Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019832.1 Corchorus olitorius cultivar O-4 contig19865, 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: 42901
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Found at i:15451 original size:21 final size:21
Alignment explanation
Indices: 15412--15460 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
15402 TCAATGCTTT
**
15412 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
15434 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
15455 A-GAAGC
1 AGGAAGC
15461 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:21322 original size:21 final size:22
Alignment explanation
Indices: 21298--21343 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
21288 GTAACACTGC
*
21298 CCACCTGGGTTATCAA-GCAAA
1 CCACCTGGGTGATCAAGGCAAA
* *
21319 CCACGTGGGTGCTCAAGGCAAA
1 CCACCTGGGTGATCAAGGCAAA
21341 CCA
1 CCA
21344 TGTAGGCGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.15
Consensus pattern (22 bp):
CCACCTGGGTGATCAAGGCAAA
Found at i:28078 original size:9 final size:9
Alignment explanation
Indices: 28052--28081 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
28042 ATCCACACAC
*
28052 CTCCATTCC
1 CTCCATTCT
28061 CTCCATTCT
1 CTCCATTCT
28070 CTCCATTCT
1 CTCCATTCT
28079 CTC
1 CTC
28082 ATACATACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.50, G:0.00, T:0.40
Consensus pattern (9 bp):
CTCCATTCT
Found at i:29804 original size:21 final size:21
Alignment explanation
Indices: 29776--29815 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
29766 CCAATTCGCC
*
29776 CTTTAGCTT-TTTTTTAATCT
1 CTTTAGCTTATTTGTTAATCT
29796 CTTTCAGCTTATTTGTTAAT
1 CTTT-AGCTTATTTGTTAAT
29816 TCAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 5 0.29
22 8 0.47
ACGTcount: A:0.17, C:0.15, G:0.07, T:0.60
Consensus pattern (21 bp):
CTTTAGCTTATTTGTTAATCT
Found at i:30212 original size:13 final size:13
Alignment explanation
Indices: 30196--30220 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30186 AAAAAAAAAT
30196 CAAAAGTGTTTTC
1 CAAAAGTGTTTTC
30209 CAAAAGTGTTTT
1 CAAAAGTGTTTT
30221 TAAGTATGTT
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:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (13 bp):
CAAAAGTGTTTTC
Found at i:41319 original size:1 final size:1
Alignment explanation
Indices: 41313--41342 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
41303 CAGCATGTTT
41313 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
41343 CTAGCTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:42732 original size:38 final size:38
Alignment explanation
Indices: 42690--42766 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
42680 ATAAAAAAAG
* *
42690 TTATATATTTATCAAAAAATTTAAAACCATTTATTATA
1 TTATATATTTACCAAAAAATTTAAAACCATTCATTATA
42728 TTATATATTTACCAAAAAATTTAAAACCATTCATTATA
1 TTATATATTTACCAAAAAATTTAAAACCATTCATTATA
42766 T
1 T
42767 CATTTGTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (38 bp):
TTATATATTTACCAAAAAATTTAAAACCATTCATTATA
Done.