Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010119.1 Corchorus capsularis cultivar CVL-1 contig10140, 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: 23668
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:2451 original size:21 final size:21
Alignment explanation
Indices: 2426--2469 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2416 TATAAGGATA
*
2426 AATGTATAAAGTGAGGGTGAT
1 AATGTATAAAGTGAGAGTGAT
* *
2447 AATGTATAAGGTTAGAGTGAT
1 AATGTATAAAGTGAGAGTGAT
2468 AA
1 AA
2470 GTCTCATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (21 bp):
AATGTATAAAGTGAGAGTGAT
Found at i:3734 original size:14 final size:14
Alignment explanation
Indices: 3715--3743 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3705 GCCTTGGAGA
3715 AAGGCGTTGTTGAC
1 AAGGCGTTGTTGAC
3729 AAGGCGTTGTTGAC
1 AAGGCGTTGTTGAC
3743 A
1 A
3744 TCCAGTTGAT
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:0.24, C:0.14, G:0.34, T:0.28
Consensus pattern (14 bp):
AAGGCGTTGTTGAC
Found at i:10067 original size:13 final size:13
Alignment explanation
Indices: 10049--10080 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
10039 GCTAGGAAGC
10049 TTTAGTTCTAAGT
1 TTTAGTTCTAAGT
*
10062 TTTAGTTTTAAGT
1 TTTAGTTCTAAGT
10075 TTTAGT
1 TTTAGT
10081 CATTACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.03, G:0.16, T:0.59
Consensus pattern (13 bp):
TTTAGTTCTAAGT
Found at i:13032 original size:35 final size:36
Alignment explanation
Indices: 12971--13044 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 36
12961 AACAAAAGGG
12971 ATGCCTCGATAGAGTTTTTGTTTGTCTATGGTTACT
1 ATGCCTCGATAGAGTTTTTGTTTGTCTATGGTTACT
13007 ATGCCTCGATAGAG-TTTTGTTTGTCTATGGTTACT
1 ATGCCTCGATAGAGTTTTTGTTTGTCTATGGTTACT
13042 ATG
1 ATG
13045 AAATTCATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 24 0.63
36 14 0.37
ACGTcount: A:0.18, C:0.14, G:0.23, T:0.46
Consensus pattern (36 bp):
ATGCCTCGATAGAGTTTTTGTTTGTCTATGGTTACT
Found at i:13255 original size:40 final size:40
Alignment explanation
Indices: 13200--13279 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
13190 TCTCCGCTAG
*
13200 CTCCTGGCTTGTTAAAATTAAACTGTGATGCAGCATTTAA
1 CTCCTGGCTTATTAAAATTAAACTGTGATGCAGCATTTAA
*
13240 CTCCTGGCTTATTAAAATTGAACTGTGATGCAGCATTTAA
1 CTCCTGGCTTATTAAAATTAAACTGTGATGCAGCATTTAA
13280 TAACAGCTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (40 bp):
CTCCTGGCTTATTAAAATTAAACTGTGATGCAGCATTTAA
Found at i:15330 original size:41 final size:43
Alignment explanation
Indices: 15272--15361 Score: 130
Period size: 42 Copynumber: 2.1 Consensus size: 43
15262 ATTAAGCCCT
* *
15272 TGAAAATGTATAAAATCAA-TAACCACTACAAATTGTAACGCC
1 TGAAAATATATAAAATCAACTAACCACTACAAATTGTAACGCA
* *
15314 TGAAAATAT-TAAAATCAACTAACCAGTACAATTTGTAACGCA
1 TGAAAATATATAAAATCAACTAACCACTACAAATTGTAACGCA
15356 TGAAAA
1 TGAAAA
15362 ACAATCAACT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 9 0.21
42 34 0.79
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.24
Consensus pattern (43 bp):
TGAAAATATATAAAATCAACTAACCACTACAAATTGTAACGCA
Found at i:15526 original size:42 final size:42
Alignment explanation
Indices: 15412--15510 Score: 171
Period size: 42 Copynumber: 2.4 Consensus size: 42
15402 ACCTAACCAC
* *
15412 TACAATATGTAACGCCTAAAAATGTTAGAATTAGCCAAACGA
1 TACAATTTGTAACGCCTAAAAATGTTAGAATTAGCCAAACAA
