Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold139
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: 1720190
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 4798 characters in sequence are not A, C, G, or T
File 11 of 11
Found at i:1611834 original size:76 final size:74
Alignment explanation
Indices: 1611623--1611831 Score: 231
Period size: 76 Copynumber: 2.7 Consensus size: 74
1611613 TTGCTCCTTA
* * * ** *
1611623 AGGACAAAGGGAAAAAGAAAAGGGAAGTGTCCTGCTTCTTGAGGGCAAAGTGAAAAAGAGTACGT
1 AGGATAAAGGAAAAAAGAAAAGGAAAGCATCCTGCTTCTTGAGGACAAA--GAAAAAGAGTACGT
*
1611688 CCTGCTTTTTG
64 CCTGCTTTTCG
* * *
1611699 AGGATAAAGGAAAAAAGAAAAGGGAAGCGTCCTGCTTCTTGAGGGCAAAGTGAAAAAGAGTACGT
1 AGGATAAAGGAAAAAAGAAAAGGAAAGCATCCTGCTTCTTGAGGACAAA--GAAAAAGAGTACGT
1611764 CCTGCTTTTCG
64 CCTGCTTTTCG
*
1611775 AGGATAAAGGAACAAAAGGAAAATGAAATGCATCCTGC-TCTTTGAGGACAAAAGAAA
1 AGGATAAAGGAA-AAAA-GAAAAGGAAA-GCATCCTGCTTC-TTGAGGAC-AAAGAAA
1611832 GAGGAAAATA
Statistics
Matches: 120, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
76 84 0.70
77 4 0.03
78 14 0.12
79 15 0.12
80 3 0.03
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (74 bp):
AGGATAAAGGAAAAAAGAAAAGGAAAGCATCCTGCTTCTTGAGGACAAAGAAAAAGAGTACGTCC
TGCTTTTCG
Found at i:1611957 original size:61 final size:61
Alignment explanation
Indices: 1611874--1612029 Score: 190
Period size: 61 Copynumber: 2.5 Consensus size: 61
1611864 ACAAAGGAGA
*
1611874 AAAGAAAAAGGCGTTCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTG-
1 AAAG-AAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGC
* * * * *
1611935 AAATGAAAAGGCGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAAGTTGTGTGGGCTTTGC
1 AAA-GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGC
* * *
1611997 AAAGAGAAA-ACATCCTGCTTTTTGAGGACTAAA
1 AAAGA-AAAGGCGTCCTGCTCTTTGAGGACTAAA
1612030 GGGCAAAAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
61 74 0.91
62 7 0.09
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (61 bp):
AAAGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGC
Found at i:1612121 original size:100 final size:100
Alignment explanation
Indices: 1611947--1612126 Score: 256
Period size: 100 Copynumber: 1.8 Consensus size: 100
1611937 ATGAAAAGGC
* *
1611947 GTCCTACTCTTTGAGGACTAGAAGGTGCCACCAAGTTGTGTGGGCTTTGCAAAGAGAAAACATCC
1 GTCCTACTCTTTGAGGACTAGAAGATGCCACCAAGTTGTGTGGGCTTTGAAAAGAGAAAACATCC
*
1612012 TGCTTTTTGAGGACTAAAGGGCAAAAAGAGATAGT
66 TGCTCTTTGAGGACTAAAGGGCAAAAAGAGATAGT
* * * * *
1612047 GTCCTGCTCTTTGAGGACTAGGAA-ATGCCACCAATTTGTGTGGTCTTT-AAAAGGAGAAAGCTT
1 GTCCTACTCTTTGAGGACTA-GAAGATGCCACCAAGTTGTGTGGGCTTTGAAAA-GAGAAAACAT
1612110 CCTGCTCTTTGAGGACT
64 CCTGCTCTTTGAGGACT
1612127 GGAAAATGCT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
99 3 0.04
100 64 0.91
101 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (100 bp):
GTCCTACTCTTTGAGGACTAGAAGATGCCACCAAGTTGTGTGGGCTTTGAAAAGAGAAAACATCC
TGCTCTTTGAGGACTAAAGGGCAAAAAGAGATAGT
Found at i:1612231 original size:155 final size:153
Alignment explanation
Indices: 1611841--1612337 Score: 479
Period size: 161 Copynumber: 3.2 Consensus size: 153
1611831 AGAGGAAAAT
* * * * *
1611841 AAAGTGCATCCTGCTCTTTGTGGAC-AAA-GG-AGAAAAGAAAAAGGCGTTCTGCTCTTTGAGGA
1 AAAG-GCATCCTGCTCTTTGAGGACTAAAGGGCA-AAAAGAGAGA-GCGTCCTGCTCTTTAAGGA
** * * * *
1611903 CTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAATGA-AAAGGCGTCCTACTCTTTGAGGACTA
63 CTAGGAAGTGCCACCAATTTGTGTGGGCTTT-AAA-GAGAAA-GCATCCTGCTCTTTGAGGACTA
** *
1611967 GAAGGTGCCACCAAGTTGTGTGGGCTTTG
125 GAAAATGCCACCAACTTGTGTGGGCTTTG
* * * *
1611996 CAAAGAGAAAACATCCTGCTTTTTGAGGACTAAAGGGCAAAAAGAGATAGTGTCCTGCTCTTTGA
1 -AAAG-G----CATCCTGCTCTTTGAGGACTAAAGGGCAAAAAGAGAGAGCGTCCTGCTCTTTAA
* * *
1612061 GGACTAGGAAATGCCACCAATTTGTGTGGTCTTTAAAAGGAGAAAGCTTCCTGCTCTTTGAGGAC
60 GGACTAGGAAGTGCCACCAATTTGTGTGGGCTTT-AAA-GAGAAAGCATCCTGCTCTTTGAGGAC
* * * *
1612126 TGGAAAATGCTAGCAACTTGTGTGGGTTTTG
123 TAGAAAATGCCACCAACTTGTGTGGGCTTTG
* * * * *
1612157 AAAGGCATCCTGCTCATTGAGGACTAAAGGGCGAAATGAGAGAGCGTCCTGCTTTTTAAGGACTG
1 AAAGGCATCCTGCTCTTTGAGGACTAAAGGGCAAAAAGAGAGAGCGTCCTGCTCTTTAAGGACTA
* * *
1612222 GGAAGTGCCACCAATTTATGTGGGCTTTAAA-AG---GCATCATGCTCTTTGAGGACTAAAAAAA
66 GGAAGTGCCACCAATTTGTGTGGGCTTTAAAGAGAAAGCATCCTGCTCTTTGAGGACT-AGAAAA
1612283 TGCCACCAACTTGTGTGGGCTTTG
130 TGCCACCAACTTGTGTGGGCTTTG
* *
1612307 AAAGGCGTCCTGTTCTTTGAGGACTGAAAGG
1 AAAGGCATCCTGCTCTTTGAGGACT-AAAGG
1612338 TGCCACGAAC
Statistics
Matches: 285, Mismatches: 46, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
149 19 0.07
150 47 0.16
151 5 0.02
152 2 0.01
154 3 0.01
155 76 0.27
156 5 0.02
159 1 0.00
160 21 0.07
161 92 0.32
162 13 0.05
163 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (153 bp):
AAAGGCATCCTGCTCTTTGAGGACTAAAGGGCAAAAAGAGAGAGCGTCCTGCTCTTTAAGGACTA
GGAAGTGCCACCAATTTGTGTGGGCTTTAAAGAGAAAGCATCCTGCTCTTTGAGGACTAGAAAAT
GCCACCAACTTGTGTGGGCTTTG
Found at i:1612271 original size:94 final size:94
Alignment explanation
Indices: 1612100--1612278 Score: 232
Period size: 94 Copynumber: 1.9 Consensus size: 94
1612090 TCTTTAAAAG
* * * * * * *
1612100 GAGAAAGCTTCCTGCTCTTTGAGGACTGGAAAATGCTAGCAACTTGTGTGGGTTTTGAAAGGCAT
1 GAGAAAGCGTCCTGCTCTTTAAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTAAAAGGCAT
*
1612165 CCTGCTCATTGAGGACTAAAGGGCGAAAT
66 CATGCTCATTGAGGACTAAAGGGCGAAAT
* * * * *
1612194 GAGAGAGCGTCCTGCTTTTTAAGGACTGGGAAGTGCCACCAATTTATGTGGGCTTTAAAAGGCAT
1 GAGAAAGCGTCCTGCTCTTTAAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTAAAAGGCAT
*
1612259 CATGCTCTTTGAGGACTAAA
66 CATGCTCATTGAGGACTAAA
1612279 AAAATGCCAC
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
94 71 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (94 bp):
GAGAAAGCGTCCTGCTCTTTAAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTAAAAGGCAT
CATGCTCATTGAGGACTAAAGGGCGAAAT
Found at i:1612361 original size:55 final size:56
Alignment explanation
Indices: 1612200--1612387 Score: 227
Period size: 55 Copynumber: 3.4 Consensus size: 56
1612190 AAATGAGAGA
* * * * * * *
1612200 GCGTCCTGCTTTTTAAGGACTGGGAA-GTGCCACCAATTTATGTGGGCTTTAAAAG
1 GCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
* * * **
1612255 GCATCATGCTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
* *
1612311 GCGTCCTGTTCTTTGAGGACT-GAAAGGTGCCACGAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
*
1612366 GCGTCTTGCTCTTTGAGGACTA
1 GCGTCCTGCTCTTTGAGGACTA
1612388 AAGGGTGAAA
Statistics
Matches: 111, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
55 68 0.61
56 43 0.39
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (56 bp):
GCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
Found at i:1612428 original size:205 final size:206
Alignment explanation
Indices: 1612051--1612547 Score: 583
Period size: 205 Copynumber: 2.4 Consensus size: 206
1612041 GATAGTGTCC
** * * * *
1612051 TGCTCTTTGAGGACT-AGGAAATGCCACCAATTTGTGTGGTCTTTAAAAGGAGAAAGCTTCCTGC
1 TGCTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTT-----GA-AAGGCATCCTGC
* * *
1612115 TCTTTGAGGACTGGAAA-ATGCTAGCAACTTGTGTGGGTTTTGAAAGGCATCCTGCTCATTGAGG
60 TCTTTGAGGACT-GAAAGGTGCCAGCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCATTGAGG
* * * *
1612179 ACTAAAGGGCGAAATGAGAGAGCGTCCTGCTTTTTAAGGACTGGGAAGTGCCACCAATTTATGTG
124 ACTAAAGGGCGAAAGGAGAGAGCATCCTGCTTTTGAAGGACTGGGAAGTGCCACCAACTTATGTG
1612244 GGCTTT-AAAAGGCATCA
189 GGCTTTAAAAAGGCATCA
* *
1612261 TGCTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGTTCTTTG
1 TGCTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTG
* * *
1612326 AGGACTGAAAGGTGCCA-CGAACTTGTGTGGGCTTTGAAAGGCGTCTTGCTCTTTGAGGACTAAA
66 AGGACTGAAAGGTGCCAGC-AACTTGTGTGGGCTTTGAAAGGCATCCTGCTCATTGAGGACTAAA
* *
1612390 GGGTGAAAGGAGAGAGCATCCTGCTCTTTGAA-GACTGGGAAGTGCCACCAACTTGTGTGGGCTT
130 GGGCGAAAGGAGAGAGCATCCTGCT-TTTGAAGGACTGGGAAGTGCCACCAACTTATGTGGGCTT
* *
1612454 TAAAAGGAAAAGGCGTCC
194 T---A--AAAAGGCATCA
* * * *
1612472 TGCTCTTTGAGGATTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTG
1 TGCTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTG
*
1612537 AAGACT-AAAGG
66 AGGACTGAAAGG
1612548 ACGAAAGGAG
Statistics
Matches: 249, Mismatches: 28, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
204 5 0.02
205 119 0.48
206 7 0.03
210 20 0.08
211 98 0.39
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (206 bp):
TGCTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTG
AGGACTGAAAGGTGCCAGCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCATTGAGGACTAAAG
GGCGAAAGGAGAGAGCATCCTGCTTTTGAAGGACTGGGAAGTGCCACCAACTTATGTGGGCTTTA
AAAAGGCATCA
Found at i:1612530 original size:56 final size:56
Alignment explanation
Indices: 1612405--1612542 Score: 170
Period size: 62 Copynumber: 2.4 Consensus size: 56
1612395 AAAGGAGAGA
**
1612405 GCATCCTGCTCTTTGAAGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GCATCCTGCTCTTTGAAGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT---A--AAAAG
* * *
1612466 GCGTCCTGCTCTTTGAGGATTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAG
1 GCATCCTGCTCTTTGAAGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG
1612522 GCATCCTGCTCTTTGAAGACT
1 GCATCCTGCTCTTTGAAGACT
1612543 AAAGGACGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
56 23 0.34
61 18 0.26
62 27 0.40
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (56 bp):
GCATCCTGCTCTTTGAAGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG
Found at i:1612533 original size:156 final size:155
Alignment explanation
Indices: 1612283--1612700 Score: 552
Period size: 156 Copynumber: 2.7 Consensus size: 155
1612273 ACTAAAAAAA
* * *
1612283 TGCCACCAACTTGTGTGGGCTTT-----GAAAGGCGTCCTGTTCTTTGAGGACT-GAAAGGTGCC
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCGTCCTGCTCTTTGAGGATTAGAAAAGTGCC
* * ** *
1612342 ACGAACTTGTGTGGGCTTTGAAAGGCGTCTTGCTCTTTGAGGACTAAAGGGTGAAAGGAGAGAGC
66 ACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGACGAAAGGAGAGAAC
*
1612407 ATCCTGCTCTTTGAAGACTGGGAAG
131 ATCCTACTCTTTGAAGACTGGGAAG
1612432 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGATTAGAAAAGTGC
1 TGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAGGCGTCCTGCTCTTTGAGGATTAGAAAAGTGC
* * *
1612497 CACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAAGACTAAAGGACGAAAGGAGAGAA
65 CACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGACGAAAGGAGAGAA
** *
1612562 TGTCCTACTCTTTGAGGACTGGGAAG
130 CATCCTACTCTTTGAAGACTGGGAAG
* * * *
1612588 TGCCACCAACTTGTGTGGGCTTTAAAAGG--A---GTCTTGCTCTTTGAGGACTAAAAAAAAATG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCGTCCTGCTCTTTGAGGA-T-TAGAAAAGTG
1612648 CCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
64 CCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACT-AAAGG
1612701 TGCCACCAAT
Statistics
Matches: 237, Mismatches: 22, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
149 23 0.10
150 16 0.07
151 1 0.00
152 51 0.22
153 6 0.03
154 1 0.00
155 23 0.10
156 116 0.49
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (155 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCGTCCTGCTCTTTGAGGATTAGAAAAGTGCC
ACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGACGAAAGGAGAGAAC
ATCCTACTCTTTGAAGACTGGGAAG
Found at i:1612626 original size:94 final size:95
Alignment explanation
Indices: 1612468--1612639 Score: 267
Period size: 94 Copynumber: 1.8 Consensus size: 95
1612458 AGGAAAAGGC
* *
1612468 GTCCTGCTCTTTGAGGATTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTC
1 GTCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTC
1612533 TTTGAAGACTAAAGGACGAAAGGAGAGAAT
66 TTTGAAGACTAAAGGACGAAAGGAGAGAAT
** *
1612563 GTCCTACTCTTTGAGGACT-GGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AGTCTTGCT
1 GTCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCA-TCCTGCT
*
1612626 CTTTGAGGACTAAA
65 CTTTGAAGACTAAA
1612640 AAAAAATGCC
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
93 1 0.01
94 52 0.74
95 17 0.24
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (95 bp):
GTCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTC
TTTGAAGACTAAAGGACGAAAGGAGAGAAT
Found at i:1612726 original size:55 final size:55
Alignment explanation
Indices: 1612563--1612748 Score: 239
Period size: 55 Copynumber: 3.3 Consensus size: 55
1612553 AGGAGAGAAT
* * * *
1612563 GTCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 GTCCTACTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
* * * *
