Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008726.1 Kokia drynarioides strain JFW-HI SEQ_123408, 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: 16995
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Found at i:2273 original size:20 final size:17
Alignment explanation
Indices: 2240--2317 Score: 56
Period size: 18 Copynumber: 4.5 Consensus size: 17
2230 ATTAAAAAAT
2240 AATTTTATACTTTTTTCAATA
1 AATTTTA-A-TTTTTT-AA-A
2261 AATTTTAATTTTTTAAA
1 AATTTTAATTTTTTAAA
2278 ATATTTTAATTATTTT---
1 A-ATTTTAATT-TTTTAAA
* *
2294 TATTTTGATTTTTT-AA
1 AATTTTAATTTTTTAAA
2310 AATTTTAA
1 AATTTTAA
2318 AAAATTCAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
14 4 0.08
15 8 0.16
16 6 0.12
17 2 0.04
18 11 0.22
19 10 0.20
20 1 0.02
21 7 0.14
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (17 bp):
AATTTTAATTTTTTAAA
Found at i:14298 original size:69 final size:69
Alignment explanation
Indices: 14214--14353 Score: 253
Period size: 69 Copynumber: 2.0 Consensus size: 69
14204 TTGAGGTTTG
14214 TTTCTGAGGTCAGGAGTTTTCTAGAGTTAGTTGGTTATTACCATTGCTTTGTCAAGGGGTTTTCA
1 TTTCTGAGGTCAGGAGTTTTCTAGAGTTAGTTGGTTATTACCATTGCTTTGTCAAGGGGTTTTCA
14279 AGCA
66 AGCA
* **
14283 TTTCTGAGGTCAGGAGTTTTCTAGGGTTAGTTGGTTATTACCATTGCTTTGTTGAGGGGTTTTCA
1 TTTCTGAGGTCAGGAGTTTTCTAGAGTTAGTTGGTTATTACCATTGCTTTGTCAAGGGGTTTTCA
14348 AGCA
66 AGCA
14352 TT
1 TT
14354 ATTGCTCCTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.42
Consensus pattern (69 bp):
TTTCTGAGGTCAGGAGTTTTCTAGAGTTAGTTGGTTATTACCATTGCTTTGTCAAGGGGTTTTCA
AGCA
Done.