Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006761.1 Corchorus capsularis cultivar CVL-1 contig06782, 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: 29974
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Found at i:56 original size:2 final size:2
Alignment explanation
Indices: 49--80 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
39 TTTAAACTTA
49 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
81 ATAAATCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7549 original size:33 final size:33
Alignment explanation
Indices: 7507--7579 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
7497 TCTCAATTGA
7507 AATTGGGACTAGGAAAGTAATGGGATAGAGAGC
1 AATTGGGACTAGGAAAGTAATGGGATAGAGAGC
7540 AATTGGGACTAGGAAAGTAATGGGATAGAGAGC
1 AATTGGGACTAGGAAAGTAATGGGATAGAGAGC
7573 AAGTTGG
1 AA-TTGG
7580 ATTTATCGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
33 35 0.90
34 4 0.10
ACGTcount: A:0.38, C:0.05, G:0.37, T:0.19
Consensus pattern (33 bp):
AATTGGGACTAGGAAAGTAATGGGATAGAGAGC
Found at i:8671 original size:30 final size:30
Alignment explanation
Indices: 8635--8691 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
8625 GTTAAAACTT
* *
8635 TAATTTGCTTTTGGGC-CAAAAAGAAAAGTG
1 TAATTTGCATTT-GGCACAAAAACAAAAGTG
8665 TAATTTGCATTTGGCACAAAAACAAAA
1 TAATTTGCATTTGGCACAAAAACAAAA
8692 CCATAATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (30 bp):
TAATTTGCATTTGGCACAAAAACAAAAGTG
Found at i:13974 original size:3 final size:3
Alignment explanation
Indices: 13966--14013 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
13956 ACCAACCCCA
*
13966 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
14014 GAAGCAACTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:14891 original size:78 final size:78
Alignment explanation
Indices: 14762--14909 Score: 296
Period size: 78 Copynumber: 1.9 Consensus size: 78
14752 ATAAACCTAT
14762 TTTTAAATTTACTTGTCAAAGTCAATTTCAGATTTGTATGATATCTCCATTACCCCCGGTCAACT
1 TTTTAAATTTACTTGTCAAAGTCAATTTCAGATTTGTATGATATCTCCATTACCCCCGGTCAACT
14827 CTGATATCTTCAG
66 CTGATATCTTCAG
14840 TTTTAAATTTACTTGTCAAAGTCAATTTCAGATTTGTATGATATCTCCATTACCCCCGGTCAACT
1 TTTTAAATTTACTTGTCAAAGTCAATTTCAGATTTGTATGATATCTCCATTACCCCCGGTCAACT
14905 CTGAT
66 CTGAT
14910 GCTTAATTAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (78 bp):
TTTTAAATTTACTTGTCAAAGTCAATTTCAGATTTGTATGATATCTCCATTACCCCCGGTCAACT
CTGATATCTTCAG
Found at i:25178 original size:50 final size:49
Alignment explanation
