Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 103 of 210
Found at i:34981876 original size:41 final size:41
Alignment explanation
Indices: 34981819--34981946 Score: 229
Period size: 41 Copynumber: 3.1 Consensus size: 41
34981809 TTTTCACCTT
*
34981819 TCAGGCCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
*
34981860 TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCTGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
34981901 TCAGGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
1 TCA-GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
34981943 TCAG
1 TCAG
34981947 NNNNNNNNNN
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
41 43 0.52
42 40 0.48
ACGTcount: A:0.17, C:0.22, G:0.34, T:0.27
Consensus pattern (41 bp):
TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
Found at i:34981922 original size:42 final size:42
Alignment explanation
Indices: 34981825--34981946 Score: 228
Period size: 42 Copynumber: 2.9 Consensus size: 42
34981815 CCTTTCAGGC
34981825 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA-GGG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGG
*
34981866 CTTTAGCGGCGTTTTTGGAGAAGCGCTGCTAATGCTCAGGGG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGG
34981908 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAG
34981947 NNNNNNNNNN
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
41 37 0.47
42 41 0.53
ACGTcount: A:0.17, C:0.21, G:0.34, T:0.28
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGG
Found at i:34988348 original size:16 final size:16
Alignment explanation
Indices: 34988327--34988382 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
34988317 CGTTTGGTTT
34988327 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
34988343 GCTGTAATTGAATAGA
1 GCTGTAATGGAATAGA
34988359 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
34988375 ACTGTAAT
1 GCTGTAAT
34988383 AGTAATTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:34988415 original size:45 final size:44
Alignment explanation
Indices: 34988361--34988456 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
34988351 TGAATAGAGC
*
34988361 TGTAATGGAATAGAACTGTAATAGTAATTCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAACTGTAATAGT-ATTC-ATGTGTTTGGTCGAA
* *
34988406 TGTAATGGAATAGAATTGTAATAGTATTCTTGTGTTTGGTCGAA
1 TGTAATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTCGAA
*
34988450 TGGAATG
1 TGTAATG
34988457 ATGTTCTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.46
45 24 0.52
ACGTcount: A:0.32, C:0.04, G:0.25, T:0.39
Consensus pattern (44 bp):
TGTAATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTCGAA
Found at i:34988826 original size:105 final size:106
Alignment explanation
Indices: 34988710--34988923 Score: 405
Period size: 105 Copynumber: 2.0 Consensus size: 106
34988700 CTACTTTATT
34988710 ATTTTTAAACTGTAA-ACCATATTTAATATGCTAAAATATCATTAATGAAACAATATTTCACATC
1 ATTTTTAAACTGTAATA-CATATTTAATATGCTAAAATATCATTAATGAAACAATATTTCACATC
34988774 CAAACATAATATTGATAAATTAACAAAAAGTTA-ATGATTTC
65 CAAACATAATATTGATAAATTAACAAAAAGTTACATGATTTC
34988815 ATTTTTAAACTGTAATACATATTTAATATGCTAAAATATCATTAATGAAACAATATTTCACATCC
1 ATTTTTAAACTGTAATACATATTTAATATGCTAAAATATCATTAATGAAACAATATTTCACATCC
34988880 AAACATAATATTGATAAATTAACAAAAAGTTACATGATTTC
66 AAACATAATATTGATAAATTAACAAAAAGTTACATGATTTC
34988921 ATT
1 ATT
34988924 AGTTTAGATG
Statistics
Matches: 107, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
105 95 0.89
106 12 0.11
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (106 bp):
ATTTTTAAACTGTAATACATATTTAATATGCTAAAATATCATTAATGAAACAATATTTCACATCC
AAACATAATATTGATAAATTAACAAAAAGTTACATGATTTC
Found at i:34994075 original size:260 final size:261
Alignment explanation
Indices: 34993614--34994136 Score: 1039
Period size: 260 Copynumber: 2.0 Consensus size: 261
34993604 TGATACCAAG
34993614 TTTTTTGACTGATGAACTTCCGCGTGTTAAGTCACTATTGGTCTATGGCTCATGTGTGGAAGATA
1 TTTTTTGACTGATGAACTTCCGCGTGTTAAGTCACTATTGGTCTATGGCTCATGTGTGGAAGATA
34993679 TTTGTCCCAAGGCAACTGGTTTTATTGCTAAAGAATATTACGAAGTTTAAGAAAATAGTGATTAA
66 TTTGTCCCAAGGCAACTGGTTTTATTGCTAAAGAATATTACGAAGTTTAAGAAAATAGTGATTAA
34993744 TTTATACTAATTTAGTCTAAATTATGTAAACTTTAATATAAAAATAAGAAATATATTTATCAAAA
131 TTTATACTAATTTAGTCTAAATTATGTAAACTTTAATATAAAAATAAGAAATATATTTATCAAAA
34993809 ATTTATATAAAAAATAAAAATTAGATAAAAATGATTTATTTAACTTTATTTTTTTAT-AAATTCT
196 ATTTATATAAAAAATAAAAATTAGATAAAAATGATTTATTTAACTTTATTTTTTTATCAAATTCT
34993873 A
261 A
34993874 TTTTTTGACTGATGAACTTCCGCGTGTTAAGTCACTATTGGTCTATGGCTCATGTGTGGAAGATA
1 TTTTTTGACTGATGAACTTCCGCGTGTTAAGTCACTATTGGTCTATGGCTCATGTGTGGAAGATA
34993939 TTTGTCCCAAGGCAACTGGTTTTATTGCTAAAGAATATTACGAAGTTTAAGAAAATAGTGATTAA
66 TTTGTCCCAAGGCAACTGGTTTTATTGCTAAAGAATATTACGAAGTTTAAGAAAATAGTGATTAA
34994004 TTTATACTAATTTAGTCTAAATTATGTAAACTTTAATATAAAAATAAGAAATATATTTATCAAAA
131 TTTATACTAATTTAGTCTAAATTATGTAAACTTTAATATAAAAATAAGAAATATATTTATCAAAA
34994069 ATTTATATAAAAAATAAAAATTAGATAAAAATGATTTATTTAACTTTATTTTTTTATCAAATTCT
196 ATTTATATAAAAAATAAAAATTAGATAAAAATGATTTATTTAACTTTATTTTTTTATCAAATTCT
34994134 A
261 A
34994135 TT
1 TT
34994137 ATACTATACA
Statistics
Matches: 262, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
260 252 0.96
261 10 0.04
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.40
Consensus pattern (261 bp):
TTTTTTGACTGATGAACTTCCGCGTGTTAAGTCACTATTGGTCTATGGCTCATGTGTGGAAGATA
TTTGTCCCAAGGCAACTGGTTTTATTGCTAAAGAATATTACGAAGTTTAAGAAAATAGTGATTAA
TTTATACTAATTTAGTCTAAATTATGTAAACTTTAATATAAAAATAAGAAATATATTTATCAAAA
ATTTATATAAAAAATAAAAATTAGATAAAAATGATTTATTTAACTTTATTTTTTTATCAAATTCT
A
Found at i:34995335 original size:4 final size:4
Alignment explanation
Indices: 34995326--34995350 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
34995316 ATATATGCAT
34995326 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
34995351 CATATATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:35010140 original size:396 final size:396
Alignment explanation
Indices: 35009408--35010199 Score: 1584
Period size: 396 Copynumber: 2.0 Consensus size: 396
35009398 AATTAGTAAA
35009408 CTCCGGTAATGCCTCGTACCCTATTTCGGTGTCGAATACGGGTAAGGGGTGTTACACATATGGTT
1 CTCCGGTAATGCCTCGTACCCTATTTCGGTGTCGAATACGGGTAAGGGGTGTTACACATATGGTT
35009473 AAAATTTCATGATTATTTGTTAATTTAGGAATGTTATAATATATTATTCATATTTTGTTGTTGAA
66 AAAATTTCATGATTATTTGTTAATTTAGGAATGTTATAATATATTATTCATATTTTGTTGTTGAA
35009538 ATTAAGATTATCGTAAAAGTATGAAAATTGAATTGAATGTTTAAAATGAGTAGAACGCAGGATTG
131 ATTAAGATTATCGTAAAAGTATGAAAATTGAATTGAATGTTTAAAATGAGTAGAACGCAGGATTG
35009603 AGTACGATCATTTCGTGGCAAAGAACGAATTGACGGATAAGACCATGGTTGGACCATGACAATGT
196 AGTACGATCATTTCGTGGCAAAGAACGAATTGACGGATAAGACCATGGTTGGACCATGACAATGT
35009668 TTAAATGTAAGACCATAGCTGAGCTATGGCATTTTAATGAAAAGACCATAACTAGGTTATGACAC
261 TTAAATGTAAGACCATAGCTGAGCTATGGCATTTTAATGAAAAGACCATAACTAGGTTATGACAC
35009733 TATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTGAGACCATAGTTGGGCTATGG
326 TATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTGAGACCATAGTTGGGCTATGG
35009798 CATTCT
391 CATTCT
35009804 CTCCGGTAATGCCTCGTACCCTATTTCGGTGTCGAATACGGGTAAGGGGTGTTACACATATGGTT
1 CTCCGGTAATGCCTCGTACCCTATTTCGGTGTCGAATACGGGTAAGGGGTGTTACACATATGGTT
35009869 AAAATTTCATGATTATTTGTTAATTTAGGAATGTTATAATATATTATTCATATTTTGTTGTTGAA
66 AAAATTTCATGATTATTTGTTAATTTAGGAATGTTATAATATATTATTCATATTTTGTTGTTGAA
35009934 ATTAAGATTATCGTAAAAGTATGAAAATTGAATTGAATGTTTAAAATGAGTAGAACGCAGGATTG
131 ATTAAGATTATCGTAAAAGTATGAAAATTGAATTGAATGTTTAAAATGAGTAGAACGCAGGATTG
35009999 AGTACGATCATTTCGTGGCAAAGAACGAATTGACGGATAAGACCATGGTTGGACCATGACAATGT
196 AGTACGATCATTTCGTGGCAAAGAACGAATTGACGGATAAGACCATGGTTGGACCATGACAATGT
35010064 TTAAATGTAAGACCATAGCTGAGCTATGGCATTTTAATGAAAAGACCATAACTAGGTTATGACAC
261 TTAAATGTAAGACCATAGCTGAGCTATGGCATTTTAATGAAAAGACCATAACTAGGTTATGACAC
35010129 TATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTGAGACCATAGTTGGGCTATGG
326 TATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTGAGACCATAGTTGGGCTATGG
35010194 CATTCT
391 CATTCT
35010200 GATGATAAGA
Statistics
Matches: 396, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
396 396 1.00
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.32
Consensus pattern (396 bp):
CTCCGGTAATGCCTCGTACCCTATTTCGGTGTCGAATACGGGTAAGGGGTGTTACACATATGGTT
AAAATTTCATGATTATTTGTTAATTTAGGAATGTTATAATATATTATTCATATTTTGTTGTTGAA
ATTAAGATTATCGTAAAAGTATGAAAATTGAATTGAATGTTTAAAATGAGTAGAACGCAGGATTG
AGTACGATCATTTCGTGGCAAAGAACGAATTGACGGATAAGACCATGGTTGGACCATGACAATGT
TTAAATGTAAGACCATAGCTGAGCTATGGCATTTTAATGAAAAGACCATAACTAGGTTATGACAC
TATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTGAGACCATAGTTGGGCTATGG
CATTCT
Found at i:35010211 original size:101 final size:100
Alignment explanation
Indices: 35010036--35010341 Score: 441
Period size: 101 Copynumber: 3.0 Consensus size: 100
35010026 AATTGACGGA
* * * *
35010036 TAAGACCATGGTTGGACCATGACAATGTTTAAATGTAAGACCATAGCTGAGCTATGGCATTTTAA
1 TAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGAGCTATGGCATTTTGA
* *
35010101 TGAAAAGACCATAACTAGGTTATGACACTATGAACG
66 TGATAAGACCATAACT-GGTTATGGCACTATGAACG
* * * *
35010137 TAAGACCATGGTTGGACCATGGCAGTGTTTATATGTGAGACCATAGTTGGGCTATGGCATTCTGA
1 TAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGAGCTATGGCATTTTGA
35010202 TGATAAGACCATAACTGGGTTATGGCACTATGAACG
66 TGATAAGACCATAACT-GGTTATGGCACTATGAACG
* * *
35010238 TAAAACCATGGTTGGACCGTGGCAGTGTTTATATGTAAGACCATAGCTGCGCTATGGCATTTTGA
1 TAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGAGCTATGGCATTTTGA
* * *
35010303 TGATAATACCATAACTGGTTTATGGCACTACGAATG
66 TGATAAGACCATAACTGG-TTATGGCACTATGAACG
35010339 TAA
1 TAA
35010342 AGGATGAATT
Statistics
Matches: 184, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
100 2 0.01
101 182 0.99
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (100 bp):
TAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGAGCTATGGCATTTTGA
TGATAAGACCATAACTGGTTATGGCACTATGAACG
Found at i:35010367 original size:24 final size:24
Alignment explanation
Indices: 35010335--35010385 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
35010325 TGGCACTACG
35010335 AATGTAAAGGATGAATTGACGGAA
1 AATGTAAAGGATGAATTGACGGAA
35010359 AATGTAAAGGATGAATTGACGGAA
1 AATGTAAAGGATGAATTGACGGAA
35010383 AAT
1 AAT
35010386 TACCCAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.47, C:0.04, G:0.27, T:0.22
Consensus pattern (24 bp):
AATGTAAAGGATGAATTGACGGAA
Found at i:35024991 original size:21 final size:21
Alignment explanation
Indices: 35024967--35025010 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
35024957 TGGATACTAC
35024967 TGGTCTACTATGGAAGGGGAG
1 TGGTCTACTATGGAAGGGGAG
35024988 TGGTCTACTATGGAAGGGGAG
1 TGGTCTACTATGGAAGGGGAG
35025009 TG
1 TG
35025011 CATAAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.43, T:0.25
Consensus pattern (21 bp):
TGGTCTACTATGGAAGGGGAG
Found at i:35028492 original size:24 final size:25
Alignment explanation
Indices: 35028440--35028498 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
35028430 ATGGCCCTAT
* *
35028440 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTATATAGTTCTTC
*
35028465 CGAGCTTCTCGTTA-ATAGTTCTTC
1 CGAGCTTCCCGTTATATAGTTCTTC
*
35028489 CGAGCATCCC
1 CGAGCTTCCC
35028499 AATTGGTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 16 0.55
25 13 0.45
ACGTcount: A:0.15, C:0.29, G:0.20, T:0.36
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATAGTTCTTC
Found at i:35028747 original size:24 final size:23
Alignment explanation
Indices: 35028683--35028755 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 23
35028673 CTTCCCATTA
*
35028683 ATGGCTCTTCA-GAGCTACCTGTT
1 ATGGCTCTT-ATGAGCTTCCTGTT
**
35028706 ATTGGCTCGCATGAGCTTCCTGATT
1 A-TGGCTCTTATGAGCTTCCTG-TT
*
35028731 ATGGCTCTTATGAGCTTTCTGTT
1 ATGGCTCTTATGAGCTTCCTGTT
35028754 AT
1 AT
35028756 AAAACCCGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
23 6 0.15
24 32 0.78
25 3 0.07
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (23 bp):
ATGGCTCTTATGAGCTTCCTGTT
Found at i:35031135 original size:7 final size:7
Alignment explanation
Indices: 35031125--35031155 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
