Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 69 of 97
Found at i:27674969 original size:80 final size:80
Alignment explanation
Indices: 27674803--27674971 Score: 212
Period size: 80 Copynumber: 2.1 Consensus size: 80
27674793 TTATACATTT
* *
27674803 TTAATATTTTAATATTTTAAAAAAGAAAATAGAGATAAAATAAAAATAAATAATCACATTAAAGG
1 TTAATATTTTAATATTTTAAAAAAGAAAATAGAGATAAAATAAAAATAAATAACCACATTAAAAG
* *
27674868 TTTAATTATAAATTA
66 TTTAATTACAAAATA
** * ** * * * * *
27674883 AAAATATTTTAATATTTTCAAATTGAAATTAGGGATAAGATAAAAATAAATAACCATATTAAAAT
1 TTAATATTTTAATATTTTAAAAAAGAAAATAGAGATAAAATAAAAATAAATAACCACATTAAAAG
27674948 TTTAATTACAAAATA
66 TTTAATTACAAAATA
27674963 TTAATATTT
1 TTAATATTT
27674972 CAAATAAATG
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
80 73 1.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (80 bp):
TTAATATTTTAATATTTTAAAAAAGAAAATAGAGATAAAATAAAAATAAATAACCACATTAAAAG
TTTAATTACAAAATA
Found at i:27675068 original size:126 final size:123
Alignment explanation
Indices: 27674926--27675243 Score: 372
Period size: 126 Copynumber: 2.6 Consensus size: 123
27674916 GATAAGATAA
* * * *
27674926 AAATAAATAACCATATTAAAATTTTAATTACAAAATATTAATATTTCAAA-TAAATGATAATTTT
1 AAATAAATAATCATATTAAAATTTTAATTATAAATTATTAATATTTCAAATTAAATGATAAATTT
* * * * * *
27674990 TTGATATTTAAATATTTTAAAAAATGAAATAATGTGATAAAATAAAATAAAAATATAAACAT
66 ATAATAGTTAAACATTTT-AAAAATGAAAT-AGGTGATAAAATAAAAT-AAAATA-AAACAG
* * * *
27675052 AAATAAATAGTCATATTAAATTTTTAATTATAAATTATTAATATTTTAAATTAAGTGATAAATTT
1 AAATAAATAATCATATTAAAATTTTAATTATAAATTATTAATATTTCAAATTAAATGATAAATTT
* * *
27675117 ATAATAGTTAAACATTTTAAAAATGAAATCGGTGATAAAATAAAATGAAATAAAATAG
66 ATAATAGTTAAACATTTTAAAAATGAAATAGGTGATAAAATAAAATAAAATAAAACAG
** * * * *
27675175 AAATAAATAATCATATTAAAGGTTTAATTATAAATTAATAATA-TT-AAACTAAATTATAAATAT
1 AAATAAATAATCATATTAAAATTTTAATTATAAATTATTAATATTTCAAATTAAATGATAAATTT
27675238 ATAATA
66 ATAATA
27675244 TTTTAAAAAT
Statistics
Matches: 166, Mismatches: 25, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
121 20 0.12
122 2 0.01
123 43 0.26
124 5 0.03
125 15 0.09
126 55 0.33
127 26 0.16
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.37
Consensus pattern (123 bp):
AAATAAATAATCATATTAAAATTTTAATTATAAATTATTAATATTTCAAATTAAATGATAAATTT
ATAATAGTTAAACATTTTAAAAATGAAATAGGTGATAAAATAAAATAAAATAAAACAG
Found at i:27675171 original size:15 final size:15
Alignment explanation
Indices: 27675151--27675184 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
27675141 GAAATCGGTG
27675151 ATAAAATA-AAATGAA
1 ATAAAATAGAAAT-AA
27675166 ATAAAATAGAAATAA
1 ATAAAATAGAAATAA
27675181 ATAA
1 ATAA
27675185 TCATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (15 bp):
ATAAAATAGAAATAA
Found at i:27689261 original size:45 final size:45
Alignment explanation
Indices: 27689197--27689356 Score: 232
Period size: 45 Copynumber: 3.6 Consensus size: 45
27689187 CTTAATGAAC
* * * *
27689197 TTACACGCCATATACAAAAACATGTTACACGCTATGGTTAGGTTA
1 TTACACGCCATGTACAAAAACATGTGACACGCTATGGTTAGATTG
* *
27689242 TTACACGCCATGTATAAAAACATGTGACAC-ATCATGGTTAGATTG
1 TTACACGCCATGTACAAAAACATGTGACACGCT-ATGGTTAGATTG
27689287 TTACACGCCATGTACAAAAACATGTGACACGCTATGGTTAGATTG
1 TTACACGCCATGTACAAAAACATGTGACACGCTATGGTTAGATTG
* *
27689332 TTATACGCCATGTATAAAAACATGT
1 TTACACGCCATGTACAAAAACATGT
27689357 TACATGCCAT
Statistics
Matches: 103, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
44 1 0.01
45 101 0.98
46 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (45 bp):
TTACACGCCATGTACAAAAACATGTGACACGCTATGGTTAGATTG
Found at i:27689316 original size:24 final size:24
Alignment explanation
Indices: 27689285--27689391 Score: 87
Period size: 24 Copynumber: 4.6 Consensus size: 24
27689275 ATGGTTAGAT
27689285 TGTTACACGCCATGTACAAAAACA
1 TGTTACACGCCATGTACAAAAACA
* * * * *
27689309 TGTGACACGCTATGGT---TAGA-T
1 TGTTACACGCCAT-GTACAAAAACA
* *
27689330 TGTTATACGCCATGTATAAAAACA
1 TGTTACACGCCATGTACAAAAACA
*
27689354 TGTTACATGCCATGTACAAAAACA
1 TGTTACACGCCATGTACAAAAACA
* *
27689378 TGTAACACGTCATG
1 TGTTACACGCCATG
27689392 GTTAGGTTGT
Statistics
Matches: 61, Mismatches: 17, Indels: 10
0.69 0.19 0.11
Matches are distributed among these distances:
20 2 0.03
21 10 0.16
22 2 0.03
23 2 0.03
24 43 0.70
25 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (24 bp):
TGTTACACGCCATGTACAAAAACA
Found at i:27689372 original size:69 final size:69
Alignment explanation
Indices: 27689285--27689436 Score: 216
Period size: 69 Copynumber: 2.2 Consensus size: 69
27689275 ATGGTTAGAT
* * *
27689285 TGTTACACGCCATGTACAAAAACATGTGACACG-CTATGGTTAGATTGTTATACGCCATGTATAA
1 TGTTACACGCCATGTACAAAAACATGTAACACGTC-ATGGTTAGATTGTTACACGCCATGTACAA
27689349 AAACA
65 AAACA
* * *
27689354 TGTTACATGCCATGTACAAAAACATGTAACACGTCATGGTTAGGTTGTTACACGTCATGTACAAA
1 TGTTACACGCCATGTACAAAAACATGTAACACGTCATGGTTAGATTGTTACACGCCATGTACAAA
27689419 AACA
66 AACA
* *
27689423 TATGACACGCCATG
1 TGTTACACGCCATG
27689437 GTTAGGTTGT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
69 72 0.99
70 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (69 bp):
TGTTACACGCCATGTACAAAAACATGTAACACGTCATGGTTAGATTGTTACACGCCATGTACAAA
AACA
Found at i:27689402 original size:114 final size:114
Alignment explanation
Indices: 27689242--27689468 Score: 355
Period size: 114 Copynumber: 2.0 Consensus size: 114
27689232 GGTTAGGTTA
* *
27689242 TTACACGCCATGTATAAAAACATGTGACACATCATGGTTAGATTGTTACACGCCATGTACAAAAA
1 TTACACGCCATGTACAAAAACATGTAACACATCATGGTTAGATTGTTACACGCCATGTACAAAAA
* * *
27689307 CATGTGACACGCTATGGTTAGATTGTTATACGCCATGTATAAAAACATG
66 CATATGACACGCCATGGTTAGATTGTTACACGCCATGTATAAAAACATG
* * * *
27689356 TTACATGCCATGTACAAAAACATGTAACACGTCATGGTTAGGTTGTTACACGTCATGTACAAAAA
1 TTACACGCCATGTACAAAAACATGTAACACATCATGGTTAGATTGTTACACGCCATGTACAAAAA
* *
27689421 CATATGACACGCCATGGTTAGGTTGTTACACGTCATGTATAAAAACAT
66 CATATGACACGCCATGGTTAGATTGTTACACGCCATGTATAAAAACAT
27689469 TTTATACGTC
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (114 bp):
TTACACGCCATGTACAAAAACATGTAACACATCATGGTTAGATTGTTACACGCCATGTACAAAAA
CATATGACACGCCATGGTTAGATTGTTACACGCCATGTATAAAAACATG
Found at i:27689418 original size:45 final size:45
Alignment explanation
Indices: 27689354--27689468 Score: 176
Period size: 45 Copynumber: 2.6 Consensus size: 45
27689344 TATAAAAACA
* * * *
27689354 TGTTACATGCCATGTACAAAAACATGTAACACGTCATGGTTAGGT
1 TGTTACACGTCATGTACAAAAACATATAACACGCCATGGTTAGGT
*
27689399 TGTTACACGTCATGTACAAAAACATATGACACGCCATGGTTAGGT
1 TGTTACACGTCATGTACAAAAACATATAACACGCCATGGTTAGGT
*
27689444 TGTTACACGTCATGTATAAAAACAT
1 TGTTACACGTCATGTACAAAAACAT
27689469 TTTATACGTC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (45 bp):
TGTTACACGTCATGTACAAAAACATATAACACGCCATGGTTAGGT
Found at i:27690225 original size:1 final size:1
Alignment explanation
Indices: 27690221--27690255 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
27690211 AAAACATCAT
27690221 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
27690256 TAAGCTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:27691848 original size:14 final size:14
Alignment explanation
Indices: 27691824--27691867 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
27691814 NNNNNNATAA
27691824 AAAATATAATAAAAT
1 AAAA-ATAATAAAAT
*
27691839 AAAAATAAT-AATT
1 AAAAATAATAAAAT
27691852 AAATAATAATAAAAT
1 AAA-AATAATAAAAT
27691867 A
1 A
27691868 CTAAAAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 6 0.24
14 11 0.44
15 8 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAATAATAAAAT
Found at i:27691862 original size:17 final size:17
Alignment explanation
Indices: 27691823--27691867 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
27691813 NNNNNNNATA
27691823 AAAAAT-ATAATAAAAT
1 AAAAATAATAATAAAAT
*
27691839 AAAAATAATAATTAAAT
1 AAAAATAATAATAAAAT
*
27691856 AATAATAA-AATA
1 AAAAATAATAATA
27691868 CTAAAAATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATAATAATAAAAT
Found at i:27699242 original size:19 final size:20
Alignment explanation
Indices: 27699213--27699252 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
27699203 TCACTTCTAA
27699213 ACTTCAAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
27699233 ACTT-AAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
27699252 A
1 A
27699253 AGTCAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (20 bp):
ACTTCAAATCATACTCCAAT
Found at i:27705611 original size:32 final size:32
Alignment explanation
Indices: 27705551--27705611 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
27705541 ATATTTTACG
* **
27705551 TAAAAAAAAACGAAAAAATGAATTAAAAAATA
1 TAAAAAAAAACGAAAAAAAGAAAAAAAAAATA
27705583 TAAAAAAAAA-GAGAAAAAAGAAAAAAAAA
1 TAAAAAAAAACGA-AAAAAAGAAAAAAAAA
27705612 TTTTCAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 2 0.08
32 23 0.92
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.10
Consensus pattern (32 bp):
TAAAAAAAAACGAAAAAAAGAAAAAAAAAATA
Found at i:27706526 original size:38 final size:38
Alignment explanation
Indices: 27706483--27706937 Score: 462
Period size: 38 Copynumber: 12.0 Consensus size: 38
27706473 AAAAGAAAAA
* * * *
27706483 AAAAGTTTCGTTACCTCAGTTTTCAAGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
