Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010782.1 Corchorus capsularis cultivar CVL-1 contig10803, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:885 original size:13 final size:13
Alignment explanation
Indices: 867--922 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
857 TATTAGGTAA
867 TAATAAATACTAT
1 TAATAAATACTAT
*
880 TAATAAATACTAG
1 TAATAAATACTAT
* * * *
893 TAAGTTATTATTAA
1 TAA-TAAATACTAT
907 TAATAAATACTAT
1 TAATAAATACTAT
920 TAA
1 TAA
923 GTTACTGGAT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
13 24 0.73
14 9 0.27
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (13 bp):
TAATAAATACTAT
Found at i:1251 original size:31 final size:31
Alignment explanation
Indices: 1210--1269 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1200 AACATTTTTG
* *
1210 AAATGTCTATTGTACCCTTATTTAACTTTCA
1 AAATGCCTATTATACCCTTATTTAACTTTCA
*
1241 AAATGCCTATTATATCCTTATTTAACTTT
1 AAATGCCTATTATACCCTTATTTAACTTT
1270 TACAGTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (31 bp):
AAATGCCTATTATACCCTTATTTAACTTTCA
Found at i:2376 original size:29 final size:30
Alignment explanation
Indices: 2316--2394 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
2306 GCTAAATATC
* * **
2316 CAAAAAAATTCCTTATGTTTTGTTTTTGGGA
1 CAAAATAATCCCTTATG-TTTGTTTTCAGGA
2347 CAAAATAATCCCTTATGTTT-TTTTCAGGA
1 CAAAATAATCCCTTATGTTTGTTTTCAGGA
* *
2376 CAAATTAATCCTTTATGTT
1 CAAAATAATCCCTTATGTT
2395 CAAAAATGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 24 0.57
30 3 0.07
31 15 0.36
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.44
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTGTTTTCAGGA
Found at i:2572 original size:29 final size:31
Alignment explanation
Indices: 2523--2596 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
2513 CCACGTCAAC
*
2523 AAGGGACTTAATTTGATCC-AAA-AAAAACAT
1 AAGGGA-TTATTTTGATCCAAAAGAAAAACAT
*
2553 AAGGGATTATTTTG-TCCCAAAAGAAAAATAT
1 AAGGGATTATTTTGAT-CCAAAAGAAAAACAT
*
2584 AAGGGATTTTTTT
1 AAGGGATTATTTT
2597 TATATTTAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 1 0.03
29 9 0.24
30 9 0.24
31 19 0.50
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.31
Consensus pattern (31 bp):
AAGGGATTATTTTGATCCAAAAGAAAAACAT
Found at i:2977 original size:30 final size:31
Alignment explanation
Indices: 2938--3008 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
2928 CTCATTTTTG
*
2938 AAACGTAAGGAATTAATTTGT-CCAAAAAAA
1 AAACATAAGGAATTAATTTGTCCCAAAAAAA
* * *
2968 AAACATAAGGGATTATTTTGTCCCAAAAACA
1 AAACATAAGGAATTAATTTGTCCCAAAAAAA
2999 AAACATAAGG
1 AAACATAAGG
3009 GATTTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.51, C:0.13, G:0.14, T:0.23
Consensus pattern (31 bp):
AAACATAAGGAATTAATTTGTCCCAAAAAAA
Found at i:3002 original size:31 final size:30
Alignment explanation
Indices: 2938--3017 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 30
2928 CTCATTTTTG
* * *
2938 AAACGTAAGGAATTAATTTGTCCAAAAAAA
1 AAACATAAGGGATTATTTTGTCCAAAAAAA
*
2968 AAACATAAGGGATTATTTTGTCCCAAAAACA
1 AAACATAAGGGATTATTTTGT-CCAAAAAAA
*
2999 AAACATAAGGGATTTTTTT
