Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006712.1 Corchorus capsularis cultivar CVL-1 contig06733, 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: 19873
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:6685 original size:29 final size:29
Alignment explanation
Indices: 6652--6712 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
6642 CTATGCCTGA
6652 TCACCATAGGTTTAATCTTAGGGATTTAG
1 TCACCATAGGTTTAATCTTAGGGATTTAG
6681 TCACCATAGGTTTAATCTTAGGGATTTAG
1 TCACCATAGGTTTAATCTTAGGGATTTAG
6710 TCA
1 TCA
6713 AGGACTGAGA
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:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (29 bp):
TCACCATAGGTTTAATCTTAGGGATTTAG
Found at i:9350 original size:15 final size:17
Alignment explanation
Indices: 9312--9352 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
9302 TCACCCAAGC
9312 AAAAAACAGATCTTGTG
1 AAAAAACAGATCTTGTG
*
9329 AATAAACAGATC-T-TG
1 AAAAAACAGATCTTGTG
9344 AAAAAACAG
1 AAAAAACAG
9353 GCCTAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 10 0.45
16 1 0.05
17 11 0.50
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.20
Consensus pattern (17 bp):
AAAAAACAGATCTTGTG
Found at i:10593 original size:74 final size:73
Alignment explanation
Indices: 10430--10892 Score: 465
Period size: 74 Copynumber: 6.3 Consensus size: 73
10420 AGGGAGTATA
* * *
10430 TATATATTTTGGCAGCGATACATTTTGTCATTG-TTAAAAGAATAAT-TTTT-TAC-ACGACCTT
1 TATATATTTTGGCAGC-A-ACATTTTGTCGTTGTTTAAAA-AAT-ATCTTTTACACAACGACTTT
*
10491 TTAGTCGTTACG
62 TTAGTCGTTACT
* * *
10503 CATATATTTTGGCAGCAACATTTTGTCGTTGTTTAAAAAACTATCTTTTACGCAACGACTTTTAA
1 TATATATTTTGGCAGCAACATTTTGTCGTTGTTTAAAAAA-TATCTTTTACACAACGACTTTTTA
*
10568 GTTGTTACT
65 GTCGTTACT
* * *
10577 TATATATTTTGACAGCAACATTTTGTCGTTG-TTAAAAGAATATTTTTTTACACGACGACTTTTT
1 TATATATTTTGGCAGCAACATTTTGTCGTTGTTTAAAA-AATA-TCTTTTACACAACGACTTTTT
*
10641 AGTCGTTACG
64 AGTCGTTACT
*** * **
10651 TATATATTTTGGCAATTACATTTTGTCGTT-TTTAAAGAACTATCTTTTATGCAACGACTTTTTA
1 TATATATTTTGGCAGCAACATTTTGTCGTTGTTTAAA-AAATATCTTTTACACAACGACTTTTTA
*
10715 GTCGTTACA
65 GTCGTTACT
* * * * * *
10724 TATATATTTTGGCAGCGACACTTTGTCGTTGTTAAAAAAATTGTCTTTTACACGACGACATTTTA
1 TATATATTTTGGCAGCAACATTTTGTCGTTGTTTAAAAAA-TATCTTTTACACAACGACTTTTTA
10789 GTCGTTA-T
65 GTCGTTACT
* * * * *
10797 ATACATATTTTGGCAACGACACTTTGTCGTTGTTAAAAAAATTATCTTTTACACAACGACTTTTT
1 -TATATATTTTGGCAGCAACATTTTGTCGTTGTTTAAAAAA-TATCTTTTACACAACGACTTTTT
*
10862 AGTTGTTA-T
64 AGTCGTTACT
* *
10871 GTACATATTTTGGCAACAACAT
1 -TATATATTTTGGCAGCAACAT
10893 CCAATTTTGC
Statistics
