Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009899.1 Corchorus capsularis cultivar CVL-1 contig09920, 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: 75802
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3926 original size:15 final size:15
Alignment explanation
Indices: 3906--3934 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3896 CAATATAACA
3906 ATGGTAATATGATTT
1 ATGGTAATATGATTT
3921 ATGGTAATATGATT
1 ATGGTAATATGATT
3935 CTTGGATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (15 bp):
ATGGTAATATGATTT
Found at i:8370 original size:23 final size:23
Alignment explanation
Indices: 8344--8388 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
8334 ACTTTATTTC
8344 TTTTAT-ATTTAATACTTTTAAAA
1 TTTTATCA-TTAATACTTTTAAAA
*
8367 TTTTCTCATTAATACTTTTAAA
1 TTTTATCATTAATACTTTTAAA
8389 CATGATCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTATCATTAATACTTTTAAAA
Found at i:12725 original size:59 final size:59
Alignment explanation
Indices: 12633--12746 Score: 219
Period size: 59 Copynumber: 1.9 Consensus size: 59
12623 TCAAGAATTG
*
12633 CTTGAGGAAGACATGCAGGGAATTGGCACATTGAGACCTTAGTCTTTACCCTCTTTGTA
1 CTTGAGGAAGACATGCAGGGAATTGGCACATTGAAACCTTAGTCTTTACCCTCTTTGTA
12692 CTTGAGGAAGACATGCAGGGAATTGGCACATTGAAACCTTAGTCTTTACCCTCTT
1 CTTGAGGAAGACATGCAGGGAATTGGCACATTGAAACCTTAGTCTTTACCCTCTT
12747 GTATCTTTCT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (59 bp):
CTTGAGGAAGACATGCAGGGAATTGGCACATTGAAACCTTAGTCTTTACCCTCTTTGTA
Found at i:19619 original size:3 final size:3
Alignment explanation
Indices: 19604--19639 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
19594 AGCAGCGCAA
19604 CAC CAC TCAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC -CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
19640 TTCAGAGCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.64, G:0.00, T:0.03
Consensus pattern (3 bp):
CAC
Found at i:29298 original size:30 final size:28
Alignment explanation
Indices: 29261--29328 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
29251 GGTGCTGATG
*
29261 GGGCAAAACATCCCAAAATTGAAGTTCAT
1 GGGCAAAACAT-CCAAAATTAAAGTTCAT
**
29290 GAGGCAAAATGTCCAAAATTAAAGTTCAT
1 G-GGCAAAACATCCAAAATTAAAGTTCAT
29319 GGGACAAAAC
1 GGG-CAAAAC
29329 TTTCAAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.06
29 23 0.70
30 8 0.24
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (28 bp):
GGGCAAAACATCCAAAATTAAAGTTCAT
Found at i:30285 original size:73 final size:73
Alignment explanation
Indices: 30166--30308 Score: 250
Period size: 73 Copynumber: 2.0 Consensus size: 73
30156 AACTAGTATT
* *
30166 ATAACACATAAGGGTAGTCATCATTTGGCTCAGTGATAAAATACTGGATTTTTAGTTCTAAACTT
1 ATAACACATAAGGGTAGTCATCATTTGACTCAGTGATAAAATACTGGACTTTTAGTTCTAAACTT
30231 CTAATATC
66 CTAATATC
* *
30239 ATAACACATAAGGGTAGTCATCATTTGACTTAGTGATAAAGTACTGGACTTTTAGTTCTAAACTT
1 ATAACACATAAGGGTAGTCATCATTTGACTCAGTGATAAAATACTGGACTTTTAGTTCTAAACTT
30304 CTAAT
66 CTAAT
30309 GGCTAAGATT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (73 bp):
ATAACACATAAGGGTAGTCATCATTTGACTCAGTGATAAAATACTGGACTTTTAGTTCTAAACTT
