Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397277.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2.0, 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: 2651878
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 95949 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:507653 original size:15 final size:14
Alignment explanation
Indices: 507633--507675 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
507623 AATCTAAAAC
507633 ATAAAAACAAATAAA
1 ATAAAAACAAAT-AA
*
507648 ATAAAAATAAATAA
1 ATAAAAACAAATAA
507662 ATAATAATACAAAT
1 ATAA-AA-ACAAAT
507676 TGAGAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.25
15 13 0.54
16 5 0.21
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAAAACAAATAA
Found at i:507665 original size:14 final size:15
Alignment explanation
Indices: 507633--507662 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
507623 AATCTAAAAC
*
507633 ATAAAAACAAATAAA
1 ATAAAAATAAATAAA
507648 ATAAAAATAAATAAA
1 ATAAAAATAAATAAA
507663 TAATAATACA
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:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (15 bp):
ATAAAAATAAATAAA
Found at i:517849 original size:38 final size:39
Alignment explanation
Indices: 517801--517888 Score: 106
Period size: 40 Copynumber: 2.3 Consensus size: 39
517791 CGAGAGGAAC
* *
517801 AAGCATAACC-TCACAAAGGCATTACCATTTCAAGGTTA
1 AAGCACAACCTTCAAAAAGGCATTACCATTTCAAGGTTA
* * * *
517839 AAGCACAACCTTTCAAAAAGTCTTTGCCTTTTCAAGGTTA
1 AAGCACAACC-TTCAAAAAGGCATTACCATTTCAAGGTTA
517879 AAGCACAACC
1 AAGCACAACC
517889 CTTTTATCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 9 0.21
40 33 0.79
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (39 bp):
AAGCACAACCTTCAAAAAGGCATTACCATTTCAAGGTTA
Found at i:528526 original size:15 final size:15
Alignment explanation
Indices: 528503--528548 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
528493 TAACTACTCT
*
528503 TAAAGTAATTTAAAA
1 TAAAATAATTTAAAA
528518 TAAAATAATTTAAAA
1 TAAAATAATTTAAAA
*
528533 TAAAATAACTTAAAA
1 TAAAATAATTTAAAA
528548 T
1 T
528549 TTAACTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
TAAAATAATTTAAAA
Found at i:528559 original size:21 final size:22
Alignment explanation
Indices: 528524--528567 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
528514 AAAATAAAAT
528524 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
528546 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
528567 A
1 A
528568 TAATCACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:534014 original size:14 final size:14
Alignment explanation
Indices: 533978--534016 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
533968 TGAAGAAGAA
533978 AAGAGCAAAAAAAT
1 AAGAGCAAAAAAAT
*
533992 AAGAG-AAAAAACT
1 AAGAGCAAAAAAAT
*
534005 ATGAGCAAAAAA
1 AAGAGCAAAAAA
534017 TTCGTATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (14 bp):
AAGAGCAAAAAAAT
Found at i:534363 original size:35 final size:35
Alignment explanation
Indices: 534312--534392 Score: 144
Period size: 35 Copynumber: 2.3 Consensus size: 35
534302 GCCTTGATAG
* *
534312 AGGTTACACTTGATCTTACAAAAGGCATGTTGTAA
1 AGGTTACACTTCATCTTACAAAAGGCATATTGTAA
534347 AGGTTACACTTCATCTTACAAAAGGCATATTGTAA
1 AGGTTACACTTCATCTTACAAAAGGCATATTGTAA
534382 AGGTTACACTT
1 AGGTTACACTT
534393 GACCCTATTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (35 bp):
AGGTTACACTTCATCTTACAAAAGGCATATTGTAA
Found at i:537493 original size:21 final size:22
Alignment explanation
Indices: 537458--537501 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
537448 CTCTTAAAGT
537458 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
537480 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
537501 A
1 A
537502 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:539440 original size:28 final size:28
Alignment explanation
Indices: 539398--539452 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
539388 TCAAAATTTA
* *
539398 CATTTAGTGAAAGGGAGTTTTACAATTG
1 CATTTAATGAAAGGGAGTTCTACAATTG
*
539426 CATTTAATGAGAGGGAGTTCTACAATT
1 CATTTAATGAAAGGGAGTTCTACAATT
539453 TTAAAACATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.35
Consensus pattern (28 bp):
CATTTAATGAAAGGGAGTTCTACAATTG
Found at i:539500 original size:74 final size:72
Alignment explanation
Indices: 539410--539562 Score: 227
Period size: 74 Copynumber: 2.1 Consensus size: 72
539400 TTTAGTGAAA
*
539410 GGGAGTTTTACAATTGCATTTAATGAGAGGGAGTTCTACAATTTTAAAACATGCTTAAGT-TCAA
1 GGGAGTTTTACAATTGCATTTAATGAGAGGGAGTTCTACAAATTTAAAACATGCTTAAGTAT-AA
539474 AAACATAG
65 AAACATAG
* * *
539482 GGTGAGTTTCTACAATTGCATTTAGTGAGGGGGAGTTCTACAAATTTCAAACATGCTTAAGTATA
1 GG-GAGTTT-TACAATTGCATTTAATGAGAGGGAGTTCTACAAATTTAAAACATGCTTAAGTATA
*
539547 AAAACTTAG
64 AAAACATAG
539556 GGGAGTT
1 GGGAGTT
539563 ATTAAATCAA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
72 2 0.03
73 11 0.15
74 59 0.81
75 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (72 bp):
GGGAGTTTTACAATTGCATTTAATGAGAGGGAGTTCTACAAATTTAAAACATGCTTAAGTATAAA
AACATAG
Found at i:539991 original size:50 final size:50
Alignment explanation
Indices: 539898--540007 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 50
539888 AAGCTTCATT
* * * *
539898 GTATCGAGACTTCACCTCTAGTCTTCAAATTCCAAAGAGCAAGT-CCAAAA
1 GTATCGAGACTTCACCTCCAGGCATCAAATTCCAAAGAACAAGTGCC-AAA
* * *
539948 GTATCGAGTCTTCACCTCCAGGCATCAATTTCCATAA-AACAAGTGGCAAA
1 GTATCGAGACTTCACCTCCAGGCATCAAATTCCA-AAGAACAAGTGCCAAA
539998 GTATCGAGAC
1 GTATCGAGAC
540008 ACACTGATGG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
50 47 0.94
51 3 0.06
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (50 bp):
GTATCGAGACTTCACCTCCAGGCATCAAATTCCAAAGAACAAGTGCCAAA
Found at i:546369 original size:19 final size:19
Alignment explanation
Indices: 546324--546374 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
546314 TTAATGTATG
546324 AATGCTATGATGAACATGC
1 AATGCTATGATGAACATGC
*
546343 -TTGCTATGATGATACATGC
1 AATGCTATGATGA-ACATGC
546362 AATG-TATGATGAA
1 AATGCTATGATGAA
546375 TCGTATGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 12 0.43
19 14 0.50
20 2 0.07
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (19 bp):
AATGCTATGATGAACATGC
Found at i:554519 original size:35 final size:36
Alignment explanation
Indices: 554466--554567 Score: 116
Period size: 35 Copynumber: 2.9 Consensus size: 36
554456 TAGAACCCTT
* * * *
554466 CTACCTTTCACTTGGGTTAATGTATAACCACACAA-
1 CTACCTTTTAATTTGGTTAAGGTATAACCACACAAC
*** *
554501 CTACCTTTTAATTTGGTTAAGGTATAATTGCTCAAC
1 CTACCTTTTAATTTGGTTAAGGTATAACCACACAAC
*
554537 CTACCTTTTAATTTGGTTAAGGTGTAACCAC
1 CTACCTTTTAATTTGGTTAAGGTATAACCAC
554568 TCATTAGTGT
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
35 27 0.50
36 27 0.50
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CTACCTTTTAATTTGGTTAAGGTATAACCACACAAC
Found at i:556600 original size:12 final size:12
Alignment explanation
Indices: 556583--556629 Score: 69
Period size: 12 Copynumber: 3.8 Consensus size: 12
556573 GAATAGTTTC
556583 TTGCTGCCTCCT
1 TTGCTGCCTCCT
556595 TTGCTGCCT-CT
1 TTGCTGCCTCCT
556606 CTTGCTGCCTCTCT
1 -TTGCTGCCTC-CT
556620 TTGCTGCCTC
1 TTGCTGCCTC
556630 AAAAATCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.06
12 18 0.56
13 10 0.31
14 2 0.06
ACGTcount: A:0.00, C:0.40, G:0.17, T:0.43
Consensus pattern (12 bp):
TTGCTGCCTCCT
Found at i:556610 original size:24 final size:25
Alignment explanation
Indices: 556581--556629 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
556571 CAGAATAGTT
556581 TCTTGCTGCCTC-CTTTGCTGCCTC
1 TCTTGCTGCCTCTCTTTGCTGCCTC
556605 TCTTGCTGCCTCTCTTTGCTGCCTC
1 TCTTGCTGCCTCTCTTTGCTGCCTC
556630 AAAAATCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.00, C:0.41, G:0.16, T:0.43
Consensus pattern (25 bp):
TCTTGCTGCCTCTCTTTGCTGCCTC
Found at i:563480 original size:22 final size:22
Alignment explanation
Indices: 563450--563492 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
563440 TTAATCTTAT
563450 TTAAGTAAAA-AAAATTCAAAAA
1 TTAAGTAAAACAAAATT-AAAAA
*
563472 TTAATTAAAACAAAATTAAAA
1 TTAAGTAAAACAAAATTAAAA
563493 CAAGCACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (22 bp):
TTAAGTAAAACAAAATTAAAAA
Found at i:566242 original size:379 final size:378
Alignment explanation
Indices: 565533--566255 Score: 990
Period size: 378 Copynumber: 1.9 Consensus size: 378
565523 ATATTTTAGT
* *
565533 ATATATATACTTTAAATATAAACATATTTACTTTCTATTTTGTGTTAAAATTACAAAATTATAAC
1 ATATATATACTTTAAATATAAACATATTTACTTTCTATTTTGTATTAAAATCACAAAATTATAAC
* * * * * *
565598 TTAAAAAATTATTAATTATAATATATATAACTTTGTTTATATAAACTTATAACATATAAACCTAA
66 TCAAAAAATTATTAATTACAACACATATAACTTTATTTATATAAACATATAACATATAAACCTAA
* * * ** *
565663 AGAGAAGTTGTGAGATTAGAATAATTATAAAACCTAGTTATTTTTTTTATTTTAAGTAATTAAGG
131 AGAGAAGTTATGAGATTAAAATAATTATAAAACCTAGTTATTTTTTTAATTGCAAGTAATTAAAG
** * * * *
565728 ACAAACCTGTATAGTTAATTAAATTAATTTATAAAATTATAATCATTAATTAAATTGTAATGTCT
196 ACAAACCCATAGAGTTAATTAAAGTAATTAATAAAACTATAATCATTAATTAAATTGTAATGTCT
** * *
565793 TTTAATATTTATACGTTATACATATATTAGATTCATTTATAAGGAATATAATTACTATTATATAT
261 TTTAATATAAATACGTTATACATACATTAGATTCATTTATAAGAAATATAATTACTATTATATAT
565858 ATATATATATATATTAAAATACTCTTAATGTGTGCGCGTGTTTGTATGTATAA
326 ATATATATATATATTAAAATACTCTTAATGTGTGCGCGTGTTTGTATGTATAA
* *
565911 ATATATGTACTTTAAATATAAACATATTTACTTTCTATTTTGTATTAACATCACAAAAATTATAA
1 ATATATATACTTTAAATATAAACATATTTACTTTCTATTTTGTATTAAAATCAC-AAAATTATAA
* * * *
565976 CTCATAAGATTATTAATTACAACACATATACCTTTATTTATATAAACATATAACATATAAATCTA
