Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 65 of 202
Found at i:19129691 original size:14 final size:14
Alignment explanation
Indices: 19129672--19129704 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
19129662 AAAATTTAAC
19129672 TATACTAAAATGAT
1 TATACTAAAATGAT
19129686 TATACTAAAATGAT
1 TATACTAAAATGAT
*
19129700 CATAC
1 TATAC
19129705 ATACAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (14 bp):
TATACTAAAATGAT
Found at i:19140497 original size:17 final size:17
Alignment explanation
Indices: 19140470--19140502 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19140460 TCACTACATT
19140470 TTTATTTCACATATTCAC
1 TTTATTTCACA-ATTCAC
19140488 TTTA-TTCACAATTCA
1 TTTATTTCACAATTCA
19140503 TAAAAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTATTTCACAATTCAC
Found at i:19140801 original size:16 final size:17
Alignment explanation
Indices: 19140782--19140814 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19140772 CTTTTCTTTC
19140782 TTTTC-TCCCTTTATTT
1 TTTTCTTCCCTTTATTT
*
19140798 TTTTCTTTCCTTTATTT
1 TTTTCTTCCCTTTATTT
19140815 CCCTTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTCTTCCCTTTATTT
Found at i:19146588 original size:18 final size:18
Alignment explanation
Indices: 19146565--19146613 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
19146555 AAAAAAGTAT
19146565 TTTAAAAATATTTTAAAA
1 TTTAAAAATATTTTAAAA
**
19146583 TTTAAAAA-AAATTAAAA
1 TTTAAAAATATTTTAAAA
*
19146600 TAATAAAAATATTT
1 T-TTAAAAATATTT
19146614 ATTATATTCG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 8 0.33
18 14 0.58
19 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAAAAATATTTTAAAA
Found at i:19147473 original size:20 final size:20
Alignment explanation
Indices: 19147445--19147486 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
19147435 GATAATTAAC
* *
19147445 CTTAGTTTAATTATATAATA
1 CTTAATTTAATTAAATAATA
19147465 CTTAATTTAATTAAATAATA
1 CTTAATTTAATTAAATAATA
19147485 CT
1 CT
19147487 CACATAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (20 bp):
CTTAATTTAATTAAATAATA
Found at i:19153951 original size:1 final size:1
Alignment explanation
Indices: 19153945--19153982 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
19153935 ATCAATTCAC
* *
19153945 TTTTTTTTTTTTATTTTTTTTCTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19153983 GGGGGGGGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.03, C:0.03, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:19154788 original size:16 final size:16
Alignment explanation
Indices: 19154759--19154791 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19154749 TTCCTATCCA
19154759 TCTTTGCTTTTTTTTT
1 TCTTTGCTTTTTTTTT
*
19154775 TCTTT-CTTTGTTTTT
1 TCTTTGCTTTTTTTTT
19154790 TC
1 TC
19154792 CCTTTGTAAA
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:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (16 bp):
TCTTTGCTTTTTTTTT
Found at i:19170880 original size:69 final size:69
Alignment explanation
Indices: 19170769--19170906 Score: 258
Period size: 69 Copynumber: 2.0 Consensus size: 69
19170759 CAAAGGTGAG
* *
19170769 AAAGAAAAAAATATATATATATACATATAATATTATACTATTATACTAATATATGAGCAGGTCAT
1 AAAGAAAAAAAAATATATATATACATATAATATTATACTATTATACTAATATATGAACAGGTCAT
19170834 AGCT
66 AGCT
19170838 AAAGAAAAAAAAATATATATATACATATAATATTATACTATTATACTAATATATGAACAGGTCAT
1 AAAGAAAAAAAAATATATATATACATATAATATTATACTATTATACTAATATATGAACAGGTCAT
19170903 AGCT
66 AGCT
19170907 CACGAAGGCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.51, C:0.09, G:0.08, T:0.33
Consensus pattern (69 bp):
AAAGAAAAAAAAATATATATATACATATAATATTATACTATTATACTAATATATGAACAGGTCAT
AGCT
Found at i:19177925 original size:3 final size:3
Alignment explanation
Indices: 19177917--19177951 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19177907 TAGAAAATAC
19177917 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19177952 ATGGGGATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19181030 original size:10 final size:11
Alignment explanation
Indices: 19180994--19181024 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
19180984 CTAATTTCAC
19180994 ATTTAAAAATT
1 ATTTAAAAATT
19181005 ATTTAAAAATT
1 ATTTAAAAATT
*
19181016 GTTTAAAAA
1 ATTTAAAAA
19181025 AATTTATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
ATTTAAAAATT
Found at i:19185229 original size:2 final size:2
Alignment explanation
Indices: 19185222--19185250 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19185212 TCAAGGGATT
19185222 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19185251 CATTTTATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19190900 original size:140 final size:140
Alignment explanation
Indices: 19190648--19191333 Score: 626
Period size: 140 Copynumber: 5.0 Consensus size: 140
19190638 ATGCTTACTG
* ** * * *** *
19190648 CGACACTTTTGGGGCGACACTTTTTTAAGTGTTGGGATAAACTTGTCGACATATGTTTTAGCCAA
1 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCAA
* * * *
19190713 CTTTTTGTATAAGAGTTGGGATATGCATGCCTAAGGTAACACTTAAATAAGAATCAGCTTTATCC
66 CTCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTCAGCTTTGTCC
19190778 AACACTATGC
131 AACACTATGC
* *
19190788 CGACACTTTTGGGCCGACACTTTCCTAAATGTTGGGATAGACTTGCCGATATACACTTTGGCCAA
1 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCAA
* *
19190853 CTCTTTATATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAG-GTCGGCTTTGTCC
66 CTCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTCAGCTTTGTCC
19190917 AACACTATGC
131 AACACTATGC
*
19190927 AGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCAA
1 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCAA
* * * * *
19190992 CCCTTTGTATAAGAGTTGGAATATGCATGCCTAAGACAACGA-TTAAATAAGAGTCAGTTTTGTT
66 CTCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAAC-ACTTAAATAAGAGTCAGCTTTGTC
*
19191056 CAACACTATGT
130 CAACACTATGC
** *** ** * * * * *
19191067 CGACACTTTT---CAAAGTGTTGTGGTAGACTTGTTGGCAT--ACGTT-TTGGTCA-ACTCTTTG
1 CGACACTTTTGGGCCGACACTT-TCCTA-A-GTGTTGGGATAGAC-TTGTCGAT-ATACACTTTG
*** *** * * *
19191125 TATAAGAGTTGGTAT---A--T-------GCATGCCTAAGGCAACACTTAAATAAGAGTCGGTTT
61 GCCAACTCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTCAGCTT
*
19191178 TGTCCAACACGATGC
126 TGTCCAACACTATGC
* * ** **
19191193 CGACACTTTTGGGCCAACACTTTCCTAAGTGTTGGGATAGACTTGCCGGCATATGCTTTGGCCAA
1 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCAA
* * * * *
19191258 CTCTTTGTATAAGGGTCGGGATATGCATGCCTAAGGCAACTA-TTAAATAAAAG-CCGATTTTGT
66 CTCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAAC-ACTTAAATAAGAGTCAG-CTTTGT
19191321 CCAACACTATGC
129 CCAACACTATGC
19191333 C
1 C
19191334 AACTTGTGTT
Statistics
Matches: 439, Mismatches: 78, Indels: 58
0.76 0.14 0.10
Matches are distributed among these distances:
125 1 0.00
126 62 0.14
127 4 0.01
128 21 0.05
129 5 0.01
133 1 0.00
135 1 0.00
137 4 0.01
138 23 0.05
139 133 0.30
140 183 0.42
141 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (140 bp):
CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCAA
CTCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTCAGCTTTGTCC
AACACTATGC
Found at i:19191166 original size:126 final size:126
Alignment explanation
Indices: 19190939--19191333 Score: 364
Period size: 126 Copynumber: 3.0 Consensus size: 126
19190929 ACACTTTTGG
* * *
19190939 GCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCAACCCTTTGTATAA
1 GCCGACACTTTTCAAAGTGTTGGGATAGACTTGTCGACATACACTTTGGCCAACCCTTTGTATAA
* *
19191004 GAGTTGGAATATGCATGCCTAAGACAACGATTAAATAAGAGTCAGTTTTGTTCAACACTAT
66 GAGTTGGAATATGCATGCCTAAGACAACGATTAAATAAGAGTCAGTTTTGTCCAACACGAT
* * * ** * *
19191065 GTCGACACTTTTCAAAGTGTTGTGG-TAGACTTGTTGGCATACGTTTTGGTCAACTCTTTGTATA
1 GCCGACACTTTTCAAAGTGTTG-GGATAGACTTGTCGACATACACTTTGGCCAACCCTTTGTATA
* * *
19191129 AGAGTTGGTATATGCATGCCTAAGGCAAC-ACTTAAATAAGAGTCGGTTTTGTCCAACACGAT
65 AGAGTTGGAATATGCATGCCTAAGACAACGA-TTAAATAAGAGTCAGTTTTGTCCAACACGAT
* * **
19191191 GCCGACACTTTTGGGCCAACACTTTCCTAAGTGTTGGGATAGACTTGCCGGCATATGCTTTGGCC
1 GCCGACACTTTT-------CA-------AAGTGTTGGGATAGACTTGTCGACATACACTTTGGCC
* * * * * * * *
19191256 AACTCTTTGTATAAGGGTCGGGATATGCATGCCTAAGGCAACTATTAAATAAAAG-CCGATTTTG
52 AACCCTTTGTATAAGAGTTGGAATATGCATGCCTAAGACAACGATTAAATAAGAGTCAG-TTTTG
*
19191320 TCCAACACTAT
116 TCCAACACGAT
19191331 GCC
1 GCC
19191334 AACTTGTGTT
Statistics
Matches: 223, Mismatches: 27, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
125 1 0.00
126 117 0.52
127 2 0.01
133 2 0.01
139 4 0.02
140 96 0.43
141 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (126 bp):
GCCGACACTTTTCAAAGTGTTGGGATAGACTTGTCGACATACACTTTGGCCAACCCTTTGTATAA
GAGTTGGAATATGCATGCCTAAGACAACGATTAAATAAGAGTCAGTTTTGTCCAACACGAT
Found at i:19191284 original size:266 final size:265
Alignment explanation
Indices: 19190844--19191331 Score: 762
Period size: 266 Copynumber: 1.8 Consensus size: 265
19190834 CGATATACAC
19190844 TTTGGCCAACTCTTTATATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGGTCGG
1 TTTGGCCAACTCTTTATATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGGTCGG
* * *
19190909 CTTTGTCCAACACTATGCAGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTC
66 CTTTGTCCAACACGATGCAGACACTTTTGGGCCAACACTTTCCTAAGTGTTGGGATAGACTTGCC
* *
19190974 GATATACACTTTGGCCAACCCTTTGTATAAGAGTTGGAATATGCATGCCTAAGACAACGATTAAA
131 GACATACACTTTGGCCAACCCTTTGTATAAGAGTCGGAATATGCATGCCTAAGACAACGATTAAA
* *
19191039 TAAGAGTCAG-TTTTGTTCAACACTATGTCGACACTTTTCAAAGTGTTGTGGTAGACTTGTTGGC
196 TAAAAG-CAGATTTTGTCCAACACTATGTCGACACTTTTCAAAGTGTTGTGGTAGACTTGTTGGC
19191103 ATACGT
260 ATACGT
* * *
19191109 TTTGGTCAACTCTTTGTATAAGAGTTGGTATATGCATGCCTAAGGCAACACTTAAATAAGAGTCG
1 TTTGGCCAACTCTTTATATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAG-GTCG
