Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014130.1 Corchorus capsularis cultivar CVL-1 contig14151, 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: 48671
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:3424 original size:15 final size:15
Alignment explanation
Indices: 3404--3436 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3394 CACATCATAT
3404 ATTCCATTAATTTGC
1 ATTCCATTAATTTGC
3419 ATTCCATTAATTTGC
1 ATTCCATTAATTTGC
3434 ATT
1 ATT
3437 AGAATAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.48
Consensus pattern (15 bp):
ATTCCATTAATTTGC
Found at i:6379 original size:30 final size:31
Alignment explanation
Indices: 6338--6408 Score: 108
Period size: 30 Copynumber: 2.3 Consensus size: 31
6328 AAGAAAAGTA
* *
6338 AAAAGGGTAATCAGTAATTAAGTTCAATAAG
1 AAAAGAGTAATCAGTAACTAAGTTCAATAAG
*
6369 AAAA-AGTAATCAGTGACTAAGTTCAATAAG
1 AAAAGAGTAATCAGTAACTAAGTTCAATAAG
6399 AAAAGAGTAA
1 AAAAGAGTAA
6409 AATGATAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 27 0.75
31 9 0.25
ACGTcount: A:0.52, C:0.07, G:0.18, T:0.23
Consensus pattern (31 bp):
AAAAGAGTAATCAGTAACTAAGTTCAATAAG
Found at i:6430 original size:22 final size:22
Alignment explanation
Indices: 6399--6508 Score: 127
Period size: 22 Copynumber: 5.0 Consensus size: 22
6389 GTTCAATAAG
6399 AAAAGAGTAAAATGATAATCAGT
1 AAAA-AGTAAAATGATAATCAGT
* *
6422 AAAAAGTAAAAAGGTAATCAGT
1 AAAAAGTAAAATGATAATCAGT
* *
6444 AAAAGGTAAAAT-AGTAATTAG-
1 AAAAAGTAAAATGA-TAATCAGT
6465 AAAAGAGTAAAATGATAATCAGT
1 AAAA-AGTAAAATGATAATCAGT
6488 AAAAAGTAAAA-GAGTAATCAG
1 AAAAAGTAAAATGA-TAATCAG
6509 GAAAGGAAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
21 6 0.08
22 59 0.80
23 9 0.12
ACGTcount: A:0.58, C:0.04, G:0.18, T:0.20
Consensus pattern (22 bp):
AAAAAGTAAAATGATAATCAGT
Found at i:6538 original size:33 final size:33
Alignment explanation
Indices: 6486--6630 Score: 157
Period size: 33 Copynumber: 4.3 Consensus size: 33
6476 ATGATAATCA
* *
6486 GTAAAAAGTAAAAGAGTAATCAGGAAAGGAAATG
1 GTAAAGAGT-AAAGAGTAATCAGGAAAGAAAATG
*
6520 GTAAAGAGTAAAGAGTAATC-GGCAAAGGAAATG
1 GTAAAGAGTAAAGAGTAATCAGG-AAAGAAAATG
* * *
6553 GTAAAGAGTGAAGAGTAATTAGTAAAGAAAAATG
1 GTAAAGAGTAAAGAGTAATCAGGAAAG-AAAATG
* * * * *
6587 GTAAAGAGTAATGAGTAATTAGTAAAAAAAATA
1 GTAAAGAGTAAAGAGTAATCAGGAAAGAAAATG
6620 GTAAAGAGTAA
1 GTAAAGAGTAA
6631 TCAGTAAAGA
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
32 2 0.02
33 59 0.60
34 38 0.38
ACGTcount: A:0.54, C:0.02, G:0.26, T:0.19
Consensus pattern (33 bp):
GTAAAGAGTAAAGAGTAATCAGGAAAGAAAATG
Found at i:6603 original size:27 final size:27
Alignment explanation
Indices: 6563--6657 Score: 100
Period size: 27 Copynumber: 3.3 Consensus size: 27
6553 GTAAAGAGTG
*
6563 AAGAGTAATTAGTAAAGAAAAATGGTA
1 AAGAGTAATCAGTAAAGAAAAATGGTA
* *
6590 AAGAGTAATGAGTAATTAGTAAAAAAAATAGTA
1 AAGAGTAATCAGTAA--AG----AAAAATGGTA
*
6623 AAGAGTAATCAGTAAAGAAGAATGGTA
1 AAGAGTAATCAGTAAAGAAAAATGGTA
6650 AAGAGTAA
1 AAGAGTAA
6658 AATATTAATC
