Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023922.1 Corchorus olitorius cultivar O-4 contig23955, 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: 30637
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Found at i:579 original size:19 final size:19
Alignment explanation
Indices: 555--610 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
545 AAAGTGTTCC
555 AATGGTTCGATCCTGACTT
1 AATGGTTCGATCCTGACTT
574 AATGGTTCGAT-CT--C--
1 AATGGTTCGATCCTGACTT
588 AATGGTTCGATCCTGACTT
1 AATGGTTCGATCCTGACTT
607 AATG
1 AATG
611 AAGCACTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.34
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 15 0.47
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (19 bp):
AATGGTTCGATCCTGACTT
Found at i:10294 original size:28 final size:28
Alignment explanation
Indices: 10263--10339 Score: 127
Period size: 28 Copynumber: 2.8 Consensus size: 28
10253 AATTTCAAAA
* *
10263 TCCAGGGGCATTTTGGTCATTTTGCATG
1 TCCAAGGGTATTTTGGTCATTTTGCATG
*
10291 TCCAAGGGTATCTTGGTCATTTTGCATG
1 TCCAAGGGTATTTTGGTCATTTTGCATG
10319 TCCAAGGGTATTTTGGTCATT
1 TCCAAGGGTATTTTGGTCATT
10340 CGCACTCAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (28 bp):
TCCAAGGGTATTTTGGTCATTTTGCATG
Found at i:13179 original size:41 final size:41
Alignment explanation
Indices: 13120--13208 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
13110 TGTTCCCGTT
* *
13120 TACAATTTGGTCCCTGATTTAAG-TTAATATTTACTATTTGA
1 TACAATTTAGTCCCTGATTTAAGATT-ATAGTTACTATTTGA
* * *
13161 TACAATTTAGTCCTTGATTTAGGATTCTAGTTACTATTTGA
1 TACAATTTAGTCCCTGATTTAAGATTATAGTTACTATTTGA
*
13202 TTCAATT
1 TACAATT
13209 GGGTCCTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 39 0.95
42 2 0.05
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (41 bp):
TACAATTTAGTCCCTGATTTAAGATTATAGTTACTATTTGA
Found at i:21304 original size:21 final size:21
Alignment explanation
Indices: 21280--21321 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21270 GCAGTTTAGG
21280 CAACTCCAATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
**
21301 CAACTCTGATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
21322 TTCTTTGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (21 bp):
CAACTCCAATGAGCTTGAAAC
Found at i:22235 original size:20 final size:21
Alignment explanation
Indices: 22197--22237 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
22187 GCAGCTTAGG
22197 CAACTCCAATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
*
22218 CAACTCCGATGA-CTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
22238 TTCTTTGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.37, C:0.29, G:0.15, T:0.20
Consensus pattern (21 bp):
CAACTCCAATGAGCTTGAAAC
Found at i:24473 original size:12 final size:11
Alignment explanation
Indices: 24445--24487 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
24435 AGGGAAGAAG
*
24445 AAAAAGAAGGA
1 AAAAAGAAAGA
24456 AGAAAAGAAAGTA
1 A-AAAAGAAAG-A
24469 AAAAAGAAA-A
1 AAAAAGAAAGA
24479 AAAAAGAAA
1 AAAAAGAAA
24488 AAAGAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 10 0.34
11 1 0.03
12 16 0.55
13 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:24477 original size:17 final size:16
Alignment explanation
Indices: 24439--24495 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
24429 TTAGTTAGGG
* **
24439 AAGAAGAAAAAGAAGG
1 AAGAAAAAAAAGAAAA
*
24455 AAGAAAAGAAAGTAAAA
1 AAGAAAAAAAAG-AAAA
