Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012798.1 Corchorus capsularis cultivar CVL-1 contig12819, 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: 14349
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Found at i:966 original size:10 final size:10
Alignment explanation
Indices: 951--977 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
941 CTGACTAGCT
951 TAATATTAAC
1 TAATATTAAC
961 TAATATTAAC
1 TAATATTAAC
971 TAATATT
1 TAATATT
978 CATTGGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (10 bp):
TAATATTAAC
Found at i:1060 original size:19 final size:20
Alignment explanation
Indices: 1031--1073 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1021 GATTTTCATC
**
1031 TTTTATCTTTTTTTGGATTT
1 TTTTATCTTTTTTTAAATTT
1051 TTTTAT-TTTTTTTAAATTT
1 TTTTATCTTTTTTTAAATTT
1070 TTTT
1 TTTT
1074 GAAGTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTATCTTTTTTTAAATTT
Found at i:1973 original size:10 final size:10
Alignment explanation
Indices: 1949--1977 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1939 GCCCTTTTTA
1949 CCAAGAACA-
1 CCAAGAACAT
1958 CCAAGAACAT
1 CCAAGAACAT
1968 CCAAGAACAT
1 CCAAGAACAT
1978 TCAAACCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.52, C:0.31, G:0.10, T:0.07
Consensus pattern (10 bp):
CCAAGAACAT
Found at i:2857 original size:21 final size:21
Alignment explanation
Indices: 2831--2875 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2821 TTTATATATA
2831 TTTTTTTTACGTTTCTGTTTT
1 TTTTTTTTACGTTTCTGTTTT
2852 TTTTTTTTACGTTTCTGTTTT
1 TTTTTTTTACGTTTCTGTTTT
2873 TTT
1 TTT
2876 ATTACTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.04, C:0.09, G:0.09, T:0.78
Consensus pattern (21 bp):
TTTTTTTTACGTTTCTGTTTT
Found at i:3677 original size:38 final size:37
Alignment explanation
Indices: 3624--3708 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 37
3614 TTTGGTCGAT
* *
3624 TTTGATAACTGCTGAAAGAGGACATGTTTCTAGTCAA
1 TTTGATAACTCCTGAAAGAGGACATGTTTCCAGTCAA
* * *
3661 CTTTGATAACTCCTGAAGGATGACCTGTTTCCAGTCAA
1 -TTTGATAACTCCTGAAAGAGGACATGTTTCCAGTCAA
3699 TTTGGATAAC
1 TTT-GATAAC
3709 AACAAAGTCG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
37 3 0.07
38 38 0.93
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (37 bp):
TTTGATAACTCCTGAAAGAGGACATGTTTCCAGTCAA
Found at i:3732 original size:97 final size:97
Alignment explanation
Indices: 3618--3805 Score: 236
Period size: 97 Copynumber: 1.9 Consensus size: 97
3608 GACTGATTTG
* * * * *
3618 GTCGATTTTGATAACTGCTGAAAGAG-GACATGTTTCTAGTCAACTTT-GATAACTCCTGAAGGA
1 GTCGACTTTGATAACTGCTGAAA-AGTAACATGTTTCCAGTCAA-TTTCGATAACTCCTAAAAGA
* *
3681 TGACCTGTTTCCAGTCAATTTGGATAACAACAAA
64 TGACATGTTTCCAGTCAATTTAGATAACAACAAA
* * *
3715 GTCGACTTTGATAACTGCTGAAAAGTAACCTGTTTCCAGTCGATTTCGATAACTTCTAAAAGATG
1 GTCGACTTTGATAACTGCTGAAAAGTAACATGTTTCCAGTCAATTTCGATAACTCCTAAAAGATG
* *
3780 ACATGTTTCTAGTCGATTTAGATAAC
66 ACATGTTTCCAGTCAATTTAGATAAC
3806 TTCTTAAGGA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
96 5 0.06
97 72 0.94
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (97 bp):