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
27 30 0.53
29 2 0.04
31 2 0.04
33 23 0.40
ACGTcount: A:0.56, C:0.01, G:0.22, T:0.21
Consensus pattern (27 bp):
AAGAGTAATCAGTAAAGAAAAATGGTA
Found at i:6624 original size:67 final size:66
Alignment explanation
Indices: 6497--6628 Score: 165
Period size: 67 Copynumber: 2.0 Consensus size: 66
6487 TAAAAAGTAA
* * ** *
6497 AAGAGTAATCAGGAAAGGAAATGGTAAAGAGTAAAGAGTAATCGGCAAAGGAAATGGTAAAGAGT
1 AAGAGTAATCAGGAAAGAAAATGGTAAAGAGTAAAGAGTAATCAGCAAAAAAAATAGTAAAGAGT
6562 G
66 G
* * * * *
6563 AAGAGTAATTAGTAAAGAAAAATGGTAAAGAGTAATGAGTAATTAGTAAAAAAAATAGTAAAGAG
1 AAGAGTAATCAGGAAAG-AAAATGGTAAAGAGTAAAGAGTAATCAGCAAAAAAAATAGTAAAGAG
6628 T
65 T
6629 AATCAGTAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
66 15 0.27
67 40 0.73
ACGTcount: A:0.52, C:0.02, G:0.27, T:0.19
Consensus pattern (66 bp):
AAGAGTAATCAGGAAAGAAAATGGTAAAGAGTAAAGAGTAATCAGCAAAAAAAATAGTAAAGAGT
G
Found at i:6628 original size:26 final size:27
Alignment explanation
Indices: 6593--6657 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
6583 AATGGTAAAG
* *
6593 AGTAATGAGTAATTAGTAAA-AAAAAT
1 AGTAAAGAGTAATCAGTAAAGAAAAAT
*
6619 AGTAAAGAGTAATCAGTAAAGAAGAAT
1 AGTAAAGAGTAATCAGTAAAGAAAAAT
*
6646 GGTAAAGAGTAA
1 AGTAAAGAGTAA
6658 AATATTAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 18 0.53
27 16 0.47
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.22
Consensus pattern (27 bp):
AGTAAAGAGTAATCAGTAAAGAAAAAT
Found at i:9614 original size:21 final size:21
Alignment explanation
Indices: 9566--9615 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
9556 TGTCACCACA
9566 ACAA-AGAAATTGGAATCACC
1 ACAATAGAAATTGGAATCACC
*
9586 AC-ATAGAAGTTGGAA-CTACC
1 ACAATAGAAATTGGAATC-ACC
9606 ACAATAGAAA
1 ACAATAGAAA
9616 AGTATACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 2 0.08
20 17 0.68
21 6 0.24
ACGTcount: A:0.50, C:0.18, G:0.16, T:0.16
Consensus pattern (21 bp):
ACAATAGAAATTGGAATCACC
Found at i:12803 original size:88 final size:87
Alignment explanation
Indices: 12651--12829 Score: 295
Period size: 88 Copynumber: 2.0 Consensus size: 87
12641 AGTGACTGAG
* * *
12651 GCAATTCTAGTGGGTTGGTAGGTGAGTCCCTTGGGTTTCCAAATGAAATAGTTATTTTGTTGATT
1 GCAATTCTAGTGGGTTGGTAGGTAAGTCCCTTGGGTTTCCAAATGAAATAGTTATTTCGATGATT
*
12716 ATCTAATTTAGTTTGGTTTTCAT
66 ATCTAATTTAGTTTGGTCTTC-T
*
12739 GCAATTCTAGTGGGTTGGTAGGTAAGTTCCTTGGGTTTCCAAATGAAATAGTTATTTCGATGATT
1 GCAATTCTAGTGGGTTGGTAGGTAAGTCCCTTGGGTTTCCAAATGAAATAGTTATTTCGATGATT
*
12804 ATCTAATTTATTTTGGTCTTCT
66 ATCTAATTTAGTTTGGTCTTCT
12826 GCAA
1 GCAA
12830 CAGTTATGTA
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
87 5 0.06
88 80 0.94
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (87 bp):
GCAATTCTAGTGGGTTGGTAGGTAAGTCCCTTGGGTTTCCAAATGAAATAGTTATTTCGATGATT
ATCTAATTTAGTTTGGTCTTCT
Found at i:13121 original size:153 final size:153
Alignment explanation
Indices: 12843--13152 Score: 593
Period size: 153 Copynumber: 2.0 Consensus size: 153
