Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 49 of 105
Found at i:9392645 original size:38 final size:40
Alignment explanation
Indices: 9392603--9392678 Score: 129
Period size: 38 Copynumber: 1.9 Consensus size: 40
9392593 TTTTTAAAGT
9392603 TTCAAAGCCTCTGTTTA-GGGGAG-CATTTTCAAACAAGA
1 TTCAAAGCCTCTGTTTAGGGGGAGCCATTTTCAAACAAGA
*
9392641 TTCAAATCCTCTGTTTAGGGGGAGCCATTTTCAAACAA
1 TTCAAAGCCTCTGTTTAGGGGGAGCCATTTTCAAACAA
9392679 AATTTTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 16 0.46
39 6 0.17
40 13 0.37
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (40 bp):
TTCAAAGCCTCTGTTTAGGGGGAGCCATTTTCAAACAAGA
Found at i:9393692 original size:144 final size:144
Alignment explanation
Indices: 9393452--9393858 Score: 412
Period size: 144 Copynumber: 2.9 Consensus size: 144
9393442 GCATTTGGGA
* * * * * * *
9393452 AAGTATAAAATTACCAAAATA-CCCTTTAAAGGTATTTTCTTAATTTACTATTCCCAAGCTTAGA
1 AAGTGTAAAATTATCAAAATACCCCTATAAAGGTATTTT-ATAATTTGCTCTTCCCAAGCTCAGA
*
9393516 CTTTCAT-AAA------A-ATCTTAATTTCATAATATTTCAT-ATTTTTTGTGCATTTGAAATCA
65 TTTTCATAAAACTTTTTAGATCTTAATTTCATAATATTTCATAATTTTTTGTGCATTTGAAATCA
* *
9393572 CAATAGTACCCTTGGA-
130 CAACAGTA-CC-TCGAC
* * * *
9393588 AA-TGTAAAATTATCAAAATATCCCTATAAAGGTATTTTCATTATTTGC-CATTCCCGAGCTCAT
1 AAGTGTAAAATTATCAAAATACCCCTATAAAGGTATTTT-ATAATTTGCTC-TTCCCAAGCTCAG
* * * *
9393651 ATTTTTATGAAATTTTTTAGATCTTAATTTCATAATATTTCATGA-TTTTTGATGCATTTGAAAT
64 ATTTTCATAAAACTTTTTAGATCTTAATTTCATAATATTTCATAATTTTTTG-TGCATTTGAAAT
* *
9393715 CATAGCAGTACCTCGAC
128 CACAACAGTACCTCGAC
* * * *
9393732 AAGTGTGAAATTATCAAAATACCCCTATAAATGTATTTTGTAATTTGCTCTTCCCAAGCTTAGAT
1 AAGTGTAAAATTATCAAAATACCCCTATAAAGGTATTTTATAATTTGCTCTTCCCAAGCTCAGAT
* * *
9393797 TTTCATAAAACTTTTTAGATCTTAATTTTATAATATTTCATAATTTTTTATGC-TTTAAAATC
66 TTTCATAAAACTTTTTAGATCTTAATTTCATAATATTTCATAATTTTTTGTGCATTTGAAATC
9393859 TCCAAAATGA
Statistics
Matches: 224, Mismatches: 31, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
135 16 0.07
136 41 0.18
137 3 0.01
143 12 0.05
144 93 0.42
145 59 0.26
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (144 bp):
AAGTGTAAAATTATCAAAATACCCCTATAAAGGTATTTTATAATTTGCTCTTCCCAAGCTCAGAT
TTTCATAAAACTTTTTAGATCTTAATTTCATAATATTTCATAATTTTTTGTGCATTTGAAATCAC
AACAGTACCTCGAC
Found at i:9397802 original size:77 final size:77
Alignment explanation
Indices: 9397720--9397863 Score: 209
Period size: 77 Copynumber: 1.9 Consensus size: 77
9397710 ACTTTTCGAG
* * * * **
9397720 ATAATCATTAGGATGTCTAGGCACAAGATAAAAATGATTTGTAAGATCT-TCGAGAATAATTTCA
1 ATAATCATCAAGATCTCTAAGCACAAGATAAAAATGATTCATAAGATCTCT-GAGAATAATTTCA
9397784 AAGATCTTCGATC
65 AAGATCTTCGATC
*
9397797 ATAATCATCAAGATCTCTAAGCACAAGATAAAAATGATTCATAAGATCTCTGAGCATAATTTCAA
1 ATAATCATCAAGATCTCTAAGCACAAGATAAAAATGATTCATAAGATCTCTGAGAATAATTTCAA
9397862 AG
66 AG
9397864 TTCTCTAGGT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
77 58 0.98
78 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (77 bp):
ATAATCATCAAGATCTCTAAGCACAAGATAAAAATGATTCATAAGATCTCTGAGAATAATTTCAA
AGATCTTCGATC
Found at i:9397809 original size:22 final size:22
Alignment explanation
Indices: 9397762--9397812 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
9397752 AATGATTTGT
*
9397762 AAGATCTTCGAGAATAATTTCA
1 AAGATCTTCGAGAATAATATCA
**
9397784 AAGATCTTCGATCATAATCATC-
1 AAGATCTTCGAGAATAAT-ATCA
9397806 AAGATCT
1 AAGATCT
9397813 CTAAGCACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (22 bp):
AAGATCTTCGAGAATAATATCA
Found at i:9398107 original size:151 final size:151
Alignment explanation
Indices: 9397931--9398282 Score: 338
Period size: 151 Copynumber: 2.3 Consensus size: 151
9397921 TTTTTTTAAA
* * * *
9397931 TTTTAAAATTATGGAGCCTTGATTTTAAAGGAGCTTTTTTAAAGTTTAGAATGATATGTAAGACC
1 TTTTAAAGTTATGGAGTCTTTATTTTAAAGGAGCTTTTTTAAAGTTTAGAATGATATGTAACACC
* * *** *
9397996 T-TAAGTCATAATTTCTAAAGTCCT-TTGGCCATGATCTATAAAACC-ATGGGATTGA-CTTTAA
66 TCAAAG-CATAATTTCTAAAGACCTCCAAG-CATGATCTATAAAACCTAT-GCA-TGATCTTTAA
*
9398057 AACGACCAAGTACCTTTTCTAAATT
127 AACGACCAAGTACCTCTTCTAAATT
* * * * * *
9398082 TTTTATAGTTGTGGAGTCTTTATTTTAAAAGG-G-TTTGTTCAAAGTTAATAATGATTTGTAACA
1 TTTTAAAGTTATGGAGTCTTTATTTT-AAAGGAGCTTT-TTTAAAGTTTAGAATGATATGTAACA
* * * *
9398145 CCTCAAAGCATACTTTCTAAAGACCTCCAAGTATGATTTATAAGACCTTAATGCATGATCTTTAA
64 CCTCAAAGCATAATTTCTAAAGACCTCCAAGCATGATCTATAAAACC-T-ATGCATGATCTTTAA
** ***
9398210 AACTTCTGGGTACCTCTTCTAAATT
127 AACGACCAAGTACCTCTTCTAAATT
*
9398235 TTTTAAAGTTATGGAGTCTTTGTTTTAAAGGAGCTTTTTTCAAAGTTT
1 TTTTAAAGTTATGGAGTCTTTATTTTAAAGGAGCTTTTTT-AAAGTTT
9398283 GGTTTGTAAG
Statistics
Matches: 159, Mismatches: 31, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
150 3 0.02
151 75 0.47
152 17 0.11
153 53 0.33
154 11 0.07
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (151 bp):
TTTTAAAGTTATGGAGTCTTTATTTTAAAGGAGCTTTTTTAAAGTTTAGAATGATATGTAACACC
TCAAAGCATAATTTCTAAAGACCTCCAAGCATGATCTATAAAACCTATGCATGATCTTTAAAACG
ACCAAGTACCTCTTCTAAATT
Found at i:9398917 original size:18 final size:18
Alignment explanation
Indices: 9398880--9398919 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
9398870 AATTTGTTTA
*
9398880 TGAAGATCAAGCTTTTTT
1 TGAAGATCAAGATTTTTT
9398898 TGAAGATCAA-ATTTTATT
1 TGAAGATCAAGATTTT-TT
9398916 TGAA
1 TGAA
9398920 TTTCTAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (18 bp):
TGAAGATCAAGATTTTTT
Found at i:9399635 original size:5 final size:5
Alignment explanation
Indices: 9399625--9399656 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
9399615 GAGGGGAGAG
9399625 AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AA
1 AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AA
9399657 CAAAACCTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AAGGA
Found at i:9400363 original size:19 final size:19
Alignment explanation
Indices: 9400341--9400377 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9400331 CTTTAAAAAA
9400341 CTTTCTTTTTCATTCTTTT
1 CTTTCTTTTTCATTCTTTT
* *
9400360 CTTTTTTTTTCTTTCTTT
1 CTTTCTTTTTCATTCTTT
9400378 ATTAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (19 bp):
CTTTCTTTTTCATTCTTTT
Found at i:9403645 original size:19 final size:19
Alignment explanation
Indices: 9403621--9403658 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9403611 CCTTTAGCCA
9403621 TTTTGAGCTTTATAAAACT
1 TTTTGAGCTTTATAAAACT
9403640 TTTTGAGCTTTATAAAACT
1 TTTTGAGCTTTATAAAACT
9403659 AACACGTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (19 bp):
TTTTGAGCTTTATAAAACT
Found at i:9405876 original size:27 final size:27
Alignment explanation
Indices: 9405845--9405899 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
9405835 ATAATAGTCC
* *
9405845 ATTGATTGCACATTGATTCCAACATGA
1 ATTGATTGCACACTAATTCCAACATGA
*
9405872 ATTGATTGCACACTAATTCTAACATGA
1 ATTGATTGCACACTAATTCCAACATGA
9405899 A
1 A
9405900 ACTAGTTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (27 bp):
ATTGATTGCACACTAATTCCAACATGA
Found at i:9406121 original size:34 final size:35
Alignment explanation
Indices: 9406078--9406148 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 35
9406068 TGCATAGGTT
*
9406078 GCATCCAAGTAATAGTAATGATGAAGTAAAGT-TC
1 GCATCCAAGTAATAATAATGATGAAGTAAAGTATC
*
9406112 GCATCCAAGTAATAATATTGATGAAGTAAAGTATC
1 GCATCCAAGTAATAATAATGATGAAGTAAAGTATC
9406147 GC
1 GC
9406149 TCCCTTGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 30 0.88
35 4 0.12
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.27
Consensus pattern (35 bp):
GCATCCAAGTAATAATAATGATGAAGTAAAGTATC
Found at i:9410776 original size:20 final size:20
Alignment explanation
Indices: 9410753--9410795 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
9410743 GCTCAAACAG
9410753 TTCAAGGATGGCTAAATCAT
1 TTCAAGGATGGCTAAATCAT
** *
9410773 TTCAATTATGGTTAAATCAT
1 TTCAAGGATGGCTAAATCAT
9410793 TTC
1 TTC
9410796 TTAAGTCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (20 bp):
TTCAAGGATGGCTAAATCAT
Found at i:9415565 original size:12 final size:12
Alignment explanation
Indices: 9415548--9415586 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
9415538 TTAATGTGTT
9415548 CTGAATCTAAAG
1 CTGAATCTAAAG
* *
9415560 CTGAATTTAAACT
1 CTGAATCTAAA-G
9415573 CTGAATCTAAAG
1 CTGAATCTAAAG
9415585 CT
1 CT
9415587 AAATTTAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (12 bp):
CTGAATCTAAAG
Found at i:9415575 original size:25 final size:25
Alignment explanation
Indices: 9415547--9415597 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
9415537 ATTAATGTGT
*
9415547 TCTGAATCTAAAGCTGAATTTAAAC
1 TCTGAATCTAAAGCTAAATTTAAAC
9415572 TCTGAATCTAAAGCTAAATTTAAAC
1 TCTGAATCTAAAGCTAAATTTAAAC
9415597 T
1 T
9415598 ATGTTGTAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (25 bp):
TCTGAATCTAAAGCTAAATTTAAAC
Found at i:9427913 original size:12 final size:12
Alignment explanation
Indices: 9427892--9427961 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 12
9427882 CACTTTATTG
9427892 CTTTTGTTTTTT-
1 CTTTT-TTTTTTC
9427904 C-TTTTTTTTTC
1 CTTTTTTTTTTC
**
9427915 CTTTAGGTTTTTC
1 CTTT-TTTTTTTC
*
9427928 CTTTTTTTATTC
1 CTTTTTTTTTTC
9427940 CTTTTTCTTTTT-
1 CTTTTT-TTTTTC
9427952 CTTTTCTTTT
1 CTTTT-TTTT
