Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 6 of 141
Found at i:1512776 original size:24 final size:24
Alignment explanation
Indices: 1512749--1512827 Score: 65
Period size: 24 Copynumber: 3.3 Consensus size: 24
1512739 GACATATGGT
1512749 GGTGGAGGTGAATGAGATGGTGGA
1 GGTGGAGGTGAATGAGATGGTGGA
* ** *
1512773 GGTGGAGACTTGTAAACATATGGTGGA
1 GGTGGAG--GTG-AATGAGATGGTGGA
*
1512800 --T-GAGGTGAATGAGATGGTGGT
1 GGTGGAGGTGAATGAGATGGTGGA
1512821 GGTGGAG
1 GGTGGAG
1512828 ACTTATAAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 12
0.66 0.15 0.20
Matches are distributed among these distances:
21 10 0.25
22 2 0.05
23 1 0.03
24 13 0.32
25 1 0.03
26 2 0.05
27 11 0.28
ACGTcount: A:0.25, C:0.03, G:0.48, T:0.24
Consensus pattern (24 bp):
GGTGGAGGTGAATGAGATGGTGGA
Found at i:1512871 original size:21 final size:21
Alignment explanation
Indices: 1512845--1512921 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 21
1512835 AATGTAAGGA
1512845 GGAGGTGGTGATGGAGATGGT
1 GGAGGTGGTGATGGAGATGGT
* * *
1512866 GGAGGTGGGGACTTGTAGATGTAAGGG
1 GGAGGTGGTGA--TG--GA-G-ATGGT
*
1512893 GGAGGTGGTGAAGGAGATGGT
1 GGAGGTGGTGATGGAGATGGT
1512914 GGAGGTGG
1 GGAGGTGG
1512922 AGACTTGTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
21 21 0.49
22 1 0.02
23 4 0.09
25 3 0.07
26 1 0.02
27 13 0.30
ACGTcount: A:0.21, C:0.01, G:0.57, T:0.21
Consensus pattern (21 bp):
GGAGGTGGTGATGGAGATGGT
Found at i:1513518 original size:27 final size:26
Alignment explanation
Indices: 1513440--1513514 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 26
1513430 GACGGAGATA
1513440 GTGGAGGTGGGGACTTGTAGACATAAG
1 GTGGAGGTGGGGACTTGTAGACAT-AG
* * * *
1513467 GTGGGGGTGGTGA--GGCAG--AT-G
1 GTGGAGGTGGGGACTTGTAGACATAG
*
1513488 GTGGAGGTGGCGACTTGTAGACATAG
1 GTGGAGGTGGGGACTTGTAGACATAG
1513514 G
1 G
1513515 GTGGTGGAGG
Statistics
Matches: 35, Mismatches: 8, Indels: 11
0.65 0.15 0.20
Matches are distributed among these distances:
21 12 0.34
23 5 0.14
25 5 0.14
26 2 0.06
27 11 0.31
ACGTcount: A:0.21, C:0.08, G:0.49, T:0.21
Consensus pattern (26 bp):
GTGGAGGTGGGGACTTGTAGACATAG
Found at i:1517845 original size:60 final size:60
Alignment explanation
Indices: 1517769--1517885 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 60
1517759 TTTAGTAATA
*
1517769 TGGAGGTGGAGGCTTGTAGACATAAGGTGGAGGAAGAGAAGGAGAAGGTGGAGGTGGAGG
1 TGGAGGTGGAGGCTTGTACACATAAGGTGGAGGAAGAGAAGGAGAAGGTGGAGGTGGAGG
* * * *
1517829 TGGAGGTGG-GGACTTGTACACATATGGTGGAGGAGGTGAAGGAGATGGTGGAGGTGG
1 TGGAGGTGGAGG-CTTGTACACATAAGGTGGAGGAAGAGAAGGAGAAGGTGGAGGTGG
1517886 TGACTTATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 2 0.04
60 49 0.96
ACGTcount: A:0.26, C:0.04, G:0.51, T:0.18
Consensus pattern (60 bp):
TGGAGGTGGAGGCTTGTACACATAAGGTGGAGGAAGAGAAGGAGAAGGTGGAGGTGGAGG
Found at i:1517866 original size:48 final size:48
Alignment explanation
Indices: 1517827--1518365 Score: 765
Period size: 48 Copynumber: 11.2 Consensus size: 48
1517817 TGGAGGTGGA
* * *
1517827 GGTGGAGGTGGGGACTTGTACACATATGGTGGAGGAGGTGAAGGAGAT
1 GGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGAAGGAGAT
* * ** * * *
1517875 GGTGGAGGTGGTGACTTATAAATGTAAGGAGGAGGTGGTGAGGGAGAT
1 GGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGAAGGAGAT
*
1517923 AGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGACA-GAGAT
1 GGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGA-AGGAGAT
* *
1517971 GGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAAGAGAT
1 GGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGAAGGAGAT
* * * * *
1518019 GGTGGAGGTGGGGACTTGTAGACATAGGGTGGAGGTGGTGAGGGAGAT
1 GGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGAAGGAGAT
* *
1518067 GGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGAAGGTGAAGGAGAT
1 GGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGAAGGAGAT
* * * * *
1518115 GGTGGAGGTGGGGACTTGTAGACATATGGTGGAGGTGGTGAAAGAGAT
1 GGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGAAGGAGAT
*
1518163 GGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGACGGAGAT
1 GGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGAAGGAGAT
*
1518211 GGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGAT
1 GGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGAAGGAGAT
* * * * *
1518259 GGTGGAGGTGGGGACTTGTAGACATATGGTGGAGGTGGTGAAAGAGAT
1 GGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGAAGGAGAT
*
1518307 GGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGAT
1 GGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGAAGGAGAT
1518355 GGTGGAGGTGG
1 GGTGGAGGTGG
1518366 TGAGGAAGAT
Statistics
Matches: 429, Mismatches: 60, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
47 1 0.00
48 428 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.19
Consensus pattern (48 bp):
GGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGAAGGAGAT
Found at i:1518005 original size:144 final size:144
Alignment explanation
Indices: 1517827--1518365 Score: 846
Period size: 144 Copynumber: 3.7 Consensus size: 144
1517817 TGGAGGTGGA
* * *
1517827 GGTGGAGGTGGGGACTTGTACACATATGGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGTGACTT
1 GGTGGAGGTGGGGACTTGTAGACATATGGTGGAGGAGGTGAAAGAGATGGTGGAGGTGGAGACTT
* ** * * *
1517892 ATAAATGTAAGGAGGAGGTGGTGAGGGAGATAGTGGAGGTGGAGACTTGTAAACATAAGGTGGAG
66 GTAAACATAAGGAGGAGGAGGTGAGGGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAG
1517957 GAGGTGACA-GAGAT
131 GAGGTGA-AGGAGAT
* * * * *
1517971 GGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAAGAGATGGTGGAGGTGGGGACTT
1 GGTGGAGGTGGGGACTTGTAGACATATGGTGGAGGAGGTGAAAGAGATGGTGGAGGTGGAGACTT
* * * *
1518036 GTAGACATAGGGTGGAGGTGGTGAGGGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAG
66 GTAAACATAAGGAGGAGGAGGTGAGGGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAG
*
1518101 AAGGTGAAGGAGAT
131 GAGGTGAAGGAGAT
*
1518115 GGTGGAGGTGGGGACTTGTAGACATATGGTGGAGGTGGTGAAAGAGATGGTGGAGGTGGAGACTT
1 GGTGGAGGTGGGGACTTGTAGACATATGGTGGAGGAGGTGAAAGAGATGGTGGAGGTGGAGACTT
* *
1518180 GTAAACATAAGGTGGAGGAGGTGACGGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAG
66 GTAAACATAAGGAGGAGGAGGTGAGGGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAG
1518245 GAGGTGAAGGAGAT
131 GAGGTGAAGGAGAT
*
1518259 GGTGGAGGTGGGGACTTGTAGACATATGGTGGAGGTGGTGAAAGAGATGGTGGAGGTGGAGACTT
1 GGTGGAGGTGGGGACTTGTAGACATATGGTGGAGGAGGTGAAAGAGATGGTGGAGGTGGAGACTT
*
1518324 GTAAACATAAGGAGGAGGAGGTGAAGGAGATGGTGGAGGTGG
66 GTAAACATAAGGAGGAGGAGGTGAGGGAGATGGTGGAGGTGG
1518366 TGAGGAAGAT
Statistics
Matches: 366, Mismatches: 28, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
143 1 0.00
144 365 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.19
Consensus pattern (144 bp):
GGTGGAGGTGGGGACTTGTAGACATATGGTGGAGGAGGTGAAAGAGATGGTGGAGGTGGAGACTT
GTAAACATAAGGAGGAGGAGGTGAGGGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAG
GAGGTGAAGGAGAT
Found at i:1518358 original size:69 final size:69
Alignment explanation
Indices: 1518140--1518434 Score: 256
Period size: 69 Copynumber: 4.2 Consensus size: 69
1518130 TTGTAGACAT
* *
1518140 ATGGTGGAGGTGGTGAAAGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGAC
1 ATGGTGGAGGTGGTGAAAGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAA
1518205 GGAG
66 GGAG
* * * * * * * * *** * *
1518209 ATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGA--AGGAGATGGTGGAGGTGG-G
1 ATGGTGGAGGT-G-G---TG-AAAGAGATGGTGGAGGTGGAGACTTGTA-AACAT-AAGGAGGAG
** * * *
1518271 GACTTGTAGACAT
58 GAGGTGAAG-GAG
1518284 ATGGTGGAGGTGGTGAAAGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAA
1 ATGGTGGAGGTGGTGAAAGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAA
1518349 GGAG
66 GGAG
* * *
1518353 ATGGTGGAGGTGGTG-AGGAAGATGGTGGTGGTGGAGACTTGTAAACATAAGGAGGGGGAGGTGA
1 ATGGTGGAGGTGGTGAAAG-AGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGA
*
1518417 ATGAG
65 AGGAG
1518422 ATGGTGGAGGTGG
1 ATGGTGGAGGTGG
1518435 GGACTTGTTA
Statistics
Matches: 173, Mismatches: 40, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
68 2 0.01
69 108 0.62
70 12 0.07
71 3 0.02
73 3 0.02
74 11 0.06
75 34 0.20
ACGTcount: A:0.29, C:0.04, G:0.48, T:0.19
Consensus pattern (69 bp):
ATGGTGGAGGTGGTGAAAGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAA
GGAG
Found at i:1518367 original size:21 final size:21
Alignment explanation
Indices: 1518337--1518386 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1518327 AACATAAGGA
*
1518337 GGAGGAGGTGAAGG-AGATGGT
1 GGAGGTGGTG-AGGAAGATGGT
1518358 GGAGGTGGTGAGGAAGATGGT
1 GGAGGTGGTGAGGAAGATGGT
*
1518379 GGTGGTGG
1 GGAGGTGG
1518387 AGACTTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.22, C:0.00, G:0.60, T:0.18
Consensus pattern (21 bp):
GGAGGTGGTGAGGAAGATGGT
Found at i:1518378 original size:165 final size:165
Alignment explanation
Indices: 1518190--1518530 Score: 533
Period size: 165 Copynumber: 2.1 Consensus size: 165
1518180 GTAAACATAA
*
1518190 GGTGGAGGAGGTGACGGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAGG
1 GGTGGAGGTGGTGACGGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAGG
* *
1518255 AGATGGTGGAGGTGGGGACTTG-TAGACATATGGTGGAGGTGGTGAAAGAGATGGTGGAGGTGGA
66 AGATGGTGGAGGTGGGGACTTGTTA-ACATAGGGTGGAGGTGGTGAAAGAGATGATGGAGGTGGA
1518319 GACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGAT
130 GACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGAT
* * *
1518355 GGTGGAGGTGGTGA-GGAAGATGGTGGTGGTGGAGACTTGTAAACATAAGGAGGGGGAGGTGAAT
1 GGTGGAGGTGGTGACGG-AGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAG
** *
1518419 GAGATGGTGGAGGTGGGGACTTGTTAACATAGGGTGGAGGTGGTGAGGGAGATGATGGAGGTGGG