Indices: 25112--26182 Score: 920
Period size: 50 Copynumber: 21.7 Consensus size: 49
25102 AGAAAACTGA
* * *
25112 ACCTTCCGACCGGGAAGGGGCATTTTGGGGAACAAAGAAAGAAAACTGGA
1 ACCTTCCGACCGGGAAGGGGCATTTT-GGAAACAAAGAAAGAAAACAGGG
* * * *
25162 ACCTTCCAACCAGGAAGGGGCATTTTTGGAAACAAAAGTAA-ACAACAGGG
1 ACCTTCCGACCGGGAAGGGGCA-TTTTGGAAAC-AAAGAAAGAAAACAGGG
*
25212 ACCTTCCGACCGGGAAGGGGCATTTTAGGAAACAAATAAAGAAAACAGGG
1 ACCTTCCGACCGGGAAGGGGCATTTT-GGAAACAAAGAAAGAAAACAGGG
** *
25262 ACCTTCCGACCGGGAAAAGGCATTTTTGGAAAC--A-AAAGAAAACATGG
1 ACCTTCCGACCGGGAAGGGGCA-TTTTGGAAACAAAGAAAGAAAACAGGG
* * * * *
25309 ACCTTCCGACCGGGAAGAGGCATTTTTGG-AATAAACAAACAAAGCAGGG
1 ACCTTCCGACCGGGAAGGGGCA-TTTTGGAAACAAAGAAAGAAAACAGGG
* * *
25358 ACCTTCCGATCGGGAAGGGGCATTTTGGGACACAAATAAAGAAAACAGGG
1 ACCTTCCGACCGGGAAGGGGCATTTT-GGAAACAAAGAAAGAAAACAGGG
* * **
25408 ACCTTCCGACCGGGAAGGGGC-TTTTTGAAA-TAAGTGTAGAAAACTA-GG
1 ACCTTCCGACCGGGAAGGGGCATTTTGGAAACAAAG-AAAGAAAAC-AGGG
** * * * * * *
25456 ACCTTCCGACCGGGAAGGGGCATTTTTTAGA-TATGTGAAGAAAACTGTG
1 ACCTTCCGACCGGGAAGGGGCATTTTGGAAACAAAG-AAAGAAAACAGGG
* * * * *
25505 ACCTTCCGACCGGAAATGGGTATTTTTGGAAACAAAAGTAA-ACAACAGGG
1 ACCTTCCGACCGGGAAGGGGCA-TTTTGGAAAC-AAAGAAAGAAAACAGGG
* * * *
25555 ACCTTCTGAACGGGAAGGGGCATTTTAGGAAACAAATAAAGAAAACAAGG
1 ACCTTCCGACCGGGAAGGGGCATTTT-GGAAACAAAGAAAGAAAACAGGG
* * ** *
25605 ACCTTCCGACCGAGAAAGGGCATTTTTGG-AATTAACAAAGAAAACAGGG
1 ACCTTCCGACCGGGAAGGGGCA-TTTTGGAAACAAAGAAAGAAAACAGGG
* * *
25654 ACCTTCCGACCGGGAAGGGGCATTTTTGAACACAAATAAAGAAAATAGGG
1 ACCTTCCGACCGGGAAGGGGCATTTTGGAA-ACAAAGAAAGAAAACAGGG
* * * * **
25704 ACCTTCTGACCCGGAAGGGGC-TTTTTGAAA-TAAGTGTAGAAAACTA-GG
1 ACCTTCCGACCGGGAAGGGGCATTTTGGAAACAAAG-AAAGAAAAC-AGGG
* * * * * ** *
25752 ACCTTCCTACC-AGAAGGGGAATTTTTGG-AA-TAAGTGAAGAAAATTGTG
1 ACCTTCCGACCGGGAAGGGGCA-TTTTGGAAACAAAG-AAAGAAAACAGGG
* * * *
25800 ACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAAAAGTAA-ACAACAAGG
1 ACCTTCCGACCGGGAAGGGGCA-TTTTGGAA-ACAAAGAAAGAAAACAGGG
* ** * *
25850 ACCTTACGATAGGGAAGGGGCATTTTGGGGAAA-AAATAAAGAAATCAGGG
1 ACCTTCCGACCGGGAAGGGGCATTTT--GGAAACAAAGAAAGAAAACAGGG
* * *
25900 ACTTTCCGACCGAGAAGGGGCATTTTGGGAAACAAACAAAGAAAACAGGG
1 ACCTTCCGACCGGGAAGGGGCATTTT-GGAAACAAAGAAAGAAAACAGGG
* * * * **
25950 ACCTTCTGACCGGGAAGAGGCATTTTGGGAAACAAATAAAGAGAACAAAG
1 ACCTTCCGACCGGGAAGGGGCATTTT-GGAAACAAAGAAAGAAAACAGGG
* * * * * * *
26000 ATCTTCCAACCAGGAAGGGGCATTTTTGGAAACAAACAGAGAAAACAAGA
1 ACCTTCCGACCGGGAAGGGGCA-TTTTGGAAACAAAGAAAGAAAACAGGG
* * *
26050 AACTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAATAGGG
1 ACCTTCCGACCGGGAAGGGGCATTTT-GGAAACAAAGAAAGAAAACAGGG
* *
26100 ACCTTCCGACCGGGAAGGGGCATTTTGGAAACAAACAAAGAAAACAAGG
1 ACCTTCCGACCGGGAAGGGGCATTTTGGAAACAAAGAAAGAAAACAGGG
*
26149 ACCTTCCGACCGAGAAGGGGCATTTTTGGAAACA
1 ACCTTCCGACCGGGAAGGGGCA-TTTTGGAAACA
26183 TAACCTTCCG
Statistics
Matches: 835, Mismatches: 148, Indels: 76
0.79 0.14 0.07
Matches are distributed among these distances:
46 2 0.00
47 51 0.06
48 87 0.10
49 220 0.26
50 439 0.53
51 31 0.04
52 5 0.01
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.18
Consensus pattern (49 bp):
ACCTTCCGACCGGGAAGGGGCATTTTGGAAACAAAGAAAGAAAACAGGG
Found at i:25285 original size:100 final size:101
Alignment explanation
Indices: 25112--26182 Score: 1032
Period size: 100 Copynumber: 10.8 Consensus size: 101
25102 AGAAAACTGA
* * * * * * *
25112 ACCTTCCGACCGGGAAGGGGCATTTTGGGGAACAAAGAAAGAAAACTGGAACCTTCCAACCAGGA
1 ACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAAACAGGGACCTTCCGACCGGGA
*
25177 AGGGGCATTTTTGGAAACAAAAGT-AA-ACAACAGGG
66 AGGGGCATTTTTGGAAACAAAA-TAAAGAAAACAGGG
* *
25212 ACCTTCCGACCGGGAAGGGGCATTTTAGGAAACAAATAAAGAAAACAGGGACCTTCCGACCGGGA
1 ACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAAACAGGGACCTTCCGACCGGGA
** *
25277 AAAGGCATTTTTGGAAAC---A-AAAGAAAACATGG
66 AGGGGCATTTTTGGAAACAAAATAAAGAAAACAGGG
* * * * *
25309 ACCTTCCGACCGGGAAGAGGCATTTTTGG-AATAAACAAACAAAGCAGGGACCTTCCGATCGGGA
1 ACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAAACAGGGACCTTCCGACCGGGA
* *
25373 AGGGGCATTTTGGGACAC-AAATAAAGAAAACAGGG
66 AGGGGCATTTTTGGAAACAAAATAAAGAAAACAGGG
* ****
25408 ACCTTCCGACCGGGAAGGGGC-TTTTT-GAAATAAGTGTAGAAAACTA-GGACCTTCCGACCGGG
1 ACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAAAC-AGGGACCTTCCGACCGGG
* * * ** * * *
25470 AAGGGGCATTTTT-TAGA-TATGTGAAGAAAACTGTG
65 AAGGGGCATTTTTGGAAACAAAATAAAGAAAACAGGG
* * * * * *
25505 ACCTTCCGACCGGAAATGGGTATTTTTGGAAACAAA-AGTAA-ACAACAGGGACCTTCTGAACGG
1 ACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACA--AAGAAAACAGGGACCTTCCGACCGG
* *
25568 GAAGGGGCATTTTAGGAAAC-AAATAAAGAAAACAAGG
64 GAAGGGGCATTTTTGGAAACAAAATAAAGAAAACAGGG
* * **
25605 ACCTTCCGACCGAGAAAGGGCATTTTTGG-AATTAACAAAGAAAACAGGGACCTTCCGACCGGGA
1 ACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAAACAGGGACCTTCCGACCGGGA
*
25669 AGGGGCATTTTT-G-AACACAAATAAAGAAAATAGGG
66 AGGGGCATTTTTGGAAACA-AAATAAAGAAAACAGGG
* * * **** * *
25704 ACCTTCTGACCCGGAAGGGGC-TTTTT-GAAATAAGTGTAGAAAACTA-GGACCTTCCTACC-AG