9427962 GCAAGCTAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
10 6 0.13
11 4 0.09
12 22 0.47
13 15 0.32
ACGTcount: A:0.03, C:0.16, G:0.04, T:0.77
Consensus pattern (12 bp):
CTTTTTTTTTTC
Found at i:9427924 original size:24 final size:25
Alignment explanation
Indices: 9427897--9427943 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
9427887 TATTGCTTTT
*
9427897 GTTTTTTCTTTTTTT-TTCCTTTAG
1 GTTTTTCCTTTTTTTATTCCTTTAG
9427921 GTTTTTCCTTTTTTTATTCCTTT
1 GTTTTTCCTTTTTTTATTCCTTT
9427944 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.74
Consensus pattern (25 bp):
GTTTTTCCTTTTTTTATTCCTTTAG
Found at i:9428922 original size:16 final size:17
Alignment explanation
Indices: 9428874--9428920 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
9428864 TGAAAAGACA
9428874 AACAAAACATGAAAAT-
1 AACAAAACATGAAAATG
* * *
9428890 AACAAAATAAGCAAATG
1 AACAAAACATGAAAATG
9428907 AACAAAACATGAAA
1 AACAAAACATGAAA
9428921 TGCAAAGCTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.68, C:0.13, G:0.09, T:0.11
Consensus pattern (17 bp):
AACAAAACATGAAAATG
Found at i:9443611 original size:10 final size:11
Alignment explanation
Indices: 9443596--9443624 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
9443586 TTATTTGCCA
9443596 TTTCTTTTC-T
1 TTTCTTTTCTT
9443606 TTTCTTTTCTT
1 TTTCTTTTCTT
9443617 TTTCTTTT
1 TTTCTTTT
9443625 TCAATTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:9444661 original size:20 final size:20
Alignment explanation
Indices: 9444636--9444678 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
9444626 CATTCAAGAG
9444636 AAACATGATGTGAACCTAGA
1 AAACATGATGTGAACCTAGA
*
9444656 AAACATGATTTGAACCTAGA
1 AAACATGATGTGAACCTAGA
9444676 AAA
1 AAA
9444679 AAAAAACTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (20 bp):
AAACATGATGTGAACCTAGA
Found at i:9446072 original size:14 final size:15
Alignment explanation
Indices: 9446053--9446081 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9446043 GGAAAAATAG
9446053 GAAAAAAATA-CAAA
1 GAAAAAAATATCAAA
9446067 GAAAAAAATATCAAA
1 GAAAAAAATATCAAA
9446082 ACTAAAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.76, C:0.07, G:0.07, T:0.10
Consensus pattern (15 bp):
GAAAAAAATATCAAA
Found at i:9455950 original size:30 final size:30
Alignment explanation
Indices: 9455914--9455971 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
9455904 GCTAATATCG
9455914 TTGGTTCACCCTTAGTGTACTTTTGTTATA
1 TTGGTTCACCCTTAGTGTACTTTTGTTATA
9455944 TTGGTTCACCCTTAGTGTACTTTTGTTA
1 TTGGTTCACCCTTAGTGTACTTTTGTTA
9455972 GGCTAGTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.16, C:0.17, G:0.17, T:0.50
Consensus pattern (30 bp):
TTGGTTCACCCTTAGTGTACTTTTGTTATA
Found at i:9458860 original size:29 final size:29
Alignment explanation
Indices: 9458802--9458862 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
9458792 TAGGAAAAGC
*
9458802 AAAAAAAGAAAAGAAAGAAAATGTGAAAA
1 AAAAAAACAAAAGAAAGAAAATGTGAAAA
* * *
9458831 AAAAAAACAAAAGCAATAAAGTGGTGAAAA
1 AAAAAAACAAAAGAAAGAAAAT-GTGAAAA
9458861 AA
1 AA
9458863 GCAAAGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.72, C:0.03, G:0.16, T:0.08
Consensus pattern (29 bp):
AAAAAAACAAAAGAAAGAAAATGTGAAAA
Found at i:9465868 original size:7 final size:7
Alignment explanation
Indices: 9465806--9465868 Score: 54
Period size: 7 Copynumber: 8.9 Consensus size: 7
9465796 TCTAAGTTAA
9465806 GGTTTAG
1 GGTTTAG
*
9465813 GATTTAG
1 GGTTTAG
* * *
9465820 GATTCAA
1 GGTTTAG
9465827 GGTTTAG
1 GGTTTAG
*
9465834 GGTTTAA
1 GGTTTAG
*
9465841 GGTTTAT
1 GGTTTAG
*
9465848 GATTTAG
1 GGTTTAG
9465855 GGTTTTAG
1 GG-TTTAG
9465863 GGTTTA
1 GGTTTA
9465869 AAGTTTTAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 37 0.84
8 7 0.16
ACGTcount: A:0.22, C:0.02, G:0.32, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:9465926 original size:57 final size:57
Alignment explanation
Indices: 9465827--9465945 Score: 150
Period size: 57 Copynumber: 2.1 Consensus size: 57
9465817 TAGGATTCAA
* * * *
9465827 GGTTTAGGGTTTAAGGTTTATGATTTAGGGTTTTAGGGTTTAAAGTTTTAAATTTAG
1 GGTTTAGAGTTTAAGATTTATGATTTAGGGTTTTAAGGTTTAAAGTTTCAAATTTAG
* * * *
9465884 GGTTTAGAGTTTAAGATTT-TGAATTTGGGGTTTTAAGGTTTAAGGTTTCCAATTTGG
1 GGTTTAGAGTTTAAGATTTATG-ATTTAGGGTTTTAAGGTTTAAAGTTTCAAATTTAG
9465941 GGTTT
1 GGTTT
9465946 TATGGAATTA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
56 2 0.04
57 51 0.96
ACGTcount: A:0.23, C:0.02, G:0.29, T:0.47
Consensus pattern (57 bp):
GGTTTAGAGTTTAAGATTTATGATTTAGGGTTTTAAGGTTTAAAGTTTCAAATTTAG
Found at i:9465937 original size:29 final size:29
Alignment explanation
Indices: 9465829--9465947 Score: 109
Period size: 29 Copynumber: 4.1 Consensus size: 29
9465819 GGATTCAAGG
* *
9465829 TTTAGGGTTTAAGG-TTTATGATTTAGGGT
1 TTTAAGGTTTAAGGTTTTA-AATTTAGGGT
* *
9465858 TTTAGGGTTTAAAGTTTTAAATTTAGGG-
1 TTTAAGGTTTAAGGTTTTAAATTTAGGGT
* * *
9465886 TTT-AGAGTTTAAGATTTTGAATTTGGGGT
1 TTTAAG-GTTTAAGGTTTTAAATTTAGGGT
** *
9465915 TTTAAGGTTTAAGGTTTCCAATTTGGGGT
1 TTTAAGGTTTAAGGTTTTAAATTTAGGGT
9465944 TTTA
1 TTTA
9465948 TGGAATTAGA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
27 1 0.01
28 21 0.28
29 48 0.63
30 6 0.08
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.48
Consensus pattern (29 bp):
TTTAAGGTTTAAGGTTTTAAATTTAGGGT
Found at i:9468295 original size:21 final size:21
Alignment explanation
Indices: 9468279--9468320 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9468269 TGAAACAACT
*
9468279 TTCAAACAAAGAAAAACAAAA
1 TTCAAAAAAAGAAAAACAAAA
9468300 TTCAAAAAAAGAAAAA-AAAA
1 TTCAAAAAAAGAAAAACAAAA
9468320 T
1 T
9468321 AAGGGTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.74, C:0.10, G:0.05, T:0.12
Consensus pattern (21 bp):
TTCAAAAAAAGAAAAACAAAA
Found at i:9472507 original size:32 final size:32
Alignment explanation
Indices: 9472444--9472507 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
9472434 TCAAGTGAGT
*
9472444 AAGAGGATTTTTGCAAGAAATTTGAGTTGAAA
1 AAGAGGATTTTTGCAAGAAATTTGAGATGAAA
*
9472476 AAGATGATTTTTG-AATG-AATTTGGAGATGAAA
1 AAGAGGATTTTTGCAA-GAAATTT-GAGATGAAA
9472508 TTTTAAGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 7 0.25
32 21 0.75
ACGTcount: A:0.41, C:0.02, G:0.25, T:0.33
Consensus pattern (32 bp):
AAGAGGATTTTTGCAAGAAATTTGAGATGAAA
Found at i:9472772 original size:16 final size:18
Alignment explanation
Indices: 9472751--9472783 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
9472741 AACATAGCGT
9472751 TTTTTAT-T-ATTTTTTA
1 TTTTTATGTGATTTTTTA
9472767 TTTTTATGTGATTTTTT
1 TTTTTATGTGATTTTTT
9472784 TATAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (18 bp):
TTTTTATGTGATTTTTTA
Found at i:9478033 original size:200 final size:200
Alignment explanation
Indices: 9477684--9478084 Score: 721
Period size: 200 Copynumber: 2.0 Consensus size: 200
9477674 GGCAACGTTC
*
9477684 AGGTTTGCATGGAGAAATGTACTACTTTGAACGTCAACACCAACATAATCTTCGAGGGAGTGACA
1 AGGTTTGCATGGAGAAATGTACTACTTTGAACATCAACACCAACATAATCTTCGAGGGAGTGACA
* * *
9477749 AACCCTACTCCCACTCTTATTGCTTGATAGCGACCTTTGTACTTACAATCTCATAAAAAAGAGCA
66 AACCCTACTCCCACTCTTATTGCTTCATAGCGACATTTGTACTTACAACCTCATAAAAAAGAGCA
*
9477814 ATCAAGTTTTTTGCATCATTGCCAAGGATTATATTGGTGCTAGAAGACTAATATTAATAACATTT
131 ATCAAGTTTTTTACATCATTGCCAAGGATTATATTGGTGCTAGAAGACTAATATTAATAACATTT
9477879 ATTTT
196 ATTTT
9477884 AGGTTTGCATGGAGAAATGTACTACTTTGAACATCAACACCAACATAATCTTCGAGGGAGTGACA
1 AGGTTTGCATGGAGAAATGTACTACTTTGAACATCAACACCAACATAATCTTCGAGGGAGTGACA
* * * *
9477949 AACCCTACTCTCATTCTTATTGCTTCATAGCGTCATTTGTACTTGCAACCTCATAAAAAAGAGCA
66 AACCCTACTCCCACTCTTATTGCTTCATAGCGACATTTGTACTTACAACCTCATAAAAAAGAGCA
9478014 ATCAAGTTTTTTACATCATTGCCAAGGATTATATTGGTGCTAGAAGACTAATATTAATAACATTT
131 ATCAAGTTTTTTACATCATTGCCAAGGATTATATTGGTGCTAGAAGACTAATATTAATAACATTT
9478079 ATTTT
196 ATTTT
9478084 A
1 A
9478085 CTTTGCAATT
Statistics
Matches: 192, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 192 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (200 bp):
AGGTTTGCATGGAGAAATGTACTACTTTGAACATCAACACCAACATAATCTTCGAGGGAGTGACA
AACCCTACTCCCACTCTTATTGCTTCATAGCGACATTTGTACTTACAACCTCATAAAAAAGAGCA
ATCAAGTTTTTTACATCATTGCCAAGGATTATATTGGTGCTAGAAGACTAATATTAATAACATTT
ATTTT
Found at i:9478142 original size:20 final size:21
Alignment explanation
Indices: 9478103--9478142 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
9478093 TTTAGACTTA
* *
9478103 TTTTTTTCTTTTAATGTGTTC
1 TTTTTTTCTTTCAATATGTTC
9478124 TTTTTTT-TTTCAATATGTT
1 TTTTTTTCTTTCAATATGTT
9478143 TGATTTCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.72
Consensus pattern (21 bp):
TTTTTTTCTTTCAATATGTTC
Found at i:9490890 original size:11 final size:11
Alignment explanation
Indices: 9490874--9490899 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9490864 ATTTAACATT
9490874 AAAAAAAATAA
1 AAAAAAAATAA
9490885 AAAAAAAATAA
1 AAAAAAAATAA
9490896 AAAA
1 AAAA
9490900 GAAGAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:9491108 original size:57 final size:58
Alignment explanation
Indices: 9490930--9491563 Score: 833
Period size: 58 Copynumber: 10.9 Consensus size: 58
9490920 TTGTGCAGGA
* * **
9490930 AAAATTGATACTTTCAACTTTTCCCCAAAATATC----TTTGAAACTTTAATTTCGAA-G
