Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 109 of 427
Found at i:28720247 original size:27 final size:27
Alignment explanation
Indices: 28720217--28720295 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 27
28720207 TAGGTAAAAA
*
28720217 GACCGTAAAGCCCTTGTAGGGTAAAGT
1 GACCGTAAAGCCCCTGTAGGGTAAAGT
28720244 GACCGTAAAGCCCCTGTAGGGTAAAGT
1 GACCGTAAAGCCCCTGTAGGGTAAAGT
* *
28720271 GACCGTAATA-CCACTGTATGGTAAA
1 GACCGTAA-AGCCCCTGTAGGGTAAA
28720296 ATTACGAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
27 47 0.98
28 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (27 bp):
GACCGTAAAGCCCCTGTAGGGTAAAGT
Found at i:28721130 original size:26 final size:26
Alignment explanation
Indices: 28721101--28721275 Score: 246
Period size: 26 Copynumber: 6.8 Consensus size: 26
28721091 GAGGAAGTGC
**
28721101 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* *
28721127 AAAAGGGCTTATGTCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
28721153 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* *
28721179 AAAAGGGCTTATGCCCTAGTCTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
28721205 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
28721231 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
28721256 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28721276 ATTAAAGAGG
Statistics
Matches: 131, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
25 33 0.25
26 98 0.75
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:28721177 original size:52 final size:51
Alignment explanation
Indices: 28721101--28721275 Score: 291
Period size: 52 Copynumber: 3.4 Consensus size: 51
28721091 GAGGAAGTGC
*
28721101 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGTCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATG-CCCAGTTTACCG
*
28721153 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTCTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCC-AGTTTACCG
28721205 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATG-CCCAGTTTACCG
28721256 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28721276 ATTAAAGAGG
Statistics
Matches: 118, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
50 10 0.08
51 23 0.19
52 85 0.72
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCAGTTTACCG
Found at i:28721529 original size:31 final size:31
Alignment explanation
Indices: 28721494--28721602 Score: 164
Period size: 31 Copynumber: 3.5 Consensus size: 31
28721484 GTTTACAGTA
* *
28721494 AAGGCTTCGGCCCAGAGATATGATTTATGGT
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
*
28721525 AAGGCTTCGGCCTAGTGATATGATTTATGAT
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
* * *
28721556 AAGGCTTCGACCCAGTGATATGATTTATAAA
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
28721587 AAGGCTTCGGCCCAGT
1 AAGGCTTCGGCCCAGT
28721603 AACCGTTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (31 bp):
AAGGCTTCGGCCCAGTGATATGATTTATGAT
Found at i:28727721 original size:27 final size:27
Alignment explanation
Indices: 28727691--28727744 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28727681 TCATACAACC
* *
28727691 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
28727718 CATGTAACAATAATTTTCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
28727745 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.41
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:28732165 original size:6 final size:6
Alignment explanation
Indices: 28732154--28732201 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
28732144 AATTGATTAT
* *
28732154 ATTAAA ATTAAA ATTAAA ATTAAA A-TATAA A-TATA ATTAAA AATAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTA-AA ATTAAA ATTAAA ATTAAA
28732201 A
1 A
28732202 AAATATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATTAAA
Found at i:28732196 original size:24 final size:23
Alignment explanation
Indices: 28732165--28732211 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
28732155 TTAAAATTAA
* *
28732165 AATTAAAATTAAAATATAAATAT
1 AATTAAAATAAAAAAATAAATAT
*
28732188 AATTAAAAATAAAAAAATATATAT
1 AATT-AAAATAAAAAAATAAATAT
28732212 TTATTATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AATTAAAATAAAAAAATAAATAT
Found at i:28732796 original size:33 final size:32
Alignment explanation
Indices: 28732688--28732797 Score: 96
Period size: 33 Copynumber: 3.3 Consensus size: 32
28732678 TATTGACTGT
*
28732688 TGGGGAGGGTAATG-ATGAAGGGGTAGAATCTAA
1 TGGGGAGGGTGATGTA-GAAGGGGTAGAATCT-A
* * * **
28732721 TGGTGAAGGTGATCTAGAAATGGTAGAATCTA
1 TGGGGAGGGTGATGTAGAAGGGGTAGAATCTA
* * *
28732753 GTGGGAAGGGTGATGTAGAAGGGGTATAAGCTGA
1 -TGGGGAGGGTGATGTAGAAGGGGTAGAATCT-A
28732787 TGGGGAGGGTG
1 TGGGGAGGGTG
28732798 TGTCTGCTAC
Statistics
Matches: 59, Mismatches: 15, Indels: 6
0.74 0.19 0.08
Matches are distributed among these distances:
32 1 0.02
33 56 0.95
34 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.44, T:0.23
Consensus pattern (32 bp):
TGGGGAGGGTGATGTAGAAGGGGTAGAATCTA
Found at i:28735042 original size:13 final size:13
Alignment explanation
Indices: 28735024--28735053 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28735014 TAGATTTTTC
28735024 CTAAATATTATCA
1 CTAAATATTATCA
*
28735037 CTAAATATTATTA
1 CTAAATATTATCA
28735050 CTAA
1 CTAA
28735054 GTAATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:28739949 original size:14 final size:15
Alignment explanation
Indices: 28739930--28739958 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28739920 TACTCCAGTC
28739930 ACAGATACA-AAATA
1 ACAGATACAGAAATA
28739944 ACAGATACAGAAATA
1 ACAGATACAGAAATA
28739959 TCATGCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.14, G:0.10, T:0.14
Consensus pattern (15 bp):
ACAGATACAGAAATA
Found at i:28740171 original size:18 final size:18
Alignment explanation
Indices: 28740148--28740182 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28740138 AATTTTAAAA
*
28740148 TTATGGGCCCACATGCCC
1 TTATGGACCCACATGCCC
28740166 TTATGGACCCACATGCC
1 TTATGGACCCACATGCC
28740183 TAGATTGGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.23
Consensus pattern (18 bp):
TTATGGACCCACATGCCC
Found at i:28747856 original size:5 final size:5
Alignment explanation
Indices: 28747846--28747872 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28747836 TTTTTAAGGG
28747846 ATTTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT AT
28747873 CTAATTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:28747879 original size:15 final size:15
Alignment explanation
Indices: 28747846--28747880 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28747836 TTTTTAAGGG
* *
28747846 ATTTTATTTTATTTT
1 ATTTTATTTTATCTA
28747861 ATTTTATTTTATCTA
1 ATTTTATTTTATCTA
28747876 ATTTT
1 ATTTT
28747881 TCTTTTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTATTTTATCTA
Found at i:28749203 original size:60 final size:60
Alignment explanation
Indices: 28749106--28749242 Score: 193
Period size: 60 Copynumber: 2.3 Consensus size: 60
28749096 TGACACTAAG
* * * * *
28749106 TGGTGTTTAGGGTTAGATGGGTGTTTCAAACCCCATATAGTGTGTTGGGATGGTCGGAGA
1 TGGTGTGTAGGGTTGGATGGGTATTTCAAACCCCATATAGGGTGTTGGGATGGTCAGAGA
* *
28749166 TGGTGTGTAGGGTTGGATGGGTATTTCAAACCTCATATGGGGTGTTGGGATGGTCAGAGA
1 TGGTGTGTAGGGTTGGATGGGTATTTCAAACCCCATATAGGGTGTTGGGATGGTCAGAGA
*
28749226 TGGTCTGTAGCGGTTGG
1 TGGTGTGTAG-GGTTGG
28749243 GGGTGGAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
60 62 0.91
61 6 0.09
ACGTcount: A:0.18, C:0.09, G:0.39, T:0.33
Consensus pattern (60 bp):
TGGTGTGTAGGGTTGGATGGGTATTTCAAACCCCATATAGGGTGTTGGGATGGTCAGAGA
Found at i:28755319 original size:55 final size:55
Alignment explanation
Indices: 28755248--28755376 Score: 186
Period size: 55 Copynumber: 2.3 Consensus size: 55
28755238 GGTAGGCACG
* *
28755248 GGCATGTCGCACGCCCGTGCTAAATTCTCAATTTCGACCACGGTGTAAAGACACA
1 GGCATGTCGCACGCCCGTGCTAAATTCTCAATTTCAACCACAGTGTAAAGACACA
* * * * **
28755303 GGCGTTTCGCACGCCCGTGCTAAATTCTCAATTTCAACCGCAGTGTAAAGATATG
1 GGCATGTCGCACGCCCGTGCTAAATTCTCAATTTCAACCACAGTGTAAAGACACA
28755358 GGCATGTCGCACGCCCGTG
1 GGCATGTCGCACGCCCGTG
28755377 TTGGTTTGAC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (55 bp):
GGCATGTCGCACGCCCGTGCTAAATTCTCAATTTCAACCACAGTGTAAAGACACA
Found at i:28756050 original size:22 final size:22
Alignment explanation
Indices: 28756019--28756063 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
28756009 CAATTTGTAG
28756019 CCTTCATTCTTCATAGATAGGT
1 CCTTCATTCTTCATAGATAGGT
*
28756041 CCTTCGTTCTTCATAGATAGGT
1 CCTTCATTCTTCATAGATAGGT
28756063 C
1 C
28756064 ATTTGTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (22 bp):
CCTTCATTCTTCATAGATAGGT
Found at i:28760913 original size:46 final size:47
Alignment explanation
Indices: 28760862--28760992 Score: 155
Period size: 46 Copynumber: 2.8 Consensus size: 47
28760852 ATGGTTGAGC
28760862 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T-G
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTC-CTTATGGATG-GAACTAG
* * *
28760909 -TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGA--GATGTAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCCTTATGGATGGAACTA-G
28760954 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTC-CTTATGG
28760993 GCGGGTTACA
Statistics
Matches: 71, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
42 2 0.03
43 5 0.07
45 3 0.04
46 29 0.41
47 29 0.41
48 2 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (47 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCCTTATGGATGGAACTAG
Found at i:28760978 original size:47 final size:46
Alignment explanation
Indices: 28760860--28760985 Score: 152
Period size: 47 Copynumber: 2.7 Consensus size: 46
28760850 GGATGGTTGA
* *
28760860 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GGATGCGAAT
*
28760908 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGA-GATG-TAACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGGATGCGAA-T
28760951 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCG
1 --GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCG
28760986 CTTATGGGCG
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
42 2 0.03
43 5 0.07
45 3 0.04
46 29 0.41
47 30 0.43
48 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGGATGCGAAT
Found at i:28770739 original size:29 final size:30
Alignment explanation
Indices: 28770697--28770754 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
