Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, 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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 27 of 29
Found at i:11943463 original size:15 final size:13
Alignment explanation
Indices: 11943424--11943523 Score: 68
Period size: 14 Copynumber: 7.6 Consensus size: 13
11943414 TACTGTTATA
11943424 ATTAAAATAAAAAT
1 ATTAAAAT-AAAAT
11943438 ATTAAAATAAAAT
1 ATTAAAATAAAAT
*
11943451 ATATAATATTAAAAT
1 AT-TAA-AATAAAAT
*
11943466 A--AAATATATAAT
1 ATTAAA-ATAAAAT
11943478 A-TAAGAATCAAAA-
1 ATTAA-AAT-AAAAT
11943491 ATTAAAATAAAAT
1 ATTAAAATAAAAT
*
11943504 A--AAATATAAAAA
1 ATTAAA-ATAAAAT
11943516 ATTAAAAT
1 ATTAAAAT
11943524 TTATATAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 23
0.71 0.05 0.23
Matches are distributed among these distances:
11 4 0.06
12 19 0.27
13 18 0.26
14 21 0.30
15 8 0.11
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (13 bp):
ATTAAAATAAAAT
Found at i:11943491 original size:22 final size:20
Alignment explanation
Indices: 11943426--11943523 Score: 107
Period size: 20 Copynumber: 5.0 Consensus size: 20
11943416 CTGTTATAAT
*
11943426 TAAAATA-AAAATATTAAAA
1 TAAAATATATAATATTAAAA
11943445 TAAAATATATAATATTAAAA
1 TAAAATATATAATATTAAAA
11943465 TAAAATATATAATA-TAAGAA
1 TAAAATATATAATATTAA-AA
*
11943485 TCAAAA-AT-TAA-AATAAAA
1 T-AAAATATATAATATTAAAA
* *
11943503 TAAAATATAAAAAATTAAAA
1 TAAAATATATAATATTAAAA
11943523 T
1 T
11943524 TTATATAATA
Statistics
Matches: 69, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.06
18 6 0.09
19 18 0.26
20 37 0.54
21 4 0.06
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (20 bp):
TAAAATATATAATATTAAAA
Found at i:11943495 original size:33 final size:33
Alignment explanation
Indices: 11943423--11943514 Score: 104
Period size: 34 Copynumber: 2.8 Consensus size: 33
11943413 ATACTGTTAT
*
11943423 AATTAAAATAAAA-ATATTAAAATAAAATATATA
1 AATTAAAATAAAATATA-TAATATAAAATATATA
11943456 ATATTAAAATAAAATATATAATATAAGAATCA-A-A
1 A-ATTAAAATAAAATATATAATATAA-AAT-ATATA
11943490 AATTAAAATAAAATA-A-AATATAAAA
1 AATTAAAATAAAATATATAATATAAAA
11943515 AATTAAAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
30 2 0.04
31 7 0.13
32 1 0.02
33 15 0.28
34 21 0.39
35 7 0.13
36 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (33 bp):
AATTAAAATAAAATATATAATATAAAATATATA
Found at i:11943535 original size:55 final size:52
Alignment explanation
Indices: 11943420--11943746 Score: 202
Period size: 57 Copynumber: 5.9 Consensus size: 52
11943410 TTTATACTGT
*
11943420 TATAAT-TAA-AATAAAAATATTAAAATAAAATATATAATATTAAAATAAAATA
1 TATAATATAAGAAT-AAAA-ATTAAAATAAAATATATAATATAAAAATAAAATA
11943472 TATAATATAAGAATCAAAAATTAAAATAAAATA-A-AATATAAAAAATTAAAATTTA
1 TATAATATAAGAAT-AAAAATTAAAATAAAATATATAATAT-AAAAA-TAAAA--TA
* *
11943527 TATAATATAGGTAA-AACAAATTAAAATAAAATATATTAAAGAAATAAAAATAAAATA
1 TATAATATAAG-AATAA-AAATTAAAATAAAATATA-T--A-ATATAAAAATAAAATA
* * * * *
11943584 TATAAGATTATAATAATAAATAAAAATAAAATATATGACAT-TAAAAATATATTTAAAA
1 TATAATATAAGAATAA-AAATTAAAATAAAATATAT-A-ATATAAAAATA-A---AATA
* * * *
11943642 TATGATATTA-TATAAAAATTAATAATAAAAAATATAAATATATTAAAAATAAAATA
1 TATAATATAAGAATAAAAATTAA-AAT--AAAATATATA-ATA-TAAAAATAAAATA
* * * *
11943698 TATAAGATTATAATAATAAATAAAAATAAAATATATGACAT-TAAAAATA
1 TATAATATAAGAATAA-AAATTAAAATAAAATATAT-A-ATATAAAAATA
11943747 TATTTAAGGG
Statistics
Matches: 221, Mismatches: 27, Indels: 52
0.74 0.09 0.17
Matches are distributed among these distances:
51 5 0.02
52 11 0.05
53 22 0.10
54 25 0.11
55 39 0.18
56 26 0.12
57 42 0.19
58 20 0.09
59 14 0.06
60 14 0.06
61 3 0.01
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (52 bp):
TATAATATAAGAATAAAAATTAAAATAAAATATATAATATAAAAATAAAATA
Found at i:11943677 original size:24 final size:24
Alignment explanation
Indices: 11943650--11943717 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
11943640 AATATGATAT
11943650 TATATAAAAATTAATAATAAAAAA
1 TATATAAAAATTAATAATAAAAAA
* *
11943674 TATA-AATATATTAA-AA-ATAAAA
1 TATATAA-AAATTAATAATAAAAAA
* *
11943696 TATATAAGATTATAATAATAAA
1 TATATAAAAAT-TAATAATAAA
11943718 TAAAAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
22 10 0.30
23 9 0.27
24 12 0.36
25 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (24 bp):
TATATAAAAATTAATAATAAAAAA
Found at i:11943698 original size:114 final size:114
Alignment explanation
Indices: 11943544--11943802 Score: 432
Period size: 114 Copynumber: 2.3 Consensus size: 114
11943534 TAGGTAAAAC
* * *
11943544 AAATTAA-AATAAAATATATTAAAGA-AATAAAAATAAAATATATAAGATTATAATAATAAATAA
1 AAATTAATAATAAAAAATA-TAAATATATTAAAAATAAAATATATAAGATTATAATAATAAATAA
*
11943607 AAATAAAATATATGACATTAAAAATATATTTAAAATATGATATTATATAA
65 AAATAAAATATATGACATTAAAAATATATTTAAAAGATGATATTATATAA
11943657 AAATTAATAATAAAAAATATAAATATATTAAAAATAAAATATATAAGATTATAATAATAAATAAA
1 AAATTAATAATAAAAAATATAAATATATTAAAAATAAAATATATAAGATTATAATAATAAATAAA
**
11943722 AATAAAATATATGACATTAAAAATATATTTAAGGGATGATATTATATAA
66 AATAAAATATATGACATTAAAAATATATTTAAAAGATGATATTATATAA
*
11943771 AAATTAATAATGAAAAATATAAATATATTAAA
1 AAATTAATAATAAAAAATATAAATATATTAAA
11943803 CTTGTATTTT
Statistics
Matches: 137, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
113 12 0.09
114 125 0.91
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (114 bp):
AAATTAATAATAAAAAATATAAATATATTAAAAATAAAATATATAAGATTATAATAATAAATAAA
AATAAAATATATGACATTAAAAATATATTTAAAAGATGATATTATATAA
Found at i:11959369 original size:2 final size:2
Alignment explanation
Indices: 11959362--11959398 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11959352 CATTGTTAAC
11959362 AG AG AG AG AG 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 AG AG AG AG AG A
11959399 AAGAAGCGAT
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11962482 original size:3 final size:3
Alignment explanation
Indices: 11962474--11962499 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11962464 CCAACCATGC
11962474 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
11962500 CTAAGAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:11970560 original size:22 final size:22
Alignment explanation
Indices: 11970535--11970577 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11970525 TAATAATACA
*
11970535 TATACATATATATATAAATATG
1 TATACATACATATATAAATATG
*
11970557 TATACATACATATATATATAT
1 TATACATACATATATAAATAT
11970578 CCTATACCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (22 bp):
TATACATACATATATAAATATG
Found at i:11975986 original size:2 final size:2
Alignment explanation
Indices: 11975979--11976025 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
11975969 TTAAAACACA
11975979 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
11976021 AT AT A
1 AT AT A
11976026 AAGGGTATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11976616 original size:14 final size:14
Alignment explanation
Indices: 11976597--11976630 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
11976587 GTGTTTGTAT
11976597 AAACATTTGATGAC
1 AAACATTTGATGAC
11976611 AAACA-TTGATGAC
1 AAACATTTGATGAC
11976624 AAACATT
1 AAACATT
11976631 AAAGCCTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (14 bp):
AAACATTTGATGAC
Found at i:11979829 original size:2 final size:2
Alignment explanation
Indices: 11979822--11979851 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11979812 TGCTTTGGAC
11979822 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
11979852 TAAGAGTGAA
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:11981266 original size:24 final size:25
Alignment explanation
Indices: 11981239--11981305 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
11981229 TCATATTAAT
*
11981239 ATTATATTGTAATTAA-AATGATAA
1 ATTATATTGTAATTAATAATAATAA
* *
11981263 ATTATATTTTAATTAATAATAATTA
1 ATTATATTGTAATTAATAATAATAA
11981288 ATTA-ATTGTTAA-TAATAA
1 ATTATATTG-TAATTAATAA
11981306 GTGTTTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 24 0.65
25 13 0.35
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
ATTATATTGTAATTAATAATAATAA
Found at i:11989798 original size:2 final size:2
Alignment explanation
Indices: 11989791--11989822 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11989781 ATAAAAATAA
11989791 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
11989823 GCCAACCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11991459 original size:11 final size:11
Alignment explanation
Indices: 11991443--11991489 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