35031115 TCTTTTATGT
35031125 TCCCTTC
1 TCCCTTC
35031132 TCCCTTC
1 TCCCTTC
35031139 TCCCTTC
1 TCCCTTC
35031146 TCCCTTC
1 TCCCTTC
35031153 TCC
1 TCC
35031156 ATATTCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (7 bp):
TCCCTTC
Found at i:35033103 original size:19 final size:19
Alignment explanation
Indices: 35033071--35033123 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
35033061 TTCTAAAAGC
*
35033071 TTTTTTGAACTTTTTTAAATT
1 TTTTTT-AA-TTTTTTAAATA
*
35033092 TTTTTTTATTTTTTAAATA
1 TTTTTTAATTTTTTAAATA
35033111 TTTTTTAATTTTT
1 TTTTTTAATTTTT
35033124 ATAATTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 22 0.76
20 1 0.03
21 6 0.21
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTTAATTTTTTAAATA
Found at i:35034111 original size:108 final size:107
Alignment explanation
Indices: 35033832--35034111 Score: 341
Period size: 106 Copynumber: 2.6 Consensus size: 107
35033822 GAAACCATAC
* * * * *
35033832 TTTG-AAGTTTTAAGAGGATATTTGGCTATTTAGTCGAACGAGAAATCAAAACCCAGCGCGTTAG
1 TTTGAAAGTTTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAG
* *
35033896 GGCACGTTCTCTCGAATTTCCAAACGCGAAACATTGCCTCGT
66 GGCACGTTCTCTCGAATTTCCAAACGCGAAACATGGCCTCAT
** * * * * * *
35033938 TTT-AGAA-TTTCGAAAGGATATTCGACTATTCGGCCAAACGAGTAATCGAAACCCACCACGTTA
1 TTTGA-AAGTTTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTA
* * * *
35034001 GGGCACGTTTTCTCGAGTTTCCAAACGCGAAATATGGCCTTAT
65 GGGCACGTTCTCTCGAATTTCCAAACGCGAAACATGGCCTCAT
*
35034044 TTTGAAAGTTTTAAAAGGGTATTTGGCTATTTTGGTCAAACGAGAAATCGAAACCCAGCACGTTA
1 TTTGAAAGTTTTAAAAGGATATTTGGCTA-TTTGGTCAAACGAGAAATCGAAACCCAGCACGTTA
35034109 GGG
65 GGG
35034112 TTTTGCTTGG
Statistics
Matches: 141, Mismatches: 28, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
106 88 0.62
107 19 0.13
108 34 0.24
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (107 bp):
TTTGAAAGTTTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAG
GGCACGTTCTCTCGAATTTCCAAACGCGAAACATGGCCTCAT
Found at i:35035199 original size:19 final size:19
Alignment explanation
Indices: 35035167--35035219 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
35035157 TTCTAAAAGC
*
35035167 TTTTTTGAACTTTTTTAAATT
1 TTTTTT-AA-TTTTTTAAATA
*
35035188 TTTTTTTATTTTTTAAATA
1 TTTTTTAATTTTTTAAATA
35035207 TTTTTTAATTTTT
1 TTTTTTAATTTTT
35035220 ATAATTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 22 0.76
20 1 0.03
21 6 0.21
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTTAATTTTTTAAATA
Found at i:35036207 original size:108 final size:107
Alignment explanation
Indices: 35035928--35036367 Score: 580
Period size: 108 Copynumber: 4.1 Consensus size: 107
35035918 GAAACCATAC
* * * * *
35035928 TTTG-AAGTTTTAAGAGGATATTTGGCTATTTAGTCGAACGAGAAATCAAAACCCAGCGCGTTAG
1 TTTGAAAGTTTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAG
* * **
35035992 GGCACGTTCTCTCGAATTTCCAAACGCGAAACATTGCCTCGT
66 GGCACGTTTTCTCGAATTTCCAAACGCGAAACATGGCCTTAT
** * * * * * *
35036034 TTT-AGAA-TTTCGAAAGGATATTCGACTATTCGGCCAAACGAGTAATCGAAACCCACCACGTTA
1 TTTGA-AAGTTTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTA
* *
35036097 GGGCACGTTTTCTCGAGTTTCCAAACGCGAAATATGGCCTTAT
65 GGGCACGTTTTCTCGAATTTCCAAACGCGAAACATGGCCTTAT
*
35036140 TTTGAAAGTTTTAAAAGGGTATTTGGCTATTTTGGTCAAACGAGAAATCGAAACCCAGCACGTTA
1 TTTGAAAGTTTTAAAAGGATATTTGGCTA-TTTGGTCAAACGAGAAATCGAAACCCAGCACGTTA
*
35036205 GGGCACGTTTTCTCGAATTTCCAAACGCGAAATATGGCCTTAT
65 GGGCACGTTTTCTCGAATTTCCAAACGCGAAACATGGCCTTAT
*
35036248 TTTGAAAGTTTTAAAAGGGTATTTGGCTATTTTGGTCAAACGAGAAATCGAAACCCAGCACGTTA
1 TTTGAAAGTTTTAAAAGGATATTTGGCTA-TTTGGTCAAACGAGAAATCGAAACCCAGCACGTTA
* * * *
35036313 GAGCACGTTTTCTCGATTTTCCAAACGCAAAACATTGCCTTAT
65 GGGCACGTTTTCTCGAATTTCCAAACGCGAAACATGGCCTTAT
* *
35036356 TTAGAAAATTTT
1 TTTGAAAGTTTT
35036368 CTTTTTTATG
Statistics
Matches: 293, Mismatches: 36, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
106 88 0.30
107 19 0.06
108 186 0.63
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (107 bp):
TTTGAAAGTTTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAG
GGCACGTTTTCTCGAATTTCCAAACGCGAAACATGGCCTTAT
Found at i:35046337 original size:17 final size:18
Alignment explanation
Indices: 35046294--35046338 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
35046284 ATACGAGTGT
35046294 ATATTTAAAAATAACATA
1 ATATTTAAAAATAACATA
** *
35046312 ATAAATAAAAA-AACGTA
1 ATATTTAAAAATAACATA
35046329 ATATTTAAAA
1 ATATTTAAAA
35046339 TTAATAATCT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (18 bp):
ATATTTAAAAATAACATA
Found at i:35054200 original size:2 final size:2
Alignment explanation
Indices: 35054193--35054224 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35054183 GATGGGTTTA
35054193 AT AT 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 AT AT
35054225 TTAGTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35057581 original size:30 final size:32
Alignment explanation
Indices: 35057527--35057594 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
35057517 TATTTTAGCT
** * *
35057527 AAATTTGGTCATCAAT-CTTTTAAAAAGAGTC
1 AAATTTGACCATCAATCCTTTAAAAAAAAGTC
35057558 AAATTTGACCATC-ATCCTTTAAAAAAAAGTC
1 AAATTTGACCATCAATCCTTTAAAAAAAAGTC
35057589 AAATTT
1 AAATTT
35057595 CTGCGTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (32 bp):
AAATTTGACCATCAATCCTTTAAAAAAAAGTC
Found at i:35058658 original size:122 final size:123
Alignment explanation
Indices: 35058513--35058759 Score: 487
Period size: 122 Copynumber: 2.0 Consensus size: 123
35058503 CAGACATAGC
35058513 ATATGCTTTGAATTCTTGCTTCTTTGAGTCACTATTTAAAAAAATTCAAATAATATAATTGGTAT
1 ATATGCTTTGAATTCTTGCTTCTTTGAGTCACTATTTAAAAAAATTCAAATAATATAATTGGTAT
35058578 ATAATTATTATTTTATTTAAAGAGTTTTAGGTGAAAAAGGATAGAGATT-TCCATATT
66 ATAATTATTATTTTATTTAAAGAGTTTTAGGTGAAAAAGGATAGAGATTATCCATATT
35058635 ATATGCTTTGAATTCTTGCTTCTTTGAGTCACTATTTAAAAAAATTCAAATAATATAATTGGTAT
1 ATATGCTTTGAATTCTTGCTTCTTTGAGTCACTATTTAAAAAAATTCAAATAATATAATTGGTAT
35058700 ATAATTATTATTTTATTTAAAGAGTTTTAGGTGAAAAAGGATAGAGATTATCCATATT
66 ATAATTATTATTTTATTTAAAGAGTTTTAGGTGAAAAAGGATAGAGATTATCCATATT
35058758 AT
1 AT
35058760 CATGATCTAT
Statistics
Matches: 124, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 114 0.92
123 10 0.08
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (123 bp):
ATATGCTTTGAATTCTTGCTTCTTTGAGTCACTATTTAAAAAAATTCAAATAATATAATTGGTAT
ATAATTATTATTTTATTTAAAGAGTTTTAGGTGAAAAAGGATAGAGATTATCCATATT
Found at i:35062964 original size:13 final size:15
Alignment explanation
Indices: 35062937--35062976 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
35062927 ACAGGGAGAA
35062937 AAAGAAA-GA-AAAG
1 AAAGAAAGGAGAAAG
35062950 AAA-AAAGG-GAAAG
1 AAAGAAAGGAGAAAG
35062963 AAAGAAAGGAGAAA
1 AAAGAAAGGAGAAA
35062977 TTAGAGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.13
13 11 0.48
14 5 0.22
15 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (15 bp):
AAAGAAAGGAGAAAG
Found at i:35071578 original size:13 final size:13
Alignment explanation
Indices: 35071562--35071609 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
35071552 GGTAATTGGG
35071562 TTGGGTTGGATAC
1 TTGGGTTGGATAC
*
35071575 TTGGTTTGG--A-
1 TTGGGTTGGATAC
35071585 TTGGGTTGGATAC
1 TTGGGTTGGATAC
35071598 TTGGGTTTGGAT
1 TTGGG-TTGGAT
35071610 TGGGTTAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
10 8 0.28
11 1 0.03
12 1 0.03
13 13 0.45
14 6 0.21
ACGTcount: A:0.12, C:0.04, G:0.40, T:0.44
Consensus pattern (13 bp):
TTGGGTTGGATAC
Found at i:35071578 original size:18 final size:18
Alignment explanation
Indices: 35071539--35071604 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
35071529 ATTTTTATGA
* * *
35071539 TTGGGTTCGGTTGGGTAA
1 TTGGGTTGGGTTGGATAC
35071557 TTGGGTTGGGTTGGATAC
1 TTGGGTTGGGTTGGATAC
35071575 TTGGTTTGGATTGGGTTGGATAC
1 TT-G---GG-TTGGGTTGGATAC
35071598 TTGGGTT
1 TTGGGTT
35071605 TGGATTGGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 19 0.47
19 3 0.08
22 3 0.08
23 15 0.38
ACGTcount: A:0.11, C:0.05, G:0.42, T:0.42
Consensus pattern (18 bp):
TTGGGTTGGGTTGGATAC
Found at i:35071583 original size:23 final size:24
Alignment explanation
Indices: 35071557--35071615 Score: 102
Period size: 23 Copynumber: 2.5 Consensus size: 24
35071547 GGTTGGGTAA
*
35071557 TTGGGTTGGGTTGGATACTT-GGT
1 TTGGATTGGGTTGGATACTTGGGT
35071580 TTGGATTGGGTTGGATACTTGGGT
1 TTGGATTGGGTTGGATACTTGGGT
35071604 TTGGATTGGGTT
1 TTGGATTGGGTT
35071616 AGGTGAATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 19 0.56
24 15 0.44
ACGTcount: A:0.10, C:0.03, G:0.42, T:0.44
Consensus pattern (24 bp):
TTGGATTGGGTTGGATACTTGGGT
Found at i:35077808 original size:25 final size:25
Alignment explanation
Indices: 35077738--35077810 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 25
35077728 CATAGTTCTT
* * *
35077738 ATGAGCATCTCGATATTTGGCTCTC
1 ATGAGCTTCCCGATAATTGGCTCTC
* **
35077763 ACGAGCTTCCTAATTAA-TGGCTCTC
1 ATGAGCTTCCCGA-TAATTGGCTCTC
*
35077788 TTGAGCTTCCCGATAATTGGCTC
1 ATGAGCTTCCCGATAATTGGCTC
35077811 GAATTAGCTT
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
24 3 0.08
25 31 0.86
26 2 0.06
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (25 bp):
ATGAGCTTCCCGATAATTGGCTCTC
Found at i:35084390 original size:25 final size:25
Alignment explanation
Indices: 35084356--35084522 Score: 107
Period size: 24 Copynumber: 6.8 Consensus size: 25
35084346 ATCTTTCATT
35084356 AGCTTCCCGATTAATGGCTCTCTAG
1 AGCTTCCCGATTAATGGCTCTCTAG
* * * *
35084381 AGCTTCCCGA-TATTAGCTCGCTTG
1 AGCTTCCCGATTAATGGCTCTCTAG
* * *
35084405 AATCTTCCCG-TTATTGGCTC-ATATG
1 -AGCTTCCCGATTAATGGCTCTCTA-G
* * *
35084430 AGCTTCCC-ATTAATAGCTCTTTGG
1 AGCTTCCCGATTAATGGCTCTCTAG
* *
35084454 AGCTTCCC-ATTAATAGCTCTCTGG
1 AGCTTCCCGATTAATGGCTCTCTAG
*
35084478 AGCTTCCCG-TTACATGGCTCAC-ATG
1 AGCTTCCCGATTA-ATGGCTCTCTA-G
*
35084503 AGCATCCCG-TTATATGGCTC
1 AGCTTCCCGATTA-ATGGCTC
35084523 GAGAGAGAGC
Statistics
Matches: 115, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
24 61 0.53
25 54 0.47
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.34
Consensus pattern (25 bp):
AGCTTCCCGATTAATGGCTCTCTAG
Found at i:35084457 original size:73 final size:74
Alignment explanation
Indices: 35084356--35084511 Score: 183
Period size: 73 Copynumber: 2.1 Consensus size: 74
35084346 ATCTTTCATT
* * * *
35084356 AGCTTCCCGATTAATGGCTCTCTAGAGCTTCCCGA-TATTAGCTCGCTTGAATCTTCCCGTTA-T
1 AGCTTCCCGATTAATAGCTCTCTAGAGCTTCCC-ATTAATAGCTCGC-TGAAGCTTCCCGTTACA
*
35084419 TGGCTCATATG
64 TGGCTCACATG
* * * *
35084430 AGCTTCCC-ATTAATAGCTCTTTGGAGCTTCCCATTAATAGCTCTCTGGAGCTTCCCGTTACATG
1 AGCTTCCCGATTAATAGCTCTCTAGAGCTTCCCATTAATAGCTCGCTGAAGCTTCCCGTTACATG
35084494 GCTCACATG
66 GCTCACATG
*
35084503 AGCATCCCG
1 AGCTTCCCG
35084512 TTATATGGCT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
72 14 0.20
73 47 0.68
74 8 0.12
ACGTcount: A:0.20, C:0.29, G:0.19, T:0.33
Consensus pattern (74 bp):
AGCTTCCCGATTAATAGCTCTCTAGAGCTTCCCATTAATAGCTCGCTGAAGCTTCCCGTTACATG
GCTCACATG
Found at i:35084540 original size:27 final size:25
Alignment explanation
Indices: 35084477--35084540 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
35084467 TAGCTCTCTG
*
35084477 GAGCTTCCCGTTACATGGCTCACAT
1 GAGCTTCCCGTTACATGGCTCACAA
* * *
35084502 GAGCATCCCGTTATATGGCTCGAGAGA
1 GAGCTTCCCGTTACATGGCTC-ACA-A
35084529 GAGCTTCCCGTT
1 GAGCTTCCCGTT
35084541 TAAGGGTTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 19 0.59
26 2 0.06
27 11 0.34
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.27
Consensus pattern (25 bp):
GAGCTTCCCGTTACATGGCTCACAA
Found at i:35098314 original size:15 final size:15
Alignment explanation
Indices: 35098294--35098322 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35098284 ATATAGCCCG
35098294 AAAATCAAAAACCAA
1 AAAATCAAAAACCAA
35098309 AAAATCAAAAACCA
1 AAAATCAAAAACCA
35098323 GTGCCGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.21, G:0.00, T:0.07
Consensus pattern (15 bp):
AAAATCAAAAACCAA
Found at i:35101800 original size:121 final size:118
Alignment explanation
Indices: 35101642--35101868 Score: 319
Period size: 121 Copynumber: 1.9 Consensus size: 118
35101632 TCGAAAATCC
