Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004976.1 Corchorus capsularis cultivar CVL-1 contig04994, 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: 12604
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:854 original size:2 final size:2
Alignment explanation
Indices: 847--936 Score: 58
Period size: 2 Copynumber: 50.5 Consensus size: 2
837 TCGAATATTG
* *
847 AT AT AT AT A- AT -T AA AT AT -T AT AT AT AT AT A- AT AA AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
884 AG AT AT AT AT A- AT -T AT AT AT AT A- AT AA AT -T AG 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
922 AT A- AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
937 ATACTATTGT
Statistics
Matches: 67, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
1 11 0.16
2 56 0.84
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:903 original size:30 final size:30
Alignment explanation
Indices: 867--939 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
857 TTAAATATTA
867 TATATATATAATAAATTAGATATATATAAT
1 TATATATATAATAAATTAGATATATATAAT
897 TATATATATAATAAATTAGATATATATAAT
1 TATATATATAATAAATTAGATATATATAAT
927 TATATATATAATA
1 TATATATATAATA
940 CTATTGTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (30 bp):
TATATATATAATAAATTAGATATATATAAT
Found at i:1263 original size:25 final size:25
Alignment explanation
Indices: 1193--1256 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
1183 GTGTTTTCTC
1193 AACGCAAGCACATGCTCGTTTGCCA
1 AACGCAAGCACATGCTCGTTTGCCA
* *
1218 AACGCAAGCACAGGCTCGTTTGCTA
1 AACGCAAGCACATGCTCGTTTGCCA
*
1243 AACGCAAGAACATG
1 AACGCAAGCACATG
1257 AGCGTTTACC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (25 bp):
AACGCAAGCACATGCTCGTTTGCCA
Found at i:3361 original size:13 final size:16
Alignment explanation
Indices: 3337--3376 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
3327 ATTTCTGAAA
*
3337 TTATAATTATA-TA-T
1 TTATTATTATATTATT
3351 TTATT-TTATATTATT
1 TTATTATTATATTATT
3366 TTATTATTATA
1 TTATTATTATA
3377 ATCAGAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 5 0.23
14 6 0.27
15 6 0.27
16 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATTATATTATT
Found at i:4885 original size:23 final size:22
Alignment explanation
Indices: 4855--4933 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
4845 TGACTTTCAT
*
4855 ATTTGGGGTTTGACCATTAAGTA
1 ATTTGGGGTTTGACCATTAA-TG
*
4878 ATTTGGGGTTTGATCA-TACATG
1 ATTTGGGGTTTGACCATTA-ATG
*
4900 ATTTAGGGTTTGACCATT-ATG
1 ATTTGGGGTTTGACCATTAATG
4921 ATTTGGGGTTTGA
1 ATTTGGGGTTTGA
4934 TCTCATTACT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
21 15 0.31
22 17 0.35
23 17 0.35
ACGTcount: A:0.23, C:0.08, G:0.28, T:0.42
Consensus pattern (22 bp):
ATTTGGGGTTTGACCATTAATG
Found at i:4908 original size:22 final size:21
Alignment explanation
Indices: 4851--4939 Score: 83
Period size: 21 Copynumber: 4.2 Consensus size: 21
4841 GGTTTGACTT
*
4851 TCAT-ATTTGGGGTTTGACCA
