Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004184.1 Hibiscus syriacus cultivar Beakdansim tig00009151_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: 68250
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:12415 original size:21 final size:21
Alignment explanation
Indices: 12391--12451 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
12381 GCATCAAGGT
12391 TTTTGTTGAAGCCATGAAATC
1 TTTTGTTGAAGCCATGAAATC
12412 TTTT-TTCGAAGCCATGAAATC
1 TTTTGTT-GAAGCCATGAAATC
**
12433 TTTTGCCGAAGCCAT-AAAT
1 TTTTGTTGAAGCCATGAAAT
12452 TCCTAGAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
20 6 0.17
21 30 0.83
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (21 bp):
TTTTGTTGAAGCCATGAAATC
Found at i:12415 original size:22 final size:21
Alignment explanation
Indices: 12398--12451 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
12388 GGTTTTTGTT
12398 GAAGCCATGAAATCTTTTTTC
1 GAAGCCATGAAATCTTTTTTC
**
12419 GAAGCCATGAAATCTTTTGCC
1 GAAGCCATGAAATCTTTTTTC
12440 GAAGCCAT-AAAT
1 GAAGCCATGAAAT
12452 TCCTAGAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (21 bp):
GAAGCCATGAAATCTTTTTTC
Found at i:17243 original size:49 final size:49
Alignment explanation
Indices: 16997--17243 Score: 305
Period size: 49 Copynumber: 5.0 Consensus size: 49
16987 AATACCATGA
* * * *
16997 GTGGCACCTTTTATGCTGAAATACACTGTTATGCATTTAACTTTCATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTT
* * * *
17046 GTGACACATTTTGTTTGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
1 GTGGCAC-CTTT-TATGCCGAAATGCACCGTTATGCATTTAACTTTCATTT
* * ** * *
17097 GTGGCACATTTTATGTCGAAATGCACTATTATACAATTAACTTTCATTT
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTT
* *
17146 GTGGCACCTTTTATGCCGAAATGCACCATTATACATTTAACTTTCATTT
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTT
* * *
17195 GTGGTACCTTTTATGCCAAAATGCACCGGTATGCATTTAACTTTCATTT
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTT
17244 ATTCATTTTA
Statistics
Matches: 172, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
49 126 0.73
50 6 0.03
51 40 0.23
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (49 bp):
GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTT
Found at i:27222 original size:23 final size:24
Alignment explanation
Indices: 27194--27243 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
27184 ATCAGCAAAG
27194 AAATTG-AAGCACTCAAAAGAAGA
1 AAATTGTAAGCACTCAAAAGAAGA
* *
27217 AAATTGTAAGCACTTAAATGAAGA
1 AAATTGTAAGCACTCAAAAGAAGA
27241 AAA
1 AAA
27244 AAAAAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.56, C:0.10, G:0.16, T:0.18
Consensus pattern (24 bp):
AAATTGTAAGCACTCAAAAGAAGA
Found at i:33282 original size:8 final size:8
Alignment explanation
Indices: 33265--33333 Score: 72
Period size: 8 Copynumber: 8.8 Consensus size: 8
33255 CTATTTTTTT
33265 AAAAAA-A
1 AAAAAACA
33272 AAAAAACA
1 AAAAAACA
33280 AAAAAAC-
1 AAAAAACA
*
33287 AAAAAGCA
1 AAAAAACA
*
33295 AAAAAGGCA
1 AAAAA-ACA
33304 AAAAAA-A
1 AAAAAACA
*
33311 AAAAAGGCA
1 AAAAA-ACA
33320 AAAAAACA
1 AAAAAACA
33328 AAAAAA
1 AAAAAA
33334 GAGCCAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
7 18 0.34
8 21 0.40
9 14 0.26
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:33290 original size:16 final size:16
Alignment explanation
Indices: 33265--33333 Score: 72
Period size: 15 Copynumber: 4.4 Consensus size: 16
33255 CTATTTTTTT
33265 AAAAAA-AAAAAAACA
1 AAAAAACAAAAAAACA
*
33280 AAAAAAC-AAAAAGCA
1 AAAAAACAAAAAAACA
*
33295 AAAAAGGCAAAAAAA-A
1 AAAAA-ACAAAAAAACA
*
33311 AAAAAGGCAAAAAAACA
1 AAAAA-ACAAAAAAACA
33328 AAAAAA
1 AAAAAA
33334 GAGCCAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
15 18 0.39
16 17 0.37
17 11 0.24
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (16 bp):
AAAAAACAAAAAAACA
Found at i:33305 original size:24 final size:24
Alignment explanation
Indices: 33271--33333 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
33261 TTTTAAAAAA
*
33271 AAAAAAACAAAAAAACAAAAA-GC
1 AAAAAAACAAAAAAAAAAAAAGGC
*
33294 AAAAAAGGCAAAAAAAAAAAAAGGC
1 AAAAAA-ACAAAAAAAAAAAAAGGC
33319 AAAAAAACAAAAAAA
1 AAAAAAACAAAAAAA
33334 GAGCCAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 6 0.17
24 21 0.60
25 8 0.23
ACGTcount: A:0.83, C:0.10, G:0.08, T:0.00
Consensus pattern (24 bp):
AAAAAAACAAAAAAAAAAAAAGGC
Found at i:33330 original size:20 final size:19
Alignment explanation
Indices: 33303--33344 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
33293 CAAAAAAGGC
*
33303 AAAAAAAAAAAAAGGCAAA
1 AAAAAAAAAAAAAGCCAAA
*
33322 AAAACAAAAAAAGAGCCAAA
1 AAAA-AAAAAAAAAGCCAAA
33342 AAA
1 AAA
33345 GCCAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.81, C:0.10, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAGCCAAA
Found at i:41542 original size:11 final size:13
Alignment explanation
Indices: 41510--41539 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
41500 TGTCCAAATA
41510 TGAAAAGGTATGT
1 TGAAAAGGTATGT
41523 TGAAAAGGTATG-
1 TGAAAAGGTATGT
41535 TGAAA
1 TGAAA
41540 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:56178 original size:19 final size:19
Alignment explanation
Indices: 56152--56201 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
56142 GAAACCCCTT
*
56152 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTTAA
*
56171 TTAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
56190 TGAATATACATG
1 TGAAAATACATG
56202 CTCTTGTCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:60108 original size:20 final size:19
Alignment explanation
Indices: 60073--60121 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
60063 GAAACCCCTT
60073 TGAAAATAC-TTGATTTTTAA
1 TGAAAATACATTGA--TTTAA
60093 TGAAAATACATT-ATTTAA
1 TGAAAATACATTGATTTAA
*
60111 TGAAGATACAT
1 TGAAAATACAT
60122 GCTCTTGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 15 0.56
20 10 0.37
21 2 0.07
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (19 bp):
TGAAAATACATTGATTTAA
Found at i:61453 original size:17 final size:18
Alignment explanation
Indices: 61418--61453 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
61408 TTAGATATTG
*
61418 TAAATTATTTTTTGTATA
1 TAAATTATTTTATGTATA
61436 TAAATTATTTTATG-ATA
1 TAAATTATTTTATGTATA
61453 T
1 T
61454 TGTGTGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (18 bp):
TAAATTATTTTATGTATA
Done.