11991433 ACACTTAAAA
11991443 ATTAATAATTT
1 ATTAATAATTT
11991454 ATTAATAAATTT
1 ATTAAT-AATTT
11991466 A-TAAT-ATTT
1 ATTAATAATTT
*
11991475 A-TATTAATTT
1 ATTAATAATTT
11991485 ATTAA
1 ATTAA
11991490 AAAATTGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 8 0.26
10 5 0.16
11 12 0.39
12 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTAATAATTT
Found at i:11991486 original size:10 final size:10
Alignment explanation
Indices: 11991445--11991486 Score: 50
Period size: 9 Copynumber: 4.1 Consensus size: 10
11991435 ACTTAAAAAT
11991445 TAATAATTTA
1 TAATAATTTA
11991455 TTAATAAATTTA
1 -TAAT-AATTTA
11991467 TAAT-ATTTA
1 TAATAATTTA
*
11991476 TATTAATTTA
1 TAATAATTTA
11991486 T
1 T
11991487 TAAAAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 8 0.29
10 6 0.21
11 8 0.29
12 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TAATAATTTA
Found at i:11995451 original size:2 final size:2
Alignment explanation
Indices: 11995444--11995472 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11995434 ATAATTATCT
11995444 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 G
11995473 GATTCGCGAT
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11996103 original size:2 final size:2
Alignment explanation
Indices: 11996096--11996122 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11996086 ATGCTCCCTT
11996096 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
11996123 AAGGCTTTTA
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:12001536 original size:26 final size:26
Alignment explanation
Indices: 12001507--12001622 Score: 75
Period size: 26 Copynumber: 4.5 Consensus size: 26
12001497 TTGAAATAAC
12001507 AACAATATTTTTTTAACATGATATGT
1 AACAATATTTTTTTAACATGATATGT
* *
12001533 AAC-AT-TTTTGTATATTACATG-TA-AT
1 AACAATATTTT-T-T-TAACATGATATGT
*
12001558 AAAAATATTTTTTTTCAACAT-AGTATGT
1 AACAATA-TTTTTTT-AACATGA-TATGT
* *
12001586 AACAAT-TTTTTTTAACCATGGTGTGT
1 AACAATATTTTTTTAA-CATGATATGT
12001612 AA-AATATTTTT
1 AACAATATTTTT
12001623 ATACAGGACG
Statistics
Matches: 69, Mismatches: 8, Indels: 26
0.67 0.08 0.25
Matches are distributed among these distances:
24 4 0.06
25 12 0.17
26 34 0.49
27 9 0.13
28 10 0.14
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (26 bp):
AACAATATTTTTTTAACATGATATGT
Found at i:12001714 original size:80 final size:80
Alignment explanation
Indices: 12001536--12001833 Score: 253
Period size: 81 Copynumber: 3.7 Consensus size: 80
12001526 GATATGTAAC
* * * * * *
12001536 ATTTTTGTATATTACATGTAATAAAAATATTTTTTTTCAACAT-AGTATGTAACAATTTTTTTTA
1 ATTTTTGTACATAACGTGTAATAATAATATTTTTTTTCAACATGA-CATGTAACAA-CTTTTTTA
* ** *
12001600 ACCATGGTGTGTAAAAT
64 ACTATAATGTGTAATAT
* ** * * *
12001617 ATTTTTATACAGGACGTGTAACAATAATATTTTTTTTCAATATGGA-ATGTAACAACCTTTTTAA
1 ATTTTTGTACATAACGTGTAATAATAATATTTTTTTTCAACAT-GACATGTAACAACTTTTTTAA
12001681 CTATAATGTGTAATAT
65 CTATAATGTGTAATAT
* * * * * *
12001697 GTTTTTGTACATAACGTGTAAAAAT-A-ATTTTTTTTCAATATAATATGTAAAAACTTTTTTTAA
1 ATTTTTGTACATAACGTGTAATAATAATATTTTTTTTCAACATGACATGTAACAAC-TTTTTTAA
* *
12001760 TTATAACGTGTAATAT
65 CTATAATGTGTAATAT
* * *
12001776 ATTTTTGTATATAATGTAGTATAATAATAATAATTTTTTTTTAACATGACATGTAACA
1 ATTTTTGTACATAACGT-G--TAATAATAAT-ATTTTTTTTCAACATGACATGTAACA
12001834 CCGTGTAATG
Statistics
Matches: 174, Mismatches: 33, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
77 1 0.01
78 24 0.14
79 36 0.21
80 40 0.23
81 44 0.25
82 6 0.03
83 2 0.01
85 21 0.12
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (80 bp):
ATTTTTGTACATAACGTGTAATAATAATATTTTTTTTCAACATGACATGTAACAACTTTTTTAAC
TATAATGTGTAATAT
Found at i:12001739 original size:29 final size:28
Alignment explanation
Indices: 12001707--12001772 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 28
12001697 GTTTTTGTAC
*
12001707 ATAACGTGTAAAAATAATTTTTTTTCAA-T
1 ATAACGTGTAAAAA-AACTTTTTTT-AATT
**
12001736 ATAATATGT--AAAAACTTTTTTTAATT
1 ATAACGTGTAAAAAAACTTTTTTTAATT
12001762 ATAACGTGTAA
1 ATAACGTGTAA
12001773 TATATTTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
25 2 0.07
26 17 0.59
27 3 0.10
29 7 0.24
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (28 bp):
ATAACGTGTAAAAAAACTTTTTTTAATT
Found at i:12001780 original size:26 final size:26
Alignment explanation
Indices: 12001674--12001789 Score: 62
Period size: 26 Copynumber: 4.5 Consensus size: 26
12001664 TGTAACAACC
* *
12001674 TTTTTAACTATAATGTGTAATAT-GTT
1 TTTTTAA-TATAACGTGTAATATACTT
* * * *
12001700 TTTGT-ACATAACGTGTAAAAATAATTT
1 TTTTTAATATAACGTGT-AATAT-ACTT
** *
12001727 TTTTTCAATATAATATGTAA-AAACTT
1 TTTTT-AATATAACGTGTAATATACTT
12001753 TTTTTAATTATAACGTGTAATATA-TT
1 TTTTTAA-TATAACGTGTAATATACTT
*
12001779 TTTGT-ATATAA
1 TTTTTAATATAA
12001790 TGTAGTATAA
Statistics
Matches: 68, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
24 13 0.19
25 8 0.12
26 28 0.41
27 9 0.13
28 2 0.03
29 8 0.12
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (26 bp):
TTTTTAATATAACGTGTAATATACTT
Found at i:12001802 original size:79 final size:78
Alignment explanation
Indices: 12001608--12001803 Score: 207
Period size: 79 Copynumber: 2.5 Consensus size: 78
12001598 TAACCATGGT
* * ** * * *
12001608 GTGTAAAATATTTTTATACAGGACGTGTAACAATAATATTTTTTTTCAATATGGAATGTAACAAC
1 GTGTAATATATTTTTGTACATAACGTGTAATAAT-A-ATTTTTTTTCAATATGAAATGTAAAAAC
*
12001673 CTTTTTAACTATAAT
64 CTTTTTAACTATAAC
* *
12001688 GTGTAATATGTTTTTGTACATAACGTGTAAAAATAATTTTTTTTCAATAT-AATATGTAAAAACT
1 GTGTAATATATTTTTGTACATAACGTGTAATAATAATTTTTTTTCAATATGAA-ATGTAAAAAC-
* *
12001752 TTTTTTAATTATAAC
64 CTTTTTAACTATAAC
* *
12001767 GTGTAATATATTTTTGTATATAATGTAGT-ATAATAAT
1 GTGTAATATATTTTTGTACATAACGT-GTAATAATAAT
12001804 AATAATTTTT
Statistics
Matches: 98, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
77 1 0.01
78 24 0.24
79 43 0.44
80 30 0.31
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.45
Consensus pattern (78 bp):
GTGTAATATATTTTTGTACATAACGTGTAATAATAATTTTTTTTCAATATGAAATGTAAAAACCT
TTTTAACTATAAC
Found at i:12037013 original size:14 final size:15
Alignment explanation
Indices: 12036987--12037016 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12036977 AATCTTTATG
12036987 ATTAATAATTAATTA
1 ATTAATAATTAATTA
12037002 ATTAAT-ATTAATTA
1 ATTAATAATTAATTA
12037016 A
1 A
12037017 AATATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAATAATTAATTA
Found at i:12037279 original size:30 final size:30
Alignment explanation
Indices: 12037245--12037303 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
12037235 AATAATTAGT
* * *
12037245 TATAAATATTTATTTGGTTTAAAATAAAAA
1 TATAAACATTTATTTAGTTCAAAATAAAAA
*
12037275 TATAAGCATTTATTTAGTTCAAAATAAAA
1 TATAAACATTTATTTAGTTCAAAATAAAA
12037304 GTAAAAGAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (30 bp):
TATAAACATTTATTTAGTTCAAAATAAAAA
Found at i:12048039 original size:29 final size:29
Alignment explanation
Indices: 12048006--12048097 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
12047996 AACTCCACTA
*
12048006 TTGTCATCATCTGTGAACGAATCCACCAC
1 TTGTCATCATCTGTGAACAAATCCACCAC
* * *
12048035 TTGTCTAT-AT-AGAGTATA-AAACTCCACTA-
1 TTGTC-ATCATCTGTG-A-ACAAA-TCCACCAC
12048064 TTGTCATCATCTGTGAACAAATCCACCAC
1 TTGTCATCATCTGTGAACAAATCCACCAC
12048093 TTGTC
1 TTGTC
12048098 TATATAGAGT
Statistics
Matches: 48, Mismatches: 7, Indels: 16
0.68 0.10 0.23
Matches are distributed among these distances:
28 11 0.23
29 26 0.54
30 11 0.23
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (29 bp):
TTGTCATCATCTGTGAACAAATCCACCAC
Found at i:12048087 original size:58 final size:58
Alignment explanation
Indices: 12047992--12048109 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
12047982 TAGCTAATCC
*
12047992 ATAAAACTCCACTATTGTCATCATCTGTGAACGAATCCACCACTTGTCTATATAGAGT
1 ATAAAACTCCACTATTGTCATCATCTGTGAACAAATCCACCACTTGTCTATATAGAGT
12048050 ATAAAACTCCACTATTGTCATCATCTGTGAACAAATCCACCACTTGTCTATATAGAGT
1 ATAAAACTCCACTATTGTCATCATCTGTGAACAAATCCACCACTTGTCTATATAGAGT
12048108 AT
1 AT
12048110 GCTCTTAGAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (58 bp):
ATAAAACTCCACTATTGTCATCATCTGTGAACAAATCCACCACTTGTCTATATAGAGT
Found at i:12051666 original size:14 final size:15
Alignment explanation
Indices: 12051647--12051675 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12051637 AGACCCTAAA
12051647 TAAAAA-TAATTTAT
1 TAAAAAGTAATTTAT
12051661 TAAAAAGTAATTTAT
1 TAAAAAGTAATTTAT
12051676 GTATTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TAAAAAGTAATTTAT
Found at i:12053016 original size:15 final size:15
