Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002188.1 Hibiscus syriacus cultivar Beakdansim tig00004456_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: 75782
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:9311 original size:25 final size:27
Alignment explanation
Indices: 9283--9332 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
9273 ACAGAAAATG
9283 CAAATGA-T-ATATGAATATATCAGAA
1 CAAATGATTCATATGAATATATCAGAA
9308 CAAATGATTCATATGAATATATCAG
1 CAAATGATTCATATGAATATATCAG
9333 CTGTTATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 7 0.30
26 1 0.04
27 15 0.65
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (27 bp):
CAAATGATTCATATGAATATATCAGAA
Found at i:11510 original size:79 final size:77
Alignment explanation
Indices: 11380--11540 Score: 279
Period size: 79 Copynumber: 2.1 Consensus size: 77
11370 AAACCTTTAT
11380 AAATTGTGAGAATGAAATGCACACAAGTATAAATTAGTTATAATTACATATTTGAAAGGTATAAG
1 AAATTGTGAGAATGAAATGCACACAAGTATAAATTAGTTATAATTACATATTTGAAAGGTATAAG
11445 AAGATGAAGTTC
66 AAGATGAAGTTC
*
11457 AAATTGTGAGAATG-AATGCACACACCAAGTATAAATTAGTTATAATTATATATTTGAAAGGTAT
1 AAATTGTGAGAATGAAATG--CACA-CAAGTATAAATTAGTTATAATTACATATTTGAAAGGTAT
11521 AAGAAGATGAAGTTC
63 AAGAAGATGAAGTTC
11536 AAATT
1 AAATT
11541 CAAAATAAAT
Statistics
Matches: 80, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
76 4 0.05
77 14 0.17
78 4 0.05
79 58 0.73
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.30
Consensus pattern (77 bp):
AAATTGTGAGAATGAAATGCACACAAGTATAAATTAGTTATAATTACATATTTGAAAGGTATAAG
AAGATGAAGTTC
Found at i:20475 original size:23 final size:23
Alignment explanation
Indices: 20443--20504 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
20433 AAACTTTATT
* *
20443 TAATTCAATTAATTATTTAAAAA
1 TAATTAAATTAATTATTAAAAAA
*
20466 TAATTAAATTAATAATTAAAAAA
1 TAATTAAATTAATTATTAAAAAA
*
20489 TAATTAATTTAATTAT
1 TAATTAAATTAATTAT
20505 GATTAATTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATTAAATTAATTATTAAAAAA
Found at i:20492 original size:11 final size:11
Alignment explanation
Indices: 20461--20495 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
20451 TTAATTATTT
20461 AAAAATAATTA
1 AAAAATAATTA
*
20472 AATTAATAATTA
1 AA-AAATAATTA
20484 AAAAATAATTA
1 AAAAATAATTA
20495 A
1 A
20496 TTTAATTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAATAATTA
Found at i:21293 original size:2 final size:2
Alignment explanation
Indices: 21286--21368 Score: 139
Period size: 2 Copynumber: 41.5 Consensus size: 2
21276 CCTCTACCCC
21286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
21328 AT AT AT AT AT AT AT AT AT TT AT AT AT TT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21369 ATGCTCCTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:37233 original size:24 final size:24
Alignment explanation
Indices: 37201--37266 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
37191 TTTCCCTCCT
37201 CCGTGCTTGAATTTCCCATGCTTC
1 CCGTGCTTGAATTTCCCATGCTTC
*
37225 CCGTGCTTGAATTTCCCATGTTTC
1 CCGTGCTTGAATTTCCCATGCTTC
*
37249 CCGTGCTTAAATTTCCCA
1 CCGTGCTTGAATTTCCCA
37267 CCATGATGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.15, C:0.32, G:0.15, T:0.38
Consensus pattern (24 bp):
CCGTGCTTGAATTTCCCATGCTTC
Found at i:37634 original size:33 final size:33
Alignment explanation
Indices: 37596--37699 Score: 181
Period size: 33 Copynumber: 3.2 Consensus size: 33
37586 ATAACCAACC
*
37596 GGTGGATAGCCTTGAGGGGGATACCCTCCAGCA
1 GGTGGATAGCCATGAGGGGGATACCCTCCAGCA
37629 GGTGGATAGCCATGAGGGGGATACCCTCCAGCA
1 GGTGGATAGCCATGAGGGGGATACCCTCCAGCA
* *
37662 GGTGGATAGCCCTGAGGGGGATACCCTCCAGCT
1 GGTGGATAGCCATGAGGGGGATACCCTCCAGCA
37695 GGTGG
1 GGTGG
37700 GTACGCACCG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.20, C:0.24, G:0.38, T:0.17
Consensus pattern (33 bp):
GGTGGATAGCCATGAGGGGGATACCCTCCAGCA
Found at i:37743 original size:12 final size:12
Alignment explanation
Indices: 37726--37751 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37716 TATCCTCCAT
37726 GACCATGAGCAA
1 GACCATGAGCAA
37738 GACCATGAGCAA
1 GACCATGAGCAA
37750 GA
1 GA
37752 TTTGAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.27, T:0.08
Consensus pattern (12 bp):
GACCATGAGCAA
Found at i:38665 original size:5 final size:5
Alignment explanation
Indices: 38657--38683 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
38647 TATTCCATTC
38657 CAATA CAATA CAATA CAATA CAATA CA
1 CAATA CAATA CAATA CAATA CAATA CA
38684 CAGGGAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.19
Consensus pattern (5 bp):
CAATA
Found at i:41213 original size:72 final size:72
