Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014609.1 Corchorus capsularis cultivar CVL-1 contig14630, 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: 10348
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Found at i:128 original size:8 final size:8
Alignment explanation
Indices: 115--148 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
105 CACCTTCTTG
115 AAAAATTC
1 AAAAATTC
123 AAAAATTC
1 AAAAATTC
*
131 AGAAACTTC
1 A-AAAATTC
140 AAAAATTC
1 AAAAATTC
148 A
1 A
149 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:239 original size:5 final size:5
Alignment explanation
Indices: 222--251 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
212 GTTATATCGA
222 AAAAT ATAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAA
252 AATTTGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:4058 original size:21 final size:21
Alignment explanation
Indices: 4032--4073 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4022 GCACAAGTGA
*
4032 CCGGCCATGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
4053 CCGGCCACGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
4074 GCTCGACCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.33, T:0.17
Consensus pattern (21 bp):
CCGGCCACGCGACTTGGAGAT
Found at i:4145 original size:33 final size:32
Alignment explanation
Indices: 4053--4145 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 32
4043 ACTTGGAGAT
* *
4053 CCGGCCACGCGACTTGGAGATGCTCGACCATCA
1 CCGGCCACGCGAC-TGGAGATGCCCGGCCATCA
*
4086 CCGGCCACGTGACTCGGAGATGCCCGGCCATCA
1 CCGGCCACGCGACT-GGAGATGCCCGGCCATCA
*
4119 CCGGCCACGCGACATGGATATGCCCGG
1 CCGGCCACGCGAC-TGGAGATGCCCGG
4146 GCACATGACT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
32 1 0.02
33 51 0.96
34 1 0.02
ACGTcount: A:0.19, C:0.38, G:0.30, T:0.13
Consensus pattern (32 bp):
CCGGCCACGCGACTGGAGATGCCCGGCCATCA
Found at i:6481 original size:8 final size:8
Alignment explanation
Indices: 6468--6519 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 8
6458 TCCCAGCCAG
6468 AAAAAAGA
1 AAAAAAGA
6476 AAAAAAGA
1 AAAAAAGA
6484 GAAAAAGAGA
1 -AAAAA-AGA
6494 AAGAAGAAGA
1 AA-AA-AAGA
6504 ATAAAAGAGA
1 A-AAAA-AGA
6514 AAAAAA
1 AAAAAA
6520 AAGAGAAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
8 9 0.24
9 12 0.32
10 15 0.39
11 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:6523 original size:20 final size:20
Alignment explanation
Indices: 6475--6526 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
6465 CAGAAAAAAG
6475 AAAAAAAGAGAAAAAGAGAA
1 AAAAAAAGAGAAAAAGAGAA
* *
6495 AGAAGAAGA-ATAAAAGAGAA
1 AAAAAAAGAGA-AAAAGAGAA
6515 AAAAAAAGAGAA
1 AAAAAAAGAGAA
6527 GAAACAATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
AAAAAAAGAGAAAAAGAGAA
Found at i:6527 original size:28 final size:28
Alignment explanation
Indices: 6472--6529 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
6462 AGCCAGAAAA
*
6472 AAGAAAAAAAGAGAAAAAGAGAAAGAAG
1 AAGAAAAAAAGAGAAAAAGAAAAAGAAG
*
6500 AAGAATAAAAGAGAAAAA-AAAAGAGAAG
1 AAGAAAAAAAGAGAAAAAGAAAA-AGAAG
6528 AA
1 AA
6530 ACAATGAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (28 bp):
AAGAAAAAAAGAGAAAAAGAAAAAGAAG
Found at i:6601 original size:44 final size:45
Alignment explanation
Indices: 6538--6643 Score: 187
Period size: 45 Copynumber: 2.4 Consensus size: 45
6528 AAACAATGAG
*
6538 GGTTTTCAAAAGGTTTTGATAAAATGG-TTTTCAAAAAGAGTCAT
1 GGTTTTCAAAAGGTTTTGATAAAACGGTTTTTCAAAAAGAGTCAT
*
6582 GGTTTTCAAAAGGTTTTGATAAAACGGTTTTTCAAAAGGAGTCAT
1 GGTTTTCAAAAGGTTTTGATAAAACGGTTTTTCAAAAAGAGTCAT
6627 GGTTTTCAAAAGGTTTT
1 GGTTTTCAAAAGGTTTT
6644 CCAAAGTTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
44 26 0.44
45 33 0.56
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.38
Consensus pattern (45 bp):
GGTTTTCAAAAGGTTTTGATAAAACGGTTTTTCAAAAAGAGTCAT
Found at i:7194 original size:10 final size:10
Alignment explanation
Indices: 7179--7222 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
7169 CATTCAAAGT
7179 AAAGAAGAAA
1 AAAGAAGAAA
7189 AAAGAA-AAA
1 AAAGAAGAAA
