Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013312.1 Corchorus olitorius cultivar O-4 contig13345, 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: 42118
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2700 original size:164 final size:164
Alignment explanation
Indices: 2394--2717 Score: 431
Period size: 164 Copynumber: 2.0 Consensus size: 164
2384 TAATGGTTAG
*
2394 AAAACGCCGCTATATATTATAGGCGTAAAGTTGCAAAAATTTCTTTGTTTTAGGAGGAGGGAATT
1 AAAACGCCGCTATATATTATAGGCGTAAAGTTGCAAAAATTTCCTTGTTTTAGGAGGAGGGAATT
* *
2459 TTTCCCTCCAAAAAAAGAGAAAAAAAAATCTCTCCCTCCATATTTTAAAATAGCGGCGTTTCCTT
66 TTTCCCTCCAAAAAAAGAGAAAAAAAAATCTCTCCCTCCATATATTAAAATAGCGACGTTTCCTT
* * *
2524 TTCAAGACGCCACTAATTAGCGGCATCTGATGTC
131 ATCAAAACGCCACTAAATAGCGGCATCTGATGTC
* * * * *
2558 AAAACGCCGCTATATATTATAGGTGTAGAGTTG-GAAACTTTCCTTGTTTTAGTGGGGAGGGAAT
1 AAAACGCCGCTATATATTATAGGCGTAAAGTTGCAAAAATTTCCTTGTTTTAG-GAGGAGGGAAT
* * *
2622 TTTTCCCTCCAAAAAAAG-GAGAAAAAAAATCTTTCTCTCCATATATTAATAT-GACGACGTCTT
65 TTTTCCCTCCAAAAAAAGAGA-AAAAAAAATCTCTCCCTCCATATATTAAAATAG-CGACGT-TT
* * *
2685 TC-TATCAAAACGCCACTAAATGGCGGCGTCTGA
127 CCTTATCAAAACGCCACTAAATAGCGGCATCTGA
2718 AACTCAGACG
Statistics
Matches: 139, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
163 19 0.14
164 117 0.84
165 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (164 bp):
AAAACGCCGCTATATATTATAGGCGTAAAGTTGCAAAAATTTCCTTGTTTTAGGAGGAGGGAATT
TTTCCCTCCAAAAAAAGAGAAAAAAAAATCTCTCCCTCCATATATTAAAATAGCGACGTTTCCTT
ATCAAAACGCCACTAAATAGCGGCATCTGATGTC
Found at i:5946 original size:6 final size:6
Alignment explanation
Indices: 5935--5974 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
5925 CCCAGTTGTC
5935 TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TCCC
1 TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TCCC
5975 CATTGTTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.30, C:0.53, G:0.00, T:0.17
Consensus pattern (6 bp):
TCCCAA
Found at i:6097 original size:6 final size:6
Alignment explanation
Indices: 6088--6117 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
6078 CGCCAACAAC
6088 AACCCA AACCCA AACCCA AACCCA AACCCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA
6118 TCAGCATCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (6 bp):
AACCCA
Found at i:6292 original size:6 final size:6
Alignment explanation
Indices: 6281--6307 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6271 TCGGTTCATC
6281 ATCAAA ATCAAA ATCAAA ATCAAA ATC
1 ATCAAA ATCAAA ATCAAA ATCAAA ATC
6308 CCTTGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.19, G:0.00, T:0.19
Consensus pattern (6 bp):
ATCAAA
Found at i:12024 original size:22 final size:22
Alignment explanation
Indices: 11999--12047 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
11989 AATTATAAAT
* *
11999 TATATAAATTATATATATATCA
1 TATATAAAATAAATATATATCA
* *
12021 TATAGAAAATAAATATATATTA
1 TATATAAAATAAATATATATCA
12043 TATAT
1 TATAT
12048 TATATATTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TATATAAAATAAATATATATCA
Found at i:12526 original size:148 final size:150
Alignment explanation
Indices: 12246--12547 Score: 455
Period size: 148 Copynumber: 2.0 Consensus size: 150
12236 AACCGAGCCG
* *
12246 GTGAGCGTCGGCTCCGTTGGATCCGGTCGGTTTCGTCAGTTAGAACTGACGAACGCCCAACCCTA
1 GTGAGCGTCGGCTCCGTTGGATCAGGTCGGTTTCGTCAGTTAGAACCGACGAACGCCCAACCCTA
* ** **
12311 CCACTCATCAAATCAGTTTGATTTCATATATATAGTACTAGAGTTACAAACAATGAGAACTTTAA
