Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005839.1 Hibiscus syriacus cultivar Beakdansim tig00013691_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: 55841
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4407 original size:14 final size:14
Alignment explanation
Indices: 4365--4504 Score: 70
Period size: 14 Copynumber: 9.2 Consensus size: 14
4355 TATTAAAATA
4365 ATTTTAAATAATTT
1 ATTTTAAATAATTT
* *
4379 A--ATAAGATTATTT
1 ATTTTAA-ATAATTT
4392 ATTTTAAATAATTT
1 ATTTTAAATAATTT
*
4406 ATTTTAAAAACAATTT
1 ATTTT--AAATAATTT
*
4422 -TTATAAAATAATTT
1 ATT-TTAAATAATTT
4436 ATTTTAAAATAAATTAT
1 ATTTT-AAAT-AATT-T
* **
4453 AATAAAATATGGATTGATTT
1 ATTTTAA-AT--A---ATTT
4473 ATTTTAAAATAATTT
1 ATTTT-AAATAATTT
4488 ATTTTAAATAATTT
1 ATTTTAAATAATTT
4502 ATT
1 ATT
4505 AGTATAGATT
Statistics
Matches: 95, Mismatches: 15, Indels: 32
0.67 0.11 0.23
Matches are distributed among these distances:
12 3 0.03
13 7 0.07
14 33 0.35
15 20 0.21
16 15 0.16
17 5 0.05
18 2 0.02
20 5 0.05
21 5 0.05
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (14 bp):
ATTTTAAATAATTT
Found at i:4433 original size:30 final size:30
Alignment explanation
Indices: 4397--4461 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
4387 TATTTATTTT
* *
4397 AAATAATTTATTTTAAAA-ACAATTTTTATA
1 AAATAATTTATTTTAAAATA-AATTATAATA
4427 AAATAATTTATTTTAAAATAAATTATAATA
1 AAATAATTTATTTTAAAATAAATTATAATA
4457 AAATA
1 AAATA
4462 TGGATTGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (30 bp):
AAATAATTTATTTTAAAATAAATTATAATA
Found at i:4443 original size:15 final size:15
Alignment explanation
Indices: 4388--4504 Score: 96
Period size: 14 Copynumber: 7.5 Consensus size: 15
4378 TAATAAGATT
4388 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
*
4402 ATTTATTTTAAAAACA
1 ATTTATTTT-AAAATA
*
4418 ATTT-TTATAAAATA
1 ATTTATTTTAAAATA
4432 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* * *
4447 AATTATAATAAAATATGGA
1 ATTTAT-TTTAAA-AT--A
4466 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
4484 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
4498 ATTTATT
1 ATTTATT
4505 AGTATAGATT
Statistics
Matches: 83, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
14 30 0.36
15 26 0.31
16 12 0.14
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.05
22 5 0.06
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:4481 original size:52 final size:47
Alignment explanation
Indices: 4425--4795 Score: 341
Period size: 54 Copynumber: 7.1 Consensus size: 47
4415 ACAATTTTTA
* *
4425 TAAAATAATTTATTTTAAAATAAATTATAATAAAATATGGATTGATTTATTT
1 TAAAATAATTTATTTT-AAAT-AATT-T-AT-TAGTATGGATTGATTTATTT
*
4477 TAAAATAATTTATTTTAAATAATTTATTAGTATAGATTGA-TTATTT
1 TAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
4523 TAAATATGGATTGATTTA-TTTAAATAATTTATTAGTATGGATTGATTTATTT
1 TAAA-AT--A---ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
4575 TAAAAATGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
1 T-AAAAT-A---ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
4627 TAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
1 T-AAA-AT--A---ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
*
4681 TAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTT
1 T-AAA-AT--A---ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
* *
4735 TAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATAT
1 T-AAA-AT--A---ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
4789 TAAAATA
1 TAAAATA
4796 TGGATTGATT
Statistics
Matches: 301, Mismatches: 7, Indels: 24
0.91 0.02 0.07
Matches are distributed among these distances:
46 10 0.03
47 12 0.04
48 2 0.01
49 2 0.01
50 5 0.02
51 40 0.13
52 71 0.24
53 8 0.03
54 151 0.50
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (47 bp):
TAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
Found at i:4620 original size:32 final size:32
Alignment explanation
Indices: 4582--4792 Score: 185
Period size: 32 Copynumber: 7.5 Consensus size: 32
4572 TTTTAAAAAT
4582 GATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATG
4614 GATTGATTTA-TTT---TAA---A--A-TATG
1 GATTGATTTATTTTAAATAATTTATTAGTATG
