Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004438.1 Kokia drynarioides strain JFW-HI SEQ_117832, 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: 6064
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Found at i:151 original size:23 final size:23
Alignment explanation
Indices: 119--263 Score: 141
Period size: 23 Copynumber: 6.3 Consensus size: 23
109 ACATTAGCGC
*
119 GCTTAGTGTTTAGCACTGTGTGT
1 GCTTACTGTTTAGCACTGTGTGT
* *
142 GCTTACTGTTCAGCACTATGTGT
1 GCTTACTGTTTAGCACTGTGTGT
* * * *
165 ACTTACTGTTCAGCACTATATGT
1 GCTTACTGTTTAGCACTGTGTGT
* *
188 GCTTACTGATTT-GTAGTGTGTGT
1 GCTTACTG-TTTAGCACTGTGTGT
* **
211 GCTTACTGTTTTGCACTGCATGT
1 GCTTACTGTTTAGCACTGTGTGT
*
234 GCCTACTGATTT-GCACTGTGTGT
1 GCTTACTG-TTTAGCACTGTGTGT
257 GCTTACT
1 GCTTACT
264 ATATCCCTAA
Statistics
Matches: 100, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
22 3 0.03
23 92 0.92
24 5 0.05
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (23 bp):
GCTTACTGTTTAGCACTGTGTGT
Found at i:4795 original size:17 final size:17
Alignment explanation
Indices: 4711--4811 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 17
4701 CCATTTTTAA
* *
4711 AATTTAAATCTAAATCT
1 AATTTAAATTTAAATTT
* *
4728 -ATTTAAATTTGAATTC
1 AATTTAAATTTAAATTT
*
4744 ACTTTAAATTTAAACTTT
1 AATTTAAATTTAAA-TTT
* * * **
4762 ATTTTGAGTTTGGATTT
1 AATTTAAATTTAAATTT
4779 AATTTAAATTTAAATTT
1 AATTTAAATTTAAATTT
* *
4796 ATTTTAAATTAAAATT
1 AATTTAAATTTAAATT
4812 AAACTTTGAA
Statistics
Matches: 63, Mismatches: 19, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
16 12 0.19
17 40 0.63
18 11 0.17
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (17 bp):
AATTTAAATTTAAATTT
Found at i:4959 original size:15 final size:15
Alignment explanation
Indices: 4885--4961 Score: 54
Period size: 15 Copynumber: 5.1 Consensus size: 15
4875 CTTTGGGCCT
4885 AATTCCAAATGACCC
1 AATTCCAAATGACCC
* *
4900 AAATTGCCTAA--ACAC
1 -AATT-CCAAATGACCC
4915 AATTCCAAATGACCC
1 AATTCCAAATGACCC
* *
4930 AAATCGCCTAA--ACCC
1 -AAT-TCCAAATGACCC
4945 AATTCCAAATGACCC
1 AATTCCAAATGACCC
4960 AA
1 AA
4962 ATTGCCGAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 15
0.67 0.12 0.22
Matches are distributed among these distances:
13 8 0.17
14 7 0.15
15 16 0.35
16 7 0.15
17 8 0.17
ACGTcount: A:0.43, C:0.32, G:0.06, T:0.18
Consensus pattern (15 bp):
AATTCCAAATGACCC
Found at i:4974 original size:15 final size:15
Alignment explanation
Indices: 4896--4977 Score: 55
Period size: 15 Copynumber: 5.5 Consensus size: 15
4886 ATTCCAAATG
*
4896 ACCCAAATTGCCTAA
1 ACCCAAATTGCCAAA
*
4911 ACAC-AATT-CCAAA
1 ACCCAAATTGCCAAA
* *
4924 TGACCCAAATCGCCTAA
1 --ACCCAAATTGCCAAA
4941 ACCC-AATT-CCAAA
1 ACCCAAATTGCCAAA
*
4954 TGACCCAAATTGCCGAA
1 --ACCCAAATTGCCAAA
4971 ACCCAAA
1 ACCCAAA
4978 CCCAAACCCA
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
13 8 0.16
14 7 0.14
15 21 0.41
16 7 0.14
17 8 0.16
ACGTcount: A:0.43, C:0.34, G:0.07, T:0.16
Consensus pattern (15 bp):
ACCCAAATTGCCAAA
Found at i:4983 original size:30 final size:30
Alignment explanation
Indices: 4885--4976 Score: 157
Period size: 30 Copynumber: 3.1 Consensus size: 30
4875 CTTTGGGCCT
*
4885 AATTCCAAATGACCCAAATTGCCTAAACAC
1 AATTCCAAATGACCCAAATTGCCTAAACCC
*
4915 AATTCCAAATGACCCAAATCGCCTAAACCC
1 AATTCCAAATGACCCAAATTGCCTAAACCC
*
4945 AATTCCAAATGACCCAAATTGCCGAAACCC
1 AATTCCAAATGACCCAAATTGCCTAAACCC
4975 AA
1 AA
4977 ACCCAAACCC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (30 bp):
AATTCCAAATGACCCAAATTGCCTAAACCC
Done.