Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012227.1 Corchorus capsularis cultivar CVL-1 contig12248, 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: 31739
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7789 original size:27 final size:25
Alignment explanation
Indices: 7733--7791 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 25
7723 TATATCAATT
7733 ATAAAG-AAAACAATTAAACTAAAA
1 ATAAAGCAAAACAATTAAACTAAAA
*
7757 ATAAAGCAAAACAAATTAAATCTAAAT
1 ATAAAGCAAAAC-AATTAAA-CTAAAA
*
7784 CTAAAGCA
1 ATAAAGCA
7792 GATTAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 6 0.20
25 5 0.17
26 7 0.23
27 12 0.40
ACGTcount: A:0.64, C:0.12, G:0.05, T:0.19
Consensus pattern (25 bp):
ATAAAGCAAAACAATTAAACTAAAA
Found at i:15335 original size:21 final size:21
Alignment explanation
Indices: 15297--15337 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15287 CCTTGGCTTA
*
15297 TGATCTTCAATACTCTTCAAT
1 TGATCTTCAATACACTTCAAT
**
15318 TGATCTTCAATGGACTTCAA
1 TGATCTTCAATACACTTCAA
15338 GCCTTCAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (21 bp):
TGATCTTCAATACACTTCAAT
Found at i:15822 original size:16 final size:16
Alignment explanation
Indices: 15801--15845 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
15791 GTGATAGCGT
15801 GGCATTCCCCATGGGC
1 GGCATTCCCCATGGGC
15817 GGCATTCCCCATGGGC
1 GGCATTCCCCATGGGC
15833 GGCATTCCCCATG
1 GGCATTCCCCATG
15846 TCGGCCAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.13, C:0.38, G:0.29, T:0.20
Consensus pattern (16 bp):
GGCATTCCCCATGGGC
Found at i:15993 original size:19 final size:19
Alignment explanation
Indices: 15963--16013 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
15953 GAGAAAATTC
15963 ATAAAATCTAAAAA-TAAAA
1 ATAAAAT-TAAAAATTAAAA
15982 ATAATAATTAAAAATTAAAA
1 ATAA-AATTAAAAATTAAAA
*
16002 TTAAAATTAAAA
1 ATAAAATTAAAA
16014 TTGGGTTGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAAAATTAAAAATTAAAA
Found at i:16015 original size:6 final size:6
Alignment explanation
Indices: 15964--16015 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
15954 AGAAAATTCA
* *
15964 TAAAAT CTAAAAA TAAAAA TAATAAT TAAAAAT TAAAAT TAAAAT TAAAAT
1 TAAAAT -TAAAAT TAAAAT TAA-AAT T-AAAAT TAAAAT TAAAAT TAAAAT
16015 T
1 T
16016 GGGTTGCCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
6 27 0.66
7 12 0.29
8 2 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (6 bp):
TAAAAT
Found at i:26344 original size:19 final size:18
Alignment explanation
Indices: 26311--26346 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
26301 TTGAAATAAT
26311 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
26329 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
26347 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:27361 original size:2 final size:2
Alignment explanation
Indices: 27354--27378 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27344 TATTACTGTG
27354 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 T
27379 CTATTGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28163 original size:9 final size:9
Alignment explanation
Indices: 28147--28221 Score: 68
Period size: 9 Copynumber: 8.6 Consensus size: 9
28137 GTATATTTAG
28147 TATT-TATA
1 TATTATATA
*
28155 TTTTATATA
1 TATTATATA
28164 TATTATATA
1 TATTATATA
28173 TATTAT-TA
1 TATTATATA
*
28181 T-TCATATA
1 TATTATATA
*
28189 TAACTTAAATA
1 T-A-TTATATA
*
28200 TATGATATA
1 TATTATATA
28209 TA-TATATA
1 TATTATATA
28217 TATTA
1 TATTA
28222 CAAAAGACGA
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
7 3 0.06
8 16 0.30
9 27 0.51
10 1 0.02
11 6 0.11
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (9 bp):
TATTATATA
Found at i:31492 original size:15 final size:15
Alignment explanation
Indices: 31472--31501 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31462 ACAATATAAC
31472 CTCTATAAAATAATA
1 CTCTATAAAATAATA
*
31487 CTCTATAAATTAATA
1 CTCTATAAAATAATA
31502 ATCCCTGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
CTCTATAAAATAATA
Done.