Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold200
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: 883113
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 55997 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:331 original size:15 final size:14
Alignment explanation
Indices: 297--329 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
287 CTCCATTTTT
297 ATTTTTTCATCATC
1 ATTTTTTCATCATC
311 ATTTTTTCAT--TC
1 ATTTTTTCATCATC
323 ATTTTTT
1 ATTTTTT
330 TTAGGAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
14 10 0.53
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTTTCATCATC
Found at i:12660 original size:186 final size:186
Alignment explanation
Indices: 12346--12718 Score: 620
Period size: 186 Copynumber: 2.0 Consensus size: 186
12336 TAGTGCCTTA
*
12346 GGGAAAATTACTAGCCCATAAATGCTAATAGCAAAGGCATCGACCCCTTTCCTCGCATCAGGGTG
1 GGGAAAATTACTAGCCCATAAATGCTAAGAGCAAAGGCATCGACCCCTTTCCTCGCATCAGGGTG
* * * * * *
12411 CCCCAAAATTAGCTCTTGCAGGTTTTTCCAAGGGATACATTTGCTTTCCCCCTTCTGCTTGATCC
66 CCCCAAAATAAACTCCTGCAGGCTTTTCCAAGGGATACATTTACTTTCCCCCTTCAGCTTGATCC
*
12476 GTGCTGTGACCCACTGCTCACTCATTCCAGTGATGTTCATCAACTTCTTTATAAAG
131 GTGCCGTGACCCACTGCTCACTCATTCCAGTGATGTTCATCAACTTCTTTATAAAG
* * * *
12532 GGGAAAATTACTAGCCCATAAATGCTTAGAGCAAAGGTATCGACCCTTTTCCTCGCATTAGGGTG
1 GGGAAAATTACTAGCCCATAAATGCTAAGAGCAAAGGCATCGACCCCTTTCCTCGCATCAGGGTG
*
12597 CCCCAAAATAAACTCCTGCAGGCTTTTCCAAGGGATACATTTACTTTCCCCCTTCAGCTTGATCT
66 CCCCAAAATAAACTCCTGCAGGCTTTTCCAAGGGATACATTTACTTTCCCCCTTCAGCTTGATCC
*
12662 GTGCCGTGACCCACTGCTCATTCATTCCAGTGATGTTCATCAACTTCTTTATAAAG
131 GTGCCGTGACCCACTGCTCACTCATTCCAGTGATGTTCATCAACTTCTTTATAAAG
12718 G
1 G
12719 TTGGAACATT
Statistics
Matches: 173, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
186 173 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (186 bp):
GGGAAAATTACTAGCCCATAAATGCTAAGAGCAAAGGCATCGACCCCTTTCCTCGCATCAGGGTG
CCCCAAAATAAACTCCTGCAGGCTTTTCCAAGGGATACATTTACTTTCCCCCTTCAGCTTGATCC
GTGCCGTGACCCACTGCTCACTCATTCCAGTGATGTTCATCAACTTCTTTATAAAG
Found at i:13821 original size:23 final size:24
Alignment explanation
Indices: 13781--13825 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
13771 CCACTTTAAA
*
13781 TTTGAAGAAAAAAGGGGAATCGAC
1 TTTGAAGAAAAAAAGGGAATCGAC
13805 TTTGAA-AAAAAAAGGGAATCG
1 TTTGAAGAAAAAAAGGGAATCG
13826 CCACCGATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (24 bp):
TTTGAAGAAAAAAAGGGAATCGAC
Found at i:16600 original size:31 final size:31
Alignment explanation
Indices: 16562--16622 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
16552 ATAAAAAATT
16562 GGGTTAAGTGCGATTGGTGTTCCAAACTATC
1 GGGTTAAGTGCGATTGGTGTTCCAAACTATC
* *
16593 GGGTTAAGTGTGATTGGTGTTCTAAACTAT
1 GGGTTAAGTGCGATTGGTGTTCCAAACTAT
16623 GTGATTCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.36
Consensus pattern (31 bp):
GGGTTAAGTGCGATTGGTGTTCCAAACTATC
Found at i:21610 original size:43 final size:44
Alignment explanation
Indices: 21560--21713 Score: 181
Period size: 43 Copynumber: 3.6 Consensus size: 44
21550 AGTGATACGG
* *
21560 GGAATCAGCAAATAGCAACC-CCTTTCACAATCAAAGATACAGT
1 GGAATCAGCACATAGCAACCACCTTTCATAATCAAAGATACAGT
* * * **
21603 GGAATCAGCACTTAGCAACCACCTTT-ATATTTAGTGATACAG-
1 GGAATCAGCACATAGCAACCACCTTTCATAATCAAAGATACAGT
* * *
21645 GGAATCAACACATAGCAACC-CCTTTCATAATCAAATATACGGT
1 GGAATCAGCACATAGCAACCACCTTTCATAATCAAAGATACAGT
*
21688 GGAATCAGCACTTAGCAACCACCTTT
1 GGAATCAGCACATAGCAACCACCTTT
21714 ATATTCAGTG
Statistics
Matches: 90, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
41 5 0.06
42 28 0.31
43 47 0.52
44 10 0.11
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.23
Consensus pattern (44 bp):
GGAATCAGCACATAGCAACCACCTTTCATAATCAAAGATACAGT
Found at i:21662 original size:42 final size:42
Alignment explanation
Indices: 21525--21749 Score: 233
Period size: 42 Copynumber: 5.3 Consensus size: 42
21515 CGGTGGATTT
*
21525 AGCACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAATC
1 AGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATC
** * * ** *
21566 AGCAAATAGCAACC-CCTTTCACAATCAAAGATACAGTGGAATC
1 AGCACTTAGCAACCACCTTT-ATATTCAGTGATAC-GGGGAATC
* *
21609 AGCACTTAGCAACCACCTTTATATTTAGTGATACAGGGAATC
1 AGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATC
* * * *
21651 AACACATAGCAACC-CCTTTCATAATCAAAT-ATACGGTGGAATC
1 AGCACTTAGCAACCACCTTT-ATATTC-AGTGATACGG-GGAATC
**
21694 AGCACTTAGCAACCACCTTTATATTCAGTGATGTGGGGAATC
1 AGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATC
21736 AGCACTTAGCAACC
1 AGCACTTAGCAACC
21750 TCTTGGGGAA
Statistics
Matches: 147, Mismatches: 28, Indels: 17
0.77 0.15 0.09
Matches are distributed among these distances:
40 2 0.01
41 19 0.13
42 59 0.40
43 57 0.39
44 10 0.07
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (42 bp):
AGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATC
Found at i:21663 original size:85 final size:85
Alignment explanation
Indices: 21525--21749 Score: 344
Period size: 85 Copynumber: 2.7 Consensus size: 85
21515 CGGTGGATTT
* *
21525 AGCACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAATCAGCAAATAGCAACCCCTTTCACA
1 AGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGCACATAGCAACCCCTTTCACA
21589 ATCAAAGATACAGTGGAATC
66 ATCAAAGATACAGTGGAATC
* * * *
21609 AGCACTTAGCAACCACCTTTATATTTAGTGATACAGGGAATCAACACATAGCAACCCCTTTCATA
1 AGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGCACATAGCAACCCCTTTCACA
* *
21674 ATCAAATATACGGTGGAATC
66 ATCAAAGATACAGTGGAATC
** *
21694 AGCACTTAGCAACCACCTTTATATTCAGTGATGTGGGGAATCAGCACTTAGCAACC
1 AGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGCACATAGCAACC
21750 TCTTGGGGAA
Statistics
Matches: 126, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 17 0.13
85 109 0.87
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (85 bp):
AGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGCACATAGCAACCCCTTTCACA
ATCAAAGATACAGTGGAATC
Found at i:21911 original size:19 final size:20
Alignment explanation
Indices: 21862--21912 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
21852 TTCAATCGAG
* *
21862 AACCTTATTTTACAACATTT
1 AACCATATTTTTCAACATTT
*
21882 TACCA-ACTTTTTCAA-ATTT
1 AACCATA-TTTTTCAACATTT
21901 AACCATATTTTT
1 AACCATATTTTT
21913 GTAATCTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (20 bp):
AACCATATTTTTCAACATTT
Found at i:27094 original size:11 final size:11
Alignment explanation
Indices: 27078--27102 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27068 TTTGGGCACC
27078 AATAAGAAGAA
1 AATAAGAAGAA
27089 AATAAGAAGAA
1 AATAAGAAGAA
27100 AAT
1 AAT
27103 GTATTTGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (11 bp):
AATAAGAAGAA
Found at i:28328 original size:40 final size:40
Alignment explanation
Indices: 28282--28498 Score: 267
Period size: 40 Copynumber: 5.5 Consensus size: 40
28272 TAATTATTGT
* * *
28282 TGAATGCATATACGTGCCCCTGTTTGAACTTCGGTACCCT
1 TGAATGCACATACGTGCCCCTATTTGAACTTCGGTACCCC
* * *
28322 TAAATGCACATACGTGCCCCTATTTAAACTTCGGTACCCT
1 TGAATGCACATACGTGCCCCTATTTGAACTTCGGTACCCC
* * * *
28362 TGAATGCACATACGTCCCCCTTTTTGTACTTCAGTACCCC
1 TGAATGCACATACGTGCCCCTATTTGAACTTCGGTACCCC
* **
28402 TGAATGCACATATGTGCCCCTATTTCTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTATTTGAACTTCGGTACCCC
* *
28442 TGAATGCACATACGTGCCCTTGTTT-ATACTTCGGTA-CCC
1 TGAATGCACATACGTGCCCCTATTTGA-ACTTCGGTACCCC
*
28481 TGAACGCACATACGTGCC
1 TGAATGCACATACGTGCC
28499 TTGTTTATAC
Statistics
Matches: 155, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
39 20 0.13
40 135 0.87
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTATTTGAACTTCGGTACCCC
Found at i:33256 original size:40 final size:40
Alignment explanation
Indices: 33210--33426 Score: 267
Period size: 40 Copynumber: 5.5 Consensus size: 40
33200 TAATTATTGT
* * *
33210 TGAATGCATATACGTGCCCCTGTTTGAACTTCGGTACCCT
1 TGAATGCACATACGTGCCCCTATTTGAACTTCGGTACCCC
* * *
33250 TAAATGCACATACGTGCCCCTATTTAAACTTCGGTACCCT
1 TGAATGCACATACGTGCCCCTATTTGAACTTCGGTACCCC
* * * *
33290 TGAATGCACATACGTCCCCCTTTTTGTACTTCAGTACCCC
1 TGAATGCACATACGTGCCCCTATTTGAACTTCGGTACCCC
* **
33330 TGAATGCACATATGTGCCCCTATTTCTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTATTTGAACTTCGGTACCCC
* *
33370 TGAATGCACATACGTGCCCTTGTTT-ATACTTCGGTA-CCC
1 TGAATGCACATACGTGCCCCTATTTGA-ACTTCGGTACCCC
*
33409 TGAACGCACATACGTGCC
1 TGAATGCACATACGTGCC
33427 TTGTTTATAC
Statistics
Matches: 155, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
39 20 0.13
40 135 0.87
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTATTTGAACTTCGGTACCCC
Found at i:38929 original size:26 final size:26
Alignment explanation
Indices: 38882--38932 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
38872 TTAGATAAAA
*
38882 AGGGGTCGCTAAGTGTATATTCCCCG
1 AGGGGTCGCTAAGTGTAGATTCCCCG
*
38908 AGGGGTTGCTAAGTGCT-GATTCCCC
1 AGGGGTCGCTAAGTG-TAGATTCCCC
38933 AAATTATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (26 bp):
AGGGGTCGCTAAGTGTAGATTCCCCG
Found at i:39000 original size:43 final size:43
Alignment explanation
Indices: 38911--39273 Score: 304
Period size: 43 Copynumber: 8.6 Consensus size: 43
38901 TTCCCCGAGG
** * *
38911 GGTTGCTAAGTGCTGATTCC-CCAAAT-TATTGATTTTAAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATAT-TTGAATATAAAGGT
* * *
38953 GGTTGCTAAGTGCTGATTCCACTGTATATTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGTATATTTGAATAT-AAAGGT
* *
38996 GGTTGCTATGTGCTGATT-CACCGTATCA-CTGAATATAAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTAT-ATTTGAATATAAAGGT
* * *
39038 GGTTGCTAAGTGCTTATTCCACCGTATATTTGATTTTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGTATATTTGAATAT-AAAGGT
* * *
39081 GGTTGCTATGTGCTGATTCC-CTGTATCA-CTGAATATAAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTAT-ATTTGAATATAAAGGT
* *
39123 GGTTGCTAAGTGCTGATTCCACCGTATCA-CTAAATATAAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTAT-ATTTGAATATAAAGGT
* * *
39166 GGTTGCTAAGTGCTGATTCCACCGTATCTTT-AACTGTGAAACG-
1 GGTTGCTAAGTGCTGATTCCACCGTATATTTGAA-TAT-AAAGGT
* * * * *
39209 GGTTGCTATGTGCTGATTCC-TCGTATCA-CTGAAT-TTAAGAT
1 GGTTGCTAAGTGCTGATTCCACCGTAT-ATTTGAATATAAAGGT
* *
39250 GGTTACTAAGTGCTGAATCCACCG
1 GGTTGCTAAGTGCTGATTCCACCG
39274 AGTAACGGAT
Statistics
Matches: 265, Mismatches: 38, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
40 2 0.01
41 28 0.11
42 89 0.34
43 131 0.49
44 15 0.06
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACCGTATATTTGAATATAAAGGT
Found at i:39051 original size:85 final size:85
Alignment explanation
Indices: 38908--39193 Score: 371
Period size: 85 Copynumber: 3.4 Consensus size: 85
38898 ATATTCCCCG
* ** * * * *
38908 AGGGGTTGCTAAGTGCTGATTCCCCAAATTATTGATTTTAAAGGTGGTTGCTAAGTGCTGATTCC
1 AGGGGTTGCTAAGTGCTGATTCACCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
* *
38973 ACTGTATATTTGATTGTGAA
66 ACCGTATATTTGATTATGAA
* *
38993 AGGGGTTGCTATGTGCTGATTCACCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTTATTCC
1 AGGGGTTGCTAAGTGCTGATTCACCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
*
39058 ACCGTATATTTGATTTTGAA
66 ACCGTATATTTGATTATGAA
*
39078 AGGGGTTGCTATGTGCTGATTC-CCTGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTC
1 AGGGGTTGCTAAGTGCTGATTCACC-GTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTC
* * *
39142 CACCGTATCA-CTAAATAT-AA
65 CACCGTAT-ATTTGATTATGAA
39162 AGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AGG-GGTTGCTAAGTGCTGATT-CACCGTATC
39194 TTTAACTGTG
Statistics
