# HG changeset patch
# User iuc
# Date 1558649842 14400
# Node ID 0d425a4b68968552db4870b2bc1e46da4530c88b
# Parent  1fbb1135da16eea8ac4f4c4106da5be359f01339
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d

diff -r 1fbb1135da16 -r 0d425a4b6896 augustus_training.xml
--- a/augustus_training.xml	Fri May 10 08:52:20 2019 -0400
+++ b/augustus_training.xml	Thu May 23 18:17:22 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="augustus_training" name="Train Augustus" profile="16.04" version="@VERSION@+galaxy1">
+<tool id="augustus_training" name="Train Augustus" profile="16.04" version="@VERSION@+galaxy2">
     <description>ab-initio gene predictor</description>
     <macros>
         <import>macros.xml</import>
@@ -8,7 +8,7 @@
         <requirement type="package" version="2.31.10">maker</requirement>
     </expand>
     <command><![CDATA[
-        cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
+        cp -r "\$AUGUSTUS_CONFIG_PATH" augustus_dir/ &&
 
         export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
 
diff -r 1fbb1135da16 -r 0d425a4b6896 test-data/augustus.hints.output.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augustus.hints.output.gtf	Thu May 23 18:17:22 2019 -0400
@@ -0,0 +1,195 @@
+# This output was generated with AUGUSTUS (version 3.2.3).
+# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
+# O. Keller, S. König, L. Gerischer and L. Romoth.
+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
+# Sources of extrinsic information: M RM E W 
+# Setting CDSpart local malus: 0.985
+# Setting UTRpart local malus: 0.973
+# reading in the file /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_14.dat ...
+# Have extrinsic information about 1 sequences (in the specified range). 
+# Initialising the parameters using config directory /Users/sargentl/miniconda3/envs/__augustus@3.2.3/config/ ...
+# fly version. Using default transition matrix.
+# Looks like /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_13.dat is in fasta format.
+# We have hints for 1 sequence and for 1 of the sequences in the input set.
+#
+# ----- prediction on sequence number 1 (length = 9950, name = chr2R) -----
+#
+# Delete group HintGroup gi|2701440, 8630-8864, mult= 1, priority= 4 4 features
+# Delete group HintGroup gi|4203815, 8630-9250, mult= 1, priority= 4 6 features
+# Delete group HintGroup gi|4245769, 8630-9250, mult= 1, priority= 4 6 features
+# Delete group HintGroup gi|4245770, 8630-9250, mult= 1, priority= 4 6 features
+# Delete group HintGroup gi|13769068, 8630-9250, mult= 1, priority= 4 6 features
+# Delete group HintGroup gi|14693753, 8630-9250, mult= 1, priority= 4 6 features
+# Delete group HintGroup gi|14695912, 8630-9250, mult= 1, priority= 4 6 features
+# Delete group HintGroup gi|14699170, 8630-9250, mult= 1, priority= 4 6 features
+# Delete group HintGroup gi|14700619, 8630-9250, mult= 1, priority= 4 6 features
+# Delete group HintGroup gi|15539951, 8630-9250, mult= 1, priority= 4 6 features
+# Delete group HintGroup gi|15543927, 8630-9250, mult= 1, priority= 4 6 features
+# Delete group HintGroup gi|38623822, 8630-9250, mult= 1, priority= 4 6 features
+# Delete group HintGroup SRR023546.8642467/1, 8630-8693, mult= 1, priority= 4 2 features
+# Delete group HintGroup gi|2871896, 8811-9250, mult= 1, priority= 4 4 features
+# Delete group HintGroup gi|15543159, 8811-9250, mult= 1, priority= 4 4 features
+# Delete group HintGroup , 8811-8864, mult= 8, priority= 4 1 features
+# Delete group HintGroup , 8811-8864, mult= 8, priority= 4 1 features
+# Delete group HintGroup gi|2700091, 9191-9250, mult= 1, priority= 4 2 features
+# Delete group HintGroup gi|2701304, 9191-9250, mult= 1, priority= 4 2 features
+# Delete group HintGroup gi|2701309, 9191-9250, mult= 1, priority= 4 2 features
+# Delete group HintGroup gi|3101873, 9191-9250, mult= 1, priority= 4 2 features
+# Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features
+# Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features
+# Deleted 23 groups because some hint was not satisfiable.
+# Constraints/Hints:
+chr2R	w2h	ep	7551	7560	5.3	.	.	mult=5;src=W "1.03743;0.992;9:0"
+chr2R	w2h	ep	7561	7570	7.4	.	.	mult=7;src=W "1.05617;0.992;13:0"
+chr2R	w2h	ep	7571	7580	9.7	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	7581	7590	10.2	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	7591	7600	9	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	7601	7610	9.7	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	7611	7620	13	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	7621	7630	15.3	.	.	mult=15;src=W "1.13933;0.992;29:0"
+chr2R	w2h	ep	7631	7640	13.4	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	7641	7650	13.7	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	7651	7660	14.4	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7661	7670	14.6	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7671	7680	16.8	.	.	mult=16;src=W "1.15043;0.992;31:0"
+chr2R	w2h	ep	7681	7690	16.7	.	.	mult=16;src=W "1.15043;0.992;31:0"
+chr2R	w2h	ep	7691	7700	17.6	.	.	mult=17;src=W "1.16167;0.992;33:0"
+chr2R	w2h	ep	7701	7710	20.3	.	.	mult=20;src=W "1.19619;0.992;39:0"
+chr2R	w2h	ep	7711	7720	20.5	.	.	mult=20;src=W "1.19619;0.992;39:0"
+chr2R	w2h	ep	7721	7730	18.8	.	.	mult=18;src=W "1.17304;0.992;35:0"
+chr2R	w2h	ep	7731	7740	16.7	.	.	mult=16;src=W "1.15043;0.992;31:0"
+chr2R	w2h	ep	7741	7750	16.8	.	.	mult=16;src=W "1.15043;0.992;31:0"
+chr2R	w2h	ep	7751	7760	15.5	.	.	mult=15;src=W "1.13933;0.992;29:0"
+chr2R	w2h	ep	7761	7770	17.4	.	.	mult=17;src=W "1.16167;0.992;33:0"
+chr2R	w2h	ep	7771	7780	19.5	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	7781	7790	19.1	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	7791	7800	20.1	.	.	mult=20;src=W "1.19619;0.992;39:0"
+chr2R	w2h	ep	7801	7810	22.7	.	.	mult=22;src=W "1.21988;0.992;43:0"
+chr2R	w2h	ep	7811	7820	24.4	.	.	mult=24;src=W "1.24409;0.992;47:0"
+chr2R	w2h	ep	7821	7830	23.6	.	.	mult=23;src=W "1.23192;0.992;45:0"
+chr2R	w2h	ep	7831	7840	19.5	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	7841	7850	16.2	.	.	mult=16;src=W "1.15043;0.992;31:0"
+chr2R	w2h	ep	7851	7860	14.8	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7861	7870	14	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7871	7880	14.3	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7881	7890	11.4	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	7891	7900	12.9	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	7901	7910	14	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7911	7920	14.8	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7921	7930	14.8	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7931	7940	14.2	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7941	7950	11.8	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	7951	7960	13.3	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	7961	7970	13.7	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	7971	7980	12.4	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	7981	7990	17.1	.	.	mult=17;src=W "1.16167;0.992;33:0"
+chr2R	w2h	ep	7991	8000	19.9	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	8001	8010	20	.	.	mult=20;src=W "1.19619;0.992;39:0"
+chr2R	w2h	ep	8011	8020	22.7	.	.	mult=22;src=W "1.21988;0.992;43:0"
+chr2R	w2h	ep	8021	8030	21.9	.	.	mult=21;src=W "1.20797;0.992;41:0"
+chr2R	w2h	ep	8031	8040	21	.	.	mult=21;src=W "1.20797;0.992;41:0"
+chr2R	w2h	ep	8041	8050	25.1	.	.	mult=25;src=W "1.25639;0.992;49:0"
+chr2R	w2h	ep	8051	8060	23.5	.	.	mult=23;src=W "1.23192;0.992;45:0"
+chr2R	w2h	ep	8061	8070	20.3	.	.	mult=20;src=W "1.19619;0.992;39:0"
+chr2R	w2h	ep	8071	8080	19.8	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	8081	8090	19.1	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	8091	8100	15.4	.	.	mult=15;src=W "1.13933;0.992;29:0"
+chr2R	w2h	ep	8101	8110	15.8	.	.	mult=15;src=W "1.13933;0.992;29:0"
+chr2R	w2h	ep	8111	8120	12.5	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	8121	8130	9.4	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	8131	8140	5.8	.	.	mult=5;src=W "1.03743;0.992;9:0"
+chr2R	w2h	ep	8210	8219	4.2	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8220	8229	4.2	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8230	8239	4.2	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8240	8249	5	.	.	mult=5;src=W "1.03743;0.992;9:0"
+chr2R	w2h	ep	8260	8269	4.8	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8270	8279	8	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8280	8289	8	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8290	8299	7.3	.	.	mult=7;src=W "1.05617;0.992;13:0"
+chr2R	w2h	ep	8300	8309	7	.	.	mult=7;src=W "1.05617;0.992;13:0"
+chr2R	w2h	ep	8310	8319	7.3	.	.	mult=7;src=W "1.05617;0.992;13:0"
+chr2R	w2h	ep	8320	8329	9.6	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	8330	8339	11.6	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	8340	8349	10.8	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	8350	8359	10.1	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	8360	8369	11	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	8370	8379	13.4	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	8380	8389	13	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	8390	8399	11.8	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	8400	8409	9	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	8410	8419	7.7	.	.	mult=7;src=W "1.05617;0.992;13:0"
+chr2R	w2h	ep	8420	8429	8.9	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8430	8439	11.5	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	8440	8449	11.4	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	8450	8459	9.8	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	8460	8469	10.2	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	8470	8479	10.8	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	8480	8489	10	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	8490	8499	8.2	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8500	8509	7.1	.	.	mult=7;src=W "1.05617;0.992;13:0"
+chr2R	w2h	ep	8510	8519	4.2	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8520	8529	4.7	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8739	8748	4.3	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8749	8758	5.7	.	.	mult=5;src=W "1.03743;0.992;9:0"
+chr2R	w2h	ep	8759	8768	8	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8769	8778	8	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8779	8788	8.6	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8789	8798	8.7	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8880	8889	12.7	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	8890	8899	15.3	.	.	mult=15;src=W "1.13933;0.992;29:0"
+chr2R	w2h	ep	8900	8909	17.6	.	.	mult=17;src=W "1.16167;0.992;33:0"
+chr2R	w2h	ep	8910	8919	17.9	.	.	mult=17;src=W "1.16167;0.992;33:0"
+chr2R	w2h	ep	8920	8929	17.2	.	.	mult=17;src=W "1.16167;0.992;33:0"
+chr2R	w2h	ep	8930	8939	18.4	.	.	mult=18;src=W "1.17304;0.992;35:0"
+chr2R	w2h	ep	8940	8949	19.9	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	8950	8959	19.1	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	8960	8969	15.2	.	.	mult=15;src=W "1.13933;0.992;29:0"
+chr2R	w2h	ep	8970	8979	13	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	8980	8989	14.7	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	8990	8999	14.5	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	9000	9009	14.5	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	9010	9019	12.5	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	9020	9029	11.9	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	9030	9039	12.1	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	9040	9049	10	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	9050	9059	9.7	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	9060	9069	10.6	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	9070	9079	12.3	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	9080	9089	13.1	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	9090	9099	13.4	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	9100	9109	12	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	9110	9119	10.7	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	9120	9129	11	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	9130	9139	10.9	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	9140	9149	7.9	.	.	mult=7;src=W "1.05617;0.992;13:0"
+chr2R	w2h	ep	9150	9159	4.9	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	9160	9169	4.4	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	9265	9274	11.4	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	9275	9284	12.8	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	9285	9294	13.1	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	9295	9304	13.6	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	9305	9314	13	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	9315	9324	12.4	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	9325	9334	9	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	9335	9344	5.2	.	.	mult=5;src=W "1.03743;0.992;9:0"
+# Predicted genes for sequence number 1 on both strands
+# start gene chr2R.g1
+chr2R	AUGUSTUS	gene	7560	9303	0.79	-	.	chr2R.g1
+chr2R	AUGUSTUS	transcript	7560	9303	0.79	-	.	chr2R.g1.t1
+chr2R	AUGUSTUS	start_codon	9301	9303	.	-	0	transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1";
+# Evidence for and against this transcript:
+# % of transcript supported by hints (any source): 57.1
+# CDS exons: 4/4
+#      W:   4 
+# CDS introns: 0/3
+# 5'UTR exons and introns: 0/0
+# 3'UTR exons and introns: 0/0
+# hint groups fully obeyed: 0
+# incompatible hint groups: 129
+#      W: 129 
+# end gene chr2R.g1
+###
+# command line:
+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_13.dat --UTR=off --genemodel=complete --hintsfile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_14.dat --extrinsicCfgFile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_15.dat --species=fly
\ No newline at end of file
diff -r 1fbb1135da16 -r 0d425a4b6896 test-data/augustus.hints_and_range.output.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augustus.hints_and_range.output.gtf	Thu May 23 18:17:22 2019 -0400
@@ -0,0 +1,165 @@
+# This output was generated with AUGUSTUS (version 3.2.3).
+# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
+# O. Keller, S. König, L. Gerischer and L. Romoth.
+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
+# Sources of extrinsic information: M RM E W 
+# Setting CDSpart local malus: 0.985
+# Setting UTRpart local malus: 0.973
+# reading in the file /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_18.dat ...
+# Have extrinsic information about 1 sequences (in the specified range). 
+# Initialising the parameters using config directory /Users/sargentl/miniconda3/envs/__augustus@3.2.3/config/ ...
+# fly version. Using default transition matrix.
+# Looks like /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_17.dat is in fasta format.
+# We have hints for 1 sequence and for 1 of the sequences in the input set.
+#
+# ----- prediction on sequence number 1 (length = 2001, name = chr2R) -----
+#
+# Delete group HintGroup gi|2701440, 1631-1865, mult= 1, priority= 4 4 features
+# Delete group HintGroup gi|4203815, 1631-1865, mult= 1, priority= 4 4 features
+# Delete group HintGroup gi|4245769, 1631-1865, mult= 1, priority= 4 4 features
+# Delete group HintGroup gi|4245770, 1631-1865, mult= 1, priority= 4 4 features
+# Delete group HintGroup gi|13769068, 1631-1865, mult= 1, priority= 4 4 features
+# Delete group HintGroup gi|14693753, 1631-1865, mult= 1, priority= 4 4 features
+# Delete group HintGroup gi|14695912, 1631-1865, mult= 1, priority= 4 4 features
+# Delete group HintGroup gi|14699170, 1631-1865, mult= 1, priority= 4 4 features
+# Delete group HintGroup gi|14700619, 1631-1865, mult= 1, priority= 4 4 features
+# Delete group HintGroup gi|15539951, 1631-1865, mult= 1, priority= 4 4 features
+# Delete group HintGroup gi|15543927, 1631-1865, mult= 1, priority= 4 4 features
+# Delete group HintGroup gi|38623822, 1631-1865, mult= 1, priority= 4 4 features
+# Delete group HintGroup SRR023546.8642467/1, 1631-1694, mult= 1, priority= 4 2 features
+# Delete group HintGroup gi|2871896, 1812-1865, mult= 1, priority= 4 2 features
+# Delete group HintGroup gi|15543159, 1812-1865, mult= 1, priority= 4 2 features
+# Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features
+# Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features
+# Deleted 17 groups because some hint was not satisfiable.
+# Constraints/Hints:
+chr2R	w2h	ep	7551	7560	5.3	.	.	mult=5;src=W "1.03743;0.992;9:0"
+chr2R	w2h	ep	7561	7570	7.4	.	.	mult=7;src=W "1.05617;0.992;13:0"
+chr2R	w2h	ep	7571	7580	9.7	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	7581	7590	10.2	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	7591	7600	9	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	7601	7610	9.7	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	7611	7620	13	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	7621	7630	15.3	.	.	mult=15;src=W "1.13933;0.992;29:0"
+chr2R	w2h	ep	7631	7640	13.4	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	7641	7650	13.7	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	7651	7660	14.4	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7661	7670	14.6	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7671	7680	16.8	.	.	mult=16;src=W "1.15043;0.992;31:0"
+chr2R	w2h	ep	7681	7690	16.7	.	.	mult=16;src=W "1.15043;0.992;31:0"
+chr2R	w2h	ep	7691	7700	17.6	.	.	mult=17;src=W "1.16167;0.992;33:0"
+chr2R	w2h	ep	7701	7710	20.3	.	.	mult=20;src=W "1.19619;0.992;39:0"
+chr2R	w2h	ep	7711	7720	20.5	.	.	mult=20;src=W "1.19619;0.992;39:0"
+chr2R	w2h	ep	7721	7730	18.8	.	.	mult=18;src=W "1.17304;0.992;35:0"
+chr2R	w2h	ep	7731	7740	16.7	.	.	mult=16;src=W "1.15043;0.992;31:0"
+chr2R	w2h	ep	7741	7750	16.8	.	.	mult=16;src=W "1.15043;0.992;31:0"
+chr2R	w2h	ep	7751	7760	15.5	.	.	mult=15;src=W "1.13933;0.992;29:0"
+chr2R	w2h	ep	7761	7770	17.4	.	.	mult=17;src=W "1.16167;0.992;33:0"
+chr2R	w2h	ep	7771	7780	19.5	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	7781	7790	19.1	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	7791	7800	20.1	.	.	mult=20;src=W "1.19619;0.992;39:0"
+chr2R	w2h	ep	7801	7810	22.7	.	.	mult=22;src=W "1.21988;0.992;43:0"
+chr2R	w2h	ep	7811	7820	24.4	.	.	mult=24;src=W "1.24409;0.992;47:0"
+chr2R	w2h	ep	7821	7830	23.6	.	.	mult=23;src=W "1.23192;0.992;45:0"
+chr2R	w2h	ep	7831	7840	19.5	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	7841	7850	16.2	.	.	mult=16;src=W "1.15043;0.992;31:0"
+chr2R	w2h	ep	7851	7860	14.8	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7861	7870	14	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7871	7880	14.3	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7881	7890	11.4	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	7891	7900	12.9	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	7901	7910	14	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7911	7920	14.8	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7921	7930	14.8	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7931	7940	14.2	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	7941	7950	11.8	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	7951	7960	13.3	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	7961	7970	13.7	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	7971	7980	12.4	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	7981	7990	17.1	.	.	mult=17;src=W "1.16167;0.992;33:0"
+chr2R	w2h	ep	7991	8000	19.9	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	8001	8010	20	.	.	mult=20;src=W "1.19619;0.992;39:0"
+chr2R	w2h	ep	8011	8020	22.7	.	.	mult=22;src=W "1.21988;0.992;43:0"
+chr2R	w2h	ep	8021	8030	21.9	.	.	mult=21;src=W "1.20797;0.992;41:0"
+chr2R	w2h	ep	8031	8040	21	.	.	mult=21;src=W "1.20797;0.992;41:0"
+chr2R	w2h	ep	8041	8050	25.1	.	.	mult=25;src=W "1.25639;0.992;49:0"
+chr2R	w2h	ep	8051	8060	23.5	.	.	mult=23;src=W "1.23192;0.992;45:0"
+chr2R	w2h	ep	8061	8070	20.3	.	.	mult=20;src=W "1.19619;0.992;39:0"
+chr2R	w2h	ep	8071	8080	19.8	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	8081	8090	19.1	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	8091	8100	15.4	.	.	mult=15;src=W "1.13933;0.992;29:0"
+chr2R	w2h	ep	8101	8110	15.8	.	.	mult=15;src=W "1.13933;0.992;29:0"
+chr2R	w2h	ep	8111	8120	12.5	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	8121	8130	9.4	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	8131	8140	5.8	.	.	mult=5;src=W "1.03743;0.992;9:0"
+chr2R	w2h	ep	8210	8219	4.2	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8220	8229	4.2	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8230	8239	4.2	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8240	8249	5	.	.	mult=5;src=W "1.03743;0.992;9:0"
+chr2R	w2h	ep	8260	8269	4.8	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8270	8279	8	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8280	8289	8	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8290	8299	7.3	.	.	mult=7;src=W "1.05617;0.992;13:0"
+chr2R	w2h	ep	8300	8309	7	.	.	mult=7;src=W "1.05617;0.992;13:0"
+chr2R	w2h	ep	8310	8319	7.3	.	.	mult=7;src=W "1.05617;0.992;13:0"
+chr2R	w2h	ep	8320	8329	9.6	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	8330	8339	11.6	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	8340	8349	10.8	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	8350	8359	10.1	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	8360	8369	11	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	8370	8379	13.4	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	8380	8389	13	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	8390	8399	11.8	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	8400	8409	9	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	8410	8419	7.7	.	.	mult=7;src=W "1.05617;0.992;13:0"
