Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 179 of 427
Found at i:49549439 original size:91 final size:93
Alignment explanation
Indices: 49549282--49549452 Score: 292
Period size: 91 Copynumber: 1.9 Consensus size: 93
49549272 CGCCCATAAG
* *
49549282 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
49549347 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
*
49549375 CGAACTCGGACTCAACTCAACGAGTTC-GACATT-GCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
49549438 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
49549453 CAAATTTCTA
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
91 44 0.59
92 4 0.05
93 26 0.35
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:49551861 original size:29 final size:29
Alignment explanation
Indices: 49551822--49551909 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
49551812 CAAAGATAAC
*
49551822 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
49551851 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
49551880 AAGATATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
49551910 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.11
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:49551880 original size:15 final size:15
Alignment explanation
Indices: 49551822--49551900 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
49551812 CAAAGATAAC
*
49551822 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
49551836 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
49551851 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
49551865 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
49551880 AAGATATCCAGGATA
1 AAGAAATCCAGAATA
49551895 AAGAAA
1 AAGAAA
49551901 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.16, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:49551909 original size:15 final size:15
Alignment explanation
Indices: 49551833--49551909 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
49551823 AGAAAACCGA
49551833 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
49551848 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
49551862 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
49551876 AATAAAGATATCCAGG
1 -ATAAAGAAATCCAAG
*
49551892 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
49551907 ATA
1 ATA
49551910 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.16, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:49554857 original size:46 final size:45
Alignment explanation
Indices: 49554790--49554963 Score: 181
Period size: 46 Copynumber: 3.8 Consensus size: 45
49554780 TGTAACCCGC
*
49554790 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
* * *
49554836 CCATAAGTGAACTCGGACTCAACT-AACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCGCAT
* *** * **
49554881 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
*
49554928 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
49554964 ATGCCCAAAT
Statistics
Matches: 103, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
45 17 0.17
46 70 0.68
47 16 0.16
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGCAT
Found at i:49554908 original size:92 final size:93
Alignment explanation
Indices: 49554797--49554968 Score: 292
Period size: 92 Copynumber: 1.9 Consensus size: 93
49554787 CGCCCATAAG
** *
49554797 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACT-A
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
49554861 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
*
49554889 CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
49554954 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
49554969 CAAATATCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 59 0.80
93 15 0.20
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:49567126 original size:42 final size:42
Alignment explanation
Indices: 49567019--49567140 Score: 165
Period size: 43 Copynumber: 2.9 Consensus size: 42
49567009 TACCGTACCA
* * * *
49567019 ATGCCATATCCCAGATATGGTCATAAATGTAATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATCG
* *
49567061 ATGCCAATAACCCAGAAATGGTCTTACACG-AAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGTAA-TCTCATATCG
49567104 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
49567141 GTAACCCTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
42 34 0.49
43 35 0.51
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATCG
Found at i:49569555 original size:21 final size:21
Alignment explanation
Indices: 49569529--49569569 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
49569519 AGCTTAAATG
49569529 ATGGTTGAATAAGTA-GAATTC
1 ATGGTTGAA-AAGTATGAATTC
49569550 ATGGTTGAAAAGTATGAATT
1 ATGGTTGAAAAGTATGAATT
49569570 GAAATTGCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.34
Consensus pattern (21 bp):
ATGGTTGAAAAGTATGAATTC
Found at i:49570281 original size:2 final size:2
Alignment explanation
Indices: 49570274--49570308 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
49570264 GACATTCGGT
49570274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49570309 GATAAATTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49570917 original size:39 final size:39
Alignment explanation
Indices: 49570861--49571019 Score: 205
Period size: 39 Copynumber: 4.1 Consensus size: 39
49570851 CATGGTATTT
* *
49570861 GAAATATATCCAGACATGAGGTCCGCAGGCTATATGCTAG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATGTGCT-G
*
49570901 G-AATATATCCGGACATGAGGTCCACAGGCTATGTGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATGTGCTG
* * *
49570939 GAAATATATCCGGACTTGAAGTCCGTAGGCTATGTGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATGTGCTG
* * *
49570978 GAAATATATCCGGACTTGTA-GTCCGTAGGCTACGTGCTG
1 GAAATATATCCGGACATG-AGGTCCGCAGGCTATGTGCTG
49571017 GAA
1 GAA
49571020 TGGTACCCGG
Statistics
Matches: 109, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
38 2 0.02
39 105 0.96
40 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (39 bp):
GAAATATATCCGGACATGAGGTCCGCAGGCTATGTGCTG
Found at i:49573150 original size:71 final size:71
Alignment explanation
Indices: 49573064--49573227 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
49573054 CGATTTGTCT
49573064 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
49573129 CTTTCA
66 CTTTCA
49573135 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
49573200 CTTTCA
66 CTTTCA
49573206 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
49573228 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:49573265 original size:71 final size:70
Alignment explanation
Indices: 49573064--49573261 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
49573054 CGATTTGTCT
* * * *
49573064 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
49573129 CTTTCA
65 CTTTCA
* * * *
49573135 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
49573200 CTTTCA
65 CTTTCA
* *
49573206 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
49573262 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:49590992 original size:28 final size:29
Alignment explanation
Indices: 49590951--49591007 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
49590941 ATTTTACAAT
*
49590951 TTAACCCCTCAATTTACACTTTTCTCAAA
1 TTAACCCCTCAATTGACACTTTTCTCAAA
* * *
49590980 TTAATCCCT-AATTGACATTTTTGTCAAA
1 TTAACCCCTCAATTGACACTTTTCTCAAA
49591008 AATCACTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (29 bp):
TTAACCCCTCAATTGACACTTTTCTCAAA
Found at i:49593919 original size:42 final size:42
Alignment explanation
Indices: 49593862--49594010 Score: 178
Period size: 42 Copynumber: 3.5 Consensus size: 42
49593852 GTTCCAATGT
* *
49593862 CATATTCC-AGATATGGTCTCACATGGAA-TCTCATATCGA-GC
1 CATA-TCCTAGATATGGTCTTACA-CGAAGTCTCATATCGATGC
* * *
49593903 CAATAGCCTAGCTATGGTCTTACACGAAGTCTCATATTGATGC
1 C-ATATCCTAGATATGGTCTTACACGAAGTCTCATATCGATGC
* * *
49593946 CATATCCCAGATATGGTCTTACACGAAGTATCATAACGATGC
1 CATATCCTAGATATGGTCTTACACGAAGTCTCATATCGATGC
49593988 CATATCCTAGATATGGTCTTACA
1 CATATCCTAGATATGGTCTTACA
49594011 TGTAATCTCA
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
41 6 0.07
42 83 0.90
43 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (42 bp):
CATATCCTAGATATGGTCTTACACGAAGTCTCATATCGATGC
Found at i:49595561 original size:14 final size:14
Alignment explanation
Indices: 49595528--49595570 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
49595518 TTAATTAAAA
49595528 TGTTAATAAAATAT
1 TGTTAATAAAATAT
49595542 CT-TTAATAAAATAT
1 -TGTTAATAAAATAT
49595556 TGTTAA-AATAATAT
1 TGTTAATAA-AATAT
49595570 T
1 T
49595571 AAATAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.12
14 22 0.85
15 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (14 bp):
TGTTAATAAAATAT
Found at i:49598315 original size:41 final size:41
Alignment explanation
Indices: 49598258--49598370 Score: 192
Period size: 41 Copynumber: 2.7 Consensus size: 41
49598248 GTAGTAGTGA
49598258 AATTAAATGGGAGGGTAAGAGAATAAAAAATTTTATAAATC
1 AATTAAATGGGAGGGTAAGAGAATAAAAAATTTTATAAATC
*
49598299 AATTAAATGGGAGGGTAAGAGAATAAAAATTTTTATAAATC
1 AATTAAATGGGAGGGTAAGAGAATAAAAAATTTTATAAATC
49598340 AATTAAATGGGAGGGTATTAGAG-ATAAAAAA
1 AATTAAATGGGAGGGTA--AGAGAATAAAAAA
49598371 AATTGTATAG
Statistics
Matches: 68, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
41 57 0.84
42 7 0.10
43 4 0.06
ACGTcount: A:0.50, C:0.02, G:0.21, T:0.27
Consensus pattern (41 bp):
AATTAAATGGGAGGGTAAGAGAATAAAAAATTTTATAAATC
Found at i:49599192 original size:10 final size:10
Alignment explanation
Indices: 49599170--49599204 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