1 TCATGATTTGGGGTTTGATCA
* *
4871 TTAAGTAATTTGGGGTTTGATCA
1 -TCA-TGATTTGGGGTTTGATCA
* *
4894 TACATGATTTAGGGTTTGACCA
1 T-CATGATTTGGGGTTTGATCA
*
4916 TTATGATTTGGGGTTTGATC-
1 TCATGATTTGGGGTTTGATCA
4936 TCAT
1 TCAT
4940 TACTAGTAGG
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
20 3 0.05
21 18 0.33
22 18 0.33
23 16 0.29
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.43
Consensus pattern (21 bp):
TCATGATTTGGGGTTTGATCA
Found at i:4972 original size:84 final size:86
Alignment explanation
Indices: 4892--5106 Score: 303
Period size: 84 Copynumber: 2.5 Consensus size: 86
4882 GGGGTTTGAT
* *
4892 CATACATGATTTAGGGTTTGACCATTATGATTTGGGGTTTGATCT-CATTACTAGTAGGGG-TT-
1 CATACATGATTTGGGGTTTGACCATTACGATTTGGGGTTTGATCTCCATTACTAGTAGGGGTTTC
*
4954 TAATCATGCTTTACGGTTTCAC
66 TAATCATGCATTA-GGTTTCAC
* * *
4976 CATACATGATTTGGGGTTTGACCATTACGCTTTGTGGTTTGAT-TCCATTATTAGTAGGGGTTTG
1 CATACATGATTTGGGGTTTGACCATTACGATTTGGGGTTTGATCTCCATTACTAGTAGGGGTTT-
**
5040 CCTAATCATGCATTAAATTTCAC
65 -CTAATCATGCATTAGGTTTCAC
5063 CATACATGATTTGGGGTTTGACCATTACGATTTGGGGTTTGATC
1 CATACATGATTTGGGGTTTGACCATTACGATTTGGGGTTTGATC
5107 GGCTAAATAA
Statistics
Matches: 115, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
83 1 0.01
84 53 0.46
85 2 0.02
87 47 0.41
88 12 0.10
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (86 bp):
CATACATGATTTGGGGTTTGACCATTACGATTTGGGGTTTGATCTCCATTACTAGTAGGGGTTTC
TAATCATGCATTAGGTTTCAC
Found at i:6905 original size:21 final size:22
Alignment explanation
Indices: 6879--6920 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
6869 CCATACATGA
6879 TTTGGGGTTTGA-CCATTACGC
1 TTTGGGGTTTGACCCATTACGC
6900 TTTGGGGTTTGATCCCATTAC
1 TTTGGGGTTTGA-CCCATTAC
6921 TAGTAGGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.40
Consensus pattern (22 bp):
TTTGGGGTTTGACCCATTACGC
Found at i:6990 original size:21 final size:22
Alignment explanation
Indices: 6964--7007 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
6954 CACTATACAT
6964 GATTTGGGGTTTGA-CCATTAC
1 GATTTGGGGTTTGACCCATTAC
6985 GATTTGGGGTTTGATCCCATTAC
1 GATTTGGGGTTTGA-CCCATTAC
7008 TAGTAGGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.67
23 7 0.33
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (22 bp):
GATTTGGGGTTTGACCCATTAC
Found at i:7016 original size:23 final size:21
Alignment explanation
Indices: 6969--7020 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
6959 TACATGATTT
* *
6969 GGGGTTTGACCATTACGATTT
1 GGGGTTTGACCATTACGAGTA
*
6990 GGGGTTTGATCCCATTACTAGTA
1 GGGGTTTGA--CCATTACGAGTA
7013 GGGGTTTG
1 GGGGTTTG
7021 TCTAATCATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 9 0.35
23 17 0.65
ACGTcount: A:0.17, C:0.13, G:0.33, T:0.37
Consensus pattern (21 bp):
GGGGTTTGACCATTACGAGTA
Found at i:7076 original size:21 final size:22
Alignment explanation
Indices: 7051--7094 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
7041 CACCATACAT
*
7051 GATTTGGGGTTTGA-CCATTAC