Alignment explanation
Indices: 12052996--12053040 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
12052986 GTTTTATATT
* *
12052996 TTATTAAAAATGTGA
1 TTATTAAAAATATAA
*
12053011 TTATTAAGAATATAA
1 TTATTAAAAATATAA
*
12053026 TTATTAAAAAAATAA
1 TTATTAAAAATATAA
12053041 CATTTACAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (15 bp):
TTATTAAAAATATAA
Found at i:12061638 original size:21 final size:21
Alignment explanation
Indices: 12061609--12061655 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12061599 ATGATTTACT
*
12061609 TAAAATTTTTTAAATAATT-TA
1 TAAAATTTTTCAAAT-ATTATA
*
12061630 TAAACTTTTTCAAATATTATA
1 TAAAATTTTTCAAATATTATA
12061651 TAAAA
1 TAAAA
12061656 GAATAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAATTTTTCAAATATTATA
Found at i:12077090 original size:17 final size:17
Alignment explanation
Indices: 12077068--12077105 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
12077058 TATTATCAAC
*
12077068 ATATAACATG-TCATATG
1 ATATAAAATGATCAT-TG
12077085 ATATAAAATGATCATTG
1 ATATAAAATGATCATTG
12077102 ATAT
1 ATAT
12077106 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (17 bp):
ATATAAAATGATCATTG
Found at i:12077129 original size:17 final size:17
Alignment explanation
Indices: 12077107--12077140 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12077097 CATTGATATT
12077107 TTAATTAATAATAATAA
1 TTAATTAATAATAATAA
* *
12077124 TTAATTATTAATTATAA
1 TTAATTAATAATAATAA
12077141 AAATTAACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATTAATAATAATAA
Found at i:12077135 original size:20 final size:20
Alignment explanation
Indices: 12077110--12077147 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12077100 TGATATTTTA
*
12077110 ATTAATAATAATAATTAATT
1 ATTAATAATAAAAATTAATT
*
12077130 ATTAATTATAAAAATTAA
1 ATTAATAATAAAAATTAA
12077148 CTTAAATCAA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTAATAATAAAAATTAATT
Found at i:12106063 original size:10 final size:10
Alignment explanation
Indices: 12106048--12106072 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12106038 ATTATTTATT
12106048 TTTTTTAAAA
1 TTTTTTAAAA
12106058 TTTTTTAAAA
1 TTTTTTAAAA
12106068 TTTTT
1 TTTTT
12106073 GTTTGACTTG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:12113857 original size:2 final size:2
Alignment explanation
Indices: 12113845--12113882 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
12113835 TGACGTAATC
* *
12113845 AT AT AT GT AT AT AT AC 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
12113883 TGATATTGTA
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:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12114358 original size:2 final size:2
Alignment explanation
Indices: 12114353--12114383 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12114343 ATATATATAT
12114353 AG AG 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 AG AG A
12114384 TAATAGAGCC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12126568 original size:5 final size:5
Alignment explanation
Indices: 12126558--12126582 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12126548 CAGATTTTAA
12126558 TCCCT TCCCT TCCCT TCCCT TCCCT
1 TCCCT TCCCT TCCCT TCCCT TCCCT
12126583 GTCCAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
TCCCT
Found at i:12140654 original size:3 final size:3
Alignment explanation
Indices: 12140646--12140670 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12140636 AGCCATTTGG
12140646 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
12140671 CGTTGGGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:12140889 original size:2 final size:2
Alignment explanation
Indices: 12140882--12140922 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
12140872 CTGAAAAAGT
*
12140882 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA 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 TA T
12140923 TTTTTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12144343 original size:2 final size:2
Alignment explanation
Indices: 12144336--12144368 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12144326 ATAGTTATGC
12144336 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 T
12144369 CTGTATCAGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12149657 original size:2 final size:2
Alignment explanation
Indices: 12149650--12149699 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
12149640 AAAAGCACCA
12149650 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
12149692 AT AT AT AT
1 AT AT AT AT
12149700 GTAGCTAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12151004 original size:29 final size:28
Alignment explanation
Indices: 12150954--12151010 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
12150944 TGTATGATGA
* *
12150954 TTTATTTAAAAAATAAGATTTAATTTTT
1 TTTAATTAAAAAATAAGATTTAAATTTT
**
12150982 TTTAATTAAAAAATTAATTTTTAAATTTT
1 TTTAATTAAAAAA-TAAGATTTAAATTTT
12151011 AAATTTAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TTTAATTAAAAAATAAGATTTAAATTTT
Found at i:12168040 original size:8 final size:8
Alignment explanation
Indices: 12168027--12168079 Score: 90
Period size: 8 Copynumber: 6.8 Consensus size: 8
12168017 TCCTGGACCA
12168027 CCATGGAC
1 CCATGGAC
12168035 CCATGGAC
1 CCATGGAC
12168043 CCATGGAC
1 CCATGGAC
12168051 CCATGGAC
1 CCATGGAC
12168059 CCATGGAC
1 CCATGGAC
*
12168067 TCATGGA-
1 CCATGGAC
12168074 CCATGG
1 CCATGG
12168080 TCCATAGCGT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
7 5 0.12
8 38 0.88
ACGTcount: A:0.25, C:0.34, G:0.26, T:0.15
Consensus pattern (8 bp):
CCATGGAC
Found at i:12168084 original size:7 final size:7
Alignment explanation
Indices: 12168026--12168084 Score: 64
Period size: 8 Copynumber: 7.7 Consensus size: 7
12168016 TTCCTGGACC
12168026 ACCATGG
1 ACCATGG
12168033 ACCCATGG
1 A-CCATGG
12168041 ACCCATGG
1 A-CCATGG
12168049 ACCCATGG
1 A-CCATGG
12168057 ACCCATGG
1 A-CCATGG
12168065 ACTCATGG
1 AC-CATGG
12168073 ACCATGG
1 ACCATGG
*
12168080 TCCAT
1 ACCAT
12168085 AGCGTGTACT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
7 11 0.22
8 38 0.78
ACGTcount: A:0.25, C:0.34, G:0.24, T:0.17
Consensus pattern (7 bp):
ACCATGG
Found at i:12168864 original size:28 final size:26
Alignment explanation
Indices: 12168820--12168871 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 26
12168810 TTAAATATAA
12168820 AAATCAAATAATCAAATAA-TATAATTAC
1 AAATCAAATAA--AAA-AATTATAATTAC
12168848 AAATCAAATAAAAAAATTATAATT
1 AAATCAAATAAAAAAATTATAATT
12168872 TTAAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 2 0.09
26 10 0.43
28 11 0.48
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (26 bp):
AAATCAAATAAAAAAATTATAATTAC
Found at i:12168865 original size:20 final size:20
Alignment explanation
Indices: 12168829--12168866 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12168819 AAAATCAAAT
* *
12168829 AATCAAATAATATAATTACA
1 AATCAAATAAAAAAATTACA
12168849 AATCAAATAAAAAAATTA
1 AATCAAATAAAAAAATTA
12168867 TAATTTTAAA
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:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (20 bp):
AATCAAATAAAAAAATTACA
Found at i:12178572 original size:3 final size:3
Alignment explanation
Indices: 12178564--12178598 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
12178554 CCTTTGCGTC
*
12178564 TCT TCT TCT TCT TCT TCT TCT TCA TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
12178599 ATACTACAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:12209984 original size:16 final size:15
Alignment explanation
Indices: 12209963--12209992 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12209953 ATTCGACCAC
12209963 CTTTCTCTATTCTTCT
1 CTTTCTCT-TTCTTCT
12209979 CTTTCTCTTTCTTC
1 CTTTCTCTTTCTTC
12209993 AACTTCTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63
Consensus pattern (15 bp):
CTTTCTCTTTCTTCT
Found at i:12210811 original size:21 final size:22
Alignment explanation
Indices: 12210771--12210815 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
12210761 TGATGTGATA
12210771 TATATAGTTGTCATTATATTAT
1 TATATAGTTGTCATTATATTAT
12210793 TATATAGTTGTCA-TATATTAT
1 TATATAGTTGTCATTATATTAT
12210814 TA
1 TA
12210816 ATTTAATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.53
Consensus pattern (22 bp):
TATATAGTTGTCATTATATTAT
Found at i:12212194 original size:7 final size:7
Alignment explanation
Indices: 12212183--12212223 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
