Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 135 of 144
Found at i:34368298 original size:34 final size:35
Alignment explanation
Indices: 34368257--34368328 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
34368247 TTGCACCAAC
34368257 TTTTTTTGTTTT-GTATA-CAAAAAAACAGCCGCTT
1 TTTTTTTGTTTTGGTA-AGCAAAAAAACAGCCGCTT
*
34368291 TTTTTTTGTTTTGGTAAGTAAAAAAACAGCCGCTT
1 TTTTTTTGTTTTGGTAAGCAAAAAAACAGCCGCTT
34368326 TTT
1 TTT
34368329 AAAAATAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
34 13 0.37
35 22 0.63
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (35 bp):
TTTTTTTGTTTTGGTAAGCAAAAAAACAGCCGCTT
Found at i:34378574 original size:24 final size:24
Alignment explanation
Indices: 34378546--34378592 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
34378536 ATTATTATAC
34378546 TTTTTATATATTTAAAATTTAATT
1 TTTTTATATATTTAAAATTTAATT
* * **
34378570 TTTTTTTATTTTTTGAATTTAAT
1 TTTTTATATATTTAAAATTTAAT
34378593 AATTTAATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTTTATATATTTAAAATTTAATT
Found at i:34384536 original size:31 final size:31
Alignment explanation
Indices: 34384501--34384571 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
34384491 GAAAACCTTA
* *
34384501 AAGTTCAAGTTTC-GATAAGAGAAAT-ATTGTT
1 AAGTTCAAATTTCAG-TAAGA-AAATAATTATT
*
34384532 AAGTTCAAATTTCAGTATGAAAATAATTATT
1 AAGTTCAAATTTCAGTAAGAAAATAATTATT
34384563 AAGTTCAAA
1 AAGTTCAAA
34384572 ATTGAACTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 4 0.11
31 30 0.86
32 1 0.03
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (31 bp):
AAGTTCAAATTTCAGTAAGAAAATAATTATT
Found at i:34393645 original size:2 final size:2
Alignment explanation
Indices: 34393638--34393689 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
34393628 TTCTTCCATC
34393638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34393680 AT -T AT AT AT A
1 AT AT AT AT AT A
34393690 CAACTTTACA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34405468 original size:3 final size:3
Alignment explanation
Indices: 34405460--34405487 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
34405450 CTTTATACCT
34405460 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
34405488 AACAGAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:34407737 original size:22 final size:22
Alignment explanation
Indices: 34407711--34407753 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
34407701 GATTTTTATG
34407711 AATGGATTTATATGTAATATTA
1 AATGGATTTATATGTAATATTA
* *
34407733 AATGGATTTTTATGTATTATT
1 AATGGATTTATATGTAATATT
34407754 TTCTAATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
AATGGATTTATATGTAATATTA
Found at i:34413897 original size:40 final size:38
Alignment explanation
Indices: 34413829--34413963 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
34413819 ACCAGAATGG
* *
34413829 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
34413869 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
34413906 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
34413947 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
34413964 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:34413961 original size:41 final size:38
Alignment explanation
Indices: 34413861--34413964 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
34413851 TTCGAAGCAA
* *
34413861 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
34413898 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
34413936 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
34413965 CTCGAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:34414894 original size:13 final size:12
Alignment explanation
Indices: 34414833--34414905 Score: 60
Period size: 13 Copynumber: 6.0 Consensus size: 12
34414823 TATATATTAG
*
34414833 TTAATAATAATA
1 TTAATTATAATA
*
34414845 ATAA-TATAATA
1 TTAATTATAATA
*
34414856 CTAATTA-AATA
1 TTAATTATAATA
* *
34414867 CTAATTTATATTA
1 TTAA-TTATAATA
34414880 TTATATTATAATA
1 TTA-ATTATAATA
34414893 TTAATTAATAATA
1 TTAATT-ATAATA
34414906 AATTAAAGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
11 17 0.34
12 11 0.22
13 21 0.42
14 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
TTAATTATAATA
Found at i:34423847 original size:31 final size:29
Alignment explanation
Indices: 34423812--34423884 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
34423802 ACGCTCTGTG
* * *
34423812 ACTAAAATGTTACAATATGATAACATAAGTA
1 ACTAAAATGTAAC-ATATCA-AACATAAATA
*
34423843 ACTAAAATGTAACATTTCAAACATAAATA
1 ACTAAAATGTAACATATCAAACATAAATA
*
34423872 ACTAAAATATAAC
1 ACTAAAATGTAAC
34423885 TTGAGACAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 21 0.57
30 4 0.11
31 12 0.32
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.27
Consensus pattern (29 bp):
ACTAAAATGTAACATATCAAACATAAATA
Found at i:34429116 original size:60 final size:59
Alignment explanation
Indices: 34429010--34429381 Score: 269
Period size: 59 Copynumber: 6.2 Consensus size: 59
34429000 AAAAAAAAAA
*
34429010 TTGGTGTTGGTCATTG-TATGGCCGACACCCTCTTTTAATTT-A-ATAAAAAAATCAAATTTT
1 TTGGTGTTGGTCA-TGCAATGGCCGACACCC-CTTTT--TTTCAGATAAAAAAATCAAATTTT
* ** * * *
34429070 TGGGTGTTGACCATGCAATGGCCGACACCCCTTTTTTGTCAGATAAAAAATTTAATTTTT
1 TTGGTGTTGGTCATGCAATGGCCGACACCCCTTTTTT-TCAGATAAAAAAATCAAATTTT
* * * * * * *
34429130 TTAGTGTTGGTCATGCCATGACCGACA-CCCTTATTTATCTGATAAGAAAAT-AATTTTTT
1 TTGGTGTTGGTCATGCAATGGCCGACACCCCTT-TTTTTCAGATAAAAAAATCAA-ATTTT
* * * * *
34429189 TTTGTGTTGGTCATGCAATGGTCGACA-TCCTCTTTTTTCAGATAAAAAATTTTAAATTTTT
1 TTGGTGTTGGTCATGCAATGGCCGACACCCCT-TTTTTTCAGATAAAAAA-ATCAAA-TTTT
* * * *
34429250 TTGGTGTTGGCCATTGC-ATGGTCGACACCCACTTTTTGTCAGATAAAAAATTCAAATTTTTT
1 TTGGTGTTGGTCA-TGCAATGGCCGACACCC-CTTTTTTTCAGATAAAAAAATCAAA--TTTT
* ** *
34429312 TTGGTGTT-GTCATGCCATGATCGACACCCCCTTTTTTATCTGAT-AAAAAATC-AATTATT
1 TTGGTGTTGGTCATGCAATGGCCGACA-CCCCTTTTTT-TCAGATAAAAAAATCAAATT-TT
*
34429371 TGGGTGTTGGT
1 TTGGTGTTGGT
34429382 TATGTCATGG
Statistics
Matches: 255, Mismatches: 38, Indels: 38
0.77 0.11 0.11
Matches are distributed among these distances:
57 2 0.01
58 5 0.02
59 77 0.30
60 71 0.28
61 57 0.22
62 41 0.16
63 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (59 bp):
TTGGTGTTGGTCATGCAATGGCCGACACCCCTTTTTTTCAGATAAAAAAATCAAATTTT
Found at i:34429336 original size:61 final size:59
Alignment explanation
Indices: 34429010--34429391 Score: 296
Period size: 60 Copynumber: 6.4 Consensus size: 59
34429000 AAAAAAAAAA
* * * * *
34429010 TTGGTGTTGGTCATTG-TATGGCCGACACCCTCTTTTAATTTA-ATAAAAAAATCAAA-TTTT
1 TTGGTGTTGGTCA-TGCCATGGTCGACACCC-CTTTTTA-TCAGAT-AAAAAATTAAATTTTT
* ** * * * *
34429070 TGGGTGTTGACCATGCAATGGCCGACACCCCTTTTTTGTCAGATAAAAAATTTAATTTTT
1 TTGGTGTTGGTCATGCCATGGTCGACACCCC-TTTTTATCAGATAAAAAATTAAATTTTT
* ** * *
34429130 TTAGTGTTGGTCATGCCATGACCGACA-CCCTTATTTATCTGATAAGAAAA-TAATTTTTT
1 TTGGTGTTGGTCATGCCATGGTCGACACCCCTT-TTTATCAGATAA-AAAATTAAATTTTT
* * *
34429189 TTTGTGTTGGTCATGCAATGGTCGACATCCTCTTTTT-TCAGATAAAAAATTTTAAATTTTT
1 TTGGTGTTGGTCATGCCATGGTCGACA-CCCCTTTTTATCAGATAAAAAA--TTAAATTTTT
* *
34429250 TTGGTGTTGGCCATTG-CATGGTCGACACCCACTTTTTGTCAGATAAAAAATTCAAATTTTTT
1 TTGGTGTTGGTCA-TGCCATGGTCGACACCC-CTTTTTATCAGATAAAAAATT-AAA-TTTTT
* * * *
34429312 TTGGTGTT-GTCATGCCATGATCGACACCCCCTTTTTTATCTGATAAAAAA-TCAATTATT
1 TTGGTGTTGGTCATGCCATGGTCGACA-CCCC-TTTTTATCAGATAAAAAATTAAATTTTT
* * *
34429371 TGGGTGTTGGTTATGTCATGG
1 TTGGTGTTGGTCATGCCATGG
34429392 GTGTAACTGG
Statistics
Matches: 262, Mismatches: 40, Indels: 40
0.77 0.12 0.12
Matches are distributed among these distances:
58 6 0.02
59 75 0.29
60 78 0.30
61 57 0.22
62 46 0.18
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.40
Consensus pattern (59 bp):
TTGGTGTTGGTCATGCCATGGTCGACACCCCTTTTTATCAGATAAAAAATTAAATTTTT
Found at i:34431328 original size:26 final size:25
Alignment explanation
Indices: 34431292--34431341 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
34431282 TTATTTTTGT
34431292 TTATTTCTTAAAATTAATTTTAATTA
1 TTATTTCTTAAAA-TAATTTTAATTA
* * *
34431318 TTATTTTTTAATATATTTTTAATT
1 TTATTTCTTAAAATAATTTTAATT
34431342 TATCGATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TTATTTCTTAAAATAATTTTAATTA
Found at i:34432169 original size:59 final size:55
Alignment explanation
Indices: 34432071--34432570 Score: 186
Period size: 59 Copynumber: 8.7 Consensus size: 55
34432061 AGGGAAAGTT
* * *
34432071 GGTGTCGGTCATTGTATGACCAACAGAAAAAAATTGATTTTTTACCAGATAAAAAAG
1 GGTGTCGGTCA-TGCATGGCCAACA-CAAAAAATTGATTTTTTACCAGATAAAAAAG
* * * *
34432128 CGGATGTCGGCCATGCAATGGCCAACACAAAAAATTCGATTTTTTTATCTGA-CAAAAAG
1 -GG-TGTCGGTCATGC-ATGGCCAACACAAAAAATT-GA-TTTTTTACCAGATAAAAAAG
* * **
34432187 AGGTGTTGATCATTGCATGGTTAACACAAAAAAATTGATTTTTTACCAGATAAAAAAGG
1 -GGTGTCGGTCA-TGCATGGCCAACAC-AAAAAATTGATTTTTTACCAGATAAAAAA-G
* * * * *
34432246 GGTGTCAGTCATGGCATGACCAACATAAAAAAAATTCGAATTTTTTATCTA-A-CAAAAAG
1 GGTGTCGGTCAT-GCATGGCCAAC--ACAAAAAATT-G-ATTTTTTA-CCAGATAAAAAAG
* * * *
34432305 AG-AT-GGTC--G-A----C-AC-CAAAAAATTTGATTTTTTATTCAGATAAAAAGG
1 GGTGTCGGTCATGCATGGCCAACACAAAAAA-TTGATTTTTTA-CCAGATAAAAAAG
* * * * * *
34432351 GGTGTCGGCCATGTAATGGCCAACACCAAAAAAATTTAAAATTTTTTATCTGA-AAAAAGG
1 GGTGTCGGTCATG-CATGGCCAACA-C-AAAAAA-TT--GATTTTTTACCAGATAAAAAAG
*** * * * * *
34432411 GGTGTCAACCATTGCCTGGCTAACACAAAAAAATT-ATTTTTTTATCAGATAAATAGG
1 GGTGTCGGTCA-TGCATGGCCAACAC-AAAAAATTGA-TTTTTTACCAGATAAAAAAG
** * * * * *
34432468 GGTGTCGACCATGGCATGACCAACACCAAAACAATTGAATTTTTTATCTGACAAAAAGG
1 GGTGTCGGTCAT-GCATGGCCAACA-CAAAA-AATTG-ATTTTTTACCAGATAAAAAAG
* *
34432527 GAGTGTTGGCCATGCATGGCCAACACCCAAAAAATTGATTTTTT
1 G-GTGTCGGTCATGCATGGCCAACA--CAAAAAATTGATTTTTT
34432571 TTATCAGATT
Statistics
Matches: 344, Mismatches: 55, Indels: 86
0.71 0.11 0.18
Matches are distributed among these distances:
44 10 0.03
45 8 0.02
46 8 0.02
47 1 0.00
48 5 0.01
49 1 0.00
50 1 0.00
52 1 0.00
53 1 0.00
54 1 0.00
55 1 0.00
56 13 0.04
57 45 0.13
58 65 0.19
59 92 0.27
60 66 0.19
61 15 0.04
62 10 0.03
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (55 bp):
GGTGTCGGTCATGCATGGCCAACACAAAAAATTGATTTTTTACCAGATAAAAAAG
Found at i:34432263 original size:58 final size:57
Alignment explanation
Indices: 34432071--34432292 Score: 180
Period size: 58 Copynumber: 3.8 Consensus size: 57
34432061 AGGGAAAGTT
* * * *
34432071 GGTGTCGGTCATTGTATGACCAACAGAAAAAAATTGATTTTTTACCAGATAAAAAAGCG
1 GGTGTCAGTCA-TGCATGGCCAACACAAAAAAATTGATTTTTTACCAGATAAAAAAG-G
* * * * * * *
34432130 GATGTCGGCCATGCAATGGCCAACAC-AAAAAATTCGATTTTTTTATCTGA-CAAAAAGA
