Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011074.1 Kokia drynarioides strain JFW-HI SEQ_126047, 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: 36861
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:222 original size:15 final size:14
Alignment explanation
Indices: 188--226 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
178 TATTTATTAA
188 TTAATAATAATATT
1 TTAATAATAATATT
202 TT--TAATAATATT
1 TTAATAATAATATT
214 TTAAATAATAATA
1 TT-AATAATAATA
227 AATCTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.55
14 2 0.09
15 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAATAATAATATT
Found at i:590 original size:25 final size:25
Alignment explanation
Indices: 556--604 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
546 GATTTGAATT
*
556 TGTTCTTATACCTCGTTTTACAATC
1 TGTTCTTATACCCCGTTTTACAATC
581 TGTTCTTATACCCCGTTTTACAAT
1 TGTTCTTATACCCCGTTTTACAAT
605 GATGGTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.47
Consensus pattern (25 bp):
TGTTCTTATACCCCGTTTTACAATC
Found at i:942 original size:17 final size:16
Alignment explanation
Indices: 922--994 Score: 74
Period size: 17 Copynumber: 4.3 Consensus size: 16
912 AAACTTTAAT
922 TTTAAATTTATAATAAA
1 TTTAAATTTA-AATAAA
**
939 TTTAAATTTCAACCAAA
1 TTTAAATTT-AAATAAA
956 TTTAAATTTAGAATAAA
1 TTTAAATTTA-AATAAA
* *
973 CTTAATTTTAAAATAAA
1 TTTAAATTT-AAATAAA
990 TTTAA
1 TTTAA
995 GCTGATTGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
16 1 0.02
17 43 0.93
18 2 0.04
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:991 original size:34 final size:34
Alignment explanation
Indices: 922--994 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
912 AAACTTTAAT
* * * *
922 TTTAAATTTATAATAAATTTAAATTTCAACCAAA
1 TTTAAATTTAGAATAAACTTAAATTTAAAACAAA
* *
956 TTTAAATTTAGAATAAACTTAATTTTAAAATAAA
1 TTTAAATTTAGAATAAACTTAAATTTAAAACAAA
990 TTTAA
1 TTTAA
995 GCTGATTGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (34 bp):
TTTAAATTTAGAATAAACTTAAATTTAAAACAAA
Found at i:2097 original size:29 final size:29
Alignment explanation
Indices: 2064--2136 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
2054 ATGGAAACTA
2064 ATTATCAACGGCTGATCTTATCACAAACC
1 ATTATCAACGGCTGATCTTATCACAAACC
** *
2093 ATTATCATGGGCTGATCTTATCTCAAACC
1 ATTATCAACGGCTGATCTTATCACAAACC
2122 ATTATCAACGGCTGA
1 ATTATCAACGGCTGA
2137 GAATATTTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (29 bp):
ATTATCAACGGCTGATCTTATCACAAACC
Found at i:15669 original size:29 final size:29
Alignment explanation
Indices: 15620--15675 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
15610 AATTTACTGT
* **
15620 TATGGACAGAAATAACCTTAAATTTTTGC
1 TATGAACAGAAATAAAATTAAATTTTTGC
*
15649 TATGAACAGAAATAAAATTAATTTTTT
1 TATGAACAGAAATAAAATTAAATTTTT
15676 TTGGATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (29 bp):
TATGAACAGAAATAAAATTAAATTTTTGC
Found at i:32024 original size:17 final size:19
Alignment explanation
Indices: 32004--32038 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
31994 TTCGGTAGAA
32004 AAGGAA-TTTGA-TTGGTT
1 AAGGAAGTTTGACTTGGTT
32021 AAGGAAGTTTGACTTGGT
1 AAGGAAGTTTGACTTGGT
32039 CAAACGGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.29, C:0.03, G:0.31, T:0.37
Consensus pattern (19 bp):
AAGGAAGTTTGACTTGGTT
Found at i:33469 original size:29 final size:30
Alignment explanation
Indices: 33412--33469 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
33402 AACTTAATCA
*
33412 AATCAAAATTTTATATATAGAATCGCACAT
1 AATCAAAATTTTATATATAGAATCACACAT
* *
33442 AATCAAAA-TTTATATATAGCATTACACA
1 AATCAAAATTTTATATATAGAATCACACA
33470 CGTATCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (30 bp):
AATCAAAATTTTATATATAGAATCACACAT
Done.