4636 GATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATG
4668 GATTGATTTA-TTT---TAA---A--A-TATG
1 GATTGATTTATTTTAAATAATTTATTAGTATG
4690 GATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATG
*
4722 TATTGATTTA-TTT---TAA---A--A-TATG
1 GATTGATTTATTTTAAATAATTTATTAGTATG
4744 GATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATG
* *
4776 AATTGATTTATATTAAA
1 GATTGATTTATTTTAAA
4793 ATATGGATTG
Statistics
Matches: 145, Mismatches: 4, Indels: 60
0.69 0.02 0.29
Matches are distributed among these distances:
22 41 0.28
23 12 0.08
25 3 0.02
26 9 0.06
28 9 0.06
29 3 0.02
31 12 0.08
32 56 0.39
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
GATTGATTTATTTTAAATAATTTATTAGTATG
Found at i:4635 original size:22 final size:22
Alignment explanation
Indices: 4610--4652 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
4600 AATTTATTAG
4610 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
4632 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
4653 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:4664 original size:54 final size:54
Alignment explanation
Indices: 4484--4809 Score: 581
Period size: 54 Copynumber: 6.1 Consensus size: 54
4474 TTTTAAAATA
*
4484 ATTTATTTTAAATAATTTATTAGTATAGATTGA-TTATTTT-AAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
4536 ATTTA-TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA-AT-GATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
4587 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
4641 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
4695 ATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
4749 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATATTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
4803 ATTTATT
1 ATTTATT
4810 ATTGTAGATG
Statistics
Matches: 265, Mismatches: 4, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
51 36 0.14
52 53 0.20
53 5 0.02
54 171 0.65
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:4689 original size:22 final size:22
Alignment explanation
Indices: 4664--4706 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
4654 AATTTATTAG
4664 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
4686 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
4707 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:4734 original size:22 final size:22
Alignment explanation
Indices: 4718--4760 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4708 AATTTATTAG
*
4718 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
4740 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
4761 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:4918 original size:21 final size:22
Alignment explanation
Indices: 4852--4916 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
4842 AATTTATTAG
4852 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
4874 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
4896 TAT-GATTGATTTACTTTTAAA
1 TATGGATTGATTTA-TTTTAAA
4917 TAATTTATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.24
22 32 0.76
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:4991 original size:30 final size:31
Alignment explanation
Indices: 4941--4998 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
4931 AATTGTATGG
*
4941 ATTATTTAAATTTCAGTATTGCAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
*
4972 ATTATTTAAA-CTGAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
4999 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:7125 original size:37 final size:37
Alignment explanation
Indices: 7084--7156 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
7074 CTCTCCCACG
7084 CCATCCGATAGAAACAATATTTAATGGAACCAAATAA
1 CCATCCGATAGAAACAATATTTAATGGAACCAAATAA
*
7121 CCATCCGATAGAAACAATATTTGATGGAACCAAATA
1 CCATCCGATAGAAACAATATTTAATGGAACCAAATA
7157 GGAATCATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (37 bp):
CCATCCGATAGAAACAATATTTAATGGAACCAAATAA
Found at i:13258 original size:22 final size:22
Alignment explanation
Indices: 13233--13286 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
13223 GGAATCAATA
*
13233 CCCCCTTGAA-GAGGAACTGATT
1 CCCCCTTGAATG-GGAACCGATT
*
