Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015033.1 Corchorus capsularis cultivar CVL-1 contig15054, 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: 57851
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38 TAGTAACTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:830 original size:30 final size:30
Alignment explanation
Indices: 794--850 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
784 TGGCCAGACA
794 CTTATGGCAATTTTTGATCATATCATACAG
1 CTTATGGCAATTTTTGATCATATCATACAG
824 CTTATGGCAATTTTTGATCATATCATA
1 CTTATGGCAATTTTTGATCATATCATA
851 TCGCTCTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (30 bp):
CTTATGGCAATTTTTGATCATATCATACAG
Found at i:4121 original size:17 final size:17
Alignment explanation
Indices: 4099--4133 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4089 GTAATTGGAG
4099 TAGTACCTTTTTAAGAA
1 TAGTACCTTTTTAAGAA
*
4116 TAGTACTTTTTTAAGAA
1 TAGTACCTTTTTAAGAA
4133 T
1 T
4134 TTTTTTGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (17 bp):
TAGTACCTTTTTAAGAA
Found at i:10533 original size:31 final size:31
Alignment explanation
Indices: 10495--10557 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
10485 CAATCAATTC
* *
10495 GTCCTGATGGAAAGCCTCTCGATGTTAAGTT
1 GTCCTGATGGAAAGCCTCCCGATGATAAGTT
*
10526 GTCCTGATGGAAAGCGTCCCGATGATAAGTT
1 GTCCTGATGGAAAGCCTCCCGATGATAAGTT
10557 G
1 G
10558 CTTTAGAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (31 bp):
GTCCTGATGGAAAGCCTCCCGATGATAAGTT
Found at i:12364 original size:109 final size:110
Alignment explanation
Indices: 12071--12344 Score: 448
Period size: 108 Copynumber: 2.5 Consensus size: 110
12061 ACTATTATAG
* *
12071 TTTTATTCTACTAGAAACTCTATTTTTATTTAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-T---TCTAATATCTTTATAATTACTT
12136 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
62 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
12185 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-TCTAATATCTTTATAATTACTTTATT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
*
12249 TTTACCAAAAAA-TTGGATATATTAAAATTTTTTCTAATATACAA
66 TTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
*
12293 TTTTATTCTACTAAAAAGTCTATTTTCATTTAATTAAATTC-AATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATA
12345 TAATTTTTTT
Statistics
Matches: 155, Mismatches: 4, Indels: 9
0.92 0.02 0.05
Matches are distributed among these distances:
107 6 0.04
108 73 0.47
109 40 0.26
114 36 0.23
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (110 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
TTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:18434 original size:14 final size:14
Alignment explanation
Indices: 18415--18453 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
18405 CTTTTTTCTA
18415 TTAAAAAATATTTT
1 TTAAAAAATATTTT
*
18429 TTAAAAATATGTTTT
1 TTAAAAA-ATATTTT
*
18444 TTGAAAAATA
1 TTAAAAAATA
18454 AAAATATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (14 bp):
TTAAAAAATATTTT
Found at i:20895 original size:30 final size:29
Alignment explanation
Indices: 20833--20895 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
20823 ACTGAACCGT
***
20833 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTATAAAGGC
*
20862 CAAATAAGCCCCTGAACTCTTATAAAAGGC
1 CAAATAAGCCCCTGAACTATTAT-AAAGGC
20892 CAAA
1 CAAA
20896 AAAACCCTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTATAAAGGC
Found at i:32415 original size:16 final size:16
Alignment explanation
Indices: 32390--32427 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
32380 CTTTTTCAAC
* *
32390 TTATTCTTCAATGAAA
1 TTATTATTCAAGGAAA
32406 TTATTATTCAAGGAAA
1 TTATTATTCAAGGAAA
32422 TTATTA
1 TTATTA
32428 CATAGTGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (16 bp):
TTATTATTCAAGGAAA
Found at i:35462 original size:13 final size:13
Alignment explanation
Indices: 35444--35468 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35434 CACATAATTA
35444 AATTCTTATATGT
1 AATTCTTATATGT
35457 AATTCTTATATG
1 AATTCTTATATG
35469 CAAAAGGGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
AATTCTTATATGT
Found at i:47075 original size:21 final size:21
Alignment explanation
Indices: 47049--47091 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
47039 TTGCCACATG
47049 TAATAGGTGACATGTGGCGTT
1 TAATAGGTGACATGTGGCGTT
47070 TAATAGGTGACATGTGGCGTT
1 TAATAGGTGACATGTGGCGTT
47091 T
1 T
47092 CAAAATTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.33, T:0.35
