Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold19
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: 2266706
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17655 characters in sequence are not A, C, G, or T
File 13 of 15
Found at i:1809838 original size:16 final size:16
Alignment explanation
Indices: 1809819--1809850 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1809809 ATATAATAAC
*
1809819 AAAATAATAACAAAAT
1 AAAATAATAAAAAAAT
1809835 AAAATAATAAAAAAAT
1 AAAATAATAAAAAAAT
1809851 TCTTTTCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATAATAAAAAAAT
Found at i:1809850 original size:11 final size:11
Alignment explanation
Indices: 1809811--1809836 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1809801 TTTAAAAAAT
1809811 ATAATAACAAA
1 ATAATAACAAA
1809822 ATAATAACAAA
1 ATAATAACAAA
1809833 ATAA
1 ATAA
1809837 AATAATAAAA
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:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAATAACAAA
Found at i:1816291 original size:60 final size:60
Alignment explanation
Indices: 1816213--1816704 Score: 571
Period size: 59 Copynumber: 8.2 Consensus size: 60
1816203 GAGAAAGACG
* *
1816213 CTTTTCTTTTAAAGCCCACACAAGTTGGCGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
1 CTTTT-TTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
* * * * *
1816274 CTTTTTTTAAAAACCCACACAAGTTAGTGGCATCCGTTTAGTCCTCAAAAAGCAGGATGC
1 CTTTTTTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
** *
1816334 C-TTTTTTAAAAGCCCACACAAGTTGGTGGCACTTGTTCAGTCCTCAAAGAGTAGGATGC
1 CTTTTTTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
** *
1816393 C-TTTTTTAAAAGCCCACACAAGTT-GTGAAACCCGTTCAATCCTCAAAGAGCAGGATGC
1 CTTTTTTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
* * * * **
1816451 CTTTTTCTTTTAAAG-CCACACAAGTTGGTGGCACCCATTCAGTCTTCAAAGAGTAGGACAC
1 C-TTTT-TTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
* * *
1816512 CTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAAGATAC
1 C-TTTT-TTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
* * * * ** * * *
1816574 CTTTTTTTAAAAGCCCACATAAGTTTGTGGCACTCGTTCAGTCTTCAAAGAATAAGACGT
1 CTTTTTTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
* ** * * *
1816634 CTTTTTTT-AAAGCCCACACAAGTTGGTGGTACCTATTTAGTCCTCAAAGAGGAGAATGC
1 CTTTTTTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
1816693 CTTTTTTTAAAA
1 CTTTTTTTAAAA
1816705 AAAAATCACA
Statistics
Matches: 366, Mismatches: 59, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
58 29 0.08
59 119 0.33
60 119 0.33
61 57 0.16
62 42 0.11
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (60 bp):
CTTTTTTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
Found at i:1816470 original size:119 final size:120
Alignment explanation
Indices: 1816213--1816704 Score: 580
Period size: 119 Copynumber: 4.1 Consensus size: 120
1816203 GAGAAAGACG
* * * *
1816213 CTTTTCTTTTAAAGCCCACACAAGTTGGCGGCACCCGTTCAGTCCTCAAAGAGCAGGATGCCTTT
1 CTTTT-TTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGTAGGACGCCTTT
* * * *
1816278 TTTTAAAAACCCACACAAGTTAGTGGCATCCGTTTAGTCCTCAAAAAGCAGGATGC
65 TTTTAAAAGCCCACACAAGTTAGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
** *
1816334 C-TTTTTTAAAAGCCCACACAAGTTGGTGGCACTTGTTCAGTCCTCAAAGAGTAGGATGCC-TTT
1 CTTTTTTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGTAGGACGCCTTTT
** *
1816397 TTTAAAAGCCCACACAAGTT-GTGAAACCCGTTCAATCCTCAAAGAGCAGGATGC
66 TTTAAAAGCCCACACAAGTTAGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
* * * *
1816451 CTTTTTCTTTTAAAG-CCACACAAGTTGGTGGCACCCATTCAGTCTTCAAAGAGTAGGACACCTT
1 C-TTTT-TTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGTAGGACGCC-T
* * * *
1816515 TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAAGATAC
63 TTT-TTTAAAAGCCCACACAAGTTAGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
* * * * * * *
1816574 CTTTTTTTAAAAGCCCACATAAGTTTGTGGCACTCGTTCAGTCTTCAAAGAATAAGACGTCTTTT
1 CTTTTTTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGTAGGACGCCTTTT
* * ** * * *
1816639 TTT-AAAGCCCACACAAGTTGGTGGTACCTATTTAGTCCTCAAAGAGGAGAATGC
66 TTTAAAAGCCCACACAAGTTAGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
1816693 CTTTTTTTAAAA
1 CTTTTTTTAAAA
1816705 AAAAATCACA
Statistics
Matches: 321, Mismatches: 42, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
117 29 0.09
118 22 0.07
119 150 0.47
120 13 0.04
121 15 0.05
122 62 0.19
123 30 0.09
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (120 bp):
CTTTTTTTAAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGTAGGACGCCTTTT
TTTAAAAGCCCACACAAGTTAGTGGCACCCGTTCAGTCCTCAAAGAGCAGGATGC
Found at i:1816831 original size:33 final size:32
Alignment explanation
Indices: 1816794--1816963 Score: 139
Period size: 33 Copynumber: 5.3 Consensus size: 32
1816784 CACTTGAGTC
* *
1816794 AAAGCCCACATAAGTCGGTGGCACCCTTTCTCA
1 AAAGCCTACACAAGTCGGTGGCACCCTTT-TCA
** * **
1816827 AAAGCCTACACAAGTTAGTGGCA-TCTTTTTT
1 AAAGCCTACACAAGTCGGTGGCACCCTTTTCA
* * *
1816858 AAAGCCTGCACAAGTCGGTGGCAACCTTCTCTA
1 AAAGCCTACACAAGTCGGTGGCACCCTTTTC-A
* * *
1816891 AAATCC-ACATAAGTCGATGGCACCCCTTTTCA
1 AAAGCCTACACAAGTCGGTGGCA-CCCTTTTCA
* * **
1816923 AAAGCCTACACAAGTTGGTGGCA-TCTTTTTT
1 AAAGCCTACACAAGTCGGTGGCACCCTTTTCA
1816954 AAAGCCTACA
1 AAAGCCTACA
1816964 GTCCACACAA
Statistics
Matches: 106, Mismatches: 27, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
31 36 0.34
32 27 0.25
33 43 0.41
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (32 bp):
AAAGCCTACACAAGTCGGTGGCACCCTTTTCA
Found at i:1817028 original size:70 final size:70
Alignment explanation
Indices: 1816894--1817029 Score: 186
Period size: 70 Copynumber: 1.9 Consensus size: 70
1816884 TTCTCTAAAA
* * *
1816894 TCCACATAAGTCGATGGCACCCCTTTTCAAAAGCCTACACAAGTTGGTGGCATCTTTTTTAAAGC
1 TCCACACAAGTCGATGGCACCCC-TTTCAAAAGCCTACACAAGTTAGTGGCATCTTTTTCAAAGC
1816959 CTACAG
65 CTACAG
* *
1816965 TCCACACAAGTCGATGGCAACTCCC-TTC-AAAGCTTACACAAGTTAGTGGTATCTTTTTCAAAG
1 TCCACACAAGTCGATGGC-AC-CCCTTTCAAAAGCCTACACAAGTTAGTGGCATCTTTTTCAAAG
1817028 CC
64 CC
1817030 CACACAAGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
70 33 0.57
71 20 0.34
72 2 0.03
73 3 0.05
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (70 bp):
TCCACACAAGTCGATGGCACCCCTTTCAAAAGCCTACACAAGTTAGTGGCATCTTTTTCAAAGCC
TACAG
Found at i:1817848 original size:23 final size:21
Alignment explanation
Indices: 1817804--1817853 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1817794 ATTTTTTGGG
*
1817804 AGAGAACAAAAAGTGGTTAAA
1 AGAGAAAAAAAAGTGGTTAAA
*
1817825 AGAGAAAAAAAAGTTGTTAAA
1 AGAGAAAAAAAAGTGGTTAAA
*
1817846 AAAGAAAA
1 AGAGAAAA
1817854 TGAGAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.64, C:0.02, G:0.20, T:0.14
Consensus pattern (21 bp):
AGAGAAAAAAAAGTGGTTAAA
Found at i:1818972 original size:10 final size:10
Alignment explanation
Indices: 1818938--1818980 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1818928 TTTCCACAAA
1818938 AAAAAAGAAT
1 AAAAAAGAAT
*
1818948 AAATAAAAAAT
1 AAA-AAAGAAT
*
1818959 AAAAAAGTAT
1 AAAAAAGAAT
*
1818969 AAAAAATAAT
1 AAAAAAGAAT
1818979 AA
1 AA
1818981 TAATAAGTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (10 bp):
AAAAAAGAAT
Found at i:1820922 original size:2 final size:2
Alignment explanation
Indices: 1820915--1820993 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
1820905 ACATTGCGAC
1820915 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
1820957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1820994 CTTACCACTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1824758 original size:39 final size:39
Alignment explanation
Indices: 1824709--1824961 Score: 98
Period size: 39 Copynumber: 6.4 Consensus size: 39
1824699 AAAACACCAT
*
1824709 AATGATCTTAAAAGTTTAGTTTTGACATAAAAATACTAA
1 AATGACCTTAAAAGTTTAGTTTTGACATAAAAATACTAA
* * * ***
1824748 CATGACCTT-AAAGACTTATTTTTGATGCAAAAATACTAA
1 AATGACCTTAAAAG-TTTAGTTTTGACATAAAAATACTAA
* ** * ** * * ***
1824787 AATAACCCAAAAAGTTTGGTTTCAATATGAAAGCGCTAA
1 AATGACCTTAAAAGTTTAGTTTTGACATAAAAATACTAA
* * ** * * * *
1824826 CATGACCATAAAGAACTTGGATTTAACAT-AAACTACTAA
1 AATGACCTTAAA-AGTTTAGTTTTGACATAAAAATACTAA
* * * * *
1824865 AAT-AGCCTTAAAGGTTTAGTTTCGATATGAAAGTACTAA
1 AATGA-CCTTAAAAGTTTAGTTTTGACATAAAAATACTAA
* * * * *
1824904 CACGACCTCAAAAGACTTAGGTTTTGACATAAAAATAATAA
1 AATGACCTTAAAAG-TTTA-GTTTTGACATAAAAATACTAA
* *
1824945 AATAACTTTAAAAGTTT
1 AATGACCTTAAAAGTTT
1824962 GATTTGGACA
Statistics
Matches: 145, Mismatches: 61, Indels: 15
0.66 0.28 0.07
Matches are distributed among these distances:
38 13 0.09
39 86 0.59
40 21 0.14
41 25 0.17
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.30
Consensus pattern (39 bp):
AATGACCTTAAAAGTTTAGTTTTGACATAAAAATACTAA
Found at i:1824904 original size:78 final size:78
Alignment explanation
Indices: 1824715--1824961 Score: 212
Period size: 78 Copynumber: 3.1 Consensus size: 78
1824705 CCATAATGAT
* * * * * ** *
1824715 CTTAAAAGTTTAGTTTTGACATAAAAATACTAACATGACCTTAAAGACTTATTTTTGATGCAAAA
1 CTTAAAAGTTTAGTTTCGATATGAAAGTACTAACATGACCATAAAGACTTAGATTTGATACAAAA
1824780 ATACTAAAATAAC
66 ATACTAAAATAAC
** * * ** *
1824793 CCAAAAAGTTTGGTTTCAATATGAAAGCGCTAACATGACCATAAAGAACTTGGATTT-A-ACATA
1 CTTAAAAGTTTAGTTTCGATATGAAAGTACTAACATGACCATAAAG-ACTTAGATTTGATACA-A
* *
1824856 AACTACTAAAATAGC
64 AAATACTAAAATAAC
* * * * *
1824871 CTTAAAGGTTTAGTTTCGATATGAAAGTACTAACACGACC-TCAAAAGACTTAGGTTTTGACATA
1 CTTAAAAGTTTAGTTTCGATATGAAAGTACTAACATGACCAT--AAAGACTTA-GATTTGATACA
*
1824935 AAAATAATAAAATAAC
63 AAAATACTAAAATAAC
*
1824951 TTTAAAAGTTT
1 CTTAAAAGTTT
1824962 GATTTGGACA
Statistics
Matches: 129, Mismatches: 33, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
77 3 0.02
78 86 0.67
79 15 0.12
80 23 0.18
81 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (78 bp):
CTTAAAAGTTTAGTTTCGATATGAAAGTACTAACATGACCATAAAGACTTAGATTTGATACAAAA
ATACTAAAATAAC
Found at i:1825799 original size:59 final size:59
Alignment explanation
Indices: 1825736--1825854 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
1825726 CAGTCAAATT
1825736 TTTTATTTTTAAGAATTTTTTGACATTTATATGTAAAATTGAGAAAATTGACTGTCGTA
1 TTTTATTTTTAAGAATTTTTTGACATTTATATGTAAAATTGAGAAAATTGACTGTCGTA
*
1825795 TTTTATTTTTAAGAATTTTTTGACGTTTATATGTAAAATTGAGAAAATTGACTGTCGTA
1 TTTTATTTTTAAGAATTTTTTGACATTTATATGTAAAATTGAGAAAATTGACTGTCGTA
1825854 T
1 T
1825855 ATTTTTACCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (59 bp):
TTTTATTTTTAAGAATTTTTTGACATTTATATGTAAAATTGAGAAAATTGACTGTCGTA
Found at i:1828532 original size:21 final size:20
Alignment explanation
Indices: 1828467--1828539 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
1828457 TTTTACAATT
* *
1828467 TGTATTGATACAATAAGTTAA
1 TGTATCGATAC-ATAAGTGAA
1828488 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
***
1828508 TGTATCGATACATGCTTGAAA
1 TGTATCGATACATAAGTG-AA
1828529 TGTATCGATAC
1 TGTATCGATAC
1828540 TGGACCATGT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 23 0.50
21 23 0.50
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:1832109 original size:17 final size:18
Alignment explanation
Indices: 1832080--1832113 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1832070 TTATGATAAT
1832080 ATTTTTAATAAAATTAAA
1 ATTTTTAATAAAATTAAA
1832098 ATTTTTAA-AAAATTAA
1 ATTTTTAATAAAATTAA
1832114 GACAAGTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTTTAATAAAATTAAA
Found at i:1833503 original size:16 final size:16
Alignment explanation
Indices: 1833476--1833515 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
1833466 AACAAAATAG
*
1833476 CATAATAATAACATGAA
1 CATAA-AATAACAAGAA
1833493 CATAAAATAACAAGAA
1 CATAAAATAACAAGAA
1833509 CATAAAA
1 CATAAAA
1833516 ATGAGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.65, C:0.12, G:0.05, T:0.17
Consensus pattern (16 bp):
CATAAAATAACAAGAA
Found at i:1833791 original size:162 final size:163
Alignment explanation
Indices: 1833585--1833950 Score: 409
Period size: 162 Copynumber: 2.2 Consensus size: 163
1833575 CACTCAAATG
* * *
1833585 TAAACTTAAGATCATCAAGTTTAAAATAAAAAAAAATAACATAATGAAACTAAATATAACAAGAA
1 TAAAC-TAGGATCATCAAGCTTAAAATAAAGAAAAATAACATAATGAAACTAAATATAACAAGAA
* * * *
1833650 CGAAAGAAAAAAATGAATGCAATTTAAACAACATAAATAGCTCAAAGTTTGACCTCCAAAAAGGT
65 AGAAAGAAAAAAATGAATGCAACTTAAACAACATAAAGAACTCAAAGTTTGACCTCCAAAAAGGT
*
1833715 TTAT-TCAACC-TTGGCTC-AACTATTACCCAAGTT
130 TTATAT--ACCTTTGGCTCAAACTATCACCCAAGTT
* * * *
1833748 T-AACTCAGGATCATCAAGCTTAAAA-ATAAGAAAAATAACATAATGAAATTAAATATGATATGA
1 TAAACT-AGGATCATCAAGCTTAAAATA-AAGAAAAATAACATAATGAAACTAAATATAACAAGA
* * * * * * * ***
1833811 AAGAAATATAAACATGAATGTAACTTACATAACATGAAGAACTCAAAGTTTGGTTTCCAAAAAGG
64 AAGAAAGAAAAAAATGAATGCAACTTAAACAACATAAAGAACTCAAAGTTTGACCTCCAAAAAGG
**
1833876 TTTATATACCTTTGGCTCAAACTATCACTTAAGTT
129 TTTATATACCTTTGGCTCAAACTATCACCCAAGTT
* * *
1833911 TAAACTAGAATAATCAAGCTTAAAATAAAGGAAAATAACA
1 TAAACTAGGATCATCAAGCTTAAAATAAAGAAAAATAACA
1833951 ATATAAATAT
Statistics
Matches: 169, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
161 5 0.03
162 114 0.67
163 45 0.27
164 5 0.03
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (163 bp):
TAAACTAGGATCATCAAGCTTAAAATAAAGAAAAATAACATAATGAAACTAAATATAACAAGAAA
GAAAGAAAAAAATGAATGCAACTTAAACAACATAAAGAACTCAAAGTTTGACCTCCAAAAAGGTT
TATATACCTTTGGCTCAAACTATCACCCAAGTT
Found at i:1834541 original size:13 final size:13
Alignment explanation
Indices: 1834523--1834547 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1834513 GATACTAGTG
1834523 TTAAAAAGTCTAA
1 TTAAAAAGTCTAA
1834536 TTAAAAAGTCTA
1 TTAAAAAGTCTA
1834548 CACATAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
TTAAAAAGTCTAA
Found at i:1835038 original size:27 final size:28
Alignment explanation
Indices: 1835008--1835074 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 28
1834998 GTCTAACCGA
1835008 AAATTCTATATATAAAAA-TTTAAATGG
1 AAATTCTATATATAAAAAGTTTAAATGG
* * *
1835035 AAATGCTATACT-TAAAAAGTTTCAATTG
1 AAATTCTATA-TATAAAAAGTTTAAATGG
*
1835063 AAAAT-TATATAT
1 AAATTCTATATAT
1835075 GCAACAAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
26 1 0.03
27 20 0.62
28 11 0.34
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.37
Consensus pattern (28 bp):
AAATTCTATATATAAAAAGTTTAAATGG
Found at i:1844828 original size:19 final size:19
Alignment explanation
Indices: 1844787--1844846 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
1844777 TAAATTTTTT
* *
1844787 AAAAATTTTAGAAAATTCA
1 AAAAATTTTATAAAAATCA
**
1844806 AAAAATTTTATAAAAATGG
1 AAAAATTTTATAAAAATCA
1844825 AAAAATTTT-T-AAAAT-A
1 AAAAATTTTATAAAAATCA
1844841 AAAAAT
1 AAAAAT
1844847 GACTTTTACA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
16 6 0.17
17 5 0.14
18 1 0.03
19 24 0.67
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (19 bp):
AAAAATTTTATAAAAATCA
Found at i:1845097 original size:22 final size:20
Alignment explanation
Indices: 1845063--1845103 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1845053 ACAAATAGAA
1845063 AAAAATTATAAATTCAAAAT
1 AAAAATTATAAATTCAAAAT
*
1845083 AAAAATTCATGAAATTTAAAA
1 AAAAATT-AT-AAATTCAAAA
1845104 ATTTTACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAATTCAAAAT
Found at i:1845384 original size:331 final size:326
Alignment explanation
Indices: 1844738--1845386 Score: 712
Period size: 331 Copynumber: 1.9 Consensus size: 326
1844728 AAAATATATA
** *
1844738 TATAAATTCAAAATAAAAATTCATAAAATTTTGAAATTGTAAATTTTTTAAAAATTTTAGAAAAT
1 TATAAATTCAAAATAAAAATTCATAAAATTTAAAAATTGTAAATTTTTTAAAAAATTTAGAAAAT
**
1844803 TCAAAAAATTTTATAAAAATGGAAAAATTTTTAAAATAAAAAATGACTTTTACAAATTCATTTGT
66 TCAAAAAATTTTATAAAAA--GAAAAATTTAAAAAATAAAAAATGACTTTTACAAATTCATTTGT
* * ** * ***
1844868 AAAAAAGAATTTGAAATTTTGAAAAAAATATAAAAATTTAAAAATTGAAATTTCAAACATTTTTA
129 -AAAAAGAA-TTGAAAATTTGAAAAAAATATAAAAAATTAAAAATAAAAATTTCAAAAAAAATTA
* *
1844933 ACTCAACATTTGGAAAAATTTTTATTTTGAAATTTTTTAAATTTTAAAAAAAATAAAAAATGAAA
192 ACTCAAAATTTGGAAAAAATTTTATTTTGAAATTTTTTAAATTTTAAAAAAAATAAAAAATGAAA
* * * *
1844998 TTTAAAAAGAAATAGAGAGAGAGGAATCAAGGATTGAAAAAGAAAAAATAAAGAAACAAATAGAA
257 TTTAAAAAGAAATAGAAAGAAAGGAATCAAAGA-TGAAAAAGAAAAAAGAAAGAAACAAATAGAA
1845063 AAAAAT
321 AAAAAT
* * *
1845069 TATAAATTCAAAATAAAAATTCATGAAATTTAAAAATT-TTACTTTTTTAAAAAAATTTA-AAAA
1 TATAAATTCAAAATAAAAATTCATAAAATTTAAAAATTGTAAATTTTTT-AAAAAATTTAGAAAA
* *
1845132 GTTCAAAAACTTTTATAAAAA-AGAAATTTAAAAAAT-AAAAA-G-CTTTTTACAAATTCATTTG
65 -TTCAAAAAATTTTATAAAAAGAAAAATTTAAAAAATAAAAAATGAC-TTTTACAAATTCATTTG
1845193 T-AAAA-AA-TGAAAATTTGAAAAATATATATTAAAATAAAATTAAAAACTAAAAATTTCAAAAA
128 TAAAAAGAATTGAAAATTTGAAAAA-A-ATA-T--AA-AAAATTAAAAA-TAAAAATTTC-AAAA
* *
1845255 AAAATTATACTCAAAATTTGGAAAAAATTTTACTTTCT-AAATTTTTTCAACTTTTTGAAAAAAT
185 AAAATTA-ACTCAAAATTTGGAAAAAATTTTA-TTT-TGAAATTTTTT-AA-ATTTT-AAAAAAA
* *
1845319 TTGAAAAATGAAATTTAAAAAG-AA-AGAAAGAAAGGAATCGAAAAGA-GAAAAAGAGAACGAAA
244 ATAAAAAATGAAATTTAAAAAGAAATAGAAAGAAAGGAATC--AAAGATGAAAAAGA-AA--AAA
1845381 GAAAGA
304 GAAAGA
1845387 GATAATGAGA
Statistics
Matches: 268, Mismatches: 28, Indels: 40
0.80 0.08 0.12
Matches are distributed among these distances:
321 14 0.05
322 1 0.00
323 5 0.02
324 5 0.02
325 1 0.00
326 21 0.08
327 15 0.06
328 20 0.07
329 7 0.03
330 34 0.13
331 75 0.28
332 24 0.09
333 8 0.03
334 30 0.11
335 8 0.03
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (326 bp):
TATAAATTCAAAATAAAAATTCATAAAATTTAAAAATTGTAAATTTTTTAAAAAATTTAGAAAAT
TCAAAAAATTTTATAAAAAGAAAAATTTAAAAAATAAAAAATGACTTTTACAAATTCATTTGTAA
AAAGAATTGAAAATTTGAAAAAAATATAAAAAATTAAAAATAAAAATTTCAAAAAAAATTAACTC
AAAATTTGGAAAAAATTTTATTTTGAAATTTTTTAAATTTTAAAAAAAATAAAAAATGAAATTTA
AAAAGAAATAGAAAGAAAGGAATCAAAGATGAAAAAGAAAAAAGAAAGAAACAAATAGAAAAAAA
T
Found at i:1849983 original size:1 final size:1
Alignment explanation
Indices: 1849977--1850066 Score: 72
Period size: 1 Copynumber: 90.0 Consensus size: 1
1849967 AAATCTTCAC
* * ** * * * **
1849977 TTTTTTTTTTTGTTTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTCTTTTTCCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
1850042 TTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1850067 CCAATTGCCA
Statistics
Matches: 69, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.87
Consensus pattern (1 bp):
T
Found at i:1850027 original size:29 final size:30
Alignment explanation
Indices: 1849979--1850068 Score: 155
Period size: 30 Copynumber: 3.0 Consensus size: 30
1849969 ATCTTCACTT
*
1849979 TTTTTTTTTGTTTTTTTTTTTTTCTTTTTCC
1 TTTTTTTTTG-TTTTGTTTTTTTCTTTTTCC
1850010 -TTTTTTTTGTTTTGTTTTTTTCTTTTTCC
1 TTTTTTTTTGTTTTGTTTTTTTCTTTTTCC
1850039 TTTTTTTTTGTTTTGTTTTTTTCTTTTTCC
1 TTTTTTTTTGTTTTGTTTTTTTCTTTTTCC
1850069 AATTGCCATG
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
29 19 0.33
30 38 0.67
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (30 bp):
TTTTTTTTTGTTTTGTTTTTTTCTTTTTCC
Found at i:1869708 original size:24 final size:24
Alignment explanation
Indices: 1869684--1869741 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1869674 TCCTCCGCAA
*
1869684 AAAAAAAAGAGACAAAAAA-AACAA
1 AAAAAAAAGA-AAAAAAAACAACAA
*
1869708 AAAAAAAACAAAAAAAAACAACAA
1 AAAAAAAAGAAAAAAAAACAACAA
*
1869732 CAACAAAAAG
1 -AAAAAAAAG
1869742 GGTCCGGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 7 0.25
24 14 0.50
25 7 0.25
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAAAACAACAA
Found at i:1869710 original size:10 final size:10
Alignment explanation
Indices: 1869697--1869728 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
1869687 AAAAAGAGAC
1869697 AAAAAAAACAA
1 AAAAAAAAC-A
1869708 AAAAAAAACA
1 AAAAAAAACA
1869718 AAAAAAAACA
1 AAAAAAAACA
1869728 A
1 A
1869729 CAACAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:1871291 original size:49 final size:49
Alignment explanation
Indices: 1871232--1872255 Score: 653
Period size: 49 Copynumber: 22.5 Consensus size: 49
1871222 AATATCACTA
* * * *
1871232 CTTGAATCAGCATATTGGCACCTTTATCTTTAGGACCAATGTCACTAGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* *
1871281 CTTGAATCAGCACATTGG---C---A-C---AAGCCCAATATCGCTGGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * *
1871320 CTTAAATCAGCACATTGG---C---A-C---AAGCCCAATATCGCTGGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * *
1871359 CTTGAATCAGCATATTGACACCTTTATCTTCAAGACCAATGTCGCTGGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* *
1871408 CTTGAATCAGCACATTGG---C---A----TAAGCCCAATATCGCTGGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * *
1871447 CTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTGGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* *
1871496 CTTGAATCAGCACATTGG---C---A-C---AAG-CCTAATATCGCTAGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC-AATATCGCTGGC
* * **
1871535 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTAAC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * * **
1871584 CTTGAATCAGTACATTGG---C---A-C---AAGCCCAATATCGCTAAC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * * * * * *
1871623 CTTGAATCAACGTATTGGCATCTTCATCTTTAAGTCCGATATCGCTAGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * * *
1871672 CTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTAGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * *
1871721 CTTGAATCAGCACATT---A---GTA-C---AAGCCCAATATCGCTGGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * * * * **
1871760 TTTGAATCAGCATATTAGCACCTTTATATTTAAGACCAATGTCACTAAC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * * * *
1871809 CTTGAATCAGTACATTGG---C---A----TAAGCCCAATATTGCTGGT
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * *
1871848 CTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCGATATCGCTGGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* *
1871897 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTGGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * * * **
1871946 CTTGAATCAGTACATTGG---C---A-C---AAGCCCAATATCGTTGAT
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * * * *
1871985 CTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * * *
1872034 CTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCGATATCGCTGGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * *
1872083 CTTGAATTAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTAGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * * * * * *
1872132 CTTGAATCAGCACATTGGCGCCTTCATTTTTAAGACCGATGTCGTTGGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* * * * *
1872181 CTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGC
1 CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
* *
1872230 CTTAAATCAGCATATTGGCATCTTTA
1 CTTGAATCAGCATATTGGCACCTTTA
1872256 GCATTCCTAA
Statistics
Matches: 776, Mismatches: 127, Indels: 144
0.74 0.12 0.14
Matches are distributed among these distances:
38 2 0.00
39 239 0.31
42 12 0.02
43 8 0.01
45 8 0.01
46 11 0.01
49 494 0.64
50 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (49 bp):
CTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGC
Found at i:1871322 original size:39 final size:39
Alignment explanation
Indices: 1871279--1871555 Score: 248
Period size: 39 Copynumber: 6.6 Consensus size: 39
1871269 AATGTCACTA
1871279 GCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTG
1 GCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTG
*
1871318 GCCTTAAATCAGCACATTGGCACAAGCCCAATATCGCTG
1 GCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTG
* * * *
1871357 GCCTTGAATCAGCATATTGACACCTTTATCTTCAAGACCAATGTCGCTG
1 GCCTTGAATCAGCACATTG---GC---A----CAAGCCCAATATCGCTG
*
1871406 GCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTG
1 GCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTG
* * * * *
1871445 GCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTG
1 GCCTTGAATCAGCACATTGG---C---A-C---AAGCCCAATATCGCTG
* *
1871494 GCCTTGAATCAGCACATTGGCACAAGCCTAATATCGCTA
1 GCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTG
*
1871533 GCCTTGAATCAGCATATTGGCAC
1 GCCTTGAATCAGCACATTGGCAC
1871556 CTTTATCTTT
Statistics
Matches: 193, Mismatches: 25, Indels: 40
0.75 0.10 0.16
Matches are distributed among these distances:
39 120 0.62
42 3 0.02
43 2 0.01
45 2 0.01
46 2 0.01
49 64 0.33
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (39 bp):
GCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTG
Found at i:1871416 original size:88 final size:88
Alignment explanation
Indices: 1871306--1872150 Score: 553
Period size: 88 Copynumber: 9.4 Consensus size: 88
1871296 TGGCACAAGC
* * * *
1871306 CCAATATCGCTGGCCTTAAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTAGCCTTGAATCAACA
* *
1871371 TATTGACACCTTTATCTTCAAGA
66 TATTGGCACCTTTATCTTTAAGA
* *
1871394 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAACA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTAGCCTTGAATCAACA
1871459 TATTGGCACCTTTATCTTTAAGA
66 TATTGGCACCTTTATCTTTAAGA
* * *
1871482 CCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGCCTAATATCGCTAGCCTTGAATCAGCA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTAGCCTTGAATCAACA
1871547 TATTGGCACCTTTATCTTTAAGA
66 TATTGGCACCTTTATCTTTAAGA
* ** * * *
1871570 CCAATGTCACTAACCTTGAATCAGTACATTGGCACAAGCCCAATATCGCTAACCTTGAATCAACG
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTAGCCTTGAATCAACA
* * *
1871635 TATTGGCATCTTCATCTTTAAGT
66 TATTGGCACCTTTATCTTTAAGA
* * * * * * * *
1871658 CCGATATCGCTAGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTAGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGG---C---A-C---AAGCCCAATATCGCTAGCCT
* * * *
1871723 TGAATCAGCACATT---A---GTA-C---AAGC
56 TGAATCAACATATTGGCACCTTTATCTTTAAGA
* * * * * * * *
1871746 CCAATATCGCTGGCTTTGAATCAGCATATTAGCACCTTTATATTTAAGACCAATGTCACTAACCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C---------AAGCCCAATATCGCTAGCCT
** * *
1871811 TGAATCAGTACATTGG---C---A----TAAGC
56 TGAATCAACATATTGGCACCTTTATCTTTAAGA
* * * * * * *
1871834 CCAATATTGCTGGTCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCGATATCGCTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGG------CA-C---AAGCCCAATATCGCTAGCCT
*
1871899 TGAATCAGCATATTGGCACCTTTATCTTTAAGA
56 TGAATCAACATATTGGCACCTTTATCTTTAAGA
* * * *
1871932 CCAATGTCACTGGCCTTGAATCAGTACATTGGCACAAGCCCAATATCG-TTGATCTTGAATCAAC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTAG-CCTTGAATCAAC
* *
1871996 ATATTGGCACCTTCATCTTTAAGT
65 ATATTGGCACCTTTATCTTTAAGA
* * * * * * * *
1872020 CCGATATCGTTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCGATATCGCTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGG------CA-C---AAGCCCAATATCGCTAGCCT
* *
1872085 TGAATTAGCATATTGGCACCTTTATCTTTAAGA
56 TGAATCAACATATTGGCACCTTTATCTTTAAGA
*
1872118 CCAATGTCGCTAGCCTTGAATCAGCACATTGGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGC
1872151 GCCTTCATTT
Statistics
Matches: 615, Mismatches: 94, Indels: 92
0.77 0.12 0.11
Matches are distributed among these distances:
82 2 0.00
85 1 0.00
87 2 0.00
88 465 0.76
91 4 0.01
92 4 0.01
94 7 0.01
95 3 0.00
98 125 0.20
99 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (88 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTAGCCTTGAATCAACA
TATTGGCACCTTTATCTTTAAGA
Found at i:1871725 original size:225 final size:225
Alignment explanation
Indices: 1871436--1872201 Score: 958
Period size: 225 Copynumber: 3.4 Consensus size: 225
1871426 CATAAGCCCA
1871436 ATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTGGCCTTGA
*
1871501 ATCAGCACATTGGCACAAGCCTAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTT
66 ATCAGCACATTGGCACAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTT
1871566 AAGACCAATGTCACTAACCTTGAATCAGTACATTGGCACAAGCCCAATATCGCTAACCTTGAATC
131 AAGACCAATGTCACTAACCTTGAATCAGTACATTGGCACAAGCCCAATATCGCTAACCTTGAATC
* *
1871631 AACGTATTGGCATCTTCATCTTTAAGTCCG
196 AACATATTGGCACCTTCATCTTTAAGTCCG
* *
1871661 ATATCGCTAGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTAGCCTTGA
1 ATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTGGCCTTGA
* * * * * *
1871726 ATCAGCACATTAGTACAAGCCCAATATCGCTGGCTTTGAATCAGCATATTAGCACCTTTATATTT
66 ATCAGCACATTGGCACAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTT
* * ***
1871791 AAGACCAATGTCACTAACCTTGAATCAGTACATTGGCATAAGCCCAATATTGCTGGTCTTGAATC
131 AAGACCAATGTCACTAACCTTGAATCAGTACATTGGCACAAGCCCAATATCGCTAACCTTGAATC
*
1871856 AGCATATTGGCACCTTCATCTTTAAGTCCG
196 AACATATTGGCACCTTCATCTTTAAGTCCG
*
1871886 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTGGCCTTGA
* * * * *
1871951 ATCAGTACATTGGCACAAGCCCAATATCG-TTGATCTTGAATCAACATATTGGCACCTTCATCTT
66 ATCAGCACATTGGCACAAGCCCAATATCGCTAG-CCTTGAATCAGCATATTGGCACCTTTATCTT
* * * ** ** ** * * *
1872015 TAAGTCCGATATCGTTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCGATATCGCT
130 TAAGACCAATGTCACTAACCTTGAATCAGTACATTGG------CA-C---AAGCCCAATATCGCT
** * * * * *
1872080 GGCCTTGAATTAGCATATTGGCACCTTTATCTTTAAGACCA
185 AACCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCG
* * * * * * * * **
1872121 ATGTCGCTAGCCTTGAATCAGCACATTGGCGCCTTCATTTTTAAGACCGATGTCGTTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTGGCCTTGA
1872186 ATCAGCACATTGGCAC
66 ATCAGCACATTGGCAC
1872202 CTTCATCTTT
Statistics
Matches: 471, Mismatches: 59, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
224 2 0.00
225 348 0.74
231 2 0.00
235 119 0.25
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (225 bp):
ATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTGGCCTTGA
ATCAGCACATTGGCACAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTT
AAGACCAATGTCACTAACCTTGAATCAGTACATTGGCACAAGCCCAATATCGCTAACCTTGAATC
AACATATTGGCACCTTCATCTTTAAGTCCG
Found at i:1871792 original size:137 final size:137
Alignment explanation
Indices: 1871523--1871817 Score: 419
Period size: 137 Copynumber: 2.2 Consensus size: 137
1871513 GCACAAGCCT
*
1871523 AATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTAACCTTG
1 AATATCGCTAGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTAACCTTG
* * * * * *
1871588 AATCAGTACATTGGCACAAGCCCAATATCGCTAACCTTGAATCAACGTATTGGCATCTTCATCTT
66 AATCAGCACATTAGCACAAGCCCAATATCGCTAACCTTGAATCAACATATTAGCACCTTCATATT
*
1871653 TAAGTCC
131 TAAGACC
* *
1871660 GATATCGCTAGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTAGCCTTG
1 AATATCGCTAGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTAACCTTG
* ** * * *
1871725 AATCAGCACATTAGTACAAGCCCAATATCGCTGGCTTTGAATCAGCATATTAGCACCTTTATATT
