Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007867.1 Hibiscus syriacus cultivar Beakdansim tig00110239_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3477501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 18
Found at i:1612508 original size:143 final size:139
Alignment explanation
Indices: 1612196--1612508 Score: 324
Period size: 143 Copynumber: 2.2 Consensus size: 139
1612186 TAATTTTAAG
1612196 AAATATATTAATTTAT-AAA-A--ATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGT
1 AAATATA-TAATTTATAAAATAGGATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGT
* * * *
1612257 GCCTTAAGACAGTTCTTTTCTTAGATATTAATAAATAAATATTAATAAAACATTTATCTTAAAAT
65 ACCTTAAGACAGCTCTTTTCTTAGATATTAAAAAATAAATAATAATAAAACATTTATCTTAAAAT
1612322 AATTAAAATATAT
130 AATT---ATATAT
* * * *
1612335 TAATATATGATTTATAAAAATAGGACATTTATTTATTTA-AGAATATTAGAAAAGGACTTCTAGG
1 AAATATATAATTTAT-AAAATAGGATATTTATTTATTTAGA-AATATCAGAAAAGGACTTCTAGG
** * *
1612399 TATTTTAAGACAGCTCTTTTCTTAGATATTAAAAAATAAATACAT-ATCAAAATATGTTTATTTT
64 TACCTTAAGACAGCTCTTTTCTTAGATATTAAAAAATAAATA-ATAAT-AAAACA--TTTA-TCT
1612463 TAAGAATAATT-TATA-
124 TAA-AATAATTATATAT
*
1612478 AAAT-TA-AATTTAT-AAATAGGATTTTTATTTA
1 AAATATATAATTTATAAAATAGGATATTTATTTA
1612509 ATAAACGAAT
Statistics
Matches: 146, Mismatches: 16, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
138 7 0.05
139 22 0.15
140 3 0.02
141 7 0.05
142 3 0.02
143 78 0.53
144 10 0.07
146 4 0.03
147 5 0.03
148 7 0.05
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (139 bp):
AAATATATAATTTATAAAATAGGATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTA
CCTTAAGACAGCTCTTTTCTTAGATATTAAAAAATAAATAATAATAAAACATTTATCTTAAAATA
ATTATATAT
Found at i:1612629 original size:15 final size:15
Alignment explanation
Indices: 1612609--1612667 Score: 68
Period size: 15 Copynumber: 4.0 Consensus size: 15
1612599 ATATCAAACG
*
1612609 TAATAATAAATAAAA
1 TAATAATAATTAAAA
1612624 TAATAATAATTAAAA
1 TAATAATAATTAAAA
* *
1612639 TGA-AAGAATTAAAA
1 TAATAATAATTAAAA
1612653 GTAATAAT-ATTAAAA
1 -TAATAATAATTAAAA
1612668 ACTAATGGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 10 0.27
15 25 0.68
16 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
TAATAATAATTAAAA
Found at i:1614061 original size:13 final size:13
Alignment explanation
Indices: 1614028--1614089 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
1614018 TTTGGGTTTG
1614028 TAATAATTATT-TA
1 TAATAA-TATTATA
1614041 TAAT-ATATTATA
1 TAATAATATTATA
1614053 TAATAATATTTAATAA
1 TAATAATA-TT-AT-A
* *
1614069 TAATAATAATATT
1 TAATAATATTATA
1614082 TAATAATA
1 TAATAATA
1614090 ATAACAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
11 4 0.10
12 7 0.17
13 15 0.36
14 4 0.10
15 3 0.07
16 9 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATAATATTATA
Found at i:1614076 original size:19 final size:19
Alignment explanation
Indices: 1614052--1614102 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1614042 AATATATTAT
1614052 ATAATAATATTTAATAATA
1 ATAATAATATTTAATAATA
1614071 ATAATAATATTTAATAATA
1 ATAATAATATTTAATAATA
*
1614090 ATAACAA-ATTTAA
1 ATAATAATATTTAA
1614103 ATGAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAATAATATTTAATAATA
Found at i:1614361 original size:77 final size:78
Alignment explanation
Indices: 1614223--1614377 Score: 240
Period size: 77 Copynumber: 2.0 Consensus size: 78
1614213 GATGGAAATG
* *
1614223 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGAT-A-CCGAAGGATTTGAAAACATCAAAAAGCT
*
1614288 CCCGAAGGTTTTTTT
64 CCCGAAGGCTTTTTT
* *
1614303 TTTGGAAACATCATGCACTGTAGGACTTACAGAT-CCGAAGGATTTGAAAACATCAAAAAGCTCC
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATACCGAAGGATTTGAAAACATCAAAAAGCTCC
1614367 CGAAGGCTTTT
66 CGAAGGCTTTT
1614378 GGAAACATCA
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
77 39 0.56
80 31 0.44
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Consensus pattern (78 bp):
TTTGAAAACATCATGCACTGAAGGACTTACAGATACCGAAGGATTTGAAAACATCAAAAAGCTCC
CGAAGGCTTTTTT
Found at i:1614419 original size:53 final size:53
Alignment explanation
Indices: 1614339--1614450 Score: 183
Period size: 53 Copynumber: 2.1 Consensus size: 53
1614329 TTACAGATCC
1614339 GAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGC-T
1 GAAGGATTTGAAAACATCAAAAAGCT-CCGAAGGCTTTTTGG-AACATCATGCAT
*
1614392 GAAGGCTTTGAAAACATCAAAAAGCTCCGAAGGCTTTTTGGAACATCATGCAT
1 GAAGGATTTGAAAACATCAAAAAGCTCCGAAGGCTTTTTGGAACATCATGCAT
1614445 GAAGGA
1 GAAGGA
1614451 CTTACAGATG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
52 18 0.33
53 37 0.67
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (53 bp):
GAAGGATTTGAAAACATCAAAAAGCTCCGAAGGCTTTTTGGAACATCATGCAT
Found at i:1614485 original size:126 final size:127
Alignment explanation
Indices: 1614262--1614516 Score: 376
Period size: 126 Copynumber: 2.0 Consensus size: 127
1614252 CAGATGACCC
* * *
1614262 GAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGTTTTTTTTTTGGAAACATCATGCACTGTAGG
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGG---TCTTTTTGGAAACATCATGCACTGAAGG
1614327 ACTTACAGATCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGC
63 ACTTACAGATCCGAAGGATTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGC
1614391 T
127 T
1614392 GAAGGCTTTGAAAACATCAAAAAGCT-CCGAAGG-CTTTTTGG-AACATCATGCA-TGAAGGACT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGTCTTTTTGGAAACATCATGCACTGAAGGACT
*
1614453 TACAGATGACCCGAAGGCTTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGC
66 TACAGAT---CCGAAGGATTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGC
1614517 ACTAAACGGA
Statistics
Matches: 117, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
123 15 0.13
124 11 0.09
125 23 0.20
126 36 0.31
129 7 0.06
130 25 0.21
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.25
Consensus pattern (127 bp):
GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGTCTTTTTGGAAACATCATGCACTGAAGGACT
TACAGATCCGAAGGATTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCT
Found at i:1614762 original size:73 final size:76
Alignment explanation
Indices: 1614392--1615571 Score: 1948
Period size: 74 Copynumber: 15.9 Consensus size: 76
1614382 ACATCATGCT
1614392 GAAGGCTTTGAAAACATCAAAAAGCT-CCGAAGGCTTTTTGG-AACATCATGCA-TGAAGGACTT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1614454 ACAGATGACCC
66 ACAGATGACCC
*
1614465 GAAGGCTTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTAAACGGACT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA-GGACT
1614529 TACAGATGACCC
65 TACAGATGACCC
1614541 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1614606 ACAGATGACCC
66 ACAGATGACCC
1614617 GAA-GCTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGACTT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1614680 ACAGATGACCC
66 ACAGATGACCC
*
1614691 GAAGGCTTTGAAAACATC-AAAAGCT-CCGAAGGCTTTTTGGAAA-ATCATGCACTGAAGGGCTT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1614753 ACAGATGACCC
66 ACAGATGACCC
*
1614764 GAAGGCTTTG-AAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1614828 ACAGATGACCC
66 ACAGATGACCC
*
1614839 GAAGGCCTTTGAAAACATCAAAAAGCTCCCAAAGGC-TTTTGGAAACATCATGCACTGAAGGACT
1 GAAGG-CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACT
1614903 TACAGATGA-CC
65 TACAGATGACCC
*
1614914 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGG-TTTTTGGAAACATCATGCACTGAAGGGCTT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1614978 ACAGATGACCC
66 ACAGATGACCC
* *
1614989 GAAGGC-TTG-AAACATTAAAAAGCTCCCAAAGGC-TTTTGGAAACATCATGCACTGAAGGACTT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1615051 ACAGATGACCC
66 ACAGATGACCC
*
1615062 GAAGGCTTTG-AAACATC-AAAAGCTCCCAAAGGCTTTTTGG-AA-A-CATGCACTGAAGGACTT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1615122 ACAGATGACCC
66 ACAGATGACCC
*
1615133 TG-AGGCTTTGAAAACATC-AAAAGCT--CAAAGGCTTTTTGGAAACATCATGCACTGAAGGACT
1 -GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACT
1615194 TACAGATGACCC
65 TACAGATGACCC
1615206 G-AGGC-TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1615269 ACAGATGACCC
66 ACAGATGACCC
*
1615280 GAAGGCTTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAAACATCATGCACTGAAGGGCT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG-AAACATCATGCACTGAAGGACT
1615344 TACAGATGACCC
65 TACAGATGACCC
*
1615356 GAAGGCTTTG-AAACATC-AAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1615419 ACAGATGA-CC
66 ACAGATGACCC
*
1615429 GAAGGCTTTGAAAACATCAAAAAGCT-CCAAAGGC-TTTTGGAAACATCATGCACTGAAGGACTT
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1615492 ACAGATGACCC
66 ACAGATGACCC
1615503 TG-AGGCTTTGAAAACATCAAAAAGCT-CCGAAGGCTTTTTGGAAACA-CATGCACTGAAGGAC-
1 -GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACT
1615564 TACAGATG
65 TACAGATG
1615572 TGGGAATAGT
Statistics
Matches: 1058, Mismatches: 16, Indels: 66
0.93 0.01 0.06
Matches are distributed among these distances:
70 14 0.01
71 49 0.05
72 43 0.04
73 256 0.24
74 311 0.29
75 173 0.16
76 150 0.14
77 62 0.06
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (76 bp):
GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
ACAGATGACCC
Found at i:1614934 original size:298 final size:299
Alignment explanation
Indices: 1614392--1615571 Score: 1985
Period size: 298 Copynumber: 4.0 Consensus size: 299
1614382 ACATCATGCT
1614392 GAAGGCTTTGAAAACATCAAAAAGCT-CCGAAGGCTTTTTGG-AACATCATGCA-TGAAGGACTT
1 GAAGGCTTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
*
1614454 ACAGATGACCCGAAGGCTTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
65 ACAGATGACCCGAAGGCTTTG-AAACATCAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCAC
* *
1614519 TAAACGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGA
129 TGAA-GGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT-CCAAAGGCTTTTTGGA
*
1614584 AACATCATGCACTGAAGGACTTACAGATGACCCGAAGCTTTGAAAACATCAAAAAGCTCCCGAAG
192 AACATCATGCACTGAAGGACTTACAGATGACCCGAGGCTTTGAAAACATCAAAAAGCTCCCGAAG
1614649 GC-TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
257 GCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
*
1614691 GAAGGCTTTGAAAACATCAAAAGCT-CCGAAGGCTTTTTGGAAA-ATCATGCACTGAAGGGCTTA
1 GAAGGCTTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
*
1614754 CAGATGACCCGAAGGCTTTGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACT
66 CAGATGACCCGAAGGCTTTGAAACATC-AAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACT
*
1614819 GAAGGGCTTACAGATGACCCGAAGGCCTTTGAAAACATCAAAAAGCTCCCAAAGGC-TTTTGGAA
130 GAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGCT-CCAAAGGCTTTTTGGAA
1614883 ACATCATGCACTGAAGGACTTACAGATGA-CCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAG
193 ACATCATGCACTGAAGGACTTACAGATGACCCG-AGGCTTTGAAAACATCAAAAAGCTCCCGAAG
*
1614947 G-TTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCC
257 GCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
* *
1614989 GAAGGC-TTG-AAACATTAAAAAGCTCCCAAAGGC-TTTTGGAAACATCATGCACTGAAGGACTT
1 GAAGGCTTTGAAAACA-TCAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
1615051 ACAGATGACCCGAAGGCTTTGAAACATCAAAAGCTCCCAAAGGCTTTTTGG-AA-A-CATGCACT
65 ACAGATGACCCGAAGGCTTTGAAACATCAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACT
1615113 GAAGGACTTACAGATGACCCTG-AGGCTTTGAAAACATC-AAAAGCT-CAAAGGCTTTTTGGAAA
130 GAAGGACTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAGCTCCAAAGGCTTTTTGGAAA
1615175 CATCATGCACTGAAGGACTTACAGATGACCCGAGGC-TTGAAAACATCAAAAAGCTCCCGAAGGC
