Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold332
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: 2744988
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 17
Found at i:1777311 original size:37 final size:39
Alignment explanation
Indices: 1777263--1777337 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 39
1777253 CTATTTTTTG
*
1777263 TTGCTGTTTACTAG-TGTTTGCT-TGCTG-TTTTTGCTAT
1 TTGCTGTTTACT-GTTGTTTACTCTGCTGATTTTTGCTAT
*
1777300 TTGCTTTTTACTGTTGTTTACTGCTGCTGATTTTTGCT
1 TTGCTGTTTACTGTTGTTTACT-CTGCTGATTTTTGCT
1777338 GTTGTTGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 1 0.03
37 18 0.56
39 5 0.16
40 8 0.25
ACGTcount: A:0.08, C:0.15, G:0.20, T:0.57
Consensus pattern (39 bp):
TTGCTGTTTACTGTTGTTTACTCTGCTGATTTTTGCTAT
Found at i:1778266 original size:20 final size:20
Alignment explanation
Indices: 1778226--1778279 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
1778216 TTTATACAAT
*
1778226 TGTATCGATACAATTAGTGAA
1 TGTATCGATAC-ATAAGTGAA
1778247 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
1778267 TGTATCGATACAT
1 TGTATCGATACAT
1778280 GTCTCAAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:1778353 original size:20 final size:20
Alignment explanation
Indices: 1778328--1778379 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1778318 GTCAAAAAAT
*
1778328 TGTATCGATACATGAATAAA
1 TGTATCGATACATGAACAAA
***
1778348 TGTATCGATACATTTCCAAA
1 TGTATCGATACATGAACAAA
1778368 TGTATCGATACA
1 TGTATCGATACA
1778380 ATTTGCTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATGAACAAA
Found at i:1780008 original size:13 final size:13
Alignment explanation
Indices: 1779990--1780014 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1779980 AATTTTATCA
1779990 TGTATCGATACAT
1 TGTATCGATACAT
1780003 TGTATCGATACA
1 TGTATCGATACA
1780015 ATGTGTCGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1780091 original size:19 final size:20
Alignment explanation
Indices: 1780063--1780116 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
1780053 ACTACCAGTT
* *
1780063 TCATGCATCGATACAATG-A
1 TCATGTATCGATACAAAGCA
*
1780082 TCATGTATCGGTACAAAGCA
1 TCATGTATCGATACAAAGCA
* *
1780102 TAATGTATTGATACA
1 TCATGTATCGATACA
1780117 TCTGGATGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
TCATGTATCGATACAAAGCA
Found at i:1788834 original size:17 final size:18
Alignment explanation
Indices: 1788812--1788901 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 18
1788802 CTGCTAGTTT
**
1788812 CATGTATCGATATTATG-
1 CATGTATCGATACAATGA
1788829 CATGTATCGATACAATGA
1 CATGTATCGATACAATGA
*
1788847 TCATGTATCGATACAAAGCA
1 -CATGTATCGATACAATG-A
* *
1788867 TAATGTATCGATACATCTGGA
1 -CATGTATCGATACA-AT-GA
*
1788888 TATGTATCGATACA
1 CATGTATCGATACA
1788902 TACAAAGGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
17 15 0.25
19 16 0.26
20 28 0.46
21 1 0.02
22 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (18 bp):
CATGTATCGATACAATGA
Found at i:1788874 original size:20 final size:19
Alignment explanation
Indices: 1788830--1788881 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
1788820 GATATTATGC
* *
1788830 ATGTATCGATACAATGATC
1 ATGTATCGATACAAAGATA
1788849 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAG-ATA
1788869 ATGTATCGATACA
1 ATGTATCGATACA
1788882 TCTGGATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (19 bp):
ATGTATCGATACAAAGATA
Found at i:1788902 original size:20 final size:20
Alignment explanation
Indices: 1788830--1788901 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
1788820 GATATTATGC
*
1788830 ATGTATCGATACAAT-GATC
1 ATGTATCGATACAATGGATA
* *
1788849 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAATGGATA
*
1788869 ATGTATCGATACATCTGGAT-
1 ATGTATCGATACA-ATGGATA
1788889 ATGTATCGATACA
1 ATGTATCGATACA
1788902 TACAAAGGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.31
20 28 0.62
21 3 0.07
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGGATA
Found at i:1793128 original size:50 final size:50
Alignment explanation
Indices: 1793070--1793307 Score: 350
Period size: 50 Copynumber: 4.8 Consensus size: 50
1793060 GGTAGAAAGT
* ** * *
1793070 ACCTTTGACAATAGAGAGGGGTGGCTGTAATTGTTGACGATTCTTGACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACAATTCTTCACCA
* *
1793120 ACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACAATTCTTTACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACAATTCTTCACCA
* * * *
1793170 ACCTTTGACAATAGAGGGAGCTGGCCAAAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACAATTCTTCACCA
* *
1793220 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGATAATTGTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACAATTCTTCACCA
*
1793270 ACCTTTGACAATAGAGAAAGGTGGCCATAATTGTTGAC
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGAC
1793308 TCTAAGTATA
Statistics
Matches: 170, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 170 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (50 bp):
ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACAATTCTTCACCA
Found at i:1793790 original size:22 final size:22
Alignment explanation
Indices: 1793762--1793813 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1793752 TTGGAGAGAG
1793762 GCCGAGTGAGATAACGGACGAT
1 GCCGAGTGAGATAACGGACGAT
1793784 GCCGAGTGAGATAACGGACGAT
1 GCCGAGTGAGATAACGGACGAT
*
1793806 GCCAAGTG
1 GCCGAGTG
1793814 GAACGAGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.19, G:0.37, T:0.13
Consensus pattern (22 bp):
GCCGAGTGAGATAACGGACGAT
Found at i:1797748 original size:50 final size:50
Alignment explanation
Indices: 1797691--1797978 Score: 477
Period size: 50 Copynumber: 5.8 Consensus size: 50
1797681 GGTGGAAAGT
*
1797691 ACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
* *
1797741 ACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCT
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
** * *
1797791 ACCTTTGACAATAGAGAGAGGTGGCTGTAATTGTTAATGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
* *
1797841 ACCTTTGACAATAGAGGGAGCTGGCCATAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
1797891 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
* *
1797941 ACCTTTGACAATAGAGAAAGGTAGCCATAATTGTTGAC
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGAC
1797979 TCTAAGTATA
Statistics
Matches: 219, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 219 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (50 bp):
ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
Found at i:1799080 original size:20 final size:20
Alignment explanation
Indices: 1799052--1799129 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
1799042 GAAAAAAAGA
**
1799052 CAAAATGTATTGATACATTG
1 CAAAATGTATCAATACATTG
*
1799072 CAGAATGTATCAATACATT-
1 CAAAATGTATCAATACATTG
*
1799091 CATACATGTATCAATACATTG
1 CA-AAATGTATCAATACATTG
* *
1799112 AAAAATGTATCGATACAT
1 CAAAATGTATCAATACAT
1799130 CTGGGTAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.04
20 45 0.94
21 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (20 bp):
CAAAATGTATCAATACATTG
Found at i:1799159 original size:51 final size:52
Alignment explanation
Indices: 1799096--1799232 Score: 213
Period size: 52 Copynumber: 2.7 Consensus size: 52
1799086 ACATTCATAC
* *
1799096 ATGTATCAATACATTGAAAAATGTATCGATACATCTGGGT-AAAAAAATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAAAACAGA
* *
1799147 ATGTATCGATACATTGAAAAATGTATGGATACATTTGGGTAAAAAAAACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAAAACAGA
* *
1799199 ATGTATAGATACATTGAAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACAT
1799233 TCATACATGT
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
51 37 0.47
52 41 0.53
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (52 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAAAACAGA
Found at i:1799221 original size:20 final size:20
Alignment explanation
Indices: 1799196--1799233 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1799186 TAAAAAAAAC
1799196 AGAATGTATAGATACATTGA
1 AGAATGTATAGATACATTGA
*
1799216 AGAATGTATCGATACATT
1 AGAATGTATAGATACATT
1799234 CATACATGTA
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:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATGTATAGATACATTGA
Found at i:1802410 original size:76 final size:75
Alignment explanation
Indices: 1802208--1802402 Score: 230
Period size: 76 Copynumber: 2.5 Consensus size: 75
1802198 TAACATTCTG
** * **
1802208 TTATCAGTTTGTTTTGGCTACTGATGGGAAATTATAGAAACCACATATTCCCCATTGTGTTCTTC
1 TTATCAGTTTGTTTTGGCTA-TG-TAAGAAATTTTAGAAACCACATATTCCCCATCATGTTCTTC
*
1802273 TTTTTCAACTTA
64 TTCTTCAACTTA
* * * *
1802285 ATATCAATATGTTTTGGCTAT-TAAGGAAAATTTTAGAAGCCACATATTCCCCATCATGTTCTTC
1 TTATCAGTTTGTTTTGGCTATGTAA-G-AAATTTTAGAAACCACATATTCCCCATCATGTTCTTC
*
1802349 TTCTTCAGCTTA
64 TTCTTCAACTTA
*
1802361 TTATCAGTTTGTTTTGGCTATTGTTAGAAATTTTAGAAACCA
1 TTATCAGTTTGTTTTGGCTA-TGTAAGAAATTTTAGAAACCA
1802403 TACATTCCAA
Statistics
Matches: 98, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
74 1 0.01
75 1 0.01
76 75 0.77
77 19 0.19
78 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (75 bp):
TTATCAGTTTGTTTTGGCTATGTAAGAAATTTTAGAAACCACATATTCCCCATCATGTTCTTCTT
CTTCAACTTA
Found at i:1803150 original size:40 final size:39
Alignment explanation
Indices: 1803106--1803217 Score: 109
Period size: 39 Copynumber: 2.8 Consensus size: 39
1803096 TTCATCCTGA
* *
1803106 TCAACCTTTTTCATGTATTGACTTGTAGGTTTTATCCCAG
1 TCAACCTTTTTCAT-TGTTAACTTGTAGGTTTTATCCCAG
* * * *
1803146 TCAA-CTTTATCATTCGTTAACTTATCGGTTTTATCCTAG
1 TCAACCTTTTTCATT-GTTAACTTGTAGGTTTTATCCCAG
* * *
1803185 CCAACCCTTTTCATTTGTTCACTTGTAGGTTTT
1 TCAACCTTTTTCA-TTGTTAACTTGTAGGTTTT
1803218 GTCCTAGTTA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
38 1 0.02
39 30 0.53
40 24 0.42
41 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.46
Consensus pattern (39 bp):
TCAACCTTTTTCATTGTTAACTTGTAGGTTTTATCCCAG
Found at i:1803223 original size:40 final size:40
Alignment explanation
Indices: 1803107--1803224 Score: 114
Period size: 40 Copynumber: 3.0 Consensus size: 40
1803097 TCATCCTGAT
* * * * * *
1803107 CAACCTTTTTCATGTATTGACTTGTAGGTTTTATCCCAGT
1 CAACCCTTTTCATTTGTTAACTTGTAGGTTTTATCCTAGC
* * *
1803147 CAA--CTTTATCATTCGTTAACTTATCGGTTTTATCCTAGC
1 CAACCCTTT-TCATTTGTTAACTTGTAGGTTTTATCCTAGC
* *
1803186 CAACCCTTTTCATTTGTTCACTTGTAGGTTTTGTCCTAG
1 CAACCCTTTTCATTTGTTAACTTGTAGGTTTTATCCTAG
1803225 TTAACCATTC
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
38 3 0.05
39 26 0.43
40 28 0.46
41 4 0.07
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (40 bp):
CAACCCTTTTCATTTGTTAACTTGTAGGTTTTATCCTAGC
Found at i:1804814 original size:26 final size:26
Alignment explanation
Indices: 1804760--1804815 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1804750 AAATCAATTC
* * *
1804760 TTTAAAATTTTATTTATTTTATGAGT
1 TTTAAAATTTTATTTATTATATCAAT
1804786 TTTAAAATTTT-TTTATATATATCAAT
1 TTTAAAATTTTATTTAT-TATATCAAT
1804812 TTTA
1 TTTA
1804816 CTCCGTAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (26 bp):
TTTAAAATTTTATTTATTATATCAAT
Found at i:1805406 original size:33 final size:32
Alignment explanation
Indices: 1805345--1805412 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
1805335 CCTTAACTGT
*
1805345 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTAACGATACATACAAGATGTATCGATACA
1805377 TTGTAACGATACATGACCAA-ATGTATCGATACA
1 TTGTAACGATACAT-A-CAAGATGTATCGATACA
1805410 TTG
1 TTG
1805413 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 17 0.52
34 3 0.09
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (32 bp):
TTGTAACGATACATACAAGATGTATCGATACA
