Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 60 of 65
Found at i:11801105 original size:29 final size:29
Alignment explanation
Indices: 11801070--11801129 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
11801060 TTTTCTGCGC
11801070 CAGAAATTCCAAGGCATTTCAATCTGCTT
1 CAGAAATTCCAAGGCATTTCAATCTGCTT
11801099 CAGAAATTCCAAGGCATTTCAATCTGCTT
1 CAGAAATTCCAAGGCATTTCAATCTGCTT
11801128 CA
1 CA
11801130 ACAACTTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (29 bp):
CAGAAATTCCAAGGCATTTCAATCTGCTT
Found at i:11809785 original size:2 final size:2
Alignment explanation
Indices: 11809778--11809816 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11809768 GCCTTCAAAT
11809778 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11809817 TTTGTGATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11810228 original size:26 final size:26
Alignment explanation
Indices: 11810177--11810228 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
11810167 AATATTTAAA
* *
11810177 TAAAAATAAAAATAAATTAAATTTTT
1 TAAAAATAAAAATAAATCAAAATTTT
*
11810203 TAAAAATATAAAAT-TATCAAAATTTT
1 TAAAAATA-AAAATAAATCAAAATTTT
11810229 AAAGTATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
TAAAAATAAAAATAAATCAAAATTTT
Found at i:11813494 original size:14 final size:16
Alignment explanation
Indices: 11813461--11813491 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11813451 ATTTTGTTAC
11813461 TGATATTGTGTTATTT
1 TGATATTGTGTTATTT
11813477 TGATATTG-GTTATTT
1 TGATATTGTGTTATTT
11813492 GATGTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (16 bp):
TGATATTGTGTTATTT
Found at i:11819089 original size:21 final size:19
Alignment explanation
Indices: 11819055--11819093 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
11819045 GATTTTTTGA
11819055 ATTTTTTTTTAAAAATAAT
1 ATTTTTTTTTAAAAATAAT
11819074 ATTTTTATTATTAAAAATAA
1 ATTTTT-TT-TTAAAAATAA
11819094 AAAATATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTTTTTTAAAAATAAT
Found at i:11819526 original size:17 final size:17
Alignment explanation
Indices: 11819506--11819539 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
11819496 TAATATTAAA
11819506 TAAAAAA-AATTTATTTT
1 TAAAAAATAA-TTATTTT
11819523 TAAAAAATAATTATTTT
1 TAAAAAATAATTATTTT
11819540 ATGTATGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAAAATAATTATTTT
Found at i:11825086 original size:2 final size:2
Alignment explanation
Indices: 11825079--11825109 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11825069 TTTTTAAGAT
11825079 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11825110 TACTAACCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11829461 original size:19 final size:19
Alignment explanation
Indices: 11829437--11829490 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
11829427 ACAAAAAGAG
11829437 AAAAG-AAAAAAAAGAAACA
1 AAAAGAAAAAAAAAGAAA-A
*
11829456 AAAAGAGAAACAAAAAGCAAA
1 AAAAGA-AAA-AAAAAGAAAA
11829477 AAAAGAAAAAAAAA
1 AAAAGAAAAAAAAA
11829491 AGGGACGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 10 0.32
20 3 0.10
21 10 0.32
22 8 0.26
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAAAAGAAAA
Found at i:11829472 original size:12 final size:12
Alignment explanation
Indices: 11829426--11829472 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
11829416 ATCCAATCAG
11829426 AACAAAAAGAGAA
1 AACAAAAAGAG-A
* *
11829439 AAGAAAAAAAAGA
1 AA-CAAAAAGAGA
11829452 AACAAAAAGAGA
1 AACAAAAAGAGA
11829464 AACAAAAAG
1 AACAAAAAG
11829473 CAAAAAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 17 0.59
13 5 0.17
14 7 0.24
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (12 bp):
AACAAAAAGAGA
Found at i:11830553 original size:32 final size:32
Alignment explanation
Indices: 11830517--11830590 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
11830507 ACATCGATAA
* *
11830517 AGATTCAATAACAAATGTTGGGGCATATTTAG
1 AGATTCAACAACAAATATTGGGGCATATTTAG
* * *
11830549 AGATTCAACATCGAATATTGGGGCATATTTGG
1 AGATTCAACAACAAATATTGGGGCATATTTAG
*
11830581 GGATTCAACA
1 AGATTCAACA
11830591 TCCTGATGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (32 bp):
AGATTCAACAACAAATATTGGGGCATATTTAG
Found at i:11831309 original size:43 final size:44
Alignment explanation
Indices: 11831210--11831333 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 44
11831200 GCGAAGGGGC
*
11831210 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAATGA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAATCA
* * * *
11831254 -ATCTACGATTTCAACTCCACGATGGAGGATATCGTGCCCA-CA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAATCA
* * *
11831296 CATCCACGGTTTCAACTTCACGACGAAGGGA-ATCGTAC
1 CATCCACGATTTCAACTCCACGACGGA-GGATATCGTAC
11831334 ACACAAGCAG
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 1 0.01
43 63 0.94
44 3 0.04
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (44 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAATCA
Found at i:11831430 original size:335 final size:335
Alignment explanation
Indices: 11830820--11831517 Score: 1164
Period size: 335 Copynumber: 2.1 Consensus size: 335
11830810 TGGTGAATGC
* *
11830820 TCAACTTCACAACGAATGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGAT
1 TCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGAT
* *
11830885 TTCAACTCCACGACGGAGGATATCGTACCAACGAAACCATGATTTCAACTCCATGACGGAGGATA
66 TTCAACTCCACGACGGAGGATATCGTACCAACGAAACCACGATTTCAACTCCACGACGGAGGATA
*
11830950 TCGTGCCCACACATTCACGGTTTCAACTTCACGACGAAGGGAATCGTACACACAAACAACATCCA
131 TCGTGCCCACACATCCACGGTTTCAACTTCACGACGAAGGGAATCGTACACACAAACAACATCCA
** * * *
11831015 TCTATAGATTGGATTTCAACTTCATGACGAAGGATGTCCAACTCAAAGAATGAGTGTCTGTCAAT
196 TCTATAGATAAGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAATGTCTGTCAAT
*
11831080 AAACTTCTCAGTTTCAAAGTCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAGCACA
261 AAACTTCTCAGTTTCAAAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAGCACA
11831145 AGCTTGGATT
326 AGCTTGGATT
* *
11831155 TCAACTTCATGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGGCGAAGGGGCCATCCACGAT
1 TCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGAT
* * * *
11831220 TTCAACTCCACGACGGAGGATATCGTACCAATGAATCTACGATTTCAACTCCACGATGGAGGATA
66 TTCAACTCCACGACGGAGGATATCGTACCAACGAAACCACGATTTCAACTCCACGACGGAGGATA
* *
11831285 TCGTGCCCACACATCCACGGTTTCAACTTCACGACGAAGGGAATCGTACACACAAGCAGCATCCA
131 TCGTGCCCACACATCCACGGTTTCAACTTCACGACGAAGGGAATCGTACACACAAACAACATCCA
* *
11831350 TCTCTAGATAAGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAATGTCTGTTAAT
196 TCTATAGATAAGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAATGTCTGTCAAT
* * *
11831415 AAACTT-TCCAGTTTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAGTAC
261 AAACTTCT-CAGTTTCAAAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAGCAC
11831479 AAGCTTGGATT
325 AAGCTTGGATT
11831490 TCAACTTCACGACGAAGGATATTCAAGT
1 TCAACTTCACGACGAAGGATATTCAAGT
11831518 TAAAACTTCA
Statistics
Matches: 337, Mismatches: 25, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
334 1 0.00
335 336 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (335 bp):
TCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGAT
TTCAACTCCACGACGGAGGATATCGTACCAACGAAACCACGATTTCAACTCCACGACGGAGGATA
TCGTGCCCACACATCCACGGTTTCAACTTCACGACGAAGGGAATCGTACACACAAACAACATCCA
TCTATAGATAAGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAATGTCTGTCAAT
AAACTTCTCAGTTTCAAAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAGCACA
AGCTTGGATT
Found at i:11831608 original size:42 final size:42
Alignment explanation
Indices: 11831545--11831674 Score: 179
Period size: 42 Copynumber: 3.1 Consensus size: 42
11831535 GAAGCAAATC
*
11831545 CATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGT
1 CATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGT
* * *
11831587 CATCAATAAGTCTTTCTAGCATGGTGTTTAAATCCTTTGGGT
1 CATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGT
* * * * *
11831629 CGTCTATAAGACTTCCGAGCATGATGCTTAAATCCTTCGGGT
1 CATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGT
11831671 CATC
1 CATC
11831675 TGTAAACCTT
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (42 bp):
CATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGT
Found at i:11831686 original size:42 final size:41
Alignment explanation
Indices: 11831560--11831694 Score: 162
Period size: 42 Copynumber: 3.2 Consensus size: 41
11831550 GTAAGTCTTT
* * *
11831560 CGAGCATGATGTTTAAATCCTTCGGGTCATCAATAAGTCTTT
1 CGAGCATGATGTTTAAATCCTTCGGGTCATCTATAA-ACTTC
* * * *
11831602 CTAGCATGGTGTTTAAATCCTTTGGGTCGTCTATAAGACTTC
1 CGAGCATGATGTTTAAATCCTTCGGGTCATCTATAA-ACTTC
* *
11831644 CGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAACCTTC
1 CGAGCATGATGTTTAAATCCTTCGGGTCATCTATAAA-CTTC
11831686 CGAGCATGA
1 CGAGCATGA
11831695 CGATCAAGTC
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 1 0.01