13255 CCCCTTTGAATGGGAACCGATT
1 CCCCCTTGAATGGGAACCGATT
13277 CCCTCCTTGA
1 CCC-CCTTGA
13287 GGGAATCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.26
Consensus pattern (22 bp):
CCCCCTTGAATGGGAACCGATT
Found at i:23517 original size:3 final size:3
Alignment explanation
Indices: 23509--23557 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
23499 AATTATTTAA
* ** *
23509 ATT ATT ATT TTT AAA ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
23557 A
1 A
23558 AATTAAATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:23527 original size:15 final size:15
Alignment explanation
Indices: 23500--23557 Score: 68
Period size: 15 Copynumber: 4.1 Consensus size: 15
23490 TTTTACTTAA
*
23500 ATTATTTAAATTATT
1 ATTATTAAAATTATT
*
23515 ATTTTTAAAATTATT
1 ATTATTAAAATTATT
23530 ATTATT---ATTATT
1 ATTATTAAAATTATT
*
23542 ATTATTAATATTATT
1 ATTATTAAAATTATT
23557 A
1 A
23558 AATTAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
12 12 0.32
15 25 0.68
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTATTAAAATTATT
Found at i:25217 original size:20 final size:19
Alignment explanation
Indices: 25192--25233 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
25182 CTATTTTATA
25192 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
25212 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
25231 AAT
1 AAT
25234 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:25229 original size:119 final size:117
Alignment explanation
Indices: 25088--25324 Score: 298
Period size: 120 Copynumber: 2.0 Consensus size: 117
25078 ATTTTAATCC
* * * *
25088 TGTTTTAATATTTATTTATTTTTCAATAT-TAAGAAATGA-CAGTCTTAAAACAACTGGATGTCT
1 TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC-
* *
25151 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAAT
65 ATTTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAA-TATATATAAAT
* * ** *
25206 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
* **
25271 CTTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAAT
65 ATTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAAT
25324 T
1 T
25325 AATATTTTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
118 19 0.19
119 28 0.27
120 38 0.37
121 17 0.17
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (117 bp):
TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
TTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAAT
Found at i:25322 original size:29 final size:29
Alignment explanation
Indices: 25289--25345 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
25279 ATATTTCTAA
25289 ATAAATAAATATTTTATTT-ATAAATATAT
1 ATAAATAAATATTTT-TTTCATAAATATAT
* *
25318 ATAAATTAATATTTTTTTCATAATTATA
1 ATAAATAAATATTTTTTTCATAAATATA
25346 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAATAAATATTTTTTTCATAAATATAT
Found at i:26118 original size:112 final size:112
Alignment explanation
Indices: 25980--26203 Score: 369
Period size: 112 Copynumber: 2.0 Consensus size: 112
25970 TATTCCTCAT
* *
25980 TCTCCTCTTTCCAGTTCCACAAAAAACAAGGATTTACAATTTGCACCAATATACTAGAGTTTTAT
1 TCTCCTCTTTCCAGTTCCACAAAAAACAAAGATTTACAATTTACACCAATATACTAGAGTTTTAT
*
26045 CTGTCAGAGATGAAGAAAACTTACTAACCATAGAAATTGAAGTTATA
66 CTATCAGAGATGAAGAAAACTTACTAACCATAGAAATTGAAGTTATA
*
26092 TCTCCTCTTTTCTA-TTCCACAAAAAACAAAGATTTACAATTTACACCAATATACTAGAGTTTTA
1 TCTCCTC-TTTCCAGTTCCACAAAAAACAAAGATTTACAATTTACACCAATATACTAGAGTTTTA
* * *
26156 TCTATTAGAGATGAAGAAAACTTATTAACTATAGAAATTGAAGTTATA
65 TCTATCAGAGATGAAGAAAACTTACTAACCATAGAAATTGAAGTTATA
26204 AGATAACTCC
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
112 99 0.95
113 5 0.05
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.33
Consensus pattern (112 bp):
TCTCCTCTTTCCAGTTCCACAAAAAACAAAGATTTACAATTTACACCAATATACTAGAGTTTTAT
CTATCAGAGATGAAGAAAACTTACTAACCATAGAAATTGAAGTTATA
Found at i:31167 original size:22 final size:22
Alignment explanation
Indices: 31113--31220 Score: 116
Period size: 22 Copynumber: 5.0 Consensus size: 22
31103 ATACAATCAT
**
31113 ACCAAGGACGAGAAGA-TGTTC
1 ACCAAGGACGAGAAGACCATTC
**
31134 ATGAA-GACGAGAAGACCATTC
1 ACCAAGGACGAGAAGACCATTC
31155 ACCAAGGACGAGAAGACCATTC
1 ACCAAGGACGAGAAGACCATTC
*