1612618 GTCTTGCTCTTTGAGGACTAAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
1 GTCCTACTCTTTGAGGACT---AGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
* *
1612676 GTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAATTTGTGTGGGCTTTGAAAGGC
1 GTCCTACTCTTTGAGGACTAGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGC
1612731 GTCCTACTCTTTGAGGAC
1 GTCCTACTCTTTGAGGAC
1612749 CAAAGGGTGA
Statistics
Matches: 114, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
54 3 0.03
55 63 0.55
58 48 0.42
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (55 bp):
GTCCTACTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
Found at i:1612743 original size:207 final size:210
Alignment explanation
Indices: 1612432--1612824 Score: 571
Period size: 207 Copynumber: 1.9 Consensus size: 210
1612422 GACTGGGAAG
*
1612432 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGATTAGAAAAGTGC
1 TGCCACCAACTTGTGTGGGCTTT---A-GAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGC
* *
1612497 CACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAAGACTAAAGGACGAAAGGAGAGAA
62 CACCAACTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTGAAGACCAAAGGACGAAAGGAGAGAA
*
1612562 TGTCCTACTCTTTGAGGACT-G-GGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCTTGC
127 CGTCCTACTCTTTGAGGACTAGAGG--GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCTTGC
1612625 TCTTTGAGGACTAAAAAAAAA
190 TCTTTGAGGACTAAAAAAAAA
*
1612646 TGCCACCAACTTGTGTGGGCTTT-G-AAAGGCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACC
1 TGCCACCAACTTGTGTGGGCTTTAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACC
* * * * ** *
1612708 AATTTGTGTGGGCTTTGAAAGGCGTCCTACTCTTTGAGGACCAAAGGGTGAAAGGAGAGAGCGTC
66 AACTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTGAAGACCAAAGGACGAAAGGAGAGAACGTC
* *
1612773 CTACTCTTTGAGGATTAGAGGGTGCCACCAACTTGTGTGGGCTTTAGAAGGA
131 CTACTCTTTGAGGACTAGAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1612825 AAAGGCATCC
Statistics
Matches: 163, Mismatches: 14, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
207 112 0.69
208 25 0.15
209 3 0.02
214 23 0.14
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (210 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACC
AACTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTGAAGACCAAAGGACGAAAGGAGAGAACGTC
CTACTCTTTGAGGACTAGAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCTTGCTCTTTG
AGGACTAAAAAAAAA
Found at i:1612743 original size:363 final size:360
Alignment explanation
Indices: 1611890--1612842 Score: 1261
Period size: 363 Copynumber: 2.6 Consensus size: 360
1611880 AAAGGCGTTC
* * *
1611890 TGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAATGAAAAGGCGTCCTAC
1 TGCTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGC-TT----TG-AAAGGCGTCCTGC
* * *
1611954 TCTTTGAGGACT-AGAAGGTGCCACCAAGTTGTGTGGGCTTTGCAAAGAGAAAACATCCTGCTTT
60 TCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-G----CGTCCTGCTCT
** * * * * * *
1612018 TTGAGGACTAAAGGGCAAAAAGAGATAGTGTCCTGCTCTTTGAGGACTAGGAAATGCCACCAATT
118 TTGAGGACTAAAGGGTGAAAGGAGAGAGCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACT
* * * * *
1612083 TGTGTGGTCTTTAAAAGGAGAAA-GCTTCCTGCTCTTTGAGGACTGGAAAATGCTAGCAACTTGT
183 TGTGTGGGCTTTAAAAGGA-AAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGT
* * * * * * * *
1612147 GTGGGTTTTGAAAGGCATCCTGCTCATTGAGGACTAAAGGGCGAAATGAGAGAGCGTCCTGCTTT
247 GTGGGCTTTAAAAGGCATCCTGCTCATTGAAGACTAAAGGACGAAAGGAGAGAACGTCCTACTCT
*
1612212 TTAAGGACTGGGAAGTGCCACCAATTTATGTGGGCTTTAAAAGGCATCA
312 TTAAGGACTGGGAAGTGCCACCAACTTATGTGGGCTTTAAAAGGCATCA
*
1612261 TGCTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGTTCTTTG
1 TGCTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTG
* *
1612326 AGGACTGAAAGGTGCCACGAACTTGTGTGGGCTTTGAAAGGCGTCTTGCTCTTTGAGGACTAAAG
66 AGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAG
* *
1612391 GGTGAAAGGAGAGAGCATCCTGCTCTTTGAAGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTA
131 GGTGAAAGGAGAGAGCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTA
* *
1612456 AAAGGAAAAGGCGTCCTGCTCTTTGAGGATTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
196 AAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAA
* * *
1612521 GGCATCCTGCTCTTTGAAGACTAAAGGACGAAAGGAGAGAATGTCCTACTCTTTGAGGACTGGGA
260 GGCATCCTGCTCATTGAAGACTAAAGGACGAAAGGAGAGAACGTCCTACTCTTTAAGGACTGGGA
* *
1612586 AGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AGTCT
325 AGTGCCACCAACTTATGTGGGCTTTAAAAGGCA-TCA
1612622 TGCTCTTTGAGGACTAAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
1 TGCTCTTTGAGGACT--AAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
* * *
1612687 TGAGGACTGAAAGGTGCCACCAATTTGTGTGGGCTTTGAAAGGCGTCCTACTCTTTGAGGACCAA
64 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAA
* *
1612752 AGGGTGAAAGGAGAGAGCGTCCTACTCTTTGAGGATTAGAGG--GTGCCACCAACTTGTGTGGGC
129 AGGGTGAAAGGAGAGAGCGTCCTGCTCTTTGAGGACT-G-GGAAGTGCCACCAACTTGTGTGGGC
* *
1612815 TTTAGAAGGAAAAGGCATCCTGTTCTTT
192 TTTAAAAGGAAAAGGCATCCTGCTCTTT
1612843 AAAGACTAAA
Statistics
Matches: 521, Mismatches: 52, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
359 3 0.01
360 106 0.20
361 125 0.24
363 186 0.36
364 2 0.00
365 6 0.01
366 49 0.09
367 3 0.01
371 17 0.03
372 24 0.05
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (360 bp):
TGCTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTG
AGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAG
GGTGAAAGGAGAGAGCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTA
AAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
GCATCCTGCTCATTGAAGACTAAAGGACGAAAGGAGAGAACGTCCTACTCTTTAAGGACTGGGAA
GTGCCACCAACTTATGTGGGCTTTAAAAGGCATCA
Found at i:1613827 original size:1 final size:1
Alignment explanation
Indices: 1613807--1613877 Score: 61
Period size: 1 Copynumber: 71.0 Consensus size: 1
1613797 CTTTTCTCTC
* * * * * * * * *
1613807 TTTTTTCTTTGTTTTGTTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTGTTTTTTTGTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1613872 TTTTTT
1 TTTTTT
1613878 GAAAAAGAAT
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.00, C:0.01, G:0.11, T:0.87
Consensus pattern (1 bp):
T
Found at i:1613836 original size:8 final size:8
Alignment explanation
Indices: 1613809--1613877 Score: 88
Period size: 8 Copynumber: 8.6 Consensus size: 8
1613799 TTTCTCTCTT
1613809 TTTTCTTTG
1 TTTT-TTTG
*
1613818 TTTTGTT-
1 TTTTTTTG
1613825 TTTTTTTG
1 TTTTTTTG
1613833 TTTTTTTG
1 TTTTTTTG
1613841 TTTTTTTG
1 TTTTTTTG
1613849 TTTTTTTTG
1 -TTTTTTTG
1613858 TTTTTTTG
1 TTTTTTTG
*
1613866 TTGTTTT-
1 TTTTTTTG
1613873 TTTTT
1 TTTTT
1613878 GAAAAAGAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
7 10 0.19
8 32 0.59
9 12 0.22
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1613836 original size:25 final size:26
Alignment explanation
Indices: 1613807--1613877 Score: 103
Period size: 25 Copynumber: 2.8 Consensus size: 26
1613797 CTTTTCTCTC
1613807 TTTTTTCT-TTGTTTTGTTTTTTTTTG
1 TTTTTT-TGTTGTTTTGTTTTTTTTTG
*
1613833 TTTTTTTGTTTTTTTG-TTTTTTTTG
1 TTTTTTTGTTGTTTTGTTTTTTTTTG
1613858 TTTTTTTGTTGTTTT-TTTTT
1 TTTTTTTGTTGTTTTGTTTTT
1613878 GAAAAAGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
25 28 0.68
26 13 0.32
ACGTcount: A:0.00, C:0.01, G:0.11, T:0.87
Consensus pattern (26 bp):
TTTTTTTGTTGTTTTGTTTTTTTTTG
Found at i:1626544 original size:122 final size:122
Alignment explanation
Indices: 1626326--1626559 Score: 328
Period size: 122 Copynumber: 1.9 Consensus size: 122
1626316 TAAAAATCGA
* * * *
1626326 GGTTGGAGTATCCCCTCGAAAATAACAGGGTTAGAGTATCCCTGATTATAGAAAATCGGTATTTT
1 GGTTGGAGTATCCCATCGAAAACAACAGGGTTAGAGTATCCCCGATTATAGAAAATCAGTATTTT
* * *
1626391 GAAAATAAAATCGGAGTTGGAGTATCCCCGATTGTGGAAATTTGGTAATAAAGTCGG
66 GAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAATTGGTAATAAAGTCGG
* * * *
1626448 GGTTGGAGTATCCCATC-AGAAACAACGGGGTTGGAGTATCCCCGATTAT-GAGAAATTAGTGTT
1 GGTTGGAGTATCCCATCGA-AAACAACAGGGTTAGAGTATCCCCGATTATAGA-AAATCAGTATT
*
1626511 TTGAAAATAAAACCGGAGTTGGAATATCTCCGATTGTGGAAAATTGGTA
64 TTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAATTGGTA
1626560 TTTTAGAAAT
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
121 3 0.03
122 95 0.97
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (122 bp):
GGTTGGAGTATCCCATCGAAAACAACAGGGTTAGAGTATCCCCGATTATAGAAAATCAGTATTTT
GAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAATTGGTAATAAAGTCGG
Found at i:1626555 original size:51 final size:51
Alignment explanation
Indices: 1626477--1626591 Score: 117
Period size: 51 Copynumber: 2.3 Consensus size: 51
1626467 AAACAACGGG
* *
1626477 GTTGGAGTATCCCCGATTATGAGAAATTAGTGTTTT-GAAAATAAAACCGGA
1 GTTGGAATATCCCCGATTATGAGAAATTAGTATTTTAG-AAATAAAACCGGA
* * * * *
1626528 GTTGGAATATCTCCGATTGTG-GAAAATTGGTATTTTAGAAATAAAATCGGG
1 GTTGGAATATCCCCGATTATGAG-AAATTAGTATTTTAGAAATAAAACCGGA
* *
1626579 GTTAGAGTATCCC
1 GTTGGAATATCCC
1626592 TTAGAAATAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
50 1 0.02
51 50 0.96
52 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31
Consensus pattern (51 bp):
GTTGGAATATCCCCGATTATGAGAAATTAGTATTTTAGAAATAAAACCGGA
Found at i:1626736 original size:78 final size:80
Alignment explanation
Indices: 1626607--1626778 Score: 278
Period size: 78 Copynumber: 2.2 Consensus size: 80
1626597 AATAACGGAA
* *
1626607 TTGGAGTATCCTCGATGACATAACGGGGTTGGAGTACCCCCGATTATG-AAAAATCAA-TATTTT
1 TTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTACCCCCGATTATGAAAAAAT-AACTATTTT
1626670 AGATAT-AAGCCGGGG
65 AGATATAAAGCCGGGG
*
1626685 TTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTACCCCCGATTATGAAAAAAATAACTTTTTT
1 TTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTACCCCCGATTATG-AAAAAATAACTATTTT
1626750 AGATATAAAGCCGGGG
65 AGATATAAAGCCGGGG
1626766 TTGGAGTATCCCC
1 TTGGAGTATCCCC
1626779 TCGAAAATAA
Statistics
Matches: 87, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
78 46 0.53
79 2 0.02
80 17 0.20
81 22 0.25
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (80 bp):
TTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTACCCCCGATTATGAAAAAATAACTATTTTA
GATATAAAGCCGGGG
Found at i:1626809 original size:81 final size:77
Alignment explanation
Indices: 1626607--1626801 Score: 214
Period size: 78 Copynumber: 2.5 Consensus size: 77
1626597 AATAACGGAA
* * * **
1626607 TTGGAGTATCCTCGATGACATAACGGGGTTGGAGTACCCCCGATTATGAAAAATCAATATTTTAG
1 TTGGAGTATCCCCGA-GAAATAACGAGGTTAAAGTACCCCCGATTATGAAAAATCAATATTTTAG
1626672 ATATAAGCCGGGG
65 ATATAAGCCGGGG
* ** *
1626685 TTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTACCCCCGATTATGAAAAAAAT-AACTTTTT
1 TTGGAGTATCCCCGA-GAAATAACGAGGTTAAAGTACCCCCGATTATG--AAAAATCAA-TATTT
1626749 TAGATATAAAGCCGGGG
62 TAGATAT-AAGCCGGGG
*
1626766 TTGGAGTATCCCCTCGA-AAATAATGAGGTTAAAGTA
1 TTGGAGTAT-CCC-CGAGAAATAACGAGGTTAAAGTA
1626802 TTCCCGATGA
Statistics
Matches: 104, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
78 46 0.44
79 2 0.02
80 17 0.16
81 33 0.32
82 3 0.03
83 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (77 bp):
TTGGAGTATCCCCGAGAAATAACGAGGTTAAAGTACCCCCGATTATGAAAAATCAATATTTTAGA
TATAAGCCGGGG
Found at i:1629356 original size:33 final size:33
Alignment explanation
Indices: 1629310--1629378 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
1629300 TACATTGTAA
* *
1629310 AATGTATCGATACAATGAGCTATGTATCGATAC
1 AATGTATCAATACAATGAGCAATGTATCGATAC
1629343 AATGTATCAATACAATGAGCAATGTATCGATAC
1 AATGTATCAATACAATGAGCAATGTATCGATAC
1629376 AAT
1 AAT
1629379 ACAAAATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (33 bp):
AATGTATCAATACAATGAGCAATGTATCGATAC
Found at i:1632169 original size:20 final size:19
Alignment explanation
Indices: 1632114--1632169 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1632104 AAAACCCTTA
*
1632114 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
1632134 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
1632154 AATGTATCGATACATG
1 AAAGTATCGATACATG
1632170 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:1632263 original size:20 final size:20
Alignment explanation
Indices: 1632220--1632271 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
1632210 GTAGCCAAAC
*
1632220 TTGTATCGATACACAAAATA
1 TTGTATCGATACACAAAAAA
1632240 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
1632259 TTGTATCGATACA
1 TTGTATCGATACA