1 GGTGTCAGTCATGC-ATGGCCAACACAAAAAAATT-GA-TTTTTTACCAGATAAAAAAGG
* **
34432188 GGTGT-TGATCATTGCATGGTTAACACAAAAAAATTGATTTTTTACCAGATAAAAAAGG
1 GGTGTCAG-TCA-TGCATGGCCAACACAAAAAAATTGATTTTTTACCAGATAAAAAAGG
* *
34432246 GGTGTCAGTCATGGCATGACCAACATAAAAAAAATTCGAATTTTTTA
1 GGTGTCAGTCAT-GCATGGCCAACA-CAAAAAAATT-G-ATTTTTTA
34432293 TCTAACAAAA
Statistics
Matches: 128, Mismatches: 23, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
57 12 0.09
58 50 0.39
59 47 0.37
60 11 0.09
61 8 0.06
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (57 bp):
GGTGTCAGTCATGCATGGCCAACACAAAAAAATTGATTTTTTACCAGATAAAAAAGG
Found at i:34432277 original size:117 final size:116
Alignment explanation
Indices: 34432092--34432588 Score: 445
Period size: 117 Copynumber: 4.3 Consensus size: 116
34432082 TTGTATGACC
* * *
34432092 AACAGAAAAAAATTGATTTTTTACCAGATAAAAAAGCGGATGTCGGCCAT-GCAATGGCCAACA-
1 AACACAAAAAAATTGATTTTTTACCAGAT-AAAAAG-GGGTGTCGGCCATGGC-ATGACCAACAC
* * *
34432155 C-AAAAAATTCGATTTTTTTATCTGACAAAAAGAGGTGTTGATCATTGCATGGTT
63 CAAAAAAATTCGAATTTTTTATCTGACAAAAAGAGGTGTTGACCA-TGCATGGCT
* * **
34432209 AACACAAAAAAATTGATTTTTTACCAGATAAAAAAGGGGTGTCAGTCATGGCATGACCAACATAA
1 AACACAAAAAAATTGATTTTTTACCAGAT-AAAAAGGGGTGTCGGCCATGGCATGACCAACACCA
* * *
34432274 AAAAAATTCGAATTTTTTATCTAACAAAAAGAGATG--G----T-C--GAC-
65 AAAAAATTCGAATTTTTTATCTGACAAAAAGAGGTGTTGACCATGCATGGCT
* * ** *
34432316 -AC-CAAAAAATTTGATTTTTTATTCAGATAAAAAGGGGTGTCGGCCATGTAATGGCCAACACCA
1 AACACAAAAAAATTGATTTTTTA-CCAGATAAAAAGGGGTGTCGGCCATGGCATGACCAACACCA
** * ** *
34432379 AAAAAATTTAAAATTTTTTATCTGA-AAAAAGGGGTGTCAACCATTGCCTGGCT
65 AAAAAA-TTCGAATTTTTTATCTGACAAAAAGAGGTGTTGACCA-TGCATGGCT
* * *
34432432 AACACAAAAAAATT-ATTTTTTTATCAGATAAATAGGGGTGTCGACCATGGCATGACCAACACCA
1 AACACAAAAAAATTGA-TTTTTTACCAGATAAAAAGGGGTGTCGGCCATGGCATGACCAACACCA
* * * *
34432496 AAACAATT-GAATTTTTTATCTGACAAAAAGGGAGTGTTGGCCATGCATGGCC
65 AAAAAATTCGAATTTTTTATCTGACAAAAAGAG-GTGTTGACCATGCATGGCT
* * *
34432548 AACACCCAAAAAATTGATTTTTTTTATCAGATTAAAAGGGG
1 AACA-CAAAAAAATTGA--TTTTTTACCAGATAAAAAGGGG
34432589 GTGTTGACCA
Statistics
Matches: 313, Mismatches: 43, Indels: 46
0.78 0.11 0.11
Matches are distributed among these distances:
105 61 0.19
106 22 0.07
108 1 0.00
110 1 0.00
111 1 0.00
112 1 0.00
113 1 0.00
115 16 0.05
116 41 0.13
117 97 0.31
118 50 0.16
119 21 0.07
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (116 bp):
AACACAAAAAAATTGATTTTTTACCAGATAAAAAGGGGTGTCGGCCATGGCATGACCAACACCAA
AAAAATTCGAATTTTTTATCTGACAAAAAGAGGTGTTGACCATGCATGGCT
Found at i:34432384 original size:105 final size:105
Alignment explanation
Indices: 34432213--34432409 Score: 254
Period size: 105 Copynumber: 1.9 Consensus size: 105
34432203 ATGGTTAACA
* * *
34432213 CAAAAAAATTGATTTTTTACCAGATAAAAAAGGGGTGTCAGTCATGGCATGACCAACATAAAAAA
1 CAAAAAAATTGATTTTTTACCAGATAAAAAAGGGGTGTCAGCCATGGAATGACCAACACAAAAAA
**
34432278 AA-TTCGAATTTTTTATCTAACAAAAAGAGATGGTCGACAC
66 AATTTAAAATTTTTTATCTAA-AAAAAGAGATGGTCGACAC
* * * * * *
34432318 CAAAAAATTTGATTTTTTATTCAGAT-AAAAAGGGGTGTCGGCCATGTAATGGCCAACACCAAAA
1 CAAAAAAATTGATTTTTTA-CCAGATAAAAAAGGGGTGTCAGCCATGGAATGACCAACACAAAAA
*
34432382 AAATTTAAAATTTTTTATCTGAAAAAAG
65 AAATTTAAAATTTTTTATCTAAAAAAAG
34432410 GGGTGTCAAC
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
105 58 0.74
106 20 0.26
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (105 bp):
CAAAAAAATTGATTTTTTACCAGATAAAAAAGGGGTGTCAGCCATGGAATGACCAACACAAAAAA
AATTTAAAATTTTTTATCTAAAAAAAGAGATGGTCGACAC
Found at i:34432410 original size:60 final size:58
Alignment explanation
Indices: 34432314--34432617 Score: 276
Period size: 59 Copynumber: 5.1 Consensus size: 58
34432304 GAGATGGTCG
* * * *
34432314 ACACCAAAAAATTTGATTTTTTATTCAGATAAAAAGGGGTGTCGGCCATGTAATGGCCA
1 ACACCAAAAAAATTAATTTTTTA-TCAGATAAAAAGGGGTGTCGACCATGTCATGGCCA
* * * *
34432373 ACACCAAAAAAATTTAAAATTTTTTATCTGA-AAAAAGGGGTGTCAACCAT-TGCCTGGCTA
1 ACACCAAAAAAA-TT--AATTTTTTATCAGATAAAAAGGGGTGTCGACCATGT-CATGGCCA
* * * *
34432433 ACA-CAAAAAAATTATTTTTTTATCAGATAAATAGGGGTGTCGACCATGGCATGACCA
1 ACACCAAAAAAATTAATTTTTTATCAGATAAAAAGGGGTGTCGACCATGTCATGGCCA
* * * * *
34432490 ACACCAAAACAATTGAATTTTTTATCTGACAAAAAGGGAGTGTTGGCCATG-CATGGCCA
1 ACACCAAAAAAATT-AATTTTTTATCAGATAAAAAGGG-GTGTCGACCATGTCATGGCCA
* * * *
34432549 ACACCCAAAAAATTGATTTTTTTTATCAGATTAAAAGGGGGTGTTGACCATG-CAATGGCCA
1 ACACCAAAAAAATT-A-ATTTTTTATCAGA-TAAAAAGGGGTGTCGACCATGTC-ATGGCCA
*
34432610 AAACCAAA
1 ACACCAAA
34432618 TTTTTTTTTT
Statistics
Matches: 200, Mismatches: 33, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
56 12 0.06
57 25 0.12
58 11 0.05
59 60 0.30
60 60 0.30
61 24 0.12
62 8 0.04
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (58 bp):
ACACCAAAAAAATTAATTTTTTATCAGATAAAAAGGGGTGTCGACCATGTCATGGCCA
Found at i:34432571 original size:59 final size:57
Alignment explanation
Indices: 34432314--34432617 Score: 290
Period size: 60 Copynumber: 5.1 Consensus size: 57
34432304 GAGATGGTCG
* *
34432314 ACACCAAAAAATTTG-ATTTTTTATTCAGATAAAAAGGGGTGTCGGCCATGTAATGGCCA
1 ACACCAAAAAA-TTGAATTTTTTA-TCAGATAAAAAGGGGTGTCGACCATG-CATGGCCA
* * * * *
34432373 ACACCAAAAAAATTTAAAATTTTTTATCTGA-AAAAAGGGGTGTCAACCATTGCCTGGCTA
1 ACACC-AAAAAA-TT-GAATTTTTTATCAGATAAAAAGGGGTGTCGACCA-TGCATGGCCA
* * * *
34432433 ACACAAAAAAATT-ATTTTTTTATCAGATAAATAGGGGTGTCGACCATGGCATGACCA
1 ACACCAAAAAATTGAATTTTTTATCAGATAAAAAGGGGTGTCGACCAT-GCATGGCCA
* * * *
34432490 ACACCAAAACAATTGAATTTTTTATCTGACAAAAAGGGAGTGTTGGCCATGCATGGCCA
1 ACACCAAAA-AATTGAATTTTTTATCAGATAAAAAGGG-GTGTCGACCATGCATGGCCA
* * *
34432549 ACACCCAAAAAATTGATTTTTTTTATCAGATTAAAAGGGGGTGTTGACCATGCAATGGCCA
1 ACA-CCAAAAAATTGA-ATTTTTTATCAGA-TAAAAAGGGGTGTCGACCATGC-ATGGCCA
*
34432610 AAACCAAA
1 ACACCAAA
34432618 TTTTTTTTTT
Statistics
Matches: 203, Mismatches: 29, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
56 13 0.06
57 30 0.15
58 6 0.03
59 47 0.23
60 77 0.38
61 22 0.11
62 8 0.04
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (57 bp):
ACACCAAAAAATTGAATTTTTTATCAGATAAAAAGGGGTGTCGACCATGCATGGCCA
Found at i:34432682 original size:58 final size:56
Alignment explanation
Indices: 34432447--34432668 Score: 153
Period size: 60 Copynumber: 3.8 Consensus size: 56
34432437 AAAAAAATTA
* * * **
34432447 TTTTTTTATCAGATAAATA-GGGGTGTCGACCATGGC-ATGACCAACACCAAAACAATTGA
1 TTTTTTTATCAGATAAAAAGGGGGTGTCGACCAT-GCAATGGCCAAAACC---A-AATTTT
* * * * * * * *
34432506 ATTTTTTATCTGACAAAAAGGGAGTGTTGGCCATGC-ATGGCCAACACCCAAAAAATTGAT
1 TTTTTTTATCAGATAAAAAGGGGGTGTCGACCATGCAATGGCCAA-AACC---AAATT-TT
* *
34432566 TTTTTTTATCAGATTAAAAGGGGGTGTTGACCATGCAATGGCCAAAACCAAATTTT
1 TTTTTTTATCAGATAAAAAGGGGGTGTCGACCATGCAATGGCCAAAACCAAATTTT
* * *
34432622 TTTTTTCTGTCAGATAAAAAAGGGGGTGTCGGCTATGCAATGGCCAA
1 TTTTTT-TATCAGAT-AAAAAGGGGGTGTCGACCATGCAATGGCCAA
34432669 CATCATTTTT
Statistics
Matches: 132, Mismatches: 25, Indels: 13
0.78 0.15 0.08
Matches are distributed among these distances:
56 7 0.05
57 12 0.09
58 27 0.20
59 28 0.21
60 50 0.38
61 8 0.06
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (56 bp):
TTTTTTTATCAGATAAAAAGGGGGTGTCGACCATGCAATGGCCAAAACCAAATTTT
Found at i:34433803 original size:239 final size:239
Alignment explanation
Indices: 34433384--34433871 Score: 949
Period size: 239 Copynumber: 2.0 Consensus size: 239
34433374 ATAAATATTC
34433384 ATTTTAAAAATGATATTGTGAAGCAAAACTATACTTTTGAATAATATTCAAATTCATTAATATTA
1 ATTTTAAAAATGATATTGTGAAGCAAAACTATACTTTTGAATAATATTCAAATTCATTAATATTA
34433449 TGATATTTTAGTAATAATATAAAAAAATTGTTGTAACTCATTATTAACATTTTTATATATGAAAT
66 TGATATTTTAGTAATAATATAAAAAAATTGTTGTAACTCATTATTAACATTTTTATATATGAAAT
34433514 ATAAATTTTTATACATTTGTAAGTAATTAATATTTTTTTTGAAAGTCGTAAGTAATTAATATTAA
131 ATAAATTTTTATACATTTGTAAGTAATTAATATTTTTTTTGAAAGTCGTAAGTAATTAATATTAA
*
34433579 TTATTTGTAAATTTTAAATTTGAATATTAATCTATATTTTAAAT
196 TTATTTGTAAAATTTAAATTTGAATATTAATCTATATTTTAAAT
*
34433623 ATTTTAAAAATGATATTGTGAAGTAAAACTATACTTTTGAATAATATTCAAATTCATTAATATTA
1 ATTTTAAAAATGATATTGTGAAGCAAAACTATACTTTTGAATAATATTCAAATTCATTAATATTA
34433688 TGATATTTTAGTAATAATATAAAAAAATTGTTGTAACTCATTATTAACATTTTTATATATGAAAT
66 TGATATTTTAGTAATAATATAAAAAAATTGTTGTAACTCATTATTAACATTTTTATATATGAAAT
34433753 ATAAATTTTTATACATTTGTAAGTAATTAATATTTTTTTTGAAAGTCGTAAGTAATTAATATTAA
131 ATAAATTTTTATACATTTGTAAGTAATTAATATTTTTTTTGAAAGTCGTAAGTAATTAATATTAA
34433818 TTATTTGTAAAATTTAAATTTGAATATTAATCTATATTTTAAAT
196 TTATTTGTAAAATTTAAATTTGAATATTAATCTATATTTTAAAT
34433862 ATTATTAAAA
1 ATT-TTAAAA
34433872 TATAACCGTT
Statistics
Matches: 246, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
239 240 0.98
240 6 0.02
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (239 bp):
ATTTTAAAAATGATATTGTGAAGCAAAACTATACTTTTGAATAATATTCAAATTCATTAATATTA
TGATATTTTAGTAATAATATAAAAAAATTGTTGTAACTCATTATTAACATTTTTATATATGAAAT
ATAAATTTTTATACATTTGTAAGTAATTAATATTTTTTTTGAAAGTCGTAAGTAATTAATATTAA
TTATTTGTAAAATTTAAATTTGAATATTAATCTATATTTTAAAT
Found at i:34441071 original size:17 final size:15
Alignment explanation
Indices: 34441048--34441087 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
34441038 ATAATAAAAA
34441048 TATAATTTTATTATTT
1 TATAATTTTATT-TTT
34441064 TAATAA-TTTATTTTT
1 T-ATAATTTTATTTTT
34441079 TATAATTTT
1 TATAATTTT
34441088 TAAAAGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.18
15 7 0.32
16 7 0.32
17 4 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATAATTTTATTTTT
Found at i:34447723 original size:20 final size:19
Alignment explanation
Indices: 34447698--34447735 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
34447688 AATTTATTTT
*
34447698 TAATTGTTATATTAATATTA
1 TAATTGATATATT-ATATTA
34447718 TAATTGATATATTATATT
1 TAATTGATATATTATATT
34447736 TTGTTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TAATTGATATATTATATTA
Found at i:34469626 original size:2 final size:2
Alignment explanation
Indices: 34469619--34469644 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34469609 AATCAGATTA
34469619 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
34469645 TAAAAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34469829 original size:55 final size:55
Alignment explanation
Indices: 34469763--34469873 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
34469753 GCAGCCAGGC
* *
34469763 ACTGTAATCGCAGGAGAAATGCTTTAAAGATGAGAGAAAATTAGACGGATGCACT
1 ACTGTAATCGCAGGAGAAATGCTTAAAAGATGAGAGAAAATTAGACGCATGCACT
*
34469818 ACTGTAATCGCAGGAGAAATGCTTAAAAGATGAGAGAAAATTAGACGCATTCACT
1 ACTGTAATCGCAGGAGAAATGCTTAAAAGATGAGAGAAAATTAGACGCATGCACT
34469873 A
1 A
