Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 47 of 125
Found at i:9508790 original size:22 final size:22
Alignment explanation
Indices: 9508765--9509466 Score: 118
Period size: 22 Copynumber: 32.8 Consensus size: 22
9508755 GTAATTATCG
* * *
9508765 ATAAGTTAATAGTAAATTAGTA
1 ATAACTTAATAGTAAATGAATA
*
9508787 ATAACTTAATAGTAAATGAATG
1 ATAACTTAATAGTAAATGAATA
* * *
9508809 ATAATTTAATAGTAAA--ATTG
1 ATAACTTAATAGTAAATGAATA
** *
9508829 ATAACTTTCTAATAAAT-AAGTA
1 ATAACTTAATAGTAAATGAA-TA
* * *
9508851 ATAA-TATAATAATATATGCATA
1 ATAACT-TAATAGTAAATGAATA
* * *
9508873 A-AACCTTAATACTAAATCAATT
1 ATAA-CTTAATAGTAAATGAATA
* *
9508895 ATAA-TATAATTGT-AATGCATA
1 ATAACT-TAATAGTAAATGAATA
* * *
9508916 ATAACATAATATTAAATCAA-A
1 ATAACTTAATAGTAAATGAATA
* ** *
9508937 GATAACTTAACA--AAACAAAAGTG
1 -ATAACTTAATAGTAAA-TGAA-TA
* * * *
9508960 ATAACTTAATAGTTAATTATTG
1 ATAACTTAATAGTAAATGAATA
* * * *
9508982 ATAACTGAGCA-AATAAATCAATG
1 ATAACTTA--ATAGTAAATGAATA
* *
9509005 ATAACTTAATAGTAAATTAGTA
1 ATAACTTAATAGTAAATGAATA
* * *
9509027 ATGATTTAATAGT-AATTAAT-
1 ATAACTTAATAGTAAATGAATA
* *
9509047 -TGAC--AATAGTAAAT-TATAA
1 ATAACTTAATAGTAAATGAAT-A
* * **
9509066 ATAGCTTAATAATAAACAAATA
1 ATAACTTAATAGTAAATGAATA
* * *
9509088 ATAAATTAATACTAAAT-AATTG
1 ATAACTTAATAGTAAATGAA-TA
* * *
9509110 ATAATTTAATAGGT-AATCATTGA
1 ATAACTTAATA-GTAAATGAAT-A
* * *
9509133 A-AACTTAAAAGTAAATCAGT-
1 ATAACTTAATAGTAAATGAATA
* *
9509153 ATAACTTAATAGTAAAT-CATCG
1 ATAACTTAATAGTAAATGAAT-A
* * * * *
9509175 ATAACATAATAGTTAATTAGTG
1 ATAACTTAATAGTAAATGAATA
*
9509197 ATAACTTAATAATAAATTG--TA
1 ATAACTTAATAGTAAA-TGAATA
* *
9509218 CATAATTTAATA-TAAAT-ATGTA
1 -ATAACTTAATAGTAAATGA-ATA
* * * *
9509240 ATAACTTAGTAATGAAT-TATA
1 ATAACTTAATAGTAAATGAATA
* * *
9509261 GATAATTTAGTAATAAATCG-ATA
1 -ATAACTTAATAGTAAAT-GAATA
* **
9509284 AT-ATTTTGTAGTAAAT-AATA
1 ATAACTTAATAGTAAATGAATA
9509304 A-AA---AATAGTAAAT-AATA
1 ATAACTTAATAGTAAATGAATA
*
9509321 ATAACATAATAGTAAAT-ATATA
1 ATAACTTAATAGTAAATGA-ATA
* * *
9509343 A-AAATATAATAGTAAATCATTA
1 ATAACT-TAATAGTAAATGAATA
*
9509365 ATAATTTAATAGTAAAT---TA
1 ATAACTTAATAGTAAATGAATA
* ** * *
9509384 ATAAGTTAGCAGTAAATCACTA
1 ATAACTTAATAGTAAATGAATA
* * *
9509406 ATAACATAATAGTAAATTATTA
1 ATAACTTAATAGTAAATGAATA
* *
9509428 ATAACTTAATTA-TAAATCAATG
1 ATAACTTAA-TAGTAAATGAATA
*
9509450 ATAATTTAATAGTAAAT
1 ATAACTTAATAGTAAAT
9509467 TAATTAATCA
Statistics
Matches: 506, Mismatches: 115, Indels: 118
0.68 0.16 0.16
Matches are distributed among these distances:
17 21 0.04
18 5 0.01
19 19 0.04
20 28 0.06
21 90 0.18
22 304 0.60
23 36 0.07
24 3 0.01
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.34
Consensus pattern (22 bp):
ATAACTTAATAGTAAATGAATA
Found at i:9508932 original size:43 final size:44
Alignment explanation
Indices: 9508851--9508935 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 44
9508841 TAAATAAGTA
*
9508851 ATAATATAATAATATATGCATAAAACCTTAATACTAAATCAATT
1 ATAATATAATAATATATGCATAAAACCATAATACTAAATCAATT
** *
9508895 ATAATATAATTGTA-ATGCATAATAA-CATAATATTAAATCAA
1 ATAATATAATAATATATGCATAA-AACCATAATACTAAATCAA
9508936 AGATAACTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 22 0.61
44 14 0.39
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (44 bp):
ATAATATAATAATATATGCATAAAACCATAATACTAAATCAATT
Found at i:9508985 original size:44 final size:44
Alignment explanation
Indices: 9508937--9509023 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 44
9508927 TTAAATCAAA
* *
9508937 GATAACTTAACAAA-ACAA-AAGTGATAACTTAATAGTTAATTATT
1 GATAACTGAACAAATA-AACAA-TGATAACTTAATAGTAAATTATT
*
9508981 GATAACTGAGCAAATAAATCAATGATAACTTAATAGTAAATTA
1 GATAACTGAACAAATAAA-CAATGATAACTTAATAGTAAATTA
9509024 GTAATGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
44 14 0.38
45 21 0.57
46 2 0.05
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (44 bp):
GATAACTGAACAAATAAACAATGATAACTTAATAGTAAATTATT
Found at i:9509162 original size:65 final size:65
Alignment explanation
Indices: 9509070--9509213 Score: 148
Period size: 65 Copynumber: 2.2 Consensus size: 65
9509060 TTATAAATAG
* * ** *
9509070 CTTAATAATAAA-CAAATAATAAATTAATACTAAATAATTGATAATTTAATAGGTAATCATTGAA
1 CTTAATAATAAATC-AGT-ATAAATTAATACTAAATAATCGATAACATAATAGGTAATCAGTGAA
9509134 AA
64 AA
* * * * * *
9509136 CTTAA-AAGTAAATCAGTATAACTTAATAGTAAATCATCGATAACATAATAGTTAATTAGTGATA
1 CTTAATAA-TAAATCAGTATAAATTAATACTAAATAATCGATAACATAATAGGTAATCAGTGAAA
9509200 A
65 A
9509201 CTTAATAATAAAT
1 CTTAATAATAAAT
9509214 TGTACATAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
65 50 0.78
66 13 0.20
67 1 0.02
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (65 bp):
CTTAATAATAAATCAGTATAAATTAATACTAAATAATCGATAACATAATAGGTAATCAGTGAAAA
Found at i:9509164 original size:43 final size:44
Alignment explanation
Indices: 9509108--9509213 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 44
9509098 ACTAAATAAT
* * *
9509108 TGATAATTTAATAGGT-AATCATTGAAAACTTAAAAGTAAATCAG
1 TGATAACTTAATA-GTAAATCATCGAAAACATAAAAGTAAATCAG
* * * *
9509152 T-ATAACTTAATAGTAAATCATCGATAACATAATAGTTAATTAG
1 TGATAACTTAATAGTAAATCATCGAAAACATAAAAGTAAATCAG
*
9509195 TGATAACTTAATAATAAAT
1 TGATAACTTAATAGTAAAT
9509214 TGTACATAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
42 2 0.04
43 33 0.63
44 17 0.33
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (44 bp):
TGATAACTTAATAGTAAATCATCGAAAACATAAAAGTAAATCAG
Found at i:9509312 original size:17 final size:17
Alignment explanation
Indices: 9509292--9509346 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 17
9509282 TAATATTTTG
9509292 TAGTAAATAATAAAAAA
1 TAGTAAATAATAAAAAA
9509309 TAGTAAATAATAATAACATAA
1 TAGTAAATAAT-A-AA-A-AA
9509330 TAGTAAATATATAAAAA
1 TAGTAAATA-ATAAAAA
9509347 TATAATAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.33
18 2 0.06
19 3 0.09
20 3 0.09
21 12 0.36
22 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.27
Consensus pattern (17 bp):
TAGTAAATAATAAAAAA
Found at i:9509375 original size:44 final size:42
Alignment explanation
Indices: 9509292--9509468 Score: 150
Period size: 44 Copynumber: 4.2 Consensus size: 42
9509282 TAATATTTTG
*
9509292 TAGTAAATAAT-AAAA--AATAGTAAAT-AATAATAACATAA
1 TAGTAAATTATAAAAATTAATAGTAAATCAATAATAACATAA
* **
9509330 TAGTAAATATATAAAAATATAATAGTAAATCATTAATAATTTAA
1 TAGTAAAT-TATAAAAAT-TAATAGTAAATCAATAATAACATAA
* * ** *
9509374 TAGTAAATTA-ATAAGTTAGCAGTAAATCACTAATAACATAA
1 TAGTAAATTATAAAAATTAATAGTAAATCAATAATAACATAA
* * **
9509415 TAGTAAATTATTAATAACTTAATTA-TAAATCAATGATAATTTAA
1 TAGTAAATTA-TAA-AAATTAA-TAGTAAATCAATAATAACATAA
9509459 TAGTAAATTA
1 TAGTAAATTA
9509469 ATTAATCACT
Statistics
Matches: 110, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
38 8 0.07
39 2 0.02
40 4 0.04
41 30 0.27
42 4 0.04
43 13 0.12
44 48 0.44
45 1 0.01
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (42 bp):
TAGTAAATTATAAAAATTAATAGTAAATCAATAATAACATAA
Found at i:9509421 original size:85 final size:84
Alignment explanation
Indices: 9509310--9509470 Score: 229
Period size: 85 Copynumber: 1.9 Consensus size: 84
9509300 AATAAAAAAT
*
9509310 AGTAAATAATAATAACATAATAGTAAA-TATATAA-AAATATAA-TAGTAAATCATTAATAATTT
1 AGTAAATAATAATAACATAATAGTAAATTAT-TAATAAAT-TAATTA-TAAATCAATAATAATTT
9509372 AATAGTAAATTAATAAGTTAGC
63 AATAGTAAATTAATAAGTTAGC
* * *
9509394 AGTAAATCACTAATAACATAATAGTAAATTATTAATAACTTAATTATAAATCAATGATAATTTAA
1 AGTAAAT-AATAATAACATAATAGTAAATTATTAATAAATTAATTATAAATCAATAATAATTTAA
9509459 TAGTAAATTAAT
65 TAGTAAATTAAT
9509471 TAATCACTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
84 7 0.10
85 54 0.78
86 8 0.12
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (84 bp):
AGTAAATAATAATAACATAATAGTAAATTATTAATAAATTAATTATAAATCAATAATAATTTAAT
AGTAAATTAATAAGTTAGC
Found at i:9509470 original size:11 final size:11
Alignment explanation
Indices: 9509307--9509386 Score: 51
Period size: 11 Copynumber: 7.4 Consensus size: 11
9509297 AATAATAAAA
9509307 AATAGTAAA-T
1 AATAGTAAATT
*
9509317 AATAATAACA-T
1 AATAGTAA-ATT
9509328 AATAGTAAA-T
1 AATAGTAAATT
*
9509338 ATATA-AAAATAT
1 A-ATAGTAAAT-T
*
9509350 AATAGTAAATC
1 AATAGTAAATT
* * *
9509361 ATTAATAATTT
1 AATAGTAAATT
9509372 AATAGTAAATT
1 AATAGTAAATT
9509383 AATA
1 AATA
9509387 AGTTAGCAGT
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
10 13 0.25
11 34 0.64
12 6 0.11
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.34
Consensus pattern (11 bp):
AATAGTAAATT
Found at i:9509621 original size:22 final size:22
Alignment explanation
Indices: 9509051--9509658 Score: 103
Period size: 22 Copynumber: 28.0 Consensus size: 22
9509041 ATTAATTGAC
* * *
9509051 AATAGTAAATTATAAATAGCTT
1 AATAATAAATTATTAATAACTT
** * *
9509073 AATAATAAACAAATAATAAATT
1 AATAATAAATTATTAATAACTT
* * * *
9509095 AATACTAAATAATTGATAATTT
1 AATAATAAATTATTAATAACTT
* *
9509117 AATAGGT-AATCATTGAA-AACTT
1 AATA-ATAAATTATT-AATAACTT
* *
9509139 AA-AAGTAAATCAGT-ATAACTT
1 AATAA-TAAATTATTAATAACTT
* * ** *
9509160 AATAGTAAATCATCGATAACAT
1 AATAATAAATTATTAATAACTT
* * * *
9509182 AATAGTTAATTAGTGATAACTT
1 AATAATAAATTATTAATAACTT
* *
9509204 AATAATAAATT-GTACATAATTT
1 AATAATAAATTATTA-ATAACTT
9509226 AAT-ATAAA-TATGTAATAACTT
1 AATAATAAATTAT-TAATAACTT
* * *
9509247 AGTAATGAATTA-TAGATAATTT
1 AATAATAAATTATTA-ATAACTT
* * *
9509269 AGTAATAAATCGA-TAAT-ATTT
1 AATAATAAAT-TATTAATAACTT
** * *
9509290 TGTAGTAAA-TAATAA-AA---
1 AATAATAAATTATTAATAACTT
* * *
9509307 AATAGTAAA-TAATAATAACAT
1 AATAATAAATTATTAATAACTT
* *
9509328 AATAGTAAA-TATATAA-AAATAT
1 AATAATAAATTAT-TAATAACT-T
* * *
9509350 AATAGTAAATCATTAATAATTT
1 AATAATAAATTATTAATAACTT
* *
9509372 AATAGT-AA--ATTAATAAGTT
1 AATAATAAATTATTAATAACTT
** * * * *
9509391 AGCAGTAAATCACTAATAACAT
1 AATAATAAATTATTAATAACTT
*
9509413 AATAGTAAATTATTAATAACTT
1 AATAATAAATTATTAATAACTT
* * * * *
9509435 AATTATAAATCAATGATAATTT
1 AATAATAAATTATTAATAACTT
* *
9509457 AATAGTAAATTAATTAATCAC-T
1 AATAATAAATT-ATTAATAACTT
* * * * *
9509479 AATTTAGTGGTAAATCATCAACAATTT
1 AA--TA---ATAAATTATTAATAACTT
* *
9509506 AAT-AGAAATTATTTATAACTT
1 AATAATAAATTATTAATAACTT
* * * * *
9509527 AATGATAAGTCATTCATAATTT
1 AATAATAAATTATTAATAACTT
*** * * *
9509549 AATGGCAAATCATTCATAAATT
1 AATAATAAATTATTAATAACTT
* *
9509571 AGA-AGTAAATTATTAATAATTT
1 A-ATAATAAATTATTAATAACTT
** *
9509593 AGCAATAAATTATTGATAACTT
1 AATAATAAATTATTAATAACTT
* * *
9509615 AATAATAAATAACTGATAACTT
1 AATAATAAATTATTAATAACTT
** *
9509637 AATTGTCAATTATTAATAACTT
1 AATAATAAATTATTAATAACTT
9509659 TTTTTATACT
Statistics
Matches: 437, Mismatches: 112, Indels: 74
0.70 0.18 0.12
Matches are distributed among these distances:
17 13 0.03
18 2 0.00
19 15 0.03
20 8 0.02
21 73 0.17
22 291 0.67
23 18 0.04
24 2 0.00
25 1 0.00
26 5 0.01
27 9 0.02
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (22 bp):
AATAATAAATTATTAATAACTT
Found at i:9510098 original size:89 final size:87
Alignment explanation
Indices: 9509934--9510142 Score: 231
Period size: 89 Copynumber: 2.3 Consensus size: 87
9509924 AAGTGATACT
* * * * * *** *
9509934 TTAGTAGTTAATCATTGATAATTTAATACTAAATCAATGATAACTTAATAGTAAATTATTTTTAC
1 TTAGTAGTAAATCATTAATAACTTAATAGTAAATCAACGATAACTTAATAGTAAATTATTAGAAA
**
9509999 TTTATTAGT-AATTAATTGATAAAC
66 TTTAAAAGTAAATTAA-T-AT-AAC
* * *
9510023 TTAGTAGTAAATCATAAATAACTTAATAGTAAATCAACGATAATTTAATAGTTAATTATTAGAAA
1 TTAGTAGTAAATCATTAATAACTTAATAGTAAATCAACGATAACTTAATAGTAAATTATTAGAAA
9510088 TTTAAAAGTAAATTAATATAAC
66 TTTAAAAGTAAATTAATATAAC
9510110 TTAGTAGTAGTTAATCATTAATAACTTAATAGT
1 TTAGTAGTA---AATCATTAATAACTTAATAGT
9510143 TAATTAACTT
Statistics
Matches: 101, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
87 12 0.12
88 2 0.02
89 61 0.60
90 26 0.26
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (87 bp):
TTAGTAGTAAATCATTAATAACTTAATAGTAAATCAACGATAACTTAATAGTAAATTATTAGAAA
TTTAAAAGTAAATTAATATAAC
Found at i:9510145 original size:22 final size:22
Alignment explanation
Indices: 9509938--9510684 Score: 141
Period size: 22 Copynumber: 33.8 Consensus size: 22
9509928 GATACTTTAG
* *
9509938 TAGTTAATCATTGATAATTTAA
1 TAGTAAATCATTGATAACTTAA
* *
9509960 TACTAAATCAATGATAACTTAA