28770687 GGAGGTGGGA
28770697 TGGGAAGGAAGTAAAATTTTAGGGAGAAAG
1 TGGGAAGGAAGTAAAATTTTAGGGAGAAAG
* * *
28770727 TGGG-AGGGAGTAAAATTTTGGGGGGAAA
1 TGGGAAGGAAGTAAAATTTTAGGGAGAAA
28770755 ATAAAAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.21
Consensus pattern (30 bp):
TGGGAAGGAAGTAAAATTTTAGGGAGAAAG
Found at i:28771910 original size:22 final size:22
Alignment explanation
Indices: 28771875--28771928 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
28771865 ATATTTATTA
*
28771875 AATAATGT-ATAACATTCCAGT
1 AATAATATGATAACATTCCAGT
28771896 AATAATATGATAACATTCCAGT
1 AATAATATGATAACATTCCAGT
28771918 AATAATATGAT
1 AATAATATGAT
28771929 CGATAAAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 7 0.23
22 24 0.77
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.33
Consensus pattern (22 bp):
AATAATATGATAACATTCCAGT
Found at i:28772394 original size:22 final size:21
Alignment explanation
Indices: 28772354--28772397 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
28772344 TATTTGTGAA
*
28772354 AAAATAAATTTTTAAAAAATT
1 AAAATAAATTTATAAAAAATT
*
28772375 AAAATAAATTTAATATAAAATT
1 AAAATAAATTT-ATAAAAAATT
28772397 A
1 A
28772398 TCAATATACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATAAATTTATAAAAAATT
Found at i:28772718 original size:16 final size:16
Alignment explanation
Indices: 28772697--28772739 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
28772687 TTTATGCTCA
*
28772697 TTTGTTTATTTTCAAG
1 TTTGTTTATTTTCAAC
*
28772713 TTTGTTTATGTTCAAC
1 TTTGTTTATTTTCAAC
28772729 TTGTGTTTATT
1 TT-TGTTTATT
28772740 AAGAACTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.16, C:0.07, G:0.14, T:0.63
Consensus pattern (16 bp):
TTTGTTTATTTTCAAC
Found at i:28772737 original size:17 final size:16
Alignment explanation
Indices: 28772685--28772738 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
28772675 CAGACTTGAA
*
28772685 TGTTTATGCTC-A-TT
1 TGTTTATGTTCAACTT
* *
28772699 TGTTTATTTTCAAGTT
1 TGTTTATGTTCAACTT
28772715 TGTTTATGTTCAACTT
1 TGTTTATGTTCAACTT
28772731 GTGTTTAT
1 -TGTTTAT
28772739 TAAGAACTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 9 0.27
15 1 0.03
16 16 0.48
17 7 0.21
ACGTcount: A:0.17, C:0.09, G:0.15, T:0.59
Consensus pattern (16 bp):
TGTTTATGTTCAACTT
Found at i:28787120 original size:16 final size:17
Alignment explanation
Indices: 28787101--28787137 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
28787091 GATATCATTA
28787101 TTTTAATA-T-ATTATAT
1 TTTTAATAGTAATTA-AT
28787117 TTTTAATAGTAATTAAT
1 TTTTAATAGTAATTAAT
28787134 TTTT
1 TTTT
28787138 TTAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 7 0.37
18 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTAATAGTAATTAAT
Found at i:28788601 original size:20 final size:20
Alignment explanation
Indices: 28788578--28788618 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
28788568 TATTCAAGTG
28788578 AGTTTAAATATAAATTTTAA
1 AGTTTAAATATAAATTTTAA
*
28788598 AGTTTACATATAAATTTTAA
1 AGTTTAAATATAAATTTTAA
28788618 A
1 A
28788619 TATTCATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (20 bp):
AGTTTAAATATAAATTTTAA
Found at i:28789076 original size:24 final size:25
Alignment explanation
Indices: 28789045--28789096 Score: 97
Period size: 24 Copynumber: 2.1 Consensus size: 25
28789035 TAATATAAAA
28789045 ATAACAAATGAAAATATATTAT-AT
1 ATAACAAATGAAAATATATTATAAT
28789069 ATAACAAATGAAAATATATTATAAT
1 ATAACAAATGAAAATATATTATAAT
28789094 ATA
1 ATA
28789097 TAACAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (25 bp):
ATAACAAATGAAAATATATTATAAT
Found at i:28799986 original size:30 final size:30
Alignment explanation
Indices: 28799952--28800018 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
28799942 CTATCTATTT
*
28799952 TTAATTTATGCTATTGTACTATTATATTAA
1 TTAATTTATGCTATTATACTATTATATTAA
*
28799982 TTAATTTATGCTCTTATACTATTATATTAA
1 TTAATTTATGCTATTATACTATTATATTAA
28800012 TTAATTT
1 TTAATTT
28800019 TTAATTTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.55
Consensus pattern (30 bp):
TTAATTTATGCTATTATACTATTATATTAA
Found at i:28802237 original size:35 final size:35
Alignment explanation
Indices: 28802193--28802359 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
28802183 TCCTCATTGA
** *
28802193 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* ***
28802228 AATGCCATACCTACATTTTTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
28802268 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
28802303 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
28802338 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
28802360 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 88 0.75
39 3 0.03
40 26 0.22
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:28802276 original size:75 final size:73
Alignment explanation
Indices: 28802188--28802359 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 73
28802178 GGTTTTCCTC
** * * ***
28802188 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTTTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
28802252 TCAGTATGG
65 TCAGTATGG
*
28802261 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
28802326 CTCAGTATGG
64 CTCAGTATGG
28802336 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
28802360 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 57 0.65
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:28805102 original size:19 final size:19
Alignment explanation
Indices: 28805078--28805120 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
28805068 GTATTTTTTT
*
28805078 TTGTTTTTTTGGACTAATG
1 TTGTTTATTTGGACTAATG
* *
28805097 TTGTTTATTTGGATTGATG
1 TTGTTTATTTGGACTAATG
28805116 TTGTT
1 TTGTT
28805121 CGCTTGTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.02, G:0.23, T:0.60
Consensus pattern (19 bp):
TTGTTTATTTGGACTAATG
Found at i:28805545 original size:44 final size:42
Alignment explanation
Indices: 28805451--28805550 Score: 114
Period size: 44 Copynumber: 2.4 Consensus size: 42
28805441 TCCCAAACAG
* * *
28805451 GGTCTTACACGAAA-TTAAATAGATGCCAATGTCCTAGATAT
1 GGTCATACACGAAATTTAAATAGATGCCAACGTCCCAGATAT
* *
28805492 GGT-ATTACACGTAAATTTCAAATCGATGCCAACGTCCCAGATGT
1 GGTCA-TACACG-AAATTT-AAATAGATGCCAACGTCCCAGATAT
28805536 GGTCATACACGAAAT
1 GGTCATACACGAAAT
28805551 CATATATCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
41 9 0.18
42 3 0.06
43 6 0.12
44 30 0.61
45 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (42 bp):
GGTCATACACGAAATTTAAATAGATGCCAACGTCCCAGATAT
Found at i:28809053 original size:21 final size:21
Alignment explanation
Indices: 28809028--28809091 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
28809018 AAAGAAACCT
28809028 ATAAGGGTTGAACAGAAGCTC
1 ATAAGGGTTGAACAGAAGCTC
* * * * * *
28809049 GTAAGAGCTGAACGGAAACCC
1 ATAAGGGTTGAACAGAAGCTC
* *
28809070 ATAAGGGTTAAACTGAAGCTC
1 ATAAGGGTTGAACAGAAGCTC
28809091 A
1 A
28809092 AAAAAGCTAA
Statistics
Matches: 30, Mismatches: 13, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
ATAAGGGTTGAACAGAAGCTC
Found at i:28813166 original size:22 final size:22
Alignment explanation
Indices: 28813141--28813184 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28813131 TATTTATTGC
*
28813141 TATTTAAAAAAATTATATATAA
1 TATTTAAAAAAATTAAATATAA
* *
28813163 TATTTACAAATATTAAATATAA
1 TATTTAAAAAAATTAAATATAA
28813185 AATATTAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TATTTAAAAAAATTAAATATAA
Found at i:28820149 original size:26 final size:26
Alignment explanation
Indices: 28820120--28820227 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
28820110 TGATACAAAT
*
28820120 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28820146 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28820172 TGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28820198 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28820224 TGAT
1 TGAT
28820228 TGGAATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28827889 original size:13 final size:13
Alignment explanation
Indices: 28827871--28827896 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28827861 AAGCCACCTT
28827871 ACACGGGCGTGTC
1 ACACGGGCGTGTC
28827884 ACACGGGCGTGTC
1 ACACGGGCGTGTC
28827897 CCTGTCGAGC
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:0.15, C:0.31, G:0.38, T:0.15
Consensus pattern (13 bp):
ACACGGGCGTGTC
Found at i:28834714 original size:29 final size:29
Alignment explanation
Indices: 28834686--28834787 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
28834676 CCTCCGAGCT
** * * *
28834686 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
28834715 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
28834744 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
28834773 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
28834788 GATCTCGTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:28842571 original size:29 final size:29
Alignment explanation
Indices: 28842543--28842644 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
28842533 CCTCCGAGCT
** * * *
28842543 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
28842572 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
28842601 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
28842630 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
28842645 GATCTCGTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:28847060 original size:41 final size:41
Alignment explanation
Indices: 28847015--28847132 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
28847005 TGAAAGATAA
28847015 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
28847056 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
28847086 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
28847127 ATGTAG
1 ATGTAG
28847133 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:28847071 original size:71 final size:71
Alignment explanation
Indices: 28846983--28847146 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
28846973 GAGATGTATC
28846983 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
28847048 AGGACA
66 AGGACA
28847054 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
28847119 AGGACA
66 AGGACA
28847125 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
28847147 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:28854651 original size:16 final size:16
Alignment explanation