*
15454 TACAATTTGTAATGCCTAAAAATGTTAGAATTAGCCAAACAA
1 TACAATTTGTAACGCCTAAAAATGTTAGAATTAGCCAAACAA
15496 TACAATTTGTAACGC
1 TACAATTTGTAACGC
15511 TTGAAAATAC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.27
Consensus pattern (42 bp):
TACAATTTGTAACGCCTAAAAATGTTAGAATTAGCCAAACAA
Found at i:15847 original size:38 final size:38
Alignment explanation
Indices: 15790--15919 Score: 119
Period size: 38 Copynumber: 3.6 Consensus size: 38
15780 GAAATCAACT
* *
15790 AACCAGTAAAATTTGTAATGCTTGAAAATGCATCACCC
1 AACCAATAAAATTTATAATGCTTGAAAATGCATCACCC
* * * *
15828 AACCATTACAATATT-TAATGCATGAAAA--C--CAACC
1 AACCAATAAAAT-TTATAATGCTTGAAAATGCATCACCC
* *
15862 AATCAATAAAATTTATAATTCTTGAAAATGCATCACCC
1 AACCAATAAAATTTATAATGCTTGAAAATGCATCACCC
* *
15900 AACTAAT-AAATTTGTAATGC
1 AACCAATAAAATTTATAATGC
15920 ATAAAAAAAT
Statistics
Matches: 72, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
33 2 0.03
34 24 0.33
36 2 0.03
37 11 0.15
38 31 0.43
39 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.28
Consensus pattern (38 bp):
AACCAATAAAATTTATAATGCTTGAAAATGCATCACCC
Found at i:15892 original size:72 final size:71
Alignment explanation
Indices: 15763--15921 Score: 203
Period size: 72 Copynumber: 2.2 Consensus size: 71
15753 TGACAAATGA
* * * * *
15763 TACAATATGTAATGCCTGAAATCAACTAACCAGTAAAATTTGTAATGCTTGAAAATGCATCACCC
1 TACAATATGTAATGCATGAAACCAACCAACCAATAAAATTTATAATGCTTGAAAATGCATCACCC
15828 AACCAT
66 AACCAT
* * *
15834 TACAATATTTAATGCATGAAAACCAACCAATCAATAAAATTTATAATTCTTGAAAATGCATCACC
1 TACAATATGTAATGCATG-AAACCAACCAACCAATAAAATTTATAATGCTTGAAAATGCATCACC
* *
15899 CAACTAA
65 CAACCAT
*
15906 TA-AATTTGTAATGCAT
1 TACAATATGTAATGCAT
15922 AAAAAAATCA
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
71 28 0.37
72 47 0.63
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (71 bp):
TACAATATGTAATGCATGAAACCAACCAACCAATAAAATTTATAATGCTTGAAAATGCATCACCC
AACCAT
Found at i:16412 original size:42 final size:42
Alignment explanation
Indices: 16308--16412 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 42
16298 ACCTGACCAA
* * * *
16308 TACAATATGTAACGCCTAAAAATGTTAGAAATAGCCAAACGG
1 TACAATTTGTAACGCCTGAAAATATTAGAAATAGCCAAACAG
* * *
16350 TACACTTTGTAACGCCTGAAAATATTAGAATTAGTCAAACAG
1 TACAATTTGTAACGCCTGAAAATATTAGAAATAGCCAAACAG
*
16392 TACAATTTGTAACGCTTGAAA
1 TACAATTTGTAACGCCTGAAA
16413 TTGCTAGAGT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (42 bp):
TACAATTTGTAACGCCTGAAAATATTAGAAATAGCCAAACAG
Found at i:16490 original size:34 final size:34
Alignment explanation
Indices: 16424--16492 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
16414 TGCTAGAGTG
* * * *
16424 AACCAACTTGTACAACCTGTAACGCGTGAAAATC
1 AACCAACTAGTACAACCTGTAAAGCCTAAAAATC
**
16458 AACCAACTAGTACAATTTGTAAAGCCTAAAAATC
1 AACCAACTAGTACAACCTGTAAAGCCTAAAAATC
16492 A
1 A
16493 GCAAAGCAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.43, C:0.23, G:0.12, T:0.22
Consensus pattern (34 bp):
AACCAACTAGTACAACCTGTAAAGCCTAAAAATC
Found at i:16730 original size:38 final size:37
Alignment explanation
Indices: 16687--16819 Score: 137
Period size: 38 Copynumber: 3.6 Consensus size: 37
16677 CTGAAATCAA
* *
16687 CCAACCAGTACAATTTGTAACACTTGAAAATGCATCAC
1 CCAACCAATACAATTTGTAACGCTTGAAAATGCAT-AC
* *
16725 CCAACCAATACAATATGTAACGCATGAAAAT-CA-A-
1 CCAACCAATACAATTTGTAACGCTTGAAAATGCATAC
