Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018320.1 Corchorus olitorius cultivar O-4 contig18353, 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: 29721
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Found at i:6758 original size:13 final size:14
Alignment explanation
Indices: 6730--6759 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6720 GACTAGACTC
6730 AAAACTGACTCGAA
1 AAAACTGACTCGAA
6744 AAAACTGACTC-AA
1 AAAACTGACTCGAA
6757 AAA
1 AAA
6760 CAAACTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.57, C:0.20, G:0.10, T:0.13
Consensus pattern (14 bp):
AAAACTGACTCGAA
Found at i:7005 original size:15 final size:15
Alignment explanation
Indices: 6985--7014 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6975 ATAATTGGAA
6985 TTCCTTTATAATTAG
1 TTCCTTTATAATTAG
7000 TTCCTTTATAATTAG
1 TTCCTTTATAATTAG
7015 GGGAATGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (15 bp):
TTCCTTTATAATTAG
Found at i:27415 original size:22 final size:21
Alignment explanation
Indices: 27346--27514 Score: 124
Period size: 22 Copynumber: 7.8 Consensus size: 21
27336 TAACCTCGAA
*
27346 ATGAAATTTTGATAA-TCTCCTT
1 ATGAAATTTTGGTAACT-TCC-T
* * * *
27368 ATGAAAATTCGGTAACATTGCA
1 ATGAAATTTTGGTAAC-TTCCT
*
27390 ATGAAATTTTGGTAATCTTTCT
1 ATGAAATTTTGGTAA-CTTCCT
** * *
27412 ATGAAATTTCAGTAACCATACT
1 ATGAAATTTTGGTAA-CTTCCT
*
27434 ATGAAATTTTGGTAACATCCCT
1 ATGAAATTTTGGTAAC-TTCCT
* *
27456 ATGAAATTATGGTAACCTCTCT
1 ATGAAATTTTGGTAACTTC-CT
*
27478 ATGAAATTTTAGTAACTTCCT
1 ATGAAATTTTGGTAACTTCCT
* *
27499 ATGAACTTTTAGTAAC
1 ATGAAATTTTGGTAAC
27515 CAACGCATGA
Statistics
Matches: 116, Mismatches: 26, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
21 19 0.16
22 93 0.80
23 3 0.03
24 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
ATGAAATTTTGGTAACTTCCT
Found at i:27437 original size:66 final size:66
Alignment explanation
Indices: 27367--27493 Score: 173
Period size: 66 Copynumber: 1.9 Consensus size: 66
27357 ATAATCTCCT
** * * *
27367 TATGAAAATTCGGTAACATTGCAATGAAATTTTGGTAATCTTTCTATGAAATTTCAGTAACCATA
1 TATGAAAATTCGGTAACATCCCAATGAAATTATGGTAACCTCTCTATGAAATTTCAGTAACCATA
27432 C
66 C
* * * *
27433 TATGAAATTTTGGTAACATCCCTATGAAATTATGGTAACCTCTCTATGAAATTTTAGTAAC
1 TATGAAAATTCGGTAACATCCCAATGAAATTATGGTAACCTCTCTATGAAATTTCAGTAAC
27494 TTCCTATGAA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 52 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.37
Consensus pattern (66 bp):
TATGAAAATTCGGTAACATCCCAATGAAATTATGGTAACCTCTCTATGAAATTTCAGTAACCATA
C
Found at i:27462 original size:44 final size:44
Alignment explanation
Indices: 27346--27516 Score: 145
Period size: 44 Copynumber: 3.9 Consensus size: 44
27336 TAACCTCGAA
* * * * * *
27346 ATGAAATTTTGATAATCTCCTTATGAAAATTCGGTAA-CATTGCA
1 ATGAAATTTTGGTAATCTCCCTATGAAATTTCAGTAACCA-TACT
**
27390 ATGAAATTTTGGTAATCTTTCTATGAAATTTCAGTAACCATACT
1 ATGAAATTTTGGTAATCTCCCTATGAAATTTCAGTAACCATACT
* *
27434 ATGAAATTTTGGTAA-CATCCCTATGAAATTAT-GGTAACC-TCTCT
1 ATGAAATTTTGGTAATC-TCCCTATGAAATT-TCAGTAACCAT-ACT
* * * *
27478 ATGAAATTTTAGTAA-CTTCCTATGAACTTTTAGTAACCA
1 ATGAAATTTTGGTAATCTCCCTATGAAATTTCAGTAACCA
27517 ACGCATGAAA
Statistics
Matches: 105, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
42 1 0.01
43 19 0.18
44 82 0.78
45 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (44 bp):
ATGAAATTTTGGTAATCTCCCTATGAAATTTCAGTAACCATACT
Found at i:27785 original size:2 final size:2
Alignment explanation
Indices: 27778--27805 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27768 TGCAATTACA
27778 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27806 TTTTCATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28242 original size:28 final size:28
Alignment explanation
Indices: 28196--28268 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
28186 GGTCATTTAG
** *
28196 GGGCATTTTAATCA-TTTGCACGTTCAA
1 GGGCATTTTGGTCATTTTGCACATTCAA
28223 GGGCATTTTGGTCATTTTGCACATTCAA
1 GGGCATTTTGGTCATTTTGCACATTCAA
*
28251 GGGCATTTCGGTCATTTT
1 GGGCATTTTGGTCATTTT
28269 AAGTTCACTG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 12 0.29
28 29 0.71
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTTGCACATTCAA
Done.