Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007022.1 Corchorus capsularis cultivar CVL-1 contig07043, 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: 14255
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:88 original size:22 final size:21
Alignment explanation
Indices: 3--230 Score: 110
Period size: 22 Copynumber: 10.6 Consensus size: 21
1 TT
3 TTTTGATAATCCTCACTATGAAA
1 TTTTGATAA-CCT-ACTATGAAA
* * * *
26 TTTTGTTAATCTCCCTATAAAA
1 TTTTGATAACCT-ACTATGAAA
* *
48 TTTTGATTTACATACTATGAAA
1 TTTTGA-TAACCTACTATGAAA
*
70 TTTTGATAACCTTCTTATGAAA
1 TTTTGATAACCTAC-TATGAAA
*
92 TTTTGA-AAACTAAACTATGAAAA
1 TTTTGATAACCT--ACTATG-AAA
*
115 TTTTTGATAACCTTCATATGAAA
1 -TTTTGATAACCTAC-TATGAAA
* * * *
138 TTTTAATATCCTCCT-TCAAA
1 TTTTGATAACCTACTATGAAA
* *
158 TTTTGATTACTCTA-TAATAAAA
1 TTTTGATAAC-CTACT-ATGAAA
* * * *
180 GTTTAATAACCTTC-CT--AA
1 TTTTGATAACCTACTATGAAA
*
198 -TTTGGTAACCATACTATGAAA
1 TTTTGATAACC-TACTATGAAA
219 TTTTGATAACCT
1 TTTTGATAACCT
231 CCCCAGAAAT
Statistics
Matches: 152, Mismatches: 36, Indels: 36
0.68 0.16 0.16
Matches are distributed among these distances:
17 8 0.05
18 4 0.03
19 1 0.01
20 13 0.09
21 17 0.11
22 76 0.50
23 19 0.12
24 10 0.07
25 4 0.03
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (21 bp):
TTTTGATAACCTACTATGAAA
Found at i:109 original size:44 final size:44
Alignment explanation
Indices: 17--141 Score: 135
Period size: 44 Copynumber: 2.8 Consensus size: 44
7 GATAATCCTC
* * * * * ** *
17 ACTATGAAATTTTGTTAATCTCCCTATAAAATTTTGATTTACAT
1 ACTATGAAATTTTGATAACCTTCATATGAAATTTTGATAAACAA
*
61 ACTATGAAATTTTGATAACCTTCTTATGAAATTTTGA-AAACTAA
1 ACTATGAAATTTTGATAACCTTCATATGAAATTTTGATAAAC-AA
105 ACTATGAAAATTTTTGATAACCTTCATATGAAATTTT
1 ACTATG-AAA-TTTTGATAACCTTCATATGAAATTTT
142 AATATCCTCC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 2 0.03
44 39 0.57
45 3 0.04
46 25 0.36
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (44 bp):
ACTATGAAATTTTGATAACCTTCATATGAAATTTTGATAAACAA
Found at i:295 original size:22 final size:22
Alignment explanation
Indices: 270--390 Score: 93
Period size: 22 Copynumber: 5.5 Consensus size: 22
260 AATCATATTT
270 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* *
292 TGAAATTTTGATAACCTCTCTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
314 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
* * * *
336 TGAAATTTTGATAATCACATTA
1 TGAAAATTTGATAACCTCTTTA
* * *
358 TGTAATTTTGATAACCTCGCTT-
1 TGAAAATTTGATAACCTC-TTTA
380 TGAAAATTTGA
1 TGAAAATTTGA
391 AATTGGACCC
Statistics
Matches: 77, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
21 3 0.04
22 69 0.90
23 5 0.06
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:365 original size:44 final size:44
Alignment explanation
Indices: 249--373 Score: 126
Period size: 44 Copynumber: 2.8 Consensus size: 44
239 ATACCACTAC
* * * * * *
249 GAAATTTTGGTAATCATATTTTGAAAATTTGATAACCTCTTTAT
1 GAAATTTTGATAATCACATTATGAAATTTTGATAACCCCTCTAT
* * * * *
293 GAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACCCCTCTAT
1 GAAATTTTGATAATCACAT-TATGAAATTTTGATAACCCCTCTAT
*
337 GAAATTTTGATAATCACATTATGTAATTTTGATAACC
1 GAAATTTTGATAATCACATTATGAAATTTTGATAACC
374 TCGCTTTGAA
Statistics
Matches: 62, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
43 1 0.02
44 60 0.97
45 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (44 bp):
GAAATTTTGATAATCACATTATGAAATTTTGATAACCCCTCTAT
Found at i:384 original size:44 final size:43
Alignment explanation
Indices: 249--390 Score: 117
Period size: 44 Copynumber: 3.2 Consensus size: 43
239 ATACCACTAC
* * * * *
249 GAAATTTTGGTAATCATATTTTGAAAATTTGATAACCTCTTTAT
1 GAAATTTTGATAATCACATTATGAAATTTTGATAACCTCCTT-T
* * * * *
293 GAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACC-CCTCTAT
1 GAAATTTTGATAATCACAT-TATGAAATTTTGATAACCTCCT-T-T
*
337 GAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTTT
1 GAAATTTTGATAATCACATTATGAAATTTTGATAACCTC-CTTT
*
381 GAAAATTTGA
1 GAAATTTTGA
391 AATTGGACCC
Statistics
Matches: 76, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
43 3 0.04
44 68 0.89
45 3 0.04
46 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (43 bp):
GAAATTTTGATAATCACATTATGAAATTTTGATAACCTCCTTT
Found at i:11951 original size:27 final size:28
Alignment explanation
Indices: 11908--11965 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
11898 AAATTTTTTT
11908 AAAGAAAAAATCATTTTCTTCTTT-AAA
1 AAAGAAAAAATCATTTTCTTCTTTGAAA
** * *
11935 AAAGAAAAAATGGTTTTTTTTTTTGAAA
1 AAAGAAAAAATCATTTTCTTCTTTGAAA
11963 AAA
1 AAA
11966 ACAGAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (28 bp):
AAAGAAAAAATCATTTTCTTCTTTGAAA
Done.