Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021025.1 Corchorus olitorius cultivar O-4 contig21058, 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: 22539
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--38 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
39 TATAGGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:723 original size:52 final size:52
Alignment explanation
Indices: 632--737 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 52
622 CATTACTCTT
* * *
632 TTGGAGTGCAATATCTCTTGGCAAAAGTGAGCAATAAAATGACGGTAAATTG
1 TTGGAGTGCAATATCTCTTGGCAAAAGTGACCAAGAAAATGAAGGTAAATTG
*
684 TTGGGGTGCAATATCTCTTGGCAAAAGTGACCAAGAAAATGAAGGTAAATTG
1 TTGGAGTGCAATATCTCTTGGCAAAAGTGACCAAGAAAATGAAGGTAAATTG
736 TT
1 TT
738 CACAATTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (52 bp):
TTGGAGTGCAATATCTCTTGGCAAAAGTGACCAAGAAAATGAAGGTAAATTG
Found at i:1240 original size:36 final size:36
Alignment explanation
Indices: 1193--1265 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1183 AAGAACAAAT
1193 ATCGGCTATAACCAAGAAAAAGGCACAATAGGTTTC
1 ATCGGCTATAACCAAGAAAAAGGCACAATAGGTTTC
*
1229 ATCGGCTATAACCAAGAAAAAGGCACAATGGGTTTC
1 ATCGGCTATAACCAAGAAAAAGGCACAATAGGTTTC
1265 A
1 A
1266 CTACTATGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (36 bp):
ATCGGCTATAACCAAGAAAAAGGCACAATAGGTTTC
Found at i:3152 original size:13 final size:13
Alignment explanation
Indices: 3130--3172 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
3120 CAAAGTTAAG
3130 AAAAACACAAAAAC
1 AAAAA-ACAAAAAC
*
3144 AAAAAACAAAAAT
1 AAAAAACAAAAAC
*
3157 ACAAAAC-AAAAC
1 AAAAAACAAAAAC
3169 AAAA
1 AAAA
3173 CTAAAGGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 7 0.28
13 13 0.52
14 5 0.20
ACGTcount: A:0.81, C:0.16, G:0.00, T:0.02
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:4958 original size:2 final size:2
Alignment explanation
Indices: 4951--4989 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4941 CCTTATTCTG
4951 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4990 ATAGAGAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6699 original size:25 final size:26
Alignment explanation
Indices: 6668--6765 Score: 139
Period size: 25 Copynumber: 3.9 Consensus size: 26
6658 TTGCTGCAGG
* *
6668 AAGTGGCGCAAGGCCTGATAGAAGG-
1 AAGTGGCGCAGGGCCTGAGAGAAGGA
*
6693 AAGTGGCGTAGGGCCTGAGA-AAGGA
1 AAGTGGCGCAGGGCCTGAGAGAAGGA
6718 AAGTGGCGCAGGGCCTGAGAG-AGGA
1 AAGTGGCGCAGGGCCTGAGAGAAGGA
*
6743 AAGTGGCACAGGGCCTGAGAGAA
1 AAGTGGCGCAGGGCCTGAGAGAA
6766 AATAAGCATT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
24 4 0.06
25 60 0.92
26 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.43, T:0.10
Consensus pattern (26 bp):
AAGTGGCGCAGGGCCTGAGAGAAGGA
Found at i:8948 original size:12 final size:12
Alignment explanation
Indices: 8931--8956 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8921 TTGATTCAAT
8931 ATTCCTATATTA
1 ATTCCTATATTA
8943 ATTCCTATATTA
1 ATTCCTATATTA
8955 AT
1 AT
8957 GGAAAGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTCCTATATTA
Found at i:10827 original size:27 final size:26
Alignment explanation
Indices: 10761--10867 Score: 187
Period size: 26 Copynumber: 4.1 Consensus size: 26
10751 TAAAGTCATC
10761 CAGGGGCATTTTGGTCATTTGTACTT
1 CAGGGGCATTTTGGTCATTTGTACTT
10787 CAGGGGCATTTTGGTCATTTGTACTT
1 CAGGGGCATTTTGGTCATTTGTACTT
10813 CAGGGGGCATTTTGGTCATTTGTACTT
1 CA-GGGGCATTTTGGTCATTTGTACTT
* *
10840 CAGGGGCACTTTGGTCTTTTGTACTT
1 CAGGGGCATTTTGGTCATTTGTACTT
10866 CA
1 CA
10868 TTTACCAGCT
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 52 0.67
27 26 0.33
ACGTcount: A:0.15, C:0.17, G:0.27, T:0.41
Consensus pattern (26 bp):
CAGGGGCATTTTGGTCATTTGTACTT
Found at i:10840 original size:53 final size:53
Alignment explanation
Indices: 10763--10867 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 53