** *
27706521 AAAAGTTTCGTTGCCTCAATTTTGAGGAGTTTATTTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
* *
27706559 -AAAGTTTCATTGCCTCAGCTTTGAGGAGTTTATTTTTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCA--TTTTT
** * *
27706598 AAAA-TTCTCGTTGCCTTTGTTTTGAAGAGTTCA-TTTT
1 AAAAGTT-TCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
* * *
27706635 AAAAGTCTCGTTGCCTCAGCTTTGGGGAGTTTTATTTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAG-TTCATTTTT
* * **
27706674 -AAAGTTTCATTGTCTCAATTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
* *
27706711 AAAAATCTT-GTTGCCTTAGCTTTGAGGAGTTCATTTTTTT
1 AAAAGT-TTCGTTGCCTCAGCTTTGAGGAGTTCA--TTTTT
*
27706751 AAAAGTTTCG-TGTCCTCAGTTTTGAGGAGTTCA-TTTT
1 AAAAGTTTCGTTG-CCTCAGCTTTGAGGAGTTCATTTTT
* *
27706788 AAAAGTCTCGTTGCCTCAGCTTTGAGGAGTTTTATTTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAG-TTCATTTTT
* * **
27706827 -AAAGTTTCATTACCTCAATTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
* * *
27706864 --CAGTTTCGTTGCCTTAACTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
*
27706900 AGAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
27706938 TTAAGTTNNN
Statistics
Matches: 345, Mismatches: 54, Indels: 36
0.79 0.12 0.08
Matches are distributed among these distances:
36 31 0.09
37 98 0.28
38 143 0.41
39 21 0.06
40 52 0.15
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (38 bp):
AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
Found at i:27706628 original size:77 final size:76
Alignment explanation
Indices: 27706484--27706937 Score: 467
Period size: 77 Copynumber: 6.0 Consensus size: 76
27706474 AAAGAAAAAA
* * * * *
27706484 AAAGTTTCGTTACCTCAGTTTTCAAGAGTTCA--TTTTTAAAAGTTTCGTTGCCTCAATTTTGAG
1 AAAGTTTCGTTGCCTCAGCTTTGAGGAGTTTATTTTTTTAAAA-TTTCGTTGCCTCAATTTTGAG
*
27706547 GAGTTTATTTTT
65 GAGTTCATTTTT
* *** *
27706559 AAAGTTTCATTGCCTCAGCTTTGAGGAGTTTATTTTTTTAAAATTCTCGTTGCCTTTGTTTTGAA
1 AAAGTTTCGTTGCCTCAGCTTTGAGGAGTTTATTTTTTTAAAATT-TCGTTGCCTCAATTTTGAG
*
27706624 GAGTTCATTTTA
65 GAGTTCATTTTT
* * * * * *
27706636 AAAGTCTCGTTGCCTCAGCTTTGGGGAGTTT-TATTTTTAAAGTTTCATTGTCTCAATTTTGAGG
1 AAAGTTTCGTTGCCTCAGCTTTGAGGAGTTTATTTTTTTAAAATTTCGTTGCCTCAATTTTGAGG
27706700 AGTTCATTTTT
66 AGTTCATTTTT
* * * *
27706711 AAAAATCTT-GTTGCCTTAGCTTTGAGGAGTTCATTTTTTTAAAAGTTTCG-TGTCCTCAGTTTT
1 -AAAGT-TTCGTTGCCTCAGCTTTGAGGAGTTTATTTTTTTAAAA-TTTCGTTG-CCTCAATTTT
*
27706774 GAGGAGTTCATTTTA
62 GAGGAGTTCATTTTT
* * * * *
27706789 AAAGTCTCGTTGCCTCAGCTTTGAGGAGTTT-TATTTTTAAAGTTTCATTACCTCAATTTTGAGG
1 AAAGTTTCGTTGCCTCAGCTTTGAGGAGTTTATTTTTTTAAAATTTCGTTGCCTCAATTTTGAGG
27706853 AGTTCATTTTT
66 AGTTCATTTTT
* * * * * **
27706864 -CAGTTTCGTTGCCTTAACTTTGAGGAGTTCA--TTTTTAGAAGTTTCGTTGCCTCAGCTTTGAG
1 AAAGTTTCGTTGCCTCAGCTTTGAGGAGTTTATTTTTTTA-AAATTTCGTTGCCTCAATTTTGAG
27706926 GAGTTCATTTTT
65 GAGTTCATTTTT
27706938 TTAAGTTNNN
Statistics
Matches: 313, Mismatches: 54, Indels: 25
0.80 0.14 0.06
Matches are distributed among these distances:
73 6 0.02
74 57 0.18
75 77 0.25
76 48 0.15
77 99 0.32
78 26 0.08
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (76 bp):
AAAGTTTCGTTGCCTCAGCTTTGAGGAGTTTATTTTTTTAAAATTTCGTTGCCTCAATTTTGAGG
AGTTCATTTTT
Found at i:27706697 original size:115 final size:115
Alignment explanation
Indices: 27706490--27706941 Score: 499
Period size: 115 Copynumber: 4.0 Consensus size: 115
27706480 AAAAAAAGTT
* * * * *
27706490 TCGTTACCTCAGTTTTCAAGAGTTCATTTTTAAAAGTTTCGTTGCCTCAATTTTGAGGAGTTTAT
1 TCGTTGCCTTAGTTTTGAAGAGTTCATTTTTAAAAGTTTCGTTGCCTCAACTTTGAGGAGTTCAT
*
27706555 TTTTAAAGTTTCATTGCCTCAGCTTTGAGGAGTTTATTTTTTTAAAATTC
66 TTTTAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTTTTAAAATTC
* * * * *
27706605 TCGTTGCCTTTGTTTTGAAGAGTTCA-TTTTAAAAGTCTCGTTGCCTCAGCTTTGGGGAGTTTTA
1 TCGTTGCCTTAGTTTTGAAGAGTTCATTTTTAAAAGTTTCGTTGCCTCAACTTTGAGGAG-TTCA
* ** *
27706669 TTTTTAAAGTTTCATTGTCTCAATTTTGAGGAGTTCA--TTTTTAAAAATC
65 TTTTTAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTTTTAAAATTC
* * * **
27706718 TTGTTGCCTTAGCTTTGAGGAGTTCATTTTTTTAAAAGTTTCG-TGTCCTCAGTTTTGAGGAGTT
1 TCGTTGCCTTAGTTTTGAAGAGTTCA--TTTTTAAAAGTTTCGTTG-CCTCAACTTTGAGGAGTT
* * * *
27706782 CATTTTAAAAGTCTCGTTGCCTCAGCTTTGAGGAGTT--TTATTTTTAAAGTT-
63 CATTTTTAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATT-TTTTTAAAATTC
* * * * * * *
27706833 TCATTACCTCAATTTTGAGGAGTTCATTTTT--CAGTTTCGTTGCCTTAACTTTGAGGAGTTCAT
1 TCGTTGCCTTAGTTTTGAAGAGTTCATTTTTAAAAGTTTCGTTGCCTCAACTTTGAGGAGTTCAT
*
27706896 TTTTAGAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTTTAA
66 TTTTA-AAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTTTTAA
27706942 GTTNNNNNNN
Statistics
Matches: 284, Mismatches: 41, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
111 29 0.10
112 30 0.11
113 45 0.16
114 31 0.11
115 113 0.40
116 36 0.13
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.46
Consensus pattern (115 bp):
TCGTTGCCTTAGTTTTGAAGAGTTCATTTTTAAAAGTTTCGTTGCCTCAACTTTGAGGAGTTCAT
TTTTAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTTTTAAAATTC
Found at i:27706790 original size:153 final size:152
Alignment explanation
Indices: 27706483--27706936 Score: 616
Period size: 153 Copynumber: 3.0 Consensus size: 152
27706473 AAAAGAAAAA
* * * * * * *
27706483 AAAAGTTTCGTTACCTCAGTTTTCAAGAG-TTCATTTTTAAAAGTTTCGTTGCCTCAATTTTGAG
1 AAAAGTCTCGTTGCCTCAGCTTTGAGGAGTTTTATTTTT-AAAGTTTCATTGCCTCAATTTTGAG
* * * *
27706547 GAGTTTATTTTTAAAGTTTCATTGCCTCAGCTTTGAGGAGTTTATTTTTTTAAAA-TTCTCGTTG
65 GAGTTCATTTTTAAAGTTTCGTTGCCTTAGCTTTGAGGAGTTCATTTTTTTAAAAGTT-TCGTTG
** *
27706611 CCTTTGTTTTGAAGAGTTCATTTT
129 CCTCAGTTTTGAGGAGTTCATTTT
* *
27706635 AAAAGTCTCGTTGCCTCAGCTTTGGGGAGTTTTATTTTTAAAGTTTCATTGTCTCAATTTTGAGG
1 AAAAGTCTCGTTGCCTCAGCTTTGAGGAGTTTTATTTTTAAAGTTTCATTGCCTCAATTTTGAGG
*
27706700 AGTTCATTTTTAAAAATCTT-GTTGCCTTAGCTTTGAGGAGTTCATTTTTTTAAAAGTTTCG-TG
66 AGTTCATTTTT-AAAGT-TTCGTTGCCTTAGCTTTGAGGAGTTCATTTTTTTAAAAGTTTCGTTG
27706763 TCCTCAGTTTTGAGGAGTTCATTTT
129 -CCTCAGTTTTGAGGAGTTCATTTT
*
27706788 AAAAGTCTCGTTGCCTCAGCTTTGAGGAGTTTTATTTTTAAAGTTTCATTACCTCAATTTTGAGG
1 AAAAGTCTCGTTGCCTCAGCTTTGAGGAGTTTTATTTTTAAAGTTTCATTGCCTCAATTTTGAGG
* * *
27706853 AGTTCATTTTT-CAGTTTCGTTGCCTTAACTTTGAGGAGTTCA--TTTTTAGAAGTTTCGTTGCC
66 AGTTCATTTTTAAAGTTTCGTTGCCTTAGCTTTGAGGAGTTCATTTTTTTAAAAGTTTCGTTGCC
*
27706915 TCAGCTTTGAGGAGTTCATTTT
131 TCAGTTTTGAGGAGTTCATTTT
27706937 TTTAAGTTNN
Statistics
Matches: 270, Mismatches: 25, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
149 37 0.14
150 4 0.01
151 25 0.09
152 59 0.22
153 141 0.52
154 4 0.01
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (152 bp):
AAAAGTCTCGTTGCCTCAGCTTTGAGGAGTTTTATTTTTAAAGTTTCATTGCCTCAATTTTGAGG
AGTTCATTTTTAAAGTTTCGTTGCCTTAGCTTTGAGGAGTTCATTTTTTTAAAAGTTTCGTTGCC
TCAGTTTTGAGGAGTTCATTTT
Found at i:27712382 original size:26 final size:26
Alignment explanation
Indices: 27712348--27712397 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
27712338 TAAAAGACGA
* *
27712348 TTAATATGATTAATACGATTAAATTT
1 TTAAGATGATTAACACGATTAAATTT
*
27712374 TTAAGATGATTAACATGATTAAAT
1 TTAAGATGATTAACACGATTAAAT
27712398 AATTTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (26 bp):
TTAAGATGATTAACACGATTAAATTT
Found at i:27738975 original size:3 final size:3
Alignment explanation
Indices: 27738967--27738993 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27738957 CAGCAACTTG
27738967 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
27738994 CTTTCACGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:27739824 original size:43 final size:44
Alignment explanation
Indices: 27739771--27739868 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 44
27739761 ACTATGTGCA
* * **
27739771 AGTAGAGAGTGCCA-ATAAGCCAAG-GATGACCCGGTTATGTGTG
1 AGTAGGGAGTGCCATATAA-CCAAGTGATGACCCAGCCATGTGTG
* *
27739814 AGTAGGGAGTG-CATATAACCCAGTGATGACCTAGCCATGTGTG
1 AGTAGGGAGTGCCATATAACCAAGTGATGACCCAGCCATGTGTG
27739857 AGTAGGGAGTGC
1 AGTAGGGAGTGC
27739869 ACATGAGCTG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
42 6 0.13
43 40 0.87
ACGTcount: A:0.29, C:0.16, G:0.34, T:0.21
Consensus pattern (44 bp):
AGTAGGGAGTGCCATATAACCAAGTGATGACCCAGCCATGTGTG
Found at i:27740309 original size:50 final size:48
Alignment explanation
Indices: 27740247--27740344 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 48
27740237 CTTCTCGCTG
* * *
27740247 CAGCGAGAAACTTTCTGTTTTCTAGGTTGCAATTTCGCTGTAGCGAGATT
1 CAGCGAGAAACTTTCTG-TTTCTAGGTTACAA-TTCGCTGCAACGAGATT
27740297 CAGCGAGAAACTTTCTGTTTCTAGGTTACAATTCGCTGCAACGAGATT
1 CAGCGAGAAACTTTCTGTTTCTAGGTTACAATTCGCTGCAACGAGATT
27740345 GAATCTCGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 15 0.33
49 13 0.29
50 17 0.38
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (48 bp):
CAGCGAGAAACTTTCTGTTTCTAGGTTACAATTCGCTGCAACGAGATT
Found at i:27743909 original size:26 final size:27
Alignment explanation
Indices: 27743871--27743924 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
27743861 TTATGTATTT
*
27743871 TATTTTTAAAAGCATAAATATTTTATA
1 TATTTTTAAAAGCATAAACATTTTATA
* *
27743898 TATTTTT-GAAGCATGAACATTTTATA
1 TATTTTTAAAAGCATAAACATTTTATA
27743924 T
1 T
27743925 TTCTACTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (27 bp):
TATTTTTAAAAGCATAAACATTTTATA
Found at i:27759258 original size:20 final size:20
Alignment explanation