194 CATCATGCACTGAAGGACTTACAGATGACCCGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1615239 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
259 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
*
1615280 GAAGGCTTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGGAAAACATCATGCACTGAAGGGCTT
1 GAAGGCTTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGG-AAACATCATGCACTGAAGGACTT
1615345 ACAGATGACCCGAAGGCTTTGAAACATCAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACT
65 ACAGATGACCCGAAGGCTTTGAAACATCAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACT
1615410 GAAGGACTTACAGATGA-CCGAAGGCTTTGAAAACATCAAAAAGCTCCAAAGGC-TTTTGGAAAC
130 GAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCAAAGGCTTTTTGGAAAC
1615473 ATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCT-CCGAAGGC
195 ATCATGCACTGAAGGACTTACAGATGACCC-GAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1615537 TTTTTGGAAACA-CATGCACTGAAGGAC-TACAGATG
259 TTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1615572 TGGGAATAGT
Statistics
Matches: 841, Mismatches: 15, Indels: 53
0.93 0.02 0.06
Matches are distributed among these distances:
290 34 0.04
291 87 0.10
292 29 0.03
293 24 0.03
294 103 0.12
295 5 0.01
296 34 0.04
297 132 0.16
298 256 0.30
299 137 0.16
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (299 bp):
GAAGGCTTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
CAGATGACCCGAAGGCTTTGAAACATCAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTG
AAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCAAAGGCTTTTTGGAAACA
TCATGCACTGAAGGACTTACAGATGACCCGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
Found at i:1615883 original size:162 final size:164
Alignment explanation
Indices: 1615576--1615891 Score: 505
Period size: 163 Copynumber: 1.9 Consensus size: 164
1615566 CAGATGTGGG
* * * *
1615576 AATAGTTTACTAAGTAAGAAACTATGGAAATTGTTTTCTTACTATTCAACAATTTCATTTTCAGA
1 AATAGTTTAATAAGTAAGAAACTAAGAAAATCGTTTTCTTACTATTCAACAATTTCATTTTCAGA
**
1615641 AAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAGATAACATGTTGATTGGG
66 AAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAGATAACATGTTGATTGGG
*
1615706 TAACATGCCCCAATCTCCAGATAAGGTTGTTGGA
131 TAACATGCCCCAATCTCAAGATAAGGTTGTTGGA
*
1615740 AATAGTTTAATAAGTAA-AAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT-A-A
1 AATAGTTTAATAAGTAAGAAACTAAGAAAATCGTTTTCTTACTATTCAACAATTTCATTTTCAGA
*
1615802 AAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTTTGAA-ATAACATGTTGATTG
66 AAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTA--TTTTTCAAGATAACATGTTGATTG
1615866 GGTAACATGCCCCAATCTCAAGATAA
129 GGTAACATGCCCCAATCTCAAGATAA
1615892 TACTCATTCT
Statistics
Matches: 141, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
161 38 0.27
162 41 0.29
163 46 0.33
164 16 0.11
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (164 bp):
AATAGTTTAATAAGTAAGAAACTAAGAAAATCGTTTTCTTACTATTCAACAATTTCATTTTCAGA
AAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAGATAACATGTTGATTGGG
TAACATGCCCCAATCTCAAGATAAGGTTGTTGGA
Found at i:1616648 original size:54 final size:51
Alignment explanation
Indices: 1616566--1616683 Score: 157
Period size: 54 Copynumber: 2.3 Consensus size: 51
1616556 CGAATAGCAG
*** *
1616566 GTTCGTAAAACATTTGACAGTGCATTCATCTTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCAT-TTTT--TGTGGCTTCTACTCAGAT
1616620 GTTCGTAAAACATTTGACAACACATTCATTTTTTGTGGCTTCTACTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTTTTTGTGGCTTCTACTCAGAT
*
1616671 GTTC-TCAAACATT
1 GTTCGTAAAACATT
1616684 GAAGCTCTCT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 8 0.14
51 21 0.36
53 4 0.07
54 26 0.44
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (51 bp):
GTTCGTAAAACATTTGACAACACATTCATTTTTTGTGGCTTCTACTCAGAT
Found at i:1617021 original size:54 final size:52
Alignment explanation
Indices: 1616939--1617057 Score: 159
Period size: 54 Copynumber: 2.3 Consensus size: 52
1616929 CGAATAGCAG
*** *
1616939 GTTCGTAAAACATTTGACAGTGCATTCATCTTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCAT-TTTT-CTGTGGCTTCTACTCAGAT
*
1616993 GTTCGTAAAACATTTGACAACACATTCATTTTTTTGTGGCTTCTACTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTTTTCTGTGGCTTCTACTCAGAT
*
1617045 GTTC-TCAAACATT
1 GTTCGTAAAACATT
1617058 GAAGCTCTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
51 8 0.14
52 21 0.36
53 4 0.07
54 26 0.44
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (52 bp):
GTTCGTAAAACATTTGACAACACATTCATTTTTCTGTGGCTTCTACTCAGAT
Found at i:1619445 original size:93 final size:93
Alignment explanation
Indices: 1619279--1619560 Score: 449
Period size: 93 Copynumber: 3.0 Consensus size: 93
1619269 CTTATTTCTA
* ** * * *
1619279 CTATGAGCAAATTCATCTTTTAAATCCAATGATTGGTTTTG-GGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATCCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAG
*
1619343 ATAACTCAAAGAACACTTCTAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
* * *
1619371 CTATGAGCACATTCATCTTCCAAATTCAATGATTCATTCTGTGGTTTCATACCAAATCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATCCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAG
*
1619436 ATAATTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
1619464 CTATGAGCACATTCATCTTCCAAATCCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATCCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAG
*
1619529 ATAACTCAAAGAACACTTCCAGAAGATA
66 ATAACTCAAAGAACACTTCCAGAAGATG
1619557 CTAT
1 CTAT
1619561 TGGGTCTTCT
Statistics
Matches: 173, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 34 0.20
93 139 0.80
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (93 bp):
CTATGAGCACATTCATCTTCCAAATCCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:1622177 original size:30 final size:31
Alignment explanation
Indices: 1622143--1622204 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1622133 CATACACAGA
1622143 AACCTTTGT-AAAAGAGGTATCCACAGGGGG
1 AACCTTTGTAAAAAGAGGTATCCACAGGGGG
1622173 AACCTTTGTAAAAAGAGGTATCCACAGGGGG
1 AACCTTTGTAAAAAGAGGTATCCACAGGGGG
1622204 A
1 A
1622205 TGAATATTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.19
Consensus pattern (31 bp):
AACCTTTGTAAAAAGAGGTATCCACAGGGGG
Found at i:1626725 original size:16 final size:17
Alignment explanation
Indices: 1626695--1626727 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1626685 AATTTTTAAG
1626695 AAAATATATTAATTTAT
1 AAAATATATTAATTTAT
*
1626712 AAAA-ATATTTATTTAT
1 AAAATATATTAATTTAT
1626728 TTAGAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAATATATTAATTTAT
Found at i:1627136 original size:15 final size:14
Alignment explanation
Indices: 1627106--1627165 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
1627096 TATCAAACGT
1627106 AATAATAAAA-TAA
1 AATAATAAAATTAA
1627119 AATAATAATAATTAA
1 AATAATAA-AATTAA
1627134 AATGAA-AGAAATTAA
1 AAT-AATA-AAATTAA
*
1627149 AAGTAATAATATTAA
1 AA-TAATAAAATTAA
1627164 AA
1 AA
1627166 ACTAATGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.20
14 2 0.05
15 25 0.62
16 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AATAATAAAATTAA
Found at i:1628074 original size:13 final size:13
Alignment explanation
Indices: 1628056--1628107 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
1628046 CTTTCGTTTT
1628056 TTTTTCTTTTCTG
1 TTTTTCTTTTCTG
*
1628069 TTTTTCGTTTC--
1 TTTTTCTTTTCTG
*
1628080 TTTTT-TTTTCTT
1 TTTTTCTTTTCTG
*
1628092 TTTTTCTTGTCTG
1 TTTTTCTTTTCTG
1628105 TTT
1 TTT
1628108 CTCTGTAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 4 0.12
11 5 0.16
12 5 0.16
13 18 0.56
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTTCTG
Found at i:1628088 original size:23 final size:24
Alignment explanation
Indices: 1628047--1628097 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1628037 TATCCCTTCC
*
1628047 TTTCGTTTTTTTTTCTTTTCTGTT
1 TTTCGTTTCTTTTTCTTTTCTGTT
*
1628071 TTTCGTTTCTTTTT-TTTTCTTTT
1 TTTCGTTTCTTTTTCTTTTCTGTT
1628094 TTTC
1 TTTC
1628098 TTGTCTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (24 bp):
TTTCGTTTCTTTTTCTTTTCTGTT
Found at i:1628563 original size:3 final size:3
Alignment explanation
Indices: 1628557--1628619 Score: 72
Period size: 3 Copynumber: 20.0 Consensus size: 3
1628547 AATAATTATT
* *
1628557 TAA TAA TAA TAT TATA TAA TAA TATT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
*
1628604 TATT TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA
1628620 CAAATTTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
3 45 0.88
4 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:1628575 original size:13 final size:13
Alignment explanation
Indices: 1628546--1628618 Score: 105
Period size: 13 Copynumber: 5.6 Consensus size: 13
1628536 TTTGGGTTTG
1628546 TAATAATTATTTAA
1 TAATAA-TATTTAA
1628560 TAATAATA-TTATA
1 TAATAATATTTA-A
1628573 TAATAATATTTAA
1 TAATAATATTTAA
*
1628586 TAATAATA-ATAA
1 TAATAATATTTAA
1628598 TAATAATATTTAA
1 TAATAATATTTAA
1628611 TAATAATA
1 TAATAATA
1628619 ACAAATTTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
12 14 0.26
13 31 0.57
14 9 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATAATATTTAA
Found at i:1628611 original size:16 final size:16
Alignment explanation
Indices: 1628546--1628619 Score: 76
Period size: 16 Copynumber: 4.4 Consensus size: 16
1628536 TTTGGGTTTG
*
1628546 TAATAATTATTTAATAA
1 TAATAA-TATATAATAA
*
1628563 TAATATTATATAATAA
1 TAATAATATATAATAA
*
1628579 TATTTAATAATAATAATAA
1 TA-ATAAT-AT-ATAATAA
*
1628598 TAATAATATTTAATAA
1 TAATAATATATAATAA
1628614 TAATAA
1 TAATAA
1628620 CAAATTTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
16 23 0.48
17 10 0.21
18 6 0.12
19 9 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAATATATAATAA
Found at i:1631699 original size:407 final size:410
Alignment explanation
Indices: 1631117--1631933 Score: 1597
Period size: 407 Copynumber: 2.0 Consensus size: 410
1631107 TCTCCCGGAC
1631117 ATCACCCTCTATATCAAAGGCTTGTCCATCTGAAGCCTCAACGATATCATATTTATCAATTATTG
1 ATCACCCTCTATATCAAAGGCTTGTCCATCTGAAGCCTCAACGATATCATATTTATCAATTATTG
1631182 GTATGTCATCGTCTATCACAAGTGGAACAAAAGTTTCATTATCCTCACTAAAATCACCAAAGATT
66 GTATGTCATCGTCTATCACAAGTGGAACAAAAGTTTCATTATCCTCACTAAAATCACCAAAGATT
1631247 TCATCGAATCTCCCGACGAGGTTATCTACATCTTCTGATGGTCCTACTTCTACAGTCATTGGTGC
131 TCATCGAATCTCCCGACGAGGTTATCTACATCTTCTGATGGTCCTACTTCTACAGTCATTGGTGC
1631312 AACACTTGATGAAGTAGGAACATCTACAGTTTCGGCAATAATCTCAATCATTTAATTATTGGAAC
196 AACACTTGATGAAGTAGGAACATCTACAGTTTCGGCAATAATCTCAATCATTTAATTATTGGAAC
1631377 ATTGATGAAGGCCAACCATAACACTTACATCGTTATCATCGTCGATCATGATTGCTTCATATTTG
261 ATTGATGAAGGCCAACCATAACACTTACATCGTTATCATCGTCGATCATGATTGCTTCATATTTG
1631442 AGCGAAGTCTCT-AAA-G-TGTG-TGATAAATCAAACTTGAAATATAACCTCTATTTTTTTTCAA
326 AGCGAAGTCTCTAAAATGATGTGTTGATAAATCAAACTTGAAATATAACCTCTA-TTTTTTTCAA
1631503 TTTTCATTTTCAATTACCGAT
390 TTTTCATTTTCAATTACCGAT
1631524 ATCACCCTCTATATCAAAGGCTTGTCCATCTGAAGCCTCAACGATATCATATTTATCAATTATTG
1 ATCACCCTCTATATCAAAGGCTTGTCCATCTGAAGCCTCAACGATATCATATTTATCAATTATTG
1631589 GTATGTCATCGTCTATCACAAGTGGAACAAAAGTTTCATTATCCTCACTAAAATCACCAAAGATT
66 GTATGTCATCGTCTATCACAAGTGGAACAAAAGTTTCATTATCCTCACTAAAATCACCAAAGATT
1631654 TCATCGAATCTCCCGACGAGGTTATCTACATCTTCTGATGGTCCTACTTCTACAGTCATTGGTGC
131 TCATCGAATCTCCCGACGAGGTTATCTACATCTTCTGATGGTCCTACTTCTACAGTCATTGGTGC
1631719 AACACTTGATGAAGTAGGAACATCTACAGTTTCGGCAATAATCTCAATCATTTAATTATTGGAAC
196 AACACTTGATGAAGTAGGAACATCTACAGTTTCGGCAATAATCTCAATCATTTAATTATTGGAAC
1631784 ATTGATGAAGGCCAACCATAACACTTACATCGTTATCATCGTCGATCATGATTGCTTCATATTTG
261 ATTGATGAAGGCCAACCATAACACTTACATCGTTATCATCGTCGATCATGATTGCTTCATATTTG
