Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006865.1 Corchorus capsularis cultivar CVL-1 contig06886, 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: 28215
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:397 original size:48 final size:47
Alignment explanation
Indices: 204--407 Score: 302
Period size: 47 Copynumber: 4.3 Consensus size: 47
194 AAAAGGGGTG
* * * *
204 ATCAGT-AATCAGTAAAAAGAGCTTAAACAGAGTCAAGGTGATGGTA
1 ATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAAGTGATGGTA
** *
250 ATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGATGGTT
1 ATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAAGTGATGGTA
297 ATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAAGTGATGGTA
1 ATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAAGTGATGGTA
* * *
344 ATCAGTAAATCAGTAAAAAGAGATTAATCAAAAGTCAAGGTAATAGTA
1 ATCAGTAAATCAGTAAAAAGAGATTAATC-AAAGTCAAAGTGATGGTA
392 ATCAGTAAATCAGTAA
1 ATCAGTAAATCAGTAA
408 TCAAGTAAAA
Statistics
Matches: 145, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 6 0.04
47 108 0.74
48 31 0.21
ACGTcount: A:0.47, C:0.09, G:0.20, T:0.24
Consensus pattern (47 bp):
ATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAAGTGATGGTA
Found at i:456 original size:71 final size:70
Alignment explanation
Indices: 368--523 Score: 183
Period size: 71 Copynumber: 2.2 Consensus size: 70
358 AAAAAGAGAT
* * *
368 TAATCAAAAGTCAAGGTAATAG-TAATCAGTAAATCAGTAATCAA-GTAAAAACATAGTAATCAG
1 TAATTAAAAGTCAAGGTAAGAGATAATCAGTAAATAAG-AATCAAGGT-AAAA-ATAGTAATCAG
*
431 TAAAT-TG
63 TAAATCAG
* * *
438 ATAATTAAGAGTCAAGGTAAGAGATTAATCAGTAATTAAGAGTCAAGGTAAAAATAGTAATCAGT
1 -TAATTAAAAGTCAAGGTAAGAGA-TAATCAGTAAATAAGAATCAAGGTAAAAATAGTAATCAGT
503 AAATCAG
64 AAATCAG
510 TAATTAAAAGTCAA
1 TAATTAAAAGTCAA
524 TGGATTGATC
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
71 48 0.66
72 10 0.14
73 15 0.21
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (70 bp):
TAATTAAAAGTCAAGGTAAGAGATAATCAGTAAATAAGAATCAAGGTAAAAATAGTAATCAGTAA
ATCAG
Found at i:504 original size:32 final size:31
Alignment explanation
Indices: 439--504 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
429 AGTAAATTGA
*
439 TAATTAAGAGTCAAGGTAAGAGATTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
470 TAATTAAGAGTCAAGGTAA-AAATAGTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAAT--TAATCAG
502 TAA
1 TAA
505 ATCAGTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 3 0.09
31 19 0.59
32 10 0.31
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAGAAATTAATCAG
Found at i:646 original size:21 final size:22
Alignment explanation
Indices: 622--670 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
612 GAGAGTAATC
*
622 AGTAAAAGAAAAAT-GGTAAAG
1 AGTAAAAGAAAAATCAGTAAAG
*
643 AGT-AAAGAATAATCAGTAAAG
1 AGTAAAAGAAAAATCAGTAAAG
664 AGTAAAA
1 AGTAAAA
671 TAGTAATCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 12 0.50
22 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.16
