Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015138.1 Corchorus olitorius cultivar O-4 contig15171, 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: 20064
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:364 original size:90 final size:89
Alignment explanation
Indices: 256--433 Score: 295
Period size: 90 Copynumber: 2.0 Consensus size: 89
246 ACACATGAAT
*
256 ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTTCAAA-TTATTGA
1 ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACC-TTAAAAGTTATTGA
320 TAATATTTAAAAATTAAAAAGGACAC
65 TAATATTT-AAAATTAAAAAGGACAC
* **
346 ATGATATATAATTTTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
1 ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
411 AATATTTAAAATTAAAAAGGACA
66 AATATTTAAAATTAAAAAGGACA
434 TTTTAGATAT
Statistics
Matches: 83, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
89 21 0.25
90 62 0.75
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (89 bp):
ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
AATATTTAAAATTAAAAAGGACAC
Found at i:492 original size:6 final size:6
Alignment explanation
Indices: 474--503 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
464 GTTTAGACTT
474 ATATAG TATATAG ATATAG ATATAG ATATA
1 ATATAG -ATATAG ATATAG ATATAG ATATA
504 ACCATCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:1835 original size:10 final size:10
Alignment explanation
Indices: 1820--1848 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1810 TCGTATTAAC
1820 AATTTTATTT
1 AATTTTATTT
1830 AATTTTATTT
1 AATTTTATTT
1840 AA-TTTATTT
1 AATTTTATTT
1849 CCTTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
AATTTTATTT
Found at i:3936 original size:11 final size:11
Alignment explanation
Indices: 3906--3944 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3896 TATTAAAGAG
* *
3906 TTTTTGTTTGT
1 TTTTTCTTTTT
*
3917 TTCTTCTTTTT
1 TTTTTCTTTTT
3928 TTTTTCTTTTT
1 TTTTTCTTTTT
3939 TTTTTC
1 TTTTTC
3945 CGATTTTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:5205 original size:7 final size:7
Alignment explanation
Indices: 5193--5230 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
5183 GCATACTTCT
5193 CAAAAAA
1 CAAAAAA
5200 CAAAAAAA
1 C-AAAAAA
5208 CAAAAAA
1 CAAAAAA
5215 CAAACAAA
1 CAAA-AAA
5223 CAAAAAA
1 CAAAAAA
5230 C
1 C
5231 TAAAGGATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAAAA
Found at i:5207 original size:8 final size:8
Alignment explanation
Indices: 5194--5229 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
5184 CATACTTCTC
5194 AAAAAACA
1 AAAAAACA
5202 AAAAAAC-
1 AAAAAACA
5209 AAAAAACA
1 AAAAAACA
*
5217 AACAAACA
1 AAAAAACA
5225 AAAAA
1 AAAAA
5230 CTAAAGGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:5213 original size:15 final size:15
Alignment explanation
Indices: 5193--5230 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
5183 GCATACTTCT
5193 CAAAAAACAAAAAAA
1 CAAAAAACAAAAAAA
*
5208 CAAAAAACAAACAAA
1 CAAAAAACAAAAAAA
5223 CAAAAAAC
1 CAAAAAAC
5231 TAAAGGATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (15 bp):
CAAAAAACAAAAAAA
Found at i:6298 original size:20 final size:20
Alignment explanation
Indices: 6272--6315 Score: 70
Period size: 22 Copynumber: 2.1 Consensus size: 20
6262 ATTATGGTAT
6272 TATATATAAAATATATTTATGA
1 TATATATAAAATATA--TATGA
6294 TATATATAAAATATATATGA
1 TATATATAAAATATATATGA
6314 TA
1 TA
6316 AATTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.32
22 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (20 bp):
TATATATAAAATATATATGA
Found at i:6318 original size:13 final size:11
Alignment explanation
Indices: 6272--6311 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
6262 ATTATGGTAT
6272 TATATATAAAA
1 TATATATAAAA
* **
6283 TATATTTATGA
1 TATATATAAAA
6294 TATATATAAAA
1 TATATATAAAA
6305 TATATAT
1 TATATAT
6312 GATAAATTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (11 bp):
TATATATAAAA
Found at i:7670 original size:20 final size:20
Alignment explanation
Indices: 7645--7684 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
7635 ATAACATATA
7645 GTTATTGAAATTGACTTTAT
1 GTTATTGAAATTGACTTTAT
7665 GTTATTGAAATTGACTTTAT
1 GTTATTGAAATTGACTTTAT
7685 TGCCAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (20 bp):
GTTATTGAAATTGACTTTAT
Done.