Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 81 of 103
Found at i:30239385 original size:21 final size:21
Alignment explanation
Indices: 30239359--30239401 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
30239349 TGTTACTATC
30239359 TAGTTGAGTTATTTTCAATTA
1 TAGTTGAGTTATTTTCAATTA
30239380 TAGTTGAGTTATTTTCAATTA
1 TAGTTGAGTTATTTTCAATTA
30239401 T
1 T
30239402 CTTGTGTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (21 bp):
TAGTTGAGTTATTTTCAATTA
Found at i:30258918 original size:23 final size:24
Alignment explanation
Indices: 30258850--30258910 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
30258840 AATATTATAT
30258850 AATTATTTTAT-T-T-AGATAAATTA
1 AATTATTTTATGTATAAG-TAAA-TA
*
30258873 AATTTTTTTATGTATAAGT-AATA
1 AATTATTTTATGTATAAGTAAATA
30258896 AATTATTTTATGTAT
1 AATTATTTTATGTAT
30258911 TTTAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 26 0.79
24 3 0.09
25 2 0.06
26 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (24 bp):
AATTATTTTATGTATAAGTAAATA
Found at i:30263725 original size:12 final size:12
Alignment explanation
Indices: 30263685--30263727 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
30263675 AATTTTATTT
30263685 TTTATTTTAATAA
1 TTTATTTTAA-AA
* * *
30263698 TTTATTATATAT
1 TTTATTTTAAAA
30263710 TTTATTTTAAAA
1 TTTATTTTAAAA
30263722 TTTATT
1 TTTATT
30263728 AAATTCATTA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTATTTTAAAA
Found at i:30267936 original size:17 final size:18
Alignment explanation
Indices: 30267896--30267936 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
30267886 AAATAAAATT
30267896 AGAAACAAAACCAAAAAAC
1 AGAAA-AAAACCAAAAAAC
*
30267915 A-AAAAAAA-CAGAAAAC
1 AGAAAAAAACCAAAAAAC
30267931 AGAAAA
1 AGAAAA
30267937 TGAAAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 8 0.40
17 8 0.40
18 3 0.15
19 1 0.05
ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00
Consensus pattern (18 bp):
AGAAAAAAACCAAAAAAC
Found at i:30268113 original size:25 final size:26
Alignment explanation
Indices: 30268057--30268118 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
30268047 ACACAAGATC
* *
30268057 ATAAAAAAAAAAAAGTAAATAAACAA
1 ATAATAAAAAAAAAGGAAATAAACAA
*
30268083 ATAATAAAAAAAAAGGAAA-AAATGAA
1 ATAATAAAAAAAAAGGAAATAAA-CAA
30268109 A-AATAAAAAA
1 ATAATAAAAAA
30268119 TAGATAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.38
26 20 0.62
ACGTcount: A:0.81, C:0.02, G:0.06, T:0.11
Consensus pattern (26 bp):
ATAATAAAAAAAAAGGAAATAAACAA
Found at i:30268384 original size:21 final size:21
Alignment explanation
Indices: 30268353--30268409 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
30268343 TTGTTATTTA
30268353 AAAAAATCAG-AAACAAAAAAC
1 AAAAAA-CAGAAAACAAAAAAC
*
30268374 GAAAAAACAGAAAACAGAAAAC
1 -AAAAAACAGAAAACAAAAAAC
*
30268396 AAAAAACAAAAAAC
1 AAAAAACAGAAAAC
30268410 GAATAATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.77, C:0.14, G:0.07, T:0.02
Consensus pattern (21 bp):
AAAAAACAGAAAACAAAAAAC
Found at i:30268396 original size:14 final size:14
Alignment explanation
Indices: 30268363--30268409 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
30268353 AAAAAATCAG
30268363 AAACAAAAAACGAAA
1 AAACAAAAAAC-AAA
* *
30268378 AAACAGAAAACAGA
1 AAACAAAAAACAAA
30268392 AAACAAAAAACAAA
1 AAACAAAAAACAAA
30268406 AAAC
1 AAAC
30268410 GAATAATGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.79, C:0.15, G:0.06, T:0.00
Consensus pattern (14 bp):
AAACAAAAAACAAA
Found at i:30268397 original size:29 final size:28
Alignment explanation
Indices: 30268355--30268409 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 28
30268345 GTTATTTAAA
30268355 AAAATCAGAAACAAAAAACGAAAAAACAG
1 AAAATCAGAAACAAAAAAC-AAAAAACAG
30268384 AAAA-CAGAAAACAAAAAACAAAAAAC
1 AAAATCAG-AAACAAAAAACAAAAAAC
30268410 GAATAATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.76, C:0.15, G:0.07, T:0.02
Consensus pattern (28 bp):
AAAATCAGAAACAAAAAACAAAAAACAG
Found at i:30268682 original size:7 final size:7
Alignment explanation
Indices: 30268672--30268748 Score: 84
Period size: 7 Copynumber: 10.9 Consensus size: 7
30268662 TAAAAAAATT
30268672 GAAAAAC
1 GAAAAAC
30268679 GAAAAAC
1 GAAAAAC
30268686 GAAAAAC
1 GAAAAAC
30268693 GAAAAAAC
1 G-AAAAAC
*
30268701 AAAAAAC
1 GAAAAAC
*
30268708 GAGAAAC
1 GAAAAAC
30268715 -AGAAAAC
1 GA-AAAAC
*
30268722 AAAAAAC
1 GAAAAAC
*
30268729 GAATAAC
1 GAAAAAC
*
30268736 GAAAAAT
1 GAAAAAC
30268743 GAAAAA
1 GAAAAA
30268749 TAGACAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
6 1 0.02
7 51 0.86
8 7 0.12
ACGTcount: A:0.73, C:0.12, G:0.13, T:0.03
Consensus pattern (7 bp):
GAAAAAC
Found at i:30268849 original size:319 final size:312
Alignment explanation
Indices: 30268103--30269598 Score: 2066
Period size: 319 Copynumber: 4.8 Consensus size: 312
30268093 AAAAGGAAAA
* * *
30268103 AATGAAAAATAAAAAATAGATAAATTAATTATTTAAAAAAA-CTCAAATTAATTATTGCAAGAGC
1 AATGAAAAATGAAAAATAGAGAAACTAATTATTTAAAAAAATCTCAAATTAATTATTGCAAGAGC
*
30268167 CAAAAAACAGGGAATAGATTATCAATATGGTAGTACAAATAACCATTTATCCACTTGCCTAAATA
66 CAAAAAACAGTGAATAGATTATCAATATGGTAGTACAAATAACCATTTATCCACTTGCCTAAATA
* * *
30268232 AAATTACCAAATAGGAAAGAACAATCATTCTTTGTCTTTCATAATTAATTTTAAAAATAGAAACC
131 AAATTACAAAATAGGAAAGAACAATCATTCTTTGTCTTTCATAATTAATTTAAAAAATGGAAACC
*
30268297 TTGTTTTTGGTAGCAACAACATGTTTTCAAACTTACTTTTTTTAAATTGTTATTTAAAAAAATC-
196 TTGTTTTTGGTAACAACAACATGTTTTCAAACTTACTTTTTTT-AATTGTTATTTAAAAAAATCG
* * * *
30268361 AGAAACAAAAAACGAAAAAACAGAAAACAGAAAACAAAAAACAAAAAACGAAT
260 AAAAACGAAAAACGAAAAAACAAAAAACAGAAAACAGAAAACAAAAAACGAAT
*
30268414 AATGAAAAATGAAAAATAGAGAAACTAATTATTTAAAAAAATCTCAAATCAATTATTGCAAGAGC
1 AATGAAAAATGAAAAATAGAGAAACTAATTATTTAAAAAAATCTCAAATTAATTATTGCAAGAGC
* * * *
30268479 TAAAAAAGAGTGAATAGGTTATCAATATGGCAGTACAAATAACCATTTATCCACTTGCCTAAATA
66 CAAAAAACAGTGAATAGATTATCAATATGGTAGTACAAATAACCATTTATCCACTTGCCTAAATA
*
30268544 AAATTACAAAATAGGAAAGAACAATCATTTTTTGTCTTTCATAATTAATTTAAAAAAATGGAAAC
131 AAATTACAAAATAGGAAAGAACAATCATTCTTTGTCTTTCATAATTAATTT-AAAAAATGGAAAC
* *
30268609 CTT-CTTTTGGTAACAACAACATGTTTTCAAACTTAATTTTTTTAATTGTTATTTAAAAAAATTG
195 CTTGTTTTTGGTAACAACAACATGTTTTCAAACTTACTTTTTTTAATTGTTATTTAAAAAAA-T-
30268673 AAAAACGAAAAACGAAAAACGAAAAAACAAAAAAC-GAGAAACAGAAAACAAAAAACGAAT
258 -----CGAAAAACGAAAAACGAAAAAACAAAAAACAGA-AAACAGAAAACAAAAAACGAAT
* * * *
30268733 AACGAAAAATGAAAAATAGACAAAATAATTATTTAAAAAAATCTCAAATCAATTATTGCAAGAGC
1 AATGAAAAATGAAAAATAGAGAAACTAATTATTTAAAAAAATCTCAAATTAATTATTGCAAGAGC
* * * *
30268798 TAAAAAAGAGTGAATAGGTTATCAATATGGTAGTACAAATAACCATTTATCCACTTACCTAAATA
66 CAAAAAACAGTGAATAGATTATCAATATGGTAGTACAAATAACCATTTATCCACTTGCCTAAATA
* *
30268863 ACATTACAAAATAGGAAAGAACAATCATTATTTGTCTTTCATAATTAATTTTAAAAAATGGAAAC
131 AAATTACAAAATAGGAAAGAACAATCATTCTTTGTCTTTCATAATTAA-TTTAAAAAATGGAAAC
* * *
30268928 CTT-CTTTTGGTAACAACAACATGTTTTCAAACTTAATTTTTTTAATTGTTATTTAAAAAAATTG
195 CTTGTTTTTGGTAACAACAACATGTTTTCAAACTTACTTTTTTTAATTGTTATTTAAAAAAATCG
* *
30268992 AAAAACG-AAAATG-------AAAAAACAGAAAAC---AAA-AAACAA--AA-
260 AAAAACGAAAAACGAAAAAACAAAAAACAGAAAACAGAAAACAAAAAACGAAT
* * *
30269030 AATGAAAAATAAAAAATAGATAAATTAATTATTT-AAAAAA-CTCAAATTAATTATTGCAAGAGC
1 AATGAAAAATGAAAAATAGAGAAACTAATTATTTAAAAAAATCTCAAATTAATTATTGCAAGAGC
*
30269093 CAAAAAACAGGGAATAGATTATCAATATGGTAGTACAAATAACCATTTATCCACTTGCCTAAATA
66 CAAAAAACAGTGAATAGATTATCAATATGGTAGTACAAATAACCATTTATCCACTTGCCTAAATA
* * *
30269158 AAATTACCAAATAGGAAAGAACAATCATTCTTTGTCTTTCATAATTAATTTTAAAAATAGAAACC
131 AAATTACAAAATAGGAAAGAACAATCATTCTTTGTCTTTCATAATTAATTTAAAAAATGGAAACC
* **
30269223 TTGTTTTTGGTAGCAACAACATGTTTTCAAACTTACTTTTTAAAAATTGTTATTTAAAAAAATCA
196 TTGTTTTTGGTAACAACAACATGTTTTCAAACTTACTTTTT-TTAATTGTTATTTAAAAAAATC-
30269288 GAAACAAAAAACGAAAAAACGAAAAAACAAAAAACAGAAAACAGAAAACGAAAAACGAAAAACGA
259 G-----AAAAACG-AAAAACGAAAAAACAAAAAACAGAAAACAGAAAAC-----A--AAAAACGA
30269353 AT
311 AT
* *
30269355 AATGACAAATGAAAAATAGAGAAACTAATTATTTTAAAAAAATCTCAAATTAATTATTGCAAAAG
1 AATGAAAAATGAAAAATAGAGAAACTAATTA-TTTAAAAAAATCTCAAATTAATTATTGCAAGAG
* * * *
30269420 CCAAAAAAAAGTGAATAGATTATCAATATGGTAGGACAAATAACCATTTATCTACATGCCTAAAT
65 CCAAAAAACAGTGAATAGATTATCAATATGGTAGTACAAATAACCATTTATCCACTTGCCTAAAT
* * *
30269485 AAAATTACAAAATAGGTAAGAACAATCATTCTTTGTCTTTCATAATTAATTCAAAAAAATGAAAA
130 AAAATTACAAAATAGGAAAGAACAATCATTCTTTGTCTTTCATAATTAATT-TAAAAAATGGAAA
* *
30269550 CCTTGTTTTTGATAACAACAATATG-TTTCGAAACTTACTTTTTTTAATT
194 CCTTGTTTTTGGTAACAACAACATGTTTTC-AAACTTACTTTTTTTAATT
30269599 CAAACAGTAA
Statistics
Matches: 1062, Mismatches: 74, Indels: 81
0.87 0.06 0.07
Matches are distributed among these distances:
294 17 0.02
295 162 0.15
296 25 0.02
297 31 0.03
298 2 0.00
300 5 0.00
301 3 0.00
302 7 0.01
304 16 0.02
305 2 0.00
311 75 0.07
312 177 0.17
313 14 0.01
314 3 0.00
318 4 0.00
319 291 0.27
320 4 0.00
322 4 0.00
324 2 0.00
325 27 0.03
326 3 0.00
327 6 0.01
328 138 0.13
329 44 0.04
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (312 bp):
AATGAAAAATGAAAAATAGAGAAACTAATTATTTAAAAAAATCTCAAATTAATTATTGCAAGAGC
CAAAAAACAGTGAATAGATTATCAATATGGTAGTACAAATAACCATTTATCCACTTGCCTAAATA
AAATTACAAAATAGGAAAGAACAATCATTCTTTGTCTTTCATAATTAATTTAAAAAATGGAAACC
TTGTTTTTGGTAACAACAACATGTTTTCAAACTTACTTTTTTTAATTGTTATTTAAAAAAATCGA
AAAACGAAAAACGAAAAAACAAAAAACAGAAAACAGAAAACAAAAAACGAAT
Found at i:30269009 original size:14 final size:15
Alignment explanation
Indices: 30268992--30269038 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
30268982 AAAAAAATTG
30268992 AAAAAC-GAAAATGA
1 AAAAACAGAAAATGA
*
30269006 AAAAACAGAAAA-CA
1 AAAAACAGAAAATGA
*
30269020 AAAAACAAAAAATGA
1 AAAAACAGAAAATGA
30269035 AAAA
1 AAAA
30269039 TAAAAAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.79, C:0.09, G:0.09, T:0.04
Consensus pattern (15 bp):
AAAAACAGAAAATGA
Found at i:30269038 original size:21 final size:21
Alignment explanation
Indices: 30268983--30269045 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
30268973 TTGTTATTTA
* **
30268983 AAAAAATTGAAAAACGAAAATG
1 AAAAAA-TGAAAAACAAAAAAC
*
30269005 AAAAAA-CAGAAAACAAAAAAC
1 AAAAAATGA-AAAACAAAAAAC
*
30269026 AAAAAATGAAAAATAAAAAA
1 AAAAAATGAAAAACAAAAAA
30269046 TAGATAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
20 1 0.03
21 25 0.76
22 7 0.21
ACGTcount: A:0.78, C:0.06, G:0.08, T:0.08
Consensus pattern (21 bp):
AAAAAATGAAAAACAAAAAAC
Found at i:30269043 original size:14 final size:14
Alignment explanation
Indices: 30268983--30269046 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
30268973 TTGTTATTTA
30268983 AAAAAATTGAAAAAC
1 AAAAAA-TGAAAAAC
*
30268998 -GAAAATGAAAAAAC
1 AAAAAATG-AAAAAC
* **
30269012 AGAAAACAAAAAAC
1 AAAAAATGAAAAAC
*
30269026 AAAAAATGAAAAAT
1 AAAAAATGAAAAAC
30269040 AAAAAAT
1 AAAAAAT
30269047 AGATAAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
13 2 0.05
14 33 0.82
15 5 0.12
ACGTcount: A:0.77, C:0.06, G:0.08, T:0.09
Consensus pattern (14 bp):
AAAAAATGAAAAAC
Found at i:30269313 original size:9 final size:8
Alignment explanation
Indices: 30269289--30269353 Score: 70
Period size: 7 Copynumber: 8.9 Consensus size: 8
30269279 AAAAAATCAG
30269289 AAAC-AAA
1 AAACGAAA
30269296 AAACGAAA
1 AAACGAAA
30269304 AAACGAAA
