Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 259 of 335
Found at i:78461030 original size:24 final size:24
Alignment explanation
Indices: 78460972--78461177 Score: 119
Period size: 24 Copynumber: 8.7 Consensus size: 24
78460962 TAAAAAGGCT
*
78460972 CTTTTAT-TATTATTTATTTTAAGTTT
1 CTTTTATATATTATTTATTTTAA---A
*
78460998 CTTTCATATATTATTTATTTTAAA
1 CTTTTATATATTATTTATTTTAAA
* *
78461022 CTATTATATA-TATTATCTTTTAAA
1 CTTTTATATATTATT-TATTTTAAA
*
78461046 TTTTTATATATTA-TT-TTTTAAA
1 CTTTTATATATTATTTATTTTAAA
* *
78461068 TTGTTTTATATGTTATTT-TTTT--A
1 --CTTTTATATATTATTTATTTTAAA
* *
78461091 --TATAT-TATTATTCATTTTAAA
1 CTTTTATATATTATTTATTTTAAA
* *
78461112 CTGTTT-TATTACTATTTATTTTAAG
1 CT-TTTATA-TATTATTTATTTTAAA
* * *
78461137 TTTTTATATATTGTTTATTTGAAA
1 CTTTTATATATTATTTATTTTAAA
*
78461161 CTTTTATTTATTTATTT
1 CTTTTATATA-TTATTT
78461178 TTAATTGTTT
Statistics
Matches: 140, Mismatches: 24, Indels: 33
0.71 0.12 0.17
Matches are distributed among these distances:
18 6 0.04
19 8 0.06
21 1 0.01
22 7 0.05
23 7 0.05
24 61 0.44
25 29 0.21
26 6 0.04
27 15 0.11
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.64
Consensus pattern (24 bp):
CTTTTATATATTATTTATTTTAAA
Found at i:78461134 original size:44 final size:42
Alignment explanation
Indices: 78461045--78461134 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 42
78461035 TATCTTTTAA
* **
78461045 ATTTT-TATATATTATTTTTTAAATTGTTTTATATGTTATTT
1 ATTTTATATATATTATTTTTTAAACTGTTTTATATACTATTT
78461086 -TTTTATATATTATTATTCATTTTAAACTGTTTTAT-TACTATTT
1 ATTTTATATA-TATTATT--TTTTAAACTGTTTTATATACTATTT
78461129 ATTTTA
1 ATTTTA
78461135 AGTTTTTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
40 4 0.10
41 4 0.10
42 7 0.17
43 6 0.15
44 20 0.49
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (42 bp):
ATTTTATATATATTATTTTTTAAACTGTTTTATATACTATTT
Found at i:78461220 original size:48 final size:45
Alignment explanation
Indices: 78461124--78461221 Score: 106
Period size: 48 Copynumber: 2.1 Consensus size: 45
78461114 GTTTTATTAC
* * * * * *
78461124 TATTTATTTTAAGTTTTTATATATTGTTTATTTGAAACTTTTATT
1 TATTTATTTTAAGTTTTTATAAATTATCTATTTGAAAATATTAGT
*
78461169 TATTTATTTTTAATTGTTTTTATAAATTATCTATTTTAAAATATTAGT
1 TATTTA-TTTTAA--GTTTTTATAAATTATCTATTTGAAAATATTAGT
78461217 TATTT
1 TATTT
78461222 TAAATTATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
45 6 0.14
46 6 0.14
48 31 0.72
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (45 bp):
TATTTATTTTAAGTTTTTATAAATTATCTATTTGAAAATATTAGT
Found at i:78463165 original size:48 final size:50
Alignment explanation
Indices: 78463109--78463219 Score: 120
Period size: 54 Copynumber: 2.2 Consensus size: 50
78463099 AGTTCTATAA
*
78463109 TTAAGACCA-TCAAAG-AGGCAATGTAACACCCTATACTC-AGCCTAGACG
1 TTAAGACCAGTCAAAGCAGGCAATGTAACACCCCATACTCGA-CCTAGACG
***
78463157 TTAAGACCAAGTTTGGAGCTCAGGCAATGTAACACCCCATACTCGACCTAGACG
1 TTAAGACC-AG-TCAAAG--CAGGCAATGTAACACCCCATACTCGACCTAGACG
78463211 TTAAGACCA
1 TTAAGACCA
78463220 AGTTTGGAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
48 8 0.15
49 1 0.02
51 3 0.06
53 1 0.02
54 38 0.73
55 1 0.02
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (50 bp):
TTAAGACCAGTCAAAGCAGGCAATGTAACACCCCATACTCGACCTAGACG
Found at i:78463207 original size:54 final size:54
Alignment explanation
Indices: 78463124--78463232 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
78463114 ACCATCAAAG
*
78463124 AGGCAATGTAACACCCTATACTCAGCCTAGACGTTAAGACCAAGTTTGGAGCTC
1 AGGCAATGTAACACCCCATACTCAGCCTAGACGTTAAGACCAAGTTTGGAGCTC
78463178 AGGCAATGTAACACCCCATACTC-GACCTAGACGTTAAGACCAAGTTTGGAGCTC
1 AGGCAATGTAACACCCCATACTCAG-CCTAGACGTTAAGACCAAGTTTGGAGCTC
78463232 A
1 A
78463233 CATCAAAATG
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
53 1 0.02
54 52 0.98
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (54 bp):
AGGCAATGTAACACCCCATACTCAGCCTAGACGTTAAGACCAAGTTTGGAGCTC
Found at i:78466161 original size:2 final size:2
Alignment explanation
Indices: 78466154--78466193 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
78466144 CAGTGAGCAA
78466154 AT AT AT AT 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 AT AT AT AT
78466194 GCTCTAAAGG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78467019 original size:17 final size:17
Alignment explanation
Indices: 78466993--78467031 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
78466983 AATGAAATGC
* *
78466993 AAAAATAAAAATAAAAT
1 AAAAAGAAAAACAAAAT
*
78467010 AAAAAGAAAAACAAATT
1 AAAAAGAAAAACAAAAT
78467027 AAAAA
1 AAAAA
78467032 ATAAATAGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (17 bp):
AAAAAGAAAAACAAAAT
Found at i:78468773 original size:40 final size:40
Alignment explanation
Indices: 78468699--78468841 Score: 160
Period size: 40 Copynumber: 3.6 Consensus size: 40
78468689 CCGCACCAAG
* * * * * * *
78468699 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAC
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
78468739 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * *
78468779 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
78468819 GCCTTCGGGTCTTAACCCGGATA
1 GCCTTCGGGTCTTAGCCCGGATA
78468842 AATTTTCAGC
Statistics
Matches: 87, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:78468877 original size:39 final size:40
Alignment explanation
Indices: 78468739--78468880 Score: 146
Period size: 40 Copynumber: 3.6 Consensus size: 40
78468729 TTGCACAAAC
* * *
78468739 GCCTTCGGGTCTTAGCCCGGATTTAA-CAACTTGCACGAA-T
1 GCCTTCGGGTCTTAGCCCGGA-TAAAGCTACTAGCAC-AATT
*
78468779 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATAAAGCTACTAGCACAATT
* ** * *
78468819 GCCTTCGGGTCTTAACCCGGATAAATTTTC-AGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATAAAGCTACTAGCACAATT
* *
78468858 GTCTTCGGGGCTTAGCCCGGATA
1 GCCTTCGGGTCTTAGCCCGGATA
78468881 TCATTCAATT
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
39 32 0.37
40 55 0.63
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATAAAGCTACTAGCACAATT
Found at i:78476875 original size:40 final size:40
Alignment explanation
Indices: 78476801--78476943 Score: 160
Period size: 40 Copynumber: 3.6 Consensus size: 40
78476791 CCGCACCAAG
* * * * * * *
78476801 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAC
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
78476841 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * *
78476881 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
78476921 GCCTTCGGGTCTTAACCCGGATA
1 GCCTTCGGGTCTTAGCCCGGATA
78476944 AAATTTTCAG
Statistics
Matches: 87, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:78476961 original size:40 final size:41
Alignment explanation
Indices: 78476841--78476983 Score: 141
Period size: 40 Copynumber: 3.6 Consensus size: 41
78476831 TTGCACAAAC
** * *
78476841 GCCTTCGGGTCTTAGCCCGGATTTAA-CAACTTGCACGAA-T
1 GCCTTCGGGTCTTAGCCCGGATAAAAGCTACTAGCAC-AATT
*
78476881 GCCTTCGGGTCTTAGCCCGGAT-ATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATAAAAGCTACTAGCACAATT
* ** * *
78476921 GCCTTCGGGTCTTAACCCGGATAAAATTTTC-AGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATAAAAGCTACTAGCACAATT
* *
78476961 GTCTTCGGGGCTTAGCCCGGATA
1 GCCTTCGGGTCTTAGCCCGGATA
78476984 TCATTCAATT
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.03
40 80 0.92
41 4 0.05
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (41 bp):
GCCTTCGGGTCTTAGCCCGGATAAAAGCTACTAGCACAATT
Found at i:78486697 original size:29 final size:29
Alignment explanation
Indices: 78486664--78486746 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
78486654 GTGTCGAGAT
78486664 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
78486693 TGGCACTAAGTGTGCGTGCTGGAAATATT
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
**
78486722 TGGCACTAAGTGTGCAAGCTGGAAA
1 TGGCACTAAGTGTGCGTGCTGGAAA
78486747 AAAAATACGG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:78489567 original size:40 final size:39
Alignment explanation
Indices: 78489512--78489719 Score: 206
Period size: 40 Copynumber: 5.2 Consensus size: 39
78489502 TGAATGATAC
* * *
78489512 CCGGGTTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTG-TTATAT
* *
78489552 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGTTATAT
* *
78489592 TCGGGCTAAGACCCGAAGGCATTCGTG-TGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCT-AG-TGTTATAT
* * *
78489632 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGT-TACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGT--TATAT
* * * *
78489672 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTTTAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGT-GTTATAT
78489712 CC-GGCTAA
1 CCGGGCTAA
78489720 ATTCCGAAGA
Statistics
Matches: 141, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
38 1 0.01
39 6 0.04
40 131 0.93
41 2 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGTTATAT
Found at i:78489713 original size:80 final size:80
Alignment explanation
Indices: 78489512--78489719 Score: 242
Period size: 80 Copynumber: 2.6 Consensus size: 80
78489502 TGAATGATAC
* * * *
78489512 CCGGGTTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCG
* *** *
78489577 TGCGAGTTGTTATAT
66 TGCAAGTTACCAAAT
* * *
78489592 TCGGGCTAAGACCCGAAGGC-ATTCGTG-TGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATT
1 CCGGGTTAAGACCCGAAGGCAATT-GTGCT-AGTGGTTATATCCGGGCTAAGACCCGAAGGCATT
*
78489655 TGTGCAAGTTACCAAAT
64 CGTGCAAGTTACCAAAT
* *
78489672 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTTTATCC-GGCTAA
1 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAA
78489720 ATTCCGAAGA
Statistics
Matches: 106, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
79 9 0.08
80 93 0.88
81 4 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCG
TGCAAGTTACCAAAT
Found at i:78489943 original size:24 final size:24
Alignment explanation
Indices: 78489922--78489974 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