66 AATCAGCACATTAGCACAAGCCCAATATCGCTAACCTTGAATCAACATATTAGCACCTTCATATT
1871790 TAAGACC
131 TAAGACC
* * *
1871797 AATGTCACTAACCTTGAATCA
1 AATATCGCTAGCCTTGAATCA
1871818 GTACATTGGC
Statistics
Matches: 138, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
137 138 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (137 bp):
AATATCGCTAGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCAATGTCACTAACCTTG
AATCAGCACATTAGCACAAGCCCAATATCGCTAACCTTGAATCAACATATTAGCACCTTCATATT
TAAGACC
Found at i:1872077 original size:186 final size:190
Alignment explanation
Indices: 1871348--1872345 Score: 758
Period size: 176 Copynumber: 5.4 Consensus size: 190
1871338 CACAAGCCCA
* * * *
1871348 ATATCGCTGGCCTTGAATCAGCATATTGACACCTTTATCTTCAAGACCAATGTCGCTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTAGCCTTGA
* * * * *
1871413 ATCAGCACATT-G-G-CAT-AAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTAT
66 ATCAGCACATTGGCGCCATCAAGACCAATATCGTTGACCTTGAATCAACACATTGGCACCTTCAT
* * * ** * *
1871474 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGG------CA-C---AAG-CCTA
131 CTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCC-G
* *
1871524 ATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTAACCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTAGCCTTGA
* * * * ** *
1871589 ATCAGTACATT-G-G-CA-CAAGCCCAATATCGCTAACCTTGAATCAACGTATTGGCATCTTCAT
66 ATCAGCACATTGGCGCCATCAAGACCAATATCGTTGACCTTGAATCAACACATTGGCACCTTCAT
* * * * * *
1871650 CTTTAAGTCCGATATCGCTAGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACCA
131 CTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCG
* * * * * * * * * *
1871710 ATGTCACTAGCCTTGAATCAGCACATT---A---GTA-C---AAGCCCAATATCGCTGGCTTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTAGCCTTGA
* * * * * ** * **
1871765 ATCAGCATATTAGCACCTTTATATTTAAGACCAATGTCACTAACCTTGAATCAGTACATTGG---
66 ATCAGCACATTGGCGCC-----A-TCAAGACCAATATCGTTGACCTTGAATCAACACATTGGCAC
* * * * *
1871827 ---CA----TAAGCCCAATATTGCTGGTCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCC
125 CTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCC
1871885 G
190 G
*
1871886 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTAGCCTTGA
* * * *
1871951 ATCAGTACATT-G-G-CA-CAAGCCCAATATCGTTGATCTTGAATCAACATATTGGCACCTTCAT
66 ATCAGCACATTGGCGCCATCAAGACCAATATCGTTGACCTTGAATCAACACATTGGCACCTTCAT
*
1872012 CTTTAAGTCCGATATCGTTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCG
131 CTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCG
* *
1872072 ATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTAGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTAGCCTTGA
* * * * *
1872137 ATCAGCACATTGGCGCCTTCATTTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATTGGCAC
66 ATCAGCACATTGGCG-C--CA---TCAAGACCAATATCGTTGACCTTGAATCAACACATTGGCAC
* * * *
1872202 CTTCATCTTTAAGTCCGATATCGTTGGCCTTAAATCAGCATATTGGCATCTTTAGCATTCCTAAG
125 CTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATC-TT--TAAG
*
1872267 -CCTA
187 TCC-G
* * ** * * * * *
1872271 ATGTCGTTGGCCTTGTCTCAGCACATTGGCA--TTCT-TCTTCAAGTCTAATGTCACTAGCCATG
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-TATCTTTAAGACCAATGTCACTAGCCTTG
1872333 AATCAGCACATTG
65 AATCAGCACATTG
1872346 TCATTCTTTG
Statistics
Matches: 658, Mismatches: 107, Indels: 93
0.77 0.12 0.11
Matches are distributed among these distances:
176 270 0.41
177 1 0.00
178 1 0.00
179 3 0.00
180 4 0.01
182 5 0.01
183 4 0.01
184 1 0.00
185 1 0.00
186 208 0.32
187 3 0.00
188 1 0.00
192 2 0.00
196 83 0.13
197 39 0.06
198 3 0.00
199 29 0.04
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (190 bp):
ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTAGCCTTGA
ATCAGCACATTGGCGCCATCAAGACCAATATCGTTGACCTTGAATCAACACATTGGCACCTTCAT
CTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCG
Found at i:1872082 original size:137 final size:137
Alignment explanation
Indices: 1871749--1872249 Score: 545
Period size: 137 Copynumber: 3.6 Consensus size: 137
1871739 TACAAGCCCA
* * * * * **
1871749 ATATCGCTGGCTTTGAATCAGCATATTAGCACCTTTATATTTAAGACCAATGTCACTAACCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATATCACTGGCCTTGA
* * * *
1871814 ATCAGTACATTGGCATAAGCCCAATATTGCTGGTCTTGAATCAGCATATTGGCACCTTCATCTTT
66 ATCAGCACATTGGCACAAGCCCAATATCGCTGATCTTGAATCAGCATATTGGCACCTTCATCTTT
1871879 AAGTCCG
131 AAGTCCG
* *
1871886 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATATCACTGGCCTTGA
* * *
1871951 ATCAGTACATTGGCACAAGCCCAATATCGTTGATCTTGAATCAACATATTGGCACCTTCATCTTT
66 ATCAGCACATTGGCACAAGCCCAATATCGCTGATCTTGAATCAGCATATTGGCACCTTCATCTTT
1872016 AAGTCCG
131 AAGTCCG
* * * * *
1872023 ATATCGTTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCGATATCGCTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATATCACTGGCCTTGA
* * * * * * *
1872088 ATTAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCT-AGCCTTGAATCAGCACATTGGCG
66 ATCAGCACATTGG---C---A-C---AAGCCCAATATCGCTGA-TCTTGAATCAGCATATTGGCA
* *
1872152 CCTTCATTTTTAAGACCG
120 CCTTCATCTTTAAGTCCG
* * * * * ** *
1872170 ATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCTTAA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATATCACTGGCCTTGA
*
1872235 ATCAGCATATTGGCA
66 ATCAGCACATTGGCA
1872250 TCTTTAGCAT
Statistics
Matches: 318, Mismatches: 35, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
137 195 0.61
140 1 0.00
141 1 0.00
143 1 0.00
144 2 0.01
146 1 0.00
147 117 0.37
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (137 bp):
ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATATCACTGGCCTTGA
ATCAGCACATTGGCACAAGCCCAATATCGCTGATCTTGAATCAGCATATTGGCACCTTCATCTTT
AAGTCCG
Found at i:1872242 original size:147 final size:149
Alignment explanation
Indices: 1871985--1872301 Score: 442
Period size: 147 Copynumber: 2.1 Consensus size: 149
1871975 TATCGTTGAT
* * * *
1871985 CTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCAACATATT
1 CTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATATCGTTGGCCTTGAATCAACACATT
* * *
1872050 GGCACCTTCATCTTTAAGTCCGATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTATC-TT-
66 GGCACCTTCATCTTTAAGTCCGATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTAGCATTC
1872113 TAAGACC-AATGTCGCTAGC
131 TAAG-CCTAATGTCGCTAGC
* * * *
1872132 CTTGAATCAGCACATTGGCGCCTTCATTTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATT
1 CTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATATCGTTGGCCTTGAATCAACACATT
* *
1872197 GGCACCTTCATCTTTAAGTCCGATATCGTTGGCCTTAAATCAGCATATTGGCATCTTTAGCATTC
66 GGCACCTTCATCTTTAAGTCCGATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTAGCATT-
* *
1872262 CTAAGCCTAATGTCGTTGGC
130 CTAAGCCTAATGTCGCTAGC
**
1872282 CTTGTCTCAGCACATTGGCA
1 CTTGAATCAGCACATTGGCA
1872302 TTCTTCTTCA
Statistics
Matches: 148, Mismatches: 18, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
147 113 0.76
148 2 0.01
149 2 0.01
150 31 0.21
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (149 bp):
CTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATATCGTTGGCCTTGAATCAACACATT
GGCACCTTCATCTTTAAGTCCGATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTAGCATTC
TAAGCCTAATGTCGCTAGC
Found at i:1872300 original size:52 final size:49
Alignment explanation
Indices: 1871971--1872345 Score: 272
Period size: 49 Copynumber: 7.6 Consensus size: 49
1871961 TGGCACAAGC
* ** * * * *
1871971 CCAATATCGTTGATCTTGAATCAACATATTGGCACCTTCATCTTTAAGT
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCAGCTTTAAGT
* * * * * *
1872020 CCGATATCGTTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGT
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCAGCTTTAAGT
* * * * * * * * *
1872069 CCGATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTATCTTTAAGA
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCAGCTTTAAGT
* * ** ** *
1872118 CCAATGTCGCTAGCCTTGAATCAGCACATTGGCGCCTTCATTTTTAAGA
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCAGCTTTAAGT
* * *
1872167 CCGATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCAGCTTTAAGT
* * * * *
1872216 CCGATATCGTTGGCCTTAAATCAGCATATTGGCATCTTTAGCATTCCTAAG-
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCAGC-TT--TAAGT
** *
1872267 CCTAATGTCGTTGGCCTTGTCTCAGCACATTGGCATTCTT---CTTCAAGT
1 CC-AATGTCGTTGGCCTTGAATCAGCACATTGGCA-TCTTCAGCTTTAAGT
* ** * *
1872315 CTAATGTCACTAGCCATGAATCAGCACATTG
1 CCAATGTCGTTGGCCTTGAATCAGCACATTG
1872346 TCATTCTTTG
Statistics
Matches: 278, Mismatches: 42, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
47 26 0.09
48 1 0.00
49 212 0.76
50 3 0.01
51 2 0.01
52 30 0.11
53 4 0.01
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (49 bp):
CCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCAGCTTTAAGT
Found at i:1874051 original size:20 final size:20
Alignment explanation
Indices: 1874006--1874051 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1873996 GTTAACAACC
*
1874006 CATGATTCATGCATTTTAAG
1 CATGTTTCATGCATTTTAAG
1874026 CTATGTTTCATGCA-TTTACAG
1 C-ATGTTTCATGCATTTTA-AG
1874047 CATGT
1 CATGT
1874052 CCAGCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTAAG
Found at i:1879384 original size:13 final size:13
Alignment explanation
Indices: 1879366--1879392 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1879356 TACAAAGATT
1879366 AATGTATCGATAC
1 AATGTATCGATAC
1879379 AATGTATCGATAC
1 AATGTATCGATAC
1879392 A
1 A
1879393 TTGAATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1879384 original size:33 final size:33
Alignment explanation
Indices: 1879346--1879412 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1879336 AAAATTTTCA
*
1879346 AATGTATCAATACAAAGATTAATGTATCGATAC
1 AATGTATCAATACAAAGAATAATGTATCGATAC
* **
1879379 AATGTATCGATACATTGAATAATGTATCGATAC
1 AATGTATCAATACAAAGAATAATGTATCGATAC
1879412 A
1 A
1879413 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (33 bp):
AATGTATCAATACAAAGAATAATGTATCGATAC
Found at i:1879485 original size:21 final size:19
Alignment explanation
Indices: 1879438--1879492 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1879428 GCAGGGTAGC
1879438 TTTGTATCGATACAACACT
1 TTTGTATCGATACAACACT
* **
1879457 TATGTATCGATACATTTACT
1 TTTGTATCGATACA-ACACT
1879477 GTTTGTATCGATACAA
1 -TTTGTATCGATACAA
1879493 ATTGTTGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACAACACT
Found at i:1883657 original size:52 final size:52
Alignment explanation
Indices: 1883590--1883707 Score: 191
Period size: 52 Copynumber: 2.3 Consensus size: 52
1883580 AATTTATCTG
* * *
1883590 CATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTA
1 CATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAATTGCCTA
* *
1883642 CATGTATCGATACATTTTATAATGTATCGATACATCTAGGCAAAATTGCCTG
1 CATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAATTGCCTA
1883694 CATGTATCGATACA
1 CATGTATCGATACA
1883708 AAGATCAGTG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (52 bp):
CATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAATTGCCTA
Found at i:1883720 original size:52 final size:51
Alignment explanation
Indices: 1883587--1883727 Score: 185
Period size: 52 Copynumber: 2.7 Consensus size: 51
1883577 GAAAATTTAT
* *
1883587 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAAATTGC
* * *
1883639 CTACATGTATCGATACATTTTATAATGTATCGATACATCTAGGCAAAATTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAAATTGC
*
1883691 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1883728 ATGTATCGAT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 2 0.03
52 76 0.97
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTAGGCAAAATTGC
Found at i:1883734 original size:13 final size:13
Alignment explanation
Indices: 1883716--1883740 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1883706 CAAAGATCAG
1883716 TGTATCGATACAA
1 TGTATCGATACAA
1883729 TGTATCGATACA
1 TGTATCGATACA
1883741 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1883824 original size:13 final size:13
Alignment explanation
Indices: 1883806--1883830 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1883796 CAAAAAAATA
1883806 TGTATCGATACAT
1 TGTATCGATACAT
1883819 TGTATCGATACA
1 TGTATCGATACA
1883831 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1883826 original size:33 final size:33
Alignment explanation
Indices: 1883784--1883850 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1883774 AGTAGCTTAA
1883784 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1883817 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1883850 A
1 A
1883851 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1888783 original size:2 final size:2
Alignment explanation
Indices: 1888776--1888801 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1888766 TTTATTCTTG
1888776 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
1888802 GTGTGTGTGT
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:1888806 original size:2 final size:2
Alignment explanation
Indices: 1888801--1888826 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1888791 TATATATATA
1888801 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
1888827 GGGAGTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1889012 original size:3 final size:3
Alignment explanation
Indices: 1889004--1889035 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1888994 GTATAATAGC
1889004 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1889036 ATAGCAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1889578 original size:2 final size:2
Alignment explanation
Indices: 1889571--1889596 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1889561 CAAGTTCAGC
1889571 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
1889597 GCTCTCTCCT
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:1890686 original size:12 final size:12
Alignment explanation
Indices: 1890669--1890696 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1890659 CACTCCTTAG
1890669 GTTTTTAGTGAC
1 GTTTTTAGTGAC
1890681 GTTTTTAGTGAC
1 GTTTTTAGTGAC
1890693 GTTT
1 GTTT
1890697 GGAACACCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.07, G:0.25, T:0.54
Consensus pattern (12 bp):
GTTTTTAGTGAC
Found at i:1904896 original size:21 final size:20
Alignment explanation
Indices: 1904866--1904904 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
1904856 CACATTTTTG
1904866 TCCAAATGTATCGATACATT
1 TCCAAATGTATCGATACATT
1904886 TCCAGAATGTATCGATACA
1 TCCA-AATGTATCGATACA
1904905 AGGTCTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (20 bp):
TCCAAATGTATCGATACATT
Found at i:1910632 original size:2 final size:2
Alignment explanation
Indices: 1910625--1910655 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1910615 ATCAATGTCA
1910625 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 T
1910656 TTGGTGCGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1912393 original size:17 final size:17
Alignment explanation
Indices: 1912355--1912395 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1912345 TTAAGATAAA
1912355 AAAATG-TAAGAAAGAG
1 AAAATGTTAAGAAAGAG
*
1912371 AAAATGTTAAGGAAGAG
1 AAAATGTTAAGAAAGAG
*
1912388 AGAATGTT
1 AAAATGTT
1912396 TCAAAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.20
Consensus pattern (17 bp):