+chr2R	w2h	ep	8420	8429	8.9	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8430	8439	11.5	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	8440	8449	11.4	.	.	mult=11;src=W "1.0964;0.992;21:0"
+chr2R	w2h	ep	8450	8459	9.8	.	.	mult=9;src=W "1.07589;0.992;17:0"
+chr2R	w2h	ep	8460	8469	10.2	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	8470	8479	10.8	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	8480	8489	10	.	.	mult=10;src=W "1.08606;0.992;19:0"
+chr2R	w2h	ep	8490	8499	8.2	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8500	8509	7.1	.	.	mult=7;src=W "1.05617;0.992;13:0"
+chr2R	w2h	ep	8510	8519	4.2	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8520	8529	4.7	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8739	8748	4.3	.	.	mult=4;src=W "1.02857;0.992;7:0"
+chr2R	w2h	ep	8749	8758	5.7	.	.	mult=5;src=W "1.03743;0.992;9:0"
+chr2R	w2h	ep	8759	8768	8	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8769	8778	8	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8779	8788	8.6	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8789	8798	8.7	.	.	mult=8;src=W "1.06592;0.992;15:0"
+chr2R	w2h	ep	8880	8889	12.7	.	.	mult=12;src=W "1.1069;0.992;23:0"
+chr2R	w2h	ep	8890	8899	15.3	.	.	mult=15;src=W "1.13933;0.992;29:0"
+chr2R	w2h	ep	8900	8909	17.6	.	.	mult=17;src=W "1.16167;0.992;33:0"
+chr2R	w2h	ep	8910	8919	17.9	.	.	mult=17;src=W "1.16167;0.992;33:0"
+chr2R	w2h	ep	8920	8929	17.2	.	.	mult=17;src=W "1.16167;0.992;33:0"
+chr2R	w2h	ep	8930	8939	18.4	.	.	mult=18;src=W "1.17304;0.992;35:0"
+chr2R	w2h	ep	8940	8949	19.9	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	8950	8959	19.1	.	.	mult=19;src=W "1.18455;0.992;37:0"
+chr2R	w2h	ep	8960	8969	15.2	.	.	mult=15;src=W "1.13933;0.992;29:0"
+chr2R	w2h	ep	8970	8979	13	.	.	mult=13;src=W "1.11756;0.992;25:0"
+chr2R	w2h	ep	8980	8989	14.7	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	8990	8999	14.5	.	.	mult=14;src=W "1.12838;0.992;27:0"
+chr2R	w2h	ep	9000	9009	14.5	.	.	mult=14;src=W "1.12838;0.992;27:0"
+# Predicted genes for sequence number 1 on both strands
+# start gene chr2R.g1
+chr2R	AUGUSTUS	gene	7560	8931	0.83	-	.	chr2R.g1
+chr2R	AUGUSTUS	transcript	7560	8931	0.83	-	.	chr2R.g1.t1
+chr2R	AUGUSTUS	start_codon	8929	8931	.	-	0	transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1";
+# Evidence for and against this transcript:
+# % of transcript supported by hints (any source): 60
+# CDS exons: 3/3
+#      W:   3 
+# CDS introns: 0/2
+# 5'UTR exons and introns: 0/0
+# 3'UTR exons and introns: 0/0
+# hint groups fully obeyed: 0
+# incompatible hint groups: 102
+#      W: 102 
+# end gene chr2R.g1
+###
+# command line:
+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_17.dat --UTR=off --genemodel=complete --hintsfile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_18.dat --extrinsicCfgFile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_19.dat --predictionStart=7000 --predictionEnd=9000 --species=fly
\ No newline at end of file
diff -r 1fbb1135da16 -r 0d425a4b6896 test-data/chr2R.truncated.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr2R.truncated.fa	Thu May 23 18:17:22 2019 -0400
@@ -0,0 +1,200 @@
+>chr2R
+TTGCAATTTGCACTTTTCAATTGCCCCAAAAGATACGCCAACGAAATGCT
+TATTAAAGTATCAAAAACAAATACCAGAAAGCTGTCACCAATCCCGCCCC
+ATAGAAAACATGCCCACTTTGCCGCAGAATTTGCATATTTGTCTCCGTCG
+GCGGTCGTCATTTTAATAAAAAAAAAATGTTTGTATAATTTCAGGTCGTC
+GTGGGATGCGGCGGCTGCTTGCttataaaattaattttaaattaaacaat
+tttaattatGATTCAATAATCAACAAACACACTGCAGCTTCGTCAATGTT
+GTCGCAGACTTTCAACAATGCAAATATTGGTTTACGGCCATAAAGGCCCA
+GCGCGACCAACCAAACCATTAATCCAACTCCGCTCGACTATTGCAAATTG
+TTTAATAGCCGCCTTTCTTTCTTTTATGTTTGCAAAAAGAATGTATTTCC
+ATAATATTGCCGCTTTATGTTTCATCTGGAACCACTTAACTTTGCCTCTG
+CTAATTCAATTAAAAGGAGAATTTAAAAACTTGAATAGCTTGTAAAGTGA
+CAAAAAATTCAGTACTTCTTTTATTGAGTTAGTAACTAATATCAATGCTA
+ATTCAATTCGCAGATGCCCTTGTTTCCACCAAAAATTTAAATTACTACAT
+TGAAAAAAAAAATAATTCTAATAAACTATATTGATTTGCAATAGTATATT
+CCCAATGCTCCATAAACTTGCTTCACATGACttaaaaaataaattaaaat
+ttataGAAAAAACTTGATTTTTGAATTTGTTCCTTGCTTGAAACTTGCTG
+AATTTTTTTATGTGCAGAAATATTTTCGATGGTAATTGAATTAACTCTTA
+ATTTGGTATTTTGCCTGTGTGGTCATAAAATTTAAAGAGCACATTAATTG
+TCTAATTGAAAAAACGGTTTGGCTGCATAAATTGCTCGACGACTTGCTCA
+TTTTTCTCATGATTATTATAGTTATGACAACCATTTGTTTAAGCTAGTTA
+CAGTGCCTCTTGGGAAGACTTACTAAGGGAATGCACCTTTAGTCAAATGC
+AACAGATATTAATTAAATATTCAGTGCTTAATCACTTGCAACAAGTTAAA
+TGTTGATTTTTGCCCAGAGCCCTCTGTGACTTTATTCAATTAGCGTTTGT
+TAACTCCCGTTCCCGAACTTCTCCAGATTTTTTGCCAATCTTTTTCGATG
+CCGGCGGGCACATCATTACATATGCCACGCCCACCTCGCCATTGCCTGCC
+CCAAGCTTTATGCTTGGTGTACGCAAAAATTTATTTACACGCATAATTTA
+AAAAACCTTTTGCGCTTTGCTTAATGGCCATTCATTTATTGTAACACACA
+CACACACTCGCTGGGTGACACTTGCATTATTGAATCTGCCACGCCCACCA
+AAAAGGCGGAGGCACATAATGGGCTGATTTCGTTAGTTGACAGCCACATG
+TTTGCGGTACTCGTTAAGCTGAAAACATGCCTTTTCAAGGGGTTTTGGCA
+TTTATTTTATAATTTAAGTATCTATGCCCATGAAGCTTTTAATATAAAAC
+CACTCAAAACATTTTAAAATACTTTTAAAATATACATTACGTTACATTAA
+ATAATCAAATCAATTGATAGTACGAAACTGACATATAAACAATATTATAG
+GAATGAACACATTTCACACTTACAAAATGTAGAATTTAATTTAAAGGCTA
+TGAAGTATAAACGTATAAAATATATCCAATTATTAAAATATTAAAACAAA
+ATATCAAGTTGAGGCCGCCACCTTTGTTTAAATCTATAAATTGGGAAACA
+GTTTGTTTATTTGTGCTGGACATTAATTGTCTGTTCGAAGAAAGGTAATT
+AAAACAAATCCACATTGTTATCCTGCGCTATCAATATGCCAGCAAATTAA
+TTATGATGTGTTAGACAGATCAATGACATTCTTGCTGAGAGCCGAGTTGC
+TGCAACTCGCTTGCCAAAGTTAAACGCACTCACTTAACTCGCACCATTCA
+GCTTTAGTCACCTGGATTTGATTCGATTTTGTCATCTGCCCGGGCAACAa
+cacatacatatatactacacatgcaaacatatacatatatgcccatatct
+acatGGCCAACTACTTCGATTCCTGGCCTTTTGTACTGGCCCCTTTCGCC
+TGTGGCAATGCTTCCTGTCTGATGTTGCACGAGTAGATGTTGCCgctgtt
+gctgttgctgttgctgttgctTGTGTGCCTTGAGTTGGCAGGCCACGTTC
+TGGTTTCGGTTGCGGTTTCGGTTTGCTGGCTGCGATGGGCGCCTGTTGAC
+GCTTTCGGCTACCCAGACATGGGTATCAGCCAGGTACCGACTTGGCTCTC
+CAGTTTATGGCCGTTTACATGCTCACCGCCCGTTTCTCATATCACTTTAT
+TTGCCAGCGGAATTCGCACGCAACTCCCTCGGTAATGATGCTCAAGAATT
+TTTAATAAAAAACTGCCAGCCAAGCAGGAGGAGCTTTGCTCTTTTATTTT
+TGTGCTGCGACTGATGAAGGCAATTGGAAGGACCTTAATGACAGGCAGCC
+TTTGTGGGTTAAGCAATATATTAATCAGCATATTAATTATGCAGCAAGGT
+AGTTTTGCCCGAGTGCGGGCGGGCATGGCCAGTGTCGAAGGTCAACGAAC
+TGCAGCGGCCGCATGCATTGTTGGGGCATATAAATTGTTTAAACAACTTT
+ACAGACAACATCCGTTGGGCCAGGCAAAATGGCCCGAAGGCGATGGGAAT
+TCGAGTACCAGGCTgccagccagccagccagccagccagccagccagcca
+gtcagccaTGTGACAGGCAGTCGGTCATTATTTCGCACTTTTGTTGCCGC
+TGCGGAAATTTCACAGCAAGAGGCAGCGGCAAACATGCGACACGTGCAAC
+ACCGAAAGTCGAGAGTCTGGGCGATACAGTGTGCCATAACAATAATGCCA
+CAACAAAGATAGAGTCCCTGCCAGTAGAGAGCAGGCTGGGCGAAAAATGT
+GTGCGGGAGTCAGGTGGAAAAGATGCACAAGTCGGTGGCAGACAAAATGG
+AATTTTAATGATATGAGAAGGCGCGCCTTCTGAATATTTTTGCAGGTGAA
+ACTGCTTACCAGCCATCCACTTGGCCACCTCCCCCTCCACCAAACAGCAC
+CAAACTCTTACCCTTTGAACTCGCGTAGTACAACCGGCACTTGAACTACG
+CCGCTTACTACGCTCTTGGCGCTCTTTTCAGTTTGTTTTTGCTGCGTTAT
+AGTGCCCGTTTTTTTTCTGTCCTGACTCAGGCGCAGGCGAGTTGGCCCAG
+AAGAGCGCAAGAGAACCGCTAAGAGCGCATTTACGATTGGCAAGCCGGTA
+AAAATAGAAAAATAAGTAGTTTGAACACAGTTTGTATGAAGGTATGCTGT
+TTCGCTTGAAATTTAATGCAGTTTATATTACAGAAATAGAAAACTAACCA
+ATTACTTTGTTTATTTTGGTATTAAATGAATGAGCTGCACTTACACTTTT
+CAAAATAGTTTATCCAAAGCACTTGACATTTTGGTGGTAGTTATTGCATA
+GTTCAGGTGCTTTTTGTAGTTTAAAACATTTTGAAACCCCTTTTAAGATA
+TCACAAGCACAAAGCACAAAGGCGCACTCACACAATTGCGAACGGCAAGC
+GCCATGTGCGCCTGGCGGTATGCAATAGTTTCTGTTTCTCTTTCGTTTCC