1 ACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAAAC-AGGGACCTTCCGACCGGG
* * * * ** *
25765 AAGGGGAATTTTTGG-AA-TAAGTGAAGAAAATTGTG
65 AAGGGGCATTTTTGGAAACAAAATAAAGAAAACAGGG
* ** * * * **
25800 ACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAAAAGTAA-ACAACAAGGACCTTACGATAGGG
1 ACCTTCCGACCGGGAAGGGGCATTTTTGGAA-ACAAACAAAGAAAACAGGGACCTTCCGACCGGG
* * *
25864 AAGGGGCATTTTGGGGAA-AAAATAAAGAAATCAGGG
65 AAGGGGCATTTTTGGAAACAAAATAAAGAAAACAGGG
* * * *
25900 ACTTTCCGACCGAGAAGGGGCATTTTGGGAAACAAACAAAGAAAACAGGGACCTTCTGACCGGGA
1 ACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAAACAGGGACCTTCCGACCGGGA
* * * **
25965 AGAGGCATTTTGGGAAAC-AAATAAAGAGAACAAAG
66 AGGGGCATTTTTGGAAACAAAATAAAGAAAACAGGG
* * * * * * *
26000 ATCTTCCAACCAGGAAGGGGCATTTTTGGAAACAAACAGAGAAAACAAGAAACTTCCGACCGGGA
1 ACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAAACAGGGACCTTCCGACCGGGA
* *
26065 AGGGGCATTTTGGGAAAC-AAATAAAGAAAATAGGG
66 AGGGGCATTTTTGGAAACAAAATAAAGAAAACAGGG
* *
26100 ACCTTCCGACCGGGAAGGGGCA-TTTTGGAAACAAACAAAGAAAACAAGGACCTTCCGACCGAGA
1 ACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAAACAGGGACCTTCCGACCGGGA
26164 AGGGGCATTTTTGGAAACA
66 AGGGGCATTTTTGGAAACA
26183 TAACCTTCCG
Statistics
Matches: 789, Mismatches: 151, Indels: 62
0.79 0.15 0.06
Matches are distributed among these distances:
96 78 0.10
97 91 0.12
98 99 0.13
99 217 0.28
100 304 0.39
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.18
Consensus pattern (101 bp):
ACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAAACAGGGACCTTCCGACCGGGA
AGGGGCATTTTTGGAAACAAAATAAAGAAAACAGGG
Found at i:25655 original size:296 final size:296
Alignment explanation
Indices: 25151--26182 Score: 1116
Period size: 296 Copynumber: 3.5 Consensus size: 296
25141 GAACAAAGAA
* * * * * * * *
25151 AGAAAACT-GGAACCTTCCAACCAGGAAGGGGCATTTTTGGAAACAAAAGT-AA-ACAACAGGGA
1 AGAAAACTAGG-ACCTTCCGACCGGGAAGGGGCATTTTT-TAGA-ATAAGTGAAGAAAACTGTGA
* * *
25213 CCTTCCGACCGGGAAGGGGCATTTTAGGAAAC-AAA-TAAAGAAAACAGGGACCTTCCGACCGGG
63 CCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAAGT-AA-ACAACAGGGACCTT-CGAACGGG
** * * *
25276 AAAAGGCATTTTTGGAAAC--A-AAAGAAAACATGGACCTTCCGACCG-GGAAGAGGCATTTTTG
125 AAGGGGCATTTTAGGAAACAAATAAAGAAAACAAGGACCTTCCGACCGAGAAAG-GGCATTTTTG
* * *
25337 GAATAAACAAACAAAGCAGGGACCTTCCGATCGGGAAGGGGCATTTTGGGACACAAATAAAGAAA
189 GAATAAACAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGACACAAATAAAGAAA
*
25402 ACAGGGACCTTCCGACCGGGAAGGGGCTTTTTGAAATAAGTGT
254 ACAGGGACCTTCCGACCAGGAAGGGGCTTTTTGAAATAAGTGT
*
