Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014068.1 Corchorus capsularis cultivar CVL-1 contig14089, 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: 28140
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Found at i:845 original size:62 final size:61
Alignment explanation
Indices: 746--879 Score: 189
Period size: 62 Copynumber: 2.2 Consensus size: 61
736 GTCAACCCAA
* * ** *
746 AAAAAAAAAAGCTCGCTAAATTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGT
1 AAAAAAAAAAGCTCGCTAAATTGAAAATCCTGAAAAGGACGACTTAGGCAAAACATAGAGC
807 AAAAAAAAAAGACTCGC-AAAGTTGAAAATCCTGAAAAGGACGACTTAGGCAAAACATAGAGC
1 AAAAAAAAAAG-CTCGCTAAA-TTGAAAATCCTGAAAAGGACGACTTAGGCAAAACATAGAGC
869 ACAAAAAAAAA
1 A-AAAAAAAAA
880 ATGAACTACG
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
61 14 0.22
62 42 0.65
63 9 0.14
ACGTcount: A:0.52, C:0.15, G:0.19, T:0.14
Consensus pattern (61 bp):
AAAAAAAAAAGCTCGCTAAATTGAAAATCCTGAAAAGGACGACTTAGGCAAAACATAGAGC
Found at i:1637 original size:16 final size:16
Alignment explanation
Indices: 1616--1650 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1606 ACGATTCAGA
1616 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
1632 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
1648 AAG
1 AAG
1651 TATTTCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:2632 original size:16 final size:16
Alignment explanation
Indices: 2611--2645 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2601 ACGATTCAGA
2611 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
2627 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
2643 AAG
1 AAG
2646 TATTTCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:5218 original size:2 final size:2
Alignment explanation
Indices: 5211--5245 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5201 CTCGTACTTT
* *
5211 TA TA TA TA GA TA TA GA 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 TA T
5246 TCTATAATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:19014 original size:129 final size:129
Alignment explanation
Indices: 18779--19028 Score: 439
Period size: 129 Copynumber: 1.9 Consensus size: 129
18769 AGTTTATAAT
* *
18779 TGGCTAAAATCTCAATTAGGGCCCTGAACTTTGCCAAAAGGGTCAAATAAGTGCCCAAACTATGA
1 TGGCTAAAATCTCAATTAGGACCCTAAACTTTGCCAAAAGGGTCAAATAAGTGCCCAAACTATGA
*
18844 AAAGGTCAAATTAGCGCCTGAACTTTTCGATTTGGGTCAATTCAGTCCAAAATGTTTTGGATTA
66 AAAGGTCAAATTAGCGCCTGAACTTTTCGATTTGAGTCAATTCAGTCCAAAATGTTTTGGATTA
*
18908 TGGCTAAAATCTCAATTAGGACCCTAAATTTTGCCAAAAGGGTCAAATAAGTGCCCAAACTATGA
1 TGGCTAAAATCTCAATTAGGACCCTAAACTTTGCCAAAAGGGTCAAATAAGTGCCCAAACTATGA
*
18973 AAAGGTCAAATTAGTGCCTGAACTTTTCGATTTGAAG-CAATTCAGTCCAAAATGTT
66 AAAGGTCAAATTAGCGCCTGAACTTTTCGATTTG-AGTCAATTCAGTCCAAAATGTT
19029 AGATTATAAG
Statistics
Matches: 115, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
129 114 0.99
130 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (129 bp):
TGGCTAAAATCTCAATTAGGACCCTAAACTTTGCCAAAAGGGTCAAATAAGTGCCCAAACTATGA
AAAGGTCAAATTAGCGCCTGAACTTTTCGATTTGAGTCAATTCAGTCCAAAATGTTTTGGATTA
Found at i:19410 original size:4 final size:4
Alignment explanation
Indices: 19403--19447 Score: 76
Period size: 4 Copynumber: 11.8 Consensus size: 4
19393 ACACACACAT
19403 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC --AC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
19448 TATATATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
4 37 0.95
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:21757 original size:31 final size:30
Alignment explanation
Indices: 21718--21776 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
21708 ATCTCATTAT
* * *
21718 AAATTCAATTTATATTTAGATTAGATTTTC
1 AAATTCAATTCAAATTTAAATTAGATTTTC
*
21748 AAATGTCAATTCAAATTTAAATTATATTT
1 AAAT-TCAATTCAAATTTAAATTAGATTT
21777 ATCTCCGATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (30 bp):
AAATTCAATTCAAATTTAAATTAGATTTTC
Found at i:22356 original size:2 final size:2
Alignment explanation
Indices: 22349--22381 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
22339 TGAATAAGAG
22349 AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22382 AAGGATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.