Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015206.1 Corchorus capsularis cultivar CVL-1 contig15227, 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: 37716
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:434 original size:15 final size:15
Alignment explanation
Indices: 416--452 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
406 TTTTTTATTT
416 TATATATATAATATA
1 TATATATATAATATA
431 TATA-ATTATAATATA
1 TATATA-TATAATATA
446 TAT-TATA
1 TATATATA
453 CAAAACGACG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATATATAATATA
Found at i:5688 original size:31 final size:31
Alignment explanation
Indices: 5653--5717 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
5643 AACTGAACTA
* *
5653 ACTCAAACATGCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGAGCTAAAGATCTGGAG
5684 ACTCAAACATCCAAGAGCTAAAGATCTGGAG
1 ACTCAAACATCCAAGAGCTAAAGATCTGGAG
5715 ACT
1 ACT
5718 GATAACCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (31 bp):
ACTCAAACATCCAAGAGCTAAAGATCTGGAG
Found at i:6370 original size:15 final size:15
Alignment explanation
Indices: 6350--6380 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6340 AGATTAATTG
*
6350 ATTTGGGAGGGTAGT
1 ATTTGGGAGGATAGT
6365 ATTTGGGAGGATAGT
1 ATTTGGGAGGATAGT
6380 A
1 A
6381 GAAATTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.42, T:0.32
Consensus pattern (15 bp):
ATTTGGGAGGATAGT
Found at i:9293 original size:2 final size:2
Alignment explanation
Indices: 9277--9312 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
9267 TCTTTTCTTC
*
9277 AT AT AT AA AT CAT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A
9313 GAGGGAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:13272 original size:23 final size:24
Alignment explanation
Indices: 13239--13283 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
13229 TTCTCCTGTT
*
13239 AGCCGATTAAAAA-AAATTGCAGC
1 AGCCGAATAAAAAGAAATTGCAGC
13262 AGCCGAATAAAAAGAAATTGCA
1 AGCCGAATAAAAAGAAATTGCA
13284 ACAGGGGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.16
Consensus pattern (24 bp):
AGCCGAATAAAAAGAAATTGCAGC
Found at i:16414 original size:54 final size:54
Alignment explanation
Indices: 16332--16441 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
16322 GTCATGGTTA
16332 TCGCAACAACTATTGTCAGATATTTTTCACGTTTCATACTTTCATTATCCATTT
1 TCGCAACAACTATTGTCAGATATTTTTCACGTTTCATACTTTCATTATCCATTT
16386 TCGCAACAACTATTGTCAGATATTTTTCACGTTTCATACTTTCATTATCCATTT
1 TCGCAACAACTATTGTCAGATATTTTTCACGTTTCATACTTTCATTATCCATTT
16440 TC
1 TC
16442 ATTTCGTTGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (54 bp):
TCGCAACAACTATTGTCAGATATTTTTCACGTTTCATACTTTCATTATCCATTT
Found at i:16720 original size:39 final size:39
Alignment explanation
Indices: 16671--16760 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 39
16661 TTTTGTATAT
16671 AAACTCAATCTTATCATATTAATCTGTCCATAAGTAAAC
1 AAACTCAATCTTATCATATTAATCTGTCCATAAGTAAAC
* *
16710 AAACTCAATCTTATCATATTAATTTGTCCATAAGTAAAT
1 AAACTCAATCTTATCATATTAATCTGTCCATAAGTAAAC
16749 AAACTCAATCTT
1 AAACTCAATCTT
16761 TTCACATAGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (39 bp):
AAACTCAATCTTATCATATTAATCTGTCCATAAGTAAAC
Found at i:18241 original size:31 final size:32
Alignment explanation
Indices: 18203--18272 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
18193 CTACTCACAC
*
18203 TTAACTTCTCCAATTTACCCTTCA-TATTTTA
1 TTAACTTCTCCAATTTACCCCTCATTATTTTA
*
18234 TTAACTTCTCCAATTTACCCCTCATTTTTTTA
1 TTAACTTCTCCAATTTACCCCTCATTATTTTA
*
18266 TCAACTT
1 TTAACTT
18273 AACATTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (32 bp):
TTAACTTCTCCAATTTACCCCTCATTATTTTA
Found at i:20767 original size:46 final size:46
Alignment explanation
