Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013475.1 Corchorus capsularis cultivar CVL-1 contig13496, 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: 20921
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Found at i:71 original size:29 final size:29
Alignment explanation
Indices: 19--119 Score: 121
Period size: 29 Copynumber: 3.4 Consensus size: 29
9 CGTTAGATTG
19 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAACGT-CCAAAATTGAAGTTC
* *
49 AGGGGGCAAAATGTCCAAGATTGAAGTTC
1 AGGGGGCAAAACGTCCAAAATTGAAGTTC
* * **
78 GGGGGGCAAAACGTCTAAACACTACAAGTTC
1 AGGGGGCAAAACGTCCAAA-A-TTGAAGTTC
109 AGGGGGCAAAA
1 AGGGGGCAAAA
120 TGGTAGATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
29 29 0.48
30 14 0.23
31 17 0.28
ACGTcount: A:0.37, C:0.18, G:0.30, T:0.16
Consensus pattern (29 bp):
AGGGGGCAAAACGTCCAAAATTGAAGTTC
Found at i:454 original size:22 final size:21
Alignment explanation
Indices: 426--694 Score: 122
Period size: 22 Copynumber: 12.5 Consensus size: 21
416 GAGGATATTG
426 AAATTTCATATGAAGGTTATCA
1 AAATTTCATATG-AGGTTATCA
* *
448 AAATTTCATAGTTTA-GTTTTCA
1 AAATTTCATA--TGAGGTTATCA
*
470 AAATTTCATAAGAGGATTATCA
1 AAATTTCATATGAGG-TTATCA
* * *
492 AAATTTCA-AAGTATGTAGATCA
1 AAATTTCATATG-AGGT-TATCA
* * *
514 AAATTTCATAGGGAGATTAACA
1 AAATTTCATA-TGAGGTTATCA
536 AAATTTCATAATGAGGTTATCA
1 AAATTTCAT-ATGAGGTTATCA
** *
558 AAAAATCATAGGGAGG-TATCA
1 AAATTTCATA-TGAGGTTATCA
*
579 AAA-TT--TGT-A-GTTATCA
1 AAATTTCATATGAGGTTATCA
* * *
595 AGATTTCATAAGAAAGTTATCA
1 AAATTTCATATG-AGGTTATCA
* * *
617 CAATTTTATAGGGAGGTTTATCA
1 AAATTTCATA-TGAGG-TTATCA
* * *
640 AAATTTTATAAGAAGATTTATCA
1 AAATTTCATATG-AG-GTTATCA
* *
663 AAATTTTATAGTGATGTTATCA
1 AAATTTCATA-TGAGGTTATCA
*
685 CAATTTCATA
1 AAATTTCATA
695 GTGTGATTAC
Statistics
Matches: 188, Mismatches: 37, Indels: 44
0.70 0.14 0.16
Matches are distributed among these distances:
15 1 0.01
16 8 0.04
17 2 0.01
18 1 0.01
19 1 0.01
20 2 0.01
21 15 0.08
22 115 0.61
23 40 0.21
24 3 0.02
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (21 bp):
AAATTTCATATGAGGTTATCA
Found at i:638 original size:23 final size:23
Alignment explanation
Indices: 611--695 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
601 CATAAGAAAG
*
611 TTATCACAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* * *
634 TTATCAAAATTTTATAAGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
657 TTATCAAAATTTTATAGTGATG-
1 TTATCAAAATTTTATAGGGAGGT
* *
679 TTATCACAATTTCATAG
1 TTATCAAAATTTTATAG
696 TGTGATTACT
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 15 0.29
23 36 0.71
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:653 original size:45 final size:45
Alignment explanation
Indices: 426--694 Score: 152
Period size: 44 Copynumber: 6.2 Consensus size: 45
416 GAGGATATTG
* * ** *
426 AAATTTCATATGAAG-GTTATCAAAATTTCATAGTTTA-GTTTTCA
1 AAATTTCATAAGAAGAGTTATCAAAATTTTATAG-GGAGGTTATCA
* * * * * *
470 AAATTTCATAAGAGGA-TTATCAAAATTTCA-AAGTATGTAGATCA
1 AAATTTCATAAGAAGAGTTATCAAAATTTTATAGGGAGGT-TATCA
* * * * **
514 AAATTTCATAGGGAGA-TTAACAAAATTTCATAATGAGGTTATCA
1 AAATTTCATAAGAAGAGTTATCAAAATTTTATAGGGAGGTTATCA
** * * *
558 AAAAATCAT-AG-GGAGGTATCAAAA--TT-T--GTA-GTTATCA
1 AAATTTCATAAGAAGAGTTATCAAAATTTTATAGGGAGGTTATCA
* *
595 AGATTTCATAAGAA-AGTTATCACAATTTTATAGGGAGGTTTATCA
