Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold177
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: 788481
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.27
Warning! 150793 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:446476 original size:2 final size:2
Alignment explanation
Indices: 446469--446494 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
446459 TTTTCTCCTA
446469 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
446495 TACTAGGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:446911 original size:3 final size:3
Alignment explanation
Indices: 446903--446944 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
446893 AATTTTAACT
446903 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
446945 GATTTTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:447079 original size:21 final size:20
Alignment explanation
Indices: 447009--447080 Score: 51
Period size: 21 Copynumber: 3.6 Consensus size: 20
446999 TATTTATATC
447009 ATAT-TAAAT-TTATTAATA
1 ATATATAAATATTATTAATA
* * * *
447027 AAATTTTTAATTTTATTAATA
1 ATA-TATAAATATTATTAATA
*
447048 ATATATCAATATTATTACATA
1 ATATATAAATATTATTA-ATA
447069 ATACTA-AAATAT
1 ATA-TATAAATAT
447081 AATTGGATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
18 2 0.05
19 1 0.02
20 15 0.36
21 22 0.52
22 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATATAAATATTATTAATA
Found at i:447273 original size:16 final size:15
Alignment explanation
Indices: 447243--447272 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
447233 TATTTTTATT
*
447243 TTTTTTTACTTAAAA
1 TTTTTTTAATTAAAA
447258 TTTTTTTAATTAAAA
1 TTTTTTTAATTAAAA
447273 AATAATGGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTTTAATTAAAA
Found at i:448318 original size:17 final size:19
Alignment explanation
Indices: 448298--448341 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
448288 TGGATAGAAA
448298 AATAAAAAAACAAA-AA-T
1 AATAAAAAAACAAATAATT
* *
448315 AATAGAAAAATAAATAATT
1 AATAAAAAAACAAATAATT
448334 AATAAAAA
1 AATAAAAA
448342 GAATTTACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 12 0.55
18 2 0.09
19 8 0.36
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (19 bp):
AATAAAAAAACAAATAATT
Found at i:448576 original size:6 final size:6
Alignment explanation
Indices: 448565--448602 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
448555 AGAACAAAGT
* *
448565 TTTGGC TTTGGC TTTGGC TTCGGC TTCGGC TTTGGC TT
1 TTTGGC TTTGGC TTTGGC TTTGGC TTTGGC TTTGGC TT
448603 CATGTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.21, G:0.32, T:0.47
Consensus pattern (6 bp):
TTTGGC
Found at i:449861 original size:24 final size:21
Alignment explanation
Indices: 449810--449869 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 21
449800 TATCCAATTT
449810 AAATTATT-TTTAAAA-TAATA
1 AAATT-TTATTTAAAATTAATA
449830 AAATTTTATTTAAAATTAATTA
1 AAATTTTATTTAAAATTAA-TA
*
449852 TAAATATTTATATAAAAT
1 -AAAT-TTTATTTAAAAT
449870 ATTTTTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 2 0.06
20 12 0.35
21 3 0.09
22 2 0.06
23 4 0.12
24 11 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATTTTATTTAAAATTAATA
Found at i:450691 original size:16 final size:17
Alignment explanation
Indices: 450670--450701 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
450660 TTATAATAAG
450670 TAAAAAACTT-AAACAA
1 TAAAAAACTTGAAACAA
450686 TAAAAAACTTGAAACA
1 TAAAAAACTTGAAACA
450702 TTTAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.66, C:0.12, G:0.03, T:0.19
Consensus pattern (17 bp):
TAAAAAACTTGAAACAA
Found at i:456004 original size:25 final size:27
Alignment explanation
Indices: 455947--456004 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 27
455937 TATAATGATC
* * *
455947 CATTTTTATAATTAATAATATTTTTCT
1 CATTTTTATAATAAATAAGATTTTTAT
455974 CA-TTTTA-AATAAATAAGATTTTTAT
1 CATTTTTATAATAAATAAGATTTTTAT
455999 -ATTTTT
1 CATTTTT
456005 GAAAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 1 0.04
25 19 0.70
26 5 0.19
27 2 0.07
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (27 bp):
CATTTTTATAATAAATAAGATTTTTAT
Found at i:456577 original size:58 final size:58
Alignment explanation
Indices: 456444--456776 Score: 139
Period size: 58 Copynumber: 5.7 Consensus size: 58
456434 AAATATTTCT
** *
456444 AAAATACATGAAATTATATGAAAGTCCTTAGATTATGAAAAATAATCTAAACGACACC
1 AAAATACATGAAATTGCATAAAAGTCCTTAGATTATGAAAAATAATCTAAACGACACC
* * * * * * * *
456502 AACATAGATCAACTTGCATAAAAGTTCTTTGATTATGGAAAATAA-CTTAAAGGAC-CTC
1 AAAATACATGAAATTGCATAAAAGTCCTTAGATTATGAAAAATAATC-TAAACGACAC-C
* * * * * * ** * **
456560 AAAATATATGAAATTGCACTGAAA-TCCCTAAATTATGGAAAATAAACTAAATTATATT
1 AAAATACATGAAATTGCA-TAAAAGTCCTTAGATTATGAAAAATAATCTAAACGACACC
** * * * **
456618 AGAGTTTACA--AAATTGCATCAAAGTCCTTAGGTTAT-AGAAAATGATCTAAATAACACC
1 A-A-AATACATGAAATTGCATAAAAGTCCTTAGATTATGA-AAAATAATCTAAACGACACC
* * ** * * **
456676 AACATAAAT-AAATTTGCATAAAAG-CCTGT-GTAACATGAAAAATAACCTAAATGACATT
1 AAAATACATGAAA-TTGCATAAAAGTCCT-TAG-ATTATGAAAAATAATCTAAACGACACC
* *
456734 AAAATTCATGAAA-TGACATAGAAGTCCTTA-AGTTATGAAAAAT
1 AAAATACATGAAATTG-CATAAAAGTCCTTAGA-TTATGAAAAAT
456777 GACTAAAATG
Statistics
Matches: 199, Mismatches: 57, Indels: 38
0.68 0.19 0.13
Matches are distributed among these distances:
56 3 0.02
57 17 0.09
58 163 0.82
59 13 0.07
60 3 0.02
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (58 bp):
AAAATACATGAAATTGCATAAAAGTCCTTAGATTATGAAAAATAATCTAAACGACACC
Found at i:459637 original size:22 final size:22
Alignment explanation
Indices: 459592--459637 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
459582 CCATGCAAGA
*
459592 TTTGGATATCACCACTAAAGCC
1 TTTGGATATCACCACGAAAGCC
459614 TTTGGATATCACCATCGAAA-CC
1 TTTGGATATCACCA-CGAAAGCC
459636 TT
1 TT
459638 GAATGTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (22 bp):
TTTGGATATCACCACGAAAGCC
Found at i:459676 original size:87 final size:87
Alignment explanation
Indices: 459580--459839 Score: 364
Period size: 87 Copynumber: 3.0 Consensus size: 87
459570 TCAAAGACTT
* *
459580 GTCCATGCAAGA-TTTGGATATCACCACTAAAGCCTTTGGATATCACCATCGAAACCTTGAATGT
1 GTCCATGCAAGATTTTGGATATCACCACTAAAGCCTTTAGATATCACCATCAAAACCTTGAATGT
* *
459644 GAAAATCCTTTTTGAATGCTTCA
66 GAAATTCTTTTTTGAATGCTT-A
459667 GTCCATGCAA-ATTTTGGATATCACCACTAAAGCCTTTAGATATCACCAAT-AAAACCTTGAATG
1 GTCCATGCAAGATTTTGGATATCACCACTAAAGCCTTTAGATATCACC-ATCAAAACCTTGAATG
* * *
459730 TGAAGTTCTTTTTTGAACGCTTT
65 TGAAATTCTTTTTTGAATGCTTA
** * * *
459753 GATTTATGCAAGATTTTGGATATCACCACTAGAGCCTTTAAATATCACCACCAAAACCTTGAATG
1 G-TCCATGCAAGATTTTGGATATCACCACTAAAGCCTTTAGATATCACCATCAAAACCTTGAATG
459818 TGAAATTCTTTTTTGAATGCTT
65 TGAAATTCTTTTTTGAATGCTT
459840 TGGCTATTGC
Statistics
Matches: 154, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
86 2 0.01
87 82 0.53
88 70 0.45
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (87 bp):
GTCCATGCAAGATTTTGGATATCACCACTAAAGCCTTTAGATATCACCATCAAAACCTTGAATGT
GAAATTCTTTTTTGAATGCTTA
Found at i:459711 original size:22 final size:22
Alignment explanation
Indices: 459683--459724 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
459673 GCAAATTTTG
* *
459683 GATATCACCACTAAAGCCTTTA
1 GATATCACCAATAAAACCTTTA
459705 GATATCACCAATAAAACCTT
1 GATATCACCAATAAAACCTT
459725 GAATGTGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (22 bp):
GATATCACCAATAAAACCTTTA
Found at i:460747 original size:17 final size:17
Alignment explanation
Indices: 460725--460757 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
460715 TTTTATCTAT
460725 TTATAT-TTATATTTAAA
1 TTATATATT-TATTTAAA
460742 TTATATATTTATTTAA
1 TTATATATTTATTTAA
460758 TATTTTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATATTTATTTAAA
Found at i:462358 original size:8 final size:8
Alignment explanation
Indices: 462347--462386 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
462337 AAACTAGAAA
462347 AAAAAAAG
1 AAAAAAAG
462355 AAAAATAA-
1 AAAAA-AAG
462363 AAAAAAGAG
1 AAAAAA-AG
462372 AAAAAAAG
1 AAAAAAAG
462380 AAAAAAA
1 AAAAAAA
462387 AGGAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 1 0.03
8 20 0.69
9 8 0.28
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:462364 original size:15 final size:15
Alignment explanation
Indices: 462344--462384 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
462334 AAAAAACTAG
462344 AAAAAAAAAAGA-AA
1 AAAAAAAAAAGAGAA
462358 AATAAAAAAAAGAGAA
1 AA-AAAAAAAAGAGAA
462374 AAAAAGAAAAA
1 AAAAA-AAAAA
462385 AAAGGAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.08
15 13 0.54
16 9 0.38
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAAGAGAA
Found at i:462366 original size:17 final size:16
Alignment explanation
Indices: 462344--462388 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
462334 AAAAAACTAG
462344 AAAAAAAAAAGAAAAA