12212173 ATGTACATAA
*
12212183 AATAATA
1 AATAATT
12212190 AATAATT
1 AATAATT
**
12212197 TTTAATT
1 AATAATT
12212204 AATAATT
1 AATAATT
12212211 AATAATT
1 AATAATT
12212218 AATAAT
1 AATAAT
12212224 AAAAATTTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATAATT
Found at i:12212238 original size:32 final size:28
Alignment explanation
Indices: 12212183--12212266 Score: 69
Period size: 29 Copynumber: 2.7 Consensus size: 28
12212173 ATGTACATAA
12212183 AATAATAAATAATTTTTAATTAATAATTAATAATT
1 AATAATAAA-AA--TTTAATTAAT--TTAA-AA-T
*
12212218 AATAATAAAAATTTACTTAATTTAAAAT
1 AATAATAAAAATTTAATTAATTTAAAAT
* *
12212246 AAAATATAAAAATTTATTTAA
1 AATA-ATAAAAATTTAATTAA
12212267 ATTTTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
28 4 0.09
29 17 0.38
30 4 0.09
32 9 0.20
34 2 0.04
35 9 0.20
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
AATAATAAAAATTTAATTAATTTAAAAT
Found at i:12213901 original size:107 final size:106
Alignment explanation
Indices: 12213752--12213946 Score: 284
Period size: 107 Copynumber: 1.8 Consensus size: 106
12213742 TCTACTTCAT
* * * *
12213752 AAAATTACAATTTAAGAAAGTCAATCTAATAGTAAAAGAAGTTAAAATAAACAAATTGTTTAGAT
1 AAAATTACAATTCAAAAAAGTCAATCTAATAGTAAAAGAAGTTAAAATAAACAAACTATTTAGAT
12213817 TCATATTAATGCCTAGAGTTTTAATAGAAATTAACACCATA
66 TCATATTAATGCCTAGAGTTTTAATAGAAATTAACACCATA
* * * *
12213858 AAAATTACAAATTCAAAAAAGTCAGTTTAATGGTAGAAA-AAGTTAAAATTAACAAACTATTTAG
1 AAAATTAC-AATTCAAAAAAGTCAATCTAATAGTA-AAAGAAGTTAAAATAAACAAACTATTTAG
*
12213922 ATTCATATTAATGCTTAGAGTTTTA
64 ATTCATATTAATGCCTAGAGTTTTA
12213947 GTGAAAAAGA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
106 8 0.10
107 67 0.86
108 3 0.04
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (106 bp):
AAAATTACAATTCAAAAAAGTCAATCTAATAGTAAAAGAAGTTAAAATAAACAAACTATTTAGAT
TCATATTAATGCCTAGAGTTTTAATAGAAATTAACACCATA
Found at i:12217173 original size:21 final size:21
Alignment explanation
Indices: 12217149--12217193 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
12217139 TATGTAAATC
12217149 TTATATATCAT-ATTTATATAT
1 TTATATATCATAATTTA-ATAT
* *
12217170 TTATGTATTATAATTTAATAT
1 TTATATATCATAATTTAATAT
12217191 TTA
1 TTA
12217194 GTATTTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATATATCATAATTTAATAT
Found at i:12217207 original size:21 final size:21
Alignment explanation
Indices: 12217160--12217208 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
12217150 TATATATCAT
12217160 ATTTATATATTTATGTATTATA
1 ATTTA-ATATTTATGTATTATA
*
12217182 ATTTAATATTTA-GTATTTTA
1 ATTTAATATTTATGTATTATA
12217202 AGTTTAA
1 A-TTTAA
12217209 GTATAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 8 0.32
21 12 0.48
22 5 0.20
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (21 bp):
ATTTAATATTTATGTATTATA
Found at i:12242437 original size:18 final size:18
Alignment explanation
Indices: 12242416--12242454 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12242406 TTCCCTTTCC
* *
12242416 TTTCCTTTTTCTTTTGTT
1 TTTCCTTTTTCATTTCTT
12242434 TTTCCTTTTTCATTTCTT
1 TTTCCTTTTTCATTTCTT
12242452 TTT
1 TTT
12242455 TTTTACATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTCCTTTTTCATTTCTT
Found at i:12254396 original size:2 final size:2
Alignment explanation
Indices: 12254389--12254422 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12254379 CTCGCTCTAA
12254389 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
12254423 GCATGCATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12263894 original size:210 final size:211
Alignment explanation
Indices: 12263542--12263949 Score: 719
Period size: 210 Copynumber: 1.9 Consensus size: 211
12263532 AACAACTACT
* * *
12263542 CAAAGTTTTCTGGGACTCAAAACTAGCAAGAAAGGGCCAGAAATGTCAGCAATGGAATGTGGTCA
1 CAAAGTTTGCTGGGACTCAAAACTAGCAAGAAAGGGCCAGAAATGTCAACAATGAAATGTGGTCA
*
12263607 TACCTGACGGCAAAGCAGCACCATCACATAAATTTGGTTTGTTGAAGTAGCCCAAGTGAAAGAGC
66 TACCTGACGGCAAAGCAGCACCATCACATAAATTTGGTTTGTTGAAGTAGCCCAAGTGAAAAAGC
*
12263672 AACTTCAATTCATTCCACACCTAAAGGTTCTTTCAAGGTTAACAGCACATTGACATGAAAGTTAC
131 AACTTCAATTCATTCCACACCTAAAGGTCCTTTCAAGGTTAACAGCACATTGACATGAAAGTTAC
12263737 GACAGTAACAACAGCA
196 GACAGTAACAACAGCA
12263753 CAAAGTTTGCTGGGACTCAAAACTAGCAAGAAAGGGCCAG-AATGTCAACAATGAAATGTGGTCA
1 CAAAGTTTGCTGGGACTCAAAACTAGCAAGAAAGGGCCAGAAATGTCAACAATGAAATGTGGTCA
*
12263817 TACCTGACGGCAAAGCAGCACCATCACATAAATTTGGTTTGTTGAAGTAGCCCAAGTGAAAAAGT
66 TACCTGACGGCAAAGCAGCACCATCACATAAATTTGGTTTGTTGAAGTAGCCCAAGTGAAAAAGC
* * * *
12263882 ACCTTCAATTCATTCCTCACCTAAAGGTCCTTTCGAGGTTAATAGCACATTGACATGAAAGTTAC
131 AACTTCAATTCATTCCACACCTAAAGGTCCTTTCAAGGTTAACAGCACATTGACATGAAAGTTAC
12263947 GAC
196 GAC
12263950 GGTGAGTAAG
Statistics
Matches: 187, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
210 148 0.79
211 39 0.21
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (211 bp):
CAAAGTTTGCTGGGACTCAAAACTAGCAAGAAAGGGCCAGAAATGTCAACAATGAAATGTGGTCA
TACCTGACGGCAAAGCAGCACCATCACATAAATTTGGTTTGTTGAAGTAGCCCAAGTGAAAAAGC
AACTTCAATTCATTCCACACCTAAAGGTCCTTTCAAGGTTAACAGCACATTGACATGAAAGTTAC
GACAGTAACAACAGCA
Found at i:12269989 original size:211 final size:211
Alignment explanation
Indices: 12269620--12270034 Score: 607
Period size: 211 Copynumber: 2.0 Consensus size: 211
12269610 TAACAAAAAA
* * * * *
12269620 TCAAAGTTTGCTGGGACTCAAATCTAGTAAGAAAGGGCCAGCAATGTCAGCATTGGAATGTGTTC
1 TCAAAGTTTGCTGGGACTCAAAGCTAGCAAGAAAGGGCCAGAAATGTCAGCAATGGAATGTGGTC
* * * *
12269685 ATACCTGACGGCAAAGCAGTACCATCACATAAATTTGGTTTGTTCAAGTAGCCCAAGTGAAATAG
66 ATACCTCACAGCAAAGCAGCACCATCACATAAATTTGGTTTGTTCAAGTAGCCCAAGTGAAAAAG
* *
12269750 CAACATCAATTCATTCCACACCTAAAGGTTCTTTCAAGGATAACAGCACAGTGACGTGAAAGTTA
131 CAACATCAATTCATTCCACACCTAAAGGTTCTTTCAAGGATAACAGCACACTGACATGAAAGTTA
*
12269815 GGACAGTGACAACAAC
196 CGACAGTGACAACAAC
* *
12269831 TCAAAGTTTGCTGGGACTCAGAGCTAGCAAGAAAGGGCCTGAAATGTCCA-CAATGGAATGTGGT
1 TCAAAGTTTGCTGGGACTCAAAGCTAGCAAGAAAGGGCCAGAAATGT-CAGCAATGGAATGTGGT
* * *
12269895 CATACCTCACAGCAAAGCAGCACCATCACATAAATTTGTTTTGTTGACGTAGCCCAAGTGAAAAA
65 CATACCTCACAGCAAAGCAGCACCATCACATAAATTTGGTTTGTTCAAGTAGCCCAAGTGAAAAA
* * * * *
12269960 GCACCTTCAATTCATTCCACACGTAAAGGTTCTTTCAGGGTTAACAGCACACTGACATGAAAGTT
130 GCAACATCAATTCATTCCACACCTAAAGGTTCTTTCAAGGATAACAGCACACTGACATGAAAGTT
*
12270025 ACGATAGTGA
195 ACGACAGTGA
12270035 GTAAGATAAA
Statistics
Matches: 180, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
211 178 0.99
212 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (211 bp):
TCAAAGTTTGCTGGGACTCAAAGCTAGCAAGAAAGGGCCAGAAATGTCAGCAATGGAATGTGGTC
ATACCTCACAGCAAAGCAGCACCATCACATAAATTTGGTTTGTTCAAGTAGCCCAAGTGAAAAAG
CAACATCAATTCATTCCACACCTAAAGGTTCTTTCAAGGATAACAGCACACTGACATGAAAGTTA
CGACAGTGACAACAAC
Found at i:12281695 original size:32 final size:32
Alignment explanation
Indices: 12281659--12281738 Score: 142
Period size: 32 Copynumber: 2.5 Consensus size: 32
12281649 AGACATGCAG
12281659 AAGAATGAGGGTGTACATTGAGCAAAAAAAAA
1 AAGAATGAGGGTGTACATTGAGCAAAAAAAAA
**
12281691 AAGAATGAGGGTGTACATTGAGGGAAAAAAAA
1 AAGAATGAGGGTGTACATTGAGCAAAAAAAAA
12281723 AAGAATGAGGGTGTAC
1 AAGAATGAGGGTGTAC
12281739 TAATAAGTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.49, C:0.05, G:0.30, T:0.16
Consensus pattern (32 bp):
AAGAATGAGGGTGTACATTGAGCAAAAAAAAA
Found at i:12287764 original size:21 final size:20
Alignment explanation
Indices: 12287738--12287792 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
12287728 TGTCGACCTT
* *
12287738 TTAATATTAATGATAATTTAA
1 TTAATAATAATAATAA-TTAA
12287759 TTAATAATAATAATAATTAA
1 TTAATAATAATAATAATTAA
* *
12287779 TTATTAAAAATAAT
1 TTAATAATAATAAT
12287793 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TTAATAATAATAATAATTAA
Found at i:12290295 original size:87 final size:87
Alignment explanation
Indices: 12290174--12290433 Score: 430
Period size: 87 Copynumber: 3.0 Consensus size: 87
12290164 ATCAACTAAG
* * *
12290174 GATTCAGGTGAGGTAGATGAGAGGCCACAGAAGAAAGCAAAGCTTGATAGTACTGTGAAAGTGTC
1 GATTCAGGTGAGGTAGATGAGAGGCCACATAAGAAAGCAAAGCTTGCTAGTGCTGTGAAAGTGTC
*
12290239 CACTGACAAGAACATGAATAAA
66 CAATGACAAGAACATGAATAAA
* * *
12290261 GATTCAAGTGAGGTAGATGAGGGGCCACATAAGAAAGCAAAGCTTGCTAGTGCTGTGAAAGTGTG
1 GATTCAGGTGAGGTAGATGAGAGGCCACATAAGAAAGCAAAGCTTGCTAGTGCTGTGAAAGTGTC
*
12290326 CAATGACAGGAACATGAATAAA
66 CAATGACAAGAACATGAATAAA
12290348 GATTCAGGTGAGGTAGATGAGAGGCCACATAAGAAAGCAAAGCTTGCTAGTGCTGTGAAAGTGTC
1 GATTCAGGTGAGGTAGATGAGAGGCCACATAAGAAAGCAAAGCTTGCTAGTGCTGTGAAAGTGTC
* *
12290413 CAGTGACAAGAACACGAATAA
66 CAATGACAAGAACATGAATAA