* *
19191174 GTTTTGTCCAACACGATGCCGACACTTTTGGGCCAACACTTTCCTAAGTGTTGGGATAGACTTGC
65 GCTTTGTCCAACACGATGCAGACACTTTTGGGCCAACACTTTCCTAAGTGTTGGGATAGACTTGC
* ** * * * * *
19191239 CGGCATATGCTTTGGCCAACTCTTTGTATAAGGGTCGGGATATGCATGCCTAAGGCAACTATTAA
130 CGACATACACTTTGGCCAACCCTTTGTATAAGAGTCGGAATATGCATGCCTAAGACAACGATTAA
*
19191304 ATAAAAGCCGATTTTGTCCAACACTATG
195 ATAAAAGCAGATTTTGTCCAACACTATG
19191332 CCAACTTGTG
Statistics
Matches: 200, Mismatches: 21, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
265 59 0.29
266 141 0.70
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (265 bp):
TTTGGCCAACTCTTTATATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGGTCGG
CTTTGTCCAACACGATGCAGACACTTTTGGGCCAACACTTTCCTAAGTGTTGGGATAGACTTGCC
GACATACACTTTGGCCAACCCTTTGTATAAGAGTCGGAATATGCATGCCTAAGACAACGATTAAA
TAAAAGCAGATTTTGTCCAACACTATGTCGACACTTTTCAAAGTGTTGTGGTAGACTTGTTGGCA
TACGT
Found at i:19193072 original size:13 final size:13
Alignment explanation
Indices: 19193054--19193130 Score: 82
Period size: 13 Copynumber: 5.9 Consensus size: 13
19193044 AGTTATTCAT
19193054 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
19193067 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
** * *
19193080 TGCCGTGGAGAAG
1 TGCTTTTGAAAAG
* *
19193093 TGCTTTTCAGAAG
1 TGCTTTTGAAAAG
* *
19193106 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
19193119 TGCTTTTGAAAA
1 TGCTTTTGAAAA
19193131 TTTTGAGTGT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 52 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:19195813 original size:36 final size:36
Alignment explanation
Indices: 19195714--19196154 Score: 389
Period size: 36 Copynumber: 12.0 Consensus size: 36
19195704 AAAAAAAATA
* * * *
19195714 CCTTATACGTGTCTATCTCAACCTTTTT-AAGGTTA
1 CCTTAGACGAGTCTATCCCAACCTTTTTAAAGGTTG
* *
19195749 CTTTAGACGAGTTTATCCCAACCTTTTTTAAAGGTTG
1 CCTTAGACGAGTCTATCCCAACC-TTTTTAAAGGTTG
*
19195786 CCTTAAACGAGTCTATCCCAACCTTTTTAAA-GTTG
1 CCTTAGACGAGTCTATCCCAACCTTTTTAAAGGTTG
* * *
19195821 CCTTAAACGGGTCTATCCCAACCTTTTTTAAAAGTTG
1 CCTTAGACGAGTCTATCCCAACC-TTTTTAAAGGTTG
** *
19195858 CCTTAGATAAGGTTTATCCCAACCTTTTT-AAGGTTG
1 CCTTAGACGA-GTCTATCCCAACCTTTTTAAAGGTTG
* *
19195894 CCTTAGACGGGTCTATCCCAACCTTTTTTAAAGGTCG
1 CCTTAGACGAGTCTATCCCAACC-TTTTTAAAGGTTG
* * * *
19195931 ACTTAGAC-ATGGTTTAT-CCAAACTTTTTAAAGGTTA
1 CCTTAGACGA--GTCTATCCCAACCTTTTTAAAGGTTG
* * *
19195967 TCTTAGAC-AGGTTTATCCCAACAATTTTTTTATAGAGGTTG
1 CCTTAGACGA-GTCTATCCCAAC---CTTTTTA-A-AGGTTG
* * *
19196008 TCTTAGACAAGGTCTATCTCAACCTTTTT-AAGGTTG
1 CCTTAGACGA-GTCTATCCCAACCTTTTTAAAGGTTG
* *
19196044 CCTTAGACG-GCTCTATCCCAACTATTTTTTAAAAGTTG
1 CCTTAGACGAG-TCTATCCCAAC--CTTTTTAAAGGTTG
*
19196082 CCTTAGACAAGTTCTATCCCAACCTTTTT-AAGGTTG
1 CCTTAGACGAG-TCTATCCCAACCTTTTTAAAGGTTG
19196118 CCTTAGACG-GATCTATCCCAACCTTTTTTAAAGGTTG
1 CCTTAGACGAG-TCTATCCCAACC-TTTTTAAAGGTTG
19196155 GTCTTGATTA
Statistics
Matches: 338, Mismatches: 45, Indels: 44
0.79 0.11 0.10
Matches are distributed among these distances:
34 1 0.00
35 86 0.25
36 94 0.28
37 77 0.23
38 31 0.09
39 23 0.07
40 1 0.00
41 13 0.04
42 12 0.04
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (36 bp):
CCTTAGACGAGTCTATCCCAACCTTTTTAAAGGTTG
Found at i:19195894 original size:73 final size:73
Alignment explanation
Indices: 19195727--19196154 Score: 520
Period size: 73 Copynumber: 5.8 Consensus size: 73
19195717 TATACGTGTC
* * * * * *
19195727 TATCTCAACCTTTTTAAGGTTACTTTAGACGAGTTTATCCCAACCTTTTTTAAAGGTTGCCTTAA
1 TATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTAAAGGTTGCCTTAG
* *
19195792 ACGA-GTC
66 ACAAGGTT
* * *
19195799 TATCCCAACCTTTTTAAAGTTGCCTTAAACGGGTCTATCCCAACCTTTTTTAAAAGTTGCCTTAG
1 TATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTAAAGGTTGCCTTAG
*
19195864 ATAAGGTT
66 ACAAGGTT
* *
19195872 TATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTAAAGGTCGACTTAG
1 TATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTAAAGGTTGCCTTAG
*
19195937 ACATGGTT
66 ACAAGGTT
* ** * * * *
19195945 TAT-CCAAACTTTTTAAAGGTTATCTTAGACAGGTTTATCCCAACAATTTTTTTATAGAGGTTGT
1 TATCCCAACCTTTTT-AAGGTTGCCTTAGACGGGTCTATCCCAAC--CTTTTTTA-A-AGGTTGC
*
19196009 CTTAGACAAGGTC
61 CTTAGACAAGGTT
* * * *
19196022 TATCTCAACCTTTTTAAGGTTGCCTTAGACGGCTCTATCCCAACTATTTTTTAAAAGTTGCCTTA
1 TATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAAC-CTTTTTTAAAGGTTGCCTTA
19196087 GACAA-GTT
65 GACAAGGTT
*
19196095 CTATCCCAACCTTTTTAAGGTTGCCTTAGACGGATCTATCCCAACCTTTTTTAAAGGTTG
1 -TATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTAAAGGTTG
19196155 GTCTTGATTA
Statistics
Matches: 303, Mismatches: 45, Indels: 15
0.83 0.12 0.04
Matches are distributed among these distances:
72 68 0.22
73 111 0.37
74 56 0.18
75 8 0.03
76 8 0.03
77 43 0.14
78 9 0.03
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (73 bp):
TATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTAAAGGTTGCCTTAG
ACAAGGTT
Found at i:19196718 original size:2 final size:2
Alignment explanation
Indices: 19196711--19196767 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
19196701 CAAAAACCTA
19196711 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
19196753 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
19196768 AAGATACATG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19201076 original size:27 final size:27
Alignment explanation
Indices: 19201045--19201098 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
19201035 ATAGTTGGAA
19201045 AATTGCCCAATTTTTGAAATTAGTCTT
1 AATTGCCCAATTTTTGAAATTAGTCTT
*
19201072 AATTGCCCAATTTTTTAAATTAGTCTT
1 AATTGCCCAATTTTTGAAATTAGTCTT
19201099 CTACATGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (27 bp):
AATTGCCCAATTTTTGAAATTAGTCTT
Found at i:19208613 original size:44 final size:42
Alignment explanation
Indices: 19208502--19208616 Score: 160
Period size: 42 Copynumber: 2.7 Consensus size: 42
19208492 ATGGCCCGGA
*
19208502 CACACGCCCATGTCCTTGCCTGTGTGGCTCACACAGCCTGGG
1 CACACGCCCATGTCCTTGCCTGTGTGGCTCAAACAGCCTGGG
*
19208544 CACACGCCCATGTCCTTGCCTGTGTGGCTCAAACAGCTTGGG
1 CACACGCCCATGTCCTTGCCTGTGTGGCTCAAACAGCCTGGG
* *
19208586 CAAACACACCCATGTCCCTAGCC-GTGTGGCT
1 C--ACACGCCCATGT-CCTTGCCTGTGTGGCT
19208617 TCGATTGTCT
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
42 41 0.62
44 19 0.29
45 6 0.09
ACGTcount: A:0.17, C:0.37, G:0.24, T:0.22
Consensus pattern (42 bp):
CACACGCCCATGTCCTTGCCTGTGTGGCTCAAACAGCCTGGG
Found at i:19210621 original size:29 final size:28
Alignment explanation
Indices: 19210584--19210642 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
19210574 AAGTAGATTG
19210584 TAAAAGGTTTCTAGTTAAGCCACAAAAGC
1 TAAAAGGTTT-TAGTTAAGCCACAAAAGC
* * *
19210613 TAAAGGGTTTTAGTTAAGCTATAAAAGC
1 TAAAAGGTTTTAGTTAAGCCACAAAAGC
19210641 TA
1 TA
19210643 GGAAGAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.29
Consensus pattern (28 bp):
TAAAAGGTTTTAGTTAAGCCACAAAAGC
Found at i:19216997 original size:9 final size:9
Alignment explanation
Indices: 19216985--19217031 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
19216975 ATATAAAAAA
19216985 AATTAACCG
1 AATTAACCG
*
19216994 AATTAACTG
1 AATTAACCG
*
19217003 ACTTAACCG
1 AATTAACCG
*
19217012 AATTAATCG
1 AATTAACCG
19217021 AATTAACCG
1 AATTAACCG
19217030 AA
1 AA
19217032 ATTTAAGTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:19231685 original size:36 final size:36
Alignment explanation
Indices: 19231645--19231715 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
19231635 TTTAAATTAA
* *
19231645 TTAAATTATCTATCGGATATTCAAATATGTTAAATG
1 TTAAATTATCGATCGGATATTCAAATATGCTAAATG
*
19231681 TTAAATTATCGGTCGGATATTCAAATATGCTAAAT
1 TTAAATTATCGATCGGATATTCAAATATGCTAAAT
19231716 ATCTACATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (36 bp):
TTAAATTATCGATCGGATATTCAAATATGCTAAATG
Found at i:19233098 original size:30 final size:30
Alignment explanation
Indices: 19233062--19233133 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
19233052 CAATTGAACT
* *
19233062 TAAATTTTTAAATTTGAAAAATA-GAGAGAC
1 TAAATTTTTAAATATAAAAAATATGAG-GAC
*
19233092 TAAATTTTTAAAAATAAAAAATATGAGGAC
1 TAAATTTTTAAATATAAAAAATATGAGGAC
19233122 TAAA-TTTTAAAT
1 TAAATTTTTAAAT
19233134 GCATAAAGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 7 0.19
30 27 0.73
31 3 0.08
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.35
Consensus pattern (30 bp):
TAAATTTTTAAATATAAAAAATATGAGGAC
Found at i:19239947 original size:99 final size:100
Alignment explanation
Indices: 19239842--19240036 Score: 322
Period size: 99 Copynumber: 2.0 Consensus size: 100
19239832 CTTAAAAATA
* *
19239842 TTTAAAATTTATATTTCATATATTAAAATATTAATAATAAATTATAATAAATT-ATTTTTATATT
1 TTTAAAATTTATATTTCATATATTAAAATATTAACAACAAATTATAATAAATTGATTTTTATATT
*
19239906 ATTACTAACG-TATCATGATATTAACTAATTTATTT
66 ATTACTAA-GATATCATAATATTAACTAATTTATTT
*
19239941 TTTAAAATTTATATTTCATATATTAAAATATTAACAACAAATTATAATAAATTGTTTTTTATATT
1 TTTAAAATTTATATTTCATATATTAAAATATTAACAACAAATTATAATAAATTGATTTTTATATT
*
19240006 CTTACTAAGATATCATAATATTAACTAATTT
66 ATTACTAAGATATCATAATATTAACTAATTT
19240037 GAACATTATT
Statistics
Matches: 89, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
99 52 0.58
100 37 0.42
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (100 bp):
TTTAAAATTTATATTTCATATATTAAAATATTAACAACAAATTATAATAAATTGATTTTTATATT
ATTACTAAGATATCATAATATTAACTAATTTATTT
Found at i:19256292 original size:2 final size:2
Alignment explanation
Indices: 19256287--19256332 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
19256277 AAAAAATACA
19256287 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
19256329 AT AT
1 AT AT
19256333 TCATATGGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19259246 original size:29 final size:29
