Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012469.1 Corchorus capsularis cultivar CVL-1 contig12490, 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: 55077
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:530 original size:31 final size:31
Alignment explanation
Indices: 495--556 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
485 CTTTTAATTG
495 TTTTTTGATACATAAA-TTTATTTAGTATTTAT
1 TTTTTTGA-ACA-AAACTTTATTTAGTATTTAT
*
527 TTTTTTGACCAAAACTTTATTTAGTATTTA
1 TTTTTTGAACAAAACTTTATTTAGTATTTA
557 GTATTGCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 3 0.11
31 17 0.61
32 8 0.29
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (31 bp):
TTTTTTGAACAAAACTTTATTTAGTATTTAT
Found at i:13945 original size:30 final size:30
Alignment explanation
Indices: 13879--13963 Score: 73
Period size: 30 Copynumber: 2.8 Consensus size: 30
13869 GGTGGTAACC
* * * *
13879 ACCACCATAACAATAATAATAACAACCACC
1 ACCACCACAACAACAATAATAACAACAACA
* * *
13909 ATCACCACAGCAACAATGATAACAACAACA
1 ACCACCACAACAACAATAATAACAACAACA
* *
13939 ACCACCACCATC-ACAATAACAACAA
1 ACCACCA-CAACAACAATAATAACAA
13964 ATCAGCTGGA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
30 40 0.93
31 3 0.07
ACGTcount: A:0.53, C:0.34, G:0.02, T:0.11
Consensus pattern (30 bp):
ACCACCACAACAACAATAATAACAACAACA
Found at i:26848 original size:95 final size:91
Alignment explanation
Indices: 26722--26907 Score: 275
Period size: 95 Copynumber: 2.0 Consensus size: 91
26712 GCTGTCCAAA
* *
26722 GATTACTAAACAACAAAAATCAAAGAACGATTCGAC-TTTTAACTTGATTACCAAAAAAAATAAA
1 GATTACCAAACAAAAAAAATCAAAGAACGATTCGACATTTT-ACTTGATTACC--AAAAAA-AAA
*
26786 AAAATCGAAGAACGATTCGACTTTTTACTT
62 AAAATCGAAGAACGATTCGACTTCTTACTT
* *
26816 GATTACCAAACAAAAAAAAATCGAAGAACGATTCGACATTTTACTTGATTACCAAACAAAAAAAA
1 GATTACCAAAC-AAAAAAAATCAAAGAACGATTCGACATTTTACTTGATTACCAAAAAAAAAAAA
26881 ATCGAAGAACGATTCGACTTCTTACTT
65 ATCGAAGAACGATTCGACTTCTTACTT
26908 CATAGGAAGC
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
92 32 0.38
93 5 0.06
94 10 0.12
95 34 0.40
96 4 0.05
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.25
Consensus pattern (91 bp):
GATTACCAAACAAAAAAAATCAAAGAACGATTCGACATTTTACTTGATTACCAAAAAAAAAAAAA
TCGAAGAACGATTCGACTTCTTACTT
Found at i:26850 original size:46 final size:46
Alignment explanation
Indices: 26722--26907 Score: 275
Period size: 46 Copynumber: 4.0 Consensus size: 46
26712 GCTGTCCAAA
* * * *
26722 GATTACTAAAC-AACAAAAATCAAAGAACGATTCGACTTTTAACTT
1 GATTACCAAACAAAAAAAAATCGAAGAACGATTCGACTTTTTACTT
*
26767 GATTACCAAAAAAAATAAAAAAATCGAAGAACGATTCGACTTTTTACTT
1 GATTACC--AAACAA-AAAAAAATCGAAGAACGATTCGACTTTTTACTT
*
26816 GATTACCAAACAAAAAAAAATCGAAGAACGATTCGACATTTTACTT
1 GATTACCAAACAAAAAAAAATCGAAGAACGATTCGACTTTTTACTT
*
26862 GATTACCAAACAAAAAAAAATCGAAGAACGATTCGACTTCTTACTT
1 GATTACCAAACAAAAAAAAATCGAAGAACGATTCGACTTTTTACTT
26908 CATAGGAAGC
Statistics
Matches: 128, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
45 6 0.05
46 76 0.59
47 8 0.06
48 1 0.01
49 37 0.29
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.25
Consensus pattern (46 bp):
GATTACCAAACAAAAAAAAATCGAAGAACGATTCGACTTTTTACTT
Found at i:27611 original size:14 final size:15
Alignment explanation
Indices: 27584--27615 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
27574 TATAATACTG
27584 TATTTAACCATGGTT
1 TATTTAACCATGGTT
27599 TATTTAA-CATGGTT
1 TATTTAACCATGGTT
27613 TAT
1 TAT
27616 GAAGAAATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.50
Consensus pattern (15 bp):
TATTTAACCATGGTT
Found at i:28385 original size:12 final size:13
Alignment explanation
Indices: 28359--28388 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28349 CATAGATTTC
28359 AAAGGGAATAAAA
1 AAAGGGAATAAAA
*
28372 AAAGGGAAAAAAA
1 AAAGGGAATAAAA
28385 AAAG
1 AAAG
28389 CAATAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.03
Consensus pattern (13 bp):
AAAGGGAATAAAA
Found at i:33702 original size:2 final size:2
Alignment explanation
Indices: 33695--33734 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
33685 AGTTTTTATT
33695 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33735 GTCTGAAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43698 original size:30 final size:30
Alignment explanation
Indices: 43664--43727 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
43654 ATAGTAACTT
43664 TATATATATCTTTTTTTTTT-GCAACATATA
1 TATATATATCTTTTTTTTTTGGCAA-ATATA
* * *
43694 TATATCTTTCTTTTTTTTTTGGTAAATATA
1 TATATATATCTTTTTTTTTTGGCAAATATA
43724 TATA
1 TATA
43728 GAGGTAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (30 bp):
TATATATATCTTTTTTTTTTGGCAAATATA
Found at i:44940 original size:24 final size:22
Alignment explanation
Indices: 44913--44961 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
44903 ATGGCTTCCT
44913 CTCACCTTCCTCCTTCTCATCTAA
1 CTCACCTTCCT-CTTC-CATCTAA
* *
44937 CTCACGTTCCTCTTCCTTCTAA
1 CTCACCTTCCTCTTCCATCTAA
44959 CTC
1 CTC
44962 CGGTAGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 4 0.17
24 10 0.43
ACGTcount: A:0.14, C:0.45, G:0.02, T:0.39
Consensus pattern (22 bp):
CTCACCTTCCTCTTCCATCTAA
Found at i:53871 original size:14 final size:13
Alignment explanation
Indices: 53846--53870 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53836 ATCGCTTCCT
53846 TTTCCTTTTTTTC
1 TTTCCTTTTTTTC
53859 TTTCCTTTTTTT
1 TTTCCTTTTTTT
53871 TTTTTTTGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTCCTTTTTTTC
Found at i:54876 original size:20 final size:21
Alignment explanation
Indices: 54848--54887 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
54838 CTTGTTCTTG
54848 GTACACATTTTCAA-TATGGA
1 GTACACATTTTCAATTATGGA
*
54868 GTACCCATTTTCAATTATGG
1 GTACACATTTTCAATTATGG
54888 CGTTTATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
GTACACATTTTCAATTATGGA
Done.