Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019990.1 Corchorus olitorius cultivar O-4 contig20023, 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: 41567
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:3213 original size:25 final size:25
Alignment explanation
Indices: 3179--3228 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3169 GACATGTGCC
3179 CGGTTACTAATCAATACTAATTTGT
1 CGGTTACTAATCAATACTAATTTGT
3204 CGGTTACTAATCAATACTAATTTGT
1 CGGTTACTAATCAATACTAATTTGT
3229 TCAAATGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (25 bp):
CGGTTACTAATCAATACTAATTTGT
Found at i:3840 original size:75 final size:75
Alignment explanation
Indices: 3715--3908 Score: 343
Period size: 75 Copynumber: 2.6 Consensus size: 75
3705 ATAGGGAGAT
* *
3715 GGAGCCGGTGCCCAAGGGGAAGATGGAGCCGGAGCTGGTGCCCAATGTTCAGTTGGTGGTGTAGT
1 GGAGCTGGTGCCCAAGGGGAAGATGGAGCCGGAGCTGGTGCCCAAGGTTCAGTTGGTGGTGTAGT
3780 TGGTACTGAA
66 TGGTACTGAA
*
3790 GGAGCTGGTGCCCAAGGGGAAGATGGAGCCGGAGCTGGCGCCCAAGGTTCAGTTGGTGGTGTAGT
1 GGAGCTGGTGCCCAAGGGGAAGATGGAGCCGGAGCTGGTGCCCAAGGTTCAGTTGGTGGTGTAGT
3855 TGGTACTGAA
66 TGGTACTGAA
* *
3865 GGAGCTGGTGCCCAAGGGGAAGATGGAGTCGGAGCCGGTGCCCA
1 GGAGCTGGTGCCCAAGGGGAAGATGGAGCCGGAGCTGGTGCCCA
3909 GCCATATGAA
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 113 1.00
ACGTcount: A:0.20, C:0.19, G:0.43, T:0.19
Consensus pattern (75 bp):
GGAGCTGGTGCCCAAGGGGAAGATGGAGCCGGAGCTGGTGCCCAAGGTTCAGTTGGTGGTGTAGT
TGGTACTGAA
Found at i:6028 original size:30 final size:30
Alignment explanation
Indices: 5994--6058 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
5984 ACAGAGGCTC
*
5994 AAATTGAGAGTTCAT-AGGGTAAAATGTCCA
1 AAATTGAGAATTCATGA-GGTAAAATGTCCA
6024 AAATTGAGAATTCATGAGGTAAAATGTCCA
1 AAATTGAGAATTCATGAGGTAAAATGTCCA
6054 AAATT
1 AAATT
6059 AAAATTTAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (30 bp):
AAATTGAGAATTCATGAGGTAAAATGTCCA
Found at i:7052 original size:51 final size:51
Alignment explanation
Indices: 6992--7143 Score: 240
Period size: 51 Copynumber: 3.0 Consensus size: 51
6982 AAGAAGGAGC
* *
6992 TGGTGCCCAAGGGGAAGATGGAGACGGAGCTGGTGCCCAAGGTTCAGTTGG
1 TGGTTCCCAAGGGGCAGATGGAGACGGAGCTGGTGCCCAAGGTTCAGTTGG
7043 TGGTTCCCAAGGGGCAGATGGAGACGGAGCTGGTGCCCAAGGTTCAGTTGG
1 TGGTTCCCAAGGGGCAGATGGAGACGGAGCTGGTGCCCAAGGTTCAGTTGG
*
7094 TGGTTCCCAA---GCAGATGGAG-CAGGAGCTGGTGCCCAAGGTTCAGCTGG
1 TGGTTCCCAAGGGGCAGATGGAGAC-GGAGCTGGTGCCCAAGGTTCAGTTGG
7142 TG
1 TG
7144 TTGCTGGCGT
Statistics
Matches: 97, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
47 1 0.01
48 37 0.38
51 59 0.61
ACGTcount: A:0.20, C:0.20, G:0.41, T:0.19
Consensus pattern (51 bp):
TGGTTCCCAAGGGGCAGATGGAGACGGAGCTGGTGCCCAAGGTTCAGTTGG
Found at i:9261 original size:26 final size:26
Alignment explanation
Indices: 9249--9298 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
9239 TTAGGTTGAT
*
9249 GAGCTAAGTTTGTTTTTTTGAATAAC
1 GAGCTAAGTTTGTTTTTTAGAATAAC
9275 GAGCTAAGTTTGTTTTTT-GAATAA
1 GAGCTAAGTTTGTTTTTTAGAATAA
9299 TGGAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.46
Consensus pattern (26 bp):
GAGCTAAGTTTGTTTTTTAGAATAAC
Found at i:9296 original size:25 final size:26
Alignment explanation
Indices: 9249--9298 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
9239 TTAGGTTGAT
9249 GAGCTAAGTTTGTTTTTTTGAATAAC
1 GAGCTAAGTTTGTTTTTTTGAATAAC
9275 GAGCTAAGTTTG-TTTTTTGAATAA
1 GAGCTAAGTTTGTTTTTTTGAATAA
9299 TGGAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.46
Consensus pattern (26 bp):
GAGCTAAGTTTGTTTTTTTGAATAAC
Found at i:13134 original size:14 final size:15
Alignment explanation
Indices: 13115--13144 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
13105 AAACCAGTTA
13115 ATACATACAT-ACAT
1 ATACATACATCACAT
13129 ATACATACATCACAT
1 ATACATACATCACAT
13144 A
1 A
13145 AAAGTTCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (15 bp):