1 AAATTTCATAAGAAGAGTTATCAAAATTTTATAGGGAGG-TTATCA
* * * *
640 AAATTTTATAAGAAGATTTATCAAAATTTTATAGTGATGTTATCA
1 AAATTTCATAAGAAGAGTTATCAAAATTTTATAGGGAGGTTATCA
*
685 CAATTTCATA
1 AAATTTCATA
695 GTGTGATTAC
Statistics
Matches: 172, Mismatches: 38, Indels: 29
0.72 0.16 0.12
Matches are distributed among these distances:
37 13 0.08
38 12 0.07
40 3 0.02
41 2 0.01
42 4 0.02
43 13 0.08
44 68 0.40
45 37 0.22
46 20 0.12
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (45 bp):
AAATTTCATAAGAAGAGTTATCAAAATTTTATAGGGAGGTTATCA
Found at i:1052 original size:41 final size:41
Alignment explanation
Indices: 1001--1143 Score: 126
Period size: 50 Copynumber: 3.2 Consensus size: 41
991 TGATAATTGT
**
1001 CATAATTATCTTTAAAGATAATATGACTAATAAATATAATC
1 CATAATTATCTTTAAAGATAATATGGTTAATAAATATAATC
1042 CATAATTATCTCTAATATTTATGTAGATAATATGGTTAATAAATATAATC
1 CATAATTATCT-T--TA---A---AGATAATATGGTTAATAAATATAATC
* ** *
1092 CATAATTATCTCTATGGATAATATGGTTAAT-TATATAATCAC
1 CATAATTATCTTTAAAGATAATATGGTTAATAAATATAAT--C
1134 CATAATTATC
1 CATAATTATC
1144 CCATAAACAT
Statistics
Matches: 85, Mismatches: 6, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
40 7 0.08
41 26 0.31
42 12 0.14
44 2 0.02
47 3 0.04
50 35 0.41
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (41 bp):
CATAATTATCTTTAAAGATAATATGGTTAATAAATATAATC
Found at i:1911 original size:30 final size:31
Alignment explanation
Indices: 1844--1918 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
1834 ACCAGTTACA
* *
1844 GGGTGTTACCTATAACGTGTGTAACAAAGTG
1 GGGTATTACCTGTAACGTGTGTAACAAAGTG
* *
1875 GGGTATTACCTGTAACGTGTGTAACCACGT-
1 GGGTATTACCTGTAACGTGTGTAACAAAGTG
*
1905 GGGTATTACTTGTA
1 GGGTATTACCTGTA
1919 GCAGGGGTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 13 0.33
31 26 0.67
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (31 bp):
GGGTATTACCTGTAACGTGTGTAACAAAGTG
Found at i:3562 original size:89 final size:89
Alignment explanation
Indices: 3450--3711 Score: 397
Period size: 88 Copynumber: 3.0 Consensus size: 89
3440 ACTTCAATGG
* *
3450 GAGTGC-TTCAGCCTCTACAAGGAGAAAATGATTCTACTACTTGGAGGGAGCATTAAGATATTGA
1 GAGTGCTTTCAACCTCTACAAGGAGAAAATGATTCTACTACTTGGAGGGAGCATTTAGATATTGA
* *
3514 GCTCGCTTTGATCAGCGGCAGTAA
66 GCTCGCTTTGATTAGCGGCAATAA
3538 GAGTGCTTTCAACCTCTACAAGGAGAAAAT-ATTCTACTACTTGGAGGGAGCATTTAGATATTGA
1 GAGTGCTTTCAACCTCTACAAGGAGAAAATGATTCTACTACTTGGAGGGAGCATTTAGATATTGA
* *
3602 GCTTGCTTTTG-TTAGCAGCAATAA
66 GCTCGC-TTTGATTAGCGGCAATAA
* * * *
3626 GAGTGCTTCCGACCTCTACAAGGAGAAAA-GATTCTGCTACTTGGAGGGAGCATTTAGATATTTA
1 GAGTGCTTTCAACCTCTACAAGGAGAAAATGATTCTACTACTTGGAGGGAGCATTTAGATATTGA
3690 GCTCGCTTTGATTAGCGGCAAT
66 GCTCGCTTTGATTAGCGGCAAT
3712 GAAAATATTT
Statistics
Matches: 158, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
87 4 0.03
88 128 0.81
89 26 0.16
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (89 bp):
GAGTGCTTTCAACCTCTACAAGGAGAAAATGATTCTACTACTTGGAGGGAGCATTTAGATATTGA
GCTCGCTTTGATTAGCGGCAATAA
Found at i:3754 original size:88 final size:87
Alignment explanation
Indices: 3450--3754 Score: 291
Period size: 88 Copynumber: 3.5 Consensus size: 87
3440 ACTTCAATGG
* * *
3450 GAGTGC-TTCAGCCTCTACAAGGAGAAA-ATGATTCTACTACTTGGAGGGAGCATTAAGATATTG
1 GAGTGCTTTCAACCTCTACAAGGAGAAATTTG-TT-T-CTACTTGGAGGGAGCATTTAGATATTG
* *
3513 AGCTCGCTTTGATCAGCGGCAGTAA
63 AGCTCGCTTTGATTAGCGGCAATAA
* *