1 AAAATTGATACTTTCAACTTTTCCTCAAAA-ATCTTTTTTTGAAAATTT-ATTTTTAAGG
* *
9490985 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTCTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATC-TTTTTTTGAAAATTTATTTTTAAGG
* *
9491044 AAAATTGATACTTTCAACTTTCCCTCAAAAA-CCTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAAGG
* * **
9491101 AAAATTGATACTTTCAACTTTT-CTCCAAAAATATTTTTTTGAAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAATCTTTTTTTGAAAA-TTTATTTTTAAGG
* * *
9491160 GAAATTGATACTTTCAACTTTCCCTCAAAAA-CCTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAAGG
* * * **
9491217 AAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTTGGAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTT-GAAAATTTATTTTTAAGG
* *
9491275 AAAATTGATACTTTCAAC-TTTCTTCAAAAA-CCTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAAGG
* *
9491331 AAAATTGATACTTTCAACTTTTCCTCAAAATTTTTTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAA---ATCTTTTTTTGAAAATTTATTTTTAAGG
*
9491392 AAAATTGATACTTGT-AACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTT-TCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAAGG
9491450 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATC---TTTTTTTGAAAATTTATTTTTAAGG
*
9491511 AAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTGAAAATTTATTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTT
9491564 ATTTTATTTA
Statistics
Matches: 511, Mismatches: 45, Indels: 43
0.85 0.08 0.07
Matches are distributed among these distances:
54 3 0.01
55 29 0.06
56 40 0.08
57 108 0.21
58 144 0.28
59 76 0.15
60 2 0.00
61 108 0.21
62 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAAGG
Found at i:9491584 original size:9 final size:9
Alignment explanation
Indices: 9491577--9491669 Score: 82
Period size: 9 Copynumber: 9.8 Consensus size: 9
9491567 TTATTTAAAG
9491577 AAAATAAAAT
1 AAAA-AAAAT
9491587 AAAAAAAAT
1 AAAAAAAAT
9491596 AAAAGTGAAAAT
1 AAAA---AAAAT
9491608 -AAAAAAAT
1 AAAAAAAAT
9491616 AAAAAAAAT
1 AAAAAAAAT
*
9491625 AAAATAAAGT
1 AAAA-AAAAT
*
9491635 AAAACAAA-
1 AAAAAAAAT
*
9491643 AATAAAAAT
1 AAAAAAAAT
9491652 AAAATAAAGAT
1 AAAA-AAA-AT
9491663 AAAAAAA
1 AAAAAAA
9491670 TATTAAATAA
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
8 11 0.16
9 26 0.38
10 18 0.26
11 9 0.13
12 5 0.07
ACGTcount: A:0.81, C:0.01, G:0.04, T:0.14
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:9491585 original size:5 final size:5
Alignment explanation
Indices: 9491577--9491680 Score: 92
Period size: 5 Copynumber: 20.6 Consensus size: 5
9491567 TTATTTAAAG
9491577 AAAAT AAAAT AAAA- AAAAT AAAAGT GAAAAT -AAA- AAAAT AAAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAAT AAAAT
* *
9491625 AAAAT AAAGT AAAACA AAAAT AAAAAT AAAAT AAAGAT AAAA- AAATAT
1 AAAAT AAAAT AAAA-T AAAAT -AAAAT AAAAT AAA-AT AAAAT AAA-AT
*
9491673 TAAAT AAA
1 AAAAT AAA
9491681 CCTAATCTAA
Statistics
Matches: 82, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
4 17 0.21
5 43 0.52
6 18 0.22
7 4 0.05
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:9491620 original size:27 final size:25
Alignment explanation
Indices: 9491577--9491716 Score: 95
Period size: 27 Copynumber: 5.2 Consensus size: 25
9491567 TTATTTAAAG
*
9491577 AAAATAAAATAA-AAAAAATAAAAGT
1 AAAATAAAAAAATAAAAAATAAAA-T
9491602 GAAAATAAAAAAATAAAAAAAATAAAAT
1 -AAAATAAAAAAAT--AAAAAATAAAAT
* *
9491630 AAAGTAAAACAAAAATAAAAATAAAAT
1 AAAATAAAA-AAATA-AAAAATAAAAT
** *
9491657 AAAGATAAAAAAATATTAAATAAACCT
1 AAA-ATAAAAAAATAAAAAATAAA-AT
9491684 AATCTAATAATAAAAATAAATAAAT-AAAT
1 AA---AATAA-AAAAATAAA-AAATAAAAT
9491713 AAAA
1 AAAA
9491717 CCTGGAGCGG
Statistics
Matches: 91, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
26 21 0.23
27 29 0.32
28 9 0.10
29 18 0.20
30 10 0.11
31 4 0.04
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (25 bp):
AAAATAAAAAAATAAAAAATAAAAT
Found at i:9491628 original size:38 final size:36
Alignment explanation
Indices: 9491577--9491669 Score: 107
Period size: 38 Copynumber: 2.5 Consensus size: 36
9491567 TTATTTAAAG
*
9491577 AAAATAAAATAAAAAAAATAAAAGTGAAAATAAAAAAAT
1 AAAATAAAATAAAAAAAATAAAA--CAAAA-AAAAAAAT
* *
9491616 AAAA-AAAATAAAATAAAGTAAAACAAAAATAAAAAT
1 AAAATAAAATAAAA-AAAATAAAACAAAAAAAAAAAT
9491652 AAAATAAAGATAAAAAAA
1 AAAATAAA-ATAAAAAAA
9491670 TATTAAATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
36 11 0.23
37 10 0.21
38 15 0.31
39 12 0.25
ACGTcount: A:0.81, C:0.01, G:0.04, T:0.14
Consensus pattern (36 bp):
AAAATAAAATAAAAAAAATAAAACAAAAAAAAAAAT
Found at i:9492679 original size:6 final size:6
Alignment explanation
Indices: 9492668--9492771 Score: 88
Period size: 6 Copynumber: 16.8 Consensus size: 6
9492658 AATACCTAAG
* *
9492668 ATAAAA ATAAAA GAAAAAA ATATATAT ATAAAAA ATAAAA ATAAAA AT-AAA
1 ATAAAA ATAAAA -ATAAAA ATA-A-AA AT-AAAA ATAAAA ATAAAA ATAAAA
* * *
9492719 ATAGAA AT-AAA ATAAAA ATGTAAA ATACAAA A-AAAA ATACAA ATAAAA
1 ATAAAA ATAAAA ATAAAA AT-AAAA ATA-AAA ATAAAA ATAAAA ATAAAA
9492767 ATAAA
1 ATAAA
9492772 TTAAAATGAA
Statistics
Matches: 79, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
5 13 0.16
6 43 0.54
7 18 0.23
8 4 0.05
9 1 0.01
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:9492681 original size:13 final size:12
Alignment explanation
Indices: 9492668--9492771 Score: 88
Period size: 11 Copynumber: 8.4 Consensus size: 12
9492658 AATACCTAAG
9492668 ATAAAAATAAAA
1 ATAAAAATAAAA
* *
9492680 GAAAAAAATATATAT
1 -ATAAAAATA-A-AA
9492695 ATAAAAAATAAAA
1 AT-AAAAATAAAA
9492708 ATAAAAAT-AAA
1 ATAAAAATAAAA
*
9492719 ATAGAAAT-AAA
1 ATAAAAATAAAA
*
9492730 ATAAAAATGTAAA
1 ATAAAAAT-AAAA
9492743 ATACAAAA-AAAA
1 ATA-AAAATAAAA
*
9492755 ATACAAATAAAA
1 ATAAAAATAAAA
9492767 ATAAA
1 ATAAA
9492772 TTAAAATGAA
Statistics
Matches: 75, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
11 23 0.31
12 20 0.27
13 17 0.23
14 7 0.09
15 8 0.11
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (12 bp):
ATAAAAATAAAA
Found at i:9492779 original size:41 final size:41
Alignment explanation
Indices: 9492668--9492777 Score: 116
Period size: 41 Copynumber: 2.7 Consensus size: 41
9492658 AATACCTAAG
* * * * **
9492668 ATAAAAATAAAAGAAAAA-AATATATATATAAAAAATAAAA
1 ATAAAAATAAAATAAAAATAAAATAAAAATGTAAAATAAAA
*
9492708 ATAAAAATAAAATAGAAATAAAATAAAAATGTAAAATACAAA
1 ATAAAAATAAAATAAAAATAAAATAAAAATGTAAAATA-AAA
*
9492750 A-AAAAATACAAATAAAAATAAATTAAAA
1 ATAAAAATA-AAATAAAAATAAAATAAAA
9492778 TGAAGAAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
40 16 0.28
41 21 0.36
42 21 0.36
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (41 bp):
ATAAAAATAAAATAAAAATAAAATAAAAATGTAAAATAAAA
Found at i:9492790 original size:36 final size:36
Alignment explanation
Indices: 9492705--9492778 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
9492695 ATAAAAAATA
* *
9492705 AAAATA-AAAATAAAATAGAAATAAAATAAAAATGT
1 AAAATACAAAAAAAAATACAAATAAAATAAAAATGT
*
9492740 AAAATACAAAAAAAAATACAAATAAAA-ATAAAT-T
1 AAAATACAAAAAAAAATACAAATAAAATAAAAATGT
9492774 AAAAT
1 AAAAT
9492779 GAAGAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 6 0.17
35 11 0.31
36 18 0.51
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (36 bp):
AAAATACAAAAAAAAATACAAATAAAATAAAAATGT
Found at i:9492952 original size:8 final size:8
Alignment explanation
Indices: 9492941--9492982 Score: 61
Period size: 7 Copynumber: 5.4 Consensus size: 8
9492931 ACCTTTTTAC
9492941 TTTTTGTT
1 TTTTTGTT
9492949 TTTTTG-T
1 TTTTTGTT
9492956 TTTTTG-T
1 TTTTTGTT
9492963 TTTTTGTTT
1 TTTTTG-TT
9492972 TTTTTGTT
1 TTTTTGTT
9492980 TTT
1 TTT
9492983 GATTAAAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.44
8 11 0.34
9 7 0.22
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTTGTT
Found at i:9492959 original size:15 final size:16
Alignment explanation
Indices: 9492941--9492982 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
9492931 ACCTTTTTAC
9492941 TTTTTGTTTTTT-TGT
1 TTTTTGTTTTTTGTGT
*
9492956 TTTTTGTTTTTTGTTT
1 TTTTTGTTTTTTGTGT
9492972 TTTTTGTTTTT
1 TTTTTGTTTTT
9492983 GATTAAAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (16 bp):
TTTTTGTTTTTTGTGT
Found at i:9492983 original size:15 final size:16
Alignment explanation
Indices: 9492941--9492983 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
9492931 ACCTTTTTAC
9492941 TTTTTGTTTTT-TTGT
1 TTTTTGTTTTTGTTGT
9492956 TTTTTGTTTTTTGTT-T
1 TTTTTG-TTTTTGTTGT
9492972 TTTTTGTTTTTG
1 TTTTTGTTTTTG
9492984 ATTAAAGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 12 0.46
16 12 0.46
17 2 0.08
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (16 bp):
TTTTTGTTTTTGTTGT
Found at i:9493204 original size:41 final size:42
Alignment explanation
Indices: 9492990--9493335 Score: 378
Period size: 41 Copynumber: 8.3 Consensus size: 42
9492980 TTTGATTAAA
* * * * *
9492990 GCTCCTTTAAACAGAGGCTCAACGACTTTGAGAAACATAAATG
1 GCTCCTCTAAACAGAGGCACCACGACTTT-AGAAAAATAAATT
** * * * *
9493033 GCTCCTCTAATTAGAGGCTCAATGACTTTAGAAAAATAAATG
1 GCTCCTCTAAACAGAGGCACCACGACTTTAGAAAAATAAATT
* * * * *
9493075 GCTCCTCTAATCAGAGGCTCAACAACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTAGAAAAATAAATT
* *
9493117 GCTCCTCTAAACAGAGGCACCACGACTTTTAG-AAAGTAAATC