1 AAACGAAA
30269312 AAAC-AAA
1 AAACGAAA
*
30269319 AAAC-AGA
1 AAACGAAA
*
30269326 AAAC-AGA
1 AAACGAAA
30269333 AAACG-AA
1 AAACGAAA
30269340 AAACG-AA
1 AAACGAAA
30269347 AAACGAA
1 AAACGAA
30269354 TAATGACAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
7 37 0.70
8 16 0.30
ACGTcount: A:0.75, C:0.14, G:0.11, T:0.00
Consensus pattern (8 bp):
AAACGAAA
Found at i:30269320 original size:37 final size:36
Alignment explanation
Indices: 30269279--30269349 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 36
30269269 TTGTTATTTA
30269279 AAAAAATCAG-AAACAAAAAACGAAAAAACGAAAAAAC
1 AAAAAA-CAGAAAACAAAAAACG-AAAAACGAAAAAAC
*
30269316 AAAAAACAGAAAACAGAAAACGAAAAACGAAAAA
1 AAAAAACAGAAAACAAAAAACGAAAAACGAAAAA
30269350 CGAATAATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 15 0.47
37 17 0.53
ACGTcount: A:0.76, C:0.13, G:0.10, T:0.01
Consensus pattern (36 bp):
AAAAAACAGAAAACAAAAAACGAAAAACGAAAAAAC
Found at i:30277676 original size:42 final size:41
Alignment explanation
Indices: 30277626--30277833 Score: 146
Period size: 42 Copynumber: 5.3 Consensus size: 41
30277616 TTAATATTTG
30277626 TAAATAAAATATTAATATTTTAATACATTAATGATTAAATTA
1 TAAATAAAATATTAATATTTTAATACATTAAT-ATTAAATTA
* * * * *
30277668 TAAATAAAATATTAACATTTAAAT-GATCAATTATTAATATTT
1 TAAATAAAATATTAATATTTTAATACATTAA-TATTAA-ATTA
*
30277710 TAAATAAATTATTAATA--TTAA-A-A--AATA--AAA-TA
1 TAAATAAAATATTAATATTTTAATACATTAATATTAAATTA
*
30277742 -AAATAAAACTA--AATAATTATAATAGCATT--T---AAATTA
1 TAAATAAAA-TATTAAT-ATTTTAATA-CATTAATATTAAATTA
* *
30277778 TAAATAAAATATTAATATTTTAAAATATTAATGATTAAATTA
1 TAAATAAAATATTAATATTTTAATACATTAAT-ATTAAATTA
30277820 TAAATAAAATATTA
1 TAAATAAAATATTA
30277834 CACCCGAGAA
Statistics
Matches: 130, Mismatches: 14, Indels: 44
0.69 0.07 0.23
Matches are distributed among these distances:
30 3 0.02
31 8 0.06
32 3 0.02
33 4 0.03
34 3 0.02
35 3 0.02
36 11 0.08
37 17 0.13
38 4 0.03
39 1 0.01
40 3 0.02
41 9 0.07
42 61 0.47
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (41 bp):
TAAATAAAATATTAATATTTTAATACATTAATATTAAATTA
Found at i:30277721 original size:20 final size:20
Alignment explanation
Indices: 30277614--30277728 Score: 99
Period size: 20 Copynumber: 5.5 Consensus size: 20
30277604 ATCCTACTCA
*
30277614 TATTAATATTTGTAAATAAAA
1 TATTAATATTT-TAAATAAAT
*
30277635 TATTAATATTTTAATACATTAAT
1 TATTAATATTTT-A-A-ATAAAT
* * *
30277658 GATTAA-ATTATAAATAAAA
1 TATTAATATTTTAAATAAAT
*
30277677 TATTAACA-TTTAAATGATCAAT
1 TATTAATATTTTAAAT-A--AAT
30277699 TATTAATATTTTAAATAAAT
1 TATTAATATTTTAAATAAAT
30277719 TATTAATATT
1 TATTAATATT
30277729 AAAAAATAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 17
0.74 0.10 0.17
Matches are distributed among these distances:
19 15 0.20
20 17 0.22
21 13 0.17
22 15 0.20
23 16 0.21
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
TATTAATATTTTAAATAAAT
Found at i:30277723 original size:23 final size:22
Alignment explanation
Indices: 30277614--30277728 Score: 70
Period size: 23 Copynumber: 5.5 Consensus size: 22
30277604 ATCCTACTCA
30277614 TATTAATATTTGTAAATAAA-A-
1 TATTAATATTT-TAAATAAATAT
*
30277635 TATTAATATTTT-AATACATTAAT
1 TATTAATATTTTAAATA-AAT-AT
* *
30277658 GATTAA-ATTATAAATAAA-A-
1 TATTAATATTTTAAATAAATAT
* *
30277677 TATTAACA-TTTAAAT-GATCAAT
1 TATTAATATTTTAAATAAAT--AT
30277699 TATTAATATTTTAAAT-AA-AT
1 TATTAATATTTTAAATAAATAT
30277719 TATTAATATT
1 TATTAATATT
30277729 AAAAAATAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
18 1 0.01
19 15 0.20
20 16 0.22
21 12 0.16
22 13 0.18
23 17 0.23
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (22 bp):
TATTAATATTTTAAATAAATAT
Found at i:30277731 original size:41 final size:43
Alignment explanation
Indices: 30277614--30277728 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 43
30277604 ATCCTACTCA
* *
30277614 TATTAATATTTGTAAATAAAATATTAATATTTTAATACATTAAT
1 TATTAATATTT-TAAATAAAATATTAATATTTAAATACATCAAT
* * * *
30277658 GATTAA-ATTATAAATAAAATATTAACATTTAAAT-GATCAAT
1 TATTAATATTTTAAATAAAATATTAATATTTAAATACATCAAT
*
30277699 TATTAATATTTTAAATAAATTATTAATATT
1 TATTAATATTTTAAATAAAATATTAATATT
30277729 AAAAAATAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 10 0.17
42 42 0.70
43 3 0.05
44 5 0.08
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (43 bp):
TATTAATATTTTAAATAAAATATTAATATTTAAATACATCAAT
Found at i:30277975 original size:27 final size:26
Alignment explanation
Indices: 30277943--30277999 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
30277933 TATTAATATT
* *
30277943 TAAATTATCAATTATTAATATTTTAAA
1 TAAATTATAAATGATTAATA-TTTAAA
*
30277970 TAAATTATAAATGATTCATATTTAAA
1 TAAATTATAAATGATTAATATTTAAA
30277996 -AAAT
1 TAAAT
30278000 AAATTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 4 0.15
26 6 0.22
27 17 0.63
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
TAAATTATAAATGATTAATATTTAAA
Found at i:30278081 original size:42 final size:40
Alignment explanation
Indices: 30278034--30278444 Score: 225
Period size: 42 Copynumber: 10.3 Consensus size: 40
30278024 ATAATAACAT
30278034 TTAAATTATAAATAAAATATTAATATTTTCAAATATTAATTA
1 TTAAATTATAAATAAAATATTAATA-TTT-AAATATTAATTA
* *
30278076 TTAAATTATAAACAAAATATTAATATTTAAATGATCAATTA
1 TTAAATTATAAATAAAATATTAATATTTAAAT-ATTAATTA
* * * * * *
30278117 TTAATATTTTATATAAATTA-TAA-ATTATTAATCTTTAA-AA
1 TTAA-ATTATAAATAAAATATTAATATT-TAAAT-ATTAATTA
* *
30278157 ATAAAATA-AAATAAAAATAATTAATGA--T-AATA--ACA-T-
1 TTAAATTATAAAT-AAAAT-ATTAAT-ATTTAAATATTA-ATTA
* * *
30278193 TTAAATTATAAATAAAATATTAACATTTTAAAAATATAATGA
1 TTAAATTATAAATAAAATATTAATA-TTTAAATAT-TAATTA
*
30278235 TTAAATTATAAATAAAATATTAATATTTAAA-AATAAGTTA
1 TTAAATTATAAATAAAATATTAATATTTAAATATTAA-TTA
* * *
30278275 TTAATATTATAAATAAATTA-TAA-ATTATTAATATTAA-GA
1 TTAA-ATTATAAATAAAATATTAATATT-TAAATATTAATTA
*** * * * * * *
30278314 AGGAACTA-ATATAAAATA--AATA-AT-CATAATAA-CA
1 TTAAATTATAAATAAAATATTAATATTTAAATATTAATTA
* * *
30278348 TTAAATTATAAATAAAATATCAATATTTTATAATGTTAATGA
1 TTAAATTATAAATAAAATATTAATA-TTTA-AATATTAATTA
*
30278390 TTAAATTATACATAAAATATTAATATTTAAATGATTAATTA
1 TTAAATTATAAATAAAATATTAATATTTAAAT-ATTAATTA
*
30278431 TTAATATTTTAAAT
1 TTAA-ATTATAAAT
30278445 TAATTATAAA
Statistics
Matches: 279, Mismatches: 56, Indels: 68
0.69 0.14 0.17
Matches are distributed among these distances:
34 12 0.04
35 15 0.05
36 14 0.05
37 19 0.07
38 9 0.03
39 18 0.06
40 30 0.11
41 71 0.25
42 90 0.32
43 1 0.00
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (40 bp):
TTAAATTATAAATAAAATATTAATATTTAAATATTAATTA
Found at i:30278096 original size:160 final size:157
Alignment explanation
Indices: 30277922--30278459 Score: 744
Period size: 159 Copynumber: 3.4 Consensus size: 157
30277912 CCACAAAAAA
* * *
30277922 TATAAACAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATTATAAATGATTC
1 TATAAACAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAATAAATTATAAATTATTA
*
30277987 ATATTTAAAAAATAAATTAAATTATAAATAAATAATCATAATAACATTTAAATTATAAATAAAAT
66 ATATTT-AAAAATAAAATAAA-TATAAATAAATAATCATAATAACATTTAAATTATAAATAAAAT
*
30278052 ATTAATATTTTCAAATATTAATTATTAAAT
129 ATTAATATTTT-AAATATTAATGATTAAAT
*
30278082 TATAAACAAAATATTAATATTTAAATGATCAATTATTAATATTTTATATAAATTATAAATTATTA
1 TATAAACAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAATAAATTATAAATTATTA
* * * *
30278147 ATCTTTAAAAATAAAATAAAATAAAAATAATTAATGATAATAACATTTAAATTATAAATAAAATA
66 ATATTTAAAAATAAAAT-AAATATAAATAAATAATCATAATAACATTTAAATTATAAATAAAATA
* *
30278212 TTAACATTTTAAAAATATAATGATTAAAT
130 TTAATATTTTAAATAT-TAATGATTAAAT
* * *
30278241 TATAAATAAAATATTAATATTTAAA-AAT-AAGTTATTAATATTATAAATAAATTATAAATTATT
1 TATAAACAAAATATTAATATTTAAATGATCAA-TTATTAATATTTTAAATAAATTATAAATTATT
* ** *
30278304 AATA-TTAAGAAGGAACT-AATATAAAATAAATAATCATAATAACA-TTAAATTATAAATAAAAT
65 AATATTTAAAAATAAAATAAATAT-AAATAAATAATCATAATAACATTTAAATTATAAATAAAAT
* *
30278366 ATCAATATTTTATAATGTTAATGATTAAAT
129 ATTAATATTTTA-AATATTAATGATTAAAT
* * * *
30278396 TATACATAAAATATTAATATTTAAATGATTAATTATTAATATTTTAAATTAATTATAAATTATT
1 TATAAACAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAATAAATTATAAATTATT
30278460 TATTTTATTC
Statistics
Matches: 339, Mismatches: 32, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
155 68 0.20
156 54 0.16
157 13 0.04
158 40 0.12
159 95 0.28
160 69 0.20
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (157 bp):
TATAAACAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAATAAATTATAAATTATTA
ATATTTAAAAATAAAATAAATATAAATAAATAATCATAATAACATTTAAATTATAAATAAAATAT
TAATATTTTAAATATTAATGATTAAAT
Found at i:30278168 original size:27 final size:27
Alignment explanation
Indices: 30278112--30278168 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
30278102 TTAAATGATC
* * *
30278112 AATTATTAATATTTTATATAAATTATA
1 AATTATTAATATTTAAAATAAAATATA
*
30278139 AATTATTAATCTTTAAAAATAAAATA-A
1 AATTATTAATATTT-AAAATAAAATATA
30278166 AAT
1 AAT
30278169 AAAAATAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
AATTATTAATATTTAAAATAAAATATA
Found at i:30278197 original size:26 final size:26
Alignment explanation
Indices: 30278168--30278235 Score: 61
Period size: 26 Copynumber: 2.6 Consensus size: 26
30278158 TAAAATAAAA
30278168 TAAAAATAATTAATGATAATAACA-TT
1 TAAAAATAA-TAATGATAATAACATTT
* * *
30278194 TAAATTATAAATAA-AATATTAACATTT
1 TAAA-AAT-AATAATGATAATAACATTT
30278221 TAAAAAT-ATAATGAT
1 TAAAAATAATAATGAT
30278236 TAAATTATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
24 4 0.12
25 2 0.06
26 14 0.42
27 11 0.33
28 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (26 bp):
TAAAAATAATAATGATAATAACATTT
Found at i:30278294 original size:11 final size:11
Alignment explanation
Indices: 30278236--30278299 Score: 53
Period size: 11 Copynumber: 6.1 Consensus size: 11
30278226 ATATAATGAT
30278236 TAAATTATAAA
1 TAAATTATAAA
* *
30278247 TAAAATATTAA
1 TAAATTATAAA
* *
30278258 T-ATTTAAAAA
1 TAAATTATAAA
* *
30278268 TAAGTTATTAA
1 TAAATTATAAA
30278279 T--ATTATAAA
1 TAAATTATAAA
30278288 TAAATTATAAA
1 TAAATTATAAA
30278299 T
1 T
30278300 TATTAATATT
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
9 7 0.18
10 6 0.15
11 26 0.67
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TAAATTATAAA
Found at i:30278433 original size:22 final size:20
Alignment explanation
Indices: 30278407--30278461 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
30278397 ATACATAAAA
30278407 TATTAATATTTAAATGATTAAT
1 TATTAATATTTAAA--ATTAAT
*
30278429 TATTAATATTTTAAATTAAT
1 TATTAATATTTAAAATTAAT
*
30278449 TATAAATTATTTA
1 TATTAA-TATTTA
30278462 TTTTATTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.38
21 5 0.17
22 13 0.45
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TATTAATATTTAAAATTAAT
Found at i:30279283 original size:22 final size:23
Alignment explanation
Indices: 30279255--30279321 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 23
30279245 ATACCATTGA
*
30279255 TAACTAAATTATTAATTTTATA-
1 TAACTAAATTATTAATTTTAAAT
* *
30279277 TAGCTAAATATATAAAATTATTAAAT
1 TAACTAAAT-TAT-TAATT-TTAAAT
30279303 TAACTAAAGTTATTAATTT
1 TAACTAAA-TTATTAATTT
30279322 AATTCTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
22 8 0.23
23 3 0.09
24 5 0.14
25 8 0.23
26 10 0.29
