Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000508.1 Hibiscus syriacus cultivar Beakdansim tig00000967_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: 47795
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Found at i:8317 original size:35 final size:35
Alignment explanation
Indices: 8277--8358 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 35
8267 GTTGCATTTT
* *
8277 GTATTTGGTTGATTTAGTAGGAATGTAAGATTATTC
1 GTATTTGGTTAATTTAGTAGGAAAGTAAGATTA-TC
*
8313 -TATTTGATTAATTTAGTAGGAAAGTAAGATTATC
1 GTATTTGGTTAATTTAGTAGGAAAGTAAGATTATC
8347 GTATTTGGTTAA
1 GTATTTGGTTAA
8359 AGGAATAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
34 2 0.05
35 39 0.95
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (35 bp):
GTATTTGGTTAATTTAGTAGGAAAGTAAGATTATC
Found at i:11286 original size:20 final size:20
Alignment explanation
Indices: 11249--11286 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11239 GGCCGTTTCT
*
11249 AGCCGTTGGGGATGATTTGG
1 AGCCGTTGGGGATAATTTGG
*
11269 AGCCGTTGGGGGTAATTT
1 AGCCGTTGGGGATAATTT
11287 TTCTACAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.11, G:0.42, T:0.32
Consensus pattern (20 bp):
AGCCGTTGGGGATAATTTGG
Found at i:11341 original size:20 final size:21
Alignment explanation
Indices: 11316--11355 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
11306 TCAGGATAGG
11316 GAGTATCGATACT-CCTTTAA
1 GAGTATCGATACTACCTTTAA
*
11336 GAGTATCGGTACTACCTTTA
1 GAGTATCGATACTACCTTTA
11356 TAATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (21 bp):
GAGTATCGATACTACCTTTAA
Found at i:15299 original size:11 final size:11
Alignment explanation
Indices: 15283--15307 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15273 TCGTAAAATT
15283 ATATTATAAAA
1 ATATTATAAAA
15294 ATATTATAAAA
1 ATATTATAAAA
15305 ATA
1 ATA
15308 ATATTCACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATTATAAAA
Found at i:24472 original size:3 final size:3
Alignment explanation
Indices: 24451--24492 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
24441 CTACCAAAAA
*
24451 TAT TAT T-T TAT TAA T-T TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
24493 ATCAATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.09
3 32 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:26351 original size:24 final size:20
Alignment explanation
Indices: 26298--26354 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 20
26288 TCCCTTTTGA
*
26298 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
26318 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
26341 ATGTGCATCGATGC
1 A-GTGCATCGATGC
26355 GCTACTCATG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:30056 original size:26 final size:28
Alignment explanation
Indices: 30027--30098 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 28
30017 ACTTAATCTC
* *
30027 TTATATTCA-TATAT-CACATATGCATA
1 TTATATTCATTATATAAACATAAGCATA
30053 -T-TATTCATTATATAAACATAAGCATA
1 TTATATTCATTATATAAACATAAGCATA
30079 -T-TATTCATTATATAAACATA
1 TTATATTCATTATATAAACATA
30099 TATTCATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.14
25 6 0.14
26 30 0.71
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42
Consensus pattern (28 bp):
TTATATTCATTATATAAACATAAGCATA
Found at i:30107 original size:28 final size:28
Alignment explanation
Indices: 30044--30114 Score: 110
Period size: 26 Copynumber: 2.6 Consensus size: 28
30034 CATATATCAC
30044 ATATGCATATTATTCATTATATAAACAT
1 ATATGCATATTATTCATTATATAAACAT
30072 A-A-GCATATTATTCATTATATAAACAT
1 ATATGCATATTATTCATTATATAAACAT
* *
30098 ATATTCATATAATTCAT
1 ATATGCATATTATTCAT
30115 ATCATACCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 25 0.64
27 2 0.05
28 12 0.31
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (28 bp):
ATATGCATATTATTCATTATATAAACAT
Found at i:30471 original size:20 final size:20
