Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022230.1 Corchorus olitorius cultivar O-4 contig22263, 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: 18490
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Found at i:734 original size:13 final size:13
Alignment explanation
Indices: 718--756 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
708 TTATTGTCTT
718 ATTAAATTGTTTA
1 ATTAAATTGTTTA
*
731 ATTAAATAGTTTTA
1 ATTAAATTG-TTTA
*
745 AATAAATTGTTT
1 ATTAAATTGTTT
757 TGGGTGCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (13 bp):
ATTAAATTGTTTA
Found at i:2715 original size:44 final size:44
Alignment explanation
Indices: 2661--2748 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
2651 TTCATTTTTA
2661 ATTTCTGGTTTTAATTTAATCAAACCCAAATGCTTATTTTCTGT
1 ATTTCTGGTTTTAATTTAATCAAACCCAAATGCTTATTTTCTGT
2705 ATTTCTGGTTTTAATTTAATCAAACCCAAATGCTTATTTTCTGT
1 ATTTCTGGTTTTAATTTAATCAAACCCAAATGCTTATTTTCTGT
2749 GGTTCTCAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (44 bp):
ATTTCTGGTTTTAATTTAATCAAACCCAAATGCTTATTTTCTGT
Found at i:9894 original size:13 final size:13
Alignment explanation
Indices: 9876--9905 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
9866 ACATTGGGAA
9876 TTTTATTTTATTT
1 TTTTATTTTATTT
9889 TTTTATTTTATTT
1 TTTTATTTTATTT
9902 TTTT
1 TTTT
9906 TTGTGGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:12606 original size:354 final size:356
Alignment explanation
Indices: 11921--12622 Score: 921
Period size: 354 Copynumber: 2.0 Consensus size: 356
11911 TTATTTATCT
* * * *
11921 AATGACCCTTATACTTTTATGCATTATGCTATTTAATTCTTTACAAATTCTAGCTTGGTCGATTT
1 AATGACCCTTATACTTTTATACATTATGCTATTTAATCCTTTACAAATTCTAGCTTGATCGATTC
* ** *
11986 AACACTTCGACTTAAATTTTTTTATTTTTTTGTTCTATTTATCCGATTAAGGTGATTCAAATGTC
66 AACACTTCGACTTAAATTTTCTTATTCCTTTGTTCTATTTATCCAATTAAGGTGATTCAAATGTC
*
12051 TATTAAAAGGTAATTTCATGATCTACAACTTTCATGGAAGACTCAAAAGCCAATCTTTATGTTTC
131 TATTAAAAGGTAATTTCATGATCTACAACTTTCATGGAAGACTCAAAAGCAAATCTTTATGTTTC
* * *
12116 AATTCTAAAAAATGCTTCCAAAATTTTATGGTTTTGATTGACAGTCTACTTAATATCGTATAATT
196 AATTCTAAAAAATACTTCCAAAATTTGATGGTTTCGATTGACAGTCTACTTAATATCGTATAATT
* *
12181 TTCGATCCACATGTCTGATTGAAATTACTCAAATATCGGTTAAAAGGTTATTTCATGATCTACGA
261 TTCGATCCACATGTCCGATTGAAATTACTCAAATATCGGTTAAAAGGTTATTTCATGATCTACAA
12246 CTTTCATGAAGAACTCGAAAGCTGAATAAAA
326 CTTTCATGAAGAACTCGAAAGCTGAATAAAA
* *
12277 AATGACCCTTATACTTTTCTACCTTATGCTATTTAATCCTTTACAAATTCTAGCTTGATCGATTC
1 AATGACCCTTATACTTTTATACATTATGCTATTTAATCCTTTACAAATTCTAGCTTGATCGATTC
* ** * * * **
12342 AACACTTC-AGTTTTCATTTTCTT-TTCCTTT-TT-TATTTGTCTAATTTAGGTGATTCAGGTGT
66 AACACTTCGA-CTTAAATTTTCTTATTCCTTTGTTCTATTTATCCAATTAAGGTGATTCAAATGT
* * * * * *
12403 CTATTAAAAGGTAATTTCATGATTTACAACTTTCATGTAGGGCTCAAAAGTAAATTTTTATGTTT
130 CTATTAAAAGGTAATTTCATGATCTACAACTTTCATGGAAGACTCAAAAGCAAATCTTTATGTTT
* * * * * * *
12468 TAGTTCTAAAAAAATACTTCCGAAATTTGGTGGTTTCGATTGACTGTCTATTTAATATCTTATAA
195 CAATTCT-AAAAAATACTTCCAAAATTTGATGGTTTCGATTGACAGTCTACTTAATATCGTATAA
* * * * *
12533 TTTTCGATTCACATGTCCGATT-AAAGTTATTTAAGTTTCGGTTAAAAGGTTATTGT-ATGATCT
259 TTTTCGATCCACATGTCCGATTGAAA-TTACTCAAATATCGGTTAAAAGGTTATT-TCATGATCT
* **
12596 ATAACTTTCATGAAGGGCTCGAAAGCT
322 ACAACTTTCATGAAGAACTCGAAAGCT
12623 AAATTTAATC
Statistics
Matches: 297, Mismatches: 45, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
353 89 0.30
354 125 0.42
355 7 0.02
356 76 0.26
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (356 bp):
AATGACCCTTATACTTTTATACATTATGCTATTTAATCCTTTACAAATTCTAGCTTGATCGATTC
AACACTTCGACTTAAATTTTCTTATTCCTTTGTTCTATTTATCCAATTAAGGTGATTCAAATGTC
TATTAAAAGGTAATTTCATGATCTACAACTTTCATGGAAGACTCAAAAGCAAATCTTTATGTTTC
AATTCTAAAAAATACTTCCAAAATTTGATGGTTTCGATTGACAGTCTACTTAATATCGTATAATT
TTCGATCCACATGTCCGATTGAAATTACTCAAATATCGGTTAAAAGGTTATTTCATGATCTACAA
CTTTCATGAAGAACTCGAAAGCTGAATAAAA
Found at i:16304 original size:38 final size:38
Alignment explanation
Indices: 16261--16357 Score: 167
Period size: 38 Copynumber: 2.6 Consensus size: 38
16251 TCGGTCAATG
16261 TCGAGCCGAGCTCGAGCTCAAGTAGCTCGAGTATCGAA
1 TCGAGCCGAGCTCGAGCTCAAGTAGCTCGAGTATCGAA
* * *
16299 TCGAGCCGAACTCAAGCTCAAGTAGCTCTAGTATCGAA
1 TCGAGCCGAGCTCGAGCTCAAGTAGCTCGAGTATCGAA
16337 TCGAGCCGAGCTCGAGCTCAA
1 TCGAGCCGAGCTCGAGCTCAA
16358 TGATGATTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (38 bp):
TCGAGCCGAGCTCGAGCTCAAGTAGCTCGAGTATCGAA
Found at i:18210 original size:22 final size:21
Alignment explanation
Indices: 18185--18232 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
18175 TCTCAACCTT
18185 AATCAATCAAAACAACATCAAA
1 AATCAA-CAAAACAACATCAAA
** *
18207 AATCAACCCAACAACATCTAA
1 AATCAACAAAACAACATCAAA
18228 AATCA
1 AATCA
18233 TGGAGGGGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (21 bp):
AATCAACAAAACAACATCAAA
Done.