27 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (23 bp):
TAACTAAATTATTAATTTTAAAT
Found at i:30279315 original size:18 final size:18
Alignment explanation
Indices: 30279289--30279323 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30279279 GCTAAATATA
30279289 TAAAATTATTAAATTAAC
1 TAAAATTATTAAATTAAC
* *
30279307 TAAAGTTATTAATTTAA
1 TAAAATTATTAAATTAA
30279324 TTCTTTTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
TAAAATTATTAAATTAAC
Found at i:30279354 original size:2 final size:2
Alignment explanation
Indices: 30279347--30279387 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30279337 TGGCCCACAN
30279347 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
30279388 GTATGTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30282128 original size:18 final size:19
Alignment explanation
Indices: 30282091--30282129 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
30282081 TGATATTTTT
*
30282091 TAATAACATTGACGTAATA
1 TAATAACATTGACATAATA
*
30282110 TAATAACA-TGTCATAATA
1 TAATAACATTGACATAATA
30282128 TA
1 TA
30282130 TGATGATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (19 bp):
TAATAACATTGACATAATA
Found at i:30289435 original size:15 final size:15
Alignment explanation
Indices: 30289415--30289444 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
30289405 TTGCGCTGCA
30289415 TCATTTCTTTATTCT
1 TCATTTCTTTATTCT
30289430 TCATTTCTTTATTCT
1 TCATTTCTTTATTCT
30289445 ATCTCACCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTATTCT
Found at i:30310419 original size:28 final size:29
Alignment explanation
Indices: 30310356--30310419 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
30310346 TAAATTTTTT
** *
30310356 AAAAATTACACTTTTGCCCCCGTAAAGTG
1 AAAAATTACACTTTTGCCCCCAAAAACTG
* * *
30310385 AAGAATTACATTTTTG-TCCCAAAAACTG
1 AAAAATTACACTTTTGCCCCCAAAAACTG
30310413 AAAAATT
1 AAAAATT
30310420 GCCCATAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (29 bp):
AAAAATTACACTTTTGCCCCCAAAAACTG
Found at i:30311983 original size:6 final size:6
Alignment explanation
Indices: 30311968--30312001 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
30311958 TTATTTTCTT
30311968 TTTATAA TTTATA TTTATA TTTATA TTTATA TTT
1 TTTAT-A TTTATA TTTATA TTTATA TTTATA TTT
30312002 GTTTGCAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:30312410 original size:7 final size:7
Alignment explanation
Indices: 30312387--30312434 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
30312377 CCTCTATATC
*
30312387 ATATTTA
1 ATATTTT
*
30312394 ATAATTT
1 ATATTTT
30312401 ATATTTT
1 ATATTTT
*
30312408 ATATATT
1 ATATTTT
30312415 ATAGTTTT
1 ATA-TTTT
*
30312423 ATATTTA
1 ATATTTT
30312430 ATATT
1 ATATT
30312435 ATAAGTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 28 0.82
8 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (7 bp):
ATATTTT
Found at i:30312435 original size:20 final size:23
Alignment explanation
Indices: 30312398--30312442 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
30312388 TATTTAATAA
30312398 TTTATATTTTATATATTAT-AGT
1 TTTATATTTTATATATTATAAGT
30312420 TTTATA-TTTA-ATATTATAAGT
1 TTTATATTTTATATATTATAAGT
30312441 TT
1 TT
30312443 AAATAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 9 0.41
22 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTATATTTTATATATTATAAGT
Found at i:30314515 original size:20 final size:23
Alignment explanation
Indices: 30314478--30314522 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
30314468 TATTTAACAA
30314478 TTTATATTTTATATATTAT-AGT
1 TTTATATTTTATATATTATAAGT
30314500 TTTATA-TTTA-ATATTATAAGT
1 TTTATATTTTATATATTATAAGT
30314521 TT
1 TT
30314523 AAATAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 9 0.41
22 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTATATTTTATATATTATAAGT
Found at i:30325666 original size:8 final size:8
Alignment explanation
Indices: 30325653--30325721 Score: 61
Period size: 8 Copynumber: 8.4 Consensus size: 8
30325643 CACTTATTTC
30325653 AAAAAAAT
1 AAAAAAAT
30325661 AAAAAAAT
1 AAAAAAAT
30325669 AACAAATAAT
1 AA-AAA-AAT
*
30325679 GAAATATAAT
1 -AAA-AAAAT
*
30325689 AAAAAAAC
1 AAAAAAAT
*
30325697 CAAAAAAT
1 AAAAAAAT
30325705 -AAAAAAT
1 AAAAAAAT
30325712 -AAAAAAT
1 AAAAAAAT
30325719 AAA
1 AAA
30325722 TTAAAAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
7 14 0.27
8 21 0.41
9 6 0.12
10 7 0.14
11 3 0.06
ACGTcount: A:0.80, C:0.04, G:0.01, T:0.14
Consensus pattern (8 bp):
AAAAAAAT
Found at i:30325708 original size:6 final size:7
Alignment explanation
Indices: 30325654--30325721 Score: 57
Period size: 7 Copynumber: 9.4 Consensus size: 7
30325644 ACTTATTTCA
30325654 AAAAAAT
1 AAAAAAT
30325661 AAAAAAAT
1 -AAAAAAT
*
30325669 AACAAAT
1 AAAAAAT
*
30325676 AATGAAAT
1 AA-AAAAT
*
30325684 ATAATAA-
1 A-AAAAAT
**
30325691 AAAAACC
1 AAAAAAT
30325698 AAAAAAT
1 AAAAAAT
30325705 AAAAAAT
1 AAAAAAT
30325712 AAAAAAT
1 AAAAAAT
30325719 AAA
1 AAA
30325722 TTAAAAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
6 3 0.06
7 31 0.63
8 14 0.29
9 1 0.02
ACGTcount: A:0.79, C:0.04, G:0.01, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:30325711 original size:28 final size:28
Alignment explanation
Indices: 30325658--30325712 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
30325648 ATTTCAAAAA
* * *
30325658 AATAAAAAAATAACAAATAATGAAATAT
1 AATAAAAAAACAAAAAATAATAAAATAT
30325686 AATAAAAAAACCAAAAAATAA-AAAATA
1 AATAAAAAAA-CAAAAAATAATAAAATA
30325713 AAAAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.16
Consensus pattern (28 bp):
AATAAAAAAACAAAAAATAATAAAATAT
Found at i:30325731 original size:36 final size:36
Alignment explanation
Indices: 30325653--30325730 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
30325643 CACTTATTTC
* * *
30325653 AAAAAAATAAAAAAATAACAAATAATGAAATATAAT
1 AAAAAAACAAAAAAATAAAAAATAATAAAATATAAT
*
30325689 AAAAAAACCAAAAAATAAAAAATAA-AAAATA-AATT
1 AAAAAAACAAAAAAATAAAAAATAATAAAATATAA-T
30325724 AAAAAAA
1 AAAAAAA
30325731 AGAGGAACAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 2 0.05
35 13 0.35
36 22 0.59
ACGTcount: A:0.79, C:0.04, G:0.01, T:0.15
Consensus pattern (36 bp):
AAAAAAACAAAAAAATAAAAAATAATAAAATATAAT
Found at i:30326254 original size:14 final size:13
Alignment explanation
Indices: 30326230--30326288 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 13
30326220 GCTAAGGAGG
30326230 GAAAGAAGAGAAA
1 GAAAGAAGAGAAA
*
30326243 GAAAGTAAGAGAGA
1 GAAAG-AAGAGAAA
*
30326257 G-AAGGA-AGAAA
1 GAAAGAAGAGAAA
30326268 GAAA-AAG-GAAA
1 GAAAGAAGAGAAA
30326279 G-AAGAAGAGA
1 GAAAGAAGAGA
30326289 GAGAGAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
10 2 0.05
11 14 0.38
12 5 0.14
13 8 0.22
14 8 0.22
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (13 bp):
GAAAGAAGAGAAA
Found at i:30326285 original size:21 final size:22
Alignment explanation
Indices: 30326229--30326295 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
30326219 AGCTAAGGAG
30326229 GGAAAGAAG-AGAAAGAAAGTAA
1 GGAAAGAAGAAGAAAGAAAG-AA
*
30326251 GAGAGAGAAGGAAGAAAGAAA-AA
1 G-GAAAGAA-GAAGAAAGAAAGAA
* *
30326274 GGAAAGAAGAAGAGAGAGAGAA
1 GGAAAGAAGAAGAAAGAAAGAA
30326296 AAGATCGGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 9 0.24
22 9 0.24
23 9 0.24
24 1 0.03
25 9 0.24
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.01
Consensus pattern (22 bp):
GGAAAGAAGAAGAAAGAAAGAA
Found at i:30326362 original size:30 final size:30
Alignment explanation
Indices: 30326328--30326395 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
30326318 GAAAAGGAAA
* *
30326328 AAGAAAGAGAAAGAGAAAGAGAAAAAA-GGG
1 AAGAAAGAG-AAGAAAAAAAGAAAAAAGGGG
30326358 AAGAAAGAGAAGAAAAAAAGAAAAAAGGGG
1 AAGAAAGAGAAGAAAAAAAGAAAAAAGGGG
30326388 AAGAAAGA
1 AAGAAAGA
30326396 TCGAGAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 15 0.43
30 20 0.57
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (30 bp):
AAGAAAGAGAAGAAAAAAAGAAAAAAGGGG
Found at i:30326368 original size:6 final size:6
Alignment explanation
Indices: 30326312--30326351 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
30326302 GGTGACAAGG
*
30326312 GAGAAA GA-AAA G-GAAA AAGAAA GAGAAA GAGAAA GAGAAA
1 GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA
30326352 AAAGGGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 7 0.23
6 23 0.77
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (6 bp):
GAGAAA
Found at i:30326384 original size:20 final size:23
Alignment explanation
Indices: 30326337--30326384 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 23
30326327 AAAGAAAGAG
*
30326337 AAAGAGAAAGAGAAAAAAGGGAAG
1 AAAGAGAAAGAGAAAAAA-GGAAA
30326361 AAAGAG-AAGA-AAAAAA-GAAA
1 AAAGAGAAAGAGAAAAAAGGAAA
30326381 AAAG
1 AAAG
30326385 GGGAAGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 7 0.30
22 6 0.26
23 4 0.17
24 6 0.26
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (23 bp):
AAAGAGAAAGAGAAAAAAGGAAA
Found at i:30329508 original size:29 final size:29
Alignment explanation
Indices: 30329447--30329509 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
30329437 AACACTTGAT
** * *
30329447 ATCTTGATCATGAACTTCGTTGCCGCTTT
1 ATCTTGATCACAAACTTCGCTGCCGCTTG
**
30329476 ATCTTGATCACAAACTTCGCTGTTGCTTG
1 ATCTTGATCACAAACTTCGCTGCCGCTTG
30329505 ATCTT
1 ATCTT
30329510 CATTTTAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (29 bp):
ATCTTGATCACAAACTTCGCTGCCGCTTG
Found at i:30331629 original size:51 final size:52
Alignment explanation
Indices: 30331574--30331671 Score: 153
Period size: 52 Copynumber: 1.9 Consensus size: 52
30331564 CTTGATCTTC
*
30331574 GCTTCAAGGGTC-TTTACGACTTGATCTTCATCACAAACACTTGATACCTTT
1 GCTTCAAGGGTCTTTTACGACTTAATCTTCATCACAAACACTTGATACCTTT
* * *
30331625 GCTTCAAGGGTCTTTTACGACTTAATCTTGATTACGAACACTTGATA
1 GCTTCAAGGGTCTTTTACGACTTAATCTTCATCACAAACACTTGATA
30331672 TCTTGATCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 12 0.29
52 30 0.71
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (52 bp):
GCTTCAAGGGTCTTTTACGACTTAATCTTCATCACAAACACTTGATACCTTT
Found at i:30333404 original size:29 final size:29
Alignment explanation
Indices: 30333362--30333581 Score: 157
Period size: 29 Copynumber: 7.6 Consensus size: 29
30333352 CCTCATAACT
*
30333362 AGGGATTACCACCTATTTTTTGCTAGAGA
1 AGGGATTACCACCTAATTTTTGCTAGAGA
** *
30333391 AGGGATTACCACCTAATTAAT-ATA-AGTTA
1 AGGGATTACCACCTAATTTTTGCTAGAG--A
* * *
30333420 TGGG-TTACCACCTAATTTTTGGTAGAAA
1 AGGGATTACCACCTAATTTTTGCTAGAGA
* * **
30333448 AGGAATTACCACTTAATTAATG-TACGTAG-
1 AGGGATTACCACCTAATTTTTGCTA-G-AGA
* * * *
30333477 TGGTATTAACACCTAATTTTTGCTAGAAA
1 AGGGATTACCACCTAATTTTTGCTAGAGA
**
30333506 AGGGATTACCACCTAATTAATG-TA-AGTTA
1 AGGGATTACCACCTAATTTTTGCTAGAG--A
* * *
30333535 TGGGATTACCGCCTAATTTTTGCTAGAAA
1 AGGGATTACCACCTAATTTTTGCTAGAGA
30333564 AGGGATTACCACCTAATT
1 AGGGATTACCACCTAATT
30333582 AATGTAAGTT
Statistics
Matches: 143, Mismatches: 35, Indels: 26
0.70 0.17 0.13
Matches are distributed among these distances:
27 3 0.02
28 24 0.17
29 109 0.76
30 6 0.04
31 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (29 bp):
AGGGATTACCACCTAATTTTTGCTAGAGA
Found at i:30333504 original size:58 final size:57