Indices: 28854630--28854662 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28854620 TGTGCTCTTT
*
28854630 TGGCAACTCAAGTTTG
1 TGGCAACTCAAATTTG
28854646 TGGCAACTCAAATTTG
1 TGGCAACTCAAATTTG
28854662 T
1 T
28854663 AGGCCACCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (16 bp):
TGGCAACTCAAATTTG
Found at i:28859200 original size:22 final size:19
Alignment explanation
Indices: 28859175--28859228 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 19
28859165 TACAAATCAA
*
28859175 ATCTCTAAGATTACAAAATTAT
1 ATCTCTAAGATTAC--AAGT-T
28859197 ATCTTCTAAGATTACAAGTT
1 ATC-TCTAAGATTACAAGTT
28859217 ATCTCTAAGATT
1 ATCTCTAAGATT
28859229 TCATATCTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 9 0.30
20 4 0.13
21 3 0.10
22 3 0.10
23 11 0.37
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (19 bp):
ATCTCTAAGATTACAAGTT
Found at i:28861599 original size:16 final size:15
Alignment explanation
Indices: 28861570--28861600 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
28861560 CTAAATGTTA
28861570 TTTATTTTATATTAT
1 TTTATTTTATATTAT
28861585 TTTATTTTCATATTAT
1 TTTATTTT-ATATTAT
28861601 AAACACTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTTTATATTAT
Found at i:28865157 original size:16 final size:16
Alignment explanation
Indices: 28865132--28865166 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28865122 TCCTAAAAGC
*
28865132 TTTGGAACTTTTAATT
1 TTTGGAACTTGTAATT
*
28865148 TTTGGGACTTGTAATT
1 TTTGGAACTTGTAATT
28865164 TTT
1 TTT
28865167 TATTTTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.06, G:0.17, T:0.57
Consensus pattern (16 bp):
TTTGGAACTTGTAATT
Found at i:28867952 original size:38 final size:40
Alignment explanation
Indices: 28867908--28868082 Score: 157
Period size: 39 Copynumber: 4.5 Consensus size: 40
28867898 TGAAACCAAT
* *
28867908 TACCAGCAC-AAGCCTGCGGGAATTTAAACCCGG-TATAA
1 TACCAGCACGAAGCCTGCGGGACTTTAAGCCCGGATATAA
* * *
28867946 TACCAGCTCGAAGCCTGCGGGACTTT-AGCCCGGACATAT
1 TACCAGCACGAAGCCTGCGGGACTTTAAGCCCGGATATAA
* * * *
28867985 TTCCAGCACGTAGCCTGC-GGACCTTAAGTCCGGATATAA
1 TACCAGCACGAAGCCTGCGGGACTTTAAGCCCGGATATAA
* ** *
28868024 TTCCAGCAC-ATAGCCTGC-GGACCCTAAGTCCGGATATAA
1 TACCAGCACGA-AGCCTGCGGGACTTTAAGCCCGGATATAA
*
28868063 TTCCAGCAC-ATAGCCTGCGG
1 TACCAGCACGA-AGCCTGCGG
28868083 ACCCTAAGTT
Statistics
Matches: 118, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
38 20 0.17
39 97 0.82
40 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.21
Consensus pattern (40 bp):
TACCAGCACGAAGCCTGCGGGACTTTAAGCCCGGATATAA
Found at i:28868023 original size:78 final size:78
Alignment explanation
Indices: 28867937--28868100 Score: 199
Period size: 78 Copynumber: 2.1 Consensus size: 78
28867927 GAATTTAAAC
* * * * *
28867937 CCGG-TATAATACCAGCTCGA-AGCCTGCGGGA-CTTTAGCCCGGACATATTTCCAGCACGTAGC
1 CCGGATATAATACCAGCAC-ATAGCCTGC-GGACCCTAAGCCCGGACATAATTCCAGCACATAGC
*
28867999 CTGCGGACCTTAAGT
64 CTGCGGACCCTAAGT
* * *
28868014 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCCAGCACATAGCCT
1 CCGGATATAATACCAGCACATAGCCTGCGGACCCTAAGCCCGGACATAATTCCAGCACATAGCCT
28868079 GCGGACCCTAAGT
66 GCGGACCCTAAGT
*
28868092 TCGGATATA
1 CCGGATATA
28868101 CATCACTGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
77 8 0.11
78 66 0.89
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (78 bp):
CCGGATATAATACCAGCACATAGCCTGCGGACCCTAAGCCCGGACATAATTCCAGCACATAGCCT
GCGGACCCTAAGT
Found at i:28868083 original size:39 final size:39
Alignment explanation
Indices: 28867975--28868100 Score: 207
Period size: 39 Copynumber: 3.2 Consensus size: 39
28867965 GGACTTTAGC
* * * *
28867975 CCGGACATATTTCCAGCACGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
28868014 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
28868053 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
*
28868092 TCGGATATA
1 CCGGATATA
28868101 CATCACTGAA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:28873904 original size:148 final size:150
Alignment explanation
Indices: 28873714--28874010 Score: 413
Period size: 148 Copynumber: 2.0 Consensus size: 150
28873704 ATTACAATTC
*
28873714 TGAGAGATTTAAAAAAAAAAGAGCGTGTTCTTAGAAGTGTTTTCAAAATAAAAACAAAATCACTT
1 TGAGAGATTTAAAAAAAAAAGAGCGTGTTCTTAAAAGTGTTTTCAAAATAAAAACAAAATCACTT
* * ** * *
28873779 GATCGAGATGTCTAAAAATAATATCCCATGAATCCTAGGATATCTGAAAAATGATGAT-AGGGAT
66 GACCGAGATGTCTAAAAATAACA-CCCAAAAATCCCAGGATATCTGAAAAATGAAGATCA-GGAT
* *
28873843 TCTTGGGTTCTGGAAACTTTTT
129 TCCTAGGTTCTGGAAACTTTTT
* *
28873865 TGAGAGATTT-TAAAAAAAA-A-TGTGTTCTTAAAAGTGTTTTCAAAATAAAAACAAAATCACTT
1 TGAGAGATTTAAAAAAAAAAGAGCGTGTTCTTAAAAGTGTTTTCAAAATAAAAACAAAATCACTT
* * * *
28873927 GACCGAGATGTTTGAAAATAACACCCAAAAATCCCGGGATATCTGGAAAATGAAGATCAGGATTC
66 GACCGAGATGTCTAAAAATAACACCCAAAAATCCCAGGATATCTGAAAAATGAAGATCAGGATTC
28873992 CTAGGTTCTGGAAACTTTT
131 CTAGGTTCTGGAAACTTTT
28874011 CATGGGGGTT
Statistics
Matches: 130, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
147 51 0.39
148 60 0.46
149 1 0.01
150 8 0.06
151 10 0.08
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (150 bp):
TGAGAGATTTAAAAAAAAAAGAGCGTGTTCTTAAAAGTGTTTTCAAAATAAAAACAAAATCACTT
GACCGAGATGTCTAAAAATAACACCCAAAAATCCCAGGATATCTGAAAAATGAAGATCAGGATTC
CTAGGTTCTGGAAACTTTTT
Found at i:28881032 original size:12 final size:12
Alignment explanation
Indices: 28881015--28881047 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
28881005 GGTCGAATTA
28881015 GGTTAATCGGTC
1 GGTTAATCGGTC
28881027 GGTTAATCGGTC
1 GGTTAATCGGTC
28881039 GGTTAATCG
1 GGTTAATCG
28881048 AATTAATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.15, G:0.33, T:0.33
Consensus pattern (12 bp):
GGTTAATCGGTC
Found at i:28881268 original size:18 final size:18
Alignment explanation
Indices: 28881245--28881282 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
28881235 AATATATATT
28881245 AACCCAAGTATCCAACCC
1 AACCCAAGTATCCAACCC
*
28881263 AACCCAATTATCCAACCC
1 AACCCAAGTATCCAACCC
28881281 AA
1 AA
28881283 TCATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.42, G:0.03, T:0.13
Consensus pattern (18 bp):
AACCCAAGTATCCAACCC
Found at i:28881349 original size:20 final size:20
Alignment explanation
Indices: 28881311--28881349 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28881301 ATTCAATAAA
* **
28881311 TAAAAATATAAATCTAAAAC
1 TAAAAATAAAAATAAAAAAC
28881331 TAAAAATAAAAATAAAAAA
1 TAAAAATAAAAATAAAAAA
28881350 ACATATAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:28881383 original size:9 final size:9
Alignment explanation
Indices: 28881369--28881427 Score: 73
Period size: 9 Copynumber: 6.6 Consensus size: 9
28881359 TTTATACAAA
28881369 TAATTCGGT
1 TAATTCGGT
*
28881378 TAATTCGAT
1 TAATTCGGT
*
28881387 TAATTCGGG
1 TAATTCGGT
*
28881396 TAATTCGGG
1 TAATTCGGT
28881405 TAATTCGGT
1 TAATTCGGT
* *
28881414 TAACTCGAT
1 TAATTCGGT
28881423 TAATT
1 TAATT
28881428 TTATACTTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (9 bp):
TAATTCGGT
Found at i:28881392 original size:18 final size:18
Alignment explanation
Indices: 28881369--28881427 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
28881359 TTTATACAAA
28881369 TAATTCGGTTAATTCGAT
1 TAATTCGGTTAATTCGAT
* **
28881387 TAATTCGGGTAATTCGGG
1 TAATTCGGTTAATTCGAT
*
28881405 TAATTCGGTTAACTCGAT
1 TAATTCGGTTAATTCGAT
28881423 TAATT
1 TAATT
28881428 TTATACTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (18 bp):
TAATTCGGTTAATTCGAT
Found at i:28883562 original size:25 final size:25
Alignment explanation
Indices: 28883534--28883584 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
28883524 ATTCAATCAG
28883534 ATAGAATACAGTCAAATAATCCTAC
1 ATAGAATACAGTCAAATAATCCTAC
*
28883559 ATAGAATATAGTCAAATAATCCTAC
1 ATAGAATACAGTCAAATAATCCTAC
28883584 A
1 A
28883585 CCCAGAACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.25
Consensus pattern (25 bp):
ATAGAATACAGTCAAATAATCCTAC
Found at i:28886203 original size:25 final size:25
Alignment explanation
Indices: 28886175--28886227 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
28886165 TGACTTTTTG
28886175 GATGGGATCTAGGCATTTTTGGGTT
1 GATGGGATCTAGGCATTTTTGGGTT
28886200 GATGGGATCTAGGCATTTTTGGGTT
1 GATGGGATCTAGGCATTTTTGGGTT
28886225 GAT
1 GAT
28886228 ATGTCTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.17, C:0.08, G:0.36, T:0.40
Consensus pattern (25 bp):
GATGGGATCTAGGCATTTTTGGGTT
Found at i:28889290 original size:35 final size:35
Alignment explanation
Indices: 28889247--28889319 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
28889237 TTTTCCCTTT
28889247 TTATTTCATTTGATTACCAAATGACCAAAATGCCC
1 TTATTTCATTTGATTACCAAATGACCAAAATGCCC
28889282 TTATTTCATTTGATTACCAAATGACCAAAATGCCC
1 TTATTTCATTTGATTACCAAATGACCAAAATGCCC
28889317 TTA
1 TTA
28889320 GGGCTTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (35 bp):
TTATTTCATTTGATTACCAAATGACCAAAATGCCC
Found at i:28890057 original size:24 final size:24
Alignment explanation
Indices: 28890007--28890057 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
28889997 TACTGTGTTT
* * * **
28890007 TTTATTTTTTATTTTTATCTCTTA
1 TTTATTTATGATTTTTATATCAAA
28890031 TTTATTTATGATTTTTATATCAAA
1 TTTATTTATGATTTTTATATCAAA
28890055 TTT
1 TTT
28890058 CTTCTTTTAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTATTTATGATTTTTATATCAAA
Found at i:28890095 original size:22 final size:22
Alignment explanation
Indices: 28890053--28890094 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
28890043 TTTTATATCA
*
28890053 AATTTCTTCTTTTACTATTTTC
1 AATTTCTTCTATTACTATTTTC
28890075 AATTTCTTC-ATTACTATTTT
1 AATTTCTTCTATTACTATTTT
28890095 TTTTCTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (22 bp):
AATTTCTTCTATTACTATTTTC
Found at i:28893640 original size:891 final size:893
Alignment explanation
Indices: 28891399--28894972 Score: 6827
Period size: 892 Copynumber: 4.0 Consensus size: 893
28891389 AAGCCATATT
* * *
28891399 TATAGTTCGAGGAGTAAAGGAGTAGACAATTTTGTCGTAGAAGACTAACACGACCCCACATGAGG
1 TATAGTTCGAGGAGTAAAGGAGTAGACAATTTTATCGTAGAAGACTAGCACAACCCCACATGAGG
* *
28891464 TTGCGACTAGGAGTATATGCGTCAAGTTCATAATCATCAGCTCCAACCCATAATTCTATATTGAT
66 TTGCGACTAGGAGTATATGCGTCAAGTTCATCATCATCAGCTCCAACCCATAATTTTATATTGAT
*
28891529 GGGTGCACCGCCTCCCAGTTAGTATGGCTCATATTTTTCTGGTGTTTTTACTAACACTATGTTTT
131 GGGTGCACCACCTCCCAGTTAGTATGGCTCATATTTTTCTGGTGTTTTTACTAACACTATGTTTT
* * *
28891594 TCACACAAGCGCCACATTATGCACTAGTATACTATGCATCAACACCTTCTTCAGGAATATATTTT
196 TCACACAAGCGCCACATTATGCACCAGTATACCATGCATCAACACCTTCTTTAGGAATATA-TTT