1 AAAAAAAAAAGAAAAA
*
462360 TAAAAAAAAGAGAAAAA
1 -AAAAAAAAAAGAAAAA
462377 AAGAAAAAAAAG
1 AA-AAAAAAAAG
462389 GAAAGTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 2 0.08
17 23 0.92
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAAGAAAAA
Found at i:463139 original size:58 final size:57
Alignment explanation
Indices: 463024--463163 Score: 156
Period size: 58 Copynumber: 2.4 Consensus size: 57
463014 CACATTAAAT
* ** * * *
463024 ATTACTATGTCATTTCATGCATTTAATTACATTTAATTCATTTTCTATAGTTTAGAA
1 ATTATTATGTCATTTCATGCATTTAAAGACATTGAAGTCATTTTCTATAGTATAGAA
*
463081 ATTATTATGTCATTTCATGCATGTTAAAGATATTGAAGTCATTTTCTAT-GATATAGAA
1 ATTATTATGTCATTTCATGCAT-TTAAAGACATTGAAGTCATTTTCTATAG-TATAGAA
* * *
463139 ACTTTTTTTGTCATTTCATGAATTT
1 A-TTATTATGTCATTTCATGCATTT
463164 TAATGGCATT
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
57 22 0.31
58 30 0.43
59 18 0.26
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.49
Consensus pattern (57 bp):
ATTATTATGTCATTTCATGCATTTAAAGACATTGAAGTCATTTTCTATAGTATAGAA
Found at i:463180 original size:59 final size:58
Alignment explanation
Indices: 463024--463183 Score: 171
Period size: 59 Copynumber: 2.8 Consensus size: 58
463014 CACATTAAAT
* * * *
463024 ATTACTATGTCATTTCATGCA-TTTAATTACATTTAATTCATTTTCTATAGTTTAGAA
1 ATTATTATGTCATTTCATGCATTTTAATGACATTTAAGTCATTTTCTATAGTATAGAA
* * * *
463081 ATTATTATGTCATTTCATGCATGTTAAAGATATTGAAGTCATTTTCTAT-GATATAGAA
1 ATTATTATGTCATTTCATGCATTTTAATGACATTTAAGTCATTTTCTATAG-TATAGAA
* * * * *
463139 ACTTTTTTTGTCATTTCATGAATTTTAATGGCATTTTAGTCATTT
1 A-TTATTATGTCATTTCATGCATTTTAATGACATTTAAGTCATTT
463184 CTCATGACTT
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
57 21 0.25
58 28 0.34
59 34 0.41
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (58 bp):
ATTATTATGTCATTTCATGCATTTTAATGACATTTAAGTCATTTTCTATAGTATAGAA
Found at i:463336 original size:58 final size:59
Alignment explanation
Indices: 463269--463397 Score: 147
Period size: 58 Copynumber: 2.2 Consensus size: 59
463259 TATGTATTCC
* * ** *
463269 CATGTATTTTAAGG-CCATTATAGTTATTTGCCATGTTTT-AGGATTATTTATGCAATTT
1 CATGTATTTTAAGGACCATTATAATAACATGCAATGTTTTAAGGATT-TTTATGCAATTT
* * * *
463327 CATGCATTTT-AGGATCATTTTAATAACATGCAATGTTTTAAGGATTTTTATGTAATTT
1 CATGTATTTTAAGGACCATTATAATAACATGCAATGTTTTAAGGATTTTTATGCAATTT
463385 CATGTATTTTAAG
1 CATGTATTTTAAG
463398 ACTATTTTGG
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
57 3 0.05
58 47 0.81
59 8 0.14
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (59 bp):
CATGTATTTTAAGGACCATTATAATAACATGCAATGTTTTAAGGATTTTTATGCAATTT
Found at i:465969 original size:20 final size:20
Alignment explanation
Indices: 465921--465958 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
465911 AGGACAATGT
*
465921 ATCGATATAATTCTTCATGC
1 ATCGATACAATTCTTCATGC
465941 ATCGATACAATTCTTCAT
1 ATCGATACAATTCTTCAT
465959 TTATTGATAC
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:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (20 bp):
ATCGATACAATTCTTCATGC
Found at i:466057 original size:20 final size:20
Alignment explanation
Indices: 466031--466084 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
466021 ACTACCAGTT
*
466031 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAAGTGA
466050 TGCATGTATCGATAC-AGTGA
1 T-CATGTATCGATACAAGTGA
466070 TCATGTATCGATACA
1 TCATGTATCGATACA
466085 TTATATCGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (20 bp):
TCATGTATCGATACAAGTGA
Found at i:471539 original size:52 final size:52
Alignment explanation
Indices: 471469--471589 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
471459 GAAAATTTAT
*
471469 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
471521 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
471573 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
471590 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:471602 original size:52 final size:51
Alignment explanation
Indices: 471469--471609 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
471459 GAAAATTTAT
471469 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
471521 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
471573 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
471610 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:471616 original size:13 final size:13
Alignment explanation
Indices: 471598--471622 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
471588 CAAAGATCAG
471598 TGTATCGATACAA
1 TGTATCGATACAA
471611 TGTATCGATACA
1 TGTATCGATACA
471623 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:471705 original size:13 final size:13
Alignment explanation
Indices: 471687--471711 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
471677 CAAAAAAATA
471687 TGTATCGATACAT
1 TGTATCGATACAT
471700 TGTATCGATACA
1 TGTATCGATACA
471712 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:471707 original size:33 final size:33
Alignment explanation
Indices: 471665--471731 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
471655 AGTAGCTTAA
471665 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
471698 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
471731 A
1 A
471732 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:472358 original size:16 final size:16
Alignment explanation
Indices: 472339--472369 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
472329 TAGTATCGAA
472339 CCTAAATTGTATCAAT
1 CCTAAATTGTATCAAT
472355 CCTAAATTGTATCAA
1 CCTAAATTGTATCAA
472370 ACAAGTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (16 bp):
CCTAAATTGTATCAAT
Found at i:481898 original size:27 final size:27
Alignment explanation
Indices: 481840--481890 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
481830 CTAAGCCCAT
481840 TTTTTCATTTTAAAAGCATACTTTAAAA
1 TTTTTCATTTTAAAAGCATA-TTTAAAA
*
481868 TTTTTCTTTTTAAAAG-AT-TTTAA
1 TTTTTCATTTTAAAAGCATATTTAA
481891 TTAATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
27 2 0.09
28 15 0.68
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (27 bp):
TTTTTCATTTTAAAAGCATATTTAAAA
Found at i:484860 original size:13 final size:13
Alignment explanation
Indices: 484839--484872 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
484829 TGGCAAATGA
*
484839 AGAAGAAAAAGAG
1 AGAAAAAAAAGAG
484852 AGAAAAAAAAGAG
1 AGAAAAAAAAGAG
484865 AGGAAAAA
1 A-GAAAAA
484873 GAGAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAGAG
Found at i:486376 original size:156 final size:156
Alignment explanation
Indices: 485947--487744 Score: 1563
Period size: 156 Copynumber: 11.5 Consensus size: 156
485937 TGTCATTGGA
*
485947 TCCACTTTTATGCTGAAGGTGGGCATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
1 TCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
* * * *
486012 CTTCGGGAGTATCAGGCACTTCTAAGTCAAAGGTATCTCATTTGGGTATTTTCGTAATTTTTTTA
66 CTTAGGGGGTATCAGGCACTTCTAAGTCAAAGGTATCTCATTAGGGTATTTTCATAATTTTTTTA
* * * * * *
486077 GAAACGAGTCTTAGGTTATCACTGGG
131 TAACCGAGTCCTAGGTTGTCACCGAG
* * * *
486103 TCCCCTTTATAT-C-GAAGGTGGTTA-TTAGGATAGGTTCATCCCATCTGTAATTCTTTTTAAGT
1 TCCACTTT-TATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGT
* * ** *
486165 CCTTTAAGGGGTATTAGGCACTTCTAAGTTGAAGGTATCTCA-TGGGGTATTTTCATAATTTTTT
65 CC-TTAGGGGGTATCAGGCACTTCTAAGTCAAAGGTATCTCATTAGGGTATTTTCATAATTTTTT
486229 TATAACCGAGTCCCTA-GTTGTCACCGAG
129 TATAACCGAGT-CCTAGGTTGTCACCGAG
*** *
486257 TTTGCTTTTATGCTGAAGGTGGGGATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
1 TCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
* * *
486322 CTTCGGGGGTATCAGGCACTTCTAAGTCGAAGGTATCTCATTTGGGTATTTTCATAATTTTTTTA
66 CTTAGGGGGTATCAGGCACTTCTAAGTCAAAGGTATCTCATTAGGGTATTTTCATAATTTTTTTA
* *
486387 TAAACGAGTCCTAGGTTATCACC-AGG
131 TAACCGAGTCCTAGGTTGTCACCGA-G
* * *
486413 TCCCCTTTTAT-ATCGAAGGTGGGTA-TTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGT
1 TCCACTTTTATGCT-GAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGT
* * * *
486476 CCTTTAAGGGGTATCGGGCACTTCTAAGTTAAAGGTATCTCATGAGGGTATTTTCATAATTTTTT
65 CC-TTAGGGGGTATCAGGCACTTCTAAGTCAAAGGTATCTCATTAGGGTATTTTCATAATTTTTT
* * * *
486541 TATGACCGAGTCCCTA-ATTGTCATCGGG
129 TATAACCGAGT-CCTAGGTTGTCACCGAG
* * * * *
486569 TTCGCTTTTATGCTGAAGGTGGGGATTTAAGATAGGTTCATCTCATCTATAATCCTTTTTAAGTC
1 TCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
* * * * * * *
486634 TTTTAGGGGGTATCAGGCATTTTTAAGTCGAAA-GCATCCCA-TAGGGACATTTTCATAATTTTC
66 -CTTAGGGGGTATCAGGCACTTCTAAGTC-AAAGGTATCTCATTAGGG-TATTTTCATAATTTTT
* * * * * * * *
486697 TCAAAATCGAGTCTTATGTTGTCGCTGGG
128 TTATAACCGAGTCCTAGGTTGTCACCGAG
** * *
486726 TCTGCTTTTATGCTGAAGGTTGGTATTTAGGATAGGTTCATCACATCTATAATCCTTTTTAAGTC
1 TCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
* * * * * * * **
486791 TTTTAAGGGGTATC-GAGTACTTCGAAGTTAAAGGTATCCTC-TAAGGGTGTTTTTGTAA-TTTT