65 CTCAAAAAATTATTAATTACAACACATATAACTTTATTTATATAAACATATAACATATAAACCTA
* * * * *
566041 AAGGGAAGTTATGAGATTAAAATACTTTTGAAACCTAGTT-TTTTTTTAATTGCATGTAATTAAA
130 AAGAGAAGTTATGAGATTAAAATAATTATAAAACCTAGTTATTTTTTTAATTGCAAGTAATTAAA
* * * * * *
566105 GATAAACCCATAGAGTTCATTAAAGTAATTAATGAAACTA-AGATTATTAATTGACTTGTAATGT
195 GACAAACCCATAGAGTTAATTAAAGTAATTAATAAAACTATA-ATCATTAATTAAATTGTAATGT
* *
566169 CTTTTAATATAAATAC-TT-TATATACATT-GAGTTCATTTATAAGAAATATAATTACTATTTTA
259 CTTTTAATATAAATACGTTATACATACATTAGA-TTCATTTATAAGAAATATAATTACTATTATA
566231 -ATATATATATATATATTAAAATACT
323 TATATATATATATATATTAAAATACT
566256 TTTAGTATAT
Statistics
Matches: 299, Mismatches: 43, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
375 27 0.09
376 37 0.12
377 3 0.01
378 133 0.44
379 99 0.33
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (378 bp):
ATATATATACTTTAAATATAAACATATTTACTTTCTATTTTGTATTAAAATCACAAAATTATAAC
TCAAAAAATTATTAATTACAACACATATAACTTTATTTATATAAACATATAACATATAAACCTAA
AGAGAAGTTATGAGATTAAAATAATTATAAAACCTAGTTATTTTTTTAATTGCAAGTAATTAAAG
ACAAACCCATAGAGTTAATTAAAGTAATTAATAAAACTATAATCATTAATTAAATTGTAATGTCT
TTTAATATAAATACGTTATACATACATTAGATTCATTTATAAGAAATATAATTACTATTATATAT
ATATATATATATATTAAAATACTCTTAATGTGTGCGCGTGTTTGTATGTATAA
Found at i:571736 original size:23 final size:23
Alignment explanation
Indices: 571686--571764 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 23
571676 GCAATGCTTA
* ** *
571686 AGTCACACAATACC-TAAAAACT
1 AGTCACGCAATACCTTACTAACC
*
571708 AGTCACGCCATACCTTACTAACC
1 AGTCACGCAATACCTTACTAACC
*
571731 AGTCACGCAATATCTTACTAACC
1 AGTCACGCAATACCTTACTAACC
571754 AGTCACGCAAT
1 AGTCACGCAAT
571765 GTCATATCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 12 0.24
23 37 0.76
ACGTcount: A:0.38, C:0.32, G:0.09, T:0.22
Consensus pattern (23 bp):
AGTCACGCAATACCTTACTAACC
Found at i:571776 original size:23 final size:23
Alignment explanation
Indices: 571708--571782 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
571698 CCTAAAAACT
* * *
571708 AGTCACGCCATACCTTACTAACC
1 AGTCACGCAATATCATACTAACC
*
571731 AGTCACGCAATATCTTACTAACC
1 AGTCACGCAATATCATACTAACC
*
571754 AGTCACGCAATGTCATA-TCAACC
1 AGTCACGCAATATCATACT-AACC
571777 AGTCAC
1 AGTCAC
571783 ATAATACCTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
22 1 0.02
23 46 0.98
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.23
Consensus pattern (23 bp):
AGTCACGCAATATCATACTAACC
Found at i:571814 original size:22 final size:22
Alignment explanation
Indices: 571789--571861 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
571779 TCACATAATA
571789 CCTAAAAATTAGTCATACAATG
1 CCTAAAAATTAGTCATACAATG
*
571811 CCTAAAAATTAATC-T-CGTAATG
1 CCTAAAAATTAGTCATAC--AATG
* * * *
571833 CCCAAAAAGTAGTTACACAATG
1 CCTAAAAATTAGTCATACAATG
571855 CCTAAAA
1 CCTAAAA
571862 GCCACCAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 37 0.93
24 1 0.03
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.25
Consensus pattern (22 bp):
CCTAAAAATTAGTCATACAATG
Found at i:575605 original size:10 final size:10
Alignment explanation
Indices: 575592--575616 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
575582 CAAAAAATGA
575592 AAAAATAAAT
1 AAAAATAAAT
575602 AAAAATAAAT
1 AAAAATAAAT
575612 AAAAA
1 AAAAA
575617 GGAGAAAAGA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:578271 original size:166 final size:165
Alignment explanation
Indices: 577993--578498 Score: 636
Period size: 165 Copynumber: 3.1 Consensus size: 165
577983 ATGTGGATCT
* * *
577993 TGACACTTTACATGTCAGCAAAAGTAAATGAACACATGACATGGTAAGTTATGATAGAATGCTTA
1 TGACACTTTACATGTAAGCAAAAATCAATGAACACATGACATGGTAAGTTATGATAGAATGCTTA
* **
578058 GACATTTTGTTGATGGTGAGAACTAATCAATCTTTCACT-AGTTTCAATTCTTTTTGGATAGTTT
66 GACACTTTGTTGATGGTGAGAACTAATCAATCTTTTGCTGA-TTTCAATTC-TTTTGGATAGTTT
* *
578122 GGTCAGTAATGTTGATCAGCCAAGTTGGTGTAAACCA
129 GGTCAGTAATGTTGATCATCCAAGTTGGTGTAGACCA
* * * ** *
578159 TGACACTTTACATGTTAGCAAAAATCATTAAACACAAAACATGGTAAGTTATGATAGAATTCTTA
1 TGACACTTTACATGTAAGCAAAAATCAATGAACACATGACATGGTAAGTTATGATAGAATGCTTA
* * * * * ** * * **
578224 AACACCTTGTTAATGGTAAGAAGTAATCTGTCTTTTGCTGATTTCAATTCTTTTGGACAATTTTA
66 GACACTTTGTTGATGGTGAGAACTAATCAATCTTTTGCTGATTTCAATTCTTTTGGATAGTTTGG
* * *
578289 TCAATAATGTTGATTATCCAAGTTGGTATAGACCA
131 TCAGTAATGTTGATCATCCAAGTTGGTGTAGACCA
* * * * *
578324 TGACACTTTACATGTAAGCAACAATCACTGAACATATGACATGGTAACTTATGATAGAGTGCTTA
1 TGACACTTTACATGTAAGCAAAAATCAATGAACACATGACATGGTAAGTTATGATAGAATGCTTA
* * * *
578389 GACACTTTGTTGATTGTGAGCACTAATCAATCTTTTGCTGGTTTTAATTCTTTTGGATAGTTTGG
66 GACACTTTGTTGATGGTGAGAACTAATCAATCTTTTGCTGATTTCAATTCTTTTGGATAGTTTGG
* *
578454 TCAGTAATGTTGATCATCCATGTTGGTGTGGACCA
131 TCAGTAATGTTGATCATCCAAGTTGGTGTAGACCA
578489 TGACACTTTA
1 TGACACTTTA
578499 TGGTGTGGAC
Statistics
Matches: 282, Mismatches: 57, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
165 186 0.66
166 95 0.34
167 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Consensus pattern (165 bp):
TGACACTTTACATGTAAGCAAAAATCAATGAACACATGACATGGTAAGTTATGATAGAATGCTTA
GACACTTTGTTGATGGTGAGAACTAATCAATCTTTTGCTGATTTCAATTCTTTTGGATAGTTTGG
TCAGTAATGTTGATCATCCAAGTTGGTGTAGACCA
Found at i:578505 original size:22 final size:22
Alignment explanation
Indices: 578477--578518 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
578467 TCATCCATGT
578477 TGGTGTGGACCATGACACTTTA
1 TGGTGTGGACCATGACACTTTA
*
578499 TGGTGTGGACCATGGCACTT
1 TGGTGTGGACCATGACACTT
578519 CACATGTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (22 bp):
TGGTGTGGACCATGACACTTTA
Found at i:578730 original size:41 final size:41
Alignment explanation
Indices: 578684--578766 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
578674 CCATGACACT
*
578684 TTACATGTTAACAAAAATCACTAAACACATGACATGGTAAG
1 TTACATGTCAACAAAAATCACTAAACACATGACATGGTAAG
* * **
578725 TTACATGTCAACAAAAATCATTGAACATGTGACATGGTAAG
1 TTACATGTCAACAAAAATCACTAAACACATGACATGGTAAG
578766 T
1 T
578767 CATGATAAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (41 bp):
TTACATGTCAACAAAAATCACTAAACACATGACATGGTAAG
Found at i:579317 original size:39 final size:38
Alignment explanation
Indices: 579230--579376 Score: 161
Period size: 38 Copynumber: 3.8 Consensus size: 38
579220 TTCTTCTCTG
* * * * *
579230 ATGCGAGATTCATAGAAAAGAAAGGTTTTTCTCCCCCG
1 ATGCGAGATTCATGGAAGAGAATGGTTTTTCTCCCTCA
* * * * * *
579268 ATGCGTGATTCATGGAAGATAGTGGTTTTTTTTTCCTTA
1 ATGCGAGATTCATGGAAGAGAATGG-TTTTTCTCCCTCA
579307 ATGC-AGGATTCATGGAAGAGAATGGTTTTTCTCCCTCA
1 ATGCGA-GATTCATGGAAGAGAATGGTTTTTCTCCCTCA
*
579345 ATGCGAGATTCATGGAAGAGAAAGGTTTTTCT
1 ATGCGAGATTCATGGAAGAGAATGGTTTTTCT
579377 TTAAAGAGTG
Statistics
Matches: 88, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
38 58 0.66
39 30 0.34
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (38 bp):
ATGCGAGATTCATGGAAGAGAATGGTTTTTCTCCCTCA
Found at i:579731 original size:13 final size:13
Alignment explanation
Indices: 579713--579737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
579703 TAATATGAAT
579713 AAAATATAAATAA
1 AAAATATAAATAA
579726 AAAATATAAATA
1 AAAATATAAATA
579738 TTGTTATTTC
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATATAAATAA
Found at i:580623 original size:125 final size:125
Alignment explanation
Indices: 580411--580726 Score: 438
Period size: 125 Copynumber: 2.5 Consensus size: 125
580401 ACATGACATA
*
580411 GTAAGTTATGATAGAGTGCTTAGACACATTGTTGATGGTGAGAACTAATCAGTCTTTTGCTAGTT
1 GTAAGTTATGATAGAGTGCTTAGACACATTGTTGATGGTGAGAACTAATAAGTCTTTTGCTAGTT
* * * * *
580476 TTAGTTATTTTCGATAGTTTGCTT-GTTAATGTTGATCATCTAGGTTGGTCACATGGCACG
66 TTAGTTATTTTCGACAATTTGCTTAG-TAATGTTGATCATCTAGGTTGATCAAATGACACG
* * * *
580536 GTAAGTTATGATAAAGTGCTTAGACACGTTGTTGATGGTGAGAA-TGAATAATTTTTTTGCTAGT
1 GTAAGTTATGATAGAGTGCTTAGACACATTGTTGATGGTGAGAACT-AATAAGTCTTTTGCTAGT
*
580600 TTTAGTTATTTTCGACAATTTGCTTAGTAATGTTGATCATCTAGGTTGATCAAATGACATG
65 TTTAGTTATTTTCGACAATTTGCTTAGTAATGTTGATCATCTAGGTTGATCAAATGACACG
* * ** ** *
580661 GTAAGTTATGATAGAGTACTTAAACATTTTGTTGATGGTGAGAACTAACCAGTCTTTTACTAGTT
1 GTAAGTTATGATAGAGTGCTTAGACACATTGTTGATGGTGAGAACTAATAAGTCTTTTGCTAGTT
580726 T
66 T
580727 CAATTTTTTG
Statistics
Matches: 167, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
124 1 0.01
125 164 0.98
126 2 0.01
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.40
Consensus pattern (125 bp):
GTAAGTTATGATAGAGTGCTTAGACACATTGTTGATGGTGAGAACTAATAAGTCTTTTGCTAGTT
TTAGTTATTTTCGACAATTTGCTTAGTAATGTTGATCATCTAGGTTGATCAAATGACACG
Found at i:581287 original size:45 final size:46
Alignment explanation
Indices: 581205--581313 Score: 114
Period size: 45 Copynumber: 2.4 Consensus size: 46
581195 GGACAAAGAG
** *
581205 TTCATGACTCCCCACTAGGACCATGACATCCCCCATT-GA-TGCGGA
1 TTCATGACTCCCCACTAAAACCATGACATCCCCCATTGGAGT-CAGA
* ****
581250 TTCATGGCTCCCCACTAAAACCATGACATTTTTCATTGGAGTCAGA
1 TTCATGACTCCCCACTAAAACCATGACATCCCCCATTGGAGTCAGA
*
581296 TTCATGACTCCCTACTAA
1 TTCATGACTCCCCACTAA
581314 GACCTTGTCT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
45 30 0.58
46 21 0.40
47 1 0.02
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.28
Consensus pattern (46 bp):
TTCATGACTCCCCACTAAAACCATGACATCCCCCATTGGAGTCAGA
Found at i:581419 original size:39 final size:37
Alignment explanation
Indices: 581333--581515 Score: 154
Period size: 38 Copynumber: 4.8 Consensus size: 37
581323 TTTTTCCCCG
* * * * **
581333 ATGTGGGATTCATGAAAAAGAGTGATTTTTCTCCCTTG
1 ATGTAGGATTCATGGAAAAGAGTGGTTTTCCT-CCTCA
*
581371 ATGTGGGATTCATGGAAAAGAGTGGTGCTTTCCTCCTCA
1 ATGTAGGATTCATGGAAAAGAGTGGT--TTTCCTCCTCA
