Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004735.1 Hibiscus syriacus cultivar Beakdansim tig00010691_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: 58067
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:4428 original size:31 final size:31
Alignment explanation
Indices: 4393--4475 Score: 118
Period size: 31 Copynumber: 2.7 Consensus size: 31
4383 TGATGGATTA
4393 TTGTAAATTGTATTAAGGATTTC-TAACACAT
1 TTGTAAATTGTATTAAGGATTTCAT-ACACAT
4424 TTGTAAATTGTATTAAGGATTTCATACACAT
1 TTGTAAATTGTATTAAGGATTTCATACACAT
*
4455 TTGTTTAATT-TATT-AGGATTT
1 TTG-TAAATTGTATTAAGGATTT
4476 TTAATTGGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
30 7 0.14
31 36 0.73
32 6 0.12
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (31 bp):
TTGTAAATTGTATTAAGGATTTCATACACAT
Found at i:6478 original size:120 final size:123
Alignment explanation
Indices: 6206--6480 Score: 317
Period size: 120 Copynumber: 2.2 Consensus size: 123
6196 TGAAAAGTGC
* * *
6206 GATACCCCTTTA-CTATTGC-TAGTTAGTCTCTTTATGAAATGATATCTGATATTGCTATAATTA
1 GATACCCC-TTAGCTATTGCTTA-TTATTCTCGTCATGAAATGATATCTGATATTGCTATAATTA
* * * * *
6269 TTTTTCGATTAGGAGATTGTATTTTTTTTAAGAACTAAATTGAGAACAAGATGAGATTGTAG
64 TTTTT--ATTAGGAGAATGTATTCTTTTTAAGAACTAAATTGAGAAAAAGAAGAGATTGGAG
* * * * **
6331 GATACCCCTTAGCTATTACTGAATATTCTCGTCATGTAATGATATCTGATATTGCTATTGTTA-T
1 GATACCCCTTAGCTATTGCTTATTATTCTCGTCATGAAATGATATCTGATATTGCTATAATTATT
* ** *
6395 TTT-TTAGGAGAATGTA-TCTTTTTCATTATTAAATTGAGAAAAAGAAGAGATTGGAG
66 TTTATTAGGAGAATGTATTCTTTTTAAGAACTAAATTGAGAAAAAGAAGAGATTGGAG
6451 GATACCCCTTAGCTATTGCTTATTATTCTC
1 GATACCCCTTAGCTATTGCTTATTATTCTC
6481 TTCAGTTTTC
Statistics
Matches: 127, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
120 59 0.46
121 12 0.09
124 7 0.06
125 48 0.38
126 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.41
Consensus pattern (123 bp):
GATACCCCTTAGCTATTGCTTATTATTCTCGTCATGAAATGATATCTGATATTGCTATAATTATT
TTTATTAGGAGAATGTATTCTTTTTAAGAACTAAATTGAGAAAAAGAAGAGATTGGAG
Found at i:11748 original size:21 final size:21
Alignment explanation
Indices: 11702--11759 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
11692 GATCCCTTTT
*
11702 CAAAAGGATCAATCCCTCAGG
1 CAAAAGGATCGATCCCTCAGG
* *
11723 AAAAATGATCGATCCCTC-GAG
1 CAAAAGGATCGATCCCTCAG-G
11744 CAAAAGGATCGATCCC
1 CAAAAGGATCGATCCC
11760 AAACTTTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.38, C:0.28, G:0.19, T:0.16
Consensus pattern (21 bp):
CAAAAGGATCGATCCCTCAGG
Found at i:15218 original size:37 final size:37
Alignment explanation
Indices: 15146--15219 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
15136 TGAAAAATAT
* *
15146 TTTATATATTTTCTTTAAAAAATTTAAATTCATAAAA
1 TTTATATATTTTCTTTAAAAAATTGAAAATCATAAAA
* *
15183 TTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAAA
1 TTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAAA
15220 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 13 0.41
38 19 0.59
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
TTTATATATTTTCTTTAAAAAATTGAAAATCATAAAA
Found at i:15693 original size:23 final size:21
Alignment explanation
Indices: 15655--15697 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
15645 ATAATTATTT
15655 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
15676 AAAAATATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
15697 A
1 A
15698 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:42535 original size:16 final size:17
Alignment explanation
Indices: 42502--42537 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
42492 TTAAATTCAT
*
42502 AATTTTAAATACATAAA
1 AATTTTAAATAAATAAA
42519 AATTTTAAA-AAATAAA
1 AATTTTAAATAAATAAA
42535 AAT
1 AAT
42538 CCAAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTTTAAATAAATAAA
Found at i:57150 original size:16 final size:16
Alignment explanation
Indices: 57129--57159 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
57119 TTAACATTTT
57129 GAAAAAAAAAAAACTA
1 GAAAAAAAAAAAACTA
57145 GAAAAAAAAAAAACT
1 GAAAAAAAAAAAACT
57160 TTATTAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06
Consensus pattern (16 bp):
GAAAAAAAAAAAACTA
Done.