65 GAGATGGTGGAGGTGGGGACTTGTTAACATAGGGTGGAGGTGGTGAAAGAGATGATGGAGGTGGA
* * *
1518484 GACTTGTAGATATAAGGTGGAGGAGGTGAAGGAGAT
130 GACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGAT
*
1518520 GGCGGAGGTGG
1 GGTGGAGGTGG
1518531 AGACTTGTAG
Statistics
Matches: 161, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
164 2 0.01
165 157 0.98
166 2 0.01
ACGTcount: A:0.27, C:0.04, G:0.50, T:0.19
Consensus pattern (165 bp):
GGTGGAGGTGGTGACGGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAGG
AGATGGTGGAGGTGGGGACTTGTTAACATAGGGTGGAGGTGGTGAAAGAGATGATGGAGGTGGAG
ACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGAT
Found at i:1518426 original size:48 final size:48
Alignment explanation
Indices: 1518355--1519186 Score: 765
Period size: 48 Copynumber: 17.3 Consensus size: 48
1518345 TGAAGGAGAT
* * * *
1518355 GGTGGAGGTGGTG-AGGAAGATGGTGGTGGTGGAGACTTGTAAACATAA
1 GGTGGAGGAGGTGAAGG-AGATGGTGGAGGTGGAGACTTGTAGACATAG
* * * *
1518403 GGAGGGGGAGGTGAATGAGATGGTGGAGGTGGGGACTTGTTA-ACATAG
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTG-TAGACATAG
* * * * * *
1518451 GGTGGAGGTGGTGAGGGAGATGATGGAGGTGGGGACTTGTAGATATAA
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
*
1518499 GGTGGAGGAGGTGAAGGAGATGGCGGAGGTGGAGACTTGTAGACATAG
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
* * ** * *
1518547 GGTGGAGGAGGAGAGGGAGATGGCAGAGATGGGGACTTGTAGACATAG
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
* * * *
1518595 GGTGGGGGAGGTGAGGGAGATGGCGGAGGTGGAGACTTGTAAACATAG
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
* * *
1518643 GGTGGAGGAGGTGAGGGAGATGGTGGAGGTGGTGACTTGTAGACATAA
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
* *
1518691 GGT---GGAGGTGAGGGAGATGGCGGAGGTGGAGACTTGTAGACATAG
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
* * * * *
1518736 GGTGGTGGAGGAGAGGGAGATGGCGGAGGTGGAGACTTGTATACATAG
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
* * *
1518784 GGTGGAGGAGGAGAGGGAGATGGCGGAGGTGGAGACTTGTAGACATAG
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
* * * *
1518832 GGTGGAGGTGGTGAAGGTGATGGTGGTGGTGGGGACTTGTAGACATAG
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
* * * * * * * * *
1518880 GGTGGAGGTGGTAAAGGTGATGGTGGTGGTGTAGACCTGTAAATATAA
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
* * * * * *
1518928 GGAGGAGGTGGAGAGGGAGATGGTGAAGGTGGAGACTTGTAGACATAA
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
* * * * *
1518976 GGCGGAAGAGGTGAAGGAGATGGTGGAGGTGGTGACTTGTAGGCATAA
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
* * * * * * * *
1519024 GGAGGAGGTGGTGAAGGTGATGGTGGTGGTGGTGGTGGGGACTTATAAACATAT
1 GGTGGAGGAGGTGAA-G-GA----GATGGTGGAGGTGGAGACTTGTAGACATAG
* * * * * * * *
1519078 GGAGGTGGTGGAGATGGAGATGGTGGAGGTGGGGACTTGTACACGTAG
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
* * * * * * * * *
1519126 GGAGGTGGAGGGGAAGGAGAAGGTGGCGGTGGGGACTTATAGGCATAC
1 GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
*
1519174 GGTGGTGGAGGTG
1 GGTGGAGGAGGTG
1519187 GGGACTTGTA
Statistics
Matches: 663, Mismatches: 109, Indels: 24
0.83 0.14 0.03
Matches are distributed among these distances:
45 42 0.06
47 2 0.00
48 574 0.87
49 5 0.01
50 2 0.00
52 2 0.00
53 1 0.00
54 35 0.05
ACGTcount: A:0.25, C:0.05, G:0.50, T:0.20
Consensus pattern (48 bp):
GGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAGACATAG
Found at i:1518480 original size:117 final size:117
Alignment explanation
Indices: 1518241--1518482 Score: 324
Period size: 117 Copynumber: 2.1 Consensus size: 117
1518231 AACATAAGGA
* * * * * *
1518241 GGAGGAGGTGAAGGAGATGGTGGAGGTGGGGACTTGTAGACATATGGTGGAGGTGGTGAAAGAGA
1 GGAGGTGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAAGAGA
*
1518306 TGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGATGGT
66 TGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGATGAT
* * *
1518358 GGAGGTGGTG-AGGAAGATGGTGGTGGTGGAGACTTGTAAACATAAGGAGGGGGAGGTGAATGAG
1 GGAGGTGGTGAAGG-AGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAAGAG
* * * * * *
1518422 ATGGTGGAGGTGGGGACTTGTTAACATAGGGTGGAGGTGGTGAGGGAGATGAT
65 ATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGATGAT
1518475 GGAGGTGG
1 GGAGGTGG
1518483 GGACTTGTAG
Statistics
Matches: 108, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
116 3 0.03
117 105 0.97
ACGTcount: A:0.27, C:0.03, G:0.50, T:0.20
Consensus pattern (117 bp):
GGAGGTGGTGAAGGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAAGAGA
TGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGATGAT
Found at i:1518503 original size:144 final size:144
Alignment explanation
Indices: 1518355--1519187 Score: 846
Period size: 144 Copynumber: 5.7 Consensus size: 144
1518345 TGAAGGAGAT
* * * * * * *
1518355 GGTGGAGGTGGTGAGGAAGATGGTGGTGGTGGAGACTTGTAAACATAAGGAGGGGGAGGTGAATG
1 GGTGGAGGAGGAGAGGGAGATGGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGGAGGTGAAGG
* *
1518420 AGATGGTGGAGGTGGGGACTTGTTA-ACATAGGGTGGAGGTGGTGAGGGAGATGATGGAGGTGGG
66 AGATGGTGGAGGTGGGGACTTG-TAGACATAGGGTGGAGGTGGTGAGGGAGATGGTGGAGGTGGA
* *
1518484 GACTTGTAGATATAA
130 GACTTGTAAACATAA
* * * * * * *
1518499 GGTGGAGGAGGTGAAGGAGATGGCGGAGGTGGAGACTTGTAGACATAGGGTGGAGGAGGAGAGGG
1 GGTGGAGGAGGAGAGGGAGATGGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGGAGGTGAAGG
** * * * *
1518564 AGATGGCAGAGATGGGGACTTGTAGACATAGGGTGGGGGAGGTGAGGGAGATGGCGGAGGTGGAG
66 AGATGGTGGAGGTGGGGACTTGTAGACATAGGGTGGAGGTGGTGAGGGAGATGGTGGAGGTGGAG
*
1518629 ACTTGTAAACATAG
131 ACTTGTAAACATAA
* * * *
1518643 GGTGGAGGAGGTGAGGGAGATGGTGGAGGTGGTGACTTGTAGACAT-A--AGGTGGAGGTGAGGG
1 GGTGGAGGAGGAGAGGGAGATGGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGGAGGTGAAGG
* * * * * *
1518705 AGATGGCGGAGGTGGAGACTTGTAGACATAGGGTGGTGGAGGAGAGGGAGATGGCGGAGGTGGAG
66 AGATGGTGGAGGTGGGGACTTGTAGACATAGGGTGGAGGTGGTGAGGGAGATGGTGGAGGTGGAG
* *
1518770 ACTTGTATACATAG
131 ACTTGTAAACATAA
* * * *
1518784 GGTGGAGGAGGAGAGGGAGATGGCGGAGGTGGAGACTTGTAGACATAGGGTGGAGGTGGTGAAGG
1 GGTGGAGGAGGAGAGGGAGATGGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGGAGGTGAAGG
* * * * * * *
1518849 TGATGGTGGTGGTGGGGACTTGTAGACATAGGGTGGAGGTGGTAAAGGTGATGGTGGTGGTGTAG
66 AGATGGTGGAGGTGGGGACTTGTAGACATAGGGTGGAGGTGGTGAGGGAGATGGTGGAGGTGGAG
* *
1518914 ACCTGTAAATATAA
131 ACTTGTAAACATAA
* * * * *
1518928 GGAGGAGGTGGAGAGGGAGATGGTGAAGGTGGAGACTTGTAGACATAAGGCGGAAGAGGTGAAGG
1 GGTGGAGGAGGAGAGGGAGATGGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGGAGGTGAAGG
* * * * * *
1518993 AGATGGTGGAGGTGGTGACTTGTAGGCATAAGGAGGAGGTGGTGAAGGTGATGGTGGTGGTGGTG
66 AGATGGTGGAGGTGGGGACTTGTAGACATAGGGTGGAGGTGGTG-AGG-GA----GATGGTGGAG
* * *
1519058 GTGGGGACTTATAAACATAT
125 GTGGAGACTTGTAAACATAA
* * * * * * * * * *
1519078 GGAGGTGGTGGAGATGGAGATGGTGGAGGTGGGGACTTGTACACGTAGGGAGGTGGAGGGGAAGG
1 GGTGGAGGAGGAGAGGGAGATGGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGGAGGTGAAGG
* * * *
1519143 AGAAGGTGGCGGTGGGGACTTATAGGCATACGGTGGTGGAGGTGG
66 AGATGGTGGAGGTGGGGACTTGTAGACATA--G-GGTGGAGGTGG
1519188 GGACTTGTAG
Statistics
Matches: 574, Mismatches: 102, Indels: 17
0.83 0.15 0.02
Matches are distributed among these distances:
141 128 0.22
143 2 0.00
144 328 0.57
145 2 0.00
146 1 0.00
150 103 0.18
153 10 0.02
ACGTcount: A:0.25, C:0.05, G:0.50, T:0.20
Consensus pattern (144 bp):
GGTGGAGGAGGAGAGGGAGATGGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGGAGGTGAAGG
AGATGGTGGAGGTGGGGACTTGTAGACATAGGGTGGAGGTGGTGAGGGAGATGGTGGAGGTGGAG
ACTTGTAAACATAA
Found at i:1518521 original size:213 final size:213
Alignment explanation
Indices: 1518140--1518569 Score: 637
Period size: 213 Copynumber: 2.0 Consensus size: 213
1518130 TTGTAGACAT
* *
1518140 ATGGTGGAGGTGGTGAAAGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGTGGAGGAGGTGAC
1 ATGGTGGAGGTGGTGAAAGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAA
*
1518205 GGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGATGGTGGAGGTGG
66 GGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGATGATGGAGGTGG
* * *
1518270 GGACTTGTAGACATATGGTGGAGGTGGTGAAAGAGATGGTGGAGGTGGAGACTTGTAAACATAAG
131 GGACTTGTAGACATAAGGTGGAGGAGGTGAAAGAGATGGCGGAGGTGGAGACTTGTAAACATAAG
*
1518335 GAGGAGGAGGTGAAGGAG
196 GAGGAGGAGGAGAAGGAG
* * *
1518353 ATGGTGGAGGTGGTG-AGGAAGATGGTGGTGGTGGAGACTTGTAAACATAAGGAGGGGGAGGTGA
1 ATGGTGGAGGTGGTGAAAG-AGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGA
* * * * * * *
1518417 ATGAGATGGTGGAGGTGGGGACTTGTTAACATAGGGTGGAGGTGGTGAGGGAGATGATGGAGGTG
65 AGGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGATGATGGAGGTG
* * * *
1518482 GGGACTTGTAGATATAAGGTGGAGGAGGTGAAGGAGATGGCGGAGGTGGAGACTTGTAGACATAG
130 GGGACTTGTAGACATAAGGTGGAGGAGGTGAAAGAGATGGCGGAGGTGGAGACTTGTAAACATAA
* *
1518547 GGTGGAGGAGGAGAGGGAG
195 GGAGGAGGAGGAGAAGGAG
1518566 ATGG
1 ATGG
1518570 CAGAGATGGG
Statistics
Matches: 193, Mismatches: 23, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
212 2 0.01
213 191 0.99
ACGTcount: A:0.28, C:0.04, G:0.49, T:0.19
Consensus pattern (213 bp):
ATGGTGGAGGTGGTGAAAGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAA
GGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGAGGAGGAGGTGAAGGAGATGATGGAGGTGG
GGACTTGTAGACATAAGGTGGAGGAGGTGAAAGAGATGGCGGAGGTGGAGACTTGTAAACATAAG
GAGGAGGAGGAGAAGGAG
Found at i:1518717 original size:24 final size:24
Alignment explanation
Indices: 1518690--1518769 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 24
1518680 TGTAGACATA
1518690 AGGTGGAGGTGAGGGAGATGGCGG
1 AGGTGGAGGTGAGGGAGATGGCGG
* * *
1518714 AGGTGGAGACTTGTA--GACATAG-GG
1 AGGTGGAG--GTG-AGGGAGATGGCGG
* *
1518738 TGGTGGAGGAGAGGGAGATGGCGG
