Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011500.1 Corchorus capsularis cultivar CVL-1 contig11521, 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: 16840
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:459 original size:22 final size:22
Alignment explanation
Indices: 431--479 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
421 ATTATATATA
*
431 AAAATCAAACTATATAAAAAAT
1 AAAATCAAACTACATAAAAAAT
** *
453 AAAATCATCCTACATAAAATAT
1 AAAATCAAACTACATAAAAAAT
475 AAAAT
1 AAAAT
480 ATTACCAAAT
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:0.63, C:0.12, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAATCAAACTACATAAAAAAT
Found at i:689 original size:21 final size:21
Alignment explanation
Indices: 663--704 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
653 AGACTAATAT
663 CTTGGCCTAATAACAATTAAA
1 CTTGGCCTAATAACAATTAAA
* *
684 CTTGGCCTGATAATAATTAAA
1 CTTGGCCTAATAACAATTAAA
705 AGTTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (21 bp):
CTTGGCCTAATAACAATTAAA
Found at i:722 original size:2 final size:2
Alignment explanation
Indices: 710--746 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
700 TTAAAAGTTC
710 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
747 TATCCTACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2339 original size:22 final size:23
Alignment explanation
Indices: 2304--2349 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
2294 ATTTCCCGTG
*
2304 TTTTGTGTATATTTTCCGTGGAC
1 TTTTATGTATATTTTCCGTGGAC
*
2327 TTTTATGT-TATTTTCCGTTGAC
1 TTTTATGTATATTTTCCGTGGAC
2349 T
1 T
2350 ACCCTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (23 bp):
TTTTATGTATATTTTCCGTGGAC
Found at i:4262 original size:22 final size:22
Alignment explanation
Indices: 4237--4875 Score: 175
Period size: 22 Copynumber: 29.5 Consensus size: 22
4227 TGTCCTTATC
4237 AAATTTTGATAACCTTCCTATG
1 AAATTTTGATAACCTTCCTATG
*
4259 AAATTATGATAA--TTACACTAT-
1 AAATTTTGATAACCTT-C-CTATG
* * *
4280 ---TTTTTATGA-CGTCCTTATG
1 AAATTTTGATAACCTTCC-TATG
* *
4299 AAATTTTTATAACCTTCTTATG
1 AAATTTTGATAACCTTCCTATG
** ** *
4321 AAATTTCAATAACGATACTATTG
1 AAATTTTGATAACCTTCCTA-TG
* * **
4344 -AATTTCGAGAACCTTTTTAT-
1 AAATTTTGATAACCTTCCTATG
* ** *
4364 AATTTTTTTTAACCTTCTTATG
1 AAATTTTGATAACCTTCCTATG
* * *
4386 AAATTTTGTTAACCTCCCTAAG
1 AAATTTTGATAACCTTCCTATG
* *
4408 GAATTTTGA-AGACC-TCATTATG
1 AAATTTTGATA-ACCTTC-CTATG
*
4430 AAATTTTGATAA-CTTCCAAATG
1 AAATTTTGATAACCTTCC-TATG
**
4452 AAATTTTGATAACCAACACTAT-
1 AAATTTTGATAACCTTC-CTATG
* *
4474 AAGATGTTGATAACC-TCCATGTG
1 AA-ATTTTGATAACCTTCC-TATG
* * *
4497 ATATATTGATAAACACAT--TATG
1 AAATTTTGAT-AAC-CTTCCTATG
* * *
4519 AAAATTTAAAAACC-TCCATATG
1 AAATTTTGATAACCTTCC-TATG
* * *
4541 -AATTGTT-AGTAATC-ACACTCTG
1 AAATT-TTGA-TAACCTTC-CTATG
*
4563 AAATTTTGAT-A-CTCACAGCTATG
1 AAATTTTGATAACCT-TC--CTATG
4586 AAATTGTT-ATAACC-TCGCTATG
1 AAATT-TTGATAACCTTC-CTATG
**
4608 AAATTTTGATAAACCTTCCTACA
1 AAATTTTGAT-AACCTTCCTATG
* * *
4631 AAATTTTGATAAATCTCCCTATA
1 AAATTTTGAT-AACCTTCCTATG
4654 AAATTTTGATAACC-TCCTTATG
1 AAATTTTGATAACCTTCC-TATG
* *
4676 AAATCTTGATAA-----CTA-C
1 AAATTTTGATAACCTTCCTATG
*
4692 AAATTTTGATAACCTCCCTAT-
1 AAATTTTGATAACCTTCCTATG
* *
4713 AATTTTTTGATAACC-TCATTATG
1 AA-ATTTTGATAACCTTC-CTATG
* *
4736 AAATTTT-ATTAATCTCCCTATG
1 AAATTTTGA-TAACCTTCCTATG
* * * *
4758 AAAATTTGATCTA-CATACTATG
1 AAATTTTGAT-AACCTTCCTATG
* *
4780 AAATTTTGATAACCCTCTTATG
1 AAATTTTGATAACCTTCCTATG
* **
4802 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-TCCTATG
* *
4824 AAACTTTGATAACCTTCATATG
1 AAATTTTGATAACCTTCCTATG
* *
4846 AAATTTTGATATCC-TCC-CTG
1 AAATTTTGATAACCTTCCTATG
4866 AAATTTTGAT
1 AAATTTTGAT
4876 TACTCCATGA
Statistics
Matches: 455, Mismatches: 103, Indels: 120
0.67 0.15 0.18