+GTAAATGGTAGTGCGCGTATAGTAgtgtgcgtttgcgtatgcgtgtgtgt
+gtgtgtgtgtgtgtgcgtTTTAGCCGACAAAGTGCAACACACAGCGCAAT
+GACCGACGTACTCGAGCGTTGACTCGTTTCTGCGACAACTTTTCTCGCTC
+CTCGCCGATGGGAATAATGATCTCAGCGTAATGACGATTTTTAGCAGCCA
+GTAAGCTTGTTGATGCTGTGCCGATGACGTTGCGAACTCGCTCTCTCCGG
+GCCGCTCGCTCTCTCTTTCCCACACTCTCTCGGCCATTTTGCGGAAGTTT
+CAACTCACCGCAAAACGCTCCAAAATGAGCAGCCAAATTGCGAGTTCCTT
+CCTTAATTGCGCACTCGTATCGTTCATTTGTATTTGTATTCCCTCCCATC
+AGCATTTTCTCTTCGGCCATATAACAGTTTTCTCTTATACTTTCGCTTCG
+GTTTATAGCACGCACATTCCCGGTGACGTCACAAGGCTTTCCCAACGCTT
+TTTCCATAGAATCAGTTGTTGTTTGGGCTGCACAAGCCGGCAATGTAAAC
+AAAACATAAAATATATGAATGGGTGAGTGAGTTGTGCGGGTGTCTGGGTT
+ATTCGACTGCTTCGGCTGAGTGGGTGGCTGTTTTGGGTGGAAATTGGGTG
+ACCCCGATGCACTGGTGTTGGTGCAAATTCGGCAATGCGTGTGCGCTGCG
+CCTGATGAATGAAAAGTTCGAGTGGCCGCGTGGAAAGCGGGAAAACATCT
+GAGCGTCAGCTGCACGGTCATATGTTTGATATTATTCCTGTGAAAGCGGA
+AAATGATTTTGAATATTAAAGGAAATCGATGCGGAAAATGTTTTGGAGTA
+TTTAATAGCCATTAAATGGATAACGTAGATTTTGTCACAGGTTTATAAAA
+TGTAGTTATAGGTAATATATTCACTAAAACAGAAACTGCCTTACACACTT
+TTAGTATATTGTTTTATTTACTTAAATTACCTAAGTAAATAAAAGTATTT
+TCAAATTGTTACAAAAAGCACACCCTTTTTTCTATTTTTGTTAATATTTG
+AATGCCCCACCAATCGATTGAATTTGAAGCCAATTCGTGATTCGGAAAGC
+GCAGAGTGTCCTGTATTAAATTCAGCCTTGCAGACAAATGCAAAAACCAT
+CGACAGGCCGTGTCAGAAAACACACGAAAATCGAGTGAGCCCCAGAGCAA
+TCGCATTTTAATTTGAATTCTTTCTGGTGAGGCCCTTACAAAAGCCCCCA
+TGCGATGTGCACGACCAAAAAATGAACTTAAGTTTCGGCCAAGAATCTTG
+TTGAAGAATTTCTATTTGAGCATTTGTCATGTCTTCGCCTTAGTCTATAA
+AATATACTGTCGGTGGATGGGGACGCGGGGTGTGTGCAAATATGCGAAAG
+CTAAATGTCAGAGTCAACCCTTTCGCAGGCCATTCTGCCTGCTTTTTTTT
+CAGCCTTTTCTGGCCGGTGTTGCCGCCTTGGCCCCTTTTTTGGGTGGAAA
+GGAAAGTTTTTATCTTAAGCTGCGCGCTGACAGGCAGCAAAGCGGCAAGC
+GAGGCAACACAAGTACAAGCCGGACAAAGAAGCCAGGGGGAGTGGGGATG
+GGCTGGCCGAACGGAAAATGGGAAATGGAAAATGGACGGGCAACGACAAG
+GCGGGCAAACGTCAAGTTATAGAAAATGCTAGTGCCTGCACAATAAGAAA
+AGTGTCATCCGAATTGCTAATCAATGGAATGATGTTGAGGAGACTCAAAA
+GAAATTTAAAGACCTACTAATAAGAAAAAACTGAAAAATCATTAAGTTTT
+TAAACTATTCAAACATATTTAAATAATAATTTGTGCAAATTTATTATTGC
+TTAAAACAACTAAATAAAAATATATAATGTCATTCAAAGTTTCAAAAAAA
+ATTTATTCAATTAAACAAAGGCCATTTTGTATCTTTTCAAAAGTATATGA
+CTTAAAAATAGGTTCATTCATTTTGCTTATGCAAGCTAAGGACTCAGCTT
+TTTGTCAAAGTGCAGAAAAGGGGAATGAAACTGGTCTTAGAGGGAGAAAA
+AATTAAAGGACATGCTGAACGCATTCCTTGGGACACGGGCTGACAGTGAG
+TGATTTGACCATACCCTCATTTGCGTGCAGCAAGGACCAAGATCCGAGCT
+CTGGGTTCCGGGTTCCGGGGTTCCGACTACCGAGATCCAGGCACACCAAT
+GGATTAATGTGCAAGGATGCGACTCGTCAGGCAGGCCAAGAAAATTACGT
+CAAGCTACGCAATGGGCCCGTGCCTTTCCCACTGCCCCCCACCACCCCAc
+aacctaaccaaatccaacccagcccagcacaacccaaaccaTTATCCTTT
+TGGAAATCTGATGATGAGCGCCGACTGCTGCGGGCGGGCGACTCAAAATG
+GGAGTGACTCATTTACGCGCTGCACTCGAGTTTCAACCGGCAGCCGGCGA
+AGGAAAAGCGGGACTCCGAGAACTTTTCCAAGCTATTTCTGCGCCCAAAT
+GACAGCGAAATGTAATAATGAAAAACTTTTTCTTTGTCAACTTGATGAGT
+ATGAAATTTTTCACaaaaaaaaaaaaagaaaaaagattaaataaaataaa
+agaCGAGCGGCAAAGGAACGGGTTGAGCTTGGGTGGCAGGGCGGTGAGCT
+AGAAATATGAAACGTCAGGACTGGTCCTTAGTCTTAGGTTGGCCTTAGTC
+TTGGTTGGCCTTCGAGATTAGTTATGGCAAAGGAATTTCCAAGCGAAGGC
+GCACGCAAATGATTGCATGCCGCATTACGCATACGCCCGGTTGTGCGTGG
+CCGGTTTTAAAATTGAATTTTAATATACAGCAGACACAAAGAGATGTACA
+TGACCATATGTATATGTATATAGCTGATCCCTGGCCATGGCTGCTATAAG
+CCAGGTTATCCAGCCACCCCGAAAAAACACATGTTCTGCATTTTTACTTT
+GTACTGGACCAGGACCCACGGTCCATCATCCCTACCATTTTGCTGCTGCA
+CCGCATCGGGGATTGCGGAATTCATAAGCTATGTGCGTTTGCTACAAAAG
+TGGAATTTTCGCCACGCCAAAGGATACCCGCTTGCAGGCTCCCAGCTCAC
+AGTTCCCACTTCCCGTTTCCTAGATCCTGAGCATGCCATTAACCCACTCG
+CAAAAAGCGCAAAATCGCTTAAATTATTGTTACAAGCTGCCAGTGCCAAG
+TGGCAGGCACAGCAACAGCAAAAACAAGAACAAGACCAGGGGggcaggtg
+gcaggtggcaggtggcaCAGGGCAAACCACCTGAGCTTTTGGCCGCGCTT
+TGCTTTGAGTGCCAGTTAGCATAACTCCGCAGGCCGCAGGCGAATATGTc
+tgttgttgctgcttttgccgctttgctactctcctgatgttgggtgctgc
+tcctgattttgctgttgccgttAGAAGTATTTGTGGCGCGGCAAAGGACA
+TCCTCTCGGCAGCCCGTTCTCACCTGCCTGCCAAGCTGCAAGCTCCAGCT
+GAAAGTGTCTTTGGTGAGCGCTACCCACCACCTAAATATACAAAGTGTGG
+GGGAAAAACAAGAAAAATAACAACCTACAATAGTCTCTTCTTTGTTACCT
+AAAAATATAAGAAAAGCACACCTCGCAATTGTGTTGAAAAAAACAAATTG
+ATACGAAAAAAAGCGATAGGGATGCCACAACAAAGCGCAATCTTATCAAA
+CGTATTAAACATTTTGCTTATCAAAACAGCGAGGTTTGCACAACAATGCG
+AAATAGGAGGAGGCAAAATTCTTATCTGCATTTCATCAGTCAAACATTTA
+CTGTAATCAAAAATCGCAACTATAAGGAACACAAGTAAAGGCCACAAATG
+AGAAGCAAATTATTGTTCGATATCCGTGAATTTGAAGGGGAACGTAATGG
+CCGGTTCCATGACGAACATGGTCTTGAATGGACGGCTGGCATCCCGATTG
+AACTCCACATGGAAATTGCGAATCAACTTGGCCACTGTGGTCTCCATTTC
+CAGATCCACCACCCGTTTGCCAATGCACATGCGGGGTCCAAAGCCAAAGG
+GAAGGAACGTGAAGGGGCTGACCTGCATCTTCTTTCCGGTCTCCGGATCC
+CTTAACCAGCGCTCCGGCAGAAATTCATCTGGTCGTGGATAATATGTAGC
+TTCCTTCATCAGCACATTTGAGCCGAGCAGGACAGTCGTTCCCTTGGGCA
+CCCGGTAACCCGAAAGTATCACATCATTTTGGCAGGTTCTCATGGTTCCC
+AAGCCATTGGGATAGTATCGCAGTGTCTCCTTGATCACAGCCCTCAAATA
+TGGCATATCCTTCATGTTCTCCTCGTTGAGTAGGGAATCCTTTGTGGGCA
+TGATGCTCAAGAGCTCCTCCCGCAGTTTGGCCTGCTTATCCGGATGCTTT
+GAGAGGCAGAGTAAAACAGCCGACAGAAGCGTGGCTGTGGCATCCACACC
+AGCGAATAGGATGTCCAGACTCATAATCACCGCCACCTTGGGATCGATCT
+CCATTAATCTCTCCAGCATACTGTTACTATTTATTTTTTCGCCAGCCTGG
+CGGCGCTTTTCCAGTGCATCCTGATTTTCCTTCAGCATTTTCTGGGCCAC
+ATTCAAACTGTCATTGAGAGTTCGCTTCATTTTCCTGTAGGTGGGCGTCG
+ATATGATCTTCCACATGGAGGGCTGAATGTCTAGCTTAAATGTGAGACGG
+AAAATATCCCTCGAGGTCTGGAAGAGGGTCAATGCATCGGAATTATCGCG
+GTTTTTTCTAATCAGACCCATTTGCCGATCGAAAGCCACCAGGCCGAGTG
+ACTCGAAAACAAGCCGGCTTATTTCATCCGTAAAATCTTCGGGGACTTCT
+AGAGTTTTTGGATCGCGGATTTCCTTAATGCTGCACAGTAAAATGGAATT
+TATTGCTATATATAAATAACAATTCAATAACAAAAATTTCTTACCGCTCT
+ATAAACTCATTATTGATATTAGACAATGGTTCATAATACATTCTCAAGCC
+CCTGGGTTGCATAAAGATGGGATTAATGGCTGATCGTAGTTTTCCCCATG
+CCTCATTTTGTCTGAAATATTCAAATTCAATTGTTTCCTTGCTACTTATT
+AGATTTTATACTCACGAAGCCACCAATCCTTGAACCTCACCGTAAACATC
+TGGTCGAACGTGTTCGCGGAAATATACAATGGAATCCAGGCCATCACGAC
+GTGGCCAGATACCCTCGTTGCGGAATACCATCTCAATGTCCTTTGTGTTG
+AAAGTGGTGACCCAATCCTTGCGGCCAAACATTCCGGGCATTACATAGAT
+ATCTCCATAGCGCTTTCGCATGGCACTGGTGTATTCCGTAATCGATGCAT
+TTTGGAATTCACCACCGGGCATGAAAGCCCTCATAAATTTGAATTTGTTG
+GGCCGCGGAATCTCATCGTAGGTCTTGTGCTCCTCCGTTATCTATAATTG
+GAAACTAATAACATGATAAATCTATTTCGACTGGATTTTGTGCATACTAA
+CACTAGATTTAGCTTGTTCATGTGCCAAAACGGAGGCTGATCTTGAAGAT
+CGAACGGGACCCACGTAAATCGCCACAGATCGCGCACTGCTCAATGTATT
+CATTCTATTCCTTTTGGTGATCAACTGCAACTAAAAACAGTTCCACTTTC
+GAGAACGTTCTTATACCAAAGGCTTATCTCTAAAACGTAGAAAAGAGAGG
+AGAGCGAATAACTTGAAATGCTTCAAAATGCAAAAATCTCAAACAAAAAC
+AAAAGCCAGCAAACAAAGCATGAGTTTCATTTTCTTATCAGCTGAACGGT
+ATAATCGCCGTGAATTGCCTACCTCACTCAACTGAAAAAATAAACAAATG
+AACGTGACTGGCTAGAAAAACAAATTGAGAGCGTTGGAACTTACAATAAA
+TACACCTCAGAGAATTTGATACTACTATTACGACTATTACATACCCGTTA
+CTCATTTAGTGGGATCGCTAGaaaaaaatctaaaatatttaaatattttt
+taaaaatttataaGGATTCTAGTTCAACGGTAGACAATTTCAAGATAAAT
+AACCAAATTAAAGAAAAATAAAAACAATTCTTAGAGTTGATCCTTGTTCT
+CTTTGCATACTGatattttatttattttttattttatttatttaCTGGCG
+CCGCTTTTCCACAGAGTCCTCGGTGTCCTTTATCATTTTCTGTGAGAACA
+TTAAGATGTCATCGAGAAGACGCATCATCATCCGAAAGTTTGGAGTGGAG
diff -r 1fbb1135da16 -r 0d425a4b6896 test-data/extrinsic.truncated.cfg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extrinsic.truncated.cfg	Thu May 23 18:17:22 2019 -0400
@@ -0,0 +1,183 @@
+==# extrinsic information configuration file for AUGUSTUS
+# 
+# protein hints
+# include with --extrinsicCfgFile=filename
+# date: 16.10.2007
+# Mario Stanke (mstanke@gwdg.de)
+
+
+# source of extrinsic information:
+# M manual anchor (required)
+# P protein database hit
+# E EST/cDNA database hit
+# C combined est/protein database hit
+# D Dialign
+# R retroposed genes
+# T transMapped refSeqs
+# W wiggle track coverage info from RNA-Seq
+
+[SOURCES]
+M RM E W
+
+#
+# individual_liability: Only unsatisfiable hints are disregarded. By default this flag is not set
+# and the whole hint group is disregarded when one hint in it is unsatisfiable.