Found at i:1810604 original size:13 final size:13
Alignment explanation
Indices: 1810586--1810610 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1810576 ATAACACTTA
1810586 TGTATCGATACAT
1 TGTATCGATACAT
1810599 TGTATCGATACA
1 TGTATCGATACA
1810611 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1810607 original size:32 final size:32
Alignment explanation
Indices: 1810566--1810629 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1810556 GTAGCTTCAT
*
1810566 TTGTATCGATATAACACTTATGTATCGATACA
1 TTGTATCGATACAACACTTATGTATCGATACA
1810598 TTGTATCGATACAACACTTATGTATCGATACA
1 TTGTATCGATACAACACTTATGTATCGATACA
1810630 AATCGTTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAACACTTATGTATCGATACA
Found at i:1810628 original size:19 final size:19
Alignment explanation
Indices: 1810567--1810630 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
1810557 TAGCTTCATT
*
1810567 TGTATCGATATAACACTTA
1 TGTATCGATACAACACTTA
1810586 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1810599 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1810618 TGTATCGATACAA
1 TGTATCGATACAA
1810631 ATCGTTGACA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
16 6 0.15
18 1 0.03
19 22 0.56
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1810815 original size:28 final size:28
Alignment explanation
Indices: 1810784--1811382 Score: 488
Period size: 28 Copynumber: 20.5 Consensus size: 28
1810774 GGTTGCATCA
*
1810784 ACTTGTGTGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
*
1810812 ACTTATGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1810840 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
*
1810868 ACTTATGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1810896 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* *
1810924 ACTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
1810954 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
*
1810982 ACTTATGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* *
1811010 ACATGTGGGCTTTTGAAGGTTGCCACTA
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* *
1811038 ACTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
* * *
1811068 ACTTGTGGGCTTTTGAAAAGGGTGCCAATA
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
* * *
1811098 ACTTGTGGGCTTAATAGGAAAAAGAG-TGCTACGG
1 ACTTGTGGGCTT--T-TG---AAG-GTTGCCACTG
* * ** * *
1811132 AGTTGTGCGCTTACAAAAGAAAATGAG-TGACACGG
1 ACTTGTGGGCTT----TTG--AA-G-GTTGCCACTG
* * * ** *
1811167 AGTTGTGGACTTTGGAAAATATGCCATTG
1 ACTTGTGGGCTTTTGAAGGT-TGCCACTG
** *
1811196 ACTTGTGGGCTTCAGGAAAGGGTGCCACTG
1 ACTTGTGGGCTT-TTG-AAGGTTGCCACTG
**
1811226 GTTTGTGGGC-TTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* * *
1811253 ACTTGTGGAC-TTTGAAAAAGATGCCACTG
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
* *
1811282 ACTTGTGGGCATTTGAAGGTTGCCATTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* * *
1811310 ACTTGTGGGCTTTGGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
** *
1811340 ACTTGTGCACTTTAGAAAACGG-TGCCACTG
1 ACTTGTGGGCTTTTG--AA-GGTTGCCACTG
1811370 ACTTGTGGGCTTT
1 ACTTGTGGGCTTT
1811383 GGAAATAGTG
Statistics
Matches: 481, Mismatches: 68, Indels: 42
0.81 0.12 0.07
Matches are distributed among these distances:
27 23 0.05
28 223 0.46
29 38 0.08
30 144 0.30
31 5 0.01
32 1 0.00
33 1 0.00
34 23 0.05
35 21 0.04
36 2 0.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.32
Consensus pattern (28 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTG
Found at i:1810989 original size:114 final size:114
Alignment explanation
Indices: 1810784--1811084 Score: 534
Period size: 114 Copynumber: 2.7 Consensus size: 114
1810774 GGTTGCATCA
* * * *
1810784 ACTTGTGTGCTTTTGAAGGTTGCCACTGACTTATGGGCTTTTG--AAGGTTGCCACTGACTTGTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTG
1810847 GGCTTTTGAAGGTTGCCACTGACTTATGGGCTTTTGAAGGTTGCCACTG
66 GGCTTTTGAAGGTTGCCACTGACTTATGGGCTTTTGAAGGTTGCCACTG
1810896 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTG
1810961 GGCTTTTGAAGGTTGCCACTGACTTATGGGCTTTTGAAGGTTGCCACTG
66 GGCTTTTGAAGGTTGCCACTGACTTATGGGCTTTTGAAGGTTGCCACTG
* *
1811010 ACATGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTG
1811075 GGCTTTTGAA
66 GGCTTTTGAA
1811085 AAGGGTGCCA
Statistics
Matches: 181, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
112 41 0.23
114 140 0.77
ACGTcount: A:0.18, C:0.17, G:0.30, T:0.35
Consensus pattern (114 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTG
GGCTTTTGAAGGTTGCCACTGACTTATGGGCTTTTGAAGGTTGCCACTG
Found at i:1811138 original size:34 final size:35
Alignment explanation
Indices: 1811100--1811174 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
1811090 TGCCAATAAC
* *
1811100 TTGTGGGCTTA-ATAGGAAAAAGAGTG-CTACGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGAC-ACGGAG
* *
1811134 TTGTGCGCTTACAAAAGAAAATGAGTGACACGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGACACGGAG
1811169 TTGTGG
1 TTGTGG
1811175 ACTTTGGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 10 0.29
35 23 0.68
36 1 0.03
ACGTcount: A:0.32, C:0.11, G:0.33, T:0.24
Consensus pattern (35 bp):
TTGTGGGCTTACAAAAGAAAAAGAGTGACACGGAG
Found at i:1811251 original size:27 final size:27
Alignment explanation
Indices: 1811188--1811383 Score: 151
Period size: 30 Copynumber: 6.8 Consensus size: 27
1811178 TTGGAAAATA
* * *
1811188 TGCCATTGACTTGTGGGCTTCAGGAAAGGG
1 TGCCACTGACTTGTGGGCTT--TG-AAGGT
**
1811218 TGCCACTGGTTTGTGGGCTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGAAGGT
* * *
1811245 TGCCACTGACTTGTGGACTTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTG--AAGGT
1811274 TGCCACTGACTTGTGGGCATTTGAAGGT
1 TGCCACTGACTTGTGGGC-TTTGAAGGT
* *
1811302 TGCCATTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTT-G--AAGGT
* **
1811332 TGCCACTAACTTGTGCACTTTAGAAAACGG-
1 TGCCACTGACTTGTGGGCTTT-G--AA-GGT
1811362 TGCCACTGACTTGTGGGCTTTG
1 TGCCACTGACTTGTGGGCTTTG
1811384 GAAATAGTGA
Statistics
Matches: 136, Mismatches: 23, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
27 26 0.19
28 22 0.16
29 21 0.15
30 65 0.48
31 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (27 bp):
TGCCACTGACTTGTGGGCTTTGAAGGT
Found at i:1811259 original size:57 final size:57
Alignment explanation
Indices: 1811188--1811387 Score: 219
Period size: 57 Copynumber: 3.5 Consensus size: 57
1811178 TTGGAAAATA
* **
1811188 TGCCATTGACTTGTGGGCTTCAGGAAAGGGTGCCACTGGTTTGTGGGC-TTTGAAGGT
1 TGCCATTGACTTGTGGGCTT-TGGAAAGGGTGCCACTGACTTGTGGGCATTTGAAGGT
* * * * *
1811245 TGCCACTGACTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCATTTGAAGGT
1 TGCCATTGACTTGTGGGCTTTGGAAAGGGTGCCACTGACTTGTGGGCATTTGAAGGT
*
1811302 TGCCATTGACTTGTGGGCTTTGGAAAAGGGTGCCACTAACTTGT--GCACTTTAGAAAACGG-
1 TGCCATTGACTTGTGGGCTTTGG-AAAGGGTGCCACTGACTTGTGGGCA-TTT-G--AA-GGT
*
1811362 TGCCACTGACTTGTGGGCTTTGGAAA
1 TGCCATTGACTTGTGGGCTTTGGAAA
1811388 TAGTGAGGAA
Statistics
Matches: 121, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
56 24 0.20
57 50 0.41
58 18 0.15
59 3 0.02
60 24 0.20
61 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.30
Consensus pattern (57 bp):
TGCCATTGACTTGTGGGCTTTGGAAAGGGTGCCACTGACTTGTGGGCATTTGAAGGT
Found at i:1813111 original size:21 final size:21
Alignment explanation
Indices: 1813049--1813157 Score: 75
Period size: 21 Copynumber: 5.1 Consensus size: 21
1813039 TAAAGATGCC
1813049 GGTGTCAATATGCTGATTCAA
1 GGTGTCAATATGCTGATTCAA
* * *
1813070 -G-GCCAATGATATCGGACTTCAA
1 GGTGTCAAT-AT-GCTGA-TTCAA
1813092 GGTGTCAATATGCTGATTCAA
1 GGTGTCAATATGCTGATTCAA
*
1813113 GGCTAG-CGATAT--TGGACTTCAA
1 GG-T-GTCAATATGCT-GA-TTCAA
*
1813135 GGTGTCAATATACTGATTCAA
1 GGTGTCAATATGCTGATTCAA
1813156 GG
1 GG
1813158 CCAGCGATAT
Statistics
Matches: 68, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
19 5 0.07
20 5 0.07
21 25 0.37
22 23 0.34
23 5 0.07
24 5 0.07
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (21 bp):
GGTGTCAATATGCTGATTCAA
Found at i:1813168 original size:43 final size:43
Alignment explanation
Indices: 1813049--1813170 Score: 199
Period size: 43 Copynumber: 2.8 Consensus size: 43
1813039 TAAAGATGCC
** *
1813049 GGTGTCAATATGCTGATTCAAGGCCAATGATATCGGACTTCAA
1 GGTGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTTCAA
*
1813092 GGTGTCAATATGCTGATTCAAGGCTAGCGATATTGGACTTCAA
1 GGTGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTTCAA
*
1813135 GGTGTCAATATACTGATTCAAGGCCAGCGATATTGG
1 GGTGTCAATATGCTGATTCAAGGCCAGCGATATTGG
1813171 GTTTAAAAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (43 bp):
GGTGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTTCAA
Found at i:1813287 original size:29 final size:29
Alignment explanation
Indices: 1813241--1813346 Score: 128
Period size: 29 Copynumber: 3.6 Consensus size: 29
1813231 AGATGCCACG
1813241 AACTTGTGTGGACTTTTGAAAGGGTTGCATC
1 AACTTGTGT-G-CTTTTGAAAGGGTTGCATC
1813272 AACTTGTGTGCTTTTG-AA-GGTTGCCA-C
1 AACTTGTGTGCTTTTGAAAGGGTTG-CATC
** *
1813299 TGTCTTGTGGGCTTTTGAAAGGGTTGCATC
1 -AACTTGTGTGCTTTTGAAAGGGTTGCATC
1813329 AACTTGTGTGCTTTTGAA
1 AACTTGTGTGCTTTTGAA
1813347 GGTTGCCACT
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
27 6 0.09
28 17 0.27
29 25 0.39
30 7 0.11
31 9 0.14
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.39
Consensus pattern (29 bp):
AACTTGTGTGCTTTTGAAAGGGTTGCATC
Found at i:1813498 original size:30 final size:29
Alignment explanation
Indices: 1813234--1813933 Score: 515
Period size: 28 Copynumber: 23.9 Consensus size: 29
1813224 TAGAAGAAGA
1813234 TGCCAC-GAACTTGTGTGGACTTTTGAAAGGGT
1 TGCCACTG-ACTTGTG-GG-CTTTTGAAA-GGT
* *
1813266 TG-CA-TCAACTTGTGTGCTTTTG-AAGGT
1 TGCCACT-GACTTGTGGGCTTTTGAAAGGT
*
1813293 TGCCACTGTCTTGTGGGCTTTTGAAAGGGT
1 TGCCACTGACTTGTGGGCTTTTGAAA-GGT
* *
1813323 TG-CA-TCAACTTGTGTGCTTTTG-AAGGT
1 TGCCACT-GACTTGTGGGCTTTTGAAAGGT
*
1813350 TGCCACTGACTTGTGAGCTTTTG-AAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAGGT
*
1813378 TGCCACTGACTTATGGGCTTTTG-AAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAGGT
* * * *
1813406 TGGCACTTACTTATGGGATTTTG-AAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAGGT
*
1813434 TGCCACTGACTTATGGGCTTTTG-AAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAGGT
*
1813462 TGCCACTGACTTGTGGGCTTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTG-AAAGGT
*
1813492 TGCCACTAACTTGTGGGCTTTTG-AAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAGGT
*
1813520 TGCCACT-AGCTTATGGGCTTTTG-AAGGT
1 TGCCACTGA-CTTGTGGGCTTTTGAAAGGT
*
1813548 TGCCACTGACTTGTAGGCTTTTG-AAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAGGT
* * *
1813576 TGCCACTAACCTGTGGGCTTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTG-AAAGGT
* *
1813606 TGCCACTAACTTGTGGGCTTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTG-AAAGGT
* ***
1813636 TGCCACTAACTTGTGGGCATAAAAGGAAAAAGAG-
1 TGCCACTGACTTGTGGGC-T--TTTG--AAAG-GT
* * * ** *
1813670 TGCTACGGAGTTGTGGGCTTACAAAAGAAAAGGAG
1 TGCCACTGACTTGTGGGCTT----TTG-AAAGG-T
* * * **
1813705 TGCCACGGAGTTGTGGAC-TTTGAAAAAT
1 TGCCACTGACTTGTGGGCTTTTGAAAGGT
* ** *
1813733 ATGCCATTGACTTGTGGGCTTCGGAAAAGGG
1 -TGCCACTGACTTGTGGGCTTTTG-AAAGGT
** *
1813764 TGCCACTGGTTTGTAGGC-TTTG-AAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAGGT
* * *
1813791 TGCCACTGACTTGTGGAC-TTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTTG-AAAGGT
*
1813820 TGCCACTGACTTGTAGGCTTTTG-AAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAGGT
* *
1813848 TGCCACTGACTTGTGGGCTTTAGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTG-AAAGGT
* * *
1813878 TGCCACTGACTTGTGGACTTTAGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTG-AAAGGT
* *
