Mercurial > repos > bgruening > repeat_masker

comparison test-data/small.fasta.cat @ 3:bdfc22c1c3e3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
author iuc
date Wed, 02 May 2018 20:18:11 -0400
parents
children 438f65cb1d14
comparison
equal deleted inserted replaced
2:5673e72241aa 3:bdfc22c1c3e3
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 67 2.94 1.43 0.00 scaffold_1 11981 12050 (2170) (CT)n#Simple_repeat 1 71 (0) c_b1s251i0
74
75 scaffold_1 11981 CTCTCTCTCTCTCCCTCTCCCTCTC-CTCTCTCTCTCTCTCTCTCTCTCT 12029
76 i i -
77 (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50
78
79 scaffold_1 12030 CTCTCTCTCTCTCTCTCTCTC 12050
80
81 (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTC 71
82
83 Matrix = Unknown
84 Transitions / transversions = 1.00 (2/0)
85 Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1)
86
87 19 15.37 2.78 0.00 scaffold_1 12078 12113 (2107) (CT)n#Simple_repeat 1 37 (0) m_b1s252i6
88
89 scaffold_1 12078 CTCGCTCTCTCACTCTCTCCCTCTCTC-CCCACTCTC 12113
90 v v i - i v
91 (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 37
92
93 Matrix = Unknown
94 Transitions / transversions = 0.67 (2/3)
95 Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1)
96
97 ## Total Sequences: 1
98 ## Total Length: 14220
99 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220
100 ## Total NonSub ( excluding all non ACGT bases ):14220
101 RepeatMasker version open-4.0.7 , default mode
102 run with rmblastn version 2.2.27+
103 RepeatMasker Combined Database: Dfam_Consensus-20170127