Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_50.0, 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: 9139585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37885 characters in sequence are not A, C, G, or T
File 11 of 19
Found at i:4192720 original size:33 final size:33
Alignment explanation
Indices: 4192682--4192746 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
4192672 ATGACATGCT
*
4192682 AACATATTATAATTAATGATAATATGATATGTA
1 AACATATTATAATTAATGATAACATGATATGTA
*
4192715 AACATATTATAATTGATGATAACATGATATGT
1 AACATATTATAATTAATGATAACATGATATGT
4192747 TAATTTGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (33 bp):
AACATATTATAATTAATGATAACATGATATGTA
Found at i:4200127 original size:2 final size:2
Alignment explanation
Indices: 4200120--4200150 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4200110 TCTATTAATC
4200120 AT AT AT 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 AT AT AT A
4200151 GTCCAATTCG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4218670 original size:2 final size:2
Alignment explanation
Indices: 4218652--4218687 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4218642 TCCAGGCAAG
* *
4218652 TA TA GA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4218688 CATACCCTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:4241292 original size:18 final size:18
Alignment explanation
Indices: 4241269--4241304 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4241259 TTATAAATTT
4241269 AATTTTAATTAATTATTA
1 AATTTTAATTAATTATTA
* *
4241287 AATTTTTATTTATTATTA
1 AATTTTAATTAATTATTA
4241305 TTATTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTTAATTAATTATTA
Found at i:4241436 original size:25 final size:25
Alignment explanation
Indices: 4241390--4241438 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
4241380 AATTGAATTC
*
4241390 TTTTTTAATTTTAACATGATAAATG
1 TTTTTTAATTTTAACATAATAAATG
*
4241415 TTTTTTATATTTTAA-TTAATAAAT
1 TTTTTTA-ATTTTAACATAATAAAT
4241439 TAATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (25 bp):
TTTTTTAATTTTAACATAATAAATG
Found at i:4241850 original size:2 final size:2
Alignment explanation
Indices: 4241843--4241872 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4241833 GGATGGGAGC
4241843 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
4241873 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4241888 original size:2 final size:2
Alignment explanation
Indices: 4241883--4241922 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4241873 NNNNNNNNNN
4241883 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
4241923 GTTTCCTTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4248950 original size:32 final size:28
Alignment explanation
Indices: 4248886--4248940 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
4248876 ATATTACAAA
4248886 CAAATAAATTACATCAAAAATAAATAAG
1 CAAATAAATTACATCAAAAATAAATAAG
* *
4248914 CAAATACATTACATCAAATATAAATAA
1 CAAATAAATTACATCAAAAATAAATAA
4248941 AATTTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.24
Consensus pattern (28 bp):
CAAATAAATTACATCAAAAATAAATAAG
Found at i:4249501 original size:18 final size:18
Alignment explanation
Indices: 4249467--4249516 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
4249457 TTGATTTTTC
4249467 ATAATT-AAA-TATATAAA
1 ATAATTAAAATTAT-TAAA
4249484 AT-ATATAAAATTATTAAA
1 ATAAT-TAAAATTATTAAA
*
4249502 TTAATTAAAATTATT
1 ATAATTAAAATTATT
4249517 TTTTGGCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 2 0.07
17 3 0.11
18 18 0.64
19 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATTAAAATTATTAAA
Found at i:4259668 original size:30 final size:30
Alignment explanation
Indices: 4259633--4259710 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
4259623 AATTATTAAT
*
4259633 TATATAAATTTATTTAATTTAAAATAAAAA-
1 TATATAAATTTATTTAA-ATAAAATAAAAAG
4259663 TATATAAATTTATTTAAATAAAATAAAAAG
1 TATATAAATTTATTTAAATAAAATAAAAAG
*
4259693 TA-A-ACATTTATTTAAATA
1 TATATAAATTTATTTAAATA
4259711 TTTTAAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 14 0.31
29 12 0.27
30 19 0.42
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (30 bp):
TATATAAATTTATTTAAATAAAATAAAAAG
Found at i:4265557 original size:20 final size:19
Alignment explanation
Indices: 4265510--4265557 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
4265500 ATTTTGACAT
* * *
4265510 AATATTTTTAAAAATTTTA
1 AATAATTTTAAAAAATGTA
*
4265529 AATTATTTTAAAAAATGTA
1 AATAATTTTAAAAAATGTA
4265548 AATAACTTTT
1 AATAA-TTTT
4265558 TATACTTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
AATAATTTTAAAAAATGTA
Found at i:4268199 original size:2 final size:2
Alignment explanation
Indices: 4268192--4268218 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4268182 TGTGAATAAC
4268192 AT 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 AT A
4268219 AGTAGGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4272238 original size:20 final size:20
Alignment explanation
Indices: 4272213--4272250 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4272203 GGCATAACAT
4272213 AGAACAAATGCACATGGTCA
1 AGAACAAATGCACATGGTCA
*
4272233 AGAACAAATGCACGTGGT
1 AGAACAAATGCACATGGT
4272251 TTATACCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (20 bp):
AGAACAAATGCACATGGTCA
Found at i:4277425 original size:43 final size:46
Alignment explanation
Indices: 4277364--4277455 Score: 138
Period size: 43 Copynumber: 2.1 Consensus size: 46
4277354 GGTCGGGCTA
4277364 GCCCTGCCCCCTCCTCCGGCTCCCAC-AGT-CCG-TTCCCCCTGCG
1 GCCCTGCCCCCTCCTCCGGCTCCCACGAGTCCCGATTCCCCCTGCG
*
4277407 GCCCTGCGCCCC-CCTCCGGCTCCCGCGAGTCCCGATTCCCCCTGCG
1 GCCCTGC-CCCCTCCTCCGGCTCCCACGAGTCCCGATTCCCCCTGCG
4277453 GCC
1 GCC
4277456 GCCGGGTTGG
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
43 20 0.45
44 7 0.16
45 3 0.07
46 14 0.32
ACGTcount: A:0.04, C:0.58, G:0.22, T:0.16
Consensus pattern (46 bp):
GCCCTGCCCCCTCCTCCGGCTCCCACGAGTCCCGATTCCCCCTGCG
Found at i:4283059 original size:2 final size:2
Alignment explanation
Indices: 4283052--4283090 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4283042 ACCGCTTTTA
4283052 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
4283091 GGTTAATTTG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4289130 original size:19 final size:20
Alignment explanation
Indices: 4289106--4289149 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
4289096 TGGGCATCTA
*
4289106 ATATCTAAAGACTCA-TTTG
1 ATATCTAAAGACTCAGTTGG
*
4289125 ATATCTCAAGACTCAGTTGG
1 ATATCTAAAGACTCAGTTGG
4289145 ATATC
1 ATATC
4289150 CATCCTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (20 bp):
ATATCTAAAGACTCAGTTGG
Found at i:4292898 original size:2 final size:2
Alignment explanation
Indices: 4292891--4292921 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4292881 CTTTTGGATG
4292891 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4292922 TGAAGTAAAT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4294642 original size:92 final size:92
Alignment explanation
Indices: 4294485--4294670 Score: 345
Period size: 92 Copynumber: 2.0 Consensus size: 92
4294475 TCCACTAACA
4294485 CTGGTGAACACTACAGTGAGATTTCTTGTGGTGAGATCCAATGAGATCTTACCAATAACTATAAT
1 CTGGTGAACACTACAGTGAGATTTCTTGTGGTGAGATCCAATGAGATCTTACCAATAACTATAAT
4294550 GGTCACTGATTAACACCATACAAGATT
66 GGTCACTGATTAACACCATACAAGATT
* * *
4294577 CTGGTGACCACTACAGTGAGATTTCTTGTGGTGAGATCCAATGAGATCTTACCAATACCTGTAAT
1 CTGGTGAACACTACAGTGAGATTTCTTGTGGTGAGATCCAATGAGATCTTACCAATAACTATAAT
4294642 GGTCACTGATTAACACCATACAAGATT
66 GGTCACTGATTAACACCATACAAGATT
4294669 CT
1 CT
4294671 TGAGCAACAA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (92 bp):
CTGGTGAACACTACAGTGAGATTTCTTGTGGTGAGATCCAATGAGATCTTACCAATAACTATAAT
GGTCACTGATTAACACCATACAAGATT
Found at i:4303352 original size:16 final size:16
Alignment explanation
Indices: 4303331--4303364 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
4303321 TATATATGGT
4303331 ATGGTACAAGATATAA
1 ATGGTACAAGATATAA
4303347 ATGGTACAAGATATAA
1 ATGGTACAAGATATAA
4303363 AT
1 AT
4303365 TTGCCTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (16 bp):