Alignment explanation
Indices: 30333364--30333591 Score: 332
Period size: 58 Copynumber: 4.0 Consensus size: 57
30333354 TCATAACTAG
* * *
30333364 GGATTACCACCTATTTTTTGCTAGAGAAGGGATTACCACCTAATTAATATAAGTTAT
1 GGATTACCACCTAATTTTTGCTAGAAAAGGGATTACCACCTAATTAATGTAAGTTAT
* * * * *
30333421 GGGTTACCACCTAATTTTTGGTAGAAAAGGAATTACCACTTAATTAATGTACG-TAGT
1 GGATTACCACCTAATTTTTGCTAGAAAAGGGATTACCACCTAATTAATGTAAGTTA-T
*
30333478 GGTATTAACACCTAATTTTTGCTAGAAAAGGGATTACCACCTAATTAATGTAAGTTAT
1 GG-ATTACCACCTAATTTTTGCTAGAAAAGGGATTACCACCTAATTAATGTAAGTTAT
*
30333536 GGGATTACCGCCTAATTTTTGCTAGAAAAGGGATTACCACCTAATTAATGTAAGTT
1 -GGATTACCACCTAATTTTTGCTAGAAAAGGGATTACCACCTAATTAATGTAAGTT
30333592 TTTTTTTTTT
Statistics
Matches: 151, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
56 2 0.01
57 48 0.32
58 97 0.64
59 4 0.03
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (57 bp):
GGATTACCACCTAATTTTTGCTAGAAAAGGGATTACCACCTAATTAATGTAAGTTAT
Found at i:30337407 original size:2 final size:2
Alignment explanation
Indices: 30337400--30337440 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
30337390 NNNNNNNNNN
30337400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30337441 GAATGCTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30337491 original size:11 final size:12
Alignment explanation
Indices: 30337468--30337497 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
30337458 TTAGAAAATC
30337468 AAAATAAACAAA
1 AAAATAAACAAA
30337480 AAAATAAA-AAA
1 AAAATAAACAAA
30337491 AAAATAA
1 AAAATAA
30337498 TAGTAAAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAATAAACAAA
Found at i:30338794 original size:16 final size:15
Alignment explanation
Indices: 30338756--30338809 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
30338746 ATTTGAGCAT
30338756 TTGTTTTATGCATTA
1 TTGTTTTATGCATTA
*
30338771 TGGTTTTATGCATTAA
1 TTGTTTTATGCATT-A
*
30338787 TTGTTTTATG-ATCA
1 TTGTTTTATGCATTA
*
30338801 TTATTTTAT
1 TTGTTTTAT
30338810 TATTTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 9 0.26
15 15 0.44
16 10 0.29
ACGTcount: A:0.22, C:0.06, G:0.13, T:0.59
Consensus pattern (15 bp):
TTGTTTTATGCATTA
Found at i:30349045 original size:61 final size:61
Alignment explanation
Indices: 30348950--30349119 Score: 331
Period size: 61 Copynumber: 2.8 Consensus size: 61
30348940 NNNNNNNNNN
30348950 CAGTTACGTTGGCACAAAGAGATTTAAGCCCAATTAAATTGGCATCCAAGATGTATAAGTC
1 CAGTTACGTTGGCACAAAGAGATTTAAGCCCAATTAAATTGGCATCCAAGATGTATAAGTC
*
30349011 CAGTTACGTTGGCACAAAGAGATTTAAGCCCAATTAAATTGGCATCCAAGATGTATGAGTC
1 CAGTTACGTTGGCACAAAGAGATTTAAGCCCAATTAAATTGGCATCCAAGATGTATAAGTC
30349072 CAGTTACGTTGGCACAAAGAGATTTAAGCCCAATTAAATTGGCATCCA
1 CAGTTACGTTGGCACAAAGAGATTTAAGCCCAATTAAATTGGCATCCA
30349120 GGCACAAAAA
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 108 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (61 bp):
CAGTTACGTTGGCACAAAGAGATTTAAGCCCAATTAAATTGGCATCCAAGATGTATAAGTC
Found at i:30349138 original size:37 final size:38
Alignment explanation
Indices: 30349082--30349156 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 38
30349072 CAGTTACGTT
* *
30349082 GGCACAAAGAGATTTAAGCCCAATTAAATTGGCATCCA
1 GGCACAAAAAGATTTAAGCCCAATTAAACTGGCATCCA
30349120 GGCACAAAAAG-TTTAAGCCCAATTAAACTGGCATCCA
1 GGCACAAAAAGATTTAAGCCCAATTAAACTGGCATCCA
30349157 AGATGTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 25 0.71
38 10 0.29
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (38 bp):
GGCACAAAAAGATTTAAGCCCAATTAAACTGGCATCCA
Found at i:30349165 original size:31 final size:31
Alignment explanation
Indices: 30348972--30349416 Score: 318
Period size: 31 Copynumber: 14.2 Consensus size: 31
30348962 CACAAAGAGA
30348972 TTTAAGCCCAATTAAATTGGCATCCAAGATG
1 TTTAAGCCCAATTAAATTGGCATCCAAGATG
* * * ** *
30349003 TATAAGTCCAGTTACGTTGGCA-CAAAGA-G
1 TTTAAGCCCAATTAAATTGGCATCCAAGATG
30349032 ATTTAAGCCCAATTAAATTGGCATCCAAGATG
1 -TTTAAGCCCAATTAAATTGGCATCCAAGATG
* * * * ** *
30349064 TATGAGTCCAGTTACGTTGGCA-CAAAGA-G
1 TTTAAGCCCAATTAAATTGGCATCCAAGATG
* *
30349093 ATTTAAGCCCAATTAAATTGGCATCCAGGCACAAAAAG
1 -TTTAAGCCCAATTAAATTGGCAT-----C-CAAGATG
*
30349131 TTTAAGCCCAATTAAACTGGCATCCAAGATG
1 TTTAAGCCCAATTAAATTGGCATCCAAGATG
* * * *
30349162 TTTAAGCCCAGTGATATTGGCA-CAAAAAGA-G
1 TTTAAGCCCAATTAAATTGGCATC--CAAGATG
* **
30349193 TCTAAGCCCAATTAAGCTGGCATCCAAGATG
1 TTTAAGCCCAATTAAATTGGCATCCAAGATG
* * * *
30349224 TTTAAGCCCAGTGATATTGGCA-CAAAAAGA-G
1 TTTAAGCCCAATTAAATTGGCATC--CAAGATG
* *
30349255 TTTAAGCCCAATTAAACTGGCATCCAAGACG
1 TTTAAGCCCAATTAAATTGGCATCCAAGATG
* * * * **
30349286 TTTAAGCCCAGTGATATTAGCATAAAAAGA-G
1 TTTAAGCCCAATTAAATTGGCAT-CCAAGATG
*
30349317 TTTAAGCCCAATTTAAACTGGCATCCAAGATG
1 TTTAAGCCCAA-TTAAATTGGCATCCAAGATG
* *
30349349 TTTAAGCCC-ATTGAGATTGGCA-CAAAGATG
1 TTTAAGCCCAATT-AAATTGGCATCCAAGATG
* *
30349379 TATAAGCCCAATTAAACTGGCATCCAAGATG
1 TTTAAGCCCAATTAAATTGGCATCCAAGATG
30349410 TTTAAGC
1 TTTAAGC
30349417 TCAGTGATAT
Statistics
Matches: 312, Mismatches: 76, Indels: 52
0.71 0.17 0.12
Matches are distributed among these distances:
29 2 0.01
30 77 0.25
31 172 0.55
32 34 0.11
36 1 0.00
37 25 0.08
38 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (31 bp):
TTTAAGCCCAATTAAATTGGCATCCAAGATG
Found at i:30349215 original size:62 final size:62
Alignment explanation
Indices: 30349120--30349450 Score: 535
Period size: 62 Copynumber: 5.4 Consensus size: 62
30349110 TTGGCATCCA
30349120 GGCAC-AAAA-AGTTTAAGCCCAATTAAACTGGCATCCAAGATGTTTAAGCCCAGTGATATT
1 GGCACAAAAAGAGTTTAAGCCCAATTAAACTGGCATCCAAGATGTTTAAGCCCAGTGATATT
* *
30349180 GGCACAAAAAGAGTCTAAGCCCAATTAAGCTGGCATCCAAGATGTTTAAGCCCAGTGATATT
1 GGCACAAAAAGAGTTTAAGCCCAATTAAACTGGCATCCAAGATGTTTAAGCCCAGTGATATT
*
30349242 GGCACAAAAAGAGTTTAAGCCCAATTAAACTGGCATCCAAGACGTTTAAGCCCAGTGATATT
1 GGCACAAAAAGAGTTTAAGCCCAATTAAACTGGCATCCAAGATGTTTAAGCCCAGTGATATT
* * * *
30349304 AGCATAAAAAGAGTTTAAGCCCAATTTAAACTGGCATCCAAGATGTTTAAGCCCATTGAGATT
1 GGCACAAAAAGAGTTTAAGCCCAA-TTAAACTGGCATCCAAGATGTTTAAGCCCAGTGATATT
* *
30349367 GGCAC--AAAGATGTATAAGCCCAATTAAACTGGCATCCAAGATGTTTAAGCTCAGTGATATT
1 GGCACAAAAAGA-GTTTAAGCCCAATTAAACTGGCATCCAAGATGTTTAAGCCCAGTGATATT
30349428 GGCACAAAAAGAGTTTAAGCCCA
1 GGCACAAAAAGAGTTTAAGCCCA
30349451 GTGATATTAG
Statistics
Matches: 248, Mismatches: 17, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
60 5 0.02
61 49 0.20
62 151 0.61
63 43 0.17
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (62 bp):
GGCACAAAAAGAGTTTAAGCCCAATTAAACTGGCATCCAAGATGTTTAAGCCCAGTGATATT
Found at i:30349431 original size:31 final size:31
Alignment explanation
Indices: 30349130--30349480 Score: 236
Period size: 31 Copynumber: 11.4 Consensus size: 31
30349120 GGCACAAAAA
* * * * *
30349130 GTTTAAGCCCAATTAAACTGGCATCCAAGAT
1 GTTTAAGCCCAGTGATATTGGCATCAAAGAT
30349161 GTTTAAGCCCAGTGATATTGGCA-CAAAAAGA-
1 GTTTAAGCCCAGTGATATTGGCATC--AAAGAT
* * * * *
30349192 GTCTAAGCCCAATTA-AGCTGGCATCCAAGAT
1 GTTTAAGCCCAGTGATA-TTGGCATCAAAGAT
30349223 GTTTAAGCCCAGTGATATTGGCA-CAAAAAGA-
1 GTTTAAGCCCAGTGATATTGGCATC--AAAGAT
* * * * * *
30349254 GTTTAAGCCCAATTAAACTGGCATCCAAGAC
1 GTTTAAGCCCAGTGATATTGGCATCAAAGAT
* *
30349285 GTTTAAGCCCAGTGATATTAGCATAAAAAGA-
1 GTTTAAGCCCAGTGATATTGGCAT-CAAAGAT
* * * * *
30349316 GTTTAAGCCCAATTTAAACTGGCATCCAAGAT
1 GTTTAAGCCC-AGTGATATTGGCATCAAAGAT
* *
30349348 GTTTAAGCCCATTGAGATTGGCA-CAAAGAT
1 GTTTAAGCCCAGTGATATTGGCATCAAAGAT
* * * * * *
30349378 GTATAAGCCCAATTAAACTGGCATCCAAGAT
1 GTTTAAGCCCAGTGATATTGGCATCAAAGAT
*
30349409 GTTTAAGCTCAGTGATATTGGCA-CAAAAAGA-
1 GTTTAAGCCCAGTGATATTGGCATC--AAAGAT
* *
30349440 GTTTAAGCCCAGTGATATTAGCA-CAAATAT
1 GTTTAAGCCCAGTGATATTGGCATCAAAGAT
*
30349470 GTATAAGCCCA
1 GTTTAAGCCCA
30349481 ATTTAGCTAA
Statistics
Matches: 248, Mismatches: 55, Indels: 35
0.73 0.16 0.10
Matches are distributed among these distances:
29 4 0.02
30 46 0.19
31 160 0.65
32 38 0.15
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (31 bp):
GTTTAAGCCCAGTGATATTGGCATCAAAGAT
Found at i:30349772 original size:12 final size:12
Alignment explanation
Indices: 30349743--30349802 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
30349733 CACCCATTTT
**
30349743 AAAAAATAAAGA
1 AAAAAATAAATC
*
30349755 ATAAAAATTAATC
1 A-AAAAATAAATC
30349768 AAAAAATAAATC
1 AAAAAATAAATC
*
30349780 AAATAATCAAAT-
1 AAAAAAT-AAATC
30349792 AATAAAATAAA
1 AA-AAAATAAA
30349803 AATAAAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 22 0.56
13 17 0.44
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (12 bp):
AAAAAATAAATC
Found at i:30350585 original size:26 final size:26
Alignment explanation
Indices: 30350537--30350586 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
30350527 ATCGGTGGAG
**
30350537 GCTTTTAGAGAGAAGGCAGAGAGGAA
1 GCTTTTAGAGAGAAAACAGAGAGGAA
30350563 GCTTTTAGAGAGAGAAACA-AGAGG
1 GCTTTTAGAGAGA-AAACAGAGAGG
30350587 GAAAAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (26 bp):
GCTTTTAGAGAGAAAACAGAGAGGAA
Found at i:30352715 original size:11 final size:11
Alignment explanation
Indices: 30352699--30352766 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 11
30352689 ATCAAATATA
*
30352699 TAAAAATGTTT
1 TAAAAATATTT
30352710 TAAAAAATATTT
1 T-AAAAATATTT
*
30352722 T-AAAATGTTAT
1 TAAAAATATT-T
30352733 TAAAAATATTTT
1 TAAAAATA-TTT
*
30352745 TAAGAACACATTT
1 TAA-AA-ATATTT
30352758 TAAAAATAT
1 TAAAAATAT
30352767 ATTATCTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
10 7 0.15
11 6 0.13
12 21 0.46
13 10 0.22
14 2 0.04
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.41
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:30352739 original size:22 final size:22
Alignment explanation
Indices: 30352692--30352744 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
30352682 TAGTAAAATC
* *
30352692 AAATATATAAAAATGTTTTAAA
1 AAATATTTTAAAATGTTTTAAA
30352714 AAATATTTTAAAATGTTATT-AA
1 AAATATTTTAAAATGTT-TTAAA
30352736 AAATATTTT
1 AAATATTTT
30352745 TAAGAACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
AAATATTTTAAAATGTTTTAAA
Found at i:30364708 original size:27 final size:25
Alignment explanation
Indices: 30364678--30364728 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
30364668 TTTAAAGAAA
30364678 AAAATTAAAATAAAATATATAATATAC
1 AAAATTAAAATAAAA-ATA-AATATAC
* *
30364705 AAAATTATATTAAAAATAAATATA
1 AAAATTAAAATAAAAATAAATATA
30364729 AAATATATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 13 0.59
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAATTAAAATAAAAATAAATATAC
Found at i:30365001 original size:15 final size:15
Alignment explanation
Indices: 30364981--30365038 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
30364971 ATTATCTTCT
*
30364981 TTGCAATCACATTGC
1 TTGCAATCACATTAC
* *
30364996 TTGCAATTACAGTAC
1 TTGCAATCACATTAC
* * *
30365011 CTACAATCACATTAT
1 TTGCAATCACATTAC
*
30365026 TTGTAATCACATT
1 TTGCAATCACATT
30365039 GTATTGTAAA
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (15 bp):
TTGCAATCACATTAC
Found at i:30367005 original size:22 final size:22
Alignment explanation
Indices: 30366980--30367033 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
30366970 TGCATCGTTA
* *
30366980 GTTTTTAGGCATTGCGTAATTG
