Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001293.1 Corchorus capsularis cultivar CVL-1 contig01293, 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: 1707
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Found at i:269 original size:22 final size:22
Alignment explanation
Indices: 241--320 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
231 TGTCTCTATC
241 TGGTTATCAAAATTCCATAAGA
1 TGGTTATCAAAATTCCATAAGA
* * *
263 TGGTTATTATAATTCCATGAGGA
1 TGGTTATCAAAATTCCAT-AAGA
* *
286 -GTTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTCCATAAG-A
*
307 TGGTTACCAAAATT
1 TGGTTATCAAAATT
321 TCATCGTGTA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.02
22 41 0.91
23 3 0.07
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTCCATAAGA
Found at i:329 original size:22 final size:22
Alignment explanation
Indices: 292--370 Score: 122
Period size: 22 Copynumber: 3.6 Consensus size: 22
282 AGGAGTTTAT
*
292 CAAAATTCCATAGTGTGGTTAC
1 CAAAATTTCATAGTGTGGTTAC
* *
314 CAAAATTTCATCGTGTAGTTAC
1 CAAAATTTCATAGTGTGGTTAC
*
336 CAAAATTTCATAGAGTGGTTAC
1 CAAAATTTCATAGTGTGGTTAC
358 CAAAATTTCATAG
1 CAAAATTTCATAG
371 GATCGGGTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGTGTGGTTAC
Found at i:513 original size:22 final size:22
Alignment explanation
Indices: 488--593 Score: 65
Period size: 22 Copynumber: 4.8 Consensus size: 22
478 AGGTTATACG
**
488 AATTTCATAGTGTGGTTAACAA
1 AATTTCATAGTAAGGTTAACAA
510 AATTTCATTAG-AAGGTT-ACTAA
1 AATTTCA-TAGTAAGGTTAAC-AA
* * ** *
532 TATTTCATTGGGAGGTTATCAA
1 AATTTCATAGTAAGGTTAACAA
* * *
554 AATTTTATAGTATGGTTATCAA
1 AATTTCATAGTAAGGTTAACAA
*
576 AATTTTATA-TGAAGGTTA
1 AATTTCATAGT-AAGGTTA
594 TAAAAGTCTC
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
21 5 0.08
22 57 0.86
23 4 0.06
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.41
Consensus pattern (22 bp):
AATTTCATAGTAAGGTTAACAA
Found at i:594 original size:22 final size:22
Alignment explanation
Indices: 544--598 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
534 TTTCATTGGG
544 AGGTTATCAAAATTTTATAGTA
1 AGGTTATCAAAATTTTATAGTA
*
566 TGGTTATCAAAATTTTATA-TGA
1 AGGTTATCAAAATTTTATAGT-A
588 AGGTTAT-AAAA
1 AGGTTATCAAAA
599 GTCTCAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 5 0.17
22 25 0.83
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.40
Consensus pattern (22 bp):
AGGTTATCAAAATTTTATAGTA
Found at i:673 original size:22 final size:22
Alignment explanation
Indices: 638--768 Score: 88
Period size: 22 Copynumber: 5.9 Consensus size: 22
628 TGATAGAAGG
*
638 TTATC-AAATCTCATAGAGTAA
1 TTATCAAAATTTCATAGAGTAA
* *
659 TTATCGAAATTTCATAAAGATAGGA
1 TTATCAAAATTTCATAGAG-TA--A
* **
684 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGAGTAA
* * *
706 TTATCAAAATTTCAAAGCG-AGG
1 TTATCAAAATTTCATAGAGTA-A
* *
728 TTATCAAAATTGCATA-ATGTGA
1 TTATCAAAATTTCATAGA-GTAA
*
750 TTATCAAAATTTTATAGAG
1 TTATCAAAATTTCATAGAG
769 GGGTCAACAA
Statistics
Matches: 85, Mismatches: 17, Indels: 15
0.73 0.15 0.13
Matches are distributed among these distances:
21 5 0.06
22 59 0.69
23 3 0.04
24 1 0.01
25 17 0.20
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGTAA
Found at i:780 original size:44 final size:44
Alignment explanation
Indices: 688--782 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 44
678 ATAGGATTAT
* * * * *
688 CAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGGTTAT
1 CAAAATTGCATAATGTTGTTATCAAAATTTCAAAGAGAGGTCAA
* * *
732 CAAAATTGCATAATG-TGATTATCAAAATTTTATAGAGGGGTCAA
1 CAAAATTGCATAATGTTG-TTATCAAAATTTCAAAGAGAGGTCAA
776 CAAAATT
1 CAAAATT
783 ATGAAATTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.34
Consensus pattern (44 bp):
CAAAATTGCATAATGTTGTTATCAAAATTTCAAAGAGAGGTCAA
Found at i:1102 original size:31 final size:31
Alignment explanation
Indices: 1037--1097 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1027 AACTTTATGT
*
1037 TTTCCGATTGTACCATTATTTTTAAAACATA
1 TTTCCAATTGTACCATTATTTTTAAAACATA
*
1068 TTTCCAATTGTACCCTT-TTTTTAAAA-ATA