ATACATACATCACAT
Found at i:13606 original size:2 final size:2
Alignment explanation
Indices: 13599--13628 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13589 TTAATGGTAC
13599 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13629 CTAGTTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15230 original size:58 final size:58
Alignment explanation
Indices: 15129--15241 Score: 158
Period size: 58 Copynumber: 1.9 Consensus size: 58
15119 ATTAATCAAA
* *
15129 TATCAAGTGACATGTTCTTTATTAGATGCATAAGAAAAGACGTTTTCGGACCGAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAGAAAAAACGTTTTAGGACCGAGACT
* *
15187 TATCGAGTGACATGTTTTTTTATTAGATGTC-TAA-AAAAAACGTTTTAGGACCGAG
1 TATCAAGTGACATG-TTCTTTATTAGATG-CATAAGAAAAAACGTTTTAGGACCGAG
15242 GCATGATGCT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 32 0.65
59 16 0.33
60 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAGAAAAAACGTTTTAGGACCGAGACT
Found at i:16562 original size:36 final size:36
Alignment explanation
Indices: 16515--16584 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
16505 TTCAATAACC
*
16515 TTACATCTTTTGT-GATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAG-TTTTGATTATCATATTTCTTA
*
16551 TTACATTTTTTGTAGTTTTGATTATCATATTTCT
1 TTACATCTTTTGTAGTTTTGATTATCATATTTCT
16585 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAGTTTTGATTATCATATTTCTTA
Found at i:17456 original size:204 final size:204
Alignment explanation
Indices: 17100--17512 Score: 713
Period size: 204 Copynumber: 2.0 Consensus size: 204
17090 GCTTAATAAC
*
17100 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGAAGTGAATAAG
*
17165 ATACAACACATTATTATTATATATAAAAACTATACCAAAAAAAAATTAAGTTGAACATTAGTGGT
66 ATACAACACATTACTATTATATATAAAAACTATACCAAAAAAAAATTAAGTTGAACATTAGTGGT
*
17230 TGATTTATTAAATTATATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
131 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
17295 TCCGA-TTA
196 TCCGATTTA
* *
17303 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGGTTACTATCAAAGTTGAAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAA-TTTTTAAGTCTAAGATTACTAACAAAGTTGAAGTGAATAA
** *
17368 GATACAATGCATTACTATTATATATACAGAACTATACCAAAAAAAAATT-AGTTGAACATTAGTG
65 GATACAACACATTACTATTATATATA-AAAACTATACCAAAAAAAAATTAAGTTGAACATTAGTG
17432 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAA
129 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAA
*
17497 TATCCGATTTA
194 GATCCGATTTA
17508 TTTAT
1 TTTAT
17513 TATTTAAGGA
Statistics
Matches: 198, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
203 24 0.12
204 145 0.73
205 29 0.15
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (204 bp):
TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGAAGTGAATAAG
ATACAACACATTACTATTATATATAAAAACTATACCAAAAAAAAATTAAGTTGAACATTAGTGGT
TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
TCCGATTTA
Found at i:17675 original size:39 final size:40
Alignment explanation
Indices: 17621--17701 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
17611 ATACCTAAGA
*
17621 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
17660 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
17700 AT
1 AT
17702 AGAAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:18739 original size:22 final size:22
Alignment explanation
Indices: 18714--18790 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
18704 TATTTTTATG
* *
18714 AAATTTCGATAATCACCCTATT
1 AAATTTTGATAATCACCCTATA
* * *
18736 AAATTTTGATAACCACCATATG
1 AAATTTTGATAATCACCCTATA
*
18758 AAATTTTGATAATTA-CCTATA
1 AAATTTTGATAATCACCCTATA
*
18779 AAATTGTGATAA
1 AAATTTTGATAA
18791 ACTCCATAAG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 15 0.33
22 31 0.67
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAATCACCCTATA
Found at i:18790 original size:43 final size:44
Alignment explanation