1632272 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:1636338 original size:15 final size:15
Alignment explanation
Indices: 1636318--1636348 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1636308 TAAAAATATC
*
1636318 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1636333 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1636348 C
1 C
1636349 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1640922 original size:20 final size:19
Alignment explanation
Indices: 1640867--1640922 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1640857 AAAACCCTTA
*
1640867 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
1640887 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
1640907 AATGTATCGATACATG
1 AAAGTATCGATACATG
1640923 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:1641010 original size:13 final size:13
Alignment explanation
Indices: 1640992--1641017 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1640982 TACACAAAAT
1640992 ATGTATCGATACA
1 ATGTATCGATACA
1641005 ATGTATCGATACA
1 ATGTATCGATACA
1641018 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1641016 original size:32 final size:33
Alignment explanation
Indices: 1640974--1641037 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1640964 TAGCCAAACT
* *
1640974 TGTATTGATACACAAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1641006 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1641038 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1642857 original size:20 final size:20
Alignment explanation
Indices: 1642815--1642862 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1642805 TGTTGAAGCA
* *
1642815 ATGTATGGATATAATTCATC
1 ATGTATCGATATAATTCACC
1642835 ATGTATCGATATAATGT-ACC
1 ATGTATCGATATAAT-TCACC
1642855 ATGTATCG
1 ATGTATCG
1642863 GTACAAACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (20 bp):
ATGTATCGATATAATTCACC
Found at i:1642922 original size:20 final size:20
Alignment explanation
Indices: 1642897--1642951 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
1642887 CTACCAATTT
**
1642897 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
1642917 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1642936 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1642952 GTATAATGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1642941 original size:19 final size:19
Alignment explanation
Indices: 1642897--1642972 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 19
1642887 CTACCAATTT
**
1642897 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1642917 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1642936 CATGTATCGATACAATGTATA
1 CATGTATCGATACAATG-A-A
*
1642957 -ATGTATCAATACAATG
1 CATGTATCGATACAATG
1642973 TATCGATACA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 19 0.37
20 31 0.61
21 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1642961 original size:39 final size:39
Alignment explanation
Indices: 1642897--1642972 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
1642887 CTACCAATTT
* *
1642897 CATGTATCGATACAATTGTCCATGTATCGATACAATGAA
1 CATGTATCGATACAATTGTCAATGTATCAATACAATGAA
*
1642936 CATGTATCGATACAA-TGTATAATGTATCAATACAATG
1 CATGTATCGATACAATTGT-CAATGTATCAATACAATG
1642973 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 3 0.09
39 30 0.91
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (39 bp):
CATGTATCGATACAATTGTCAATGTATCAATACAATGAA
Found at i:1645846 original size:20 final size:21
Alignment explanation
Indices: 1645802--1645853 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
1645792 TTACTGTGCA
*
1645802 TGTATCGATACATACTTGAAT
1 TGTATCGATACATACGTGAAT
*
1645823 TGTATCGATACATA-GTGTAT
1 TGTATCGATACATACGTGAAT
1645843 TGTATCGATAC
1 TGTATCGATAC
1645854 TGCCGCAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATACGTGAAT
Found at i:1646569 original size:23 final size:22
Alignment explanation
Indices: 1646526--1646574 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
1646516 GTAAAAAAGG
* **
1646526 AAAATAACAGACAAATTTACAC
1 AAAATAAAAGACAAAAGTACAC
*
1646548 AAAATAAAAGCACAAAAGTACAT
1 AAAATAAAAG-ACAAAAGTACAC
1646571 AAAA
1 AAAA
1646575 AGTAGGGATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.65, C:0.14, G:0.06, T:0.14
Consensus pattern (22 bp):
AAAATAAAAGACAAAAGTACAC
Found at i:1646910 original size:51 final size:51
Alignment explanation
Indices: 1646846--1646957 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
1646836 AACGGCGTTG
*
1646846 GAGTATCCCCGATTATGGAAAATC-ATTATTTTGAAAATAAAA-CTAGGGTTA
1 GAGTATCCCCGATTATGAAAAATCGA-TATTTTGAAAATAAAATC-AGGGTTA
** * * * *
1646897 GAGTATCTGCGATTGTGAAAAATCGATGTTTTGGAAATAAAATCAGGGTTC
1 GAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAATCAGGGTTA
1646948 GAGTATCCCC
1 GAGTATCCCC
1646958 TTGGAAATAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
51 48 0.96
52 2 0.04
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAATCAGGGTTA
Found at i:1647028 original size:130 final size:130
Alignment explanation
Indices: 1646795--1647033 Score: 329
Period size: 130 Copynumber: 1.8 Consensus size: 130
1646785 AAGTTTGATA
* * *
1646795 TTTTGGAGATAAAACCAGGGTTGGAGTATTCCCTTGAAAATAACGGCGTTGGAGTATCCCCGATT
1 TTTTGGAAATAAAACCAGGGTTCGAGTATCCCCTTGAAAATAACGGCGTTGGAGTATCCCCGATT
* *
1646860 ATGGAAAATCATTATTTTGAAAATAAAACTAGGGTTAGAGTATCTGCGATTGTGAAAAATCGATG
66 ATGAAAAATCATTATTTTAAAAATAAAACTAGGGTTAGAGTATCTGCGATTGTGAAAAATCGATG
* * * *
1646925 TTTTGGAAATAAAATCAGGGTTCGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCTCGATT
1 TTTTGGAAATAAAACCAGGGTTCGAGTATCCCCTTGAAAATAACGGCGTTGGAGTATCCCCGATT
* * * *
1646990 TTGAAAAATTGA-TGTTTTAAAAATAAAA-TCGGGGTTAGAGTATC
66 ATGAAAAA-TCATTATTTTAAAAATAAAACT-AGGGTTAGAGTATC
1647034 CCCTTGAAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
129 1 0.01
130 91 0.97
131 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (130 bp):
TTTTGGAAATAAAACCAGGGTTCGAGTATCCCCTTGAAAATAACGGCGTTGGAGTATCCCCGATT
ATGAAAAATCATTATTTTAAAAATAAAACTAGGGTTAGAGTATCTGCGATTGTGAAAAATCGATG
Found at i:1647182 original size:77 final size:79
Alignment explanation
Indices: 1646876--1647188 Score: 364
Period size: 79 Copynumber: 3.9 Consensus size: 79
1646866 AATCATTATT
* ** * *
1646876 TTGAAAATAAAACTAGGGTTAGAGTATCTGCGATTGTGAAAAATCGATGTTTTGGAAATAAAATC
1 TTGAAAAT--AAC-AGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAATC
*
1646941 AGGGTTCGAGTATCCCC
63 AGGGTTGGAGTATCCCC
* * * * ** *
1646958 TTGGAAATAACGGGGTTGGAGTATCCTCGATTTTGAAAAATTGATGTTTTAAAAATAAAATCGGG
1 TTGAAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAATCAGG
*
1647023 GTTAGAGTATCCCC
66 GTTGGAGTATCCCC
** * * *
1647037 TTGAAAATAACACAGTTGGAGTATCCCCGATTATGGAAAACTGATGTTTTGGAAATAAAAT-TGA
1 TTGAAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAATCAG-
*
1647101 GGTTGGAGTATCCTC
65 GGTTGGAGTATCCCC
*
1647116 TT-AAAATAACAGGGTTGGAGTATCCCCG-TTATGAAAAATT-AGTGTTTTGGAAATAAAACCAG
1 TTGAAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATTGA-TGTTTTGGAAATAAAATCAG
1647178 GGTTGGAGTAT
65 GGTTGGAGTAT
1647189 TCTCAATTAT
Statistics
Matches: 198, Mismatches: 30, Indels: 11
0.83 0.13 0.05
Matches are distributed among these distances:
76 1 0.01
77 37 0.19
78 26 0.13
79 124 0.63
80 3 0.02
82 7 0.04
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.30
Consensus pattern (79 bp):
TTGAAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAATCAGG
GTTGGAGTATCCCC
Found at i:1647210 original size:128 final size:130
Alignment explanation
Indices: 1647051--1647321 Score: 318
Period size: 128 Copynumber: 2.1 Consensus size: 130
1647041 AAATAACACA
* * ** * *
1647051 GTTGGAGTATCCCCGATTATGGAAAACTGATGTTTTGGAAATAAAA-TTGAGGTTGGAGTA-TCC
1 GTTGGAGTATCCCCAATTATGAAAAACTGATGTTTTGGAAATAAAACCAGA-GTTGAAGTATTCA
* *
1647114 TCTT-AAAATAAC-AGGGTTGGAGTATCCCCG-TTATGAAAAATTAGTGTTTTGGAAATAAAACC
65 T-TTGAAAATAACGA-GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAACC
1647176 AGG
128 AGG
* * *
1647179 GTTGGAGTATTCTCAATTATGAAAAATTGATGTTTTGGAAATAAAACCAGAGTTGAAGTATTCAT
1 GTTGGAGTATCCCCAATTATGAAAAACTGATGTTTTGGAAATAAAACCAGAGTTGAAGTATTCAT
* * * * *
1647244 TTGGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGG
66 TTGAAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAACCAGG
**
1647309 GTTAAAGTATCCC
1 GTTGGAGTATCCC
1647322 TTCAAAAATA
Statistics
Matches: 118, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
128 51 0.43
129 27 0.23
130 40 0.34
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (130 bp):
GTTGGAGTATCCCCAATTATGAAAAACTGATGTTTTGGAAATAAAACCAGAGTTGAAGTATTCAT
TTGAAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAACCAGG
Found at i:1647213 original size:51 final size:51
Alignment explanation
Indices: 1647125--1647241 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
1647115 CTTAAAATAA
**
1647125 CAGGGTTGGAGTA-TCCCCGTTATGAAAAATTAGTGTTTTGGAAATAAAAC
1 CAGGGTTGGAGTATTCCCAATTATGAAAAATTAGTGTTTTGGAAATAAAAC
*
1647175 CAGGGTTGGAGTATTCTCAATTATGAAAAATT-GATGTTTTGGAAATAAAAC
1 CAGGGTTGGAGTATTCCCAATTATGAAAAATTAG-TGTTTTGGAAATAAAAC
* *
1647226 CAGAGTTGAAGTATTC
1 CAGGGTTGGAGTATTC
1647242 ATTTGGAAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
50 14 0.23
51 46 0.77
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (51 bp):
CAGGGTTGGAGTATTCCCAATTATGAAAAATTAGTGTTTTGGAAATAAAAC
Found at i:1647250 original size:286 final size:286
Alignment explanation
Indices: 1646795--1647399 Score: 776
Period size: 286 Copynumber: 2.1 Consensus size: 286
1646785 AAGTTTGATA
* *
1646795 TTTTGGAGATAAAACCAGGGTTGGAGTATTCCCTTGAAAATAACGGCGTTGGAGTATCCCCGATT
1 TTTTGGAAATAAAA-CTGGGTTGGAGTA-TCCCTTGAAAATAACGGCGTTGGAGTATCCCCGATT
* * * * *
1646860 ATGGAAAATCATTATTTTGAAAATAAAACTAGGGTTAGAGTATCTGCGATTGTGAAAAATCGATG
64 ATGAAAAATCAGTATTTTGAAAATAAAACCAGGGTTAGAGTATCTGCAATTATGAAAAATCGATG
* * * *
1646925 TTTTGGAAATAAAATCAGGGTTCGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCTCGATT
129 TTTTGGAAATAAAACCAGAGTTCGAGTATCCACTTGGAAATAACGAGGTTGGAGTATCCTCGATT
* * * * *
1646990 TTGAAAAATTGATGTTTTAAAAATAAAATCGGGGTTAGAGTATCCCCTT-GAAAATAACACAG-T
194 GTGAAAAATTGATATTTTAAAAATAAAATCAGGGTTAAAGTAT-CCCTTCAAAAATAACA-AGAT
* * *
1647053 TGGAGTATCCCCGATTATGGAAAA-CTGATG
257 TCGAGTATCCCCGATTATGAAAAATCAG-TG
*
1647083 TTTTGGAAATAAAATTGAGGTTGGAGTATCCTCTT-AAAATAACAGG-GTTGGAGTATCCCCG-T
1 TTTTGGAAATAAAACTG-GGTTGGAGTATCC-CTTGAAAATAAC-GGCGTTGGAGTATCCCCGAT
* * * * *
1647145 TATGAAAAATTAGTGTTTTGGAAATAAAACCAGGGTTGGAGTATTCT-CAATTATGAAAAATTGA
63 TATGAAAAATCAGTATTTTGAAAATAAAACCAGGGTTAGAGTA-TCTGCAATTATGAAAAATCGA
* *
1647209 TGTTTTGGAAATAAAACCAGAGTT-GAAGTATTCATTTGGAAATAACGAGGTTGGAGTATCCTCG
127 TGTTTTGGAAATAAAACCAGAGTTCG-AGTATCCACTTGGAAATAACGAGGTTGGAGTATCCTCG
* * * *
1647273 ATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGGGTTAAAGTATCCCTTCAAAAATAATAGGA
191 ATTGTGAAAAATTGATATTTTAAAAATAAAATCAGGGTTAAAGTATCCCTTCAAAAATAACAAGA
*
1647338 TTCTAGTATCCCCGATTATGAAAAATCAGTG
256 TTCGAGTATCCCCGATTATGAAAAATCAGTG
1647369 TTTTGGAAATAAAACTGGGTTGGAGTATCCC
1 TTTTGGAAATAAAACTGGGTTGGAGTATCCC
1647400 CGATTATGAA
Statistics
Matches: 276, Mismatches: 33, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
284 1 0.00
285 20 0.07
286 195 0.71
287 32 0.12
288 28 0.10
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (286 bp):
TTTTGGAAATAAAACTGGGTTGGAGTATCCCTTGAAAATAACGGCGTTGGAGTATCCCCGATTAT
GAAAAATCAGTATTTTGAAAATAAAACCAGGGTTAGAGTATCTGCAATTATGAAAAATCGATGTT
TTGGAAATAAAACCAGAGTTCGAGTATCCACTTGGAAATAACGAGGTTGGAGTATCCTCGATTGT
GAAAAATTGATATTTTAAAAATAAAATCAGGGTTAAAGTATCCCTTCAAAAATAACAAGATTCGA
GTATCCCCGATTATGAAAAATCAGTG
Found at i:1647331 original size:79 final size:77
Alignment explanation
Indices: 1647178--1647399 Score: 219
Period size: 79 Copynumber: 2.8 Consensus size: 77
1647168 ATAAAACCAG
* * * * * *
1647178 GGTTGGAGTATTCTCAATTATGAAAAATTGATGTTTTGGAAATAAAACCAGAGTTGAAGTATTCA
1 GGTTGGAGTATCCTCGATTATGAAAAATTGGTGTTTTGGAAATAAAA-CAGGGTTGAAGTATCCC
***
1647243 TTTGGAAATAACGA
65 TTCAAAAATAA-GA
* * * *
1647257 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGGGTTAAAGTATCCC
1 GGTTGGAGTATCCTCGATTATGAAAAATTGGTGTTTTGGAAATAAAA-CAGGGTTGAAGTATCCC
*
1647322 TTCAAAAATAATA
65 TTCAAAAATAAGA
** * ** * *
1647335 GGATTCTAGTATCCCCGATTATGAAAAATCAGTGTTTTGGAAATAAAACTGGGTTGGAGTATCCC
1 GG-TTGGAGTATCCTCGATTATGAAAAATTGGTGTTTTGGAAATAAAACAGGGTTGAAGTATCCC
1647400 CGATTATGAA
Statistics
Matches: 116, Mismatches: 26, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