1813908 TGCCACTAACTTGTGGGCTTTGGAAA
1 TGCCACTGACTTGTGGGCTTTTGAAA
1813934 AAGTGAGGAA
Statistics
Matches: 555, Mismatches: 79, Indels: 71
0.79 0.11 0.10
Matches are distributed among these distances:
27 33 0.06
28 236 0.43
29 67 0.12
30 157 0.28
31 13 0.02
32 2 0.00
33 3 0.01
34 25 0.05
35 19 0.03
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTTGAAAGGT
Found at i:1813542 original size:114 final size:113
Alignment explanation
Indices: 1813234--1813653 Score: 505
Period size: 114 Copynumber: 3.7 Consensus size: 113
1813224 TAGAAGAAGA
*
1813234 TGCCAC-GAACTTGTGTGGACTTTTGAAAGGGTTG-CA-TCAACTTGTGTGCTTTTGAAGGTTGC
1 TGCCACTG-ACTTGTG-GG-CTTTTGAAAGGG-TGCCACT-AACTTGTGGGCTTTTGAAGGTTGC
* * *
1813296 CACT-GTCTTGTGGGCTTTTGAAAGGGTTG-CA-TCAACTTGTGTGCTTTTGAAGGT
61 CACTAG-CTTATGGGCTTTTG-AA-GGTTGCCACT-GACTTGTGGGCTTTTGAAGGT
* * * * *
1813350 TGCCACTGACTTGTGAGCTTTTG-AAGGTTGCCACTGACTTATGGGCTTTTGAAGGTTGGCACTT
1 TGCCACTGACTTGTGGGCTTTTGAAAGGGTGCCACTAACTTGTGGGCTTTTGAAGGTTGCCAC-T
* *
1813414 A-CTTATGGGATTTTGAAGGTTGCCACTGACTTATGGGCTTTTGAAGGT
65 AGCTTATGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGT
1813462 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACT
1 TGCCACTGACTTGTGGGCTTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACT
*
1813527 AGCTTATGGGCTTTTGAAGGTTGCCACTGACTTGTAGGCTTTTGAAGGT
65 AGCTTATGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGT
* * *
1813576 TGCCACTAACCTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGCCA
1 TGCCACTGACTTGTGGGCTTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTTG--AAGGTTGCCA
* *
1813641 CTAACTTGTGGGC
63 CTAGCTTATGGGC
1813654 ATAAAAGGAA
Statistics
Matches: 268, Mismatches: 24, Indels: 24
0.85 0.08 0.08
Matches are distributed among these distances:
111 5 0.02
112 46 0.17
113 44 0.16
114 138 0.51
115 1 0.00
116 33 0.12
117 1 0.00
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.35
Consensus pattern (113 bp):
TGCCACTGACTTGTGGGCTTTTGAAAGGGTGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTA
GCTTATGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGT
Found at i:1813684 original size:34 final size:35
Alignment explanation
Indices: 1813646--1813720 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
1813636 TGCCACTAAC
* *
1813646 TTGTGGGCATA-AAAGGAAAAAGAGTGCTACGGAG
1 TTGTGGGCATACAAAAGAAAAAGAGTGCCACGGAG
* *
1813680 TTGTGGGCTTACAAAAGAAAAGGAGTGCCACGGAG
1 TTGTGGGCATACAAAAGAAAAAGAGTGCCACGGAG
1813715 TTGTGG
1 TTGTGG
1813721 ACTTTGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 10 0.28
35 26 0.72
ACGTcount: A:0.33, C:0.11, G:0.36, T:0.20
Consensus pattern (35 bp):
TTGTGGGCATACAAAAGAAAAAGAGTGCCACGGAG
Found at i:1813797 original size:27 final size:27
Alignment explanation
Indices: 1813759--1813929 Score: 139
Period size: 30 Copynumber: 6.0 Consensus size: 27
1813749 GGCTTCGGAA
* **
1813759 AAGGGTGCCACTGGTTTGTAGGCTTTG
1 AAGGTTGCCACTGACTTGTAGGCTTTG
1813786 AAGGTTGCCACTGACTTGT-GGACTTTG
1 AAGGTTGCCACTGACTTGTAGG-CTTTG
* *
1813813 AAAAAGATGCCACTGACTTGTAGGCTTTTG
1 --AAGGTTGCCACTGACTTGTAGGC-TTTG
*
1813843 AAGGTTGCCACTGACTTGTGGGCTTTAG
1 AAGGTTGCCACTGACTTGTAGGCTTT-G
*
1813871 AAAAGGGTGCCACTGACTTGT-GGACTTTAG
1 --AAGGTTGCCACTGACTTGTAGG-CTTT-G
* * *
1813901 AAAAGGGTGCCACTAACTTGTGGGCTTTG
1 --AAGGTTGCCACTGACTTGTAGGCTTTG
1813930 GAAAAAGTGA
Statistics
Matches: 124, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
26 2 0.02
27 24 0.19
28 21 0.17
29 21 0.17
30 54 0.44
31 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (27 bp):
AAGGTTGCCACTGACTTGTAGGCTTTG
Found at i:1813805 original size:57 final size:57
Alignment explanation
Indices: 1813734--1813934 Score: 253
Period size: 57 Copynumber: 3.5 Consensus size: 57
1813724 TTGAAAAATA
* * **
1813734 TGCCATTGACTTGTGGGCTTCGGAAAAGGGTGCCACTGGTTTGTAGGCTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTAGGCTTTGAAGGT
* * *
1813791 TGCCACTGACTTGTGGACTTT-GAAAAAGATGCCACTGACTTGTAGGCTTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTAGGC-TTTGAAGGT
* *
1813848 TGCCACTGACTTGTGGGCTTTAGAAAAGGGTGCCACTGACTTGT-GGACTTTAGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTAGG-CTTT-G--AAGGT
*
1813908 TGCCACTAACTTGTGGGCTTTGGAAAA
1 TGCCACTGACTTGTGGGCTTTGGAAAA
1813935 AGTGAGGAAT
Statistics
Matches: 125, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
56 22 0.18
57 52 0.42
58 22 0.18
60 29 0.23
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (57 bp):
TGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTAGGCTTTGAAGGT
Found at i:1815706 original size:22 final size:22
Alignment explanation
Indices: 1815681--1815752 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
1815671 AATATGCTGA
1815681 TTCAAGGCCAACGATATCGGAC
1 TTCAAGGCCAACGATATCGGAC
*** * *
1815703 TTCAAGG-TGTCAATATGCTGA-
1 TTCAAGGCCAACGATAT-CGGAC
* *
1815724 TTCAAGGCCAGCGATATTGGAC
1 TTCAAGGCCAACGATATCGGAC
1815746 TTCAAGG
1 TTCAAGG
1815753 TGTCAATATG
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
21 14 0.39
22 22 0.61
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (22 bp):
TTCAAGGCCAACGATATCGGAC
Found at i:1815727 original size:21 final size:21
Alignment explanation
Indices: 1815665--1815773 Score: 73
Period size: 21 Copynumber: 5.1 Consensus size: 21
1815655 TAAAGATGCC
1815665 GGTGTCAATATGCTGATTCAA
1 GGTGTCAATATGCTGATTCAA
*** * *
1815686 GGCCAACGATAT-CGGACTTCAA
1 GG-TGTCAATATGCTGA-TTCAA
1815708 GGTGTCAATATGCTGATTCAA
1 GGTGTCAATATGCTGATTCAA
* *
1815729 GGCCAG-CGATAT--TGGACTTCAA
1 GG--TGTCAATATGCT-GA-TTCAA
1815751 GGTGTCAATATGCTGATTCAA
1 GGTGTCAATATGCTGATTCAA
1815772 GG
1 GG
1815774 CGAGTGATAT
Statistics
Matches: 64, Mismatches: 14, Indels: 20
0.65 0.14 0.20
Matches are distributed among these distances:
20 2 0.03
21 31 0.48
22 29 0.45
23 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (21 bp):
GGTGTCAATATGCTGATTCAA
Found at i:1815783 original size:43 final size:43
Alignment explanation
Indices: 1815665--1815784 Score: 204
Period size: 43 Copynumber: 2.8 Consensus size: 43
1815655 TAAAGATGCC
* *
1815665 GGTGTCAATATGCTGATTCAAGGCCAACGATATCGGACTTCAA
1 GGTGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTTCAA
1815708 GGTGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTTCAA
1 GGTGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTTCAA
* *
1815751 GGTGTCAATATGCTGATTCAAGGCGAGTGATATT
1 GGTGTCAATATGCTGATTCAAGGCCAGCGATATT
1815785 TGGTTTAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (43 bp):
GGTGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTTCAA
Found at i:1815921 original size:28 final size:28
Alignment explanation
Indices: 1815889--1816515 Score: 571
Period size: 28 Copynumber: 21.5 Consensus size: 28
1815879 GGTTGCATCA
*
1815889 ACTTGTGTGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
*
1815917 ACTTGTGGGCTTTTGAAGGTTGTCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* *
1815945 ACTTATGGGCTTTTGAACGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
*
1815973 ACTTGTGGGCTTTTAAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* *
1816001 ACTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
1816031 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* *
1816059 ACTTATGGGCTTTTGAAGGTTACCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1816087 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* * *
1816115 ACTTGTGCGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
*
1816145 ACTTGTGGGCTTTTGAAAACGG-TGCCACTA
1 ACTTGTGGGCTTTTG--AA-GGTTGCCACTG
1816175 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
*
1816203 ACTTGTGGGCTTTTGAAGGTTGCCACTA
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
** * *
1816231 ACTTGTGGGCTTAAAAGGAAAAAGAG-TGCTACGG
1 ACTTGTGGGCTT---TTG---AAG-GTTGCCACTG
* *
1816265 AGTTGTGGGCTTATTAAAGAAAAGGAGTGCCA-TGG
1 ACTTGTGGGCTT-TT---G--AAGG-TTGCCACT-G
* * * * * *
1816300 AGTTGTGGACTTTGGAAAAGATGCCATTG
1 ACTTGTGGGCTTTTG-AAGGTTGCCACTG
** *
1816329 ACTTGTGGGCTTCGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
**
1816359 GTTTGTGGGC-TTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* * *
1816386 ACTTGTGGAC-TTTGAAAAAGATGCCACTG
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
1816415 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* * *
1816443 ACTTATGGGCTTTGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
* * *
1816473 ACTTGTGGACTTTAGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
*
1816503 ACTTGTAGGCTTT
1 ACTTGTGGGCTTT
1816516 GGAAAAAGTG
Statistics
Matches: 509, Mismatches: 64, Indels: 50
0.82 0.10 0.08
Matches are distributed among these distances:
27 25 0.05
28 239 0.47
29 40 0.08
30 156 0.31
31 4 0.01
32 1 0.00
33 1 0.00
34 25 0.05
35 18 0.04
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (28 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTG
Found at i:1816070 original size:86 final size:85
Alignment explanation
Indices: 1815858--1816515 Score: 571
Period size: 86 Copynumber: 7.5 Consensus size: 85
1815848 GACGCCATGA
* * *
1815858 ACTTGTGTGGACTTTTGAAAGGGTTG-CA-TCAACTTGTGTGCTTTTGAAGGTTGCCACTGACTT
1 ACTTGTG-GG-CTTTTGAAA-GGTTGCCACT-GACTTGTGGGCTTTTAAAGGTTGCCACTGACTT
*
1815921 GTGGGCTTTTGAAGGTTGTCACTG
62 GTGGGCTTTTGAAGGTTGCCACTG
* *
1815945 ACTTATGGGCTTTTG-AACGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGG
1 ACTTGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGG
* *
1816009 GCTTTTGAAAAGGGTGCCACTA
66 GCTTTTG--AAGGTTGCCACTG
* * *
1816031 ACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTATGGGCTTTTGAAGGTTACCACTGACTTGTGG
1 ACTTGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGG
1816095 GCTTTTGAAGGTTGCCACTG
66 GCTTTTGAAGGTTGCCACTG
* * * *
1816115 ACTTGTGCGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAACGG-TGCCACTAACTT
1 ACTTGTGGGCTTTTG-AAAGGTTGCCACTGACTTGTGGGCTTTT--AAA-GGTTGCCACTGACTT
1816179 GTGGGCTTTTGAAGGTTGCCACTG
62 GTGGGCTTTTGAAGGTTGCCACTG
* * * * *
1816203 ACTTGTGGGCTTTTG-AAGGTTGCCACTAACTTGTGGGC-TTAAAAGGAAAAAGAGTGCTACGGA
1 ACTTGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTAAA-G-----G-TTGCCACTGA
* *
1816266 GTTGTGGGCTTATTAAAGAAAAGGAGTGCCA-TGG
59 CTTGTGGGCTT-TT---G--AAGG-TTGCCACT-G
* * * * * * ** * **
1816300 AGTTGTGGACTTTGGAAAAGATGCCATTGACTTGTGGGCTTCGGAAAAGGGTGCCACTGGTTTGT
1 ACTTGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTT--TTAAAGGTTGCCACTGACTTGT
1816365 GGGC-TTTGAAGGTTGCCACTG
64 GGGCTTTTGAAGGTTGCCACTG
* * * * *
1816386 ACTTGTGGAC-TTTGAAAAAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTATG
1 ACTTGTGGGCTTTTG-AAAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTG
* *
1816450 GGCTTTGGAAAAGGGTGCCACTG
65 GGCTTTTG--AAGGTTGCCACTG
* * * *
1816473 ACTTGTGGACTTTAGAAAAGGGTGCCACTGACTTGTAGGCTTT
1 ACTTGTGGGCTTTTG-AAAGGTTGCCACTGACTTGTGGGCTTT
1816516 GGAAAAAGTG
Statistics
Matches: 477, Mismatches: 60, Indels: 67
0.79 0.10 0.11
Matches are distributed among these distances:
83 8 0.02
84 89 0.19
85 15 0.03
86 164 0.34
87 33 0.07
88 79 0.17
89 3 0.01
90 16 0.03
91 2 0.00
92 2 0.00
93 1 0.00
94 16 0.03
95 1 0.00
96 5 0.01
97 18 0.04
98 19 0.04
99 1 0.00
100 1 0.00
101 4 0.01
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.32
Consensus pattern (85 bp):
ACTTGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGG
GCTTTTGAAGGTTGCCACTG
Found at i:1816073 original size:114 final size:115
Alignment explanation
Indices: 1815889--1816520 Score: 636
Period size: 114 Copynumber: 5.4 Consensus size: 115
1815879 GGTTGCATCA
* * * *
1815889 ACTTGTGTGCTTTTG--AAGGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTGTCACTGACTTAT
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAAGGTTGCCACTGACTTGT
*
1815951 GGGCTTTTGAACGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTG
66 GGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTG
* *
1816001 ACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTAT
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAAGGTTGCCACTGACTTGT
* *
1816065 GGGCTTTTGAAGGTTACCACTGACTTGTGGGCTTTTGAAGGTTGCCACTG
66 GGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTG
* * *
1816115 ACTTGTGCGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAACGG-TGCCACTAACTT
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG-AAA-GGTTGCCACTGACTT
* *
1816179 GTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTA
64 GTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTG
** * * * * *
1816231 ACTTGTGGGCTTAAAAGGAAAAAGAGTGCTACGGAGTTGTGGGCTTATTAAAGAAAAGGAGTGCC
1 ACTTGTGGGCTT---TTG-AAAAGGGTGCCACTGACTTGTGGGCTT-TT---G-AAAGG-TTGCC
* * * * * * ** *
1816296 A-TGGAGTTGTGGACTTTGGAAAAGATGCCATTGACTTGTGGGCTTCGGAAAAGGGTGCCACTG
56 ACT-GACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTT--TTAAAGGTTGCCACTG
** * * * *
1816359 GTTTGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGAC-TTTGAAAAAGATGCCACTGACTTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG-AAAGGTTGCCACTGACTTG
* * *
1816420 TGGGCTTTTGAAGGTTGCCACTGACTTATGGGCTTTGGAAAAGGGTGCCACTG
65 TGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT--TAAAGGTTGCCACTG
* * * *
1816473 ACTTGTGGACTTTAGAAAAGGGTGCCACTGACTTGTAGGCTTTGGAAA
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAA
1816521 AAGTGAGGAA
Statistics
Matches: 434, Mismatches: 60, Indels: 47
0.80 0.11 0.09
Matches are distributed among these distances:
112 14 0.03
114 178 0.41
115 21 0.05
116 80 0.18
117 25 0.06
118 3 0.01
119 3 0.01
120 23 0.05
121 19 0.04
123 2 0.00
124 7 0.02
125 17 0.04
126 22 0.05
127 1 0.00
128 19 0.04
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.32
Consensus pattern (115 bp):
ACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAAGGTTGCCACTGACTTGT
GGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTG
Found at i:1816276 original size:34 final size:34
Alignment explanation
Indices: 1816233--1816307 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 34
1816223 TGCCACTAAC
*
1816233 TTGTGGGCTTA-AAAGGAAAAAGAGTGCTACGGAG
1 TTGTGGGCTTATAAA-GAAAAAGAGTGCCACGGAG
* *
1816267 TTGTGGGCTTATTAAAGAAAAGGAGTGCCATGGAG
1 TTGTGGGCTTA-TAAAGAAAAAGAGTGCCACGGAG
1816302 TTGTGG
1 TTGTGG
1816308 ACTTTGGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 11 0.31
35 22 0.61
36 3 0.08
ACGTcount: A:0.31, C:0.08, G:0.36, T:0.25
Consensus pattern (34 bp):
TTGTGGGCTTATAAAGAAAAAGAGTGCCACGGAG
Found at i:1816384 original size:27 final size:27
Alignment explanation
Indices: 1816321--1816516 Score: 167
Period size: 30 Copynumber: 6.8 Consensus size: 27
1816311 TTGGAAAAGA
* * *
1816321 TGCCATTGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTT-TG--AAGGT
**
1816351 TGCCACTGGTTTGTGGGCTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGAAGGT
* * *
1816378 TGCCACTGACTTGTGGACTTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTG--AAGGT
1816407 TGCCACTGACTTGTGGGCTTTTGAAGGT
1 TGCCACTGACTTGTGGGC-TTTGAAGGT
* *
1816435 TGCCACTGACTTATGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTT-G--AAGGT
* *
1816465 TGCCACTGACTTGTGGACTTTAGAAAAGGG
1 TGCCACTGACTTGTGGGCTTT-G--AAGGT
*
1816495 TGCCACTGACTTGTAGGCTTTG
1 TGCCACTGACTTGTGGGCTTTG
1816517 GAAAAAGTGA
Statistics
Matches: 140, Mismatches: 20, Indels: 13
0.81 0.12 0.08
Matches are distributed among these distances:
27 26 0.19
28 21 0.15
29 22 0.16
30 71 0.51
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (27 bp):
TGCCACTGACTTGTGGGCTTTGAAGGT
Found at i:1816405 original size:57 final size:57
Alignment explanation
Indices: 1816321--1816523 Score: 246
Period size: 57 Copynumber: 3.5 Consensus size: 57
1816311 TTGGAAAAGA
* * * **
1816321 TGCCATTGACTTGTGGGCTTCGGAAAAGGGTGCCACTGGTTTGTGGGCTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGAAAAAGGGTGCCACTGACTTGTGGGCTTTGAAGGT
* *
1816378 TGCCACTGACTTGTGGACTTTGAAAAA-GATGCCACTGACTTGTGGGCTTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGAAAAAGGGTGCCACTGACTTGTGGGC-TTTGAAGGT
* * * *
1816435 TGCCACTGACTTATGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGACTTTAGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAAGGGTGCCACTGACTTGTGGGCTTT-G--AAGGT
*
1816495 TGCCACTGACTTGTAGGCTTTGGAAAAAG
1 TGCCACTGACTTGTGGGCTTT-GAAAAAG
1816524 TGAGGAATGT
Statistics
Matches: 124, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
56 17 0.14
57 59 0.48
58 19 0.15
60 23 0.19
61 6 0.05
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.30
Consensus pattern (57 bp):
TGCCACTGACTTGTGGGCTTTGAAAAAGGGTGCCACTGACTTGTGGGCTTTGAAGGT
Found at i:1818292 original size:22 final size:22
Alignment explanation
Indices: 1818267--1818338 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
1818257 AATATGCTGA
1818267 TTCAAGGCCAACGATATCGGAC
1 TTCAAGGCCAACGATATCGGAC
*** * *
1818289 TTCAAGG-TGTCAATATGCTGA-
1 TTCAAGGCCAACGATAT-CGGAC
* *
1818310 TTCAAGGCCAGCGATATTGGAC
1 TTCAAGGCCAACGATATCGGAC
1818332 TTCAAGG
1 TTCAAGG
1818339 TGTCAATATG
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
21 14 0.39
22 22 0.61
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (22 bp):
TTCAAGGCCAACGATATCGGAC
Found at i:1818313 original size:21 final size:21
Alignment explanation
Indices: 1818251--1818359 Score: 73
Period size: 21 Copynumber: 5.1 Consensus size: 21
1818241 TAAAGATGCC
1818251 GGTGTCAATATGCTGATTCAA
1 GGTGTCAATATGCTGATTCAA
*** * *
1818272 GGCCAACGATAT-CGGACTTCAA
1 GG-TGTCAATATGCTGA-TTCAA
1818294 GGTGTCAATATGCTGATTCAA
1 GGTGTCAATATGCTGATTCAA
* *
1818315 GGCCAG-CGATAT--TGGACTTCAA
1 GG--TGTCAATATGCT-GA-TTCAA
1818337 GGTGTCAATATGCTGATTCAA
1 GGTGTCAATATGCTGATTCAA
1818358 GG
1 GG
1818360 CGAGTGATAT
Statistics
Matches: 64, Mismatches: 14, Indels: 20
0.65 0.14 0.20
Matches are distributed among these distances:
20 2 0.03
21 31 0.48
22 29 0.45
23 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (21 bp):
GGTGTCAATATGCTGATTCAA
Found at i:1818369 original size:43 final size:43
Alignment explanation
Indices: 1818251--1818372 Score: 208
Period size: 43 Copynumber: 2.8 Consensus size: 43
1818241 TAAAGATGCC
* *
1818251 GGTGTCAATATGCTGATTCAAGGCCAACGATATCGGACTTCAA
1 GGTGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTTCAA
1818294 GGTGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTTCAA
1 GGTGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTTCAA
* *
1818337 GGTGTCAATATGCTGATTCAAGGCGAGTGATATTGG
1 GGTGTCAATATGCTGATTCAAGGCCAGCGATATTGG
1818373 GTTTAAAAGA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (43 bp):
GGTGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTTCAA
Found at i:1818507 original size:28 final size:28
Alignment explanation
Indices: 1818475--1819101 Score: 544
Period size: 28 Copynumber: 21.5 Consensus size: 28
1818465 GGTTGCATCA
*
1818475 ACTTGTGTGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
*
1818503 ACTTGTGGGCTTTTGAAGGTTGTCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* * *
1818531 ACTTATGGGCTTTTGAACGTTGCCACTA
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
*
1818559 ACTTGTGGGCTTTTAAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
*
1818587 ACTTGTGGGCTTTTGAAAATGG-TGCCACTA
1 ACTTGTGGGCTTTTG--AA-GGTTGCCACTG
1818617 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* *
1818645 ACTTATGGGCTTTTGAAGGTTACCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1818673 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* * *
1818701 ACTTGTGCGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
*
1818731 ACTTGTGGGCTTTTGAAAACGG-TGCCACTA
1 ACTTGTGGGCTTTTG--AA-GGTTGCCACTG
1818761 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
*
1818789 ACTTGTGGGCTTTTGAAGGTTGCCACTA
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
** * *
1818817 ACTTGTGGGCTTAAAAGGAAAAAGAG-TGCTACGG
1 ACTTGTGGGCTT---TTG---AAG-GTTGCCACTG
* * *
1818851 AGTTGTGGGCTTATTAAAGAAAAGGAGTGCCACGG
1 ACTTGTGGGCTT-TT---G--AAGG-TTGCCACTG
* * * * * *
1818886 AGTTGTGGACTTTGGAAAAGATGCCATTG
1 ACTTGTGGGCTTTTG-AAGGTTGCCACTG
** *
1818915 ACTTGTGGGCTTCGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
**
1818945 GTTTGTGGGC-TTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* * * *
1818972 ACTTGTAGAC-TTTGAAAAAGATGCCACTG
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
1819001 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* * *
1819029 ACTTATGGGCTTTGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
** * *
1819059 ACTTGTGGAATTTAGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
*
1819089 ACTTGTAGGCTTT
1 ACTTGTGGGCTTT
1819102 GGAAAAAGTG
Statistics
Matches: 504, Mismatches: 69, Indels: 50
0.81 0.11 0.08
Matches are distributed among these distances:
27 26 0.05
28 235 0.47
29 39 0.08
30 151 0.30
31 6 0.01
32 1 0.00
33 1 0.00
34 25 0.05
35 20 0.04
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.32
Consensus pattern (28 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTG
Found at i:1818659 original size:114 final size:113
Alignment explanation
Indices: 1818475--1819101 Score: 557
Period size: 114 Copynumber: 5.4 Consensus size: 113
1818465 GGTTGCATCA
* * *
1818475 ACTTGTGTGCTTTTG--AAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGTCACTGACTTATG
1 ACTTGTGGGCTTTTGAAAAGG-TGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTATG
* * *
1818538 GGCTTTTGAACGTTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTG
65 GGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTG
1818587 ACTTGTGGGCTTTTGAAAATGGTGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTATG
1 ACTTGTGGGCTTTTGAAAA-GGTGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTATG
*
1818652 GGCTTTTGAAGGTTACCACTGACTTGTGGGCTTTTGAAGGTTGCCACTG
65 GGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTG
* *
1818701 ACTTGTGCGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAACGG-TGCCACTAACTT
1 ACTTGTGGGCTTTTGAAAA-GGTGCCACTAACTTGTGGGCTTTTG--AA-GGTTGCCACTGACTT
* *
1818765 GTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTA
62 ATGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTG
** * ** * *
1818817 ACTTGTGGGCTTAAAAGGAAAAAGAGTGCTACGGAGTTGTGGGCTTATTAAAGAAAAGGAGTGCC
1 ACTTGTGGGCTT---TTG-AAAAG-GTGCCACTAACTTGTGGGCTT-TT---G--AAGG-TTGCC
* * * * * * * * ** *
1818882 ACGGAGTTGTGGACTTTGGAAAAGATGCCATTGACTTGTGGGCTTCGGAAAAGGGTGCCACTG
54 ACTGACTTATGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTTG--AAGGTTGCCACTG
** * * * * * *
1818945 GTTTGTGGGC-TTTG--AAGGTTGCCACTGACTTGTAGAC-TTTGAAAAAGATGCCACTGACTTG
1 ACTTGTGGGCTTTTGAAAAGG-TGCCACTAACTTGTGGGCTTTTG--AAGGTTGCCACTGACTTA
* * *
1819006 TGGGCTTTTGAAGGTTGCCACTGACTTATGGGCTTTGGAAAAGGGTGCCACTG
63 TGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG--AAGGTTGCCACTG
** * * *
1819059 ACTTGTGGAATTTAGAAAAGGGTGCCACTGACTTGTAGGCTTT
1 ACTTGTGGGCTTTTGAAAA-GGTGCCACTAACTTGTGGGCTTT
1819102 GGAAAAAGTG
Statistics
Matches: 431, Mismatches: 58, Indels: 46
0.81 0.11 0.09
Matches are distributed among these distances:
112 14 0.03
114 175 0.41
115 24 0.06
116 79 0.18
117 21 0.05
118 4 0.01
119 4 0.01
120 23 0.05
121 18 0.04
123 2 0.00
124 6 0.01
125 18 0.04
126 23 0.05
127 1 0.00
128 19 0.04
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.32
Consensus pattern (113 bp):
ACTTGTGGGCTTTTGAAAAGGTGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTATGG
GCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTG
Found at i:1818862 original size:34 final size:34
