Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012347.1 Kokia drynarioides strain JFW-HI SEQ_127349, 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: 31591
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Found at i:393 original size:30 final size:30
Alignment explanation
Indices: 324--392 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
314 AAAAAATCTT
324 TAAACTTTTTCGAAAAATGCAATTAAATCC
1 TAAACTTTTTCGAAAAATGCAATTAAATCC
354 TAAACTTTTTCGAAAAATGCAATTAAATCC
1 TAAACTTTTTCGAAAAATGCAATTAAATCC
*
384 T-TACTTTTT
1 TAAACTTTTT
393 TTACACTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 7 0.18
30 31 0.82
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (30 bp):
TAAACTTTTTCGAAAAATGCAATTAAATCC
Found at i:10009 original size:31 final size:30
Alignment explanation
Indices: 9966--10032 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
9956 ATTATATTAA
* * *
9966 TAATTTATAAAATATAAATTAAATTAATATT
1 TAATATATAAAAT-TAAATAAAATTAAAATT
*
9997 TAATATATAAAATTACATAAAATTAAAATT
1 TAATATATAAAATTAAATAAAATTAAAATT
10027 T-ATATA
1 TAATATA
10033 ATATTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 5 0.16
30 15 0.47
31 12 0.38
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (30 bp):
TAATATATAAAATTAAATAAAATTAAAATT
Found at i:10038 original size:27 final size:28
Alignment explanation
Indices: 10000--10066 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
9990 TAATATTTAA
*
10000 TATATAAAATTACATA-AAATTAAAATT
1 TATATAAAATTACATATAAACTAAAATT
* *
10027 TATATAATATTACATATTAGACTAAAATT
1 TATATAAAATTACATA-TAAACTAAAATT
*
10056 TATATATAATT
1 TATATAAAATT
10067 TTCAACATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 15 0.45
29 18 0.55
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (28 bp):
TATATAAAATTACATATAAACTAAAATT
Found at i:10229 original size:2 final size:2
Alignment explanation
Indices: 10222--10255 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10212 AGAAACTGGA
10222 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10256 TGAAAGACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10267 original size:6 final size:6
Alignment explanation
Indices: 10258--10288 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
10248 AGAGAGAGTG
*
10258 AAAGAC AAAGAC AAAGAC AACGAC AAAGAC A
1 AAAGAC AAAGAC AAAGAC AAAGAC AAAGAC A
10289 CAACAACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.19, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAC
Found at i:24050 original size:25 final size:25
Alignment explanation
Indices: 24016--24087 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
24006 TGAAGTACTT
* *
24016 AACAGAAGCACATA-AGTGTTGGGGA
1 AACAGAAGCACACACAGTGCT-GGGA
*
24041 AACAGAAGCACACACAGTGCTGGGT
1 AACAGAAGCACACACAGTGCTGGGA
24066 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
24088 AATAGTAAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
25 38 0.88
26 5 0.12
ACGTcount: A:0.39, C:0.21, G:0.28, T:0.12
Consensus pattern (25 bp):
AACAGAAGCACACACAGTGCTGGGA
Done.