7198 AAA-AAGAGAA
1 AAAGAAGA-AA
7208 AAA-AAGAAA
1 AAAGAAGAAA
7217 AAAGAA
1 AAAGAA
7223 AAGAAAAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 2 0.06
9 12 0.39
10 17 0.55
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAGAAGAAA
Found at i:7195 original size:7 final size:7
Alignment explanation
Indices: 7183--7224 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
7173 CAAAGTAAAG
7183 AAGAAAA
1 AAGAAAA
7190 AAGAAAA
1 AAGAAAA
7197 AA-AAAA
1 AAGAAAA
*
7203 GAGAAAAA
1 AAG-AAAA
7211 AAGAAAA
1 AAGAAAA
7218 AAGAAAA
1 AAGAAAA
7225 GAAAAACCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 5 0.16
7 20 0.65
8 6 0.19
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:7207 original size:13 final size:12
Alignment explanation
Indices: 7186--7230 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
7176 AGTAAAGAAG
7186 AAAAAAG-AAAA
1 AAAAAAGAAAAA
*
7197 AAAAAAG--AGA
1 AAAAAAGAAAAA
7207 AAAAAAGAAAAA
1 AAAAAAGAAAAA
*
7219 AGAAAAGAAAAA
1 AAAAAAGAAAAA
7231 CCTTGGCCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.31
11 7 0.24
12 13 0.45
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:7209 original size:20 final size:20
Alignment explanation
Indices: 7179--7230 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
7169 CATTCAAAGT
7179 AAAGAAGAAAAAAGAAAAAAA
1 AAAG-AGAAAAAAGAAAAAAA
*
7200 AAAGAGAAAAAAAGAAAAAAG
1 AAAGAG-AAAAAAGAAAAAAA
7221 AAA-AGAAAAA
1 AAAGAGAAAAA
7231 CCTTGGCCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.17
20 4 0.14
21 20 0.69
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAGAGAAAAAAGAAAAAAA
Found at i:7210 original size:21 final size:20
Alignment explanation
Indices: 7186--7230 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
7176 AGTAAAGAAG
7186 AAAAAAGAAAAAAAAAAGAGA
1 AAAAAAGAAAAAAAAAA-AGA
*
7207 AAAAAAGAAAAAAGAAAAGA
1 AAAAAAGAAAAAAAAAAAGA
7227 AAAA
1 AAAA
7231 CCTTGGCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAAAAGA
Found at i:7838 original size:7 final size:7
Alignment explanation
Indices: 7809--7856 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
7799 AAAGAAAAAG
7809 AAAAGAA
1 AAAAGAA
*
7816 AAAAGGGA
1 AAAA-GAA
* *
7824 GAAGGAA
1 AAAAGAA
7831 AAAAGAA
1 AAAAGAA
7838 AAAAG-A
1 AAAAGAA
7844 AAAAGAA
1 AAAAGAA
7851 AAAAGA
1 AAAAGA
7857 GAATGAAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 6 0.18
7 23 0.70
8 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:7859 original size:33 final size:34
Alignment explanation
Indices: 7799--7870 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 34
7789 GAAGTGCACG
7799 AAAG-AAAAAGAAAAGAAAAAAGGGAGAAGGAA-A
1 AAAGAAAAAAGAAAAGAAAAAA-GGAGAAGGAAGA
*
7832 AAAGAAAAAAGAAAAAGAAAAAA-GAGAATGAAGA
1 AAAGAAAAAAG-AAAAGAAAAAAGGAGAAGGAAGA
7866 AAAGA
1 AAAGA
7871 GACTCTAGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
33 12 0.34
34 12 0.34
35 11 0.31
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (34 bp):
AAAGAAAAAAGAAAAGAAAAAAGGAGAAGGAAGA
Found at i:7868 original size:14 final size:13
Alignment explanation
Indices: 7832--7872 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
7822 GAGAAGGAAA
*
7832 AAAGAAAAAAGAA
1 AAAGAAAAAAGAG
7845 AAAGAAAAAAGAG
1 AAAGAAAAAAGAG
*
7858 AATGAAGAAAAGAG
1 AAAGAA-AAAAGAG
7872 A
1 A
7873 CTCTAGGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAAGAG
Found at i:8849 original size:69 final size:69
Alignment explanation
Indices: 8707--9071 Score: 411
Period size: 69 Copynumber: 5.3 Consensus size: 69
8697 CGAATGCTCC
*
8707 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCATT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGTTTAGCTTTGGTTCCATCCAAGCATT
* *
8772 TAGG
66 AAGA
*
8776 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCTAGCTTTGGTTCCAT-CAAGACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAG-TTTAGCTTTGGTTCCATCCAAG-CA
8840 -TAAGA
64 TTAAGA
* * * * *
8845 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGAT-AGTTTCAGATTCGGTTCCATCCAAGCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAG-TCAGTTT-AGCTTTGGTTCCATCCAAGCA