31177 ACCAAGGACGAGAAGGCCATTC
1 ACCAAGGACGAGAAGACCATTC
* *
31199 A-TAAAGAC-ATGAAGACCATTC
1 ACCAAGGACGA-GAAGACCATTC
31220 A
1 A
31221 TAAAGACATG
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
20 11 0.15
21 25 0.34
22 38 0.51
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (22 bp):
ACCAAGGACGAGAAGACCATTC
Found at i:31217 original size:21 final size:21
Alignment explanation
Indices: 31131--31265 Score: 132
Period size: 21 Copynumber: 6.3 Consensus size: 21
31121 CGAGAAGATG
*
31131 TTCATGAAGACGAGAAGACCA
1 TTCATAAAGACGAGAAGACCA
* *
31152 TTCACCAAGGACGAGAAGACCA
1 TTCA-TAAAGACGAGAAGACCA
* * *
31174 TTCACCAAGGACGAGAAGGCCA
1 TTCA-TAAAGACGAGAAGACCA
31196 TTCATAAAGAC-ATGAAGACCA
1 TTCATAAAGACGA-GAAGACCA
*
31217 TTCATAAAGAC-ATGAAGACCC
1 TTCATAAAGACGA-GAAGACCA
31238 TTCATAAAGAC-ATGAAGACCA
1 TTCATAAAGACGA-GAAGACCA
31259 CTTCATA
1 -TTCATA
31266 TGGGAGGTAA
Statistics
Matches: 102, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
20 1 0.01
21 56 0.55
22 45 0.44
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (21 bp):
TTCATAAAGACGAGAAGACCA
Found at i:31235 original size:64 final size:64
Alignment explanation
Indices: 31113--31241 Score: 147
Period size: 64 Copynumber: 2.0 Consensus size: 64
31103 ATACAATCAT
** * *
31113 ACCAAGGACGAGAAGATGTTCATGAAGACGAGAAGACCATTCACCAAGGACGAGAAGACCATTC
1 ACCAAGGACGAGAAGACATTCATAAAGACGAGAAGACCATTCACCAAAGACGAGAAGACCATTC
* * *
31177 ACCAAGGACGAGAAGGCCATTCATAAAGAC-ATGAAGACCATTCA-TAAAGAC-ATGAAGACCCT
1 ACCAAGGACGAGAA-GACATTCATAAAGACGA-GAAGACCATTCACCAAAGACGA-GAAGACCAT
31239 TC
63 TC
31241 A
1 A
31242 TAAAGACATG
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
63 1 0.02
64 31 0.56
65 23 0.42
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14
Consensus pattern (64 bp):
ACCAAGGACGAGAAGACATTCATAAAGACGAGAAGACCATTCACCAAAGACGAGAAGACCATTC
Found at i:35382 original size:125 final size:125
Alignment explanation
Indices: 35126--35390 Score: 376
Period size: 125 Copynumber: 2.1 Consensus size: 125
35116 AGAACATTCA
* * *
35126 AGTTATGAT-ATGTTGGGGCACGACTGTACCCACATCATGTTGAGATGACAAGATTCGGACCAAG
1 AGTTAAGATAATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAG
* * *
35190 GAGGCATGAAGAATGATCCTTACAATTTAAGGTGATGGGGGTATTTTGAAGGCCCGTACC
66 AAGGCATGAAGAATGAGCCTTACAATTTAAGGTGATGGGGGCATTTTGAAGGCCCGTACC
*
35250 AGTTAAGATAATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATAT-AGACCAA
1 AGTTAAGATAATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGAT-TCAGACCAA
* * *
35314 GAAGGCCTTG-AGAATGAGCCTTACAATTTGAGGTG-TTGGGGCATTTTGAAGGCCCGTACC
65 GAAGG-CATGAAGAATGAGCCTTACAATTTAAGGTGATGGGGGCATTTTGAAGGCCCGTACC
*
35374 AGTATAAGATGATGTTG
1 AGT-TAAGATAATGTTG
35391 CAGCACTAGT
Statistics
Matches: 126, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
124 34 0.27
125 88 0.70
126 4 0.03
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (125 bp):
AGTTAAGATAATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAG
AAGGCATGAAGAATGAGCCTTACAATTTAAGGTGATGGGGGCATTTTGAAGGCCCGTACC
Found at i:36562 original size:37 final size:35
Alignment explanation
Indices: 36521--36626 Score: 124
Period size: 37 Copynumber: 2.9 Consensus size: 35
36511 GGCAAAGTCA
*
36521 ATCTTAAGCCTTCACCGAAGATTAGTGAAGCAACTCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAA-T-C
*
36558 ATCTTAAGCCTTCACCGAAGAGT-GTTGAAGCTGATC
1 ATCTTAAGCCTTCACCGAAGAGTAG-TGAAGC-AATC
* *
36594 AGTCTTAAGCCTTTACCGAAGAGTATTGAAGCA
1 A-TCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
36627 TGTATGTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
36 3 0.05
37 56 0.93
38 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (35 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATC
Found at i:36993 original size:54 final size:54
Alignment explanation
Indices: 36928--37312 Score: 493
Period size: 54 Copynumber: 7.1 Consensus size: 54
36918 AAGATTATTT
* * * * ** *
36928 GAGTTCCATACTTCTTAAAGAAAGAAGGAGC-AATCCCGTTTGAAGAAGACGTTC
1 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAA-CCCGTAAGAAGAAGATGTTC
* *
36982 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATTTTC
1 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTC
** * *
37036 GAGTTCTATACTCGTTGAAAGAAAGAGGGAGCAAACCCGTAAGAAGAGGATGTTC
1 GAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTC
* * * *
37091 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAAAAGATTTTT
1 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTC
*
37145 GAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTT
1 GAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTC
* * * * *
37200 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCATAAGAAGATGATGTTT
1 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTC
* * *
37254 GAGTTCTATACTCCCTAGAGAAAGAGGGAGTGAACCCATAAGAAGAAGATTGTTC
1 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGA-TGTTC
37309 GAGT
1 GAGT
37313 CTTCTAATCT
Statistics
Matches: 293, Mismatches: 34, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
54 185 0.63
55 108 0.37
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (54 bp):
GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTC
Found at i:37106 original size:109 final size:108
Alignment explanation
Indices: 36915--37312 Score: 537
Period size: 109 Copynumber: 3.6 Consensus size: 108
36905 AGTGAAGCAA
* * * * * ** *
36915 AAGAAGATTATTTGAGTTCCATACTTCTTAAAGAAAGAAGGAGCAATCCCGTTTGAAGAAGACGT
1 AAGAAGATT-TTTGAGTTCTATACTCCCTAAAGAAAGAGGGAGCAAACCCGTAAGAAGAAGATGT
36980 TCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
65 TCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* ** *
37024 AAGAAGATTTTCGAGTTCTATACTCGTTGAAAGAAAGAGGGAGCAAACCCGTAAGAAGAGGATGT
1 AAGAAGATTTTTGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCAAACCCGTAAGAAGAAGATGT
37089 TCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
65 TCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* *
37133 AAAAAGATTTTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGT
1 AAGAAGATTTTTGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCAAACCCGTAAGAAGAAGATGT
* * *
37198 TTGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCATAAG
65 TCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTAAG
* * * ** *
37242 AAGATGATGTTTGAGTTCTATACTCCCTAGAGAAAGAGGGAGTGAACCCATAAGAAGAAGATTGT
1 AAGAAGATTTTTGAGTTCTATACTCCCTAAAGAAAGAGGGAGCAAACCCGTAAGAAGAAGA-TGT
37307 TCGAGT
65 TCGAGT
37313 CTTCTAATCT
Statistics
Matches: 260, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
108 46 0.18
109 214 0.82
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (108 bp):
AAGAAGATTTTTGAGTTCTATACTCCCTAAAGAAAGAGGGAGCAAACCCGTAAGAAGAAGATGTT
CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
Found at i:37360 original size:55 final size:55
Alignment explanation
Indices: 37298--37485 Score: 292
Period size: 55 Copynumber: 3.4 Consensus size: 55
37288 CCCATAAGAA
* *
37298 GAAGATTGTTCGAGTCTTCTAATCTCTGAACGAATAGAGAGCGGACACGATTGTT
1 GAAGATTGTTCGAGTCTTCTACTCTTTGAACGAATAGAGAGCGGACACGATTGTT
* *
37353 GAAGATTGTTCGAGTCTTTTACTCTTTGAACGAATAGAGAGCGGACACGATTATT
1 GAAGATTGTTCGAGTCTTCTACTCTTTGAACGAATAGAGAGCGGACACGATTGTT
37408 GAAGATTGTTCGAGTC-TCATACTCTTTGAA-GAAATAGAGAGCGGACACGATTGTT
1 GAAGATTGTTCGAGTCTTC-TACTCTTTGAACG-AATAGAGAGCGGACACGATTGTT
*
37463 GAAGATTGTTCGAGT-TCCTACTC
1 GAAGATTGTTCGAGTCTTCTACTC
37486 CCTAAAGAAA
Statistics
Matches: 123, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
54 7 0.06
55 116 0.94
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTCTACTCTTTGAACGAATAGAGAGCGGACACGATTGTT
Found at i:37521 original size:54 final size:54
Alignment explanation
Indices: 37463--37577 Score: 194
Period size: 54 Copynumber: 2.1 Consensus size: 54
37453 CACGATTGTT
* *
37463 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGAGAACCCGTTGGCA
1 GAAGATTGATCAAGTTCCTACTCCCTAAAGAAAGAGGGAGAGAACCCGTTGGCA
* *
37517 GAAGATTGATCAAGTTTCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
1 GAAGATTGATCAAGTTCCTACTCCCTAAAGAAAGAGGGAGAGAACCCGTTGGCA
37571 GAAGATT
1 GAAGATT
37578 TTTCAAGTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (54 bp):
GAAGATTGATCAAGTTCCTACTCCCTAAAGAAAGAGGGAGAGAACCCGTTGGCA
Found at i:37585 original size:54 final size:54
Alignment explanation
Indices: 36915--37565 Score: 430
Period size: 54 Copynumber: 11.9 Consensus size: 54
