Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008844.1 Corchorus capsularis cultivar CVL-1 contig08865, 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: 19142
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:3484 original size:6 final size:5
Alignment explanation
Indices: 3400--3472 Score: 101
Period size: 5 Copynumber: 13.8 Consensus size: 5
3390 AGAACAGGAG
*
3400 AAAAA AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC -AAAAC
3451 AAAAAC AAAAAC AAAAAC AAAA
1 -AAAAC -AAAAC -AAAAC AAAA
3473 ACACACAAAC
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
5 43 0.65
6 23 0.35
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:5676 original size:13 final size:13
Alignment explanation
Indices: 5658--5684 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5648 TCTGAGTTTT
5658 AAGGGGAAGAGGG
1 AAGGGGAAGAGGG
5671 AAGGGGAAGAGGG
1 AAGGGGAAGAGGG
5684 A
1 A
5685 GGTGGTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (13 bp):
AAGGGGAAGAGGG
Found at i:6340 original size:161 final size:156
Alignment explanation
Indices: 6121--6630 Score: 541
Period size: 158 Copynumber: 3.2 Consensus size: 156
6111 TTTAGCAACA
* * * *
6121 TAATCTTTTATGTTTTGACCTCATTAGTC-TTTCAGCCACGTGTGAGTAATAGTTGTTACATGTA
1 TAATC-TTTATGTTTTGACCTCATCAGTCTTTTTAGCCACGTGTGAGTAATGGTTGTTACATGCA
* * * * *
6185 ACTTACATATATGTTTCACGTTGAATTATGTTGTCACATGGACGTAAAATACAT-AAATTTTTGT
65 ACTTACATGTACGTTTCACGTTGAATGATGTTGTCACGTGGACGTAAAATCCATAAAATTTTTGT
6249 TTTACTCAAAACAGATAAAGTAAGGTACG
130 TTTACTCAAAACAGATAAAGTAA--TACG
* ** *
6278 TAATCTTCTATGTTTTTTACCTCATCAGTCTTTATGTAGCCACGCATGAGTGATGGTTGTTACAT
1 TAATCTT-TATG-TTTTGACCTCATCAGTCTTT-T-TAGCCACGTGTGAGTAATGGTTGTTACAT
* *
6343 GCAACTTACATGTACGTTTTACGTTGAATGATGTTGTCATGTGGACGTAAAATCCATAAAATTTT
62 GCAACTTACATGTACGTTTCACGTTGAATGATGTTGTCACGTGGACGTAAAATCCATAAAATTTT
*
6408 TGTTTTACTCAAAACAGAT--AGTAAT-CTTT
127 TGTTTTACTCAAAACAGATAAAGTAATAC--G
** * * * * *
6437 TATAT-TTTGACCTAATT-AGCTCATTAGCCTTTTTATAGTCACGTGTGAGTAATGGTTGTTACA
1 TA-ATCTTT-ATGT-TTTGACCTCATCAGTC-TTTT-TAGCCACGTGTGAGTAATGGTTGTTACA
** * * * *
6500 TGCAACTTATGTGTACGTTCCGCATTGAATGATGTTGTTACGTGGACGTAAAATCCATAAAATTT
61 TGCAACTTACATGTACGTTTCACGTTGAATGATGTTGTCACGTGGACGTAAAATCCATAAAATTT
6565 TTGTTTTACTCAAAACAGATAAAGTAATATACG
126 TTGTTTTACTCAAAACAGATAAAGT-A-ATACG
6598 TAATCTTTAATGTTTTGACCTCATTC-GTCTTTT
1 TAATCTTT-ATGTTTTGACCTCA-TCAGTCTTTT
6631 CGCAGTCACA
Statistics
Matches: 290, Mismatches: 43, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
156 2 0.01
157 10 0.03
158 129 0.44
159 12 0.04
160 19 0.07
161 88 0.30
162 29 0.10
163 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (156 bp):
TAATCTTTATGTTTTGACCTCATCAGTCTTTTTAGCCACGTGTGAGTAATGGTTGTTACATGCAA
CTTACATGTACGTTTCACGTTGAATGATGTTGTCACGTGGACGTAAAATCCATAAAATTTTTGTT
TTACTCAAAACAGATAAAGTAATACG
Found at i:6690 original size:319 final size:318
Alignment explanation
Indices: 6157--6732 Score: 712
Period size: 319 Copynumber: 1.8 Consensus size: 318
6147 GTCTTTCAGC
* * * * *
6157 CACGTGTGAGTAATAGTTGTTACATGTAACTTACATATATGTTTCACGTTGAATTATGTTGTCAC
1 CACGTGTGAGTAATAGTTGTTACATGCAACTTACATATACGTTCCACATTGAATGATGTTGTCAC
*
6222 ATGGACGTAAAATACATAAATTTTTGTTTTACTCAAAACAGATAAAGTAAGGTACGTAATCTTCT
