Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021829.1 Corchorus olitorius cultivar O-4 contig21862, 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: 51353
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:1228 original size:15 final size:15
Alignment explanation
Indices: 1210--1246 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1200 TTATTGTTCA
1210 CACCATTGTTATTCG
1 CACCATTGTTATTCG
* *
1225 CACCATTGTTGTTTG
1 CACCATTGTTATTCG
1240 CACCATT
1 CACCATT
1247 CACCCTAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.41
Consensus pattern (15 bp):
CACCATTGTTATTCG
Found at i:1457 original size:24 final size:26
Alignment explanation
Indices: 1425--1488 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
1415 AGGATTTTGG
* *
1425 TTATCCACACCATT-GTTGA-TGGCA
1 TTATTCACACCATTACTTGATTGGCA
*
1449 TTATTCACACCATTCACTTGATTTGCA
1 TTATTCACACCATT-ACTTGATTGGCA
1476 TTATTCACACCAT
1 TTATTCACACCAT
1489 GATGGAGAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.38
26 4 0.12
27 17 0.50
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.38
Consensus pattern (26 bp):
TTATTCACACCATTACTTGATTGGCA
Found at i:2145 original size:49 final size:46
Alignment explanation
Indices: 2063--2206 Score: 182
Period size: 49 Copynumber: 3.0 Consensus size: 46
2053 GAGCGTGCCA
* * *
2063 ATCAATTTTGTCAAAAAATTGAAAAAAAGTGCAATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAA-GAAAAATAAAAG
2110 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAG-AAAAATAAAAG
* * *
2159 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGAAAAGTAAAAG
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGAAAAATAAAAG
2205 AT
1 AT
2207 TGCTTTGAGT
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
46 11 0.13
47 14 0.16
48 19 0.22
49 42 0.49
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (46 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGAAAAATAAAAG
Found at i:3501 original size:9 final size:9
Alignment explanation
Indices: 3481--3509 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3471 TTAATTCATT
3481 TAATTTCC-
1 TAATTTCCA
3489 TAATTTCCA
1 TAATTTCCA
3498 TAATTTCCA
1 TAATTTCCA
3507 TAA
1 TAA
3510 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:4553 original size:81 final size:81
Alignment explanation
Indices: 4460--4624 Score: 312
Period size: 81 Copynumber: 2.0 Consensus size: 81
4450 GTATCTAACG
*
4460 TGTTAAAAGTTATTTCATGGAGAAATTTCGGAAACGAGCAGCTCCCAACAAAAAGCTTCTATGGT
1 TGTTAAAAGTTATTTCATGGAGAAATTTCGGAAACGAGCAGCTCCCAACAAAAAACTTCTATGGT
4525 AATGCCTTCATCCTTC
66 AATGCCTTCATCCTTC
*
4541 TGTTAAAAGTTATTTCATGGAGAAATTTTGGAAACGAGCAGCTCCCAACAAAAAACTTCTATGGT
1 TGTTAAAAGTTATTTCATGGAGAAATTTCGGAAACGAGCAGCTCCCAACAAAAAACTTCTATGGT
4606 AATGCCTTCATCCTTC
66 AATGCCTTCATCCTTC
4622 TGT
1 TGT
4625 CATCCTTTCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (81 bp):
TGTTAAAAGTTATTTCATGGAGAAATTTCGGAAACGAGCAGCTCCCAACAAAAAACTTCTATGGT
AATGCCTTCATCCTTC
Found at i:5579 original size:5 final size:5
Alignment explanation
Indices: 5566--5600 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
5556 AGCCAGGAAA
*
5566 AAAAT AAAAG AAAAG AAAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG AAAA
5601 AACTTAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:5590 original size:16 final size:16
Alignment explanation
Indices: 5565--5601 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
5555 AAGCCAGGAA
*
5565 AAAAATAAAAGAAAAG
1 AAAAAGAAAAGAAAAG
5581 AAAAAGAAAAGAAAAG
1 AAAAAGAAAAGAAAAG
5597 AAAAA
1 AAAAA
5602 ACTTAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAG
Found at i:9643 original size:9 final size:9
Alignment explanation
Indices: 9611--9636 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
9601 GAGTTGAACT
9611 AAAAATTTC
1 AAAAATTTC
9620 AAAAATTTC
1 AAAAATTTC
9629 AAAAATTT
1 AAAAATTT
9637 AATAAATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAAATTTC
Found at i:15265 original size:52 final size:52
Alignment explanation
Indices: 15164--15266 Score: 152
Period size: 52 Copynumber: 2.0 Consensus size: 52
15154 AAAAGAGGAT