ATGGTACAAGATATAA
Found at i:4305645 original size:34 final size:35
Alignment explanation
Indices: 4305579--4305646 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
4305569 CATGGAAGAG
*
4305579 AAGAAAGGGTGTTTGTGAGAAGCCTGGAAAAAATA
1 AAGAAAGGGTGTTTGAGAGAAGCCTGGAAAAAATA
* *
4305614 AAGAGAGGGT-TTTGAGAGAAGCTTGTGAAAAAA
1 AAGAAAGGGTGTTTGAGAGAAGCCTG-GAAAAAA
4305647 AATTATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 13 0.45
35 16 0.55
ACGTcount: A:0.43, C:0.04, G:0.32, T:0.21
Consensus pattern (35 bp):
AAGAAAGGGTGTTTGAGAGAAGCCTGGAAAAAATA
Found at i:4306337 original size:40 final size:39
Alignment explanation
Indices: 4306283--4306362 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 39
4306273 TAATGTCATC
*
4306283 TCTTAAATATATTTTTAATGTCATATATTTAATTTTGATT
1 TCTTAAATATATTTTTAATATCATATATTTAATTTT-ATT
* * *
4306323 TCTT-AATATAATTTTTTATATTATATATTTTATTTTATT
1 TCTTAAATAT-ATTTTTAATATCATATATTTAATTTTATT
4306362 T
1 T
4306363 TATTTCCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 9 0.26
40 26 0.74
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (39 bp):
TCTTAAATATATTTTTAATATCATATATTTAATTTTATT
Found at i:4307597 original size:46 final size:46
Alignment explanation
Indices: 4307485--4307597 Score: 115
Period size: 46 Copynumber: 2.5 Consensus size: 46
4307475 TAAAATATAA
* * *
4307485 AAAAT-AATTTTGATAAAAAATTCATACATAAAAATATCCTTTTGAC
1 AAAATCAATTTCGAT-AAAAATTCATACATAAAAATATACTTATGAC
* * * *
4307531 AAAATCTA-TTCTG-TAGAAAATTTATAGATAAAATTATACTTATGAC
1 AAAATCAATTTC-GATA-AAAATTCATACATAAAAATATACTTATGAC
4307577 AAAATCAATTTCGATAAAAAT
1 AAAATCAATTTCGATAAAAAT
4307598 ATTTATTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
45 1 0.02
46 46 0.85
47 7 0.13
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.35
Consensus pattern (46 bp):
AAAATCAATTTCGATAAAAATTCATACATAAAAATATACTTATGAC
Found at i:4309081 original size:2 final size:2
Alignment explanation
Indices: 4309074--4309117 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4309064 TTCAATTTCT
4309074 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4309116 TA
1 TA
4309118 AAATATTTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4313521 original size:14 final size:14
Alignment explanation
Indices: 4313502--4313528 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4313492 CAAGAAAAGC
4313502 CTAAAATCTTTAAA
1 CTAAAATCTTTAAA
4313516 CTAAAATCTTTAA
1 CTAAAATCTTTAA
4313529 TCAAGACGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (14 bp):
CTAAAATCTTTAAA
Found at i:4314732 original size:17 final size:17
Alignment explanation
Indices: 4314712--4314745 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4314702 CAGCGGTAAA
*
4314712 AATAACTGTAATAACAG
1 AATAACTGTAACAACAG
4314729 AATAACTGTAACAACAG
1 AATAACTGTAACAACAG
4314746 GAAAGGAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.21
Consensus pattern (17 bp):
AATAACTGTAACAACAG
Found at i:4325722 original size:16 final size:16
Alignment explanation
Indices: 4325681--4325722 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4325671 AAAGATAAGA
*
4325681 TATTTTTAAAATTAAC
1 TATTTTTAATATTAAC
* *
4325697 TTTTTTTAATTTTAAC
1 TATTTTTAATATTAAC
4325713 TATTTTTAAT
1 TATTTTTAAT
4325723 CAAGTTAGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTTTAATATTAAC
Found at i:4325919 original size:26 final size:26
Alignment explanation
Indices: 4325872--4325922 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4325862 AAAAGTGTTA
* *
4325872 TTATTACACGTTATAATTAAAAAAAG
1 TTATTACACGCTATAATGAAAAAAAG
4325898 TTATTACACGCTAT-ATCGAAAAAAA
1 TTATTACACGCTATAAT-GAAAAAAA
4325923 AATTGTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (26 bp):
TTATTACACGCTATAATGAAAAAAAG
Found at i:4326012 original size:29 final size:30
Alignment explanation
Indices: 4325955--4326018 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
4325945 TAAAAACATG
4325955 TTACATACCATGTTGAAAAAAATATTATTA
1 TTACATACCATGTTGAAAAAAATATTATTA
* * *
4325985 TTACATACTATGTT-AAAAAAATGTTATTG
1 TTACATACCATGTTGAAAAAAATATTATTA
4326014 TTACA
1 TTACA
4326019 CGTTATATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (30 bp):
TTACATACCATGTTGAAAAAAATATTATTA
Found at i:4333806 original size:33 final size:32
Alignment explanation
Indices: 4333706--4334039 Score: 120
Period size: 33 Copynumber: 10.4 Consensus size: 32
4333696 TATAAATGTA
4333706 ATATA-TTTATATTTT-T-TATTA-TTAATTTTT
1 ATATATTTTAT-TTTTATATATTATTTAA-TTTT
* *
4333736 ATATAATATTATTTTTTAAATATATT-TTTAATATT
1 ATAT-ATTTTA-TTTTT--ATATATTATTTAATTTT
*
4333771 ATATATTTTATTTTTATTTATTATTATAATTTT
1 ATATATTTTATTTTTATATATTATT-TAATTTT
4333804 ATATATTTTATTTTTA-ATA-TATTTATATTTT
1 ATATATTTTATTTTTATATATTATTTA-ATTTT
* * * *
4333835 TTAT-TATTTATTTTTATGTA--ATATCATCTCTT
1 ATATAT-TTTATTTTTATATATTATTTAAT-T-TT
*
4333867 AAATATATTTTTAATGTTATATATATT-TTT-A-TTT
1 --ATATA-TTTT-AT-TTTTATATATTATTTAATTTT
* * *
4333901 AT-TATTATA-ATTT-TATATT-TTTATTTTT
1 ATATATTTTATTTTTATATATTATTTAATTTT
* *
4333929 A-ATATTTTAATATTATATA-T-TTT-ATTTT
1 ATATATTTTATTTTTATATATTATTTAATTTT
* *
4333957 ATTTTATTTTATCTATATTATATA-AATTTTAATTTT
1 A-TATATTTTAT-T-T-TTATATATTA-TTTAATTTT
* * * * *
4333993 TTATATTTTA-TTTTATTTTTTAATTTTTATATT
1 ATATATTTTATTTTTATATATT-A-TTTAATTTT
4334026 ATATATTTTATTTT
1 ATATATTTTATTTT
4334040 AATTATAACA
Statistics
Matches: 231, Mismatches: 34, Indels: 74
0.68 0.10 0.22
Matches are distributed among these distances:
26 9 0.04
27 2 0.01
28 15 0.06
29 7 0.03
30 23 0.10
31 41 0.18
32 18 0.08
33 54 0.23
34 13 0.06
35 23 0.10
36 16 0.07
37 8 0.03
38 2 0.01
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (32 bp):
ATATATTTTATTTTTATATATTATTTAATTTT
Found at i:4333829 original size:114 final size:113
Alignment explanation
Indices: 4333704--4334039 Score: 384
Period size: 114 Copynumber: 3.0 Consensus size: 113
4333694 AATATAAATG
*
4333704 TAATATATTTATATTTTTTATTATTAATTTTTATATAATATTATTTTTTAAATATATTTTTAATA
1 TAATATATTTATATTTTTTATTATT-ATTTTTATATAATATTATTTATTAAATATATTTTTAATA
4333769 TTATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTT
65 TTATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTT
* * * * *
4333818 TAATATATTTATATTTTTTATTATTTATTTTTATGTAATATCATCTCTTAAATATATTTTTAATG
1 TAATATATTTATATTTTTTATTA-TTATTTTTATATAATATTATTTATTAAATATATTTTTAATA
4333883 TTATATA---TATTTTTATTTATTATTATAATTTTATAT-TTTTATTTT
65 TTATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTT
* * * * * * *
4333928 TAATAT-TTTAATATTATATATT-TTA-TTTTATTTTATTTTATCTATATTATATA-AATTTTAA
1 TAATATATTT-ATATTTTTTATTATTATTTTTATATAATATTAT-T-TATTAAATATATTTTTAA
* * * * * *
4333989 TTTTTTATATTTTA-TTTTATTTTTTAATTTTTATATTATATATTTTATTTT
63 TATTATATATTTTATTTTTATTTATT-ATTATAATTTTATATATTTTATTTT
4334040 AATTATAACA
Statistics
Matches: 192, Mismatches: 21, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
107 12 0.06
108 17 0.09
109 10 0.05
110 35 0.18
111 43 0.22
112 9 0.05
114 64 0.33
115 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.67
Consensus pattern (113 bp):
TAATATATTTATATTTTTTATTATTATTTTTATATAATATTATTTATTAAATATATTTTTAATAT
TATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTT
Found at i:4333835 original size:83 final size:82
Alignment explanation
Indices: 4333730--4334039 Score: 217
Period size: 84 Copynumber: 3.7 Consensus size: 82
4333720 TTTATTATTA
*
4333730 ATTTTT-ATATAATATTATTTTTTAAATATATTTTTAATATTATATATTTTATTTTTATTTATTA
1 ATTTTTAATATAAT-TTATTTTTTATATATATTTTT-ATATTATATATTTTATTTTTATTTATTA
*
4333794 TTATAATTTTATATATTTT
64 TTATAATTATATATATTTT
* * * * ** *
4333813 ATTTTTAATATATTTATATTTTTTATTATTTATTTTTATGTAATATCATCTCTTAAATATATTT-
1 ATTTTTAATATAATT-TATTTTTTA-TATATATTTTTATATTATAT-AT-T-TTATTTTTATTTA
*
4333877 TTA--AT-GTTATATATATTTTT
61 TTATTATAATTATATATA-TTTT
* * *
4333897 ATTTATTATTATAATTTTATATTTTTATTTTTAATATTTTAATATTATATATTTTA-TTTTATTT
1 ATTT-TTAATATAA-TTTAT-TTTTTA--TAT-ATATTTTTATATTATATATTTTATTTTTA-TT
*
4333961 TATT-TTATCTATATTATATAAATTTT
59 TATTATTA--TA-ATTATATATATTTT
* * *
4333987 AATTTTT--TATATTTTATTTTATTTTTTA-ATTTTTATATTATATATTTTATTTT
1 -ATTTTTAATATAATTTATTTT-TTATATATATTTTTATATTATATATTTTATTTT
4334040 AATTATAACA