GTCGACTTTGATAACTGCTGAAAAGTAACATGTTTCCAGTCAATTTCGATAACTCCTAAAAGATG
ACATGTTTCCAGTCAATTTAGATAACAACAAA
Found at i:3752 original size:59 final size:59
Alignment explanation
Indices: 3655--3767 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
3645 ACATGTTTCT
* * *
3655 AGTCAACTTTGATAACTCCTGAAGGATGACCTGTTTCCAGTCAATTTGGATAACAACAA
1 AGTCAACTTTGATAACTCCTGAAAGATAACCTGTTTCCAGTCAATTTCGATAACAACAA
* * *
3714 AGTCGACTTTGATAACTGCTGAAA-AGTAACCTGTTTCCAGTCGATTTCGATAAC
1 AGTCAACTTTGATAACTCCTGAAAGA-TAACCTGTTTCCAGTCAATTTCGATAAC
3768 TTCTAAAAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 1 0.02
59 46 0.98
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (59 bp):
AGTCAACTTTGATAACTCCTGAAAGATAACCTGTTTCCAGTCAATTTCGATAACAACAA
Found at i:3766 original size:38 final size:39
Alignment explanation
Indices: 3714--4143 Score: 454
Period size: 38 Copynumber: 11.3 Consensus size: 39
3704 ATAACAACAA
* *
3714 AGTCGACTTTGATAACTGCTGAAAAG-TAACCTGTTTCC
1 AGTCGATTTTGATAACTGCTGAAAAGATGACCTGTTTCC
* * * *
3752 AGTCGATTTCGATAACTTCT-AAAAGATGACATGTTTCT
1 AGTCGATTTTGATAACTGCTGAAAAGATGACCTGTTTCC
* * * *
3790 AGTCGATTTAGATAACTTCT-TAAGGATGACCTGTTTCC
1 AGTCGATTTTGATAACTGCTGAAAAGATGACCTGTTTCC
* * * *
3828 AGTCAACTTCGATAACTGGT-AAAAGATGACCTGTTTCC
1 AGTCGATTTTGATAACTGCTGAAAAGATGACCTGTTTCC
* * * *
3866 AGTCAACTTCGATAACT-TTGAAAA-ATGACCTGTTTCC
1 AGTCGATTTTGATAACTGCTGAAAAGATGACCTGTTTCC
*
3903 AGTCGATTTTGATAGC-GTCTG-AAAGATGACCTGTTTCC
1 AGTCGATTTTGATAACTG-CTGAAAAGATGACCTGTTTCC
* * *
3941 AGTCGATTTTGATAATTGGT-AAAAGATGACTTGTTTCC
1 AGTCGATTTTGATAACTGCTGAAAAGATGACCTGTTTCC
* * **
3979 AGTCAACTTTGATAACTTTTGAAAA-ATGACCTGTTTCC
1 AGTCGATTTTGATAACTGCTGAAAAGATGACCTGTTTCC
4017 AGTCGATTTTGATAACTGCT-AAAAGATGACCTGTTTCC
1 AGTCGATTTTGATAACTGCTGAAAAGATGACCTGTTTCC
* * ** *
4055 AGTCAACTTTGATAACTTTTGAAAA-ATGACCTATTTCC
1 AGTCGATTTTGATAACTGCTGAAAAGATGACCTGTTTCC
* * *
4093 AATCGATTTTAATAACTTCTG-AAAGATGACCTGTTTCC
1 AGTCGATTTTGATAACTGCTGAAAAGATGACCTGTTTCC
4131 AGTCGATTTTGAT
1 AGTCGATTTTGAT
4144 GACCTGTTTC
Statistics
Matches: 330, Mismatches: 51, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
37 41 0.12
38 280 0.85
39 9 0.03
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (39 bp):
AGTCGATTTTGATAACTGCTGAAAAGATGACCTGTTTCC
Found at i:4057 original size:114 final size:115
Alignment explanation
Indices: 3714--4396 Score: 673
Period size: 114 Copynumber: 6.1 Consensus size: 115
3704 ATAACAACAA
* * * *
3714 AGTCGACTTTGATAACTGCTGAAAAG-TAACCTGTTTCCAGTCGA-TTTCGATAACTTCT-AAAA
1 AGTCAACTTTGATAATTGCTGAAAAGATGACCTGTTTCCAGTCAACTTT-GATAACTTCTGAAAA
* * * * * *
3776 GATGACATGTTTCTAGTCGATTTAGATAACTTCTTAAGGATGACCTGTTTCC
65 -ATGACCTGTTTCCAGTCGATTTTGATAACTGCTGAAAGATGACCTGTTTCC
* * * *
3828 AGTCAACTTCGATAACTGGT-AAAAGATGACCTGTTTCCAGTCAACTTCGATAACTT-TGAAAAA
1 AGTCAACTTTGATAATTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCTGAAAAA
*
3891 TGACCTGTTTCCAGTCGATTTTGATAGC-GTCTGAAAGATGACCTGTTTCC
66 TGACCTGTTTCCAGTCGATTTTGATAACTG-CTGAAAGATGACCTGTTTCC
* * * * *
3941 AGTCGATTTTGATAATTGGT-AAAAGATGACTTGTTTCCAGTCAACTTTGATAACTTTTGAAAAA
1 AGTCAACTTTGATAATTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCTGAAAAA
*
4005 TGACCTGTTTCCAGTCGATTTTGATAACTGCTAAAAGATGACCTGTTTCC
66 TGACCTGTTTCCAGTCGATTTTGATAACTGCTGAAAGATGACCTGTTTCC
* * * * * * *
4055 AGTCAACTTTGATAACTT-TTGAAAA-ATGACCTATTTCCAATCGATTTTAATAACTTCTGAAAG
1 AGTCAACTTTGATAA-TTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCTGAAAA
4118 ATGACCTGTTTCCAGTCGA---T--T---T--T----GATGACCTGTTTCC
65 ATGACCTGTTTCCAGTCGATTTTGATAACTGCTGAAAGATGACCTGTTTCC
* * *
4155 AGTCAACTTTGATGATTGCTG-AAAGATGACCTGTTTCTAGTCAAC-TTGATAACTTCTGAAAGA
1 AGTCAACTTTGATAATTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCTGAAAAA
* * * * *
4218 TGACCTGTTTCCAGTCAACTTCGATAGCTACTGAAAGATGACCTGTTTCC
66 TGACCTGTTTCCAGTCGATTTTGATAACTGCTGAAAGATGACCTGTTTCC
* * * * * * * * *
4268 AGTCAACTTTAATAGCTT-TTGACAA-ATGACCTGTTTCCAGCCAACTTCGGTAACTGCTGAAAG
1 AGTCAACTTTGATA-ATTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCTGAAAA
* * * * * *
4331 ATTACCTGTTTCCAGTCAACTTTGGTAACTGCTGAGAGATGACCTGTTCCC
65 ATGACCTGTTTCCAGTCGATTTTGATAACTGCTGAAAGATGACCTGTTTCC
4382 AGTCAACTTTGATAA
1 AGTCAACTTTGATAA
4397 CTTCTTTGAG
Statistics
Matches: 481, Mismatches: 61, Indels: 55
0.81 0.10 0.09
Matches are distributed among these distances:
99 39 0.08
100 45 0.09
104 2 0.00
106 1 0.00
107 1 0.00
109 2 0.00
111 1 0.00
113 145 0.30
114 236 0.49
115 9 0.02
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (115 bp):
AGTCAACTTTGATAATTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCTGAAAAA
TGACCTGTTTCCAGTCGATTTTGATAACTGCTGAAAGATGACCTGTTTCC
Found at i:4149 original size:24 final size:24
Alignment explanation
Indices: 4117--4169 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
4107 ACTTCTGAAA
* *
4117 GATGACCTGTTTCCAGTCGATTTT
1 GATGACCTGTTTCCAGTCAACTTT
4141 GATGACCTGTTTCCAGTCAACTTT
1 GATGACCTGTTTCCAGTCAACTTT
4165 GATGA
1 GATGA
4170 TTGCTGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (24 bp):
GATGACCTGTTTCCAGTCAACTTT
Found at i:4197 original size:38 final size:38
Alignment explanation
Indices: 4141--4398 Score: 331
Period size: 38 Copynumber: 6.8 Consensus size: 38
4131 AGTCGATTTT
* *
4141 GATGACCTGTTTCCAGTCAACTTTGATGATTGCTGAAA
1 GATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAA
* *
4179 GATGACCTGTTTCTAGTCAAC-TTGATAACTTCTGAAA
1 GATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAA
* * *
4216 GATGACCTGTTTCCAGTCAACTTCGATAGCTACTGAAA
1 GATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAA
* * **
4254 GATGACCTGTTTCCAGTCAACTTTAATAGCTTTTGACAA
1 GATGACCTGTTTCCAGTCAACTTTGATAACTGCTGA-AA
* * *
4293 -ATGACCTGTTTCCAGCCAACTTCGGTAACTGCTGAAA
1 GATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAA
* * *
4330 GATTACCTGTTTCCAGTCAACTTTGGTAACTGCTGAGA
1 GATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAA
*
4368 GATGACCTGTTCCCAGTCAACTTTGATAACT
1 GATGACCTGTTTCCAGTCAACTTTGATAACT
4399 TCTTTGAGTT
Statistics
Matches: 191, Mismatches: 26, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
37 35 0.18
38 154 0.81
39 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (38 bp):
GATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAA
Found at i:4267 original size:137 final size:138
