Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015268.1 Corchorus capsularis cultivar CVL-1 contig15289, 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: 12624
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Found at i:573 original size:21 final size:21
Alignment explanation
Indices: 531--581 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
521 AATTATAATC
*
531 AATTATAATGACAGTTTTTTTT
1 AATTTTAATGACAG-TTTTTTT
553 AATTCTTAATGACAG-TTTTTT
1 AATT-TTAATGACAGTTTTTTT
574 AATTTTAA
1 AATTTTAA
582 GTTTATATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 4 0.15
21 10 0.37
22 4 0.15
23 9 0.33
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (21 bp):
AATTTTAATGACAGTTTTTTT
Found at i:580 original size:27 final size:27
Alignment explanation
Indices: 549--632 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 27
539 TGACAGTTTT
549 TTTTAATTCTTAATGACAGTTTTTTAA
1 TTTTAATTCTTAATGACAGTTTTTTAA
*
576 TTTTAAGT-TT-AT-ATCTA-TTTTTT--
1 TTTTAATTCTTAATGA-C-AGTTTTTTAA
* *
599 TGTTGAATTCCTAATGACAGTTTTTTAA
1 T-TTTAATTCTTAATGACAGTTTTTTAA
627 TTTTAA
1 TTTTAA
633 GTTTATATCT
Statistics
Matches: 43, Mismatches: 5, Indels: 18
0.65 0.08 0.27
Matches are distributed among these distances:
23 1 0.02
24 6 0.14
25 11 0.26
26 12 0.28
27 12 0.28
28 1 0.02
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.57
Consensus pattern (27 bp):
TTTTAATTCTTAATGACAGTTTTTTAA
Found at i:608 original size:51 final size:49
Alignment explanation
Indices: 545--647 Score: 179
Period size: 51 Copynumber: 2.1 Consensus size: 49
535 ATAATGACAG
*
545 TTTTTTTTAATTCTTAATGACAGTTTTTTAATTTTAAGTTTATATCTAT
1 TTTTTTTTAATTCCTAATGACAGTTTTTTAATTTTAAGTTTATATCTAT
594 TTTTTTGTTGAATTCCTAATGACAGTTTTTTAATTTTAAGTTTATATCTAT
1 TTTTTT-TT-AATTCCTAATGACAGTTTTTTAATTTTAAGTTTATATCTAT
645 TTT
1 TTT
648 AAATATTTTC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 6 0.12
50 2 0.04
51 43 0.84
ACGTcount: A:0.25, C:0.07, G:0.08, T:0.60
Consensus pattern (49 bp):
TTTTTTTTAATTCCTAATGACAGTTTTTTAATTTTAAGTTTATATCTAT
Found at i:724 original size:2 final size:2
Alignment explanation
Indices: 717--753 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
707 GGTTTTGGTG
717 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
754 GGTATTGGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1624 original size:187 final size:189
Alignment explanation
Indices: 1289--1637 Score: 578
Period size: 187 Copynumber: 1.9 Consensus size: 189
1279 AATAACAAAT
*
1289 CATAATAATAGAAAGTGAAATTACCTAAAAACCAATCCAACCTTAACATTTAAGAACAAATGAGA
1 CATAATAATAGAAAGTGAAATCACCTAAAAACCAATCCAACCTTAACATTTAAGAACAAATGAGA
1354 ACAAATGAGGAGGGTATTTTGGTACTTTAATGTTCGGTTTTTTCGTTATTTGAATTGATGATCGA
66 ACAAATGAGGAGGGTATTTTGGTACTTTAATGTTCGGTTTTTTCGTTATTTGAATTGATGATCGA
*
1419 GGGTATTGTGGGAACTTTGTGAAAGAGTTACTTTTTTAATTTAATTTTAATTAATTAAC
131 GGGTATTGTAGGAACTTTGTGAAAGAGTTACTTTTTTAATTTAATTTTAATTAATTAAC
* * * * *
1478 CATAATAATAGAAATTGAAATCACCTAAAAACCAATGCAACCTTAACATTTCA-TA-AATTGAAG
