Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007098.1 Corchorus capsularis cultivar CVL-1 contig07119, 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: 25235
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4260 original size:17 final size:16
Alignment explanation
Indices: 4220--4270 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
4210 CATGTAATCT
*
4220 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
4236 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
4253 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
4270 T
1 T
4271 GGGGGTGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:7515 original size:21 final size:22
Alignment explanation
Indices: 7479--7520 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
7469 AACCGACGGG
7479 TCGGTTCCGTCGGGTTCTCGGA
1 TCGGTTCCGTCGGGTTCTCGGA
7501 TCGGTTCCG-CGGGTTCTCGG
1 TCGGTTCCGTCGGGTTCTCGG
7521 GTCTAGTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.02, C:0.29, G:0.38, T:0.31
Consensus pattern (22 bp):
TCGGTTCCGTCGGGTTCTCGGA
Found at i:7594 original size:18 final size:18
Alignment explanation
Indices: 7573--7628 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 18
7563 ATAAAAGTAA
7573 ATATATATTTATTATAAT
1 ATATATATTTATTATAAT
7591 ATATATA---ATTATAAT
1 ATATATATTTATTATAAT
7606 -TATA-ATTTA-TATAAT
1 ATATATATTTATTATAAT
*
7621 AAATATAT
1 ATATATAT
7629 AGAAAGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.03
14 4 0.12
15 14 0.44
16 4 0.12
17 2 0.06
18 7 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATTTATTATAAT
Found at i:11420 original size:24 final size:24
Alignment explanation
Indices: 11393--11441 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
11383 TGAAACTGCA
11393 TGAATATCATAAACCAATCATTTT
1 TGAATATCATAAACCAATCATTTT
11417 TGAATATCATAAACCAATCATTTT
1 TGAATATCATAAACCAATCATTTT
11441 T
1 T
11442 TAAATTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.39
Consensus pattern (24 bp):
TGAATATCATAAACCAATCATTTT
Found at i:15077 original size:36 final size:36
Alignment explanation
Indices: 15019--15088 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
15009 TGCATTATCA
*
15019 AACAAAATTAATGTGTAAGTTTATAGAGTTAATCGC
1 AACAAAATTAATGTGTAAGTTTATAAAGTTAATCGC
* * *
15055 AACAAAATTAGTTTGTAGGTTTATAAAGTTAATC
1 AACAAAATTAATGTGTAAGTTTATAAAGTTAATC
15089 ATAACAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (36 bp):
AACAAAATTAATGTGTAAGTTTATAAAGTTAATCGC
Found at i:15095 original size:36 final size:35
Alignment explanation
Indices: 15015--15096 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 35
15005 AAATTGCATT
*
15015 ATCAAACAAAATTAATGTGTAAGTTTATAGAGTTA
1 ATCAAACAAAATTAATGTGTAAGTTTATAAAGTTA
* * * *
15050 ATCGCAACAAAATTAGTTTGTAGGTTTATAAAGTTA
1 ATC-AAACAAAATTAATGTGTAAGTTTATAAAGTTA
15086 ATCATAACAAA
1 ATCA-AACAAA
15097 TAAAAATAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
35 3 0.08
36 36 0.92
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (35 bp):
ATCAAACAAAATTAATGTGTAAGTTTATAAAGTTA
Found at i:20734 original size:143 final size:142
Alignment explanation
Indices: 20400--20804 Score: 650
Period size: 145 Copynumber: 2.8 Consensus size: 142
20390 TTGTTTCGTC
* * *
20400 TTTTCCCACTTGGCCAATTACTTAAATGCCCTAACTTTTGATTCTTAAGGTGATTAAATAACTAG
1 TTTTTCCACTTGGCCGATTACTTAAATG-CCTAACTTTTGATTCTTGAGGTGATTAAATAACTAG
* * *
20465 ACTTTTTGGTCATTTATCAATTGATTTTAATAGAGTAG-GGAATTACTAAAAGATCCCTACCCCG
65 ACTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACT--AA-ATCCCTAACCCG
*
20529 AATTAATATTTCCATC
127 AATTAATATTTCCATA
*
20545 TTTTTCCACTTGGCTGATTACTTAAATGCTCTAACTTTTGATTCTTGAGGTGATTAAATAACTAG
1 TTTTTCCACTTGGCCGATTACTTAAATGC-CTAACTTTTGATTCTTGAGGTGATTAAATAACTAG
*
20610 ACTTTTTGGTCATTTCTCAATTAACTTTAATAGAGTAGTGGAATTACTAAATCCCTAACCCGAAT
65 ACTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAATCCCTAACCCGAAT
*
20675 TAATATTTCCGTA
130 TAATATTTCCATA
20688 TTTTTCCACTTGGCCGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGTGATTAAATAACTAG
1 TTTTTCCACTTGGCCGATTACTTAAATG-CCTAACTTTTGATTCTTGAGGTGATTAAATAACTAG
20753 ACTTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAA
65 AC-TTTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAA
20805 AGATCCCTAC
Statistics
Matches: 244, Mismatches: 12, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
143 89 0.36
144 52 0.21
145 94 0.39
146 9 0.04
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.40
Consensus pattern (142 bp):
TTTTTCCACTTGGCCGATTACTTAAATGCCTAACTTTTGATTCTTGAGGTGATTAAATAACTAGA
CTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAATCCCTAACCCGAATT
AATATTTCCATA
Found at i:21066 original size:166 final size:166
Alignment explanation
Indices: 20695--21107 Score: 587
Period size: 166 Copynumber: 2.5 Consensus size: 166
20685 GTATTTTTCC
* *
20695 ACTTGGCCGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGTGATTAAATAACTAGACTTTTT
1 ACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA-AC-TTTT
* * * * * *
20760 TGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGGCTTGC
64 TGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGA
** * * *
20825 TTTTGGAGTTAGAGAACTTATTTTTTTCGTCTTTTCCT
129 TGATGGAGCTAGAGAACTAATTTTTTTCGTCTTTACCT
* *
20863 ACTTGGTAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCTTTTT
1 ACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAA-CTTTTT
*
20928 GGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCATCAAGGATTGAT
65 GGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGAT
20993 GAT-GAGCTAGAGAACTAATCTTTTTT-GTCTTTACCT
130 GATGGAGCTAGAGAACTAAT-TTTTTTCGTCTTTACCT
* *
21029 ACTTGGCAGATTACTTAAATGTCCTATCTTTTGATTCTTGAGGGGATTAAATAACTAAAATTTTT
1 ACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACT-AACTTTTT
* *
21094 GATCATTTATCAAT
65 GGTCATTTCTCAAT
21108 TGACAAATGA
Statistics
Matches: 220, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
166 93 0.42
167 73 0.33
168 54 0.25
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (166 bp):
ACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAACTTTTTG
GTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGATG
ATGGAGCTAGAGAACTAATTTTTTTCGTCTTTACCT
Found at i:21581 original size:15 final size:16
Alignment explanation
Indices: 21561--21594 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
21551 GTTTTCTAAG
*
21561 ATTATATGTATTAT-A
1 ATTATATGAATTATCA
21576 ATTATATGAATTATCA
1 ATTATATGAATTATCA
21592 ATT
1 ATT
21595 GTTTTAGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTATATGAATTATCA
Found at i:21975 original size:77 final size:78
Alignment explanation
Indices: 21848--22020 Score: 201
Period size: 77 Copynumber: 2.2 Consensus size: 78
21838 CCCGTGTCTC
* *
21848 AGGGGGTTAAACTGCTGGTAAGAGTGGATCCGCACCTCAGGGGTTTAAACTGA-TGGTAAAGAGT
1 AGGGGGTTAAACTGTTGGTAAGAGTGGATCCGCACCTCAGGGGTTAAAACTGATTGGTAAAGAGT
*
21912 GGACCCATATCAT
66 GGACCCATACCAT
* ***
21925 AGGGGGTTAAACTGTTGGTGAGAGTGGA-CTCGTGTCTCAAGGGG-TAAAACTGATTGGTAAAGA
1 AGGGGGTTAAACTGTTGGTAAGAGTGGATC-CGCACCTC-AGGGGTTAAAACTGATTGGTAAAGA
* * * *
21988 GTGGATCCGTGCCTT
64 GTGGACCCATACCAT
22003 AGGGGGTT-AACTGTTGGT
1 AGGGGGTTAAACTGTTGGT
22021 TAGACTCGAG
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
76 1 0.01
77 49 0.60
78 32 0.39
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.26
Consensus pattern (78 bp):
AGGGGGTTAAACTGTTGGTAAGAGTGGATCCGCACCTCAGGGGTTAAAACTGATTGGTAAAGAGT
GGACCCATACCAT
Found at i:22007 original size:39 final size:37
Alignment explanation
Indices: 21832--22020 Score: 157
Period size: 38 Copynumber: 4.9 Consensus size: 37
21822 GGCTGTGCAT
*
21832 AGTGGACCCGTGTCTCAGGGGGTTAAACTGCTGGTAAG
1 AGTGGACCCGTGTCTCA-GGGGTTAAACTGTTGGTAAG
* *** *
21870 AGTGGATCCGCACCTCAGGGGTTTAAACTGATGGTAAAG
1 AGTGGACCCGTGTCTCAGGGG-TTAAACTGTTGGT-AAG
* * *
21909 AGTGGACCCATATCAT-AGGGGGTTAAACTGTTGGTGAG
1 AGTGGACCCGTGTC-TCA-GGGGTTAAACTGTTGGTAAG
* *
21947 AGTGGACTCGTGTCTCAAGGGGTAAAACTGATTGGTAAAG
1 AGTGGACCCGTGTCTC-AGGGGTTAAACTG-TTGGT-AAG
* * *
21987 AGTGGATCCGTGCCTTAGGGGGTT-AACTGTTGGT
1 AGTGGACCCGTGTCTCA-GGGGTTAAACTGTTGGT
22021 TAGACTCGAG
Statistics
Matches: 121, Mismatches: 21, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
37 5 0.04
38 54 0.45
39 38 0.31
40 24 0.20
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.26
Consensus pattern (37 bp):
AGTGGACCCGTGTCTCAGGGGTTAAACTGTTGGTAAG
Found at i:22060 original size:6 final size:6
Alignment explanation
Indices: 22049--22074 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
22039 CATTAACGGA
22049 TGATTG TGATTG TGATTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TG
22075 GTGCAGCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:24993 original size:3 final size:3
Alignment explanation
Indices: 24987--25044 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
24977 AAAAAAAAGT
* *
24987 ATA ATA AT- ATA A-A ATA A-A ATA A-A ATA ATA ATA ATA ATA GTA TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
25031 ATG ATG ATA ATA AT
1 ATA ATA ATA ATA AT
25045 GAAAATGTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
2 8 0.17
3 38 0.83
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Done.