Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014076.1 Corchorus capsularis cultivar CVL-1 contig14097, 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: 65441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2292 original size:20 final size:21
Alignment explanation
Indices: 2250--2292 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
2240 CCAAGGTGAG
*
2250 TTTTCCAGTTTCCTTTTTCTT
1 TTTTCCAGTTTCCTCTTTCTT
2271 TTTTCCA-TTTCCTGCTTT-TT
1 TTTTCCAGTTTCCT-CTTTCTT
2291 TT
1 TT
2293 CAGCTCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.05, C:0.23, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTCCAGTTTCCTCTTTCTT
Found at i:7514 original size:20 final size:17
Alignment explanation
Indices: 7491--7533 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
7481 AACTTAACAA
7491 TTAACTAACTAGGTTTAAC
1 TTAACTAA--AGGTTTAAC
7510 TTTAACT-AAGGTTTAAC
1 -TTAACTAAAGGTTTAAC
7527 TTAACTA
1 TTAACTA
7534 CTAACTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
19 1 0.05
20 6 0.27
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (17 bp):
TTAACTAAAGGTTTAAC
Found at i:7523 original size:17 final size:16
Alignment explanation
Indices: 7491--7533 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
7481 AACTTAACAA
7491 TTAAC-TAACT-AGGT
1 TTAACTTAACTAAGGT
7505 TTAACTTTAACTAAGGT
1 TTAAC-TTAACTAAGGT
7522 TTAACTTAACTA
1 TTAACTTAACTA
7534 CTAACTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.19
16 12 0.46
17 9 0.35
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (16 bp):
TTAACTTAACTAAGGT
Found at i:9810 original size:31 final size:31
Alignment explanation
Indices: 9742--9812 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
9732 GGCATTTTTA
*
9742 ACACATGGCGTGCCACGTGGCATTTTTCTGT
1 ACACATGGCGTGCCACATGGCATTTTTCTGT
* *
9773 GCACATGGCGTGCCACATGTCATTTTT-TGGT
1 ACACATGGCGTGCCACATGGCATTTTTCT-GT
*
9804 ATACATGGC
1 ACACATGGC
9813 ATGCATGCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.32
Consensus pattern (31 bp):
ACACATGGCGTGCCACATGGCATTTTTCTGT
Found at i:15652 original size:14 final size:14
Alignment explanation
Indices: 15633--15661 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
15623 TATCTTATAA
15633 TGGGTAGTTTTTAT
1 TGGGTAGTTTTTAT
15647 TGGGTAGTTTTTAT
1 TGGGTAGTTTTTAT
15661 T
1 T
15662 TTATTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.59
Consensus pattern (14 bp):
TGGGTAGTTTTTAT
Found at i:28150 original size:5 final size:5
Alignment explanation
Indices: 28140--28168 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28130 TTAGTTTTAT
28140 ACTCA ACTCA ACTCA ACTCA ACTCA ACTC
1 ACTCA ACTCA ACTCA ACTCA ACTCA ACTC
28169 TTAAAGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (5 bp):
ACTCA
Found at i:33335 original size:2 final size:2
Alignment explanation
Indices: 33330--33356 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33320 TTTTTTGGAT
33330 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 T
33357 GATTGTGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35545 original size:13 final size:13
Alignment explanation
Indices: 35527--35552 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35517 AATGTATATT
35527 GAATATATTTTTA
1 GAATATATTTTTA
35540 GAATATATTTTTA
1 GAATATATTTTTA
35553 ATATTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
GAATATATTTTTA
Found at i:35580 original size:21 final size:20
Alignment explanation
Indices: 35521--35581 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 20
35511 AAATGAAATG
*
35521 TATATTGAATATATTTTTAGAA
1 TATATT-AATAT-TTTTTATAA
** * *
35543 TATATTTTTAATATTTATATA
1 TATATTAATATTTTTTATA-A
35564 TATATTAATATTTTTTAT
1 TATATTAATATTTTTTAT
35582 CATAAAAAAT
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
20 6 0.21
21 17 0.59
22 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATATTAATATTTTTTATAA
Found at i:41446 original size:28 final size:30
Alignment explanation
Indices: 41410--41469 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 30
41400 AATGGGCTCC
41410 AAATTGAAGTTCAT-A-GGCAAAACATCCA
1 AAATTGAAGTTCATAAGGGCAAAACATCCA
*
41438 AAATTGAAGTTCATAAGGGCAAAACGTCCA
1 AAATTGAAGTTCATAAGGGCAAAACATCCA
41468 AA
1 AA
41470 CTGTACAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 14 0.48
29 1 0.03
30 14 0.48
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.20
Consensus pattern (30 bp):
AAATTGAAGTTCATAAGGGCAAAACATCCA
Found at i:43497 original size:1 final size:1
Alignment explanation
Indices: 43461--43488 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
43451 AGAATCACAG
43461 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