* * * **
581410 ATGTAGGATTCATGGAAGAGATTGGTTTTTCC-CTTTG
1 ATGTAGGATTCATGGAAAAGAGTGG-TTTTCCTCCTCA
*
581447 ATG-AGAGATTCATGGAAAAGAGTGGTTTCCCCTCCTCCTA
1 ATGTAG-GATTCATGGAAAAGAGTGGTTT-TCCTCCT-C-A
*
581487 ATGTAGGATTCATGGAAAAGAGTGATTTT
1 ATGTAGGATTCATGGAAAAGAGTGGTTTT
581516 TCTCTAAAGA
Statistics
Matches: 117, Mismatches: 19, Indels: 17
0.76 0.12 0.11
Matches are distributed among these distances:
36 5 0.04
37 24 0.21
38 31 0.26
39 25 0.21
40 30 0.26
41 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (37 bp):
ATGTAGGATTCATGGAAAAGAGTGGTTTTCCTCCTCA
Found at i:581439 original size:77 final size:78
Alignment explanation
Indices: 581333--581519 Score: 247
Period size: 77 Copynumber: 2.4 Consensus size: 78
581323 TTTTTCCCCG
* * * *
581333 ATGTGGGATTCATGAAAAAGAGTGATTTTTCTCCCTTGATGTGGGATTCATGGAAAAGAGTGGTG
1 ATGTAGGATTCATGGAAAAGAGTGATTTTTCTCCCTTGATGAGAGATTCATGGAAAAGAGTGGT-
*
581398 CTT-TCCTCCT-C-A
65 -TTCCCCTCCTCCTA
* * * *
581410 ATGTAGGATTCATGGAAGAGATTGGTTTTTC-CCTTTGATGAGAGATTCATGGAAAAGAGTGGTT
1 ATGTAGGATTCATGGAAAAGAGTGATTTTTCTCCCTTGATGAGAGATTCATGGAAAAGAGTGGTT
581474 TCCCCTCCTCCTA
66 TCCCCTCCTCCTA
581487 ATGTAGGATTCATGGAAAAGAGTGATTTTTCTC
1 ATGTAGGATTCATGGAAAAGAGTGATTTTTCTC
581520 TAAAGAGTAG
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
74 2 0.02
75 6 0.06
76 30 0.32
77 55 0.59
78 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (78 bp):
ATGTAGGATTCATGGAAAAGAGTGATTTTTCTCCCTTGATGAGAGATTCATGGAAAAGAGTGGTT
TCCCCTCCTCCTA
Found at i:584171 original size:16 final size:16
Alignment explanation
Indices: 584152--584186 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
584142 AAAGGAAAAA
584152 TATTGATAAAATCTTT
1 TATTGATAAAATCTTT
* *
584168 TATTGATGAAATTTTT
1 TATTGATAAAATCTTT
584184 TAT
1 TAT
584187 ATTTATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.54
Consensus pattern (16 bp):
TATTGATAAAATCTTT
Found at i:586165 original size:2 final size:2
Alignment explanation
Indices: 586160--586228 Score: 111
Period size: 2 Copynumber: 34.5 Consensus size: 2
586150 TGTGTATATA
* *
586160 TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TA
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
586202 TG TG TG TG TG TG TG TG TG TA TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
586229 CACTATAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.04, C:0.00, G:0.45, T:0.51
Consensus pattern (2 bp):
TG
Found at i:586165 original size:12 final size:12
Alignment explanation
Indices: 586147--586220 Score: 98
Period size: 12 Copynumber: 6.3 Consensus size: 12
586137 CAAGCATTTG
*
586147 GTGTGTGTATAT
1 GTGTGTGTATGT
* *
586159 ATGTGTGTGTGT
1 GTGTGTGTATGT
586171 GTGTGTGTATGT
1 GTGTGTGTATGT
586183 GTGTGTG--TGT
1 GTGTGTGTATGT
586193 GTGTGTGTATGT
1 GTGTGTGTATGT
*
586205 GTGTGTGTGTGT
1 GTGTGTGTATGT
586217 GTGT
1 GTGT
586221 ATGTGTGTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
10 10 0.19
12 44 0.81
ACGTcount: A:0.07, C:0.00, G:0.43, T:0.50
Consensus pattern (12 bp):
GTGTGTGTATGT
Found at i:586172 original size:20 final size:20
Alignment explanation
Indices: 586147--586228 Score: 110
Period size: 20 Copynumber: 4.1 Consensus size: 20
586137 CAAGCATTTG
* * *
586147 GTGTGTGTATATATGTGTGT
1 GTGTGTGTGTGTATATGTGT
*
586167 GTGTGTGTGTGTATGTGTGT
1 GTGTGTGTGTGTATATGTGT
*
586187 GTGTGTGTGTGTGTATGTGT
1 GTGTGTGTGTGTATATGTGT
*
586207 GTGTGTGTGTGTGTATGTGT
1 GTGTGTGTGTGTATATGTGT
586227 GT
1 GT
586229 CACTATAATA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.07, C:0.00, G:0.43, T:0.50
Consensus pattern (20 bp):
GTGTGTGTGTGTATATGTGT
Found at i:586175 original size:22 final size:22
Alignment explanation
Indices: 586147--586228 Score: 128
Period size: 22 Copynumber: 3.7 Consensus size: 22
586137 CAAGCATTTG
*
586147 GTGTGTGTATATATGTGTGTGT
1 GTGTGTGTATATGTGTGTGTGT
*
586169 GTGTGTGTGTATGTGTGTGTGT
1 GTGTGTGTATATGTGTGTGTGT
*
586191 GTGTGTGTGTATGTGTGTGTGT
1 GTGTGTGTATATGTGTGTGTGT
*
586213 GTGTGTGTATGTGTGT
1 GTGTGTGTATATGTGT
586229 CACTATAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.07, C:0.00, G:0.43, T:0.50
Consensus pattern (22 bp):
GTGTGTGTATATGTGTGTGTGT
Found at i:587429 original size:68 final size:67
Alignment explanation
Indices: 587343--587592 Score: 247
Period size: 68 Copynumber: 3.7 Consensus size: 67
587333 ATCTTATAAG
* *
587343 GTATATTGAAA-ATGCATCATATACATAATCTCATGGCATTCATCATG-ATTTTTCAATCATCTC
1 GTATA-TGAAATATACATCATATACATAATCTCATGGCATTCATCATGCATATTT-AATCATCTC
587406 ATAT
64 ATAT
* * *
587410 AGTATATGAAATATACATCATATACATAATCTCATGGCATTTATCATGCGTACTTAATCA-CTTC
1 -GTATATGAAATATACATCATATACATAATCTCATGGCATTCATCATGCATATTTAATCATC-TC
587474 ATAT
64 ATAT
* * * * * * * * *
587478 GATATAT-AGAATTTACATTATATACAAAATTTTATAGTATACATCATGCATATTTAGTCATCTC
1 G-TATATGA-AATATACATCATATACATAATCTCATGGCATTCATCATGCATATTTAATCATCTC
587542 ATAT
64 ATAT
* * * *
587546 GGTATATGAAATTTATATTATATACATAATCTTATGGCATTCATCAT
1 -GTATATGAAATATACATCATATACATAATCTCATGGCATTCATCAT
587593 ACCAAACATG
Statistics
Matches: 151, Mismatches: 23, Indels: 16
0.79 0.12 0.08
Matches are distributed among these distances:
67 8 0.05
68 137 0.91
69 6 0.04
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (67 bp):
GTATATGAAATATACATCATATACATAATCTCATGGCATTCATCATGCATATTTAATCATCTCAT
AT
Found at i:589032 original size:24 final size:24
Alignment explanation
Indices: 589003--589048 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
588993 GGAAGAGTTG
*
589003 AGAAAGGAAAAAGAAGAGAAAGGA
1 AGAAAGGAAAAAGAAGAAAAAGGA
* *
589027 AGAAAGGAGAAAGGAGAAAAAG
1 AGAAAGGAAAAAGAAGAAAAAG
589049 AGAAAAGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (24 bp):
AGAAAGGAAAAAGAAGAAAAAGGA
Found at i:589039 original size:7 final size:7
Alignment explanation
Indices: 589002--589045 Score: 52
Period size: 7 Copynumber: 5.9 Consensus size: 7
588992 AGGAAGAGTT
589002 GAGAAAG
1 GAGAAAG
*
589009 GAAAAAG
1 GAGAAAG
589016 AAGAGAAAG
1 --GAGAAAG
589025 GAAGAAAG
1 G-AGAAAG
589033 GAGAAAG
1 GAGAAAG
589040 GAGAAA
1 GAGAAA
589046 AAGAGAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 19 0.59
8 7 0.22
9 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (7 bp):
GAGAAAG
Found at i:589051 original size:15 final size:14
Alignment explanation
Indices: 589002--589053 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 14
588992 AGGAAGAGTT
589002 GAGAAAGGAAAAAGAA
1 GAGAAAGG-AAAA-AA
*
589018 GAGAAAGGAAGAAAG
1 GAGAAAGGAA-AAAA
589033 GAGAAAGGAGAAAAA
1 GAGAAAGGA-AAAAA
589048 GAGAAA
1 GAGAAA
589054 AGAAGGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 21 0.66
16 11 0.34
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (14 bp):
GAGAAAGGAAAAAA
Found at i:594608 original size:29 final size:28
Alignment explanation
Indices: 594576--594636 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
594566 GGACATGTAC
*
594576 TTATTTAATGTAAATAAGCTAGGCTGGTT
1 TTATTTAATGTAAATAAGC-AGGCTAGTT
* *
594605 TTATTTTATGTAAATAAGCAGGGTAGTT
1 TTATTTAATGTAAATAAGCAGGCTAGTT
594633 TTAT
1 TTAT
594637 AGGTAATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (28 bp):
TTATTTAATGTAAATAAGCAGGCTAGTT
Found at i:600540 original size:47 final size:47
Alignment explanation
Indices: 600470--601071 Score: 368
Period size: 47 Copynumber: 12.9 Consensus size: 47
600460 GATAGGGTTT
* *
600470 AGAGTTTGGTGACACGA-CATGGAGGGAATCTGTGACACTCCAAAGTTC
1 AGAGTTT-GTGACAC-ACCATGGAGGGAATCTGTGACACGCCAGAGTTC
* * * ** *
600518 AGAGTTTATGACACACCATGGAGAGAATTTGTGACACTTCAGAGTTT
1 AGAGTTTGTGACACACCATGGAGGGAATCTGTGACACGCCAGAGTTC
* * * * *
600565 AGAGTTTGTGACACAGCATGGATGGAATCTGTGACACGACATTA-TTT
1 AGAGTTTGTGACACACCATGGAGGGAATCTGTGACACGCCA-GAGTTC
** * *
600612 AGAGTTTGTGACA-ATCCATGGAGGGAATCTGTGACACGGTAGTGTTT
1 AGAGTTTGTGACACA-CCATGGAGGGAATCTGTGACACGCCAGAGTTC
* * * *
600659 A-AGGTTTGTGACACGCCATGGAGGGAATTTGTGACACGCTAGTGTTC
1 AGA-GTTTGTGACACACCATGGAGGGAATCTGTGACACGCCAGAGTTC
* * ** *
600706 AGAGTTGGTGACATGA-CATGGAGGGAATCTGTGACACTTCAAAG-TC
1 AGAGTTTGTGACA-CACCATGGAGGGAATCTGTGACACGCCAGAGTTC
* * * * * ** *
600752 TAGAG-TT-TGACACAGCATGGATGAAATTTATGACACGATAGGGTTC
1 -AGAGTTTGTGACACACCATGGAGGGAATCTGTGACACGCCAGAGTTC
* * * ** *
600798 ATG-CTTTGTGGCACGCCATGGAGGGAATCTGTGACACATCAGTGTTC
1 A-GAGTTTGTGACACACCATGGAGGGAATCTGTGACACGCCAGAGTTC
* ** * *
600845 AGAGTTGGTGACACAGTATGGAGGGAATCTGTGAGACGCCAAAGTTC
1 AGAGTTTGTGACACACCATGGAGGGAATCTGTGACACGCCAGAGTTC
* ** * * **
600892 AGAG-TT-TGATACGGCATGGATGGAATCTGTGACATGGTAGTA-TTC
1 AGAGTTTGTGACACACCATGGAGGGAATCTGTGACACGCCAG-AGTTC
* * * * * *
600937 AAAGTTTATGACACGCCATGGAGGGACTCTGTGACACGTCAGTGTTC
1 AGAGTTTGTGACACACCATGGAGGGAATCTGTGACACGCCAGAGTTC
* ** ** * * *
600984 AGAGTTGGTGACACGGCA-GCGAAAGACATTTGTGACACGGCAGCGTTC
1 AGAGTTTGTGACACACCATG-GAGGGA-ATCTGTGACACGCCAGAGTTC
* * * * *
601032 AG-GGTTGTGACACGCCATTGAGAGAATCTGTGACATGCCA
1 AGAGTTTGTGACACACCATGGAGGGAATCTGTGACACGCCA
601072 TGTGTGTGTT
Statistics
Matches: 428, Mismatches: 104, Indels: 46
0.74 0.18 0.08
Matches are distributed among these distances:
44 1 0.00
45 56 0.13
46 29 0.07
47 314 0.73
48 28 0.07
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (47 bp):
AGAGTTTGTGACACACCATGGAGGGAATCTGTGACACGCCAGAGTTC
Found at i:600842 original size:139 final size:138
Alignment explanation
Indices: 600515--600997 Score: 465
Period size: 139 Copynumber: 3.5 Consensus size: 138
600505 CACTCCAAAG
* * * * * * * *
600515 TTCAGAGTTTATGACACACCATGGAGAGAATTTGTGACACTTCAGAGTTTAGAGTTTGTGACACA
1 TTCAAAGTTTGTGACACGCCATGGAGGGAATCTGTGACAC-TCAGTGTTCAGAGTTGGTGACACA
* * * * * * * *