78 17 0.15
79 99 0.85
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (77 bp):
GGTTGGAGTATCCTCGATTATGAAAAATTGGTGTTTTGGAAATAAAACAGGGTTGAAGTATCCCT
TCAAAAATAAGA
Found at i:1647400 original size:50 final size:51
Alignment explanation
Indices: 1647342--1647449 Score: 166
Period size: 50 Copynumber: 2.1 Consensus size: 51
1647332 ATAGGATTCT
* *
1647342 AGTATCCCCGATTATGAAAAATC-AGTGTTTTGGAAATAAAA-CTGGGTTGG
1 AGTATCCCCGATTATGAAAAATCGA-TGTTTTAGAAATAAAACCGGGGTTGG
*
1647392 AGTATCCCCGATTATGAAAAATCGATGTTTTAGAATTAAAACCGGGGTTGG
1 AGTATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAAACCGGGGTTGG
1647443 AGTATCC
1 AGTATCC
1647450 TCTTGGAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
50 37 0.70
51 16 0.30
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (51 bp):
AGTATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAAACCGGGGTTGG
Found at i:1647421 original size:208 final size:207
Alignment explanation
Indices: 1646958--1647608 Score: 735
Period size: 208 Copynumber: 3.1 Consensus size: 207
1646948 GAGTATCCCC
* * * * *
1646958 TTGGAAAT--AACGGGGTTGGAGTATCCTCGATTTTGAAAAATTGATGTTTTAAAAATAAAATCG
1 TTGGAAATAAAACTGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCG
* * * * * * * * *
1647021 GGGTT-AGAGTATCCCCTTGAAAATAACACAGTTGGAGTATCCCCGATTATGGAAAACTGATGTT
66 GGGTTGA-AGTATTCCTTTGGAAATAACACGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTT
* * * *
1647085 TTGGAAATAAAAT-TGAGGTTGGAGTATCCTCTT-AAAATAACAGGGTTGGAGTATCCCCG-TTA
130 TTAGAAATAAAATCAG-GGTTGAAGTATCC-CTTCAAAATAACAGGATTGGAGTATCCCCGATTA
*
1647147 TGAAAAATTAGTGTT
193 TGAAAAATCAGTGTT
* * * * *
1647162 TTGGAAATAAAACCAGGGTTGGAGTATTCTCAATTATGAAAAATTGATGTTTTGGAAATAAAACC
1 TTGGAAATAAAA-CTGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACC
* * * *
1647227 AGAGTTGAAGTATTCATTTGGAAATAACGA-GGTTGGAGTATCCTCGATTGTGAAAAATTGGTAT
65 GGGGTTGAAGTATTCCTTTGGAAATAAC-ACGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGT
* * **
1647291 TTTAGAAATAAAATCAGGGTTAAAGTATCCCTTCAAAAATAATAGGATTCTAGTATCCCCGATTA
129 TTTAGAAATAAAATCAGGGTTGAAGTATCCCTTC-AAAATAACAGGATTGGAGTATCCCCGATTA
1647356 TGAAAAATCAGTGTT
193 TGAAAAATCAGTGTT
* *
1647371 TTGGAAATAAAACTGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTAGAATTAAAACCG
1 TTGGAAATAAAACTGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCG
* * * * *
1647436 GGGTTGGAGTA-TCCTCTTGGAAATAACAGGGTTGGAGTATCTTTGATTGTAAAAAATTGGTGTT
66 GGGTTGAAGTATTCCT-TTGGAAATAACACGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTT
* * * *
1647500 TTAGAAATAAAATCGGGGTTGAAGTATCCCCTCGAAAATAACGGGATTGGAGTAACCCCGATTAT
130 TTAGAAATAAAATCAGGGTTGAAGTATCCCTTC-AAAATAACAGGATTGGAGTATCCCCGATTAT
*
1647565 G-AAAATCGGTGTT
194 GAAAAATCAGTGTT
** *
1647578 TCAGAAATAAAATTGGGGTTGGAGTATCCCC
1 TTGGAAATAAAACT-GGGTTGGAGTATCCCC
1647609 TCGAAAATAA
Statistics
Matches: 378, Mismatches: 57, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
204 8 0.02
206 5 0.01
207 142 0.38
208 194 0.51
209 29 0.08
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (207 bp):
TTGGAAATAAAACTGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCG
GGGTTGAAGTATTCCTTTGGAAATAACACGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTT
TAGAAATAAAATCAGGGTTGAAGTATCCCTTCAAAATAACAGGATTGGAGTATCCCCGATTATGA
AAAATCAGTGTT
Found at i:1647598 original size:78 final size:78
Alignment explanation
Indices: 1647385--1647618 Score: 290
Period size: 79 Copynumber: 3.0 Consensus size: 78
1647375 AAATAAAACT
* * *
1647385 GGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTAGAATTAAAACCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTATG-AAAATCGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
* * *
1647450 TCTTGGAAATAACA
65 CCTCGAAAATAACA
*** * * * *
1647464 GGGTTGGAGTATCTTTGATTGTAAAAAATTGGTGTTTTAGAAATAAAATCGGGGTTGAAGTATCC
1 GGGTTGGAGTATCCCCGATTAT-GAAAATCGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
1647529 CCTCGAAAATAAC-
65 CCTCGAAAATAACA
* * *
1647542 GGGATTGGAGTAACCCCGATTATGAAAATCGGTGTTTCAGAAATAAAATTGGGGTTGGAGTATCC
1 GGG-TTGGAGTATCCCCGATTATGAAAATCGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
1647607 CCTCGAAAATAA
65 CCTCGAAAATAA
1647619 AAACATAAAT
Statistics
Matches: 130, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
78 52 0.40
79 78 0.60
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (78 bp):
GGGTTGGAGTATCCCCGATTATGAAAATCGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC
CTCGAAAATAACA
Found at i:1652422 original size:79 final size:77
Alignment explanation
Indices: 1652337--1652824 Score: 512
Period size: 79 Copynumber: 6.2 Consensus size: 77
1652327 TATTTCTGAG
* * *
1652337 GGGATACTCCAACTCCGGTTTTATTTCCAAAGCATCGATTTTTCACAATCGGGGATACTCCAACC
1 GGGATACTCCAAC-CCGGTTTTATTTCCAAAACATCAATTTTTCACAATCGGAGATACTCCAACC
1652402 CCGTTATTTCCAA
65 CCGTTATTTCCAA
* * *
1652415 GGAGATACTCCAACCCTGGTTTTATTTCAAAAACA-CTAATTTTTAATAATCGGAGATACTCCAA
1 GG-GATACTCCAACCC-GGTTTTATTTCCAAAACATC-AATTTTTCACAATCGGAGATACTCCAA
* *
1652479 CACCGTTATTTCCTAG
63 CCCCGTTATTTCC-AA
* * * * *
1652495 GGGATACTCCAACCCCGATTTTATTTCGAAAACACCAATTTTTCACAATTGGGGATACTCCAACC
1 GGGATACTCCAA-CCCGGTTTTATTTCCAAAACATCAATTTTTCACAATCGGAGATACTCCAACC
**
1652560 CCGTTATTTTTGAA
65 CCGTTA-TTTCCAA
* * * *
1652574 AGGATACTCTAACCTCGGTTTTATTTCCAAAACATCGATTTTTCATAATCGGAGATACTCCAACC
1 GGGATACTCCAACC-CGGTTTTATTTCCAAAACATCAATTTTTCACAATCGGAGATACTCCAACC
* *
1652639 CTGTTATTTTCGAA
65 CCGTTA-TTTCCAA
* ** * * *
1652653 GGGATACTCCAATCCCAGTTTTATTTTTAAAACACCGATTTTTCACAATCGGGGATACTCCAACC
1 GGGATACTCCAA-CCCGGTTTTATTTCCAAAACATCAATTTTTCACAATCGGAGATACTCCAACC
* *
1652718 CCGTTATTTCTGAG
65 CCGTTATTTC-CAA
* * *
1652732 GGGATACTCCAACCCCAGTTTTA-TTCCAAAACATTAACTTTTCACAATCGGAGATACTCCAACC
1 GGGATACTCCAA-CCCGGTTTTATTTCCAAAACATCAATTTTTCACAATCGGAGATACTCCAACC
*** * *
1652796 TTATTATTTTCGA
65 CCGTTATTTCCAA
1652809 GGAGATACTCCAACCC
1 GG-GATACTCCAACCC
1652825 TAGGTTTTGT
Statistics
Matches: 345, Mismatches: 54, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
77 5 0.01
78 61 0.18
79 267 0.77
80 12 0.03
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (77 bp):
GGGATACTCCAACCCGGTTTTATTTCCAAAACATCAATTTTTCACAATCGGAGATACTCCAACCC
CGTTATTTCCAA
Found at i:1652712 original size:237 final size:236
Alignment explanation
Indices: 1652338--1652795 Score: 638
Period size: 237 Copynumber: 1.9 Consensus size: 236
1652328 ATTTCTGAGG
* *
1652338 GGATACTCCAACTCCGGTTTTATTTCCAAAGCATCGATTTTTCACAATCGGGGATACTCCAACCC
1 GGATACTCCAACTCCGGTTTTATTTCCAAAACATCGATTTTTCACAATCGGAGATACTCCAACCC
* * *
1652403 CGTTATTTCCAAGGAGATACTCCAACCCTGGTTTTATTTCAAAAACACTAATTTTTAATAATCGG
66 CGTTATTTCCAAGGAGATACTCCAACCCTAGTTTTATTTCAAAAACACCAATTTTTAACAATCGG
*
1652468 AGATACTCCAACACCGTTATTTCCT-AGGGGATACTCCAACCCC-GATTTTATTTCGAAAACACC
131 AGATACTCCAACACCGTTATTT-CTGAGGGGATACTCCAACCCCAG-TTTTA-TTCCAAAACACC
* * *
1652531 AATTTTTCACAATTGGGGATACTCCAACCCCGTTATTTTTGAAA
193 AACTTTTCACAATCGGAGATACTCCAACCCCGTTATTTTTGAAA
* *
1652575 GGATACTCTAAC-CTCGGTTTTATTTCCAAAACATCGATTTTTCATAATCGGAGATACTCCAACC
1 GGATACTCCAACTC-CGGTTTTATTTCCAAAACATCGATTTTTCACAATCGGAGATACTCCAACC
* * ** * *
1652639 CTGTTATTTTCGAAGG-GATACTCCAATCCC-AGTTTTATTTTTAAAACACCGATTTTTCACAAT
65 CCGTTA-TTTCCAAGGAGATACTCCAA-CCCTAGTTTTATTTCAAAAACACCAATTTTTAACAAT
* * **
1652702 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCAGTTTTATTCCAAAACATT
128 CGGAGATACTCCAACACCGTTATTTCTGAGGGGATACTCCAACCCCAGTTTTATTCCAAAACACC
1652767 AACTTTTCACAATCGGAGATACTCCAACC
193 AACTTTTCACAATCGGAGATACTCCAACC
1652796 TTATTATTTT
Statistics
Matches: 195, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
236 38 0.19
237 145 0.74
238 12 0.06
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (236 bp):
GGATACTCCAACTCCGGTTTTATTTCCAAAACATCGATTTTTCACAATCGGAGATACTCCAACCC
CGTTATTTCCAAGGAGATACTCCAACCCTAGTTTTATTTCAAAAACACCAATTTTTAACAATCGG
AGATACTCCAACACCGTTATTTCTGAGGGGATACTCCAACCCCAGTTTTATTCCAAAACACCAAC
TTTTCACAATCGGAGATACTCCAACCCCGTTATTTTTGAAA
Found at i:1652832 original size:158 final size:157
Alignment explanation
Indices: 1652329--1652832 Score: 636
Period size: 158 Copynumber: 3.2 Consensus size: 157
1652319 AATGTTTTTA
* *
1652329 TTTCTGAGGGGATACTCCAACTCC-GGTTTTATTTCCAAAGCATCGATTTTTCACAATCGGGGAT
1 TTTC-GAGGGGATACTCCAAC-CCAGGTTTTATTTCCAAAACACCGATTTTTCACAATCGGGGAT
** * * * *
1652393 ACTCCAACCCCGTTATTTCCAAGGAGATACTCCAACCCTGGTTTTATTTCAAAAACACTAATTTT
64 ACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATTAATTTT
* *
1652458 TAATAATCGGAGATACTCCAACACCGTTAT
129 TCATAATCGGAGATACTCCAAC-CTGTTAT
* * * * * * *
1652488 TTCCTAGGGGATACTCCAACCCCGATTTTATTTCGAAAACACCAATTTTTCACAATTGGGGATAC
1 TTTCGAGGGGATACTCCAACCCAGGTTTTATTTCCAAAACACCGATTTTTCACAATCGGGGATAC
* ** * * **
1652553 TCCAACCCCGTTATTTTTGAAAGGATACTCTAACCTCGGTTTTATTTCCAAAACATCGATTTTTC
66 TCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATTAATTTTTC
1652618 ATAATCGGAGATACTCCAACCCTGTTAT
131 ATAATCGGAGATACTCCAA-CCTGTTAT
* **
1652646 TTTCGAAGGGATACTCCAATCCCA-GTTTTATTTTTAAAACACCGATTTTTCACAATCGGGGATA
1 TTTCGAGGGGATACTCCAA-CCCAGGTTTTATTTCCAAAACACCGATTTTTCACAATCGGGGATA
* *
1652710 CTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCAGTTTTA-TTCCAAAACATTAACTTTT
65 CTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATTAATTTTT
* *
1652774 CACAATCGGAGATACTCCAACCTTATTAT
130 CATAATCGGAGATACTCCAACC-TGTTAT
*
1652803 TTTCGAGGAGATACTCCAACCCTAGGTTTT
1 TTTCGAGGGGATACTCCAACCC-AGGTTTT
1652833 GTCTCCGAAA
Statistics
Matches: 294, Mismatches: 45, Indels: 13
0.84 0.13 0.04
Matches are distributed among these distances:
156 5 0.02
157 60 0.20
158 222 0.76
159 7 0.02
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.33
Consensus pattern (157 bp):
TTTCGAGGGGATACTCCAACCCAGGTTTTATTTCCAAAACACCGATTTTTCACAATCGGGGATAC
TCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATTAATTTTTC
ATAATCGGAGATACTCCAACCTGTTAT
Found at i:1654622 original size:61 final size:61
Alignment explanation
Indices: 1654362--1655044 Score: 831
Period size: 61 Copynumber: 11.4 Consensus size: 61
1654352 AAGAGGGAGA
* * * * *
1654362 CGTCCTGCACTTTGGGGACT-AGAAGGTTCCACCAAC-T-TATGGGCTTTAAAAGG-AAAGG
1 CGTCCTACTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* * *
1654420 TGCCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAACA-G----GG
1 CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAA-AGGAAAAGG
** * * *
1654477 CGTCCTACTCTTTGAGGACTGAAAGGTATCACCAACTTGTATAGGATTTAAAAGG----GG
1 CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* *
1654534 CGTCCTACTCTTTAAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGG
1 CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* * * *
1654595 CATCATGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGG
1 CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* * **
1654656 CGTCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTTGCATGGGCTTTAAAAGG-AAAGG
1 CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* * * * *
1654716 TGTCATACTCTTTGAGGACTGAAAGGCGCCACCAACTTGTGTAGGCTTTTAAAGGAAAAGG
1 CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* * *
1654777 CGTCTTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGG
1 CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* * * *
1654838 CATCATCCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
1 CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* **
1654899 CGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAACAA--AAAAAA
1 CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AAGGAAAAGG
* * * *
1654959 TGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGAGCTTTAAAAGGAAAAGA
1 CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* *
1655020 CGTCCTACTTTTTGAGGACAGAAAG
1 CGTCCTACTCTTTGAGGACTGAAAG
1655045 ATTAAAAGGT
Statistics
Matches: 547, Mismatches: 65, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
56 1 0.00
57 98 0.18
58 29 0.05
59 4 0.01
60 117 0.21
61 296 0.54
62 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (61 bp):
CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
Found at i:1654792 original size:182 final size:182
Alignment explanation
Indices: 1654362--1655044 Score: 863
Period size: 182 Copynumber: 3.8 Consensus size: 182
1654352 AAGAGGGAGA
* * * * * * *
1654362 CGTCCTGCACTTTGGGGACT-AGAAGGTTCCACCAAC-T-TATGGGCTTTAAAAGG-AAAGGTGC
1 CGTCCTACTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
1654423 CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAACA-G----GGCGTCCT
