Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008616.1 Corchorus capsularis cultivar CVL-1 contig08637, 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: 15938
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:6939 original size:12 final size:13
Alignment explanation
Indices: 6917--6945 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6907 TTGAACAAGA
6917 AAAACTAAAAAAT
1 AAAACTAAAAAAT
6930 AAAA-TAAAAAAT
1 AAAACTAAAAAAT
6942 AAAA
1 AAAA
6946 AAAGTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAACTAAAAAAT
Found at i:7462 original size:53 final size:55
Alignment explanation
Indices: 7399--7506 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 55
7389 TTCAGGTTTC
7399 AGTTTTTACTCG-CTATTTCCCAAAACACCCTTCCCGGACGGAAGACACT-ATTT
1 AGTTTTTACTCGCCTATTTCCCAAAACACCCTTCCCGGACGGAAGACACTGATTT
* * * *
7452 AGTTTTTACTCGCCTCTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTGATTT
1 AGTTTTTACTCGCCTATTTCCCAAAACACCCTTCCCGGACGGAAGACACTGATTT
7507 TTACCTGTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
53 12 0.24
54 33 0.67
55 4 0.08
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.31
Consensus pattern (55 bp):
AGTTTTTACTCGCCTATTTCCCAAAACACCCTTCCCGGACGGAAGACACTGATTT
Found at i:7625 original size:48 final size:49
Alignment explanation
Indices: 7401--7730 Score: 251
Period size: 48 Copynumber: 6.7 Consensus size: 49
7391 CAGGTTTCAG
* * ** * * *
7401 TTTTTACTCGCTATTTCCCAAAACACCCTTCCCGGACGGAAGACACTATTTA
1 TTTTTACTCGCTTTTTCCTAAAATGCCCTTCCCGGATGGAAGGCGC---TTA
* * * * *
7453 GTTTTTACTCGCCTCTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTGA
1 -TTTTTACTCG-CTTTTTCCTAAAATGCCCTTCCCGGATGGAAGGCGCTTA
* * * * * * *
7504 TTTTTAC-CTG-TTGTTTTCTAAAACGCCCTTCCTGGACGGAAGACACTAA
1 TTTTTACTC-GCTT-TTTCCTAAAATGCCCTTCCCGGATGGAAGGCGCTTA
* *
7553 TCTTTA---GCTTTTTCCTAAAATGCCCTTCCCGGATGGAAGACGCTTA
1 TTTTTACTCGCTTTTTCCTAAAATGCCCTTCCCGGATGGAAGGCGCTTA
* * * * * *
7599 TTTTTAC-CACTTTTCCCTAAAGTGCCCTTCCCGGACGGAAGGCACTAA
1 TTTTTACTCGCTTTTTCCTAAAATGCCCTTCCCGGATGGAAGGCGCTTA
* * *
7647 TTTTTACTTGCTTTTTTCTAAAACGCCCTTCCCGGATGGAAGGCG-TTA
1 TTTTTACTCGCTTTTTCCTAAAATGCCCTTCCCGGATGGAAGGCGCTTA
* * *
7695 GTTTTACTCGCTTTTTCTTAAAATGCCCTTTCCGGA
1 TTTTTACTCGCTTTTTCCTAAAATGCCCTTCCCGGA
7731 CGAAAGGCAA
Statistics
Matches: 230, Mismatches: 40, Indels: 19
0.80 0.14 0.07
Matches are distributed among these distances:
46 36 0.16
47 2 0.01
48 73 0.32
49 67 0.29
50 8 0.03
51 2 0.01
53 10 0.04
54 32 0.14
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (49 bp):
TTTTTACTCGCTTTTTCCTAAAATGCCCTTCCCGGATGGAAGGCGCTTA
Found at i:8843 original size:15 final size:16
Alignment explanation
Indices: 8823--8860 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
8813 GATTAATCTC
*