42 78 0.99
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (41 bp):
CGAGCATGATGTTTAAATCCTTCGGGTCATCTATAAACTTC
Found at i:11831717 original size:42 final size:41
Alignment explanation
Indices: 11831640--11831726 Score: 95
Period size: 42 Copynumber: 2.1 Consensus size: 41
11831630 GTCTATAAGA
* * * *
11831640 CTTCCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAAC
1 CTTCCGAGCATGACGATCAAATCCTTCGGGCCATCT-TAAAC
* *
11831682 CTTCCGAGCATGACGATCAAGTCC-TCTGGGCCATCTTAAGC
1 CTTCCGAGCATGACGATCAAATCCTTC-GGGCCATCTTAAAC
11831723 CTTC
1 CTTC
11831727 ACCAAAGAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 10 0.26
42 28 0.74
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.29
Consensus pattern (41 bp):
CTTCCGAGCATGACGATCAAATCCTTCGGGCCATCTTAAAC
Found at i:11831755 original size:37 final size:37
Alignment explanation
Indices: 11831714--11831785 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
11831704 CCTCTGGGCC
11831714 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCA
11831751 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAAT
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAAT
11831786 ATAAGATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCA
Found at i:11832003 original size:113 final size:113
Alignment explanation
Indices: 11831796--11832391 Score: 786
Period size: 113 Copynumber: 5.3 Consensus size: 113
11831786 ATAAGATTTT
* *
11831796 ATATTCCCTTCAG-AGTAAGCGAAACA-AGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAG
1 ATATTCCC-TCAGAAG-AAGCGGAACAGA-TCCCTCTTTTCCAAGATTTGATATTCCCTTCAGAG
*
11831859 TAAGTGGAACAAGTCTTACCACGATTCAATGGATCAACTCTCCCAGATCTG
63 TAAGTGGAACAAGTCTTGCCACGATTCAATGGATCAACTCTCCCAGATCTG
* * *
11831910 ATATTCCCTCAGAATAAGCGAAACA-AGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTA
1 ATATTCCCTCAGAAGAAGCGGAACAGA-TCCCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTA
11831974 AGTGGAACAAGTCTTGCCACGATTCAATGGATCAACTCTCCCAGATCTG
65 AGTGGAACAAGTCTTGCCACGATTCAATGGATCAACTCTCCCAGATCTG
* * *
11832023 ATATTCTCTCAAAAGAAGCGGAACAGATCCCTCTTATCCAAGATTTGATATTCCCTTCAGAGTAA
1 ATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAA
* *
11832088 GTAGAACAAGTCTTGCCACGATTCAATGGATCAATTCTCCCAGATCTG
66 GTGGAACAAGTCTTGCCACGATTCAATGGATCAACTCTCCCAGATCTG
* * **
11832136 ATATTCCCTCAGAAGAAGCGGAACAGATCCTTGTTTTTTAAGATTTGATATTCCC-T--GAGTGA
1 ATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTTTTCCAAGATTTGATATTCCCTTCAGAGT-A
* *
11832198 CAGCGGAACAAGTCTTGCCATGATTCAATGGATCAACTCTCCCAGATCTG
65 -AGTGGAACAAGTCTTGCCACGATTCAATGGATCAACTCTCCCAGATCTG
* *
11832248 ATATTCCCTCAGAAGAAGCGGAATAGATCCCTCTTTTTCAAGATTTGATATTCCC-T--GAGTGA
1 ATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTTTTCCAAGATTTGATATTCCCTTCAGAGT-A
* * *
11832310 CAGTGGAACAAGTC-TACC-CTGATTCAATAGATCAACATC-CTCAGATCTG
65 -AGTGGAACAAGTCTTGCCAC-GATTCAATGGATCAAC-TCTCCCAGATCTG
* *
11832359 ATATTCCCTGAG-TGACAGCGGAACAGATCCCTC
1 ATATTCCCTCAGAAGA-AGCGGAACAGATCCCTC
11832392 ATCATATTTC
Statistics
Matches: 442, Mismatches: 33, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
110 6 0.01
111 55 0.12
112 119 0.27
113 252 0.57
114 10 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (113 bp):
ATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAA
GTGGAACAAGTCTTGCCACGATTCAATGGATCAACTCTCCCAGATCTG
Found at i:11834540 original size:2 final size:2
Alignment explanation
Indices: 11834535--11834562 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11834525 CAAGATATGG
11834535 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
11834563 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:11834567 original size:2 final size:2
Alignment explanation
Indices: 11834562--11834613 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
11834552 ACACACACAC
11834562 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
11834604 AT AT AT AT AT
1 AT AT AT AT AT
11834614 CCTTTTGTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11838456 original size:20 final size:20
Alignment explanation
Indices: 11838431--11838523 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
11838421 TTTTCCCAAT
11838431 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
11838451 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
11838471 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
11838492 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
11838513 TCGCAATGCGA
1 TCGCAATGCGA
11838524 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:11838473 original size:41 final size:41
Alignment explanation
Indices: 11838428--11838523 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
11838418 CGATTTTCCC
11838428 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
11838469 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
11838510 AAATCGCAATGCGA
1 AATTCGCAATGCGA
11838524 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:11838477 original size:21 final size:20
Alignment explanation
Indices: 11838431--11838523 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
11838421 TTTTCCCAAT
*
11838431 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
11838451 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
11838471 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
11838492 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
11838513 TCGCAATGCGA
1 TCGCAATGCGA
11838524 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:11838536 original size:41 final size:41
Alignment explanation
Indices: 11838450--11838584 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
11838440 GAATAAGTAA
* * *
11838450 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
11838491 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
11838532 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
11838573 TTCGCAACGCGA
1 ATCGCAACGCGA
11838585 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:11838537 original size:20 final size:20
Alignment explanation
Indices: 11838512--11838605 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
11838502 AATTGGGAAA
*
11838512 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
11838532 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
11838553 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
11838573 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
11838593 TTCGCAACGCGAT
1 ATCGCAACGCGAT
11838606 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:11839187 original size:19 final size:19
Alignment explanation
Indices: 11839163--11839207 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
11839153 GCAACGAGAT
*
11839163 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
11839182 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
11839201 AATCGCA
1 AATCGCA
11839208 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:11839225 original size:19 final size:19
Alignment explanation
Indices: 11839203--11839292 Score: 137
Period size: 19 Copynumber: 4.7 Consensus size: 19
11839193 GAAACCAAAA
11839203 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
11839222 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
11839241 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
11839260 TCGCGGTTGCGATTTTCATT
1 TCGC-ATTGCGATTTTCATT
11839280 TCG-AGTTGCGATT
1 TCGCA-TTGCGATT
11839293 GTCTGGTCGC
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
19 49 0.73
20 18 0.27
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:11839312 original size:33 final size:33
Alignment explanation
Indices: 11839275--11839362 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
11839265 GTTGCGATTT
* * *
11839275 TCATTTCGAGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
11839308 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
11839341 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
11839363 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.24, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:11839364 original size:20 final size:20
Alignment explanation
Indices: 11839330--11839387 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
11839320 GCGATTCTCT
**
11839330 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
11839350 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
11839370 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
11839388 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:11841468 original size:42 final size:42
Alignment explanation
Indices: 11841388--11841510 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
11841378 GCCCGACTCG
* * * * * * *
11841388 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGGGTCCCCTCCCACCGTTCAAGAGGCC
11841430 CCTATCATTCCTCGAGGGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGGGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
