Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010465.1 Corchorus capsularis cultivar CVL-1 contig10486, 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: 69107
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:262 original size:2 final size:2
Alignment explanation
Indices: 255--282 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
245 GTACCAAATT
255 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
283 CTGAATAAAT
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:620 original size:16 final size:17
Alignment explanation
Indices: 587--627 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
577 GGTAATTGGG
587 CGGGTTC-GGATCATTT
1 CGGGTTCGGGATCATTT
*
603 CGGGTTCGGGTTCA-TT
1 CGGGTTCGGGATCATTT
*
619 CGGGGTCGG
1 CGGGTTCGG
628 TCTCGGGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.07, C:0.20, G:0.41, T:0.32
Consensus pattern (17 bp):
CGGGTTCGGGATCATTT
Found at i:2300 original size:33 final size:33
Alignment explanation
Indices: 2238--2306 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 33
2228 ATGTAATAGT
* *
2238 TTTTATTAGTATACCTCTTTTGTAGACTCTTTGA
1 TTTTATTAGTAAACCTCTTTTGTAAACTCTTT-A
*
2272 TTTTATTAGTAAATCTC-TTTGTAAACTCTTTA
1 TTTTATTAGTAAACCTCTTTTGTAAACTCTTTA
2304 TTT
1 TTT
2307 GTTAAGACGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 4 0.12
33 13 0.41
34 15 0.47
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (33 bp):
TTTTATTAGTAAACCTCTTTTGTAAACTCTTTA
Found at i:6940 original size:2 final size:2
Alignment explanation
Indices: 6933--6971 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
6923 CGCCCCGGAG
*
6933 TA TA TA TA TA TA TA TA TT TA TA TA TA TA T- TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6972 GTTTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:21452 original size:15 final size:15
Alignment explanation
Indices: 21432--21504 Score: 58
Period size: 16 Copynumber: 4.7 Consensus size: 15
21422 TCTGAATCTA
21432 AATCCGAAAAACACG
1 AATCCGAAAAACACG
* *
21447 AATCCGAAAAAGCTCA
1 AATCCGAAAAA-CACG
* *
21463 AACCCGAAAAAACCCG
1 AATCCG-AAAAACACG
*
21479 AACCCGAAAAA-ATCCG
1 AATCCGAAAAACA--CG
21495 AATCCGAAAA
1 AATCCGAAAA
21505 TTTATGAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
15 16 0.34
16 26 0.55
17 5 0.11
ACGTcount: A:0.52, C:0.29, G:0.12, T:0.07
Consensus pattern (15 bp):
AATCCGAAAAACACG
Found at i:21696 original size:32 final size:31
Alignment explanation
Indices: 21652--21759 Score: 155
Period size: 32 Copynumber: 3.4 Consensus size: 31
21642 ACTCAAACAG
21652 AACCCGAACCCGAATTAACCTGATCCAAATTC
1 AACCCGAACCCGAATTAACCTGA-CCAAATTC
*
21684 AATCCGAACCCGAATTAACCTGACCAAAATT-
1 AACCCGAACCCGAATTAACCTGACC-AAATTC
* *
21715 AACCCGAACCCGAATTAATCTGACCCAAATCC
1 AACCCGAACCCGAATTAACCTGA-CCAAATTC
21747 AACCCGAACCCGA
1 AACCCGAACCCGA
21760 CTCAAGCCCG
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
31 27 0.39
32 42 0.61
ACGTcount: A:0.39, C:0.35, G:0.10, T:0.16
Consensus pattern (31 bp):
AACCCGAACCCGAATTAACCTGACCAAATTC
Found at i:25659 original size:12 final size:12
Alignment explanation
Indices: 25644--25685 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
25634 AGGTCACGTG
25644 TCTTTTTTATTT
1 TCTTTTTTATTT
*
25656 TCTTTTTTAATT
1 TCTTTTTTATTT
25668 TCTATTTTTATTT
1 TCT-TTTTTATTT
25681 T-TTTT
1 TCTTTT
25686 ATTAAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 3 0.11
12 15 0.56
13 9 0.33
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (12 bp):
TCTTTTTTATTT
Found at i:25850 original size:106 final size:104