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTAGAAAAATAAATT
*
9493159 GCTCCTCTAAACAGAGGCACCACGACTTTAG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTAGAAAAATAAATT
* * *
9493200 GCTCCTTTAAACAGAGGCACCACAACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTAGAAAAATAAATT
* *
9493241 GCTCCTCTCAACAGAGGCACCATGACTTT-GAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTAGAAAAATAAATT
* * * *
9493282 GCTCTTCTAAACAAAGGCACCACGACTTT-GGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTAGAAAAATAAATT
*
9493323 ACTCCTCTAAACA
1 GCTCCTCTAAACA
9493336 AAGTAAATTG
Statistics
Matches: 268, Mismatches: 33, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
40 1 0.00
41 133 0.50
42 105 0.39
43 29 0.11
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTAGAAAAATAAATT
Found at i:9493380 original size:63 final size:63
Alignment explanation
Indices: 9493276--9493398 Score: 192
Period size: 63 Copynumber: 2.0 Consensus size: 63
9493266 CTTTGAAAAA
*
9493276 TAAATTGCTCTTCTAAACAAAGGCACCACGACTTTGGAAAGTAAATTACTCCTCTAAACAAAG
1 TAAATTGCTCTTCTAAACAAAGGCACCACGACTTTGAAAAGTAAATTACTCCTCTAAACAAAG
* * * * *
9493339 TAAATTGCTCTTTTAAATAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTCAACA
1 TAAATTGCTCTTCTAAACAAAGGCACCACGACTTTGAAAAGTAAATTACTCCTCTAAACA
9493399 GAGGCACCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (63 bp):
TAAATTGCTCTTCTAAACAAAGGCACCACGACTTTGAAAAGTAAATTACTCCTCTAAACAAAG
Found at i:9493402 original size:41 final size:42
Alignment explanation
Indices: 9493335--9493434 Score: 148
Period size: 41 Copynumber: 2.4 Consensus size: 42
9493325 TCCTCTAAAC
* * *
9493335 AAAGTAAATTGCTCTTTTAAATAGAGGCACCACGACTTT-GA
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGA
* *
9493376 AAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGGG
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGA
9493418 AAAGTAAATTGCTCCTC
1 AAAGTAAATTGCTCCTC
9493435 GACAATCATG
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 35 0.66
42 18 0.34
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (42 bp):
AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGA
Found at i:9493411 original size:104 final size:105
Alignment explanation
Indices: 9493231--9493434 Score: 311
Period size: 104 Copynumber: 2.0 Consensus size: 105
9493221 ACAACTTTGA
* * *
9493231 AAAGTAAATTGCTCCTCTCAACAGAGGCACCATGACTTTGAAAAATAAATTGCTCTTCTAAACAA
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAA
9493296 AGGCACCACGACTTT-GGAAAGTAAATTACTCCTCTAAAC
66 AGGCACCACGACTTTGGGAAAGTAAATTACTCCTCTAAAC
* * * * * *
9493335 AAAGTAAATTGCTCTTTTAAATAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTCAACAG
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAA
*
9493400 AGGCACCACGACTTTGGGAAAGTAAATTGCTCCTC
66 AGGCACCACGACTTTGGGAAAGTAAATTACTCCTC
9493435 GACAATCATG
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
104 71 0.80
105 18 0.20
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (105 bp):
AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAA
AGGCACCACGACTTTGGGAAAGTAAATTACTCCTCTAAAC
Found at i:9494411 original size:24 final size:23
Alignment explanation
Indices: 9494383--9494456 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 23
9494373 TTGAGTCCTC
9494383 TTTTTCATTCACTTTTTTCATTTT
1 TTTTTCATTCA-TTTTTTCATTTT
**
9494407 TTTTTCATTCATTTTTTTTTCATTCA
1 TTTTTCATTCA---TTTTTTCATTTT
9494433 TTTTT--TTCATTTTTTCATTTT
1 TTTTTCATTCATTTTTTCATTTT
9494454 TTT
1 TTT
9494457 AATCTTTTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
21 13 0.30
24 15 0.35
26 15 0.35
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTCATTCATTTTTTCATTTT
Found at i:9494419 original size:15 final size:15
Alignment explanation
Indices: 9494399--9494439 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
9494389 ATTCACTTTT
9494399 TTCATTTTTTTTTCA
1 TTCATTTTTTTTTCA
9494414 TTCATTTTTTTTTCA
1 TTCATTTTTTTTTCA
9494429 TTCATTTTTTT
1 TTCATTTTTTT
9494440 CATTTTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCATTTTTTTTTCA
Found at i:9494425 original size:17 final size:17
Alignment explanation
Indices: 9494403--9494456 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
9494393 ACTTTTTTCA
9494403 TTTTTTTTTCATTCA--
1 TTTTTTTTTCATTCATT
9494418 TTTTTTTTTCATTCATT
1 TTTTTTTTTCATTCATT
9494435 TTTTTCATTTT--TTCATT
1 TTTTT--TTTTCATTCATT
9494452 TTTTT
1 TTTTT
9494457 AATCTTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 15 0.43
17 16 0.46
19 4 0.11
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTTTTCATTCATT
Found at i:9494453 original size:7 final size:8
Alignment explanation
Indices: 9494390--9494472 Score: 57
Period size: 8 Copynumber: 10.2 Consensus size: 8
9494380 CTCTTTTTCA
9494390 TTCACTTTT
1 TTCA-TTTT
9494399 TTCATTTT
1 TTCATTTT
*
9494407 TT--TTTCA
1 TTCATTT-T
9494414 TTCATTTT
1 TTCATTTT
*
9494422 TT--TTTCA
1 TTCATTT-T
9494429 TTCATTTTT
1 TTCA-TTTT
9494438 TTCATTTT
1 TTCATTTT
9494446 TTCATTTTT
1 TTCA-TTTT
* *
9494455 TTAATCTT
1 TTCATTTT
9494463 TTCATTTT
1 TTCATTTT
9494471 TT
1 TT
9494473 TCAAGCATAG
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
6 6 0.10
7 4 0.07
8 27 0.47
9 18 0.31
10 3 0.05
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (8 bp):
TTCATTTT
Found at i:9494456 original size:11 final size:11
Alignment explanation
Indices: 9494395--9494447 Score: 52
Period size: 13 Copynumber: 4.3 Consensus size: 11
9494385 TTTCATTCAC
9494395 TTTTTTCATTTTT
1 TTTTTTCA--TTT
9494408 TTTTCATTCATTT
1 TTTT--TTCATTT
9494421 TTTTTTCATTCAT
1 TTTTTTCATT--T
9494434 TTTTTTCATTT
1 TTTTTTCATTT
9494445 TTT
1 TTT
9494448 CATTTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
11 10 0.28
13 22 0.61
15 4 0.11
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:9494464 original size:17 final size:17
Alignment explanation
Indices: 9494429--9494473 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
9494419 TTTTTTTTCA
* *
9494429 TTCATTTTTTTCATTTT
1 TTCATTTTTTTAATCTT
9494446 TTCATTTTTTTAATCTT
1 TTCATTTTTTTAATCTT
9494463 TTCATTTTTTT
1 TTCATTTTTTT
9494474 CAAGCATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCATTTTTTTAATCTT
Found at i:9494506 original size:19 final size:17
Alignment explanation
Indices: 9494468--9494506 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
9494458 ATCTTTTCAT
*
9494468 TTTTTTCAAGCATAGTA
1 TTTTTTCAAGCATAGAA
9494485 TTTTTTCACAGCATCAGAA
1 TTTTTTCA-AGCAT-AGAA
9494504 TTT
1 TTT
9494507 ATAGAGTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 5 0.26
19 6 0.32
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (17 bp):
TTTTTTCAAGCATAGAA
Found at i:9501682 original size:15 final size:16
Alignment explanation
Indices: 9501664--9501694 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9501654 GTTAAATGTG
9501664 ATGAAT-AAAAATGCA
1 ATGAATGAAAAATGCA
9501679 ATGAATGAAAAATGCA
1 ATGAATGAAAAATGCA
9501695 TGTATGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.19
Consensus pattern (16 bp):
ATGAATGAAAAATGCA
Found at i:9504977 original size:59 final size:56
Alignment explanation
Indices: 9504846--9505188 Score: 360
Period size: 57 Copynumber: 5.9 Consensus size: 56
9504836 TTTGTGCAGG
*
9504846 GAAAATTGATACTTTCAACTTTTCCTCAAAAATTCATTTTTGAAAATTTATTTTTAA-A
1 GAAAATTGATACTTTCAACTTTCCCTCAAAAATT--TTTTTGAAAATTTA-TTTTAAGA
* *
9504904 GAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTCGAAAACTTTAATTTTGAGA
1 GAAAATTGATACTTTCAAC-TTTCCCTCAAAAAT-TTTTTT-GAAAA-TTT-ATTTTAAGA
9504964 G-AAATTGATACTTTCAACTTTCCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGA
1 GAAAATTGATACTTTCAACTTTCCCTCAAAAA-TTTTTTTGAAAATTTA-TTTTAAGA
* * * *
9505021 -AAAATTGATATTTTCAACTTTTCCC-CAAAAATATTTTTCTAGAAACTTTAATTT-CGA
1 GAAAATTGATACTTTCAAC-TTTCCCTCAAAAAT-TTTTT-T-GAAAATTTATTTTAAGA
* * *
9505078 GGAAAATTGATACTTTCAAC-TTCCCTCAAAAACCTTTTCTGAAACTTTATTTTAAG-
1 -GAAAATTGATACTTTCAACTTTCCCTCAAAAA-TTTTTTTGAAAATTTATTTTAAGA
* *
9505134 GAAAATTGATACTTTCAACTTTTCCTTAAAAATCTTTTTTTGAAAATTTATTTTA
1 GAAAATTGATACTTTCAACTTTCCCTCAAAAA--TTTTTTTGAAAATTTATTTTA
9505189 TTTTATTTAA
Statistics
Matches: 247, Mismatches: 17, Indels: 43
0.80 0.06 0.14
Matches are distributed among these distances:
55 19 0.08
56 24 0.10
57 70 0.28
58 61 0.25
59 69 0.28
60 4 0.02
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (56 bp):
GAAAATTGATACTTTCAACTTTCCCTCAAAAATTTTTTTGAAAATTTATTTTAAGA
Found at i:9505028 original size:57 final size:56
Alignment explanation
Indices: 9504847--9505187 Score: 359
Period size: 59 Copynumber: 5.9 Consensus size: 56
9504837 TTGTGCAGGG
*
9504847 AAAATTGATACTTTCAACTTTTCCTCAAAAATTCATTTTTGAAAATTTATTTTTAA-A
1 AAAATTGATACTTTCAACTTTCCCTCAAAAATT--TTTTTGAAAATTTATTTTTAAGA
* * *
9504904 GAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTCGAAAACTTTAATTTTGAGA
1 -AAAATTGATACTTTCAAC-TTTCCCTCAAAAAT-TTTTTT-GAAAA-TTTATTTTTAAGA
*
9504964 GAAATTGATACTTTCAACTTTCCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTCCCTCAAAAA-TTTTTTTGAAAATTTATTTTTAAGA
* * * ** *
9505021 AAAATTGATATTTTCAACTTTTCCC-CAAAAATATTTTTCTAGAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAAC-TTTCCCTCAAAAAT-TTTTT-T-GAAAATTTATTTTTAAGA
* * * *