78489912 GTTGATGAAG
78489922 TGTGAAGTAAGTATGATTATGAGAA
1 TGTGAAGTAA-TATGATTATGAGAA
* *
78489947 TGTGTATTAATATGATTATGAGAA
1 TGTGAAGTAATATGATTATGAGAA
78489971 TGTG
1 TGTG
78489975 TATTAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (24 bp):
TGTGAAGTAATATGATTATGAGAA
Found at i:78489975 original size:24 final size:24
Alignment explanation
Indices: 78489933--78489982 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
78489923 GTGAAGTAAG
78489933 TATGATTATGAGAATGTGTATTAA
1 TATGATTATGAGAATGTGTATTAA
78489957 TATGATTATGAGAATGTGTATTAA
1 TATGATTATGAGAATGTGTATTAA
78489981 TA
1 TA
78489983 AAGTGATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (24 bp):
TATGATTATGAGAATGTGTATTAA
Found at i:78492598 original size:27 final size:27
Alignment explanation
Indices: 78492563--78492628 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
78492553 TAGTTGAACT
*
78492563 ATGGCAAAGTGATAAAGCGTGTCAAAC
1 ATGGCAAAGTGATAAAGCGTGCCAAAC
* * *
78492590 ATGGTAAAGTGATAAAGTGTGCCAAAT
1 ATGGCAAAGTGATAAAGCGTGCCAAAC
78492617 ATGGCAAAGTGA
1 ATGGCAAAGTGA
78492629 AATGTGACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.27, T:0.21
Consensus pattern (27 bp):
ATGGCAAAGTGATAAAGCGTGCCAAAC
Found at i:78495315 original size:50 final size:49
Alignment explanation
Indices: 78495208--78495405 Score: 182
Period size: 50 Copynumber: 4.0 Consensus size: 49
78495198 CAATTATAGA
* * * * *
78495208 AAATCAAATATAATATCACATATGTGCATACCTATATGGCCGAATATGC
1 AAATCAAATATAACATCAAATATGTACATACTTATATGGCCGAATATAC
* * *
78495257 AAGATCAAATTTAACATTAAATATGTACTTACTTATATGGCCGAATATAC
1 AA-ATCAAATATAACATCAAATATGTACATACTTATATGGCCGAATATAC
* * * * * *
78495307 GAATTCAAATATAATATCAAATTTGTGCATACCTT-CATGGCCGAATATTC
1 -AAATCAAATATAACATCAAATATGTACATA-CTTATATGGCCGAATATAC
* * * * *
78495357 TAAATCCAATATAACATCACATACGTACATACCTATGTGGCCGAATATA
1 -AAATCAAATATAACATCAAATATGTACATACTTATATGGCCGAATATA
78495406 TACAAGGTCA
Statistics
Matches: 116, Mismatches: 29, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
49 4 0.03
50 107 0.92
51 5 0.04
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (49 bp):
AAATCAAATATAACATCAAATATGTACATACTTATATGGCCGAATATAC
Found at i:78495398 original size:100 final size:100
Alignment explanation
Indices: 78495211--78495405 Score: 259
Period size: 100 Copynumber: 1.9 Consensus size: 100
78495201 TTATAGAAAA
* * *
78495211 TCAAATATAATATCACATATGTGCATACCTATATGGCCGAATATGCAAGATCAAATTTAACATTA
1 TCAAATATAATATCAAATATGTGCATACCTATATGGCCGAATATGCAAGATCAAATATAACATCA
* * *
78495276 AATATGTACTTACTTATATGGCCGAATATACGAAT
66 AATACGTACATACCTATATGGCCGAATATACGAAT
* * *
78495311 TCAAATATAATATCAAATTTGTGCATACCT-TCATGGCCGAATATTCTAA-ATCCAATATAACAT
1 TCAAATATAATATCAAATATGTGCATACCTAT-ATGGCCGAATATGC-AAGATCAAATATAACAT
* *
78495374 CACATACGTACATACCTATGTGGCCGAATATA
64 CAAATACGTACATACCTATATGGCCGAATATA
78495406 TACAAGGTCA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
99 1 0.01
100 79 0.96
101 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31
Consensus pattern (100 bp):
TCAAATATAATATCAAATATGTGCATACCTATATGGCCGAATATGCAAGATCAAATATAACATCA
AATACGTACATACCTATATGGCCGAATATACGAAT
Found at i:78502325 original size:27 final size:27
Alignment explanation
Indices: 78502293--78502358 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
78502283 TAGTTGAACT
78502293 ATGGCAAAGTGATAAAGTGTGCCAAAC
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
*
78502320 ATGGCAAAGTGATAAAGTGTGCCAAAT
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
78502347 ATGGCAAAGTGA
1 ATGGCAAAGTGA
78502359 AATGTGACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (27 bp):
ATGGCAAAGTGATAAAGTGTGCCAAAC
Found at i:78504450 original size:40 final size:40
Alignment explanation
Indices: 78504405--78504612 Score: 195
Period size: 40 Copynumber: 5.2 Consensus size: 40
78504395 CGGAATACAA
* *
78504405 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
* * * *
78504445 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
*
78504485 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
* ** * * *
78504525 CCGGATTTGGTC-ACTAGCA-TAATTGCCTTCGGGTCTTAAC
1 CCGGATAT-AACAACTTGCACGAA-TGCCTTCGGGTCTTAGC
* * * * ** * *
78504565 CCAGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
78504605 CCGGATAT
1 CCGGATAT
78504613 CATTTAATTG
Statistics
Matches: 140, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
39 3 0.02
40 134 0.96
41 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
Found at i:78504552 original size:80 final size:81
Alignment explanation
Indices: 78504405--78504610 Score: 236
Period size: 80 Copynumber: 2.6 Consensus size: 81
78504395 CGGAATACAA
* * * *
78504405 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
78504469 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* ** * *
78504485 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTTGGTC-ACTAGCATAATT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
78504549 GCCTTCGGGTCTTAAC
66 GCCTTCGGGTATTAAC
* * * ** * *
78504565 CCAGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
78504611 ATCATTTAAT
Statistics
Matches: 107, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 104 0.97
81 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (81 bp):
CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Found at i:78510569 original size:23 final size:22
Alignment explanation
Indices: 78510538--78510581 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
78510528 TTGATTGTAT
*
78510538 GTTTAGGTATGATTTTAGTTTAA
1 GTTTAGGTATGAATTTA-TTTAA
*
78510561 GTTTTGGTATGAATTTATTTA
1 GTTTAGGTATGAATTTATTTA
78510582 TGAATTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (22 bp):
GTTTAGGTATGAATTTATTTAA
Found at i:78517388 original size:40 final size:40
Alignment explanation
Indices: 78517318--78517495 Score: 297
Period size: 40 Copynumber: 4.5 Consensus size: 40
78517308 AAACCAAGTA
* * *
78517318 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
78517357 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
78517397 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
78517437 CCTTCGGCACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
78517477 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
78517496 TTATTATCCG
Statistics
Matches: 132, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 14 0.11
40 118 0.89
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:78519800 original size:9 final size:9
Alignment explanation
Indices: 78519788--78519844 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
78519778 TTTGATAAAC
78519788 ATGATATGT
1 ATGATATGT
*
78519797 ATGATATGCAC
1 ATGATATG--T
*
78519808 ATGACATGT
1 ATGATATGT
*
78519817 ATGATATGCAC
1 ATGATATG--T
78519828 ATGATATGT
1 ATGATATGT
78519837 ATGATATG
1 ATGATATG
78519845 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:78519811 original size:20 final size:20
Alignment explanation
Indices: 78519786--78519856 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
78519776 ATTTTGATAA
78519786 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
78519806 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
78519826 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
78519846 ACATGAGATGT
1 ACATGATATGT
78519857 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:78519833 original size:11 final size:11
Alignment explanation
Indices: 78519797--78519851 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
78519787 CATGATATGT
78519797 ATGATATGCAC
1 ATGATATGCAC
* *
78519808 ATGACATG--T
1 ATGATATGCAC
78519817 ATGATATGCAC
1 ATGATATGCAC
*
78519828 ATGATATG--T
1 ATGATATGCAC
78519837 ATGATATGCAC
1 ATGATATGCAC
78519848 ATGA
1 ATGA
78519852 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:78519928 original size:24 final size:24
Alignment explanation
Indices: 78519901--78520091 Score: 280
Period size: 24 Copynumber: 8.0 Consensus size: 24
78519891 GGAGGAAGTG
78519901 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
78519925 CAAAAGGGCTTATGCCTCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
78519949 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
78519973 -TAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
78519996 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
78520020 -TAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
78520043 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
78520067 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
78520092 ATGATAAAGC
Statistics
Matches: 154, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
23 44 0.29
24 99 0.64
25 11 0.07
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:78519996 original size:47 final size:47
Alignment explanation
Indices: 78519901--78520070 Score: 295
Period size: 47 Copynumber: 3.6 Consensus size: 47
78519891 GGAGGAAGTG
* *
78519901 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCTCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
78519949 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
78519996 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
78520043 TAAAAGGGCTTTTGCCCCAGTTATTAAA
1 CAAAAGGGCTTATGCCCCAGTTATTAAA
78520071 AGAGGCTAGG
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
47 94 0.80
48 24 0.20
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (47 bp):
CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:78520019 original size:71 final size:71
Alignment explanation
Indices: 78519902--78520092 Score: 296
Period size: 71 Copynumber: 2.7 Consensus size: 71
78519892 GAGGAAGTGC
*
78519902 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCTCAGTTATCAAAAGGGCTTATGCCCC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCC
78519967 AGTTATT
65 AGTTATT
*
78519974 -AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCA
78520038 GTTATT
66 GTTATT
* * *