Statistics
Matches: 180, Mismatches: 24, Indels: 45
0.72 0.10 0.18
Matches are distributed among these distances:
83 35 0.19
84 39 0.22
85 30 0.17
86 18 0.10
87 22 0.12
88 17 0.09
89 1 0.01
90 6 0.03
91 12 0.07
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (82 bp):
ATTTTTAATATAATTTATTTTTTATATATATTTTTATATTATATATTTTATTTTTATTTATTATT
ATAATTATATATATTTT
Found at i:4333920 original size:7 final size:7
Alignment explanation
Indices: 4333888--4334036 Score: 69
Period size: 7 Copynumber: 20.4 Consensus size: 7
4333878 TAATGTTATA
4333888 TATATTT
1 TATATTT
4333895 T-TA-TT
1 TATATTT
*
4333900 TAT-TAT
1 TATATTT
4333906 TATAATTT
1 TAT-ATTT
4333914 TATATTT
1 TATATTT
4333921 T-TATTTT
1 TATA-TTT
4333928 TAATATTT
1 T-ATATTT
*
4333936 TAATATTA
1 T-ATATTT
4333944 TATATTT
1 TATATTT
4333951 TATTTTATTT
1 TA---TATTT
*
4333961 TATTTTAT
1 TATATT-T
4333969 CTATATTAT
1 -TATATT-T
*
4333978 ATAAATTT
1 -TATATTT
4333986 TA-ATTT
1 TATATTT
*
4333992 TTTATATT
1 TATAT-TT
4334000 T-TATTT
1 TATATTT
*
4334006 TATTTTT
1 TATATTT
4334013 TA-ATTTT
1 TATA-TTT
*
4334020 TATATTA
1 TATATTT
4334027 TATATTT
1 TATATTT
4334034 TAT
1 TAT
4334037 TTTAATTATA
Statistics
Matches: 112, Mismatches: 13, Indels: 34
0.70 0.08 0.21
Matches are distributed among these distances:
5 3 0.03
6 17 0.15
7 49 0.44
8 22 0.20
9 14 0.12
10 7 0.06
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (7 bp):
TATATTT
Found at i:4333946 original size:5 final size:5
Alignment explanation
Indices: 4333946--4334040 Score: 56
Period size: 5 Copynumber: 19.4 Consensus size: 5
4333936 TAATATTATA
* * * * *
4333946 TATTT TATTT TATTT TATTT TA-TC TATAT TATATA AATTT TAATTT T-TTA
1 TATTT TATTT TATTT TATTT TATTT TATTT TAT-TT TATTT T-ATTT TATTT
* * *
4333996 TATTT TATTT TA-TT T-TTT AATTTT TATAT TA-TA TATTT TATTT TA
1 TATTT TATTT TATTT TATTT TA-TTT TATTT TATTT TATTT TATTT TA
4334041 ATTATAACAA
Statistics
Matches: 66, Mismatches: 16, Indels: 16
0.67 0.16 0.16
Matches are distributed among these distances:
4 13 0.20
5 42 0.64
6 11 0.17
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (5 bp):
TATTT
Found at i:4333965 original size:30 final size:30
Alignment explanation
Indices: 4333774--4334002 Score: 90
Period size: 28 Copynumber: 7.6 Consensus size: 30
4333764 TAATATTATA
*
4333774 TATTTTATTTT-TATTTATTATTATA-ATTT
1 TATTTTATTTTAT-TTTAATATTATATATTT
* *
4333803 TA-TATATTTTATTTTTAATATATTTATATTT
1 TATTTTATTTTA-TTTTAATAT-TATATATTT
* * *
4333834 T-TTATTA-TTTATTTTTATGTAATATCATCTCT
1 TATT-TTATTTTATTTTAATATTATAT-AT-T-T
* * *
4333866 TAAATATATTTTTAATGTT-ATA-TATAT-TTT
1 T-ATTTTA-TTTT-ATTTTAATATTATATATTT
* *
4333896 TA-TTTA--TTATTATAATTTTATAT-TTT
1 TATTTTATTTTATTTTAATATTATATATTT
**
4333922 TATTTT-TAATATTTTAATATTATATATTT
1 TATTTTATTTTATTTTAATATTATATATTT
4333951 TATTTTATTTTATTTTATCTATATTATATAAATTT
1 TATTTTATTTTATTTTA---ATATTATAT--ATTT
*
4333986 TAATTTT-TTATATTTTA
1 T-ATTTTATTTTATTTTA
4334003 TTTTATTTTT
Statistics
Matches: 150, Mismatches: 23, Indels: 48
0.68 0.10 0.22
Matches are distributed among these distances:
24 3 0.02
25 4 0.03
26 10 0.07
27 3 0.02
28 24 0.16
29 22 0.15
30 23 0.15
31 12 0.08
32 5 0.03
33 11 0.07
34 5 0.03
35 19 0.13
36 9 0.06
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (30 bp):
TATTTTATTTTATTTTAATATTATATATTT
Found at i:4334003 original size:26 final size:26
Alignment explanation
Indices: 4333892--4334031 Score: 75
Period size: 26 Copynumber: 5.6 Consensus size: 26
4333882 GTTATATATA
4333892 TTTTTAT-TTATTAT-TATAATTTT-AT
1 TTTTTATATT-TTATATA-AATTTTAAT
4333917 ATTTTTAT-TTTTA-AT--ATTTTAAT
1 -TTTTTATATTTTATATAAATTTTAAT
* * **
4333940 ATTATATATTTTAT-TTTATTTT-AT
1 TTTTTATATTTTATATAAATTTTAAT
* * *
4333964 TTTATCTATATTATATAAATTTTAAT
1 TTTTTATATTTTATATAAATTTTAAT
* **
4333990 TTTTTATATTTTATTTTATTTTTTAA-
1 TTTTTATATTTTA-TATAAATTTTAAT
*
4334016 TTTTTATATTATATAT
1 TTTTTATATTTTATAT
4334032 TTTATTTTAA
Statistics
Matches: 90, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
22 10 0.11
23 8 0.09
24 13 0.14
25 17 0.19
26 33 0.37
27 9 0.10
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (26 bp):
TTTTTATATTTTATATAAATTTTAAT
Found at i:4334024 original size:50 final size:51
Alignment explanation
Indices: 4333911--4334030 Score: 144
Period size: 50 Copynumber: 2.4 Consensus size: 51
4333901 ATTATTATAA
4333911 TTTTATATTTTTAT-TT-T-TAATATTTTAATATTATATATTTTATTTTATT
1 TTTTA-ATTTTTATATTATATAATATTTTAATATTATATATTTTATTTTATT
* * *
4333960 TTATT--TTATCTATATTATATAA-ATTTTAATTTTTTATATTTTATTTTATT
1 TT-TTAATT-TTTATATTATATAATATTTTAATATTATATATTTTATTTTATT
4334010 TTTTAATTTTTATATTATATA
1 TTTTAATTTTTATATTATATA
4334031 TTTTATTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
47 2 0.03
48 4 0.07
49 6 0.10
50 43 0.72
51 5 0.08
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (51 bp):
TTTTAATTTTTATATTATATAATATTTTAATATTATATATTTTATTTTATT
Found at i:4334039 original size:26 final size:26
Alignment explanation
Indices: 4333932--4334043 Score: 102
Period size: 26 Copynumber: 4.1 Consensus size: 26
4333922 TATTTTTAAT
*
4333932 ATTTTAATATTATATATTTTATTTTA
1 ATTTTTATATTATATATTTTATTTTA
* * **
4333958 TTTTATTTTATCTATATTATATAAATTTTA
1 ATTT-TTATAT-TATA-TAT-TTTATTTTA
4333988 ATTTTTTATATT-T-TATTTTATTTTTTA
1 A-TTTTTATATTATATATTTTA--TTTTA
4334015 ATTTTTATATTATATATTTTATTTTA
1 ATTTTTATATTATATATTTTATTTTA
4334041 ATT
1 ATT
4334044 ATAACAATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
25 2 0.03
26 24 0.35
27 11 0.16
28 12 0.18
29 4 0.06
30 12 0.18
31 3 0.04
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (26 bp):
ATTTTTATATTATATATTTTATTTTA
Found at i:4334065 original size:78 final size:80
Alignment explanation
Indices: 4333911--4334067 Score: 180
Period size: 78 Copynumber: 2.0 Consensus size: 80
4333901 ATTATTATAA
* * * *
4333911 TTTTATATTTTTATTTTTAATATTTTAATATTATATATTTTATTTTATTTTATTTTATCTATATT
1 TTTTATATTTTTATTTTTAATATTTTAATATTATATATTTTATTTTATTTTATTATAACAATATA
*
4333976 ATATAAATTTTAATT
66 AAATAAATTTTAATT
* *
4333991 TTTTATA-TTTTA-TTTT-ATTTTTTAAT-TTTTATATTATATATTTTATTTTAATTATAACAAT
1 TTTTATATTTTTATTTTTAATATTTTAATATTATATATT-T-TATTTTATTTT-ATTATAACAAT
*
4334052 ATAAAAT-ATTTTTAAT
63 ATAAAATAAATTTTAAT
4334068 AAGATAATAA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
76 8 0.12
77 10 0.15
78 23 0.35
79 18 0.27
80 7 0.11
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (80 bp):
TTTTATATTTTTATTTTTAATATTTTAATATTATATATTTTATTTTATTTTATTATAACAATATA
AAATAAATTTTAATT
Found at i:4335304 original size:2 final size:2
Alignment explanation
Indices: 4335291--4335326 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4335281 AAGAACCATA
* *
4335291 AT AT AT AC AT AT AT AC 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
4335327 GAGAATCTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4341706 original size:22 final size:22
Alignment explanation
Indices: 4341675--4341724 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
4341665 TATTATCTTT
*
4341675 TTATTTAGAGTTAAATAAATTC
1 TTATTAAGAGTTAAATAAATTC
*
4341697 TTATTAAGAGTTAAATAAATTT
1 TTATTAAGAGTTAAATAAATTC
4341719 TTATTA
1 TTATTA
4341725 GTAATGATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (22 bp):
TTATTAAGAGTTAAATAAATTC
Found at i:4343144 original size:5 final size:5
Alignment explanation
Indices: 4343134--4343166 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
4343124 CCTTCGTTAA
*
4343134 AAAAG AAAAG AAAAG AAACG AAAAG -AAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
4343167 TATATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:4351541 original size:2 final size:2
Alignment explanation
Indices: 4351534--4351573 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4351524 GAACAAGCAG
4351534 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4351574 GTCTGTCTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4368631 original size:25 final size:25
Alignment explanation
Indices: 4368603--4368654 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
4368593 ACCTTACAAT
*
4368603 TAGGAATATTCAAATTTTATGGTAA
1 TAGGAATATTCAAATTTTATGGAAA
4368628 TAGGAATATTCAAATTTTATGGAAA
1 TAGGAATATTCAAATTTTATGGAAA