24472 AAGAAAAAAAAAGAAAA
1 AAG-AAAAAAAAGAAAA
24489 AAGAAAA
1 AAGAAAA
24496 TGTCTGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 14 0.41
17 12 0.35
18 8 0.24
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (16 bp):
AAGAAAAAAAAGAAAA
Found at i:28184 original size:424 final size:424
Alignment explanation
Indices: 27387--28225 Score: 1270
Period size: 424 Copynumber: 2.0 Consensus size: 424
27377 ATCCAACATG
* *
27387 GCCAATAGGAATGTTCCACATCATCTTTAGCATCTGAATTTTCGTCCAAAACATTCTACAAGACG
1 GCCAATAGGAATGCTCCACATCATCTTTAGCATCTGAATTTTCATCCAAAACATTCTACAAGACG
* * * * *
27452 GTTTAGGAGAAGATCAATTATGTCCAGAAATTTTAAGGGCAAAATAGTCCACTGGAACGGCAGAA
66 GTTCAGGAAAAGATCAATTATGTCCAAAAATTTTAAGAGCAAAATAGTCCACCGGAACGGCAGAA
*
27517 TTAGGTCTCGAGATAACATAAAAGTTGTAGATCTTGGAATCCTCTTTCCAACGGTAGCTCATTTG
131 TTAGGTCTCGAGATAACATAAAAGTTGTAGATCTTGGAATCCTCTTTCCAACGGTACCTCATTTG
* * *
27582 CATTTTTAAGAGCTTTGAATCAAAAGTTATGAATTTTCTTCCAACACTGCTCTTGTGAAGTCCTC
196 CATTTTTAAGAGCTCTGAATCAAAAGTTATGAATTTCCTTCCAAAACTGCTCTTGTGAAGTCCTC
* *
27647 CTCTGAAATAGATTTAACAATGCTGCATCAGGGCTGAAACATTACTGCATCATAATTACTGATTG
261 CTCTGAAATAGATTTAACAATGCTACATCAGGACTGAAACATTACTGCATCATAATTACTGATTG
*
27712 GACTTAGACTTCTTCTTTGGGCTTCCATATTAACGAAATAGGTCTAAGAATATCAGATTTAAACT
326 GACTTAGACTCCTTCTTTGGGCTTCCATATTAACGAAATAGGTCTAAGAATATCAGATTTAAACT
*
27777 TCAAGACATCTGGGTTGGCAATTTGAGCTTCATA
391 TCAAGACATCTGGCTTGGCAATTTGAGCTTCATA
* * * *
27811 GCCAATAGGAATGCTCTACATCATCTTTAGCATCTGAATTTTCATCCAAAACATTCTCCATGTCG
1 GCCAATAGGAATGCTCCACATCATCTTTAGCATCTGAATTTTCATCCAAAACATTCTACAAGACG
* *
27876 GTTCAGGAAAAGATCAATTCTGTCCAAAAATTTTAAGAGCAAAATTGTCCACCGGAACGGCAGAA
66 GTTCAGGAAAAGATCAATTATGTCCAAAAATTTTAAGAGCAAAATAGTCCACCGGAACGGCAGAA
* *
27941 TTAGGTCTGGAGATAACATAAAAGTTGTAGATCTTGGAATCTTCTTTCCAACGGTACCTCATTTG
131 TTAGGTCTCGAGATAACATAAAAGTTGTAGATCTTGGAATCCTCTTTCCAACGGTACCTCATTTG
** *
28006 CATTTTTCTGAGCTCTGGATCAAAAGTTATGAATTTCCTTCCAAAACTGCTCTTGTGAAGTCCTC
196 CATTTTTAAGAGCTCTGAATCAAAAGTTATGAATTTCCTTCCAAAACTGCTCTTGTGAAGTCCTC
* ** * * *
28071 CTTTG-AATAGGATTTAACAATTTTACATCAGGATTGAATCATTACTGCATCATAATTATTGATT
261 CTCTGAAATA-GATTTAACAATGCTACATCAGGACTGAAACATTACTGCATCATAATTACTGATT
* * * * **
28135 GGA-TTTGAACTCCTTTTTTGGGCTTCCATATTAACG-AATTGGTTCTAAGAATATCATATTTGG
325 GGACTTAG-ACTCCTTCTTTGGGCTTCCATATTAACGAAATAGG-TCTAAGAATATCAGATTTAA
**
28198 GTTTCAAGACATCTGGCTTGGCAATTTG
388 ACTTCAAGACATCTGGCTTGGCAATTTG
28226 GGTTTCATGG
Statistics
Matches: 372, Mismatches: 40, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
423 12 0.03
424 360 0.97
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (424 bp):
GCCAATAGGAATGCTCCACATCATCTTTAGCATCTGAATTTTCATCCAAAACATTCTACAAGACG
GTTCAGGAAAAGATCAATTATGTCCAAAAATTTTAAGAGCAAAATAGTCCACCGGAACGGCAGAA
TTAGGTCTCGAGATAACATAAAAGTTGTAGATCTTGGAATCCTCTTTCCAACGGTACCTCATTTG
CATTTTTAAGAGCTCTGAATCAAAAGTTATGAATTTCCTTCCAAAACTGCTCTTGTGAAGTCCTC
CTCTGAAATAGATTTAACAATGCTACATCAGGACTGAAACATTACTGCATCATAATTACTGATTG
GACTTAGACTCCTTCTTTGGGCTTCCATATTAACGAAATAGGTCTAAGAATATCAGATTTAAACT
TCAAGACATCTGGCTTGGCAATTTGAGCTTCATA
Found at i:30103 original size:7 final size:7
Alignment explanation
Indices: 30091--30120 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
30081 TTTTTGGATA
30091 TTTCTCT
1 TTTCTCT
30098 TTTCTCT
1 TTTCTCT
30105 TTTCTCT
1 TTTCTCT
30112 TTTCT-T
1 TTTCTCT
30118 TTT
1 TTT
30121 ATATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTCTCT
Done.