66 -CTTAGGGGGTATCAG-GCACTTCTAAGTCAAAGGTAT-CTCATTAGGGTATTTTCATAATTTTT
* * ** * *
486853 TTAGAATCGAGTCCTAGGTCATCATCGGG
128 TTATAACCGAGTCCTAGGTTGTCACCGAG
* * * * * * *
486882 TCCACTTTTATGCCGAATGTGAGTATTTAGAATAGGTTCATCTCATCTGTAATCCTTTTAAAGTC
1 TCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
* * * *
486947 TTTTAGGGAGTAT-AGGACACTTCTAAGCCGAAGGTATCTC-TTAGGGGTATTTT-AGTAATTTT
66 -CTTAGGGGGTATCAGG-CACTTCTAAGTCAAAGGTATCTCATTA-GGGTATTTTCA-TAATTTT
* * * *
487009 TTCATAACTGAGTCTTAGGTCGTCACCGAG
127 TTTATAACCGAGTCCTAGGTTGTCACCGAG
* * * * * *
487039 TCCATTTTTATGCCGAAGGTTGGTATTTAGGATAGGTTCATCCCATTTATAAGCTTTTTTAAGTC
1 TCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
* * ** * * * *
487104 CTTTA-AGGATATTGGGCACTTCTAAGTCAAAGGTATC-CCTAAGCGCATTTT-AGTAATTTCTC
66 C-TTAGGGGGTATCAGGCACTTCTAAGTCAAAGGTATCTCATTAGGGTATTTTCA-TAATTT-T-
** * *
487166 TAAAATCAAGTCCTAGGTTAAGTCCTAGGTTGTCATCGAA
127 T-TTAT-AA--CC---G---AGTCCTAGGTTGTCACCGAG
* * * **
487206 TCTACTTTTATACCGAATATGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
1 TCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
* * * * * **
487271 TTTTAGGGGGTATCAGGCACTTCTAAGTTAAAGGTATCCCCTAAGGGTATTTTTGT-A-TTTTTT
66 -CTTAGGGGGTATCAGGCACTTCTAAGTCAAAGGTATCTCATTAGGGTATTTTCATAATTTTTTT
* * * * *
487334 AGAATCGAATCTTAGGTTGTCA-CTAGG
130 ATAACCGAGTCCTAGGTTGTCACCGA-G
487361 TCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAAT-CTTTTTAAGTC
1 TCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
* *
487425 TTTTAGGGGGTAT-AGGACACTTCTAAGT-AGAAGGTATCTC-TTGGGGGTATTTT-AGTAATTT
66 -CTTAGGGGGTATCAGG-CACTTCTAAGTCA-AAGGTATCTCATT-AGGGTATTTTCA-TAATTT
* * * *
487486 TTTCATAACCGATTCTTAGGTTGTCACCGGG
126 TTTTATAACCGAGTCCTAGGTTGTCACCGAG
** * * * *
487517 TCTGCCTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAAGCTTTTTTAAGTC
1 TCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
* ** * *
487582 CTTTA-GGGATATTTGGCACTTCTAAATCAAAGGTATCT--TTAAGGGTATTTT-AGTAATTTCT
66 C-TTAGGGGGTATCAGGCACTTCTAAGTCAAAGGTATCTCATT-AGGGTATTTTCA-TAATTTTT
* * * * ** *
487643 CTAGAACCAAGTCCTAAGTTGTCATTGAA
128 TTATAACCGAGTCCTAGGTTGTCACCGAG
* * * * * *
487672 TCTACTTGTATACCGAAGGTAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTGAGTC
1 TCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
487737 CTTTAGGG
66 C-TTAGGG
487745 TTACTATAAT
Statistics
Matches: 1345, Mismatches: 237, Indels: 120
0.79 0.14 0.07
Matches are distributed among these distances:
153 8 0.01
154 138 0.10
155 318 0.24
156 447 0.33
157 294 0.22
158 12 0.01
159 2 0.00
161 2 0.00
163 2 0.00
164 2 0.00
165 1 0.00
166 1 0.00
167 77 0.06
168 28 0.02
169 13 0.01
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.38
Consensus pattern (156 bp):
TCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTC
CTTAGGGGGTATCAGGCACTTCTAAGTCAAAGGTATCTCATTAGGGTATTTTCATAATTTTTTTA
TAACCGAGTCCTAGGTTGTCACCGAG
Found at i:487666 original size:311 final size:310
Alignment explanation
Indices: 485951--487741 Score: 1662
Period size: 313 Copynumber: 5.7 Consensus size: 310
485941 ATTGGATCCA
* *
485951 CTTTTATGCTGAAGGTGGGCATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCC-TT
1 CTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTT
* * *
486015 CGGGAGTATCAGGCACTTCTAAGTCAAAGGTATCTCATT-TGGGTATTTTCGTAATTTTTTTAGA
66 AGGGA-TATCAGGCACTTCTAAGTCAAAGGTATCTC-TTAAGGGTATTTTAGTAA-TTTTTTAGA
* * * * *
486079 AACGAGTCTTAGGTTATCACTGGGTCCCCTTTATAT-C-GAAGGTGGTTA-TTAGGATAGGTTCA
128 ACCGAGTCTTAGGTTGTCACTAGGTCCACTTT-TATGCTGAAGGTGGGTATTTAGGATAGGTTCA
* *
486141 TCCCATCTGTAATTCTTTTTAAGTCCTTTAAGGGGTATTAGG-CACTTCTAAGTTGAAGGTATCT
192 TCCCATCTATAA-TCTTTTTAAGTCCTTTAAGGGGTA-TAGGACACTTCTAAG-TAAAGGTATCT
* * * *
486205 CAT-GGGGTATTTTCA-TAATTTTTTTATAACCGAGTCCCTA-GTTGTCACCGAGTTTG
254 CATGGGGGTATTTT-AGTAATTTTTTTATAACCGA-TTCCTAGGTTGTCATCGGGTCTG
* * *
486261 CTTTTATGCTGAAGGTGGGGATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTC
1 CTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTT
* * * * *
486326 GGGGGTATCAGGCACTTCTAAGTCGAAGGTATCTCATT-TGGGTATTTTCA-TAATTTTTTTATA
66 AGGGATATCAGGCACTTCTAAGTCAAAGGTATCTC-TTAAGGGTATTTT-AGTAA-TTTTTTAGA
* * * * * *
486389 AACGAGTCCTAGGTTATCACCAGGTCCCCTTTTAT-ATCGAAGGTGGGTA-TTAGGATAGGTTCA
128 ACCGAGTCTTAGGTTGTCACTAGGTCCACTTTTATGCT-GAAGGTGGGTATTTAGGATAGGTTCA
* *
486452 TCCCATCTATAATTCTTTTTAAGTCCTTTAAGGGGTATCGGGCACTTCTAAGTTAAAGGTATCTC
192 TCCCATCTATAA-TCTTTTTAAGTCCTTTAAGGGGTATAGGACACTTCTAAG-TAAAGGTATCTC
* * * *
486517 ATGAGGGTATTTTCA-TAATTTTTTTATGACCGAGTCCCTA-ATTGTCATCGGGT-TCG
255 ATGGGGGTATTTT-AGTAATTTTTTTATAACCGA-TTCCTAGGTTGTCATCGGGTCT-G
* * * * *
486573 CTTTTATGCTGAAGGTGGGGATTTAAGATAGGTTCATCTCATCTATAATCCTTTTTAAGTCTTTT
1 CTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTT
* * * * * * * *
486638 AGGGGGTATCAGGCATTTTTAAGTCGAAA-GCATCCCAT-AGGGACATTTTCA-TAATTTTCTCA
66 A-GGGATATCAGGCACTTCTAAGTC-AAAGGTATCTCTTAAGGG-TATTTT-AGTAATTTT-TTA
* * * * * ** *
486700 AAATCGAGTCTTATGTTGTCGCTGGGTCTGCTTTTATGCTGAAGGTTGGTATTTAGGATAGGTTC
126 GAACCGAGTCTTAGGTTGTCACTAGGTCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTC
* * * * *
486765 ATCACATCTATAATCCTTTTTAAGTCTTTTAAGGGGTAT-CGAGTACTTCGAAGTTAAAGGTATC
191 ATCCCATCTATAAT-CTTTTTAAGTCCTTTAAGGGGTATAGGA-CACTTCTAAG-TAAAGGTAT-
* * * * * ** **
486829 CTCTAAGGGTGT-TTTT-GTAA-TTTTTTAGAATCGAGTCCTAGGTCATCATCGGGTCCA
252 CTC-ATGGGGGTATTTTAGTAATTTTTTTATAACCGATTCCTAGGTTGTCATCGGGTCTG
* * * * * * *
486886 CTTTTATGCCGAATGTGAGTATTTAGAATAGGTTCATCTCATCTGTAATCCTTTTAAAGTCTTTT
1 CTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTT
* * * *
486951 AGGGAGTAT-AGGACACTTCTAAGCCGAAGGTATCTCTTAGGGGTATTTTAGTAATTTTTTCATA
66 AGGGA-TATCAGG-CACTTCTAAGTCAAAGGTATCTCTTAAGGGTATTTTAGTAATTTTTT-AGA
* * * * * *
487015 ACTGAGTCTTAGGTCGTCAC-CGAGTCCATTTTTATGCCGAAGGTTGGTATTTAGGATAGGTTCA
128 ACCGAGTCTTAGGTTGTCACTAG-GTCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCA
* * * * *
487079 TCCCATTTATAAGCTTTTTTAAGTCCTTTAA-GGATATTGGGCACTTCTAAGTCAAAGGTATC-C
192 TCCCATCTATAATC-TTTTTAAGTCCTTTAAGGGGTATAGGACACTTCTAAGT-AAAGGTATCTC
* ** * * ** * **
487142 CTAAGCGCATTTTAGTAATTTCTCTAAAATCAAGTCCTAGGTTAAGTCCTAGGTTGTCATCGAAT
255 ATGGGGGTATTTTAGTAATTT-T-T-TTAT-AA--CC---G---ATTCCTAGGTTGTCATCGGGT
*
487207 CTA
308 CTG
* ** *
487210 CTTTTATACCGAATATGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCTTTT
1 CTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTT
* * * * * *
487275 AGGGGGTATCAGGCACTTCTAAGTTAAAGGTATCCCCTAAGGGTATTTTTGT-ATTTTTTAGAAT
66 A-GGGATATCAGGCACTTCTAAGTCAAAGGTATCTCTTAAGGGTATTTTAGTAATTTTTTAGAAC
*
487339 CGAATCTTAGGTTGTCACTAGGTCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCC
130 CGAGTCTTAGGTTGTCACTAGGTCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCC
* * *
487404 CATCTATAATCTTTTTAAGTCTTTTAGGGGGTATAGGACACTTCTAAGTAGAAGGTATCTCTTGG
195 CATCTATAATCTTTTTAAGTCCTTTAAGGGGTATAGGACACTTCTAAGTA-AAGGTATCTCATGG
* * *
487469 GGGTATTTTAGTAATTTTTTCATAACCGATTCTTAGGTTGTCACCGGGTCTG
259 GGGTATTTTAGTAATTTTTTTATAACCGATTCCTAGGTTGTCATCGGGTCTG
* * *
487521 CCTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAAGCTTTTTTAAGTCCTTT
1 CTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTT
** * *
487586 AGGGATATTTGGCACTTCTAAATCAAAGGTATCT-TTAAGGGTATTTTAGTAATTTCTCTAGAAC
66 AGGGATATCAGGCACTTCTAAGTCAAAGGTATCTCTTAAGGGTATTTTAGTAATTT-TTTAGAAC
* * * * * * * * * *
487650 CAAGTCCTAAGTTGTCA-TTGAATCTACTTGTATACCGAAGGTAGGTATTTAGGATAGGTTCATC
130 CGAGTCTTAGGTTGTCACTAG-GTCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATC
*
487714 CCATCTATAATCCTTTTTGAGTCCTTTA
194 CCATCTATAAT-CTTTTTAAGTCCTTTA
487742 GGGTTACTAT
Statistics
Matches: 1233, Mismatches: 193, Indels: 108
0.80 0.13 0.07
Matches are distributed among these distances:
309 19 0.02
310 185 0.15
311 239 0.19
312 168 0.14
313 267 0.22
314 77 0.06
315 8 0.01
316 7 0.01
317 2 0.00
318 1 0.00
319 2 0.00
320 2 0.00
321 17 0.01
322 95 0.08
323 25 0.02
324 113 0.09
325 6 0.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (310 bp):
CTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTT
AGGGATATCAGGCACTTCTAAGTCAAAGGTATCTCTTAAGGGTATTTTAGTAATTTTTTAGAACC
GAGTCTTAGGTTGTCACTAGGTCCACTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCC
ATCTATAATCTTTTTAAGTCCTTTAAGGGGTATAGGACACTTCTAAGTAAAGGTATCTCATGGGG
GTATTTTAGTAATTTTTTTATAACCGATTCCTAGGTTGTCATCGGGTCTG
Found at i:490869 original size:13 final size:13
Alignment explanation
Indices: 490851--490876 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
490841 CAATTTTTTG
490851 TGTATCGATACAT
1 TGTATCGATACAT
490864 TGTATCGATACAT
1 TGTATCGATACAT
490877 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:491625 original size:21 final size:21
Alignment explanation
Indices: 491584--491627 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
491574 CTCCCCTTTA
* *
491584 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