36905 AGTGAAGCAA
* * * * * * **
36915 AAGAAGATTATTTGAGTTCCATACTTCTTAAAGAAAGAAGGAGC-AATCCCGTTTG
1 AAGAAGATTGTTCGAGTTTC-TACTCCCTAAAGAAAGAGGGAGCGAA-CCCGTAAG
* * *
36970 AAGAAGA-CGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
1 AAGAAGATTGTTCGAGTT-TCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
* ** *
37024 AAGAAGATT-TTCGAGTTCTATACTCGTTGAAAGAAAGAGGGAGCAAACCCGTAAG
1 AAGAAGATTGTTCGAGTT-TCTACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAAG
* * *
37079 AAGAGGA-TGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
1 AAGAAGATTGTTCGAGTT-TCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
* * *
37133 AAAAAGATT-TTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTAAG
1 AAGAAGATTGTTCGAGTT-TCTACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAAG
* * * *
37188 AAGAAGA-TGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCATAAG
1 AAGAAGATTGTTCGAGTTTC-TACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
* * * * * *
37242 AAGATGA-TGTTTGAGTTCTATACTCCCTAGAGAAAGAGGGAGTGAACCCATAAG
1 AAGAAGATTGTTCGAGTT-TCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
* * * * * *
37296 AAGAAGATTGTTCGAGTCTTCTAATCTCTGAACGAATAGA--GAGCGGACACG-ATTG
1 AAGAAGATTGTTCGAGT-TTCTACTCCCT-AAAGAA-AGAGGGAGCGAACCCGTA-AG
** * ** * * * *
37351 TTGAAGATTGTTCGAGTCTTTTACTCTTTGAACGAATAGA--GAGCGGACACGATTA-
1 AAGAAGATTGTTCGAGT-TTCTACTCCCT-AAAGAA-AGAGGGAGCGAACCCG-TAAG
** * ** * * * * * *
37406 TTGAAGATTGTTCGAGTCTCATACTCTTTGAAGAAATAGAGAGCGGACACG-ATTG
1 AAGAAGATTGTTCGAGTTTC-TACTCCCTAAAGAAAGAGGGAGCGAACCCGTA-AG
** * * **
37461 TTGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGAGAACCCGTTGG
1 AAGAAGATTGTTCGAGTTTCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
* * *
37515 CAGAAGATTGATCAAGTTTCTACTCCCTAAAGAAAGAGGGAGCGAACCCGT
1 AAGAAGATTGTTCGAGTTTCTACTCCCTAAAGAAAGAGGGAGCGAACCCGT
37566 TGGCAGAAGA
Statistics
Matches: 495, Mismatches: 78, Indels: 47
0.80 0.13 0.08
Matches are distributed among these distances:
53 2 0.00
54 258 0.52
55 227 0.46
56 5 0.01
57 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (54 bp):
AAGAAGATTGTTCGAGTTTCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
Found at i:45932 original size:20 final size:20
Alignment explanation
Indices: 45907--45956 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
45897 ATTTATTCAA
45907 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
45927 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
*
45947 TGGTGTATCG
1 TGGTGCATCG
45957 GTACACTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:46617 original size:22 final size:20
Alignment explanation
Indices: 46581--46684 Score: 68
Period size: 22 Copynumber: 4.9 Consensus size: 20
46571 AGATCCAATC
*
46581 AAAATAAAGAGAAGAAACAAAGA
1 AAAAAAAAGA-AAGAAA-AAA-A
*
46604 AAAAAAAAGAAAGAGCAAAAA
1 AAAAAAAAGAAAGA-AAAAAA
* *
46625 AAGAAAGAGCAAAGAGAAAAAA
1 AAAAAAAAG-AAAGA-AAAAAA
*
46647 ATAAAGAAAA-AAAG-AAAAAG
1 A-AAA-AAAAGAAAGAAAAAAA
*
46667 AAAAAAAACAAAGAAAAA
1 AAAAAAAAGAAAGAAAAA
46685 GGGACGAGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
18 4 0.06
19 7 0.10
20 10 0.15
21 8 0.12
22 23 0.34
23 12 0.18
24 3 0.04
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGAAAGAAAAAAA
Found at i:46625 original size:15 final size:15
Alignment explanation
Indices: 46605--46637 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
46595 AAACAAAGAA
46605 AAAAAAAGAAAGAGC
1 AAAAAAAGAAAGAGC
46620 AAAAAAAGAAAGAGC
1 AAAAAAAGAAAGAGC
46635 AAA
1 AAA
46638 GAGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAGAGC
Found at i:46627 original size:25 final size:27
Alignment explanation
Indices: 46581--46684 Score: 76
Period size: 27 Copynumber: 4.0 Consensus size: 27
46571 AGATCCAATC
*
46581 AAAATAAAGAGAAGAAACAAAGAAAAA
1 AAAAGAAAGAGAAGAAACAAAGAAAAA
* *
46608 AAAAGAAAGAGCA-AAA-AAAGAAAGAG
1 AAAAGAAAGAGAAGAAACAAAGAAA-AA
* * *
46634 CAAAG--AGA-AAAAAATAAAGAAAAA
1 AAAAGAAAGAGAAGAAACAAAGAAAAA
* *
46658 AAGAA-AAAGAAAAAAAACAAAGAAAAA
1 AA-AAGAAAGAGAAGAAACAAAGAAAAA
46685 GGGACGAGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
23 1 0.02
24 8 0.13
25 16 0.26
26 11 0.18
27 26 0.42