4368653 TA
1 TA
4368655 ATGAAACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.38
Consensus pattern (25 bp):
TAGGAATATTCAAATTTTATGGAAA
Found at i:4377178 original size:4 final size:4
Alignment explanation
Indices: 4377169--4377201 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
4377159 TAAAATAATA
4377169 ATTT ATTT ATTT ATTT ATTT ATTT A-TT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
4377202 CCCTTAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:4394732 original size:18 final size:20
Alignment explanation
Indices: 4394698--4394734 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
4394688 ATTTCACATA
4394698 TTTATAATATAAAATAATAT
1 TTTATAATATAAAATAATAT
4394718 TTTATAAT-T-AAATAATA
1 TTTATAATATAAAATAATA
4394735 GAACATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTATAATATAAAATAATAT
Found at i:4396387 original size:2 final size:2
Alignment explanation
Indices: 4396380--4396404 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4396370 GAACACAGAA
4396380 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
4396405 TAATGCTATT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4404792 original size:10 final size:10
Alignment explanation
Indices: 4404777--4404801 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4404767 CAATTTGCCT
4404777 TTTTTTTTTG
1 TTTTTTTTTG
4404787 TTTTTTTTTG
1 TTTTTTTTTG
4404797 TTTTT
1 TTTTT
4404802 CAAAGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:4417690 original size:70 final size:70
Alignment explanation
Indices: 4417555--4417691 Score: 211
Period size: 70 Copynumber: 2.0 Consensus size: 70
4417545 TCCACTAAAA
* * *
4417555 CCAGTTCTCAAATTCATAATGACTACTTGTTTCAATCCTAATGAATTCTTATAATACTTGCAAGG
1 CCAGTTCTCAAATTCACAATGACTACTTGTTTCAATCCCAATGAATTCTTATAATACTTACAAGG
4417620 ATTTT
66 ATTTT
* * * *
4417625 CCAGTTCTCAAATTCACAATGAGTAGTTGTTTCAATCCCAATGAATTGTTATAATACTTATAAGG
1 CCAGTTCTCAAATTCACAATGACTACTTGTTTCAATCCCAATGAATTCTTATAATACTTACAAGG
4417690 AT
66 AT
4417692 GTCAAGTGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.38
Consensus pattern (70 bp):
CCAGTTCTCAAATTCACAATGACTACTTGTTTCAATCCCAATGAATTCTTATAATACTTACAAGG
ATTTT
Found at i:4418899 original size:2 final size:2
Alignment explanation
Indices: 4418892--4418918 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4418882 GTTAGCACTA
4418892 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
4418919 AATATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4445854 original size:35 final size:35
Alignment explanation
Indices: 4445806--4445893 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
4445796 TTCATATGAA
* * *
4445806 AAGTAGCGTTTCACTTGTTTTAGTT-TTTCTGCT-TG
1 AAGTAGTGCTTCACTTGTTCTAGTTGTTTC-G-TATG
4445841 AAGTAGTGCTTCACTTGTTCTAGTTGTTTCGTATG
1 AAGTAGTGCTTCACTTGTTCTAGTTGTTTCGTATG
* *
4445876 AAATAGTACTTCACTTGT
1 AAGTAGTGCTTCACTTGT
4445894 AAAGGTTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 1 0.02
35 41 0.89
36 4 0.09
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (35 bp):
AAGTAGTGCTTCACTTGTTCTAGTTGTTTCGTATG
Found at i:4449340 original size:2 final size:2
Alignment explanation
Indices: 4449323--4449360 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
4449313 GTGCTTGTAC
* *
4449323 AT AT AA AT AC 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
4449361 CTGTCTGTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4458653 original size:2 final size:2
Alignment explanation
Indices: 4458646--4458678 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4458636 AAACCTTCGC
4458646 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4458679 GGTCAGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4459555 original size:17 final size:18
Alignment explanation
Indices: 4459535--4459576 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
4459525 AATTATAAAA
4459535 TATATATACAAAT-TATG
1 TATATATACAAATATATG
* *
4459552 TATAAAT-TAAATATATG
1 TATATATACAAATATATG
4459569 TATATATA
1 TATATATA
4459577 TGATATGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (18 bp):
TATATATACAAATATATG
Found at i:4459990 original size:36 final size:36
Alignment explanation
Indices: 4459950--4460020 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
4459940 AGTATAATTA
4459950 TATAAATAA-ATATTATAAAT-TATAGTAATGTTTATG
1 TATAAATAATATA-TATAAATATATA-TAATGTTTATG
* *
4459986 TATAAATTATATATATATATATATATAATGTTTAT
1 TATAAATAATATATATAAATATATATAATGTTTAT
4460021 ACAATTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 24 0.77
37 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (36 bp):
TATAAATAATATATATAAATATATATAATGTTTATG
Found at i:4460012 original size:23 final size:21
Alignment explanation
Indices: 4459945--4460013 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 21
4459935 TATTAAGTAT
*
4459945 AATTATATAAATAAATATTATA
1 AATTATAT-AATATATATTATA
* *
4459967 AATTATAGTAATGTTTATGTATA
1 AATTATA-TAATATATAT-TATA
4459990 AATTATATATATATATATATATA
1 AATTATATA-ATATATAT-TATA
4460013 A
1 A
4460014 TGTTTATACA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 15 0.39
23 23 0.61
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
AATTATATAATATATATTATA
Found at i:4461856 original size:135 final size:132
Alignment explanation
Indices: 4461701--4461963 Score: 321
Period size: 135 Copynumber: 2.0 Consensus size: 132
4461691 GTATAAACAC
* * * * *
4461701 TATATATATTTAATTTATACATAAATATTACTATAACTTCTAAT-TTTTATTTTTATAATTACAC
1 TATATATATTTAATTTATACATAAATAATACTATAAATTATAATACTTTATTTATATAATTACAC
*
4461765 TTAATAACTTTTAATTATCATCCGAGTTTTTATAACATATTATTTATAATTAGTTATTATTTATA
66 TTAATAA---TTAATTA-CATCCGAATTTTTATAACATATTATTTATAATTAGTTATTATTTATA
4461830 TATGCA
127 TATGCA
* * * *
4461836 TATATATGTTTAATTTATACATAAGTAATACTGTAAATTATAATAAACTTTATTTATATGATTAC
1 TATATATATTTAATTTATACATAAATAATACTATAAATTATAAT--ACTTTATTTATATAATTAC
* * ** * *
4461901 ACTTCATAATTAGTTACATCTTAATTTTTATAATATATTGTTTATAATTAGTTATTATTTATA
64 ACTTAATAATTAATTACATCCGAATTTTTATAACATATTATTTATAATTAGTTATTATTTATA
4461964 CAAAGTTTGA
Statistics
Matches: 109, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
134 42 0.39
135 44 0.40
138 23 0.21
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.51
Consensus pattern (132 bp):
TATATATATTTAATTTATACATAAATAATACTATAAATTATAATACTTTATTTATATAATTACAC
TTAATAATTAATTACATCCGAATTTTTATAACATATTATTTATAATTAGTTATTATTTATATATG
CA
Found at i:4462048 original size:17 final size:19
Alignment explanation
Indices: 4462013--4462052 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4462003 TCATTAATTT
4462013 CATATATATAATATATATA
1 CATATATATAATATATATA
*
4462032 CATATATTTAAT-T-TATA
1 CATATATATAATATATATA
4462049 CATA
1 CATA
4462053 ATCTGTATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
19 11 0.55
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (19 bp):
CATATATATAATATATATA
Found at i:4463452 original size:7 final size:8
Alignment explanation
Indices: 4463435--4463491 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 8
4463425 ATTTAAGTTG
4463435 TTATATTA
1 TTATATTA
4463443 TTAT-TTA
1 TTATATTA
4463450 TTATAATATA
1 TTAT-AT-TA
4463460 TTAATATT-
1 TT-ATATTA
*
4463468 TTATATCA
1 TTATATTA
4463476 TTAT-TTA
1 TTATATTA
4463483 TTATATTA
1 TTATATTA
4463491 T
1 T
4463492 ATTAAAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 17 0.41
8 14 0.34
9 2 0.05
10 6 0.15
11 2 0.05
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATATTA
Found at i:4465833 original size:20 final size:21
Alignment explanation
Indices: 4465794--4465833 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4465784 AAATAAATAT
4465794 TTAAAATTTTAATATATTTAA
1 TTAAAATTTTAATATATTTAA
*
4465815 TTAAAATTTT-ATATTTTTA
1 TTAAAATTTTAATATATTTA
4465834 TTTTGAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAAAATTTTAATATATTTAA
Found at i:4465863 original size:30 final size:30
Alignment explanation
Indices: 4465827--4465884 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4465817 AAAATTTTAT
*
4465827 ATTTTTATTTTGAATCAAATAAGCTCTTAC
1 ATTTTTATTTTGAATCAAATAAACTCTTAC
* *
4465857 ATTTTTATTTTTAGTCAAATAAACTCTT
1 ATTTTTATTTTGAATCAAATAAACTCTT