1 AGGTGGAGGTGAGGGAGATGGCGG
1518762 AGGTGGAG
1 AGGTGGAG
1518770 ACTTGTATAC
Statistics
Matches: 41, Mismatches: 9, Indels: 12
0.66 0.15 0.19
Matches are distributed among these distances:
21 1 0.02
22 1 0.02
23 5 0.12
24 26 0.63
25 5 0.12
26 2 0.05
27 1 0.02
ACGTcount: A:0.24, C:0.05, G:0.56, T:0.15
Consensus pattern (24 bp):
AGGTGGAGGTGAGGGAGATGGCGG
Found at i:1518790 original size:27 final size:27
Alignment explanation
Indices: 1518712--1518890 Score: 97
Period size: 27 Copynumber: 7.3 Consensus size: 27
1518702 GGGAGATGGC
1518712 GGAGGTGGAGACTTGTAGACATAGGGT
1 GGAGGTGGAGACTTGTAGACATAGGGT
* * * * *
1518739 GGTGGAGGAGA---G-GGAGAT--GGC
1 GGAGGTGGAGACTTGTAGACATAGGGT
*
1518760 GGAGGTGGAGACTTGTATACATAGGGT
1 GGAGGTGGAGACTTGTAGACATAGGGT
* * * *
1518787 GGAGGAGGAGA---G-GGAGAT--GGC
1 GGAGGTGGAGACTTGTAGACATAGGGT
1518808 GGAGGTGGAGACTTGTAGACATAGGGT
1 GGAGGTGGAGACTTGTAGACATAGGGT
* **
1518835 GGAGGTGGTGA-AGGT-G--AT--GGT
1 GGAGGTGGAGACTTGTAGACATAGGGT
* *
1518856 GGTGGTGGGGACTTGTAGACATAGGGT
1 GGAGGTGGAGACTTGTAGACATAGGGT
1518883 GGAGGTGG
1 GGAGGTGG
1518891 TAAAGGTGAT
Statistics
Matches: 106, Mismatches: 28, Indels: 36
0.62 0.16 0.21
Matches are distributed among these distances:
21 35 0.33
22 2 0.02
23 10 0.09
24 4 0.04
25 10 0.09
26 2 0.02
27 43 0.41
ACGTcount: A:0.23, C:0.06, G:0.51, T:0.20
Consensus pattern (27 bp):
GGAGGTGGAGACTTGTAGACATAGGGT
Found at i:1519082 original size:54 final size:54
Alignment explanation
Indices: 1518996--1519109 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 54
1518986 GTGAAGGAGA
* * ** * *
1518996 TGGTGGAGGTGGTGACTTGTAGGCATAAGGAGGAGGTGGTGAAGGTGATGGTGG
1 TGGTGGAGGTGGGGACTTATAAACATAAGGAGGAGGTGGAGAAGGAGATGGTGG
* * * *
1519050 TGGTGGTGGTGGGGACTTATAAACATATGGAGGTGGTGGAGATGGAGATGGTGG
1 TGGTGGAGGTGGGGACTTATAAACATAAGGAGGAGGTGGAGAAGGAGATGGTGG
*
1519104 AGGTGG
1 TGGTGG
1519110 GGACTTGTAC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.21, C:0.04, G:0.51, T:0.25
Consensus pattern (54 bp):
TGGTGGAGGTGGGGACTTATAAACATAAGGAGGAGGTGGAGAAGGAGATGGTGG
Found at i:1519096 original size:15 final size:15
Alignment explanation
Indices: 1519076--1519105 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1519066 TTATAAACAT
*
1519076 ATGGAGGTGGTGGAG
1 ATGGAGATGGTGGAG
1519091 ATGGAGATGGTGGAG
1 ATGGAGATGGTGGAG
1519106 GTGGGGACTT
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:0.23, C:0.00, G:0.57, T:0.20
Consensus pattern (15 bp):
ATGGAGATGGTGGAG
Found at i:1519181 original size:30 final size:30
Alignment explanation
Indices: 1519147--1519247 Score: 94
Period size: 30 Copynumber: 3.4 Consensus size: 30
1519137 GGAAGGAGAA
* *
1519147 GGTGGCGGTGGGGACTTATAGGCATACGGT
1 GGTGGTGGTGGGGACTTATAGGCATAAGGT
* * * **
1519177 GGTGGAGGTGGGGACTTGTAGACATAAGAA
1 GGTGGTGGTGGGGACTTATAGGCATAAGGT
* * ** *
1519207 GGTGGTGGTGGAGAGTTATAGGTGTATGGT
1 GGTGGTGGTGGGGACTTATAGGCATAAGGT
1519237 GGTGGTGGTGG
1 GGTGGTGGTGG
1519248 TGATGGTAGA
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.19, C:0.06, G:0.50, T:0.26
Consensus pattern (30 bp):
GGTGGTGGTGGGGACTTATAGGCATAAGGT
Found at i:1521902 original size:23 final size:23
Alignment explanation
Indices: 1521860--1521903 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1521850 ATACAAGGGT
*
1521860 AAAATTATAGTTTAACTCTCATA
1 AAAATTATAATTTAACTCTCATA
1521883 AAAATATATAATTTAA-TCTCA
1 AAAAT-TATAATTTAACTCTCA
1521904 ACCCCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (23 bp):
AAAATTATAATTTAACTCTCATA
Found at i:1526747 original size:14 final size:14
Alignment explanation
Indices: 1526725--1526756 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1526715 TAAGACCATA
*
1526725 AAATTAAAAATTTT
1 AAATAAAAAATTTT
1526739 AAATAAAAAATTTT
1 AAATAAAAAATTTT
1526753 AAAT
1 AAAT
1526757 TATTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATAAAAAATTTT
Found at i:1527225 original size:500 final size:500
Alignment explanation
Indices: 1526401--1527400 Score: 2000
Period size: 500 Copynumber: 2.0 Consensus size: 500
1526391 TTATCCCTTT
1526401 CCAATAGGAGAATGACAAATCAGATTTTTCCTCCTGATTTCTAGCATTTTTTTGTTGAATTTGAA
1 CCAATAGGAGAATGACAAATCAGATTTTTCCTCCTGATTTCTAGCATTTTTTTGTTGAATTTGAA
1526466 TTTTTTAGTAGGAAAAACTGAAATCAGGAAGAAAATTCTGATTTGACATTCTTCTATTAGAAAGA
66 TTTTTTAGTAGGAAAAACTGAAATCAGGAAGAAAATTCTGATTTGACATTCTTCTATTAGAAAGA
1526531 GATAGGGATGACGTGGAATCATAATTTCATACAATCCTTTCTCTCTTTGTGTCACATTACACTAA
131 GATAGGGATGACGTGGAATCATAATTTCATACAATCCTTTCTCTCTTTGTGTCACATTACACTAA
1526596 CAGAAAGCTTACGTGGCATATAACAGTGCAAATGTGGCACCCAAGTCAGCAATTTTAATTTAAGT
196 CAGAAAGCTTACGTGGCATATAACAGTGCAAATGTGGCACCCAAGTCAGCAATTTTAATTTAAGT
1526661 AATTTATGTTGAGAATATAATTATATATTTGATAATTAATTTCTTTTATGTATGTAAGACCATAA
261 AATTTATGTTGAGAATATAATTATATATTTGATAATTAATTTCTTTTATGTATGTAAGACCATAA
1526726 AATTAAAAATTTTAAATAAAAAATTTTAAATTATTTAAATTTAAATTTTAGAAGTGAAAAAATTT
326 AATTAAAAATTTTAAATAAAAAATTTTAAATTATTTAAATTTAAATTTTAGAAGTGAAAAAATTT
1526791 TATTTAGAAAAATATAATTTAATTATGATTGATTGGAAAGTCAAAGTAAAATTCCACTATAACAT
391 TATTTAGAAAAATATAATTTAATTATGATTGATTGGAAAGTCAAAGTAAAATTCCACTATAACAT
1526856 TACTCCTATTTTATATTTTTTAAGGACTTATAGACAAATTTATTA
456 TACTCCTATTTTATATTTTTTAAGGACTTATAGACAAATTTATTA
1526901 CCAATAGGAGAATGACAAATCAGATTTTTCCTCCTGATTTCTAGCATTTTTTTGTTGAATTTGAA
1 CCAATAGGAGAATGACAAATCAGATTTTTCCTCCTGATTTCTAGCATTTTTTTGTTGAATTTGAA
1526966 TTTTTTAGTAGGAAAAACTGAAATCAGGAAGAAAATTCTGATTTGACATTCTTCTATTAGAAAGA
66 TTTTTTAGTAGGAAAAACTGAAATCAGGAAGAAAATTCTGATTTGACATTCTTCTATTAGAAAGA
1527031 GATAGGGATGACGTGGAATCATAATTTCATACAATCCTTTCTCTCTTTGTGTCACATTACACTAA
131 GATAGGGATGACGTGGAATCATAATTTCATACAATCCTTTCTCTCTTTGTGTCACATTACACTAA
1527096 CAGAAAGCTTACGTGGCATATAACAGTGCAAATGTGGCACCCAAGTCAGCAATTTTAATTTAAGT
196 CAGAAAGCTTACGTGGCATATAACAGTGCAAATGTGGCACCCAAGTCAGCAATTTTAATTTAAGT
1527161 AATTTATGTTGAGAATATAATTATATATTTGATAATTAATTTCTTTTATGTATGTAAGACCATAA
261 AATTTATGTTGAGAATATAATTATATATTTGATAATTAATTTCTTTTATGTATGTAAGACCATAA
1527226 AATTAAAAATTTTAAATAAAAAATTTTAAATTATTTAAATTTAAATTTTAGAAGTGAAAAAATTT
326 AATTAAAAATTTTAAATAAAAAATTTTAAATTATTTAAATTTAAATTTTAGAAGTGAAAAAATTT
1527291 TATTTAGAAAAATATAATTTAATTATGATTGATTGGAAAGTCAAAGTAAAATTCCACTATAACAT
391 TATTTAGAAAAATATAATTTAATTATGATTGATTGGAAAGTCAAAGTAAAATTCCACTATAACAT
1527356 TACTCCTATTTTATATTTTTTAAGGACTTATAGACAAATTTATTA
456 TACTCCTATTTTATATTTTTTAAGGACTTATAGACAAATTTATTA
1527401 TTTTTAGAGG
Statistics
Matches: 500, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
500 500 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (500 bp):
CCAATAGGAGAATGACAAATCAGATTTTTCCTCCTGATTTCTAGCATTTTTTTGTTGAATTTGAA
TTTTTTAGTAGGAAAAACTGAAATCAGGAAGAAAATTCTGATTTGACATTCTTCTATTAGAAAGA
GATAGGGATGACGTGGAATCATAATTTCATACAATCCTTTCTCTCTTTGTGTCACATTACACTAA
CAGAAAGCTTACGTGGCATATAACAGTGCAAATGTGGCACCCAAGTCAGCAATTTTAATTTAAGT
AATTTATGTTGAGAATATAATTATATATTTGATAATTAATTTCTTTTATGTATGTAAGACCATAA
AATTAAAAATTTTAAATAAAAAATTTTAAATTATTTAAATTTAAATTTTAGAAGTGAAAAAATTT
TATTTAGAAAAATATAATTTAATTATGATTGATTGGAAAGTCAAAGTAAAATTCCACTATAACAT
TACTCCTATTTTATATTTTTTAAGGACTTATAGACAAATTTATTA
Found at i:1527247 original size:14 final size:14
Alignment explanation
Indices: 1527225--1527256 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1527215 TAAGACCATA
*
1527225 AAATTAAAAATTTT
1 AAATAAAAAATTTT
1527239 AAATAAAAAATTTT
1 AAATAAAAAATTTT
1527253 AAAT
1 AAAT
1527257 TATTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATAAAAAATTTT
Found at i:1528258 original size:8 final size:8
Alignment explanation
Indices: 1528234--1528272 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
1528224 AATTAAAATT
1528234 TTATAAAA
1 TTATAAAA
1528242 TT-TAAAAA
1 TTAT-AAAA
1528250 TTATAAAA
1 TTATAAAA
1528258 TTATAAAA
1 TTATAAAA
1528266 TTATAAA
1 TTATAAA
1528273 TCAATTCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.03
8 27 0.93
9 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TTATAAAA
Found at i:1529034 original size:34 final size:34
Alignment explanation
Indices: 1528995--1529066 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
1528985 TTAATTATAA
1528995 TTTTATTAATAAAATAATATATATCACAATATTT
1 TTTTATTAATAAAATAATATATATCACAATATTT
1529029 TTTTATTAATAAAATAATATATATCACAATATTT
1 TTTTATTAATAAAATAATATATATCACAATATTT
1529063 TTTT
1 TTTT
1529067 CTTTTTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (34 bp):
TTTTATTAATAAAATAATATATATCACAATATTT
Found at i:1532505 original size:2 final size:2
Alignment explanation
Indices: 1532498--1532527 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1532488 AGTTGGTGTG
1532498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1532528 TTGCAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1536765 original size:18 final size:18
Alignment explanation
Indices: 1536742--1536776 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1536732 GGTCATTGAA
*
1536742 TTTGATAATTAAGTTTAT
1 TTTGATAATTAAATTTAT
*
1536760 TTTGATATTTAAATTTA
1 TTTGATAATTAAATTTA
1536777 AAAAATATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (18 bp):
TTTGATAATTAAATTTAT
Found at i:1537494 original size:18 final size:19
Alignment explanation
Indices: 1537468--1537507 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1537458 TTTACATATT
*
1537468 TTTATAATTA-TACTTAAA
1 TTTAAAATTATTACTTAAA
*
1537486 TTTAAAATTATTATTTAAA
1 TTTAAAATTATTACTTAAA
1537505 TTT
1 TTT
1537508 GATTTGAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAAATTATTACTTAAA
Found at i:1540542 original size:203 final size:205
Alignment explanation
Indices: 1540147--1540753 Score: 584
Period size: 210 Copynumber: 2.9 Consensus size: 205
1540137 TTAAACACGT
* * * *
