Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012491.1 Corchorus olitorius cultivar O-4 contig12524, 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: 14421
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:1242 original size:31 final size:31
Alignment explanation
Indices: 1182--1245 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1172 AGTAGGGGTT
* **
1182 TTGTAAAACTTTTGAATCGCGTATTATACCC
1 TTGTAAAACTTTTGAATCGCCTAACATACCC
* *
1213 TTGTTAAACTTTTGATTCGCCTAACATACCC
1 TTGTAAAACTTTTGAATCGCCTAACATACCC
1244 TT
1 TT
1246 ATTTTTTCGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (31 bp):
TTGTAAAACTTTTGAATCGCCTAACATACCC
Found at i:1387 original size:93 final size:93
Alignment explanation
Indices: 1285--1469 Score: 316
Period size: 93 Copynumber: 2.0 Consensus size: 93
1275 TTATTTAAAT
*
1285 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAACTA
* *
1350 TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTATTTTTACCATATTACTAATTTAC
* *
1378 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAACTA
*
1443 TTTTATTTTTACGATATTACTAATTTA
66 TTTTATTTTTACCATATTACTAATTTA
1470 ATTAAAAAGT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATATTACTAATTTAC
Found at i:7160 original size:37 final size:37
Alignment explanation
Indices: 7110--7185 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
7100 AGGTGTTATG
7110 AGATTTCAATTGTATTCGGTAATG-TAGCTAATCATGT
1 AGATTTCAATTGTATTCGGTAA-GCTAGCTAATCATGT
7147 AGATTTCAATTGTATTCGGTAAGCTAGCTAATCATGT
1 AGATTTCAATTGTATTCGGTAAGCTAGCTAATCATGT
7184 AG
1 AG
7186 CGGTGTACGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 1 0.03
37 37 0.97
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (37 bp):
AGATTTCAATTGTATTCGGTAAGCTAGCTAATCATGT
Found at i:10846 original size:12 final size:12
Alignment explanation
Indices: 10829--10859 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
10819 ACACAGACAC
*
10829 ACAGACACGTAA
1 ACAGACACATAA
10841 ACAGACACATAA
1 ACAGACACATAA
10853 ACAGACA
1 ACAGACA
10860 GATACATAGA
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:0.55, C:0.26, G:0.13, T:0.06
Consensus pattern (12 bp):
ACAGACACATAA
Found at i:13263 original size:11 final size:12
Alignment explanation
Indices: 13247--13278 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
13237 GAAGTTCGTG
13247 TTTGAAGACT-A
1 TTTGAAGACTAA
13258 TTTGAAGA-TAA
1 TTTGAAGACTAA
13269 TTTGAAGACT
1 TTTGAAGACT
13279 TGAAGATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 17 0.89
12 1 0.05
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTAA
Found at i:13283 original size:19 final size:18
Alignment explanation
Indices: 13259--13294 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13249 TGAAGACTAT
13259 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
13278 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
13295 ATTATTTCCA
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:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Done.