Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013159.1 Corchorus olitorius cultivar O-4 contig13192, 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: 16543
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Found at i:3254 original size:21 final size:20
Alignment explanation
Indices: 3230--3277 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
3220 TTTTATCAAA
*
3230 CCCATTTTCTCCGATTTGAG
1 CCCATTTTCTCCAATTTGAG
3250 TCCCATTTTCTCCAATTTGAG
1 -CCCATTTTCTCCAATTTGAG
3271 -CCATTTT
1 CCCATTTT
3278 TATCAAACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 7 0.27
21 19 0.73
ACGTcount: A:0.17, C:0.29, G:0.10, T:0.44
Consensus pattern (20 bp):
CCCATTTTCTCCAATTTGAG
Found at i:4036 original size:3 final size:3
Alignment explanation
Indices: 4028--4059 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4018 CAGCTCCTAA
4028 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
4060 TATATGTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:4277 original size:21 final size:21
Alignment explanation
Indices: 4251--4294 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
4241 TTTTATCAAA
4251 CCCATTTTCTCCGATTTGAGC
1 CCCATTTTCTCCGATTTGAGC
4272 CCCATTTTCTCCGATTTGAGC
1 CCCATTTTCTCCGATTTGAGC
4293 CC
1 CC
4295 TTTTTATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.36, G:0.14, T:0.36
Consensus pattern (21 bp):
CCCATTTTCTCCGATTTGAGC
Found at i:5438 original size:21 final size:21
Alignment explanation
Indices: 5412--5455 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5402 TTTTATCAAA
5412 CCCATTTTCTCCGATTTGAGC
1 CCCATTTTCTCCGATTTGAGC
*
5433 CCCATTTTCTCCGGTTTGAGC
1 CCCATTTTCTCCGATTTGAGC
5454 CC
1 CC
5456 TTTTTATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.36, G:0.16, T:0.36
Consensus pattern (21 bp):
CCCATTTTCTCCGATTTGAGC
Found at i:6364 original size:21 final size:21
Alignment explanation
Indices: 6340--6381 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6330 CATTTTGTGA
6340 AGGAGAAAGG-GGAGGGGCTCG
1 AGGAG-AAGGAGGAGGGGCTCG
*
6361 AGGAGGAGGAGGAGGGGCTCG
1 AGGAGAAGGAGGAGGGGCTCG
6382 TACCACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.26, C:0.10, G:0.60, T:0.05
Consensus pattern (21 bp):
AGGAGAAGGAGGAGGGGCTCG
Found at i:6516 original size:4 final size:4
Alignment explanation
Indices: 6507--6551 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
6497 TGATGTATAA
* * * *
6507 ATTT ATTT ATTA ATTT ATTT TTTT ATTA ATTT ATTT GTTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
6552 CTAATTTAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:6523 original size:12 final size:12
Alignment explanation
Indices: 6506--6559 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
6496 ATGATGTATA
6506 AATTTATTTATT
1 AATTTATTTATT
*
6518 AATTTATTTTTT
1 AATTTATTTATT
* *
6530 TATTAATTTATT
1 AATTTATTTATT
** *
6542 TGTTTATTTACT
1 AATTTATTTATT
6554 AATTTA
1 AATTTA
6560 ATATATGTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
AATTTATTTATT
Found at i:6531 original size:16 final size:16
Alignment explanation
Indices: 6507--6549 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
6497 TGATGTATAA
6507 ATTTATTTATTAATTT
1 ATTTATTTATTAATTT
*
6523 ATTTTTTTATTAATTT
1 ATTTATTTATTAATTT
*
6539 ATTTGTTTATT
1 ATTTATTTATT
6550 TACTAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
ATTTATTTATTAATTT
Found at i:6733 original size:14 final size:14
Alignment explanation
Indices: 6714--6744 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
6704 AGAGGTATTC
6714 TAATTTTTTTTCTT
1 TAATTTTTTTTCTT
6728 TAA-TTTTTTTCTT
1 TAATTTTTTTTCTT
6741 TAAT
1 TAAT
6745 CATACCACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.81
14 3 0.19
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (14 bp):
TAATTTTTTTTCTT
Found at i:6855 original size:18 final size:18
Alignment explanation
Indices: 6832--6871 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
6822 GACGCGATAC
6832 AACTTACCTTACGCC-CGA
1 AACTTACCTTAC-CCTCGA
6850 AACTTACCTTACCCTCGA
1 AACTTACCTTACCCTCGA
6868 AACT
1 AACT
6872 GATGATGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.30, C:0.38, G:0.07, T:0.25
Consensus pattern (18 bp):
AACTTACCTTACCCTCGA
Found at i:8095 original size:26 final size:26
Alignment explanation
Indices: 8066--8117 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
8056 TATATTCGTC
8066 TGAAATAATCACCTATCAGAATTCAG
1 TGAAATAATCACCTATCAGAATTCAG
*
8092 TGAAATAATCATCTATCAGAATTCAG
1 TGAAATAATCACCTATCAGAATTCAG
8118 AATTGGTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (26 bp):
TGAAATAATCACCTATCAGAATTCAG
Found at i:16421 original size:60 final size:60
Alignment explanation
Indices: 16285--16421 Score: 184
Period size: 60 Copynumber: 2.3 Consensus size: 60
16275 ATTTATTGTT
* * * *
16285 GTGGGGGATGCCCACTGGGTCGTACGATAGAGCTATGCTCGACTATTCTTTATCGTTGGC
1 GTGGGGGATGCCCACTTGGTCGTACGATAGAGCGATGCTCGACTATTCGTTATCGTTGCC
* * * * * *
16345 GTGGGGGATGCCCACTTGTTTGTACGATCGAGGGATGCTCGACTCTTCGTTATTGTTGCC
1 GTGGGGGATGCCCACTTGGTCGTACGATAGAGCGATGCTCGACTATTCGTTATCGTTGCC
16405 GTGGGGGATGCCCACTT
1 GTGGGGGATGCCCACTT
16422 CTTTATATGT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.15, C:0.22, G:0.33, T:0.31
Consensus pattern (60 bp):
GTGGGGGATGCCCACTTGGTCGTACGATAGAGCGATGCTCGACTATTCGTTATCGTTGCC
Done.