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (27 bp):
AAAAGAAAGAGAAGAAACAAAGAAAAA
Found at i:46656 original size:12 final size:13
Alignment explanation
Indices: 46635--46684 Score: 64
Period size: 14 Copynumber: 3.7 Consensus size: 13
46625 AAGAAAGAGC
*
46635 AAAGAGAAAAAAAT
1 AAAGA-AAAAAAAA
46649 AAAGAAAAAAAGAA
1 AAAGAAAAAAA-AA
*
46663 AAAGAAAAAAAAC
1 AAAGAAAAAAAAA
46676 AAAGAAAAA
1 AAAGAAAAA
46685 GGGACGAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 16 0.48
14 17 0.52
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:46658 original size:14 final size:13
Alignment explanation
Indices: 46603--46684 Score: 67
Period size: 13 Copynumber: 6.2 Consensus size: 13
46593 AGAAACAAAG
46603 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
*
46616 GAGCAAAAAAAGAAA
1 -A-AAAAAAAAGAAA
* ** *
46631 GAGCAAAGAG-AA
1 AAAAAAAAAGAAA
*
46643 AAAAATAAAGAAA
1 AAAAAAAAAGAAA
46656 AAAAGAAAAAGAAA
1 AAAA-AAAAAGAAA
*
46670 AAAAACAAAGAAA
1 AAAAAAAAAGAAA
46683 AA
1 AA
46685 GGGACGAGAA
Statistics
Matches: 52, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
12 7 0.13
13 21 0.40
14 13 0.25
15 11 0.21
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.01
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:46671 original size:15 final size:15
Alignment explanation
Indices: 46599--46674 Score: 64
Period size: 15 Copynumber: 4.8 Consensus size: 15
46589 GAGAAGAAAC
46599 AAAGAAAAAAAAAGAA
1 AAAG-AAAAAAAAGAA
* *
46615 AGAGCAAAAAAAGAA
1 AAAGAAAAAAAAGAA
* *
46630 AGAGCAAAGAGAAAAAAA
1 AAAG-AAA-A-AAAAGAA
46648 TAAAG-AAAAAAAGAA
1 -AAAGAAAAAAAAGAA
46663 AAAGAAAAAAAA
1 AAAGAAAAAAAA
46675 CAAAGAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
14 4 0.08
15 27 0.55
16 6 0.12
17 3 0.06
18 6 0.12
19 3 0.06
ACGTcount: A:0.80, C:0.03, G:0.16, T:0.01
Consensus pattern (15 bp):
AAAGAAAAAAAAGAA
Found at i:46685 original size:19 final size:18
Alignment explanation
Indices: 46643--46685 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
46633 GCAAAGAGAA
* *
46643 AAAAATAAAGAAAAAAAG
1 AAAAAGAAAAAAAAAAAG
46661 AAAAAGAAAAAAAACAAAG
1 AAAAAGAAAAAAAA-AAAG
46680 AAAAAG
1 AAAAAG
46686 GGACGAGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAAAG
Found at i:48074 original size:131 final size:131
Alignment explanation
Indices: 47729--48064 Score: 398
Period size: 131 Copynumber: 2.6 Consensus size: 131
47719 GTTTGAAGTG
* ** * *
47729 TGTCATCCACCGACCAGACCTCCTCATCAC--AGAAGTTGTGTCATCC-CTAGATAACTAACCGT
1 TGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCA-CCACTAGATAACCAACTGT
*
47791 CCTCATCATGTAAGAACCGTGTTATCATCCCTAAAGATGGTCTATCATCCTCATCACATAAGAAC
65 CCTCATCATGTAAGAACCGTGTTATCATCCCTAAAGATGGTCTACCATCCTCATCACATAAGAAC
47856 CA
130 CA
* * * *
47858 TGTCATCCACCGACTAGACCTCCTCATCATGTAGGAGCCGTGTCACCCCTAGATAACCATCTGTC
1 TGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCACTAGATAACCAACTGTC
* *** *
47923 CTCATCATGTAAGAACCGTGTTATCATCCCTAAAGAT-GTCTAGCCATCCTTATCGTGTAGGAAC
66 CTCATCATGTAAGAACCGTGTTATCATCCCTAAAGATGGTCTA-CCATCCTCATCACATAAGAAC
**
47987 TG
130 CA
* *
47989 TGTCATCTC-TCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCATTAGA-AGACCAGACT
1 TGTCATC-CACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCACTAGATA-ACCA-ACT
*
48052 -TCTTCATCATGTA
63 GTCCTCATCATGTA
48065 TGAGTCGTGT
Statistics
Matches: 177, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
129 28 0.16
130 8 0.05
131 138 0.78
132 3 0.02
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (131 bp):
TGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCACTAGATAACCAACTGTC
CTCATCATGTAAGAACCGTGTTATCATCCCTAAAGATGGTCTACCATCCTCATCACATAAGAACC
A
Found at i:50706 original size:26 final size:26
Alignment explanation
Indices: 50644--50711 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
50634 ATGTGATTTG
** *
50644 CTTTGTAACTAGGCATGTATGCCTTA
1 CTTTGTAACCGGGCCTGTATGCCTTA
*
50670 CTTTGTAACCGGGCCTGTGTGCCTTA
1 CTTTGTAACCGGGCCTGTATGCCTTA
50696 CTTTGTAACCGGGCCT
1 CTTTGTAACCGGGCCT
50712 TCGGGCTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (26 bp):
CTTTGTAACCGGGCCTGTATGCCTTA
Found at i:50742 original size:12 final size:12
Alignment explanation