Alignment explanation
Indices: 25700--25960 Score: 382
Period size: 106 Copynumber: 2.5 Consensus size: 104
25690 AGTTTAACCT
*
25700 TAATTTTACTAAGTTTAGCCTCAAATTAAAATTTTATTTTTATTTTAAGGGTAAACTTCAAAATT
1 TAATTTCACTAAGTTTAGCC-CAAATTAAAATTTTATTTTTATTTTAAGGGTAAACTTCAAAATT
25765 AATAATTTATTGTTATAGAATTTTAGAAATAAAATACGA-AAC
65 AATAA--TATTGTTATAGAATTTTAGAAATAAAATA-GATAAC
* *
25807 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCATAATTA
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAACTTCAAAATTA
* ** *
25872 ATAATATTGTTCTAGGGTTTTAGAAATAAAATATATAAC
66 ATAATATTGTTATAGAATTTTAGAAATAAAATAGATAAC
** *
25911 TAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
25961 TAGAAAAATT
Statistics
Matches: 143, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
103 45 0.31
104 32 0.22
106 47 0.33
107 19 0.13
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (104 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAACTTCAAAATTA
ATAATATTGTTATAGAATTTTAGAAATAAAATAGATAAC
Found at i:28847 original size:31 final size:31
Alignment explanation
Indices: 28806--28884 Score: 124
Period size: 31 Copynumber: 2.5 Consensus size: 31
28796 CATTTCTGTT
*
28806 TTTAGGCTCAAATTGGTCAACTTTTGAAAGA
1 TTTAGACTCAAATTGGTCAACTTTTGAAAGA
*
28837 TTTAGACTCAAATTGAG-CAACTTTTGAAAGG
1 TTTAGACTCAAATTG-GTCAACTTTTGAAAGA
28868 TTTAGACTCAAATTGGT
1 TTTAGACTCAAATTGGT
28885 GGCTAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 1 0.02
31 42 0.95
32 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (31 bp):
TTTAGACTCAAATTGGTCAACTTTTGAAAGA
Found at i:33247 original size:17 final size:19
Alignment explanation
Indices: 33225--33259 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
33215 ATTCCATATA
33225 TTTCTTAT-TTA-ATTATT
1 TTTCTTATATTATATTATT
33242 TTTCTTATATTATATTAT
1 TTTCTTATATTATATTAT
33260 ATAATCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTCTTATATTATATTATT
Found at i:35804 original size:20 final size:20
Alignment explanation
Indices: 35779--35817 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
35769 TCTTATCGTA
35779 GAATTATTAAGATTCTTACT
1 GAATTATTAAGATTCTTACT
35799 GAATTATTAAGATTCTTAC
1 GAATTATTAAGATTCTTAC
35818 CAAAGACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (20 bp):
GAATTATTAAGATTCTTACT
Found at i:36849 original size:41 final size:41
Alignment explanation
Indices: 36792--36873 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
36782 AAAGGAGTTG
*
36792 TGGGTCAGCGTATTTAACTTACATAAGCTCTGATATACTGA
1 TGGGTCAGCGTATTTAACTTACACAAGCTCTGATATACTGA
* * *
36833 TGGGTTAGCGTGTTTAACTTACACAAGTTCTGATATACTGA
1 TGGGTCAGCGTATTTAACTTACACAAGCTCTGATATACTGA
36874 CATGGATCCC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (41 bp):
TGGGTCAGCGTATTTAACTTACACAAGCTCTGATATACTGA
Found at i:38439 original size:30 final size:30
Alignment explanation
Indices: 38395--38460 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
38385 ATTCACTTAT
* *
38395 CCTTATTTGCAAAATACGAAAATGTTTTGC
1 CCTTATGTGCAAAATACGAAAATATTTTGC
*
38425 CCTTATGTGTAAAATACGAAAATATTTTGC
1 CCTTATGTGCAAAATACGAAAATATTTTGC
38455 CCTTAT
1 CCTTAT
38461 TTATTAATCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (30 bp):
CCTTATGTGCAAAATACGAAAATATTTTGC
Found at i:39685 original size:32 final size:32
Alignment explanation
Indices: 39644--39709 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
39634 GGACGGATAG
39644 CTCGGTCTTTGAACAGGTCTACGCCAGACAAA
1 CTCGGTCTTTGAACAGGTCTACGCCAGACAAA
*
39676 CTCGGTCTTTGAACAGGTCTACGCTAGACAAA
1 CTCGGTCTTTGAACAGGTCTACGCCAGACAAA