1 CATAATAATAGAAAGTGAAATCACCTAAAAACCAATCCAACCTTAACATTTAAGAACAAATG-AG
* *
1541 CACAAATGAGGAGGGTATTTTGGTACTTTAATGTTCGG-TTTTTCGTTATTTGAATTGATGATTG
65 AACAAATGAGGAGGGTATTTTGGTACTTTAATGTTCGGTTTTTTCGTTATTTGAATTGATGATCG
*
1605 AGGGTATTTTAGGAACTTTGTGAAAGAGTTACT
130 AGGGTATTGTAGGAACTTTGTGAAAGAGTTACT
1638 ATTTATGGGT
Statistics
Matches: 149, Mismatches: 10, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
187 60 0.40
188 40 0.27
189 49 0.33
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (189 bp):
CATAATAATAGAAAGTGAAATCACCTAAAAACCAATCCAACCTTAACATTTAAGAACAAATGAGA
ACAAATGAGGAGGGTATTTTGGTACTTTAATGTTCGGTTTTTTCGTTATTTGAATTGATGATCGA
GGGTATTGTAGGAACTTTGTGAAAGAGTTACTTTTTTAATTTAATTTTAATTAATTAAC
Found at i:5507 original size:13 final size:13
Alignment explanation
Indices: 5489--5513 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5479 GTTTCTAAAT
5489 TAATCGATTCTGA
1 TAATCGATTCTGA
5502 TAATCGATTCTG
1 TAATCGATTCTG
5514 GAATGTGGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TAATCGATTCTGA
Found at i:6817 original size:2 final size:2
Alignment explanation
Indices: 6806--6835 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6796 ATACTTTTAT
6806 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6836 CATACATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7203 original size:2 final size:2
Alignment explanation
Indices: 7196--7233 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
7186 CTAAATTGAA
7196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
7234 AAAGTATCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7301 original size:31 final size:30
Alignment explanation
Indices: 7263--7327 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 30
7253 AACTTTATGT
7263 TTTCCGATTGTACCCATTTTTTCAAATATA
1 TTTCCGATTGTACCCATTTTTTCAAATATA
*
7293 GTTTCCGATTGTACCCTTTTTTTCAAATATA
1 -TTTCCGATTGTACCCATTTTTTCAAATATA
7324 TTTC
1 TTTC
7328 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.23, C:0.20, G:0.08, T:0.49
Consensus pattern (30 bp):
TTTCCGATTGTACCCATTTTTTCAAATATA
Found at i:8520 original size:21 final size:22
Alignment explanation
Indices: 8469--8565 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
8459 TGGTCATCAT
* *
8469 AATTTCATGAG-GAGGTTATCAA
1 AATTTCAT-AGTGTGGTTACCAA
* * *
8491 AAATCCATAGTGTGGTTACCCA
1 AATTTCATAGTGTGGTTACCAA
*
8513 AA-TTCATA-TG-GAAGTTATCAA
1 AATTTCATAGTGTG--GTTACCAA
8534 AATTTCATAGTGTGGTTACCAA
1 AATTTCATAGTGTGGTTACCAA
8556 AATTTCATAG
1 AATTTCATAG
8566 GATCGAGTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
19 1 0.02
20 2 0.03
21 15 0.25
22 39 0.65
23 2 0.03
24 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTACCAA
Found at i:8581 original size:24 final size:23
Alignment explanation
Indices: 8464--8591 Score: 76
Period size: 22 Copynumber: 5.7 Consensus size: 23
8454 TAAGATGGTC
*
8464 ATCATAATTTCATGAGGA-G-GTT
1 ATCAAAATTTCAT-AGGATGAGTT
* *
8486 ATCAAAAATCCATAGTG-TG-GTT
1 ATCAAAATTTCATAG-GATGAGTT
* *
8508 ACCCAAA-TTCATATGGA--AGTT
1 ATCAAAATTTCATA-GGATGAGTT
8529 ATCAAAATTTCATAGTG-TG-GTT