+# 1group1gene: Try to predict a single gene that covers all hints of a given group. This is relevant for
+# hint groups with gaps, e.g. when two ESTs, say 5' and 3', from the same clone align nearby.
+#
+[SOURCE-PARAMETERS]
+
+
+#   feature        bonus         malus   gradelevelcolumns
+#		r+/r-
+#
+# the gradelevel colums have the following format for each source
+# sourcecharacter numscoreclasses boundary    ...  boundary    gradequot  ...  gradequot
+# 
+
+[GENERAL]
+      start        1        1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
+       stop        1        1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
+        tss        1        1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
+        tts        1        1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
+        ass        1        1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
+        dss        1        1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
+   exonpart        1     .992  M    1  1e+100  RM  1     1    E 1    1    W 1  1.005
+       exon        1        1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
+ intronpart        1        1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
+     intron        1       .8  M    1  1e+100  RM  1     1    E 1    1000 W 1    1
+    CDSpart        1  1 0.985  M    1  1e+100  RM  1     1    E 1    1	  W 1    1
+        CDS        1        1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
+    UTRpart        1   1 .973  M    1  1e+100  RM  1     1    E 1    1    W 1    1
+        UTR        1        1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
+     irpart        1        1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
+nonexonpart        1        1  M    1  1e+100  RM  1     1.01 E 1    1    W 1    1
+  genicpart        1        1  M    1  1e+100  RM  1     1    E 1    1    W 1    1
+
+#
+# Explanation: 
+# 
+# The gff/gtf file containint the hints must contain somewhere in the last
+# column an entry source=?, where ? is one of the source characters listed in
+# the line after [SOURCES] above. You can use different sources when you have
+# hints of different reliability of the same type, e.g. exon hints from ESTs
+# and exon hints from evolutionary conservation information.
+# 
+# In the [GENERAL] section the entries second column specify a bonus for obeying
+# a hint and the entry in the third column specify a malus (penalty) for
+# predicting a feature that is not supported by any hint. The bonus and the
+# malus is a factor that is multiplied to the posterior probability of gene
+# structueres. 
+# Example: 
+#   CDS     1000  0.7  ....
+# means that, when AUGUSTUS is searching for the most likely gene structure,
+# every gene structure that has a CDS exactly as given in a hint gets
+# a bonus factor of 1000. Also, for every CDS that is not supported the
+# probability of the gene structure gets a malus of 0.7. Increase the bonus to
+# make AUGUSTUS obey more hints, decrease the malus to make AUGUSTUS predict few
+# features that are not supported by hints. The malus helps increasing
+# specificity, e.g. when the exons predicted by AUGUSTUS are suspicious because
+# there is no evidence from ESTs, mRNAs, protein databases, sequence
+# conservation, transMapped expressed sequences.
+# Setting the malus to 1.0 disables those penalties. Setting the bonus to 1.0
+# disables the boni. 
+# 
+#       start: translation start (start codon), specifies an interval that contains
+#              the start codon. The interval can be larger than 3bp, in which case
+#              every ATG in the interval gets a bonus. The highest bonus is given
+#              to ATGs in the middle of the interval, the bonus fades off towards the ends.
+#        stop: translation end  (stop codon), see 'start'
+#         tss: transcription start site, see 'start'
+#         tts: transcription termination site, see 'start'
+#         ass: acceptor (3') splice site, the last intron position
+#         dss: donor (5') splice site, the first intron position
+#    exonpart: part of an exon in the biological sense. The bonus applies only
+#              to exons that contain the interval from the hint. Just
+#              overlapping means no bonus at all. The malus applies to every
+#              base of an exon. Therefore the malus for an exon is exponential
+#              in the length of an exon: malus=exonpartmalus^length.
+# 	     Therefore the malus should be close to 1, e.g. 0.99.
+#        exon: exon in the biological sense. Only exons that exactly match the
+#              hint get a bonus. Exception: The exons that contain the start
+#              codon and stop codon. This malus applies to a complete exon
+#              independent of its length.
+#  intronpart: introns both between coding and non-coding exons. The bonus
+#              applies to every intronic base in the interval of the hint.
+#      intron: An intron gets the bonus if and only if it is exactly as in the hint.
+#     CDSpart: part of the coding part of an exon. (CDS = coding sequence)
+#         CDS: coding part of an exon with exact boundaries. For internal exons
+#              of a multi exon gene this is identical to the biological
+#              boundaries of the exon. For the first and the last coding exon
+#              the boundaries are the boundaries of the coding sequence (start, stop).
+#         UTR: exact boundaries of a UTR exon or the untranslated part of a
+#              partially coding exon.
+#     UTRpart: The hint interval must be included in the UTR part of an exon.
+#      irpart: The bonus applies to every base of the intergenic region. If UTR
+#              prediction is turned on (--UTR=on) then UTR is considered
+#              genic. If you choose against the usual meaning the bonus of
+#              irparts to be much smaller than 1 in the configuration file you
+#              can force AUGUSTUS to not predict an intergenic region in the
+#              specified interval. This is useful if you want to tell AUGUSTUS
+#              that two distant exons belong to the same gene, when AUGUSTUS
+#              tends to split that gene into smaller genes.
+# nonexonpart: intergenic region or intron. The bonus applies to very non-exon
+#              base that overlaps with the interval from the hint. It is
+#              geometric in the length of that overlap, so choose it close to
+#              1.0. This is useful as a weak kind of masking, e.g. when it is
+#              unlikely that a retroposed gene contains a coding region but you
+#              do not want to completely forbid exons.
+#   genicpart: everything that is not intergenic region, i.e. intron or exon or UTR if
+#              applicable. The bonus applies to every genic base that overlaps with the
+#              interval from the hint. This can be used in particular to make Augustus
+#              predict one gene between positions a and b if a and b are experimentally
+#              confirmed to be part of the same gene, e.g. through ESTs from the same clone.
+#              alias: nonirpart
+#
+# Any hints of types dss, intron, exon, CDS, UTR that (implicitly) suggest a donor splice
+# site allow AUGUSTUS to predict a donor splice site that has a GC instead of the much more common GT.
+# AUGUSTUS does not predict a GC donor splice site unless there is a hint for one.
+# 
+# Starting in column number 4 you can tell AUGUSTUS how to modify the bonus 
+# depending on the source of the hint and the score of the hint. 
+# The score of the hints is specified in the 6th column of the hint gff/gtf.
+# If the score is used at all, the score is not used directly through some
+# conversion formula but by distinguishing different classes of scores, e.g. low
+# score, medium score, high score. The format is the following:
+# First, you specify the source character, then the number of classes (say n), then you
+# specify the score boundaries that separate the classes (n-1 thresholds) and then you specify
+# for each score class the multiplicative modifier to the bonus (n factors). 
+# 
+# Examples:
+# 
+# M 1 1e+100
+# means for the manual hint there is only one score class, the bonus for this
+# type of hint is multiplied by 10^100. This practically forces AUGUSTUS to obey
+# all manual hints.
+# 
+# T    2       1.5 1 5e29
+# For the transMap hints distinguish 2 classes. Those with a score below 1.5 and
+# with a score above 1.5. The bonus if the lower score hints is unchanged and
+# the bonus of the higher score hints is multiplied by 5x10^29.
+# 
+# D    8     1.5  2.5  3.5  4.5  5.5  6.5  7.5  0.58  0.4  0.2  2.9  0.87  0.44 0.31  7.3
+# Use 8 score classes for the DIALIGN hints. DIALIGN hints give a score, a strand and
+# reading frame information for CDSpart hints. The strand and reading frame are often correct but not
+# often enough to rely on them. To account for that I generated hints for all
+# 6 combinations of a strand and reading frame and then used 2x2x2=8 different
+# score classes:
+# {low score, high score} x {DIALIGN strand, opposite strand} x {DIALIGN reading frame, other reading frame}
+# This example shows that scores don't have to be monotonous. A higher score
+# does not have to mean a higher bonus. They are merely a way of classifying the
+# hints into categories as you wish. In particular, you could get the effect of
+# having different sources by having just hints of one source and then distinguishing
+# more scores classes.
+# 
+# 
+# Future plans:
+# - Add fuzzy intron hints. Introns get a bonus only when they approximately
+# have the same boundaries as in the hint.
+# - Make the splice site hints fuzzy also. Allow a hint interval that contains a
+# likely splice site, as opposed to only an individual position.
+# - Write a program that automatically optimizes the boni and mali given an
+# annotated test set of genes and hints for that set of sequences.