600580 GCATGGATGGAATCTGTGACACGACATTA-TTTAGAGTTTGTGACA-ATCCATGGAGGGAATCTG
65 GCATGGAGGGAATCTGTGACACGCCA-AAGTTCAGAG-TT-TGACACA-GCATGGATGAAATCTA
*
600643 TGACACGGTAGTG-
126 TGACACGATAG-GA
* * * * *
600656 TTTAAGGTTTGTGACACGCCATGGAGGGAATTTGTGACACGCTAGTGTTCAGAGTTGGTGACA-T
1 TTCAAAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTC-AGTGTTCAGAGTTGGTGACACA
** *
600720 GACATGGAGGGAATCTGTGACACTTCAAAG-TCTAGAGTTTGACACAGCATGGATGAAATTTATG
65 G-CATGGAGGGAATCTGTGACACGCCAAAGTTC-AGAGTTTGACACAGCATGGATGAAATCTATG
*
600784 ACACGATAGGG
128 ACACGATAGGA
* *
600795 TTC-ATGCTTTGTGGCACGCCATGGAGGGAATCTGTGACACATCAGTGTTCAGAGTTGGTGACAC
1 TTCAAAG-TTTGTGACACGCCATGGAGGGAATCTGTGACAC-TCAGTGTTCAGAGTTGGTGACAC
* * * * * *
600859 AGTATGGAGGGAATCTGTGAGACGCCAAAGTTCAGAGTTTGATACGGCATGGATGGAATCTGTGA
64 AGCATGGAGGGAATCTGTGACACGCCAAAGTTCAGAGTTTGACACAGCATGGATGAAATCTATGA
* * *
600924 CATGGTAGTA
129 CACGATAGGA
* *
600934 TTCAAAGTTTATGACACGCCATGGAGGGACTCTGTGACACGTCAGTGTTCAGAGTTGGTGACAC
1 TTCAAAGTTTGTGACACGCCATGGAGGGAATCTGTGACAC-TCAGTGTTCAGAGTTGGTGACAC
600998 GGCAGCGAAA
Statistics
Matches: 285, Mismatches: 46, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
138 3 0.01
139 192 0.67
140 13 0.05
141 77 0.27
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (138 bp):
TTCAAAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCAGTGTTCAGAGTTGGTGACACAG
CATGGAGGGAATCTGTGACACGCCAAAGTTCAGAGTTTGACACAGCATGGATGAAATCTATGACA
CGATAGGA
Found at i:601648 original size:31 final size:31
Alignment explanation
Indices: 601606--601884 Score: 378
Period size: 31 Copynumber: 9.0 Consensus size: 31
601596 TAGTGTCATG
* *
601606 ACATTTGACTTGTTATGCACGGCGTGTCACC
1 ACATTTTACTTGTTATGCATGGCGTGTCACC
* *
601637 ATATTTTACTTGTTATGCATGGTGTGTCACC
1 ACATTTTACTTGTTATGCATGGCGTGTCACC
* * *
601668 GCATTTTACTTGTTATGCATGGTGTGTCACG
1 ACATTTTACTTGTTATGCATGGCGTGTCACC
* * *
601699 ACCTTTTACTTGTTATGCATGGCATGTCACT
1 ACATTTTACTTGTTATGCATGGCGTGTCACC
* *
601730 ACCTTTTACTTGTTATGCATGGCGTGTCACG
1 ACATTTTACTTGTTATGCATGGCGTGTCACC
*
601761 ACATTTTACTTGTTATGCATGACGTGTCACC
1 ACATTTTACTTGTTATGCATGGCGTGTCACC
* * *
601792 ACATTTTACTTCTTATGCATGGCATGTCACA
1 ACATTTTACTTGTTATGCATGGCGTGTCACC
* *
601823 ACCTTTTTACTTGTTATGCATGGCGTGTAACC
1 A-CATTTTACTTGTTATGCATGGCGTGTCACC
*
601855 ACTTTTTACTTGTTATGCATGGCGTGTCAC
1 ACATTTTACTTGTTATGCATGGCGTGTCAC
601885 AACCTTTGTC
Statistics
Matches: 220, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
31 194 0.88
32 26 0.12
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (31 bp):
ACATTTTACTTGTTATGCATGGCGTGTCACC
Found at i:613677 original size:24 final size:24
Alignment explanation
Indices: 613645--613690 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
613635 ATAGGATAAT
613645 ACTTGATATAACCTTGATTCTAAA
1 ACTTGATATAACCTTGATTCTAAA
613669 ACTTGATATAACCTTGATTCTA
1 ACTTGATATAACCTTGATTCTA
613691 TATCACCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (24 bp):
ACTTGATATAACCTTGATTCTAAA
Found at i:627023 original size:21 final size:22
Alignment explanation
Indices: 626988--627030 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
626978 ATGGGATCAT
626988 TTTGCCTAAAATGTATCGATAC
1 TTTGCCTAAAATGTATCGATAC
* *
627010 TTTGCCT-CAATGTATTGATAC
1 TTTGCCTAAAATGTATCGATAC
627031 ATTTATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (22 bp):
TTTGCCTAAAATGTATCGATAC
Found at i:633509 original size:2 final size:2
Alignment explanation
Indices: 633502--633527 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
633492 GTTGCTAGGG
633502 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
633528 TAAGGTAGGC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:639267 original size:21 final size:21
Alignment explanation
Indices: 639243--639298 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
639233 AGCTACTGAA
*
639243 AATCTTGTTGCAGCCAAAATG
1 AATCTTGCTGCAGCCAAAATG
* *
639264 AATCTTGCTGTAGCCAAGATG
1 AATCTTGCTGCAGCCAAAATG
**
639285 AATCTCACTGCAGC
1 AATCTTGCTGCAGC
639299 AAGAAACTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (21 bp):
AATCTTGCTGCAGCCAAAATG
Found at i:644536 original size:60 final size:60
Alignment explanation
Indices: 644443--644563 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
644433 ACTTTAAGAG
*
644443 TGGTTTTGTTTCCTTCAAAGTGCCTTTCATAGTCTGAAAATGGGAAAAGCTAAAGTATGC
1 TGGTTTTGTTTCCTTCAAAGTGACTTTCATAGTCTGAAAATGGGAAAAGCTAAAGTATGC
644503 TGGTTTTGTTTCCTTCAAAGTGACTTTCATAGTCTGAAAATGGGAAAAGCTAAAGTATGC
1 TGGTTTTGTTTCCTTCAAAGTGACTTTCATAGTCTGAAAATGGGAAAAGCTAAAGTATGC
644563 T
1 T
644564 TTGGAATTCT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (60 bp):
TGGTTTTGTTTCCTTCAAAGTGACTTTCATAGTCTGAAAATGGGAAAAGCTAAAGTATGC
Found at i:645392 original size:18 final size:19
Alignment explanation
Indices: 645352--645395 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
645342 ATTAATATTT
645352 AATATTATTTTATTAACAAA
1 AATATTATTTTATT-ACAAA
*
645372 AATATTATTTTATT-TAAA
1 AATATTATTTTATTACAAA
645390 AATATT
1 AATATT
645396 CTTTCCGCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
20 14 0.61
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTATTTTATTACAAA
Found at i:645486 original size:26 final size:27
Alignment explanation
Indices: 645448--645504 Score: 98
Period size: 26 Copynumber: 2.1 Consensus size: 27
645438 AATATCCTTT
645448 ATTATCCTCAATAGAGTCTCATCAATC
1 ATTATCCTCAATAGAGTCTCATCAATC
*
645475 ATTA-CCTTAATAGAGTCTCATCAATC
1 ATTATCCTCAATAGAGTCTCATCAATC
645501 ATTA
1 ATTA
645505 AATAAGGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (27 bp):
ATTATCCTCAATAGAGTCTCATCAATC
Found at i:649400 original size:34 final size:34
Alignment explanation
Indices: 649361--649425 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
649351 GTAATGATCT
*
649361 TTGGAGACATTGA-GGATGATGATATGCCCTAACA
1 TTGGAGA-ATTGAGGGATAATGATATGCCCTAACA
* *
649395 TTGGAGATTTTAGGGATAATGATATGCCCTA
1 TTGGAGAATTGAGGGATAATGATATGCCCTA
649426 TATTTGGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 3 0.11
34 24 0.89
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (34 bp):
TTGGAGAATTGAGGGATAATGATATGCCCTAACA
Found at i:657585 original size:38 final size:38
Alignment explanation
Indices: 657534--657607 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
657524 AATTCAAGTA
*
657534 TGTCTACCCAAATCACGAATCAAATCACCTAAGTGACG
1 TGTCTACCCAAATCACAAATCAAATCACCTAAGTGACG
657572 TGTCTACCCAAATCACAAATCAAATCACCTAAGTGA
1 TGTCTACCCAAATCACAAATCAAATCACCTAAGTGA
657608 TGTGAACATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (38 bp):
TGTCTACCCAAATCACAAATCAAATCACCTAAGTGACG
Found at i:666819 original size:2 final size:2
Alignment explanation
Indices: 666772--666806 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
666762 CTTTCAATTT
666772 GA GA GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
666807 TGAGTCCAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:684569 original size:2 final size:2
Alignment explanation
Indices: 684562--684595 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
684552 GTTTACTTTA
* *
684562 AT AT AT AT AT AT AT AT AT GT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
684596 GGTTAGGTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:684575 original size:10 final size:10
Alignment explanation
Indices: 684562--684595 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
684552 GTTTACTTTA
*
684562 ATATATATAT
1 ATATATATGT
684572 ATATATATGT
1 ATATATATGT
684582 ATATATATGT
1 ATATATATGT
684592 ATAT
1 ATAT
684596 GGTTAGGTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATATATATGT
Found at i:687283 original size:2 final size:2
Alignment explanation
Indices: 687276--687301 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
687266 ATCGCACCAC
687276 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
687302 GGCATTGAAT
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:696651 original size:29 final size:29
Alignment explanation
Indices: 696609--696685 Score: 138
Period size: 29 Copynumber: 2.7 Consensus size: 29
696599 GATAATGATT
696609 GTGATGCCACCTGTGTGAGAATACTTCGA
1 GTGATGCCACCTGTGTGAGAATACTTCGA
696638 GTGATGCCACCTGTGTGAGAATACTTCGA
1 GTGATGCCACCTGTGTGAGAATACTTCGA
*
696667 GTGATGCCAACTGT-TGAGA
1 GTGATGCCACCTGTGTGAGA
696686 GATTACTCTG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 5 0.11
29 42 0.89
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (29 bp):
GTGATGCCACCTGTGTGAGAATACTTCGA
Found at i:702551 original size:30 final size:30
Alignment explanation
Indices: 702515--702583 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
702505 TTCTCTTGTT
702515 TCAAAATGACTCAATGGTCACCTTTTATAG
1 TCAAAATGACTCAATGGTCACCTTTTATAG
702545 TCAAAATGACTCAATGGTCACCTTTTATAG
1 TCAAAATGACTCAATGGTCACCTTTTATAG
702575 TCAAAATGA
1 TCAAAATGA
702584 TGTTTGGAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (30 bp):
TCAAAATGACTCAATGGTCACCTTTTATAG
Found at i:720068 original size:35 final size:35
Alignment explanation
Indices: 720022--720097 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
720012 NNNNNNNNNN
*
720022 TAAATTGTTTAATTAAGTTATTGGGCCTAATTAAT
1 TAAATTGTTTAATTAAGTTATTGGACCTAATTAAT
* *
720057 TAAATTGTTTAATTAAGTTTTTGGACCTAATTGAT
1 TAAATTGTTTAATTAAGTTATTGGACCTAATTAAT
720092 TAAATT
1 TAAATT
720098 AAACAATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (35 bp):
TAAATTGTTTAATTAAGTTATTGGACCTAATTAAT
Found at i:720106 original size:35 final size:35
Alignment explanation
Indices: 720032--720116 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 35
720022 TAAATTGTTT