491605 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
491626 TC
1 TC
491628 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:493452 original size:13 final size:13
Alignment explanation
Indices: 493434--493471 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
493424 ATAATCACCC
*
493434 TGTATCGATACAG
1 TGTATCGATACAA
493447 TGTATCGATACAA
1 TGTATCGATACAA
493460 TGTATCGATACA
1 TGTATCGATACA
493472 TTGAATTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:495551 original size:15 final size:15
Alignment explanation
Indices: 495531--495561 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
495521 ATTTCGTTTG
*
495531 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
495546 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
495561 G
1 G
495562 GACATTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:497395 original size:21 final size:21
Alignment explanation
Indices: 497366--497410 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
497356 AAGTTTTCAT
*
497366 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
497386 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
497408 TTT
1 TTT
497411 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:498017 original size:12 final size:12
Alignment explanation
Indices: 498002--498027 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
497992 TCTGAGTCAC
498002 CATCTTCATCAA
1 CATCTTCATCAA
498014 CATCTTCATCAA
1 CATCTTCATCAA
498026 CA
1 CA
498028 CTTGCATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (12 bp):
CATCTTCATCAA
Found at i:500665 original size:13 final size:13
Alignment explanation
Indices: 500633--500667 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
500623 AATACTAAAG
500633 CAATGTATCGATA
1 CAATGTATCGATA
*
500646 CATTGTATCGATA
1 CAATGTATCGATA
*
500659 TAATGTATC
1 CAATGTATC
500668 AGTATAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:507465 original size:15 final size:13
Alignment explanation
Indices: 507434--507458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
507424 TAATGATAAA
507434 TGTATCGATACAT
1 TGTATCGATACAT
507447 TGTATCGATACA
1 TGTATCGATACA
507459 AATTGTAAAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:507893 original size:14 final size:14
Alignment explanation
Indices: 507874--507902 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
507864 CACAATGTAT
507874 TGATACATGAACAG
1 TGATACATGAACAG
507888 TGATACATGAACAG
1 TGATACATGAACAG
507902 T
1 T
507903 AATGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (14 bp):
TGATACATGAACAG
Found at i:510609 original size:19 final size:19
Alignment explanation
Indices: 510585--510647 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
510575 AACAAGTAAC
*
510585 TGTATCAATACATAAGTGT
1 TGTATCGATACATAAGTGT
510604 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
510617 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
510636 TGTATCGATACA
1 TGTATCGATACA
510648 ATGTATCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
15 2 0.05
17 2 0.05
19 22 0.59
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:510622 original size:13 final size:13
Alignment explanation
Indices: 510604--510628 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
510594 ACATAAGTGT
510604 TGTATCGATACAA
1 TGTATCGATACAA
510617 TGTATCGATACA
1 TGTATCGATACA
510629 TAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:510628 original size:32 final size:32
Alignment explanation
Indices: 510585--510654 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
510575 AACAAGTAAC
510585 TGTATCAATACATAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAGTGTTGTATCGATACAA
*
510617 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAGTGTTGTATCGATACAA
510649 TGTATC
1 TGTATC
510655 TTTACGAAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCAATACATAAGTGTTGTATCGATACAA
Found at i:510718 original size:13 final size:13
Alignment explanation
Indices: 510700--510727 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
510690 ATTACTCAAA
510700 TGTATCGATACAT
1 TGTATCGATACAT
510713 TGTATCGATACAT
1 TGTATCGATACAT
510726 TG
1 TG
510728 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:513909 original size:20 final size:20
Alignment explanation
Indices: 513884--513932 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
513874 TTCCAGATGA
513884 ATCGATACAAAGA-TCAATGT
1 ATCGATACAAAGAGT-AATGT
*
513904 ATCGATACAATGAGTAATGT
1 ATCGATACAAAGAGTAATGT
513924 ATCGATACA
1 ATCGATACA
513933 TTTCCTTGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (20 bp):
ATCGATACAAAGAGTAATGT
Found at i:513988 original size:19 final size:20
Alignment explanation
Indices: 513964--514016 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
513954 AGCGATACAT
513964 TGTATCGATACAATACT-TA
1 TGTATCGATACAATACTATA
* *
513983 TGTATCGATACAGTTACTATT
1 TGTATCGATACA-ATACTATA
514004 TGTATCGATACAA
1 TGTATCGATACAA
514017 ATTGTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (20 bp):
TGTATCGATACAATACTATA
Found at i:517036 original size:166 final size:165
Alignment explanation
Indices: 516771--517418 Score: 658
Period size: 166 Copynumber: 3.9 Consensus size: 165
516761 ATTTTTCAGG
* * * * * * *
516771 AAAAATAG-AATTTCAAAG-AAAAATCAAAAACTTATGAAAATAAATTAATTTTTTAGAACTGAA
1 AAAAAGAGAAATTTCAAGGAAAAAACCAAAAACTCATGAAAATGAATTTATTTTTTAAAACTGAA
** *
516834 TTAATATGAACCAAATAATGATGTTTGATAAATTTTAAAAATTGAAAACCAAGAAAAATCAGCTC
66 TTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCA-CTC
516899 AAAAAAATTTACGGAGTAGAAAATACCATATTTCAA
130 AAAAAAATTTACGGAGTAGAAAATACCATATTTCAA
* *
516935 AAAAAGGGAAATTTCAAGGAAAAAACCAAAAACTCATAAAAATGAATTTATTTTTTAAAACTGAA
1 AAAAAGAGAAATTTCAAGGAAAAAACCAAAAACTCATGAAAATGAATTTATTTTTTAAAACTGAA
* * * *
517000 TTAATATAAAATAAATAATGATTTTTGATGAATTTTAAAAATTTAAAACCAAGAAAAATACCCTC
66 TTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAAT-CACTC
* * * * *
517065 GAAAATATTTACGGAGTAGAAAATACCGTAATTCGA
130 AAAAAAATTTACGGAGTAGAAAATACCATATTTCAA
*
517101 AAAAAGAGAAATTTCAAGAAAAAAATCC-AAAACTCATGAAAATGAATTTATTTTCTTACAAA--
1 AAAAAGAGAAATTTCAAGGAAAAAA-CCAAAAACTCATGAAAATGAATTTATTTT-TTA-AAACT
517163 -AATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATC-C
63 GAATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCAC
*** * * *
517226 -CATAAAAAATTTAAAAAGTAGAAAACACTATATTCTTGAA
128 TCA-AAAAAATTTACGGAGTAGAAAATACCATA-T-TTCAA
* ** * * * *
517266 AAAAA-AG-AATTTCAGGGAAAACATTCAAAAACTCATGAAAATTAA-TTACTTTTTAAAAATTA
1 AAAAAGAGAAATTTCAAGGAAAA-AACCAAAAACTCATGAAAATGAATTTATTTTTTAAAACTGA
* *** * * * * * *
517328 ATTTAAT-GGGGGTCAAATTATAATATTTGATGAATTTTAAAAATTTTAAATCTAAG-AAAATC-
65 A-TTAATATGAAAT-AAATAATGATGTTTGATGAATTTTAAAAA-TTGAAAACCAAGAAAAATCA
*
517390 CTCATGAAAAAATTTACGGAGAAGAAAAT
127 CTCA--AAAAAATTTACGGAGTAGAAAAT
517419 CCCGTAATTT
Statistics
Matches: 405, Mismatches: 60, Indels: 35
0.81 0.12 0.07
Matches are distributed among these distances:
161 3 0.01
162 4 0.01
163 42 0.10
164 31 0.08
165 113 0.28
166 185 0.46
167 24 0.06
168 3 0.01
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29
Consensus pattern (165 bp):
AAAAAGAGAAATTTCAAGGAAAAAACCAAAAACTCATGAAAATGAATTTATTTTTTAAAACTGAA
TTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCACTCA
AAAAAATTTACGGAGTAGAAAATACCATATTTCAA
Found at i:520842 original size:13 final size:13
Alignment explanation
Indices: 520824--520850 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
520814 ACATTATGCT
520824 TTGTATCGATACA
1 TTGTATCGATACA
520837 TTGTATCGATACA
1 TTGTATCGATACA
520850 T
1 T
520851 GCTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:520859 original size:19 final size:19
Alignment explanation
Indices: 520835--520890 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
520825 TGTATCGATA
*
520835 CATTGTATCGATACATGCT
1 CATTGTATCGATACATGCC
* *
520854 CATTGTATCGATATATACC
1 CATTGTATCGATACATGCC
520873 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
520891 AAACTAACAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGCC
Found at i:520953 original size:13 final size:13
Alignment explanation
Indices: 520935--520964 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
520925 GATACATGGG
520935 ACATTGTATCGAT
1 ACATTGTATCGAT
*
520948 ACATTGTATTGAT
1 ACATTGTATCGAT
520961 ACAT
1 ACAT
520965 GAAGAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:520962 original size:33 final size:33
Alignment explanation
Indices: 520919--520985 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
520909 CTAAGTGAAA
*
520919 TGTATCGATACATG-GGACATTGTATCGATACAT
1 TGTATCGATACATGAAGA-ATTGTATCGATACAT
*
520952 TGTATTGATACATGAAGAATTGTATCGATACAT
1 TGTATCGATACATGAAGAATTGTATCGATACAT
520985 T
1 T
520986 ATGCCCAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATGAAGAATTGTATCGATACAT
Found at i:524882 original size:19 final size:19
Alignment explanation
Indices: 524855--524910 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
524845 TGTATCGATA
*
524855 CATTATATCGATACATGCT
1 CATTGTATCGATACATGCT
*
524874 CATTGTATCGATACATACT
1 CATTGTATCGATACATGCT
524893 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
524911 AAACTGGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:524964 original size:20 final size:19
Alignment explanation
Indices: 524939--525037 Score: 78
Period size: 20 Copynumber: 5.7 Consensus size: 19
524929 TTAAGTGAAA
524939 TGTATCGATACATGGGACAT
1 TGTATCGATACAT-GGACAT
524959 TGTATC----CAT--ACAT
1 TGTATCGATACATGGACAT
*
524972 TGTATTGATACATGAGACAT
1 TGTATCGATACATG-GACAT
524992 TGTATCGAT--A---A-AT
1 TGTATCGATACATGGACAT
525005 TGTATCGATACATGGGACAT
1 TGTATCGATACAT-GGACAT
525025 TGTATCGATACAT
1 TGTATCGATACAT
525038 TATGTCCAAC
Statistics
Matches: 63, Mismatches: 2, Indels: 28
0.68 0.02 0.30
Matches are distributed among these distances:
13 20 0.32
14 1 0.02
15 1 0.02
16 3 0.05
17 3 0.05
18 1 0.02
19 1 0.02
20 33 0.52
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Consensus pattern (19 bp):
TGTATCGATACATGGACAT
Found at i:524982 original size:33 final size:33
Alignment explanation
Indices: 524939--525038 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
524929 TTAAGTGAAA
*
524939 TGTATCGATACATGGGACATTGTATCCATACAT
1 TGTATCGATACATGGGACATTGTATCGATACAT
* * *
524972 TGTATTGATACATGAGACATTGTATCGATAAAT
1 TGTATCGATACATGGGACATTGTATCGATACAT
525005 TGTATCGATACATGGGACATTGTATCGATACAT
1 TGTATCGATACATGGGACATTGTATCGATACAT
525038 T
1 T
525039 ATGTCCAACG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATGGGACATTGTATCGATACAT
Found at i:525008 original size:13 final size:13
Alignment explanation
Indices: 524990--525014 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
524980 TACATGAGAC
524990 ATTGTATCGATAA
1 ATTGTATCGATAA
525003 ATTGTATCGATA
1 ATTGTATCGATA
525015 CATGGGACAT
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
ATTGTATCGATAA
Found at i:527730 original size:20 final size:20
Alignment explanation
Indices: 527707--527779 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
527697 ACAATTCAAA
527707 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
527727 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
527748 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
527768 GTATCGATACAT
1 GTATCGATACAT
527780 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:527751 original size:21 final size:21
Alignment explanation
Indices: 527725--527800 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
527715 ACATGTTGCA
527725 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
527746 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
527766 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
527787 ATGTATCGATACAT
1 ATGTATCGATACAT
527801 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:527758 original size:41 final size:41
Alignment explanation
Indices: 527707--527800 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
527697 ACAATTCAAA
*
527707 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
527748 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
527789 GTATCGATACAT
1 GTATCGATACAT
527801 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:527857 original size:13 final size:13
Alignment explanation
Indices: 527839--527864 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
527829 TACAGCAAGT
527839 ATGTATCGATACA
1 ATGTATCGATACA
527852 ATGTATCGATACA
1 ATGTATCGATACA
527865 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:531948 original size:15 final size:15
Alignment explanation
Indices: 531928--531966 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
531918 TAAAAATGTC
*
531928 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
531943 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
531958 CCAAATGAA
1 CAAAATGAA
531967 ATTGATGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:534051 original size:20 final size:21
Alignment explanation
Indices: 533972--534050 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
533962 AATGTCCAAA
*
533972 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
533992 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
534017 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
534037 TTGTATCGATACAT
1 ATGTATCGATACAT
534051 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:534055 original size:13 final size:13
Alignment explanation
Indices: 534037--534075 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
534027 ACATTTTTCT
534037 TTGTATCGATACA
1 TTGTATCGATACA
534050 TTGTATCGATACA
1 TTGTATCGATACA
*
534063 CTGTATCGATACA
1 TTGTATCGATACA
534076 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:536396 original size:20 final size:20
Alignment explanation
Indices: 536373--536445 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
536363 ACAATTCAAA
536373 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
536393 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
536414 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
536434 GTATCGATACAT
1 GTATCGATACAT
536446 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:536417 original size:21 final size:21
Alignment explanation
Indices: 536391--536466 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
536381 ACATGTTGCA
536391 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
536412 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
536432 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
536453 ATGTATCGATACAT
1 ATGTATCGATACAT
536467 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:536424 original size:41 final size:41
Alignment explanation
Indices: 536373--536466 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
536363 ACAATTCAAA
*
536373 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
536414 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
536455 GTATCGATACAT
1 GTATCGATACAT
536467 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:536523 original size:13 final size:13
Alignment explanation
Indices: 536505--536530 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
536495 TACAGCAAGT
536505 ATGTATCGATACA
1 ATGTATCGATACA
536518 ATGTATCGATACA
1 ATGTATCGATACA
536531 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:537530 original size:20 final size:21
Alignment explanation
Indices: 537505--537546 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
537495 GTATTTCATG
*
537505 TCAATTGAATTA-AATAATTA
1 TCAATTGAATGAGAATAATTA
*
537525 TCAATTTAATGAGAATAATTA
1 TCAATTGAATGAGAATAATTA
537546 T
1 T
537547 TAAATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (21 bp):
TCAATTGAATGAGAATAATTA
Found at i:539903 original size:3 final size:3
Alignment explanation
Indices: 539895--539933 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
539885 ATTTTAGATC
539895 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TCAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TA
539934 TGTATTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:544973 original size:16 final size:17
Alignment explanation
Indices: 544953--545014 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 17
544943 TAATATACAC
544953 ATAAAATAAAAAATAAT
1 ATAAAATAAAAAATAAT
* *
544970 -TAAAATAATATATAAT
1 ATAAAATAAAAAATAAT
*
544986 ATAAAAATAATAATATGAAT
1 AT-AAAATAA-AAAAT-AAT
545006 ATATAAATA
1 ATA-AAATA
545015 TATTAAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 14 0.38
17 1 0.03
18 7 0.19
19 5 0.14
20 10 0.27
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
ATAAAATAAAAAATAAT
Found at i:545008 original size:20 final size:18
Alignment explanation
Indices: 544971--545014 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
544961 AAAAATAATT
544971 AAAATAATATATAATATA
1 AAAATAATATATAATATA
544989 AAAATAATAATATGAATATA
1 AAAATAAT-ATAT-AATATA
*
545009 TAAATA
1 AAAATA
545015 TATTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 4 0.17
20 11 0.48
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAATAATATATAATATA
Found at i:545016 original size:33 final size:34
Alignment explanation
Indices: 544974--545063 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 34
544964 AATAATTAAA
544974 ATAATATATAATATAAAA-ATA-ATAATATGAATAT
1 ATAATATAT-AT-TAAAATATATATAATATGAATAT
*
545008 ATAA-ATATATTAAAATTTATATAATATGAATGAT
1 ATAATATATATTAAAATATATATAATATGAAT-AT
545042 -TAA-A-ATATTAAAAT-TGATATAA
1 ATAATATATATTAAAATAT-ATATAA
545064 ATATATAATA
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
31 6 0.12
32 20 0.39
33 19 0.37
34 6 0.12
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (34 bp):
ATAATATATATTAAAATATATATAATATGAATAT