+
diff -r 1fbb1135da16 -r 0d425a4b6896 test-data/hints.truncated.adjusted.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hints.truncated.adjusted.gff	Thu May 23 18:17:22 2019 -0400
@@ -0,0 +1,482 @@
+chr2R	b2h	ep	8895	9191	0	.	.	grp=gi|2700091;pri=4;src=E
+chr2R	b2h	ep	8895	9191	0	.	.	grp=gi|2700091;pri=4;src=E
+chr2R	b2h	ep	9252	9338	0	.	.	grp=gi|2700091;pri=4;src=E
+chr2R	b2h	ep	9252	9338	0	.	.	grp=gi|2700091;pri=4;src=E
+chr2R	b2h	ep	8878	9191	0	.	.	grp=gi|2701304;pri=4;src=E
+chr2R	b2h	ep	8878	9191	0	.	.	grp=gi|2701304;pri=4;src=E
+chr2R	b2h	ep	9252	9338	0	.	.	grp=gi|2701304;pri=4;src=E
+chr2R	b2h	ep	9252	9338	0	.	.	grp=gi|2701304;pri=4;src=E
+chr2R	b2h	ep	8880	9191	0	.	.	grp=gi|2701309;pri=4;src=E
+chr2R	b2h	ep	8880	9191	0	.	.	grp=gi|2701309;pri=4;src=E
+chr2R	b2h	ep	9252	9338	0	.	.	grp=gi|2701309;pri=4;src=E
+chr2R	b2h	ep	9252	9338	0	.	.	grp=gi|2701309;pri=4;src=E
+chr2R	b2h	ep	8559	8630	0	.	.	grp=gi|2701440;pri=4;src=E
+chr2R	b2h	ep	8559	8630	0	.	.	grp=gi|2701440;pri=4;src=E
+chr2R	b2h	ep	8866	9172	0	.	.	grp=gi|2701440;pri=4;src=E
+chr2R	b2h	ep	8866	9172	0	.	.	grp=gi|2701440;pri=4;src=E
+chr2R	b2h	ep	8782	8811	0	.	.	grp=gi|2871896;pri=4;src=E
+chr2R	b2h	ep	8782	8811	0	.	.	grp=gi|2871896;pri=4;src=E
+chr2R	b2h	ep	9252	9360	0	.	.	grp=gi|2871896;pri=4;src=E
+chr2R	b2h	ep	9252	9360	0	.	.	grp=gi|2871896;pri=4;src=E
+chr2R	b2h	ep	9077	9191	0	.	.	grp=gi|3101873;pri=4;src=E
+chr2R	b2h	ep	9077	9191	0	.	.	grp=gi|3101873;pri=4;src=E
+chr2R	b2h	ep	9252	9337	0	.	.	grp=gi|3101873;pri=4;src=E
+chr2R	b2h	ep	9252	9337	0	.	.	grp=gi|3101873;pri=4;src=E
+chr2R	b2h	ep	8489	8630	0	.	.	grp=gi|4203815;pri=4;src=E
+chr2R	b2h	ep	8489	8630	0	.	.	grp=gi|4203815;pri=4;src=E
+chr2R	b2h	ep	9252	9339	0	.	.	grp=gi|4203815;pri=4;src=E
+chr2R	b2h	ep	9252	9339	0	.	.	grp=gi|4203815;pri=4;src=E
+chr2R	b2h	ep	8575	8630	0	.	.	grp=gi|4245769;pri=4;src=E
+chr2R	b2h	ep	8575	8630	0	.	.	grp=gi|4245769;pri=4;src=E
+chr2R	b2h	ep	9252	9340	0	.	.	grp=gi|4245769;pri=4;src=E
+chr2R	b2h	ep	9252	9340	0	.	.	grp=gi|4245769;pri=4;src=E
+chr2R	b2h	ep	8563	8630	0	.	.	grp=gi|4245770;pri=4;src=E
+chr2R	b2h	ep	8563	8630	0	.	.	grp=gi|4245770;pri=4;src=E
+chr2R	b2h	ep	9252	9340	0	.	.	grp=gi|4245770;pri=4;src=E
+chr2R	b2h	ep	9252	9340	0	.	.	grp=gi|4245770;pri=4;src=E
+chr2R	b2h	ep	8487	8630	0	.	.	grp=gi|13769068;pri=4;src=E
+chr2R	b2h	ep	8487	8630	0	.	.	grp=gi|13769068;pri=4;src=E
+chr2R	b2h	ep	9252	9340	0	.	.	grp=gi|13769068;pri=4;src=E
+chr2R	b2h	ep	9252	9340	0	.	.	grp=gi|13769068;pri=4;src=E
+chr2R	b2h	ep	8550	8630	0	.	.	grp=gi|14693753;pri=4;src=E
+chr2R	b2h	ep	8550	8630	0	.	.	grp=gi|14693753;pri=4;src=E
+chr2R	b2h	ep	9252	9372	0	.	.	grp=gi|14693753;pri=4;src=E
+chr2R	b2h	ep	9252	9372	0	.	.	grp=gi|14693753;pri=4;src=E
+chr2R	b2h	ep	8613	8630	0	.	.	grp=gi|14695912;pri=4;src=E
+chr2R	b2h	ep	8613	8630	0	.	.	grp=gi|14695912;pri=4;src=E
+chr2R	b2h	ep	9252	9372	0	.	.	grp=gi|14695912;pri=4;src=E
+chr2R	b2h	ep	9252	9372	0	.	.	grp=gi|14695912;pri=4;src=E
+chr2R	b2h	ep	8551	8630	0	.	.	grp=gi|14699170;pri=4;src=E
+chr2R	b2h	ep	8551	8630	0	.	.	grp=gi|14699170;pri=4;src=E
+chr2R	b2h	ep	9252	9372	0	.	.	grp=gi|14699170;pri=4;src=E
+chr2R	b2h	ep	9252	9372	0	.	.	grp=gi|14699170;pri=4;src=E
+chr2R	b2h	ep	8614	8630	0	.	.	grp=gi|14700619;pri=4;src=E
+chr2R	b2h	ep	8614	8630	0	.	.	grp=gi|14700619;pri=4;src=E
+chr2R	b2h	ep	9252	9372	0	.	.	grp=gi|14700619;pri=4;src=E
+chr2R	b2h	ep	9252	9372	0	.	.	grp=gi|14700619;pri=4;src=E
+chr2R	b2h	ep	8536	8630	0	.	.	grp=gi|15539951;pri=4;src=E
+chr2R	b2h	ep	8536	8630	0	.	.	grp=gi|15539951;pri=4;src=E
+chr2R	b2h	ep	9252	9346	0	.	.	grp=gi|15539951;pri=4;src=E
+chr2R	b2h	ep	9252	9346	0	.	.	grp=gi|15539951;pri=4;src=E
+chr2R	b2h	ep	7756	8449	0	.	.	grp=gi|15542574;pri=4;src=E
+chr2R	b2h	ep	7756	8449	0	.	.	grp=gi|15542574;pri=4;src=E
+chr2R	b2h	ep	8705	8811	0	.	.	grp=gi|15543159;pri=4;src=E
+chr2R	b2h	ep	8705	8811	0	.	.	grp=gi|15543159;pri=4;src=E
+chr2R	b2h	ep	9252	9342	0	.	.	grp=gi|15543159;pri=4;src=E
+chr2R	b2h	ep	9252	9342	0	.	.	grp=gi|15543159;pri=4;src=E
+chr2R	b2h	ep	8492	8630	0	.	.	grp=gi|15543927;pri=4;src=E
+chr2R	b2h	ep	8492	8630	0	.	.	grp=gi|15543927;pri=4;src=E
+chr2R	b2h	ep	9252	9359	0	.	.	grp=gi|15543927;pri=4;src=E
+chr2R	b2h	ep	9252	9359	0	.	.	grp=gi|15543927;pri=4;src=E
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+chr2R	b2h	ep	8508	8630	0	.	.	grp=gi|38623822;pri=4;src=E
+chr2R	b2h	ep	9252	9355	0	.	.	grp=gi|38623822;pri=4;src=E
+chr2R	b2h	ep	9252	9355	0	.	.	grp=gi|38623822;pri=4;src=E
+chr2R	b2h	exon	8695	8811	0	.	.	grp=gi|2701440;pri=4;src=E
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+chr2R	b2h	exon	8866	9191	0	.	.	grp=gi|2871896;pri=4;src=E
+chr2R	b2h	exon	8866	9191	0	.	.	grp=gi|2871896;pri=4;src=E
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+chr2R	b2h	exon	8866	9191	0	.	.	grp=gi|15543159;pri=4;src=E
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+chr2R	b2h	intron	8631	8694	0	.	.	grp=gi|2701440;pri=4;src=E
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+chr2R	b2h	intron	8631	8694	0	.	.	grp=gi|4245769;pri=4;src=E
+chr2R	b2h	intron	8631	8694	0	.	.	grp=gi|4245770;pri=4;src=E
+chr2R	b2h	intron	8631	8694	0	.	.	grp=gi|4245770;pri=4;src=E
+chr2R	b2h	intron	8631	8694	0	.	.	grp=gi|13769068;pri=4;src=E
+chr2R	b2h	intron	8631	8694	0	.	.	grp=gi|13769068;pri=4;src=E
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+chr2R	b2h	intron	8631	8694	0	.	.	grp=gi|14700619;pri=4;src=E
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+chr2R	b2h	intron	8631	8694	0	.	.	grp=gi|15539951;pri=4;src=E
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+chr2R	b2h	intron	8631	8694	0	.	.	grp=gi|38623822;pri=4;src=E
+chr2R	b2h	intron	8631	8694	0	.	.	grp=gi|38623822;pri=4;src=E
+chr2R	b2h	intron	8812	8865	0	.	.	grp=gi|2701440;pri=4;src=E
+chr2R	b2h	intron	8812	8865	0	.	.	grp=gi|2701440;pri=4;src=E
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+chr2R	b2h	intron	8812	8865	0	.	.	grp=gi|2871896;pri=4;src=E
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+chr2R	b2h	intron	8812	8865	0	.	.	grp=gi|4203815;pri=4;src=E
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+chr2R	b2h	intron	8812	8865	0	.	.	grp=gi|4245769;pri=4;src=E
+chr2R	b2h	intron	8812	8865	0	.	.	grp=gi|4245770;pri=4;src=E
+chr2R	b2h	intron	8812	8865	0	.	.	grp=gi|4245770;pri=4;src=E
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+chr2R	b2h	intron	8812	8865	0	.	.	grp=gi|13769068;pri=4;src=E
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+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|4245770;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|13769068;pri=4;src=E