65 CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAA-AGGAAAAGGCGTCCT
** * *
1654483 ACTCTTTGAGGACTGAAAGGTATCACCAACTTGTATAGGATTTAAAAGG---GG
129 ACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAGG
* * *
1654534 CGTCCTACTCTTTAAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCATC
1 CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
* * *
1654599 ATGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCGTCCTGC
66 CTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTAC
* *
1654664 TCTTTGAGGATTGAAAGGTGCCACCAACTTGCATGGGCTTTAAAAGGAAAGG
131 TCTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAGG
* * * * *
1654716 TGTCATACTCTTTGAGGACTGAAAGGCGCCACCAACTTGTGTAGGCTTTTAAAGGAAAAGGCGTC
1 CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
* * * * *
1654781 TTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCATCATCC
66 CTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTAC
* *
1654846 TCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
131 TCTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGGCTTTAAAAGG-AAAGG
* ***
1654899 CGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAACAA--AAAAAATGT
1 CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AAGGAAAAGGCGT
* * * *
1654962 CCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGAGCTTTAAAAGGAAAAGACGTCCTA
65 CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTA
* *
1655027 CTTTTTGAGGACAGAAAG
130 CTCTTTGAGGACTGAAAG
1655045 ATTAAAAGGT
Statistics
Matches: 439, Mismatches: 58, Indels: 18
0.85 0.11 0.03
Matches are distributed among these distances:
172 29 0.07
173 2 0.00
174 16 0.04
175 52 0.12
179 50 0.11
182 238 0.54
183 50 0.11
184 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (182 bp):
CGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
CTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTAC
TCTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAGG
Found at i:1654840 original size:243 final size:242
Alignment explanation
Indices: 1654371--1655044 Score: 940
Period size: 243 Copynumber: 2.8 Consensus size: 242
1654361 ACGTCCTGCA
* * *
1654371 CTTTGGGGACT-AGAAGGTTCCACCAACTTA--TGGGCTTTAAAAGG-AAAGGTGCCCTGCTCTT
1 CTTTGGGGACTGA-AAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTT
*
1654432 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAACAG---GGCGTCCTACTCTTTGAGG
65 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAA-AGAAAGGTGTCCTACTCTTTGAGG
** * * *
1654494 ACTGAAAGGTATCACCAACTTGTATAGGATTTAAAAGG----GGCGTCCTACTCTTTAAGGACTG
129 ACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCGTCCTACTCTTTGAGGACTG
* * *
1654555 AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCATCATGCT
194 AAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCATCATCCT
*
1654604 CTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTT
1 CTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTT
* ** *
1654669 GAGGATTGAAAGGTGCCACCAACTTGCATGGGCTTTAAAAGGAAAGGTGTCATACTCTTTGAGGA
66 GAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAGGTGTCCTACTCTTTGAGGA
* * * *
1654734 CTGAAAGGCGCCACCAACTTGTGTAGGCTTTTAAAGGAAAAGGCGTCTTGCTCTTTGAGGACTGA
130 CTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCGTCCTACTCTTTGAGGACTGA
1654799 AAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCATCATCCT
195 AAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCATCATCCT
* *
1654847 CTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCTTT
1 CTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTT
* * **
1654912 GAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAACAAAAAAAATGTCCTACTCTTTGAGGA
66 GAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AAGAAAGGTGTCCTACTCTTTGAGGA
* * * *
1654977 CTAAAAGGTGCCACCAACTTGTGT-GAGCTTTAAAAGGAAAAGACGTCCTACTTTTTGAGGACAG
130 CTGAAAGGTGCCACCAACTTGTGTAG-GCTTTAAAAGGAAAAGGCGTCCTACTCTTTGAGGACTG
1655041 AAAG
194 AAAG
1655045 ATTAAAAGGT
Statistics
Matches: 387, Mismatches: 40, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
233 26 0.07
234 1 0.00
235 15 0.04
236 53 0.14
239 49 0.13
242 1 0.00
243 240 0.62
244 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (242 bp):
CTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTT
GAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGTGTCCTACTCTTTGAGGAC
TGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCGTCCTACTCTTTGAGGACTGAA
AGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCATCATCCT
Found at i:1656039 original size:1 final size:1
Alignment explanation
Indices: 1656028--1656079 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
1656018 TTCTTTTCTC
* * * * * *
1656028 TTTTCTTTTTTTCTTTTTTTTTCTTTTTTTATTTTGTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1656080 GAAAAAGGAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.02, C:0.06, G:0.04, T:0.88
Consensus pattern (1 bp):
T
Found at i:1656041 original size:25 final size:23
Alignment explanation
Indices: 1656021--1656079 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
1656011 GGTTCTTTTC
*
1656021 TTTTCTCTTTTCTTT-TTTTCTTT
1 TTTTTTCTTTT-TTTATTTTCTTT
*
1656044 TTTTTTCTTTTTTTATTTTGTTT
1 TTTTTTCTTTTTTTATTTTCTTT
*
1656067 TTGTTT-TTTTTTT
1 TTTTTTCTTTTTTT
1656080 GAAAAAGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.31
23 22 0.69
ACGTcount: A:0.02, C:0.08, G:0.03, T:0.86
Consensus pattern (23 bp):
TTTTTTCTTTTTTTATTTTCTTT
Found at i:1656049 original size:18 final size:19
Alignment explanation
Indices: 1656016--1656076 Score: 79
Period size: 18 Copynumber: 3.2 Consensus size: 19
1656006 AAGTAGGTTC
1656016 TTTTCTTTTCTCTTTTCTTT
1 TTTTCTTTTCT-TTTTCTTT
1656036 TTTTCTTTT-TTTTTCTTT
1 TTTTCTTTTCTTTTTCTTT
* * *
1656054 TTTTATTTTGTTTTTGTTT
1 TTTTCTTTTCTTTTTCTTT
1656073 TTTT
1 TTTT
1656077 TTTGAAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 16 0.42
19 13 0.34
20 9 0.24
ACGTcount: A:0.02, C:0.10, G:0.03, T:0.85
Consensus pattern (19 bp):
TTTTCTTTTCTTTTTCTTT
Found at i:1668486 original size:51 final size:52
Alignment explanation
Indices: 1668417--1668531 Score: 157
Period size: 51 Copynumber: 2.2 Consensus size: 52
1668407 AAAATAATGG
*
1668417 GGTTGGAGTATCCTCGATTATGAAAAATCAATGTTTT-AGAAATAAAA-CTAA
1 GGTTGGAGTATCCTCGATTATGAAAAATCAATGTTTTGA-AAATAAAATCGAA
* *
1668468 GGTTGGAGTAT-CTCCGATTGTGAAAAATCAGTGTTTTGAAAATAAAATCGAA
1 GGTTGGAGTATCCT-CGATTATGAAAAATCAATGTTTTGAAAATAAAATCGAA
1668520 -GTTGGAGTATCC
1 GGTTGGAGTATCC
1668532 CTTTGGAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
50 2 0.04
51 50 0.88
52 5 0.09
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (52 bp):
GGTTGGAGTATCCTCGATTATGAAAAATCAATGTTTTGAAAATAAAATCGAA
Found at i:1668542 original size:130 final size:127
Alignment explanation
Indices: 1668379--1669128 Score: 552
Period size: 130 Copynumber: 5.8 Consensus size: 127
1668369 TATTTTGGAG
* * * * * *
1668379 AATAAACCGAGGTTAGAGTAT-CCTCTCGAAAATAATGGGGTTGGAGTATCCTCGATTATGAAAA
1 AATAAAACGAGGTTGGAGTATCCCT-TTGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAA
**
1668443 ATCAATGTTTTAGAAATAAAACTAAGGTTGGAGTATCTCCGATTGTGAAAAATCAGTGTTTTGAA
65 ATCAATGTTTTAGAAATAAAA-TGGGGTTGGAGTATCTCCGATTGTGAAAAAT-AGTGTTTTGAA
* * * * * *
1668508 AATAAAATCGAAGTTGGAGTATCCCTTTGGAAATAACAGGGTTAGAGTATCCCCAATGATGGAAA
1 AATAAAA-CGAGGTTGGAGTATCCCTTTGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAA
*** * * * * * *
1668573 ATTGGTGTTTTAAAAATAAAACCGGGGTTGGAGTATCTCCAATTATGAAAAATTGATGTTTTGGA
65 ATCAATGTTTTAGAAATAAAA-TGGGGTTGGAGTATCTCCGATTGTGAAAAATAG-TGTTTTGAA
* * *** * *
1668638 AATAAAACCAGGGTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATTATGAAAA
1 AATAAAACGA-GGTTGGAGTATCCCTTTGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAA
* * * * * * *
1668703 ATCGATGTTTTGGAAATAAATTGGGGTTGAAGTAT-TGCCGATTATGAAAAATTGATGTTTTGGA
65 ATCAATGTTTTAGAAATAAAATGGGGTTGGAGTATCT-CCGATTGTGAAAAATAG-TGTTTTGAA
* * * *
1668767 AATAAAATTGGGGTTGGAGTATCTCC-TTGGAAATAACGGGGTTGGAGGATCCCCGATTGTGAAA
1 AATAAAA-CGAGGTTGGAGTATC-CCTTTGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAA
** * **** * *
1668831 AATTGATGTTTTAGAAATAAAATCGGGGTTAGAGTATCCTCTCGAAAATAATG-GGGTTAGAGTA
64 AATCAATGTTTTAGAAATAAAAT-GGGGTTGGAGTAT-CTC-CG---AT--TGTGAAAAATAGTG
*
1668895 TCTTTGAT
121 T-TTTGAA
* * * * * *
1668903 TATAAAA--A--ATCGA-TGT---TTTGGAAATAAAATCGGGGTTGAAGTATCCCTGATTATGAA
1 AATAAAACGAGGTTGGAGTATCCCTTTGGAAAT--AA-CGGGGTTGGAGTATCCCCGATTATGAA
* * ** *
1668960 AAATCAGTGTTTTAGAAATAAAATCAGGGTTAAAGTATCCCCGATTGTGAAAAATCAGTGTTTTG
63 AAATCAATGTTTTAGAAATAAAAT-GGGGTTGGAGTATCTCCGATTGTGAAAAAT-AGTGTTTTG
1669025 AA
126 AA
* * *
1669027 AATAAAACCGAGGTTTGAGTATCCCTTTGGAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAA
1 AATAAAA-CGAGGTTGGAGTATCCCTTTGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAA
* * * *
1669092 ATTAGTATTTTAGAAATAAAATCGGGGTTGAAGTATC
65 ATCAATGTTTTAGAAATAAAAT-GGGGTTGGAGTATC
1669129 CCTTCAGAAA
Statistics
Matches: 488, Mismatches: 101, Indels: 63
0.75 0.15 0.10
Matches are distributed among these distances:
123 2 0.00
124 13 0.03
125 6 0.01
127 9 0.02
128 3 0.01
129 124 0.25
130 292 0.60
131 9 0.02
132 3 0.01
133 9 0.02
135 4 0.01
136 13 0.03
137 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.30
Consensus pattern (127 bp):
AATAAAACGAGGTTGGAGTATCCCTTTGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
TCAATGTTTTAGAAATAAAATGGGGTTGGAGTATCTCCGATTGTGAAAAATAGTGTTTTGAA
Found at i:1668615 original size:51 final size:51
Alignment explanation
Indices: 1668544--1668663 Score: 168
Period size: 51 Copynumber: 2.4 Consensus size: 51
1668534 TTGGAAATAA
* * *
1668544 CAGGGTTAGAGTATCCCCAATGATGGAAAATTGGTGTTTTAAAAATAAAAC
1 CAGGGTTGGAGTATCCCCAATGATGAAAAATTGATGTTTTAAAAATAAAAC
* * * **
1668595 CGGGGTTGGAGTATCTCCAATTATGAAAAATTGATGTTTTGGAAATAAAAC
1 CAGGGTTGGAGTATCCCCAATGATGAAAAATTGATGTTTTAAAAATAAAAC
1668646 CAGGGTTGGAGTATCCCC
1 CAGGGTTGGAGTATCCCC
1668664 TCAAAAATAA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (51 bp):
CAGGGTTGGAGTATCCCCAATGATGAAAAATTGATGTTTTAAAAATAAAAC
Found at i:1668744 original size:50 final size:51
Alignment explanation
Indices: 1668690--1668788 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 51
1668680 TAGAGTATCC
1668690 CCGATTATGAAAAATCGATGTTTTGGAAAT-AAATTGGGGTTGAAGTATTG
1 CCGATTATGAAAAATCGATGTTTTGGAAATAAAATTGGGGTTGAAGTATTG
* *
1668740 CCGATTATGAAAAATTGATGTTTTGGAAATAAAATTGGGGTTGGAGTAT
1 CCGATTATGAAAAATCGATGTTTTGGAAATAAAATTGGGGTTGAAGTAT
1668789 CTCCTTGGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 29 0.63
51 17 0.37
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (51 bp):
CCGATTATGAAAAATCGATGTTTTGGAAATAAAATTGGGGTTGAAGTATTG
Found at i:1668823 original size:79 final size:79
Alignment explanation
Indices: 1668740--1668948 Score: 267
Period size: 79 Copynumber: 2.6 Consensus size: 79
1668730 TGAAGTATTG
* * *
1668740 CCGATTATGAAAAATTGATGTTTTGGAAATAAAATTGGGGTTGGAGTAT-CTCCTTGGAAATAAC
1 CCGATTATGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCT-CTCGAAAATAAC
*
1668804 GGGGTTGGAGGATCC
65 GGGGTTAGAGGATCC
* * * *
1668819 CCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTAGAGTATCCTCTCGAAAATAATG
1 CCGATTATGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCTCTCGAAAATAACG
* *
1668884 GGGTTAGAGTATCT
66 GGGTTAGAGGATCC
** * * *
1668898 TTGATTATAAAAAATCGATGTTTTGGAAATAAAATCGGGGTTGAAGTATCC
1 CCGATTATGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCC
1668949 CTGATTATGA
Statistics
Matches: 111, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
79 109 0.98
80 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (79 bp):
CCGATTATGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCTCTCGAAAATAACG
GGGTTAGAGGATCC
Found at i:1668850 original size:208 final size:209
Alignment explanation
Indices: 1668595--1668983 Score: 559
Period size: 208 Copynumber: 1.9 Consensus size: 209
1668585 AAAATAAAAC
* * * *
1668595 CGGGGTTGGAGTATCTCCAATTATGAAAAATTGATGTTTTGGAAATAAAACCAGGGTTGGAGTAT
1 CGGGGTTGGAGGATCCCCAATTATGAAAAATTGATGTTTTAGAAATAAAACCAGGGTTAGAGTAT
*
1668660 CCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATTATGAAAAATCGATGTTTTGGAAAT-AAAT
66 CCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATTATAAAAAATCGATGTTTTGGAAATAAAAT
* * * *
1668724 TGGGGTTGAAGTATTGCC-GATTATGAAAAAT-TGATGTTTTGGAAATAAAATTGGGGTTGGAGT
131 CGGGGTTGAAGTA-TCCCTGATTATGAAAAATCAG-TGTTTTAGAAATAAAATTGGGGTTGGAGT