Indices: 20700--20792 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
20690 ACAAAAAGAT
* *
20700 AACCAGAATACTCCTACTTCACTATGCTATACATAAACCCAACCAC
1 AACCAAAATACTCCTACTTCACTATGCTATACATAAACCAAACCAC
20746 AACCAAAATACTCCTACTTCACTATGCTATACATAAACCAAACCAC
1 AACCAAAATACTCCTACTTCACTATGCTATACATAAACCAAACCAC
20792 A
1 A
20793 TCTTGGATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.42, C:0.33, G:0.03, T:0.22
Consensus pattern (46 bp):
AACCAAAATACTCCTACTTCACTATGCTATACATAAACCAAACCAC
Found at i:30765 original size:31 final size:31
Alignment explanation
Indices: 30712--30816 Score: 120
Period size: 31 Copynumber: 3.4 Consensus size: 31
30702 TTATCAATTT
* ** * *
30712 ACCCTACTAAAATTGAAGTTTTATAGTATTG
1 ACCCCACTAAAATAAAAATTTTATAGTATTA
*
30743 ACCCCATTAAAATAAAAATTTTATAGTATTA
1 ACCCCACTAAAATAAAAATTTTATAGTATTA
* * *
30774 ACCCCACTAAAATCAAAGTTTTATAGTATTT
1 ACCCCACTAAAATAAAAATTTTATAGTATTA
*
30805 ACCCCACAAAAA
1 ACCCCACTAAAA
30817 ATGTTGGATC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (31 bp):
ACCCCACTAAAATAAAAATTTTATAGTATTA
Found at i:33269 original size:116 final size:116
Alignment explanation
Indices: 33037--33270 Score: 391
Period size: 116 Copynumber: 2.0 Consensus size: 116
33027 CAATGCAGTA
33037 TACCTCCATCAAACAAAGACCTTGACTTACCATCATTCATGTTATAAGATGACTAACATCAAAGT
1 TACCTCCATCAAACAAAGACCTTGACTTACCATCATTCATGTTATAAGATGACTAACATCAAAGT
33102 TTGGTACAAATATGAATTTTTCAGAGAAAATGATGCTACTAGCTGAATAAG
66 TTGGTACAAATATGAATTTTTCAGAGAAAATGATGCTACTAGCTGAATAAG
* * *
33153 TACCTCCATCAAACAAAGATCTTGAGTTACCATCATTCATTTTATAAGATGACTAACATCAAAAG
1 TACCTCCATCAAACAAAGACCTTGACTTACCATCATTCATGTTATAAGATGACTAACATC-AAAG
* *
33218 TTTGGTACAAATATGATTTTTTCAGAGAAAATGCA-GCTACTA-CTGATTAAG
65 TTTGGTACAAATATGAATTTTTCAGAGAAAATG-ATGCTACTAGCTGAATAAG
33269 TA
1 TA
33271 TGGCTTATTT
Statistics
Matches: 111, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
116 67 0.60
117 43 0.39
118 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (116 bp):
TACCTCCATCAAACAAAGACCTTGACTTACCATCATTCATGTTATAAGATGACTAACATCAAAGT
TTGGTACAAATATGAATTTTTCAGAGAAAATGATGCTACTAGCTGAATAAG
Found at i:35557 original size:23 final size:23
Alignment explanation
Indices: 35530--35606 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
35520 CAAACGTACC
35530 ATCATAAAGATTTTCATTATTTA
1 ATCATAAAGATTTTCATTATTTA
* * *
35553 ATCATAAAAATTGAATCA-TA-ATA
1 ATCATAAAGATT--TTCATTATTTA
*
35576 ATCATAAAGATTTTCATCATTTA
1 ATCATAAAGATTTTCATTATTTA
*
35599 ATTATAAA
1 ATCATAAA
35607 CCATACCCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
21 3 0.07
22 1 0.02
23 33 0.79
24 2 0.05
25 3 0.07
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (23 bp):
ATCATAAAGATTTTCATTATTTA
Found at i:35894 original size:21 final size:21
Alignment explanation
Indices: 35810--35900 Score: 112
Period size: 21 Copynumber: 4.3 Consensus size: 21
35800 GTTTCAACCA
*
35810 TTTCAGCAGCACATTTAAC-C
1 TTTCAGCAGCAGATTTAACAC
* * *
35830 ATTTTAGCAGTAGATTTAACTC
1 -TTTCAGCAGCAGATTTAACAC
*
35852 TTTCAGCAGCATATTTAACAC
1 TTTCAGCAGCAGATTTAACAC
*
35873 TTTCAGCAGCAGATTTAGCAC
1 TTTCAGCAGCAGATTTAACAC
35894 TTTCAGC
1 TTTCAGC
35901 TGGAGTAGCT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
21 59 0.98
22 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (21 bp):
TTTCAGCAGCAGATTTAACAC
Found at i:36462 original size:21 final size:21
Alignment explanation
Indices: 36436--36476 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
36426 TACATACAAT
36436 ACTATCATAACAAACTCTCAC
1 ACTATCATAACAAACTCTCAC
*
36457 ACTATCATAACAGACTCTCA
1 ACTATCATAACAAACTCTCA
36477 TGAGTCTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.32, G:0.02, T:0.24
Consensus pattern (21 bp):
ACTATCATAACAAACTCTCAC
Done.