Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 77 of 290
Found at i:23341064 original size:15 final size:15
Alignment explanation
Indices: 23340996--23341064 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
23340986 AACAAATAAT
23340996 AAGAAA-CC-GAATA
1 AAGAAATCCAGAATA
23341009 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
23341024 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
23341039 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
*
23341054 AAGAGATCCAG
1 AAGAAATCCAG
23341065 GAAAAAAACC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
13 6 0.13
14 3 0.06
15 37 0.79
16 1 0.02
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:23344128 original size:46 final size:44
Alignment explanation
Indices: 23343979--23344152 Score: 183
Period size: 46 Copynumber: 3.9 Consensus size: 44
23343969 TGTAACCCGC
* *
23343979 CCATAAGTGAACTCGGACTCAACTCAA-GAGCTAGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATTCGCAT
*
23344023 CCATAAGTGAACTC-GACTCAACTCAACGAGCTCGGATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATTCGC-A--T
* *** *
23344068 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG--ATTCGCAT
*
23344115 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGAT
23344153 GCCCAAACAT
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 1 0.01
43 15 0.14
44 23 0.21
45 5 0.05
46 34 0.31
47 25 0.23
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (44 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATTCGCAT
Found at i:23344152 original size:93 final size:90
Alignment explanation
Indices: 23343987--23344155 Score: 266
Period size: 93 Copynumber: 1.8 Consensus size: 90
23343977 GCCCATAAGT
**
23343987 GAACTCGGACTCAACTCAAGAGCTAGGTGTTCGCATCCATAAGTGAACTCGACTCAACTCAACGA
1 GAACTCGGACTCAACTCAAGAGCTAGGCATTCGCATCCATAAGTGAACTCGACTCAACTCAACGA
23344052 GCTCGGATGCCTAGTTACATCTCTC
66 GCTCGGATGCCTAGTTACATCTCTC
* *
23344077 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAA-GAGCTAGG-CATTCGCATCCATAAGTGAACTC-GACTCAACTCAA
*
23344142 CGAGTTCGGATGCC
63 CGAGCTCGGATGCC
23344156 CAAACATCCT
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
90 19 0.27
91 6 0.08
92 21 0.30
93 25 0.35
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (90 bp):
GAACTCGGACTCAACTCAAGAGCTAGGCATTCGCATCCATAAGTGAACTCGACTCAACTCAACGA
GCTCGGATGCCTAGTTACATCTCTC
Found at i:23344170 original size:46 final size:46
Alignment explanation
Indices: 23344028--23344170 Score: 134
Period size: 46 Copynumber: 3.1 Consensus size: 46
23344018 CGCATCCATA
* *
23344028 AGTGAACTC-GACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATC-CT
* * * * *
23344076 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCCT
*
23344120 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
23344166 AGTGA
1 AGTGA
23344171 CATGTCACTT
Statistics
Matches: 75, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
44 8 0.11
46 39 0.52
47 24 0.32
49 4 0.05
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
Found at i:23345619 original size:6 final size:6
Alignment explanation
Indices: 23345601--23345682 Score: 62
Period size: 6 Copynumber: 13.3 Consensus size: 6
23345591 AAGAAACATT
* *
23345601 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAG- GTGACAGA ATCAGA ATCAAA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA
* *
23345650 ATCAGT ATCAGGTA AT-AGA ATCAAA ATCAGA AT