49599160 ATTTTAAAAT
49599170 TTTTTATAT-
1 TTTTTATATA
49599179 TTTTTATATA
1 TTTTTATATA
*
49599189 TTTTCATATA
1 TTTTTATATA
49599199 TTTTTA
1 TTTTTA
49599205 ATTTAATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTATATA
Found at i:49599216 original size:21 final size:21
Alignment explanation
Indices: 49599174--49599216 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
49599164 TAAAATTTTT
* * *
49599174 TATATTTTTTATATATTTTCA
1 TATATTTTTAATATAATATCA
*
49599195 TATATTTTTAATTTAATATCA
1 TATATTTTTAATATAATATCA
49599216 T
1 T
49599217 TTAATCATAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
TATATTTTTAATATAATATCA
Found at i:49599690 original size:20 final size:20
Alignment explanation
Indices: 49599665--49599703 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
49599655 TATAATTGAT
* *
49599665 TATTGATGAAAATGGATATA
1 TATTGATAAAAATAGATATA
49599685 TATTGATAAAAATAGATAT
1 TATTGATAAAAATAGATAT
49599704 GGATTTCATT
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:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (20 bp):
TATTGATAAAAATAGATATA
Found at i:49601287 original size:45 final size:45
Alignment explanation
Indices: 49601222--49601352 Score: 183
Period size: 45 Copynumber: 2.9 Consensus size: 45
49601212 ATGAAATCTA
*
49601222 AACTCATTTGAGTTGTGGTCTGAGTTCATGATAAATGTGACGTCCG
1 AACTCA-TTGAGTTGTGGTCTGAGTTCATGATATATGTGACGTCCG
* *
49601268 AACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGATGTCTG
1 AACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGACGTCCG
* * *
49601313 AATTCATTGAGTTGTGATATGAGTT-AGTGATATATGTGAC
1 AACTCATTGAGTTGTGGTCTGAGTTCA-TGATATATGTGAC
49601353 ACATGTTTTG
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
44 1 0.01
45 70 0.91
46 6 0.08
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.38
Consensus pattern (45 bp):
AACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGACGTCCG
Found at i:49601596 original size:15 final size:15
Alignment explanation
Indices: 49601564--49601592 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
49601554 ATTTTTAGTG
49601564 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
49601579 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
49601593 ATTTTCGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:49601935 original size:27 final size:27
Alignment explanation
Indices: 49601904--49601958 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
49601894 AAAAGAAAGA
49601904 AAGAAAAGAAAGCTTTAGGTATTCGGC
1 AAGAAAAGAAAGCTTTAGGTATTCGGC
* *
49601931 AAGAAAAGGAAGCTTTAGGTATTGGGC
1 AAGAAAAGAAAGCTTTAGGTATTCGGC
49601958 A
1 A
49601959 CTTTGGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (27 bp):
AAGAAAAGAAAGCTTTAGGTATTCGGC
Found at i:49602701 original size:43 final size:43
Alignment explanation
Indices: 49602637--49602808 Score: 167
Period size: 43 Copynumber: 4.0 Consensus size: 43
49602627 CATAGGATTT
* *
49602637 TCGATATGTG-TTCTCGTGTAAGACCACGTCTAGGACGTTGGCA
1 TCGATATGTGATT-TCGAGTAAGACCACGTCTGGGACGTTGGCA
* * *
49602680 TTGATATGTGATTTCGAGTAAGACCATGTCTGGGACATTGGCA
1 TCGATATGTGATTTCGAGTAAGACCACGTCTGGGACGTTGGCA
* * *
49602723 TCG-TAATTGTGA-TTCGTGTAAGACC-TGTCTGGAACAG-TGGCA
1 TCGAT-A-TGTGATTTCGAGTAAGACCACGTCTGGGAC-GTTGGCA
* *
49602765 TCGACATGTGATTAC-ATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGATTTCGA-GTAAGACCACGTCTGGGACGTTGGCA
49602808 T
1 T
49602809 TGTACGATAT
Statistics
Matches: 106, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
41 5 0.05
42 30 0.28
43 64 0.60
44 7 0.07
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
TCGATATGTGATTTCGAGTAAGACCACGTCTGGGACGTTGGCA
Found at i:49602775 original size:85 final size:86
Alignment explanation
Indices: 49602650--49602808 Score: 209
Period size: 85 Copynumber: 1.9 Consensus size: 86
49602640 ATATGTGTTC
* * * *
49602650 TCGTGTAAGACCACGTCTAGGACGTTGGCATTGATATGTGATTTCGA-GTAAGACCATGTCTGGG
1 TCGTGTAAGACCACGTCTAGGACGTTGGCATCGACATGTGATTAC-ATGTAAGACCACGTCTGGG
49602714 ACATTGGCATCGTAATTGTGAT
65 ACATTGGCATCGTAATTGTGAT
*
49602736 TCGTGTAAGACC-TGTCT-GGAACAG-TGGCATCGACATGTGATTACATGTAAGACCACGTCTGG
1 TCGTGTAAGACCACGTCTAGG-AC-GTTGGCATCGACATGTGATTACATGTAAGACCACGTCTGG
*
49602798 GACGTTGGCAT
64 GACATTGGCAT
49602809 TGTACGATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
84 3 0.05
85 48 0.75
86 13 0.20
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (86 bp):
TCGTGTAAGACCACGTCTAGGACGTTGGCATCGACATGTGATTACATGTAAGACCACGTCTGGGA
CATTGGCATCGTAATTGTGAT
Found at i:49605742 original size:14 final size:14
Alignment explanation
Indices: 49605702--49605765 Score: 67
Period size: 14 Copynumber: 4.6 Consensus size: 14
49605692 ACCTAAACCG
*
49605702 ACCAATTCATTCAT
1 ACCATTTCATTCAT
* *
49605716 ACCCCTTT-GTTCAT
1 A-CCATTTCATTCAT
49605730 ACCATTTCATTCAT
1 ACCATTTCATTCAT
* *
49605744 ACAATTTCGTTCAT
1 ACCATTTCATTCAT
49605758 ACCATTTC
1 ACCATTTC
49605766 GACCATTCCT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 5 0.12
14 31 0.77
15 4 0.10
ACGTcount: A:0.27, C:0.30, G:0.03, T:0.41
Consensus pattern (14 bp):
ACCATTTCATTCAT
Found at i:49605742 original size:28 final size:28
Alignment explanation
Indices: 49605702--49605765 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
49605692 ACCTAAACCG
* **
49605702 ACCAATTCATTCATACCCCTTT-GTTCAT
1 ACCATTTCATTCATA-CAATTTCGTTCAT
49605730 ACCATTTCATTCATACAATTTCGTTCAT
1 ACCATTTCATTCATACAATTTCGTTCAT
49605758 ACCATTTC
1 ACCATTTC
49605766 GACCATTCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 4 0.12
28 28 0.88
ACGTcount: A:0.27, C:0.30, G:0.03, T:0.41
Consensus pattern (28 bp):
ACCATTTCATTCATACAATTTCGTTCAT
Found at i:49605766 original size:14 final size:14
Alignment explanation
Indices: 49605711--49605766 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
49605701 GACCAATTCA
*
49605711 TTCATACCCCTTT-G
1 TTCATA-CCATTTCG
*
49605725 TTCATACCATTTCA
1 TTCATACCATTTCG
*
49605739 TTCATACAATTTCG
1 TTCATACCATTTCG
49605753 TTCATACCATTTCG
1 TTCATACCATTTCG
49605767 ACCATTCCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
13 5 0.14
14 31 0.86
ACGTcount: A:0.23, C:0.29, G:0.05, T:0.43
Consensus pattern (14 bp):
TTCATACCATTTCG
Found at i:49607372 original size:17 final size:18
Alignment explanation
Indices: 49607330--49607378 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
49607320 AGTTGAAAAG
49607330 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
49607349 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
49607366 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
49607379 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:49608282 original size:40 final size:38
Alignment explanation
Indices: 49608201--49608367 Score: 149
Period size: 40 Copynumber: 4.2 Consensus size: 38
49608191 AAATTGAATG
* * *
49608201 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTG-GAAATT
1 ATATCCGGGCTAAGACCCGAAG-GAATTGTGCAGTG--ATT
* *
49608240 ATATCCGGGTTAAGACCCGAAGGTAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGG-AATTGTGC-AGTGATT
* * *
49608280 ATATCCGGGCTAAGGCCCGAAGGCATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGAATT-GTGC-AGTGATT
* *
49608320 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGG-AATTGTGCA-GTGATT
49608360 ATATCCGG
1 ATATCCGG
49608368 TTATATTCCG
Statistics
Matches: 104, Mismatches: 17, Indels: 13
0.78 0.13 0.10
Matches are distributed among these distances:
39 17 0.16
40 83 0.80
41 3 0.03
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (38 bp):
ATATCCGGGCTAAGACCCGAAGGAATTGTGCAGTGATT
Found at i:49616341 original size:31 final size:31
Alignment explanation
Indices: 49616303--49616364 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
49616293 TGAAGGTTCG
49616303 TAGTATTTAGCTAACATCCACATTAGTACCA
1 TAGTATTTAGCTAACATCCACATTAGTACCA
* *
49616334 TAGTATTTAGCTAACATCTACGTTAGTACCA
1 TAGTATTTAGCTAACATCCACATTAGTACCA
49616365 ACTCCCAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (31 bp):
TAGTATTTAGCTAACATCCACATTAGTACCA
Found at i:49618435 original size:24 final size:24
Alignment explanation
Indices: 49618403--49618498 Score: 88
Period size: 24 Copynumber: 3.9 Consensus size: 24
49618393 TAAGCTAATG
* *
49618403 AACAATAAGCTCTATCGAGCT-AGA
1 AACAGTAAGCTCTAACGAGCTGA-A
49618427 AACAGTAAGCTCTAACGAGCTGAA
1 AACAGTAAGCTCTAACGAGCTGAA
* * *
49618451 AATAGTAAGCTCTTACGAGTTGATA
1 AACAGTAAGCTCTAACGAGCTGA-A
*
49618476 TATCAGTAAGCT-TATACGAGCTG
1 -AACAGTAAGCTCTA-ACGAGCTG
49618499 TGGTGAATCC
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
24 40 0.68
25 3 0.05
26 16 0.27
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (24 bp):
AACAGTAAGCTCTAACGAGCTGAA
Found at i:49627564 original size:31 final size:33
Alignment explanation
Indices: 49627526--49627597 Score: 94
Period size: 31 Copynumber: 2.2 Consensus size: 33
49627516 CCTTAATTCC
*
49627526 TAAAAAATCCTAACCCTAACCC-TAACAAAA-T
1 TAAAAAATCCTAACCCTAACCCTTAAAAAAAGT
* *
49627557 TAAAAAATCCTCATCCTAACCCTTAAAAAAAGT
1 TAAAAAATCCTAACCCTAACCCTTAAAAAAAGT
49627590 TAAGAAAA
1 TAA-AAAA
49627598 GAGAGAGTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 20 0.57
32 7 0.20
33 4 0.11
34 4 0.11
ACGTcount: A:0.53, C:0.24, G:0.03, T:0.21
Consensus pattern (33 bp):
TAAAAAATCCTAACCCTAACCCTTAAAAAAAGT
Found at i:49628556 original size:30 final size:30
Alignment explanation
Indices: 49628522--49628582 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
49628512 ATTTTATTGT
*
49628522 TAATTTTGTTATTATTTTAAAGGCATTTGC
1 TAATTTTGTTATTATCTTAAAGGCATTTGC
*
49628552 TAATTTTGTTATTATCTTAGAGGCATTTGC
1 TAATTTTGTTATTATCTTAAAGGCATTTGC
