Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023809.1 Corchorus olitorius cultivar O-4 contig23842, 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: 27049
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Found at i:9838 original size:32 final size:32
Alignment explanation
Indices: 9761--9839 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
9751 AAATAGCCCA
* * *
9761 TTTGCCCCCTAAACTTTGCAAATTTTGGCCAG
1 TTTGCCCCCTGAACTTTCCAAATTTAGGCCAG
9793 TTTGCCCCCTGAACTTTCCAAATTTAGGCCAG
1 TTTGCCCCCTGAACTTTCCAAATTTAGGCCAG
*
9825 TTTGCCCCATGAACT
1 TTTGCCCCCTGAACT
9840 AGTAATTGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (32 bp):
TTTGCCCCCTGAACTTTCCAAATTTAGGCCAG
Found at i:13734 original size:51 final size:51
Alignment explanation
Indices: 13664--13863 Score: 373
Period size: 51 Copynumber: 3.9 Consensus size: 51
13654 ATTAAAGAGT
*
13664 CGTCTTCCGCTTATCCTTTGAATTGTCTTCCAATTCAATCTTAAAAAGGAC
1 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
* *
13715 CGTCTTCCACTTATCCTTTGAACTGTCTTCCAATTCAATCTCAAAAAGGAC
1 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
13766 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
1 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
13817 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAA
1 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAA
13864 AAATCATCTT
Statistics
Matches: 144, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 144 1.00
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.36
Consensus pattern (51 bp):
CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
Found at i:15266 original size:12 final size:12
Alignment explanation
Indices: 15249--15279 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
15239 TTGTTAAAAA
15249 TGCCCCATATAT
1 TGCCCCATATAT
*
15261 TGCCCCATATGT
1 TGCCCCATATAT
15273 TGCCCCA
1 TGCCCCA
15280 CTAAAAGAGA
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:0.19, C:0.39, G:0.13, T:0.29
Consensus pattern (12 bp):
TGCCCCATATAT
Found at i:15301 original size:19 final size:19
Alignment explanation
Indices: 15277--15315 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
15267 ATATGTTGCC
15277 CCACTAAAAGAGACCTTCT
1 CCACTAAAAGAGACCTTCT
15296 CCACTAAAAGAGACCTTCT
1 CCACTAAAAGAGACCTTCT
15315 C
1 C
15316 AAAAAGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (19 bp):
CCACTAAAAGAGACCTTCT
Found at i:16399 original size:14 final size:13
Alignment explanation
Indices: 16374--16417 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 13
16364 TAAAAGACTC
16374 AAAACC-TTTTTG
1 AAAACCTTTTTTG
16386 AAAACCTATTTTTG
1 AAAACCT-TTTTTG
16400 AAAACCTTTTCTTG
1 AAAACCTTTT-TTG
16414 AAAA
1 AAAA
16418 TAATTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.21
13 3 0.10
14 20 0.69
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (13 bp):
AAAACCTTTTTTG
Found at i:16424 original size:26 final size:25
Alignment explanation
Indices: 16374--16424 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
16364 TAAAAGACTC
*
16374 AAAACCTTTTTGAAAACCTATTTTTG
1 AAAACCTTTTTGAAAA-CTAATTTTG
16400 AAAACCTTTTCTTGAAAA-TAATTTT
1 AAAACC-TTT-TTGAAAACTAATTTT
16425 CTTGAAAGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 12 0.55
27 3 0.14
28 7 0.32
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (25 bp):
AAAACCTTTTTGAAAACTAATTTTG
Done.