Indices: 27759173--27759259 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
27759163 GGTGTTTTAA
27759173 TTATTTTA--TTAGTT-TAGT
1 TTATTTTATGTTAGTTAT-GT
*
27759191 TTATTATATGTT--TTAATGT
1 TTATTTTATGTTAGTT-ATGT
* * *
27759210 TTATTTTAAGTTAATAATG-
1 TTATTTTATGTTAGTTATGT
27759229 TTAGTTTTATGTTAGTTATGT
1 TTA-TTTTATGTTAGTTATGT
27759250 TTATTTTATG
1 TTATTTTATG
27759260 ATTTTATAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
18 9 0.17
19 15 0.28
20 26 0.48
21 4 0.07
ACGTcount: A:0.25, C:0.00, G:0.13, T:0.62
Consensus pattern (20 bp):
TTATTTTATGTTAGTTATGT
Found at i:27760376 original size:14 final size:15
Alignment explanation
Indices: 27760357--27760390 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
27760347 TTATTGCTTT
*
27760357 GATTTTT-TTAGTTA
1 GATTTTTGTTAATTA
27760371 GATTTTTGTTAATTA
1 GATTTTTGTTAATTA
27760386 GATTT
1 GATTT
27760391 AGTTAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (15 bp):
GATTTTTGTTAATTA
Found at i:27760393 original size:25 final size:26
Alignment explanation
Indices: 27760363--27760412 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
27760353 CTTTGATTTT
27760363 TTTAGTTAGATTTTT-GTT-AATTAGA
1 TTTAGTTAG-TTTTTAGTTGAATTAGA
27760388 TTTAGTTAGTTTTTAGTTGAATTAG
1 TTTAGTTAGTTTTTAGTTGAATTAG
27760413 TTATTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.22
25 12 0.52
26 6 0.26
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (26 bp):
TTTAGTTAGTTTTTAGTTGAATTAGA
Found at i:27773127 original size:73 final size:74
Alignment explanation
Indices: 27773050--27773247 Score: 240
Period size: 73 Copynumber: 2.7 Consensus size: 74
27773040 TGGCCAGTTG
* ** *
27773050 AGAAACAAAGATGACTTAATCGACTAAGAAGCATTTTTAGTCGACTAAGAGCC-TACTACCAGAA
1 AGAAACAGAGATGACTTAATCGACTAAGAAGCATAATTAGTCGACTAAGAGCCTTACTACCAAAA
*
27773114 ATTAGG-TTA
66 ACT-GGATTA
** * * *
27773123 AGAAACAGAGACAACTTAATCGACTAAGAAGCATAGTTAGTCAACTAAGA-CCTTACTGCCAAAA
1 AGAAACAGAGATGACTTAATCGACTAAGAAGCATAATTAGTCGACTAAGAGCCTTACTACCAAAA
*
27773187 ACTGGATTT
66 ACTGGATTA
* * *
27773196 AGAGATAGAGATGACTTAATCGACTAAGAAGCATAATTAGTTGACTAAGAGC
1 AGAAACAGAGATGACTTAATCGACTAAGAAGCATAATTAGTCGACTAAGAGC
27773248 ATTCTGTCTA
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
72 4 0.04
73 100 0.95
74 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (74 bp):
AGAAACAGAGATGACTTAATCGACTAAGAAGCATAATTAGTCGACTAAGAGCCTTACTACCAAAA
ACTGGATTA
Found at i:27776596 original size:20 final size:20
Alignment explanation
Indices: 27776571--27776610 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
27776561 GGAGATGAGT
27776571 TTGAAAACTTCTGTAATGAA
1 TTGAAAACTTCTGTAATGAA
*
27776591 TTGAAAACTTTTGTAATGAA
1 TTGAAAACTTCTGTAATGAA
27776611 AAGGGGTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (20 bp):
TTGAAAACTTCTGTAATGAA
Found at i:27781636 original size:73 final size:73
Alignment explanation
Indices: 27781552--27781741 Score: 254
Period size: 73 Copynumber: 2.6 Consensus size: 73
27781542 TCAAAAACAG
* * * * * * *
27781552 AGACGACTTAATTGACTAAGAAGTATTGTTAGTCGACTAAGAGCCTACTGCCAGAAATTGGGTTC
1 AGACGACTTAATCGACTAAGAAGCATAGTTAGTCGACTAAGAGCCTACTACCAAAAACTGGATTC
27781617 AGAGACAA
66 AGAGACAA
* * * * * *
27781625 AGACAACTTAATCGATTAAAAAGCATAGTTAATCAACTAAGAGCTTACTACCAAAAACTGGATTC
1 AGACGACTTAATCGACTAAGAAGCATAGTTAGTCGACTAAGAGCCTACTACCAAAAACTGGATTC
27781690 AGAGACAA
66 AGAGACAA
*
27781698 AGACGACTTAATCGACTAAGAAGCATAGTTAGTTGACTAAGAGC
1 AGACGACTTAATCGACTAAGAAGCATAGTTAGTCGACTAAGAGC
27781742 ATTTTGTCTA
Statistics
Matches: 98, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 98 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (73 bp):
AGACGACTTAATCGACTAAGAAGCATAGTTAGTCGACTAAGAGCCTACTACCAAAAACTGGATTC
AGAGACAA
Found at i:27785206 original size:90 final size:90
Alignment explanation
Indices: 27785045--27785218 Score: 215
Period size: 90 Copynumber: 1.9 Consensus size: 90
27785035 ACGTTTTAGA
* * * * * **
27785045 ATTATTTTGTTTTTATCATCTTCAAGTTTCAAAAGGATTTCAATGATTGGGTTTTGATCAATGGT
1 ATTATTTTGTTTTCATCATCTCCAAGTTGCAAAAGGATTTCAATAATTGGGTTTTAATCAATAAT
*
27785110 TTTAGCAAATCAGGCAAGTAATGGT
66 TGTAGCAAATCAGGCAAGTAATGGT
* ***
27785135 ATTATTTTGTTTTCATCATCTCCAAGTTGGAAAAGGATTTCAATAATT-GGTCTTTAATTTCTAA
1 ATTATTTTGTTTTCATCATCTCCAAGTTGCAAAAGGATTTCAATAATTGGGT-TTTAATCAATAA
*
27785199 TTGTAGCAAATCAGGTAAGT
65 TTGTAGCAAATCAGGCAAGT
27785219 GACTTGATAT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
89 3 0.04
90 67 0.96
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (90 bp):
ATTATTTTGTTTTCATCATCTCCAAGTTGCAAAAGGATTTCAATAATTGGGTTTTAATCAATAAT
TGTAGCAAATCAGGCAAGTAATGGT
Found at i:27785726 original size:73 final size:73
Alignment explanation
Indices: 27785607--27785752 Score: 229
Period size: 73 Copynumber: 2.0 Consensus size: 73
27785597 GATGGATAAT
* *
27785607 TGTCAAGCCCAGCTCTACAATATGTTTATTATGCCATTCCTACATAAGAATGCATATTTGCTTAC
1 TGTCAAGCCCAACTCTACAATATGTTTATTATGCCATTCCTACATAAGAATGCATATTTGCTAAC
27785672 TTGAGTAC
66 TTGAGTAC
* * * *
27785680 TGTCAAGCCCAACTCTGCAATATGTTTATTATGTCATTCTTACATAAGAATGCATGTTTGCTAAC
1 TGTCAAGCCCAACTCTACAATATGTTTATTATGCCATTCCTACATAAGAATGCATATTTGCTAAC
*
27785745 TTGGGTAC
66 TTGAGTAC
27785753 CTCAGAAATC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (73 bp):
TGTCAAGCCCAACTCTACAATATGTTTATTATGCCATTCCTACATAAGAATGCATATTTGCTAAC
TTGAGTAC
Found at i:27792588 original size:25 final size:25
Alignment explanation
Indices: 27792560--27792648 Score: 108
Period size: 25 Copynumber: 3.5 Consensus size: 25
27792550 GAGTCGTGAC
27792560 AATAATTTTACCATCAGAATCTAAG
1 AATAATTTTACCATCAGAATCTAAG
* *
27792585 AATAATTTTACCACCAGAAGT-TGATG
1 AATAATTTTACCATCAGAA-TCT-AAG
* * *
27792611 GATAATTATACCATCATAATCTAAG
1 AATAATTTTACCATCAGAATCTAAG
27792636 AATAATTTTACCA
1 AATAATTTTACCA
27792649 CTAGAAGTGA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
25 33 0.63
26 19 0.37
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.33
Consensus pattern (25 bp):
AATAATTTTACCATCAGAATCTAAG
Found at i:27792622 original size:26 final size:26
Alignment explanation
Indices: 27792561--27792674 Score: 85
Period size: 25 Copynumber: 4.5 Consensus size: 26
27792551 AGTCGTGACA
* * *
27792561 ATAATTTTACCATCAGAA-TCT-AAGA
1 ATAATTTTACCACCAGAAGT-TGATGG
27792586 ATAATTTTACCACCAGAAGTTGATGG
1 ATAATTTTACCACCAGAAGTTGATGG
* * * * *
27792612 ATAATTATACCATCATAA-TCT-AAGA
1 ATAATTTTACCACCAGAAGT-TGATGG
*
27792637 ATAATTTTACCACTAGAAG-TGAATGG
1 ATAATTTTACCACCAGAAGTTG-ATGG
27792663 ATAATTTTACCA
1 ATAATTTTACCA
27792675 TCAAAAGTGG
Statistics
Matches: 69, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
24 1 0.01
25 35 0.51
26 33 0.48
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (26 bp):
ATAATTTTACCACCAGAAGTTGATGG
Found at i:27792637 original size:51 final size:51
Alignment explanation
Indices: 27792561--27792677 Score: 191
Period size: 51 Copynumber: 2.3 Consensus size: 51
27792551 AGTCGTGACA
27792561 ATAATTTTACCATCAGAATCTAAGAATAATTTTACCACCAGAAGTTG-ATGG
1 ATAATTTTACCATCAGAATCTAAGAATAATTTTACCACCAGAAG-TGAATGG
* * *
27792612 ATAATTATACCATCATAATCTAAGAATAATTTTACCACTAGAAGTGAATGG
1 ATAATTTTACCATCAGAATCTAAGAATAATTTTACCACCAGAAGTGAATGG
27792663 ATAATTTTACCATCA
1 ATAATTTTACCATCA
27792678 AAAGTGGATG
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 2 0.03
51 59 0.97
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (51 bp):
ATAATTTTACCATCAGAATCTAAGAATAATTTTACCACCAGAAGTGAATGG
Found at i:27792682 original size:26 final size:25
Alignment explanation
Indices: 27792560--27792683 Score: 101
Period size: 26 Copynumber: 4.9 Consensus size: 25
27792550 GAGTCGTGAC
*
27792560 AATAATTTTACCATCAGAA-TCTAAG
1 AATAATTTTACCATCAGAAGT-GAAG
* *
27792585 AATAATTTTACCACCAGAAGTTGATG
1 AATAATTTTACCATCAGAAG-TGAAG
* * * *
27792611 GATAATTATACCATCATAA-TCTAAG
1 AATAATTTTACCATCAGAAGT-GAAG
27792636 AATAATTTTACCA-CTAGAAGTGAATG
1 AATAATTTTACCATC-AGAAGTGAA-G
* *
27792662 GATAATTTTACCATCAAAAGTG
1 AATAATTTTACCATCAGAAGTG
27792684 GATGAATGCC
Statistics
Matches: 77, Mismatches: 15, Indels: 13
0.73 0.14 0.12
Matches are distributed among these distances:
24 2 0.03
25 36 0.47
26 37 0.48
27 2 0.03
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (25 bp):
AATAATTTTACCATCAGAAGTGAAG
Found at i:27792771 original size:18 final size:18
Alignment explanation
Indices: 27792730--27792772 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
27792720 ATAATATACT
*
27792730 AAAAGTGGATAACCAATC
1 AAAAGTGGATAACCAACC
* * *
27792748 ATAAGTGGATCACCCACC
1 AAAAGTGGATAACCAACC
27792766 AAAAGTG
1 AAAAGTG
27792773 AACGGATACT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (18 bp):
AAAAGTGGATAACCAACC
Found at i:27792809 original size:28 final size:28
Alignment explanation
Indices: 27792778--27792836 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
27792768 AAGTGAACGG
* *
27792778 ATACTTATAATCTAAAAAAAGTGGATGA
1 ATACTTATAACCCAAAAAAAGTGGATGA
* **
27792806 ATACTTTTAACCCACCAAAAGTGGATGA
1 ATACTTATAACCCAAAAAAAGTGGATGA
27792834 ATA
1 ATA
27792837 ATGAAAAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (28 bp):
ATACTTATAACCCAAAAAAAGTGGATGA
Found at i:27792855 original size:14 final size:15
Alignment explanation
Indices: 27792836--27792865 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