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
23345683 ATGAATGCAA
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
5 5 0.08
6 46 0.77
7 6 0.10
8 3 0.05
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:23345638 original size:31 final size:31
Alignment explanation
Indices: 23345610--23345678 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
23345600 TATCAGAACT
*
23345610 AGAATCAGAATCAGAATCAGGTGACAGAATC
1 AGAATCAAAATCAGAATCAGGTGACAGAATC
* * *
23345641 AGAATCAAAATCAGTATCAGGTAATAGAATC
1 AGAATCAAAATCAGAATCAGGTGACAGAATC
*
23345672 AAAATCA
1 AGAATCA
23345679 GAATATGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.19
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGGTGACAGAATC
Found at i:23346166 original size:27 final size:27
Alignment explanation
Indices: 23346136--23346448 Score: 385
Period size: 27 Copynumber: 11.6 Consensus size: 27
23346126 AACACCCTAG
** * *
23346136 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
23346163 GGGTAAAA-TGATAATTCTGTAAATCGA
1 GGGTAAAACAG-TAATTCTGTAAATCGA
* *
23346190 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
23346217 GGGTAAAATAGTAATTCTGTCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
23346244 GGGTAAAATAGTAATTCTGTCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
23346271 GGGTAAAACAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
23346298 GGGTAAAACAGTAATTCTGTAAATCAA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
23346325 GGGTAAAACAATAATTCTATAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
23346352 GGGTACAACGGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * * * *
23346379 GGGTAAAACTGAAATTTTATAAATCAA
1 GGGTAAAACAGTAATTCTGTAAATCGA
23346406 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
23346433 TGGTAGAACAGTAATT
1 GGGTAAAACAGTAATT
23346449 TTTTTAATTC
Statistics
Matches: 252, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
26 1 0.00
27 250 0.99
28 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (27 bp):
GGGTAAAACAGTAATTCTGTAAATCGA
Found at i:23346487 original size:27 final size:25
Alignment explanation
Indices: 23346450--23346534 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 25
23346440 ACAGTAATTT
*
23346450 TTTTAATTCGAGGGTACTTTGA-TAA
1 TTTTAATTCGAGGGTA-TTTCAGTAA
23346475 TTTTACATGTCGAGGGTATTTCAGTAA
1 TTTTA-AT-TCGAGGGTATTTCAGTAA
* *
23346502 TTTTGCAA-ACTGAGGGTATTTCGGTAA
1 TTTT--AATTC-GAGGGTATTTCAGTAA
23346529 TTTTAA
1 TTTTAA
23346535 AAATTGAGGA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
25 7 0.14
26 7 0.14
27 35 0.69
28 1 0.02
29 1 0.02
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.42
Consensus pattern (25 bp):
TTTTAATTCGAGGGTATTTCAGTAA
Found at i:23346531 original size:54 final size:53
Alignment explanation
Indices: 23346459--23346611 Score: 155
Period size: 54 Copynumber: 2.8 Consensus size: 53
23346449 TTTTTAATTC
* ** *
23346459 GAGGGTACTTTGATAATTTTACATGTCGAGGGTATTTCAGTAATTTTGCAAACT
1 GAGGGTACTTTGGTAATTTTACAAAT-GAGGGTATTTCAGTAATTTTACAAACT
* * ** * *
23346513 GAGGGTA-TTTCGGTAATTTTAAAAATTGAGGATATTTGGGTAATTTTATAAATT
1 GAGGGTACTTT-GGTAATTTTACAAA-TGAGGGTATTTCAGTAATTTTACAAACT
* * *
23346567 GGGGGTACTTTGGTAATTTTACAACTGGGGGTATTTCAGTAATTT
1 GAGGGTACTTTGGTAATTTTACAAATGAGGGTATTTCAGTAATTT
23346612 GGTAAACTAA
Statistics
Matches: 79, Mismatches: 17, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