49628582 T
1 T
49628583 TATTAAGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52
Consensus pattern (30 bp):
TAATTTTGTTATTATCTTAAAGGCATTTGC
Found at i:49629422 original size:126 final size:125
Alignment explanation
Indices: 49629064--49629503 Score: 659
Period size: 125 Copynumber: 3.5 Consensus size: 125
49629054 TAATTAAATT
* * *
49629064 AGGATGCACTGTCAGCAAAATTACTGAAAAAGCTTTCACGTGGATGCTCTTTTGCTACAGTAGTA
1 AGGATGCACTATCAGCAAAATTACTGAAAAAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTA
* * *
49629129 TTTAAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTTCAAAACGCTTCAAGC
66 TCTAAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCCAAAACACTTCAAGC
* *
49629189 AGGATGCACTGTCAGTAAAATTACTGAAAAAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTA
1 AGGATGCACTATCAGCAAAATTACTGAAAAAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTA
* * * *
49629254 TCTGAAAAAATAATTTTGAAAAGATGTTTTTGAACAAATAGTGTCCAAAACACTTCAAGC
66 TCTAAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCCAAAACACTTCAAGC
* * * *
49629314 AGGATGCACTATCAGCAAAATTACTGAAAAAAGCTTCTACGTAGACGCTCTTTTGCTACAATAAT
1 AGGATGCACTATCAGCAAAATTACTG-AAAAAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGT
* *
49629379 ATCAAAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCCAAAACACGTCAAGC
65 ATCTAAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCCAAAACACTTCAAGC
* *
49629440 AGGATGCACTATCAG-AAGAATTACTAAAAGAAGC-CCCACGTGGACGCTCTTTTGCTACAGTAG
1 AGGATGCACTATCAGCAA-AATTACTGAAA-AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAG
49629503 T
64 T
49629504 TCCTATTTGG
Statistics
Matches: 284, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
125 169 0.60
126 115 0.40
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (125 bp):
AGGATGCACTATCAGCAAAATTACTGAAAAAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTA
TCTAAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCCAAAACACTTCAAGC
Found at i:49633061 original size:18 final size:18
Alignment explanation
Indices: 49633035--49633077 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
49633025 GACTAGGAAA
* * *
49633035 AGGAAACATATAAGGGTT
1 AGGATACATATAAAGGCT
49633053 AGGATACATATAAAGGCT
1 AGGATACATATAAAGGCT
49633071 AGGATAC
1 AGGATAC
49633078 GCACTTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAAGGCT
Found at i:49633902 original size:20 final size:19
Alignment explanation
Indices: 49633861--49633902 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
49633851 ATACAATTAT
*
49633861 ATTATAAATCTATGTAATA
1 ATTATAAATCTATATAATA
49633880 ATTATAAAATCTAATATAA-A
1 ATTAT-AAATCT-ATATAATA
49633900 ATT
1 ATT
49633903 TACCTTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 10 0.50
21 5 0.25
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
ATTATAAATCTATATAATA
Found at i:49634789 original size:21 final size:20
Alignment explanation
Indices: 49634765--49634812 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
49634755 CTTTTTTGCA
49634765 AAAATT-AAAGAAAGCTTTGAG
1 AAAATTGAAAGAAA--TTTGAG
49634786 AAAATTTGAAAGAAATTTGAG
1 AAAA-TTGAAAGAAATTTGAG
*
49634807 AGAATT
1 AAAATT
49634813 TGGAGAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 13 0.54
22 2 0.08
23 7 0.29
ACGTcount: A:0.52, C:0.02, G:0.19, T:0.27
Consensus pattern (20 bp):
AAAATTGAAAGAAATTTGAG
Found at i:49634813 original size:21 final size:21
Alignment explanation
Indices: 49634771--49634834 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 21
49634761 TGCAAAAATT
*
49634771 AAAGAAAGCTTTGAGAAAATTTG
1 AAAGAAA--TTTGAGAGAATTTG
49634794 AAAGAAATTTGAGAGAATTTG
1 AAAGAAATTTGAGAGAATTTG
*
49634815 -GAGAGAATTTAGAGAGAATT
1 AAAGA-AATTT-GAGAGAATT
49634835 ATGAGATGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
20 3 0.08
21 18 0.49
22 9 0.24
23 7 0.19
ACGTcount: A:0.47, C:0.02, G:0.25, T:0.27
Consensus pattern (21 bp):
AAAGAAATTTGAGAGAATTTG
Found at i:49634828 original size:9 final size:10
Alignment explanation
Indices: 49634780--49634840 Score: 68
Period size: 11 Copynumber: 5.7 Consensus size: 10
49634770 TAAAGAAAGC
*
49634780 TTTGAGAAAA
1 TTTGAGAGAA
*
49634790 TTTGAAAGAAA
1 TTTGAGAG-AA
49634801 TTTGAGAGAA
1 TTTGAGAGAA
49634811 TTTGGAGAGAA
1 TTT-GAGAGAA
49634822 TTTAGAGAGAA
1 TTT-GAGAGAA
49634833 TTATGAGA
1 TT-TGAGA
49634841 TGACTTTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
10 11 0.25
11 32 0.73
12 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (10 bp):
TTTGAGAGAA
Found at i:49641234 original size:9 final size:9
Alignment explanation
Indices: 49641216--49641249 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
49641206 CTATCCGCTC
49641216 AAATAGGCT
1 AAATAGGCT
*
49641225 AAATAAGCT
1 AAATAGGCT
49641234 AAATAGGCT
1 AAATAGGCT
49641243 AAATAGG
1 AAATAGG
49641250 TTTCTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.21
Consensus pattern (9 bp):
AAATAGGCT
Found at i:49642329 original size:24 final size:24
Alignment explanation
Indices: 49642284--49642330 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
49642274 AAATATGAGT
*
49642284 AGGAAAGAATTCAACTTGAGATTG
1 AGGAAAGAATTAAACTTGAGATTG
49642308 AGGAAAGAATTGAAACTT-AGATT
1 AGGAAAGAATT-AAACTTGAGATT
49642331 TAAAGGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (24 bp):
AGGAAAGAATTAAACTTGAGATTG
Found at i:49642920 original size:19 final size:19
Alignment explanation
Indices: 49642898--49642981 Score: 61
Period size: 19 Copynumber: 4.6 Consensus size: 19
49642888 ATGTTGAATA
49642898 TTATTTAATTTTTTTTCAT
1 TTATTTAATTTTTTTTCAT
* **
49642917 TTATGTAATTTTAATT-A-
1 TTATTTAATTTTTTTTCAT
* **
49642934 AT-TTTAA--TTTTTGAAT
1 TTATTTAATTTTTTTTCAT
49642950 ATTATTTAATTTTTTTTCAT
1 -TTATTTAATTTTTTTTCAT
*
49642970 TTATGTAATTTT
1 TTATTTAATTTT
49642982 AATTAATTTG
Statistics
Matches: 47, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
14 3 0.06
15 1 0.02
16 4 0.09
17 2 0.04
18 6 0.13
19 24 0.51
20 7 0.15
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (19 bp):
TTATTTAATTTTTTTTCAT
Found at i:49642990 original size:19 final size:19
Alignment explanation
Indices: 49642915--49642990 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
49642905 ATTTTTTTTC
49642915 ATTTATGTAATTTTAATTA
1 ATTTATGTAATTTTAATTA
*
49642934 A-TT-T-TAATTTT--TGA
1 ATTTATGTAATTTTAATTA
* ** *
49642948 ATATTATTTAATTTTTTTTC
1 AT-TTATGTAATTTTAATTA
49642968 ATTTATGTAATTTTAATTA
1 ATTTATGTAATTTTAATTA
49642987 ATTT
1 ATTT
49642991 GTATTTTATA
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
14 3 0.07
16 9 0.20
17 2 0.05
18 9 0.20
19 18 0.41
20 3 0.07
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (19 bp):
ATTTATGTAATTTTAATTA
Found at i:49642997 original size:53 final size:53
Alignment explanation
Indices: 49642881--49642990 Score: 202
Period size: 53 Copynumber: 2.1 Consensus size: 53
49642871 GTAACGGTTT
* *
49642881 ATTTTAAATGTTGAATATTATTTAATTTTTTTTCATTTATGTAATTTTAATTA
1 ATTTTAATTTTTGAATATTATTTAATTTTTTTTCATTTATGTAATTTTAATTA
49642934 ATTTTAATTTTTGAATATTATTTAATTTTTTTTCATTTATGTAATTTTAATTA
1 ATTTTAATTTTTGAATATTATTTAATTTTTTTTCATTTATGTAATTTTAATTA
49642987 ATTT
1 ATTT
49642991 GTATTTTATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (53 bp):
ATTTTAATTTTTGAATATTATTTAATTTTTTTTCATTTATGTAATTTTAATTA
Found at i:49644475 original size:30 final size:30
Alignment explanation
Indices: 49644435--49644506 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
49644425 GATGATGGGA
*
49644435 CGGGCGCATCAACAGCGCCCACACAATCAC
1 CGGGCCCATCAACAGCGCCCACACAATCAC
* * * *
49644465 CGGGCCCATCAATAGTGCCTACACAATCAT
1 CGGGCCCATCAACAGCGCCCACACAATCAC
49644495 CGGGCCCATCAA
1 CGGGCCCATCAA
49644507 AAGTATCTAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.29, C:0.39, G:0.19, T:0.12
Consensus pattern (30 bp):
CGGGCCCATCAACAGCGCCCACACAATCAC
Found at i:49644517 original size:30 final size:30
Alignment explanation
Indices: 49644455--49644524 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
49644445 AACAGCGCCC
* *
49644455 ACACAATCACCGGGCCCATCAATAGTGCCT
1 ACACAATCACCGGGCCCATCAAAAGTACCT
* *
49644485 ACACAATCATCGGGCCCATCAAAAGTATCT
1 ACACAATCACCGGGCCCATCAAAAGTACCT
49644515 ACACAATCAC
1 ACACAATCAC
49644525 TAGGCCCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.36, C:0.34, G:0.13, T:0.17
Consensus pattern (30 bp):
ACACAATCACCGGGCCCATCAAAAGTACCT
Found at i:49644531 original size:30 final size:30
Alignment explanation
Indices: 49644455--49644532 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
49644445 AACAGCGCCC
* * *
49644455 ACACAATCACCGGGCCCATCAATAGTGCCT
1 ACACAATCACTGGGCCCATCAAAAGTACCT
*
49644485 ACACAATCA-TCGGGCCCATCAAAAGTATCT
1 ACACAATCACT-GGGCCCATCAAAAGTACCT
*
49644515 ACACAATCACTAGGCCCA
1 ACACAATCACTGGGCCCA
49644533 ATGCCTCAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 40 0.98
31 1 0.02
ACGTcount: A:0.35, C:0.35, G:0.14, T:0.17
Consensus pattern (30 bp):
ACACAATCACTGGGCCCATCAAAAGTACCT
Found at i:49649317 original size:16 final size:14
Alignment explanation
Indices: 49649290--49649323 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
49649280 CTCTCTTTTG
49649290 TTTTCTTTTTTTAT
1 TTTTCTTTTTTTAT
49649304 TTTTCTCTTCTTTTAT
1 TTTTCT-TT-TTTTAT
49649320 TTTT
1 TTTT
49649324 TTACAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 2 0.11
16 10 0.56
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTCTTTTTTTAT
Found at i:49653115 original size:10 final size:10
Alignment explanation
Indices: 49653100--49653126 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
49653090 TAAGTTGAAG
49653100 TTGAGCTGAT
1 TTGAGCTGAT
49653110 TTGAGCTGAT
1 TTGAGCTGAT