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+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|14695912;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|14695912;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|14699170;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|14699170;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|14700619;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|14700619;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|15539951;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|15539951;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|15543159;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|15543159;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|15543927;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|15543927;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|38623822;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	grp=gi|38623822;pri=4;src=E
+chr2R	b2h	intron	8631	8694	0	.	.	grp=SRR023546.8642467/1;pri=4;src=E
+chr2R	b2h	intron	8631	8694	0	.	.	grp=SRR023546.8642467/1;pri=4;src=E
+chr2R	b2h	intron	8812	8865	0	.	.	mult=8;pri=4;src=E
+chr2R	b2h	intron	8812	8865	0	.	.	mult=8;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	mult=3;pri=4;src=E
+chr2R	b2h	intron	9192	9251	0	.	.	mult=3;pri=4;src=E
+chr2R	w2h	ep	7551	7560	5.300	.	.	src=W;mult=5;
+chr2R	w2h	ep	7551	7560	5.300	.	.	src=W;mult=5;
+chr2R	w2h	ep	7561	7570	7.400	.	.	src=W;mult=7;
+chr2R	w2h	ep	7561	7570	7.400	.	.	src=W;mult=7;
+chr2R	w2h	ep	7571	7580	9.700	.	.	src=W;mult=9;
+chr2R	w2h	ep	7571	7580	9.700	.	.	src=W;mult=9;
+chr2R	w2h	ep	7581	7590	10.200	.	.	src=W;mult=10;
+chr2R	w2h	ep	7581	7590	10.200	.	.	src=W;mult=10;
+chr2R	w2h	ep	7591	7600	9.000	.	.	src=W;mult=9;
+chr2R	w2h	ep	7591	7600	9.000	.	.	src=W;mult=9;
+chr2R	w2h	ep	7601	7610	9.700	.	.	src=W;mult=9;
+chr2R	w2h	ep	7601	7610	9.700	.	.	src=W;mult=9;
+chr2R	w2h	ep	7611	7620	13.000	.	.	src=W;mult=13;
+chr2R	w2h	ep	7611	7620	13.000	.	.	src=W;mult=13;
+chr2R	w2h	ep	7621	7630	15.300	.	.	src=W;mult=15;
+chr2R	w2h	ep	7621	7630	15.300	.	.	src=W;mult=15;
+chr2R	w2h	ep	7631	7640	13.400	.	.	src=W;mult=13;
+chr2R	w2h	ep	7631	7640	13.400	.	.	src=W;mult=13;
+chr2R	w2h	ep	7641	7650	13.700	.	.	src=W;mult=13;
+chr2R	w2h	ep	7641	7650	13.700	.	.	src=W;mult=13;
+chr2R	w2h	ep	7651	7660	14.400	.	.	src=W;mult=14;
+chr2R	w2h	ep	7651	7660	14.400	.	.	src=W;mult=14;
+chr2R	w2h	ep	7661	7670	14.600	.	.	src=W;mult=14;
+chr2R	w2h	ep	7661	7670	14.600	.	.	src=W;mult=14;
+chr2R	w2h	ep	7671	7680	16.800	.	.	src=W;mult=16;
+chr2R	w2h	ep	7671	7680	16.800	.	.	src=W;mult=16;
+chr2R	w2h	ep	7681	7690	16.700	.	.	src=W;mult=16;
+chr2R	w2h	ep	7681	7690	16.700	.	.	src=W;mult=16;
+chr2R	w2h	ep	7691	7700	17.600	.	.	src=W;mult=17;
+chr2R	w2h	ep	7691	7700	17.600	.	.	src=W;mult=17;
+chr2R	w2h	ep	7701	7710	20.300	.	.	src=W;mult=20;
+chr2R	w2h	ep	7701	7710	20.300	.	.	src=W;mult=20;
+chr2R	w2h	ep	7711	7720	20.500	.	.	src=W;mult=20;
+chr2R	w2h	ep	7711	7720	20.500	.	.	src=W;mult=20;
+chr2R	w2h	ep	7721	7730	18.800	.	.	src=W;mult=18;
+chr2R	w2h	ep	7721	7730	18.800	.	.	src=W;mult=18;
+chr2R	w2h	ep	7731	7740	16.700	.	.	src=W;mult=16;
+chr2R	w2h	ep	7731	7740	16.700	.	.	src=W;mult=16;
+chr2R	w2h	ep	7741	7750	16.800	.	.	src=W;mult=16;
+chr2R	w2h	ep	7741	7750	16.800	.	.	src=W;mult=16;
+chr2R	w2h	ep	7751	7760	15.500	.	.	src=W;mult=15;
+chr2R	w2h	ep	7751	7760	15.500	.	.	src=W;mult=15;
+chr2R	w2h	ep	7761	7770	17.400	.	.	src=W;mult=17;
+chr2R	w2h	ep	7761	7770	17.400	.	.	src=W;mult=17;
+chr2R	w2h	ep	7771	7780	19.500	.	.	src=W;mult=19;
+chr2R	w2h	ep	7771	7780	19.500	.	.	src=W;mult=19;
+chr2R	w2h	ep	7781	7790	19.100	.	.	src=W;mult=19;
+chr2R	w2h	ep	7781	7790	19.100	.	.	src=W;mult=19;
+chr2R	w2h	ep	7791	7800	20.100	.	.	src=W;mult=20;
+chr2R	w2h	ep	7791	7800	20.100	.	.	src=W;mult=20;
+chr2R	w2h	ep	7801	7810	22.700	.	.	src=W;mult=22;
+chr2R	w2h	ep	7801	7810	22.700	.	.	src=W;mult=22;
+chr2R	w2h	ep	7811	7820	24.400	.	.	src=W;mult=24;
+chr2R	w2h	ep	7811	7820	24.400	.	.	src=W;mult=24;
+chr2R	w2h	ep	7821	7830	23.600	.	.	src=W;mult=23;
+chr2R	w2h	ep	7821	7830	23.600	.	.	src=W;mult=23;
+chr2R	w2h	ep	7831	7840	19.500	.	.	src=W;mult=19;
+chr2R	w2h	ep	7831	7840	19.500	.	.	src=W;mult=19;
+chr2R	w2h	ep	7841	7850	16.200	.	.	src=W;mult=16;
+chr2R	w2h	ep	7841	7850	16.200	.	.	src=W;mult=16;
+chr2R	w2h	ep	7851	7860	14.800	.	.	src=W;mult=14;
+chr2R	w2h	ep	7851	7860	14.800	.	.	src=W;mult=14;
+chr2R	w2h	ep	7861	7870	14.000	.	.	src=W;mult=14;
+chr2R	w2h	ep	7861	7870	14.000	.	.	src=W;mult=14;
+chr2R	w2h	ep	7871	7880	14.300	.	.	src=W;mult=14;
+chr2R	w2h	ep	7871	7880	14.300	.	.	src=W;mult=14;
+chr2R	w2h	ep	7881	7890	11.400	.	.	src=W;mult=11;
+chr2R	w2h	ep	7881	7890	11.400	.	.	src=W;mult=11;
+chr2R	w2h	ep	7891	7900	12.900	.	.	src=W;mult=12;
+chr2R	w2h	ep	7891	7900	12.900	.	.	src=W;mult=12;
+chr2R	w2h	ep	7901	7910	14.000	.	.	src=W;mult=14;
+chr2R	w2h	ep	7901	7910	14.000	.	.	src=W;mult=14;
+chr2R	w2h	ep	7911	7920	14.800	.	.	src=W;mult=14;
+chr2R	w2h	ep	7911	7920	14.800	.	.	src=W;mult=14;
+chr2R	w2h	ep	7921	7930	14.800	.	.	src=W;mult=14;
+chr2R	w2h	ep	7921	7930	14.800	.	.	src=W;mult=14;
+chr2R	w2h	ep	7931	7940	14.200	.	.	src=W;mult=14;
+chr2R	w2h	ep	7931	7940	14.200	.	.	src=W;mult=14;
+chr2R	w2h	ep	7941	7950	11.800	.	.	src=W;mult=11;
+chr2R	w2h	ep	7941	7950	11.800	.	.	src=W;mult=11;
+chr2R	w2h	ep	7951	7960	13.300	.	.	src=W;mult=13;
+chr2R	w2h	ep	7951	7960	13.300	.	.	src=W;mult=13;
+chr2R	w2h	ep	7961	7970	13.700	.	.	src=W;mult=13;
+chr2R	w2h	ep	7961	7970	13.700	.	.	src=W;mult=13;
+chr2R	w2h	ep	7971	7980	12.400	.	.	src=W;mult=12;
+chr2R	w2h	ep	7971	7980	12.400	.	.	src=W;mult=12;
+chr2R	w2h	ep	7981	7990	17.100	.	.	src=W;mult=17;
+chr2R	w2h	ep	7981	7990	17.100	.	.	src=W;mult=17;
+chr2R	w2h	ep	7991	8000	19.900	.	.	src=W;mult=19;
+chr2R	w2h	ep	7991	8000	19.900	.	.	src=W;mult=19;
+chr2R	w2h	ep	8001	8010	20.000	.	.	src=W;mult=20;
+chr2R	w2h	ep	8001	8010	20.000	.	.	src=W;mult=20;
+chr2R	w2h	ep	8011	8020	22.700	.	.	src=W;mult=22;
+chr2R	w2h	ep	8011	8020	22.700	.	.	src=W;mult=22;
+chr2R	w2h	ep	8021	8030	21.900	.	.	src=W;mult=21;
+chr2R	w2h	ep	8021	8030	21.900	.	.	src=W;mult=21;
+chr2R	w2h	ep	8031	8040	21.000	.	.	src=W;mult=21;
+chr2R	w2h	ep	8031	8040	21.000	.	.	src=W;mult=21;
+chr2R	w2h	ep	8041	8050	25.100	.	.	src=W;mult=25;
+chr2R	w2h	ep	8041	8050	25.100	.	.	src=W;mult=25;
+chr2R	w2h	ep	8051	8060	23.500	.	.	src=W;mult=23;
+chr2R	w2h	ep	8051	8060	23.500	.	.	src=W;mult=23;
+chr2R	w2h	ep	8061	8070	20.300	.	.	src=W;mult=20;
+chr2R	w2h	ep	8061	8070	20.300	.	.	src=W;mult=20;
+chr2R	w2h	ep	8071	8080	19.800	.	.	src=W;mult=19;
+chr2R	w2h	ep	8071	8080	19.800	.	.	src=W;mult=19;
+chr2R	w2h	ep	8081	8090	19.100	.	.	src=W;mult=19;
+chr2R	w2h	ep	8081	8090	19.100	.	.	src=W;mult=19;
+chr2R	w2h	ep	8091	8100	15.400	.	.	src=W;mult=15;
+chr2R	w2h	ep	8091	8100	15.400	.	.	src=W;mult=15;
+chr2R	w2h	ep	8101	8110	15.800	.	.	src=W;mult=15;
+chr2R	w2h	ep	8101	8110	15.800	.	.	src=W;mult=15;
+chr2R	w2h	ep	8111	8120	12.500	.	.	src=W;mult=12;
+chr2R	w2h	ep	8111	8120	12.500	.	.	src=W;mult=12;
+chr2R	w2h	ep	8121	8130	9.400	.	.	src=W;mult=9;
+chr2R	w2h	ep	8121	8130	9.400	.	.	src=W;mult=9;
+chr2R	w2h	ep	8131	8140	5.800	.	.	src=W;mult=5;
+chr2R	w2h	ep	8131	8140	5.800	.	.	src=W;mult=5;
+chr2R	w2h	ep	8210	8219	4.200	.	.	src=W;mult=4;
+chr2R	w2h	ep	8210	8219	4.200	.	.	src=W;mult=4;
+chr2R	w2h	ep	8220	8229	4.200	.	.	src=W;mult=4;
+chr2R	w2h	ep	8220	8229	4.200	.	.	src=W;mult=4;
+chr2R	w2h	ep	8230	8239	4.200	.	.	src=W;mult=4;