12290434 CGTGCTTAAC
Statistics
Matches: 159, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 159 1.00
ACGTcount: A:0.38, C:0.14, G:0.29, T:0.19
Consensus pattern (87 bp):
GATTCAGGTGAGGTAGATGAGAGGCCACATAAGAAAGCAAAGCTTGCTAGTGCTGTGAAAGTGTC
CAATGACAAGAACATGAATAAA
Found at i:12296063 original size:18 final size:18
Alignment explanation
Indices: 12296040--12296086 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
12296030 CCTCGCTATT
12296040 GAAGAAGAAGAGGAAGAG
1 GAAGAAGAAGAGGAAGAG
*
12296058 GAAGAAGAAGAGGAGGAG
1 GAAGAAGAAGAGGAAGAG
*
12296076 GAGGAAGAAGA
1 GAAGAAGAAGA
12296087 ACATCATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAGAGGAAGAG
Found at i:12320323 original size:7 final size:7
Alignment explanation
Indices: 12320311--12320426 Score: 50
Period size: 7 Copynumber: 16.4 Consensus size: 7
12320301 TTCATGTTAT
12320311 TATATAA
1 TATATAA
12320318 TATATAA
1 TATATAA
*
12320325 TTTATATA
1 TATATA-A
*
12320333 TATTTAA
1 TATATAA
12320340 TATACT-A
1 TATA-TAA
12320347 TATA-AA
1 TATATAA
12320353 -AT-TAA
1 TATATAA
12320358 TATATAA
1 TATATAA
*
12320365 CT-TATGCA
1 -TATAT-AA
*
12320373 TA-ATGA
1 TATATAA
12320379 TATATAA
1 TATATAA
12320386 -AGTCACTAA
1 TA-T-A-TAA
12320395 TATTATTAA
1 TA-TA-TAA
12320404 TAT-TAA
1 TATATAA
*
12320410 TATTTAA
1 TATATAA
12320417 TATATAA
1 TATATAA
12320424 TAT
1 TAT
12320427 TTATTTATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 30
0.68 0.08 0.24
Matches are distributed among these distances:
5 4 0.05
6 13 0.15
7 46 0.55
8 10 0.12
9 9 0.11
10 2 0.02
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (7 bp):
TATATAA
Found at i:12320426 original size:14 final size:13
Alignment explanation
Indices: 12320400--12320441 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
12320390 ACTAATATTA
12320400 TTAATATTAATAT
1 TTAATATTAATAT
12320413 TTAATATATAATAT
1 TTAATAT-TAATAT
*
12320427 TTATTTATTAATAT
1 TTA-ATATTAATAT
12320441 T
1 T
12320442 ATTTTATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 7 0.27
14 16 0.62
15 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTAATATTAATAT
Found at i:12320643 original size:15 final size:17
Alignment explanation
Indices: 12320623--12320654 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
12320613 ATAATAAAAA
12320623 TAAAT-ATTTA-ATATT
1 TAAATAATTTATATATT
12320638 TAAATAATTTATATATT
1 TAAATAATTTATATATT
12320655 CGAGTATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATAATTTATATATT
Found at i:12326684 original size:51 final size:51
Alignment explanation
Indices: 12326629--12326739 Score: 150
Period size: 51 Copynumber: 2.2 Consensus size: 51
12326619 TACCCTTTAA
* *
12326629 AACATCAATTAACACTACCAAGCAGCTTTTTTCTAAACATATACTTTTTTG
1 AACATCAATTAACACTACCAAGCAGCTTTTTTCTAAACATACACTTTTTCG
* * ** * *
12326680 AACATCAATTTACACTACCATGTTGCTTTTTTCTGAACATGCACTTTTTCG
1 AACATCAATTAACACTACCAAGCAGCTTTTTTCTAAACATACACTTTTTCG
12326731 AACATCAAT
1 AACATCAAT
12326740 ATACTCTATC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (51 bp):
AACATCAATTAACACTACCAAGCAGCTTTTTTCTAAACATACACTTTTTCG
Found at i:12334395 original size:23 final size:23
Alignment explanation
Indices: 12334352--12334395 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
12334342 CAGAAAAAAG
*
12334352 AAGAAAGCTATTGACAACATGAC
1 AAGAAAGCTATTGAAAACATGAC
*
12334375 AAGAAATC-ATTGAAAAGCATG
1 AAGAAAGCTATTGAAAA-CATG
12334396 GCAACATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.18
Consensus pattern (23 bp):
AAGAAAGCTATTGAAAACATGAC
Found at i:12349478 original size:30 final size:29
Alignment explanation
Indices: 12349420--12349479 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
12349410 ATTAGAATAA
* * *
12349420 ATTTTGATTATATTTAATTAATTTTTTAT
1 ATTTTGATTATAATTAAATAAATTTTTAT
*
12349449 ATTTTTATTATAAATTAAATAAATTTTTAT
1 ATTTTGATTAT-AATTAAATAAATTTTTAT
12349479 A
1 A
12349480 ATAAAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTTTGATTATAATTAAATAAATTTTTAT
Found at i:12352437 original size:4 final size:4
Alignment explanation
Indices: 12352430--12352459 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
12352420 TATATATATA
*
12352430 TATG TATG TATG TATG TATG TATG CATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
12352460 GTTTTATGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.03, G:0.23, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:12357742 original size:123 final size:122
Alignment explanation
Indices: 12357553--12357785 Score: 306
Period size: 123 Copynumber: 1.9 Consensus size: 122
12357543 TTCAAGCCCT
* * * * * * * *
12357553 GCCTGAGCATTCACTGGCGCCGGTGGAATACAACAATGCGTTGGAAAAACACTCCCTGAATTTCA
1 GCCTGAGCATTCAATGGCCCCAGAGGAATACAACAATGCATTGGAAAAACACTACCTAAATCTCA
* *
12357618 AAGCTTCTTGTTGCCGTAAGGATTAAATGGCAACTGGCACGAGTCCTGATTTATAAA
66 AAACTTCTTGTTGCCGTAAGGATTAAATGGCAACTGGAACGAGTCCTGATTTATAAA
*
12357675 GCCTGAGCATTCAATGGCCCCAGAGGAAT-CTGAACAATGCATTGGAACAACACTACCTAAATCT
1 GCCTGAGCATTCAATGGCCCCAGAGGAATAC--AACAATGCATTGGAAAAACACTACCTAAATCT
* * * *
12357739 CAAAACTTCTTGTTGCTGTCAGGATTCAGTGGCAACTGGAACGAGTC
64 CAAAACTTCTTGTTGCCGTAAGGATTAAATGGCAACTGGAACGAGTC
12357786 AGTATTTTAC
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
121 1 0.01
122 25 0.27
123 68 0.72
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (122 bp):
GCCTGAGCATTCAATGGCCCCAGAGGAATACAACAATGCATTGGAAAAACACTACCTAAATCTCA
AAACTTCTTGTTGCCGTAAGGATTAAATGGCAACTGGAACGAGTCCTGATTTATAAA
Found at i:12359203 original size:29 final size:30
Alignment explanation
Indices: 12359171--12359241 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
12359161 ATATTTAAAA
12359171 TTTTTTGAATTCTTAAATATATTCTTATTT
1 TTTTTTGAATTCTTAAATATATTCTTATTT
* * *
12359201 TTTTATT--ATTTTTAATTATATTTTTATTT
1 TTTT-TTGAATTCTTAAATATATTCTTATTT
12359230 TTATTTTGAATT
1 TT-TTTTGAATT
12359242 AAATAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
29 23 0.68
30 6 0.18
31 5 0.15
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (30 bp):
TTTTTTGAATTCTTAAATATATTCTTATTT
Found at i:12359230 original size:6 final size:6
Alignment explanation
Indices: 12359190--12359236 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
12359180 TTCTTAAATA
* * * *
12359190 TATTCT TATTTT T-TTAT TATTTT TAATTA TATTTT TATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
12359237 GAATTAAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (6 bp):
TATTTT
Found at i:12359233 original size:24 final size:23
Alignment explanation
Indices: 12359196--12359242 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
12359186 AATATATTCT
*
12359196 TATTTTTTTATTATTTTTAATTA
1 TATTTTTTTATTATTTTGAATTA
*
12359219 TATTTTTATTTTTATTTTGAATTA
1 TATTTTT-TTATTATTTTGAATTA
12359243 AATAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (23 bp):
TATTTTTTTATTATTTTGAATTA
Found at i:12359270 original size:29 final size:28
Alignment explanation
Indices: 12359220--12359284 Score: 94
Period size: 29 Copynumber: 2.3 Consensus size: 28
12359210 TTTTAATTAT
* *
12359220 ATTTTTATTTTTATTTTGAATTAAATAA
1 ATTTTTATGTTTATTTTAAATTAAATAA
12359248 ATTTTATATGTTTATTTTAAATTAAATAA
1 ATTTT-TATGTTTATTTTAAATTAAATAA
*
12359277 GTTTTTAT
1 ATTTTTAT
12359285 ACTTAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 8 0.24
29 25 0.76
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (28 bp):
ATTTTTATGTTTATTTTAAATTAAATAA
Found at i:12360254 original size:19 final size:18
Alignment explanation
Indices: 12360213--12360256 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
12360203 TAACATATAG
12360213 TTTAATTGATAAAAATTA
1 TTTAATTGATAAAAATTA
*
12360231 ATTAATT-ATTAAAAATTTA
1 TTTAATTGA-TAAAAA-TTA
12360250 TTTAATT
1 TTTAATT
12360257 TAAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 12 0.55
19 9 0.41
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTTAATTGATAAAAATTA
Found at i:12363444 original size:55 final size:55
Alignment explanation
Indices: 12363383--12363492 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
12363373 AAAAGAAAAA
12363383 GAGAGGAATTGAAATTTTATTATGATTTTGACATTCAAGCTATCAATAATCTTAC
1 GAGAGGAATTGAAATTTTATTATGATTTTGACATTCAAGCTATCAATAATCTTAC
*
12363438 GAGAGGAATTGAAATTTTATTATGATTTTGACATTCAAGCTATTAATAATCTTAC
1 GAGAGGAATTGAAATTTTATTATGATTTTGACATTCAAGCTATCAATAATCTTAC
12363493 TTATTGTCAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (55 bp):
GAGAGGAATTGAAATTTTATTATGATTTTGACATTCAAGCTATCAATAATCTTAC
Found at i:12377055 original size:88 final size:88
Alignment explanation