49653120 TTGAGCT
1 TTGAGCT
49653127 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:49656775 original size:126 final size:126
Alignment explanation
Indices: 49656550--49656921 Score: 507
Period size: 126 Copynumber: 3.0 Consensus size: 126
49656540 AAGCATGAAC
* * * * * *
49656550 TACTGTAGAAAAAGAGCATCCATGTGGGAGCTTTTTTTAGAAATTTTGTTGACAGTGCATCTTGC
1 TACTGTAGAAAAAGAGCGTTCACGTGGAAGCTTTTTTTAGAAATTTTGCTGACAGTGCATCCTGC
* *
49656615 TTGAAACGTTTTTGACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAAGAAT
66 TTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAAGAAT
* * *
49656676 TACTGTAGGAAAAGAGTGTTCACGTGGAAGCTTTTTTTAGAAATTTTGCTGACAATGCATCCTGC
1 TACTGTAGAAAAAGAGCGTTCACGTGGAAGCTTTTTTTAGAAATTTTGCTGACAGTGCATCCTGC
* * *
49656741 TTGAAGCGTTTTTGACAATATTTGTTTAGAAACGTTTTCTCAAAATTATTTTTTCAAGAAT
66 TTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAAGAAT
* * *
49656802 TACTGTAGAAAAAGAACGTTCACAT-GAGAGCTTTTTTCTA-TAATTTTGCTGACAGTGCATCCT
1 TACTGTAGAAAAAGAGCGTTCACGTGGA-AGCTTTTTT-TAGAAATTTTGCTGACAGTGCATCCT
** * * *
49656865 TATTGAAGCGTTTTTGACACTATTTGTTCAG-AACATCTTTTCAATATTATTTTTTCA
64 GCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCA
49656922 GGGTCAAAAT
Statistics
Matches: 216, Mismatches: 28, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
125 24 0.11
126 190 0.88
127 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (126 bp):
TACTGTAGAAAAAGAGCGTTCACGTGGAAGCTTTTTTTAGAAATTTTGCTGACAGTGCATCCTGC
TTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAAGAAT
Found at i:49657013 original size:28 final size:30
Alignment explanation
Indices: 49656979--49657058 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
49656969 TAAAAAAACT
* *
49656979 GAACCCTAATTTAATTAATTT-TAACCCTA
1 GAACCCTAATTTAATTAATTTAAAACCATA
*
49657008 -AACCCTAATTTAATTTATTTAAAACCATA
1 GAACCCTAATTTAATTAATTTAAAACCATA
49657037 GAACCCTAATTTAATTAATTTA
1 GAACCCTAATTTAATTAATTTA
49657059 TTTAAACACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 19 0.42
29 6 0.13
30 20 0.44
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (30 bp):
GAACCCTAATTTAATTAATTTAAAACCATA
Found at i:49657044 original size:30 final size:29
Alignment explanation
Indices: 49656980--49657170 Score: 128
Period size: 34 Copynumber: 6.4 Consensus size: 29
49656970 AAAAAAACTG
* * *
49656980 AACCCTAATTTAATTAATTT-TAACCCTA
1 AACCCTAATTTAATTTATTTAAAACCATA
49657008 AACCCTAATTTAATTTATTTAAAACCATA
1 AACCCTAATTTAATTTATTTAAAACCATA
49657037 GAACCCTAATTTAATTAATTTATTTAAACACCATA
1 -AACCCTAA--T--TTAATTTATTTAAA-ACCATA
* * **
49657072 AACCCTAGTTTCATTCCTTT------A-A
1 AACCCTAATTTAATTTATTTAAAACCATA
* *
49657094 AACCCTAATTTTATTTATTTAAAACCCTAA
1 AACCCTAATTTAATTTATTTAAAACCAT-A
*
49657124 AACCCTAATTTACTTAATTTATTTAAAAATCATA
1 AACCCTAA--T--TTAATTTATTT-AAAACCATA
49657158 AACCCTAATTTAA
1 AACCCTAATTTAA
49657171 ATATTTTTTA
Statistics
Matches: 128, Mismatches: 15, Indels: 38
0.71 0.08 0.21
Matches are distributed among these distances:
22 17 0.13
23 1 0.01
28 19 0.15
29 6 0.05
30 29 0.23
32 4 0.03
34 40 0.31
35 12 0.09
ACGTcount: A:0.41, C:0.19, G:0.01, T:0.39
Consensus pattern (29 bp):
AACCCTAATTTAATTTATTTAAAACCATA
Found at i:49657097 original size:22 final size:22
Alignment explanation
Indices: 49657071--49657123 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
49657061 TAAACACCAT
* *
49657071 AAACCCTAGTTTCATTCCTTTA
1 AAACCCTAATTTCATTCATTTA
* *
49657093 AAACCCTAATTTTATTTATTTA
1 AAACCCTAATTTCATTCATTTA
49657115 AAACCCTAA
1 AAACCCTAA
49657124 AACCCTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.40
Consensus pattern (22 bp):
AAACCCTAATTTCATTCATTTA
Found at i:49657110 original size:86 final size:86
Alignment explanation
Indices: 49657007--49657164 Score: 262
Period size: 86 Copynumber: 1.8 Consensus size: 86
49656997 TTTTAACCCT
* *
49657007 AAACCCTAATTTAATTTATTTAAAACCATAGAACCCTAATTTAATTAATTTATTTAAACACCATA
1 AAACCCTAATTTAATTTATTTAAAACCATAAAACCCTAATTTAATTAATTTATTTAAAAACCATA
49657072 AACCCTAGTTTCATTCCTTTA
66 AACCCTAGTTTCATTCCTTTA
* * * *
49657093 AAACCCTAATTTTATTTATTTAAAACCCTAAAACCCTAATTTACTTAATTTATTTAAAAATCATA
1 AAACCCTAATTTAATTTATTTAAAACCATAAAACCCTAATTTAATTAATTTATTTAAAAACCATA
49657158 AACCCTA
66 AACCCTA
49657165 ATTTAAATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 66 1.00
ACGTcount: A:0.41, C:0.20, G:0.01, T:0.38
Consensus pattern (86 bp):
AAACCCTAATTTAATTTATTTAAAACCATAAAACCCTAATTTAATTAATTTATTTAAAAACCATA
AACCCTAGTTTCATTCCTTTA
Found at i:49658077 original size:27 final size:28
Alignment explanation
Indices: 49658033--49658089 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
49658023 CATTTAATTC
*
49658033 AAATAAAATAAATTATTAAAAATTTATAA
1 AAATAAAATAAATAATTAAAAA-TTATAA
*
49658062 AAAT-AAA-AAATAATTATAAATTATAA
1 AAATAAAATAAATAATTAAAAATTATAA
49658088 AA
1 AA
49658090 TACGATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 8 0.31
27 11 0.42
28 3 0.12
29 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (28 bp):
AAATAAAATAAATAATTAAAAATTATAA
Found at i:49658089 original size:18 final size:18
Alignment explanation
Indices: 49658040--49658091 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
49658030 TTCAAATAAA
*
49658040 ATAAATTATTAAAA-ATTT
1 ATAAATTA-TAAAATAATT
* *
49658058 ATAAAAATAAAAAATAATT
1 AT-AAATTATAAAATAATT
49658077 ATAAATTATAAAATA
1 ATAAATTATAAAATA
49658092 CGATTTAACC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAATTATAAAATAATT
Found at i:49661843 original size:8 final size:8
Alignment explanation
Indices: 49661823--49661860 Score: 67
Period size: 8 Copynumber: 4.6 Consensus size: 8
49661813 TCGAGGTTTT
49661823 TTTTTAAA
1 TTTTTAAA
49661831 TTTTTTAAA
1 -TTTTTAAA
49661840 TTTTTAAA
1 TTTTTAAA
49661848 TTTTTAAA
1 TTTTTAAA
49661856 TTTTT
1 TTTTT
49661861 TTTAATTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTTAAA
Found at i:49669150 original size:27 final size:27
Alignment explanation
Indices: 49669096--49669206 Score: 136
Period size: 27 Copynumber: 4.1 Consensus size: 27
49669086 AACATGGCTG
* *
49669096 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
49669122 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
* *
49669149 CCAAAACAGAT-ATATGTGGCAGAGACA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* * *
49669176 CCAGATCAGATAAATGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
49669203 CCAG
1 CCAG
49669207 GACGCTTCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 15 0.21
27 57 0.78
28 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.23, T:0.15
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:49669178 original size:54 final size:53
Alignment explanation
Indices: 49669100--49669205 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 53
49669090 TGGCTGCCAG
* *
49669100 AACAGATAATGTGACAGAGTCACCAGAACAGATAATTGTGGCAGAGCCACCAA
1 AACAGATAATGTGACAGAGACACCAGAACAGATAAATGTGGCAGAGCCACCAA
* * *
49669153 AACAGATATATGTGGCAGAGACACCAGATCAGATAAATGTGGCATAGCCACCA
1 AACAGATA-ATGTGACAGAGACACCAGAACAGATAAATGTGGCAGAGCCACCA
49669206 GGACGCTTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 8 0.17
54 39 0.83
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.16
Consensus pattern (53 bp):
AACAGATAATGTGACAGAGACACCAGAACAGATAAATGTGGCAGAGCCACCAA
Found at i:49672327 original size:29 final size:29
Alignment explanation
Indices: 49672294--49672452 Score: 171
Period size: 29 Copynumber: 5.5 Consensus size: 29
49672284 GTGACGAGAT
49672294 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
49672323 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
49672352 TGGCACTAAGTGTGCATGCTGGAAAT-TA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
49672380 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
49672409 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
49672438 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
49672453 GAAATCGAGT
Statistics
Matches: 110, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 22 0.20
29 88 0.80
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:49672364 original size:58 final size:58
Alignment explanation
Indices: 49672290--49672454 Score: 176
Period size: 57 Copynumber: 2.9 Consensus size: 58
49672280 TACGGTGACG
*
49672290 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGC-ATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGA-GCTCGAA
* * **
49672347 ATATATGGCACTAAGTGTGCATGCTGGAAAT-TACGGCACTGGGTGTGCGAGCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGAGCTCGAA
* * * ** * *
49672404 GGGTATGGCACTATGTGTGCGGGCT-TAAATCACATGGCACTAAGTGTGCGA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAT-ATATGGCACTAAGTGTGCGA
49672455 AATCGAGTAT
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
56 4 0.05
57 42 0.48
58 42 0.48
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGAGCTCGAA
Found at i:49680390 original size:29 final size:29
Alignment explanation
Indices: 49680357--49680515 Score: 171
Period size: 29 Copynumber: 5.5 Consensus size: 29
49680347 GTGACGAGAT
49680357 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
49680386 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
49680415 TGGCACTAAGTGTGCATGCTGGAAAT-TA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
49680443 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
49680472 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
49680501 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
49680516 GAAATCGAGT
Statistics
Matches: 110, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 22 0.20
29 88 0.80
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:49680427 original size:58 final size:58
