Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013168.1 Kokia drynarioides strain JFW-HI SEQ_128187, 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: 17747
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Found at i:5265 original size:15 final size:13
Alignment explanation
Indices: 5235--5291 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
5225 ATTATTTATC
*
5235 TTTTCTTTAATTT
1 TTTTCTTTCATTT
* *
5248 TTCTATTTCATTT
1 TTTTCTTTCATTT
5261 TTTTCTTTCTATTT
1 TTTTCTTTC-ATTT
5275 TTTATCCTTTCATTT
1 TTT-T-CTTTCATTT
5290 TT
1 TT
5292 CCTTTCATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 17 0.47
14 7 0.19
15 7 0.19
16 5 0.14
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTCTTTCATTT
Found at i:5277 original size:16 final size:15
Alignment explanation
Indices: 5253--5291 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
5243 AATTTTTCTA
5253 TTTCATTTTTT-T-C
1 TTTCATTTTTTATCC
5266 TTTCTATTTTTTATCC
1 TTTC-ATTTTTTATCC
5282 TTTCATTTTT
1 TTTCATTTTT
5292 CCTTTCATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.17
14 7 0.30
15 7 0.30
16 5 0.22
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCATTTTTTATCC
Found at i:13137 original size:23 final size:23
Alignment explanation
Indices: 13111--13256 Score: 210
Period size: 23 Copynumber: 6.3 Consensus size: 23
13101 ACACTAGCAC
13111 GCTTACT-ATTTAGCACTGTGTGT
1 GCTTACTGA-TTAGCACTGTGTGT
13134 GCTTACT-ATTTAGCACTGTGTGT
1 GCTTACTGA-TTAGCACTGTGTGT
*
13157 GCTTACTGATTCGCACTGTGTGT
1 GCTTACTGATTAGCACTGTGTGT
*
13180 GCTTACTGTATT-GCATTGTGTGT
1 GCTTACTG-ATTAGCACTGTGTGT
13203 GCTTACTGATTAGCACTGTGTGT
1 GCTTACTGATTAGCACTGTGTGT
13226 GCTTACTGGATT-GCACTGTGTGT
1 GCTTACT-GATTAGCACTGTGTGT
13249 GCTTACTG
1 GCTTACTG
13257 TTGCCCAACA
Statistics
Matches: 116, Mismatches: 3, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
22 4 0.03
23 104 0.90
24 8 0.07
ACGTcount: A:0.15, C:0.18, G:0.25, T:0.42
Consensus pattern (23 bp):
GCTTACTGATTAGCACTGTGTGT
Found at i:13281 original size:25 final size:25
Alignment explanation
Indices: 13246--13308 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
13236 TTGCACTGTG
*
13246 TGTGCTTACTGTTGCCCAACACTTA
1 TGTGCTCACTGTTGCCCAACACTTA
13271 TGTGCTCACTGTTGCCCAACACTTA
1 TGTGCTCACTGTTGCCCAACACTTA
13296 TGTGCTCACTGTT
1 TGTGCTCACTGTT
13309 TAGTACTTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (25 bp):
TGTGCTCACTGTTGCCCAACACTTA
Found at i:14790 original size:24 final size:24
Alignment explanation
Indices: 14729--14791 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
14719 GAGACTAATA
*
14729 AGAGTTTAACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* * *
14753 AGAGTTTAATTGAAACTAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
14777 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
14792 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:16729 original size:24 final size:24
Alignment explanation
Indices: 16713--16763 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
16703 AGTTTGACTT
16713 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
16737 AAACAAATAAATAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
16761 AAA
1 AAA
16764 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:17134 original size:20 final size:21
Alignment explanation
Indices: 17091--17134 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
17081 AATGAGAGAA
17091 AGAAGAAATAAGTTTGAATCTG
1 AGAAGAAATAAGTTTG-ATCTG
*
17113 AGAAGAATTAAGTTTG-TCTG
1 AGAAGAAATAAGTTTGATCTG
17133 AG
1 AG
17135 TGAGAGGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
22 15 0.71
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.30
Consensus pattern (21 bp):
AGAAGAAATAAGTTTGATCTG
Done.