Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009047.1 Hibiscus syriacus cultivar Beakdansim tig00112458_pilon, 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: 186478
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:185228 original size:27 final size:28
Alignment explanation
Indices: 185146--185229 Score: 68
Period size: 27 Copynumber: 3.0 Consensus size: 28
185136 AAAGGGAGAT
*
185146 GAAAGATAGAAATA-AAAGAAAAATAAAAAA
1 GAAAG-TA-AAATAGAAA-AAAAATAATAAA
* *
185176 GAAAGTAAAA-ATGAATAAATAA-AATAGA
1 GAAAGTAAAATA-GAA-AAAAAATAATAAA
185204 -AAAGTAAAATAGAAAAAAAATAATAA
1 GAAAGTAAAATAGAAAAAAAATAATAA
185230 TAATAATAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
26 5 0.11
27 17 0.39
28 8 0.18
29 8 0.18
30 6 0.14
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (28 bp):
GAAAGTAAAATAGAAAAAAAATAATAAA
Found at i:185247 original size:12 final size:11
Alignment explanation
Indices: 185151--185244 Score: 64
Period size: 11 Copynumber: 7.9 Consensus size: 11
185141 GAGATGAAAG
185151 ATAGAAATAAA
1 ATAGAAATAAA
* *
185162 AGAAAAATAAA
1 ATAGAAATAAA
*
185173 AAAGAAAGTAAAA
1 ATAGAAA-T-AAA
*
185186 ATGAATAAATAAA
1 AT--AGAAATAAA
185199 ATAGAAAAGTAAA
1 ATAG-AAA-TAAA
*
185212 ATAGAAAAAAA
1 ATAGAAATAAA
185223 ATA-ATAATAATA
1 ATAGA-AATAA-A
185235 ATAGAAATAA
1 ATAGAAATAA
185245 TAAAATAGTA
Statistics
Matches: 65, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
10 1 0.02
11 25 0.38
12 16 0.25
13 18 0.28
14 1 0.02
15 4 0.06
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (11 bp):
ATAGAAATAAA
Found at i:185250 original size:37 final size:38
Alignment explanation
Indices: 185156--185257 Score: 120
Period size: 37 Copynumber: 2.7 Consensus size: 38
185146 GAAAGATAGA
* *
185156 AATAAAAGAAAAATAAAAAAGAAAGTAAAAATGAATAAAT
1 AATAATAGAAAAATAAAATAGAAA--AAAAATGAATAAAT
*
185196 AA-AATAGAAAAGTAAAATAGAAAAAAAAT-AAT-AAT
1 AATAATAGAAAAATAAAATAGAAAAAAAATGAATAAAT
*
185231 AATAATAGAAATAATAAAATAGTAAAA
1 AATAATAGAAA-AATAAAATAGAAAAA
185258 GAGTATAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
35 5 0.09
36 11 0.20
37 19 0.35
39 18 0.33
40 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (38 bp):
AATAATAGAAAAATAAAATAGAAAAAAAATGAATAAAT
Found at i:185369 original size:12 final size:12
Alignment explanation
Indices: 185306--185391 Score: 54
Period size: 12 Copynumber: 7.0 Consensus size: 12
185296 TACATATATG
185306 AAATA-AAAAAT
1 AAATATAAAAAT
185317 -AATATTAAAAAT
1 AAATA-TAAAAAT
*
185329 -AATACTAATAAT
1 AAATA-TAAAAAT
*
185341 AGTTATAGTAAAAAT
1 A--AATA-TAAAAAT
*
185356 AAATATAAATAT
1 AAATATAAAAAT
*
185368 AAATAT-AAAAC
1 AAATATAAAAAT
185379 AAATAGTAAAAAT
1 AAATA-TAAAAAT
185392 GACCATGACG
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
10 4 0.07
11 8 0.14
12 29 0.50
13 7 0.12
15 10 0.17
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.28
Consensus pattern (12 bp):
AAATATAAAAAT
Found at i:185370 original size:18 final size:18
Alignment explanation
Indices: 185345--185391 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
185335 AATAATAGTT
*
185345 ATAGTAAAAATAAATATAA
1 ATAGTAAAAATAAA-ACAA
*
185364 ATA-TAAATATAAAACAA
1 ATAGTAAAAATAAAACAA
185381 ATAGTAAAAAT
1 ATAGTAAAAAT
185392 GACCATGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 6 0.25
18 15 0.62
19 3 0.12
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (18 bp):
ATAGTAAAAATAAAACAA
Done.