1540147 GTTTGATCATTGGGTTTTTTTAATTATTTTATTTAAATATGATATAAAAGTACGAAAAGATAAAA
1 GTTTGATCATT-GG-ATTTGTAATTATTTTATTTAAAAATGATATAAAAGTACGAAAAGACAAAA
* * * *
1540212 ATGAAATCATAATAATATTAATTATAATTTAAAAGGAGTATTTCTATAATTTCATAATTGAGTTG
64 GTGAAATCACAATAACATTAATTATAATTTAAAAGGAGTATTTCTATAATTTCATAATTAAGTTG
* * * * ** * *
1540277 GTGATCCAGTTAAGGGTGACATTAGCTCCTTAAATTGCTTAAATATAAGTATTAGGTTAGATATT
129 GTGATCCAATTAAAGGTGACACTAACTCAGTAAAGTGCTTAAATATAAGTATTAGATTAGATATT
*
1540342 -A-A-ATA-TGC
194 AACACATATTCC
* *
1540350 GTTTGATCATTGGATTTGTAATTATATTATTTAAAAATGATATAAAAGTACGAAAAGAGAAAAGT
1 GTTTGATCATTGGATTTGTAATTATTTTATTTAAAAATGATATAAAAGTACGAAAAGACAAAAGT
* * *
1540415 GACATCACAATAACATTGATTATAATTTTACAAAAGGGGTATTTCTATAATTTCATAATTAAGTT
66 GAAATCACAATAACATTAATTATAA-TTT--AAAAGGAGTATTTCTATAATTTCATAATTAAGTT
* * *
1540480 GGTGA-CCAATTAAAGGTGACACTAACTCAGTAACGTGTTTAAATATAAGTATTATATTAGATAT
128 GGTGATCCAATTAAAGGTGACACTAACTCAGTAAAGTGCTTAAATATAAGTATTAGATTAGATAT
1540544 TGAACACATATTCC
193 T-AACACATATTCC
* * **
1540558 GTCCTTGGAT--TTGTAATTTGTAATTATTTTATTTGAAAATGATATAAAAGTATAAAAAGACAA
1 GT--TT-GATCATTG-GATTTGTAATTATTTTATTTAAAAATGATATAAAAGTACGAAAAGACAA
** *** * * * *
1540621 AAGTGTTATTGTAATAATATTAATTATAATTTAAAAGAAATGATATTTTTATAATTTCATAATTG
62 AAGTGAAATCACAATAACATTAATTATAATTTAAAAG-GA-G-TATTTCTATAATTTCATAATTA
* * * * * * * ** *
1540686 AGTAGG-CAGTTCAATT-AAGAGCGATACTAACTCAGTAAAATACTTAAATACGAGTATTATATT
124 AGTTGGTGA-TCCAATTAAAG-GTGACACTAACTCAGTAAAGTGCTTAAATATAAGTATTAGATT
1540749 AGATA
187 AGATA
1540754 CGTTAAATAT
Statistics
Matches: 334, Mismatches: 52, Indels: 28
0.81 0.13 0.07
Matches are distributed among these distances:
201 67 0.20
202 5 0.01
203 60 0.18
204 37 0.11
205 1 0.00
206 1 0.00
207 8 0.02
208 4 0.01
209 8 0.02
210 95 0.28
211 48 0.14
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (205 bp):
GTTTGATCATTGGATTTGTAATTATTTTATTTAAAAATGATATAAAAGTACGAAAAGACAAAAGT
GAAATCACAATAACATTAATTATAATTTAAAAGGAGTATTTCTATAATTTCATAATTAAGTTGGT
GATCCAATTAAAGGTGACACTAACTCAGTAAAGTGCTTAAATATAAGTATTAGATTAGATATTAA
CACATATTCC
Found at i:1550496 original size:16 final size:18
Alignment explanation
Indices: 1550457--1550490 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1550447 TAAGTTTATA
1550457 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
1550474 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
1550491 AATTTAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:1552118 original size:16 final size:16
Alignment explanation
Indices: 1552099--1552148 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1552089 TTTTTAAAAG
1552099 AATATTTATTTATTTT
1 AATATTTATTTATTTT
* *
1552115 AATATTTAATAATTTT
1 AATATTTATTTATTTT
*
1552131 -ATACATTATTT-TTTT
1 AATA-TTTATTTATTTT
1552146 AAT
1 AAT
1552149 GTGTTTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
AATATTTATTTATTTT
Found at i:1553066 original size:17 final size:19
Alignment explanation
Indices: 1553039--1553074 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1553029 TCTAGCCTCG
1553039 ATATAATATTAAT-TTTAA
1 ATATAATATTAATATTTAA
1553057 ATAT-ATATTAATATTTAA
1 ATATAATATTAATATTTAA
1553075 TTTCGAATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATAATATTAATATTTAA
Found at i:1553257 original size:89 final size:89
Alignment explanation
Indices: 1553150--1553315 Score: 237
Period size: 89 Copynumber: 1.9 Consensus size: 89
1553140 ACTCTTAAAC
* * * * * * *
1553150 TTTTTCACAAAAAACAATTAAGCTATTGATTTT-TTTTGCATTTAATTGGGTATTTAAACTTTCA
1 TTTTTCACAAAAAACAATTAAGCCATT-ATTTTCTCTTACACTCAATTGAGTACTTAAACTTTCA
1553214 AAATGCATCAAAAAGGTCCTCAAAA
65 AAATGCATCAAAAAGGTCCTCAAAA
1553239 TTTTTCA-AAAAAAGCAATTAAGCCATTATTTTCTCTTACACTCAATTGAGTACTTAAACTTTCA
1 TTTTTCACAAAAAA-CAATTAAGCCATTATTTTCTCTTACACTCAATTGAGTACTTAAACTTTCA
1553303 AAATGCATCAAAA
65 AAATGCATCAAAA
1553316 GGCCTTCAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
88 11 0.16
89 57 0.84
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (89 bp):
TTTTTCACAAAAAACAATTAAGCCATTATTTTCTCTTACACTCAATTGAGTACTTAAACTTTCAA
AATGCATCAAAAAGGTCCTCAAAA
Found at i:1553382 original size:87 final size:88
Alignment explanation
Indices: 1553158--1553402 Score: 225
Period size: 87 Copynumber: 2.8 Consensus size: 88
1553148 ACTTTTTCAC
* * * * * *
1553158 AAAAAA-CAATTAAGCTATTGATTTT-TTTTGCATTTAATTGGGTATTTAAACTTTCAAAATGCA
1 AAAAAAGCAATTAAGCCA-TGATTTTCTCTTACACTCAATTGGGTACTTAAACTTTCAAAATGCA
* **
1553221 TCAAAAAGGTCCTCAAAATTTTTCA
65 TC-AAAAGGTCCTCAAAATCTTAAA
* *
1553246 AAAAAAGCAATTAAGCCATTATTTTCTCTTACACTCAATTGAGTACTTAAACTTTCAAAATGCAT
1 AAAAAAGCAATTAAGCCATGATTTTCTCTTACACTCAATTGGGTACTTAAACTTTCAAAATGCAT
1553311 CAAAAGG-CCTTC-AAA-CTTAAA
66 CAAAAGGTCC-TCAAAATCTTAAA
* * * * * *
1553332 AAAAAATCAATTAAGCCCCTGCTTTT-TTTTCCCACTCAATTGGGTACTTAAA-TTGCCAAAATG
1 AAAAAAGCAATTAAG-CCATGATTTTCTCTT-ACACTCAATTGGGTACTTAAACTT-TCAAAATG
*
1553395 CATTAAAA
63 CATCAAAA
1553403 ATATCTTTTG
Statistics
Matches: 131, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
86 22 0.17
87 45 0.34
88 20 0.15
89 44 0.34
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (88 bp):
AAAAAAGCAATTAAGCCATGATTTTCTCTTACACTCAATTGGGTACTTAAACTTTCAAAATGCAT
CAAAAGGTCCTCAAAATCTTAAA
Found at i:1553554 original size:20 final size:20
Alignment explanation
Indices: 1553529--1553566 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1553519 AAAAATAAAA
* *
1553529 TTAATATAAATTATTAAATT
1 TTAATAAAAAATATTAAATT
1553549 TTAATAAAAAATATTAAA
1 TTAATAAAAAATATTAAA
1553567 AAATTATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAATAAAAAATATTAAATT
Found at i:1554441 original size:21 final size:21
Alignment explanation
Indices: 1554415--1554457 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1554405 GTTCGGACTC
*
1554415 TAAGAAAGTGTGGGAAAATCT
1 TAAGAAAGTGCGGGAAAATCT
1554436 TAAGAAAGTGCGGGAAAATCT
1 TAAGAAAGTGCGGGAAAATCT
1554457 T
1 T
1554458 GTAACTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.28, T:0.23
Consensus pattern (21 bp):
TAAGAAAGTGCGGGAAAATCT
Found at i:1574659 original size:3 final size:3
Alignment explanation
Indices: 1574653--1574678 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1574643 ATAAAAAAAA
1574653 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1574679 AAAGTGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1582034 original size:21 final size:22
Alignment explanation
Indices: 1582001--1582044 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1581991 ATACAGCATG
*
1582001 TATATTATTTTAATTTTAATTA
1 TATATTATTTTAATTATAATTA
1582023 TATATT-TTTTAATTATAATTA
1 TATATTATTTTAATTATAATTA
1582044 T
1 T
1582045 TAATTTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATATTATTTTAATTATAATTA
Found at i:1582686 original size:4 final size:4
Alignment explanation
Indices: 1582677--1582709 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1582667 AGCCAATTTG
1582677 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1582710 CATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:1583505 original size:133 final size:134
Alignment explanation
Indices: 1583348--1583619 Score: 528
Period size: 133 Copynumber: 2.0 Consensus size: 134
1583338 ATTTAATATT
*
1583348 TTATTAAAAATAAAATTTTAATTTTGATCCAAAATTTTATAATTTTATTTCCTCCCTTAAACAAA
1 TTATAAAAAATAAAATTTTAATTTTGATCCAAAATTTTATAATTTTATTTCCTCCCTTAAACAAA
1583413 TTTCATAACTTCACACCAATGACATTGCTTCTTTTTCCACCAATATTTATTATGCTTAAATTAAA
66 TTTCATAACTTCACACCAATGACATTGCTTCTTTTTCCACCAATATTTATTATGCTTAAATTAAA
1583478 ATAA
131 ATAA
1583482 TTATAAAAAATAAAA-TTTAATTTTGATCCAAAATTTTATAATTTTATTTCCTCCCTTAAACAAA
1 TTATAAAAAATAAAATTTTAATTTTGATCCAAAATTTTATAATTTTATTTCCTCCCTTAAACAAA
1583546 TTTCATAACTTCACACCAATGACATTGCTTCTTTTTCCACCAATATTTATTATGCTTAAATTAAA
66 TTTCATAACTTCACACCAATGACATTGCTTCTTTTTCCACCAATATTTATTATGCTTAAATTAAA
1583611 ATAA
131 ATAA
1583615 TTATA
1 TTATA
1583620 TAAATCAAAA
Statistics
Matches: 137, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
133 123 0.90
134 14 0.10
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (134 bp):
TTATAAAAAATAAAATTTTAATTTTGATCCAAAATTTTATAATTTTATTTCCTCCCTTAAACAAA
TTTCATAACTTCACACCAATGACATTGCTTCTTTTTCCACCAATATTTATTATGCTTAAATTAAA
ATAA
Found at i:1592684 original size:19 final size:19
Alignment explanation
Indices: 1592662--1592699 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1592652 CTGTGTTAAA
* *
1592662 AGTTTTTAAATTTTAAATT
1 AGTTTTCAAACTTTAAATT
1592681 AGTTTTCAAACTTTAAATT
1 AGTTTTCAAACTTTAAATT
1592700 TTTCTAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (19 bp):
AGTTTTCAAACTTTAAATT
Found at i:1619107 original size:2 final size:2
Alignment explanation
Indices: 1619100--1619126 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1619090 AAAACTTTAA
1619100 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1619127 TTACAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1620024 original size:29 final size:29
Alignment explanation
Indices: 1619982--1620055 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
1619972 ATAGGTATCT
1619982 AATCAAATTAGTCCCTCTGTTATTAAATG
1 AATCAAATTAGTCCCTCTGTTATTAAATG
1620011 AATCAAATTAGTCCCTCTGTTATTAAATG
1 AATCAAATTAGTCCCTCTGTTATTAAATG
* *
1620040 AAACAATTTAGTCCCT
1 AATCAAATTAGTCCCT
1620056 ATACTAGTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (29 bp):
AATCAAATTAGTCCCTCTGTTATTAAATG
Found at i:1620066 original size:29 final size:29
Alignment explanation
Indices: 1619985--1620081 Score: 77
Period size: 29 Copynumber: 3.3 Consensus size: 29
1619975 GGTATCTAAT
* ** * *
1619985 CAAATTAGTCCCTCTGTTATTAAATGAAT
1 CAAATTAGTCCCTATACTAGTAAATGAAA
* ** *
1620014 CAAATTAGTCCCTCTGTTATTAAATGAAA