8823 TCGGGTTGA-TCAGGT
1 TCGGGTCGATTCAGGT
8838 TCGGGTCGATTCAGGT
1 TCGGGTCGATTCAGGT
*
8854 TTGGGTC
1 TCGGGTC
8861 ATTAAAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.11, C:0.16, G:0.39, T:0.34
Consensus pattern (16 bp):
TCGGGTCGATTCAGGT
Found at i:10090 original size:21 final size:21
Alignment explanation
Indices: 10053--10092 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
10043 AATAAAAATC
*
10053 ATATTAAATATTAATGGTGAT
1 ATATTAAATACTAATGGTGAT
10074 ATATTAAATTACT-ATGGTG
1 ATATTAAA-TACTAATGGTG
10093 TGATTATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (21 bp):
ATATTAAATACTAATGGTGAT
Found at i:10946 original size:18 final size:18
Alignment explanation
Indices: 10889--10946 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 18
10879 TACTCCCTCC
*
10889 CATTCAAAATAAGTGCAA
1 CATTCAAATTAAGTGCAA
*
10907 CATTTCAAGATT---TGCAGT
1 CA-TTCAA-ATTAAGTGCA-A
10925 CATTCAAATTAAGTGCAA
1 CATTCAAATTAAGTGCAA
10943 CATT
1 CATT
10947 TATAAACCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 12
0.67 0.07 0.26
Matches are distributed among these distances:
16 3 0.10
17 9 0.29
18 8 0.26
19 9 0.29
20 2 0.06
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (18 bp):
CATTCAAATTAAGTGCAA
Found at i:13545 original size:204 final size:204
Alignment explanation
Indices: 13195--13603 Score: 773
Period size: 204 Copynumber: 2.0 Consensus size: 204
13185 TAAAACATCT
* * *
13195 GTTTTTCACCTCAAATGCAATATCAAATAAGTTTTGGTTTGTATTAGAAGTTGATTTTGACAGTA
1 GTTTTTCACCTCAAATACAATACCAAATAAGTTTTGGTTTGTATTAGAAGTTGATTTTGACAGCA
* *
13260 AAAGCTAATCTTTAGGTGTTTTTGCGTTTCACAAGTTCTTTTAGACATCAAATTACTAAAATCTT
66 AAAGCTAATCTTTAGGTGCTTTTGCGTTTCACAAGTTCTTTTAGACACCAAATTACTAAAATCTT
13325 TTAATAATTTTCTATTCCCTTTTTAACTTATATCTTTTTTAGACATTTTATCTTTTTATCATATT
131 TTAATAATTTTCTATTCCCTTTTTAACTTATATCTTTTTTAGACATTTTATCTTTTTATCATATT
13390 TTTTCCAAG
196 TTTTCCAAG
13399 GTTTTTCACCTCAAATACAATACCAAATAAGTTTTGGTTTGTATTAGAAGTTGATTTTGACAGCA
1 GTTTTTCACCTCAAATACAATACCAAATAAGTTTTGGTTTGTATTAGAAGTTGATTTTGACAGCA
13464 AAAGCTAATCTTTAGGTGCTTTTGCGTTTCACAAGTTCTTTTAGACACCAAATTACTAAAATCTT
66 AAAGCTAATCTTTAGGTGCTTTTGCGTTTCACAAGTTCTTTTAGACACCAAATTACTAAAATCTT
13529 TTAATAATTTTCTATTCCCTTTTTAACTTATATCTTTTTTAGACATTTTATCTTTTTATCATATT
131 TTAATAATTTTCTATTCCCTTTTTAACTTATATCTTTTTTAGACATTTTATCTTTTTATCATATT
13594 TTTTCCAAG
196 TTTTCCAAG
13603 G
1 G
13604 CAATACCAAA
Statistics
Matches: 200, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
204 200 1.00
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (204 bp):
GTTTTTCACCTCAAATACAATACCAAATAAGTTTTGGTTTGTATTAGAAGTTGATTTTGACAGCA
AAAGCTAATCTTTAGGTGCTTTTGCGTTTCACAAGTTCTTTTAGACACCAAATTACTAAAATCTT
TTAATAATTTTCTATTCCCTTTTTAACTTATATCTTTTTTAGACATTTTATCTTTTTATCATATT
TTTTCCAAG
Done.