* * *
35101642 GATGATATTCGGACCCACACTCGTATCTGACACTTACAAGTAGGTTACTGGGTTTAAGTCGACAC
1 GATGATATTCGGACCCACACTCATATCTGACACTTACAAGTAGGTTACTAGGTTTAA-TAGA-AC
* * * *
35101707 ATGGATATGCAGATATGGCTTTGAAACATGAAAAAATGTAGAAATGTAGAAAAAAT
64 ATCGATATGCAGATATGACCTCGAAACATG-AAAAATGTAGAAATGTAGAAAAAAT
* ** *
35101763 GATGATATTCGGACCCATACTCATATCTGACGGTTACAAGTAGGTTACTAGGTTTAATATAACAT
1 GATGATATTCGGACCCACACTCATATCTGACACTTACAAGTAGGTTACTAGGTTTAATAGAACAT
*
35101828 CGATATGCGGATATGACCTCGAAACATGAAAAATGTAGAAA
66 CGATATGCAGATATGACCTCGAAACATGAAAAATGTAGAAA
35101869 ATCCGACTAC
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
118 13 0.14
119 27 0.29
120 2 0.02
121 52 0.55
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (118 bp):
GATGATATTCGGACCCACACTCATATCTGACACTTACAAGTAGGTTACTAGGTTTAATAGAACAT
CGATATGCAGATATGACCTCGAAACATGAAAAATGTAGAAATGTAGAAAAAAT
Found at i:35110956 original size:7 final size:7
Alignment explanation
Indices: 35110946--35110970 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
35110936 CATCATCACC
35110946 ACAATGA
1 ACAATGA
35110953 ACAATGA
1 ACAATGA
35110960 ACAATGA
1 ACAATGA
35110967 ACAA
1 ACAA
35110971 CAACAATAAT
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:0.60, C:0.16, G:0.12, T:0.12
Consensus pattern (7 bp):
ACAATGA
Found at i:35111235 original size:3 final size:3
Alignment explanation
Indices: 35111227--35111258 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
35111217 TATGTATCCT
35111227 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
35111259 CTGTTAGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:35111874 original size:3 final size:3
Alignment explanation
Indices: 35111868--35111895 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
35111858 TGATGATGAT
35111868 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
35111896 CTGATATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35116700 original size:31 final size:31
Alignment explanation
Indices: 35116657--35116715 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
35116647 GTTGTTAAAC
35116657 TATTCGAAAGTTTTCATTTAAGTCATTGAAT
1 TATTCGAAAGTTTTCATTTAAGTCATTGAAT
* *
35116688 TATTTGAAAGTTTTTATTTAAGTCATTG
1 TATTCGAAAGTTTTCATTTAAGTCATTG
35116716 GGTAGTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.49
Consensus pattern (31 bp):
TATTCGAAAGTTTTCATTTAAGTCATTGAAT
Found at i:35121735 original size:18 final size:18
Alignment explanation
Indices: 35121712--35121793 Score: 59
Period size: 17 Copynumber: 4.8 Consensus size: 18
35121702 TGTTATTTTA
35121712 AAAATATTATAAAATCAT
1 AAAATATTATAAAATCAT
* *
35121730 AAAATA-TATAAATTTTAT
1 AAAATATTATAAA-ATCAT
* *
35121748 AAAA-ATGA-AAAATTAT
1 AAAATATTATAAAATCAT
*
35121764 AAAATATTA-AAAGTACAT
1 AAAATATTATAAAAT-CAT
35121782 AAAA-ATT-TAAAA
1 AAAATATTATAAAA
35121794 ATATATTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
16 8 0.16
17 23 0.45
18 20 0.39
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAATATTATAAAATCAT
Found at i:35121759 original size:26 final size:25
Alignment explanation
Indices: 35121713--35121785 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 25
35121703 GTTATTTTAA
35121713 AAATATTATAAAATCATAAAATATAT
1 AAATATTATAAAATCATAAAAT-TAT
* *
35121739 AAATTTTATAAAAATGA-AAAATTAT
1 AAATATTAT-AAAATCATAAAATTAT
*
35121764 AAAATATTA-AAAGTACATAAAA
1 -AAATATTATAAAAT-CATAAAA
35121786 ATTTAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
24 4 0.11
25 4 0.11
26 24 0.63
27 6 0.16
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (25 bp):
AAATATTATAAAATCATAAAATTAT
Found at i:35121775 original size:16 final size:17
Alignment explanation
Indices: 35121712--35121775 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 17
35121702 TGTTATTTTA
*
35121712 AAAATATTATAAAATCAT
1 AAAATA-TATAAAATTAT
*
35121730 AAAATATATAAATTTTAT
1 AAAATATATAAA-ATTAT
35121748 AAAA-ATGA-AAAATTAT
1 AAAATAT-ATAAAATTAT
35121764 AAAATAT-TAAAA
1 AAAATATATAAAA
35121776 GTACATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
16 12 0.31
17 13 0.33
18 14 0.36
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATATATAAAATTAT
Found at i:35127818 original size:18 final size:18
Alignment explanation
Indices: 35127795--35127832 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
35127785 CACCAATTTG
*
35127795 TTATTTGAGTTATTCGAA
1 TTATTTGAGTTATTCAAA
35127813 TTATTTGAGTTATTCAAA
1 TTATTTGAGTTATTCAAA
35127831 TT
1 TT
35127833 GTAAAATTTA
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:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (18 bp):
TTATTTGAGTTATTCAAA
Found at i:35131005 original size:14 final size:14
Alignment explanation
Indices: 35130987--35131029 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 14
35130977 AGTATATATA
35130987 AAAAAGTAAAAAAAC
1 AAAAA-TAAAAAAAC
35131002 AAAAATAAAAAAAAC
1 AAAAAT-AAAAAAAC
35131017 AAAAATAAAAAAA
1 AAAAATAAAAAAA
35131030 ATAAAACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.86, C:0.05, G:0.02, T:0.07
Consensus pattern (14 bp):
AAAAATAAAAAAAC
Found at i:35131013 original size:16 final size:15
Alignment explanation
Indices: 35130994--35131035 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
35130984 ATAAAAAAGT
35130994 AAAAAAACAAAAATA
1 AAAAAAACAAAAATA
35131009 AAAAAAACAAAAATA
1 AAAAAAACAAAAATA
*
35131024 AAAAAAATAAAA
1 AAAAAAACAAAA
35131036 CATATGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.88, C:0.05, G:0.00, T:0.07
Consensus pattern (15 bp):
AAAAAAACAAAAATA
Found at i:35131020 original size:20 final size:20
Alignment explanation
Indices: 35130996--35131037 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
35130986 AAAAAAGTAA
* *
35130996 AAAAACAAAAATAAAAAAAAC
1 AAAAATAAAAA-AAATAAAAC
35131017 AAAAATAAAAAAAATAAAAC
1 AAAAATAAAAAAAATAAAAC
35131037 A
1 A
35131038 TATGTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (20 bp):
AAAAATAAAAAAAATAAAAC
Found at i:35131035 original size:14 final size:13
Alignment explanation
Indices: 35130986--35131035 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
35130976 AAGTATATAT
*
35130986 AAAAAAGTAAAAA
1 AAAAAAATAAAAA
35130999 AACAAAAATAAAAAA
1 AA-AAAAAT-AAAAA
35131014 AACAAAAATAAAAA
1 AA-AAAAATAAAAA
35131028 AAATAAAA
1 AAA-AAAA
35131036 CATATGTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
13 3 0.09
14 16 0.48
15 14 0.42
ACGTcount: A:0.86, C:0.04, G:0.02, T:0.08
Consensus pattern (13 bp):
AAAAAAATAAAAA
Found at i:35131173 original size:3 final size:3
Alignment explanation
Indices: 35131165--35131217 Score: 72
Period size: 3 Copynumber: 17.3 Consensus size: 3
35131155 AGTAAATGAT
*
35131165 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATGGA AAA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT--A ATA ATA ATA
35131211 ATA ATA A
1 ATA ATA A
35131218 GGGTGATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 41 0.91
5 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:35133340 original size:45 final size:45
Alignment explanation
Indices: 35133134--35133326 Score: 180
Period size: 45 Copynumber: 4.3 Consensus size: 45
35133124 GCCAATCCAT
* *
35133134 GAAGACAAGATCTGCTGTCTTGGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGTTGTCTTCGATCTACTTCGCCACCAGTATGG
* *
35133179 GAAGACAAGATCTGATT-TCTTCAATCTA-TTCCACCACCAGTATGG
1 GAAGACAAGATCTG-TTGTCTTCGATCTACTT-CGCCACCAGTATGG
* * * * * ***
35133224 GGAGACAATATCTGTTGTATTTGATCTACTT---CACGCTGATACAT
1 GAAGACAAGATCTGTTGTCTTCGATCTACTTCGCCAC-CAG-TATGG
* * *
35133268 GAGGACAAGATCTATTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGTTGTCTTCGATCTACTTCGCCACCAGTATGG
35133313 GAAGACAAGATCTG
1 GAAGACAAGATCTG
35133327 GTATCTTTAA
Statistics
Matches: 113, Mismatches: 26, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
42 3 0.03
43 2 0.02
44 30 0.27
45 70 0.62
46 5 0.04
47 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (45 bp):
GAAGACAAGATCTGTTGTCTTCGATCTACTTCGCCACCAGTATGG
Found at i:35133771 original size:132 final size:128
Alignment explanation
Indices: 35133315--35134480 Score: 1211
Period size: 132 Copynumber: 8.9 Consensus size: 128
35133305 CAGTATGGGA
** * * *
35133315 AGACAAGATCTGGTATCTTTAATCTATTCCACTGCTACCTAGGGAAGTAGAATTACTGGCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGG-AGTAGAATTACTGGCTTCAA
35133380 TGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAG
65 TGTACTCCACTGT-ACC-CAGGGAGGTAAAAT-CGCCATCTTTGATCTGCTCCACTACTGCTTAG
*
35133445 GA
127 GG
* * * * *
35133447 AGACAAGATCT-ACAATCTTCAACCTACTCCACTGCTGCTCAGGGAG-ACAA-GACTGGTAGCTT
1 AGACAAGATCTGA-AATCTTCAATCTATTCCACTGCTGCCCAGGGAGTAGAATTACT-G--GCTT
* * * ** * * * * * *
35133509 AAACCTGCTTC-CCTACTATA--TTGGGAAGCTAAGATTCACCGTCTTTGATCTACTCCACTATT
62 CAA--TG-TACTCC-ACTGTACCCAGGG-AGGTAA-AATCGCCATCTTTGATCTGCTCCACTACT
*
35133571 GTTTAGGG
121 GCTTAGGG
* * * * *** * * ** *
35133579 AGACAGGGTCT-ACAATCTTCAACCTACTCCACTGCTGGTAAGGGAGATAGGACTGGTGGCTTAA
1 AGACAAGATCTGA-AATCTTCAATCTATTCCACTGCTGCCCAGGGAG-TAGAATTACTGGCTTCA
** * * ** * * *
35133643 ACCTGCTTCC-CTACTACCTTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTT
64 ATGTAC-TCCACT-GTACCCAGGG-AGGTAA-AATCGCCATCTTTGATCTGCTCCACTACTGCTT
35133707 AGGG
125 AGGG
* *
35133711 AGACAAGATCTGAAATATTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGG-AGTAGAATTACTGGCTTCAA
* * *
35133776 TGTGCTCCACTGTAACCACAGGGAGGTAAAACCCTCCATCTTTGATCTGCTCCACTACTGCTTAG
65 TGTACTCCACTGT-ACC-CAGGGAGGTAAAA-TCGCCATCTTTGATCTGCTCCACTACTGCTTAG
35133841 GG
127 GG
* *
35133843 AGACAAGATCTGAAATCTTCAATCTATTCCACTACTGCCTAGGGAGATAGAATTACTGGCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAG-TAGAATTACTGGCTTCAA
*
35133908 TGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGTTTAG
65 TGTACTCCACTGT-ACC-CAGGGAGGTAAAATC-GCCATCTTTGATCTGCTCCACTACTGCTTAG
35133973 GG
127 GG
*
35133975 AGAC-A-A---GAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTATTGGCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGG-AGTAGAATTACTGGCTTCAA
*
35134035 --TACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGTTTAG
65 TGTACTCCACTGT-ACC-CAGGGAGGTAAAATC-GCCATCTTTGATCTGCTCCACTACTGCTTAG
35134098 GG
127 GG
35134100 AGAC-A-A---GAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGG-AGTAGAATTACTGGCTTCAA
* * *
35134160 TGTACTCCATTGTAACTACAGGGAGGTAAAATCTGCTATCTTTGATCTGCTCCACTACTGCTTAG
65 TGTACTCCACTGT-AC-CCAGGGAGGTAAAATC-GCCATCTTTGATCTGCTCCACTACTGCTTAG
35134225 GG
127 GG
* * *
35134227 AGACAAGATATGAAATCTTCAATATATTCCACTGCTGCCCAGGGAGATAGAATTACCGGCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAG-TAGAATTACTGGCTTCAA
**
35134292 TGTACTCCACTGTAACCACAATGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAG
65 TGTACTCCACTGT-ACC-CAGGGAGGTAAAAT-CGCCATCTTTGATCTGCTCCACTACTGCTTAG
35134357 GG
127 GG
* * *
35134359 AGACAAGATCTGTAATCTTCAATCTATTCCGCTGCTGCCCAGAGAAGTAGAATTACTGGCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAG-GGAGTAGAATTACTGGCTTCAA
*
35134424 TGTACTCCACTGTAACCACAGGGAGGTAAAACCGCCATCTTTGATCTGCTCCACTAC
65 TGTACTCCACTGT-ACC-CAGGGAGGTAAAATCGCCATCTTTGATCTGCTCCACTAC
35134481 AACCGAGGGA
Statistics
Matches: 899, Mismatches: 96, Indels: 79
0.84 0.09 0.07
Matches are distributed among these distances:
125 124 0.14
127 112 0.12
128 3 0.00
129 8 0.01
130 7 0.01
131 43 0.05
132 575 0.64
133 12 0.01
134 8 0.01
135 7 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (128 bp):
AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAGTAGAATTACTGGCTTCAAT
GTACTCCACTGTACCCAGGGAGGTAAAATCGCCATCTTTGATCTGCTCCACTACTGCTTAGGG
Found at i:35135734 original size:8 final size:7
Alignment explanation
Indices: 35135697--35135731 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
35135687 TTTGCCTCTC
35135697 CATTTTT
1 CATTTTT
35135704 CATTTTT
1 CATTTTT
35135711 CA-TTTT
1 CATTTTT
35135717 CATCTTTT
1 CAT-TTTT
35135725 CATTTTT
1 CATTTTT
35135732 TCACATCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.23
7 13 0.50
8 7 0.27
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:35139813 original size:29 final size:29
Alignment explanation
Indices: 35139771--35139832 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
35139761 GGAGTCAGTT