66 ATGGACGTAAAATACATAAATTTTTGTTTTACTCAAAACAGATAAAGTAAGATACGTAATCTTCT
* * * * * ** **
6287 ATGTTTTTTACCTCATCAGTCTTTATGTAGCCACGCATGAGTGATGGTTGTTACATGCAACTTAC
131 ATGTTTTTGACCTCATCAGTCTTTATGCAGCCACACATGAATAATACTTAATACATGCAACTTAC
* * * *
6352 ATGTACGTTTTACGTTGAATGATGTTGTCATGTGGACGTAAAATCCATAAAATTTTTGTTTTACT
196 ATGTACATTGTACGTTGAATCATGTTGTCACGTGGACGTAAAATCCAT-AAATTTTTGTTTTACT
6417 CAAAACAGATAGTAATCTTTTATATTTTGACCTAATTAGCTCATTAGCCTTTTTATAGT
260 CAAAACAGATAGTAATCTTTTATATTTTGACCTAATTAGCTCATTAGCCTTTTTATAGT
* ** * * *
6476 CACGTGTGAGTAATGGTTGTTACATGCAACTTATGTGTACGTTCCGCATTGAATGATGTTGTTAC
1 CACGTGTGAGTAATAGTTGTTACATGCAACTTACATATACGTTCCACATTGAATGATGTTGTCAC
* * *
6541 GTGGACGTAAAATCCATAAAATTTTTGTTTTACTCAAAACAGATAAAGTAATATACGTAATCTT-
66 ATGGACGTAAAATACAT-AAATTTTTGTTTTACTCAAAACAGATAAAGTAAGATACGTAATCTTC
* * * *
6605 TAATG-TTTTGACCTCATTC-GTCTTT-TCGCAGTCACACGTGAATAATACTTAATATATGTACA
130 T-ATGTTTTTGACCTCA-TCAGTCTTTAT-GCAGCCACACATGAATAATACTTAATACATGCA-A
* * * *** *
6667 C-TACGTGTACATTGTATGTTGAATCATGTTGTCACGTGGATGTATTTTCTATAAATTTTTGTTT
191 CTTACATGTACATTGTACGTTGAATCATGTTGTCACGTGGACGTAAAATCCATAAATTTTTGTTT
6731 TA
256 TA
6733 TTAAAAAAAA
Statistics
Matches: 213, Mismatches: 39, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
318 15 0.07
319 147 0.69
320 51 0.24
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (318 bp):
CACGTGTGAGTAATAGTTGTTACATGCAACTTACATATACGTTCCACATTGAATGATGTTGTCAC
ATGGACGTAAAATACATAAATTTTTGTTTTACTCAAAACAGATAAAGTAAGATACGTAATCTTCT
ATGTTTTTGACCTCATCAGTCTTTATGCAGCCACACATGAATAATACTTAATACATGCAACTTAC
ATGTACATTGTACGTTGAATCATGTTGTCACGTGGACGTAAAATCCATAAATTTTTGTTTTACTC
AAAACAGATAGTAATCTTTTATATTTTGACCTAATTAGCTCATTAGCCTTTTTATAGT
Found at i:7457 original size:112 final size:112
Alignment explanation
Indices: 7063--7466 Score: 429
Period size: 111 Copynumber: 3.6 Consensus size: 112
7053 GCGCGTACAG
* * *
7063 ATTCCAAGTCCACGTGACAACATCATTAAATGTGGAATGCACACGTAAGGTGCTTGTAACAAGCA
1 ATTCCATGTCCACGTGACAACATCATTAAATGTGGAATGTACACGTAAGGTGCTTGTAACAACCA
* ** * ** *
7128 TTACTTACGCGTGGATACATTTTTTTTTGTGAAA-AGGAGCGTATGA
66 TTACTTACGCGTGGATACACTTTTTTAGGTAAAACAAAAGTGTATGA
* * * * **
7174 ATTCCACGTTCACGTGACAACATCATTAAATGCGGAATGTACACGTAAGGCGCTTGTAACAACTG
1 ATTCCATGTCCACGTGACAACATCATTAAATGTGGAATGTACACGTAAGGTGCTTGTAACAACCA
** * * *
7239 TTACTTACGCGTGGATA-TGTTTTTTGGGTAAAACGAAAGTGTATGG
66 TTACTTACGCGTGGATACACTTTTTTAGGTAAAACAAAAGTGTATGA
* * * * *
7285 ATTCCATATCCACGTGACAATATCACTAAACGTGGAATGTACATGTAA-GT-CATTTGTAACAAC
1 ATTCCATGTCCACGTGACAACATCATTAAATGTGGAATGTACACGTAAGGTGC--TTGTAACAAC
* * * *
7348 CATTACTTACGTGTGGATACACCTTTTTAGGTAAAACAAAAATGTATGC
64 CATTACTTACGCGTGGATACACTTTTTTAGGTAAAACAAAAGTGTATGA
* * * * * * *
7397 ATTCCATGTCCACGTGACAGCATCATTCAATATGTAATGTACACGTAAGGTGTTTATAACAACCG
1 ATTCCATGTCCACGTGACAACATCATTAAATGTGGAATGTACACGTAAGGTGCTTGTAACAACCA
7462 TTACT
66 TTACT
7467 CACCTGTGAC
Statistics
Matches: 238, Mismatches: 49, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
109 1 0.00
110 12 0.05
111 147 0.62
112 76 0.32
113 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (112 bp):
ATTCCATGTCCACGTGACAACATCATTAAATGTGGAATGTACACGTAAGGTGCTTGTAACAACCA
TTACTTACGCGTGGATACACTTTTTTAGGTAAAACAAAAGTGTATGA
Found at i:12287 original size:3 final size:3
Alignment explanation
