Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002261.1 Kokia drynarioides strain JFW-HI SEQ_114275, 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: 7223
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Found at i:142 original size:21 final size:21
Alignment explanation
Indices: 118--192 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 21
108 AATAACTCAC
*
118 AAATCTAGCAAATGTATGTGT
1 AAATGTAGCAAATGTATGTGT
139 AAATGTATGTTTCATAAT-TAATGTGT
1 AAATGTA-G---CA-AATGT-ATGTGT
*
165 AAATGTAGAAAATGTATGTGT
1 AAATGTAGCAAATGTATGTGT
186 AAATGTA
1 AAATGTA
193 TGTTTCAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
21 22 0.49
22 3 0.07
25 4 0.09
26 16 0.36
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (21 bp):
AAATGTAGCAAATGTATGTGT
Found at i:144 original size:12 final size:12
Alignment explanation
Indices: 127--195 Score: 65
Period size: 12 Copynumber: 5.8 Consensus size: 12
117 CAAATCTAGC
127 AAATGTATGTGT
1 AAATGTATGTGT
*
139 AAATGTATGTTT
1 AAATGTATGTGT
151 CATAAT-TAATGTGT
1 -A-AATGT-ATGTGT
*
165 AAATGTA---GA
1 AAATGTATGTGT
174 AAATGTATGTGT
1 AAATGTATGTGT
186 AAATGTATGT
1 AAATGTATGT
196 TTCAAAATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
9 8 0.17
12 26 0.57
13 4 0.09
14 8 0.17
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (12 bp):
AAATGTATGTGT
Found at i:169 original size:26 final size:26
Alignment explanation
Indices: 133--207 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 26
123 TAGCAAATGT
*
133 ATGTGTAAATGTATGTTTCATAATTA
1 ATGTGTAAATGTATGTTTCAAAATTA
159 ATGTGTAAATGTA-G----AAAATGT-
1 ATGTGTAAATGTATGTTTCAAAAT-TA
180 ATGTGTAAATGTATGTTTCAAAATTA
1 ATGTGTAAATGTATGTTTCAAAATTA
206 AT
1 AT
208 ATGATTTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
21 17 0.41
22 2 0.05
25 2 0.05
26 20 0.49
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.41
Consensus pattern (26 bp):
ATGTGTAAATGTATGTTTCAAAATTA
Found at i:196 original size:47 final size:47
Alignment explanation
Indices: 118--207 Score: 153
Period size: 47 Copynumber: 1.9 Consensus size: 47
108 AATAACTCAC
* *
118 AAATCTAGCAAATGTATGTGTAAATGTATGTTTCATAATTAATGTGT
1 AAATCTAGAAAATGTATGTGTAAATGTATGTTTCAAAATTAATGTGT
*
165 AAATGTAGAAAATGTATGTGTAAATGTATGTTTCAAAATTAAT
1 AAATCTAGAAAATGTATGTGTAAATGTATGTTTCAAAATTAAT
208 ATGATTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.39
Consensus pattern (47 bp):
AAATCTAGAAAATGTATGTGTAAATGTATGTTTCAAAATTAATGTGT
Found at i:334 original size:21 final size:21
Alignment explanation
Indices: 308--383 Score: 73
Period size: 21 Copynumber: 3.4 Consensus size: 21
298 CACAGTACAT
308 TAAATGTAGCAATTGTATGTG
1 TAAATGTAGCAATTGTATGTG
*
329 TAAATGTATGTTTCATAATT-AATGTG
1 TAAATGTA-G---C--AATTGTATGTG
*
355 TAAATGTAGCAACTGTATGTG
1 TAAATGTAGCAATTGTATGTG
376 TAAATGTA
1 TAAATGTA
384 TGTTTCATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
20 3 0.07
21 21 0.47
22 2 0.04
25 2 0.04
26 13 0.29
27 4 0.09
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (21 bp):
TAAATGTAGCAATTGTATGTG
Found at i:338 original size:12 final size:12
Alignment explanation
Indices: 321--386 Score: 50
Period size: 12 Copynumber: 5.6 Consensus size: 12
311 ATGTAGCAAT
321 TGTATGTGTAAA
1 TGTATGTGTAAA
*
333 TGTATGTTTCATAA
1 TGTATGTGT-A-AA
347 T-TAATGTGTAAA
1 TGT-ATGTGTAAA
* *
359 TGTA---GCAAC
1 TGTATGTGTAAA
368 TGTATGTGTAAA
1 TGTATGTGTAAA
380 TGTATGT
1 TGTATGT
387 TTCATAATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
9 7 0.17
12 22 0.54
13 4 0.10
14 8 0.20
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (12 bp):
TGTATGTGTAAA
Found at i:353 original size:26 final size:26
Alignment explanation
Indices: 321--394 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
311 ATGTAGCAAT
321 TGTATGTGTAAATGTATGTTTCATAA
1 TGTATGTGTAAATGTATGTTTCATAA
*
347 T-TAATGTGTAAATGTA-G---CA-AC
1 TGT-ATGTGTAAATGTATGTTTCATAA
368 TGTATGTGTAAATGTATGTTTCATAA
1 TGTATGTGTAAATGTATGTTTCATAA
394 T
1 T
395 CAATATGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
21 15 0.38
22 4 0.10
25 4 0.10
26 16 0.41
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (26 bp):
TGTATGTGTAAATGTATGTTTCATAA
Found at i:1198 original size:48 final size:48
Alignment explanation
Indices: 1142--1235 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
1132 GTTGGCAGTA
*
1142 AAGGTGGTGAGGGTTTAGATGCTAGCAATAAGGGTGGTGAGGGTGATG
1 AAGGTGGTGAGGGTTTAGAAGCTAGCAATAAGGGTGGTGAGGGTGATG
* * * *
1190 AAGGTGGTGAGGGTTTGGAAGCTGGTAGTAAGGGTGGTGAGGGTGA
1 AAGGTGGTGAGGGTTTAGAAGCTAGCAATAAGGGTGGTGAGGGTGA
1236 GGGAGATGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.23, C:0.03, G:0.49, T:0.24
Consensus pattern (48 bp):
AAGGTGGTGAGGGTTTAGAAGCTAGCAATAAGGGTGGTGAGGGTGATG
Found at i:5263 original size:31 final size:32
Alignment explanation
Indices: 5228--5290 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
5218 TTCAACTCAT
5228 CGATTAAAC-AAACAGCAATATCGATTAAACA
1 CGATTAAACAAAACAGCAATATCGATTAAACA
*
5259 CGATTAAACAAAACAGTAATATCGATTAAACA
1 CGATTAAACAAAACAGCAATATCGATTAAACA
5291 AAATATCAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (32 bp):
CGATTAAACAAAACAGCAATATCGATTAAACA
Found at i:5287 original size:22 final size:22
Alignment explanation
Indices: 5255--5312 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
5245 ATATCGATTA
5255 AACA-CGATTAAACAAAACAGT-
1 AACATCGATTAAACAAAACA-TC
* *
5276 AATATCGATTAAACAAAATATC
1 AACATCGATTAAACAAAACATC
5298 AACATCGATTAAACA
1 AACATCGATTAAACA
5313 TGATTAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (22 bp):
AACATCGATTAAACAAAACATC
Done.