*
28891659 TTGCACCACCTTCATCCATAGGAACATATTACCTGCCATTGTTGTCAACAACACCAATGTATATG
260 TTGCACCACCTTCATCCATAGGAACATATTACATGCCATTGTTGTCAACAACACCAATGTATATG
28891724 TCATTACATACAATTCCAACATTCTATGCACAACTAGGTTTTTTGACACCATATACTCCTTCGTC
325 TCATTACATACAATTCCAACATTCTATGCACAACTAGGTTTTTTGACACCATATACTCCTTCGTC
28891789 AATAGTGTTGCAAACACCCCCAAAATCACTGTTCTTCAAAGGTGGGTTATCTTCTCAACCACCTA
390 AATAGTGTTGCAAACACCCCCAAAATCACTGTTCTTCAAAGGTGGGTTATCTTCTCAACCACCTA
28891854 TTAATACAACCGAAGATATATGATGACAACCTAGGATGCAAATACAATCTAGCACGAAAGAACAA
455 TTAATACAACCGAAGATATATGATGACAACCTAGGATGCAAATACAATCTAGCACGAAAGAACAA
*
28891919 GATGAAGATGAAGATAGTGTTAGAGATAAAGATAAATATGAAGATCAAGATAGAGGTTAGAGATA
520 GATGAAGATGAAGATAGTGTTAGAGATAAAGATAAATATGAAGATCAAGATAGAGATTAGAGATA
*
28891984 GAAGTGAAGATGAAGATGATGAGCCAGAACTTTGACCACGACGGAATACTCCTCGTAACTAACAC
585 GAAGTGAAGATGAAGATGAAGAGCCAGAACTTTGACCACGACGGAATACTCCTCGTAACTAACAC
28892049 CCACAGGGTTATCGCACACATTTGGGTTGACGAATGAGATAACTTTCTAATTTAAATTTCTGTCA
650 CCACAGGGTTATCGCACACATTTGGGTTGACGAATGAGATAACTTTCTAATTTAAATTTCTGTCA
* *
28892114 TGTACATCATCATTTAGTTTGTTAACTTTTAATTTTTATTGTATCGATTTTTTACATCCATAATC
715 TGTACATCATCATTTAGTTTGTTAACTTTGAATTTTTATTCTATCGATTTTTTACATCCATAATC
28892179 GACTTATTCACATTATATAAAAAAATGTTTGTTTA-TTTTTCATTTTGGATGCTTATAAAAAAAA
780 GACTTATTCACATTATATAAAAAAATGTTTGTTTATTTTTTCATTTTGGATGCTTATAAAAAAAA
28892243 AGAACAAATTGTTTGTATTGTATGTTGTAATTAATTTTTACATCAATAA
845 AGAACAAATTGTTTGTATTGTATGTTGTAATTAATTTTTACATCAATAA
28892292 TATAGTTCGAGGAGTAAAGGAGTAGACAATTTTATCGTAGAAGACTAGCACAACCCCACATGAGG
1 TATAGTTCGAGGAGTAAAGGAGTAGACAATTTTATCGTAGAAGACTAGCACAACCCCACATGAGG
28892357 TTGCGACTAGGAGTATATGCGTCAAGTTCATCATCATCAGCTCCAACCCATAATTTTATATTGAT
66 TTGCGACTAGGAGTATATGCGTCAAGTTCATCATCATCAGCTCCAACCCATAATTTTATATTGAT
28892422 GGGTGCACCACCTCCCAGTTAGTATGGCTCATATTTTTCTGGTGTTTTTACTAACACTATGTTTT
131 GGGTGCACCACCTCCCAGTTAGTATGGCTCATATTTTTCTGGTGTTTTTACTAACACTATGTTTT
28892487 TCACACAAGCGCCACATTATGCACCAGTATACCATGCATCAACACCTTCTTTAGGAATATATTTT
196 TCACACAAGCGCCACATTATGCACCAGTATACCATGCATCAACACCTTCTTTAGGAATATATTTT
28892552 TGCACCACCTTCATCCATAGGAACATATTACATGCCATTGTTGTCAACAACACCAATGTATATGT
261 TGCACCACCTTCATCCATAGGAACATATTACATGCCATTGTTGTCAACAACACCAATGTATATGT
28892617 CATTACATACAATTCCAACATTCTATGCACAACTAGGTTTTTTGACACCATATACTCCTTCGTCA
326 CATTACATACAATTCCAACATTCTATGCACAACTAGGTTTTTTGACACCATATACTCCTTCGTCA
28892682 ATAGTGTTGCAAACACCCCCAAAATCACTGTTCTTCAAAGGTGGGTTATCTTCTCAACCACCTAT
391 ATAGTGTTGCAAACACCCCCAAAATCACTGTTCTTCAAAGGTGGGTTATCTTCTCAACCACCTAT
28892747 TAATACAACCGAAGATATATGATGACAACCTAGGATGCAAATACAATCTAGCACGAAAGAACAAG
456 TAATACAACCGAAGATATATGATGACAACCTAGGATGCAAATACAATCTAGCACGAAAGAACAAG
28892812 ATGAAGATGAAGATAGTGTTAGAGATAAAGATAAATATGAAGATCAAGATAGAGATTAGAGATAG
521 ATGAAGATGAAGATAGTGTTAGAGATAAAGATAAATATGAAGATCAAGATAGAGATTAGAGATAG
28892877 AAGTGAAGATGAAGATGAAGAGCCAGAACTTTGACCACGACGGAATACTCCTCGTAACTAACACC
586 AAGTGAAGATGAAGATGAAGAGCCAGAACTTTGACCACGACGGAATACTCCTCGTAACTAACACC
*
28892942 CACAGGGTTATCGCACACATTTGGGTTGACGAATGAGATAACTTTCTGATTTAAATTTCTGTCAT
651 CACAGGGTTATCGCACACATTTGGGTTGACGAATGAGATAACTTTCTAATTTAAATTTCTGTCAT
28893007 GTACATCATCATTTAGTTTGTTAACTTTGAATTTTTATTCTATCGATTTTTTACATCCATAATCG
716 GTACATCATCATTTAGTTTGTTAACTTTGAATTTTTATTCTATCGATTTTTTACATCCATAATCG
28893072 ACTTATTCACATTATAT-AAAAAATGTTTGTTTATTTTTTCATTTTGGATGCTTAT-AAAAAAAA
781 ACTTATTCACATTATATAAAAAAATGTTTGTTTATTTTTTCATTTTGGATGCTTATAAAAAAAAA
28893135 GAACAAATTGTTTGTATTGTATGTTGTAATTAATTTTTACATCAATAA
846 GAACAAATTGTTTGTATTGTATGTTGTAATTAATTTTTACATCAATAA
28893183 TATAGTTCGAGGAGTAAAGGAGTAGACAATTTTATCGTAGAAGACTAGCACAACCCCACATGAGG
1 TATAGTTCGAGGAGTAAAGGAGTAGACAATTTTATCGTAGAAGACTAGCACAACCCCACATGAGG
28893248 TTGCGACTAGGAGTATATGCGTCAAGTTCATCATCATCAGCTCCAACCCATAATTTTATATTGAT
66 TTGCGACTAGGAGTATATGCGTCAAGTTCATCATCATCAGCTCCAACCCATAATTTTATATTGAT
28893313 GGGTGCACCACCTCCCAGTTAGTATGGCTCATATTTTTCTGGTGTTTTTACTAACACTATGTTTT
131 GGGTGCACCACCTCCCAGTTAGTATGGCTCATATTTTTCTGGTGTTTTTACTAACACTATGTTTT
28893378 TCACACAAGCGCCACATTATGCACCAGTATACCATGCATCAACACCTTCTTTAGGAATATATTTT
196 TCACACAAGCGCCACATTATGCACCAGTATACCATGCATCAACACCTTCTTTAGGAATATATTTT
28893443 TGCACCACCTTCATCCATAGGAACATATTACATGCCATTGTTGTCAACAACACCAATGTATATGT
261 TGCACCACCTTCATCCATAGGAACATATTACATGCCATTGTTGTCAACAACACCAATGTATATGT
28893508 CATTACATACAATTCCAACATTCTATGCACAACTAGGTTTTTTGACACCATATACTCCTTCGTCA
326 CATTACATACAATTCCAACATTCTATGCACAACTAGGTTTTTTGACACCATATACTCCTTCGTCA
28893573 ATAGTGTTGCAAACACCCCCAAAATCACTGTTCTTCAAAGGTGGGTTATCTTCTCAACCACCTAT
391 ATAGTGTTGCAAACACCCCCAAAATCACTGTTCTTCAAAGGTGGGTTATCTTCTCAACCACCTAT
28893638 TAATACAACCGAAGATATATGATGACAACCTAGGATGCAAATACAATCTAGCACGAAAGAACAAG
456 TAATACAACCGAAGATATATGATGACAACCTAGGATGCAAATACAATCTAGCACGAAAGAACAAG
28893703 ATGAAGATGAAGATAGTGTTAGAGATAAAGATAAATATGAAGATCAAGATAGAGATTAGAGATAG
521 ATGAAGATGAAGATAGTGTTAGAGATAAAGATAAATATGAAGATCAAGATAGAGATTAGAGATAG
28893768 AAGTGAAGATGAAGATGAAGAGCCAGAACTTTGACCACGACGGAATACTCCTCGTAACTAACACC
586 AAGTGAAGATGAAGATGAAGAGCCAGAACTTTGACCACGACGGAATACTCCTCGTAACTAACACC
*
28893833 CACAGGGTTATCGCACACATTTGGGTTGACGAATGAGATAACTTTCTGATTTAAATTTCTGTCAT
651 CACAGGGTTATCGCACACATTTGGGTTGACGAATGAGATAACTTTCTAATTTAAATTTCTGTCAT
28893898 GTACATCATCATTTAGTTTGTTAACTTTGAATTTTTATTCTATCGATTTTTTACATCCATAATCG
716 GTACATCATCATTTAGTTTGTTAACTTTGAATTTTTATTCTATCGATTTTTTACATCCATAATCG
28893963 ACTTATTCACATTATATAAAAAAATGTTTGTTTATTTTTTCATTTTGGATGCTTAT-AAAAAAAA
781 ACTTATTCACATTATATAAAAAAATGTTTGTTTATTTTTTCATTTTGGATGCTTATAAAAAAAAA
28894027 GAACAAATTGTTTGTATTGTATGTTGTAATTAATTTTTACATCAATAA
846 GAACAAATTGTTTGTATTGTATGTTGTAATTAATTTTTACATCAATAA
28894075 TATAGTTCGAGGAGTAAAGGAGTAGACAATTTTATCGTAGAAGACTAGCACAACCCCACATGAGG
1 TATAGTTCGAGGAGTAAAGGAGTAGACAATTTTATCGTAGAAGACTAGCACAACCCCACATGAGG
28894140 TTGCGACTAGGAGTATATGCGTCAAGTTCATCATCATCAGCTCCAACCCATAATTTTATATTGAT
66 TTGCGACTAGGAGTATATGCGTCAAGTTCATCATCATCAGCTCCAACCCATAATTTTATATTGAT
28894205 GGGTGCACCACCTCCCAGTTAGTATGGCTCATATTTTTCTGGTGTTTTTACTAACACTATGTTTT
131 GGGTGCACCACCTCCCAGTTAGTATGGCTCATATTTTTCTGGTGTTTTTACTAACACTATGTTTT
28894270 TCACACAAGCGCCACATTATGCACCAGTATACCATGCATCAACACCTTCTTTAGGAATATATTTT
196 TCACACAAGCGCCACATTATGCACCAGTATACCATGCATCAACACCTTCTTTAGGAATATATTTT
28894335 TGCACCACCTTCATCCATAGGAACATATTACATGCCATTGTTGTCAACAACACCAATGTATATGT
261 TGCACCACCTTCATCCATAGGAACATATTACATGCCATTGTTGTCAACAACACCAATGTATATGT
28894400 CATTACATACAATTCCAACATTCTATGCACAACTAGGTTTTTTGACACCATATACTCCTTCGTCA
326 CATTACATACAATTCCAACATTCTATGCACAACTAGGTTTTTTGACACCATATACTCCTTCGTCA
*
28894465 ATAGTGTTGCAAACACCCCCAAAATCACTGTTCTTCAAAGGTGGGTTATCTTCTTAACCACCTAT
391 ATAGTGTTGCAAACACCCCCAAAATCACTGTTCTTCAAAGGTGGGTTATCTTCTCAACCACCTAT
* *
28894530 TAATACAACCGAAGATATATGATGACAACCTATGATGCAAATACAATCTAGCACAAAAGAACAAG
456 TAATACAACCGAAGATATATGATGACAACCTAGGATGCAAATACAATCTAGCACGAAAGAACAAG
* *
28894595 ATGAAGATGAAGACAGTGTTAGAGATAAAGATAAATATGAAGATCAAGATAGAGGTTAGAGATAG
521 ATGAAGATGAAGATAGTGTTAGAGATAAAGATAAATATGAAGATCAAGATAGAGATTAGAGATAG
28894660 AAGTGAAGATGAAGATGAAGAGCCAGAACTTTGACCACGACGGAATACTCCTCGTAACTAACACC
586 AAGTGAAGATGAAGATGAAGAGCCAGAACTTTGACCACGACGGAATACTCCTCGTAACTAACACC
* *
28894725 CACAGGGTTGTGGCACACATTTGGGTTGACGAATGAGATAACTTTCTAATTTAAATTTCTGTCAT
651 CACAGGGTTATCGCACACATTTGGGTTGACGAATGAGATAACTTTCTAATTTAAATTTCTGTCAT
* *
28894790 GTACATCATCATTTAGTTTGTTAACATTT-AATTTGTATTGTATCGATTTTTTACATCCATAATC
716 GTACATCATCATTTAGTTTGTTAAC-TTTGAATTTTTATTCTATCGATTTTTTACATCCATAATC
*
28894854 TACTTATTCACATTATATAAAAAAATGTTTGTTTATTTTTTTCATTTTGGATGCTTATAAAAAAA
780 GACTTATTCACATTATATAAAAAAATGTTTGTTTA-TTTTTTCATTTTGGATGCTTATAAAAAAA
*
28894919 AAGAACAAATTGTTTGTATGGTATGTTGT-ATTGAATTTTTACATCAATAA
844 AAGAACAAATTGTTTGTATTGTATGTTGTAATT-AATTTTTACATCAATAA
28894969 TATA
1 TATA
28894973 TGTATTTACA
Statistics
Matches: 2648, Mismatches: 27, Indels: 11
0.99 0.01 0.00
Matches are distributed among these distances:
891 869 0.33
892 1449 0.55
893 275 0.10
894 55 0.02
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (893 bp):
TATAGTTCGAGGAGTAAAGGAGTAGACAATTTTATCGTAGAAGACTAGCACAACCCCACATGAGG
TTGCGACTAGGAGTATATGCGTCAAGTTCATCATCATCAGCTCCAACCCATAATTTTATATTGAT
GGGTGCACCACCTCCCAGTTAGTATGGCTCATATTTTTCTGGTGTTTTTACTAACACTATGTTTT
TCACACAAGCGCCACATTATGCACCAGTATACCATGCATCAACACCTTCTTTAGGAATATATTTT
TGCACCACCTTCATCCATAGGAACATATTACATGCCATTGTTGTCAACAACACCAATGTATATGT
CATTACATACAATTCCAACATTCTATGCACAACTAGGTTTTTTGACACCATATACTCCTTCGTCA
ATAGTGTTGCAAACACCCCCAAAATCACTGTTCTTCAAAGGTGGGTTATCTTCTCAACCACCTAT
TAATACAACCGAAGATATATGATGACAACCTAGGATGCAAATACAATCTAGCACGAAAGAACAAG
ATGAAGATGAAGATAGTGTTAGAGATAAAGATAAATATGAAGATCAAGATAGAGATTAGAGATAG
AAGTGAAGATGAAGATGAAGAGCCAGAACTTTGACCACGACGGAATACTCCTCGTAACTAACACC
CACAGGGTTATCGCACACATTTGGGTTGACGAATGAGATAACTTTCTAATTTAAATTTCTGTCAT
GTACATCATCATTTAGTTTGTTAACTTTGAATTTTTATTCTATCGATTTTTTACATCCATAATCG
ACTTATTCACATTATATAAAAAAATGTTTGTTTATTTTTTCATTTTGGATGCTTATAAAAAAAAA
GAACAAATTGTTTGTATTGTATGTTGTAATTAATTTTTACATCAATAA
Found at i:28894672 original size:37 final size:36
Alignment explanation
Indices: 28894592--28894680 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 36
28894582 ACAAAAGAAC
*
28894592 AAGATGAAGATGAAGACAGTGTTAGAGATAAAGATA
1 AAGATGAAGATGAAGACAGGGTTAGAGATAAAGATA
* * * *
28894628 AATATGAAGATCAAGATAGAGGTTAGAGATAGAAG-TG
1 AAGATGAAGATGAAGACAG-GGTTAGAGATA-AAGATA
28894665 AAGATGAAGATGAAGA
1 AAGATGAAGATGAAGA
28894681 GCCAGAACTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
36 16 0.36
37 25 0.57
38 3 0.07
ACGTcount: A:0.49, C:0.02, G:0.29, T:0.19
Consensus pattern (36 bp):
AAGATGAAGATGAAGACAGGGTTAGAGATAAAGATA
Found at i:28903910 original size:21 final size:21
Alignment explanation
Indices: 28903880--28903951 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 21
28903870 CACATACGTG
*
28903880 CCCCT-ATTTGTACTTTGGTA
1 CCCCTGATTTGTACTTAGGTA
* * * *
28903900 CCCCTGATTTGCACATACGTG
1 CCCCTGATTTGTACTTAGGTA
* *
28903921 CCCTTG-TTTGTACTTCGGTA
1 CCCCTGATTTGTACTTAGGTA
28903941 CCCCTGATTTG
1 CCCCTGATTTG
28903952 CACAAACATG
Statistics
Matches: 38, Mismatches: 12, Indels: 3
0.72 0.23 0.06
Matches are distributed among these distances:
20 19 0.50
21 19 0.50
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.39
Consensus pattern (21 bp):
CCCCTGATTTGTACTTAGGTA
Found at i:28903912 original size:41 final size:41
Alignment explanation
Indices: 28903867--28904070 Score: 273
Period size: 41 Copynumber: 5.0 Consensus size: 41
28903857 TACTGTTGAG
* * * *