34469874 AAGCAGTGCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (55 bp):
ACTGTAATCGCAGGAGAAATGCTTAAAAGATGAGAGAAAATTAGACGCATGCACT
Found at i:34478636 original size:15 final size:15
Alignment explanation
Indices: 34478616--34478669 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
34478606 ATACTACAAA
34478616 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
34478631 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
34478648 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
34478665 ATATT
1 ATATT
34478670 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:34478733 original size:16 final size:16
Alignment explanation
Indices: 34478702--34478738 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
34478692 ATGTGAAGAA
34478702 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
34478718 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
34478734 TATTA
1 TATTA
34478739 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:34480224 original size:26 final size:25
Alignment explanation
Indices: 34480166--34480224 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 25
34480156 CTAAACTCAC
34480166 TTTT-AAAATATGTATATTTAATAA
1 TTTTAAAAATATGTATATTTAATAA
*
34480190 TATTGAAAAATATGTATATTTTAATAA
1 T-TTTAAAAATATGTATA-TTTAATAA
34480217 TTTTAAAA
1 TTTTAAAA
34480225 TATTTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 1 0.03
25 2 0.07
26 18 0.60
27 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (25 bp):
TTTTAAAAATATGTATATTTAATAA
Found at i:34480260 original size:17 final size:17
Alignment explanation
Indices: 34480240--34480312 Score: 85
Period size: 17 Copynumber: 4.2 Consensus size: 17
34480230 TTAAAAATAA
*
34480240 AAATTTAATTTAAGTTT
1 AAATTTAATTTAAATTT
*
34480257 AAATTTAATTTAAGTTT
1 AAATTTAATTTAAATTT
*
34480274 AAATTTATTTTTAAATTT
1 AAATTTA-ATTTAAATTT
*
34480292 AAAATT-ATTCTAAATTT
1 AAATTTAATT-TAAATTT
34480309 AAAT
1 AAAT
34480313 AATTAAAATG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
16 2 0.04
17 34 0.69
18 13 0.27
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (17 bp):
AAATTTAATTTAAATTT
Found at i:34480292 original size:6 final size:6
Alignment explanation
Indices: 34480240--34480312 Score: 64
Period size: 6 Copynumber: 12.7 Consensus size: 6
34480230 TTAAAAATAA
* * **
34480240 AAATTT -AATTT AAGTTT AAATTT -AATTT AAGTTT AAATTT ATTTTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
34480286 AAATTT AAAATT --ATTCT AAATTT AAAT
1 AAATTT AAATTT AAATT-T AAATTT AAAT
34480313 AATTAAAATG
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
4 2 0.04
5 11 0.21
6 36 0.69
7 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:34481063 original size:13 final size:13
Alignment explanation
Indices: 34481030--34481083 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
34481020 TATATTAGAT
*
34481030 ATAATTAATAAGTA
1 ATAAATAATAA-TA
* *
34481044 TTAAATAATATTA
1 ATAAATAATAATA
34481057 ATAAATAATAATA
1 ATAAATAATAATA
*
34481070 AT-AATATTAATA
1 ATAAATAATAATA
34481082 AT
1 AT
34481084 TGTTAGTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 11 0.32
13 15 0.44
14 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (13 bp):
ATAAATAATAATA
Found at i:34482361 original size:59 final size:58
Alignment explanation
Indices: 34482260--34482581 Score: 303
Period size: 59 Copynumber: 5.5 Consensus size: 58
34482250 TTTGACCCCC
* * ** * **
34482260 CAAACTTTCCAAAAATTA-TACTTTGACCCTCGAACTTACCAAAACTCACATTTTTGCTTT
1 CAAAC-TTCCAAAAATTACCA-TTTTACCCTTAAACTT-CCAAAAATCACATTTTTGCCCT
* * *
34482320 CGAACTTCTAAAAATTACCATTTTACCCCTTAACCTTCCAAAAATCACA-TTTTGCCCT
1 CAAACTTCCAAAAATTACCATTTTA-CCCTTAAACTTCCAAAAATCACATTTTTGCCCT
* * *
34482378 -GAACTTCCAAAAATTACCATTTTACCCTCAAACTTAACAAAAATCACATTTTTGCCC-
1 CAAACTTCCAAAAATTACCATTTTACCCTTAAACTT-CCAAAAATCACATTTTTGCCCT
* * * *
34482435 CTAAACTTTCAAAAATTACCATTTTACCCCTAAATCTTTCAAAAATAACATTTTTGCCCT
1 C-AAACTTCCAAAAATTACCATTTTACCCTTAAA-CTTCCAAAAATCACATTTTTGCCCT
* * * * **
34482495 CAAACTTCCAAAAATAATCATTTTAACCTTAAACTTCCAAAAATTACATTTTTAACCT
1 CAAACTTCCAAAAATTACCATTTTACCCTTAAACTTCCAAAAATCACATTTTTGCCCT
* *
34482553 CGAACCTTCCAAAAATCA-CATTTTTACCC
1 C-AAACTTCCAAAAATTACCA-TTTTACCC
34482582 CCGAACTACC
Statistics
Matches: 220, Mismatches: 32, Indels: 21
0.81 0.12 0.08
Matches are distributed among these distances:
56 9 0.04
57 34 0.15
58 39 0.18
59 121 0.55
60 17 0.08
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (58 bp):
CAAACTTCCAAAAATTACCATTTTACCCTTAAACTTCCAAAAATCACATTTTTGCCCT
Found at i:34482363 original size:30 final size:29
Alignment explanation
Indices: 34482322--34482640 Score: 237
Period size: 29 Copynumber: 10.9 Consensus size: 29
34482312 TTTGCTTTCG
* *
34482322 AACTTCTAAAAATTACCATTTTACCCCTTA
1 AACTTCCAAAAATTA-CATTTTACCCCTGA
* * *
34482352 ACCTTCCAAAAATCACATTTT-GCCCTG-
1 AACTTCCAAAAATTACATTTTACCCCTGA
*
34482379 AACTTCCAAAAATTACCATTTTA-CCCTCA
1 AACTTCCAAAAATTA-CATTTTACCCCTGA
* * *
34482408 AACTTAACAAAAATCACATTTTTGCCCCT-A
1 AACTT-CCAAAAATTACA-TTTTACCCCTGA
*
34482438 AACTTTCAAAAATTACCATTTTACCCCT-A
1 AACTTCCAAAAATTA-CATTTTACCCCTGA
* * ** *
34482467 AATCTTTCAAAAATAACATTTTTGCCCTCA
1 AA-CTTCCAAAAATTACATTTTACCCCTGA
* * *
34482497 AACTTCCAAAAATAATCATTTTA-ACCTTA
1 AACTTCCAAAAATTA-CATTTTACCCCTGA
*
34482526 AACTTCCAAAAATTACATTTTTA-ACCTCGA
1 AACTTCCAAAAATTACA-TTTTACCCCT-GA
* * *
34482556 ACCTTCCAAAAATCACATTTTTACCCCCG-
1 AACTTCCAAAAATTACA-TTTTACCCCTGA
*
34482585 AACTACCAAAAATTACCATTTTACCCC-G-
1 AACTTCCAAAAATTA-CATTTTACCCCTGA
34482613 AA-TGTCCAAAAATTACATTTTTACCCCT
1 AACT-TCCAAAAATTACA-TTTTACCCCT
34482641 AACTGCCCCC
Statistics
Matches: 241, Mismatches: 31, Indels: 35
0.79 0.10 0.11
Matches are distributed among these distances:
27 16 0.07
28 38 0.16
29 103 0.43
30 78 0.32
31 6 0.02
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTACCCCTGA
Found at i:34482594 original size:59 final size:57
Alignment explanation
Indices: 34482296--34482639 Score: 198
Period size: 59 Copynumber: 5.9 Consensus size: 57
34482286 CCCTCGAACT
* * * * * * * *
34482296 TACCAAAACTCACATTTTTGCTTTCGAACTTCTAAAAATTACCA-TTTTACCCCTTAACC
1 TACCAAAAATTACATTTTTAC-CTCGAACTTCCAAAAA-TAACATTTTTACCCC-CAAAC
* * ** * *
34482355 TTCCAAAAATCACATTTTGCCCT-GAACTTCCAAAAATTACCA-TTTTACCCTCAAAC
1 TACCAAAAATTACATTTTTACCTCGAACTTCCAAAAA-TAACATTTTTACCCCCAAAC
* * * * * * * *
34482411 TTAACAAAAATCACATTTTTGCCCCTAAACTTTCAAAAATTACCA-TTTTACCCCTAAATC
1 -TACCAAAAATTACATTTTTACCTC-GAACTTCCAAAAA-TAACATTTTTACCCCCAAA-C
** * * * * **
34482471 TTTCAAAAATAACATTTTTGCCCTCAAACTTCCAAAAATAATCA-TTTTAACCTTAAAC
1 TACCAAAAATTACATTTTT-ACCTCGAACTTCCAAAAATAA-CATTTTTACCCCCAAAC
* * *
34482529 TTCCAAAAATTACATTTTTAACCTCGAACCTTCCAAAAATCACATTTTTACCCCCGAAC
1 TACCAAAAATTACATTTTT-ACCTCGAA-CTTCCAAAAATAACATTTTTACCCCCAAAC
* *
34482588 TACCAAAAATTACCA-TTTTACCCCGAA-TGTCCAAAAATTACATTTTTACCCC
1 TACCAAAAATTA-CATTTTTACCTCGAACT-TCCAAAAATAACATTTTTACCCC
34482640 TAACTGCCCC
Statistics
Matches: 235, Mismatches: 40, Indels: 22
0.79 0.13 0.07
Matches are distributed among these distances:
56 4 0.02
57 66 0.28
58 36 0.15
59 123 0.52
60 6 0.03
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.33
Consensus pattern (57 bp):
TACCAAAAATTACATTTTTACCTCGAACTTCCAAAAATAACATTTTTACCCCCAAAC
Found at i:34482634 original size:28 final size:28
Alignment explanation
Indices: 34482257--34482644 Score: 239
Period size: 30 Copynumber: 13.3 Consensus size: 28
34482247 CGTTTTGACC
* * * *
34482257 CCCCAAACTTTCCAAAAATTATACTTTGA
1 CCCCGAAC-TTCCAAAAATTACATTTTTA
* * *
34482286 CCCTCGAACTTACCAAAACTCACATTTTTG
1 CCC-CGAACTT-CCAAAAATTACATTTTTA
** *
34482316 CTTTCGAACTTCTAAAAATTACCA-TTTTA
1 C-CCCGAACTTCCAAAAATTA-CATTTTTA
* * *
34482345 CCCCTTAACCTTCCAAAAATCACA-TTTTG
1 CCCC-GAA-CTTCCAAAAATTACATTTTTA
*
34482374 CCCTGAACTTCCAAAAATTACCA-TTTTA
1 CCCCGAACTTCCAAAAATTA-CATTTTTA
* * * *
34482402 CCCTCAAACTTAACAAAAATCACATTTTTG
1 CCC-CGAACTT-CCAAAAATTACATTTTTA
* *
34482432 CCCCTAAACTTTCAAAAATTACCA-TTTTA
1 CCCC-GAACTTCCAAAAATTA-CATTTTTA
* * * *
34482461 CCCCTAAATCTTTCAAAAATAACATTTTTG
1 CCCC-GAA-CTTCCAAAAATTACATTTTTA
* * *
34482491 CCCTCAAACTTCCAAAAATAATCATTTTAA
1 CCC-CGAACTTCCAAAAATTA-CATTTTTA
***
34482521 CCTTAAACTTCCAAAAATTACATTTTTAA
1 CCCCGAACTTCCAAAAATTACATTTTT-A
* *
34482550 CCTCGAACCTTCCAAAAATCACATTTTTA
1 CCCCGAA-CTTCCAAAAATTACATTTTTA
*
34482579 CCCCCGAACTACCAAAAATTACCA-TTTTA
1 -CCCCGAACTTCCAAAAATTA-CATTTTTA
34482608 CCCCGAA-TGTCCAAAAATTACATTTTTA
1 CCCCGAACT-TCCAAAAATTACATTTTTA
*
34482636 CCCCTAACT
1 CCCCGAACT
34482645 GCCCCCCCGA
Statistics
Matches: 288, Mismatches: 48, Indels: 46
0.75 0.13 0.12
Matches are distributed among these distances:
27 15 0.05
28 46 0.16
29 109 0.38
30 117 0.41
31 1 0.00
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.32
Consensus pattern (28 bp):
CCCCGAACTTCCAAAAATTACATTTTTA
Found at i:34482665 original size:41 final size:41
Alignment explanation
Indices: 34482608--34482691 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
34482598 TACCATTTTA
34482608 CCCCGAATGTCCAAAAATTACATTTTTACCCCTAACTGCCC
1 CCCCGAATGTCCAAAAATTACATTTTTACCCCTAACTGCCC
* *
34482649 CCCCGAATGTCCAAAAATTACATTTTTACCCCTGATTGCCC
1 CCCCGAATGTCCAAAAATTACATTTTTACCCCTAACTGCCC
34482690 CC
1 CC
34482692 AAAATTACCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.37, G:0.08, T:0.27
Consensus pattern (41 bp):
CCCCGAATGTCCAAAAATTACATTTTTACCCCTAACTGCCC
Found at i:34489767 original size:3 final size:3
Alignment explanation
Indices: 34489746--34489804 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
34489736 GAGTGAAAGA
* * **
34489746 AAT AAA AAT AAT AAA AAT AAT ATAT ATAT TTT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT
34489793 AAT AAT AAT AAT
1 AAT AAT AAT AAT
34489805 TGATAAAGTA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 41 0.87
4 6 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:34493674 original size:26 final size:27
Alignment explanation
Indices: 34493634--34493684 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
34493624 AATTTAGTAT
34493634 TGTTTTTGAAAAGTA-TTGTGAAAAAG
1 TGTTTTTGAAAAGTACTTGTGAAAAAG
** *
34493660 TGTTTTTGATGAGTACTTTTGAAAA
1 TGTTTTTGAAAAGTACTTGTGAAAA
34493685 GTTTGATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (27 bp):
TGTTTTTGAAAAGTACTTGTGAAAAAG
Found at i:34493912 original size:30 final size:30
Alignment explanation
Indices: 34493861--34493917 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
34493851 ATAACTTGTT
* *
34493861 AATATTTTAATATATGAAATATAAATTTTA