Alignment explanation
Indices: 1818819--1818893 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 34
1818809 TGCCACTAAC
*
1818819 TTGTGGGCTTA-AAAGGAAAAAGAGTGCTACGGAG
1 TTGTGGGCTTATAAA-GAAAAAGAGTGCCACGGAG
*
1818853 TTGTGGGCTTATTAAAGAAAAGGAGTGCCACGGAG
1 TTGTGGGCTTA-TAAAGAAAAAGAGTGCCACGGAG
1818888 TTGTGG
1 TTGTGG
1818894 ACTTTGGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 11 0.30
35 23 0.62
36 3 0.08
ACGTcount: A:0.31, C:0.09, G:0.36, T:0.24
Consensus pattern (34 bp):
TTGTGGGCTTATAAAGAAAAAGAGTGCCACGGAG
Found at i:1818970 original size:27 final size:27
Alignment explanation
Indices: 1818907--1819102 Score: 149
Period size: 30 Copynumber: 6.8 Consensus size: 27
1818897 TTGGAAAAGA
* * *
1818907 TGCCATTGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTT-TG--AAGGT
**
1818937 TGCCACTGGTTTGTGGGCTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGAAGGT
* * * *
1818964 TGCCACTGACTTGTAGACTTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTG--AAGGT
1818993 TGCCACTGACTTGTGGGCTTTTGAAGGT
1 TGCCACTGACTTGTGGGC-TTTGAAGGT
* *
1819021 TGCCACTGACTTATGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTT-G--AAGGT
** *
1819051 TGCCACTGACTTGTGGAATTTAGAAAAGGG
1 TGCCACTGACTTGTGGGCTTT-G--AAGGT
*
1819081 TGCCACTGACTTGTAGGCTTTG
1 TGCCACTGACTTGTGGGCTTTG
1819103 GAAAAAGTGA
Statistics
Matches: 136, Mismatches: 24, Indels: 13
0.79 0.14 0.08
Matches are distributed among these distances:
27 25 0.18
28 21 0.15
29 21 0.15
30 69 0.51
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (27 bp):
TGCCACTGACTTGTGGGCTTTGAAGGT
Found at i:1818991 original size:57 final size:57
Alignment explanation
Indices: 1818870--1819109 Score: 230
Period size: 57 Copynumber: 4.1 Consensus size: 57
1818860 CTTATTAAAG
* * * * * * * * *
1818870 AAAAGGAGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCATTGACTTGTGGGCTTCGG
1 AAAAGG-GTGCCACTGACTTGTGGGCTTT-G-AAGGTTGCCACTGACTTGTAGGCTTTGA
** *
1818930 AAAAGGGTGCCACTGGTTTGTGGGCTTTGAAGGTTGCCACTGACTTGTAGACTTTGA
1 AAAAGGGTGCCACTGACTTGTGGGCTTTGAAGGTTGCCACTGACTTGTAGGCTTTGA
* * * *
1818987 AAAA-GATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTATGGGCTTTGG
1 AAAAGGGTGCCACTGACTTGTGGGC-TTTGAAGGTTGCCACTGACTTGTAGGCTTTGA
** *
1819044 AAAAGGGTGCCACTGACTTGTGGAATTTAGAAAAGGGTGCCACTGACTTGTAGGCTTTGGA
1 AAAAGGGTGCCACTGACTTGTGGGCTTT-G--AAGGTTGCCACTGACTTGTAGGCTTT-GA
1819105 AAAAG
1 AAAAG
1819110 TGAGGAATGT
Statistics
Matches: 149, Mismatches: 25, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
56 17 0.11
57 60 0.40
58 19 0.13
59 18 0.12
60 29 0.19
61 6 0.04
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.28
Consensus pattern (57 bp):
AAAAGGGTGCCACTGACTTGTGGGCTTTGAAGGTTGCCACTGACTTGTAGGCTTTGA
Found at i:1826873 original size:13 final size:13
Alignment explanation
Indices: 1826855--1826879 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1826845 ATAATGCACA
1826855 GTATCAATACATT
1 GTATCAATACATT
1826868 GTATCAATACAT
1 GTATCAATACAT
1826880 GACCACTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
GTATCAATACATT
Found at i:1826986 original size:13 final size:13
Alignment explanation
Indices: 1826968--1826993 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1826958 ACATATAAGA
1826968 TGTATCGATACAT
1 TGTATCGATACAT
1826981 TGTATCGATACAT
1 TGTATCGATACAT
1826994 GACCAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1827009 original size:33 final size:32
Alignment explanation
Indices: 1826948--1827015 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
1826938 CCTTAACTGT
*
1826948 TTGTATCGATACATATAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
1826980 TTGTATCGATACATGACCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATGTATCGATACA
1827013 TTG
1 TTG
1827016 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 17 0.52
34 2 0.06
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:1827775 original size:15 final size:15
Alignment explanation
Indices: 1827755--1827794 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1827745 GAGCTTTCAA
1827755 ATTTTATATTT-CTTT
1 ATTTTAT-TTTACTTT
*
1827770 ATTTTATTTTATTTT
1 ATTTTATTTTACTTT
1827785 ATTTTATTTT
1 ATTTTATTTT
1827795 TGACTAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (15 bp):
ATTTTATTTTACTTT
Found at i:1827777 original size:5 final size:5
Alignment explanation
Indices: 1827767--1827794 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1827757 TTTATATTTC
1827767 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1827795 TGACTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:1830012 original size:19 final size:20
Alignment explanation
Indices: 1829988--1830038 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1829978 TAGCCAAACT
**
1829988 TGTATCGATACA-CACAGTA
1 TGTATCGATACACCACAAAA
*
1830007 TGTATCGATACACCATAAAA
1 TGTATCGATACACCACAAAA
1830027 TGTATCGATACA
1 TGTATCGATACA
1830039 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACCACAAAA
Found at i:1831639 original size:9 final size:9
Alignment explanation
Indices: 1831625--1831654 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1831615 CATCAAGGAC
1831625 GATGAAGAT
1 GATGAAGAT
1831634 GATGAAGAT
1 GATGAAGAT
*
1831643 GATGATGAT
1 GATGAAGAT
1831652 GAT
1 GAT
1831655 TGTGACTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (9 bp):
GATGAAGAT
Found at i:1836222 original size:13 final size:13
Alignment explanation
Indices: 1836204--1836242 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1836194 ATAGCATTCT
1836204 TTGTATCGATACA
1 TTGTATCGATACA
*
1836217 TTGTATTGATACA
1 TTGTATCGATACA
*
1836230 CTGTATCGATACA
1 TTGTATCGATACA
1836243 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1836651 original size:19 final size:19
Alignment explanation
Indices: 1836627--1836691 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
1836617 TAGCCAAACT
1836627 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
1836646 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
1836659 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
1836680 TGTATCGATACA
1 TGTATCGATACA
1836692 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:1836663 original size:13 final size:13
Alignment explanation
Indices: 1836645--1836670 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1836635 TACACAAAAT
1836645 ATGTATCGATACA
1 ATGTATCGATACA
1836658 ATGTATCGATACA
1 ATGTATCGATACA
1836671 CAAAAAATAT
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:1836668 original size:32 final size:33
Alignment explanation
Indices: 1836627--1836691 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
1836617 TAGCCAAACT
1836627 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
1836659 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
1836692 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:1837597 original size:20 final size:20
Alignment explanation
Indices: 1837562--1837602 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1837552 CAAATTTCTT
1837562 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
1837584 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
1837603 TTCAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:1839974 original size:13 final size:13
Alignment explanation
Indices: 1839956--1839980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1839946 ACACACAGTA
1839956 TGTATCGATACAT
1 TGTATCGATACAT
1839969 TGTATCGATACA
1 TGTATCGATACA
1839981 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1839977 original size:32 final size:33
Alignment explanation
Indices: 1839936--1840003 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1839926 GTAGCCAAAC
**
1839936 TTGTATCGATACA-CACAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
1839968 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
1840001 TTG
1 TTG
1840004 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:1846263 original size:21 final size:21
Alignment explanation
Indices: 1846239--1846294 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
1846229 AGGGTGGTTT
*
1846239 TGTATTGATACATTTCAGC-CA
1 TGTATCGATACATTTCA-CTCA
*
1846260 TGTATCGATACA-TTCACTTA
1 TGTATCGATACATTTCACTCA
1846280 TGTATCGATACATTT
1 TGTATCGATACATTT
1846295 ACTATTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 17 0.55
21 13 0.42
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
TGTATCGATACATTTCACTCA
Found at i:1846282 original size:20 final size:21
Alignment explanation
Indices: 1846259--1846312 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1846249 CATTTCAGCC
1846259 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTAT
*
1846279 ATGTATCGATACATTTACTAT
1 ATGTATCGATACATTCACTAT
* *
1846300 TTATATCGATACA
1 ATGTATCGATACA
1846313 AATTGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:1858791 original size:31 final size:31
Alignment explanation
Indices: 1858753--1858863 Score: 163
Period size: 31 Copynumber: 3.5 Consensus size: 31
1858743 AAAAAAAAAA
1858753 TCCACGACTCAGTGGCAATCTCTTCTCAAAG
1 TCCACGACTCAGTGGCAATCTCTTCTCAAAG
*
1858784 TCCACGACTCAGTGGCAATCTCTGCTCAAAG
1 TCCACGACTCAGTGGCAATCTCTTCTCAAAG
*
1858815 TCCACGACACAGTGGC-ATC-CTTCTCTTTAAAG
1 TCCACGACTCAGTGGCAATCTCTTCTC---AAAG
1858847 TCCACGACTCAGTGGCA
1 TCCACGACTCAGTGGCA
1858864 TTTTTTCTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
29 5 0.07
30 3 0.04
31 45 0.62
32 19 0.26
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24
Consensus pattern (31 bp):
TCCACGACTCAGTGGCAATCTCTTCTCAAAG
Found at i:1858876 original size:31 final size:31
Alignment explanation
Indices: 1858753--1858927 Score: 156
Period size: 31 Copynumber: 5.5 Consensus size: 31
1858743 AAAAAAAAAA
* *
1858753 TCCACGACTCAGTGGCAATCTCTTC-TCAAAG
1 TCCACGACTCAGTGGC-ATCTTTTCTTTAAAG
* * *
1858784 TCCACGACTCAGTGGCAATCTCTGC-TCAAAG
1 TCCACGACTCAGTGGC-ATCTTTTCTTTAAAG
* *
1858815 TCCACGACACAGTGGCATCCTTCTCTTTAAAG
1 TCCACGACTCAGTGGCAT-CTTTTCTTTAAAG
*
1858847 TCCACGACTCAGTGGCATTTTTTCTTTAAAG
1 TCCACGACTCAGTGGCATCTTTTCTTTAAAG
* * * * *
1858878 CCCACAACTCCGTGGCACCTTGTTCCTTTTAAG
1 TCCACGACTCAGTGGCATCTT-TT-CTTTAAAG
* *
1858911 TCCACAACTCCGTGGCA
1 TCCACGACTCAGTGGCA
1858928 CCCTTTTAAA
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
30 2 0.02
31 75 0.60
32 24 0.19
33 23 0.19
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (31 bp):
TCCACGACTCAGTGGCATCTTTTCTTTAAAG
Found at i:1858990 original size:62 final size:62
Alignment explanation
Indices: 1858871--1859324 Score: 486
Period size: 62 Copynumber: 7.0 Consensus size: 62
1858861 GCATTTTTTC
* * * *
1858871 TTTAAAGCCCACAACTCCGTGGCACCTTGTTC-CTTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTCTTTAAAGCCCACAACTCCGTGGCACCCT
* *
1858932 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTT-AAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTC-TCTTTAAAGCCCACAACTCCGTGGCACCCT
* * * * *
1858994 TTTAAAGCCCACAATTCTGTGGCACCTTTTTCATCTTT-AAGTCCACAACTCCGTGGCACCCG
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTC-TCTTTAAAGCCCACAACTCCGTGGCACCCT
* *
1859056 TTT-AAGCCCAGAACTCCGTGGCACCTTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
1 TTTAAAGCCCACAACTCCGTGGCA-CTTTTTTCTCTTTAAAGCCCACAACTCCGTGGCACC----
1859120 TCT
61 -CT
* *
1859123 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTT
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC-TTT-AAAGCCCACAACTCCGTGGCACC--
1859188 TTTCT
61 ---CT
* *
1859193 GTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTC
1 -TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC-TTT-AAAGCCCACAACTCCGTGGCACCC
1859258 -
62 T
* * * *
1859258 TTTAAAGTCCACAACTTCGTGGCACCTTTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
