Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009786.1 Corchorus capsularis cultivar CVL-1 contig09807, 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: 19947
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:73 original size:3 final size:3
Alignment explanation
Indices: 58--92 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
48 TCTATTGTCT
58 ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
93 CAAGTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:845 original size:73 final size:74
Alignment explanation
Indices: 753--908 Score: 242
Period size: 73 Copynumber: 2.1 Consensus size: 74
743 TTAAGGAAGA
*
753 AAAATGTGTAATTACGAAAAAGGGTAAAAGGAAAAGGAATTGGGGAAACTCA-TAAAGGACTTTT
1 AAAA-GTGTAATTACGAAAAAGGGTAAAAGGAAAAGGAATAGGGGAAACTCATTAAAGGACTTTT
*
817 TAGTCATCCG
65 TAGTCACCCG
* * * *
827 AAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATTTAGGGGCTTTTT
1 AAAAGTGTAATTACGAAAAAGGGTAAAAGGAAAAGGAATAGGGGAAACTCATTAAAGGACTTTTT
892 AGTCACCCG
66 AGTCACCCG
901 AAAAGTGT
1 AAAAGTGT
909 GAAAAGACCA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
73 45 0.60
74 30 0.40
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.22
Consensus pattern (74 bp):
AAAAGTGTAATTACGAAAAAGGGTAAAAGGAAAAGGAATAGGGGAAACTCATTAAAGGACTTTTT
AGTCACCCG
Found at i:1899 original size:2 final size:2
Alignment explanation
Indices: 1892--1924 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1882 AACAATTCAA
1892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1925 GGTCATCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1971 original size:2 final size:2
Alignment explanation
Indices: 1964--1992 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1954 ATTGTCTATC
1964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1993 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1998 original size:3 final size:3
Alignment explanation
Indices: 1990--2017 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1980 ATATATATAT
1990 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2018 CAAGTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2769 original size:73 final size:74
Alignment explanation
Indices: 2677--2832 Score: 233
Period size: 73 Copynumber: 2.1 Consensus size: 74
2667 TTAAGGAAGA
* *
2677 AAAATGTGTAATTACGAAAAAGGGTAAAAGGAAAAGGAATGGGGGAAACTCA-TAAAGGACTTTT
1 AAAA-GTGTAATTACGAAAAAAGGTAAAAGGAAAAGGAATAGGGGAAACTCATTAAAGGACTTTT
*
2741 TAGTCATCCG
65 TAGTCACCCG
* * * *
2751 AAAAGTGTAATTACGAAAAAAGGTAGAAGGAAAAGGAATAGGGGAAACTCATTTAGGGGCTTTTT
1 AAAAGTGTAATTACGAAAAAAGGTAAAAGGAAAAGGAATAGGGGAAACTCATTAAAGGACTTTTT
2816 AGTCACCCG
66 AGTCACCCG
2825 AAAAGTGT
1 AAAAGTGT
2833 GAAAAGACCA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
73 44 0.59
74 30 0.41
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.22
Consensus pattern (74 bp):
AAAAGTGTAATTACGAAAAAAGGTAAAAGGAAAAGGAATAGGGGAAACTCATTAAAGGACTTTTT
AGTCACCCG
Found at i:5748 original size:27 final size:27
Alignment explanation
Indices: 5718--5773 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5708 AGTTCATATA
5718 TCTCTGAATAGTTTACCTATTTTGGTT
