Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002677.1 Kokia drynarioides strain JFW-HI SEQ_114937, 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: 7179
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:1440 original size:52 final size:50
Alignment explanation
Indices: 1395--1493 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 50
1385 TCATTTTCAC
1395 TTTATTT-ATTTTATTTTAGTTTAGTTTTTTTGTTTAATATTTTCATCACTTTA
1 TTTATTTCATTTTATTTTAGTTT--TTTTTTTGTTTAATATTTTCAT--CTTTA
1448 TTTATTTCATTTTATTTTAGTTTTTTTTTTGTTTAATATTTTCATC
1 TTTATTTCATTTTATTTTAGTTTTTTTTTTGTTTAATATTTTCATC
1494 ACTAAACCCC
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
50 1 0.02
52 22 0.49
53 7 0.16
54 15 0.33
ACGTcount: A:0.19, C:0.06, G:0.05, T:0.70
Consensus pattern (50 bp):
TTTATTTCATTTTATTTTAGTTTTTTTTTTGTTTAATATTTTCATCTTTA
Found at i:1460 original size:49 final size:50
Alignment explanation
Indices: 1391--1496 Score: 169
Period size: 49 Copynumber: 2.1 Consensus size: 50
1381 AACTTCATTT
*
1391 TCACTTTATTTATTTTATTTTAGTTTAG-TTTTTTTGTTTAATATTTTCA
1 TCACTTTATTTATTTCATTTTAGTTTAGTTTTTTTTGTTTAATATTTTCA
*
1440 TCACTTTATTTATTTCATTTTATTTTAGTTTTTTTTTTGTTTAATATTTTCA
1 TCACTTTATTTATTTCATTTTAGTTTAG--TTTTTTTTGTTTAATATTTTCA
1492 TCACT
1 TCACT
1497 AAACCCCCTT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
49 26 0.50
52 26 0.50
ACGTcount: A:0.20, C:0.08, G:0.05, T:0.67
Consensus pattern (50 bp):
TCACTTTATTTATTTCATTTTAGTTTAGTTTTTTTTGTTTAATATTTTCA
Found at i:1514 original size:52 final size:52
Alignment explanation
Indices: 1398--1517 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 52
1388 TTTTCACTTT
** ***
1398 ATTTATTTTATTTTAGTTTAGTTTTTTTGTTTAATATTTTCATCACTTTATTT
1 ATTTATTTTATTTTAGTTTA-TTTTTTTGTTTAATATTTTCATCACTAAACCC
1451 ATTTCATTTTATTTTAGTTT-TTTTTTTGTTTAATATTTTCATCACTAAACCCC
1 ATTT-ATTTTATTTTAGTTTATTTTTTTGTTTAATATTTTCATCACTAAA-CCC
* *
1504 CTTTAATTTATTTT
1 ATTTATTTTATTTT
1518 CAGGAAGCTC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
52 36 0.62
53 7 0.12
54 15 0.26
ACGTcount: A:0.22, C:0.10, G:0.04, T:0.64
Consensus pattern (52 bp):
ATTTATTTTATTTTAGTTTATTTTTTTGTTTAATATTTTCATCACTAAACCC
Found at i:3201 original size:39 final size:39
Alignment explanation
Indices: 3145--3219 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
3135 GCTGGGGCAA
* *
3145 CTGCTGTTGTTGTTGCAGCTG-GGAGAGTTGCTGCTGCTG
1 CTGCTGCTGTTGCTGCAGCTGAGG-GAGTTGCTGCTGCTG
*
3184 CTGCTGCTGTTGCTGCAGCTGAGGGAGTTGTTGCTG
1 CTGCTGCTGTTGCTGCAGCTGAGGGAGTTGCTGCTG
3220 TTGCAAATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 30 0.94
40 2 0.06
ACGTcount: A:0.08, C:0.19, G:0.39, T:0.35
Consensus pattern (39 bp):
CTGCTGCTGTTGCTGCAGCTGAGGGAGTTGCTGCTGCTG
Found at i:3256 original size:15 final size:15
Alignment explanation
Indices: 3236--3282 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
3226 ATGTGGGAGC
3236 GGCTGTTGCTGCTGT
1 GGCTGTTGCTGCTGT
3251 GGCTGTTGCTGCTGCT
1 GGCTGTTGCTGCTG-T
* *
3267 -GTTGTTGCAGCTGT
1 GGCTGTTGCTGCTGT
3281 GG
1 GG
3283 GAGCTGCTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.02, C:0.19, G:0.40, T:0.38
Consensus pattern (15 bp):
GGCTGTTGCTGCTGT
Found at i:3299 original size:33 final size:33
Alignment explanation
Indices: 3252--3327 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
3242 TGCTGCTGTG
*
3252 GCTGTTGCTGCTGCTGTTGTTGCAGCTGTGGGA
1 GCTGCTGCTGCTGCTGTTGTTGCAGCTGTGGGA
3285 GCTGCTGCTGCTGCTGTTGTTGCAGCTGTGGGA
1 GCTGCTGCTGCTGCTGTTGTTGCAGCTGTGGGA
*
3318 CCTGCTGCTG
1 GCTGCTGCTG
3328 TGGCATCTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.05, C:0.22, G:0.38, T:0.34
Consensus pattern (33 bp):
GCTGCTGCTGCTGCTGTTGTTGCAGCTGTGGGA
Found at i:3340 original size:33 final size:33
Alignment explanation
Indices: 3237--3327 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
3227 TGTGGGAGCG
* *
3237 GCTGTTGCTGCTGT-GG--CTGTTGCTGCTGCT
1 GCTGTTGCAGCTGTGGGACCTGCTGCTGCTGCT
* *
3267 GTTGTTGCAGCTGTGGGAGCTGCTGCTGCTGCT
1 GCTGTTGCAGCTGTGGGACCTGCTGCTGCTGCT
*
3300 GTTGTTGCAGCTGTGGGACCTGCTGCTG
1 GCTGTTGCAGCTGTGGGACCTGCTGCTG
3328 TGGCATCTGT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
30 12 0.22
31 2 0.04
33 40 0.74
ACGTcount: A:0.04, C:0.22, G:0.38, T:0.35
Consensus pattern (33 bp):
GCTGTTGCAGCTGTGGGACCTGCTGCTGCTGCT
Done.