AAAATGTTAAGAAAGAG
Found at i:1918853 original size:3 final size:3
Alignment explanation
Indices: 1918845--1918874 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1918835 TACCTCTTTT
1918845 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1918875 ATAAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1918879 original size:4 final size:4
Alignment explanation
Indices: 1918870--1918897 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1918860 TAATAATAAT
1918870 AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA
1918898 TCTCTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:1921135 original size:40 final size:39
Alignment explanation
Indices: 1920919--1921292 Score: 172
Period size: 38 Copynumber: 9.6 Consensus size: 39
1920909 AAAGGTTTGG
* * * *
1920919 TTTTGACATAAAAATACCAACATGACCCTCAAGAC-CAA
1 TTTTGACATGAAAATACTAAAATGACCCTAAAGACTCAA
** * * * *
1920957 TTTTGACACAAAAATACTAAAATGACCTTAATAG-TTTAG
1 TTTTGACATGAAAATACTAAAATGACCCTAA-AGACTCAA
* * **
1920996 TTTTGACATGAAAGTACTAATAT-AATCT-AA-ACTCAA
1 TTTTGACATGAAAATACTAAAATGACCCTAAAGACTCAA
* ** * *
1921032 TTTTGACAT-AAAATACTAAAATAACTTTAAAGATTCAG
1 TTTTGACATGAAAATACTAAAATGACCCTAAAGACTCAA
* * * **
1921070 TTTTGACAAGAAAGTGCTAGCATGACCCTAAATGACTCAA
1 TTTTGACATGAAAATACTAAAATGACCCTAAA-GACTCAA
* * ***
1921110 TTTTGACATGAAAATATTAAAATGACCCTAAA-AGTTTG
1 TTTTGACATGAAAATACTAAAATGACCCTAAAGACTCAA
* * * * * * * *
1921148 GTTTGATATGAAAGTACTAATACGATCCTAGAAAACTTAA
1 TTTTGACATGAAAATACTAAAATGACCCTA-AAGACTCAA
* **
1921188 TTTTGACATGAAAATA-TAAAAATGACCATAAAGGTTCAA
1 TTTTGACATGAAAATACT-AAAATGACCCTAAAGACTCAA
* * * * * * **
1921227 -TTTGCACGTGAAAGTGCTAACATAACTCTAAAAGGACTTGA
1 TTTTG-ACATGAAAATACTAAAATGACCCT-AAA-GACTCAA
* *
1921268 TTATGACATAAAAATACTAAAATGA
1 TTTTGACATGAAAATACTAAAATGA
1921293 TCTTATAGGT
Statistics
Matches: 237, Mismatches: 83, Indels: 29
0.68 0.24 0.08
Matches are distributed among these distances:
35 11 0.05
36 15 0.06
37 3 0.01
38 69 0.29
39 60 0.25
40 59 0.25
41 17 0.07
42 3 0.01
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.29
Consensus pattern (39 bp):
TTTTGACATGAAAATACTAAAATGACCCTAAAGACTCAA
Found at i:1921153 original size:78 final size:77
Alignment explanation
Indices: 1920895--1921292 Score: 254
Period size: 78 Copynumber: 5.1 Consensus size: 77
1920885 ATCTAAAACA
* * * * *
1920895 ACTAAAATGACTCTAAAGGTTTGGTTTTGACATA-AAAATACCAACATGACCCTCAAGAC-CAAT
1 ACTAAAATGACCCTAAAAGTTTGG-TTTGACA-AGAAAGTACTAACATGACCCTAAAGACTCAAT
**
1920958 TTTGACACAAAAAT
64 TTTGACATGAAAAT
* * * * * **
1920972 ACTAAAATGACCTTAATAGTTTAGTTTTGACATGAAAGTACTAATAT-AATCT-AA-ACTCAATT
1 ACTAAAATGACCCTAAAAGTTT-GGTTTGACAAGAAAGTACTAACATGACCCTAAAGACTCAATT
1921034 TTGACAT-AAAAT
65 TTGACATGAAAAT
* * * * * * *
1921046 ACTAAAAT-AACTTTAAAGATTCAGTTTTGACAAGAAAGTGCTAGCATGACCCTAAATGACTCAA
1 ACTAAAATGACCCTAAAAG-TT-TGGTTTGACAAGAAAGTACTAACATGACCCTAAA-GACTCAA
1921110 TTTTGACATGAAAAT
63 TTTTGACATGAAAAT
* * * * * * * *
1921125 ATTAAAATGACCCTAAAAGTTTGGTTTGATATGAAAGTACTAATACGATCCTAGAAAACTTAATT
1 ACTAAAATGACCCTAAAAGTTTGGTTTGACAAGAAAGTACTAACATGACCCTA-AAGACTCAATT
1921190 TTGACATGAAAAT
65 TTGACATGAAAAT
* * *** ** * * * **
1921203 A-TAAAAATGACCATAAAGGTTCAATTTGCACGTGAAAGTGCTAACATAACTCTAAAAGGACTTG
1 ACT-AAAATGACCCTAAAAGTTTGGTTTG-ACAAGAAAGTACTAACATGACCCT-AAA-GACTCA
* *
1921267 ATTATGACATAAAAAT
62 ATTTTGACATGAAAAT
1921283 ACTAAAATGA
1 ACTAAAATGA
1921293 TCTTATAGGT
Statistics
Matches: 250, Mismatches: 54, Indels: 31
0.75 0.16 0.09
Matches are distributed among these distances:
73 7 0.03
74 37 0.15
75 16 0.06
76 5 0.02
77 36 0.14
78 80 0.32
79 34 0.14
80 34 0.14
81 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.29
Consensus pattern (77 bp):
ACTAAAATGACCCTAAAAGTTTGGTTTGACAAGAAAGTACTAACATGACCCTAAAGACTCAATTT
TGACATGAAAAT
Found at i:1922084 original size:21 final size:20
Alignment explanation
Indices: 1922035--1922088 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1922025 TCATCAAGCT
*
1922035 TAAA-ATAACAT-ATTAAAG
1 TAAATATAACATAATGAAAG
1922053 TAAATATAACAATAATGAAAG
1 TAAATATAAC-ATAATGAAAG
1922074 TGAAATA-AACATAAT
1 T-AAATATAACATAAT
1922089 AATAAAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 4 0.13
19 5 0.16
20 7 0.23
21 10 0.32
22 5 0.16
ACGTcount: A:0.61, C:0.06, G:0.07, T:0.26
Consensus pattern (20 bp):
TAAATATAACATAATGAAAG
Found at i:1922134 original size:54 final size:54
Alignment explanation
Indices: 1922053--1922155 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
1922043 CATATTAAAG
* * *
1922053 TAAATATAACAATAATGAAAGTGAAATAAACATAATAATAAAATGAGCATGAAA
1 TAAATATAAAAATAATGAAAGTAAAATAAACAAAATAATAAAATGAGCATGAAA
* *
1922107 TAAATATAAAAATATTAGAAA-TAAAATAAACAAAATAATAACATGAGCA
1 TAAATATAAAAATAAT-GAAAGTAAAATAAACAAAATAATAAAATGAGCA
1922156 ATGTTCTTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 39 0.91
55 4 0.09
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.22
Consensus pattern (54 bp):
TAAATATAAAAATAATGAAAGTAAAATAAACAAAATAATAAAATGAGCATGAAA
Found at i:1924098 original size:36 final size:37
Alignment explanation
Indices: 1923998--1924099 Score: 91
Period size: 36 Copynumber: 2.8 Consensus size: 37
1923988 AAATTCATAT
* * * *
1923998 TGAAATGTCCTTAGGA-AAGGCTCTTAAAATACCTTGG
1 TGAAATATCCTTAAGAGAA-GCTCTAAAAATACCTTGA
* * ** *
1924035 TGAAATATCTTTAAGCGTTGCTTTAAAAATA-CTTGA
1 TGAAATATCCTTAAGAGAAGCTCTAAAAATACCTTGA
*
1924071 TGAAATATCCTTCAGAGAAGCTCTAAAAA
1 TGAAATATCCTTAAGAGAAGCTCTAAAAA
1924100 ATGTTTGCTT
Statistics
Matches: 49, Mismatches: 15, Indels: 3
0.73 0.22 0.04
Matches are distributed among these distances:
36 27 0.55
37 22 0.45
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (37 bp):
TGAAATATCCTTAAGAGAAGCTCTAAAAATACCTTGA
Found at i:1925150 original size:33 final size:33
Alignment explanation
Indices: 1925075--1925152 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 33
1925065 AGGCCTCAAG
* * *
1925075 GTATGGATACAAACCATGCAATGTGCCTATGCA
1 GTATCGATACAAACCATGCAATATGCCTATACA
* * * *
1925108 ATATTGATACAAACCATGCAGTATGCCTATATA
1 GTATCGATACAAACCATGCAATATGCCTATACA
1925141 GTATCGATACAA
1 GTATCGATACAA
1925153 CTCATGTAGG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (33 bp):
GTATCGATACAAACCATGCAATATGCCTATACA
Found at i:1926365 original size:13 final size:13
Alignment explanation
Indices: 1926347--1926371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1926337 TACCAAGAAC
1926347 ATGTATCGATACA
1 ATGTATCGATACA
1926360 ATGTATCGATAC
1 ATGTATCGATAC
1926372 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1926369 original size:32 final size:33
Alignment explanation
Indices: 1926328--1926392 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1926318 ACAGTTCATG
1926328 ATGTATCGATACCAAG-AACATGTATCGATACA
1 ATGTATCGATACCAAGCAACATGTATCGATACA
* * *
1926360 ATGTATCGATACTAAGCAATATGTATTGATACA
1 ATGTATCGATACCAAGCAACATGTATCGATACA
1926393 TCTGGATGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACCAAGCAACATGTATCGATACA
Found at i:1929464 original size:21 final size:23
Alignment explanation
Indices: 1929440--1929487 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 23
1929430 GCAAATTTTT
*
1929440 ATTTTTCTTATT-TAATTCA-TC
1 ATTTTTCTTATTGCAATTCATTC
*
1929461 A-TTTTCTTCTTGCAATTCATTC
1 ATTTTTCTTATTGCAATTCATTC
1929483 ATTTT
1 ATTTT
1929488 CTTCTCTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 9 0.41
21 7 0.32
22 3 0.14
23 3 0.14
ACGTcount: A:0.21, C:0.17, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTTTCTTATTGCAATTCATTC
Found at i:1929500 original size:21 final size:20
Alignment explanation
Indices: 1929442--1929492 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
1929432 AAATTTTTAT
* *
1929442 TTTTCTTATTTAATTCATCA
1 TTTTCTTCTTCAATTCATCA
1929462 TTTTCTTCTTGCAATTCATTCA
1 TTTTCTTCTT-CAATTCA-TCA
1929484 TTTTCTTCT
1 TTTTCTTCT
1929493 CTAGTTCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 9 0.33
21 6 0.22
22 12 0.44
ACGTcount: A:0.18, C:0.20, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTCTTCTTCAATTCATCA
Found at i:1934853 original size:53 final size:52
Alignment explanation
Indices: 1934788--1934928 Score: 180
Period size: 49 Copynumber: 2.8 Consensus size: 52
1934778 AATGCTAATG
* **
1934788 TGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGATGAAGGCGCCAATA
1 TGCTGATTCAAGGCTAACGACATT-GGACTTAAAGATGATGAAGGCGCCAATA
* * * *
1934841 TGCTGATGCAAGGCTAACGATATTGGACTT-AA-A-GATGAAGGTGCCAATG
1 TGCTGATTCAAGGCTAACGACATTGGACTTAAAGATGATGAAGGCGCCAATA
*
1934890 TGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAT
1 TGCTGATTCAAGGCTAACGACATTGGACTTAAAGATGAT
1934929 TGTCGTAACG
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
49 41 0.55
50 3 0.04
51 3 0.04
52 7 0.09
53 21 0.28
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.26
Consensus pattern (52 bp):
TGCTGATTCAAGGCTAACGACATTGGACTTAAAGATGATGAAGGCGCCAATA
Found at i:1938044 original size:20 final size:21
Alignment explanation
Indices: 1938018--1938074 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1938008 ATTTACCTGC
1938018 ATGTATCGATACATTT-AATA
1 ATGTATCGATACATTTGAATA
* *
1938038 GTGTATCGATACATTTGAGTA
1 ATGTATCGATACATTTGAATA
1938059 ATGTATCGATACATTT
1 ATGTATCGATACATTT
1938075 TTTGGCAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATTTGAATA
Found at i:1938118 original size:20 final size:20
Alignment explanation
Indices: 1938089--1938146 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1938079 GCAGTAGCTT
1938089 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
1938108 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
1938128 CTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
1938147 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:1938508 original size:49 final size:49
Alignment explanation
Indices: 1938436--1938821 Score: 565
Period size: 49 Copynumber: 7.7 Consensus size: 49
1938426 TGTCTACAGC
*
1938436 TGAAGGCGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGA
1 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
* * *
1938485 TGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA
1 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
1938534 TGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
1 TG---AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
* * *
1938586 TGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
1 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-GA
*
1938638 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTTGACTTAAAGA
1 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
** *
1938687 TGAAGGTACCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
1 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-GA
*
1938739 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTTGACTTAAAGA
1 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
**
1938788 TGAAGGTACCAATATGCTGATTCAAGGCCAGCGA
1 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGA
1938822 CATTCGTCCC
Statistics
Matches: 304, Mismatches: 24, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
49 162 0.53
50 6 0.02
51 6 0.02
52 130 0.43
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (49 bp):
TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
Found at i:1938613 original size:101 final size:101
Alignment explanation
Indices: 1938436--1938825 Score: 699
Period size: 101 Copynumber: 3.9 Consensus size: 101
1938426 TGTCTACAGC
* * *
1938436 TGAAGGCGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
1 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTACCAATATG
1938501 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
66 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
** * *
1938537 CAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
1 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTACCAATATG
1938602 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
66 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
*
1938638 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTTGACTTAAAGATGAAGGTACCAATATG
1 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTACCAATATG
1938703 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
66 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
*
1938739 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTTGACTTAAAGATGAAGGTACCAATATG
1 TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTACCAATATG
1938804 CTGATTCAAGGCCAGCGACATT
66 CTGATTCAAGGCCAGCGACATT
1938826 CGTCCCCACA
Statistics
Matches: 281, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 281 1.00
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (101 bp):
TGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTACCAATATG
CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
Found at i:1939701 original size:24 final size:24
Alignment explanation
Indices: 1939673--1939744 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
1939663 ACAATGTATC
*
1939673 GATACATGAACAGTGATGAATAGT
1 GATACATGAACAGTGATGAACAGT
1939697 GATACATGAACAGTGATGAACAGT
1 GATACATGAACAGTGATGAACAGT
** *
1939721 GATATGTGAACAGTGATGGACAGT
1 GATACATGAACAGTGATGAACAGT
1939745 AATGTATCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.39, C:0.10, G:0.28, T:0.24
Consensus pattern (24 bp):
GATACATGAACAGTGATGAACAGT
Found at i:1943631 original size:15 final size:16
Alignment explanation
Indices: 1943611--1943643 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1943601 TTCTGTTCTC
*
1943611 TTTTCTCTTTCA-TTT
1 TTTTCTCATTCACTTT
1943626 TTTTCTCATTCACTTT
1 TTTTCTCATTCACTTT
1943642 TT
1 TT
1943644 ATTATTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTCTCATTCACTTT
Found at i:1944895 original size:134 final size:134
Alignment explanation
Indices: 1944743--1945018 Score: 543
Period size: 134 Copynumber: 2.1 Consensus size: 134
1944733 TTTTGCCACA
1944743 CTCATTTTTTGGTTAAAAATTACCAAAACAATCTTTTAACCTGTTGAAAGAAAAAGCCACCCATG
1 CTCATTTTTTGGTTAAAAATTACCAAAACAATCTTTTAACCTGTTGAAAGAAAAAGCCACCCATG
1944808 ATGAAGTGGCTTGAGATTCGAACCCAGGCCACCCATGTTGAAGTAGTAGCACCCAACCACTCTAC
66 ATGAAGTGGCTTGAGATTCGAACCCAGGCCACCCATGTTGAAGTAGTAGCACCCAACCACTCTAC
1944873 CATG
131 CATG
1944877 CTCATTTTTTGGTTAAAAATTACCAAAACAATCTTTTAACCTGTTGAAAGAAAAAGCCACCCATG
1 CTCATTTTTTGGTTAAAAATTACCAAAACAATCTTTTAACCTGTTGAAAGAAAAAGCCACCCATG
*
1944942 ATGAAGTGGCTTGAGATTCGAACTCAGGCCACCCATGTTGAAGTAGTAGCACCCAACCACTCTAC
66 ATGAAGTGGCTTGAGATTCGAACCCAGGCCACCCATGTTGAAGTAGTAGCACCCAACCACTCTAC
1945007 CATG
131 CATG
1945011 CTCATTTT
1 CTCATTTT
1945019 CTAGATAAAA
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 141 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (134 bp):
CTCATTTTTTGGTTAAAAATTACCAAAACAATCTTTTAACCTGTTGAAAGAAAAAGCCACCCATG
ATGAAGTGGCTTGAGATTCGAACCCAGGCCACCCATGTTGAAGTAGTAGCACCCAACCACTCTAC
CATG
Found at i:1947791 original size:62 final size:62
Alignment explanation
Indices: 1947694--1947837 Score: 207
Period size: 62 Copynumber: 2.3 Consensus size: 62
1947684 GCTATCGCCT
* ** * *
1947694 TCGTGAGTAACCCTCTGCATAGGCATAGCAATAACTTTTAGGATATAAATTACCTATGTGTC
1 TCGTGAGTAACCCTCTGCATAGGAATAGCAATAACTTCCAGGAGATAAATTACCTATGTCTC
* * * *
1947756 TCGTGAGTAACCCTTTGCATAGGAATAGCAATAACTTCCGGGAGGTAAATTATCTATGTCTC