11841472 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AG-GGTCCCCTCCCACCGTTCAAGAG
11841511 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 60 0.90
43 3 0.04
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGGGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:11841509 original size:21 final size:20
Alignment explanation
Indices: 11841450--11841510 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
11841440 CTCGAGGGTC
11841450 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
11841470 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCACCGTTCAAGAGG
*
11841491 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
11841511 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:11842888 original size:14 final size:14
Alignment explanation
Indices: 11842869--11842904 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
11842859 ATTGTTTAAT
11842869 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
11842883 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
11842897 TGATTTGT
1 TGATTTGT
11842905 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:11843105 original size:19 final size:19
Alignment explanation
Indices: 11843083--11843180 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
11843073 CGAAATTAAA
*
11843083 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
11843102 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
11843118 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
11843135 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
11843151 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
11843168 TTCGCATTGCGAT
1 TTCGCATTGCGAT
11843181 AGTAATTTCC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 12 0.19
16 13 0.21
17 13 0.21
19 24 0.39
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:11843129 original size:33 final size:33
Alignment explanation
Indices: 11843087--11843180 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
11843077 ATTAAATTCG
11843087 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
11843120 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
11843153 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
11843181 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:11845492 original size:12 final size:12
Alignment explanation
Indices: 11845475--11845499 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11845465 TCTTCGGGGA
11845475 CTTTTTCTTCTT
1 CTTTTTCTTCTT
11845487 CTTTTTCTTCTT
1 CTTTTTCTTCTT
11845499 C
1 C
11845500 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:11846996 original size:14 final size:14
Alignment explanation
Indices: 11846977--11847013 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
11846967 CATCAATTAA
11846977 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
11846991 ACAAATCATCTTTT
1 ACAAATCAACATTT
11847005 ACAAATCAA
1 ACAAATCAA
11847014 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:11847385 original size:20 final size:20
Alignment explanation
Indices: 11847360--11847410 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
11847350 ATTCATTTGA
11847360 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGTGAAAATGG
11847380 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGTGAAAATGG
*
11847400 TTATCGCAACG
1 CTATCGCAACG
11847411 AGAATATCGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (20 bp):
CTATCGCAACGTGAAAATGG
Found at i:11847460 original size:14 final size:15
Alignment explanation
Indices: 11847440--11847512 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
11847430 TGATAATCGC
11847440 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
11847455 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
11847472 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
11847490 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
11847506 -TTGCGAT
1 ATTGCGAT
11847513 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:11847477 original size:19 final size:19
Alignment explanation
Indices: 11847436--11847502 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
11847426 GAAATGATAA
11847436 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
11847452 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
11847469 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
11847487 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
11847503 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:11847638 original size:14 final size:14
Alignment explanation
Indices: 11847619--11847655 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
11847609 CATCAATTAA
11847619 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
11847633 ACAAATCATCTTTT
1 ACAAATCAACATTT
11847647 ACAAATCAA
1 ACAAATCAA
11847656 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:11849558 original size:20 final size:19
Alignment explanation
Indices: 11849523--11849578 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
11849513 GAAACTTAAA
11849523 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
11849542 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
*
11849562 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
11849579 AAACCGCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:11849600 original size:14 final size:14
Alignment explanation
Indices: 11849578--11849635 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
11849568 ATGCGAAATG
*
11849578 AAAACCGCAACGAC
1 AAAATCGCAACGAC
*
11849592 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
11849608 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
11849624 AAAATCGCAACG
1 AAAATCGCAACG
11849636 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.28, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:11849624 original size:32 final size:33
Alignment explanation
Indices: 11849562--11849640 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
11849552 GGAAATGGCT
*
11849562 ATCGCAATGCGAAATGAAAACCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAACCGCAACGACAAA
*
11849595 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAACCGCAACGACAAA
11849627 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
11849641 CACAAATTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.25, G:0.19, T:0.09
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAACCGCAACGACAAA
Found at i:11849674 original size:19 final size:19
Alignment explanation
Indices: 11849652--11849780 Score: 75
Period size: 20 Copynumber: 7.3 Consensus size: 19
11849642 ACAAATTGCA
11849652 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
11849671 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
11849685 TTGCGA-TTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
11849703 TTGCGA--TT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
11849716 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
***
11849735 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
** *
11849755 TTGCGATAGTCATTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
11849775 TTGCGA
1 TTGCGA
11849781 AAGTAAACTA
Statistics
Matches: 87, Mismatches: 11, Indels: 23
0.72 0.09 0.19
Matches are distributed among these distances:
13 8 0.09
14 11 0.13
15 4 0.05
16 4 0.05
17 4 0.05
18 11 0.13
19 19 0.22
20 23 0.26
21 3 0.03
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:11849699 original size:32 final size:33
Alignment explanation
Indices: 11849652--11849741 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
11849642 ACAAATTGCA
11849652 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
11849685 TTGCGA-TTTCATTTCGCGTTGCGA-TTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
11849716 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
11849742 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
31 13 0.24
32 35 0.65
33 6 0.11
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:11850273 original size:18 final size:18
Alignment explanation
Indices: 11850247--11850291 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
11850237 GTCGATCAGA
11850247 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGTGAGG
* *
11850265 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTAGGTGAGG
11850283 TGATGGCTC
1 TGATGGCTC
11850292 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.42, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTAGGTGAGG
Found at i:11851628 original size:20 final size:20
Alignment explanation
Indices: 11851603--11851640 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11851593 AATAGTTTCT
11851603 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
11851623 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
11851641 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:11852160 original size:20 final size:20
Alignment explanation
Indices: 11852135--11852228 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