53 19 0.24
54 56 0.71
55 4 0.05
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (53 bp):
GAGGGTACTTTGGTAATTTTACAAATGAGGGTATTTCAGTAATTTTACAAACT
Found at i:23346619 original size:27 final size:27
Alignment explanation
Indices: 23346486--23346611 Score: 121
Period size: 27 Copynumber: 4.7 Consensus size: 27
23346476 TTTACATGTC
* **
23346486 GAGGGTATTTCAGTAATTTTGCAAACT
1 GAGGGTATTTCGGTAATTTTATAAACT
* *
23346513 GAGGGTATTTCGGTAATTTTAAAAATT
1 GAGGGTATTTCGGTAATTTTATAAACT
* * *
23346540 GAGGATATTTGGGTAATTTTATAAATT
1 GAGGGTATTTCGGTAATTTTATAAACT
* *
23346567 GGGGGTACTTT-GGTAATTTTA-CAACT
1 GAGGGTA-TTTCGGTAATTTTATAAACT
* *
23346593 GGGGGTATTTCAGTAATTT
1 GAGGGTATTTCGGTAATTT
23346612 GGTAAACTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
25 3 0.04
26 17 0.20
27 62 0.73
28 3 0.04
ACGTcount: A:0.29, C:0.06, G:0.25, T:0.40
Consensus pattern (27 bp):
GAGGGTATTTCGGTAATTTTATAAACT
Found at i:23359694 original size:46 final size:46
Alignment explanation
Indices: 23359605--23359724 Score: 170
Period size: 46 Copynumber: 2.6 Consensus size: 46
23359595 TCTGAACCCG
* *
23359605 TTGAGTTGCGTTCCGAGTTTACTTATGGATGCAAGCATCCGAGCTCA
1 TTGAGTTGCGTTCCGAGTTCA-TTATGGATGCAAGCACCCGAGCTCA
* * *
23359652 TTGAGTTGTGTTCCGAGTTCATTATGGATGTGAA-CACCCGAGCTCG
1 TTGAGTTGCGTTCCGAGTTCATTATGGATG-CAAGCACCCGAGCTCA
23359698 TTGAGTTGCGTTCCGAGTTCATTATGG
1 TTGAGTTGCGTTCCGAGTTCATTATGG
23359725 GTGAAATTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
46 45 0.68
47 21 0.32
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (46 bp):
TTGAGTTGCGTTCCGAGTTCATTATGGATGCAAGCACCCGAGCTCA
Found at i:23380233 original size:32 final size:32
Alignment explanation
Indices: 23380166--23380233 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
23380156 CTGTAAACCA
*
23380166 ACACGCCCAAATTGGCCTTGCCCATGTGACTC
1 ACACGCCCAAATTGGCCTTGCCCATGTGACCC
* * ** *
23380198 ACACGCCTAGATTGGCCTTGCCTGTGTGGCCC
1 ACACGCCCAAATTGGCCTTGCCCATGTGACCC
23380230 ACAC
1 ACAC
23380234 AACATGGCCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.19, C:0.37, G:0.22, T:0.22
Consensus pattern (32 bp):
ACACGCCCAAATTGGCCTTGCCCATGTGACCC
Found at i:23386135 original size:46 final size:44
Alignment explanation
Indices: 23386082--23386194 Score: 138
Period size: 46 Copynumber: 2.5 Consensus size: 44
23386072 TGAGAACTAT
23386082 TGTAAGACATGTCTGGGACATGCATTAGCCT-CGAGATGTAAGCCAG
1 TGTAAGACATGTCTGGGACATGCA-TAGCCTACGAGATGT--GCCAG
* * * * *
23386128 TGTAAGACATGTCAGGGACATACATCGGCTACGAGATGTGTCAG
1 TGTAAGACATGTCTGGGACATGCATAGCCTACGAGATGTGCCAG
23386172 TGTAAGACCATGTCTGGGACATG
1 TGTAAGA-CATGTCTGGGACATG
23386195 GCATCGGCAC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
44 11 0.19
45 17 0.29
46 30 0.52
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (44 bp):
TGTAAGACATGTCTGGGACATGCATAGCCTACGAGATGTGCCAG
Found at i:23386226 original size:48 final size:48
Alignment explanation
Indices: 23386125--23386349 Score: 218
Period size: 49 Copynumber: 4.7 Consensus size: 48
23386115 AGATGTAAGC
* * *
23386125 CAGTGTAAGA-CATGTCAGGGACAT-ACATCGGCTACG---AGATGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGTATAGAGGTGT
23386169 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGT
* *
23386217 CAGTTTAAGACCATGTCTGGGACATGGCATCGGCACGGATATGTAGAG-GT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATA-G-AG-GTGT
* * * * *
