Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002229.1 Kokia drynarioides strain JFW-HI SEQ_114227, 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: 3057
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Found at i:683 original size:22 final size:21
Alignment explanation
Indices: 632--698 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
622 GAATTGAATT
*
632 TAAATAATAAAAAAATATTT-
1 TAAATAATTAAAAAATATTTA
*
652 TAATTTTAATTATAAAAATATTTA
1 TAA--ATAATTA-AAAAATATTTA
676 TAAATAATTAAAAATATACTTTA
1 TAAATAATTAAAAA-ATA-TTTA
699 ATGTTTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 3 0.08
21 4 0.11
22 14 0.37
23 14 0.37
24 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATAATTAAAAAATATTTA
Found at i:1247 original size:28 final size:27
Alignment explanation
Indices: 1209--1266 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
1199 TTTTATTATT
*
1209 TATAATATTTATTACATTTATA-ATTTTA
1 TATAATATTTATT--ATTTATATAATTTA
*
1237 TATAATTTTTATTATTTATATAATTTA
1 TATAATATTTATTATTTATATAATTTA
1264 TAT
1 TAT
1267 TTAAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 7 0.26
27 8 0.30
28 12 0.44
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (27 bp):
TATAATATTTATTATTTATATAATTTA
Found at i:1248 original size:11 final size:10
Alignment explanation
Indices: 1227--1266 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
1217 TTATTACATT
1227 TATAATTTTA
1 TATAATTTTA
1237 TATAATTTT-
1 TATAATTTTA
*
1246 TATTA-TTTA
1 TATAATTTTA
1255 TATAA-TTTA
1 TATAATTTTA
1264 TAT
1 TAT
1267 TTAAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 3 0.11
9 15 0.56
10 9 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATAATTTTA
Found at i:1252 original size:44 final size:43
Alignment explanation
Indices: 1181--1264 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 43
1171 ACATTACTCA
1181 ATTTACAATTTTAAATATTTTTATTATTTATA-ATATTTATTAC
1 ATTTACAATTTTAAATATTTTTATTATTTATATA-ATTTATTAC
* *
1224 ATTTATAATTTTATATAATTTTTATTATTTATATAATTTAT
1 ATTTACAATTTTAAAT-ATTTTTATTATTTATATAATTTAT
1265 ATTTAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
43 14 0.38
44 22 0.59
45 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (43 bp):
ATTTACAATTTTAAATATTTTTATTATTTATATAATTTATTAC
Found at i:1267 original size:18 final size:18
Alignment explanation
Indices: 1190--1265 Score: 86
Period size: 18 Copynumber: 4.3 Consensus size: 18
1180 AATTTACAAT
* *
1190 TTTA-AATATTTTTATTA
1 TTTATAATATTTATATAA
1207 TTTATAATATTTAT-TACA
1 TTTATAATATTTATATA-A
1225 TTTATAAT-TTTATATAA
1 TTTATAATATTTATATAA
* *
1242 TTTTTATTATTTATATAA
1 TTTATAATATTTATATAA
1260 TTTATA
1 TTTATA
1266 TTTAAATTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
17 17 0.34
18 33 0.66
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATAATATTTATATAA
Found at i:1929 original size:21 final size:22
Alignment explanation
Indices: 1882--1922 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1872 AATATGGTAC
* *
1882 AAATGTTTTAATTATGATTTGA
1 AAATTTTTTAATAATGATTTGA
1904 AAATTTTTTAATAAT-ATTT
1 AAATTTTTTAATAATGATTT
1923 ATAAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (22 bp):
AAATTTTTTAATAATGATTTGA
Done.