Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012807.1 Corchorus olitorius cultivar O-4 contig12840, 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: 21221
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:490 original size:29 final size:27
Alignment explanation
Indices: 458--515 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
448 TAATTATTCC
458 AATT-AAGACTTAAAATCAATAAATATTAT
1 AATTCAAGAC-TAAAA--AATAAATATTAT
* *
487 AATTCAAGGCTAAAAAATAATTATTAT
1 AATTCAAGACTAAAAAATAAATATTAT
514 AA
1 AA
516 GAGTATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 13 0.50
29 9 0.35
30 4 0.15
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (27 bp):
AATTCAAGACTAAAAAATAAATATTAT
Found at i:1889 original size:21 final size:22
Alignment explanation
Indices: 1852--1910 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1842 GGTTTGGTAG
*
1852 AATTAATA-ACTTCATTTAT-AA
1 AATTAATATA-TTAATTTATCAA
*
1873 AATTAATATATTAATTTATCTA
1 AATTAATATATTAATTTATCAA
*
1895 AATTAAAATATTAATT
1 AATTAATATATTAATT
1911 ATTCCTATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTAATATATTAATTTATCAA
Found at i:2211 original size:156 final size:157
Alignment explanation
Indices: 2006--2306 Score: 421
Period size: 156 Copynumber: 1.9 Consensus size: 157
1996 ACAATTATTG
* * * *
2006 GCTCTTCACGGGTGCCCCTAGGGCACCCATTAGCCAAACAGTTTGTTTAATTGTGATAAGGTTTG
1 GCTCTTCACAGGTGCCACTAGGGCACCCATTAGCCAAACAGTTTGTTTAACTGTGATAAGGCTTG
* * * * * * *
2071 GTGGAATTAATTATAACTTCACTTATGTAA-TCA-ATCTATTACTTTATCT-AATTAAAATATTG
66 GTAGAATT-A--ATAACCTCACTTATGAAATTAATATATATTAATTTATCTAAATTAAAATATTA
2133 ATTATTCCAACTGAGATGGTGTAATAATTT
128 ATTATTCCAACTGAGATGGTGTAATAATTT
* *
2163 GCTCTTCACAGGTGCCACT-GGGCACCCATTAGCCAAACTGTTTGTTTAACTGTGTTAAGGCTTG
1 GCTCTTCACAGGTGCCACTAGGGCACCCATTAGCCAAACAGTTTGTTTAACTGTGATAAGGCTTG
2227 GTAGAATTAATAACCTCACTTATGAAATTAATATATATTAATTTATCTAAATTAAAATATTAATT
66 GTAGAATTAATAACCTCACTTATGAAATTAATATATATTAATTTATCTAAATTAAAATATTAATT
*
2292 ATTCCAATTGAGATG
131 ATTCCAACTGAGATG
2307 ATGAAACCCT
Statistics
Matches: 127, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
153 16 0.13
154 2 0.02
155 15 0.12
156 77 0.61
157 17 0.13
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (157 bp):
GCTCTTCACAGGTGCCACTAGGGCACCCATTAGCCAAACAGTTTGTTTAACTGTGATAAGGCTTG
GTAGAATTAATAACCTCACTTATGAAATTAATATATATTAATTTATCTAAATTAAAATATTAATT
ATTCCAACTGAGATGGTGTAATAATTT
Found at i:3381 original size:21 final size:21
Alignment explanation
Indices: 3339--3400 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
3329 TCAGGTTTGG
* *
3339 TAAAATTAATA-ACTTCACTTA
1 TAAAATTAATATA-TTAATTTA
3360 TAAAATTAATATATTAATTTA
1 TAAAATTAATATATTAATTTA
* *
3381 TCTAAATTAAAATATTAATT
1 T-AAAATTAATATATTAATT
3401 ATTCCAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATTAATATATTAATTTA
Found at i:3905 original size:21 final size:21
Alignment explanation
Indices: 3867--3910 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3857 TGGAATCAAT
*
3867 ATATTAATTTATCTAATTAAA
1 ATATTAATTTATCCAATTAAA
*
3888 ATATTAA-TTATTCCAATTGAA
1 ATATTAATTTA-TCCAATTAAA
3909 AT
1 AT
3911 GGCGTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (21 bp):
ATATTAATTTATCCAATTAAA
Found at i:5317 original size:4 final size:4
Alignment explanation
Indices: 5304--5337 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
5294 ATAATTAAAT
*
5304 GAAA -AAA GAAA GAAA GAAA GAAA GAAG GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
5338 GATTCGTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:9200 original size:22 final size:22
Alignment explanation
Indices: 9172--9214 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
9162 AATAATCTAC
9172 ACTATACTTCCAAACTTTTTTT
1 ACTATACTTCCAAACTTTTTTT
9194 ACTATACTTCCAAACTTTTTT
1 ACTATACTTCCAAACTTTTTT
9215 GTTTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (22 bp):
ACTATACTTCCAAACTTTTTTT