Indices: 12376896--12377087 Score: 368
Period size: 88 Copynumber: 2.2 Consensus size: 88
12376886 GCTGAAAACC
*
12376896 CTTCT-TTGGATTTTCTTTTTCTGCTTGGGTCTTGTAGCAGCTGCAATAGGGATGAAATGCACAA
1 CTTCTCTTGGTTTTTCTTTTTCTGCTTGGGTCTTGTAGCAGCTGCAATAGGGATGAAATGCACAA
12376960 TGTTAGTAGTCCATAATTTTAGT
66 TGTTAGTAGTCCATAATTTTAGT
12376983 CTTCTCTTGGTTTTTCTTTTTCTGCTTGGGTCTTGTAGCAGCTGCAATAGGGATGAAATGCACAA
1 CTTCTCTTGGTTTTTCTTTTTCTGCTTGGGTCTTGTAGCAGCTGCAATAGGGATGAAATGCACAA
12377048 TGTTAGTAGTCCATAATTTTAGT
66 TGTTAGTAGTCCATAATTTTAGT
12377071 CTTCTCTTGGTTTTTCT
1 CTTCTCTTGGTTTTTCT
12377088 ACTCATAGTA
Statistics
Matches: 103, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
87 5 0.05
88 98 0.95
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (88 bp):
CTTCTCTTGGTTTTTCTTTTTCTGCTTGGGTCTTGTAGCAGCTGCAATAGGGATGAAATGCACAA
TGTTAGTAGTCCATAATTTTAGT
Found at i:12386894 original size:21 final size:21
Alignment explanation
Indices: 12386870--12386910 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12386860 ATTGATAAAA
* *
12386870 TAATTAAATTTTATAAATATC
1 TAATTAAAATTTAAAAATATC
12386891 TAATTAAAATTTAAAAATAT
1 TAATTAAAATTTAAAAATAT
12386911 TTATTGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATTAAAATTTAAAAATATC
Found at i:12386983 original size:93 final size:92
Alignment explanation
Indices: 12386882--12387156 Score: 383
Period size: 93 Copynumber: 3.0 Consensus size: 92
12386872 ATTAAATTTT
** ** *
12386882 ATAAATATCTAATTAAAATTTAAAAATATTTATTGAAATTCATATTTTAATATTTGAGACATAAC
1 ATAAATATCTAATTAAAATTTAAAAATATTTATCAAAATTTGTATTTTAATATTTTAGACAT-AC
*
12386947 TCATTAAATACATACTTTATTTTACAAA
65 TCATTAAATACATACTTAATTTTACAAA
*
12386975 ATAAATATCTAATTAAAATTTTAAAAA-ATTTATCAAAATTTGTTTTTTAATATTTTAGACACTA
1 ATAAATATCTAATTAAAA-TTTAAAAATATTTATCAAAATTTGTATTTTAATATTTTAGACA-TA
*
12387039 CTCATTAAATACATACTCAATTTTACAAA
64 CTCATTAAATACATACTTAATTTTACAAA
* * *
12387068 TTAAATATCTAATTAAAATTTATAAATATTCATCAAAATTTGTATTTCT-ATATTTTAGACATTA
1 ATAAATATCTAATTAAAATTTAAAAATATTTATCAAAATTTGTATTT-TAATATTTTAGACA-TA
*
12387132 CTCATTAAATACATACTTGATTTTA
64 CTCATTAAATACATACTTAATTTTA
12387157 TAAGTCTAAA
Statistics
Matches: 163, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
92 7 0.04
93 146 0.90
94 10 0.06
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (92 bp):
ATAAATATCTAATTAAAATTTAAAAATATTTATCAAAATTTGTATTTTAATATTTTAGACATACT
CATTAAATACATACTTAATTTTACAAA
Found at i:12390906 original size:31 final size:31
Alignment explanation
Indices: 12390871--12390930 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
12390861 AACATGTGTT
*
12390871 TGGCCCTCTTCACAATTGAAAACGCTCACGC
1 TGGCCCTCTTCACAATTGAAAACACTCACGC
*
12390902 TGGCCCTCTTCACATTTGAAAACACTCAC
1 TGGCCCTCTTCACAATTGAAAACACTCAC
12390931 TCCTCTAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.35, G:0.13, T:0.25
Consensus pattern (31 bp):
TGGCCCTCTTCACAATTGAAAACACTCACGC
Found at i:12397039 original size:2 final size:2
Alignment explanation
Indices: 12397032--12397060 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12397022 TACAGCAGCC
12397032 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 T
12397061 CCATGTCAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12397409 original size:14 final size:14
Alignment explanation
Indices: 12397392--12397419 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12397382 TTTTGTCAGT
12397392 ATTGTTTGAGCAAA
1 ATTGTTTGAGCAAA
12397406 ATTGTTTGAGCAAA
1 ATTGTTTGAGCAAA
12397420 CTCGAGTATA
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:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
ATTGTTTGAGCAAA
Found at i:12414879 original size:87 final size:87
Alignment explanation
Indices: 12414777--12414951 Score: 341
Period size: 87 Copynumber: 2.0 Consensus size: 87
12414767 CAGGCAATAA
12414777 TTCCAGATCTGAAATGGAGAATGAAGTCTTCACATAAAGCAATTTCTCTGAGTTTAGAAAGTTTG
1 TTCCAGATCTGAAATGGAGAATGAAGTCTTCACATAAAGCAATTTCTCTGAGTTTAGAAAGTTTG
12414842 ACAATAAATTAATTTAATTAAG
66 ACAATAAATTAATTTAATTAAG
*
12414864 TTCCAGATCTGAAATGTAGAATGAAGTCTTCACATAAAGCAATTTCTCTGAGTTTAGAAAGTTTG
1 TTCCAGATCTGAAATGGAGAATGAAGTCTTCACATAAAGCAATTTCTCTGAGTTTAGAAAGTTTG
12414929 ACAATAAATTAATTTAATTAAG
66 ACAATAAATTAATTTAATTAAG
12414951 T
1 T
12414952 GCTATGTAGA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (87 bp):
TTCCAGATCTGAAATGGAGAATGAAGTCTTCACATAAAGCAATTTCTCTGAGTTTAGAAAGTTTG
ACAATAAATTAATTTAATTAAG
Found at i:12426135 original size:87 final size:87
Alignment explanation
Indices: 12425989--12426171 Score: 357
Period size: 87 Copynumber: 2.1 Consensus size: 87
12425979 CCACTATATT
12425989 CCTCTATTAATCCAGCTACCTAAAGTCACTCAACCAAAGTATTCATTTGCACAACTTACTTCTAT
1 CCTCTATTAATCCAGCTACCTAAAGTCACTCAACCAAAGTATTCATTTGCACAACTTACTTCTAT
12426054 GACCTTATTAACTGTGAACTTC
66 GACCTTATTAACTGTGAACTTC
12426076 CCTCTATTAATCCAGCTACCTAAAGTCACTCAACCAAAGTATTCATTTGCACAACTTACTTCTAT
1 CCTCTATTAATCCAGCTACCTAAAGTCACTCAACCAAAGTATTCATTTGCACAACTTACTTCTAT
12426141 GACCTTATTAACTGTGAACTTC
66 GACCTTATTAACTGTGAACTTC
12426163 CCTACTATT
1 CCT-CTATT
12426172 CCATTTCAAA
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 90 0.95
88 5 0.05
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.34
Consensus pattern (87 bp):
CCTCTATTAATCCAGCTACCTAAAGTCACTCAACCAAAGTATTCATTTGCACAACTTACTTCTAT
GACCTTATTAACTGTGAACTTC
Found at i:12453726 original size:68 final size:68
Alignment explanation
Indices: 12453617--12453753 Score: 240
Period size: 68 Copynumber: 2.0 Consensus size: 68
12453607 TGCGTAGTTT
12453617 TCCGGGTATTTTCATTGAAGGAAACGCGTGTTTAGGTTTGGAGAAAAAGAAAAGTCTACAAAAAA
1 TCCGGGTATTTTCATTGAAGGAAACGCGTGTTTAGGTTTGGAGAAAAAGAAAAGTCTACAAAAAA
12453682 ACC
66 ACC
**
12453685 TCCGGGTATTTTCATTGAAGGAAACGAC-TGTTTAGGTTTGGAGAAAAAGAAAAGTCTACACCAA
1 TCCGGGTATTTTCATTGAAGGAAACG-CGTGTTTAGGTTTGGAGAAAAAGAAAAGTCTACAAAAA
12453749 AACC
65 AACC
12453753 T
1 T
12453754 TTCTCCGCCT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 65 0.98
69 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.26
Consensus pattern (68 bp):
TCCGGGTATTTTCATTGAAGGAAACGCGTGTTTAGGTTTGGAGAAAAAGAAAAGTCTACAAAAAA
ACC
Found at i:12478036 original size:23 final size:23
Alignment explanation
Indices: 12478009--12478057 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
12477999 TTGAGACCAG
12478009 TTTTTAGTTTCTGCT-TTCTTTTTC
1 TTTTTAGTTTCT--TATTCTTTTTC
*
12478033 TTTTTGGTTTCTTATTCTTTTTC
1 TTTTTAGTTTCTTATTCTTTTTC
12478056 TT
1 TT
12478058 CTTCCAACGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 1 0.04
23 11 0.48
24 11 0.48
ACGTcount: A:0.04, C:0.14, G:0.08, T:0.73
Consensus pattern (23 bp):
TTTTTAGTTTCTTATTCTTTTTC
Found at i:12501253 original size:2 final size:2
Alignment explanation
Indices: 12501248--12501286 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
12501238 CGCTTTAGTT
*
12501248 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12501287 TTACTCTGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:12520381 original size:2 final size:2
Alignment explanation
Indices: 12520374--12520404 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12520364 ATTCGTTTTC
12520374 AG AG 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 AG AG A
12520405 AAAGAAGAAG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12525473 original size:93 final size:94
Alignment explanation
Indices: 12525312--12525498 Score: 358
Period size: 93 Copynumber: 2.0 Consensus size: 94
12525302 GTTTATTAGG
12525312 TAAGTGGTGGGACATTTAAGACAGGGTTTCTAGCCAACCATGTTATTCGGATTTGAATATTTGAG
1 TAAGTGGTGGGACATTTAAGACA-GGTTTCTAGCCAACCATGTTATTCGGATTTGAATATTTGAG
12525377 CCATCAATCACAAAATGTTAATTCTATTGA
65 CCATCAATCACAAAATGTTAATTCTATTGA
12525407 TAAGTGGTGGGACATTTAAGAC-GGTTTCTAGCCAACCATGTTATTCGGATTTGAATATTTGAGC
1 TAAGTGGTGGGACATTTAAGACAGGTTTCTAGCCAACCATGTTATTCGGATTTGAATATTTGAGC
12525471 CATCAATCACAAAATGTTAATTCTATTG
66 CATCAATCACAAAATGTTAATTCTATTG
12525499 CTGAAAAAGA
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
93 70 0.76
95 22 0.24
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (94 bp):
TAAGTGGTGGGACATTTAAGACAGGTTTCTAGCCAACCATGTTATTCGGATTTGAATATTTGAGC
CATCAATCACAAAATGTTAATTCTATTGA
Found at i:12539338 original size:3 final size:3
Alignment explanation
Indices: 12539330--12539355 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12539320 CCCTCTCTCT
12539330 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
12539356 ATGTTTGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:12546554 original size:24 final size:25