Matches are distributed among these distances:
16 11 0.02
17 3 0.01
18 11 0.02
19 2 0.00
20 16 0.04
21 45 0.10
22 269 0.59
23 89 0.20
24 7 0.02
25 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACCTTCCTATG
Found at i:4272 original size:62 final size:62
Alignment explanation
Indices: 4175--4325 Score: 230
Period size: 62 Copynumber: 2.4 Consensus size: 62
4165 TATTGATACG
* * *
4175 AAATTATGATAACCTTCATATTAAATTATGATAATTACACTATTTTTGATGATGTCCTTATC
1 AAATTTTGATAACCTTCATATGAAATTATGATAATTACACTATTTTTGATGACGTCCTTATC
* * *
4237 AAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATGACGTCCTTATG
1 AAATTTTGATAACCTTCATATGAAATTATGATAATTACACTATTTTTGATGACGTCCTTATC
* *
4299 AAATTTTTATAACCTTCTTATGAAATT
1 AAATTTTGATAACCTTCATATGAAATT
4326 TCAATAACGA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 81 1.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.44
Consensus pattern (62 bp):
AAATTTTGATAACCTTCATATGAAATTATGATAATTACACTATTTTTGATGACGTCCTTATC
Found at i:4341 original size:62 final size:62
Alignment explanation
Indices: 4175--4342 Score: 185
Period size: 62 Copynumber: 2.7 Consensus size: 62
4165 TATTGATACG
* * * * ** *
4175 AAATTATGATAACCTTCATATTAAATTATGATAATTACACTATTTTTGATGATGTCCTTATC
1 AAATTTTGATAACCTTCCTATGAAATTATAATAACGACACTATTTTTGATGACGTCCTTATC
* ** * *
4237 AAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATGACGTCCTTATG
1 AAATTTTGATAACCTTCCTATGAAATTATAATAACGACACTATTTTTGATGACGTCCTTATC
* * *
4299 AAATTTTTATAACCTTCTTATGAAATT-TCAATAACGATACTATT
1 AAATTTTGATAACCTTCCTATGAAATTAT-AATAACGACACTATT
4343 GAATTTCGAG
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
61 1 0.01
62 92 0.99
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (62 bp):
AAATTTTGATAACCTTCCTATGAAATTATAATAACGACACTATTTTTGATGACGTCCTTATC
Found at i:4634 original size:23 final size:23
Alignment explanation
Indices: 4608--4670 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
4598 CCTCGCTATG
*
4608 AAATTTTGATAAACCTTCCTACA
1 AAATTTTGATAAACCTCCCTACA
* *
4631 AAATTTTGATAAATCTCCCTATA
1 AAATTTTGATAAACCTCCCTACA
4654 AAATTTTGAT-AACCTCC
1 AAATTTTGATAAACCTCC
4671 TTATGAAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 6 0.17
23 30 0.83
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTACA
Found at i:5033 original size:22 final size:22
Alignment explanation
Indices: 4982--5032 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
4972 ATCACATTTC
* * *
4982 GAAAATTTGATAACCTCTTTAT
1 GAAATTTTAATAACCTCTCTAT
5004 GAAATTTTAATAACCTCTCTAT
1 GAAATTTTAATAACCTCTCTAT
5026 -AAATTTT
1 GAAATTTT
5033 TGTTGACCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (22 bp):
GAAATTTTAATAACCTCTCTAT
Found at i:5075 original size:22 final size:22
Alignment explanation
Indices: 5048--5101 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5038 ACCCCTCCAT
5048 GAAATTTTGATAATCAC-ATTA
1 GAAATTTTGATAATCACGATTA
* *
5069 TGTAATTTTGATAATCTCGATTA
1 -GAAATTTTGATAATCACGATTA
5092 GAAATTTTGA
1 GAAATTTTGA
5102 AATTGGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (22 bp):
GAAATTTTGATAATCACGATTA
Found at i:5250 original size:37 final size:37
Alignment explanation
Indices: 5159--5253 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 37
5149 ATCTAATGCC
*
5159 AAATAGGACGTTGGAGACAAAGACAAAAAGCAAAATT
1 AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
** *
5196 AAATACAACGGTT-GAAACAAAGACAAAAGGCAAAATT
1 AAATAGGAC-GTTGGAAACAAAGACAAAAAGCAAAATT
5233 AAATAGGACGTTGGAAACAAA
1 AAATAGGACGTTGGAAACAAA
5254 AAGACAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
36 3 0.06
37 44 0.88
38 3 0.06
ACGTcount: A:0.55, C:0.12, G:0.20, T:0.14
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
Found at i:5408 original size:31 final size:31
Alignment explanation