9505080 AAAATTGATACTTTCAAC-TTCCCTCAAAAACCTTTTCTGAAACTTTA-TTTTAAGG
1 AAAATTGATACTTTCAACTTTCCCTCAAAAA-TTTTTTTGAAAATTTATTTTTAAGA
* *
9505135 AAAATTGATACTTTCAACTTTTCCTTAAAAATCTTTTTTTGAAAATTTATTTT
1 AAAATTGATACTTTCAACTTTCCCTCAAAAA--TTTTTTTGAAAATTTATTTT
9505188 ATTTTATTTA
Statistics
Matches: 244, Mismatches: 23, Indels: 32
0.82 0.08 0.11
Matches are distributed among these distances:
55 24 0.10
56 20 0.08
57 63 0.26
58 60 0.25
59 75 0.31
60 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.43
Consensus pattern (56 bp):
AAAATTGATACTTTCAACTTTCCCTCAAAAATTTTTTTGAAAATTTATTTTTAAGA
Found at i:9505053 original size:116 final size:116
Alignment explanation
Indices: 9504845--9505187 Score: 468
Period size: 116 Copynumber: 3.0 Consensus size: 116
9504835 TTTTGTGCAG
*
9504845 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA-TTCATTTTTGAAAATTTATTTTTAA-AGAAA
1 GGAAAATTGATACTTTCAACTTTCCCTCAAAAACTT--TTTTTGAAAATTTATTTTTAAGA-AAA
*
9504908 ATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTCGAAAACTTTAATTTTGA
63 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTCGAAAACTTTAATTTTGA
9504962 -GAGAAATTGATACTTTCAACTTTCCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGAAAAAT
1 GGA-AAATTGATACTTTCAACTTTCCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGAAAAAT
* * *
9505026 TGATATTTTCAACTTTTCCCCAAAAATA-TTTTTCTAGAAACTTTAATTTCGA
65 TGATACTTTCAACTTTTCCCCAAAAATATTTTTTCGA-AAACTTTAATTTTGA
* * * *
9505078 GGAAAATTGATACTTTCAAC-TTCCCTCAAAAACCTTTTCTGAAACTTTA-TTTTAAGGAAAATT
1 GGAAAATTGATACTTTCAACTTTCCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGAAAAATT
** * *
9505141 GATACTTTCAACTTTTCCTTAAAAATCTTTTTTTGAAAA-TTT-ATTTT
66 GATACTTTCAACTTTTCCCCAAAAATATTTTTTCGAAAACTTTAATTTT
9505188 ATTTTATTTA
Statistics
Matches: 204, Mismatches: 16, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
112 4 0.02
113 3 0.01
114 39 0.19
115 39 0.19
116 85 0.42
117 32 0.16
118 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (116 bp):
GGAAAATTGATACTTTCAACTTTCCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGAAAAATT
GATACTTTCAACTTTTCCCCAAAAATATTTTTTCGAAAACTTTAATTTTGA
Found at i:9505271 original size:44 final size:46
Alignment explanation
Indices: 9505196--9505283 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 46
9505186 TTATTTTATT
**
9505196 TAAAGAAAATAAAATAATAAAACAAAATAAAACTGAAATAAAAAAA
1 TAAAGAAAATAAAATAATAAAACAAAATAAAACAAAAATAAAAAAA
*
9505242 TAAA-AAAATAAAA-AATAAAGA-AAAGTAAAACAAAAATAAAAA
1 TAAAGAAAATAAAATAATAAA-ACAAAATAAAACAAAAATAAAAA
9505284 TAAAATAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 24 0.63
45 10 0.26
46 4 0.11
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (46 bp):
TAAAGAAAATAAAATAATAAAACAAAATAAAACAAAAATAAAAAAA
Found at i:9505277 original size:37 final size:36
Alignment explanation
Indices: 9505201--9505283 Score: 89
Period size: 37 Copynumber: 2.3 Consensus size: 36
9505191 TTATTTAAAG
* * *
9505201 AAAATAAAATAATAAAACAAAATAAAACTGAAATAAA
1 AAAATAAAAAAATAAAAAAAAAGAAAACTGAAAT-AA
*
9505238 AAAATAAAAAAATAAAAAATAAAGAAAAGT-AAA-ACA
1 AAAATAAAAAAATAAAAAA-AAAGAAAACTGAAATA-A
9505274 AAAATAAAAA
1 AAAATAAAAA
9505284 TAAAATAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 1 0.03
36 11 0.28
37 20 0.50
38 8 0.20
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.13
Consensus pattern (36 bp):
AAAATAAAAAAATAAAAAAAAAGAAAACTGAAATAA
Found at i:9506190 original size:21 final size:19
Alignment explanation
Indices: 9506154--9506223 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 19
9506144 TTCTAGTCGG
* *
9506154 ATAAATAAAAAAAATAAAA
1 ATAAATCAAGAAAATAAAA
9506173 ATAAATCAAATGAAAATAAATCA
1 ATAAATC-AA-GAAAATAAA--A
9506196 GATAAATCAAGAAAATTAACAA
1 -ATAAATCAAGAAAA-TAA-AA
9506218 ATAAAT
1 ATAAAT
9506224 TAAAATTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
19 6 0.14
20 2 0.05
21 14 0.33
22 6 0.14
23 6 0.14
24 8 0.19
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (19 bp):
ATAAATCAAGAAAATAAAA
Found at i:9506193 original size:15 final size:15
Alignment explanation
Indices: 9506165--9506201 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
9506155 TAAATAAAAA
9506165 AAATAAAAATAAATC
1 AAATAAAAATAAATC
*
9506180 AAATGAAAATAAATC
1 AAATAAAAATAAATC
*
9506195 AGATAAA
1 AAATAAA
9506202 TCAAGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.19
Consensus pattern (15 bp):
AAATAAAAATAAATC
Found at i:9506357 original size:6 final size:6
Alignment explanation
Indices: 9506346--9506455 Score: 88
Period size: 6 Copynumber: 19.0 Consensus size: 6
9506336 AATACCTAAG
* * * *
9506346 ATAAAA ATAAAA GA-AAAA A-ATAT ATAAAA ACAATA ATAAAA ATAAAA
1 ATAAAA ATAAAA -ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
* * *
9506393 ATAAAA AT-AAA AT-ACA A-AAAA ATAAAA ATGTAAA ATACAA AT-AAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT-AAAA ATAAAA ATAAAA
*
9506438 ATACAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA
9506456 TGAAGAAAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
5 19 0.23
6 57 0.70
7 6 0.07
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:9506390 original size:18 final size:16
Alignment explanation
Indices: 9506346--9506455 Score: 73
Period size: 15 Copynumber: 6.8 Consensus size: 16
9506336 AATACCTAAG
*
9506346 ATAAAAATAAAAGAAA
1 ATAAAAATAAAAAAAA
* *
9506362 A-AAATATATAAAAACA
1 ATAAAAATA-AAAAAAA
* *
9506378 ATAATAA-AAATAAAA
1 ATAAAAATAAAAAAAA
* *
9506393 ATAAAAATAAAATACA
1 ATAAAAATAAAAAAAA
9506409 A-AAAAATAAAAATGTAAA
1 ATAAAAATAAAAA---AAA
* *
9506427 ATACAAATAAAATACAA
1 ATAAAAATAAAA-AAAA
9506444 ATAAAAATAAAA
1 ATAAAAATAAAA
9506456 TGAAGAAAAA
Statistics
Matches: 70, Mismatches: 16, Indels: 15
0.69 0.16 0.15
Matches are distributed among these distances:
15 27 0.39
16 14 0.20
17 16 0.23
18 3 0.04
19 9 0.13
20 1 0.01
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (16 bp):
ATAAAAATAAAAAAAA
Found at i:9506427 original size:16 final size:15
Alignment explanation
Indices: 9506395--9506456 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 15
9506385 AAATAAAAAT
9506395 AAAAATAAAATACAA
1 AAAAATAAAATACAA
9506410 AAAAATAAAAATGTA-AA
1 AAAAAT-AAAA--TACAA
9506427 ATACAAATAAAATACAAA
1 A-A-AAATAAAATAC-AA
9506445 TAAAAATAAAAT
1 -AAAAATAAAAT
9506457 GAAGAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
15 6 0.15
16 6 0.15
17 12 0.31
18 10 0.26
19 5 0.13
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.18
Consensus pattern (15 bp):
AAAAATAAAATACAA
Found at i:9506428 original size:34 final size:35
Alignment explanation
Indices: 9506346--9506455 Score: 118
Period size: 34 Copynumber: 3.2 Consensus size: 35
9506336 AATACCTAAG
* * * * *
9506346 ATAAAAATAAAAGAAAAAAAT-ATATAAAAACAATA
1 ATAAAAATAAAA-ATAAAAATAAAATACAAATAAAA
9506381 ATAAAAATAAAAATAAAAATAAAATAC-AA-AAAA
1 ATAAAAATAAAAATAAAAATAAAATACAAATAAAA
* *
9506414 ATAAAAATGTAAAATACAAATAAAATACAAATAAAA
1 ATAAAAAT-AAAAATAAAAATAAAATACAAATAAAA
9506450 ATAAAA
1 ATAAAA
9506456 TGAAGAAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
33 11 0.17
34 26 0.40
35 18 0.28
36 10 0.15
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (35 bp):
ATAAAAATAAAAATAAAAATAAAATACAAATAAAA
Found at i:9506833 original size:24 final size:24
Alignment explanation
Indices: 9506795--9506847 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
9506785 ACATATAATA
*
9506795 TATTTAACATGTAAATTATTTATT
1 TATTTAACATATAAATTATTTATT
*
9506819 TATTTAATATATAAATTATTTATT
1 TATTTAACATATAAATTATTTATT
9506843 TATTT
1 TATTT
9506848 GTGTATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
TATTTAACATATAAATTATTTATT
Found at i:9512605 original size:18 final size:18
Alignment explanation
Indices: 9512582--9512617 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
9512572 TCTGCTACTC
9512582 ATACAATGGAAGATTATG
1 ATACAATGGAAGATTATG
9512600 ATACAATGGAAGATTATG
1 ATACAATGGAAGATTATG
9512618 CTCCGAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (18 bp):
ATACAATGGAAGATTATG
Found at i:9529476 original size:13 final size:13
Alignment explanation
Indices: 9529446--9529495 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
9529436 TCACTTAGGA
9529446 TTTAGGGTTT--T
1 TTTAGGGTTTCAT
9529457 GTTTAGGGTTTCAT
1 -TTTAGGGTTTCAT
9529471 TTTAGGGTTTCAT
1 TTTAGGGTTTCAT
*
9529484 TTTAAGGTTTCA
1 TTTAGGGTTTCA
9529496 CATTAAGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
12 10 0.29
13 24 0.69
14 1 0.03
ACGTcount: A:0.16, C:0.06, G:0.24, T:0.54
Consensus pattern (13 bp):
TTTAGGGTTTCAT
Found at i:9529505 original size:26 final size:26
Alignment explanation
Indices: 9529458--9529507 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
9529448 TAGGGTTTTG
* ** *
9529458 TTTAGGGTTTCATTTTAGGGTTTCAT
1 TTTAAGGTTTCACATTAAGGTTTCAT
9529484 TTTAAGGTTTCACATTAAGGTTTC
1 TTTAAGGTTTCACATTAAGGTTTC
9529508 GAGTTTCATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (26 bp):
TTTAAGGTTTCACATTAAGGTTTCAT
Found at i:9531645 original size:25 final size:24
Alignment explanation
Indices: 9531603--9531651 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
9531593 CATTTTAGCC
* *
9531603 TTTTTAACCTTTTTTTTATAATTT
1 TTTTTAACATTTTATTTATAATTT
*