+chr2R	w2h	ep	8230	8239	4.200	.	.	src=W;mult=4;
+chr2R	w2h	ep	8240	8249	5.000	.	.	src=W;mult=5;
+chr2R	w2h	ep	8240	8249	5.000	.	.	src=W;mult=5;
+chr2R	w2h	ep	8260	8269	4.800	.	.	src=W;mult=4;
+chr2R	w2h	ep	8260	8269	4.800	.	.	src=W;mult=4;
+chr2R	w2h	ep	8270	8279	8.000	.	.	src=W;mult=8;
+chr2R	w2h	ep	8270	8279	8.000	.	.	src=W;mult=8;
+chr2R	w2h	ep	8280	8289	8.000	.	.	src=W;mult=8;
+chr2R	w2h	ep	8280	8289	8.000	.	.	src=W;mult=8;
+chr2R	w2h	ep	8290	8299	7.300	.	.	src=W;mult=7;
+chr2R	w2h	ep	8290	8299	7.300	.	.	src=W;mult=7;
+chr2R	w2h	ep	8300	8309	7.000	.	.	src=W;mult=7;
+chr2R	w2h	ep	8300	8309	7.000	.	.	src=W;mult=7;
+chr2R	w2h	ep	8310	8319	7.300	.	.	src=W;mult=7;
+chr2R	w2h	ep	8310	8319	7.300	.	.	src=W;mult=7;
+chr2R	w2h	ep	8320	8329	9.600	.	.	src=W;mult=9;
+chr2R	w2h	ep	8320	8329	9.600	.	.	src=W;mult=9;
+chr2R	w2h	ep	8330	8339	11.600	.	.	src=W;mult=11;
+chr2R	w2h	ep	8330	8339	11.600	.	.	src=W;mult=11;
+chr2R	w2h	ep	8340	8349	10.800	.	.	src=W;mult=10;
+chr2R	w2h	ep	8340	8349	10.800	.	.	src=W;mult=10;
+chr2R	w2h	ep	8350	8359	10.100	.	.	src=W;mult=10;
+chr2R	w2h	ep	8350	8359	10.100	.	.	src=W;mult=10;
+chr2R	w2h	ep	8360	8369	11.000	.	.	src=W;mult=11;
+chr2R	w2h	ep	8360	8369	11.000	.	.	src=W;mult=11;
+chr2R	w2h	ep	8370	8379	13.400	.	.	src=W;mult=13;
+chr2R	w2h	ep	8370	8379	13.400	.	.	src=W;mult=13;
+chr2R	w2h	ep	8380	8389	13.000	.	.	src=W;mult=13;
+chr2R	w2h	ep	8380	8389	13.000	.	.	src=W;mult=13;
+chr2R	w2h	ep	8390	8399	11.800	.	.	src=W;mult=11;
+chr2R	w2h	ep	8390	8399	11.800	.	.	src=W;mult=11;
+chr2R	w2h	ep	8400	8409	9.000	.	.	src=W;mult=9;
+chr2R	w2h	ep	8400	8409	9.000	.	.	src=W;mult=9;
+chr2R	w2h	ep	8410	8419	7.700	.	.	src=W;mult=7;
+chr2R	w2h	ep	8410	8419	7.700	.	.	src=W;mult=7;
+chr2R	w2h	ep	8420	8429	8.900	.	.	src=W;mult=8;
+chr2R	w2h	ep	8420	8429	8.900	.	.	src=W;mult=8;
+chr2R	w2h	ep	8430	8439	11.500	.	.	src=W;mult=11;
+chr2R	w2h	ep	8430	8439	11.500	.	.	src=W;mult=11;
+chr2R	w2h	ep	8440	8449	11.400	.	.	src=W;mult=11;
+chr2R	w2h	ep	8440	8449	11.400	.	.	src=W;mult=11;
+chr2R	w2h	ep	8450	8459	9.800	.	.	src=W;mult=9;
+chr2R	w2h	ep	8450	8459	9.800	.	.	src=W;mult=9;
+chr2R	w2h	ep	8460	8469	10.200	.	.	src=W;mult=10;
+chr2R	w2h	ep	8460	8469	10.200	.	.	src=W;mult=10;
+chr2R	w2h	ep	8470	8479	10.800	.	.	src=W;mult=10;
+chr2R	w2h	ep	8470	8479	10.800	.	.	src=W;mult=10;
+chr2R	w2h	ep	8480	8489	10.000	.	.	src=W;mult=10;
+chr2R	w2h	ep	8480	8489	10.000	.	.	src=W;mult=10;
+chr2R	w2h	ep	8490	8499	8.200	.	.	src=W;mult=8;
+chr2R	w2h	ep	8490	8499	8.200	.	.	src=W;mult=8;
+chr2R	w2h	ep	8500	8509	7.100	.	.	src=W;mult=7;
+chr2R	w2h	ep	8500	8509	7.100	.	.	src=W;mult=7;
+chr2R	w2h	ep	8510	8519	4.200	.	.	src=W;mult=4;
+chr2R	w2h	ep	8510	8519	4.200	.	.	src=W;mult=4;
+chr2R	w2h	ep	8520	8529	4.700	.	.	src=W;mult=4;
+chr2R	w2h	ep	8520	8529	4.700	.	.	src=W;mult=4;
+chr2R	w2h	ep	8739	8748	4.300	.	.	src=W;mult=4;
+chr2R	w2h	ep	8739	8748	4.300	.	.	src=W;mult=4;
+chr2R	w2h	ep	8749	8758	5.700	.	.	src=W;mult=5;
+chr2R	w2h	ep	8749	8758	5.700	.	.	src=W;mult=5;
+chr2R	w2h	ep	8759	8768	8.000	.	.	src=W;mult=8;
+chr2R	w2h	ep	8759	8768	8.000	.	.	src=W;mult=8;
+chr2R	w2h	ep	8769	8778	8.000	.	.	src=W;mult=8;
+chr2R	w2h	ep	8769	8778	8.000	.	.	src=W;mult=8;
+chr2R	w2h	ep	8779	8788	8.600	.	.	src=W;mult=8;
+chr2R	w2h	ep	8779	8788	8.600	.	.	src=W;mult=8;
+chr2R	w2h	ep	8789	8798	8.700	.	.	src=W;mult=8;
+chr2R	w2h	ep	8789	8798	8.700	.	.	src=W;mult=8;
+chr2R	w2h	ep	8880	8889	12.700	.	.	src=W;mult=12;
+chr2R	w2h	ep	8880	8889	12.700	.	.	src=W;mult=12;
+chr2R	w2h	ep	8890	8899	15.300	.	.	src=W;mult=15;
+chr2R	w2h	ep	8890	8899	15.300	.	.	src=W;mult=15;
+chr2R	w2h	ep	8900	8909	17.600	.	.	src=W;mult=17;
+chr2R	w2h	ep	8900	8909	17.600	.	.	src=W;mult=17;
+chr2R	w2h	ep	8910	8919	17.900	.	.	src=W;mult=17;
+chr2R	w2h	ep	8910	8919	17.900	.	.	src=W;mult=17;
+chr2R	w2h	ep	8920	8929	17.200	.	.	src=W;mult=17;
+chr2R	w2h	ep	8920	8929	17.200	.	.	src=W;mult=17;
+chr2R	w2h	ep	8930	8939	18.400	.	.	src=W;mult=18;
+chr2R	w2h	ep	8930	8939	18.400	.	.	src=W;mult=18;
+chr2R	w2h	ep	8940	8949	19.900	.	.	src=W;mult=19;
+chr2R	w2h	ep	8940	8949	19.900	.	.	src=W;mult=19;
+chr2R	w2h	ep	8950	8959	19.100	.	.	src=W;mult=19;
+chr2R	w2h	ep	8950	8959	19.100	.	.	src=W;mult=19;
+chr2R	w2h	ep	8960	8969	15.200	.	.	src=W;mult=15;
+chr2R	w2h	ep	8960	8969	15.200	.	.	src=W;mult=15;
+chr2R	w2h	ep	8970	8979	13.000	.	.	src=W;mult=13;
+chr2R	w2h	ep	8970	8979	13.000	.	.	src=W;mult=13;
+chr2R	w2h	ep	8980	8989	14.700	.	.	src=W;mult=14;
+chr2R	w2h	ep	8980	8989	14.700	.	.	src=W;mult=14;
+chr2R	w2h	ep	8990	8999	14.500	.	.	src=W;mult=14;
+chr2R	w2h	ep	8990	8999	14.500	.	.	src=W;mult=14;
+chr2R	w2h	ep	9000	9009	14.500	.	.	src=W;mult=14;
+chr2R	w2h	ep	9000	9009	14.500	.	.	src=W;mult=14;
+chr2R	w2h	ep	9010	9019	12.500	.	.	src=W;mult=12;
+chr2R	w2h	ep	9010	9019	12.500	.	.	src=W;mult=12;
+chr2R	w2h	ep	9020	9029	11.900	.	.	src=W;mult=11;
+chr2R	w2h	ep	9020	9029	11.900	.	.	src=W;mult=11;
+chr2R	w2h	ep	9030	9039	12.100	.	.	src=W;mult=12;
+chr2R	w2h	ep	9030	9039	12.100	.	.	src=W;mult=12;
+chr2R	w2h	ep	9040	9049	10.000	.	.	src=W;mult=10;
+chr2R	w2h	ep	9040	9049	10.000	.	.	src=W;mult=10;
+chr2R	w2h	ep	9050	9059	9.700	.	.	src=W;mult=9;
+chr2R	w2h	ep	9050	9059	9.700	.	.	src=W;mult=9;
+chr2R	w2h	ep	9060	9069	10.600	.	.	src=W;mult=10;
+chr2R	w2h	ep	9060	9069	10.600	.	.	src=W;mult=10;
+chr2R	w2h	ep	9070	9079	12.300	.	.	src=W;mult=12;
+chr2R	w2h	ep	9070	9079	12.300	.	.	src=W;mult=12;
+chr2R	w2h	ep	9080	9089	13.100	.	.	src=W;mult=13;
+chr2R	w2h	ep	9080	9089	13.100	.	.	src=W;mult=13;
+chr2R	w2h	ep	9090	9099	13.400	.	.	src=W;mult=13;
+chr2R	w2h	ep	9090	9099	13.400	.	.	src=W;mult=13;
+chr2R	w2h	ep	9100	9109	12.000	.	.	src=W;mult=12;
+chr2R	w2h	ep	9100	9109	12.000	.	.	src=W;mult=12;
+chr2R	w2h	ep	9110	9119	10.700	.	.	src=W;mult=10;
+chr2R	w2h	ep	9110	9119	10.700	.	.	src=W;mult=10;
+chr2R	w2h	ep	9120	9129	11.000	.	.	src=W;mult=11;
+chr2R	w2h	ep	9120	9129	11.000	.	.	src=W;mult=11;
+chr2R	w2h	ep	9130	9139	10.900	.	.	src=W;mult=10;
+chr2R	w2h	ep	9130	9139	10.900	.	.	src=W;mult=10;
+chr2R	w2h	ep	9140	9149	7.900	.	.	src=W;mult=7;
+chr2R	w2h	ep	9140	9149	7.900	.	.	src=W;mult=7;
+chr2R	w2h	ep	9150	9159	4.900	.	.	src=W;mult=4;
+chr2R	w2h	ep	9150	9159	4.900	.	.	src=W;mult=4;
+chr2R	w2h	ep	9160	9169	4.400	.	.	src=W;mult=4;
+chr2R	w2h	ep	9160	9169	4.400	.	.	src=W;mult=4;
+chr2R	w2h	ep	9265	9274	11.400	.	.	src=W;mult=11;
+chr2R	w2h	ep	9265	9274	11.400	.	.	src=W;mult=11;
+chr2R	w2h	ep	9275	9284	12.800	.	.	src=W;mult=12;
+chr2R	w2h	ep	9275	9284	12.800	.	.	src=W;mult=12;
+chr2R	w2h	ep	9285	9294	13.100	.	.	src=W;mult=13;
+chr2R	w2h	ep	9285	9294	13.100	.	.	src=W;mult=13;
+chr2R	w2h	ep	9295	9304	13.600	.	.	src=W;mult=13;
+chr2R	w2h	ep	9295	9304	13.600	.	.	src=W;mult=13;
+chr2R	w2h	ep	9305	9314	13.000	.	.	src=W;mult=13;
+chr2R	w2h	ep	9305	9314	13.000	.	.	src=W;mult=13;
+chr2R	w2h	ep	9315	9324	12.400	.	.	src=W;mult=12;
+chr2R	w2h	ep	9315	9324	12.400	.	.	src=W;mult=12;
+chr2R	w2h	ep	9325	9334	9.000	.	.	src=W;mult=9;
+chr2R	w2h	ep	9325	9334	9.000	.	.	src=W;mult=9;
+chr2R	w2h	ep	9335	9344	5.200	.	.	src=W;mult=5;
+chr2R	w2h	ep	9335	9344	5.200	.	.	src=W;mult=5;