Indices: 5373--5438 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
5363 TGGTAATTTA
* * *
5373 GAAATATGTTTTTTAAAA-AAGGGTATAATTG
1 GAAATATG-TTTTAAAAATAAAGGTACAATTG
5404 GAAATATGTTTTAAAAATAAAGGTACAATTG
1 GAAATATGTTTTAAAAATAAAGGTACAATTG
5435 GAAA
1 GAAA
5439 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.33
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAAGGTACAATTG
Found at i:5493 original size:21 final size:20
Alignment explanation
Indices: 5467--5510 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
5457 TTCGTACTTT
* *
5467 TATATATAGTATATATTATTA
1 TATATATACTATATACTA-TA
5488 TATATATACTATATACTATA
1 TATATATACTATATACTATA
5508 TAT
1 TAT
5511 TATTTTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (20 bp):
TATATATACTATATACTATA
Found at i:8372 original size:2 final size:2
Alignment explanation
Indices: 8365--8389 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8355 TGGTAAAAAC
8365 AT 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 A
8390 GAAAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9828 original size:4 final size:4
Alignment explanation
Indices: 9810--9848 Score: 62
Period size: 4 Copynumber: 9.8 Consensus size: 4
9800 TGGTTTATAG
9810 TTTA -TTA TATTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
9849 TTGAGAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.09
4 26 0.79
5 4 0.12
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:11766 original size:15 final size:15
Alignment explanation
Indices: 11743--11772 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11733 ATCGGTTGAA
*
11743 ATATTGTGTATCGTG
1 ATATCGTGTATCGTG
11758 ATATCGTGTATCGTG
1 ATATCGTGTATCGTG
11773 GCGGCCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
ATATCGTGTATCGTG
Found at i:14056 original size:19 final size:19
Alignment explanation
Indices: 14032--14069 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
14022 AAGAAAAGAG
14032 TTTCAGTTATTTTCTTCGA
1 TTTCAGTTATTTTCTTCGA
14051 TTTCAGTTATTTTCTTCGA
1 TTTCAGTTATTTTCTTCGA
14070 CAACAACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.58
Consensus pattern (19 bp):
TTTCAGTTATTTTCTTCGA
Found at i:15153 original size:16 final size:17
Alignment explanation
Indices: 15111--15153 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
15101 TAAAAAACCC
*
15111 GAACCTGAAAAAATTCA
1 GAACCCGAAAAAATTCA
15128 -AACCCG-AAAAATT-A
1 GAACCCGAAAAAATTCA
15142 GAACCCGAAAAA
1 GAACCCGAAAAA
15154 TCTGAAACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 13 0.57
16 9 0.39
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.12
Consensus pattern (17 bp):
GAACCCGAAAAAATTCA
Found at i:15403 original size:32 final size:32
Alignment explanation
Indices: 15366--15475 Score: 112
Period size: 32 Copynumber: 3.4 Consensus size: 32
15356 ACCCAATTCG
* *
15366 AGCCCGAAGCCGAATTAACCTGACCCAAAATT
1 AGCCCGAACCCGAATCAACCTGACCCAAAATT
* * * * *
15398 GGCCCGAATCCGAATCAACTTGACCTAAATTT
1 AGCCCGAACCCGAATCAACCTGACCCAAAATT
* * *
15430 AACCCGAACCCGAATCAACCCGACCCAAATTT
1 AGCCCGAACCCGAATCAACCTGACCCAAAATT
* *
15462 AACCCAAACCCGAA
1 AGCCCGAACCCGAA
15476 AACGACCTGA
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.37, C:0.35, G:0.13, T:0.15
Consensus pattern (32 bp):
AGCCCGAACCCGAATCAACCTGACCCAAAATT
Found at i:15451 original size:16 final size:17
Alignment explanation
Indices: 15425--15475 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
15415 ACTTGACCTA
*
15425 AATTTAACCCGAACCCG
1 AATTCAACCCGAACCCG
*
15442 AA-TCAACCCG-ACCCA
1 AATTCAACCCGAACCCG
* *
15457 AATTTAACCCAAACCCG
1 AATTCAACCCGAACCCG
15474 AA
1 AA
15476 AACGACCTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 6 0.22
16 13 0.48
17 8 0.30
ACGTcount: A:0.41, C:0.37, G:0.08, T:0.14
Consensus pattern (17 bp):
AATTCAACCCGAACCCG
Done.