35139771 ACGCACGAGGAAGGGTTAGCACCCTCGTA
1 ACGCACGAGGAAGGGTTAGCACCCTCGTA
35139800 ACGCACGAGGAAGGGTTAGCACCCTCGTA
1 ACGCACGAGGAAGGGTTAGCACCCTCGTA
35139829 ACGC
1 ACGC
35139833 CCAAAATTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.27, C:0.29, G:0.31, T:0.13
Consensus pattern (29 bp):
ACGCACGAGGAAGGGTTAGCACCCTCGTA
Found at i:35148435 original size:2 final size:2
Alignment explanation
Indices: 35148428--35148459 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35148418 AGGCTTAGTG
35148428 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
35148460 ATGTACTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:35148544 original size:28 final size:28
Alignment explanation
Indices: 35148510--35148602 Score: 75
Period size: 28 Copynumber: 3.3 Consensus size: 28
35148500 GTGTGTGTGT
35148510 ATGTATGTACTCACTATCTAACGAAGTC
1 ATGTATGTACTCACTATCTAACGAAGTC
* * * *** *
35148538 ATGTATGTA-TGTA-TGTGTGTGTGTATGT-
1 ATGTATGTACT-CACTATCT-AACG-AAGTC
35148566 ATGTATGTACTCACTATCTAACGAAGTC
1 ATGTATGTACTCACTATCTAACGAAGTC
35148594 ATGTATGTA
1 ATGTATGTA
35148603 TGTATGTATG
Statistics
Matches: 45, Mismatches: 14, Indels: 12
0.63 0.20 0.17
Matches are distributed among these distances:
27 7 0.16
28 31 0.69
29 7 0.16
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (28 bp):
ATGTATGTACTCACTATCTAACGAAGTC
Found at i:35148547 original size:4 final size:4
Alignment explanation
Indices: 35148538--35148666 Score: 152
Period size: 4 Copynumber: 31.2 Consensus size: 4
35148528 TAACGAAGTC
* * * * *
35148538 ATGT ATGT ATGT ATGT GTGT GTGT ATGT ATGT ATGT ACTCACT ATCT AACG-
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-T--GT ATGT -ATGT
*
35148589 AAGT CATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT -ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
35148638 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
35148667 CTCAATATCT
Statistics
Matches: 112, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
3 2 0.02
4 102 0.91
5 5 0.04
6 1 0.01
7 2 0.02
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.46
Consensus pattern (4 bp):
ATGT
Found at i:35148557 original size:56 final size:56
Alignment explanation
Indices: 35148441--35148630 Score: 321
Period size: 56 Copynumber: 3.4 Consensus size: 56
35148431 TGTGTGTGTG
* * *
35148441 TGTGTGTGTGTGTGTGTGTATGTACTCAATATCTAACGAAGTCATGTATGTATGTA
1 TGTGTGTGTGTATGTATGTATGTACTCACTATCTAACGAAGTCATGTATGTATGTA
35148497 TGTGTGTGTG--TGTATGTATGTACTCACTATCTAACGAAGTCATGTATGTATGTA
1 TGTGTGTGTGTATGTATGTATGTACTCACTATCTAACGAAGTCATGTATGTATGTA
35148551 TGTGTGTGTGTATGTATGTATGTACTCACTATCTAACGAAGTCATGTATGTATGTA
1 TGTGTGTGTGTATGTATGTATGTACTCACTATCTAACGAAGTCATGTATGTATGTA
* *
35148607 TGTATGTATGTATGTATGTATGTA
1 TGTGTGTGTGTATGTATGTATGTA
35148631 TGTATGTATG
Statistics
Matches: 128, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
54 52 0.41
56 76 0.59
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (56 bp):
TGTGTGTGTGTATGTATGTATGTACTCACTATCTAACGAAGTCATGTATGTATGTA
Found at i:35150572 original size:24 final size:24
Alignment explanation
Indices: 35150545--35150616 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
35150535 GAACCAAGCC
35150545 ATAGAAATAAAAACAATTTACTTA
1 ATAGAAATAAAAACAATTTACTTA
35150569 ATAGAAATAAAAACAATTTACTTA
1 ATAGAAATAAAAACAATTTACTTA
35150593 ATAGAAATAAAAACAATTTACTTA
1 ATAGAAATAAAAACAATTTACTTA
35150617 CTTTCAGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.29
Consensus pattern (24 bp):
ATAGAAATAAAAACAATTTACTTA
Found at i:35151870 original size:23 final size:23
Alignment explanation
Indices: 35151816--35151905 Score: 103
Period size: 23 Copynumber: 4.0 Consensus size: 23
35151806 AAGCTATCAC
* *
35151816 CCAT-CAAACATAACCA-ATTTA
1 CCATCCAAACACAACCATATGTA
*
35151837 CCCTCCAAACACAACCATATGTA
1 CCATCCAAACACAACCATATGTA
* * *
35151860 CCATCCGAACACAACCAAATATA
1 CCATCCAAACACAACCATATGTA
*
35151883 CCTTCCAAACACAACCATATGTA
1 CCATCCAAACACAACCATATGTA
35151906 TAACCTCTGA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 3 0.05
22 11 0.20
23 42 0.75
ACGTcount: A:0.43, C:0.34, G:0.03, T:0.19
Consensus pattern (23 bp):
CCATCCAAACACAACCATATGTA
Found at i:35151891 original size:46 final size:46
Alignment explanation
Indices: 35151838--35151947 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 46
35151828 ACCAATTTAC
35151838 CCTCCAAACACAACCATATG-T-ACCATCCGAACACAACCAAATATA
1 CCTCCAAACACAACCATATGATAACC-TCCGAACACAACCAAATATA
* *
35151883 CCTTCCAAACACAACCATATGTATAACCTCTGAACACAACCAAGTATA
1 CC-TCCAAACACAACCATATG-ATAACCTCCGAACACAACCAAATATA
*
35151931 GCCTCTAAACACAACCA
1 -CCTCCAAACACAACCA
35151948 ATATACCTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
45 2 0.04
46 18 0.32
48 32 0.56
49 5 0.09
ACGTcount: A:0.43, C:0.35, G:0.05, T:0.17
Consensus pattern (46 bp):
CCTCCAAACACAACCATATGATAACCTCCGAACACAACCAAATATA
Found at i:35151935 original size:23 final size:22
Alignment explanation
Indices: 35151867--35151955 Score: 99
Period size: 23 Copynumber: 3.9 Consensus size: 22
35151857 GTACCATCCG
* *
35151867 AACACAACCAAATATACCTTCCA
1 AACACAACCAAGTATACC-TCTA
*
35151890 AACACAACCATATGTATAACCTCTG
1 AACACAACCA-A-GTAT-ACCTCTA
35151915 AACACAACCAAGTATAGCCTCTA
1 AACACAACCAAGTATA-CCTCTA
35151938 AACACAACCAA-TATACCT
1 AACACAACCAAGTATACCT
35151956 TTCAATATAT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
21 3 0.05
22 5 0.09
23 30 0.52
24 2 0.03
25 15 0.26
26 3 0.05
ACGTcount: A:0.45, C:0.31, G:0.04, T:0.19
Consensus pattern (22 bp):
AACACAACCAAGTATACCTCTA
Found at i:35152823 original size:54 final size:54
Alignment explanation
Indices: 35152756--35152868 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
35152746 TGAGTAGGGT
* *
35152756 CACACGACCGTGTCGTAGGCCATGTGCCAAGCCATGTAACTCTCCGAGTTGCCA
1 CACACGACCGTGTCGCAGGCCATGTGCCAAGCCATGTAACTCTCCAAGTTGCCA
* * ** * *
35152810 TACACGACTGTGTCGCAGGCTGTGTGCCAAGCCGTGTAACTCTCTAAGTTGCCA
1 CACACGACCGTGTCGCAGGCCATGTGCCAAGCCATGTAACTCTCCAAGTTGCCA
35152864 CACAC
1 CACAC
35152869 AGTTGTGTGC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.22, C:0.32, G:0.24, T:0.22
Consensus pattern (54 bp):
CACACGACCGTGTCGCAGGCCATGTGCCAAGCCATGTAACTCTCCAAGTTGCCA
Found at i:35152889 original size:54 final size:54
Alignment explanation
Indices: 35152756--35152889 Score: 137
Period size: 54 Copynumber: 2.5 Consensus size: 54
35152746 TGAGTAGGGT
* * * * *
35152756 CACACGACCGTGTCGTAGGCCATGTGCCAAGCCATGTAACTCTCCGAGTTGCCA
1 CACACGACTGTGTCGCAAGCCGTGTGCCAAGCCATGTAACTCTCCAAGTTGCCA
* * * * *
35152810 TACACGACTGTGTCGCAGGCTGTGTGCCAAGCCGTGTAACTCTCTAAGTTGCCA
1 CACACGACTGTGTCGCAAGCCGTGTGCCAAGCCATGTAACTCTCCAAGTTGCCA
*
35152864 CACAC-AGTTGTGT-GCCAAGCCGTGTG
1 CACACGA-CTGTGTCG-CAAGCCGTGTG
35152890 ACAGTCCGTG
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
53 2 0.03
54 64 0.97
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (54 bp):
CACACGACTGTGTCGCAAGCCGTGTGCCAAGCCATGTAACTCTCCAAGTTGCCA
Found at i:35166908 original size:12 final size:11
Alignment explanation
Indices: 35166878--35166921 Score: 54
Period size: 10 Copynumber: 4.0 Consensus size: 11
35166868 ATATAAAAGT
35166878 TAAAAAAAATA
1 TAAAAAAAATA
**
35166889 TAGAAAAACGTA
1 TA-AAAAAAATA
35166901 TAAAAAAAA-A
1 TAAAAAAAATA
35166911 TAAAAAAAATA
1 TAAAAAAAATA
35166922 AGAAAAATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 10 0.37
11 8 0.30
12 9 0.33
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (11 bp):
TAAAAAAAATA
Found at i:35179384 original size:20 final size:20
Alignment explanation
Indices: 35179359--35179397 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35179349 GATATCCTTT
*
35179359 CATTGATTCCTCCTAAATTG
1 CATTGATTCATCCTAAATTG
*
35179379 CATTGATTTATCCTAAATT
1 CATTGATTCATCCTAAATT
35179398 TTTCATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.44
Consensus pattern (20 bp):
CATTGATTCATCCTAAATTG
Found at i:35180876 original size:14 final size:14
Alignment explanation
Indices: 35180831--35180880 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
35180821 TCTAATGTTC
35180831 AATTTTATATATG-
1 AATTTTATATATGA
* *
35180844 AATTTTGATTTTGTGA
1 AATTTT-A-TATATGA
35180860 AATTTTATATATGA
1 AATTTTATATATGA
35180874 AATTTTA
1 AATTTTA
35180881 ATTTAATTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 6 0.20
14 13 0.43
15 5 0.17
16 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (14 bp):
AATTTTATATATGA
Found at i:35180894 original size:30 final size:29
Alignment explanation
Indices: 35180828--35180895 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
35180818 TGGTCTAATG
* **
35180828 TTCAATTTTATATATGAATTTTGATTTTG
1 TTCAATTTTATATATGAATTTTAATTTAA
**
35180857 TGAAATTTTATATATGAAATTTTAATTTAA
1 TTCAATTTTATATATG-AATTTTAATTTAA
35180887 TTCAATTTT
1 TTCAATTTT
35180896 CACAAATTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (29 bp):
TTCAATTTTATATATGAATTTTAATTTAA
Found at i:35184613 original size:31 final size:31
Alignment explanation
Indices: 35184575--35184659 Score: 136
Period size: 31 Copynumber: 2.7 Consensus size: 31
35184565 GGCCCATTTT
35184575 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAG
1 TATTTTAAAAATATTT-AAAAATTAAAAAAAG
*
35184606 TATTTTAAAAATATTTTAAAATTAAAAAAAG
1 TATTTTAAAAATATTTAAAAATTAAAAAAAG
35184637 TATTTTAAAAATATTTTAAAAAT
1 TATTTTAAAAATA-TTTAAAAAT
35184660 ATTTTAAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
31 39 0.78
32 11 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (31 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAAG
Found at i:35184621 original size:42 final size:42
Alignment explanation
Indices: 35184575--35184698 Score: 141
Period size: 41 Copynumber: 3.0 Consensus size: 42
35184565 GGCCCATTTT
**
35184575 TATTTTAAAAATTTTAAAAA-ATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAAATTAAAAAAAGATTAAAAAAA-TATTTTAAAAA
**
35184617 TATTTT-AAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAA
1 TATTTTAAAAATTAAAAAAAG-ATTAAAAAAATATTTTAAAAA
35184659 TATTTT-AAAATT-AAAAAAGTATGT-AAAAAATATTTTAAAA
1 TATTTTAAAAATTAAAAAAAG-AT-TAAAAAAATATTTTAAAA
35184699 TTAAAAAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
41 36 0.49
42 30 0.41
43 8 0.11
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (42 bp):
TATTTTAAAAATTAAAAAAAGATTAAAAAAATATTTTAAAAA
Found at i:35184698 original size:11 final size:11
Alignment explanation
Indices: 35184575--35184668 Score: 92
Period size: 11 Copynumber: 8.9 Consensus size: 11
35184565 GGCCCATTTT
35184575 TATTTT-AAAA
1 TATTTTAAAAA
35184585 -ATTTTAAAAA
1 TATTTTAAAAA
**
35184595 -ATTAAAAAAA
1 TATTTTAAAAA
35184605 GTATTTTAAAAA
1 -TATTTTAAAAA
35184617 TATTTT--AAA
1 TATTTTAAAAA
**
35184626 -ATTAAAAAAA
1 TATTTTAAAAA
35184636 GTATTTTAAAAA
1 -TATTTTAAAAA
35184648 TATTTTAAAAA
1 TATTTTAAAAA
35184659 TATTTTAAAA
1 TATTTTAAAA
35184669 TTAAAAAAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
8 3 0.04
9 8 0.12
10 15 0.22
11 27 0.39
12 16 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:35190791 original size:21 final size:21
Alignment explanation
Indices: 35190762--35190805 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
35190752 GTCACTCGCA
*
35190762 ATACCAAAAAAACAGAATTAT
1 ATACAAAAAAAACAGAATTAT
35190783 ATACAAAAAAAACAGAATTAT
1 ATACAAAAAAAACAGAATTAT
35190804 AT
1 AT
35190806 TAAGCATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.64, C:0.11, G:0.05, T:0.20
Consensus pattern (21 bp):
ATACAAAAAAAACAGAATTAT
Found at i:35196494 original size:10 final size:9
Alignment explanation
Indices: 35196477--35196565 Score: 56
Period size: 9 Copynumber: 9.4 Consensus size: 9
35196467 AAAAAAGATT
35196477 AAAA-AATA
1 AAAATAATA
35196485 AAAATCAATA
1 AAAAT-AATA
*
35196495 AAAATTATA
1 AAAATAATA
35196504 AAAATAATTA
1 AAAATAA-TA
**
35196514 AATTTTAATA
1 AA-AATAATA
*
35196524 AAATATATAAA
1 AAA-ATA-ATA
*
35196535 AAAATATTA
1 AAAATAATA
*
35196544 AAAATTATA
1 AAAATAATA
35196553 AAAA-ATATA
1 AAAATA-ATA
35196562 AAAA
1 AAAA
35196566 ATTGTAAAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
8 4 0.06
9 28 0.45
10 22 0.35
11 8 0.13
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAATAATA
Found at i:35196515 original size:19 final size:19
Alignment explanation
Indices: 35196477--35196565 Score: 60
Period size: 19 Copynumber: 4.7 Consensus size: 19
35196467 AAAAAAGATT
35196477 AAAAA-ATAAAAATCAA-TA
1 AAAAATATAAAAAT-AATTA
*
35196495 AAAATTATAAAAATAATTA
1 AAAAATATAAAAATAATTA
*** *
35196514 AATTTTA-ATAAAATATATAA
1 AAAAATATA-AAAATA-ATTA
*
35196534 AAAAATATTAAAAATTA-TA
1 AAAAATA-TAAAAATAATTA
35196553 AAAAATATAAAAA
1 AAAAATATAAAAA
35196566 ATTGTAAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
18 13 0.23
19 29 0.52
20 8 0.14
21 5 0.09
22 1 0.02
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATATAAAAATAATTA
Found at i:35196523 original size:29 final size:30
Alignment explanation
Indices: 35196483--35196566 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 30
35196473 GATTAAAAAA
* *
35196483 TAAAAATCAATAAAAATTATAAAAATA-AT
1 TAAAAATTAATAAAAATTATAAAAAAATAT
**
35196512 TAAATTTTAAT-AAAATATATAAAAAAATAT
1 TAAAAATTAATAAAAAT-TATAAAAAAATAT
*
35196542 TAAAAATT-ATAAAAAATATAAAAAA
1 TAAAAATTAATAAAAATTATAAAAAA
35196567 TTGTAAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 5 0.11
29 28 0.62
30 12 0.27
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (30 bp):
TAAAAATTAATAAAAATTATAAAAAAATAT
Found at i:35196566 original size:19 final size:19
Alignment explanation
Indices: 35196523--35196574 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
35196513 AAATTTTAAT
*
35196523 AAAATATATAAAAAAATATTA
1 AAAAT-TAT-AAAAAATATAA
35196544 AAAATTATAAAAAATATAA
1 AAAATTATAAAAAATATAA
*
35196563 AAAATTGTAAAA
1 AAAATTATAAAA
35196575 TTTTATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 21 0.72
20 3 0.10
21 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAATTATAAAAAATATAA
Found at i:35196573 original size:10 final size:10
Alignment explanation
Indices: 35196513--35196584 Score: 65
Period size: 10 Copynumber: 7.1 Consensus size: 10
35196503 AAAAATAATT
*
35196513 AAATTTTAATA
1 AAATTATAA-A
35196524 AAATATATAAA
1 AAAT-TATAAA
* *
35196535 AAAATATTAA
1 AAATTATAAA
35196545 AAATTATAAA
1 AAATTATAAA
35196555 AAA-TATAAA
1 AAATTATAAA
*
35196564 AAATTGTAAA
1 AAATTATAAA
**
35196574 ATTTTATAAA
1 AAATTATAAA
35196584 A
1 A
35196585 GTCATACAAG
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
9 9 0.18
10 29 0.58
11 8 0.16
12 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (10 bp):
AAATTATAAA
Found at i:35196580 original size:29 final size:28
Alignment explanation
Indices: 35196492--35196584 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 28
35196482 ATAAAAATCA
* *
35196492 ATAAAAATTATAAAAATAATT-AAATTTT
1 ATAAAAAATATAAAAA-ATTTAAAATTTT
* *
35196520 AATAAAATATATAAAAAAATATTAAAA-ATT
1 -ATAAAAAATAT-AAAAAAT-TTAAAATTTT
35196550 ATAAAAAATATAAAAAATTGTAAAATTTT
1 ATAAAAAATATAAAAAATT-TAAAATTTT
35196579 ATAAAA
1 ATAAAA
35196585 GTCATACAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
27 1 0.02
28 12 0.23
29 28 0.53
30 9 0.17
31 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (28 bp):
ATAAAAAATATAAAAAATTTAAAATTTT
Found at i:35196724 original size:140 final size:141
Alignment explanation
Indices: 35196449--35196724 Score: 341
Period size: 140 Copynumber: 2.0 Consensus size: 141
35196439 TGTCTCAACC
35196449 ACAACGTGACATGTGGCAAAAAAAGATTAAAAAATAAAAATCAATAAAAATTATAAAAATAATTA
1 ACAACGTGACATGTGGCAAAAAAAGATTAAAAAATAAAAATCAATAAAAATTATAAAAATAATTA
* *
35196514 AATTTTAATAAAATATATAAAAAAATATTAAAAATTATAAAAAATATAAAAAATTGTAAAATTTT
66 AATTTTAATAAAATATATAAAAAAATATTAAAAATTATAAAAAATATAAAAAATCGTAAAATATT
35196579 ATAAAAGTCAT
131 ATAAAAGTCAT
* * * *
35196590 ACAA-GTGACATGTGGTAAAAAAATGA-TAAAAATTAAAAATCAATAAAATTTATAGAAATGAA-
1 ACAACGTGACATGTGGCAAAAAAA-GATTAAAAAATAAAAATCAATAAAAATTATAAAAAT-AAT
* * ** *
35196652 TAAGTTTTAATAAAA-ATATTTAAAATTTATTAAAAAATTGA-ATAAAACTAT-AAAAATCGTAA
64 TAAATTTTAATAAAATATA-TAAAAAAATATT-AAAAATT-ATA-AAAAATATAAAAAATCGTAA
*
35196714 AA-ATTGTAAAA
125 AATATTATAAAA
35196725 TATATAAAAC
Statistics
Matches: 117, Mismatches: 12, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
139 3 0.03
140 78 0.67
141 28 0.24
142 8 0.07
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (141 bp):
ACAACGTGACATGTGGCAAAAAAAGATTAAAAAATAAAAATCAATAAAAATTATAAAAATAATTA
AATTTTAATAAAATATATAAAAAAATATTAAAAATTATAAAAAATATAAAAAATCGTAAAATATT
ATAAAAGTCAT
Found at i:35196733 original size:17 final size:16
Alignment explanation
Indices: 35196713--35196765 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
35196703 AAAAATCGTA
35196713 AAAATTGTAAAATATAT
1 AAAA-TGTAAAATATAT
35196730 AAAACTGTAAAAATATAT
1 AAAA-TGT-AAAATATAT
*
35196748 AGAAATGTAAAAAATAT
1 A-AAATGTAAAATATAT
35196765 A
1 A
35196766 TATATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 16 0.50
18 13 0.41
19 3 0.09
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (16 bp):
AAAATGTAAAATATAT
Found at i:35196757 original size:35 final size:35
Alignment explanation
Indices: 35196693--35196765 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
35196683 AAAAAATTGA
* *
35196693 ATAAAACTATAAAAATCGTAAAAATTGTAAAATAT
1 ATAAAACTATAAAAATCATAAAAATTGTAAAAAAT
*
35196728 ATAAAACTGTAAAAAT-ATATAGAAA-TGTAAAAAAT
1 ATAAAACTATAAAAATCATA-A-AAATTGTAAAAAAT
35196763 ATA
1 ATA
35196766 TATATAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 2 0.06
35 28 0.85
36 3 0.09
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (35 bp):
ATAAAACTATAAAAATCATAAAAATTGTAAAAAAT
Found at i:35196762 original size:19 final size:18
Alignment explanation
Indices: 35196693--35196767 Score: 75
Period size: 18 Copynumber: 4.2 Consensus size: 18
35196683 AAAAAATTGA
* *
35196693 ATAAAACTATAAAAATCGT
1 ATAAAACTGTAAAAAT-AT
*
35196712 A-AAAATTGT-AAAATAT
1 ATAAAACTGTAAAAATAT
35196728 ATAAAACTGTAAAAATAT
1 ATAAAACTGTAAAAATAT
35196746 ATAGAAA-TGTAAAAAATAT
1 ATA-AAACTGT-AAAAATAT
35196765 ATA
1 ATA
35196768 TATAAAATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.04
17 12 0.25
18 19 0.40
19 15 0.31
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (18 bp):
ATAAAACTGTAAAAATAT
Found at i:35197095 original size:19 final size:19
Alignment explanation
Indices: 35197044--35197094 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
35197034 TTTTGATGTA
**
35197044 TTTTATAATTTTTTATGAT
1 TTTTATAATTTTTTACAAT
**
35197063 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTACAAT
35197082 TTTTAT-ATTTTTT
1 TTTTATAATTTTTT
35197095 TTAATTTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:35197123 original size:26 final size:26
Alignment explanation
Indices: 35197071--35197126 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
35197061 ATTTTTATAA
*
35197071 AATTTTACAATTTTTATATTTTTTTT
1 AATTTTACAATTTTTATATTATTTTT
35197097 AATTTTAACAAATTTTTA-A-TATTTTT
1 AATTTT-AC-AATTTTTATATTATTTTT
35197123 AATT
1 AATT
35197127 AAAATTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 16 0.59
27 3 0.11
28 8 0.30
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (26 bp):
AATTTTACAATTTTTATATTATTTTT
Found at i:35197178 original size:9 final size:9
Alignment explanation
Indices: 35197044--35197179 Score: 60
Period size: 9 Copynumber: 14.4 Consensus size: 9
35197034 TTTTGATGTA
35197044 TTTTATAATT
1 TTTTATAA-T
*
35197054 TTTTATGAT
1 TTTTATAAT
*
35197063 TTTTATAAAA
1 TTTTAT-AAT
*
35197073 TTTTACAAT
1 TTTTATAAT
*
35197082 TTTTATATT
1 TTTTATAAT
*
35197091 TTTTTTAAT
1 TTTTATAAT
* *
35197100 TTTAACAAAT
1 TTTTA-TAAT
35197110 TTTTA-ATAT
1 TTTTATA-AT
*
35197119 TTTTAATTAAAA
1 TTTT-A-T-AAT
*
35197131 TTTAATAAT
1 TTTTATAAT
* *
35197140 ATTTATAAA
1 TTTTATAAT
**
35197149 TTTTATTGT
1 TTTTATAAT
*
35197158 TTTT-TATTT
1 TTTTATA-AT
35197167 TTTTATAAT
1 TTTTATAAT
35197176 TTTT
1 TTTT
35197180 TGTCACATGT
Statistics
Matches: 91, Mismatches: 26, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
8 2 0.02
9 59 0.65
10 24 0.26
11 1 0.01
12 4 0.04
13 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:35200855 original size:18 final size:18
Alignment explanation
Indices: 35200832--35200866 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
35200822 TAACACAAAT
35200832 TCATTTAAGTGTTTAATC
1 TCATTTAAGTGTTTAATC
35200850 TCATTTAAGTGTTTAAT
1 TCATTTAAGTGTTTAAT
35200867 TTGTAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TCATTTAAGTGTTTAATC
Found at i:35215246 original size:2 final size:2
Alignment explanation
Indices: 35215241--35215280 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
35215231 CTATTATATA
35215241 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
35215281 AATTCATGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:35224361 original size:20 final size:20
Alignment explanation
Indices: 35224336--35224380 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
35224326 ATTATAGTAG
*
35224336 TTTTAC-ATATTCTTATCATT
1 TTTTACGATATT-TGATCATT
*
35224356 TTTTACGATATTTGATTATT
1 TTTTACGATATTTGATCATT
35224376 TTTTA
1 TTTTA
35224381 ACGTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTTACGATATTTGATCATT
Found at i:35225359 original size:21 final size:22
Alignment explanation
Indices: 35225335--35225375 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
35225325 ATTAAAGTGT
35225335 AAATTTATC-ATTTCTATTAAA
1 AAATTTATCAATTTCTATTAAA
*
35225356 AAATTTATCAATTTTTATTA
1 AAATTTATCAATTTCTATTA
35225376 TTAAAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTTATCAATTTCTATTAAA
Found at i:35226008 original size:36 final size:35
Alignment explanation
Indices: 35225968--35226045 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 35
35225958 TTTTTTTTTT
35225968 AAACAC-AGAACTTTGAAACACAATAATAATTTTTGA
1 AAACACAAGAACTTTGAAACACAA-AAT-ATTTTTGA
** * *
35226004 AAACACGAAGATTTTTGAAACACGAAATTTTTTTGA
1 AAACAC-AAGAACTTTGAAACACAAAATATTTTTGA
35226040 AAACAC
1 AAACAC
35226046 GGAATTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 19 0.53
37 3 0.08
38 14 0.39
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.28
Consensus pattern (35 bp):
AAACACAAGAACTTTGAAACACAAAATATTTTTGA
Found at i:35226024 original size:17 final size:17
Alignment explanation
Indices: 35225995--35226054 Score: 77
Period size: 17 Copynumber: 3.4 Consensus size: 17
35225985 ACACAATAAT
35225995 AATTTTTGAAAACACGA
1 AATTTTTGAAAACACGA
35226012 AGATTTTTG-AAACACGA
1 A-ATTTTTGAAAACACGA
*
35226029 AATTTTTTTGAAAACACGG
1 AA--TTTTTGAAAACACGA
35226048 AATTTTT
1 AATTTTT
35226055 TTTAAAAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
16 1 0.03
17 15 0.39
18 13 0.34
19 9 0.24
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (17 bp):
AATTTTTGAAAACACGA
Found at i:35226037 original size:19 final size:19
Alignment explanation
Indices: 35225997--35226061 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
35225987 ACAATAATAA
35225997 TTTTTGAAAACACGAAGA--
1 TTTTTGAAAACACGAA-ATT
35226015 TTTTTG-AAACACGAAATT
1 TTTTTGAAAACACGAAATT
*
35226033 TTTTTGAAAACACGGAATT
1 TTTTTGAAAACACGAAATT
*
35226052 TTTTTTAAAA
1 TTTTTGAAAA
35226062 ACAAGGAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
16 1 0.02
17 9 0.21
18 12 0.29
19 20 0.48
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38
Consensus pattern (19 bp):
TTTTTGAAAACACGAAATT
Found at i:35226055 original size:36 final size:38
Alignment explanation
Indices: 35225979--35226054 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 38
35225969 AACACAGAAC
35225979 TTTGAAACACAATAATAATTTTTGAAAACACGAAGATT
1 TTTGAAACACAATAATAATTTTTGAAAACACGAAGATT
* * *
35226017 TTTGAAACACGA-AAT-TTTTTTGAAAACACGGA-ATT
1 TTTGAAACACAATAATAATTTTTGAAAACACGAAGATT
35226052 TTT
1 TTT
35226055 TTTAAAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 6 0.17
36 15 0.43
37 3 0.09
38 11 0.31
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.36
Consensus pattern (38 bp):
TTTGAAACACAATAATAATTTTTGAAAACACGAAGATT
Found at i:35226074 original size:19 final size:19
Alignment explanation
Indices: 35226027--35226074 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
35226017 TTTGAAACAC
* *
35226027 GAAATTTTTTTGAAAACACG
1 GAAA-TTTTTTAAAAACAAG
*
35226047 GAATTTTTTTTAAAAACAAG
1 GAA-ATTTTTTAAAAACAAG
35226067 GAAATTTT
1 GAAATTTT
35226075 CGATACATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (19 bp):