1668787 ATCTCCTTGGAAATAA
194 ATCTCCTTGGAAATAA
* * * *
1668803 CGGGGTTGGAGGATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTAGAGTAT
1 CGGGGTTGGAGGATCCCCAATTATGAAAAATTGATGTTTTAGAAATAAAACCAGGGTTAGAGTAT
* * * * ***
1668868 CCTCTCGAAAATAATGGGGTTAGAGTATCTTTGATTATAAAAAATCGATGTTTTGGAAATAAAAT
66 CCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATTATAAAAAATCGATGTTTTGGAAATAAAAT
1668933 CGGGGTTGAAGTATCCCTGATTATGAAAAATCAGTGTTTTAGAAATAAAAT
131 CGGGGTTGAAGTATCCCTGATTATGAAAAATCAGTGTTTTAGAAATAAAAT
1668984 CAGGGTTAAA
Statistics
Matches: 158, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
208 112 0.71
209 45 0.28
210 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (209 bp):
CGGGGTTGGAGGATCCCCAATTATGAAAAATTGATGTTTTAGAAATAAAACCAGGGTTAGAGTAT
CCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATTATAAAAAATCGATGTTTTGGAAATAAAAT
CGGGGTTGAAGTATCCCTGATTATGAAAAATCAGTGTTTTAGAAATAAAATTGGGGTTGGAGTAT
CTCCTTGGAAATAA
Found at i:1668954 original size:51 final size:51
Alignment explanation
Indices: 1668899--1669052 Score: 195
Period size: 51 Copynumber: 3.0 Consensus size: 51
1668889 AGAGTATCTT
*
1668899 TGATTATAAAAAATC-GATGTTTTGGAAATAAAATCGGGGTTGAAGTATCCC
1 TGATTATGAAAAATCAG-TGTTTTGGAAATAAAATCGGGGTTGAAGTATCCC
* * *
1668950 TGATTATGAAAAATCAGTGTTTTAGAAATAAAATCAGGGTTAAAGTATCCC
1 TGATTATGAAAAATCAGTGTTTTGGAAATAAAATCGGGGTTGAAGTATCCC
* * * * *
1669001 CGATTGTGAAAAATCAGTGTTTTGAAAATAAAACCGAGGTTTG-AGTATCCC
1 TGATTATGAAAAATCAGTGTTTTGGAAATAAAATCG-GGGTTGAAGTATCCC
1669052 T
1 T
1669053 TTGGAAATAA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
51 83 0.94
52 5 0.06
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (51 bp):
TGATTATGAAAAATCAGTGTTTTGGAAATAAAATCGGGGTTGAAGTATCCC
Found at i:1669079 original size:79 final size:78
Alignment explanation
Indices: 1668986--1669220 Score: 285
Period size: 79 Copynumber: 3.0 Consensus size: 78
1668976 AATAAAATCA
*
1668986 GGGTTAAAGTATCCCCGATTGTGAAAAATCAGTGTTTTGAAAATAAAACCGAGGTTTGAGTATCC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGAAAATAAAACCG-GGTTTGAGTATCC
** *
1669051 CTTTGGAAATAATG
65 CTTCAGAAATAACG
* * * * *
1669065 GGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTT-AGAAATAAAATCGGGGTTGAAGTATC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGA-AAATAAAACCGGGTTTG-AGTATC
1669129 CCTTCAGAAATAACG
64 CCTTCAGAAATAACG
* * * *
1669144 GGGTTAGAGTATCCCCAATTATGGAAAATC-GATGTTTTGAAAATAAAACCGGGGTTGGAGTATC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATCAG-TGTTTTGAAAATAAAACC-GGGTTTGAGTATC
*
1669208 CCCTCAGAAATAA
64 CCTTCAGAAATAA
1669221 AAACATAAAT
Statistics
Matches: 132, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
78 7 0.05
79 119 0.90
80 6 0.05
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (78 bp):
GGGTTAGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGAAAATAAAACCGGGTTTGAGTATCCC
TTCAGAAATAACG
Found at i:1672298 original size:61 final size:61
Alignment explanation
Indices: 1672169--1672827 Score: 888
Period size: 61 Copynumber: 10.8 Consensus size: 61
1672159 GCCACTGACT
* * *
1672169 TGTGGGCTTTGAAAGGAAAAGGCATCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTA
1 TGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTG
* * * *
1672229 TGTGGGCTTTAAAAAGAGAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCTACCAACTTG
1 TGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTG
* * *
1672290 TGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTTG
1 TGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTG
* * *
1672351 TGTGGGCTTTAAAAGGAAAAGACGTCCTACTCTTTGAGGATTGAAAGGTGCCACCAACTTG
1 TGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTG
* ** * *
1672412 TGTGGGCTTTAAAAGGAGAAGGTGTCCTACTCTTTGAGGATTAAAAGGTGCCACCAACTTG
1 TGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTG
* * * * * *
1672473 TGTGGGCTTTAAAAGGAGAAGGCATCTTGCTCTTTGACGACTGAAATGTGCCACCAACTTA
1 TGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTG
* *
1672534 TGTGGGCTTTAAAAGGAAAAGGCATCTTTCTCTTTGAGGACTGAAAGGTGCCACCAACTTG
1 TGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTG
* * * * * *
1672595 TGTAGGTTTTAAAAGGAAAAGACGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTG
1 TGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTG
* * * **
1672656 TGTGGGCTTTAAAAGAAAAAGGCATCCTACTCTTTGAAGACTAAAACTTGCCACCAACTTG
1 TGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTG
* ** * ** * *
1672717 TGGGGGCTTTAACAAAAAAAAAGTGTCCTACTCTTTGAGGACTAAAAGGTACCACCAACTTG
1 TGTGGGCTTTAA-AAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTG
*
1672779 TGTGGGCTTTAAAAGGAAAAGACATCCTACTCTTTGAGGACTGAAAGGT
1 TGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAGGT
1672828 TAAAAGGTTT
Statistics
Matches: 534, Mismatches: 63, Indels: 3
0.89 0.10 0.00
Matches are distributed among these distances:
60 39 0.07
61 443 0.83
62 52 0.10
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (61 bp):
TGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTG
Found at i:1673811 original size:12 final size:12
Alignment explanation
Indices: 1673794--1673864 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 12
1673784 TTAAGCAGGT
1673794 TCTTTTTTTTTC
1 TCTTTTTTTTTC
*
1673806 TCTTTTTTCTTTT
1 TCTTTTTT-TTTC
*
1673819 TCCTCTTTTTTTC
1 T-CTTTTTTTTTC
* *
1673832 T-TTTGTTTTTG
1 TCTTTTTTTTTC
* *
1673843 TCTTTGTTTTTG
1 TCTTTTTTTTTC
1673855 T-TTTTTTTTT
1 TCTTTTTTTTT
1673865 AAAGGAATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
11 16 0.33
12 19 0.39
13 8 0.16
14 6 0.12
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.82
Consensus pattern (12 bp):
TCTTTTTTTTTC
Found at i:1673824 original size:16 final size:16
Alignment explanation
Indices: 1673796--1673835 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1673786 AAGCAGGTTC
1673796 TTTT-TTTTTCTC-TT
1 TTTTCTTTTTCTCTTT
1673810 TTTTCTTTTTCCTCTTT
1 TTTTCTTTTT-CTCTTT
1673827 TTTTCTTTT
1 TTTTCTTTT
1673836 GTTTTTGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.17
15 5 0.22
16 3 0.13
17 11 0.48
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTTCTCTTT
Found at i:1673841 original size:6 final size:6
Alignment explanation
Indices: 1673832--1673864 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1673822 TCTTTTTTTC
*
1673832 TTTTGT TTTTGT CTTTGT TTTTGT TTTT-T TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
1673865 AAAGGAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:1676054 original size:20 final size:19
Alignment explanation
Indices: 1676029--1676176 Score: 139
Period size: 20 Copynumber: 7.8 Consensus size: 19
1676019 TTTTCACAAT
1676029 TTGTATCGATACATTATTCA
1 TTGTATCGATACATT-TTCA
1676049 TTGTATCGATACATTTTGCA
1 TTGTATCGATACATTTT-CA
**
1676069 TTGTATCGATACATGGCTCA
1 TTGTATCGATACAT-TTTCA
*
1676089 TTGAATCGAT--A----CA
1 TTGTATCGATACATTTTCA
1676102 TTGTATCGATACATTGCTT-A
1 TTGTATCGATACATT--TTCA
*
1676122 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATT-TTCA
1676142 TTGTATCGATACATTTTACA
1 TTGTATCGATACATTTT-CA
*
1676162 ATGTATCGATACATT
1 TTGTATCGATACATT
1676177 CAGGCATTTT
Statistics
Matches: 108, Mismatches: 8, Indels: 24
0.77 0.06 0.17
Matches are distributed among these distances:
13 11 0.10
15 1 0.01
18 1 0.01
19 4 0.04
20 90 0.83
21 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.41
Consensus pattern (19 bp):
TTGTATCGATACATTTTCA
Found at i:1676109 original size:13 final size:13
Alignment explanation
Indices: 1676087--1676117 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1676077 ATACATGGCT
1676087 CATTGAATCGATA
1 CATTGAATCGATA
*
1676100 CATTGTATCGATA
1 CATTGAATCGATA
1676113 CATTG
1 CATTG
1676118 CTTATTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (13 bp):
CATTGAATCGATA
Found at i:1676109 original size:33 final size:33
Alignment explanation
Indices: 1676067--1676137 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1676057 ATACATTTTG
1676067 CATTGTATCGATACATGGCTCATTGAATCGATA
1 CATTGTATCGATACATGGCTCATTGAATCGATA
* * *
1676100 CATTGTATCGATACATTGCTTATTGTATCGATA
1 CATTGTATCGATACATGGCTCATTGAATCGATA
1676133 CATTG
1 CATTG
1676138 CTCATTGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (33 bp):
CATTGTATCGATACATGGCTCATTGAATCGATA
Found at i:1676127 original size:53 final size:52
Alignment explanation
Indices: 1676047--1676156 Score: 168
Period size: 53 Copynumber: 2.1 Consensus size: 52
1676037 ATACATTATT
1676047 CATTGTATCGATACATTTTGCATTGTATCGATACATGGCTCATTGAATCGATA
1 CATTGTATCGATACATTTT-CATTGTATCGATACATGGCTCATTGAATCGATA
* *
1676100 CATTGTATCGATACATTGCTT-ATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATT--TTCATTGTATCGATACATGGCTCATTGAATCGATA
1676153 CATT
1 CATT
1676157 TTACAATGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
53 51 0.96
55 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (52 bp):
CATTGTATCGATACATTTTCATTGTATCGATACATGGCTCATTGAATCGATA
Found at i:1678358 original size:19 final size:19
Alignment explanation
Indices: 1678334--1678395 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
1678324 ATTCAACGAT
1678334 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1678353 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
1678367 -TGTATTGATACATAAGTG
1 TTGTATCGATACATAAGTG
1678385 TTGTATCGATA
1 TTGTATCGATA
1678396 TATTAGGATC
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
13 10 0.29
15 2 0.06
17 2 0.06
19 21 0.60
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1678371 original size:32 final size:32
Alignment explanation
Indices: 1678335--1678395 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1678325 TTCAACGATT
1678335 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1678367 TGTATTGATACATAAGTGTTGTATCGATA
1 TGTATCGATACATAAGTGTTGTATCGATA
1678396 TATTAGGATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1678689 original size:20 final size:20
Alignment explanation
Indices: 1678664--1678718 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1678654 AAAACCCTTA
1678664 AAAGTATCGATACATAATT-C
1 AAAGTATCGATACAT-ATTGC
*
1678684 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATATTGC
*
1678704 AATGTATCGATACAT
1 AAAGTATCGATACAT
1678719 CAAAAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AAAGTATCGATACATATTGC
Found at i:1678808 original size:13 final size:13
Alignment explanation
Indices: 1678790--1678815 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1678780 ACACCAAAGT
1678790 ATGTATCGATACA
1 ATGTATCGATACA
1678803 ATGTATCGATACA
1 ATGTATCGATACA
1678816 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1678813 original size:33 final size:33
Alignment explanation
Indices: 1678771--1678835 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1678761 TAGCCAAACT
* *
1678771 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
1678804 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1678836 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1684072 original size:130 final size:130
Alignment explanation
Indices: 1683839--1684099 Score: 513
Period size: 130 Copynumber: 2.0 Consensus size: 130
1683829 CAAAAGATTT
1683839 CAAATGGATCAAGTCAAACCATGTGAAACTCCGATGAGTACTTCAACGAAGCTTGAAAAAGATGA
1 CAAATGGATCAAGTCAAACCATGTGAAACTCCGATGAGTACTTCAACGAAGCTTGAAAAAGATGA
1683904 AGGAGGTAATGTTATCAACACTAAACTTTATAGGTCTATGATTGGCTCATTGTTATATCTCACTG
66 AGGAGGTAATGTTATCAACACTAAACTTTATAGGTCTATGATTGGCTCATTGTTATATCTCACTG
1683969 CAAATGGATCAAGTCAAACCATGTGAAACTCCGATGAGTACTTCAACGAAGCTTGAAAAAGATGA
1 CAAATGGATCAAGTCAAACCATGTGAAACTCCGATGAGTACTTCAACGAAGCTTGAAAAAGATGA
*
1684034 AGGAGGTAATGTTATCGACACTAAACTTTATAGGTCTATGATTGGCTCATTGTTATATCTCACTG
66 AGGAGGTAATGTTATCAACACTAAACTTTATAGGTCTATGATTGGCTCATTGTTATATCTCACTG
1684099 C
1 C
1684100 TAGTAGACCG
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 130 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (130 bp):
CAAATGGATCAAGTCAAACCATGTGAAACTCCGATGAGTACTTCAACGAAGCTTGAAAAAGATGA
AGGAGGTAATGTTATCAACACTAAACTTTATAGGTCTATGATTGGCTCATTGTTATATCTCACTG
Found at i:1685129 original size:13 final size:13
Alignment explanation
Indices: 1685111--1685149 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1685101 ACATTTTTCT
1685111 TTGTATCGATACA
1 TTGTATCGATACA
1685124 TTGTATCGATACA
1 TTGTATCGATACA
* *
1685137 CTGCATCGATACA
1 TTGTATCGATACA
1685150 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1685313 original size:20 final size:20
Alignment explanation