1 AATATTTTAAGAAATGAAATATAAATTTTA
*
34493891 AATATTTTTAAGAAATG-AATATTAATT
1 AATA-TTTTAAGAAATGAAATATAAATT
34493918 ATATATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 13 0.57
31 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (30 bp):
AATATTTTAAGAAATGAAATATAAATTTTA
Found at i:34498479 original size:22 final size:22
Alignment explanation
Indices: 34498451--34498501 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
34498441 TGATTGGTTT
34498451 TGTCTTTTTAATTGTGTATTTA
1 TGTCTTTTTAATTGTGTATTTA
34498473 TGTCTTTTTAATTGTGTATTTA
1 TGTCTTTTTAATTGTGTATTTA
34498495 TGTCTTT
1 TGTCTTT
34498502 GCTGGTTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.16, C:0.06, G:0.14, T:0.65
Consensus pattern (22 bp):
TGTCTTTTTAATTGTGTATTTA
Found at i:34501585 original size:19 final size:16
Alignment explanation
Indices: 34501550--34501602 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
34501540 ATTATATTAA
34501550 TAATAAATTTTTATTT
1 TAATAAATTTTTATTT
34501566 TAATAAATTATTTAATTT
1 TAATAAATT-TTT-ATTT
*
34501584 T--TCAA-TTTTATTT
1 TAATAAATTTTTATTT
34501597 TAATAA
1 TAATAA
34501603 TAAATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 5 0.16
14 3 0.10
15 3 0.10
16 12 0.39
17 3 0.10
18 5 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATAAATTTTTATTT
Found at i:34504207 original size:33 final size:33
Alignment explanation
Indices: 34504169--34504233 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
34504159 ATTTTAGTTA
*
34504169 TTTTTTCGTGTTGTATTCATGTTATTCTTTTTTT
1 TTTTTTCGTGAT-TATTCATGTTATTCTTTTTTT
*
34504203 TTTTTTTGTGATTATTCATGTTATTCTTTTT
1 TTTTTTCGTGATTATTCATGTTATTCTTTTT
34504234 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 19 0.66
34 10 0.34
ACGTcount: A:0.11, C:0.08, G:0.11, T:0.71
Consensus pattern (33 bp):
TTTTTTCGTGATTATTCATGTTATTCTTTTTTT
Found at i:34515832 original size:3 final size:3
Alignment explanation
Indices: 34515826--34515854 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
34515816 AACAAATGCA
34515826 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
34515855 TCAATAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34522106 original size:33 final size:33
Alignment explanation
Indices: 34522064--34522128 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
34522054 ACCATCCATT
*
34522064 ATGTGTACATACTAGAGTTGAGTAATATCACTA
1 ATGTGTACATACTACAGTTGAGTAATATCACTA
34522097 ATGTGTACATACTACAGTTGAGTAATATCACT
1 ATGTGTACATACTACAGTTGAGTAATATCACT
34522129 TCTATAGACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (33 bp):
ATGTGTACATACTACAGTTGAGTAATATCACTA
Found at i:34522686 original size:15 final size:14
Alignment explanation
Indices: 34522665--34522716 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
34522655 TTAAAGGTGT
34522665 TTTTAATATTTAAA
1 TTTTAATATTTAAA
* *
34522679 TATTTAATTTTCTAAT
1 T-TTTAATATT-TAAA
*
34522695 TTTTTATATTTTAAA
1 TTTTAATA-TTTAAA
34522710 TTTTAAT
1 TTTTAAT
34522717 TTAATATTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
14 1 0.03
15 22 0.76
16 6 0.21
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTAATATTTAAA
Found at i:34524665 original size:3 final size:3
Alignment explanation
Indices: 34524657--34524683 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
34524647 CTTGATAAAA
34524657 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
34524684 TTCTTCCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:34528011 original size:24 final size:22
Alignment explanation
Indices: 34527978--34528022 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
34527968 TGTCACCATT
34527978 AAATCTATTTGAATCCAAATAATTC
1 AAATCTATTT-AA--CAAATAATTC
34528003 AAAT-TATTTAACAAATAATT
1 AAATCTATTTAACAAATAATT
34528023 AATCTACTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 9 0.45
23 2 0.10
24 5 0.25
25 4 0.20
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATCTATTTAACAAATAATTC
Found at i:34531464 original size:16 final size:16
Alignment explanation
Indices: 34531445--34531475 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34531435 AGAATGTTCG
34531445 TTTGAGTGAATAAATC
1 TTTGAGTGAATAAATC
*
34531461 TTTGGGTGAATAAAT
1 TTTGAGTGAATAAAT
34531476 TTGATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (16 bp):
TTTGAGTGAATAAATC
Found at i:34541699 original size:55 final size:55
Alignment explanation
Indices: 34541638--34541748 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
34541628 ATTAACTGAG
* *
34541638 TCTACTTAAACGAATCTCATGTCATTGATTGATTTTATATTATACCCAGTGACGA
1 TCTACTTAAACGAATCTCACGTCATTGATTGATTTTATATTACACCCAGTGACGA
*
34541693 TCTACTTAAACGAATCTCACGTCATTGATTGATTTTATATTACACTCAGTGACGA
1 TCTACTTAAACGAATCTCACGTCATTGATTGATTTTATATTACACCCAGTGACGA
34541748 T
1 T
34541749 TGACGAACCC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (55 bp):
TCTACTTAAACGAATCTCACGTCATTGATTGATTTTATATTACACCCAGTGACGA
Found at i:34552320 original size:20 final size:20
Alignment explanation
Indices: 34552295--34552347 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
34552285 TAAAATAATT
34552295 TTATAAATATATTTTTTTAA
1 TTATAAATATATTTTTTTAA
*
34552315 TTATAAATATATATTTTTAA
1 TTATAAATATATTTTTTTAA
34552335 -TATAAA-ATATTTT
1 TTATAAATATATTTT
34552348 CGTTCACCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.19
19 6 0.19
20 19 0.61
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATAAATATATTTTTTTAA
Found at i:34553543 original size:16 final size:16
Alignment explanation
Indices: 34553514--34553547 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
34553504 TAACAGCACT
34553514 TTTATATTTAAAAAAA
1 TTTATATTTAAAAAAA
*
34553530 TTTATCTTTTAAAAAAA
1 TTTAT-ATTTAAAAAAA
34553547 T
1 T
34553548 AAAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTATATTTAAAAAAA
Found at i:34553969 original size:16 final size:17
Alignment explanation
Indices: 34553927--34553970 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
34553917 TTTTAAATTT
34553927 TAAAATTTTTATTTAAA
1 TAAAATTTTTATTTAAA
**
34553944 TTTAATTTTT-TTTAAA
1 TAAAATTTTTATTTAAA
*
34553960 TAAAAATTTTA
1 TAAAATTTTTA
34553971 ATGTAACATT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAAAATTTTTATTTAAA
Found at i:34554750 original size:90 final size:95
Alignment explanation
Indices: 34554650--34554838 Score: 244
Period size: 102 Copynumber: 2.0 Consensus size: 95
34554640 ATTTTATTTA
**
34554650 ATAATTTTTAGTTACTCACAT-A-TGAAT-A-G-AAGAAATTTTTCAGACATATTTTGAAAATGT
1 ATAATTTTTAGCCACTCACATAATTGAATAATGAAAGAAATTTTTCAGACATATTTTGAAAATGT
34554710 TCTATTTTTTATTAAAATTTTGCTCAATTG
66 TCTATTTTTTATTAAAATTTTGCTCAATTG
34554740 ATAATTTTTAGCCACTCACATAAATTGTTTTGAATGAATGAAAGAAATTTTTCAGACATATTTTG
1 ATAATTTTTAGCCACTCACAT-AA-----TTGAAT-AATGAAAGAAATTTTTCAGACATATTTTG
* *
34554805 ATAATGTTGTATTTTTTATTAAAATTTTGCTCAA
59 AAAATGTTCTATTTTTTATTAAAATTTTGCTCAA
34554839 AATTTTAATT
Statistics
Matches: 83, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
90 19 0.23
92 1 0.01
98 5 0.06
100 1 0.01
101 1 0.01
102 56 0.67
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (95 bp):
ATAATTTTTAGCCACTCACATAATTGAATAATGAAAGAAATTTTTCAGACATATTTTGAAAATGT
TCTATTTTTTATTAAAATTTTGCTCAATTG
Found at i:34559114 original size:31 final size:30
Alignment explanation
Indices: 34559063--34559123 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
34559053 TAAATTTTTT
* **
34559063 TAGTTAAATTTGACTTTTAATCTTTTAAAAA
1 TAGTCAAATTTGACCATTAAT-TTTTAAAAA
*
34559094 TAGTCAAATTTGACCATTAATTTTTCAAAA
1 TAGTCAAATTTGACCATTAATTTTTAAAAA
34559124 CGAGTCAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (30 bp):
TAGTCAAATTTGACCATTAATTTTTAAAAA
Found at i:34559130 original size:31 final size:31
Alignment explanation
Indices: 34559068--34559130 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
34559058 TTTTTTAGTT
** *
34559068 AAATTTGACTTTTAATCTTTTAAAAATAGTC
1 AAATTTGACCATTAATCTTTTAAAAAGAGTC
*
34559099 AAATTTGACCATTAAT-TTTTCAAAACGAGTC
1 AAATTTGACCATTAATCTTTT-AAAAAGAGTC
34559130 A
1 A
34559131 GATTATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.40
Consensus pattern (31 bp):
AAATTTGACCATTAATCTTTTAAAAAGAGTC
Found at i:34562313 original size:57 final size:57
Alignment explanation
Indices: 34562185--34562328 Score: 180
Period size: 57 Copynumber: 2.5 Consensus size: 57
34562175 TTTATATATT
* * ** **
34562185 AAAAAAATAAAAAAATAAAATTATATTAGTGGAGGATTATCAAATAACGGTATTACAG
1 AAAAAAAT-AAAAAATAATATTATATTAGCGGAGGATTATCAAATAACGACACCACAG
***
34562243 AAAAAAATAAAAAATAATATTATATTAGCGGAGGATTATCAAATGGTGACACCACAAG
1 AAAAAAATAAAAAATAATATTATATTAGCGGAGGATTATCAAATAACGACACCAC-AG
*
34562301 AACAAAATAAAAAATAATATTATATTAG
1 AAAAAAATAAAAAATAATATTATATTAG
34562329 TGAAAATTTA
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
57 38 0.51
58 37 0.49
ACGTcount: A:0.56, C:0.07, G:0.12, T:0.25
Consensus pattern (57 bp):
AAAAAAATAAAAAATAATATTATATTAGCGGAGGATTATCAAATAACGACACCACAG
Found at i:34562463 original size:34 final size:33
Alignment explanation
Indices: 34562420--34562728 Score: 109
Period size: 34 Copynumber: 8.9 Consensus size: 33
34562410 CAAAATATAC
34562420 AAAAATTAAATAACAAATCAATTAAAAATAACTT
1 AAAAATTAAATAACAAATCAATTAAAAATAA-TT
* *
34562454 AAAAATTAAATAACAAAT-AA--AAATATTAAAT
1 AAAAATTAAATAACAAATCAATTAAA-AATAATT
* * * * *
34562485 AACAAATCAATTAA-AAATTACTTAAAAATTAAAT
1 AA-AAATTAAATAACAAATCAATTAAAAA-TAATT
* * * * * *
34562519 AACAAATCAATTAA-AAATTAAATTTACCCAACTAAATA
1 AA-AAATTAAATAACAAA-TCAA-TTA--AAAAT-AATT
* *
34562557 AAAACATTAAATAAAAAATTAATTAAAAATTAAATAAAAAT
1 AAAA-ATTAAATAACAAATCAATTAAAAA-T-AAT-----T
34562598 AAAAACATTAAATAACAAATCAATTAAAAATAACTT
1 -AAAA-ATTAAATAACAAATCAATTAAAAATAA-TT
*
34562634 AAAAATTAAATAAC--A--AA-TAAAAATATTT
1 AAAAATTAAATAACAAATCAATTAAAAATAATT
* * * * *
34562662 AAAAATTAATTAA-AAATTAAATTTACTCAACTAAATA
1 AAAAATTAAATAACAAA-TCAA-TTA--AAAAT-AATT
34562699 AAAACATTAAATAACAAATCAATTAAAAAT
1 AAAA-ATTAAATAACAAATCAATTAAAAAT
34562729 TAAATCAAAA
Statistics
Matches: 212, Mismatches: 30, Indels: 65
0.69 0.10 0.21
Matches are distributed among these distances:
28 14 0.07
29 9 0.04
30 2 0.01
31 10 0.05
32 17 0.08
33 3 0.01
34 55 0.26
35 11 0.05
36 12 0.06
37 15 0.07
38 27 0.13
39 6 0.03
40 2 0.01
41 2 0.01
42 27 0.13
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (33 bp):
AAAAATTAAATAACAAATCAATTAAAAATAATT
Found at i:34562482 original size:54 final size:53
Alignment explanation
Indices: 34562420--34562525 Score: 194
Period size: 54 Copynumber: 2.0 Consensus size: 53
34562410 CAAAATATAC