4465885 GCAACTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (30 bp):
ATTTTTATTTTGAATCAAATAAACTCTTAC
Found at i:4466522 original size:19 final size:20
Alignment explanation
Indices: 4466500--4466537 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4466490 TACTCTTTTA
*
4466500 TTATATT-TACATAAAATCT
1 TTATATTGTACAAAAAATCT
*
4466519 TTATTTTGTACAAAAAATC
1 TTATATTGTACAAAAAATC
4466538 AGCATTTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.45
Consensus pattern (20 bp):
TTATATTGTACAAAAAATCT
Found at i:4467279 original size:2 final size:2
Alignment explanation
Indices: 4467274--4467304 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4467264 TTATGTGTGC
4467274 AT AT AT 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 AT AT AT A
4467305 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4467309 original size:2 final size:2
Alignment explanation
Indices: 4467304--4467330 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4467294 ATATATATAT
4467304 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
4467331 AGTATGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4468810 original size:22 final size:22
Alignment explanation
Indices: 4468780--4468826 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
4468770 ATTTTAAATA
* *
4468780 ATTTGTAATTATTATATA-TAGT
1 ATTTATAATTA-TACATAGTAGT
4468802 ATTTATAATTATACATAGTAGT
1 ATTTATAATTATACATAGTAGT
4468824 ATT
1 ATT
4468827 AAACAAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
ATTTATAATTATACATAGTAGT
Found at i:4469572 original size:40 final size:40
Alignment explanation
Indices: 4469512--4469590 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
4469502 TTAACATTAA
4469512 TTTTATATTGCTAATACATTATCTTAGTTTCAAGTTACGG
1 TTTTATATTGCTAATACATTATCTTAGTTTCAAGTTACGG
*
4469552 TTTTATATTGCTAATGCATTATCTTAGTTTCAAGTTACG
1 TTTTATATTGCTAATACATTATCTTAGTTTCAAGTTACG
4469591 ACTTAGTGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.48
Consensus pattern (40 bp):
TTTTATATTGCTAATACATTATCTTAGTTTCAAGTTACGG
Found at i:4471211 original size:22 final size:22
Alignment explanation
Indices: 4471182--4471236 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
4471172 CCCGCGCCTA
**
4471182 TTTCTTTTCTGTTTTGTCTT-TT
1 TTTCTTTTCAATTTTGT-TTCTT
*
4471204 TTTTTTTTCAATTTTGTTTCTT
1 TTTCTTTTCAATTTTGTTTCTT
4471226 TTTCTTTTCAA
1 TTTCTTTTCAA
4471237 AGCCAACTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.07, C:0.13, G:0.05, T:0.75
Consensus pattern (22 bp):
TTTCTTTTCAATTTTGTTTCTT
Found at i:4474616 original size:64 final size:64
Alignment explanation
Indices: 4474515--4474642 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
4474505 TTAGTAGAAA
*
4474515 GTGTAAGTGCTTTTATCTATGTCTATCAAGCTTATGTACATGTGTATTGGTGTGTGTACTCGTG
1 GTGTAAGTGCTTTTATCTATGTCTATCAAGCTTATGTACATGTGTATTGGTGTGTATACTCGTG
*
4474579 GTGTAAGTGTTTTTATCTATGTCTATCAAGCTTATGTACATGTGTATTGGTGTGTATACTCGTG
1 GTGTAAGTGCTTTTATCTATGTCTATCAAGCTTATGTACATGTGTATTGGTGTGTATACTCGTG
4474643 CGTCAACATG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.45
Consensus pattern (64 bp):
GTGTAAGTGCTTTTATCTATGTCTATCAAGCTTATGTACATGTGTATTGGTGTGTATACTCGTG
Found at i:4483468 original size:3 final size:3
Alignment explanation
Indices: 4483460--4483496 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
4483450 GAAAGTGAAG
*
4483460 GAA GAA GAA GCA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
4483497 CAGCAGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4485429 original size:111 final size:113
Alignment explanation
Indices: 4485232--4485445 Score: 337
Period size: 111 Copynumber: 1.9 Consensus size: 113
4485222 CTTCTAACTG
*
4485232 TGACATTGGTTCTGCAATTTGAGAAAAGAGAGGGGGGAAGTTGTGTTACTGAAATATGACAAAAG
1 TGACATTGGTTCTGCAATTTGAGAAAAGAGAGAGGGGAAGTTGTGTTACTGAAATATGACAAAAG
*
4485297 TATGTGGTGCTGAAAGATCCTTGTGAGTAGTTTTAGAACTGTAGCAAGA
66 TATGTGGTGCTGAAAGATCCTTGTGAGT-CTTTTAGAACTGTAGCAAGA
* *
4485346 TGACATTGGTTCTGCCATTTG-GAAAAGA-A-AGGGGAAGGTTGTGTTACTGGAAT-TGACAAAA
1 TGACATTGGTTCTGCAATTTGAGAAAAGAGAGAGGGGAA-GTTGTGTTACTGAAATATGACAAAA
*
4485407 GTATGTGGTGCTGAAAGATCCTTTTGAGTCTTTTAGAAC
65 GTATGTGGTGCTGAAAGATCCTTGTGAGTCTTTTAGAAC
4485446 CATATCAAGA
Statistics
Matches: 94, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
110 9 0.10
111 42 0.45
112 16 0.17
113 7 0.07
114 20 0.21
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.30
Consensus pattern (113 bp):
TGACATTGGTTCTGCAATTTGAGAAAAGAGAGAGGGGAAGTTGTGTTACTGAAATATGACAAAAG
TATGTGGTGCTGAAAGATCCTTGTGAGTCTTTTAGAACTGTAGCAAGA
Found at i:4491333 original size:94 final size:94
Alignment explanation
Indices: 4491185--4491433 Score: 229
Period size: 94 Copynumber: 2.7 Consensus size: 94
4491175 CATGCTAAGG
* * ** * * **
4491185 CTATATATGTTACCATATATGTAAATTTTT-TTTTAATCATCTTATAAATTTATGTGAGAGAAGA
1 CTATATATGTTACCATATATG-CACTTTTTCCCTTAATTATCTTATGAACCTATGTGAGAGAAGA
*
4491249 AAAATCCAGC-ATAAATTACATAAAAATCTA
65 AAAATCCA-CTATAAATTACACAAAAATCTA
* * * *
4491279 CTATATATGTTACCATGTATGCA-TGTTCTT-CCTTAATTGTCTTATGAACCTATGTAAGAGATG
1 CTATATATGTTACCATATATGCACT-TT-TTCCCTTAATTATCTTATGAACCTATGTGAGAGAAG
* ** ** *
4491342 AAAAGTTTACTATAAATTATGCAAAAATCTG
64 AAAAATCCACTATAAATTACACAAAAATCTA
* * *
4491373 TTATATATGTTACCATATATGTACTTTTTCCCTTAATTATCTTATGAACCTATATG-GAGAA
1 CTATATATGTTACCATATATGCACTTTTTCCCTTAATTATCTTATGAACCTATGTGAGAGAA
4491434 AAATTTTACT
Statistics
Matches: 125, Mismatches: 25, Indels: 11
0.78 0.16 0.07
Matches are distributed among these distances:
92 1 0.01
93 10 0.08
94 113 0.90
95 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (94 bp):
CTATATATGTTACCATATATGCACTTTTTCCCTTAATTATCTTATGAACCTATGTGAGAGAAGAA
AAATCCACTATAAATTACACAAAAATCTA
Found at i:4493649 original size:17 final size:18
Alignment explanation
Indices: 4493626--4493689 Score: 80
Period size: 17 Copynumber: 3.7 Consensus size: 18
4493616 TTTATTTTAT
4493626 TTTAAAATATTATTATAA
1 TTTAAAATATTATTATAA
4493644 -TTAAAATATTA--ATAA
1 TTTAAAATATTATTATAA
* *
4493659 TTTAAATTAGTTATTAAAA
1 TTTAAAATA-TTATTATAA
4493678 TTTAAAATATTA
1 TTTAAAATATTA
4493690 ATTTTTATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 4 0.10
16 7 0.18
17 14 0.36
18 3 0.08
19 11 0.28
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTTAAAATATTATTATAA
Found at i:4493660 original size:15 final size:15
Alignment explanation
Indices: 4493627--4493712 Score: 52
Period size: 15 Copynumber: 5.4 Consensus size: 15
4493617 TTATTTTATT
4493627 TTAAAATATTATTATAA
1 TTAAAATATTA--ATAA
4493644 TTAAAATATTAATAA
1 TTAAAATATTAATAA
4493659 TTTAAATTAGTTATTAA-AA
1 -TTAAA--A--TATTAATAA
**
4493678 TTTAAAATATTAATTT
1 -TTAAAATATTAATAA
*
4493694 TTATAATA-T-ATAA
1 TTAAAATATTAATAA
4493707 TTAAAA
1 TTAAAA
4493713 ACTTAAACTC
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
13 7 0.12
14 1 0.02
15 17 0.30
16 5 0.09
17 12 0.21
18 1 0.02
19 8 0.14
20 6 0.11
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (15 bp):
TTAAAATATTAATAA
Found at i:4493667 original size:27 final size:27
Alignment explanation
Indices: 4493626--4493690 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
4493616 TTTATTTTAT
4493626 TTTAAAATATT--ATTA-TAATTAAAA
1 TTTAAAATATTAAATTAGTAATTAAAA
*
4493650 TATTAATAAT-TTAAATTAGTTATTAAAA
1 T-TTAA-AATATTAAATTAGTAATTAAAA
4493678 TTTAAAATATTAA
1 TTTAAAATATTAA
4493691 TTTTTATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
24 1 0.03
25 6 0.18
26 6 0.18
27 12 0.35
28 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
TTTAAAATATTAAATTAGTAATTAAAA
Found at i:4493710 original size:35 final size:35
Alignment explanation
Indices: 4493644--4493712 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
4493634 ATTATTATAA
*
4493644 TTAAAATATTAATAATTTAAATTAGTTATTAAAAT
1 TTAAAATATTAATAATTTAAATTAGTAATTAAAAT
*
4493679 TTAAAATATTAAT-TTTTATAATATA-TAATTAAAA
1 TTAAAATATTAATAATTTA-AAT-TAGTAATTAAAA
4493713 ACTTAAACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 4 0.13
35 24 0.80
36 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (35 bp):
TTAAAATATTAATAATTTAAATTAGTAATTAAAAT
Found at i:4493996 original size:19 final size:20
Alignment explanation