1631849 AGCGAAGTCTCTAAAATGATGTGTTGATAAATCAAACTTGAAATATAACCTCTATTTTTTTCAAT
326 AGCGAAGTCTCTAAAATGATGTGTTGATAAATCAAACTTGAAATATAACCTCTATTTTTTTCAAT
1631914 TTTCATTTTCAATTACCGAT
391 TTTCATTTTCAATTACCGAT
1631934 GAGATACATC
Statistics
Matches: 406, Mismatches: 0, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
407 337 0.83
408 3 0.01
409 1 0.00
410 35 0.09
411 30 0.07
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (410 bp):
ATCACCCTCTATATCAAAGGCTTGTCCATCTGAAGCCTCAACGATATCATATTTATCAATTATTG
GTATGTCATCGTCTATCACAAGTGGAACAAAAGTTTCATTATCCTCACTAAAATCACCAAAGATT
TCATCGAATCTCCCGACGAGGTTATCTACATCTTCTGATGGTCCTACTTCTACAGTCATTGGTGC
AACACTTGATGAAGTAGGAACATCTACAGTTTCGGCAATAATCTCAATCATTTAATTATTGGAAC
ATTGATGAAGGCCAACCATAACACTTACATCGTTATCATCGTCGATCATGATTGCTTCATATTTG
AGCGAAGTCTCTAAAATGATGTGTTGATAAATCAAACTTGAAATATAACCTCTATTTTTTTCAAT
TTTCATTTTCAATTACCGAT
Found at i:1632799 original size:22 final size:20
Alignment explanation
Indices: 1632774--1632813 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1632764 TTCCACAAGA
1632774 AATATTAAAATATTAGATCCGG
1 AATA-TAAAAT-TTAGATCCGG
*
1632796 AATATAAAATTTATATCC
1 AATATAAAATTTAGATCC
1632814 AATGAAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.35
Consensus pattern (20 bp):
AATATAAAATTTAGATCCGG
Found at i:1638299 original size:8 final size:7
Alignment explanation
Indices: 1638271--1638297 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1638261 ATGCAAGGCT
1638271 GAAAAAG
1 GAAAAAG
1638278 GAAAAAG
1 GAAAAAG
1638285 GAAAAAG
1 GAAAAAG
1638292 GAAAAA
1 GAAAAA
1638298 AGAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
GAAAAAG
Found at i:1640048 original size:22 final size:22
Alignment explanation
Indices: 1640018--1640070 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1640008 AAAATGTTGA
1640018 ACAAAGAATTTCTTAATTTCTC
1 ACAAAGAATTTCTTAATTTCTC
*
1640040 ATAAAGAATTTCTTAATTTCTC
1 ACAAAGAATTTCTTAATTTCTC
1640062 ACAAAGAAT
1 ACAAAGAAT
1640071 CAGCTGAGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.38
Consensus pattern (22 bp):
ACAAAGAATTTCTTAATTTCTC
Found at i:1645904 original size:3 final size:3
Alignment explanation
Indices: 1645896--1645946 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
1645886 TCATTTCGTT
1645896 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1645942 TTA TT
1 TTA TT
1645947 TAATAAATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1647418 original size:16 final size:17
Alignment explanation
Indices: 1647399--1647440 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1647389 TTTAGTCATT
1647399 ATTTATTTATATTT-TA
1 ATTTATTTATATTTGTA
1647415 ATTTTATTT-TATTTGTA
1 A-TTTATTTATATTTGTA
*
1647432 ATATATTTA
1 ATTTATTTA
1647441 ATTATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
ATTTATTTATATTTGTA
Found at i:1647422 original size:17 final size:17
Alignment explanation
Indices: 1647400--1647433 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1647390 TTAGTCATTA
1647400 TTTATTTATATTT-TAAT
1 TTTATTT-TATTTGTAAT
1647417 TTTATTTTATTTGTAAT
1 TTTATTTTATTTGTAAT
1647434 ATATTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTATTTTATTTGTAAT
Found at i:1647439 original size:21 final size:24
Alignment explanation
Indices: 1647415--1647468 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
1647405 TTATATTTTA
1647415 ATTTTATT-TTATT-TGTAA-TA-T
1 ATTTTATTATTATTAT-TAAGTATT
*
1647436 ATTTAATTATTATTATTAAGTATT
1 ATTTTATTATTATTATTAAGTATT
1647460 ATTTTATTA
1 ATTTTATTA
1647469 ATATATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 7 0.26
22 8 0.30
23 3 0.11
24 9 0.33
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
ATTTTATTATTATTATTAAGTATT
Found at i:1647462 original size:24 final size:25
Alignment explanation
Indices: 1647434--1647500 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 25
1647424 TATTTGTAAT
*
1647434 ATATTTAATTATTATTATTA-AGTA
1 ATATTTAATTATTATTATAATAGTA
* * *
1647458 TTATTTTATTAATA-TATAATAGTA
1 ATATTTAATTATTATTATAATAGTA
*
1647482 ATATTTATTTATT-TTATAA
1 ATATTTAATTATTATTATAA
1647501 ATATCCTATT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
23 4 0.12
24 29 0.88
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (25 bp):
ATATTTAATTATTATTATAATAGTA
Found at i:1650686 original size:15 final size:14
Alignment explanation
Indices: 1650645--1650685 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1650635 ATTTTAAATA
1650645 ATTTACATTTTTGC
1 ATTTACATTTTTGC
1650659 ATTTATGCA-TTTTGC
1 ATTTA--CATTTTTGC
1650674 ATTTACATTTTT
1 ATTTACATTTTT
1650686 TATTTGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 11 0.46
16 2 0.08
ACGTcount: A:0.22, C:0.12, G:0.07, T:0.59
Consensus pattern (14 bp):
ATTTACATTTTTGC
Found at i:1653200 original size:7 final size:7
Alignment explanation
Indices: 1653190--1653248 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
1653180 AGAAGAAGGA
*
1653190 AAAAAAC
1 AAAAAAG
*
1653197 AAAAAGG
1 AAAAAAG
*
1653204 AAAAAGG
1 AAAAAAG
1653211 AAAAAAGG
1 AAAAAA-G
1653219 AAAAAA-
1 AAAAAAG
*
1653225 CAAAAAG
1 AAAAAAG
*
1653232 GAAAAAG
1 AAAAAAG
1653239 AAAAAA-
1 AAAAAAG
1653245 AAAA
1 AAAA
1653249 GGAAAATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
6 9 0.20
7 28 0.64
8 7 0.16
ACGTcount: A:0.81, C:0.03, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1653210 original size:22 final size:22
Alignment explanation
Indices: 1653189--1653247 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1653179 AAGAAGAAGG
**
1653189 AAAAAAACAAAAAGGAAAAAGGA
1 AAAAAAA-AAAAAACAAAAAGGA
**
1653212 AAAAAGGAAAAAACAAAAAGGA
1 AAAAAAAAAAAAACAAAAAGGA
1653234 AAAAGAAAAAAAAA
1 AAAA-AAAAAAAAA
1653248 AGGAAAATTG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.81, C:0.03, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAAACAAAAAGGA
Found at i:1653228 original size:29 final size:30
Alignment explanation
Indices: 1653174--1653245 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 30
1653164 CTCATCCAGC
1653174 AAAGAAAGAAGAAGGAAAAAAACAAAAAGGAA
1 AAAGAAA-AA-AAGGAAAAAAACAAAAAGGAA
*
1653206 AAAGGAAAAAAGG-AAAAAACAAAAAGGAA
1 AAAGAAAAAAAGGAAAAAAACAAAAAGGAA
1653235 AAAGAAAAAAA
1 AAAGAAAAAAA
1653246 AAAGGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 26 0.68
30 4 0.11
31 2 0.05
32 6 0.16
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (30 bp):
AAAGAAAAAAAGGAAAAAAACAAAAAGGAA
Found at i:1653244 original size:15 final size:15
Alignment explanation
Indices: 1653174--1653245 Score: 85
Period size: 15 Copynumber: 4.7 Consensus size: 15
1653164 CTCATCCAGC
1653174 AAAGAAAGAAGAAGGAA
1 AAAGAAA-AA-AAGGAA
1653191 AAA-AACAAAAAGGAA
1 AAAGAA-AAAAAGGAA
*
1653206 AAAGGAAAAAAGGAA
1 AAAGAAAAAAAGGAA
*
1653221 AAA-ACAAAAAGGAA
1 AAAGAAAAAAAGGAA
1653235 AAAGAAAAAAA
1 AAAGAAAAAAA
1653246 AAAGGAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
14 12 0.25
15 27 0.56
16 5 0.10
17 4 0.08
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAGGAA
Found at i:1653254 original size:7 final size:7
Alignment explanation
Indices: 1653197--1653254 Score: 68
Period size: 7 Copynumber: 8.6 Consensus size: 7
1653187 GGAAAAAAAC
1653197 AAAAAGG
1 AAAAAGG
1653204 AAAAAGG
1 AAAAAGG
1653211 AAAAAAGG
1 -AAAAAGG
**
1653219 AAAAAAC
1 AAAAAGG
1653226 AAAAAGG
1 AAAAAGG
1653233 AAAAA-G
1 AAAAAGG
1653239 AAAAA--
1 AAAAAGG
1653244 AAAAAGG
1 AAAAAGG
1653251 AAAA
1 AAAA
1653255 TTGAATCAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
5 5 0.11
6 6 0.14
7 26 0.59
8 7 0.16
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:1658842 original size:76 final size:76
Alignment explanation
Indices: 1658716--1659003 Score: 549
Period size: 76 Copynumber: 3.8 Consensus size: 76
1658706 ATATTTCCCA
1658716 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1658781 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1658792 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1658857 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1658868 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAT
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1658933 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1658944 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
1659004 GTTATTTTGA
Statistics
Matches: 208, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 208 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1659227 original size:76 final size:76
Alignment explanation
Indices: 1659128--1659461 Score: 587
Period size: 76 Copynumber: 4.4 Consensus size: 76
1659118 CTATTTCCCA
*
1659128 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1659193 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1659204 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1659269 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1659280 CATCTGTAAGTCCAACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1659345 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1659356 CATCTGTAAGTCCTACAGTGCATAATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1659421 AACCTTAGGGT
66 AGCCTTAGGGT
* * *
1659432 CATCTGTAAGCCCTTCACTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
1659462 TCAACATTTC
Statistics
Matches: 245, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 245 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1659355 original size:412 final size:412
Alignment explanation
Indices: 1658591--1659415 Score: 1474
Period size: 412 Copynumber: 2.0 Consensus size: 412
1658581 CCAATCAACA
**
1658591 TGTTATTTTGAAAAATAATGAGAAAACGATTTTTATAGTTTCTCATTCAATCTTTTCTAAAAATG
1 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
*
1658656 AAATTGTTGAAAAGTAAGAAAACGATTTTCATAGTTTCTTACATAGTAAAATATTTCCCACATCT
66 AAATTGTTAAAAAGTAAGAAAACGATTTTCATAGTTTCTTACATAGTAAAATATTTCCCACATCT
*
1658721 GTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCT
131 GTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCT
1658786 TAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
196 TAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
*
1658851 TTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG
261 TTTCAAAGCCTTAGGGTCATCTGTAAGTCCAACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG
* *
1658916 CTTTTTGATGTTTTCATAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAA
326 CTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATAATGTTTCCAAAAA
1658981 GCCTTCGAGAGCTTTTTGATGT
391 GCCTTCGAGAGCTTTTTGATGT
**
1659003 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTTTATCTTTTCT-AAAATG
1 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
* * * * *
1659067 AAATTGTTAAAAAGTAAGAAAATGATTTTCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
66 AAATTGTTAAAAAGTAAGAAAACGATTTTCATAG-TTTCTTACATAGTAAAATATTTCCCACATC
1659132 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCC
130 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCC
1659197 TTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC-GAGAGCTTTTTGAT
195 TTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAG-GAGCTTTTTGAT
*
1659261 GTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCAACAGTGCATGATGTTTTCAAAAAGCCTTCGGG
259 GTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCAACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
1659326 AGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATAATGTTTCCAAA
324 AGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATAATGTTTCCAAA
*
1659391 AAGCCTTCGGGAGCTTTTTGATGT
389 AAGCCTTCGAGAGCTTTTTGATGT
1659415 T
1 T
1659416 TTCAAAACCT
