Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009231.1 Corchorus capsularis cultivar CVL-1 contig09252, 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: 20073
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4963 original size:1 final size:1
Alignment explanation
Indices: 4957--4983 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
4947 AGCAATTAAG
4957 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
4984 GTAAAAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5713 original size:16 final size:16
Alignment explanation
Indices: 5693--5749 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
5683 GTCCGAACCC
5693 GAACCCGAAAAAGCTCA
1 GAACCCGAAAAA-CTCA
*
5710 -AACCCGAAAAATTCA
1 GAACCCGAAAAACTCA
*
5725 GAACCCGAAAAAAC-CC
1 GAACCCG-AAAAACTCA
5741 GAACCCGAA
1 GAACCCGAA
5750 TAAAAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 5 0.14
16 25 0.71
17 5 0.14
ACGTcount: A:0.49, C:0.32, G:0.14, T:0.05
Consensus pattern (16 bp):
GAACCCGAAAAACTCA
Found at i:6167 original size:10 final size:10
Alignment explanation
Indices: 6151--6197 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
6141 TTTTTTTTTA
6151 AATTATTGATT
1 AATTATT-ATT
6162 -ATTATTAATT
1 AATTATT-ATT
*
6172 ATTTAATTATT
1 AATT-ATTATT
6183 AATTATTATT
1 AATTATTATT
6193 AATTA
1 AATTA
6198 CAATTTTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 20 0.65
11 8 0.26
12 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (10 bp):
AATTATTATT
Found at i:6307 original size:33 final size:33
Alignment explanation
Indices: 6257--6363 Score: 133
Period size: 33 Copynumber: 3.2 Consensus size: 33
6247 CGCCCCAAGA
* * *
6257 GGGCGGCAAACCATGGCTCATGCCATCCCAGGG
1 GGGCGGCATACCATGGCTCATGCCACCCCACGG
* * * *
6290 GGGCGGCATACCGTGGCTCATGCCGCCCCCCTG
1 GGGCGGCATACCATGGCTCATGCCACCCCACGG
* *
6323 GGGCGGCATACCATGGCTCATGCCACCCTACTG
1 GGGCGGCATACCATGGCTCATGCCACCCCACGG
6356 GGGCGGCA
1 GGGCGGCA
6364 CGGTCATCAG
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.16, C:0.36, G:0.34, T:0.14
Consensus pattern (33 bp):
GGGCGGCATACCATGGCTCATGCCACCCCACGG
Found at i:6558 original size:22 final size:21
Alignment explanation
Indices: 6533--6577 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
6523 GCAAAAGTGT
*
6533 AAAAAGTGGGGCGGTGTTTAGC
1 AAAAA-TGGGGCGGTATTTAGC
6555 AAAAATGGGGCGGTATTTAGC
1 AAAAATGGGGCGGTATTTAGC
6576 AA
1 AA
6578 CACCCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.33, C:0.09, G:0.36, T:0.22
Consensus pattern (21 bp):
AAAAATGGGGCGGTATTTAGC
Found at i:7182 original size:166 final size:164
Alignment explanation
Indices: 6888--7330 Score: 539
Period size: 166 Copynumber: 2.7 Consensus size: 164
6878 GATTAATGAG
* * * *** * *
6888 GAGCGAGAGAACTAATTTTTTCGTCTTTTCAC-ACATGATTGATTACCTAAATGCCCTAACTTTT
1 GAGCTAGAGAACTATTTTTTTCGTCTTTTC-CTACTTGGCAGATTACTTAAATGTCCTAACTTTT
* * * * * * * *
6952 GATTCTTGAGGTGATTAAAAAACTAGACTTTTTGGTCATTTATCAATTGATTTTAATGGAGTAGT
65 GATTCTTGAGGGGATTAAATAACTA-AATTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGT
* * * * * *
7017 GCAATTACCAAAAGAT-CCCTACCAATGCTTGATTTT
129 GAAATTAACAAAAGATACTC-ACCAAGGATTGATGTT
* * *
7053 GGAGTTAGAGAACTTTTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAGTGTCCTAACTTTT
1 -GAGCTAGAGAACTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTT
*
7118 GATTCTTGAGGGGATTAAATAAGTAATATTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGT
65 GATTCTTGAGGGGATTAAATAACTAA-ATTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGT
* *
7183 GAAATTAATAAAAGATACTCATCAAGGATTGATGTT
129 GAAATTAACAAAAGATACTCACCAAGGATTGATGTT
*
7219 GAGCTAGAGAACTAATTTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTT
1 GAGCTAGAGAACT-ATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTT
*
7284 GATTTTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
65 GATTCTTGAGGGGATTAAATAACTAAA-TTTTTGGTCATTTCTCAAT
7331 TGACAAATGA
Statistics
Matches: 238, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
165 15 0.06
166 221 0.93
167 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (164 bp):
GAGCTAGAGAACTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTG
ATTCTTGAGGGGATTAAATAACTAAATTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGA
AATTAACAAAAGATACTCACCAAGGATTGATGTT
Found at i:7427 original size:14 final size:12
Alignment explanation
Indices: 7406--7438 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7396 AAGAATTAGT
7406 TTATATAT-TTA
1 TTATATATATTA
7417 TTATCATATATTA
1 TTAT-ATATATTA
7430 TTATATATA
1 TTATATATA
7439 AATAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 9 0.45
13 7 0.35
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATATATATTA
Found at i:11501 original size:11 final size:11
Alignment explanation
Indices: 11485--11530 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
11475 AGATTAACAT
11485 ATAAATAAAAC
1 ATAAATAAAAC
11496 ATAAATAAAAC
1 ATAAATAAAAC
11507 ATAAA-ATAAA-
1 ATAAATA-AAAC
*
11517 ATAAATAAAGC
1 ATAAATAAAAC
11528 ATA
1 ATA
11531 TGAAACATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
10 8 0.26
11 23 0.74
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.20
Consensus pattern (11 bp):
ATAAATAAAAC
Found at i:11515 original size:12 final size:12
Alignment explanation
Indices: 11480--11517 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
11470 AAGAGAGATT
11480 AACATATAAATAA
1 AACATA-AAATAA
11493 AACAT-AAATAA
1 AACATAAAATAA
11504 AACATAAAATAA
1 AACATAAAATAA
11516 AA
1 AA
11518 TAAATAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 8 0.33
13 5 0.21
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (12 bp):
AACATAAAATAA
Found at i:11522 original size:21 final size:24
Alignment explanation
Indices: 11480--11531 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 24
11470 AAGAGAGATT
11480 AACATATAAATAAAACATAAATAA
1 AACATATAAATAAAACATAAATAA
11504 AACATA-AAAT-AAA-ATAAATAA
1 AACATATAAATAAAACATAAATAA
*
11525 AGCATAT
1 AACATAT
11532 GAAACATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 13 0.50
22 3 0.12
23 4 0.15
24 6 0.23
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (24 bp):
AACATATAAATAAAACATAAATAA
Found at i:11524 original size:32 final size:31
Alignment explanation
Indices: 11485--11548 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 31
11475 AGATTAACAT
11485 ATAAATAAAACATAAATAAAACATAAAA-TAAA
1 ATAAATAAAACAT--ATAAAACATAAAATTAAA
* *
11517 ATAAATAAAGCATATGAAACATAAAATTAAA
1 ATAAATAAAACATATAAAACATAAAATTAAA
11548 A
1 A
11549 CAATAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 12 0.41
31 5 0.17
32 12 0.41
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.20
Consensus pattern (31 bp):
ATAAATAAAACATATAAAACATAAAATTAAA
Found at i:15226 original size:28 final size:27
Alignment explanation
Indices: 15194--15261 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 27
15184 TTAAAATTAG
*