1 GATTTGAGGTTTGACCCATTAC
7072 GATTTGAGGTTTGATCCCATTAC
1 GATTTGAGGTTTGA-CCCATTAC
7095 TAGGAGGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (22 bp):
GATTTGAGGTTTGACCCATTAC
Found at i:7147 original size:43 final size:45
Alignment explanation
Indices: 7100--7193 Score: 106
Period size: 43 Copynumber: 2.2 Consensus size: 45
7090 ATTACTAGGA
*
7100 GGGGTTTGTCA-AAT-TATGCTTTACAGTTTGACCATTAAAATTT
1 GGGGTTTGTCACAATGGATGCTTTACAGTTTGACCATTAAAATTT
*** * *
7143 GGGG-TT-TCACAATGGATGCTTTGGGGTTTGATCATTAATATTT
1 GGGGTTTGTCACAATGGATGCTTTACAGTTTGACCATTAAAATTT
7186 GGGGTTTG
1 GGGGTTTG
7194 ACTTTCATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
41 3 0.07
42 5 0.12
43 31 0.76
44 2 0.05
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (45 bp):
GGGGTTTGTCACAATGGATGCTTTACAGTTTGACCATTAAAATTT
Found at i:7149 original size:21 final size:21
Alignment explanation
Indices: 7125--7195 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
7115 ATGCTTTACA
7125 GTTTGACCATTAAAATTTGGG
1 GTTTGACCATTAAAATTTGGG
* * * ***
7146 GTTTCACAATGGATGCTTTGGG
1 GTTTGACCAT-TAAAATTTGGG
* *
7168 GTTTGATCATTAATATTTGGG
1 GTTTGACCATTAAAATTTGGG
7189 GTTTGAC
1 GTTTGAC
7196 TTTCATATTT
Statistics
Matches: 35, Mismatches: 14, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
21 21 0.60
22 14 0.40
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.41
Consensus pattern (21 bp):
GTTTGACCATTAAAATTTGGG
Found at i:7149 original size:87 final size:87
Alignment explanation
Indices: 6825--7122 Score: 506
Period size: 87 Copynumber: 3.4 Consensus size: 87
6815 ATTATTTAGC
* *
6825 CCCATTACTAGTAGGGATTTGTCTAATCATGCTTTACAGTTTCACCATACATGATTTGGGGTTTG
1 CCCATTACTAGTAGGGGTTTGTCTAATCATGCTTTA-AATTTCACCATACATGATTTGGGGTTTG
*
6890 ACCATTACGCTTTGGGGTTTGAT
65 ACCATTACGATTTGGGGTTTGAT
* *
6913 CCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTAAATTTCACTATACATGATTTGGGGTTTGA
1 CCCATTACTAGTAGGGGTTTGTCTAATCATGCTTTAAATTTCACCATACATGATTTGGGGTTTGA
6978 CCATTACGATTTGGGGTTTGAT
66 CCATTACGATTTGGGGTTTGAT
7000 CCCATTACTAGTAGGGGTTTGTCTAATCATGCTTTAAATTTCACCATACATGATTTGGGGTTTGA
1 CCCATTACTAGTAGGGGTTTGTCTAATCATGCTTTAAATTTCACCATACATGATTTGGGGTTTGA
*
7065 CCATTACGATTTGAGGTTTGAT
66 CCATTACGATTTGGGGTTTGAT
* * *
7087 CCCATTACTAGGAGGGGTTTGTCAAATTATGCTTTA
1 CCCATTACTAGTAGGGGTTTGTCTAATCATGCTTTA
7123 CAGTTTGACC
Statistics
Matches: 199, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
87 165 0.83
88 34 0.17
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (87 bp):
CCCATTACTAGTAGGGGTTTGTCTAATCATGCTTTAAATTTCACCATACATGATTTGGGGTTTGA
CCATTACGATTTGGGGTTTGAT
Found at i:7606 original size:2 final size:2
Alignment explanation
Indices: 7599--7634 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
7589 TTTAGTGTTT
7599 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7635 GTATGTATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:9017 original size:16 final size:16
Alignment explanation