* * * *
16759 CCAACCAACAAAATTTATAATGCTTGAAAATGCATAGC
1 CCAACCAATACAATTTGTAACGCTTGAAAATGCATA-C
* *
16797 CCAACTAGTACAATTTGTAACGC
1 CCAACCAATACAATTTGTAACGC
16820 ATAAAAATCA
Statistics
Matches: 75, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
34 25 0.33
35 3 0.04
36 1 0.01
37 2 0.03
38 44 0.59
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.23
Consensus pattern (37 bp):
CCAACCAATACAATTTGTAACGCTTGAAAATGCATAC
Found at i:16736 original size:114 final size:116
Alignment explanation
Indices: 16542--16750 Score: 287
Period size: 114 Copynumber: 1.8 Consensus size: 116
16532 TCAGCTAGCC
* * * * **
16542 AATACAATATGTGTACCGCATGAAAATCAGCCAACTAGTACAATCAGTAACTGTCTGAAAATGCA
1 AATACAATATATGTAACGCATGAAAATCAACCAACCAGTACAATCAGTAACACTCTGAAAATGCA
** *
16607 TCACTTAACCAATACAATATGTAATGCATGGAAGGTTAGAATCTGACAAAT
66 TCACCCAACCAATACAATATGTAACGCATGGAAGGTTAGAATCTGACAAAT
* * **
16658 AATACAATATATGTAATGCCTG-AAATCAACCAACCAGTACAATTTGTAACACT-TGAAAATGCA
1 AATACAATATATGTAACGCATGAAAATCAACCAACCAGTACAATCAGTAACACTCTGAAAATGCA
16721 TCACCCAACCAATACAATATGTAACGCATG
66 TCACCCAACCAATACAATATGTAACGCATG
16751 AAAATCAACC
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
114 37 0.46
115 25 0.31
116 18 0.22
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.24
Consensus pattern (116 bp):
AATACAATATATGTAACGCATGAAAATCAACCAACCAGTACAATCAGTAACACTCTGAAAATGCA
TCACCCAACCAATACAATATGTAACGCATGGAAGGTTAGAATCTGACAAAT
Found at i:16852 original size:72 final size:72
Alignment explanation
Indices: 16680--16855 Score: 219
Period size: 72 Copynumber: 2.4 Consensus size: 72
16670 GTAATGCCTG
* **
16680 AAATCAACCAACCAGTACAATTTGTAACACTTGAAAATGCATCACCCAACCAATACAATATGTAA
1 AAATCAACCAACCAATACAATTTGTAATGCTTGAAAATGCATCACCCAACCAATACAATATGTAA
*
16745 CGCATGA
66 CGCATAA
* * * * * *
16752 AAATCAACCAACCAACAAAATTTATAATGCTTGAAAATGCAT-AGCCCAACTAGTACAATTTGTA
1 AAATCAACCAACCAATACAATTTGTAATGCTTGAAAATGCATCA-CCCAACCAATACAATATGTA
16816 ACGCATAA
65 ACGCATAA
* * *
16824 AAATCAGCCAGCCAATACAATATGTAATGCTT
1 AAATCAACCAACCAATACAATTTGTAATGCTT
16856 AGGACTGCAT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
71 1 0.01
72 86 0.99
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (72 bp):
AAATCAACCAACCAATACAATTTGTAATGCTTGAAAATGCATCACCCAACCAATACAATATGTAA
CGCATAA
Found at i:17643 original size:33 final size:34
Alignment explanation
Indices: 17587--17650 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
17577 TTAAATACAA
* *
17587 ATCCTAGAAAAAAAAATGTAAGCATAACCTTTCC
1 ATCCAAGAAAAAAAAATGCAAGCATAACCTTTCC
*
17621 ATCCAAGAAAAAAAAA-GCAAGCATATCCTT
1 ATCCAAGAAAAAAAAATGCAAGCATAACCTT
17651 AAATACAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 12 0.44
34 15 0.56
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.20
Consensus pattern (34 bp):
ATCCAAGAAAAAAAAATGCAAGCATAACCTTTCC
Found at i:20430 original size:21 final size:21
Alignment explanation
Indices: 20404--20456 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
20394 ACACTGGAGT
* * *
20404 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
20425 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
20446 ACAT-GGGCGCC
1 ACATGGGGCGCC
20457 CAGCGCTAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.26, C:0.32, G:0.32, T:0.09
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Done.