Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016518.1 Corchorus capsularis cultivar CVL-1 contig16539, 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: 12900
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:630 original size:6 final size:6
Alignment explanation
Indices: 611--647 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
601 CTAAGCAAAG
*
611 TAAAT- TAAAGC TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TA
648 TAGCAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (6 bp):
TAAATC
Found at i:2030 original size:19 final size:18
Alignment explanation
Indices: 1998--2035 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1988 TTGAATGAAT
*
1998 TCTTCAATTGTCTTCAAA
1 TCTTCAATTATCTTCAAA
2016 TCTTCAAATTATCTTCAAA
1 TCTTC-AATTATCTTCAAA
2035 T
1 T
2036 AATCTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.45
Consensus pattern (18 bp):
TCTTCAATTATCTTCAAA
Found at i:2031 original size:11 final size:11
Alignment explanation
Indices: 2014--2045 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2004 ATTGTCTTCA
2014 AATCTTCAAAT
1 AATCTTCAAAT
*
2025 TATCTTCAAAT
1 AATCTTCAAAT
2036 AATCTTCAAA
1 AATCTTCAAA
2046 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:7836 original size:19 final size:18
Alignment explanation
Indices: 7804--7841 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
7794 TTGAATGAAT
*
7804 TCTTCAATTGTCTTCAAA
1 TCTTCAATTATCTTCAAA
7822 TCTTCAAATTATCTTCAAA
1 TCTTC-AATTATCTTCAAA
7841 T
1 T
7842 AATCTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.45
Consensus pattern (18 bp):
TCTTCAATTATCTTCAAA
Found at i:7837 original size:11 final size:11
Alignment explanation
Indices: 7820--7851 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
7810 ATTGTCTTCA
7820 AATCTTCAAAT
1 AATCTTCAAAT
*
7831 TATCTTCAAAT
1 AATCTTCAAAT
7842 AATCTTCAAA
1 AATCTTCAAA
7852 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:10146 original size:6 final size:6
Alignment explanation
Indices: 10135--10172 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
10125 ATTAATTTGC
10135 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
10173 GCTTTGCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (6 bp):
TTTAGA
Found at i:10543 original size:25 final size:25
Alignment explanation
Indices: 10492--10543 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
10482 AAAAAAAAAG
* *
10492 TTTGCGTTGAAAAAAAAAATTTGTT
1 TTTGCGTCGAAAAAAAAAAGTTGTT
10517 TTTGCGTCGATAAAAAAAAAGTT-TT
1 TTTGCGTCGA-AAAAAAAAAGTTGTT
10542 TT
1 TT
10544 CCGTTTTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (25 bp):
TTTGCGTCGAAAAAAAAAAGTTGTT
Done.