11852125 GATTATGTAT
11852135 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
11852155 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
11852175 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
11852196 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
11852216 TATCGCATTGCGA
1 TATCGCGTTGCGA
11852229 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:11852200 original size:41 final size:42
Alignment explanation
Indices: 11852155--11852290 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
11852145 CGAAAGTCAG
* * * *
11852155 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
11852196 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
11852238 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
11852279 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
11852291 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:11852229 original size:20 final size:20
Alignment explanation
Indices: 11852115--11852229 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
11852105 CGCTTTGAAA
*
11852115 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
11852136 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
11852156 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
11852176 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
11852197 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
11852217 ATCGCATTGCGAT
1 ATCGCATTGCGAT
11852230 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:11852262 original size:20 final size:20
Alignment explanation
Indices: 11852218--11852310 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
11852208 ATAGTCAGTA
*
11852218 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
11852239 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
11852259 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
11852280 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
11852300 TCGCATTGCGA
1 TCGCATTGCGA
11852311 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:11852291 original size:41 final size:41
Alignment explanation
Indices: 11852218--11852313 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
11852208 ATAGTCAGTA
* *
11852218 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
11852259 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
11852300 TCGCATTGCGAATT
1 TCGCATTGCGAATT
11852314 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:11858052 original size:21 final size:21
Alignment explanation
Indices: 11858026--11858070 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11858016 GATTTCTGGG
* *
11858026 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
11858047 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
11858068 CAA
1 CAA
11858071 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:11859753 original size:149 final size:149
Alignment explanation
Indices: 11859571--11859874 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
11859561 GAGTCGAGGG
*
11859571 TCTACGCGGTTCTTTAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTCAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
11859636 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
11859701 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
11859720 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTCAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
11859785 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
11859850 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
11859869 TCTACG
1 TCTACG
11859875 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTCAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:11859897 original size:23 final size:23
Alignment explanation
Indices: 11859853--11859897 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11859843 ATCATTATAT
*
11859853 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
11859876 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
11859898 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:11863005 original size:21 final size:21
Alignment explanation
Indices: 11862979--11863023 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11862969 GATTTCTGGG
* *
11862979 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
11863000 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
11863021 CAA
1 CAA
11863024 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:11864704 original size:149 final size:149
Alignment explanation
Indices: 11864522--11864825 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
11864512 GAGTCGAGGG
*
11864522 TCTACGCGGTTCTTTAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTCAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
11864587 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
11864652 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
11864671 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTCAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
11864736 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
11864801 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
11864820 TCTACG
1 TCTACG
11864826 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTCAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:11864848 original size:23 final size:23
Alignment explanation
Indices: 11864804--11864848 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11864794 ATCATTATAT
*
11864804 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
11864827 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
11864849 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:11870466 original size:20 final size:20
Alignment explanation
Indices: 11870441--11870478 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11870431 TTTTGGTACA
*
11870441 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
11870461 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
11870479 TTTGAAGGGG
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:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:11882510 original size:30 final size:31
Alignment explanation
Indices: 11882464--11882537 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
11882454 TAATCTTTAG
* *
11882464 TGACTACATCTTAATTAAATAAAAAT-AAAA
1 TGACTAAATATTAATTAAATAAAAATGAAAA
* *
11882494 TGATTAAATATTAATTAAATAAAAATGAAAG
1 TGACTAAATATTAATTAAATAAAAATGAAAA
*
11882525 TGACTAGATATTA
1 TGACTAAATATTA
11882538 TGTTTGTTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 23 0.62
31 14 0.38
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (31 bp):
TGACTAAATATTAATTAAATAAAAATGAAAA
Found at i:11884845 original size:3 final size:3
Alignment explanation
Indices: 11884837--11884889 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
11884827 TGTAATTATT
* *
11884837 TAA TAA TAA TATA TAA TAA TAAA TAA -AA TTA TAA TAA T-A TAT TAA
1 TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
11884882 TAA TAA TA
1 TAA TAA TA
11884890 TTAAAAACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.10
3 32 0.76
4 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:11884852 original size:10 final size:10
Alignment explanation
Indices: 11884839--11884886 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
11884829 TAATTATTTA
11884839 ATAATAATAT
1 ATAATAATAT
*
11884849 ATAATAATAA
1 ATAATAATAT
11884859 ATAA-AAT-T
1 ATAATAATAT
11884867 ATAATAATAT
1 ATAATAATAT
11884877 ATTAATAATA
1 A-TAATAATA
11884887 ATATTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 4 0.12
9 6 0.18
10 15 0.45
11 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATAATAT
Found at i:11884870 original size:25 final size:25
Alignment explanation
Indices: 11884842--11884892 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
11884832 TTATTTAATA
11884842 ATAAT-ATATAATAATAAATAAAATT
1 ATAATAATATAATAAT-AATAAAATT
* *
11884867 ATAATAATATATTAATAATAATATT
1 ATAATAATATAATAATAATAAAATT
11884892 A
1 A
11884893 AAAACAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAATAATATAATAATAATAAAATT
Found at i:11885728 original size:241 final size:235
Alignment explanation
Indices: 11885143--11885901 Score: 977
Period size: 236 Copynumber: 3.2 Consensus size: 235
11885133 TGCTCCTTAT
* *
11885143 TCTTCAGATGAGTTCTTCTCATTATGAACACTTCT-GAAAATGTTGATGCTGGTCTATCTCCTTC
1 TCTTCAGATGAGTTCTTCTCATTATGAACATTTCTGGAAAA-GTTGATGCTGATCTATCTCCTTC
11885207 TGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAG
65 TGTGATAGAGTCA-GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAG
11885272 ATAAGTTCTTCTCATTATGAACTTCTCTGGAAA----AGTTGATCCATCGAATGATGAATTCAAA
129 ATAAGTTCTTCTCATTATGAACTTCTCTGGAAATGTGAGTTGATCCATCGAATGATGAATTC-AA
* * * *
11885333 CAAAAGGTTTGACCAAATTCTTCTCATTATGAATTTCTTCTTCC
193 CAAAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
* * *