1 TAGTAAATCATTGATAACTTAA
* * * *
9509982 TAGTAAATTATT-TTTACTTTAT
1 TAGTAAATCATTGATAAC-TTAA
* * *
9510004 TAGTAATTAATTGATAAACTTAG
1 TAGTAAATCATTGAT-AACTTAA
**
9510027 TAGTAAATCATAAATAACTTAA
1 TAGTAAATCATTGATAACTTAA
** *
9510049 TAGTAAATCAACGATAATTTAA
1 TAGTAAATCATTGATAACTTAA
* * *
9510071 TAGTTAATTATTAGA-AATTTAA
1 TAGTAAATCATT-GATAACTTAA
* * *
9510093 AAGTAAATTAAT-ATAACTTAGTA
1 TAGTAAATCATTGATAACTTA--A
* *
9510116 GTAGTTAATCATTAATAACTTAA
1 -TAGTAAATCATTGATAACTTAA
*
9510139 TAGT---T-AAT--TAACTTAA
1 TAGTAAATCATTGATAACTTAA
* * *
9510155 TAGTAAATTATGGATAATTTAA
1 TAGTAAATCATTGATAACTTAA
* * * *
9510177 TA-TAAATTAGTGGTAACTTTA
1 TAGTAAATCATTGATAACTTAA
* * * * *
9510198 TAATGAATCA-TGCTTAATTTAG
1 TAGTAAATCATTG-ATAACTTAA
** ** * * **
9510220 TAACAAATC-TAAAATGATTTTT
1 TAGTAAATCAT-TGATAACTTAA
* *
9510242 TAGTAAATAATTGAAAAC-TAA
1 TAGTAAATCATTGATAACTTAA
* * * *
9510263 GTAGTAAATTAATAATAACATAA
1 -TAGTAAATCATTGATAACTTAA
* *
9510286 TAGTAAATGCA-TAATAACATAA
1 TAGTAAAT-CATTGATAACTTAA
* * * *
9510308 TAGTGAATAATTGATAATTTGGA
1 TAGTAAATCATTGATAACTT-AA
*
9510331 TA-TAAATTATTGATAACTTAA
1 TAGTAAATCATTGATAACTTAA
* * *
9510352 T-GTTAAATCACTAATAACTTAG
1 TAG-TAAATCATTGATAACTTAA
* * * *
9510374 TTGTAAATC-TATGACAATTTAG
1 TAGTAAATCAT-TGATAACTTAA
* * * *
9510396 TAGTAAATTAGTTAATCAGTGATAA
1 TAGTAAATCA-TTGATAACT--TAA
* * *
9510421 CTTTGTAGTAAATCATCGATAAATTAA
1 --TAGT---AAATCATTGATAACTTAA
* *
9510448 TAGTAAAT--TTGTTTTAACTTTA
1 TAGTAAATCATTG--ATAACTTAA
* * * *
9510470 TAATAAATCATTAACAA-TATAG
1 TAGTAAATCATTGATAACT-TAA
* ** * *
9510492 TAGTAAATTATCAATAATTTAG
1 TAGTAAATCATTGATAACTTAA
* *
9510514 TAGTAAATCATTCATAATTTAA
1 TAGTAAATCATTGATAACTTAA
* * * * *
9510536 TAATAAATCACTAATAAATTAG
1 TAGTAAATCATTGATAACTTAA
* * * *
9510558 TAGTAAATCAATGCTAATTTAG
1 TAGTAAATCATTGATAACTTAA
* * * *
9510580 TACTAAATCATTAATAATTTAG
1 TAGTAAATCATTGATAACTTAA
* * * * *
9510602 TTGTATATAACTGATAATTTAA
1 TAGTAAATCATTGATAACTTAA
*
9510624 TAGTAAATCGTTGATAA-TATAA
1 TAGTAAATCATTGATAACT-TAA
* * *
9510646 TAGTAAATTAATGATAATTTAA
1 TAGTAAATCATTGATAACTTAA
* *
9510668 TTGTCAATCATTGATAA
1 TAGTAAATCATTGATAA
9510685 ATTTTTTTTA
Statistics
Matches: 522, Mismatches: 157, Indels: 92
0.68 0.20 0.12
Matches are distributed among these distances:
16 12 0.02
18 2 0.00
19 2 0.00
20 4 0.01
21 32 0.06
22 394 0.75
23 34 0.07
24 13 0.02
25 13 0.02
27 6 0.01
29 5 0.01
30 5 0.01
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.39
Consensus pattern (22 bp):
TAGTAAATCATTGATAACTTAA
Found at i:9510152 original size:16 final size:16
Alignment explanation
Indices: 9510127--9510164 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
9510117 TAGTTAATCA
9510127 TTAA-TAACTTAATAG
1 TTAATTAACTTAATAG
9510142 TTAATTAACTTAATAG
1 TTAATTAACTTAATAG
*
9510158 TAAATTA
1 TTAATTA
9510165 TGGATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (16 bp):
TTAATTAACTTAATAG
Found at i:9510539 original size:66 final size:66
Alignment explanation
Indices: 9510469--9510600 Score: 171
Period size: 66 Copynumber: 2.0 Consensus size: 66
9510459 TTTTAACTTT
* * * *
9510469 ATAATAAATCATTAAC-AATATAGTAGTAAAT-TAT-CAATAATTTAGTAGTAAATCATTCATAA
1 ATAATAAATCACTAACAAAT-TAGTAGTAAATCAATGC--TAATTTAGTACTAAATCATTAATAA
9510531 TTTA
63 TTTA
*
9510535 ATAATAAATCACTAATAAATTAGTAGTAAATCAATGCTAATTTAGTACTAAATCATTAATAATTT
1 ATAATAAATCACTAACAAATTAGTAGTAAATCAATGCTAATTTAGTACTAAATCATTAATAATTT
9510600 A
66 A
9510601 GTTGTATATA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
66 52 0.90
67 5 0.09
68 1 0.02
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.37
Consensus pattern (66 bp):
ATAATAAATCACTAACAAATTAGTAGTAAATCAATGCTAATTTAGTACTAAATCATTAATAATTT
A
Found at i:9510620 original size:44 final size:43
Alignment explanation
Indices: 9510492--9510684 Score: 179
Period size: 44 Copynumber: 4.4 Consensus size: 43
9510482 AACAATATAG
* * * *
9510492 TAGTAAATTATCAATAATTTAGTAGTAAATCATTCATAATTTAA
1 TAGTAAATCATTAATAATTTAGTAGTAAAT-AATGATAATTTAA
* * * * *
9510536 TAATAAATCACTAATAAATTAGTAGTAAATCAATGCTAATTTAG
1 TAGTAAATCATTAATAATTTAGTAGTAAAT-AATGATAATTTAA
* * *
9510580 TACTAAATCATTAATAATTTAGTTGTATATAACTGATAATTTAA
1 TAGTAAATCATTAATAATTTAGTAGTAAATAA-TGATAATTTAA
* * * *
9510624 TAGTAAATCGTTGATAATATAATAGTAAATTAATGATAATTTAA
1 TAGTAAATCATTAATAATTTAGTAGTAAA-TAATGATAATTTAA
* * *
9510668 TTGTCAATCATTGATAA
1 TAGTAAATCATTAATAA
9510685 ATTTTTTTTA
Statistics
Matches: 121, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
43 2 0.02
44 116 0.96
45 3 0.02
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (43 bp):
TAGTAAATCATTAATAATTTAGTAGTAAATAATGATAATTTAA
Found at i:9510653 original size:66 final size:66
Alignment explanation
Indices: 9510505--9510671 Score: 172
Period size: 66 Copynumber: 2.5 Consensus size: 66
9510495 TAAATTATCA
* ** * *
9510505 ATAATTTAGTAGTAAATCATTCATAATTTAATAATAAATCACTAATAAATTAGTAGTAAATCAAT
1 ATAATTTAGTAGTAAATCATTAATAATTTAATTGTAAATAACTAATAAATTAATAGTAAATCAAT
9510570 G
66 G
* * * * * * **
9510571 CTAATTTAGTACTAAATCATTAATAATTTAGTTGTATATAACTGATAATTTAATAGTAAATCGTT
1 ATAATTTAGTAGTAAATCATTAATAATTTAATTGTAAATAACTAATAAATTAATAGTAAATCAAT
9510636 G
66 G
* * * * *
9510637 ATAATATAATAGTAAATTAATGATAATTTAATTGT
1 ATAATTTAGTAGTAAATCATTAATAATTTAATTGT
9510672 CAATCATTGA
Statistics
Matches: 80, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
66 80 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (66 bp):
ATAATTTAGTAGTAAATCATTAATAATTTAATTGTAAATAACTAATAAATTAATAGTAAATCAAT
G
Found at i:9511006 original size:21 final size:21
Alignment explanation
Indices: 9510982--9511035 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
9510972 GTTATTTACT
*
9510982 AAAATTATATTAA-GAAATACC
1 AAAATTATATCAATG-AATACC
* *
9511003 AAAATTTTATCAATGATTACC
1 AAAATTATATCAATGAATACC
*
9511024 AAAATTACATCA
1 AAAATTATATCA
9511036 TAAATTACCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAATTATATCAATGAATACC
Found at i:9512546 original size:68 final size:68
Alignment explanation
Indices: 9512390--9512575 Score: 185
Period size: 68 Copynumber: 2.7 Consensus size: 68
9512380 CCTATACCAA
* ** * * *
9512390 TCACAAATTGATTCAATTGATAAAATCATCAGCCCCAACATAATTGTTTTTGGATACGAATTTTA
1 TCACAAATTGATTCAATTGATAAAATCGTCA-ATCCAATATAATTGTTTGTCGATACGAATTTTA
**
9512455 TTAT
65 CAAT
* *
9512459 TCACAAATTAATTCAATTGATAAAATCGTCAATCCAATATAATTGTTTGTCGATTCGAATTTTAA
1 TCACAAATTGATTCAATTGATAAAATCGTCAATCCAATATAATTGTTTGTCGATACGAATTTT-A
9512524 CAAT
65 CAAT
* * * * * * *
9512528 T-ATAAATTGACTCTATTGATAAGACCGTCAATCCGATCATAACTGTTT
1 TCACAAATTGATTCAATTGATAAAATCGTCAATCCAAT-ATAATTGTTT
9512576 TTGATTCAAA
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
68 55 0.57
69 42 0.43
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (68 bp):
TCACAAATTGATTCAATTGATAAAATCGTCAATCCAATATAATTGTTTGTCGATACGAATTTTAC
AAT
Found at i:9521327 original size:221 final size:215
Alignment explanation
Indices: 9520680--9521340 Score: 636
Period size: 221 Copynumber: 3.0 Consensus size: 215
9520670 TGTCTAATAT
* * * *
9520680 TTATTTGGATTGTTGACTTTTAATTTTCTTGTATTCATTTTTTTTAAACCATTATTTTAAAATGT
1 TTATTTGAATTATTGACTTTTAATTTTCTTGTATTCATTTTTTTAAAACCATTATTTTAAAATTT
* * * *
9520745 ATTCATCAACCTTTTAGTTTTGTAACATTTATATTTTTCGCTTTTGATTTTCTTATGACTTATGA
66 ATTGATCAAAC-TTTAGTTTTGTAACATTTATATTTTACTCTTTTGATTTTCTTATGACTTATGA
* * *
9520810 TCTTCTATCTCTTTAAAGGGTGAGA-ATTATATGAGTGTCTTTTATGTCTTTATTACACTTTTTT
130 TTTTC-ATCTTTTTAAAGGGTGAGAGATTATATGAGTGTCTTTTATGTCTCTATTACACTTTTTT
* * *
9520874 CTTTCAATTATTGTTTGTCATA
194 CTCTCAATTCTTATTTGTCATA
* * *
9520896 TTATTCT-TATTATTTACTCTTAATTTTCTTGTATTCATTTTATTTAAAACCATTATTTGTTAAA
1 TTATT-TGAATTATTGACTTTTAATTTTCTTGTATTCATTTT-TTTAAAACCATTA-TT-TTAAA
* ** * *
9520960 ATTTACTGATCAAACCCTAGATTTTGTAACATTTATATTTTTGACTTAATTTTGATTTTCTTATA
62 ATTTATTGATCAAACTTTAG-TTTTGTAACATTTATA-TTTT-AC-T-CTTTTGATTTTCTTATG
* * * * * *
9521025 ATTTATGATTTT-ATATTTCTTTTAAGGGTGAGAG-TTATATGAATTGT-TTTCATGTCTCTTTT
122 ACTTATGATTTTCAT-CTT-TTTAAAGGGTGAGAGATTATATG-AGTGTCTTTTATGTCTCTATT
* *
9521087 ATA-TTTTTTTTC-CAATTCTTATTTGTCATA
184 ACACTTTTTTCTCTCAATTCTTATTTGTCATA
* * * **
9521117 TTATTTGAATTATTGACTTTTGATTTTTTTATATTCATTTTCTTTAAAATTATTATCTATTAAAA
1 TTATTTGAATTATTGACTTTTAATTTTCTTGTATTCATTTT-TTTAAAACCATTAT-T-TTAAAA
* **
9521182 TTTATTGATCAAATCTTTAGTTTTATAACATTTATATTTTAAC-CTTTTGATTTTCTTGGGACTT
63 TTTATTGATCAAA-CTTTAGTTTTGTAACATTTATATTTT-ACTCTTTTGATTTTCTTATGACTT
* *** * **
9521246 ATAGTTTTTCATCTTTTTCAAAATATAAGAGATTATATGAGTGTCTTTTATACCTCTATTACACT
126 AT-GATTTTCATCTTTTT-AAAGGGTGAGAGATTATATGAGTGTCTTTTATGTCTCTATTACACT
* * * *
9521311 TTCTTCTCTAAATTCTTATTTATCGTA
189 TTTTTCTCTCAATTCTTATTTGTCATA
9521338 TTA
1 TTA
9521341 CTAATTATGC
Statistics
Matches: 355, Mismatches: 67, Indels: 41
0.77 0.14 0.09
Matches are distributed among these distances:
216 35 0.10
217 34 0.10
218 23 0.06
219 54 0.15
220 19 0.05
221 115 0.32
222 12 0.03
223 59 0.17
224 4 0.01
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (215 bp):
TTATTTGAATTATTGACTTTTAATTTTCTTGTATTCATTTTTTTAAAACCATTATTTTAAAATTT
ATTGATCAAACTTTAGTTTTGTAACATTTATATTTTACTCTTTTGATTTTCTTATGACTTATGAT
TTTCATCTTTTTAAAGGGTGAGAGATTATATGAGTGTCTTTTATGTCTCTATTACACTTTTTTCT
CTCAATTCTTATTTGTCATA
Found at i:9526287 original size:18 final size:19
Alignment explanation
Indices: 9526254--9526290 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
9526244 AAAAATAGTA
9526254 AAAAAAAAAGTAAAATGAAG
1 AAAAAAAAAG-AAAATGAAG
9526274 AAAAAAAAAG-AAATGAA
1 AAAAAAAAAGAAAATGAA
9526291 TGCCATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAAAAAAAGAAAATGAAG
Found at i:9526673 original size:8 final size:8
Alignment explanation
Indices: 9526645--9526692 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
9526635 TAATGGATGG
*
9526645 GAAAAGAT
1 GAAAAAAT
*
9526653 GAAAAAGAA
1 GAAAAA-AT
9526662 GAAAAAAT
1 GAAAAAAT
9526670 GAAAAAAT
1 GAAAAAAT
9526678 GAAAAAAGT
1 GAAAAAA-T
9526687 GAAAAA
1 GAAAAA
9526693 TAAAAAGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
8 21 0.60
9 14 0.40
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (8 bp):
GAAAAAAT
Found at i:9526693 original size:16 final size:16
Alignment explanation
Indices: 9526645--9526692 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
9526635 TAATGGATGG
* *
9526645 GAAAAGATGAAAAAGAA
1 GAAAAAATGAAAAA-AT
9526662 GAAAAAATGAAAAAAT
1 GAAAAAATGAAAAAAT
9526678 GAAAAAAGTGAAAAA
1 GAAAAAA-TGAAAAA
9526693 TAAAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.29
17 20 0.71
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (16 bp):
GAAAAAATGAAAAAAT
Found at i:9528012 original size:79 final size:79
Alignment explanation
Indices: 9527916--9528391 Score: 627
Period size: 79 Copynumber: 6.0 Consensus size: 79
9527906 GTTTGGATTT
* * * *
9527916 TCAAATAAGAATCTTTGAATTTCAAATGAGAATCTATGAGGTGTGAAACCCAAAATTTATCGAAT
1 TCAAATGAGAATATTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATTGAAT
*
9527981 GTGAATCTTCAAAC
66 GTGAATCTTCGAAC
*
9527995 TCAAATGAGAATATTTGAATTTCAAATGAGAATCTTTGAAGTGTGAAACCCAAAATTTATTGAAT
1 TCAAATGAGAATATTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATTGAAT
*
9528060 GTGAATCTTCAAAC
66 GTGAATCTTCGAAC
* * * *
9528074 TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTAAGATGTGAAACCCAAAATTTATCGAAT
1 TCAAATGAGAATATTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATTGAAT
9528139 GTGAATCTTCGAAC
66 GTGAATCTTCGAAC
* * * *
9528153 TCAAATGAGAATATTTAAATTTCAAGTGAGAATCTTTGAGGTGTAAAACCCAAAATTTGTTGAAT
1 TCAAATGAGAATATTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATTGAAT
* *
9528218 GTAAATCTTTGAAC
66 GTGAATCTTCGAAC
* * * * *
9528232 TCAAATGAAAATATTTAAATTTCAAATGAGAATCTTTGAGGTGTGAAATCTAAAATTTGTTGAAT
1 TCAAATGAGAATATTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATTGAAT
9528297 GTGAATCTTCGAAC
66 GTGAATCTTCGAAC
* * ** * *
9528311 TCAAATAAGAATCTTTGTGTTTCAAAT-A-AAGTTATTTGAGGTGTGAAACCC-TAATGTTCATT
1 TCAAATGAGAATATTTGAATTTCAAATGAGAA--TCTTTGAGGTGTGAAACCCAAAAT-TT-ATT
9528373 -AGATGTGAATCTTCGAAC
62 GA-ATGTGAATCTTCGAAC
9528391 T
1 T
9528392 AGAATGAAAA
