Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019485.1 Corchorus olitorius cultivar O-4 contig19518, 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: 42631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2947 original size:21 final size:19
Alignment explanation
Indices: 2906--2961 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
2896 TTTAGCAACG
2906 GTACAGATGAGATTATACT
1 GTACAGATGAGATTATACT
*
2925 GTACAGATTAGATTACGTACT
1 GTACAGATGAGATTA--TACT
*
2946 GTACAAATGAGATTAT
1 GTACAGATGAGATTAT
2962 TAGAGCAGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 15 0.47
21 17 0.53
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (19 bp):
GTACAGATGAGATTATACT
Found at i:27743 original size:48 final size:48
Alignment explanation
Indices: 27672--27770 Score: 180
Period size: 48 Copynumber: 2.1 Consensus size: 48
27662 GTTCGGCAAC
*
27672 GGGGGAATGAGACGGAGGAGCCAAAACTGGGGCCGGAGACGATGCTTT
1 GGGGGAATGAGACGGAGGAGCCAAAACCGGGGCCGGAGACGATGCTTT
*
27720 GGGGGAATGAGCCGGAGGAGCCAAAACCGGGGCCGGAGACGATGCTTT
1 GGGGGAATGAGACGGAGGAGCCAAAACCGGGGCCGGAGACGATGCTTT
27768 GGG
1 GGG
27771 AGGATTGGCG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.25, C:0.18, G:0.45, T:0.11
Consensus pattern (48 bp):
GGGGGAATGAGACGGAGGAGCCAAAACCGGGGCCGGAGACGATGCTTT
Found at i:27819 original size:63 final size:63
Alignment explanation
Indices: 27720--27838 Score: 202
Period size: 63 Copynumber: 1.9 Consensus size: 63
27710 ACGATGCTTT
* *
27720 GGGGGAATGAGCCGGAGGAGCCAAAACCGGGGCCGGAGACGATGCTTTGGGAGGATTGGCGAC
1 GGGGGAATGAGCCGGAGGAGCCAAAACCGGAGCCGGAGACGATGCCTTGGGAGGATTGGCGAC
* *
27783 GGGGGAATGAGGCGGAGGAGCCAAACCCGGAGCCGGAGACGATGCCTTGGGAGGAT
1 GGGGGAATGAGCCGGAGGAGCCAAAACCGGAGCCGGAGACGATGCCTTGGGAGGAT
27839 GAACAACAGG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.24, C:0.19, G:0.46, T:0.10
Consensus pattern (63 bp):
GGGGGAATGAGCCGGAGGAGCCAAAACCGGAGCCGGAGACGATGCCTTGGGAGGATTGGCGAC
Found at i:27865 original size:63 final size:63
Alignment explanation
Indices: 27725--27855 Score: 158
Period size: 63 Copynumber: 2.1 Consensus size: 63
27715 GCTTTGGGGG
* * * * * * *
27725 AATGAGCCGGAGGAGCCAAAACCGGGGCCGGAGACGATGCTTTGGGAGGATTGGCGACGGGGG
1 AATGAGGCGGAGGAGCCAAAACCGGAGCCGGAGACGATGCCTTGGGAGGATTGACAACGAGGA
*
27788 AATGAGGCGGAGGAGCCAAACCCGGAGCCGGAGACGATGCCTTGGGAGGA-TGAACAAC-AGGA
1 AATGAGGCGGAGGAGCCAAAACCGGAGCCGGAGACGATGCCTTGGGAGGATTG-ACAACGAGGA
27850 ACATGA
1 A-ATGA
27856 TGCTTAGGAG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 5 0.09
63 53 0.91
ACGTcount: A:0.29, C:0.20, G:0.41, T:0.10
Consensus pattern (63 bp):
AATGAGGCGGAGGAGCCAAAACCGGAGCCGGAGACGATGCCTTGGGAGGATTGACAACGAGGA
Found at i:29415 original size:14 final size:14
Alignment explanation
Indices: 29396--29427 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
29386 TTAATATACC
29396 TTATTTCAAACATT
1 TTATTTCAAACATT
29410 TTATTTCAAACATT
1 TTATTTCAAACATT
29424 TTAT
1 TTAT
29428 ATATACACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATTTCAAACATT
Found at i:31274 original size:64 final size:65
Alignment explanation
Indices: 31156--31287 Score: 239
Period size: 64 Copynumber: 2.0 Consensus size: 65
31146 CACAAAGGTG
31156 GCAATTCGGCTCAATAGCTAACCCCTTGCGACACAAAACTTCCGATGTGTTCAAACAATTAAAAA
1 GCAATTCGGCTCAATAGCTAACCCCTTGCGACACAAAACTTCCGATGTGTTCAAACAATTAAAAA
* *
31221 GCAATTCGGCTCAATAGCTAACCCTTTGCG-CACAAAACTTCCGATGTGTTCAAACATTTAAAAA
1 GCAATTCGGCTCAATAGCTAACCCCTTGCGACACAAAACTTCCGATGTGTTCAAACAATTAAAAA
31285 GCA
1 GCA
31288 GGAGCCAAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 36 0.55
