Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018653.1 Corchorus olitorius cultivar O-4 contig18686, 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: 59941
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:3718 original size:12 final size:11
Alignment explanation
Indices: 3691--3723 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
3681 ATTATTCTTT
3691 CAAAAAATAAA
1 CAAAAAATAAA
3702 CAAAAAATAAA
1 CAAAAAATAAA
3713 CGAAAAAATAA
1 C-AAAAAATAA
3724 GCATTGCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (11 bp):
CAAAAAATAAA
Found at i:4757 original size:40 final size:40
Alignment explanation
Indices: 4702--4781 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
4692 ATAAAGTTTG
*
4702 TTCATAATTTTGTTAATGTATATTAAGTAGTATTTTATTA
1 TTCATAATTTTGTTAATGTATATTAAGTAGTATTGTATTA
*
4742 TTCATAATTTTGTTAATGTATATTAAGTATTATTGTATTA
1 TTCATAATTTTGTTAATGTATATTAAGTAGTATTGTATTA
4782 ATTAGAATGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.55
Consensus pattern (40 bp):
TTCATAATTTTGTTAATGTATATTAAGTAGTATTGTATTA
Found at i:12485 original size:20 final size:21
Alignment explanation
Indices: 12447--12488 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12437 TCCTTTGTTG
12447 ATGATCTCCAATGGGCTTTAA
1 ATGATCTCCAATGGGCTTTAA
*
12468 ATGATCTCCGAT-GGCTTTAA
1 ATGATCTCCAATGGGCTTTAA
12488 A
1 A
12489 CTCTTCAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (21 bp):
ATGATCTCCAATGGGCTTTAA
Found at i:12591 original size:21 final size:21
Alignment explanation
Indices: 12565--12617 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
12555 CATTGGGCCT
12565 AATGGCATCTTCAATGGATCA
1 AATGGCATCTTCAATGGATCA
12586 AATGGCATCTTCAATGGATCA
1 AATGGCATCTTCAATGGATCA
12607 AATGGCATCTT
1 AATGGCATCTT
12618 AGGCAACTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (21 bp):
AATGGCATCTTCAATGGATCA
Found at i:14968 original size:97 final size:98
Alignment explanation
Indices: 14801--14979 Score: 351
Period size: 97 Copynumber: 1.8 Consensus size: 98
14791 TAAAAAAGTA
14801 GAGACATTTAAAGCAGTTCTTACCTTTTGAATCTGTTTGGAGATGCAACTTGTGGAGGAGAGGAA
1 GAGACATTTAAAGCAGTTCTTACCTTTTGAATCTGTTTGGAGATGCAACTTGTGGAGGAGAGGAA
14866 GTCATGTGTGGTGTGGAGATGCAACTTGTGGAG
66 GTCATGTGTGGTGTGGAGATGCAACTTGTGGAG
14899 GAGACATTTAAAGCAGTTCTTACCTTTTG-ATCTGTTTGGAGATGCAACTTGTGGAGGAGAGGAA
1 GAGACATTTAAAGCAGTTCTTACCTTTTGAATCTGTTTGGAGATGCAACTTGTGGAGGAGAGGAA
14963 GTCATGTGTGGTGTGGA
66 GTCATGTGTGGTGTGGA
14980 CTAACAAGTA
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
97 52 0.64
98 29 0.36
ACGTcount: A:0.25, C:0.11, G:0.32, T:0.31
Consensus pattern (98 bp):
GAGACATTTAAAGCAGTTCTTACCTTTTGAATCTGTTTGGAGATGCAACTTGTGGAGGAGAGGAA
GTCATGTGTGGTGTGGAGATGCAACTTGTGGAG
Found at i:17634 original size:13 final size:13
Alignment explanation
Indices: 17596--17655 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 13
17586 ATAAGTATGC
17596 AAATTATTTGGAT
1 AAATTATTTGGAT
* *
17609 ATATTA--T-GTT
1 AAATTATTTGGAT
17619 AAATTATTTGGAT
1 AAATTATTTGGAT
*
17632 AAATTA--T-GTT
1 AAATTATTTGGAT
17642 AAATTATTTGGAT
1 AAATTATTTGGAT
17655 A
1 A
17656 TAATAAGTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
10 15 0.43
11 2 0.06
12 2 0.06
13 16 0.46
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.48
Consensus pattern (13 bp):
AAATTATTTGGAT
Found at i:17694 original size:23 final size:23
Alignment explanation
Indices: 17596--17687 Score: 139
Period size: 23 Copynumber: 4.0 Consensus size: 23