Found at i:545067 original size:33 final size:33
Alignment explanation
Indices: 544995--545063 Score: 106
Period size: 32 Copynumber: 2.1 Consensus size: 33
544985 TATAAAAATA
*
544995 ATAATATGAATATATAAATATATTAAAATTTAT
1 ATAATATGAATATATAAATATATTAAAATTGAT
545028 ATAATATGAATGAT-TAAA-ATATTAAAATTGAT
1 ATAATATGAAT-ATATAAATATATTAAAATTGAT
545060 ATAA
1 ATAA
545064 ATATATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 17 0.50
33 15 0.44
34 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (33 bp):
ATAATATGAATATATAAATATATTAAAATTGAT
Found at i:545134 original size:26 final size:26
Alignment explanation
Indices: 545058--545139 Score: 85
Period size: 26 Copynumber: 3.1 Consensus size: 26
545048 ATTAAAATTG
* *
545058 ATATAAATATATAATATTTTAAAAAT
1 ATATAAATTTATAATATTTTAAATAT
* ** *
545084 A-ATTAAAATTATAATATATAAAAATTT
1 ATA-TAAATTTATAATAT-TTTAAATAT
545111 ATATAAATTTATAATATTTTAAATAT
1 ATATAAATTTATAATATTTTAAATAT
545137 ATA
1 ATA
545140 AAAGTATATG
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
25 1 0.02
26 22 0.51
27 19 0.44
28 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATATAAATTTATAATATTTTAAATAT
Found at i:545139 original size:16 final size:16
Alignment explanation
Indices: 545061--545142 Score: 58
Period size: 16 Copynumber: 4.8 Consensus size: 16
545051 AAAATTGATA
*
545061 TAAATATATAATATTT
1 TAAATATATAAAATTT
* *
545077 TAAAAATAATTAAAATTA
1 TAAATAT-A-TAAAATTT
545095 T-AATATATAAAAATTTAT
1 TAAATATAT-AAAA-TT-T
* *
545113 ATAAATTTATAATATTT
1 -TAAATATATAAAATTT
545130 TAAATATATAAAA
1 TAAATATATAAAA
545143 GTATATGAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
15 1 0.02
16 22 0.44
17 8 0.16
18 9 0.18
19 4 0.08
20 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATATATAAAATTT
Found at i:545727 original size:16 final size:16
Alignment explanation
Indices: 545686--545728 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
545676 ATTCATATCA
545686 TTTT-TTAAATTTAAT
1 TTTTATTAAATTTAAT
*
545701 TTTTAAT-AATTTAAT
1 TTTTATTAAATTTAAT
545716 TTTTATTAAATTT
1 TTTTATTAAATTT
545729 TAAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATTAAATTTAAT
Found at i:547533 original size:19 final size:19
Alignment explanation
Indices: 547509--547552 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
547499 TCAATTACAC
547509 GTGGCTTTAAATTTTTTAT
1 GTGGCTTTAAATTTTTTAT
547528 GTGGCTTTAAATTTTTTAT
1 GTGGCTTTAAATTTTTTAT
547547 GTGGCT
1 GTGGCT
547553 AAAATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.18, C:0.07, G:0.20, T:0.55
Consensus pattern (19 bp):
GTGGCTTTAAATTTTTTAT
Found at i:547557 original size:18 final size:19
Alignment explanation
Indices: 547509--547557 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
547499 TCAATTACAC
*
547509 GTGGCTTTAAATTTTTTAT
1 GTGGCTTAAAATTTTTTAT
*
547528 GTGGCTTTAAATTTTTTAT
1 GTGGCTTAAAATTTTTTAT
547547 GTGGC-TAAAAT
1 GTGGCTTAAAAT
547558 ATTAATGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 5 0.17
19 24 0.83
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.51
Consensus pattern (19 bp):
GTGGCTTAAAATTTTTTAT
Found at i:548287 original size:2 final size:2
Alignment explanation
Indices: 548280--548312 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
548270 ACTATTATTT
*
548280 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
548313 GTCACGGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:553007 original size:31 final size:32
Alignment explanation
Indices: 552967--553034 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 32
552957 ATCTTTTGCA
552967 AACCTAGTTCCCTTAAACTCTTTCGGCTTAGG
1 AACCTAGTTCCCTTAAACTCTTTCGGCTTAGG
552999 AACC-AGTTCCCTTAAACTCTTTCGGCTTAGG
1 AACCTAGTTCCCTTAAACTCTTTCGGCTTAGG
553030 AACCT
1 AACCT
553035 CGATCTTGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (32 bp):
AACCTAGTTCCCTTAAACTCTTTCGGCTTAGG
Found at i:554058 original size:187 final size:188
Alignment explanation
Indices: 553737--554138 Score: 583
Period size: 187 Copynumber: 2.1 Consensus size: 188
553727 TTAATGGAAG
*
553737 ACTAGAATTAATATTTATCTATAAAATCTAGAACTCAGATAAGTTTAAACTCTATTACTCTATTT
1 ACTAGAATTAATATTTATCTATAAAATCTAGAACTCAGATAAGTTTAAACTCTATTACTCTACTT
* * * * * * *
553802 TTATAGAGTTTTAATTAAGCTGAAGTAGTTGTAGTTAACTGACTTTCTAAATTTTTAGAAACTTA
66 CTATAAAGTTCTAATTAAGCTGAAATAGTTGTAGTTAACTAACTCTCCAAATTTTTAGAAACTTA
*
553867 AGT-AACTGAATCTTTTAAAACTCTTGAAA-TATTAAATTTATTTTGATAAATTAAATT
131 AGTAAACTGAATCTTTTAAAACTCTT-AAAGTATTAAATTTATTTTAATAAATTAAATT
* * * *
553924 ACTAGGATTAATATTTATCTATAAAATCTAGAATTTAGATAAGTTTAAACTCTATTATTCTACTT
1 ACTAGAATTAATATTTATCTATAAAATCTAGAACTCAGATAAGTTTAAACTCTATTACTCTACTT
* * *
553989 CTATAAAGTTCTAATTAAGTTTAAATAGTTGTAGTTGACTAACTCTCCAAATTTTTAGAAACTTA
66 CTATAAAGTTCTAATTAAGCTGAAATAGTTGTAGTTAACTAACTCTCCAAATTTTTAGAAACTTA
* * * *
554054 AGTAAACTGAATTTTTTAAAATTCTTAAAGTGTTGAATTTATTTTAATAAATTAAATT
131 AGTAAACTGAATCTTTTAAAACTCTTAAAGTATTAAATTTATTTTAATAAATTAAATT
* *
554112 ACTAAAATTAATATTTATTTATAAAAT
1 ACTAGAATTAATATTTATCTATAAAAT
554139 TTAAATAAAT
Statistics
Matches: 190, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
187 121 0.64
188 69 0.36
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (188 bp):
ACTAGAATTAATATTTATCTATAAAATCTAGAACTCAGATAAGTTTAAACTCTATTACTCTACTT
CTATAAAGTTCTAATTAAGCTGAAATAGTTGTAGTTAACTAACTCTCCAAATTTTTAGAAACTTA
AGTAAACTGAATCTTTTAAAACTCTTAAAGTATTAAATTTATTTTAATAAATTAAATT
Found at i:554179 original size:15 final size:15
Alignment explanation
Indices: 554143--554184 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
554133 TAAAATTTAA
*
554143 ATAAATTTAAATTTT
1 ATAAATTTTAATTTT
* *
554158 AT-TATTTTATTTTT
1 ATAAATTTTAATTTT
554172 ATAAATTTTAATT
1 ATAAATTTTAATT
554185 AAATTAAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATAAATTTTAATTTT
Found at i:558854 original size:59 final size:57
Alignment explanation
Indices: 558752--558867 Score: 169
Period size: 59 Copynumber: 2.0 Consensus size: 57
558742 AAGAATTTGA
* * * *
558752 ATACTTATGGCAGGAAATATTACACTACATGATTTCTTCCAATAAAATTCATTCAAT
1 ATACTCATGGAAGGAAATATTACACTACATGACTTCTTACAATAAAATTCATTCAAT
*
558809 ATACTCATGGAAGGAAATATTATATACTACATGACTTCTTACAATAAAATTCATTCAAT
1 ATACTCATGGAAGGAAATA-T-TACACTACATGACTTCTTACAATAAAATTCATTCAAT
558868 CAACAAAGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
57 17 0.33
58 1 0.02
59 34 0.65
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (57 bp):
ATACTCATGGAAGGAAATATTACACTACATGACTTCTTACAATAAAATTCATTCAAT
Found at i:561546 original size:2 final size:2
Alignment explanation
Indices: 561539--561660 Score: 64
Period size: 2 Copynumber: 61.0 Consensus size: 2
561529 AAAGTGTAAA
* * * * * **
561539 AT AT AT AT AT AT AT AT GT GT GT AT AT AT AT AT AT AT GT GT GC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * ** * * * *
561581 AT AT AT AT AT AT AT GT GT GC AT AT AT AT AT AT AT GT GT GT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
561623 GT GT GT GT 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
561661 CATGTCCTCA
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 106 1.00
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (2 bp):
AT
Found at i:561660 original size:20 final size:20
Alignment explanation
Indices: 561540--561620 Score: 144
Period size: 20 Copynumber: 4.0 Consensus size: 20
561530 AAGTGTAAAA
561540 TATATATATATATATGTGTG
1 TATATATATATATATGTGTG
561560 TATATATATATATATGTGTG
1 TATATATATATATATGTGTG
*
561580 CATATATATATATATGTGTG
1 TATATATATATATATGTGTG
*
561600 CATATATATATATATGTGTG
1 TATATATATATATATGTGTG
561620 T
1 T
561621 GTGTGTGTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (20 bp):
TATATATATATATATGTGTG
Found at i:566128 original size:44 final size:44
Alignment explanation
Indices: 566074--566197 Score: 212
Period size: 44 Copynumber: 2.8 Consensus size: 44
566064 GGTGTTTTTA
* *
566074 TTATTTATTTTTCTGTGGTTTGGCATAGCCACCCAATTGCATAT
1 TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATAT
*
566118 TTATTTATTTTTCCGTGGATTAGCATAGCCACCCAATTGCATAT
1 TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATAT
*
566162 TTATTTATTTTTCCATGGATTGGCATAGCCACCCAA
1 TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAA
566198 ATTCTAACAA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 75 1.00
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (44 bp):
TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATAT
Found at i:570920 original size:44 final size:44
Alignment explanation
Indices: 570804--570927 Score: 176
Period size: 44 Copynumber: 2.8 Consensus size: 44
570794 GGTATTTTTA
* * * *
570804 TTATTTATTTTTCTGTGGTTTGGCATAGCCATCCAATTGCATAT
1 TTATTTATTTTTCTGTGGATTGACATAGTCAACCAATTGCATAT
* * *
570848 TTATTTATTTTTCCGTAGATTGACATAGTCACCCAATTGCATAT
1 TTATTTATTTTTCTGTGGATTGACATAGTCAACCAATTGCATAT
*
570892 TTATTTATTTTTCTGTGGATTGATATAGTCAACCAA
