Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001359.1 Hibiscus syriacus cultivar Beakdansim tig00002649_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: 183523
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:162439 original size:13 final size:13
Alignment explanation
Indices: 162423--162461 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
162413 CTTTGATTTA
162423 TTTATTATGTTTT
1 TTTATTATGTTTT
*
162436 TTTATTATGTTTA
1 TTTATTATGTTTT
* *
162449 TTTGTTTTGTTTT
1 TTTATTATGTTTT
162462 GTTTCATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (13 bp):
TTTATTATGTTTT
Found at i:162448 original size:26 final size:26
Alignment explanation
Indices: 162406--162470 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
162396 TAACTATTCA
*
162406 TTTTTTTCTTTGATTTATTTATTATG
1 TTTTTTTATTTGATTTATTTATTATG
* *
162432 TTTTTTTATTATG-TTTATTTGTTTTG
1 TTTTTTTATT-TGATTTATTTATTATG
162458 TTTTGTTTCATTT
1 TTTT-TTT-ATTT
162471 TTTTCTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 24 0.73
27 6 0.18
28 3 0.09
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.75
Consensus pattern (26 bp):
TTTTTTTATTTGATTTATTTATTATG
Found at i:162690 original size:13 final size:13
Alignment explanation
Indices: 162672--162701 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
162662 CGAATCGGGT
162672 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
162685 TTTTAATTTTTAA
1 TTTTAAATTTTAA
162698 TTTT
1 TTTT
162702 TTGTGATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:163600 original size:24 final size:24
Alignment explanation
Indices: 163562--163614 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
163552 AGGATCATGC
163562 CACAAGAGCAAAGAAAATATG-AGT
1 CACAAGAGCAAAGAAAA-ATGAAGT
* *
163586 CACAAGAGTAGAGAAAAATGAAGT
1 CACAAGAGCAAAGAAAAATGAAGT
163610 CACAA
1 CACAA
163615 TGACAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.55, C:0.13, G:0.21, T:0.11
Consensus pattern (24 bp):
CACAAGAGCAAAGAAAAATGAAGT
Found at i:163723 original size:86 final size:86
Alignment explanation
Indices: 163607--163785 Score: 288
Period size: 86 Copynumber: 2.1 Consensus size: 86
163597 AGAAAAATGA
*
163607 AGTCACAATGACAGAAAATCTAATTTAAAATTAAAAAGATTCAAACAAAAAATATAAAAGATATA
1 AGTCACAATGACAG-AAATCTAATTTAAAATTAAAAAGACTCAAACAAAAAATATAAAAGATATA
163672 ACATAAAAAACAATAGAATTAAT
65 ACAT-AAAAACAATAGAATTAAT
* * *
163695 AGTCATAATGACAG-AATCTAATTTAAAATTAAAAATACTCAAGCAAAAAATATAAAAGATATAA
1 AGTCACAATGACAGAAATCTAATTTAAAATTAAAAAGACTCAAACAAAAAATATAAAAGATATAA
*
163759 CATAAAAATAATAGAATTAAT
66 CATAAAAACAATAGAATTAAT
163780 AGTCAC
1 AGTCAC
163786 CGACAGTTAG
Statistics
Matches: 85, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
85 22 0.26
86 50 0.59
88 13 0.15
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.24
Consensus pattern (86 bp):
AGTCACAATGACAGAAATCTAATTTAAAATTAAAAAGACTCAAACAAAAAATATAAAAGATATAA
CATAAAAACAATAGAATTAAT
Found at i:166866 original size:19 final size:19
Alignment explanation
Indices: 166842--166904 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 19
166832 TTATAAATAT
*
166842 CTCCCATTT-CATTTTCTTC
1 CTCCCATTTCCA-CTTCTTC
166861 CTCCCATTTTCCACTTCTTC
1 CTCCCA-TTTCCACTTCTTC
166881 CTCCCATTTTCCACTTCTTC
1 CTCCCA-TTTCCACTTCTTC
166901 CTCC
1 CTCC
166905 TTAAGCCACT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
19 6 0.15
20 33 0.80
21 2 0.05
ACGTcount: A:0.10, C:0.44, G:0.00, T:0.46
Consensus pattern (19 bp):
CTCCCATTTCCACTTCTTC