Statistics
Matches: 395, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
411 38 0.10
412 357 0.90
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (412 bp):
TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
AAATTGTTAAAAAGTAAGAAAACGATTTTCATAGTTTCTTACATAGTAAAATATTTCCCACATCT
GTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCT
TAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
TTTCAAAGCCTTAGGGTCATCTGTAAGTCCAACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG
CTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATAATGTTTCCAAAAA
GCCTTCGAGAGCTTTTTGATGT
Found at i:1659597 original size:3 final size:3
Alignment explanation
Indices: 1659591--1659658 Score: 75
Period size: 3 Copynumber: 22.3 Consensus size: 3
1659581 TTATTTCGTT
** *
1659591 TTA TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
1659640 TTA -TA TATA TTA CTA TTA T
1 TTA TTA T-TA TTA TTA TTA T
1659659 GTAATAAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 46 0.85
4 6 0.11
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1659669 original size:22 final size:22
Alignment explanation
Indices: 1659625--1659669 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1659615 TTATTATTAT
* *
1659625 TATTAATATTATATATTATATA
1 TATTAATATTATATAATAAATA
* *
1659647 TATTACTATTATGTAATAAATA
1 TATTAATATTATATAATAAATA
1659669 T
1 T
1659670 TACAAGCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTAATATTATATAATAAATA
Found at i:1671271 original size:73 final size:73
Alignment explanation
Indices: 1671152--1671298 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
1671142 CTGATGACAG
1671152 GCGATCAACATCTGGTCAGTGTGTCTATCCTGGGAATCATTTGCTATCATAGAATGCTAGGAAAC
1 GCGATCAACATCTGGTCAGTGTGTCTATCCTGGGAATCATTTGCTATCATAGAATGCTAGGAAAC
1671217 AACGATTT
66 AACGATTT
*
1671225 GCGATCAACATCTGGTCAGTGTGTCTATCTTGGGAATCATTTGCTATCATAGAATGCTAGGAAAC
1 GCGATCAACATCTGGTCAGTGTGTCTATCCTGGGAATCATTTGCTATCATAGAATGCTAGGAAAC
1671290 AACGATTT
66 AACGATTT
1671298 G
1 G
1671299 TTTCTGATTC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (73 bp):
GCGATCAACATCTGGTCAGTGTGTCTATCCTGGGAATCATTTGCTATCATAGAATGCTAGGAAAC
AACGATTT
Found at i:1676065 original size:21 final size:21
Alignment explanation
Indices: 1676018--1676074 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1676008 GTTGACCGTT
* *
1676018 ACGGTGCTGACGTGATAGTTC
1 ACGGTGCTGACGTGGTAGTCC
* *
1676039 ATGGTGCTGACGTGGTGGTCC
1 ACGGTGCTGACGTGGTAGTCC
*
1676060 ACGGTGTTGACGTGG
1 ACGGTGCTGACGTGG
1676075 CAGTTTATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.14, C:0.18, G:0.40, T:0.28
Consensus pattern (21 bp):
ACGGTGCTGACGTGGTAGTCC
Found at i:1676225 original size:21 final size:21
Alignment explanation
Indices: 1676174--1676225 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1676164 ATTGTGGACC
* *
1676174 GTCACGTCAATACCGTGAACT
1 GTCACGTCAGTACCGTAAACT
1676195 GTCACGTCAGTACCGTAAACT
1 GTCACGTCAGTACCGTAAACT
1676216 GTCACGTCAG
1 GTCACGTCAG
1676226 CACTGTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (21 bp):
GTCACGTCAGTACCGTAAACT
Found at i:1676233 original size:21 final size:21
Alignment explanation
Indices: 1676174--1676233 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
1676164 ATTGTGGACC
** *
1676174 GTCACGTCAATACCGTGAACT
1 GTCACGTCAGCACCGTAAACT
*
1676195 GTCACGTCAGTACCGTAAACT
1 GTCACGTCAGCACCGTAAACT
*
1676216 GTCACGTCAGCACTGTAA
1 GTCACGTCAGCACCGTAA
1676234 TGGTCAAACG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (21 bp):
GTCACGTCAGCACCGTAAACT
Found at i:1676881 original size:16 final size:15
Alignment explanation
Indices: 1676855--1676884 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1676845 GTCACAATTT
1676855 TTTAAATTGATTTTA
1 TTTAAATTGATTTTA
1676870 TTTAACATTGATTTT
1 TTTAA-ATTGATTTT
1676885 TTAAAAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (15 bp):
TTTAAATTGATTTTA
Found at i:1677806 original size:26 final size:25
Alignment explanation
Indices: 1677766--1677831 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 25
1677756 GAACAAGATA
*
1677766 AAGATAAAAAA-AACATAAATGAAAT
1 AAGA-AAAAAATAACATAAATAAAAT
*
1677791 AGAGAAAAAAATAACATGAATAAAAT
1 A-AGAAAAAAATAACATAAATAAAAT
1677817 AAGAAATAATAATAA
1 AAGAAA-AA-AATAA
1677832 TGTATGCCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 12 0.34
26 18 0.51
27 5 0.14
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (25 bp):
AAGAAAAAAATAACATAAATAAAAT
Found at i:1677974 original size:4 final size:4
Alignment explanation
Indices: 1677965--1677990 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1677955 AATAAAAGAA
1677965 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1677991 TATGAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1678136 original size:9 final size:9
Alignment explanation
Indices: 1678122--1678159 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
1678112 ATATATATAT
1678122 AAAAATAAA
1 AAAAATAAA
1678131 AAAAAT-AA
1 AAAAATAAA
1678139 AAAAATAAA
1 AAAAATAAA
1678148 AAATAATAAA
1 AAA-AATAAA
1678158 AA
1 AA
1678160 TGAAATGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.30
9 11 0.41
10 8 0.30
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAATAAA
Found at i:1678144 original size:17 final size:18
Alignment explanation
Indices: 1678122--1678159 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
1678112 ATATATATAT
1678122 AAAAATAAAAAA-AATAA
1 AAAAATAAAAAATAATAA
1678139 AAAAATAAAAAATAATAA
1 AAAAATAAAAAATAATAA
1678157 AAA
1 AAA
1678160 TGAAATGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (18 bp):
AAAAATAAAAAATAATAA
Found at i:1680244 original size:17 final size:17
Alignment explanation
Indices: 1680222--1680259 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1680212 ATTTTTTTCA
* *
1680222 AAAAAACAAAATAAGGC
1 AAAAAACAAAAAAAGCC
1680239 AAAAAACAAAAAAAGCC
1 AAAAAACAAAAAAAGCC
1680256 AAAA
1 AAAA
1680260 TTTCAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.76, C:0.13, G:0.08, T:0.03
Consensus pattern (17 bp):
AAAAAACAAAAAAAGCC
Found at i:1686966 original size:34 final size:32
Alignment explanation
Indices: 1686904--1686973 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1686894 ACCTTACAAC
* *
1686904 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
1686936 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
1686970 TCCC
1 TCCC
1686974 CTTTAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:1687282 original size:21 final size:21
Alignment explanation
Indices: 1687256--1687297 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1687246 CCAGAATGGG
*
1687256 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1687277 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1687298 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1687430 original size:15 final size:15
Alignment explanation
Indices: 1687410--1687466 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
1687400 AAACCATGCA
1687410 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
1687425 GGGGAATC-GATACCC
1 GGGGAATCTG-TACCC
*
1687440 TTGGGGGGAATCTGTTCCC
1 ----GGGGAATCTGTACCC
1687459 GGGGAATC
1 GGGGAATC
1687467 GATACCCCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 21 0.60
19 12 0.34
20 1 0.03
ACGTcount: A:0.19, C:0.23, G:0.37, T:0.21
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:1687487 original size:35 final size:34
Alignment explanation
Indices: 1687410--1687493 Score: 141
Period size: 34 Copynumber: 2.4 Consensus size: 34
1687400 AAACCATGCA
* *
1687410 GGGGAATCTGTACCCGGGGAATCGATACCCTTGG
1 GGGGAATCTGTTCCCGGGGAATCGATACCCCTGG
1687444 GGGGAATCTGTTCCCGGGGAATCGATACCCCCTGG
1 GGGGAATCTGTTCCCGGGGAATCGATA-CCCCTGG
1687479 GGGGAATCTGTTCCC
1 GGGGAATCTGTTCCC
1687494 TCTGGGCAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 26 0.55
35 21 0.45
ACGTcount: A:0.18, C:0.26, G:0.35, T:0.21
Consensus pattern (34 bp):
GGGGAATCTGTTCCCGGGGAATCGATACCCCTGG
Found at i:1690790 original size:21 final size:21
Alignment explanation
Indices: 1690765--1690806 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1690755 CCAGAATGGG
*
1690765 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1690786 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1690807 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1690993 original size:35 final size:34
Alignment explanation
Indices: 1690919--1691003 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
1690909 AAACCATGCA
* *
1690919 GGGGGAATCTGTACTCGGGGAATCGATACCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
*
1690953 GGGGGAATCTATTCCCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATA-CCCCTG
1690988 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
1691004 TCTGGGCAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 25 0.54
35 21 0.46
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (34 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
Found at i:1691200 original size:25 final size:25
Alignment explanation
Indices: 1691172--1691219 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1691162 ACAAAGTATA
* *
1691172 AATGTAAATAGAATTATATTATATT
1 AATGTAAATAAAATTATAATATATT
1691197 AATGTAAATAAAATTATAATATA
1 AATGTAAATAAAATTATAATATA
1691220 ATTTGTAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (25 bp):
AATGTAAATAAAATTATAATATATT
Found at i:1693735 original size:2 final size:2
Alignment explanation
Indices: 1693728--1693785 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
1693718 GATTGCTGAA
* *
1693728 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1693770 AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT
1693786 GAAAATAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1695734 original size:3 final size:3
Alignment explanation
Indices: 1695726--1695755 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1695716 TCCATTTTCC
1695726 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1695756 GTTGTTGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1697308 original size:29 final size:29
Alignment explanation
Indices: 1697275--1697362 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
1697265 TCCCCAAGCA
* *
1697275 TAGGTCGCCATGCCCCCCGGGCGACCTTG
1 TAGGTCGCCATGCACGCCGGGCGACCTTG
* * *
1697304 TAGGTCGCCATGCACGCCAGGCGACATGG
1 TAGGTCGCCATGCACGCCGGGCGACCTTG
*
1697333 TAGGTCGCCATGCACGCAGGGCGACCTTG
1 TAGGTCGCCATGCACGCCGGGCGACCTTG
1697362 T
1 T
1697363 CCTGCGCCCT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.16, C:0.34, G:0.33, T:0.17
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCGGGCGACCTTG
Found at i:1697396 original size:22 final size:22
Alignment explanation
Indices: 1697370--1697422 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1697360 TGTCCTGCGC
*
1697370 CCTGCTCCCCGCTGCATGCTCG
1 CCTGCTCCCCACTGCATGCTCG
1697392 CCTGCTCCCCACTGCATGCTCG
1 CCTGCTCCCCACTGCATGCTCG
1697414 CCTGCTCCC
1 CCTGCTCCC
1697423 GCTTCTCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.06, C:0.53, G:0.19, T:0.23
Consensus pattern (22 bp):
CCTGCTCCCCACTGCATGCTCG
Found at i:1697470 original size:25 final size:24
Alignment explanation
Indices: 1697442--1697548 Score: 66
Period size: 22 Copynumber: 4.7 Consensus size: 24
1697432 TGCACCTTTA
1697442 TTCGCTGCATT-ATTGCAGCATAATT
1 TTCGCTGC-TTCA-TGCAGCATAATT
* *
1697467 TTCGTTGCTTCATGCAGCATCA-T
1 TTCGCTGCTTCATGCAGCATAATT
* * *
1697490 TT-GTTGCTTCATGCAACATCA-T
1 TTCGCTGCTTCATGCAGCATAATT
* * *
1697512 TT-GTTCCTTCATGCAGCATCA-T
1 TTCGCTGCTTCATGCAGCATAATT
*