78520044 AAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-CCAGTTATA
78520093 TGATAAAGCA
Statistics
Matches: 110, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
70 23 0.21
71 76 0.69
72 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (71 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCA
GTTATT
Found at i:78526507 original size:40 final size:40
Alignment explanation
Indices: 78526430--78526610 Score: 222
Period size: 40 Copynumber: 4.5 Consensus size: 40
78526420 ACCCAAGTAT
* ** *
78526430 CTTCGGGATTTAG-CCGGATATAACCACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
78526469 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
78526509 CTTCGGGACTTAGCCCGGATATAGTCGCCAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
** * *
78526549 CTTCGGGTTTTAGCCCGGATATAG-CAACTCGCACAAAAGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
78526589 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
78526611 CATTCGAATA
Statistics
Matches: 120, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
39 12 0.10
40 108 0.90
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:78529842 original size:23 final size:22
Alignment explanation
Indices: 78529811--78529854 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
78529801 TTGATCGTAT
*
78529811 GTTTAGGTATGATTTTAGTTTAA
1 GTTTAGGTATGAATTTA-TTTAA
*
78529834 GTTTTGGTATGAATTTATTTA
1 GTTTAGGTATGAATTTATTTA
78529855 TGAATTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (22 bp):
GTTTAGGTATGAATTTATTTAA
Found at i:78535711 original size:37 final size:37
Alignment explanation
Indices: 78535653--78535774 Score: 208
Period size: 37 Copynumber: 3.3 Consensus size: 37
78535643 TATAAAAGAA
* *
78535653 GTCTTACCCGGACATATTCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
78535690 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
78535727 GTCTTACCCGGTCATAATCTCCACATGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
78535764 GTCTCACCCGG
1 GTCTTACCCGG
78535775 AACATATCCC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 81 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:78535930 original size:49 final size:49
Alignment explanation
Indices: 78535870--78536188 Score: 548
Period size: 49 Copynumber: 6.5 Consensus size: 49
78535860 CATATATTTT
* * *
78535870 ACATTGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCAGC
1 ACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCATC
*
78535919 ACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACC
1 ACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCATC
* *
78535968 ACATCAGCCATTAGGCCTCATCACATATACATACACTTTCACATTCATC
1 ACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCATC
*
78536017 ACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATC
1 ACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCATC
*
78536066 ACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATC
1 ACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCATC
*
78536115 ACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCATC
1 ACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCATC
*
78536164 ACATTGGCCATTAGGCCTTATCACA
1 ACATCGGCCATTAGGCCTTATCACA
78536189 CATATATGTA
Statistics
Matches: 257, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 257 1.00
ACGTcount: A:0.31, C:0.31, G:0.09, T:0.30
Consensus pattern (49 bp):
ACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCATC
Found at i:78538828 original size:9 final size:9
Alignment explanation
Indices: 78538794--78538928 Score: 75
Period size: 9 Copynumber: 15.0 Consensus size: 9
78538784 TATTACGTAA
*
78538794 GTAAGTTTT
1 GTAAGTTAT
*
78538803 GTAAGTTTT
1 GTAAGTTAT
78538812 GTAAGTTAT
1 GTAAGTTAT
78538821 GTAAGTTAT
1 GTAAGTTAT
*
78538830 G-ATA-TGAT
1 GTA-AGTTAT
* *
78538838 ATACATTTAT
1 GTA-AGTTAT
*
78538848 GT-A-TTAC
1 GTAAGTTAT
*
78538855 GTAAGTTAA
1 GTAAGTTAT
*
78538864 GTCAGGTATGAT
1 GT-AAGT-T-AT
* *
78538876 ATATATTTAT
1 GTA-AGTTAT
78538886 GT-A-TTAT
1 GTAAGTTAT
78538893 GTAAGTTAT
1 GTAAGTTAT
*
78538902 GTAAGTTTT
1 GTAAGTTAT
78538911 GTAAGTTAT
1 GTAAGTTAT
78538920 GTAAGTTAT
1 GTAAGTTAT
78538929 TATATGATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
7 11 0.11
8 8 0.08
9 64 0.65
10 10 0.10
11 3 0.03
12 3 0.03
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:78539165 original size:15 final size:15
Alignment explanation
Indices: 78539147--78539201 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
78539137 AAAAATTTAT
78539147 TTTAATTAAATAATA
1 TTTAATTAAATAATA
* *
78539162 TTTAAATAAATTAT-
1 TTTAATTAAATAATA
*
78539176 TTTAGTTAAATAATA
1 TTTAATTAAATAATA
*
78539191 TTTAAGTAAAT
1 TTTAATTAAAT
78539202 TAATCCAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
14 11 0.34
15 21 0.66
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (15 bp):
TTTAATTAAATAATA
Found at i:78539175 original size:29 final size:29
Alignment explanation
Indices: 78539143--78539203 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
78539133 TGGAAAAAAT
78539143 TTATTTTAATTAAATAATATTTAAATAAA
1 TTATTTTAATTAAATAATATTTAAATAAA
* *
78539172 TTATTTTAGTTAAATAATATTTAAGTAAA
1 TTATTTTAATTAAATAATATTTAAATAAA
78539201 TTA
1 TTA
78539204 ATCCAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
TTATTTTAATTAAATAATATTTAAATAAA
Found at i:78539305 original size:194 final size:194
Alignment explanation
Indices: 78538975--78539368 Score: 682
Period size: 194 Copynumber: 2.0 Consensus size: 194
78538965 TTCCCTTTAA
* *
78538975 AAATTATTTTAATTAAATAATATTTAAATTAATTAATCCAAATTATGTAATTTAAAAAATTGTGT
1 AAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAAATTGTGT
* *
78539040 ATAAAAAGTTGAAAATCGTATAAGATGAAATATCAACTTTGTTACATGAAAAAGAAATAATAAAC
66 ATAAAAAGTTGAAAACCGTATAAGATGAAATATCAACTTTGTTACATGAAAAAGAAATAATAAAA
78539105 ATAAAATTTGACGATGTGGAAAATCACATGGAAA-AAATTTATTTTAATTAAATAATATTTAAAT
131 ATAAAATTTGACGATGTGGAAAATCACATGGAAATAAA-TTATTTTAATTAAATAATATTTAAAT
* *
78539169 AAATTATTTTAGTTAAATAATATTTAAGTAAATTAATCCAAATTATATAATTTAAAAAATTGTGT
1 AAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAAATTGTGT
* *
78539234 ATAAAAAGTTGAAAACCGTATAAGATGAAATGTCAACTTTGTTCCATGAAAAAGAAATAATAAAA
66 ATAAAAAGTTGAAAACCGTATAAGATGAAATATCAACTTTGTTACATGAAAAAGAAATAATAAAA
* *
78539299 ATAAAATTTGATGATGTGGAAAATCACATGGAAATAAATTATTTTAATTAAATGATATTTAAAT
131 ATAAAATTTGACGATGTGGAAAATCACATGGAAATAAATTATTTTAATTAAATAATATTTAAAT
78539363 AAATTA
1 AAATTA
78539369 ATCCAAAATA
Statistics
Matches: 189, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
194 186 0.98
195 3 0.02
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (194 bp):
AAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAAATTGTGT
ATAAAAAGTTGAAAACCGTATAAGATGAAATATCAACTTTGTTACATGAAAAAGAAATAATAAAA
ATAAAATTTGACGATGTGGAAAATCACATGGAAATAAATTATTTTAATTAAATAATATTTAAAT
Found at i:78539502 original size:14 final size:14
Alignment explanation
Indices: 78539483--78539513 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
78539473 CTTGTTTTAA
*
78539483 TATGGTAATGGCAT
1 TATGGTAATGACAT
78539497 TATGGTAATGACAT
1 TATGGTAATGACAT
78539511 TAT
1 TAT
78539514 CGACTAACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (14 bp):
TATGGTAATGACAT
Found at i:78539784 original size:24 final size:24
Alignment explanation
Indices: 78539752--78539798 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
78539742 TTAACTTAAA
*
78539752 TGATAAAATGGATGATAATATTTG
1 TGATAAAATGGATGAGAATATTTG
78539776 TGATAAAATGGATGAGAATATTT
1 TGATAAAATGGATGAGAATATTT
78539799 CAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (24 bp):
TGATAAAATGGATGAGAATATTTG
Found at i:78542296 original size:17 final size:19
Alignment explanation
Indices: 78542260--78542296 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
78542250 ATAAAATTTG
*
78542260 AAATCTTGAGAATTATTTA
1 AAATCTTGAGAATTAATTA
78542279 AAAT-TTGA-AATTAATTA
1 AAATCTTGAGAATTAATTA
78542296 A
1 A
78542297 TATATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (19 bp):
AAATCTTGAGAATTAATTA
Found at i:78542444 original size:7 final size:7
Alignment explanation
Indices: 78542434--78542520 Score: 77
Period size: 7 Copynumber: 12.0 Consensus size: 7
78542424 AACCCCTGTC
78542434 CCCTTAA
1 CCCTTAA
78542441 CCCTTAAA
1 CCCTT-AA
*
78542449 CCCCTAA
1 CCCTTAA
* *
78542456 CCCATAT
1 CCCTTAA
78542463 CCCATTAA
1 CCC-TTAA
*
78542471 CCCCTAAA
1 -CCCTTAA
78542479 CCCTTAA
1 CCCTTAA
78542486 CCCTTAA
1 CCCTTAA
*
78542493 CCCCTAA
1 CCCTTAA
78542500 CCAC-TAA
1 CC-CTTAA
78542507 CCCTTAA
1 CCCTTAA
*
78542514 CCTTTAA
1 CCCTTAA
78542521 ATCCTAAATC
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
6 1 0.02
7 50 0.76
8 12 0.18
9 3 0.05
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (7 bp):
CCCTTAA
Found at i:78542458 original size:30 final size:30
Alignment explanation
Indices: 78542410--78542488 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 30
78542400 CTAAACCTTA
* * * * *
78542410 AACCCC-AAACTCCAAACCCCTGTCCCCTT
1 AACCCCTAAACCCCTAACCCATATCCCATT
*
78542439 AACCCTTAAACCCCTAACCCATATCCCATT
1 AACCCCTAAACCCCTAACCCATATCCCATT
*
78542469 AACCCCTAAACCCTTAACCC
1 AACCCCTAAACCCCTAACCC
78542489 TTAACCCCTA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 5 0.12
30 36 0.88
ACGTcount: A:0.32, C:0.48, G:0.01, T:0.19
Consensus pattern (30 bp):
AACCCCTAAACCCCTAACCCATATCCCATT
Found at i:78542475 original size:22 final size:21
Alignment explanation
Indices: 78542438--78542515 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 21
78542428 CCTGTCCCCT
78542438 TAACCCTTAAACCCCTAACCCA
1 TAACCCTT-AACCCCTAACCCA
* *
78542460 TATCCCATTAACCCCTAAACCCT
1 TAACCC-TTAACCCCT-AACCCA
78542483 TAACCCTTAACCCCTAA-CCA
1 TAACCCTTAACCCCTAACCCA
78542503 CTAACCCTTAACC
1 -TAACCCTTAACC
78542516 TTTAAATCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
20 2 0.04
21 14 0.29
22 21 0.43
23 12 0.24
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.22