Alignment explanation
Indices: 19259185--19259248 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
19259175 CAAGTAAAAT
* *
19259185 AAAAAAATTTCACTAACCCTATTTCGTTC
1 AAAAAAATTTCACGAACCCTATTTCATTC
* *
19259214 -AAAAAATTTGAGGAACCCTATTTCATTC
1 AAAAAAATTTCACGAACCCTATTTCATTC
19259242 AAAAAAA
1 AAAAAAA
19259249 ATTTAGCAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAAAAATTTCACGAACCCTATTTCATTC
Found at i:19260301 original size:3 final size:3
Alignment explanation
Indices: 19260293--19260342 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
19260283 TAGTAATGGA
19260293 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
19260341 GA
1 GA
19260343 GATAATGAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:19266606 original size:21 final size:21
Alignment explanation
Indices: 19266567--19266608 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
19266557 AGGGGAACTC
19266567 AATATTTCAATAATTTTAAGTA
1 AATATTTCAAT-ATTTTAAGTA
19266589 AATATTTTCAAT-TTTTAAGT
1 AATA-TTTCAATATTTTAAGT
19266609 GAACACACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 7 0.37
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
AATATTTCAATATTTTAAGTA
Found at i:19268282 original size:27 final size:26
Alignment explanation
Indices: 19268250--19268363 Score: 111
Period size: 27 Copynumber: 4.2 Consensus size: 26
19268240 TTAGATCGCA
*
19268250 ACAAAGGCTTTCATATCTTAATTCACC
1 ACAAAGGCTTTCATCTCTTAA-TCACC
* * **
19268277 AAAAAGGCTTTCATTTCTTAGATCGTC
1 ACAAAGGCTTTCATCTCTTA-ATCACC
* *
19268304 ACAAAGTCTTTCATCTCTTAGGTCACC
1 ACAAAGGCTTTCATCTCTTA-ATCACC
* *
19268331 ACAAAGGCTTTTATCTCTTAAATCGCC
1 ACAAAGGCTTTCATCTCTT-AATCACC
19268358 ACAAAG
1 ACAAAG
19268364 ACTTCTATCT
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
27 69 0.97
28 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (26 bp):
ACAAAGGCTTTCATCTCTTAATCACC
Found at i:19268308 original size:54 final size:53
Alignment explanation
Indices: 19268230--19268363 Score: 151
Period size: 54 Copynumber: 2.5 Consensus size: 53
19268220 TGCCACACGG
* *
19268230 TTTCTATTTTTTAGATCGCAACAAAGGCTTTCATATCTTAATTCACCAAAAAGGC
1 TTTC-ATTTCTTAGATCGC-ACAAAGGCTTTCATATCTTAAGTCACCAAAAAGGC
* * * *
19268285 TTTCATTTCTTAGATCGTCACAAAGTCTTTCATCTCTTAGGTCACCACAAAGGC
1 TTTCATTTCTTAGATCG-CACAAAGGCTTTCATATCTTAAGTCACCAAAAAGGC
* * *
19268339 TTTTATCTCTTAAATCGCCACAAAG
1 TTTCATTTCTTAGATCG-CACAAAG
19268364 ACTTCTATCT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
54 63 0.93
55 5 0.07
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (53 bp):
TTTCATTTCTTAGATCGCACAAAGGCTTTCATATCTTAAGTCACCAAAAAGGC
Found at i:19268372 original size:27 final size:26
Alignment explanation
Indices: 19268240--19268373 Score: 90
Period size: 27 Copynumber: 5.0 Consensus size: 26
19268230 TTTCTATTTT
* * *
19268240 TTAGATCGCAACAAAGGCTTTCATATC
1 TTAGATCGCCACAAAGACTTT-ATCTC
* * * *
19268267 TTA-ATTCACCAAAAAGGCTTTCATTTC
1 TTAGA-TCGCCACAAAGACTTT-ATCTC
* *
19268294 TTAGATCGTCACAAAGTCTTTCATCTC
1 TTAGATCGCCACAAAGACTTT-ATCTC
* * *
19268321 TTAGGTCACCACAAAGGCTTTTATCTC
1 TTAGATCGCCACAAAGAC-TTTATCTC
*
19268348 TTAAATCGCCACAAAGACTTCTATCT
1 TTAGATCGCCACAAAGACTT-TATCT
19268374 TTTTGGTATG
Statistics
Matches: 86, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
26 3 0.03
27 79 0.92
28 4 0.05
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.34
Consensus pattern (26 bp):
TTAGATCGCCACAAAGACTTTATCTC
Found at i:19269589 original size:43 final size:43
Alignment explanation
Indices: 19269535--19269654 Score: 142
Period size: 42 Copynumber: 2.8 Consensus size: 43
19269525 ATAATAAGAG
*
19269535 GAACATATAATAAATCAATACATTGATAGAAT-ATAAT-TA-TGAT
1 GAACATGTAATAAATCAATA-A-T-ATAGAATCATAATATATTGAT
* *
19269578 GAACATGTAATAAATCAAT-ATATATAATCATTATATATTGAT
1 GAACATGTAATAAATCAATAATATAGAATCATAATATATTGAT
*
19269620 GAACATGTAATAAATCAAT-ATATATAATCATAATA
1 GAACATGTAATAAATCAATAATATAGAATCATAATA
19269655 AGGGGGAATG
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
39 6 0.09
40 5 0.07
41 3 0.04
42 38 0.54
43 18 0.26
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (43 bp):
GAACATGTAATAAATCAATAATATAGAATCATAATATATTGAT
Found at i:19278966 original size:20 final size:22
Alignment explanation
Indices: 19278936--19279020 Score: 80
Period size: 22 Copynumber: 3.7 Consensus size: 22
19278926 ATTTATTACG
19278936 TATATATATATTGTAGAATATATAAA
1 TATATATATA-TG-A-AATATA-AAA
*
19278962 AATATATATATGAAATATAAAA
1 TATATATATATGAAATATAAAA
* * *
19278984 TATATACATAAGAAAAATAAAA
1 TATATATATATGAAATATAAAA
* *
19279006 TATATACATAAGAAA
1 TATATATATATGAAA
19279021 AATATGGATT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
22 36 0.67
23 6 0.11
24 1 0.02
25 2 0.04
26 9 0.17
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (22 bp):
TATATATATATGAAATATAAAA
Found at i:19279021 original size:22 final size:22
Alignment explanation
Indices: 19278957--19279024 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
19278947 TGTAGAATAT
* * *
19278957 ATAAAA-ATATATATATGAAAT
1 ATAAAATATATACATAAGAAAA
19278978 ATAAAATATATACATAAGAAAA
1 ATAAAATATATACATAAGAAAA
19279000 ATAAAATATATACATAAGAAAA
1 ATAAAATATATACATAAGAAAA
19279022 ATA
1 ATA
19279025 TGGATTGTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
21 6 0.14
22 37 0.86
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.26
Consensus pattern (22 bp):
ATAAAATATATACATAAGAAAA
Found at i:19279115 original size:26 final size:27
Alignment explanation
Indices: 19279083--19279145 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
19279073 GTATGAAAAT
*
19279083 ATGTGTATATATGTACATAAATTA-AA
1 ATGTGTATATATATACATAAATTATAA
* *
19279109 ATGTGTATATGTATATATAAATTATAA
1 ATGTGTATATATATACATAAATTATAA
*
19279136 A-GTATATATA
1 ATGTGTATATA
19279146 AAATAAAGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 28 0.90
27 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (27 bp):
ATGTGTATATATATACATAAATTATAA
Found at i:19279163 original size:18 final size:17
Alignment explanation
Indices: 19279119--19279155 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
19279109 ATGTGTATAT
19279119 GTATATATAAATTATAAA
1 GTATATATAAA-TATAAA
19279137 GTATATATAAA-ATAAA
1 GTATATATAAATATAAA
19279153 GTA
1 GTA
19279156 GGTATATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (17 bp):
GTATATATAAATATAAA
Found at i:19279232 original size:3 final size:3
Alignment explanation
Indices: 19279218--19279269 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
19279208 GGTATAAATG
19279218 AAT AAGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19279264 AAT AAT
1 AAT AAT
19279270 GATAGTAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19280018 original size:5 final size:5
Alignment explanation
Indices: 19280008--19280045 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
19279998 AAAAAAATCA
* *
19280008 AAAAT AAAAT -AAAT AAAAT AAAAT AAAAC AAGAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
19280046 AACGGAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:19280025 original size:14 final size:14
Alignment explanation
Indices: 19280008--19280034 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19279998 AAAAAAATCA
19280008 AAAATAAAATAAAT
1 AAAATAAAATAAAT
19280022 AAAATAAAATAAA
1 AAAATAAAATAAA
19280035 ACAAGATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:19282413 original size:13 final size:13
Alignment explanation
Indices: 19282395--19282439 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
19282385 AGTTTTTTTT
19282395 TTAAATATTATCA
1 TTAAATATTATCA
*
19282408 TTAAATAAT-TCA
1 TTAAATATTATCA
19282420 --AAATATTATCA
1 TTAAATATTATCA
*
19282431 CTAAATATT
1 TTAAATATT
19282440 TCAAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 6 0.22
11 3 0.11
12 3 0.11
13 15 0.56
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (13 bp):
TTAAATATTATCA
Found at i:19282427 original size:23 final size:23
Alignment explanation
Indices: 19282397--19282446 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
19282387 TTTTTTTTTT
*
19282397 AAATATTATCATTAAATAATTCA
1 AAATATTATCACTAAATAATTCA
*
19282420 AAATATTATCACTAAATATTTCA
1 AAATATTATCACTAAATAATTCA
19282443 AAAT
1 AAAT
19282447 TTAAAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATATTATCACTAAATAATTCA
Found at i:19293678 original size:128 final size:128
Alignment explanation
Indices: 19293450--19293692 Score: 477
Period size: 128 Copynumber: 1.9 Consensus size: 128
19293440 GAATGTCTAA
19293450 TTATGGCTTGTTAATATACGTAATGTTGATAGTAGATAGACATAAAATTGGGTGAGAAGCATGGC
1 TTATGGCTTGTTAATATACGTAATGTTGATAGTAGATAGACATAAAATTGGGTGAGAAGCATGGC
19293515 TTGTAAAATGACCTATTTTCGTTCACAAGAGCAGAGACACGGGCATGTGTGTTATATGGCTTG
66 TTGTAAAATGACCTATTTTCGTTCACAAGAGCAGAGACACGGGCATGTGTGTTATATGGCTTG
*
19293578 TTATGGCTTGTTAATATACGTAATGTTGATAGTAGATAGACATAAAATTGGGTGAGAAGTATGGC
1 TTATGGCTTGTTAATATACGTAATGTTGATAGTAGATAGACATAAAATTGGGTGAGAAGCATGGC
19293643 TTGTAAAATGACCTATTTTCGTTCACAAGAGCAGAGACACGGGCATGTGT
66 TTGTAAAATGACCTATTTTCGTTCACAAGAGCAGAGACACGGGCATGTGT
19293693 CCCCTATTTC
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 114 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.32
Consensus pattern (128 bp):
TTATGGCTTGTTAATATACGTAATGTTGATAGTAGATAGACATAAAATTGGGTGAGAAGCATGGC
TTGTAAAATGACCTATTTTCGTTCACAAGAGCAGAGACACGGGCATGTGTGTTATATGGCTTG
Found at i:19294846 original size:2 final size:2
Alignment explanation
Indices: 19294839--19294925 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
19294829 GTATAAATGT
19294839 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19294881 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19294923 TA T
1 TA T