1697534 TT-GTTGCTTCATGCA
1 TTCGCTGCTTCATGCA
1697549 TCAATTATTG
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
22 53 0.71
23 3 0.04
24 11 0.15
25 8 0.11
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (24 bp):
TTCGCTGCTTCATGCAGCATAATT
Found at i:1697562 original size:22 final size:22
Alignment explanation
Indices: 1697455--1697548 Score: 143
Period size: 22 Copynumber: 4.2 Consensus size: 22
1697445 GCTGCATTAT
*
1697455 TGCAGCATAATTTTCGTTGCTTCA
1 TGCAGCATCA-TTT-GTTGCTTCA
1697479 TGCAGCATCATTTGTTGCTTCA
1 TGCAGCATCATTTGTTGCTTCA
* *
1697501 TGCAACATCATTTGTTCCTTCA
1 TGCAGCATCATTTGTTGCTTCA
1697523 TGCAGCATCATTTGTTGCTTCA
1 TGCAGCATCATTTGTTGCTTCA
1697545 TGCA
1 TGCA
1697549 TCAATTATTG
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
22 53 0.82
23 3 0.05
24 9 0.14
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.40
Consensus pattern (22 bp):
TGCAGCATCATTTGTTGCTTCA
Found at i:1699472 original size:18 final size:18
Alignment explanation
Indices: 1699449--1699486 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1699439 AGGCATTTGA
*
1699449 TCCTCTGGTCGTGCTTGT
1 TCCTCTGGTCGAGCTTGT
*
1699467 TCCTCTGGTGGAGCTTGT
1 TCCTCTGGTCGAGCTTGT
1699485 TC
1 TC
1699487 ATCGTGCTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.26, G:0.29, T:0.42
Consensus pattern (18 bp):
TCCTCTGGTCGAGCTTGT
Found at i:1701108 original size:23 final size:23
Alignment explanation
Indices: 1701076--1701119 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1701066 TCCCCTGTGG
1701076 GGGGAATCAGTTCCCCTTCAAAA
1 GGGGAATCAGTTCCCCTTCAAAA
*
1701099 GGGGATTCAGTTCCCCTTCAA
1 GGGGAATCAGTTCCCCTTCAA
1701120 GAGAGGTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (23 bp):
GGGGAATCAGTTCCCCTTCAAAA
Found at i:1704910 original size:20 final size:21
Alignment explanation
Indices: 1704839--1704911 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 21
1704829 TTGAAAGTAA
*
1704839 ATTTTGCAAATCTA-AAATTTT
1 ATTTT-CAAATCTACTAATTTT
* * * *
1704860 CTTTTCAAACTCTTCTAGTTTG
1 ATTTTCAAA-TCTACTAATTTT
*
1704882 ATTTGCAAATC-ACTAATTTT
1 ATTTTCAAATCTACTAATTTT
1704902 ATTTTCAAAT
1 ATTTTCAAAT
1704912 TCTTTGTTGG
Statistics
Matches: 39, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
20 19 0.49
21 9 0.23
22 11 0.28
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.48
Consensus pattern (21 bp):
ATTTTCAAATCTACTAATTTT
Found at i:1704984 original size:22 final size:21
Alignment explanation
Indices: 1704942--1704981 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1704932 GAGCTTATTT
*
1704942 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1704963 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1704982 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1707336 original size:18 final size:19
Alignment explanation
Indices: 1707308--1707343 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1707298 AAATTTTCAT
1707308 TTTATTTATTTTAAATTAG
1 TTTATTTATTTTAAATTAG
1707327 TTTA-TTATTTTAAATTA
1 TTTATTTATTTTAAATTA
1707344 TTAGTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTATTTATTTTAAATTAG
Found at i:1707373 original size:17 final size:17
Alignment explanation
Indices: 1707351--1707384 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1707341 TTATTAGTTT
1707351 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
1707368 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
1707385 CTAAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (17 bp):
GTTAGTTTAGGGTTAGG
Found at i:1707577 original size:15 final size:15
Alignment explanation
Indices: 1707559--1707608 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1707549 AAAAATTGTT
1707559 TATTAGTTTAAGTTA
1 TATTAGTTTAAGTTA
**
1707574 TATTAAAGAAT-AGTT-
1 TATT--AGTTTAAGTTA
1707589 TATTAGTTTAAGTTA
1 TATTAGTTTAAGTTA
1707604 TATTA
1 TATTA
1707609 AAAAATAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 3 0.11
14 4 0.15
15 13 0.48
16 4 0.15
17 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (15 bp):
TATTAGTTTAAGTTA
Found at i:1707590 original size:30 final size:30
Alignment explanation
Indices: 1707522--1707626 Score: 147
Period size: 30 Copynumber: 3.4 Consensus size: 30
1707512 TTTAGTTAAT
* * *
1707522 TAGTTTTTTAGTAGTAAATTATAATTAAAAAA
1 TAGTTTATTAGT-TTAAGTTAT-ATTAAAAAA
* *
1707554 TTGTTTATTAGTTTAAGTTATATTAAAGAA
1 TAGTTTATTAGTTTAAGTTATATTAAAAAA
1707584 TAGTTTATTAGTTTAAGTTATATTAAAAAA
1 TAGTTTATTAGTTTAAGTTATATTAAAAAA
1707614 TAGTTTATTAGTT
1 TAGTTTATTAGTT
1707627 GTTTAAGGGA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 49 0.74
31 7 0.11
32 10 0.15
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAGTTATATTAAAAAA
Found at i:1707709 original size:15 final size:16
Alignment explanation
Indices: 1707681--1707714 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1707671 GTTTGTTACT
1707681 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
1707697 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
1707712 TTA
1 TTA
1707715 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:1709532 original size:17 final size:17
Alignment explanation
Indices: 1709510--1709551 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
1709500 TTAGTATCAA
1709510 AATAATTAAATATTAAT
1 AATAATTAAATATTAAT
* *
1709527 AATAATTCATTATTAAT
1 AATAATTAAATATTAAT
1709544 AATAATTA
1 AATAATTA
1709552 GTAAATCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAATTAAATATTAAT
Found at i:1709547 original size:60 final size:59
Alignment explanation
Indices: 1709453--1709582 Score: 199
Period size: 60 Copynumber: 2.2 Consensus size: 59
1709443 GATTTTTAGT
* *
1709453 ATTAAATCATTATTATAATTTCATTATTAGTAATAATTAGTAAATCATTAGTATCAAAATA
1 ATTAAAT-ATTATAATAATTTCATTATTAATAATAATTAGTAAATCATTAGTATC-AAATA
*
1709514 ATTAAATATTAATAATAA-TTCATTATTAATAATAATTAGTAAATCATTAGTATCAAATC
1 ATTAAATATT-ATAATAATTTCATTATTAATAATAATTAGTAAATCATTAGTATCAAATA
1709573 ATTAAATATT
1 ATTAAATATT
1709583 TAAAAATCAT
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
59 14 0.22
60 38 0.58
61 13 0.20
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (59 bp):
ATTAAATATTATAATAATTTCATTATTAATAATAATTAGTAAATCATTAGTATCAAATA
Found at i:1709700 original size:14 final size:14
Alignment explanation
Indices: 1709679--1709958 Score: 160
Period size: 14 Copynumber: 21.3 Consensus size: 14
1709669 ATTAGTAATA
1709679 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1709693 AGTATTAAATCATT
1 ATTATTAAATCATT
*
1709707 ATTA-TAAA--ATC
1 ATTATTAAATCATT
*
1709718 ATTACTAAATC---
1 ATTATTAAATCATT
1709729 ATTATTAAATCATT
1 ATTATTAAATCATT
1709743 -TCTATTAAATCATT
1 AT-TATTAAATCATT
*
1709757 ATTA-T-AATGATT
1 ATTATTAAATCATT
1709769 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1709783 GTTA-T---T-ATT
1 ATTATTAAATCATT
1709792 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1709806 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1709818 ATTACTAAAT-ATT
1 ATTATTAAATCATT
*
1709831 ATTA-T-AATGATT
1 ATTATTAAATCATT
* *
1709843 CTTATCAAATCATT
1 ATTATTAAATCATT
*
1709857 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1709869 ATTATCAAATCATT
1 ATTATTAAATCATT
*
1709883 ACTAAATCATCAAATCATT
1 A-T---T-ATTAAATCATT
* *
1709902 AAATATTAAA--ATC
1 -ATTATTAAATCATT
*
1709915 ATTATTAAATAATT
1 ATTATTAAATCATT
*
1709929 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1709941 ATTACTAAATCATT
1 ATTATTAAATCATT
1709955 ATTA
1 ATTA
1709959 AATCATAATA
Statistics
Matches: 210, Mismatches: 24, Indels: 64
0.70 0.08 0.21
Matches are distributed among these distances:
9 6 0.03
10 2 0.01
11 19 0.09
12 59 0.28
13 22 0.10
14 81 0.39
15 7 0.03
16 1 0.00
18 1 0.00
19 11 0.05
20 1 0.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:1709781 original size:26 final size:26
Alignment explanation
Indices: 1709666--1709980 Score: 263
Period size: 26 Copynumber: 12.7 Consensus size: 26
1709656 TTATTCCATA
* * *
1709666 ATTATTAGT-AATAATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATG
* *
1709690 ATTAGTATTAAATCATTATTATAA-A
1 ATTATTATTAAATCATTATTATAATG
* * *
1709715 ATCATTACTAAATCATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATG
1709740 ATT-TCTATTAAATCATTATTATAATG
1 ATTAT-TATTAAATCATTATTATAATG
*
1709766 ATTATTATTAAATCATTGTTAT--T-
1 ATTATTATTAAATCATTATTATAATG
1709789 ATTATTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
*
1709815 ATTATTACTAAAT-ATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
* *
1709840 ATTCTTATCAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
* * *
1709866 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATTAAATCATTATTATAATG
* *
1709891 ATCAAATCATT-AA--A-TATTA-AA--
1 AT--TATTATTAAATCATTATTATAATG
* *
1709912 ATCATTATTAAATAATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
* *
1709938 ATTATTACTAAATCATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATG
*
1709963 A-TAATATTAAAATCATTA
1 ATTATTATT-AAATCATTA
1709981 CTAAATCATC
Statistics
Matches: 239, Mismatches: 32, Indels: 39
0.77 0.10 0.13
Matches are distributed among these distances:
19 5 0.02
20 2 0.01
21 2 0.01
22 1 0.00
23 32 0.13
24 19 0.08
25 86 0.36
26 87 0.36
27 5 0.02
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (26 bp):
ATTATTATTAAATCATTATTATAATG
Found at i:1709807 original size:20 final size:21
Alignment explanation
Indices: 1709766--1709810 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
1709756 TATTATAATG
1709766 ATTATTATTAAATCATTGTTATT
1 ATTATTATTAAATCA-T-TTATT
1709789 ATTATTATTAAATCA-TTATT
1 ATTATTATTAAATCATTTATT
1709809 AT
1 AT
1709811 AATGATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
23 15 0.68
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTATTATTAAATCATTTATT
Found at i:1709909 original size:100 final size:96
Alignment explanation
Indices: 1709699--1710000 Score: 300
Period size: 100 Copynumber: 3.1 Consensus size: 96
1709689 CATTAGTATT
* * * *
1709699 AAATCATT-ATTA-TAAAATCATTACTAAATCATTATTA-AATCATTTCTATTAAATCATTATTA
1 AAATCATTAAATATTAAAATCATTACTAAATAATTATTATAATGATTT-TATCAAATCATTATTA
* * * *
1709761 TAATGATTATTATTAAATCATTGTTATTATTATTATT
65 TAATGATTATTA-TAAATCA---TTACTA-AATCATC
* * *
1709798 AAATCATT-ATTA-TAATGATTATTACTAAAT-ATTATTATAATGATTCTTATCAAATCATTATT
1 AAATCATTAAATATTAA-AATCATTACTAAATAATTATTATAATGATT-TTATCAAATCATTATT
1709860 ATAATGATTATTATCAAATCATTACTAAATCATC
64 ATAATGATTATTAT-AAATCATTACTAAATCATC
*
1709894 AAATCATTAAATATTAAAATCATTATTAAATAATTATTATAATGATTATTA-CTAAATCATTATT
1 AAATCATTAAATATTAAAATCATTACTAAATAATTATTATAATGATT-TTATC-AAATCATTATT
*
1709958 A-AATCATAATATTA-AAATCATTACTAAATCATC
64 ATAATGAT--TATTATAAATCATTACTAAATCATC
1709991 AAAT-ATTAAA
1 AAATCATTAAA
1710001 ATCATTACAA
Statistics
Matches: 179, Mismatches: 14, Indels: 23
0.83 0.06 0.11
Matches are distributed among these distances:
96 18 0.10
97 48 0.27
98 33 0.18
99 28 0.16
100 51 0.28
101 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (96 bp):
AAATCATTAAATATTAAAATCATTACTAAATAATTATTATAATGATTTTATCAAATCATTATTAT
AATGATTATTATAAATCATTACTAAATCATC
Found at i:1709930 original size:123 final size:123
Alignment explanation
Indices: 1709792--1710057 Score: 369
Period size: 124 Copynumber: 2.2 Consensus size: 123
1709782 TGTTATTATT
* *
1709792 ATTATTAAATCATTATTATAATGATTATTACTAAAT-ATTATTATAATGAT-TCTTATCAAATCA
1 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTA-AATCATATATTA--AAATCA
* * * * * *
1709855 TTATTATAATGAT-TATTA-TCAAATCATTACTAAATCATCAAATCATTAAATATTAAAATC
63 TTACTA-AATCATCAAATATTAAAATCATTACAAAATCATCAAATCATTAAATATTAAAATC
*