12833 TTATGTATGA
* *
12843 TTAAATCATGGTTTTTGAAATTGGACCGATCAGTTCGATCGATTAAATTGGGTATCGGAAGTCTG
1 TTAAATCATGGTTTTTGAAATCGGACCGATCAGTTCGATCGATTAAATTGGGTATCGGAAGCCTG
12908 TTCGGTCCAGATAATCTGGAATTTTCGATCAATCAACAATCGATGGTTGAACCGACCTGATAATC
66 TTCGGTCCAGATAATCTGGAATTTTCGATCAATCAACAATCGATGGTTGAACCGACCTGATAATC
12973 AGACCGGTTTTGAAAAAAATTTG
131 AGACCGGTTTTGAAAAAAATTTG
12996 TTAAATCATGGTTTTTGAAATCGGACCGATCAGTTCGATCGATTAAATTGGGTATCGGAAGCCTG
1 TTAAATCATGGTTTTTGAAATCGGACCGATCAGTTCGATCGATTAAATTGGGTATCGGAAGCCTG
*
13061 TTCGGTCCAGATAGTCTGGAATTTTCGATCAATCAACAATCGATGGTTGAACCGACCTGATAATC
66 TTCGGTCCAGATAATCTGGAATTTTCGATCAATCAACAATCGATGGTTGAACCGACCTGATAATC
13126 AGACCGGTTTTGAAAAAAATTTG
131 AGACCGGTTTTGAAAAAAATTTG
13149 TTAA
1 TTAA
13153 TGGTTGGATT
Statistics
Matches: 154, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 154 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (153 bp):
TTAAATCATGGTTTTTGAAATCGGACCGATCAGTTCGATCGATTAAATTGGGTATCGGAAGCCTG
TTCGGTCCAGATAATCTGGAATTTTCGATCAATCAACAATCGATGGTTGAACCGACCTGATAATC
AGACCGGTTTTGAAAAAAATTTG
Found at i:20332 original size:38 final size:37
Alignment explanation
Indices: 20277--20354 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 37
20267 TTGTTATCAT
*
20277 TTAGGCTTTGGTTATCAATTTTCCTCTTAGACTAATA
1 TTAGGCTTTGGTTATCAATTTTCCTCTTAGACAAATA
*
20314 TTAGCGCTTTGGTTATCAATTTTTCTCTTAGACAAATA
1 TTAG-GCTTTGGTTATCAATTTTCCTCTTAGACAAATA
20352 TTA
1 TTA
20355 TCAATATTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 4 0.11
38 34 0.89
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (37 bp):
TTAGGCTTTGGTTATCAATTTTCCTCTTAGACAAATA
Found at i:22187 original size:17 final size:17
Alignment explanation
Indices: 22165--22198 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22155 TAAAGAAGTT
22165 TTTGTAGTTAGCCTATG
1 TTTGTAGTTAGCCTATG
22182 TTTGTAGTTAGCCTATG
1 TTTGTAGTTAGCCTATG
22199 CGCATACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.47
Consensus pattern (17 bp):
TTTGTAGTTAGCCTATG
Found at i:24514 original size:17 final size:18
Alignment explanation
Indices: 24492--24526 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
24482 TTAAGGGAGA
24492 ATAAAGAAAGA-ATTAAG
1 ATAAAGAAAGAGATTAAG
24509 ATAAAGAAAGAGATTAAG
1 ATAAAGAAAGAGATTAAG
24527 GAAGTTGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (18 bp):
ATAAAGAAAGAGATTAAG
Found at i:27133 original size:41 final size:41
Alignment explanation
Indices: 27065--27149 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
27055 TATGGAACCC
*
27065 AAACCCTAACAAACAATATAAACCCTAGGTGAGAT-AAAAG
1 AAACCCTAAAAAACAATATAAACCCTAGGTGAGATAAAAAG
*
27105 AAACCCTCAAAAAAC-ATATTAAATCCTAGGTGAGATAAAAAG
1 AAACCCT-AAAAAACAATA-TAAACCCTAGGTGAGATAAAAAG
27147 AAA
1 AAA
27150 AAACATGAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 10 0.25
41 22 0.55
42 8 0.20
ACGTcount: A:0.54, C:0.18, G:0.12, T:0.16
Consensus pattern (41 bp):
AAACCCTAAAAAACAATATAAACCCTAGGTGAGATAAAAAG
Done.