19294926 GAAATTGATC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19295132 original size:24 final size:24
Alignment explanation
Indices: 19295056--19295132 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
19295046 CTGCTCGGAA
* *
19295056 GAGCATCCTGTTAATAGCCCTCTC-
1 GAGCTTCCTGTTAATAGCTCT-TCG
* *
19295080 GAGCTTCCCGTT-ATATGATTCTT-G
1 GAGCTTCCTGTTAATA-G-CTCTTCG
19295104 CGAGCTTCCTGTTAATAGCTCTTCG
1 -GAGCTTCCTGTTAATAGCTCTTCG
19295129 GAGC
1 GAGC
19295133 ATCCAGATCG
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
23 3 0.07
24 20 0.49
25 15 0.37
26 3 0.07
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (24 bp):
GAGCTTCCTGTTAATAGCTCTTCG
Found at i:19295291 original size:25 final size:25
Alignment explanation
Indices: 19295263--19295311 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
19295253 TTGCTTGAAC
19295263 TTCCCAA-TATATGGCTATTCGGAGT
1 TTCCCAATTA-ATGGCTATTCGGAGT
* *
19295288 TTCCCGATTAATGGCTCTTCGGAG
1 TTCCCAATTAATGGCTATTCGGAG
19295312 CTACCCGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (25 bp):
TTCCCAATTAATGGCTATTCGGAGT
Found at i:19295340 original size:74 final size:75
Alignment explanation
Indices: 19295196--19295369 Score: 178
Period size: 74 Copynumber: 2.4 Consensus size: 75
19295186 AGTGTCCGTC
* * * * * * *
19295196 ATATGGCTCTTCGTGAGCTTCCCGATTAAAGTCTCTTTGTGAGCTTCCTGATATGGCTTGCTTGA
1 ATATGGCTATTCGTGAGCTTCCCGATTAAAGGCTCTTCGTGAGCTACCCGATATGGCTCGCATGA
19295261 ACTTCCCAAT
66 ACTTCCCAAT
* * *
19295271 ATATGGCTATTCG-GAGTTTCCCGATTAATGGCTCTTCG-GAGCTACCCGTTATGGGCTCGCATG
1 ATATGGCTATTCGTGAGCTTCCCGATTAAAGGCTCTTCGTGAGCTACCCGATAT-GGCTCGCATG
* *
19295334 AGCTTCCTAAT
65 AACTTCCCAAT
* *
19295345 -TATGGCTCTT-ATGAGCTTCCC-ATTA
1 ATATGGCTATTCGTGAGCTTCCCGATTA
19295370 TACAGCCCCG
Statistics
Matches: 82, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
72 4 0.05
73 28 0.34
74 38 0.46
75 12 0.15
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (75 bp):
ATATGGCTATTCGTGAGCTTCCCGATTAAAGGCTCTTCGTGAGCTACCCGATATGGCTCGCATGA
ACTTCCCAAT
Found at i:19300044 original size:3 final size:3
Alignment explanation
Indices: 19300036--19300061 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19300026 ATAACGAACA
19300036 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
19300062 ACGTGTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19302425 original size:2 final size:2
Alignment explanation
Indices: 19302418--19302442 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19302408 TTCTTGTTGC
19302418 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19302443 TTGTATTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19303765 original size:20 final size:21
Alignment explanation
Indices: 19303734--19303773 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
19303724 GTTAAAAAAA
19303734 TTAGTAAAAATATATATAATG
1 TTAGTAAAAATATATATAATG
*
19303755 TTAGT-AAAATATATTTAAT
1 TTAGTAAAAATATATATAAT
19303774 TACTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (21 bp):
TTAGTAAAAATATATATAATG
Found at i:19303780 original size:18 final size:19
Alignment explanation
Indices: 19303740--19303782 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
19303730 AAAATTAGTA
*
19303740 AAAATATATATAATGTTAGT
1 AAAATATATATAA-GTTACT
*
19303760 AAAATATATTTAA-TTACT
1 AAAATATATATAAGTTACT
19303778 AAAAT
1 AAAAT
19303783 TAATAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
20 12 0.57
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (19 bp):
AAAATATATATAAGTTACT
Found at i:19305312 original size:26 final size:22
Alignment explanation
Indices: 19305260--19305302 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
19305250 ATGTGAATAA
19305260 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
19305282 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
19305303 ACTATCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:19309426 original size:17 final size:17
Alignment explanation
Indices: 19309383--19309426 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
19309373 ATAGGATTAA
*
19309383 AAATATGTAAAATATAT
1 AAATATATAAAATATAT
19309400 AAATATTATAAAATA-AT
1 AAATA-TATAAAATATAT
19309417 AATATATATA
1 AA-ATATATA
19309427 CGTATGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
AAATATATAAAATATAT
Found at i:19311123 original size:83 final size:84
Alignment explanation
Indices: 19311026--19311564 Score: 325
Period size: 83 Copynumber: 6.4 Consensus size: 84
19311016 ATTTCTTCTG
* *
19311026 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCT-CTCTGCAACCTCAGAAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCCACTGCAACCTCAGAAA
19311090 GATAAGATCTGGATGTTAA
66 GATAAGATCTGGATGTTAA
* * * * * *
19311109 TCTGCTCCACTGCAACTTCAGGGAGATAGGA-TTGATTTCTTCTG-TCTGCTCCACTGTAACTTT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGA----TGC-GATCTGCTCCACTGCAACCTC
* *
19311172 AGGAAGATAAGA-CTGGATG-TGA
61 AGAAAGATAAGATCTGGATGTTAA
* * ** ** * * *
19311194 TCTGCT-CTCTGCAACCTCAGAAAGATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTGGATG-CGATCTGCTCCACTGCAACCTCAGA
* * * *
19311258 GAGATAGGAT-T-GATTTCTTCTA
64 AAGATAAGATCTGGA--TGTT-AA
* * * *
19311280 TCTGCTCCCCTGCAACTTCAGAGAGATAAGACTGGATACGATCTGCT-CTCTGCAACCTCAGAAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCCACTGCAACCTCAGAAA
19311344 GATAAGATCTGGATGTTAA
66 GATAAGATCTGGATGTTAA
* * * * * * *
19311363 TCCGCTCCACTGCAACTTCAGGGAGAT-AGAATTGATTTCTTCTATCTGCTCCCCTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGA----TGCGATCTGCTCCACTGCAACCTCA
** ***
19311427 GGGAGATAAGA-CTGGAT-ACGA
62 GAAAGATAAGATCTGGATGTTAA
* * ** ** * * *
19311448 TCTGCT-CTCTGCAACCTCAGAAAGATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTGGATG-CGATCTGCTCCACTGCAACCTCAGA
* * * **
19311512 GAGATAGGAT-T-GATTTCTTCTG
64 AAGATAAGATCTGGA--TGTT-AA
19311534 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
19311565 TTGTTTCACC
Statistics
Matches: 350, Mismatches: 74, Indels: 60
0.72 0.15 0.12
Matches are distributed among these distances:
82 15 0.04
83 112 0.32
84 60 0.17
85 25 0.07
86 57 0.16
87 81 0.23
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (84 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCCACTGCAACCTCAGAAA
GATAAGATCTGGATGTTAA
Found at i:19311129 original size:127 final size:127
Alignment explanation
Indices: 19310898--19311564 Score: 1190
Period size: 127 Copynumber: 5.3 Consensus size: 127
19310888 GCTATTTTTA
* *
19310898 GTCTACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACCTCAGAAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
19310963 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
66 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
*
19311025 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACCTCAGAAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
*
19311090 GATAAGATCTGGATGTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
66 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
* * * *
19311152 GTCTGCTCCACTGTAACTTTAGGAAGATAAGACTGGATGTGATCTGCTCTCTGCAACCTCAGAAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
19311217 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
66 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
* * * *
19311279 ATCTGCTCCCCTGCAACTTCAGAGAGATAAGACTGGATACGATCTGCTCTCTGCAACCTCAGAAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
*
19311344 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGAATTGATTTCTTCT
66 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
* * *
19311406 ATCTGCTCCCCTGCAACTTCAGGGAGATAAGACTGGATACGATCTGCTCTCTGCAACCTCAGAAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
19311471 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
66 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
19311533 GTCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGA
19311565 TTGTTTCACC
Statistics
Matches: 519, Mismatches: 21, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 519 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (127 bp):
GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
Found at i:19312766 original size:14 final size:13
Alignment explanation
Indices: 19312734--19312769 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
19312724 TCTCCTTTCC
19312734 CTTTTTTTTCTTTT
1 CTTTTTTTTC-TTT
*
19312748 CTTTTCTTTCTTT
1 CTTTTTTTTCTTT
19312761 CTTTTTTTT
1 CTTTTTTTT
19312770 AAGAAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
CTTTTTTTTCTTT
Found at i:19316321 original size:25 final size:25
Alignment explanation
Indices: 19316286--19316347 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
19316276 ATTATGAAAT
*
19316286 GAAT-AAAGAATGATGTA-GAAAAAA
1 GAATAAAAGAATAAT-TACGAAAAAA
**
19316310 GAATAAAAGAATAATTACTCAAAAA
1 GAATAAAAGAATAATTACGAAAAAA
19316335 GAATAAAAGAATA
1 GAATAAAAGAATA
19316348 CTGGCTCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.18
25 27 0.82
ACGTcount: A:0.65, C:0.03, G:0.15, T:0.18
Consensus pattern (25 bp):
GAATAAAAGAATAATTACGAAAAAA
Found at i:19316355 original size:25 final size:25
Alignment explanation
Indices: 19316305--19316359 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
19316295 ATGATGTAGA
*
19316305 AAAAAGAATAAAAGAATAATTACTC
1 AAAAAGAATAAAAGAATAATGACTC
* *
19316330 AAAAAGAATAAAAGAATACTGGCTC
1 AAAAAGAATAAAAGAATAATGACTC
19316355 AAAAA
1 AAAAA
19316360 TGCATACGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.16
Consensus pattern (25 bp):
AAAAAGAATAAAAGAATAATGACTC
Found at i:19323799 original size:17 final size:17
Alignment explanation
Indices: 19323756--19323799 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
19323746 ATAGGATTAA
*
19323756 AAATATGTAAAATATAT
1 AAATATATAAAATATAT
