Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015650.1 Corchorus olitorius cultivar O-4 contig15683, 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: 27571
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:3279 original size:18 final size:18
Alignment explanation
Indices: 3253--3287 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3243 TTTGAGTTCG
* *
3253 AGGAGTTCTTCGTCTTCA
1 AGGACTTCTTCGGCTTCA
3271 AGGACTTCTTCGGCTTC
1 AGGACTTCTTCGGCTTC
3288 CACCAGGAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.37
Consensus pattern (18 bp):
AGGACTTCTTCGGCTTCA
Found at i:5790 original size:2 final size:2
Alignment explanation
Indices: 5785--5824 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5775 CTCTTGATTA
5785 AT AT AT 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 AT AT AT
5825 TGCCTTGCGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14755 original size:22 final size:21
Alignment explanation
Indices: 14721--14763 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
14711 TTTTTTTTAC
14721 AAAAATTGCATTTTATATAAACAA
1 AAAAATT-CA-TTTA-ATAAACAA
14745 AAAAATT-ATTTAATAAACA
1 AAAAATTCATTTAATAAACA
14764 TTTTTTCCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 1 0.05
24 7 0.37
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAAATTCATTTAATAAACAA
Found at i:20892 original size:178 final size:179
Alignment explanation
Indices: 20482--20902 Score: 485
Period size: 178 Copynumber: 2.3 Consensus size: 179
20472 TTAAAATTGT
* * * * * * *
20482 ATAATTTTCGTTCCGGATATCCGATTAAGGTGATTCAAGTGTTTATTAAAAAGTTGTTTCATTAT
1 ATAATTTTTGCTCCAGATGTCCGATTGAGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCATTAT
* *
20547 CTACAACTTTCATGAAAGACTCAAAAACTGAATTAATTAATGTTTAAAGTATCAAAAATACTTCC
66 CTACAACTTTCATGAAAGAATCAAAAACTGAA-TAATTAATGTTTAAAGTATAAAAAATACTTCC
*
20612 GAAAAATTAGTTGTTTCGGTTGATGGGAATGGACGTTCCACTTAATATTAC
130 GAAAAATTAGTTGTTTCGGTT-ATGGGAATGGACGGTCCACTTAATATTAC
* * * * * * *
20663 ATAACTTCTGCTCCAAATGTCTGATTGAGGTGATGC-AGCTGTCTCTTAAAAGGTTGTTTTATTA
1 ATAATTTTTGCTCCAGATGTCCGATTGAGGTGATTCAAG-TGTCTATTAAAAGGTTGTTTCATTA
* * * * ** *
20727 TCTACAACTTTCAT-ACAGAATTATAAAGCT-AA-ATTTAATGTTTCGAGTATAAAAAATGCTTC
65 TCTACAACTTTCATGAAAGAATCA-AAAACTGAATAATTAATGTTTAAAGTATAAAAAATACTTC
*
20789 C-AAAAATTTAGTTGTTTCGGTT-TGCGAGAATGGATGGTCCACTTAATATTAC
129 CGAAAAA-TTAGTTGTTTCGGTTATG-G-GAATGGACGGTCCACTTAATATTAC
** *
20841 ATAATTTTTGCTCCAGATGTCCGATTGAGGTGATTCAAGTACCTGTTAAAAGGTTGTTTCAT
1 ATAATTTTTGCTCCAGATGTCCGATTGAGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCAT
20903 GATATGTGAC
Statistics
Matches: 200, Mismatches: 34, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
176 2 0.01
177 6 0.03
178 114 0.57
179 2 0.01
180 10 0.05
181 66 0.33
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (179 bp):
ATAATTTTTGCTCCAGATGTCCGATTGAGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCATTAT
CTACAACTTTCATGAAAGAATCAAAAACTGAATAATTAATGTTTAAAGTATAAAAAATACTTCCG
AAAAATTAGTTGTTTCGGTTATGGGAATGGACGGTCCACTTAATATTAC