66 CCACTCACCAAATCAGTGAGATTTCATATATATAGTACTAGAGTTACAAACAATGAGAACTCGAA
*
12376 CTAAACGGTTTAGCCAACAT
131 CTAAACGGTTTAGCCAACAA
* * * * *
12396 GTGA-CGTCGGCTCCTTTGGATTAGGTCGGTTTCGTCGGTTGGAACCG-CGAACGCCCAGCCCTA
1 GTGAGCGTCGGCTCCGTTGGATCAGGTCGGTTTCGTCAGTTAGAACCGACGAACGCCCAACCCTA
*
12459 TCACTCACCAAATCAGTGAGATTTCATATATATAGTACTAGAGTTACAAACAATGAGAACTCGAA
66 CCACTCACCAAATCAGTGAGATTTCATATATATAGTACTAGAGTTACAAACAATGAGAACTCGAA
*
12524 CTACACGGTTTAGCCAACAA
131 CTAAACGGTTTAGCCAACAA
12544 GTGA
1 GTGA
12548 TAAGGATAGA
Statistics
Matches: 137, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
148 96 0.70
149 37 0.27
150 4 0.03
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (150 bp):
GTGAGCGTCGGCTCCGTTGGATCAGGTCGGTTTCGTCAGTTAGAACCGACGAACGCCCAACCCTA
CCACTCACCAAATCAGTGAGATTTCATATATATAGTACTAGAGTTACAAACAATGAGAACTCGAA
CTAAACGGTTTAGCCAACAA
Found at i:17600 original size:15 final size:16
Alignment explanation
Indices: 17567--17606 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
17557 TTATTTTGCT
17567 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
17583 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
17598 TTGCTTTCT
1 TTGTTTTCT
17607 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:20574 original size:21 final size:21
Alignment explanation
Indices: 20540--20586 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
20530 CCATTCACCA
*
20540 TGCCATCACCGGTTAAGCCCG
1 TGCCACCACCGGTTAAGCCCG
* * *
20561 TGCCACCACTGGTTATGCCTG
1 TGCCACCACCGGTTAAGCCCG
20582 TGCCA
1 TGCCA
20587 TCGCCATTCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.36, G:0.23, T:0.23
Consensus pattern (21 bp):
TGCCACCACCGGTTAAGCCCG
Found at i:23883 original size:15 final size:16
Alignment explanation
Indices: 23850--23889 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
23840 TTACTTTGCT
23850 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
23866 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
23881 TTGCTTTCT
1 TTGTTTTCT
23890 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:30396 original size:109 final size:109
Alignment explanation
Indices: 30270--30483 Score: 401
Period size: 109 Copynumber: 2.0 Consensus size: 109
30260 CATTTTGGTG
*
30270 CTTGTATTTTTTTTTAAATCCAATAATTCATTGCACTTTGTATTGTTTGGTATGTGTGCTTATTT
1 CTTGTATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTTTGGTATGTGTGCTTATTT
30335 AATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGGTA
66 AATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGGTA
*
30379 CTTGTATTTTTCTTTAAATCCAATAATTCATTGCATTTTGTATTGTTTGGTATGTGTGCTTATTT
1 CTTGTATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTTTGGTATGTGTGCTTATTT
*
30444 AATAGGTTCAATTGAATAAACCACACAATTAATAATAATA
66 AATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
30484 TATACAAGTG
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 102 1.00
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (109 bp):
CTTGTATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTTTGGTATGTGTGCTTATTT
AATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGGTA
Found at i:35403 original size:57 final size:57
Alignment explanation
Indices: 35329--35442 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
35319 TATTTTGTAA
*
35329 AATAATCAAGTAGAGATAGGGGTGATAGGATTTATTATAACATTTATTGTGTGAAAG
1 AATAATCAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAG
* *
35386 AATAATTAAGTATAGATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAG
1 AATAATCAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAG
35443 GAAACGGATA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.34
Consensus pattern (57 bp):
AATAATCAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAG
Found at i:36396 original size:178 final size:178
Alignment explanation
Indices: 36084--36421 Score: 502
Period size: 178 Copynumber: 1.9 Consensus size: 178
36074 TTCCACCATA
* * *
36084 AGCACAAATTATGTAATATTAAGTAGACAGTCTATTTCCGATAACCGAATCAACAAATTCTTTGG
1 AGCACAAATTATATAATATTAAGTAGACAGTCTATTCCCGATAACCGAAACAACAAATTCTTTGG
* *
36149 AAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTGCATGAAAGTTGTAGATCAT
66 AAGCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAATCCTGCATGAAAGTTGTAGATCAT
*
36214 GGAACAACCTTTCAAGAGACACTTGAATCATCTCAATCAGACATCCGG
131 GGAACAACCTTTCAAGAGACACTTAAATCATCTCAATCAGACATCCGG
* * * *
36262 AGCA-AAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAATCGAAACAACAAAATT-TTT
1 AGCACAAA-TTATATAATATTAAGTAGACAGTCTATTCCCGATAACCGAAACAAC-AAATTCTTT
*
36325 GGAAGCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAATCCTTCATGAAAGTTGTAGAT
64 GGAAGCATTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAATCCTGCATGAAAGTTGTAGAT
* * *
36389 CATGGAACAATCTTTTAATAGACACTTAAATCA
128 CATGGAACAACCTTTCAAGAGACACTTAAATCA
36422 CCTAAAGCGG
Statistics
Matches: 143, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
177 7 0.05
178 131 0.92
179 5 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (178 bp):
AGCACAAATTATATAATATTAAGTAGACAGTCTATTCCCGATAACCGAAACAACAAATTCTTTGG
AAGCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAATCCTGCATGAAAGTTGTAGATCAT
GGAACAACCTTTCAAGAGACACTTAAATCATCTCAATCAGACATCCGG
Found at i:37042 original size:2 final size:2
Alignment explanation
Indices: 37035--37067 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
37025 GGCCTATCTA
37035 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 A
37068 GTGTAGACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37159 original size:27 final size:27
Alignment explanation
Indices: 37121--37207 Score: 122
Period size: 27 Copynumber: 3.2 Consensus size: 27
37111 TTTACTTCCT
37121 ATTTTGGTCATTTGCATGTCCAAGGGC
1 ATTTTGGTCATTTGCATGTCCAAGGGC
*
37148 ATTTTGGTCATTTACATGTCC-AGGCGC
1 ATTTTGGTCATTTGCATGTCCAAGG-GC
** *
37175 ATTTTGGTCATTTGCACATCCAGGGGC
1 ATTTTGGTCATTTGCATGTCCAAGGGC
37202 ATTTTG
1 ATTTTG
37208 ATCACTTCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
26 3 0.06
27 48 0.91
28 2 0.04
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (27 bp):
ATTTTGGTCATTTGCATGTCCAAGGGC
Found at i:39345 original size:69 final size:70
Alignment explanation
Indices: 39259--39410 Score: 234
Period size: 69 Copynumber: 2.2 Consensus size: 70
39249 AACAACTCAT
* * *
39259 GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTTTA-ATTTGCGCTCTTCAACAGCACAA
1 GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCAACAGCACAA
39323 GTCCG
66 GTCCG
* * *
39328 GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTTTGCATTCCTCAACAGCCCAA
1 GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCAACAGCACAA
*
39393 GTCCT
66 GTCCG
39398 GGACAGGACTTGG
1 GGACAGGACTTGG
39411 CCAAGATCTG
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
69 40 0.53
70 35 0.47
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (70 bp):
GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCAACAGCACAA
GTCCG
Done.