Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017338.1 Corchorus olitorius cultivar O-4 contig17371, 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: 14894
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5646 original size:31 final size:32
Alignment explanation
Indices: 5588--5652 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
5578 CACACAACAC
*
5588 AATTTTTTTTTTTTAAATTAAAGACGCAAAGA
1 AATTTTTTTTTTTCAAATTAAAGACGCAAAGA
*
5620 AATTTTTTTTTTTCAGAA-TAAA-ACGCAGAGA
1 AATTTTTTTTTTTCA-AATTAAAGACGCAAAGA
5651 AA
1 AA
5653 AAGAAATACG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 10 0.33
32 18 0.60
33 2 0.07
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (32 bp):
AATTTTTTTTTTTCAAATTAAAGACGCAAAGA
Found at i:5965 original size:15 final size:16
Alignment explanation
Indices: 5941--5980 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
5931 AGAGGTTGAA
*
5941 AGAAATCAATTAAAC-
1 AGAAAACAATTAAACT
5956 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
5972 AGAAAACAA
1 AGAAAACAA
5981 ATCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:8754 original size:12 final size:12
Alignment explanation
Indices: 8724--8754 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
8714 CCTGGCAATC
*
8724 CGTGTTCCGTGT
1 CGTGTTTCGTGT
8736 CGTGTTTCGTGT
1 CGTGTTTCGTGT
8748 CGTGTTT
1 CGTGTTT
8755 ACATAGGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.19, G:0.32, T:0.48
Consensus pattern (12 bp):
CGTGTTTCGTGT
Found at i:9325 original size:18 final size:19
Alignment explanation
Indices: 9302--9346 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
9292 AATCATGTCC
9302 GACACGAT-TCAAACACGA
1 GACACGATATCAAACACGA
9320 GACACGATAAGTCAAACACGA
1 GACACGAT-A-TCAAACACGA
9341 -ACACGA
1 GACACGA
9347 CTAAACGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
20 6 0.25
21 10 0.42
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
GACACGATATCAAACACGA
Found at i:9709 original size:5 final size:6
Alignment explanation
Indices: 9694--9718 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9684 TAAAATTCTG
9694 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
9719 CATGAGGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:10429 original size:19 final size:18
Alignment explanation
Indices: 10405--10440 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10395 TGAAGATTTA
10405 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
10424 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
10441 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Done.