Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009788.1 Corchorus capsularis cultivar CVL-1 contig09809, 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: 57729
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:3163 original size:33 final size:33
Alignment explanation
Indices: 3126--3233 Score: 91
Period size: 33 Copynumber: 3.3 Consensus size: 33
3116 AGCACTAGTG
*
3126 ACCGGCCATGCGACTTGGAGAAGCCCGGCCA-A
1 ACCGGCCATGCGACTTGGACAAGCCCGGCCACA
* * * *
3158 CACCGGCCACGCGACATGGACATGTCCGGCCACA
1 -ACCGGCCATGCGACTTGGACAAGCCCGGCCACA
3192 ACCGGCCAT-CG-CTTGGCGCACCAA--CCGGCCACA
1 ACCGGCCATGCGACTT-G-G-A-CAAGCCCGGCCACA
3225 ACCGGCCAT
1 ACCGGCCAT
3234 CGATAGGGTC
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
31 2 0.03
32 3 0.05
33 53 0.85
34 2 0.03
35 2 0.03
ACGTcount: A:0.23, C:0.41, G:0.27, T:0.09
Consensus pattern (33 bp):
ACCGGCCATGCGACTTGGACAAGCCCGGCCACA
Found at i:3753 original size:18 final size:18
Alignment explanation
Indices: 3732--3768 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3722 ACGTAAGTCA
3732 AGTTAATCAATAAAGTTG
1 AGTTAATCAATAAAGTTG
* *
3750 AGTTGATTAATAAAGTTG
1 AGTTAATCAATAAAGTTG
3768 A
1 A
3769 CGATTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (18 bp):
AGTTAATCAATAAAGTTG
Found at i:6665 original size:6 final size:6
Alignment explanation
Indices: 6603--6662 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
6593 TGTCTCTATA
6603 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTG-T TTTG-T
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT
6649 TTTGTT TTT-TT TTT
1 TTTGTT TTTGTT TTT
6663 TTTCCTAAGC
Statistics
Matches: 53, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
5 15 0.28
6 38 0.72
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTGTT
Found at i:12809 original size:13 final size:13
Alignment explanation
Indices: 12793--12823 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
12783 ATATAAATAA
12793 ATTTAAATATTAT
1 ATTTAAATATTAT
12806 ATTTAAATATTAT
1 ATTTAAATATTAT
12819 ATTTA
1 ATTTA
12824 TGTTATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTAAATATTAT
Found at i:22915 original size:51 final size:51
Alignment explanation
Indices: 22874--22977 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
22864 TAGAACAAAC
22874 TGTCCCTGAATTTTAAATTGTGTCACTTTTTTCATTGAATTTGAAAAATCA
1 TGTCCCTGAATTTTAAATTGTGTCACTTTTTTCATTGAATTTGAAAAATCA
22925 TGTCCCTGAATTTTAAATTGTGTCACTTTTTTCATTGAATTTGAAAAATCA
1 TGTCCCTGAATTTTAAATTGTGTCACTTTTTTCATTGAATTTGAAAAATCA
22976 TG
1 TG
22978 ACAATGCCCC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.45
Consensus pattern (51 bp):
TGTCCCTGAATTTTAAATTGTGTCACTTTTTTCATTGAATTTGAAAAATCA
Found at i:28589 original size:6 final size:6
Alignment explanation
Indices: 28578--28610 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
28568 AGGTGGCAAT
28578 TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC TGC
1 TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC TGC
28611 CCACTTGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.18, T:0.48
Consensus pattern (6 bp):
TGCTTC
Found at i:29077 original size:12 final size:12
Alignment explanation
Indices: 29060--29084 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29050 GCTCCAGCAG
29060 CTAATGATACAA
1 CTAATGATACAA
29072 CTAATGATACAA
1 CTAATGATACAA
29084 C
1 C
29085 AGCACGAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (12 bp):
CTAATGATACAA
Found at i:30241 original size:7 final size:7
Alignment explanation
Indices: 30231--30257 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
30221 AACGCGTCAA
30231 TTCAAAT
1 TTCAAAT
30238 TTCAAAT
1 TTCAAAT
30245 TTCAAAT
1 TTCAAAT
30252 TTCAAA
1 TTCAAA
30258 ACAAGGCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (7 bp):
TTCAAAT
Found at i:37466 original size:16 final size:16
Alignment explanation
Indices: 37445--37478 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
37435 ATAATTTGTG
37445 GAATATTTTATACATT
1 GAATATTTTATACATT
37461 GAATATTTTATACATT
1 GAATATTTTATACATT
37477 GA
1 GA
37479 CAAACTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (16 bp):
GAATATTTTATACATT
Done.