Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002964.1 Corchorus capsularis cultivar CVL-1 contig02972, 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: 13857
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--33 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 TA TA TA 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 TA TA TA T
34 TAACTAACTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:681 original size:32 final size:32
Alignment explanation
Indices: 624--704 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
614 AATGAATAGA
* *
624 TACTTAATCCTTAAAATTTCGTTCCAAAGAAAT
1 TACTTAATCC-TAAAGTTTCGTTCCAAAAAAAT
657 TACTTAATCCTAAAGTTTCGTTCCAAAAAAAT
1 TACTTAATCCTAAAGTTTCGTTCCAAAAAAAT
689 TACTTAATCCTAAAGT
1 TACTTAATCCTAAAGT
705 AGATTGAGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 36 0.78
33 10 0.22
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.36
Consensus pattern (32 bp):
TACTTAATCCTAAAGTTTCGTTCCAAAAAAAT
Found at i:1165 original size:22 final size:22
Alignment explanation
Indices: 1111--1165 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1101 CTTTCTAATC
* *
1111 TTAAACTTTTTATAGAAAAACT
1 TTAAACCTTTTATAAAAAAACT
*
1133 TTAAACTTTTTATAAAAAAACT
1 TTAAACCTTTTATAAAAAAACT
**
1155 TTCTACCTTTT
1 TTAAACCTTTT
1166 TACTTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (22 bp):
TTAAACCTTTTATAAAAAAACT
Found at i:1167 original size:23 final size:22
Alignment explanation
Indices: 1111--1156 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1101 CTTTCTAATC
*
1111 TTAAACTTTTTATAGAAAAACT
1 TTAAACTTTTTATAAAAAAACT
1133 TTAAACTTTTTATAAAAAAACT
1 TTAAACTTTTTATAAAAAAACT
1155 TT
1 TT
1157 CTACCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAAACTTTTTATAAAAAAACT
Found at i:1326 original size:19 final size:19
Alignment explanation
Indices: 1302--1339 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1292 TGTATATGGA
1302 CACTTTGACAAATTAGTCT
1 CACTTTGACAAATTAGTCT
1321 CACTTTGACAAATTAGTCT
1 CACTTTGACAAATTAGTCT
1340 TTCTTACGTA
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:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (19 bp):
CACTTTGACAAATTAGTCT
Found at i:1690 original size:29 final size:29
Alignment explanation
Indices: 1650--1711 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
1640 TTTAACTAAA
* *
1650 AAATTAGGAGTTAAATCATGTCGGATTCT
1 AAATAAGGAGTTAAATCATGTAGGATTCT
* *
1679 AAATAAGGAGTTAAATCGTGTAGGATTGT
1 AAATAAGGAGTTAAATCATGTAGGATTCT
1708 AAAT
1 AAAT
1712 GATAGAAAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (29 bp):
AAATAAGGAGTTAAATCATGTAGGATTCT
Found at i:3195 original size:156 final size:156
Alignment explanation
Indices: 2967--3387 Score: 625
Period size: 156 Copynumber: 2.7 Consensus size: 156
2957 TTGGCTGAAT
* * *
2967 TCGAGCTCTCCTTCATGGTGAACTTGGTTTCACACCCCAAACTATCCTTAACTGAAAAACGTGTA
1 TCGAACTCTCCTTCATGGTGAACTTGGTTTCACACCCCAAACTGTCCTTAACTGAAAAACGTGCA
* ** *
3032 TAAGTTTTTCATCTTAACTCCGATAAAGCTGAAATTTCACC-AGTAGACTTAGATTATCTCCATA
66 TAAGTTTTTCATCTTAAGTCCGATTGAGATGAAATTTCACCAAG-AGACTTAGATTATCTCCATA
3096 AGACTATGGAAAAAATTCTAAGTAAAA
130 AGACTATGGAAAAAATTCTAAGTAAAA
* *
3123 TCGAACTCTCCTTCATGGTGAAGTTGGTTTCACAACCCAAACTGTCCTTAACTGAAAAACGTGCA
1 TCGAACTCTCCTTCATGGTGAACTTGGTTTCACACCCCAAACTGTCCTTAACTGAAAAACGTGCA
** *
3188 TAAGTTTTTCATCTTAAGTTTGATTGAGATGAAACTTT-ACCAAGAGGCTTAGATTATCTCCATA
66 TAAGTTTTTCATCTTAAGTCCGATTGAGATGAAA-TTTCACCAAGAGACTTAGATTATCTCCATA
3252 AGACTATGGAAAAAATTCTAAGTAAAA
130 AGACTATGGAAAAAATTCTAAGTAAAA
* * ** *
3279 -CCAAGCTCTCCTTGATGGTGAACTTGGTTTCATTCCCCAAA-TGTCCTTAATTGAAAAACGTGC
1 TCGAA-CTCTCCTTCATGGTGAACTTGGTTTCACACCCCAAACTGTCCTTAACTGAAAAACGTGC
*
3342 ATAAGTTTTTCATCTTAAGTCCGATTGAGATGAAATTTCGCCAAGA
65 ATAAGTTTTTCATCTTAAGTCCGATTGAGATGAAATTTCACCAAGA
3388 TGACCTACAT
Statistics
Matches: 239, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
154 3 0.01
155 63 0.26
156 168 0.70
157 5 0.02
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (156 bp):
TCGAACTCTCCTTCATGGTGAACTTGGTTTCACACCCCAAACTGTCCTTAACTGAAAAACGTGCA