34562420 AAAAATTAAATAACAAATCAATTAAAAATAACTTAAAAATTAAATAACAAATA
1 AAAAATTAAATAACAAATCAATTAAAAATAACTTAAAAATTAAATAACAAATA
*
34562473 AAAATATTAAATAACAAATCAATTAAAAATTACTTAAAAATTAAATAACAAAT
1 AAAA-ATTAAATAACAAATCAATTAAAAATAACTTAAAAATTAAATAACAAAT
34562526 CAATTAAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 4 0.08
54 47 0.92
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (53 bp):
AAAAATTAAATAACAAATCAATTAAAAATAACTTAAAAATTAAATAACAAATA
Found at i:34562570 original size:50 final size:48
Alignment explanation
Indices: 34562508--34562733 Score: 222
Period size: 50 Copynumber: 4.7 Consensus size: 48
34562498 AAAATTACTT
34562508 AAAA-ATTAAATAACAAATCAATTAAAAATTAAATTTACCCAACTAAATA
1 AAAACATTAAATAACAAATCAATTAAAAATTAAATTTA-CCAAC-AAATA
* *
34562557 AAAACATTAAATAAAAAATTAATTAAAAATTAAA--T---AA-AAATA
1 AAAACATTAAATAACAAATCAATTAAAAATTAAATTTACCAACAAATA
* **
34562599 AAAACATTAAATAACAAATCAATTAAAAATAACTTAAAAATTAAATAACAAATA
1 AAAACATTAAATAACAAATCAATT--AAA-AA-TT--AAATTTACCAACAAATA
* *
34562653 AAAATATT---TAA-AAATTAATTAAAAATTAAATTTACTCAACTAAATA
1 AAAACATTAAATAACAAATCAATTAAAAATTAAATTTAC-CAAC-AAATA
34562699 AAAACATTAAATAACAAATCAATTAAAAATTAAAT
1 AAAACATTAAATAACAAATCAATTAAAAATTAAAT
34562734 CAAAACAAAA
Statistics
Matches: 146, Mismatches: 12, Indels: 37
0.75 0.06 0.19
Matches are distributed among these distances:
42 27 0.18
44 11 0.08
45 5 0.03
46 16 0.11
47 2 0.01
48 7 0.05
49 7 0.05
50 54 0.37
51 3 0.02
53 2 0.01
54 12 0.08
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (48 bp):
AAAACATTAAATAACAAATCAATTAAAAATTAAATTTACCAACAAATA
Found at i:34562582 original size:84 final size:87
Alignment explanation
Indices: 34562420--34562683 Score: 265
Period size: 92 Copynumber: 3.0 Consensus size: 87
34562410 CAAAATATAC
* *
34562420 AAAAATTAAATAACAAATCAATTAAAAATAACTTAAAAATTAAATAACAAATAAAAATATTAAAT
1 AAAAATTAAATAACAAATCAATT-AAAATAACTTAAAAATTAAACAACAAATAAAAACATTAAAT
* **
34562485 AACAAATCAATTAAAAATTACTT
65 AAAAAATCAATTAAAAATTAAAT
* **
34562508 AAAAATTAAATAACAAATCAATT-AAA-AA-TT-AAATTTACCCAACTAAATAAAAACATTAAAT
1 AAAAATTAAATAACAAATCAATTAAAATAACTTAAAAATTAAACAAC-AAATAAAAACATTAAAT
*
34562569 AAAAAATTAATTAAAAATTAAATAAAAAT
65 AAAAAATCAATTAAAAA-T---T--AAAT
* *
34562598 AAAAACATTAAATAACAAATCAATTAAAAATAACTTAAAAATTAAATAACAAATAAAAATATT--
1 -AAAA-ATTAAATAACAAATCAATT-AAAATAACTTAAAAATTAAACAACAAATAAAAACATTAA
*
34562661 -T-AAAAATTAATTAAAAATTAAAT
63 ATAAAAAATCAATTAAAAATTAAAT
34562684 TTACTCAACT
Statistics
Matches: 148, Mismatches: 14, Indels: 30
0.77 0.07 0.16
Matches are distributed among these distances:
83 9 0.06
84 33 0.22
85 3 0.02
86 7 0.05
88 25 0.17
90 2 0.01
91 5 0.03
92 35 0.24
93 1 0.01
94 3 0.02
95 2 0.01
96 14 0.09
97 9 0.06
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (87 bp):
AAAAATTAAATAACAAATCAATTAAAATAACTTAAAAATTAAACAACAAATAAAAACATTAAATA
AAAAATCAATTAAAAATTAAAT
Found at i:34562624 original size:92 final size:97
Alignment explanation
Indices: 34562508--34562733 Score: 265
Period size: 92 Copynumber: 2.4 Consensus size: 97
34562498 AAAATTACTT
** *
34562508 AAAA-ATTAAATAACAAATCAATTAAAAATTAAATTTACCCAACTAAATAAAAACAT-TAAATA-
1 AAAACATTAAATAACAAATCAATTAAAAATTAAATTTA-AAAACTAAATAAAAA-ATAAAAATAT
34562570 AAAAATTAATTAAAAATT-AA-A-T-AA-AAATA
64 AAAAATTAATTAAAAATTAAATACTCAACAAATA
* * *
34562599 AAAACATTAAATAACAAATCAATTAAAAA-T-AACTTAAAAATTAAATAACAAATAAAAATATTT
1 AAAACATTAAATAACAAATCAATTAAAAATTAAATTTAAAAACTAAATAAAAAATAAAAATA--T
34562662 AAAAATTAATTAAAAATTAAATTTACTCAACTAAATA
64 AAAAATTAATTAAAAATTAAA--TACTCAAC-AAATA
34562699 AAAACATTAAATAACAAATCAATTAAAAATTAAAT
1 AAAACATTAAATAACAAATCAATTAAAAATTAAAT
34562734 CAAAACAAAA
Statistics
Matches: 113, Mismatches: 7, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
88 2 0.02
89 16 0.14
90 5 0.04
91 5 0.04
92 42 0.37
93 2 0.02
96 1 0.01
97 1 0.01
98 2 0.02
100 34 0.30
101 1 0.01
102 2 0.02
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (97 bp):
AAAACATTAAATAACAAATCAATTAAAAATTAAATTTAAAAACTAAATAAAAAATAAAAATATAA
AAATTAATTAAAAATTAAATACTCAACAAATA
Found at i:34562664 original size:28 final size:28
Alignment explanation
Indices: 34562565--34562678 Score: 96
Period size: 28 Copynumber: 4.1 Consensus size: 28
34562555 TAAAAACATT
34562565 AAATAAAAAATTAA-TTAAAAATTAAATAA
1 AAAT-AAAAA-TAACTTAAAAATTAAATAA
* * *
34562594 AAATAAAAA-CA-TTAAATAA-CAAAT-C
1 AAATAAAAATAACTTAAA-AATTAAATAA
*
34562619 AATTAAAAATAACTTAAAAATTAAATAA
1 AAATAAAAATAACTTAAAAATTAAATAA
* *
34562647 CAAATAAAAAT-ATTTAAAAATTAATTAA
1 -AAATAAAAATAACTTAAAAATTAAATAA
34562675 AAAT
1 AAAT
34562679 TAAATTTACT
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
25 8 0.12
26 13 0.19
27 15 0.22
28 20 0.29
29 13 0.19
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.27
Consensus pattern (28 bp):
AAATAAAAATAACTTAAAAATTAAATAA
Found at i:34562666 original size:10 final size:10
Alignment explanation
Indices: 34562570--34562678 Score: 57
Period size: 11 Copynumber: 10.6 Consensus size: 10
34562560 ACATTAAATA
34562570 AAAAATTAATT
1 AAAAA-TAATT
*
34562581 AAAAATTAAAT
1 AAAAA-TAATT
34562592 AAAAATAA--
1 AAAAATAATT
* *
34562600 AAACATTAAAT
1 AAA-AATAATT
34562611 AACAAATCAATT
1 AA-AAAT-AATT
34562623 AAAAATAACTT
1 AAAAATAA-TT
34562634 --AAA-AATT
1 AAAAATAATT
* *
34562641 AAATAACAAAT
1 AAA-AATAATT
*
34562652 AAAAATATTT
1 AAAAATAATT
34562662 AAAAATTAATT
1 AAAAA-TAATT
34562673 AAAAAT
1 AAAAAT
34562679 TAAATTTACT
Statistics
Matches: 78, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
7 2 0.03
8 5 0.06
9 8 0.10
10 17 0.22
11 40 0.51
12 6 0.08
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAAATAATT
Found at i:34562682 original size:28 final size:30
Alignment explanation
Indices: 34562493--34562682 Score: 99
Period size: 29 Copynumber: 6.2 Consensus size: 30
34562483 ATAACAAATC
*
34562493 AATTAAAAATTACTTAAAAATTAAATAACA
1 AATTAAAAATAACTTAAAAATTAAATAACA
* * ***
34562523 AATCAATTAAA-AA-TT-AAATTTACCCAACTA
1 AATTAA--AAATAACTTAAAAATTAAATAAC-A
* * * *
34562553 AATAAAAACATTAAATAAAAAATTAATTAA-A
1 AATTAAAA-A-TAACTTAAAAATTAAATAACA
* *
34562584 AATTAAATAA-AAATAAAAACATTAAATAACAAA
1 AATTAAA-AATAACTTAAAA-ATTAAATAAC--A
34562617 TCAATTAAAAATAACTTAAAAATTAAATAACA
1 --AATTAAAAATAACTTAAAAATTAAATAACA
* *
34562649 AA-TAAAAAT-ATTTAAAAATTAATTAA-A
1 AATTAAAAATAACTTAAAAATTAAATAACA
34562676 AATTAAA
1 AATTAAA
34562683 TTTACTCAAC
Statistics
Matches: 125, Mismatches: 18, Indels: 36
0.70 0.10 0.20
Matches are distributed among these distances:
27 3 0.02
28 21 0.17
29 26 0.21
30 23 0.18
31 11 0.09
32 6 0.05
33 9 0.07
34 12 0.10
35 14 0.11
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (30 bp):
AATTAAAAATAACTTAAAAATTAAATAACA
Found at i:34562756 original size:31 final size:33
Alignment explanation
Indices: 34562711--34562776 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 33
34562701 AACATTAAAT
*
34562711 AACAAATCAATTAAAA-ATTAAAT-CAAAACAA
1 AACAAATCAATTAAAACAATAAATACAAAACAA
*
34562742 AACAAAT-AATTTAAAACAATAAATACTAAACAA
1 AACAAATCAA-TTAAAACAATAAATACAAAACAA
34562775 AA
1 AA
34562777 TATAACTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 2 0.07
31 13 0.43
32 6 0.20
33 9 0.30
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (33 bp):
AACAAATCAATTAAAACAATAAATACAAAACAA
Found at i:34563024 original size:21 final size:21
Alignment explanation
Indices: 34562998--34563065 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
34562988 CTTCGTTATT
34562998 TTTTTCGTGTATTTTGTATAA
1 TTTTTCGTGTATTTTGTATAA
* *** *
34563019 TTTTTCAATGT-TCAAGTAT-T
1 TTTTTC-GTGTATTTTGTATAA
*
34563039 TTTTTCGTGTATTTTATATAA
1 TTTTTCGTGTATTTTGTATAA
34563060 TTTTTC
1 TTTTTC
34563066 TCCGTAGTGC
Statistics
Matches: 33, Mismatches: 11, Indels: 6
0.66 0.22 0.12
Matches are distributed among these distances:
19 3 0.09
20 10 0.30
21 17 0.52
22 3 0.09
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (21 bp):
TTTTTCGTGTATTTTGTATAA
Found at i:34569538 original size:16 final size:15
Alignment explanation
Indices: 34569517--34569549 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
34569507 TTTTTTAGTA
34569517 TTTTTTAAAATTCATT
1 TTTTTTAAAATT-ATT
34569533 TTTTTTAAAATTATT
1 TTTTTTAAAATTATT
34569548 TT
1 TT
34569550 ACTGAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTAAAATTATT
Found at i:34577796 original size:42 final size:42
Alignment explanation
Indices: 34577750--34577831 Score: 94
Period size: 42 Copynumber: 2.0 Consensus size: 42
34577740 TAGATTTATT
* *
34577750 TTTTA-TTAAATATTTATAATCAAATTAAAATTAAATTTTTAG
1 TTTTAGTTAAATATTTATAAT-AAATAAAAATTAAAATTTTAG
** * *
34577792 TTTTAGTTTTATTTTTATAATTAATAAAAATTAAAATTTT
1 TTTTAGTTAAATATTTATAATAAATAAAAATTAAAATTTT
34577832 GTGTAATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
42 21 0.64
43 12 0.36
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (42 bp):
TTTTAGTTAAATATTTATAATAAATAAAAATTAAAATTTTAG
Found at i:34580946 original size:16 final size:18
Alignment explanation
Indices: 34580916--34580948 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
34580906 AAGAAAGTAT
34580916 AGGATAAAAAGGAAAAAG
1 AGGATAAAAAGGAAAAAG
34580934 AGGA-AAAAA-GAAAAA
1 AGGATAAAAAGGAAAAA
34580949 AACGCCCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (18 bp):
AGGATAAAAAGGAAAAAG
Found at i:34584523 original size:29 final size:29
Alignment explanation
Indices: 34584478--34584534 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
34584468 AAATTTCTAT
*
34584478 ACATTATTTTCAATCAATCGTTTTACTAC
1 ACATTATTTTCAATCAATCATTTTACTAC
* *
34584507 ACATTATTTTTAGTCAATCATTTTACTA
1 ACATTATTTTCAATCAATCATTTTACTA
34584535 TTTATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.47
Consensus pattern (29 bp):
ACATTATTTTCAATCAATCATTTTACTAC
Found at i:34589148 original size:25 final size:23
Alignment explanation
Indices: 34589099--34589160 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
34589089 ATTAATAAAA
*
34589099 TTTT-TAATTCTAAAAATTAATT
1 TTTTATAATTTTAAAAATTAATT
34589121 TTTTATGAATTTTAAAAA-TAATTAT
1 TTTTAT-AATTTTAAAAATTAA-T-T
34589146 TTTTATATATTTTAA
1 TTTTATA-ATTTTAA
34589161 GTTTTATCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
22 4 0.12
23 4 0.12
24 12 0.35
25 14 0.41
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTTATAATTTTAAAAATTAATT
Found at i:34590473 original size:18 final size:19
Alignment explanation
Indices: 34590446--34590481 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
34590436 AAATAACAAA
*
34590446 AATAATATAAGT-ATTTTT
1 AATAAAATAAGTGATTTTT