* * *
15164 AGAGACCCAAGTGCTTGAACTATCCAAAAGTGAAGAAAACGCTTGAACTATG
1 AGAGACCCAAGTGCTTGAACTATCCAAAAGTGAAGAAAACACCTAAACTATG
* * *
15216 AGAGATCCAAGTGTTTGAACTATCCAAAAGTGGAGAAAACACCTAAACTAT
1 AGAGACCCAAGTGCTTGAACTATCCAAAAGTGAAGAAAACACCTAAACTAT
15267 CAATAAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (52 bp):
AGAGACCCAAGTGCTTGAACTATCCAAAAGTGAAGAAAACACCTAAACTATG
Found at i:19979 original size:16 final size:16
Alignment explanation
Indices: 19958--19991 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
19948 AGAAGTTCAC
19958 ACCTTAACTTGGTTTT
1 ACCTTAACTTGGTTTT
19974 ACCTTAACTTGGTTTT
1 ACCTTAACTTGGTTTT
19990 AC
1 AC
19992 TCTGAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (16 bp):
ACCTTAACTTGGTTTT
Found at i:35382 original size:216 final size:217
Alignment explanation
Indices: 34959--35395 Score: 752
Period size: 216 Copynumber: 2.0 Consensus size: 217
34949 CAAATAGAAT
*
34959 AAAAAATACAAAAATAAAAGCCGACACATTAAATCGTCCAACCCATAATTGTAAAGGATTAAATA
1 AAAAAAAACAAAAATAAAAGCCGACACATTAAATCGTCCAACCCATAATTGTAAAGGATTAAATA
35024 GCATAAAACATAAAAGTATGAGGATCATTCGATAAATAATCCAACAAAAAATATTTCTTTATGGA
66 GCATAAAACATAAAAGTATGAGGATCATTCGATAAATAATCCAACAAAAAATATTTCTTTATGGA
* * *
35089 GAATGGGTCCCACGGAGGGTAACTTTTTTGGAAATTTCCCAAAACACCCTCGGTCCTCAACCAAA
131 GAATGGGCCCCACGGAGGGTAACTTTTTTGCAAATTTCCCAAAACACCCTCGATCCTCAACCAAA
35154 ATAACAAAAAAAAC-GAGTATG
196 ATAACAAAAAAAACTGAGTATG
*
35175 AAAAAAAACAAAAATAAAAGCCGACACATTAAATCGTCCAACCCATGATTGTAAAGGATTAAATA
1 AAAAAAAACAAAAATAAAAGCCGACACATTAAATCGTCCAACCCATAATTGTAAAGGATTAAATA
* *
35240 GCATAAAACATAAAAGTATGAGGATCATTCGATAAATAATTCAACAAAAAAATATTTCTTTGTGG
66 GCATAAAACATAAAAGTATGAGGATCATTCGATAAATAATCCAAC-AAAAAATATTTCTTTATGG
* * *
35305 AGAATGGGCCCCATGGAGGGTAACTTTTTTGCAAATTTCTCAAAACGCCCTCGATCCTCAACCAA
130 AGAATGGGCCCCACGGAGGGTAACTTTTTTGCAAATTTCCCAAAACACCCTCGATCCTCAACCAA
*
35370 AATAA-GAAAAAAACTGAGTATG
195 AATAACAAAAAAAACTGAGTATG
35392 AAAA
1 AAAA
35396 TACTGAAATA
Statistics
Matches: 208, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
216 115 0.55
217 93 0.45
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (217 bp):
AAAAAAAACAAAAATAAAAGCCGACACATTAAATCGTCCAACCCATAATTGTAAAGGATTAAATA
GCATAAAACATAAAAGTATGAGGATCATTCGATAAATAATCCAACAAAAAATATTTCTTTATGGA
GAATGGGCCCCACGGAGGGTAACTTTTTTGCAAATTTCCCAAAACACCCTCGATCCTCAACCAAA
ATAACAAAAAAAACTGAGTATG
Found at i:39054 original size:72 final size:73
Alignment explanation
Indices: 38919--39062 Score: 245
Period size: 72 Copynumber: 2.0 Consensus size: 73
38909 TAATTTATAT
* *
38919 AATCCGCTACCTATCAAACAAACAAACAAATAAACTAAACTCACATCCCATGAGAATTGAATTCA
1 AATCCGCTACCTACCAAACAAACAAACAAATAAACTAAACTCACATCCCATAAGAATTGAATTCA
38984 GACCTCAC
66 GACCTCAC
* *
38992 AATCCGCTACCTACCAAACAAATAAACAAA-AAACTAAACTCACATCCCATAAGACTTGAATTCA
1 AATCCGCTACCTACCAAACAAACAAACAAATAAACTAAACTCACATCCCATAAGAATTGAATTCA
39056 GACCTCA
66 GACCTCA
39063 TGATCCAGAT
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
72 39 0.58
73 28 0.42
ACGTcount: A:0.46, C:0.29, G:0.06, T:0.19
Consensus pattern (73 bp):
AATCCGCTACCTACCAAACAAACAAACAAATAAACTAAACTCACATCCCATAAGAATTGAATTCA
GACCTCAC
Found at i:40481 original size:21 final size:20
Alignment explanation
Indices: 40437--40483 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
40427 TAGAATGTAC
*
40437 GCAAAATAAAACATTATGAT
1 GCAAAATAAAAAATTATGAT
40457 -CAAAATAAAAAAATT-TAGAT
1 GCAAAAT-AAAAAATTAT-GAT
40477 GCAAAAT
1 GCAAAAT
40484 GACAATTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 7 0.30
20 10 0.43
21 6 0.26
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (20 bp):
GCAAAATAAAAAATTATGAT
Found at i:47339 original size:40 final size:40
Alignment explanation
Indices: 47284--47363 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
47274 ATTCACATAA
*
47284 ATGTTATGATAAATCCTATCCCCCTTAATTATCTAGAATT
1 ATGTTATAATAAATCCTATCCCCCTTAATTATCTAGAATT
47324 ATGTTATAATAAATCCTATCCCCCTTAATTATCTAGAATT
1 ATGTTATAATAAATCCTATCCCCCTTAATTATCTAGAATT
47364 GTAACCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (40 bp):
ATGTTATAATAAATCCTATCCCCCTTAATTATCTAGAATT
Done.