* ****
720032 AATTAAGTTATTGGGCCTAATTAATTAAATTGTTT
1 AATTAAGTTATTGGACCTAATTAATTAAATTAAAC
* *
720067 AATTAAGTTTTTGGACCTAATTGATTAAATTAAAC
1 AATTAAGTTATTGGACCTAATTAATTAAATTAAAC
720102 AATTAAGTTAATTGG
1 AATTAAGTT-ATTGG
720117 GCTTCTTAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 37 0.90
36 4 0.10
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (35 bp):
AATTAAGTTATTGGACCTAATTAATTAAATTAAAC
Found at i:729943 original size:115 final size:116
Alignment explanation
Indices: 729741--729969 Score: 415
Period size: 115 Copynumber: 2.0 Consensus size: 116
729731 CACAAAAGTA
*
729741 GAGAAAGAAGCTAATTATTGAAGCTTTATGATCTTAATTGTCTCTCAAATTCTCAATTTTTCTTA
1 GAGAAAGAAGCTAATTATTGAAGCTTTATGATCTTAATTGTCTCTCAAATTCTCAAGTTTTCTTA
*
729806 CTTTGTTCTTGCCTCCAAATCTCCAGAATTGATGCCTCTTCTT-AAAAATT
66 CTTTGTTCTTGCCTCCAAATCTCCAAAATTGATGCCTCTTCTTGAAAAATT
*
729856 GAGAAAGAAGCTAATTATTGAAGCTTTATGATCTTAATTGTCTCTCAAATTCTCAAGTTTTCTTG
1 GAGAAAGAAGCTAATTATTGAAGCTTTATGATCTTAATTGTCTCTCAAATTCTCAAGTTTTCTTA
*
729921 CTTTGTTCTTGGCTCCAAATCTCCAAAATTGATGCCTCTTCTTGAAAAA
66 CTTTGTTCTTGCCTCCAAATCTCCAAAATTGATGCCTCTTCTTGAAAAA
729970 ATTTGATAAA
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
115 104 0.95
116 5 0.05
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (116 bp):
GAGAAAGAAGCTAATTATTGAAGCTTTATGATCTTAATTGTCTCTCAAATTCTCAAGTTTTCTTA
CTTTGTTCTTGCCTCCAAATCTCCAAAATTGATGCCTCTTCTTGAAAAATT
Found at i:730690 original size:21 final size:22
Alignment explanation
Indices: 730655--730698 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
730645 CTCTTAAAGT
730655 AATTTAAAACAAAATAACATAA
1 AATTTAAAACAAAATAACATAA
* *
730677 AATTT-AACCAAAATAACTTAA
1 AATTTAAAACAAAATAACATAA
730698 A
1 A
730699 TTAACTACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.25
Consensus pattern (22 bp):
AATTTAAAACAAAATAACATAA
Found at i:735270 original size:28 final size:28
Alignment explanation
Indices: 735230--735307 Score: 156
Period size: 28 Copynumber: 2.8 Consensus size: 28
735220 CTTATATCTG
735230 CATAGCAAAAGGTAGAAAGGTTTCTCTA
1 CATAGCAAAAGGTAGAAAGGTTTCTCTA
735258 CATAGCAAAAGGTAGAAAGGTTTCTCTA
1 CATAGCAAAAGGTAGAAAGGTTTCTCTA
735286 CATAGCAAAAGGTAGAAAGGTT
1 CATAGCAAAAGGTAGAAAGGTT
735308 ATACTTCCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (28 bp):
CATAGCAAAAGGTAGAAAGGTTTCTCTA
Found at i:757290 original size:13 final size:13
Alignment explanation
Indices: 757272--757296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
757262 GAAAAACAAA
757272 CTAATTAAATAAG
1 CTAATTAAATAAG
757285 CTAATTAAATAA
1 CTAATTAAATAA
757297 ATGCAAGCCA
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:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (13 bp):
CTAATTAAATAAG
Found at i:757751 original size:19 final size:19
Alignment explanation
Indices: 757727--757765 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
757717 CATATTTGAA
757727 TAAACATCGACATAACTTT
1 TAAACATCGACATAACTTT
757746 TAAACATCGACATAACTTT
1 TAAACATCGACATAACTTT
757765 T
1 T
757766 CAAAATAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (19 bp):
TAAACATCGACATAACTTT
Found at i:769336 original size:28 final size:28
Alignment explanation
Indices: 769257--769495 Score: 203
Period size: 28 Copynumber: 8.4 Consensus size: 28
769247 TTTTACATGT
**
769257 TTTGTCTTAATTTAGATGAGAAAACATA
1 TTTGTCTTAATTTAGACAAGAAAACATA
* *
769285 TTTGATTTTAATTTAAACAAGAAAACATA
1 TTTG-TCTTAATTTAGACAAGAAAACATA
* * *
769314 TTTGTCTTAGTTTAGATAAGAAAACATG
1 TTTGTCTTAATTTAGACAAGAAAACATA
* * *
769342 CTTGTCTTAGTTTAGACAAGAAAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACAT-A
* * * * * *
769371 TTTGCCTGAATTTAGAGATGAACACATG
1 TTTGTCTTAATTTAGACAAGAAAACATA
* *
769399 TTTATCTTAATTTATGATAAG-AAA-ATA
1 TTTGTCTTAATTTA-GACAAGAAAACATA
* *
769426 TGTTGTCTTAATCTAAACAAGAAAACATA
1 T-TTGTCTTAATTTAGACAAGAAAACATA
* * * *
769455 TTTGTCTCAATTTATACAAGATAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACAT-A
769484 TTTGTCTTAATT
1 TTTGTCTTAATT
769496 AAAGAAAAGA
Statistics
Matches: 167, Mismatches: 37, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
27 7 0.04
28 97 0.58
29 63 0.38
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (28 bp):
TTTGTCTTAATTTAGACAAGAAAACATA
Found at i:769492 original size:85 final size:83
Alignment explanation
Indices: 769275--769495 Score: 228
Period size: 85 Copynumber: 2.6 Consensus size: 83
769265 AATTTAGATG
* * * *
769275 AGAAAACATATTTGATTTTAATTTAAACAAGAAAACATATTTGTCTTAGTTTAGATAAGAAAACA
1 AGAAAACATATTTG-TCTCAATTTAAACAAG-AAACATGTTTGTCTTAATTTAGATAAGAAAACA
* * *
769340 TGCTTGTCTTAGTTTAGACA
64 TGCTTGTCTTAATCTAAACA
* * * * * * * *
769360 AGAAAACATGTTTTGCCTGAATTTAGAGATGAACACATGTTTATCTTAATTTATGATAAGAAAAT
1 AGAAAACAT-ATTTGTCTCAATTTAAACAAGAA-ACATGTTTGTCTTAATTTA-GATAAGAAAAC
769425 ATG-TTGTCTTAATCTAAACA
63 ATGCTTGTCTTAATCTAAACA
*
769445 AGAAAACATATTTGTCTCAATTTATACAAGATAACATGTTTTGTCTTAATT
1 AGAAAACATATTTGTCTCAATTTAAACAAGA-AACATG-TTTGTCTTAATT
769496 AAAGAAAAGA
Statistics
Matches: 110, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
84 23 0.21
85 70 0.64
86 17 0.15
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (83 bp):
AGAAAACATATTTGTCTCAATTTAAACAAGAAACATGTTTGTCTTAATTTAGATAAGAAAACATG
CTTGTCTTAATCTAAACA
Found at i:771197 original size:32 final size:34
Alignment explanation
Indices: 771150--771242 Score: 127
Period size: 32 Copynumber: 2.7 Consensus size: 34
771140 TCTCAAGCAC
*
771150 TTGATTAAAATTGTTTAATTAAGTTG-T-GCCTAA
1 TTGATT-AAATTGTTTAATCAAGTTGTTAGCCTAA
771183 TTGATTAAATTGTTTAATCAAGTTGTTAGGCCTAA
1 TTGATTAAATTGTTTAATCAAGTTGTTA-GCCTAA
*
771218 TTGATTAAATTTATTTAATCAAGTT
1 TTGATTAAA-TTGTTTAATCAAGTT
771243 ATTGGGCTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
32 18 0.33
33 7 0.13
35 15 0.28
36 14 0.26
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.46
Consensus pattern (34 bp):
TTGATTAAATTGTTTAATCAAGTTGTTAGCCTAA
Found at i:771242 original size:36 final size:34
Alignment explanation
Indices: 771150--771256 Score: 128
Period size: 36 Copynumber: 3.1 Consensus size: 34
771140 TCTCAAGCAC
*
771150 TTGATTAAAATTGTTTAATTAAGTTG-T-GCCTAA
1 TTGATT-AAATTGTTTAATCAAGTTGTTGGCCTAA
771183 TTGATTAAATTGTTTAATCAAGTTGTTAGGCCTAA
1 TTGATTAAATTGTTTAATCAAGTTGTT-GGCCTAA
* * *
771218 TTGATTAAATTTATTTAATCAAGTTATTGGGCTTAA
1 TTGATTAAA-TTGTTTAATCAAGTTGTT-GGCCTAA
771254 TTG
1 TTG
771257 NNNNNNNNNN
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
32 18 0.28
33 7 0.11
35 15 0.23
36 25 0.38
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.46
Consensus pattern (34 bp):
TTGATTAAATTGTTTAATCAAGTTGTTGGCCTAA
Found at i:783542 original size:20 final size:20
Alignment explanation
Indices: 783505--783541 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
783495 AATAAGGGGG
783505 ATTTAACAATCAAATTTTGC
1 ATTTAACAATCAAATTTTGC
*
783525 ATTTAA-AATCAAGTTTT
1 ATTTAACAATCAAATTTT
783542 TTTACAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (20 bp):
ATTTAACAATCAAATTTTGC
Found at i:784888 original size:35 final size:36
Alignment explanation
Indices: 784835--784903 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
784825 AGGTGTAGTA
*
784835 GTTGTGCCTGAACGAT-AAAGGCATTGTATTGAAAG
1 GTTGTGCCTGAACCATAAAAGGCATTGTATTGAAAG
* *
784870 GTTGTGCTTGATCCATAAAAGGCATTGTATTGAA
1 GTTGTGCCTGAACCATAAAAGGCATTGTATTGAA
784904 CTTTATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 13 0.43
36 17 0.57
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (36 bp):
GTTGTGCCTGAACCATAAAAGGCATTGTATTGAAAG
Found at i:789781 original size:22 final size:21
Alignment explanation
Indices: 789740--789789 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
789730 AAATGCAAAT
*
789740 AAATAAAACATAATTCAAAAG
1 AAATAAAACATAATTCAAAAC
* *
789761 AAATAAAACTGTAGTTCAAAAC
1 AAATAAAAC-ATAATTCAAAAC
789783 AAA-AAAA
1 AAATAAAA
789790 TTTCAAACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.66, C:0.10, G:0.06, T:0.18
Consensus pattern (21 bp):
AAATAAAACATAATTCAAAAC
Found at i:800936 original size:11 final size:11
Alignment explanation
Indices: 800920--800969 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 11
800910 TAAGCTTAAA
800920 ATTTTTTATTT
1 ATTTTTTATTT
*
800931 ATTTTTCA-TT
1 ATTTTTTATTT
*
800941 ATTTTAT-TTT
1 ATTTTTTATTT
800951 A-TTTTTATTT
1 ATTTTTTATTT
*
800961 AATTTTTAT
1 ATTTTTTAT
800970 GTCATTTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 4 0.12
10 14 0.44
11 14 0.44
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTTTTTATTT
Found at i:813091 original size:21 final size:20
Alignment explanation
Indices: 813063--813101 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
813053 TAATTGATGC
813063 TTGGCTTTAAATGATGGCTA
1 TTGGCTTTAAATGATGGCTA
*
813083 TTGGACTTTGAATGATGGC
1 TTGG-CTTTAAATGATGGC
813102 ATTATTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.38
Consensus pattern (20 bp):
TTGGCTTTAAATGATGGCTA
Found at i:819323 original size:125 final size:125
Alignment explanation
Indices: 819097--819348 Score: 477
Period size: 125 Copynumber: 2.0 Consensus size: 125
819087 CCCCCAAAGC
819097 ATAATTCAACATCTCCAAATCCCTACTTGAACATTTTACTGAGAGCTAGTTTCCAATTATTTAAA
1 ATAATTCAACATCTCCAAATCCCTACTTGAACATTTTACTGAGAGCTAGTTTCCAATTATTTAAA
819162 TTTCACTTCAGCCTATTGTTGGCCCCCTTCCCCTCTTAATCAGCCAATGTTCCTTGATAA
66 TTTCACTTCAGCCTATTGTTGGCCCCCTTCCCCTCTTAATCAGCCAATGTTCCTTGATAA
*
819222 ATAATTCAACATCTCCAAATCCCTACTTGAGCATTTTACTGAGAGCTAGTTTCCAATTATTTAAA
1 ATAATTCAACATCTCCAAATCCCTACTTGAACATTTTACTGAGAGCTAGTTTCCAATTATTTAAA
* *
