Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014468.1 Corchorus olitorius cultivar O-4 contig14501, 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: 51167
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:6932 original size:19 final size:19
Alignment explanation
Indices: 6908--6946 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6898 TACAATTCAA
6908 ATAAACTACATATATACCT
1 ATAAACTACATATATACCT
6927 ATAAACTACATATATACCT
1 ATAAACTACATATATACCT
6946 A
1 A
6947 CCAAATAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAACTACATATATACCT
Found at i:9462 original size:29 final size:29
Alignment explanation
Indices: 9393--9452 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
9383 CATTGAGTGG
* *
9393 TATCTAACTTTCTTCTCATAAATGAAAAT
1 TATCAAACTTTATTCTCATAAATGAAAAT
9422 TATCAAACTTTATTCTCATAAATGAAAAT
1 TATCAAACTTTATTCTCATAAATGAAAAT
9451 TA
1 TA
9453 CATTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (29 bp):
TATCAAACTTTATTCTCATAAATGAAAAT
Found at i:11987 original size:17 final size:17
Alignment explanation
Indices: 11967--12000 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11957 GCTAATAATA
*
11967 ATTATTCCATAATTATT
1 ATTATTCAATAATTATT
11984 ATTATTCAATAATTATT
1 ATTATTCAATAATTATT
12001 CCTAATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATTCAATAATTATT
Found at i:13497 original size:28 final size:27
Alignment explanation
Indices: 13455--13509 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
13445 ACTGAGACTA
*
13455 GACTCGAAACTGACTCGAAAAAACAAACT
1 GACTCGAAACCGACTC--AAAAACAAACT
13484 GACTC-AAACCGACTCAAAAACAAACT
1 GACTCGAAACCGACTCAAAAACAAACT
13510 CAAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 11 0.44
28 9 0.36
29 5 0.20
ACGTcount: A:0.49, C:0.27, G:0.11, T:0.13
Consensus pattern (27 bp):
GACTCGAAACCGACTCAAAAACAAACT
Found at i:19418 original size:20 final size:20
Alignment explanation
Indices: 19393--19430 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19383 TTCTCTGTTT
*
19393 TCTTTGTTTTTTTTAAGGAG
1 TCTTTGTTTTTTATAAGGAG
19413 TCTTTGTTTTTTATAAGG
1 TCTTTGTTTTTTATAAGG
19431 TTCTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.05, G:0.18, T:0.61
Consensus pattern (20 bp):
TCTTTGTTTTTTATAAGGAG
Found at i:19435 original size:19 final size:20
Alignment explanation
Indices: 19392--19436 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
19382 CTTCTCTGTT
*
19392 TTCTTTGTTTTTTTTAAGGA
1 TTCTTTGTTTTTTATAAGGA
*
19412 GTCTTTGTTTTTTATAAGG-
1 TTCTTTGTTTTTTATAAGGA
19431 TTCTTT
1 TTCTTT
19437 TTATTTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.13, C:0.07, G:0.16, T:0.64
Consensus pattern (20 bp):
TTCTTTGTTTTTTATAAGGA
Found at i:29371 original size:300 final size:300
Alignment explanation
Indices: 28829--29402 Score: 1078
Period size: 300 Copynumber: 1.9 Consensus size: 300
28819 TATTTCTCTC
28829 TCTCTCTCTCTTTTTCTCACAAATTAAAACCTTTCAAACACTTTACTTTTGAGAATCGAATCTGG
1 TCTCTCTCTCTTTTTCTCACAAATTAAAACCTTTCAAACACTTTACTTTTGAGAATCGAATCTGG
28894 AATCGATGATTTAAATGTTTCGATGTGACTTTGATCCAGTTTTTGCAATTCACTCTGATTTATTT
66 AATCGATGATTTAAATGTTTCGATGTGACTTTGATCCAGTTTTTGCAATTCACTCTGATTTATTT
28959 TTCGCTGCAACGCGCACAACATCATGTGTCTACAACTCTGTCATTTTTGACAAAATGACTGACAC
131 TTCGCTGCAACGCGCACAACATCATGTGTCTACAACTCTGTCATTTTTGACAAAATGACTGACAC
* *