1709915 ATTATTAAATAATTATTATAATGATTATTACTAAATCATTATTAAATCATAATATTAAAATCATT
1 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTAAATCAT-ATATTAAAATCATT
1709980 ACTAAATCATCAAATATTAAAATCATTACAAAATCATCAAATCATTAAATATTAAAATC
65 ACTAAATCATCAAATATTAAAATCATTACAAAATCATCAAATCATTAAATATTAAAATC
*
1710039 ATTATTAAATCATTTTTAT
1 ATTATTAAATCATTATTAT
1710058 GGTTAATTGA
Statistics
Matches: 127, Mismatches: 11, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
122 5 0.04
123 54 0.43
124 64 0.50
125 4 0.03
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.42
Consensus pattern (123 bp):
ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTAAATCATATATTAAAATCATTA
CTAAATCATCAAATATTAAAATCATTACAAAATCATCAAATCATTAAATATTAAAATC
Found at i:1709995 original size:27 final size:27
Alignment explanation
Indices: 1709947--1710028 Score: 123
Period size: 27 Copynumber: 3.1 Consensus size: 27
1709937 GATTATTACT
*
1709947 AAATCATTATTAAATCAT--AATATTA
1 AAATCATTACTAAATCATCAAATATTA
1709972 AAATCATTACTAAATCATCAAATATTA
1 AAATCATTACTAAATCATCAAATATTA
*
1709999 AAATCATTACAAAATCATCAAATCATTA
1 AAATCATTACTAAATCATCAAAT-ATTA
1710027 AA
1 AA
1710029 TATTAAAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
25 17 0.33
27 29 0.56
28 6 0.12
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATCATTACTAAATCATCAAATATTA
Found at i:1710002 original size:8 final size:9
Alignment explanation
Indices: 1709968--1710052 Score: 63
Period size: 8 Copynumber: 9.3 Consensus size: 9
1709958 AAATCATAAT
1709968 ATTAAAATC
1 ATTAAAATC
1709977 ATTACTAAATC
1 ATTA--AAATC
*
1709988 A-TCAAAT-
1 ATTAAAATC
1709995 ATTAAAATC
1 ATTAAAATC
1710004 ATTACAAAATC
1 ATT--AAAATC
*
1710015 A-TCAAATC
1 ATTAAAATC
1710023 ATT-AAAT-
1 ATTAAAATC
1710030 ATTAAAATC
1 ATTAAAATC
1710039 ATTATTAAATC
1 ATTA--AAATC
1710050 ATT
1 ATT
1710053 TTTATGGTTA
Statistics
Matches: 62, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
7 4 0.06
8 23 0.37
9 12 0.19
10 2 0.03
11 21 0.34
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAAATC
Found at i:1710030 original size:35 final size:35
Alignment explanation
Indices: 1709983--1710051 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
1709973 AATCATTACT
1709983 AAATCATCAAATATTAAAATCATTACAAAATCATC
1 AAATCATCAAATATTAAAATCATTACAAAATCATC
* **
1710018 AAATCATTAAATATTAAAATCATTATTAAATCAT
1 AAATCATCAAATATTAAAATCATTACAAAATCAT
1710052 TTTTATGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (35 bp):
AAATCATCAAATATTAAAATCATTACAAAATCATC
Found at i:1710322 original size:49 final size:49
Alignment explanation
Indices: 1710259--1710570 Score: 534
Period size: 49 Copynumber: 6.3 Consensus size: 49
1710249 ATTACTAATA
* * *
1710259 ATTACTAAATCATTACTATCAAATCATTAAATATTAACAATAATTTAATT
1 ATTACT-AATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
*
1710309 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTAATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
*
1710358 ATTACTAATCATTACTACCAAATTATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
*
1710407 ATTACTAATAATTACTACCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
*
1710456 ATGACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
*
1710505 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
*
1710554 ATTACTAATAATTACTA
1 ATTACTAATCATTACTA
1710571 AATAATTATT
Statistics
Matches: 251, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
49 245 0.98
50 6 0.02
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
Found at i:1710513 original size:18 final size:18
Alignment explanation
Indices: 1710486--1710566 Score: 55
Period size: 18 Copynumber: 4.8 Consensus size: 18
1710476 AATCATTAAA
*
1710486 TATTAATAATAATTTCAT
1 TATTACTAATAATTTCAT
* *
1710504 TATTACTAATCA-TT-AC
1 TATTACTAATAATTTCAT
* * **
1710520 TA-T-CAAATCATTAAAT
1 TATTACTAATAATTTCAT
*
1710536 -ATTAATAATAATTTCAT
1 TATTACTAATAATTTCAT
1710553 TATTACTAATAATT
1 TATTACTAATAATT
1710567 ACTAAATAAT
Statistics
Matches: 46, Mismatches: 12, Indels: 10
0.68 0.18 0.15
Matches are distributed among these distances:
14 6 0.13
15 3 0.07
16 5 0.11
17 10 0.22
18 22 0.48
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTACTAATAATTTCAT
Found at i:1711538 original size:17 final size:17
Alignment explanation
Indices: 1711483--1711544 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
1711473 ATAATATAAA
*
1711483 TTAAACAAAATATTTTT
1 TTAAACACAATATTTTT
* *
1711500 TTAAAACAACACTAAATATTT
1 TT-AAAC-ACA--ATATTTTT
1711521 TTAAACACAATATTTTT
1 TTAAACACAATATTTTT
1711538 TTAAACA
1 TTAAACA
1711545 GAAATTATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 15 0.42
18 4 0.11
19 5 0.14
20 4 0.11
21 8 0.22
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAACACAATATTTTT
Found at i:1711636 original size:14 final size:14
Alignment explanation
Indices: 1711617--1711643 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1711607 CACATACACA
1711617 ACAACAAAAAATAG
1 ACAACAAAAAATAG
1711631 ACAACAAAAAATA
1 ACAACAAAAAATA
1711644 ATAAATTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
ACAACAAAAAATAG
Found at i:1711636 original size:17 final size:17
Alignment explanation
Indices: 1711614--1711646 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1711604 TTGCACATAC
1711614 ACAACAACAAAA-AATAG
1 ACAACAA-AAAATAATAG
1711631 ACAACAAAAAATAATA
1 ACAACAAAAAATAATA
1711647 AATTACCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
ACAACAAAAAATAATAG
Found at i:1712070 original size:28 final size:30
Alignment explanation
Indices: 1712030--1712092 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
1712020 ATTTTTTATA
1712030 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1712060 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1712088 TAATA
1 TAATA
1712093 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:1712099 original size:28 final size:28
Alignment explanation
Indices: 1712034--1712099 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
1712024 TTTATATAAT
1712034 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
1712062 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
1712090 ATAATTTATA
1 ATAATATATA
1712100 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:1712102 original size:21 final size:21
Alignment explanation
Indices: 1712069--1712117 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1712059 CTAATATAAT
1712069 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1712090 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1712111 ATTAACT
1 A-TAACT
1712118 AATTTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1712586 original size:29 final size:29
Alignment explanation
Indices: 1712554--1712662 Score: 114
Period size: 29 Copynumber: 3.8 Consensus size: 29
1712544 GTCGCGGGGC
*
1712554 GTGCTTGACGACCTACCAT-GTCGCCGCGA
1 GTGCATGACGACCT-CCATGGTCGCCGCGA
** *
1712583 GTGCATGACGACCTCTTTGGTCGCCGGGA
1 GTGCATGACGACCTCCATGGTCGCCGCGA
**
1712612 GTGCATGACGACCTCTTTGGTCGCC-CGAA
1 GTGCATGACGACCTCCATGGTCGCCGCG-A
* *
1712641 GTGCATGGCGACCTCCTTGGTC
1 GTGCATGACGACCTCCATGGTC
1712663 TCCCGGAGGG
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
28 3 0.04
29 68 0.96
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.24
Consensus pattern (29 bp):
GTGCATGACGACCTCCATGGTCGCCGCGA
Found at i:1712635 original size:58 final size:58
Alignment explanation
Indices: 1712540--1712676 Score: 152
Period size: 58 Copynumber: 2.4 Consensus size: 58
1712530 GGGTTAAAAG
* * *
1712540 CTTGGTCGCGGGGCGTGCTTGACGACCTACCATGTCGCCGCG-AGTGCATGACGACCTC
1 CTTGGTCGCCGGGAGTGCATGACGACCTACCATGTCGCC-CGAAGTGCATGACGACCTC
* ** *
1712598 TTTGGTCGCCGGGAGTGCATGACGACCT-CTTTGGTCGCCCGAAGTGCATGGCGACCTC
1 CTTGGTCGCCGGGAGTGCATGACGACCTACCAT-GTCGCCCGAAGTGCATGACGACCTC
* * *
1712656 CTTGGTCTCCCGGAGGGCATG
1 CTTGGTCGCCGGGAGTGCATG
1712677 GCTACCTATG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 4 0.06
58 62 0.94
ACGTcount: A:0.13, C:0.31, G:0.34, T:0.23
Consensus pattern (58 bp):
CTTGGTCGCCGGGAGTGCATGACGACCTACCATGTCGCCCGAAGTGCATGACGACCTC
Found at i:1712678 original size:29 final size:29
Alignment explanation
Indices: 1712573--1712676 Score: 138
Period size: 29 Copynumber: 3.6 Consensus size: 29
1712563 GACCTACCAT
1712573 GTCG-CCGCGAGTGCATGACGACCTCTTTG
1 GTCGCCCG-GAGTGCATGACGACCTCTTTG
*
1712602 GTCGCCGGGAGTGCATGACGACCTCTTTG
1 GTCGCCCGGAGTGCATGACGACCTCTTTG
* * *
1712631 GTCGCCCGAAGTGCATGGCGACCTCCTTG
1 GTCGCCCGGAGTGCATGACGACCTCTTTG
* *
1712660 GTCTCCCGGAGGGCATG
1 GTCGCCCGGAGTGCATG
1712677 GCTACCTATG
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
29 64 0.97
30 2 0.03
ACGTcount: A:0.13, C:0.31, G:0.34, T:0.22
Consensus pattern (29 bp):
GTCGCCCGGAGTGCATGACGACCTCTTTG
Found at i:1713456 original size:34 final size:34
Alignment explanation
Indices: 1713411--1713477 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
1713401 AATAGGAATT
*
1713411 ACAACTTCTCTC-GATATACCAAGGAGAAAACAATG
1 ACAACTTCTCTCTGATA-A-AAAGGAGAAAACAATG
1713446 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
1713478 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 5 0.17
36 4 0.14
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATG
Found at i:1719062 original size:15 final size:15
Alignment explanation
Indices: 1719042--1719071 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1719032 CGTTATTTTA
1719042 AAATTAAATAAATTT
1 AAATTAAATAAATTT
*
1719057 AAATTAAATTAATTT
1 AAATTAAATAAATTT
1719072 TTTTCATATC
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATTAAATAAATTT
Found at i:1719839 original size:12 final size:12
Alignment explanation
Indices: 1719831--1719863 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1719821 ACGCAACCAC
1719831 ATCCGCAACAAA
1 ATCCGCAACAAA
1719843 ATCCGCAACAAA
1 ATCCGCAACAAA
1719855 ATCCGCAAC
1 ATCCGCAAC
1719864 CCCACGCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.45, C:0.36, G:0.09, T:0.09
Consensus pattern (12 bp):
ATCCGCAACAAA
Found at i:1723399 original size:29 final size:29
Alignment explanation
Indices: 1723367--1723423 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1723357 AATAAAAATT
*
1723367 ATTTTAATTAAAATTAATA-GTCAAATAAA
1 ATTTTAATCAAAATTAA-AGGTCAAATAAA
* *
1723396 ATTTTAGTCATAATTAAAGGTCAAATAA
1 ATTTTAATCAAAATTAAAGGTCAAATAA
1723424 GATAATTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (29 bp):
ATTTTAATCAAAATTAAAGGTCAAATAAA
Found at i:1723881 original size:16 final size:15
Alignment explanation
Indices: 1723862--1723893 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1723852 ATGGATAAAA
1723862 ATAAAGATAAGAATAG
1 ATAAAGATAA-AATAG
1723878 ATAAAGATAAAATAG
1 ATAAAGATAAAATAG
1723893 A
1 A
1723894 GATACGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.19
Consensus pattern (15 bp):
ATAAAGATAAAATAG
Found at i:1731172 original size:21 final size:21
Alignment explanation
Indices: 1731148--1731190 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1731138 AATGAAATGG
*
1731148 AAGTAGATGAAGTACCTTGGT
1 AAGTAGATAAAGTACCTTGGT
*
1731169 AAGTAGATAAAGTGCCTTGGT
1 AAGTAGATAAAGTACCTTGGT
1731190 A
1 A
1731191 GAAGGTGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (21 bp):
AAGTAGATAAAGTACCTTGGT
Found at i:1732239 original size:24 final size:24
Alignment explanation
Indices: 1732212--1732267 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
1732202 AACTACCCCG
**
1732212 TAGAATTTGCACTGAAGTACCACA
1 TAGAATTTGCACCAAAGTACCACA
* *
1732236 TAGAATATGCACCAAAGTGCCACA
1 TAGAATTTGCACCAAAGTACCACA
1732260 TAG-ATTTG
1 TAGAATTTG