819287 TTTCACTTCAGCCTATTGTTGGCCCCCTTCCTCTCTTGATCAGCCAATGTTCCTTGATAA
66 TTTCACTTCAGCCTATTGTTGGCCCCCTTCCCCTCTTAATCAGCCAATGTTCCTTGATAA
819347 AT
1 AT
819349 CACAAGAATA
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 124 1.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.37
Consensus pattern (125 bp):
ATAATTCAACATCTCCAAATCCCTACTTGAACATTTTACTGAGAGCTAGTTTCCAATTATTTAAA
TTTCACTTCAGCCTATTGTTGGCCCCCTTCCCCTCTTAATCAGCCAATGTTCCTTGATAA
Found at i:821778 original size:54 final size:54
Alignment explanation
Indices: 821696--821802 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 54
821686 CACATTATTG
* *
821696 GAACAATTGGAAAAGAATCAGAAGCTGTTGCTCACGTGCACCCACAGTTGATTA
1 GAACAACTGGAAAAGAATCAGAAGCTGTTGCTCACGTGCACCCACAATTGATTA
821750 GAACAACTGGAAAAGAATCAGAAGCTGTTGCTCACGTGCACCCACAATTGATT
1 GAACAACTGGAAAAGAATCAGAAGCTGTTGCTCACGTGCACCCACAATTGATT
821803 TCTTCAGAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (54 bp):
GAACAACTGGAAAAGAATCAGAAGCTGTTGCTCACGTGCACCCACAATTGATTA
Found at i:823632 original size:186 final size:188
Alignment explanation
Indices: 823278--823646 Score: 609
Period size: 187 Copynumber: 2.0 Consensus size: 188
823268 AAGAACCCCC
* *
823278 TACACTACAATCAACTCAAGTTCTATAGGCCTTCATCACATTCTAGAACGGCCTCAAACTAGAAT
1 TACACTACAATCAACTCAAGTTCTATAGGCCTTCATCACATTCTAGAACGACCTAAAACTAGAAT
*
823343 CTATACAGTCCATGCTGATGCATCTATTGGCTTTCATCACATCTCACCAAAGCATATTAGATGAC
66 CTATACAGTCCATGCTGATGCATCTATTGGCTTTCATCACATCTCACCAAAGCATATTAGACGAC
*
823408 TAAAAATTATGTTGTCTTCAATTCACACAGCCTGAGACAATGAACTTATCTCACACCT
131 TAAAAATTATGTTGTCTTCAATTCACACAGCATGAGACAATGAACTTATCTCACACCT
* * * *
823466 TACACTACCATCAACTCAAGTTCTATGGGCCTTCATCTC-TTAC-CGAACGACCTAAAACTAGAA
1 TACACTACAATCAACTCAAGTTCTATAGGCCTTCATCACATT-CTAGAACGACCTAAAACTAGAA
* * *
823529 TCTATACAGTCCATGCTGATGCATCTGTTGGCTTTCATCGCATCTTACCAAA-CATATTAGACGA
65 TCTATACAGTCCATGCTGATGCATCTATTGGCTTTCATCACATCTCACCAAAGCATATTAGACGA
823593 CTAAAAATTATGTTGTCTTCAATTCACACAGCATGAGACAATGAACTTATCTCA
130 CTAAAAATTATGTTGTCTTCAATTCACACAGCATGAGACAATGAACTTATCTCA
823647 TACTTGTTAC
Statistics
Matches: 169, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
186 64 0.38
187 68 0.40
188 37 0.22
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.30
Consensus pattern (188 bp):
TACACTACAATCAACTCAAGTTCTATAGGCCTTCATCACATTCTAGAACGACCTAAAACTAGAAT
CTATACAGTCCATGCTGATGCATCTATTGGCTTTCATCACATCTCACCAAAGCATATTAGACGAC
TAAAAATTATGTTGTCTTCAATTCACACAGCATGAGACAATGAACTTATCTCACACCT
Found at i:825613 original size:17 final size:18
Alignment explanation
Indices: 825579--825618 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
825569 GTTAATTATA
825579 TTAAATAAATATAATATT
1 TTAAATAAATATAATATT
825597 TTAAA-AAAT-TAACTA-T
1 TTAAATAAATATAA-TATT
825613 TTAAAT
1 TTAAAT
825619 TTATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 9 0.45
17 6 0.30
18 5 0.25
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAATAAATATAATATT
Found at i:825650 original size:17 final size:17
Alignment explanation
Indices: 825630--825662 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
825620 TATATTTTTG
825630 AATTTA-AAATATTTAAC
1 AATTTATAAAT-TTTAAC
825647 AATTTATAAATTTTAA
1 AATTTATAAATTTTAA
825663 TTTATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTATAAATTTTAAC
Found at i:826027 original size:253 final size:254
Alignment explanation
Indices: 825735--826202 Score: 602
Period size: 253 Copynumber: 1.8 Consensus size: 254
825725 TTTTAAACAC
* * * *
825735 TAAAAATTAAGGTAAAAAATTATAAAAGTACAATAAGTATTATCAAAATATTGACGTCACACGTG
1 TAAAAATTAACGTAAAAAATTATAAAAGTACAATAAGTATTATCAAAATATTAACGT-AAACATG
* * * *
825800 TGAGATTTAATATAACAAATCAATTAA-TTCAAATAAATATAAATTTTTTTAA-AATTAAACATT
65 TGAAATTTAAGATAACAAATCAATTAAGTTAAAATAAATAT-AATTTTTATAAGAATTAAACATT
* * * *
825863 AAAATTTTTATT-CTCAACTTTAAATTATTTAACGGTTTAGAAATTTTAATATACAAATGAATAA
129 AAAATTTTTATTACTCAAC-TAAAAGTATTTAAAGATTTAGAAATTTTAATATACAAATGAATAA
* *
825927 TAGTAAGGAT-AAAAATAATTATTGTAAAATTTTTTAGTTAAAAAATTTTTACGTAAACTTA
193 TAATAAAGATAAAAAATAATTATTGTAAAATTTTTTAGTTAAAAAATTTTTACGTAAACTTA
* * * ** * *
825988 TAAAAATTAACTTAAGAAATTATAAAGGTGGAATAAGTATTGTCAAAATATTAACGTAAATATGT
1 TAAAAATTAACGTAAAAAATTATAAAAGTACAATAAGTATTATCAAAATATTAACGTAAACATGT
* * * *
826053 GAAATTTAAGATAACAAGTCAATTAAGTTAAAATAAGTATAATTTTTATAAGAATTAAATATTTA
66 GAAATTTAAGATAACAAATCAATTAAGTTAAAATAAATATAATTTTTATAAGAATTAAACATTAA
* * * * * *
826118 AATTTTTATTATTGAGCTAAAAGTATTTAAAGATTTATAAATTTTAATTTATAAATGAATAATAA
131 AATTTTTATTACTCAACTAAAAGTATTTAAAGATTTAGAAATTTTAATATACAAATGAATAATAA
826183 TAAAGATAAAAAATAATTAT
196 TAAAGATAAAAAATAATTAT
826203 AGTTAAAAAA
Statistics
Matches: 180, Mismatches: 31, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
252 38 0.21
253 127 0.71
254 15 0.08
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (254 bp):
TAAAAATTAACGTAAAAAATTATAAAAGTACAATAAGTATTATCAAAATATTAACGTAAACATGT
GAAATTTAAGATAACAAATCAATTAAGTTAAAATAAATATAATTTTTATAAGAATTAAACATTAA
AATTTTTATTACTCAACTAAAAGTATTTAAAGATTTAGAAATTTTAATATACAAATGAATAATAA
TAAAGATAAAAAATAATTATTGTAAAATTTTTTAGTTAAAAAATTTTTACGTAAACTTA
Found at i:834244 original size:18 final size:18
Alignment explanation
Indices: 834217--834256 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
834207 AATGCTTTTC
*
834217 CTCTTTTCTTTTGCTTCT
1 CTCTTATCTTTTGCTTCT
*
834235 CTCTTATCTTTTTCTTCT
1 CTCTTATCTTTTGCTTCT
834253 -TCTT
1 CTCTT
834257 CTTTAAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.03, C:0.28, G:0.03, T:0.68
Consensus pattern (18 bp):
CTCTTATCTTTTGCTTCT
Found at i:844204 original size:22 final size:22
Alignment explanation
Indices: 844155--844204 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
844145 AATTTTACAT
*
844155 AATTAAATATATAAAATTATTT
1 AATTAAATATATAAAATTATTA
*
844177 AGTTAAATATATAAAATTATTA
1 AATTAAATATATAAAATTATTA
844199 AATTAA
1 AATTAA
844205 TAAAATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AATTAAATATATAAAATTATTA
Found at i:845811 original size:2 final size:2
Alignment explanation
Indices: 845804--845834 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
845794 TGTTATGTAA
845804 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
845835 CTATGTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:846252 original size:37 final size:38
Alignment explanation
Indices: 846138--846272 Score: 125
Period size: 37 Copynumber: 3.5 Consensus size: 38
846128 ACCGAATGTT
* *
846138 TTTTCAAGGATCAAGCACAACCTTCACCAAAGTCATTAATA--
1 TTTT-AAGGATCAAGCACAACCTTCA-C-AA-CCA-AAATACC
* *
846179 TTTTAA-GATCGAGCACAACCTTCATAACCAAAATACC
1 TTTTAAGGATCAAGCACAACCTTCACAACCAAAATACC
* *
846216 TTTTAAGGATCAAGCACAACCTTTACAACC-ATATACC
1 TTTTAAGGATCAAGCACAACCTTCACAACCAAAATACC
* *
846253 ATTTAAGGATCATGCACAAC
1 TTTTAAGGATCAAGCACAAC
846273 ATTTTAACCT
Statistics
Matches: 81, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
35 4 0.05
36 2 0.02
37 32 0.40
38 20 0.25
39 17 0.21
40 2 0.02
41 4 0.05
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.26
Consensus pattern (38 bp):
TTTTAAGGATCAAGCACAACCTTCACAACCAAAATACC
Found at i:852789 original size:38 final size:38
Alignment explanation
Indices: 852693--852790 Score: 135
Period size: 38 Copynumber: 2.6 Consensus size: 38
852683 CTACTTTTTT
*
852693 AGGATCAAGCACAACCTTTACAACCAAAATGCCTCTTA
1 AGGATCAAGCACAACCTTTATAACCAAAATGCCTCTTA
* *
852731 AAGATCAAGCACAACCTTTATAAGCAAAATGCCT-TTGA
1 AGGATCAAGCACAACCTTTATAACCAAAATGCCTCTT-A
* *
852769 AGGATCAAGCATAATCTTTATA
1 AGGATCAAGCACAACCTTTATA
852791 CCTTTTGCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
37 2 0.04
38 51 0.96
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.24
Consensus pattern (38 bp):
AGGATCAAGCACAACCTTTATAACCAAAATGCCTCTTA
Found at i:853790 original size:26 final size:25
Alignment explanation
Indices: 853743--853791 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
853733 GAATAAATTT
**
853743 TTCTTTCCATTCAATTGACAATTGA
1 TTCTTTCCATTCAAAAGACAATTGA
*
853768 TTCTTTTCATTCAAAAGATCAATT
1 TTCTTTCCATTCAAAAGA-CAATT
853792 CTTAAGGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.45
Consensus pattern (25 bp):
TTCTTTCCATTCAAAAGACAATTGA
Found at i:855810 original size:22 final size:21
Alignment explanation
Indices: 855785--855830 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
855775 ATAGTTAACT
855785 GAATGCACCATCATACAATATG
1 GAATGCACCATCATA-AATATG
* **
855807 GAATTCTGCATCATAAATATG
1 GAATGCACCATCATAAATATG
855828 GAA
1 GAA
855831 ATGCTTTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.26
Consensus pattern (21 bp):
GAATGCACCATCATAAATATG
Found at i:858068 original size:21 final size:21
Alignment explanation
Indices: 858044--858091 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
858034 AATTATTTTT
858044 ATTTCAAGCAATTTTAGTTCA
1 ATTTCAAGCAATTTTAGTTCA
*
858065 ATTTCAAGTAATTTTAGTTCA
1 ATTTCAAGCAATTTTAGTTCA
858086 ATTTCA
1 ATTTCA
858092 TGTTAAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (21 bp):
ATTTCAAGCAATTTTAGTTCA
Found at i:903320 original size:35 final size:36
Alignment explanation
Indices: 903281--903360 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
903271 CTAGCCTTGG
903281 TAAAAGGCATG-TGTAAAGGTTACGCCCGATCCTAT
1 TAAAAGGCATGTTGTAAAGGTTACGCCCGATCCTAT
* ** *
903316 TAAAAGGCATGTTGTAAAGGTTGCGCTTGATCTTAT
1 TAAAAGGCATGTTGTAAAGGTTACGCCCGATCCTAT
*
903352 TGAAAGGCA
1 TAAAAGGCA
903361 AGCCGATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 11 0.28
36 28 0.72
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (36 bp):
TAAAAGGCATGTTGTAAAGGTTACGCCCGATCCTAT
