Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007343.1 Hibiscus syriacus cultivar Beakdansim tig00019675_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: 43998
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:8577 original size:2 final size:2
Alignment explanation
Indices: 8570--8603 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
8560 AATATAAATG
8570 TA TA TA TA 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 TA TA TA TA
8604 ATTCAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9460 original size:18 final size:20
Alignment explanation
Indices: 9437--9479 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
9427 CTTGATTTCC
*
9437 ATTCAATTTCATT-CAT-AA
1 ATTCAACTTCATTACATCAA
*
9455 ATTCAACTTCTTTACATCAA
1 ATTCAACTTCATTACATCAA
9475 ATTCA
1 ATTCA
9480 TGTTCTTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.52
19 3 0.14
20 7 0.33
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTCAACTTCATTACATCAA
Found at i:11509 original size:25 final size:25
Alignment explanation
Indices: 11481--11529 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
11471 TAATTAAATC
* *
11481 ATTAATAATTATGTTAAGAGATTGT
1 ATTAATAATCATATTAAGAGATTGT
*
11506 ATTAATAGTCATATTAAGAGATTG
1 ATTAATAATCATATTAAGAGATTG
11530 GATTTCGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (25 bp):
ATTAATAATCATATTAAGAGATTGT
Found at i:11652 original size:28 final size:26
Alignment explanation
Indices: 11617--11670 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
11607 ATATATGATT
*
11617 TAATTAATTAATTTAAATTAAGATTTAA
1 TAATTAA-TAATTTAAATCAA-ATTTAA
*
11645 TAATTAATAATTTTAATCAAATTTAA
1 TAATTAATAATTTAAATCAAATTTAA
11671 GTGAACAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.25
27 11 0.46
28 7 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
TAATTAATAATTTAAATCAAATTTAA
Found at i:14790 original size:51 final size:52
Alignment explanation
Indices: 14728--14829 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 52
14718 ATTTCAATTT
14728 AATCATAATTTAAATTTAATTTAATAATTTTTTATTTAATCGGGTGGTGACC
1 AATCATAATTTAAATTTAATTTAATAATTTTTTATTTAATCGGGTGGTGACC
14780 AATCA-AATTTAAATTTAATTTAATAATTTTTTATTTAATCGGGTGGTGAC
1 AATCATAATTTAAATTTAATTTAATAATTTTTTATTTAATCGGGTGGTGAC
14830 ACGATTGGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 45 0.90
52 5 0.10
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (52 bp):
AATCATAATTTAAATTTAATTTAATAATTTTTTATTTAATCGGGTGGTGACC
Found at i:35995 original size:18 final size:17
Alignment explanation
Indices: 35972--36005 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35962 CAACACGTAT
35972 GCACGCATATGCATAAAA
1 GCACGCAT-TGCATAAAA
*
35990 GCACGCCTTGCATAAA
1 GCACGCATTGCATAAA
36006 GTGAGTCAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (17 bp):
GCACGCATTGCATAAAA
Found at i:36236 original size:181 final size:182
Alignment explanation
Indices: 35932--36275 Score: 618
Period size: 181 Copynumber: 1.9 Consensus size: 182
35922 AATCCTCCGC
* *
35932 ATAAAAGCACACATAGTTTTAGGCTTTATCCAACACGTATGCACGCATATGCATAAAAGCACGCC
1 ATAAAAGCACACATAGTTTTAGGCTTTATCCAACACGCATGCACACATATGCATAAAAGCACGCC
35997 TTGCATAAAGTGAGTCAGGATAGAGTGACTTGGATAGAACATACCACCATTGAGTTTCGGAAAG-
66 TTGCATAAAGTGAGTCAGGATAGAGTGACTTGGATAGAACATACCACCATTGAGTTTCGGAAAGT
*
36061 TTGACTTTTGGTTTTGGATTGTAAAAGAGATGTATGTTGTTGCTGTTGTTAA
131 TTGACTTTTGGCTTTGGATTGTAAAAGAGATGTATGTTGTTGCTGTTGTTAA
* *
36113 ATAAAAGCACACATAGTTTTAGGCTTTATCCAACACGCATGCACACTTATGCATAAAAGCACTCC
1 ATAAAAGCACACATAGTTTTAGGCTTTATCCAACACGCATGCACACATATGCATAAAAGCACGCC
*
36178 TTGCATAAAGTGAGTCAGGATCGAGTGACTTGGATAGAACATACCACCATTGAGTTTCGGAAAGT
66 TTGCATAAAGTGAGTCAGGATAGAGTGACTTGGATAGAACATACCACCATTGAGTTTCGGAAAG-
36243 TTTGACTTTTGGCTTTGGATTGTAAAAGAGATG
130 TTTGACTTTTGGCTTTGGATTGTAAAAGAGATG
36276 CTGATGATAT
Statistics
Matches: 155, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
181 124 0.80
183 31 0.20
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (182 bp):
ATAAAAGCACACATAGTTTTAGGCTTTATCCAACACGCATGCACACATATGCATAAAAGCACGCC
TTGCATAAAGTGAGTCAGGATAGAGTGACTTGGATAGAACATACCACCATTGAGTTTCGGAAAGT
TTGACTTTTGGCTTTGGATTGTAAAAGAGATGTATGTTGTTGCTGTTGTTAA
Found at i:37317 original size:28 final size:28
Alignment explanation
Indices: 37277--37334 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
37267 CTCAACCAGA
37277 ATGTTTCATTTTTCCTTTTGTTCTGCAT
1 ATGTTTCATTTTTCCTTTTGTTCTGCAT
*
37305 ATGTTTCTTTTTTCCTTTTGTTCTGCAT
1 ATGTTTCATTTTTCCTTTTGTTCTGCAT
37333 AT
1 AT
37335 CTGCTTCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.10, C:0.17, G:0.10, T:0.62
Consensus pattern (28 bp):
ATGTTTCATTTTTCCTTTTGTTCTGCAT
Done.