43489 ACATTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:50687 original size:16 final size:16
Alignment explanation
Indices: 50666--50720 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
50656 TCACTGGATT
50666 TGTTTGTTGGGGAATG
1 TGTTTGTTGGGGAATG
**
50682 TGTTTGTT-GGCTA-G
1 TGTTTGTTGGGGAATG
* *
50696 CG-ATGTTGGGGAATG
1 TGTTTGTTGGGGAATG
50711 TGTTTGTTGG
1 TGTTTGTTGG
50721 CTAGCGATGT
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
13 4 0.14
14 5 0.18
15 5 0.18
16 14 0.50
ACGTcount: A:0.11, C:0.04, G:0.42, T:0.44
Consensus pattern (16 bp):
TGTTTGTTGGGGAATG
Found at i:50712 original size:29 final size:29
Alignment explanation
Indices: 50670--50730 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
50660 TGGATTTGTT
50670 TGTTGGGGAATGTGTTTGTTGGCTAGCGA
1 TGTTGGGGAATGTGTTTGTTGGCTAGCGA
50699 TGTTGGGGAATGTGTTTGTTGGCTAGCGA
1 TGTTGGGGAATGTGTTTGTTGGCTAGCGA
50728 TGT
1 TGT
50731 ATGGTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.13, C:0.07, G:0.41, T:0.39
Consensus pattern (29 bp):
TGTTGGGGAATGTGTTTGTTGGCTAGCGA
Found at i:51510 original size:18 final size:19
Alignment explanation
Indices: 51489--51531 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
51479 ACTCAGACTC
*
51489 AAACT-AACTGACTCAAAA
1 AAACTGAACTAACTCAAAA
51507 AAACTGAACTAACTC-AAA
1 AAACTGAACTAACTCAAAA
51525 AAACTGA
1 AAACTGA
51532 CTGAACCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.56, C:0.21, G:0.07, T:0.16
Consensus pattern (19 bp):
AAACTGAACTAACTCAAAA
Found at i:61972 original size:29 final size:30
Alignment explanation
Indices: 61940--61997 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
61930 GTGAACTTCA
*
61940 ATTTTGATCAATTAAACTCC-TG-AAACTCG
1 ATTTTGACCAATTAAA-TCCTTGCAAACTCG
*
61969 ATTTTGGCCAATTAAATCCTTGCAAACTC
1 ATTTTGACCAATTAAATCCTTGCAAACTC
61998 CGTTAAGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 16 0.64
30 6 0.24
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.34
Consensus pattern (30 bp):
ATTTTGACCAATTAAATCCTTGCAAACTCG
Found at i:62219 original size:60 final size:60
Alignment explanation
Indices: 62144--62308 Score: 199
Period size: 60 Copynumber: 2.8 Consensus size: 60
62134 ACTCATTGTT
* * * *
62144 CAAATAAGGGTCTAACGTTTGCCAAAATGTTCAAATAAGAGTCTGATTTTTTAATT-TGAC
1 CAAATAAGGGCCTAACATTTGCCAAAATGTTCAAATAAGAGTCTGATCTTTTAATTCAG-C
* * *
62204 CAAATAAGGGCCTAACATTTTCGAAAATGTTCAAATAAGGGTCTGATCTTTTAATTCAGC
1 CAAATAAGGGCCTAACATTTGCCAAAATGTTCAAATAAGAGTCTGATCTTTTAATTCAGC
* * * *
62264 CAAATAAGGGCCTAACATTAT-CGAAAATGCTCTAATAAGGGTCTG
1 CAAATAAGGGCCTAACATT-TGCCAAAATGTTCAAATAAGAGTCTG
62309 GTGTCGAAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
60 92 0.98
61 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (60 bp):
CAAATAAGGGCCTAACATTTGCCAAAATGTTCAAATAAGAGTCTGATCTTTTAATTCAGC
Found at i:62224 original size:29 final size:28
Alignment explanation
Indices: 62192--62282 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 28
62182 GAGTCTGATT
62192 TTTTAATTTGACCAAATAAGGGCCTAACA
1 TTTTAA-TTGACCAAATAAGGGCCTAACA
* ** * *
62221 TTTTCGAAAATGTTCAAATAAGGGTCTGATC-
1 TTTT---AATTGACCAAATAAGGGCCT-AACA
*
62252 TTTTAATTCAGCCAAATAAGGGCCTAACA
1 TTTTAATTGA-CCAAATAAGGGCCTAACA
62281 TT
1 TT
62283 ATCGAAAATG
Statistics
Matches: 45, Mismatches: 11, Indels: 12
0.66 0.16 0.18
Matches are distributed among these distances:
28 5 0.11
29 18 0.40
31 18 0.40
32 4 0.09
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (28 bp):
TTTTAATTGACCAAATAAGGGCCTAACA
Found at i:62458 original size:57 final size:58
Alignment explanation
Indices: 62344--62506 Score: 193
Period size: 57 Copynumber: 2.8 Consensus size: 58
62334 CAAACTGACG
* ** * * * *
62344 TCAGGCCCTTATTTGAGCATTTTCGGTAATATTAGGCCCTTATTTGGCTAAATTAAAAGA
1 TCAGACCCTTATTTGAGCATTTTC-G-AACGTTAGACTCTTATTTGGCCAAATTAAAAAA
62404 TCAGACCCTTATTTGAGCATTTTC-AACGTTAGACTCTTATTTGGCCAAATTAAAAAA
1 TCAGACCCTTATTTGAGCATTTTCGAACGTTAGACTCTTATTTGGCCAAATTAAAAAA
* * *
62461 TCAAATCCTTATTTGAGCATTTTGGCAAACGTTAGACTCTTATTTG
1 TCAGACCCTTATTTGAGCATTTT--CGAACGTTAGACTCTTATTTG
62507 AACAATTAAC
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
57 48 0.53
59 1 0.01
60 42 0.46
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (58 bp):
TCAGACCCTTATTTGAGCATTTTCGAACGTTAGACTCTTATTTGGCCAAATTAAAAAA
Found at i:65408 original size:2 final size:2
Alignment explanation
Indices: 65401--65433 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
65391 GAAGCAAAAC
65401 AT AT AT AT 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 AT AT AT AT A
65434 AAATAAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.