Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012378.1 Corchorus olitorius cultivar O-4 contig12411, 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: 14239
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:3622 original size:20 final size:21
Alignment explanation
Indices: 3589--3628 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3579 TGATTGATTA
3589 AGAACTCTAGTAGA-ATTTAT
1 AGAACTCTAGTAGACATTTAT
3609 AGAACTCT-GTTAGACATTTA
1 AGAACTCTAG-TAGACATTTA
3629 ATTTTGTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 12 0.67
21 5 0.28
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (21 bp):
AGAACTCTAGTAGACATTTAT
Found at i:3884 original size:14 final size:14
Alignment explanation
Indices: 3865--3898 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3855 GCTGAGAAAG
3865 TTGAGTCATGACTC
1 TTGAGTCATGACTC
*
3879 TTGAGTCTTGACTC
1 TTGAGTCATGACTC
*
3893 ATGAGT
1 TTGAGT
3899 TTAAGAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (14 bp):
TTGAGTCATGACTC
Found at i:9452 original size:13 final size:13
Alignment explanation
Indices: 9434--9461 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
9424 CTCTTTTAAT
9434 TATCTTATCTTAC
1 TATCTTATCTTAC
9447 TATCTTATCTTAC
1 TATCTTATCTTAC
9460 TA
1 TA
9462 CTATATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (13 bp):
TATCTTATCTTAC
Found at i:10897 original size:22 final size:22
Alignment explanation
Indices: 10865--10924 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
10855 CAAATTTCCT
*
10865 TTACTATTATTTCATAAGGAGG
1 TTACTAATATTTCATAAGGAGG
**
10887 TTACTAATATTTCATGGGGAGG
1 TTACTAATATTTCATAAGGAGG
*
10909 TTA-TCAAAATTTCATA
1 TTACT-AATATTTCATA
10925 GTATGGTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (22 bp):
TTACTAATATTTCATAAGGAGG
Found at i:11115 original size:22 final size:22
Alignment explanation
Indices: 11090--11262 Score: 123
Period size: 22 Copynumber: 7.9 Consensus size: 22
11080 TATAGGAATA
**
11090 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* *
11112 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
11134 TTATCAAAATTACATAATGTA-A
1 TTATCAAAATTTCATAGTG-AGG
* * * *
11156 TTATTAAAATTTTATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
11178 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGTGAGG
**
11200 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
11222 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
*
11244 TTACCAAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
11263 GTATTTCTGG
Statistics
Matches: 116, Mismatches: 33, Indels: 4
0.76 0.22 0.03
Matches are distributed among these distances:
22 115 0.99
23 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:11476 original size:110 final size:103
Alignment explanation
Indices: 11275--11508 Score: 335
Period size: 110 Copynumber: 2.2 Consensus size: 103
11265 ATTTCTGGGG
* *
11275 AGGTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAACTTTTATTATAGAGT
1 AGGTTATCACAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAACTTTTATTATAGAAT
11340 AATCAAAATTTCAGGGAGGATATCAAAATTTCATATG-A
66 AATCAAAATTTCAGGGAGGATATCAAAATTTCATA-GCA
*
11378 ATGTTATCACAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATTATTTATTAAACTTTTATT
1 AGGTTATCACAATTTCATAGTATGGTTACCAAATTAGGAAGG-------TTATTAAACTTTTATT
* * *
11443 ATGGAATAATCAAATTTTCAGGGAGGATATCAAAATTTCATAGCG
59 ATAGAATAATCAAAATTTCAGGGAGGATATCAAAATTTCATAGCA
11488 AGGTTATCACAATTTCATAGT
1 AGGTTATCACAATTTCATAGT
11509 GTGATTATCA
Statistics
Matches: 116, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
