Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013963.1 Kokia drynarioides strain JFW-HI SEQ_128994, 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: 14124
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Found at i:314 original size:14 final size:15
Alignment explanation
Indices: 295--335 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
285 TATGTGTGCT
295 TAATTCTTGATTTAG
1 TAATTCTTGATTTAG
* *
310 T-ATTCTTGATATAT
1 TAATTCTTGATTTAG
324 TAATTCTTGATT
1 TAATTCTTGATT
336 GATGTGCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.56
Consensus pattern (15 bp):
TAATTCTTGATTTAG
Found at i:1003 original size:18 final size:19
Alignment explanation
Indices: 980--1039 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 19
970 AGCCATTTTA
*
980 TTATTATTT-ATTTTTATT
1 TTATTATTTCACTTTTATT
998 TTATTATTTGCACTTTTATT
1 TTATTATTT-CACTTTTATT
* *
1018 TTAATTTTTTTCCCTTTTATT
1 TT-A-TTATTTCACTTTTATT
1039 T
1 T
1040 GCTTCTAGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 9 0.26
20 10 0.29
21 11 0.31
22 5 0.14
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.72
Consensus pattern (19 bp):
TTATTATTTCACTTTTATT
Found at i:1016 original size:20 final size:21
Alignment explanation
Indices: 991--1039 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
981 TATTATTTAT
991 TTTTATTTT-ATTATTTGCAC
1 TTTTATTTTAATTATTTGCAC
* * *
1011 TTTTATTTTAATTTTTTTCCC
1 TTTTATTTTAATTATTTGCAC
1032 TTTTATTT
1 TTTTATTT
1040 GCTTCTAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTATTTTAATTATTTGCAC
Found at i:3945 original size:22 final size:22
Alignment explanation
Indices: 3896--3958 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
3886 AATTAGTATA
* *
3896 TTTATTTTCATTTTCATATTTAGG
1 TTTATTTT-ATTTT-ATTTTTAAG
*
3920 TTTATTTTATTTTATTTTTAAT
1 TTTATTTTATTTTATTTTTAAG
*
3942 TTTATTTTA-ATTATTTT
1 TTTATTTTATTTTATTTT
3959 GTTTTTTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.20
22 15 0.43
23 5 0.14
24 8 0.23
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.71
Consensus pattern (22 bp):
TTTATTTTATTTTATTTTTAAG
Found at i:4867 original size:9 final size:10
Alignment explanation
Indices: 4845--4881 Score: 58
Period size: 9 Copynumber: 3.7 Consensus size: 10
4835 AAGAAGAAGA
4845 AAAAAAAGTCG
1 AAAAAAA-TCG
4856 AAAAAAAT-G
1 AAAAAAATCG
4865 AAAAAAATCG
1 AAAAAAATCG
4875 AAAAAAA
1 AAAAAAA
4882 GAAAATTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.36
10 9 0.36
11 7 0.28
ACGTcount: A:0.76, C:0.05, G:0.11, T:0.08
Consensus pattern (10 bp):
AAAAAAATCG
Found at i:4870 original size:19 final size:18
Alignment explanation
Indices: 4845--4886 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 18
4835 AAGAAGAAGA
4845 AAAAAAAGTCGAAAAAAATG
1 AAAAAAA-TCGAAAAAAA-G
4865 AAAAAAATCGAAAAAAAG
1 AAAAAAATCGAAAAAAAG
4883 AAAA
1 AAAA
4887 TTCAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.23
19 10 0.45
20 7 0.32
ACGTcount: A:0.76, C:0.05, G:0.12, T:0.07
Consensus pattern (18 bp):
AAAAAAATCGAAAAAAAG
Done.