23386267 -AGTGTAAGACCATGTCTGGGACAAGGCGTCAGCCTCGATTTCA-A--TAGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATC-GGCACG-TAT-AGAGGT-GT
23386315 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
23386350 TTATACCCTA
Statistics
Matches: 151, Mismatches: 16, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
44 10 0.07
45 16 0.11
46 7 0.05
48 50 0.33
49 57 0.38
50 8 0.05
51 2 0.01
52 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.23
Consensus pattern (48 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGT
Found at i:23386338 original size:98 final size:95
Alignment explanation
Indices: 23386032--23386349 Score: 282
Period size: 98 Copynumber: 3.4 Consensus size: 95
23386022 TATGAGAGCT
* * * * *
23386032 AGTGTAAGTCCATGTCTGGGACATGGCATCGACATTGAGATG-AGAACTATTGTAAGA-CATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CGAGATGTAG-AGTAGTGTAAGACCATGTC
* * * * *
23386095 TGGGAC-ATGCATTAGCCTCGAGAT-GTAAGCC
64 TGGGACAAGGCATCAGCCTCGATATAAT-AGTC
* *
23386126 AGTGTAAGA-CATGTCAGGGACAT-ACATCGGCTACGAGATGT---GTCAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGAGATGTAGAGT-AGTGTAAGACCATGTC
* * *
23386186 TGGGACATGGCATC-GGCACG-TATAGAGGT-GTC
64 TGGGACAAGGCATCAGCCTCGATATA-A--TAGTC
* *
23386218 AGTTTAAGACCATGTCTGGGACATGGCATCGGCACGGATATGTAGAGGTAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GAGATGTAGA-GTAGTGTAAGACCATGTC
* *
23386283 TGGGACAAGGCGTCAGCCTCGATTTCAATAGTC
64 TGGGACAAGGCATCAGCCTCGATAT-AATAGTC
23386316 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA
23386350 TTATACCCTA
Statistics
Matches: 179, Mismatches: 25, Indels: 36
0.75 0.10 0.15
Matches are distributed among these distances:
89 1 0.01
90 10 0.06
91 16 0.09
92 26 0.15
93 29 0.16
94 22 0.12
97 29 0.16
98 42 0.23
99 3 0.02
100 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (95 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGAGATGTAGAGTAGTGTAAGACCATGTCTG
GGACAAGGCATCAGCCTCGATATAATAGTC
Found at i:23387364 original size:28 final size:28
Alignment explanation
Indices: 23387312--23387365 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
23387302 CACGGGCTAA
* *
23387312 GACACGGGCGTGTCGAGGCCGTGTGAGG
1 GACACGGGCGTGTCCAGGCCATGTGAGG
23387340 GACACGGGCGTGTGCCA-GCCATGTGA
1 GACACGGGCGTGT-CCAGGCCATGTGA
23387366 AATCCCCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.17, C:0.24, G:0.44, T:0.15
Consensus pattern (28 bp):
GACACGGGCGTGTCCAGGCCATGTGAGG
Found at i:23390859 original size:43 final size:43
Alignment explanation
Indices: 23390798--23390962 Score: 124
Period size: 43 Copynumber: 3.8 Consensus size: 43
23390788 CAACGCGAAC
* *
23390798 GTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCC-ACT
1 GTCCCAGAAG-GGTCTTACACGTAATCACATATCGATGCCAACT
* * *
23390841 GTCCCAGATAGGGTCTTACACG-AA-CTCATATACGTTGCCGA-T
1 GTCCCAGA-AGGGTCTTACACGTAATCACATAT-CGATGCCAACT
** * * *
23390883 GTCCCAGACATAGTCTTACATGTAAATCATAAATCGATGCCAAC-
1 GTCCCAGA-AGGGTCTTACACGT-AATCACATATCGATGCCAACT
* * *
23390927 GTCTCAGACGTGGTCTTACACGCAATCACATATCGA
1 GTCCCAGAAG-GGTCTTACACGTAATCACATATCGA
23390963 AATCCTATGT
Statistics
Matches: 93, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
41 6 0.06
42 27 0.29
43 30 0.32
44 26 0.28
45 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
GTCCCAGAAGGGTCTTACACGTAATCACATATCGATGCCAACT
Found at i:23392063 original size:13 final size:13
Alignment explanation