Matches: 179, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
84 7 0.04
85 163 0.91
86 7 0.04
87 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (85 bp):
AGGGGTTGCTAAGTGCTGATTCACCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
ACCGTATATTTGATTATGAA
Found at i:39159 original size:128 final size:126
Alignment explanation
Indices: 38911--39273 Score: 450
Period size: 128 Copynumber: 2.8 Consensus size: 126
38901 TTCCCCGAGG
** *
38911 GGTTGCTAAGTGCTGATTCC-CCAAATTATTGATTTT-AAAGGTGGTTGCTAAGTGCTGATTCCA
1 GGTTGCTAAGTGCTGATTCCACCGTATT-TTGATTTTGAAAGG-GGTTGCTATGTGCTGATTCC-
* * * *
38974 CTGTAT-ATTTGATTGTGAAAGG-GGTTGCTATGTGCTGATT-CACCGTATCACTGAATATAAAG
63 CTGTATCA-CTGAAT-T-AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTAAATATAAAG
39036 GT
125 GT
*
39038 GGTTGCTAAGTGCTTATTCCACCGTATATTTGATTTTGAAAGGGGTTGCTATGTGCTGATTCCCT
1 GGTTGCTAAGTGCTGATTCCACCGTAT-TTTGATTTTGAAAGGGGTTGCTATGTGCTGATTCCCT
39103 GTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTAAATATAAAGGT
65 GTATCACTGAAT-TAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTAAATATAAAGGT
* * * *
39166 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAACTGTGAAACGGGTTGCTATGTGCTGATT-CCT
1 GGTTGCTAAGTGCTGATTCCACCGTAT-TTTGATTTTGAAAGGGGTTGCTATGTGCTGATTCCCT
* * * *
39230 CGTATCACTGAATTTAAGATGGTTACTAAGTGCTGAATCCACCG
65 -GTATCACTGAATTAAAGGTGGTTGCTAAGTGCTGATTCCACCG
39274 AGTAACGGAT
Statistics
Matches: 210, Mismatches: 19, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
126 5 0.02
127 77 0.37
128 122 0.58
129 6 0.03
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (126 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTTTGATTTTGAAAGGGGTTGCTATGTGCTGATTCCCTG
TATCACTGAATTAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTAAATATAAAGGT
Found at i:56743 original size:17 final size:18
Alignment explanation
Indices: 56729--56812 Score: 80
Period size: 19 Copynumber: 4.4 Consensus size: 18
56719 ATAATCTTCG
56729 AGGATATGCAATCTTAGA
1 AGGATATGCAATCTTAGA
*
56747 TATGATATGCAATCTTAGA
1 -AGGATATGCAATCTTAGA
*
56766 TATGATATATGCAATCTTAGA
1 -A-G-GATATGCAATCTTAGA
* *
56787 TATGATATGTAATCTTAGA
1 -AGGATATGCAATCTTAGA
56806 A-GATATG
1 AGGATATG
56813 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
17 6 0.11
18 1 0.02
19 33 0.58
21 17 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (18 bp):
AGGATATGCAATCTTAGA
Found at i:56755 original size:19 final size:19
Alignment explanation
Indices: 56731--56805 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
56721 AATCTTCGAG
56731 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
56750 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
56769 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
56790 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
56806 AGATATGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 34 0.64
21 19 0.36
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:56777 original size:21 final size:21
Alignment explanation
Indices: 56732--56794 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
56722 ATCTTCGAGG
56732 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
56751 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
56772 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
56793 AT
1 AT
56795 GTAATCTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.45
21 23 0.55
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:56824 original size:23 final size:22
Alignment explanation
Indices: 56744--56828 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 22
56734 ATGCAATCTT
*
56744 AGATATGATATGCAATCTTAG-
1 AGATATGATATGTAATCTTAGA
* *
56765 ATATGAT-ATATGCAATCTT---
1 AGAT-ATGATATGTAATCTTAGA
56784 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
56806 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
56829 GATTTAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.26
21 15 0.28
22 10 0.19
23 13 0.24
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:56838 original size:22 final size:23
Alignment explanation
Indices: 56794--56838 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
56784 AGATATGATA
*
56794 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
56817 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
56839 GTACATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:61698 original size:6 final size:6
Alignment explanation
Indices: 61689--61727 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
61679 TAAAAGTGAT
61689 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA- AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
61728 TGGAGAGTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:63003 original size:44 final size:45
Alignment explanation
Indices: 62921--63559 Score: 624
Period size: 44 Copynumber: 14.5 Consensus size: 45
62911 GCAGATCAGT
* * * *
62921 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* *
62965 GAAGATA-CAAATCTTGTCTTCCTATATTAGTGGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * * *
63009 GAAGAAAGCAGATATTGTCTTCATTTATTGG-CGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * *
63053 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * *
63097 GAAGAT-GCAGATATTGTCTTCATTTATTGG-CGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * *
63140 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* *
63185 GAAGAT-GCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * **
63229 GAAGAAAGCAGATCTTGTCTTCATGTATTGGT-GTAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * * * *
63273 AAAGATAGTAGGTCCTATCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * *
63317 GAAGAT-GCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* ** * ***
63361 GAAGAAAGCAGATCTTGTCTTTATGTATTGG-CATGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * *
63405 GAAAATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * *
63449 GAAGAT-GCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * *
63493 GAAGAAAGCAGATCTTGTCTT-ATGTATTGGT-GTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
*
63536 GAAGATAGCAGATCTTGCCTTCCT
1 GAAGATAGCAGATCTTGTCTTCCT
63560 GCACCGACAG
Statistics
Matches: 477, Mismatches: 104, Indels: 28
0.78 0.17 0.05
Matches are distributed among these distances:
42 1 0.00
43 127 0.27
44 261 0.55
45 88 0.18
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
Found at i:63179 original size:132 final size:132
Alignment explanation
Indices: 62921--63559 Score: 797
Period size: 132 Copynumber: 4.8 Consensus size: 132
62911 GCAGATCAGT
* * * * * * * *
62921 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATA-CAAATCTTGTCT
1 GAAGAT-GCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
* * * * ** * * *
62984 TCCTATATTAGTG-GCGAAGTAGATCGAAGAAAGCAGATATTGTCTTCATTTATTGG-CGTGAAG
65 TCATGTATT-G-GCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAG-GAAG
*
63047 TAGATC
127 TGGATC
* * * * * * * *
63053 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATATTGTCT
1 GAAGAT-GCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
*
63116 TCATTTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTG
65 TCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAG-GAAGTG
63181 GATC
129 GATC
63185 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
1 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* * * * * *
63250 CATGTATTGGTGTAAAGTAGATCAAAGATAGTAGGTCCTATCTTCCTATATTGGTAGGAAGTGGA
66 CATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGA
63315 TC
131 TC
*
63317 GAAGATGCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
1 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* * * *
63382 TATGTATTGGCATGAAGTAGATCGAAAATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGA
66 CATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGA
63447 TC
131 TC
*
63449 GAAGATGCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
1 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* * *
63514 -ATGTATTGGTGTGAAGTAGATCGAAGATAGCAGATCTTGCCTTCCT
66 CATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCT
63560 GCACCGACAG
Statistics
Matches: 457, Mismatches: 45, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
130 1 0.00
131 100 0.22
132 292 0.64
133 64 0.14
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (132 bp):
GAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
CATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGA
TC
Found at i:63745 original size:44 final size:44
Alignment explanation
Indices: 63680--63885 Score: 238
Period size: 44 Copynumber: 4.7 Consensus size: 44
63670 TGACCTCAAC
* *
63680 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTTTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
63724 CCTATCTCCCTGGTCAACAGTGGAATAGGGTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * *
63768 TCTATCTCCCTGGGCAGTAGTGGAAT-GGATTGAAGATTGT-AGGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGG-TTGAAGATTGTGA-AT
* * *
63812 CCTATCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATCGTGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
63856 CCTATCTCCCTGAGT-AGCACTGGAGTAGGT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGT
63886 GAAAAATAGC
Statistics
Matches: 135, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
43 3 0.02
44 128 0.95
45 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:64420 original size:128 final size:129
Alignment explanation
Indices: 64192--64434 Score: 310
Period size: 128 Copynumber: 1.9 Consensus size: 129
64182 ATGGCAAATT
* * * * * *
64192 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCAATAATCCTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTAAAGTTGCAGTGGAACAGACTAAAGTAAATAATCCTATCTCCCTAAAGTTGCAGC
* * * *
64257 GAAGCGGATTAAAACCTTGGGTCTTATCTCTCTGAAGTTTCAG-AGAGCAAAATGTATCTAGTC
66 GAAGCGGATTAAAACCATGGATCTTATCTCTCTGAAATTACAGTAGAGCAAAATGTATCTAGTC
* *
64320 TTATCTCTCTAAAGTTGCAGTGGAACAGACTAAA-TAAACTAATCCTATCTCCCTAAAGTTGTAG
1 TTATCTCCCTAAAGTTGCAGTGGAACAGACTAAAGTAAA-TAATCCTATCTCCCTAAAGTTGCAG
* * * **
64384 CGGAGTGGATTAGAATGATGGATCTTATCTCTCTGAAATTACAGTAGAGCA
65 CGAAGCGGATTAAAACCATGGATCTTATCTCTCTGAAATTACAGTAGAGCA
64435 GATCGCATCA
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
127 3 0.03
128 87 0.91
129 6 0.06
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (129 bp):
TTATCTCCCTAAAGTTGCAGTGGAACAGACTAAAGTAAATAATCCTATCTCCCTAAAGTTGCAGC
GAAGCGGATTAAAACCATGGATCTTATCTCTCTGAAATTACAGTAGAGCAAAATGTATCTAGTC
Found at i:64749 original size:19 final size:19
Alignment explanation
Indices: 64725--64799 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
64715 AATCTTCGAG
64725 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
64744 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
64763 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
64784 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
64800 AGTTATGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 34 0.64
21 19 0.36
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:64771 original size:21 final size:21
Alignment explanation
Indices: 64726--64788 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
64716 ATCTTCGAGG
64726 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
64745 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
64766 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
64787 AT
1 AT
64789 GTAATCTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.45
