Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012049.1 Corchorus capsularis cultivar CVL-1 contig12070, 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: 27315
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Found at i:1377 original size:12 final size:12
Alignment explanation
Indices: 1360--1385 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1350 ATTTGCCATC
1360 TTCTCCAATGAT
1 TTCTCCAATGAT
1372 TTCTCCAATGAT
1 TTCTCCAATGAT
1384 TT
1 TT
1386 AAGGAGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (12 bp):
TTCTCCAATGAT
Found at i:4481 original size:24 final size:25
Alignment explanation
Indices: 4452--4512 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 25
4442 TCTTCATCAA
4452 ATATATCAATAATTATCATTGTAAT
1 ATATATCAATAATTATCATTGTAAT
4477 AATATACTCAATAATTATCATTGT--T
1 -ATATA-TCAATAATTATCATTGTAAT
4502 ATATATCAATA
1 ATATATCAATA
4513 TATGAAATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.18
24 5 0.15
25 1 0.03
26 5 0.15
27 17 0.50
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (25 bp):
ATATATCAATAATTATCATTGTAAT
Found at i:5920 original size:170 final size:169
Alignment explanation
Indices: 5553--6056 Score: 935
Period size: 170 Copynumber: 3.0 Consensus size: 169
5543 AGATAAATAA
* *
5553 ATTACACAGCGGAGAAACCAAAGATGACCAAACATCAGACAAACTCTGACTAGGTGTCATTCCCA
1 ATTACACAGCGGAGAAACCAAAGATGACCAAACATCAGACAAACTCTGACTAGTTGTCACTCCCA
5618 CGCGTGCACTCCCACGGCGTTGACCAAGAG---AAAAAAA-AACAACGGCTGAAGACAAAACAAC
66 CGCGTGCACTCCCACGGCGTTGACCAAGAGAAAAAAAAAACAACAACGGCTGAAGACAAAACAAC
5679 AACAAAGGGAAAAAGAGGATAATAAAAACCAGGCCAAGC
131 AACAAAGGGAAAAAGAGGATAATAAAAACCAGGCCAAGC
5718 ATTACACAGCGGAGAAACCAAAGATGACCAAACATCAGACAAACTCTGACTAGTTGTCACTCCCA
1 ATTACACAGCGGAGAAACCAAAGATGACCAAACATCAGACAAACTCTGACTAGTTGTCACTCCCA
*
5783 CGCGTGCACTCCCACGGTGTTGACCAAGAGAAAAAAAAAAACAACAACGGCTGAAGACAAAACAA
66 CGCGTGCACTCCCACGGCGTTGACCAAGAG-AAAAAAAAAACAACAACGGCTGAAGACAAAACAA
5848 CAACAAAGGGAAAAAGAGGATAATAAAAACCAGGCCAAGC
130 CAACAAAGGGAAAAAGAGGATAATAAAAACCAGGCCAAGC
5888 ATTACACAGCGGAGAAACCAAAGATGACCAAACATCAGACAAACTCTGACTAGTTGTCACTCCCA
1 ATTACACAGCGGAGAAACCAAAGATGACCAAACATCAGACAAACTCTGACTAGTTGTCACTCCCA
*
5953 CGCGTGCACTCCCACGACGTTGACCAAGAGAAAAAAAAAACAACAACGGCTGAAGACAAAACAAC
66 CGCGTGCACTCCCACGGCGTTGACCAAGAGAAAAAAAAAACAACAACGGCTGAAGACAAAACAAC
6018 AACAAAGGGAAAAAGAGGATAATAAAAACCAGGCCAAGC
131 AACAAAGGGAAAAAGAGGATAATAAAAACCAGGCCAAGC
6057 CAAGCCCAAA
Statistics
Matches: 329, Mismatches: 5, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
165 92 0.28
169 81 0.25
170 156 0.47
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (169 bp):
ATTACACAGCGGAGAAACCAAAGATGACCAAACATCAGACAAACTCTGACTAGTTGTCACTCCCA
CGCGTGCACTCCCACGGCGTTGACCAAGAGAAAAAAAAAACAACAACGGCTGAAGACAAAACAAC
AACAAAGGGAAAAAGAGGATAATAAAAACCAGGCCAAGC
Found at i:6229 original size:25 final size:25
Alignment explanation
Indices: 6195--6243 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
6185 TCACATAAAT
* *
6195 AAACATGATTTGTAAGGAGAATTAC
1 AAACACGATTTGTAAGGAAAATTAC
6220 AAACACGATTTGTAAGGAAAATTA
1 AAACACGATTTGTAAGGAAAATTA
6244 AACCCACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (25 bp):
AAACACGATTTGTAAGGAAAATTAC
Found at i:6307 original size:28 final size:28
Alignment explanation
Indices: 6254--6314 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
6244 AACCCACATG
*
6254 AATAAACAATCCATATACATATATATCA
1 AATAAACAATCCATATACATATATATAA
*
6282 AATAAACAA-CCATAATA-AGATAATATAA