Indices: 23392045--23392069 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23392035 ACAAACAATA
23392045 AAATTTTCACACG
1 AAATTTTCACACG
23392058 AAATTTTCACAC
1 AAATTTTCACAC
23392070 ATATCAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:23395562 original size:17 final size:17
Alignment explanation
Indices: 23395540--23395572 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23395530 CACTTGAACT
23395540 TAACAAATAATT-TCAAA
1 TAACAAA-AATTATCAAA
23395557 TAACAAAAATTATCAA
1 TAACAAAAATTATCAA
23395573 GTCAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (17 bp):
TAACAAAAATTATCAAA
Found at i:23402105 original size:12 final size:14
Alignment explanation
Indices: 23402080--23402108 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
23402070 ACTTCTATCC
23402080 TCTCTCATTCTTTT
1 TCTCTCATTCTTTT
23402094 TCTCTCATT-TTTT
1 TCTCTCATTCTTTT
23402107 TC
1 TC
23402109 ATTTCAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.66
Consensus pattern (14 bp):
TCTCTCATTCTTTT
Found at i:23408231 original size:47 final size:47
Alignment explanation
Indices: 23408162--23408255 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
23408152 TAGTGATCTC
23408162 TCCTACTCTATTTGTTGCGGCAACCATCTTTTTGGTTTAGCCCAAAT
1 TCCTACTCTATTTGTTGCGGCAACCATCTTTTTGGTTTAGCCCAAAT
23408209 TCCTACTCTATTTGTTGCGGCAACCATCTTTTTGGTTTAGCCCAAAT
1 TCCTACTCTATTTGTTGCGGCAACCATCTTTTTGGTTTAGCCCAAAT
23408256 ATTCTAAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (47 bp):
TCCTACTCTATTTGTTGCGGCAACCATCTTTTTGGTTTAGCCCAAAT
Found at i:23409052 original size:43 final size:43
Alignment explanation
Indices: 23409000--23409083 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 43
23408990 TTGTAGAAAG
*
23409000 GAAACAAATCAATTGAAACAAAATCT-CAATCGAGAAACCTAGA
1 GAAACAAATCAAGTGAAACAAAAT-TACAATCGAGAAACCTAGA
* * * * *
23409043 GAAAGAAATCTAGTGAAATAAAATTACAATTGGGAAACCTA
1 GAAACAAATCAAGTGAAACAAAATTACAATCGAGAAACCTA
23409084 TTAGAAAATC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.03
43 33 0.97
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.19
Consensus pattern (43 bp):
GAAACAAATCAAGTGAAACAAAATTACAATCGAGAAACCTAGA
Found at i:23409159 original size:36 final size:36
Alignment explanation
Indices: 23409119--23409193 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
23409109 TCCTGAAGAA
23409119 AGAAAGAAATCACCATTGCCTTCTCCTGTTTCCACT
1 AGAAAGAAATCACCATTGCCTTCTCCTGTTTCCACT
23409155 AGAAAGAAATCACCATTGCCTTCTCCTGTTTCCACT
1 AGAAAGAAATCACCATTGCCTTCTCCTGTTTCCACT
23409191 AGA
1 AGA
23409194 TCAGCTGTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (36 bp):
AGAAAGAAATCACCATTGCCTTCTCCTGTTTCCACT
Found at i:23411517 original size:17 final size:15
Alignment explanation
Indices: 23411480--23411510 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
23411470 GTGTAGCATG
23411480 GTTTAATGAAATAGA
1 GTTTAATGAAATAGA
23411495 GTTTAATGAAATAGA
1 GTTTAATGAAATAGA
23411510 G
1 G
23411511 CGTTTAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (15 bp):
GTTTAATGAAATAGA
Found at i:23418070 original size:36 final size:36
Alignment explanation
Indices: 23418023--23418097 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
23418013 TCGTTTGGAG
23418023 ATAGTTTATTGCATAAAGCTTACTTGTCATACGTAC
1 ATAGTTTATTGCATAAAGCTTACTTGTCATACGTAC
23418059 ATAGTTTATTGCATAAAGCTTACTTGTCATACGTAC
1 ATAGTTTATTGCATAAAGCTTACTTGTCATACGTAC
