Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010177.1 Corchorus capsularis cultivar CVL-1 contig10198, 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: 7582
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Found at i:503 original size:25 final size:25
Alignment explanation
Indices: 458--506 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
448 ATTTGAACTC
*
458 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
483 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
507 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:506 original size:21 final size:21
Alignment explanation
Indices: 458--508 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
448 ATTTGAACTC
458 ATTATT-TATTATTTAAAATAT
1 ATTATTAT-TTATTTAAAATAT
479 ATTTATTATTTATTTAATAATAT
1 A-TTATTATTTATTTAA-AATAT
502 A-TATTAT
1 ATTATTAT
509 ATCTAAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 7 0.26
22 13 0.48
23 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATTATTTATTTAAAATAT
Found at i:1196 original size:167 final size:167
Alignment explanation
Indices: 885--1207 Score: 443
Period size: 167 Copynumber: 1.9 Consensus size: 167
875 TTGTCAATTG
* * *
885 AGAAATGACCAATAAGTTTAGTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTAAGTAA
1 AGAAATGACCAAAAAGATTAGTTATTTAATCCCCTCAAGAAGAAAAAATTAGGACATTTAAGTAA
* * * * ** * * *
950 TCTGCCAAGTAGGTAAAGACGAAAAAATGTTAGTTCTCTAGCTCATCATCAATCCTTGAAGGGGA
66 TCTGCCAAGTAGGAAAAGACGAAAAAATATAAGTTCTCTAACTCAAAAGCAAGCCTTGAAGGAGA
*
1015 TCATTTATTAATTCCACTACTCTATTCAAATCCATTT
131 TCATTTAGTAATTCCACTACTCTATTCAAATCCATTT
* * * *
1052 AGAAATGACTAAAAAGATTATTTATTTAATCCCCTCAAGAAGCAAAAGTTAGGACATTTAAGTAA
1 AGAAATGACCAAAAAGATTAGTTATTTAATCCCCTCAAGAAGAAAAAATTAGGACATTTAAGTAA
*
1117 TCTGCCAAGTAGGAAAAGACGAAAAAA-ATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTA-GA
66 TCTGCCAAGTAGGAAAAGACGAAAAAATATAAGTTCTCTAACT-CAAAAGCAAGCCTTG-AAGGA
*
1180 GATCTTTTAGTAATTCCACTACTCTATT
129 GATCATTTAGTAATTCCACTACTCTATT
1208 AAAGTTTAGG
Statistics
Matches: 135, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
166 12 0.09
167 122 0.90
168 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (167 bp):
AGAAATGACCAAAAAGATTAGTTATTTAATCCCCTCAAGAAGAAAAAATTAGGACATTTAAGTAA
TCTGCCAAGTAGGAAAAGACGAAAAAATATAAGTTCTCTAACTCAAAAGCAAGCCTTGAAGGAGA
TCATTTAGTAATTCCACTACTCTATTCAAATCCATTT
Found at i:1838 original size:321 final size:322
Alignment explanation
Indices: 1011--1799 Score: 1303
Period size: 323 Copynumber: 2.4 Consensus size: 322
1001 ATCCTTGAAG
* * * * *
1011 GGGATCATTTATTAATTCCACTACTCTATTCAAATCCATTTAGAAATGACTAAAAAGATTATTTA
1 GGGATCTTTTAGTAATTCCACTACTCTATTCAAATCCATTGAGAAATGACCAAAAAGATTACTTA
*
1076 TTTAATCCCCTCAAGAAGCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAA
66 TTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAA
*
1141 AAAATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGAGATCTTTTAGTAATTCCACTACTCTA