1732268 TCCCCGAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (24 bp):
TAGAATTTGCACCAAAGTACCACA
Found at i:1732300 original size:23 final size:24
Alignment explanation
Indices: 1732260--1732310 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
1732250 AAGTGCCACA
* * *
1732260 TAGATTTGTCCCCGAAGGATCGCG
1 TAGAGTTGTCCCCGAAGGACCGAG
1732284 TAGAGTTGT-CCCGAAGGACCGAG
1 TAGAGTTGTCCCCGAAGGACCGAG
1732307 TAGA
1 TAGA
1732311 ACCCTCAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (24 bp):
TAGAGTTGTCCCCGAAGGACCGAG
Found at i:1736944 original size:23 final size:23
Alignment explanation
Indices: 1736918--1736983 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
1736908 AATGATCGCG
*
1736918 TAGAATTGTCCCAAAGGACCATA
1 TAGAATTGTCCCGAAGGACCATA
*
1736941 TAGAATTGTCCTGAAGGACCATA
1 TAGAATTGTCCCGAAGGACCATA
1736964 TAGAATTGTCCCGAAGGACC
1 TAGAATTGTCCCGAAGGACC
1736984 GCGTAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGGACCATA
Found at i:1736991 original size:23 final size:23
Alignment explanation
Indices: 1736890--1736983 Score: 98
Period size: 23 Copynumber: 4.1 Consensus size: 23
1736880 CATGAAAGTG
* *
1736890 CCACATAGATTTGTCCCAAATGA
1 CCACATAGAATTGTCCCAAAGGA
* * *
1736913 TCGCGTAGAATTGTCCCAAAGGA
1 CCACATAGAATTGTCCCAAAGGA
* **
1736936 CCATATAGAATTGTCCTGAAGGA
1 CCACATAGAATTGTCCCAAAGGA
* *
1736959 CCATATAGAATTGTCCCGAAGGA
1 CCACATAGAATTGTCCCAAAGGA
1736982 CC
1 CC
1736984 GCGTAGAACC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (23 bp):
CCACATAGAATTGTCCCAAAGGA
Found at i:1743348 original size:24 final size:26
Alignment explanation
Indices: 1743320--1743367 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
1743310 AAAAATGTTA
*
1743320 TTTTAAAAATA-TATAAT-ATATATG
1 TTTTAAAAAAATTATAATCATATATG
1743344 TTTTAAAAAAATTATAATCATATA
1 TTTTAAAAAAATTATAATCATATA
1743368 ATATACTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 6 0.29
26 5 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
TTTTAAAAAAATTATAATCATATATG
Found at i:1743437 original size:37 final size:37
Alignment explanation
Indices: 1743386--1743553 Score: 178
Period size: 37 Copynumber: 4.8 Consensus size: 37
1743376 TCAGATAATA
* *
1743386 TTTT-AAAATTATATATTATATATTTTTTAAAAATGT
1 TTTTAAAAATCATATATTATATATATTTTAAAAATGT
* * *
1743422 TTTCAAAAATCATATATTATATA-GTTTTCAAAATG-
1 TTTTAAAAATCATATATTATATATATTTTAAAAATGT
1743457 TTTT--AAA--AT-TATTATATA-ATTTTAAAAATGT
1 TTTTAAAAATCATATATTATATATATTTTAAAAATGT
*
1743488 TTTTAAAAATCATATATTATATATATTTCAAAAATGT
1 TTTTAAAAATCATATATTATATATATTTTAAAAATGT
* * *
1743525 TTTTTAAAA-C-CATACTATATATATTTTAA
1 TTTTAAAAATCATATATTATATATATTTTAA
1743554 TTTTATTTTA
Statistics
Matches: 112, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
30 19 0.17
31 6 0.05
33 6 0.05
35 21 0.19
36 23 0.21
37 37 0.33
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (37 bp):
TTTTAAAAATCATATATTATATATATTTTAAAAATGT
Found at i:1743470 original size:30 final size:31
Alignment explanation
Indices: 1743399--1743533 Score: 101
Period size: 36 Copynumber: 4.0 Consensus size: 31
1743389 TAAAATTATA
* *
1743399 TATTATATATTTTTTAAAAATGTTTTCAAAAATCAT
1 TATTATATA-ATTTTAAAAATGTTTT--TAAA--AT
* *
1743435 ATATTATATAGTTTTCAAAATG-TTTTAAAAT
1 -TATTATATAATTTTAAAAATGTTTTTAAAAT
1743466 TATTATATAATTTTAAAAATGTTTTTAAAAATCAT
1 TATTATATAATTTTAAAAATGTTTTT--AAA--AT
*
1743501 ATATTATATATATTTCAAAAATGTTTTTTAAAA
1 -TATTATATA-ATTTTAAAAATG-TTTTTAAAA
1743534 CCATACTATA
Statistics
Matches: 84, Mismatches: 6, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
30 19 0.23
31 6 0.07
33 6 0.07
34 1 0.01
35 5 0.06
36 22 0.26
37 20 0.24
38 5 0.06
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (31 bp):
TATTATATAATTTTAAAAATGTTTTTAAAAT
Found at i:1743481 original size:66 final size:68
Alignment explanation
Indices: 1743399--1743527 Score: 210
Period size: 66 Copynumber: 1.9 Consensus size: 68
1743389 TAAAATTATA
*
1743399 TATTATATATTTTTTAAAAATGTTTTCAAAAATCATATATTATATAGT-TTTC-AAAATGTTTTA
1 TATTATATATATTTTAAAAATGTTTTCAAAAATCATATATTATATA-TATTTCAAAAATGTTTTA
1743462 AAAT
65 AAAT
*
1743466 TATTATATA-ATTTTAAAAATGTTTTTAAAAATCATATATTATATATATTTCAAAAATGTTTT
1 TATTATATATATTTTAAAAATGTTTTCAAAAATCATATATTATATATATTTCAAAAATGTTTT
1743528 TTAAAACCAT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
65 1 0.02
66 38 0.66
67 19 0.33
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (68 bp):
TATTATATATATTTTAAAAATGTTTTCAAAAATCATATATTATATATATTTCAAAAATGTTTTAA
AAT
Found at i:1743667 original size:29 final size:29
Alignment explanation
Indices: 1743612--1743667 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
1743602 AACTATATAT
* * *
1743612 TATACATTTTCAAAAATATTTCCAAAAGC
1 TATACATTTTCAAAAAAAATTCAAAAAGC
* *
1743641 TATATATTTTTAAAAAAAATTCAAAAA
1 TATACATTTTCAAAAAAAATTCAAAAA
1743668 ACCATATTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.36
Consensus pattern (29 bp):
TATACATTTTCAAAAAAAATTCAAAAAGC
Found at i:1744567 original size:84 final size:84
Alignment explanation
Indices: 1744318--1745019 Score: 805
Period size: 84 Copynumber: 8.4 Consensus size: 84
1744308 AATGCAATCA
* * * * *
1744318 AACTCGGAGGTCTTCGGTTGACAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
1744383 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * * *
1744402 AACTTGAAGGTCTTTGG-TGACAGATAACCCTTCTTGACTGAAGCTATGTTACAAATG--ATGCC
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
1744464 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* *
1744483 AACTCGAAGATCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
1744548 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * * * * *
1744567 AACTTGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAGATGATGTGT
1 AACTCGAAGGTC-TTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-
* * * * *
1744631 CCTCGAAGCTGAGTGTAATCA
64 CCTTGGAGCTGAGCGTAGTCG
*
1744652 AACTCGAGGGTCTTTGGTTGGA-AGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGC
1 AACTCGAAGGTCTTTGGTT-GACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGC
1744716 CTTGGAGCTGAGCGTAGTCG
65 CTTGGAGCTGAGCGTAGTCG
* * * * * * *
1744736 AACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAGATGATGTGT
1 AACTCGAAGGTC-TTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-
* * ** *
1744800 CCTCGAAGCTGAATGTAATCG
64 CCTTGGAGCTGAGCGTAGTCG
* * * * ** ** *
1744821 AACTTGAGGGTCTTT-G--G-CAGATAGCCCTTATCGACTTAAACTATGCTATAAATGATGTGCC
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
1744882 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
*
1744901 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
* *
1744966 TTGGAACTGAGCATAGTCG
66 TTGGAGCTGAGCGTAGTCG
*
1744985 AACTCGAAGGTCTTTTGG-TGACAAATAACCCTTCT
1 AACTCGAAGGTC-TTTGGTTGACAGATAACCCTTCT
1745020 AGATCCTCGA
Statistics
Matches: 514, Mismatches: 89, Indels: 30
0.81 0.14 0.05
Matches are distributed among these distances:
80 29 0.06
81 71 0.14
82 35 0.07
83 39 0.08
84 236 0.46
85 102 0.20
86 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (84 bp):
AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
TTGGAGCTGAGCGTAGTCG
Found at i:1744697 original size:169 final size:168
Alignment explanation
Indices: 1744297--1744949 Score: 840
Period size: 165 Copynumber: 3.9 Consensus size: 168
1744287 ATTTGGCTTG
* * *
1744297 CCTCTAAGCTGAATGCAATCAAACTCG-GAGGTCTTCGGTT-GACAGATAACCCTTCTCGACTTA
1 CCTCGAAGCTGAATGTAATCAAACTCGAG-GGTCTTTGGTTGGA-AGATAACCCTTCTCGACTTA
* * *
1744360 AGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGGTGACAG
64 AGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* * ** *
1744425 ATAACCCTTCTTGAC-TGAAGCTATGTTACAAATGA--TG-
129 ATAACCCTTCTAGACTTG-AGTTATGTTGTAGATGATGTGT
* * ** * * * * *
1744462 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTTGGCAGATAACCCTTCTCGACTTAAG
1 CCTCGAAGCTGAATGTAATCAAACTCGAGGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAG
* *
1744527 TTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTGACAGA
66 CTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGA
*
1744592 TAACCCTTCTAGCCTTGAGTTATGTTGTAGATGATGTGT
130 TAACCCTTCTAGACTTGAGTTATGTTGTAGATGATGTGT
*
1744631 CCTCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAG
1 CCTCGAAGCTGAATGTAATCAAACTCGAGGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAG
*
1744696 TTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGA
66 CTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGA
*
1744761 TAACCCTTCTAGCCTTGAGTTATGTTGTAGATGATGTGT
130 TAACCCTTCTAGACTTGAGTTATGTTGTAGATGATGTGT
* * * * * *
1744800 CCTCGAAGCTGAATGTAATCGAACTTGAGGGTC--T--TTGGCAGATAGCCCTTATCGACTTAAA
1 CCTCGAAGCTGAATGTAATCAAACTCGAGGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAG
** * *
1744861 CTATGCTATAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGA
66 CTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGA
* *
1744926 TAACCCTTCTCGACTTAAGTTATG
130 TAACCCTTCTAGACTTGAGTTATG
1744950 CTGCAAATGA
Statistics
Matches: 435, Mismatches: 45, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
164 5 0.01
165 197 0.45
166 38 0.09
167 3 0.01
168 2 0.00
169 190 0.44
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (168 bp):
CCTCGAAGCTGAATGTAATCAAACTCGAGGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAG
CTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
AACCCTTCTAGACTTGAGTTATGTTGTAGATGATGTGT
Found at i:1744731 original size:334 final size:333
Alignment explanation
Indices: 1744297--1744949 Score: 870
Period size: 334 Copynumber: 2.0 Consensus size: 333
1744287 ATTTGGCTTG
*
1744297 CCTCTAAGCTGAATGCAATCAAACTCGGAGGTCTTCGGTTGACAGATAACCCTTCTCGACTTAAG
1 CCTCGAAGCTGAATGCAATCAAACTCGGAGGTCTTCGGTTGACAGATAACCCTTCTCGACTTAAG
* *
1744362 CTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTC-TTTGGTGACAGA
66 CTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGA
* * * * *
1744426 TAACCCTTCTTGAC-TGAAGCTATGTTACAAATGA-TG-CCTTGGAGCTGAGCGTAGTCGAACTC
131 TAACCCTTCTAGACTTG-AGCTATGTTACAAATGAGTGTCCTCGAAGCTGAACGTAATCGAACTC
* ** *
1744488 GAAGATCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGA
195 GAAGATC--T--TTGGCAGATAACCCTTATCGACTTAAACTATGCTACAAATGATATGCCTTGGA
* * *
1744553 GCTGAGCGTAGTCGAACTTGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGT
256 GCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGT
1744617 TGTAGATGATGTGT
320 TGTAGATGATGTGT
* * *
1744631 CCTCGAAGCTGAGTGTAATCAAACTC-GAGGGTCTTTGGTTGGA-AGATAACCCTTCTCGACTTA
1 CCTCGAAGCTGAATGCAATCAAACTCGGA-GGTCTTCGGTT-GACAGATAACCCTTCTCGACTTA
* *
1744694 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACA
64 AGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACA
* * ** * *
1744759 GATAACCCTTCTAGCCTTGAGTTATGTTGTAGATGATGTGTCCTCGAAGCTGAATGTAATCGAAC
129 GATAACCCTTCTAGACTTGAGCTATGTTACAAATGA-GTGTCCTCGAAGCTGAACGTAATCGAAC
* * * * * *
1744824 TTGAGGGTCTTTGGCAGATAGCCCTTATCGACTTAAACTATGCTATAAATGATGTGCCTTGGAGC
193 TCGAAGATCTTTGGCAGATAACCCTTATCGACTTAAACTATGCTACAAATGATATGCCTTGGAGC
* *
1744889 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
258 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATG
1744950 CTGCAAATGA
Statistics
Matches: 277, Mismatches: 34, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
333 7 0.03
334 201 0.73
335 39 0.14
336 3 0.01
337 2 0.01
338 25 0.09
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (333 bp):
CCTCGAAGCTGAATGCAATCAAACTCGGAGGTCTTCGGTTGACAGATAACCCTTCTCGACTTAAG
CTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGA
TAACCCTTCTAGACTTGAGCTATGTTACAAATGAGTGTCCTCGAAGCTGAACGTAATCGAACTCG