21 23 0.55
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:82986 original size:15 final size:15
Alignment explanation
Indices: 82966--82996 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
82956 TGAAGAAGAA
*
82966 CCACTAGTGAATGTC
1 CCACTAGTGAAAGTC
82981 CCACTAGTGAAAGTC
1 CCACTAGTGAAAGTC
82996 C
1 C
82997 TTTGGCGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (15 bp):
CCACTAGTGAAAGTC
Found at i:91626 original size:25 final size:25
Alignment explanation
Indices: 91598--91672 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
91588 AACAACCTCT
91598 CAAATTAGATAATCACGTAACTTAA
1 CAAATTAGATAATCACGTAACTTAA
* * **
91623 CAAA-TCG-TCAA--AC--AACCTCT
1 CAAATTAGAT-AATCACGTAACTTAA
91643 CAAATTAGATAATCACGTAACTTAA
1 CAAATTAGATAATCACGTAACTTAA
91668 CAAAT
1 CAAAT
91673 CATCCTAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
20 8 0.23
21 4 0.11
22 3 0.09
23 3 0.09
24 4 0.11
25 13 0.37
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.25
Consensus pattern (25 bp):
CAAATTAGATAATCACGTAACTTAA
Found at i:91637 original size:45 final size:45
Alignment explanation
Indices: 91588--91673 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
91578 CCTAAGCAAG
91588 AACAACCTCTCAAATTAGATAATCACGTAACTTAACAAATCGTCA
1 AACAACCTCTCAAATTAGATAATCACGTAACTTAACAAATCGTCA
91633 AACAACCTCTCAAATTAGATAATCACGTAACTTAACAAATC
1 AACAACCTCTCAAATTAGATAATCACGTAACTTAACAAATC
91674 ATCCTAAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.24
Consensus pattern (45 bp):
AACAACCTCTCAAATTAGATAATCACGTAACTTAACAAATCGTCA
Found at i:96535 original size:43 final size:43
Alignment explanation
Indices: 96488--96617 Score: 165
Period size: 43 Copynumber: 3.0 Consensus size: 43
96478 CATGGTCGTA
*
96488 TCACTTTGCCGTGTGTCACACATGGCTGAGACACACACCTGTG
1 TCACTTTGCCGTGTGTCACACATGGCTGAGACACACACCCGTG
* * * *
96531 TCACTTGGCTGTGTGTCACACATGACTGAGACATACACCCGTG
1 TCACTTTGCCGTGTGTCACACATGGCTGAGACACACACCCGTG
* * *
96574 T--CTCTGCCCGTGTGTCACACACGGCTGAGACACACACCCATG
1 TCACTTTG-CCGTGTGTCACACATGGCTGAGACACACACCCGTG
96616 TC
1 TC
96618 TCTGCTCGTG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
41 3 0.04
42 31 0.42
43 39 0.53
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (43 bp):
TCACTTTGCCGTGTGTCACACATGGCTGAGACACACACCCGTG
Found at i:96602 original size:42 final size:42
Alignment explanation
Indices: 96496--96629 Score: 178
Period size: 42 Copynumber: 3.2 Consensus size: 42
96486 TATCACTTTG
* * *
96496 CCGTGTGTCACACATGGCTGAGACACACACCTGTGTCACTTGG
1 CCGTGTGTCACACATGGCTGAGACACACACCCGTGTCTC-TGC
* * *
96539 CTGTGTGTCACACATGACTGAGACATACACCCGTGTCTCTGC
1 CCGTGTGTCACACATGGCTGAGACACACACCCGTGTCTCTGC
* *
96581 CCGTGTGTCACACACGGCTGAGACACACACCCATGTCTCTGC
1 CCGTGTGTCACACATGGCTGAGACACACACCCGTGTCTCTGC
*
96623 TCGTGTG
1 CCGTGTG
96630 GATGAAAATA
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 45 0.57
43 34 0.43
ACGTcount: A:0.20, C:0.32, G:0.24, T:0.24
Consensus pattern (42 bp):
CCGTGTGTCACACATGGCTGAGACACACACCCGTGTCTCTGC
Found at i:105887 original size:26 final size:26
Alignment explanation
Indices: 105835--105887 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
105825 CACCAATATC
* *
105835 GCAGCATAGCTGCCAATAGTAATAAT
1 GCAGCAGAGCTGCCAATAGTAAGAAT
* *
105861 GCAGCAGAGCTGCCAGTAGTCAGAAT
1 GCAGCAGAGCTGCCAATAGTAAGAAT
105887 G
1 G
105888 GCTAAAAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (26 bp):
GCAGCAGAGCTGCCAATAGTAAGAAT
Found at i:105935 original size:22 final size:22
Alignment explanation
Indices: 105881--105945 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
105871 TGCCAGTAGT
*
105881 CAGAATGGCTAAAAGCTGTAAA
1 CAGAATGGCTAAAAGCTATAAA
* * *
105903 CAGGATAGCTATAAGCTATAAA
1 CAGAATGGCTAAAAGCTATAAA
* * *
105925 TAGAATGGCTACAAGCCATAA
1 CAGAATGGCTAAAAGCTATAA
105946 GTACAGTAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (22 bp):
CAGAATGGCTAAAAGCTATAAA
Found at i:105992 original size:32 final size:32
Alignment explanation
Indices: 105937--106107 Score: 227
Period size: 32 Copynumber: 5.4 Consensus size: 32
105927 GAATGGCTAC
* *
105937 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
105968 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
106000 CAGCCATCAGTAACAGTAATATGATCAGCACC
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
106032 AAGCCATCAGTAACGGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
106064 AAGCCATCAGTAACGGTAATATGATCGGCATA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
106096 AAGCCATTAGTA
1 AAGCCATCAGTA
106108 GTATCGCAGT
Statistics
Matches: 122, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
31 10 0.08
32 112 0.92
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:106353 original size:27 final size:27
Alignment explanation
Indices: 106315--106735 Score: 563
Period size: 27 Copynumber: 15.6 Consensus size: 27
106305 CCACTAGGGC
* *
106315 ATTACGGTTATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
106342 ATTACGGTTATTTTACCCTATAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
** *
106369 ATTACAATCATTATACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
106396 ATTACGATCATTTTACCCTACAGTGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
*
106423 ATTACAGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
106450 ATTACGGTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
**
106477 ATTACGACCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
106504 ATTACAGTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
106531 ATTCCGGTCATTTTACCGTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
106558 ATTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** * *
106585 ATTATAGTCATTTTACCCTATAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
106612 ATTACGATCATTTTACCCTACATGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
106639 ATTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
106666 ATTACGGTCATTTTACCCTACGGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
**
106693 ATTACGGTCATTTGGCCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
106720 ATTACGGTTATTTTAC
1 ATTACGGTCATTTTAC
106736 AAATATTGGG
Statistics
Matches: 345, Mismatches: 49, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 345 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:108779 original size:43 final size:43
Alignment explanation
Indices: 108726--108886 Score: 159
Period size: 43 Copynumber: 3.8 Consensus size: 43
108716 TTCGAGGTGT
* *
108726 GATTTCGTGTAATACCATGTCTGGGACATTGGCATCGATATGA
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATATGA
* * *
108769 GATTACGTGTAAGGCCATGTCTAGGACGTTGGCATCG-TAT-A
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATATGA
* * ** *
108810 TGATT-TGTGTAAGACCCTGTCTGGGACAGAGGCATCGATATGT
1 -GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATATGA
* * * *
108853 GATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCAT
108887 TGTATGTGAT
Statistics
Matches: 94, Mismatches: 20, Indels: 9
0.76 0.16 0.07
Matches are distributed among these distances:
41 26 0.28
42 18 0.19
43 50 0.53
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATATGA
Found at i:110042 original size:18 final size:18
Alignment explanation
Indices: 110021--110057 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
110011 GGAGGACATT
110021 GATATGATTGAATTTGAA
1 GATATGATTGAATTTGAA
110039 GATATGATTGAATTTGAA
1 GATATGATTGAATTTGAA
110057 G
1 G
110058 CACGGTTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (18 bp):
GATATGATTGAATTTGAA
Found at i:111946 original size:24 final size:24
Alignment explanation
Indices: 111902--111948 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
111892 ACGAGCTCAA
* *
111902 AATCGGTATGCTCTTACGAGCTGT
1 AATCGGTAAGCTCCTACGAGCTGT
111926 AATCGGTAAGCTCCT-CTGAGCTG
1 AATCGGTAAGCTCCTAC-GAGCTG
111949 AATAATGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (24 bp):
AATCGGTAAGCTCCTACGAGCTGT
Found at i:121749 original size:57 final size:58
Alignment explanation
Indices: 121670--121785 Score: 225
Period size: 57 Copynumber: 2.0 Consensus size: 58
121660 TAATTACTGA
121670 TTGATTGAAATATTTTTTGAAAATATGGATAGAAAATTTTAATGATTTAGTGCCTAAT
1 TTGATTGAAATATTTTTTGAAAATATGGATAGAAAATTTTAATGATTTAGTGCCTAAT
121728 TTGATTGAAAT-TTTTTTGAAAATATGGATAGAAAATTTTAATGATTTAGTGCCTAAT
1 TTGATTGAAATATTTTTTGAAAATATGGATAGAAAATTTTAATGATTTAGTGCCTAAT
121785 T
1 T
121786 GAATTTTTAG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 47 0.81
58 11 0.19
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.44
Consensus pattern (58 bp):
TTGATTGAAATATTTTTTGAAAATATGGATAGAAAATTTTAATGATTTAGTGCCTAAT
Found at i:129048 original size:51 final size:51
Alignment explanation
Indices: 128968--129155 Score: 206
Period size: 51 Copynumber: 3.7 Consensus size: 51
128958 TATCGCTGAA
* * * *
128968 CACGTGTGTAGTACTATGGGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGATAAATATTGGT
* *
129019 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-TTGGT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGATAAA--TATTGGT
* * * *
129070 CACGTGTGTAGTACTATA-TGGAGGCTACTATGTGGACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTA-AGTGAAGGCTACTACGTGTACCGATAAATA-TTGGT
*
129120 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGTA
129156 TCGAATGATA
Statistics
Matches: 116, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
50 38 0.33
51 76 0.66
52 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGATAAATATTGGT
Found at i:129155 original size:101 final size:102
Alignment explanation
Indices: 128968--129160 Score: 257
Period size: 101 Copynumber: 1.9 Consensus size: 102
128958 TATCGCTGAA
* * *
128968 CACGTGTGTAGTACTATGGGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGGGAAGGCTACTACGTGGACCGATAAATAATGATCACATGTGTAGTAC
*
129033 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTACGTGTACCGAAAAGCTTTGGT
* * * *
129070 CACGTGTGTAGTACTATATGG-AGGCTACTATGTGGACCG-TAAA-ACTTGATCACGTGTGTAGT
1 CACGTGTGTAGTACTAT-GGGAAGGCTACTACGTGGACCGATAAATA-ATGATCACATGTGTAGT
* *
129132 ACTATGTGAAGGCTACTACGTGTATCGAA
64 ACTAAGTGAAGGCTACTACGTGTACCGAA
129161 TGATAATAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
100 1 0.01
101 44 0.56
102 32 0.41
103 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGGGAAGGCTACTACGTGGACCGATAAATAATGATCACATGTGTAGTAC
TAAGTGAAGGCTACTACGTGTACCGAAAAGCTTTGGT
Found at i:135757 original size:51 final size:51
Alignment explanation
Indices: 135677--136016 Score: 340
Period size: 51 Copynumber: 6.7 Consensus size: 51
135667 TATCGCTGAA
* * * * *
135677 CACGTGTGTAGTACTATGGGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGATAAATATTGGT
* * *
135728 CACATGTGTAGTCCTAAGTGAAGGATACTATGTGTACCGA-AAAGCT-TTGGT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGATAAA--TATTGGT
* * *
135779 CACGTGTGTAGTACTATA-TGGAGGCTACTATGTGGACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTA-AGTGAAGGCTACTATGTGTACCGATAAATA-TTGGT
* * * * *
135829 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCAATAAATAATGGT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGATAAATATTGGT
*
135880 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-TTGGT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGATAAA--TATTGGT
* * *
135931 CACGTGTGTAGTACTATA-TGGAGGCTACTATGTGGACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTA-AGTGAAGGCTACTATGTGTACCGATAAATA-TTGGT
* *
135981 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTA
136017 TCGAATGATA
Statistics
