Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014123.1 Corchorus capsularis cultivar CVL-1 contig14144, 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: 46567
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:9345 original size:18 final size:19
Alignment explanation
Indices: 9322--9361 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
9312 TTCTTGAAAT
9322 AATTCTTC-AATGATCTTC
1 AATTCTTCAAATGATCTTC
*
9340 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATGATCTTC
9359 AAT
1 AAT
9362 AAATCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTCTTCAAATGATCTTC
Found at i:9346 original size:30 final size:30
Alignment explanation
Indices: 9312--9372 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
9302 CAATTCTTGC
* *
9312 TTCTTGAAATAATTCTTCAAT-GATCTTCAA
1 TTCTTCAAATAA-TCTTCAATAAATCTTCAA
*
9342 TTCTTCAAATTATCTTCAATAAATCTTCAA
1 TTCTTCAAATAATCTTCAATAAATCTTCAA
9372 T
1 T
9373 CACGAACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.34, C:0.18, G:0.03, T:0.44
Consensus pattern (30 bp):
TTCTTCAAATAATCTTCAATAAATCTTCAA
Found at i:18916 original size:10 final size:12
Alignment explanation
Indices: 18889--18922 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
18879 TCCCATGCAA
18889 TGGCCGGTCATG
1 TGGCCGGTCATG
18901 TGGCCGGTC-T-
1 TGGCCGGTCATG
18911 TGGCCGGTCATG
1 TGGCCGGTCATG
18923 GTTCCATGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.45
11 2 0.10
12 9 0.45
ACGTcount: A:0.06, C:0.26, G:0.41, T:0.26
Consensus pattern (12 bp):
TGGCCGGTCATG
Found at i:20840 original size:33 final size:33
Alignment explanation
Indices: 20785--20874 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
20775 CTCTTTCTTT
***
20785 TCAACCAAAACAGTCCTATTTTCAATGCTATGA
1 TCAACCAAAACAGAATTATTTTCAATGCTATGA
* * * *
20818 TCATCCAAAACAGATTTGTTTTCCATGCTATGA
1 TCAACCAAAACAGAATTATTTTCAATGCTATGA
20851 TCAACCAAAACAGAATTATTTTCA
1 TCAACCAAAACAGAATTATTTTCA
20875 TCACAAGTAG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (33 bp):
TCAACCAAAACAGAATTATTTTCAATGCTATGA
Found at i:25728 original size:31 final size:29
Alignment explanation
Indices: 25689--25761 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 29
25679 CAGAAATGTT
25689 ACCAAATTGAGTC-GATTTGGAAAGGTTTGGC
1 ACCAAATTGAG-CAGATTT--AAAGGTTTGGC
*
25720 ACTC-AATTGAGCAGCTTTAAAGGTTTGGC
1 AC-CAAATTGAGCAGATTTAAAGGTTTGGC
25749 ACCAAATTGAGCA
1 ACCAAATTGAGCA
25762 TTTAGCCCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
28 1 0.03
29 22 0.58
30 1 0.03
31 13 0.34
32 1 0.03
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (29 bp):
ACCAAATTGAGCAGATTTAAAGGTTTGGC
Found at i:26562 original size:21 final size:21
Alignment explanation
Indices: 26536--26618 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 21
26526 TATCTTAGAT
26536 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
26557 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
**
26578 ATAAATAATGA-ATTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
26600 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
26619 TTACTAAACG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
21 19 0.37
22 22 0.43
23 10 0.20
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:26566 original size:25 final size:25
Alignment explanation
Indices: 26538--26586 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
26528 TCTTAGATAT
*
26538 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
26563 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
26587 GAATTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:31201 original size:21 final size:20
Alignment explanation
Indices: 31163--31201 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31153 TTATAGCTAT
* *
31163 TTTTCTATACTTTTTACCAC
1 TTTTATATACTTTATACCAC
31183 TTTTATATACATTTATACC
1 TTTTATATAC-TTTATACC
31202 TTATTTTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTATATACTTTATACCAC
Found at i:32204 original size:20 final size:20
Alignment explanation
Indices: 32181--32221 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
32171 GTATTTCTTG
32181 GATCTCTGTATGAATTCTAT
1 GATCTCTGTATGAATTCTAT
32201 GATCTCTGTATGAATTCTAT
1 GATCTCTGTATGAATTCTAT
32221 G
1 G
32222 TTGCTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (20 bp):
GATCTCTGTATGAATTCTAT
Found at i:32720 original size:15 final size:16
Alignment explanation
Indices: 32702--32735 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
32692 AATTGCTTTC
*
32702 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
32717 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
32733 TTA
1 TTA
32736 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:41261 original size:19 final size:18
Alignment explanation
Indices: 41237--41272 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41227 AAGTTCGTGC
41237 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
41256 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
41273 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:42575 original size:15 final size:16
Alignment explanation
Indices: 42555--42588 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42545 GATTGCTTTC
*
42555 TTAGTT-AATTTACTT
1 TTAGTTAAATTTAATT
42570 TTAGTTAAATTTAATT
1 TTAGTTAAATTTAATT
42586 TTA
1 TTA
42589 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (16 bp):
TTAGTTAAATTTAATT
Done.