Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000241.1 Kokia drynarioides strain JFW-HI SEQ_110971, 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: 12976
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:2000 original size:34 final size:34
Alignment explanation
Indices: 1956--2109 Score: 202
Period size: 34 Copynumber: 4.5 Consensus size: 34
1946 TACTACTGAT
1956 TTGATTTGTTATAAGCATATTAATTGCTATCGTA
1 TTGATTTGTTATAAGCATATTAATTGCTATCGTA
* * * *
1990 TCGATATGTTATAAGCATTTTAATTGCTACCGTA
1 TTGATTTGTTATAAGCATATTAATTGCTATCGTA
*
2024 TTGATTTGTTATAAGCATATTAATTACTATCGTA
1 TTGATTTGTTATAAGCATATTAATTGCTATCGTA
* * * * *
2058 TTGATCTATTATAACCACATTAATTGCTA-CAATA
1 TTGATTTGTTATAAGCATATTAATTGCTATC-GTA
2092 TTGATTTGTTATAAGCAT
1 TTGATTTGTTATAAGCAT
2110 GCGACATTGC
Statistics
Matches: 100, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
33 1 0.01
34 99 0.99
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (34 bp):
TTGATTTGTTATAAGCATATTAATTGCTATCGTA
Found at i:2041 original size:68 final size:68
Alignment explanation
Indices: 1956--2109 Score: 227
Period size: 68 Copynumber: 2.3 Consensus size: 68
1946 TACTACTGAT
* * * ** *
1956 TTGATTTGTTATAAGCATATTAATTGCTATCGTATCGATATGTTATAAGCATTTTAATTGCTACC
1 TTGATTTGTTATAAGCATATTAATTACTATCGTATCGATATATTATAACCACATTAATTGCTACA
*
2021 GTA
66 ATA
* *
2024 TTGATTTGTTATAAGCATATTAATTACTATCGTATTGATCTATTATAACCACATTAATTGCTACA
1 TTGATTTGTTATAAGCATATTAATTACTATCGTATCGATATATTATAACCACATTAATTGCTACA
2089 ATA
66 ATA
2092 TTGATTTGTTATAAGCAT
1 TTGATTTGTTATAAGCAT
2110 GCGACATTGC
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 77 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (68 bp):
TTGATTTGTTATAAGCATATTAATTACTATCGTATCGATATATTATAACCACATTAATTGCTACA
ATA
Found at i:3255 original size:18 final size:18
Alignment explanation
Indices: 3232--3266 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3222 TTACATTTGA
3232 AAAGTAAAAACTAAAAAT
1 AAAGTAAAAACTAAAAAT
*
3250 AAAGTAAAACCTAAAAA
1 AAAGTAAAAACTAAAAA
3267 AGAGAGAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.14
Consensus pattern (18 bp):
AAAGTAAAAACTAAAAAT
Found at i:4225 original size:27 final size:27
Alignment explanation
Indices: 4194--4245 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
4184 ATTTTTTATT
*
4194 TTGAAATTCATTCCAAAATAAAAATGA
1 TTGAAATTCATTACAAAATAAAAATGA
4221 TTGAAATTCATTACAAAATAAAAAT
1 TTGAAATTCATTACAAAATAAAAAT
4246 TCTTTCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.31
Consensus pattern (27 bp):
TTGAAATTCATTACAAAATAAAAATGA
Found at i:5227 original size:15 final size:15
Alignment explanation
Indices: 5207--5240 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5197 TTTTTAAAAA
5207 TATTTGTTTATTTAT
1 TATTTGTTTATTTAT
*
5222 TATTTGTTTGTTTAT
1 TATTTGTTTATTTAT
5237 TATT
1 TATT
5241 CATTATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (15 bp):
TATTTGTTTATTTAT
Found at i:6285 original size:22 final size:22
Alignment explanation
Indices: 6260--6302 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6250 ATTACCATGT
6260 TTATCTAATA-TGTTATAGATAA
1 TTATCTAATATTGTTAT-GATAA
*
6282 TTATTTAATATTGTTATGATA
1 TTATCTAATATTGTTATGATA
6303 CTTACTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
TTATCTAATATTGTTATGATAA
Found at i:11791 original size:6 final size:7
Alignment explanation
Indices: 11774--11799 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
11764 TTATGGTTCT
11774 TTTTTTC
1 TTTTTTC
11781 TTTTTTC
1 TTTTTTC
11788 TTTTTTC
1 TTTTTTC
11795 TTTTT
1 TTTTT
11800 AATCACCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Done.