Alignment explanation
Indices: 49680353--49680517 Score: 176
Period size: 57 Copynumber: 2.9 Consensus size: 58
49680343 TACGGTGACG
*
49680353 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGC-ATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGA-GCTCGAA
* * **
49680410 ATATATGGCACTAAGTGTGCATGCTGGAAAT-TACGGCACTGGGTGTGCGAGCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGAGCTCGAA
* * * ** * *
49680467 GGGTATGGCACTATGTGTGCGGGCT-TAAATCACATGGCACTAAGTGTGCGA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAT-ATATGGCACTAAGTGTGCGA
49680518 AATCGAGTAT
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
56 4 0.05
57 42 0.48
58 42 0.48
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGAGCTCGAA
Found at i:49682004 original size:24 final size:24
Alignment explanation
Indices: 49681969--49682045 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
49681959 CCAACACCAT
*
49681969 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
49681993 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
* *
49682017 TCTCCCTTATCAGCTCCCAAATCT
1 TCTCCCTTATCAGCTCCTAAATCC
49682041 TCTCC
1 TCTCC
49682046 TGACAGCCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.21, C:0.43, G:0.04, T:0.32
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:49682086 original size:25 final size:25
Alignment explanation
Indices: 49682052--49682106 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
49682042 CTCCTGACAG
49682052 CCTTTCACTTCAGTTCCACTGCTTA
1 CCTTTCACTTCAGTTCCACTGCTTA
49682077 CCTTTCACTTCAGTTCCACTGCTTA
1 CCTTTCACTTCAGTTCCACTGCTTA
49682102 CCTTT
1 CCTTT
49682107 TCTGTACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.15, C:0.36, G:0.07, T:0.42
Consensus pattern (25 bp):
CCTTTCACTTCAGTTCCACTGCTTA
Found at i:49682655 original size:27 final size:26
Alignment explanation
Indices: 49682607--49682666 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
49682597 AGCGAGGCTG
*
49682607 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
49682634 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
49682660 CAGATAT
1 CAGATAT
49682667 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:49683262 original size:81 final size:81
Alignment explanation
Indices: 49683118--49683367 Score: 338
Period size: 81 Copynumber: 3.1 Consensus size: 81
49683108 GGGGCAACAT
* * * * * * *
49683118 GGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACATGGGTATTTTAGTATTTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
*
49683183 CCTACAATGGTATTTC
66 CCTACAAGGGTATTTC
*
49683199 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
* *
49683264 CCTACAGGGGTATTTT
66 CCTACAAGGGTATTTC
* * * * *
49683280 AGTAATTCTACCTTACAGGGCTATTTCAGTAATTCTACCTTACAGGGGTATTTCGGTATTTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
*
49683345 CTTACAAGGGTATTTC
66 CCTACAAGGGTATTTC
*
49683361 GATAATT
1 GGTAATT
49683368 TTACAAATTG
Statistics
Matches: 147, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 147 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (81 bp):
GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
CCTACAAGGGTATTTC
Found at i:49683361 original size:27 final size:27
Alignment explanation
Indices: 49683119--49683360 Score: 297
Period size: 27 Copynumber: 9.0 Consensus size: 27
49683109 GGGCAACATG
* * * *
49683119 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
49683146 GTAATTCTACCCTACATGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCA
* * *
49683173 GTATTTCTACCCTACAATGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
*
49683200 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
*
49683227 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
49683254 GTAATTCTACCCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCA
*
49683281 GTAATTCTACCTTAC-AGGGCTATTTCA
1 GTAATTCTACCCTACAAGGG-TATTTCA
* * *
49683308 GTAATTCTACCTTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
49683335 GTATTTCTACCTTACAAGGGTATTTC
1 GTAATTCTACCCTACAAGGGTATTTC
49683361 GATAATTTTA
Statistics
Matches: 190, Mismatches: 23, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
26 3 0.02
27 184 0.97
28 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:49683386 original size:81 final size:79
Alignment explanation
Indices: 49683135--49683394 Score: 306
Period size: 81 Copynumber: 3.2 Consensus size: 79
49683125 TTACCCCACA
* * * * *
49683135 AGGGTATCTCGGTAATTCTACCCTACATGGGTATTTTAGTATTTCTACCCTACAATGGTATTTCG
1 AGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCG
* *
49683200 GTAATTCTACCCTAC
66 ATAATTCTA-CCTTC
* *
49683215 AGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTT-
1 A-GGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTC
*
49683279 TAGTAATTCTACCTTAC
65 GA-TAATTCTACCTT-C
* * *
49683296 AGGGCTATTTCAGTAATTCTACCTTACAGGGGTATTTCGGTATTTCTACCTTACAAGGGTATTTC
1 AGGG-TATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTC
* * *
49683361 GATAATTTTACAAATTG
65 GATAATTCTAC--CTTC
49683378 AGGGTATTTCAGTAATT
1 AGGGTATTTCAGTAATT
49683395 TAACAATCGA
Statistics
Matches: 154, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
80 7 0.05
81 140 0.91
82 5 0.03
83 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (79 bp):
AGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCG
ATAATTCTACCTTC
Found at i:49683616 original size:27 final size:27
Alignment explanation
Indices: 49683351--49683627 Score: 251
Period size: 27 Copynumber: 10.3 Consensus size: 27
49683341 CTACCTTACA
**
49683351 AGGGTATTTC-GATAATTTTACAAATTG
1 AGGGTATTTCAG-TAATTTTACAAACCG
* *
49683378 AGGGTATTTCAGTAATTTAAC-AATCG
1 AGGGTATTTCAGTAATTTTACAAACCG
* * *
49683404 ACGGTATTTCGGTAATTTTATAAACCG
1 AGGGTATTTCAGTAATTTTACAAACCG
* * * *
49683431 GGGGTACTTT-GGAAATTTTACAAGCCG
1 AGGGTA-TTTCAGTAATTTTACAAACCG
* * * *
49683458 AGGGTATTTCAATAATTTTGCAAATCA
1 AGGGTATTTCAGTAATTTTACAAACCG
* *
49683485 AGGGTATTTCAGTAATTTTGCAAACTG
1 AGGGTATTTCAGTAATTTTACAAACCG
* **
49683512 AGGGTATTTCAATAATTTTACAAATTG
1 AGGGTATTTCAGTAATTTTACAAACCG
*
49683539 AGGGTATTTCAGTAATTTTAC-AATCG
1 AGGGTATTTCAGTAATTTTACAAACCG
* *
49683565 ACGGTATTTCAGTAATTTTATAAACCG
1 AGGGTATTTCAGTAATTTTACAAACCG
* *
49683592 GGGGTACTTT-GGTAATTTTACAAACC-
1 AGGGTA-TTTCAGTAATTTTACAAACCG
49683618 AGGGGTATTT
1 A-GGGTATTT
49683628 TGGTGATTTG
Statistics
Matches: 206, Mismatches: 37, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
26 50 0.24
27 149 0.72
28 7 0.03
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTACAAACCG
Found at i:49683631 original size:27 final size:27
Alignment explanation
Indices: 49683214--49683627 Score: 201
Period size: 27 Copynumber: 15.4 Consensus size: 27
49683204 TTCTACCCTA
* **
49683214 CAGGGGTATTTCAGTAATTCTACCCTA-
1 CAGGGGTATTTCAGTAATTTTA-CAAAC
* **
49683241 CAGGGGTATTTCAGTAATTCTACCCTA-
1 CAGGGGTATTTCAGTAATTTTA-CAAAC
* * **
49683268 CAGGGGTATTTTAGTAATTCTACCTTA-
1 CAGGGGTATTTCAGTAATTTTA-CAAAC
* * **
49683295 CAGGGCTATTTCAGTAATTCTACCTTA-
1 CAGGGGTATTTCAGTAATTTTA-CAAAC
* **
49683322 CAGGGGTATTTCGGT-ATTTCTACCTTA-
1 CAGGGGTATTTCAGTAATTT-TA-CAAAC
*
49683349 CAAGGGTATTTC-GATAATTTTACAAA-
1 CAGGGGTATTTCAG-TAATTTTACAAAC
** * *
49683375 TTGAGGGTATTTCAGTAATTTAACAATC
1 CAG-GGGTATTTCAGTAATTTTACAAAC
* * * *
49683403 GA-CGGTATTTCGGTAATTTTATAAAC
1 CAGGGGTATTTCAGTAATTTTACAAAC
* * * *
49683429 CGGGGGTACTTT-GGAAATTTTACAAGC
1 CAGGGGTA-TTTCAGTAATTTTACAAAC
* * *
49683456 C-GAGGGTATTTCAATAATTTTGCAAAT
1 CAG-GGGTATTTCAGTAATTTTACAAAC
* *
49683483 CAAGGGTATTTCAGTAATTTTGCAAA-
1 CAGGGGTATTTCAGTAATTTTACAAAC
* *
49683509 CTGAGGGTATTTCAATAATTTTACAAA-
1 CAG-GGGTATTTCAGTAATTTTACAAAC
** *
49683536 TTGAGGGTATTTCAGTAATTTTACAATC
1 CAG-GGGTATTTCAGTAATTTTACAAAC
* * *
49683564 GA-CGGTATTTCAGTAATTTTATAAAC
1 CAGGGGTATTTCAGTAATTTTACAAAC
* *
49683590 CGGGGGTACTTT-GGTAATTTTACAAAC
1 CAGGGGTA-TTTCAGTAATTTTACAAAC
49683617 CAGGGGTATTT
1 CAGGGGTATTT
49683628 TGGTGATTTG
Statistics
Matches: 318, Mismatches: 54, Indels: 31
0.79 0.13 0.08
Matches are distributed among these distances:
26 54 0.17
27 253 0.80
28 11 0.03
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (27 bp):
CAGGGGTATTTCAGTAATTTTACAAAC
Found at i:49683643 original size:27 final size:27
Alignment explanation
Indices: 49683576--49683643 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
49683566 CGGTATTTCA
* *
49683576 GTAATTTTATAAACCGGGGGTACTTTG
1 GTAATTTGATAAACCAGGGGTACTTTG
* * *
49683603 GTAATTTTACAAACCAGGGGTATTTTG
1 GTAATTTGATAAACCAGGGGTACTTTG
* *
49683630 GTGATTTGGTAAAC
1 GTAATTTGATAAAC
49683644 TAAAGTATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (27 bp):
GTAATTTGATAAACCAGGGGTACTTTG
Found at i:49683652 original size:80 final size:79
Alignment explanation
Indices: 49683363--49683652 Score: 239
Period size: 80 Copynumber: 3.6 Consensus size: 79
49683353 GGTATTTCGA
** * * * *
49683363 TAATTTTACAAATTGAGGGTATTTCAGTAATTT-AACAATCGACGGTATTTCGGTAATTTTATAA
1 TAATTTTACAAACCGAGGGTATTTCAGTAATTTGTA-AA-CTAAGGTATTTCAGTAATTTTATAA
49683427 ACCGGGGGTACTTTGG
64 ACCGGGGGTACTTTGG
* * * * **
49683443 AAATTTTACAAGCCGAGGGTATTTCAATAATTTTGCAAA-TCAAGGGTATTTCAGTAATTTTGCA
1 TAATTTTACAAACCGAGGGTATTTCAGTAA-TTTGTAAACT-AA-GGTATTTCAGTAATTTTATA
* * **
49683507 AACTGAGGGTA-TTTCAA
63 AACCGGGGGTACTTT-GG
** * *
49683524 TAATTTTACAAATTGAGGGTATTTCAGTAATTT-TACAATCGACGGTATTTCAGTAATTTTATAA
1 TAATTTTACAAACCGAGGGTATTTCAGTAATTTGTA-AA-CTAAGGTATTTCAGTAATTTTATAA
49683588 ACCGGGGGTACTTTGG
64 ACCGGGGGTACTTTGG
** * *
49683604 TAATTTTACAAACC-AGGGGTATTTTGGTGATTTGGTAAACTAAAGTATT
1 TAATTTTACAAACCGA-GGGTATTTCAGTAATTT-GTAAACTAAGGTATT
49683653 CTAAATAGGG
Statistics