Found at i:166905 original size:23 final size:20
Alignment explanation
Indices: 166855--166904 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
166845 CCATTTCATT
166855 TTCTTCCTCCCATTTTCCAC
1 TTCTTCCTCCCATTTTCCAC
166875 TTCTTCCTCCCATTTTCCAC
1 TTCTTCCTCCCATTTTCCAC
166895 TTCTTCCTCC
1 TTCTTCCTCC
166905 TTAAGCCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.08, C:0.46, G:0.00, T:0.46
Consensus pattern (20 bp):
TTCTTCCTCCCATTTTCCAC
Found at i:169018 original size:22 final size:22
Alignment explanation
Indices: 168988--169029 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
168978 GGGTCTACGC
*
168988 GGTCTTTCGGGACATATACAGA
1 GGTCCTTCGGGACATATACAGA
169010 GGTCCTTCGGGACATATACA
1 GGTCCTTCGGGACATATACA
169030 CATGTCATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (22 bp):
GGTCCTTCGGGACATATACAGA
Found at i:171364 original size:18 final size:18
Alignment explanation
Indices: 171341--171377 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
171331 AGGCATTTGA
171341 TCCTCTGGCT-GTGCTTGT
1 TCCTCT-GCTCGTGCTTGT
171359 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
171377 T
1 T
171378 GCTTGTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.00, C:0.30, G:0.24, T:0.46
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:173020 original size:23 final size:23
Alignment explanation
Indices: 172935--173014 Score: 144
Period size: 23 Copynumber: 3.5 Consensus size: 23
172925 CCAAAACCCC
172935 AAGGGGGAATCGGTTCCCCTTCA
1 AAGGGGGAATCGGTTCCCCTTCA
172958 AAGGGGGAATCGGTTCCCCTTCA
1 AAGGGGGAATCGGTTCCCCTTCA
172981 AAGGGGGAATCGGTTCCCCTTC-
1 AAGGGGGAATCGGTTCCCCTTCA
*
173003 AAGGGGGTATCG
1 AAGGGGGAATCG
173015 ATTTCCTCTG
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 11 0.20
23 45 0.80
ACGTcount: A:0.21, C:0.24, G:0.34, T:0.21
Consensus pattern (23 bp):
AAGGGGGAATCGGTTCCCCTTCA
Found at i:179271 original size:20 final size:20
Alignment explanation
Indices: 179242--179290 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
179232 ATTTGTAGGA
*
179242 GCATTAATGCATTAAGAGGT
1 GCATTGATGCATTAAGAGGT
*
179262 GCATTGATGCATTAAGGGGT
1 GCATTGATGCATTAAGAGGT
*
179282 GCATCGATG
1 GCATTGATG
179291 TATGGATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.29
Consensus pattern (20 bp):
GCATTGATGCATTAAGAGGT
Found at i:180604 original size:21 final size:21
Alignment explanation
Indices: 180580--180619 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
180570 TGCCAAAGTT
180580 ACTGTAACAGTGCATCGATGC
1 ACTGTAACAGTGCATCGATGC
*
180601 ACTGTAGCAGTGCATCGAT
1 ACTGTAACAGTGCATCGAT
180620 ACACAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
ACTGTAACAGTGCATCGATGC
Found at i:183349 original size:21 final size:21
Alignment explanation
Indices: 183323--183379 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
183313 TCTGGGCAGG
183323 TGCATCGATGCACTATGAGTA
1 TGCATCGATGCACTATGAGTA
183344 TGCATCGATGCACTATGAGTA
1 TGCATCGATGCACTATGAGTA
* *
183365 TGTACCGATGCACTA
1 TGCATCGATGCACTA
183380 AGATAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCACTATGAGTA
Found at i:183418 original size:20 final size:20
Alignment explanation
Indices: 183393--183446 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
183383 TAAATTTTGA
*
183393 AGGTGCATTAATGCATTAAG
1 AGGTGCATCAATGCATTAAG
*
183413 AGGTGCATCGATGCATTAAG
1 AGGTGCATCAATGCATTAAG
* *
183433 GGGTGCATCGATGC
1 AGGTGCATCAATGC
183447 TGGATATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (20 bp):
AGGTGCATCAATGCATTAAG
Done.