1 AAACATAAGGGATTATTTT
3018 TGGGTATTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 18 0.41
31 26 0.59
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (30 bp):
AAACATAAGGGATTATTTTGTCCAAAAAAA
Found at i:3918 original size:17 final size:18
Alignment explanation
Indices: 3890--3923 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3880 AAACTAATTG
*
3890 GTTTTGTTTTAATTTAAT
1 GTTTTGTTTTAAATTAAT
3908 GTTTT-TTTTAAATTAA
1 GTTTTGTTTTAAATTAA
3924 AAATGTCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (18 bp):
GTTTTGTTTTAAATTAAT
Found at i:11539 original size:44 final size:44
Alignment explanation
Indices: 11476--11563 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
11466 AAGAATAATT
11476 TTAATGGAGACTCCAACACACAAACACAATTTTATTAACTAACC
1 TTAATGGAGACTCCAACACACAAACACAATTTTATTAACTAACC
*
11520 TTAATGGAGGCTCCAACACACAAACACAATTTTATTAACTAACC
1 TTAATGGAGACTCCAACACACAAACACAATTTTATTAACTAACC
11564 CTAACTGGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (44 bp):
TTAATGGAGACTCCAACACACAAACACAATTTTATTAACTAACC
Found at i:12360 original size:72 final size:72
Alignment explanation
Indices: 12232--12382 Score: 198
Period size: 72 Copynumber: 2.1 Consensus size: 72
12222 TTTTTGCAAG
* * *
12232 CAAACCATCAAGATCAATTTTTGACAATCTAAAAATTTCAGCAAAAACTTTCGCATCCAAACCAA
1 CAAACCATCAAGATCAATTTTTGACAACCTAAAAACTTCAGCAAAAACTTTCGCATCAAAACCAA
12297 AATCCCA
66 AATCCCA
* * * *
12304 CAAACCTTCAA-AGTCAATTTTTGACAACCTCAAGACTTCAGCAGAAAACTTT-GCATCAAAACT
1 CAAACCATCAAGA-TCAATTTTTGACAACCTAAAAACTTCAGCA-AAAACTTTCGCATCAAAACC
*
12367 AGAATCCCA
64 AAAATCCCA
12376 CAAACCA
1 CAAACCA
12383 AGACCTTCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 1 0.01
72 59 0.87
73 8 0.12
ACGTcount: A:0.43, C:0.27, G:0.07, T:0.23
Consensus pattern (72 bp):
CAAACCATCAAGATCAATTTTTGACAACCTAAAAACTTCAGCAAAAACTTTCGCATCAAAACCAA
AATCCCA
Found at i:15713 original size:14 final size:15
Alignment explanation
Indices: 15694--15723 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15684 TTGCATAAAT
15694 ATAGACA-AAAAAAA
1 ATAGACATAAAAAAA
15708 ATAGACATAAAAAAA
1 ATAGACATAAAAAAA
15723 A
1 A
15724 ACCCCTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (15 bp):
ATAGACATAAAAAAA
Found at i:16210 original size:18 final size:18
Alignment explanation
Indices: 16184--16218 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16174 AATCTTTCTG
*
16184 TTTTTTTTTTCATTTTTA
1 TTTTATTTTTCATTTTTA
*
16202 TTTTATTTTTTATTTTT
1 TTTTATTTTTCATTTTT
16219 GATATCGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTATTTTTCATTTTTA
Found at i:22257 original size:11 final size:11
Alignment explanation
Indices: 22243--22280 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
22233 ATTCATAACA
22243 AATTTATAATT
1 AATTTATAATT
22254 AATTTATAATT
1 AATTTATAATT
22265 -ATTTGATAATT
1 AATTT-ATAATT
*
22276 TATTT
1 AATTT
22281 TATATATAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:26580 original size:26 final size:28
Alignment explanation
Indices: 26547--26599 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
26537 TTGGTTATTA
26547 TATTATATA-TA-TA-TATAATAATATAT