GAAATTTTTTAAAAACAAG
Found at i:35226212 original size:18 final size:18
Alignment explanation
Indices: 35226176--35226281 Score: 103
Period size: 17 Copynumber: 6.0 Consensus size: 18
35226166 TTGAAAACAC
*
35226176 GAAAACATGAAAA-TTTT
1 GAAAACACGAAAATTTTT
35226193 GAAAACACGAAAATTTTT
1 GAAAACACGAAAATTTTT
* *
35226211 G-AAACATGAGAATTTTTT
1 GAAAACACGA-AAATTTTT
35226229 GAAAACACGAAAAATTTTT
1 GAAAACACG-AAAATTTTT
* **
35226248 -TAAACACGGGAATTTTT
1 GAAAACACGAAAATTTTT
*
35226265 GAAAACATG-AAATTTTT
1 GAAAACACGAAAATTTTT
35226282 TATTTTTTAT
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
17 33 0.45
18 26 0.36
19 13 0.18
20 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.32
Consensus pattern (18 bp):
GAAAACACGAAAATTTTT
Found at i:35226236 original size:36 final size:35
Alignment explanation
Indices: 35226189--35226282 Score: 125
Period size: 36 Copynumber: 2.6 Consensus size: 35
35226179 AACATGAAAA
*
35226189 TTTTGAAAACACGAAAATTTTTGAAACATGAGAATT
1 TTTTGAAAACACGAAAATTTTTGAAACACGAGAA-T
* *
35226225 TTTTGAAAACACGAAAAATTTTTTAAACACGGGAAT
1 TTTTGAAAACACG-AAAATTTTTGAAACACGAGAAT
* *
35226261 TTTTGAAAACATGAAATTTTTT
1 TTTTGAAAACACGAAAATTTTT
35226283 ATTTTTTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
35 8 0.15
36 26 0.50
37 18 0.35
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (35 bp):
TTTTGAAAACACGAAAATTTTTGAAACACGAGAAT
Found at i:35226282 original size:18 final size:18
Alignment explanation
Indices: 35226176--35226282 Score: 89
Period size: 18 Copynumber: 6.0 Consensus size: 18
35226166 TTGAAAACAC
*
35226176 GAAAACATGAAA-ATTTT
1 GAAAACATGAAATTTTTT
* *
35226193 GAAAACACGAAAATTTTT
1 GAAAACATGAAATTTTTT
35226211 G-AAACATGAGAATTTTTT
1 GAAAACATGA-AATTTTTT
*
35226229 GAAAACACGAAAAATTTTTT
1 GAAAACATG--AAATTTTTT
* *
35226249 --AAACACGGGAA-TTTTT
1 GAAAACA-TGAAATTTTTT
35226265 GAAAACATGAAATTTTTT
1 GAAAACATGAAATTTTTT
35226283 ATTTTTTATT
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
16 5 0.07
17 23 0.32
18 28 0.39
19 7 0.10
20 8 0.11
21 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (18 bp):
GAAAACATGAAATTTTTT
Found at i:35226315 original size:17 final size:17
Alignment explanation
Indices: 35226295--35226339 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
35226285 TTTTTATTTT
35226295 TTTTAAAAACACGGAAA
1 TTTTAAAAACACGGAAA
*
35226312 TTTT-AAAACATGGAAA
1 TTTTAAAAACACGGAAA
*
35226328 CTTTAAAAACAC
1 TTTTAAAAACAC
35226340 AAATTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (17 bp):
TTTTAAAAACACGGAAA
Found at i:35226358 original size:20 final size:22
Alignment explanation
Indices: 35226333--35226374 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
35226323 GGAAACTTTA
35226333 AAAACACAA-ATTTTT-TTTTT
1 AAAACACAAGATTTTTATTTTT
35226353 AAAACACAAGATTTTTATTTTT
1 AAAACACAAGATTTTTATTTTT
35226375 TTTATTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 6 0.30
22 5 0.25
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (22 bp):
AAAACACAAGATTTTTATTTTT
Found at i:35226996 original size:22 final size:22
Alignment explanation
Indices: 35226968--35227023 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
35226958 CTTTTTATTT
*
35226968 TCTTTTTTTCTTTC-CTTTTTC
1 TCTTTTTTTCTTCCTCTTTTTC
* *
35226989 TCTCTTTTTCTTCCTCTTTTTT
1 TCTTTTTTTCTTCCTCTTTTTC
35227011 TCTTTTTTTCTTC
1 TCTTTTTTTCTTC
35227024 TTCTCTTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
TCTTTTTTTCTTCCTCTTTTTC
Found at i:35227035 original size:22 final size:21
Alignment explanation
Indices: 35226967--35227036 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 21
35226957 ACTTTTTATT
35226967 TTCTTTTTTTCTTTCCTT-TTTC
1 TTCTTTTTTTC-TT-CTTCTTTC
*
35226989 TCTCTTTTTCTTCCTCTT-TTT-
1 T-TCTTTTT-TTCTTCTTCTTTC
35227010 TTCTTTTTTTCTTCTTCTCTTC
1 TTCTTTTTTTCTTCTTCT-TTC
35227032 TTCTT
1 TTCTT
35227037 GTCTCAAAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 7 0.17
20 8 0.20
21 3 0.07
22 12 0.29
23 8 0.20
24 3 0.07
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (21 bp):
TTCTTTTTTTCTTCTTCTTTC
Found at i:35227705 original size:29 final size:29
Alignment explanation
Indices: 35227576--35227735 Score: 110
Period size: 30 Copynumber: 5.4 Consensus size: 29
35227566 GCAAAGCTTC
** *
35227576 TGGGG-CAAAAGTGTAATTTTAGCAAAAATA
1 TGGGGTCAAAA-TGTAATTTTAG-AAAGTTT
* * *
35227606 T-GGGCCAAAATGTAATTTCTTGAGAGTTT
1 TGGGGTCAAAATGTAATTT-TAGAAAGTTT
** * * *
35227635 AAGGGTCAAAGTGCAATTTTGAGAAAGTCT
1 TGGGGTCAAAATGTAATTTT-AGAAAGTTT
** * *
35227665 AAGTGTCGAAATGTAATTTTAGAAAGTTT
1 TGGGGTCAAAATGTAATTTTAGAAAGTTT
35227694 TGGGGTCAAAATGTAAATTTTAGAAAAG-TT
1 TGGGGTCAAAATGT-AATTTTAG-AAAGTTT
35227724 TGGGGTCAAAAT
1 TGGGGTCAAAAT
35227736 ATAAAATTTG
Statistics
Matches: 103, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
29 33 0.32
30 66 0.64
31 4 0.04
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (29 bp):
TGGGGTCAAAATGTAATTTTAGAAAGTTT
Found at i:35227743 original size:31 final size:30
Alignment explanation
Indices: 35227679--35227751 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
35227669 GTCGAAATGT
*
35227679 AATTTTAG-AAAGTTTTGGGGTCAAAATGTA
1 AATTTTAGAAAAG-TTTGGGGTCAAAATATA
35227709 AATTTTAGAAAAGTTTGGGGTCAAAATATA
1 AATTTTAGAAAAGTTTGGGGTCAAAATATA
*
35227739 AAATTT-GAAAAGT
1 AATTTTAGAAAAGT
35227752 ATAAGGGTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 7 0.17
30 29 0.73
31 4 0.10
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (30 bp):
AATTTTAGAAAAGTTTGGGGTCAAAATATA
Found at i:35228310 original size:89 final size:83
Alignment explanation
Indices: 35228045--35230168 Score: 1664
Period size: 76 Copynumber: 26.8 Consensus size: 83
35228035 CGACATGTGC
* *
35228045 CCCGAGGTTCAACTCAAC-TCTCGCAATATGAGTTGA-TTTTTG----AAAAACATG-AA-TT-G
1 CCCGAGGCTCAACTC-ACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACA-GAAATTTAA
*
35228101 AAAAATACCTCGGCGT--GA
64 AAAAATACCTCAGCGTGCGA
* *
35228119 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG----AAAAACAAAAATTTAAAA
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACAGAAATTTAAAA
** *
35228179 GAAATACCTC-G-GTATGG
66 -AAATACCTCAGCGTGCGA
* * *
35228196 TCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAAAAAACAGAAAT
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTG----A-A-AAAAAAACAGAAAT
35228261 TTAAAAAAATACCTCAGCGTGCGA
60 TTAAAAAAATACCTCAGCGTGCGA
35228285 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAAAAAAAACAGAAATTTAAAA
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACAGAAATTT-AAA
35228349 AAAATACCTCAGCGTGCGA
65 AAAATACCTCAGCGTGCGA
35228368 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA---TTT---AAAAAAACAGAAATTTTTAA
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACAGAAA--TTTAA
*
35228427 AAAAATACCTCAGCGTGCAA
64 AAAAATACCTCAGCGTGCGA
35228447 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTG-AAAAAAAACAGAAATTTTAAA
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACAGAAA-TTTAAA
*
35228510 AAAATACCTCAGTGTGCGA
65 AAAATACCTCAGCGTGCGA
35228529 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTG-AAAAAAAACAGAAATTTAAAA
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACAGAAATTTAAAA
35228592 AAATACCTCAGCGTGCGA
66 AAATACCTCAGCGTGCGA
* *
35228610 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTG-AAAAAAAATAGAAATTAAAAA
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACAGAAATTTAAAA
35228673 AAATACCTCAGCGTGCGA
66 AAATACCTCAGCGTGCGA
* * *
35228691 CCCGAGGCTCAACTCACTTTTCGCAATATGAGTTGA---TTT---AAAAAAATAGAATTTTTTAA
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACAGAA--ATTTAA
35228750 AAAAATACCTCAGCGTGCGA
64 AAAAATACCTCAGCGTGCGA
* * *
35228770 CCCGAGGCTCAACTCACTTTTCGCAATATGAGTTGA---TTT---AAAAAAATAGAATTTTTTAA
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACAGAA--ATTTAA
35228829 AAAAATACCTCAGCGTGCGA
64 AAAAATACCTCAGCGTGCGA
* * *
35228849 CCCAATGTTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAAAAAAAAACAGAAATTTTAA
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTG-AAAAAAAAACAGAAA-TTTAA
35228913 AAAAATACCTCAGCGTGCGA
64 AAAAATACCTCAGCGTGCGA
* * *
35228933 CCCAATGTTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAAAAAAAAACAGAAATTTTAA
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTG-AAAAAAAAACAGAAA-TTTAA
35228997 AAAAATACCTCAGCGTGCGA
64 AAAAATACCTCAGCGTGCGA
* * * *
35229017 CCCAATGTTCGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAAAAA-ACGAAAA
1 CCC---G--AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACA-GAAAT
* * * *
35229081 TT-GAAAAATACCTCGGCATGTGA
60 TTAAAAAAATACCTCAGCGTGCGA
* * * *
35229104 CCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTG--AAAAAAACA-AAAATTGAAA
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACAGAAATTTAAAA
* * *
35229166 AAATACCTCGGCATGTGA
66 AAATACCTCAGCGTGCGA
* * * *
35229184 CCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTCG--AAAAAAACA-AAAATT-AA
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTT-GAAAAAAAAACAGAAATTTAAA
* * *
35229245 AAAATACCTCGGCATGTGA
65 AAAATACCTCAGCGTGCGA
* * * ***** * *
35229264 CCCGAAGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTTTTGAAAAACATAAA-TT--G
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTTGAAAAAAAAACAGAAATTTAAA
35229326 AAAATACCTCAGCGT--GA
65 AAAATACCTCAGCGTGCGA
* * * * * *
35229343 CCTGAGGTTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTAAAAAAAAACAG-AAGTT--A
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTTGAAAAAAAAACAGAAATTTAAA
35229405 AAAATACCTCAGCGT--GA
65 AAAATACCTCAGCGTGCGA
* * * **
35229422 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA--TTTAAAAAAAAAAGACTA-AAA-TT--
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAA-AC-AGAAATTTAA
35229480 AAAAATACCTCAGCGT--GA
64 AAAAATACCTCAGCGTGCGA
* * * * **
35229498 CCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGA--TTTAAAAAAAAAAGACTA-AAA-TT--
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAA-AC-AGAAATTTAA
35229556 AAAAATACCTCAGCGT--GA
64 AAAAATACCTCAGCGTGCGA
* * * * **
35229574 CCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGA--TTTAAAAAAAAAAGACTA-AAA-TT--
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAA-AC-AGAAATTTAA
35229632 AAAAATACCTCAGCGT--GA
64 AAAAATACCTCAGCGTGCGA
* * * * **
35229650 CCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGA--TTTAAAAAAAAAAGACTA-AAA-TT--
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAA-AC-AGAAATTTAA
35229708 AAAAATACCTCAGCGT--GA
64 AAAAATACCTCAGCGTGCGA
* * * * **
35229726 CCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGA--TTTAAAAAAAAAAGACTA-AAA-TT--
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAA-AC-AGAAATTTAA
35229784 AAAAATACCTCAGCGT--GA
64 AAAAATACCTCAGCGTGCGA
* * * * **
35229802 CCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGA--TTTAAAAAAAAAAGACTA-AAA-TT--
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAA-AC-AGAAATTTAA
35229860 AAAAATACCTCAGCGT--GA
64 AAAAATACCTCAGCGTGCGA
* * * * **
35229878 CCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGA--TTTAAAAAAAAAAGACTA-AAA-TT--
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAA-AC-AGAAATTTAA
35229936 AAAAATACCTCAGCGT--GA
64 AAAAATACCTCAGCGTGCGA
* * * * **
35229954 CCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGA--TTTAAAAAAAAAAGACTA-AAA-TT--
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAA-AC-AGAAATTTAA
35230012 AAAAATACCTCAGCGT--GA
64 AAAAATACCTCAGCGTGCGA
* * * * **
35230030 CCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGA--TTTAAAAAAAAAAGACTA-AAA-TT--
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAA-AC-AGAAATTTAA
35230088 AAAAATACCTCAGCGT--GA
64 AAAAATACCTCAGCGTGCGA
* * * * * *
35230106 CCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTCTTG--AAAAAAACAGAATTTTAAAA
1 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACAGAAATTTAAAA
35230168 A
66 A
35230169 TATTTCTTGA
Statistics
Matches: 1921, Mismatches: 69, Indels: 116
0.91 0.03 0.06
Matches are distributed among these distances:
73 2 0.00
74 48 0.02
75 19 0.01
76 675 0.35
77 59 0.03
78 39 0.02
79 289 0.15