Indices: 12273--12310 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
12263 GAATTTGAAA
12273 AAG AACG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
12311 TCTTAGTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.03, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16518 original size:12 final size:12
Alignment explanation
Indices: 16500--16583 Score: 69
Period size: 12 Copynumber: 7.0 Consensus size: 12
16490 TCTGGAGCAC
*
16500 TGGTGGTGGTGG
1 TGGTGGTGGCGG
* *
16512 AGGTGGTTGCGG
1 TGGTGGTGGCGG
* * *
16524 TGGAGGCGGAGG
1 TGGTGGTGGCGG
16536 TGGTGGTGGCGG
1 TGGTGGTGGCGG
* *
16548 TTGTGGGGGCGG
1 TGGTGGTGGCGG
*
16560 TGGTGGAGGCGG
1 TGGTGGTGGCGG
* *
16572 TTGCGGTGGCGG
1 TGGTGGTGGCGG
16584 AGGCGGCGGT
Statistics
Matches: 54, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 54 1.00
ACGTcount: A:0.05, C:0.08, G:0.64, T:0.23
Consensus pattern (12 bp):
TGGTGGTGGCGG
Found at i:16553 original size:15 final size:15
Alignment explanation
Indices: 16505--16580 Score: 56
Period size: 15 Copynumber: 5.5 Consensus size: 15
16495 AGCACTGGTG
*
16505 GTGGTGGAGGTGGTT
1 GTGGTGGAGGCGGTT
* **
16520 GCGGTGGAGGCGGAG
1 GTGGTGGAGGCGGTT
*
16535 GTGGTGGTGGCGGTT
1 GTGGTGGAGGCGGTT
16550 GT-G-GG-GGC-G--
1 GTGGTGGAGGCGGTT
16559 GTGGTGGAGGCGGTT
1 GTGGTGGAGGCGGTT
*
16574 GCGGTGG
1 GTGGTGG
16581 CGGAGGCGGC
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
9 2 0.04
10 1 0.02
11 3 0.07
12 6 0.13
13 3 0.07
14 1 0.02
15 30 0.65
ACGTcount: A:0.05, C:0.08, G:0.64, T:0.22
Consensus pattern (15 bp):
GTGGTGGAGGCGGTT
Found at i:16746 original size:22 final size:22
Alignment explanation
Indices: 16721--16767 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
16711 AAAATACTGC
16721 TAATA-CTAATTTCTGCAATATT
1 TAATACCTAATTTCTGCAAT-TT
*
16743 TAATATCCTTATTTCTGCAATTT
1 TAATA-CCTAATTTCTGCAATTT
16766 TA
1 TA
16768 TATATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 4 0.18
24 13 0.59
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.49
Consensus pattern (22 bp):
TAATACCTAATTTCTGCAATTT
Found at i:16777 original size:22 final size:23
Alignment explanation
Indices: 16729--16778 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
16719 GCTAATACTA
*
16729 ATTTCTGCAATATTTAATATCCTT
1 ATTTCTGCAATATTTAATAT-CAT
16753 ATTTCTGCAAT-TTTATATAT-AT
1 ATTTCTGCAATATTTA-ATATCAT
16775 ATTT
1 ATTT
16779 ATGATCCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.21
23 4 0.17
24 15 0.62
ACGTcount: A:0.30, C:0.12, G:0.04, T:0.54
Consensus pattern (23 bp):
ATTTCTGCAATATTTAATATCAT
Found at i:18086 original size:2 final size:2
Alignment explanation
Indices: 18079--18106 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18069 AATATAAATT
18079 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
18107 ATAACTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18881 original size:11 final size:11
Alignment explanation
Indices: 18865--18898 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
18855 TCGAAGTTCG
18865 TATTTGAAGAT
1 TATTTGAAGAT
18876 TATTTGAAGA-
1 TATTTGAAGAT
18886 TATTTTGAAGAT
1 TA-TTTGAAGAT
18898 T
1 T
18899 TGAAGACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.10
11 18 0.86
12 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (11 bp):
TATTTGAAGAT
Done.