Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014504.1 Corchorus capsularis cultivar CVL-1 contig14525, 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: 33336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10240 original size:27 final size:27
Alignment explanation
Indices: 10210--10268 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
10200 ACTCCTTGCT
*
10210 TGCAGATTCTTCTCCAAAATTTGAAGA
1 TGCAGATTCTTCTACAAAATTTGAAGA
10237 TGCAGATTCTTCTACAAAATTTGAAGA
1 TGCAGATTCTTCTACAAAATTTGAAGA
10264 TGCAG
1 TGCAG
10269 GTGATGCGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (27 bp):
TGCAGATTCTTCTACAAAATTTGAAGA
Found at i:11874 original size:15 final size:15
Alignment explanation
Indices: 11854--12005 Score: 151
Period size: 15 Copynumber: 10.1 Consensus size: 15
11844 CTCTGTAAAT
*
11854 CTGAATTTGCACCTG
1 CTGAATTCGCACCTG
* **
11869 CTGAATGCAAACCTG
1 CTGAATTCGCACCTG
*
11884 CTGAATTCGAACCTG
1 CTGAATTCGCACCTG
* *
11899 CTAAATTCGAACCTG
1 CTGAATTCGCACCTG
* * *
11914 CTGAATTCACATCTA
1 CTGAATTCGCACCTG
*
11929 CTGAATTCGAACCTG
1 CTGAATTCGCACCTG
* *
11944 CTGAATTCACATCTG
1 CTGAATTCGCACCTG
*
11959 CTGAATTCACACCTG
1 CTGAATTCGCACCTG
*
11974 CTGAATTCGCATCTG
1 CTGAATTCGCACCTG
* *
11989 TTGAATTCACACCTG
1 CTGAATTCGCACCTG
12004 CT
1 CT
12006 AAAGTATTAA
Statistics
Matches: 111, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 111 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (15 bp):
CTGAATTCGCACCTG
Found at i:11890 original size:30 final size:30
Alignment explanation
Indices: 11854--12005 Score: 178
Period size: 30 Copynumber: 5.1 Consensus size: 30
11844 CTCTGTAAAT
* * *
11854 CTGAATTTGCACCTGCTGAATGCAAACCTG
1 CTGAATTCGCATCTGCTGAATTCAAACCTG
* * * *
11884 CTGAATTCGAACCTGCTAAATTCGAACCTG
1 CTGAATTCGCATCTGCTGAATTCAAACCTG
* * *
11914 CTGAATTCACATCTACTGAATTCGAACCTG
1 CTGAATTCGCATCTGCTGAATTCAAACCTG
* *
11944 CTGAATTCACATCTGCTGAATTCACACCTG
1 CTGAATTCGCATCTGCTGAATTCAAACCTG
* *
11974 CTGAATTCGCATCTGTTGAATTCACACCTG
1 CTGAATTCGCATCTGCTGAATTCAAACCTG
12004 CT
1 CT
12006 AAAGTATTAA
Statistics
Matches: 107, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 107 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (30 bp):
CTGAATTCGCATCTGCTGAATTCAAACCTG
Found at i:11913 original size:45 final size:45
Alignment explanation
Indices: 11863--12005 Score: 180
Period size: 45 Copynumber: 3.2 Consensus size: 45
11853 TCTGAATTTG
* *
11863 CACCTGCTGAATGCAAACCTGCTGAATTCGAACCTGCTAAATTCGA
1 CACCTGCTGAATTCACACCTGCTGAATTCGAACCTGCTAAATTC-A
* * *
11909 -ACCTGCTGAATTCACATCTACTGAATTCGAACCTGCTGAATTCA
1 CACCTGCTGAATTCACACCTGCTGAATTCGAACCTGCTAAATTCA
* * * * *
11953 CATCTGCTGAATTCACACCTGCTGAATTCGCATCTGTTGAATTCA
1 CACCTGCTGAATTCACACCTGCTGAATTCGAACCTGCTAAATTCA
11998 CACCTGCT
1 CACCTGCT
12006 AAAGTATTAA
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
44 1 0.01
45 83 0.99
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (45 bp):
CACCTGCTGAATTCACACCTGCTGAATTCGAACCTGCTAAATTCA
Found at i:16762 original size:13 final size:13
Alignment explanation
Indices: 16744--16768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16734 ATTAATGGTC
16744 AAAATCTAAAGAT
1 AAAATCTAAAGAT
16757 AAAATCTAAAGA
1 AAAATCTAAAGA
16769 AAATGGTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (13 bp):
AAAATCTAAAGAT
Found at i:20828 original size:12 final size:13
Alignment explanation
Indices: 20813--20842 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
20803 TTTCCAGAAA
20813 ATTTTCTTCA-TT
1 ATTTTCTTCAGTT
20825 ATTTTCTTCAGTT
1 ATTTTCTTCAGTT
20838 ATTTT
1 ATTTT
20843 TCATATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.17, C:0.13, G:0.03, T:0.67
Consensus pattern (13 bp):
ATTTTCTTCAGTT
Found at i:23624 original size:13 final size:13
Alignment explanation
Indices: 23606--23636 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
23596 CCCTATACCC
23606 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
23619 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
*
23632 GGAAA
1 AGAAA
23637 TGTGCCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAA
Found at i:24910 original size:1 final size:1
Alignment explanation
Indices: 24904--24930 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
24894 TTATATATTT
24904 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
24931 CCCTCAGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.