1 AATAAACAATCCAT-ATACATAT-ATATAA
6310 AATAA
1 AATAA
6315 TGGCTTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.61, C:0.13, G:0.02, T:0.25
Consensus pattern (28 bp):
AATAAACAATCCATATACATATATATAA
Found at i:6436 original size:21 final size:21
Alignment explanation
Indices: 6395--6439 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6385 AGATTGAGTG
*
6395 ATATAATTTAACTAAATTTAA
1 ATATAATTTAAATAAATTTAA
* *
6416 ATATGATTTAAATCAAATTAAA
1 ATATAATTTAAAT-AAATTTAA
6438 AT
1 AT
6440 TAAACATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (21 bp):
ATATAATTTAAATAAATTTAA
Found at i:6567 original size:30 final size:30
Alignment explanation
Indices: 6531--6602 Score: 96
Period size: 27 Copynumber: 2.5 Consensus size: 30
6521 AATAATGCCA
6531 AAGGAGATAAAAAAAAATGACATGAAGCCT-
1 AAGGAGA-AAAAAAAAATGACATGAAGCCTC
*
6561 AAGGAG--ACAAAAAATGACATGAAGCCTC
1 AAGGAGAAAAAAAAAATGACATGAAGCCTC
*
6589 AAGGAGACAAAAAA
1 AAGGAGAAAAAAAA
6603 TGACATAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 20 0.54
28 6 0.16
30 11 0.30
ACGTcount: A:0.57, C:0.12, G:0.21, T:0.10
Consensus pattern (30 bp):
AAGGAGAAAAAAAAAATGACATGAAGCCTC
Found at i:6580 original size:27 final size:28
Alignment explanation
Indices: 6542--6608 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
6532 AGGAGATAAA
6542 AAAAAATGACATGAAGCCT-AAGGAGAC
1 AAAAAATGACATGAAGCCTCAAGGAGAC
6569 AAAAAATGACATGAAGCCTCAAGGAGAC
1 AAAAAATGACATGAAGCCTCAAGGAGAC
6597 AAAAAATGACAT
1 AAAAAATGACAT
6609 AACATGTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
27 19 0.49
28 20 0.51
ACGTcount: A:0.54, C:0.15, G:0.19, T:0.12
Consensus pattern (28 bp):
AAAAAATGACATGAAGCCTCAAGGAGAC
Found at i:6989 original size:25 final size:25
Alignment explanation
Indices: 6955--7003 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
6945 TCACATAAAT
*
6955 AAACATGATTTGTAAGGAGAATTAC
1 AAACATGATTTGTAAGGAAAATTAC
6980 AAACATGATTTGTAAGGAAAATTA
1 AAACATGATTTGTAAGGAAAATTA
7004 AACCCACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (25 bp):
AAACATGATTTGTAAGGAAAATTAC
Found at i:7196 original size:21 final size:21
Alignment explanation
Indices: 7154--7196 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
7144 AGATTGAGTG
*
7154 ATATAATTTAACTAAATCTAA
1 ATATAATTTAAATAAATCTAA
*
7175 ATATGATTTAAATCAAAT-TAA
1 ATATAATTTAAAT-AAATCTAA
7196 A
1 A
7197 CATTAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATAATTTAAATAAATCTAA
Found at i:7342 original size:27 final size:28
Alignment explanation
Indices: 7304--7372 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
7294 GAGACAAAAA
* *
7304 AAAAAAAGACATGAAG-CTTAAGGAGAC
1 AAAAAATGACATGAAGTCTCAAGGAGAC
7331 AAAAAATGACATGAAGTCTCAAGGAGAC
1 AAAAAATGACATGAAGTCTCAAGGAGAC
7359 AAAAAATGACATGA
1 AAAAAATGACATGA
7373 CATGAGATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 15 0.38
28 24 0.62
ACGTcount: A:0.55, C:0.12, G:0.20, T:0.13
Consensus pattern (28 bp):
AAAAAATGACATGAAGTCTCAAGGAGAC
Found at i:8779 original size:163 final size:166
Alignment explanation
Indices: 8503--8836 Score: 494
Period size: 163 Copynumber: 2.0 Consensus size: 166
8493 TATTGAATTT
* * * * *
8503 AATTAAATAAACATAGATTTTTTAGTAGAATAAAACTATAACAGTTTAAATAATGTCATTTAAGA
1 AATTAAATAAACATAGAGTTTGTAGTAGAATAAAACTATAAAAGCTTAAACAATGTCATTTAAGA
* *
8568 AATATATTTTAAAAATTCTAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGATAAAAGTAA
66 AATATATTTTAAAAATTCTAATATATCTAAGATTTTTAATTAAAATAGTAAAATGATAAAAATAA
8633 AATAGTTATAAAGATATTAGA-T-TAATTAAATAAA
