Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008598.1 Corchorus capsularis cultivar CVL-1 contig08619, 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: 11103
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:602 original size:23 final size:24
Alignment explanation
Indices: 560--605 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
550 ATTATAGTTG
560 TGAGAGCAAAGAAAATGAAGCTTC
1 TGAGAGCAAAGAAAATGAAGCTTC
584 TGAGAGCAAAG-AAATGAAGCTT
1 TGAGAGCAAAGAAAATGAAGCTT
606 GAAGGAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.46, C:0.11, G:0.26, T:0.17
Consensus pattern (24 bp):
TGAGAGCAAAGAAAATGAAGCTTC
Found at i:1675 original size:16 final size:16
Alignment explanation
Indices: 1626--1676 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
1616 ATTCATATAT
1626 AATTTTCTTATAAAAA
1 AATTTTCTTATAAAAA
** * *
1642 AACATTCATATAAGAA
1 AATTTTCTTATAAAAA
*
1658 AATTTTCTTTTAAAAA
1 AATTTTCTTATAAAAA
1674 AAT
1 AAT
1677 AATATTATGT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (16 bp):
AATTTTCTTATAAAAA
Found at i:1834 original size:16 final size:15
Alignment explanation
Indices: 1812--1855 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
1802 TTATAGTTTG
*
1812 AATTCAGTACTTATGA
1 AATTCAGTACTTA-AA
*
1828 GATTCAGTA-TTAAA
1 AATTCAGTACTTAAA
1842 AATTCAGTACTTAA
1 AATTCAGTACTTAA
1856 TCTTTCAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.38
15 7 0.29
16 8 0.33
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (15 bp):
AATTCAGTACTTAAA
Found at i:1877 original size:14 final size:15
Alignment explanation
Indices: 1844--1877 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1834 GTATTAAAAA
*
1844 TTCAGTACTTAATCT
1 TTCAGCACTTAATCT
1859 TTCAGCACTTAAT-T
1 TTCAGCACTTAATCT
1873 TTCAG
1 TTCAG
1878 TTTTATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (15 bp):
TTCAGCACTTAATCT
Found at i:4796 original size:16 final size:16
Alignment explanation
Indices: 4775--4808 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
4765 ATTACATTAT
4775 AATATTTTT-TTGTATA
1 AATATTTTTATTG-ATA
4791 AATATTTTTATTGATA
1 AATATTTTTATTGATA
4807 AA
1 AA
4809 AATGAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
AATATTTTTATTGATA
Found at i:5444 original size:9 final size:8
Alignment explanation
Indices: 5423--5457 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
5413 TCAAAGATGA
5423 GGCACTTG
1 GGCACTTG
5431 GGCACTTAG
1 GGCACTT-G
5440 GGCACTTG
1 GGCACTTG
5448 GGC-CTTG
1 GGCACTTG
5455 GGC
1 GGC
5458 TTTAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.27
8 11 0.42
9 8 0.31
ACGTcount: A:0.11, C:0.26, G:0.40, T:0.23
Consensus pattern (8 bp):
GGCACTTG
Found at i:5547 original size:25 final size:26
Alignment explanation
Indices: 5519--5569 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
5509 TAAGCCTATA
* *
5519 GGAATTTATTTAATAAATTC-TTTTT
1 GGAATTTAATCAATAAATTCGTTTTT
5544 GGAATTTAATCAATAAATTCGTTTTT
1 GGAATTTAATCAATAAATTCGTTTTT
5570 TACCATGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (26 bp):
GGAATTTAATCAATAAATTCGTTTTT
Found at i:10687 original size:25 final size:26
Alignment explanation
Indices: 10659--10709 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
10649 TAAGCCTATA
* *
10659 GGAATTTATTTAATAAATTC-TTTTT
1 GGAATTTAATCAATAAATTCGTTTTT
10684 GGAATTTAATCAATAAATTCGTTTTT
1 GGAATTTAATCAATAAATTCGTTTTT
10710 TACCATGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (26 bp):
GGAATTTAATCAATAAATTCGTTTTT
Done.