Consensus pattern (22 bp):
AGTAAAAGAAAAATCAGTAAAG
Found at i:747 original size:21 final size:21
Alignment explanation
Indices: 723--933 Score: 106
Period size: 21 Copynumber: 9.5 Consensus size: 21
713 TCAGTAGAAG
* *
723 GTAATCATTAAGAGTAAAACA
1 GTAATCAGTAAGAGTAAAATA
* * * *
744 GTAACCAGTGAA-AGCAAAGTG
1 GTAATCAGT-AAGAGTAAAATA
* *
765 GTAATTAGTAAGAGTCAAATA
1 GTAATCAGTAAGAGTAAAATA
*
786 GTAATCAGTAAGAAGTAAAAGA
1 GTAATCAGTAAG-AGTAAAATA
*
808 GTAATCAGTAAAAAAGGAGCAGAAAATA
1 GTAATCAGT----AA-GAG--TAAAATA
* *
836 GTAATCAGTAAAATAGTAAAATG
1 GTAATCAGT--AAGAGTAAAATA
* *
859 GTAATCAGTAAAAAGTAGAAA-G
1 GTAATCAGT-AAGAGTA-AAATA
**
881 GTAATCAACAAGAGTAAAATA
1 GTAATCAGTAAGAGTAAAATA
*
902 GTAATCAGTACAAAGTAAAGA-A
1 GTAATCAGTA-AGAGTAAA-ATA
924 -TAATCAGTAA
1 GTAATCAGTAA
934 AATAATGATG
Statistics
Matches: 148, Mismatches: 28, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
20 6 0.04
21 58 0.39
22 41 0.28
23 18 0.12
25 2 0.01
26 8 0.05
27 1 0.01
28 14 0.09
ACGTcount: A:0.53, C:0.08, G:0.19, T:0.20
Consensus pattern (21 bp):
GTAATCAGTAAGAGTAAAATA
Found at i:817 original size:15 final size:15
Alignment explanation
Indices: 799--854 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
789 ATCAGTAAGA
*
799 AGTAAAAGAGTAATC
1 AGTAAAATAGTAATC
* * *
814 AGTAAAAAAG-GAGC
1 AGTAAAATAGTAATC
828 AG-AAAATAGTAATC
1 AGTAAAATAGTAATC
842 AGTAAAATAGTAA
1 AGTAAAATAGTAA
855 AATGGTAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
13 6 0.18
14 8 0.24
15 19 0.58
ACGTcount: A:0.57, C:0.05, G:0.20, T:0.18
Consensus pattern (15 bp):
AGTAAAATAGTAATC
Found at i:883 original size:22 final size:23
Alignment explanation
Indices: 774--920 Score: 101
Period size: 22 Copynumber: 6.4 Consensus size: 23
764 GGTAATTAGT
* *
774 AAGAGTCAAATAGTAATCAGTAA
1 AAGAGTAAAATGGTAATCAGTAA
*
797 GA-AGTAAAA-GAGTAATCAGTAAAA
1 AAGAGTAAAATG-GTAATCAGT--AA
* *
821 AAGGAGCAGAAAATAGTAATCAGTAA
1 AA-GAG--TAAAATGGTAATCAGTAA
*
847 AATAGTAAAATGGTAATCAGTAA
1 AAGAGTAAAATGGTAATCAGTAA
*
870 AA-AGTAGAAA-GGTAATCA--AC
1 AAGAGTA-AAATGGTAATCAGTAA
* *
890 AAGAGTAAAATAGTAATCAGTAC
1 AAGAGTAAAATGGTAATCAGTAA
913 AA-AGTAAA
1 AAGAGTAAA
921 GAATAATCAG
Statistics
Matches: 100, Mismatches: 11, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
20 6 0.06
21 11 0.11
22 33 0.33
23 26 0.26
24 3 0.03
25 2 0.02
26 6 0.06
28 13 0.13
ACGTcount: A:0.55, C:0.07, G:0.19, T:0.19
Consensus pattern (23 bp):
AAGAGTAAAATGGTAATCAGTAA
Found at i:6448 original size:3 final size:3
Alignment explanation
Indices: 6440--6474 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
6430 CGGCTAACCG
*
6440 GAA GAA GAA AAA GAA GAA GTAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA G
6475 GAAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:8948 original size:25 final size:25
Alignment explanation
Indices: 8933--9015 Score: 157
Period size: 25 Copynumber: 3.3 Consensus size: 25
8923 CGCTCATGTT
8933 CTTGCGTTTGGCAAACGAGCCTGTG