9531627 TTTTATAACATTTTATTTATTATTT
1 TTTT-TAACATTTTATTTATAATTT
9531652 ATCTTATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTTAACATTTTATTTATAATTT
Found at i:9532373 original size:33 final size:33
Alignment explanation
Indices: 9532325--9532406 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
9532315 TCAATGCTAG
* * *
9532325 CTAAATTAGGTTTAAAATTTCATTGGATGCCAA
1 CTAAATTGGGCTTAAAATTTCATTAGATGCCAA
* * *
9532358 TTAAATTGGGCTTAAAATTTCATTAGATGCTAG
1 CTAAATTGGGCTTAAAATTTCATTAGATGCCAA
*
9532391 CTAAACTGGGCTTAAA
1 CTAAATTGGGCTTAAA
9532407 TTTTTATCGA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (33 bp):
CTAAATTGGGCTTAAAATTTCATTAGATGCCAA
Found at i:9532491 original size:35 final size:35
Alignment explanation
Indices: 9532451--9532567 Score: 182
Period size: 35 Copynumber: 3.3 Consensus size: 35
9532441 TCATTAGGCA
* **
9532451 CCAACTAAACTA-GACTTAAAACTTCCTCATGAGTG
1 CCAACTAAACTATG-CTTAAAATTTTTTCATGAGTG
*
9532486 CCAACTAAACTATGCTTAAAATTTTTTTATGAGTG
1 CCAACTAAACTATGCTTAAAATTTTTTCATGAGTG
9532521 CCAACTAAACTATGCTTAAAATTTTTTCATGAGTG
1 CCAACTAAACTATGCTTAAAATTTTTTCATGAGTG
9532556 CCAACTAAACTA
1 CCAACTAAACTA
9532568 GGTTAAATTT
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 75 0.99
36 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (35 bp):
CCAACTAAACTATGCTTAAAATTTTTTCATGAGTG
Found at i:9532936 original size:22 final size:21
Alignment explanation
Indices: 9532857--9532937 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 21
9532847 TATACTTTTT
* *
9532857 CAGCTAATCTAGGTTTACATG
1 CAGCTAATCTAGGCTTACGTG
* *
9532878 CAACTAATCTTGGCTTACGTG
1 CAGCTAATCTAGGCTTACGTG
* *
9532899 CCAGCTAAAT-TGGGCTTATGTG
1 -CAGCT-AATCTAGGCTTACGTG
9532921 CTAGCTAATCTAGGCTT
1 C-AGCTAATCTAGGCTT
9532938 GTGTGTCAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
21 21 0.44
22 24 0.50
23 3 0.06
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (21 bp):
CAGCTAATCTAGGCTTACGTG
Found at i:9533819 original size:17 final size:17
Alignment explanation
Indices: 9533786--9533819 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9533776 AACTAAGTAA
* *
9533786 ATTGATGCGTAATTCCC
1 ATTGATGCATAACTCCC
9533803 ATTGATGCATAACTCCC
1 ATTGATGCATAACTCCC
9533820 TTCATTTAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (17 bp):
ATTGATGCATAACTCCC
Found at i:9538209 original size:13 final size:14
Alignment explanation
Indices: 9538181--9538218 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
9538171 AAAATGTAGG
9538181 AAAATG-AAATGAAA
1 AAAATGTAAA-GAAA
*
9538195 AAAAAGTAAAGAAA
1 AAAATGTAAAGAAA
9538209 AAAATGTAAA
1 AAAATGTAAA
9538219 TCCTAATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 18 0.86
15 3 0.14
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (14 bp):
AAAATGTAAAGAAA
Found at i:9538634 original size:24 final size:22
Alignment explanation
Indices: 9538600--9538662 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 22
9538590 TTTGCTAGAA
*
9538600 AAATTCTAAAAATAA-ACTCAAG
1 AAATTCTAAAAA-AAGAATCAAG
9538622 AAATTCATGAAAAAAAGAATCAAG
1 AAATTC-T-AAAAAAAGAATCAAG
*
9538646 AAACTCTATTAAAAAAG
1 AAATTCTA--AAAAAAG
9538663 CAATGTAGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 7 0.21
23 4 0.12
24 23 0.68
ACGTcount: A:0.60, C:0.11, G:0.08, T:0.21
Consensus pattern (22 bp):
AAATTCTAAAAAAAGAATCAAG
Found at i:9543169 original size:20 final size:20
Alignment explanation
Indices: 9543146--9543189 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
9543136 GGAATTTTGG
9543146 TTTTTACATTGTTGT-TATT
1 TTTTTACATTGTTGTGTATT
*
9543165 TTTTTACATTTTTGTGTATT
1 TTTTTACATTGTTGTGTATT
9543185 TTTTT
1 TTTTT
9543190 CGATTGTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.14, C:0.05, G:0.09, T:0.73
Consensus pattern (20 bp):
TTTTTACATTGTTGTGTATT
Found at i:9548497 original size:17 final size:16
Alignment explanation
Indices: 9548476--9548506 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9548466 TATGGTATGA
*
9548476 AAAAAATAAAGGAAAT
1 AAAAAATAAAAGAAAT
9548492 AAAAAATAAAAGAAA
1 AAAAAATAAAAGAAA
9548507 GAGTTTCCTT
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:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAAAATAAAAGAAAT
Found at i:9548501 original size:778 final size:767
Alignment explanation
Indices: 9546990--9548537 Score: 2399
Period size: 778 Copynumber: 2.0 Consensus size: 767
9546980 GTAGTTCACA
* *
9546990 TAGTATCTATAACTACATTCTCATGTGATGGTTGTATAAGTGATCCTTTGACTTGAGATTACTTA
1 TAGTATCTATAACTACATTCTCATGTGATGGTTATATAAGTGATCATTTGACTTGAGATTACTTA
9547055 TGATCTTATATGATGAATATTATATTTTGACTTTACTTTATTTATGGTTCTAACCAAGAATGCAC
66 TGATCTTATATGATGAATATTATATTTTGACTTTACTTTATTTATGGTTCTAACCAAGAATGCAC
* *
9547120 CAATCAAGCATTGTTGTGTATAACACGAGGCATATGAAGATGCATGAAGTAATCAAGATGGAATT
131 CAATCAAGCATTGTTGGGTATAACACGAGGCATATAAAGATGCATGAAGTAATCAAGATGGAATT
* * *
9547185 TATCATCTTATGTAATCAAAAGAGTATTTCAATTAGTCTTGATTGAATTAACTTAAGAAATCTTT
196 CATCATCTTATGTAATCAAAAGAGTATTTCAACTAGTATTGATTGAATTAACTTAAGAAATCTTT
* *
9547250 GGCCAAAGCGAAATAAAACTTTAGAATTGATCTAAAACTTATTTTTGAGTTAATGTCAAGGATAA
261 AGCCAAAGCGAAATAAAACTTTAGAATTGATCTAAAACTTATTTGTGAGTTAATGTCAAGGATAA
*
9547315 GACTTAACATGGTAAACAAGATTGAGTAAACACTAAAAACTAAACCATATTCAATGTTCAAACCG
326 GACTTAACATGGTAAACAAGATTGAGTAAACAC----AACTAAACCATATTCAATATTCAAACCG
* * * *
9547380 AGATACTTTGTGATGAAAGAATACTAATTATATACAAAGATATTCACGGATAGGTTGTCAAGCCA
387 ACATACTATGTGATGAAAGAATACTAATTATACACAAAGAAATTCACGGATAGGTTGTCAAGCCA
*
9547445 TATTGACTTTTCTTTAACAATTAGGGGTCATGACAATAAAGCTAGCATTGATCATGATCTATAAA
452 TATTGACTTTTCTTTAACAATTAAGGGTCATGACAATAAAGCTAGCATTGATCATGATCTATAAA
* *
9547510 CATAAGGTTGGTTAATTAGAGAATTGGTGATGAAGACAAAAAGTTTGTTTCATCTATAGCTGAAT
517 CATAAGGCTGGTTAATTAGAGAATTGGTGATGAAGACAAAAAGTTTGTTTCATCTATAACTGAAT
*
9547575 ACTAAAGCTTATAATGCTTATATTTATTGCCAACATACTAAAGAACCTAATGTATCACACACAAT
582 ACTAAAGCTTATAATGCTTATATTTATTGCCAACATACTAAAGAACCTAATGGATCACACACAAT
* *
9547640 AGGACAAGTGTGAAAGATTAAAATTGGGACAAATTAAGTTAGACTTAATTTGATTTTGGTACGAC
647 AGGACAAGTGTGAAAGATTAAAATTAGGACAAATTAAGTTAGACTTAATTTGATTATGGTACGAC
9547705 AAAAAATAAAGGAAATAAAAAACAAAAGAAAGAGTTTCCTTTATTTTGTAAATTCGACTAGCT
712 AAAAAATAAAGGAAAT-------AAAAGAAAGAGTTTCCTTTATTTTGTAAATTCGACTAGCT
* *
9547768 TAGTGTCTATAGCTACATTCTCATGTGATGGTTATATAAGTGATCATTTGACTTGAGATTACTTA
1 TAGTATCTATAACTACATTCTCATGTGATGGTTATATAAGTGATCATTTGACTTGAGATTACTTA
* *
9547833 TGATCTTATATTATGAATGTTATATTTTGACTTTACTTTATTTATGGTTCTAACCAAGAATGCAC
66 TGATCTTATATGATGAATATTATATTTTGACTTTACTTTATTTATGGTTCTAACCAAGAATGCAC
* * ** * * *
9547898 TAGTCAAGTGTTGTTGGGTATAACATGAGGCATATAAA-AGTTCATGAAGTAATCAAGATGGGAT
131 CAATCAAGCATTGTTGGGTATAACACGAGGCATATAAAGA-TGCATGAAGTAATCAAGATGGAAT
* * *
9547962 TCATCTTCTTGTGTAATCAAAAGAGTATTTCAACTAGTATTGATTGAATTAACTTGAGAAATCTT
195 TCATCATCTTATGTAATCAAAAGAGTATTTCAACTAGTATTGATTGAATTAACTTAAGAAATCTT
* * *
9548027 TAGCCAAAGCGAAATAAGACTTTAGAATTGGTCTCAAACTTATTTGTGAGTTAATGTCAAGGATA
260 TAGCCAAAGCGAAATAAAACTTTAGAATTGATCTAAAACTTATTTGTGAGTTAATGTCAAGGATA
* *
9548092 AGACTTAACATGGTAAA-GAGATTGAGT-AA-AC-ACTAAACCATATTCAATATTCAAACTGACA
325 AGACTTAACATGGTAAACAAGATTGAGTAAACACAACTAAACCATATTCAATATTCAAACCGACA
*
9548153 TACTATGTGATGAAAGAATACTAATTATACACAAAGACAATTCACGGATAGGTTGTGAAGCCATA
390 TACTATGTGATGAAAGAATACTAATTATACACAAAGA-AATTCACGGATAGGTTGTCAAGCCATA
* * *
9548218 TTGATTTTTCTTTAGCAATTAAGGGTCATGGCAATAAAGCTAGCATTGATCAT-ACTCTATAAAC
454 TTGACTTTTCTTTAACAATTAAGGGTCATGACAATAAAGCTAGCATTGATCATGA-TCTATAAAC
*
9548282 ATAAGGCTGGTTAATTGGAGAATTGGTGATGAAGACAAAAAGTTTGTTTCATCTATAACTGAATT
518 ATAAGGCTGGTTAATTAGAGAATTGGTGATGAAGACAAAAAGTTTGTTTCATCTATAACTGAA-T
* *
9548347 ACTAAAGCTTATAATGCTTGTATTTATTGCCAACATGCTAAAGAACCTAATGGATCACACACAAT
582 ACTAAAGCTTATAATGCTTATATTTATTGCCAACATACTAAAGAACCTAATGGATCACACACAAT
* * *
9548412 AGGACAATTGTGAAAGATTAAAATTAGGACAAATTAAGTTGGACTTAATTTGATTATGGTATGA-
647 AGGACAAGTGTGAAAGATTAAAATTAGGACAAATTAAGTTAGACTTAATTTGATTATGGTACGAC
*
9548476 AAAAAATAAAGGAAATAAAAAATAAAAGAAAGAGTTTCCTTTATTTTGTAAATTTGACTAGC
712 AAAAAATAAAGG-------AAATAAAAGAAAGAGTTTCCTTTATTTTGTAAATTCGACTAGC
9548538 ATAGAGTTAA
Statistics
Matches: 709, Mismatches: 50, Indels: 29
0.90 0.06 0.04
Matches are distributed among these distances:
770 63 0.09
771 193 0.27
772 122 0.17
775 2 0.00
776 2 0.00
777 10 0.01
778 317 0.45
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (767 bp):
TAGTATCTATAACTACATTCTCATGTGATGGTTATATAAGTGATCATTTGACTTGAGATTACTTA
TGATCTTATATGATGAATATTATATTTTGACTTTACTTTATTTATGGTTCTAACCAAGAATGCAC
CAATCAAGCATTGTTGGGTATAACACGAGGCATATAAAGATGCATGAAGTAATCAAGATGGAATT
CATCATCTTATGTAATCAAAAGAGTATTTCAACTAGTATTGATTGAATTAACTTAAGAAATCTTT
AGCCAAAGCGAAATAAAACTTTAGAATTGATCTAAAACTTATTTGTGAGTTAATGTCAAGGATAA
GACTTAACATGGTAAACAAGATTGAGTAAACACAACTAAACCATATTCAATATTCAAACCGACAT
ACTATGTGATGAAAGAATACTAATTATACACAAAGAAATTCACGGATAGGTTGTCAAGCCATATT
GACTTTTCTTTAACAATTAAGGGTCATGACAATAAAGCTAGCATTGATCATGATCTATAAACATA
AGGCTGGTTAATTAGAGAATTGGTGATGAAGACAAAAAGTTTGTTTCATCTATAACTGAATACTA
AAGCTTATAATGCTTATATTTATTGCCAACATACTAAAGAACCTAATGGATCACACACAATAGGA
CAAGTGTGAAAGATTAAAATTAGGACAAATTAAGTTAGACTTAATTTGATTATGGTACGACAAAA
AATAAAGGAAATAAAAGAAAGAGTTTCCTTTATTTTGTAAATTCGACTAGCT
Found at i:9549699 original size:17 final size:16