Found at i:905117 original size:61 final size:61
Alignment explanation
Indices: 905052--905233 Score: 269
Period size: 61 Copynumber: 3.0 Consensus size: 61
905042 TATATTCCAT
* * **
905052 TGTAAAAGGTAATGTAAGGTTATACCTCCATTGAAATAGCAACGTAAGGTTATACCTCCTC
1 TGTAAAAGGTAGTGTAAGGTTATACCTCCATTGAAATAGTAGTGTAAGGTTATACCTCCTC
905113 TGTAAAAGGTAGTGTAAGGTTATACCTCCATTGAAATAGTAGTGTAAGGTTATACCTCCTC
1 TGTAAAAGGTAGTGTAAGGTTATACCTCCATTGAAATAGTAGTGTAAGGTTATACCTCCTC
* *
905174 TGTAAAAGGTAGTGTATA-CTTACACCTCCATTGTAAA-ATGTAGTGTAAGGTTATACCTCC
1 TGTAAAAGGTAGTGTA-AGGTTATACCTCCATTG-AAATA-GTAGTGTAAGGTTATACCTCC
905234 ATAGAAAAGG
Statistics
Matches: 112, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
61 87 0.78
62 25 0.22
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (61 bp):
TGTAAAAGGTAGTGTAAGGTTATACCTCCATTGAAATAGTAGTGTAAGGTTATACCTCCTC
Found at i:905133 original size:31 final size:31
Alignment explanation
Indices: 905047--905245 Score: 225
Period size: 31 Copynumber: 6.5 Consensus size: 31
905037 GCAGTTATAT
*
905047 TCCATTGTAAAAGGTAATGTAAGGTTATACC
1 TCCATTGTAAAAGGTAGTGTAAGGTTATACC
* **
905078 TCCATTG-AAATA-GCAACGTAAGGTTATACC
1 TCCATTGTAAA-AGGTAGTGTAAGGTTATACC
905108 TCC-TCTGTAAAAGGTAGTGTAAGGTTATACC
1 TCCAT-TGTAAAAGGTAGTGTAAGGTTATACC
905139 TCCATTG-AAATA-GTAGTGTAAGGTTATACC
1 TCCATTGTAAA-AGGTAGTGTAAGGTTATACC
* *
905169 TCC-TCTGTAAAAGGTAGTGTATA-CTTACACC
1 TCCAT-TGTAAAAGGTAGTGTA-AGGTTATACC
*
905200 TCCATTGTAAAATGTAGTGTAAGGTTATACC
1 TCCATTGTAAAAGGTAGTGTAAGGTTATACC
*
905231 TCCATAG-AAAAGGTA
1 TCCATTGTAAAAGGTA
905246 AAGAAATGTT
Statistics
Matches: 144, Mismatches: 12, Indels: 25
0.80 0.07 0.14
Matches are distributed among these distances:
29 2 0.01
30 60 0.42
31 79 0.55
32 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (31 bp):
TCCATTGTAAAAGGTAGTGTAAGGTTATACC
Found at i:905630 original size:20 final size:20
Alignment explanation
Indices: 905583--905674 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
905573 AAGCTTCTAT
* * *
905583 ATCTAATCGATAGATTTCAAA
1 ATCT-ATCGATACATTGCTAA
*
905604 ATCTATCAATACATTGCTAA
1 ATCTATCGATACATTGCTAA
* * *
905624 ATTTATCGATA-AATGATGAA
1 ATCTATCGATACATTGCT-AA
*
905644 ATATATCGATACATTGCTAA
1 ATCTATCGATACATTGCTAA
905664 ATCTATCGATA
1 ATCTATCGATA
905675 GATGATGAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
19 4 0.07
20 45 0.79
21 8 0.14
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (20 bp):
ATCTATCGATACATTGCTAA
Found at i:905656 original size:40 final size:40
Alignment explanation
Indices: 905602--905694 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 40
905592 ATAGATTTCA
* *
905602 AAATCTATCAATACATTGCTAAATTTATCGATAAATGATG
1 AAATCTATCGATACATTGCTAAATCTATCGATAAATGATG
* *
905642 AAATATATCGATACATTGCTAAATCTATCGATAGATGATG
1 AAATCTATCGATACATTGCTAAATCTATCGATAAATGATG
*
905682 AAATCTATTGATA
1 AAATCTATCGATA
905695 GATTTCATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (40 bp):
AAATCTATCGATACATTGCTAAATCTATCGATAAATGATG
Found at i:905685 original size:20 final size:20
Alignment explanation
Indices: 905622--905697 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
905612 ATACATTGCT
* *
905622 AAATTTATCGATAAATGATG
1 AAATCTATCGATAGATGATG
* * *
905642 AAATATATCGATACATTGCT-
1 AAATCTATCGATAGA-TGATG
905662 AAATCTATCGATAGATGATG
1 AAATCTATCGATAGATGATG
*
905682 AAATCTATTGATAGAT
1 AAATCTATCGATAGAT
905698 TTCATCATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 3 0.06
20 41 0.87
21 3 0.06
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (20 bp):
AAATCTATCGATAGATGATG
Found at i:928486 original size:85 final size:86
Alignment explanation
Indices: 928372--928544 Score: 330
Period size: 86 Copynumber: 2.0 Consensus size: 86
928362 CTCTATGACA
*
928372 TAGAGTTATTTGGTTTAAAATTTAGCTACTAAGTTGCTA-GTTTTTGAGTTTTAGCATAGATTTT
1 TAGAGTTATTTGGTCTAAAATTTAGCTACTAAGTTGCTAGGTTTTTGAGTTTTAGCATAGATTTT
928436 AAGTGTTTTTAGTTATTTATT
66 AAGTGTTTTTAGTTATTTATT
928457 TAGAGTTATTTGGTCTAAAATTTAGCTACTAAGTTGCTAGGTTTTTGAGTTTTAGCATAGATTTT
1 TAGAGTTATTTGGTCTAAAATTTAGCTACTAAGTTGCTAGGTTTTTGAGTTTTAGCATAGATTTT
928522 AAGTGTTTTTAGTTATTTATT
66 AAGTGTTTTTAGTTATTTATT
928543 TA
1 TA
928545 ATTATAGTTA
Statistics
Matches: 86, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
85 38 0.44
86 48 0.56
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (86 bp):
TAGAGTTATTTGGTCTAAAATTTAGCTACTAAGTTGCTAGGTTTTTGAGTTTTAGCATAGATTTT
AAGTGTTTTTAGTTATTTATT
Found at i:930199 original size:21 final size:21
Alignment explanation
Indices: 930175--930245 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
930165 ACAATACTTC
930175 TTTTAAATTTAAATAAATTAA
1 TTTTAAATTTAAATAAATTAA
* * *
930196 TTTTAAATGTAATTAATATTTA
1 TTTTAAATTTAAATAA-ATTAA
* *
930218 -CTTAAATTTAAACAAATTAA
1 TTTTAAATTTAAATAAATTAA
*
930238 ATTTAAAT
1 TTTTAAAT
930246 ATAATGAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 4 0.10
21 31 0.79
22 4 0.10
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (21 bp):
TTTTAAATTTAAATAAATTAA
Found at i:934624 original size:21 final size:20
Alignment explanation
Indices: 934600--934669 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
934590 ATAGGATTTT
934600 TTTAAATTTAAACAAATTAAA
1 TTTAAATTT-AACAAATTAAA
* * **
934621 TTTAAATGTAATAAATCTTTA
1 TTTAAATTTAACAAAT-TAAA
934642 TTTAAATTTGAACAAATTAAA
1 TTTAAATTT-AACAAATTAAA
934663 TTTAAAT
1 TTTAAAT
934670 ATAATGGCTT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 6 0.15
21 27 0.69
22 6 0.15
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (20 bp):
TTTAAATTTAACAAATTAAA
Found at i:937951 original size:20 final size:20
Alignment explanation
Indices: 937926--937968 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
937916 AAATTAAGGC
* *
937926 AAATGTATCAATACATTACA
1 AAATGTATCAACACATCACA
937946 AAATGTATCAACACATCACA
1 AAATGTATCAACACATCACA
937966 AAA
1 AAA
937969 GAAAGGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.19, G:0.05, T:0.23
Consensus pattern (20 bp):
AAATGTATCAACACATCACA
Found at i:940306 original size:80 final size:80
Alignment explanation
Indices: 940097--940308 Score: 264
Period size: 80 Copynumber: 2.6 Consensus size: 80
940087 AAGTACATGT
* * * * *
940097 TTTGCTTATAGTGCATATGACTATCTTAACACATACATCTTATGGCATAAATTTCATAACCTCAT
1 TTTGCCTATAGTGTATATGACTATCTCAACACATACATATTATGGCATACATTTCATAACCTCAT
* *
940162 AAATCACTTACACGC
66 AAATCACTCACACAC
* * * *
940177 TTAGTCC-ATAGTTTATATGACTATCTCATCACATACATATCATGGCATACATTTCATAACCTCA
1 TTTG-CCTATAGTGTATATGACTATCTCAACACATACATATTATGGCATACATTTCATAACCTCA
* *
940241 TAAATTACTCACATAC
65 TAAATCACTCACACAC
* * *
940257 TTTGCCTATAATGTATATGACTATCTCAACATATACAAATTATGGCATACAT
1 TTTGCCTATAGTGTATATGACTATCTCAACACATACATATTATGGCATACAT
940309 GTTACAATCT
Statistics
Matches: 110, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
79 2 0.02
80 107 0.97
81 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (80 bp):
TTTGCCTATAGTGTATATGACTATCTCAACACATACATATTATGGCATACATTTCATAACCTCAT
AAATCACTCACACAC
Found at i:948853 original size:21 final size:21
Alignment explanation
Indices: 948827--948871 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
948817 TAACTATTCC
948827 TAAAGT-AAATTAAAGCAAAAA
1 TAAAGTAAAATTAAA-CAAAAA
*
948848 TAAAGTAAAATTAAACTAAAA
1 TAAAGTAAAATTAAACAAAAA
948869 TAA
1 TAA
948872 CTTGAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (21 bp):
TAAAGTAAAATTAAACAAAAA
Found at i:948857 original size:11 final size:11
Alignment explanation
Indices: 948827--948869 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
948817 TAACTATTCC
948827 TAAAGT-AAAT
1 TAAAGTAAAAT
* *
948837 TAAAGCAAAAA
1 TAAAGTAAAAT
948848 TAAAGTAAAAT
1 TAAAGTAAAAT
*
948859 TAAACTAAAAT
1 TAAAGTAAAAT
948870 AACTTGAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 5 0.19
11 22 0.81
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (11 bp):
TAAAGTAAAAT
Found at i:958329 original size:58 final size:57
Alignment explanation
Indices: 958239--958357 Score: 184
Period size: 58 Copynumber: 2.1 Consensus size: 57
958229 CATAATCATC
* * *
958239 CAAAGTACTTTGCATGTGCTAGATTTATTTTATACAATTTAATAAATGCTATGCAATG
1 CAAAGTACTATGCATGTGATAGATTTATTTTATACAATTTAATAAATGCTATAC-ATG
* *
958297 CAAAGTAGTATGCATGTGATAGATTTATTTTATACGATTTAATAAATGCTATACATG
1 CAAAGTACTATGCATGTGATAGATTTATTTTATACAATTTAATAAATGCTATACATG
958354 CAAA
1 CAAA
958358 AATGAGATCC
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 7 0.12
58 49 0.88
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (57 bp):
CAAAGTACTATGCATGTGATAGATTTATTTTATACAATTTAATAAATGCTATACATG
Found at i:963907 original size:12 final size:13
Alignment explanation
Indices: 963888--963923 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
963878 CAGAATAGTT
963888 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
963901 T-TTGCTGCCT-C
1 TCTTGCTGCCTCC
963912 TCTTGCTGCCTC
1 TCTTGCTGCCTC
963924 AAAAATCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 18 0.86
13 1 0.05
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (13 bp):
TCTTGCTGCCTCC
Found at i:964605 original size:21 final size:22
Alignment explanation
Indices: 964570--964613 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
964560 CTCTTAAAGT
964570 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
964592 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
964613 A
1 A
964614 TTAATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:968373 original size:12 final size:13
Alignment explanation
Indices: 968354--968397 Score: 67
Period size: 12 Copynumber: 3.6 Consensus size: 13