Consensus pattern (21 bp):
TAACCCTTAACCCCTAACCCA
Found at i:78542545 original size:8 final size:7
Alignment explanation
Indices: 78542472--78542551 Score: 56
Period size: 7 Copynumber: 11.1 Consensus size: 7
78542462 TCCCATTAAC
78542472 CCCTAAA
1 CCCTAAA
*
78542479 CCCTTAA
1 CCCTAAA
*
78542486 CCCTTAAC
1 CCC-TAAA
78542494 CCCT-AA
1 CCCTAAA
78542500 CCACT-AA
1 CC-CTAAA
*
78542507 CCCTTAA
1 CCCTAAA
*
78542514 CCTTTAAA
1 CC-CTAAA
*
78542522 TCCTAAA
1 CCCTAAA
*
78542529 TCCTAAA
1 CCCTAAA
78542536 CCCATAAA
1 CCC-TAAA
78542544 CCCTAAA
1 CCCTAAA
78542551 C
1 C
78542552 TATAATGATA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
6 5 0.08
7 38 0.64
8 16 0.27
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.23
Consensus pattern (7 bp):
CCCTAAA
Found at i:78542861 original size:303 final size:300
Alignment explanation
Indices: 78542423--78542998 Score: 847
Period size: 303 Copynumber: 1.9 Consensus size: 300
78542413 CCCAAACTCC
* * * * *
78542423 AAACCCCTGTCCCCTTAACCCTTAAACCCCTAACCCATATCCCATTAACCCCTAAACCCTTAACC
1 AAACCCCTGTCCCCTTAACCCCTAAACCCCTAACCAATAACCCACTAAACCCTAAACCC-TAACC
* * * * ** *
78542488 CTTAACCCCTAACCACTAACCCTTAACCTTTAAATCCTAAATCCTAAACCCATAAACCCTAAACT
65 CTTAAACCCTAACCACTAACCATAAACCTTAAAATAATAAATCATAAACCCATAAACCCTAAACT
78542553 ATAATGATAATTAATTCAATATTTTAAAATTAATATTATCTCTTTTACGATTATATAAGAATTTA
130 ATAATGATAATTAATTCAATATTTTAAAATTAATATTATCTCTTTTACGATTATATAAGAATTTA
*
78542618 TTTAATATATAAATTGACAAACATTCAGTCATATACCCAAAAAACCTTAAAATTATTTTAAATAA
195 TTTAATATATAAATTGACAAACAATCAGTCATATACCC-AAAAACCTTAAAA--A-TTTAAATAA
78542683 TAGTATTTTAATTTTTTAACATATATTTTTCACACTAATTACCCT
256 TAGTATTTTAATTTTTTAACATATATTTTTCACACTAATTACCCT
**
78542728 AAACCCCTGTCCCCTTAACCCCT-AACCCCTAACCAATAACCC-CTAAACTTTAAATCCC-AACC
1 AAACCCCTGTCCCCTTAACCCCTAAACCCCTAACCAATAACCCACTAAACCCTAAA-CCCTAACC
* * *
78542790 TTTAAACCCTAAACC-CATAATCCATAAACCTTAAAATAATAACTCATAAA-CCATAAATCCTAA
65 CTTAAACCCT-AACCAC-TAA-CCATAAACCTTAAAATAATAAATCATAAACCCATAAACCCTAA
78542853 ACTATAATGATAATTAATTCAATATTTTAAAATTAATATTATCTCTTTTACGATTATATAAGAAT
127 ACTATAATGATAATTAATTCAATATTTTAAAATTAATATTATCTCTTTTACGATTATATAAGAAT
* *
78542918 TTATTTAATATATAAATTGACAAACAATCAGTCATATACCCAAAAAGCTTTAAAATTTAAATAAT
192 TTATTTAATATATAAATTGACAAACAATCAGTCATATACCCAAAAACCTTAAAAATTTAAATAAT
*
78542983 AGTATTTTTATTTTTT
257 AGTATTTTAATTTTTT
78542999 CATTTTTAAC
Statistics
Matches: 246, Mismatches: 21, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
299 25 0.10
300 1 0.00
302 24 0.10
303 132 0.54
304 42 0.17
305 22 0.09
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.34
Consensus pattern (300 bp):
AAACCCCTGTCCCCTTAACCCCTAAACCCCTAACCAATAACCCACTAAACCCTAAACCCTAACCC
TTAAACCCTAACCACTAACCATAAACCTTAAAATAATAAATCATAAACCCATAAACCCTAAACTA
TAATGATAATTAATTCAATATTTTAAAATTAATATTATCTCTTTTACGATTATATAAGAATTTAT
TTAATATATAAATTGACAAACAATCAGTCATATACCCAAAAACCTTAAAAATTTAAATAATAGTA
TTTTAATTTTTTAACATATATTTTTCACACTAATTACCCT
Found at i:78543234 original size:40 final size:40
Alignment explanation
Indices: 78543189--78543264 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
78543179 TATAGTGGAG
78543189 TTTTTCAAAAAGCACCGCTAATGCTCGATCTATAGCTGCA
1 TTTTTCAAAAAGCACCGCTAATGCTCGATCTATAGCTGCA
* * * * *
78543229 TTTTTCAGAAAGCGCTGCTAATGCTTGATCTGTAGC
1 TTTTTCAAAAAGCACCGCTAATGCTCGATCTATAGC
78543265 ACCGCTAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.33
Consensus pattern (40 bp):
TTTTTCAAAAAGCACCGCTAATGCTCGATCTATAGCTGCA
Found at i:78543368 original size:40 final size:40
Alignment explanation
Indices: 78543324--78543429 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 40
78543314 TTTTTTTGTG
* * *
78543324 GCATTTTTAAAAAAGCACCGCTAATGGTCGAGCTATAGTA
1 GCATTTTTAAAAAAGCGCCGCTAATGCTCGAGCTATAGCA
** * *
78543364 GCATTTTTTGAAAAGCGCCGCTAATGCTCGATCTATAGCG
1 GCATTTTTAAAAAAGCGCCGCTAATGCTCGAGCTATAGCA
* *
78543404 GCATTTTTCAAAAAGTGCCGCTAATG
1 GCATTTTTAAAAAAGCGCCGCTAATG
78543430 ACGCTAAAGC
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (40 bp):
GCATTTTTAAAAAAGCGCCGCTAATGCTCGAGCTATAGCA
Found at i:78546064 original size:13 final size:14
Alignment explanation
Indices: 78546046--78546092 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
78546036 TGAAATGGCA
78546046 AATATGAGAA-ATG
1 AATATGAGAATATG
78546059 AATATGAGAATATG
1 AATATGAGAATATG
*
78546073 AGAAATGA-AATATG
1 A-ATATGAGAATATG
78546087 AA-ATGA
1 AATATGA
78546093 TGAAATAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 4 0.13
13 11 0.35
14 11 0.35
15 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.23
Consensus pattern (14 bp):
AATATGAGAATATG
Found at i:78546070 original size:21 final size:21
Alignment explanation
Indices: 78546045--78546095 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
78546035 TTGAAATGGC
78546045 AAATATGAGAAATG-AATATG
1 AAATATGAGAAATGAAATATG
78546065 AGAATATGAGAAATGAAATATG
1 A-AATATGAGAAATGAAATATG
78546087 AAATGATGA
1 AAAT-ATGA
78546096 AATAAGATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 1 0.04
21 16 0.57
22 11 0.39
ACGTcount: A:0.55, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
AAATATGAGAAATGAAATATG
Found at i:78546071 original size:8 final size:8
Alignment explanation
Indices: 78546046--78546099 Score: 50
Period size: 8 Copynumber: 7.5 Consensus size: 8
78546036 TGAAATGGCA
78546046 AATATGAG
1 AATATGAG
78546054 AA-AT--G
1 AATATGAG
78546059 AATATGAG
1 AATATGAG
78546067 AATATGAG
1 AATATGAG
78546075 AA-ATGA-
1 AATATGAG
78546081 AATATGA-
1 AATATGAG
78546088 AATGATGA-
1 AAT-ATGAG
78546096 AATA
1 AATA
78546100 AGATGTGGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
5 3 0.07
6 4 0.10
7 14 0.34
8 20 0.49
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (8 bp):
AATATGAG
Found at i:78553248 original size:20 final size:20
Alignment explanation
Indices: 78553220--78553277 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
78553210 CATTGTAATG
78553220 CAAATAGAGGCACCGAAGTA
1 CAAATAGAGGCACCGAAGTA
* * *
78553240 CAAACAGAGGCATCGAAGTG
1 CAAATAGAGGCACCGAAGTA
78553260 C-AATAGAGGCACCGAAGT
1 CAAATAGAGGCACCGAAGT
78553278 GCAATCCTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.41, C:0.21, G:0.28, T:0.10
Consensus pattern (20 bp):
CAAATAGAGGCACCGAAGTA
Found at i:78553269 original size:19 final size:19
Alignment explanation
Indices: 78553222--78553282 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
78553212 TTGTAATGCA
*
78553222 AATAGAGGCACCGAAGTAC
1 AATAGAGGCACCGAAGTGC
* *
78553241 AAACAGAGGCATCGAAGTGC
1 -AATAGAGGCACCGAAGTGC
78553261 AATAGAGGCACCGAAGTGC
1 AATAGAGGCACCGAAGTGC
78553280 AAT
1 AAT
78553283 CCTGTACAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.41, C:0.20, G:0.28, T:0.11
Consensus pattern (19 bp):
AATAGAGGCACCGAAGTGC
Found at i:78554225 original size:17 final size:18
Alignment explanation
Indices: 78554191--78554226 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
78554181 TGAATTTCTA
78554191 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
78554209 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
78554226 T
1 T
78554227 AACTCACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:78554607 original size:11 final size:12
Alignment explanation
Indices: 78554593--78554624 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
78554583 TTAGTTTCTC
78554593 CTTT-TTCTTTT
1 CTTTCTTCTTTT
78554604 CTTTCTTC-TTT
1 CTTTCTTCTTTT
78554615 CTTTCTTCTT
1 CTTTCTTCTT
78554625 ATTTCCGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
CTTTCTTCTTTT
Found at i:78561509 original size:27 final size:28
Alignment explanation
Indices: 78561453--78561522 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
78561443 AAATTTGTAC
78561453 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
78561481 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
78561508 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
78561523 GACTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:78561533 original size:27 final size:27
Alignment explanation
Indices: 78561453--78561534 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
78561443 AAATTTGTAC
* *
78561453 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
78561481 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
78561508 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
78561535 GCTTTTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.02
27 30 0.61
28 18 0.37
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:78567172 original size:43 final size:43
Alignment explanation
Indices: 78567106--78567255 Score: 173
Period size: 43 Copynumber: 3.5 Consensus size: 43
78567096 TTGTACAATA
* *
78567106 CCAACGTCCCTA-ACGTGGTCTTACATGTAATCTCATATTGATT
1 CCAACGTCCC-AGACGTGGTCTTACATGTAATCACATATTGATG
* *
78567149 CC-ACTGTCCCAGACAG-GGTCTTAC-TCTTAAACACATATTGATG
1 CCAAC-GTCCCAGAC-GTGGTCTTACAT-GTAATCACATATTGATG
* *
78567192 CCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATG
1 CCAACGTCCCAGACGTGGTCTTACATGTAATCACATATTGATG
*
78567235 CCAACGTCCCGGACGTGGTCT
1 CCAACGTCCCAGACGTGGTCT
78567256 AATACATGAT
Statistics
Matches: 91, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
42 5 0.05
43 83 0.91
44 3 0.03
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (43 bp):
CCAACGTCCCAGACGTGGTCTTACATGTAATCACATATTGATG
Found at i:78568295 original size:15 final size:13
Alignment explanation
Indices: 78568266--78568292 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
78568256 GCTCGGCAGG
78568266 GACACGCCCGTGT
1 GACACGCCCGTGT
78568279 GACACGCCCGTGT
1 GACACGCCCGTGT
78568292 G
1 G
78568293 TGATTACTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:78568676 original size:43 final size:43
Alignment explanation
Indices: 78568615--78568943 Score: 451
Period size: 43 Copynumber: 7.7 Consensus size: 43
78568605 CGGTTTATCA
*
78568615 TGGTCTTATACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