Alignment explanation
Indices: 4004--4271 Score: 385
Period size: 137 Copynumber: 1.9 Consensus size: 138
3994 CTTTTGAAAA
* *
4004 ATGACCTGTTTCCAGTCGATTTTGATAACTGCTAAAAGATGACCTGTTTCCAGTCAACTTTGATA
1 ATGACCTGTTTCCAGTCAACTTTGATAACTGCTAAAAGATGACCTGTTTCCAGTCAACTTTGATA
* * * * *
4069 ACTTTTGAAAAATGACCTATTTCCAATCGATTTTAATAACTTCTGAAAGATGACCTGTTTCCAGT
66 ACTTCTGAAAAATGACCTATTTCCAATCAACTTCAATAACTACTGAAAGATGACCTGTTTCCAGT
4134 CGATTTTG
131 CGATTTTG
* * * *
4142 ATGACCTGTTTCCAGTCAACTTTGATGATTGCTGAAAGATGACCTGTTTCTAGTCAAC-TTGATA
1 ATGACCTGTTTCCAGTCAACTTTGATAACTGCTAAAAGATGACCTGTTTCCAGTCAACTTTGATA
* * * * *
4206 ACTTCTGAAAGATGACCTGTTTCCAGTCAACTTCGATAGCTACTGAAAGATGACCTGTTTCCAGT
66 ACTTCTGAAAAATGACCTATTTCCAATCAACTTCAATAACTACTGAAAGATGACCTGTTTCCAGT
4271 C
131 C
4272 AACTTTAATA
Statistics
Matches: 114, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
137 62 0.54
138 52 0.46
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (138 bp):
ATGACCTGTTTCCAGTCAACTTTGATAACTGCTAAAAGATGACCTGTTTCCAGTCAACTTTGATA
ACTTCTGAAAAATGACCTATTTCCAATCAACTTCAATAACTACTGAAAGATGACCTGTTTCCAGT
CGATTTTG
Found at i:4297 original size:213 final size:214
Alignment explanation
Indices: 3927--4347 Score: 583
Period size: 213 Copynumber: 2.0 Consensus size: 214
3917 GCGTCTGAAA
* * * *
3927 GATGACCTGTTTCCAGTCGATTTTGATAATTGGTAAAAGATGACTTGTTTCCAGTCAACTTTGAT
1 GATGACCTGTTTCCAGTCAACTTTGATAATTGCTAAAAGATGACCTGTTTCCAGTCAACTTTGAT
* * * * *
3992 AACTTTTGAAAAATGACCTGTTTCCAGTCGATTTTGATAACTGCTAAAAGATGACCTGTTTCCAG
66 AACTTCTGAAAAATGACCTGTTTCCAGTCAACTTCGATAACTACTAAAAGATGACCTGTTTCCAG
* * * * * *
4057 TCAACTTTGATAACTTTTGAAAAATGACCTATTTCCAATCGATTTTAATAACTTCTGAAAGATGA
131 TCAACTTTAATAACTTTTGAAAAATGACCTATTTCCAACCAACTTCAATAACTGCTGAAAGATGA
4122 CCTGTTTCCAGTCGATTTT
196 CCTGTTTCCAGTCGATTTT
* * *
4141 GATGACCTGTTTCCAGTCAACTTTGATGATTGCTGAAAGATGACCTGTTTCTAGTCAAC-TTGAT
1 GATGACCTGTTTCCAGTCAACTTTGATAATTGCTAAAAGATGACCTGTTTCCAGTCAACTTTGAT
* * *
4205 AACTTCTGAAAGATGACCTGTTTCCAGTCAACTTCGATAGCTACTGAAAGATGACCTGTTTCCAG
66 AACTTCTGAAAAATGACCTGTTTCCAGTCAACTTCGATAACTACTAAAAGATGACCTGTTTCCAG
* * * * ** *
4270 TCAACTTTAATAGCTTTTGACAAATGACCTGTTTCCAGCCAACTTCGGTAACTGCTGAAAGATTA
131 TCAACTTTAATAACTTTTGAAAAATGACCTATTTCCAACCAACTTCAATAACTGCTGAAAGATGA
4335 CCTGTTTCCAGTC
196 CCTGTTTCCAGTC
4348 AACTTTGGTA
Statistics
Matches: 179, Mismatches: 28, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
213 127 0.71
214 52 0.29
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (214 bp):
GATGACCTGTTTCCAGTCAACTTTGATAATTGCTAAAAGATGACCTGTTTCCAGTCAACTTTGAT
AACTTCTGAAAAATGACCTGTTTCCAGTCAACTTCGATAACTACTAAAAGATGACCTGTTTCCAG
TCAACTTTAATAACTTTTGAAAAATGACCTATTTCCAACCAACTTCAATAACTGCTGAAAGATGA
CCTGTTTCCAGTCGATTTT
Found at i:13817 original size:10 final size:10
Alignment explanation
Indices: 13793--13821 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
13783 GCCCTTTTTA
13793 CCAAGAACA-
1 CCAAGAACAT
13802 CCAAGAACAT
1 CCAAGAACAT
13812 CCAAGAACAT
1 CCAAGAACAT
13822 TCAAAGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.52, C:0.31, G:0.10, T:0.07
Consensus pattern (10 bp):
CCAAGAACAT
Done.