34590464 AATAAAATAAGTGATTTT
1 AATAAAATAAGTGATTTT
34590482 ATTATAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (19 bp):
AATAAAATAAGTGATTTTT
Found at i:34593394 original size:3 final size:3
Alignment explanation
Indices: 34593388--34593413 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
34593378 TTGCTGTTGT
34593388 TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TG
34593414 TGGCTACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.35, T:0.35
Consensus pattern (3 bp):
TGC
Found at i:34594286 original size:17 final size:18
Alignment explanation
Indices: 34594253--34594286 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
34594243 TATGGCACCA
*
34594253 TCAGCAACAATATATTCC
1 TCAGCAACAAAATATTCC
34594271 TCAGCAA-AAAATATTC
1 TCAGCAACAAAATATTC
34594287 GTTTTAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (18 bp):
TCAGCAACAAAATATTCC
Found at i:34598229 original size:15 final size:15
Alignment explanation
Indices: 34598187--34598227 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
34598177 TTAAAATGTA
34598187 TAAAAATTAAATTTT
1 TAAAAATTAAATTTT
* *
34598202 TAATATTTAAATTTT
1 TAAAAATTAAATTTT
34598217 TAAAAAATTAA
1 T-AAAAATTAA
34598228 TTAATTACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAAAATTAAATTTT
Found at i:34601581 original size:31 final size:31
Alignment explanation
Indices: 34601510--34601663 Score: 81
Period size: 31 Copynumber: 5.2 Consensus size: 31
34601500 TACTTGAACA
* * **
34601510 TAAAAT-TTTTGAAATTTTTTATTAAACTTT
1 TAAAATCTTTTAAAATTTTTAATTAAACCAT
* * *
34601540 TATAACCTTTTAAAATTTTTAATTAACCCAT
1 TAAAATCTTTTAAAATTTTTAATTAAACCAT
* * * * * *
34601571 TAAAATCTTTTATAAGTTCT-GTT-GACCTT
1 TAAAATCTTTTAAAATTTTTAATTAAACCAT
*
34601600 TAAAA-CTTTTAAAA--GTTAATTAAACCTAT
1 TAAAATCTTTTAAAATTTTTAATTAAACC-AT
* *
34601629 CAAAAT-TTTCTAAAA-TTTTAATTCAACCAT
1 TAAAATCTTT-TAAAATTTTTAATTAAACCAT
*
34601659 CAAAA
1 TAAAA
34601664 CTTAAATCTC
Statistics
Matches: 92, Mismatches: 25, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
26 1 0.01
27 2 0.02
28 11 0.12
29 16 0.17
30 18 0.20
31 44 0.48
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.44
Consensus pattern (31 bp):
TAAAATCTTTTAAAATTTTTAATTAAACCAT
Found at i:34608595 original size:30 final size:30
Alignment explanation
Indices: 34608559--34608618 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
34608549 TATTATGGAT
34608559 TTAAGATTAAAACTTTCATATCAATATTGA
1 TTAAGATTAAAACTTTCATATCAATATTGA
34608589 TTAAGATTAAAACTTTCATATCAATATTGA
1 TTAAGATTAAAACTTTCATATCAATATTGA
34608619 AATTTTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (30 bp):
TTAAGATTAAAACTTTCATATCAATATTGA
Found at i:34609837 original size:15 final size:15
Alignment explanation
Indices: 34609817--34609846 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34609807 GTATTACATA
34609817 CAGCACCGAAGAATT
1 CAGCACCGAAGAATT
34609832 CAGCACCGAAGAATT
1 CAGCACCGAAGAATT
34609847 AAACACGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (15 bp):
CAGCACCGAAGAATT
Found at i:34610483 original size:23 final size:23
Alignment explanation
Indices: 34610362--34610472 Score: 141
Period size: 23 Copynumber: 4.8 Consensus size: 23
34610352 GCTGGGGAAA
34610362 CAGTAAGCACACACAGTGTAAAT
1 CAGTAAGCACACACAGTGTAAAT
* * ** *
34610385 CAGTAGGCACACGCAGTACAAAA
1 CAGTAAGCACACACAGTGTAAAT
*
34610408 CAGTAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGTAAAT
* * *
34610431 CAGTAAGCACATATAGTGTGAAT
1 CAGTAAGCACACACAGTGTAAAT
34610454 CAGTAAGCACACACAGTGT
1 CAGTAAGCACACACAGTGT
34610473 TGAATAGTAA
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGTAAAT
Found at i:34624407 original size:549 final size:549
Alignment explanation
Indices: 34623349--34625011 Score: 2466
Period size: 549 Copynumber: 3.0 Consensus size: 549
34623339 AAACCCACTA
**
34623349 TTTCCTCCCTCAATTGACCATTCTCTTCGATTTTAGTTCTCAGGTCCTCTTCCAGTTCACCTTTC
1 TTTCCTCCCTCAGCTGACCATTCTCTTCGATTTTAGTTCTCAGGTCCTCTTCCAGTTCACCTTTC
*
34623414 TGGTTCTTTAGAGAAATGACCTCCAATTCTAGTTCCTTCATTTGTGCCAACAAACTCTCTTTCTC
66 TGGTTCTTTAGAGAAATGACCTCCAATTCTAGTTCCTTCATTTGTGCCAACAAACCCTCTTTCTC
* * *
34623479 CTGCAGAACTCTCTGTTGATCCTCAGTCTTGCTTACGATCTCTTCTTTTGCCTTTTCTATCTCGA
131 CTGCAGAACTCTCTGTTGATCCTCGGTCTTGCTTACTATCTCTTCTTTTGCCTTTTCTATCTCAA
* * * *
34623544 TCATATAATCTGAAATAGCTTGAGTTTTACTCTCAAGCTGAACTTCAAGTTCAGCTTTCTGGCTA
196 TCAAATGATCGGAAATAGCTTGAGTTTTACTCTCAAGCTGAACTTCAAGTTCTGCTTTCTGGCTA
* * * * *
34623609 TGCATGGATTCCAGTTTCTGCTGCAATGTATTTATTTGATCCATCAAGCTCTTGACTTGA-TTCG
261 TGCA-GGACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACTTGAGTT-G
* *
34623673 ATGCTTCATCGCCTTTAACTACAATATGTTCTTCCAACTGAGCTTTCTCGGT-CCT-CAGCGACT
324 ATGCTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCTCGGTGCGTAC-GCGACT
* * * * *
34623736 CCATGTCTCCTAGCAGATTGTTAATCTGCACAGTCAAATTATCCACTCTAGATAATGATTCTGTC
388 CCATGTCTGCTAGCAGATTGTTGATCTGCACTGTCAAATTCTCCACTCTAGATAATGATTCTTTC
* * *
34623801 TCATTATCCTCAAACTTCTTTCTGAGAATCAAAAGTTCTTCTTGTCT-TGTCTTTGATATCATTT
453 TCATTATCCTCAAACTTCTTTGTGAGAGTCAAAAGTTCTTCTTGTCTCTGT-TTTGATATCATCT
* *
34623865 CGAGTTCTGAAATTTGAGATTGCAGTCCCATAT
517 CGAGTTCTGAAATTTGGGATTGCAGTCCTATAT
* *
34623898 TTTCCACCCTCAGCTGACCATTCTCTTCAATTTTAGTTCTCAGGTCCTCTTCCAGTTCACCTTTC
1 TTTCCTCCCTCAGCTGACCATTCTCTTCGATTTTAGTTCTCAGGTCCTCTTCCAGTTCACCTTTC
34623963 TGGTTCTTTAGAGAAATGACCTCCAATTCTAGTTCCTTCATTTGTGCCAACAAACCCTCTTTCTC
66 TGGTTCTTTAGAGAAATGACCTCCAATTCTAGTTCCTTCATTTGTGCCAACAAACCCTCTTTCTC
*
34624028 CTGCAGAACTCTCTGTTGATCCTCGGTCTTGCTTACTATCTCTTCTTTTGCCTTCTCTATCTCAA
131 CTGCAGAACTCTCTGTTGATCCTCGGTCTTGCTTACTATCTCTTCTTTTGCCTTTTCTATCTCAA
* *
34624093 TCAAATGATCGGAAATAGCTTGAGTTTTTCTCTCAAGCTGAACTTCCAGTTCTGCTTTCTGGCTA
196 TCAAATGATCGGAAATAGCTTGAGTTTTACTCTCAAGCTGAACTTCAAGTTCTGCTTTCTGGCTA
*
34624158 TGCAGGAACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACCTGAGTTGA
261 TGCAGG-ACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACTTGAGTTGA
34624223 TGCTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCT-GGATGCGTACG-GACTC
325 TGCTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCTCGG-TGCGTACGCGACTC
* *
34624286 CATGTCTGCTAGCAAATTGTTGATCTGCACTGTCAAATTCTCTACTCTAGATAGA-GATTCTTTC
389 CATGTCTGCTAGCAGATTGTTGATCTGCACTGTCAAATTCTCCACTCTAGATA-ATGATTCTTTC
* * * *
34624350 TCGTTGTCCTCAAACTTCTTTGTGAGTGTCCAAAGTTCTTCTTGTCTCTGTTTTGATATCATCTC
453 TCATTATCCTCAAACTTCTTTGTGAGAGTCAAAAGTTCTTCTTGTCTCTGTTTTGATATCATCTC
* *
34624415 GAGTTCTGAAATTTGGGATTGCAGTCCTAAAC
518 GAGTTCTGAAATTTGGGATTGCAGTCCTATAT
* ** **
34624447 TTTCCTCCCTCAGCTGGCCATTCTCTTCGATTTTAGTTCTCAAATCCTCTTCCAACTCACCTTTC
1 TTTCCTCCCTCAGCTGACCATTCTCTTCGATTTTAGTTCTCAGGTCCTCTTCCAGTTCACCTTTC
* * * * *
34624512 TGATTCTTTA-ACGAATTGACATCAAATTCTAGTTCCTTCATTTGTGCCAGCAAACCCTCTTTCT
66 TGGTTCTTTAGA-GAAATGACCTCCAATTCTAGTTCCTTCATTTGTGCCAACAAACCCTCTTTCT
* * * *
34624576 CCTGCAGAACTCTTTGTTGATCCTCGGTCTTGCTTGCTATCTCTTCTTTTGCATTTTCGATCTCA
130 CCTGCAGAACTCTCTGTTGATCCTCGGTCTTGCTTACTATCTCTTCTTTTGCCTTTTCTATCTCA
* * * *
34624641 ATCACATGATCGGAAATCGCTCGAGTTTTACTCTCAAGCTGAACTTCAAGTTCTGCTTTCTGACT
195 ATCAAATGATCGGAAATAGCTTGAGTTTTACTCTCAAGCTGAACTTCAAGTTCTGCTTTCTGGCT
* * * *
34624706 CTGCAGGGACTCCAGCTCCTGCTGCAAATTATTTATCTGATCCATCAAGCTTTTGACTTGAGTGG
260 ATGCA-GGACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACTTGAGTTG
** * *
34624771 ATGCTTCATCATCTTTCACTGCAATATGTTCTTCCAACTGAGCTTTCTCGGTGCGTA-GTGACTC
324 ATGCTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCTCGGTGCGTACGCGACTC
* *
34624835 CATGTCTGCTAGCAGATTGTTGATCTGCACTGTCAAGTTCTCCACTCTAGACAATGATTCTTTCT
389 CATGTCTGCTAGCAGATTGTTGATCTGCACTGTCAAATTCTCCACTCTAGATAATGATTCTTTCT
** * * *
34624900 CATTATCCTCAATTTTCTTTGCGAGAGTCAAAAGTTCTTCTTCTCTCT-TTTCTGACATCATCTC
454 CATTATCCTCAAACTTCTTTGTGAGAGTCAAAAGTTCTTCTTGTCTCTGTTT-TGATATCATCTC
*
34624964 AAGTTCTGAAATTTGGGATTGCAGTCCTATAT
518 GAGTTCTGAAATTTGGGATTGCAGTCCTATAT
*
34624996 TTACCTCTCC-CAGCTG
1 TTTCCTC-CCTCAGCTG
34625012 CTTTGCTTCA
Statistics
Matches: 1011, Mismatches: 89, Indels: 28
0.90 0.08 0.02
Matches are distributed among these distances:
548 10 0.01
549 985 0.97
550 15 0.01
551 1 0.00
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (549 bp):
TTTCCTCCCTCAGCTGACCATTCTCTTCGATTTTAGTTCTCAGGTCCTCTTCCAGTTCACCTTTC
TGGTTCTTTAGAGAAATGACCTCCAATTCTAGTTCCTTCATTTGTGCCAACAAACCCTCTTTCTC
CTGCAGAACTCTCTGTTGATCCTCGGTCTTGCTTACTATCTCTTCTTTTGCCTTTTCTATCTCAA
TCAAATGATCGGAAATAGCTTGAGTTTTACTCTCAAGCTGAACTTCAAGTTCTGCTTTCTGGCTA
TGCAGGACTCCAGCTCCTGCTGCAAAGTATTTATCTGATCCATCAAGCTCTTGACTTGAGTTGAT
GCTTCATCGCCTTTCACTACAATATGTTCTTCCAACTGAGCTTTCTCGGTGCGTACGCGACTCCA
TGTCTGCTAGCAGATTGTTGATCTGCACTGTCAAATTCTCCACTCTAGATAATGATTCTTTCTCA
TTATCCTCAAACTTCTTTGTGAGAGTCAAAAGTTCTTCTTGTCTCTGTTTTGATATCATCTCGAG
TTCTGAAATTTGGGATTGCAGTCCTATAT
Found at i:34629179 original size:18 final size:18
Alignment explanation
Indices: 34629152--34629190 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
34629142 AGTTTTATAT
* *
34629152 AATAATAAAAAGGAGAAA
1 AATAAAAAAAAGAAGAAA
*
34629170 AATAAAAAAAATAAGAAA
1 AATAAAAAAAAGAAGAAA
34629188 AAT
1 AAT
34629191 GGTTAGAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (18 bp):
AATAAAAAAAAGAAGAAA
Found at i:34630637 original size:117 final size:117
Alignment explanation
Indices: 34630473--34630957 Score: 553
Period size: 117 Copynumber: 4.2 Consensus size: 117
34630463 CTTTGAGTTT
* * * * *
34630473 GATTCATTCATTGCATTTTTGCTTGCATTCATTGAATCCCTCA-ACTTCCTCAGCTCAGCTTCAC
1 GATTCAGTCAATGCATTTTTGCCTGCCTCCATTGAATCCCT-AGACTTCCTCAGCTCAGCTTCAC
* * * *
34630537 TACTGGCAAGCTTCTCTTTAAGCTCTCCATTTTCGTGTTCTAGCCTTGAAATG
65 AACTAGCAAGCTTCTCTTTAAGCTGTCCATTTTCGTGCTCTAGCCTTGAAATG
* * * * *
34630590 GATTCAGTCAATGAATTCTTGCCTCCCTCCATTGAATCCCTAGACTTCCTCAGTTCAACTTCACA
1 GATTCAGTCAATGCATTTTTGCCTGCCTCCATTGAATCCCTAGACTTCCTCAGCTCAGCTTCACA
* * * * *
34630655 ACTGGTAAGCTTCTCTTTATGTTGTCCATTTTCGTGCTGTAGCCTTGAAATG
66 ACTAGCAAGCTTCTCTTTAAGCTGTCCATTTTCGTGCTCTAGCCTTGAAATG
* * * *
34630707 GATTCAGTCAATGCCTTTTTGCCTGCCTCCGTTGAATCCCTAGATTTCCTTAGCTC-GACTTCAC
1 GATTCAGTCAATGCATTTTTGCCTGCCTCCATTGAATCCCTAGACTTCCTCAGCTCAG-CTTCAC
** * * *
34630771 AGGTATCAAGCTTCTCTTTAAGGTGTCCATTTTCGTGCTTTAGCCTTGAAATG
65 AACTAGCAAGCTTCTCTTTAAGCTGTCCATTTTCGTGCTCTAGCCTTGAAATG
* * * *
34630824 GATTCAGTCCATGCATTTTTGCATGCCTCCATAGTAT-CCTAGACTTCCTCAGCTCAGCTTCACA
1 GATTCAGTCAATGCATTTTTGCCTGCCTCCATTGAATCCCTAGACTTCCTCAGCTCAGCTTCACA
* * * * * * * * *
34630888 AGTAGCAAGCTTCTCTCTGAGCTTTCTATTATCTTGCTCTAGCCTTGAATTC
66 ACTAGCAAGCTTCTCTTTAAGCTGTCCATTTTCGTGCTCTAGCCTTGAAATG