28903867 TTGCACATACGTGCCCCTATTTGTACTTTGGTACCCCTGAT
1 TTGCACAAACATGCCCCTGTTTGTACTTCGGTACCCCTGAT
* * *
28903908 TTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCCTGAT
1 TTGCACAAACATGCCCCTGTTTGTACTTCGGTACCCCTGAT
* * *
28903949 TTGCACAAACATGCCCCTGTTTGTACTTCGGTACCCTTAAA
1 TTGCACAAACATGCCCCTGTTTGTACTTCGGTACCCCTGAT
* * *
28903990 TTGCACAACCATGCCCCTGTTTGTATTTCGGTACCCCTGAC
1 TTGCACAAACATGCCCCTGTTTGTACTTCGGTACCCCTGAT
* *
28904031 TTACACAAACATGCCCCTGTTTGTACTTCGGTACCGCTGA
1 TTGCACAAACATGCCCCTGTTTGTACTTCGGTACCCCTGA
28904071 ATGCACTTTT
Statistics
Matches: 145, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 145 1.00
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.33
Consensus pattern (41 bp):
TTGCACAAACATGCCCCTGTTTGTACTTCGGTACCCCTGAT
Found at i:28905124 original size:14 final size:14
Alignment explanation
Indices: 28905105--28905132 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28905095 TTTCTAGGGC
28905105 CTTGAGGGCTTTAT
1 CTTGAGGGCTTTAT
28905119 CTTGAGGGCTTTAT
1 CTTGAGGGCTTTAT
28905133 TTAGGTACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (14 bp):
CTTGAGGGCTTTAT
Found at i:28906842 original size:46 final size:45
Alignment explanation
Indices: 28906748--28906913 Score: 167
Period size: 46 Copynumber: 3.6 Consensus size: 45
28906738 GTGCTAATGC
28906748 CATGTCCCAGACATGGTCTTACACTAGC--ACATCTCGTAGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTTACATCTCG-AGCCGATG
* * *
28906793 CATGTCCGAGACATGTCTTACACTAGCTTACGTCTCGAGGCCGAAG
1 CATGTCCCAGACATGTCTTACACTAGCTTACATCTCGA-GCCGATG
* * * * * *
28906839 CATGTCCCACACATATCTTACACTAG-TGTTCCTCTCAATGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCT-TACATCTCGA-GCCGATG
*
28906885 CCATGTCCTAGACATGTCTTACACTAGCT
1 -CATGTCCCAGACATGTCTTACACTAGCT
28906914 CACACAAGTG
Statistics
Matches: 100, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
44 13 0.13
45 15 0.15
46 48 0.48
47 23 0.23
48 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTAGCTTACATCTCGAGCCGATG
Found at i:28914416 original size:46 final size:44
Alignment explanation
Indices: 28914327--28914500 Score: 136
Period size: 46 Copynumber: 3.8 Consensus size: 44
28914317 GTATTTCTAT
28914327 GCCGATGCCATGTCCCAGACATGGTCTCACACTGGCACATCTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTCACACTGGCACATCTCG-AG
* **
28914373 GCCGATGCATGTCCCAGACATGTACT-ACATTGGCTTATGTCTCGAG
1 GCCGATGCATGTCCCAGACATGT-CTCACACTGGC--ACATCTCGAG
* * ** * * *
28914419 GCCGAAGCATGTCTCAGACATGTCTTTCACTAGTGCTCATCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTCACACT-G-GCACATCTCGAG
* *
28914465 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGC
1 GCCGATG-CATGTCCCAGACAT-GTCTCACACTGGC
28914501 TCTCATAATG
Statistics
Matches: 103, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
44 9 0.09
45 19 0.18
46 49 0.48
47 15 0.15
48 11 0.11
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (44 bp):
GCCGATGCATGTCCCAGACATGTCTCACACTGGCACATCTCGAG
Found at i:28926603 original size:25 final size:25
Alignment explanation
Indices: 28926575--28926623 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
28926565 TACAGTCTAT
*
28926575 CTATAGTAGTCTT-AGTATATACTAC
1 CTATAGTAAT-TTCAGTATATACTAC
28926600 CTATAGTAATTTCAGTATATACTA
1 CTATAGTAATTTCAGTATATACTA
28926624 TCAAAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (25 bp):
CTATAGTAATTTCAGTATATACTAC
Found at i:28927797 original size:2 final size:2
Alignment explanation
Indices: 28927790--28927817 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28927780 GACCATGTAA
28927790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28927818 CAGTCAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28928673 original size:31 final size:31
Alignment explanation
Indices: 28928638--28928710 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
28928628 TGGAAGGAGA
28928638 AGAAAGAAATGCTAGATTATTTTTCCAGCAG
1 AGAAAGAAATGCTAGATTATTTTTCCAGCAG
28928669 AGAAAGAAATGCTAGATTATTTTTCCAGCAG
1 AGAAAGAAATGCTAGATTATTTTTCCAGCAG
28928700 AGAGAA-AAATG
1 AGA-AAGAAATG
28928711 AATTTTGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 39 0.95
32 2 0.05
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (31 bp):
AGAAAGAAATGCTAGATTATTTTTCCAGCAG
Found at i:28929504 original size:40 final size:41
Alignment explanation
Indices: 28929419--28929648 Score: 207
Period size: 41 Copynumber: 5.7 Consensus size: 41
28929409 TATGCCTCTA
* * * *
28929419 TTTGTACTTCGGCACCCCTGATTTACACATACGTACCCCTG
1 TTTGTACTTCGGTACCCCTGATTTGCACAAACGTGCCCCTG
* ** *
28929460 TTTGTACTT-GGTACCCCTGATTTGCACAAATGTGCCATTA
1 TTTGTACTTCGGTACCCCTGATTTGCACAAACGTGCCCCTG
** *
28929500 TTTGTACTTTAGTACCCCTGAATTGCACAAACGTGCCCCTG
1 TTTGTACTTCGGTACCCCTGATTTGCACAAACGTGCCCCTG
* * * * * *
28929541 TTTGTACTTCGATACCCTTGACTTGCATATACGTG-CCTTG
1 TTTGTACTTCGGTACCCCTGATTTGCACAAACGTGCCCCTG
* * * *
28929581 TTTGTACTTCGGTA-CCCTGGTATTAG-ACAAACATACCCTTG
1 TTTGTACTTCGGTACCCCT-G-ATTTGCACAAACGTGCCCCTG
* *
28929622 TTTGTACTTCGGTACCCTTGACTTGCA
1 TTTGTACTTCGGTACCCCTGATTTGCA
28929649 TATACATGCC
Statistics
Matches: 150, Mismatches: 33, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.02
40 58 0.39
41 86 0.57
42 3 0.02
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (41 bp):
TTTGTACTTCGGTACCCCTGATTTGCACAAACGTGCCCCTG
Found at i:28929585 original size:81 final size:81
Alignment explanation
Indices: 28929411--28929677 Score: 263
Period size: 81 Copynumber: 3.3 Consensus size: 81
28929401 TGTACATATA
** * * * *
28929411 TGCCTCTATTTGTACTTCGGCACCCCTGATTTACACATACGTACCCCTGTTTGTACTT-GGTACC
1 TGCCT-TATTTGTACTTTAGTACCCCTGAATTGCACAAACGTACCCCTGTTTGTACTTCGGTACC
* * * * *
28929475 CCTGATTTGCACAAATG
65 CTTGACTTGCATATACG
* *
28929492 TGCCATTATTTGTACTTTAGTACCCCTGAATTGCACAAACGTGCCCCTGTTTGTACTTCGATACC
1 TGCC-TTATTTGTACTTTAGTACCCCTGAATTGCACAAACGTACCCCTGTTTGTACTTCGGTACC
28929557 CTTGACTTGCATATACG
65 CTTGACTTGCATATACG
* ** * * *
28929574 TGCCTTGTTTGTACTTCGGTA-CCCTGGTATTAG-ACAAACATACCCTTGTTTGTACTTCGGTAC
1 TGCCTTATTTGTACTTTAGTACCCCT-GAATT-GCACAAACGTACCCCTGTTTGTACTTCGGTAC
*
28929637 CCTTGACTTGCATATACA
64 CCTTGACTTGCATATACG
* *
28929655 TGCCCTCTTTGTA-TTTCAGTACC
1 TGCCTTATTTGTACTTT-AGTACC
28929678 TCTTAATGCA
Statistics
Matches: 154, Mismatches: 26, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
80 6 0.04
81 124 0.81
82 24 0.16
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.36
Consensus pattern (81 bp):
TGCCTTATTTGTACTTTAGTACCCCTGAATTGCACAAACGTACCCCTGTTTGTACTTCGGTACCC
TTGACTTGCATATACG
Found at i:28929677 original size:40 final size:40
Alignment explanation
Indices: 28929500--28929677 Score: 148
Period size: 41 Copynumber: 4.4 Consensus size: 40
28929490 TGTGCCATTA
* * * * * *
28929500 TTTGTACTTTAGTACCCCTGAATTGCACAAACGTGCCCCTG
1 TTTGTACTTCAGTACCCTTGACTTGCATATACATG-CCCTG
* *
28929541 TTTGTACTTC-GATACCCTTGACTTGCATATACGTGCCTTG
1 TTTGTACTTCAG-TACCCTTGACTTGCATATACATGCCCTG
* * *
28929581 TTTGTACTTCGGTACCCTGGTA-TTAGACA-A-ACATACCCTTG
1 TTTGTACTTCAGTACCCTTG-ACTT-G-CATATACATGCCC-TG
* *
28929622 TTTGTACTTCGGTACCCTTGACTTGCATATACATGCCCTC
1 TTTGTACTTCAGTACCCTTGACTTGCATATACATGCCCTG
*
28929662 TTTGTATTTCAGTACC
1 TTTGTACTTCAGTACC
28929678 TCTTAATGCA
Statistics
Matches: 113, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
39 2 0.02
40 47 0.42
41 62 0.55
42 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.37
Consensus pattern (40 bp):
TTTGTACTTCAGTACCCTTGACTTGCATATACATGCCCTG
Found at i:28938722 original size:137 final size:138
Alignment explanation
Indices: 28938256--28938814 Score: 807
Period size: 138 Copynumber: 4.1 Consensus size: 138
28938246 AAGAACATAG
**
28938256 ATATAATTAATATATGAATTTGAACCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * *
28938321 AATATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGAAATGAAAATTAGTATTTTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGAAATGAAAATTAATATTCTTT
*
28938386 TAAAAAGA
131 TGAAAAGA
* *
28938394 ATATAATTAATATATGAATTTGATTCACACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * * * *
28938459 AATGTAGACAATTATACTAATTAATTTCGGTTAAAATATAAAATAAATGAAAATTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGAAATGAAAATTAATATTCTTT
28938524 TGAAAAGA
131 TGAAAAGA
* * *
28938532 ATATAATCAATATATGAATTTGATTCATACAAAAAATTATTTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * *
28938597 AATATAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAA-TAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGAAATGAAAATTAATATTCTTT
* *
28938661 TGAACATA
131 TGAAAAGA
* * *
28938669 ATATAATTAATATATGATTTTGATTCATACAAAATATTACTTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * * * * *
28938734 TATATAAATAGA-TATATTAATTAATTTCGGTTAAAATATAAAAGATACGAAAATTAATATTATT
66 AATATAAACA-ATTATATTAATTAATTTCGGTCAAAATATAAAAGAAATGAAAATTAATATTCTT
* *
28938798 TTGGAAAGG
130 TTGAAAAGA
28938807 ATATAATT
1 ATATAATT
28938815 CATTTTTCTA
Statistics
Matches: 374, Mismatches: 45, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
137 122 0.33
138 252 0.67
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.41
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGAAATGAAAATTAATATTCTTT
TGAAAAGA
Found at i:28938813 original size:275 final size:276
Alignment explanation
Indices: 28938255--28938813 Score: 843
Period size: 275 Copynumber: 2.0 Consensus size: 276
28938245 AAAGAACATA
* *
28938255 GATATAATTAATATATGAATTTGAACCATACAAAATATTAATTGTATATATTTTACCGAATTTAT
1 GATATAATCAATATATGAATTTGAACCATACAAAAAATTAATTGTATATATTTTACCGAATTTAT
** * *
28938320 TAATATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGAAATGAAAATTAGTATTTTT
66 TAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGAAATGAAAATTAATATTCTT
28938385 TTAAAAAGAATATAATTAATATATGAATTTGATTCACACAAAATATTAATTGTATATATTTTACT
131 TTAAAAAGAATATAATTAATATATGAATTTGATTCACACAAAATATTAATTGTATATATTTTACT
* * * *
28938450 GAATTTATTAATGTAGACAATTATACTAATTAATTTCGGTTAAAATATAAAATAAATGAAAATTA
196 GAATTTATTAATATAAACAATTATACTAATTAATTTCGGTTAAAATATAAAAGAAACGAAAATTA
*
28938515 ATATTCTTTTGAAAAG
261 ATATTATTTTGAAAAG
* ** *
28938531 AATATAATCAATATATGAATTTGATTCATACAAAAAATTATTTGTATATATTTTACCGAATTTAT
1 GATATAATCAATATATGAATTTGAACCATACAAAAAATTAATTGTATATATTTTACCGAATTTAT
* *
28938596 TAATATAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAA-TAATATTCTT
66 TAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGAAATGAAAATTAATATTCTT
* * * * * *
28938660 TTGAACATAATATAATTAATATATGATTTTGATTCATACAAAATATTACTTGTATATATTTTACT
