Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017405.1 Corchorus olitorius cultivar O-4 contig17438, 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: 23284
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:420 original size:16 final size:16
Alignment explanation
Indices: 399--430 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
389 TTCATAAGGT
399 TATTAAAAAATTATAA
1 TATTAAAAAATTATAA
*
415 TATTAAATAATTATAA
1 TATTAAAAAATTATAA
431 AATCACAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATTAAAAAATTATAA
Found at i:680 original size:20 final size:21
Alignment explanation
Indices: 657--695 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
647 AGGTAAAAGT
657 TTAATAAAGTTA-TAAAAATG
1 TTAATAAAGTTATTAAAAATG
*
677 TTAATAAGGTTATTAAAAA
1 TTAATAAAGTTATTAAAAA
696 GCTTATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (21 bp):
TTAATAAAGTTATTAAAAATG
Found at i:4816 original size:429 final size:429
Alignment explanation
Indices: 4160--5038 Score: 1136
Period size: 429 Copynumber: 2.0 Consensus size: 429
4150 TATCTTGATT
* * * * *
4160 GGACAAATAGAACAAAGAAAAAAATTAAAGCGTTAAATCGAGTAAAATAGAATTTGTAAAGGACT
1 GGACAAATAGAAAAAAAAAAAAAATTAAAGCGTTAAACCGAGTAAAATAGAATTAGTAAAGAACT
* *
4225 AAGTAGTATAAAGTAAAAAAGTATGAGGGTGATTTGATAAATAATCCAAATAAAAAAGATGTTTG
66 AAGTAG-ATAAAGTAAAAAAGTATGAGGGTCATTTCATAAATAATCCAAATAAAAAAGATGTTTG
* * *
4290 TTGATAGAGATCTTCAAACATAAAAATTCCCTTTTAAACCCTTCATGAAACTTGTAGATCAAATT
130 TTGATAGAGATCTTCAAACAT--AAATT-CC--TTAAACACTTAATGAAACTCGTAGATCAAATT
*
4355 TAGCTTTCAAGTACTTCATGAAAGTCGTAGATCACGCAATAACCTTTAAACTGACACTT-A-AAT
190 TAGCTTTCAAGTACTTCATGAAAGTCGTAGATCACGCAATAACCTTTAAACCGACACTTGAGAA-
* * * *
4418 CACTTTAATCGGACATG-TGAATAT-AAAATTATATGGTATTAAATAGACCGACAATCAAAACCA
254 -ACATTAACCGCACATGTTG-AT-TGAAAATTATATGATATTAAATAGACCGACAATCAAAACCA
* ** * **
4481 CCAAATTTGGGAAGCATTTTTTCTTTGAATTGAAATGTAAAAATTGGCTTTTGAGTTTTTCATGA
316 CCAAATTTCGGAAGCA--TTTT-TTTGAATTGAAACATAAAAATTGGCTTTTAAGTCCTTCATGA
* * *
4546 AAGTTGGAGATCATGAAATTACCTTTTAATCGACACCTGAATCACCTTAATG
378 AAGTTGGAAATCATGAAATTACCTTTTAATAGACACCTGAATCACCTTAATC
* *
4598 GGACAAATAGAAAAAAAAAAATAAAGCTT-AAGCGTTAAACCGATTAAGATTAGAATTAGTAAAG
1 GGACAAATAGAAAAAAAAAAA-AAA--TTAAAGCGTTAAACCGAGTAA-AATAGAATTAGTAAAG
4662 AACTAAGTAG-TAAAGTAGAAAAA-TATGAGGGTCATTTCATAAATAATCCAAATAAAAAA-ATG
62 AACTAAGTAGATAAAGTA-AAAAAGTATGAGGGTCATTTCATAAATAATCCAAATAAAAAAGATG
* * *
4724 TTTGTTGATGGAGATCTTGAAACAT-AA-T-C-TGAACACTTAATGAAACTCGTAGATCAAATTT
126 TTTGTTGATAGAGATCTTCAAACATAAATTCCTTAAACACTTAATGAAACTCGTAGATCAAATTT
** * * * *
4785 AGCTTTCGGGTCCTTCATGAAAGTTGTAGATCATGCAATAACCTTTTAACCGACACTTGAGAAAC
191 AGCTTTCAAGTACTTCATGAAAGTCGTAGATCACGCAATAACCTTTAAACCGACACTTGAGAAAC
* * * *
4850 ATTAGCCGCACATGTTGATTGAAAATTATATGATATTAAATAGATCGGCAATCAAAATCACCAAA
256 ATTAACCGCACATGTTGATTGAAAATTATATGATATTAAATAGACCGACAATCAAAACCACCAAA
*
4915 TTTCGGAAGCATTTTTTTGAATTGAAACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTTGTA
321 TTTCGGAAGCATTTTTTTGAATTGAAACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTTGGA
*
4980 AATCATGAAATTACCTTTTAATAGACACCTGGATCACCTTAATC
386 AATCATGAAATTACCTTTTAATAGACACCTGAATCACCTTAATC
5024 GGACAAATA-AAAAAA
1 GGACAAATAGAAAAAA
5039 TTTAAAAAAA
Statistics
Matches: 391, Mismatches: 41, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
425 6 0.02
426 93 0.24
427 4 0.01
428 1 0.00
429 143 0.37
430 3 0.01
431 2 0.01
432 1 0.00
434 1 0.00
435 2 0.01
438 45 0.12
439 44 0.11
440 21 0.05
441 25 0.06
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (429 bp):
GGACAAATAGAAAAAAAAAAAAAATTAAAGCGTTAAACCGAGTAAAATAGAATTAGTAAAGAACT
AAGTAGATAAAGTAAAAAAGTATGAGGGTCATTTCATAAATAATCCAAATAAAAAAGATGTTTGT
TGATAGAGATCTTCAAACATAAATTCCTTAAACACTTAATGAAACTCGTAGATCAAATTTAGCTT
TCAAGTACTTCATGAAAGTCGTAGATCACGCAATAACCTTTAAACCGACACTTGAGAAACATTAA
CCGCACATGTTGATTGAAAATTATATGATATTAAATAGACCGACAATCAAAACCACCAAATTTCG
GAAGCATTTTTTTGAATTGAAACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTTGGAAATCA
TGAAATTACCTTTTAATAGACACCTGAATCACCTTAATC
Found at i:8257 original size:17 final size:17
Alignment explanation
Indices: 8235--8272 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
8225 ATAAATACCG
*
8235 GTGATCTT-GCATCACTT
1 GTGATCTTAG-ATCACTA
8252 GTGATCTTAGATCACTA
1 GTGATCTTAGATCACTA
8269 GTGA
1 GTGA
8273 ACTGAGGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (17 bp):
GTGATCTTAGATCACTA
Found at i:9014 original size:27 final size:27
Alignment explanation
Indices: 8977--9035 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
8967 ACACATAACT
* * *
8977 TTTGAGTCTCACATAACCTGCAGCTTC
1 TTTGAGACTCACATAACATGCAACTTC
*
9004 TTTGAGACTCACATAACATGGAACTTC
1 TTTGAGACTCACATAACATGCAACTTC
9031 TTTGA
1 TTTGA
9036 ATCTCACCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (27 bp):
TTTGAGACTCACATAACATGCAACTTC
Found at i:9041 original size:27 final size:27
Alignment explanation
Indices: 8977--9042 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
8967 ACACATAACT
* * *
8977 TTTGAGTCTCACATAACCTGCAGCTTC
1 TTTGAATCTCACATAACATGCAACTTC
*
9004 TTTGAGA-CTCACATAACATGGAACTTC
1 TTTGA-ATCTCACATAACATGCAACTTC
9031 TTTGAATCTCAC
1 TTTGAATCTCAC
9043 CTAGAATTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (27 bp):
TTTGAATCTCACATAACATGCAACTTC
Found at i:13794 original size:22 final size:23
Alignment explanation
Indices: 13769--13812 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
13759 CTAAACAATT
* *
13769 TTTTATTTGATTGTTG-ACAAGA
1 TTTTATTTAACTGTTGAACAAGA
*
13791 TTTTTTTTAACTGTTGAACAAG
1 TTTTATTTAACTGTTGAACAAG
13813 TAATGAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.50
Consensus pattern (23 bp):
TTTTATTTAACTGTTGAACAAGA
Found at i:16316 original size:19 final size:20
Alignment explanation
Indices: 16283--16323 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
16273 TTTATTGTAT
*
16283 TTTATTTTTTTTTATATTTA
1 TTTATTTTTTATTATATTTA
16303 TTTA-TTTTTATTATATTTA
1 TTTATTTTTTATTATATTTA
16322 TT
