Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020730.1 Corchorus olitorius cultivar O-4 contig20763, 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: 29820
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4514 original size:5 final size:5
Alignment explanation
Indices: 4504--4542 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
4494 TTCTCTCCTT
* *
4504 CTTTC CTTTC CTTTC CTTTG CTTTG CTTTC CTTTC CTTT
1 CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTTT
4543 TTCCCCTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.00, C:0.33, G:0.05, T:0.62
Consensus pattern (5 bp):
CTTTC
Found at i:5869 original size:21 final size:19
Alignment explanation
Indices: 5845--5902 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
5835 ACTGTTCTAA
5845 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
5866 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
*
5885 TAATCTCATCTATACAGT
1 TAATCTCATCTGTACAGT
5903 TGCTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:14706 original size:61 final size:61
Alignment explanation
Indices: 14633--14755 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
14623 CCTCCTACTC
14633 ACTATCTCTCTTCATAAATTCTGTTACCACTAGCAAGGGTAACTTGGGTAAGTTAAGTAAA
1 ACTATCTCTCTTCATAAATTCTGTTACCACTAGCAAGGGTAACTTGGGTAAGTTAAGTAAA
14694 ACTATCTCTCTTCATAAATTCTGTTACCACTAGCAAGGGTAACTTGGGTAAGTTAAGTAAA
1 ACTATCTCTCTTCATAAATTCTGTTACCACTAGCAAGGGTAACTTGGGTAAGTTAAGTAAA
14755 A
1 A
14756 TATGCATTAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (61 bp):
ACTATCTCTCTTCATAAATTCTGTTACCACTAGCAAGGGTAACTTGGGTAAGTTAAGTAAA
Found at i:16558 original size:17 final size:17
Alignment explanation
Indices: 16536--16569 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16526 TGTCGCGTAC
16536 CTGGTTATCGTGGGTGA
1 CTGGTTATCGTGGGTGA
16553 CTGGTTATCGTGGGTGA
1 CTGGTTATCGTGGGTGA
16570 GTCTCACAAC
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:0.12, C:0.12, G:0.41, T:0.35
Consensus pattern (17 bp):
CTGGTTATCGTGGGTGA
Found at i:22616 original size:2 final size:2
Alignment explanation
Indices: 22609--22641 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22599 AATCCAAAGT
22609 TA TA TA TA TA TA TA 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 T
22642 GGTGAGATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23044 original size:59 final size:59
Alignment explanation
Indices: 22972--23092 Score: 242
Period size: 59 Copynumber: 2.1 Consensus size: 59
22962 TAGGCTGTTT
22972 TTAGAAAAGAATATTGTTACCTCACTTGTTGCTTATGTTAAAAATCTTTTTACCCATGC
1 TTAGAAAAGAATATTGTTACCTCACTTGTTGCTTATGTTAAAAATCTTTTTACCCATGC
23031 TTAGAAAAGAATATTGTTACCTCACTTGTTGCTTATGTTAAAAATCTTTTTACCCATGC
1 TTAGAAAAGAATATTGTTACCTCACTTGTTGCTTATGTTAAAAATCTTTTTACCCATGC
23090 TTA
1 TTA
23093 CAACAGTACT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (59 bp):
TTAGAAAAGAATATTGTTACCTCACTTGTTGCTTATGTTAAAAATCTTTTTACCCATGC
Found at i:23503 original size:30 final size:30
Alignment explanation
Indices: 23445--23504 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
23435 GCTTATTCAT
* *
23445 TTTGCTTTGCATTTGTTATCGTTGTCCTCA
1 TTTGCTTTGCATTTGCTATCGTTATCCTCA
23475 TTTGCTTTGCATTTGCTATC-TCTATCCTCA
1 TTTGCTTTGCATTTGCTATCGT-TATCCTCA
23505 AAGCTACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.12, C:0.23, G:0.13, T:0.52
Consensus pattern (30 bp):
TTTGCTTTGCATTTGCTATCGTTATCCTCA
Found at i:26412 original size:30 final size:30
Alignment explanation
Indices: 26371--26430 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
26361 GCTTATTTAT
26371 TTTGCTTTGCATTCGTTATCTCTATCCTCA
1 TTTGCTTTGCATTCGTTATCTCTATCCTCA
* *
26401 TTTGTTTTGCATTTGTTATCTCTATCCTCA
1 TTTGCTTTGCATTCGTTATCTCTATCCTCA
26431 AAACTACTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.13, C:0.23, G:0.10, T:0.53
Consensus pattern (30 bp):
TTTGCTTTGCATTCGTTATCTCTATCCTCA
Found at i:26540 original size:21 final size:21
Alignment explanation
Indices: 26510--26551 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
26500 ATAATGTATG
*
26510 GAAAATAGATCACATTCCAAA
1 GAAAAAAGATCACATTCCAAA
26531 GAAAAAAGATCACATTCCAAA
1 GAAAAAAGATCACATTCCAAA
26552 ACTCATACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.19, G:0.10, T:0.17
Consensus pattern (21 bp):
GAAAAAAGATCACATTCCAAA
Found at i:27176 original size:23 final size:23
Alignment explanation
Indices: 27133--27176 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
27123 AATTTTTTTT
*
27133 AATTAAAATAGTAAAATGATAAA
1 AATTAAAATAGTAAAAGGATAAA
*
27156 AATT-AAATAGTTATAAGGATA
1 AATTAAAATAG-TAAAAGGATA
27177 TTATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (23 bp):
AATTAAAATAGTAAAAGGATAAA
Found at i:28904 original size:3 final size:3
Alignment explanation
Indices: 28894--28939 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
28884 TTTGGAATTT
28894 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
28940 TATTAGTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:29074 original size:2 final size:2
Alignment explanation
Indices: 29067--29106 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29057 TAATATGGAG
29067 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
29107 ACTAACTTTA
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:29704 original size:11 final size:11
Alignment explanation
Indices: 29690--29724 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
29680 TTTTCTGTTT
29690 TTTTGTTTTTG
1 TTTTGTTTTTG
*
29701 TTTTGTTTTCG
1 TTTTGTTTTTG
29712 TTTTGTTTTTG
1 TTTTGTTTTTG
29723 TT
1 TT
29725 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Done.