1 TATTATATAGTAGTATTAT-ATAATATAT
26573 TATTATATAGTAGTATTATATAATATA
1 TATTATATAGTAGTATTATATAATATA
26600 GTACCAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 9 0.38
27 2 0.08
28 10 0.42
29 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
TATTATATAGTAGTATTATATAATATAT
Found at i:26598 original size:18 final size:17
Alignment explanation
Indices: 26542--26602 Score: 57
Period size: 14 Copynumber: 4.0 Consensus size: 17
26532 ACAATTTGGT
26542 TATTATAT--TATA-TA
1 TATTATATAATATAGTA
26556 TA-TATATAATA-A-TA
1 TATTATATAATATAGTA
26570 TATTAT-T-ATATAGTA
1 TATTATATAATATAGTA
26585 GTATTATATAATATAGTA
1 -TATTATATAATATAGTA
26603 CCAAAAGCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 8 0.21
14 9 0.23
15 7 0.18
16 6 0.15
17 1 0.03
18 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
TATTATATAATATAGTA
Found at i:32858 original size:149 final size:148
Alignment explanation
Indices: 32430--32884 Score: 506
Period size: 149 Copynumber: 3.0 Consensus size: 148
32420 AACACATTAA
* * *
32430 ACGCGTGACCAGCAAACACAAAGAGGATAAACGACAAAG-TTTTGGTCTATTCCACGAGGAAATT
1 ACGCGTGACC-GCAAACACAAAGAGGATAAACGACAAAGATTTT-GTCTATTACAAGAGGAAATC
* * * *
32494 GACAACAATTATTGCATCTTTTATAAGAACAATTCATTTTAATGGCTTCTAACTATGCCACCATG
64 GATAACAA-TATTGCATC--TT-T---AACGATTCATTTTAACGG-TTCTAACTATACCACCATG
* **
32559 CATTCAAAACAGAGGATCTAAAATGAAC
121 CATTCAAAACAGAGAATCTAAAACAAAC
* * * * *
32587 GCACGTGACAC-CAAATACAAAGAGGATAAACGACAAAGATTTTGTCTATTACATGAAGAAATCG
1 ACGCGTGAC-CGCAAACACAAAGAGGATAAACGACAAAGATTTTGTCTATTACAAGAGGAAATCG
* * *
32651 ATAACAATCATTGCATCGTTTAACGGTTCATTTTAACGGTTTCT-A-TATATCACCATGCATCCA
65 ATAACAAT-ATTGCATC-TTTAACGATTCATTTTAACGG-TTCTAACTATACCACCATGCATTCA
32714 AAACAGAGAATCTAAAACAAAC
127 AAACAGAGAATCTAAAACAAAC
* * **
32736 ACGCGTGACCGGCAAAGACAAAGAGGATAAACAACAAAGATTTTGTCTATTTTAAGAGGAAATCG
1 ACGCGTGACC-GCAAACACAAAGAGGATAAACGACAAAGATTTTGTCTATTACAAGAGGAAATCG
* *
32801 ATAACAATATTGCATC-TTAACGATTCATTTTAACGGTTCCTAACTATACCAGCATGCATTTAAA
65 ATAACAATATTGCATCTTTAACGATTCATTTTAACGGTT-CTAACTATACCACCATGCATTCAAA
*
32865 ACAAAGAATCTAAAACAAAC
129 ACAGAGAATCTAAAACAAAC
32885 GACAAAATCC
Statistics
Matches: 257, Mismatches: 33, Indels: 24
0.82 0.11 0.08
Matches are distributed among these distances:
146 2 0.01
147 21 0.08
148 2 0.01
149 84 0.33
150 56 0.22
151 19 0.07
154 1 0.00
155 3 0.01
156 57 0.22
157 11 0.04
158 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (148 bp):
ACGCGTGACCGCAAACACAAAGAGGATAAACGACAAAGATTTTGTCTATTACAAGAGGAAATCGA
TAACAATATTGCATCTTTAACGATTCATTTTAACGGTTCTAACTATACCACCATGCATTCAAAAC
AGAGAATCTAAAACAAAC
Found at i:35386 original size:2 final size:2
Alignment explanation
Indices: 35379--35412 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
35369 TAATATGTAG
35379 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35413 TGATTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35400 original size:17 final size:17
Alignment explanation
Indices: 35380--35412 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35370 AATATGTAGT
35380 ATATATATATATATATA
1 ATATATATATATATATA
35397 ATATATATATATATAT