27792826 GTGGATGAAT
27792836 AATGAAAAG-ATAAA
1 AATGAAAAGAATAAA
27792850 AATGAAAAGAATAAA
1 AATGAAAAGAATAAA
27792865 A
1 A
27792866 GGAATATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AATGAAAAGAATAAA
Found at i:27797242 original size:23 final size:23
Alignment explanation
Indices: 27797214--27797257 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
27797204 TTCTTTATTC
27797214 TCTTTAATTGTT-TTTTCAAATTA
1 TCTTTAATTGTTCTTTT-AAATTA
*
27797237 TCTTTATTTGTTCTTTTAAAT
1 TCTTTAATTGTTCTTTTAAAT
27797258 GATATTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.23, C:0.09, G:0.05, T:0.64
Consensus pattern (23 bp):
TCTTTAATTGTTCTTTTAAATTA
Found at i:27797508 original size:24 final size:24
Alignment explanation
Indices: 27797478--27797530 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
27797468 TTATTATTTG
*
27797478 TAATATTTTAATATTAAATA-TAAA
1 TAATATTTTAATAATAAATAGT-AA
27797502 TAATATTTTAATAATAAATAGTAA
1 TAATATTTTAATAATAAATAGTAA
27797526 TAATA
1 TAATA
27797531 ATATATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TAATATTTTAATAATAAATAGTAA
Found at i:27801065 original size:17 final size:17
Alignment explanation
Indices: 27801045--27801090 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
27801035 ATTGGTCCAT
27801045 TTTTAAAACTTTAAAAA
1 TTTTAAAACTTTAAAAA
27801062 TTTTAAAACTTTAAAAA
1 TTTTAAAACTTTAAAAA
*
27801079 TTTTAAACCTTT
1 TTTTAAAACTTT
27801091 TATCTCCACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTTAAAACTTTAAAAA
Found at i:27801066 original size:9 final size:9
Alignment explanation
Indices: 27801043--27801085 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
27801033 CCATTGGTCC
*
27801043 ATTTTTAAA
1 ATTTTAAAA
*
27801052 ACTTTAAAA
1 ATTTTAAAA
27801061 ATTTT-AAA
1 ATTTTAAAA
*
27801069 ACTTTAAAA
1 ATTTTAAAA
27801078 ATTTTAAA
1 ATTTTAAA
27801086 CCTTTTATCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:27801748 original size:27 final size:27
Alignment explanation
Indices: 27801718--27801769 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
27801708 TTGTCATACA
*
27801718 TCATGTTCAAAAAAATGTTATTACACG
1 TCATGTTAAAAAAAATGTTATTACACG
*
27801745 TCATGTTAAAAAAAATGTTGTTACA
1 TCATGTTAAAAAAAATGTTATTACA
27801770 TGCCATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (27 bp):
TCATGTTAAAAAAAATGTTATTACACG
Found at i:27801780 original size:27 final size:27
Alignment explanation
Indices: 27801726--27801780 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
27801716 CATCATGTTC
* *
27801726 AAAAAAATGTTATTACACGTCATGTTA
1 AAAAAAATGTTATTACACGCCATATTA
* *
27801753 AAAAAAATGTTGTTACATGCCATATTA
1 AAAAAAATGTTATTACACGCCATATTA
27801780 A
1 A
27801781 GGTGTTTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (27 bp):
AAAAAAATGTTATTACACGCCATATTA
Found at i:27801904 original size:153 final size:153
Alignment explanation
Indices: 27801626--27801904 Score: 350
Period size: 153 Copynumber: 1.8 Consensus size: 153
27801616 TGTCATGTTG
* * *
27801626 AAGGTGTTTAATTCCTAGAGTTTATATGCTAATGAAATATAAAGATAGAGACAAAGTTACACGCC
1 AAGGTGTTTAACTCCAAGAGTTTATATGCTAATGAAATATAAAGATAGAGACAAAGTTAAACGCC
** * * * * *
27801691 TTGTTTAAAAAATAATATTGTCATACATCATGTTCAAAAAAATGTTATTACACGTCATGTTAAAA
66 ACGTTGAAAAAATAATATTGTCACACAGCATGTTAAAAAAAAAGTTATTACACGTCATGTTAAAA
27801756 AAAATGTTGTTACATGCCATATT
131 AAAATGTTGTTACATGCCATATT
* * *
27801779 AAGGTGTTTAACTCCAAGAGTTTATGT-CTTAGTGAAATATAAAGATAGAGATC-AAGTTAAATG
1 AAGGTGTTTAACTCCAAGAGTTTATATGC-TAATGAAATATAAAGATAGAGA-CAAAGTTAAACG
* * *
27801842 TCACGTTGAAAAAA-AA-ATTGTTACACAGCATGTTGGAAAAAAAAAGTTATTACACGTTATGTT
64 CCACGTTGAAAAAATAATATTGTCACACAGCATGTT--AAAAAAAAAGTTATTACACGTCATGTT
27801905 TAAAGTGTTT
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
151 15 0.14
152 3 0.03
153 87 0.82
154 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (153 bp):
AAGGTGTTTAACTCCAAGAGTTTATATGCTAATGAAATATAAAGATAGAGACAAAGTTAAACGCC
ACGTTGAAAAAATAATATTGTCACACAGCATGTTAAAAAAAAAGTTATTACACGTCATGTTAAAA
AAAATGTTGTTACATGCCATATT
Found at i:27802068 original size:125 final size:124
Alignment explanation
Indices: 27801726--27802078 Score: 388
Period size: 127 Copynumber: 2.8 Consensus size: 124
27801716 CATCATGTTC
* * * * * * **
27801726 AAAAAAATGTTATTACACGTCATGTTAAAAAAAATGTTGTTACATGCCATA-TTAAGGTGTTTAA
1 AAAAAAAAGTTGTTACACATCATGTTAAAAAAAA-ATTATTACACGTTATATTTAAGGTGTTTAA
* * * *
27801790 CTCCAAGAGTTTATGTCTTAGTGAAATATAAAGATAGAGATCAAGTTAAATGTCACGTTG
65 CTCCAAGAGTTTATGTCTTAGTGAAATACAAAGATAGAGATCAAGTTAAACGACACATTG
* * * *
27801850 AAAAAAAAATTGTTACACAGCATGTTGGAAAAAAAAAGTTATTACACGTTATGTTTAAAGTGTTT
1 AAAAAAAAGTTGTTACACATCATGTT--AAAAAAAAA-TTATTACACGTTATATTTAAGGTGTTT
* * * * * * *
27801915 AACTCCAATAATTTATGTTTTAATGAAATACAAAAATAGAGA-CTAAGTTACACGACATATTG
63 AACTCCAAGAGTTTATGTCTTAGTGAAATACAAAGATAGAGATC-AAGTTAAACGACACATTG
*
27801977 AAATAAAAGTTGTTACACATCATGTTAAAAAAAGAATTATTACACGTTATATTTAAGGTGTTTAA
1 AAAAAAAAGTTGTTACACATCATGTTAAAAAAA-AATTATTACACGTTATATTTAAGGTGTTTAA
* *
27802042 TTCTTAA-AGTTTATGTCTTAGTGAAATACAAAGATAG
65 CTC-CAAGAGTTTATGTCTTAGTGAAATACAAAGATAG
27802079 GAAATATGTT
Statistics
Matches: 188, Mismatches: 34, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
124 21 0.11
125 62 0.33
126 23 0.12
127 82 0.44
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (124 bp):
AAAAAAAAGTTGTTACACATCATGTTAAAAAAAAATTATTACACGTTATATTTAAGGTGTTTAAC
TCCAAGAGTTTATGTCTTAGTGAAATACAAAGATAGAGATCAAGTTAAACGACACATTG
Found at i:27802648 original size:10 final size:9
Alignment explanation
Indices: 27802619--27802654 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
27802609 ATAATTTTTT
27802619 AAAAAATAA
1 AAAAAATAA
**
27802628 TTAAAATAA
1 AAAAAATAA
27802637 AAAAAATAA
1 AAAAAATAA
27802646 AAAAAATAA
1 AAAAAATAA
27802655 TTTTATGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAAATAA
Found at i:27803786 original size:228 final size:227
Alignment explanation
Indices: 27803036--27803928 Score: 818
Period size: 228 Copynumber: 3.9 Consensus size: 227
27803026 CTCGTACAAG
* * *
27803036 ATGCAGATCTTCGTGAAAACCCTAACCGGCAAAACCATCACCCTCGAGGTGGAGAGCTCAGACAC
1 ATGCAGATCTTCGTGAAAACCCTAACCGG-AAAACCATCACTCTTGAGGTGGAGAGCTCTGACAC
* * * * * * *
27803101 CATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAAGGCATTCCTCCTGATCAACAGCGCTTGA
65 AATCGACAACGTCAAGGCCAAAATCCAAGACAAGGAAGGGATCCCTCCGGATCAACAGAGGTTGA
* * * *
27803166 TCTTCGCCGGCAAGCAACTT-GAAGACGGCCGAACCCTTGCGGATTACAATATCCAAAAGGAATC
130 TCTTCGCCGGCAAGC-AGTTGGAGGACGGCCGAACCCTTGCGGATTACAACATCCAGAAGGAATC
* * * * * * * *
27803230 GACTCTCCACCTGGTACTCCGTCTCCGTGGCGGC
194 AACCCTTCACCTTGTGCTCAGGCTCCGTGGAGGC
* * * * *
27803264 ATGCAGATCTTCGTCAAAACCCTAACCGGCAAGACCATCACTCTTGAAGTCGAAAGCTCTGACAC
1 ATGCAGATCTTCGTGAAAACCCTAACCGG-AAAACCATCACTCTTGAGGTGGAGAGCTCTGACAC
* * * * * *
27803329 GATCGACAACGTTAAGGCCAAGATCCAAGACAAGG-AGGGCATCCCTCCGGACCAACAGCGATTG
65 AATCGACAACGTCAAGGCCAAAATCCAAGACAAGGAAGGG-ATCCCTCCGGATCAACAGAGGTTG
* * * * * * *
27803393 ATCTTCGCTGGCAAGCAGCTCGAGGACGGCCGCACCCTGGCGGACTACAATATCCAGAAGGAATC
129 ATCTTCGCCGGCAAGCAGTTGGAGGACGGCCGAACCCTTGCGGATTACAACATCCAGAAGGAATC
* *
27803458 AACCCTTCACCTTGTGCTCAGGCTGCGCGGAGGC
194 AACCCTTCACCTTGTGCTCAGGCTCCGTGGAGGC
* * * * * * * * * * *
27803492 ATGCAGATTTTCGTTAAAACCTTGACCGGGAAAACTATTACTCTGGAGGTAGAGAGTTCGGATAC
1 ATGCAGATCTTCGTGAAAACCCTAACC-GGAAAACCATCACTCTTGAGGTGGAGAGCTCTGACAC
* * * * * *
27803557 AATTGATAACGTCAAGGCAAAAATCCAGGATAAGGAAGGGATCCCTCCGGATCAGCAGAGGTTGA
65 AATCGACAACGTCAAGGCCAAAATCCAAGACAAGGAAGGGATCCCTCCGGATCAACAGAGGTTGA
* * * * * *
27803622 TATTCGCCGGGAAGCAGTTGGAGGACGGCAGGACCCTTGCGGATTACAACATCCAGAAGGAGTCC
130 TCTTCGCCGGCAAGCAGTTGGAGGACGGCCGAACCCTTGCGGATTACAACATCCAGAAGGAATCA
* * *
27803687 ACTCTTCACCTTGTGCTGAGGCTCCGTGGAGGG
195 ACCCTTCACCTTGTGCTCAGGCTCCGTGGAGGC
* * * * * * * * *
27803720 ATGCAGATCTTCGTGAAGACGCTGACTGGAAAGACGATTACGCTTGAGGTGGAGAGTTCTGATAC
1 ATGCAGATCTTCGTGAAAACCCTAACCGGAAA-ACCATCACTCTTGAGGTGGAGAGCTCTGACAC
* * * * * * * * * * * *
27803785 AATCGATAACGTGAAGGCGAAAATTCAAGATAAGGAGGGGATTCCACCTGATCAGCAGAGGCTCA
65 AATCGACAACGTCAAGGCCAAAATCCAAGACAAGGAAGGGATCCCTCCGGATCAACAGAGGTTGA
* * * * * * * * * * *
27803850 TTTTCGCTGGGAAGCAATTGGAGGATGGGCGTACTCTTGCAGATTACAACATCCAGAAGGAGTCT
130 TCTTCGCCGGCAAGCAGTTGGAGGACGGCCGAACCCTTGCGGATTACAACATCCAGAAGGAATCA
27803915 ACCCTTCACCTTGT
195 ACCCTTCACCTTGT
27803929 CCTTCGGCTT
Statistics
Matches: 551, Mismatches: 109, Indels: 10
0.82 0.16 0.01
Matches are distributed among these distances:
227 10 0.02
228 535 0.97
229 6 0.01
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.20
Consensus pattern (227 bp):
ATGCAGATCTTCGTGAAAACCCTAACCGGAAAACCATCACTCTTGAGGTGGAGAGCTCTGACACA
ATCGACAACGTCAAGGCCAAAATCCAAGACAAGGAAGGGATCCCTCCGGATCAACAGAGGTTGAT
CTTCGCCGGCAAGCAGTTGGAGGACGGCCGAACCCTTGCGGATTACAACATCCAGAAGGAATCAA
CCCTTCACCTTGTGCTCAGGCTCCGTGGAGGC
Found at i:27805561 original size:32 final size:32
Alignment explanation
Indices: 27805524--27805596 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
27805514 CTGAAATCCA
27805524 TTTCCTTCTCTTTTGAATAACATGTTGATTTC
1 TTTCCTTCTCTTTTGAATAACATGTTGATTTC
*
27805556 TTTCCTTCTCTTTTGAATAACGTGTTGATTTC
1 TTTCCTTCTCTTTTGAATAACATGTTGATTTC
27805588 TTTCCTTCT
1 TTTCCTTCT