Indices: 4493961--4494001 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
4493951 TCATTTAATA
4493961 ATTTAAATATTAATATT-TT
1 ATTTAAATATTAATATTATT
*
4493980 ATTTATAAT-TTAGTATTATT
1 ATTTA-AATATTAATATTATT
4494000 AT
1 AT
4494002 GACTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTTAAATATTAATATTATT
Found at i:4493999 original size:28 final size:28
Alignment explanation
Indices: 4493939--4494000 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
4493929 TTTTCATTTT
*
4493939 TTATTTATATTTTCATTTAATAATTTAA
1 TTATTAATATTTTCATTTAATAATTTAA
*
4493967 ATATTAATATTTT-ATTT-ATAATTTAGTA
1 TTATTAATATTTTCATTTAATAATTTA--A
4493995 TTATTA
1 TTATTA
4494001 TGACTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 8 0.28
27 4 0.14
28 17 0.59
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
TTATTAATATTTTCATTTAATAATTTAA
Found at i:4499833 original size:2 final size:2
Alignment explanation
Indices: 4499826--4499865 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
4499816 AATAGTGCTG
* *
4499826 TA TA TA TA TA TA TA TA TG TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4499866 AAGGTAATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4500780 original size:21 final size:22
Alignment explanation
Indices: 4500744--4500789 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
4500734 TTATTAAGTT
4500744 TATTTAAATTAAATATATTAAAA
1 TATTTAAA-TAAATATATTAAAA
4500767 TATTTAAA-AAATATATTAAAA
1 TATTTAAATAAATATATTAAAA
4500788 TA
1 TA
4500790 AAAATAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 15 0.65
23 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TATTTAAATAAATATATTAAAA
Found at i:4509177 original size:16 final size:15
Alignment explanation
Indices: 4509155--4509205 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
4509145 GAAATAGATA
4509155 AAAATTAAATAAAAT
1 AAAATTAAATAAAAT
* *
4509170 AATTATTACATAAAAAT
1 AA-AATTAAAT-AAAAT
*
4509187 AAAATAAAATAAAAT
1 AAAATTAAATAAAAT
4509202 AAAA
1 AAAA
4509206 ATAATTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 11 0.38
16 11 0.38
17 7 0.24
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATTAAATAAAAT
Found at i:4509206 original size:16 final size:16
Alignment explanation
Indices: 4509152--4509209 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
4509142 CAAGAAATAG
*
4509152 ATAAAAATTAAATAAA
1 ATAAAAATAAAATAAA
** * *
4509168 ATAATTATTACATAAA
1 ATAAAAATAAAATAAA
4509184 A-ATAAAATAAAATAAA
1 ATA-AAAATAAAATAAA
4509200 ATAAAAATAA
1 ATAAAAATAA
4509210 TTATTATGAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 1 0.03
16 31 0.94
17 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAATAAAATAAA
Found at i:4509209 original size:27 final size:27
Alignment explanation
Indices: 4509152--4509205 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
4509142 CAAGAAATAG
* * * *
4509152 ATAAAAATTAAATAAAATAATTATTAC
1 ATAAAAATAAAATAAAATAAATATAAA
4509179 ATAAAAATAAAATAAAATAAA-ATAAA
1 ATAAAAATAAAATAAAATAAATATAAA
4509205 A
1 A
4509206 ATAATTATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (27 bp):
ATAAAAATAAAATAAAATAAATATAAA
Found at i:4509372 original size:27 final size:26
Alignment explanation
Indices: 4509322--4509374 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
4509312 ATTTTATTTT
**
4509322 TTAAATATTAATAATTTATAATTTAA
1 TTAAATATTAATAATCAATAATTTAA
*
4509348 TTAAACTATTAATAATCAATCATTTAA
1 TTAAA-TATTAATAATCAATAATTTAA
4509375 ATATTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAAATATTAATAATCAATAATTTAA
Found at i:4509457 original size:42 final size:41
Alignment explanation
Indices: 4509373--4509457 Score: 93
Period size: 42 Copynumber: 2.0 Consensus size: 41
4509363 TCAATCATTT
**
4509373 AAATATTAATATTTTATTTATAATTTAATATTATTATGATTA
1 AAATATTAATATTTTATTTAT-ATTTAATATTAAAATGATTA
*
4509415 AAATATTAATAATTTTAATTTAT-TTTCATATTTAAAAT-ATTA
1 AAATATTAAT-ATTTT-ATTTATATTTAATA-TTAAAATGATTA
4509457 A
1 A
4509458 TTTTATAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
42 21 0.57
43 10 0.27
44 6 0.16
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (41 bp):
AAATATTAATATTTTATTTATATTTAATATTAAAATGATTA
Found at i:4509739 original size:16 final size:16
Alignment explanation
Indices: 4509714--4509744 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4509704 TTATGTTTTC
4509714 ATTAAAAATTTAATAT
1 ATTAAAAATTTAATAT
*
4509730 ATTAATAATTTAATA
1 ATTAAAAATTTAATA
4509745 AGATAAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAAAAATTTAATAT
Found at i:4514772 original size:11 final size:12
Alignment explanation
Indices: 4514752--4514786 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
4514742 TTTATATATT
4514752 ATATATTTTTTA
1 ATATATTTTTTA
*
4514764 ATA-ATTTTTAA
1 ATATATTTTTTA
4514775 ATATATTTTTTA
1 ATATATTTTTTA
4514787 TTAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATATATTTTTTA
Found at i:4514800 original size:23 final size:23
Alignment explanation
Indices: 4514752--4514802 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
4514742 TTTATATATT
**
4514752 ATATATTTTTTAATAATTTTTAA
1 ATATATTTTTTAATAATAATTAA
*
4514775 ATATATTTTTTATTAAATAATT-A
1 ATATATTTTTTAAT-AATAATTAA
4514798 ATATA
1 ATATA
4514803 ATTAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATATATTTTTTAATAATAATTAA
Found at i:4515673 original size:15 final size:18
Alignment explanation
Indices: 4515641--4515677 Score: 53
Period size: 15 Copynumber: 2.2 Consensus size: 18
4515631 TATTTACATG
4515641 TTATAAAATTATTATTTA
1 TTATAAAATTATTATTTA
4515659 TTAT-AAATT-TT-TTTA
1 TTATAAAATTATTATTTA
4515674 TTAT
1 TTAT
4515678 TAATGGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
16 2 0.11
17 5 0.26
18 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATAAAATTATTATTTA
Found at i:4518663 original size:3 final size:3
Alignment explanation
Indices: 4518655--4518681 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4518645 GTTAACATCC
4518655 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
4518682 GACTACTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:4522828 original size:2 final size:2
Alignment explanation
Indices: 4522821--4522851 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4522811 GAGTTTCATA
4522821 AT AT AT 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 AT AT AT A
4522852 AGGCTTATTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4561869 original size:19 final size:20
Alignment explanation
Indices: 4561847--4561888 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
4561837 ATTGATATAT
* *
4561847 TTTAATATTTAAT-TTATTA
1 TTTAATATATAATGTCATTA
*
4561866 TTTAGTATATAATGTCATTA
1 TTTAATATATAATGTCATTA
4561886 TTT
1 TTT
4561889 TAAAAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTAATATATAATGTCATTA
Found at i:4564599 original size:7 final size:7
Alignment explanation
Indices: 4564587--4564614 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
4564577 CTATGATCTT
4564587 AGGTTTA
1 AGGTTTA
4564594 AGGTTTA
1 AGGTTTA
4564601 AGGTTTA
1 AGGTTTA
4564608 AGGTTTA
1 AGGTTTA
4564615 GTTTGTCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (7 bp):
AGGTTTA
Found at i:4567929 original size:2 final size:2
Alignment explanation
Indices: 4567922--4567952 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4567912 GCTTTTCATT
4567922 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
4567953 GAGACAAACG
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4572049 original size:2 final size:2
Alignment explanation
Indices: 4572042--4572070 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4572032 AAGGCAAAAT
4572042 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4572071 TTGCAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4583829 original size:18 final size:18
Alignment explanation
Indices: 4583808--4583875 Score: 51
Period size: 18 Copynumber: 4.1 Consensus size: 18
4583798 AATAATAATT
4583808 AATTAATTTAATTATATA
1 AATTAATTTAATTATATA
*
4583826 AATTTATTT-ATT-T-TA
1 AATTAATTTAATTATATA
* *
4583841 AAATAA---AAATATATA
1 AATTAATTTAATTATATA
4583856 AATTTAATTTAA-TATATA
1 AA-TTAATTTAATTATATA
4583874 AA
1 AA
