Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015609.1 Corchorus capsularis cultivar CVL-1 contig15630, 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: 12160
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:3880 original size:16 final size:18
Alignment explanation
Indices: 3861--3903 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3851 TGTAAAGAAA
3861 AAGAAAA-T-GACAAAAG
1 AAGAAAAGTCGACAAAAG
*
3877 AAGAAGAAGTCGATAAAAG
1 AAGAA-AAGTCGACAAAAG
3896 AAGAAAAG
1 AAGAAAAG
3904 AAGAGGACGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 5 0.22
17 2 0.09
18 4 0.17
19 12 0.52
ACGTcount: A:0.65, C:0.05, G:0.23, T:0.07
Consensus pattern (18 bp):
AAGAAAAGTCGACAAAAG
Found at i:4246 original size:31 final size:30
Alignment explanation
Indices: 4211--4300 Score: 103
Period size: 29 Copynumber: 3.0 Consensus size: 30
4201 AAAAAGCCTA
4211 TAATTGTGCCAACTCGAAAACGTTTGGCCCT
1 TAATTGTGCCAACTCG-AAACGTTTGGCCCT
*
4242 TAATTGAT--CAAATCGAAACGTTTGGCCCT
1 TAATTG-TGCCAACTCGAAACGTTTGGCCCT
* * *
4271 TAATTGAGCCGACGCGCAAACGTTTGGCCC
1 TAATTGTGCCAACTCG-AAACGTTTGGCCC
4301 CATATTGAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
29 20 0.40
30 10 0.20
31 19 0.38
32 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (30 bp):
TAATTGTGCCAACTCGAAACGTTTGGCCCT
Found at i:5830 original size:112 final size:111
Alignment explanation
Indices: 5714--5919 Score: 376
Period size: 112 Copynumber: 1.8 Consensus size: 111
5704 GAAAATTATA
*
5714 AAAAACAATAAGAAGGAGAAGTGAAATTACAACAAAACCAAGGTAAAGATTCAAACTTATTGAAT
1 AAAAACAATAAGAAGGAAAAGTGAAATTACAACAAAACCAAGGTAAAGATTCAAACTTATTGAAT
5779 TGGGTACTATTGGAGTTGGCTTTCTGGTAAAAAACAATAAGAAGGAG
66 TGGGTACTATTGGAGTTGGCTTT-TGGTAAAAAACAATAAGAAGGAG
*
5826 AAAAACAATAAGAAGGAAAAGTGAAATTACAACAAAACCAAGGTAAAGATTCAAGCTTATTGAAT
1 AAAAACAATAAGAAGGAAAAGTGAAATTACAACAAAACCAAGGTAAAGATTCAAACTTATTGAAT
*
5891 TGGGTACTATTGGAGTTTGCTTTTGGTAA
66 TGGGTACTATTGGAGTTGGCTTTTGGTAA
5920 TTTCAACCCA
Statistics
Matches: 91, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
111 6 0.07
112 85 0.93
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (111 bp):
AAAAACAATAAGAAGGAAAAGTGAAATTACAACAAAACCAAGGTAAAGATTCAAACTTATTGAAT
TGGGTACTATTGGAGTTGGCTTTTGGTAAAAAACAATAAGAAGGAG
Found at i:5831 original size:18 final size:18
Alignment explanation
Indices: 5808--5842 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5798 CTTTCTGGTA
5808 AAAAACAATAAGAAGGAG
1 AAAAACAATAAGAAGGAG
5826 AAAAACAATAAGAAGGA
1 AAAAACAATAAGAAGGA
5843 AAAGTGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.20, T:0.06
Consensus pattern (18 bp):
AAAAACAATAAGAAGGAG
Found at i:8922 original size:40 final size:40
Alignment explanation
Indices: 8877--9000 Score: 96
Period size: 40 Copynumber: 3.1 Consensus size: 40
8867 GTAAAATTGT
8877 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
1 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
* * ** * * * * * *
8917 AAAATAGAGTTTTTAGTTGAGTAAAATAG---TAA-AATGGT-
1 AAAATATAATAGTTA--TAAGGATATTAGATTTAATTAT-ATA
8955 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
1 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
8995 AAAATA
1 AAAATA
9001 GAGTTTTTAG
Statistics
Matches: 56, Mismatches: 20, Indels: 16
0.61 0.22 0.17
Matches are distributed among these distances:
36 8 0.14
38 13 0.23
39 8 0.14
40 19 0.34
42 8 0.14
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (40 bp):
AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
Found at i:8930 original size:78 final size:77
Alignment explanation
Indices: 8860--9098 Score: 368
Period size: 78 Copynumber: 3.2 Consensus size: 77
8850 TTTTTTTAAC
8860 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
8925 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
8938 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
9003 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
9016 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
9074 TTTTTAGTTGAG
66 TTTTTAGTTGAG
9086 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
9099 ACCTAAATAA
Statistics
Matches: 156, Mismatches: 3, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
70 56 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 89 0.57
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:9057 original size:70 final size:70
Alignment explanation
Indices: 8944--9098 Score: 240
Period size: 70 Copynumber: 2.2 Consensus size: 70
8934 TGAGTAAAAT
* * * * *
8944 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
9009 AGTTG
66 AGTTG
*
9014 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
9079 AGTTG
66 AGTTG
9084 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
9099 ACCTAAATAA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
70 76 0.97
71 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (70 bp):
AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTG
Done.