Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 165 of 255
Found at i:54064624 original size:141 final size:141
Alignment explanation
Indices: 54064453--54064742 Score: 472
Period size: 141 Copynumber: 2.1 Consensus size: 141
54064443 GTCTAGGATA
* **
54064453 TGGCATTGGCCTCGATATAAGAGAGACAGTGTAAGACCATGTCTGGGACATGGCATCGACTCGAT
1 TGGCATCGGCCTCGATATAAGAGAGACAGTGTAAGACCATGTCTAAGACATGGCATCGACTCGAT
*
54064518 ATGTGATTAAATGTAAGACAAAGTCTGGGACATTGGCATTGTATTGTGATTTCGTGTAAGACCCT
66 ATGTGATTAAATGTAAGACAAAGTCTGGGACATTGGCATTGTATTGTGATTTCATGTAAGACCCT
54064583 GTGTCGGACAG
131 GTGTCGGACAG
* * *
54064594 TGGCATCGGCCTTGATATAAGAGAGTCAGTGTAAGACCATGTCTAAGACATGGCATCGACTCGGT
1 TGGCATCGGCCTCGATATAAGAGAGACAGTGTAAGACCATGTCTAAGACATGGCATCGACTCGAT
* * * *
54064659 ATGTGATTAAATGTAATACCATGTCTGGGACATTTGCATTGTATTGTGATTTCATGTAAGACCCT
66 ATGTGATTAAATGTAAGACAAAGTCTGGGACATTGGCATTGTATTGTGATTTCATGTAAGACCCT
*
54064724 GTGTGGGACAG
131 GTGTCGGACAG
54064735 TGGCATCG
1 TGGCATCG
54064743 ATATCTGATA
Statistics
Matches: 137, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
141 137 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (141 bp):
TGGCATCGGCCTCGATATAAGAGAGACAGTGTAAGACCATGTCTAAGACATGGCATCGACTCGAT
ATGTGATTAAATGTAAGACAAAGTCTGGGACATTGGCATTGTATTGTGATTTCATGTAAGACCCT
GTGTCGGACAG
Found at i:54064691 original size:47 final size:47
Alignment explanation
Indices: 54064482--54064691 Score: 169
Period size: 47 Copynumber: 4.5 Consensus size: 47
54064472 AGAGAGACAG
54064482 TGTAAGACCATGTCTGGGACATGGCATCGACTCGATATGTGATTAAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACTCGATATGTGATTAAA
* * * ***
54064529 TGTAAGACAAAGTCTGGGACATTGGCATTG--T--AT-TGTGATTTCG
1 TGTAAGACCATGTCTGGGACA-TGGCATCGACTCGATATGTGATTAAA
* * * * * * * * *
54064572 TGTAAGACCCTGTGTCGGACAGTGGCATCGGCCTTGATATAAGAGAGTCAG
1 TGTAAGACCATGTCTGGGACA-TGGCATC-GACTCGATAT--GTGATTAAA
** *
54064623 TGTAAGACCATGTCTAAGACATGGCATCGACTCGGTATGTGATTAAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACTCGATATGTGATTAAA
*
54064670 TGTAATACCATGTCTGGGACAT
1 TGTAAGACCATGTCTGGGACAT
54064692 TTGCATTGTA
Statistics
Matches: 123, Mismatches: 31, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
43 29 0.24
44 3 0.02
46 2 0.02
47 43 0.35
48 9 0.07
49 8 0.07
50 7 0.06
51 22 0.18
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (47 bp):
TGTAAGACCATGTCTGGGACATGGCATCGACTCGATATGTGATTAAA
Found at i:54092327 original size:50 final size:50
Alignment explanation
Indices: 54092259--54092387 Score: 156
Period size: 49 Copynumber: 2.6 Consensus size: 50
54092249 TGTGTCAGTA
* * *
54092259 TAAGACCATGTCTAGGACATGGCATCGGCACGGATATGT-GAGAG-CTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCACGCA-ATGTCGAGAGTC-AATG
* * * *
54092309 TAAGACCATGTCTGGGACATGGCATCAGC-CTCAATTTCGATAGTCAATG
1 TAAGACCATGTCTGGGACATGGCATCGGCACGCAATGTCGAGAGTCAATG
54092358 TAAGACCATGTCTGGGACATGGCATCGGCA
1 TAAGACCATGTCTGGGACATGGCATCGGCA
54092388 TTATACCCTA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
48 3 0.04
49 37 0.54
50 28 0.41
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATCGGCACGCAATGTCGAGAGTCAATG
Found at i:54095833 original size:15 final size:15
Alignment explanation
Indices: 54095813--54095847 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
54095803 CCGTGTGTCG
54095813 CACACGGCTGAGACA
1 CACACGGCTGAGACA
*
54095828 CACACGGTTGAGACA
1 CACACGGCTGAGACA
54095843 CACAC
1 CACAC
54095848 CCGTGTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.34, C:0.34, G:0.23, T:0.09
Consensus pattern (15 bp):
CACACGGCTGAGACA
Found at i:54096846 original size:23 final size:21
Alignment explanation
Indices: 54096750--54096847 Score: 79
Period size: 23 Copynumber: 4.3 Consensus size: 21
54096740 TAATAAACAA
*
54096750 TAAGCTCTATTGAGCTGAATAG
1 TAAGCTCTA-TGAGCTAAATAG
*
54096772 TAAGCTCTATCGAGCTAAATCGG
1 TAAGCTCTAT-GAGCTAAAT-AG
* *
54096795 TAAGCCCCAATGAGCTAAAATAG
1 TAAG-CTCTATGAGCT-AAATAG
* *
54096818 TAAGCTCTTATGAGCTGAATCGG
1 TAAGCTC-TATGAGCTAAAT-AG
54096841 TAAGCTC
1 TAAGCTC
54096848 ATACCAGCTA
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
21 1 0.02
22 22 0.36
23 30 0.49
24 8 0.13
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (21 bp):
TAAGCTCTATGAGCTAAATAG
Found at i:54103546 original size:40 final size:40
Alignment explanation
Indices: 54103491--54103695 Score: 272
Period size: 40 Copynumber: 5.2 Consensus size: 40
54103481 CGGATGATAA
*
54103491 CGAAGGCATTTGTGCTAGTTACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
* *
54103531 CGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* *
54103571 CGAAGGCATTTGTGGGAGTTACTCTATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * *
54103611 CGAAGGCATTGGTGCGAGATACTATATCCGGGCTAAGCCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * *
54103651 CGAAGGCATTTGAGCGAG-TAGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCC
54103690 CGAAGG
1 CGAAGG
54103696 TACTTGGTTT
Statistics
Matches: 148, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 15 0.10
40 132 0.89
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:54106645 original size:22 final size:22
Alignment explanation
Indices: 54106618--54106739 Score: 79
Period size: 22 Copynumber: 5.3 Consensus size: 22
54106608 CATGCATATG
54106618 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * * *
54106640 TGTGATGAATG-TGAACGTGCAAATA
1 TGTGAT-AAGGCCGAATG-GC-CA-A
54106665 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
54106687 TGTGATGAATG-TGAACAT-GCAAATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
54106712 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
54106734 TGTGAT
1 TGTGAT
54106740 GAATGTGAAC
Statistics
Matches: 74, Mismatches: 14, Indels: 24
0.66 0.12 0.21
Matches are distributed among these distances:
22 25 0.34
23 15 0.20
24 15 0.20
25 19 0.26
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.24
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:54106647 original size:47 final size:47
Alignment explanation
Indices: 54106596--54106789 Score: 325
Period size: 47 Copynumber: 4.1 Consensus size: 47
54106586 GATTCTATGA
* *
54106596 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
*
54106643 GATGAATGTGAACGTGCAAATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
54106690 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
* * **
54106737 GATGAATGTGAACATGCATATATGTGATAGGGTAGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
54106784 GATGAA
1 GATGAA
54106790 CGTGGAAGCG
Statistics
Matches: 139, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 139 1.00
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.25
Consensus pattern (47 bp):
GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
Found at i:54115561 original size:40 final size:40
Alignment explanation
Indices: 54115506--54115774 Score: 416
Period size: 40 Copynumber: 6.7 Consensus size: 40
54115496 CGGATGATAA
* *
54115506 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
* *
54115546 CGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
54115586 CGAAGGCATTTGTGTGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
54115626 CAAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
54115666 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * *
54115706 CGAAGGCATTGGTGCGAGCTACTATATCCGGGCTAAGCCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
54115746 CGAAGGCATTTGAGCGAG-TAGCTATATCC
1 CGAAGGCATTTGTGCGAGTTA-CTATATCC
54115775 AGTTAAATCT
Statistics
Matches: 216, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
39 2 0.01
40 213 0.99
41 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:54120474 original size:24 final size:23
Alignment explanation
Indices: 54120447--54120522 Score: 84
Period size: 24 Copynumber: 3.3 Consensus size: 23
54120437 TGATAAACAA
54120447 TAAGCTCTATTGAGCAGAAAACGG
1 TAAGCTCTATTGAGC-GAAAACGG
*
54120471 TAAGCTCTATTGAGCTGAATA--G
1 TAAGCTCTATTGAGC-GAAAACGG
* * *
54120493 TAAGCTCTATCGAGCTAAATCGG
1 TAAGCTCTATTGAGCGAAAACGG
54120516 TAAGCTC
1 TAAGCTC
54120523 CAATGAGCTG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.05
22 15 0.34
23 8 0.18
24 19 0.43
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (23 bp):
TAAGCTCTATTGAGCGAAAACGG
Found at i:54120502 original size:46 final size:46
Alignment explanation
Indices: 54120447--54120543 Score: 133
Period size: 46 Copynumber: 2.1 Consensus size: 46
54120437 TGATAAACAA
* * *
54120447 TAAGCTCTATTGAGCAGAAAACGGTAAGCTCTATTGAGCTG-AATAG
1 TAAGCTCTATCGAGC-GAAAACGGTAAGCTCCAATGAGCTGAAATAG
* *
54120493 TAAGCTCTATCGAGCTAAATCGGTAAGCTCCAATGAGCTGAAATAG
1 TAAGCTCTATCGAGCGAAAACGGTAAGCTCCAATGAGCTGAAATAG
54120539 TAAGC
1 TAAGC
54120544 ACTCATGAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
45 21 0.47
46 24 0.53
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (46 bp):
TAAGCTCTATCGAGCGAAAACGGTAAGCTCCAATGAGCTGAAATAG
Found at i:54120530 original size:23 final size:23
Alignment explanation
Indices: 54120468--54120567 Score: 64
Period size: 23 Copynumber: 4.4 Consensus size: 23
54120458 GAGCAGAAAA
* * *
54120468 CGGTAAGCTCTATTGAGCTGAAT
1 CGGTAAGCTCCAATGAGCTAAAT
* *
54120491 -AGTAAGCT-CTATCGAGCTAAAT
1 CGGTAAGCTCCAAT-GAGCTAAAT
54120513 CGGTAAGCTCCAATGAGCTGAAAT
1 CGGTAAGCTCCAATGAGCT-AAAT
* * * *
54120537 -AGTAAGCACTC-ATGAGTTGAAT
1 CGGTAAGCTC-CAATGAGCTAAAT
54120559 CGGTAAGCT
1 CGGTAAGCT
54120568 AATACGAGTT
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
21 1 0.02
22 18 0.31
23 31 0.53
24 8 0.14
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (23 bp):
CGGTAAGCTCCAATGAGCTAAAT
Found at i:54120560 original size:46 final size:45
Alignment explanation
Indices: 54120468--54120567 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 45
54120458 GAGCAGAAAA
* * *
54120468 CGGTAAGCTCTATTGAGCTGAATAGTAAGCTCTATCGAGCTAAAT
1 CGGTAAGCTCCAATGAGCTGAATAGTAAGCACTATCGAGCTAAAT
* *
54120513 CGGTAAGCTCCAATGAGCTGAAATAGTAAGCACTCAT-GAGTTGAAT
1 CGGTAAGCTCCAATGAGCTG-AATAGTAAGCACT-ATCGAGCTAAAT
54120559 CGGTAAGCT
1 CGGTAAGCT
54120568 AATACGAGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 18 0.38
46 28 0.58
47 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (45 bp):
CGGTAAGCTCCAATGAGCTGAATAGTAAGCACTATCGAGCTAAAT
Found at i:54124070 original size:47 final size:47
Alignment explanation
Indices: 54123960--54124229 Score: 134
Period size: 46 Copynumber: 5.7 Consensus size: 47
54123950 ATTTGTGTGA
*
54123960 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAGATTATGAGAT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAGATGATGAGAT
54124007 -CTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGA-GACT-AG-T
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA--GATGA-TGAGAT
* ** * * * *
54124054 GCTAGTGTAAGACATGTTTGGGGTATGCATCAGCCTCG-GGACGTA-A-
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-AGATGATG-AGAT
* * * * * * *
54124100 GCCAGTTTAAGACATGTCTGGAACATGCATCGACTACAAGAT--G-T
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAGATGATGAGAT
* * * * *
54124144 GTTAGTGTAAAACCATGTCTGGGGCATGGCATCGACAAGGTTATG-TGAGA-
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA-G--ATGATGAGAT
*
54124194 GCTAGTGTAAGGCCATGTCTGGGACATGGCATCGGC
1 GCTAGTGTAA-GACATGTCTGGGACAT-GCATCGGC
54124230 ACTTTACCCA
Statistics
Matches: 165, Mismatches: 34, Indels: 45
0.68 0.14 0.18
Matches are distributed among these distances:
44 8 0.05
45 12 0.07
46 57 0.35
47 30 0.18
48 22 0.13
49 5 0.03
50 31 0.19
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.25
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAGATGATGAGAT
Found at i:54133850 original size:41 final size:41
Alignment explanation
Indices: 54133789--54133979 Score: 235
Period size: 41 Copynumber: 4.7 Consensus size: 41
54133779 CTATCTTAAA
*
54133789 TCGCACACTAAGTGCCATATATAGCTGAAGCTATCTTGATC
1 TCGCACACTAAGTGCCATATATAGCTGAAGCTATCTCGATC
* * *
54133830 TCGTAAACTAAGTGCCATATATAGCCT-AAACTATCTCGATC
1 TCGCACACTAAGTGCCATATATAG-CTGAAGCTATCTCGATC
* * * *
54133871 TTGCACACTAAGTGCTATATATAGCCGAAGCTATGTCGATC
1 TCGCACACTAAGTGCCATATATAGCTGAAGCTATCTCGATC
* *
54133912 TCGCACACTAAGTGCCATATATAG-TCGAAGCTATGTCGA-A
1 TCGCACACTAAGTGCCATATATAGCT-GAAGCTATCTCGATC
* *
54133952 TCGCACACTAAGTGCCACATGTAGCTGA
1 TCGCACACTAAGTGCCATATATAGCTGA
54133980 TTTGTCATCG
Statistics
Matches: 129, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
40 25 0.19
41 102 0.79
42 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (41 bp):
TCGCACACTAAGTGCCATATATAGCTGAAGCTATCTCGATC
Found at i:54133901 original size:82 final size:81
Alignment explanation
Indices: 54133746--54133968 Score: 252
Period size: 82 Copynumber: 2.7 Consensus size: 81
54133736 AATACTCGAC
* * ** * **
54133746 ATCTCACACACTAAGTGCTGTACATAGCC-AAAGCTATCTTAAATCGCACACTAAGTGCCATATA
1 ATCTCGCAAACTAAGTGCCATATATAGCCGAAA-CTATCTCGAATCGCACACTAAGTGCCATATA
* *
54133810 TAGCTGAAGCTATCTTG
65 TAGCCGAAGCTATCTCG
* * *
54133827 ATCTCGTAAACTAAGTGCCATATATAGCCTAAACTATCTCG-ATCTTGCACACTAAGTGCTATAT
1 ATCTCGCAAACTAAGTGCCATATATAGCCGAAACTATCTCGAATC--GCACACTAAGTGCCATAT
*
54133891 ATAGCCGAAGCTATGTCG
64 ATAGCCGAAGCTATCTCG
* * * *
54133909 ATCTCGCACACTAAGTGCCATATATAGTCGAAGCTATGTCGAATCGCACACTAAGTGCCA
1 ATCTCGCAAACTAAGTGCCATATATAGCCGAAACTATCTCGAATCGCACACTAAGTGCCA
54133969 CATGTAGCTG
Statistics
Matches: 119, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
80 3 0.03
81 43 0.36
82 70 0.59
83 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (81 bp):
ATCTCGCAAACTAAGTGCCATATATAGCCGAAACTATCTCGAATCGCACACTAAGTGCCATATAT
AGCCGAAGCTATCTCG
Found at i:54134314 original size:8 final size:9
Alignment explanation
Indices: 54134294--54134319 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
54134284 TTATTAACTA
54134294 TTTTACCAT
1 TTTTACCAT
54134303 TTTTACCAT
1 TTTTACCAT
54134312 TTTTACCA
1 TTTTACCA
54134320 CTTGCCAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (9 bp):
TTTTACCAT
Found at i:54135897 original size:19 final size:19
Alignment explanation
Indices: 54135875--54135913 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54135865 TATAAATCAC
54135875 ATCAATGATCATAAT-TTAA
1 ATCAATGATCA-AATATTAA
*
54135894 ATCAATTATCAAATATTAA
1 ATCAATGATCAAATATTAA
54135913 A
1 A
54135914 ATCATATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (19 bp):
ATCAATGATCAAATATTAA
Found at i:54140715 original size:43 final size:43
Alignment explanation
Indices: 54140630--54140711 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
54140620 ATATAGTACA
* *
54140630 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGCAATCACATATCG
* *
54140673 ATGCCACTGTCCCAGACATGGTCTTACTTGC-A-CACATAT
1 ATGCCAATGTCCCAGACATGGTCTTACATGCAATCACATAT
54140712 ATCGGAGTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 7 0.20
42 1 0.03
43 27 0.77
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGCAATCACATATCG
Found at i:54140749 original size:56 final size:56
Alignment explanation
Indices: 54140663--54140769 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 56
54140653 TTACATGTAA
* * * * *
54140663 TCACATATCGATGCCACTGTCCCAGACATGGTCTTACTTGCACACATATATCGGAG
1 TCACATATCGATGCCAATGTACAAAACATGGTCTTACTCGCACACATATATCGGAG
*
54140719 TCACATATCGATGCCAATGTATAAAACATGGTCTTACTCGCACACATATAT
1 TCACATATCGATGCCAATGTACAAAACATGGTCTTACTCGCACACATATAT
54140770 TGATGCCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (56 bp):
TCACATATCGATGCCAATGTACAAAACATGGTCTTACTCGCACACATATATCGGAG
Found at i:54142579 original size:25 final size:26
Alignment explanation
Indices: 54142544--54142598 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
54142534 CGTGGATTTA
* *
54142544 ATTTGCCTTTTCAACCGAAACGAAGT
1 ATTTGCCTTTTCAACCAAAACAAAGT
54142570 ATTT-CCTTTTCAACCAAAACAAAGT
1 ATTTGCCTTTTCAACCAAAACAAAGT
54142595 ATTT
1 ATTT
54142599 TCTTCCATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (26 bp):
ATTTGCCTTTTCAACCAAAACAAAGT
Found at i:54161337 original size:27 final size:27
Alignment explanation
Indices: 54161306--54161481 Score: 201
Period size: 27 Copynumber: 6.5 Consensus size: 27
54161296 TAAATTGTAC
54161306 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
54161333 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54161359 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
54161387 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
54161415 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54161442 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54161469 AGCACTGAGTGTG
1 AGCACTAAGTGTG
54161482 TGGACTCAAT
Statistics
Matches: 127, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:54161420 original size:82 final size:81
Alignment explanation
Indices: 54161307--54161462 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54161297 AAATTGTACA
* *
54161307 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
54161371 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
54161388 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
54161453 TGCGAGTTGA
65 TGCGAATTGA
54161463 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:54161474 original size:82 final size:81
Alignment explanation
Indices: 54161303--54161481 Score: 225
Period size: 82 Copynumber: 2.2 Consensus size: 81
54161293 GATTAAATTG
* *
54161303 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
54161368 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
54161384 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
54161448 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
54161466 TATAGCACTGAGTGTG
1 TACAGCACTAAGTGTG
54161482 TGGACTCAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.22
82 64 0.78
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:54164167 original size:55 final size:55
Alignment explanation
Indices: 54164080--54164230 Score: 234
Period size: 55 Copynumber: 2.8 Consensus size: 55
54164070 TAAATTGTGC
*
54164080 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGA-TATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
54164134 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
* * * *
54164190 AGCACTAGGTGTGCGAGCTGATTATATAGCACT-AGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
54164231 CACTTAATAT
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
54 24 0.27
55 45 0.50
56 21 0.23
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:54164169 original size:28 final size:28
Alignment explanation
Indices: 54164080--54164230 Score: 220
Period size: 27 Copynumber: 5.5 Consensus size: 28
54164070 TAAATTGTGC
*
54164080 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
54164107 AGCACTAAGTGTGCGAGTTTGA-TATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
54164134 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
54164162 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* * * *
54164190 AGCACTAGGTGTGCGAG-CTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
54164217 AGCACT-AGTGTGCG
1 AGCACTAAGTGTGCG
54164231 CACTTAATAT
Statistics
Matches: 116, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
26 7 0.06
27 57 0.49
28 52 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:54167067 original size:43 final size:43
Alignment explanation
Indices: 54167020--54167171 Score: 163
Period size: 43 Copynumber: 3.6 Consensus size: 43
54167010 GTTCTCATGA
*
54167020 AAGACCACGTCTAGGA-AGTTGGCATCGATATGTGATTATGTGT
1 AAGACCACGTCTAGGACAGTTGGCATCGATATGTGATT-CGTGT
* * * * *
54167063 AAGACCATGTCTGGGACA-TTGGCATCG-TATTTAATTCGTAT
1 AAGACCACGTCTAGGACAGTTGGCATCGATATGTGATTCGTGT
* *
54167104 AAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGATTGCATGT
1 AAGACCAC-GTCTAGGACAGTTGGCATCGATATGTGATT-CGTGT
54167147 AAGACCACGTCTAGGAC-GTTGGCAT
1 AAGACCACGTCTAGGACAGTTGGCAT
54167172 TGTATGATAT
Statistics
Matches: 90, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
41 27 0.30
42 15 0.17
43 46 0.51
44 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (43 bp):
AAGACCACGTCTAGGACAGTTGGCATCGATATGTGATTCGTGT
Found at i:54174802 original size:41 final size:41
Alignment explanation
Indices: 54174599--54174821 Score: 285
Period size: 41 Copynumber: 5.5 Consensus size: 41
54174589 AAAACTCGAT
* * * *
54174599 ATCTCACACACTAAGTGTCGTACATAGCCGAAGCTATCTC-
1 ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCG
*
54174639 A-CATCGCACACTAAGTGCCATATATAGCCGAAGCTATCTTG
1 ATC-TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCG
* * *
54174680 ATCTCACACACTAAGTGCCATATATAGCTGAAGCTATCTTG
1 ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCG
* *
54174721 ATCTCG-AGCACTAAGTGCCATATATAGCCGAAGCTCTGTCG
1 ATCTCGCA-CACTAAGTGCCATATATAGCCGAAGCTATCTCG
*
54174762 ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTATGTCGG
1 ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTC-G
54174804 A--TCGCACACTAAGTGCCA
1 ATCTCGCACACTAAGTGCCA
54174822 CATGTAGCTG
Statistics
Matches: 164, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
39 1 0.01
40 51 0.31
41 108 0.66
42 4 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (41 bp):
ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCG
Found at i:54176710 original size:21 final size:21
Alignment explanation
Indices: 54176670--54176710 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54176660 ATTGTTGAGA
* *
54176670 AGGAAGTTGCTATTGCAGAAG
1 AGGAAGTTGCTACTGAAGAAG
*
54176691 AGGAAGTTGTTACTGAAGAA
1 AGGAAGTTGCTACTGAAGAA
54176711 AAAGTTGTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.32, T:0.24
Consensus pattern (21 bp):
AGGAAGTTGCTACTGAAGAAG
Found at i:54179618 original size:27 final size:27
Alignment explanation
Indices: 54179584--54179734 Score: 160
Period size: 27 Copynumber: 5.6 Consensus size: 27
54179574 TAAATTGTAC
* *
54179584 AGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
54179610 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
54179638 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
54179666 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
54179693 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
54179720 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54179735 GACTCAATAT
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 84 0.78
28 23 0.21
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:54179681 original size:55 final size:54
Alignment explanation
Indices: 54179583--54179734 Score: 171
Period size: 55 Copynumber: 2.8 Consensus size: 54
54179573 TTAAATTGTA
** *
54179583 CAGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTGCGAATTGACCATG
1 CAGCACTAAGTGTGCGAGTTGAATATGTA-GCACTAAGTGTGCGAATTGACCACG
* * * **
54179637 CGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG
1 CAGCACTAAGTGTGCGAG-TTGAATATGTAGCACTAAGTGTGCGAATTGACCACG
* * * *
54179692 TAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 CAGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
54179735 GACTCAATAT
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 38 0.46
55 44 0.53
56 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (54 bp):
CAGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAATTGACCACG
Found at i:54179725 original size:82 final size:82
Alignment explanation
Indices: 54179584--54179734 Score: 187
Period size: 82 Copynumber: 1.8 Consensus size: 82