4583876 AATTTTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
13 2 0.05
14 1 0.03
15 10 0.26
16 4 0.11
17 3 0.08
18 16 0.42
19 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTAATTTAATTATATA
Found at i:4583840 original size:23 final size:23
Alignment explanation
Indices: 4583777--4583841 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
4583767 TAAATATAAA
4583777 AATAAT-ATT-ATTATTTTAATT
1 AATAATAATTAATTATTTTAATT
*
4583798 AATAATAATTAATTAATTTAATT
1 AATAATAATTAATTATTTTAATT
* *
4583821 ATATAA-ATTTATTTATTTTAA
1 A-ATAATAATTAATTATTTTAA
4583842 AATAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.16
22 3 0.08
23 24 0.65
24 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATAATAATTAATTATTTTAATT
Found at i:4590975 original size:5 final size:5
Alignment explanation
Indices: 4590960--4590991 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
4590950 TTTTCATCAC
4590960 CATCT -ATCT CATCT CATCT CATCT CATCT CAT
1 CATCT CATCT CATCT CATCT CATCT CATCT CAT
4590992 TTCAACCGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.41
Consensus pattern (5 bp):
CATCT
Found at i:4594881 original size:2 final size:2
Alignment explanation
Indices: 4594870--4594908 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
4594860 AATTTTTGAA
4594870 AT AT -T AT AT AT A- AT AT -T A- 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
4594908 A
1 A
4594909 AAATAACAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.12
2 29 0.88
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4626804 original size:2 final size:2
Alignment explanation
Indices: 4626797--4626826 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4626787 TCTTAACAAC
4626797 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
4626827 TCGCATCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4628660 original size:42 final size:42
Alignment explanation
Indices: 4628601--4628685 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
4628591 GATATTCCAA
4628601 TGATTTGATATTTTAGAAAGAATTTGAATGACAAAAAGATTG
1 TGATTTGATATTTTAGAAAGAATTTGAATGACAAAAAGATTG
4628643 TGATTTGATATTTTAGAAAGAATTTGAATGACAAAAAGATTG
1 TGATTTGATATTTTAGAAAGAATTTGAATGACAAAAAGATTG
4628685 T
1 T
4628686 TGCAGCACGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.36
Consensus pattern (42 bp):
TGATTTGATATTTTAGAAAGAATTTGAATGACAAAAAGATTG
Found at i:4630186 original size:11 final size:11
Alignment explanation
Indices: 4630170--4630198 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
4630160 TTGGCAGAGC
4630170 AAGAAAACTCA
1 AAGAAAACTCA
4630181 AAGAAAACTCA
1 AAGAAAACTCA
4630192 AAGAAAA
1 AAGAAAA
4630199 AGAACGCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.69, C:0.14, G:0.10, T:0.07
Consensus pattern (11 bp):
AAGAAAACTCA
Found at i:4632681 original size:19 final size:19
Alignment explanation
Indices: 4632645--4632682 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
4632635 TTTTTTATTT
*
4632645 TTTAATATTTTATTATACA
1 TTTAATATTTTATGATACA
4632664 TTTAATAATTTT-TGATACA
1 TTTAAT-ATTTTATGATACA
4632683 ATTATTATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTAATATTTTATGATACA
Found at i:4656004 original size:17 final size:17
Alignment explanation
Indices: 4655978--4656010 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4655968 AGCTAATTGT
4655978 TTATAAATAAAAGACAG
1 TTATAAATAAAAGACAG
*
4655995 TTATATATAAAAGACA
1 TTATAAATAAAAGACA
4656011 ATTGATGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (17 bp):
TTATAAATAAAAGACAG
Found at i:4656127 original size:47 final size:47
Alignment explanation
Indices: 4656075--4656177 Score: 188
Period size: 47 Copynumber: 2.2 Consensus size: 47
4656065 ATTCAATACC
4656075 ATTAGAATTAAGAAAAACATATTTTGATATAAAAGTCAATGAATGCA
1 ATTAGAATTAAGAAAAACATATTTTGATATAAAAGTCAATGAATGCA
*
4656122 ATTAGAATTAAGAAAAACATATTTTGATATAAAAGTCATTGAATGCA
1 ATTAGAATTAAGAAAAACATATTTTGATATAAAAGTCAATGAATGCA
*
4656169 ATTACAATT
1 ATTAGAATT
4656178 CTTATTTATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.32
Consensus pattern (47 bp):
ATTAGAATTAAGAAAAACATATTTTGATATAAAAGTCAATGAATGCA
Found at i:4680855 original size:12 final size:12
Alignment explanation
Indices: 4680838--4680864 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4680828 TGTCATGGTG
4680838 TCTAACTATACT
1 TCTAACTATACT
4680850 TCTAACTATACT
1 TCTAACTATACT
4680862 TCT
1 TCT
4680865 TGTCATGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (12 bp):
TCTAACTATACT
Found at i:4681217 original size:25 final size:25
Alignment explanation
Indices: 4681185--4681236 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
4681175 AATATTTTTT
*
4681185 ATATTTTTATATAAAAATAATAAATA
1 ATATTTTAAT-TAAAAATAATAAATA
* *
4681211 ATATTTTAATTAATAATAATTAATA
1 ATATTTTAATTAAAAATAATAAATA
4681236 A
1 A
4681237 ATCATTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATTTTAATTAAAAATAATAAATA
Found at i:4690073 original size:29 final size:29
Alignment explanation
Indices: 4690000--4690081 Score: 78
Period size: 31 Copynumber: 2.8 Consensus size: 29
4689990 TTTGAATTTT
*
4690000 TTTTAATTTAATTTTT-TATTTAAAATTG
1 TTTTAATTTAATTTTTATATTTAAAATTA
** *
4690028 TAATATTTTAAATTTTT-TATTTTAAAAATTA
1 TTTTAATTT-AATTTTTATA-TTT-AAAATTA
4690059 TTTTAATTTAATTTTTAATATTT
1 TTTTAATTTAATTTTT-ATATTT
4690082 TTAATTTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
28 6 0.14
29 9 0.21
30 10 0.24
31 15 0.36
32 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (29 bp):
TTTTAATTTAATTTTTATATTTAAAATTA
Found at i:4690138 original size:18 final size:18
Alignment explanation
Indices: 4690115--4690158 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
4690105 CTTGACATTA
4690115 ATGTGACATCCAATATTG
1 ATGTGACATCCAATATTG
*
4690133 ATGTGACGTCCAATATTG
1 ATGTGACATCCAATATTG
4690151 ATGTGACA
1 ATGTGACA
4690159 GTGACACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (18 bp):
ATGTGACATCCAATATTG
Found at i:4698755 original size:13 final size:13
Alignment explanation
Indices: 4698737--4698761 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4698727 ACTACATAAA
4698737 GTCAAAATTTTAT
1 GTCAAAATTTTAT
4698750 GTCAAAATTTTA
1 GTCAAAATTTTA
4698762 CATGTGAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
GTCAAAATTTTAT
Found at i:4700446 original size:15 final size:15
Alignment explanation
Indices: 4700428--4700468 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4700418 AAATTTAAAA
4700428 TTATAAAATTATAAT
1 TTATAAAATTATAAT
* *
4700443 TTATATAATGATAAT
1 TTATAAAATTATAAT
*
4700458 TTTTAAAATTA
1 TTATAAAATTA
4700469 ATAAAAAGTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TTATAAAATTATAAT
Found at i:4709947 original size:2 final size:2
Alignment explanation
Indices: 4709940--4709976 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4709930 ATAACTTCAT
4709940 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 T
4709977 CCTTTCCTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4710896 original size:77 final size:77
Alignment explanation
Indices: 4710792--4710948 Score: 269
Period size: 77 Copynumber: 2.0 Consensus size: 77
4710782 TGTTTAGAAA
* *
4710792 TTGCATAATCTTATAACAGCGCTTATATTTGATTCAACGTGGAAACAACTAAGGTTGTTGCAAGT
1 TTGCATAATCTTATAACAGCGCTTATATTTGATTCAAAGGGGAAACAACTAAGGTTGTTGCAAGT
*
4710857 CTTGGGTGGTCT
66 CTTGAGTGGTCT
* *
4710869 TTGCATAATCTTATTACAGGGCTTATATTTGATTCAAAGGGGAAACAACTAAGGTTGTTGCAAGT
1 TTGCATAATCTTATAACAGCGCTTATATTTGATTCAAAGGGGAAACAACTAAGGTTGTTGCAAGT
4710934 CTTGAGTGGTCT
66 CTTGAGTGGTCT
4710946 TTG
1 TTG
4710949 TTAGTTAGGG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (77 bp):
TTGCATAATCTTATAACAGCGCTTATATTTGATTCAAAGGGGAAACAACTAAGGTTGTTGCAAGT
CTTGAGTGGTCT
Found at i:4711276 original size:14 final size:14
Alignment explanation
Indices: 4711259--4711288 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4711249 TTTTCACATT
4711259 AAAATTAAGAATGA
1 AAAATTAAGAATGA
4711273 AAAATTAAGAATGA
1 AAAATTAAGAATGA
4711287 AA
1 AA
4711289 GTGAAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (14 bp):
AAAATTAAGAATGA
Found at i:4733805 original size:6 final size:6
Alignment explanation
Indices: 4733794--4733827 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
