Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002585.1 Kokia drynarioides strain JFW-HI SEQ_114790, 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: 1789
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Found at i:1165 original size:29 final size:29
Alignment explanation
Indices: 1132--1403 Score: 171
Period size: 30 Copynumber: 9.3 Consensus size: 29
1122 GTCCCTAAAT
*
1132 CTTCCAAAAATTACTATTTTACCCCCGAA
1 CTTCCAAAAATTACCATTTTACCCCCGAA
* * ** *
1161 CTTCCAAAAA-TCCCATTTTTGATCATCAAA
1 CTTCCAAAAATTACCA-TTTT-ACCCCCGAA
* * *
1191 CTCCCAAAAA-TCCCATTTTTGA-TCCCGAA
1 CTTCCAAAAATTACCA-TTTT-ACCCCCGAA
* **
1220 CCTTCCAAAAATTACTATTTTACCCCTAAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
* *
1250 CTTCCAAAAA-TCCCATTTTTAACCCCGAA
1 CTTCCAAAAATTACCA-TTTTACCCCCGAA
** *
1279 CCTTCTTAAAATTACCATTTTACCCCCAAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
* * **
1309 CTTCCAACAA-TCCCATTTTTTA-CCTTGAA
1 CTTCCAAAAATTACCA--TTTTACCCCCGAA
* * *
1338 CCTTCCAAAAATTACTATTTT-TCCTCGAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
* *
1367 TTTCCAAAAATTACCATTTTACCCTCGAA
1 CTTCCAAAAATTACCATTTTACCCCCGAA
1396 CTTCCAAA
1 CTTCCAAA
1404 GATCCTATTT
Statistics
Matches: 187, Mismatches: 42, Indels: 28
0.73 0.16 0.11
Matches are distributed among these distances:
28 28 0.15
29 73 0.39
30 76 0.41
31 10 0.05
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (29 bp):
CTTCCAAAAATTACCATTTTACCCCCGAA
Found at i:1228 original size:30 final size:29
Alignment explanation
Indices: 1148--1434 Score: 167
Period size: 30 Copynumber: 9.8 Consensus size: 29
1138 AAAATTACTA
1148 TTTTACCCCCGAA-CTTCCAAAAATCCCAT
1 TTTTA-CCCCGAACCTTCCAAAAATCCCAT
** * *
1177 TTTTGATCATC-AAACTCCCAAAAATCCCAT
1 TTTT-A-CCCCGAACCTTCCAAAAATCCCAT
* **
1207 TTTTGATCCCGAACCTTCCAAAAATTAC-T
1 TTTT-ACCCCGAACCTTCCAAAAATCCCAT
* *
1236 ATTTTACCCCTAAACTTCCAAAAATCCCAT
1 -TTTTACCCCGAACCTTCCAAAAATCCCAT
* * *
1266 TTTTAACCCCGAACCTTCTTAAAATTACCA-
1 TTTT-ACCCCGAACCTTC-CAAAAATCCCAT
* * *
1296 TTTTACCCCCAAACTTCCAACAATCCCATT
1 TTTTACCCCGAACCTTCCAAAAATCCCA-T
** * *
1326 TTTTACCTTGAACCTTCCAAAAATTACTAT
1 TTTTACCCCGAACCTTCCAAAAA-TCCCAT
* * *
1356 TTTT-CCTCGAA-TTTCCAAAAATTACCA-
1 TTTTACCCCGAACCTTCCAAAAA-TCCCAT
* *
1383 TTTTACCCTCGAA-CTTCCAAAGATCCTAT
1 TTTTACCC-CGAACCTTCCAAAAATCCCAT
** *
1412 TTTTGATTCCGAACATTCCAAAA
1 TTTT-ACCCCGAACCTTCCAAAA
1435 CTATCATTCT
Statistics
Matches: 197, Mismatches: 46, Indels: 29
0.72 0.17 0.11
Matches are distributed among these distances:
27 4 0.02
28 26 0.13
29 67 0.34
30 89 0.45
31 11 0.06
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
TTTTACCCCGAACCTTCCAAAAATCCCAT
Found at i:1384 original size:59 final size:58
Alignment explanation
Indices: 1187--1403 Score: 242
Period size: 59 Copynumber: 3.7 Consensus size: 58
1177 TTTTGATCAT
* * *
1187 CAAACTCCCAAAAATCCCATTTTTGATCCCGAACCTTCCAAAAATTACTATTTTACCC
1 CAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACTATTTTACCC
** *
1245 CTAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCTTAAAATTACCATTTTACCCC
1 C-AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACTATTTTA-CCC
* * ** * *
1305 CAAACTTCCAACAATCCCATTTTTTACCTTGAACCTTCCAAAAATTACTATTTTTCCT
1 CAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACTATTTTACCC
* * *
1363 CGAATTTCCAAAAATTACCA-TTTT-ACCCTCGAA-CTTCCAAA
1 CAAACTTCCAAAAA-TCCCATTTTTAACCC-CGAACCTTCCAAA
1404 GATCCTATTT
Statistics
Matches: 134, Mismatches: 21, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
57 11 0.08
58 21 0.16
59 98 0.73
60 4 0.03
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (58 bp):
CAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACTATTTTACCC
Done.