1 ATATATATATATATAT
35413 TGATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:36990 original size:20 final size:20
Alignment explanation
Indices: 36965--37006 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
36955 GATTCAATGC
36965 TCTCTCTCTTCATGAGAGTT
1 TCTCTCTCTTCATGAGAGTT
*
36985 TCTCTCTCTTCTTGAGAGTT
1 TCTCTCTCTTCATGAGAGTT
37005 TC
1 TC
37007 CCTTTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.48
Consensus pattern (20 bp):
TCTCTCTCTTCATGAGAGTT
Found at i:37014 original size:20 final size:20
Alignment explanation
Indices: 36968--37022 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
36958 TCAATGCTCT
* *
36968 CTCTCTTCATGAGAGTTTCT
1 CTCTCTTCTTGAGAGTTTCC
36988 CTCTCTTCTTGAGAGTTTCC
1 CTCTCTTCTTGAGAGTTTCC
* *
37008 CTTTCTTTTTGAGAG
1 CTCTCTTCTTGAGAG
37023 ATCCGATCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.24, G:0.16, T:0.47
Consensus pattern (20 bp):
CTCTCTTCTTGAGAGTTTCC
Found at i:39867 original size:107 final size:107
Alignment explanation
Indices: 39681--39895 Score: 385
Period size: 107 Copynumber: 2.0 Consensus size: 107
39671 TTTTTCTTCC
* * *
39681 TAATACAGACCCTCTGAAATTGATATCTAGAAACTATTTTGAGTCTAACCTAATTTTTAGTTGAA
1 TAATACAAACCCTCTGAAATTAATATCTAGAAACTACTTTGAGTCTAACCTAATTTTTAGTTGAA
39746 CCACACCGAACTTCAAACCGAGGAAAACTCTCTTATCACCTA
66 CCACACCGAACTTCAAACCGAGGAAAACTCTCTTATCACCTA
*
39788 TAATACAAACCCTCTGAAATTAATATCTAGAAACTACTTTGAGTCTAACTTAATTTTTAGTTGAA
1 TAATACAAACCCTCTGAAATTAATATCTAGAAACTACTTTGAGTCTAACCTAATTTTTAGTTGAA
*
39853 CCACACCGGACTTCAAACCGAGGAAAACTCTCTTATCACCTA
66 CCACACCGAACTTCAAACCGAGGAAAACTCTCTTATCACCTA
39895 T
1 T
39896 TTTCTTGTCC
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (107 bp):
TAATACAAACCCTCTGAAATTAATATCTAGAAACTACTTTGAGTCTAACCTAATTTTTAGTTGAA
CCACACCGAACTTCAAACCGAGGAAAACTCTCTTATCACCTA
Found at i:40719 original size:38 final size:38
Alignment explanation
Indices: 40677--40749 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
40667 ACATAATGTG
*
40677 ATTATCAAAAAATCATAGGGAGGTTATCAAAATTTGTA
1 ATTATCAAAAAATCATAAGGAGGTTATCAAAATTTGTA
* **
40715 ATTATCAAGATTTCATAAGGAGGTTATCAAAATTT
1 ATTATCAAAAAATCATAAGGAGGTTATCAAAATTT
40750 TATAGGGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (38 bp):
ATTATCAAAAAATCATAAGGAGGTTATCAAAATTTGTA
Found at i:40732 original size:60 final size:61
Alignment explanation
Indices: 40656--40772 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 61
40646 CAAAGCGAGG
* *
40656 TTATCAAAATTACATAATGTGATTATCAAAAAATCATAGGGAG-GTTATCAAAATTTGTAA
1 TTATCAAAATTACATAAGGAGATTATCAAAAAATCATAGGGAGAGTTATCAAAATTTGTAA
* * * ** * *
40716 TTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGATTTATCAAAATTT
1 TTATCAAAATTACATAAGGAGATTATCAAAAAATCATAGGGAGAGTTATCAAAATTT
40773 TATAGGAAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
60 35 0.74
61 12 0.26
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.36
Consensus pattern (61 bp):
TTATCAAAATTACATAAGGAGATTATCAAAAAATCATAGGGAGAGTTATCAAAATTTGTAA
Found at i:40768 original size:23 final size:22
Alignment explanation
Indices: 40637--41086 Score: 186