Statistics
Matches: 353, Mismatches: 39, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
77 2 0.01
78 4 0.01
79 328 0.93
80 19 0.05
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (79 bp):
TCAAATGAGAATATTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATTGAAT
GTGAATCTTCGAAC
Found at i:9528021 original size:21 final size:21
Alignment explanation
Indices: 9527995--9528034 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9527985 ATCTTCAAAC
9527995 TCAAATGAGAATATTTGAATT
1 TCAAATGAGAATATTTGAATT
*
9528016 TCAAATGAGAATCTTTGAA
1 TCAAATGAGAATATTTGAA
9528035 GTGTGAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (21 bp):
TCAAATGAGAATATTTGAATT
Found at i:9528085 original size:20 final size:20
Alignment explanation
Indices: 9528057--9528109 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
9528047 AAATTTATTG
*
9528057 AATGTGAATCTTCAAACTCA
1 AATGAGAATCTTCAAACTCA
* **
9528077 AATGAGAATCTTTGAATTTCA
1 AATGAGAATC-TTCAAACTCA
9528098 AATGAGAATCTT
1 AATGAGAATCTT
9528110 TAAGATGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (20 bp):
AATGAGAATCTTCAAACTCA
Found at i:9528243 original size:20 final size:21
Alignment explanation
Indices: 9528215--9528270 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
9528205 AAATTTGTTG
*
9528215 AATGTAAATCTTTGAA-CTCA
1 AATGAAAATCTTTGAATCTCA
* * *
9528235 AATGAAAATATTTAAATTTCA
1 AATGAAAATCTTTGAATCTCA
*
9528256 AATGAGAATCTTTGA
1 AATGAAAATCTTTGA
9528271 GGTGTGAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (21 bp):
AATGAAAATCTTTGAATCTCA
Found at i:9528907 original size:42 final size:42
Alignment explanation
Indices: 9528786--9529078 Score: 243
Period size: 42 Copynumber: 7.0 Consensus size: 42
9528776 CATGATTATC
* * * *
9528786 GAGGAGCAATTTATTTTTTCCAAAGTTGTTGTGCCTTTCTTTA
1 GAGGAGCAATTTATTTTTT-AAAAGTTGTGGTGCCTCTGTTTA
* * * * **
9528829 AATGAGCAATTTATTTTTTCAAAGTTATAATGCCTCTGTTTA
1 GAGGAGCAATTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTA
* * *
9528871 GAGGAGCAATTTATTTTCTAAAAGTTGTGGTACCTCTGTTTT
1 GAGGAGCAATTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTA
* * * * *
9528913 GAGAAGTAATTTATTTTTTGAAAGTTGTGGTGCATTTGTTTA
1 GAGGAGCAATTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTA
* * *
9528955 GAGGAGCAATTTA--TTTCAAAAGTCGTGGTGCCTCTATTTA
1 GAGGAGCAATTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTA
* * * * * *
9528995 AAGGAGTATTTTATTTTTTAAAA-TTATTGTACCTCTGTTTA
1 GAGGAGCAATTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTA
** ** * * *
9529036 GAGGAGCCTTTTACCTTTT-AAAGTTATTGAGCCTCTGTTTA
1 GAGGAGCAATTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTA
9529077 GA
1 GA
9529079 AGAGTTTTGT
Statistics
Matches: 199, Mismatches: 48, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
40 34 0.17
41 45 0.23
42 103 0.52
43 17 0.09
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (42 bp):
GAGGAGCAATTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTA
Found at i:9530790 original size:8 final size:8
Alignment explanation
Indices: 9530767--9530796 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
9530757 TAGTGTTTTA
9530767 TATTATAT
1 TATTATAT
9530775 TA-TATAT
1 TATTATAT
9530782 TATTATAT
1 TATTATAT
9530790 TATTATA
1 TATTATA
9530797 CTATATAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTATAT
Found at i:9530886 original size:15 final size:16
Alignment explanation
Indices: 9530866--9530898 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
9530856 CTTAAATTTA
*
9530866 TTTTATTTTTC-ATAT
1 TTTTATTTGTCAATAT
9530881 TTTTATTTGTCAATAT
1 TTTTATTTGTCAATAT
9530897 TT
1 TT
9530899 CTTCTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTATTTGTCAATAT
Found at i:9538136 original size:23 final size:23
Alignment explanation
Indices: 9538110--9538171 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
9538100 CTCGCTCGAT
9538110 TAAGCTCGATTAGTATGTAAAAA
1 TAAGCTCGATTAGTATGTAAAAA
9538133 TAAGCTCGATTAGTATGTAAAAA
1 TAAGCTCGATTAGTATGTAAAAA
*
9538156 TAAGCTCGATTCGTAT
1 TAAGCTCGATTAGTAT
9538172 ACTCGACAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (23 bp):
TAAGCTCGATTAGTATGTAAAAA
Found at i:9547394 original size:28 final size:28
Alignment explanation
Indices: 9547359--9547419 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
9547349 TGTATGCATT
9547359 TGCATCATTT-TCATATCATTTCATTCTA
1 TGCATCATTTCT-ATATCATTTCATTCTA
9547387 TGCATCATTTCTATATCATTTCATTCTA
1 TGCATCATTTCTATATCATTTCATTCTA
9547415 TGCAT
1 TGCAT
9547420 TATTATATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.25, C:0.21, G:0.05, T:0.49
Consensus pattern (28 bp):
TGCATCATTTCTATATCATTTCATTCTA
Found at i:9547426 original size:25 final size:27
Alignment explanation
Indices: 9547371--9547430 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 27
9547361 CATCATTTTC
*
9547371 ATATCATTTCATTCTATGCATCATTTCT
1 ATATCATTTCATTCTATGCAT-ATATCT
9547399 ATATCATTTCATTCTATGCAT-TAT-T
1 ATATCATTTCATTCTATGCATATATCT
9547424 ATATCAT
1 ATATCAT
9547431 CCTATGCATC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 8 0.26
26 2 0.06
28 21 0.68
ACGTcount: A:0.28, C:0.18, G:0.03, T:0.50
Consensus pattern (27 bp):
ATATCATTTCATTCTATGCATATATCT
Found at i:9547583 original size:26 final size:26
Alignment explanation
Indices: 9547545--9547597 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
9547535 TACATGCATT
9547545 ACACATAAAGCATATAATTTCTGATC
1 ACACATAAAGCATATAATTTCTGATC
* *
9547571 ACACATAAGGCATATCATTTCTGATC
1 ACACATAAAGCATATAATTTCTGATC
9547597 A
1 A
9547598 TAATTGTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (26 bp):
ACACATAAAGCATATAATTTCTGATC
Found at i:9550289 original size:18 final size:18
Alignment explanation
Indices: 9550267--9550310 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
9550257 GGGAAAAGAC
*
9550267 GAAAAAGAAGAAAAAA-T
1 GAAAAAAAAGAAAAAAGT
*
9550284 GAAAAAAATGAAAAAAGT
1 GAAAAAAAAGAAAAAAGT
9550302 GAAAAAAAA
1 GAAAAAAAA
9550311 AAAGAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (18 bp):
GAAAAAAAAGAAAAAAGT
Found at i:9550299 original size:9 final size:9
Alignment explanation
Indices: 9550277--9550309 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
9550267 GAAAAAGAAG
9550277 AAAAAATGA
1 AAAAAATGA
9550286 AAAAAATGA
1 AAAAAATGA
*
9550295 AAAAAGTGA
1 AAAAAATGA
9550304 AAAAAA
1 AAAAAA
9550310 AAAAGAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (9 bp):
AAAAAATGA
Found at i:9550324 original size:9 final size:8
Alignment explanation
Indices: 9550267--9550322 Score: 51
Period size: 9 Copynumber: 6.6 Consensus size: 8
9550257 GGGAAAAGAC
9550267 GAAAAAGAA
1 GAAAAA-AA
*
9550276 GAAAAAAT
1 GAAAAAAA
9550284 GAAAAAAA
1 GAAAAAAA
*
9550292 TGAAAAAAGT
1 -GAAAAAA-A
9550302 GAAAAAAA
1 GAAAAAAA
9550310 -AAAAGAAA
1 GAAAA-AAA
9550318 GAAAA
1 GAAAA
9550323 GATGAAGAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 4 0.10
8 11 0.28
9 24 0.62
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (8 bp):
GAAAAAAA
Found at i:9551300 original size:11 final size:9
Alignment explanation
Indices: 9551267--9551292 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
9551257 TTGACATCCA
9551267 CATTACATG
1 CATTACATG
9551276 CATTACATG
1 CATTACATG
9551285 CATTACAT
1 CATTACAT
9551293 TTGCATTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (9 bp):
CATTACATG
Found at i:9551627 original size:20 final size:21
Alignment explanation
Indices: 9551599--9551655 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
9551589 AAATTTATCG
*
9551599 AATGTGAATCTTT-AAACTCA
1 AATGAGAATCTTTGAAACTCA
* **
9551619 AATGAGAATATTTGAATTTCA
1 AATGAGAATCTTTGAAACTCA
9551640 AATGAGAATCTTTGAA
1 AATGAGAATCTTTGAA
9551656 GTGTGAAACC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (21 bp):
AATGAGAATCTTTGAAACTCA
Found at i:9551638 original size:79 final size:79
Alignment explanation
Indices: 9551537--9552012 Score: 571
Period size: 79 Copynumber: 6.0 Consensus size: 79
9551527 GTCTGGATTT
* * *
9551537 TCAAATAAGAATCTTTTAATTTCAAATGAGAATCTATGAGGTGTGAAACCCAAAATTTATCGAAT
1 TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATCGAAT
*
9551602 GTGAATCTTTAAAC
66 GTGAATCTTCAAAC
* * * *
9551616 TCAAATGAGAATATTTGAATTTCAAATGAGAATCTTTGAAGTGTGAAACCTAAAATTTATTGAAT
1 TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATCGAAT
*
9551681 GTGAATTTTCAAAC
66 GTGAATCTTCAAAC
* * * * * ** *
9551695 TAAAATGATAATATTTGAATTTCAAATGTGAATCTTTAAAATGTGAAACCCAAAATTTGTCGAAT
1 TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATCGAAT
*
9551760 GTGAATCTTCGAAC
66 GTGAATCTTCAAAC
* * * *
9551774 TCAAATGAGAATCTTTAAATTTCAAGTGAGAATCTTTGAGGTGTGAAACCCAAAATTTGTTGAAT
1 TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATCGAAT
* **
9551839 GTAAATCTTTGAAC
66 GTGAATCTTCAAAC
* * * * * *
9551853 TCAAATAAGAATCTTTGAATTTTAAATGAGAATATTTGAGGTGTGAAATCCAAAATTTGTTGAAT
1 TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATCGAAT
*
9551918 ATGAATCTTCAAAC
66 GTGAATCTTCAAAC
** *
9551932 TCAAATGAGAATCTTTGTGTTTCAAAT-A-AAGTTCTTTGAGGTGTGAAACCC-TAATGTTCATC
1 TCAAATGAGAATCTTTGAATTTCAAATGAGAA--TCTTTGAGGTGTGAAACCCAAAAT-TT-ATC
*
9551994 GGATGTGAATCTTCAAAC
62 GAATGTGAATCTTCAAAC
9552012 T
1 T
9552013 AGAATGAAAA
Statistics
Matches: 341, Mismatches: 52, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
77 2 0.01
78 4 0.01
79 317 0.93
80 18 0.05
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (79 bp):
TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATCGAAT
GTGAATCTTCAAAC
Found at i:9552472 original size:42 final size:42
Alignment explanation
Indices: 9552408--9552663 Score: 214
Period size: 42 Copynumber: 6.1 Consensus size: 42
9552398 ATGATTATCG
* * * * *
9552408 AGGAGCAATTTATTTTTCCAAAGTTGTTGTGCCTTTCTTTAA
1 AGGAGCAATTTATTTTTTCAAAGTTATGGTGCCTCTATTTAA
* ** * *
9552450 ATGAGCAATTTATTTTTTCAAAGTTATAATGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTTCAAAGTTATGGTGCCTCTATTTAA
* * * * * *
9552492 AGGAGCAATTTATTTTCTAAAAGTTGTGGTACATCTATTTTA
1 AGGAGCAATTTATTTTTTCAAAGTTATGGTGCCTCTATTTAA
** *
9552534 AGGAATAATTTATTTTTTCAAAGTTACGGTGCCTCTATTTAGA
1 AGGAGCAATTTATTTTTTCAAAGTTATGGTGCCTCTATTTA-A
* ** *
9552577 A-GAGTAATTTA--TTTTCAAAAGTCGTGGTGCTTCTATTTAA
1 AGGAGCAATTTATTTTTTC-AAAGTTATGGTGCCTCTATTTAA
* * * * *
9552617 AGGAGTATTTTA-TTTTTCAAAGTTATTGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTTCAAAGTTATGGTGCCTCTATTTAA
9552658 AGGAGC
1 AGGAGC
9552664 TTTTTACCTT
Statistics
Matches: 169, Mismatches: 41, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
40 7 0.04
41 49 0.29
42 111 0.66
43 2 0.01
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (42 bp):
AGGAGCAATTTATTTTTTCAAAGTTATGGTGCCTCTATTTAA
Found at i:9552548 original size:84 final size:83
Alignment explanation
Indices: 9552456--9552663 Score: 283
Period size: 84 Copynumber: 2.5 Consensus size: 83
9552446 TTAAATGAGC
* *
9552456 AATTTATTTTTTCAAAGTTATAATGCCTCTGTTTAGAGGAGCAATTTATTTTCTAAAAGTTGTGG
1 AATTTATTTTTTCAAAGTTATAGTGCCTCTGTTTAGAGGAGCAATTTATTTTC-AAAAGTCGTGG
*
9552521 TACATCTATTTTAAGGAAT
65 TACATCTATTTAAAGGAAT
** * * *
9552540 AATTTATTTTTTCAAAGTTACGGTGCCTCTATTTAGAAGAGTAATTTATTTTCAAAAGTCGTGGT
1 AATTTATTTTTTCAAAGTTATAGTGCCTCTGTTTAGAGGAGCAATTTATTTTCAAAAGTCGTGGT
* * *
9552605 GCTTCTATTTAAAGGAGT
66 ACATCTATTTAAAGGAAT
* *
9552623 ATTTTA-TTTTTCAAAGTTATTGTGCCTCTGTTTAGAGGAGC
1 AATTTATTTTTTCAAAGTTATAGTGCCTCTGTTTAGAGGAGC
9552664 TTTTTACCTT
Statistics
Matches: 107, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
82 30 0.28
83 30 0.28
84 47 0.44
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (83 bp):
AATTTATTTTTTCAAAGTTATAGTGCCTCTGTTTAGAGGAGCAATTTATTTTCAAAAGTCGTGGT
ACATCTATTTAAAGGAAT
Found at i:9552669 original size:41 final size:41
Alignment explanation
Indices: 9552407--9552699 Score: 175
Period size: 42 Copynumber: 7.0 Consensus size: 41
9552397 CATGATTATC
* * * *
9552407 GAGGAGCAATTTATTTTTCCAAAGTTGTTGTGCCTTTCTTTA
1 GAGGAGCTATTTATTTTT-CAAAGTTGTGGTGCCTCTGTTTA
* * * * **
9552449 AATGAGCAATTTATTTTTTCAAAGTTATAATGCCTCTGTTTA
1 GAGGAGCTATTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTTA
* * * * *
9552491 GAGGAGCAATTTATTTTCTAAAAGTTGTGGTACATCTATTTTA
1 GAGGAGCTATTTATTTT-TCAAAGTTGTGGTGCCTCT-GTTTA
* ** *
9552534 -AGGA-ATAATTTATTTTTTCAAAGTTACGGTGCCTCTATTTA
1 GAGGAGCT-ATTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTTA
* * * *
9552575 GAAGAG-TAATTTA-TTTTCAAAAGTCGTGGTGCTTCTATTTA
1 GAGGAGCT-ATTTATTTTTC-AAAGTTGTGGTGCCTCTGTTTA
* * *
9552616 AAGGAG-TATTTTATTTTTCAAAGTTATTGTGCCTCTGTTTA
1 GAGGAGCTA-TTTATTTTTCAAAGTTGTGGTGCCTCTGTTTA
* * * * *
9552657 GAGGAGCTTTTTACCTTGT-AAAGTTGTTGAGCCTCTGTTTA
1 GAGGAGCTATTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTTA
9552698 GA
1 GA
9552700 AGAGTTTTGT
Statistics
Matches: 197, Mismatches: 42, Indels: 25
0.75 0.16 0.09
Matches are distributed among these distances:
40 6 0.03
41 83 0.42
42 95 0.48
43 13 0.07
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.44
Consensus pattern (41 bp):
GAGGAGCTATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTA
Found at i:9554395 original size:5 final size:5
Alignment explanation
Indices: 9554385--9554426 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
9554375 TGGATAGTGT
9554385 TTATA TTATA TTATA TTATA TTATA -TATA TATATA TATATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA T-TATA T-TATA T
9554427 AAACTCAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.11
5 20 0.57
6 11 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:9554413 original size:2 final size:2
Alignment explanation
Indices: 9554386--9554427 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
9554376 GGATAGTGTT
9554386 TA TA T- TA TA T- TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9554424 TA TA
1 TA TA
9554428 AACTCAATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.11
2 32 0.89
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:9554419 original size:8 final size:8
Alignment explanation
Indices: 9554386--9554427 Score: 56
Period size: 7 Copynumber: 5.8 Consensus size: 8
9554376 GGATAGTGTT
9554386 TATAT-TA
1 TATATATA
9554393 TAT-TATA
1 TATATATA
9554400 T-TATAT-
1 TATATATA
9554406 TATATATA
1 TATATATA
9554414 TATATATA
1 TATATATA
9554422 TATATA
1 TATATA
9554428 AACTCAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 3 0.10
7 14 0.45
8 14 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
TATATATA
Found at i:9555789 original size:2 final size:2
Alignment explanation
Indices: 9555782--9555810 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9555772 ATAAAGAGTT
9555782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9555811 GACTAGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9556672 original size:66 final size:69
Alignment explanation
Indices: 9556526--9556675 Score: 159
Period size: 66 Copynumber: 2.2 Consensus size: 69
9556516 GAAGAAATAG
* * *
9556526 AAAAGATAAAGAAAGCTAAAGATACACAATTAATTACATACATATTACTTTTTAAATTCAAACAA
1 AAAAGGTAAAGAAAGCTAAAGAAACACAATTAATTACATAAATATTACTTTTTAAATTCAAACAA
*
9556591 ATGA
66 ATCA
* * * * *
9556595 AAAA-GTCAAGAAAG-TCAAGAAAACACAATTGA-TATATAAATATTA-TTTTTAAATTGAATA-
1 AAAAGGTAAAGAAAGCTAAAG-AAACACAATTAATTACATAAATATTACTTTTTAAATTCAA-AC
9556655 AAA-CA
64 AAATCA
9556660 AAAAGGTAAAGAAAGC
1 AAAAGGTAAAGAAAGC
9556676 CCAAAAAAGT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
65 5 0.07
66 24 0.36
67 16 0.24
68 18 0.27
69 4 0.06
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.25
Consensus pattern (69 bp):
AAAAGGTAAAGAAAGCTAAAGAAACACAATTAATTACATAAATATTACTTTTTAAATTCAAACAA
ATCA
Found at i:9573374 original size:26 final size:26
Alignment explanation
Indices: 9573345--9573396 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
9573335 AAATTTAGAT
*
9573345 GAAATTTCTCACCTAGAAATTT-TATA
1 GAAATTTATCACCTA-AAATTTCTATA
*
9573371 GAAATTTATCACTTAAAATTTCTATA
1 GAAATTTATCACCTAAAATTTCTATA
9573397 AATTCCATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (26 bp):
GAAATTTATCACCTAAAATTTCTATA
Found at i:9577299 original size:3 final size:3
Alignment explanation
Indices: 9577285--9577331 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
9577275 AAATGGAATT
*
9577285 GAA GAA GCA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
9577332 TTGATTTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:9579505 original size:30 final size:29
Alignment explanation
Indices: 9579437--9579507 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
9579427 TGTCCAATCA
* *
9579437 AAGGTTTAATTGAATGAAAATATATGTAC
1 AAGGTTCAATTGAATGAAAATAAATGTAC
* **
9579466 AAGGATTCAATTGGATGAAAATAAATGTTTT
1 AAGG-TTCAATTGAATGAAAATAAATG-TAC
9579497 AAGGTTCAATT
1 AAGGTTCAATT
9579508 AATTTGAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 4 0.11
30 26 0.74
31 5 0.14
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.35
Consensus pattern (29 bp):
AAGGTTCAATTGAATGAAAATAAATGTAC
Found at i:9580841 original size:22 final size:20
Alignment explanation
Indices: 9580786--9580832 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
9580776 ATAAGATGAT
*
9580786 ATTATTTAACCAATATATAA
1 ATTATTTAACTAATATATAA
9580806 ATTATTTAACTAATATATAA
1 ATTATTTAACTAATATATAA
9580826 ATTATTT
1 ATTATTT
9580833 CATTTTAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTATTTAACTAATATATAA
Found at i:9580902 original size:27 final size:26
Alignment explanation
Indices: 9580872--9580931 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
9580862 AAATAAGATG
9580872 ATATTATTTAATTTAATCTTATTTATA
1 ATATTATTTAATTTAATCTTA-TTATA
* * *
9580899 ATATTATTTTATTTTATTTTATTATA
1 ATATTATTTAATTTAATCTTATTATA
*
9580925 ATCTTAT
1 ATATTAT
9580932 ATATCAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (26 bp):
ATATTATTTAATTTAATCTTATTATA
Found at i:9582707 original size:14 final size:13
Alignment explanation
Indices: 9582688--9582725 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
9582678 TGTTAAATTC
9582688 ATTATTTATCTTTT
1 ATTATTTA-CTTTT
9582702 ATTATTTACTTTT
1 ATTATTTACTTTT
9582715 -TTATTT-CTTTT
1 ATTATTTACTTTT
9582726 GCACTGATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 5 0.21
12 6 0.25
13 5 0.21
14 8 0.33
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTATTTACTTTT
Found at i:9584862 original size:21 final size:21
Alignment explanation
Indices: 9584807--9584863 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
9584797 TTTGGAAGTG
* * *
9584807 CATATTTTATAAAATAATTATA
1 CATATATTAT-AATTAAATATA
*
9584829 CATGTA-TATTAATTAAATATA
1 CATATATTA-TAATTAAATATA
9584850 CATATATTATAATT
1 CATATATTATAATT
9584864 TTGAATAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (21 bp):
CATATATTATAATTAAATATA
Found at i:9585375 original size:325 final size:324
Alignment explanation
Indices: 9584785--9585420 Score: 1087
Period size: 325 Copynumber: 2.0 Consensus size: 324
9584775 ATGTAATTAC
* *
9584785 TTTATTTTATTTTTTGGAAGTGCATATTTTATAAAATAATTATACATGTATATTAATTAAATATA
1 TTTATTTTATTTTTTGGAAGTGCATATTTTATAAAATAATTATACATATATATTAACTAAATATA
* *
9584850 CATATATTATAATTTTGAATAAAGATCATTGAACATTACAATTACAAAAATAATTTTAATTTTAT
66 CATATATTATAATTTTGAATAAAAATAATTGAACATTACAATTACAAAAATAATTTTAATTTTAT
*
9584915 TTATTAATATATTATTATTTTTTCACTAATTATTTTTAAGATGGTACGAATTAATAAATATTTGT
131 TTATTAATATATTATTATTTTTTCACTAATTATTTTTAAGATGATACGAATTAATAAATATTTGT
* *
9584980 GTTACTTTTTGGAAATTTCCCTCAATAAAAGGACTGATGTTTGGGCTGTCTTCCATTACTTAGAT
196 GTTACTTTTCGGAAATTTCCCGCAATAAAAGGACTGATGTTTGGGCTGTCTTCCATTACTTAGAT
*
9585045 AAGAAAGGAAGAAAAAAACCAAGAAGATCCCGACAAGAAAAGAAGTGATGGGCAATAAATTTTAT
261 AAGAAAGGAAGAAAAAAA-CAAGAAGATCCCGACAAGAAAAGAAGCGATGGGCAATAAATTTTAT
9585110 TTTATTTTATTTTTTGGAAGTGCATATTTTATAAAATAATTATACATATATATTAACTAAATATA
1 TTTATTTTATTTTTTGGAAGTGCATATTTTATAAAATAATTATACATATATATTAACTAAATATA
* * *
9585175 CCTATATTATAATTTTGAATAAAAATAATTGAACATTACGATTATAAAAATAATTTTCAATTTTA
66 CATATATTATAATTTTGAATAAAAATAATTGAACATTACAATTACAAAAATAATTTT-AATTTTA
* * *
9585240 TTTATTAATAT-TTATTGTTTTTTCAGTAATTATTTTTAATATGATACGAATTAATAAATATTTG
130 TTTATTAATATATTATTATTTTTTCACTAATTATTTTTAAGATGATACGAATTAATAAATATTTG
*
9585304 TGTTACTTTTCGGAAATTTCCCGCAATAAAAGGACTGAT-TTTCGGGCTGTCTTCCATTGCTTAG
195 TGTTACTTTTCGGAAATTTCCCGCAATAAAAGGACTGATGTTT-GGGCTGTCTTCCATTACTTAG
*
9585368 ATAAGAAAGGAAGAATAAAACAAGAAGATCCCGACAAGAAAAGAAGCGATGGG
259 ATAAGAAAGGAAGAAAAAAACAAGAAGATCCCGACAAGAAAAGAAGCGATGGG
9585421 TAACGACTTT
Statistics
Matches: 293, Mismatches: 16, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
324 35 0.12
325 240 0.82
326 18 0.06
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (324 bp):
TTTATTTTATTTTTTGGAAGTGCATATTTTATAAAATAATTATACATATATATTAACTAAATATA
CATATATTATAATTTTGAATAAAAATAATTGAACATTACAATTACAAAAATAATTTTAATTTTAT
TTATTAATATATTATTATTTTTTCACTAATTATTTTTAAGATGATACGAATTAATAAATATTTGT
GTTACTTTTCGGAAATTTCCCGCAATAAAAGGACTGATGTTTGGGCTGTCTTCCATTACTTAGAT
AAGAAAGGAAGAAAAAAACAAGAAGATCCCGACAAGAAAAGAAGCGATGGGCAATAAATTTTAT
Found at i:9597591 original size:51 final size:52
Alignment explanation
Indices: 9597513--9597638 Score: 166
Period size: 51 Copynumber: 2.4 Consensus size: 52
9597503 CCCTCTCCTC
* * * * *
9597513 TTAGAATTCTT-TTTCTGTAAGTTAAACTTGCCTATTAAGAATCAT-TTTCTT
1 TTAGAATTCTTCTTT-TGCAAGTCAAACTTACCTATTAAAAATCATCTTTCTG
* *
9597564 TTAGAATTCTTCTCTTGCAAGTCAAACTTACCTATTAAAAATCTTCTTTCTG
1 TTAGAATTCTTCTTTTGCAAGTCAAACTTACCTATTAAAAATCATCTTTCTG
9597616 TTAGAATTCTTCTTTTGCAAGTC
1 TTAGAATTCTTCTTTTGCAAGTC
9597639 TTCTTATCCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
51 36 0.55
52 29 0.45
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (52 bp):
TTAGAATTCTTCTTTTGCAAGTCAAACTTACCTATTAAAAATCATCTTTCTG
Found at i:9597701 original size:11 final size:11
Alignment explanation
Indices: 9597665--9597704 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
9597655 AATATCTGAC
9597665 AAATCTCAAAT
1 AAATCTCAAAT
* * *
9597676 AAATTTCTAAC
1 AAATCTCAAAT
9597687 AAATCTCAAAT
1 AAATCTCAAAT
9597698 AAATCTC
1 AAATCTC
9597705 TTATGGGATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATCTCAAAT
Found at i:9598020 original size:25 final size:25
Alignment explanation
Indices: 9597943--9598045 Score: 109
Period size: 25 Copynumber: 4.1 Consensus size: 25
9597933 CAAACCATGT
*
9597943 TCTTCTCACATCTCAAACCTTCAGC
1 TCTTCTCACATCTCGAACCTTCAGC
** * * *
9597968 TCTTCTCATGTCTTGAACATT-TGAC
1 TCTTCTCACATCTCGAACCTTCAG-C
* *
9597993 TCTTCTCACGTTTCGAACCTTCAGC
1 TCTTCTCACATCTCGAACCTTCAGC
*
9598018 TCTTCCCACATCTCGAACCTTCAGC
1 TCTTCTCACATCTCGAACCTTCAGC
9598043 TCT
1 TCT
9598046 GATACTACTA
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
24 1 0.02
25 60 0.97
26 1 0.02
ACGTcount: A:0.19, C:0.36, G:0.09, T:0.36
Consensus pattern (25 bp):
TCTTCTCACATCTCGAACCTTCAGC
Found at i:9598726 original size:52 final size:51
Alignment explanation
Indices: 9598641--9598766 Score: 130
Period size: 52 Copynumber: 2.4 Consensus size: 51
9598631 CCTCTCCTCC
* * * *
9598641 TAGAATTCTTCTTCTGTAAGTCAAACTTGCCTATTAAGAA-TCT-TTTTTCTTT
1 TAGAATTCTTCTT-TGCAAGTCAAACTTACCTATTAAAAATTCTCTTTGTC--T
* *
9598693 TAGAATTCTTCTCTTGCAAGTTAAATTTACCTATTAAAAATTCTCTTTGTCT
1 TAGAATTCTTCT-TTGCAAGTCAAACTTACCTATTAAAAATTCTCTTTGTCT
*
9598745 TAAAATTCTTCTTTTGCAAGTC
1 TAGAATTCTTC-TTTGCAAGTC
9598767 TTCTTATCCA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
52 52 0.84
53 5 0.08
54 5 0.08
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.47
Consensus pattern (51 bp):
TAGAATTCTTCTTTGCAAGTCAAACTTACCTATTAAAAATTCTCTTTGTCT
Found at i:9604005 original size:21 final size:22
Alignment explanation
Indices: 9603974--9604015 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
9603964 TGATGAAGTC
9603974 TGAATTTTCAAATAAGAATCTT
1 TGAATTTTCAAATAAGAATCTT
*
9603996 TGAA-TTTCAAATGAGAATCT
1 TGAATTTTCAAATAAGAATCT
9604016 ATGAGGTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (22 bp):
TGAATTTTCAAATAAGAATCTT
Found at i:9604077 original size:79 final size:78
Alignment explanation
Indices: 9603981--9604393 Score: 565
Period size: 79 Copynumber: 5.2 Consensus size: 78
9603971 GTCTGAATTT
* * *
9603981 TCAAATAAGAATCTTTGAATTTCAAATGAGAATCTATGAGGTGTGAAACACAAAATTTATCGAAT