*
8909 TTCAG-
64 TTAAGA
* * *
8914 GAGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCTAGCTTCGGTTCCATCCAGGCA
1 G-GCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAG-TTTAGCTTTGGTTCCATCCAAGCA
*
8979 --AGATA
64 TTA-AGA
* * * *
8984 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGAT-AGTTTAAGATTTGGTTCCATCCAAGCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAG-TCAGTTT-AGCTTTGGTTCCATCCAAGCA
* *
9048 TTTAGG
64 TTAAGA
*
9054 GGCTTTTCCATAAGCCAA
1 GGCTTTTCCACAAGCCAA
9072 GTTCAGTAAG
Statistics
Matches: 252, Mismatches: 29, Indels: 29
0.81 0.09 0.09
Matches are distributed among these distances:
68 4 0.02
69 148 0.59
70 98 0.39
71 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (69 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGTTTAGCTTTGGTTCCATCCAAGCATT
AAGA
Found at i:8956 original size:139 final size:137
Alignment explanation
Indices: 8707--9071 Score: 554
Period size: 139 Copynumber: 2.6 Consensus size: 137
8697 CGAATGCTCC
* * * *
8707 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAG-TCAGTTTAGCCTTGGTTCCATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGAT-AGTTTAG-ATTGGTTCCATCCAAGCAT
*
8771 TTAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCTAGCTTTGGTTCCATCAA
64 TTAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCTAGCTTCGGTTCCATCAA
8836 GACATA-AGA
129 GACA-AGAGA
8845 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTCAGATTCGGTTCCATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTT-AGATT-GGTTCCATCCAAGCAT
* * *
8910 TCAGGAGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCTAGCTTCGGTTCCATCCA
64 TTAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCTAGCTTCGGTTCCATCAA
* *
8975 GGCAAGATA
129 GACAAGAGA
8984 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTAAGATTTGGTTCCATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTT-AGA-TTGGTTCCATCCAAGCAT
*
9049 TTAGGGGCTTTTCCATAAGCCAA
64 TTAGGGGCTTTTCCACAAGCCAA
9072 GTTCAGTAAG
Statistics
Matches: 208, Mismatches: 14, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
138 40 0.19
139 166 0.80
140 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (137 bp):
GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTAGATTGGTTCCATCCAAGCATTT
AGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCTAGCTTCGGTTCCATCAAGA
CAAGAGA
Found at i:9254 original size:47 final size:47
Alignment explanation
Indices: 9181--9418 Score: 341
Period size: 47 Copynumber: 5.0 Consensus size: 47
9171 ATCCAGGCAA
* * * *
9181 TCTTCTCTCACTTCCACGCGGGTTTTCAATTTAATGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
*
9228 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTGGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
* *
9275 TCTTTTCTCGCTTCCATGCGAGTTTTCAATCTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
* *
9322 TCTTTTCTCGCTTCCACGCGGGTTTTCAATTTACTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
* * * * *
9369 TCTTTCTCTCGCTTCCATGCGAGTCTGCAATTTAGTGACCAGAGTTGG
1 TCTTT-TCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
9417 TC
1 TC
9419 AACGGGTTTT
Statistics
Matches: 171, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
47 134 0.78
48 37 0.22
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.36
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
Found at i:10090 original size:14 final size:14
Alignment explanation
Indices: 10073--10100 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10063 GCATATTAAC
10073 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
10087 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
10101 ATTACTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:10315 original size:20 final size:20
Alignment explanation
Indices: 10290--10328 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10280 AAATACAAGG
10290 CATTTGATTTACAAATTGGA
1 CATTTGATTTACAAATTGGA
*
10310 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
10329 TGCTCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Done.