54179574 TAAATTGTAC
* * *
54179584 AGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTG
1 AGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGTGCGAATTGACCATACAGCACTAAGTG
54179649 TGCGAGTTTGACTATGT
66 TGCGAGTTTGACTATGT
** * * ** * *
54179666 AGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGT
1 AGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGTGTGCGAATTGACCATACAGCACTAAGT
54179730 GTGCG
65 GTGCG
54179735 GACTCAATAT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
81 1 0.02
82 56 0.98
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (82 bp):
AGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGTGCGAATTGACCATACAGCACTAAGTG
TGCGAGTTTGACTATGT
Found at i:54195714 original size:31 final size:31
Alignment explanation
Indices: 54195676--54195744 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 31
54195666 TACTAAGCCA
54195676 AAGCCTTTTCATAAATCAAATCACTGGGCCG
1 AAGCCTTTTCATAAATCAAATCACTGGGCCG
* *
54195707 AAGCC-TTTCATAAATCATATCACTGTGCCG
1 AAGCCTTTTCATAAATCAAATCACTGGGCCG
54195737 AAGCCTTT
1 AAGCCTTT
54195745 ATTATAAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 28 0.80
31 7 0.20
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (31 bp):
AAGCCTTTTCATAAATCAAATCACTGGGCCG
Found at i:54195828 original size:42 final size:42
Alignment explanation
Indices: 54195768--54195858 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
54195758 TGGCCCATAG
*
54195768 GCCCATTTCAATAACACATGAAATATCAATGAATGTATGCAA
1 GCCCATTTCAATAACACATGAAATACCAATGAATGTATGCAA
*
54195810 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATAACACATGAAATACCAATGAATGTATGCAA
54195852 GCCCATT
1 GCCCATT
54195859 CGGGGAGACT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (42 bp):
GCCCATTTCAATAACACATGAAATACCAATGAATGTATGCAA
Found at i:54196075 original size:26 final size:26
Alignment explanation
Indices: 54196004--54196126 Score: 196
Period size: 26 Copynumber: 4.8 Consensus size: 26
54195994 CCTCTTTAAT
**
54196004 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
54196029 AACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
**
54196054 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
54196080 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
54196106 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
54196127 GCACTTCCTC
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 33 0.36
26 58 0.64
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:54196115 original size:52 final size:51
Alignment explanation
Indices: 54196004--54196126 Score: 230
Period size: 52 Copynumber: 2.4 Consensus size: 51
54195994 CCTCTTTAAT
54196004 AACTGGGGCA-AAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATA
54196054 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCA-AAGCCCTTTTCAATA
54196106 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
54196127 GCACTTCCTC
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
50 10 0.14
51 25 0.35
52 36 0.51
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (51 bp):
AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATA
Found at i:54196201 original size:20 final size:20
Alignment explanation
Indices: 54196176--54196250 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
54196166 TTATGAATTC
* *
54196176 ATCATGTGGATCTCATACAT
1 ATCATGTGCATATCATACAT
54196196 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
54196216 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
54196236 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
54196251 TCCCACGTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
18 8 0.15
20 42 0.81
21 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:54196207 original size:11 final size:11
Alignment explanation
Indices: 54196193--54196231 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
54196183 GGATCTCATA
54196193 CATATCATGTG
1 CATATCATGTG
*
54196204 CATATCA--TA
1 CATATCATGTG
54196213 CATATCATGTG
1 CATATCATGTG
54196224 CATATCAT
1 CATATCAT
54196232 ATCAATCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 8 0.33
11 16 0.67
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (11 bp):
CATATCATGTG
Found at i:54196248 original size:9 final size:10
Alignment explanation
Indices: 54196193--54196249 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
54196183 GGATCTCATA
54196193 CATATCATGT
1 CATATCATGT
*
54196203 GCATATCAT-A
1 -CATATCATGT
54196213 CATATCATGT
1 CATATCATGT
*
54196223 GCATATCATAT
1 -CATATCATGT
54196234 CA-ATCATGT
1 CATATCATGT
54196243 -ATATCAT
1 CATATCAT
54196250 ATCCCACGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 19 0.49
10 2 0.05
11 17 0.44
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (10 bp):
CATATCATGT
Found at i:54196979 original size:27 final size:27
Alignment explanation
Indices: 54196949--54197029 Score: 112
Period size: 27 Copynumber: 3.0 Consensus size: 27
54196939 GGGCATATTC
*
54196949 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACCATACAGGGGCT-TTACG
*
54196976 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCATACAGGGGCTTTACG
54197003 GTCACTTTACCCA-ACAGGGGCTTTACG
1 GTCACTTTA-CCATACAGGGGCTTTACG
54197030 ATCTTTTTAC
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
27 46 0.94
28 3 0.06
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (27 bp):
GTCACTTTACCATACAGGGGCTTTACG
Found at i:54197197 original size:27 final size:27
Alignment explanation
Indices: 54197181--54197309 Score: 161
Period size: 27 Copynumber: 4.8 Consensus size: 27
54197171 CTTTGTAAAT
54197181 TAGGGGTATTTTGGTAATTTTACAAA-
1 TAGGGGTATTTTGGTAATTTTACAAAC
* * *
54197207 TTGAGGGTATTTCGGTAATTTCACAAAC
1 TAG-GGGTATTTTGGTAATTTTACAAAC
* *
54197235 CAAGGGTATTTTGGTAATTTTACAAAC
1 TAGGGGTATTTTGGTAATTTTACAAAC
54197262 TAGGGGTATTTTGGTAATTTTACAAAC
1 TAGGGGTATTTTGGTAATTTTACAAAC
* * **
54197289 CAAGGGTATTTAAGTAATTTT
1 TAGGGGTATTTTGGTAATTTT
54197310 GTAAATCGAG
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
26 2 0.02
27 85 0.98
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
TAGGGGTATTTTGGTAATTTTACAAAC
Found at i:54197242 original size:54 final size:54
Alignment explanation
Indices: 54197184--54197323 Score: 192
Period size: 54 Copynumber: 2.6 Consensus size: 54
54197174 TGTAAATTAG
54197184 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
* * *
54197238 GGGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATTGA-GGGTATTTCGGTAATTTCACAAACCAA
** ** *
54197292 GGGTATTTAAGTAATTTTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTA
54197324 AAACAGTAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 73 0.97
55 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
Found at i:54197295 original size:81 final size:81
Alignment explanation
Indices: 54197154--54197308 Score: 213
Period size: 81 Copynumber: 1.9 Consensus size: 81
54197144 TTTATAAAGT
** * ***
54197154 CAAGGGTATTTCTGTAACTTTGTAAATTAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTT
1 CAAGGGTATTTCTGTAACTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
**
54197219 CGGTAATTTCACAAAC
66 AAGTAATTTCACAAAC
*
54197235 CAAGGGTATTT-TGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATT
1 CAAGGGTATTTCT-GTAACTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATT
54197299 TAAGTAATTT
65 TAAGTAATTT
54197309 TGTAAATCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
80 1 0.02
81 63 0.98
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (81 bp):
CAAGGGTATTTCTGTAACTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
AAGTAATTTCACAAAC
Found at i:54197333 original size:54 final size:54
Alignment explanation
Indices: 54197275--54197498 Score: 157
Period size: 54 Copynumber: 4.1 Consensus size: 54
54197265 GGGTATTTTG
* ** * *
54197275 GTAATTTTACAAACCAAGGGT-ATTTAAGTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTACAAACCAAGGGTAAAAT-AGTAATTCTATAAATCGAGGGTAAAACA
** * *
54197329 GTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
** * * ** * *
54197383 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAAC-
1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
* ** * * ** * * *
54197436 GATAATTATGTAAATCGAGGGTAAAACGGTAATTATGTAAATC-AGGGGTAAAACG
1 G-TAATTCTACAAACCAAGGGTAAAATAGTAATTCTATAAATCGA-GGGTAAAACA
54197491 GTAATTCT
1 GTAATTCT
54197499 GTAAATCGGG
Statistics
Matches: 148, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
53 2 0.01
54 143 0.97
55 3 0.02
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (54 bp):
GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
Found at i:54197350 original size:81 final size:80
Alignment explanation
Indices: 54197265--54197567 Score: 241
Period size: 81 Copynumber: 3.7 Consensus size: 80
54197255 TACAAACTAG
* * *
54197265 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTAA-GTAATTTTGTAAATCGAGGGTAAAACA
1 GGGTAATTTGGTAATTTTACAAATCAAGGGTA--AAACGTAATTTTGTAAATCGAGGGTAAAACA
54197329 GTAATTCTGTAAATCAA
64 GTAATTCTGTAAATCAA
** * * * * * *
54197346 GGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGG
1 GGGTAATTTGGTAATTTTACAAATCAAGGGTAAAAC-GTAATTTTGTAAATCGAGGGTAAAACAG
* *
54197411 TAATTCTGTAAGTCGA
65 TAATTCTGTAAATCAA
*** * * ** * * *
54197427 GGGTAAAACGATAATTATGTAAATCGAGGGTAAAACGGTAATTATGTAAATC-AGGGGTAAAACG
1 GGGTAATTTGGTAATTTTACAAATCAAGGGTAAAAC-GTAATTTTGTAAATCGA-GGGTAAAACA
**
54197491 GTAATTCTGTAAATCGG
64 GTAATTCTGTAAATCAA
* * * *** **
54197508 GGGTACTTTGGTAATTTTACAAGTCAAAGGTATTTCGGTAATTTTACAAATCGAGGGTAA
1 GGGTAATTTGGTAATTTTACAAATCAAGGGTAAAAC-GTAATTTTGTAAATCGAGGGTAA
54197568 TTCAGTATTT
Statistics
Matches: 180, Mismatches: 38, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
79 2 0.01
80 1 0.01
81 176 0.98
82 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.30
Consensus pattern (80 bp):
GGGTAATTTGGTAATTTTACAAATCAAGGGTAAAACGTAATTTTGTAAATCGAGGGTAAAACAGT
AATTCTGTAAATCAA
Found at i:54197523 original size:27 final size:27
Alignment explanation
Indices: 54197302--54197512 Score: 307
Period size: 27 Copynumber: 7.8 Consensus size: 27
54197292 GGGTATTTAA
* *
54197302 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
54197329 GTAATTCTGTAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
54197356 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
54197383 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
54197410 GTAATTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
54197437 ATAATTATGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
54197464 GTAATTATGTAAATC-AGGGGTAAAACG
1 GTAATTCTGTAAATCGA-GGGTAAAACG
*
54197491 GTAATTCTGTAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
54197513 CTTTGGTAAT
Statistics
Matches: 167, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
26 1 0.01
27 166 0.99
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:54197566 original size:27 final size:27
Alignment explanation
Indices: 54197518--54197607 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 27
54197508 GGGTACTTTG
* * *
54197518 GTAATTTTACAAGTCAAAGGTATTTCG
1 GTAATTTTACAAATCAAGGGTATTTCA
* *
54197545 GTAATTTTACAAATCGAGGGTAATTCA
1 GTAATTTTACAAATCAAGGGTATTTCA
* *
54197572 GTATTTTTACAAA-CTAAGGGTATTTTA
1 GTAATTTTACAAATC-AAGGGTATTTCA
54197599 GTAATTTTA
1 GTAATTTTA
54197608 GTAAACTAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
26 1 0.02
27 51 0.98
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAATCAAGGGTATTTCA
Found at i:54199866 original size:31 final size:31
Alignment explanation
Indices: 54199828--54199906 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
54199818 TTTAACGGTT
