Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002186.1 Kokia drynarioides strain JFW-HI SEQ_114156, 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: 14475
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Found at i:1560 original size:30 final size:30
Alignment explanation
Indices: 1481--1561 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
1471 AATATTAAAT
* *
1481 TTATACATAAACTTTGATTTAATGTGCAATG
1 TTATACATGAACTTTGATTT-ATGTCCAATG
*
1512 TTATACATGAACTTTGATTT-TGTCCAATT
1 TTATACATGAACTTTGATTTATGTCCAATG
* *
1541 TTATATATGGAATTTTGATTT
1 TTATACAT-GAACTTTGATTT
1562 GATTTAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 14 0.32
30 11 0.25
31 19 0.43
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (30 bp):
TTATACATGAACTTTGATTTATGTCCAATG
Found at i:3235 original size:26 final size:26
Alignment explanation
Indices: 3206--3259 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3196 CAATTAAGTC
3206 CCTGATGATATGAATATTGTTAAAAT
1 CCTGATGATATGAATATTGTTAAAAT
3232 CCTGATGATATGAATATTGTTAAAAT
1 CCTGATGATATGAATATTGTTAAAAT
3258 CC
1 CC
3260 ATACTTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (26 bp):
CCTGATGATATGAATATTGTTAAAAT
Found at i:5815 original size:29 final size:29
Alignment explanation
Indices: 5758--5815 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5748 TATGGTTTGA
*
5758 TGTGCAATTATATACATGAACTTTGATTT
1 TGTGCAATTATATACATGAACTTTAATTT
* *
5787 TGTGCAATTTTAT-CATGAAATTTTAATTT
1 TGTGCAATTATATACATG-AACTTTAATTT
5816 GATCCAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (29 bp):
TGTGCAATTATATACATGAACTTTAATTT
Found at i:5816 original size:28 final size:29
Alignment explanation
Indices: 5758--5816 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
5748 TATGGTTTGA
* *
5758 TGTGCAATTATATACATGAACTTTGATTT
1 TGTGCAATTATATACATGAAATTTGAATT
* *
5787 TGTGCAATTTTAT-CATGAAATTTTAATT
1 TGTGCAATTATATACATGAAATTTGAATT
5815 TG
1 TG
5817 ATCCAATTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (29 bp):
TGTGCAATTATATACATGAAATTTGAATT
Found at i:8277 original size:15 final size:16
Alignment explanation
Indices: 8245--8277 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
8235 TATTTTCAAA
8245 TTTATCATTTTAATTT
1 TTTATCATTTTAATTT
*
8261 TTTATTATTTT-ATTT
1 TTTATCATTTTAATTT
8276 TT
1 TT
8278 AAAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATCATTTTAATTT
Found at i:8495 original size:5 final size:5
Alignment explanation
Indices: 8485--8518 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
8475 ACGCAAAGTT
8485 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
8519 TAATTTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Done.