Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011344.1 Kokia drynarioides strain JFW-HI SEQ_126324, 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: 4916
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:1029 original size:29 final size:30
Alignment explanation
Indices: 966--1038 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
956 TAAACATTCC
* * *
966 AAAATTTATATTTTTACACCTAGACTTTTT
1 AAAAATTATATTTTGACACCTAGAATTTTT
*
996 AAAAATTATATTTTGACACTTA-AATTTTCT
1 AAAAATTATATTTTGACACCTAGAATTTT-T
1026 AAAAATTA-ATTTT
1 AAAAATTATATTTT
1039 AGACCCCCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 10 0.26
30 28 0.74
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.48
Consensus pattern (30 bp):
AAAAATTATATTTTGACACCTAGAATTTTT
Found at i:2237 original size:70 final size:70
Alignment explanation
Indices: 2149--2295 Score: 251
Period size: 70 Copynumber: 2.1 Consensus size: 70
2139 GATTGGTGGT
* * *
2149 GACTCCCATTTTCCAATTTTTAGATAATT-TTCGAAACTAACGTACAAAAAAATGGTTTCAATAG
1 GACTCCAATTTTCCAATTTTTAAATAATTCTT-GAAACTAACGTACAAAAAAATGGTTTCAACAG
2213 CTTGGC
65 CTTGGC
2219 GACTCCAATTTTCCAATTTTTAAATAATTCTTGAAACTAACGTACAAAAAAATGGTTTCAACAGC
1 GACTCCAATTTTCCAATTTTTAAATAATTCTTGAAACTAACGTACAAAAAAATGGTTTCAACAGC
2284 TTGGC
66 TTGGC
2289 GACTCCA
1 GACTCCA
2296 CTGGGGACCA
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
70 71 0.97
71 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (70 bp):
GACTCCAATTTTCCAATTTTTAAATAATTCTTGAAACTAACGTACAAAAAAATGGTTTCAACAGC
TTGGC
Done.