11885377 TTCTTCAGATGAGTTCTTCTTATTATGAACTCTTTCTGGAAAAGTTGATGTTGATCTATCTCCTT
1 -TCTTCAGATGAGTTCTTCTCATTATGAAC-ATTTCTGGAAAAGTTGATGCTGATCTATCTCCTT
*
11885442 CTGTGATAGAGTCA-CAAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTATTCTTCCTCTTC
64 CTGTGATAGAGTCAGC--AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTC
* * ***
11885506 AGATAAGTTCTTCTCATTATGAGCTTCTTCTGGAAATGTTGATGTTGATCTATCTCCTGTGATAG
127 AGATAAGTTCTTCTCATTATGAACTTC-TCTGGAAATG-TGA-GTTGATCCA--TCGAATGAT-G
*
11885571 AA-TCATACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCC
186 AATTCA-ACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
* * * *
11885621 TCTTCAGATAAGTTCTTCTCATTATTAAC-TTTCTGGAAATGTTGATGCTGATCTATCTCATTCT
1 TCTTCAGATGAGTTCTTCTCATTATGAACATTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCT
* * **
11885685 GTGATAGAATCGAGCAAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
66 GTGATAGAGTC-AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
* *
11885750 TAAGTTCTTCTCGTTATGAACTTCTCTGGAAATGCTGA----A-CCATCGAATGATGAATTCGAG
130 TAAGTTCTTCTCATTATGAACTTCTCTGGAAATG-TGAGTTGATCCATCGAATGATGAATTC-AA
* *
11885810 CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTT
193 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-C
* *
11885854 TCTTCAGATGGGTTCTTCTCATTATGAACTTCTTCTGGAAAAGTTGAT
1 TCTTCAGATGAGTTCTTCTCATTATGAACAT-TTCTGGAAAAGTTGAT
11885902 CCATCGAATG
Statistics
Matches: 460, Mismatches: 42, Indels: 44
0.84 0.08 0.08
Matches are distributed among these distances:
231 3 0.01
232 48 0.10
233 27 0.06
234 4 0.01
235 44 0.10
236 110 0.24
237 13 0.03
240 13 0.03
241 110 0.24
242 2 0.00
243 35 0.08
244 33 0.07
245 15 0.03
246 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (235 bp):
TCTTCAGATGAGTTCTTCTCATTATGAACATTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCT
GTGATAGAGTCAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT
AAGTTCTTCTCATTATGAACTTCTCTGGAAATGTGAGTTGATCCATCGAATGATGAATTCAACAA
AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
Found at i:11885747 original size:121 final size:119
Alignment explanation
Indices: 11885333--11886014 Score: 619
Period size: 121 Copynumber: 5.7 Consensus size: 119
11885323 TGAATTCAAA
* * * * *
11885333 CAAAAGGTTTGACCAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 CAAAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
* * *
11885398 ATTATGAACTCTTTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCA-
64 ATTATGAA--CTTTCTGGAAAAGTTGATGCTGATCTATCT-CATCTGTGATAGAATCAG
* *
11885456 CAAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATAAGTTCTTCTC
1 C--AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTC
* * * *
11885521 ATTATGAGCTTCTTCTGGAAATGTTGATGTTGATCTATCTC--CTGTGATAGAATCATA
64 ATTATGAAC-T-TTCTGGAAAAGTTGATGCTGATCTATCTCATCTGTGATAGAATCA-G
* *
11885578 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATAAGTTCTTCTCAT
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
* *
11885643 TATTAACTTTCTGGAAATGTTGATGCTGATCTATCTCATTCTGTGATAGAATCGAG
66 TATGAACTTTCTGGAAAAGTTGATGCTGATCTATCTCA-TCTGTGATAGAATC-AG
* * *
11885699 CAAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCGT
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
11885764 TATGAACTTCTCTGG--AA----ATGCTGA---A-C-CATC-GAATGAT-GAATTCGAG
66 TATGAACTT-TCTGGAAAAGTTGATGCTGATCTATCTCATCTG--TGATAGAA-TC-AG
* * * **
11885810 CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGGGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATAAGTTCTTCTCA
* * *
11885875 TTATGAACTTCTTCTGGAAAAGTTGAT-C----C-ATC-GA---ATGAT-GAATTCAAA
65 TTATGAAC-T-TTCTGGAAAAGTTGATGCTGATCTATCTCATCTGTGATAGAA-TC-AG
* * * * * *
11885923 CAAAAGGTTTGACCAAATTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 CAAAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
11885988 ATTATGAACTATTTCTGG-AAAGTTGAT
64 ATTATGAAC--TTTCTGGAAAAGTTGAT
11886015 CCATCGAATG
Statistics
Matches: 486, Mismatches: 45, Indels: 66
0.81 0.08 0.11
Matches are distributed among these distances:
109 1 0.00
110 5 0.01
111 49 0.10
112 27 0.06
113 33 0.07
114 64 0.13
115 3 0.01
116 8 0.02
117 2 0.00
118 29 0.06
119 3 0.01
120 81 0.17
121 82 0.17
122 9 0.02
123 53 0.11
124 31 0.06
125 6 0.01
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (119 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
TATGAACTTTCTGGAAAAGTTGATGCTGATCTATCTCATCTGTGATAGAATCAG
Found at i:11885964 original size:114 final size:112
Alignment explanation
Indices: 11885699--11886035 Score: 464
Period size: 113 Copynumber: 3.0 Consensus size: 112
11885689 TAGAATCGAG
* * * *
11885699 CAAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCGT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
11885764 TATGAACTTC-TCTGGAAATGCTGAACCATCGAATGATGAATTCGAG
66 TATGAACTTCTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
* ** *
11885810 CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGGGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCA
11885875 TTATGAACTTCTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
65 TTATGAACTTCTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
* * * *
11885923 CAAAAGGTTTGACCAAATTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 CAAAAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTC
11885988 ATTATGAACTAT-TTCTGG-AAAGTTGATCCATCGAATGATGAATTCAAA
64 ATTATGAACT-TCTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
11886036 TCTTTTCTAA
Statistics
Matches: 200, Mismatches: 21, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
111 38 0.19
112 29 0.14
113 67 0.34
114 64 0.32
115 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTCTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
Found at i:11887203 original size:18 final size:18
Alignment explanation
Indices: 11887180--11887243 Score: 89
Period size: 18 Copynumber: 3.7 Consensus size: 18
11887170 AAAATAAAAG
*
11887180 AATAAATTGAATTTCGAA
1 AATAAATTAAATTTCGAA
11887198 AATAAATTAAATTTCGAA
1 AATAAATTAAATTTCGAA
*
11887216 AATAAATTAAATCTC-AA
1 AATAAATTAAATTTCGAA
11887233 AA-AAA-TAAATT
1 AATAAATTAAATT
11887244 GAATTTAGAG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
15 5 0.12
16 3 0.07
17 4 0.09
18 31 0.72
ACGTcount: A:0.58, C:0.06, G:0.05, T:0.31
Consensus pattern (18 bp):
AATAAATTAAATTTCGAA
Found at i:11887623 original size:10 final size:9
Alignment explanation
Indices: 11887603--11887636 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
11887593 TTGACCCTCC
11887603 TTTTTTATT
1 TTTTTTATT
11887612 TTTTTTATT
1 TTTTTTATT
*
11887621 TTTTTTCTT
1 TTTTTTATT
11887630 TCTTTTT
1 T-TTTTT
11887637 TCATTTCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTATT
Found at i:11895002 original size:15 final size:15
Alignment explanation
Indices: 11894979--11895010 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11894969 TGCAATGAAT
11894979 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
11894994 AATGCATGTATGCAA
1 AATGAATGTATGCAA
11895009 AA
1 AA
11895011 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:11898371 original size:28 final size:26
Alignment explanation
Indices: 11898316--11898373 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
11898306 AAATATTAAT
*
11898316 AAAATAATATATATATAAATACTATG
1 AAAATAATATATATATAAAAACTATG
* *
11898342 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TATATATAAAAACTATG
11898370 AAAA
1 AAAA
11898374 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATATATATAAAAACTATG
Found at i:11899038 original size:33 final size:29
Alignment explanation
Indices: 11899001--11899076 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 29
11898991 AAAAAATAGA
*
11899001 TTAATATATAATTTATAAAAATAGGATATTTAT
1 TTAATATAT-ATTTATAAAAA-A-CATA-TTAT
11899034 TTAATATATA--TATAAAAAACATATTAT
1 TTAATATATATTTATAAAAAACATATTAT
11899061 TTAATATATATTTATA
1 TTAATATATATTTATA
11899077 TGAATAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 14 0.35
28 3 0.08
29 5 0.12
30 8 0.20
32 1 0.03
33 9 0.22
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (29 bp):
TTAATATATATTTATAAAAAACATATTAT
Found at i:11899077 original size:31 final size:33
Alignment explanation
Indices: 11899001--11899077 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 33
11898991 AAAAAATAGA
**
11899001 TTAATATATAATTTATA-AAAATAGGATATTTAT
1 TTAATATAT-ATTTATATAAAATAACATATTTAT
11899034 TT-A-ATATA--TATATAAAA-AACATA-TTAT
1 TTAATATATATTTATATAAAATAACATATTTAT
11899061 TTAATATATATTTATAT
1 TTAATATATATTTATAT
11899078 GAATAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
27 6 0.16
28 9 0.24
29 9 0.24
30 1 0.03
31 9 0.24
32 1 0.03
33 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (33 bp):
TTAATATATATTTATATAAAATAACATATTTAT
Found at i:11899149 original size:13 final size:13
Alignment explanation
Indices: 11899082--11899173 Score: 50
Period size: 13 Copynumber: 6.8 Consensus size: 13