1 CAAATTAGTCCCTATACTAGTAAATGAAA
* * *
1620043 CAATTTAGTCCCTATACTAGTAAAAGAAT
1 CAAATTAGTCCCTATACTAGTAAATGAAA
*
1620072 CAAATAAGTC
1 CAAATTAGTC
1620082 TAAATTGTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (29 bp):
CAAATTAGTCCCTATACTAGTAAATGAAA
Found at i:1621877 original size:31 final size:31
Alignment explanation
Indices: 1621842--1621915 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
1621832 AAGTATTAAT
1621842 TTGAACCAAAAAGCCAAGTTTAGGTACCAAA
1 TTGAACCAAAAAGCCAAGTTTAGGTACCAAA
** * *
1621873 TTGAA-CATTGAGGCCAAGTTTAGGTACCTAA
1 TTGAACCA-AAAAGCCAAGTTTAGGTACCAAA
* *
1621904 TTGGACAAAAAA
1 TTGAACCAAAAA
1621916 AACCTTATGT
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
30 2 0.06
31 29 0.91
32 1 0.03
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (31 bp):
TTGAACCAAAAAGCCAAGTTTAGGTACCAAA
Found at i:1622643 original size:32 final size:33
Alignment explanation
Indices: 1622602--1622683 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
1622592 AATATTAATC
*
1622602 AAGCATCTCAAAAATTTTAAAAATTCTC-ATTA
1 AAGCCTCTCAAAAATTTTAAAAATTCTCTATTA
** * *
1622634 AAGCCTCTCAAATTCTTTTGAAAATTTTCTATTA
1 AAGCCTCTCAAA-AATTTTAAAAATTCTCTATTA
*
1622668 AACCCTC-CAAAAATTT
1 AAGCCTCTCAAAAATTT
1622684 GGAAACTCTC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
32 14 0.35
33 16 0.40
34 10 0.25
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.37
Consensus pattern (33 bp):
AAGCCTCTCAAAAATTTTAAAAATTCTCTATTA
Found at i:1624062 original size:19 final size:19
Alignment explanation
Indices: 1624023--1624062 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1624013 ACTCATTGGT
* *
1624023 TTTTATTTAATATTTAGTA
1 TTTTATATAATATGTAGTA
*
1624042 TTTTATATAATATGTATTA
1 TTTTATATAATATGTAGTA
1624061 TT
1 TT
1624063 CCTTTTATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTATATAATATGTAGTA
Found at i:1628133 original size:137 final size:138
Alignment explanation
Indices: 1627966--1628231 Score: 392
Period size: 137 Copynumber: 1.9 Consensus size: 138
1627956 AATTTATCGA
* * ** * *
1627966 AAACCCAATTTTTTTTAAAAATTAAACATATTATGTCGATTATTCATTCATATCTC-AATTCGAG
1 AAACCCAATTTATTTAAAAAAAAAAACATATTACGTCAATTATTCATTCATATC-CAAATTCGAG
1628030 TAATAAAAAAATTAAAAACAACCATGTAAAAATATGAGGAAGAGAAAACAAAGTGAAAAGATAAA
65 TAATAAAAAAATTAAAAACAACCATGTAAAAATATGAGGAAGAGAAAACAAAGTGAAAAGATAAA
1628095 ATTAATCCG
130 ATTAATCCG
1628104 AAACCCAA-TTATTTAAAAAAAAAAACATATTACGTCAATTATTCATTCATATCCAAATTCGAGT
1 AAACCCAATTTATTTAAAAAAAAAAACATATTACGTCAATTATTCATTCATATCCAAATTCGAGT
* ** * * * *
1628168 AATAAAAAGATTAAAAAGGAGCATGTAAGAATATGAGGATGAGAAAGCAAAGTGAAAAGATAAA
66 AATAAAAAAATTAAAAACAACCATGTAAAAATATGAGGAAGAGAAAACAAAGTGAAAAGATAAA
1628232 GTGATAAAAG
Statistics
Matches: 114, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
136 1 0.01
137 105 0.92
138 8 0.07
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (138 bp):
AAACCCAATTTATTTAAAAAAAAAAACATATTACGTCAATTATTCATTCATATCCAAATTCGAGT
AATAAAAAAATTAAAAACAACCATGTAAAAATATGAGGAAGAGAAAACAAAGTGAAAAGATAAAA
TTAATCCG
Found at i:1644039 original size:20 final size:20
Alignment explanation
Indices: 1644014--1644056 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1644004 TTAGTTGATG
1644014 TGTGGCATTGATGGACCTTA
1 TGTGGCATTGATGGACCTTA
1644034 TGTGGCATTGATGGACCTTA
1 TGTGGCATTGATGGACCTTA
1644054 TGT
1 TGT
1644057 AATTTTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.14, G:0.30, T:0.37
Consensus pattern (20 bp):
TGTGGCATTGATGGACCTTA
Found at i:1647003 original size:21 final size:21
Alignment explanation
Indices: 1646979--1647018 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1646969 GATCAAACAG
*
1646979 AAAACTAAT-CATTTATGTTA
1 AAAAATAATGCATTTATGTTA
*
1646999 AAAAATTATGCATTTATGTT
1 AAAAATAATGCATTTATGTT
1647019 GCTAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAAATAATGCATTTATGTTA
Found at i:1648503 original size:31 final size:30
Alignment explanation
Indices: 1648446--1648505 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
1648436 ATAGCTCAGT
*
1648446 GACTTAAATAAAATTTTAAAATAGTTTAGA
1 GACTTAAATAAAACTTTAAAATAGTTTAGA
**
1648476 GACTTAAATAAAAACTTTCGAATAGTTTAG
1 GACTTAAAT-AAAACTTTAAAATAGTTTAG
1648506 TGACCAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.35
Consensus pattern (30 bp):
GACTTAAATAAAACTTTAAAATAGTTTAGA
Found at i:1656378 original size:66 final size:65
Alignment explanation
Indices: 1656288--1656458 Score: 261
Period size: 66 Copynumber: 2.6 Consensus size: 65
1656278 TGGTTAAACA
* * * * *
1656288 GAATAAATTATCGAATTTTTATTTAATTGAATCAATTATGTTTGATTATTTTATTCGGTTTTATG
1 GAATAAATTATCG-ATTTTGATTTAATTGAATAAATTATATTTGATTAGTTTATTCGATTTTATG
1656353 T
65 T
1656354 GAATAAATTATCGATTTTCGATTTAATTGAATAAATTATATTTGATTAGTTTATTCGATTTTATG
1 GAATAAATTATCGATTTT-GATTTAATTGAATAAATTATATTTGATTAGTTTATTCGATTTTATG
1656419 T
65 T
*
1656420 GAATAAATTATCAATTTTTGATTTAATTGAATAAATTAT
1 GAATAAATTATCGA-TTTTGATTTAATTGAATAAATTAT
1656459 CGATTTTATA
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
65 5 0.05
66 88 0.91
67 4 0.04
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.50
Consensus pattern (65 bp):
GAATAAATTATCGATTTTGATTTAATTGAATAAATTATATTTGATTAGTTTATTCGATTTTATGT
Found at i:1656443 original size:29 final size:28
Alignment explanation
Indices: 1656410--1656465 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1656400 TAGTTTATTC
*
1656410 GATTTTATGTGAATAAATTATCAATTTTT
1 GATTTAAT-TGAATAAATTATCAATTTTT
*
1656439 GATTTAATTGAATAAATTATCGATTTT
1 GATTTAATTGAATAAATTATCAATTTT
1656466 ATATTTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.50
Consensus pattern (28 bp):
GATTTAATTGAATAAATTATCAATTTTT
Found at i:1657267 original size:16 final size:16
Alignment explanation
Indices: 1657246--1657297 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
1657236 TTTAGTTCGC
*
1657246 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAGG
1657262 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
1657278 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
1657294 TGTA
1 TGTA
1657298 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:1657344 original size:45 final size:44
Alignment explanation
Indices: 1657278--1657372 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
1657268 GGATTAGAGG
*
1657278 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
1657323 TGTAATGGAATAGAGGCGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
1657367 TGTAAT
1 TGTAAT
1657373 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 22 0.49
45 23 0.51
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:1657554 original size:18 final size:17
Alignment explanation
Indices: 1657533--1657567 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1657523 TTATTATTAA
*
1657533 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1657551 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1657568 TCTATTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1657558 original size:34 final size:34
Alignment explanation
Indices: 1657519--1657626 Score: 82
Period size: 34 Copynumber: 3.2 Consensus size: 34
1657509 ATATTTAAAC
1657519 ATAATTATTATTAAATATATTTTAATTAAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATAT
* * * *
1657553 ATAATT-TAATAAAATTCTATTTGTATAATT-TAA-A-
1 ATAATTATTATTAAA-TATA-TT-T-TAATTAAAATAT
* *
1657587 ATAATTATTATTACATATAATTTAA-TAATAATAT
1 ATAATTATTATTAAATATATTTTAATTAA-AATAT
1657621 ATAATT
1 ATAATT
1657627 TCATAAAATT
Statistics
Matches: 55, Mismatches: 10, Indels: 18
0.66 0.12 0.22
Matches are distributed among these distances:
30 1 0.02
31 3 0.05
32 3 0.05
33 8 0.15
34 24 0.44
35 8 0.15
36 3 0.05
37 5 0.09
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (34 bp):
ATAATTATTATTAAATATATTTTAATTAAAATAT
Found at i:1657605 original size:26 final size:28
Alignment explanation
Indices: 1657576--1657636 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
1657566 ATTCTATTTG
*
1657576 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
1657602 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
1657630 TAAAATT
1 TATAATT
1657637 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:1657605 original size:68 final size:69
Alignment explanation
Indices: 1657511--1657638 Score: 206
Period size: 68 Copynumber: 1.9 Consensus size: 69
1657501 ATTTAATCAT
*
1657511 ATTTAAACATAATTATTATTAAATATATTTTAATTAA-AATATATAATTTAATAAAATTCTATTT
1 ATTTAAACATAATTATTATTAAATATAATTTAA-TAATAATATATAATTTAATAAAATTCTATTT
1657575 GTATA
65 GTATA
* *
1657580 ATTTAAA-ATAATTATTATTACATATAATTTAATAATAATATATAATTTCATAAAATTCT
1 ATTTAAACATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTCT
1657639 TGATAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
67 3 0.05
68 45 0.82
69 7 0.13
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (69 bp):
ATTTAAACATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTCTATTTG
TATA
Found at i:1657677 original size:93 final size:92
Alignment explanation
Indices: 1657579--1657760 Score: 285
Period size: 93 Copynumber: 2.0 Consensus size: 92
1657569 CTATTTGTAT
* * *
1657579 AATTTAAAATAATTATTATTACATATAATT-TAATAATAATATATAATTTCATAAAATTCTTGAT
1 AATTTAAAATAATTAATATTAAATATAATTAT-ATAATAATATATAATTTCATAAAATTCTTAAT
*
1657643 AATAAAAATTTTCTTATATGAATTTATAC
65 AAT-AAAATGTTCTTATATGAATTTATAC
* *
1657672 AATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCATAAAATTCTTAATA
1 AATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCATAAAATTCTTAATA
1657737 ATAAAATGTTCTTATATGAATTTA
66 ATAAAATGTTCTTATATGAATTTA
1657761 CTAAAATCAA
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