Alignment explanation
Indices: 9549671--9549702 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
9549661 TAACATGCAA
9549671 TTAAACTAAATTAAAC
1 TTAAACTAAATTAAAC
9549687 TTAAACATAAATTAAA
1 TTAAAC-TAAATTAAA
9549703 TCAACTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
TTAAACTAAATTAAAC
Found at i:9559515 original size:20 final size:20
Alignment explanation
Indices: 9559445--9559515 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
9559435 TACATGAATT
*
9559445 TTCATCATCTTTCTTCAAGA
1 TTCATCATCTTCCTTCAAGA
9559465 TTCATCATCTT-CTTCAAGA
1 TTCATCATCTTCCTTCAAGA
9559484 TTCATCATCTTCCTTCAAGA
1 TTCATCATCTTCCTTCAAGA
9559504 TTCATCATCTTC
1 TTCATCATCTTC
9559516 AACTCTATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.38
20 31 0.62
ACGTcount: A:0.24, C:0.28, G:0.04, T:0.44
Consensus pattern (20 bp):
TTCATCATCTTCCTTCAAGA
Found at i:9559671 original size:10 final size:10
Alignment explanation
Indices: 9559628--9559675 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
9559618 CAAAATATGA
9559628 TCAAGAATCAT
1 TCAAGAATC-T
* *
9559639 CCAAGAATCA
1 TCAAGAATCT
*
9559649 TCAA-AAACT
1 TCAAGAATCT
9559658 TCAAGAATCT
1 TCAAGAATCT
9559668 TCAAGAAT
1 TCAAGAAT
9559676 TACTAAGGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
9 7 0.23
10 15 0.50
11 8 0.27
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.23
Consensus pattern (10 bp):
TCAAGAATCT
Found at i:9560719 original size:16 final size:17
Alignment explanation
Indices: 9560698--9560732 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
9560688 CATTGAAAGA
9560698 TTTTTTTTTTGGT-TTT
1 TTTTTTTTTTGGTATTT
9560714 TTTTTTTTTTGGTATTT
1 TTTTTTTTTTGGTATTT
9560731 TT
1 TT
9560733 GAGTAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTTGGTATTT
Found at i:9563568 original size:16 final size:16
Alignment explanation
Indices: 9563549--9563615 Score: 55
Period size: 16 Copynumber: 4.2 Consensus size: 16
9563539 ATTTAATCTT
9563549 AAATTAATTTAAATTC
1 AAATTAATTTAAATTC
* **
9563565 AAATTAGTTCGAATTGC
1 AAATTAATTTAAATT-C
* *
9563582 AAA-TAATTTCAACTC
1 AAATTAATTTAAATTC
* *
9563597 AAATTTATTTTAATTC
1 AAATTAATTTAAATTC
9563613 AAA
1 AAA
9563616 ATGATTTTTA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
15 4 0.10
16 31 0.79
17 4 0.10
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.40
Consensus pattern (16 bp):
AAATTAATTTAAATTC
Found at i:9566172 original size:62 final size:62
Alignment explanation
Indices: 9566093--9566211 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 62
9566083 CACGGTCCAT
* * * *
9566093 ACCAACTTATGAGATATTATTTGCTTTGACCTCATTGGGTCTCACAATTTTGTTCAAGTTGG
1 ACCAACTTATAAGATATTATTCGCTTTAACCTCATTAGGTCTCACAATTTTGTTCAAGTTGG
* * * *
9566155 ACCAACTTGTAAGATATTATTCGTTTTAACCTTATTAGGTCTCACGATTTTGTTCAA
1 ACCAACTTATAAGATATTATTCGCTTTAACCTCATTAGGTCTCACAATTTTGTTCAA
9566212 ATTAAAGTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 49 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (62 bp):
ACCAACTTATAAGATATTATTCGCTTTAACCTCATTAGGTCTCACAATTTTGTTCAAGTTGG
Found at i:9567641 original size:24 final size:24
Alignment explanation
Indices: 9567613--9567668 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
9567603 ATTTAATAAG
* *
9567613 TTTTTATTTGTATTATATTTATTA
1 TTTTTATTTATACTATATTTATTA
* *
9567637 TTTTTACTTATGCTATATTTATTA
1 TTTTTATTTATACTATATTTATTA
9567661 TTTTTATT
1 TTTTTATT
9567669 AAATTAATGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTTATTTATACTATATTTATTA
Found at i:9567814 original size:16 final size:16
Alignment explanation
Indices: 9567793--9567827 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
9567783 ACCAATTCGA
9567793 GTTTGGGTTGATTTGG
1 GTTTGGGTTGATTTGG
*
9567809 GTTTGGGTTGATTTTG
1 GTTTGGGTTGATTTGG
9567825 GTT
1 GTT
9567828 CAAGTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.00, G:0.40, T:0.54
Consensus pattern (16 bp):
GTTTGGGTTGATTTGG
Found at i:9569007 original size:19 final size:19
Alignment explanation
Indices: 9568983--9569022 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
9568973 TAAATAAAAA
9568983 AAATAAAATTTATTTAA-AT
1 AAATAAAA-TTATTTAATAT
*
9569002 AAATAATATTATTTAATAT
1 AAATAAAATTATTTAATAT
9569021 AA
1 AA
9569023 TTAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATAAAATTATTTAATAT
Found at i:9569015 original size:18 final size:19
Alignment explanation
Indices: 9568992--9569027 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9568982 AAAATAAAAT
9568992 TTATTTAA-ATAAATAATA
1 TTATTTAATATAAATAATA
*
9569010 TTATTTAATATAATTAAT
1 TTATTTAATATAAATAAT
9569028 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTTAATATAAATAATA
Found at i:9577399 original size:6 final size:6
Alignment explanation
Indices: 9577388--9577429 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
9577378 ATGCCTACAC
9577388 ATATGT ATATGT ATATGT ATATGT -TATGT ATATGT ATATGT A
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT A
9577430 CGTATACGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:9577417 original size:17 final size:18
Alignment explanation
Indices: 9577388--9577429 Score: 77
Period size: 17 Copynumber: 2.4 Consensus size: 18
9577378 ATGCCTACAC
9577388 ATATGTATATGTATATGT
1 ATATGTATATGTATATGT
9577406 ATATGT-TATGTATATGT
1 ATATGTATATGTATATGT
9577423 ATATGTA
1 ATATGTA
9577430 CGTATACGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (18 bp):
ATATGTATATGTATATGT
Found at i:9581608 original size:22 final size:23
Alignment explanation
Indices: 9581567--9581616 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 23
9581557 AAATAACAAA
9581567 AAAATTATTAAATTTCAAAT-AC
1 AAAATTATTAAATTTCAAATAAC
9581589 AAAATTA-TAAATTAAT-AAATAAC
1 AAAATTATTAAATT--TCAAATAAC
9581612 AAAAT
1 AAAAT
9581617 CAAATCATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.24
22 11 0.44
23 8 0.32
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAATTATTAAATTTCAAATAAC
Found at i:9584239 original size:22 final size:22
Alignment explanation
Indices: 9584186--9584240 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
9584176 AATTTTATAT
9584186 AAATATTTATAAATTAATGAAA
1 AAATATTTATAAATTAATGAAA
* *
9584208 ATAATA-TTATAAATTTATTAAA
1 A-AATATTTATAAATTAATGAAA
9584230 AAATATTTATA
1 AAATATTTATA
9584241 TAAATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATATTTATAAATTAATGAAA
Found at i:9592799 original size:13 final size:14
Alignment explanation
Indices: 9592779--9592810 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
9592769 ATAAATAAAA
9592779 TTTAAAAACTATTT
1 TTTAAAAACTATTT
9592793 TTTAAAAACTATTT
1 TTTAAAAACTATTT
9592807 TTTA
1 TTTA
9592811 TCGAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTAAAAACTATTT
Found at i:9593099 original size:16 final size:15
Alignment explanation
Indices: 9593079--9593132 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
9593069 ATTAAAAAAA
9593079 AAAAAAAGAGAGAAG
1 AAAAAAAGAGAGAAG
*
9593094 AGAAAAGAGAGAGAAG
1 A-AAAAAAGAGAGAAG
*
9593110 AAAAGAAAGA-AAAATG
1 AAAA-AAAGAGAGAA-G
9593126 AAAAAAA
1 AAAAAAA
9593133 ATTTTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 10 0.30
16 23 0.70
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (15 bp):
AAAAAAAGAGAGAAG
Found at i:9593101 original size:14 final size:15
Alignment explanation
Indices: 9593082--9593120 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
9593072 AAAAAAAAAA
9593082 AAAAGAGAGAAG-AG
1 AAAAGAGAGAAGAAG
9593096 AAAAGAGAG-AGAAG
1 AAAAGAGAGAAGAAG
*
9593110 AAAAGAAAGAA
1 AAAAGAGAGAA
9593121 AAATGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 2 0.09
14 19 0.86
15 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
AAAAGAGAGAAGAAG
Found at i:9593156 original size:15 final size:15
Alignment explanation
Indices: 9593138--9593173 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
9593128 AAAAAATTTT
*
9593138 AAATTTAATAATTCA
1 AAATTTAATAATTAA
*
9593153 AAATTTATTAATTAA
1 AAATTTAATAATTAA
9593168 AAATTT
1 AAATTT
9593174 TACTTTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTTAATAATTAA
Found at i:9593359 original size:14 final size:15
Alignment explanation
Indices: 9593340--9593386 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
9593330 AAAAGAAAAA
9593340 AAAAAT-AAAGAGGG
1 AAAAATAAAAGAGGG
*
9593354 AAAAATAAAATAGGG
1 AAAAATAAAAGAGGG
**
9593369 AAAAGGAAAAGAAGGG
1 AAAAATAAAAG-AGGG
9593385 AA
1 AA
9593387 GATGAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 6 0.22
15 15 0.56
16 6 0.22
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.06
Consensus pattern (15 bp):
AAAAATAAAAGAGGG
Found at i:9594599 original size:8 final size:8
Alignment explanation
Indices: 9594588--9594617 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
9594578 GAACTCTGAC
9594588 TCTCTCTG
1 TCTCTCTG
*
9594596 TCTCTCTC
1 TCTCTCTG
9594604 TCTCTCTG
1 TCTCTCTG
9594612 TCTCTC
1 TCTCTC
9594618 ATGTACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.43, G:0.07, T:0.50
Consensus pattern (8 bp):
TCTCTCTG
Found at i:9595009 original size:2 final size:2
Alignment explanation
Indices: 9595002--9595034 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9594992 TACACATGAA