Matches: 331, Mismatches: 47, Indels: 23
0.83 0.12 0.06
Matches are distributed among these distances:
71 17 0.05
72 12 0.04
73 78 0.24
74 223 0.67
75 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (73 bp):
TATATATTTTGGCAGCAACATTTTGTCGTTGTTTAAAAAATATCTTTTACACAACGACTTTTTAG
TCGTTACT
Found at i:10711 original size:147 final size:147
Alignment explanation
Indices: 10430--10892 Score: 605
Period size: 147 Copynumber: 3.1 Consensus size: 147
10420 AGGGAGTATA
* *
10430 TATATATTTTGGCAGCGATACATTTTGTCATTGTTAAAAGAATAATTTTTTACACGAC--CTTTT
1 TATATATTTTGGCAGC-A-ACATTTTGTCGTTGTTAAAAGAATATTTTTTTACACGACGACTTTT
* *
10493 AGTCGTTACGCATATATTTTGGCAGCAACATTTTGTCGTTGTTTAAAAAACTATCTTTTACGCAA
64 AGTCGTTACGTATATATTTTGGCAACAACATTTTGTCGTTGTTTAAAAAACTATCTTTTACGCAA
*
10558 CGACTTTTAAGTTGTTACT
129 CGACTTTTTAGTTGTTACT
*
10577 TATATATTTTGACAGCAACATTTTGTCGTTGTTAAAAGAATATTTTTTTACACGACGACTTTTTA
1 TATATATTTTGGCAGCAACATTTTGTCGTTGTTAAAAGAATATTTTTTTACACGACGAC-TTTTA
** * *
10642 GTCGTTACGTATATATTTTGGCAATTACATTTTGTCGTT-TTTAAAGAACTATCTTTTATGCAAC
65 GTCGTTACGTATATATTTTGGCAACAACATTTTGTCGTTGTTTAAAAAACTATCTTTTACGCAAC
* *
10706 GACTTTTTAGTCGTTACA
130 GACTTTTTAGTTGTTACT
* *
10724 TATATATTTTGGCAGCGACACTTTGTCGTTGTTAAAA-AA-ATTGTCTTTTACACGACGACATTT
1 TATATATTTTGGCAGCAACATTTTGTCGTTGTTAAAAGAATATT-T-TTTTACACGACGAC-TTT
** * * * * * *
10787 TAGTCGTTATATACATATTTTGGCAACGACACTTTGTCGTTGTTAAAAAAATTATCTTTTACACA
63 TAGTCGTTACGTATATATTTTGGCAACAACATTTTGTCGTTGTTTAAAAAACTATCTTTTACGCA
10852 ACGACTTTTTAGTTGTTA-T
128 ACGACTTTTTAGTTGTTACT
* *
10871 GTACATATTTTGGCAACAACAT
1 -TATATATTTTGGCAGCAACAT
10893 CCAATTTTGC
Statistics
Matches: 276, Mismatches: 33, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
145 40 0.14
146 4 0.01
147 140 0.51
148 92 0.33
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (147 bp):
TATATATTTTGGCAGCAACATTTTGTCGTTGTTAAAAGAATATTTTTTTACACGACGACTTTTAG
TCGTTACGTATATATTTTGGCAACAACATTTTGTCGTTGTTTAAAAAACTATCTTTTACGCAACG
ACTTTTTAGTTGTTACT
Found at i:10825 original size:221 final size:221
Alignment explanation
Indices: 10483--10886 Score: 564
Period size: 221 Copynumber: 1.8 Consensus size: 221
10473 AATTTTTTAC
* * *
10483 ACGACCTTTTAGTCGTTACGCATATATTTTGGCAGCAACATTTTGTCGTTGTTTAAAAAACTATC
1 ACGACCTTTTAGTCGTTACACATATATTTTGGCAGCAACACTTTGTCGTTGTTAAAAAAACTATC
* * * * *
10548 TTTTACGCAACGACTTTTAAGTTGTTACTTATATATTTTGACAGCAACATTTTGTCGTTGTTAAA
66 TTTTACACAACGACTTTTAAGTCGTTACTTACATATTTTGACAACAACACTTTGTCGTTGTTAAA
* *
10613 AGAATATT-T-TTTTACACGACGACTTTTTAGTCGTTACGTATATATTTTGGCAATTACATTTTG