131 AATAGTTATAAAGATATTAGATTATAATTAAATAAA
* * * * *
8667 AATTAAATAAATATGGAGTTTGTAGTCGAATCAAACTGTAAAAGCTTAAACAATGTCATTTAAGA
1 AATTAAATAAACATAGAGTTTGTAGTAGAATAAAACTATAAAAGCTTAAACAATGTCATTTAAGA
* * *
8732 AATCTA-TTTAAAAATTCTAATATATCTAAGATTTTTAATTGAAATAGTAAAATGGTAAAAATAA
66 AATATATTTTAAAAATTCTAATATATCTAAGATTTTTAATTAAAATAGTAAAATGATAAAAATAA
8796 AATAGTTATAAAGATATTAGATTTAATAATTAAATAAA
131 AATAGTTATAAAGATATTAGA-TT-ATAATTAAATAAA
8834 AAT
1 AAT
8837 AGAGTATGGA
Statistics
Matches: 151, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
163 75 0.50
164 60 0.40
165 1 0.01
167 15 0.10
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.36
Consensus pattern (166 bp):
AATTAAATAAACATAGAGTTTGTAGTAGAATAAAACTATAAAAGCTTAAACAATGTCATTTAAGA
AATATATTTTAAAAATTCTAATATATCTAAGATTTTTAATTAAAATAGTAAAATGATAAAAATAA
AATAGTTATAAAGATATTAGATTATAATTAAATAAA
Found at i:12043 original size:31 final size:31
Alignment explanation
Indices: 12008--12076 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
11998 AGTTTTATAA
* * * *
12008 AACTTTTGAAACGTCCGTTGTATCTTTATTT
1 AACTTTTGAAACATCCATTATATCCTTATTT
* *
12039 AACTTTTGAAATATCTATTATATCCTTATTT
1 AACTTTTGAAACATCCATTATATCCTTATTT
12070 AACTTTT
1 AACTTTT
12077 ACAGTTTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (31 bp):
AACTTTTGAAACATCCATTATATCCTTATTT
Found at i:14584 original size:106 final size:106
Alignment explanation
Indices: 14378--14670 Score: 298
Period size: 110 Copynumber: 2.8 Consensus size: 106
14368 TTTTCTAAAG
* * * * * *
14378 CTTAAAATAAAATTTTAATTTTAATTT-GGGTTAAACTTGATG-AATTAGTTATATA-TTT-TAT
1 CTTAAAATAAAA-ATAAAATTTAATTTGGGGCTAAACTTGGTGAAATTAGTTTTATATTTTATAT
* ** **
14439 TTCTAAAACCCTATAGCAATATTATTAATTATGGAATTTACC
65 TTATAAAACCCTATAAAAATATTATTAATTATAAAATTTACC
*
14481 CTTAAAAT-AAAA-AAAA-TTAATTTGGGGCTAAACTTGGTGAAATTAGTTTTGTATTTTATAAT
1 CTTAAAATAAAAATAAAATTTAATTTGGGGCTAAACTTGGTGAAATTAGTTTTATATTTTAT-AT
*
14543 TTATAAAACCCTATAAAAATAAATTATTAATTTTAAAATTTACC
65 TTATAAAACCCTATAAAAAT--ATTATTAATTATAAAATTTACC
* * * *
14587 CTTAAAATAAAAATAAAATTTAAATTTGGAGCTAAATTTAGAGAAATTAGTTTTATA-TTT-TAT
1 CTTAAAATAAAAATAAAATTT-AATTTGGGGCTAAACTTGGTGAAATTAGTTTTATATTTTATAT
* * *
14650 TTCTAAAACTCTATAATAATA
65 TTATAAAACCCTATAAAAATA
14671 ATAAAAAAAA
Statistics
Matches: 158, Mismatches: 21, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
99 7 0.04
100 15 0.09
101 11 0.07
102 6 0.04
103 9 0.06
104 19 0.12
105 1 0.01
106 27 0.17
107 23 0.15
108 5 0.03
109 5 0.03
110 30 0.19
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (106 bp):
CTTAAAATAAAAATAAAATTTAATTTGGGGCTAAACTTGGTGAAATTAGTTTTATATTTTATATT
TATAAAACCCTATAAAAATATTATTAATTATAAAATTTACC
Found at i:16300 original size:12 final size:12
Alignment explanation
Indices: 16271--16333 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
16261 ATCCTCAGCA
*
16271 ACCGCCTCCACC
1 ACCGCCACCACC
* *
16283 AACGCCACCGCC
1 ACCGCCACCACC
*
16295 ACCGCCACCCCC
1 ACCGCCACCACC
**
16307 ACAACCACCACC
1 ACCGCCACCACC
*
16319 TCCGCCACCACC
1 ACCGCCACCACC
16331 ACC
1 ACC
16334 CCAGGAAACA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.24, C:0.65, G:0.08, T:0.03
Consensus pattern (12 bp):
ACCGCCACCACC
Found at i:16657 original size:2 final size:2
Alignment explanation
Indices: 16650--16681 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16640 TTTTTATTTA
16650 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
16682 TATTGGCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.