Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015279.1 Corchorus capsularis cultivar CVL-1 contig15300, 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: 29738
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:351 original size:25 final size:25
Alignment explanation
Indices: 323--402 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 25
313 ACTAATTATC
323 CTCTTCTTAATTATTACCACTTTTA
1 CTCTTCTTAATTATTACCACTTTTA
* *
348 CTCTTCTT-TTTCTCTACCA-TTTTA
1 CTCTTCTTAATTAT-TACCACTTTTA
* * *
372 CTCTT-TGAATTACTGATCACCTTTTA
1 CTCTTCTTAATTA-TTACCA-CTTTTA
398 CTCTT
1 CTCTT
403 TATTGATTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
23 1 0.02
24 18 0.42
25 14 0.33
26 10 0.23
ACGTcount: A:0.19, C:0.26, G:0.03, T:0.53
Consensus pattern (25 bp):
CTCTTCTTAATTATTACCACTTTTA
Found at i:607 original size:26 final size:27
Alignment explanation
Indices: 561--628 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
551 CTCTTTACTG
**
561 ATTACTATTTT-ACCCTCTTGAACTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
*
587 ATTACTATTTTCATTCT-TTGAATTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
* *
613 ATCACAATTTGTCATT
1 ATTACTATTT-TCATT
629 TTACTCTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 27 0.77
27 8 0.23
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.50
Consensus pattern (27 bp):
ATTACTATTTTCATTCTCTTGAACTTA
Found at i:780 original size:32 final size:32
Alignment explanation
Indices: 743--831 Score: 133
Period size: 32 Copynumber: 2.8 Consensus size: 32
733 TCTTGATTAC
* *
743 CATTTTACCGATTGCTTCTTTTACTTTCACTA
1 CATTTTACTGATTACTTCTTTTACTTTCACTA
* *
775 TATTTTACTGATTACTTCTTTTACTTTCACTC
1 CATTTTACTGATTACTTCTTTTACTTTCACTA
*
807 CATTTTACTGATTACTTCCTTTACT
1 CATTTTACTGATTACTTCTTTTACT
832 GATTACTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.19, C:0.24, G:0.04, T:0.53
Consensus pattern (32 bp):
CATTTTACTGATTACTTCTTTTACTTTCACTA
Found at i:829 original size:16 final size:16
Alignment explanation
Indices: 778--840 Score: 69
Period size: 16 Copynumber: 3.9 Consensus size: 16
768 TTCACTATAT
*
778 TTTACTGATTACTTCT
1 TTTACTGATTACTTCC
794 TTTACT--TTCAC-TCC
1 TTTACTGATT-ACTTCC
808 ATTTTACTGATTACTTCC
1 --TTTACTGATTACTTCC
826 TTTACTGATTACTTC
1 TTTACTGATTACTTC
841 TCTTGGTTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
14 4 0.10
15 2 0.05
16 27 0.68
17 2 0.05
18 5 0.12
ACGTcount: A:0.19, C:0.24, G:0.05, T:0.52
Consensus pattern (16 bp):
TTTACTGATTACTTCC
Found at i:6017 original size:17 final size:17
Alignment explanation
Indices: 5995--6031 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5985 CAACAGCTAT
*
5995 ATTGTTCATCATAGTAA
1 ATTGTTCACCATAGTAA
*
6012 ATTGTTCCCCATAGTAA
1 ATTGTTCACCATAGTAA
6029 ATT
1 ATT
6032 ACCTTGCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (17 bp):
ATTGTTCACCATAGTAA
Found at i:12115 original size:35 final size:36
Alignment explanation
Indices: 12069--12299 Score: 307
Period size: 35 Copynumber: 6.6 Consensus size: 36
12059 TTCTTACTAA
*
12069 ACTTAATTACCCTGAATTAAATTACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
12104 ACTTAATTACCCTGAATTAAGTTACTTATT-AACTC
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
*
12139 ACTTAATTACCCTGAATTAAGTTACTTATTGAA-TT
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
12174 ACTTAATTACCCTGAATTAAGTTACTTATT-AACTC
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
*
12209 ACTTAATTACCCTGAATTAAGGTTGA-TTACTG-ACTC
1 ACTTAATTACCCTGAATTAA-GTT-ACTTATTGAACTC
* ** *
12245 ACTTAATTGCCCTGAATTAAGTTGA-TTACCG-ACTT
1 ACTTAATTACCCTGAATTAAGTT-ACTTATTGAACTC
*
12280 ACTTAATTACCCCGAATTAA
1 ACTTAATTACCCTGAATTAA
12300 ATTGCTCATT
Statistics
Matches: 181, Mismatches: 9, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
