Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007412.1 Kokia drynarioides strain JFW-HI SEQ_122031, 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: 32405
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1128 original size:6 final size:6
Alignment explanation
Indices: 1117--1211 Score: 67
Period size: 6 Copynumber: 16.7 Consensus size: 6
1107 CACTTGTATT
* * *
1117 AATTTA AATTTA AATTT- AACTCA AATTTA TAA--TA AATTTA AATTTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
* * * * *
1163 AA-GTA AATTTA AACTTA AA-ATA AATTTA ATTTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
1208 AATT
1 AATT
1212 CTATGGGCCC
Statistics
Matches: 67, Mismatches: 15, Indels: 14
0.70 0.16 0.15
Matches are distributed among these distances:
4 2 0.03
5 16 0.24
6 47 0.70
7 2 0.03
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:1135 original size:17 final size:17
Alignment explanation
Indices: 1117--1211 Score: 109
Period size: 17 Copynumber: 5.6 Consensus size: 17
1107 CACTTGTATT
* *
1117 AATTTAAATTTAAATTT
1 AATTTAAATTTAAAATA
* * *
1134 AACTCAAATTTATAATA
1 AATTTAAATTTAAAATA
* *
1151 AATTTAAATTTTAAGTA
1 AATTTAAATTTAAAATA
*
1168 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
*
1185 AATTTAATTTTAAAATA
1 AATTTAAATTTAAAATA
1202 AATTTAAATT
1 AATTTAAATT
1212 CTATGGGCCC
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 62 1.00
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:3810 original size:3 final size:3
Alignment explanation
Indices: 3802--3830 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3792 AAACAGGACG
3802 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3831 TTTTGAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4119 original size:40 final size:39
Alignment explanation
Indices: 4074--4173 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 39
4064 GAAGTTAATT
*** *
4074 TTTTTATAATATTATTAATTAATTAAATTGGTTTTTTTTA
1 TTTTTATAATATTATTAATTAATTAAA-TCAATTTTTATA
* *
4114 TTTTTATAATATCATTAACTAATTAAATCAATTTTTATA
1 TTTTTATAATATTATTAATTAATTAAATCAATTTTTATA
**
4153 TTTTTATAACGTTATTAATTA
1 TTTTTATAATATTATTAATTA
4174 GTTCAAATAA
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 25 0.50
40 25 0.50
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (39 bp):
TTTTTATAATATTATTAATTAATTAAATCAATTTTTATA
Found at i:29022 original size:20 final size:21
Alignment explanation
Indices: 28986--29027 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
28976 TGCAATTGAA
* *
28986 TATTTATAAATATATTTTTAT
1 TATTTATAAAAATATTTCTAT
29007 TATTTA-AAAAATATTTCTAT
1 TATTTATAAAAATATTTCTAT
29027 T
1 T
29028 TCGTAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTATAAAAATATTTCTAT
Found at i:30279 original size:6 final size:6
Alignment explanation
Indices: 30268--30293 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30258 AAAGGGGACC
30268 TCGCCT TCGCCT TCGCCT TCGCCT TC
1 TCGCCT TCGCCT TCGCCT TCGCCT TC
30294 AGAGTGAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.15, T:0.35
Consensus pattern (6 bp):
TCGCCT
Done.