131 A-AA-ATTATCTTTTACACAACGACTTTTTAGTCGTTACGTACATATTTTGGCAATTACATTTTG
10676 TCGTTTTTAAAGAACTATCTTTTATGCA
194 TCGTTTTTAAAGAACTATCTTTTATGCA
* * * * *
10704 ACGACTTTTTAGTCGTTACATATATATTTTGGCAGCGACACTTTGTCGTTGTTAAAAAAATTGTC
1 ACGACCTTTTAGTCGTTACACATATATTTTGGCAGCAACACTTTGTCGTTGTTAAAAAAACTATC
* * *
10769 TTTTACACGACGACATTTT-AGTCGTTA-TATACATATTTTGGCAACGACACTTTGTCGTTGTTA
66 TTTTACACAACGAC-TTTTAAGTCGTTACT-TACATATTTTGACAACAACACTTTGTCGTTGTTA
* *
10832 AAAAAATTATCTTTTACACAACGACTTTTTAGTTGTTATGTACATATTTTGGCAA
129 AAAAAATTATCTTTTACACAACGACTTTTTAGTCGTTACGTACATATTTTGGCAA
10887 CAACATCCAA
Statistics
Matches: 159, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
219 3 0.02
220 4 0.03
221 148 0.93
222 4 0.03
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.42
Consensus pattern (221 bp):
ACGACCTTTTAGTCGTTACACATATATTTTGGCAGCAACACTTTGTCGTTGTTAAAAAAACTATC
TTTTACACAACGACTTTTAAGTCGTTACTTACATATTTTGACAACAACACTTTGTCGTTGTTAAA
AAAATTATCTTTTACACAACGACTTTTTAGTCGTTACGTACATATTTTGGCAATTACATTTTGTC
GTTTTTAAAGAACTATCTTTTATGCA
Found at i:14583 original size:16 final size:16
Alignment explanation
Indices: 14564--14638 Score: 116
Period size: 16 Copynumber: 4.7 Consensus size: 16
14554 TTCGGGCGGG
14564 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
14580 TTCGGGTTCGGG-ATTT
1 TTCGGGTTCGGGTA-TT
* *
14596 TTCGAGTTCGGGTTTT
1 TTCGGGTTCGGGTATT
14612 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
14628 TTCGGGTTCGG
1 TTCGGGTTCGG
14639 TCTCGGATCG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
15 1 0.02
16 52 0.98
ACGTcount: A:0.05, C:0.13, G:0.37, T:0.44
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:14591 original size:32 final size:32
Alignment explanation
Indices: 14550--14623 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
14540 GGCAATTGGG
* *
14550 CGGGTTCGGGCGGGTTCGGGTTCGGGTATTTT
1 CGGGTTCGGGAGGGTTCGAGTTCGGGTATTTT
*** *
14582 CGGGTTCGGGATTTTTCGAGTTCGGGTTTTTT
1 CGGGTTCGGGAGGGTTCGAGTTCGGGTATTTT
14614 CGGGTTCGGG
1 CGGGTTCGGG
14624 TATTTTCGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.04, C:0.15, G:0.43, T:0.38
Consensus pattern (32 bp):
CGGGTTCGGGAGGGTTCGAGTTCGGGTATTTT
Found at i:14677 original size:23 final size:23
Alignment explanation
Indices: 14628--14682 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
14618 TTCGGGTATT
* *
14628 TTCGGGTTCGGTCTCGGATCGAA
1 TTCGGGTTCGGGCCCGGATCGAA
* **
14651 TTCGGGTTCGGGCCCGGGTCGGG
1 TTCGGGTTCGGGCCCGGATCGAA
14674 TTCGGGTTC
1 TTCGGGTTC
14683 ACTTTCGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.05, C:0.24, G:0.42, T:0.29
