Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013816.1 Corchorus olitorius cultivar O-4 contig13849, 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: 6768
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:941 original size:29 final size:29
Alignment explanation
Indices: 885--942 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
875 CTTGAAATAA
* *
885 ATCTTCAATGGTCTTCAAGTCTCCAATTT
1 ATCTTCAATGGTCTTCAAGACACCAATTT
*
914 ATCTTCAAATGGTCTTCAA-ACACGAATTT
1 ATCTTC-AATGGTCTTCAAGACACCAATTT
943 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
Found at i:2363 original size:40 final size:40
Alignment explanation
Indices: 2312--2387 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
2302 TAATTAAATG
*
2312 CAATTTGGTCCCTAATTTAGGATTCT-ATATACTGTTGATA
1 CAATTTAGTCCCTAATTTAGGATTCTAAT-TACTGTTGATA
*
2352 CAATTTAGTCCCTGATTTAGGATTCTAATTACTGTT
1 CAATTTAGTCCCTAATTTAGGATTCTAATTACTGTT
2388 TGGCTCAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.43
Consensus pattern (40 bp):
CAATTTAGTCCCTAATTTAGGATTCTAATTACTGTTGATA
Found at i:6180 original size:9 final size:9
Alignment explanation
Indices: 6143--6169 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
6133 AAAAAAAAAT
6143 GAAAATAAA
1 GAAAATAAA
6152 GAAAATAAA
1 GAAAATAAA
6161 GAAAATAAA
1 GAAAATAAA
6170 AAATGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
GAAAATAAA
Found at i:6575 original size:6 final size:6
Alignment explanation
Indices: 6564--6609 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
6554 AAAAATCTAA
*
6564 AAAAAT AAAAAT -AAAAT AAAAAT -AAAAT -AAAAT CAAAAT CAAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT
6610 CAAATCAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
5 15 0.42
6 16 0.44
7 5 0.14
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:6579 original size:5 final size:5
Alignment explanation
Indices: 6547--6630 Score: 55
Period size: 5 Copynumber: 15.6 Consensus size: 5
6537 CAAGAAGTTC
*
6547 AAATA AAA-A AAATCT AAA-A AAATAA AAATA AAATAA AAATA AAATA
1 AAATA AAATA AAAT-A AAATA AAAT-A AAATA AAAT-A AAATA AAATA
* *
6593 AAATCA AAATCAA AAATC AAATC AAATCA AAATCA AAA
1 AAAT-A AAAT--A AAATA AAATA AAAT-A AAAT-A AAA
6631 GAGAATTGAT
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
4 7 0.11
5 27 0.41
6 27 0.41
7 5 0.08
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:6579 original size:11 final size:11
Alignment explanation
Indices: 6565--6614 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
6555 AAAATCTAAA
6565 AAAATAAAAAT
1 AAAATAAAAAT
6576 AAAATAAAAAT
1 AAAATAAAAAT
6587 AAAAT-AAAAT
1 AAAATAAAAAT
6597 CAAAATCAAAAAT
1 -AAAAT-AAAAAT
*
6610 CAAAT
1 AAAAT
6615 CAAATCAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
10 5 0.14
11 21 0.60
12 4 0.11
13 5 0.14
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:6625 original size:6 final size:6
Alignment explanation
Indices: 6565--6630 Score: 70
Period size: 5 Copynumber: 11.7 Consensus size: 6
6555 AAAATCTAAA
* *
6565 AAAATA AAAAT- AAAATA AAAAT- AAAAT- AAAATC AAAATC AAAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC -AAAATC
6611 -AAATC -AAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAA
6631 GAGAATTGAT
Statistics
Matches: 56, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
5 25 0.45
6 25 0.45
7 6 0.11
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATC
Done.