Alignment explanation
Indices: 41096--41239 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
41086 GATAATCTGA
41096 GAGTGGAACGTGCAAACCAAGCATATATTGAGATGCGAAAACAGAGTAGCAAATGCTCTAACTGA
1 GAGTGGAACGTGCAAACCAAGCATATATTGAGATGCGAAAACAGAGTAGCAAATGCTCTAACTGA
41161 ATAAGCC
66 ATAAGCC
41168 GAGTGGAACGTGCAAACCAAGCATATATTGAGATGCGAAAACAGAGTAGCAAATGCTCTAACTGA
1 GAGTGGAACGTGCAAACCAAGCATATATTGAGATGCGAAAACAGAGTAGCAAATGCTCTAACTGA
41233 ATAAGCC
66 ATAAGCC
41240 TCGACACTCC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (72 bp):
GAGTGGAACGTGCAAACCAAGCATATATTGAGATGCGAAAACAGAGTAGCAAATGCTCTAACTGA
ATAAGCC
Found at i:42035 original size:15 final size:15
Alignment explanation
Indices: 42003--42032 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
41993 AGTTTTTTTA
42003 ATAAAATATAATATT
1 ATAAAATATAATATT
42018 ATAAAATAATAATAT
1 ATAAAAT-ATAATAT
42033 ATATGATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAAATATAATATT
Found at i:42036 original size:20 final size:20
Alignment explanation
Indices: 42002--42041 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41992 AAGTTTTTTT
*
42002 AATAAAATATAATATTATAA
1 AATAAAATATAATATGATAA
42022 AATAATAATAT-ATATGATAA
1 AATAA-AATATAATATGATAA
42042 TTATTTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
AATAAAATATAATATGATAA
Found at i:53827 original size:20 final size:20
Alignment explanation
Indices: 53802--53873 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 20
53792 TTAAAGTTTA
53802 AAAATATAATATATTTAAAT
1 AAAATATAATATATTTAAAT
* *
53822 AAAATACTATAAAAATAAAGTTTTAA-
1 -AAA-A-TAT---AATATA-TTTAAAT
53848 AAAATATAATATATTTAAAT
1 AAAATATAATATATTTAAAT
53868 AAAATA
1 AAAATA
53874 AAAATAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 15
0.68 0.07 0.25
Matches are distributed among these distances:
19 5 0.12
20 11 0.28
21 3 0.08
22 1 0.03
23 6 0.15
24 1 0.03
25 3 0.08
26 5 0.12
27 5 0.12
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (20 bp):
AAAATATAATATATTTAAAT
Found at i:53834 original size:44 final size:46
Alignment explanation
Indices: 53785--53873 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
53775 GAAAACGTAG
*
53785 TATAAAATTAAAG-TTT-AAAAATATAATATATTTAAATAAAATAC
1 TATAAAAATAAAGTTTTAAAAAATATAATATATTTAAATAAAATAC
53829 TATAAAAATAAAGTTTTAAAAAATATAATATATTTAAATAAAATA
1 TATAAAAATAAAGTTTTAAAAAATATAATATATTTAAATAAAATA
53874 AAAATAATTA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 12 0.29
45 3 0.07
46 27 0.64
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (46 bp):
TATAAAAATAAAGTTTTAAAAAATATAATATATTTAAATAAAATAC
Found at i:62411 original size:2 final size:2
Alignment explanation
Indices: 62406--62430 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
62396 GACCCAAAAA
62406 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
62431 GTTTTACCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65158 original size:20 final size:21
Alignment explanation
Indices: 65133--65173 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
65123 ATATTATTCG
65133 TTAAATTTTGTTAAT-TAAAT
1 TTAAATTTTGTTAATCTAAAT
65153 TTAAATTTTGTTAATCTAAAT
1 TTAAATTTTGTTAATCTAAAT
65174 GGATATGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (21 bp):
TTAAATTTTGTTAATCTAAAT
Found at i:66541 original size:13 final size:14
Alignment explanation
Indices: 66517--66546 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
66507 TTCTTAACAT
66517 ATAAATATTTATTG
1 ATAAATATTTATTG
66531 ATAAA-ATTTATTG
1 ATAAATATTTATTG
66544 ATA
1 ATA
66547 TTTTAATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
ATAAATATTTATTG
Found at i:66956 original size:66 final size:66
Alignment explanation
Indices: 66886--67018 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
66876 AATTTGTTTT
66886 TAACTTTCTAATTTTATAAAATATGTAATAAAAATTAAATATTTTTTATACGAAGTATGAGGGAT
1 TAACTTTCTAATTTTATAAAATATGTAATAAAAATTAAATATTTTTTATACGAAGTATGAGGGAT
66951 A
66 A
66952 TAACTTTCTAATTTTATAAAATATGTAATAAAAATTAAATATTTTTTATACGAAGTATGAGGGAT
1 TAACTTTCTAATTTTATAAAATATGTAATAAAAATTAAATATTTTTTATACGAAGTATGAGGGAT
67017 A
66 A
67018 T
1 T
67019 TGTTCAAAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.41
Consensus pattern (66 bp):
TAACTTTCTAATTTTATAAAATATGTAATAAAAATTAAATATTTTTTATACGAAGTATGAGGGAT
A
Found at i:71285 original size:18 final size:19
Alignment explanation
Indices: 71250--71286 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
71240 TACGGAATGT
71250 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
71270 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
71287 TGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Done.