Found at i:20987 original size:178 final size:177
Alignment explanation
Indices: 20583--20987 Score: 399
Period size: 178 Copynumber: 2.3 Consensus size: 177
20573 ACTGAATTAA
*
20583 TTAATGTTT-AAAGTATCAAAAATACTTCCG-AAAAATTAGTTGTTTCGGTTGATGGGAATGGAC
1 TTAATGTTTCAAA-TACCAAAAATACTT-CGAAAAAATTAGTTGTTTCGGTT-ATGGGAATGGAC
* * **
20646 GTTCCACTTAATATTACATAACTTCTGCTCCAAATGTCTGATTGAGGTGATGCAGCTGTCTCTTA
63 GGTCCACTTAATATTACATAACTTCTGCTCCAAATGTCCGATTGAGGTGATGCAGCTACCTCTTA
* * * * *
20711 AAAGGTTGTTTTATTATCTACAACTTTCATACAGAATTATAAAGCTAAAT
128 AAAGGTTGTTTCATGATATACAACTTTCATACAGAACTAGAAAGCTAAAT
* * ** * * * *
20761 TTAATGTTTCGAGTATAAAAAATGCTTCCAAAAATTTAGTTGTTTCGGTT-TGCGAGAATGGATG
1 TTAATGTTTCAAATACCAAAAATACTTCGAAAAAATTAGTTGTTTCGGTTATG-G-GAATGGACG
* * * * *
20825 GTCCACTTAATATTACATAATTTTTGCTCCAGATGTCCGATTGAGGTGATTCAAG-TACCTGTTA
64 GTCCACTTAATATTACATAACTTCTGCTCCAAATGTCCGATTGAGGTGATGC-AGCTACCTCTTA
*** * * *
20889 AAAGGTTGTTTCATGATATGTGACTTTCATGA-AGGACTCGAAATCTAAAT
128 AAAGGTTGTTTCATGATATACAACTTTCAT-ACAGAACTAGAAAGCTAAAT
* * * *
20939 TTGATTTTTCAAATACCAAAAATTCTTCTGAAAAAATT-GTTATTTCGGT
1 TTAATGTTTCAAATACCAAAAATACTTC-GAAAAAATTAGTTGTTTCGGT
20988 GGATTTTTTA
Statistics
Matches: 183, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
176 2 0.01
177 2 0.01
178 168 0.92
179 11 0.06
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (177 bp):
TTAATGTTTCAAATACCAAAAATACTTCGAAAAAATTAGTTGTTTCGGTTATGGGAATGGACGGT
CCACTTAATATTACATAACTTCTGCTCCAAATGTCCGATTGAGGTGATGCAGCTACCTCTTAAAA
GGTTGTTTCATGATATACAACTTTCATACAGAACTAGAAAGCTAAAT
Found at i:21618 original size:29 final size:31
Alignment explanation
Indices: 21559--21618 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 31
21549 ATCTCACCAT
* * * *
21559 GAAAATATGATGAGATTTTAAAAGAAGAAAA
1 GAAAATATGATCAGATTATAAAAAAAAAAAA
21590 GAAAATA-GATCA-ATTATAAAAAAAAAAAA
1 GAAAATATGATCAGATTATAAAAAAAAAAAA
21619 AAATCATGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 14 0.56
30 4 0.16
31 7 0.28
ACGTcount: A:0.65, C:0.02, G:0.13, T:0.20
Consensus pattern (31 bp):
GAAAATATGATCAGATTATAAAAAAAAAAAA
Found at i:23567 original size:2 final size:2
Alignment explanation
Indices: 23560--23587 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23550 GAAAGCATAA
23560 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
23588 TATTCCTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25278 original size:8 final size:8
Alignment explanation
Indices: 25265--25290 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
25255 ATTTCTTTCT
25265 CTCTCTCC
1 CTCTCTCC
25273 CTCTCTCC
1 CTCTCTCC
25281 CTCTCTCC
1 CTCTCTCC
25289 CT
1 CT
25291 ATCTGTCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (8 bp):
CTCTCTCC
Found at i:27274 original size:2 final size:2
Alignment explanation
Indices: 27262--27294 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
27252 ATCAAACCAA
27262 AT AT A- 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
27295 CATGTCTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.