1 TCGTGAGTAACCCTCTGCATAGGAATAGCAATAACTTCCAGGAGATAAATTACCTATGTCTC
1947818 TCGTGAGTAACCCTCTGCAT
1 TCGTGAGTAACCCTCTGCAT
1947838 TTGCATAGGA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (62 bp):
TCGTGAGTAACCCTCTGCATAGGAATAGCAATAACTTCCAGGAGATAAATTACCTATGTCTC
Found at i:1951280 original size:16 final size:18
Alignment explanation
Indices: 1951259--1951308 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
1951249 AAAGTCAAAA
*
1951259 GCAAAAGCACAAAAAA-T
1 GCAAAAGCAAAAAAAAGT
1951276 G-AAAAG-AAAAAAAAGT
1 GCAAAAGCAAAAAAAAGT
1951292 GCAAAAGCAAAATAAAA
1 GCAAAAGCAAAA-AAAA
1951309 AAGGGAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 7 0.25
16 7 0.25
17 6 0.21
18 4 0.14
19 4 0.14
ACGTcount: A:0.70, C:0.10, G:0.14, T:0.06
Consensus pattern (18 bp):
GCAAAAGCAAAAAAAAGT
Found at i:1951324 original size:38 final size:38
Alignment explanation
Indices: 1951247--1951327 Score: 94
Period size: 38 Copynumber: 2.1 Consensus size: 38
1951237 CAAAATGATG
* *
1951247 AAAAAGTCAAAAGCAAAAGCACAAAAAATGAAAAGAAA
1 AAAAAGTCAAAAGCAAAAGCACAAAAAAGGAAAACAAA
* *
1951285 AAAAAGTGCAAAAGCAAAA-TA-AAAAAGGGAACAACAAA
1 AAAAAGT-CAAAAGCAAAAGCACAAAAAAGGAA-AACAAA
1951323 AAAAA
1 AAAAA
1951328 AACGAGGACA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 8 0.22
38 18 0.49
39 11 0.30
ACGTcount: A:0.72, C:0.10, G:0.14, T:0.05
Consensus pattern (38 bp):
AAAAAGTCAAAAGCAAAAGCACAAAAAAGGAAAACAAA
Found at i:1952814 original size:32 final size:32
Alignment explanation
Indices: 1952748--1952883 Score: 172
Period size: 32 Copynumber: 4.4 Consensus size: 32
1952738 TAAAGCCCAT
* *
1952748 AAGTCAGTGGC-A-TCATTTCGAAG-CC-CAC
1 AAGTCGGTGGCAACTCATTTCAAAGCCCACAC
1952776 AAGTCGGTGGCAACTCATTTCAAAGCCCACAC
1 AAGTCGGTGGCAACTCATTTCAAAGCCCACAC
* * *
1952808 AAGTCGGTGGAAACTTATTTGAAAGCCCACAC
1 AAGTCGGTGGCAACTCATTTCAAAGCCCACAC
* *
1952840 AAGTCGGTGGCAACCCGTTTCAAAGCCCACAC
1 AAGTCGGTGGCAACTCATTTCAAAGCCCACAC
*
1952872 AAGTCCGTGGCA
1 AAGTCGGTGGCA
1952884 CCCTTTTAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
28 10 0.11
29 1 0.01
30 10 0.11
31 2 0.02
32 70 0.75
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.19
Consensus pattern (32 bp):
AAGTCGGTGGCAACTCATTTCAAAGCCCACAC
Found at i:1953038 original size:58 final size:57
Alignment explanation
Indices: 1952638--1953306 Score: 478
Period size: 58 Copynumber: 11.5 Consensus size: 57
1952628 AGTCCATGAT
* * * * *
1952638 TCAGTGGCATTTCTTTTCAAAGTCCACAACTCAGTGGCATCCTTTT--AAGTCCACAAC
1 TCAGTGGCA-TCCTTTTCAAAGCCCACAAGTCAGTGGCAT-CTTTTCAAAGCCCACAAG
* * * * * * * *
1952695 TCTGTGGCATCCTTTT-AAAGTCCATAACTCTGAGGCACCCTTTT-AAAGCCCATAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAG
* * * *
1952751 TCAGTGGCAT-CATTTCGAAGCCCACAAGTCGGTGGCAACTCATTTCAAAGCCCACACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGC-A-TCTTTTCAAAG-CC-CACAAG
* * * * * * * *
1952811 TCGGTGGAAACTTATTTGAAAGCCCACACAAGTCGGTGGCAACCCGTTTCAAAGCCCACACAAG
1 TCAGTGGCATCCT-TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCTTTTCAAAG-CC-CACAAG
* * * * **
1952875 TCCGTGGCACCCTTTT-AAAGCCCATAAGTCAGTGGCACCCTTTT-AAAATCCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAG
* * * * * * * *
1952931 TCAGTGGTA-CCCTTCCAAAACCCATAAGTCAGTGACACCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAG
* * * *
1952987 TCATTGACATACCTTTTCAAAGCCCACAAGTTAGTGGCA-CATTTTCAAAGCCCATAAG
1 TCAGTGGCAT-CCTTTTCAAAGCCCACAAGTCAGTGGCATC-TTTTCAAAGCCCACAAG
* * * * *
1953045 ACAATGGAAT-CTTTTCAAAGCCTACAAGTCAGTGGCATCTTTTCAAAAGCCCATAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC-AAAGCCCACAAG
* * *
1953102 TCAGTGGCATCCTTTTCAAAGCTCACAAGTTAGTGGCATCCTTTCAAAGCCCACATAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCAC--AAG
* * * * * *
1953161 TCGGTGGTAACTCTATTGTCAAAGCCCACAAGACAGTGGTATCTTTTCAAAGCCCACAGG
1 TCAGTGGCATC-CT-TT-TCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAG
* * **
1953221 TTAGTGGCATCC-TTTCAAAAGCCCATAAGTCAGTGTTATCCTTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTTC-AAAGCCCACAAGTCAGTGGCAT-CTTTTCAAAGCCCACAAG
*
1953279 TTAGTGGCATCCTTTTCAAAGCCCACAA
1 TCAGTGGCATCCTTTTCAAAGCCCACAA
1953307 ATTAGTAGCA
Statistics
Matches: 495, Mismatches: 90, Indels: 53
0.78 0.14 0.08
Matches are distributed among these distances:
55 36 0.07
56 117 0.24
57 65 0.13
58 119 0.24
59 25 0.05
60 35 0.07
61 4 0.01
62 44 0.09
63 5 0.01
64 45 0.09
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (57 bp):
TCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAG
Found at i:1953227 original size:148 final size:144
Alignment explanation
Indices: 1952857--1953307 Score: 491
Period size: 148 Copynumber: 3.1 Consensus size: 144
1952847 TGGCAACCCG
* * * * * * **
1952857 TTTCAAAGCCCACACAAGTCCGTGGCACCCTT-TTAAAGCCCATAAGTCAGTGGCACCCTTTT-A
1 TTTCAAAGCCCACA-AAGTCAGTGGCA-CATTGTCAAAGCCCACAAGACAATGG-AATCTTTTCA
** * * * *
1952920 AAATCCACAAGTCAGTGGTACCCTTCCAAAA-CCCATAAGTCAGTGACA-CCCTTTCAAAGCCCA
63 AAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCATAAGTCAGTGACATCCTTTTCAAAGCCCA
* * *
1952983 CAAGTCATTGACATACCT
128 CAAGTTAGTGGCAT-CCT
* * *
1953001 TTTCAAAGCCCAC-AAGTTAGTGGCACATTTTCAAAGCCCATAAGACAATGGAATCTTTTCAAAG
1 TTTCAAAGCCCACAAAGTCAGTGGCACATTGTCAAAGCCCACAAGACAATGGAATCTTTTCAAAG
* * * *
1953065 CCTACAAGTCAGTGGCATCTTTTCAAAAGCCCATAAGTCAGTGGCATCCTTTTCAAAGCTCACAA
66 CCCACAAGTCAGTGGCATCCTTTCAAAAGCCCATAAGTCAGTGACATCCTTTTCAAAGCCCACAA
1953130 GTTAGTGGCATCC-
131 GTTAGTGGCATCCT
* * * *
1953143 TTTCAAAGCCCACATAAGTCGGTGGTAACTCTATTGTCAAAGCCCACAAGACAGTGGTATCTTTT
1 TTTCAAAGCCCACA-AAGTCAGTGG---CAC-ATTGTCAAAGCCCACAAGACAATGGAATCTTTT
* * **
1953208 CAAAGCCCACAGGTTAGTGGCATCCTTTCAAAAGCCCATAAGTCAGTGTTATCCTTTTCAAAGCC
61 CAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCATAAGTCAGTGACATCCTTTTCAAAGCC
1953273 CACAAGTTAGTGGCATCCT
126 CACAAGTTAGTGGCATCCT
1953292 TTTCAAAGCCCACAAA
1 TTTCAAAGCCCACAAA
1953308 TTAGTAGCAT
Statistics
Matches: 261, Mismatches: 35, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
141 9 0.03
142 66 0.25
143 18 0.07
144 45 0.17
147 2 0.01
148 107 0.41
149 14 0.05
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (144 bp):
TTTCAAAGCCCACAAAGTCAGTGGCACATTGTCAAAGCCCACAAGACAATGGAATCTTTTCAAAG
CCCACAAGTCAGTGGCATCCTTTCAAAAGCCCATAAGTCAGTGACATCCTTTTCAAAGCCCACAA
GTTAGTGGCATCCT
Found at i:1953318 original size:29 final size:29
Alignment explanation
Indices: 1952638--1953306 Score: 513
Period size: 28 Copynumber: 23.0 Consensus size: 29
1952628 AGTCCATGAT
* * *
1952638 TCAGTGGCATTTCTTTTCAAAGTCCACAAC
1 TCAGTGGCA-TCCTTTTCAAAGCCCACAAG
* *
1952668 TCAGTGGCATCCTTTT--AAGTCCACAAC
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* * * *
1952695 TCTGTGGCATCCTTTT-AAAGTCCATAAC
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* * * *
1952723 TCTGAGGCACCCTTTT-AAAGCCCATAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* *
1952751 TCAGTGGCAT-CATTTCGAAGCCCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* * *
1952779 TCGGTGGCAACTCATTTCAAAGCCCACACAAG
1 TCAGTGGCATC-CTTTTCAAAG-CC-CACAAG
* * * * *
1952811 TCGGTGGAAACTTATTTGAAAGCCCACACAAG
1 TCAGTGGCATCCT-TTTCAAAG-CC-CACAAG
* * *
1952843 TCGGTGGCAACCCGTTTCAAAGCCCACACAAG
1 TCAGTGGC-ATCCTTTTCAAAG-CC-CACAAG
* * *
1952875 TCCGTGGCACCCTTTT-AAAGCCCATAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* **
1952903 TCAGTGGCACCCTTTT-AAAATCCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* * * * *
1952931 TCAGTGGTA-CCCTTCCAAAACCCATAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* *
1952959 TCAGTGACA-CCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* *
1952987 TCATTGACATACCTTTTCAAAGCCCACAAG
1 TCAGTGGCAT-CCTTTTCAAAGCCCACAAG
* * *
1953017 TTAGTGGCA-CATTTTCAAAGCCCATAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* * * *
1953045 ACAATGGAAT-CTTTTCAAAGCCTACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
*
1953073 TCAGTGGCAT-CTTTTCAAAAGCCCATAAG
1 TCAGTGGCATCCTTTTC-AAAGCCCACAAG
*
1953102 TCAGTGGCATCCTTTTCAAAGCTCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
*
1953131 TTAGTGGCATCC-TTTCAAAGCCCACATAAG
1 TCAGTGGCATCCTTTTCAAAGCCCAC--AAG
* * *
1953161 TCGGTGGTAACTCTATTGTCAAAGCCCACAAG
1 TCAGTGGCATC-CT-TT-TCAAAGCCCACAAG
* * *
1953193 ACAGTGGTAT-CTTTTCAAAGCCCACAGG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* *
1953221 TTAGTGGCATCC-TTTCAAAAGCCCATAAG
1 TCAGTGGCATCCTTTTC-AAAGCCCACAAG
**
1953250 TCAGTGTTATCCTTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
*
1953279 TTAGTGGCATCCTTTTCAAAGCCCACAA
1 TCAGTGGCATCCTTTTCAAAGCCCACAA
1953307 ATTAGTAGCA
Statistics
Matches: 531, Mismatches: 85, Indels: 47
0.80 0.13 0.07
Matches are distributed among these distances:
27 34 0.06
28 223 0.42
29 107 0.20
30 68 0.13
31 10 0.02
32 74 0.14
33 4 0.01
34 11 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (29 bp):
TCAGTGGCATCCTTTTCAAAGCCCACAAG
Found at i:1954543 original size:32 final size:33
Alignment explanation
Indices: 1954441--1954792 Score: 534
Period size: 33 Copynumber: 10.8 Consensus size: 33
1954431 ACCTTCAAAA
* *
1954441 CCACACAAGTTGGTGGCAACCATTCTCTAAAGC
1 CCACACAAGTCGGTGGCAACCCTTCTCTAAAGC
* * * *
1954474 CCATACAAATTGGTGGCAACCATTCTCTAAAGC
1 CCACACAAGTCGGTGGCAACCCTTCTCTAAAGC
1954507 CCACACAAGTCGGTGGCAACCCTTCTC-AAAGC
1 CCACACAAGTCGGTGGCAACCCTTCTCTAAAGC
1954539 CCACACAAGTCAGGTGGCAACCCTTCTC-AAAGC
1 CCACACAAGTC-GGTGGCAACCCTTCTCTAAAGC
1954572 CCACACAAGTCGGTGGCAACCCTTCT-TAAAGC
1 CCACACAAGTCGGTGGCAACCCTTCTCTAAAGC
*
1954604 CCACACAAGTCGGTGGCAACCCTT-TCCAAAGC
1 CCACACAAGTCGGTGGCAACCCTTCTCTAAAGC
* *
1954636 CCACAAAAGTCGGTGGCAACCTTTCTC-AAAGC
1 CCACACAAGTCGGTGGCAACCCTTCTCTAAAGC
*
1954668 CCACAAAAGTCGGTGGCAACCCTTCTCTAAAGC
1 CCACACAAGTCGGTGGCAACCCTTCTCTAAAGC
*
1954701 CCACACAAGTTGGTGGCAACCCTTCTCTAAAGC
1 CCACACAAGTCGGTGGCAACCCTTCTCTAAAGC
* * *
1954734 CCACACAAGTTGGTGGCAATCATTCTCTAAAGC
1 CCACACAAGTCGGTGGCAACCCTTCTCTAAAGC
1954767 CCACACAAGTCGGTGGCAACCCTTCT
1 CCACACAAGTCGGTGGCAACCCTTCT
1954793 AAGGCCAATA
Statistics
Matches: 297, Mismatches: 17, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
31 1 0.00
32 118 0.40
33 178 0.60
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.19
Consensus pattern (33 bp):
CCACACAAGTCGGTGGCAACCCTTCTCTAAAGC
Found at i:1954900 original size:43 final size:43
Alignment explanation
Indices: 1954838--1955447 Score: 390
Period size: 43 Copynumber: 13.1 Consensus size: 43
1954828 GCACCTTCAT
* *
1954838 CTTTAAGTCCAATGTAGCTGGCCTTGAATAAGCACATTGGCAC
1 CTTTAAGTCCAATGCAGCTGGCCTTGAATCAGCACATTGGCAC
*
1954881 CTTTAAGTCCAATGCAGCTGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGCAGCTGGCCTTGAATCAGCACATTGGCAC
** *
1954924 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATGCAGCTGGCCTTGAATCAGCACATTGGCA----C
* *
1954971 AATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCAC
1 ---CTTTAAGTCCAATGCAGCTGGCCTTGAATCAGCACATTGGCAC
* *
1955017 CTTTAAGTCCAATATC-GCTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAAT-GCAGCTGGCCTTGAATCAGCACATTGGCA----C
* *
1955064 ATCTTTAAGTCTAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATGCAGCTGGCCTTGAATCAGCACATTGGCAC
** * *
1955109 CTCCAAGTCCAATATC-GCTGGCCTTGAATCAGCATATTGGCACCCTC
1 CTTTAAGTCCAAT-GCAGCTGGCCTTGAATCAGCACATTGGCA----C
*
1955156 ATCTTTTAAGCCCAATGTC-GCTGGCCTTGAATCAGCACATTGGCAC
1 --C-TTTAAGTCCAATG-CAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
1955202 CTTTAAGTCCAATATC-GCTAGGCCTTGAATCAGCATATTGGTGCCTTTGTCAT
1 CTTTAAGTCCAAT-GCAGCT-GGCCTTGAATCAGCACA-T--TG-----G-CAC
* * * *
1955255 CTTTAAGTCTAATATC-GCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCAT
1 CTTTAAGTCCAAT-GCAGCTGGCCTTGAATCAGCACATT---G-----G-CAC
*
1955307 CTTTAAGCCCAATGTC-GCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATG-CAGCTGGCCTTGAATCAGCACATTGGCAC
* * * * *
1955350 CTTTAAGTCCAATATC-GCTAGCCTTGGATCAGCATATTAGCACCTTTGTCAT
1 CTTTAAGTCCAAT-GCAGCTGGCCTTGAATCAGC-----A-CA---TTGGCAC
1955402 CTTTAAGTCCAATGTCA-CTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATG-CAGCTGGCCTTGAATCAGCACATTGGCAC
1955445 CTT
1 CTT
1955448 CATCTTTAAC
Statistics
Matches: 465, Mismatches: 51, Indels: 102
0.75 0.08 0.17
Matches are distributed among these distances:
43 203 0.44
44 18 0.04
45 2 0.00
46 4 0.01
47 6 0.01
48 1 0.00
49 42 0.09
50 74 0.16
51 1 0.00
52 94 0.20
53 20 0.04
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATGCAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1955015 original size:93 final size:92
Alignment explanation
Indices: 1954838--1955456 Score: 641
Period size: 93 Copynumber: 6.6 Consensus size: 92
1954828 GCACCTTCAT
* * * * *
1954838 CTTTAAGTCCAATGTAGCTGGCCTTGAATAAGCACATTGGCA----C--CTTTAAGTCCAATGCA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
1954897 GCTGACCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
1954924 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAATCTTTAAGTCCAATGT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTC-ATCTTTAAGTCCAATGT
*
1954989 AGCTGGCCTTGAATCAACACATTGGCAC
65 AGCTGGCCTTGAATCAGCACATTGGCAC
*
1955017 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCTAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1955082 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
** * *
1955109 CTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTCATCTTTTAAGCCCAATGT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TTTAAGTCCAATGT
*
1955174 CGCTGGCCTTGAATCAGCACATTGGCAC
65 AGCTGGCCTTGAATCAGCACATTGGCAC
** *
1955202 CTTTAAGTCCAATATCGCTAGGCCTTGAATCAGCATATTGGTGCCTTTGTCATCTTTAAGTCTAA
1 CTTTAAGTCCAATATCGCT-GGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAA
* * * *
1955267 TATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCAT
62 TGTAGCTGGCCTTGAATCAGCACATT---G-----G-CAC
* * * * *
1955307 CTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
* * * *
1955366 GCTAGCCTTGGATCAGCATATTAGCACCTTTGTCAT
66 GCTGGCCTTGAATCAGC-----A-CA---TTGGCAC
* * *
1955402 CTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAA
1955457 CATTCCTAAG
Statistics
Matches: 460, Mismatches: 37, Indels: 57
0.83 0.07 0.10
Matches are distributed among these distances:
86 39 0.08
90 1 0.00
92 90 0.20
93 142 0.31
94 23 0.05
95 73 0.16
96 33 0.07
97 6 0.01
99 2 0.00
100 1 0.00
101 8 0.02
104 23 0.05
105 19 0.04
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (92 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1955119 original size:185 final size:185
Alignment explanation
Indices: 1954838--1955295 Score: 651
Period size: 185 Copynumber: 2.5 Consensus size: 185
1954828 GCACCTTCAT
* * * * * *
1954838 CTTTAAGTCCAATGTAGCTGGCCTTGAATAAGCACATTGGCA----C--CTTTAAGTCCAATGCA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCTAATGTA
* **
1954897 GCTGACCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
66 GCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
* *
1954962 GGCACCTTCAATC-TTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCAC
131 GGCACCCTC-ATCTTTTAAGCCCAATGTAGCTGGCCTTGAATCAACACATTGGCAC
1955017 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCTAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCTAATGTA
*
1955082 GCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
66 GCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
* *