Alignment explanation
Indices: 30446--30483 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30436 TCCCCTTTGA
*
30446 AGTGCATCGATGTATTCTAC
1 AGTGCATCGATGCATTCTAC
*
30466 AGTGCATTGATGCATTCT
1 AGTGCATCGATGCATTCT
30484 TTGATATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:30568 original size:64 final size:64
Alignment explanation
Indices: 30491--30652 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 64
30481 TCTTTGATAT
* * *
30491 GTGCATCGATGCACTACTCATGCATCGTTACACAAATCACCTTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACTACTCATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
* * * * ** *
30555 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTTCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTACTCATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
* *
30619 GTGCATCGATGCACTTC-CTGTGCATCGATACACA
1 GTGCATCGATGCACTACTC-ATGCATCGATACACA
30653 CTGAACAATT
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
64 75 0.93
65 6 0.07
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACTCATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:34649 original size:24 final size:20
Alignment explanation
Indices: 34594--34631 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
34584 TCCCCTTTGA
34594 AGTGCATCGATGTATTCTAC
1 AGTGCATCGATGTATTCTAC
34614 AGTGCATCGATGTATTCT
1 AGTGCATCGATGTATTCT
34632 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATGTATTCTAC
Found at i:38774 original size:24 final size:20
Alignment explanation
Indices: 38719--38756 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
38709 TCCCCTTTGA
38719 AGTGCATCGATGTATTCTAC
1 AGTGCATCGATGTATTCTAC
38739 AGTGCATCGATGTATTCT
1 AGTGCATCGATGTATTCT
38757 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATGTATTCTAC
Found at i:42474 original size:32 final size:32
Alignment explanation
Indices: 42430--42491 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
42420 TCTTACTTGT
*
42430 ACTAACTAATTTCACTTCTTTTGTTTGTGTAC
1 ACTAACTAATTTCACTTCTTTTCTTTGTGTAC
* **
42462 ACTAACTTATTTCTTTTCTTTTCTTTGTGT
1 ACTAACTAATTTCACTTCTTTTCTTTGTGT
42492 CATTTTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.56
Consensus pattern (32 bp):
ACTAACTAATTTCACTTCTTTTCTTTGTGTAC
Found at i:43043 original size:19 final size:20
Alignment explanation
Indices: 42999--43043 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
42989 TTGGGATCAA
42999 CATTTTTGCATCTGCATTTG
1 CATTTTTGCATCTGCATTTG
*
43019 CA-TTTTGCATCTGTATTT-
1 CATTTTTGCATCTGCATTTG
43037 CATTTTT
1 CATTTTT
43044 TAAGAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 19 0.83
20 2 0.09
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.56
Consensus pattern (20 bp):
CATTTTTGCATCTGCATTTG
Found at i:44341 original size:13 final size:13
Alignment explanation
Indices: 44323--44374 Score: 72
Period size: 13 Copynumber: 4.0 Consensus size: 13
44313 GATAAATAAA
44323 CAAAGAGAAAAAG
1 CAAAGAGAAAAAG
44336 CAAAGA-AAAAGAG
1 CAAAGAGAAAA-AG
44349 CAAA-AGAAAAAG
1 CAAAGAGAAAAAG
44361 CAAAGAGCAAAAAG
1 CAAAGAG-AAAAAG
44375 AAAACAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
12 11 0.31
13 18 0.51
14 6 0.17
ACGTcount: A:0.69, C:0.10, G:0.21, T:0.00
Consensus pattern (13 bp):
CAAAGAGAAAAAG
Found at i:45774 original size:31 final size:31
Alignment explanation
Indices: 45730--45806 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 31
45720 CATTAAGGCA
45730 GTTTCTTTAGAAACACAAA-ATCTTTGAGTAT-
1 GTTTCTTTAGAAACA-AAACATCTTTGAG-ATC
45761 GTTTCTGTT-GAAACAAAACCATCTTTGAGATC
1 GTTTCT-TTAGAAACAAAA-CATCTTTGAGATC
45793 GTTTCATTTA-AAAC
1 GTTTC-TTTAGAAAC
45807 GAATTTTGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
30 3 0.08
31 14 0.35
32 22 0.55
33 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (31 bp):
GTTTCTTTAGAAACAAAACATCTTTGAGATC
Done.