23418095 ATA
1 ATA
23418098 ATAATATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (36 bp):
ATAGTTTATTGCATAAAGCTTACTTGTCATACGTAC
Found at i:23424744 original size:7 final size:7
Alignment explanation
Indices: 23424732--23424815 Score: 132
Period size: 7 Copynumber: 12.0 Consensus size: 7
23424722 AAGTTGCGAA
*
23424732 TGCCTAT
1 TGCCTGT
*
23424739 TGCCTAT
1 TGCCTGT
*
23424746 TGCCTAT
1 TGCCTGT
*
23424753 TGCCTAT
1 TGCCTGT
23424760 TGCCTGT
1 TGCCTGT
23424767 TGCCTGT
1 TGCCTGT
23424774 TGCCTGT
1 TGCCTGT
23424781 TGCCTGT
1 TGCCTGT
23424788 TGCCTGT
1 TGCCTGT
23424795 TGCCTGT
1 TGCCTGT
23424802 TGCCTGT
1 TGCCTGT
23424809 TGCCTGT
1 TGCCTGT
23424816 GCCGGACTTA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
7 76 1.00
ACGTcount: A:0.05, C:0.29, G:0.24, T:0.43
Consensus pattern (7 bp):
TGCCTGT
Found at i:23432381 original size:54 final size:55
Alignment explanation
Indices: 23432288--23432391 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 55
23432278 GAAATGATGA
*
23432288 AATGGAGAAACATGAAACATTGGGAAATGATTAAAGTTTTCTCCAAAATTAAAAT
1 AATGGAGAAACATGAAACATTGGGAAATGAATAAAGTTTTCTCCAAAATTAAAAT
* ***
23432343 AATGGAG-AA-ATGAAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATT
1 AATGGAGAAACATGAAA-CATTGGGAAATGAATAAAGTTTTCTCCAAAATT
23432392 GAAGTGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
53 6 0.14
54 30 0.70
55 7 0.16
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (55 bp):
AATGGAGAAACATGAAACATTGGGAAATGAATAAAGTTTTCTCCAAAATTAAAAT
Found at i:23432407 original size:6 final size:6
Alignment explanation
Indices: 23432396--23432422 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
23432386 AAAATTGAAG
23432396 TGAAAA TGAAAA TGAAAA TGAAAA TGA
1 TGAAAA TGAAAA TGAAAA TGAAAA TGA
23432423 GAAACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.19, T:0.19
Consensus pattern (6 bp):
TGAAAA
Found at i:23447706 original size:64 final size:64
Alignment explanation
Indices: 23447632--23447755 Score: 221
Period size: 64 Copynumber: 1.9 Consensus size: 64
23447622 ATATGTCTCG
*
23447632 ACCGAAGCAATTATGTGCAAGAGATTTGAAGATGGTTTGAACAAATATATCTGCTTGTTACTCA
1 ACCGAAGCAATTATGTGCAAGAGATTTGAAGATGGTTTGAACAAATATATCTACTTGTTACTCA
* *
23447696 ACCGAAGCAATTATGTGCAATATATTTGAAGATGGTTTGAACAAATATATCTACTTGTTA
1 ACCGAAGCAATTATGTGCAAGAGATTTGAAGATGGTTTGAACAAATATATCTACTTGTTA
23447756 GTTGGGATTC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (64 bp):
ACCGAAGCAATTATGTGCAAGAGATTTGAAGATGGTTTGAACAAATATATCTACTTGTTACTCA
Found at i:23452584 original size:20 final size:20
Alignment explanation
Indices: 23452545--23452584 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
23452535 CTAAAAGAAA
23452545 GAAATCGAAATTAGATCGAGG
1 GAAATCGAAATTA-ATCGAGG
23452566 GAAATCGAAAGTT-ATCGAG
1 GAAATCGAAA-TTAATCGAG
23452585 TAATCGATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 10 0.56
22 2 0.11
ACGTcount: A:0.42, C:0.10, G:0.28, T:0.20
Consensus pattern (20 bp):
GAAATCGAAATTAATCGAGG
Found at i:23470542 original size:44 final size:43
Alignment explanation
Indices: 23470398--23470555 Score: 180
Period size: 43 Copynumber: 3.7 Consensus size: 43
23470388 AGCTAGTATA
* * * *
23470398 ATGCCAATGTCCCAAATATGGTCTTACATGT-AATCAAATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATC-AATATTG
** *
23470441 ATGCCGCTGTCCCAGACAGGGTCTTACACG-AAATCAA-ATATG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCAATAT-TG