Alignment explanation
Indices: 12546527--12546579 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
12546517 AAAAAATAAA
*
12546527 ATTAAATTTATATA-CATTATATAT
1 ATTAAATATATATATCATTATATAT
**
12546551 ATT-AATATATATATTTTTATATAT
1 ATTAAATATATATATCATTATATAT
12546575 ATTAA
1 ATTAA
12546580 GAAGAGTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 9 0.38
24 14 0.58
25 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTAAATATATATATCATTATATAT
Found at i:12546561 original size:12 final size:12
Alignment explanation
Indices: 12546544--12546579 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12546534 TTATATACAT
12546544 TATATATATTAA
1 TATATATATTAA
**
12546556 TATATATATTTT
1 TATATATATTAA
12546568 TATATATATTAA
1 TATATATATTAA
12546580 GAAGAGTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATATATATTAA
Found at i:12546878 original size:27 final size:29
Alignment explanation
Indices: 12546831--12546900 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 29
12546821 ATATTTTTTA
12546831 ATATAAAATATTATAAATATATATAA-TT
1 ATATAAAATATTATAAATATATATAATTT
* *
12546859 ATATAAAA-ATTATATATATATTTAATTT
1 ATATAAAATATTATAAATATATATAATTT
*
12546887 ATATACAAGTATTA
1 ATATA-AAATATTA
12546901 CTATAACTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 15 0.42
28 15 0.42
29 2 0.06
30 4 0.11
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (29 bp):
ATATAAAATATTATAAATATATATAATTT
Found at i:12547312 original size:230 final size:226
Alignment explanation
Indices: 12546843--12547328 Score: 567
Period size: 230 Copynumber: 2.1 Consensus size: 226
12546833 ATAAAATATT
* * * * **
12546843 ATAAATATAT-ATA-ATTATATA-A-AAAT-TATATATATATTTAATTTATATACAAGTATTACT
1 ATAAATATATAATATATTATATATATATATATAAACATATATTTAATTTATACACAACCATTACT
*
12546903 ATAACTTATAATAAACTTTATTTATCTGATTACACTTAATAATCTTATTAATTATCAACTTAATT
66 ATAACTTATAATAAACTTTATTTATATGATTACACTTAATAATCTTATTAATTATCAACTTAATT
*
12546968 TTTATAACATATTATTTATAATTAGTTATTATTTATACAAACTTTGATATAAAGTATTATAACAT
131 TTTATAACATATTATTTATAATTAGTTATTATTTATACAAACTTTGATATAAAATATTATAACAT
* * *
12547033 ATAAGTTGTGTTATTAATTTCATATATACATA
196 ATAACTTGTGTAATTAATATCATATATA-ATA
*
12547065 ATAAAATTATATAATATATGTATATATATATATATAAACATATATTTAATTTATACATAACCATT
1 AT-AAA-TATATAATATAT-TATATATATATATATAAACATATATTTAATTTATACACAACCATT
* * * * * * * *
12547130 GCTATAATTTATAATAGATTTTATTTATATGGTTACACTTAATAATTTTATTAGTTATCATCTTA
63 ACTATAACTTATAATAAACTTTATTTATATGATTACACTTAATAATCTTATTAATTATCAACTTA
* * * * *
12547195 ATTTTTATAACATATTGTTTATACTTAGTTATTATTTATACATATTTTAATATAAAAATTAAAAT
128 ATTTTTATAACATATTATTTATAATTAGTTATTATTTATACAAACTTT--GAT----A-TAAAAT
*
12547260 ATTATAACATGTAACTTGTGTAATTAATATCATATAT-ATA
186 ATTATAACATATAACTTGTGTAATTAATATCATATATAATA
*
12547300 AT-AA-A-GTAATATATTATATATATATATAT
1 ATAAATATATAATATATTATATATATATATAT
12547329 TTAATTTATA
Statistics
Matches: 222, Mismatches: 27, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
222 2 0.01
223 3 0.01
224 5 0.02
225 3 0.01
226 2 0.01
227 6 0.03
228 1 0.00
229 18 0.08
230 133 0.60
231 1 0.00
232 2 0.01
233 2 0.01
235 5 0.02
236 1 0.00
237 38 0.17
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (226 bp):
ATAAATATATAATATATTATATATATATATATAAACATATATTTAATTTATACACAACCATTACT
ATAACTTATAATAAACTTTATTTATATGATTACACTTAATAATCTTATTAATTATCAACTTAATT
TTTATAACATATTATTTATAATTAGTTATTATTTATACAAACTTTGATATAAAATATTATAACAT
ATAACTTGTGTAATTAATATCATATATAATA
Found at i:12549862 original size:23 final size:23
Alignment explanation
Indices: 12549835--12549878 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12549825 AAATTTATTA
12549835 ATTAATTGATAAATTAATAATTT
1 ATTAATTGATAAATTAATAATTT
** *
12549858 ATTAATTTTTATATTAATAAT
1 ATTAATTGATAAATTAATAAT
12549879 AAAAAAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTAATTGATAAATTAATAATTT
Found at i:12549874 original size:35 final size:35
Alignment explanation
Indices: 12549826--12549897 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
12549816 ACATGTTGAA
* **
12549826 AATTTATTAATTAATTGATAAATTAA-TAATTTATT
1 AATTTATTAATTAA-TAATAAAAAAATTAATTTATT
12549861 AATTT-TTATATTAATAATAAAAAAATTAATTTATT
1 AATTTATTA-ATTAATAATAAAAAAATTAATTTATT
12549896 AA
1 AA
12549898 AGTATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 11 0.34
35 21 0.66
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (35 bp):
AATTTATTAATTAATAATAAAAAAATTAATTTATT
Found at i:12550214 original size:44 final size:44
Alignment explanation
Indices: 12550164--12550251 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
12550154 AAAATAAAAC
** *
12550164 GTAAGATATTTTTTGAAATCAATTATGGTTTTTCTCATTAACTG
1 GTAAGATATTTTGGGAAATCAATGATGGTTTTTCTCATTAACTG
* *
12550208 GTAAGATATTTTGGGTAATCAATGATTGTTTTTCTCATTAACTG
1 GTAAGATATTTTGGGAAATCAATGATGGTTTTTCTCATTAACTG
12550252 ATAAATTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (44 bp):
GTAAGATATTTTGGGAAATCAATGATGGTTTTTCTCATTAACTG
Found at i:12550262 original size:44 final size:44
Alignment explanation
Indices: 12550165--12550263 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
12550155 AAATAAAACG
** * * *
12550165 TAAGATATTTTTTGAAATCAATTATGGTTTTTCTCATTAACTGG
1 TAAGATATTTTGGGTAATCAATGATGGTTTTTCTCATTAACTGA
*
12550209 TAAGATATTTTGGGTAATCAATGATTGTTTTTCTCATTAACTGA
1 TAAGATATTTTGGGTAATCAATGATGGTTTTTCTCATTAACTGA
12550253 TAA-ATTATTTT
1 TAAGA-TATTTT
12550264 ACATTTGAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 1 0.02
44 47 0.98
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.48
Consensus pattern (44 bp):
TAAGATATTTTGGGTAATCAATGATGGTTTTTCTCATTAACTGA
Found at i:12552118 original size:17 final size:17
Alignment explanation
Indices: 12552096--12552128 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12552086 TGGAATGCAT
12552096 ATTCCTAATTTTATGAC
1 ATTCCTAATTTTATGAC
12552113 ATTCCTAATTTTATGA
1 ATTCCTAATTTTATGA
12552129 TTGATGGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.48
Consensus pattern (17 bp):
ATTCCTAATTTTATGAC
Found at i:12559993 original size:2 final size:2
Alignment explanation
Indices: 12559976--12560010 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
12559966 AAGCATTAGC
* *
12559976 AT AT AC AT AC 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 A
12560011 ATTAAAGGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:12565722 original size:14 final size:15
Alignment explanation
Indices: 12565692--12565724 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12565682 CACTACATAA
*
12565692 AAAAATATGTTACTT
1 AAAAATATGTTAATT
12565707 AAAAATATG-TAATT
1 AAAAATATGTTAATT
12565721 AAAA
1 AAAA
12565725 TCTAAATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (15 bp):
AAAAATATGTTAATT
Found at i:12578648 original size:30 final size:30
Alignment explanation
Indices: 12578612--12578673 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
12578602 AAAAAAGAAC
12578612 AGTCCATCAACAAAGAGTAAGGAGGAAGCA
1 AGTCCATCAACAAAGAGTAAGGAGGAAGCA
12578642 AGTCCATCAACAAAGAGTAAGGAGGAAGCA
1 AGTCCATCAACAAAGAGTAAGGAGGAAGCA
12578672 AG
1 AG
12578674 AAGAACAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.47, C:0.16, G:0.27, T:0.10
Consensus pattern (30 bp):
AGTCCATCAACAAAGAGTAAGGAGGAAGCA
Found at i:12578851 original size:24 final size:22
Alignment explanation
Indices: 12578812--12578856 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
12578802 TTATAAAATA
*
12578812 ATTTAAATTAATTAATTTAATT
1 ATTTAAATTAACTAATTTAATT
12578834 ATTTAAAATTTAACTAATTTAAT
1 ATTT-AAA-TTAACTAATTTAAT
12578857 AAAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 3 0.15
24 13 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTAAATTAACTAATTTAATT
Found at i:12579248 original size:40 final size:38
Alignment explanation
Indices: 12579194--12579276 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 38
12579184 AAAAGTTAAA
*
12579194 TTTTATATTAAAAATATAAATTTATTCAATTTATA-TAT-T
1 TTTTATAAT-AAAA-ATAAATTTATT-AATTTATATTATAT
*
12579233 TTTTATACATAAAAATAATTTTATTAATTTATATTATAT
1 TTTTATA-ATAAAAATAAATTTATTAATTTATATTATAT
12579272 TTTTA
1 TTTTA
12579277 ATAAAATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 8 0.21
38 13 0.33
39 17 0.44
40 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (38 bp):
TTTTATAATAAAAATAAATTTATTAATTTATATTATAT
Found at i:12579402 original size:15 final size:16
Alignment explanation
Indices: 12579372--12579404 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12579362 TTATAAAATT
12579372 ATATTTCAACAATTAC
1 ATATTTCAACAATTAC
*
12579388 ATATTT-AATAATTAC