131 TTAAAAAGAATATAATTAATATATGAATTTGATTCACACAAAATATTAATTGTATATATTTTACT
* * * *
28938725 GAATTTATTTATATAAATAGA-TATATTAATTAATTTCGGTTAAAATATAAAAGATACGAAAATT
196 GAATTTATTAATATAAACA-ATTATACTAATTAATTTCGGTTAAAATATAAAAGAAACGAAAATT
*
28938789 AATATTATTTTGGAAAG
260 AATATTATTTTGAAAAG
28938806 GATATAAT
1 GATATAAT
28938814 TCATTTTTCT
Statistics
Matches: 253, Mismatches: 29, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
275 143 0.57
276 110 0.43
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.41
Consensus pattern (276 bp):
GATATAATCAATATATGAATTTGAACCATACAAAAAATTAATTGTATATATTTTACCGAATTTAT
TAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGAAATGAAAATTAATATTCTT
TTAAAAAGAATATAATTAATATATGAATTTGATTCACACAAAATATTAATTGTATATATTTTACT
GAATTTATTAATATAAACAATTATACTAATTAATTTCGGTTAAAATATAAAAGAAACGAAAATTA
ATATTATTTTGAAAAG
Found at i:28939331 original size:33 final size:33
Alignment explanation
Indices: 28939289--28939355 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
28939279 ATTCTAAGTC
28939289 TAGAGTTTTATCAGAGTTATCTTAGTCTTATTT
1 TAGAGTTTTATCAGAGTTATCTTAGTCTTATTT
28939322 TAGAGTTTTATCAGAGTTATCTTAGTCTTATTT
1 TAGAGTTTTATCAGAGTTATCTTAGTCTTATTT
28939355 T
1 T
28939356 CAAAAGTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (33 bp):
TAGAGTTTTATCAGAGTTATCTTAGTCTTATTT
Found at i:28942406 original size:18 final size:18
Alignment explanation
Indices: 28942385--28942432 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
28942375 TTCTCTTTAG
28942385 TCTCAGCTTCCTCTTCGT
1 TCTCAGCTTCCTCTTCGT
* *
28942403 TCTCAGTTTCCTCTTTGT
1 TCTCAGCTTCCTCTTCGT
28942421 TCTCAGCTTCCT
1 TCTCAGCTTCCT
28942433 TTTAGTTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.06, C:0.35, G:0.10, T:0.48
Consensus pattern (18 bp):
TCTCAGCTTCCTCTTCGT
Found at i:28944007 original size:24 final size:24
Alignment explanation
Indices: 28943976--28944024 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
28943966 TTTTTGGTAG
28943976 AAACAATTATATTATGACAATGTC
1 AAACAATTATATTATGACAATGTC
*
28944000 AAACAATTATATTGTGACAATGTC
1 AAACAATTATATTATGACAATGTC
28944024 A
1 A
28944025 GCTAAGTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (24 bp):
AAACAATTATATTATGACAATGTC
Found at i:28944868 original size:20 final size:20
Alignment explanation
Indices: 28944845--28944889 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
28944835 AAAAAGAAAT
28944845 TAGAAATTATAAAA-TATAAA
1 TAGAAATTA-AAAATTATAAA
*
28944865 TAGATATTAAAAATTATAAA
1 TAGAAATTAAAAATTATAAA
*
28944885 AAGAA
1 TAGAA
28944890 TCAAATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (20 bp):
TAGAAATTAAAAATTATAAA
Found at i:28944955 original size:16 final size:16
Alignment explanation
Indices: 28944917--28944947 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28944907 TCAAAAAAAT
28944917 TATAAATCAACATTAA
1 TATAAATCAACATTAA
*
28944933 TAAAAATCAACATTA
1 TATAAATCAACATTA
28944948 GAATAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (16 bp):
TATAAATCAACATTAA
Found at i:28946195 original size:43 final size:44
Alignment explanation
Indices: 28946114--28946206 Score: 143
Period size: 43 Copynumber: 2.1 Consensus size: 44
28946104 AGTGGCGACA
*
28946114 TTTAACAAGGTTTGTCTACACAAACACCGCTAAAGAACATGACT
1 TTTAACAAGGTTTGTCTACAAAAACACCGCTAAAGAACATGACT
* * *
28946158 TTTAACAAGGTTT-TTTCCAAAAACTCCGCTAAAGAACATGACT
1 TTTAACAAGGTTTGTCTACAAAAACACCGCTAAAGAACATGACT
28946201 TTTAAC
1 TTTAAC
28946207 GGCACTTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 32 0.71
44 13 0.29
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.29
Consensus pattern (44 bp):
TTTAACAAGGTTTGTCTACAAAAACACCGCTAAAGAACATGACT
Found at i:28950670 original size:31 final size:32
Alignment explanation
Indices: 28950611--28950670 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
28950601 AACCCTTCCT
* *
28950611 GCATTAAATCCAACCAAAAAATAACAAATATA
1 GCATGAAATCCAACCAAAAAACAACAAATATA
*
28950643 GCATGAAATCCAACC-AAAAACAGCAAAT
1 GCATGAAATCCAACCAAAAAACAACAAAT
28950671 GTAACATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 11 0.44
32 14 0.56
ACGTcount: A:0.57, C:0.22, G:0.07, T:0.15
Consensus pattern (32 bp):
GCATGAAATCCAACCAAAAAACAACAAATATA
Found at i:28951396 original size:13 final size:14
Alignment explanation
Indices: 28951370--28951398 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28951360 ACTAATGACA
28951370 AATTAAACCATTAT
1 AATTAAACCATTAT
28951384 AATTAAA-CATTAT
1 AATTAAACCATTAT
28951397 AA
1 AA
28951399 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:28956168 original size:29 final size:28
Alignment explanation
Indices: 28956134--28956236 Score: 127
Period size: 29 Copynumber: 3.6 Consensus size: 28
28956124 TAATCGATCA
*
28956134 CGCACACTTAGTGCCATGTGATTTAAGCT
1 CGCACACTTAGTGCCATAT-ATTTAAGCT
* *
28956163 CGCACACATAGTGCCATATAATTTAAGTT
1 CGCACACTTAGTGCCATAT-ATTTAAGCT
28956192 CGCACACTTAGTGCCATACT-TTTCAAGCT
1 CGCACACTTAGTGCCATA-TATTT-AAGCT
*
28956221 TGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
28956237 ATCTTGTCAC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
28 3 0.05
29 61 0.94
30 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTTAAGCT
Found at i:28959775 original size:9 final size:9
Alignment explanation
Indices: 28959761--28959923 Score: 142
Period size: 9 Copynumber: 18.7 Consensus size: 9
28959751 TAACTCTAAT
28959761 TAAGTTATG
1 TAAGTTATG
28959770 TAAGTTATG
1 TAAGTTATG
* * *
28959779 ATATGATATA
1 -TAAGTTATG
*
28959789 T-ATTTATG
1 TAAGTTATG
28959797 T-A-TTATG
1 TAAGTTATG
28959804 TAAGTTATG
1 TAAGTTATG
*
28959813 TAAATTATG
1 TAAGTTATG
*
28959822 TGAGTTATG
1 TAAGTTATG
*
28959831 TGAGTTATG
1 TAAGTTATG
*
28959840 TGAGTTATG
1 TAAGTTATG
*
28959849 TAAGTTATA
1 TAAGTTATG
28959858 TAAGTTATG
1 TAAGTTATG
* *
28959867 TGAGTTATA
1 TAAGTTATG
28959876 TAAGTTATG
1 TAAGTTATG
28959885 TGAA-TTA--
1 T-AAGTTATG
* *
28959892 T-ATTTATA
1 TAAGTTATG
28959900 TAAGTTATG
1 TAAGTTATG
28959909 TAAGTTATG
1 TAAGTTATG
28959918 TAAGTT
1 TAAGTT
28959924 CAAGTATATA
Statistics
Matches: 127, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
5 1 0.01
6 3 0.02
7 7 0.06
8 7 0.06
9 101 0.80
10 8 0.06
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:28960216 original size:29 final size:29
Alignment explanation
Indices: 28960185--28960309 Score: 119
Period size: 29 Copynumber: 4.2 Consensus size: 29
28960175 TTATGGAAAA
*
28960185 AAATTATTTTAATTAAATAATATTTATAA-
1 AAATTATATTAATTAAATAATATTTA-AAC
* *
28960214 AAATTATATTAATTTAATAATATTTAAAT
1 AAATTATATTAATTAAATAATATTTAAAC
* * * *
28960243 AAATTA-ATCCAAATTATATTATTAATTAAACC
1 AAATTATAT--TAATTA-AATAATATTTAAA-C
*
28960275 AAATTATATTAATTAAATAATATTTAAAT
1 AAATTATATTAATTAAATAATATTTAAAC
28960304 AAATTA
1 AAATTA
28960310 ATCCAAATTA
Statistics
Matches: 77, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
28 4 0.05
29 36 0.47
30 14 0.18
31 15 0.19
32 6 0.08
33 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (29 bp):
AAATTATATTAATTAAATAATATTTAAAC
Found at i:28960283 original size:61 final size:62
Alignment explanation
Indices: 28960214--28960329 Score: 216
Period size: 61 Copynumber: 1.9 Consensus size: 62
28960204 ATATTTATAA
*
28960214 AAATTATATTAATTTAATAATATTTAAATAAATTAATCCAAATTATATT-ATTAATTAAACC
1 AAATTATATTAATTAAATAATATTTAAATAAATTAATCCAAATTATATTAATTAATTAAACC
28960275 AAATTATATTAATTAAATAATATTTAAATAAATTAATCCAAATTATATTAATTAA
1 AAATTATATTAATTAAATAATATTTAAATAAATTAATCCAAATTATATTAATTAA
28960330 ATAATATTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
61 48 0.91
62 5 0.09
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (62 bp):
AAATTATATTAATTAAATAATATTTAAATAAATTAATCCAAATTATATTAATTAATTAAACC
Found at i:28960286 original size:19 final size:19
Alignment explanation
Indices: 28960262--28960369 Score: 87
Period size: 19 Copynumber: 5.6 Consensus size: 19
28960252 CAAATTATAT
28960262 TATTAATTAAACCAAATTA
1 TATTAATTAAACCAAATTA
*
28960281 TATTAATTAAA-TAATATTTA
1 TATTAATTAAACCAA-A-TTA
* * *
28960301 AATAAATTAATCCAAATTA
1 TATTAATTAAACCAAATTA
*
28960320 TATTAATTAAA-TAATATT-
1 TATTAATTAAACCAA-ATTA
* *
28960338 TAAATAAGTTAATCCAAATTA
1 T-ATTAA-TTAAACCAAATTA
28960359 TATTAATTAAA
1 TATTAATTAAA
28960370 ATAAGATTGA
Statistics
Matches: 67, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
18 5 0.07
19 34 0.51
20 23 0.34
21 5 0.07
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.41
Consensus pattern (19 bp):
TATTAATTAAACCAAATTA
Found at i:28960295 original size:27 final size:26
Alignment explanation
Indices: 28960237--28960295 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 26
28960227 TTAATAATAT
*
28960237 TTAAATAAATTAATCCAAATTATATTA
1 TTAAAT-AATTAAACCAAATTATATTA
28960264 -T---TAATTAAACCAAATTATATTAA
1 TTAAATAATTAAACCAAATTATATT-A
28960287 TTAAATAAT
1 TTAAATAAT
28960296 ATTTAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
22 18 0.69
23 2 0.08
24 1 0.04
26 1 0.04
27 4 0.15
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (26 bp):
TTAAATAATTAAACCAAATTATATTA
Found at i:28960316 original size:39 final size:39
Alignment explanation
Indices: 28960266--28960369 Score: 190
Period size: 39 Copynumber: 2.7 Consensus size: 39
28960256 TTATATTATT
*
28960266 AATTAAACCAAATTATATTAATTAAATAATATTTAAATA
1 AATTAATCCAAATTATATTAATTAAATAATATTTAAATA
28960305 AATTAATCCAAATTATATTAATTAAATAATATTTAAATA
1 AATTAATCCAAATTATATTAATTAAATAATATTTAAATA
*
28960344 AGTTAATCCAAATTATATTAATTAAA
1 AATTAATCCAAATTATATTAATTAAA
28960370 ATAAGATTGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (39 bp):
AATTAATCCAAATTATATTAATTAAATAATATTTAAATA
Found at i:28960616 original size:24 final size:24
Alignment explanation
Indices: 28960584--28960630 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28960574 TTAACTTAAA
*
28960584 TGATAAAAC-AGACGATAATATTTG
1 TGATAAAACGA-ACGAGAATATTTG
28960608 TGATAAAACGAACGAGAATATTT
1 TGATAAAACGAACGAGAATATTT
28960631 CAATAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.28
Consensus pattern (24 bp):
TGATAAAACGAACGAGAATATTTG
Found at i:28963016 original size:40 final size:40
Alignment explanation
Indices: 28962967--28963044 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
28962957 TTTAGCGGCC
* *
28962967 CTTTTTTAAAAACGCCGCT-ATAGGTCGATCTATAGCGGTG
1 CTTTCTTAAAAACGCCGCTAAT-GCTCGATCTATAGCGGTG
* * *
28963007 CTTTCTTAAAAATGCTGCTAATGCTCGATCTTTAGCGG
1 CTTTCTTAAAAACGCCGCTAATGCTCGATCTATAGCGG