54199828 ACTGGGCCGAAGCCTTTTCATAAATCAAATC
1 ACTGGGCCGAAGCCTTTTCATAAATCAAATC
*
54199859 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCAAATC
*
54199890 ACTGGGTCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
54199907 ATTATAAACG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCAAATC
Found at i:54200186 original size:26 final size:26
Alignment explanation
Indices: 54200134--54200335 Score: 309
Period size: 26 Copynumber: 7.8 Consensus size: 26
54200124 CCTCTTTAAT
54200134 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* **
54200159 AACTGGGGCA-AAGCCTTTTTTCAATA
1 AACTGGGGCATAAGCC-CTTTTCGGTA
54200185 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
54200211 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* **
54200237 AACTAGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
54200263 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
**
54200289 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
54200315 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
54200336 GCACTTCCTC
Statistics
Matches: 161, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
25 15 0.09
26 141 0.88
27 5 0.03
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:54200410 original size:20 final size:20
Alignment explanation
Indices: 54200385--54200459 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
54200375 TTATGAATTC
*
54200385 ATCATGTGCATCTCATACAT
1 ATCATGTGCATATCATACAT
54200405 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54200425 ATCATGAGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
54200445 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
54200460 TCCCGCGTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 8 0.16
20 41 0.80
21 2 0.04
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:54201210 original size:27 final size:27
Alignment explanation
Indices: 54201163--54201241 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 27
54201153 TATTCATCAT
* *
54201163 TTTACCATACATGGG-TATTACGGTCAC
1 TTTACCCTACAGGGGCT-TTACGGTCAC
*
54201190 TTTACCCT-CTAGGGGCTTTACGGTCAG
1 TTTACCCTAC-AGGGGCTTTACGGTCAC
54201217 TTTACCCTACAGGGGCTTTACGGTC
1 TTTACCCTACAGGGGCTTTACGGTC
54201242 TTTTGGCCTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
26 1 0.02
27 43 0.93
28 2 0.04
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (27 bp):
TTTACCCTACAGGGGCTTTACGGTCAC
Found at i:54201333 original size:27 final size:27
Alignment explanation
Indices: 54201303--54201354 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
54201293 GTAAATCTAC
54201303 AAACAAAAGGTATTTC-AGTAATTTTGT
1 AAACAAAAGGTATTTCTA-TAATTTTGT
* *
54201330 AAACCAATGGTATTTCTATAATTTT
1 AAACAAAAGGTATTTCTATAATTTT
54201355 TATAAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (27 bp):
AAACAAAAGGTATTTCTATAATTTTGT
Found at i:54201397 original size:27 final size:27
Alignment explanation
Indices: 54201311--54201559 Score: 143
Period size: 27 Copynumber: 9.1 Consensus size: 27
54201301 ACAAACAAAA
* * *
54201311 GGTATTTCAGTAATTTTGTAAACCAAT
1 GGTATTTCTGTAATTTTGTAAATCAAG
* *
54201338 GGTATTTCTATAATTTTTATAAAGTCAAG
1 GGTATTTCTGTAA-TTTTGTAAA-TCAAG
*
54201367 GGTATTTCTGTAACTTTGTAAATCAAG
1 GGTATTTCTGTAATTTTGTAAATCAAG
** **
54201394 GGTATTT-TGGTAATTTTACAAATTGAG
1 GGTATTTCT-GTAATTTTGTAAATCAAG
*** *
54201421 GGTATTT-TGGTAATTTCACAAACCAAG
1 GGTATTTCT-GTAATTTTGTAAATCAAG
** *
54201448 GGTATTT-TGGTAATTTTACAAA-CTAGG
1 GGTATTTCT-GTAATTTTGTAAATC-AAG
** *
54201475 GGTATTT-TGGTAATTTTACAAACCAAG
1 GGTATTTCT-GTAATTTTGTAAATCAAG
*
54201502 GGTATTT-TAGTAATTTTATAAATCGAA-
1 GGTATTTCT-GTAATTTTGTAAATC-AAG
*** *
54201529 GGTAAAACAGTAATTTTGTAAATCAAG
1 GGTATTTCTGTAATTTTGTAAATCAAG
54201556 GGTA
1 GGTA
54201560 AAACAGTAAT
Statistics
Matches: 186, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
26 4 0.02
27 149 0.80
28 18 0.10
29 15 0.08
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.39
Consensus pattern (27 bp):
GGTATTTCTGTAATTTTGTAAATCAAG
Found at i:54201448 original size:54 final size:54
Alignment explanation
Indices: 54201390--54201524 Score: 218
Period size: 54 Copynumber: 2.5 Consensus size: 54
54201380 CTTTGTAAAT
54201390 CAAGGGTATTTTGGTAATTTTACAAATT-GAGGGTATTTTGGTAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAATTAG-GGGTATTTTGGTAATTTCACAAAC
* *
54201444 CAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAATTAGGGGTATTTTGGTAATTTCACAAAC
* *
54201498 CAAGGGTATTTTAGTAATTTTATAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
54201525 CGAAGGTAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
54 74 0.99
55 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (54 bp):
CAAGGGTATTTTGGTAATTTTACAAATTAGGGGTATTTTGGTAATTTCACAAAC
Found at i:54201542 original size:54 final size:54
Alignment explanation
Indices: 54201390--54201597 Score: 175
Period size: 54 Copynumber: 3.9 Consensus size: 54
54201380 CTTTGTAAAT
* * * **** *
54201390 CAAGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTCACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAACGGTAATTTTACAAAC
* * * ****
54201444 CAAGGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAATCGA-GGGTAAAACGGTAATTTTACAAAC
* * ** *
54201498 CAAGGGTATTTTAGTAATTTTATAAATCGAAGGTAAAACAGTAATTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAACGGTAATTTTACAAAC
**** *
54201552 CAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATT
1 CAAGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAACGGTAATT
54201598 CTGTAAGTCG
Statistics
Matches: 130, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.01
54 127 0.98
55 2 0.02
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.35
Consensus pattern (54 bp):
CAAGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAACGGTAATTTTACAAAC
Found at i:54201559 original size:81 final size:81
Alignment explanation
Indices: 54201376--54201559 Score: 192
Period size: 81 Copynumber: 2.3 Consensus size: 81
54201366 GGGTATTTCT
* *** *
54201376 GTAACTTTGTAAATCAAGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTCACA
1 GTAATTTTGTAAATCAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTCACA
*****
54201441 AACCAAGGGTATTTTG
66 AACCAAGGGTAAAACA
** * * *
54201457 GTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTAT
1 GTAATTTTGTAAATC-AAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTCAC
*
54201521 AAATCGAA-GGTAAAACA
65 AAA-CCAAGGGTAAAACA
54201538 GTAATTTTGTAAATCAAGGGTA
1 GTAATTTTGTAAATCAAGGGTA
54201560 AAACAGTAAT
Statistics
Matches: 81, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
80 1 0.01
81 76 0.94
82 4 0.05
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.38
Consensus pattern (81 bp):
GTAATTTTGTAAATCAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTCACA
AACCAAGGGTAAAACA
Found at i:54201569 original size:81 final size:81
Alignment explanation
Indices: 54201484--54201688 Score: 198
Period size: 81 Copynumber: 2.5 Consensus size: 81
54201474 GGGTATTTTG
* **** * *
54201484 GTAATTTTACAAACCAAGGGTATTTTAGTAATTTTATAAATCGAAGGTAAAAC-AGTAATTTTGT
1 GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTATAAATCGAAGGTAAAACGA-TAATTATGT
54201548 AAATCAAGGGTAAAACA
65 AAATCAAGGGTAAAACA
* * * * * * *
54201565 GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAACGATAATTATGTA
1 GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTATAAATCGAAGGTAAAACGATAATTATGTA
* *
54201630 AATCGAGGGTAAAACG
66 AATCAAGGGTAAAACA
* ** *
54201646 GTAATTATGTAAATCAAGGGTAAAAC-GATAATTCTATAAATCG
1 GTAATTCTACAAACCAAGGGTAAAACAG-TAATTCTATAAATCG
54201689 GGGGTACTTT
Statistics
Matches: 101, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
80 1 0.01
81 99 0.98
82 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (81 bp):
GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTATAAATCGAAGGTAAAACGATAATTATGTA
AATCAAGGGTAAAACA
Found at i:54201693 original size:27 final size:27
Alignment explanation
Indices: 54201520--54201694 Score: 210
Period size: 27 Copynumber: 6.5 Consensus size: 27
54201510 AGTAATTTTA
* *
54201520 TAAATCGAAGGTAAAAC-AGTAATTTTG
1 TAAATCGAGGGTAAAACGA-TAATTCTG
* *
54201547 TAAATCAAGGGTAAAAC-AGTAATTCTA
1 TAAATCGAGGGTAAAACGA-TAATTCTG
*
54201574 TAAATCGAGGGTAAAACGGTAATTCTG
1 TAAATCGAGGGTAAAACGATAATTCTG
* *
54201601 TAAGTCGAGGGTAAAACGATAATTATG
1 TAAATCGAGGGTAAAACGATAATTCTG
* *
54201628 TAAATCGAGGGTAAAACGGTAATTATG
1 TAAATCGAGGGTAAAACGATAATTCTG
* *
54201655 TAAATCAAGGGTAAAACGATAATTCTA
1 TAAATCGAGGGTAAAACGATAATTCTG
*
54201682 TAAATCGGGGGTA
1 TAAATCGAGGGTA
54201695 CTTTGGTAAT
Statistics
Matches: 129, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
27 129 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.26
Consensus pattern (27 bp):
TAAATCGAGGGTAAAACGATAATTCTG
Found at i:54201694 original size:81 final size:81
Alignment explanation
Indices: 54201512--54201694 Score: 242
Period size: 81 Copynumber: 2.3 Consensus size: 81
54201502 GGTATTTTAG
* * * *
54201512 TAATTTTATAAATCGAAGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATAA
1 TAATTCTATAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAGTAATTATATAA
* *
54201577 ATCGAGGGTAAAACGG
66 ATCAAGGGTAAAACGA
* * * * *
54201593 TAATTCTGTAAGTCGAGGGTAAAAC-GATAATTATGTAAATCGAGGGTAAAACGGTAATTATGTA
1 TAATTCTATAAATCGAGGGTAAAACAG-TAATTATGTAAATCAAGGGTAAAACAGTAATTATATA
54201657 AATCAAGGGTAAAACGA
65 AATCAAGGGTAAAACGA
*
54201674 TAATTCTATAAATCGGGGGTA
1 TAATTCTATAAATCGAGGGTA
54201695 CTTTGGTAAT
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 1 0.01
81 86 0.99
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (81 bp):
TAATTCTATAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAGTAATTATATAA
ATCAAGGGTAAAACGA
Found at i:54201705 original size:54 final size:54
Alignment explanation
Indices: 54201512--54201694 Score: 260
Period size: 54 Copynumber: 3.4 Consensus size: 54
54201502 GGTATTTTAG
* * * *
54201512 TAATTTTATAAATCGAAGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAAC-A
1 TAATTCTATAAATCGAGGGTAAAACGGTAATTATGTAAATCAAGGGTAAAACGA
* * *
54201565 GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAACGA
1 -TAATTCTATAAATCGAGGGTAAAACGGTAATTATGTAAATCAAGGGTAAAACGA
* *
54201620 TAATTATGTAAATCGAGGGTAAAACGGTAATTATGTAAATCAAGGGTAAAACGA
1 TAATTCTATAAATCGAGGGTAAAACGGTAATTATGTAAATCAAGGGTAAAACGA
*
54201674 TAATTCTATAAATCGGGGGTA
1 TAATTCTATAAATCGAGGGTA
54201695 CTTTGGTAAT
Statistics
Matches: 114, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
54 113 0.99
55 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (54 bp):
TAATTCTATAAATCGAGGGTAAAACGGTAATTATGTAAATCAAGGGTAAAACGA
Found at i:54201721 original size:27 final size:27
Alignment explanation
Indices: 54201700--54201789 Score: 119
Period size: 27 Copynumber: 3.3 Consensus size: 27
54201690 GGGTACTTTG
*
54201700 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
*
54201727 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
* * *
54201754 GTATTTTTACAAA-CTAAGGGTATTTCG
1 GTAATTTTACAAATCGAA-GGTATTTCA
54201781 GTAATTTTA
1 GTAATTTTA
54201790 GTAAACAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.04
27 53 0.96
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAATCGAAGGTATTTCA
Found at i:54204304 original size:40 final size:40
Alignment explanation
Indices: 54204259--54204483 Score: 346
Period size: 40 Copynumber: 5.6 Consensus size: 40
54204249 ACTACTTGCT
* *
54204259 CAAATGCCTTCAGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
54204299 CAAATGCCTTCGGGTCTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
54204339 CAAATGCCTTCGGGACTTAGCCCGGGTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