Matches: 161, Mismatches: 37, Indels: 24
0.73 0.17 0.11
Matches are distributed among these distances:
79 2 0.01
80 94 0.58
81 62 0.39
82 3 0.02
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (79 bp):
TAATTTTACAAACCGAGGGTATTTCAGTAATTTGTAAACTAAGGTATTTCAGTAATTTTATAAAC
CGGGGGTACTTTGG
Found at i:49691766 original size:12 final size:12
Alignment explanation
Indices: 49691749--49691773 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49691739 TTACTTTGAT
49691749 AGATCCTGGATC
1 AGATCCTGGATC
49691761 AGATCCTGGATC
1 AGATCCTGGATC
49691773 A
1 A
49691774 ATGCATTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (12 bp):
AGATCCTGGATC
Found at i:49694890 original size:40 final size:40
Alignment explanation
Indices: 49694841--49694994 Score: 114
Period size: 40 Copynumber: 3.9 Consensus size: 40
49694831 CGAAATTTAA
* * *
49694841 CCGGATATAGCGACTCGCTCGATTGTCTTCGGGACA-TAGC
1 CCGGATATAGCGACTCGCACAATTGCCTTCGGGA-ATTAGC
* * *
49694881 CCGGTTATAGTGATTCGCACAATTGCCTTCGGGAATTAGC
1 CCGGATATAGCGACTCGCACAATTGCCTTCGGGAATTAGC
* ** * * *
49694921 CCGGATTTAGTAACTCGCACGAATT-CCTTCGAGACTTAAC
1 CCGGATATAGCGACTCGCAC-AATTGCCTTCGGGAATTAGC
* * * ** *
49694961 CCGGTTTTGGTAACTCGCACAAATGCCTTCGGGA
1 CCGGATATAGCGACTCGCACAATTGCCTTCGGGA
49694995 CTTAACTCGG
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 4 0.04
40 86 0.91
41 4 0.04
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (40 bp):
CCGGATATAGCGACTCGCACAATTGCCTTCGGGAATTAGC
Found at i:49694997 original size:40 final size:40
Alignment explanation
Indices: 49694867--49695045 Score: 187
Period size: 40 Copynumber: 4.5 Consensus size: 40
49694857 GCTCGATTGT
* * * * *
49694867 CTTCGGGACATAGCCCGGTTATAGTGATTCGCACAATTGC
1 CTTCGGGACTTAGCCCGGTTTTAGTAACTCGCACAAATGC
* * * *
49694907 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACGAATTC
1 CTTCGGGACTTAGCCCGGTTTTAGTAACTCGCACAAATGC
* * *
49694947 CTTCGAGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGTTTTAGTAACTCGCACAAATGC
* * * * * *
49694987 CTTCGGGACTTAACTCGGTTTTGGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAGCCCGGTTTTAGTAAC-TCGCACAAATGC
49695028 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAGCCCGG
49695046 GCACCATTCG
Statistics
Matches: 115, Mismatches: 23, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
40 89 0.77
41 26 0.23
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGTTTTAGTAACTCGCACAAATGC
Found at i:49702476 original size:17 final size:17
Alignment explanation
Indices: 49702454--49702487 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
49702444 TGGCTACTTC
49702454 GGGCC-ATGTGGCCCAAT
1 GGGCCAATG-GGCCCAAT
49702471 GGGCCAATGGGCCCAAT
1 GGGCCAATGGGCCCAAT
49702488 TGGATAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.21, C:0.29, G:0.35, T:0.15
Consensus pattern (17 bp):
GGGCCAATGGGCCCAAT
Found at i:49702688 original size:27 final size:27
Alignment explanation
Indices: 49702658--49702890 Score: 245
Period size: 27 Copynumber: 8.6 Consensus size: 27
49702648 TTAGTTTACC
49702658 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
49702685 AAATCACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
49702712 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
49702739 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
49702766 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
49702793 AAATTACCAAAATACCCCTGATTTATG
1 AAATTACCAAAATACCCCTGGTTTGTA
** * **
49702820 AAATTACTGAAATA-CCTTGGACCTGTA
1 AAATTACCAAAATACCCCTGG-TTTGTA
** **
49702847 AAATTATTAAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
*
49702874 AAATTACCAAAGTACCC
1 AAATTACCAAAATACCC
49702891 TTGATTTACA
Statistics
Matches: 172, Mismatches: 31, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
26 4 0.02
27 165 0.96
28 3 0.02
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:49702943 original size:27 final size:27
Alignment explanation
Indices: 49702846--49702944 Score: 74
Period size: 27 Copynumber: 3.7 Consensus size: 27
49702836 TTGGACCTGT
** * **
49702846 AAAATTATTAAAATACCCTCGACTTGT
1 AAAATTATCGAAATACCCTCGATTTAC
* *
49702873 AAAATTA-CCAAAGTACCCTTGATTTAC
1 AAAATTATCGAAA-TACCCTCGATTTAC
* * ***
49702900 AGAATTACCGTTTTACCCTCGATTTAC
1 AAAATTATCGAAATACCCTCGATTTAC
49702927 AAAATTATCGAAATACCC
1 AAAATTATCGAAATACCC
49702945 CTGCAAGGTA
Statistics
Matches: 53, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
26 3 0.06
27 49 0.92
28 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATTATCGAAATACCCTCGATTTAC
Found at i:49702959 original size:27 final size:27
Alignment explanation
Indices: 49702929--49703317 Score: 494
Period size: 27 Copynumber: 14.3 Consensus size: 27
49702919 CGATTTACAA
* * *
49702929 AATTATCGAAATACCCCTGCAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
49702956 AATTATCGAAATACCCCTACCCCTGTAAGGTAG
1 AATTACCGAAATA------CCCCTGTAGGGTAG
* * *
49702989 AATTACTGGAATACCTCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
49703016 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
49703043 AATTACCGGAATACCCCTGTA-GGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
49703069 AATTACCGGAATACCCCTTTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
49703096 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
49703123 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
49703150 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
49703177 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
49703204 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
49703231 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
49703258 AATTACTAAAATACCCTTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
49703285 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
49703311 AATTACC
1 AATTACC
49703318 ATTTTGCCCC
Statistics
Matches: 330, Mismatches: 25, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
26 42 0.13
27 265 0.80
33 23 0.07
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:49703002 original size:33 final size:33
Alignment explanation
Indices: 49702940--49703033 Score: 94
Period size: 33 Copynumber: 3.0 Consensus size: 33
49702930 ATTATCGAAA
* *
49702940 TACCCCTGCAAGGTAGAATTA-TCGAAATACCCC
1 TACCCCTGTAAGGTAGAATTACT-GGAATACCCC
49702973 TACCCCTGTAAGGTAGAATTACTGGAATA--CC
1 TACCCCTGTAAGGTAGAATTACTGGAATACCCC
* *
49703004 T----CTGTAGGGTAGAATTACCGGAATACCCC
1 TACCCCTGTAAGGTAGAATTACTGGAATACCCC
49703033 T
1 T
49703034 GTAGGGTAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
27 22 0.41
29 3 0.06
31 3 0.06
33 25 0.46
34 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (33 bp):
TACCCCTGTAAGGTAGAATTACTGGAATACCCC
Found at i:49703479 original size:16 final size:16
Alignment explanation
Indices: 49703458--49703488 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49703448 CAAATATGGG
49703458 CATGACATGCTGCATA
1 CATGACATGCTGCATA
*
49703474 CATGACATGTTGCAT
1 CATGACATGCTGCAT
49703489 GGGTTGGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (16 bp):
CATGACATGCTGCATA
Found at i:49703777 original size:22 final size:22
Alignment explanation
Indices: 49703744--49703808 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
49703734 TTAAAGCCTT
* *
49703744 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
49703766 CT-ATATATGGCTCTGTGCCAAC
1 CTGAT-TATGGCTCTGTGCCAAC
*
49703788 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
49703809 ACGTATTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 2 0.05
22 34 0.89
23 2 0.05
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:49704068 original size:27 final size:26
Alignment explanation
Indices: 49703967--49704068 Score: 105
Period size: 27 Copynumber: 3.8 Consensus size: 26
49703957 GTTCTGTTAA
* * *
49703967 GTGGCTTTGCCACATTACCTGTTTCTG
1 GTGGCTCTGCCACAATATCTG-TTCTG
* *
49703994 GTGGCTATGCCACAAATATCTATTCTG
1 GTGGCTCTGCCAC-AATATCTGTTCTG
*
49704021 GTGGCGCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGT-TCTG
* *
49704048 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
49704069 ATAACTGAGC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
26 8 0.13
27 50 0.79
28 5 0.08
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.34
Consensus pattern (26 bp):
GTGGCTCTGCCACAATATCTGTTCTG
Found at i:49704243 original size:6 final size:6
Alignment explanation
Indices: 49704205--49704350 Score: 77
Period size: 6 Copynumber: 23.3 Consensus size: 6
49704195 TTGCATTCAC
* * *
49704205 ATTCTG ACTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG A-TTCTG ATTCTG
* * * *
49704256 -TTACCTG ATACTG ATTTTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
* *
49704306 ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG ATTCT- AGTTCTG AT
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
49704351 AATGTTTCTT
Statistics
Matches: 108, Mismatches: 16, Indels: 32
0.69 0.10 0.21
Matches are distributed among these distances:
5 8 0.07
6 74 0.69
7 22 0.20
8 4 0.04
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:49704244 original size:25 final size:26
Alignment explanation
Indices: 49704234--49704336 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 26
49704224 TTACCTGATA
* *
49704234 CTGATTCTGATTTTTGATTCTGTTAC
1 CTGATACTGATTTCTGATTCTGTTAC
*
49704260 CTGATACTGATTTTGATTTTGATTCTGTTAC
1 CTGATACTGA---T--TTCTGATTCTGTTAC
*
49704291 CTGATACTGA-TTCTGATTCTGTCAC
1 CTGATACTGATTTCTGATTCTGTTAC
* *
49704316 CTAATTCTGA-TTCTGATTCTG
1 CTGATACTGATTTCTGATTCTG
49704337 ATTCTAGTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
25 32 0.48
26 9 0.13
29 1 0.01
31 25 0.37
ACGTcount: A:0.18, C:0.17, G:0.16, T:0.49