1 TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAAC-CAAAATTTATTGAAT
9604046 GTGAATCTTCAAAC
65 GTGAATCTTCAAAC
* *
9604060 TCAAATGAGAATATTTGAATTTCAAATGAGAATCTTTGAAGTGTGAAACCCAAAATTTATTGAAT
1 TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAA-CCAAAATTTATTGAAT
*
9604125 GTGAATTTTCAAAC
65 GTGAATCTTCAAAC
* * *
9604139 TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTAAGATGTGAAACCCAAAATTTGTTGAAT
1 TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAA-CCAAAATTTATTGAAT
* *
9604204 GTGAATATTCGAAC
65 GTGAATCTTCAAAC
* * * *
9604218 TCAAATGAGAATCTTTAAATTTCAAGTGAGAATCTTTGAGGTGCGAAACCTAAAATTTATTAAAT
1 TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACC-AAAATTTATTGAAT
* **
9604283 GTAAATCTTTGAAC
65 GTGAATCTTCAAAC
* * *
9604297 TCAAATGAGAATCTTTGAATTTCAAATAAGAATCTTTGAGGTGTGAAACCTAAAATTTGTCGAAT
1 TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACC-AAAATTTATTGAAT
*
9604362 GTAAATCTTCAAAC
65 GTGAATCTTCAAAC
* *
9604376 TTAAATGAGAATATTTGA
1 TCAAATGAGAATCTTTGA
9604394 GGTGTGAAAT
Statistics
Matches: 298, Mismatches: 34, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
78 2 0.01
79 295 0.99
80 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (78 bp):
TCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCAAAATTTATTGAATG
TGAATCTTCAAAC
Found at i:9604086 original size:21 final size:21
Alignment explanation
Indices: 9604060--9604099 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9604050 ATCTTCAAAC
9604060 TCAAATGAGAATATTTGAATT
1 TCAAATGAGAATATTTGAATT
*
9604081 TCAAATGAGAATCTTTGAA
1 TCAAATGAGAATATTTGAA
9604100 GTGTGAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (21 bp):
TCAAATGAGAATATTTGAATT
Found at i:9604150 original size:20 final size:21
Alignment explanation
Indices: 9604122--9604175 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
9604112 AAATTTATTG
*
9604122 AATGTGAAT-TTTCAAACTCA
1 AATGAGAATCTTTCAAACTCA
* **
9604142 AATGAGAATCTTTGAATTTCA
1 AATGAGAATCTTTCAAACTCA
9604163 AATGAGAATCTTT
1 AATGAGAATCTTT
9604176 AAGATGTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (21 bp):
AATGAGAATCTTTCAAACTCA
Found at i:9604309 original size:20 final size:21
Alignment explanation
Indices: 9604286--9604335 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
9604276 ATTAAATGTA
*
9604286 AATCTTTGAA-CTCAAATGAG
1 AATCTTTGAATCTCAAATAAG
*
9604306 AATCTTTGAATTTCAAATAAG
1 AATCTTTGAATCTCAAATAAG
9604327 AATCTTTGA
1 AATCTTTGA
9604336 GGTGTGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (21 bp):
AATCTTTGAATCTCAAATAAG
Found at i:9604397 original size:58 final size:58
Alignment explanation
Indices: 9604318--9604450 Score: 187
Period size: 58 Copynumber: 2.3 Consensus size: 58
9604308 TCTTTGAATT
9604318 TCAAATAAGAATCTTTGAGGTGTGAAA-CCTAAAATTTGTCGAATGTAAATCTTCAAAC
1 TCAAATAAGAATCTTTGAGGTGTGAAATCC-AAAATTTGTCGAATGTAAATCTTCAAAC
* * * * * * *
9604376 TTAAATGAGAATATTTGAGGTGTGAAATCCAAAATTTGTTGAATGTGAATTTTCGAAC
1 TCAAATAAGAATCTTTGAGGTGTGAAATCCAAAATTTGTCGAATGTAAATCTTCAAAC
9604434 TCAAATAAGAATCTTTG
1 TCAAATAAGAATCTTTG
9604451 TGTTTCAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 62 0.97
59 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (58 bp):
TCAAATAAGAATCTTTGAGGTGTGAAATCCAAAATTTGTCGAATGTAAATCTTCAAAC
Found at i:9605005 original size:42 final size:42
Alignment explanation
Indices: 9604912--9605240 Score: 353
Period size: 42 Copynumber: 7.9 Consensus size: 42
9604902 GATTGTCGAT
* *
9604912 GAGCAATTTATTTTTTCAAAGTTGTAGTGTCTCTGTTTAGAG
1 GAGCAATTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * *
9604954 GAG-TATTTATTTTTTCAAAATTGTGGTGCCTTTGTTTAGAG
1 GAGCAATTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * * *
9604995 GAGCAATTTATTTTTCCAAAGTTGTGGTGCCTCTCTTTAAAT
1 GAGCAATTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * *
9605037 GAGCAATTTATTTTTTTAAAGTTATAGTGCCTCTGTTTAGAG
1 GAGCAATTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * * * * *
9605079 GAGAAATTTA-TTTTCCAAAATTGTGGTACCTCTATTTTGAG
1 GAGCAATTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
** *
9605120 GAATAATTTATTTTTTCAAAGTTGTGGTACCTCTGTTTAGAG
1 GAGCAATTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * * *
9605162 GAGCAATTTA--TTTTCAAAGGTCGTGGTGCCTCTATTTAAAA
1 GAGCAATTTATTTTTTCAAA-GTTGTGGTGCCTCTGTTTAGAG
* * * *
9605203 GAGTATTTTATTTTTT-AAAGTTGTTGTGTCTCTGTTTA
1 GAGCAATTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTA
9605241 AAGAAGCCTT
Statistics
Matches: 235, Mismatches: 47, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
40 8 0.03
41 107 0.46
42 116 0.49
43 4 0.02
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (42 bp):
GAGCAATTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
Found at i:9605051 original size:83 final size:83
Alignment explanation
Indices: 9604912--9605240 Score: 385
Period size: 83 Copynumber: 4.0 Consensus size: 83
9604902 GATTGTCGAT
* * * * * *
9604912 GAGCAATTTATTTTTTCAAAGTTGTAGTGTCTCTGTTTAGAGGAGT-ATTTATTTTTTCAAAATT
1 GAGCAATTTA-TTTTCCAAAGTTGTGGTGCCTCTATTTAAAGGAGTAATTTATTTTTTCAAAGTT
*
9604976 GTGGTGCCTTTGTTTAGAG
65 GTGGTGCCTCTGTTTAGAG
* * * *
9604995 GAGCAATTTATTTTTCCAAAGTTGTGGTGCCTCTCTTTAAATGAGCAATTTATTTTTTTAAAGTT
1 GAGCAATTTA-TTTTCCAAAGTTGTGGTGCCTCTATTTAAAGGAGTAATTTATTTTTTCAAAGTT
* *
9605060 ATAGTGCCTCTGTTTAGAG
65 GTGGTGCCTCTGTTTAGAG
* * * ** *
9605079 GAGAAATTTATTTTCCAAAATTGTGGTACCTCTATTTTGAGGAATAATTTATTTTTTCAAAGTTG
1 GAGCAATTTATTTTCCAAAGTTGTGGTGCCTCTATTTAAAGGAGTAATTTATTTTTTCAAAGTTG
*
9605144 TGGTACCTCTGTTTAGAG
66 TGGTGCCTCTGTTTAGAG
* * *
9605162 GAGCAATTTATTTT-CAAAGGTCGTGGTGCCTCTATTTAAAAGAGTATTTTATTTTTT-AAAGTT
1 GAGCAATTTATTTTCCAAA-GTTGTGGTGCCTCTATTTAAAGGAGTAATTTATTTTTTCAAAGTT
* *
9605225 GTTGTGTCTCTGTTTA
65 GTGGTGCCTCTGTTTA
9605241 AAGAAGCCTT
Statistics
Matches: 207, Mismatches: 37, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
82 23 0.11
83 143 0.69
84 41 0.20
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (83 bp):
GAGCAATTTATTTTCCAAAGTTGTGGTGCCTCTATTTAAAGGAGTAATTTATTTTTTCAAAGTTG
TGGTGCCTCTGTTTAGAG
Found at i:9605132 original size:125 final size:125
Alignment explanation
Indices: 9604910--9605175 Score: 372
Period size: 125 Copynumber: 2.1 Consensus size: 125
9604900 ATGATTGTCG
* * * *
9604910 ATGAGCAATTTATTTTTTCAAAGTTGTAGTGTCTCTGTTTAGAGGAGTATTTATTTTTTCAAAAT
1 ATGAGCAATTTATTTTTTCAAAGTTATAGTGCCTCTGTTTAGAGGAGAATTTATTTTTCCAAAAT
* * * * *
9604975 TGTGGTGCCTTTGTTTAGAGGAGCAATTTATTTTTCCAAAGTTGTGGTGCCTCTCTTTAA
66 TGTGGTACCTCTATTTAGAGGAACAATTTATTTTTCCAAAGTTGTGGTACCTCTCTTTAA
*
9605035 ATGAGCAATTTATTTTTTTAAAGTTATAGTGCCTCTGTTTAGAGGAGAAATTTA-TTTTCCAAAA
1 ATGAGCAATTTATTTTTTCAAAGTTATAGTGCCTCTGTTTAGAGGAG-AATTTATTTTTCCAAAA
* * * * *
9605099 TTGTGGTACCTCTATTTTGAGGAATAATTTATTTTTTCAAAGTTGTGGTACCTCTGTTTAG
65 TTGTGGTACCTCTATTTAGAGGAACAATTTATTTTTCCAAAGTTGTGGTACCTCTCTTTAA
*
9605160 AGGAGCAATTTATTTT
1 ATGAGCAATTTATTTT
9605176 CAAAGGTCGT
Statistics
Matches: 124, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
125 119 0.96
126 5 0.04
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45
Consensus pattern (125 bp):
ATGAGCAATTTATTTTTTCAAAGTTATAGTGCCTCTGTTTAGAGGAGAATTTATTTTTCCAAAAT
TGTGGTACCTCTATTTAGAGGAACAATTTATTTTTCCAAAGTTGTGGTACCTCTCTTTAA
Found at i:9605241 original size:41 final size:41
Alignment explanation
Indices: 9604912--9605283 Score: 325
Period size: 41 Copynumber: 9.0 Consensus size: 41
9604902 GATTGTCGAT
* *
9604912 GAGCAATTTATTTTTTCAAAGTTGTAGTGTCTCTGTTTAGAG
1 GAGCAATTTATTTTTT-AAAGTTGTGGTGCCTCTGTTTAGAG
* * *
9604954 GAG-TATTTATTTTTTCAAAATTGTGGTGCCTTTGTTTAGAG
1 GAGCAATTTATTTTTT-AAAGTTGTGGTGCCTCTGTTTAGAG
* * * *
9604995 GAGCAATTTATTTTTCCAAAGTTGTGGTGCCTCTCTTTAAAT
1 GAGCAATTTATTTTT-TAAAGTTGTGGTGCCTCTGTTTAGAG
* *
9605037 GAGCAATTTATTTTTTTAAAGTTATAGTGCCTCTGTTTAGAG
1 GAGCAATTTA-TTTTTTAAAGTTGTGGTGCCTCTGTTTAGAG
* ** * * * *
9605079 GAGAAATTTATTTTCCAAAATTGTGGTACCTCTATTTTGAG
1 GAGCAATTTATTTTTTAAAGTTGTGGTGCCTCTGTTTAGAG
** *
9605120 GAATAATTTATTTTTTCAAAGTTGTGGTACCTCTGTTTAGAG
1 GAGCAATTTATTTTTT-AAAGTTGTGGTGCCTCTGTTTAGAG
* * * * *
9605162 GAGCAATTTA-TTTTCAAAGGTCGTGGTGCCTCTATTTAAAA
1 GAGCAATTTATTTTTTAAA-GTTGTGGTGCCTCTGTTTAGAG
* * * * *
9605203 GAGTATTTTATTTTTTAAAGTTGTTGTGTCTCTGTTTAAAG
1 GAGCAATTTATTTTTTAAAGTTGTGGTGCCTCTGTTTAGAG
* ** ** * * *
9605244 AAGCCTTTTACCTTTTAAAGTTGTTGAGCCTCTTTTTAGA
1 GAGCAATTTATTTTTTAAAGTTGTGGTGCCTCTGTTTAGA
9605284 AGAATCTTGT
Statistics
Matches: 265, Mismatches: 59, Indels: 13
0.79 0.18 0.04
Matches are distributed among these distances:
40 3 0.01
41 148 0.56
42 109 0.41
43 5 0.02
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (41 bp):
GAGCAATTTATTTTTTAAAGTTGTGGTGCCTCTGTTTAGAG
Found at i:9611176 original size:18 final size:16
Alignment explanation
Indices: 9611151--9611193 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
9611141 TTATTATGTT
*
9611151 TTATATTTAAAATATTA
1 TTATATTTAAAA-AATA
9611168 TTGATATTTAAAAAATA
1 TT-ATATTTAAAAAATA
9611185 TTATATTTA
1 TTATATTTA
9611194 TTTTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 7 0.29
18 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TTATATTTAAAAAATA
Found at i:9614676 original size:8 final size:8
Alignment explanation
Indices: 9614655--9614766 Score: 147
Period size: 8 Copynumber: 13.8 Consensus size: 8
9614645 CTATGCTTGA
9614655 AAAAAATG
1 AAAAAATG
9614663 ACAAAAATG
1 A-AAAAATG
*
9614672 GAAAAATG
1 AAAAAATG
*
9614680 GAAAAATG
1 AAAAAATG
9614688 -AAAAATG
1 AAAAAATG
9614695 AAAAAATG
1 AAAAAATG
9614703 AAAAAAATG
1 -AAAAAATG
9614712 AAAAAATG
1 AAAAAATG
9614720 AAAAAAATG
1 -AAAAAATG
9614729 AAAAAATG
1 AAAAAATG
9614737 -AAAAATG
1 AAAAAATG
9614744 AAAAAATG
1 AAAAAATG
*
9614752 AAAATGATG
1 AAAA-AATG
9614761 AAAAAA
1 AAAAAA
9614767 GGTGAACAAG
Statistics
Matches: 95, Mismatches: 3, Indels: 12
0.86 0.03 0.11
Matches are distributed among these distances:
7 14 0.15
8 51 0.54
9 30 0.32
ACGTcount: A:0.72, C:0.01, G:0.14, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:9614690 original size:15 final size:15
Alignment explanation
Indices: 9614656--9614766 Score: 141
Period size: 17 Copynumber: 6.9 Consensus size: 15
9614646 TATGCTTGAA
9614656 AAAAATGACAAAAATGG
1 AAAAATGA-AAAAAT-G
*
9614673 AAAAATGGAAAAATG
1 AAAAATGAAAAAATG
9614688 AAAAATGAAAAAATG
1 AAAAATGAAAAAATG
9614703 AAAAAAATGAAAAAATG
1 --AAAAATGAAAAAATG
9614720 AAAAAAATGAAAAAATG
1 --AAAAATGAAAAAATG
9614737 AAAAATGAAAAAATG
1 AAAAATGAAAAAATG
9614752 AAAATGATGAAAAAA
1 AAAA--ATGAAAAAA
9614767 GGTGAACAAG
Statistics
Matches: 88, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
15 34 0.39
16 6 0.07
17 48 0.55
ACGTcount: A:0.72, C:0.01, G:0.14, T:0.13
Consensus pattern (15 bp):
AAAAATGAAAAAATG
Found at i:9614726 original size:49 final size:48
Alignment explanation
Indices: 9614652--9614766 Score: 176
Period size: 49 Copynumber: 2.4 Consensus size: 48
9614642 ATACTATGCT
* *
9614652 TGAAAAAAATGACAAAAATGGAAAAATGGAAAAATGAAAAATGAAAAAA
1 TGAAAAAAATGA-AAAAATGAAAAAATGAAAAAATGAAAAATGAAAAAA
9614701 TGAAAAAAATGAAAAAATGAAAAAAATGAAAAAATGAAAAATGAAAAAA
1 TGAAAAAAATGAAAAAATG-AAAAAATGAAAAAATGAAAAATGAAAAAA
**
9614750 TGAAAATGATGAAAAAA
1 TGAAAAAAATGAAAAAA
9614767 GGTGAACAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 7 0.11
49 54 0.89
ACGTcount: A:0.71, C:0.01, G:0.15, T:0.13
Consensus pattern (48 bp):
TGAAAAAAATGAAAAAATGAAAAAATGAAAAAATGAAAAATGAAAAAA
Found at i:9615827 original size:42 final size:42
Alignment explanation
Indices: 9615781--9616190 Score: 562
Period size: 42 Copynumber: 10.0 Consensus size: 42
9615771 GTCTAGGAGT
*
9615781 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
9615823 ATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
9615863 ATTTAC-TTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
* *
9615903 ATTTACTCTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
9615945 ATTTACTTTT-CAAAGTTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG--TCGTGGTGCCTCTGTTTAGAGGAGCA
9615986 ATTTAC-TTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