TAAGTTTTTCATCTTAAGTCCGATTGAGATGAAATTTCACCAAGAGACTTAGATTATCTCCATAA
GACTATGGAAAAAATTCTAAGTAAAA
Found at i:4707 original size:107 final size:105
Alignment explanation
Indices: 4556--4818 Score: 404
Period size: 107 Copynumber: 2.5 Consensus size: 105
4546 AGTTTAGCCT
* *
4556 TAATTTCACTAAGTTTAGCCCCAATTTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
*
4621 AATAATTTATTTTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
4663 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* * *
4728 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAT
66 AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
**
4768 TAA-TTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATT-TTATTTTTATTTTAAGGGT
4819 TAGAAAAATT
Statistics
Matches: 146, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
103 14 0.10
104 31 0.21
105 34 0.23
107 67 0.46
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:6155 original size:15 final size:16
Alignment explanation
Indices: 6125--6156 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6115 TTAAGATTTG
6125 AATTCAGTACTTATAA
1 AATTCAGTACTTATAA
6141 AATTCAGTA-TTATAA
1 AATTCAGTACTTATAA
6156 A
1 A
6157 TTATGTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (16 bp):
AATTCAGTACTTATAA
Found at i:7520 original size:23 final size:20
Alignment explanation
Indices: 7500--7543 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
7490 GAAATAATCA
7500 TATAAAATAATAATAACTAAT
1 TATAAAA-AATAATAACTAAT
* *
7521 TTTTAAAAATAATAACTAAT
1 TATAAAAAATAATAACTAAT
7541 TAT
1 TAT
7544 TAATTGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TATAAAAAATAATAACTAAT
Found at i:7533 original size:20 final size:20
Alignment explanation
Indices: 7508--7546 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
7498 CATATAAAAT
*
7508 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
7528 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
7547 TTGAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:8703 original size:8 final size:9
Alignment explanation
Indices: 8692--8728 Score: 51
Period size: 8 Copynumber: 4.2 Consensus size: 9
8682 TTTAAAGTTT
8692 TAATA-ATA
1 TAATATATA
8700 TAATATATA
1 TAATATATA
8709 T-ATATATA
1 TAATATATA
8717 TATATATATA
1 TA-ATATATA
8727 TA
1 TA
8729 CTATGCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 13 0.50
9 4 0.15
10 9 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TAATATATA
Found at i:8709 original size:2 final size:2
Alignment explanation
Indices: 8697--8728 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
8687 AGTTTTAATA
8697 AT AT A- 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
8729 CTATGCTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8936 original size:5 final size:5
Alignment explanation
Indices: 8929--8959 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
8919 TTAAAACACC
*
8929 CAACC CAACA CAACA CAACA CAACA CAACA C
1 CAACA CAACA CAACA CAACA CAACA CAACA C
8960 GCGCACTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (5 bp):
CAACA
Found at i:9275 original size:2 final size:2
Alignment explanation
Indices: 9268--9296 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9258 CGACCCAAAC
9268 TA 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 TA T
9297 TTGCTTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12273 original size:2 final size:2
Alignment explanation
Indices: 12268--12296 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12258 TTGGTAAAAA
12268 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 A
12297 ACCGGGACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13675 original size:21 final size:22
Alignment explanation
Indices: 13633--13674 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
13623 AATATAGGGG
**
13633 TTTGCTATTTACCGCCCCCCCT
1 TTTGCTAAATACCGCCCCCCCT
13655 TTTGCTAAATACCGCCCCCC
1 TTTGCTAAATACCGCCCCCC
13675 TCCCCCTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.45, G:0.10, T:0.31
Consensus pattern (22 bp):
TTTGCTAAATACCGCCCCCCCT
Done.