131 AAAATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTA
**
1206 TTAAAGTTTAGGACATTTAAGTAATCTGCCAGGTAGGTAAAGACGAAAAAGATTACTTCTCCAGC
196 TTAAAGTTTA-GACATTTAAGTAATCTGCCAAATAGGTAAAGACGAAAAAGATTACTTCTCCAGC
* *
1271 TCATCATTAATCCGGGTAGGGATCTTTTAGTAATTCCATCCAACTTATCATTAATTCGTGGTA
260 TCATCATTAATCCGGGTAGGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGTA
* *
1334 GAGATCTTTTAGTAATTCCACTACTCTTTTCAAATCCATTGAGAAATGACCAAAAAGATTACTTA
1 GGGATCTTTTAGTAATTCCACTACTCTATTCAAATCCATTGAGAAATGACCAAAAAGATTACTTA
* * **
1399 TTTAATCCCCTCAAGAATCAAAAGTTAGGACATTCAAGTAATCTACCAAGTAAAAAAAGACGAAA
66 TTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAA
1464 AAAATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTA
131 AAAATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTA
*
1529 TTAAAG-TT-GACATTTAAGTAATCTGCCAAATAGGTAAAGACGAAAAAGATTACTTCTCCTGCT
196 TTAAAGTTTAGACATTTAAGTAATCTGCCAAATAGGTAAAGACGAAAAAGATTACTTCTCCAGCT
* *
1592 CATCATTAATCTGGGGTAGGGATCTTTTAGTAATTCCACCCAGCTTATCATTAATTCGGGGTA
261 CATCATTAATC-CGGGTAGGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGTA
* *
1655 GGGATCTTTTAGTAATTTCACTGCTCTATTCAAATCCATTGAGAAATGACCAAAAAGATTACTTA
1 GGGATCTTTTAGTAATTCCACTACTCTATTCAAATCCATTGAGAAATGACCAAAAAGATTACTTA
* * *
1720 TTTAATCCCCTCAAGAATCAAAAGTTAGGGCATTTAAGTAATCGGCCAAGTGGGAAAAGACGGAA
66 TTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGAC-GAA
*
1785 AAAAATTAGTTCTCT
130 AAAAATAAGTTCTCT
1800 CGCTCCTCAT
Statistics
Matches: 432, Mismatches: 32, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
320 63 0.15
321 162 0.38
322 19 0.04
323 188 0.44
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (322 bp):
GGGATCTTTTAGTAATTCCACTACTCTATTCAAATCCATTGAGAAATGACCAAAAAGATTACTTA
TTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAA
AAAATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTA
TTAAAGTTTAGACATTTAAGTAATCTGCCAAATAGGTAAAGACGAAAAAGATTACTTCTCCAGCT
CATCATTAATCCGGGTAGGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGTA
Found at i:5519 original size:9 final size:8
Alignment explanation
Indices: 5507--5601 Score: 65
Period size: 9 Copynumber: 11.8 Consensus size: 8
5497 GTGACCCGCA
5507 ACCCAGATG
1 ACCC-GATG
5516 ACCCGA-G
1 ACCCGATG
5523 ACCCGAATG
1 ACCCG-ATG
*
5532 ACCCG-TA
1 ACCCGATG
*
5539 ACTCAGATG
1 AC-CCGATG
*
5548 ACCCGA-A
1 ACCCGATG
5555 ACCCGAATG
1 ACCCG-ATG
*
5564 ACCCG-TA
1 ACCCGATG
5571 ACCCGAGTG
1 ACCCGA-TG
5580 ACCCGA-G
1 ACCCGATG
5587 ACCCGTATG
1 ACCCG-ATG
5596 ACCCGA
1 ACCCGA
5602 AACCCGAATA
Statistics
Matches: 68, Mismatches: 8, Indels: 21
0.70 0.08 0.22
Matches are distributed among these distances:
7 26 0.38
8 11 0.16
9 31 0.46
ACGTcount: A:0.31, C:0.37, G:0.22, T:0.11
Consensus pattern (8 bp):
ACCCGATG
Found at i:5607 original size:32 final size:32
Alignment explanation
Indices: 5483--5606 Score: 169
Period size: 32 Copynumber: 3.9 Consensus size: 32
5473 GAATCCGCCC
* *
5483 GACCCGAAACCCGAGTGACCCGCAACCCAGAT
1 GACCCGAAACCCGAATGACCCGTAACCCAGAT