** * * *
78568658 TGGTCTTATGCGTAATCACGTATCGATGCCAACGTCCCAAACT
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
* * * * *
78568701 TGGTCTTACAAGTAATAACATATTGATGCCAACATCCCAGATG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
** * *
78568744 TGGTCTTATGCTTAATCACATATCGATGCCAACATCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
*
78568787 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGAAG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
* *
78568830 TGGTCTTACGCGTAATCACATATCGATGCCAATGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
* ** *
78568873 TGGCCTTATGCGTAATCACATGTCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
*
78568916 TAGTCTTACACGTAATCACATATCGATG
1 TGGTCTTACACGTAATCACATATCGATG
78568944 TCTCATATAT
Statistics
Matches: 248, Mismatches: 38, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 248 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (43 bp):
TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
Found at i:78569055 original size:2 final size:2
Alignment explanation
Indices: 78569048--78569083 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
78569038 CTATAGTCGA
78569048 AT AT 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 AT AT
78569084 TCATGATTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78571339 original size:46 final size:46
Alignment explanation
Indices: 78571289--78571461 Score: 169
Period size: 46 Copynumber: 3.7 Consensus size: 46
78571279 TGGTTGAGCA
78571289 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATG
* * * *
78571335 TCCGAACTCGTTGAGTTGAGTCCT-AGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGT-CTGAGTTCACTTATGGATGCAA--ATG
* *
78571380 CATCCGAACTCGTTGAGTTGAGT-TCGAGTTCATTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCT-GAGTTCACTTATGGATGCAAATG
* *
78571428 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAA-CTCGTTGAGTTGAGTCTGAGTTCACTTA
78571462 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
43 6 0.06
45 9 0.09
46 51 0.50
47 28 0.27
48 4 0.04
50 5 0.05
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.32
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATG
Found at i:78571445 original size:93 final size:93
Alignment explanation
Indices: 78571286--78571456 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
78571276 GGATGGTTGA
*
78571286 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCCAACTCGTTGAGT
*
78571351 TGAGTCCTAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
78571379 GCATCCGAACTCGTTGAGTTGAGT-TCGAGTTCATTTATGGATGCGAATG-CCCAAGCTCGTTGA
1 GCATCCGAACTCGTTGAGTTGAGTCT-GAGTTCACTTATGGATGCAAATGTCCCAA-CTCGTTGA
78571442 GTTGAGTCCGAGTTC
64 GTTGAGTCCGAGTTC
78571457 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
92 5 0.07
93 67 0.93
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:78578845 original size:46 final size:46
Alignment explanation
Indices: 78578795--78578967 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
78578785 TGGTTGAGCA
*
78578795 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
78578841 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
78578888 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
78578934 -CCTGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
78578968 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 13, Indels: 16
0.79 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
45 5 0.05
46 58 0.55
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:78578951 original size:93 final size:93
Alignment explanation
Indices: 78578792--78578962 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
78578782 GGATGGTTGA
* *
78578792 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCATTGAGT
78578857 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
78578885 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG-CCTGAGCTCATTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC-GAACTCATTGAG
78578949 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
78578963 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:78582177 original size:26 final size:26
Alignment explanation
Indices: 78582148--78582197 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
78582138 CATAGTGTCT
78582148 GTACCTCGTTCGAAAAGCAGTCTTCC
1 GTACCTCGTTCGAAAAGCAGTCTTCC
*
78582174 GTACCTCGTTCGGAAAGCAGTCTT
1 GTACCTCGTTCGAAAAGCAGTCTT
78582198 TGGCACATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (26 bp):
GTACCTCGTTCGAAAAGCAGTCTTCC
Found at i:78585354 original size:69 final size:69
Alignment explanation
Indices: 78585228--78585365 Score: 181
Period size: 69 Copynumber: 2.0 Consensus size: 69
78585218 GACGTGGTCT
* * * *
78585228 TACATGTAATCTCATATCGATACCACTATCCCAGACAGGGTCTTACTCTTAAACACATATCGATG
1 TACACGTAATCACATATCGATACCACTATCCCAGACAGGGTCTTACACGTAAACACATATCGATG
78585293 CCAA
66 CCAA
* * *
78585297 TACACGTAATCACATATCGATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATCGA
1 TACACGTAATCACATATCGATACC-ACTATCCCAGACAG-GGTCTTACACGTAAACACATATCGA
78585360 TGCCAA
64 TGCCAA
78585366 CACCCCAAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
68 1 0.02
69 57 0.95
70 2 0.03
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (69 bp):
TACACGTAATCACATATCGATACCACTATCCCAGACAGGGTCTTACACGTAAACACATATCGATG
CCAA
Found at i:78585358 original size:43 final size:43
Alignment explanation
Indices: 78585297--78585576 Score: 398
Period size: 43 Copynumber: 6.5 Consensus size: 43
78585287 TCGATGCCAA
*
78585297 TACACGTAATCACATATCGATGCCAACGTCCCAGACGTGGTCT
1 TACACGTAATCACATATCGATGCCAACATCCCAGACGTGGTCT
* * * *
78585340 TACACGTAATCACATATCGATGCCAACACCCCAAATGTGGTTT
1 TACACGTAATCACATATCGATGCCAACATCCCAGACGTGGTCT
* * * *
78585383 TACATGTAATCACTTATCGATGCCAACATCCCAGACATGGTTT
1 TACACGTAATCACATATCGATGCCAACATCCCAGACGTGGTCT
* **
78585426 TACACGTAATCACATATCGATGCTAATGTCCCAGACGTGGTCT
1 TACACGTAATCACATATCGATGCCAACATCCCAGACGTGGTCT
* * *
78585469 TACGCGTAATCACATATCGATGCCAACGTCCTAGACGTGGTCT
1 TACACGTAATCACATATCGATGCCAACATCCCAGACGTGGTCT
* **
78585512 TACACGTAATCACATATCAATGCCAACATCCTGGACGTGGTCT
1 TACACGTAATCACATATCGATGCCAACATCCCAGACGTGGTCT
78585555 TACACGTAATCACATATCGATG
1 TACACGTAATCACATATCGATG
78585577 TCTCATGTAT
Statistics
Matches: 210, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 210 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (43 bp):
TACACGTAATCACATATCGATGCCAACATCCCAGACGTGGTCT
Found at i:78585689 original size:2 final size:2
Alignment explanation
Indices: 78585682--78585707 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
78585672 ATATAGTCGA
78585682 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
78585708 CCATGATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78586349 original size:15 final size:15
Alignment explanation
Indices: 78586326--78586356 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
78586316 TCAAAATTTC
78586326 CAATACAAAACATAT
1 CAATACAAAACATAT
*
78586341 CAATCCAAAACATAT
1 CAATACAAAACATAT
78586356 C
1 C
78586357 TTTCATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:78593163 original size:18 final size:20
Alignment explanation
Indices: 78593125--78593164 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
78593115 AGGACTTGTC
*
78593125 TACTGCATTATTTGATGCTG
1 TACTGCATTATTTGATACTG
78593145 TACTG-ATTA-TTGATACTG
1 TACTGCATTATTTGATACTG
78593163 TA
1 TA
78593165 ATGGGTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.45
Consensus pattern (20 bp):
TACTGCATTATTTGATACTG
Found at i:78595257 original size:40 final size:39
Alignment explanation
Indices: 78595188--78595319 Score: 201
Period size: 40 Copynumber: 3.3 Consensus size: 39
78595178 AACCCAAGTA
* **
78595188 CCTTCGGGATTTAGCCGGATATAACAACTCGCACAAATG
1 CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG
*
78595227 CCTTTGGGACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGC-CGGATATAGTAACTCGCACAAATG
*
78595267 CCTTCAGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATG
78595307 CCTTCGGGACTTA
1 CCTTCGGGACTTA
78595320 ACCCGCACTA
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
39 13 0.15
40 70 0.83
41 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG
Found at i:78595361 original size:12 final size:12
Alignment explanation
Indices: 78595344--78595369 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
78595334 AAAATAGGGC
78595344 TTTAGCGGCGTT
1 TTTAGCGGCGTT
78595356 TTTAGCGGCGTT
1 TTTAGCGGCGTT
78595368 TT
1 TT
78595370 ATCAAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTAGCGGCGTT
Found at i:78595468 original size:41 final size:41
Alignment explanation
Indices: 78595423--78595642 Score: 311
Period size: 41 Copynumber: 5.4 Consensus size: 41
78595413 GCGTTTTACC
* * ** *
78595423 AAAAACGCCACTAAAAA-CAGAGCAATAGCGATG-TTTTAGTA
1 AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTT-G-G
* **
78595464 AAAAATGCCGC-AAAAAATAGAGCATTAGCGGCGCTTTTGG
1 AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
78595504 AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
1 AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
78595545 AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
1 AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
*
78595586 AAAAACGCCGCTAAAAACCAAAGCATTAGCGGCGCTTTTGG
1 AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
*
78595627 TAAAACGCCGCTAAAA
1 AAAAACGCCGCTAAAA
78595643 GTCATATAAC
Statistics
Matches: 164, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
40 15 0.09
41 145 0.88
42 4 0.02
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.18
Consensus pattern (41 bp):
AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
Found at i:78595814 original size:7 final size:7
Alignment explanation
Indices: 78595799--78595852 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
78595789 TTAATTATCA
*
78595799 TTATAGT
1 TTATGGT
78595806 TTATGGT
1 TTATGGT
78595813 TTATGGT
1 TTATGGT
* *