19323773 AAATATTATAAAATA-AT
1 AAATA-TATAAAATATAT
19323790 AATATATATA
1 AA-ATATATA
19323800 CGTATGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
AAATATATAAAATATAT
Found at i:19325956 original size:2 final size:2
Alignment explanation
Indices: 19325949--19325983 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19325939 CAAAATAAAC
19325949 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 A
19325984 ACTCTGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19326148 original size:19 final size:19
Alignment explanation
Indices: 19326124--19326168 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
19326114 AAATGTACTA
* *
19326124 ATTAATTTTTTTGGGCCAC
1 ATTAATTTCTTTGGACCAC
19326143 ATTAATTTCTTTGGACCAC
1 ATTAATTTCTTTGGACCAC
19326162 ATTAATT
1 ATTAATT
19326169 AAAGATCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47
Consensus pattern (19 bp):
ATTAATTTCTTTGGACCAC
Found at i:19327013 original size:24 final size:26
Alignment explanation
Indices: 19326965--19327014 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
19326955 ACATTATTTT
19326965 AATGTAATAGAATAATAATGTATAAAA
1 AATGTAATAGAATAAT-ATGTATAAAA
*
19326992 AATGTGATAGAATAAT-TG-ATAAA
1 AATGTAATAGAATAATATGTATAAA
19327015 TTTATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 2 0.09
27 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30
Consensus pattern (26 bp):
AATGTAATAGAATAATATGTATAAAA
Found at i:19329710 original size:17 final size:17
Alignment explanation
Indices: 19329683--19329728 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 17
19329673 AAAGTTTAGG
19329683 GGGGAAATAAAAAGTTTT
1 GGGGAAAT-AAAAGTTTT
19329701 GGGG-AATAAAAG-TTT
1 GGGGAAATAAAAGTTTT
19329716 GAGGGAAAGTAAA
1 G-GGGAAA-TAAA
19329729 TAGGGGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 5 0.20
18 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.22
Consensus pattern (17 bp):
GGGGAAATAAAAGTTTT
Found at i:19330015 original size:30 final size:31
Alignment explanation
Indices: 19329973--19330033 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
19329963 GGGTTGGGAG
* *
19329973 GGGAAGGGAGTAAAAGTTTTGGGGGGAAAGT
1 GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
19330004 GGGAA-GGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
19330034 AAAAAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (31 bp):
GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:19330096 original size:9 final size:9
Alignment explanation
Indices: 19330082--19330118 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
19330072 TATAGTTTGA
19330082 TATTCGAAT
1 TATTCGAAT
19330091 TATTCGAAT
1 TATTCGAAT
*
19330100 TATTCGAGT
1 TATTCGAAT
19330109 TATTCGAAT
1 TATTCGAAT
19330118 T
1 T
19330119 CGAAAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:19330189 original size:9 final size:9
Alignment explanation
Indices: 19330172--19330202 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19330162 TTGAGTTGAT
19330172 TCGAATAAC
1 TCGAATAAC
*
19330181 TCGATTAAC
1 TCGAATAAC
19330190 TCGAATAAC
1 TCGAATAAC
19330199 TCGA
1 TCGA
19330203 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:19334988 original size:207 final size:207
Alignment explanation
Indices: 19334605--19334994 Score: 462
Period size: 207 Copynumber: 1.9 Consensus size: 207
19334595 TTGTTTATAA
* * **
19334605 AATCAAGGTTCGAAGGTGAAGAGCTGCAACCTCTAACACAGTTAGCGAGAACAAAGCTCTTAAAT
1 AATCAAGGTTAGAAGGTGAAAAGCTGCAACCTCTAACACAGTTAGCGAGAACAAAGCTCCCAAAT
* * *
19334670 GTAAAATCAATGTTAGCTGGATAAGAGCCACGACCTTTAACACAGTTAGCGAGAGTAAAGCTCCT
66 GTAAAATCAATGTTAGCTGGATAAGAGCCACGACCTCTAACACAGTTAGCGAGAGCAAAGATCCT
* * * *
19334735 AGCTGTAAAATCAAGGCTCGCAGGCGAAGAGCCGCGACCCCTAACACAGTTAGCGAAAGTAAAGG
131 AGCTGTAAAATCAAAGCTCGCAAGCAAAGAGCCACGACCCCTAACACAGTTAGCGAAAGTAAAGG
19334800 TCCTAGTGTTAG
196 TCCTAGTGTTAG
* * * * * **
19334812 AATCAAGGTTAGCAGGTGAAAAGTTGCGAA-CTCTAACATAGTTAGTGAGAGCAAAGCTCCCAGT
1 AATCAAGGTTAGAAGGTGAAAAGCTGC-AACCTCTAACACAGTTAGCGAGAACAAAGCTCCCAAA
* * * * * * *
19334876 TGTAAAGTCAATGTTCG-TAGGCA-AAGAGTCATGACCTCTAACATAGTTAGCTAGAGCAAATAT
65 TGTAAAATCAATGTTAGCT-GG-ATAAGAGCCACGACCTCTAACACAGTTAGCGAGAGCAAAGAT
* * * * *
19334939 TCTAGTTGTAAAATCAAAGTTCGCAAGCAAAGAGTCACGACCTCTAACACAGTTAG
128 CCTAGCTGTAAAATCAAAGCTCGCAAGCAAAGAGCCACGACCCCTAACACAGTTAG
19334995 TGAGAGCAAA
Statistics
Matches: 150, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
206 1 0.01
207 146 0.97
208 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (207 bp):
AATCAAGGTTAGAAGGTGAAAAGCTGCAACCTCTAACACAGTTAGCGAGAACAAAGCTCCCAAAT
GTAAAATCAATGTTAGCTGGATAAGAGCCACGACCTCTAACACAGTTAGCGAGAGCAAAGATCCT
AGCTGTAAAATCAAAGCTCGCAAGCAAAGAGCCACGACCCCTAACACAGTTAGCGAAAGTAAAGG
TCCTAGTGTTAG
Found at i:19335025 original size:69 final size:69
Alignment explanation
Indices: 19334633--19335166 Score: 389
Period size: 69 Copynumber: 7.8 Consensus size: 69
19334623 AAGAGCTGCA
* * ** * * *
19334633 ACCTCTAACACAGTTAGCGAGAACAAAGCTCTTAAATGTAAAATCAATGTTAGCTGG-ATAAGAG
1 ACCTCTAACACAGTTAGCGAGAGCAAAGCTCCTAGCTGTAAAATCAAAGTTCGCAGGCA-AAGAG
19334697 CCACG
65 CCACG
* * * * *
19334702 ACCTTTAACACAGTTAGCGAGAGTAAAGCTCCTAGCTGTAAAATCAAGGCTCGCAGGCGAAGAGC
1 ACCTCTAACACAGTTAGCGAGAGCAAAGCTCCTAGCTGTAAAATCAAAGTTCGCAGGCAAAGAGC
*
19334767 CGCG
66 CACG
* * * * * * * *
19334771 ACCCCTAACACAGTTAGCGAAAGTAAAGGTCCTAG-TGTTAGAATCAAGGTTAGCAGGTGAAA-A
1 ACCTCTAACACAGTTAGCGAGAGCAAAGCTCCTAGCTG-TAAAATCAAAGTTCGCAGG-CAAAGA
***
19334834 GTTGCG
64 GCCACG
* * * * * * * * *
19334840 AACTCTAACATAGTTAGTGAGAGCAAAGCTCCCAGTTGTAAAGTCAATGTTCGTAGGCAAAGAGT
1 ACCTCTAACACAGTTAGCGAGAGCAAAGCTCCTAGCTGTAAAATCAAAGTTCGCAGGCAAAGAGC
*
19334905 CATG
66 CACG
* * ** * * * *
19334909 ACCTCTAACATAGTTAGCTAGAGCAAATATTCTAGTTGTAAAATCAAAGTTCGCAAGCAAAGAGT
1 ACCTCTAACACAGTTAGCGAGAGCAAAGCTCCTAGCTGTAAAATCAAAGTTCGCAGGCAAAGAGC
19334974 CACG
66 CACG
* * * * * * *
19334978 ACCTCTAACACAGTTAGTGAGAGCAAAACACCTAGCTGTAAAATCAAAATTCACAAGCGAAGAGC
1 ACCTCTAACACAGTTAGCGAGAGCAAAGCTCCTAGCTGTAAAATCAAAGTTCGCAGGCAAAGAGC
*
19335043 CGCG
66 CACG
* * * * * * ** *
19335047 ACCACTAA-AGCAATTAACGAGAGCAAAACACCTAGCTGTAAAATCAAATTTTACAGGCGAAGAG
1 ACCTCTAACA-CAGTTAGCGAGAGCAAAGCTCCTAGCTGTAAAATCAAAGTTCGCAGGCAAAGAG
* *
19335111 CCGCA
65 CCACG
* * *
19335116 ACCAC-AA-AGCAGTTAGCGAGAGTAAAGCTTCC-AGTTGTAAAATCAAAGTTC
1 ACCTCTAACA-CAGTTAGCGAGAGCAAAGC-TCCTAGCTGTAAAATCAAAGTTC
19335167 ACAAGTGAAG
Statistics
Matches: 377, Mismatches: 81, Indels: 15
0.80 0.17 0.03
Matches are distributed among these distances:
68 41 0.11
69 332 0.88
70 4 0.01
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (69 bp):
ACCTCTAACACAGTTAGCGAGAGCAAAGCTCCTAGCTGTAAAATCAAAGTTCGCAGGCAAAGAGC
CACG
Found at i:19341843 original size:16 final size:16
Alignment explanation
Indices: 19341822--19341858 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
19341812 TCCAAAGTAC
19341822 AATTTTATCATTAATT
1 AATTTTATCATTAATT
19341838 AATTTTATCATTAATT
1 AATTTTATCATTAATT
19341854 AATTT
1 AATTT
19341859 ATAAAGACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTTATCATTAATT
Found at i:19344169 original size:15 final size:16
Alignment explanation
Indices: 19344132--19344169 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
19344122 TGGATACCTA
*
19344132 AAAAAAATATAAATTT
1 AAAAAAATATAAACTT
*
19344148 TAAAAAAT-TAAACTT
1 AAAAAAATATAAACTT
19344163 AAAAAAA
1 AAAAAAA
19344170 CCCAAACTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAAAATATAAACTT
Found at i:19344991 original size:60 final size:60
Alignment explanation
Indices: 19344918--19345040 Score: 237
Period size: 60 Copynumber: 2.0 Consensus size: 60
19344908 ATAATAAGTC
19344918 TTTTCAGTTTAGACTTGCTTATAGGGTGGGCCACTCGGCCCGGCCTGAAAAATGGGAGTA
1 TTTTCAGTTTAGACTTGCTTATAGGGTGGGCCACTCGGCCCGGCCTGAAAAATGGGAGTA
*
19344978 TTTTCAGTTTAGACTTGCTTATAGGGTGGGCCACTCGGTCCGGCCTGAAAAATGGGAGTA
1 TTTTCAGTTTAGACTTGCTTATAGGGTGGGCCACTCGGCCCGGCCTGAAAAATGGGAGTA
19345038 TTT
1 TTT
19345041 AAGTAAAAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (60 bp):
TTTTCAGTTTAGACTTGCTTATAGGGTGGGCCACTCGGCCCGGCCTGAAAAATGGGAGTA
Found at i:19351599 original size:25 final size:25
Alignment explanation
Indices: 19351518--19351586 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
19351508 GGTCACCGAT
19351518 TTCAGCTCGCATGAGCTTCCCATTA
1 TTCAGCTCGCATGAGCTTCCCATTA
* *
19351543 TTCAACTTGCATGAGCTTCCCATTA
1 TTCAGCTCGCATGAGCTTCCCATTA
19351568 TTCAGCTCGCATGAGCTTC
1 TTCAGCTCGCATGAGCTTC
19351587 TTGCTATTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.33
Consensus pattern (25 bp):
TTCAGCTCGCATGAGCTTCCCATTA
Found at i:19359277 original size:35 final size:35
Alignment explanation
Indices: 19359237--19359331 Score: 156
Period size: 35 Copynumber: 2.7 Consensus size: 35
19359227 TCTCTATTTG
*
19359237 GCGTGTTTCGATTGGACTAGCTCTTATAAGCACTGA
1 GCGTGTTTCGGTTGGACTAGCTCTTATAAGCA-TGA
*
19359273 -CGTGTTTCGGTTGGACTAGCTCTTATAAGCATTA
1 GCGTGTTTCGGTTGGACTAGCTCTTATAAGCATGA
19359307 GCGTGTTTCGGTTGGACTAGCTCTT
1 GCGTGTTTCGGTTGGACTAGCTCTT
19359332 GTGAGCATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
34 2 0.04
35 54 0.96
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (35 bp):
GCGTGTTTCGGTTGGACTAGCTCTTATAAGCATGA
Found at i:19361915 original size:35 final size:36
Alignment explanation
Indices: 19361821--19362289 Score: 333
Period size: 35 Copynumber: 12.9 Consensus size: 36
19361811 TGAGACAAAA
* * *
19361821 TCTATCCCAACCTTTTTT-AGTTTACCTTAGACGGG
1 TCTATCCCAACTTTTTTTAAGGTTGCCTTAGACGGG
* * *
19361856 TTTA-CCCTAAC-CTTTTTACGGTTGCCTTAGACGGG
1 TCTATCCC-AACTTTTTTTAAGGTTGCCTTAGACGGG
* * * **
19361891 TTTATCCTAACTTTTTTTAA-GTTGCCTTGGAAAAGG
1 TCTATCCCAACTTTTTTTAAGGTTGCCTTAG-ACGGG
* * * * *