29024 ACCCCACACTGTCATTTAGTTTTTATCGCAAAAACTTTTCAAGAGATTTTTGGTGCAACACTTGT
196 ACCCCACACTGTCATTTAATTTTTATCGCAAAAACTTTTCAAGAGATTTTTGGTGCAACACTTAT
29089 TATGATTGAATTCCCCCCTCCCCCACAATTAGTTGTTATT
261 TATGATTGAATTCCCCCCTCCCCCACAATTAGTTGTTATT
29129 TCTCTCTCTCTTTTTCTCACAAATTAAAACCTTTCAAACACTTTACTTTTGAGAATCGAATCTGG
1 TCTCTCTCTCTTTTTCTCACAAATTAAAACCTTTCAAACACTTTACTTTTGAGAATCGAATCTGG
29194 AATCGATGATTTAAATGTTTCGATGTGAC-TTGATCCAGTTTTTGCAATTCACTCTGATTTATTT
66 AATCGATGATTTAAATGTTTCGATGTGACTTTGATCCAGTTTTTGCAATTCACTCTGATTTATTT
*
29258 TTCGCTGCAACGCGCACAACATCATGTGTCTACAACTCTGTCATTTTTTACAAAATGACTGACAC
131 TTCGCTGCAACGCGCACAACATCATGTGTCTACAACTCTGTCATTTTTGACAAAATGACTGACAC
* * *
29323 GCTCCACACTGTCATTTAATTTTTATCGCAAAAAACTTTTCAAGAGATTTTTTGTGCAACACTTA
196 ACCCCACACTGTCATTTAATTTTTATCGC-AAAAACTTTTCAAGAGATTTTTGGTGCAACACTTA
29388 TTATGATTGAATTCC
260 TTATGATTGAATTCC
29403 AACCCCCCCC
Statistics
Matches: 267, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
299 125 0.47
300 142 0.53
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.38
Consensus pattern (300 bp):
TCTCTCTCTCTTTTTCTCACAAATTAAAACCTTTCAAACACTTTACTTTTGAGAATCGAATCTGG
AATCGATGATTTAAATGTTTCGATGTGACTTTGATCCAGTTTTTGCAATTCACTCTGATTTATTT
TTCGCTGCAACGCGCACAACATCATGTGTCTACAACTCTGTCATTTTTGACAAAATGACTGACAC
ACCCCACACTGTCATTTAATTTTTATCGCAAAAACTTTTCAAGAGATTTTTGGTGCAACACTTAT
TATGATTGAATTCCCCCCTCCCCCACAATTAGTTGTTATT
Found at i:39825 original size:24 final size:24
Alignment explanation
Indices: 39793--39840 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
39783 TCCGATGTCA
39793 TTGCTTTTGTCGGCGCTGGTGGTG
1 TTGCTTTTGTCGGCGCTGGTGGTG
*
39817 TTGCTTTTGTCGGCGTTGGTGGTG
1 TTGCTTTTGTCGGCGCTGGTGGTG
39841 CTGCCCCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.00, C:0.15, G:0.42, T:0.44
Consensus pattern (24 bp):
TTGCTTTTGTCGGCGCTGGTGGTG
Found at i:41001 original size:31 final size:29
Alignment explanation
Indices: 40939--41002 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 29
40929 AGATTGGGTA
*
40939 CTTAAATGACCTTTTCTAAAGATCAGGCC
1 CTTAAATGACCTTTTCTAAAGATCAGACC
*
40968 CTTAAATGACCTTTTCCCTAAAGGTCAGACC
1 CTTAAATGACCTTTT--CTAAAGATCAGACC
40999 CTTA
1 CTTA
41003 TTTGAACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 15 0.48
31 16 0.52
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (29 bp):
CTTAAATGACCTTTTCTAAAGATCAGACC
Found at i:41013 original size:31 final size:31
Alignment explanation
Indices: 40939--41013 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
40929 AGATTGGGTA
* *
40939 CTTAAATGACCTTTT--CTAAAGATCAGGCC
1 CTTAAATGAACTTTTCCCTAAAGATCAGACC
* *
40968 CTTAAATGACCTTTTCCCTAAAGGTCAGACC
1 CTTAAATGAACTTTTCCCTAAAGATCAGACC
**
40999 CTTATTTGAACTTTT
1 CTTAAATGAACTTTT
41014 AGCCTTAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 15 0.38
31 24 0.62
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (31 bp):
CTTAAATGAACTTTTCCCTAAAGATCAGACC
Found at i:42272 original size:19 final size:19
Alignment explanation
Indices: 42250--42300 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
42240 GGGCTGAAAT
42250 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
42269 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
42288 TAATT-ATTATTAA
1 TAATTAATTATTAA
42301 AAATCTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Done.