Matches: 237, Mismatches: 36, Indels: 33
0.77 0.12 0.11
Matches are distributed among these distances:
50 77 0.32
51 155 0.65
52 5 0.02
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGATAAATATTGGT
Found at i:135913 original size:26 final size:26
Alignment explanation
Indices: 135833--135915 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
135823 CTTGATCACG
*
135833 TGTGTAGTACTATGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
* * *
135859 CGTGTA-TCAATAAAT-AATGG-TCAC-A
1 TGTGTAGT-ACTAAGTGAA-GGCT-ACTA
135884 TGTGTAGTACTAAGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
135910 TGTGTA
1 TGTGTA
135916 CCGAAAAGCT
Statistics
Matches: 43, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
25 19 0.44
26 24 0.56
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGAAGGCTACTA
Found at i:136016 original size:101 final size:100
Alignment explanation
Indices: 135677--136021 Score: 367
Period size: 101 Copynumber: 3.4 Consensus size: 100
135667 TATCGCTGAA
* * * * *
135677 CACGTGTGTAGTACTATGGGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAGTC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGA-AAACT-TTGGTCACGTGTGTAGTA
*
135741 CTA-AGTGAAGGATACTATGTGTACCG-AAAAGCTTTGGT
64 CTATA-TGAAGGCTACTATGTGTACCGTAAAA-C-TTGGT
* * * * *
135779 CACGTGTGTAGTACTATATGGAGGCTACTATGTGGACCGTAAAAC-TTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCG-AAAACTTTGGTCACGTGTGTAGTAC
* * ** *
135843 TATGTGAAGGCTACTACGTGTATCAATAAATA-ATGGT
65 TATATGAAGGCTACTATGTGTA-CCGTAAA-ACTTGGT
* * *
135880 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAAAA-CTTTGGTCACGTGTGTAGTAC
* * *
135945 TATATGGAGGCTACTATGTGGACCGTAAAACTTGAT
65 TATATGAAGGCTACTATGTGTACCGTAAAACTTGGT
*
135981 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAA
136022 TGATAATAAT
Statistics
Matches: 200, Mismatches: 34, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
100 5 0.03
101 117 0.58
102 73 0.37
103 4 0.02
104 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (100 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAAAACTTTGGTCACGTGTGTAGTACT
ATATGAAGGCTACTATGTGTACCGTAAAACTTGGT
Found at i:136053 original size:152 final size:153
Alignment explanation
Indices: 135677--136031 Score: 651
Period size: 152 Copynumber: 2.3 Consensus size: 153
135667 TATCGCTGAA
* *
135677 CACGTGTGTAGTACTATGGGAAGGCTACTACGTGTATCG-ATAAATAATGGTCACATGTGTAGTC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATAAATAATGGTCACATGTGTAGTA
135741 CTAAGTGAAGGATACTATGTGTACCGAAAAGCTTTGGTCACGTGTGTAGTACTATATGGAGGCTA
66 CTAAGTGAAGGATACTATGTGTACCGAAAAGCTTTGGTCACGTGTGTAGTACTATATGGAGGCTA
135806 CTATGTGGACCGTAAAACTTGAT
131 CTATGTGGACCGTAAAACTTGAT
135829 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATC-AATAAATAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATAAATAATGGTCACATGTGTAGTA
*
135893 CTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGTAGTACTATATGGAGGCTA
66 CTAAGTGAAGGATACTATGTGTACCGAAAAGCTTTGGTCACGTGTGTAGTACTATATGGAGGCTA
135958 CTATGTGGACCGTAAAACTTGAT
131 CTATGTGGACCGTAAAACTTGAT
135981 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGATAATAAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAT-A-AATAAT
136032 AACATTGGTA
Statistics
Matches: 196, Mismatches: 3, Indels: 5
0.96 0.01 0.02
Matches are distributed among these distances:
152 186 0.95
153 3 0.02
154 1 0.01
155 6 0.03
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (153 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATAAATAATGGTCACATGTGTAGTA
CTAAGTGAAGGATACTATGTGTACCGAAAAGCTTTGGTCACGTGTGTAGTACTATATGGAGGCTA
CTATGTGGACCGTAAAACTTGAT
Found at i:145407 original size:25 final size:25
Alignment explanation
Indices: 145373--145420 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
145363 TTTAAAGGGG
*
145373 GTAAGACATTTTGCATGAATTTTTA
1 GTAAGACATTTCGCATGAATTTTTA
145398 GTAAGACATTTCGCATGAATTTT
1 GTAAGACATTTCGCATGAATTTT
145421 AAAGCATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (25 bp):
GTAAGACATTTCGCATGAATTTTTA
Found at i:154406 original size:16 final size:15
Alignment explanation
Indices: 154379--154412 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
154369 ATAACTAGTA
*
154379 TATAATTATATTTAT
1 TATAATTATATTAAT
154394 TATAATATATATTAAT
1 TATAAT-TATATTAAT
154410 TAT
1 TAT
154413 TATCGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:156674 original size:48 final size:48
Alignment explanation
Indices: 156622--156715 Score: 179
Period size: 48 Copynumber: 2.0 Consensus size: 48
156612 TAATCGGTCA
*
156622 GTTAACCAAATTTTTTCGGTCCGGGGTCGGTTAATTATTTTTTGATCG
1 GTTAACCAAATTTTTTCGGTCCAGGGTCGGTTAATTATTTTTTGATCG
156670 GTTAACCAAATTTTTTCGGTCCAGGGTCGGTTAATTATTTTTTGAT
1 GTTAACCAAATTTTTTCGGTCCAGGGTCGGTTAATTATTTTTTGAT
156716 TTTTCGGTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.20, C:0.14, G:0.21, T:0.45
Consensus pattern (48 bp):
GTTAACCAAATTTTTTCGGTCCAGGGTCGGTTAATTATTTTTTGATCG
Found at i:156866 original size:18 final size:18
Alignment explanation
Indices: 156833--156885 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
156823 ATTCACCTAA
*
156833 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
156852 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
156870 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
156886 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:156997 original size:9 final size:9
Alignment explanation
Indices: 156983--157049 Score: 107
Period size: 9 Copynumber: 7.4 Consensus size: 9
156973 GTAGTGATTC
*
156983 AATTCGATT
1 AATTCGGTT
156992 AATTCGGTT
1 AATTCGGTT
157001 AATTCGGTT
1 AATTCGGTT
157010 AATTCGGTT
1 AATTCGGTT
*
157019 AATTCGGGT
1 AATTCGGTT
*
157028 AATCCGGTT
1 AATTCGGTT
157037 AATTCGGTT
1 AATTCGGTT
157046 AATT
1 AATT
157050 TTTAACCAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:162396 original size:26 final size:26
Alignment explanation
Indices: 162358--162519 Score: 175
Period size: 26 Copynumber: 6.2 Consensus size: 26
162348 AAAATTATTA
*
162358 AAATTACTGAAATACCCTTAATGGGT
1 AAATTACTAAAATACCCTTAATGGGT
* *
162384 AAATTACTAAAATACCCCTAATGAGT
1 AAATTACTAAAATACCCTTAATGGGT
* *
162410 AAATTATTAAAATACCCTTGATGGGT
1 AAATTACTAAAATACCCTTAATGGGT
** *
162436 AAATTACCGAAATACCCTTGATGGGT
1 AAATTACTAAAATACCCTTAATGGGT
*
162462 AAATTAC-AGAAATA-CATCTAATGGGT
1 AAATTACTA-AAATACCCT-TAATGGGT
* ** *
162488 AAATTACTGAAATACCCTCGATGGAT
1 AAATTACTAAAATACCCTTAATGGGT
162514 AAATTA
1 AAATTA
162520 TCGAAATACC
Statistics
Matches: 114, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
25 2 0.02
26 110 0.96
27 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.29
Consensus pattern (26 bp):
AAATTACTAAAATACCCTTAATGGGT
Found at i:162490 original size:78 final size:78
Alignment explanation
Indices: 162358--162530 Score: 240
Period size: 78 Copynumber: 2.2 Consensus size: 78
162348 AAAATTATTA
* * *
162358 AAATTACTGAAATACCCTTAATGGGTAAATTACTAAAATACCCCTAATGAGTAAATTATTAAAAT
1 AAATTACCGAAATACCCTTAATGGGTAAATTACTAAAATACACCTAATGAGTAAATTACTAAAAT
* *
162423 ACCCTTGATGGGT
66 ACCCTCGATGGAT
* * * *
162436 AAATTACCGAAATACCCTTGATGGGTAAATTAC-AGAAATACATCTAATGGGTAAATTACTGAAA
1 AAATTACCGAAATACCCTTAATGGGTAAATTACTA-AAATACACCTAATGAGTAAATTACTAAAA
162500 TACCCTCGATGGAT
65 TACCCTCGATGGAT
*
162514 AAATTATCGAAATACCC
1 AAATTACCGAAATACCC
162531 CCAAAGGGTC
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
77 1 0.01
78 83 0.99
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (78 bp):
AAATTACCGAAATACCCTTAATGGGTAAATTACTAAAATACACCTAATGAGTAAATTACTAAAAT
ACCCTCGATGGAT
Found at i:162505 original size:52 final size:53
Alignment explanation
Indices: 162358--162530 Score: 203
Period size: 52 Copynumber: 3.3 Consensus size: 53
162348 AAAATTATTA
* * * * *
162358 AAATTA-CTGAAATACCCTTAATGGGTAAATTACTAAAATACCCCTAATGAGT
1 AAATTATCAGAAATACCCTTAATGGGTAAATTACTGAAATACCCTTGATGGGT
* * *
162410 AAATTATTA-AAATACCCTTGATGGGTAAATTACCGAAATACCCTTGATGGGT
1 AAATTATCAGAAATACCCTTAATGGGTAAATTACTGAAATACCCTTGATGGGT
* * *
162462 AAATTA-CAGAAATA-CATCTAATGGGTAAATTACTGAAATACCCTCGATGGAT
1 AAATTATCAGAAATACCCT-TAATGGGTAAATTACTGAAATACCCTTGATGGGT
162514 AAATTATC-GAAATACCC
1 AAATTATCAGAAATACCC
162531 CCAAAGGGTC
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
51 3 0.03
52 96 0.95
53 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (53 bp):
AAATTATCAGAAATACCCTTAATGGGTAAATTACTGAAATACCCTTGATGGGT
Found at i:166815 original size:11 final size:11
Alignment explanation
Indices: 166799--166851 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
166789 CTTCATTCAT
166799 CATCCCTCAAG
1 CATCCCTCAAG
*
166810 CATCCCTGAAG
1 CATCCCTCAAG
* * *
166821 CAGCCCCCAAT
1 CATCCCTCAAG
*
166832 CATCCCTCAAT
1 CATCCCTCAAG
*
166843 CATTCCTCA
1 CATCCCTCA
166852 TTCATTCTCA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.26, C:0.45, G:0.08, T:0.21
Consensus pattern (11 bp):
CATCCCTCAAG
Found at i:175502 original size:30 final size:29
Alignment explanation
Indices: 175434--175503 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 29
175424 CTGCAGCTCA
* *
175434 ATTTCAGCTCCCTTAGCTCAATTCGACTCC
1 ATTT-AGCTCACTTAGCTCAATTCCACTCC
* *
175464 AATTAGCTCACTTGAGCTCAATTCCAC-CT
1 ATTTAGCTCACTT-AGCTCAATTCCACTCC
175493 ATTTGAGCTCA
1 ATTT-AGCTCA
175504 ATTTAGCTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.24, C:0.31, G:0.11, T:0.33
Consensus pattern (29 bp):
ATTTAGCTCACTTAGCTCAATTCCACTCC
Found at i:190471 original size:31 final size:30
Alignment explanation
Indices: 190431--190491 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
190421 TCAAGTTTCC
*
190431 ATATACATGTAACATCCATAT-CATGTATTT
1 ATATACATGTAAAAT-CATATCCATGTATTT
*
190461 ATATATCATGTAAAATCATTTCCATGTATTT
1 ATATA-CATGTAAAATCATATCCATGTATTT
190492 CATGTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.43
Consensus pattern (30 bp):
ATATACATGTAAAATCATATCCATGTATTT
Found at i:190664 original size:25 final size:25
Alignment explanation
Indices: 190635--190684 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
190625 ATCCTGTATA
*
190635 GGTATGCT-TATACGAGCTGTAAATC
1 GGTATGCTCTAT-CGAACTGTAAATC
*
190660 GGTATGCTCTCTCGAACTGTAAATC
1 GGTATGCTCTATCGAACTGTAAATC
190685 AGTAAGCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (25 bp):
GGTATGCTCTATCGAACTGTAAATC
Found at i:204868 original size:95 final size:96
Alignment explanation
Indices: 204755--204945 Score: 375
Period size: 95 Copynumber: 2.0 Consensus size: 96
204745 TACAATCCAA
204755 CTATTGGATTTATCAATATATTTGTACTTGTCAAGCATTTAAATTTTTAAATTGATCCGATATTT
1 CTATTGGATTTATCAATATATTTGTACTTGTCAAGCATTTAAATTTTTAAATTGATCCGATATTT
204820 CTAGTATACTGATCTAAAATATTGTATATAT
66 CTAGTATACTGATCTAAAATATTGTATATAT
204851 CTATTGGA-TTATCAATATATTTGTACTTGTCAAGCATTTAAATTTTTAAATTGATCCGATATTT
1 CTATTGGATTTATCAATATATTTGTACTTGTCAAGCATTTAAATTTTTAAATTGATCCGATATTT
204915 CTAGTATACTGATCTAAAATATTGTATATAT
66 CTAGTATACTGATCTAAAATATTGTATATAT
204946 TAATATGTAT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 87 0.92
96 8 0.08
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (96 bp):
CTATTGGATTTATCAATATATTTGTACTTGTCAAGCATTTAAATTTTTAAATTGATCCGATATTT
CTAGTATACTGATCTAAAATATTGTATATAT
Found at i:205386 original size:21 final size:23
Alignment explanation
Indices: 205362--205409 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
205352 TCATATTTAA
* *
205362 AAAAATTCTAATTTTC-AA-AAT
1 AAAAATTATAATATTCTAATAAT
205383 AAAAATTATAATATTCTAATAAT
1 AAAAATTATAATATTCTAATAAT
205406 AAAA