80 126 0.07
81 183 0.10
82 143 0.07
83 75 0.04
84 114 0.06
85 11 0.01
87 29 0.02
88 27 0.01
89 76 0.04
90 6 0.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (83 bp):
CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACAGAAATTTAAAA
AAATACCTCAGCGTGCGA
Found at i:35229495 original size:76 final size:78
Alignment explanation
Indices: 35228264--35230143 Score: 1829
Period size: 76 Copynumber: 23.7 Consensus size: 78
35228254 CAGAAATTTA
* * **
35228264 AAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAA
1 AAAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTAAAA
35228329 AAAAAA-AC-AGAAATTT
63 AAAAAAGACTA-AAA-TT
* *
35228345 AAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTT-AA
1 --AAAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAA
* **
35228409 AAAAACAGA--AATTTTT
62 AAAAAAAGACTAA-AATT
* *
35228425 AAAAAAATACCTCAGCGTGCAACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 -AAAAAATACCTCAGCGTG--ACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTT-A
* **
35228490 AAAAAAACAGA--AATTTT
60 AAAAAAAAAGACTAAAATT
* * * ***
35228507 AAAAAAATACCTCAGTGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 -AAAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAA
35228572 AAAAAA-AC-AGAAATTT
63 AAAAAAGACTA-AAA-TT
* * ***
35228588 AAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 -AAAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAA
35228653 AAAAAA-A-TAGAAATT
63 AAAAAAGACTA-AAATT
* * *
35228668 AAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTTTCGCAATATGAGTTGATTT-AA
1 --AAAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAA
* * ***
35228732 AAAAATAGAAT-TTTTT
62 AAAAAAAGACTAAAATT
* * *
35228748 AAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTTTCGCAATATGAGTTGATTT-AAA
1 -AAAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAA
* * ***
35228812 AAAATAGAAT-TTTTT
63 AAAAAAGACTAAAATT
* * * * * *
35228827 AAAAAAATACCTCAGCGTGCGACCCAATGTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 -AAAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTAA
35228892 AAAAAAAA-AC-AGAAATTTT
61 AAAAAAAAGACTA-AAA--TT
* * * * * *
35228911 AAAAAAATACCTCAGCGTGCGACCCAATGTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 -AAAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTAA
35228976 AAAAAAAA-AC-AGAAATTTT
61 AAAAAAAAGACTA-AAA--TT
*
35228995 AAAAAAATACCTCAGCGTGCGACCCAATGTTCGGCTCAACTCACCTCTCGCATTATGAGTTGATT
1 -AAAAAATACCTCAGCGT--GACCC---G--AGGCTCAACTCACCTCTCGCATTATGAGTTGA--
* *
35229060 TTTTGAAAAAAAAA-ACGAAAATT
56 -TTTAAAAAAAAAAGACTAAAATT
* * ****
35229083 GAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGA
1 AAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAA
*
35229148 AAAAA-ACAAAAATT
64 AAAAAGACTAAAATT
* * ***
35229162 GAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTC
1 -AAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTAAA
* *
35229227 GAAAAAA-ACAAAAATT
62 AAAAAAAGACTAAAATT
* * **
35229243 AAAAAATACCTCGGCATGTGACCCGAAGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTT
1 AAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA---TTTAA
****
35229308 TTTGAAAA-AC-ATAAATT
61 AAAAAAAAGACTA-AAATT
* * * **
35229325 -GAAAATACCTCAGCGTGACCTGAGGTTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTAA
1 AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA---TTTAAAA
*
35229389 AAAAAA-AC-AGAAGTT
63 AAAAAAGACTA-AAATT
*
35229404 -AAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAA
1 AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAA
35229467 AAAGACTAAAATT
66 AAAGACTAAAATT
* *
35229480 -AAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAA
1 AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAA
35229543 AAAGACTAAAATT
66 AAAGACTAAAATT
* *
35229556 -AAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAA
1 AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAA
35229619 AAAGACTAAAATT
66 AAAGACTAAAATT
* *
35229632 -AAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAA
1 AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAA
35229695 AAAGACTAAAATT
66 AAAGACTAAAATT
* *
35229708 -AAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAA
1 AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAA
35229771 AAAGACTAAAATT
66 AAAGACTAAAATT
* *
35229784 -AAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAA
1 AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAA
35229847 AAAGACTAAAATT
66 AAAGACTAAAATT
* *
35229860 -AAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAA
1 AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAA
35229923 AAAGACTAAAATT
66 AAAGACTAAAATT
* *
35229936 -AAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAA
1 AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAA
35229999 AAAGACTAAAATT
66 AAAGACTAAAATT
* *
35230012 -AAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAA
1 AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAA
35230075 AAAGACTAAAATT
66 AAAGACTAAAATT
* *
35230088 -AAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTT
1 AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTT
35230144 CTTGAAAAAA
Statistics
Matches: 1687, Mismatches: 70, Indels: 87
0.91 0.04 0.05
Matches are distributed among these distances:
75 11 0.01
76 669 0.40
77 2 0.00
78 14 0.01
79 304 0.18
80 127 0.08
81 188 0.11
82 119 0.07
83 70 0.04
84 113 0.07
87 18 0.01
88 2 0.00
89 29 0.02
90 20 0.01
91 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (78 bp):
AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAA
AAAGACTAAAATT
Found at i:35229654 original size:228 final size:232
Alignment explanation
Indices: 35228053--35230143 Score: 1905
Period size: 228 Copynumber: 8.8 Consensus size: 232
35228043 GCCCCGAGGT
* * *** * * * *
35228053 TCAACTCAACTCTCGCAATATGAGTTGATTT-TTGAAAAACA-T-GAATTGAAAAATACCTCGGC
1 TCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAAACTAAAATTAAAAAATACCTCAGC
* * * *
35228115 GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTTAAA--
66 GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTT-AAAAAAAAAAACTAAAATT
* * ** ** * *
35228178 AGAAATACCTCGGTATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA
128 AAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA---TTT--AAA
* *
35228243 ACATAAAAAAAC-AGAAATTTAAAAAAATACCTCAGCGTGCGACCCGAGGC
188 A-A-AAAAAGACTA-AAA-TT-AAAAAATACCTCAGCGT-CGACCCGAAGC
* * **
35228293 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAAAAAAC-AGAAATTTAAAAAAAATACC
1 TCAACTCACCTCTCGCATTATGAGTTGA-TTTAAAAAAAAAAACTA-AAA-TT--AAAAAATACC
* * *
35228357 TCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTAAAAAAACAGAAATT
61 TCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAA-A-AAA-C
** * *
35228422 TTTAA--AAAAATACCTCAGCGTGCAACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
121 TAAAATTAAAAATACCTCAGCGTG--ACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--
* ** * *
35228485 TTTGAAAAAAAACAGA--AATTTTAAAAAAATACCTCAGTGTGCGACCCGAGGC
182 TTT-AAAAAAAAAAGACTAAAATT-AAAAAATACCTCAGCGT-CGACCCGAAGC
* * ***
35228537 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAAAAAC-AGAAATTTAAAAAAATACCTC
1 TCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAAACTA-AAA-TT-AAAAAATACCTC
* * ***
35228601 AGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAAAAA-TAGAA
63 AGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAAACTA-AA
* * *
35228665 ATTAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTTTCGCAATATGAGTTGATTT
125 ATT---AAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTT
* * *** *
35228730 -AAAAAAATAGAAT-TTTTTAAAAAAATACCTCAGCGTGCGACCCGAGGC
185 AAAAAAAAAAGACTAAAATT-AAAAAATACCTCAGCGT-CGACCCGAAGC
* * * * ***
35228778 TCAACTCACTTTTCGCAATATGAGTTGATTTAAAAAAATAGAA-T-TTTTTAAAAAAATACCTCA
1 TCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAA-AAAACTAAAATT-AAAAAATACCTCA
* * * * * *
35228841 GCGTGCGACCCAATGTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAAAAAAAC-AGA
64 GCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTAAAAAAAAAAACTA-A
* * * * *
35228905 AATTTTAAAAAAATACCTCAGCGTGCGACCCAATGTTCAACTCACTTCTCGCAATATGAGTTGAT
124 AA--TT--AAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-
*
35228970 TTTTGAAAAAAAAA-AC-AGAAATTTTAAAAAAATACCTCAGCGTGCGACCC-AATGTTCGGC
182 -TTTAAAAAAAAAAGACTA-AAA--TT-AAAAAATACCTCAGCGT-CGACCCGAA------GC
* * *
35229030 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAAAAAACGAAAATTGAAAAATACCTC
1 TCAACTCACCTCTCGCATTATGAGTTGA---TTTAAAAAAAAAAACTAAAATTAAAAAATACCTC
* **** *
35229095 GGCATGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAAACAAAAA
63 AGC--GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAAACTAAAA
* * *
35229160 TTGAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTT
126 TT--AAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTA
*** * *
35229225 TCGAAAAAA-ACAAAAATTAAAAAATACCTCGGCATGT-GACCCGAAGC
186 AAAAAAAAAGACTAAAATTAAAAAATACCTCAGC--GTCGACCCGAAGC
****** *
35229272 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTTTTGAAAAAC-ATAAATT-GAAAATACCT
1 TCAACTCACCTCTCGCATTATGAGTTGA---TTTAAAAAAAAAAACTA-AAATTAAAAAATACCT
* * **
35229335 CAGCGTGACCTGAGGTTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTAAAAAAAAAC-AG
62 CAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA---TTTAAAAAAAAAAACTA-
* *
35229399 AAGTTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAA
123 AAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAA
35229463 AAAAAAAGACTAAAATT-AAAAATACCTCAGCGT-GACCCGAAGC
188 AAAAAAAGACTAAAATTAAAAAATACCTCAGCGTCGACCCGAAGC
*
35229506 TCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAAAAGACTAAAATT-AAAAATACCTCAG
1 TCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAA-ACTAAAATTAAAAAATACCTCAG
* *
35229569 CGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAAAAGACTAAAATTA
65 CGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAA-ACTAAAATTA
* *
35229633 AAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAAA
129 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAA
35229697 AGACTAAAATT-AAAAATACCTCAGCGT-GACCCGAAGC
194 AGACTAAAATTAAAAAATACCTCAGCGTCGACCCGAAGC
*
35229734 TCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAAAAGACTAAAATT-AAAAATACCTCAG
1 TCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAA-ACTAAAATTAAAAAATACCTCAG
* *
35229797 CGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAAAAGACTAAAATTA
65 CGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAA-ACTAAAATTA
* *
35229861 AAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAAA
129 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAA
35229925 AGACTAAAATT-AAAAATACCTCAGCGT-GACCCGAAGC
194 AGACTAAAATTAAAAAATACCTCAGCGTCGACCCGAAGC
*
35229962 TCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAAAAGACTAAAATT-AAAAATACCTCAG
1 TCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAA-ACTAAAATTAAAAAATACCTCAG
* *
35230025 CGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAAAAGACTAAAATTA
65 CGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAA-ACTAAAATTA
* *
35230089 AAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTT
129 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTT
35230144 CTTGAAAAAA
Statistics
Matches: 1650, Mismatches: 132, Indels: 150
0.85 0.07 0.08
Matches are distributed among these distances:
227 11 0.01
228 517 0.31
229 1 0.00
230 20 0.01
231 42 0.03
232 1 0.00
233 13 0.01
234 25 0.02
236 22 0.01
237 20 0.01
238 26 0.02
239 97 0.06
240 52 0.03
241 101 0.06
242 195 0.12
243 23 0.01
244 117 0.07
245 11 0.01
246 9 0.01
247 70 0.04
248 8 0.00
249 61 0.04
250 20 0.01
251 82 0.05
252 27 0.02
253 16 0.01
254 4 0.00
255 55 0.03
256 2 0.00
257 2 0.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (232 bp):
TCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAAACTAAAATTAAAAAATACCTCAGC
GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAAACTAAAATTAAA
AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAAG
ACTAAAATTAAAAAATACCTCAGCGTCGACCCGAAGC
Found at i:35230198 original size:30 final size:30
