Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011958.1 Corchorus capsularis cultivar CVL-1 contig11979, 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: 5477
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1173 original size:11 final size:11
Alignment explanation
Indices: 1136--1177 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
1126 TATACTATAT
1136 CTAA-TAATAG
1 CTAATTAATAG
*
1146 CTAATTAATAA
1 CTAATTAATAG
*
1157 CGAATTAATAG
1 CTAATTAATAG
*
1168 TTAATTAATA
1 CTAATTAATA
1178 ATGAACAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 4 0.15
11 22 0.85
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:4190 original size:37 final size:37
Alignment explanation
Indices: 4129--5473 Score: 1390
Period size: 37 Copynumber: 36.6 Consensus size: 37
4119 GTGTCAAAGT
*
4129 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAATTC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * * *
4166 CTTATTTATGGTCCCTGTTTAGGTGTCTAATCAAAAT-
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATC-AAATC
* * * *
4203 CTTGTTCAAGATCCCTGTTTAAGTGTGTTATCAAACC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * **
4240 CTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAAA
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* *
4277 CTTGTTCAAGATCCCTGTTTAGGTGTCTTATTAAATC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* *
4314 CTTGTTTAAGGA-CCCTGTTTAGGTGTCTCATCTAAAAC
1 CTTGTTTAA-GATCCCTGTTTAGGTGTCTTATC-AAATC
* *
4352 CTTGTTCAAGATCCTTGTTTTAGGTGTCTTATCAAATC
1 CTTGTTTAAGATCCCTG-TTTAGGTGTCTTATCAAATC
* *
4390 C---TTT--G-----T-TTTAGGTGTCTCATCAAAAC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* *
4416 CTTGTTCAAGATCCATGTTTAGGTGTCTTATCAAATC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* *
4453 CTTGTTTAAGATCCCTGTTTAGGTGTCTCATCAAAAC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * * *
4490 CTTGTTCAAGATCCCTATTTACGTGTCTTATCAAATT
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * * *
4527 CTTGCTTAAGGTCCCTATTTAGGTGTCTCATCAAAAT-
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATC-AAATC
* *
4564 CTT-TTTCAAGATCCCTTTTTAGGTGTATTATCAAATC
1 CTTGTTT-AAGATCCCTGTTTAGGTGTCTTATCAAATC
* * * *
4601 CTTGTTTAAGGTCCATGTTTAGGTGTCTCATCAAAAC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
*
4638 CTTGTTCAAGATCCCTGTTTAGGTGTCTTATCAAATC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * * *
4675 CATGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAAC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * *
4712 CTTGTTCAAGACCCCTGGTTAGGTGTCTTATCAAATC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * * *
4749 CATGTTTAATG-TCACTGGTTAGGTGTCTCATCAAAAT-
1 CTTGTTTAA-GATCCCTGTTTAGGTGTCTTATC-AAATC
* * *
4786 CTTGTTCAAGATCCCTGTTTAGTTATCTTATCAAATC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * *
4823 CTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAAC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* *
4860 CTTGTTCAAGATCCATGTTTAGGTGTCTTATCAAATC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * ** *
4897 CTTGTTTAAGGTCCCTGTTTAGCTGTCACATCAAAAC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
*
4934 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATGAAATC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * *
4971 TTTGTTTAAGGTCCCTGTTTAGGTGTCTTATCAAATT
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * *
5008 CTT-TCTTAAGGTCCCTATTTAGGTGTCTCATCAAAAT-
1 CTTGT-TTAAGATCCCTGTTTAGGTGTCTTATC-AAATC
* * * *
5045 CTTTTTTCAAGATCCCTTTTTAGGTCTCTTATTAAATC
1 CTTGTTT-AAGATCCCTGTTTAGGTGTCTTATCAAATC
* * * *
5083 CTTGTTTAAGGTCCCTATTTAGGTGTCTCATCAAAAC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* *
5120 CTTGTTCAAGATCCCTGTTTAGGTGTCTTATCAAATT
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * * *
5157 CTTGCTTAAGGTCCCTCTTTAGGTGTCTCATCAAAAT-
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATC-AAATC
* * * *
5194 CTAT-TTCAAGATTCATGTTTAGTTGTCTTATCAAATC
1 CT-TGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * * *
5231 CTTGTTTAAGGTCCCTGTTTTGGTGTCTCATCAAAAC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * *
5268 CTTGTTCT-AGATCCATGATTAGGTGTCTTATCAAATA
1 CTTGTT-TAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * *
5305 CTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAAC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
*
5342 CTT-TTTCAATATCCCAT-TTTAGGTGTCTTATCAAATC
1 CTTGTTT-AAGATCCC-TGTTTAGGTGTCTTATCAAATC
* * * *
5379 CTTGTTTAAGGTCCCTATTTAGGTGTCTCATCAAAAC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
* * *
5416 CTTGTTCAAGATCCAT-TTTAAGTGTCTTATCAAATC
1 CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
**
5452 CTTGTTTAAGGCCCCTGTTTAG
1 CTTGTTTAAGATCCCTGTTTAG
5474 ATGT
Statistics
Matches: 1070, Mismatches: 197, Indels: 82
0.79 0.15 0.06
Matches are distributed among these distances:
26 19 0.02
28 1 0.00
29 2 0.00
31 1 0.00
33 1 0.00
35 2 0.00
36 55 0.05
37 896 0.84
38 79 0.07
39 14 0.01
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (37 bp):
CTTGTTTAAGATCCCTGTTTAGGTGTCTTATCAAATC
Found at i:4392 original size:25 final size:25
Alignment explanation
Indices: 4357--4421 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 25
4347 AAAACCTTGT
*
4357 TCAAGATCCTTGTTTTAGGTGTCTTA
1 TCAA-ATCCTTGTTTTAGGTGTCTCA
4383 TCAAATCCTTTGTTTTAGGTGTCTCA
1 TCAAATCC-TTGTTTTAGGTGTCTCA
*
4409 TCAAAACCTTGTT
1 TCAAATCCTTGTT
4422 CAAGATCCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 9 0.25
26 27 0.75
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (25 bp):
TCAAATCCTTGTTTTAGGTGTCTCA
Done.