Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010433.1 Kokia drynarioides strain JFW-HI SEQ_125323, 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, 753
Length: 1255
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.39
Found at i:214 original size:9 final size:9
Alignment explanation
Indices: 188--221 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
178 TTTTGTTTTT
*
188 TTATTATTA
1 TTATTAATA
197 TTCATTAATA
1 TT-ATTAATA
207 TTATTAATA
1 TTATTAATA
216 TTATTA
1 TTATTA
222 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (9 bp):
TTATTAATA
Found at i:241 original size:17 final size:17
Alignment explanation
Indices: 219--253 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
209 ATTAATATTA
219 TTATTAAAAATAAATAT
1 TTATTAAAAATAAATAT
**
236 TTATTATTAATAAATAT
1 TTATTAAAAATAAATAT
253 T
1 T
254 ATGAAACCGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATTAAAAATAAATAT
Found at i:297 original size:16 final size:16
Alignment explanation
Indices: 273--310 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
263 CCCACTTGTC
273 ATTAATGTCAT-TATTT
1 ATTAATGTCATCTA-TT
*
289 ATTACTGTCATCTATT
1 ATTAATGTCATCTATT
305 ATTAAT
1 ATTAAT
311 ATTATTCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 17 0.89
17 2 0.11
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (16 bp):
ATTAATGTCATCTATT
Found at i:1035 original size:6 final size:6
Alignment explanation
Indices: 1026--1103 Score: 58
Period size: 6 Copynumber: 13.7 Consensus size: 6
1016 TTTTAGCCTT
* * * *
1026 ATTTAA ATTTAT A-GTAA TTTTAA ATTTGAA A-ATAA ATTTAA A-TTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
* *
1072 A-TTAA ATTTAA ATTCAA A-ATAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
1104 TTAAACAAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
5 18 0.33
6 34 0.62
7 3 0.05
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:1074 original size:11 final size:11
Alignment explanation
Indices: 1045--1102 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
1035 TATAGTAATT
1045 TTAAATTTGAAA
1 TTAAATTT-AAA
*
1057 ATAAATTTAAA
1 TTAAATTTAAA
1068 TTAAA-TTAAA
1 TTAAATTTAAA
*
1078 TTTAAATTCAAA
1 -TTAAATTTAAA
*
1090 ATAAATTTAAA
1 TTAAATTTAAA
1101 TT
1 TT
1103 TTTAAACAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 5 0.13
11 22 0.58
12 11 0.29
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:1096 original size:17 final size:17
Alignment explanation
Indices: 1026--1136 Score: 116
Period size: 18 Copynumber: 6.4 Consensus size: 17
1016 TTTTAGCCTT
* *
1026 ATTTAAATTTATAGTAA
1 ATTTAAATTTAAAATAA
*
1043 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
*
1061 ATTTAAA-TTAAATTAA
1 ATTTAAATTTAAAATAA
*
1077 ATTTAAATTCAAAATAA
1 ATTTAAATTTAAAATAA
* *
1094 ATTTAAATTTTTAAACAA
1 ATTTAAA-TTTAAAATAA
*
1112 ATTTAATTTTTAAAATAA
1 ATTTAA-ATTTAAAATAA
1130 ATTTAAA
1 ATTTAAA
1137 GGGAGTTTGG
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
16 13 0.17
17 25 0.33
18 38 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Done.