Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016827.1 Corchorus olitorius cultivar O-4 contig16860, 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: 35145
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:8013 original size:13 final size:13
Alignment explanation
Indices: 7995--8021 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7985 GCACTTGTAG
7995 GTCTATTTAGAGA
1 GTCTATTTAGAGA
8008 GTCTATTTAGAGA
1 GTCTATTTAGAGA
8021 G
1 G
8022 AAAGTTGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (13 bp):
GTCTATTTAGAGA
Found at i:12689 original size:21 final size:21
Alignment explanation
Indices: 12641--12692 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
12631 AACTCATCTT
*
12641 GATGATATGAAGTCCATTGGA
1 GATGATTTGAAGTCCATTGGA
12662 GATGATTTGAAGT-CATTTGGA
1 GATGATTTGAAGTCCA-TTGGA
12683 GATGATTTGA
1 GATGATTTGA
12693 GCAAGAAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.35
Consensus pattern (21 bp):
GATGATTTGAAGTCCATTGGA
Found at i:14132 original size:14 final size:14
Alignment explanation
Indices: 14113--14141 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
14103 CTAACCACTC
14113 ATACTTTCAAATAT
1 ATACTTTCAAATAT
14127 ATACTTTCAAATAT
1 ATACTTTCAAATAT
14141 A
1 A
14142 GGATCGAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (14 bp):
ATACTTTCAAATAT
Found at i:26827 original size:22 final size:22
Alignment explanation
Indices: 26797--26839 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
26787 AAAATTCAGA
* *
26797 ACAAGTCCTGTCCAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
26819 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
26840 TTGCGGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTGG
Found at i:28540 original size:10 final size:10
Alignment explanation
Indices: 28525--28551 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
28515 AAGAAGAGGG
28525 TTAAGAATAA
1 TTAAGAATAA
28535 TTAAGAATAA
1 TTAAGAATAA
28545 TTAAGAA
1 TTAAGAA
28552 GAAAATAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (10 bp):
TTAAGAATAA
Found at i:28643 original size:15 final size:15
Alignment explanation
Indices: 28625--28658 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
28615 AGAAAACAAT
28625 AATAATTAAGAAGAA
1 AATAATTAAGAAGAA
28640 AATAATTAAGAAGAA
1 AATAATTAAGAAGAA
28655 AATA
1 AATA
28659 GAGGGTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.21
Consensus pattern (15 bp):
AATAATTAAGAAGAA
Found at i:28679 original size:29 final size:29
Alignment explanation
Indices: 28640--28719 Score: 115
Period size: 32 Copynumber: 2.7 Consensus size: 29
28630 TTAAGAAGAA
28640 AATAATTAAGAAGAAAATAGAGGGTTAAG
1 AATAATTAAGAAGAAAATAGAGGGTTAAG
**
28669 AATAATTAAGACACAGAAAGCAGAGGGTTAAG
1 AATAATTAAG--A-AGAAAATAGAGGGTTAAG
28701 AATAATTAAGAAGAAAATA
1 AATAATTAAGAAGAAAATA
28720 ACTAAACTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
29 16 0.36
30 1 0.02
31 1 0.02
32 26 0.59
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.19
Consensus pattern (29 bp):
AATAATTAAGAAGAAAATAGAGGGTTAAG
Found at i:32168 original size:29 final size:29
Alignment explanation
Indices: 32134--32268 Score: 121
Period size: 29 Copynumber: 4.6 Consensus size: 29
32124 TGGTCATCCA
* *
32134 AGGGCATTATAGTCATTTCTGCACAATCT
1 AGGGCATTTTGGTCATTTCTGCACAATCT
* * * * *
32163 GGGGCATTTTGGTCATTTTTAC-CCATCCA
1 AGGGCATTTTGGTCATTTCTGCACAAT-CT
* *
32192 AGGGCATTATGGTCATTTTTGCAC-ATCT
1 AGGGCATTTTGGTCATTTCTGCACAATCT
* * *
32220 AGGGGGTATTTTAGTCATTTCTGCACAATCC
1 A--GGGCATTTTGGTCATTTCTGCACAATCT
32251 AGGGCATTTTGGTCATTT
1 AGGGCATTTTGGTCATTT
32269 TGGTTTTATT
Statistics
Matches: 83, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
28 5 0.06
29 54 0.65
30 20 0.24
31 4 0.05
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (29 bp):
AGGGCATTTTGGTCATTTCTGCACAATCT
Found at i:32192 original size:58 final size:58
Alignment explanation
Indices: 32128--32239 Score: 163
Period size: 58 Copynumber: 1.9 Consensus size: 58
32118 GTATTTTGGT
*
32128 CATCCAAGGGCATTATAGTCATTTCTGCACAATCT-GGGGCATTTTGGTCATTTTTACC
1 CATCCAAGGGCATTATAGTCATTTCTGCAC-ATCTAGGGGCATTTTAGTCATTTTTACC
* * *
32186 CATCCAAGGGCATTATGGTCATTTTTGCACATCTAGGGGGTATTTTAGTCATTT
1 CATCCAAGGGCATTATAGTCATTTCTGCACATCTA-GGGGCATTTTAGTCATTT
32240 CTGCACAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
57 4 0.08
58 28 0.58
59 16 0.33
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (58 bp):
CATCCAAGGGCATTATAGTCATTTCTGCACATCTAGGGGCATTTTAGTCATTTTTACC
Found at i:34931 original size:29 final size:29
Alignment explanation
Indices: 34875--34932 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
34865 CTTGAAATAA
* *
34875 ATCTTCAATGGTCTTCAAGTCTCCAATTT
1 ATCTTCAATGGTCTTCAAGACACCAATTT
*
34904 ATCTTCAAATGGTCTTCAA-ACACGAATTT
1 ATCTTC-AATGGTCTTCAAGACACCAATTT
34933 CGAATCTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38
Consensus pattern (29 bp):
ATCTTCAATGGTCTTCAAGACACCAATTT
Done.