19361927 TCTATACCAAC-TTTTTTACGGTTGCTTTAAATGGG
1 TCTATCCCAACTTTTTTTAAGGTTGCCTTAGACGGG
* * * *
19361962 TCTATCCCAAC-ATTTTTAAGGTTGTCTTAAACGAG
1 TCTATCCCAACTTTTTTTAAGGTTGCCTTAGACGGG
* *
19361997 TCAATCCCAACTTTTTTTAAAAGTTGCCTTAGACAGGG
1 TCTATCCCAACTTTTTTT-AAGGTTGCCTTAGAC-GGG
* ** * * * **
19362035 TCTATCCTAAC-CCTTTTATGGTTGCTTTAGGCATG
1 TCTATCCCAACTTTTTTTAAGGTTGCCTTAGACGGG
* *
19362070 TCTATCCCAACCTTTTTTGAAGGTTGCCTTAGACAAGG
1 TCTATCCCAA-CTTTTTTTAAGGTTGCCTTAGAC-GGG
* * *
19362108 TTTATCCCAACTTTTTTAAAAGGTTGCCTTAGACTGG
1 TCTATCCCAACTTTTTT-TAAGGTTGCCTTAGACGGG
* * *
19362145 CCTCTCCCAACTTTTTTTAAAGGTTGCCTTAGACAAGG
1 TCTATCCCAACTTTTTTT-AAGGTTGCCTTAGAC-GGG
* * **
19362183 TCTATCCCAAC-CTTTTTAAGGTTACCTTAGACGAA
1 TCTATCCCAACTTTTTTTAAGGTTGCCTTAGACGGG
* * ** *
19362218 TCTATCCCAATCTTTTTTAAAGGTTACCTTAGATAAGA
1 TCTATCCCAA-CTTTTTTTAAGGTTGCCTTAGA-CGGG
* *
19362256 TCTATCCTAAATTTTTTTAAAGGTTGCCTTAGAC
1 TCTATCCCAACTTTTTTT-AAGGTTGCCTTAGAC
19362290 AAGGTTTACT
Statistics
Matches: 339, Mismatches: 76, Indels: 36
0.75 0.17 0.08
Matches are distributed among these distances:
34 8 0.02
35 104 0.31
36 58 0.17
37 98 0.29
38 71 0.21
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (36 bp):
TCTATCCCAACTTTTTTTAAGGTTGCCTTAGACGGG
Found at i:19362052 original size:73 final size:73
Alignment explanation
Indices: 19361821--19362341 Score: 368
Period size: 73 Copynumber: 7.2 Consensus size: 73
19361811 TGAGACAAAA
* * * * * * *
19361821 TCTATCCCAACCTTTTTTAGTTTACCTTAGACGGGTTTA-CCCTAAC-CTTTTT-ACGGTTGCCT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATCCC-AACTTTTTTTAAAGGTTGCCT
*
19361883 TAGAC-GGG
65 TAGACAAGG
* * * * ** * * *
19361891 TTTATCCTAACTTTTTTTAA-GTTGCCTTGGAAAAGGTCTATACCAAC-TTTTTT-ACGGTTGCT
1 TCTATCCCAAC-CTTTTTAAGGTTGCCTTAGACGA-GTCTATCCCAACTTTTTTTAAAGGTTGCC
*
19361953 TTA-A-ATGGG
64 TTAGACA-AGG
* * * * *
19361962 TCTATCCCAACATTTTTAAGGTTGTCTTAAACGAGTCAATCCCAACTTTTTTTAAAAGTTGCCTT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATCCCAACTTTTTTTAAAGGTTGCCTT
*
19362027 AGACAGGG
66 AGACAAGG
* * * * * * *
19362035 TCTATCCTAACCCTTTTATGGTTGCTTTAGGC-ATGTCTATCCCAACCTTTTTTGAAGGTTGCCT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGA-GTCTATCCCAACTTTTTTTAAAGGTTGCCT
19362099 TAGACAAGG
65 TAGACAAGG
* * * *
19362108 TTTATCCCAACTTTTTTAAAAGGTTGCCTTAGACTG-GCCTCTCCCAACTTTTTTTAAAGGTTGC
1 TCTATCCCAACCTTTTT--AAGGTTGCCTTAGAC-GAGTCTATCCCAACTTTTTTTAAAGGTTGC
19362172 CTTAGACAAGG
63 CTTAGACAAGG
* * *
19362183 TCTATCCCAACCTTTTTAAGGTTACCTTAGACGAATCTATCCCAA-TCTTTTTTAAAGGTTACCT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATCCCAACT-TTTTTTAAAGGTTGCCT
* *
19362247 TAGATAAGA
65 TAGACAAGG
* ** * * * * * **
19362256 TCTATCCTAAATTTTTTTAAAGGTTGCCTTAGACAAGGTTTA-CTCAACTTTTTTAAAAGATTAT
1 TCTATCC-CAACCTTTTT-AAGGTTGCCTTAGACGA-GTCTATCCCAACTTTTTTTAAAGGTTGC
*
19362320 CTTAGAC-TGG
63 CTTAGACAAGG
*
19362330 TCTATCCTAACC
1 TCTATCCCAACC
19362342 ACTTTCAAAG
Statistics
Matches: 353, Mismatches: 77, Indels: 39
0.75 0.16 0.08
Matches are distributed among these distances:
70 35 0.10
71 56 0.16
72 14 0.04
73 129 0.37
74 16 0.05
75 99 0.28
76 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (73 bp):
TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATCCCAACTTTTTTTAAAGGTTGCCTT
AGACAAGG
Found at i:19362173 original size:148 final size:148
Alignment explanation
Indices: 19362001--19362289 Score: 400
Period size: 148 Copynumber: 2.0 Consensus size: 148
19361991 AACGAGTCAA
* * * * * *
19362001 TCCCAACTTTTTTTAAAAGTTGCCTTAGACAGGGTCTATCCTAACCCTTTTATGGTTGCTTTAGG
1 TCCCAACTTTTTTTAAAAGTTGCCTTAGACAAGGTCTATCCCAACCCTTTTAAGGTTACCTTAGA
* * * * * *
19362066 C-ATGTCTATCCCAACCTTTTTTGAAGGTTGCCTTAGACAAGGTTTATCCCAACTTTTTTAAAAG
66 CGA-ATCTATCCCAACCTTTTTTAAAGGTTACCTTAGACAAGATCTATCCCAAATTTTTTAAAAG
19362130 GTTGCCTTAGACTGGCCTC
130 GTTGCCTTAGACTGGCCTC
* *
19362149 TCCCAACTTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTACCTTAGA
1 TCCCAACTTTTTTTAAAAGTTGCCTTAGACAAGGTCTATCCCAACCCTTTTAAGGTTACCTTAGA
* * * *
19362214 CGAATCTATCCCAATCTTTTTTAAAGGTTACCTTAGATAAGATCTATCCTAAATTTTTTTAAAGG
66 CGAATCTATCCCAACCTTTTTTAAAGGTTACCTTAGACAAGATCTATCCCAAATTTTTTAAAAGG
19362279 TTGCCTTAGAC
131 TTGCCTTAGAC
19362290 AAGGTTTACT
Statistics
Matches: 122, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
148 121 0.99
149 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (148 bp):
TCCCAACTTTTTTTAAAAGTTGCCTTAGACAAGGTCTATCCCAACCCTTTTAAGGTTACCTTAGA
CGAATCTATCCCAACCTTTTTTAAAGGTTACCTTAGACAAGATCTATCCCAAATTTTTTAAAAGG
TTGCCTTAGACTGGCCTC
Found at i:19362304 original size:148 final size:147
Alignment explanation
Indices: 19362001--19362346 Score: 392
Period size: 148 Copynumber: 2.3 Consensus size: 147
19361991 AACGAGTCAA
* * * * * *
19362001 TCCCAACTTTTTTTAAAAGTTGCCTTAGACAGGGTCTATCCTAACCCTTTTATGGTTGCTTTAGG
1 TCCCAACTTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCTAACCCTTTTAAGGTTACCTTAGA
* * * * * *
19362066 CATGTCTATCCCAACCTTTTTTGAAGGTTGCCTTAGACAAGGTTTATCCCAACTTTTTTAAAAGG
66 CATATCTATCCCAACCTTTTTTAAAGGTTACCTTAGACAAGATCTATCCCAAATTTTTTAAAAGG
*
19362131 TTGCCTTAGACTGGCCTC
131 TTGCCTTAGACAGG-CTC
* *
19362149 TCCCAACTTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTACCTTAGA
1 TCCCAACTTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCTAACCCTTTTAAGGTTACCTTAGA
* * * *
19362214 CGA-ATCTATCCCAATCTTTTTTAAAGGTTACCTTAGATAAGATCTATCCTAAATTTTTTTAAAG
66 C-ATATCTATCCCAACCTTTTTTAAAGGTTACCTTAGACAAGATCTATCCCAAATTTTTTAAAAG
*
19362278 GTTGCCTTAGACAAGG-TT
130 GTTGCCTTAGAC-AGGCTC
* * * ** *
19362296 TACTCAACTTTTTTAAAAGATTATCTTAGAC-TGGTCTATCCTAACCACTTT
1 T-CCCAACTTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCTAACC-CTTT
19362347 CAAAGGTTGG
Statistics
Matches: 166, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
147 15 0.09
148 148 0.89
149 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (147 bp):
TCCCAACTTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCTAACCCTTTTAAGGTTACCTTAGA
CATATCTATCCCAACCTTTTTTAAAGGTTACCTTAGACAAGATCTATCCCAAATTTTTTAAAAGG
TTGCCTTAGACAGGCTC
Found at i:19364037 original size:12 final size:12
Alignment explanation
Indices: 19364016--19364048 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
19364006 CTCTTCTAGT
19364016 TCATCATCATCC
1 TCATCATCATCC
*
19364028 TCATCCTCATCC
1 TCATCATCATCC
19364040 TCATCATCA
1 TCATCATCA
19364049 ACCCCACGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.42, G:0.00, T:0.33
Consensus pattern (12 bp):
TCATCATCATCC
Found at i:19372274 original size:16 final size:17
Alignment explanation
Indices: 19372253--19372294 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
19372243 GAAATAACCT
*
19372253 ATAATTTGAA-TTAAAA
1 ATAATTTAAACTTAAAA
19372269 ATAATTTAAACTT-AAA
1 ATAATTTAAACTTAAAA
*
19372285 ATAACTTAAA
1 ATAATTTAAA
19372295 AACCCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (17 bp):
ATAATTTAAACTTAAAA
Found at i:19375514 original size:12 final size:12
Alignment explanation
Indices: 19375493--19375523 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19375483 GGGAATCCAT
*
19375493 GAGAGAGAGAGA
1 GAGAGTGAGAGA
19375505 GAGAGTGAGAGA
1 GAGAGTGAGAGA
19375517 GAGAGTG
1 GAGAGTG
19375524 TGTGTGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.52, T:0.06
Consensus pattern (12 bp):
GAGAGTGAGAGA
Found at i:19377539 original size:20 final size:20
Alignment explanation
Indices: 19377514--19377553 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
19377504 ATTTATTATT
19377514 ATTTCAATTTATATTTGAAG
1 ATTTCAATTTATATTTGAAG
19377534 ATTTCAATTTATATTTGAAG
1 ATTTCAATTTATATTTGAAG
19377554 TTCTAAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (20 bp):
ATTTCAATTTATATTTGAAG
Found at i:19381541 original size:8 final size:7
Alignment explanation
Indices: 19381511--19381538 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
19381501 TATTAATTTT
19381511 TAAAAAA
1 TAAAAAA
19381518 TAAAAAA
1 TAAAAAA
19381525 TAAAAAA
1 TAAAAAA
19381532 TAAAAAA
1 TAAAAAA
19381539 ATACATATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
TAAAAAA
Found at i:19381723 original size:21 final size:21
Alignment explanation
Indices: 19381697--19381740 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19381687 TTTATAATGT
19381697 ATGTATAT-TATTATAAAAATA
1 ATGTATATGTA-TATAAAAATA
*
19381718 ATGTATATGTATATAATAATA
1 ATGTATATGTATATAAAAATA
19381739 AT
1 AT
19381741 AATAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
ATGTATATGTATATAAAAATA
Found at i:19381738 original size:3 final size:3
Alignment explanation
Indices: 19381730--19381811 Score: 164
Period size: 3 Copynumber: 27.3 Consensus size: 3
19381720 GTATATGTAT
19381730 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19381778 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
19381812 GTTGGGATTA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:19383363 original size:6 final size:6
Alignment explanation
Indices: 19383348--19383401 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
19383338 GGTTTTCTCC
* * * * *
19383348 AAATGA AAATTG AAATGA AAATGG AAATGG AAATGT AAATGA AAATGAG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATG-G
19383397 AAATG
1 AAATG
19383402 ATTCATTTAC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
6 34 0.87
7 5 0.13
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.20
Consensus pattern (6 bp):
AAATGG
Found at i:19383375 original size:18 final size:18
Alignment explanation
Indices: 19383348--19383402 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
19383338 GGTTTTCTCC
*
19383348 AAATGAAAATTGAAATGA
1 AAATGAAAATGGAAATGA
* *
19383366 AAATGGAAATGGAAATGT
1 AAATGAAAATGGAAATGA
19383384 AAATGAAAATGAGAAATGA
1 AAATGAAAATG-GAAATGA