Consensus pattern (26 bp):
CTGATACTGATTTCTGATTCTGTTAC
Found at i:49704249 original size:32 final size:32
Alignment explanation
Indices: 49704205--49704308 Score: 183
Period size: 32 Copynumber: 3.3 Consensus size: 32
49704195 TTGCATTCAC
*
49704205 ATTCTGACTTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTTGATTCTGTTACCTGATACTG
49704237 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTTGATTCTGTTACCTGATACTG
*
49704269 ATTTTGA-TTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTTGATTCTGTTACCTGATACTG
49704300 ATTCTGATT
1 ATTCTGATT
49704309 CTGTCACCTA
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
31 30 0.44
32 38 0.56
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.50
Consensus pattern (32 bp):
ATTCTGATTTTTGATTCTGTTACCTGATACTG
Found at i:49706875 original size:27 final size:26
Alignment explanation
Indices: 49706827--49706878 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
49706817 GCGAGGCTGC
*
49706827 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
49706853 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
49706879 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:49707551 original size:27 final size:27
Alignment explanation
Indices: 49707521--49707590 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
49707511 TACCCCATGA
* *
49707521 GGGTATCTCGGTAATTCTACCATACAG
1 GGGTATTTCAGTAATTCTACCATACAG
* *
49707548 GGGTATTTCAGTAATTCTACCCTACTG
1 GGGTATTTCAGTAATTCTACCATACAG
49707575 GGGTATTTCAGTAATT
1 GGGTATTTCAGTAATT
49707591 TAACAAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (27 bp):
GGGTATTTCAGTAATTCTACCATACAG
Found at i:49707604 original size:27 final size:27
Alignment explanation
Indices: 49707546--49707618 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
49707536 TCTACCATAC
* **
49707546 AGGGGTATTTCAGTAATTCTACCCTACT
1 AGGGGTATTTCAGTAATT-TAACAAACT
*
49707574 -GGGGTATTTCAGTAATTTAACAAATT
1 AGGGGTATTTCAGTAATTTAACAAACT
**
49707600 AGGGGTATTTTGGTAATTT
1 AGGGGTATTTCAGTAATTT
49707619 TACTAATCGA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 5 0.13
27 33 0.87
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (27 bp):
AGGGGTATTTCAGTAATTTAACAAACT
Found at i:49707689 original size:27 final size:27
Alignment explanation
Indices: 49707602--49707680 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
49707592 AACAAATTAG
*
49707602 GGGTATTTTGGTAATTTTACTAATCGA
1 GGGTATTTTGGTAATTTTGCTAATCGA
49707629 GGGTATTTTGGTAATTTTGCTAATCGA
1 GGGTATTTTGGTAATTTTGCTAATCGA
*
49707656 GGGTATTTTGGTAATTTGGCTAATC
1 GGGTATTTTGGTAATTTTGCTAATC
49707681 TAAAGTATTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTGCTAATCGA
Found at i:49707830 original size:17 final size:18
Alignment explanation
Indices: 49707808--49707845 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
49707798 AATCTAGCCA
*
49707808 ATTGGGCCCGTA-GGCCC
1 ATTGGGCCCATATGGCCC
49707825 ATTGGGCCCATATGGCCC
1 ATTGGGCCCATATGGCCC
49707843 ATT
1 ATT
49707846 TCGGCCCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.24
Consensus pattern (18 bp):
ATTGGGCCCATATGGCCC
Found at i:49713677 original size:40 final size:40
Alignment explanation
Indices: 49713601--49713848 Score: 356
Period size: 40 Copynumber: 6.2 Consensus size: 40
49713591 TCTTCGGAAT
* ** * *
49713601 TTAG-CCGGATATAACCACAAGCACAATTGCCGTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * *
49713640 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
49713680 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* *
49713720 TTAGCCCAGATATAACAACTCGCACAAATGCCTTTGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
49713760 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * *
49713800 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAA-CAACTCGCACAAATGCCTTCGGGTC
49713840 TTAGCCCGG
1 TTAGCCCGG
49713849 GTATCATTCA
Statistics
Matches: 189, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
39 3 0.02
40 185 0.98
41 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
Found at i:49715687 original size:80 final size:80
Alignment explanation
Indices: 49715603--49715751 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
49715593 TATGGTAACC
* * * *
49715603 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
49715667 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
49715683 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
49715748 CCGG
66 CCGG
49715752 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:49715693 original size:40 final size:38
Alignment explanation
Indices: 49715644--49715751 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
49715634 ATCACGATTT
*
49715644 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
49715684 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
49715724 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
49715752 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:49723809 original size:80 final size:80
Alignment explanation
Indices: 49723725--49723873 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
49723715 TATGGTAACC
* * * *
49723725 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
49723789 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
49723805 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
49723870 CCGG
66 CCGG
49723874 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:49723815 original size:40 final size:38
Alignment explanation
Indices: 49723766--49723873 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
49723756 ATCACGATTT
*
49723766 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
49723806 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
49723846 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
49723874 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:49727067 original size:29 final size:29
Alignment explanation
Indices: 49727029--49727101 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
49727019 GTTGTGAGAT
* * *
49727029 TGGCAATAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
49727058 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
49727087 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
49727102 ATGGTTGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:49737878 original size:31 final size:31
Alignment explanation
Indices: 49737840--49737902 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
49737830 TTTGAAGTAT
49737840 GTTTCCATCTTCCCTGCCAACTTCCAATCGA
1 GTTTCCATCTTCCCTGCCAACTTCCAATCGA
**
49737871 GTTTCCATCTTTGCTGCCAACTTCCAATCGA
1 GTTTCCATCTTCCCTGCCAACTTCCAATCGA
49737902 G
1 G
49737903 ACAAATGGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.35, G:0.13, T:0.33
Consensus pattern (31 bp):
GTTTCCATCTTCCCTGCCAACTTCCAATCGA
Found at i:49739245 original size:19 final size:20
Alignment explanation
Indices: 49739221--49739258 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
49739211 GGTACCACCA
49739221 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
49739240 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
49739259 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:49739647 original size:93 final size:93
Alignment explanation
Indices: 49739488--49739657 Score: 268
Period size: 93 Copynumber: 1.8 Consensus size: 93
49739478 CCCCTAAGTG
* * * *
49739488 AACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
49739553 GAGTTCGGATGCCTAGTTACATCTCACA
66 GAGTTCGGATGCCTAGTTACATCTCACA
* * * *
49739581 AACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCTATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
49739646 GAGTTCGGATGC
66 GAGTTCGGATGC
49739658 TCAACCATCC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCACA
Found at i:49739648 original size:46 final size:46
Alignment explanation
Indices: 49739482--49739651 Score: 159
Period size: 46 Copynumber: 3.7 Consensus size: 46
49739472 AACCCGCCCC
* * * * * * *
49739482 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCTA
* * * *
49739528 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC--A-GAC-ATTTGCATCT-A
*
49739579 -CA---AACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCTA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCTA
49739621 TAAGTGAACTCGGACTCAACTCAACGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
49739652 GGATGCTCAA
Statistics
Matches: 100, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
42 1 0.01
43 9 0.09
44 2 0.02
45 1 0.01
46 53 0.53
47 25 0.25
49 2 0.02
50 6 0.06
51 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCTA
Found at i:49740111 original size:30 final size:30
Alignment explanation
Indices: 49740077--49740136 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
49740067 ATTTAATACG
49740077 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
49740107 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
49740137 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:49745665 original size:43 final size:43
Alignment explanation
Indices: 49745643--49745738 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 43
49745633 ATGTGTTTTT
*
49745643 GTGTAAGACCATGTCTAGGACATTGGCATCGACTTATGATTTAC
1 GTGTAAGACCATGTCTAGGACATAGGCATCGAC-TATGATTTAC
* * *
49745687 GTGTAAGACCATGTCTGGGACATCGGCATCGTAAT-TGATTT-C
1 GTGTAAGACCATGTCTAGGACATAGGCATCG-ACTATGATTTAC
*
49745729 GTGTAGGACC
1 GTGTAAGACC
49745739 TTTTCTCGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 10 0.21
43 6 0.13
44 30 0.64
45 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCATGTCTAGGACATAGGCATCGACTATGATTTAC
Found at i:49748662 original size:31 final size:31
Alignment explanation