1 GTTTTTAGGCATTGCATAACTG
*
30367002 G-TTTTAGGCATTGCATGACTG
1 GTTTTTAGGCATTGCATAACTG
*
30367023 ATTTTTAGGCA
1 GTTTTTAGGCA
30367034 ATGCTTAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.20, C:0.11, G:0.26, T:0.43
Consensus pattern (22 bp):
GTTTTTAGGCATTGCATAACTG
Found at i:30367121 original size:23 final size:23
Alignment explanation
Indices: 30367063--30367115 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
30367053 CCTAAAAACT
* *
30367063 AGTCACGCAACG-TCTTACTAAGC
1 AGTCACGCAATGCT-TTACTAACC
*
30367086 AGTCATGCAATGCTTTACTAACC
1 AGTCACGCAATGCTTTACTAACC
30367109 AGTCACG
1 AGTCACG
30367116 TTATGCCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (23 bp):
AGTCACGCAATGCTTTACTAACC
Found at i:30367272 original size:22 final size:22
Alignment explanation
Indices: 30367216--30367273 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
30367206 AATTAGTGAC
30367216 GTAATGCCTAAAAAATGGTCAT
1 GTAATGCCTAAAAAATGGTCAT
* * * * *
30367238 GCAATACCCAAAAACTGGTTAT
1 GTAATGCCTAAAAAATGGTCAT
30367260 GTAATGCCTAAAAA
1 GTAATGCCTAAAAA
30367274 TCACCAAAAC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (22 bp):
GTAATGCCTAAAAAATGGTCAT
Found at i:30368793 original size:211 final size:213
Alignment explanation
Indices: 30368420--30368837 Score: 597
Period size: 211 Copynumber: 2.0 Consensus size: 213
30368410 TCTATAATTA
* * * * * *
30368420 TATATATATGAAATTAATGATATAACTTATATGTTATAATGTTTTATATCAAAGTTTGTATAAAT
1 TATATATAT-AAATTAATAATACAAATTATATGCTAAAATATTTTATATCAAAGTTTGTATAAAT
* *** * *
30368485 AATACCTAATTATAAACAATATGTAATAAAATCTAAAGTGATCGTTGATAAACTTATTAAGTGTA
65 AATAACTAATTATAAACAATATGTAATAAAATCTAAAGTGATAACTAATAAAATTATTAAGTGTA
* * *
30368550 ATCATATAAATAAAATTTATTATAAGTTATAGTAATGCTTATGTATAAATTGAATATATGTATAT
130 ATCATATAAATAAAATCTATTATAAATTATAGTAATGCTTATGTATAAATTAAATATATGTATAT
30368615 ATACAATATATTGCTTTAT
195 ATACAATATATTGCTTTAT
30368634 TATATATAT-AATTAATAATACAAATTATATGCTAAAATATTTTATA-CAAAGTTTGTATAAATA
1 TATATATATAAATTAATAATACAAATTATATGCTAAAATATTTTATATCAAAGTTTGTATAAATA
* * * *
30368697 ATAACTAATTATAAACAATATGTTATAGAATCTAACGTGATAACTAATAAAATTATTAATTGTAA
66 ATAACTAATTATAAACAATATGTAATAAAATCTAAAGTGATAACTAATAAAATTATTAAGTGTAA
* ** *
30368762 TTATATAAATAATGTCTATTCTAAATTATAGTAATGCTTATGTATAAATTAAATATATGTATATA
131 TCATATAAATAAAATCTATTATAAATTATAGTAATGCTTATGTATAAATTAAATATATGTATATA
*
30368827 TATAATATATT
196 TACAATATATT
30368838 TATACAATTA
Statistics
Matches: 180, Mismatches: 24, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
211 140 0.78
212 31 0.17
214 9 0.05
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (213 bp):
TATATATATAAATTAATAATACAAATTATATGCTAAAATATTTTATATCAAAGTTTGTATAAATA
ATAACTAATTATAAACAATATGTAATAAAATCTAAAGTGATAACTAATAAAATTATTAAGTGTAA
TCATATAAATAAAATCTATTATAAATTATAGTAATGCTTATGTATAAATTAAATATATGTATATA
TACAATATATTGCTTTAT
Found at i:30368822 original size:17 final size:17
Alignment explanation
Indices: 30368800--30368854 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
30368790 TAGTAATGCT
30368800 TATGTATAAATTAAATA
1 TATGTATAAATTAAATA
*
30368817 TATGTATATA-TATAATA
1 TATGTATAAATTA-AATA
* *
30368834 TATTTATACAATTATATA
1 TATGTATA-AATTAAATA
30368852 TAT
1 TAT
30368855 ATTCATAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 2 0.06
17 20 0.65
18 7 0.23
19 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (17 bp):
TATGTATAAATTAAATA
Found at i:30370023 original size:17 final size:18
Alignment explanation
Indices: 30370003--30370038 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
30369993 AAATTAAAGA
30370003 TAATTTTT-AAAAAAATT
1 TAATTTTTGAAAAAAATT
*
30370020 TAATTTTTGAAAAATATT
1 TAATTTTTGAAAAAAATT
30370038 T
1 T
30370039 TTTGATGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATTTTTGAAAAAAATT
Found at i:30370878 original size:22 final size:22
Alignment explanation
Indices: 30370853--30370895 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
30370843 AACAGCTCCC
30370853 TCTT-TCTTTCCCTTTCCTTTTT
1 TCTTCTCTTTCCC-TTCCTTTTT
30370875 TCTTCTCTTTCCCTTCCTTTT
1 TCTTCTCTTTCCCTTCCTTTT
30370896 GCCGCCAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (22 bp):
TCTTCTCTTTCCCTTCCTTTTT
Found at i:30382887 original size:115 final size:117
Alignment explanation
Indices: 30382701--30382984 Score: 350
Period size: 115 Copynumber: 2.5 Consensus size: 117
30382691 TTAAAAGAGC
** * * *
30382701 GCGTGTAGTTCA-TCAACAATTTAAAATAGAATATGCATA-TTAGTTATAAGTTTTTCAACTTCA
1 GCGTGTAGTTCACT-AATGATTTAAGATTGAATATGCATATTTAGTTATAAGTTTTACAACTTCA
** * * * *
30382764 AGGTGTGTATA-TAGCAATAATGATTTAGATTAAATATGCATATTACAAC-AGT
65 AGACGTGTATATTA-CAATAATGATTTAGACTAAATATGCATATAAAAACAACT
*
30382816 GCGTGTAGTTCACTAATGATTTAAGATTGAATATGCATATTTA-TTATAAGTTTTACAATTTCAA
1 GCGTGTAGTTCACTAATGATTTAAGATTGAATATGCATATTTAGTTATAAGTTTTACAACTTCAA
*
30382880 GACGTGTATATTATAATAATGATTTAGACTAAATATGCATATAAAAACAACT
66 GACGTGTATATTACAATAATGATTTAGACTAAATATGCATATAAAAACAACT
* *
30382932 -CGCGTAGTTCACTGATGATTTAAGATTGAATATG--TATGTTAGTTATAAGTTTT
1 GCGTGTAGTTCACTAATGATTTAAGATTGAATATGCATAT-TTAGTTATAAGTTTT
30382985 GCATTTTCTA
Statistics
Matches: 148, Mismatches: 15, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
113 3 0.02
114 3 0.02
115 134 0.91
116 8 0.05
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (117 bp):
GCGTGTAGTTCACTAATGATTTAAGATTGAATATGCATATTTAGTTATAAGTTTTACAACTTCAA
GACGTGTATATTACAATAATGATTTAGACTAAATATGCATATAAAAACAACT
Found at i:30383015 original size:115 final size:113
Alignment explanation
Indices: 30382719--30383019 Score: 320
Period size: 115 Copynumber: 2.6 Consensus size: 113
30382709 TTCATCAACA
* * * * *
30382719 ATTTAAAATAGAATATGCATATTAGTTATAAGTTTTTCAACTTCA-AGGTGTGTATATAGCAATA
1 ATTTAAGATTGAATATGTAT-TTAGTTATAAGTTTTACAATTTCAGAGGTGTGTAT-T-GCAATA
* * * * *
30382783 ATGATTTAGATTAAATATGCATATTACAACAGTGCGTGTAGTTCACTAATG
63 ATGATTTAGACTAAATATGCATATAAAAACACTGCGCGTAGTTCACTAATG
* * **
30382834 ATTTAAGATTGAATATGCATATTTA-TTATAAGTTTTACAATTTCAAGACGTGTATATTATAATA
1 ATTTAAGATTGAATATG--TATTTAGTTATAAGTTTTACAATTTC-AGAGGTGTGTATTGCAATA
*
30382898 ATGATTTAGACTAAATATGCATATAAAAACAACT-CGCGTAGTTCACTGATG
63 ATGATTTAGACTAAATATGCATATAAAAAC-ACTGCGCGTAGTTCACTAATG
* * * * *
30382949 ATTTAAGATTGAATATGTATGTTAGTTATAAGTTTTGCATTTTCTAGAGGAGTGGATTGCACTAA
1 ATTTAAGATTGAATATGTAT-TTAGTTATAAGTTTTACAATTTC-AGAGGTGTGTATTGCAATAA
30383014 TGATTT
64 TGATTT
30383020 TAGAAGGATT
Statistics
Matches: 154, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
113 3 0.02
114 3 0.02
115 131 0.85
116 7 0.05
117 10 0.06
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (113 bp):
ATTTAAGATTGAATATGTATTTAGTTATAAGTTTTACAATTTCAGAGGTGTGTATTGCAATAATG
ATTTAGACTAAATATGCATATAAAAACACTGCGCGTAGTTCACTAATG
Found at i:30390464 original size:25 final size:26
Alignment explanation
Indices: 30390436--30390485 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
30390426 GATGTAATGT
*
30390436 ATCTAATCTTG-TAAATAATATGTTC
1 ATCTAATCTTGATAAATAACATGTTC
* *
30390461 ATCTAATTTTGATAAGTAACATGTT
1 ATCTAATCTTGATAAATAACATGTT
30390486 GAAGTCTGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (26 bp):
ATCTAATCTTGATAAATAACATGTTC
Found at i:30392555 original size:6 final size:6
Alignment explanation
Indices: 30392531--30392576 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
30392521 ACATATTAAC
* *
30392531 AAATAA AAATGA AGA-AA AAAT-A AAAT-A AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
30392576 A
1 A
30392577 TAATCATGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
5 13 0.38
6 21 0.62
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:30392579 original size:16 final size:17
Alignment explanation
Indices: 30392531--30392576 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
30392521 ACATATTAAC
*
30392531 AAATAAAAATGAAGA-AA
1 AAATAAAAAT-AAAATAA
30392548 AAAT-AAAATAAAATAA
1 AAATAAAAATAAAATAA
30392564 AAATAAAAATAAA
1 AAATAAAAATAAA
30392577 TAATCATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 3 0.12
16 11 0.42
17 12 0.46
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.15
Consensus pattern (17 bp):
AAATAAAAATAAAATAA
Found at i:30397380 original size:198 final size:198
Alignment explanation
Indices: 30397042--30397433 Score: 696
Period size: 198 Copynumber: 2.0 Consensus size: 198
30397032 GCCATCCCTT
*
30397042 CCCCCACTTTCTTCCCTTTTTAATTGGATTTCTAGTCTAGATGAAACGGTGTGGAAAGAAATGCA
1 CCCCCACTTTCTTCCCTTTTTAATTGGATTCCTAGTCTAGATGAAACGGTGTGGAAAGAAATGCA
* *
30397107 AGTGGATGATATGATCGCACCTGACTTATTACCATTACTGTCCTTAAACAAGATACCTACGTTAA
66 AGTGGATGATATGATCGCACCTCACTTATCACCATTACTGTCCTTAAACAAGATACCTACGTTAA
* *
30397172 TTGTTGTATTATCATAACTTTCTTCTTCTATTTTGTTC-GTTGGTTTTGCTGCCCTTGAATGATA
131 TTGTTGTATTATCATAACTTTCTTCTTCAATTTTG-TCAGTTGGTTTTGCTGCCCTGGAATGATA
30397236 CCTC
195 CCTC
* *
30397240 CCCCCACTTTCTTCCCTTTTTCATTGGATTCCTAGTCTAGATGAAATGGTGTGGAAAGAAATGCA
1 CCCCCACTTTCTTCCCTTTTTAATTGGATTCCTAGTCTAGATGAAACGGTGTGGAAAGAAATGCA
*
30397305 AGTGGATGATATGATCGCACCTCACTTATCACCATTACTGTCCTTAAACAAGATACCTATGTTAA
66 AGTGGATGATATGATCGCACCTCACTTATCACCATTACTGTCCTTAAACAAGATACCTACGTTAA
30397370 TTGTTGTATTATCATAACTTTCTTCTTCAATTTTGTCAGTTGGTTTTGCTGCCCTGGAATGATA
131 TTGTTGTATTATCATAACTTTCTTCTTCAATTTTGTCAGTTGGTTTTGCTGCCCTGGAATGATA
30397434 TAACTGACTC
Statistics
Matches: 185, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
197 2 0.01
198 183 0.99
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (198 bp):
CCCCCACTTTCTTCCCTTTTTAATTGGATTCCTAGTCTAGATGAAACGGTGTGGAAAGAAATGCA
AGTGGATGATATGATCGCACCTCACTTATCACCATTACTGTCCTTAAACAAGATACCTACGTTAA
TTGTTGTATTATCATAACTTTCTTCTTCAATTTTGTCAGTTGGTTTTGCTGCCCTGGAATGATAC
CTC
Found at i:30398054 original size:38 final size:37
Alignment explanation
Indices: 30397997--30398069 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
30397987 TGATAAAAAG
30397997 TATGTTCATTAATTCTACTAAACAATATGTTCAAGTC
1 TATGTTCATTAATTCTACTAAACAATATGTTCAAGTC
* *
30398034 TATGTTCATCTAATTTTACTAAATAATATGTTCAAG
1 TATGTTCAT-TAATTCTACTAAACAATATGTTCAAG
30398070 CATTAGTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 9 0.27
38 24 0.73
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (37 bp):
TATGTTCATTAATTCTACTAAACAATATGTTCAAGTC
Found at i:30398420 original size:2 final size:2
Alignment explanation
Indices: 30398413--30398438 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30398403 CTGCCTGGAT
30398413 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
30398439 TCTTCTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30399813 original size:19 final size:19
Alignment explanation
Indices: 30399774--30399813 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
30399764 TATATATTGG
*
30399774 TTTAGGATATTTTAGATTA
1 TTTAGGATATTTTAGAGTA
* *
30399793 TTTAGGTTATTTTATAGTA
1 TTTAGGATATTTTAGAGTA
30399812 TT
1 TT
30399814 AATTAGTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (19 bp):
TTTAGGATATTTTAGAGTA
Found at i:30411127 original size:15 final size:15
Alignment explanation
Indices: 30411104--30411133 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30411094 TTAGTTAGTA
*
30411104 TTAATTTATTTATAT
1 TTAAATTATTTATAT
30411119 TTAAATTATTTATAT
1 TTAAATTATTTATAT