1 TTTAAAGCCCACAACTCCGTGGCA-CTTTTTTCTC-TTTAAAGCCCACAACTCCGTGGCACCCT
1859322 TTT
1 TTT
1859325 TCCCTTTTAA
Statistics
Matches: 352, Mismatches: 25, Indels: 29
0.87 0.06 0.07
Matches are distributed among these distances:
61 50 0.14
62 114 0.32
63 27 0.08
64 36 0.10
65 2 0.01
66 1 0.00
67 6 0.02
68 24 0.07
69 3 0.01
70 30 0.09
71 59 0.17
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (62 bp):
TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTCTTTAAAGCCCACAACTCCGTGGCACCCT
Found at i:1859070 original size:27 final size:27
Alignment explanation
Indices: 1859029--1859080 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1859019 CTTTTTCATC
*
1859029 TTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAGCCCACAACTCCGTGGCACCCG
*
1859056 TTTAAGCCCAGAACTCCGTGGCACC
1 TTTAAGCCCACAACTCCGTGGCACC
1859081 TTTTTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (27 bp):
TTTAAGCCCACAACTCCGTGGCACCCG
Found at i:1859106 original size:35 final size:35
Alignment explanation
Indices: 1859059--1859357 Score: 334
Period size: 37 Copynumber: 8.7 Consensus size: 35
1859049 GCACCCGTTT
*
1859059 AAGCCCAGAACTCCGTGGCACCTTTTTTCTTTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
1859094 AAGCCCACAACTCCGTGGCACC-TTTTTC-TTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
* * *
1859127 AAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCA
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-TCTTTTTA
*
1859164 AAGCCCACAACTCCGTGGCACC-TTTTTCTGTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
*
1859198 AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCA
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-TCTTTTTA
*
1859235 AAGCCCACGACTCCGTGGCA-C-----TC--TTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
* * *
1859262 AAGTCCACAACTTCGTGGCACCTTTTTTTTCTTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCT-TTTTA
* *
1859298 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-
1 AAGCCCACAACTCCGTGGCAC-CTTTTTTCTTTTTA
* *
1859333 AAGTCCACAACTCCGTGGCATCTTT
1 AAGCCCACAACTCCGTGGCACCTTT
1859358 CTCCCTTCCT
Statistics
Matches: 224, Mismatches: 23, Indels: 35
0.79 0.08 0.12
Matches are distributed among these distances:
27 20 0.09
28 1 0.00
29 2 0.01
33 26 0.12
34 37 0.17
35 50 0.22
36 33 0.15
37 55 0.25
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (35 bp):
AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
Found at i:1859170 original size:37 final size:33
Alignment explanation
Indices: 1858835--1859357 Score: 463
Period size: 34 Copynumber: 16.0 Consensus size: 33
1858825 AGTGGCATCC
* * * *
1858835 TTCTCTTTAAAGTCCACGACTCAGTGGCA-TTTT
1 TTCT-TTTAAAGCCCACAACTCCGTGGCACCTTT
1858868 TTC-TTTAAAGCCCACAACTCCGTGGCACCTTGT
1 TTCTTTTAAAGCCCACAACTCCGTGGCACCTT-T
* *
1858901 TCCTTTT-AAGTCCACAACTCCGTGGCACC---
1 TTCTTTTAAAGCCCACAACTCCGTGGCACCTTT
* *
1858930 --CTTTTAAAGCCCACAATTCCGTGGCACTTTT
1 TTCTTTTAAAGCCCACAACTCCGTGGCACCTTT
*
1858961 TTCATCTTT-AAGTCCACAACTCCGTGGCACC---
1 TTC-T-TTTAAAGCCCACAACTCCGTGGCACCTTT
* *
1858992 --CTTTTAAAGCCCACAATTCTGTGGCACCTTT
1 TTCTTTTAAAGCCCACAACTCCGTGGCACCTTT
*
1859023 TTCATCTTT-AAGTCCACAACTCCGTGGCACC---
1 TTC-T-TTTAAAGCCCACAACTCCGTGGCACCTTT
* *
1859054 --CGTTT-AAGCCCAGAACTCCGTGGCACCTTTT
1 TTCTTTTAAAGCCCACAACTCCGTGGCACC-TTT
1859085 TTCTTTTTAAAGCCCACAACTCCGTGGCACCTTT
1 TTC-TTTTAAAGCCCACAACTCCGTGGCACCTTT
*
1859119 TTCTTTTAAAGCCCACAACTCTGTGGCACTCTTT
1 TTCTTTTAAAGCCCACAACTCCGTGGCAC-CTTT
1859153 TTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTT
1 TT--CTTTT-AAAGCCCACAACTCCGTGGCACCTTT
1859189 TTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTT
1 TTCT-TTTAAAGCCCACAACTCCGTGGCAC-C-TTT
*
1859225 TCTCTTTTCAAAGCCCACGACTCCGTGGCA-C---
1 T-TCTTTT-AAAGCCCACAACTCCGTGGCACCTTT
* *
1859256 -TC-TTTAAAGTCCACAACTTCGTGGCACCTTTTTT
1 TTCTTTTAAAGCCCACAACTCCGTGGCACC---TTT
1859290 TTCTTTTAAAGCCCACAACTCCGTGGCACTCTTT
1 TTCTTTTAAAGCCCACAACTCCGTGGCAC-CTTT
* *
1859324 TTCCCTTTT-AAGTCCACAACTCCGTGGCATCTTT
1 TT--CTTTTAAAGCCCACAACTCCGTGGCACCTTT
1859358 CTCCCTTCCT
Statistics
Matches: 409, Mismatches: 33, Indels: 95
0.76 0.06 0.18
Matches are distributed among these distances:
27 49 0.12
28 43 0.11
29 4 0.01
31 21 0.05
32 2 0.00
33 55 0.13
34 91 0.22
35 53 0.13
36 46 0.11
37 45 0.11
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (33 bp):
TTCTTTTAAAGCCCACAACTCCGTGGCACCTTT
Found at i:1859264 original size:27 final size:26
Alignment explanation
Indices: 1859234--1859286 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1859224 TTCTCTTTTC
*
1859234 AAAGCCCACGACTCCGTGGCACTCTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTT
* *
1859261 AAAGTCCACAACTTCGTGGCACCTTT
1 AAAGCCCACAACTCCGTGGCACCTTT
1859287 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.25
Consensus pattern (26 bp):
AAAGCCCACAACTCCGTGGCACCTTT
Found at i:1859405 original size:33 final size:35
Alignment explanation
Indices: 1859362--1859431 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 35
1859352 ATCTTTCTCC
*
1859362 CTTCCTAAAGCCCACACAAGTCGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGGCGGTGGCAACCCTT
*
1859396 CTTCC-AAAGCCCACATAAGGCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGGCGGTGGCAACCCTT
1859430 CT
1 CT
1859432 AAGCCCAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 22 0.67
34 11 0.33
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.20
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGGCGGTGGCAACCCTT
Found at i:1859495 original size:49 final size:49
Alignment explanation
Indices: 1859431--1859993 Score: 634
Period size: 49 Copynumber: 11.8 Consensus size: 49
1859421 GCAACCCTTC
* * *
1859431 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
*
1859480 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
1859523 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA--TCTT-CATCTT
* * * *
1859575 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTAGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
1859624 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * *
1859667 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
1859716 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
1859759 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATC-TTCATCTT
* *
1859809 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
1859858 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * * * *
1859901 TAAGTCCAATATAGCTGGCCTTAAATCAGCATATCGACACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA--TCTT-CATCTT
* *
1859953 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATC
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATC
1859994 CTTTTTCATC
Statistics
Matches: 437, Mismatches: 46, Indels: 61
0.80 0.08 0.11
Matches are distributed among these distances:
43 153 0.35
45 3 0.01
47 1 0.00
48 1 0.00
49 161 0.37
50 44 0.10
52 74 0.17
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
Found at i:1859729 original size:92 final size:92
Alignment explanation
Indices: 1859572--1859931 Score: 489
Period size: 92 Copynumber: 3.9 Consensus size: 92
1859562 CCTTTTCCAT
* * * * *
1859572 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTAGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
1859637 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
1859664 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
1859729 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
1859756 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCCATCTTTAAGTCCAATGT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATC-TTCATCTTTAAGTCCAATGT
*
1859821 AGCTGGCCTTGACTCAGCACATTGGCACCTTC
65 AGCTGGCCTTGAATCAGCACATTGGCA----C
* *
1859853 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATA
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
*
1859912 TAGCTGGCCTTAAATCAGCA
64 TAGCTGGCCTTGAATCAGCA
1859932 TATCGACACC
Statistics
Matches: 246, Mismatches: 15, Indels: 14
0.89 0.05 0.05
Matches are distributed among these distances:
92 160 0.65
93 45 0.18
94 1 0.00
97 1 0.00
99 39 0.16
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (92 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1860833 original size:33 final size:33
Alignment explanation
Indices: 1860796--1860862 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1860786 TTCAACGATT
1860796 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1860829 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1860862 T
1 T
1860863 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1860834 original size:13 final size:13
Alignment explanation
Indices: 1860816--1860840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1860806 CATAAAATGT
1860816 TGTATCGATACAA
1 TGTATCGATACAA
1860829 TGTATCGATACA
1 TGTATCGATACA
1860841 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1861067 original size:52 final size:52
Alignment explanation
Indices: 1860939--1861059 Score: 206
Period size: 52 Copynumber: 2.3 Consensus size: 52
1860929 GACGGATCTT
* **
1860939 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACAATAAAA
*
1860991 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACAATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACAATAAAA
1861043 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1861060 ATAAATTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACAATAAAA
Found at i:1865769 original size:13 final size:13
Alignment explanation
Indices: 1865751--1865776 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1865741 TACAGCAAGT
1865751 ATGTATCGATACA
1 ATGTATCGATACA
1865764 ATGTATCGATACA
1 ATGTATCGATACA
1865777 CAAAAAATTT
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:1868456 original size:26 final size:26
Alignment explanation
Indices: 1868426--1868477 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1868416 CGTTGCTGCA
1868426 GTTGCATGCTGGAGCTGCTACCGTTG
1 GTTGCATGCTGGAGCTGCTACCGTTG
* *
1868452 GTTGCATGCTGGAGCTGTTACTGTTG
1 GTTGCATGCTGGAGCTGCTACCGTTG
1868478 CTGGAACTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.19, G:0.35, T:0.35
Consensus pattern (26 bp):
GTTGCATGCTGGAGCTGCTACCGTTG
Found at i:1868625 original size:34 final size:34
Alignment explanation
Indices: 1868582--1868684 Score: 145
Period size: 34 Copynumber: 3.0 Consensus size: 34
1868572 ATGCTTGTTG
**
1868582 CTTTACAGCTC-CATGTTGCTATTTGAAGCTGCCT
1 CTTTACAGCTCTC-TGTTGCTATTTGGTGCTGCCT
* *
1868616 CTTTACAGCTCTCTGCTGCTATTAGGTGCTGCCT
1 CTTTACAGCTCTCTGTTGCTATTTGGTGCTGCCT
*
1868650 CTTTGCAGCTCTCTGTTGCTATTTGGTGCTGCCT
1 CTTTACAGCTCTCTGTTGCTATTTGGTGCTGCCT
1868684 C
1 C
1868685 CTCCCCCCTT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
34 60 0.98
35 1 0.02
ACGTcount: A:0.12, C:0.28, G:0.20, T:0.40
Consensus pattern (34 bp):
CTTTACAGCTCTCTGTTGCTATTTGGTGCTGCCT
Found at i:1877657 original size:21 final size:20
Alignment explanation
Indices: 1877609--1877665 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
1877599 TCAAAAACCC
*
1877609 AAAATGTATCAATAC-AATG
1 AAAATGTATCGATACAAATG
1877628 AATAATGTATCGATACAAATAG
1 AA-AATGTATCGATACAAAT-G
*
1877650 TAAATGTATCGATACA
1 AAAATGTATCGATACA
1877666 TTTCCTTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 12 0.36
21 17 0.52
22 2 0.06
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (20 bp):
AAAATGTATCGATACAAATG
Found at i:1877721 original size:21 final size:21
Alignment explanation
Indices: 1877693--1877748 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
1877683 AGGGTGGTTT
1877693 TGTATCGATACATTTCAACCAA
1 TGTATCGATACATTTC-ACCAA
**
1877715 T-TATCGATACA-TTCACTTA