39708 CT
1 CT
39710 TTGGGTTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (32 bp):
CTCGGTCTTTGAACAGGTCTACGCCAGACAAA
Found at i:47434 original size:16 final size:17
Alignment explanation
Indices: 47415--47449 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
47405 TTAACCAGAG
47415 AAGC-AAAAGTTTTGAA
1 AAGCAAAAAGTTTTGAA
*
47431 AAGCAAAAATTTTTGAA
1 AAGCAAAAAGTTTTGAA
47448 AA
1 AA
47450 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (17 bp):
AAGCAAAAAGTTTTGAA
Found at i:49031 original size:3 final size:3
Alignment explanation
Indices: 49025--49064 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
49015 AAAAAAAAAT
49025 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
49065 TAAAAACAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:59297 original size:49 final size:49
Alignment explanation
Indices: 59240--59388 Score: 289
Period size: 49 Copynumber: 3.0 Consensus size: 49
59230 TAAATTCATC
*
59240 ATAAATTATTAATATAATTGATTTAATTTTAGTGATTATTCATATAATT
1 ATAAATTATTCATATAATTGATTTAATTTTAGTGATTATTCATATAATT
59289 ATAAATTATTCATATAATTGATTTAATTTTAGTGATTATTCATATAATT
1 ATAAATTATTCATATAATTGATTTAATTTTAGTGATTATTCATATAATT
59338 ATAAATTATTCATATAATTGATTTAATTTTAGTGATTATTCATATAATT
1 ATAAATTATTCATATAATTGATTTAATTTTAGTGATTATTCATATAATT
59387 AT
1 AT
59389 TTTTCTTTTG
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 99 1.00
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (49 bp):
ATAAATTATTCATATAATTGATTTAATTTTAGTGATTATTCATATAATT
Found at i:59298 original size:19 final size:18
Alignment explanation
Indices: 59274--59356 Score: 65
Period size: 19 Copynumber: 4.8 Consensus size: 18
59264 AATTTTAGTG
59274 ATTATTCATATAATTATAA
1 ATTATTCATATAATTAT-A
59293 ATTATTCATATAATTGAT-
1 ATTATTCATATAATT-ATA
*
59311 -TTA---AT-T--TTAGTG
1 ATTATTCATATAATTA-TA
59323 ATTATTCATATAATTATAA
1 ATTATTCATATAATTAT-A
59342 ATTATTCATATAATT
1 ATTATTCATATAATT
59357 GATTTAATTT
Statistics
Matches: 52, Mismatches: 1, Indels: 22
0.69 0.01 0.29
Matches are distributed among these distances:
10 1 0.02
11 3 0.06
13 4 0.08
14 2 0.04
16 2 0.04
17 4 0.08
18 1 0.02
19 33 0.63
20 2 0.04
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.51
Consensus pattern (18 bp):
ATTATTCATATAATTATA
Found at i:65730 original size:3 final size:3
Alignment explanation
Indices: 65722--65751 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
65712 TCCAAGTGTG
65722 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65752 CTTTTCTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:67805 original size:27 final size:28
Alignment explanation
Indices: 67749--67805 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
67739 TAACTATCCA
*
67749 TTTTGGGACAAATTGGTCCCTTAACTTT
1 TTTTGGGACAAATTGGCCCCTTAACTTT
*
67777 TTTTGGGATAAATTGGCCCCTTAACTTT
1 TTTTGGGACAAATTGGCCCCTTAACTTT
67805 T
1 T
67806 AAAAATGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (28 bp):
TTTTGGGACAAATTGGCCCCTTAACTTT
Found at i:68540 original size:28 final size:27
Alignment explanation
Indices: 68498--68554 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
68488 TCTCGTTTTT
68498 AAAAGTTAAGGGGCCAATTTGTTCCCCAA
1 AAAAGTTAAGGGGCCAATTTG-T-CCCAA
68527 AAAAGTTAA-GGGCCAATTTGTCCCAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAA
68553 AA
1 AA
68555 TGAATAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 7 0.25
27 1 0.04
28 11 0.39
29 9 0.32
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (27 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAA
Done.