65 29 0.45
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (65 bp):
GCAATTCGGCTCAATAGCTAACCCCTTGCGACACAAAACTTCCGATGTGTTCAAACAATTAAAAA
Found at i:31780 original size:22 final size:22
Alignment explanation
Indices: 31709--31774 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
31699 CAATTCGAAG
31709 AACAATTATCAGGACTCTCAGC
1 AACAATTATCAGGACTCTCAGC
*
31731 AACAATAATCAGGACTCTCAGC
1 AACAATTATCAGGACTCTCAGC
31753 AACAATTATCAGGACTCTCAGC
1 AACAATTATCAGGACTCTCAGC
31775 GTCAATAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (22 bp):
AACAATTATCAGGACTCTCAGC
Found at i:33315 original size:47 final size:47
Alignment explanation
Indices: 33257--33355 Score: 164
Period size: 47 Copynumber: 2.1 Consensus size: 47
33247 CCAAACCAGC
*
33257 CATGGAGGAAA-TTGTTAGAAAATTGGCTGAGTTGCACCAAAAAAATG
1 CATGCAGGAAATTTGTTAG-AAATTGGCTGAGTTGCACCAAAAAAATG
*
33304 CATGCAGGAAATTTGTTAGAAATTGGCTGAGTTGCACCAAAAAATTG
1 CATGCAGGAAATTTGTTAGAAATTGGCTGAGTTGCACCAAAAAAATG
33351 CATGC
1 CATGC
33356 TGCAACACTT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 42 0.86
48 7 0.14
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.25
Consensus pattern (47 bp):
CATGCAGGAAATTTGTTAGAAATTGGCTGAGTTGCACCAAAAAAATG
Found at i:33368 original size:48 final size:48
Alignment explanation
Indices: 33268--33368 Score: 150
Period size: 47 Copynumber: 2.1 Consensus size: 48
33258 ATGGAGGAAA
* *
33268 TTGTTAGAAAATTGGCTGAGTTGCACCAAAAAAATGCATGCAGGAAAT
1 TTGTTAGAAAATTGGCTGAGTTGCACCAAAAAAATGCATGCAGCAAAC
* *
33316 TTGTTAG-AAATTGGCTGAGTTGCACCAAAAAATTGCATGCTGCAACAC
1 TTGTTAGAAAATTGGCTGAGTTGCACCAAAAAAATGCATGCAGCAA-AC
33364 TTGTT
1 TTGTT
33369 CAAAAGAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 35 0.73
48 13 0.27
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (48 bp):
TTGTTAGAAAATTGGCTGAGTTGCACCAAAAAAATGCATGCAGCAAAC
Found at i:34279 original size:41 final size:41
Alignment explanation
Indices: 34233--34314 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
34223 TTGTATAACC
* *
34233 GATAATTACATTGGATCTGATTAATCCAAAGTGATAATTAT
1 GATAATTACATTAGATCTGACTAATCCAAAGTGATAATTAT
34274 GATAATTACATTAGATCTGACTAATCCAAAGTGATAATTAT
1 GATAATTACATTAGATCTGACTAATCCAAAGTGATAATTAT
34315 ATTGAATCCG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (41 bp):
GATAATTACATTAGATCTGACTAATCCAAAGTGATAATTAT
Found at i:34309 original size:32 final size:32
Alignment explanation
Indices: 34273--34337 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
34263 GTGATAATTA
*
34273 TGATAATTACATT-AGATCTGACTAATCCAAAG
1 TGATAATTACATTGA-ATCCGACTAATCCAAAG
* *
34305 TGATAATTATATTGAATCCGACTAATCTAAAG
1 TGATAATTACATTGAATCCGACTAATCCAAAG
34337 T
1 T
34338 TGAATTGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (32 bp):
TGATAATTACATTGAATCCGACTAATCCAAAG
Found at i:34465 original size:1 final size:1
Alignment explanation
Indices: 34461--34486 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
34451 TTTTTTTAGG
34461 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
34487 AAGGTAGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:34506 original size:30 final size:29
Alignment explanation
Indices: 34472--34541 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 29
34462 TTTTTTTTTT
*
34472 TTTTTTTTTTTTTTTAAGGTAGGTGATAC
1 TTTTTTTTTTTTTTTAAGGGAGGTGATAC
* * *
34501 GTTTTTTTTTCTTTTTATGGGAGGTGATGC
1 -TTTTTTTTTTTTTTTAAGGGAGGTGATAC
34531 TTTTTTTTTTT
1 TTTTTTTTTTT
34542 CGATTCTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 10 0.29
30 25 0.71