9616028 ATTTAC-TTTCCAAAGTCGTGGTGCCTCTATTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
9616069 ATTTA-TTTTTC-AAGTTCGT--TGCCTCTATTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
*
9616108 ATTTACATTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* * * *
9616150 ATTTACTTTCCCAAAGTCGTTGAGCCTCTGCTTAGAGGAGC
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
9616191 TTTGGTAAAA
Statistics
Matches: 336, Mismatches: 15, Indels: 34
0.87 0.04 0.09
Matches are distributed among these distances:
39 28 0.08
40 83 0.25
41 89 0.26
42 132 0.39
43 4 0.01
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (42 bp):
ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:9616133 original size:122 final size:122
Alignment explanation
Indices: 9615781--9616190 Score: 666
Period size: 122 Copynumber: 3.3 Consensus size: 122
9615771 GTCTAGGAGT
9615781 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGC
1 ATTTAC-TTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGC
9615846 CTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
65 CTCTGTTTAGAGGAGCAATTTACTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
9615903 ATTTACTCTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTTCGTTG
1 ATTTACT-TTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TTCGTTG
9615968 CCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
64 CCTCTGTTTAGAGGAGCAATTTACTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* * *
9616028 ATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAGAGGAGCAATTTATTTTTC-AAGTTCGTTGCC
1 ATTTACTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCC
*
9616092 TCTATTTAGAGGAGCAATTTACATTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
66 TCTGTTTAGAGGAGCAATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
9616150 ATTTACTTTCCCAAAGTCGTTG-AGCCTCTGCTTAGAGGAGC
1 ATTTACTTT-CCAAAGTCGTGGTA-CCTCTGTTTAGAGGAGC
9616191 TTTGGTAAAA
Statistics
Matches: 272, Mismatches: 8, Indels: 15
0.92 0.03 0.05
Matches are distributed among these distances:
121 1 0.00
122 124 0.46
123 74 0.27
124 46 0.17
125 27 0.10
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (122 bp):
ATTTACTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCC
TCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:9616138 original size:205 final size:205
Alignment explanation
Indices: 9615781--9616190 Score: 634
Period size: 205 Copynumber: 2.0 Consensus size: 205
9615771 GTCTAGGAGT
*
9615781 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGC
1 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTCGTTGC
* *
9615846 CTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTC
66 CTCTATTTAGAGGAGCAATTTACTTTCCAAAGTTCGTTGCCTCTATTTAGAGGAGCAATTTACTC
*
9615911 TTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTT-TCAAAGTTTCGTT-GCCTCTG
131 TTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCCAAAG--TCGTTAGCCTCTG
*
9615974 TTTAGAGGAGCA
194 CTTAGAGGAGCA
*
9615986 ATTTAC-TTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG-TCGTGG
1 ATTTACTTTTCC-AAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTCGT--
* *
9616049 TGCCTCTATTTAGAGGAGCAATTTATTTTTC-AAGTTCGTTGCCTCTATTTAGAGGAGCAATTTA
63 TGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAGTTCGTTGCCTCTATTTAGAGGAGCAATTTA
*
9616113 CAT-TTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCCAAAGTCGTTGAGCCT
128 C-TCTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCCAAAGTCGTT-AGCCT
9616177 CTGCTTAGAGGAGC
191 CTGCTTAGAGGAGC
9616191 TTTGGTAAAA
Statistics
Matches: 189, Mismatches: 9, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
204 14 0.07
205 124 0.66
206 51 0.27
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (205 bp):
ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTCGTTGC
CTCTATTTAGAGGAGCAATTTACTTTCCAAAGTTCGTTGCCTCTATTTAGAGGAGCAATTTACTC
TTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCCAAAGTCGTTAGCCTCTGCT
TAGAGGAGCA
Found at i:9616203 original size:1 final size:1
Alignment explanation
Indices: 9616197--9616311 Score: 95
Period size: 1 Copynumber: 115.0 Consensus size: 1
9616187 GAGCTTTGGT
* * * * * * * *
9616197 AAAAAAAAAAAAACAAAAAAACAAAACAAAAAACAAAAAAACAAAAAAAAACAAAACAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
9616262 ACAAAAAAACAAAAAAAAGACAAAAAAAAACAAAAAAAGAATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9616312 GTTGCTTCTA
Statistics
Matches: 84, Mismatches: 30, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 84 1.00
ACGTcount: A:0.87, C:0.10, G:0.02, T:0.01
Consensus pattern (1 bp):
A
Found at i:9616216 original size:10 final size:10
Alignment explanation
Indices: 9616198--9616311 Score: 122
Period size: 11 Copynumber: 10.8 Consensus size: 10
9616188 AGCTTTGGTA
*
9616198 AAAAAAAAAA
1 AAAAAAAAAC
9616208 AACAAAAAAAC
1 AA-AAAAAAAC
9616219 AAAACAAAAA-
1 AAAA-AAAAAC
*
9616229 ACAAAAAAAC
1 AAAAAAAAAC
9616239 AAAAAAAAAC
1 AAAAAAAAAC
*
9616249 AAAACAAAACAA
1 AAAA-AAAA-AC
9616261 AACAAAAAAAC
1 AA-AAAAAAAC
9616272 AAAAAAAAGAC
1 AAAAAAAA-AC
9616283 AAAAAAAAAC
1 AAAAAAAAAC
*
9616293 AAAAAAAGAAT
1 AAAAAAA-AAC
9616304 AAAAAAAA
1 AAAAAAAA
9616312 GTTGCTTCTA
Statistics
Matches: 90, Mismatches: 6, Indels: 16
0.80 0.05 0.14
Matches are distributed among these distances:
9 5 0.06
10 36 0.40
11 40 0.44
12 7 0.08
13 2 0.02
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.01
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:9616227 original size:20 final size:20
Alignment explanation
Indices: 9616199--9616311 Score: 140
Period size: 20 Copynumber: 5.5 Consensus size: 20
9616189 GCTTTGGTAA
9616199 AAAAAAAAAAACAAAAAAAC
1 AAAAAAAAAAACAAAAAAAC
*
9616219 AAAACAAAAAACAAAAAAAC
1 AAAAAAAAAAACAAAAAAAC
*
9616239 AAAAAAAAACAA-AACAAAAC
1 AAAAAAAAA-AACAAAAAAAC
9616259 AAAACAAAAAAACAAAAAAA-
1 AAAA-AAAAAAACAAAAAAAC
*
9616279 AGACAAAAAAAAACAAAAAAAG
1 A-A-AAAAAAAAACAAAAAAAC
9616301 AATAAAAAAAA
1 AA-AAAAAAAA
9616312 GTTGCTTCTA
Statistics
Matches: 82, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
20 41 0.50
21 38 0.46
22 3 0.04
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.01
Consensus pattern (20 bp):
AAAAAAAAAAACAAAAAAAC
Found at i:9616409 original size:14 final size:14
Alignment explanation
Indices: 9616390--9616443 Score: 81
Period size: 14 Copynumber: 3.7 Consensus size: 14
9616380 TTTTTTTTTT
9616390 AAAAAAAAGTAAAA
1 AAAAAAAAGTAAAA
9616404 AAAAAAAAGTAAAA
1 AAAAAAAAGTAAAA
*
9616418 AAAAAAAAGAAAACA
1 AAAAAAAAGTAAA-A
9616433 AAAGAAAAAGT
1 AAA-AAAAAGT
9616444 TGCCTCTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
14 26 0.72
15 4 0.11
16 6 0.17
ACGTcount: A:0.83, C:0.02, G:0.09, T:0.06
Consensus pattern (14 bp):
AAAAAAAAGTAAAA
Found at i:9616430 original size:10 final size:10
Alignment explanation
Indices: 9616390--9616441 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
9616380 TTTTTTTTTT
*
9616390 AAAAAAAAGT
1 AAAAAAAAGA
9616400 AAAAAAAA-A
1 AAAAAAAAGA
**
9616409 AAAGTAAA-A
1 AAAAAAAAGA
9616418 AAAAAAAAGA
1 AAAAAAAAGA
*
9616428 AAACAAAAGA
1 AAAAAAAAGA
9616438 AAAA
1 AAAA
9616442 GTTGCCTCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
9 13 0.38
10 21 0.62
ACGTcount: A:0.87, C:0.02, G:0.08, T:0.04
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:9616542 original size:20 final size:19
Alignment explanation
Indices: 9616514--9616551 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
9616504 GAGCTTTGGT
*
9616514 AAAAAAAAAAACACAAAAG
1 AAAAAAAAAAAAACAAAAG
9616533 AAAAACAAAAAAAACAAAA
1 AAAAA-AAAAAAAACAAAA
9616552 AAATGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAACAAAAG
Found at i:9616759 original size:31 final size:28
Alignment explanation
Indices: 9616723--9616796 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 28
9616713 TTATTATTAT
*
9616723 TTTATTTTTTATTTTATGTATATCCTATATA
1 TTTATTTTTTATTTTAT-TAT-TACTA-ATA
* *
9616754 TTTATTATTTA-CTTATTATTACTAATA
1 TTTATTTTTTATTTTATTATTACTAATA
*
9616781 TATATTTTTTTATTTT
1 TTTA-TTTTTTATTTT
9616797 TATCTTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
27 6 0.17
28 10 0.29
29 5 0.14
30 4 0.11
31 10 0.29
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.66
Consensus pattern (28 bp):
TTTATTTTTTATTTTATTATTACTAATA
Found at i:9616826 original size:22 final size:21
Alignment explanation
Indices: 9616783--9616826 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
9616773 TACTAATATA
* *
9616783 TATTTTTTTATTTTTATCTTT
1 TATTTTTTTATTTTCATATTT
*
9616804 TATTTTATTTATTTTCGTATTT
1 TATTTT-TTTATTTTCATATTT
9616826 T
1 T
9616827 TATATATCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (21 bp):
TATTTTTTTATTTTCATATTT
Found at i:9617272 original size:31 final size:31
Alignment explanation
Indices: 9617237--9617302 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
9617227 TTTCAGATTC
* * ** *
9617237 CGGCAAAAATTTCGGCGAATTTTGAATTTTT
1 CGGCAAAAATTCCGGCCAACCTTGAAGTTTT
*
9617268 CGGCAAACATTCCGGCCAACCTTGAAGTTTT
1 CGGCAAAAATTCCGGCCAACCTTGAAGTTTT
9617299 CGGC
1 CGGC
9617303 GACCAACCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (31 bp):
CGGCAAAAATTCCGGCCAACCTTGAAGTTTT
Found at i:9617381 original size:19 final size:20
Alignment explanation
Indices: 9617357--9617395 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
9617347 TCCGGCCAAC
9617357 TTCCGGCGA-AATTTCCAGA
1 TTCCGGCGACAATTTCCAGA
* *
9617376 TTCCGGTGACATTTTCCAGA
1 TTCCGGCGACAATTTCCAGA
9617396 ATTCGACACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (20 bp):
TTCCGGCGACAATTTCCAGA
Found at i:9617768 original size:17 final size:19
Alignment explanation
Indices: 9617746--9617784 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
9617736 TGTAATATTC
9617746 TTTTTATTTA-T-TTTTAT
1 TTTTTATTTATTATTTTAT
9617763 TTTTTATTTATTATTTTAT
1 TTTTTATTTATTATTTTAT
9617782 TTT
1 TTT
9617785 CTTTAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.50
18 1 0.05
19 9 0.45
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTATTTATTATTTTAT
Found at i:9617872 original size:57 final size:56
Alignment explanation
Indices: 9617811--9618373 Score: 764
Period size: 57 Copynumber: 9.7 Consensus size: 56
9617801 AAAATTCCAA
*
9617811 AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
1 AAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
9617868 AAAAAAAAATATTTTTAGGGAAAAGTTG-AA--ATCAATTTTCCTTAGAAATAAATTTCC
1 ---AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT-C
* * *
9617925 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTCAGAAATAAATTTC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
9617981 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 ---AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT-C
*
9618041 AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC
* *
9618098 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
9618154 AAAAAAAATATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 ----AAAA-A-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT-C
*
9618217 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC
9618274 AAAAAA-AGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTCC
1 AAAAAATA---TTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTT-C
9618335 AAAAAATATTTTT-GGG-AAAGTTGAAAGTATCAATTTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
9618374 CTACAAAAAA
Statistics
Matches: 463, Mismatches: 14, Indels: 55
0.87 0.03 0.10
Matches are distributed among these distances:
54 24 0.05
55 2 0.00
56 30 0.06
57 201 0.43
58 13 0.03
59 119 0.26
60 13 0.03
61 11 0.02
62 49 0.11
63 1 0.00
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (56 bp):
AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
Found at i:9617926 original size:116 final size:115
Alignment explanation
Indices: 9617805--9618373 Score: 764
Period size: 116 Copynumber: 4.9 Consensus size: 115
9617795 AAATAAAAAA
9617805 TTCCAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAA
1 TTCCAAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC--
9617870 AAAAAAATATTTTTAGGGAAAAGTTG-AA-ATCAATTTTCCTTAGAAATAAAT