19383403 TTCATTTACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
18 25 0.81
19 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.22, T:0.20
Consensus pattern (18 bp):
AAATGAAAATGGAAATGA
Found at i:19383394 original size:12 final size:12
Alignment explanation
Indices: 19383348--19383394 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
19383338 GGTTTTCTCC
19383348 AAATGAAAAT-T
1 AAATGAAAATGT
*
19383359 GAAATGAAAATGG
1 -AAATGAAAATGT
*
19383372 AAATGGAAATGT
1 AAATGAAAATGT
19383384 AAATGAAAATG
1 AAATGAAAATG
19383395 AGAAATGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.21
Consensus pattern (12 bp):
AAATGAAAATGT
Found at i:19386794 original size:27 final size:27
Alignment explanation
Indices: 19386756--19386811 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
19386746 TTAATAACTT
* *
19386756 TTATAGTATTGTTTTGGATATAGATCA
1 TTATAGCATTGTTTTGGATATACATCA
19386783 TTATAGCATTGTTTTGGATATACATCA
1 TTATAGCATTGTTTTGGATATACATCA
19386810 TT
1 TT
19386812 TATTTGCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (27 bp):
TTATAGCATTGTTTTGGATATACATCA
Found at i:19396091 original size:11 final size:11
Alignment explanation
Indices: 19396075--19396103 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
19396065 CGAGTCAATG
19396075 CGACTATATTT
1 CGACTATATTT
19396086 CGACTATATTT
1 CGACTATATTT
19396097 CGACTAT
1 CGACTAT
19396104 CGACAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (11 bp):
CGACTATATTT
Found at i:19402742 original size:36 final size:36
Alignment explanation
Indices: 19402697--19402768 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
19402687 ATTTTAACAA
*
19402697 TTATATTTAATGCAATAAAATATTTATTATATTTAT
1 TTATATTTAATACAATAAAATATTTATTATATTTAT
* *
19402733 TTATTTTTAATATAATAAAATATTTATTATATTTAT
1 TTATATTTAATACAATAAAATATTTATTATATTTAT
19402769 GATAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (36 bp):
TTATATTTAATACAATAAAATATTTATTATATTTAT
Found at i:19402762 original size:26 final size:27
Alignment explanation
Indices: 19402725--19402775 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
19402715 AATATTTATT
*
19402725 ATATTTATTTATTTTTAAT-ATAATAAA
1 ATATTTATTTATATTT-ATGATAATAAA
19402752 ATATTTA-TTATATTTATGATAATA
1 ATATTTATTTATATTTATGATAATA
19402776 TTTTTCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 2 0.09
26 13 0.59
27 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
ATATTTATTTATATTTATGATAATAAA
Found at i:19403324 original size:16 final size:16
Alignment explanation
Indices: 19403303--19403364 Score: 97
Period size: 16 Copynumber: 3.9 Consensus size: 16
19403293 TTTGGTTCGC
19403303 TGTAATGGAATAGATG
1 TGTAATGGAATAGATG
*
19403319 TGTAATGGAATAGAGG
1 TGTAATGGAATAGATG
*
19403335 TGTAATGAAATAGATG
1 TGTAATGGAATAGATG
*
19403351 CGTAATGGAATAGA
1 TGTAATGGAATAGA
19403365 GGCGTAATAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.40, C:0.02, G:0.31, T:0.27
Consensus pattern (16 bp):
TGTAATGGAATAGATG
Found at i:19403347 original size:32 final size:32
Alignment explanation
Indices: 19403303--19403372 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
19403293 TTTGGTTCGC
* *
19403303 TGTAATGGAATAGATGTGTAATGGAATAGAGG
1 TGTAATGAAATAGATGCGTAATGGAATAGAGG
19403335 TGTAATGAAATAGATGCGTAATGGAATAGAGG
1 TGTAATGAAATAGATGCGTAATGGAATAGAGG
*
19403367 CGTAAT
1 TGTAAT
19403373 AGGTAAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.39, C:0.03, G:0.31, T:0.27
Consensus pattern (32 bp):
TGTAATGAAATAGATGCGTAATGGAATAGAGG
Found at i:19403369 original size:16 final size:16
Alignment explanation
Indices: 19403304--19403372 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
19403294 TTGGTTCGCT
* *
19403304 GTAATGGAATAGATGT
1 GTAATGGAATAGAGGC
*
19403320 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
* *
19403336 GTAATGAAATAGATGC
1 GTAATGGAATAGAGGC
19403352 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
19403368 GTAAT
1 GTAAT
19403373 AGGTAAATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:19403417 original size:46 final size:44
Alignment explanation
Indices: 19403354--19403442 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
19403344 ATAGATGCGT
* *
19403354 AATGGAATAGAGGCGTAATAGGTAAATCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGCCGTAAT-GGT-AATCTTGTGTTTGGTTGAATGG
*
19403400 AATGGAATAGAGCCGTAATGGTATTCTTGTGTTTGGTTGAATG
1 AATGGAATAGAGCCGTAATGGTAATCTTGTGTTTGGTTGAATG
19403443 TAATAGAGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 19 0.47
45 3 0.08
46 18 0.45
ACGTcount: A:0.28, C:0.06, G:0.30, T:0.36
Consensus pattern (44 bp):
AATGGAATAGAGCCGTAATGGTAATCTTGTGTTTGGTTGAATGG
Found at i:19403538 original size:16 final size:16
Alignment explanation
Indices: 19403517--19403578 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
19403507 TTTGGTTCCC
19403517 TGTAATGGAATAGATG
1 TGTAATGGAATAGATG
*
19403533 TGTAATGGAATAGAGG
1 TGTAATGGAATAGATG
*
19403549 TGTAATGAAATAGATG
1 TGTAATGGAATAGATG
* *
19403565 CGTAATGTAATAGA
1 TGTAATGGAATAGA
19403579 GGCGTAATAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.40, C:0.02, G:0.29, T:0.29
Consensus pattern (16 bp):
TGTAATGGAATAGATG
Found at i:19403553 original size:32 final size:32
Alignment explanation
Indices: 19403517--19403586 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
19403507 TTTGGTTCCC
* *
19403517 TGTAATGGAATAGATGTGTAATGGAATAGAGG
1 TGTAATGAAATAGATGCGTAATGGAATAGAGG
*
19403549 TGTAATGAAATAGATGCGTAATGTAATAGAGG
1 TGTAATGAAATAGATGCGTAATGGAATAGAGG
*
19403581 CGTAAT
1 TGTAAT
19403587 AGGTAAATCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.39, C:0.03, G:0.30, T:0.29
Consensus pattern (32 bp):
TGTAATGAAATAGATGCGTAATGGAATAGAGG
Found at i:19403583 original size:16 final size:16
Alignment explanation
Indices: 19403518--19403586 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
19403508 TTGGTTCCCT
* *
19403518 GTAATGGAATAGATGT
1 GTAATGGAATAGAGGC
*
19403534 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
* *
19403550 GTAATGAAATAGATGC
1 GTAATGGAATAGAGGC
*
19403566 GTAATGTAATAGAGGC
1 GTAATGGAATAGAGGC
19403582 GTAAT
1 GTAAT
19403587 AGGTAAATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.39, C:0.03, G:0.30, T:0.28
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:19403655 original size:44 final size:46
Alignment explanation
Indices: 19403568--19403656 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 46
19403558 ATAGATGCGT
* * *
19403568 AATGTAATAGAGGCGTAATAGGTAAATCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGCCGTAATAGGTAAATCTTGTGTTTGGTTGAATGG
*
19403614 AATGGAATAGAGCCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATG
1 AATGGAATAGAGCCGTAATAGGTAAATCTTGTGTTTGGTTGAATG
19403657 TAATAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 19 0.49
45 3 0.08
46 17 0.44
ACGTcount: A:0.28, C:0.06, G:0.29, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGCCGTAATAGGTAAATCTTGTGTTTGGTTGAATGG
Found at i:19403662 original size:214 final size:212
Alignment explanation
Indices: 19403293--19403722 Score: 824
Period size: 214 Copynumber: 2.0 Consensus size: 212
19403283 TTACAGCACG
*
19403293 TTTGGTTCGCTGTAATGGAATAGATGTGTAATGGAATAGAGGTGTAATGAAATAGATGCGTAATG
1 TTTGGTTCCCTGTAATGGAATAGATGTGTAATGGAATAGAGGTGTAATGAAATAGATGCGTAATG
19403358 GAATAGAGGCGTAATAGGTAAATCTTTTGTTTGGTTGAATGGAATGGAATAGAGCCGTAATGGTA
66 GAATAGAGGCGTAATAGGTAAATCTTTTGTTTGGTTGAATGGAATGGAATAGAGCCGTAATGGTA
19403423 TTCTTGTGTTTGGTTGAATGTAATAGAGGTGTAATAGCATAAGAAAAAAAAAACTAAAATGACTA
131 TTCTTGTGTTTGGTTGAATGTAATAGAGGTGTAATAGCATAAG--AAAAAAAACTAAAATGACTA
19403488 GAATACCCTTTGCAGAATT
194 GAATACCCTTTGCAGAATT
19403507 TTTGGTTCCCTGTAATGGAATAGATGTGTAATGGAATAGAGGTGTAATGAAATAGATGCGTAATG
1 TTTGGTTCCCTGTAATGGAATAGATGTGTAATGGAATAGAGGTGTAATGAAATAGATGCGTAATG
*
19403572 TAATAGAGGCGTAATAGGTAAATCTTTTGTTTGGTTGAATGGAATGGAATAGAGCCGTAATGGTA
66 GAATAGAGGCGTAATAGGTAAATCTTTTGTTTGGTTGAATGGAATGGAATAGAGCCGTAATGGTA
19403637 TTCTTGTGTTTGGTTGAATGTAATAGAGGTGTAATAGCATAAGAAAAAAAACTAAAATGACTAGA
131 TTCTTGTGTTTGGTTGAATGTAATAGAGGTGTAATAGCATAAGAAAAAAAACTAAAATGACTAGA
19403702 ATACCCTTTGCAGAATT
196 ATACCCTTTGCAGAATT
19403719 TTTG
1 TTTG
19403723 TTAGGTAGAT
Statistics
Matches: 214, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
212 43 0.20
214 171 0.80
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (212 bp):
TTTGGTTCCCTGTAATGGAATAGATGTGTAATGGAATAGAGGTGTAATGAAATAGATGCGTAATG
GAATAGAGGCGTAATAGGTAAATCTTTTGTTTGGTTGAATGGAATGGAATAGAGCCGTAATGGTA
TTCTTGTGTTTGGTTGAATGTAATAGAGGTGTAATAGCATAAGAAAAAAAACTAAAATGACTAGA
ATACCCTTTGCAGAATT
Found at i:19403671 original size:39 final size:41
Alignment explanation
Indices: 19403568--19403673 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 41
19403558 ATAGATGCGT
*
19403568 AATGTAATAGAGGCGTAATAGGTAAATCTTTTGTTTGGTTG
1 AATGTAATAGAGGCGTAATAGGTAAATCTTGTGTTTGGTTG
* *
19403609 AATGGAATGGAATAGAGCCGTAAT-GGT-ATTCTTGTGTTTGGTTG
1 AAT-G--T--AATAGAGGCGTAATAGGTAAATCTTGTGTTTGGTTG
*
19403653 AATGTAATAGAGGTGTAATAG
1 AATGTAATAGAGGCGTAATAG
19403674 CATAAGAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
39 12 0.22
40 1 0.02
41 4 0.07
42 1 0.02
43 1 0.02
44 19 0.35
45 3 0.06
46 13 0.24
ACGTcount: A:0.30, C:0.05, G:0.29, T:0.36
Consensus pattern (41 bp):
AATGTAATAGAGGCGTAATAGGTAAATCTTGTGTTTGGTTG
Found at i:19403872 original size:18 final size:17
Alignment explanation
Indices: 19403820--19403872 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
19403810 TTATTATTAA
19403820 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
19403838 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
19403855 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
19403873 CATAATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 9 0.27