Period size: 22 Copynumber: 20.6 Consensus size: 22
40627 TGGTCCGATT
* *
40637 TCAAAATTTCAAAGCGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* ** * *
40659 TCAAAATTACATAATGTGATTA
1 TCAAAATTTCATAGGGAGGTTA
**
40681 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
*
40703 TCAAAATTT-GTA---A--TTA
1 TCAAAATTTCATAGGGAGGTTA
* *
40719 TCAAGATTTCATAAGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* *
40741 TCAAAATTTTATAGGGAGATTTA
1 TCAAAATTTCATAGGGAG-GTTA
* *
40764 TCAAAATTTTATAGGAAGGTTTA
1 TCAAAATTTCATAGGGAGG-TTA
* *
40787 TCAAAATGTCATAGCGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * * *
40809 TCACAATTTCATAGTGTGATTA
1 TCAAAATTTCATAGGGAGGTTA
* * * *
40831 TCAAAATTTCAGAGTGTGATTA
1 TCAAAATTTCATAGGGAGGTTA
* * * *
40853 CTGACAA-TTCATATGGAGGTTT
1 -TCAAAATTTCATAGGGAGGTTA
* * ** *
40875 TTAAATTTTCATAACGTGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * *
40897 TCAATATATCATATGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* ** *
40919 TCAACATCTT-ATAGTGTTGATTA
1 TCAAAAT-TTCATAG-GGAGGTTA
* *
40942 TCAAAATTTCATAGTGAGATCT-
1 TCAAAATTTCATAGGGAGGT-TA
* * *
40964 TTAAAATTCCTTAGGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * *
40986 ACAAAATTTCATAAGAAGGTTAAA
1 TCAAAATTTCATAGGGAGGTT--A
*** *
41010 T-AAAATTT-ATAAAAAGGTTC
1 TCAAAATTTCATAGGGAGGTTA
* * * *
41030 TCGAAATTCCATA-GTATCGTTA
1 TCAAAATTTCATAGGGA-GGTTA
** *
41052 TTGAAATTTCATAGGAAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
41074 TCAAAATTTCATA
1 TCAAAATTTCATA
41087 AGGATGTCAT
Statistics
Matches: 314, Mismatches: 93, Indels: 42
0.70 0.21 0.09
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
20 2 0.01
21 12 0.04
22 217 0.69
23 68 0.22
24 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATAGGGAGGTTA
Found at i:41007 original size:111 final size:109
Alignment explanation
Indices: 40715--41007 Score: 238
Period size: 111 Copynumber: 2.6 Consensus size: 109
40705 AAAATTTGTA
* * * * * * * * *
40715 ATTATCAAGATTTCATAAG-GAGGTTATCAAAATTTTATAGGGAGATTTATCAAAATTTTATAGG
1 ATTATCAAAATTTCA-GAGTGAGATTATGAAAA-TTCATAGGGAG-GTTAACAAAATTTCATAAG
*
40779 AAGGTTTATCAAAATGTCATAGCGAGGTTATCACAATTTCATAGTGTG
63 AAGG-TTATCAAAATATCATAGCGAGGTTATCACAATTTCATAGTGTG
* * * *** *
40827 ATTATCAAAATTTCAGAGTGTGATTACTGACAATTCATATGGAGGTTTTTAAATTTTCATAACG-
1 ATTATCAAAATTTCAGAGTGAGATTA-TGAAAATTCATAGGGAGGTTAACAAAATTTCATAA-GA
* *
40891 TGGTTATCAATATATCATATG-GAGGTTATCA-ACATCTT-ATAGTGTTG
64 AGGTTATCAAAATATCATA-GCGAGGTTATCACA-AT-TTCATAGTG-TG
* * *
40938 ATTATCAAAATTTCATAGTGAGATCT-TTAAAATTCCTTAGGGAGGTTAACAAAATTTCATAAGA
1 ATTATCAAAATTTCAGAGTGAGAT-TATGAAAATT-CATAGGGAGGTTAACAAAATTTCATAAGA
41002 AGGTTA
64 AGGTTA
41008 AATAAAATTT
Statistics
Matches: 143, Mismatches: 28, Indels: 21
0.74 0.15 0.11
Matches are distributed among these distances:
109 1 0.01
110 39 0.27
111 69 0.48
112 30 0.21
113 4 0.03
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (109 bp):
ATTATCAAAATTTCAGAGTGAGATTATGAAAATTCATAGGGAGGTTAACAAAATTTCATAAGAAG
GTTATCAAAATATCATAGCGAGGTTATCACAATTTCATAGTGTG
Found at i:41130 original size:62 final size:65
Alignment explanation