Consensus pattern (23 bp):
TTCGGGTTCGGGCCCGGATCGAA
Found at i:15450 original size:17 final size:17
Alignment explanation
Indices: 15424--15465 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
15414 TATTTTGATC
*
15424 TCGGGCTCGGGTCGGG-T
1 TCGGGTTCGGG-CGGGTT
15441 TCGGGTTCGGGCGGGTT
1 TCGGGTTCGGGCGGGTT
15458 TCGGGTTC
1 TCGGGTTC
15466 ATTTTGCCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.00, C:0.21, G:0.50, T:0.29
Consensus pattern (17 bp):
TCGGGTTCGGGCGGGTT
Found at i:17962 original size:130 final size:130
Alignment explanation
Indices: 17712--17951 Score: 322
Period size: 130 Copynumber: 1.8 Consensus size: 130
17702 ATTTCAACCT
** * * * *
17712 TTATGATTTCACAGTGACTTTGTTTTTGTTGTTACGAAAATTGTAAGCATTAGCAGCGACTAAAA
1 TTATGATTTCACAACGACTTTATTTTTGTTGTTACGAAAACTGTAAGCATTAGCAACAACTAAAA
* * * *
17777 AAGTGTTGTGTAAAATACCATCAAAATTATTTAGGCAACGACTTTAAAAAATTGTTACGAATAGA
66 AAGTGTTGTGTAAAATACCATCAAAATCACTAAGGCAACAACTTTAAAAAATTGTTACGAATAGA
* * *
17842 TTATGATTTCTCAACGACTTTATTTTTGTTGTTACG-AAACTGTAAGCATTGGCAACAATTAAAA
1 TTATGATTTCACAACGACTTTATTTTTGTTGTTACGAAAACTGTAAGCATTAGCAACAACTAAAA
*
17906 AACTTGTTG-GCTAAAATACCATCAAAATCACTAAGGCAACAACTTT
66 AA-GTGTTGTG-TAAAATACCATCAAAATCACTAAGGCAACAACTTT
17952 TAATTATTGT
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
129 26 0.28
130 68 0.72
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (130 bp):
TTATGATTTCACAACGACTTTATTTTTGTTGTTACGAAAACTGTAAGCATTAGCAACAACTAAAA
AAGTGTTGTGTAAAATACCATCAAAATCACTAAGGCAACAACTTTAAAAAATTGTTACGAATAGA
Found at i:19341 original size:29 final size:30
Alignment explanation
Indices: 19288--19350 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
19278 AATTTGTAGT
* * *
19288 TTTTGGACGTTTTATCCTATGAACT-TTAA
1 TTTTGGACATTTTATCCTATAAACTCTCAA
19317 TTTTGGACATTTTACTCC-ATAAACTCTCAA
1 TTTTGGACATTTTA-TCCTATAAACTCTCAA
19347 TTTT
1 TTTT
19351 TGAAGTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (30 bp):
TTTTGGACATTTTATCCTATAAACTCTCAA
Found at i:19590 original size:29 final size:30
Alignment explanation
Indices: 19525--19599 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 30
19515 CTTTGAGAGG
19525 GGGCAAAACGTCCAAAATAGAGAGTTTAGA
1 GGGCAAAACGTCCAAAATAGAGAGTTTAGA
* * *
19555 GGACAAAATGTCCAAAATTGA-AGTTTA-A
1 GGGCAAAACGTCCAAAATAGAGAGTTTAGA
19583 TGGGCAAAACGTCCAAA
1 -GGGCAAAACGTCCAAA
19600 CGCTACAAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.03
29 20 0.51
30 18 0.46
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.19
Consensus pattern (30 bp):
GGGCAAAACGTCCAAAATAGAGAGTTTAGA
Done.