Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008916.1 Corchorus capsularis cultivar CVL-1 contig08937, 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: 39148
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:966 original size:19 final size:18
Alignment explanation
Indices: 925--975 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
915 ACGGCCCTGT
*
925 CCTCTC-TTCTCCACTCC
1 CCTCTCTTTCTCAACTCC
*
942 CTTCTCTTTCTCAACTCCC
1 CCTCTCTTTCTCAACT-CC
*
961 CCTCTCTCTCTCAAC
1 CCTCTCTTTCTCAAC
976 ATTTCTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 5 0.18
18 8 0.29
19 15 0.54
ACGTcount: A:0.10, C:0.53, G:0.00, T:0.37
Consensus pattern (18 bp):
CCTCTCTTTCTCAACTCC
Found at i:1657 original size:21 final size:22
Alignment explanation
Indices: 1631--1675 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
1621 TCAAAGGGTG
*
1631 TTGCTAAACATCG-CCCCCTTT
1 TTGCTAAACACCGCCCCCCTTT
1652 TTGCTAAACACCGCCCCCCTTT
1 TTGCTAAACACCGCCCCCCTTT
1674 TT
1 TT
1676 TAGTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.18, C:0.40, G:0.09, T:0.33
Consensus pattern (22 bp):
TTGCTAAACACCGCCCCCCTTT
Found at i:1886 original size:33 final size:33
Alignment explanation
Indices: 1842--1929 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 33
1832 GGCTAATGAC
*
1842 CGTGCCGCCCCAGGAGGGCGGCATGCCGTGG-T
1 CGTGCCGCCCCAGGAGGGCGGCATGCAGTGGCT
** *
1874 ATTTGCCGCCCCAGGAGGACGGCATGCAGTGGCT
1 -CGTGCCGCCCCAGGAGGGCGGCATGCAGTGGCT
*
1908 CGTGCCGCCCTAGGAGGGCGGC
1 CGTGCCGCCCCAGGAGGGCGGC
1930 TGTGCCACGG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
33 45 0.98
34 1 0.02
ACGTcount: A:0.12, C:0.33, G:0.41, T:0.14
Consensus pattern (33 bp):
CGTGCCGCCCCAGGAGGGCGGCATGCAGTGGCT
Found at i:2084 original size:13 final size:13
Alignment explanation
Indices: 2063--2133 Score: 72
Period size: 13 Copynumber: 5.2 Consensus size: 13
2053 TACTTACAAA
*
2063 AAAATATTACTTAC
1 AAAA-ATTACATAC
2077 AAAAATTACATAC
1 AAAAATTACATAC
2090 AATAAAAATTAACATA-
1 ---AAAAATT-ACATAC
*
2106 AAAAATTACTTAC
1 AAAAATTACATAC
2119 AAAAATTACATAC
1 AAAAATTACATAC
2132 AA
1 AA
2134 TAATAATTAC
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
12 4 0.08
13 29 0.59
14 4 0.08
16 7 0.14
17 5 0.10
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAAATTACATAC
Found at i:2110 original size:29 final size:30
Alignment explanation
Indices: 2051--2123 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
2041 TTGTTGTGAG
* *
2051 ATTACTTACAAAAAAATATTACTTACAAAA
1 ATTACTTACAAAAAAATATAACATACAAAA
*
2081 ATTACATACAATAAAAAT-TAACATA-AAAA
1 ATTACTTACAA-AAAAATATAACATACAAAA
2110 ATTACTTACAAAAA
1 ATTACTTACAAAAA
2124 TTACATACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 14 0.37
30 15 0.39
31 6 0.16
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.27
Consensus pattern (30 bp):
ATTACTTACAAAAAAATATAACATACAAAA
Found at i:2122 original size:42 final size:43
Alignment explanation
Indices: 2062--2142 Score: 146
Period size: 42 Copynumber: 1.9 Consensus size: 43
2052 TTACTTACAA
2062 AAAAATATTACTTACAAAAATTACATACAATAAAAATTAACAT
1 AAAAATATTACTTACAAAAATTACATACAATAAAAATTAACAT
*
2105 AAAAA-ATTACTTACAAAAATTACATACAATAATAATTA
1 AAAAATATTACTTACAAAAATTACATACAATAAAAATTA
2143 CAAACATGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
42 32 0.86
43 5 0.14
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.28
