Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008744.1 Corchorus capsularis cultivar CVL-1 contig08765, 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: 6922
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Found at i:358 original size:201 final size:200
Alignment explanation
Indices: 1--585 Score: 685
Period size: 201 Copynumber: 3.0 Consensus size: 200
* * *
1 TAACGG-GTATTGTATAATTTTTCTTATAGAATTATTATATAATACACTGTCAATGTAAATTTTG
1 TAACGGTGTATTGTATAAATTTTCTTATAGAATTATTATACAATACACTGTCAGTGTAAATTTTG
* * * * *
65 AACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAAAAATTTTATATTAAT
66 GACTCCATAAACGGGTTAAGAAGTTGACACATACCACATTTCATAATTAAATATTTAATATTAAT
*
130 ACATATTCCCTAAGGATACATATGTCAACCCTTAAAGTTAAATCCC-GCACGTGCAGTCTGCTAA
131 ACATATTCCCTAAGGGTACATATGTCAACCCTTAAA-TTAAA-CCCAGCACGTGCAGTCTGCTAA
194 ACTCCAC
194 ACTCCAC
* * * *
201 TGACGGTGTATTGTATAAATTTTCTTATAGAATTTTTATACAATACACTATCAGTGTGAATTTTG
1 TAACGGTGTATTGTATAAATTTTCTTATAGAATTATTATACAATACACTGTCAGTGTAAATTTTG
*
266 GACTCCATAAACGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAAATATTTAATATTAAT
66 GACTCCATAAACGGGTTAAGAAGTTGACACATACCACATTTCATAATTAAATATTTAATATTAAT
* * *
331 ATATATTCCCTAAGGGTACACATGTCAACCC-----TTAAACCCAGCACTTGCAGTCTGCTAAAC
131 ACATATTCCCTAAGGGTACATATGTCAACCCTTAAATTAAACCCAGCACGTGCAGTCTGCTAAAC
391 TCCAC
196 TCCAC
* * * * *
396 TAAAGGTGTATTGTAT-AATTTTTTTATAGGATTATTATACAATACATTGTCAGCGTAAATTTTG
1 TAACGGTGTATTGTATAAATTTTCTTATAGAATTATTATACAATACACTGTCAGTGTAAATTTTG
* * *
460 GTCTTCAT-AA-GCG----G--G-TGACACATACCACATTTCAAAATTAATTAAATATTTAATAT
66 GACTCCATAAACGGGTTAAGAAGTTGACACATACCACATTTC---A-TAATTAAATATTTAATAT
* * * *
516 TAATACATATTCCCTAAGGGGACATATATCAA--C-T--CTTAAA-CCACGCACGTGTAGTCTGC
127 TAATACATATTCCCTAAGGGTACATATGTCAACCCTTAAATTAAACCCA-GCACGTGCAGTCTGC
575 TAAACTCCAC
191 TAAACTCCAC
585 T
1 T
586 GACAATATAA
Statistics
Matches: 341, Mismatches: 35, Indels: 29
0.84 0.09 0.07
Matches are distributed among these distances:
185 17 0.05
186 1 0.00
187 1 0.00
188 5 0.01
189 75 0.22
192 2 0.01
193 2 0.01
194 50 0.15
195 43 0.13
200 5 0.01
201 140 0.41
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (200 bp):
TAACGGTGTATTGTATAAATTTTCTTATAGAATTATTATACAATACACTGTCAGTGTAAATTTTG
GACTCCATAAACGGGTTAAGAAGTTGACACATACCACATTTCATAATTAAATATTTAATATTAAT
ACATATTCCCTAAGGGTACATATGTCAACCCTTAAATTAAACCCAGCACGTGCAGTCTGCTAAAC
TCCAC
Found at i:1857 original size:26 final size:27
Alignment explanation
Indices: 1828--1881 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
1818 TCTACATAAA
*
1828 TTTATTAACCTCACATTCTTAG-AATT
1 TTTAGTAACCTCACATTCTTAGTAATT
* * *
1854 TTTAGTAATCTTATATTCTTAGTAATT
1 TTTAGTAACCTCACATTCTTAGTAATT
1881 T
1 T
1882 ATTTCTGAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.52
Consensus pattern (27 bp):
TTTAGTAACCTCACATTCTTAGTAATT
Found at i:5545 original size:127 final size:126
Alignment explanation
Indices: 5355--5588 Score: 382
Period size: 127 Copynumber: 1.8 Consensus size: 126
5345 ATACAAAGAA
*
5355 ATTGGCAAGAAGGATTTAACTTTCTATAGTATATCATTTTTATATGAGTTAATTAAGGGTTAATT
1 ATTGGCAAAAAGGATTTAACTTTCTATAGTATATCATTTTTATATGAGTTAATTAAGGGTTAATT
* *
5420 GAATTTGTATTAGTTATTGAATTTTGACATTATTAATCAAAAAGTTCCGTGTAATTCAAAT
66 GAATTGGTATTAGTTATTCAATTTTGACATTATTAATCAAAAAGTTCCGTGTAATTCAAAT
* *
5481 ATTGGCAAAAATGATTTAACTTTCTATCTA-TAGTAT-TTTTTTATATGAGTTAATTAAGGGTTA
1 ATTGGCAAAAAGGATTTAACTTTCTA--TAGTA-TATCATTTTTATATGAGTTAATTAAGGGTTA
5544 ATTGAATTGGTATTAGTTATTCAATTTTGACATTATTAATCAAAA
63 ATTGAATTGGTATTAGTTATTCAATTTTGACATTATTAATCAAAA
5589 TTGATTTGGA
Statistics
Matches: 100, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
126 24 0.24
127 71 0.71
128 5 0.05
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (126 bp):
ATTGGCAAAAAGGATTTAACTTTCTATAGTATATCATTTTTATATGAGTTAATTAAGGGTTAATT
GAATTGGTATTAGTTATTCAATTTTGACATTATTAATCAAAAAGTTCCGTGTAATTCAAAT
Found at i:5742 original size:5 final size:5
Alignment explanation
Indices: 5725--5757 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
5715 AAATATTTAT
*
5725 ATATG ATAAG ATATG ATATG ATAT- ATATG ATAT
1 ATATG ATATG ATATG ATATG ATATG ATATG ATAT
5758 ATGATAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (5 bp):
ATATG
Found at i:6231 original size:22 final size:23
Alignment explanation
Indices: 6181--6231 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
6171 TATGCATGAC
6181 ATTTGGCTCTTTTTCATGCTCAAT
1 ATTTGGCTCTTTTT-ATGCTCAAT
*
6205 ATTTGGCTCTTCTTT-TGCT-GAT
1 ATTTGGCTCTT-TTTATGCTCAAT
6227 ATTTG
1 ATTTG
6232 TACAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 7 0.28
23 4 0.16
24 11 0.44
25 3 0.12
ACGTcount: A:0.14, C:0.18, G:0.16, T:0.53
Consensus pattern (23 bp):
ATTTGGCTCTTTTTATGCTCAAT
Found at i:6893 original size:2 final size:2
Alignment explanation
Indices: 6886--6912 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6876 CATATGCATG
6886 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6913 TTCATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.