92 21 0.26
93 60 0.73
94 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCATAAAATTCTTAATA
ATAAAATGTTCTTATATGAATTTATAC
Found at i:1661454 original size:29 final size:29
Alignment explanation
Indices: 1661422--1661478 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
1661412 TATTTTATCC
1661422 TATACTTT-ATAATTAAATTTAAATAAAAG
1 TATACTTTAATAATTAAATTTAAA-AAAAG
* *
1661451 TATATTTTAATTATTAAATTTAAAAAAA
1 TATACTTTAATAATTAAATTTAAAAAAA
1661479 CCCTTGCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
TATACTTTAATAATTAAATTTAAAAAAAG
Found at i:1668003 original size:29 final size:30
Alignment explanation
Indices: 1667948--1668010 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
1667938 TTGGTCTTAT
* *
1667948 TTAATTCTTTTTAATAATATAGAGACTAAA
1 TTAATTCTATTTAATAATAAAGAGACTAAA
*
1667978 TTAA-TCTATTTAATAATAAATG-GACTAAT
1 TTAATTCTATTTAATAATAAA-GAGACTAAA
1668007 TTAA
1 TTAA
1668011 ATCAATTCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (30 bp):
TTAATTCTATTTAATAATAAAGAGACTAAA
Found at i:1668034 original size:31 final size:29
Alignment explanation
Indices: 1667957--1668034 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
1667947 TTTAATTCTT
* *
1667957 TTTAATAATATAGAGACTAAATTAATCTA
1 TTTAATAATATAGGGACTAAATTAATCAA
* * *
1667986 TTTAATAATAAATGGACTAATTTAAATCAA
1 TTTAATAATATAGGGACTAAATT-AATCAA
1668016 TTCCT-ATAATATAGGGACT
1 TT--TAATAATATAGGGACT
1668035 TCCAAGTTAC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 19 0.49
30 7 0.18
31 12 0.31
32 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (29 bp):
TTTAATAATATAGGGACTAAATTAATCAA
Found at i:1670563 original size:30 final size:29
Alignment explanation
Indices: 1670529--1670611 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
1670519 AATGCTCGAC
*
1670529 CTTTTTAAAAGTGTTCAAATAAAGGTCAAA
1 CTTTTTAAAA-TGATCAAATAAAGGTCAAA
* *
1670559 CTTTTCAAAATGATCCAATAAAGGTCAAA
1 CTTTTTAAAATGATCAAATAAAGGTCAAA
* * *
1670588 CCTTTTCGAAAATGCTCCAATAAA
1 -CTTTT-TAAAATGATCAAATAAA
1670612 AGCTTCTCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 17 0.37
30 14 0.30
31 15 0.33
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (29 bp):
CTTTTTAAAATGATCAAATAAAGGTCAAA
Found at i:1670578 original size:29 final size:31
Alignment explanation
Indices: 1670546--1670611 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
1670536 AAAGTGTTCA
1670546 AATAAAGGTCAAA-CTTTTC-AAAATGATCC
1 AATAAAGGTCAAACCTTTTCGAAAATGATCC
*
1670575 AATAAAGGTCAAACCTTTTCGAAAATGCTCC
1 AATAAAGGTCAAACCTTTTCGAAAATGATCC
1670606 AATAAA
1 AATAAA
1670612 AGCTTCTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 13 0.38
30 6 0.18
31 15 0.44
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (31 bp):
AATAAAGGTCAAACCTTTTCGAAAATGATCC
Found at i:1674839 original size:9 final size:8
Alignment explanation
Indices: 1674825--1674876 Score: 59
Period size: 9 Copynumber: 5.9 Consensus size: 8
1674815 TTTGGTTAAA
1674825 AATTACGCG
1 AATTAC-CG
1674834 AATTACCCG
1 AATTA-CCG
1674843 AATTATCCG
1 AATTA-CCG
1674852 AATTAACCG
1 AATT-ACCG
1674861 AATTAACCG
1 AATT-ACCG
1674870 AATTACC
1 AATTACC
1674877 AAAAAATACC
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
8 3 0.08
9 35 0.88
10 2 0.05
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (8 bp):
AATTACCG
Found at i:1674853 original size:18 final size:18
Alignment explanation
Indices: 1674832--1674876 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1674822 AAAAATTACG
*
1674832 CGAATTACCCGAATTATC
1 CGAATTACCCGAATTAAC
*
1674850 CGAATTAACCGAATTAAC
1 CGAATTACCCGAATTAAC
1674868 CGAATTACC
1 CGAATTACC
1674877 AAAAAATACC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (18 bp):
CGAATTACCCGAATTAAC
Found at i:1674932 original size:9 final size:8
Alignment explanation
Indices: 1674917--1674942 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1674907 ATTTTTTATT
1674917 TTTAAAAA
1 TTTAAAAA
1674925 TTTAAAAA
1 TTTAAAAA
1674933 TTTAAAAA
1 TTTAAAAA
1674941 TT
1 TT
1674943 ATTAAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TTTAAAAA
Found at i:1675059 original size:13 final size:13
Alignment explanation
Indices: 1675041--1675070 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1675031 TTTTAGTTTT
1675041 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
1675054 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
1675067 ATTG
1 ATTG
1675071 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:1675941 original size:31 final size:31
Alignment explanation
Indices: 1675847--1675942 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 31
1675837 TTTTTCTTTA
* *
1675847 TTTTTTGGGTTTTGTATTAATTTTCTATATG
1 TTTTATGGGTTTTGTATTAATTTTCGATATG
* * * * *
1675878 TCTAATGGATTTTGTTTTACTTTTCGATATG
1 TTTTATGGGTTTTGTATTAATTTTCGATATG
*
1675909 TTTTGTGGGTTTTGTATTAATTTTCGATATG
1 TTTTATGGGTTTTGTATTAATTTTCGATATG
1675940 TTT
1 TTT
1675943 GGTGTTTCTT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.17, C:0.05, G:0.18, T:0.60
Consensus pattern (31 bp):
TTTTATGGGTTTTGTATTAATTTTCGATATG
Found at i:1680645 original size:2 final size:2
Alignment explanation
Indices: 1680638--1680664 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1680628 TTCCACCTCA
1680638 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1680665 AAAGTCACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1686555 original size:34 final size:34
Alignment explanation
Indices: 1686512--1686576 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
1686502 TAAGGCAGAA
1686512 TTGTAGTAAAATTCAAGCTACCATTGTTCTTTAC
1 TTGTAGTAAAATTCAAGCTACCATTGTTCTTTAC
*
1686546 TTGTAGTAAAATTCAAGTTACCATTGTTCTT
1 TTGTAGTAAAATTCAAGCTACCATTGTTCTT
1686577 CTTCTTACGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.43
Consensus pattern (34 bp):
TTGTAGTAAAATTCAAGCTACCATTGTTCTTTAC
Found at i:1695915 original size:20 final size:22
Alignment explanation
Indices: 1695882--1695931 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
1695872 AAAGAATTCA
*
1695882 ATAAATA-AAAAATATATT-AT
1 ATAAATATTAAAATATATTAAT
*
1695902 -TAAATATTAAAATATTTTAAT
1 ATAAATATTAAAATATATTAAT
1695923 ATAAATATT
1 ATAAATATT
1695932 TTAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.24
20 9 0.36
21 2 0.08
22 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAAATATTAAAATATATTAAT
Found at i:1701813 original size:18 final size:18
Alignment explanation
Indices: 1701791--1701826 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1701781 TTTTTTATAA
*
1701791 AAAAATTATTAATTATTTC
1 AAAAATT-TTAATAATTTC
1701810 AAAAATTTTAATAATTT
1 AAAAATTTTAATAATTT
1701827 TAATTAAACA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAAATTTTAATAATTTC
Found at i:1703556 original size:18 final size:18
Alignment explanation
Indices: 1703534--1703569 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1703524 TTTTTTATAA
*
1703534 AAAAATTATTAATTATTTC
1 AAAAATT-TTAATAATTTC
1703553 AAAAATTTTAATAATTT
1 AAAAATTTTAATAATTT
1703570 TAATTAAACA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAAATTTTAATAATTTC
Found at i:1705093 original size:4 final size:4
Alignment explanation
Indices: 1705084--1705108 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1705074 AAACAAGATA
1705084 GCAT GCAT GCAT GCAT GCAT GCAT G
1 GCAT GCAT GCAT GCAT GCAT GCAT G
1705109 TAAATCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (4 bp):
GCAT
Found at i:1716974 original size:10 final size:10
Alignment explanation
Indices: 1716959--1716984 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1716949 AGCCAGTACC
1716959 TGTATTGATA
1 TGTATTGATA
1716969 TGTATTGATA
1 TGTATTGATA
1716979 TGTATT
1 TGTATT
1716985 AACCCATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (10 bp):
TGTATTGATA
Found at i:1720123 original size:12 final size:12
Alignment explanation
Indices: 1720106--1720130 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1720096 TCTCCGACAC
1720106 TGATTGTTAAAT
1 TGATTGTTAAAT
1720118 TGATTGTTAAAT
1 TGATTGTTAAAT
1720130 T
1 T
1720131 TAACTCAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TGATTGTTAAAT
Found at i:1721723 original size:22 final size:21
Alignment explanation
Indices: 1721682--1721723 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1721672 TTGAGTATCA
* *
1721682 AAATATATAACTTTGTCAAAT
1 AAATATATAAATTTGACAAAT
1721703 AAATATATCAAATTTGACAAA
1 AAATATAT-AAATTTGACAAA
1721724 AATAATACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (21 bp):
AAATATATAAATTTGACAAAT
Found at i:1731079 original size:1 final size:1
Alignment explanation
Indices: 1731068--1731120 Score: 97
Period size: 1 Copynumber: 53.0 Consensus size: 1
1731058 TGGGACTTTC
*
1731068 TTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1731121 GTGTGTGTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.00, G:0.02, T:0.98
Consensus pattern (1 bp):
T
Found at i:1738035 original size:10 final size:10
Alignment explanation
Indices: 1738022--1738046 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1738012 AAATGTAAAA
1738022 AAAAACTTAT
1 AAAAACTTAT
1738032 AAAAACTTAT
1 AAAAACTTAT
1738042 AAAAA
1 AAAAA
1738047 ATATTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAACTTAT
Found at i:1738201 original size:6 final size:7
Alignment explanation
Indices: 1738182--1738206 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1738172 NNNNNNNNNN
1738182 TATTTTT
1 TATTTTT
1738189 TATTTTT
1 TATTTTT
1738196 TATTTTT
1 TATTTTT
1738203 TATT
1 TATT
1738207 GGCAAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TATTTTT
Found at i:1738418 original size:3 final size:3