78595820 TTAAGAT
1 TTATGGT
*
78595827 ATATGGT
1 TTATGGT
*
78595834 TTAGGGT
1 TTATGGT
*
78595841 TTAAGGT
1 TTATGGT
78595848 TTATG
1 TTATG
78595853 AGTTAACTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (7 bp):
TTATGGT
Found at i:78595831 original size:21 final size:21
Alignment explanation
Indices: 78595807--78595937 Score: 100
Period size: 21 Copynumber: 5.9 Consensus size: 21
78595797 CATTATAGTT
*
78595807 TATGGTTTATGGTTTAAGATA
1 TATGGTTTAGGGTTTAAGATA
* *
78595828 TATGGTTTAGGGTTTAAGGTT
1 TATGGTTTAGGGTTTAAGATA
** *
78595849 TATGAGTTAACTATAGTTTAATATA
1 TATG-GTT---TAGGGTTTAAGATA
* *
78595874 TATGGTTTAGGGTTTAAGGTT
1 TATGGTTTAGGGTTTAAGATA
**
78595895 TATGAGTTAACTATAGTTTAAGATA
1 TATG-GTT---TAGGGTTTAAGATA
78595920 TATGGTTTAGGGTTTAAG
1 TATGGTTTAGGGTTTAAG
78595938 GTTTAGGAGT
Statistics
Matches: 83, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
21 44 0.53
22 6 0.07
24 6 0.07
25 27 0.33
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.45
Consensus pattern (21 bp):
TATGGTTTAGGGTTTAAGATA
Found at i:78595875 original size:46 final size:46
Alignment explanation
Indices: 78595818--78595953 Score: 254
Period size: 46 Copynumber: 3.0 Consensus size: 46
78595808 ATGGTTTATG
78595818 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAACTATA
1 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAACTATA
*
78595864 GTTTAATATATATGGTTTAGGGTTTAAGGTTTATGAGTTAACTATA
1 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAACTATA
*
78595910 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTA
1 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAACTA
78595954 GTATTTGAAG
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.43
Consensus pattern (46 bp):
GTTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAACTATA
Found at i:78595877 original size:25 final size:25
Alignment explanation
Indices: 78595839--78595923 Score: 79
Period size: 25 Copynumber: 3.6 Consensus size: 25
78595829 ATGGTTTAGG
* *
78595839 GTTTAAGGTTTATGAGTTAACTATA
1 GTTTAAGATATATGAGTTAACTATA
* **
78595864 GTTTAATATATATG-GTT---TAGG
1 GTTTAAGATATATGAGTTAACTATA
* *
78595885 GTTTAAGGTTTATGAGTTAACTATA
1 GTTTAAGATATATGAGTTAACTATA
78595910 GTTTAAGATATATG
1 GTTTAAGATATATG
78595924 GTTTAGGGTT
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
21 13 0.30
22 3 0.07
24 3 0.07
25 25 0.57
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (25 bp):
GTTTAAGATATATGAGTTAACTATA
Found at i:78596009 original size:7 final size:7
Alignment explanation
Indices: 78595980--78596106 Score: 105
Period size: 7 Copynumber: 18.1 Consensus size: 7
78595970 GATGAATTAT
78595980 GGGTTTA
1 GGGTTTA
*
78595987 GGGATTA
1 GGGTTTA
* *
78595994 TGATTTA
1 GGGTTTA
78596001 GGGTTTA
1 GGGTTTA
*
78596008 GGGGTTA
1 GGGTTTA
78596015 GGG-TT-
1 GGGTTTA
78596020 GGAGTTTA
1 GG-GTTTA
* *
78596028 AGGTGTAA
1 GGGT-TTA
*
78596036 GGGTTTG
1 GGGTTTA
*
78596043 GGGTTAA
1 GGGTTTA
*
78596050 GGGTTAA
1 GGGTTTA
78596057 GGGTTTA
1 GGGTTTA
*
78596064 GAGTTTA
1 GGGTTTA
*
78596071 GTGTTTA
1 GGGTTTA
*
78596078 GTGTTTA
1 GGGTTTA
78596085 GGGTTTA
1 GGGTTTA
78596092 GGGTTTA
1 GGGTTTA
*
78596099 AGGTTTA
1 GGGTTTA
78596106 G
1 G
78596107 TGGCATTTTT
Statistics
Matches: 96, Mismatches: 20, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
5 2 0.02
6 3 0.03
7 85 0.89
8 6 0.06
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (7 bp):
GGGTTTA
Found at i:78596402 original size:14 final size:14
Alignment explanation
Indices: 78596379--78596423 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
78596369 TTAATTATCA
78596379 TTATAGTTTAGGGT
1 TTATAGTTTAGGGT
78596393 TTAT-GATTTAGGGT
1 TTATAG-TTTAGGGT
*
78596407 ATATAGTTTAGGGT
1 TTATAGTTTAGGGT
78596421 TTA
1 TTA
78596424 AGGTGTACGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (14 bp):
TTATAGTTTAGGGT
Found at i:78596465 original size:29 final size:29
Alignment explanation
Indices: 78596433--78596491 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
78596423 AAGGTGTACG
78596433 AATTACTAATTTACGGGTTACAATTATGT
1 AATTACTAATTTACGGGTTACAATTATGT
78596462 AATTACTAATTTACGGGTTACAATTATGT
1 AATTACTAATTTACGGGTTACAATTATGT
78596491 A
1 A
78596492 GTACTTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.41
Consensus pattern (29 bp):
AATTACTAATTTACGGGTTACAATTATGT
Found at i:78601459 original size:24 final size:24
Alignment explanation
Indices: 78601432--78601499 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
78601422 ATTATTATTG
* *
78601432 AAATATTCTTGTCCGTTTTATCAT
1 AAATATTATTGTCCGTTTTATCAC
*
78601456 AAATATTATTCTCCGTTTTATCAC
1 AAATATTATTGTCCGTTTTATCAC
*
78601480 AAATATTATCGTCCGTTTTA
1 AAATATTATTGTCCGTTTTA
78601500 CCGTTTAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (24 bp):
AAATATTATTGTCCGTTTTATCAC
Found at i:78601833 original size:9 final size:9
Alignment explanation
Indices: 78601821--78601941 Score: 118
Period size: 9 Copynumber: 13.6 Consensus size: 9
78601811 TATTTGATAT
*
78601821 CATAATTTA
1 CATAACTTA
78601830 CATAACTTA
1 CATAACTTA
* *
78601839 TATAACATA
1 CATAACTTA
*
78601848 TATAACTTA
1 CATAACTTA
78601857 CATAACTTA
1 CATAACTTA
* *
78601866 TATAACATA
1 CATAACTTA
78601875 CATAACTTA
1 CATAACTTA
* * *
78601884 TATAGCATA
1 CATAACTTA
78601893 CATAACTTA
1 CATAACTTA
*
78601902 TATAACTTA
1 CATAACTTA
* *
78601911 GATAA-ATA
1 CATAACTTA
*
78601919 TATAACTTA
1 CATAACTTA
78601928 CATAACTTA
1 CATAACTTA
78601937 CATAA
1 CATAA
78601942 TACTTAAATA
Statistics
Matches: 90, Mismatches: 21, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
8 6 0.07
9 84 0.93
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.36
Consensus pattern (9 bp):
CATAACTTA
Found at i:78601843 original size:18 final size:18
Alignment explanation
Indices: 78601821--78601941 Score: 145
Period size: 18 Copynumber: 6.8 Consensus size: 18
78601811 TATTTGATAT
* *
78601821 CATAATTTACATAACTTA
1 CATAACTTATATAACTTA
* *
78601839 TATAACATATATAACTTA
1 CATAACTTATATAACTTA
*
78601857 CATAACTTATATAACATA
1 CATAACTTATATAACTTA
* *
78601875 CATAACTTATATAGCATA
1 CATAACTTATATAACTTA
78601893 CATAACTTATATAACTTA
1 CATAACTTATATAACTTA
* *
78601911 GATAA-ATATATAACTTA
1 CATAACTTATATAACTTA
*
78601928 CATAACTTACATAA
1 CATAACTTATATAA
78601942 TACTTAAATA
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
17 15 0.17
18 72 0.83
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.36
Consensus pattern (18 bp):
CATAACTTATATAACTTA
Found at i:78601852 original size:27 final size:27
Alignment explanation
Indices: 78601817--78601941 Score: 135
Period size: 27 Copynumber: 4.6 Consensus size: 27
78601807 AATATATTTG
* *
78601817 ATATCATAATTTACATAACTTATATAAC
1 ATAT-ATAACTTACATAACATATATAAC
*
78601845 ATATATAACTTACATAACTTATATAAC
1 ATATATAACTTACATAACATATATAAC
* * * *
78601872 ATACATAACTTATATAGCATACATAAC
1 ATATATAACTTACATAACATATATAAC
* *
78601899 TTATATAACTTAGATAA-ATATATAAC
1 ATATATAACTTACATAACATATATAAC
* *
78601925 TTACATAACTTACATAA
1 ATATATAACTTACATAA
78601942 TACTTAAATA
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 23 0.27
27 57 0.68
28 4 0.05
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (27 bp):
ATATATAACTTACATAACATATATAAC
Found at i:78603819 original size:12 final size:12
Alignment explanation
Indices: 78603802--78603827 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
78603792 AAGATCGAGG
78603802 GATGAATCTGAT
1 GATGAATCTGAT
78603814 GATGAATCTGAT
1 GATGAATCTGAT
78603826 GA
1 GA
78603828 AGATGATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:78606291 original size:40 final size:40
Alignment explanation
Indices: 78606246--78606412 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
78606236 CGGAATATAA
78606246 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
78606286 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
78606326 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
78606366 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
78606405 CCGGATAT
1 CCGGATAT
78606413 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:78614250 original size:40 final size:40
Alignment explanation
Indices: 78614205--78614371 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
78614195 CGGAATATAA
78614205 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
78614245 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
78614285 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
78614325 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
78614364 CCGGATAT
1 CCGGATAT
78614372 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:78618052 original size:19 final size:20
Alignment explanation
Indices: 78618018--78618055 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
78618008 AGTCCTTACA
78618018 CTAAATTAACCTTAATTAAG
1 CTAAATTAACCTTAATTAAG
*
78618038 CTAAATTTA-CTTAATTAA
1 CTAAATTAACCTTAATTAA
78618056 AATCTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
CTAAATTAACCTTAATTAAG
Found at i:78619650 original size:140 final size:140
Alignment explanation
Indices: 78619398--78619654 Score: 394
Period size: 140 Copynumber: 1.8 Consensus size: 140
78619388 ATTGTTGGCT
* * *
78619398 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTTTGG
1 AGTGTAAGACATGTCTGAGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGG
*
78619463 GACATGGCATCGGCATTGAGACGAGAGCCAGTGTAAGACATGTCTGGGACATTCATCAGCCTCGA
66 GACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACATGTCTGGGACATTCATCAGCCTCGA
78619528 AACGTAAGTC
131 AACGTAAGTC
* * *
78619538 AGTGTAAGACATGTCTGAGACATGCATCGGCTACGA-GATGATAGCTAGTGTAAGACCATGTCTG
1 AGTGTAAGACATGTCTGAGACATGCATCGGCCAC-ATGATGAGAGCCAGTGTAAGACCATGTCTG
*
78619602 GGACATGGCATCGAC-TTGAGA-TATGAGCCAGTGTAAGACCATGTCTGGGACAT
65 GGACATGGCATCGACATTGAGACGA-GAGCCAGTGTAAGA-CATGTCTGGGACAT
78619655 GGCATTGGCA
Statistics
Matches: 106, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
138 1 0.01
139 20 0.19
140 84 0.79