30411134 ATTTAATAAT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTAAATTATTTATAT
Found at i:30418434 original size:2 final size:2
Alignment explanation
Indices: 30418429--30418455 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30418419 TAAAAATAAT
30418429 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
30418456 CAACTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30419848 original size:28 final size:29
Alignment explanation
Indices: 30419798--30419902 Score: 104
Period size: 28 Copynumber: 3.5 Consensus size: 29
30419788 AATATTTGAG
*
30419798 GGACTAAATTGAAAAAATAAAAAGTTTAGA
1 GGACTAAATT-AAAAAATGAAAAGTTTAGA
* *
30419828 AGACTAAATT-AAAAATGAAAAATTTAGA
1 GGACTAAATTAAAAAATGAAAAGTTTAGA
** *
30419856 GGGTTAAATTAAAAAGAATGAAAAAGTTTGGA
1 GGACTAAATT-AAAA-AATG-AAAAGTTTAGA
*
30419888 GGACCAAATTAAAAA
1 GGACTAAATTAAAAA
30419903 GAAGTAAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 23 0.38
30 13 0.22
31 8 0.13
32 16 0.27
ACGTcount: A:0.56, C:0.04, G:0.17, T:0.23
Consensus pattern (29 bp):
GGACTAAATTAAAAAATGAAAAGTTTAGA
Found at i:30419879 original size:31 final size:31
Alignment explanation
Indices: 30419765--30419913 Score: 132
Period size: 31 Copynumber: 4.9 Consensus size: 31
30419755 CCTTTGGAAT
* *
30419765 GAGGACTAAATTGAAAAGAA-AAAAA-TATTT
1 GAGGACTAAATTAAAAAGAATAAAAAGT-TTA
*
30419795 GAGGGACTAAATTGAAAA-AATAAAAAGTTTA
1 GA-GGACTAAATTAAAAAGAATAAAAAGTTTA
*
30419826 GAAGACTAAATT--AAA-AATGAAAAA-TTTA
1 GAGGACTAAATTAAAAAGAAT-AAAAAGTTTA
** *
30419854 GAGGGTTAAATTAAAAAGAATGAAAAAGTTTG
1 GAGGACTAAATTAAAAAGAAT-AAAAAGTTTA
*
30419886 GAGGACCAAATTAAAAAGAAGTAAAAAG
1 GAGGACTAAATTAAAAAGAA-TAAAAAG
30419914 GTAGGGACTA
Statistics
Matches: 101, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
28 19 0.19
29 5 0.05
30 16 0.16
31 33 0.33
32 27 0.27
33 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.21
Consensus pattern (31 bp):
GAGGACTAAATTAAAAAGAATAAAAAGTTTA
Found at i:30421075 original size:2 final size:2
Alignment explanation
Indices: 30421068--30421123 Score: 103
Period size: 2 Copynumber: 27.5 Consensus size: 2
30421058 TGTCATGTGG
30421068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
30421111 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
30421124 ATGATTTATG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 51 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30423073 original size:30 final size:30
Alignment explanation
Indices: 30423039--30423157 Score: 95
Period size: 30 Copynumber: 4.0 Consensus size: 30
30423029 GTCATAAAGG
30423039 CTTATTTGACTCAAAATAAAAATAAAAGAA
1 CTTATTTGACTCAAAATAAAAATAAAAGAA
* * *
30423069 CTTATTTGGCTCAAAATAAAAGTATAAGAGA
1 CTTATTTGACTCAAAATAAAAATAAAAGA-A
*
30423100 -TTGA-TTGAACACGATAAA-AAAAATAAAAG--
1 CTT-ATTTG-ACTC-A-AAATAAAAATAAAAGAA
* * *
30423129 CTCATTTGACTTAAAATAAAAATATAAGA
1 CTTATTTGACTCAAAATAAAAATAAAAGA
30423158 GCCTAGTTGA
Statistics
Matches: 69, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
27 3 0.04
28 11 0.16
29 3 0.04
30 35 0.51
31 4 0.06
32 10 0.14
33 3 0.04
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (30 bp):
CTTATTTGACTCAAAATAAAAATAAAAGAA
Found at i:30427809 original size:353 final size:357
Alignment explanation
Indices: 30427153--30427865 Score: 1332
Period size: 353 Copynumber: 2.0 Consensus size: 357
30427143 TATAAATTCT
*
30427153 AATATATATATATATACAGGTGTTAAGTGTATATTTGGTTTAGTTTTTTTTCAATTTATTTACAT
1 AATAAATATATATATACAGGTGTTAAGTGTATATTTGGTTTAGTTTTTTTTCAATTTATTTACAT
30427218 CTTAAAAGTAAAAATCAGGTTAAATATGATTTTTTTGATAAGTTTTTTTTTTTAAAATAAAATTT
66 CTTAAAAGTAAAAATCAGGTTAAATATGATTTTTTTGATAAGTTTTTTTTTTTAAAATAAAATTT
30427283 TTAAAAAAGAAATTTAAAAAAAAGCTTTTTTTTTAAATATATTAATTTTCAAAGAATACCCTTCT
131 TTAAAAAAGAAATTTAAAAAAAAGCTTTTTTTTTAAATATATTAATTTTCAAAGAATACCCTTCT
30427348 CTCAATTAATTTTTTTTTCCTCTCATTCTCTTTACAAATTACCATTCTTCAACGTAAATCACGAT
196 CTCAATTAATTTTTTTTTCCTCTCATTCTCTTTACAAATTACCATTCTTCAACGTAAATCACGAT
30427413 TTGTTTATTTTTTACTTCTCTCTACAAAAACTAATAAAAAAACAAAAGATCCAACAATATAATAT
261 TTGTTTATTTTTTACTTCTCTCTACAAAAACTAATAAAAAAACAAAAGATCCAACAATATAATAT
30427478 CAAAATCTATAATTTTTTTTTATTTTTACAAA
326 CAAAATCTATAATTTTTTTTTATTTTTACAAA
*
30427510 AATAANATATATATATA-AGTTGGTTAAGTGTATATTTGGTTTTAG-TTTTTTTCAATTTATTTA
1 AATAA-ATATATATATACAGGT-GTTAAGTGTATATTTGG-TTTAGTTTTTTTTCAATTTATTTA
30427573 CATCTTAAAAGTAAAAATCAGGTTAAATATGATTTTTTTGATAAG-TTTTTTTTTT-AAATAAAA
63 CATCTTAAAAGTAAAAATCAGGTTAAATATGATTTTTTTGATAAGTTTTTTTTTTTAAAATAAAA
30427636 -TTTT-AAAAAG-AATTTAAAAAAAAGCTTTTTTTTTAAATATATTAATTTTCAAAGAATACCCT
128 TTTTTAAAAAAGAAATTTAAAAAAAAGCTTTTTTTTTAAATATATTAATTTTCAAAGAATACCCT
30427698 TCTCTCAATTAATTTTTTTTTCCTCTCATTCTCTTTACAAATTACCATTCTTCAACGTAAATCAC
193 TCTCTCAATTAATTTTTTTTTCCTCTCATTCTCTTTACAAATTACCATTCTTCAACGTAAATCAC
30427763 GATTTGTTTATTTTTTACTTCTCTCTACAAAAACTAATAAAAAAACAAAAGATCCAACAATATAA
258 GATTTGTTTATTTTTTACTTCTCTCTACAAAAACTAATAAAAAAACAAAAGATCCAACAATATAA
30427828 TATCAAAATCTATAATTTTTTTTTATTTTTACAAA
323 TATCAAAATCTATAATTTTTTTTTATTTTTACAAA
30427863 AAT
1 AAT
30427866 TAAGAAAAAA
Statistics
Matches: 351, Mismatches: 2, Indels: 10
0.97 0.01 0.03
Matches are distributed among these distances:
353 220 0.63
354 6 0.02
355 4 0.01
356 8 0.02
357 17 0.05
358 91 0.26
359 5 0.01
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (357 bp):
AATAAATATATATATACAGGTGTTAAGTGTATATTTGGTTTAGTTTTTTTTCAATTTATTTACAT
CTTAAAAGTAAAAATCAGGTTAAATATGATTTTTTTGATAAGTTTTTTTTTTTAAAATAAAATTT
TTAAAAAAGAAATTTAAAAAAAAGCTTTTTTTTTAAATATATTAATTTTCAAAGAATACCCTTCT
CTCAATTAATTTTTTTTTCCTCTCATTCTCTTTACAAATTACCATTCTTCAACGTAAATCACGAT
TTGTTTATTTTTTACTTCTCTCTACAAAAACTAATAAAAAAACAAAAGATCCAACAATATAATAT
CAAAATCTATAATTTTTTTTTATTTTTACAAA
Found at i:30428263 original size:19 final size:19
Alignment explanation
Indices: 30428221--30428269 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
30428211 AACAATTTAC
30428221 TAAACAGTTTTACTTTAATCA
1 TAAA-AGTTTTACTTT-ATCA
30428242 TAAAAGTTATTACTTT-TCA
1 TAAAAGTT-TTACTTTATCA
*
30428261 TAAGAGTTT
1 TAAAAGTTT
30428270 AATAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 1 0.04
19 10 0.38
20 4 0.15
21 11 0.42
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (19 bp):
TAAAAGTTTTACTTTATCA
Found at i:30429758 original size:60 final size:59
Alignment explanation
Indices: 30429678--30429800 Score: 169
Period size: 60 Copynumber: 2.1 Consensus size: 59
30429668 AAAGTAAAAG
*
30429678 AACTTATTTGATTAAAAATAAAAATATAAGAGATTGATTG-AGCGCAATAAAAAAAATAAA
1 AACTCATTTGATTAAAAATAAAAATATAAGAGATTGATTGAAG-GCAAT-AAAAAAATAAA
* * *
30429738 AACTCATTTGACTT-AAAATAAAAATATAAGAGCTTGGTTGAAGGTAATAAAAAAATAAA
1 AACTCATTTGA-TTAAAAATAAAAATATAAGAGATTGATTGAAGGCAATAAAAAAATAAA
30429797 AACT
1 AACT
30429801 TATATGAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
59 15 0.26
60 38 0.67
61 4 0.07
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.27
Consensus pattern (59 bp):
AACTCATTTGATTAAAAATAAAAATATAAGAGATTGATTGAAGGCAATAAAAAAATAAA
Found at i:30432989 original size:55 final size:54
Alignment explanation
Indices: 30432927--30433104 Score: 194
Period size: 55 Copynumber: 3.2 Consensus size: 54
30432917 TGAAGAGTTA
* *
30432927 TTTTAGCGTGTCATGGCTGTTACTGGCGTGTTGTGGGTTAACTAGTTATTTGAGT
1 TTTTAGCGTGTCATGGCTGTTCCTGGCGTGTCGTGGGTTAACTAGTT-TTTGAGT
* * * * * * * *
30432982 TGTTAGCGTGTCACGACTGTTCCTGGGGTGTGGTGGGTTAACTGAATTTATGGGT
1 TTTTAGCGTGTCATGGCTGTTCCTGGCGTGTCGTGGGTTAACT-AGTTTTTGAGT
* * * * *
30433037 TTTTGGTGTGTCATGGCTGTTCCTGGTGTGTCGTGGGTTAACTGGTTTTTTAGGT
1 TTTTAGCGTGTCATGGCTGTTCCTGGCGTGTCGTGGGTTAACTAGTTTTTGA-GT
30433092 TTTTAGCGTGTCA
1 TTTTAGCGTGTCA
30433105 CGGATGTTGG
Statistics
Matches: 98, Mismatches: 23, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
54 4 0.04
55 91 0.93
56 3 0.03
ACGTcount: A:0.12, C:0.12, G:0.33, T:0.43
Consensus pattern (54 bp):
TTTTAGCGTGTCATGGCTGTTCCTGGCGTGTCGTGGGTTAACTAGTTTTTGAGT
Found at i:30433183 original size:23 final size:23
Alignment explanation
Indices: 30433144--30433270 Score: 164
Period size: 23 Copynumber: 5.5 Consensus size: 23
30433134 TAGTGATTGA
* *
30433144 CGTGTCACAACAGTGATGCATGG
1 CGTGTCACGACACTGATGCATGG
* *
30433167 CGTGTAACGATACTGATGCATGG
1 CGTGTCACGACACTGATGCATGG
* *
30433190 AGTGTCACGACAGTGATGCATGG
1 CGTGTCACGACACTGATGCATGG
* *
30433213 CGTGTCATGACAGTGATGCATGG
1 CGTGTCACGACACTGATGCATGG
* *
30433236 CGTGTAACGATACTGATGCATGG
1 CGTGTCACGACACTGATGCATGG
30433259 CGTGTCACGACA
1 CGTGTCACGACA
30433271 TTTGACTTGA
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 88 1.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (23 bp):
CGTGTCACGACACTGATGCATGG
Found at i:30433286 original size:31 final size:31
Alignment explanation
Indices: 30433251--30433332 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
30433241 AACGATACTG
*
30433251 ATGCATGGCGTGTCACGACATTTGAC-TTGAT
1 ATGCATGGCGTGTCACAACATTTGACATT-AT
* * * *
30433282 ATGCATGGAGTGTTACAATATTTTACATTAT
1 ATGCATGGCGTGTCACAACATTTGACATTAT
* *
30433313 TTGCATGGCGTGTAACAACA
1 ATGCATGGCGTGTCACAACA
30433333 CGACTGACAA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 39 0.95
32 2 0.05
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (31 bp):
ATGCATGGCGTGTCACAACATTTGACATTAT
Found at i:30436865 original size:31 final size:32
Alignment explanation
Indices: 30436802--30437108 Score: 283
Period size: 31 Copynumber: 9.9 Consensus size: 32
30436792 AATAAGGAAT
* *
30436802 AAATG-TGAGACACGCCATGCATAAAAAG-TA
1 AAATGTTGTGACACGCCATGCATAACAAGATA
* * *
30436832 AAATGTTGTGACATGCCGTGCATATCAA-ATA
1 AAATGTTGTGACACGCCATGCATAACAAGATA
* * *
30436863 AAATATTGTAACACGCCATTCATAACAAGA-A
1 AAATGTTGTGACACGCCATGCATAACAAGATA
*** *
30436894 AAATGAAATGACACGTCATGCATAACAAG-TA
1 AAATGTTGTGACACGCCATGCATAACAAGATA
30436925 AAATGTTGTGACACGCCATGCATAACAAGATA
1 AAATGTTGTGACACGCCATGCATAACAAGATA
* * * * *
30436957 AACT-TGGTGACACGCCAAGGATAACAAG-CA
1 AAATGTTGTGACACGCCATGCATAACAAGATA
* * *
30436987 CAATGTTCTGACACACCATGCATAACAAG-TA
1 AAATGTTGTGACACGCCATGCATAACAAGATA
* *
30437018 AAAGGTTGTGACACGCCATGCATAACAAG-TT
1 AAATGTTGTGACACGCCATGCATAACAAGATA
* * *
30437049 AAACGTTGTGACACACCATGCATAACAA-TTA
1 AAATGTTGTGACACGCCATGCATAACAAGATA
* * * *
30437080 AATTGTTCTGACTCGTCATGCATAACAAG
1 AAATGTTGTGACACGCCATGCATAACAAG
30437109 TTCTGGTGTG
Statistics
Matches: 220, Mismatches: 49, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
30 8 0.04
31 206 0.94
32 6 0.03
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (32 bp):
AAATGTTGTGACACGCCATGCATAACAAGATA
Found at i:30436970 original size:93 final size:92
Alignment explanation
Indices: 30436810--30437109 Score: 341
Period size: 93 Copynumber: 3.2 Consensus size: 92
30436800 ATAAATGTGA
* * * * * *
30436810 GACACGCCATGCATAAAAAGTAAAATGTTGTGACATGCCGTGCATATCAA-ATAAAATATTGTAA
1 GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGAT-AAA-CTTGTGA
* ***
30436874 CACGCCATTCATAACAAGAAAAATGAAAT
64 CACGCCATGCATAACAAGAAAAATGTTCT
*
30436903 GACACGTCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGATAAACTTGGTGAC
1 GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGATAAACTT-GTGAC
* * * *
30436968 ACGCCAAGGATAACAAGCACAATGTTCT
65 ACGCCATGCATAACAAGAAAAATGTTCT
