Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021753.1 Corchorus olitorius cultivar O-4 contig21786, 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: 85505
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4685 original size:13 final size:13
Alignment explanation
Indices: 4667--4693 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4657 AAACAACTAA
4667 AAAGCACTTCTGG
1 AAAGCACTTCTGG
4680 AAAGCACTTCTGG
1 AAAGCACTTCTGG
4693 A
1 A
4694 TTTTCCGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAGCACTTCTGG
Found at i:5541 original size:46 final size:46
Alignment explanation
Indices: 5488--5580 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
5478 CAAGCAGGGC
5488 ATATTAATGAATTTAATGGTCTTTAACCAACTAAGTAAAAAAAAAA
1 ATATTAATGAATTTAATGGTCTTTAACCAACTAAGTAAAAAAAAAA
5534 ATATTAATGAATTTAATGGTCTTTAACCAACTAAGTAAAAAAAAAA
1 ATATTAATGAATTTAATGGTCTTTAACCAACTAAGTAAAAAAAAAA
5580 A
1 A
5581 ACTAAAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.30
Consensus pattern (46 bp):
ATATTAATGAATTTAATGGTCTTTAACCAACTAAGTAAAAAAAAAA
Found at i:10362 original size:15 final size:15
Alignment explanation
Indices: 10330--10371 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
10320 AAATTGAAGT
* *
10330 TTTTTCCAGAAAAGC
1 TTTTTCCAGAAGACC
*
10345 TTTTTCCAGAAGCCC
1 TTTTTCCAGAAGACC
10360 TTTTT-CAGAAGA
1 TTTTTCCAGAAGA
10372 GTTTTAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (15 bp):
TTTTTCCAGAAGACC
Found at i:15248 original size:13 final size:14
Alignment explanation
Indices: 15225--15257 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
15215 AATGGAATAT
15225 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
15239 AAAAAG-AAAAAAG
1 AAAAAGAAAAAAAG
15252 AAAAAG
1 AAAAAG
15258 TGAATTCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:18542 original size:23 final size:23
Alignment explanation
Indices: 18510--18563 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
18500 TGAGAAAGTT
18510 ATTTTCCCTATCTAACTTACCAC
1 ATTTTCCCTATCTAACTTACCAC
*
18533 ATTTTTCCTATCTAACTTACCAC
1 ATTTTCCCTATCTAACTTACCAC
18556 ATTTTCCC
1 ATTTTCCC
18564 ATTACTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.24, C:0.33, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTTCCCTATCTAACTTACCAC
Found at i:19069 original size:18 final size:18
Alignment explanation
Indices: 19046--19081 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19036 ATCAAAAATT
* *
19046 AAAATTATCAATTGAAAG
1 AAAATTACCAATTAAAAG
19064 AAAATTACCAATTAAAAG
1 AAAATTACCAATTAAAAG
19082 GTAAAAATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.25
Consensus pattern (18 bp):
AAAATTACCAATTAAAAG
Found at i:22039 original size:2 final size:2
Alignment explanation
Indices: 22032--22062 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22022 CATAATTTTG
22032 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 T
22063 TTTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22999 original size:12 final size:13
Alignment explanation
Indices: 22961--23002 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
22951 TTTTGAAAAA
*
22961 AAAAACAAAAGAG
1 AAAAATAAAAGAG
22974 AAAAATTAAAAGAG
1 AAAAA-TAAAAGAG
*
22988 AAAAA-GAAAGAG
1 AAAAATAAAAGAG
23000 AAA
1 AAA
23003 GGACTTAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 9 0.35
13 5 0.19
14 12 0.46
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (13 bp):
AAAAATAAAAGAG
Found at i:23523 original size:29 final size:29
Alignment explanation
Indices: 23481--23541 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
23471 TATTACTTAT
*
23481 ACCAAATTTTAA-TTTTATCCAAATAATTA
1 ACCAAAATTTAATTTTTAT-CAAATAATTA
*
23510 ACCAAAATTTAATTTTTATCTAATAATTA
1 ACCAAAATTTAATTTTTATCAAATAATTA
23539 ACC
1 ACC
23542 TGCCACATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (29 bp):
ACCAAAATTTAATTTTTATCAAATAATTA
Found at i:26294 original size:11 final size:11
Alignment explanation
Indices: 26278--26303 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
26268 CTGTTTATTT
26278 TTTTATTTTTA
1 TTTTATTTTTA
26289 TTTTATTTTTA