28963045 CGTTTTTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 30 0.94
41 2 0.06
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (40 bp):
CTTTCTTAAAAACGCCGCTAATGCTCGATCTATAGCGGTG
Found at i:28963016 original size:153 final size:155
Alignment explanation
Indices: 28962739--28963051 Score: 409
Period size: 153 Copynumber: 2.0 Consensus size: 155
28962729 ATTGTGGTGT
* * * *
28962739 TTTTTTGAGGAAGCGCCGCTAATGCCACTGAAGCTCAAAATATACGACGTCGTTCTGTTTAATAT
1 TTTTTTGAGGAAGCGCCGCTAATGCCACTGAAGCTCAAAAAAAACGACGTCGTTCTCTTTAATAC
** *
28962804 TTTAGCGGTGTTTTTAAAAAAGCGCGGCTAGAGATCGACCTATAGCGGCGCTTTCTTAAAAACGC
66 TTTAGCGGCCTTTTTAAAAAAGCGCCGCTAGAGATCGACCTATAGCGGCGCTTTCTTAAAAACGC
* *
28962869 CGCTAATGTTGGATCTATT-GCAGCG
131 CGCTAATGCTCGATCT-TTAGCAGCG
* *
28962894 TTTTTTG-GGAAGCGCCGCTAATGCCACTGAAGCT-AAAAAAAACGATGTCGTTCTCTTTAATCC
1 TTTTTTGAGGAAGCGCCGCTAATGCCACTGAAGCTCAAAAAAAACGACGTCGTTCTCTTTAATAC
* * * * * *
28962957 TTTAGCGGCCCTTTTTTAAAAA-CGCCGCTATAGGTCGATCTATAGCGGTGCTTTCTTAAAAATG
66 TTTAGCGG-CCTTTTTAAAAAAGCGCCGCTAGAGATCGACCTATAGCGGCGCTTTCTTAAAAACG
* *
28963021 CTGCTAATGCTCGATCTTTAGCGGCG
130 CCGCTAATGCTCGATCTTTAGCAGCG
28963047 TTTTT
1 TTTTT
28963052 CAAATACTCA
Statistics
Matches: 137, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
152 2 0.01
153 91 0.66
154 37 0.27
155 7 0.05
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (155 bp):
TTTTTTGAGGAAGCGCCGCTAATGCCACTGAAGCTCAAAAAAAACGACGTCGTTCTCTTTAATAC
TTTAGCGGCCTTTTTAAAAAAGCGCCGCTAGAGATCGACCTATAGCGGCGCTTTCTTAAAAACGC
CGCTAATGCTCGATCTTTAGCAGCG
Found at i:28963633 original size:41 final size:41
Alignment explanation
Indices: 28963537--28963719 Score: 235
Period size: 41 Copynumber: 4.5 Consensus size: 41
28963527 TCCAAACGCG
*
28963537 CTATAGCCCTAACCTTTTGTGGCGTTTATGAAAAAAATGTCA
1 CTATAGCCTTAACCTTTTGTGGCGTTTATG-AAAAAATGTCA
* * * *
28963579 TTATAACCTTAACATTTTGTGGTGTTTATGAAAAAATGTCA
1 CTATAGCCTTAACCTTTTGTGGCGTTTATGAAAAAATGTCA
* *
28963620 CTATAGCCCTAACATTTTGTGGCGTTTAT-AAAAAATCGTCA
1 CTATAGCCTTAACCTTTTGTGGCGTTTATGAAAAAAT-GTCA
* * * *
28963661 CTATAGCCTTAACCTTTTGCGGCATTTATGAAAAAA-GCCT
1 CTATAGCCTTAACCTTTTGTGGCGTTTATGAAAAAATGTCA
28963701 CTATAGCCTTAACCTTTTG
1 CTATAGCCTTAACCTTTTG
28963720 CAATGTTTTT
Statistics
Matches: 124, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 28 0.23
41 65 0.52
42 31 0.25
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (41 bp):
CTATAGCCTTAACCTTTTGTGGCGTTTATGAAAAAATGTCA
Found at i:28964214 original size:24 final size:24
Alignment explanation
Indices: 28964186--28964237 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
28964176 TTTCTAAAAG
* *
28964186 ATTTAGTATTTATTAATATAATAT
1 ATTTAGCATTTATTAACATAATAT
*
28964210 ATTTAGCATTTATTAACATAATTT
1 ATTTAGCATTTATTAACATAATAT
28964234 ATTT
1 ATTT
28964238 GACCTACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAACATAATAT
Found at i:28970820 original size:16 final size:17
Alignment explanation
Indices: 28970783--28970820 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
28970773 TCTTTGGAAT
28970783 TTTATTTTTAATTTGGG
1 TTTATTTTTAATTTGGG
* *
28970800 ATTATTTTTGATTT-GG
1 TTTATTTTTAATTTGGG
28970816 TTTAT
1 TTTAT
28970821 AACTGCTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.18, C:0.00, G:0.16, T:0.66
Consensus pattern (17 bp):
TTTATTTTTAATTTGGG
Found at i:28976159 original size:35 final size:35
Alignment explanation
Indices: 28976113--28976181 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
28976103 ATAACCTCTT
28976113 TTAAAATATAAATTTATTAATATATGTAAAAAAAC
1 TTAAAATATAAATTTATTAATATATGTAAAAAAAC
28976148 TTAAAATATAAATTTATTAATATATGTAAAAAAA
1 TTAAAATATAAATTTATTAATATATGTAAAAAAA
28976182 ATTTTCCGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (35 bp):
TTAAAATATAAATTTATTAATATATGTAAAAAAAC
Found at i:28977719 original size:46 final size:46
Alignment explanation
Indices: 28977667--28977835 Score: 184
Period size: 46 Copynumber: 3.7 Consensus size: 46
28977657 CGCCCCTAAA
* * *
28977667 TGAACTCAGACTCAAATCAACGAGCTCGGGCATTCGCATCCATAAG
1 TGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAG
* * * * *
28977713 TGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTT-ACAT--TTCA-
1 TGAACTCAGACTCAACTCAACGAGTTC-G--GAC-A-TTCGCATCCATAAG
28977760 TGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAG
1 TGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAG
*
28977806 TGAACTCGGACTCAACTCAACGAGTTCGGA
1 TGAACTCAGACTCAACTCAACGAGTTCGGA
28977836 TGCACAACCA
Statistics
Matches: 101, Mismatches: 13, Indels: 18
0.77 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 54 0.53
47 27 0.27
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (46 bp):
TGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAG
Found at i:28977780 original size:93 final size:93
Alignment explanation
Indices: 28977666--28977838 Score: 310
Period size: 93 Copynumber: 1.9 Consensus size: 93
28977656 CCGCCCCTAA
*
28977666 ATGAACTCAGACTCAAATCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTC
1 ATGAACTCAGACTCAAATCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
28977731 AACGAGTTCAGATGCCTAGTTACATTTC
66 AACGAGTTCAGATGCCTAGTTACATTTC
* *
28977759 ATGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
1 ATGAACTCAGACTCAAATCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
*
28977824 AACGAGTTCGGATGC
66 AACGAGTTCAGATGC
28977839 ACAACCATCC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (93 bp):
ATGAACTCAGACTCAAATCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
AACGAGTTCAGATGCCTAGTTACATTTC
Found at i:28977854 original size:46 final size:47
Alignment explanation
Indices: 28977661--28977854 Score: 131
Period size: 46 Copynumber: 4.2 Consensus size: 47
28977651 ATAACCCGCC
* * * * **
28977661 CCTAAATGAACTCAGACTCAAATCAACGAGCTCGG--GCA-TTCGCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCACAAC-CAT
*
28977706 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGC-CTAGTTA-CAT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCAC-A---ACCAT
* * * **
28977756 -TTCA-TGAACTCAGACTCAACTCAACGAGTTCGGA--CA-TTCGCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCACAAC-CAT
28977799 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCACAACCAT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCACAACCAT
28977847 CCT-AGTGA
1 CCTAAGTGA
28977855 CATGTCACTT
Statistics
Matches: 114, Mismatches: 18, Indels: 33
0.69 0.11 0.20
Matches are distributed among these distances:
43 3 0.03
45 5 0.04
46 62 0.54
47 29 0.25
48 11 0.10
49 1 0.01
50 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (47 bp):
CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCACAACCAT
Found at i:28978289 original size:30 final size:30
Alignment explanation
Indices: 28978255--28978314 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
28978245 ATTTAATACG
28978255 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
28978285 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
28978315 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:28985275 original size:46 final size:46
Alignment explanation
Indices: 28985208--28985379 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
28985198 TAACCCCCCC
* *
28985208 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* * *
28985254 TAAGTGAACTCGGACTCAACTCAACGAGTTCGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG--GAC--GTTCGCATCCA
* * *
28985301 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
28985346 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28985380 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 87 0.82
47 2 0.02
48 2 0.02
49 3 0.03
50 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
Found at i:28985324 original size:92 final size:93
Alignment explanation
Indices: 28985213--28985382 Score: 306
Period size: 92 Copynumber: 1.8 Consensus size: 93
28985203 CCCCCTAAGT
* *
28985213 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28985278 CGAGTTC-GATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
28985305 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28985370 CGAGTTCGGATGC
66 CGAGTTCGGATGC
28985383 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 69 0.93
93 5 0.07
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:28985832 original size:30 final size:30
Alignment explanation
Indices: 28985798--28985857 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
28985788 ATTTAATACG
28985798 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * * *
28985828 AACTTTTGCATAATTACACTTTTTCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
28985858 GGCTTGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:28986719 original size:7 final size:7
Alignment explanation
Indices: 28986707--28986731 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28986697 ATATGGTAAT
28986707 TCTGGTA
1 TCTGGTA
28986714 TCTGGTA
1 TCTGGTA
28986721 TCTGGTA
1 TCTGGTA
28986728 TCTG
1 TCTG
28986732 ATTATTCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.28, T:0.44
Consensus pattern (7 bp):
TCTGGTA
Found at i:28988253 original size:19 final size:18
Alignment explanation
Indices: 28988231--28988278 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
28988221 TTTATTTAAA
28988231 ATTTTTTGAATAATTTGAT
1 ATTTTTTGAAT-ATTTGAT
* *
28988250 ATTTTAT-AATATTTTAT
1 ATTTTTTGAATATTTGAT
28988267 ATATTTTTGAAT
1 AT-TTTTTGAAT
28988279 TATGTATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 8 0.33
18 7 0.29
19 9 0.38
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (18 bp):
ATTTTTTGAATATTTGAT
Found at i:29005691 original size:7 final size:7
Alignment explanation
Indices: 29005652--29005811 Score: 54
Period size: 7 Copynumber: 22.7 Consensus size: 7
29005642 TTTATTTTAT
29005652 TTTAGGG
1 TTTAGGG
*
29005659 TTTATGG
1 TTTAGGG
* * *
29005666 TCTATGA
1 TTTAGGG
*
29005673 TTTAAGG
1 TTTAGGG
29005680 TTTAGGG
1 TTTAGGG
*
29005687 TTTAGGA
1 TTTAGGG
**
29005694 TTTAGTA
1 TTTAGGG
*
29005701 TTTATGGT
1 TTTA-GGG
*
29005709 TTTAGGT
1 TTTAGGG
* *
29005716 TTTATGT
1 TTTAGGG
*
29005723 TTTATGG
1 TTTAGGG
* *
29005730 TTTATGA
1 TTTAGGG
**
29005737 TTTATAG
1 TTTAGGG
* *
29005744 TTTAAGA
1 TTTAGGG
29005751 TTT-GGAG
1 TTTAGG-G
*
29005758 TTTGGGG
1 TTTAGGG
**
29005765 TTTAATG
1 TTTAGGG
**
29005772 TTTAGAT
1 TTTAGGG
*
29005779 TTTAAGG
1 TTTAGGG
29005786 TTTAGGG
1 TTTAGGG
29005793 TTTA-GG
1 TTTAGGG
29005799 TTTAGAGG
1 TTTAG-GG
29005807 TTTAG
1 TTTAG
29005812 ATAAAAATGC