18 24 0.73
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:19415390 original size:51 final size:50
Alignment explanation
Indices: 19415323--19415516 Score: 219
Period size: 51 Copynumber: 3.8 Consensus size: 50
19415313 AAATGATACC
* * * *
19415323 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCA-TATCATT
* * * * * *
19415374 CGATACACGTAGTAGCCTGCAGATAGTACTACACACGTGATCAAAGCTATT
1 CGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATATC-ATT
* * * * *
19415425 TGGTACGCATAGTTGCCTGCACATAGTACTACACATGCGACC-TATCATTT
1 CGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATATCA-TT
19415475 CGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACC
19415517 TAGCAACTTC
Statistics
Matches: 115, Mismatches: 26, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
49 1 0.01
50 42 0.37
51 72 0.63
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (50 bp):
CGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATATCATT
Found at i:19415508 original size:101 final size:101
Alignment explanation
Indices: 19415330--19415514 Score: 282
Period size: 101 Copynumber: 1.8 Consensus size: 101
19415320 ACCCGGTTCA
* * *
19415330 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TATCATCCGATACACATAGTAGCCTGCA
*
19415395 GATAGTACTACACACGTGATCAAAGCTATTTGGTACG
65 CATAGTACTACACACGTGATCAAAGCTATTTGGTACG
* * *
19415432 CATAGTTGCCTGCACATAGTACTACACATGCGACC-TATCATTTCGGTACACATAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATATCA-TCCGATACACATAGTAGCCTGCA
19415496 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
19415515 CCTAGCAACT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
100 4 0.05
101 38 0.51
102 33 0.44
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATATCATCCGATACACATAGTAGCCTGCAC
ATAGTACTACACACGTGATCAAAGCTATTTGGTACG
Found at i:19423447 original size:21 final size:19
Alignment explanation
Indices: 19423423--19423471 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
19423413 TGTGTAACTA
19423423 AATTGTGTAATTATATGCTTG
1 AATTGTGTAATTATATG--TG
** *
19423444 AATTGAATAATTGTATGTG
1 AATTGTGTAATTATATGTG
19423463 AATTGTGTA
1 AATTGTGTA
19423472 TTGGCCATGT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 9 0.39
21 14 0.61
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (19 bp):
AATTGTGTAATTATATGTG
Found at i:19423799 original size:26 final size:26
Alignment explanation
Indices: 19423764--19423847 Score: 95
Period size: 26 Copynumber: 3.3 Consensus size: 26
19423754 GAGCGTCTTG
19423764 TATATGGCTCTTTGTGAGCTTCCTGAT
1 TATATGGCTCTTTGTGAGCTTCCTG-T
19423791 TATA-GGCTCTTTGTGAGCTTCCTGT
1 TATATGGCTCTTTGTGAGCTTCCTGT
** * *
19423816 TAT-T-GCTCGCT-TGAACTTCCCGT
1 TATATGGCTCTTTGTGAGCTTCCTGT
19423839 TATATGGCT
1 TATATGGCT
19423848 ATCCGGTGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
23 13 0.26
24 6 0.12
25 7 0.14
26 20 0.40
27 4 0.08
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (26 bp):
TATATGGCTCTTTGTGAGCTTCCTGT
Found at i:19423896 original size:24 final size:24
Alignment explanation
Indices: 19423864--19423914 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
19423854 TGATTCCTGA
*
19423864 TTAAGTGCTTTTCGAAGCTACCCG
1 TTAAGTGCTCTTCGAAGCTACCCG
* *
19423888 TTAAGTGCTCTTCGGAGGTACCCG
1 TTAAGTGCTCTTCGAAGCTACCCG
19423912 TTA
1 TTA
19423915 TATGCTCGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (24 bp):
TTAAGTGCTCTTCGAAGCTACCCG
Found at i:19429142 original size:14 final size:14
Alignment explanation
Indices: 19429123--19429152 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
19429113 AGGAGATAGT
19429123 GAAAATGGCTCAAG
1 GAAAATGGCTCAAG
19429137 GAAAATGGCTCAAG
1 GAAAATGGCTCAAG
19429151 GA
1 GA
19429153 CTCGAGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.30, T:0.13
Consensus pattern (14 bp):
GAAAATGGCTCAAG
Found at i:19430517 original size:20 final size:21
Alignment explanation
Indices: 19430489--19430527 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
19430479 TGTAAACTTG
*
19430489 AGTGTTTAAATTG-TATTTTT
1 AGTGGTTAAATTGTTATTTTT
19430509 AGTGGTTAAATTGTTATTT
1 AGTGGTTAAATTGTTATTT
19430528 AAGCTTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (21 bp):
AGTGGTTAAATTGTTATTTTT
Found at i:19432939 original size:26 final size:26
Alignment explanation
Indices: 19432872--19432955 Score: 114
Period size: 26 Copynumber: 3.2 Consensus size: 26
19432862 GAAGAAGCTT
* * * *
19432872 TTTCTTTCACATTCTGCCACACAGGC
1 TTTCCTTCATATTATGCCACAAAGGC
*
19432898 TTTTCCTTCATGTTATGCCACAAAGGC
1 -TTTCCTTCATATTATGCCACAAAGGC
19432925 TTTCCTTCATATTATGCCACAAAGGC
1 TTTCCTTCATATTATGCCACAAAGGC
19432951 TTTCC
1 TTTCC
19432956 ACTTGAGAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 30 0.59
27 21 0.41
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (26 bp):
TTTCCTTCATATTATGCCACAAAGGC
Found at i:19437377 original size:48 final size:47
Alignment explanation
Indices: 19437319--19437433 Score: 167
Period size: 48 Copynumber: 2.4 Consensus size: 47
19437309 TAGCTGCAAT
*
19437319 TATGTAGTGGTGTATCCACGATGTGCTATGTGACCGTTCATCGATATC
1 TATGTGGTGGT-TATCCACGATGTGCTATGTGACCGTTCATCGATATC
* * *
19437367 TATGTGGTGGTTTATCCTCGATGTGCTATGTGACTGTTCATCGGTATC
1 TATGTGGTGG-TTATCCACGATGTGCTATGTGACCGTTCATCGATATC
19437415 TATGTGGTGGCTTATCCAC
1 TATGTGGTGG-TTATCCAC
19437434 AAACTGGTGT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 59 0.98
49 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.38
Consensus pattern (47 bp):
TATGTGGTGGTTATCCACGATGTGCTATGTGACCGTTCATCGATATC
Found at i:19437846 original size:14 final size:15
Alignment explanation
Indices: 19437819--19437847 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19437809 TTATTATGGA
19437819 CTTTAAATTGGTTTT
1 CTTTAAATTGGTTTT
19437834 CTTTAAA-TGGTTTT
1 CTTTAAATTGGTTTT
19437848 GATACTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (15 bp):
CTTTAAATTGGTTTT
Found at i:19441473 original size:30 final size:31
Alignment explanation
Indices: 19441437--19441495 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
19441427 AGCAGTCGGT
*
19441437 GTGGG-CCTAAGCCCAGTACAGTAA-CAGTGA
1 GTGGGCCCT-AGCCCAATACAGTAATCAGTGA
19441467 GTGGGCCCTAGCCCAATACAGTAATCAGT
1 GTGGGCCCTAGCCCAATACAGTAATCAGT
19441496 ATAATGCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (31 bp):
GTGGGCCCTAGCCCAATACAGTAATCAGTGA
Found at i:19441883 original size:27 final size:27
Alignment explanation
Indices: 19441853--19441995 Score: 198
Period size: 27 Copynumber: 5.3 Consensus size: 27
19441843 TATAATAGTC
*
19441853 ATTTTACCCCTCGGGGGTATTTCGATA
1 ATTTTACCCTTCGGGGGTATTTCGATA
* *
19441880 ATTTTACCCTTTGGGGGTATTTAGATA
1 ATTTTACCCTTCGGGGGTATTTCGATA
*
19441907 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGGGGGTATTTCGATA
* * *
19441934 ATTTTATCCTTCGGGGCTATTTCGGTA
1 ATTTTACCCTTCGGGGGTATTTCGATA
* *
19441961 ATTTTACCCTTCGAGGGTATTTCGGTA
1 ATTTTACCCTTCGGGGGTATTTCGATA
19441988 A-TTTACCC
1 ATTTTACCC
19441996 CTCAAGTCGC
Statistics
Matches: 103, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 7 0.07
27 96 0.93
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTTCGGGGGTATTTCGATA
Found at i:19442950 original size:17 final size:19
Alignment explanation
Indices: 19442914--19442953 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
19442904 AACCAACAAC
*
19442914 AAGAGAAGAAGAAACTGAA
1 AAGAGAAGAAGAAACAGAA
19442933 AAGA-AAGAAGAAA-AGAA
1 AAGAGAAGAAGAAACAGAA
19442950 AAGA
1 AAGA
19442954 TGAGGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.70, C:0.03, G:0.25, T:0.03
Consensus pattern (19 bp):
AAGAGAAGAAGAAACAGAA
Found at i:19444684 original size:23 final size:21
Alignment explanation
Indices: 19444658--19444698 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19444648 AAGTATCTAT
*
19444658 ATATATATAAATTATAAAAAA
1 ATATATATATATTATAAAAAA
*
19444679 ATATATGTATATTATAAAAA
1 ATATATATATATTATAAAAA
19444699 CGTATGCAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATATATATATTATAAAAAA
Found at i:19447103 original size:17 final size:19
Alignment explanation
Indices: 19447067--19447106 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
19447057 AATCGGCAAC
*
19447067 AAGAGAAGAAGAAATCGAA
1 AAGAGAAGAAGAAATAGAA
19447086 AAGA-AAGAAGAAA-AGAA
1 AAGAGAAGAAGAAATAGAA
19447103 AAGA
1 AAGA
19447107 TGAGGGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.70, C:0.03, G:0.25, T:0.03
Consensus pattern (19 bp):
AAGAGAAGAAGAAATAGAA
Found at i:19451164 original size:27 final size:25
Alignment explanation
Indices: 19451100--19451160 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
19451090 TGTATGTTCG
19451100 CACAAGCTGT-AATCAGAATGCTCA
1 CACAAGCTGTGAATCAGAATGCTCA
*
19451124 CACGAGCTGTGAATCAGAATGCTCA
1 CACAAGCTGTGAATCAGAATGCTCA
19451149 CACAAGCTGTGA
1 CACAAGCTGTGA
19451161 GAATGGGCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 9 0.26
25 25 0.74
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (25 bp):
CACAAGCTGTGAATCAGAATGCTCA
Found at i:19456060 original size:15 final size:16
Alignment explanation
Indices: 19456031--19456060 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19456021 CAACCATGCT
19456031 TTAACACATTATCAAA
1 TTAACACATTATCAAA
19456047 TTAACACA-TATCAA
1 TTAACACATTATCAA
19456061 TAATGTACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:19461565 original size:5 final size:5
Alignment explanation
Indices: 19461555--19461608 Score: 108
Period size: 5 Copynumber: 10.8 Consensus size: 5
19461545 TGCTCTTTAT
19461555 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
19461605 TATT
1 TATT
19461609 TTCTAGTTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 49 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Done.