1 TTTTATTTTTA
26300 TTTT
1 TTTT
26304 TTATTCTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:26304 original size:18 final size:19
Alignment explanation
Indices: 26271--26308 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
26261 TAACTATCTG
*
26271 TTTATTTTTTTATTTTTAT
1 TTTATTTTTATATTTTTAT
26290 TTTATTTTTAT-TTTTTAT
1 TTTATTTTTATATTTTTAT
26308 T
1 T
26309 CTGCTCTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTATTTTTATATTTTTAT
Found at i:28551 original size:3 final size:3
Alignment explanation
Indices: 28543--28570 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28533 GCTCAAAAGT
28543 CAC CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC C
28571 GATGCTTGAA
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:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:47439 original size:10 final size:10
Alignment explanation
Indices: 47420--47461 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
47410 ATTGGATTTT
47420 TTTTGTATGA
1 TTTTGTATGA
*
47430 TTTTGGATGA
1 TTTTGTATGA
*
47440 TTTT-TTTGA
1 TTTTGTATGA
47449 TTTTGTATGA
1 TTTTGTATGA
47459 TTT
1 TTT
47462 GAATTGAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.17, C:0.00, G:0.19, T:0.64
Consensus pattern (10 bp):
TTTTGTATGA
Found at i:56236 original size:5 final size:5
Alignment explanation
Indices: 56226--56253 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
56216 TGACCAGCAA
56226 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
56254 TGGAATAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:58939 original size:16 final size:15
Alignment explanation
Indices: 58917--58960 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
58907 TTAAAGTTTG
*
58917 AATTCAGTACTTATGA
1 AATTCAGTACTTA-AA
*
58933 GATTCAGTA-TTAAA
1 AATTCAGTACTTAAA
58947 AATTCAGTACTTAA
1 AATTCAGTACTTAA
58961 TCTTTCAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.38
15 7 0.29
16 8 0.33
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (15 bp):
AATTCAGTACTTAAA
Found at i:58982 original size:14 final size:15
Alignment explanation
Indices: 58949--58982 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
58939 GTATTAAAAA
*
58949 TTCAGTACTTAATCT
1 TTCAGCACTTAATCT
58964 TTCAGCACTTAAT-T
1 TTCAGCACTTAATCT
58978 TTCAG
1 TTCAG
58983 TTTTATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (15 bp):
TTCAGCACTTAATCT
Found at i:67641 original size:7 final size:7
Alignment explanation
Indices: 67609--67650 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
67599 ACAAAAAATC
67609 TTTTGCT
1 TTTTGCT
*
67616 TTTAGCT
1 TTTTGCT
67623 TAATTTGC-
1 T--TTTGCT
67631 TTTTGCT
1 TTTTGCT
67638 TTTTGCT
1 TTTTGCT
67645 TTTTGC
1 TTTTGC
67651 GTTTGTGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
6 5 0.17
7 20 0.67
8 1 0.03
9 4 0.13
ACGTcount: A:0.07, C:0.14, G:0.14, T:0.64
Consensus pattern (7 bp):
TTTTGCT
Found at i:81350 original size:11 final size:11
Alignment explanation
Indices: 81334--81364 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
81324 GAATTTGGAT
81334 TAAAGAATACA
1 TAAAGAATACA
81345 TAAAG-ATACA
1 TAAAGAATACA
81355 TAAAGAATAC
1 TAAAGAATAC
81365 CAGCAGCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.19
Consensus pattern (11 bp):
TAAAGAATACA
Found at i:81913 original size:6 final size:6
Alignment explanation
Indices: 81902--81948 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
81892 CCTACTCTCA
* *
81902 AGTCTG AGTCTG AGTCCG AGTCCG AGTCCG AGTCCG AGTCCG AGTCC
1 AGTCCG AGTCCG AGTCCG AGTCCG AGTCCG AGTCCG AGTCCG AGTCC
81949 AATAAGAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.17, C:0.30, G:0.32, T:0.21
Consensus pattern (6 bp):
AGTCCG
Found at i:83364 original size:15 final size:15
Alignment explanation
Indices: 83344--83375 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
83334 ATTCCAAATC
83344 AGGGAATGGAAGGAA
1 AGGGAATGGAAGGAA
83359 AGGGAATGGAAGGAA
1 AGGGAATGGAAGGAA
83374 AG
1 AG
83376 TGATTATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.47, T:0.06
Consensus pattern (15 bp):
AGGGAATGGAAGGAA
Done.