Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015335.1 Corchorus capsularis cultivar CVL-1 contig15356, 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: 53597
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:12458 original size:19 final size:19
Alignment explanation
Indices: 12430--12491 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
12420 TATGAGAAAG
*
12430 TGATCCTTGTTTGGTGTAA
1 TGATCATTGTTTGGTGTAA
*
12449 TGATCATTGTTTGGTCTAA
1 TGATCATTGTTTGGTGTAA
* *
12468 TGGCATCTTTTTTTGGTGTAA
1 T-G-ATCATTGTTTGGTGTAA
12489 TGA
1 TGA
12492 AAAATCTCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 15 0.42
ACGTcount: A:0.18, C:0.10, G:0.24, T:0.48
Consensus pattern (19 bp):
TGATCATTGTTTGGTGTAA
Found at i:12941 original size:26 final size:26
Alignment explanation
Indices: 12900--12965 Score: 107
Period size: 26 Copynumber: 2.5 Consensus size: 26
12890 AATCACATCC
12900 AATGGTGGATGGAGTCTGGAAAAAAAA
1 AATGGTGGATGGAGTCT-GAAAAAAAA
*
12927 AA-GGTGGATGTAGTCTGAAAAAAAA
1 AATGGTGGATGGAGTCTGAAAAAAAA
12952 AATGGTGGATGGAG
1 AATGGTGGATGGAG
12966 CCATGGAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 11 0.31
26 23 0.64
27 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.35, T:0.20
Consensus pattern (26 bp):
AATGGTGGATGGAGTCTGAAAAAAAA
Found at i:16418 original size:15 final size:18
Alignment explanation
Indices: 16398--16434 Score: 53
Period size: 15 Copynumber: 2.2 Consensus size: 18
16388 TTAACTTTTT
16398 AAAATTAA-AA-T-ATAA
1 AAAATTAATAACTCATAA
16413 AAAATTAATAACTCATAA
1 AAAATTAATAACTCATAA
16431 AAAA
1 AAAA
16435 CAAAAAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
16 2 0.11
17 1 0.05
18 8 0.42
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATTAATAACTCATAA
Found at i:16974 original size:6 final size:6
Alignment explanation
Indices: 16965--16992 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
16955 GGTTGGTTTT
16965 GGAGTA GGAGTA GGAGTA GGAGTA GGAG
1 GGAGTA GGAGTA GGAGTA GGAGTA GGAG
16993 AGAGGCAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.54, T:0.14
Consensus pattern (6 bp):
GGAGTA
Found at i:22665 original size:20 final size:20
Alignment explanation
Indices: 22642--22685 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
22632 TTAATCAATT
*
22642 ATTAATTCTAATAATTCATA
1 ATTAATTCCAATAATTCATA
22662 ATTAATTCCAATAATTCATA
1 ATTAATTCCAATAATTCATA
22682 ATTA
1 ATTA
22686 GATTAATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTAATTCCAATAATTCATA
Found at i:29685 original size:14 final size:14
Alignment explanation
Indices: 29668--29720 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
29658 TTTTTTTCTT
29668 AATTTGAATTTCAA
1 AATTTGAATTTCAA
*
29682 AATTCGAATTTCAA
1 AATTTGAATTTCAA
* * *
29696 ATTTTAAAATTC-A
1 AATTTGAATTTCAA
29709 AATTTCGAATTT
1 AATTT-GAATTT
29721 TGGCGGGCTG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
13 5 0.17
14 25 0.83
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (14 bp):
AATTTGAATTTCAA
Found at i:29721 original size:21 final size:21
Alignment explanation
Indices: 29668--29721 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
29658 TTTTTTTCTT
* *
29668 AATTT-GAATTTCAAAATTCG
1 AATTTCGAATTTTAAAATTCA
*
29688 AATTTCAAATTTTAAAATTCA
1 AATTTCGAATTTTAAAATTCA
29709 AATTTCGAATTTT
1 AATTTCGAATTTT
29722 GGCGGGCTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 5 0.17
21 24 0.83
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (21 bp):
AATTTCGAATTTTAAAATTCA
Found at i:30320 original size:21 final size:22
Alignment explanation
Indices: 30285--30330 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
30275 TTAACTGGGG
*
30285 GTTTTGGTGTTTTGGATTAAGT
1 GTTTTGATGTTTTGGATTAAGT
*
30307 GTTTTGAT-TTTTGGTTTAAGT
1 GTTTTGATGTTTTGGATTAAGT
30328 GTT
1 GTT
30331 CCTTTTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.13, C:0.00, G:0.28, T:0.59
Consensus pattern (22 bp):
GTTTTGATGTTTTGGATTAAGT
Found at i:33738 original size:74 final size:75
Alignment explanation
Indices: 33508--33773 Score: 403
Period size: 75 Copynumber: 3.6 Consensus size: 75
33498 ACGTTCTGCA
* * *
33508 GTCTGCTTAGG-CGCTCGACCTCGCTCGG-AGTAAAACGGGGGCGCCGGTCTAGGCGCTCAGCCG
1 GTCTGCTT-GGACGCTCGACCTCGCT-GGAAGTTATACGGGGGCGCCAGTCTAGGCGCTCAGCCG
*
33571 TTTGCGGGTGGC
64 TCTGCGGGTGGC
* * *
33583 GTCTGCTTGGACGCTCGACCTCGCTCGAAGTTATACGGGGGCGCCAGTCTAGGCGTTCAGCTGTC
1 GTCTGCTTGGACGCTCGACCTCGCTGGAAGTTATACGGGGGCGCCAGTCTAGGCGCTCAGCCGTC
*
33648 TGCGGCTGGC
66 TGCGGGTGGC
*
33658 GTCTGCTTGGACGCTTGACCTCGCTGGAAGTTATAC-GGGGCGCCAGTCTAGGCGCTCAGCCGTC
1 GTCTGCTTGGACGCTCGACCTCGCTGGAAGTTATACGGGGGCGCCAGTCTAGGCGCTCAGCCGTC
33722 TGCGGGTGGC
66 TGCGGGTGGC
*
33732 GTCTGCTTTGACGCTCGACCTCGCTGGAAGTTATACGGGGGC
1 GTCTGCTTGGACGCTCGACCTCGCTGGAAGTTATACGGGGGC
33774 TTGCACAAAT
Statistics
Matches: 173, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
74 72 0.42
75 101 0.58
ACGTcount: A:0.12, C:0.29, G:0.36, T:0.23
Consensus pattern (75 bp):
GTCTGCTTGGACGCTCGACCTCGCTGGAAGTTATACGGGGGCGCCAGTCTAGGCGCTCAGCCGTC
TGCGGGTGGC
Found at i:52846 original size:12 final size:12
Alignment explanation
Indices: 52829--52855 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52819 AATATCGGAT
52829 ATAGATATTAAA
1 ATAGATATTAAA
52841 ATAGATATTAAA
1 ATAGATATTAAA
52853 ATA
1 ATA
52856 TTGTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (12 bp):
ATAGATATTAAA
Done.