17586 ATAAGTATGC
17596 AAATTATTTGGATATATTATGTT
1 AAATTATTTGGATATATTATGTT
*
17619 AAATTATTTGGATAAATTATGTT
1 AAATTATTTGGATATATTATGTT
* *
17642 AAATTATTTGGATATAATAAGTT
1 AAATTATTTGGATATATTATGTT
*
17665 AAATTATTTGTGTTATATTATGT
1 AAATTATTTG-GATATATTATGT
17688 AATTTATATT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
23 52 0.85
24 9 0.15
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (23 bp):
AAATTATTTGGATATATTATGTT
Found at i:39012 original size:35 final size:35
Alignment explanation
Indices: 38972--39046 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
38962 AGTTCGTTTA
38972 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
*
39007 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
39042 TGTTC
1 TGTTC
39047 GTTTATATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (35 bp):
TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
Found at i:39109 original size:16 final size:16
Alignment explanation
Indices: 39088--39119 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39078 TATAACTATT
39088 TATATATTAATAATAA
1 TATATATTAATAATAA
*
39104 TATATATTATTAATAA
1 TATATATTAATAATAA
39120 AAATTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:40322 original size:20 final size:20
Alignment explanation
Indices: 40256--40345 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 20
40246 CCTAAATAAA
* *
40256 AAATAATAATTAATTCTAGT
1 AAATAATAAATAATTATAGT
*
40276 AAATCAA-AATTATAATTA-ATT
1 AAAT-AATAA--ATAATTATAGT
40297 ACAATAATAAATAATTATAGT
1 A-AATAATAAATAATTATAGT
40318 AAATAAT---TAATTATAGT
1 AAATAATAAATAATTATAGT
40335 CAAATAATAAA
1 -AAATAATAAA
40346 ATAACTAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
17 10 0.18
18 7 0.12
20 19 0.34
21 10 0.18
22 10 0.18
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (20 bp):
AAATAATAAATAATTATAGT
Found at i:40328 original size:17 final size:17
Alignment explanation
Indices: 40287--40342 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
40277 AATCAAAATT
* *
40287 ATAATTAATTACAAT-A
1 ATAATTAATTATAGTAA
*
40303 ATAAATAATTATAGTAA
1 ATAATTAATTATAGTAA
40320 ATAATTAATTATAGTCAA
1 ATAATTAATTATAGT-AA
40338 ATAAT
1 ATAAT
40343 AAAATAACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 12 0.35
17 15 0.44
18 7 0.21
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (17 bp):
ATAATTAATTATAGTAA
Found at i:40694 original size:19 final size:19
Alignment explanation
Indices: 40670--40708 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
40660 CATGATGTTC
40670 TTGAAGAAGTTTAGAGAGT
1 TTGAAGAAGTTTAGAGAGT
*
40689 TTGAAGAAGTTTTGAGAGT
1 TTGAAGAAGTTTAGAGAGT
40708 T
1 T
40709 AGAAAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (19 bp):
TTGAAGAAGTTTAGAGAGT
Found at i:41881 original size:62 final size:62
Alignment explanation
Indices: 41778--41899 Score: 219
Period size: 62 Copynumber: 2.0 Consensus size: 62
41768 TTGAATTCTA
*
41778 ATTTTGATGTTTGGGCATAGAGATTTATTTGAATTGTAATGAGATTTCACTGGGTTTGTTTTC
1 ATTTAGATGTTTGGGCATAGAGATTTATTTGAATTGTAATGAGATTTCACTGGG-TTGTTTTC
41841 ATTTAGATGTTTGGGCAT-GAGATTTATTTGAATTGTAATGAGATTTCACTGGGTTGTTT
1 ATTTAGATGTTTGGGCATAGAGATTTATTTGAATTGTAATGAGATTTCACTGGGTTGTTT
41900 GTTGGCTAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
61 6 0.10
62 35 0.60
63 17 0.29
ACGTcount: A:0.23, C:0.06, G:0.25, T:0.47
Consensus pattern (62 bp):
ATTTAGATGTTTGGGCATAGAGATTTATTTGAATTGTAATGAGATTTCACTGGGTTGTTTTC
Done.