ACGTcount: A:0.11, C:0.04, G:0.19, T:0.66
Consensus pattern (29 bp):
TTTTTTTTTTTTTTTAAGGGAGGTGATAC
Found at i:34666 original size:18 final size:17
Alignment explanation
Indices: 34625--34658 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
34615 ATCTAATGAA
*
34625 AAATAGCCACAATAACC
1 AAATAACCACAATAACC
34642 AACATAACCACAATAAC
1 AA-ATAACCACAATAAC
34659 TTAAATAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 2 0.13
18 13 0.87
ACGTcount: A:0.56, C:0.29, G:0.03, T:0.12
Consensus pattern (17 bp):
AAATAACCACAATAACC
Found at i:37612 original size:13 final size:13
Alignment explanation
Indices: 37594--37628 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
37584 ATATATATCT
37594 TATCTTATTTTAC
1 TATCTTATTTTAC
*
37607 TATCTTATCTTAC
1 TATCTTATTTTAC
37620 TATCTTATT
1 TATCTTATT
37629 ATTTTACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (13 bp):
TATCTTATTTTAC
Found at i:39618 original size:44 final size:44
Alignment explanation
Indices: 39570--39697 Score: 148
Period size: 44 Copynumber: 2.9 Consensus size: 44
39560 TGATTAGTGT
* * * * * **
39570 GGTTATCAAAATTCCACAGTGTGGTTATCAAATTTGCATAGGGA
1 GGTTATCAAAATTTCATAATGAGGTTATCAAATTTGCACAAAGA
** * *
39614 GGTTATTGAAATTTCATAATGAGGTTATCAAATTTTCACAAATA
1 GGTTATCAAAATTTCATAATGAGGTTATCAAATTTGCACAAAGA
*
39658 GGTTATCAAAATTTCATAATGAGGTTATCAAATTTTCACA
1 GGTTATCAAAATTTCATAATGAGGTTATCAAATTTGCACA
39698 GTGCGATTGT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAATGAGGTTATCAAATTTGCACAAAGA
Found at i:39694 original size:22 final size:22
Alignment explanation
Indices: 39592--39695 Score: 122
Period size: 22 Copynumber: 4.7 Consensus size: 22
39582 TCCACAGTGT
* **
39592 GGTTATCAAATTTGCATAGGGA
1 GGTTATCAAATTTTCATAATGA
*
39614 GGTTATTGAAA-TTTCATAATGA
1 GGTTA-TCAAATTTTCATAATGA
*
39636 GGTTATCAAATTTTCACAAAT-A
1 GGTTATCAAATTTTCA-TAATGA
*
39658 GGTTATCAAAATTTCATAATGA
1 GGTTATCAAATTTTCATAATGA
39680 GGTTATCAAATTTTCA
1 GGTTATCAAATTTTCA
39696 CAGTGCGATT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
21 7 0.10
22 55 0.80
23 7 0.10
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
GGTTATCAAATTTTCATAATGA
Found at i:42592 original size:22 final size:22
Alignment explanation
Indices: 42297--42613 Score: 198
Period size: 22 Copynumber: 14.3 Consensus size: 22
42287 ACAATCAAAC
* * *
42297 CAAAATTACATAGGAAGTTTAT
1 CAAAATTTCATAGGGAGGTTAT
* *
42319 CAAAATTTCATAATGTA-GTTA-
1 CAAAATTTCAT-AGGGAGGTTAT
*
42340 CAAAAATTTCATATGGAGGTTAT
1 C-AAAATTTCATAGGGAGGTTAT
* * * *
42363 CAAAACTTCA-AAGTATAGTTAT
1 CAAAATTTCATAGGGA-GGTTAT
** *
42385 CAAAATTTCATACAGAGGTTAC
1 CAAAATTTCATAGGGAGGTTAT
***
42407 CAAAATTTCATAAAAAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* *
42429 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATAGGGAGGTTAT
* *
42451 CAAAATTTCATACGAAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* * *
42473 CGAAAGTTT-ATAGTGTGGTTAT
1 C-AAAATTTCATAGGGAGGTTAT
* *** *
42495 CAAAATCTCATAAAAAGGTTAA
1 CAAAATTTCATAGGGAGGTTAT
*
42517 CAAAATATCATAGGGAGGGAGATTAT
1 CAAAATTTCATAGGGA--G-G-TTAT
* * *
42543 CAAAATTTCCTA--GAGATTAA
1 CAAAATTTCATAGGGAGGTTAT
42563 CAAAATTTCATAGGGAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* *
42585 GAAAATTTTAT-GGAGAGGTTAT
1 CAAAATTTCATAGG-GAGGTTAT
42607 CAAAATT
1 CAAAATT
42614 ATATATAGAG
Statistics
Matches: 226, Mismatches: 54, Indels: 30
0.73 0.17 0.10
Matches are distributed among these distances:
20 14 0.06
21 15 0.07
22 168 0.74
23 12 0.05
24 3 0.01
25 1 0.00
26 13 0.06
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGGGAGGTTAT
Done.