Indices: 1685270--1685315 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1685260 AAATCTTTTG
1685270 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1685291 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1685311 CAAAA
1 CAAAA
1685316 CTAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1687585 original size:20 final size:21
Alignment explanation
Indices: 1687562--1687616 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
1687552 ATAATTCAAA
* *
1687562 GTATCGATACATGTTACA-AT
1 GTATCGATACATGTAAAATAT
**
1687582 GTATCGATACATCAAAAATAT
1 GTATCGATACATGTAAAATAT
1687603 GTATCGATACATGT
1 GTATCGATACATGT
1687617 CATTGGGATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (21 bp):
GTATCGATACATGTAAAATAT
Found at i:1687683 original size:13 final size:13
Alignment explanation
Indices: 1687665--1687690 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1687655 ACACCAAAGT
1687665 ATGTATCGATACA
1 ATGTATCGATACA
1687678 ATGTATCGATACA
1 ATGTATCGATACA
1687691 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1687688 original size:33 final size:33
Alignment explanation
Indices: 1687646--1687710 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1687636 TAGCCAAACT
* *
1687646 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
1687679 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1687711 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1688600 original size:52 final size:52
Alignment explanation
Indices: 1688518--1688643 Score: 198
Period size: 52 Copynumber: 2.4 Consensus size: 52
1688508 ATCGATACAT
* * * *
1688518 TGTATCGATACACGCAGTCAAATTTTCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATGAAA
* *
1688570 TGTATTGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACCATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATGAAA
1688622 TGTATCGATACATGCAGGCAAA
1 TGTATCGATACATGCAGGCAAA
1688644 ATTTCATATT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATGAAA
Found at i:1692112 original size:51 final size:50
Alignment explanation
Indices: 1692037--1692215 Score: 191
Period size: 51 Copynumber: 3.5 Consensus size: 50
1692027 AAATTTCTAG
* * * *
1692037 ATTTTTCAT-CTCGGAGATACTCCAA-TCCCGGTTTCATTTCCAAAACATCA
1 ATTTTTCATAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACA-CA
* * *
1692087 ATTTTTCTTAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACCC
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACA-CA
* * * *
1692138 ATTTTCCATAATCGGGGATACTTCAACTCTGATTTTATTTCCAAAACACTG
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC-A
* *
1692189 ACTTTTCACAATCGGGGATACTCCAAC
1 ATTTTTCATAATCGGGGATACTCCAAC
1692216 CCCATTATTT
Statistics
Matches: 108, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
50 9 0.08
51 98 0.91
52 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (50 bp):
ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACA
Found at i:1692394 original size:79 final size:79
Alignment explanation
Indices: 1692152--1692510 Score: 356
Period size: 79 Copynumber: 4.6 Consensus size: 79
1692142 TCCATAATCG
* * * * * * * * *
1692152 GGGATACTTCAACTCTGATTTTATTTCCAAAACACTGACTTTTCACAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATTAATTTTTCATAATCGAGGATACTCCAACC
*
1692217 CCATTATTTTC-GA
66 CCATTATTTTCAAA
* * * * *
1692230 GGCGACACTCCAACCCCGATTTTATTTCTAAAGCATCAA-TTTT--T-ATCGGGGATATTCCAAC
1 GG-GATACTCCAACCCCGATTTTATTTCTAAAACATTAATTTTTCATAATCGAGGATACTCCAAC
*
1692291 CCCGTTATTTTCAAA
65 CCCATTATTTTCAAA
*
1692306 GGGATACTCCAACCCC-AGTTTTATTTCTAAAACATTAATTTTTCATAGTCGAGGATACTCCAAC
1 GGGATACTCCAACCCCGA-TTTTATTTCTAAAACATTAATTTTTCATAATCGAGGATACTCCAAC
* * * *
1692370 CCCGTTATTTCCGAG
65 CCCATTATTTTCAAA
* * ** *
1692385 GGGATACTCCAATCCCGATTTTATTT-TGAAATCATCGATTTTTCACAATCGAGGATACTCCAAC
1 GGGATACTCCAACCCCGATTTTATTTCT-AAAACATTAATTTTTCATAATCGAGGATACTCCAAC
1692449 CCCATTATTTTCAAA
65 CCCATTATTTTCAAA
* * *
1692464 GGGATACTCCAACCCCG-TTATTATCTCCAAAATATTAAATTTTTCAT
1 GGGATACTCCAACCCCGATT-TTATTTCTAAAACATT-AATTTTTCAT
1692511 CAGGAAATGT
Statistics
Matches: 229, Mismatches: 40, Indels: 22
0.79 0.14 0.08
Matches are distributed among these distances:
74 1 0.00
75 58 0.25
76 7 0.03
78 10 0.04
79 144 0.63
80 9 0.04
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (79 bp):
GGGATACTCCAACCCCGATTTTATTTCTAAAACATTAATTTTTCATAATCGAGGATACTCCAACC
CCATTATTTTCAAA
Found at i:1698783 original size:55 final size:55
Alignment explanation
Indices: 1698651--1699279 Score: 604
Period size: 55 Copynumber: 11.0 Consensus size: 55
1698641 TTTTCTTTTT
* * *
1698651 AAAGCCTACACAAGTTAGTGGCACCTTT-AGTCCTCAAAGAGCAGGATGCCTTTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC-TTTC
*
1698706 TTTTTAAAGCCCACACAGGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
1 -----AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
* *
1698766 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTTAAAGAGCAAGACGCCTTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
* * * *
1698821 AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAACAAGACGTCTTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
*
1698876 AAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTC
1 AAAGCCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAGAGCAGGACGCC-TTTC
** *
1698932 TTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCAGGACGCCTTTC
1 -----AAAGCCCACACAAGTTGGTGGCA-CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
** * * * * *
1698993 AAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGTAGGATGACTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
* * * *
1699048 AAAG-CCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACACTTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTC
* **
1699103 AAAGCCTACACAAGTTGGTGGCACCTTT-AGTTTTCAAAGATG-AGGACGCCTTTTCCTTTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGA-GCAGGACG------CC-TTTC
** * * * *
1699164 AAAGCCCACATGAGTTGGTGGCACCTTCCAATCCTCAAAGAGAAGGATGCCTTTTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC--TTTC
** *
1699221 ATTTTAAAGCCCACACAAGTTACTGGCACCTTT-AGTCCTCAAAGAGCGGGACGCACTTT
1 -----AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC-CTTT
1699280 ATTCCCCTTT
Statistics
Matches: 486, Mismatches: 54, Indels: 58
0.81 0.09 0.10
Matches are distributed among these distances:
54 40 0.08
55 203 0.42
56 50 0.10
57 5 0.01
60 33 0.07
61 93 0.19
62 60 0.12
63 2 0.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (55 bp):
AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
Found at i:1699119 original size:227 final size:224
Alignment explanation
Indices: 1698645--1699267 Score: 786
Period size: 227 Copynumber: 2.7 Consensus size: 224
1698635 CGCCTTTTTT
* *
1698645 CTTTTTAAAGCCTACACAAGTTAGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTT
1 CTTTTTAAAGCCTACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT
*
1698710 TAAAGCCCACACAGGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
66 TAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
* *
1698775 ACAAGTTGGTGGCACCTTTCAGTCCTTAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGT
131 ACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACGACTTTCAAAGCCCACACAAGTTGGT
1698840 GGCACCTTTTAGTCCTCAAAGAACAAGAC
196 GGCACCTTTTAGTCCTCAAAGAACAAGAC
* * * *
1698869 GTCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTCT
1 CT-TTTTAAAGCCTACACAAGTTGGTGGCACCTT--TAGTCCTCAAAGAGCAGGACGCCTTTTCT
** *
1698933 TTTTAAAGCCCACACAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGC
63 TTTTAAAGCCCACACAAGTTGGTGGCA-CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGC
** * * * * *
1698998 CCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGTAGGATGACTTTTAAAG-CCACACAAGT
127 CCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACGACTTTCAAAGCCCACACAAGT
* * *
1699062 TGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGAC
192 TGGTGGCACCTTT-TAGTCCTCAAAGAACAAGAC
**
1699096 ACTTTTTAAAGCCTACACAAGTTGGTGGCACCTTTAGTTTTCAAAGATG-AGGACGCCTTTTCCT
1 -CTTTTTAAAGCCTACACAAGTTGGTGGCACCTTTAGTCCTCAAAGA-GCAGGACGCCTTTT-CT
* ** * * * *
1699160 TTTCAAAGCCCACATGAGTTGGTGGCACCTTCCAATCCTCAAAGAGAAGGATGCCTTTTTCATTT
63 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC--TTTC----
**
1699225 TAAAGCCCACACAAGTTACTGGCACCTTT-AGTCCTCAAAGAGC
122 -AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGC
1699268 GGGACGCACT
Statistics
Matches: 340, Mismatches: 43, Indels: 24
0.84 0.11 0.06
Matches are distributed among these distances:
224 4 0.01
225 24 0.07
226 118 0.35
227 149 0.44
228 8 0.02
232 13 0.04
233 24 0.07
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (224 bp):
CTTTTTAAAGCCTACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT
TAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
ACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACGACTTTCAAAGCCCACACAAGTTGGT
GGCACCTTTTAGTCCTCAAAGAACAAGAC
Found at i:1699181 original size:61 final size:61
Alignment explanation
Indices: 1699099--1699284 Score: 196
Period size: 62 Copynumber: 3.0 Consensus size: 61
1699089 GCAGGACACT
* **
1699099 TTTTAAAGCCTACACAAGTTGGTGGCACCTTTAGTTTTCAAAGATG-AGGACGCC-TTTTCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGA-GAAGGACGCCTTTTTCC
** * * * *
1699159 TTTTCAAAGCCCACATGAGTTGGTGGCACCTTCCAATCCTCAAAGAGAAGGATGCCTTTTTCA
1 TTTT-AAAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTCAAAGAGAAGGACGCCTTTTTCC
** **
1699222 TTTTAAAGCCCACACAAGTTACTGGCACCTTTAGTCCTCAAAGAGCGGGACGCACTTTATTCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGAAGGACGC-CTTT-TTCC
1699285 CCTTTGTCCT
Statistics
Matches: 101, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
60 4 0.04
61 42 0.42
62 43 0.43
63 12 0.12
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (61 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGAAGGACGCCTTTTTCC
Found at i:1699419 original size:61 final size:61
Alignment explanation
Indices: 1699323--1699638 Score: 363
Period size: 61 Copynumber: 5.2 Consensus size: 61
1699313 TCATTTCCTT
* *
1699323 CTTTTCCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCAGGATAC
1 CTTTT-CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGATAC
* **
1699386 CTTTTCCTTTCAAAG-CCACACAAGTTCGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGC
1 CTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATAC
* * * * *
1699446 CTTTTCCTTTCAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCCTCAAAAAGCAAGAT-G
1 CTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATAC
* ** * * *
1699506 C-TTTCTCTTTGCAAAGCCCACACAAGATGGTGGCACCTTCCAGTCCTCAAAGAGTAGGATGC
1 CTTTTC-CTTT-CAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATAC
* * * *
1699568 C-TTTCTTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGTAGGACAC
1 CTTTTC-CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGATAC
1699629 CTTTTCCTTT
1 CTTTTCCTTT
1699639 TCTCCTTTGT
Statistics
Matches: 218, Mismatches: 29, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
59 4 0.02
60 44 0.20
61 141 0.65
62 24 0.11
63 5 0.02
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (61 bp):
CTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATAC
Found at i:1699539 original size:354 final size:343
Alignment explanation
Indices: 1698987--1699691 Score: 854
Period size: 354 Copynumber: 2.0 Consensus size: 343
1698977 GAGCAGGACG
* *
1698987 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGTAGGATGACTTTTAAAG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGACTTTTAAAG
* *
1699052 CCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACACTTTTTAAAGCCTACACAAG
66 CCACACAAGTTCGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACACTTTTTAAAGCCCACACAAG
** * * * ** *
1699117 TTGGTGGCACCTTTAGTTTTCAAAGATGAGGACGCCTTTTCCTTTTCAAAGCCCACATGAGTTGG
131 TTGGTGGCACCTTTAGTCCTCAAAGAAGAAGACGCCTTTTCCTTTGCAAAGCCCACACAAGATGG
*
1699182 TGGCACCTTCCAATCCTCAAAGAGAAGGATGCCTTT-TTCATTTTAAAGCCCACACAAGTTACTG
196 TGGCACCTTCCAATCCTCAAAGAGAAGGATGCCTTTCTT--TTTCAAAGCCCACACAAGTTACTG
* * *
1699246 GCAC-CTTTAGTCCTCAAAGAGCGGGACGCAC-TT-TATTCCCCTTTGTCCTCAAAGAGTAGGAC
259 GCACTCTTTAGTCCTCAAAGAGCAGGACAC-CTTTCTATTCCCCTTTGTCCTCAAAGAGCAGGAC
*
1699308 ACACTTCATTTCCTTCTTTTC
323 ACACTTCATTCCCTTCTTTTC
1699329 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCAGGAT-ACCTTTTCC
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTTTAGTCCTCAAAGAGCAGGATGA-C---T--
*
1699393 TTTCAAAGCCACACAAGTTCGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTC
59 TTT-AAAGCCACACAAGTTCGTGGCACTTTTCTAGTCCTCAAAGAGCAGGAC-AC--TT--TTT-
* * *
1699457 AAAGCCCACATAAGTTGGTGGCA-TTTTCCAGTCCTCAAA-AAGCAAGATG-C-TTTCTCTTTGC
117 AAAGCCCACACAAGTTGGTGGCACCTTT--AGTCCTCAAAGAAG-AAGACGCCTTTTC-CTTTGC
* *
1699518 AAAGCCCACACAAGATGGTGGCACCTTCCAGTCCTCAAAGAGTAGGATGCCTTTCTTTTTCAAAG
178 AAAGCCCACACAAGATGGTGGCACCTTCCAATCCTCAAAGAGAAGGATGCCTTTCTTTTTCAAAG
* ** * * * *
1699583 CCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGTAGGACACCTTTTCCTTTTCTCCTTTG
243 CCCACACAAGTTACTGGCACTCTTTAGTCCTCAAAGAGCAGGACACC-TTT-CTATTCCCCTTTG
*
1699648 TCCTCAAAGAGCAGGACGCACTTCATTCCCTTCTTTTC
306 TCCTCAAAGAGCAGGACACACTTCATTCCCTTCTTTTC
1699686 CCTTTT
1 CCTTTT
1699692 GTCCTCAAAG
Statistics
Matches: 308, Mismatches: 31, Indels: 33
0.83 0.08 0.09
Matches are distributed among these distances:
342 29 0.09
343 25 0.08
346 1 0.00
348 28 0.09
349 22 0.07
351 2 0.01
353 35 0.11
354 99 0.32
355 16 0.05
357 51 0.17
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (343 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGACTTTTAAAG
CCACACAAGTTCGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACACTTTTTAAAGCCCACACAAG
TTGGTGGCACCTTTAGTCCTCAAAGAAGAAGACGCCTTTTCCTTTGCAAAGCCCACACAAGATGG
TGGCACCTTCCAATCCTCAAAGAGAAGGATGCCTTTCTTTTTCAAAGCCCACACAAGTTACTGGC
ACTCTTTAGTCCTCAAAGAGCAGGACACCTTTCTATTCCCCTTTGTCCTCAAAGAGCAGGACACA
CTTCATTCCCTTCTTTTC
Found at i:1699652 original size:38 final size:39
Alignment explanation
Indices: 1699609--1699751 Score: 112
Period size: 42 Copynumber: 3.5 Consensus size: 39
1699599 GCACTTTTTA
*
1699609 GTCCTCAAAGAGTAGGACAC-CTTTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAGGACACTCTTTTCCTTTTCTCCTTT
* * *
1699647 GTCCTCAAAGAGCAGGACGCACTTCATTCCCTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAGGA--CAC-TCTTTTCCTT-TTCT-CC-TTT
*
1699692 GTCCTCAAAGAGCAGGATGCACTTTATTTTCCTCTTTCT--TTT
1 GTCCTCAAAGAGCAGGA--CAC--TCTTTTCCT-TTTCTCCTTT
*
1699734 GTCCTCAAAGAGTAGGAC
1 GTCCTCAAAGAGCAGGAC
1699752 GCATTTCATT
Statistics
Matches: 86, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
38 16 0.19
40 4 0.05
42 26 0.30
43 3 0.03
44 2 0.02
45 24 0.28
46 10 0.12
47 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.36
Consensus pattern (39 bp):
GTCCTCAAAGAGCAGGACACTCTTTTCCTTTTCTCCTTT
Found at i:1699699 original size:45 final size:44
Alignment explanation
Indices: 1699635--1699761 Score: 154
Period size: 45 Copynumber: 2.9 Consensus size: 44
1699625 ACACCTTTTC
1699635 CTTTTCTCC-TTTGTCCTCAAAGAGCAGGACGCACTTCATTCCCTT
1 CTTTTC-CCTTTTGTCCTCAAAGAGCAGGACGCACTTCATTCCC-T
* * *
1699680 CTTTTCCCTTTTGTCCTCAAAGAGCAGGATGCACTTTATTTTCCT
1 CTTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTCA-TTCCCT
* *
1699725 C-TTT--CTTTTGTCCTCAAAGAGTAGGACGCATTTCATT
1 CTTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTCATT
1699762 TTTTTTTTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
41 2 0.03
42 27 0.37
44 5 0.07
45 35 0.48
46 4 0.05
ACGTcount: A:0.19, C:0.28, G:0.14, T:0.39
Consensus pattern (44 bp):
CTTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTCATTCCCT
Found at i:1699763 original size:42 final size:42
Alignment explanation
Indices: 1699630--1699763 Score: 148
Period size: 42 Copynumber: 3.1 Consensus size: 42
1699620 GTAGGACACC
*
1699630 TTTTCCT-TTTCTCCTTTGTCCTCAAAGAGCAGGACGCACTTCA
1 TTTTCCTCTTTCT--TTTGTCCTCAAAGAGCAGGACGCATTTCA
* *
1699673 -TTCCCTTCTTTTCCCTTTTGTCCTCAAAGAGCAGGATGCACTTT-A
1 TTTTCC-TC-TTT--CTTTTGTCCTCAAAGAGCAGGACGCA-TTTCA
*
1699718 TTTTCCTCTTTCTTTTGTCCTCAAAGAGTAGGACGCATTTCA
1 TTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGGACGCATTTCA
1699760 TTTT
1 TTTT
1699764 TTTTTTTTCC
Statistics
Matches: 77, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
41 3 0.04
42 33 0.43
43 1 0.01
44 3 0.04
45 29 0.38
46 6 0.08
47 2 0.03
ACGTcount: A:0.18, C:0.27, G:0.13, T:0.42
Consensus pattern (42 bp):
TTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGGACGCATTTCA
Found at i:1701042 original size:51 final size:51
Alignment explanation
Indices: 1700952--1701130 Score: 218
Period size: 51 Copynumber: 3.5 Consensus size: 51
1700942 AAATTTCTAG
* * * * *
1700952 ATTTTTCAT-CTCGGGGATACTCTAA-TCCCGGTTTCATTTCCAAAACATCA
1 ATTTTTCATAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACCA
* * * *
1701002 ATTTTTCTTAATCGGGGATCCTCCAACTCCGATTTTATTTCTAAAACACCC
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCA
* *
1701053 ATTTTCCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCG
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCA
* *
1701104 ACTTTTCACAATCGGGGATACTCCAAC
1 ATTTTTCATAATCGGGGATACTCCAAC
1701131 CCCGTTATTT
Statistics
Matches: 110, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
50 8 0.07
51 101 0.92
52 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (51 bp):
ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCA
Found at i:1701160 original size:28 final size:28
Alignment explanation
Indices: 1701118--1701195 Score: 131
Period size: 28 Copynumber: 2.8 Consensus size: 28
1701108 TTCACAATCG
*
1701118 GGGATACTCCAACCCCGTTATTTTC-GA
1 GGGATACTCCAACCCCGTTATTTTCAAA
1701145 GGCGATACTCCAACCCCGTTATTTTCAAA
1 GG-GATACTCCAACCCCGTTATTTTCAAA
1701174 GGGATACTCCAACCCCGTTATT
1 GGGATACTCCAACCCCGTTATT
1701196 ATCTCCAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
27 2 0.04
28 43 0.90
29 3 0.06
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTTCAAA
Found at i:1703162 original size:32 final size:32
Alignment explanation
Indices: 1703116--1703210 Score: 113
Period size: 32 Copynumber: 3.0 Consensus size: 32
1703106 CTAAGTGATT
*
1703116 GAGAGGTTCTATCTTAGCCTTGAAAGATAGTG
1 GAGATGTTCTATCTTAGCCTTGAAAGATAGTG
* *
1703148 TAGATGTTCTATCTTAGCCCGTGAAAAGATAG-G
1 GAGATGTTCTATCTTAG-CCTTG-AAAGATAGTG
* *
1703181 GAGGT-TTCTATCTTAGCTTTGAAAGATAGT
1 GAGATGTTCTATCTTAGCCTTGAAAGATAGT
1703211 ATTGTAAGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
30 8 0.15
31 3 0.06
32 26 0.49
33 8 0.15
34 8 0.15
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (32 bp):
GAGATGTTCTATCTTAGCCTTGAAAGATAGTG
Found at i:1705803 original size:13 final size:13
Alignment explanation
Indices: 1705785--1705810 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1705775 TACACCAAGT
1705785 ATGTATCGATACA
1 ATGTATCGATACA
1705798 ATGTATCGATACA
1 ATGTATCGATACA
1705811 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1705808 original size:32 final size:33
Alignment explanation
Indices: 1705767--1705830 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1705757 TAGCCAAACT
* **
1705767 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1705799 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1705831 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1715295 original size:169 final size:169
Alignment explanation
Indices: 1715014--1715351 Score: 561
Period size: 169 Copynumber: 2.0 Consensus size: 169
1715004 TCCAATGCCA
1715014 TAAGACACATCTCTCCTTAATTCAGCATTTGTTGAGAAACTTTGATCATCAAGTTTTCTATTTGA
1 TAAGACACATCTCTCCTTAATTCAGCATTTGTTGAGAAACTTTGATCATCAAGTTTTCTATTTGA
**
1715079 GCTATAAAGATTGTTTTTCTCGAGTGTTAATCCGATAAAGAAGATTAGGCTCTGATACCAATTGT
66 GCTATAAAGATCATTTTTCTCGAGTGTTAATCCGATAAAGAAGATTAGGCTCTGATACCAATTGT
1715144 AAGCTCTAGGATTGGATGAACCAAAAGGGGGGTGAATTG
131 AAGCTCTAGGATTGGATGAACCAAAAGGGGGGTGAATTG
* * *
1715183 TAAGACACATTTCTCCTTTATTCAGCATTTGTTGAGAAGCTTTGATCATCAAGTTTTCTATTTGA
1 TAAGACACATCTCTCCTTAATTCAGCATTTGTTGAGAAACTTTGATCATCAAGTTTTCTATTTGA
* * * * *
1715248 GCTATAAAGATCATTTCTT-TCGGGTGTTAATTCGATGAAGGAGATTAGGCTCTGATATCAATTG
66 GCTATAAAGATCATTT-TTCTCGAGTGTTAATCCGATAAAGAAGATTAGGCTCTGATACCAATTG
*
1715312 TAAGCTCTAGGATTGGATGAACCAAGAGGGGGGTGAATTG
130 TAAGCTCTAGGATTGGATGAACCAAAAGGGGGGTGAATTG
1715352 GTTCTTTTCG
Statistics
Matches: 157, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
169 155 0.99
170 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (169 bp):
TAAGACACATCTCTCCTTAATTCAGCATTTGTTGAGAAACTTTGATCATCAAGTTTTCTATTTGA
GCTATAAAGATCATTTTTCTCGAGTGTTAATCCGATAAAGAAGATTAGGCTCTGATACCAATTGT
AAGCTCTAGGATTGGATGAACCAAAAGGGGGGTGAATTG
Found at i:1716071 original size:20 final size:20
Alignment explanation
Indices: 1716046--1716099 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1716036 GATGGGCACA
* *
1716046 ATGTATCGATACATTTTACT-
1 ATGTATCGATACAATGT-CTC
1716066 ATGTATCGATACAATGTCTC
1 ATGTATCGATACAATGTCTC
1716086 ATGTATCGATACAA
1 ATGTATCGATACAA
1716100 ACAGTGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATGTCTC
Found at i:1716151 original size:20 final size:20
Alignment explanation
Indices: 1716126--1716163 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1716116 TACTGTCAGT
*
1716126 TTCATGTATCGATGCAATTC
1 TTCATGTATCGATACAATTC
1716146 TTCATGTATCGATACAAT
1 TTCATGTATCGATACAAT
1716164 GTATTGATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (20 bp):
TTCATGTATCGATACAATTC
Found at i:1718012 original size:22 final size:21
Alignment explanation
Indices: 1717987--1718042 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
1717977 ACAGTGATGT
1717987 ATGAATAGTGATGTATCGATAC
1 ATGAA-AGTGATGTATCGATAC
*
1718009 ATGAAAGTAATGTATCGATAC
1 ATGAAAGTGATGTATCGATAC
1718030 ATGAACAGTGATG
1 ATGAA-AGTGATG
1718043 AATAGTGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (21 bp):
ATGAAAGTGATGTATCGATAC
Found at i:1718049 original size:10 final size:10
Alignment explanation
Indices: 1718030--1718060 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1718020 GTATCGATAC
1718030 ATGAACAGTG
1 ATGAACAGTG
*
1718040 ATGAATAGTG
1 ATGAACAGTG
1718050 ATGAACAGTG
1 ATGAACAGTG
1718060 A
1 A
1718061 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1718148 original size:53 final size:53
Alignment explanation
Indices: 1718084--1718220 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
1718074 CTACTACCAA
1718084 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
1718137 TGTATCGATACATATTGTGTGTATCGATACAAATTTTGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1718190 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
1718221 TATGCAATCT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:1718253 original size:20 final size:20
Alignment explanation
Indices: 1718190--1718260 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1718180 GCCAATGTCC
**
1718190 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
1718210 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
1718230 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1718250 TGTATCGATAC
1 TGTATCGATAC
1718261 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1718732 original size:16 final size:17
Alignment explanation
Indices: 1718713--1718745 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1718703 AAAAGAATTC
1718713 GAGTT-AAAAAAAATAT
1 GAGTTGAAAAAAAATAT
1718729 GAGTTGAAAAAAAATAT
1 GAGTTGAAAAAAAATAT
1718746 AATAAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (17 bp):
GAGTTGAAAAAAAATAT
Found at i:1719026 original size:15 final size:15
Alignment explanation
Indices: 1719006--1719036 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1718996 GTTGGTTTTG
1719006 GGTTGGATCATTTCA
1 GGTTGGATCATTTCA
*
1719021 GGTTGGATTATTTCA
1 GGTTGGATCATTTCA
1719036 G
1 G
1719037 ATTTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (15 bp):
GGTTGGATCATTTCA
Found at i:1719095 original size:16 final size:16
Alignment explanation
Indices: 1719076--1719139 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 16
1719066 TGATCGTTTA
* *
1719076 GAGTTCAGGTTATTTC
1 GAGTTCGGGTCATTTC
*
1719092 GAGTTTGGGTCATTTC
1 GAGTTCGGGTCATTTC
* * *
1719108 AAGTTCGGATTATTTC
1 GAGTTCGGGTCATTTC
*
1719124 GGGTTCGGGTCATTTC
1 GAGTTCGGGTCATTTC
1719140 AGATTCGAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.16, C:0.14, G:0.28, T:0.42
Consensus pattern (16 bp):
GAGTTCGGGTCATTTC
Found at i:1719113 original size:32 final size:32
Alignment explanation
Indices: 1719077--1719140 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1719067 GATCGTTTAG
*
1719077 AGTTCAGG-TTATTTCGAGTTTGGGTCATTTCA
1 AGTTC-GGATTATTTCGAGTTCGGGTCATTTCA
*
1719109 AGTTCGGATTATTTCGGGTTCGGGTCATTTCA
1 AGTTCGGATTATTTCGAGTTCGGGTCATTTCA
1719141 GATTCGAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 2 0.07
32 27 0.93
ACGTcount: A:0.17, C:0.14, G:0.27, T:0.42
Consensus pattern (32 bp):
AGTTCGGATTATTTCGAGTTCGGGTCATTTCA
Done.