1 TCTCTGAATAGTTTACCTATTTTGGTT
5745 TCTCTGAATAGTTTACCTATTTTGGTT
1 TCTCTGAATAGTTTACCTATTTTGGTT
5772 TC
1 TC
5774 CACTAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.52
Consensus pattern (27 bp):
TCTCTGAATAGTTTACCTATTTTGGTT
Found at i:5781 original size:27 final size:27
Alignment explanation
Indices: 5721--5781 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
5711 TCATATATCT
*
5721 CTGAATAGTTTACCTATTTTGGTTTCT
1 CTGAATAGTTTACCTATTTTGGTTTCA
5748 CTGAATAGTTTACCTATTTTGGTTTCCA
1 CTGAATAGTTTACCTATTTTGGTTT-CA
5776 CT-AATA
1 CTGAATA
5782 AAGGATTCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.48
Consensus pattern (27 bp):
CTGAATAGTTTACCTATTTTGGTTTCA
Found at i:16290 original size:57 final size:57
Alignment explanation
Indices: 16199--16314 Score: 178
Period size: 57 Copynumber: 2.0 Consensus size: 57
16189 AGTTTGCAAT
* *
16199 ATCTCCAAGCACCAAATCTGCACAGTCCTTTATTTGTAATTCACAAAGCATCGGAAG
1 ATCTCCAAGCACCAAATCTGCACACTCCTCTATTTGTAATTCACAAAGCATCGGAAG
* * * *
16256 ATCTCCAAGCACCAACTCTGCACACTCCTCTATTTGTAATTGACACAGCATTGGAAG
1 ATCTCCAAGCACCAAATCTGCACACTCCTCTATTTGTAATTCACAAAGCATCGGAAG
16313 AT
1 AT
16315 TTGAAAGTGA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.27
Consensus pattern (57 bp):
ATCTCCAAGCACCAAATCTGCACACTCCTCTATTTGTAATTCACAAAGCATCGGAAG
Found at i:19603 original size:33 final size:33
Alignment explanation
Indices: 19549--19613 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
19539 CACTTTCACT
19549 GAGTCTCCCCACTAGGACGGC-TCAGCCACGGCG
1 GAGTCTCCCCACTAGGACGGCTTC-GCCACGGCG
* * *
19582 GAGTCTCCCCATTGGGGCGGCTTCGCCACGGC
1 GAGTCTCCCCACTAGGACGGCTTCGCCACGGC
19614 AGGCCGCCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.14, C:0.38, G:0.32, T:0.15
Consensus pattern (33 bp):
GAGTCTCCCCACTAGGACGGCTTCGCCACGGCG
Found at i:19739 original size:32 final size:33
Alignment explanation
Indices: 19692--19776 Score: 109
Period size: 32 Copynumber: 2.6 Consensus size: 33
19682 AAAATAGCCG
* *
19692 AGCCGCCCCATTGGGGCGGCCTGCC-CTGGCGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCTATGGCGA
* **
19724 AGCCACCCCAGTGGGGCGGCCTGCCTATGGTTA
1 AGCCGCCCCAGTGGGGCGGCCTGCCTATGGCGA
*
19757 AGCCGCCTCAGTGGGGCGGC
1 AGCCGCCCCAGTGGGGCGGC
19777 TTGAGCCATG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 23 0.51
33 22 0.49
ACGTcount: A:0.12, C:0.36, G:0.38, T:0.14
Consensus pattern (33 bp):
AGCCGCCCCAGTGGGGCGGCCTGCCTATGGCGA
Found at i:19792 original size:33 final size:33
Alignment explanation
Indices: 19692--19797 Score: 110
Period size: 33 Copynumber: 3.2 Consensus size: 33
19682 AAAATAGCCG
* * **
19692 AGCCGCCCCATTGGGGCGGCCTGCC-CTGGCGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCTATGGTTA
*
19724 AGCCACCCCAGTGGGGCGGCCTGCCTATGGTTA
1 AGCCGCCCCAGTGGGGCGGCCTGCCTATGGTTA
* *
19757 AGCCGCCTCAGTGGGGCGGCTTGAGCC-ATGG-TA
1 AGCCGCCCCAGTGGGGCGGCCT--GCCTATGGTTA
19790 AGCCGCCC
1 AGCCGCCC
19798 TCTTGGGGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
32 23 0.37
33 32 0.52
34 4 0.06
35 3 0.05
ACGTcount: A:0.13, C:0.36, G:0.36, T:0.15
Consensus pattern (33 bp):
AGCCGCCCCAGTGGGGCGGCCTGCCTATGGTTA
Done.