103 40 0.34
109 1 0.01
110 75 0.65
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (103 bp):
AGGTTATCACAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAACTTTTATTATAGAAT
AATCAAAATTTCAGGGAGGATATCAAAATTTCATAGCA
Found at i:11495 original size:22 final size:22
Alignment explanation
Indices: 11465--11705 Score: 125
Period size: 22 Copynumber: 10.9 Consensus size: 22
11455 AATTTTCAGG
* *
11465 GAGGATATCAAAATTTCATAGC
1 GAGGTTATCAAAATTTCATAGT
*
11487 GAGGTTATCACAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* * *
11509 GTGATTATCAAAATTTCAGAGT
1 GAGGTTATCAAAATTTCATAGT
* *
11531 GTGATTA-CTAACAA-TTCATA-T
1 GAGGTTATC-AA-AATTTCATAGT
* * * *
11552 GGAGGTTTTTAAATTTTCATA-A
1 -GAGGTTATCAAAATTTCATAGT
* * *
11574 CATGGTTATCAATATATCATA-T
1 GA-GGTTATCAAAATTTCATAGT
* * * *
11596 GGAGGTTTTTAACATCTCATAGT
1 -GAGGTTATCAAAATTTCATAGT
* * *
11619 GTTGGTTATCAAAATTTCATTGG
1 G-AGGTTATCAAAATTTCATAGT
*
11642 GAAGTTATCAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
** * *
11664 GAGGTCT-TCAAAATCCCTTAGG
1 GAGGT-TATCAAAATTTCATAGT
*
11686 GAGGTTAACAAAATTTCATA
1 GAGGTTATCAAAATTTCATA
11706 AAAAGGCTAA
Statistics
Matches: 162, Mismatches: 46, Indels: 22
0.70 0.20 0.10
Matches are distributed among these distances:
21 5 0.03
22 137 0.85
23 20 0.12
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGT
Found at i:11797 original size:22 final size:22
Alignment explanation
Indices: 11622--11799 Score: 80
Period size: 22 Copynumber: 8.1 Consensus size: 22
11612 TCATAGTGTT
**
11622 GGTTATCAAAATTTCATTGGGAA
1 GGTTATCAAAATTTCA-TAAGAA
*
11645 -GTTATCAAAATTTCAT-AGTGA
1 GGTTATCAAAATTTCATAAG-AA
** * * *
11666 GGTCT-TCAAAATCCCTTAGGGA
1 GGT-TATCAAAATTTCATAAGAA
* *
11688 GGTTAACAAAATTTCATAAAAA
1 GGTTATCAAAATTTCATAAGAA
* ** *
11710 GGCTAAAAAAAATTT-ATAAAAA
1 GG-TTATCAAAATTTCATAAGAA
* * * *
11732 GGCTCTC-AAATTCCAT-AGTAT
1 GGTTATCAAAATTTCATAAG-AA
* * *
11753 CGTTATTAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAAGAA
11775 GGTTATCAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
11797 GGT
1 GGT
11800 CATAAAAAAT
Statistics
Matches: 112, Mismatches: 33, Indels: 21
0.67 0.20 0.13
Matches are distributed among these distances:
20 7 0.06
21 9 0.08
22 83 0.74
23 13 0.12
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGAA
Found at i:11807 original size:22 final size:22
Alignment explanation
Indices: 11760--11807 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
11750 TATCGTTATT
* * *
11760 AAAATTTCATAGGAAGGTTATC
1 AAAATTTCATAAGAAGGTCATA
11782 AAAATTTCATAAGAAGGTCATA
1 AAAATTTCATAAGAAGGTCATA
11804 AAAA
1 AAAA
11808 ATATTGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAAGAAGGTCATA
Found at i:13090 original size:13 final size:13
Alignment explanation
Indices: 13072--13101 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
13062 AACCGTTAAT
13072 ATCAAAATCATAA
1 ATCAAAATCATAA
*
13085 ATCAAAGTCATAA
1 ATCAAAATCATAA
13098 ATCA
1 ATCA
13102 GAGTAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (13 bp):
ATCAAAATCATAA
Found at i:14192 original size:2 final size:2
Alignment explanation
Indices: 14185--14232 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
14175 CTTCATTTAT
*
14185 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TCA -A AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
14226 TA TA TA T
1 TA TA TA T
14233 TTTACGG
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
1 2 0.05
2 39 0.93
3 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.