* *
5515 GACCCGAGACCCGAATGACCCGTAACTCAGAT
1 GACCCGAAACCCGAATGACCCGTAACCCAGAT
5547 GACCCGAAACCCGAATGACCCGTAACCC-GAGT
1 GACCCGAAACCCGAATGACCCGTAACCCAGA-T
* * *
5579 GACCCGAGACCCGTATGACCCGAAACCC
1 GACCCGAAACCCGAATGACCCGTAACCC
5607 GAATAACCCA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 2 0.02
32 80 0.98
ACGTcount: A:0.31, C:0.39, G:0.22, T:0.09
Consensus pattern (32 bp):
GACCCGAAACCCGAATGACCCGTAACCCAGAT
Found at i:5615 original size:16 final size:16
Alignment explanation
Indices: 5483--5615 Score: 144
Period size: 16 Copynumber: 8.3 Consensus size: 16
5473 GAATCCGCCC
*
5483 GACCCGAAACCCGAGT
1 GACCCGAAACCCGAAT
*
5499 GACCCGCAACCC-AGAT
1 GACCCGAAACCCGA-AT
*
5515 GACCCGAGACCCGAAT
1 GACCCGAAACCCGAAT
* *
5531 GACCCGTAACTC-AGAT
1 GACCCGAAACCCGA-AT
5547 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
* *
5563 GACCCGTAACCCGAGT
1 GACCCGAAACCCGAAT
* *
5579 GACCCGAGACCCGTAT
1 GACCCGAAACCCGAAT
5595 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
*
5611 AACCC
1 GACCC
5616 AAGAAGTTAA
Statistics
Matches: 95, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
15 2 0.02
16 91 0.96
17 2 0.02
ACGTcount: A:0.32, C:0.38, G:0.21, T:0.09
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:7228 original size:20 final size:20
Alignment explanation
Indices: 7192--7229 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7182 TTTAGAAGCA
**
7192 ATTAATTAAAAGTATTAAAC
1 ATTAATTAAAACAATTAAAC
7212 ATTAATTAAAACAATTAA
1 ATTAATTAAAACAATTAA
7230 GGAAGGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (20 bp):
ATTAATTAAAACAATTAAAC
Found at i:7322 original size:74 final size:74
Alignment explanation
Indices: 7236--7392 Score: 244
Period size: 74 Copynumber: 2.1 Consensus size: 74
7226 TTAAGGAAGG
* * * * *
7236 GAAATGTGTAATTACGAAAAAGGGTAGAAGGAGAAGGAATGGGGGAAACTCATAGAGGGGCTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGAAATAGGGGAAACTCATAGAGGGACTTTT
7301 TAGTCATCC-
66 TAGTCA-CCT
*
7310 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGAAATAGGGGAAACTCATAGATGGACTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGAAATAGGGGAAACTCATAGAGGGACTTTT
7375 TAGTCACCT
66 TAGTCACCT
7384 GAAAAGTGT
1 GAAAAGTGT
7393 GAAAAGACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
73 2 0.03
74 74 0.97
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (74 bp):
GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGAAATAGGGGAAACTCATAGAGGGACTTTT
TAGTCACCT
Found at i:7507 original size:15 final size:15
Alignment explanation
Indices: 7475--7525 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
7465 GTTAAAAATA
7475 ATATATAGTATATATAT
1 ATATATAGTA-AT-TAT
7492 ATATATAGTAATTAT
1 ATATATAGTAATTAT
*
7507 A-ATATAATAAATTAT
1 ATATATAGT-AATTAT
7522 -TATA
1 ATATA
7526 AAAAAGTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
14 6 0.19
15 13 0.42
16 2 0.06
17 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (15 bp):
ATATATAGTAATTAT
Done.