Alignment explanation
Indices: 35230140--35230198 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
35230130 TTATGAGTTG
*
35230140 ATTTCTTGAAAAAAACAGAATTTTAAAAAT
1 ATTTCTTGAAAAAAACAGAATTTCAAAAAT
* **
35230170 ATTTCTTGAAAGAAACAGGGTTTCAAAAA
1 ATTTCTTGAAAAAAACAGAATTTCAAAAA
35230199 ACATCAGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (30 bp):
ATTTCTTGAAAAAAACAGAATTTCAAAAAT
Found at i:35231050 original size:18 final size:16
Alignment explanation
Indices: 35231029--35231084 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
35231019 TTGATTTTTC
* *
35231029 TTTTTCTTTTCTTTGT
1 TTTTTTTTTTTTTTGT
*
35231045 TTTTTTTGTTTTTTTAT
1 TTTTTTT-TTTTTTTGT
*
35231062 TTTTTGTTATTTTTTGT
1 TTTTT-TTTTTTTTTGT
35231079 TTTTTT
1 TTTTTT
35231085 GTCCATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 7 0.21
17 24 0.73
18 2 0.06
ACGTcount: A:0.04, C:0.04, G:0.07, T:0.86
Consensus pattern (16 bp):
TTTTTTTTTTTTTTGT
Found at i:35231057 original size:25 final size:25
Alignment explanation
Indices: 35231023--35231084 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 25
35231013 TTCATCTTGA
* *
35231023 TTTTTCTTTTTCTT-TTCTTTGTT-T
1 TTTTTGTTTTT-TTATTTTTTGTTAT
35231047 TTTTTGTTTTTTTATTTTTTGTTAT
1 TTTTTGTTTTTTTATTTTTTGTTAT
35231072 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
35231085 GTCCATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 14 0.41
ACGTcount: A:0.03, C:0.05, G:0.06, T:0.85
Consensus pattern (25 bp):
TTTTTGTTTTTTTATTTTTTGTTAT
Found at i:35231064 original size:15 final size:16
Alignment explanation
Indices: 35231046--35231075 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35231036 TTTCTTTGTT
35231046 TTTTTTGTT-TTTTTA
1 TTTTTTGTTATTTTTA
35231061 TTTTTTGTTATTTTT
1 TTTTTTGTTATTTTT
35231076 TGTTTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.87
Consensus pattern (16 bp):
TTTTTTGTTATTTTTA
Found at i:35231085 original size:18 final size:18
Alignment explanation
Indices: 35231035--35231086 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
35231025 TTTCTTTTTC
35231035 TTTTCTTTGTTTTTTT-TG
1 TTTT-TTTGTTTTTTTGTG
*
35231053 TTTTTTT-ATTTTTTGT-
1 TTTTTTTGTTTTTTTGTG
35231069 TATTTTTTGTTTTTTTGT
1 T-TTTTTTGTTTTTTTGT
35231087 CCATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 7 0.24
17 10 0.34
18 12 0.41
ACGTcount: A:0.04, C:0.02, G:0.10, T:0.85
Consensus pattern (18 bp):
TTTTTTTGTTTTTTTGTG
Found at i:35236921 original size:19 final size:18
Alignment explanation
Indices: 35236899--35236958 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
35236889 AACACGAAGA
35236899 TTTTTGAAACAC-GAAAAT
1 TTTTTGAAACACAG-AAAT
*
35236917 TTTTTGAAAACACAGAATTT
1 TTTTTG-AAACACAGAA-AT
35236937 TTTTTGAAA-ACAAGGAAAT
1 TTTTTGAAACAC-A-GAAAT
35236956 TTT
1 TTT
35236959 CGATACATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 8 0.23
19 16 0.46
20 11 0.31
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (18 bp):
TTTTTGAAACACAGAAAT
Found at i:35236941 original size:20 final size:19
Alignment explanation
Indices: 35236881--35237179 Score: 107
Period size: 18 Copynumber: 16.3 Consensus size: 19
35236871 ACAATAATAA
* *
35236881 TTTTCGAAAACACGAAGA-
1 TTTTTGAAAACACGAAAAT
35236899 TTTTTG-AAACACGAAAAT
1 TTTTTGAAAACACGAAAAT
**
35236917 TTTTTGAAAACACAGAATTT
1 TTTTTGAAAACAC-GAAAAT
* *
35236937 TTTTTGAAAACAAGGAAA-
1 TTTTTGAAAACACGAAAAT
* * * *
35236955 TTTTCG-ATACATGAGAAT
1 TTTTTGAAAACACGAAAAT
35236973 TTTTTG---ACACGAAAA-
1 TTTTTGAAAACACGAAAAT
*
35236988 ATTTTGAAAACACGAAAA-
1 TTTTTGAAAACACGAAAAT
*
35237006 -TTTTGAAAACATG---AT
1 TTTTTGAAAACACGAAAAT
** * **
35237021 TTTTTTTAAATACG-ATTT
1 TTTTTGAAAACACGAAAAT
* * *
35237039 TTTTTAAAAACATGAGAATTT
1 TTTTTGAAAACACGA-AA-AT
35237060 TTTTTGAAAACACGAAAACAT
1 TTTTTGAAAACACG-AAA-AT
* *
35237081 GAAAATTTTGAAAAAACGAAAA-
1 ----TTTTTGAAAACACGAAAAT
* *
35237103 TTTTTG-AAACATGAGAAT
1 TTTTTGAAAACACGAAAAT
* *
35237121 TTTTTGAAAACATGAAAAAA
1 TTTTTGAAAACACG-AAAAT
**
35237141 TTTTT--AAACACGGGAA-
1 TTTTTGAAAACACGAAAAT
*
35237157 TTTTTGATAACACG-AAAT
1 TTTTTGAAAACACGAAAAT
35237175 TTTTT
1 TTTTT
35237180 ATTTTTTATT
Statistics
Matches: 211, Mismatches: 45, Indels: 50
0.69 0.15 0.16
Matches are distributed among these distances:
14 1 0.00
15 5 0.02
16 21 0.10
17 41 0.19
18 69 0.33
19 15 0.07
20 25 0.12
21 17 0.08
22 1 0.00
23 1 0.00
24 3 0.01
25 12 0.06
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (19 bp):
TTTTTGAAAACACGAAAAT
Found at i:35236958 original size:21 final size:20
Alignment explanation
Indices: 35236899--35236948 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
35236889 AACACGAAGA
**
35236899 TTTTTG-AAACAC-GAAAAT
1 TTTTTGAAAACACAGAATTT
35236917 TTTTTGAAAACACAGAATTT
1 TTTTTGAAAACACAGAATTT
35236937 TTTTTGAAAACA
1 TTTTTGAAAACA
35236949 AGGAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 6 0.21
19 6 0.21
20 16 0.57
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (20 bp):
TTTTTGAAAACACAGAATTT
Found at i:35237010 original size:17 final size:17
Alignment explanation
Indices: 35236879--35237016 Score: 75
Period size: 17 Copynumber: 7.8 Consensus size: 17
35236869 ACACAATAAT
35236879 AATTTTCGAAAACACGAA
1 AATTTT-GAAAACACGAA
*
35236897 GATTTTTG-AAACACGAA
1 -AATTTTGAAAACACGAA
35236914 AATTTTTTGAAAACACAGAA
1 AA--TTTTGAAAACAC-GAA
** * *
35236934 TTTTTTTTGAAAACAAGGA
1 --AATTTTGAAAACACGAA
* * *
35236953 AATTTTCG-ATACATGAG
1 AATTTT-GAAAACACGAA
***
35236970 AATTTT-TTGACACGAAA
1 AATTTTGAAAACACG-AA
35236987 AATTTTGAAAACACGAA
1 AATTTTGAAAACACGAA
35237004 AATTTTGAAAACA
1 AATTTTGAAAACA
35237017 TGATTTTTTT
Statistics
Matches: 90, Mismatches: 19, Indels: 22
0.69 0.15 0.17
Matches are distributed among these distances:
16 5 0.06
17 46 0.51
18 12 0.13
19 13 0.14
20 14 0.16
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (17 bp):
AATTTTGAAAACACGAA
Found at i:35237212 original size:17 final size:17
Alignment explanation
Indices: 35237192--35237252 Score: 63
Period size: 16 Copynumber: 3.7 Consensus size: 17
35237182 TTTTTATTTT
35237192 TTTTAAAAACACGAAAA
1 TTTTAAAAACACGAAAA
* *
35237209 TTTT-AAAACATGGAAA
1 TTTTAAAAACACGAAAA
**
35237225 -TTTAAAAACACGAATT
1 TTTTAAAAACACGAAAA
*
35237241 TTTTTAAAACAC
1 TTTTAAAAACAC
35237253 AAGTTTTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
15 3 0.09
16 18 0.51
17 14 0.40
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (17 bp):
TTTTAAAAACACGAAAA
Found at i:35237259 original size:17 final size:17
Alignment explanation
Indices: 35237229--35237262 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
35237219 TGGAAATTTA
35237229 AAAACACGAATTTTTTT
1 AAAACACGAATTTTTTT
*
35237246 AAAACAC-AAGTTTTTT
1 AAAACACGAATTTTTTT
35237262 A
1 A
35237263 TTTTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (17 bp):
AAAACACGAATTTTTTT
Found at i:35237861 original size:23 final size:23
Alignment explanation
Indices: 35237835--35237879 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
35237825 GGCTGCTGTT
35237835 TTTTATTTTTTTATTACTTTTTA
1 TTTTATTTTTTTATTACTTTTTA
* * *
35237858 TTTTCTTTTTTTCTTTCTTTTT
1 TTTTATTTTTTTATTACTTTTT
35237880 TCTCTCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTATTTTTTTATTACTTTTTA
Found at i:35237880 original size:11 final size:11
Alignment explanation
Indices: 35237841--35237915 Score: 55
Period size: 11 Copynumber: 6.5 Consensus size: 11
35237831 TGTTTTTTAT
* *
35237841 TTTTTTATTAC
1 TTTTTTCTTTC
35237852 TTTTTAT-TTTC
1 TTTTT-TCTTTC
35237863 TTTTTTTCTTTC
1 -TTTTTTCTTTC
*
35237875 TTTTTTCTCTC
1 TTTTTTCTTTC
35237886 -TTTTTCTTCCTC
1 TTTTTTCTT--TC
*
35237898 TTTTTTTTTTTC
1 -TTTTTTCTTTC
35237910 TTTTTT
1 TTTTTT
35237916 TTCTTCTTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
10 7 0.13
11 25 0.47
12 14 0.26
14 7 0.13
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:35237880 original size:35 final size:34
Alignment explanation
Indices: 35237851--35237920 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 34
35237841 TTTTTTATTA
*
35237851 CTTTTTATT-TTCTTTTTTTCTTTCTTTTTTCTCT
1 CTTTTTATTCCTCTTTTTTTCTTTCTTTTTT-TCT
* *
35237885 CTTTTTCTTCCTCTTTTTTTTTTTCTTTTTTT-T
1 CTTTTTATTCCTCTTTTTTTCTTTCTTTTTTTCT
35237918 CTT
1 CTT
35237921 CTTCTCTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 4 0.12
34 9 0.28
35 19 0.59
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (34 bp):
CTTTTTATTCCTCTTTTTTTCTTTCTTTTTTTCT
Found at i:35237906 original size:27 final size:27
Alignment explanation
Indices: 35237869--35237931 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
35237859 TTTCTTTTTT
35237869 TCTTTC-TTTTTTCTCTCTTTTTCTTCC
1 TCTTTCTTTTTTTCT-TCTTTTTCTTCC
* * *
35237896 TCTTTTTTTTTTTCTTTTTTTTCTTCT
1 TCTTTCTTTTTTTCTTCTTTTTCTTCC
35237923 TCTCTTCTT
1 TCT-TTCTT
35237932 CTTGTCTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 18 0.60
28 12 0.40
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (27 bp):
TCTTTCTTTTTTTCTTCTTTTTCTTCC
Found at i:35237916 original size:11 final size:11
Alignment explanation
Indices: 35237833--35237923 Score: 74
Period size: 12 Copynumber: 7.8 Consensus size: 11
35237823 TGGGCTGCTG
*
35237833 TTTTTTATTTT
1 TTTTTTCTTTT
*
35237844 TTTATTACTTTT
1 TTT-TTTCTTTT
*
35237856 TATTTTCTTTT
1 TTTTTTCTTTT
35237867 TTTCTTTCTTTT
1 TTT-TTTCTTTT
* *
35237879 TTCTCTCTTTT
1 TTTTTTCTTTT
**
35237890 TCTTCCTCTTTTT
1 T-TTTTTC-TTTT
35237903 TTTTTTCTTTT
1 TTTTTTCTTTT
35237914 TTTTCTTCTT
1 TTTT-TTCTT
35237924 CTCTTCTTCT
Statistics
Matches: 64, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
11 28 0.44
12 31 0.48
13 5 0.08
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:35238599 original size:29 final size:29
Alignment explanation
Indices: 35238477--35238639 Score: 134
Period size: 30 Copynumber: 5.5 Consensus size: 29
35238467 CAAAGCTTCT
**
35238477 GGGG-CAAAAGTGTAATTTTAGCAAA-AATA
1 GGGGTCAAAA-TGTAATTTTAG-AAAGTTTA
* * * *
35238506 TGGGCCAAAATGTAATTTCTTGAGAGTTTA
1 GGGGTCAAAATGTAATTT-TAGAAAGTTTA
* * *
35238536 GGGGTCAAAGTGAAATTTTGAGAAAGTATA
1 GGGGTCAAAATGTAATTTT-AGAAAGTTTA
* ** *
35238566 AGGGTTGAAATGTAATTTTAGAAAGTTTT
1 GGGGTCAAAATGTAATTTTAGAAAGTTTA
35238595 GGGGTCAAAATGTAAATTTTAGAAAAGTTT-
1 GGGGTCAAAATGT-AATTTTAG-AAAGTTTA
35238625 GGGGTCAAAATGTAA
1 GGGGTCAAAATGTAA
35238640 AATTTTAAAA
Statistics
Matches: 106, Mismatches: 22, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
29 34 0.32
30 65 0.61
31 7 0.07
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTAGAAAGTTTA
Found at i:35238613 original size:30 final size:30
Alignment explanation
Indices: 35238511--35238646 Score: 136
Period size: 30 Copynumber: 4.5 Consensus size: 30
35238501 AAATATGGGC
* *
35238511 CAAAATGT-AATTTCTTGAGAGTTTAGGGGT
1 CAAAATGTAAATTT-TAGAAAGTTTAGGGGT
* * *
35238541 CAAAGTG-AAATTTTGAGAAAGTATAAGGGT
1 CAAAATGTAAATTTT-AGAAAGTTTAGGGGT
** *
35238571 TGAAATGT-AATTTTAGAAAGTTTTGGGGT
1 CAAAATGTAAATTTTAGAAAGTTTAGGGGT
35238600 CAAAATGTAAATTTTAGAAAAGTTT-GGGGT
1 CAAAATGTAAATTTTAG-AAAGTTTAGGGGT
35238630 CAAAATGTAAAATTTTA
1 CAAAATGT-AAATTTTA
35238647 AAATTACAGG
Statistics
Matches: 87, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
29 19 0.22
30 53 0.61
31 15 0.17
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.35
Consensus pattern (30 bp):
CAAAATGTAAATTTTAGAAAGTTTAGGGGT
Found at i:35238636 original size:59 final size:59
Alignment explanation
Indices: 35238476--35238639 Score: 149
Period size: 59 Copynumber: 2.8 Consensus size: 59
35238466 GCAAAGCTTC
* * * * *
35238476 TGGGG-CAAAAGTGT-AATTTTAGCAAAAATATGGGCCAAAATGTAATTTCTTGAGAGTTT
1 TGGGGTCAAAA-TGTAAATTTTAG-AAAAGTTTGGGTCAAAATGTAATTTCTAGAAAGTTT
* * * **
35238535 AGGGGTCAAAGTG-AAATTTT-GAGAAAGTATAAGGGTTGAAATGTAATTT-TAGAAAGTTT
1 TGGGGTCAAAATGTAAATTTTAGA-AAAGT-T-TGGGTCAAAATGTAATTTCTAGAAAGTTT
35238594 TGGGGTCAAAATGTAAATTTTAGAAAAGTTTGGGGTCAAAATGTAA
1 TGGGGTCAAAATGTAAATTTTAGAAAAGTTT-GGGTCAAAATGTAA
35238640 AATTTTAAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
57 1 0.01
58 5 0.06
59 44 0.54
60 30 0.37
61 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.32
Consensus pattern (59 bp):
TGGGGTCAAAATGTAAATTTTAGAAAAGTTTGGGTCAAAATGTAATTTCTAGAAAGTTT
Done.