11899072 TTATATGAAT
11899082 AAATAATAATACTTA
1 AAATAATAA-A-TTA
11899097 ATAATAAT-AATTA
1 A-AATAATAAATTA
* *
11899110 AATATATTACAAATA
1 AA-ATAATA-AATTA
11899125 AACAT-ATAAAATTA
1 AA-ATAAT-AAATTA
11899139 AAATAATAAATT-
1 AAATAATAAATTA
*
11899151 AAATTA-AAATATA
1 AAATAATAAAT-TA
11899164 AAAT-ATAAAT
1 AAATAATAAAT
11899174 AAATAGTGAC
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
11 4 0.06
12 8 0.13
13 23 0.37
14 10 0.16
15 11 0.18
16 6 0.10
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATAATAAATTA
Found at i:11899158 original size:24 final size:23
Alignment explanation
Indices: 11899131--11899177 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
11899121 AATAAACATA
11899131 TAAAAT-TAAAATAATAAATTAAAT
1 TAAAATATAAAAT-ATAAA-TAAAT
11899155 TAAAATATAAAATATAAATAAAT
1 TAAAATATAAAATATAAATAAAT
11899178 AGTGACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.23
24 11 0.50
25 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAAATATAAAATATAAATAAAT
Found at i:11899167 original size:18 final size:19
Alignment explanation
Indices: 11899102--11899173 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 19
11899092 ACTTAATAAT
11899102 AATAATTAAATAT--ATTACA
1 AATAA-TAAATATAAATTA-A
*
11899121 AATAA-ACATATAAAATTAA
1 AATAATAAATAT-AAATTAA
11899140 AATAATAAAT-TAAATTAA
1 AATAATAAATATAAATTAA
11899158 AAT-ATAAAATATAAAT
1 AATAAT-AAATATAAAT
11899174 AAATAGTGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
17 7 0.16
18 14 0.31
19 17 0.38
20 7 0.16
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAATAAATATAAATTAA
Found at i:11899176 original size:18 final size:19
Alignment explanation
Indices: 11899122--11899173 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
11899112 TATATTACAA
11899122 ATAAACATATAAAATTAAAAT
1 ATAAA-ATAT-AAATTAAAAT
11899143 A-ATAAAT-TAAATTAAAAT
1 ATA-AAATATAAATTAAAAT
11899161 ATAAAATATAAAT
1 ATAAAATATAAAT
11899174 AAATAGTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 15 0.54
19 7 0.25
20 3 0.11
21 3 0.11
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAAATATAAATTAAAAT
Found at i:11900336 original size:3 final size:3
Alignment explanation
Indices: 11900316--11900386 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
11900306 GCCTGAAGTG
* * *
11900316 TAA TAA -AA TAA TAT TAA TAA TAA TAA T-A TAA TTA TAA T-A TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
11900361 TAA -AA TAA AAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
11900387 AAAATGGATA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 8 0.15
3 46 0.85
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:11900352 original size:11 final size:11
Alignment explanation
Indices: 11900332--11900368 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
11900322 AATAATATTA
*
11900332 ATAATAATAAT
1 ATAATTATAAT
11900343 ATAATTATAAT
1 ATAATTATAAT
*
11900354 ATAATTATAAA
1 ATAATTATAAT
11900365 ATAA
1 ATAA
11900369 AAATAATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAATTATAAT
Found at i:11903493 original size:3 final size:3
Alignment explanation
Indices: 11903482--11903531 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
11903472 ATATATGATG
11903482 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11903529 ATA
1 ATA
11903532 GAGAGAGAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:11904592 original size:14 final size:14
Alignment explanation
Indices: 11904575--11904602 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11904565 TTCATAACAA
11904575 AATTATATAACTAT
1 AATTATATAACTAT
11904589 AATTATATAACTAT
1 AATTATATAACTAT
11904603 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:11905583 original size:35 final size:36
Alignment explanation
Indices: 11905518--11905598 Score: 114
Period size: 35 Copynumber: 2.3 Consensus size: 36
11905508 TATTAAAAAT
*
11905518 AATTATTATATATATAATATTAATAAATTTAATTTA
1 AATTAATATATATATAATATTAATAAATTTAATTTA
* *
11905554 AATTAATATATATAT-ATATTTATATATTTAATTTA
1 AATTAATATATATATAATATTAATAAATTTAATTTA
11905589 AA-T-ATATATA
1 AATTAATATATA
11905599 CCCGGCCCGA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 7 0.17
34 1 0.02
35 20 0.48
36 14 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
AATTAATATATATATAATATTAATAAATTTAATTTA
Found at i:11909159 original size:35 final size:33
Alignment explanation
Indices: 11909103--11909175 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 33
11909093 TGCATGTTCA
11909103 AAATTCCAAAACACTTATTACATTCTAAACCCC
1 AAATTCCAAAACACTTATTACATTCTAAACCCC
* * * *
11909136 AAATTCTAAAATACTTTAATTACATTTTAAACCCT
1 AAATTCCAAAACAC-TT-ATTACATTCTAAACCCC
11909171 AAATT
1 AAATT
11909176 AAAGTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 12 0.35
34 2 0.06
35 20 0.59
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (33 bp):
AAATTCCAAAACACTTATTACATTCTAAACCCC
Found at i:11909220 original size:35 final size:35
Alignment explanation
Indices: 11909171--11909247 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
11909161 TTTAAACCCT
* * *
11909171 AAATTAAAGTATTTTAAAATTTGGGGTTTAAAATG
1 AAATTGAATTATTTTAAAATTTAGGGTTTAAAATG
* * *
11909206 TAATTGAATTATTTTAGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTAAAATTTAGGGTTTAAAATG
11909241 AAATTGA
1 AAATTGA
11909248 GGACTATGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAAAATTTAGGGTTTAAAATG
Found at i:11911383 original size:23 final size:23
Alignment explanation
Indices: 11911357--11911419 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
11911347 TAAGCTACCA
11911357 AAAGGAAAATAAACATGTGTCAT
1 AAAGGAAAATAAACATGTGTCAT
11911380 AAA-GACAGAGATAAAC--GTGTCAT
1 AAAGGA-A-A-ATAAACATGTGTCAT
*
11911403 AAAGGCAAAT-AACATGT
1 AAAGGAAAATAAACATGT
11911420 CACAATGACA
Statistics
Matches: 33, Mismatches: 1, Indels: 13
0.70 0.02 0.28
Matches are distributed among these distances:
20 3 0.09
21 2 0.06
22 5 0.15
23 15 0.45
24 2 0.06
25 6 0.18
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (23 bp):
AAAGGAAAATAAACATGTGTCAT
Found at i:11921405 original size:38 final size:39
Alignment explanation
Indices: 11921354--11921438 Score: 136
Period size: 38 Copynumber: 2.2 Consensus size: 39
11921344 TCAGGACAAC
* *
11921354 GTCAGTCTGATAACTCCGAGGGCTTGTCTGTCGAGAAG-
1 GTCAGTCGGATAACTCCGAGGGCTTGTCTATCGAGAAGA
11921392 GTCAGTCGGATAACTCCGAGGGCTTGTCTATCGAGAAGA
1 GTCAGTCGGATAACTCCGAGGGCTTGTCTATCGAGAAGA
11921431 GTCTAGTC
1 GTC-AGTC
11921439 TTCATTTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 36 0.84
39 3 0.07
40 4 0.09
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (39 bp):
GTCAGTCGGATAACTCCGAGGGCTTGTCTATCGAGAAGA
Found at i:11921714 original size:16 final size:17
Alignment explanation
Indices: 11921683--11921717 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
11921673 CGTATCGCCG
*
11921683 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
11921700 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
11921716 AC
1 AC
11921718 GTGAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:11936440 original size:3 final size:3
Alignment explanation
Indices: 11936432--11936471 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
11936422 AATATTTATT
* *
11936432 TAA TAA TAA TAA TAA TAA TACA TAT TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
11936472 AAGAAAAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:11936713 original size:45 final size:45
Alignment explanation
Indices: 11936648--11937262 Score: 977
Period size: 45 Copynumber: 13.8 Consensus size: 45
11936638 GAGGTCTTAT
* * * ** *
11936648 CATCTTGCACTGTAGGTCTTACAGATGACCCGAAGACTTTAAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
11936693 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
11936738 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* * *
11936783 CATCATTCACTGAAGGGCTTACAGATGATCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* **
11936828 CATCATGCACTGAAGGGCTTACAGATGACCTGAAGACTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
11936873 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG-AAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
11936917 -A-CAT-CACTGAAGAGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
11936959 CATCATGCACTGAAGGGCTTACAGATGATCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* * * *
11937004 TATCATGCACTGAAGGGCTTACAAATAACCCAAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* *
11937049 CATCATGCACTGAATGGCTTACAGATGACCCAAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
11937094 CATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
11937139 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
11937184 CATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
11937229 CATAATGCACTGAAGGGCTTACAGATGACCCGAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAA
11937263 TTAAAAAGCT
Statistics