Indices: 41056--41210 Score: 217
Period size: 65 Copynumber: 2.4 Consensus size: 65
41046 TCGTTATTGA
* *
41056 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGATGTCAT-AAAAA-A-TAGTGTAATTATAAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGAACGTCATAAAAAATACTAGTGTAATTATAAT
* * *
41118 AATTTCATAGGAATGTTATCAAAATTTCATAAGAACGTTATAAAAAATACTAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGAACGTCATAAAAAATACTAGTGTAATTATAAT
* * *
41183 AATTTAATAGGAAGATTATCATAATTTC
1 AATTTCATAGGAAGGTTATCAAAATTTC
41211 GTATGAATAT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
62 37 0.46
63 5 0.06
64 1 0.01
65 38 0.47
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (65 bp):
AATTTCATAGGAAGGTTATCAAAATTTCATAAGAACGTCATAAAAAATACTAGTGTAATTATAAT
Found at i:41163 original size:22 final size:22
Alignment explanation
Indices: 41111--41163 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
41101 AATAGTGTAA
* * *
41111 TTATAATAATTTCATAGGAATG
1 TTATAAAAATTTCATAAGAACG
*
41133 TTATCAAAATTTCATAAGAACG
1 TTATAAAAATTTCATAAGAACG
41155 TTATAAAAA
1 TTATAAAAA
41164 ATACTAGTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (22 bp):
TTATAAAAATTTCATAAGAACG
Found at i:45015 original size:32 final size:32
Alignment explanation
Indices: 44974--45038 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
44964 CCCAGGCTGT
44974 TCAGTCCACATCAAACACCTCATGCAACAATC
1 TCAGTCCACATCAAACACCTCATGCAACAATC
45006 TCAGTCCACATCAAACACCTCATGCAACAATC
1 TCAGTCCACATCAAACACCTCATGCAACAATC
45038 T
1 T
45039 TTCTCCTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.37, G:0.06, T:0.20
Consensus pattern (32 bp):
TCAGTCCACATCAAACACCTCATGCAACAATC
Found at i:52764 original size:16 final size:16
Alignment explanation
Indices: 52743--52779 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
52733 GCAATCGCTC
52743 TTTTGTTAGAACATGG
1 TTTTGTTAGAACATGG
52759 TTTTGTTAGAACATGG
1 TTTTGTTAGAACATGG
*
52775 GTTTG
1 TTTTG
52780 CTCACTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.05, G:0.27, T:0.46
Consensus pattern (16 bp):
TTTTGTTAGAACATGG
Found at i:56425 original size:14 final size:14
Alignment explanation
Indices: 56406--56434 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56396 TTGCTTGTTG
56406 GGTTATTGTATCTA
1 GGTTATTGTATCTA
56420 GGTTATTGTATCTA
1 GGTTATTGTATCTA
56434 G
1 G
56435 TTTTAAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.24, T:0.48
Consensus pattern (14 bp):
GGTTATTGTATCTA
Found at i:56888 original size:12 final size:12
Alignment explanation
Indices: 56871--56896 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
56861 ATGAACATCC
56871 TTCACTTAGTTA
1 TTCACTTAGTTA
56883 TTCACTTAGTTA
1 TTCACTTAGTTA
56895 TT
1 TT
56897 ATGAGAGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (12 bp):
TTCACTTAGTTA
Found at i:69337 original size:2 final size:2
Alignment explanation
Indices: 69330--69356 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
69320 TCTTTTTATT
69330 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
69357 TTGTTTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.