1 TT
16324 AAAATTGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTATTTTTTATTATATTTA
Found at i:16319 original size:15 final size:15
Alignment explanation
Indices: 16280--16323 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
16270 AAGTTTATTG
*
16280 TATTTTATTTTTTTT
1 TATTTTATTTATTTT
16295 TATATTTATTTATTTT
1 TAT-TTTATTTATTTT
*
16311 TATTATATTTATT
1 TATTTTATTTATT
16324 AAAATTGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTTATTTATTTT
Found at i:20023 original size:29 final size:31
Alignment explanation
Indices: 19991--20057 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
19981 ATGCAATTTG
19991 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
*
20020 GGATATAACGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
*
20051 AGATATA
1 GGATATA
20058 GTCCGTTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:20225 original size:31 final size:31
Alignment explanation
Indices: 20187--20265 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
20177 CTAACTGATT
*
20187 ATATCCTTAATTGCTTGAAATCGAAAACGTC
1 ATATCCTTAATTGCTTGAAATAGAAAACGTC
*
20218 ATATCCTTAATTGCTTGAAATAGAAAACGTT
1 ATATCCTTAATTGCTTGAAATAGAAAACGTC
*
20249 ATATCATTAATTGCTTG
1 ATATCCTTAATTGCTTG
20266 TTTTGTAACA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATAGAAAACGTC
Found at i:20314 original size:31 final size:31
Alignment explanation
Indices: 20185--20321 Score: 127
Period size: 31 Copynumber: 4.5 Consensus size: 31
20175 GCCTAACTGA
20185 TTATATCCTTAATTGCTTGAAATC-GAAAACG
1 TTATATCCTTAATTGCTTGAAA-CAGAAAACG
* *
20216 TCATATCCTTAATTGCTTGAAATAGAAAACG
1 TTATATCCTTAATTGCTTGAAACAGAAAACG
* **** * *
20247 TTATATCATTAATTGCTTG-TTTTG-TAACA
1 TTATATCCTTAATTGCTTGAAACAGAAAACG
** *
20276 TTATATCCTTAATTGCTTGTGACAGCAAACG
1 TTATATCCTTAATTGCTTGAAACAGAAAACG
*
20307 TTATATCCTAAATTG
1 TTATATCCTTAATTG
20322 ATTATTTGAC
Statistics
Matches: 86, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
29 21 0.24
30 3 0.03
31 62 0.72
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAACAGAAAACG
Found at i:21141 original size:29 final size:30
Alignment explanation
Indices: 21109--21175 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
21099 ATGCAATTTG
21109 GGATATAACGTTAC-AAAACAAACAATTAA
1 GGATATAACGTTACAAAAACAAACAATTAA
* *
21138 GGATATAACGTTACGAAAAACGAGCAATTAA
1 GGATATAACGTTAC-AAAAACAAACAATTAA
21169 GGATATA
1 GGATATA
21176 GTCCGTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
31 20 0.59
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (30 bp):
GGATATAACGTTACAAAAACAAACAATTAA
Found at i:21573 original size:6 final size:6
Alignment explanation
Indices: 21562--21592 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
21552 GCAGTTCTCT
21562 CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG C
1 CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG C
21593 AACTTCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.16, T:0.32
Consensus pattern (6 bp):
CTCCTG
Done.