Found at i:10798 original size:1 final size:1
Alignment explanation
Indices: 10792--10822 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
10782 CGATTCTTGT
10792 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10823 CTCATATACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11630 original size:25 final size:25
Alignment explanation
Indices: 11596--11644 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
11586 CCAAATAATC
11596 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
*
11621 TTGAGCACTCTCGTTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
11645 CAAGCCAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:12969 original size:29 final size:28
Alignment explanation
Indices: 12921--12975 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
12911 AAGTGGAGCG
*
12921 AAAATAGCAAATTGGTCCCTCAAGTGAA
1 AAAATAGCAAATTAGTCCCTCAAGTGAA
* *
12949 AAAATATGCAATTTAGTCCCTGAAGTG
1 AAAATA-GCAAATTAGTCCCTCAAGTG
12976 GAGTTAACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (28 bp):
AAAATAGCAAATTAGTCCCTCAAGTGAA
Found at i:13184 original size:30 final size:31
Alignment explanation
Indices: 13130--13187 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
13120 AGGGTTGACA
*
13130 CAATTGCTCAATTAACTCCACTTCAGGGTCT
1 CAATTGCTCAACTAACTCCACTTCAGGGTCT
* *
13161 CAATTGCTC-ACTAAGTTCACTTCAGGG
1 CAATTGCTCAACTAACTCCACTTCAGGG
13188 ACCCATTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.31
Consensus pattern (31 bp):
CAATTGCTCAACTAACTCCACTTCAGGGTCT
Found at i:14051 original size:30 final size:31
Alignment explanation
Indices: 14015--14081 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
14005 GTGCAAATGG
14015 GTCCCTGAAG-TGAACTT-AGTGAGCAATTGA
1 GTCCCTGAAGTTGAA-TTAAGTGAGCAATTGA
* *
14045 GTCCCTGAAGTTGAATTAATTGAGCAATTGG
1 GTCCCTGAAGTTGAATTAAGTGAGCAATTGA
14076 GTCCCT
1 GTCCCT
14082 CACCAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (31 bp):
GTCCCTGAAGTTGAATTAAGTGAGCAATTGA
Found at i:15701 original size:2 final size:2
Alignment explanation
Indices: 15694--15723 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15684 ATCAAATAGT
15694 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
15724 CTATTTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20451 original size:44 final size:44
Alignment explanation
Indices: 20383--20527 Score: 281
Period size: 44 Copynumber: 3.3 Consensus size: 44
20373 CTTCTTCTTC
*
20383 TTCTTTGTCCTCTTCTTCTTGTTCCTGCGATGGTCGTTTTAAAT
1 TTCTCTGTCCTCTTCTTCTTGTTCCTGCGATGGTCGTTTTAAAT
20427 TTCTCTGTCCTCTTCTTCTTGTTCCTGCGATGGTCGTTTTAAAT
1 TTCTCTGTCCTCTTCTTCTTGTTCCTGCGATGGTCGTTTTAAAT
20471 TTCTCTGTCCTCTTCTTCTTGTTCCTGCGATGGTCGTTTTAAAT
1 TTCTCTGTCCTCTTCTTCTTGTTCCTGCGATGGTCGTTTTAAAT
20515 TTCTCTGTCCTCT
1 TTCTCTGTCCTCT
20528 ACTCCTCTCC
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 100 1.00
ACGTcount: A:0.08, C:0.26, G:0.15, T:0.51
Consensus pattern (44 bp):
TTCTCTGTCCTCTTCTTCTTGTTCCTGCGATGGTCGTTTTAAAT
Found at i:20563 original size:88 final size:85
Alignment explanation
Indices: 20380--20568 Score: 211
Period size: 88 Copynumber: 2.2 Consensus size: 85
20370 CTTCTTCTTC
*
20380 TTCTTCTTTGTCCTCTTCTTCTTGTTCCTGCGATGGTCGTTTTAAATTTCTCTGTCCTCTTCTTC
1 TTCTTCTCTGTCCTCTTCTTCTTGTTCCTGCGATGGTCGTTTTAAATTTCTCTGTCCTCTTCTTC
* * * * *
20445 TTGTTCCTGCGATGGTCGTT
66 CTCTTCCTGCAATGCTCGTG
*
20465 TTAAATTTCTCTGTCCTCTTCTTCTTGTTCCTGCGATGGTCGTTTTAAATTTCTCTGTCCTCTAC
1 TT---CTTCTCTGTCCTCTTCTTCTTGTTCCTGCGATGGTCGTTTTAAATTTCTCTGTCCTCT--
* *
20530 TCCTCTCCTCTTCC-GTAACTTCTC-TG
61 T-CT-TCCTCTTCCTGCAA-TGCTCGTG
20556 TTCTTCTCTGTCC
1 TTCTTCTCTGTCC
20569 AAAGTCCTTT
Statistics
Matches: 86, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
85 2 0.02
88 66 0.77
90 1 0.01
91 7 0.08
92 10 0.12
ACGTcount: A:0.08, C:0.29, G:0.13, T:0.50
Consensus pattern (85 bp):
TTCTTCTCTGTCCTCTTCTTCTTGTTCCTGCGATGGTCGTTTTAAATTTCTCTGTCCTCTTCTTC
CTCTTCCTGCAATGCTCGTG
Done.