Consensus pattern (43 bp):
AAAAATATTACTTACAAAAATTACATACAATAAAAATTAACAT
Found at i:2143 original size:25 final size:26
Alignment explanation
Indices: 2093--2146 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
2083 TACATACAAT
*
2093 AAAAATTAACATAAAAAATTACTTAC
1 AAAAATTAACATAAAAAATTAATTAC
*
2119 AAAAATT-ACATACAATAA-TAATTAC
1 AAAAATTAACATA-AAAAATTAATTAC
2144 AAA
1 AAA
2147 CATGTCTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (26 bp):
AAAAATTAACATAAAAAATTAATTAC
Found at i:7090 original size:33 final size:33
Alignment explanation
Indices: 7048--7119 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
7038 GTTGATTGCA
* **
7048 ATGACACTAAATCTGATTTAGG-TGCTGTTTGTG
1 ATGAAACTAAATCTG-TTTAGGATGCTAATTGTG
*
7081 ATGAAACTAAATCTGTTTTGGATGCTAATTGTG
1 ATGAAACTAAATCTGTTTAGGATGCTAATTGTG
7114 ATGAAA
1 ATGAAA
7120 ACAAACCTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 5 0.15
33 29 0.85
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.38
Consensus pattern (33 bp):
ATGAAACTAAATCTGTTTAGGATGCTAATTGTG
Found at i:7163 original size:33 final size:33
Alignment explanation
Indices: 7126--7188 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
7116 GAAAACAAAC
* *
7126 CTGTTTTTGTTGATCATAGCATTGCAAATAATT
1 CTGTTTTGGTTGATCATAGCATTGAAAATAATT
7159 CTGTTTTGGTTGATCATAGCATTGAAAATA
1 CTGTTTTGGTTGATCATAGCATTGAAAATA
7189 GGACTGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (33 bp):
CTGTTTTGGTTGATCATAGCATTGAAAATAATT
Found at i:7196 original size:33 final size:33
Alignment explanation
Indices: 7126--7200 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
7116 GAAAACAAAC
* * **
7126 CTGTTTTTGTTGATCATAGCATTGCAAATAATT
1 CTGTTTTGGTTGATCATAGCATTGAAAATAAGA
*
7159 CTGTTTTGGTTGATCATAGCATTGAAAATAGGA
1 CTGTTTTGGTTGATCATAGCATTGAAAATAAGA
7192 CTGTTTTGG
1 CTGTTTTGG
7201 GTAAAAAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (33 bp):
CTGTTTTGGTTGATCATAGCATTGAAAATAAGA
Found at i:12447 original size:21 final size:21
Alignment explanation
Indices: 12409--12449 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12399 CCTTGGCTTA
*
12409 TGATCTTCAATACTCTTCAAT
1 TGATCTTCAATACACTTCAAT
**
12430 TGATCTTCAATGGACTTCAA
1 TGATCTTCAATACACTTCAA
12450 GCCTTCAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (21 bp):
TGATCTTCAATACACTTCAAT
Found at i:12583 original size:30 final size:30
Alignment explanation
Indices: 12547--12607 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
12537 CAAAGGATCA
12547 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
12577 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
12607 A
1 A
12608 TTGATGTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.18, C:0.30, G:0.20, T:0.33
Consensus pattern (30 bp):
AATGGCATCTTTGGTGCGATTCCTCCATCC
Found at i:12618 original size:30 final size:30
Alignment explanation
Indices: 12547--12628 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 30
12537 CAAAGGATCA
*
12547 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGACATCTTTGGTGCGATTCCTCCATCC
*
12577 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGACATCTTTGGTGCGATTCCTCCATCC
* **
12607 ATTGATGTCTTTGGTGCG-TTCC
1 AATGACATCTTTGGTGCGATTCC
12629 CATCTCCTCC
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 4 0.08
30 44 0.92
ACGTcount: A:0.15, C:0.27, G:0.22, T:0.37