*
34630940 GATTCAGACAATGCATTT
1 GATTCAGTCAATGCATTT
34630958 CTGGCCGTCT
Statistics
Matches: 309, Mismatches: 56, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
116 80 0.26
117 229 0.74
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (117 bp):
GATTCAGTCAATGCATTTTTGCCTGCCTCCATTGAATCCCTAGACTTCCTCAGCTCAGCTTCACA
ACTAGCAAGCTTCTCTTTAAGCTGTCCATTTTCGTGCTCTAGCCTTGAAATG
Found at i:34630991 original size:233 final size:235
Alignment explanation
Indices: 34630484--34631042 Score: 566
Period size: 233 Copynumber: 2.4 Consensus size: 235
34630474 ATTCATTCAT
* * * * * **
34630484 TGCATTTTTGCTTGCATTCATTGAATCCCTCA-ACTTCCTCAGCTCAGCTTCACTA-CTGGCAAG
1 TGCATTTTGGCCTGCCTCCATTGAATCCCT-AGACTTCCTTAGCTCAGCTTCAC-AGGAGGCAAG
* *
34630547 CTTCTCTTTAAGCTCTCCATTTTCGTG-TTCTAGCCTTGAAATGGATTCAGTCAATGAATTCTTG
64 CTTCTCTTTAAGGTGTCCATTTTCGTGCTTCTAGCCTTGAAATGGATTCAGTCAATGAATTCTTG
* * * * * *
34630611 CCTCCCTCCATTGAATCCCTAGACTTCCTCAGTTCAACTTCACAACTGGTAAGCTTCTCTTTATG
129 CATCCCTCCATAGAATCCCTAGACTTCCTCAGCTCAACTTCACAACTAGCAAGCTTCTCTTGATG
* * * *
34630676 TTGTCCATTTTCGTGCTGTAGCCTTGAAATGGATTCAGTCAA
194 TTGTCCATTATCGTGCTCTAGCCTTGAAATCGATTCAGACAA
* * * * *
34630718 TGCCTTTTTGCCTGCCTCCGTTGAATCCCTAGATTTCCTTAGCTC-GACTTCACAGGTA-TCAAG
1 TGCATTTTGGCCTGCCTCCATTGAATCCCTAGACTTCCTTAGCTCAG-CTTCACAGG-AGGCAAG
* * *
34630781 CTTCTCTTTAAGGTGTCCATTTTCGTGCTT-TAGCCTTGAAATGGATTCAGTCCATGCATTTTTG
64 CTTCTCTTTAAGGTGTCCATTTTCGTGCTTCTAGCCTTGAAATGGATTCAGTCAATGAATTCTTG
* * * *
34630845 CATGCCTCCATAGTAT-CCTAGACTTCCTCAGCTCAGCTTCACAAGTAGCAAGCTTCTCTCTGA-
129 CATCCCTCCATAGAATCCCTAGACTTCCTCAGCTCAACTTCACAACTAGCAAGCTTCTCT-TGAT
* * *
34630908 GCTT-TCTATTATCTTGCTCTAGCCTTGAATTCGATTCAGACAA
193 G-TTGTCCATTATCGTGCTCTAGCCTTGAAATCGATTCAGACAA
* ** * * * *
34630951 TGCATTTCTGGCC-GTCTTTATTGAATTCCTTA-ACTTCCTTATCTCAGCTTCACCGGAGGCAAC
1 TGCATTT-TGGCCTGCCTCCATTGAA-TCCCTAGACTTCCTTAGCTCAGCTTCACAGGAGGCAAG
* *
34631014 CTTCTCTCTAA-GTGCTCCATTTTCTTGCT
64 CTTCTCTTTAAGGTG-TCCATTTTCGTGCT
34631043 CCAGCATCTT
Statistics
Matches: 267, Mismatches: 46, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
232 4 0.01
233 133 0.50
234 128 0.48
235 2 0.01
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.37
Consensus pattern (235 bp):
TGCATTTTGGCCTGCCTCCATTGAATCCCTAGACTTCCTTAGCTCAGCTTCACAGGAGGCAAGCT
TCTCTTTAAGGTGTCCATTTTCGTGCTTCTAGCCTTGAAATGGATTCAGTCAATGAATTCTTGCA
TCCCTCCATAGAATCCCTAGACTTCCTCAGCTCAACTTCACAACTAGCAAGCTTCTCTTGATGTT
GTCCATTATCGTGCTCTAGCCTTGAAATCGATTCAGACAA
Found at i:34633252 original size:96 final size:96
Alignment explanation
Indices: 34633088--34633282 Score: 372
Period size: 96 Copynumber: 2.0 Consensus size: 96
34633078 CATCACATAC
*
34633088 AAAATTTAATACATAATTATGTATTTAAAGTTAAAAAATCGTTATTATAAGTAACAAACAATTCT
1 AAAATTTAATACATAATCATGTATTTAAAGTTAAAAAATCGTTATTATAAGTAACAAACAATTCT
34633153 TGCTCATACCATTACGGGTGAGAGACTAATA
66 TGCTCATACCATTACGGGTGAGAGACTAATA
34633184 AAAATTTAATACATAATCATGTATTTAAAGTTAAAAAATCGTTATTATAAGTAACAAACAATTCT
1 AAAATTTAATACATAATCATGTATTTAAAGTTAAAAAATCGTTATTATAAGTAACAAACAATTCT
*
34633249 TGCTCATACCATTACGGGTGGGAGACTAATA
66 TGCTCATACCATTACGGGTGAGAGACTAATA
34633280 AAA
1 AAA
34633283 CTCTGAGAAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (96 bp):
AAAATTTAATACATAATCATGTATTTAAAGTTAAAAAATCGTTATTATAAGTAACAAACAATTCT
TGCTCATACCATTACGGGTGAGAGACTAATA
Found at i:34642674 original size:34 final size:34
Alignment explanation
Indices: 34642631--34642700 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
34642621 TGTAAACGTA
*
34642631 ACATTAGGTATAAATAATAGGATTTGTTAACTCG
1 ACATTAGGTATAAATAATAAGATTTGTTAACTCG
34642665 ACATTAGGTATAAATAATAAGATTTGTTAACTCG
1 ACATTAGGTATAAATAATAAGATTTGTTAACTCG
34642699 AC
1 AC
34642701 TCGATTTGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (34 bp):
ACATTAGGTATAAATAATAAGATTTGTTAACTCG
Found at i:34643999 original size:29 final size:28
Alignment explanation
Indices: 34643970--34644027 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
34643960 AAATTTATAT
34643970 TTAAAATATAAAACTTATAATTTAATTATTC
1 TTAAAA-A-AAAACTTATAATTTAATTA-TC
*
34644001 TTCAAAAAAAACTTATAATTTAATTAT
1 TTAAAAAAAAACTTATAATTTAATTAT
34644028 GTTTATTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 19 0.73
30 1 0.04
31 5 0.19
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (28 bp):
TTAAAAAAAAACTTATAATTTAATTATC
Found at i:34645134 original size:25 final size:26
Alignment explanation
Indices: 34645106--34645160 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
34645096 TAACTATTAA
34645106 AAATATTA-ACTA-ATTTAAAAAATTT
1 AAATATTATA-TAGATTTAAAAAATTT
* **
34645131 AAATTTTATATAGATTTAAAAGTTTT
1 AAATATTATATAGATTTAAAAAATTT
34645157 AAAT
1 AAAT
34645161 TAGATATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (26 bp):
AAATATTATATAGATTTAAAAAATTT
Found at i:34645167 original size:26 final size:26
Alignment explanation
Indices: 34645118--34645168 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
34645108 ATATTAACTA
**
34645118 ATTTAAAAAATTTAAATTTTATATAG
1 ATTTAAAAAATTTAAATTAGATATAG
**
34645144 ATTTAAAAGTTTTAAATTAGATATA
1 ATTTAAAAAATTTAAATTAGATATA
34645169 ATTCATTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (26 bp):
ATTTAAAAAATTTAAATTAGATATAG
Found at i:34647835 original size:8 final size:9
Alignment explanation
Indices: 34647811--34647837 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
34647801 GCTATAGTTA
34647811 AAATTTTTT
1 AAATTTTTT
34647820 AAATTTTTT
1 AAATTTTTT
34647829 AAATTTTTT
1 AAATTTTTT
34647838 CTTAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
AAATTTTTT
Found at i:34647901 original size:22 final size:23
Alignment explanation
Indices: 34647853--34647894 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
34647843 TAATAATTGT
34647853 AAATGAAATTAAAAATATCATAA
1 AAATGAAATTAAAAATATCATAA
34647876 AAAT-AAA-TAAAAAT-TCATA
1 AAATGAAATTAAAAATATCATA
34647895 TGAAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 7 0.37
22 3 0.16
23 4 0.21
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (23 bp):
AAATGAAATTAAAAATATCATAA
Found at i:34649638 original size:25 final size:26
Alignment explanation
Indices: 34649597--34649646 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
34649587 TAAAGATTTT
*
34649597 GGATAATTTTCTTTAATGCATCACAA
1 GGATAACTTTCTTTAATGCATCACAA
*
34649623 GGATAACTTT-TTTAATGTATCACA
1 GGATAACTTTCTTTAATGCATCACA
34649647 TGCTCAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (26 bp):
GGATAACTTTCTTTAATGCATCACAA
Found at i:34650743 original size:15 final size:15
Alignment explanation
Indices: 34650714--34650756 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
34650704 AACTTAATAC
* *
34650714 TATAAATTATATATT
1 TATAAATAATTTATT
34650729 TATAAATAATTTATT
1 TATAAATAATTTATT
*
34650744 CATAACATAATTT
1 TATAA-ATAATTT
34650757 TCATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
TATAAATAATTTATT
Found at i:34670388 original size:22 final size:22
Alignment explanation
Indices: 34670367--34670407 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
34670357 TCTAAATTTA
*
34670367 AATTTATA-CTAATTATTTTTT
1 AATTTATATCTAACTATTTTTT
*
34670388 ATTTTATATCTAACTATTTT
1 AATTTATATCTAACTATTTT
34670408 AACGCATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (22 bp):
AATTTATATCTAACTATTTTTT
Found at i:34672230 original size:25 final size:25
Alignment explanation
Indices: 34672180--34672228 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
34672170 ACACACTCTC
* * *
34672180 TTTAAAATTAATTTATTTCTTAAAT
1 TTTAAAAATAATCTATTTATTAAAT
34672205 TTTAAAAATAATCTATTTAATTAA
1 TTTAAAAATAATCTATTT-ATTAA
34672229 TTAAAAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTAAAAATAATCTATTTATTAAAT
Found at i:34672408 original size:32 final size:32
Alignment explanation
Indices: 34672372--34672437 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
34672362 TTATCATGTG
34672372 ATGGAGACAACTATGCAATCTTAAACAATAAT
1 ATGGAGACAACTATGCAATCTTAAACAATAAT
* *
34672404 ATGGAGACAACTATGTAATCTTATACAATAAT
1 ATGGAGACAACTATGCAATCTTAAACAATAAT
34672436 AT
1 AT
34672438 TACTAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (32 bp):
ATGGAGACAACTATGCAATCTTAAACAATAAT
Found at i:34674177 original size:13 final size:12
Alignment explanation
Indices: 34674131--34674177 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
34674121 CTAACATTTA
34674131 ATTTAATATTAT
1 ATTTAATATTAT
* *
34674143 CTTAAAATATT-T
1 ATT-TAATATTAT
34674155 ATTTAATATTAT
1 ATTTAATATTAT
34674167 ATTTAAGTATT
1 ATTTAA-TATT
34674178 TGATTAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
11 6 0.21
12 12 0.43
13 10 0.36
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (12 bp):
ATTTAATATTAT
Found at i:34674177 original size:24 final size:25
Alignment explanation
Indices: 34674126--34674178 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
34674116 ATAGTCTAAC
*
34674126 ATTTAATTTAATATTATCTTAAAAT
1 ATTTAATTTAATATTATATTAAAAT
* *
34674151 ATTT-ATTTAATATTATATTTAAGT
1 ATTTAATTTAATATTATATTAAAAT
34674175 ATTT
1 ATTT
34674179 GATTAAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTAATTTAATATTATATTAAAAT
Found at i:34700371 original size:21 final size:20
Alignment explanation
Indices: 34700329--34700371 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
34700319 TTAAAAAAAA
* *
34700329 TAAATATTAATGATTTTAAT
1 TAAATATTAATAATTATAAT
34700349 TAAATATTAATCAATTATAAT
1 TAAATATTAAT-AATTATAAT
34700370 TA
1 TA
34700372 TCATAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TAAATATTAATAATTATAAT
Found at i:34704665 original size:31 final size:31
Alignment explanation
Indices: 34704630--34704695 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
34704620 TGATTACACC
34704630 AAATCAAAATTCATATATCAAACTACACATT
1 AAATCAAAATTCATATATCAAACTACACATT
* * * *
34704661 AAATCAAAGTTTATATATCAAATTACATATT
1 AAATCAAAATTCATATATCAAACTACACATT
34704692 AAAT
1 AAAT
34704696 ACTCTCGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.33
Consensus pattern (31 bp):
AAATCAAAATTCATATATCAAACTACACATT
Found at i:34709024 original size:55 final size:55
Alignment explanation
Indices: 34708940--34709072 Score: 230
Period size: 55 Copynumber: 2.4 Consensus size: 55
34708930 GTTACAAAAA
*
34708940 GATGACGCGAGAATATTAAAGTGGAACTTAATTGAGTGGAGATGAGATTGCTAGT
1 GATGACGCGAGAATATTAAAGTGGAACTTAATTGAGTGGAGATGAGATCGCTAGT
* *
34708995 GATGACGCGAGAATATTAAAGTGGAACTTACTTGAGTGGAGATGAGATCGTTAGT
1 GATGACGCGAGAATATTAAAGTGGAACTTAATTGAGTGGAGATGAGATCGCTAGT
*