AAGATCTTTGGCAGATAACCCTTATCGACTTAAACTATGCTACAAATGATATGCCTTGGAGCTGA
GCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGTTGTAGA
TGATGTGT
Found at i:1745164 original size:84 final size:83
Alignment explanation
Indices: 1745058--1745511 Score: 490
Period size: 84 Copynumber: 5.5 Consensus size: 83
1745048 TCGAGGGTCT
**
1745058 TTGGCAGATAGTCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1745123 CGAACTCGAAGGTCTTTAG
66 CGAACTCGAAGGTCTTT-G
* * * * *
1745142 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCTCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC-CTTGGAGCTGAGCGTAG
*
1745207 TCGAACT-TAAGGGTC--T-
65 TCGAACTCGAA-GGTCTTTG
* * *
1745223 TTGGCAAATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* *
1745288 CAAACTCAAAGGTCTTTGG
66 CGAACTCGAAGGTCTTT-G
* ** * * *
1745307 TTGGCAGATAACCCTTCTTGACTTAATTTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTGGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1745372 CGAACTCGAAGGTCTTTTG
66 CGAACTCGAAGGTC-TTTG
* * * * * * ** * * * *
1745391 ATGACAGATAACCCTTCTAGCCTTTAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
* *
1745456 TGGAACTCGAGGGTC--T-
65 TCGAACTCGAAGGTCTTTG
* *
1745472 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAAT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAT
1745512 AGTTTGTATA
Statistics
Matches: 307, Mismatches: 54, Indels: 21
0.80 0.14 0.05
Matches are distributed among these distances:
80 23 0.07
81 75 0.24
82 2 0.01
83 1 0.00
84 153 0.50
85 53 0.17
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (83 bp):
TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTG
Found at i:1745302 original size:165 final size:165
Alignment explanation
Indices: 1745025--1745346 Score: 545
Period size: 165 Copynumber: 2.0 Consensus size: 165
1745015 CTTCTAGATC
* * *
1745025 CTCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGGCAGATAGTCCTTCTCGACTTAAGCTATG
1 CTCGAAGCTGAGTGTAATCAAACTCAAGGGTCTTTGGCAAATAGCCCTTCTCGACTTAAGCTATG
* *
1745090 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGTTGGCAGATAACC
66 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTAGTTGGCAGATAACC
1745155 CTTCTCGACTTAAGTTATGCTGCAAATGATGTGCT
131 CTTCTCGACTTAAGTTATGCTGCAAATGATGTGCT
* * *
1745190 CTCGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAAATAGCCCTTCTTGACTTAAGCTATG
1 CTCGAAGCTGAGTGTAATCAAACTCAAGGGTCTTTGGCAAATAGCCCTTCTCGACTTAAGCTATG
*
1745255 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACC
66 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTAGTTGGCAGATAACC
* *
1745320 CTTCTTGACTTAATTTATGCTGCAAAT
131 CTTCTCGACTTAAGTTATGCTGCAAAT
1745347 AATATGCCTT
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
165 146 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (165 bp):
CTCGAAGCTGAGTGTAATCAAACTCAAGGGTCTTTGGCAAATAGCCCTTCTCGACTTAAGCTATG
CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTAGTTGGCAGATAACC
CTTCTCGACTTAAGTTATGCTGCAAATGATGTGCT
Found at i:1745404 original size:389 final size:391
Alignment explanation
Indices: 1744630--1745410 Score: 1226
Period size: 389 Copynumber: 2.0 Consensus size: 391
1744620 AGATGATGTG
1744630 TCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAA
1 TCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTC-TT-GTTGGAAGATAACCCTTCTCGACTTAA
* *
1744695 GTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAG
64 GCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGGTGACAG
* * * * *
1744760 ATAACCCTTCTAGCCTTGAGTTATGTTGTAGATGATGTGTCCTCGAAGCTGAATGTAATCGAACT
129 ATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGTCCTCGAAGCTGAATGTAATCGAACT
* * *
1744825 TGAGGGTCTTTGGCAGATAGCCCTTATCGACTTAAACTATGCTATAAATGATGTGCCTTGGAGCT
194 TAAGGGTCTTTGGCAAATAGCCCTTATCGACTTAAACTATGCTACAAATGATGTGCCTTGGAGCT
* *
1744890 GAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
259 GAGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
* *
1744955 AATGATATGCCTTGGAACTGAGCATAGTCGAACTCGAAGGTCTTTTGGTGACAAATAACCCTTCT
324 AATAATATGCCTTGGAACTGAGCATAGTCGAACTCGAAGGTCTTTTGATGACAAATAACCCTTCT
1745020 AGA
389 AGA
* **
1745023 TCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTC-T-TTGGCAGATAGTCCTTCTCGACTTAAGC
1 TCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTGTTGGAAGATAACCCTTCTCGACTTAAGC
* * *
1745086 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGTTGGCAGAT
66 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGGTGACAGAT
* *
1745151 AACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CTCTCGAAGCTGAGTGTAATCGAACTT
131 AACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGTC-CTCGAAGCTGAATGTAATCGAACTT
* * * *
1745215 AAGGGTCTTTGGCAAATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTG
195 AAGGGTCTTTGGCAAATAGCCCTTATCGACTTAAACTATGCTACAAATGATGTGCCTTGGAGCTG
* *
1745280 AGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAATTTATGCTGCAA
260 AGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAA
* * * *
1745345 ATAATATGCCTTGGAGCTGAGCGTGGTCGAACTCGAAGGTCTTTTGATGACAGATAACCCTTCTA
325 ATAATATGCCTTGGAACTGAGCATAGTCGAACTCGAAGGTCTTTTGATGACAAATAACCCTTCTA
1745410 G
390 G
1745411 CCTTTAGTTA
Statistics
Matches: 355, Mismatches: 32, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
388 1 0.00
389 319 0.90
391 1 0.00
393 34 0.10
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (391 bp):
TCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTGTTGGAAGATAACCCTTCTCGACTTAAGC
TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGGTGACAGAT
AACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGTCCTCGAAGCTGAATGTAATCGAACTTA
AGGGTCTTTGGCAAATAGCCCTTATCGACTTAAACTATGCTACAAATGATGTGCCTTGGAGCTGA
GCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAA
TAATATGCCTTGGAACTGAGCATAGTCGAACTCGAAGGTCTTTTGATGACAAATAACCCTTCTAG
A
Found at i:1745478 original size:165 final size:163
Alignment explanation
Indices: 1745025--1745512 Score: 473
Period size: 165 Copynumber: 3.0 Consensus size: 163
1745015 CTTCTAGATC
* * * ** *
1745025 CTCGAAGCTGAGTGTAATCAAACTCG-AGGGTCTTTGGCAGATAGTCCTTCTCGACTTAAGCTAT
1 CTCGAAGCTGAGCGTAATCGAACT-GAAGGGTCTTTGGCAAATAACCCTTCTAGACTTAAGCTAT
* * * * * *
1745089 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGTTGGCAGATAAC
65 GCTACAAATGATGTGCCTCGAAGCTGAGCGTAATCAAACTCAAAGGTC-TT-GTTGGCAGATAAC
* *
1745154 CCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCT
128 CCTTCTCGACTTAAGTTATGCTGCAAATAATATGCT
* * * *
1745190 CTCGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAAATAGCCCTTCTTGACTTAAGCTATG
1 CTCGAAGCTGAGCGTAATCGAACTGAAGGGTCTTTGGCAAATAACCCTTCTAGACTTAAGCTATG
* * * *
1745255 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACC
66 CTACAAATGATGTGCCTCGAAGCTGAGCGTAATCAAACTCAAAGGTC-TT-GTTGGCAGATAACC
* *
1745320 CTTCTTGACTTAATTTATGCTGCAAATAATATGC-
129 CTTCTCGACTTAAGTTATGCTGCAAATAATATGCT
* * ** * * *
1745354 CTTGGAGCTGAGCGTGGTCGAACTCGAA-GGTCTTTTGATGACAGATAACCCTTCTAGCCTTTAG
1 CTCGAAGCTGAGCGTAATCGAACT-GAAGGGTC-TTTG--G-CAAATAACCCTTCTAGACTTAAG
* * * ** * *
1745418 TTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAATGGAACTCGAGGGTC-T-TTGGCAGAT
61 CTATGCTACAAATGATGTG-CCTCGAAGCTGAGCGTAATCAAACTCAAAGGTCTTGTTGGCAGAT
* * *
1745481 AGCCCTTCTCGACTTAAGCTATACTGCAAATA
125 AACCCTTCTCGACTTAAGTTATGCTGCAAATA
1745513 GTTTGTATAA
Statistics
Matches: 277, Mismatches: 39, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
164 23 0.08
165 193 0.70
167 2 0.01
168 34 0.12
169 25 0.09
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (163 bp):
CTCGAAGCTGAGCGTAATCGAACTGAAGGGTCTTTGGCAAATAACCCTTCTAGACTTAAGCTATG
CTACAAATGATGTGCCTCGAAGCTGAGCGTAATCAAACTCAAAGGTCTTGTTGGCAGATAACCCT
TCTCGACTTAAGTTATGCTGCAAATAATATGCT
Found at i:1745497 original size:249 final size:249
Alignment explanation
Indices: 1745058--1745511 Score: 701
Period size: 249 Copynumber: 1.8 Consensus size: 249
1745048 TCGAGGGTCT
** * *
1745058 TTGGCAGATAGTCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTAGT
* * * *
1745123 CGAACTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
66 CGAACTCGAAGGTCTTTAGATGACAGATAACCCTTCTAGACTTAAGTTATGCTACAAATGATGTG
* * *
1745188 CTCTCGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAAATAGCCCTTCTTGACTTAAGCTA
131 CCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAAATAGCCCTTCTCGACTTAAGCTA
*
1745253 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGG
196 TACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGG
* ** *
1745307 TTGGCAGATAACCCTTCTTGACTTAATTTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTGGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTAGT
* * * *
1745372 CGAACTCGAAGGTCTTTTGATGACAGATAACCCTTCTAGCCTTTAGTTATGCTATAAATGATGTG
66 CGAACTCGAAGGTCTTTAGATGACAGATAACCCTTCTAGACTTAAGTTATGCTACAAATGATGTG
* * *
1745437 CCCTCGAAGCTGAGTGTAATGGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
131 CCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAAATAGCCCTTCTCGACTTAAGCTA
1745502 TACTGCAAAT
196 TACTGCAAAT
1745512 AGTTTGTATA
Statistics
Matches: 182, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
249 182 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (249 bp):
TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTAGATGACAGATAACCCTTCTAGACTTAAGTTATGCTACAAATGATGTG
CCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAAATAGCCCTTCTCGACTTAAGCTA
TACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGG
Found at i:1750777 original size:8 final size:8
Alignment explanation
Indices: 1750755--1750792 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1750745 AAAAAAAGAG
1750755 ATAATAAA
1 ATAATAAA
1750763 A-AATAAA
1 ATAATAAA
1750770 ATAATAAA
1 ATAATAAA
*
1750778 ATATTAAAA
1 ATAAT-AAA
1750787 ATAATA
1 ATAATA
1750793 CAAACAAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 7 0.27
8 12 0.46
9 7 0.27
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
ATAATAAA
Found at i:1752171 original size:22 final size:22
Alignment explanation
Indices: 1752146--1752195 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1752136 AATGAAATGA
* * *
1752146 AAAAAATAAATGAATATACAAT
1 AAAAAATAAATAAAAATAAAAT
*
1752168 AAAAAATAATTAAAAATAAAAT
1 AAAAAATAAATAAAAATAAAAT
1752190 AAAAAA
1 AAAAAA
1752196 ATGTTATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (22 bp):
AAAAAATAAATAAAAATAAAAT
Found at i:1752242 original size:33 final size:34
Alignment explanation
Indices: 1752200--1752466 Score: 137
Period size: 35 Copynumber: 7.9 Consensus size: 34
1752190 AAAAAAATGT
*
1752200 TATTTTAAAAATATATACTATATATGTTTTAAAAA
1 TATTTTAAAAATATATA-TATATATCTTTTAAAAA
*
1752235 -A-TTT-AAAATCATATA-ATATA-CTTTCAAATAA
1 TATTTTAAAAAT-ATATATATATATCTTTTAAA-AA
* *
1752266 TATTTTAAAATTATATATTATATATTTTTTAAAAA
1 TATTTTAAAAATATATA-TATATATCTTTTAAAAA
* * * *
1752301 TGTTTT-CAAATATCATATATTATATATTTTCAAAA
1 TATTTTAAAAATAT-ATATA-TATATCTTTTAAAAA
* * * *
1752336 TTTTTTAAAACTAT-TATATA-AT-TTTCAAAATG
1 TATTTTAAAAATATATATATATATCTTTTAAAA-A
* * * *
1752368 TTTTTTAAAAATCATATTTTATATATATTTCAAAAA
1 TATTTTAAAAAT-ATA-TATATATATCTTTTAAAAA
* ** *
1752404 TGTTTTTTAAAACCATACTATATATA--TTTCAAAAA
1 --TATTTTAAAAATATA-TATATATATCTTTTAAAAA
*
1752439 -ATTTTAAAAACTATATA-ATATATGTTTT
1 TATTTTAAAAA-TATATATATATATCTTTT
1752467 TTTTAAATGT
Statistics
Matches: 183, Mismatches: 27, Indels: 46
0.71 0.11 0.18
Matches are distributed among these distances:
30 6 0.03
31 18 0.10
32 29 0.16
33 26 0.14
34 16 0.09
35 47 0.26
36 13 0.07
37 18 0.10
38 10 0.05
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.48
Consensus pattern (34 bp):
TATTTTAAAAATATATATATATATCTTTTAAAAA
Done.