968344 CAGAATAGTT
968354 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
968367 T-TTGCTGCCT-C
1 TCTTGCTGCCTCC
968378 TCTTGCTGCCT-C
1 TCTTGCTGCCTCC
968390 TCTTGCTG
1 TCTTGCTG
968398 GCTTAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 2 0.07
12 27 0.90
13 1 0.03
ACGTcount: A:0.00, C:0.39, G:0.18, T:0.43
Consensus pattern (13 bp):
TCTTGCTGCCTCC
Found at i:969081 original size:21 final size:22
Alignment explanation
Indices: 969046--969089 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
969036 CTCTTAAAGT
969046 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
969068 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
969089 A
1 A
969090 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:985661 original size:8 final size:8
Alignment explanation
Indices: 985648--985688 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
985638 CTTCTTCCAT
985648 CTTTCTTC
1 CTTTCTTC
985656 CTTTCTCTC
1 CTTTCT-TC
* *
985665 TTTTCTTT
1 CTTTCTTC
985673 CTTTCTTC
1 CTTTCTTC
985681 CTTTCTTC
1 CTTTCTTC
985689 TCCTTTCATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (8 bp):
CTTTCTTC
Found at i:985675 original size:25 final size:26
Alignment explanation
Indices: 985647--985695 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
985637 TCTTCTTCCA
*
985647 TCTTTCTTCCTTTC-TCTCTTTTCTT
1 TCTTTCTTCCTTTCTTCTCCTTTCTT
985672 TCTTTCTTCCTTTCTTCTCCTTTC
1 TCTTTCTTCCTTTCTTCTCCTTTC
985696 ATCTTTTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (26 bp):
TCTTTCTTCCTTTCTTCTCCTTTCTT
Found at i:985700 original size:25 final size:25
Alignment explanation
Indices: 985636--985701 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
985626 TCTTTTTTTT
* *
985636 TTCTTCTTCCATCTTTCTTCCTTTC
1 TTCTCCTTTCATCTTTCTTCCTTTC
* *
985661 -TCTCTTTTCTTTCTTTCTTCCTTTC
1 TTCTCCTTTC-ATCTTTCTTCCTTTC
985686 TTCTCCTTTCATCTTT
1 TTCTCCTTTCATCTTT
985702 TCTCCTTGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 6 0.18
25 19 0.58
26 8 0.24
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (25 bp):
TTCTCCTTTCATCTTTCTTCCTTTC
Found at i:985703 original size:18 final size:16
Alignment explanation
Indices: 985634--985704 Score: 56
Period size: 17 Copynumber: 4.4 Consensus size: 16
985624 TTTCTTTTTT
*
985634 TTTTC-TTCTTCCATC
1 TTTTCTTTCTTTCATC
* *
985649 -TTTCTTCCTTTCTCTC
1 TTTTCTTTCTTTC-ATC
*
985665 TTTTCTTTCTTTCTTC
1 TTTTCTTTCTTTCATC
*
985681 CTTTCTTCTCCTTTCATC
1 TTTTCTT-T-CTTTCATC
985699 TTTTCT
1 TTTTCT
985705 CCTTGGTAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
14 4 0.09
15 5 0.12
16 10 0.23
17 12 0.28
18 12 0.28
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTCTTTCTTTCATC
Found at i:990437 original size:35 final size:35
Alignment explanation
Indices: 990339--990461 Score: 108
Period size: 35 Copynumber: 3.5 Consensus size: 35
990329 GTTAAAAACC
* *
990339 ATTGTTAAAGGGTTCCTT-TTAT-TCACATGAAAAAGC
1 ATTGTT-AAGGGTT-CTTCTT-TCTCATATGAAAAAGT
* * * *
990375 ATTG-TAACGGTTCTGCTTGCTCCTATGAAAAAGT
1 ATTGTTAAGGGTTCTTCTTTCTCATATGAAAAAGT
* *
990409 GTTGTTAAGGGTTCTTCTTTCTCATATGAAAAATT
1 ATTGTTAAGGGTTCTTCTTTCTCATATGAAAAAGT
* *
990444 ATTGTTGAGGGTTTTTCT
1 ATTGTTAAGGGTTCTTCT
990462 CACTCTCATG
Statistics
Matches: 69, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
33 2 0.03
34 22 0.32
35 41 0.59
36 4 0.06
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (35 bp):
ATTGTTAAGGGTTCTTCTTTCTCATATGAAAAAGT
Found at i:990473 original size:35 final size:35
Alignment explanation
Indices: 990339--990476 Score: 93
Period size: 35 Copynumber: 3.9 Consensus size: 35
990329 GTTAAAAACC
* * * *
990339 ATTGTTAAAGGGTTCCTT-TTATTCACATGAAAAAGC
1 ATTGTT-AAGGGTT-CTTCTCACTCATATGAAAAAGT
* * ** *
990375 ATTG-TAACGGTTCTGCTTGCTCCTATGAAAAAGT
1 ATTGTTAAGGGTTCTTCTCACTCATATGAAAAAGT
* ** *
990409 GTTGTTAAGGGTTCTTCTTTCTCATATGAAAAATT
1 ATTGTTAAGGGTTCTTCTCACTCATATGAAAAAGT
* *
990444 ATTGTTGAGGGTTTTTCTCACTC-TCATGAAAAA
1 ATTGTTAAGGGTTCTTCTCACTCAT-ATGAAAAA
990477 ACGTTGTGAG
Statistics
Matches: 81, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
33 2 0.02
34 23 0.28
35 52 0.64
36 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.39
Consensus pattern (35 bp):
ATTGTTAAGGGTTCTTCTCACTCATATGAAAAAGT
Found at i:990785 original size:19 final size:21
Alignment explanation
Indices: 990763--990830 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 21
990753 TTTGCTTTAA
990763 TTTATGTT-TTAATGTTTA-T
1 TTTATGTTATTAATGTTTAGT
* *
990782 TTTAAGTTAATAATG-TTAGT
1 TTTATGTTATTAATGTTTAGT
* * *
990802 TTTATATTATTTATGTTTATT
1 TTTATGTTATTAATGTTTAGT
990823 TTTATGTT
1 TTTATGTT
990831 TTTCTAAGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 10 0.26
20 17 0.45
21 11 0.29
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (21 bp):
TTTATGTTATTAATGTTTAGT
Found at i:1005150 original size:73 final size:74
Alignment explanation
Indices: 1005007--1005191 Score: 223
Period size: 73 Copynumber: 2.5 Consensus size: 74
1004997 CAGACAAAAT
* * *
1005007 GCTCTAAATCGACTAAC-ATGCTTTTTAGTCGATTAAGTCATTTTTGTCTTCTGATCCTAGCTTC
1 GCTCTTAATCGACTAACAATGCTTCTTAGTCGATTAAGTCATTTTTGTCTTCTGAACCTAGCTTC
**
1005071 TGGTAGT-G
66 AAGTAGTAG
* *
1005079 AGCTCTTAATCGACTAGCAATGCTTCTTAGTCGATTAAGTCATTTTTGTC-TCTGAACCTAGTTT
1 -GCTCTTAATCGACTAACAATGCTTCTTAGTCGATTAAGTCATTTTTGTCTTCTGAACCTAGCTT
1005143 CAAGTAGTAG
65 CAAGTAGTAG
* * * * * *
1005153 GTTCTTACTCGACTAACAATACCTCTTGGTCGACTAAGT
1 GCTCTTAATCGACTAACAATGCTTCTTAGTCGATTAAGT
1005192 GTTCTTTGTT
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
73 65 0.68
74 31 0.32
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (74 bp):
GCTCTTAATCGACTAACAATGCTTCTTAGTCGATTAAGTCATTTTTGTCTTCTGAACCTAGCTTC
AAGTAGTAG
Found at i:1018632 original size:18 final size:20
Alignment explanation
Indices: 1018604--1018644 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
1018594 GAGAGGAAAT
*
1018604 AATTCTAAAGCTTGATGC-A
1 AATTCTAAAGCTAGATGCTA
1018623 AATT-TAAAGCTAGATGCTA
1 AATTCTAAAGCTAGATGCTA
1018642 AAT
1 AAT
1018645 GAGAAAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (20 bp):
AATTCTAAAGCTAGATGCTA
Found at i:1034741 original size:21 final size:20
Alignment explanation
Indices: 1034710--1034760 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1034700 GTTTTATTAA
*
1034710 TTTTG-TTTTCTATCTTTTGT
1 TTTTGTTTTTCTATCTTAT-T
*
1034730 TTTTGTTTTTCTTTCTTATT
1 TTTTGTTTTTCTATCTTATT
1034750 TTTTGTGTTTT
1 TTTTGT-TTTT
1034761 GTTTTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.04, C:0.08, G:0.10, T:0.78
Consensus pattern (20 bp):
TTTTGTTTTTCTATCTTATT
Found at i:1034753 original size:26 final size:26
Alignment explanation
Indices: 1034716--1034766 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
1034706 TTAATTTTGT
1034716 TTTCTATCTTTTGT-TTTTGTTTTTC
1 TTTCTATCTTTTGTGTTTTGTTTTTC
*
1034741 TTTCTTATTTTTTGTGTTTTGTTTTT
1 TTTC-TATCTTTTGTGTTTTGTTTTT
1034767 TCATAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 9 0.39
27 10 0.43
ACGTcount: A:0.04, C:0.08, G:0.10, T:0.78
Consensus pattern (26 bp):
TTTCTATCTTTTGTGTTTTGTTTTTC
Found at i:1042264 original size:16 final size:16
Alignment explanation
Indices: 1042230--1042263 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1042220 GAAACCAAAA
*
1042230 TTTGGATTTTGATTCT
1 TTTGAATTTTGATTCT
1042246 TTTGAATTTTGATT-T
1 TTTGAATTTTGATTCT
1042261 TTT
1 TTT
1042264 TTTATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.15, C:0.03, G:0.15, T:0.68
Consensus pattern (16 bp):
TTTGAATTTTGATTCT
Found at i:1044935 original size:31 final size:30
Alignment explanation
Indices: 1044862--1045055 Score: 138
Period size: 28 Copynumber: 6.7 Consensus size: 30
1044852 TAAAATATTT
* * * *
1044862 TGTCTAAATTGAG-CCAAACA-TGTTTTCT
1 TGTCTAAATTAAGACAAAACATTTTTTTCC
* *
1044890 TGTCTAGATTAAGACAAAACATTTTTTTCT
1 TGTCTAAATTAAGACAAAACATTTTTTTCC
* * * *
1044920 TATTTTAAATTAAGAC-ATACATGTTTTTCC
1 T-GTCTAAATTAAGACAAAACATTTTTTTCC
* *
1044950 TGTCTAAATTAAGAAAAAACAAGTTTTTT--
1 TGTCTAAATTAAGACAAAAC-ATTTTTTTCC
* *
1044979 TGTCTAAATTAAGA-AAAA-A-TGTTTTCA
1 TGTCTAAATTAAGACAAAACATTTTTTTCC
* * *
1045006 TGTCTAAATTAAGA-TAAACA-TGTTTTCA
1 TGTCTAAATTAAGACAAAACATTTTTTTCC
*
1045034 TGTCTAAATAAAGACAAAACAT
1 TGTCTAAATTAAGACAAAACAT
1045056 GTCTAAATTA
Statistics
Matches: 136, Mismatches: 20, Indels: 18
0.78 0.11 0.10
Matches are distributed among these distances:
25 5 0.04
26 1 0.01
27 17 0.12
28 37 0.27
29 36 0.26
30 23 0.17
31 17 0.12
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (30 bp):
TGTCTAAATTAAGACAAAACATTTTTTTCC
Found at i:1044958 original size:29 final size:28
Alignment explanation
Indices: 1044861--1045057 Score: 189
Period size: 29 Copynumber: 6.9 Consensus size: 28
1044851 ATAAAATATT
* *
1044861 TTGTCTAAATTGAGCCAAACATGTTTTC
1 TTGTCTAAATTAAGACAAACATGTTTTC
* *
1044889 TTGTCTAGATTAAGACAAAACATTTTTTTC
1 TTGTCTAAATTAAGAC-AAACA-TGTTTTC
* * *
1044919 TTATTTTAAATTAAGACATACATGTTTTTC
1 TT-GTCTAAATTAAGACAAACATG-TTTTC
* * * *
1044949 CTGTCTAAATTAAGAAAAAACAAGTTTTT
1 TTGTCTAAATTAAG-ACAAACATGTTTTC
*
1044978 TTGTCTAAATTAAGA-AAAAATGTTTTC
1 TTGTCTAAATTAAGACAAACATGTTTTC
* *
1045005 ATGTCTAAATTAAGATAAACATGTTTTC
1 TTGTCTAAATTAAGACAAACATGTTTTC
* *
1045033 ATGTCTAAATAAAGACAAAACATGT
1 TTGTCTAAATTAAGAC-AAACATGT
1045058 CTAAATTAAG
Statistics
Matches: 138, Mismatches: 24, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
27 23 0.17
28 39 0.28
29 41 0.30
30 24 0.17
31 11 0.08
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (28 bp):
TTGTCTAAATTAAGACAAACATGTTTTC
Done.