1 ATCAAAATTTCATAG-GATGAGTT
*
8551 ACCAAAATTTCATAGGATCGAGTT
1 ATCAAAATTTCATAGGAT-GAGTT
* *
8575 ATTAAAATTTCTTAGGA
1 ATCAAAATTTCATAGGA
8592 ATTTCATAGT
Statistics
Matches: 82, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
21 18 0.22
22 46 0.56
23 1 0.01
24 17 0.21
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (23 bp):
ATCAAAATTTCATAGGATGAGTT
Found at i:8936 original size:22 final size:22
Alignment explanation
Indices: 8920--9273 Score: 132
Period size: 22 Copynumber: 16.0 Consensus size: 22
8910 ATCATGGGGA
8920 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
**
8942 GGTTATCAAAATTTTTTAGTGT
1 GGTTATCAAAATTTCATAGTGT
* *
8964 GGTTATCAAAATTTCAT-TTGAA
1 GGTTATCAAAATTTCATAGTG-T
*
8986 GGTTAT-AAAAGTCTCAATTTCA-TGAT
1 GGTTATCAAAA-TTTC-A--T-AGTG-T
* * **
9012 GAG-TACCAAAATTTGATAG-AA
1 G-GTTATCAAAATTTCATAGTGT
* * *
9033 AGTTATC-AAATCTCATAGAGT
1 GGTTATCAAAATTTCATAGTGT
* * *
9054 GATTATCGAAATTTCATAGAGAT
1 GGTTATCAAAATTTCATAGTG-T
*
9077 CGGATTATCAAAATTT-ATAG-GAA
1 -GG-TTATCAAAATTTCATAGTG-T
* *
9100 GATTATCAAAATTTCATGGTGT
1 GGTTATCAAAATTTCATAGTGT
* * ***
9122 TGTTATCAAAATTTCAGAGCAA
1 GGTTATCAAAATTTCATAGTGT
* *
9144 GGTTATCAAAATTACATAATGT
1 GGTTATCAAAATTTCATAGTGT
** * *
9166 TATTATCAAAATTTTATAGAG-
1 GGTTATCAAAATTTCATAGTGT
* * * ** *
9187 GGTCAACAAAATTTTATAAAGA
1 GGTTATCAAAATTTCATAGTGT
* ****
9209 GGTTATCAAAAATTCATAAACA
1 GGTTATCAAAATTTCATAGTGT
* * *
9231 GGTTATCAAATTTTCAAAATGT
1 GGTTATCAAAATTTCATAGTGT
* *
9253 GATTACCAAAATTTCATAGTG
1 GGTTATCAAAATTTCATAGTG
9274 GTATTTCTGG
Statistics
Matches: 244, Mismatches: 69, Indels: 38
0.70 0.20 0.11
Matches are distributed among these distances:
20 10 0.04
21 42 0.17
22 155 0.64
23 6 0.02
24 5 0.02
25 13 0.05
26 8 0.03
27 5 0.02
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:9399 original size:22 final size:22
Alignment explanation
Indices: 9343--9799 Score: 147
Period size: 22 Copynumber: 21.0 Consensus size: 22
9333 AAACTTGTAT
*
9343 TATGGA-GTAATCAAAATTTC-
1 TATGGAGGTTATCAAAATTTCA
* *
9363 -AGGGAGGATATCAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
*
9384 TATGAAGGTTATCAAAATTT--
1 TATGGAGGTTATCAAAATTTCA
* *
9404 TATGGTTTA-GTTTTCAAAATTTCG
1 TATGG---AGGTTATCAAAATTTCA
*
9428 TA-AGAGGGTTATCAAAATTTCA
1 TATGGA-GGTTATCAAAATTTCA
*
9450 TAGTGTGTA-G--ATCAAAATTCCA
1 TA-TG-G-AGGTTATCAAAATTTCA
* ** * *
9472 TAGGGATATTAACAAAATTTAA
1 TATGGAGGTTATCAAAATTTCA
**
9494 TAAT-GAGGTTATCAAAAAAATCA
1 T-ATGGAGGTTATC-AAAATTTCA
* *
9517 TACGGAGATTATCAAAA--T--
1 TATGGAGGTTATCAAAATTTCA
* *
9535 T-TGTA-GTTATCAAGATTTCA
1 TATGGAGGTTATCAAAATTTCA
* *
9555 TAAGGAGGTTATCAAAATTTTA
1 TATGGAGGTTATCAAAATTTCA
* *
9577 TAGGGAGGTTTATCAAAATTTTA
1 TATGGAGG-TTATCAAAATTTCA
*
9600 TA-GGAATGTTTATCAAAATTTCA
1 TATGG-A-GGTTATCAAAATTTCA
** * *
9623 TAACGAGGTTATTACAATTTCA
1 TATGGAGGTTATCAAAATTTCA
*
9645 TA--G-TGTGTATCAAAATTTCA
1 TATGGAGGT-TATCAAAATTTCA
* *
9665 GAGTGTGA--TTA-CTAACAA-TACA
1 TA-TG-GAGGTTATC-AA-AATTTCA
* * *
9687 TATGGAGGTTTTTAAATTTTCA
1 TATGGAGGTTATCAAAATTTCA
