Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014287.1 Corchorus olitorius cultivar O-4 contig14320, 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: 40554
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:301 original size:8 final size:8
Alignment explanation
Indices: 288--312 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
278 ATCAAATTCC
288 TCAAATTT
1 TCAAATTT
296 TCAAATTT
1 TCAAATTT
304 TCAAATTT
1 TCAAATTT
312 T
1 T
313 GGAGAAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (8 bp):
TCAAATTT
Found at i:301 original size:17 final size:16
Alignment explanation
Indices: 279--312 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
269 ACCTTTTCCA
279 TCAAATTCCTCAAATTT
1 TCAAATT-CTCAAATTT
*
296 TCAAATTTTCAAATTT
1 TCAAATTCTCAAATTT
312 T
1 T
313 GGAGAAGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (16 bp):
TCAAATTCTCAAATTT
Found at i:2512 original size:4 final size:4
Alignment explanation
Indices: 2505--2531 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2495 TTTGAAAAAA
2505 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
2532 AAAAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:9024 original size:2 final size:2
Alignment explanation
Indices: 9017--9050 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9007 TCATCTTAAG
9017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9051 CATGAGGCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25479 original size:21 final size:21
Alignment explanation
Indices: 25437--25475 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25427 TAAGGATCCA
*
25437 ACATTTCAATTTTTCAGTGTT
1 ACATGTCAATTTTTCAGTGTT
25458 ACATGTCAATTTTT-AGTG
1 ACATGTCAATTTTTCAGTG
25476 GTTAACAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.49
Consensus pattern (21 bp):
ACATGTCAATTTTTCAGTGTT
Found at i:27941 original size:9 final size:9
Alignment explanation
Indices: 27927--27952 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
27917 ACGCTTATAA
27927 AATCGTGTT
1 AATCGTGTT
27936 AATCGTGTT
1 AATCGTGTT
27945 AATCGTGT
1 AATCGTGT
27953 CGTGTACGCA
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:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (9 bp):
AATCGTGTT
Found at i:28295 original size:13 final size:13
Alignment explanation
Indices: 28277--28304 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28267 TCTCATAAGC
28277 AAACTCTCAATCT
1 AAACTCTCAATCT
28290 AAACTCTCAATCT
1 AAACTCTCAATCT
28303 AA
1 AA
28305 TCAACCCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (13 bp):
AAACTCTCAATCT
Found at i:37285 original size:81 final size:82
Alignment explanation
Indices: 37150--37315 Score: 325
Period size: 81 Copynumber: 2.0 Consensus size: 82
37140 AACTCTGTCA
37150 CAACTGTAAAAAAACTTCAGTCTATGCTTTGTTTAGCAAATTTGCCTTTTCTGCAGAGTGATGTG
1 CAACTGTAAAAAAACTTCAGTCTATGCTTTGTTTAGCAAATTTGCCTTTTCTGCAGAGTGATGTG
37215 CTGTTGT-AGTAACTAG
66 CTGTTGTGAGTAACTAG
37231 CAACTGTAAAAAAACTTCAGTCTATGCTTTGTTTAGCAAATTTGCCTTTTCTGCAGAGTGATGTG
1 CAACTGTAAAAAAACTTCAGTCTATGCTTTGTTTAGCAAATTTGCCTTTTCTGCAGAGTGATGTG
37296 CTGTTGTGAGTAACTAG
66 CTGTTGTGAGTAACTAG
37313 CAA
1 CAA
37316 GATGGACTAT
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 72 0.86
82 12 0.14
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (82 bp):
CAACTGTAAAAAAACTTCAGTCTATGCTTTGTTTAGCAAATTTGCCTTTTCTGCAGAGTGATGTG
CTGTTGTGAGTAACTAG
Found at i:39506 original size:186 final size:183
Alignment explanation
Indices: 39195--39563 Score: 702
Period size: 186 Copynumber: 2.0 Consensus size: 183
39185 GCACAAAACC
*
39195 CACACGCAACTAATATGGTGAGACTTGAACCTACTTCGTGGTTAGGAAGCATCCACCTTATCATT
1 CACACGCAACGAATATGGTGAGACTTGAACCTACTTCGTGGTTAGGAAGCATCCACCTTATCATT
39260 GAGCCAACTAATATAATAGCCTCACTATGATATGTCAAATATTAGGTTTTGAAGGGTTGTTTCAA
66 GAGCCAACTAATATAATAGCCTCACTATGATATGTCAAATATTAGGTTTTGAAGGGTTGTTTCAA
39325 TTTTCTATTTTGCTTTGATTTTTTTTAAGGGTTGATCAATTTTTTTTCGATTA
131 TTTTCTATTTTGCTTTGATTTTTTTTAAGGGTTGATCAATTTTTTTTCGATTA
39378 CACACGCAACGAATATGGTGAGACTTGAACCTAAGACTTCGTGGTTAGGAAGCATCCACCTTATC
1 CACACGCAACGAATATGGTGAGACTTGAACCT---ACTTCGTGGTTAGGAAGCATCCACCTTATC
39443 ATTGAGCCAACTAATATAATAGCCTCACTATGATATGTCAAATATTAGGTTTTGAAGGGTTGTTT
63 ATTGAGCCAACTAATATAATAGCCTCACTATGATATGTCAAATATTAGGTTTTGAAGGGTTGTTT
39508 CAATTTTCTATTTTGCTTTGATTTTTTTTAAGGGTTGATCAATTTTTTTTCGATTA
128 CAATTTTCTATTTTGCTTTGATTTTTTTTAAGGGTTGATCAATTTTTTTTCGATTA
39564 TTTTATCAAG
Statistics
Matches: 182, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
183 31 0.17
186 151 0.83
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (183 bp):
CACACGCAACGAATATGGTGAGACTTGAACCTACTTCGTGGTTAGGAAGCATCCACCTTATCATT
GAGCCAACTAATATAATAGCCTCACTATGATATGTCAAATATTAGGTTTTGAAGGGTTGTTTCAA
TTTTCTATTTTGCTTTGATTTTTTTTAAGGGTTGATCAATTTTTTTTCGATTA
Found at i:39869 original size:2 final size:2
Alignment explanation
Indices: 39864--39893 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39854 TTTCATTGAA
39864 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39894 GAACTCTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40307 original size:48 final size:47
Alignment explanation
Indices: 40243--40346 Score: 147
Period size: 48 Copynumber: 2.2 Consensus size: 47
40233 AGGAGCAATA
* * * *
40243 AAAAGTAAAAGATCAATTTTTTATTAAAAATTGAGAAAAAAGTGCGAGG
1 AAAAGTAAAGGTTCAATTTTGTAGTAAAAATTGAG-AAAAAGTGC-AGG
40292 AAAA-TAAAGGTTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGG
1 AAAAGTAAAGGTTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGG
40338 AAAAGTAAA
1 AAAAGTAAA
40347 AGATTGCTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
46 7 0.14
47 13 0.26
48 26 0.52
49 4 0.08
ACGTcount: A:0.52, C:0.04, G:0.19, T:0.25
Consensus pattern (47 bp):
AAAAGTAAAGGTTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGG
Done.