* * *
30436996 GACACACCATGCATAACAAGTAAAAGGTTGTGACACGCCATGCATAACAAGTTAAACGTTGTGAC
1 GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGATAAAC-TTGTGAC
* ** *
30437061 ACACCATGCATAACAATTAAATTGTTCT
65 ACGCCATGCATAACAAGAAAAATGTTCT
* *
30437089 GACTCGTCATGCATAACAAGT
1 GACACGCCATGCATAACAAGT
30437110 TCTGGTGTGT
Statistics
Matches: 175, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
92 2 0.01
93 169 0.97
94 4 0.02
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.22
Consensus pattern (92 bp):
GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGATAAACTTGTGACA
CGCCATGCATAACAAGAAAAATGTTCT
Found at i:30437803 original size:15 final size:13
Alignment explanation
Indices: 30437780--30437825 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
30437770 GTTTACAATG
30437780 AATTGTATACAAAA
1 AATTGTATA-AAAA
*
30437794 AATATGTATAAAATG
1 AAT-TGTATAAAA-A
30437809 AATTGTATAAAAA
1 AATTGTATAAAAA
30437822 AATT
1 AATT
30437826 TATGTGTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 4 0.14
14 15 0.54
15 9 0.32
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.33
Consensus pattern (13 bp):
AATTGTATAAAAA
Found at i:30439488 original size:156 final size:156
Alignment explanation
Indices: 30439192--30439674 Score: 626
Period size: 156 Copynumber: 3.1 Consensus size: 156
30439182 CGACTGGGTC
* * * *
30439192 AACTACAATAACATATATAATTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCG
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCG
* * ** * * * *
30439257 TTACAACTTTAATATCCTAACTGGTGGCTCGTTAGCAGTCTGTGGTGGAGCCGGATCGATTGATG
66 TTACAACTTTAATATCCTTACCGCCGGCTCGTTAGCAGTCTGCGATGGAGCCGGATCGATCGGTG
*
30439322 CTTTAGGACCTGTCGTCGCTTTCGCA
131 CTTCAGGACCTGTCGTCGCTTTCGCA
* * * * * *
30439348 TACTGTAATTACATATTTAACTGTGTTATTCAATAATCATGTATGAAATTATTGAACATTAACTG
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCG
* * *
30439413 TTACAACTTTAATATCTTTACCGCCGGCTCGTTAGCAGTCTACGATGGAGCCGGATAGATCGGTG
66 TTACAACTTTAATATCCTTACCGCCGGCTCGTTAGCAGTCTGCGATGGAGCCGGATCGATCGGTG
* * *
30439478 CTTCATGACCTGTCGTCGCTTCCACA
131 CTTCAGGACCTGTCGTCGCTTTCGCA
* *
30439504 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTTTGGAATTGTTGAACACTAACCG
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCG
* ** * * *
30439569 TTACAACTTTAATATCCTTACCGCCGACTCGTTAGTTGTCTGCGGTTGG-GCTGGACCGATCGGT
66 TTACAACTTTAATATCCTTACCGCCGGCTCGTTAGCAGTCTGC-GATGGAGCCGGATCGATCGGT
* * *
30439633 GCTTGAGGACCTGTCCTCGCTTTCGTA
130 GCTTCAGGACCTGTCGTCGCTTTCGCA
30439660 AACTGCAATTACATA
1 AACTGCAATTACATA
30439675 AATTACTATG
Statistics
Matches: 278, Mismatches: 48, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
156 274 0.99
157 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (156 bp):
AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCG
TTACAACTTTAATATCCTTACCGCCGGCTCGTTAGCAGTCTGCGATGGAGCCGGATCGATCGGTG
CTTCAGGACCTGTCGTCGCTTTCGCA
Found at i:30439687 original size:156 final size:156
Alignment explanation
Indices: 30439213--30439727 Score: 595
Period size: 156 Copynumber: 3.3 Consensus size: 156
30439203 CATATATAAT
* *
30439213 TGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCGTTACAACTTTAATATCCTAAC
1 TGTGTTATTCAATAATCATATATGGAATTGTTGAACACTAACCGTTACAACTTTAATATCCTTAC
* ** * * * *
30439278 TGGTGGCTCGTTAGCAGTCTGTGGTGGAGCCGGATCGATTGATGCTTTAGGACCTGTCGTCGCTT
66 CGCCGGCTCGTTAGCAGTCTGCGGTGGAGCCGGATCGATCGGTGCTTCAGGACCTGTCGTCGCTT
* * *
30439343 TCGCATACTGTAATTACAT-ATTTAAC
131 TCGCAAACTGCAATTACATAAATT-AC
* * * * * *
30439369 TGTGTTATTCAATAATCATGTATGAAATTATTGAACATTAACTGTTACAACTTTAATATCTTTAC
1 TGTGTTATTCAATAATCATATATGGAATTGTTGAACACTAACCGTTACAACTTTAATATCCTTAC
* * * *
30439434 CGCCGGCTCGTTAGCAGTCTACGATGGAGCCGGATAGATCGGTGCTTCATGACCTGTCGTCGCTT
66 CGCCGGCTCGTTAGCAGTCTGCGGTGGAGCCGGATCGATCGGTGCTTCAGGACCTGTCGTCGCTT
* * * *
30439499 CCACAAACTGCAATTACATATATAAC
131 TCGCAAACTGCAATTACATAAATTAC
* *
30439525 TGTGTTATTCAATAATCATGTTTGGAATTGTTGAACACTAACCGTTACAACTTTAATATCCTTAC
1 TGTGTTATTCAATAATCATATATGGAATTGTTGAACACTAACCGTTACAACTTTAATATCCTTAC
* ** * * * *
30439590 CGCCGACTCGTTAGTTGTCTGCGGTTGG-GCTGGACCGATCGGTGCTTGAGGACCTGTCCTCGCT
66 CGCCGGCTCGTTAGCAGTCTGCGG-TGGAGCCGGATCGATCGGTGCTTCAGGACCTGTCGTCGCT
*
30439654 TTCGTAAACTGCAATTACATAAATTAC
130 TTCGCAAACTGCAATTACATAAATTAC
* * * * * * *
30439681 TATGTTACTCGATAAACATATGTGGGAA-TGTAGAACACAAACCGTTA
1 TGTGTTATTCAATAATCATATAT-GGAATTGTTGAACACTAACCGTTA
30439728 GAACCGATCT
Statistics
Matches: 302, Mismatches: 54, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
156 294 0.97
157 8 0.03
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (156 bp):
TGTGTTATTCAATAATCATATATGGAATTGTTGAACACTAACCGTTACAACTTTAATATCCTTAC
CGCCGGCTCGTTAGCAGTCTGCGGTGGAGCCGGATCGATCGGTGCTTCAGGACCTGTCGTCGCTT
TCGCAAACTGCAATTACATAAATTAC
Found at i:30441383 original size:31 final size:31
Alignment explanation
Indices: 30441318--30441612 Score: 317
Period size: 31 Copynumber: 9.5 Consensus size: 31
30441308 AATAAGGAAT
* *
30441318 AAATATTGTGACATGCCATGCAT-TGCAA-TCA
1 AAATGTTGTGACACGCCATGCATAT-CAAGT-A
*
30441349 AAATATTGTGACACGCCATGCATAAT-AAGTA
1 AAATGTTGTGACACGCCATGCAT-ATCAAGTA
* * * *
30441380 AAATGTTGTGACACGTCATGCAAAACAAGTT
1 AAATGTTGTGACACGCCATGCATATCAAGTA
* * *
30441411 AAACGTTGTGACACACCATGCATATCAAGTT
1 AAATGTTGTGACACGCCATGCATATCAAGTA
* *
30441442 AAACGTTATGACACGCCATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGTA
* * * *
30441473 AAATGCTGTCAAACGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGTA
* *
30441504 AAATGCTGTGACACGACATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGTA
* *
30441535 AAATGCTGTCACACGCCATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGTA
* * *
30441566 AAATGCTGTCACACGCTATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGTA
* *
30441597 AAATGCTGTCACACGC
1 AAATGTTGTGACACGC
30441613 TAATAACTAA
Statistics
Matches: 233, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
30 1 0.00
31 230 0.99
32 1 0.00
33 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATATCAAGTA
Found at i:30442168 original size:53 final size:52
Alignment explanation
Indices: 30442101--30442200 Score: 164
Period size: 53 Copynumber: 1.9 Consensus size: 52
30442091 TGTTAGCTGC
* *
30442101 TCAAGCACTACCGTGTCACGCACTCTAAACCATGACCATGGCATGTCAGCTTT
1 TCAAGCAATACCGTGTCACACACTCTAAA-CATGACCATGGCATGTCAGCTTT
*
30442154 TCAAGCAATGCCGTGTCACACACTCTAAACATGACCATGGCATGTCA
1 TCAAGCAATACCGTGTCACACACTCTAAACATGACCATGGCATGTCA
30442201 CCAACTCTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 18 0.41
53 26 0.59
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (52 bp):
TCAAGCAATACCGTGTCACACACTCTAAACATGACCATGGCATGTCAGCTTT
Found at i:30442261 original size:47 final size:47
Alignment explanation
Indices: 30442188--30442489 Score: 322
Period size: 47 Copynumber: 6.4 Consensus size: 47
30442178 CTAAACATGA
* * * *
30442188 CCATGGCATGTCACCAACTCTGAACTCTGGCATGTCACAGATTTCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* **
30442235 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTCTCACAGATTCAAT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * * * ** *
30442282 CCATGGCATCTCACTAACCCTGAAAGCTGGCATGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * *
30442329 CCAT-GCTATGTCACCAACTCTTAA-TCTGACGTGTCATAGATTCCCT
1 CCATGGC-GTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * * *
30442375 CCATGGCGTTTCACCAACTCTAAACGCTGCCGTGTCACACATTCCCAT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCC-T
* * *
30442423 -CATGGCGTGTCACAAACTCTTAACTCTGGTGTCTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
*
30442469 CCATGGCGTCTCACCAACTCT
1 CCATGGCGTGTCACCAACTCT
30442490 GAGCGGTGCC
Statistics
Matches: 207, Mismatches: 43, Indels: 10
0.80 0.17 0.04
Matches are distributed among these distances:
46 39 0.19
47 167 0.81
48 1 0.00
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.27
Consensus pattern (47 bp):
CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
Found at i:30442267 original size:24 final size:24
Alignment explanation
Indices: 30442191--30442265 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
30442181 AACATGACCA
*
30442191 TGGCATGTCACCAACTCTGAACTC
1 TGGCATGTCACCAACTCTTAACTC
*
30442215 TGGCATGTCA-CAGA-T-TT-CCTCC
1 TGGCATGTCACCA-ACTCTTAACT-C
*
30442237 ATGGCGTGTCACCAACTCTTAACTC
1 -TGGCATGTCACCAACTCTTAACTC
30442262 TGGC
1 TGGC
30442266 GTCTCACAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 13 0.32
24 18 0.45
25 3 0.08
26 2 0.05
ACGTcount: A:0.21, C:0.32, G:0.19, T:0.28
Consensus pattern (24 bp):
TGGCATGTCACCAACTCTTAACTC
Found at i:30442312 original size:94 final size:94
Alignment explanation
Indices: 30442188--30442491 Score: 373
Period size: 94 Copynumber: 3.2 Consensus size: 94
30442178 CTAAACATGA
* ** *
30442188 CCATGGCATGTCACCAACTCTGAACTCTGGCATGTCACAGATTTCCTCCATGGCGTGTCACCAAC
1 CCATGGCATCTCACCAACTCTGAAAGCTGGCATGTCACAGATTCCCTCCATGGCGTGTCACCAAC
**
30442253 TCTTAACTCTGGCGTCTCACAGATTCAAT
66 TCTTAACTCTGGCGTCTCACAGATTCCCT
* * *
30442282 CCATGGCATCTCACTAACCCTGAAAGCTGGCATGTCACAGATTCCCTCCAT-GCTATGTCACCAA
1 CCATGGCATCTCACCAACTCTGAAAGCTGGCATGTCACAGATTCCCTCCATGGC-GTGTCACCAA
* * *
30442346 CTCTTAA-TCTGACGTGTCATAGATTCCCT
65 CTCTTAACTCTGGCGTCTCACAGATTCCCT
* * * * * *
30442375 CCATGGCGTTTCACCAACTCT-AAACGCTGCCGTGTCACACATTCCCAT-CATGGCGTGTCACAA
1 CCATGGCATCTCACCAACTCTGAAA-GCTGGCATGTCACAGATTCCC-TCCATGGCGTGTCACCA
*
30442438 ACTCTTAACTCTGGTGTCTCACAGATTCCCT
64 ACTCTTAACTCTGGCGTCTCACAGATTCCCT
*
30442469 CCATGGCGTCTCACCAACTCTGA
1 CCATGGCATCTCACCAACTCTGA
30442492 GCGGTGCCGT
Statistics
Matches: 178, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
92 3 0.02
93 72 0.40
94 102 0.57
95 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.27
Consensus pattern (94 bp):
CCATGGCATCTCACCAACTCTGAAAGCTGGCATGTCACAGATTCCCTCCATGGCGTGTCACCAAC
TCTTAACTCTGGCGTCTCACAGATTCCCT
Found at i:30442500 original size:94 final size:94
Alignment explanation
Indices: 30442188--30442536 Score: 364
Period size: 94 Copynumber: 3.7 Consensus size: 94
30442178 CTAAACATGA
* * * * * * * *
30442188 CCATGGCATGTCACCAACTCTGAACTCTGGCATGTCACAGATTTCC-TCCATGGCGTGTCACCAA
1 CCATGGCGTCTCACCAACTCTGAACGCTGCCGTGTCACACATTCCCAT-CATGGCGTGTCACAAA
**
30442252 CTCTTAACTCTGGCGTCTCACAGATTCAAT
65 CTCTTAACTCTGGCGTCTCACAGATTCCCT
* * * * * * * * *
30442282 CCATGGCATCTCACTAACCCTGAAAGCTGGCATGTCACAGATTCCC-TCCAT-GCTATGTCACCA
1 CCATGGCGTCTCACCAACTCTGAACGCTGCCGTGTCACACATTCCCAT-CATGGC-GTGTCACAA
* * *
30442345 ACTCTTAA-TCTGACGTGTCATAGATTCCCT
64 ACTCTTAACTCTGGCGTCTCACAGATTCCCT
* *
30442375 CCATGGCGTTTCACCAACTCTAAACGCTGCCGTGTCACACATTCCCATCATGGCGTGTCACAAAC
1 CCATGGCGTCTCACCAACTCTGAACGCTGCCGTGTCACACATTCCCATCATGGCGTGTCACAAAC
*
30442440 TCTTAACTCTGGTGTCTCACAGATTCCCT
66 TCTTAACTCTGGCGTCTCACAGATTCCCT
* * * * * *
30442469 CCATGGCGTCTCACCAACTCTGAGCGGTGCCGTGTCATACATTCCCAACATGACGTTTCACAAAC
1 CCATGGCGTCTCACCAACTCTGAACGCTGCCGTGTCACACATTCCCATCATGGCGTGTCACAAAC
30442534 TCT
66 TCT
30442537 AAACCCTGCC
Statistics
Matches: 216, Mismatches: 35, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
93 74 0.34
94 142 0.66
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.27
Consensus pattern (94 bp):