Indices: 8998--9104 Score: 83
Period size: 16 Copynumber: 6.7 Consensus size: 16
8988 CCCGACCCGA
*
8998 ATGACCCGCAACCCAG
1 ATGACCCGAAACCCAG
* *
9014 ATGACCCGAGACCCAA
1 ATGACCCGAAACCCAG
* *
9030 ATGACTCGTAACCCAG
1 ATGACCCGAAACCCAG
* *
9046 ATAACCCAAAACCC-G
1 ATGACCCGAAACCCAG
* * *
9061 AATAATCCGTAACCCAG
1 -ATGACCCGAAACCCAG
9078 ATGACCCGAAACCC-G
1 ATGACCCGAAACCCAG
*
9093 AATAACCCGAAA
1 -ATGACCCGAAA
9105 AGTTAACCCG
Statistics
Matches: 70, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
15 2 0.03
16 67 0.96
17 1 0.01
ACGTcount: A:0.39, C:0.36, G:0.15, T:0.10
Consensus pattern (16 bp):
ATGACCCGAAACCCAG
Found at i:9027 original size:32 final size:32
Alignment explanation
Indices: 8992--9101 Score: 139
Period size: 32 Copynumber: 3.4 Consensus size: 32
8982 AACCCGCCCG
* * *
8992 ACCCGAATGACCCGCAACCCAGATGACCCGAG
1 ACCCGAATAACCCGTAACCCAGATGACCCGAA
* * * * *
9024 ACCCAAATGACTCGTAACCCAGATAACCCAAA
1 ACCCGAATAACCCGTAACCCAGATGACCCGAA
*
9056 ACCCGAATAATCCGTAACCCAGATGACCCGAA
1 ACCCGAATAACCCGTAACCCAGATGACCCGAA
9088 ACCCGAATAACCCG
1 ACCCGAATAACCCG
9102 AAAAGTTAAC
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.37, C:0.37, G:0.15, T:0.10
Consensus pattern (32 bp):
ACCCGAATAACCCGTAACCCAGATGACCCGAA
Found at i:10999 original size:23 final size:23
Alignment explanation
Indices: 10972--11018 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
10962 GAACCCGCCC
10972 AACCC-GA-GACCCGGTAGACCCGA
1 AACCCAGATGACCCGG-A-ACCCGA
10995 AACCCAGATGACCCGGAACCCGA
1 AACCCAGATGACCCGGAACCCGA
11018 A
1 A
11019 TAACCCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 12 0.55
24 3 0.14
25 7 0.32
ACGTcount: A:0.34, C:0.38, G:0.23, T:0.04
Consensus pattern (23 bp):
AACCCAGATGACCCGGAACCCGA
Found at i:11007 original size:16 final size:16
Alignment explanation
Indices: 10988--11059 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 16
10978 AGACCCGGTA
10988 GACCCGAAACCC-AGAT
1 GACCCGAAACCCGA-AT
*
11004 GACCCGGAACCCGAAT
1 GACCCGAAACCCGAAT
* *
11020 AACCC-AAATCC-AGAT
1 GACCCGAAACCCGA-AT
*
11035 AACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
11051 GACCCGAAA
1 GACCCGAAA
11060 AAACTGTCTG
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
14 1 0.02
15 11 0.24
16 32 0.70
17 2 0.04
ACGTcount: A:0.40, C:0.36, G:0.17, T:0.07
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:11040 original size:31 final size:32
Alignment explanation
Indices: 10972--11059 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 32
10962 GAACCCGCCC
* *
10972 AACCCGAGACCCG-GTAGACCCGAAACCCAGAT
1 AACCCGAAACCCGAATA-ACCCGAAACCCAGAT
* * *
11004 GACCCGGAACCCGAATAACCC-AAATCCAGAT
1 AACCCGAAACCCGAATAACCCGAAACCCAGAT
*
11035 AACCCGAAACCCGAATGACCCGAAA
1 AACCCGAAACCCGAATAACCCGAAA
11060 AAACTGTCTG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 27 0.59
32 17 0.37
33 2 0.04
ACGTcount: A:0.39, C:0.36, G:0.18, T:0.07
Consensus pattern (32 bp):
AACCCGAAACCCGAATAACCCGAAACCCAGAT
Done.