141 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (140 bp):
AGTGTAAGACATGTCTGAGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACATGTCTGGGACATTCATCAGCCTCGA
AACGTAAGTC
Found at i:78619659 original size:47 final size:45
Alignment explanation
Indices: 78619398--78619655 Score: 236
Period size: 47 Copynumber: 5.5 Consensus size: 45
78619388 ATTGTTGGCT
*
78619398 AGTGTAAGACATGTCTGGGACATGCATCGGC-C-ACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTCGAGA-TAT--GAGCC
* * *
78619444 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGACGA-GAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TCGAGA-TATGAGCC
* * * ** * *
78619492 AGTGTAAGACATGTCTGGGACATTCATCAGCCTCGAAACGTAAGTC
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCTCGAGATATGAGCC
* *
78619538 AGTGTAAGACATGTCTGAGACATGCATCGGCTACGAGATGAT-AGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCT-CGAGAT-ATGAGCC
* *
78619584 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATATGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTCGAGATATGAGCC
78619631 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
78619656 GCATTGGCAC
Statistics
Matches: 174, Mismatches: 26, Indels: 24
0.78 0.12 0.11
Matches are distributed among these distances:
45 3 0.02
46 64 0.37
47 74 0.43
48 30 0.17
51 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTCGAGATATGAGCC
Found at i:78621528 original size:43 final size:43
Alignment explanation
Indices: 78621372--78621530 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 43
78621362 CAATACCATA
* ** * *
78621372 TCCCAGATATGGTCTTACATGTTATCACAT-ATCGATGCCGATAG
1 TCCCAGACATGGTCTTACACATAATCACATGAT-GATGCCAAT-G
* * * * * *
78621416 -CCCAG-CTATGTTCTTACACGA-AATCAAATAACGATGTCAATT
1 TCCCAGAC-ATGGTCTTACAC-ATAATCACATGATGATGCCAATG
78621458 TCCCAGACATGGTCTTACACATAATCACATGATGATGCCAATG
1 TCCCAGACATGGTCTTACACATAATCACATGATGATGCCAATG
*
78621501 TCCCCGACATGGTCTTACACATAATCACAT
1 TCCCAGACATGGTCTTACACATAATCACAT
78621531 CTCGTTAATC
Statistics
Matches: 92, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
42 1 0.01
43 89 0.97
44 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.28
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACATAATCACATGATGATGCCAATG
Found at i:78622199 original size:31 final size:31
Alignment explanation
Indices: 78622164--78622225 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
78622154 ATTCATCAGT
78622164 GGCACTTTACAAAATCATTAAAAACTTCAAA
1 GGCACTTTACAAAATCATTAAAAACTTCAAA
78622195 GGCACTTTACAAAATCATTAAAAACTTCAAA
1 GGCACTTTACAAAATCATTAAAAACTTCAAA
78622226 AACTAAGGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (31 bp):
GGCACTTTACAAAATCATTAAAAACTTCAAA
Found at i:78624363 original size:48 final size:48
Alignment explanation
Indices: 78624230--78624363 Score: 162
Period size: 48 Copynumber: 2.8 Consensus size: 48
78624220 ATGTGAGAGC
* * * *
78624230 TCTTTTCAAAGAATATGTGAACTGTCACTGTAATGTATGTGTGAATTA
1 TCTTTTCAAAGAATATGCGAACTGTCAATGTAATGTATATGTGAACTA
*
78624278 TCTTTTCAAA-AAGTATGCGAACTATCAATGTAATGTATATGTGAACTA
1 TCTTTTCAAAGAA-TATGCGAACTGTCAATGTAATGTATATGTGAACTA
* * * * *
78624326 TCTTTTCAAAGGATATGCAAATTGTCATTGTATTGTAT
1 TCTTTTCAAAGAATATGCGAACTGTCAATGTAATGTAT
78624364 GCATGAATTG
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
47 2 0.03
48 70 0.96
49 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (48 bp):
TCTTTTCAAAGAATATGCGAACTGTCAATGTAATGTATATGTGAACTA
Found at i:78624406 original size:96 final size:96
Alignment explanation
Indices: 78624230--78624413 Score: 208
Period size: 96 Copynumber: 1.9 Consensus size: 96
78624220 ATGTGAGAGC
** ** * *
78624230 TCTTTTCAAAGAATATGTGAACTGTCACTGTAATGTATGTGTGAATTATCTTTTCAAAAAGTATG
1 TCTTTTCAAAGAATATGCAAACTGTCACTGTAATGTATGCATGAATTATCGTTGCAAAAAGTATG
*
78624295 CGAACTATCAATGTAATGTATATGTGAACTA
66 CGAACTATCAATGTAAAGTATATGTGAACTA
* * * * *
78624326 TCTTTTCAAAGGATATGCAAATTGTCATTGTATTGTATGCATGAATTGTCGTTGCACAAAA-TAT
1 TCTTTTCAAAGAATATGCAAACTGTCACTGTAATGTATGCATGAATTATCGTTGCA-AAAAGTAT
* * * *
78624390 GTGAACTGTTATTGTAAAGTATAT
65 GCGAACTATCAATGTAAAGTATAT
78624414 TAAACCGACC
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
96 67 0.94
97 4 0.06
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (96 bp):
TCTTTTCAAAGAATATGCAAACTGTCACTGTAATGTATGCATGAATTATCGTTGCAAAAAGTATG
CGAACTATCAATGTAAAGTATATGTGAACTA
Found at i:78635653 original size:15 final size:14
Alignment explanation
Indices: 78635628--78635685 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
78635618 AGAGTTCAAG
*
78635628 ATAAGGAAATCCATA
1 ATAAAGAAATCCA-A
*
78635643 ATGAAGAAATCCAGA
1 ATAAAGAAATCCA-A
* *
78635658 TTATAGAAATCCAA
1 ATAAAGAAATCCAA
78635672 CATAAAGAAATCCA
1 -ATAAAGAAATCCA
78635686 GAAGAAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 1 0.03
15 33 0.97
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (14 bp):
ATAAAGAAATCCAA
Found at i:78636780 original size:12 final size:12
Alignment explanation
Indices: 78636763--78636803 Score: 73
Period size: 12 Copynumber: 3.3 Consensus size: 12
78636753 GCTATTGTAA
78636763 ACCTTTATTCAT
1 ACCTTTATTCAT
78636775 ACCTTTATTCAT
1 ACCTTTATTCAT
78636787 ACCTTTATTCAT
1 ACCTTTATTCAT
78636799 CACCT
1 -ACCT
78636804 AGTTTTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 24 0.86
13 4 0.14
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.46
Consensus pattern (12 bp):
ACCTTTATTCAT
Found at i:78638307 original size:46 final size:46
Alignment explanation
Indices: 78638238--78638338 Score: 148
Period size: 46 Copynumber: 2.2 Consensus size: 46
78638228 GAAAAAAGTT
* *
78638238 ATTGTGAATGTGGTTGTTCAAATTGGAATTGAGTATATGTGTTTGA
1 ATTGTGAATGTGGTTGTTCAAATTAGAATTGAGCATATGTGTTTGA
* * * *
78638284 CTTGTGAATGTGGTTGTTGAAATTAGAATTGGGCCTATGTGTTTGA
1 ATTGTGAATGTGGTTGTTCAAATTAGAATTGAGCATATGTGTTTGA
78638330 ATTGTGAAT
1 ATTGTGAAT
78638339 TAGATTGGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.25, C:0.04, G:0.29, T:0.43
Consensus pattern (46 bp):
ATTGTGAATGTGGTTGTTCAAATTAGAATTGAGCATATGTGTTTGA
Found at i:78639375 original size:28 final size:29
Alignment explanation
Indices: 78639344--78639398 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
78639334 GATTTTGAGT
*
78639344 AAAAATGCATATT-AGGGATTAAATTGAC
1 AAAAATGCAAATTGAGGGATTAAATTGAC
* * *
78639372 AAAAGTGTAAATTGAGGGGTTAAATTG
1 AAAAATGCAAATTGAGGGATTAAATTG
78639399 TGAAATAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 10 0.45
29 12 0.55
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.29
Consensus pattern (29 bp):
AAAAATGCAAATTGAGGGATTAAATTGAC
Found at i:78639949 original size:43 final size:43
Alignment explanation
Indices: 78639896--78640035 Score: 149
Period size: 43 Copynumber: 3.3 Consensus size: 43
78639886 TGTGATTACA
* *
78639896 TGTAATACCATGTCTGGGACATTGGCATTG-TATTTTGAATACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGTTA-TTTGAATACG
* * *
78639939 TGTAAGACCATGTCTAGGACATTGGCATCGTTATTTGATTTCG
1 TGTAAGACCATGTCTGGGACATTGGCATCGTTATTTGAATACG
* * * * * *
78639982 TGTAAGACCCTGTCTGGGACAGTGGCGTCGATATGTG-ATAACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGTTATTTGAAT-ACG
78640025 TGTAAGACCAT
1 TGTAAGACCAT
78640036 ATTTGGGATA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
42 1 0.01
43 77 0.96
44 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGTTATTTGAATACG
Found at i:78641963 original size:24 final size:24
Alignment explanation
Indices: 78641912--78642079 Score: 248
Period size: 24 Copynumber: 7.0 Consensus size: 24
78641902 GCTTTATCAT
*
78641912 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
78641937 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
78641961 ATAACTGGGGTATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
78641985 CTAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
78642009 GTAACTGGGGCATAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
*
78642033 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
78642057 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
78642080 GCACTTCCTC
Statistics
Matches: 132, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
24 120 0.91
25 12 0.09
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:78642154 original size:20 final size:20
Alignment explanation
Indices: 78642129--78642195 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
78642119 TTATGAATAC
78642129 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
78642149 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
78642169 GTCATGTGTATATCATACAT
1 ATCATGTGCATATCATACAT
*
78642189 ACCATGT
1 ATCATGT
78642196 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:78649708 original size:9 final size:9
Alignment explanation
Indices: 78649694--78649731 Score: 69
Period size: 9 Copynumber: 4.3 Consensus size: 9
78649684 AATAATCCCG
78649694 AAAAGAAGT
1 AAAAGAAGT
78649703 AAAAGAAGT
1 AAAAGAAGT
78649712 AAAAGAAGT
1 AAAAGAAGT
78649721 AAAAGAA-T
1 AAAAGAAGT
78649729 AAA
1 AAA
78649732 TAATAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 4 0.14
9 25 0.86
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (9 bp):
AAAAGAAGT
Found at i:78650259 original size:24 final size:24
Alignment explanation
Indices: 78650208--78650373 Score: 248
Period size: 24 Copynumber: 7.0 Consensus size: 24
78650198 GCTTTATAAT
*
78650208 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
78650233 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
78650257 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
78650281 GTAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
78650304 ATAACT-GGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
78650327 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
78650351 ATAACTGGGGCATAAGCTCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
78650374 GCACTTCCTC
Statistics
Matches: 134, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
22 16 0.12