27805597 ATTTCTTCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.15, C:0.21, G:0.10, T:0.55
Consensus pattern (32 bp):
TTTCCTTCTCTTTTGAATAACATGTTGATTTC
Found at i:27826016 original size:33 final size:33
Alignment explanation
Indices: 27825974--27826039 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
27825964 GGTAAGCAGG
27825974 ACGGTGGTAAGAGTCTCGCCTATGATTCCCGTC
1 ACGGTGGTAAGAGTCTCGCCTATGATTCCCGTC
27826007 ACGGTGGTAAGAGTCTCGCCTATGATTCCCGTC
1 ACGGTGGTAAGAGTCTCGCCTATGATTCCCGTC
27826040 TATAGTGCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (33 bp):
ACGGTGGTAAGAGTCTCGCCTATGATTCCCGTC
Found at i:27826177 original size:73 final size:73
Alignment explanation
Indices: 27826043--27826179 Score: 170
Period size: 73 Copynumber: 1.9 Consensus size: 73
27826033 TCCCGTCTAT
* *
27826043 AGTGCTTTAATGAGTACCAGTTTTGTCTACAAAGATGGTGGTAAACAAGGACGATGGTAAAAGTT
1 AGTGCTTTAATGAGTACCAGTTTTCTCTACAAAGATGGTGGTAAACAAGGACGATGATAAAAGTT
27826108 CTGCCTAC
66 CTGCCTAC
* ** * **
27826116 AGTGCTTTGATGAGTACCAGTTTTACT-TGTAATGATGGTGGTAAGTAAGGAC-AGTGATAAAAG
1 AGTGCTTTAATGAGTACCAGTTTT-CTCTACAAAGATGGTGGTAAACAAGGACGA-TGATAAAAG
27826179 T
64 T
27826180 CAAGCTTGTG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
72 1 0.02
73 52 0.96
74 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (73 bp):
AGTGCTTTAATGAGTACCAGTTTTCTCTACAAAGATGGTGGTAAACAAGGACGATGATAAAAGTT
CTGCCTAC
Found at i:27826253 original size:16 final size:16
Alignment explanation
Indices: 27826232--27826262 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27826222 TTTTGCCTGC
*
27826232 AGGGATGGTGGTAAGT
1 AGGGATAGTGGTAAGT
27826248 AGGGATAGTGGTAAG
1 AGGGATAGTGGTAAG
27826263 AGTCCCGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (16 bp):
AGGGATAGTGGTAAGT
Found at i:27826273 original size:86 final size:86
Alignment explanation
Indices: 27826116--27826280 Score: 213
Period size: 86 Copynumber: 1.9 Consensus size: 86
27826106 TTCTGCCTAC
* * *
27826116 AGTGCTTTGATGAGTACCAGTTTTACTTGTAATGATGGTGGTAAGTAAGGACAGTGATAAAAGTC
1 AGTGCTTTGATGAGTACCAGTTTTACCTGCAAGGATGGTGGTAAGTAAGGACAGTGATAAAAGTC
27826181 AAGCTTGTGATTCTTGCCTGT
66 AAGCTTGTGATTCTTGCCTGT
** * * * * * *
27826202 AGTGCTTTGATGAGTATTAGTTTTGCCTGCAGGGATGGTGGTAAGTAGGGATAGTGGTAAGAGTC
1 AGTGCTTTGATGAGTACCAGTTTTACCTGCAAGGATGGTGGTAAGTAAGGACAGTGATAAAAGTC
**
27826267 CCGCTTGTGATTCT
66 AAGCTTGTGATTCT
27826281 CCGATGTAAT
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
86 66 1.00
ACGTcount: A:0.24, C:0.12, G:0.30, T:0.35
Consensus pattern (86 bp):
AGTGCTTTGATGAGTACCAGTTTTACCTGCAAGGATGGTGGTAAGTAAGGACAGTGATAAAAGTC
AAGCTTGTGATTCTTGCCTGT
Found at i:27826398 original size:39 final size:39
Alignment explanation
Indices: 27826355--27826456 Score: 123
Period size: 39 Copynumber: 2.6 Consensus size: 39
27826345 GGTGGCTAGA
* * * **
27826355 GCATTGGACAATGATTTTGATATTCCATCTATGGTTACG
1 GCATTGGACGATGACTTTGATATTCCATCAATGACTACG
* * **
27826394 GCATTGGATGATAACTTTGATATTCTGTCAATGACTACG
1 GCATTGGACGATGACTTTGATATTCCATCAATGACTACG
27826433 GCATTGGACGATGACTTTGATATT
1 GCATTGGACGATGACTTTGATATT
27826457 TAGTTAGTGA
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (39 bp):
GCATTGGACGATGACTTTGATATTCCATCAATGACTACG
Found at i:27827314 original size:34 final size:34
Alignment explanation
Indices: 27827276--27827343 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
27827266 TTATTAATTA
*
27827276 ATATGAATGCATGCTACTTAAATGAAATCTGTTG
1 ATATGAATGCATGATACTTAAATGAAATCTGTTG
27827310 ATATGAATGCATGATACTTAAATGAAATCTGTTG
1 ATATGAATGCATGATACTTAAATGAAATCTGTTG
27827344 GTGGGATAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (34 bp):
ATATGAATGCATGATACTTAAATGAAATCTGTTG
Found at i:27837529 original size:74 final size:71
Alignment explanation
Indices: 27837374--27837530 Score: 163
Period size: 74 Copynumber: 2.2 Consensus size: 71
27837364 TATTATCACT
* * * * *
27837374 ATGTGCACTCCCATACTGCACACAGTTATTGTGTCATGAGCTCTTCCATACCATAAACCACTATT
1 ATGTGCACTCCCACACCGCACACAGTTATTGTGCCATGAGCTCTCCCACACCATAAACCACTATT
27837439 ACAATC
66 ACAATC
* * * * *
27837445 TTGTACACTCCCACACCGCACACATGGTTATAAT-TGCCATGAGCTCTCCCACATCGTACACCAC
1 ATGTGCACTCCCACACCGCACACA--GTTAT--TGTGCCATGAGCTCTCCCACACCATAAACCAC
**
27837509 TATTACCGTC
62 TATTACAATC
27837519 ATGTGCACTCCC
1 ATGTGCACTCCC
27837531 TCAATGCACA
Statistics
Matches: 68, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
71 20 0.29
73 5 0.07
74 42 0.62
75 1 0.01
ACGTcount: A:0.27, C:0.34, G:0.12, T:0.27
Consensus pattern (71 bp):
ATGTGCACTCCCACACCGCACACAGTTATTGTGCCATGAGCTCTCCCACACCATAAACCACTATT
ACAATC
Found at i:27842900 original size:23 final size:22
Alignment explanation
Indices: 27842874--27842919 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
27842864 ACCCTAACAT
*
27842874 ATTTGGAGAAGAGAAAATTTGAA
1 ATTTAGAGAAGA-AAAATTTGAA
* *
27842897 ATTTAGAGAATAAAACTTTGAA
1 ATTTAGAGAAGAAAAATTTGAA
27842919 A
1 A
27842920 CTTGAAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.28
Consensus pattern (22 bp):
ATTTAGAGAAGAAAAATTTGAA
Found at i:27846924 original size:32 final size:37
Alignment explanation
Indices: 27846871--27846943 Score: 111
Period size: 34 Copynumber: 2.1 Consensus size: 37
27846861 AAAATAAAAA
27846871 AATAAAATATATAATATAGG-AATTAAAAA-TTA-AT
1 AATAAAATATATAATATAGGAAATTAAAAATTTATAT
27846905 AATAAAATA-A-AATATAGGAAATTAAAAATTTATAT
1 AATAAAATATATAATATAGGAAATTAAAAATTTATAT
27846940 AATA
1 AATA
27846944 TAGGAAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
32 8 0.22
33 10 0.28
34 12 0.33
35 6 0.17
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (37 bp):
AATAAAATATATAATATAGGAAATTAAAAATTTATAT
Found at i:27847026 original size:11 final size:11
Alignment explanation
Indices: 27847012--27847061 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
27847002 AATAAAATAT
27847012 ATAAGATTATA
1 ATAAGATTATA
*
27847023 ATAAGAATTGAAA
1 ATAAG-ATT-ATA
*
27847036 ATAA-AATAT-
1 ATAAGATTATA
27847045 ATAAGATTATA
1 ATAAGATTATA
27847056 ATAAGA
1 ATAAGA
27847062 AATGAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
9 4 0.13
10 5 0.16
11 13 0.42
12 3 0.10
13 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (11 bp):
ATAAGATTATA
Found at i:27847035 original size:33 final size:33
Alignment explanation
Indices: 27846992--27847079 Score: 167
Period size: 33 Copynumber: 2.7 Consensus size: 33
27846982 AATTGTATTA
27846992 AAGAAATGAAAATAAAATATATAAGATTATAAT
1 AAGAAATGAAAATAAAATATATAAGATTATAAT
*
27847025 AAGAATTGAAAATAAAATATATAAGATTATAAT
1 AAGAAATGAAAATAAAATATATAAGATTATAAT
27847058 AAGAAATGAAAATAAAATATAT
1 AAGAAATGAAAATAAAATATAT
27847080 GATATTAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (33 bp):
AAGAAATGAAAATAAAATATATAAGATTATAAT
Found at i:27858453 original size:116 final size:116
Alignment explanation
Indices: 27858234--27858577 Score: 268
Period size: 116 Copynumber: 3.0 Consensus size: 116
27858224 TACTTAGGGC
* * * * * * *
27858234 AACAAGCGATGTGCCTCAACACACATCTAGTACCATAGCACTTGCTAGATAAGAAT-AACAAGTA
1 AACAAGCCATGTGCCACAACACACGTCTAGCACCATAGC-CTTACTAGAT-AGGATCAACAAGCA
* * * * * * *
27858298 TGTGATTTACTCGTTGC-A-A-ATGTCTAGCACTAGAACCCCTGCTAGATGGGAA-
64 TGTGACTTA-TC--TACAACACATGTCTAGCACCATAGCCCCTACTAGATAGGAAT
** * * *
27858350 AACAAGCCATGTGTGACAGCACACGTCTAGCACCATAGCCCTTATTAGATAGGAAT-GACAAGCA
1 AACAAGCCATGTGCCACAACACACGTCTAGCACCATAG-CCTTACTAGATAGG-ATCAACAAGCA
* *
27858414 TGTGACTTATCTACAACACATGTCTAGCACGATAGCCCCTATTAGATAGGAAT
64 TGTGACTTATCTACAACACATGTCTAGCACCATAGCCCCTACTAGATAGGAAT
* * * * * * * * * *
27858467 GACGAGCGATGTGCCCCAACACATGTCTAGCACCATAGCGTTGCTATATAGGGTCAATAAGCATG
1 AACAAGCCATGTGCCACAACACACGTCTAGCACCATAGCCTTACTAGATAGGATCAACAAGCATG
** * *
27858532 TGACTTATCTACTGCACATGTCTAGCACCATGGCCCCTAATAGATA
66 TGACTTATCTACAACACATGTCTAGCACCATAGCCCCTACTAGATA
27858578 CGGTCAACAA
Statistics
Matches: 181, Mismatches: 40, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
113 2 0.01
114 1 0.01
115 6 0.03
116 141 0.78
117 31 0.17
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (116 bp):
AACAAGCCATGTGCCACAACACACGTCTAGCACCATAGCCTTACTAGATAGGATCAACAAGCATG
TGACTTATCTACAACACATGTCTAGCACCATAGCCCCTACTAGATAGGAAT
Found at i:27858655 original size:58 final size:58
Alignment explanation
Indices: 27858584--27858702 Score: 175
Period size: 58 Copynumber: 2.1 Consensus size: 58
27858574 GATACGGTCA
*
27858584 ACAAGCATATGTCTCACCATTGCACATGTCAAACACCACGCCTTGCTAGATGGGCCTC
1 ACAAGCATATGTCTCACCATTGCACATGTCAAACACCACGCCTTGCTAAATGGGCCTC
* * ** * *
27858642 ACAAGCATGTGTCTCGCCATTGCACATGTTTAGCACCATGCCTTGCTAAATGGGCCTC
1 ACAAGCATATGTCTCACCATTGCACATGTCAAACACCACGCCTTGCTAAATGGGCCTC
27858700 ACA
1 ACA
27858703 TACCATTTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.24
Consensus pattern (58 bp):
ACAAGCATATGTCTCACCATTGCACATGTCAAACACCACGCCTTGCTAAATGGGCCTC
Found at i:27858922 original size:24 final size:23
Alignment explanation
Indices: 27858891--27858953 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 23
27858881 CTCTGCAAAT
*
27858891 TTCA-ATACTATATAGTATAGTCA
1 TTCATATACTATATAGCATAG-CA
27858914 TTCATATACTATATAGCATAGCA
1 TTCATATACTATATAGCATAGCA
27858937 TTCATATACATATATAG
1 TTCATATAC-TATATAG
27858954 ATGCCGTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
23 15 0.41
24 22 0.59