1 AAAA
205410 TTCATTAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.61
22 2 0.09
23 7 0.30
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAAATTATAATATTCTAATAAT
Found at i:205484 original size:20 final size:21
Alignment explanation
Indices: 205447--205496 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
205437 TTGATAAATT
205447 TTACAAATATAATTTTATTTA
1 TTACAAATATAATTTTATTTA
*
205468 TTACAAA-ATATTTTTATTTA
1 TTACAAATATAATTTTATTTA
*
205488 ATA-AAATAT
1 TTACAAATAT
205497 GAATAATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 3 0.12
20 16 0.62
21 7 0.27
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
TTACAAATATAATTTTATTTA
Found at i:213179 original size:22 final size:21
Alignment explanation
Indices: 213140--213180 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
213130 ATCAAATAGT
**
213140 TCAATTCACATCCCATCATTC
1 TCAATTCACATCAAATCATTC
213161 TCAATTCAACATCAAATCAT
1 TCAATTC-ACATCAAATCAT
213181 CATTTCATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.37, C:0.32, G:0.00, T:0.32
Consensus pattern (21 bp):
TCAATTCACATCAAATCATTC
Found at i:215367 original size:13 final size:13
Alignment explanation
Indices: 215332--215388 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
215322 TCTACATGGT
*
215332 TCGCACATTTAGC
1 TCGCACATTGAGC
* *
215345 TTGCATATTGAGC
1 TCGCACATTGAGC
*
215358 TCGCACATTGGGC
1 TCGCACATTGAGC
* **
215371 TCACGTATTGAGC
1 TCGCACATTGAGC
215384 TCGCA
1 TCGCA
215389 TGACGCTAAG
Statistics
Matches: 32, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (13 bp):
TCGCACATTGAGC
Found at i:219532 original size:72 final size:73
Alignment explanation
Indices: 219389--219536 Score: 235
Period size: 72 Copynumber: 2.0 Consensus size: 73
219379 ATGACACTCA
* * *
219389 AGAATTTTGAAAACAATTATTCCCTAGGTTATTCAGAACTTACAAGGAAAAAACTACTTGGTCAA
1 AGAATTTCGAAAACAATTATTCCCTAGGTTATTCAGAACCTACAAGGAAAAAACTACTTGGTAAA
219454 TATTATTG
66 TATTATTG
* * *
219462 AGAATTTCGAAAATAATTATTCCCTAGGTTGTT-AGAACCTATAAGGAAAAAACTACTTGGTAAA
1 AGAATTTCGAAAACAATTATTCCCTAGGTTATTCAGAACCTACAAGGAAAAAACTACTTGGTAAA
219526 TATTATTG
66 TATTATTG
219534 AGA
1 AGA
219537 TGGCGTTGAA
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 39 0.57
73 30 0.43
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (73 bp):
AGAATTTCGAAAACAATTATTCCCTAGGTTATTCAGAACCTACAAGGAAAAAACTACTTGGTAAA
TATTATTG
Found at i:221520 original size:22 final size:22
Alignment explanation
Indices: 221492--221536 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
221482 ACGAGCTCAA
221492 TCAAAAAGAGGCATTTTGACAT
1 TCAAAAAGAGGCATTTTGACAT
*
221514 TCAAAAAGAGGTATTTTGACAT
1 TCAAAAAGAGGCATTTTGACAT
221536 T
1 T
221537 GAAGTACCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (22 bp):
TCAAAAAGAGGCATTTTGACAT
Found at i:222265 original size:30 final size:27
Alignment explanation
Indices: 222203--222273 Score: 72
Period size: 30 Copynumber: 2.5 Consensus size: 27
222193 ATATTCTATT
*
222203 ATATATTTTTAAATAATTTAAAATCACC
1 ATAT-TTTTTAAATAATTTAAAATCACA
222231 ATATTTTTCTAAATAATTTTTAAAAAT-ACA
1 ATATTTTT-TAAATAA--TTT-AAAATCACA
*
222261 ATATTTTATAAAT
1 ATATTTTTTAAAT
222274 TTTTGTGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 4 0.11
28 11 0.30
29 5 0.14
30 12 0.32
31 5 0.14
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATTTTTTAAATAATTTAAAATCACA
Found at i:242483 original size:29 final size:29
Alignment explanation
Indices: 242409--242512 Score: 93
Period size: 29 Copynumber: 3.6 Consensus size: 29
242399 CACCATTGGT
* *
242409 ACATAGTACTTGATAAATATAACACCGGC
1 ACATAGTACTTGATAACTGTAACACCGGC
* * * * *
242438 ATAGT-GTGCCTGGTAACTGTAACACCGGT
1 ACA-TAGTACTTGATAACTGTAACACCGGC
* *
242467 ACAAAGTACTTGATAACTGTAATCACCGAC
1 ACATAGTACTTGATAACTGTAA-CACCGGC
*
242497 ACATAGTGCTTGATAA
1 ACATAGTACTTGATAA
242513 ACCCTAATGA
Statistics
Matches: 56, Mismatches: 16, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
29 36 0.64
30 20 0.36
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (29 bp):
ACATAGTACTTGATAACTGTAACACCGGC
Found at i:242509 original size:30 final size:29
Alignment explanation
Indices: 242451--242512 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
242441 GTGTGCCTGG
**
242451 TAACTGTAACACCGGTACAAAGTACTTGA
1 TAACTGTAACACCGACACAAAGTACTTGA
* *
242480 TAACTGTAATCACCGACACATAGTGCTTGA
1 TAACTGTAA-CACCGACACAAAGTACTTGA
242510 TAA
1 TAA
242513 ACCCTAATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (29 bp):
TAACTGTAACACCGACACAAAGTACTTGA
Found at i:242598 original size:52 final size:52
Alignment explanation
Indices: 242536--242642 Score: 205
Period size: 52 Copynumber: 2.1 Consensus size: 52
242526 GTCATTTATA
*
242536 TCCTAGCTATCCACTGAGTTCACATGGACCCTGTATCTCGTATTCAATCTTT
1 TCCTAGCTATCCACTGAGTTCACATGGACCCTGTATCTCGTATTCAATCCTT
242588 TCCTAGCTATCCACTGAGTTCACATGGACCCTGTATCTCGTATTCAATCCTT
1 TCCTAGCTATCCACTGAGTTCACATGGACCCTGTATCTCGTATTCAATCCTT
242640 TCC
1 TCC
242643 ATTCTTTTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.36
Consensus pattern (52 bp):
TCCTAGCTATCCACTGAGTTCACATGGACCCTGTATCTCGTATTCAATCCTT
Found at i:245924 original size:50 final size:50
Alignment explanation
Indices: 245806--246048 Score: 315
Period size: 50 Copynumber: 4.8 Consensus size: 50
245796 GATAATAACA
* * * ** * *
245806 TGCCAAAGCCATGTCCCAGACATGGTTTTACATGGGATGTTCTCATATTGG
1 TGCCAACGCCATGTCTCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * *
245857 TTCCCATGCCATGTCTCAGACATGGTCTTACAAGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCTCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
245907 TGGCAACGTCATGTCTCAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCTCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
245957 TGCCAACGCCATGTCCCAGACATAGTCTTACATGGCACCTCTCATCTCGG
1 TGCCAACGCCATGTCTCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
246007 TGCCAACGCCATGTCGCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCTCAGACATGGTCTTACATGGGACCTCT
246049 TTACCCAAAT
Statistics
Matches: 166, Mismatches: 26, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 135 0.81
51 31 0.19
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCTCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:250666 original size:5 final size:5
Alignment explanation
Indices: 250656--250691 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
250646 ATGTTTGAAA
250656 AAAAT AAAAT AAAAT AAAAT AAATAT ATAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAA-AT A-AAAT AAAA
250692 GTATATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 21 0.72
6 6 0.21
7 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:255313 original size:22 final size:22
Alignment explanation
Indices: 255288--255333 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
255278 GTTTTGCAAT
255288 TACAATTGTATAAAATTTTATA
1 TACAATTGTATAAAATTTTATA
255310 TACAATTGTATAAAATTTTATA
1 TACAATTGTATAAAATTTTATA
255332 TA
1 TA
255334 ACACCATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (22 bp):
TACAATTGTATAAAATTTTATA
Found at i:255347 original size:15 final size:15
Alignment explanation
Indices: 255324--255361 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
255314 ATTGTATAAA
*
255324 ATTTTATATAACACC
1 ATTTAATATAACACC
255339 ATTTAATATAACACC
1 ATTTAATATAACACC
255354 ATTTAATA
1 ATTTAATA
255362 ACCAAATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTTAATATAACACC
Found at i:257744 original size:43 final size:42
Alignment explanation
Indices: 257633--257761 Score: 132
Period size: 43 Copynumber: 3.0 Consensus size: 42
257623 AAAACTCGTA
* * * *
257633 CAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCATATAT
1 CAATG-CAACGTCCCAGACGTGGTCTTACACGTAAACACAAAT
* * **
257676 CAATGCCACTGTCCTAGACAAGGTCTTACACGTAAACACAAAT
1 CAATGCAAC-GTCCCAGACGTGGTCTTACACGTAAACACAAAT
* * *
257719 CGATGCTAACGTCCCAAACGTGGTCTTACACGAAAACACAAAT
1 CAATGC-AACGTCCCAGACGTGGTCTTACACGTAAACACAAAT
257762 AAAAAATCAC
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 3 0.04
43 64 0.93
44 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (42 bp):
CAATGCAACGTCCCAGACGTGGTCTTACACGTAAACACAAAT
Found at i:267891 original size:114 final size:115
Alignment explanation
Indices: 267756--267985 Score: 453
Period size: 114 Copynumber: 2.0 Consensus size: 115
267746 TTGGTTGAAT
267756 ATTTTATTATTTTATTATAAGATATTTATTAATATTTTATTTAATTAAAATTAGTATTCAAAGAA
1 ATTTTATTATTTTATTATAAGATATTTATTAATATTTTATTTAATTAAAATTAGTATTCAAAGAA
267821 AGAAAGATGAATAACATCTTTCACCAAAGCTTCTAGCGTCCATGAAAGAG
66 AGAAAGATGAATAACATCTTTCACCAAAGCTTCTAGCGTCCATGAAAGAG
267871 ATTTTATTA-TTTATTATAAGATATTTATTAATATTTTATTTAATTAAAATTAGTATTCAAAGAA
1 ATTTTATTATTTTATTATAAGATATTTATTAATATTTTATTTAATTAAAATTAGTATTCAAAGAA
267935 AGAAAGATGAATAACATCTTTCACCAAAGCTTCTAGCGTCCATGAAAGAG
66 AGAAAGATGAATAACATCTTTCACCAAAGCTTCTAGCGTCCATGAAAGAG
267985 A
1 A
267986 GATGAAAGAA
Statistics
Matches: 115, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
114 106 0.92
115 9 0.08
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (115 bp):
ATTTTATTATTTTATTATAAGATATTTATTAATATTTTATTTAATTAAAATTAGTATTCAAAGAA
AGAAAGATGAATAACATCTTTCACCAAAGCTTCTAGCGTCCATGAAAGAG
Found at i:270621 original size:17 final size:17
Alignment explanation
Indices: 270599--270631 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
270589 CGTCAGGTGC
270599 GGTACAATGACCAAAAA
1 GGTACAATGACCAAAAA
*
270616 GGTACAATGCCCAAAA
1 GGTACAATGACCAAAA
270632 GTCAATAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.12
Consensus pattern (17 bp):
GGTACAATGACCAAAAA
Found at i:274860 original size:35 final size:35
Alignment explanation
Indices: 274821--274892 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
274811 TGTTTTATAA
* *
274821 ATTATACATA-TTTTTATTTTAAATTTAATAAACTC
1 ATTATA-ATATTTTTTATTTCAAATGTAATAAACTC
* *
274856 ATTATATTATTTTTTATTTCGAATGTAATAAACTC
1 ATTATAATATTTTTTATTTCAAATGTAATAAACTC
274891 AT
1 AT
274893 CATATCAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 2 0.06
35 30 0.94
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (35 bp):
ATTATAATATTTTTTATTTCAAATGTAATAAACTC
Found at i:275076 original size:24 final size:21
Alignment explanation
Indices: 275049--275091 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 21
275039 TGATTTAATT
275049 TAATTTATTTCTATTTTATTATTA
1 TAATTT-TTT-TATTTT-TTATTA
275073 TAATTTTTTTATTTTTTAT
1 TAATTTTTTTATTTTTTAT
275092 CAATTTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 3 0.16
24 6 0.32
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (21 bp):
TAATTTTTTTATTTTTTATTA
Found at i:275306 original size:54 final size:54
Alignment explanation
Indices: 275231--275336 Score: 194
Period size: 54 Copynumber: 2.0 Consensus size: 54
275221 TTAAAGACGC
* *
275231 ATAGACTTAATGAGATTTATTTAAATCTTTTCAAGCATTTCAATTAAAATTTAG
1 ATAGACATAATGAGATATATTTAAATCTTTTCAAGCATTTCAATTAAAATTTAG
275285 ATAGACATAATGAGATATATTTAAATCTTTTCAAGCATTTCAATTAAAATTT
1 ATAGACATAATGAGATATATTTAAATCTTTTCAAGCATTTCAATTAAAATTT
275337 TATTTATTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (54 bp):
ATAGACATAATGAGATATATTTAAATCTTTTCAAGCATTTCAATTAAAATTTAG
Found at i:279940 original size:111 final size:111
Alignment explanation
Indices: 279753--279958 Score: 331
Period size: 111 Copynumber: 1.9 Consensus size: 111
279743 AATTCTGCAT
* *
279753 TGGGTAAATCCATCTAGACTTACCATAACACATACGTTCGCAGAGAGTGAAAACGAACTGTCTAT
1 TGGGTAAATCCACCTAAACTTACCATAACACATACGTTCGCAGAGAGTGAAAACGAACTGTCTAT