9595002 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9595035 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9595039 original size:2 final size:2
Alignment explanation
Indices: 9595034--9595064 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9595024 TCTCTCTCTC
*
9595034 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9595065 GCTTTTCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9596400 original size:21 final size:21
Alignment explanation
Indices: 9596375--9596415 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9596365 TTTTTTTAAA
9596375 TAAAT-TATATCAATAAAATTT
1 TAAATCTAT-TCAATAAAATTT
*
9596396 TAAATCTATTTAATAAAATT
1 TAAATCTATTCAATAAAATT
9596416 ATCCTGTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATCTATTCAATAAAATTT
Found at i:9596901 original size:25 final size:25
Alignment explanation
Indices: 9596859--9596912 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
9596849 TAAATTTTAG
*
9596859 AATTTTTTACCAAATTTTCTACAAA
1 AATTTTTTACCAAATTTTCTAAAAA
* *
9596884 AATTTTTTA-CAGATTTTTTTAAAAA
1 AATTTTTTACCA-AATTTTCTAAAAA
9596909 AATT
1 AATT
9596913 CTACAAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (25 bp):
AATTTTTTACCAAATTTTCTAAAAA
Found at i:9599145 original size:14 final size:13
Alignment explanation
Indices: 9599128--9599160 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
9599118 GAGCTGCTGA
9599128 TTTGACTTATGATT
1 TTTG-CTTATGATT
9599142 TTTGCTTATGA-T
1 TTTGCTTATGATT
9599154 TTTGCTT
1 TTTGCTT
9599161 GAATGCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 7 0.37
14 4 0.21
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.61
Consensus pattern (13 bp):
TTTGCTTATGATT
Found at i:9599670 original size:3 final size:3
Alignment explanation
Indices: 9599662--9599697 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
9599652 ACACTATCTC
9599662 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9599698 AGGAAACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9600322 original size:11 final size:11
Alignment explanation
Indices: 9600290--9600322 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
9600280 TAGAAATTTC
9600290 AAAA-TTTTTT
1 AAAATTTTTTT
9600300 AGAAATTTTTTT
1 A-AAATTTTTTT
9600312 AAAATTTTTTT
1 AAAATTTTTTT
9600323 GAATACTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 13 0.62
12 7 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (11 bp):
AAAATTTTTTT
Found at i:9607494 original size:3 final size:3
Alignment explanation
Indices: 9607486--9607511 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9607476 GAGGAAGGTG
9607486 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
9607512 GTTAGATGGA
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:9608043 original size:19 final size:21
Alignment explanation
Indices: 9608002--9608046 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
9607992 CAAAACAAAA
9608002 TTAATCAAATTATATTATTTT
1 TTAATCAAATTATATTATTTT
*
9608023 TTAATCCAATTA-ATT-TTTT
1 TTAATCAAATTATATTATTTT
9608042 TTAAT
1 TTAAT
9608047 TTTAAAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.39
20 3 0.13
21 11 0.48
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAATCAAATTATATTATTTT
Found at i:9608100 original size:17 final size:17
Alignment explanation
Indices: 9608080--9608119 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
9608070 GATCAATTAA
9608080 TTAAATAATAAAATATT
1 TTAAATAATAAAATATT
* **
9608097 TTAAATTATATTATATT
1 TTAAATAATAAAATATT
9608114 TTAAAT
1 TTAAAT
9608120 TTTTAGTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAATAATAAAATATT
Found at i:9612869 original size:15 final size:15
Alignment explanation
Indices: 9612845--9612887 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
9612835 GAAGTGCCTT
9612845 GAAA-AAAAAAAAGA
1 GAAAGAAAAAAAAGA
9612859 GAAAGAAAAAAAA-A
1 GAAAGAAAAAAAAGA
*
9612873 GAAAGGAAAAAAAGA
1 GAAAGAAAAAAAAGA
9612888 AGTTTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
GAAAGAAAAAAAAGA
Found at i:9612869 original size:16 final size:15
Alignment explanation
Indices: 9612848--9612885 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
9612838 GTGCCTTGAA
9612848 AAAAAAAAAGAGAAAG
1 AAAAAAAAAGA-AAAG
*
9612864 AAAAAAAAAGAAAGG
1 AAAAAAAAAGAAAAG
9612879 AAAAAAA
1 AAAAAAA
9612886 GAAGTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:9612888 original size:13 final size:14
Alignment explanation
Indices: 9612845--9612885 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
9612835 GAAGTGCCTT
9612845 GAAA-AAAAAAAAGA
1 GAAAGAAAAAAAA-A
9612859 GAAAGAAAAAAAAA
1 GAAAGAAAAAAAAA
9612873 GAAAGGAAAAAAA
1 GAAA-GAAAAAAA
9612886 GAAGTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
GAAAGAAAAAAAAA
Found at i:9614141 original size:24 final size:23
Alignment explanation
Indices: 9614104--9614180 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 23
9614094 ATGAAAAGGG
9614104 GAAAGAAAATGAAAGAAAGAAAAA
1 GAAA-AAAATGAAAGAAAGAAAAA
*
9614128 TGAAAAAAATGAAAAAAAGAAGAAA
1 -GAAAAAAATGAAAGAAAGAA-AAA
9614153 -AAAAGAAA-GAAAAGAAAGAAAAAA
1 GAAAA-AAATG-AAAGAAAG-AAAAA
9614177 GAAA
1 GAAA
9614181 TTGAATGACT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
23 5 0.11
24 28 0.62
25 12 0.27
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (23 bp):
GAAAAAAATGAAAGAAAGAAAAA
Found at i:9614147 original size:28 final size:28
Alignment explanation
Indices: 9614105--9614180 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
9614095 TGAAAAGGGG
*
9614105 AAAGAAAATGAAAGAAAGAAAAATGAAA-A
1 AAAGAAAA--AAAGAAAGAAAAAAGAAAGA
9614134 AAATGAAAAAAAG-AAGAAAAAAAGAAAGA
1 AAA-GAAAAAAAGAAAG-AAAAAAGAAAGA
*
9614163 AAAGAAAGAAA-AAAGAAA
1 AAAGAAAAAAAGAAAGAAA
9614181 TTGAATGACT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
27 6 0.15
28 23 0.56
29 7 0.17
30 5 0.12
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (28 bp):
AAAGAAAAAAAGAAAGAAAAAAGAAAGA
Found at i:9614152 original size:20 final size:21
Alignment explanation
Indices: 9614104--9614180 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 21
9614094 ATGAAAAGGG
9614104 GAAAGAAAATGAAAGAAAG-AAA
1 GAAAGAAAA--AAAGAAAGAAAA
*
9614126 -AATGAAAAAAATGAAA-AAAA
1 GAAAGAAAAAAA-GAAAGAAAA
9614146 G-AAGAAAAAAAGAAAGAAAA
1 GAAAGAAAAAAAGAAAGAAAA
9614166 GAAAG-AAAAAAGAAA
1 GAAAGAAAAAAAGAAA
9614181 TTGAATGACT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
19 7 0.15
20 31 0.65
21 10 0.21
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (21 bp):
GAAAGAAAAAAAGAAAGAAAA
Found at i:9614157 original size:11 final size:11
Alignment explanation
Indices: 9614138--9614176 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
9614128 TGAAAAAAAT
9614138 GAAAAAAAGAA
1 GAAAAAAAGAA
9614149 GAAAAAAAGAAA
1 GAAAAAAAG-AA
9614161 GAAAAGAAAGAA
1 GAAAA-AAAGAA
9614173 -AAAA
1 GAAAA
9614177 GAAATTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 13 0.50
12 9 0.35
13 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
GAAAAAAAGAA
Found at i:9614165 original size:9 final size:9
Alignment explanation
Indices: 9614104--9614174 Score: 62
Period size: 9 Copynumber: 8.0 Consensus size: 9
9614094 ATGAAAAGGG
9614104 GAAAGAAAA
1 GAAAGAAAA
9614113 TGAAAGAAAGA
1 -GAAAGAAA-A
*
9614124 AAAATGAAAA
1 GAAA-GAAAA
9614134 -AAATGAAAA
1 GAAA-GAAAA
9614143 -AAAG--AA
1 GAAAGAAAA
9614149 GAAA-AAAA
1 GAAAGAAAA
9614157 GAAAGAAAA
1 GAAAGAAAA
9614166 GAAAGAAAA
1 GAAAGAAAA
9614175 AAGAAATTGA
Statistics
Matches: 54, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
6 2 0.04
7 3 0.06
8 7 0.13
9 25 0.46
10 12 0.22
11 5 0.09
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.04
Consensus pattern (9 bp):
GAAAGAAAA
Found at i:9616091 original size:40 final size:40
Alignment explanation
Indices: 9616042--9616208 Score: 149
Period size: 40 Copynumber: 4.2 Consensus size: 40
9616032 AATGAGTATT
*
9616042 TGATTTCCAAGACTTTC-GAGCACAATCTTAGACTTTTGAA
1 TGATTTCCAAGACTTTCAG-GCAAAATCTTAGACTTTTGAA
* *
9616082 TGATTTCCAAAGACTTTCAGGCAAAATTTTAGATTTTTGAA
1 TGATTTCC-AAGACTTTCAGGCAAAATCTTAGACTTTTGAA
* * * * * * ** *
9616123 TGATTTCCTAGACTTCCAAGTAAAACCTTAAAAGTTTAAA
1 TGATTTCCAAGACTTTCAGGCAAAATCTTAGACTTTTGAA
* * * *
9616163 TGATTTCCAATATCTTT-AGGCAAAATCATAGATTTTTAAA
1 TGATTTCCAAGA-CTTTCAGGCAAAATCTTAGACTTTTGAA
9616203 TGATTT
1 TGATTT
9616209 TCAAAGACAT
Statistics
Matches: 101, Mismatches: 23, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
40 62 0.61
41 38 0.38
42 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (40 bp):
TGATTTCCAAGACTTTCAGGCAAAATCTTAGACTTTTGAA
Found at i:9616409 original size:22 final size:22
Alignment explanation
Indices: 9616375--9616470 Score: 86
Period size: 22 Copynumber: 4.4 Consensus size: 22
9616365 GTGTAATCTT
*
9616375 AAAGTCTTTTGAGCACAATTTC
1 AAAGTCTTCTGAGCACAATTTC
* * *
9616397 AATGTCTTCTGAGCACGATCTC
1 AAAGTCTTCTGAGCACAATTTC
* * * *
9616419 TAAGTCTTTTGGGTACAATTTC
1 AAAGTCTTCTGAGCACAATTTC
* *
9616441 AAAGTCATCT-AGGCATAATTTC
1 AAAGTCTTCTGA-GCACAATTTC
9616463 AAAGTCTT
1 AAAGTCTT
9616471 TTGGGTACAA
Statistics
Matches: 55, Mismatches: 18, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (22 bp):
AAAGTCTTCTGAGCACAATTTC
Done.