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (23 bp):
TTCATATACTATATAGCATAGCA
Found at i:27863362 original size:17 final size:17
Alignment explanation
Indices: 27863340--27863372 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27863330 CCAAAACTTC
*
27863340 CCCAAAGTTTTCAACAT
1 CCCAAAGTTTTAAACAT
27863357 CCCAAAGTTTTAAACA
1 CCCAAAGTTTTAAACA
27863373 AAAATGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.27, G:0.06, T:0.27
Consensus pattern (17 bp):
CCCAAAGTTTTAAACAT
Found at i:27866248 original size:13 final size:13
Alignment explanation
Indices: 27866230--27866254 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27866220 ATTTAGAATA
27866230 ATTACTTGAATTC
1 ATTACTTGAATTC
27866243 ATTACTTGAATT
1 ATTACTTGAATT
27866255 AATTCCTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (13 bp):
ATTACTTGAATTC
Found at i:27873356 original size:19 final size:19
Alignment explanation
Indices: 27873332--27873369 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
27873322 CCATTTAACT
*
27873332 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
27873351 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
27873370 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:27873576 original size:28 final size:29
Alignment explanation
Indices: 27873535--27873594 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
27873525 GTCTATGGGC
* *
27873535 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGGCAAAAATGT
* *
27873563 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCACTTTTA-GGGGGCAAAAATGT
27873593 AA
1 AA
27873595 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.38
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGGCAAAAATGT
Found at i:27874737 original size:16 final size:16
Alignment explanation
Indices: 27874716--27874750 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
27874706 ATAAAATATT
*
27874716 ATGTTTTCTAATTAAA
1 ATGTTTTCTAATAAAA
*
27874732 ATGTTTTTTAATAAAA
1 ATGTTTTCTAATAAAA
27874748 ATG
1 ATG
27874751 AGATTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (16 bp):
ATGTTTTCTAATAAAA
Found at i:27882383 original size:13 final size:13
Alignment explanation
Indices: 27882365--27882389 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27882355 AGAGAAATTG
27882365 TGATTTTATAAAA
1 TGATTTTATAAAA
27882378 TGATTTTATAAA
1 TGATTTTATAAA
27882390 TTTTCTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:27888498 original size:28 final size:27
Alignment explanation
Indices: 27888446--27888498 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
27888436 GGACAAGTGT
* **
27888446 CCTTGTGGTGGAAAATTACTGTTTTGC
1 CCTTGGGGTGGAAAATTACCATTTTGC
27888473 CCTTGGGGTGGCAAAATTACCATTTT
1 CCTTGGGGTGG-AAAATTACCATTTT
27888499 ATCCGTATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.38
Consensus pattern (27 bp):
CCTTGGGGTGGAAAATTACCATTTTGC
Found at i:27889550 original size:20 final size:20
Alignment explanation
Indices: 27889525--27889570 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
27889515 TTTTGGCCCC
27889525 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
27889545 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
27889565 ATTTGA
1 ATTTGA
27889571 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:27889646 original size:28 final size:27
Alignment explanation
Indices: 27889615--27889667 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
27889605 TTTAGAGTAT
*
27889615 AGGGATAAAATGGTAATTTTGCCACCTC
1 AGGGACAAAATGGTAATTTT-CCACCTC
* *
27889643 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGACAAAATGGTAATTTTCCACC
27889668 ACCAGGATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (27 bp):
AGGGACAAAATGGTAATTTTCCACCTC
Found at i:27897583 original size:25 final size:25
Alignment explanation
Indices: 27897555--27897638 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 25
27897545 ATGGACTTCT
27897555 CCCATTTCTT-TTTAATTGGGCCATG
1 CCCATTTCTTCTTT-ATTGGGCCATG
*
27897580 CCCA-TTCTTCCTTTATTGGACCATG
1 CCCATTTCTT-CTTTATTGGGCCATG
* *
27897605 TCCATTT-TTCTTGCTTGTTGGGCCATG
1 CCCATTTCTTC-T--TTATTGGGCCATG
27897632 CCCATTT
1 CCCATTT
27897639 TCCTTTCTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
24 6 0.12
25 20 0.42
26 5 0.10
27 17 0.35
ACGTcount: A:0.13, C:0.27, G:0.15, T:0.44
Consensus pattern (25 bp):
CCCATTTCTTCTTTATTGGGCCATG
Found at i:27897630 original size:27 final size:26
Alignment explanation
Indices: 27897570--27897650 Score: 83
Period size: 27 Copynumber: 3.1 Consensus size: 26
27897560 TTCTTTTTAA
* * *
27897570 TTGGGCCATGCCCATTCTTCCT-TTA
1 TTGGGCCATGCCCATTTTTCTTCTTG
* *
27897595 TTGGACCATGTCCATTTTTCTTGCTTG
1 TTGGGCCATGCCCATTTTTCTT-CTTG
*
27897622 TTGGGCCATGCCCATTTTCCTTTCTTG
1 TTGGGCCATGCCCATTTTTC-TTCTTG
27897649 TT
1 TT
27897651 ATTTTCTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
25 18 0.40
27 25 0.56
28 2 0.04
ACGTcount: A:0.10, C:0.27, G:0.17, T:0.46
Consensus pattern (26 bp):
TTGGGCCATGCCCATTTTTCTTCTTG
Found at i:27897701 original size:4 final size:5
Alignment explanation
Indices: 27897636--27897700 Score: 75
Period size: 5 Copynumber: 13.6 Consensus size: 5
27897626 GCCATGCCCA
* *
27897636 TTTTC CTTTC TTGTTA TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTC
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
27897686 -TTTC -TTTC -TTTC TTT
1 TTTTC TTTTC TTTTC TTT
27897701 CCTCCACCAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
4 16 0.30
5 34 0.63
6 4 0.07
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:27898064 original size:34 final size:34
Alignment explanation
Indices: 27898016--27898093 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
27898006 GCACTTTTTG
27898016 GCCTCCAAAA-TAGCAAAAAAATAGCTCTTTTCA
1 GCCTCCAAAATTAGCAAAAAAATAGCTCTTTTCA
* *
27898049 GCCTCTAAAATTAGCAGAAAAATAGCTCTTTTCA
1 GCCTCCAAAATTAGCAAAAAAATAGCTCTTTTCA
*
27898083 GCGTCCAAAAT
1 GCCTCCAAAAT
27898094 CAACCCTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 9 0.22
34 31 0.77
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.26
Consensus pattern (34 bp):
GCCTCCAAAATTAGCAAAAAAATAGCTCTTTTCA
Found at i:27909180 original size:2 final size:2
Alignment explanation
Indices: 27909169--27909216 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
27909159 ACTTAGGTTT
27909169 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27909210 TA TA TA T
1 TA TA TA T
27909217 TACTTGTNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27910390 original size:2 final size:2
Alignment explanation
Indices: 27910383--27910413 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
27910373 TGTAGTAATA
*
27910383 AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27910414 GGTGACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27919627 original size:30 final size:31
Alignment explanation
Indices: 27919593--27919650 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
27919583 TCATAAGAGC
*
27919593 TTATTTGAT-TCAAAAT-TAAAGTATAAATAT
1 TTATTT-ATCTCAAAATAAAAAGTATAAATAT
27919623 TTATTTATCTCAAAATAAAAAGTATAAA
1 TTATTTATCTCAAAATAAAAAGTATAAA
27919651 GACTTCATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 2 0.08
30 13 0.52
31 10 0.40
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (31 bp):
TTATTTATCTCAAAATAAAAAGTATAAATAT
Found at i:27920785 original size:20 final size:20
Alignment explanation
Indices: 27920760--27920805 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
27920750 TTTTGGCCCC
27920760 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
27920780 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
27920800 ATTTGA
1 ATTTGA
27920806 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:27920886 original size:27 final size:27
Alignment explanation
Indices: 27920850--27920902 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
27920840 TTTGGAGTAT
*
27920850 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGAAAAATGGTAATTTT-CCACCTC
*
27920878 AGGGGAAAAATTGTAATTTTCCACC
1 AGGGGAAAAATGGTAATTTTCCACC
27920903 ACCAAGGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGAAAAATGGTAATTTTCCACCTC
Found at i:27993990 original size:18 final size:17
Alignment explanation
Indices: 27993960--27993993 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
27993950 GTAGAAGGCT
27993960 CATGCATGAATGCAAAA
1 CATGCATGAATGCAAAA
*
27993977 CATGTCATGTATGCAAA
1 CATG-CATGAATGCAAA
27993994 GGAACGTGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (17 bp):
CATGCATGAATGCAAAA
Found at i:27994612 original size:13 final size:13
Alignment explanation
Indices: 27994594--27994641 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
27994584 TCTTTCTTTA
*
27994594 ATTTATTTTTATT
1 ATTTATTATTATT
27994607 ATTTATTCATT-TT
1 ATTTATT-ATTATT
*
27994620 ATTCATTATTATT
1 ATTTATTATTATT
27994633 ATTTATTAT
1 ATTTATTAT
27994642 ATTTTTTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 3 0.10
13 25 0.83
14 2 0.07
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTATTATTATT
Found at i:27995725 original size:3 final size:3
Alignment explanation
Indices: 27995717--27995745 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
27995707 GCTTTAAAAC
27995717 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