3538 GAGTGCTTTCAACCTCTACAAGGAGAAAATATT-CTACTACTTGGAGGGAGCATTTAGATATTGA
1 GAGTGCTTTCAACCTCTACAAGGAG-AAAT-TTGTTTCTACTTGGAGGGAGCATTTAGATATTGA
* *
3602 GCTTGCTTTTG-TTAGCAGCAATAA
64 GCTCGC-TTTGATTAGCGGCAATAA
* * * *
3626 GAGTGCTTCCGACCTCTACAAGGAGAAA--AGATTCTGCTACTTGGAGGGAGCATTTAGATATTT
1 GAGTGCTTTCAACCTCTACAAGGAGAAATTTG-TT-T-CTACTTGGAGGGAGCATTTAGATATTG
3689 AGCTCGCTTTGATTAGCGGCAATGAA
63 AGCTCGCTTTGATTAGCGGCAAT-AA
* ** * * *
3715 -AATATTTTTTAAACTCTACAGGGAGAAATTTGTTTCTACT
1 GAGT-GCTTTCAACCTCTACAAGGAGAAATTTGTTTCTACT
3755 ACCTGGAGTA
Statistics
Matches: 177, Mismatches: 26, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
86 1 0.01
87 7 0.04
88 120 0.68
89 41 0.23
90 6 0.03
91 1 0.01
92 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (87 bp):
GAGTGCTTTCAACCTCTACAAGGAGAAATTTGTTTCTACTTGGAGGGAGCATTTAGATATTGAGC
TCGCTTTGATTAGCGGCAATAA
Found at i:3890 original size:35 final size:35
Alignment explanation
Indices: 3844--3929 Score: 145
Period size: 35 Copynumber: 2.5 Consensus size: 35
3834 TATATATGGA
* *
3844 GTGGCGTCATAGGCCAAGGTAATAGTTCATGATAT
1 GTGGCGACATAGGCCAAGGTAATAGTACATGATAT
*
3879 GTGGCGACATAGGCCAAGGTAATTGTACATGATAT
1 GTGGCGACATAGGCCAAGGTAATAGTACATGATAT
3914 GTGGCGACATAGGCCA
1 GTGGCGACATAGGCCA
3930 TTTAATATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.24
Consensus pattern (35 bp):
GTGGCGACATAGGCCAAGGTAATAGTACATGATAT
Found at i:3994 original size:33 final size:31
Alignment explanation
Indices: 3935--4000 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 31
3925 GGCCATTTAA
3935 TATATATGCGCGACATAGGCCATTGTTGTTG
1 TATATATGCGCGACATAGGCCATTGTTGTTG
3966 TATATATG-GCGACATAGGCCATTGTTGTTG
1 TATATATGCGCGACATAGGCCATTGTTGTTG
3996 TATAT
1 TATAT
4001 GTAAACATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 27 0.77
31 8 0.23
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (31 bp):
TATATATGCGCGACATAGGCCATTGTTGTTG
Found at i:4008 original size:28 final size:29
Alignment explanation
Indices: 3947--4009 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
3937 TATATGCGCG
**
3947 ACATAGGCCATTGTTGTTGTATATATGGCG
1 ACATAGGCCATTGTTGTTG-ATATATGGAA
*
3977 ACATAGGCCATTGTTGTTG-TATATGTAA
1 ACATAGGCCATTGTTGTTGATATATGGAA
4005 ACATA
1 ACATA
4010 TGGTTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 11 0.37
30 19 0.63
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.37
Consensus pattern (29 bp):
ACATAGGCCATTGTTGTTGATATATGGAA
Found at i:4039 original size:5 final size:5
Alignment explanation
Indices: 4014--4082 Score: 61
Period size: 5 Copynumber: 13.2 Consensus size: 5
4004 AACATATGGT
* *
4014 TTTTT TTTTG CTTTTG CTTTTG TTTTTG TTTTG TGTTG TTTTTG TTTTG
1 TTTTG TTTTG -TTTTG -TTTTG -TTTTG TTTTG TTTTG -TTTTG TTTTG
4063 TTTT- TTTT- TTTTGG TTTTG T
1 TTTTG TTTTG TTTT-G TTTTG T
4083 GACTGAACTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
4 8 0.14
5 24 0.43
6 24 0.43
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (5 bp):
TTTTG
Found at i:4039 original size:11 final size:10
Alignment explanation
Indices: 4014--4082 Score: 61
Period size: 11 Copynumber: 6.6 Consensus size: 10
4004 AACATATGGT
*
4014 TTTTTTTTTG
1 TTTTGTTTTG
4024 CTTTTGCTTTTG
1 -TTTTG-TTTTG
4036 TTTTTGTTTTG
1 -TTTTGTTTTG
*
4047 TGTTGTTTTTG
1 TTTTG-TTTTG
4058 TTTTGTTTT-
1 TTTTGTTTTG
4067 TTTT-TTTTGG
1 TTTTGTTTT-G
4077 TTTTGT
