Mercurial > repos > bgruening > repeat_masker

comparison test-data/small_dfam.fasta.cat @ 10:bfc70c8cc5ca draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
author iuc
date Fri, 11 Dec 2020 22:26:02 +0000
parents
children 72aade318318
comparison
equal deleted inserted replaced
9:438f65cb1d14 10:bfc70c8cc5ca
1 18 0.00 0.00 0.00 scaffold_1 613 632 (13519) (GT)n#Simple_repeat 1 20 (0) m_b1s252i0
2
3 scaffold_1 613 GTGTGTGTGTGTGTGTGTGT 632
4
5 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGT 20
6
7 Matrix = Unknown
8 Transitions / transversions = 1.00 (0/0)
9 Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0)
10
11 16 18.30 2.22 2.22 scaffold_1 780 824 (13327) (ATAATA)n#Simple_repeat 1 45 (0) m_b1s252i1
12
13 scaffold_1 780 ATATTAAT-ATACTAAATAATGATAATATTAATTCTAATAATGATA 824
14 v - v - i v vv i
15 (ATAATA)n#Sim 1 ATAATAATAATAAT-AATAATAATAATAATAATAATAATAATAATA 45
16
17 Matrix = Unknown
18 Transitions / transversions = 0.40 (2/5)
19 Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2)
20
21 12 23.88 4.55 0.00 scaffold_1 2231 2274 (11877) (CAGA)n#Simple_repeat 1 46 (0) m_b1s252i2
22
23 scaffold_1 2231 CAGA-AAACAGTCAGCCAATCAGA-GGACAGACTCAGAGACAGACA 2274
24 - i v v iv -i vv v
25 (CAGA)n#Simpl 1 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 46
26
27 Matrix = Unknown
28 Transitions / transversions = 0.50 (3/6)
29 Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2)
30
31 15 18.42 10.20 0.00 scaffold_1 4853 4901 (9250) (TC)n#Simple_repeat 1 54 (0) m_b1s252i3
32
33 scaffold_1 4853 TCTATTTTTCTCTCTCTCTCT-TCGGTCAGTTTCTCT-TCT-TCTC-CTC 4898
34 v i i - vv vv i - - -
35 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50
36
37 scaffold_1 4899 -CTC 4901
38 -
39 (TC)n#Simple_ 51 TCTC 54
40
41 Matrix = Unknown
42 Transitions / transversions = 0.60 (3/5)
43 Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.00 (5 / 5)
44
45 13 19.07 1.82 7.69 scaffold_1 6230 6284 (7867) (TAATTAA)n#Simple_repeat 1 52 (0) m_b1s252i4
46
47 scaffold_1 6230 TAATGAGT-ATTACTAATTAATAATTGGATGAGTTTATGAATTCATCATT 6278
48 v i - v -i - i v - v v
49 (TAATTAA)n#Si 1 TAATTAATAATTAATAATTAATAATT-AAT-AATTAAT-AATTAATAATT 47
50
51 scaffold_1 6279 AAATAA 6284
52 -
53 (TAATTAA)n#Si 48 -AATAA 52
54
55 Matrix = Unknown
56 Transitions / transversions = 0.60 (3/5)
57 Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5)
58
59 15 28.31 0.00 3.51 scaffold_1 6548 6606 (7545) (GACA)n#Simple_repeat 1 57 (0) m_b1s252i5
60
61 scaffold_1 6548 GACAGAGAGATAAACAGACAGACATGGAAACAGAGGGACATAGAAAACAA 6597
62 v i i viv i vi v -v i -
63 (GACA)n#Simpl 1 GACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA-CAGAC-A 48
64
65 scaffold_1 6598 GACAGAGAG 6606
66 v
67 (GACA)n#Simpl 49 GACAGACAG 57
68
69 Matrix = Unknown
70 Transitions / transversions = 0.86 (6/7)
71 Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2)
72
73 180 25.44 1.41 5.88 scaffold_1 8140 8210 (5941) C AmnL2-1#LINE/L2 (11) 2602 2535 m_b1s601i0
74
75 scaffold_1 8140 ACAACATTATTTTGTCTA-CACCCTGCATACAGCACAGTATATTAAATTT 8188
76 v v - ii i v i- v vii ---
77 C AmnL2-1#LINE/ 2602 ACAACTTTATTTTGTATAGCGTCTTTCATACAA-ACTGTATCCCAAA--- 2557
78
79 scaffold_1 8189 AGGTTTTATTAAGTTAAGTAAT 8210
80 v i ivi i
81 C AmnL2-1#LINE/ 2556 ACGCTTTACAGAGTTAAATAAT 2535
82
83 Matrix = 25p39g.matrix
84 Kimura (with divCpGMod) = 29.45
85 Transitions / transversions = 1.43 (10/7)
86 Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5)
87
88 67 2.94 1.43 0.00 scaffold_1 11981 12050 (2170) (CT)n#Simple_repeat 1 71 (0) c_b1s251i0
89
90 scaffold_1 11981 CTCTCTCTCTCTCCCTCTCCCTCTC-CTCTCTCTCTCTCTCTCTCTCTCT 12029
91 i i -
92 (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50
93
94 scaffold_1 12030 CTCTCTCTCTCTCTCTCTCTC 12050
95
96 (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTC 71
97
98 Matrix = Unknown
99 Transitions / transversions = 1.00 (2/0)
100 Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1)
101
102 19 15.37 2.78 0.00 scaffold_1 12078 12113 (2107) (CT)n#Simple_repeat 1 37 (0) m_b1s252i6
103
104 scaffold_1 12078 CTCGCTCTCTCACTCTCTCCCTCTCTC-CCCACTCTC 12113
105 v v i - i v
106 (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 37
107
108 Matrix = Unknown
109 Transitions / transversions = 0.67 (2/3)
110 Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1)
111
112 ## Total Sequences: 1
113 ## Total Length: 14220
114 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220
115 ## Total NonSub ( excluding all non ACGT bases ):14220
116 RepeatMasker version 4.1.1 , default mode
117 run with rmblastn version 2.10.0+
118 RM Library: CONS-Dfam_3.2