CTAATATC
Found at i:38220 original size:16 final size:16
Alignment explanation
Indices: 38199--38232 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
38189 CTGTTGGTAT
38199 CTTTTCACAGGTGGAC
1 CTTTTCACAGGTGGAC
38215 CTTTTCACAGGTGGAC
1 CTTTTCACAGGTGGAC
38231 CT
1 CT
38233 AGTTCTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (16 bp):
CTTTTCACAGGTGGAC
Found at i:53287 original size:135 final size:131
Alignment explanation
Indices: 53026--53291 Score: 342
Period size: 135 Copynumber: 2.0 Consensus size: 131
53016 AATTGGTTGA
*
53026 TGATTCAAGTGATTCGTCACTTCTTTCCCAAAGTCTTGAGTTCGAAGTCATGCGAATGAAGAAAA
1 TGATTCAAGTGATTCGTCACTTCTTTCCCAAAGTCTCGAGTTCGAAGTCATGCGAATGAAGAAAA
* * *
53091 CTATTCATAGAGAGTTTATTTTCATAATGAACCGATCTTATTAAAAAAGAATTAATCGTAAACCA
66 CTATTCATAGAGAGTTTATCTTCATAATGAACCAATCTGATTAAAAAAGAATTAATCGTAAACCA
53156 T
131 T
*
53157 TGATTCAAGTGATTCGTCACTCTTCTTTCCCAAA-TCTCGAGTTC-AGAGTCTTGC-AGATGAAG
1 TGATTCAAGTGATTCGTCA--CTTCTTTCCCAAAGTCTCGAGTTCGA-AGTCATGCGA-ATGAAG
* * * * *
53219 ATAAACTATTCATAGGAGAGGTTTATCTTCATGATGGACTAATCTGACTT-GAATAGAATTAATC
62 A-AAACTATTCATA-GAGA-GTTTATCTTCATAATGAACCAATCTGA-TTAAAAAAGAATTAATC
53283 GTAAACCAT
123 GTAAACCAT
53292 GAAAAAGGAT
Statistics
Matches: 117, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
131 21 0.18
132 23 0.20
133 25 0.21
134 4 0.03
135 42 0.36
136 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (131 bp):
TGATTCAAGTGATTCGTCACTTCTTTCCCAAAGTCTCGAGTTCGAAGTCATGCGAATGAAGAAAA
CTATTCATAGAGAGTTTATCTTCATAATGAACCAATCTGATTAAAAAAGAATTAATCGTAAACCA
T
Found at i:59668 original size:14 final size:14
Alignment explanation
Indices: 59633--59660 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
59623 ATCATGTTAC
59633 ACCAAAACCAATGT
1 ACCAAAACCAATGT
59647 ACCAAAACCAATGT
1 ACCAAAACCAATGT
59661 TCATAAACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.29, G:0.07, T:0.14
Consensus pattern (14 bp):
ACCAAAACCAATGT
Found at i:74051 original size:30 final size:30
Alignment explanation
Indices: 74017--74079 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
74007 GCTCTTTTTC
* * *
74017 AGAAATGAAGAAGAAGTATTTGTGACATTG
1 AGAAATCAAGAAGAAGTATCTGTGACATCG
* * *
74047 AGAAATCATGAAGAATTATCTGTGTCATCG
1 AGAAATCAAGAAGAAGTATCTGTGACATCG
74077 AGA
1 AGA
74080 GACGGGTGGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (30 bp):
AGAAATCAAGAAGAAGTATCTGTGACATCG
Found at i:74590 original size:3 final size:3
Alignment explanation
Indices: 74582--74606 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
74572 GGTGTGGACC
74582 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
74607 GCAAAACTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:75764 original size:2 final size:2
Alignment explanation
Indices: 75753--75802 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
75743 ACACCCATTA
75753 AT AT AT -T AT AT AT AT 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 AT AT AT AT AT AT AT AT
75794 AT AT AT AT A
1 AT AT AT AT A
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.