Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018417.1 Corchorus olitorius cultivar O-4 contig18450, 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: 25188
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:3170 original size:21 final size:20
Alignment explanation
Indices: 3129--3167 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3119 TATAGCATCT
3129 TTTTAAAATTTTTATTATTA
1 TTTTAAAATTTTTATTATTA
*
3149 TTTTATAAGTTTTT-TTATT
1 TTTTA-AAATTTTTATTATT
3168 TATATTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTAAAATTTTTATTATTA
Found at i:3601 original size:36 final size:36
Alignment explanation
Indices: 3561--3633 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
3551 ATCTTATTGC
*
3561 TATTTAACTTGATTTTTTCGTCATTTCAATATTGGT
1 TATTTAACTTGATTTTTTCGCCATTTCAATATTGGT
3597 TATTTAACTTGATTTTTTCGCCATTTCAATATTGGT
1 TATTTAACTTGATTTTTTCGCCATTTCAATATTGGT
3633 T
1 T
3634 TTTTCGTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.12, G:0.11, T:0.55
Consensus pattern (36 bp):
TATTTAACTTGATTTTTTCGCCATTTCAATATTGGT
Found at i:4040 original size:178 final size:178
Alignment explanation
Indices: 3771--4093 Score: 510
Period size: 178 Copynumber: 1.8 Consensus size: 178
3761 CCGATTAAGG
* *
3771 TGATTTAAGTGTCTAATAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTAATAAAAGATTGTTCCATGATCTACAACTTTCATAAAGGACTCGAAAACTA
* *
3836 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAA-AATTTGTTGTTTCGGTTAAC-GAGAATA
66 AATTTAATGTTTCAAGTATAAAAAATGCTTCC-AAAGAATTAGTTGTTTCGGTTAACAGA-AATA
*
3899 GATGGTCCACTTAATATTATATAACTTTTGCTCCAAATGTTTGATTGAGA
129 GACGGTCCACTTAATATTATATAACTTTTGCTCCAAATGTTTGATTGAGA
**
3949 TGATTCAAGTGTCTCTTGAAAAG-TTGTTCCATGATCTACAACTTTCATAAAGGACTCGAAAACT
1 TGATTCAAGTGTCTAAT-AAAAGATTGTTCCATGATCTACAACTTTCATAAAGGACTCGAAAACT
4013 AAATTTAATG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACAGAAATA
65 AAATTTAATGTTTCAA-GTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACAGAAATA
*
4077 GACGGTCTACTTAATAT
129 GACGGTCCACTTAATAT
4094 AACATAATTT
Statistics
Matches: 133, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
177 8 0.06
178 118 0.89
179 7 0.05
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (178 bp):
TGATTCAAGTGTCTAATAAAAGATTGTTCCATGATCTACAACTTTCATAAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACAGAAATAGA
CGGTCCACTTAATATTATATAACTTTTGCTCCAAATGTTTGATTGAGA
Found at i:11639 original size:179 final size:178
Alignment explanation
Indices: 11258--11712 Score: 497
Period size: 179 Copynumber: 2.6 Consensus size: 178
11248 TATCCGATCA
* * *
11258 AGGTGATTCAACTGTCTATTAAAAGGTTGTTCCATGATCTACAACTTTCATGAAAGACTCGAAAA
1 AGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTC-AAAA
* * * *
11323 -CT-AATTTAATGTTTCAAGTATCAAAAAAGCTTCCGAATAATTAGTTGTTTCGGTTAACGGGAA
65 GCTAAATTTAATGTTTCAAGTATCAAAAAAGCTTCCAAAAAATTAATTGTTTCGGTTAACGAGAA
* * * **
11386 TGGACGATCCACTTAATATAACATTACTTTTGCTCCAGATGTCTTATTG
130 TGAACGATCCACTTAATATAACATAACTTTTGCTCCAAATGTCCGATTG