10753 AAGTCATCCA
*
10763 GGGGCATTTTGGTCATTTGTACTTCAGGGGCATTTTGGTCATTTGTACTTCAG
1 GGGGCATTTTGGTCATTTGTACTTCAGGGGCACTTTGGTCATTTGTACTTCAG
*
10816 GGGGCATTTTGGTCATTTGTACTTCAGGGGCACTTTGGTCTTTTGTACTTCA
1 GGGGCATTTTGGTCATTTGTACTTCAGGGGCACTTTGGTCATTTGTACTTCA
10868 TTTACCAGCT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.14, C:0.16, G:0.28, T:0.42
Consensus pattern (53 bp):
GGGGCATTTTGGTCATTTGTACTTCAGGGGCACTTTGGTCATTTGTACTTCAG
Found at i:11196 original size:9 final size:9
Alignment explanation
Indices: 11183--11214 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
11173 GTAAAGTAGG
*
11183 AAAATACAG
1 AAAATACAA
11192 AAAATACAA
1 AAAATACAA
11201 AAAATACAA
1 AAAATACAA
11210 AAAAT
1 AAAAT
11215 TGGAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.75, C:0.09, G:0.03, T:0.12
Consensus pattern (9 bp):
AAAATACAA
Found at i:18362 original size:10 final size:10
Alignment explanation
Indices: 18344--18390 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
18334 TTCCCATAAA
*
18344 AAATAAAAAT
1 AAATGAAAAT
18354 AAATGAAAAT
1 AAATGAAAAT
*
18364 AAATGAATGAAA
1 AAATGAA--AAT
18376 AAATGAAAAT
1 AAATGAAAAT
18386 AAATG
1 AAATG
18391 CACTTGGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 23 0.72
12 9 0.28
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (10 bp):
AAATGAAAAT
Found at i:18757 original size:4 final size:4
Alignment explanation
Indices: 18748--18778 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
18738 AAGAAATTCA
18748 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
18779 ATCAATCGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:18795 original size:14 final size:13
Alignment explanation
Indices: 18745--18806 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
18735 ATCAAGAAAT
*
18745 TCAAAATAAATAAA
1 TCAAAA-AAATCAA
* *
18759 T-AAATAAATAAA
1 TCAAAAAAATCAA
18771 T-AAATAAAATCAA
1 TCAAA-AAAATCAA
18784 TCGAAAAAAATCAA
1 TC-AAAAAAATCAA
18798 TCAAAAAAA
1 TCAAAAAAA
18807 AGAGAAGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
12 11 0.26
13 17 0.40
14 11 0.26
15 3 0.07
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.19
Consensus pattern (13 bp):
TCAAAAAAATCAA
Found at i:18807 original size:14 final size:14
Alignment explanation
Indices: 18776--18807 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
18766 ATAAATAAAT
*
18776 AAAATCAATCGAAA
1 AAAATCAATCAAAA
18790 AAAATCAATCAAAA
1 AAAATCAATCAAAA
18804 AAAA
1 AAAA
18808 GAGAAGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.72, C:0.12, G:0.03, T:0.12
Consensus pattern (14 bp):
AAAATCAATCAAAA
Found at i:18831 original size:6 final size:6
Alignment explanation
Indices: 18820--18852 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
18810 GAAGAAAGAA
*
18820 AAAATC AAAATC AAAATC AAAAT- AAAAAC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
18853 AGAATTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:19171 original size:15 final size:15
Alignment explanation
Indices: 19138--19175 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
19128 TCAAGTGCAC
*
19138 AGAAAAAA-AAAGAG
1 AGAAAAAAGAAAAAG
*
19152 TGAAAAAAGAAAAAG
1 AGAAAAAAGAAAAAG
19167 AGAAAAAAG
1 AGAAAAAAG
19176 GAAAGAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (15 bp):
AGAAAAAAGAAAAAG
Found at i:20817 original size:30 final size:30
Alignment explanation
Indices: 20778--21560 Score: 1165
Period size: 30 Copynumber: 25.9 Consensus size: 30
20768 TCATTGCGTG
* *
20778 ATTGTTTTATTTTAATCCTGGTTTAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* * *
20808 ATTGCTTTATATCAATCCTGTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
*
20838 ATTGCTTTATTTTAATCCTAGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
*
20868 ATTGCTTTATTTTAATCTTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* *
20898 GTTGCTCTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