Indices: 18710--18810 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 44
18700 TGAATATTTT
* * * *
18710 TATGAAATTTCGATAATCACCCTATTAAATTTTGATAACCACCA
1 TATGAAATTTTGATAATCACCCTATAAAATTGTGATAAACACCA
* *
18754 TATGAAATTTTGATAATTA-CCTATAAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAATCACCCTATAAAATTGTGATAAACACCA
* *
18797 TAAGAAACTTTGAT
1 TATGAAATTTTGAT
18811 GACCTAACTA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 32 0.65
44 17 0.35
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACCCTATAAAATTGTGATAAACACCA
Found at i:29690 original size:21 final size:23
Alignment explanation
Indices: 29648--29691 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29638 GATGACTGGG
*
29648 AAAACAACATGAGATCGTTAGCAA
1 AAAACAACATGAGATC-ATAGCAA
29672 AAAACAA-ATGAGAT-ATAGCA
1 AAAACAACATGAGATCATAGCA
29692 GGACCATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
23 7 0.37
24 7 0.37
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.16
Consensus pattern (23 bp):
AAAACAACATGAGATCATAGCAA
Found at i:33729 original size:178 final size:177
Alignment explanation
Indices: 33408--33871 Score: 538
Period size: 178 Copynumber: 2.6 Consensus size: 177
33398 TATCCTATCA
* * *
33408 AGGTGATTCAAGTGTCTATTAAAAGGTTGTTCCATGATCTACAACTTTCATGAAAGACTCGAAAA
1 AGGTGATTCAAGTGTCTA-TAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCGAAAG
* * * *
33473 CTAAATTTAATGTTTCAAGTATAAAAAAAGCTTCCGAATAATTAGTTGTTTCGGTTAGCGGGAAT
65 CTAAATTTAATGTTTCAAGTATAAAAAATGCTTCCGAAAAATTAATTCTTTCGGTTAGCGGGAAT
* * * ***
33538 GGACGATCCACTTAGT-ATAACATTACTTTTGCTCCAGATGTCTTCTTG
130 GAACGATCCACTTAATAAT-ACATAACTTTTGCTCCAGATGTCCGATTG
* * * * *
33586 AGTTGATCCAAGTGTCTCATAAAAGGTTATTTTATGATCTACAACTTTCATGCAGGACTCGAAAG
1 AGGTGATTCAAGTGTCT-ATAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCGAAAG
*
33651 CTAAATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAAAATTAATTCTTTCGGTTAG-GGAGAA
65 CTAAATTTAATGTTTCAAGTATAAAAAATGCTTCCGAAAAATTAATTCTTTCGGTTAGCGG-GAA
* *
33715 TGAACAGA-CCACTTAATAATACATAATTTTTGCTTCAGATGTCCGATTG
129 TGAAC-GATCCACTTAATAATACATAACTTTTGCTCCAGATGTCCGATTG
* * * * * * * *
33764 AGGTGATTTAAGTGTCTGTTAAAAGGCTGTTTCATGATCTTCAGCTTTCGTGTAGGACTTGAAAG
1 AGGTGATTCAAGTGTCT-ATAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCGAAAG
* * * ** *
33829 CTAAATTTTATTTTTCAAATACCAAAAATGCTTCTGAAAAATT
65 CTAAATTTAATGTTTCAAGTATAAAAAATGCTTCCGAAAAATT
33872 TATATTTCGG
Statistics
Matches: 241, Mismatches: 41, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
177 2 0.01
178 234 0.97
179 5 0.02
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (177 bp):
AGGTGATTCAAGTGTCTATAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCGAAAGC
TAAATTTAATGTTTCAAGTATAAAAAATGCTTCCGAAAAATTAATTCTTTCGGTTAGCGGGAATG
AACGATCCACTTAATAATACATAACTTTTGCTCCAGATGTCCGATTG
Found at i:37464 original size:18 final size:18
Alignment explanation
Indices: 37441--37494 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
37431 AAAAAAGCAA
* *
37441 AGAGCACATGATGCCATG
1 AGAGCACACGATGCCACG
37459 AGAGCACACGATGCCACG
1 AGAGCACACGATGCCACG
* *
37477 AGAGCTCACAATGCCACG
1 AGAGCACACGATGCCACG
37495 CTTTGGGCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.33, C:0.30, G:0.26, T:0.11
Consensus pattern (18 bp):
AGAGCACACGATGCCACG
Found at i:40185 original size:40 final size:40
Alignment explanation
Indices: 40141--40221 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
40131 ATTTGTCTCT
40141 CCTAATAATTAAGGCAATAAATTAAA-TCTAGGTTTAGCCC
1 CCTAATAATTAAGGCAATAAATTAAATTC-AGGTTTAGCCC
*
40181 CCTAATAATTAAGGTAATAAATTAAATTCAGGTTTAGCCC
1 CCTAATAATTAAGGCAATAAATTAAATTCAGGTTTAGCCC
40221 C
1 C
40222 TAGTTATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 37 0.95
41 2 0.05
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (40 bp):
CCTAATAATTAAGGCAATAAATTAAATTCAGGTTTAGCCC
Done.