Matches: 531, Mismatches: 35, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
41 33 0.06
42 6 0.01
43 2 0.00
44 6 0.01
45 484 0.91
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (45 bp):
CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
Found at i:11936802 original size:26 final size:26
Alignment explanation
Indices: 11936772--11936847 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
11936762 ATGACCCGAA
11936772 GGCTTTGAAAACATCATTCACTGAAG
1 GGCTTTGAAAACATCATTCACTGAAG
* * *
11936798 GGC-TT--ACAGATGA-TC-C-GAA-
1 GGCTTTGAAAACATCATTCACTGAAG
*
11936817 GGCTTTGAAAACATCATGCACTGAAG
1 GGCTTTGAAAACATCATTCACTGAAG
11936843 GGCTT
1 GGCTT
11936848 ACAGATGACC
Statistics
Matches: 36, Mismatches: 7, Indels: 14
0.63 0.12 0.25
Matches are distributed among these distances:
19 3 0.08
20 5 0.14
21 1 0.03
22 7 0.19
23 6 0.17
24 1 0.03
25 5 0.14
26 8 0.22
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (26 bp):
GGCTTTGAAAACATCATTCACTGAAG
Found at i:11938040 original size:22 final size:22
Alignment explanation
Indices: 11937963--11938042 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
11937953 AATAAAGTTT
*
11937963 TCATCTTTGAAAAAAGAATCTA
1 TCATCTTTGAAGAAAGAATCTA
11937985 TCATCTTTGAAGAGAA-AATCTA
1 TCATCTTTGAAGA-AAGAATCTA
11938007 TCATCTTTGAAGAAAGAATCTA
1 TCATCTTTGAAGAAAGAATCTA
11938029 TCATCTTTGAAGAA
1 TCATCTTTGAAGAA
11938043 TGTAGATGTA
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
21 2 0.04
22 51 0.93
23 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAAAGAATCTA
Found at i:11938514 original size:54 final size:54
Alignment explanation
Indices: 11938411--11938568 Score: 174
Period size: 54 Copynumber: 2.9 Consensus size: 54
11938401 TAATTGGTTC
* * ** *
11938411 GTAAAACATTTGACAACACATTCATCATCTCATGTGGTTTCTGCTCAGATGCTA
1 GTAAAACATTTGACAACACATTCATCCTTTCATGTACTTTCTGCCCAGATGCTA
* * * *
11938465 GTAAAACATTTAACAACACATTCATCCTTTCCTGTAACTTT-TGCCCAGATGTTC
1 GTAAAACATTTGACAACACATTCATCCTTTCATGT-ACTTTCTGCCCAGATGCTA
* * * **
11938519 GTAAAGCATTTGACAATACATTCATTCTTTCATGTGGTTTCTGCCCAGAT
1 GTAAAACATTTGACAACACATTCATCCTTTCATGTACTTTCTGCCCAGAT
11938569 TTTTGGTTAA
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 3 0.03
54 80 0.93
55 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCCTTTCATGTACTTTCTGCCCAGATGCTA
Found at i:11943093 original size:19 final size:18
Alignment explanation
Indices: 11943060--11943095 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11943050 TTGTTTATCA
*
11943060 CATTTTCAATTAATTCTC
1 CATTTTCAATAAATTCTC
11943078 CATTTATCAATAAATTCT
1 CATTT-TCAATAAATTCT
11943096 TGAATTCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (18 bp):
CATTTTCAATAAATTCTC
Found at i:11944123 original size:20 final size:21
Alignment explanation
Indices: 11944093--11944145 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
11944083 ATATAAAATG
*
11944093 AAAATGTAAATG-AAA-ATATA
1 AAAATGCAAATGCAAACATA-A
*
11944113 GAAATGCAAATGCAAACATAA
1 AAAATGCAAATGCAAACATAA
11944134 AAAATGCAAATG
1 AAAATGCAAATG
11944146 TAATGAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.36
21 15 0.54
22 3 0.11
ACGTcount: A:0.60, C:0.08, G:0.13, T:0.19
Consensus pattern (21 bp):
AAAATGCAAATGCAAACATAA
Found at i:11944156 original size:21 final size:21
Alignment explanation
Indices: 11944087--11944157 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 21
11944077 ATGCAAATAT
*
11944087 AAAATGAAAATGTAAATGAAAATA
1 AAAATGCAAATGT-AATG-AAA-A
* ** *
11944111 TAGAAATGCAAATGCAAACATAA
1 -A-AAATGCAAATGTAATGAAAA
11944134 AAAATGCAAATGTAATGAAAA
1 AAAATGCAAATGTAATGAAAA
11944155 AAA
1 AAA
11944158 TACGAATGCA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
21 19 0.53
22 1 0.03
23 1 0.03
24 2 0.06
25 3 0.08
26 10 0.28
ACGTcount: A:0.63, C:0.06, G:0.13, T:0.18
Consensus pattern (21 bp):
AAAATGCAAATGTAATGAAAA
Found at i:11947164 original size:19 final size:16
Alignment explanation
Indices: 11947139--11947180 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
11947129 TGTCCTTTCT
11947139 TAATATTTGAAAAATAAA
1 TAATATTT-AAAAAT-AA
11947157 TAA-ATATTAAAAATAA
1 TAATAT-TTAAAAATAA
11947173 TAATATTT
1 TAATATTT
11947181 CCTAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 7 0.32
17 10 0.45
18 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TAATATTTAAAAATAA
Found at i:11947378 original size:2 final size:2
Alignment explanation
Indices: 11947371--11947451 Score: 153
Period size: 2 Copynumber: 40.5 Consensus size: 2
11947361 AACAAAGCAA
11947371 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
*
11947413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11947452 AGCAGGATAT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:11947749 original size:15 final size:15
Alignment explanation
Indices: 11947726--11947767 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
11947716 ATCAAAATAA
11947726 AATAA-ATTAAAAGC
1 AATAATATTAAAAGC
*
11947740 AATAATATTAAATTGC
1 AATAATATTAAA-AGC
11947756 AA-AATATTAAAA
1 AATAATATTAAAA
11947768 ATTCAGGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 5 0.21
15 15 0.62
16 4 0.17
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (15 bp):
AATAATATTAAAAGC
Found at i:11948934 original size:3 final size:3
Alignment explanation
Indices: 11948926--11948958 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
11948916 TTTATTTAAC
11948926 AAT AAT AAT AAT AAT ATAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA
11948959 AAGGAAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11948948 original size:16 final size:16
Alignment explanation
Indices: 11948927--11948957 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
11948917 TTATTTAACA
11948927 ATAATAATAATAATAT
1 ATAATAATAATAATAT
11948943 ATAATAATAATAATA
1 ATAATAATAATAATA
11948958 AAAGGAAAAG
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATAATAATAATAT
Found at i:11967456 original size:13 final size:13
Alignment explanation
Indices: 11967438--11967463 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11967428 AGTATTAAAC
11967438 AAGAACCCTAATT
1 AAGAACCCTAATT
11967451 AAGAACCCTAATT
1 AAGAACCCTAATT
11967464 TATTGTTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
AAGAACCCTAATT
Found at i:11976172 original size:19 final size:20
Alignment explanation
Indices: 11976148--11976187 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
11976138 TGACATATAT
11976148 ATGTAGATTATTAA-TGTTC
1 ATGTAGATTATTAATTGTTC
*
11976167 ATGTAGGTTATTAATTGTTC
1 ATGTAGATTATTAATTGTTC
11976187 A
1 A
11976188 AATATGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.47
Consensus pattern (20 bp):
ATGTAGATTATTAATTGTTC
Found at i:11976652 original size:93 final size:93
Alignment explanation
Indices: 11976493--11976747 Score: 492
Period size: 93 Copynumber: 2.7 Consensus size: 93
11976483 AATACATAAT
*
11976493 TAATCTCCTAATATATTTGTTATTAAATAATAGCAAATTAGGGTAATAATTGTTGCAGTATTTTA
1 TAATCTCCTAATCTATTTGTTATTAAATAATAGCAAATTAGGGTAATAATTGTTGCAGTATTTTA
11976558 TTAACAACAAATAGGCTTTATATTTTAA
66 TTAACAACAAATAGGCTTTATATTTTAA
11976586 TAATCTCCTAATCTATTTGTTATTAAATAATAGCAAATTAGGGTAATAATTGTTGCAGTATTTTA
1 TAATCTCCTAATCTATTTGTTATTAAATAATAGCAAATTAGGGTAATAATTGTTGCAGTATTTTA
11976651 TTAACAACAAATAGGCTTTATATTTTAA
66 TTAACAACAAATAGGCTTTATATTTTAA
*
11976679 TAATCTCCTAATCTATTTGTTATTAAATAATAGCAAATTAGGGTAATAATTGCTGCAGTATTTTA
1 TAATCTCCTAATCTATTTGTTATTAAATAATAGCAAATTAGGGTAATAATTGTTGCAGTATTTTA
11976744 TTAA
66 TTAA
11976748 ACAGGCTTTA
Statistics
Matches: 160, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 160 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (93 bp):
TAATCTCCTAATCTATTTGTTATTAAATAATAGCAAATTAGGGTAATAATTGTTGCAGTATTTTA
TTAACAACAAATAGGCTTTATATTTTAA
Found at i:11976664 original size:46 final size:46
Alignment explanation
Indices: 11976521--11976664 Score: 109
Period size: 46 Copynumber: 3.1 Consensus size: 46
11976511 GTTATTAAAT
11976521 AATAGCAAATTAGGGTAATAATTGTTGCAGTATTTTATTAACAACA
1 AATAGCAAATTAGGGTAATAATTGTTGCAGTATTTTATTAACAACA
** *** ** * * *
11976567 AATAGGC-TTTATATTTTAATAATCTCCT-AATCTATTTGTTATT-A-AA-T
1 AATA-GCAAAT-TAGGGTAATAAT-TGTTGCA-GTA-TT-TTATTAACAACA
11976614 AATAGCAAATTAGGGTAATAATTGTTGCAGTATTTTATTAACAACA
1 AATAGCAAATTAGGGTAATAATTGTTGCAGTATTTTATTAACAACA
11976660 AATAG
1 AATAG
11976665 GCTTTATATT
Statistics
Matches: 67, Mismatches: 20, Indels: 22
0.61 0.18 0.20
Matches are distributed among these distances:
43 5 0.07
44 3 0.04
45 6 0.09
46 22 0.33
47 17 0.25
48 6 0.09
49 3 0.04
50 5 0.07
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (46 bp):
AATAGCAAATTAGGGTAATAATTGTTGCAGTATTTTATTAACAACA
Found at i:11981491 original size:17 final size:17
Alignment explanation
Indices: 11981469--11981503 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
11981459 AAAAAATGCC
11981469 CCACACATATAACAGTT
1 CCACACATATAACAGTT
11981486 CCACACATATAACAGTT