Indices: 50720--50770 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
50710 CTTCGGGCTT
*
50720 TATAAATAATAA
1 TATATATAATAA
* *
50732 TATTTATAATAT
1 TATATATAATAA
50744 TATATATAATAA
1 TATATATAATAA
50756 CGTATATAT-ATAA
1 --TATATATAATAA
50769 TA
1 TA
50771 ATCGTCACTC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.06
12 19 0.59
13 4 0.12
14 7 0.22
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (12 bp):
TATATATAATAA
Found at i:51010 original size:42 final size:42
Alignment explanation
Indices: 50950--51141 Score: 119
Period size: 42 Copynumber: 4.5 Consensus size: 42
50940 GTGCTCCTGC
* *
50950 TTCACTACTCTTCTGTGAAGGTTGA-ATGATTGAGAATCTAAT
1 TTCACTACTCTTCCGTGAAGATTGACATGATTGAGAATCT-AT
* ** *
50992 TTCACTACTCTTCCGTGAAGATCAGACTCACAATTG-G-AT-TAC
1 TTCACTACTCTTCCGTGAAGAT-TGA--CATGATTGAGAATCTAT
* * * * *
51034 TTCACTACTCTTCCGTGAAGTTTGTATACTTTG-CTGAAAATCTGT
1 TTCACTACTCTTCCGTGAAGATTG---AC-ATGATTGAGAATCTAT
* * * *
51079 TCCACTACTCTTCCGTGAAAACTGA-ATGATTGAGAACCTAAT
1 TTCACTACTCTTCCGTGAAGATTGACATGATTGAGAATCT-AT
51121 TTCACTACTCTT-CGTGAAGAT
1 TTCACTACTCTTCCGTGAAGAT
51142 CAAACTCGTA
Statistics
Matches: 110, Mismatches: 27, Indels: 27
0.67 0.16 0.16
Matches are distributed among these distances:
40 2 0.02
41 15 0.14
42 58 0.53
43 3 0.03
44 5 0.05
45 22 0.20
46 5 0.05
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (42 bp):
TTCACTACTCTTCCGTGAAGATTGACATGATTGAGAATCTAT
Found at i:52027 original size:22 final size:22
Alignment explanation
Indices: 51999--52044 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
51989 AAAGCTTTCT
51999 TCTTTGAAAACAGAATCTATCA
1 TCTTTGAAAACAGAATCTATCA
*
52021 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAACAGAATCTATCA
52043 TC
1 TC
52045 CTTACGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (22 bp):
TCTTTGAAAACAGAATCTATCA
Found at i:55572 original size:29 final size:28
Alignment explanation
Indices: 55539--55669 Score: 142
Period size: 29 Copynumber: 4.6 Consensus size: 28
55529 TATTCTGTGG
*
55539 TTTAGTCCTTGAGTTTCTATTTTTGTTAT
1 TTTAGTCCTTAAGTTTCTATTTTT-TTAT
* *
55568 TTTAGTTCTTAAATTTCTATTTTTTCTAT
1 TTTAGTCCTTAAGTTTCTATTTTTT-TAT
* *
55597 TTTAGTCCCTTGAGTTT-T-TATTTTTAT
1 TTTAGT-CCTTAAGTTTCTATTTTTTTAT
55624 TTTAGTCCTTTAAGTTTCTATTTTTTT-T
1 TTTAGTCC-TTAAGTTTCTATTTTTTTAT
55652 ATTTAGTCCTTTAAGTTT
1 -TTTAGTCC-TTAAGTTT
55670 ATGTTTTTGC
Statistics
Matches: 87, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
26 2 0.02
27 16 0.18
28 8 0.09
29 54 0.62
30 7 0.08
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (28 bp):
TTTAGTCCTTAAGTTTCTATTTTTTTAT
Found at i:55657 original size:56 final size:59
Alignment explanation
Indices: 55539--55669 Score: 164
Period size: 56 Copynumber: 2.3 Consensus size: 59
55529 TATTCTGTGG
* *
55539 TTTAGT-CCTTGAGTTTCTATTTTTGTTATTTTAGTTCTTAAATTTCTATTTTTTCTAT
1 TTTAGTCCCTTGAGTTTCTATATTTGTTATTTTAGTCCTTAAATTTCTATTTTTTCTAT
* *
55597 TTTAGTCCCTTGAGTTT-T-TATTT-TTATTTTAGTCCTTTAAGTTTCTATTTTTTTTA-
1 TTTAGTCCCTTGAGTTTCTATATTTGTTATTTTAGTCC-TTAAATTTCTATTTTTTCTAT
* *
55653 TTTAGTCCTTTAAGTTT
1 TTTAGTCCCTTGAGTTT
55670 ATGTTTTTGC
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
56 26 0.40
57 22 0.34
58 7 0.11
59 10 0.15
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (59 bp):
TTTAGTCCCTTGAGTTTCTATATTTGTTATTTTAGTCCTTAAATTTCTATTTTTTCTAT
Found at i:55683 original size:29 final size:28
Alignment explanation
Indices: 55539--55684 Score: 100
Period size: 29 Copynumber: 5.1 Consensus size: 28
55529 TATTCTGTGG
* * *
55539 TTTAGTCC-TTGAGTTTCTATTTTTGTTA
1 TTTAGTCCTTTAAGTTTATATTTTT-CTA
* * *
55567 TTTTAGTTC-TTAAATTTCTATTTTTTCTA
1 -TTTAGTCCTTTAAGTTTATA-TTTTTCTA
* * * *
55596 TTTTAGTCCCTTGAGTTTTTATTTTTAT-
1 T-TTAGTCCTTTAAGTTTATATTTTTCTA
* *
55624 TTTAGTCCTTTAAGTTTCTATTTTTTTTA
1 TTTAGTCCTTTAAGTTTATA-TTTTTCTA
*
55653 TTTAGTCCTTTAAGTTTATGTTTTTGCTA
1 TTTAGTCCTTTAAGTTTATATTTTT-CTA
55682 TTT
1 TTT
55685 GTGTCCTGTA
Statistics
Matches: 95, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
27 16 0.17
28 13 0.14
29 53 0.56
30 13 0.14
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.64
Consensus pattern (28 bp):
TTTAGTCCTTTAAGTTTATATTTTTCTA
Done.