1 TTTCCAATTGTACCATTATTTTTAAAACATA
1097 T
1 T
1098 ATTTCTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.14
30 9 0.32
31 15 0.54
ACGTcount: A:0.31, C:0.16, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCATTATTTTTAAAACATA
Found at i:1163 original size:20 final size:21
Alignment explanation
Indices: 1126--1166 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1116 CTAAATAATA
**
1126 TTTTTAATTATTCCATTATTT
1 TTTTTAATTATTAAATTATTT
1147 TTTTTAATTA-TAAATTATTT
1 TTTTTAATTATTAAATTATTT
1167 CATTATATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTAATTATTAAATTATTT
Found at i:1241 original size:22 final size:22
Alignment explanation
Indices: 1216--1322 Score: 162
Period size: 22 Copynumber: 4.9 Consensus size: 22
1206 TCCATGAGGA
*
1216 GGTTATCAAAA-TTCTATAGTGT
1 GGTTACCAAAATTTC-ATAGTGT
*
1238 GGTTACCAAAATTTCATTGTGT
1 GGTTACCAAAATTTCATAGTGT
1260 GGTTACCAAAATTTCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
* *
1282 AGTTACCAAAATTTCATAGAGT
1 GGTTACCAAAATTTCATAGTGT
1304 GGTTACCAAAATTTCATAG
1 GGTTACCAAAATTTCATAG
1323 GATCAAGTTA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
22 75 0.96
23 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGTGT
Found at i:1361 original size:22 final size:22
Alignment explanation
Indices: 1216--1376 Score: 108
Period size: 22 Copynumber: 7.2 Consensus size: 22
1206 TCCATGAGGA
* *
1216 GGTTATCAAAA-TTCTATAGTGT
1 GGTTATTAAAATTTC-ATAGGGT
** * *
1238 GGTTACCAAAATTTCATTGTGT
1 GGTTATTAAAATTTCATAGGGT
** *
1260 GGTTACCAAAATTTCATAGTGT
1 GGTTATTAAAATTTCATAGGGT
* ** *
1282 AGTTACCAAAATTTCATAGAGT
1 GGTTATTAAAATTTCATAGGGT
** *
1304 GGTTACCAAAATTTCATAGGAT
1 GGTTATTAAAATTTCATAGGGT
* * *
1326 CAAGTTATTAAAATTTCTTAGGTT
1 --GGTTATTAAAATTTCATAGGGT
*
1350 GGTTATTGAAATTTCATAGGGT
1 GGTTATTAAAATTTCATAGGGT
1372 GGTTA
1 GGTTA
1377 ATTATCACAA
Statistics
Matches: 119, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
22 99 0.83
23 3 0.03
24 17 0.14
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGGT
Found at i:1626 original size:22 final size:21
Alignment explanation
Indices: 1557--1675 Score: 73
Period size: 21 Copynumber: 5.5 Consensus size: 21
1547 TAAAAGTCTC
* * *
1557 AATTTCATA-AGGAGTACCAA
1 AATTTCATAGATGATTATCAA
* * *
1577 AATTTGATAGAAGGTTATC-A
1 AATTTCATAGATGATTATCAA
* *
1597 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGA-TGATTATCAA
1619 AATTTCATAAAGATATGATTATCAA
1 AATTTCAT--AG--ATGATTATCAA
*
1644 AATTT-ATATGAAGATTATCAAA
1 AATTTCATA-GATGATTATC-AA
1666 AATTTCATAG
1 AATTTCATAG
1676 TGTTGTTATC
Statistics
Matches: 77, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
20 18 0.23
21 19 0.25
22 17 0.22
23 4 0.05
24 4 0.05
25 14 0.18
26 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (21 bp):
AATTTCATAGATGATTATCAA
Found at i:1646 original size:25 final size:24
Alignment explanation
Indices: 1609--1674 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 24
1599 TCTCATAGAG
*
1609 TGATTATCGAAATTTCATAAAGATA
1 TGATTATCAAAATTTCATAAAGA-A
*
1634 TGATTATCAAAATTT-AT-ATGAA
1 TGATTATCAAAATTTCATAAAGAA
1656 -GATTATCAAAAATTTCATA
1 TGATTATC-AAAATTTCATA
1675 GTGTTGTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 7 0.19
22 8 0.22
23 5 0.14
24 2 0.06
25 14 0.39
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (24 bp):
TGATTATCAAAATTTCATAAAGAA
Found at i:1689 original size:22 final size:22
Alignment explanation
Indices: 1574--1674 Score: 75
Period size: 22 Copynumber: 4.5 Consensus size: 22
1564 TAAGGAGTAC
* *
1574 CAAAATTTGATA-GAAGGTTAT
1 CAAAATTTCATATGAAGATTAT
* *
1595 C-AAATCTCATA-GAGTGATTAT
1 CAAAATTTCATATGA-AGATTAT
* *
1616 CGAAATTTCATAAAGATATGATTAT
1 CAAAATTTCAT-ATGA-A-GATTAT
1641 CAAAATTT-ATATGAAGATTAT
1 CAAAATTTCATATGAAGATTAT
1662 CAAAAATTTCATA
1 C-AAAATTTCATA
1675 GTGTTGTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
20 10 0.16
21 14 0.22
22 16 0.25
23 7 0.11
24 4 0.06
25 13 0.20
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATATGAAGATTAT
Done.