1955147 GGCACCCTCATCTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
131 GGCACCCTCATCTTTTAAGCCCAATGTAGCTGGCCTTGAATCAACACATTGGCAC
**
1955202 CTTTAAGTCCAATATCGCTAGGCCTTGAATCAGCATATTGGTGCCTTTGTCATCTTTAAGTCTAA
1 CTTTAAGTCCAATATCGCT-GGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCTAA
* * *
1955267 TATCGCTGGCCTTGAATCAGCATATTGGC
62 TGTAGCTGGCCTTGAATCAGCACATTGGC
1955296 GTCTTTGTCA
Statistics
Matches: 249, Mismatches: 19, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
179 38 0.15
183 1 0.00
184 3 0.01
185 141 0.57
186 23 0.09
188 1 0.00
189 42 0.17
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (185 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCTAATGTA
GCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
GGCACCCTCATCTTTTAAGCCCAATGTAGCTGGCCTTGAATCAACACATTGGCAC
Found at i:1955291 original size:52 final size:52
Alignment explanation
Indices: 1955202--1955447 Score: 285
Period size: 52 Copynumber: 4.9 Consensus size: 52
1955192 ACATTGGCAC
*
1955202 CTTTAAGTCCAATATCGCTAGGCCTTGAATCAGCATATTGGTGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCT-GGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
* *
1955255 CTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
* * * *
1955307 CTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATT---G-----G-CAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
* * * *
1955350 CTTTAAGTCCAATATCGCTAGCCTTGGATCAGCATATTAGCACCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
* * * *
1955402 CTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTT
1955448 CATCTTTAAC
Statistics
Matches: 163, Mismatches: 21, Indels: 19
0.80 0.10 0.09
Matches are distributed among these distances:
43 35 0.21
44 1 0.01
49 1 0.01
51 1 0.01
52 107 0.66
53 18 0.11
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.33
Consensus pattern (52 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
Found at i:1955381 original size:95 final size:95
Alignment explanation
Indices: 1955255--1955447 Score: 314
Period size: 95 Copynumber: 2.0 Consensus size: 95
1955245 CCTTTGTCAT
* * * **
1955255 CTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCATCTTTAAGCCCAAT
1 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTAGCACCTTTGTCATCTTTAAGCCCAAT
*
1955320 GTCGCTGGCCTTGAATCAGCACATTGGCAC
66 GTCACTGGCCTTGAATCAGCACATTGGCAC
* *
1955350 CTTTAAGTCCAATATCGCTAGCCTTGGATCAGCATATTAGCACCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTAGCACCTTTGTCATCTTTAAGCCCAAT
1955415 GTCACTGGCCTTGAATCAGCACATTGGCAC
66 GTCACTGGCCTTGAATCAGCACATTGGCAC
1955445 CTT
1 CTT
1955448 CATCTTTAAC
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (95 bp):
CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTAGCACCTTTGTCATCTTTAAGCCCAAT
GTCACTGGCCTTGAATCAGCACATTGGCAC
Found at i:1956344 original size:19 final size:19
Alignment explanation
Indices: 1956301--1956404 Score: 139
Period size: 19 Copynumber: 5.7 Consensus size: 19
1956291 ATTTCAACGA
1956301 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACAT-AAGT
*
1956321 GTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1956340 CTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1956359 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1956374 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1956391 TTTGTATCGATACA
1 TTTGTATCGATACA
1956405 ATGTAAGCTA
Statistics
Matches: 75, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
13 11 0.15
15 2 0.03
17 2 0.03
19 46 0.61
20 14 0.19
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1956379 original size:13 final size:13
Alignment explanation
Indices: 1956361--1956385 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1956351 ACATAAGTTT
1956361 TGTATCGATACAA
1 TGTATCGATACAA
1956374 TGTATCGATACA
1 TGTATCGATACA
1956386 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1956383 original size:32 final size:32
Alignment explanation
Indices: 1956303--1956409 Score: 142
Period size: 32 Copynumber: 3.1 Consensus size: 32
1956293 TTCAACGATT
*
1956303 TGTATCGATACATAAAGTGTTGTATCGATACATAA
1 TGTATCGATACAT-AAGTTTTGTATCGATAC--AA
1956338 GTCTTGTATCGATACATAAGTTTTGTATCGATACAA
1 ----TGTATCGATACATAAGTTTTGTATCGATACAA
1956374 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
1956406 TGTA
1 TGTA
1956410 AGCTACTGCC
Statistics
Matches: 67, Mismatches: 1, Indels: 7
0.89 0.01 0.09
Matches are distributed among these distances:
32 36 0.54
36 2 0.03
38 16 0.24
39 13 0.19
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:1956525 original size:52 final size:52
Alignment explanation
Indices: 1956480--1956608 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
1956470 CACTGATCTT
1956480 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
1956532 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1956584 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1956609 TCATATTTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:1959736 original size:32 final size:32
Alignment explanation
Indices: 1959695--1959798 Score: 129
Period size: 32 Copynumber: 3.2 Consensus size: 32
1959685 AACAGCATCC
1959695 TTTCAAAGCCCACACAAGTTGGTGGCAACTCT
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCT
* * *
1959727 TTTCAAAGCCCACATAAGTTAGTGGC-ACTTTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCAAC--TCT
* * *
1959760 TTTAAAAGCCCACACAAGTTGATGGCAACCCT
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCT
1959792 TTTCAAA
1 TTTCAAA
1959799 TCACCACTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
31 2 0.03
32 31 0.53
33 24 0.41
34 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTTGGTGGCAACTCT
Found at i:1965657 original size:19 final size:19
Alignment explanation
Indices: 1965611--1965682 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
1965601 TTTCAACAAT
*
1965611 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACATA-AGT-A
*
1965632 CTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
*
1965651 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTA
*
1965670 TTGTATTGATACA
1 TTGTATCGATACA
1965683 ATGTATCGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 30 0.65
20 3 0.07
21 13 0.28
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:1970042 original size:20 final size:20
Alignment explanation
Indices: 1970017--1970057 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1970007 TCATCCCTTG
1970017 TGTCGTCCATAGCTTACACT
1 TGTCGTCCATAGCTTACACT
*
1970037 TGTCGTCCATAGCTTGCACT
1 TGTCGTCCATAGCTTACACT
1970057 T
1 T
1970058 ATAGTCATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (20 bp):
TGTCGTCCATAGCTTACACT
Found at i:1974136 original size:31 final size:31
Alignment explanation
Indices: 1974101--1974435 Score: 297
Period size: 34 Copynumber: 10.5 Consensus size: 31
1974091 ACAGTCTACG
* *
1974101 ACTCAGTGGCATCTTTTCTTCAATGTTCACA
1 ACTCAGTGGCATCTTTTCTTCAAAGTCCACA
* *
1974132 ACTCAGTGGCATC-TCTCTTCAAAGTCCACG
1 ACTCAGTGGCATCTTTTCTTCAAAGTCCACA
* *
1974162 ACTTAGTGGTATCTTTTCTTCAAAGTCCACA
1 ACTCAGTGGCATCTTTTCTTCAAAGTCCACA
* *
1974193 ACTCAGTGGCATC-TCTCTTCAAAGTCCACG
1 ACTCAGTGGCATCTTTTCTTCAAAGTCCACA
* *
1974223 ACTTAGTGGTATCTTTTCTTCAAAGTCCACA
1 ACTCAGTGGCATCTTTTCTTCAAAGTCCACA
*
1974254 ACTCAGTGGCATCTTTTTTTCTTCAAAGTCCACG
1 ACTCAGTGGCATC---TTTTCTTCAAAGTCCACA
1974288 ACTCAGTGGCATCTTTTCTCTTTCCAAAGTCCACA
1 ACTCAGTGGCATC-TTT-TC-TT-CAAAGTCCACA
* * *
1974323 ACTCCGTGGCATC-CTT-TT--AAGCCCACA
1 ACTCAGTGGCATCTTTTCTTCAAAGTCCACA
** *
1974350 ACTCCA-TGGCATTCTTTTTCCTTTTAAGCCCACA
1 ACT-CAGTGGCA-TC-TTTT-CTTCAAAGTCCACA
* **
1974384 ACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACA
1 ACTCAGTGGCA-TC-TTTT-CTTCAAAGTCCACA
*
1974418 ACTCTGTGGCATCCTTTT
1 ACTCAGTGGCAT-CTTTT
1974436 AAGCCCACAA
Statistics
Matches: 257, Mismatches: 29, Indels: 34
0.80 0.09 0.11
Matches are distributed among these distances:
27 16 0.06
28 3 0.01
30 54 0.21
31 65 0.25
32 7 0.03
33 9 0.04
34 81 0.32
35 22 0.09
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (31 bp):
ACTCAGTGGCATCTTTTCTTCAAAGTCCACA
Found at i:1974176 original size:61 final size:61
Alignment explanation
Indices: 1974079--1974335 Score: 334
Period size: 61 Copynumber: 4.0 Consensus size: 61
1974069 AATTCTTCAA
* * * *
1974079 ATCTCTCTTCTCACAGTCTACGACTCAGTGGCATCTTTTCTTCAATGTTCACAACTCAGTGGC
1 ATCTCTC-T-TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGC
* *
1974142 ATCTCTCTTCAAAGTCCACGACTTAGTGGTATCTTTTCTTCAAAGTCCACAACTCAGTGGC
1 ATCTCTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGC
* *
1974203 ATCTCTCTTCAAAGTCCACGACTTAGTGGTATCTTTTCTTCAAAGTCCACAACTCAGTGGC
1 ATCTCTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGC
* *
1974264 ATCTTTTTTTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCTCTTTCCAAAGTCCACAACTCCG
1 ATC----TCTCTTCAAAGTCCACGACTCAGTGGCATC-TTT-TC-TT-CAAAGTCCACAACTCAG
1974329 TGGC
58 TGGC
1974333 ATC
1 ATC
1974336 CTTTTAAGCC
Statistics
Matches: 176, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
61 111 0.63
62 1 0.01
63 7 0.04
65 27 0.15
66 3 0.02
67 2 0.01
68 2 0.01
69 23 0.13
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (61 bp):
ATCTCTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGC
Found at i:1974348 original size:27 final size:27
Alignment explanation
Indices: 1974318--1974461 Score: 128
Period size: 34 Copynumber: 4.9 Consensus size: 27
1974308 TTTCCAAAGT
1974318 CCACAACTCCGTGGCATCCTTTTAAGC
1 CCACAACTCCGTGGCATCCTTTTAAGC
*
1974345 CCACAACTCCATGGCATTCTTTTTCCTTTTAAGC
1 CCACAACTCCGTGGCA-------TCCTTTTAAGC
*
1974379 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCA-------TCCTTTTAAGC
*
1974413 CCACAACTCTGTGGCATCCTTTTAAGC
1 CCACAACTCCGTGGCATCCTTTTAAGC
1974440 CCACAACTCCGTGGCA-CCTTTT
1 CCACAACTCCGTGGCATCCTTTT
1974462 TCTTTTTAAA
Statistics
Matches: 103, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
26 6 0.06
27 40 0.39
34 57 0.55
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (27 bp):
CCACAACTCCGTGGCATCCTTTTAAGC
Found at i:1974368 original size:95 final size:94
Alignment explanation
Indices: 1974101--1974465 Score: 299
Period size: 95 Copynumber: 3.9 Consensus size: 94
1974091 ACAGTCTACG
* * * * *
1974101 ACTCAGTGGCATC-TTT-TC-TTCAATGTTCACAACTCAGTGGCATCTCTCTTCAAAGTCCACGA
1 ACTCAGTGGCATCTTTTCTCTTTCAAAGTCCACAACTCAGTGGCATC-CT-TT-TAAGCCCACAA
* *
1974163 CT-TAGTGGTA-TC-TTTTCTTCAAAGTCCACA
63 CTCCA-TGGCATTCTTTTTCTTCAAAGTCCACA
* * * * *
1974193 ACTCAGTGGCATC---TCTC-TTCAAAGTCCACGACTTAGTGGTATCTTTTCTTCAAAGTCCACA
1 ACTCAGTGGCATCTTTTCTCTTTCAAAGTCCACAACTCAGTGGCATC-CTT-TT--AAGCCCACA
* *
1974254 ACT-CAGTGGCATCTTTTTTTCTTCAAAGTCCACG
62 ACTCCA-TGGCAT-TCTTTTTCTTCAAAGTCCACA
*
1974288 ACTCAGTGGCATCTTTTCTCTTTCCAAAGTCCACAACTCCGTGGCATCCTTTTAAGCCCACAACT
1 ACTCAGTGGCATCTTTTCTCTTT-CAAAGTCCACAACTCAGTGGCATCCTTTTAAGCCCACAACT
** *
1974353 CCATGGCATTCTTTTTCCTTTTAAGCCCACA
65 CCATGGCATTCTTTTT-CTTCAAAGTCCACA
* * *
1974384 ACTCCGTGGCACTCTTTT-TCCTTT-TAAGTCCACAACTCTGTGGCATCCTTTTAAGCCCACAAC
1 ACTCAGTGGCA-TCTTTTCT-CTTTCAAAGTCCACAACTCAGTGGCATCCTTTTAAGCCCACAAC
* *
1974447 TCCGTGGCA-CCTTTTTCTT
64 TCCATGGCATTCTTTTTCTT
1974466 TTTAAAGCCC
Statistics
Matches: 229, Mismatches: 28, Indels: 31
0.80 0.10 0.11
Matches are distributed among these distances:
90 2 0.01
91 26 0.11
92 30 0.13
93 3 0.01
94 7 0.03
95 81 0.35
96 38 0.17
97 12 0.05
98 6 0.03
99 4 0.02
100 20 0.09
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (94 bp):
ACTCAGTGGCATCTTTTCTCTTTCAAAGTCCACAACTCAGTGGCATCCTTTTAAGCCCACAACTC
CATGGCATTCTTTTTCTTCAAAGTCCACA
Found at i:1974372 original size:34 final size:33
Alignment explanation
Indices: 1974334--1974594 Score: 293
Period size: 34 Copynumber: 8.0 Consensus size: 33
1974324 CTCCGTGGCA
* *
1974334 TCCTTTTAAGCCCACAACTCCATGGCATTCTTTT
1 TCCTTTTAAGCCCACAACTCCGTGGCA-CCTTTT
1974368 TCCTTTTAAGCCCACAACTCCGTGGCACTCTTTT
1 TCCTTTTAAGCCCACAACTCCGTGGCAC-CTTTT
* *
1974402 TCCTTTTAAGTCCACAACTCTGTGGCA------
1 TCCTTTTAAGCCCACAACTCCGTGGCACCTTTT
1974429 TCCTTTTAAGCCCACAACTCCGTGGCACCTTTT
1 TCCTTTTAAGCCCACAACTCCGTGGCACCTTTT
* * * * *
1974462 TCTTTTTAAAGCCCATAACTTCGTGACACCTTGT
1 TCCTTTT-AAGCCCACAACTCCGTGGCACCTTTT
* * *
1974496 TCCGTTTAAGTCCACAACTCTGTGGCACCTTTT
1 TCCTTTTAAGCCCACAACTCCGTGGCACCTTTT
*
1974529 TCCTTTTAAGCCCACACCTCCGTGGCATCCCTTTT
1 TCCTTTTAAGCCCACAACTCCGTGGCA--CCTTTT
* *
1974564 TCC-TTTAAGACCACAACTCCATGGCACCTTT
1 TCCTTTTAAGCCCACAACTCCGTGGCACCTTT
1974595 AAGTCCAATA
Statistics
Matches: 191, Mismatches: 26, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
27 25 0.13
32 5 0.03
33 49 0.26
34 103 0.54
35 9 0.05
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (33 bp):
TCCTTTTAAGCCCACAACTCCGTGGCACCTTTT
Found at i:1974387 original size:130 final size:127
Alignment explanation
Indices: 1974101--1974435 Score: 330
Period size: 130 Copynumber: 2.7 Consensus size: 127
1974091 ACAGTCTACG
* ** *
1974101 ACTCAGTGGCATCTTTTCTTCAATGTTCACAACTCAGTGGCATC----TCTCTTCAAAGTCCACG
1 ACTCAGTGGCATCTTTTCTTCAAAGCCCACAACTCAGTGGCATCTTTTTTTCTTCAAAGTCCACG
* * * *
1974162 ACTTAGTGGTATC-TTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTCTTCAAAGTCCACG
66 ACTCAGTGGCATCTTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTCTTCAAAGCCCACA
* * *
1974223 ACTTAGTGGTATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTTTTCTTCAAAGTCCACG
1 ACTCAGTGGCATCTTTTCTTCAAAGCCCACAACTCAGTGGCATCTTTTTTTCTTCAAAGTCCACG
* *
1974288 ACTCAGTGGCATCTTTTCTCTTTCCAAAGTCCACAACTCCGTGGCATC-CT-TT-TAAGCCCACA
66 ACTCAGTGGCATCTTTT-TC-TT-CAAAGTCCACAACTCAGTGGCATCTCTCTTCAAAGCCCACA
** * * **
1974350 ACTCCA-TGGCATTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCA-CTCTTTTTCCTTTTAAGT
1 ACT-CAGTGGCA-TC-TTTT-CTTCAAAGCCCACAACTCAGTGGCATCT-TTTTTTCTTCAAAGT
* * *
1974413 CCACAACTCTGTGGCATCCTTTT
61 CCACGACTCAGTGGCATCTTTTT
1974436 AAGCCCACAA
Statistics
Matches: 177, Mismatches: 23, Indels: 19
0.81 0.11 0.09
Matches are distributed among these distances:
122 40 0.23
126 27 0.15
127 17 0.10
128 7 0.04
129 11 0.06
130 75 0.42
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (127 bp):
ACTCAGTGGCATCTTTTCTTCAAAGCCCACAACTCAGTGGCATCTTTTTTTCTTCAAAGTCCACG
ACTCAGTGGCATCTTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTCTTCAAAGCCCACA
Found at i:1974433 original size:61 final size:60
Alignment explanation
Indices: 1974368--1974563 Score: 214
Period size: 61 Copynumber: 3.1 Consensus size: 60
1974358 GCATTCTTTT
*
1974368 TCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTTAAGCCCACAACTCTGTGGCA
* * *
1974429 TCCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCATAACT-TCGTGACA
1 TCCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCCTTTT-AAGCCCACAACTCT-GTGGCA
* * * * *
1974490 CCTTGTTCCGTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAGCCCACACCTCCGTGGC
1 ------TCCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGCCCACAACTCTGTGGC
1974555 A
60 A
1974556 TCCCTTTT
1 T-CCTTTT
1974564 TCCTTTAAGA
Statistics
Matches: 112, Mismatches: 13, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
60 13 0.12
61 48 0.43
66 15 0.13
67 36 0.32
ACGTcount: A:0.19, C:0.33, G:0.13, T:0.35
Consensus pattern (60 bp):
TCCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGCCCACAACTCTGTGGCA
Found at i:1974462 original size:27 final size:27
Alignment explanation
Indices: 1974402--1974461 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
1974392 GCACTCTTTT
* *
1974402 TCCTTTTAAGTCCACAACTCTGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
1974429 TCCTTTTAAGCCCACAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
1974456 -CCTTTT
1 TCCTTTT
1974462 TCTTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 6 0.19
27 25 0.81
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (27 bp):
TCCTTTTAAGCCCACAACTCCGTGGCA
Found at i:1974521 original size:67 final size:66
Alignment explanation
Indices: 1974433--1974594 Score: 200
Period size: 67 Copynumber: 2.4 Consensus size: 66
1974423 GTGGCATCCT
* * * *
1974433 TTTAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCATAACTTCGTGACA-CCTTGTT
1 TTTAAGACCACAACTCCGTGGCACCTTTTTCCTTTT-AAGCCCACAACTCCGTGACACCCTTGTT
1974497 CC
65 CC
* * * * *
1974499 GTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAGCCCACACCTCCGTGGCATCCCTTTT
1 -TTTAAGACCACAACTCCGTGGCACCTTTTTCCTTTTAAGCCCACAACTCCGTGACA-CCCTTGT
1974564 TCC
64 TCC
*
1974567 TTTAAGACCACAACTCCATGGCACCTTT
1 TTTAAGACCACAACTCCGTGGCACCTTT
1974595 AAGTCCAATA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
66 16 0.20
67 58 0.71
68 8 0.10
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.34
Consensus pattern (66 bp):
TTTAAGACCACAACTCCGTGGCACCTTTTTCCTTTTAAGCCCACAACTCCGTGACACCCTTGTTC
C
Found at i:1974664 original size:49 final size:49
Alignment explanation
Indices: 1974591--1975530 Score: 775
Period size: 49 Copynumber: 19.8 Consensus size: 49
1974581 TCCATGGCAC
* * *
1974591 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
1974640 CTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
1974683 CTTTAAGCCCAATATTGCTGGCC-----TCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
1974727 ATTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
1974770 CTTTAAGCCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * ** * * *
1974819 CTTGAAGACCGCTGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAACCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT---TCAT
* * *
1974871 CTTTAAGACCAATGTTGCTGGCCTTGAATTAGCACATTGGCA----C--
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
1974914 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
1974962 CTCTAAGACCAATGTCACTGGCCTTGAATCAGCACATT---A---GCA-
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * * **
1975004 ---TAAGCCCAATTTCGCTAGCCTTGAATCAGCATAGTGGCA-CTTTGT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
1975049 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG------CA-
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
1975091 C---AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG-AGCCTTTGTTAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CC--T-TCAT
*
1975140 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
1975189 TTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCAT
* *
1975241 CTTTAAGTCTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
1975290 CTTTAAGTCCAATATCTCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCAT
** * *
1975342 CTTTAAGTCCGGTGTCGTTGGCCTTGAATCAACACATTGGCACCTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
1975391 TTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T--TCAT
* * *
1975443 CTTTAAGACCAATGTCACTGGCCTTGAATTAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
1975492 CCTTACGTCCGATGTCGTTGGCCATGAATCAGCACATTG
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
1975531 TCATTCTTCG
Statistics
Matches: 713, Mismatches: 119, Indels: 118
0.75 0.13 0.12
Matches are distributed among these distances:
38 13 0.02
39 62 0.09
42 3 0.00
43 93 0.13
44 19 0.03
45 4 0.01
47 1 0.00
48 66 0.09
49 249 0.35
50 4 0.01
51 3 0.00
52 195 0.27
53 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (49 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:1974736 original size:87 final size:88
Alignment explanation
Indices: 1974585--1974863 Score: 389
Period size: 92 Copynumber: 3.1 Consensus size: 88
1974575 CACAACTCCA
* *
1974585 TGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACC
1 TGGCACCTTTAAGCCCAATATCGCTGGCC----ATCAGCATATTGGCACCTTCATCTTTAAGACC
1974650 AATGTCGTTGGCCTTGAATCAGCACAT
62 AATGTCGTTGGCCTTGAATCAGCACAT
* *
1974677 TGGCACCTTTAAGCCCAATATTGCTGGCC-TCAGCATATTGGCACCTTCATATTTAAGACCAATG
1 TGGCACCTTTAAGCCCAATATCGCTGGCCATCAGCATATTGGCACCTTCATCTTTAAGACCAATG
*
1974741 TCGCTGGCCTTGAATCAGCACAT
66 TCGTTGGCCTTGAATCAGCACAT
* *
1974764 TGGCACCTTTAAGCCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTCATCTTGAAGACC
1 TGGCACCTTTAAGCCCAATATCGCTGGCC----ATCAGCATATTGGCACCTTCATCTTTAAGACC
**
1974829 GCTGTCGTTGGCCTTGAATCAGCACAT
62 AATGTCGTTGGCCTTGAATCAGCACAT
*
1974856 CGGCACCT
1 TGGCACCT
1974864 CAACCATCTT
Statistics
Matches: 169, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
87 84 0.50
92 85 0.50
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (88 bp):
TGGCACCTTTAAGCCCAATATCGCTGGCCATCAGCATATTGGCACCTTCATCTTTAAGACCAATG
TCGTTGGCCTTGAATCAGCACAT
Found at i:1974899 original size:231 final size:223
Alignment explanation
Indices: 1974599--1975091 Score: 637
Period size: 231 Copynumber: 2.2 Consensus size: 223
1974589 ACCTTTAAGT
* * * * *
1974599 CCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGTTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTCCATCTTTAAGACCAATGTCGCTGGCCT
*
1974664 TGAATCAGCACATTGGCACCTTTAAGCCCAATATTGCTGGCC-TCAGCATATTGGCACCTTCATA
66 TGAATCAGCACATTGGCACCTTTAAGCCCAATATCGCTGGCCATCAGCATATTGGCACCTT-ATA
* * * *
1974728 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATCGCTGGCC
130 TCTAAGACCAATGTCACTGGCCTTGAATCAGCACATTAGCA----TAAGCCCAATATCGCTAGCC
* *
1974793 TTGAATTAGCATATTGGCACCTTCATCTTGAAGA
191 TTGAATCAGCATAGTGGCA-CTTCATCTTGAAGA
** * * *
1974827 CCGCTGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAACCATCTTTAAGACCAATGTTGCTGG
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT---CCATCTTTAAGACCAATGTCGCTGG
* *
1974892 CCTTGAATTAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
63 CCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATCGCTGGCC----ATCAGCATATTGGCAC
* * *
1974957 CTTGTCTCTAAGACCAATGTCACTGGCCTTGAATCAGCACATTAGCATAAGCCCAATTTCGCTAG
124 CTTATATCTAAGACCAATGTCACTGGCCTTGAATCAGCACATTAGCATAAGCCCAATATCGCTAG
** *
1975022 CCTTGAATCAGCATAGTGGCACTTTGTCTTTAAGA
189 CCTTGAATCAGCATAGTGGCACTTCATCTTGAAGA
1975057 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1975092 AAGTCCAATA
Statistics
Matches: 228, Mismatches: 29, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
228 30 0.13
230 42 0.18
231 99 0.43
235 39 0.17
236 18 0.08
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (223 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTCCATCTTTAAGACCAATGTCGCTGGCCT
TGAATCAGCACATTGGCACCTTTAAGCCCAATATCGCTGGCCATCAGCATATTGGCACCTTATAT
CTAAGACCAATGTCACTGGCCTTGAATCAGCACATTAGCATAAGCCCAATATCGCTAGCCTTGAA
TCAGCATAGTGGCACTTCATCTTGAAGA
Found at i:1974905 original size:144 final size:143
Alignment explanation
Indices: 1974728--1975488 Score: 498
Period size: 153 Copynumber: 5.3 Consensus size: 143
1974718 CACCTTCATA
1974728 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATCGCTGGCC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATCGCTGGCC
* ** **
1974793 TTGAATTAGCATATTGGCACCTTCATCT-TGAAGACCGCTGTCGTTGGCCTTGAATCAGCACATC
66 TTGAATCAGCATATTGGCACCTT-ATCTCT-AAGACCAATGTCACTGGCCTTGAATCAGCACATC
1974857 GGCACCTCAACCATC
129 GGCACCTCAACCATC
* * *
1974872 TTTAAGACCAATGTTGCTGGCCTTGAATTAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATCGCTGGCC
*
1974937 TTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCACTGGCCTTGAATCAGCACAT---
66 TTGAATCAGCATATTGGCACCTTATCTCTAAGACCAATGTCACTGGCCTTGAATCAGCACATCGG
*
1974999 ----T--AGCA--
131 CACCTCAACCATC
* * * * * * *
1975004 --TAAGCCCAATTTCGCTAGCCTTGAATCAGCATAGTGGCACTTTGTCTTTAAGACCAATGTCGC
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC-----CTTTAAGCCCAATATCGC
* * * * *
1975067 TGGCCTTGAATCAGCACATTGG---C--A---C-AAGTCCAATATCGCTGGCCTTGAATCAGCAT
61 TGGCCTTGAATCAGCATATTGGCACCTTATCTCTAAGACCAATGTCACTGGCCTTGAATCAGCAC
* *****
1975123 ATTGG-AGCCTTTGTTATC
126 ATCGGCA-CCTCAACCATC
* *
1975141 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATTTTTAAGTCCAATATCG
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC------TTTAAGCCCAATATCG
* * * * * * *
1975206 CTGGCCTTAAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCTAATGTCGCTAGCCTTGAATC
60 CTGGCCTTGAATCAGCATATTGGCACC--T-T-ATCTCTAAGACCAATGTCACTGGCCTTGAATC
* *
1975271 AGCACATTGGCACCT---TCATC
121 AGCACATCGGCACCTCAACCATC
* * * * * * ** *
1975291 TTTAAGTCCAATATCTCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCGGTG
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT---G-----G-CACCTTTAAGCCCAATA
* * * * * * * **
1975356 TCGTTGGCCTTGAATCAACACATTGGCACCTTCATTTTTAAGTCCAATATCGTTGGCCTTGAATC
57 TCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTCTAAGACCAATGTCACTGGCCTTGAATC
* * **
1975421 AGCATATTGGCACCTTC-GTCATC
121 AGCACATCGGCACC-TCAACCATC
* *
1975444 TTTAAGACCAATGTCACTGGCCTTGAATTAGCACATTGGCACCTT
1 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
1975489 CATCCTTACG
Statistics
Matches: 499, Mismatches: 67, Indels: 102
0.75 0.10 0.15
Matches are distributed among these distances:
126 29 0.06
127 1 0.00
130 33 0.07
132 1 0.00
133 1 0.00
134 4 0.01
135 38 0.08
136 1 0.00
139 35 0.07
140 35 0.07
143 33 0.07
144 90 0.18
145 1 0.00
149 1 0.00
150 81 0.16
151 2 0.00
153 108 0.22
154 1 0.00
158 1 0.00
159 3 0.01
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (143 bp):
TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATCGCTGGCC
TTGAATCAGCATATTGGCACCTTATCTCTAAGACCAATGTCACTGGCCTTGAATCAGCACATCGG
CACCTCAACCATC
Found at i:1975025 original size:39 final size:39
Alignment explanation
Indices: 1974965--1975121 Score: 134
Period size: 39 Copynumber: 3.8 Consensus size: 39
1974955 ACCTTGTCTC
* *
1974965 TAAGACCAATGTCACTGGCCTTGAATCAGCACATTAGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTAGCA
* * * * *
1975004 TAAGCCCAATTTCGCTAGCCTTGAATCAGCATAGTGGCACTTTGTCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGC--A----CA-TTAG-C-A
* *
1975052 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTAGCA
* *
1975091 CAAGTCCAATATCGCTGGCCTTGAATCAGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCA
1975122 TATTGGAGCC
Statistics
Matches: 95, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
39 54 0.57
40 1 0.01
41 4 0.04
42 2 0.02
45 2 0.02
46 4 0.04
47 1 0.01
48 27 0.28
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (39 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCACATTAGCA
Found at i:1975043 original size:87 final size:87
Alignment explanation
Indices: 1974870--1975484 Score: 521
Period size: 101 Copynumber: 6.5 Consensus size: 87
1974860 ACCTCAACCA
* *
1974870 TCTTTAAGACCAATGTTGCTGGCCTTGAATTAGCACATTGGCACCTTTAAGTCCAATATCGCTGG
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----TAAGTCCAATATCGCTGG
1974935 CCTTGAATCAGCATATTGGCACCTTG
62 CCTTGAATCAGCATATTGGCACCTTG
* * * * * *
1974961 TCTCTAAGACCAATGTCACTGGCCTTGAATCAGCACATTAGCATAAGCCCAATTTCGCTAGCCTT
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGTCCAATATCGCTGGCCTT
* *
1975026 GAATCAGCATAGTGGCACTTTG
66 GAATCAGCATATTGGCACCTTG
*
1975048 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGTCCAATATCGCTGGCCTT
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGTCCAATATCGCTGGCCTT
1975113 GAATCAGCATATTGG-AGCCTTTG
66 GAATCAGCATATTGGCA-CC-TTG
*
1975136 TTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATTTTTAAGTCCAA
1 ---TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG---C---A----TAAGTCCAA
* *
1975201 TATCGCTGGCCTTAAATCAGCATATTGGCGCCTTTG
53 TATCGCTGGCCTTGAATCAGCATATTGGCACC-TTG
* * *
1975237 TCATCTTTAAGTCTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
1 ---TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG------CA----TAAGTCCAA
* *
1975302 TATCTCTGGCCTTGAATCAGCATATTGGCGCCTTTG
53 TATCGCTGGCCTTGAATCAGCATATTGGCACC-TTG
* ** * *
1975338 TCATCTTTAAGTCCGGTGTCGTTGGCCTTGAATCAACACATTGGCACCTTCATTTTTAAGTCCAA
1 ---TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG------CA----TAAGTCCAA
*
1975403 TATCGTTGGCCTTGAATCAGCATATTGGCACCTTCG
53 TATCGCTGGCCTTGAATCAGCATATTGGCACCTT-G
* *
1975439 TCATCTTTAAGACCAATGTCACTGGCCTTGAATTAGCACATTGGCA
1 ---TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1975485 CCTTCATCCT
Statistics
Matches: 456, Mismatches: 48, Indels: 36
0.84 0.09 0.07
Matches are distributed among these distances:
86 1 0.00
87 112 0.25
88 3 0.01
91 78 0.17
94 1 0.00
95 2 0.00
97 1 0.00
100 2 0.00
101 254 0.56
104 2 0.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (87 bp):
TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGTCCAATATCGCTGGCCTT
GAATCAGCATATTGGCACCTTG
Found at i:1975267 original size:101 final size:101
Alignment explanation
Indices: 1975092--1975530 Score: 644
Period size: 101 Copynumber: 4.3 Consensus size: 101
1975082 ACATTGGCAC
* *
1975092 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGAGCCTTTGTTATCTTTAAGTCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
*
1975157 CTGGCCTTGAATCAGCACATTGGCACCTTTATTTTT
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATTTTT
* *
1975193 AAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCTAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
* *
1975258 CTAGCCTTGAATCAGCACATTGGCACCTTCATCTTT
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATTTTT
* **
1975294 AAGTCCAATATCTCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCGGTGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
* *
1975359 TTGGCCTTGAATCAACACATTGGCACCTTCATTTTT
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATTTTT
* * * * *
1975395 AAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCA
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
* **
1975460 CTGGCCTTGAATTAGCACATTGGCACCTTCATCCTT
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATTTTT
* * * * * *
1975496 ACGTCCGATGTCGTTGGCCATGAATCAGCACATTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
1975531 TCATTCTTCG
Statistics
Matches: 304, Mismatches: 34, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 304 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.33
Consensus pattern (101 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
CTGGCCTTGAATCAGCACATTGGCACCTTCATTTTT
Found at i:1975525 original size:202 final size:197
Alignment explanation
Indices: 1974591--1975486 Score: 826
Period size: 202 Copynumber: 4.7 Consensus size: 197
1974581 TCCATGGCAC
* * * * * *
1974591 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATTTTTAAGTCCAATATC
* * * * *
1974656 GTTGGCCTTGAATCAGCACATTGGCA-------C--CTTTAAGCCCAATATTGCTGGCC-----T
66 GCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAAT
* * * *
1974707 CAGCATATTGGCACCTTCATATTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT---G---
131 CAGCACATTGGCA-C--C--ATTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCT
*
1974766 --G-CAC
191 TTGTCAT
* * * * * * * ** *