4733784 AGAAAAGCTA
* *
4733794 TTATTG TTATTG TTATTG TTATTA TTATTA TTAT
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTAT
4733828 CAAATATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (6 bp):
TTATTG
Found at i:4757227 original size:2 final size:2
Alignment explanation
Indices: 4757220--4757244 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4757210 ATGAAGCAAA
4757220 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
4757245 ATCCAACACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4762394 original size:55 final size:55
Alignment explanation
Indices: 4762223--4762586 Score: 174
Period size: 55 Copynumber: 6.6 Consensus size: 55
4762213 ATGTGTAATT
* * * * *
4762223 ATTTTTTTATCATAACGTGTAACAATTAAATTTTTCAATATAACATGTG-ACAACTAA
1 ATTTTTTAAT-ATAACGTGTAATAACTAAA-TTTTCAATATATCATG-GAACAATTAA
* * ** * * * * * *
4762280 A-TTATAAATATAGTGTGTAATAATTATATTTTTCAACAT-TACATGTAATAATTAT
1 ATTTTTTAATATAACGTGTAATAACTA-AATTTTCAATATAT-CATGGAACAATTAA
* *
4762335 ATTTTTTAATATGATGTGTAATAACTAAATTTTCAATATATCATGGAACAATTAA
1 ATTTTTTAATATAACGTGTAATAACTAAATTTTCAATATATCATGGAACAATTAA
* * * * * *
4762390 ATTTTTCAACT-TAACATATAATAACTAAATTTT-AA-ACATAATGTGTAATAATTAA
1 ATTTTTTAA-TATAACGTGTAATAACTAAATTTTCAATATATCATG-G-AACAATTAA
* * ** * * * * **
4762445 A-TCTTTAACATGGCGTGTGACAACTAAATTTTTTAACATGA-CATATAACAATTAA
1 ATTTTTTAATATAACGTGTAATAACTAAA-TTTTCAATAT-ATCATGGAACAATTAA
* * *
4762500 ATTTTTTAACATAACGTGTAATAATTAAATTTTCAATATGA--AGTGTAACAATTAA
1 ATTTTTTAATATAACGTGTAATAACTAAATTTTCAATAT-ATCA-TGGAACAATTAA
* * * * *
4762555 A-TCTTCAACATAACGTGTAATAAATACATTTT
1 ATTTTTTAATATAACGTGTAATAACTAAATTTT
4762587 TTAATATGAC
Statistics
Matches: 234, Mismatches: 58, Indels: 33
0.72 0.18 0.10
Matches are distributed among these distances:
53 6 0.03
54 48 0.21
55 124 0.53
56 51 0.22
57 4 0.02
58 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (55 bp):
ATTTTTTAATATAACGTGTAATAACTAAATTTTCAATATATCATGGAACAATTAA
Found at i:4762428 original size:110 final size:110
Alignment explanation
Indices: 4762309--4762598 Score: 253
Period size: 110 Copynumber: 2.6 Consensus size: 110
4762299 ATAATTATAT
* * * * * * * *
4762309 TTTTCAACATTACATGTAATAATTATATTTTTTAATATGATGTGTAATAACTAAA-TTTTCAATA
1 TTTTAAACATAACATGTAATAATTA-AATCTTTAACATGACGTGTAACAACTAAATTTTTCAACA
* *
4762373 T-ATCATGGAACAATTAAATTTTTCAACTTAACATATAATAACTAAA
65 TGA-CATAGAACAATTAAATTTTTCAACATAACATATAATAACTAAA
** * * *
4762419 TTTTAAACATAATGTGTAATAATTAAATCTTTAACATGGCGTGTGACAACTAAATTTTTTAACAT
1 TTTTAAACATAACATGTAATAATTAAATCTTTAACATGACGTGTAACAACTAAATTTTTCAACAT
* * * * *
4762484 GACATATAACAATTAAATTTTTTAACATAACGTGTAATAATTAAA
66 GACATAGAACAATTAAATTTTTCAACATAACATATAATAACTAAA
* * * * * * * * * * *
4762529 TTTTCAATATGAA-GTGTAACAATTAAATCTTCAACATAACGTGTAATAAATACATTTTTTAATA
1 TTTTAAACAT-AACATGTAATAATTAAATCTTTAACATGACGTGTAACAACTAAATTTTTCAACA
4762593 TGACAT
65 TGACAT
4762599 GAAATAACTA
Statistics
Matches: 146, Mismatches: 31, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
109 22 0.15
110 121 0.83
111 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (110 bp):
TTTTAAACATAACATGTAATAATTAAATCTTTAACATGACGTGTAACAACTAAATTTTTCAACAT
GACATAGAACAATTAAATTTTTCAACATAACATATAATAACTAAA
Found at i:4762611 original size:110 final size:110
Alignment explanation
Indices: 4762381--4762672 Score: 275
Period size: 110 Copynumber: 2.7 Consensus size: 110
4762371 TATATCATGG
* * * * * *
4762381 AACAATTAAATTTTTCAACTTAACATATAATAACTAAATTTTAAACATAATGTGTAATAATTAAA
1 AACAACTAAATTTTTAAACATAACGTGTAATAACTAAATTTTAAACATAATGTGTAACAATTAAA
* ** * *
4762446 TCTTTAACATGGCGTGTGACAACTAAATTTTTTAACATGACATAT
66 TCTTCAACATAACGTGTAACAAATAAATTTTTTAACATGACATAT
* * * * *
4762491 AACAATTAAATTTTTTAACATAACGTGTAATAATTAAATTTTCAATATGAA-GTGTAACAATTAA
1 AACAACTAAATTTTTAAACATAACGTGTAATAACTAAATTTTAAACAT-AATGTGTAACAATTAA
* * *
4762555 ATCTTCAACATAACGTGTAATAAATACATTTTTTAATATGACATGA-
65 ATCTTCAACATAACGTGTAACAAATAAATTTTTTAACATGACAT-AT
* * * * * * ** *
4762601 AATAACTAAA-TTTTAAACATAGCGTGTAACAGCTACATGTTTCAACATAGCGTATAACAATTAA
1 AACAACTAAATTTTTAAACATAACGTGTAATAACTAAAT-TTTAAACATAATGTGTAACAATTAA
*
4762665 ATTTTCAA
65 ATCTTCAA
4762673 TACGATTTTC
Statistics
Matches: 150, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
109 23 0.15
110 124 0.83
111 3 0.02
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (110 bp):
AACAACTAAATTTTTAAACATAACGTGTAATAACTAAATTTTAAACATAATGTGTAACAATTAAA
TCTTCAACATAACGTGTAACAAATAAATTTTTTAACATGACATAT
Found at i:4762620 original size:55 final size:54
Alignment explanation
Indices: 4762233--4762629 Score: 172
Period size: 55 Copynumber: 7.2 Consensus size: 54
4762223 ATTTTTTTAT
* * * * ** * *
4762233 CATAACGTGTAACAATTAAATTTTTCAATATAACATGTGACAACTAAATTATAAA
1 CATAACGTGTAATAAAT-AATTTTTTAATATGACATGAAACAATTAAATTTTAAA
* ** * * * * * * * *
4762288 TATAGTGTGTAATAATTATATTTTTCAACATTACATGTAATAATTATATTTTTTAA
1 CATAACGTGTAATAAATA-ATTTTTTAATATGACATGAAACAATTA-AATTTTAAA
* * * * * * * *
4762344 TATGATGTGTAATAACTAAATTTTCAATAT-ATCATGGAACAATTAAATTTTTCAA
1 CATAACGTGTAATAAATAATTTTTTAATATGA-CATGAAACAATTAAA-TTTTAAA
* * * * * * * * ** * *
4762399 CTTAACATATAATAACTAAATTTTAAACATAATGTGTAATAATTAAATCTTT-AA
1 CATAACGTGTAATAAATAATTTTTTAATATGACATGAAACAATTAAAT-TTTAAA
** * * * * *
4762453 CATGGCGTGTGACAACTAAATTTTTTAACATGACAT-ATAACAATTAAATTTTTTAA
1 CATAACGTGTAATAAAT-AATTTTTTAATATGACATGA-AACAATTAAA-TTTTAAA
* * * * * *
4762509 CATAACGTGTAATAATTAAATTTTCAATATGA-AGTGTAACAATTAAATCTTCAA
1 CATAACGTGTAATAAATAATTTTTTAATATGACA-TGAAACAATTAAATTTTAAA
* *
4762563 CATAACGTGTAATAAATACATTTTTTAATATGACATGAAATAACTAAATTTTAAA
1 CATAACGTGTAATAAATA-ATTTTTTAATATGACATGAAACAATTAAATTTTAAA
*
4762618 CATAGCGTGTAA
1 CATAACGTGTAA
4762630 CAGCTACATG
Statistics
Matches: 261, Mismatches: 67, Indels: 28
0.73 0.19 0.08
Matches are distributed among these distances:
54 39 0.15
55 184 0.70
56 38 0.15
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.38
Consensus pattern (54 bp):
CATAACGTGTAATAAATAATTTTTTAATATGACATGAAACAATTAAATTTTAAA
Found at i:4762659 original size:165 final size:164
Alignment explanation
Indices: 4762233--4762669 Score: 416
Period size: 165 Copynumber: 2.6 Consensus size: 164
4762223 ATTTTTTTAT
* * * * * * * *
4762233 CATAACGTGTAACAATTAAATTTTTCAATATAACATGTGACAACTAAATTATAAATATAGTGTGT
1 CATAACGTGTAATAAAT-AATTTTTAAATATAACATGTAATAACTAAATTTTAAACATAGCGTGT
* * * * * * * * *
4762298 AATAATTATATTTTTCAACATTA-CATGTAATAATTATATTTTTTAATATGATGTGTAATAACTA
65 AACAACTAAATTTTTCAACA-TAGCATATAACAATTAAATTTTTTAACATAACGTGTAATAACTA
*
4762362 AATTTTCAATATATCATGGAACAATTAAATTTTTCAA
129 AATTTTCAATATA-CATGGAACAATTAAATTCTTCAA
* * * * * * ** * *
4762399 CTTAACATATAATAACTAAATTTTAAACATAATGTGTAATAATTAAATCTTT-AACATGGCGTGT
1 CATAACGTGTAATAAATAATTTTTAAATATAACATGTAATAACTAAAT-TTTAAACATAGCGTGT
* * *
4762463 GACAACTAAATTTTTTAACAT-GACATATAACAATTAAATTTTTTAACATAACGTGTAATAATTA
65 AACAACTAAATTTTTCAACATAG-CATATAACAATTAAATTTTTTAACATAACGTGTAATAACTA
*
4762527 AATTTTCAATATGA-AGTGTAACAATTAAA-TCTTCAA
129 AATTTTCAATAT-ACA-TGGAACAATTAAATTCTTCAA
* * *
4762563 CATAACGTGTAATAAATACATTTTTTAATATGACATGAAATAACTAAATTTTAAACATAGCGTGT
1 CATAACGTGTAATAAATA-ATTTTTAAATATAACATGTAATAACTAAATTTTAAACATAGCGTGT
* * * *
4762628 AACAGCTACATGTTTCAACATAGCGTATAACAATTAAATTTT
65 AACAACTAAATTTTTCAACATAGCATATAACAATTAAATTTT
4762670 CAATACGATT
Statistics
Matches: 213, Mismatches: 50, Indels: 17
0.76 0.18 0.06
Matches are distributed among these distances:
164 25 0.12
165 172 0.81
166 16 0.08
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (164 bp):
CATAACGTGTAATAAATAATTTTTAAATATAACATGTAATAACTAAATTTTAAACATAGCGTGTA
ACAACTAAATTTTTCAACATAGCATATAACAATTAAATTTTTTAACATAACGTGTAATAACTAAA
TTTTCAATATACATGGAACAATTAAATTCTTCAA
Found at i:4767410 original size:21 final size:23
Alignment explanation
Indices: 4767391--4767436 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
4767381 TGACTTTAAA
4767391 AATGATGAAATACCAATTAATTCAC
1 AATGATGAAATACCAATTAA-T-AC
*
4767416 TATGATGAAATACCAATTAAT
1 AATGATGAAATACCAATTAAT
4767437 TTAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (23 bp):
AATGATGAAATACCAATTAATAC
Done.