34709050 GATGACGCGAGAATATTTAAGTG
1 GATGACGCGAGAATATTAAAGTG
34709073 ATATCACTAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 74 1.00
ACGTcount: A:0.34, C:0.08, G:0.31, T:0.27
Consensus pattern (55 bp):
GATGACGCGAGAATATTAAAGTGGAACTTAATTGAGTGGAGATGAGATCGCTAGT
Found at i:34717496 original size:18 final size:17
Alignment explanation
Indices: 34717467--34717500 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
34717457 AAGTTTGTAC
34717467 AATTTTTCATTTTTATA
1 AATTTTTCATTTTTATA
34717484 AATTTTATCATTTTTAT
1 AATTTT-TCATTTTTAT
34717501 TAAGAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTTTTCATTTTTATA
Found at i:34727357 original size:5 final size:6
Alignment explanation
Indices: 34727341--34727365 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34727331 TTTTTTTCGA
34727341 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
34727366 AATCCATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:34739920 original size:153 final size:151
Alignment explanation
Indices: 34739641--34739937 Score: 416
Period size: 153 Copynumber: 2.0 Consensus size: 151
34739631 AGAACATCAA
* * *
34739641 TTTTAACATTCCAATGACTTAAATGAAAACTTTCGATAGTTCGATTACCAGTTTGTAACTTTTGA
1 TTTTAACATTCCAATAACTTAAATAAAAACTTTCGATAGTTCAATTACCAGTTTGTAACTTTTGA
* * * *
34739706 AGTTGAGTAATCAAAAAGTAAATCTACTAATAGTTTAGTGATATTGGATATAGTCACTTTACCCC
66 AGTCGAATAATCAAAAAGTAAATCTACTAATAGTTTAATAATATTGGATATAGTCACTTTACCCC
34739771 TCTATTTATTGTTTTTTGGCTT
131 TCTATTTATT-TTTTTTGGCTT
* ** *
34739793 TTTTAACATTCCAATAACTTAAATAAAAATTTTCGAATAGTTCAATTATTATTTTGTAACTTTTG
1 TTTTAACATTCCAATAACTTAAATAAAAACTTTCG-ATAGTTCAATTACCAGTTTGTAACTTTTG
* * * *
34739858 TAGTCGAATGATCAAAAAGTAAA-CTTACTAATAGTTTAATAATATTGGATATAGTCATTTTACT
65 AAGTCGAATAATCAAAAAGTAAATC-TACTAATAGTTTAATAATATTGGATATAGTCACTTTACC
*
34739922 CCTGTATTTATTTTTT
129 CCTCTATTTATTTTTT
34739938 GATTTTTTTA
Statistics
Matches: 127, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
152 37 0.29
153 90 0.71
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.43
Consensus pattern (151 bp):
TTTTAACATTCCAATAACTTAAATAAAAACTTTCGATAGTTCAATTACCAGTTTGTAACTTTTGA
AGTCGAATAATCAAAAAGTAAATCTACTAATAGTTTAATAATATTGGATATAGTCACTTTACCCC
TCTATTTATTTTTTTTGGCTT
Found at i:34741416 original size:14 final size:15
Alignment explanation
Indices: 34741393--34741421 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
34741383 ATAATTTAAA
34741393 AATTATAAAAAAATT
1 AATTATAAAAAAATT
34741408 AATTA-AAAAAAATT
1 AATTATAAAAAAATT
34741422 GAAGTACCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATTATAAAAAAATT
Found at i:34756887 original size:29 final size:27
Alignment explanation
Indices: 34756821--34756887 Score: 62
Period size: 31 Copynumber: 2.3 Consensus size: 27
34756811 GAGTTTCACG
*
34756821 TGTATAATTGCACCAAATTAAAATTCA
1 TGTATAATTGCACCAAATCAAAATTCA
* * *
34756848 TGTATACAATTGCACATTAAATCAAAGTTTA
1 TGTAT--AATTGCAC--CAAATCAAAATTCA
34756879 TGTATAATT
1 TGTATAATT
34756888 TTGAGATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 5 0.16
29 12 0.38
31 15 0.47
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (27 bp):
TGTATAATTGCACCAAATCAAAATTCA
Found at i:34766380 original size:24 final size:25
Alignment explanation
Indices: 34766348--34766394 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
34766338 TAAAAGTTCA
34766348 AACCTATTCAAATTTAAAACCCAGT
1 AACCTATTCAAATTTAAAACCCAGT
* *
34766373 AACC-ATTCATATTTCAAACCCA
1 AACCTATTCAAATTTAAAACCCA
34766395 AATTGATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.28
Consensus pattern (25 bp):
AACCTATTCAAATTTAAAACCCAGT
Found at i:34766617 original size:6 final size:6
Alignment explanation
Indices: 34766608--34766632 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34766598 AATTTGAAAT
34766608 AAATTA AAATTA AAATTA AAATTA A
1 AAATTA AAATTA AAATTA AAATTA A
34766633 TATGATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:34779102 original size:7 final size:8
Alignment explanation
Indices: 34779072--34779105 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
34779062 TTATGGTTTG
34779072 AATTTTTT
1 AATTTTTT
34779080 AATTTTTT
1 AATTTTTT
34779088 AATTTTTT
1 AATTTTTT
*
34779096 ATTTTTTT
1 AATTTTTT
34779104 AA
1 AA
34779106 ATTATTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
AATTTTTT
Found at i:34794219 original size:33 final size:32
Alignment explanation
Indices: 34794151--34794220 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
34794141 ATTTTGATAT
* *
34794151 TTAAACTTGATATATTTTTTTTAATTTAGTAC
1 TTAAACTTGAAATATTTTTTTTAATTGAGTAC
* *
34794183 TTAAACTTGAAAGTTTTTTTTTTAAGTTGA-TGC
1 TTAAACTTGAAA-TATTTTTTTTAA-TTGAGTAC
34794216 TTAAA
1 TTAAA
34794221 ATTTTTGGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 11 0.34
33 18 0.56
34 3 0.09
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (32 bp):
TTAAACTTGAAATATTTTTTTTAATTGAGTAC
Found at i:34795181 original size:3 final size:3
Alignment explanation
Indices: 34795173--34795206 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
34795163 CCCTATAAAT
34795173 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
34795207 ATTAATCCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:34826536 original size:29 final size:31
Alignment explanation
Indices: 34826500--34826557 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
34826490 TATTTCTATA
34826500 ATTTTTAAAAA-ATTAAATT-AAATTTTACC
1 ATTTTTAAAAATATTAAATTGAAATTTTACC
*
34826529 ATTTTTAAAAATATTAAATTGTAATTTTA
1 ATTTTTAAAAATATTAAATTGAAATTTTA
34826558 TTTTTACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.42
30 8 0.31
31 7 0.27
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (31 bp):
ATTTTTAAAAATATTAAATTGAAATTTTACC
Found at i:34835718 original size:25 final size:25
Alignment explanation
Indices: 34835664--34835721 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
34835654 CAAGCTCCTC
*
34835664 TAAAATTTAAAAACTATTAAAAATA
1 TAAAATTTAAAAAATATTAAAAATA
* **
34835689 GAAAATTATAAAAAAT-TTAAACTTA
1 TAAAATT-TAAAAAATATTAAAAATA
34835714 TAAAATTT
1 TAAAATTT
34835722 TTATTAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 1 0.04
25 19 0.70
26 7 0.26
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (25 bp):
TAAAATTTAAAAAATATTAAAAATA
Found at i:34849945 original size:9 final size:8
Alignment explanation
Indices: 34849924--34849948 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
34849914 TAGTATAATT
34849924 ATTTTTAA
1 ATTTTTAA
34849932 ATTTTTAA
1 ATTTTTAA
34849940 ATTTTTAA
1 ATTTTTAA
34849948 A
1 A
34849949 AAATCTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTTTAA
Found at i:34850150 original size:17 final size:18
Alignment explanation
Indices: 34850118--34850152 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
34850108 AGGAAAAAGT
*
34850118 AGTTACAAGAATATGAAA
1 AGTTACAAGAAGATGAAA
34850136 AGTTA-AAGAAGATGAAA
1 AGTTACAAGAAGATGAAA
34850153 GATTAAGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (18 bp):
AGTTACAAGAAGATGAAA
Found at i:34860507 original size:27 final size:27
Alignment explanation
Indices: 34860469--34860530 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
34860459 TATAAATGGG
34860469 TGGTGCCTACCTGACAGGCGGCACCAA
1 TGGTGCCTACCTGACAGGCGGCACCAA
* * *
34860496 TGGTGCCTACCTGTCAGGCGGCAGCAG
1 TGGTGCCTACCTGACAGGCGGCACCAA
34860523 TGGTGCCT
1 TGGTGCCT
34860531 TTCTATCAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.16, C:0.31, G:0.34, T:0.19
Consensus pattern (27 bp):
TGGTGCCTACCTGACAGGCGGCACCAA
Found at i:34860539 original size:27 final size:27
Alignment explanation
Indices: 34860469--34860549 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
34860459 TATAAATGGG
34860469 TGGTGCCTACCTGA-CAGGCGGCACCAA
1 TGGTGCCTACCT-ATCAGGCGGCACCAA
* * *
34860496 TGGTGCCTACCTGTCAGGCGGCAGCAG
1 TGGTGCCTACCTATCAGGCGGCACCAA
** *
34860523 TGGTGCCTTTCTATCAGGTGGCACCAA
1 TGGTGCCTACCTATCAGGCGGCACCAA
34860550 CTCGTATTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.19, C:0.30, G:0.31, T:0.21
Consensus pattern (27 bp):
TGGTGCCTACCTATCAGGCGGCACCAA
Found at i:34860697 original size:20 final size:20
Alignment explanation
Indices: 34860635--34860700 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
34860625 TAAATAATAT
* *
34860635 AAATATATATATATATTTTAAT
1 AAATAT-TATATA-ATTTAAAA
*
34860657 AAATA-TA-AGAATTGTAGAAA
1 AAATATTATATAATT-TA-AAA
34860677 AAATATTATATAATTTAAAA
1 AAATATTATATAATTTAAAA
34860697 AAAT
1 AAAT
34860701 TAAATTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 16 0.44
21 4 0.11
22 10 0.28
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
AAATATTATATAATTTAAAA
Found at i:34860819 original size:57 final size:55
Alignment explanation
Indices: 34860705--34860835 Score: 142
Period size: 57 Copynumber: 2.4 Consensus size: 55
34860695 AAAAATTAAA
* * *
34860705 TTAAATATTAAATAAAAATAACTCAATATTTTTAAATAAATAATATAAAAAATAT
1 TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
** * *
34860760 TTATTTATCAAAATAATAATAATCTCCAGATTTTTACAAT-AATAATATAAGAGAA-AT
1 TTAAATAT-AAAATAATAATAA-CTCAAGATTTTTA-AATAAATAATATAA-AAAATAT
34860817 TTAAATATAAAA-AATAATA
1 TTAAATATAAAATAATAATA
34860836 CACTTTTATA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
55 13 0.21
56 15 0.24
57 29 0.46
58 6 0.10
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.36
Consensus pattern (55 bp):
TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
Found at i:34860942 original size:27 final size:27
Alignment explanation
Indices: 34860901--34860961 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
34860891 TTTTACAAGA
34860901 GGTGCCTACCAGGTAGGCGGCACTAGT
1 GGTGCCTACCAGGTAGGCGGCACTAGT
**
34860928 GGTGCCTACTGGGTAGGCGGCACTAGT
1 GGTGCCTACCAGGTAGGCGGCACTAGT
34860955 GGTGCCT
1 GGTGCCT
34860962 TTGTCAATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.15, C:0.25, G:0.39, T:0.21
Consensus pattern (27 bp):
GGTGCCTACCAGGTAGGCGGCACTAGT
Found at i:34861046 original size:29 final size:26
Alignment explanation
Indices: 34861014--34861079 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
34861004 AATTTTTGAA
*
34861014 GAAAGAATAACAGTAAATTTTTGAAGAAG
1 GAAAGAA-AACA--AAAGTTTTGAAGAAG
*
34861043 GAAAGGAAACAAAAGTTTTGAAGAAG
1 GAAAGAAAACAAAAGTTTTGAAGAAG
* *
34861069 AAAAGGAAACA
1 GAAAGAAAACA
34861080 GAAGGTTAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 24 0.71
28 4 0.12
29 6 0.18
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.17
Consensus pattern (26 bp):
GAAAGAAAACAAAAGTTTTGAAGAAG
Done.