1974770 CTTTAAGCCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTCATCTTGAAGACCGCTGTC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATTTTTAAGTCCAATATC
* * * ** *
1974835 GTTGGCCTTGAATCAGCACATCGGCACC-TCAACCATCTTTAAGACCAATGTTGCTGGCCTTGAA
66 GCTGGCCTTGAATCAGCATATTGGCACCTTC-GTCATCTTTAAGACCAATGTCGCTGGCCTTGAA
* *
1974899 TTAGCACATTGGCACC-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTGT
130 TCAGCACATTGGCACCATTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGT
1974962 C-T
195 CAT
* * * * *
1974964 C--TAAGACCAATGTCACTGGCCTTGAATCAGCACATT---A---GCA----TAAGCCCAATTTC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATTTTTAAGTCCAATATC
* * *
1975017 GCTAGCCTTGAATCAGCATAGTGGCA-CTT--T-GTCTTTAAGACCAATGTCGCTGGCCTTGAAT
66 GCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAAT
* *
1975078 CAGCACATTGGCA-C----AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGAGCCTTTGTT
131 CAGCACATTGGCACCATTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTC
1975138 AT
196 AT
*
1975140 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATTTTTAAGTCCAATATC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATTTTTAAGTCCAATATC
* * * * * *
1975205 GCTGGCCTTAAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCTAATGTCGCTAGCCTTGAAT
66 GCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAAT
*
1975270 CAGCACATTGGCACCTTCATCTTTAAGTCCAATATCTCTGGCCTTGAATCAGCATATTGGCGCCT
131 CAGCACATTGGCA-C--CA--TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCT
1975335 TTGTCAT
191 TTGTCAT
** * *
1975342 CTTTAAGTCCGGTGTCGTTGGCCTTGAATCAACACATTGGCACCTTCATTTTTAAGTCCAATATC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATTTTTAAGTCCAATATC
* *
1975407 GTTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCACTGGCCTTGAAT
66 GCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAAT
*
1975472 TAGCACATTGGCACC
131 CAGCACATTGGCACC
1975487 TTCATCCTTA
Statistics
Matches: 596, Mismatches: 70, Indels: 82
0.80 0.09 0.11
Matches are distributed among these distances:
174 38 0.06
175 4 0.01
176 2 0.00
177 1 0.00
178 74 0.12
179 84 0.14
181 2 0.00
182 30 0.05
184 1 0.00
186 3 0.01
187 34 0.06
188 54 0.09
189 4 0.01
190 1 0.00
191 1 0.00
192 71 0.12
193 12 0.02
194 2 0.00
195 1 0.00
196 1 0.00
199 1 0.00
201 1 0.00
202 174 0.29
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (197 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATTTTTAAGTCCAATATC
GCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAAT
CAGCACATTGGCACCATTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTC
AT
Found at i:1976327 original size:19 final size:19
Alignment explanation
Indices: 1976303--1976365 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
1976293 CAAATAGAAC
1976303 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
**
1976322 TGTATC---A-AT-AG-AA
1 TGTATCGATACATAAGTGT
1976335 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
1976354 TGTATCGATACA
1 TGTATCGATACA
1976366 ACGTATCGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
13 6 0.18
14 2 0.06
15 2 0.06
16 2 0.06
17 2 0.06
18 2 0.06
19 18 0.53
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:1976341 original size:32 final size:32
Alignment explanation
Indices: 1976295--1976378 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
1976285 TATCGATACA
1976295 AATAGAACTGTATCGATACATAAGTGTTGTATC
1 AATAGAA-TGTATCGATACATAAGTGTTGTATC
1976328 AATAGAATGTATCGATACATAAGTGTTGTATC
1 AATAGAATGTATCGATACATAAGTGTTGTATC
* * * *
1976360 GATACAACGTATCGCTACA
1 AATAGAATGTATCGATACA
1976379 AAGCTACTAC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 40 0.85
33 7 0.15
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (32 bp):
AATAGAATGTATCGATACATAAGTGTTGTATC
Found at i:1976435 original size:13 final size:13
Alignment explanation
Indices: 1976417--1976444 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1976407 CATTACTCAA
1976417 TGTATCGATACAT
1 TGTATCGATACAT
1976430 TGTATCGATACAT
1 TGTATCGATACAT
1976443 TG
1 TG
1976445 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1976500 original size:16 final size:16
Alignment explanation
Indices: 1976479--1976509 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1976469 ATTTTACCTA
1976479 GATGTATCGATACATT
1 GATGTATCGATACATT
1976495 GATGTATCGATACAT
1 GATGTATCGATACAT
1976510 GCAAGCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (16 bp):
GATGTATCGATACATT
Found at i:1981855 original size:29 final size:29
Alignment explanation
Indices: 1981784--1982178 Score: 446
Period size: 29 Copynumber: 13.6 Consensus size: 29
1981774 ACTATCATCT
*
1981784 AGTGGCATCTTTTCAAAA-CCCACAAGTC
1 AGTGGCATCCTTTCAAAAGCCCACAAGTC
**
1981812 AGTGGCATTTTTTTCAAAAGCCCACAAGTC
1 AGTGGCA-TCCTTTCAAAAGCCCACAAGTC
*
1981842 AGTGGCATCCTTTCAAAAGCCCACAAGTT
1 AGTGGCATCCTTTCAAAAGCCCACAAGTC
*
1981871 AGTGGTATCCTTTTCAAAA-CCCACAAGTCC
1 AGTGGCATCC-TTTCAAAAGCCCACAAGT-C
* *
1981901 A-TGGTATCCTTTTCGAAAGCCCACAAGTC
1 AGTGGCATCC-TTTCAAAAGCCCACAAGTC
*
1981930 AGTGGCATCCTTTCAAAAGCCCACTAGTC
1 AGTGGCATCCTTTCAAAAGCCCACAAGTC
* *
1981959 AGGGGCATCATTTCAAAAGCCCACAAGTC
1 AGTGGCATCCTTTCAAAAGCCCACAAGTC
* * *
1981988 AGTGGTATCCTTTTC-AAAGCCCATAAGTG
1 AGTGGCATCC-TTTCAAAAGCCCACAAGTC
* * *
1982017 AGTGGCATCATTTTC-AAAGCCTACAAGTT
1 AGTGGCATC-CTTTCAAAAGCCCACAAGTC
*
1982046 AGTAGCATCCTTTCAAAAGCCCACAAGTC
1 AGTGGCATCCTTTCAAAAGCCCACAAGTC
*
1982075 AATGGCATCCTTTTC-AAAGCCCACAAGTC
1 AGTGGCATCC-TTTCAAAAGCCCACAAGTC
*
1982104 AGTGGCATCCTTTTC-AAAGCTCACAAGTC
1 AGTGGCATCC-TTTCAAAAGCCCACAAGTC
* *
1982133 AGTGGCGTCATTTTC-AAAGCCCACAAGTC
1 AGTGGCATC-CTTTCAAAAGCCCACAAGTC
* *
1982162 AATGGTATCCTTTCAAA
1 AGTGGCATCCTTTCAAA
1982179 GCCTGCAAGT
Statistics
Matches: 317, Mismatches: 38, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
28 15 0.05
29 252 0.79
30 50 0.16
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (29 bp):
AGTGGCATCCTTTCAAAAGCCCACAAGTC
Found at i:1982054 original size:87 final size:87
Alignment explanation
Indices: 1981783--1982181 Score: 504
Period size: 87 Copynumber: 4.6 Consensus size: 87
1981773 TACTATCATC
* * * **
1981783 TAGTGGCATCTTTTCAAAA-CCCACAAGTCAGTGGCATTTTTTTCAAAAGCCCACAAGTCAGTGG
1 TAGTGGCATCATTTCAAAAGCCCACAAGTCAATGGTATCCTTTTC-AAAGCCCACAAGTCAGTGG
1981847 CATCCTTTCAAAAGCCCACAAGT
65 CATCCTTTCAAAAGCCCACAAGT
* * *
1981870 TAGTGGTATCCTTTTCAAAA-CCCACAAGTCCATGGTATCCTTTTCGAAAGCCCACAAGTCAGTG
1 TAGTGGCAT-CATTTCAAAAGCCCACAAGTCAATGGTATCCTTTTC-AAAGCCCACAAGTCAGTG
*
1981934 GCATCCTTTCAAAAGCCCACTAGT
64 GCATCCTTTCAAAAGCCCACAAGT
* * * * *
1981958 CAGGGGCATCATTTCAAAAGCCCACAAGTCAGTGGTATCCTTTTCAAAGCCCATAAGTGAGTGGC
1 TAGTGGCATCATTTCAAAAGCCCACAAGTCAATGGTATCCTTTTCAAAGCCCACAAGTCAGTGGC
* *
1982023 ATCATTTTC-AAAGCCTACAAGT
66 ATC-CTTTCAAAAGCCCACAAGT
* * *
1982045 TAGTAGCATCCTTTCAAAAGCCCACAAGTCAATGGCATCCTTTTCAAAGCCCACAAGTCAGTGGC
1 TAGTGGCATCATTTCAAAAGCCCACAAGTCAATGGTATCCTTTTCAAAGCCCACAAGTCAGTGGC
*
1982110 ATCCTTTTC-AAAGCTCACAAGT
66 ATCC-TTTCAAAAGCCCACAAGT
* *
1982132 CAGTGGCGTCATTTTC-AAAGCCCACAAGTCAATGGTATCC-TTTCAAAGCC
1 TAGTGGCATCA-TTTCAAAAGCCCACAAGTCAATGGTATCCTTTTCAAAGCC
1982182 TGCAAGTTAG
Statistics
Matches: 272, Mismatches: 35, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
86 10 0.04
87 154 0.57
88 108 0.40
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (87 bp):
TAGTGGCATCATTTCAAAAGCCCACAAGTCAATGGTATCCTTTTCAAAGCCCACAAGTCAGTGGC
ATCCTTTCAAAAGCCCACAAGT
Found at i:1983627 original size:13 final size:12
Alignment explanation
Indices: 1983608--1983650 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
1983598 GGTTCAACTA
1983608 AAAAAAAGAGAG
1 AAAAAAAGAGAG
*
1983620 AGAAAAAAGGGAG
1 A-AAAAAAGAGAG
1983633 AAAGAAAAGAGA-
1 AAA-AAAAGAGAG
1983645 AAAAAA
1 AAAAAA
1983651 TAAAAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 3 0.11
12 6 0.22
13 18 0.67
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAGAG
Found at i:1985511 original size:96 final size:96
Alignment explanation
Indices: 1985375--1985600 Score: 310
Period size: 96 Copynumber: 2.3 Consensus size: 96
1985365 ACTCCAATCA
* * * * *
1985375 ATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAGCACATCAAAGTTTAAATTTTGTTCTCACT
1 ATTCCTCC-AAGGGATACTCCAACCCCGTTTTTAAACACATCAAAGTTTAAATCTTATTCTCACT
* * *
1985440 TAAATTGTCACCATTGGGGACACTTCAA-CCC
65 TAAATTGTCACCATTGGGAACAATCCAACCCC
1985471 ATTCCTCCAAGGGAATACTCCAACCCCGTTTTTAAACACATCAAAGTTTAAATCTTATTCTCACT
1 ATTCCTCCAAGGG-ATACTCCAACCCCGTTTTTAAACACATCAAAGTTTAAATCTTATTCTCACT
*
1985536 TAAATTGTCATCATTGGGAACAATCCAACCCC
65 TAAATTGTCACCATTGGGAACAATCCAACCCC
* * *
1985568 ATTCCTCCAAAAGGATACTCCAATCTCGTTTTT
1 ATTCCTCC-AAGGGATACTCCAACCCCGTTTTT
1985601 CAATCAAAAA
Statistics
Matches: 115, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
95 4 0.03
96 79 0.69
97 28 0.24
98 4 0.03
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.31
Consensus pattern (96 bp):
ATTCCTCCAAGGGATACTCCAACCCCGTTTTTAAACACATCAAAGTTTAAATCTTATTCTCACTT
AAATTGTCACCATTGGGAACAATCCAACCCC
Found at i:1988667 original size:55 final size:55
Alignment explanation
Indices: 1988520--1988708 Score: 258
Period size: 55 Copynumber: 3.4 Consensus size: 55
1988510 CTACCATTTA
* * *
1988520 GTGGCATTTCTTTTCAAAGTCTACAACTCCGTGGCATCTTTTTAAGTCCACAACTCC
1 GTGGCA-TCCTTTT-AAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCC
*
1988577 GTGGCA--CTTTTTAAGTCCACAACAT-CGTGGCATCCTTTTAAGTCCACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAAC-TCCGTGGCATCCTTTTAAGTCCACAACTCC
* *
1988630 GTGGCATCCTTTTAAAGTCCACAACTCCGTGGTATCCTTTTAAGTCCACAACTCA
1 GTGGCATCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCC
* *
1988685 GTGGCATCCTTTCAAAGCCCACAA
1 GTGGCATCCTTTTAAAGTCCACAA
1988709 GCTAGGAACA
Statistics
Matches: 120, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
53 43 0.36
54 7 0.06
55 64 0.53
57 6 0.05
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.31
Consensus pattern (55 bp):
GTGGCATCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCC
Found at i:1988693 original size:27 final size:27
Alignment explanation
Indices: 1988536--1988696 Score: 245
Period size: 27 Copynumber: 6.0 Consensus size: 27
1988526 TTTCTTTTCA
* *
1988536 AAGTCTACAACTCCGTGGCATCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
1988563 AAGTCCACAACTCCGTGGCA-CTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
1988589 AAGTCCACAACAT-CGTGGCATCCTTTT
1 AAGTCCACAAC-TCCGTGGCATCCTTTT
1988616 AAGTCCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
1988643 AAAGTCCACAACTCCGTGGTATCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
*
1988671 AAGTCCACAACTCAGTGGCATCCTTT
1 AAGTCCACAACTCCGTGGCATCCTTT
1988697 CAAAGCCCAC
Statistics
Matches: 125, Mismatches: 5, Indels: 8
0.91 0.04 0.06
Matches are distributed among these distances:
26 25 0.20
27 74 0.59
28 26 0.21
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCATCCTTTT
Found at i:1988817 original size:29 final size:29
Alignment explanation
Indices: 1988603--1989742 Score: 1009
Period size: 29 Copynumber: 39.8 Consensus size: 29
1988593 CCACAACATC
* * * *
1988603 GTGGCATCCTTT--TAAGTCCACAACTCC
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* * * *
1988630 GTGGCATCCTTT-TAAAGTCCACAACTCC
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* * * *
1988658 GTGGTATCCTTT--TAAGTCCACAACTCA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
1988685 GTGGCATCCTTTC-AAAGCCCACAAG-CTA
1 GTGGCATCCTTTCAAAAGCCCACAAGTC-A
*
1988713 G-GAACA-CCTTTTC-AAAGCCCACAAGAT-A
1 GTG-GCATCC-TTTCAAAAGCCCACAAG-TCA
* * *
1988741 GTGGCATCTTTTC-AAGGCCCATAAGAT-A
1 GTGGCATCCTTTCAAAAGCCCACAAG-TCA
* *
1988769 GTGGCAT-CTTTTATAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* *
1988797 ATGGCATCCTTTCAAAAGCCCCCAAGTCA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
*
1988826 GTGGCATCCCTTTC-AAAGCCCACAAGACA
1 GTGGCAT-CCTTTCAAAAGCCCACAAGTCA
* * *
1988855 GTGGCATCTTTTC-AAATCTCACAAGTCA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* ** * *
1988883 GTGGTATTTTTTCAAATGCCCATAAGTCA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* * * *
1988912 ATGACATCCTTTCAAAAGCCCACAAATAA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* * * *
1988941 ATGGCATCCTTTCAAAAACTCACAAGAC-
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
*
1988969 GTGGCATCTTTTC-AAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* * *
1988997 GTGGCATCTTTTCAAAAGCTCACAAGAC-
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* * *
1989025 GTGGCATCTTTTCAAAAGCTCACAAGAC-
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* * * *
1989053 GTGGCATCTTTTC-AAAGCTCACATGTTA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* *
1989081 GTGGCATCTTTTCAAAAGCCCATAAGTCA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
*
1989110 GTGGCATCCTTTCAAAAGCCCATAAGTCA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* * * * *
1989139 ATGGTATCTTTTCAAAAGCCCACAAATTA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* * *
1989168 GTGGCATCTTTTCAAAAGCCTACAAGCCA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* *
1989197 CTAGCATCCTTTCAAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* * * *
1989226 CTGGTATCCTTTTC-AAAGCCCATAAGTGA
1 GTGGCATCC-TTTCAAAAGCCCACAAGTCA
* * *
1989255 ATGTCATCATTTTC-AAAGCCCACAAGTCA
1 GTGGCATC-CTTTCAAAAGCCCACAAGTCA
*
1989284 GTGGTATCCTTTTC-AAAGCCCACAAGTCCA
1 GTGGCATCC-TTTCAAAAGCCCACAAGT-CA
* *
1989314 -TGGCATCCTTTTCAAAAACCCACAAATCA
1 GTGGCATCC-TTTCAAAAGCCCACAAGTCA
* *
1989343 GTGGCATCCTTTCAAAAGCCCATAAGTTA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* *
1989372 ATGGCATCCTTTCAAAAGCCCACAAGTTA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* *
1989401 GTGGTATCCTTTTC-AAAGCCCATAAGTCCA
1 GTGGCATCC-TTTCAAAAGCCCACAAGT-CA
*
1989431 -TGGCATCCTTTTCAAAAGCCCACAAATCA
1 GTGGCATCC-TTTCAAAAGCCCACAAGTCA
1989460 GTGGCATCCTTTCAAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
*
1989489 GTGGCATCCTTTCAAAAGCCCACAAGTTA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
* * *
1989518 GTGGTATCCTTTTCAAAA-CCCATAAGTGA
1 GTGGCATCC-TTTCAAAAGCCCACAAGTCA
* *
1989547 ATGGCATCCTTTTC-AAAGCCCACAAGTTA
1 GTGGCATCC-TTTCAAAAGCCCACAAGTCA
*
1989576 GTGGCATCCTTTCAAAAGGCCACAAGTCCA
1 GTGGCATCCTTTCAAAAGCCCACAAGT-CA
*
1989606 -TGGCATCCTTTTC-AAAGCCCACAAGTTA
1 GTGGCATCC-TTTCAAAAGCCCACAAGTCA
* *
1989634 GTGGCATCCTTTTC-AAAGCTCACAAGTTA
1 GTGGCATCC-TTTCAAAAGCCCACAAGTCA
* *
1989663 GTGGCAACATTTTC-AAAGCCCACAAGTCA
1 GTGGCATC-CTTTCAAAAGCCCACAAGTCA
*
1989692 GTGGCATCCTTTC-AAAGTCCACAAGTCA
1 GTGGCATCCTTTCAAAAGCCCACAAGTCA
*
1989720 GTGGCAACCATTTTC-AAAGCCCA
1 GTGGCATCC--TTTCAAAAGCCCA
1989743 TACAAGTTAA
Statistics
Matches: 940, Mismatches: 136, Indels: 71
0.82 0.12 0.06
Matches are distributed among these distances:
27 66 0.07
28 238 0.25
29 557 0.59
30 79 0.08
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.26
Consensus pattern (29 bp):
GTGGCATCCTTTCAAAAGCCCACAAGTCA
Found at i:1991124 original size:14 final size:15
Alignment explanation
Indices: 1991105--1991136 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1991095 AGGTTCAACT
1991105 AAAAAAAAGAG-GAA
1 AAAAAAAAGAGAGAA
1991119 AAAAAAAAGAGAGAA
1 AAAAAAAAGAGAGAA
1991134 AAA
1 AAA
1991137 TATAGAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAGAGAA
Done.