1 CTTGCGTTTGGCAAACGAGCCTGTG
8958 CTTGCGTTTGGCAAACGAGCCTGTG
1 CTTGCGTTTGGCAAACGAGCCTGTG
*
8983 CTTGCGTTTGGCAAGCGAGCCTGTG
1 CTTGCGTTTGGCAAACGAGCCTGTG
9008 CTTGCGTT
1 CTTGCGTT
9016 GAGAAAACAC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.13, C:0.24, G:0.33, T:0.30
Consensus pattern (25 bp):
CTTGCGTTTGGCAAACGAGCCTGTG
Found at i:13094 original size:25 final size:25
Alignment explanation
Indices: 13060--13163 Score: 171
Period size: 25 Copynumber: 4.3 Consensus size: 25
13050 TGCTCATGTT
*
13060 CTTGTGTTTGGCAAACGAGCCTGTG
1 CTTGCGTTTGGCAAACGAGCCTGTG
13085 CTTGCGTTTGGCAAACGAGCCTGTG
1 CTTGCGTTTGGCAAACGAGCCTGTG
13110 CTTGCGTTTGGCAAACGAGCCTGTG
1 CTTGCGTTTGGCAAACGAGCCTGTG
13135 CTTGCGTTT----AACGAGCCTGTG
1 CTTGCGTTTGGCAAACGAGCCTGTG
13156 CTTGCGTT
1 CTTGCGTT
13164 GAGAAAACAC
Statistics
Matches: 78, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
21 20 0.26
25 58 0.74
ACGTcount: A:0.14, C:0.23, G:0.31, T:0.32
Consensus pattern (25 bp):
CTTGCGTTTGGCAAACGAGCCTGTG
Found at i:15471 original size:2 final size:2
Alignment explanation
Indices: 15426--15451 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15416 TTTGAGAGAT
15426 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
15452 AACCTAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20014 original size:12 final size:12
Alignment explanation
Indices: 19997--20051 Score: 92
Period size: 12 Copynumber: 4.5 Consensus size: 12
19987 TTAATACAGG
19997 TATCGACGGATA
1 TATCGACGGATA
20009 TATCGAACGGATA
1 TATCG-ACGGATA
*
20022 TATCGACGAATA
1 TATCGACGGATA
20034 TATCGACGGATA
1 TATCGACGGATA
20046 TATCGA
1 TATCGA
20052 GGTATCGATG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
12 28 0.70
13 12 0.30
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:20034 original size:25 final size:24
Alignment explanation
Indices: 19997--20051 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 24
19987 TTAATACAGG
*
19997 TATCGACGGATATATCGAACGGATA
1 TATCGACGAATATATCG-ACGGATA
20022 TATCGACGAATATATCGACGGATA
1 TATCGACGAATATATCGACGGATA
20046 TATCGA
1 TATCGA
20052 GGTATCGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (24 bp):
TATCGACGAATATATCGACGGATA
Found at i:22089 original size:10 final size:10
Alignment explanation
Indices: 22077--22112 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
22067 AATTTAATAT
* *
22077 GGATATGTAT
1 GGATATTTAC
22087 GGATATTTAC
1 GGATATTTAC
22097 GGATATTTAC
1 GGATATTTAC
22107 GGATAT
1 GGATAT
22113 ATCGAGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.39
Consensus pattern (10 bp):
GGATATTTAC
Found at i:22240 original size:12 final size:12
Alignment explanation
Indices: 22223--22261 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
22213 GTACAGATAT
22223 CGGATATATCGA
1 CGGATATATCGA
22235 CGGATATATCGA
1 CGGATATATCGA
22247 -GG---TATCGA
1 CGGATATATCGA
22255 CGGATAT
1 CGGATAT
22262 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Done.