Alignment explanation
Indices: 1738412--1738446 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1738402 AAAAAAATTG
1738412 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1738447 TAAATTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1751467 original size:3 final size:3
Alignment explanation
Indices: 1751459--1751498 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1751449 TAGTTACCAC
1751459 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1751499 GCAAACAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:1758123 original size:111 final size:111
Alignment explanation
Indices: 1757888--1758133 Score: 327
Period size: 111 Copynumber: 2.2 Consensus size: 111
1757878 TCATCAAAGT
* * * *
1757888 CATGCAAACAGAATATAACCGAGTCATTCCGATCCGTCGATCTAGCCATTAATCTAACCCTAAAC
1 CATGGAAACAGAACATAACCAAGTCATTCCGATCCGTCAATCTAGCCATTAATCTAACCCTAAAC
* * *
1757953 TTTGAAATTTCTGGCGAAATTAAATAAGGCTCAAAAGTGTTAGAAG
66 TTTCAAATTTCTGGCGAAATTAAAGAAGGCTCAAAAGTGTAAGAAG
* * **
1757999 CATGGAAACAGAACATAACCAAGTCCTTCCGTTCCGTCAATCTAGCGGTTAATCTAACCCTAAAC
1 CATGGAAACAGAACATAACCAAGTCATTCCGATCCGTCAATCTAGCCATTAATCTAACCCTAAAC
* *
1758064 -TTCAAATTT-TCGAGTGAAA-TCAAGAAGGCTCAAAAGTGTAAGAAG
66 TTTCAAATTTCT-G-GCGAAATTAAAGAAGGCTCAAAAGTGTAAGAAG
1758109 CATGGAAACAAGAACATAACCAAGT
1 CATGGAAAC-AGAACATAACCAAGT
1758134 AAAACCAGAT
Statistics
Matches: 119, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
109 1 0.01
110 41 0.34
111 77 0.65
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.24
Consensus pattern (111 bp):
CATGGAAACAGAACATAACCAAGTCATTCCGATCCGTCAATCTAGCCATTAATCTAACCCTAAAC
TTTCAAATTTCTGGCGAAATTAAAGAAGGCTCAAAAGTGTAAGAAG
Found at i:1759956 original size:3 final size:3
Alignment explanation
Indices: 1759948--1759991 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1759938 GAAAATGTTG
1759948 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1759992 ATTCTTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1761540 original size:13 final size:13
Alignment explanation
Indices: 1761522--1761582 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
1761512 CTCAAATTTT
*
1761522 TCAAAAGTACTTC
1 TCAAAAGCACTTC
*
1761535 TCAAAAGCACTTT
1 TCAAAAGCACTTC
* * * *
1761548 TCCACAGCATTTT
1 TCAAAAGCACTTC
*
1761561 TCAAAAGCACTTT
1 TCAAAAGCACTTC
1761574 TCAAAAGCA
1 TCAAAAGCA
1761583 ATGAAGAACT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.30
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:1761582 original size:26 final size:26
Alignment explanation
Indices: 1761519--1761582 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
1761509 ACACTCAAAT
*
1761519 TTTTCAAAAGTACTTCTCAAAAGCAC
1 TTTTCAAAAGCACTTCTCAAAAGCAC
* * * *
1761545 TTTTCCACAGCATTTTTCAAAAGCAC
1 TTTTCAAAAGCACTTCTCAAAAGCAC
1761571 TTTTCAAAAGCA
1 TTTTCAAAAGCA
1761583 ATGAAGAACT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (26 bp):
TTTTCAAAAGCACTTCTCAAAAGCAC
Found at i:1761867 original size:19 final size:21
Alignment explanation
Indices: 1761843--1761883 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1761833 TCATATGTAC
1761843 TTTAT-GTTATTTT-TAATTT
1 TTTATGGTTATTTTATAATTT
*
1761862 TTTATGGTTTTTTTATAATTT
1 TTTATGGTTATTTTATAATTT
1761883 T
1 T
1761884 AAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 7 0.37
21 7 0.37
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (21 bp):
TTTATGGTTATTTTATAATTT
Found at i:1762699 original size:29 final size:29
Alignment explanation
Indices: 1762666--1762732 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
1762656 ATAAGGACAT
* *
1762666 GATCAAATTAATCAT-TTTACTATTAAATA
1 GATCAAATTAATC-TCTATACTATTAAAAA
**
1762695 GATCATTTTAATCTCTATACTATTAAAAA
1 GATCAAATTAATCTCTATACTATTAAAAA
1762724 GAATCAAAT
1 G-ATCAAAT
1762733 AAGTTCAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.03
29 24 0.80
30 5 0.17
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (29 bp):
GATCAAATTAATCTCTATACTATTAAAAA
Found at i:1763104 original size:31 final size:31
Alignment explanation
Indices: 1763040--1763139 Score: 125
Period size: 31 Copynumber: 3.3 Consensus size: 31
1763030 ACAAAGTTTA
* *
1763040 TCAAATGAA-AGCCAAA-C-TTTTCAAAGTGA
1 TCAAAT-AAGAGCCAAACCTTTTTAAAAGTGC
1763069 TCAAATAAGAGCCAAACCTTTTTAAAAGTGC
1 TCAAATAAGAGCCAAACCTTTTTAAAAGTGC
* * *
1763100 TCAAATAAGAGTCAAACCTTTTTGAAAGTAC
1 TCAAATAAGAGCCAAACCTTTTTAAAAGTGC
1763131 TCAAATAAG
1 TCAAATAAG
1763140 GGCTTCTCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
28 2 0.03
29 13 0.21
30 1 0.02
31 47 0.75
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (31 bp):
TCAAATAAGAGCCAAACCTTTTTAAAAGTGC
Found at i:1770799 original size:10 final size:9
Alignment explanation
Indices: 1770749--1770800 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 9
1770739 TTATTTACCT
*
1770749 TTTTTTTTT
1 TTTTTTTTC
*
1770758 TTTTTTCTTT
1 TTTTTT-TTC
1770768 TTTTTTTTCC
1 TTTTTTTT-C
1770778 TTTTTTTT-
1 TTTTTTTTC
1770786 TTTTTTTTC
1 TTTTTTTTC
1770795 ATTTTT
1 -TTTTT
1770801 CTCAGCTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
8 8 0.21
9 8 0.21
10 22 0.58
ACGTcount: A:0.02, C:0.08, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1770800 original size:1 final size:1
Alignment explanation
Indices: 1770748--1770793 Score: 65
Period size: 1 Copynumber: 46.0 Consensus size: 1
1770738 TTTATTTACC
* **
1770748 TTTTTTTTTTTTTTTTCTTTTTTTTTTTCCTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1770794 CATTTTTCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:1777281 original size:28 final size:28
Alignment explanation
Indices: 1777249--1777304 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
1777239 GTCCTTGCTA
1777249 AACGATAACTGTTAAAGTCATTAAGTTT
1 AACGATAACTGTTAAAGTCATTAAGTTT
* *
1777277 AACGATAATTGTTAAATTCATTAAGTTT
1 AACGATAACTGTTAAAGTCATTAAGTTT
1777305 TGCTATTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (28 bp):
AACGATAACTGTTAAAGTCATTAAGTTT
Found at i:1777942 original size:30 final size:30
Alignment explanation
Indices: 1777906--1777965 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1777896 GTTATAATAG
1777906 GAACTCGTATTAACAAGCTGGATATTATCT
1 GAACTCGTATTAACAAGCTGGATATTATCT
1777936 GAACTCGTATTAACAAGCTGGATATTATCT
1 GAACTCGTATTAACAAGCTGGATATTATCT
1777966 TTCTTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (30 bp):
GAACTCGTATTAACAAGCTGGATATTATCT
Found at i:1777961 original size:15 final size:15
Alignment explanation
Indices: 1777913--1777962 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1777903 TAGGAACTCG
1777913 TATTAACAAGCTGGA
1 TATTAACAAGCTGGA
* *
1777928 TATTATCTGAA-CTCG-
1 TATTAAC--AAGCTGGA
1777943 TATTAACAAGCTGGA
1 TATTAACAAGCTGGA
1777958 TATTA
1 TATTA
1777963 TCTTTCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 2 0.07
14 3 0.11
15 17 0.63
16 3 0.11
17 2 0.07
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (15 bp):
TATTAACAAGCTGGA
Found at i:1787400 original size:33 final size:33
Alignment explanation
Indices: 1787358--1787421 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
1787348 TTTTCACTGG
1787358 GGTAGGATTGAAATATATAGTAAATACTAACGA
1 GGTAGGATTGAAATATATAGTAAATACTAACGA
**
1787391 GGTAGGATTGAGCTATATAGTAAATACTAAC
1 GGTAGGATTGAAATATATAGTAAATACTAAC
1787422 ACAGATAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (33 bp):
GGTAGGATTGAAATATATAGTAAATACTAACGA
Found at i:1798943 original size:21 final size:21
Alignment explanation
Indices: 1798918--1798962 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1798908 CTTTTGTTTC
*
1798918 AATTATTGTTTTTTTAG-TGAA
1 AATTATTATTTTTTT-GTTGAA
1798939 AATTATTATTTTTTTGTTGAA
1 AATTATTATTTTTTTGTTGAA
1798960 AAT
1 AAT
1798963 AAAGAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (21 bp):
AATTATTATTTTTTTGTTGAA
Found at i:1807015 original size:86 final size:86
Alignment explanation
Indices: 1806920--1807082 Score: 254
Period size: 86 Copynumber: 1.9 Consensus size: 86
1806910 CTTAATTCAT
* *
1806920 TGTGATGTATGCATCCACAATCCCAATTTAAATCTTGAGTTTGGTAAGTTTTTATGTCAGCTTTA
1 TGTGATGTATGCATCCACAATCCCAATTTAAATCTCGAGTTTGGTAAGCTTTTATGTCAGCTTTA
1806985 AGTAGAATTATCTTAACTAAC
66 AGTAGAATTATCTTAACTAAC
* ***
1807006 TGTGATGTATGCATCCGCAATTTTAATTTAAATCTCGAGTTTGGTAAGCTTTTATGTCAGCTTTA
1 TGTGATGTATGCATCCACAATCCCAATTTAAATCTCGAGTTTGGTAAGCTTTTATGTCAGCTTTA
* *
1807071 GGTGGAATTATC
66 AGTAGAATTATC
1807083 AAGCATACAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 69 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (86 bp):
TGTGATGTATGCATCCACAATCCCAATTTAAATCTCGAGTTTGGTAAGCTTTTATGTCAGCTTTA
AGTAGAATTATCTTAACTAAC
Found at i:1808325 original size:86 final size:86
Alignment explanation
Indices: 1808230--1808392 Score: 254
Period size: 86 Copynumber: 1.9 Consensus size: 86
1808220 CTTAATTCAT
* *
1808230 TGTGATGTATGCATCCACAATCCCAATTTAAATCTTGAGTTTGGTAAGTTTTTATGTCAGCTTTA
1 TGTGATGTATGCATCCACAATCCCAATTTAAATCTCGAGTTTGGTAAGCTTTTATGTCAGCTTTA
1808295 AGTAGAATTATCTTAACTAAC
66 AGTAGAATTATCTTAACTAAC
* ***
1808316 TGTGATGTATGCATCCGCAATTTTAATTTAAATCTCGAGTTTGGTAAGCTTTTATGTCAGCTTTA
1 TGTGATGTATGCATCCACAATCCCAATTTAAATCTCGAGTTTGGTAAGCTTTTATGTCAGCTTTA
* *
1808381 GGTGGAATTATC
66 AGTAGAATTATC
1808393 AAGCATACAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 69 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (86 bp):
TGTGATGTATGCATCCACAATCCCAATTTAAATCTCGAGTTTGGTAAGCTTTTATGTCAGCTTTA
AGTAGAATTATCTTAACTAAC
Found at i:1814131 original size:15 final size:16
Alignment explanation
Indices: 1814106--1814135 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1814096 CATTCTAATA
1814106 AATTATTTAATATTTC