CCATGGCGTCTCACCAACTCTGAACGCTGCCGTGTCACACATTCCCATCATGGCGTGTCACAAAC
TCTTAACTCTGGCGTCTCACAGATTCCCT
Found at i:30442513 original size:47 final size:47
Alignment explanation
Indices: 30442188--30442546 Score: 231
Period size: 47 Copynumber: 7.7 Consensus size: 47
30442178 CTAAACATGA
* * * * * * * *
30442188 CCATGGCATGTCACCAACTCTGAACTCTGGCATGTCACAGATTTCCT
1 CCATGGCGTCTCACCAACTCTAAACGCTGCCGTGTCACACATTCCCT
* * * * * * **
30442235 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTCTCACAGATTCAAT
1 CCATGGCGTCTCACCAACTCTAAACGCTGCCGTGTCACACATTCCCT
* * * * * *
30442282 CCATGGCATCTCACTAACCCTGAAA-GCTGGCATGTCACAGATTCCCT
1 CCATGGCGTCTCACCAACTCT-AAACGCTGCCGTGTCACACATTCCCT
* * * * * * *
30442329 CCAT-GCTATGTCACCAACTCTTAA-TCTGACGTGTCATAGATTCCCT
1 CCATGGC-GTCTCACCAACTCTAAACGCTGCCGTGTCACACATTCCCT
*
30442375 CCATGGCGTTTCACCAACTCTAAACGCTGCCGTGTCACACATTCCCAT
1 CCATGGCGTCTCACCAACTCTAAACGCTGCCGTGTCACACATTCCC-T
* * * * ** * *
30442423 -CATGGCGTGTCACAAACTCTTAACTCTGGTGTCTCACAGATTCCCT
1 CCATGGCGTCTCACCAACTCTAAACGCTGCCGTGTCACACATTCCCT
* * * * *
30442469 CCATGGCGTCTCACCAACTCTGAGCGGTGCCGTGTCATACATTCCCA
1 CCATGGCGTCTCACCAACTCTAAACGCTGCCGTGTCACACATTCCCT
* * * * *
30442516 ACATGACGTTTCACAAACTCTAAACCCTGCC
1 CCATGGCGTCTCACCAACTCTAAACGCTGCC
30442547 CTGCGACAGC
Statistics
Matches: 246, Mismatches: 60, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
46 41 0.17
47 202 0.82
48 3 0.01
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (47 bp):
CCATGGCGTCTCACCAACTCTAAACGCTGCCGTGTCACACATTCCCT
Found at i:30453091 original size:22 final size:22
Alignment explanation
Indices: 30453063--30453104 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
30453053 CAGGTCTCTT
30453063 GTTTCCTATTAAAA-CACTACTG
1 GTTTCCTA-TAAAAGCACTACTG
30453085 GTTTCCTATAAAAGCACTAC
1 GTTTCCTATAAAAGCACTAC
30453105 GAACAGTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (22 bp):
GTTTCCTATAAAAGCACTACTG
Found at i:30454795 original size:10 final size:11
Alignment explanation
Indices: 30454776--30454822 Score: 73
Period size: 10 Copynumber: 4.5 Consensus size: 11
30454766 AAAATTTTGG
30454776 TTATTTATTTA
1 TTATTTATTTA
30454787 TTA-TTATTTA
1 TTATTTATTTA
30454797 TTATTTA-TTA
1 TTATTTATTTA
30454807 TTATTTA-TTA
1 TTATTTATTTA
30454817 TTATTT
1 TTATTT
30454823 TTAGTACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
10 29 0.83
11 6 0.17
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:30454797 original size:7 final size:7
Alignment explanation
Indices: 30454776--30454822 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
30454766 AAAATTTTGG
30454776 TTATTTA
1 TTATTTA
30454783 TT-TATTA
1 TTAT-TTA
30454790 TTATTTA
1 TTATTTA
30454797 TTATTTA
1 TTATTTA
30454804 TTA-TTA
1 TTATTTA
30454810 TT-TATTA
1 TTAT-TTA
30454817 TTATTT
1 TTATTT
30454823 TTAGTACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
6 6 0.17
7 27 0.77
8 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATTTA
Found at i:30454802 original size:17 final size:17
Alignment explanation
Indices: 30454780--30454818 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
30454770 TTTTGGTTAT
30454780 TTATTTATTATTATTTA
1 TTATTTATTATTATTTA
30454797 TTATTTATTATTATTTA
1 TTATTTATTATTATTTA
30454814 TTATT
1 TTATT
30454819 ATTTTTAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTATTATTATTTA
Found at i:30459806 original size:17 final size:17
Alignment explanation
Indices: 30459780--30459873 Score: 63
Period size: 17 Copynumber: 5.6 Consensus size: 17
30459770 TCCCGATTTA
30459780 TTTTTT-TTTTATATAT
1 TTTTTTATTTTATATAT
*
30459796 TTTTTTATTTTATTTAT
1 TTTTTTATTTTATATAT
*
30459813 TTATTTA-TTTA-AT-T
1 TTTTTTATTTTATATAT
** *
30459827 TAATTTAATTTATAT-T
1 TTTTTTATTTTATATAT
*
30459843 TATTTATTATTATTATTTAT
1 T-TTT-TTATT-TTATATAT
*
30459863 TATTTTATTTT
1 TTTTTTATTTT
30459874 TTTAATTTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
14 7 0.11
15 5 0.08
16 14 0.23
17 18 0.29
18 9 0.15
19 7 0.11
20 2 0.03
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTATTTTATATAT
Found at i:30459809 original size:13 final size:13
Alignment explanation
Indices: 30459776--30459883 Score: 67
Period size: 13 Copynumber: 7.8 Consensus size: 13
30459766 GCCATCCCGA
30459776 TTTATTTT-TTTT
1 TTTATTTTATTTT
*
30459788 TTATATATTTTTTTAT
1 TT-TAT-TTTATTT-T
*
30459804 TTTA-TTTATTTA
1 TTTATTTTATTTT
*
30459816 TTTATTTAATTTAAT
1 TTTATTTTATTT--T
* *
30459831 TTAATTTATATTTA
1 TTTATTT-TATTTT
30459845 TTTATTATTATTATT
1 TTTATT-TTATT-TT
30459860 TATTATTTTATTTT
1 T-TTATTTTATTTT
*
30459874 TTTAATTTAT
1 TTTATTTTAT
30459884 GTGTCTACAC
Statistics
Matches: 75, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
12 6 0.08
13 23 0.31
14 15 0.20
15 19 0.25
16 12 0.16
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATTTTATTTT
Found at i:30459813 original size:4 final size:4
Alignment explanation
Indices: 30459775--30459883 Score: 79
Period size: 4 Copynumber: 27.5 Consensus size: 4
30459765 AGCCATCCCG
* * *
30459775 ATTT ATTT -TTT TTTT ATAT ATTT TTTT ATTTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT
30459823 AATTT AATTT AATTT A--T ATTT ATTT A-TT A-TT A-TT ATTT A-TT ATTTT
1 -ATTT -ATTT -ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT
*
30459869 ATTT TTTT AATTT AT
1 ATTT ATTT -ATTT AT
30459884 GTGTCTACAC
Statistics
Matches: 89, Mismatches: 7, Indels: 18
0.78 0.06 0.16
Matches are distributed among these distances:
2 2 0.02
3 15 0.17
4 48 0.54
5 24 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:30459842 original size:29 final size:27
Alignment explanation
Indices: 30459799--30459882 Score: 86
Period size: 26 Copynumber: 3.1 Consensus size: 27
30459789 TATATATTTT
*
30459799 TTTATTTTATT-TATTTATTTATTTAA
1 TTTAATTTATTATATTTATTTATTTAA
30459825 TTTAATTTAATTTATATTTATTTA-TT-A
1 TTTAATTT-A-TTATATTTATTTATTTAA
* *
30459852 TTATTATTTATTAT-TTTATTTTTTTAA
1 TT-TAATTTATTATATTTATTTATTTAA
30459879 TTTA
1 TTTA
30459883 TGTGTCTACA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
25 7 0.15
26 14 0.29
27 8 0.17
28 9 0.19
29 10 0.21
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTAATTTATTATATTTATTTATTTAA
Found at i:30459881 original size:21 final size:21
Alignment explanation
Indices: 30459782--30459883 Score: 75
Period size: 21 Copynumber: 4.7 Consensus size: 21
30459772 CCGATTTATT
* * *
30459782 TTTTTTTTATATATTTTTTTA
1 TTTTTTTAATTTATTATTTTA
*
30459803 TTTTATTT-ATTTATTTATTTAA
1 TTTT-TTTAATTTA-TTATTTTA
*
30459825 TTTAATTTAATTTA-TA-TTTA
1 TTT-TTTTAATTTATTATTTTA
30459845 TTTATTATTATTATTTATTATTTTA
1 TTT-TT-TTA--ATTTATTATTTTA
30459870 TTTTTTTAATTTAT
1 TTTTTTTAATTTAT
30459884 GTGTCTACAC
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
20 8 0.12
21 19 0.29
22 15 0.23
23 13 0.20
24 4 0.06
25 7 0.11
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTTTAATTTATTATTTTA
Found at i:30470672 original size:19 final size:19
Alignment explanation
Indices: 30470648--30470696 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
30470638 AAAAATATTA
30470648 ATATATATATATATAATAT
1 ATATATATATATATAATAT
*
30470667 ATATATATATATATACTAT
1 ATATATATATATATAATAT
30470686 AT-TATATATAT
1 ATATATATATAT
30470697 TAGGGGCCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 9 0.31
19 20 0.69
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATATATATATAATAT
Found at i:30470713 original size:2 final size:2
Alignment explanation
Indices: 30470567--30470696 Score: 89
Period size: 2 Copynumber: 66.5 Consensus size: 2
30470557 TTCCTACTTT
*
30470567 TA TA TA TA TA TA TA TA GA GTA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
30470610 TA CTA -A TA AA T- TA -A CTA NA GTA -A TGA CA -A AA AA TA T- TA
1 TA -TA TA TA TA TA TA TA -TA TA -TA TA T-A TA TA TA TA TA TA TA
30470648 -A TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA CTA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
30470688 TA TA TA TA T
1 TA TA TA TA T
30470697 TAGGGGCCAG
Statistics
Matches: 105, Mismatches: 8, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
1 9 0.09
2 88 0.84
3 8 0.08
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (2 bp):
TA
Found at i:30474057 original size:97 final size:98
Alignment explanation
Indices: 30473890--30474087 Score: 292
Period size: 97 Copynumber: 2.0 Consensus size: 98
30473880 CAGTTTCCTC
* * * * **
30473890 CCATCTCTTCATCGGCCTATCCTTCCCCCTTTTGGACTGAACATTCTCCATTAAATCACATTATC
1 CCATCTCTTCATCAGACTACCCTTCCCCCTTTTGGAATGAACATTCTCCATTAAATCACAGAATC
*
30473955 AAAAAGGAACATTTAGGCCTCTGTCCCACATGA
66 AAAAAGGAACATTTAGACCTCTGTCCCACATGA
30473988 CCATCTCTTCATCAGACTACCCTT-CCCCTTTTGGAATGAACATTCTCCA-TAAATTCACAGAAT
1 CCATCTCTTCATCAGACTACCCTTCCCCCTTTTGGAATGAACATTCTCCATTAAA-TCACAGAAT
* *
30474051 CAAAAAGGAGCATTTAGACCTTTGTCCCACATGA
65 CAAAAAGGAACATTTAGACCTCTGTCCCACATGA
30474085 CCA
1 CCA
30474088 AACCAACTTA
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
96 4 0.04
97 65 0.72
98 21 0.23
ACGTcount: A:0.29, C:0.31, G:0.11, T:0.29
Consensus pattern (98 bp):
CCATCTCTTCATCAGACTACCCTTCCCCCTTTTGGAATGAACATTCTCCATTAAATCACAGAATC
AAAAAGGAACATTTAGACCTCTGTCCCACATGA
Found at i:30477254 original size:29 final size:30
Alignment explanation
Indices: 30477212--30477269 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
30477202 GGCAAAATTT
** *
30477212 CTCTAAATGATTAAGAATATC-CCTAAATA
1 CTCTAAAAAATTAACAATATCTCCTAAATA
30477241 CTCTAAAAAATTAACAATATCTCCTAAAT
1 CTCTAAAAAATTAACAATATCTCCTAAAT
30477270 TATAACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (30 bp):
CTCTAAAAAATTAACAATATCTCCTAAATA
Found at i:30484962 original size:31 final size:31
Alignment explanation
Indices: 30484920--30484981 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
30484910 ATTAGGCTAC
*
30484920 TGCTCTGTCAATGCTTCTCT-TGCAACTGCCT
1 TGCTCTCTCAATGCTTCT-TGTGCAACTGCCT
*
30484951 TGCTCTCTCAATGCTTCTTGTGCTACTGCCT
1 TGCTCTCTCAATGCTTCTTGTGCAACTGCCT
30484982 GAAGGCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.11, C:0.32, G:0.16, T:0.40
Consensus pattern (31 bp):
TGCTCTCTCAATGCTTCTTGTGCAACTGCCT
Found at i:30496675 original size:15 final size:15
Alignment explanation
Indices: 30496655--30496688 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
30496645 TTTCGTTGCC
*
30496655 TTAAAAAATGAATTT
1 TTAAAAAATAAATTT
30496670 TTAAAAAATAAATTT
1 TTAAAAAATAAATTT
30496685 TTAA
1 TTAA
30496689 TTCTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TTAAAAAATAAATTT
Found at i:30502180 original size:2 final size:2
Alignment explanation
Indices: 30502173--30502204 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30502163 AGAACTAACA
30502173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30502205 GCATTGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30504801 original size:19 final size:19
Alignment explanation
Indices: 30504766--30504803 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30504756 TACCTCACAA
* *
30504766 CTTTTTTTTATTGTTTTTC
1 CTTTTTTTTAGTCTTTTTC
30504785 CTTTTTTTTAGTCTTTTTC
1 CTTTTTTTTAGTCTTTTTC
30504804 TAACTCCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.76
Consensus pattern (19 bp):
CTTTTTTTTAGTCTTTTTC
Done.