27995746 TAAAGGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:27996323 original size:16 final size:15
Alignment explanation
Indices: 27996278--27996319 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
27996268 GGCCTAGTCC
* *
27996278 TTTTCTCCCTTCTTT
1 TTTTCTTCCTTCTTA
27996293 TTTTCTTTCCTTCTTA
1 TTTTC-TTCCTTCTTA
27996309 TTTTCTTCCTT
1 TTTTCTTCCTT
27996320 TCTTCTTCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTCTTCCTTCTTA
Found at i:27996825 original size:22 final size:21
Alignment explanation
Indices: 27996796--27996843 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
27996786 CCCTCCCCTT
*
27996796 TTTC-CTTTTTTCTTTTTTTTG
1 TTTCTCTTTTTT-TTTTTTGTG
27996817 TTTCTCTTTTTTTTTTTTGTG
1 TTTCTCTTTTTTTTTTTTGTG
27996838 TATTCT
1 T-TTCT
27996844 AGCTAGTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.79
Consensus pattern (21 bp):
TTTCTCTTTTTTTTTTTTGTG
Found at i:27998712 original size:17 final size:19
Alignment explanation
Indices: 27998692--27998731 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
27998682 AAAAAATTTA
27998692 ATTTATTTTAT-AATTC-T
1 ATTTATTTTATAAATTCAT
*
27998709 ATTTGTTTTATAAATTCAT
1 ATTTATTTTATAAATTCAT
27998728 ATTT
1 ATTT
27998732 TTCTCATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 5 0.25
19 5 0.25
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTTATTTTATAAATTCAT
Found at i:27999918 original size:28 final size:29
Alignment explanation
Indices: 27999854--27999918 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
27999844 GAGTAATTTT
* *
27999854 TAAAATTTACACTTTTACCCCCATAAAAG
1 TAAAAATTACACTTTTACCCCCATAAAAC
* *
27999883 TAATAATTACATTTTTA-CCCCA-AAAAC
1 TAAAAATTACACTTTTACCCCCATAAAAC
27999910 TGAAAAATT
1 T-AAAAATT
27999919 GCCCATAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 5 0.17
28 11 0.37
29 14 0.47
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (29 bp):
TAAAAATTACACTTTTACCCCCATAAAAC
Found at i:28087448 original size:6 final size:6
Alignment explanation
Indices: 28087439--28087463 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28087429 CTTAGACTTA
28087439 GGGCTT GGGCTT GGGCTT GGGCTT G
1 GGGCTT GGGCTT GGGCTT GGGCTT G
28087464 AAATTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGGCTT
Found at i:28094334 original size:33 final size:31
Alignment explanation
Indices: 28094287--28094357 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 31
28094277 TAAATTATAT
* * *
28094287 AATATAGAAAATTATATTAAGAAATGAAAATAA
1 AATATATAAAATTATAATAAAAAAT-AAAA-AA
* *
28094320 AATATATAAGATTATAATAAAAAATTAAAAA
1 AATATATAAAATTATAATAAAAAATAAAAAA
28094351 AATATAT
1 AATATAT
28094358 GACATTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 9 0.27
32 3 0.09
33 21 0.64
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.30
Consensus pattern (31 bp):
AATATATAAAATTATAATAAAAAATAAAAAA
Found at i:28097270 original size:19 final size:19
Alignment explanation
Indices: 28097248--28097285 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28097238 CTGCCAAACC
*
28097248 CTCAAATTATACTCAAATA
1 CTCAAATAATACTCAAATA
*
28097267 CTCAAATAATACTCCAATA
1 CTCAAATAATACTCAAATA
28097286 AGTCAAATGG
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:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATAATACTCAAATA
Found at i:28097735 original size:15 final size:15
Alignment explanation
Indices: 28097698--28097745 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
28097688 TCTTCCCTGC
* * *
28097698 AATCACACTATTTGC
1 AATCACATTACTTGT
28097713 AATCACATTACTTGT
1 AATCACATTACTTGT
28097728 AATCACATTACATTGT
1 AATCACATTAC-TTGT
28097744 AA
1 AA
28097746 AGTACCAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 23 0.79
16 6 0.21
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (15 bp):
AATCACATTACTTGT
Found at i:28100012 original size:19 final size:19
Alignment explanation
Indices: 28099988--28100025 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28099978 CCATTTAACT
*
28099988 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
28100007 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
28100026 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:28131534 original size:12 final size:12
Alignment explanation
Indices: 28131517--28131610 Score: 62
Period size: 12 Copynumber: 7.3 Consensus size: 12
28131507 ATGTCATGTA
28131517 TTTTATTTTTAT
1 TTTTATTTTTAT
28131529 TTTTATTTTTAT
1 TTTTATTTTTAT
* *
28131541 TATAATTTTATAT
1 TTTTATTTT-TAT
*
28131554 ATTTTATTTTCAT
1 -TTTTATTTTTAT
* * *
28131567 TTCTTAATATAATT
1 TT-TTATTTTTA-T
*
28131581 TTTTATATTATAT
1 TTTTAT-TTTTAT
*
28131594 ATTTTATTTTAAT
1 -TTTTATTTTTAT
28131607 TTTT
1 TTTT
28131611 TTCTCTAAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
12 25 0.40
13 19 0.31
14 18 0.29
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:28131557 original size:33 final size:32
Alignment explanation
Indices: 28131523--28131603 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 32
28131513 TGTATTTTAT
*
28131523 TTTTATTTTTATTTTTATTATAATTTTATATA
1 TTTTATTTTTATTTTTAATATAATTTTATATA
* *
28131555 TTTTATTTTCATTTCTTAATATAATTTTTTATA
1 TTTTATTTTTATTT-TTAATATAATTTTATATA
*
28131588 TTATATATTTTATTTT
1 TTTTAT-TTTTATTTT
28131604 AATTTTTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 13 0.31
33 22 0.52
34 7 0.17
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (32 bp):
TTTTATTTTTATTTTTAATATAATTTTATATA
Found at i:28131601 original size:78 final size:75
Alignment explanation
Indices: 28131459--28131610 Score: 180
Period size: 78 Copynumber: 2.0 Consensus size: 75
28131449 ATACTTGTAT
* *
28131459 TTTTTATTATTAATTTTTATATAATATTATCTTTCAAATATATTTTTAATGTCATGTATTTTATT
1 TTTTTATTATTAATTTTTATATAATATTATCTTTCAAATATATTTTTAATATCATATATTTTATT
*
28131524 TTTATTTTTA
66 TTAATTTTTA
** * * * *
28131534 TTTTTATTA-TAATTTTATATATTTTATTTTCATTTCTTAATATAATTTTTTATATTATATATTT
1 TTTTTATTATTAATTTT-TATATAATATTATC-TTTC-AAATAT-ATTTTTAATATCATATATTT
28131598 TATTTTAATTTTT
62 TATTTTAATTTTT
28131611 TTCTCTAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
74 7 0.11
75 20 0.31
76 4 0.06
77 5 0.08
78 28 0.44
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (75 bp):
TTTTTATTATTAATTTTTATATAATATTATCTTTCAAATATATTTTTAATATCATATATTTTATT
TTAATTTTTA
Found at i:28132207 original size:5 final size:5
Alignment explanation
Indices: 28132199--28132291 Score: 55
Period size: 5 Copynumber: 17.4 Consensus size: 5
28132189 TAATATCATA
* *
28132199 TATTT TATTT TCATTT CTATTAT AATTT TA-TA TATTT TATTT TCATTTT
1 TATTT TATTT T-ATTT -TATT-T TATTT TATTT TATTT TATTT T-A-TTT
* * *
28132248 TAATA TATTT TATTG TATTAT ATATTT TATTT TAATTT T-TTT TA
1 TATTT TATTT TATTT TATT-T -TATTT TATTT T-ATTT TATTT TA
28132292 AATGACAATA
Statistics
Matches: 68, Mismatches: 10, Indels: 20
0.69 0.10 0.20
Matches are distributed among these distances:
4 7 0.10
5 33 0.49
6 18 0.26
7 10 0.15
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (5 bp):
TATTT
Found at i:28132212 original size:15 final size:15
Alignment explanation
Indices: 28132180--28132244 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
28132170 CATCTCTTAA
* *
28132180 ATATATTTTTAATATC
1 ATATA-TTTTATTTTC
28132196 ATATATTTTATTTTC
1 ATATATTTTATTTTC
* *
28132211 ATTTCTATTATAATTTT-
1 A--TATATT-TTATTTTC
28132228 ATATATTTTATTTTC
1 ATATATTTTATTTTC
28132243 AT
1 AT
28132245 TTTTAATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
14 6 0.15
15 16 0.41
16 5 0.13
17 6 0.15
18 6 0.15
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATATTTTATTTTC
Found at i:28132236 original size:32 final size:31
Alignment explanation
Indices: 28132196--28132260 Score: 103
Period size: 32 Copynumber: 2.1 Consensus size: 31
28132186 TTTTAATATC
*
28132196 ATATATTTTATTTTCATTTCTATTATAATTTT
1 ATATATTTTATTTTCATTTCTAATAT-ATTTT
*
28132228 ATATATTTTATTTTCATTTTTAATATATTTT
1 ATATATTTTATTTTCATTTCTAATATATTTT
28132259 AT
1 AT
28132261 TGTATTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 7 0.23
32 24 0.77
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (31 bp):
ATATATTTTATTTTCATTTCTAATATATTTT
Found at i:28132251 original size:27 final size:27
Alignment explanation
Indices: 28132184--28132253 Score: 77
Period size: 32 Copynumber: 2.4 Consensus size: 27
28132174 TCTTAAATAT
28132184 ATTTTTAATATCATATATTTTATTTTC
1 ATTTTTAATATCATATATTTTATTTTC
* *
28132211 ATTTCTATTATAATTTTATATATTTTATTTTC
1 A--T-T-TT-TAATATCATATATTTTATTTTC
28132243 ATTTTTAATAT
1 ATTTTTAATAT
28132254 ATTTTATTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
27 6 0.17
28 2 0.06
29 2 0.06
30 2 0.06
31 2 0.06
32 21 0.60
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (27 bp):
ATTTTTAATATCATATATTTTATTTTC
Found at i:28132261 original size:27 final size:27
Alignment explanation
Indices: 28132184--28132266 Score: 69
Period size: 32 Copynumber: 2.9 Consensus size: 27
28132174 TCTTAAATAT
*
28132184 ATTTTTAATATCA-TATATTTTATTTTC
1 ATTTTTAATAT-ATTTTATTTTATTTTC
* *
28132211 ATTTCTATTATAATTTTATATATTTTATTTTC
1 ATTT-T-TAAT-ATATT-T-TATTTTATTTTC
*
28132243 ATTTTTAATATATTTTATTGTATT
1 ATTTTTAATATATTTTATTTTATT
28132267 ATATATTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
27 12 0.27