Statistics
Matches: 117, Mismatches: 31, Indels: 9
0.75 0.20 0.06
Matches are distributed among these distances:
6 7 0.06
7 96 0.82
8 14 0.12
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.51
Consensus pattern (7 bp):
TTTAGGG
Found at i:29005719 original size:22 final size:22
Alignment explanation
Indices: 29005687--29005746 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
29005677 AGGTTTAGGG
29005687 TTTAGGATTTA-GTATTTATGGT
1 TTTAGGATTTATGT-TTTATGGT
*
29005709 TTTAGGTTTTATGTTTTATGG-
1 TTTAGGATTTATGTTTTATGGT
*
29005730 TTTATGATTTATAGTTT
1 TTTAGGATTTAT-GTTT
29005747 AAGATTTGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 10 0.30
22 21 0.64
23 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (22 bp):
TTTAGGATTTATGTTTTATGGT
Found at i:29005741 original size:21 final size:21
Alignment explanation
Indices: 29005659--29005746 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
29005649 TATTTTAGGG
* * * *
29005659 TTTATGGTCTATGATTTAAGG
1 TTTATGGTTTAGGATTTATGT
*
29005680 TTTAGGGTTTAGGATTTA-GT
1 TTTATGGTTTAGGATTTATGT
*
29005700 ATTTATGGTTTTAGGTTTTATGT
1 -TTTATGG-TTTAGGATTTATGT
*
29005723 TTTATGGTTTATGATTTATAGT
1 TTTATGGTTTAGGATTTAT-GT
29005745 TT
1 TT
29005747 AAGATTTGGA
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
20 1 0.02
21 31 0.56
22 21 0.38
23 2 0.04
ACGTcount: A:0.20, C:0.01, G:0.23, T:0.56
Consensus pattern (21 bp):
TTTATGGTTTAGGATTTATGT
Found at i:29005795 original size:21 final size:20
Alignment explanation
Indices: 29005652--29005811 Score: 63
Period size: 21 Copynumber: 7.6 Consensus size: 20
29005642 TTTATTTTAT
* * *
29005652 TTTAGGGTTTATGGTCTATGA
1 TTTAAGGTTTAGGGTTTA-GA
29005673 TTTAAGGTTTAGGGTTTAGGA
1 TTTAAGGTTTAGGGTTTA-GA
* * *
29005694 TTT-AGTATTTATGGTTTTAGGT
1 TTTAAG-GTTTA-GGGTTTA-GA
* * *
29005716 TTTATGTTTTATGGTTTATGA
1 TTTAAGGTTTAGGGTTTA-GA
* * *
29005737 TTTATA-GTTTAAGATTTGGA
1 TTTA-AGGTTTAGGGTTTAGA
** **
29005757 GTTTGGGGTTTAATGTTTAGA
1 -TTTAAGGTTTAGGGTTTAGA
*
29005778 TTTTAAGGTTTAGGGTTTAGG
1 -TTTAAGGTTTAGGGTTTAGA
29005799 TTTAGAGGTTTAG
1 TTTA-AGGTTTAG
29005812 ATAAAAATGC
Statistics
Matches: 103, Mismatches: 29, Indels: 14
0.71 0.20 0.10
Matches are distributed among these distances:
20 8 0.08
21 79 0.77
22 15 0.15
23 1 0.01
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.51
Consensus pattern (20 bp):
TTTAAGGTTTAGGGTTTAGA
Found at i:29006618 original size:41 final size:41
Alignment explanation
Indices: 29006571--29006684 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 41
29006561 ACAAAAGGTA
* *
29006571 AGCAATAGC-AGCATTTTTGTTCCAAATGCCGCAAAAAGTTG
1 AGCAATAGCGA-CATTTTTGGTCCAAACGCCGCAAAAAGTTG
* *
29006612 AGCAATAGCGACGTTTTTGGTCCAAACGCCGCTAAAAGTTG
1 AGCAATAGCGACATTTTTGGTCCAAACGCCGCAAAAAGTTG
** * * *
29006653 AGCAATAATGGCTTTTTTGGTCCAAACACCGC
1 AGCAATAGCGACATTTTTGGTCCAAACGCCGC
29006685 GAATATGTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 62 0.98
42 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (41 bp):
AGCAATAGCGACATTTTTGGTCCAAACGCCGCAAAAAGTTG
Found at i:29008836 original size:93 final size:93
Alignment explanation
Indices: 29008728--29008898 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
29008718 GCCCATAGGT
* * * *
29008728 GAACTCGGACTCAACTCAATGA-TCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGAACTCAACTCAACGAGT-TCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
29008792 ACGAGTTCGGATGCCTAGTTACATTTCAC
65 ACGAGTTCGGATGCCTAGTTACATTTCAC
29008821 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29008886 CGAGTTCGGATGC
66 CGAGTTCGGATGC
29008899 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
93 72 0.99
94 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:29008895 original size:46 final size:46
Alignment explanation
Indices: 29008720--29008895 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 46
29008710 TGTAACCCGC
* * * *
29008720 CCATAGGTGAACTCGGACTCAACTCAATGA-TCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGT-TCGGACATTCGCAT
*
29008766 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * * *
29008816 --TTCA-CGAACTCGAACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
29008859 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
29008896 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 60 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:29009352 original size:30 final size:30
Alignment explanation
Indices: 29009318--29009377 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29009308 ATTTAATATG
29009318 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
29009348 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
29009378 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:29014055 original size:43 final size:44
Alignment explanation
Indices: 29013966--29014082 Score: 114
Period size: 43 Copynumber: 2.7 Consensus size: 44
29013956 TGCTTTTATC
* * * * *
29013966 AAAAACGCAGCTAAAAGTCATTTTCTTTAG-TAGTGTTTGTTAG
1 AAAAACACCGCTAAAGGTCATGTTCTTTAGCTAGTGTTTGTGAG
* *
29014009 AAAAGCACCGCTAAAGGTCATGTTCTTTAGCT-GTGTTTGTGGG
1 AAAAACACCGCTAAAGGTCATGTTCTTTAGCTAGTGTTTGTGAG
* * *
29014052 AAAAACGCCAC-AGAAGGTCATGTTCTATAGC
1 AAAAACACCGCTA-AAGGTCATGTTCTTTAGC
29014083 GGCTTTTTCC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
42 1 0.02
43 59 0.97
44 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (44 bp):
AAAAACACCGCTAAAGGTCATGTTCTTTAGCTAGTGTTTGTGAG
Found at i:29021703 original size:38 final size:38
Alignment explanation
Indices: 29021644--29021751 Score: 189
Period size: 38 Copynumber: 2.8 Consensus size: 38
29021634 TCAATCATGC
*
29021644 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTTCATAAT
*
29021683 ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
29021721 ACTGGGCCGAAGCCTTTTCATATTTCATATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATT
29021752 ACTGGGCCGA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
38 55 0.83
39 11 0.17
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (38 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
Found at i:29021709 original size:31 final size:31
Alignment explanation
Indices: 29021667--29021768 Score: 132
Period size: 31 Copynumber: 3.1 Consensus size: 31
29021657 CCTTTTCATA
29021667 TTTCATATTTCATAATACTGGGCCGAAGCCTTTTCAT
1 TTTCATATTTCATAATACTGGGCCGAAG-C----C-T
29021704 GTTTCATATTTCATAATACTGGGCCGAAGCCT
1 -TTTCATATTTCATAATACTGGGCCGAAGCCT
*
29021736 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
29021767 TT
1 TT
29021769 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
31 32 0.51
32 1 0.02
33 1 0.02
37 1 0.02
38 28 0.44
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:29022005 original size:23 final size:24
Alignment explanation
Indices: 29021960--29022075 Score: 143
Period size: 23 Copynumber: 4.9 Consensus size: 24
29021950 GCTTTATCAT
*
29021960 ATAACTGGAGGCCT-AGCCTCTTT-A
1 ATAACTGG-GGCATAAGCC-CTTTCA
29021984 ATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGGGG-CATAAGCCCTTTCA
*
29022008 ATAACTGGGGCATAAGCCCTTT-T
1 ATAACTGGGGCATAAGCCCTTTCA
*
29022031 ATAACTGGGGCATAAGCCCTTTCG
1 ATAACTGGGGCATAAGCCCTTTCA
29022055 ATAACT-GGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTT
29022076 TTCACTTCCT
Statistics
Matches: 84, Mismatches: 3, Indels: 11
0.86 0.03 0.11
Matches are distributed among these distances:
23 45 0.54
24 39 0.46
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTCA
Found at i:29022038 original size:47 final size:47
Alignment explanation
Indices: 29021960--29022076 Score: 159
Period size: 47 Copynumber: 2.5 Consensus size: 47
29021950 GCTTTATCAT
* *
29021960 ATAACTGGAGGCCT-AGCCTCTTTAATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTATAACTGGGG-CATAAGCCCTTTCA
*
29022008 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTCG
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTCA
29022055 ATAACT-GGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
29022077 TCACTTCCTC
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
46 18 0.28
47 34 0.53
48 12 0.19
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (47 bp):
ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTCA
Found at i:29022152 original size:20 final size:20
Alignment explanation
Indices: 29022127--29022186 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
29022117 TATGATTACC
29022127 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
* *
29022147 TCATGTGCGTATCATACATT
1 TCATGTGCATATCATACATA
29022167 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
29022187 CCATATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:29030004 original size:31 final size:31
Alignment explanation
Indices: 29029962--29030062 Score: 123
Period size: 38 Copynumber: 3.1 Consensus size: 31
29029952 CCTTTTCATA
29029962 TTTCATATTTCATAATACTGGGCCGAAGCCTTTTCAT
1 TTTCATATTTCATAATACTGGGCCGAAG-C----C-T
29029999 GTTTCATATTTCATAATACT-GGCCGAAGCCT
1 -TTTCATATTTCATAATACTGGGCCGAAGCCT
*
29030030 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
29030061 TT
1 TT
29030063 ACTGTAAACG
Statistics
Matches: 61, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
30 18 0.30
31 14 0.23
32 1 0.02
36 1 0.02
37 8 0.13
38 19 0.31
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.40
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:29030032 original size:37 final size:38
Alignment explanation
Indices: 29029939--29030045 Score: 180
Period size: 38 Copynumber: 2.8 Consensus size: 38
29029929 TCAATCATGC
*
29029939 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTTCATAAT
*
29029978 ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
29030016 ACT-GGCCGAAGCCTTTTCATATTTCATATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATT
29030046 ACTGGGCCGA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
37 26 0.40
38 28 0.43
39 11 0.17
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.40
Consensus pattern (38 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
Found at i:29030036 original size:30 final size:31
Alignment explanation
Indices: 29030000--29030062 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
29029990 CCTTTTCATG
29030000 TTTCATATTTCATAATACT-GGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
29030030 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
29030061 TT
1 TT
29030063 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Done.