15194 TCAACGATTAATTTTTTTT-ACAACTTAA
1 TCAACG-TTAATTTTTTTTGA-AACATAA
** *
15222 TCAACGTTTTTTTTTTTTGAAAGATAA
1 TCAACGTTAATTTTTTTTGAAACATAA
15249 TCAACGTTTAATT
1 TCAACG-TTAATT
15262 AATAATAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (27 bp):
TCAACGTTAATTTTTTTTGAAACATAA
Found at i:15235 original size:27 final size:27
Alignment explanation
Indices: 15205--15257 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
15195 CAACGATTAA
*
15205 TTTTTTTT-ACAACTTAATCAACGTTTT
1 TTTTTTTTGA-AACATAATCAACGTTTT
*
15232 TTTTTTTTGAAAGATAATCAACGTTT
1 TTTTTTTTGAAACATAATCAACGTTT
15258 AATTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (27 bp):
TTTTTTTTGAAACATAATCAACGTTTT
Found at i:17417 original size:7 final size:7
Alignment explanation
Indices: 17394--17427 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
17384 GAATTTACTT
17394 TTTTGTA
1 TTTTGTA
*
17401 CTTTTATA
1 -TTTTGTA
17409 TTTTGTA
1 TTTTGTA
17416 TTTTGTA
1 TTTTGTA
17423 TTTTG
1 TTTTG
17428 GGAAGTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.15, C:0.03, G:0.12, T:0.71
Consensus pattern (7 bp):
TTTTGTA
Found at i:17745 original size:27 final size:27
Alignment explanation
Indices: 17715--17783 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
17705 AAGTGAACTT
*
17715 AAAATGACCTAAATGCCCTTGAATGTA
1 AAAATGACCTAAATGCCCCTGAATGTA
17742 AAAATGACCTAAATGCCCCTGAATGTA
1 AAAATGACCTAAATGCCCCTGAATGTA
*
17769 AAAATGACCAAAATG
1 AAAATGACCTAAATG
17784 ACAAAGAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (27 bp):
AAAATGACCTAAATGCCCCTGAATGTA
Found at i:18962 original size:178 final size:178
Alignment explanation
Indices: 18648--18971 Score: 456
Period size: 178 Copynumber: 1.8 Consensus size: 178
18638 AAGGTGATTT
*
18648 AAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATTAAGGACTCGAAAACTAAATTTA
1 AAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
* * *
18713 ATGTTTCAAGTATCAAAAATGCTCCCGAAAAATTTGTTCTTTCGGTTAACGGGAATAGACAGTCC
66 ATGTTTCAAGTATAAAAAATGCTCCCGAAAAATTAGTTCTTTCGGTCAACGGGAATAGACAGTCC
*
18778 ACTTAATATTATATAACTTTTACTCCAGATGTCTGATTGAGATAATTC
131 ACTTAATATTACATAACTTTTACTCCAGATGTCTGATTGAGATAATTC
* * * *
18826 AAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTC
1 AAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
* * * * *
18891 ATG-TTCAATGTGTAAAAAATGCTTCC-AAAGAATTAGTTGTTTCGGTCAA-TGGAATTAGACGG
66 ATGTTTCAA-GTATAAAAAATGCTCCCGAAA-AATTAGTTCTTTCGGTCAACGGGAA-TAGACAG
**
18953 TTTACTTAATATTACATAA
128 TCCACTTAATATTACATAA
18972 TTTGTGCTTA
Statistics
Matches: 127, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
177 12 0.09
178 115 0.91
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (178 bp):
AAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
ATGTTTCAAGTATAAAAAATGCTCCCGAAAAATTAGTTCTTTCGGTCAACGGGAATAGACAGTCC
ACTTAATATTACATAACTTTTACTCCAGATGTCTGATTGAGATAATTC
Found at i:19825 original size:2 final size:2
Alignment explanation
Indices: 19814--19842 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19804 TTTTATAGTG
19814 AT AT -T 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
19843 GTTTTGACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:20049 original size:2 final size:2
Alignment explanation
Indices: 20044--20073 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20034 GCAAAAAGAA
20044 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
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.