1 TTATTTATTTTTCTGTGGATTGACATAGTCAACCAA
570928 ATTTTAACAA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 70 1.00
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (44 bp):
TTATTTATTTTTCTGTGGATTGACATAGTCAACCAATTGCATAT
Found at i:574822 original size:13 final size:13
Alignment explanation
Indices: 574804--574830 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
574794 TATTTATTAA
574804 TTTTTAATTTATT
1 TTTTTAATTTATT
574817 TTTTTAATTTATT
1 TTTTTAATTTATT
574830 T
1 T
574831 ATTTGATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTAATTTATT
Found at i:578076 original size:2 final size:2
Alignment explanation
Indices: 578071--578095 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
578061 TCTCTCTCTC
578071 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 T
578096 GTGGCTTACT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:579478 original size:14 final size:13
Alignment explanation
Indices: 579454--579489 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 13
579444 AATTAAGATT
579454 ATTAAATTATATTA
1 ATTAAA-TATATTA
579468 CATTAAATATATTA
1 -ATTAAATATATTA
579482 ATTAAATA
1 ATTAAATA
579490 AATATAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 7 0.33
15 6 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAATATATTA
Found at i:579501 original size:18 final size:17
Alignment explanation
Indices: 579471--579508 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
579461 TATATTACAT
*
579471 TAAATATATTAATTAAA
1 TAAATATAGTAATTAAA
579488 TAAATATAAGTAATTAAA
1 TAAATAT-AGTAATTAAA
579506 TAA
1 TAA
579509 TATTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
TAAATATAGTAATTAAA
Found at i:585005 original size:3 final size:3
Alignment explanation
Indices: 584997--585041 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
584987 TGCAAATTAC
584997 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
585042 TTGCTTATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:588076 original size:16 final size:16
Alignment explanation
Indices: 588055--588086 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
588045 AGACCACAAA
588055 CATGGAAATCAAATTT
1 CATGGAAATCAAATTT
588071 CATGGAAATCAAATTT
1 CATGGAAATCAAATTT
588087 TGGCTGCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (16 bp):
CATGGAAATCAAATTT
Found at i:589949 original size:10 final size:10
Alignment explanation
Indices: 589930--589960 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
589920 ATAAAAAAGA
589930 AATG-AATGG
1 AATGCAATGG
589939 AATGCAATGG
1 AATGCAATGG
589949 AATGCAATGG
1 AATGCAATGG
589959 AA
1 AA
589961 CGGAATAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.45, C:0.06, G:0.29, T:0.19
Consensus pattern (10 bp):
AATGCAATGG
Found at i:590998 original size:2 final size:2
Alignment explanation
Indices: 590985--591015 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
590975 AAGATTATTA
*
590985 AG AG AA 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
591016 AGGGGAAGGT
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:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:591400 original size:18 final size:19
Alignment explanation
Indices: 591362--591401 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
591352 ATTTATTTAT
* *
591362 TATTTTATCATAATTATAA
1 TATTTTATCAAAATAATAA
591381 TATTTTA-CAAAATAATAA
1 TATTTTATCAAAATAATAA
591399 TAT
1 TAT
591402 CTCATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTTTATCAAAATAATAA
Found at i:591433 original size:14 final size:14
Alignment explanation
Indices: 591414--591445 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
591404 CATAATAAAT
591414 TTTAATTAAAATAA
1 TTTAATTAAAATAA
*
591428 TTTAATTATAATAA
1 TTTAATTAAAATAA
591442 TTTA
1 TTTA
591446 TAAATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAAAATAA
Found at i:591461 original size:5 final size:5
Alignment explanation
Indices: 591451--591491 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
591441 ATTTATAAAT
*
591451 TTATA TTATA TT-TA -TATA TTTTA TTATA TTATA TTTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TTATA TT
591492 TAATATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
3 1 0.03
4 4 0.13
5 21 0.68
6 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TTATA
Found at i:591474 original size:28 final size:26
Alignment explanation
Indices: 591433--591512 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 26
591423 AATAATTTAA
591433 TTATAATAATTTATAAATTTATATTATAT
1 TTAT-ATAATTTAT--ATTTATATTATAT
*
591462 TTATATATTTTATTATATTATATTTATAT
1 TTATATAATTTA-TAT-TTATA-TTATAT
591491 TTAATATAATTTATATTTATAT
1 TT-ATATAATTTATATTTATAT
591513 AAATTTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
27 3 0.07
28 17 0.38
29 16 0.36
30 9 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATATAATTTATATTTATATTATAT
Found at i:591477 original size:23 final size:24
Alignment explanation
Indices: 591451--591513 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 24
591441 ATTTATAAAT
*
591451 TTATATTATATTTATATATT-TTA
1 TTATATTATATTTATATATTAATA
591474 TTATATTATATTTATAT-TTAATA
1 TTATATTATATTTATATATTAATA
*
591497 TAAT-TTATATTTATATA
1 TTATATTATATTTATATA
591514 AATTTTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTATATTATATTTATATATTAATA
Found at i:591513 original size:15 final size:15
Alignment explanation
Indices: 591424--591514 Score: 72
Period size: 16 Copynumber: 6.3 Consensus size: 15
591414 TTTAATTAAA
591424 ATAATTTA-A-TTAT
1 ATAATTTATATTTAT
*
591437 AATAATTTATAAATT-T
1 -ATAATTTAT-ATTTAT
591453 AT-A-TTATATTTAT
1 ATAATTTATATTTAT
591466 AT-ATTT-TA-TTAT
1 ATAATTTATATTTAT
591478 ATTATATTTATATTTAAT
1 A-TA-ATTTATATTT-AT
591496 ATAATTTATATTTAT
1 ATAATTTATATTTAT
591511 ATAA
1 ATAA
591515 ATTTTAAATA
Statistics
Matches: 65, Mismatches: 1, Indels: 21
0.75 0.01 0.24
Matches are distributed among these distances:
12 8 0.12
13 11 0.17
14 11 0.17
15 12 0.18
16 14 0.22
17 6 0.09
18 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATAATTTATATTTAT
Found at i:593275 original size:14 final size:16
Alignment explanation
Indices: 593242--593272 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
593232 TTAAAAATAT
593242 ATATTTATATATTAAA
1 ATATTTATATATTAAA
*
593258 ATATTTATATTTTAA
1 ATATTTATATATTAA
593273 TATAAAAATT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATTTATATATTAAA
Found at i:596517 original size:28 final size:28
Alignment explanation
Indices: 596485--596558 Score: 111
Period size: 24 Copynumber: 2.8 Consensus size: 28
596475 AATAAAAAAT
596485 TTTTATAAATAAAAATAAATTAAATTAA
1 TTTTATAAATAAAAATAAATTAAATTAA
596513 TTTTATAAATAAAAAT--A--AAATTAA
1 TTTTATAAATAAAAATAAATTAAATTAA
*
596537 TTTTATAAATTAAAATAAATTA
1 TTTTATAAATAAAAATAAATTA
596559 GATTTTAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 22 0.54
26 2 0.05
28 17 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
TTTTATAAATAAAAATAAATTAAATTAA
Found at i:596659 original size:22 final size:23
Alignment explanation
Indices: 596626--596668 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
596616 AAAAAATATT
596626 TTAACAATTAATTTTACAAATCA
1 TTAACAATTAATTTTACAAATCA
*
596649 TTAA-AATTAATTTTATAAAT
1 TTAACAATTAATTTTACAAAT
596669 TAAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAACAATTAATTTTACAAATCA
Found at i:596732 original size:121 final size:122
Alignment explanation
Indices: 596528--596770 Score: 479
Period size: 121 Copynumber: 2.0 Consensus size: 122
596518 TAAATAAAAA
596528 TAAAATTAATTTTATAAATTAAAATAAATTAGATTTTAATTTTTTTAAATTACTTAAAAAAATTA
1 TAAAATTAATTTTATAAATTAAAATAAATTAGATTTTAATTTTTTTAAATTACTTAAAAAAATTA
596593 AATTAAATTTTTATAATTATATCAAAAAATATTTTAACAATTAATTTTACAAATCAT
66 AATTAAATTTTTATAATTATATCAAAAAATATTTTAACAATTAATTTTACAAATCAT
596650 TAAAATTAATTTTATAAATTAAAATAAATTAGATTTTAA-TTTTTTAAATTACTTAAAAAAATTA
1 TAAAATTAATTTTATAAATTAAAATAAATTAGATTTTAATTTTTTTAAATTACTTAAAAAAATTA
596714 AATTAAATTTTTATAATTATATCAAAAAATATTTTAACAATTAATTTTACAAATCAT
66 AATTAAATTTTTATAATTATATCAAAAAATATTTTAACAATTAATTTTACAAATCAT
596771 ACCTTAATTT
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
121 82 0.68
122 39 0.32
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (122 bp):
TAAAATTAATTTTATAAATTAAAATAAATTAGATTTTAATTTTTTTAAATTACTTAAAAAAATTA
AATTAAATTTTTATAATTATATCAAAAAATATTTTAACAATTAATTTTACAAATCAT
Found at i:596856 original size:14 final size:14
Alignment explanation
Indices: 596839--596868 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
596829 ATACATGTAA
*
596839 AAATAAATTAAATT
1 AAATAAAATAAATT
596853 AAATAAAATAAATT
1 AAATAAAATAAATT
596867 AA
1 AA
596869 TTTTATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAAAATAAATT
Found at i:596895 original size:22 final size:22
Alignment explanation
Indices: 596852--596895 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