Indices: 49748624--49748702 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
49748614 TTTAACGGTT
*
49748624 ACTGGGCCGAAGCCTTTTAATAAATTATATC
1 ACTGGGCCGAAGCCTTTTAATAAATCATATC
*
49748655 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTAATAAATCATATC
*
49748686 ATTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
49748703 ACTGTAAACG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTAATAAATCATATC
Found at i:49748773 original size:42 final size:42
Alignment explanation
Indices: 49748726--49748817 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
49748716 TGGCCCTTAG
* ** * *
49748726 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGGAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
49748768 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
49748810 GCCCATTT
1 GCCCATTT
49748818 GGGGAGACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:49748990 original size:25 final size:26
Alignment explanation
Indices: 49748962--49749109 Score: 194
Period size: 25 Copynumber: 5.8 Consensus size: 26
49748952 CCTCTTTAAT
49748962 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
49748987 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* **
49749012 AACTAGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* *
49749037 AACTAGGGCATAAGCCCCTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* * **
49749063 AACTGGGGCATAAGCCATTTCCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
49749089 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
49749110 GCACTTCCTC
Statistics
Matches: 108, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
25 57 0.53
26 51 0.47
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.24
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:49749947 original size:27 final size:26
Alignment explanation
Indices: 49749912--49749994 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
49749902 GGGCATATTC
* *
49749912 GTCATTTTACCATACAGGGGTATTACG
1 GTCACTTTACCCTACAGGGGT-TTACG
49749939 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGG-TTTACG
* *
49749966 GTCACTTTACCCTAAAGGGCTTTACG
1 GTCACTTTACCCTACAGGGGTTTACG
49749992 GTC
1 GTC
49749995 TTTTTACCTA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 9 0.18
27 41 0.80
28 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (26 bp):
GTCACTTTACCCTACAGGGGTTTACG
Found at i:49750093 original size:27 final size:27
Alignment explanation
Indices: 49750055--49750106 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
49750045 ATAAATCTAC
49750055 AAACCAATGGTATTT-CAGTAATTTTGT
1 AAACCAATGGTATTTCCA-TAATTTTGT
*
49750082 AAACTAATGGTATTTCCATAATTTT
1 AAACCAATGGTATTTCCATAATTTT
49750107 TAGAAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (27 bp):
AAACCAATGGTATTTCCATAATTTTGT
Found at i:49750158 original size:27 final size:27
Alignment explanation
Indices: 49750104--49750335 Score: 132
Period size: 27 Copynumber: 8.6 Consensus size: 27
49750094 TTTCCATAAT
* *
49750104 TTTTAGAAAGTCAAGGGTATTTCT-GTAA
1 TTTTATAAA-TCAGGGGTATTT-TGGTAA
* *
49750132 CTTTGTAAATCAGGGGTATTTTGGTAA
1 TTTTATAAATCAGGGGTATTTTGGTAA
* * * * *
49750159 TTTTAAAAATTAAGGGTATTTCGATAA
1 TTTTATAAATCAGGGGTATTTTGGTAA
* * * *
49750186 TTTCACAAACCAGTGGTATTTTGGTAA
1 TTTTATAAATCAGGGGTATTTTGGTAA
* * * * *
49750213 TTTTACAAACCAGTGGTATTTTAGCAA
1 TTTTATAAATCAGGGGTATTTTGGTAA
* *
49750240 TTTTACAGA-CTA-GGGTATTTTGGTAA
1 TTTTATAAATC-AGGGGTATTTTGGTAA
*
49750266 TTTTACT-GATC-GAGGGTATTTTGGTAA
1 TTTTA-TAAATCAG-GGGTATTTTGGTAA
* * * **
49750293 TTTTGTAAACCAAGGGTATTTTACTAA
1 TTTTATAAATCAGGGGTATTTTGGTAA
*
49750320 TTTTGTAAATCGAGGG
1 TTTTATAAATC-AGGG
49750336 TAAAATAGTA
Statistics
Matches: 160, Mismatches: 35, Indels: 18
0.75 0.16 0.08
Matches are distributed among these distances:
26 21 0.13
27 130 0.81
28 9 0.06
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
TTTTATAAATCAGGGGTATTTTGGTAA
Found at i:49750332 original size:54 final size:54
Alignment explanation
Indices: 49750289--49750445 Score: 179
Period size: 54 Copynumber: 2.9 Consensus size: 54
49750279 GGGTATTTTG
* *** * *
49750289 GTAATTTTGTAAACCAAGGGTATTTTACTAATTTTGTAAATCGAGGGTAAAATA
1 GTAATTCTGTAAACCAAGGGTAAAATACTAATTCTATAAATCGAGGGTAAAATA
* * **
49750343 GTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAACCAAGGGTAAAATACTAATTCTATAAATCGAGGGTAAAATA
* * ***
49750397 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTA
1 GTAATTCTGTAAACCAAGGGTAAAATACTAATTCTATAAATCGAGGGTA
49750446 CTTTGGTAAT
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 90 1.00
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (54 bp):
GTAATTCTGTAAACCAAGGGTAAAATACTAATTCTATAAATCGAGGGTAAAATA
Found at i:49750456 original size:27 final size:27
Alignment explanation
Indices: 49750317--49750445 Score: 186
Period size: 27 Copynumber: 4.8 Consensus size: 27
49750307 GGTATTTTAC
* *
49750317 TAATTTTGTAAATCGAGGGTAAAATAG
1 TAATTCTGTAAATCGAGGGTAAAATGG
* *
49750344 TAATTCTGTAAATCAAGGGTAAAATAG
1 TAATTCTGTAAATCGAGGGTAAAATGG
* *
49750371 TAATTCTATAAATCGAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
*
49750398 TAATTCTGTAAATCGAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
*
49750425 TAATTCTATAAATCGAGGGTA
1 TAATTCTGTAAATCGAGGGTA
49750446 CTTTGGTAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 94 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (27 bp):
TAATTCTGTAAATCGAGGGTAAAATGG
Found at i:49752833 original size:3 final size:3
Alignment explanation
Indices: 49752825--49752897 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
49752815 TGTTTATGAA
49752825 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
49752873 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
49752898 ATTAAATATG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:49754312 original size:11 final size:10
Alignment explanation
Indices: 49754280--49754325 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
49754270 CATGAGACCT
49754280 TGATAT-ACA
1 TGATATGACA
*
49754289 TGATTTGACA
1 TGATATGACA
49754299 TGATATGCACA
1 TGATATG-ACA
*
49754310 TGATATG-TA
1 TGATATGACA
49754319 TGATATG
1 TGATATG
49754326 TATATGATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 13 0.41
10 9 0.28
11 10 0.31
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.37
Consensus pattern (10 bp):
TGATATGACA
Found at i:49754470 original size:25 final size:26
Alignment explanation
Indices: 49754381--49754478 Score: 135
Period size: 26 Copynumber: 3.8 Consensus size: 26
49754371 GAGGAAGTGC
* *
49754381 AAAAGGGCTTTTGTCCTAGTTTACCG
1 AAAAGGGCTTTTGCCCCAGTTTACCG
*
49754407 AAAAGGGCTTTTGCCCCAATTTACCG
1 AAAAGGGCTTTTGCCCCAGTTTACCG
* * *
49754433 AAAAGGGCTTTTGCCCTAGTTTATCA
1 AAAAGGGCTTTTGCCCCAGTTTACCG
49754459 AAAAGGGC-TTTGCCCCAGTT
1 AAAAGGGCTTTTGCCCCAGTT
49754479 ATTAAAAGAG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
25 11 0.17
26 53 0.83
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (26 bp):
AAAAGGGCTTTTGCCCCAGTTTACCG
Found at i:49756460 original size:47 final size:47
Alignment explanation
Indices: 49756406--49756535 Score: 163
Period size: 47 Copynumber: 2.8 Consensus size: 47
49756396 TCAATCGATA
49756406 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACT-TATCCCGG
1 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCT-TCCCGG
* * ***
49756453 AGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTCTTCGTTG
1 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCTTCCCGG
* * * *
49756500 AATACCAATACCATGGCCTATAGCCAAATTAAGGTA
1 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTA
49756536 TTATTCACAC
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
47 70 0.99
48 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (47 bp):
AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCTTCCCGG
Found at i:49761697 original size:22 final size:22
Alignment explanation
Indices: 49761658--49761699 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
49761648 AGATCATCAC
49761658 AAATATAATCGCATACATATTA
1 AAATATAATCGCATACATATTA
*
49761680 AAATATCAATCTCA-ACATAT
1 AAATAT-AATCGCATACATAT
49761700 CAATCATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATATAATCGCATACATATTA
Found at i:49763730 original size:2 final size:2
Alignment explanation
Indices: 49763723--49763754 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49763713 GTGAACTGCA
49763723 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
49763755 CAATCACATA
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:49767431 original size:30 final size:31
Alignment explanation
Indices: 49767350--49767432 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
49767340 TCAGTCTCGA
49767350 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
49767380 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
49767411 CATATCACT-GGCCTAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
49767433 ACTGATACGA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 17 0.33
31 34 0.67
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:49767634 original size:27 final size:28
Alignment explanation
Indices: 49767567--49767624 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
49767557 AAGGATTCAA
*
49767567 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGGTTATGGATA-GAAGTTTATGT
*
49767596 AGATGGGGTTATGGATA-AAGTTTTTGT
1 AGATGGGGTTATGGATAGAAGTTTATGT
49767623 AG
1 AG
49767625 GTTTGGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 11 0.41
29 16 0.59
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.40
Consensus pattern (28 bp):
AGATGGGGTTATGGATAGAAGTTTATGT
Done.