25445 AGAAAACTAGGACCTTCCGACCGGGAAGGGGCATTTTTTAG-ATATGTGAAGAAAACTGTGACCT
1 AGAAAACTAGGACCTTCCGACCGGGAAGGGGCATTTTTTAGAATAAGTGAAGAAAACTGTGACCT
* * *
25509 TCCGACCGGAAATGGGTATTTTTGGAAACAAAAGTAAACAACAGGGACCTTCTGAACGGGAAGGG
66 TCCGACCGGGAAGGGGCATTTTTGGAAACAAAAGTAAACAACAGGGACCTTC-GAACGGGAAGGG
*
25574 GCATTTTAGGAAACAAATAAAGAAAACAAGGACCTTCCGACCGAGAAAGGGCATTTTTGGAATTA
130 GCATTTTAGGAAACAAATAAAGAAAACAAGGACCTTCCGACCGAGAAAGGGCATTTTTGGAATAA
* * *
25639 ACAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTTGAACACAAATAAAGAAAATAGGG
195 ACAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGACACAAATAAAGAAAACAGGG
* *
25704 ACCTTCTGACCCGGAAGGGGCTTTTTGAAATAAGTGT
260 ACCTTCCGACCAGGAAGGGGCTTTTTGAAATAAGTGT
* * * * *
25741 AGAAAACTAGGACCTTCCTACC-AGAAGGGG-AATTTTTGGAATAAGTGAAGAAAATTGTGACCT
1 AGAAAACTAGGACCTTCCGACCGGGAAGGGGCATTTTTTAGAATAAGTGAAGAAAACTGTGACCT
*
25804 TCCGACCGGGAAGGGGCATTTTTGGAATA-AAAAGTAAACAACAAGGACCTTACGATA-GGGAAG
66 TCCGACCGGGAAGGGGCATTTTTGGAA-ACAAAAGTAAACAACAGGGACCTT-CGA-ACGGGAAG
* * * * * *
25867 GGGCATTTTGGGGAAA-AAATAAAGAAATCAGGGACTTTCCGACCGAGAAGGGGCATTTTGGGAA
128 GGGCATTTT-AGGAAACAAATAAAGAAAACAAGGACCTTCCGACCGAGAAAGGGCATTTTTGG-A
* * * * *
25931 ACAAACAAAGAAAACAGGGACCTTCTGACCGGGAAGAGGCATTTTGGGAAACAAATAAAGAGAAC
191 ATAAACAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGACACAAATAAAGAAAAC
** * * * **
25996 AAAGATCTTCCAACCAGGAAGGGGCATTTTTGGAAACAAACAG-
256 AGGGACCTTCCGACCAGGAAGGGGC-TTTTT-GAAA-TAAGTGT
* * * ** * * * *
26039 AGAAAACAAGAAACTTCCGACCGGGAAGGGGCA-TTTTGGGAAACAAATAAAGAAAA-TAGGGAC
1 AGAAAACTAGGACCTTCCGACCGGGAAGGGGCATTTTTTAG-AATAAGTGAAGAAAACT-GTGAC
* * * *
26102 CTTCCGACCGGGAAGGGGCA-TTTTGGAAACAAACA--AAGAAAACAAGGACCTTCCGACCGAGA
64 CTTCCGACCGGGAAGGGGCATTTTTGGAAACAAA-AGTAA-ACAACAGGGACCTT-CGAACGGGA
*
26164 AGGGGCATTTTTGGAAACA
126 AGGGGCATTTTAGGAAACA
26183 TAACCTTCCG
Statistics
Matches: 632, Mismatches: 78, Indels: 51
0.83 0.10 0.07
Matches are distributed among these distances:
291 4 0.01
292 3 0.00
293 71 0.11
294 45 0.07
295 135 0.21
296 238 0.38
297 9 0.01
298 30 0.05
299 59 0.09
300 38 0.06
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.18
Consensus pattern (296 bp):
AGAAAACTAGGACCTTCCGACCGGGAAGGGGCATTTTTTAGAATAAGTGAAGAAAACTGTGACCT
TCCGACCGGGAAGGGGCATTTTTGGAAACAAAAGTAAACAACAGGGACCTTCGAACGGGAAGGGG
CATTTTAGGAAACAAATAAAGAAAACAAGGACCTTCCGACCGAGAAAGGGCATTTTTGGAATAAA
CAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGACACAAATAAAGAAAACAGGGA
CCTTCCGACCAGGAAGGGGCTTTTTGAAATAAGTGT
Done.