** * * * *
9709 TAACGTGGTTATTAATATATCA
1 TATGGAGGTTATCAAAATTTCA
* *
9731 TATGGAGGTTATCAACATCTCA
1 TATGGAGGTTATCAAAATTTCA
*
9753 TATAGTGTTGGTTATCAAAATTTCA
1 TAT-G-G-AGGTTATCAAAATTTCA
*
9778 T-TGGGAAGTTATCAAAATTTCA
1 TAT-GGAGGTTATCAAAATTTCA
9800 AAATGAGGAC
Statistics
Matches: 321, Mismatches: 71, Indels: 88
0.67 0.15 0.18
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
19 7 0.02
20 35 0.11
21 7 0.02
22 178 0.55
23 56 0.17
24 9 0.03
25 16 0.05
26 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.37
Consensus pattern (22 bp):
TATGGAGGTTATCAAAATTTCA
Found at i:9593 original size:23 final size:23
Alignment explanation
Indices: 9541--9620 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
9531 AAATTTGTAG
* * *
9541 TTATCAAGATTTCATAAGGAGG-
1 TTATCAAAATTTTATAGGGAGGT
9563 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
9586 TTATCAAAATTTTATAGGAATGT
1 TTATCAAAATTTTATAGGGAGGT
9609 TTATCAAAATTT
1 TTATCAAAATTT
9621 CATAACGAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
22 19 0.37
23 33 0.63
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:9631 original size:46 final size:42
Alignment explanation
Indices: 9540--9664 Score: 106
Period size: 45 Copynumber: 2.8 Consensus size: 42
9530 AAAATTTGTA
* * * * **
9540 GTTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCAT-A-GTGTTTATCAAAATTTCATAACGAG
*
9584 GTTTATCAAAATTTTATAGGAATGTTTATCAAAATTTCATAACGAG
1 G-TTATCAAAATTTCATA-G--TGTTTATCAAAATTTCATAACGAG
* * *
9630 GTTATTACAATTTCATAGTGTGTATCAAAATTTCA
1 GTTATCAAAATTTCATAGTGTTTATCAAAATTTCA
9665 GAGTGTGATT
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
42 16 0.24
44 5 0.07
45 26 0.39
46 20 0.30
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (42 bp):
GTTATCAAAATTTCATAGTGTTTATCAAAATTTCATAACGAG
Found at i:9837 original size:22 final size:22
Alignment explanation
Indices: 9812--9860 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
9802 ATGAGGACTT
* *
9812 CAAAATTCCTTAAGAAGGTTAA
1 CAAAATTCCATAAGAAGGGTAA
*
9834 CAAAATTTCATAAGAAGGGTAA
1 CAAAATTCCATAAGAAGGGTAA
*
9856 AAAAA
1 CAAAA
9861 AATAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.22
Consensus pattern (22 bp):
CAAAATTCCATAAGAAGGGTAA
Found at i:9925 original size:22 final size:22
Alignment explanation
Indices: 9900--9969 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
9890 TATTGTTGTT
*
9900 AAAATTTCATAGGAAGTTTATC
1 AAAATTTCATAGGAAGATTATC
*
9922 AAAATTTCTTAGGAAGATTATC
1 AAAATTTCATAGGAAGATTATC
* *
9944 AAAATTTTATAAGG-AGATTATA
1 AAAATTTCAT-AGGAAGATTATC
9966 AAAA
1 AAAA
9970 ATAGTGTCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
22 39 0.93
23 3 0.07
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (22 bp):
AAAATTTCATAGGAAGATTATC
Found at i:10086 original size:2 final size:2
Alignment explanation
Indices: 10079--10111 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10069 AAAACTAGTG
10079 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10112 TAGGAGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.