54204379 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
54204419 CAAATGCCTT-TGGAGCTTAGCTCGGA-ATTAGTCACTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATA-TAGTAACTCGCA
54204459 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
54204484 TTATCATCCA
Statistics
Matches: 170, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
39 4 0.02
40 163 0.96
41 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:54212310 original size:40 final size:40
Alignment explanation
Indices: 54212257--54212520 Score: 381
Period size: 40 Copynumber: 6.6 Consensus size: 40
54212247 ACTACTTGCT
* *
54212257 CAAATGCCCTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
54212297 CAAATGCCTTCGGGTCTGAGCCCGGATATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
54212337 CAACTGCCTTCGGGACTTAGCCAGG-TATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
54212376 CAAATGCCTTCGGGACGTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
54212416 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
54212456 CAAATGCCTTC-GGAGCTTAGCCCGGA-ATTAGTCACTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATA-TAGTAACTCGCA
* *
54212496 CAAATTCCTTCGGGACTTGGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
54212521 TTATCATCCA
Statistics
Matches: 202, Mismatches: 18, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
39 39 0.19
40 160 0.79
41 3 0.01
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:54212438 original size:119 final size:120
Alignment explanation
Indices: 54212257--54212520 Score: 388
Period size: 119 Copynumber: 2.2 Consensus size: 120
54212247 ACTACTTGCT
* * *
54212257 CAAATGCCCTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGTCTGAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTGAGCCCGG
* * * *
54212322 ATATAGTAACTTGCACAACTGCCTTCGG-GACTTAGCCAGGTA-TAGTAACTCGCA
66 ATATAGTAACTCGCACAAATGCCTTCGGAG-CTTAGCCAGGAATTAGTAACTAGCA
* *
54212376 CAAATGCCTTCGGGACGTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTGAGCCCGG
* *
54212441 ATATAGTAACTCGCACAAATGCCTTCGGAGCTTAGCCCGGAATTAGTCACTAGCA
66 ATATAGTAACTCGCACAAATGCCTTCGGAGCTTAGCCAGGAATTAGTAACTAGCA
* *
54212496 CAAATTCCTTCGGGACTTGGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
54212521 TTATCATCCA
Statistics
Matches: 129, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
119 96 0.74
120 33 0.26
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (120 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTGAGCCCGG
ATATAGTAACTCGCACAAATGCCTTCGGAGCTTAGCCAGGAATTAGTAACTAGCA
Found at i:54221789 original size:40 final size:40
Alignment explanation
Indices: 54221603--54221864 Score: 347
Period size: 39 Copynumber: 6.6 Consensus size: 40
54221593 GGATTGATAC
*
54221603 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
*
54221643 CCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
54221682 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
* * *
54221721 CCGGGCTAAG-CCTGAAGGCATTCGTGCGAGTTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-T
* * * *
54221760 CCGGGCTAAGTCTCGAAGGCATTTTTGCGAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-T
* * *
54221800 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTA-ATT
54221841 -CGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54221865 AGCTAGTAGC
Statistics
Matches: 202, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
38 2 0.01
39 109 0.54
40 90 0.45
42 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
Found at i:54221897 original size:39 final size:40
Alignment explanation
Indices: 54221606--54221897 Score: 192
Period size: 39 Copynumber: 7.4 Consensus size: 40
54221596 TTGATACCCG
* * * * *
54221606 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATCC
* * * * *
54221645 GGGCTAA-GCCCGAAGGCATTTGTGCAAGTGACTA-ATTCC
1 -GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATCC
* * * *
54221684 GGGCTAA-GCCCGAAGGCATTTGTGCGAGTGACTA-ATTCC
1 -GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATCC
* * * *
54221723 GGGCTAA-GCCTGAAGGCATTCGTGCGAGTTACTAT-ATCC
1 -GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATCC
* * ** *
54221762 GGGCTAAGTCTCGAAGGCATTTTTGCGAGTTACTATAA-CTG
1 -GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATC-C
* * *
54221803 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATCG
1 GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATCC
* *
54221843 GGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTAT-ATCC
1 GGCTAACTCCCGAAGGCATTTGAGCGAGTTA-CTATAATCC
54221882 GGCTAAACT-CCGAAGG
1 GGCT-AACTCCCGAAGG
54221898 TACTTGGTTT
Statistics
Matches: 226, Mismatches: 19, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
39 125 0.55
40 99 0.44
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATCC
Found at i:54226010 original size:15 final size:16
Alignment explanation
Indices: 54225990--54226019 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54225980 TGCATATGTA
54225990 TGAATG-AATTTTATT
1 TGAATGAAATTTTATT
54226005 TGAATGAAATTTTAT
1 TGAATGAAATTTTAT
54226020 GGCCTGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (16 bp):
TGAATGAAATTTTATT
Found at i:54228981 original size:38 final size:38
Alignment explanation
Indices: 54228938--54229010 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
54228928 TTTTAAATTA
54228938 ACATGTATAACCGTGACATATCCACTTAGCACCACATT
1 ACATGTATAACCGTGACATATCCACTTAGCACCACATT
* * **
54228976 ACATGTTTAATCGTGGTATATCCACTTAGCACCAC
1 ACATGTATAACCGTGACATATCCACTTAGCACCAC
54229011 GTTAATGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (38 bp):
ACATGTATAACCGTGACATATCCACTTAGCACCACATT
Found at i:54229037 original size:47 final size:48
Alignment explanation
Indices: 54228983--54229112 Score: 208
Period size: 48 Copynumber: 2.7 Consensus size: 48
54228973 ATTACATGTT
54228983 TAATCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
1 TAATCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
* * *
54229030 TAATCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAATCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
**
54229078 TAATATTGGTATATCCACTTAGCACCACGTTACAT
1 TAATCGTGGTATATCCACTTAGCACCACGTTACAT
54229113 TTATAACCGT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
47 31 0.41
48 45 0.59
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (48 bp):
TAATCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
Found at i:54230113 original size:6 final size:6
Alignment explanation
Indices: 54230096--54230133 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
54230086 GCGCTTCTTC
54230096 TCCCCTT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
54230134 TTGAAATCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
TCCCCT
Found at i:54231367 original size:17 final size:18
Alignment explanation
Indices: 54231334--54231368 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54231324 TGTTTTCTTT
*
54231334 GAGGTCCATGATAATTGG
1 GAGGTCCAAGATAATTGG
54231352 GAGGTCCAAG-TAATTGG
1 GAGGTCCAAGATAATTGG
54231369 AAATTCCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (18 bp):
GAGGTCCAAGATAATTGG
Found at i:54233653 original size:20 final size:19
Alignment explanation
Indices: 54233609--54233654 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
54233599 CATCCAAACA
54233609 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
* *
54233628 CTAGAAAAGTAAATTATTTT
1 CCAGAAAAGTAAATCA-TTT
54233648 CCAGAAA
1 CCAGAAA
54233655 TCATTTTCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:54238265 original size:89 final size:87
Alignment explanation
Indices: 54238114--54238274 Score: 220
Period size: 89 Copynumber: 1.8 Consensus size: 87
54238104 GGATGGTTGA
* * *
54238114 GCATCCGAACTCGTGAGTTGGTCGATTTCACTTATGGATGCAATGTCCGAACTCGTTGAGTTGAG
1 GCATCCGAACTCGTGAGTTGGTCGAGTTCACTCATGGATGCAACGTCCGAACTCGTTGAGTTG-G
54238179 TCCGAGTTCATGAGATGTTACTAG
65 T-CGAGTTCATGAGATGTTACTAG
*
54238203 GCATCCGAACTCGTTGAGTTGAGTCGAGTTCA-TCATGGATGCGAACG-CCG-AGTCGTTGAGTT
1 GCATCCGAACTCG-TGAGTTG-GTCGAGTTCACTCATGGATGC-AACGTCCGAACTCGTTGAGTT
54238265 GGTCGAGTTC
63 GGTCGAGTTC
54238275 GCTTATGGCG
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
87 7 0.11
88 2 0.03
89 25 0.38
90 19 0.29
91 12 0.18
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (87 bp):
GCATCCGAACTCGTGAGTTGGTCGAGTTCACTCATGGATGCAACGTCCGAACTCGTTGAGTTGGT
CGAGTTCATGAGATGTTACTAG
Found at i:54251752 original size:38 final size:39
Alignment explanation
Indices: 54251664--54251877 Score: 265
Period size: 38 Copynumber: 5.5 Consensus size: 39
54251654 GCCATGAACG
* * * * **
54251664 GCCTTCGGGTCTGAGCCCGGATATGGTAACTTGCATTAAT
1 GCCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAAT
*
54251704 GCCTTCGGGACTTAGCCCAGATAT-GTACTCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAAT
*
54251742 GCCTTCGGGACGTAGCCCGGATATAGTACT-GCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAAT
* *
54251780 GCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAAT
*
54251820 GCCTTC-GGACTTAGCCCGGATATAGTCACTAGCACAAA-
1 GCCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAAT
*
54251858 GCCTTCGGGACTTGGCCCGG
1 GCCTTCGGGACTTAGCCCGG
54251878 TTATCATCCA
Statistics
Matches: 154, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
38 69 0.45
39 50 0.32
40 35 0.23
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (39 bp):
GCCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAAT
Found at i:54251821 original size:116 final size:116
Alignment explanation
Indices: 54251664--54251877 Score: 306
Period size: 116 Copynumber: 1.8 Consensus size: 116
54251654 GCCATGAACG
* * * **
54251664 GCCTTCGGGTCTGAGCCCGGATATGGTAACTTGCATTAATGCCTTCGGGACTTAGCCCAGATAT-
1 GCCTTCGGGTCTGAGCCCGGATATAGCAACTCGCACAAATGCCTTC-GGACTTAGCCCAGATATA
*
54251728 GT-ACTCGCACAAATGCCTTCGGGACGTAGCCCGGATATAGTACTGCACAAAT
65 GTCACTAGCACAAA-GCCTTCGGGACGTAGCCCGGATATAGTACTGCACAAAT
* *
54251780 GCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGACTTAGCCCGGATATAG
1 GCCTTCGGGTCTGAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGACTTAGCCCAGATATAG
* *
54251845 TCACTAGCACAAAGCCTTCGGGACTTGGCCCGG
66 TCACTAGCACAAAGCCTTCGGGACGTAGCCCGG
54251878 TTATCATCCA
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
115 16 0.19
116 60 0.70
117 10 0.12
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (116 bp):
GCCTTCGGGTCTGAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGACTTAGCCCAGATATAG
TCACTAGCACAAAGCCTTCGGGACGTAGCCCGGATATAGTACTGCACAAAT
Found at i:54251876 original size:78 final size:75
Alignment explanation
Indices: 54251664--54251877 Score: 252
Period size: 78 Copynumber: 2.8 Consensus size: 75
54251654 GCCATGAACG
* * * * *
54251664 GCCTTCGGGTC-TGAGCCCGGATATGGTAACTTGCATTAATGCCTTCGGGACTTAGCCCAGATAT
1 GCCTTCGGGACGT-AGCCCGGATATAGT-AC-TGCA-CAAAGCCTTCGGGACTTAGCCCGGATAT
*
54251728 GTACTCGCACAAAT
62 GAACTCGCACAAAT
*
54251742 GCCTTCGGGACGTAGCCCGGATATAGTACTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGC
1 GCCTTCGGGACGTAGCCCGGATATAGTACTGCACAAA-GCCTTCGGGACTTAGCCCGGATAT-G-
54251807 AACTCGCACAAAT
63 AACTCGCACAAAT
* *
54251820 GCCTTC-GGACTTAGCCCGGATATAGTCACTAGCACAAAGCCTTCGGGACTTGGCCCGG
1 GCCTTCGGGACGTAGCCCGGATATAGT-ACT-GCACAAAGCCTTCGGGACTTAGCCCGG
54251878 TTATCATCCA
Statistics
Matches: 120, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
75 2 0.02
76 26 0.22
77 22 0.18
78 62 0.52
79 8 0.07
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (75 bp):
GCCTTCGGGACGTAGCCCGGATATAGTACTGCACAAAGCCTTCGGGACTTAGCCCGGATATGAAC
TCGCACAAAT
Found at i:54261358 original size:40 final size:40
Alignment explanation
Indices: 54261172--54261433 Score: 347
