Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009852.1 Kokia drynarioides strain JFW-HI SEQ_124581, 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: 33631
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:241 original size:21 final size:23
Alignment explanation
Indices: 206--247 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
196 AAAAAGAATG
206 GATCTAGCTCTAGA-TCAAACCA
1 GATCTAGCTCTAGATTCAAACCA
228 GATCTAGC-CTAGATTCAAAC
1 GATCTAGCTCTAGATTCAAAC
248 AGTTTTCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (23 bp):
GATCTAGCTCTAGATTCAAACCA
Found at i:495 original size:17 final size:16
Alignment explanation
Indices: 473--514 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
463 TAATATTATT
473 AATATTATTATTAAAAA
1 AATATTATTATT-AAAA
*
490 AATATTTATTATTAATA
1 AATA-TTATTATTAAAA
507 AATATTAT
1 AATATTAT
515 GAAAACCGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 8 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATTATTATTAAAA
Found at i:608 original size:16 final size:15
Alignment explanation
Indices: 561--609 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
551 TACTGTCATC
*
561 TATTATTAACATTAT
1 TATTATTAATATTAT
* *
576 TCTTATTAACTAATAT
1 TATTATTAA-TATTAT
592 TATTATTAATATTTAT
1 TATTATTAATA-TTAT
608 TA
1 TA
610 CTGCAATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTATTAATATTAT
Found at i:1292 original size:6 final size:6
Alignment explanation
Indices: 1283--1379 Score: 69
Period size: 6 Copynumber: 16.7 Consensus size: 6
1273 TTTTAGCTTT
* * * *
1283 ATTTAA ATTTAT A-GTAA TTTTAA ATTTGAA A-ATAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
* * * *
1330 A-TTAA ATTTAAA ATTCAA A-ATAA ATTTAA ATTGAA A-ATAA ATTTAA
1 ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
1376 ATTT
1 ATTT
1380 TTAAACAAAT
Statistics
Matches: 68, Mismatches: 16, Indels: 14
0.69 0.16 0.14
Matches are distributed among these distances:
5 16 0.24
6 44 0.65
7 8 0.12
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:1322 original size:35 final size:35
Alignment explanation
Indices: 1283--1412 Score: 152
Period size: 35 Copynumber: 3.7 Consensus size: 35
1273 TTTTAGCTTT
* * * *
1283 ATTTAAATTTATAGTAATTTTAAATTTGAAAATAA
1 ATTTAAATTTAAAATAAATTTAAATTTCAAAATAA
* *
1318 ATTTAAATTTAAATTAAATTTAAAATTCAAAATAA
1 ATTTAAATTTAAAATAAATTTAAATTTCAAAATAA
* ** *
1353 ATTTAAATTGAAAATAAATTTAAATTTTTAAACAA
1 ATTTAAATTTAAAATAAATTTAAATTTCAAAATAA
*
1388 ATTTAATTTTTAAAATAAATTTAAA
1 ATTTAA-ATTTAAAATAAATTTAAA
1413 GGGAGTTTGG
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
35 65 0.80
36 16 0.20
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (35 bp):
ATTTAAATTTAAAATAAATTTAAATTTCAAAATAA
Found at i:1337 original size:17 final size:17
Alignment explanation
Indices: 1283--1412 Score: 143
Period size: 18 Copynumber: 7.4 Consensus size: 17
1273 TTTTAGCTTT
* *
1283 ATTTAAATTTATAGTAA
1 ATTTAAATTTAAAATAA
*
1300 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
*
1318 ATTTAAATTTAAATTAA
1 ATTTAAATTTAAAATAA
*
1335 ATTTAAAATTCAAAATAA
1 ATTT-AAATTTAAAATAA
*
1353 ATTTAAATTGAAAATAA
1 ATTTAAATTTAAAATAA
* *
1370 ATTTAAATTTTTAAACAA
1 ATTTAAA-TTTAAAATAA
*
1388 ATTTAATTTTTAAAATAA
1 ATTTAA-ATTTAAAATAA
1406 ATTTAAA
1 ATTTAAA
1413 GGGAGTTTGG
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
17 38 0.40
18 56 0.60
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:2197 original size:2 final size:2
Alignment explanation
Indices: 2190--2215 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2180 TGTTTTGTAC
2190 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2216 ACTATGCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13008 original size:81 final size:83
Alignment explanation
Indices: 12920--13072 Score: 240
Period size: 86 Copynumber: 1.8 Consensus size: 83
12910 TCACCAAAAA
* *
12920 AAATCTAAATATT-AA-AAA-TAAAATATAAACATATAATATACAAGTTATTATTACAAACAAAC
1 AAATCTAAATATTAAATAAATTAAAATATAAAAATATAATATACAAATTATTATTACAAACAAA-
12982 AAAAAAAGTCTTAAATATT
65 AAAAAAAGTCTTAAATATT
13001 AAATCTAAATATTAACAATAAATTAAAATATAAAAATATAATATACAAATTATTATTACAAACAA
1 AAATCTAAATATT-A-AATAAATTAAAATATAAAAATATAATATACAAATTATTATTACAAACAA
13066 AAAAAAA
64 AAAAAAA
13073 TACCTTAAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
81 13 0.20
84 2 0.03
85 9 0.14
86 41 0.63
ACGTcount: A:0.62, C:0.08, G:0.01, T:0.29
Consensus pattern (83 bp):
AAATCTAAATATTAAATAAATTAAAATATAAAAATATAATATACAAATTATTATTACAAACAAAA
AAAAAAGTCTTAAATATT
Found at i:30276 original size:2 final size:2
Alignment explanation
Indices: 30269--30300 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30259 GTTCATAACC
30269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30301 TCATAAGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.