1 TGTATCGATACATTTCACCAA
1877734 TGTATCGATACATTT
1 TGTATCGATACATTT
1877749 ACTGTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.13
20 13 0.43
21 12 0.40
22 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTTCACCAA
Found at i:1877739 original size:20 final size:20
Alignment explanation
Indices: 1877693--1877766 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
1877683 AGGGTGGTTT
**
1877693 TGTATCGATACATTTCAACCAA
1 TGTATCGATACA-TTC-ACTTA
1877715 T-TATCGATACATTCACTTA
1 TGTATCGATACATTCACTTA
* *
1877734 TGTATCGATACATTTACTGTT
1 TGTATCGATACATTCACT-TA
*
1877755 TATATCGATACA
1 TGTATCGATACA
1877767 AATTATAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.09
20 18 0.40
21 22 0.49
22 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:1877762 original size:21 final size:20
Alignment explanation
Indices: 1877716--1877766 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1877706 TTCAACCAAT
*
1877716 TATCGATACATTCACTTATG
1 TATCGATACATTCACTTATA
* *
1877736 TATCGATACATTTACTGTTTA
1 TATCGATACATTCACT-TATA
1877757 TATCGATACA
1 TATCGATACA
1877767 AATTATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (20 bp):
TATCGATACATTCACTTATA
Found at i:1879595 original size:29 final size:29
Alignment explanation
Indices: 1879553--1879844 Score: 207
Period size: 29 Copynumber: 9.7 Consensus size: 29
1879543 CACCCTTAAA
1879553 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1879582 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1879611 AAAGTCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
** *
1879638 AAAGCCCACAAACCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * *
1879668 GAAGCCCACAAGTCAGTGGCATCTTCTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
1879697 AAAGTCCACAACTCCGTGGCACTCCTTTTCTTTTG
1 AAAGCCCACAAGTCAGTGGCA-T-C---T-TTTTC
* * *
1879732 TAAGCCCACAACTTC-GTAGCACTCTTTTTCC
1 AAAGCCCACAA-GTCAGTGGCA-TCTTTTT-C
* * * *
1879763 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ---AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1879795 AAAAGCCCATAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
1879823 AAAAGCCCACAAGTCAGTGGCA
1 -AAAGCCCACAAGTCAGTGGCA
1879845 ACCTTCAAAA
Statistics
Matches: 210, Mismatches: 38, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
27 21 0.10
28 25 0.12
29 72 0.34
30 45 0.21
31 2 0.01
32 1 0.00
33 6 0.03
34 18 0.09
35 18 0.09
36 2 0.01
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:1879687 original size:57 final size:57
Alignment explanation
Indices: 1879553--1879707 Score: 186
Period size: 57 Copynumber: 2.7 Consensus size: 57
1879543 CACCCTTAAA
* * ** *
1879553 AAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAAC-TCTTCAAAGCCCACAAACCAGTGGCACCTTTTTC
*
1879611 AAAGTCCACAAGTCAGTGGCAAC-CTTCAAAGCCCACAAACCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCCACAAACCAGTGGCA-CCTTTTTC
* * * *
1879668 GAAGCCCACAAGTCAGTGGCATCTTCTCCAAAGTCCACAA
1 AAAGCCCACAAGTCAGTGGCAAC-TCTTCAAAGCCCACAA
1879708 CTCCGTGGCA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
56 22 0.27
57 27 0.33
58 21 0.25
59 13 0.16
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCCACAAACCAGTGGCACCTTTTTC
Found at i:1879700 original size:86 final size:85
Alignment explanation
Indices: 1879553--1879717 Score: 249
Period size: 86 Copynumber: 1.9 Consensus size: 85
1879543 CACCCTTAAA
** * * *
1879553 AAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGTCC
1 AAAGCCCACAAACCAGTGGCACCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTCTCCAAAGTCC
*
1879618 ACAAGTCAGTGGCAACCTTC
66 ACAACTCAGTGGCAACCTTC
*
1879638 AAAGCCCACAAACCAGTGGCACCCTTTTTCGAAGCCCACAAGTCAGTGGCATCTTCTCCAAAGTC
1 AAAGCCCACAAACCAGTGGCA-CCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTCTCCAAAGTC
*
1879703 CACAACTCCGTGGCA
65 CACAACTCAGTGGCA
1879718 CTCCTTTTCT
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 19 0.27
86 52 0.73
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.22
Consensus pattern (85 bp):
AAAGCCCACAAACCAGTGGCACCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTCTCCAAAGTCC
ACAACTCAGTGGCAACCTTC
Found at i:1879754 original size:35 final size:34
Alignment explanation
Indices: 1879702--1879794 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 34
1879692 TCTCCAAAGT
* *
1879702 CCACAACTCCGTGGCACTCCTTTTCTTTTGTAAGC
1 CCACAACTTCGTGGCACTCCTTTTCCTTT-TAAGC
* *
1879737 CCACAACTTCGTAGCACTCTTTTTCCTTTTAAGC
1 CCACAACTTCGTGGCACTCCTTTTCCTTTTAAGC
* *
1879771 CCACAAGTTAGTGGCAC-CCTTTTC
1 CCACAACTTCGTGGCACTCCTTTTC
1879795 AAAAGCCCAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
33 6 0.12
34 19 0.38
35 25 0.50
ACGTcount: A:0.19, C:0.33, G:0.13, T:0.34
Consensus pattern (34 bp):
CCACAACTTCGTGGCACTCCTTTTCCTTTTAAGC
Found at i:1879793 original size:34 final size:35
Alignment explanation
Indices: 1879702--1879793 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 35
1879692 TCTCCAAAGT
** *
1879702 CCACAACTCCGTGGCACTCC-TTTTCTTTTGTAAGC
1 CCACAACTTAGTGGCAC-CCTTTTTCCTTTGTAAGC
* * *
1879737 CCACAACTTCGTAGCACTCTTTTTCCTTT-TAAGC
1 CCACAACTTAGTGGCACCCTTTTTCCTTTGTAAGC
*
1879771 CCACAAGTTAGTGGCACCCTTTT
1 CCACAACTTAGTGGCACCCTTTT
1879794 CAAAAGCCCA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
34 25 0.52
35 23 0.48
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.35
Consensus pattern (35 bp):
CCACAACTTAGTGGCACCCTTTTTCCTTTGTAAGC
Found at i:1879836 original size:28 final size:28
Alignment explanation
Indices: 1879767--1879864 Score: 142
Period size: 28 Copynumber: 3.4 Consensus size: 28
1879757 TTTTCCTTTT
* *
1879767 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC--TTCAA
*
1879797 AAGCCCATAAGTCAGTGGCAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTCAA
1879825 AAGCCCACAAGTCAGTGGCAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTCAA
*
1879853 AAGCACACAAGT
1 AAGCCCACAAGT
1879865 TGATGCAACC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
28 43 0.68
30 20 0.32
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTCAA
Found at i:1879877 original size:28 final size:29
Alignment explanation
Indices: 1879767--1879903 Score: 115
Period size: 28 Copynumber: 4.7 Consensus size: 29
1879757 TTTTCCTTTT
* *
1879767 AAGCCCACAAGTT-AGTGGCACCCTTTTCAA
1 AAGCACACAAGTTGAGTGGCAACC--TTCAA
* * *
1879797 AAGCCCATAAG-TCAGTGGCAACCTTCAA
1 AAGCACACAAGTTGAGTGGCAACCTTCAA
* *
1879825 AAGCCCACAAG-TCAGTGGCAACCTTCAA
1 AAGCACACAAGTTGAGTGGCAACCTTCAA
1879853 AAGCACACAAGTTGA-T-GCAACCCTTTCAA
1 AAGCACACAAGTTGAGTGGCAA-CC-TTCAA
1879882 AAGTCCACACAAGTTG-GTGGCA
1 AAG--CACACAAGTTGAGTGGCA
1879904 TCTTCTTCTA
Statistics
Matches: 94, Mismatches: 5, Indels: 14
0.83 0.04 0.12
Matches are distributed among these distances:
27 4 0.04
28 45 0.48
29 11 0.12
30 19 0.20
31 12 0.13
32 3 0.03
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.19
Consensus pattern (29 bp):
AAGCACACAAGTTGAGTGGCAACCTTCAA
Found at i:1880004 original size:21 final size:21
Alignment explanation
Indices: 1879980--1880088 Score: 80
Period size: 21 Copynumber: 5.1 Consensus size: 21
1879970 ATATCGCTGG
1879980 CCTTGAATCAGCATATTGACA
1 CCTTGAATCAGCATATTGACA
* ***
1880001 CCTTGAAGCTC-G-ATATCGTTGG
1 CCTTGAA--TCAGCATATTG-ACA
1880023 CCTTGAATCAGCATATTGACA
1 CCTTGAATCAGCATATTGACA
* * **
1880044 CCTTGAAGTCTG-ATATCGTTA
1 CCTTGAA-TCAGCATATTGACA
1880065 GCCTTGAATCAGCATATTGACA
1 -CCTTGAATCAGCATATTGACA
1880087 CC
1 CC
1880089 GGCATCTTTA
Statistics
Matches: 64, Mismatches: 16, Indels: 16
0.67 0.17 0.17
Matches are distributed among these distances:
20 2 0.03
21 31 0.48
22 29 0.45
23 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGACA
Found at i:1880031 original size:43 final size:43
Alignment explanation
Indices: 1879970--1880088 Score: 204
Period size: 43 Copynumber: 2.8 Consensus size: 43
1879960 TTTAAACCCA
*
1879970 ATATCGCTGGCCTTGAATCAGCATATTGACACCTTGAAG-CTCG
1 ATATCGTTGGCCTTGAATCAGCATATTGACACCTTGAAGTCT-G
1880013 ATATCGTTGGCCTTGAATCAGCATATTGACACCTTGAAGTCTG
1 ATATCGTTGGCCTTGAATCAGCATATTGACACCTTGAAGTCTG
*
1880056 ATATCGTTAGCCTTGAATCAGCATATTGACACC
1 ATATCGTTGGCCTTGAATCAGCATATTGACACC
1880089 GGCATCTTTA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
43 71 0.97
44 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (43 bp):
ATATCGTTGGCCTTGAATCAGCATATTGACACCTTGAAGTCTG
Found at i:1880038 original size:22 final size:21
Alignment explanation
Indices: 1879970--1880081 Score: 59
Period size: 22 Copynumber: 5.2 Consensus size: 21
1879960 TTTAAACCCA
*
1879970 ATATCGCTGGCCTTGAATCAGC
1 ATATCG-TCGCCTTGAATCAGC
* * *
1879992 ATATTGACACCTTGAAGCTC-G-
1 ATATCGTCGCCTTGAA--TCAGC
*
1880013 ATATCGTTGGCCTTGAATCAGC
1 ATATCG-TCGCCTTGAATCAGC
* * * *
1880035 ATATTGACACCTTGAAGTCTG-
1 ATATCGTCGCCTTGAA-TCAGC
*
1880056 ATATCGTTAGCCTTGAATCAGC
1 ATATCG-TCGCCTTGAATCAGC
1880078 ATAT
1 ATAT
1880082 TGACACCGGC
Statistics
Matches: 64, Mismatches: 18, Indels: 16
0.65 0.18 0.16
Matches are distributed among these distances:
20 2 0.03
21 28 0.44
22 32 0.50
23 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (21 bp):
ATATCGTCGCCTTGAATCAGC
Found at i:1880996 original size:19 final size:17
Alignment explanation
Indices: 1880970--1881036 Score: 70
Period size: 19 Copynumber: 3.9 Consensus size: 17
1880960 ATTCAACGAT
1880970 TTGTATCGATACATAAG
1 TTGTATCGATACATAAG
1880987 TGTGGTATCGATAC--AA-
1 T-T-GTATCGATACATAAG
1881003 -TGTATCGATACATAAG
1 TTGTATCGATACATAAG
1881019 TATTGTATCGATACATAA
1 --TTGTATCGATACATAA
1881037 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
15 2 0.05
17 3 0.07
18 1 0.02
19 25 0.60
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (17 bp):
TTGTATCGATACATAAG
Found at i:1881007 original size:32 final size:32
Alignment explanation
Indices: 1880971--1881033 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1880961 TTCAACGATT
*
1880971 TGTATCGATACATAAGTGTGGTATCGATACAA
1 TGTATCGATACATAAGTATGGTATCGATACAA
*
1881003 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATGGTATCGATACA
1881034 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATAAGTATGGTATCGATACAA
Found at i:1894535 original size:32 final size:30
Alignment explanation
Indices: 1894491--1894590 Score: 114
Period size: 31 Copynumber: 3.2 Consensus size: 30
1894481 CGTCCGCCGC
*
1894491 AAAAAAACAAAAACAACAAAAAAATA-AACA
1 AAAAAAACAAAAAAAACAAAAAAA-ACAACA
*
1894521 AAAAAAACCAAAAAAAAGAAAAAAAACAA-A
1 AAAAAAA-CAAAAAAAACAAAAAAAACAACA
1894551 AACAAAAACAAAAACAAAACAAAAAAAACAACA
1 AA-AAAAAC-AAAA-AAAACAAAAAAAACAACA
*
1894584 ACAAAAA
1 AAAAAAA
1894591 GGGTCCGGAT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
30 12 0.20
31 26 0.43
32 20 0.33
33 2 0.03
ACGTcount: A:0.84, C:0.14, G:0.01, T:0.01
Consensus pattern (30 bp):
AAAAAAACAAAAAAAACAAAAAAAACAACA
Found at i:1894549 original size:40 final size:41
Alignment explanation
Indices: 1894491--1894581 Score: 132
Period size: 40 Copynumber: 2.2 Consensus size: 41
1894481 CGTCCGCCGC
* *
1894491 AAAAAAACAAAAACAACAAAAA-AATAAACAAAAA-AAACCA
1 AAAAAAACAAAAAAAACAAAAACAA-AAACAAAAACAAAACA
*
1894531 AAAAAAAGAAAAAAAACAAAAACAAAAACAAAAACAAAACA
1 AAAAAAACAAAAAAAACAAAAACAAAAACAAAAACAAAACA
1894572 AAAAAAACAA
1 AAAAAAACAA
1894582 CAACAAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
40 29 0.64
41 16 0.36
ACGTcount: A:0.85, C:0.13, G:0.01, T:0.01
Consensus pattern (41 bp):
AAAAAAACAAAAAAAACAAAAACAAAAACAAAAACAAAACA
Found at i:1894587 original size:6 final size:6
Alignment explanation
Indices: 1894493--1894584 Score: 84
Period size: 6 Copynumber: 15.3 Consensus size: 6
1894483 TCCGCCGCAA
* * * *