Period size: 39 Copynumber: 6.6 Consensus size: 40
54261162 GGATTGATAC
*
54261172 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
*
54261212 CCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
54261251 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
* * *
54261290 CCGGGCTAAG-CCTGAAGGCATTCGTGCGAGTTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-T
* * * *
54261329 CCGGGCTAAGTCTCGAAGGCATTTTTGCGAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-T
* * *
54261369 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTA-ATT
54261410 -CGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54261434 AGCTAGTAGC
Statistics
Matches: 202, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
38 2 0.01
39 109 0.54
40 90 0.45
42 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
Found at i:54261466 original size:39 final size:40
Alignment explanation
Indices: 54261175--54261466 Score: 192
Period size: 39 Copynumber: 7.4 Consensus size: 40
54261165 TTGATACCCG
* * * * *
54261175 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATCC
* * * * *
54261214 GGGCTAA-GCCCGAAGGCATTTGTGCAAGTGACTA-ATTCC
1 -GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATCC
* * * *
54261253 GGGCTAA-GCCCGAAGGCATTTGTGCGAGTGACTA-ATTCC
1 -GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATCC
* * * *
54261292 GGGCTAA-GCCTGAAGGCATTCGTGCGAGTTACTAT-ATCC
1 -GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATCC
* * ** *
54261331 GGGCTAAGTCTCGAAGGCATTTTTGCGAGTTACTATAA-CTG
1 -GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATC-C
* * *
54261372 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATCG
1 GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATCC
* *
54261412 GGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTAT-ATCC
1 GGCTAACTCCCGAAGGCATTTGAGCGAGTTA-CTATAATCC
54261451 GGCTAAACT-CCGAAGG
1 GGCT-AACTCCCGAAGG
54261467 TACTTGGTTT
Statistics
Matches: 226, Mismatches: 19, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
39 125 0.55
40 99 0.44
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GGCTAACTCCCGAAGGCATTTGAGCGAGTTACTATAATCC
Found at i:54265577 original size:15 final size:16
Alignment explanation
Indices: 54265557--54265586 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54265547 TGCATATGTA
54265557 TGAATG-AATTTTATT
1 TGAATGAAATTTTATT
54265572 TGAATGAAATTTTAT
1 TGAATGAAATTTTAT
54265587 GGCCTGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (16 bp):
TGAATGAAATTTTATT
Found at i:54268545 original size:38 final size:38
Alignment explanation
Indices: 54268502--54268574 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
54268492 TTTTAAATTA
54268502 ACATGTATAACCGTGACATATCCACTTAGCACCACATT
1 ACATGTATAACCGTGACATATCCACTTAGCACCACATT
* * **
54268540 ACATGTTTAATCGTGGTATATCCACTTAGCACCAC
1 ACATGTATAACCGTGACATATCCACTTAGCACCAC
54268575 GTTAATGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (38 bp):
ACATGTATAACCGTGACATATCCACTTAGCACCACATT
Found at i:54268601 original size:47 final size:48
Alignment explanation
Indices: 54268547--54268676 Score: 208
Period size: 48 Copynumber: 2.7 Consensus size: 48
54268537 ATTACATGTT
54268547 TAATCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
1 TAATCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
* * *
54268594 TAATCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAATCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
**
54268642 TAATATTGGTATATCCACTTAGCACCACGTTACAT
1 TAATCGTGGTATATCCACTTAGCACCACGTTACAT
54268677 TTATAACCGT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
47 31 0.41
48 45 0.59
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (48 bp):
TAATCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
Found at i:54270917 original size:17 final size:18
Alignment explanation
Indices: 54270884--54270918 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54270874 TGTTTTCTTT
*
54270884 GAGGTCCATGATAATTGG
1 GAGGTCCAAGATAATTGG
54270902 GAGGTCCAAG-TAATTGG
1 GAGGTCCAAGATAATTGG
54270919 AAATTCCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (18 bp):
GAGGTCCAAGATAATTGG
Found at i:54273204 original size:20 final size:19
Alignment explanation
Indices: 54273160--54273205 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
54273150 CATCCAAACA
54273160 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
* *
54273179 CTAGAAAAGTAAATTATTTT
1 CCAGAAAAGTAAATCA-TTT
54273199 CCAGAAA
1 CCAGAAA
54273206 TCATTTTCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:54277956 original size:46 final size:46
Alignment explanation
Indices: 54277906--54278081 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
54277896 TGGTTGAGCA
* *
54277906 TCCGAACTCGTTGAGTTGAGTCCGATTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* ** *
54277952 TCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATGTTACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C-AAACG
* *
54277999 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
54278045 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54278082 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 64 0.59
47 32 0.30
48 2 0.02
50 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:54278062 original size:93 final size:93
Alignment explanation
Indices: 54277903--54278073 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
54277893 GGATGGTTGA
* * * *
54277903 GCATCCGAACTCGTTGAGTTGAGTCCGATTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
54277968 TGAGTCCGAGTTCATGAGATGTTACTAG
66 TGAGTCCGAGTTCATGAGATGTTACTAG
* *
54277996 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
54278061 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
54278074 GCTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCATGAGATGTTACTAG
Found at i:54285538 original size:46 final size:46
Alignment explanation
Indices: 54285488--54285663 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
54285478 TGGTTGAGCA
* *
54285488 TCCGAACTCGTTGAGTTGAGTCCGATTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
54285534 TCCGAACTCGTTAAGTTGAGTCCGAGTTCA-TGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
54285581 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
54285627 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54285664 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 62 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:54285644 original size:93 final size:93
Alignment explanation
Indices: 54285485--54285655 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
54285475 GGATGGTTGA
* * * *
54285485 GCATCCGAACTCGTTGAGTTGAGTCCGATTTCACTTATGGATGCAAATGTCCGAACTCGTTAAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTAAGT
54285550 TGAGTCCGAGTTCATGAGATGTAACTAG
66 TGAGTCCGAGTTCATGAGATGTAACTAG
* * *
54285578 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTAAGT
54285643 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
54285656 GCTTATGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTAAGT
TGAGTCCGAGTTCATGAGATGTAACTAG
Found at i:54288319 original size:137 final size:135
Alignment explanation
Indices: 54288016--54288437 Score: 634
Period size: 137 Copynumber: 3.1 Consensus size: 135
54288006 TAGAAAAATG
54288016 AATTATATTCTTTCCAAAAAATTATTAATTTACATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATA-TCTTTCCAAAAAA-TATTAATTTACATGTCTTTTATATTTTGACTGAAATTAATTAA
* *
54288081 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
64 TATAA-TTTTTATATTAATAAATTCCGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
54288146 CATATATT
128 CATATATT
* * * *
54288154 AACTATATTTTTTCAAAGAAATATTAATTTACATGTCTTTTATATTTTGACCGAAATTAATTAAT
1 AATTATATCTTTCCAAA-AAATATTAATTTACATGTCTTTTATATTTTGACTGAAATTAATTAAT
54288219 ATAATTGTTTATATTAATAAATTCCGTAAAATA-ATACAATTAATATTTTGTATGAATCAAATTC
65 ATAATT-TTTATATTAATAAATTCCGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
54288283 ATATATT
129 ATATATT
* * *
54288290 AATTATGATCTTTCCAAAACAATACTAATTTCCA-GATCTTTTATATTTTGACTAAAATTAATTA
1 AATTAT-ATCTTTCCAAAA-AATATTAATTTACATG-TCTTTTATATTTTGACTGAAATTAATTA
*
54288354 ATATAACTTTTTATTTTAATAAA-TCCAGTAAAATATATACAATTAATATTTTGTATGAATCAAA
63 ATATAA-TTTTTATATTAATAAATTCC-GTAAAATATATACAATTAATATTTTGTATGAATCAAA
*
54288418 TTTATATATT
126 TTCATATATT
54288428 AATTATATCT
1 AATTATATCT
54288438 ATGTTCTCTA
Statistics
Matches: 261, Mismatches: 15, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
136 49 0.19
137 158 0.61
138 54 0.21
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (135 bp):
AATTATATCTTTCCAAAAAATATTAATTTACATGTCTTTTATATTTTGACTGAAATTAATTAATA
TAATTTTTATATTAATAAATTCCGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCAT
ATATT
Found at i:54290016 original size:20 final size:20
Alignment explanation
Indices: 54289980--54290018 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54289970 ATTTGTGTTG
*
54289980 TAATTCATAATTCTATTTTC
1 TAATTCATAATTATATTTTC
54290000 TAATTC-TAATATATATTTT
1 TAATTCATAAT-TATATTTT
54290019 ATTATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATTCATAATTATATTTTC
Found at i:54306961 original size:74 final size:73
Alignment explanation
Indices: 54306827--54307080 Score: 368
Period size: 74 Copynumber: 3.4 Consensus size: 73
54306817 GCAAGACACT
* * *
54306827 AAATGTATCCGGCTAAAGTCCCGCAGGCTTCGTGCTGGAATATATTCGGGCCAAGTCCGCAGGCT
1 AAATGTATCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAA-ATATCCGGGCAAAGTCCGCAGGCT
54306892 TCGTGCTGG
65 TCGTGCTGG
54306901 AAATGTATCTGGGCT-AAGTCCCGCAGGC-TCGTGCTGGAAATATCCGGGCTAAAGTCCCGCAGG
1 AAATGTATC-GGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATATCCGGGC-AAAGT-CCGCAGG
54306964 CTTCGTGCTGG
63 CTTCGTGCTGG
* * *
54306975 AAATATATCCGGCCAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGCCAAAGTCCGCAGG
1 AAATGTATCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAA--TATCCGGG-CAAAGTCCGCAGG
54307040 CTTCGTGCTGG
63 CTTCGTGCTGG
*
54307051 AAATGTATCGGGTTAAAGTCCCGCAGGCTT
1 AAATGTATCGGGCTAAAGTCCCGCAGGCTT
54307081 TATGCTGATA
Statistics
Matches: 162, Mismatches: 10, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
72 9 0.06
73 18 0.11
74 61 0.38
75 16 0.10
76 44 0.27
77 13 0.08
78 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.23
Consensus pattern (73 bp):
AAATGTATCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATATCCGGGCAAAGTCCGCAGGCTT
CGTGCTGG
Found at i:54307087 original size:38 final size:38
Alignment explanation
Indices: 54306827--54307080 Score: 344
Period size: 38 Copynumber: 6.8 Consensus size: 38
54306817 GCAAGACACT
*
54306827 AAATGTATCCGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
54306865 -AATATATTCGGGC-CAAGT-CCGCAGGCTTCGTGCTGG
1 AAATGTA-TCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
54306901 AAATGTATCTGGGCT-AAGTCCCGCAGGC-TCGTGCTGG
1 AAATGTATC-GGGCTAAAGTCCCGCAGGCTTCGTGCTGG
54306938 AAA--TATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTAT-CGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* * *
54306975 AAATATATCCGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
54307013 AAATGTATCCGGGCCAAAGT-CCGCAGGCTTCGTGCTGG
1 AAATGTAT-CGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
54307051 AAATGTATCGGGTTAAAGTCCCGCAGGCTT
1 AAATGTATCGGGCTAAAGTCCCGCAGGCTT
54307081 TATGCTGATA
Statistics
Matches: 194, Mismatches: 10, Indels: 24
0.85 0.04 0.11
Matches are distributed among these distances:
35 8 0.04
36 34 0.18
37 55 0.28
38 84 0.43
39 13 0.07
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.23
Consensus pattern (38 bp):
AAATGTATCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:54310125 original size:1 final size:1
Alignment explanation
Indices: 54310119--54310144 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
54310109 CTAAGTTGAC
54310119 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
54310145 TGTGTAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:54337130 original size:39 final size:39
Alignment explanation
Indices: 54336859--54337123 Score: 449
Period size: 39 Copynumber: 6.8 Consensus size: 39
54336849 AAGACACTAA
54336859 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* * *
54336898 AAATATATTCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
54336937 AAATGTATCTGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
54336976 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
54337015 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
54337054 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
54337093 AAATGTATCCGGGTTAAAGTCCCGCAGGCTT
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTT
54337124 TATGCTGATA
Statistics
Matches: 213, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 213 1.00
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (39 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:54339000 original size:40 final size:40
Alignment explanation
Indices: 54338849--54338993 Score: 154
Period size: 40 Copynumber: 3.6 Consensus size: 40
54338839 CGAATGATGT
* * *
54338849 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAATA
* *
54338888 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATT
1 -CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATA
*
54338929 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-A
* *
54338969 CTGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54338994 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
39 3 0.03
40 76 0.85
41 10 0.11
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
Found at i:54339012 original size:80 final size:80
Alignment explanation
Indices: 54338848--54339000 Score: 184
Period size: 80 Copynumber: 1.9 Consensus size: 80
54338838 TCGAATGATG
* *
54338848 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
54338913 GTGCGAGTTACTAAT
66 GAACGAGTTACTAAT
* * * * * *
54338928 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACTGGGCTATG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
54338991 TTGAACGAGT
64 TTGAACGAGT
54339001 AGCTATATCC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
79 1 0.02
80 53 0.87
81 7 0.11
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTTACTAAT
Found at i:54349394 original size:47 final size:47
Alignment explanation
Indices: 54349313--54349707 Score: 549
Period size: 47 Copynumber: 8.4 Consensus size: 47
54349303 AATGTGAAAG
*
54349313 TGTATATGTGTGAATAGGGCCGAATGGCCAATGTGATGAAAGTGAACA
1 TGTATATGTGTG-ATAAGGCCGAATGGCCAATGTGATGAAAGTGAACA
54349361 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACA
1 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACA
* * *
54349408 TGTGTATGTGTGAATAGGGCCGAATGGCCAATGTGATGAATGTGAACA
1 TGTATATGTGTG-ATAAGGCCGAATGGCCAATGTGATGAAAGTGAACA
* * * * *
54349456 TGCATATATGAGATAAGGCCGAATGACCAATGTGATGAATGTGAACA
1 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACA
* * *
54349503 TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACA
1 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACA
54349550 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACA
1 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACA
* * * *
54349597 TGTGTATGTGTGATAAGGCCGAGTGGCCAATGTGATGAATGTGAGCA
1 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACA
* * * * *
54349644 TGTGTATGTGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAA-A
1 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACA
**
54349690 GTGTATAAATGTGATAAG
1 -TGTATATGTGTGATAAG
54349708 TCCCGAAGGG
Statistics
Matches: 317, Mismatches: 28, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
46 1 0.00
47 263 0.83
48 53 0.17
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.26
Consensus pattern (47 bp):
TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACA
Found at i:54349882 original size:37 final size:37
Alignment explanation
Indices: 54349826--54349905 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
54349816 CCGGGCTCTA
* * *
54349826 AAGACCCGATGACTGCGTGTGG-GAATTTTGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAG-ATTATGTCCGGGT
*
54349863 AAGACTCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
54349900 AAGACT
1 AAGACT
54349906 TCGTAATAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (37 bp):
AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
Found at i:54360806 original size:14 final size:14
Alignment explanation
Indices: 54360775--54360826 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
54360765 TGCAAACAGA
*
54360775 TTTTACATTATAAG
1 TTTTACATTATAAC
* * *
54360789 TTTTTCTTTGTAAC
1 TTTTACATTATAAC
54360803 TTTTACATTATAAC
1 TTTTACATTATAAC
54360817 TTTTACATTA
1 TTTTACATTA
54360827 CAACCTGACC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.56
Consensus pattern (14 bp):
TTTTACATTATAAC
Found at i:54361659 original size:26 final size:27
Alignment explanation
Indices: 54361630--54361682 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
54361620 ATACATATTG
54361630 CAAAATTATTTCAAAAATAAG-AAATA
1 CAAAATTATTTCAAAAATAAGTAAATA
54361656 CAAAATTATTTCAAAAATAAGTAAATA
1 CAAAATTATTTCAAAAATAAGTAAATA
54361683 ACCTAGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.28
Consensus pattern (27 bp):
CAAAATTATTTCAAAAATAAGTAAATA
Found at i:54364291 original size:38 final size:38
Alignment explanation
Indices: 54364247--54364322 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
54364237 GATAAGGTAA
54364247 CTAAGTTTCCAAAATGACTTAAAAAATAGTTTTTCCCT
1 CTAAGTTTCCAAAATGACTTAAAAAATAGTTTTTCCCT
54364285 CTAAGTTTCCAAAATGACTTAAAAAATAGTTTTTCCCT
1 CTAAGTTTCCAAAATGACTTAAAAAATAGTTTTTCCCT
54364323 GCATTAGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (38 bp):
CTAAGTTTCCAAAATGACTTAAAAAATAGTTTTTCCCT
Found at i:54366094 original size:28 final size:28
Alignment explanation
Indices: 54366047--54366111 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
54366037 AAATTAACCC
*
54366047 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
54366075 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
54366103 TAGGGGTAT
1 TAGGGGTAT
54366112 TCTAGTACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:54373751 original size:27 final size:27
Alignment explanation
Indices: 54373700--54373789 Score: 110
Period size: 27 Copynumber: 3.2 Consensus size: 27
54373690 GTGACAGAGT
54373700 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* * *
54373729 CACCAGAAGAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
54373756 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
54373784 CACCAG
1 CACCAG
54373790 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 23 0.43
28 23 0.43
29 7 0.13
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:54373942 original size:28 final size:28
Alignment explanation
Indices: 54373895--54373987 Score: 159
Period size: 28 Copynumber: 3.3 Consensus size: 28
54373885 AAATTAACCC
* *
54373895 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
54373923 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
*
54373951 TAAGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
54373979 TAGGGGTAT
1 TAGGGGTAT
54373988 TCTAGTACAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:54377748 original size:50 final size:50
Alignment explanation
Indices: 54377694--54378074 Score: 306
Period size: 50 Copynumber: 7.5 Consensus size: 50
54377684 CTGGTATGCA
*
54377694 TAGTAGCCTGCACTTAGTACTACACATTCGACCTAATAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATTCGACCTAACAATCTGGTACACG
* * * * ** ** *
54377744 TAGTAGCCTGCACTTAGTACTACACACGT-GATCGAAGCTATCAAGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACA-TTCGACCTAA-CAATCTGGTACACG
* * * *
54377795 TAGTAGACTGCACTTAGTACTACACATGCGACCTAACAACCTGGTATACG
1 TAGTAGCCTGCACTTAGTACTACACATTCGACCTAACAATCTGGTACACG
* ** *
54377845 TAGTAGCCTGCACTTAGTACTACACATGT-GACCTAACCATCTTATACATG
1 TAGTAGCCTGCACTTAGTACTACACAT-TCGACCTAACAATCTGGTACACG
* * * * * ***
54377895 TAGTAGCTTGCAC-TATGTACTACACA--CGTAATCGAAGCTATCGGGTACGTA
1 TAGTAGCCTGCACTTA-GTACTACACATTCG--ACCTAA-CAATCTGGTACACG
* *
54377946 TAGTAGCCTGAACTTAGTACTACACATGCGACCTAACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATTCGACCTAACAATCTGGTACACG
* * * *** *
54377996 TAGTAGCCTGCAATTAGTACTACACACGT-GACCTAAAACCATCTTAAACACA
1 TAGTAGCCTGCACTTAGTACTACACA-TTCGACCT--AACAATCTGGTACACG
*
54378048 TAGTAGCCTGCACATAGTACTACACAT
1 TAGTAGCCTGCACTTAGTACTACACAT
54378075 GTGTTCTCAC
Statistics
Matches: 257, Mismatches: 59, Indels: 29
0.74 0.17 0.08
Matches are distributed among these distances:
48 1 0.00
49 2 0.01
50 144 0.56
51 71 0.28
52 37 0.14
53 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATTCGACCTAACAATCTGGTACACG
Found at i:54377806 original size:101 final size:101
Alignment explanation
Indices: 54377687--54377875 Score: 324
Period size: 101 Copynumber: 1.9 Consensus size: 101
54377677 AAGCTCTCTG
* * * *
54377687 GTATGCATAGTAGCCTGCACTTAGTACTACACATTCGACCTAATAATCTGGTACACGTAGTAGCC
1 GTATGCATAGTAGACTGCACTTAGTACTACACATGCGACCTAACAACCTGGTACACGTAGTAGCC
54377752 TGCACTTAGTACTACACACGTGATCGAAGCTATCAA
66 TGCACTTAGTACTACACACGTGATCGAAGCTATCAA
*
54377788 GTATGCATAGTAGACTGCACTTAGTACTACACATGCGACCTAACAACCTGGTATACGTAGTAGCC
1 GTATGCATAGTAGACTGCACTTAGTACTACACATGCGACCTAACAACCTGGTACACGTAGTAGCC
*
54377853 TGCACTTAGTACTACACATGTGA
66 TGCACTTAGTACTACACACGTGA
54377876 CCTAACCATC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 82 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (101 bp):
GTATGCATAGTAGACTGCACTTAGTACTACACATGCGACCTAACAACCTGGTACACGTAGTAGCC
TGCACTTAGTACTACACACGTGATCGAAGCTATCAA
Found at i:54377961 original size:151 final size:152
Alignment explanation
Indices: 54377684--54378073 Score: 536
Period size: 151 Copynumber: 2.6 Consensus size: 152
54377674 CCAAAGCTCT
* * ** **
54377684 CTGGTATGCATAGTAGCCTGCACTTAGTACTACACAT-TCGACCTAATAATCTGGTACACGTAGT
1 CTGGTATACGTAGTAGCCTGCACTTAGTACTACACATGT-GACCTAACCATCTTATACACGTAGT
* * *
54377748 AGCCTGCACT-TAGTACTACACACGTGATCGAAGCTATCAAGTATGCATAGTAGACTGCACTTAG
65 AGCCTGCACTATAGTACTACACACGTAATCGAAGCTATCAAGTACGCATAGTAGACTGAACTTAG
54377812 TACTACACATGCGACCTAACAAC
130 TACTACACATGCGACCTAACAAC
*
54377835 CTGGTATACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTTATACATGTAGTA
1 CTGGTATACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTTATACACGTAGTA
* ** * *
54377900 GCTTGCACTAT-GTACTACACACGTAATCGAAGCTATCGGGTACGTATAGTAGCCTGAACTTAGT
66 GCCTGCACTATAGTACTACACACGTAATCGAAGCTATCAAGTACGCATAGTAGACTGAACTTAGT
*
54377964 ACTACACATGCGACCTAACAAT
131 ACTACACATGCGACCTAACAAC
* * * * *
54377986 CTGGTACACGTAGTAGCCTGCAATTAGTACTACACACGTGACCTAAAACCATCTTAAACACATAG
1 CTGGTATACGTAGTAGCCTGCACTTAGTACTACACATGTGACCT--AACCATCTTATACACGTAG
54378051 TAGCCTGCAC-ATAGTACTACACA
64 TAGCCTGCACTATAGTACTACACA
54378074 TGTGTTCTCA
Statistics
Matches: 211, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
151 172 0.82
152 4 0.02
153 35 0.17
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (152 bp):
CTGGTATACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTTATACACGTAGTA
GCCTGCACTATAGTACTACACACGTAATCGAAGCTATCAAGTACGCATAGTAGACTGAACTTAGT
ACTACACATGCGACCTAACAAC
Found at i:54380010 original size:40 final size:40
Alignment explanation
Indices: 54379980--54380229 Score: 367
