Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003314.1 Kokia drynarioides strain JFW-HI SEQ_116003, 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: 3563
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1400 original size:26 final size:26
Alignment explanation
Indices: 1330--1401 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 26
1320 ATATCTGATG
*
1330 CTGAAAAATAAAT-GACAAACTAATTA
1 CTGAAAAATAAATAG-CAAACTAAGTA
** **
1356 CTG-AAAGCAAATAATAAACTAAGTA
1 CTGAAAAATAAATAGCAAACTAAGTA
*
1381 CTGAAAAATAAATAGGAAACT
1 CTGAAAAATAAATAGCAAACT
1402 GTAAATGGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
25 19 0.54
26 16 0.46
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.21
Consensus pattern (26 bp):
CTGAAAAATAAATAGCAAACTAAGTA
Found at i:2708 original size:74 final size:74
Alignment explanation
Indices: 2577--2725 Score: 217
Period size: 74 Copynumber: 2.0 Consensus size: 74
2567 CTTTACAAAA
* * * *
2577 TGAAAGTGAACAGCCGTCATTCATCATTCATAAATGAATGTGTTGTTTCATAGAAAAACTCTTGA
1 TGAAAGTGAACAACCATCATTCATCAATCATAAATGAATGTGTTGATTCATAGAAAAACTCTTGA
2642 ATGAAACAT
66 ATGAAACAT
* **
2651 TGAATGTGAACAACCATCATTCATCAATCATAAATGAATGTGTTGATTCATTTAAAAACTCTTGA
1 TGAAAGTGAACAACCATCATTCATCAATCATAAATGAATGTGTTGATTCATAGAAAAACTCTTGA
* *
2716 GTGGAACAT
66 ATGAAACAT
2725 T
1 T
2726 TTATCCCTCC
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (74 bp):
TGAAAGTGAACAACCATCATTCATCAATCATAAATGAATGTGTTGATTCATAGAAAAACTCTTGA
ATGAAACAT
Done.