Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017022.1 Corchorus olitorius cultivar O-4 contig17055, 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: 13396
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6947 original size:31 final size:30
Alignment explanation
Indices: 6893--6997 Score: 106
Period size: 31 Copynumber: 3.5 Consensus size: 30
6883 AGGCTTGGCT
* *
6893 AAATGCTCAATTTGCTACCAAACCTTTTAA
1 AAATGCTCAATTTGATACTAAACCTTTTAA
* *
6923 GAAATGCTCAATTTGATGCTAAACC-TTCAA
1 -AAATGCTCAATTTGATACTAAACCTTTTAA
**
6953 AGTTGCTCAATTTGATACTAAA-CTTTTCAA
1 AAATGCTCAATTTGATACTAAACCTTTT-AA
*
6983 AATTAGCTCAATTTG
1 AAAT-GCTCAATTTG
6998 GTATTTTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
28 1 0.02
29 21 0.34
30 9 0.15
31 31 0.50
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATGCTCAATTTGATACTAAACCTTTTAA
Found at i:8446 original size:24 final size:24
Alignment explanation
Indices: 8351--8477 Score: 121
Period size: 24 Copynumber: 5.3 Consensus size: 24
8341 AAGCATAAAC
* *
8351 AAGTAGGTGCTGATGTTAATGAAC
1 AAGTAGGTGCTGAGGTTAATGAAG
*
8375 AATTAGGTGCTGAGGTTAATGAAG
1 AAGTAGGTGCTGAGGTTAATGAAG
* * *
8399 AATTAGGAGGTGAGGTTAATGAAG
1 AAGTAGGTGCTGAGGTTAATGAAG
** *
8423 AAGTAGGTGGAGAAGTTAATGAAG
1 AAGTAGGTGCTGAGGTTAATGAAG
* * *
8447 -AGTTAGGAGGTGAGGTGAATGAAG
1 AAG-TAGGTGCTGAGGTTAATGAAG
*
8471 AATTAGG
1 AAGTAGG
8478 AGGTCTGGGT
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
23 2 0.02
24 84 0.97
25 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.36, T:0.25
Consensus pattern (24 bp):
AAGTAGGTGCTGAGGTTAATGAAG
Found at i:8478 original size:24 final size:24
Alignment explanation
Indices: 8365--8524 Score: 153
Period size: 24 Copynumber: 6.7 Consensus size: 24
8355 AGGTGCTGAT
* * *
8365 GTTAATGAACAATTAGGTGCTGAG
1 GTTAATGAAGAATTAGGAGGTGAG
8389 GTTAATGAAGAATTAGGAGGTGAG
1 GTTAATGAAGAATTAGGAGGTGAG
* * * *
8413 GTTAATGAAGAAGTAGGTGGAGAA
1 GTTAATGAAGAATTAGGAGGTGAG
*
8437 GTTAATGAAGAGTTAGGAGGTGAG
1 GTTAATGAAGAATTAGGAGGTGAG
*
8461 GTGAATGAAGAATTAGGAGGTCTG-G
1 GTTAATGAAGAATTAGGAGG--TGAG
* * *
8486 GTTTA-GAAGAATTAAGAGGTCAG
1 GTTAATGAAGAATTAGGAGGTGAG
***
8509 GGGCATGAAGAATTAG
1 GTTAATGAAGAATTAG
8525 TTGTTGATAA
Statistics
Matches: 110, Mismatches: 22, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
22 1 0.01
23 3 0.03
24 100 0.91
25 4 0.04
26 2 0.02
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.24
Consensus pattern (24 bp):
GTTAATGAAGAATTAGGAGGTGAG
Found at i:8750 original size:12 final size:12
Alignment explanation
Indices: 8716--8771 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
8706 TTTAGATGAT
*
8716 GATGAAGGGTTA
1 GATGAAAGGTTA
*
8728 GCT-AAAGGGTTA
1 GATGAAA-GGTTA
8740 GATGAAAGGTTA
1 GATGAAAGGTTA
8752 GATG-AAGAGTTA
1 GATGAAAG-GTTA
8764 GATGAAAG
1 GATGAAAG
8772 TGGTTTAGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
11 5 0.14
12 26 0.70
13 6 0.16
ACGTcount: A:0.39, C:0.02, G:0.36, T:0.23
Consensus pattern (12 bp):
GATGAAAGGTTA
Found at i:8750 original size:24 final size:24
Alignment explanation
Indices: 8716--8771 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
8706 TTTAGATGAT
* * *
8716 GATGAAGGGTTAGCTAAAGGGTTA
1 GATGAAAGGTTAGATAAAGAGTTA
*
8740 GATGAAAGGTTAGATGAAGAGTTA
1 GATGAAAGGTTAGATAAAGAGTTA
8764 GATGAAAG
1 GATGAAAG
8772 TGGTTTAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.39, C:0.02, G:0.36, T:0.23
Consensus pattern (24 bp):
GATGAAAGGTTAGATAAAGAGTTA
Found at i:10222 original size:31 final size:28
Alignment explanation
Indices: 10187--10258 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 28
10177 TTTTTTCCTC
10187 TCTTTTTTTTTT-TGAATTTTCACATTTTT
1 TCTTTTTTTTTTAT-AATTTTCA-ATTTTT
*
10216 AATCTTTTTTTATTTATAATTTTGAATTTTT
1 --TCTTTTTTT-TTTATAATTTTCAATTTTT
*
10247 CCTTTTTTTTTT
1 TCTTTTTTTTTT
10259 GGATTCTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 3 0.08
29 8 0.22
31 15 0.41
32 10 0.27
33 1 0.03
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (28 bp):
TCTTTTTTTTTTATAATTTTCAATTTTT
Found at i:10915 original size:21 final size:23
Alignment explanation
Indices: 10887--10950 Score: 87
Period size: 21 Copynumber: 2.9 Consensus size: 23
10877 TTAAGCCTAA
*
10887 TTTAATTCTATTTTCTAAATTAC
1 TTTAATTCTAATTTCTAAATTAC
*
10910 -TT-ATTCTAATATCTAAATTAC
1 TTTAATTCTAATTTCTAAATTAC
*
10931 TTTAATTATAATTTCTAAAT
1 TTTAATTCTAATTTCTAAAT
10951 CATTTATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 17 0.49
22 4 0.11
23 14 0.40
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAATTCTAATTTCTAAATTAC
Found at i:10989 original size:17 final size:17
Alignment explanation
Indices: 10967--11007 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
10957 TATATGAAAT
*
10967 CTAAATTAATTTAAAAA
1 CTAAATTAATCTAAAAA
*
10984 CTAAATTAATCTCAAAA
1 CTAAATTAATCTAAAAA
*
11001 TTAAATT
1 CTAAATT
11008 GAAAAAGGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (17 bp):
CTAAATTAATCTAAAAA
Done.