28 2 0.05
29 7 0.16
30 6 0.14
31 1 0.02
32 16 0.36
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (27 bp):
ATTTTTAATATATTTTATTTTATTTTC
Found at i:28132278 original size:22 final size:20
Alignment explanation
Indices: 28132224--28132287 Score: 71
Period size: 17 Copynumber: 3.2 Consensus size: 20
28132214 TCTATTATAA
28132224 TTTTATATATTTTATTTTCAT
1 TTTTATATATTTTATTTT-AT
*
28132245 TTTTAATATATTTTATTGTA-
1 TTTT-ATATATTTTATTTTAT
28132265 --TTATATATTTTATTTTAAT
1 TTTTATATATTTTATTTT-AT
28132284 TTTT
1 TTTT
28132288 TTTAAATGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
17 13 0.36
18 3 0.08
21 7 0.19
22 13 0.36
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTATATATTTTATTTTAT
Found at i:28141557 original size:34 final size:35
Alignment explanation
Indices: 28141488--28141561 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
28141478 AAATTTAAAT
* *
28141488 TTAAATAATCAAAAACAAATATCTCAAATATCAAC
1 TTAAATAATCAAAAACAAATATCTCAAACAACAAC
*
28141523 TTAAATAATTAAAAACAAATAT-TCAAACAACAAC
1 TTAAATAATCAAAAACAAATATCTCAAACAACAAC
28141557 TTAAA
1 TTAAA
28141562 CATTACAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 15 0.42
35 21 0.58
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (35 bp):
TTAAATAATCAAAAACAAATATCTCAAACAACAAC
Found at i:28143409 original size:18 final size:18
Alignment explanation
Indices: 28143386--28143422 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28143376 TTTTCTTGCT
28143386 CAAGCTACCTGATTGAAA
1 CAAGCTACCTGATTGAAA
28143404 CAAGCTACCTGATTGAAA
1 CAAGCTACCTGATTGAAA
28143422 C
1 C
28143423 TGGCTTCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (18 bp):
CAAGCTACCTGATTGAAA
Found at i:28146914 original size:24 final size:24
Alignment explanation
Indices: 28146887--28146939 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
28146877 GATGGAAAAG
28146887 ACAAAGGTGCTCTTTCCCCTAATT
1 ACAAAGGTGCTCTTTCCCCTAATT
28146911 ACAAAGGTGCTCTTTCCCCTAATT
1 ACAAAGGTGCTCTTTCCCCTAATT
28146935 ACAAA
1 ACAAA
28146940 AGATGCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.30
Consensus pattern (24 bp):
ACAAAGGTGCTCTTTCCCCTAATT
Found at i:28151811 original size:28 final size:28
Alignment explanation
Indices: 28151770--28151832 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
28151760 GAACAAATGG
*
28151770 AATAGAAATGAATAAAATAAATAAATAAA
1 AATAAAAATGAATAAAATAAATAAA-AAA
* *
28151799 AATAAAAAT-AATAATATAAATTAAAAA
1 AATAAAAATGAATAAAATAAATAAAAAA
*
28151826 ATTAAAA
1 AATAAAA
28151833 TTAAATGAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 9 0.30
28 13 0.43
29 8 0.27
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (28 bp):
AATAAAAATGAATAAAATAAATAAAAAA
Found at i:28152415 original size:2 final size:2
Alignment explanation
Indices: 28152408--28152441 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28152398 TCACAAAAAC
28152408 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28152442 ATTTTATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28153644 original size:24 final size:24
Alignment explanation
Indices: 28153615--28153664 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
28153605 ACTTTCGAGT
28153615 GAGATCTAAACTTAGCATGTAAAA
1 GAGATCTAAACTTAGCATGTAAAA
28153639 GAGATCTAAACTTAGCATGTAAAA
1 GAGATCTAAACTTAGCATGTAAAA
28153663 GA
1 GA
28153665 CAGTAGGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (24 bp):
GAGATCTAAACTTAGCATGTAAAA
Found at i:28154358 original size:17 final size:17
Alignment explanation
Indices: 28154338--28154374 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
28154328 ATTTTCAACT
* *
28154338 TAAAACAATAAAATAAA
1 TAAAAAAATAAAAAAAA
28154355 TAAAAAAATAAAAAAAA
1 TAAAAAAATAAAAAAAA
28154372 TAA
1 TAA
28154375 TTTTCATCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (17 bp):
TAAAAAAATAAAAAAAA
Found at i:28161619 original size:5 final size:5
Alignment explanation
Indices: 28161602--28161634 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
28161592 TCATGCAAGA
*
28161602 AAAAG AAAA- AAAAG AAAAG AAAAG AGAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
28161635 AGGTTTGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:28162368 original size:11 final size:11
Alignment explanation
Indices: 28162352--28162393 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
28162342 CATGAAACCA
28162352 AAAAAAAGAAG
1 AAAAAAAGAAG
28162363 AAAAAATAG-AG
1 AAAAAA-AGAAG
*
28162374 AAAGAAAAGAAA
1 AAA-AAAAGAAG
28162386 AAAAAAAG
1 AAAAAAAG
28162394 GAATGGTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:28162877 original size:35 final size:35
Alignment explanation
Indices: 28162816--28162883 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
28162806 TGAAAAATGT
* * *
28162816 AAAAAAAAAAAAGATAATGATGAAAAAGTGATGAA
1 AAAAAAAAAAAAGAAAAAGATAAAAAAGTGATGAA
*
28162851 AAAAATAAAAAAAGAAAAAGA-AAAAAATTGATG
1 AAAAA-AAAAAAAGAAAAAGATAAAAAAGTGATG
28162884 GAAAGGCATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 15 0.54
36 13 0.46
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (35 bp):
AAAAAAAAAAAAGAAAAAGATAAAAAAGTGATGAA
Found at i:28167044 original size:18 final size:19
Alignment explanation
Indices: 28167021--28167057 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
28167011 TGTTAACCAT
28167021 GGTTACAAGGCAAA-AACA
1 GGTTACAAGGCAAATAACA
28167039 GGTTACAAGGCAAATAACA
1 GGTTACAAGGCAAATAACA
28167058 TGAGCAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.14
Consensus pattern (19 bp):
GGTTACAAGGCAAATAACA
Found at i:28168355 original size:12 final size:12
Alignment explanation
Indices: 28168335--28168366 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
28168325 CTAAGAAAAT
28168335 AATTGAGAGAAG
1 AATTGAGAGAAG
*
28168347 AATTTAGAGAAG
1 AATTGAGAGAAG
28168359 AATTGAGA
1 AATTGAGA
28168367 AAAAACTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.28, T:0.22
Consensus pattern (12 bp):
AATTGAGAGAAG
Found at i:28168397 original size:30 final size:29
Alignment explanation
Indices: 28168362--28168418 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
28168352 AGAGAAGAAT
*
28168362 TGAGA-AAAAACTTCTAGTTTATTTCTCA
1 TGAGAGAAAAACTTCTAGTTCATTTCTCA
* *
28168390 TGAGAGAAGAACTTCTGGTTCATTTCTCA
1 TGAGAGAAAAACTTCTAGTTCATTTCTCA
28168419 CTATTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (29 bp):
TGAGAGAAAAACTTCTAGTTCATTTCTCA
Found at i:28170779 original size:39 final size:38
Alignment explanation
Indices: 28170684--28170793 Score: 130
Period size: 39 Copynumber: 2.8 Consensus size: 38
28170674 TCATGGGGTT
** * * *
28170684 GTGCCTTTTCAGGGGCAATAAGCTCATCTGGAGCAATTC
1 GTGCCTTTT-AGGGGCAATGGGCTCTTCTGAAACAATTC
**
28170723 GTGCCTTTTTAAAGGCAATGGGCTCTTCTGAAACAATTC
1 GTGCC-TTTTAGGGGCAATGGGCTCTTCTGAAACAATTC
28170762 GTGCCTCTTTAGGGGCAATGGGCTCTTCTGAA
1 GTGCCT-TTTAGGGGCAATGGGCTCTTCTGAA
28170794 GCGGATTCGT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
38 1 0.02
39 55 0.92
40 4 0.07
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (38 bp):
GTGCCTTTTAGGGGCAATGGGCTCTTCTGAAACAATTC
Found at i:28173718 original size:24 final size:24
Alignment explanation
Indices: 28173686--28173733 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
28173676 GTTCTCAGAG
28173686 GTCTATCACCACTTTAGGGAGACA
1 GTCTATCACCACTTTAGGGAGACA
*
28173710 GTCTATCACCACTTTAGGGGGACA
1 GTCTATCACCACTTTAGGGAGACA
28173734 AAGATATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (24 bp):
GTCTATCACCACTTTAGGGAGACA
Found at i:28173911 original size:12 final size:12
Alignment explanation
Indices: 28173882--28173921 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
28173872 ATATACTAAA
*
28173882 AAAATAATTGAG
1 AAAAGAATTGAG
* *
28173894 AGAAGAATTTAG
1 AAAAGAATTGAG
28173906 AAAAGAATTGAG
1 AAAAGAATTGAG
28173918 AAAA
1 AAAA
28173922 AAACTTTTGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (12 bp):
AAAAGAATTGAG
Found at i:28174264 original size:33 final size:33
Alignment explanation
Indices: 28174227--28174296 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
28174217 AATTAACATG
* *
28174227 TCATATTATCATCAATTATGATATGTTAGTATA
1 TCATATCATCATCAATTATAATATGTTAGTATA
* *
28174260 TCATATCATTATCAATTATAATATGTTAGTATG
1 TCATATCATCATCAATTATAATATGTTAGTATA
28174293 TCAT
1 TCAT
28174297 GTTAGCGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.46
Consensus pattern (33 bp):
TCATATCATCATCAATTATAATATGTTAGTATA
Found at i:28176439 original size:34 final size:34
Alignment explanation
Indices: 28176395--28176470 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
28176385 GTGACTTATC
*
28176395 TATTTGAGTTATTGATTTTGTTTGTATCTTATAA
1 TATTAGAGTTATTGATTTTGTTTGTATCTTATAA
28176429 TATTAGAGTTATTGATTTTGTTTGTATCTTATAA
1 TATTAGAGTTATTGATTTTGTTTGTATCTTATAA
28176463 TATTAGAG
1 TATTAGAG
28176471 ATTGAAAAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.26, C:0.03, G:0.16, T:0.55
Consensus pattern (34 bp):
TATTAGAGTTATTGATTTTGTTTGTATCTTATAA
Found at i:28184424 original size:2 final size:2
Alignment explanation
Indices: 28184417--28184447 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28184407 AACACAACTA
28184417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28184448 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.