* * * *
11435 AGCTGATTCAAGTGTCTCA-TAAAAGGTTATTTTATGATCTACAACTTTCATGCAGGACTCAAAA
1 AGGTGATTCAAGTGTCT-ATTAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCAAAA
* * *
11499 GCTAAATTTAATGTTTCAAGTATTAAAAAATGCTTCCAAAAAATTAATTTTTTCGGTTAGCGAGA
65 GCTAAATTTAATGTTTCAAGTATCAAAAAA-GCTTCCAAAAAATTAATTGTTTCGGTTAACGAGA
* * * * *
11564 ATGAATGGTCCACTTAGTA-ATACATAATTTTTGTTCCAAATGTCCGATTG
129 ATGAACGATCCACTTAATATA-ACATAACTTTTGCTCCAAATGTCCGATTG
* * * * * * * **
11614 AGGTGATTTAAGTGTCTGTTAAAAGGATGTTTCGTGATGTTCAACTTTCATGTAGGACTTGAAAG
1 AGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCAAAAG
* * * *
11679 CTAAATCTT-ATTTTTCAAATACCAAAAATGCTTC
66 CTAAAT-TTAATGTTTCAAGTATCAAAAAAGCTTC
11713 TGAAAAGTTT
Statistics
Matches: 230, Mismatches: 41, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
176 4 0.02
177 53 0.23
178 32 0.14
179 139 0.60
180 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (178 bp):
AGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCAAAAG
CTAAATTTAATGTTTCAAGTATCAAAAAAGCTTCCAAAAAATTAATTGTTTCGGTTAACGAGAAT
GAACGATCCACTTAATATAACATAACTTTTGCTCCAAATGTCCGATTG
Found at i:12534 original size:2 final size:2
Alignment explanation
Indices: 12527--12552 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12517 CAAATGAAAC
12527 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12553 GGCTAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13089 original size:60 final size:60
Alignment explanation
Indices: 12996--13115 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
12986 GTGGCATTTT
12996 CACGTCAGCTCTCATATGGGCCCCACCTTAGCATTTAGGGTCATATGGGCCCACATGAGC
1 CACGTCAGCTCTCATATGGGCCCCACCTTAGCATTTAGGGTCATATGGGCCCACATGAGC
13056 CACGTCAGCTCTCATATGGGCCCCACCTTAGCATTTAGGGTCATATGGGCCCACATGAGC
1 CACGTCAGCTCTCATATGGGCCCCACCTTAGCATTTAGGGTCATATGGGCCCACATGAGC
13116 ACTGACGTGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.22, C:0.32, G:0.23, T:0.23
Consensus pattern (60 bp):
CACGTCAGCTCTCATATGGGCCCCACCTTAGCATTTAGGGTCATATGGGCCCACATGAGC
Found at i:13107 original size:29 final size:29
Alignment explanation
Indices: 13007--13107 Score: 114
Period size: 29 Copynumber: 3.4 Consensus size: 29
12997 ACGTCAGCTC
13007 TCATATGGGCCCCACCTTAGCATTTAGGG
1 TCATATGGGCCCCACCTTAGCATTTAGGG
* * * * **
13036 TCATATGGG-CCCACATGAGCCACGTCAGCTC
1 TCATATGGGCCCCACCTTAG-CA-TTTAG-GG
13067 TCATATGGGCCCCACCTTAGCATTTAGGG
1 TCATATGGGCCCCACCTTAGCATTTAGGG
13096 TCATATGGGCCC
1 TCATATGGGCCC
13108 ACATGAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
28 8 0.14
29 23 0.41
30 6 0.11
31 11 0.20
32 8 0.14
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.25
Consensus pattern (29 bp):
TCATATGGGCCCCACCTTAGCATTTAGGG
Found at i:18070 original size:2 final size:2
Alignment explanation
Indices: 18063--18092 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18053 AGACCTTATT
18063 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
18093 AAACTAATTA
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
Done.