1 ATATTTCAACAATTAC
12579403 AT
1 AT
12579405 TCTGAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATTTCAACAATTAC
Found at i:12579956 original size:14 final size:14
Alignment explanation
Indices: 12579937--12579969 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
12579927 CAAACCAAAA
12579937 ATATATACATATAT
1 ATATATACATATAT
12579951 ATATATACATATAT
1 ATATATACATATAT
12579965 ATATA
1 ATATA
12579970 ATAACAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATATACATATAT
Found at i:12580230 original size:12 final size:12
Alignment explanation
Indices: 12580215--12580252 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
12580205 AAAAAAAACA
*
12580215 AGAGAGAGAGAG
1 AGAGAGATAGAG
*
12580227 AGAGACATAGAG
1 AGAGAGATAGAG
12580239 AGAGAGATAGAG
1 AGAGAGATAGAG
12580251 AG
1 AG
12580253 TTGTAAGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.50, C:0.03, G:0.42, T:0.05
Consensus pattern (12 bp):
AGAGAGATAGAG
Found at i:12581161 original size:12 final size:12
Alignment explanation
Indices: 12581144--12581172 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
12581134 TATGTGTGTG
12581144 AGATAAGTCATA
1 AGATAAGTCATA
12581156 AGATAAGTCATA
1 AGATAAGTCATA
12581168 AGATA
1 AGATA
12581173 GCAAAGAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.24
Consensus pattern (12 bp):
AGATAAGTCATA
Found at i:12582632 original size:2 final size:2
Alignment explanation
Indices: 12582625--12582655 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12582615 ACAAGTTTTG
*
12582625 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12582656 ACTTTTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:12594657 original size:19 final size:20
Alignment explanation
Indices: 12594600--12594658 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
12594590 AAATTTTTAT
12594600 TTTATTGTATTTAAATATTTAA
1 TTTATTGTATTTAAATA--TAA
* * *
12594622 TTTATT-AATTGATATATAA
1 TTTATTGTATTTAAATATAA
12594641 TTT-TTGTATTTAAATATA
1 TTTATTGTATTTAAATATA
12594659 GTCTGTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 2 0.07
19 15 0.50
21 7 0.23
22 6 0.20
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTATTGTATTTAAATATAA
Found at i:12596098 original size:3 final size:3
Alignment explanation
Indices: 12596090--12596118 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12596080 GAAGCACAAA
12596090 AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
12596119 AAAAAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:12600561 original size:130 final size:127
Alignment explanation
Indices: 12600372--12600715 Score: 357
Period size: 128 Copynumber: 2.7 Consensus size: 127
12600362 TCATCAACAA
* * * * * * * * *
12600372 TTTTCTTTTTAATAATTGATTAAGCGTTATGTTTATTTGCCAATTAAGGTGAGTCAGAGATACAT
1 TTTTCTTTTCAATAATTGATTAAACGTTATGCTCATTTGTCAATCAAAGTGAATCAGAGATACAC
* * * * *
12600437 GCA-AGCATGTGCTTTTATTATTATGTCAAATATATCTCAAAGTTTGGTTTCACTGCTTCGACAT
66 GCACA-CA--TCCTTTTATCATTACGTCAAATAAATCTCAAAGTTCGGTTTCACTGCTTCGACAT
* * *
12600501 TTTTCTGTTTCAATAATTGATTAAACGTTATGCTCATTGGTCGATCAAAGTGAATCAGAGATATA
1 TTTTCT-TTTCAATAATTGATTAAACGTTATGCTCATTTGTCAATCAAAGTGAATCAGAGATACA
* * * * *
12600566 CGCACACATCCTTTTGTCATTACGTTAAATAAATTTCAAAGTTCGGTTTCAGTGCTTCGACGT
65 CGCACACATCCTTTTATCATTACGTCAAATAAATCTCAAAGTTCGGTTTCACTGCTTCGACAT
* * * * *
12600629 TCTTCTCTTTCAATAATTGATTAAACGTTGTACTCATTTGTCAATCAAAGTGAATCAGAAATATA
1 TTTTCT-TTTCAATAATTGATTAAACGTTATGCTCATTTGTCAATCAAAGTGAATCAGAGATACA
* * * *
12600694 CACGCACATACTTTTGTCATTA
65 CGCACACATCCTTTTATCATTA
12600716 TGGTGAATAT
Statistics
Matches: 181, Mismatches: 32, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
128 122 0.67
129 6 0.03
130 52 0.29
131 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.40
Consensus pattern (127 bp):
TTTTCTTTTCAATAATTGATTAAACGTTATGCTCATTTGTCAATCAAAGTGAATCAGAGATACAC
GCACACATCCTTTTATCATTACGTCAAATAAATCTCAAAGTTCGGTTTCACTGCTTCGACAT
Found at i:12600730 original size:128 final size:128
Alignment explanation
Indices: 12600464--12600730 Score: 372
Period size: 128 Copynumber: 2.1 Consensus size: 128
12600454 TTATTATGTC
* * * *
12600464 AAATATATCTCAAAGTTTGGTTTCACTGCTTCGACATTTTTCTGTTTCAATAATTGATTAAACGT
1 AAATATATTTCAAAGTTCGGTTTCACTGCTTCGACATTCTTCTCTTTCAATAATTGATTAAACGT
* * * * * *
12600529 TATGCTCATTGGTCGATCAAAGTGAATCAGAGATATACGCACACATCCTTTTGTCATTACGTT
66 TATACTCATTGGTCAATCAAAGTGAATCAGAAATATACACACACATACTTTTGTCATTACGGT
* * *
12600592 AAATAAATTTCAAAGTTCGGTTTCAGTGCTTCGACGTTCTTCTCTTTCAATAATTGATTAAACGT
1 AAATATATTTCAAAGTTCGGTTTCACTGCTTCGACATTCTTCTCTTTCAATAATTGATTAAACGT
* * * *
12600657 TGTACTCATTTGTCAATCAAAGTGAATCAGAAATATACACGCACATACTTTTGTCATTATGGT
66 TATACTCATTGGTCAATCAAAGTGAATCAGAAATATACACACACATACTTTTGTCATTACGGT
*
12600720 GAATATATTTC
1 AAATATATTTC
12600731 GACATTGTTC
Statistics
Matches: 120, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
128 120 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (128 bp):
AAATATATTTCAAAGTTCGGTTTCACTGCTTCGACATTCTTCTCTTTCAATAATTGATTAAACGT
TATACTCATTGGTCAATCAAAGTGAATCAGAAATATACACACACATACTTTTGTCATTACGGT
Found at i:12602746 original size:22 final size:22
Alignment explanation
Indices: 12602697--12602748 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
12602687 TTACGTAATC
*
12602697 GATTTTTGGGTATTGCATAACT
1 GATTTTTAGGTATTGCATAACT
*
12602719 -AGTTTTTAGGTATTGCATGACT
1 GA-TTTTTAGGTATTGCATAACT
12602741 GATTTTTA
1 GATTTTTA
12602749 ATTATTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 24 0.92
23 1 0.04
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.48
Consensus pattern (22 bp):
GATTTTTAGGTATTGCATAACT
Found at i:12602754 original size:22 final size:22
Alignment explanation
Indices: 12602706--12602766 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
12602696 CGATTTTTGG
* *
12602706 GTATTGCATAACTAGTTTTTAG
1 GTATTGCATGACTAGTTTTTAA
12602728 GTATTGCATGACT-GATTTTTAA
1 GTATTGCATGACTAG-TTTTTAA
* * *
12602750 TTATTACATGATTAGTT
1 GTATTGCATGACTAGTT
12602767 GATTTAACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (22 bp):
GTATTGCATGACTAGTTTTTAA
Found at i:12602835 original size:23 final size:23
Alignment explanation
Indices: 12602774--12602841 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
12602764 GTTGATTTAA
12602774 CATTGCGTGACTGGTTAGT-AGG
1 CATTGCGTGACTGGTTAGTAAGG
* * *
12602796 CATTACGTCATTGGTTAGTAAGG
1 CATTGCGTGACTGGTTAGTAAGG
* *
12602819 CATTGCATGACTAGTTAGTAAGG
1 CATTGCGTGACTGGTTAGTAAGG
12602842 TATTATGTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 16 0.43
23 21 0.57
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.32
Consensus pattern (23 bp):
CATTGCGTGACTGGTTAGTAAGG
Found at i:12602912 original size:22 final size:22
Alignment explanation
Indices: 12602887--12602945 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
12602877 TCAACCACAC
* *
12602887 AATGCCTAAAAACTATTCACGT
1 AATGCCTAAAAACCAGTCACGT
12602909 AATGCCT-AAAACCAGTCACGT
1 AATGCCTAAAAACCAGTCACGT
* *
12602930 AATTCCTAAATACCAG
1 AATGCCTAAAAACCAG
12602946 AGATACAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (22 bp):
AATGCCTAAAAACCAGTCACGT
Found at i:12602985 original size:22 final size:22
Alignment explanation
Indices: 12602960--12603023 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
12602950 ACAATAATTA
*
12602960 AGTTACATAATACTTAAAACTC
1 AGTTACATAATACTTAAAAATC
* *
12602982 AGTTTCACAATAGC-TAAAAATC
1 AGTTACATAATA-CTTAAAAATC
* *
12603004 AGTGACATAATGCTTAAAAA
1 AGTTACATAATACTTAAAAA
12603024 CTAGTAATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (22 bp):
AGTTACATAATACTTAAAAATC
Found at i:12609923 original size:27 final size:27
Alignment explanation
Indices: 12609867--12609925 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
12609857 AGCTTCTTCA
* * **
12609867 CTTCATTAACAGCTTTCTTAGGCTTTT
1 CTTCATGAACAACTTTCTTAGGCTCGT
*
12609894 CTTCATGAACAACTTTGTTAGGCTCGT
1 CTTCATGAACAACTTTCTTAGGCTCGT
12609921 CTTCA
1 CTTCA
12609926 GGTATTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (27 bp):
CTTCATGAACAACTTTCTTAGGCTCGT
Found at i:12620112 original size:9 final size:9
Alignment explanation
Indices: 12620098--12620131 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
12620088 GGAAAGAAGA
12620098 GGAGGTGGT
1 GGAGGTGGT
12620107 GGAGGTGGT
1 GGAGGTGGT
*
12620116 GGAGGTGGA
1 GGAGGTGGT
12620125 GGAGGTG
1 GGAGGTG
12620132 CAGATCTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.15, C:0.00, G:0.68, T:0.18
Consensus pattern (9 bp):
GGAGGTGGT
Done.