63 AAAAAAATATTTTTAGGGAAAAGTTGAAAGATCAATTTTCCTTAGAAATAAAT
* *
9617921 TTCC--AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTCAGAAATAAATTTCAAA
1 TTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC--A
9617984 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAT
64 AAAAAATATTTTTAGGGAAAAGTTGAAAG-ATCAATTTTCCTTAGAAATAAAT
* *
9618037 TTCC--AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC-A
1 TTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA-TTTCAA
* *
9618099 AAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAAT
65 AAAAATATTTTTAGGGAAAAGTTGAAAG-ATCAATTTTCCTTAGAAATAAAT
* *
9618151 TTCAAAAAAAATATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
1 TTC-CAAAAAA-A-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
* *
9618216 CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAT
63 AAAAAAATATTTTTAGGGAAAAGTTGAAAG-ATCAATTTTCCTTAGAAATAAAT
* *** *
9618270 TTTCAAAAAAAGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCT-TGAAAATCGAAATTT
1 TTCCAAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTCAG-AAAT--AAATTT
*
9618333 CCAAAAAATATTTTT-GGG-AAAGTTGAAAGTATCAATTTTCC
62 CAAAAAAATATTTTTAGGGAAAAGTTGAAAG-ATCAATTTTCC
9618374 CTACAAAAAA
Statistics
Matches: 422, Mismatches: 17, Indels: 28
0.90 0.04 0.06
Matches are distributed among these distances:
113 77 0.18
114 61 0.14
115 2 0.00
116 138 0.33
117 12 0.03
118 32 0.08
119 100 0.24
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (115 bp):
TTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAA
AAAATATTTTTAGGGAAAAGTTGAAAGATCAATTTTCCTTAGAAATAAAT
Found at i:9618357 original size:292 final size:286
Alignment explanation
Indices: 9617811--9618373 Score: 920
Period size: 292 Copynumber: 1.9 Consensus size: 286
9617801 AAAATTCCAA
9617811 AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAAAAAAA
1 AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAAAAAAA
9617876 ATATTTTTAGGGAAAAGTTGAAATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATTTTTGGG
66 ATATTTTTAGGGAAAAGTTGAAATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATTTTTGGG
* *
9617941 GAAAAGTTGAAAGTATCAATTTTTCTCAGAAATAAATTTCAAAAAAAAATATTTTTAGGGAAAAG
131 GAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAAAAAAAATATTTTGAGGGAAAAG
9618006 TTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATTTTTAAGGAAAAGTTGAAAGT
196 TTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATTTTT-AGGAAAAGTTGAAAGT
9618071 ATCAATTTTCCTTAGAAATAAATTTTC
260 ATCAATTTTCCTTAGAAATAAATTTTC
*
9618098 AAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAAAAAAA
1 AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC-AAAAAAA
9618162 TATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATT
65 -A-ATATTTTTAGGGAAAAGTTG-AA--ATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATT
* **
9618227 TTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAAAAGGGT-TTTTGA
125 TTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA-TTTCAAAAAAA-AATATTTTGA
*
9618291 -GGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTCCAAAAAATATTTTT-GGGAA
188 GGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTCCAAAAAATATTTTTAGGAAA
9618353 AGTTGAAAGTATCAATTTTCC
250 AGTTGAAAGTATCAATTTTCC
9618374 CTACAAAAAA
Statistics
Matches: 258, Mismatches: 7, Indels: 17
0.91 0.02 0.06
Matches are distributed among these distances:
286 50 0.19
287 12 0.05
288 1 0.00
289 20 0.08
290 2 0.01
291 1 0.00
292 134 0.52
293 16 0.06
294 22 0.09
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (286 bp):
AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAAAAAAA
ATATTTTTAGGGAAAAGTTGAAATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATTTTTGGG
GAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAAAAAAAATATTTTGAGGGAAAAG
TTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATTTTTAGGAAAAGTTGAAAGTA
TCAATTTTCCTTAGAAATAAATTTTC
Found at i:9620181 original size:18 final size:19
Alignment explanation
Indices: 9620149--9620184 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9620139 AAGATAGAAA
*
9620149 AAAATAAAAGTAAAAAAGT
1 AAAATAAAAGAAAAAAAGT
9620168 AAAAT-AAAGAAAAAAAG
1 AAAATAAAAGAAAAAAAG
9620185 AGAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAATAAAAGAAAAAAAGT
Found at i:9620190 original size:19 final size:19
Alignment explanation
Indices: 9620149--9620194 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
9620139 AAGATAGAAA
* *
9620149 AAAATAAAAGTAAAAAAGT
1 AAAATAAAAGAAAAAAAGG
9620168 AAAAT-AAAGAAAAAAAGAG
1 AAAATAAAAGAAAAAAAG-G
9620187 AAAA-AAAA
1 AAAATAAAA
9620195 TAAATGTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (19 bp):
AAAATAAAAGAAAAAAAGG
Found at i:9620554 original size:8 final size:8
Alignment explanation
Indices: 9620541--9620635 Score: 94
Period size: 7 Copynumber: 12.0 Consensus size: 8
9620531 GAAGATATCA
9620541 AAAAAATG
1 AAAAAATG
9620549 AAAAAAAT-
1 -AAAAAATG
9620557 AAAAGAAT-
1 AAAA-AATG
*
9620565 AAAAAATA
1 AAAAAATG
9620573 AAAAAATG
1 AAAAAATG
9620581 AAAAAA-G
1 AAAAAATG
9620588 AAAAGAAGTG
1 AAAA-AA-TG
9620598 AAAAAATG
1 AAAAAATG
9620606 AAAAAAATG
1 -AAAAAATG
9620615 -AAAAATG
1 AAAAAATG
9620622 -AAAAA-G
1 AAAAAATG
9620628 AAAAAATG
1 AAAAAATG
9620636 TGAAAAGGAA
Statistics
Matches: 77, Mismatches: 1, Indels: 17
0.81 0.01 0.18
Matches are distributed among these distances:
6 1 0.01
7 29 0.38
8 25 0.32
9 17 0.22
10 5 0.06
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:9620554 original size:9 final size:9
Alignment explanation
Indices: 9620540--9620619 Score: 84
Period size: 8 Copynumber: 9.6 Consensus size: 9
9620530 GGAAGATATC
9620540 AAAAAAATG
1 AAAAAAATG
9620549 AAAAAAAT-
1 AAAAAAATG
*
9620557 AAAAGAAT-
1 AAAAAAATG
9620565 -AAAAAAT-
1 AAAAAAATG
9620572 AAAAAAATG
1 AAAAAAATG
9620581 -AAAAAA-G
1 AAAAAAATG
*
9620588 AAAAGAAGTG
1 AAAA-AAATG
9620598 -AAAAAATG
1 AAAAAAATG
9620606 AAAAAAATG
1 AAAAAAATG
9620615 AAAAA
1 AAAAA
9620620 TGAAAAAGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
7 7 0.11
8 27 0.44
9 26 0.43
10 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:9620603 original size:34 final size:32
Alignment explanation
Indices: 9620540--9620633 Score: 120
Period size: 34 Copynumber: 2.9 Consensus size: 32
9620530 GGAAGATATC
*
9620540 AAAAAAATGAAAAAAATAAAAGAATAAAAAAT-
1 AAAAAAATG-AAAAAAGAAAAGAATAAAAAATG
9620572 AAAAAAATGAAAAAAGAAAAGAAGTGAAAAAATG
1 AAAAAAATGAAAAAAGAAAAGAA-T-AAAAAATG
*
9620606 AAAAAAATGAAAAATGAAAAAGAA-AAAA
1 AAAAAAATGAAAAAAG-AAAAGAATAAAA
9620634 TGTGAAAAGG
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
31 13 0.23
32 14 0.25
33 7 0.12
34 15 0.27
35 7 0.12
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (32 bp):
AAAAAAATGAAAAAAGAAAAGAATAAAAAATG
Found at i:9621667 original size:22 final size:21
Alignment explanation
Indices: 9621632--9621807 Score: 239
Period size: 22 Copynumber: 8.3 Consensus size: 21
9621622 TAAGATAAAA
*
9621632 CTTTAAGTTTCAAATGAGAAT
1 CTTTGAGTTTCAAATGAGAAT
* * *
9621653 CTTTGAGTTTTCAAATAAAAAA
1 CTTTGAG-TTTCAAATGAGAAT
9621675 CTTTGAGTTTTCAAATGAGAAT
1 CTTTGAG-TTTCAAATGAGAAT
* *
9621697 CTTTGAGTTTCGAATAAGAAT
1 CTTTGAGTTTCAAATGAGAAT
* *
9621718 CTTTGAATTTTCAAATGAAAAT
1 CTTTG-AGTTTCAAATGAGAAT
9621740 CTTTGAGTTTCAAATGAG-AT
1 CTTTGAGTTTCAAATGAGAAT
9621760 CTTTGAGTTTCAAATGAGAAT
1 CTTTGAGTTTCAAATGAGAAT
9621781 CTTT-AGTTTCAAATGAGAAT
1 CTTTGAGTTTCAAATGAGAAT
9621801 CTTTGAG
1 CTTTGAG
9621808 ATGCAAAACC
Statistics
Matches: 136, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
20 40 0.29
21 42 0.31
22 54 0.40
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (21 bp):
CTTTGAGTTTCAAATGAGAAT
Found at i:9621676 original size:43 final size:42
Alignment explanation
Indices: 9621628--9621794 Score: 203
Period size: 43 Copynumber: 4.0 Consensus size: 42
9621618 CTCTTAAGAT
9621628 AAAACTTTAAGTTTCAAATGAGAATCTTTGAGTTTTCAAATAA
1 AAAACTTTAAGTTTCAAATGAGAATCTTTGAG-TTTCAAATAA
* *
9621671 AAAACTTTGAGTTTTCAAATGAGAATCTTTGAGTTTCGAATAA
1 AAAACTTTAAG-TTTCAAATGAGAATCTTTGAGTTTCAAATAA
* * * * *
9621714 GAATCTTTGAATTTTCAAATGAAAATCTTTGAGTTTCAAAT-G
1 AAAACTTT-AAGTTTCAAATGAGAATCTTTGAGTTTCAAATAA
* * *
9621756 AGATCTTTGAGTTTCAAATGAGAATCTTT-AGTTTCAAAT
1 AAAACTTTAAGTTTCAAATGAGAATCTTTGAGTTTCAAAT
9621795 GAGAATCTTT
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
40 10 0.09
41 18 0.17
42 6 0.06
43 52 0.48
44 22 0.20
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (42 bp):
AAAACTTTAAGTTTCAAATGAGAATCTTTGAGTTTCAAATAA
Found at i:9622358 original size:16 final size:16
Alignment explanation
Indices: 9622308--9622366 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
9622298 TGAAATCTTG
*
9622308 CGAATCTAAATTTTTA
1 CGAATCTAAAATTTTA
* * *
9622324 TGAAGCTGAAAAATCTTA
1 CGAATCT--AAAATTTTA
9622342 CGAATCTAAAATTTTA
1 CGAATCTAAAATTTTA
9622358 CGAAT-TAAA
1 CGAATCTAAA
9622367 TTCTCGTGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 4 0.12
16 18 0.53
18 12 0.35
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (16 bp):
CGAATCTAAAATTTTA
Found at i:9622494 original size:15 final size:15
Alignment explanation
Indices: 9622474--9622503 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9622464 TCTTATGAGT
9622474 CTTTGAATTGCGAAC
1 CTTTGAATTGCGAAC
*
9622489 CTTTGAATTTCGAAC
1 CTTTGAATTGCGAAC
9622504 TCAAATTGTG
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:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (15 bp):
CTTTGAATTGCGAAC
Found at i:9622642 original size:47 final size:45
Alignment explanation
Indices: 9622571--9622804 Score: 189
Period size: 47 Copynumber: 5.2 Consensus size: 45
9622561 GTCGAGGAGC
* *
9622571 TTTATTTA-TTTTCAAAGTTGTTGAGCCTCTGATTAAATGAGCCTTA
1 TTTATTTATTTTTTAAAGTTGTTGAGCCTCTGATTAGA-GAGCC-TA
*
9622617 TTTATTTATTTTTTAAAGTTGTTGAGCCTTTGATTAGAGAAG--T-
1 TTTATTTATTTTTTAAAGTTGTTGAGCCTCTGATTAGAG-AGCCTA
* *
9622660 TTTATTTATTTTCTTAAAGTTGATAAGCCTCTGATTAGAGGAG-CTA
1 TTTATTTATTTT-TTAAAGTTGTTGAGCCTCTGATTAGA-GAGCCTA
* * * *
9622706 TTTA--T-TTTTTCAAAGTTATTGAGCCT-TTACTTAAATGAGCCCTA
1 TTTATTTATTTTTTAAAGTTGTTGAGCCTCTGA-TTAGA-GAG-CCTA
* * * *
9622750 TTTATTTTTTTTTTCAAAGTTGTTAAGCCTCTAATTAGAGAAACCTTA
1 TTTATTTATTTTTT-AAAGTTGTTGAGCCTCTGATTAGAG-AGCC-TA
9622798 TTTATTT
1 TTTATTT
9622805 TCCAAAGTCG
Statistics
Matches: 153, Mismatches: 19, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
41 2 0.01
42 20 0.13
43 16 0.10
44 34 0.22
45 2 0.01
46 14 0.09
47 36 0.24
48 27 0.18
49 2 0.01
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (45 bp):
TTTATTTATTTTTTAAAGTTGTTGAGCCTCTGATTAGAGAGCCTA
Found at i:9622695 original size:44 final size:43
Alignment explanation
Indices: 9622617--9622722 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 43
9622607 ATGAGCCTTA
* * *
9622617 TTTATTTATTTTTTAAAGTTGTTGAGCCTTTGATTAGAGAAGT
1 TTTATTTATTTTTTAAAGTTGATAAGCCTCTGATTAGAGAAGT
*
9622660 TTTATTTATTTTCTTAAAGTTGATAAGCCTCTGATTAGAGGAG-
1 TTTATTTATTTT-TTAAAGTTGATAAGCCTCTGATTAGAGAAGT
*
9622703 -CTATTTATTTTTTCAAAGTT
1 TTTATTTATTTTTT-AAAGTT
9622723 ATTGAGCCTT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
41 2 0.04
42 16 0.29
43 12 0.21
44 26 0.46
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (43 bp):
TTTATTTATTTTTTAAAGTTGATAAGCCTCTGATTAGAGAAGT
Found at i:9622752 original size:86 final size:87
Alignment explanation
Indices: 9622619--9622789 Score: 197
Period size: 86 Copynumber: 2.0 Consensus size: 87
9622609 GAGCCTTATT
* * ***
9622619 TATTTATTTTTTAAAGTTGTTGAGCCTTTGATTAGAGAAGTTTTATTTA-TTTTCTT-AAAGTTG
1 TATTTATTTTTTAAAGTTATTGAGCCTTTGATTAAAGAAGCCCTATTTATTTTTCTTCAAAGTTG
*
9622682 ATAAGCCTCTGATTAGAGGAGC
66 ATAAGCCTCTAATTAGAGGAGC
*
9622704 TATTTATTTTTTCAAAGTTATTGAGCCTTT-ACTTAAATG-AGCCCTATTTATTTTTTTTTTCAA
1 TATTTATTTTTT-AAAGTTATTGAGCCTTTGA-TTAAA-GAAGCCCTATTTA--TTTTTCTTCAA
*
9622767 AGTTGTTAAGCCTCTAATTAGAG
61 AGTTGATAAGCCTCTAATTAGAG
9622790 AAACCTTATT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
85 13 0.18
86 28 0.39
87 1 0.01
89 6 0.08
90 23 0.32
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.47
Consensus pattern (87 bp):