Consensus pattern (30 bp):
AATGACATCTTTGGTGCGATTCCTCCATCC
Found at i:18872 original size:6 final size:6
Alignment explanation
Indices: 18858--18938 Score: 51
Period size: 6 Copynumber: 13.7 Consensus size: 6
18848 AATTTCTTAC
* * * * *
18858 CTTTAT CTTTTT CTTTTT C--GTT ATTTTT CTTTTT ATTTTT CGTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
* * *
18904 GTTTATT TTTATTT CTTTTT CTTTTT -ATTTT CTTT
1 CTTT-TT CTT-TTT CTTTTT CTTTTT CTTTTT CTTT
18939 GGTACTTTTA
Statistics
Matches: 56, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
4 2 0.04
5 4 0.07
6 41 0.73
7 8 0.14
8 1 0.02
ACGTcount: A:0.07, C:0.11, G:0.04, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:18912 original size:22 final size:22
Alignment explanation
Indices: 18865--18934 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
18855 TACCTTTATC
* *
18865 TTTTTCTTTTTCGTTATTTTTC
1 TTTTTATTTTTCGTTATTTTTA
18887 TTTTTATTTTTCGTT-TTGTTTA
1 TTTTTATTTTTCGTTATT-TTTA
* *
18909 TTTTTATTTCTT-TTTCTTTTTA
1 TTTTTATTT-TTCGTTATTTTTA
18931 TTTT
1 TTTT
18935 CTTTGGTACT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.05
22 36 0.86
23 4 0.10
ACGTcount: A:0.07, C:0.09, G:0.04, T:0.80
Consensus pattern (22 bp):
TTTTTATTTTTCGTTATTTTTA
Found at i:18928 original size:16 final size:16
Alignment explanation
Indices: 18883--18938 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
18873 TTTCGTTATT
*
18883 TTTCTTTTTATTTTTCG
1 TTTCTTTTTATTTTT-A
*
18900 TTT-TGTTTATTTTTA
1 TTTCTTTTTATTTTTA
*
18915 TTTCTTTTTCTTTTTA
1 TTTCTTTTTATTTTTA
18931 TTTTCTTT
1 -TTTCTTT
18939 GGTACTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 3 0.09
16 20 0.61
17 10 0.30
ACGTcount: A:0.07, C:0.09, G:0.04, T:0.80
Consensus pattern (16 bp):
TTTCTTTTTATTTTTA
Found at i:20943 original size:21 final size:22
Alignment explanation
Indices: 20904--20944 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20894 CAAAATGTGA
*
20904 CATGTTTTTATGGTCATTTTTC
1 CATGTTTTTATGGGCATTTTTC
*
20926 CATGTTTTTA-GGGGATTTT
1 CATGTTTTTATGGGCATTTT
20945 GGGCTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.15, C:0.10, G:0.20, T:0.56
Consensus pattern (22 bp):
CATGTTTTTATGGGCATTTTTC
Found at i:32762 original size:35 final size:35
Alignment explanation
Indices: 32486--32762 Score: 309
Period size: 35 Copynumber: 7.8 Consensus size: 35
32476 CGAGTCAGTG
* * *
32486 ATAAGTAACTTAATTCAGGATAATTAAGCAAG-TCG
1 ATAAGTAACTTAATTCAGGGTAATTAAG-TAGTTCA
* * * *
32521 GTAA-TCAACTTAATTCAGAGTAGTTAAGCAAG-TCAGTA
1 ATAAGT-AACTTAATTCAGGGTAATTAAG-TAGTTC---A
*
32559 ATAAGCAACTTAATTCAGGGTAATTAAGTGAG-TCA
1 ATAAGTAACTTAATTCAGGGTAATTAAGT-AGTTCA
*
32594 GTAA-TAAACTTTAATTCAGGGTAATTAAGTGAGTT-A
1 ATAAGT-AAC-TTAATTCAGGGTAATTAAGT-AGTTCA
*
32630 ATAAGTAACTTAAATCA-GGTAATTAAGTAGTTCA
1 ATAAGTAACTTAATTCAGGGTAATTAAGTAGTTCA
32664 ATAAGTAACTTAATTCAGGGTAATTAAGTGAGTT-A
1 ATAAGTAACTTAATTCAGGGTAATTAAGT-AGTTCA
32699 ATAAGTAACTTAATTCAGGGTAATTAAGTAGTTCA
1 ATAAGTAACTTAATTCAGGGTAATTAAGTAGTTCA
32734 ATAAGTAACTTAATTCAGGGTAATTAAGT
1 ATAAGTAACTTAATTCAGGGTAATTAAGT
32763 TTAGTAAGAA
Statistics
Matches: 213, Mismatches: 15, Indels: 28
0.83 0.06 0.11
Matches are distributed among these distances:
33 4 0.02
34 33 0.15
35 113 0.53
36 34 0.16
37 2 0.01
38 27 0.13
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (35 bp):
ATAAGTAACTTAATTCAGGGTAATTAAGTAGTTCA
Done.