1 TTTTGT
4083 GACTGAACTT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
8 4 0.08
9 4 0.08
10 12 0.24
11 19 0.39
12 10 0.20
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (10 bp):
TTTTGTTTTG
Found at i:6993 original size:41 final size:41
Alignment explanation
Indices: 6942--7084 Score: 126
Period size: 50 Copynumber: 3.2 Consensus size: 41
6932 TGATAATTGT
**
6942 CATAATTATCTTTAAAGATAATATGACTAATAAATATAATC
1 CATAATTATCTTTAAAGATAATATGGTTAATAAATATAATC
6983 CATAATTATCTCTAATATTTATGTAGATAATATGGTTAATAAATATAATC
1 CATAATTATCT-T--TA---A---AGATAATATGGTTAATAAATATAATC
* ** *
7033 CATAATTATCTCTATGGATAATATGGTTAAT-TATATAATCAC
1 CATAATTATCTTTAAAGATAATATGGTTAATAAATATAAT--C
7075 CATAATTATC
1 CATAATTATC
7085 CCATAAACAT
Statistics
Matches: 85, Mismatches: 6, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
40 7 0.08
41 26 0.31
42 12 0.14
44 2 0.02
47 3 0.04
50 35 0.41
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (41 bp):
CATAATTATCTTTAAAGATAATATGGTTAATAAATATAATC
Found at i:7626 original size:23 final size:22
Alignment explanation
Indices: 7578--7633 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
7568 TGAGGTCTTC
* *
7578 AAAA-TTCATTAAGGAGGTTAAC
1 AAAATTTCA-TAAGAAGGTTAAA
7600 AAAATTTCATAAGAAGGTTATAA
1 AAAATTTCATAAGAAGGTTA-AA
7623 AAAATTT-ATAA
1 AAAATTTCATAA
7634 AAAGATGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.30
Consensus pattern (22 bp):
AAAATTTCATAAGAAGGTTAAA
Found at i:7676 original size:22 final size:22
Alignment explanation
Indices: 7645--7698 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
7635 AAGATGCTCG
* * * *
7645 AAATTCCATAGTATCGTTATTA
1 AAATTTCATAGGAACGTTATCA
*
7667 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAACGTTATCA
7689 AAATTTCATA
1 AAATTTCATA
7699 ATGGGATCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGGAACGTTATCA
Found at i:7741 original size:22 final size:22
Alignment explanation
Indices: 7713--7756 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
7703 GATCATAAAA
7713 AATAGTGTA-ATTATCATAATTT
1 AATAGTG-AGATTATCATAATTT
*
7735 AATAGTGAGGTTATCATAATTT
1 AATAGTGAGATTATCATAATTT
7757 CATATGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (22 bp):
AATAGTGAGATTATCATAATTT
Found at i:9377 original size:15 final size:16
Alignment explanation
Indices: 9342--9378 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
9332 TTCTTTTTTC
*
9342 TTTTTATTATTTTTAT
1 TTTTTATTATTTTGAT
9358 TTTTTATT-TTTTGAT
1 TTTTTATTATTTTGAT
9373 TTTTTA
1 TTTTTA
9379 ATTGGGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTATTATTTTGAT
Found at i:10147 original size:27 final size:27
Alignment explanation
Indices: 10111--10164 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
10101 AAATTTTTTT
*
10111 CAACACCTGTGGTACGATTGTCATTAA
1 CAACACCTGTGGTACGATTGCCATTAA
10138 CAACACCTGTGGTACGATTGCCATTAA
1 CAACACCTGTGGTACGATTGCCATTAA
10165 ATTGGCACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (27 bp):
CAACACCTGTGGTACGATTGCCATTAA
Found at i:18368 original size:15 final size:16
Alignment explanation
Indices: 18341--18370 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18331 CACAAGGAAC
18341 AATTAATTTCTATCAT
1 AATTAATTTCTATCAT
18357 AATTAA-TTCTATCA
1 AATTAATTTCTATCA
18371 GAGAAGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAATTTCTATCAT
Done.