Consensus pattern (21 bp):
TAATAGGTGACATGTGGCGTT
Found at i:47255 original size:202 final size:201
Alignment explanation
Indices: 46904--47272 Score: 675
Period size: 202 Copynumber: 1.8 Consensus size: 201
46894 GGTTTAGACG
46904 TTTTGCCCTTGAAATATTATTGTGAAAATTTTACTCCCCCAACTTTTATTTTAAGGCTATGTTGT
1 TTTTGCCCTTGAAATATTATTGTGAAAATTTTACTCCCCCAACTTTTATTTTAAGGCTATGTTGT
* *
46969 CCCTTCAGTCAATTGAATGATTAATGGTGCTGACGTGGAATGCCATATCAATATTGAGTAATGCA
66 CCCTTCAGTCAATTGAATGATTAATGGTGCTGACGTGGAATGCCACATCAACATTGAGTAATGCA
47034 TGGACTTGCCACATGTAATAGGTGACATGTGGCGTTTAATAGGTGACATGTGGCGTTTCAAAATT
131 TGGACTTGCCACATGTAATAGGTGACATGTGGCGTTTAATAGGTGACATGTGGCGTTTCAAAATT
47099 ATCATT
196 ATCATT
* *
47105 TTTTGCCCCTTGAAATATTATTGTGAAAATTTTGCTCCCCCAACTTTTATTTTAAGGTTATGTTG
1 TTTTG-CCCTTGAAATATTATTGTGAAAATTTTACTCCCCCAACTTTTATTTTAAGGCTATGTTG
47170 TCCCTTCAGTCAATTGAATGATTAATGGTGCTGACGTGGAATGCCACATCAACATTGAGTAATGC
65 TCCCTTCAGTCAATTGAATGATTAATGGTGCTGACGTGGAATGCCACATCAACATTGAGTAATGC
* *
47235 ATGGATTTGCCACATGTAATAGGTGACATGTGGTGTTT
130 ATGGACTTGCCACATGTAATAGGTGACATGTGGCGTTT
47273 CAAAATTGTC
Statistics
Matches: 161, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
201 5 0.03
202 156 0.97
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (201 bp):
TTTTGCCCTTGAAATATTATTGTGAAAATTTTACTCCCCCAACTTTTATTTTAAGGCTATGTTGT
CCCTTCAGTCAATTGAATGATTAATGGTGCTGACGTGGAATGCCACATCAACATTGAGTAATGCA
TGGACTTGCCACATGTAATAGGTGACATGTGGCGTTTAATAGGTGACATGTGGCGTTTCAAAATT
ATCATT
Found at i:48786 original size:38 final size:38
Alignment explanation
Indices: 48735--48812 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
48725 TTTCAACAAA
*
48735 TTCAACTATCTTACATTCTTACTTAATACTTT-ACATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGA-ATTT
*
48773 TTCAACAATCTTACATTCTTACTTATTACTTTGAATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
48811 TT
1 TT
48813 GGTAATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 36 0.97
39 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.01, T:0.51
Consensus pattern (38 bp):
TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
Found at i:49811 original size:29 final size:29
Alignment explanation
Indices: 49769--49831 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
49759 TAATCATTAA
* * * *
49769 AATTCCGTCTACCAATATACGTGCTACAT
1 AATTCCATATACCAATAAACGCGCTACAT
*
49798 AATTCCATATACCAATAAACGCGTTACAT
1 AATTCCATATACCAATAAACGCGCTACAT
49827 AATTC
1 AATTC
49832 TTTAGTTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (29 bp):
AATTCCATATACCAATAAACGCGCTACAT
Found at i:50146 original size:14 final size:14
Alignment explanation
Indices: 50129--50158 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
50119 ATATATATAT
50129 ATATATACACACAC
1 ATATATACACACAC
50143 ATATATACACACAC
1 ATATATACACACAC
50157 AT
1 AT
50159 TATCAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (14 bp):
ATATATACACACAC
Found at i:50146 original size:16 final size:16
Alignment explanation
Indices: 50127--50157 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50117 ATATATATAT
*
50127 ATATATATACACACAC
1 ATATATACACACACAC
50143 ATATATACACACACA
1 ATATATACACACACA
50158 TTATCAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (16 bp):
ATATATACACACACAC
Found at i:51672 original size:20 final size:19
Alignment explanation
Indices: 51638--51675 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
51628 GATTACTAAA
*
51638 AAAACAATTAGAGGTTATC
1 AAAACAATTAAAGGTTATC
51657 AAAACAATTATAAGGTTAT
1 AAAACAATTA-AAGGTTAT
51676 TAATAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAACAATTAAAGGTTATC
Found at i:53726 original size:2 final size:2
Alignment explanation
Indices: 53715--53749 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
53705 AGTTTAGACT
53715 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53750 AGTGAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:54673 original size:38 final size:38
Alignment explanation
Indices: 54616--54695 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 38
54606 ATTCATATAT
54616 ATATATAAACTAAATAATTTAATTAAA-AAAT-TAAATAC
1 ATATATAAACTAAATAATTT-ATTAAATAAATAT-AATAC
*
54654 ATATATAAAGTTAAA-AATTTATTAAATAAATATAATAC
1 ATATATAAA-CTAAATAATTTATTAAATAAATATAATAC
54692 ATAT
1 ATAT
54696 TTATGTTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
37 6 0.16
38 27 0.71
39 5 0.13
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (38 bp):
ATATATAAACTAAATAATTTATTAAATAAATATAATAC
Done.