1894493 AAAAAC AAAAAC AACAA- AAAAAT AAACAAA AAAAACC AAAAA- AAAGAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAA-AAC AAAAA-C AAAAAC AAA-AAC
1894542 AAAAAC AAAAAC AAAAAC AAAAAC -AAAAC AAAAA- AAACAAC AA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAA-AAC AA
1894585 CAAAAAGGGT
Statistics
Matches: 73, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
5 15 0.21
6 43 0.59
7 15 0.21
ACGTcount: A:0.84, C:0.14, G:0.01, T:0.01
Consensus pattern (6 bp):
AAAAAC
Found at i:1894590 original size:1 final size:1
Alignment explanation
Indices: 1894491--1894578 Score: 59
Period size: 1 Copynumber: 88.0 Consensus size: 1
1894481 CGTCCGCCGC
* * * * * ** * * *
1894491 AAAAAAACAAAAACAACAAAAAAATAAACAAAAAAAACCAAAAAAAAGAAAAAAAACAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
1894556 AAACAAAAACAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
1894579 CAACAACAAA
Statistics
Matches: 63, Mismatches: 24, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.85, C:0.12, G:0.01, T:0.01
Consensus pattern (1 bp):
A
Found at i:1896086 original size:27 final size:27
Alignment explanation
Indices: 1896014--1896128 Score: 79
Period size: 29 Copynumber: 4.0 Consensus size: 27
1896004 GACATTCCTC
* *
1896014 ACCTTTCAAAAGCCCACAAGTCAATGGTA
1 ACCTTTC--AAGCCCACAAGTCAGTGGCA
* *
1896043 TCTTTTTCAAAGCCCACAAGTCAGTGGCA
1 AC-CTTTC-AAGCCCACAAGTCAGTGGCA
** *
1896072 ACC-TTCAAGGCCCACAAACCAGTGGCC
1 ACCTTTCAA-GCCCACAAGTCAGTGGCA
*
1896099 CCCTTTTCCGAAGCCCACAAGTCAGTGGCA
1 ACC-TTT-C-AAGCCCACAAGTCAGTGGCA
1896129 TCTTCTCCAA
Statistics
Matches: 67, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
26 2 0.03
27 20 0.30
29 23 0.34
30 20 0.30
31 2 0.03
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (27 bp):
ACCTTTCAAGCCCACAAGTCAGTGGCA
Found at i:1896210 original size:34 final size:35
Alignment explanation
Indices: 1896142--1896213 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
1896132 TCTCCAAAGT
* *
1896142 CCACAACTCCATGGCACTCCTTTTCTTTTGTAAGC
1 CCACAACTCCATAGCACTCCTTTTCCTTTGTAAGC
* *
1896177 CCACAACTCCGTAGCACTCTTTTTCCTTT-TAAGC
1 CCACAACTCCATAGCACTCCTTTTCCTTTGTAAGC
1896211 CCA
1 CCA
1896214 TAAGTTAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
34 8 0.24
35 25 0.76
ACGTcount: A:0.21, C:0.36, G:0.10, T:0.33
Consensus pattern (35 bp):
CCACAACTCCATAGCACTCCTTTTCCTTTGTAAGC
Found at i:1896242 original size:30 final size:29
Alignment explanation
Indices: 1896207--1896358 Score: 134
Period size: 28 Copynumber: 5.3 Consensus size: 29
1896197 TTTTCCTTTT
* *
1896207 AAGCCCATAAGTTAGGGGCACCCTTTTCAA
1 AAGCCCACAAGTTAGGGGCAACC-TTTCAA
*
1896237 AAGCCCACAAG-TCGGTGGCAACCTTT-AA
1 AAGCCCACAAGTTAGG-GGCAACCTTTCAA
* *
1896265 AAGCCCACAAGTCAGTGGCAACC-TTCAA
1 AAGCCCACAAGTTAGGGGCAACCTTTCAA
* * *
1896293 AAGCCCACAACTCAGTGGCAACC-TTCAA
1 AAGCCCACAAGTTAGGGGCAACCTTTCAA
* **
1896321 AAGCACACAAGTT-GATGCAACCCTTTCAA
1 AAGCCCACAAGTTAGGGGCAA-CCTTTCAA
*
1896350 AAGTCCACA
1 AAGCCCACA
1896359 CCAGTTGGTG
Statistics
Matches: 103, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
27 7 0.07
28 61 0.59
29 19 0.18
30 16 0.16
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.18
Consensus pattern (29 bp):
AAGCCCACAAGTTAGGGGCAACCTTTCAA
Found at i:1896273 original size:28 final size:28
Alignment explanation
Indices: 1896232--1896332 Score: 166
Period size: 28 Copynumber: 3.6 Consensus size: 28
1896222 GGGCACCCTT
*
1896232 TTCAAAAGCCCACAAGTCGGTGGCAACC
1 TTCAAAAGCCCACAAGTCAGTGGCAACC
*
1896260 TTTAAAAGCCCACAAGTCAGTGGCAACC
1 TTCAAAAGCCCACAAGTCAGTGGCAACC
*
1896288 TTCAAAAGCCCACAACTCAGTGGCAACC
1 TTCAAAAGCCCACAAGTCAGTGGCAACC
*
1896316 TTCAAAAGCACACAAGT
1 TTCAAAAGCCCACAAGT
1896333 TGATGCAACC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 67 1.00
ACGTcount: A:0.37, C:0.31, G:0.17, T:0.16
Consensus pattern (28 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACC
Found at i:1896345 original size:28 final size:29
Alignment explanation
Indices: 1896232--1896358 Score: 147
Period size: 28 Copynumber: 4.5 Consensus size: 29
1896222 GGGCACCCTT
*
1896232 TTCAAAAGCCCACAAG-TCGGTGGCAACC
1 TTCAAAAGCCCACAAGTTCAGTGGCAACC
*
1896260 TTTAAAAGCCCACAAG-TCAGTGGCAACC
1 TTCAAAAGCCCACAAGTTCAGTGGCAACC
*
1896288 TTCAAAAGCCCACAA-CTCAGTGGCAACC
1 TTCAAAAGCCCACAAGTTCAGTGGCAACC
* *
1896316 TTCAAAAGCACACAAGTTGA-T-GCAACCC
1 TTCAAAAGCCCACAAGTTCAGTGGCAA-CC
*
1896344 TTTCAAAAGTCCACA
1 -TTCAAAAGCCCACA
1896359 CCAGTTGGTG
Statistics
Matches: 87, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
27 4 0.05
28 69 0.79
29 14 0.16
ACGTcount: A:0.36, C:0.31, G:0.16, T:0.17
Consensus pattern (29 bp):
TTCAAAAGCCCACAAGTTCAGTGGCAACC
Found at i:1896472 original size:21 final size:21
Alignment explanation
Indices: 1896448--1896556 Score: 78
Period size: 21 Copynumber: 5.1 Consensus size: 21
1896438 ATATCGCTGG
1896448 CCTTGAATCAGCATATTGACA
1 CCTTGAATCAGCATATTGACA
* * ***
1896469 CCTTGAAGTCCG-ATATCGTTGG
1 CCTTGAA-TCAGCATATTG-ACA
1896491 CCTTGAATCAGCATATTGACA
1 CCTTGAATCAGCATATTGACA
* * ***
1896512 CCTTGAAGTCCG-ATATCGTTGG
1 CCTTGAA-TCAGCATATTG-ACA
1896534 CCTTGAATCAGCATATTGACA
1 CCTTGAATCAGCATATTGACA
1896555 CC
1 CC
1896557 GGCATCTTTA
Statistics
Matches: 62, Mismatches: 20, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
21 32 0.52
22 30 0.48
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGACA
Found at i:1896496 original size:22 final size:22
Alignment explanation
Indices: 1896469--1896540 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
1896459 CATATTGACA
1896469 CCTTGAAGTCCGATATCGTTGG
1 CCTTGAAGTCCGATATCGTTGG
* * ***
1896491 CCTTGAA-TCAGCATATTG-ACA
1 CCTTGAAGTCCG-ATATCGTTGG
1896512 CCTTGAAGTCCGATATCGTTGG
1 CCTTGAAGTCCGATATCGTTGG
1896534 CCTTGAA
1 CCTTGAA
1896541 TCAGCATATT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
21 15 0.41
22 22 0.59
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (22 bp):
CCTTGAAGTCCGATATCGTTGG
Found at i:1896499 original size:43 final size:43
Alignment explanation
Indices: 1896438--1896556 Score: 229
Period size: 43 Copynumber: 2.8 Consensus size: 43
1896428 TTTAAACCCA
*
1896438 ATATCGCTGGCCTTGAATCAGCATATTGACACCTTGAAGTCCG
1 ATATCGTTGGCCTTGAATCAGCATATTGACACCTTGAAGTCCG
1896481 ATATCGTTGGCCTTGAATCAGCATATTGACACCTTGAAGTCCG
1 ATATCGTTGGCCTTGAATCAGCATATTGACACCTTGAAGTCCG
1896524 ATATCGTTGGCCTTGAATCAGCATATTGACACC
1 ATATCGTTGGCCTTGAATCAGCATATTGACACC
1896557 GGCATCTTTA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (43 bp):
ATATCGTTGGCCTTGAATCAGCATATTGACACCTTGAAGTCCG
Found at i:1896549 original size:22 final size:21
Alignment explanation
Indices: 1896438--1896549 Score: 75
Period size: 22 Copynumber: 5.2 Consensus size: 21
1896428 TTTAAACCCA
1896438 ATATCGCTGGCCTTGAATCAGC
1 ATATCG-TGGCCTTGAATCAGC
* *** *
1896460 ATATTGACACCTTGAAGTCCG-
1 ATATCGTGGCCTTGAA-TCAGC
1896481 ATATCGTTGGCCTTGAATCAGC
1 ATATCG-TGGCCTTGAATCAGC
* *** *
1896503 ATATTGACACCTTGAAGTCCG-
1 ATATCGTGGCCTTGAA-TCAGC
1896524 ATATCGTTGGCCTTGAATCAGC
1 ATATCG-TGGCCTTGAATCAGC
1896546 ATAT
1 ATAT
1896550 TGACACCGGC
Statistics
Matches: 64, Mismatches: 20, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
21 30 0.47
22 34 0.53
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (21 bp):
ATATCGTGGCCTTGAATCAGC
Found at i:1897460 original size:19 final size:18
Alignment explanation
Indices: 1897435--1897502 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
1897425 AATTCAACGA
*
1897435 TTTGTATTGATACATAAG
1 TTTGTATCGATACATAAG
1897453 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1897469 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1897485 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
1897503 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 1 0.02
19 26 0.62
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1897473 original size:32 final size:32
Alignment explanation
Indices: 1897437--1897499 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1897427 TTCAACGATT
* *
1897437 TGTATTGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1897469 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1897500 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1897474 original size:13 final size:13
Alignment explanation
Indices: 1897456--1897480 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1897446 ACATAAGTGT
1897456 TGTATCGATACAA
1 TGTATCGATACAA
1897469 TGTATCGATACA
1 TGTATCGATACA
1897481 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1911449 original size:9 final size:9
Alignment explanation
Indices: 1911432--1911525 Score: 122
Period size: 9 Copynumber: 10.4 Consensus size: 9
1911422 CGTCCTCCGC
1911432 AAAAAAACA
1 AAAAAAACA
*
1911441 AAAACAACA
1 AAAAAAACA
1911450 AAAAAAACA
1 AAAAAAACA
1911459 AAAAAAACA
1 AAAAAAACA
1911468 AAAAAAA-A
1 AAAAAAACA
1911476 AAAAAAACA
1 AAAAAAACA
1911485 AAAAAAA-A
1 AAAAAAACA
*
1911493 ACAAAAACA
1 AAAAAAACA
1911502 AAACAAAA-A
1 AAA-AAAACA
1911511 AAACAACAACA
1 AAA-AA-AACA
1911522 AAAA
1 AAAA
1911526 GGGTCCGGAT
Statistics
Matches: 76, Mismatches: 4, Indels: 9
0.85 0.04 0.10
Matches are distributed among these distances:
8 15 0.20
9 50 0.66
10 7 0.09
11 4 0.05
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:1911460 original size:26 final size:24
Alignment explanation
Indices: 1911431--1911525 Score: 113
Period size: 24 Copynumber: 3.8 Consensus size: 24
1911421 GCGTCCTCCG
1911431 CAAAAAAACAAAAACAACAAAAAAAA
1 CAAAAAAA-AAAAACAA-AAAAAAAA
1911457 CAAAAAAAACAAAA-AAAAAAAAAA
1 CAAAAAAAA-AAAACAAAAAAAAAA
*
1911481 -AACAAAAAAAAAACAAAAACAAAA
1 CAA-AAAAAAAAAACAAAAAAAAAA
1911505 CAAAAAAAACAACAACAAAAA
1 CAAAAAAAA-AA-AACAAAAA
1911526 GGGTCCGGAT
Statistics
Matches: 62, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
23 6 0.10
24 29 0.47
25 7 0.11
26 20 0.32
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (24 bp):
CAAAAAAAAAAAACAAAAAAAAAA
Found at i:1911525 original size:1 final size:1
Alignment explanation
Indices: 1911432--1911513 Score: 83
Period size: 1 Copynumber: 82.0 Consensus size: 1
1911422 CGTCCTCCGC
* * * * * * *
1911432 AAAAAAACAAAAACAACAAAAAAAACAAAAAAAACAAAAAAAAAAAAAAAACAAAAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
1911497 AAACAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAA
1911514 CAACAACAAA
Statistics
Matches: 63, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1912996 original size:29 final size:29
Alignment explanation
Indices: 1912957--1913248 Score: 171
Period size: 29 Copynumber: 9.7 Consensus size: 29
1912947 TCACCCTTCA
1912957 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
1912986 AAAGCCCACAAGTTAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1913015 AAAGTCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
** * * *
1913042 AAAGCCCACAAACCAGTGGCACCCATTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * *
1913072 GAAGCCCACAAGTCAGTGGCATCTTCTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1913101 AAAGTCCACAACTCCA-TGGCACTCCTTTTCTTTTG
1 AAAGCCCACAAGT-CAGTGGCA-T-C---T-TTTTC
* * * *
1913136 TAAGCCCACAACTCCGTAGCACTCTTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTT-C
* * * *
1913167 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ---AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
1913199 AAAAACCCACAAGTCAATGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
1913227 AAAAGCCCACAAGTCAGTGGCA
1 -AAAGCCCACAAGTCAGTGGCA
1913249 ACCTTCAAAA
Statistics
Matches: 205, Mismatches: 43, Indels: 31
0.73 0.15 0.11
Matches are distributed among these distances:
27 21 0.10
28 24 0.12
29 68 0.33
30 45 0.22
31 2 0.01
32 1 0.00
33 5 0.02
34 20 0.10
35 19 0.09
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Done.