Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012297.1 Corchorus olitorius cultivar O-4 contig12330, 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: 50020
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:365 original size:25 final size:25
Alignment explanation
Indices: 311--357 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
301 ACGTTTGCAC
311 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTTGAATTAAAA
336 AAATACCTAAGAATTT-AATTAA
1 AAATACCTAAGAATTTGAATTAA
358 TGTAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (25 bp):
AAATACCTAAGAATTTGAATTAAAA
Found at i:407 original size:39 final size:40
Alignment explanation
Indices: 348--428 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
338 ATACCTAAGA
*
348 ATTTAATTAATGTAAATATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
* *
387 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
427 AT
1 AT
429 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
Found at i:656 original size:2 final size:2
Alignment explanation
Indices: 644--693 Score: 64
Period size: 2 Copynumber: 24.0 Consensus size: 2
634 AGTTTAGACT
* *
644 TA TA TA GTA TA TA GA TA TA TA TA TA TA TA TG TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
687 TA CTA TA
1 TA -TA TA
694 AATTATCTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 38 0.90
3 4 0.10
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:11552 original size:15 final size:16
Alignment explanation
Indices: 11534--11563 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11524 GGTTTTTACC
11534 ACCTGA-TGTTTTGTA
1 ACCTGATTGTTTTGTA
11549 ACCTGATTGTTTTGT
1 ACCTGATTGTTTTGT
11564 TGAATGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.17, C:0.13, G:0.20, T:0.50
Consensus pattern (16 bp):
ACCTGATTGTTTTGTA
Found at i:16243 original size:15 final size:15
Alignment explanation
Indices: 16223--16272 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
16213 AAAAATCATA
16223 GCAGAATATGCGTAT
1 GCAGAATATGCGTAT
* *
16238 GCAGAATTACTTCTGCAT
1 GCAGAA-TA-TGC-GTAT
16256 GCAGAATATGCGTAT
1 GCAGAATATGCGTAT
16271 GC
1 GC
16273 GTATGCAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 11 0.39
16 4 0.14
17 4 0.14
18 9 0.32
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (15 bp):
GCAGAATATGCGTAT
Found at i:17708 original size:18 final size:19
Alignment explanation
Indices: 17662--17713 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 19
17652 TTCACATCTA
17662 ATAAGGTTATTAAAAAAAACT
1 ATAAGGTTA-T-AAAAAAACT
17683 ATAGAGGTTATAAAAAAA-T
1 ATA-AGGTTATAAAAAAACT
*
17702 TTAAGGTTATAA
1 ATAAGGTTATAA
17714 CTCCAACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 9 0.31
19 3 0.10
20 7 0.24
21 4 0.14
22 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.13, T:0.31
Consensus pattern (19 bp):
ATAAGGTTATAAAAAAACT
Found at i:24741 original size:26 final size:26
Alignment explanation
Indices: 24712--24769 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
24702 TCCATGCGGA
* *
24712 CTGGGCCGTGCGCCAAGCCTAGCACG
1 CTGGGCCGCGCGCCAAGCCCAGCACG
* *
24738 CTGGGCCGCGTGCCTAGCCCAGCACG
1 CTGGGCCGCGCGCCAAGCCCAGCACG
24764 CTGGGC
1 CTGGGC
24770 TGCACTGGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.12, C:0.40, G:0.36, T:0.12
Consensus pattern (26 bp):
CTGGGCCGCGCGCCAAGCCCAGCACG
Found at i:25336 original size:28 final size:28
Alignment explanation
Indices: 25296--25364 Score: 129
Period size: 28 Copynumber: 2.5 Consensus size: 28
25286 GGAGCATAGA
25296 AGAGAGAGAAAATAACTTTGTAATTTGT
1 AGAGAGAGAAAATAACTTTGTAATTTGT
*
25324 AGAGAGAGAAAATAGCTTTGTAATTTGT
1 AGAGAGAGAAAATAACTTTGTAATTTGT
25352 AGAGAGAGAAAAT
1 AGAGAGAGAAAAT
25365 GAAGGTGAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.45, C:0.03, G:0.25, T:0.28
Consensus pattern (28 bp):
AGAGAGAGAAAATAACTTTGTAATTTGT
Found at i:30890 original size:6 final size:6
Alignment explanation
Indices: 30879--30908 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
30869 ATATTGAGCT
*
30879 AGAGAA AGAGAA AGAGAA AGAGAG AGAGAA
1 AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA
30909 CATAAAAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (6 bp):
AGAGAA
Found at i:44851 original size:4 final size:4
Alignment explanation
Indices: 44844--44875 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
44834 TTGAAAAAAA
*
44844 AGAC AGAC AGAC AGAC AGAC AGAA AGAC AGAC
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC
44876 GTAAACAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.53, C:0.22, G:0.25, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:49714 original size:36 final size:36
Alignment explanation
Indices: 49667--49736 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
49657 TTCAATAACC
* *
49667 TTACATCTTTTGTGATTTTGGTTACCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTACCATATTTCTTA
* *
49703 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTACCATATTTCT
49737 CTAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.59
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTACCATATTTCTTA
Done.