279818 TTGAGCAAAGTGTATTGTATGCGTGTTGCTTAGTATAAATTTGTAG
66 TTGAGCAAAGTGTATTGTATGCGTGTTGCTTAGTATAAATTTGTAG
* * ***
279864 TGGGTAAATCCACCTAAACTTACCGTAACACATATGTTCGCAGAGAGTGAAGGTGAACTGTCTAT
1 TGGGTAAATCCACCTAAACTTACCATAACACATACGTTCGCAGAGAGTGAAAACGAACTGTCTAT
**
279929 TTGAGTGAAGTGTATTGTATGCGTGTTGCT
66 TTGAGCAAAGTGTATTGTATGCGTGTTGCT
279959 AATATTCATA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 86 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (111 bp):
TGGGTAAATCCACCTAAACTTACCATAACACATACGTTCGCAGAGAGTGAAAACGAACTGTCTAT
TTGAGCAAAGTGTATTGTATGCGTGTTGCTTAGTATAAATTTGTAG
Found at i:280690 original size:15 final size:15
Alignment explanation
Indices: 280670--280699 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
280660 TGTATTTTAG
*
280670 CATATGTATTAAAAT
1 CATATGTAATAAAAT
280685 CATATGTAATAAAAT
1 CATATGTAATAAAAT
280700 ATCATATATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (15 bp):
CATATGTAATAAAAT
Found at i:282757 original size:28 final size:26
Alignment explanation
Indices: 282726--282779 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
282716 ATATTACTTA
282726 TAAAATATTATTATTTTAAGTAAAATAT
1 TAAAATATTATTATTTTAA--AAAATAT
*
282754 TAAATTATTATTATTTTAAAAAATAT
1 TAAAATATTATTATTTTAAAAAATAT
282780 AATTCAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 7 0.28
28 18 0.72
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TAAAATATTATTATTTTAAAAAATAT
Found at i:283423 original size:21 final size:22
Alignment explanation
Indices: 283383--283423 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
283373 TATTGCACCT
*
283383 TAAAAAATTTATTATTAATTAA
1 TAAAAAATTTATTATAAATTAA
*
283405 TAAAAATTTTA-TATAAATT
1 TAAAAAATTTATTATAAATT
283424 GAAATTCTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAAAAATTTATTATAAATTAA
Found at i:289590 original size:21 final size:21
Alignment explanation
Indices: 289564--289624 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
289554 GGGTACATGA
289564 GCGTGTGGAATG-GCCACACGG
1 GCGTGTGGAA-GAGCCACACGG
*
289585 GCGTGTGGGAGAGCCACACGG
1 GCGTGTGGAAGAGCCACACGG
** *
289606 ATGTGTGGTAGAGCCACAC
1 GCGTGTGGAAGAGCCACAC
289625 AGCCGTATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 1 0.03
21 34 0.97
ACGTcount: A:0.21, C:0.23, G:0.41, T:0.15
Consensus pattern (21 bp):
GCGTGTGGAAGAGCCACACGG
Found at i:295036 original size:27 final size:27
Alignment explanation
Indices: 295006--295060 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
294996 ATTTACAAGA
* *
295006 TTAGCATAAATGTTAATTAAATTTTAG
1 TTAGCATAAAGGTTAATTAAAATTTAG
*
295033 TTAGTATAAAGGTTAATTAAAATTTAG
1 TTAGCATAAAGGTTAATTAAAATTTAG
295060 T
1 T
295061 CCCTTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.44
Consensus pattern (27 bp):
TTAGCATAAAGGTTAATTAAAATTTAG
Found at i:296770 original size:54 final size:54
Alignment explanation
Indices: 296707--297099 Score: 380
Period size: 54 Copynumber: 7.3 Consensus size: 54
296697 TATGGTCTGT
* * * *
296707 TGATTTACGATCACGACCTTTTACTTATGGGATTTTACGAATCTCGTGGCCCAT
1 TGATTTACGATCACGACCTTTTACTTACGGGATTTTACGAATCTCGCGGTCCAC
* * * *
296761 TGATTTACGATCACAACCTTTTACTTATGGGATTTTACGAATCTCACGGTCCGC
1 TGATTTACGATCACGACCTTTTACTTACGGGATTTTACGAATCTCGCGGTCCAC
* * * * * * *
296815 TGATTTACAATCATGACATTTTACATACGAGATTTAACGAATCTCGCAGTCCAC
1 TGATTTACGATCACGACCTTTTACTTACGGGATTTTACGAATCTCGCGGTCCAC
* * * * * * *
296869 TGATTTATGATCACAACCTTTTAGTTACGAGATTTTATGAATCTTGCGGTCCGC
1 TGATTTACGATCACGACCTTTTACTTACGGGATTTTACGAATCTCGCGGTCCAC
* * * *
296923 TGATTTACGA-AATGACCTTTTACTTACGAGATTTTACGAATCTCGCGAT-CAGC
1 TGATTTACGATCACGACCTTTTACTTACGGGATTTTACGAATCTCGCGGTCCA-C
** * * **
296976 TGATTTAAAATCACGACCTTTTACTTACAGGATTTTATGAATCTCTTGGT-CAGC
1 TGATTTACGATCACGACCTTTTACTTACGGGATTTTACGAATCTCGCGGTCCA-C
* * * * * *
297030 TGATTTACAATCACGACCTTCTACTTACATGG-TTTTATGAATCTCGCGGTTCAT
1 TGATTTACGATCACGACCTTTTACTTAC-GGGATTTTACGAATCTCGCGGTCCAC
*
297084 TGATTTATGATCACGA
1 TGATTTACGATCACGA
297100 TCTTCTGCAT
Statistics
Matches: 279, Mismatches: 56, Indels: 8
0.81 0.16 0.02
Matches are distributed among these distances:
52 1 0.00
53 41 0.15
54 233 0.84
55 4 0.01
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (54 bp):
TGATTTACGATCACGACCTTTTACTTACGGGATTTTACGAATCTCGCGGTCCAC
Found at i:297092 original size:215 final size:216
Alignment explanation
Indices: 296707--297097 Score: 500
Period size: 215 Copynumber: 1.8 Consensus size: 216
296697 TATGGTCTGT
* * * * * * **
296707 TGATTTACGATCACGACCTTTTACTTATGGGATTTTACGAATCTCGTGGCCCATTGATTTACGAT
1 TGATTTACGATAACGACCTTTTACTTACGAGATTTTACGAATCTCGTCGACCACTGATTTAAAAT
** * * *
296772 CACAACCTTTTACTTATGGGATTTTACGAATCTCACGGTCCGCTGATTTACAATCATGACATTTT
66 CACAACCTTTTACTTACAGGATTTTACGAATCTCACGGTCAGCTGATTTACAATCACGACATTCT
296837 ACATACGAGATTTAACGAATCTCGCAGTCCACTGATTTATGATCACAACCTTTTAGTTACGAGAT
131 ACATACGAGATTTAACGAATCTCGCAGTCCACTGATTTATGATCACAACCTTTTAGTTACGAGAT
296902 TTTATGAATCTTGCGGTCCGC
196 TTTATGAATCTTGCGGTCCGC
* *
296923 TGATTTACGA-AATGACCTTTTACTTACGAGATTTTACGAATCTCG-CGATCAGCTGATTTAAAA
1 TGATTTACGATAACGACCTTTTACTTACGAGATTTTACGAATCTCGTCGACCA-CTGATTTAAAA
* * ** *
296986 TCACGACCTTTTACTTACAGGATTTTATGAATCTCTTGGTCAGCTGATTTACAATCACGACCTTC
65 TCACAACCTTTTACTTACAGGATTTTACGAATCTCACGGTCAGCTGATTTACAATCACGACATTC
* * * * * * *
297051 TACTTAC-ATGGTTTTATGAATCTCGCGGTTCATTGATTTATGATCAC
130 TACATACGA-GATTTAACGAATCTCGCAGTCCACTGATTTATGATCAC
297098 GATCTTCTGC
Statistics
Matches: 146, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
214 4 0.03
215 132 0.90
216 10 0.07
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (216 bp):
TGATTTACGATAACGACCTTTTACTTACGAGATTTTACGAATCTCGTCGACCACTGATTTAAAAT
CACAACCTTTTACTTACAGGATTTTACGAATCTCACGGTCAGCTGATTTACAATCACGACATTCT
ACATACGAGATTTAACGAATCTCGCAGTCCACTGATTTATGATCACAACCTTTTAGTTACGAGAT
TTTATGAATCTTGCGGTCCGC
Found at i:297099 original size:108 final size:107
Alignment explanation
Indices: 296707--297097 Score: 432
Period size: 108 Copynumber: 3.6 Consensus size: 107
296697 TATGGTCTGT
* * * * * * *
296707 TGATTTACGATCACGACCTTTTACTTATGGGATTTTACGAATCTCGTGGCCCATTGATTTACGAT
1 TGATTTACAATCACGACCTTTTACTTACGAGATTTTACGAATCTCGCGGTCCACTGATTTATGAT
* * *
296772 CACAACCTTTTACTTATGGGATTTTACGAATCTCACGGTCCGC
66 CACAACCTTTTACTTA-CGGATTTTATGAATCTCTCGGTCCGC
* * * * *
296815 TGATTTACAATCATGACATTTTACATACGAGATTTAACGAATCTCGCAGTCCACTGATTTATGAT
1 TGATTTACAATCACGACCTTTTACTTACGAGATTTTACGAATCTCGCGGTCCACTGATTTATGAT
*
296880 CACAACCTTTTAGTTACGAGATTTTATGAATCT-TGCGGTCCGC
66 CACAACCTTTTACTTACG-GATTTTATGAATCTCT-CGGTCCGC
* * **
296923 TGATTTACGAA--ATGACCTTTTACTTACGAGATTTTACGAATCTCGCGAT-CAGCTGATTTAAA
1 TGATTTAC-AATCACGACCTTTTACTTACGAGATTTTACGAATCTCGCGGTCCA-CTGATTTATG
* * *
296985 ATCACGACCTTTTACTTACAGGATTTTATGAATCTCTTGGTCAGC
64 ATCACAACCTTTTACTTAC-GGATTTTATGAATCTCTCGGTCCGC
* * * * *
297030 TGATTTACAATCACGACCTTCTACTTAC-ATGGTTTTATGAATCTCGCGGTTCATTGATTTATGA
1 TGATTTACAATCACGACCTTTTACTTACGA-GATTTTACGAATCTCGCGGTCCACTGATTTATGA
297094 TCAC
65 TCAC
297098 GATCTTCTGC
Statistics
Matches: 238, Mismatches: 35, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
106 4 0.02
107 88 0.37
108 142 0.60
109 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (107 bp):
TGATTTACAATCACGACCTTTTACTTACGAGATTTTACGAATCTCGCGGTCCACTGATTTATGAT
CACAACCTTTTACTTACGGATTTTATGAATCTCTCGGTCCGC
Found at i:297162 original size:23 final size:23
Alignment explanation
Indices: 297135--297310 Score: 153
Period size: 23 Copynumber: 7.6 Consensus size: 23
297125 TCTTATGTAT
297135 TACAATACAGTTCGTAGAAATTC
1 TACAATACAGTTCGTAGAAATTC
297158 TACAATACAGTTCGTAGAAATTC
1 TACAATACAGTTCGTAGAAATTC
* * *
297181 TACAATACAATTCATAG-TATTGC
1 TACAATACAGTTCGTAGAAATT-C
* * *
297204 TATAAATACAGTTCGTTGTAATTC
1 TA-CAATACAGTTCGTAGAAATTC
* * *
297228 TACAACACAATTC--ACAATATTTC
1 TACAATACAGTTCGTAGAA-A-TTC
* ** *
297251 TATAAATACAGTTCACAGTAATTC
1 TA-CAATACAGTTCGTAGAAATTC
*
297275 TACAATACAGTTCGT-GACATTC
1 TACAATACAGTTCGTAGAAATTC
297297 TACAATACAGTTCG
1 TACAATACAGTTCG
297311 CAACATTTTT
Statistics
Matches: 121, Mismatches: 24, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
21 1 0.01
22 23 0.19
23 64 0.53
24 27 0.22
25 4 0.03
26 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (23 bp):
TACAATACAGTTCGTAGAAATTC
Found at i:297216 original size:47 final size:47
Alignment explanation
Indices: 297161--297283 Score: 174
Period size: 47 Copynumber: 2.6 Consensus size: 47
297151 GAAATTCTAC
* * *
297161 AATACAGTTCGTAGAAATTCTACAATACAATTCATAGTATTGCTATA
1 AATACAGTTCGTAGTAATTCTACAATACAATTCACAATATTGCTATA
* * *
297208 AATACAGTTCGTTGTAATTCTACAACACAATTCACAATATTTCTATA
1 AATACAGTTCGTAGTAATTCTACAATACAATTCACAATATTGCTATA
**
297255 AATACAGTTCACAGTAATTCTACAATACA
1 AATACAGTTCGTAGTAATTCTACAATACA
297284 GTTCGTGACA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (47 bp):
AATACAGTTCGTAGTAATTCTACAATACAATTCACAATATTGCTATA
Found at i:297227 original size:70 final size:70
Alignment explanation
Indices: 297138--297336 Score: 178
Period size: 70 Copynumber: 2.9 Consensus size: 70
297128 TATGTATTAC
* * * *
297138 AATACAGTTCGTAGAAATTCTACAATACAGTTCGTAGAA-A-TTCTA-CAATACAATTCATAGT-
1 AATACAGTTCGTTG-AATTCTACAATACAGTTCG-ACAATATTTCTATAAATACAATTCACAGTA
297199 ATTGCTATA
64 ATT-CTA-A
* * *
297208 AATACAGTTCGTTGTAATTCTACAACACAATTC-ACAATATTTCTATAAATACAGTTCACAGTAA
1 AATACAGTTCGTTG-AATTCTACAATACAGTTCGACAATATTTCTATAAATACAATTCACAGTAA
*
297272 TTCTAC
65 TTCTAA
* * * * *
297278 AATACAGTTCG-TGACATTCTACAATACAGTTCG-CAACATTTTTGTAAATATAGTTCACA
1 AATACAGTTCGTTGA-ATTCTACAATACAGTTCGACAATATTTCTATAAATACAATTCACA
297337 AAATATTCTA
Statistics
Matches: 108, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
68 4 0.04
69 40 0.37
70 45 0.42
71 16 0.15
72 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (70 bp):
AATACAGTTCGTTGAATTCTACAATACAGTTCGACAATATTTCTATAAATACAATTCACAGTAAT
TCTAA
Found at i:297332 original size:24 final size:24
Alignment explanation
Indices: 297300--297409 Score: 114
Period size: 24 Copynumber: 4.6 Consensus size: 24
297290 GACATTCTAC
*
297300 AATACAGTTCGCAACATTTTTGTA
1 AATACAGTTCGCAACATTTCTGTA
* * * *
297324 AATATAGTTCACAAAATATTCTAT-
1 AATACAGTTCGCAACAT-TTCTGTA
* * *
297348 AATATAGTTCGCGACATTTCTATA
1 AATACAGTTCGCAACATTTCTGTA
* *
297372 AATACAGTTCGTAGCATTTCTGTA
1 AATACAGTTCGCAACATTTCTGTA
297396 AATACAGTTCGCAA
1 AATACAGTTCGCAA
297410 TATTCTACAA
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
23 6 0.09
24 59 0.86
25 4 0.06
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (24 bp):
AATACAGTTCGCAACATTTCTGTA
Found at i:297396 original size:72 final size:69
Alignment explanation
Indices: 297246--297419 Score: 197
Period size: 72 Copynumber: 2.5 Consensus size: 69
297236 AATTCACAAT
* ** * *
297246 ATTTCTATAAATACAGTTCACAGTAATTCTACAATACAGTTCGTGACATTCTACAATACAGTTCG
1 ATTTCTGTAAATACAGTTCACAAAAATTCTACAATACAGTTCGCGACATTCTAAAATACAGTTCG
297311 CAAC
66 CAAC
* * * *
297315 ATTTTTGTAAATATAGTTCACAAAATATTCTATAATATAGTTCGCGACATTTCTATAAATACAGT
1 ATTTCTGTAAATACAGTTCACAAAA-ATTCTACAATACAGTTCGCGACA-TTCTA-AAATACAGT
* *
297380 TCGTAGC
63 TCGCAAC
* *
297387 ATTTCTGTAAATACAGTTCGC-AATATTCTACAA
1 ATTTCTGTAAATACAGTTCACAAAAATTCTACAA
297420 CATGGTTCGT
Statistics
Matches: 86, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
69 20 0.23
70 28 0.33
71 7 0.08
72 31 0.36
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (69 bp):
ATTTCTGTAAATACAGTTCACAAAAATTCTACAATACAGTTCGCGACATTCTAAAATACAGTTCG
CAAC
Found at i:302250 original size:40 final size:38