Period size: 40 Copynumber: 6.3 Consensus size: 40
54379970 GGACTAAGAT
* * * * *
54379980 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAATTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
54380020 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
*
54380060 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
54380100 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* *
54380140 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* * * * * *
54380180 CCGAAGGCATT-GTGTGAGTTACTAAAACCGAGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
54380219 CCGAAGGCATT
1 CCGAAGGCATT
54380230 TGAACGAGGA
Statistics
Matches: 195, Mismatches: 15, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
39 33 0.17
40 162 0.83
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
Found at i:54380142 original size:120 final size:119
Alignment explanation
Indices: 54379927--54380229 Score: 367
Period size: 120 Copynumber: 2.5 Consensus size: 119
54379917 TTGAATGCTG
* * * * * * * *
54379927 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCG-GACTAAGAT-CCGAAGGCCT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGAG-CTAAG-TCCCGAAGGCAT
* *
54379990 TTGTGCGAGATACTAAATCCGGGTTAATTCCCGAAGGCATTCGTGCGAGTTATTAAA
63 TCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
** * * *
54380047 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGAGCTAAGTCCCGAAGGCATTC
* * *
54380112 GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
65 GTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
54380167 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGAGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGAGCTAAGTCCCGAAGGCATT
54380230 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
119 33 0.21
120 120 0.76
121 5 0.03
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGAGCTAAGTCCCGAAGGCATTCG
TGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:54387331 original size:40 final size:39
Alignment explanation
Indices: 54387248--54387504 Score: 207
Period size: 40 Copynumber: 6.5 Consensus size: 39
54387238 TTGAATGCTG
* * * * *
54387248 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGT-ACTAAA
** * *
54387288 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAG-TACTAAA
**
54387328 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTACTAAA
**
54387367 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TACTAAA
* *
54387407 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TACTAAA
* * * * ** * *
54387446 ACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTA-CTAAA
*
54387486 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
54387505 TACGTGATTT
Statistics
Matches: 184, Mismatches: 26, Indels: 15
0.82 0.12 0.07
Matches are distributed among these distances:
39 86 0.47
40 89 0.48
41 9 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTACTAAA
Found at i:54387377 original size:39 final size:40
Alignment explanation
Indices: 54387248--54387469 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
54387238 TTGAATGCTG
* * * * * *
54387248 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
54387288 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
54387328 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
54387367 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
54387407 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
54387446 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
54387470 TGAACGAGGA
Statistics
Matches: 160, Mismatches: 18, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
39 73 0.46
40 79 0.49
41 8 0.05
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:54387397 original size:79 final size:79
Alignment explanation
Indices: 54387248--54387469 Score: 232
Period size: 79 Copynumber: 2.8 Consensus size: 79
54387238 TTGAATGCTG
* * * * * * * * *
54387248 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
*
54387312 TGTGCGAGATACTAAA
64 CGTGCGAGATACTAAA
* * *
54387328 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* **
54387392 GTGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* * *
54387407 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
54387470 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
78 9 0.08
79 82 0.68
80 25 0.21
81 4 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACTAAA
Found at i:54387489 original size:79 final size:79
Alignment explanation
Indices: 54387323--54387504 Score: 215
Period size: 79 Copynumber: 2.3 Consensus size: 79
54387313 GTGCGAGATA
* * *
54387323 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAATCCGGGTTAAGTCCCGAAGGC
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTCTAAAACCGGGCTAAGTCCCGAAGGC
** **
54387388 ATTCGTGCGAGTTG
66 ATTCGAACGAGGAG
* * * *
54387402 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-CTAAAACCGGGCTAAGTCCCGAAGG
*
54387466 CATTTGAACGAGGAG
65 CATTCGAACGAGGAG
* *
54387481 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
54387505 TACGTGATTT
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
78 22 0.26
79 64 0.74
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTCTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAG
Found at i:54392057 original size:40 final size:40
Alignment explanation
Indices: 54391661--54392053 Score: 590
Period size: 40 Copynumber: 9.8 Consensus size: 40
54391651 ATTACCACAA
* * * ** *
54391661 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
* * *
54391701 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
* *
54391741 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTC
54391783 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
54391823 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
54391863 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
54391903 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
*
54391943 GCACAAATGCCTGCAGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
* * *
54391983 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTGCGGGTCTTAGCCCGGAT-ATATCAACTC
* * *
54392023 GCACAATTGCCTTCGGGACTTAGCCCGGATA
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATA
54392054 AAATTCAAAT
Statistics
Matches: 331, Mismatches: 19, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
39 1 0.00
40 289 0.87
41 4 0.01
42 37 0.11
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
Found at i:54402333 original size:28 final size:26
Alignment explanation
Indices: 54402293--54402353 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
54402283 TTAAAAGAAA
* *
54402293 GCCTTTGTAGCAATATCTGTCAAATGAT
1 GCCTTTATAGC-A-ATCTATCAAATGAT
*
54402321 GCCTTTATGGCAATCTATCAAATGAT
1 GCCTTTATAGCAATCTATCAAATGAT
54402347 GCCTTTA
1 GCCTTTA
54402354 GGGTAAGACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 20 0.67
27 1 0.03
28 9 0.30
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (26 bp):
GCCTTTATAGCAATCTATCAAATGAT
Found at i:54403535 original size:18 final size:19
Alignment explanation
Indices: 54403507--54403543 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
54403497 CAATATTTTC
54403507 CTTTAGAGCTTACTAAGTT
1 CTTTAGAGCTTACTAAGTT
*
54403526 CTTT-GAGCTTACTTAGTT
1 CTTTAGAGCTTACTAAGTT
54403544 ACCTTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (19 bp):
CTTTAGAGCTTACTAAGTT
Found at i:54405928 original size:21 final size:21
Alignment explanation
Indices: 54405904--54405971 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
54405894 TGATATGAAC
54405904 TCATTGAGTTGTGGTCTGAGT
1 TCATTGAGTTGTGGTCTGAGT
* * *
54405925 TCA-TGATATATGTGACATCTGAGC
1 TCATTGA-GT-TGTG--GTCTGAGT
54405949 TCATTGAGTTGTGGTCTGAGT
1 TCATTGAGTTGTGGTCTGAGT
54405970 TC
1 TC
54405972 TGATGTATAC
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
20 3 0.08
21 12 0.33
22 4 0.11
23 4 0.11
24 10 0.28
25 3 0.08
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (21 bp):
TCATTGAGTTGTGGTCTGAGT
Found at i:54418064 original size:47 final size:47
Alignment explanation
Indices: 54418001--54418381 Score: 645
Period size: 47 Copynumber: 8.0 Consensus size: 47
54417991 ATGATAGTAT
54418001 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
54418048 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
54418095 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
54418142 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
54418191 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
54418240 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* *
54418287 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* * * * * *
54418334 GGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
54418381 G
1 G
54418382 TCCCGAAGGG
Statistics
Matches: 320, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 226 0.71
49 94 0.29
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
Found at i:54418326 original size:192 final size:188
Alignment explanation
Indices: 54418001--54418379 Score: 659
Period size: 192 Copynumber: 2.0 Consensus size: 188
54417991 ATGATAGTAT
54418001 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
54418066 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
66 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * *
54418131 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
131 ATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATA-A-ATGTGATAG
54418191 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATG
54418256 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
64 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
* * *
54418321 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATA
129 ATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATA
54418380 AGTCCCGAAG
Statistics
Matches: 180, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
190 41 0.23
191 1 0.01
192 138 0.77
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (188 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
ATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATAG
Found at i:54424524 original size:21 final size:21
Alignment explanation
Indices: 54424500--54424621 Score: 72
Period size: 21 Copynumber: 5.8 Consensus size: 21
54424490 GTCCTTAATC
*
54424500 CACACGGGCGTATGCCTCAGT
1 CACACGGGCGTGTGCCTCAGT
* **
54424521 CACAC-GGTGTGTGCCTCTCTT
1 CACACGGGCGTGTGCCTC-AGT
** *
54424542 CACACGGGTATGTGCCTCAGC
1 CACACGGGCGTGTGCCTCAGT
* * *
54424563 CACAC-GACGATATGCTTCTC-TT
1 CACACGGGCG-TGTGC--CTCAGT
*
54424585 CACACGGGCGTGTGCCTCAGC
1 CACACGGGCGTGTGCCTCAGT
54424606 CACAC-GGCTGTGTGCC
1 CACACGGGC-GTGTGCC
54424622 CCTCTTCAGA
Statistics
Matches: 75, Mismatches: 18, Indels: 16
0.69 0.17 0.15
Matches are distributed among these distances:
20 17 0.23
21 32 0.43
22 20 0.27
23 6 0.08
ACGTcount: A:0.16, C:0.34, G:0.26, T:0.23
Consensus pattern (21 bp):
CACACGGGCGTGTGCCTCAGT
Found at i:54424627 original size:43 final size:43
Alignment explanation
Indices: 54424500--54424629 Score: 165
Period size: 43 Copynumber: 3.0 Consensus size: 43
54424490 GTCCTTAATC
* *
54424500 CACACGGGCGTATGCCTCAGTCACACGG-TGTGTGCCTCTCTT
1 CACACGGGCGTGTGCCTCAGCCACACGGCTGTGTGCCTCTCTT
** * * *
54424542 CACACGGGTATGTGCCTCAGCCACACGAC-GATATGCTTCTCTT
1 CACACGGGCGTGTGCCTCAGCCACACGGCTG-TGTGCCTCTCTT
*
54424585 CACACGGGCGTGTGCCTCAGCCACACGGCTGTGTGCCCCTCTT
1 CACACGGGCGTGTGCCTCAGCCACACGGCTGTGTGCCTCTCTT
54424628 CA
1 CA
54424630 GACAAGCTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
42 24 0.33
43 47 0.65
44 1 0.01
ACGTcount: A:0.16, C:0.35, G:0.25, T:0.24
Consensus pattern (43 bp):
CACACGGGCGTGTGCCTCAGCCACACGGCTGTGTGCCTCTCTT
Done.