1 CCACACATATAACAGTT
11981503 C
1 C
11981504 TACTTTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.31, G:0.06, T:0.23
Consensus pattern (17 bp):
CCACACATATAACAGTT
Found at i:11984224 original size:15 final size:16
Alignment explanation
Indices: 11984194--11984224 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11984184 ACGAGGGGAG
11984194 TCATCCCATCACTCTA
1 TCATCCCATCACTCTA
11984210 TCATCCCAT-ACTCTA
1 TCATCCCATCACTCTA
11984225 GGTGAAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.26, C:0.42, G:0.00, T:0.32
Consensus pattern (16 bp):
TCATCCCATCACTCTA
Found at i:11984366 original size:2 final size:2
Alignment explanation
Indices: 11984359--11984396 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11984349 TCATAACCTC
11984359 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
11984397 TTCCAGCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11991720 original size:14 final size:15
Alignment explanation
Indices: 11991701--11991739 Score: 62
Period size: 14 Copynumber: 2.6 Consensus size: 15
11991691 TCATGTACCT
11991701 AGAAAAATAAATG-A
1 AGAAAAATAAATGAA
11991715 AGAAAAATAAATGAA
1 AGAAAAATAAATGAA
11991730 AGTAAAAATA
1 AG-AAAAATA
11991740 TAAAGCTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 13 0.57
15 3 0.13
16 7 0.30
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (15 bp):
AGAAAAATAAATGAA
Found at i:11996061 original size:18 final size:18
Alignment explanation
Indices: 11996038--11996072 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11996028 ACTGAATATT
*
11996038 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
11996056 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
11996073 GATAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:11996733 original size:64 final size:64
Alignment explanation
Indices: 11996665--11996786 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
11996655 ACATAAATCC
* * * * *
11996665 CATTCAATGTTTGTATTTTAAGGGGGTGCATCGATGCA-CTACTTGTGCATCGATACACTAATGA
1 CATTCAATGTTTGTATTTGAAAGGAGTGCATCGATACACCT-CATGTGCATCGATACACTAATGA
* *
11996729 CATTCGATGTTTTTATTTGAAAGGAGTGCATCGATACACCTCATGTGCATCGATACAC
1 CATTCAATGTTTGTATTTGAAAGGAGTGCATCGATACACCTCATGTGCATCGATACAC
11996787 CTTGAACAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 48 0.96
65 2 0.04
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
CATTCAATGTTTGTATTTGAAAGGAGTGCATCGATACACCTCATGTGCATCGATACACTAATGA
Found at i:12007551 original size:10 final size:10
Alignment explanation
Indices: 12007531--12007588 Score: 66
Period size: 10 Copynumber: 5.8 Consensus size: 10
12007521 ATCTAAATAT
12007531 TATTT-AAAA
1 TATTTAAAAA
12007540 TATTTAAAAA
1 TATTTAAAAA
12007550 TA-TTAAATAA
1 TATTTAAA-AA
*
12007560 TTTTATAAAAA
1 TATT-TAAAAA
*
12007571 TATTAAAAAA
1 TATTTAAAAA
12007581 TATTTAAA
1 TATTTAAA
12007589 TGCATAAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 10 0.24
10 21 0.51
11 6 0.15
12 4 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTTAAAAA
Found at i:12007570 original size:21 final size:22
Alignment explanation
Indices: 12007536--12007586 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
12007526 AATATTATTT
12007536 AAAATA-TT-TAAAAATATTAA
1 AAAATATTTATAAAAATATTAA
*
12007556 ATAAT-TTTATAAAAATATTAA
1 AAAATATTTATAAAAATATTAA
12007577 AAAATATTTA
1 AAAATATTTA
12007587 AATGCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 6 0.23
21 16 0.62
22 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATATTTATAAAAATATTAA
Found at i:12013699 original size:22 final size:23
Alignment explanation
Indices: 12013667--12013710 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
12013657 TATTTTTATT
12013667 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
12013690 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
12013711 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:12013726 original size:31 final size:32
Alignment explanation
Indices: 12013663--12013739 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 32
12013653 TATTTATTTT
12013663 TATTTATTAATATTTATAATAATATAATATTA
1 TATTTATTAATATTTATAATAATATAATATTA
*
12013695 TATTT-TTAATA-TTAT-ATAAAATAATCAATTA
1 TATTTATTAATATTTATAATAATATAAT--ATTA
*
12013726 TATTATAATAATAT
1 TATT-TATTAATAT
12013740 AAGATATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 9 0.24
30 4 0.11
31 14 0.37
32 6 0.16
33 5 0.13
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TATTTATTAATATTTATAATAATATAATATTA
Found at i:12013856 original size:23 final size:23
Alignment explanation
Indices: 12013830--12013874 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12013820 AATAATATTT
12013830 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
12013853 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
12013875 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:12013968 original size:21 final size:21
Alignment explanation
Indices: 12013942--12014037 Score: 79
Period size: 21 Copynumber: 4.5 Consensus size: 21
12013932 AAAATATAAA
* *
12013942 AAAATTATTATTTTTATTAAT
1 AAAATTATAATTATTATTAAT
* *
12013963 AAAATTATAAAAATAATATTTAAT
1 AAAATTAT--AATTATTA-TTAAT
*
12013987 AATAAATA-AATTATT-TTAAT
1 AA-AATTATAATTATTATTAAT
* *
12014007 AAAATTATTATTTTTATTAAT
1 AAAATTATAATTATTATTAAT
12014028 AAAATTATAA
1 AAAATTATAA
12014038 AAATAATATT
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
19 4 0.07
20 12 0.21
21 22 0.38
22 5 0.09
23 4 0.07
24 7 0.12
25 4 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATTATAATTATTATTAAT
Found at i:12013993 original size:17 final size:16
Alignment explanation
Indices: 12013969--12014060 Score: 64
Period size: 17 Copynumber: 5.6 Consensus size: 16
12013959 TAATAAAATT
12013969 ATAAAAATAATATTTA
1 ATAAAAATAATATTTA
12013985 ATAATAAATAAATTATTTTA
1 ATAA-AAAT-AA-TA-TTTA
* *
12014005 ATAAAATTATTATTT-
1 ATAAAAATAATATTTA
* ** *
12014020 TTATTAATAA-AATT-
1 ATAAAAATAATATTTA
12014034 ATAAAAATAATATTTA
1 ATAAAAATAATATTTA
12014050 ATAATAAATAA
1 ATAA-AAATAA
12014061 ATTATTTGAA
Statistics
Matches: 57, Mismatches: 12, Indels: 13
0.70 0.15 0.16
Matches are distributed among these distances:
14 10 0.18
15 8 0.14
16 11 0.19
17 12 0.21
18 3 0.05
19 5 0.09
20 8 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAAATAATATTTA
Found at i:12013998 original size:30 final size:30
Alignment explanation
Indices: 12013964--12014065 Score: 100
Period size: 30 Copynumber: 3.2 Consensus size: 30
12013954 TTTATTAATA
12013964 AAATTATAAAAATAATATTTAATAATAAAT
1 AAATTATAAAAATAATATTTAATAATAAAT
* * *
12013994 AAATTATTTTAATAAAATTATTATTT--TTATTAAT
1 AAATTA---T-A-AAAA-TAATATTTAATAATAAAT
12014028 AAAATTATAAAAATAATATTTAATAATAAAT
1 -AAATTATAAAAATAATATTTAATAATAAAT
12014059 AAATTAT
1 AAATTAT
12014066 TTGAAACCCT
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
29 7 0.12
30 17 0.30
31 7 0.12
32 1 0.02
33 1 0.02
34 7 0.12
35 10 0.18
36 7 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
AAATTATAAAAATAATATTTAATAATAAAT
Found at i:12014063 original size:65 final size:65
Alignment explanation
Indices: 12013942--12014067 Score: 252
Period size: 65 Copynumber: 1.9 Consensus size: 65
12013932 AAAATATAAA
12013942 AAAATTATTATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAAATTATTTTAAT
1 AAAATTATTATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAAATTATTTTAAT
12014007 AAAATTATTATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAAATTATTT
1 AAAATTATTATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAAATTATTT
12014068 GAAACCCTAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (65 bp):
AAAATTATTATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAAATTATTTTAAT
Found at i:12014984 original size:3 final size:3
Alignment explanation
Indices: 12014976--12015008 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
12014966 TTTACGTTGA
*
12014976 ATG ATG ATG ATG ATG ATG ATG ATA ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
12015009 GTATAAAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:12018382 original size:25 final size:22
Alignment explanation
Indices: 12018337--12018384 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 22
12018327 AAAATCTTTC
*
12018337 CCTCCCCCGTTCCCTCTCCTCT
1 CCTCCCCCGTTCCCCCTCCTCT
12018359 CCTCCCCCGTTCATCCCCTCCCTCT
1 CCTCCCCCGTTC--CCCCT-CCTCT
12018384 C
1 C
12018385 ATTGTACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 12 0.55
24 4 0.18
25 6 0.27
ACGTcount: A:0.02, C:0.65, G:0.04, T:0.29
Consensus pattern (22 bp):
CCTCCCCCGTTCCCCCTCCTCT
Found at i:12023858 original size:2 final size:2
Alignment explanation
Indices: 12023851--12023875 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12023841 TAATAATTTA
12023851 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
12023876 CTTATACACT
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
Done.