20928 ATTGCTTTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
*
20958 ATTGCTTTATTTCAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* *
20988 GTTGCTTTATTTTAATCCTGGTTTAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
*
21018 ATTGCTTTATTTGAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
21048 ATTGCTTTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
21078 ATTGCTTTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* *
21108 ATTGCTTTATTTCAATCTTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
*
21138 ATTGCGTGATTGTTTTATTTTAATCCTGGTTTAGGATC
1 ATTGC--------TTTATTTTAATCCTGGTTGAGGATC
* * *
21176 ATTGCTTTATATCAATCCTGTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
*
21206 ATTGCTTTATTTTAATCCTAGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
*
21236 ATTGCTTTATTTTAATCTTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* *
21266 GTTGCTCTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
21296 ATTGCTTTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
21326 ATTGCTTTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
21356 ATTGCTTTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* *
21386 ATTGCTTTATTTCAATCCTGATTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* *
21416 GTTGCTTCATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* * *
21446 GTTGTTTTATTTTAAGCCTGGTTGAGGAT-
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* *
21475 ATGTGCATCATTTTAATCCTGGTTGAGGATC
1 AT-TGCTTTATTTTAATCCTGGTTGAGGATC
21506 ATTG-TTTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* *
21535 ATTGCTTTATTTAAATCCTAGTTGAG
1 ATTGCTTTATTTTAATCCTGGTTGAG
21561 TATAATTTTA
Statistics
Matches: 680, Mismatches: 62, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
29 28 0.04
30 623 0.92
31 2 0.00
38 27 0.04
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.46
Consensus pattern (30 bp):
ATTGCTTTATTTTAATCCTGGTTGAGGATC
Found at i:21168 original size:38 final size:38
Alignment explanation
Indices: 21108--21180 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
21098 GTTGAGGATC
*
21108 ATTGCTTTATTTCAATCTTGGTTGAGGATCATTGCGTG
1 ATTGCTTTATTTCAATCCTGGTTGAGGATCATTGCGTG
* * *
21146 ATTGTTTTATTTTAATCCTGGTTTAGGATCATTGC
1 ATTGCTTTATTTCAATCCTGGTTGAGGATCATTGC
21181 TTTATATCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.48
Consensus pattern (38 bp):
ATTGCTTTATTTCAATCCTGGTTGAGGATCATTGCGTG
Found at i:22141 original size:27 final size:26
Alignment explanation
Indices: 22111--22241 Score: 181
Period size: 26 Copynumber: 5.0 Consensus size: 26
22101 AGTCATCCAA
* *
22111 GGGCATTTTGGTCATTTGTATTTCAGG
1 GGGCATTTTGGTCTTTTGTACTTCA-G
*
22138 GGGCATTTTTGTCTTTTGTACTTCAG
1 GGGCATTTTGGTCTTTTGTACTTCAG
** *
22164 GGGCATTTTGGTCAATTGAACTTCAGG
1 GGGCATTTTGGTCTTTTGTACTTCA-G
22191 GGGCATTTTGGTCTTTTGTACTTCAG
1 GGGCATTTTGGTCTTTTGTACTTCAG
*
22217 GGGCACTTTGGTCTTTTGTACTTCA
1 GGGCATTTTGGTCTTTTGTACTTCA
22242 TTTACCAGCT
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
26 47 0.51
27 45 0.49
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.44
Consensus pattern (26 bp):
GGGCATTTTGGTCTTTTGTACTTCAG
Found at i:22240 original size:53 final size:53
Alignment explanation
Indices: 22111--22241 Score: 208
Period size: 53 Copynumber: 2.5 Consensus size: 53
22101 AGTCATCCAA
* *
22111 GGGCATTTTGGTCATTTGTATTTCAGGGGGCATTTTTGTCTTTTGTACTTCAG
1 GGGCATTTTGGTCATTTGTACTTCAGGGGGCATTTTGGTCTTTTGTACTTCAG
* *
22164 GGGCATTTTGGTCAATTGAACTTCAGGGGGCATTTTGGTCTTTTGTACTTCAG
1 GGGCATTTTGGTCATTTGTACTTCAGGGGGCATTTTGGTCTTTTGTACTTCAG
* *
22217 GGGCACTTTGGTCTTTTGTACTTCA
1 GGGCATTTTGGTCATTTGTACTTCA
22242 TTTACCAGCT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 70 1.00
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.44
Consensus pattern (53 bp):
GGGCATTTTGGTCATTTGTACTTCAGGGGGCATTTTGGTCTTTTGTACTTCAG
Done.