1 AATTATTTAATATTTC
1814122 AATT-TTTAATATTT
1 AATTATTTAATATTT
1814136 TATTTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTATTTAATATTTC
Found at i:1814663 original size:13 final size:13
Alignment explanation
Indices: 1814641--1814670 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1814631 TCATGGTTTG
*
1814641 AAGAAGAAGAAAA
1 AAGAAAAAGAAAA
1814654 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
1814667 AAGA
1 AAGA
1814671 GAATGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:1815802 original size:6 final size:6
Alignment explanation
Indices: 1815751--1815787 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1815741 ACGAAGAAGA
1815751 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
1815788 GAATGAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1817434 original size:6 final size:6
Alignment explanation
Indices: 1817423--1817451 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1817413 TTTATGAACA
1817423 ATATGT ATATGT ATATGT ATATGT ATATG
1 ATATGT ATATGT ATATGT ATATGT ATATG
1817452 ATTACAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (6 bp):
ATATGT
Found at i:1821345 original size:168 final size:168
Alignment explanation
Indices: 1821065--1821396 Score: 490
Period size: 168 Copynumber: 2.0 Consensus size: 168
1821055 AAATGACTTT
* *
1821065 TATTAAAAATCACATTTTTACATTTAATATATATATTTTTTAAAAATACATAGTGAGAAGAATTA
1 TATTAAAAATCACATTTTTACATTTAATATATATATTTTTTAAAAATACATAATGAGAAGAATCA
* * **
1821130 GAAGATAATTGAAGCAACTGGCAATAAAAAAAATTAACCTGTATATAAAACATTAAAAAATAAAT
66 GAAGATAATTGAAGCAACTAGCAATAAAAAAAACTAACCCATATATAAAACATTAAAAAATAAAT
1821195 TATGAGGTGATGAAAGTTAATAACAAATTTGATTATGA
131 TATGAGGTGATGAAAGTTAATAACAAATTTGATTATGA
* * * *
1821233 TATTAAAAAT-ACATTTTTACATTTAATATAT-TTTTTAATTTCAAAATACTTAATGATAAGAAT
1 TATTAAAAATCACATTTTTACATTTAATATATATATTT--TTTAAAAATACATAATGAGAAGAAT
* * * *
1821296 CAGAAGATAATTGAAGCAACTAGTAA-ACAAAAAAGCTAACCCATATATAAAATATTAATAAATA
64 CAGAAGATAATTGAAGCAACTAGCAATA-AAAAAAACTAACCCATATATAAAACATTAAAAAATA
1821360 AATTATGAGGTGATGAAAGTTAATAACAAATTTGATT
128 AATTATGAGGTGATGAAAGTTAATAACAAATTTGATT
1821397 TGAGAAAATT
Statistics
Matches: 147, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
166 4 0.03
167 22 0.15
168 121 0.82
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.33
Consensus pattern (168 bp):
TATTAAAAATCACATTTTTACATTTAATATATATATTTTTTAAAAATACATAATGAGAAGAATCA
GAAGATAATTGAAGCAACTAGCAATAAAAAAAACTAACCCATATATAAAACATTAAAAAATAAAT
TATGAGGTGATGAAAGTTAATAACAAATTTGATTATGA
Found at i:1821640 original size:11 final size:11
Alignment explanation
Indices: 1821620--1821649 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1821610 ATAAAAAATA
1821620 AAAAAGTATTTT
1 AAAAA-TATTTT
1821632 AAAAATATTTT
1 AAAAATATTTT
1821643 AAAAATA
1 AAAAATA
1821650 AATAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:1829775 original size:28 final size:28
Alignment explanation
Indices: 1829710--1829765 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1829700 TTAGGAGCTG
1829710 GTGCATAATTCAGGGAAATAATCTACTA
1 GTGCATAATTCAGGGAAATAATCTACTA
1829738 GTGCATAATTCAGGGAAATAATCTACTA
1 GTGCATAATTCAGGGAAATAATCTACTA
1829766 AGGATGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (28 bp):
GTGCATAATTCAGGGAAATAATCTACTA
Found at i:1846347 original size:20 final size:20
Alignment explanation
Indices: 1846324--1846362 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1846314 CTGGTTTTCT
*
1846324 AATTTTTTAATGTATTTTTA
1 AATTTTTTAATGAATTTTTA
*
1846344 AATTTTTTTATGAATTTTT
1 AATTTTTTAATGAATTTTT
1846363 TTTTTCTGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
AATTTTTTAATGAATTTTTA
Found at i:1848461 original size:16 final size:15
Alignment explanation
Indices: 1848435--1848489 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
1848425 ATTAAGATTT
*
1848435 TAAATTTAAAAAATA
1 TAAAATTAAAAAATA
1848450 TAGAAATT-AAAAATGA
1 TA-AAATTAAAAAAT-A
*
1848466 TAAATTTAAAAAATA
1 TAAAATTAAAAAATA
1848481 T-AAATTAAA
1 TAAAATTAAA
1848490 TACATAACTC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 7 0.21
15 14 0.41
16 13 0.38
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (15 bp):
TAAAATTAAAAAATA
Found at i:1856222 original size:31 final size:29
Alignment explanation
Indices: 1856184--1856261 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
1856174 CTAACGGCTT
* *
1856184 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
1856215 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
1856244 AGTGACTAAAATGTAACA
1 AGTGACTAAAATGTAACA
1856262 TGAGCCAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.56
30 3 0.07
31 15 0.37
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:1856278 original size:31 final size:29
Alignment explanation
Indices: 1856209--1856282 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
1856199 ACAACGTGAT
**
1856209 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATGCCA
*
1856238 AACATAAGTGACTAAAATGTAACATGAGCCA
1 AACATAAGTGACTAAAACGTAACAT--GCCA
*
1856269 AACAAAAGTGACTA
1 AACATAAGTGACTA
1856283 TTTTAGAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATGCCA
Found at i:1857477 original size:30 final size:31
Alignment explanation
Indices: 1857443--1857503 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
1857433 GTAAAAAAAT
*
1857443 TTAAAATATAAATTTATTAGTATAA-GTAAA
1 TTAAAATATAAATTTATTAATATAATGTAAA
1857473 TTAAAATATAAATTTATTAATATAATGTAAA
1 TTAAAATATAAATTTATTAATATAATGTAAA
1857504 AACAATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (31 bp):
TTAAAATATAAATTTATTAATATAATGTAAA
Found at i:1857491 original size:16 final size:16
Alignment explanation
Indices: 1857443--1857492 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1857433 GTAAAAAAAT
1857443 TTAAAATATAAATTTA
1 TTAAAATATAAATTTA
* * **
1857459 TT--AGTATAAGTAAA
1 TTAAAATATAAATTTA
1857473 TTAAAATATAAATTTA
1 TTAAAATATAAATTTA
1857489 TTAA
1 TTAA
1857493 TATAATGTAA
Statistics
Matches: 24, Mismatches: 8, Indels: 4
0.67 0.22 0.11
Matches are distributed among these distances:
14 10 0.42
16 14 0.58
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
TTAAAATATAAATTTA
Found at i:1887077 original size:12 final size:12
Alignment explanation
Indices: 1887060--1887093 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1887050 TAGTATTTAT
1887060 ATTAAATTATAA
1 ATTAAATTATAA
*
1887072 ATTAAAATATAA
1 ATTAAATTATAA
*
1887084 AATAAATTAT
1 ATTAAATTAT
1887094 CTATATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATTAAATTATAA
Found at i:1891234 original size:12 final size:13
Alignment explanation
Indices: 1891217--1891254 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1891207 TAGCTTTTCC
1891217 TTTTTA-ATAATT
1 TTTTTATATAATT
*
1891229 TTTTTATATTTATT
1 TTTTTATA-TAATT
1891243 TTTTTATATAAT
1 TTTTTATATAAT
1891255 GTCTAGAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTATATAATT
Found at i:1907600 original size:2 final size:2
Alignment explanation
Indices: 1907593--1907622 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1907583 AAAGGTAATT
1907593 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1907623 AAACAAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1919301 original size:77 final size:77
Alignment explanation
Indices: 1919174--1919333 Score: 284
Period size: 77 Copynumber: 2.1 Consensus size: 77
1919164 TCCCCCAATT
*
1919174 TTTTACAACTTAGTTTCACGCCCCATGAAATAGCTTTACATGTCACATATCTGCGAACCAAAATC
1 TTTTACAACTTAGTTTCACGCCCCATGAAATAGCTTTACATGTCACATATCTACGAACCAAAATC
1919239 TAAACAATTTTC
66 TAAACAATTTTC
* * *
1919251 TTTTATAACTTAGTTTCAGGCCCCATGAAATAGCTTTACATGTCACATATCTACGAACTAAAATC
1 TTTTACAACTTAGTTTCACGCCCCATGAAATAGCTTTACATGTCACATATCTACGAACCAAAATC
1919316 TAAACAATTTTC
66 TAAACAATTTTC
1919328 TTTTAC
1 TTTTAC
1919334 GATCTTCGAC
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.35
Consensus pattern (77 bp):
TTTTACAACTTAGTTTCACGCCCCATGAAATAGCTTTACATGTCACATATCTACGAACCAAAATC
TAAACAATTTTC
Found at i:1924267 original size:16 final size:16
Alignment explanation
Indices: 1924234--1924267 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1924224 TAATTCTCTG
**
1924234 TACAAGCTGCTTTTTT
1 TACAAGCTGCTTGGTT
1924250 TACAAGCTGCTTGGTT
1 TACAAGCTGCTTGGTT
1924266 TA
1 TA
1924268 ATGTTGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (16 bp):
TACAAGCTGCTTGGTT
Found at i:1936443 original size:26 final size:27
Alignment explanation
Indices: 1936401--1936451 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
1936391 AGGTCAAGAG
*
1936401 TCAAATTTAACTAAAAAA-GAATAAAGT
1 TCAAATTTAAC-AAAAAATAAATAAAGT
1936428 TCAAA-TTAACAAAAAATAAATAAA
1 TCAAATTTAACAAAAAATAAATAAA
1936452 AATAAACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 11 0.50
27 5 0.23
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.24
Consensus pattern (27 bp):
TCAAATTTAACAAAAAATAAATAAAGT
Found at i:1944667 original size:13 final size:14
Alignment explanation
Indices: 1944640--1944668 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1944630 ATTTCTTCAG
1944640 TTTTTTTTTCTCTT
1 TTTTTTTTTCTCTT
1944654 TTTTTTTTTC-CTT
1 TTTTTTTTTCTCTT
1944667 TT
1 TT
1944669 CGTTCAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTCTCTT
Found at i:1945069 original size:13 final size:13
Alignment explanation
Indices: 1945051--1945082 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1945041 GCCTAATGTG
1945051 ATATGTGCTTTGA
1 ATATGTGCTTTGA
1945064 ATATGTGCTTTGA
1 ATATGTGCTTTGA
1945077 ATATGT
1 ATATGT
1945083 TCAATGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (13 bp):
ATATGTGCTTTGA
Done.