23 11 0.08
24 95 0.71
25 12 0.09
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:78650318 original size:70 final size:72
Alignment explanation
Indices: 78650208--78650373 Score: 250
Period size: 70 Copynumber: 2.3 Consensus size: 72
78650198 GCTTTATAAT
*
78650208 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAA
78650272 GCCCTTTT-
64 GCCCTTTTG
*
78650280 AGTAACTGGGGCATAAGCCCTTTT-ATAACT-GGGCATAAGCCCTTTTGATAACTGGGGCATAAG
1 A-TAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAG
78650343 CCCTTTTG
65 CCCTTTTG
*
78650351 ATAACTGGGGCATAAGCTCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
78650374 GCACTTCCTC
Statistics
Matches: 88, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
70 60 0.68
71 7 0.08
72 10 0.11
73 11 0.12
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (72 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGC
CCTTTTG
Found at i:78650448 original size:20 final size:20
Alignment explanation
Indices: 78650423--78650489 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
78650413 TTATGAATAC
78650423 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
78650443 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
78650463 GTCATGTGTATATCATACAT
1 ATCATGTGCATATCATACAT
*
78650483 ACCATGT
1 ATCATGT
78650490 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:78650558 original size:25 final size:25
Alignment explanation
Indices: 78650526--78650573 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
78650516 ATATATAAAC
* * *
78650526 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
78650551 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
78650574 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:78653813 original size:35 final size:35
Alignment explanation
Indices: 78653774--78653874 Score: 121
Period size: 35 Copynumber: 2.9 Consensus size: 35
78653764 GATATGGCTG
*
78653774 AATATACAAATTCAATATAACCTCACATGTAATCA
1 AATATACAAATTCAATATAACCTCACATGTAACCA
* * * * * *
78653809 AATATACAAGTTCAATATAACTTCACAAGCAGCCG
1 AATATACAAATTCAATATAACCTCACATGTAACCA
* *
78653844 AATATACAAACTCAATATGACCTCACATGTA
1 AATATACAAATTCAATATAACCTCACATGTA
78653875 CATACTTATG
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.26
Consensus pattern (35 bp):
AATATACAAATTCAATATAACCTCACATGTAACCA
Found at i:78657326 original size:40 final size:40
Alignment explanation
Indices: 78657254--78657433 Score: 166
Period size: 40 Copynumber: 4.5 Consensus size: 40
78657244 GCTCGATTGT
* * * * *
78657254 CTTCGGGACATAGCACAG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGACTTAGCCCAGATT-TAGTAACTCGCACAAATGC
* * *
78657294 CTTCGGGAATTAGCCCAGATTTAATAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCAGATTTAGTAACTCGCACAAATGC
* * * *
78657334 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCAGATTTAGTAACTCGCACAAATGC
* * * * *
78657374 CTTCGGGAGTT-GACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAG-CCCAGATTTAGTAAC-TCGCACAAATGC
78657415 CTTCGGGACTTAGCCCAGA
1 CTTCGGGACTTAGCCCAGA
78657434 CACCATTCGA
Statistics
Matches: 112, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
40 84 0.75
41 27 0.24
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCAGATTTAGTAACTCGCACAAATGC
Found at i:78659898 original size:16 final size:16
Alignment explanation
Indices: 78659859--78659892 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
78659849 GAAAACATCT
*
78659859 CAAAAGAATAAAGATAA
1 CAAAA-AATAAAGAAAA
78659876 CAAAAAATAAAGAAAA
1 CAAAAAATAAAGAAAA
78659892 C
1 C
78659893 CCAAAACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.74, C:0.09, G:0.09, T:0.09
Consensus pattern (16 bp):
CAAAAAATAAAGAAAA
Found at i:78662197 original size:6 final size:6
Alignment explanation
Indices: 78662180--78662221 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
78662170 TTCAACATAT
* *
78662180 AAATAA AGATAA AAAT-A AAGTAA AAATAAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAAT-AA AAATAA AAATAA
78662222 TAGGTGTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 4 0.13
6 20 0.67
7 6 0.20
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:78662205 original size:11 final size:12
Alignment explanation
Indices: 78662180--78662221 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
78662170 TTCAACATAT
78662180 AAATAAAGATAA
1 AAATAAAGATAA
78662192 AAATAAAG-TAA
1 AAATAAAGATAA
*
78662203 AAATAAAAAATAA
1 AAAT-AAAGATAA
78662216 AAATAA
1 AAATAA
78662222 TAGGTGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 7 0.26
12 13 0.48
13 7 0.26
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (12 bp):
AAATAAAGATAA
Found at i:78666637 original size:29 final size:29
Alignment explanation
Indices: 78666605--78666765 Score: 171
Period size: 29 Copynumber: 5.6 Consensus size: 29
78666595 AATTTAAGCC
* *** *
78666605 CGCACACATAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCT
** * *
78666634 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCT
* * * *
78666663 TGCACACATAGTGTCATATTTTTCCAGCAT
1 CGCACACTTAGTGCCATATATTTCCAGC-T
*
78666693 -GCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCT
*
78666721 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCT
78666750 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
78666766 ATCTCGTCAC
Statistics
Matches: 114, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
29 113 0.99
30 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCT
Found at i:78678765 original size:12 final size:12
Alignment explanation
Indices: 78678748--78678780 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
78678738 GGTGCACAGA
78678748 GAGAAGCTTGGG
1 GAGAAGCTTGGG
78678760 GAGAAGCTTGGG
1 GAGAAGCTTGGG
*
78678772 GAAAAGCTT
1 GAGAAGCTT
78678781 TTGGGAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.42, T:0.18
Consensus pattern (12 bp):
GAGAAGCTTGGG
Found at i:78688920 original size:26 final size:26
Alignment explanation
Indices: 78688883--78688948 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
78688873 AGACCTCTTA
*
78688883 AATTTTAAAATTTTATTAAATTATT-T
1 AATTTTTAAATTTTATT-AATTATTAT
*
78688909 AATTTTTCAA-TTTATTAATTATTAGT
1 AATTTTTAAATTTTATTAATTATTA-T
78688935 AATTTTTAAATTTT
1 AATTTTTAAATTTT
78688949 TGAGAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 7 0.21
25 6 0.18
26 18 0.53
27 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
AATTTTTAAATTTTATTAATTATTAT
Found at i:78695522 original size:6 final size:6
Alignment explanation
Indices: 78695492--78695593 Score: 75
Period size: 6 Copynumber: 16.7 Consensus size: 6
78695482 AAGAAACATT
* * *
78695492 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * *
78695541 ATCAGA ATCAAA ATCAGA ATCAGA ATTAG- GTGACAGA ATCAGA ATCAGT
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA
78695590 ATCA
1 ATCA
78695594 AGTAAGTTAA
Statistics
Matches: 75, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
5 3 0.04
6 64 0.85
7 6 0.08
8 2 0.03
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:78695556 original size:37 final size:37
Alignment explanation
Indices: 78695501--78695587 Score: 138
Period size: 37 Copynumber: 2.4 Consensus size: 37
78695491 TATCAGAACT
* * *
78695501 AGAATCAAAATGAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAAAATCAGAATCAGAATCAGGTGAC
*
78695538 AGAATCAGAATCAAAATCAGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAAAATCAGAATCAGAATCAGGTGAC
78695575 AGAATCAGAATCA
1 AGAATCAGAATCA
78695588 GTATCAAGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.17
Consensus pattern (37 bp):
AGAATCAGAATCAAAATCAGAATCAGAATCAGGTGAC
Found at i:78695774 original size:27 final size:26
Alignment explanation
Indices: 78695734--78695841 Score: 101
Period size: 27 Copynumber: 4.0 Consensus size: 26
78695724 AGCATGGCTG
*
78695734 CCAGAACAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGACAGAGCCA
* *
78695760 CCAGATACATATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGACAGAGCCA
* *
78695787 CCAGAATAGATATTTGTCG-CATAGCCA
1 CCAGAACAGATA-TTGT-GACAGAGCCA
* * *
78695814 CCAGAAACAGATAATGTGGCAAAGCCA
1 CCAG-AACAGATATTGTGACAGAGCCA
78695841 C
1 C
78695842 TTAATAGAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
26 11 0.16
27 49 0.72
28 8 0.12
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.19
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGAGCCA
Found at i:78697495 original size:36 final size:37
Alignment explanation
Indices: 78697447--78697518 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 37
78697437 TACGAAGTCT
78697447 TACCCAGACATAATCTCCACACGTAGTCATCGGGTCG
1 TACCCAGACATAATCTCCACACGTAGTCATCGGGTCG
78697484 TACCC-GACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCAGACATAATCTCCACACGTAGTCATCGGGTC
78697519 TCACCCGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 30 0.86
37 5 0.14
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.22
Consensus pattern (37 bp):
TACCCAGACATAATCTCCACACGTAGTCATCGGGTCG
Found at i:78697670 original size:49 final size:49
Alignment explanation
Indices: 78697603--78697899 Score: 533
Period size: 49 Copynumber: 6.1 Consensus size: 49
78697593 TACCACATAT
78697603 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
* *
78697652 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
78697701 ATATATATACA-TTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
78697749 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
* *
78697798 ATATGTATACACTTTCACATTCATCACGTCGGCCATTAGGACTTATCAC
1 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
* *
78697847 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
78697896 ATAT
1 ATAT
78697900 TATTATGTAC
Statistics
Matches: 238, Mismatches: 9, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
48 47 0.20
49 191 0.80
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.34
Consensus pattern (49 bp):
ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
Done.