Alignment explanation
Indices: 302102--302262 Score: 124
Period size: 41 Copynumber: 3.9 Consensus size: 38
302092 ATGCCATCGC
* * *
302102 ATAGCCGAAGCTATTATAATCCCACACACTAAGTGCCTTAC
1 ATAGCCGAAGCTATT-CAAT--CACACACTAAGTGCCATAA
* * *
302143 ATAGCTGAAGCTATCTCAGTCTTGCACACTAAGTGCCATATATA
1 ATAGCCGAAGCTAT-TCAATC--ACACACTAAGTGCC--ATA-A
* *
302187 TATAGCCAAAGCTATTCTAAATCACACACTAACTGCCATAA
1 -ATAGCCGAAGCTATTC--AATCACACACTAAGTGCCATAA
302228 ATAGCCGAAGCTATCTCGAATCACACACTAAGTGC
1 ATAGCCGAAGCTAT-TC-AATCACACACTAAGTGC
302263 TAAACATAGT
Statistics
Matches: 96, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
39 1 0.01
40 29 0.30
41 31 0.32
42 4 0.04
43 2 0.02
44 14 0.15
45 12 0.12
46 3 0.03
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (38 bp):
ATAGCCGAAGCTATTCAATCACACACTAAGTGCCATAA
Found at i:305938 original size:93 final size:94
Alignment explanation
Indices: 305825--305998 Score: 244
Period size: 93 Copynumber: 1.9 Consensus size: 94
305815 CTGTGTTACG
* * *
305825 TAATTAATGGAAGCAATAAAAA-ACATTGCTAAATCAACCAAAATGCTGAATGTTAGG-TATTTA
1 TAATTAATGGAAGCAATAAAAAGA-ATTGCTAAAGCAACCAAAATACAGAATGTTAGGATATTTA
*
305888 TGGGGAATTATATATTAAAGCTTTGATACA
65 TGGGGAATTATAAATTAAAGCTTTGATACA
** * * *
305918 TAATTAATGTCAGGAATAAAAAGAATTGTTAAAGCAACCAAATTACAGAATGTTAGGATATTTAT
1 TAATTAATGGAAGCAATAAAAAGAATTGCTAAAGCAACCAAAATACAGAATGTTAGGATATTTAT
305983 GGGGAATTATAAATTA
66 GGGGAATTATAAATTA
305999 TTCATACGTA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
93 47 0.67
94 23 0.33
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (94 bp):
TAATTAATGGAAGCAATAAAAAGAATTGCTAAAGCAACCAAAATACAGAATGTTAGGATATTTAT
GGGGAATTATAAATTAAAGCTTTGATACA
Found at i:306892 original size:14 final size:14
Alignment explanation
Indices: 306859--306893 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
306849 AGTGTTGTGA
*
306859 AAAAAGTACTTTAG
1 AAAAATTACTTTAG
*
306873 AAAAATTACTTTTG
1 AAAAATTACTTTAG
306887 AAAAATT
1 AAAAATT
306894 CGATAGTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (14 bp):
AAAAATTACTTTAG
Found at i:307730 original size:18 final size:18
Alignment explanation
Indices: 307690--307730 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
307680 ATATTATGCT
* *
307690 TTTTTTTATTTTTTTATA
1 TTTTTCTATTCTTTTATA
*
307708 ATTTTCTATTCTTTTATA
1 TTTTTCTATTCTTTTATA
307726 TTTTT
1 TTTTT
307731 TTGGGATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTCTATTCTTTTATA
Found at i:315129 original size:3 final size:3
Alignment explanation
Indices: 315121--315148 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
315111 CTTTGATTCA
315121 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
315149 CTCCTCTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:315215 original size:3 final size:3
Alignment explanation
Indices: 315207--315238 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
315197 GCTGAGTAAC
315207 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
315239 TATTGGAAAA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:315725 original size:17 final size:16
Alignment explanation
Indices: 315703--315916 Score: 123
Period size: 17 Copynumber: 12.5 Consensus size: 16
315693 GAATTTTTTC
315703 TTTTGAAAACACGAGAA-
1 TTTTG-AAACACGA-AAT
*
315720 TTTTG-AACTAC-AATT
1 TTTTGAAAC-ACGAAAT
315735 TTTTTGAAAACACGAAAAT
1 T-TTTG-AAACACG-AAAT
*
315754 TTTTGAGACACGAAA-
1 TTTTGAAACACGAAAT
*
315769 ATTTGAAAACAC-AAAT
1 TTTTG-AAACACGAAAT
* * *
315785 TTTTGATACATGAATTT
1 TTTTGAAACACGAA-AT
*
315802 TTTTAAAACACGAAAAT
1 TTTTGAAACACG-AAAT
315819 TTTTGAAAACACGAAAAT
1 TTTTG-AAACACG-AAAT
315837 TTTTGAAACACGAGAAT
1 TTTTGAAACACGA-AAT
315854 TTTTGAAACACGGGAAATTT
1 TTTTGAAACAC--GAAA--T
* *
315874 TTTTGAAAACACTAAAAA
1 TTTTG-AAACAC-GAAAT
* *
315892 TTTCGAAACACCGGAAT
1 TTTTGAAACA-CGAAAT
315909 TTTTGAAA
1 TTTTGAAA
315917 ACATGAAGAT
Statistics
Matches: 155, Mismatches: 22, Indels: 40
0.71 0.10 0.18
Matches are distributed among these distances:
14 1 0.01
15 16 0.10
16 21 0.14
17 63 0.41
18 33 0.21
19 6 0.04
20 9 0.06
21 6 0.04
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (16 bp):
TTTTGAAACACGAAAT
Found at i:315758 original size:18 final size:18
Alignment explanation
Indices: 315735--315976 Score: 161
Period size: 17 Copynumber: 13.9 Consensus size: 18
315725 AACTACAATT
315735 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
315753 TTTTTG-AGACACGAAAA
1 TTTTTGAAAACACGAAAA
315770 --TTTGAAAACAC--AAA
1 TTTTTGAAAACACGAAAA
* * *
315784 TTTTTG-ATACATG-AAT
1 TTTTTGAAAACACGAAAA
*
315800 TTTTTTAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
315818 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
315836 TTTTTG-AAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
315853 TTTTTG-AAACACGGGAAATT
1 TTTTTGAAAACAC--GAAA-A
*
315873 TTTTTGAAAACACTAAAA
1 TTTTTGAAAACACGAAAA
* * *
315891 ATTTCG-AAACACCG-GAA
1 TTTTTGAAAACA-CGAAAA
* *
315908 TTTTTGAAAACATGAAGA
1 TTTTTGAAAACACGAAAA
* * *
315926 TTTAT-AAAATATC-AGAA
1 TTTTTGAAAACA-CGAAAA
* * *
315943 TTTTTGAAAACATGAGGAT
1 TTTTTGAAAACACGA-AAA
315962 TTTTTG-AAACACGAA
1 TTTTTGAAAACACGAA
315977 TTTTTCGATT
Statistics
Matches: 172, Mismatches: 35, Indels: 35
0.71 0.14 0.14
Matches are distributed among these distances:
14 3 0.02
15 8 0.05
16 16 0.09
17 60 0.35
18 59 0.34
19 14 0.08
20 6 0.03
21 6 0.03
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:315967 original size:19 final size:17
Alignment explanation
Indices: 315907--315970 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
315897 AAACACCGGA
315907 ATTTTTGAAAACATGAAG
1 ATTTTTGAAAACATG-AG
* * *
315925 ATTTAT-AAAATATCAG
1 ATTTTTGAAAACATGAG
315941 AATTTTTGAAAACATGAGG
1 -ATTTTTGAAAACATGA-G
315960 ATTTTTTGAAA
1 A-TTTTTGAAA
315971 CACGAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
16 2 0.06
17 11 0.31
18 13 0.36
19 10 0.28
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.38
Consensus pattern (17 bp):
ATTTTTGAAAACATGAG
Found at i:316295 original size:16 final size:16
Alignment explanation
Indices: 316259--316301 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
316249 TACCTTGTTT
*
316259 ATTAAAAT-AATTTAA
1 ATTAAAATAAAATTAA
*
316274 AATAAAATAAAATTAA
1 ATTAAAATAAAATTAA
*
316290 ATTAAATTAAAA
1 ATTAAAATAAAA
316302 ATATAGATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTAAAATAAAATTAA
Found at i:316509 original size:20 final size:21
Alignment explanation
Indices: 316484--316539 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
316474 TTGGGCCCTT
316484 TTTTTTCTTTTTT-TCTTCCC
1 TTTTTTCTTTTTTCTCTTCCC
**
316504 TTTTTTCTTTTCTTCTCTTTTC
1 TTTTTTCTTTT-TTCTCTTCCC
316526 -TTTTTCTTTTTTCT
1 TTTTTTCTTTTTTCT
316540 ACTGGGCTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
21 12 0.38
22 5 0.16
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTTCTTTTTTCTCTTCCC
Found at i:316516 original size:17 final size:16
Alignment explanation
Indices: 316493--316533 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
316483 TTTTTTTCTT
*
316493 TTTTTCTTCCCTTTTT
1 TTTTTCTTCCCTTTTC
*
316509 TCTTTTCTTCTCTTTTC
1 T-TTTTCTTCCCTTTTC
316526 TTTTTCTT
1 TTTTTCTT
316534 TTTTCTACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCTTCCCTTTTC
Found at i:316577 original size:17 final size:17
Alignment explanation
Indices: 316538--316588 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
316528 TTTCTTTTTT
*
316538 CTACTGGG-CTGTTGGG
1 CTACTGGGCCTGCTGGG
*
316554 CGAACTGGGCCTGCTGGG
1 C-TACTGGGCCTGCTGGG
316572 CTACTGCAGGCCTGCTG
1 CTACTG--GGCCTGCTG
316589 CTGATGGCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 1 0.04
17 10 0.36
18 8 0.29
19 9 0.32
ACGTcount: A:0.10, C:0.27, G:0.39, T:0.24
Consensus pattern (17 bp):
CTACTGGGCCTGCTGGG
Found at i:316627 original size:19 final size:19
Alignment explanation
Indices: 316593--316629 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
316583 CTGCTGCTGA
*
316593 TGGCCTGCTGATTTGGGCC
1 TGGCCTGCTGAGTTGGGCC
*
316612 TGGCCTGCTGCGTTGGGC
1 TGGCCTGCTGAGTTGGGC
316630 TGCTGCTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.27, G:0.41, T:0.30
Consensus pattern (19 bp):
TGGCCTGCTGAGTTGGGCC
Found at i:316818 original size:11 final size:11
Alignment explanation
Indices: 316802--316829 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
316792 TCCTTCTTTC
316802 TTCTTCCCCTT
1 TTCTTCCCCTT
316813 TTCTTCCCCTT
1 TTCTTCCCCTT
316824 TTCTTC
1 TTCTTC
316830 TTTCTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (11 bp):
TTCTTCCCCTT
Found at i:316835 original size:7 final size:7
Alignment explanation
Indices: 316823--316868 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
316813 TTCTTCCCCT
316823 TTTCTTC
1 TTTCTTC
*
316830 TTTCTTT
1 TTTCTTC
316837 TTTCTTC
1 TTTCTTC
316844 --T-TTC
1 TTTCTTC
316848 TTTCTTC
1 TTTCTTC
316855 TTTCTTC
1 TTTCTTC
316862 TTTCTTC
1 TTTCTTC
316869 CTTACTTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 3 0.09
5 1 0.03
6 1 0.03
7 29 0.85
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTCTTC
Found at i:316836 original size:4 final size:4
Alignment explanation
Indices: 316823--316881 Score: 56
Period size: 4 Copynumber: 16.0 Consensus size: 4
316813 TTCTTCCCCT
316823 TTTC -TTC TTTC TTT- TTTC -TTC TTTC TTTC -TTC TTTC -TTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* * *
316866 TTCC TTAC TTCC TTTC
1 TTTC TTTC TTTC TTTC
316882 CCGATCAGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
3 15 0.33
4 31 0.67
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:317397 original size:30 final size:29
Alignment explanation
Indices: 317363--317459 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 29
317353 GGCCAAAACA
*
317363 TAATTTTAAGAAAGTTTAAGGGTTAAAATG
1 TAATTTTAA-AAAGTTTAAGGGTTGAAATG
* *
317393 TAATTTTGAAAAATTTTAGGGGTTGAAATG
1 TAATTTT-AAAAAGTTTAAGGGTTGAAATG
* *
317423 TAATTTCAAAAAAAG-TTAAGGGTCGAAATG
1 TAATTT--TAAAAAGTTTAAGGGTTGAAATG
*
317453 CAATTTT
1 TAATTTT
317460 TTTAAAAACA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
30 48 0.87
31 7 0.13
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (29 bp):
TAATTTTAAAAAGTTTAAGGGTTGAAATG
Found at i:317744 original size:76 final size:78
Alignment explanation
Indices: 317676--318554 Score: 914
Period size: 79 Copynumber: 11.3 Consensus size: 78
317666 TGAGTTGACC
* * * * *
317676 TTTGAAAAATAGAAATT-GAAAAATACATCGGTATGTGACCTGAGGCTCAACTCACCTCTCGCAA
1 TTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAA
317740 TATGAGTTGA-TT
66 TATGAGTTGATTT
* * ** * *
317752 TTTGAAAAA-A-AAATT-AAAAAATACCTCAGTATGTGACTGGAAGCTCAACTCACCTCTAGCAA
1 TTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAA
*
317814 TATAAGTTGA-TT
66 TATGAGTTGATTT
* * * * * * *
317826 TTTGAAAAGCAGAAATT-GAAAAATACCTTGGTATGTGACCCGAGACTCAACTCACTTGTCGCAA
1 TTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAA
317890 TATGAGTTGATTT
66 TATGAGTTGATTT
* *
317903 TTTGAAGAGCAAAAAAAAAATTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTC
1 TTT---GA--AAAACAGAAATTAAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTC
317968 TCGCAATATGAGTTGATTTT
60 TCGCAATATGAGTTGA-TTT
* *
317988 TTTGAAAAACAAAAATTAAAAAAATACCTCGGCGTGTGACCCGAGAGGCTCAACTCACCTCTCGC
1 TTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCC--GAGGCTCAACTCACCTCTCGC
318053 AATATGAGTTGA-TT
64 AATATGAGTTGATTT
* ** *
318067 ATTGAAAAAACAGAAATTTAAAAGAAATACCTTAGCATGTG-TCCGAGGCTCAACTCACCTCTCG