34 6 0.03
35 142 0.78
36 32 0.18
37 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.39
Consensus pattern (36 bp):
ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
Found at i:12298 original size:106 final size:105
Alignment explanation
Indices: 12069--12302 Score: 339
Period size: 106 Copynumber: 2.2 Consensus size: 105
12059 TTCTTACTAA
*
12069 ACTTAATTACCCTGAATTAAATTACTTATTGAACTACTTAATTACCCTGAATTAAGTTACTTATT
1 ACTTAATTACCCTGAATTAAATTACTTATTGAACTACTTAATTACCCTGAATTAAGTTACTTACT
**
12134 AACTCACTTAATTACCCTGAATTAAGTTACTTATTGAATT
66 AACTCACTTAATTACCCTGAATTAAGTTACTTACCGAATT
*
12174 ACTTAATTACCCTGAATTAAGTTACTTATT-AACTCACTTAATTACCCTGAATTAAGGTTGA-TT
1 ACTTAATTACCCTGAATTAAATTACTTATTGAACT-ACTTAATTACCCTGAATTAA-GTT-ACTT
* * *
12237 ACTGACTCACTTAATTGCCCTGAATTAAGTTGA-TTACCGACTT
63 ACTAACTCACTTAATTACCCTGAATTAAGTT-ACTTACCGAATT
*
12280 ACTTAATTACCCCGAATTAAATT
1 ACTTAATTACCCTGAATTAAATT
12303 GCTCATTACT
Statistics
Matches: 116, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
104 4 0.03
105 49 0.42
106 61 0.53
107 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.39
Consensus pattern (105 bp):
ACTTAATTACCCTGAATTAAATTACTTATTGAACTACTTAATTACCCTGAATTAAGTTACTTACT
AACTCACTTAATTACCCTGAATTAAGTTACTTACCGAATT
Found at i:15915 original size:22 final size:22
Alignment explanation
Indices: 15887--15930 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
15877 CTATAAACTA
*
15887 TACTAAATACCAAAATTGAATT
1 TACTAAATACCAAAAGTGAATT
* *
15909 TACTAAATGCCAAGAGTGAATT
1 TACTAAATACCAAAAGTGAATT
15931 AGAAAATGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (22 bp):
TACTAAATACCAAAAGTGAATT
Found at i:16107 original size:22 final size:22
Alignment explanation
Indices: 16068--16124 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
16058 GGTTACCGAG
* *
16068 ATTTTATAAGGAGGTTATTAAA
1 ATTTTATATGGAGATTATTAAA
* *
16090 ATTTTATATGGATATTATTGAA
1 ATTTTATATGGAGATTATTAAA
**
16112 ATTCGATATGGAG
1 ATTTTATATGGAG
16125 GCTATTTCAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (22 bp):
ATTTTATATGGAGATTATTAAA
Found at i:16312 original size:21 final size:21
Alignment explanation
Indices: 16288--16337 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
16278 AAGAGGTTGA
*
16288 CAAAATTCATTAC-ATGGTTAT
1 CAAAATTCA-TACGAAGGTTAT
16309 CAAAATTTCATACGAAGGTTAT
1 CAAAA-TTCATACGAAGGTTAT
16331 CAAAATT
1 CAAAATT
16338 TTGATTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (21 bp):
CAAAATTCATACGAAGGTTAT
Found at i:18782 original size:42 final size:42
Alignment explanation
Indices: 18721--18815 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
18711 CGAGAGTGGC
* * * * * *
18721 GATTTGGCTTCCAAGAGAGATACGGTTTCTGATTGAGATTCT
1 GATTTGGCTCCCAACAGAGATACCGTCTCCGATTGAGATCCT
18763 GATTTGGCTCCCAACAGAGATACCGTCTCCGATTGAGATCCT
1 GATTTGGCTCCCAACAGAGATACCGTCTCCGATTGAGATCCT
*
18805 GATTTGCCTCC
1 GATTTGGCTCC
18816 ATCGTCGGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (42 bp):
GATTTGGCTCCCAACAGAGATACCGTCTCCGATTGAGATCCT
Found at i:29070 original size:12 final size:12
Alignment explanation
Indices: 29050--29080 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29040 AGGCAGAGGG
*
29050 TTGCCTGATCAC
1 TTGCATGATCAC
29062 TTGCATGATCAC
1 TTGCATGATCAC
29074 TTGCATG
1 TTGCATG
29081 TGTCTCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.35
Consensus pattern (12 bp):
TTGCATGATCAC
Found at i:29187 original size:6 final size:6
Alignment explanation
Indices: 29176--29217 Score: 75
Period size: 6 Copynumber: 6.8 Consensus size: 6
29166 TAAAATGTAA
29176 TATATC TATATC TATATC TATATC TATATC TATATAC TATAT
1 TATATC TATATC TATATC TATATC TATATC TATAT-C TATAT
29218 AAGTCTAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Done.