TATTTATTTTTTAAAGTTATTGAGCCTTTGATTAAAGAAGCCCTATTTATTTTTCTTCAAAGTTG
ATAAGCCTCTAATTAGAGGAGC
Found at i:9622806 original size:90 final size:87
Alignment explanation
Indices: 9622619--9622854 Score: 218
Period size: 90 Copynumber: 2.7 Consensus size: 87
9622609 GAGCCTTATT
* ** *
9622619 TATTTATTTTT-TAAAGTTGTTGAGCCTTTGA-TTAG-AGAAG-TTTTATTTATTTTCTT-AAAG
1 TATTTATTTTTCCAAAGTCATTGAGCCTTT-ACTTAGAAG-AGCTTTTATTT-TTTTTTTCAAAG
* * *
9622679 TTGATAAGCCTCTGATTAGAGGAGC
63 TTGATAAGCCTCTAATTAGAGAACC
* *
9622704 TATTTATTTTTTCAAAGTTATTGAGCCTTTACTTA-AATGAGCCCTATTTATTTTTTTTTTCAAA
1 TATTTATTTTTCCAAAGTCATTGAGCCTTTACTTAGAA-GAG--CT-TTTATTTTTTTTTTCAAA
*
9622768 GTTGTTAAGCCTCTAATTAGAGAAACC
62 GTTGATAAGCCTCTAATTAGAG-AACC
* * *
9622795 TTATTTA-TTTTCCAAAGTCGTTGAGCTTTTATTTAGAAGAGCTTTTA-TTTTTTTTTCAAA
1 -TATTTATTTTTCCAAAGTCATTGAGCCTTTACTTAGAAGAGCTTTTATTTTTTTTTTCAAA
9622855 AGTCGTGGAG
Statistics
Matches: 127, Mismatches: 12, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
85 12 0.09
86 22 0.17
87 14 0.11
88 4 0.03
89 9 0.07
90 30 0.24
91 28 0.22
92 8 0.06
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (87 bp):
TATTTATTTTTCCAAAGTCATTGAGCCTTTACTTAGAAGAGCTTTTATTTTTTTTTTCAAAGTTG
ATAAGCCTCTAATTAGAGAACC
Found at i:9622848 original size:133 final size:133
Alignment explanation
Indices: 9622567--9622848 Score: 331
Period size: 133 Copynumber: 2.1 Consensus size: 133
9622557 GATTGTCGAG
* *
9622567 GAGC-TTTATTTATTTTCAAAGTTGTTGAGCCTCTGATTAAATGAGCCTTATTTATTTATTTTTT
1 GAGCTTTTATTT-TTTTCAAAGTTATTGAGCCTCTGATTAAATGAGCCCTATTTATTTATTTTTT
* * * *** * *
9622631 AAAGTTGTTGAGCCTTTGATTAGAGAAGTTTTATTTATTTTCTTAAAGTTGATAAGCCTCTGATT
65 AAAGTTGTTAAGCCTCTAATTAGAGAAACCTTATTTATTTTCTCAAAGTCGATAAGCCTCTGATT
*
9622696 AGAG
130 AGAA
* *
9622700 GAGCTATTTA-TTTTTTCAAAGTTATTGAGCCT-TTACTTAAATGAGCCCTATTTATTTTTTTTT
1 GAGCT-TTTATTTTTTTCAAAGTTATTGAGCCTCTGA-TTAAATGAGCCCTATTTATTTATTTTT
* * * *
9622763 TCAAAGTTGTTAAGCCTCTAATTAGAGAAACCTTATTTATTTTC-CAAAGTCGTTGAG-CTTTTA
64 T-AAAGTTGTTAAGCCTCTAATTAGAGAAACCTTATTTATTTTCTCAAAGTCGATAAGCCTCTGA
9622826 TTTAGAA
128 -TTAGAA
9622833 GAGCTTTTATTTTTTT
1 GAGCTTTTATTTTTTT
9622849 TTCAAAAGTC
Statistics
Matches: 126, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
132 10 0.08
133 74 0.59
134 38 0.30
135 4 0.03
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (133 bp):
GAGCTTTTATTTTTTTCAAAGTTATTGAGCCTCTGATTAAATGAGCCCTATTTATTTATTTTTTA
AAGTTGTTAAGCCTCTAATTAGAGAAACCTTATTTATTTTCTCAAAGTCGATAAGCCTCTGATTA
GAA
Found at i:9623095 original size:19 final size:18
Alignment explanation
Indices: 9623073--9623112 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
9623063 AATAAAAAAC
9623073 AAAAAACAAAAAAATAGAA
1 AAAAAACAAAAAAAT-GAA
**
9623092 AAAAAATGAAAAAATGAA
1 AAAAAACAAAAAAATGAA
9623110 AAA
1 AAA
9623113 TTAGGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.82, C:0.03, G:0.07, T:0.07
Consensus pattern (18 bp):
AAAAAACAAAAAAATGAA
Found at i:9625479 original size:183 final size:183
Alignment explanation
Indices: 9625170--9625531 Score: 589
Period size: 183 Copynumber: 2.0 Consensus size: 183
9625160 ATTAATATAA
* *
9625170 AAAATAATCAATAAATAATTAAATCTCTCATGAAGATCTTTAAATTAGTATTATTTCAATTAATT
1 AAAATAATCAATAAACAATTAAATCTCTCATAAAGATCTTTAAATTAGTATTATTTCAATTAATT
* * * * *
9625235 TGTTGACCCATGATAGCTCTATTCTTGTCTATTATTTGTTTTGATTGTTTGTTAGATATCATTTT
66 TGCTGACCCACGATAGCTCCATTCTTGTCTATTATTTGTTTTGATTGTTTGTTAAATATCATATT
* * * *
9625300 CGGTTTCTTTCTTTCACACTTTATTATTGAAGCTAATTGAGGCAAAGATGTAG
131 CAGTTTCTTTCTTTCACACTTAATTATTGAAACTAAATGAGGCAAAGATGTAG
*
9625353 AAAATAATCAATAAACAATTAAATCTCTCATAAATATCTTTAAATTAGTATTATTTCAATTAATT
1 AAAATAATCAATAAACAATTAAATCTCTCATAAAGATCTTTAAATTAGTATTATTTCAATTAATT
* * *
9625418 TGCTGACCCACGATAGCTCCATTTTTGTTTATTGTTTGTTTTGATTGTTTGTTAAATATCATATT
66 TGCTGACCCACGATAGCTCCATTCTTGTCTATTATTTGTTTTGATTGTTTGTTAAATATCATATT
9625483 CAGTTTCTTTCTTTCACACTTAATTATTGAAACTAAATGAGGCAAAGAT
131 CAGTTTCTTTCTTTCACACTTAATTATTGAAACTAAATGAGGCAAAGAT
9625532 TATAGTTAAA
Statistics
Matches: 164, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
183 164 1.00
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (183 bp):
AAAATAATCAATAAACAATTAAATCTCTCATAAAGATCTTTAAATTAGTATTATTTCAATTAATT
TGCTGACCCACGATAGCTCCATTCTTGTCTATTATTTGTTTTGATTGTTTGTTAAATATCATATT
CAGTTTCTTTCTTTCACACTTAATTATTGAAACTAAATGAGGCAAAGATGTAG
Found at i:9625619 original size:34 final size:33
Alignment explanation
Indices: 9625581--9625648 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
9625571 AATGTAAATT
9625581 TTTA-TAAAATAAAATTAATAATTTTATATAAAAA
1 TTTATTAAAAT-AAATTAA-AATTTTATATAAAAA
* * *
9625615 TTTATTTAAATATATTAAAATTTTATATGAAAA
1 TTTATTAAAATAAATTAAAATTTTATATAAAAA
9625648 T
1 T
9625649 AATATATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 15 0.50
34 10 0.33
35 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (33 bp):
TTTATTAAAATAAATTAAAATTTTATATAAAAA
Found at i:9625668 original size:33 final size:32
Alignment explanation
Indices: 9625591--9625669 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
9625581 TTTATAAAAT
* * *
9625591 AAAATTAATAATTTTATATAAAAATTTATTTA
1 AAAATTAAAAATTTTATATAAAAATATATATA
*
9625623 AATATATT-AAAATTTTATATGAAAATAATATATA
1 AA-A-ATTAAAAATTTTATATAAAAAT-ATATATA
9625657 AAAATTAAAAATT
1 AAAATTAAAAATT
9625670 GATTAACCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
32 5 0.13
33 24 0.62
34 10 0.26
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (32 bp):
AAAATTAAAAATTTTATATAAAAATATATATA
Found at i:9628374 original size:30 final size:33
Alignment explanation
Indices: 9628340--9628401 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
9628330 TAATTCGAAA
* *
9628340 AAGATCAAA-TTTT-AA-ATTTGTATTTGATTC
1 AAGATAAAATTTTTAAATATTTGAATTTGATTC
9628370 AAGATAAAATTTTTAAATATTTGAATTTGATT
1 AAGATAAAATTTTTAAATATTTGAATTTGATT
9628402 GATTAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 8 0.30
31 4 0.15
32 2 0.07
33 13 0.48
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (33 bp):
AAGATAAAATTTTTAAATATTTGAATTTGATTC
Found at i:9629032 original size:20 final size:21
Alignment explanation
Indices: 9628994--9629032 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9628984 TGTAGAGAAA
*
9628994 AAAAAAAACATATAGTATATT
1 AAAAAAAACATATAATATATT
*
9629015 AAAAAAAAGA-ATAATATA
1 AAAAAAAACATATAATATA
9629033 AGATTAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (21 bp):
AAAAAAAACATATAATATATT
Found at i:9629622 original size:21 final size:19
Alignment explanation
Indices: 9629596--9629648 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
9629586 TAATTTTTTA
9629596 AAAATTTTAATTAAATATATT
1 AAAATTTTAATTAAA-A-ATT
9629617 AAAATTTT-ATATAAAAATT
1 AAAATTTTAAT-TAAAAATT
*
9629636 AAAA-ATTAATTAA
1 AAAATTTTAATTAA
9629649 TCAAATTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.17
19 9 0.31
20 3 0.10
21 12 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTTTAATTAAAAATT
Found at i:9629683 original size:21 final size:20
Alignment explanation
Indices: 9629654--9629701 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
9629644 ATTAATCAAA
9629654 TTGAATTTA-ATCGATAAAAAT
1 TTGAATTTATA-C-ATAAAAAT
*
9629675 TTGATTTTATACATAAAAAT
1 TTGAATTTATACATAAAAAT
*
9629695 TTAAATT
1 TTGAATT
9629702 AAATTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 13 0.57
21 9 0.39
22 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (20 bp):
TTGAATTTATACATAAAAAT
Found at i:9632137 original size:19 final size:20
Alignment explanation
Indices: 9632092--9632138 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
9632082 TATTTTATAA
*
9632092 AATAATTGTACATATATATT
1 AATAAATGTACATATATATT
*
9632112 AACTAAATGTACATATCTATT
1 AA-TAAATGTACATATATATT
9632133 -ATAAAT
1 AATAAAT
9632139 TTAAATTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 3 0.12
21 16 0.67
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (20 bp):
AATAAATGTACATATATATT
Found at i:9632299 original size:16 final size:17
Alignment explanation
Indices: 9632277--9632315 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
9632267 AAAAGAAGTG
9632277 ATCGGT-CATGGCTTTT
1 ATCGGTACATGGCTTTT
*
9632293 GTCGGTCACATGGCTTTT
1 ATCGGT-ACATGGCTTTT
9632311 ATCGG
1 ATCGG
9632316 CCACTATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 5 0.26
18 14 0.74
ACGTcount: A:0.13, C:0.21, G:0.28, T:0.38
Consensus pattern (17 bp):
ATCGGTACATGGCTTTT
Found at i:9632792 original size:24 final size:25
Alignment explanation
Indices: 9632748--9632815 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
9632738 TAATAAAAAA
* *
9632748 TAAATTTAATTTTTATATTTAATTT
1 TAAATTTAATTTATATATTTAAATT
*
9632773 TAAA-TTAATTTATATGTTTAAATT
1 TAAATTTAATTTATATATTTAAATT
* *
9632797 TAACTTTGAATTGATATAT
1 TAAATTT-AATTTATATAT
9632816 ATAATAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
24 20 0.57
25 6 0.17
26 9 0.26
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (25 bp):
TAAATTTAATTTATATATTTAAATT
Found at i:9632817 original size:30 final size:30
Alignment explanation
Indices: 9632759--9632817 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
9632749 AAATTTAATT
* * *
9632759 TTTATATTTAATTTTAAATTAATTTATATG
1 TTTAAATTTAACTTTAAATTAATATATATG
* *
9632789 TTTAAATTTAACTTTGAATTGATATATAT
1 TTTAAATTTAACTTTAAATTAATATATAT
9632818 AATAAAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (30 bp):
TTTAAATTTAACTTTAAATTAATATATATG
Found at i:9634544 original size:22 final size:21
Alignment explanation
Indices: 9634519--9634561 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
9634509 TTTGATTTTA
9634519 GAGTTTGGAGATTTTAGGGTTT
1 GAGTTTGGAGATTTT-GGGTTT
* *
9634541 GAGTTTTGAGGTTTTGGGTTT
1 GAGTTTGGAGATTTTGGGTTT
9634562 TTGATATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.14, C:0.00, G:0.37, T:0.49
Consensus pattern (21 bp):
GAGTTTGGAGATTTTGGGTTT
Found at i:9634598 original size:16 final size:15
Alignment explanation
Indices: 9634573--9634687 Score: 70
Period size: 16 Copynumber: 7.3 Consensus size: 15
9634563 TGATATAAGG
9634573 GTTTGGATTTTAGGA
1 GTTTGGATTTTAGGA
9634588 GTTTCGGATTTTAAGG-
1 GTTT-GGATTTT-AGGA
*
9634604 GATTTGGATTTAAGAGA
1 G-TTTGGATTTTAG-GA
* * *
9634621 TTTTAGATTTTAGGG
1 GTTTGGATTTTAGGA
*
9634636 GTTTCGGATTTTAAGGG
1 GTTT-GGATTTT-AGGA
* *
9634653 GTTTGAATTTAAAGGA
1 GTTTGGATTT-TAGGA
* * *
9634669 TTTTGAATTTTAGGG
1 GTTTGGATTTTAGGA
9634684 GTTT
1 GTTT
9634688 TAGAAACTTA
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
15 16 0.21
16 48 0.62
17 14 0.18
ACGTcount: A:0.23, C:0.02, G:0.30, T:0.45
Consensus pattern (15 bp):
GTTTGGATTTTAGGA
Found at i:9634613 original size:32 final size:30
Alignment explanation
Indices: 9634568--9634687 Score: 91
Period size: 32 Copynumber: 3.8 Consensus size: 30
9634558 GTTTTTGATA
9634568 TAAGGG-TTTGGATTTTAGGAGTTTCGGATTT
1 TAAGGGATTTGGATTTTAGGAGTTT--GATTT
* *
9634599 TAAGGGATTTGGATTTAAGAGATTTTAGATTT
1 TAAGGGATTTGGATTTTAG-GAGTTT-GATTT
* * *
9634631 T-AGGGGTTTCGGATTTTAAGGGGTTTGAATT
1 TAAGGGATTT-GGATTTT-AGGAGTTTGATTT
* * *
9634662 TAAAGGATTTTGAATTTTAGGGGTTT
1 TAAGGGA-TTTGGATTTTAGGAGTTT
9634688 TAGAAACTTA
Statistics
Matches: 72, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
31 26 0.36
32 36 0.50
33 10 0.14
ACGTcount: A:0.24, C:0.02, G:0.30, T:0.44
Consensus pattern (30 bp):
TAAGGGATTTGGATTTTAGGAGTTTGATTT
Found at i:9634634 original size:48 final size:47
Alignment explanation
Indices: 9634569--9634687 Score: 159
Period size: 48 Copynumber: 2.5 Consensus size: 47
9634559 TTTTTGATAT
* * * *
9634569 AAGGGTTTGGATTTTAGGAGTTTCGGATTTTAAGGGATTTGGATTT-
1 AAGGATTTTGATTTTAGGGGTTTCGGATTTTAAGGGATTTGAATTTA
*
9634615 AAGAGATTTTAGATTTTAGGGGTTTCGGATTTTAAGGGGTTTGAATTTA
1 AAG-GATTTT-GATTTTAGGGGTTTCGGATTTTAAGGGATTTGAATTTA
9634664 AAGGATTTTGAATTTTAGGGGTTT
1 AAGGATTTTG-ATTTTAGGGGTTT
9634688 TAGAAACTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
46 3 0.05
47 5 0.08
48 53 0.83
49 3 0.05
ACGTcount: A:0.24, C:0.02, G:0.30, T:0.44
Consensus pattern (47 bp):
AAGGATTTTGATTTTAGGGGTTTCGGATTTTAAGGGATTTGAATTTA
Done.