1 TTTG-AAAAACAGAAA-TTAAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCG
*
318131 TAATATGAGTTGA-TT
63 CAATATGAGTTGATTT
* * **
318146 TTTGAAAAACA-AATTTAAAAGAAATACCTCGGCATATG-TTCGAGGCTCAACTCACCTCTCGCA
1 TTTGAAAAACAGAAATTAAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCA
**
318209 ATATGAGTCAATTTT
65 ATATGAGTTGA-TTT
* ** * *
318224 TTTGAAAAATAGAAATTAAAAAAAATACCTCGGCATGTG-TTCGAGGTTCAACTCACCTCTCGTA
1 TTTGAAAAACAGAAATT-AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCA
318288 ATATGAGTTGATTT
65 ATATGAGTTGATTT
** ** * * *
318302 TTTTTAAAACAGAAATTAAAAAAAATATTTTGGCGTGCGACCCGAGGCTCAACTCACCTCTCGCA
1 TTTGAAAAACAGAAATT-AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCA
318367 ATATGAGTTGATTTT
65 ATATGAGTTGA-TTT
* * *
318382 TTTGAAAAATAGAAATT--AAAAATACCTCAGC--GTAACCCGAGGCTCAACTCACCTCTCGCAA
1 TTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAA
318443 TATGAGTTGATCTT
66 TATGAGTTGAT-TT
*** * * * * * * *
318457 TTTGAAAAGTGGAAATT--GAAAATACCTCAGCGTGCGGCCCAAGGCTCAACTCACCTCTCGCAT
1 TTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAA
318520 TATGAGTTGATTT
66 TATGAGTTGATTT
* *
318533 TTTGAAAAACATAAATTGAAAA
1 TTTGAAAAACAGAAATTAAAAA
318555 TATAATTCTT
Statistics
Matches: 688, Mismatches: 88, Indels: 52
0.83 0.11 0.06
Matches are distributed among these distances:
74 65 0.09
75 70 0.10
76 128 0.19
77 53 0.08
78 55 0.08
79 146 0.21
80 48 0.07
81 41 0.06
82 25 0.04
83 2 0.00
84 49 0.07
85 6 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (78 bp):
TTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGATTT
Found at i:318250 original size:155 final size:157
Alignment explanation
Indices: 317676--318541 Score: 903
Period size: 155 Copynumber: 5.6 Consensus size: 157
317666 TGAGTTGACC
* * * * *
317676 TTTGAAAAATAGAAATT-GAAAAATACATCGGTATGTGACCTGAGGCTCAACTCACCTCTCGCAA
1 TTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAA
* ** *
317740 TATGAGTTGA--TTTTTGAAAAA-A-AAATT--AAAAAATACCTCAGTATGTGACTGGAAGCTCA
66 TATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAAAAATACCTCAGCATGTG-CCCGAGGCTCA
* *
317799 ACTCACCTCTAGCAATATAAGTTGA-TT
130 ACTCACCTCTCGCAATATGAGTTGATTT
* * * * * * *
317826 TTTGAAAAGCAGAAATT-GAAAAATACCTTGGTATGTGACCCGAGACTCAACTCACTTGTCGCAA
1 TTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAA
* * * * *
317890 TATGAGTTGATTTTTTGAAGAGCAAAAAAAAAATTAAAAGAAATACCTCGGCATGTGACCCGAGG
66 TATGAGTTGATTTTTT--TGA--AAAATAGAAATTAAAAAAAATACCTCAGCATGTG-CCCGAGG
317955 CTCAACTCACCTCTCGCAATATGAGTTGATTTT
126 CTCAACTCACCTCTCGCAATATGAGTTGA-TTT
* *
317988 TTTGAAAAACAAAAATTAAAAAAATACCTCGGCGTGTGACCCGAGAGGCTCAACTCACCTCTCGC
1 TTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCC--GAGGCTCAACTCACCTCTCGC
* * * * *
318053 AATATGAGTTGA--TTATTGAAAAAACAGAAATTTAAAAGAAATACCTTAGCATGTGTCCGAGGC
64 AATATGAGTTGATTTTTTTG-AAAAATAGAAA-TTAAAAAAAATACCTCAGCATGTGCCCGAGGC
*
318116 TCAACTCACCTCTCGTAATATGAGTTGA-TT
127 TCAACTCACCTCTCGCAATATGAGTTGATTT
* * **
318146 TTTGAAAAACA-AATTTAAAAGAAATACCTCGGCATATG-TTCGAGGCTCAACTCACCTCTCGCA
1 TTTGAAAAACAGAAATTAAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCA
** * ** *
318209 ATATGAGTCAATTTTTTTGAAAAATAGAAATTAAAAAAAATACCTCGGCATGTGTTCGAGGTTCA
65 ATATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAAAAATACCTCAGCATGTGCCCGAGGCTCA
*
318274 ACTCACCTCTCGTAATATGAGTTGATTT
130 ACTCACCTCTCGCAATATGAGTTGATTT
** ** * * *
318302 TTTTTAAAACAGAAATTAAAAAAAATATTTTGGCGTGCGACCCGAGGCTCAACTCACCTCTCGCA
1 TTTGAAAAACAGAAATT-AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCA
*
318367 ATATGAGTTGATTTTTTTGAAAAATAGAAATT---AAAAATACCTCAGC--GTAACCCGAGGCTC
65 ATATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAAAAATACCTCAGCATGT-GCCCGAGGCTC
318427 AACTCACCTCTCGCAATATGAGTTGATCTT
129 AACTCACCTCTCGCAATATGAGTTGAT-TT
*** * * * * * * *
318457 TTTGAAAAGTGGAAATT--GAAAATACCTCAGCGTGCGGCCCAAGGCTCAACTCACCTCTCGCAT
1 TTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAA
318520 TATGAGTTGA-TTTTTTGAAAAA
66 TATGAGTTGATTTTTTTGAAAAA
318542 CATAAATTGA
Statistics
Matches: 610, Mismatches: 80, Indels: 51
0.82 0.11 0.07
Matches are distributed among these distances:
150 66 0.11
151 12 0.02
152 52 0.09
153 2 0.00
154 35 0.06
155 113 0.19
156 25 0.04
157 30 0.05
158 90 0.15
160 91 0.15
161 23 0.04
162 18 0.03
163 23 0.04
165 30 0.05
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (157 bp):
TTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAAAAATACCTCAGCATGTGCCCGAGGCTCAA
CTCACCTCTCGCAATATGAGTTGATTT
Found at i:318358 original size:234 final size:234
Alignment explanation
Indices: 317717--318554 Score: 923
Period size: 234 Copynumber: 3.6 Consensus size: 234
317707 TATGTGACCT
317717 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAA-A-AAATTAAAAAATACCT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAAATACCT
* ** * * * * *
317778 CAGTATGTGACTGGAAGCTCAACTCACCTCTAGCAATATAAGTTGA-TTTTTGAAAAGCAGAAAT
66 CAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAGAAAT
* * * * *
317842 T--GAAAAATACCTTGGTATGTGACCCGAGACTCAACTCACTTGTCGCAATATGAGTTGATTTTT
131 TAAAAAAAATACCTTGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*
317905 TGAAGAGCAAAAAAAAAATTAAAAGAAATACCTCGGCATGTGACCC
196 T-----G-AAAAAAAAAATTAAAAGAAATACCTCGGCATATG-CCC
* *
317951 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTAAAAAAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATT-AAAAAATACC
* * * **
318016 TCGGCGTGTGACCCGAGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTATTGAAAAAACAGA
65 TCAGCATGTGACCC--GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAGA
* * * *
318081 AATTTAAAAGAAATACCTTAGCATGTG-TCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGA-
128 AA-TTAAAAAAAATACCTTGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* * **
318144 TTTTTGAAAAACAAATTTAAAAGAAATACCTCGGCATATGTTC
192 TTTTTGAAAAAAAAAATTAAAAGAAATACCTCGGCATATGCCC
**
318187 GAGGCTCAACTCACCTCTCGCAATATGAGTCAATTTTTTTGAAAAATAGAAATTAAAAAAAATAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATT--AAAAAATAC
* ** * * *
318252 CTCGGCATGTG-TTCGAGGTTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTTAAAACAGAA
64 CTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAGAA
** * *
318316 ATTAAAAAAAATATTTTGGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
129 ATTAAAAAAAATACCTTGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT
* * * *
318381 TTTTGAAAAATAGAAATT--AA-AAATACCTCAGCGTA-ACCC
193 TTTTGAAAAA-AAAAATTAAAAGAAATACCTCGGCATATGCCC
* * * *
318420 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTTTGAAAAGTGGAAATT-GAAAATACCT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAAATACCT
* * * * * * *
318484 CAGCGTGCGGCCCAAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACATAAAT
66 CAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAGAAAT
*
318549 TGAAAA
131 TAAAAA
318555 TATAATTCTT
Statistics
Matches: 513, Mismatches: 74, Indels: 37
0.82 0.12 0.06
Matches are distributed among these distances:
230 15 0.03
231 51 0.10
233 68 0.13
234 125 0.24
235 2 0.00
236 74 0.14
237 56 0.11
238 6 0.01
239 19 0.04
241 30 0.06
242 13 0.03
243 7 0.01
244 31 0.06
245 16 0.03
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (234 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAAATACCT
CAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAGAAAT
TAAAAAAAATACCTTGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
TGAAAAAAAAAATTAAAAGAAATACCTCGGCATATGCCC
Found at i:319436 original size:29 final size:31
Alignment explanation
Indices: 319404--319466 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
319394 TTCATCTTGA
319404 TTTTTATTTTTCTTTT-CTT-TTCTTTTTTG
1 TTTTTATTTTTCTTTTACTTATTCTTTTTTG
* * * *
319433 TTTTTGTTTTTGTTTTATTTATTTTTTTTTG
1 TTTTTATTTTTCTTTTACTTATTCTTTTTTG
319464 TTT
1 TTT
319467 CCTTTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 14 0.50
30 2 0.07
31 12 0.43
ACGTcount: A:0.05, C:0.05, G:0.06, T:0.84
Consensus pattern (31 bp):
TTTTTATTTTTCTTTTACTTATTCTTTTTTG
Found at i:321297 original size:18 final size:19
Alignment explanation
Indices: 321262--321297 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
321252 CGAATCTATT
321262 AATTAAACACGAAACAGAA
1 AATTAAACACGAAACAGAA
*
321281 AATTAAA-ACGCAACAGA
1 AATTAAACACGAAACAGA
321298 TCACAACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.17, G:0.11, T:0.11
Consensus pattern (19 bp):
AATTAAACACGAAACAGAA
Found at i:321632 original size:107 final size:107
Alignment explanation
Indices: 321446--322075 Score: 1251
Period size: 107 Copynumber: 5.9 Consensus size: 107
321436 AAACACAATA
*
321446 AAAGAATTGAAATAAGTTAGATAAAGAAAACGGCACAAGCAGAATTTAAAAGAAAGAATGACCAG
1 AAAGATTTGAAATAAGTTAGATAAAGAAAACGGCACAAGCAGAATTTAAAAGAAAGAATGACCAG
321511 CAAGAAATAAAAGATAAAGTCCTAAGAAGCCTTGAAATCCCG
66 CAAGAAATAAAAGATAAAGTCCTAAGAAGCCTTGAAATCCCG
321553 AAAGATTTGAAATAAGTTAGATAAAGAAAACGGCACAAGCAGAATTTAAAAGAAAGAATGACCAG
1 AAAGATTTGAAATAAGTTAGATAAAGAAAACGGCACAAGCAGAATTTAAAAGAAAGAATGACCAG
321618 CAAGAAATAAAAGATAAAGTCCTAAGAAGCCTTGAAATCCCG
66 CAAGAAATAAAAGATAAAGTCCTAAGAAGCCTTGAAATCCCG
321660 AAAGATTTGAAATAAGTTAGATAAAGAAAACGGCACAAGCAGAATTTAAAAGAAAGAATGACCAG
1 AAAGATTTGAAATAAGTTAGATAAAGAAAACGGCACAAGCAGAATTTAAAAGAAAGAATGACCAG
321725 CAAGAAATAAAAGATAAAGTCCTAAGAAGCCTTGAAATCCCG
66 CAAGAAATAAAAGATAAAGTCCTAAGAAGCCTTGAAATCCCG
321767 AAAGATTTGAAATAAGTTAGATAAAGAAAACGGCACAAGCAGAATTTAAAAGAAAGAATGACCAG
1 AAAGATTTGAAATAAGTTAGATAAAGAAAACGGCACAAGCAGAATTTAAAAGAAAGAATGACCAG
321832 CAAGAAATAAAAGATAAAGTCCTAAGAAGCCTTGAAATCCCG
66 CAAGAAATAAAAGATAAAGTCCTAAGAAGCCTTGAAATCCCG
321874 AAAGATTTGAAATAAGTTAGATAAAGAAAACGGCACAAGCAGAATTTAAAAGAAAGAATGACCAG
1 AAAGATTTGAAATAAGTTAGATAAAGAAAACGGCACAAGCAGAATTTAAAAGAAAGAATGACCAG
321939 CAAGAAATAAAAGATAAAGTCCTAAGAAGCCTTGAAATCCCG
66 CAAGAAATAAAAGATAAAGTCCTAAGAAGCCTTGAAATCCCG
321981 AAAGATTTGAAATAAGTTAGATAAAGAAAACGGCACAAGCAGAATTTAAAAGAAAGAATGACCAG
1 AAAGATTTGAAATAAGTTAGATAAAGAAAACGGCACAAGCAGAATTTAAAAGAAAGAATGACCAG
322046 CAAGAAATAAAAGATAAAGTCCTAAGAAGC
66 CAAGAAATAAAAGATAAAGTCCTAAGAAGC
322076 GGACTGAATT
Statistics
Matches: 522, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 522 1.00
ACGTcount: A:0.52, C:0.13, G:0.19, T:0.17
Consensus pattern (107 bp):
AAAGATTTGAAATAAGTTAGATAAAGAAAACGGCACAAGCAGAATTTAAAAGAAAGAATGACCAG
CAAGAAATAAAAGATAAAGTCCTAAGAAGCCTTGAAATCCCG
Found at i:323978 original size:8 final size:8
Alignment explanation
Indices: 323965--323993 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
323955 TTTCTTGATC
323965 CTTCTTAG
1 CTTCTTAG
323973 CTTCTTAG
1 CTTCTTAG
323981 CTTCTTAG
1 CTTCTTAG
323989 CTTCT
1 CTTCT
323994 GTTGAACAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.28, G:0.10, T:0.52
Consensus pattern (8 bp):
CTTCTTAG
Found at i:329571 original size:16 final size:16
Alignment explanation
Indices: 329550--329582 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
329540 TAACAAAACA
329550 GAAGGACGGATCCAAG
1 GAAGGACGGATCCAAG
329566 GAAGGACGGATCCAAG
1 GAAGGACGGATCCAAG
329582 G
1 G
329583 TGCCCTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.39, T:0.06
Consensus pattern (16 bp):
GAAGGACGGATCCAAG
Found at i:330430 original size:11 final size:11
Alignment explanation
Indices: 330414--330438 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
330404 GCTTGGGAAG
330414 ATCAGAGGTGT
1 ATCAGAGGTGT
330425 ATCAGAGGTGT
1 ATCAGAGGTGT
330436 ATC
1 ATC
330439 CTTCCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (11 bp):
ATCAGAGGTGT
Done.