Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009980.1 Kokia drynarioides strain JFW-HI SEQ_124731, 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: 18030
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Warning! 117 characters in sequence are not A, C, G, or T
Found at i:228 original size:29 final size:28
Alignment explanation
Indices: 191--546 Score: 245
Period size: 29 Copynumber: 12.2 Consensus size: 28
181 CCCTAAACCA
191 TCCAAAAATTACCATTTTACCCCCGAACT
1 TCCAAAAATTACCATTTTA-CCCCGAACT
* *
220 T-CAAAAAATCCCATTTTTGACCCCGAATCT
1 TCCAAAAATTACCA-TTTT-ACCCCGAA-CT
* *
250 TCCAAAAATTACTATTTTACCCCCAAACT
1 TCCAAAAATTACCATTTTA-CCCCGAACT
*
279 TCCAAAAA-T-CCAATTTTTGACCTCGAACCT
1 TCCAAAAATTACC-A-TTTT-ACCCCGAA-CT
* *
309 TCCAAAAATTACTATTTTACCCCCAAACT
1 TCCAAAAATTACCATTTTA-CCCCGAACT
338 TCCAAAAA-T-CCTATTTTTGACCCCGAATCT
1 TCCAAAAATTACC-A-TTTT-ACCCCGAA-CT
368 TCC-AAAATTACCA-TTTACCCCCGAACT
1 TCCAAAAATTACCATTTTA-CCCCGAACT
*
395 TCCAAAAA-T-CTCATTTTTGACCTCGAACCT
1 TCCAAAAATTAC-CA-TTTT-ACCCCGAA-CT
* * *
425 TCTAAAAATTACCGTTTTACCCCTAA-T
1 TCCAAAAATTACCATTTTACCCCGAACT
452 TCCAAAAA-T-CTCATTTTTAACCCCGAACCT
1 TCCAAAAATTAC-CA-TTTT-ACCCCGAA-CT
*
482 TTCAAAAATTACCATTTTACCCCCGAACT
1 TCCAAAAATTACCATTTTA-CCCCGAACT
* *
511 TACAAAAA-T-CCATTTTTGACTCCGAACCT
1 TCCAAAAATTACCA-TTTT-ACCCCGAA-CT
540 TCCAAAA
1 TCCAAAA
547 CTACCTATTT
Statistics
Matches: 263, Mismatches: 26, Indels: 76
0.72 0.07 0.21
Matches are distributed among these distances:
25 1 0.00
26 3 0.01
27 26 0.10
28 46 0.17
29 91 0.35
30 75 0.29
31 18 0.07
32 3 0.01
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (28 bp):
TCCAAAAATTACCATTTTACCCCGAACT
Found at i:286 original size:59 final size:59
Alignment explanation
Indices: 186--564 Score: 500
Period size: 59 Copynumber: 6.5 Consensus size: 59
176 GAGGTCCCTA
* *
186 AACCATCCAAAAATTACCATTTTACCCCCGAACTTCAAAAAATCCCATTTTTGACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * *
245 AATCTTCCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCAATTTTTGACCTCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
304 AACCTTCCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCTATTTTTGACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
363 AATCTTCC-AAAATTACCA-TTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * *
420 AACCTTCTAAAAATTACCGTTTTA-CCCCTAA-TTCCAAAAATCTCATTTTTAACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
477 AACCTTTCAAAAATTACCATTTTACCCCCGAACTTACAAAAAT-CCATTTTTGACTCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
535 AACCTTCC-AAAACTACCTATTTTGCCCCCG
1 AACCTTCCAAAAATTACC-ATTTTACCCCCG
565 TGCATCCGAA
Statistics
Matches: 282, Mismatches: 33, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
57 94 0.33
58 60 0.21
59 128 0.45
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (59 bp):
AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:2331 original size:21 final size:21
Alignment explanation
Indices: 2305--2348 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2295 TGTGCATAAA
*
2305 CTTTATAGATTAAAGA-AAGCT
1 CTTTATAGACTAAA-ACAAGCT
2326 CTTTATAGACTAAAACAAGCT
1 CTTTATAGACTAAAACAAGCT
2347 CT
1 CT
2349 ACAAGCTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (21 bp):
CTTTATAGACTAAAACAAGCT
Found at i:4099 original size:5 final size:5
Alignment explanation
Indices: 4089--4113 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4079 CCAACATGAT
4089 GAGCA GAGCA GAGCA GAGCA GAGCA
1 GAGCA GAGCA GAGCA GAGCA GAGCA
4114 ACCGCATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
GAGCA
Found at i:11715 original size:15 final size:15
Alignment explanation
Indices: 11695--11724 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11685 TGTGTTATTT
11695 ACCTTAAAAATTATG
1 ACCTTAAAAATTATG
11710 ACCTTAAAAATTATG
1 ACCTTAAAAATTATG
11725 TATAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
ACCTTAAAAATTATG
Found at i:13292 original size:2 final size:2
Alignment explanation
Indices: 13285--13313 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13275 AGAAGGAAAC
13285 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13314 TTGGTTTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.