596842 TAAATTAAAT
*
596852 TAAATAAAATAAATTAATTTTA
1 TAAATAAAATAAATTAACTTTA
*
596874 TAAATAAAA-AAATATTACTTTA
1 TAAATAAAATAAAT-TAACTTTA
596896 AAAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATAAAATAAATTAACTTTA
Found at i:597092 original size:3 final size:3
Alignment explanation
Indices: 597084--597122 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
597074 ATAATTTTAT
597084 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
597123 GAAATTCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:597289 original size:15 final size:14
Alignment explanation
Indices: 597266--597327 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
597256 TTTTAAATTT
597266 AATTAATTTATAAAAA
1 AATT-ATTT-TAAAAA
597282 AATTATTTT-AAAA
1 AATTATTTTAAAAA
597295 AA-TATTTTACAAAA
1 AATTATTTTA-AAAA
*
597309 AACTTA-TTTACAAA
1 AA-TTATTTTAAAAA
597323 AATTA
1 AATTA
597328 AAAAAAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
12 6 0.15
13 9 0.22
14 12 0.29
15 8 0.20
16 6 0.15
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTATTTTAAAAA
Found at i:597309 original size:28 final size:28
Alignment explanation
Indices: 597272--597325 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
597262 ATTTAATTAA
*
597272 TTTATAAAAAAATTATTTTA-AAAAATAT
1 TTTACAAAAAAATTA-TTTACAAAAATAT
*
597300 TTTACAAAAAACTTATTTACAAAAAT
1 TTTACAAAAAAATTATTTACAAAAAT
597326 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (28 bp):
TTTACAAAAAAATTATTTACAAAAATAT
Found at i:597411 original size:2 final size:2
Alignment explanation
Indices: 597401--597431 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
597391 TGACACACAC
*
597401 AT AT GT 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
597432 CATCACAGGT
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:604518 original size:3 final size:3
Alignment explanation
Indices: 604510--604537 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
604500 AATAACAATC
604510 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
604538 TAATAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:606057 original size:34 final size:33
Alignment explanation
Indices: 606009--606229 Score: 248
Period size: 34 Copynumber: 6.5 Consensus size: 33
605999 TGGTAAAAAC
*
606009 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
606042 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* * *
606076 CACCCATTTAATCAATAATGGTAAGCTATCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** * *
606110 TTCTCATTTAATCAATAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
606144 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
606178 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
606212 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
606230 TCTCCCACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 23 0.14
34 131 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:606130 original size:68 final size:67
Alignment explanation
Indices: 606011--606229 Score: 278
Period size: 68 Copynumber: 3.2 Consensus size: 67
606001 GTAAAAACCA
* * *
606011 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
606076 CAC
65 CAC
* * * * * *
606079 CCATTTAATCAATAATGGTAAGCTATCAAATTTCTCATTTAATCAATAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
606144 CTC
65 CAC
* * * *
606147 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
606212 CA-
65 CAC
606214 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
606230 TCTCCCACTT
Statistics
Matches: 128, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
67 17 0.13
68 110 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:606153 original size:102 final size:101
Alignment explanation
Indices: 606009--606229 Score: 334
Period size: 102 Copynumber: 2.2 Consensus size: 101
605999 TGGTAAAAAC
* *
606009 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* * *
606074 ATCACCCATTTAATCAATAATGGTAAGCTATCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * * *
606110 TTCTCATTTAATCAATAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
606175 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
606212 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
606230 TCTCCCACTT
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
101 15 0.14
102 90 0.86
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:608885 original size:36 final size:36
Alignment explanation
Indices: 608838--608910 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
608828 AACCTCAATC
608838 TATTTTGCTTACTTAAAACACAATGCTCACAGAAAG
1 TATTTTGCTTACTTAAAACACAATGCTCACAGAAAG
608874 TATTTTGCTTACTTAAAACACAATGCTCACAGAAAG
1 TATTTTGCTTACTTAAAACACAATGCTCACAGAAAG
608910 T
1 T
608911 TCCACCCACG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (36 bp):
TATTTTGCTTACTTAAAACACAATGCTCACAGAAAG
Found at i:609129 original size:281 final size:281
Alignment explanation
Indices: 608626--609154 Score: 1049
Period size: 281 Copynumber: 1.9 Consensus size: 281
608616 TTCCAGATTC
*
608626 AAGTTCCACCCGCGCTTTGTATACTTTGAAAACTGGAAATACATCTGCTTTACTTTTGATTGGAT
1 AAGTTCCACCCACGCTTTGTATACTTTGAAAACTGGAAATACATCTGCTTTACTTTTGATTGGAT
608691 ACACCCAACATCTTCTGGAGAAATCATCAATAAATGACACAAAGTATTTTGCTCCTCCTAGAGAC
66 ACACCCAACATCTTCTGGAGAAATCATCAATAAATGACACAAAGTATTTTGCTCCTCCTAGAGAC
608756 ATAACCGGTGCTTGCCAAACATCTGAATGAATTAACTCCAGAATGCACTTACTTCTAGCATTAGA
131 ATAACCGGTGCTTGCCAAACATCTGAATGAATTAACTCCAGAATGCACTTACTTCTAGCATTAGA
608821 TGTGCTGAACCTCAATCTATTTTGCTTACTTAAAACACAATGCTCACAGAAAGTATTTTGCTTAC
196 TGTGCTGAACCTCAATCTATTTTGCTTACTTAAAACACAATGCTCACAGAAAGTATTTTGCTTAC
608886 TTAAAACACAATGCTCACAGA
261 TTAAAACACAATGCTCACAGA
608907 AAGTTCCACCCACGCTTTGTATACTTTGAAAACTGGAAATACATCTGCTTTACTTTTGATTGGAT
1 AAGTTCCACCCACGCTTTGTATACTTTGAAAACTGGAAATACATCTGCTTTACTTTTGATTGGAT
608972 ACACCCAACATCTTCTGGAGAAATCATCAATAAATGACACAAAGTATTTTGCTCCTCCTAGAGAC
66 ACACCCAACATCTTCTGGAGAAATCATCAATAAATGACACAAAGTATTTTGCTCCTCCTAGAGAC
609037 ATAACCGGTGCTTGCCAAACATCTGAATGAATTAACTCCAGAATGCACTTACTTCTAGCATTAGA
131 ATAACCGGTGCTTGCCAAACATCTGAATGAATTAACTCCAGAATGCACTTACTTCTAGCATTAGA
609102 TGTGCTGAACCTCAATCTATTTTGCTTACTTAAAACACAATGCTCACAGAAAG
196 TGTGCTGAACCTCAATCTATTTTGCTTACTTAAAACACAATGCTCACAGAAAG
609155 GTAGGCTTAC
Statistics
Matches: 247, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
281 247 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (281 bp):
AAGTTCCACCCACGCTTTGTATACTTTGAAAACTGGAAATACATCTGCTTTACTTTTGATTGGAT
ACACCCAACATCTTCTGGAGAAATCATCAATAAATGACACAAAGTATTTTGCTCCTCCTAGAGAC
ATAACCGGTGCTTGCCAAACATCTGAATGAATTAACTCCAGAATGCACTTACTTCTAGCATTAGA
TGTGCTGAACCTCAATCTATTTTGCTTACTTAAAACACAATGCTCACAGAAAGTATTTTGCTTAC
TTAAAACACAATGCTCACAGA
Found at i:610964 original size:34 final size:33
Alignment explanation
Indices: 610916--611135 Score: 264
Period size: 34 Copynumber: 6.5 Consensus size: 33
610906 TGGTAAAAAC
*
610916 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
610949 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
610983 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
611017 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
611051 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
611085 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
611119 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
611136 AATAAATATA
Statistics
Matches: 161, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 22 0.14
34 133 0.83
35 6 0.04
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:611032 original size:68 final size:67
Alignment explanation
Indices: 610918--611135 Score: 294
Period size: 68 Copynumber: 3.2 Consensus size: 67
610908 GTAAAAACCA
* * *
610918 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
610983 CAC
65 CAC
* * * *
610986 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
611051 CTC
65 CAC
* * * *
611054 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
611119 CA-
65 CAC
611121 CCATTTAATCAACAA
1 CCATTTAATCAACAA
611136 AATAAATATA
Statistics
Matches: 131, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
67 16 0.12
68 114 0.87
69 1 0.01
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:611060 original size:102 final size:101
Alignment explanation
Indices: 610916--611135 Score: 350
Period size: 102 Copynumber: 2.2 Consensus size: 101
610906 TGGTAAAAAC
* *
610916 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
610981 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
611017 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
611082 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
611119 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
611136 AATAAATATA
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 15 0.14
102 92 0.86
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Done.