23470483 ATGCCAATGTCCCAGACATGGTCTTACACGTAAAT-AATAGGTTG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCAATA--TTG
*
23470527 ATGCCAATGTCCCAGACGTGGTCTTACAC
1 ATGCCAATGTCCCAGACATGGTCTTACAC
23470556 AAATACACAT
Statistics
Matches: 98, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
41 2 0.02
42 32 0.33
43 33 0.34
44 30 0.31
45 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCAATATTG
Found at i:23481115 original size:42 final size:43
Alignment explanation
Indices: 23481013--23481126 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
23481003 AGCTCGTACA
* * *
23481013 ATGCTAACGTCCCAGAC-GTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACAG-GGTCTTACACGAAATCAAATATCG
* *
23481056 ATGCC-ACTATCCTAGACAGGGTCTTACACGAAATCAAATA-CG
1 ATGCCAAC-GTCCCAGACAGGGTCTTACACGAAATCAAATATCG
*
23481098 ATGCCAACGTCCCAGACATGGTCTTACAC
1 ATGCCAACGTCCCAGACAGGGTCTTACAC
23481127 AAAAAAACAT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
42 27 0.45
43 32 0.53
44 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACACGAAATCAAATATCG
Found at i:23482393 original size:26 final size:26
Alignment explanation
Indices: 23482362--23482413 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
23482352 ATTTTAGAAG
23482362 TTCCACTTAAACCCTTAAATATTTAT
1 TTCCACTTAAACCCTTAAATATTTAT
23482388 TTCCACTTAAACCCTTAAATATTTAT
1 TTCCACTTAAACCCTTAAATATTTAT
23482414 AAACAAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (26 bp):
TTCCACTTAAACCCTTAAATATTTAT
Found at i:23486948 original size:50 final size:49
Alignment explanation
Indices: 23486772--23487183 Score: 229
Period size: 46 Copynumber: 8.7 Consensus size: 49
23486762 TAGGGTAAAA
* * * ** *
23486772 TGCCGATACCATGTCCCAGACATGGTCTTACACTGGCT-T-ATCCATCA
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATATCG
* ** * * *
23486819 AGTTGATGCCATGTCCCAGACATGGTCTTACACT-GACTATCA-AAATCG
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTAG-CTCTCATATATCG
* * *
23486867 AGGCCGACGCCGTGTCCCAAACATGGTCTTACACTAGCTCTCATATATCTG
1 -TGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATATC-G
* * * *
23486918 TGTCGATGCCATGTCTCAAACATGGTCTTACACTAACACCTC-TATA-CG
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTAGC-TCTCATATATCG
* * ** * *
23486966 TGCCGATGCCATGTCCCAAACACGGTC-TA-AC-A-TTAACACATCTCG
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATATCG
* * * *
23487011 TAGCTGATG-CATGTCCCAGACAT-GTCTTACACTAGCT-T-ACATCTCG
1 T-GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATATCG
* * * *
23487057 AGGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTC--ATCTCAA
1 -TGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATATC-G
* * * * *
23487104 TGCTGATGACATGTCCCAGACATGGTCTTCCACTGGCTCTCATA-AT-G
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATATCG
* **
23487151 TGGCCGATG-CATTTCCCAGGCAT-GTCTTACACT
1 T-GCCGATGCCATGTCCCAAACATGGTCTTACACT
23487184 GGCGCACAAA
Statistics
Matches: 292, Mismatches: 49, Indels: 49
0.75 0.13 0.13
Matches are distributed among these distances:
43 1 0.00
44 5 0.02
45 18 0.06
46 73 0.25
47 63 0.22
48 51 0.17
49 36 0.12
50 41 0.14
51 4 0.01
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (49 bp):
TGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATATCG
Found at i:23487161 original size:94 final size:96
Alignment explanation
Indices: 23486773--23487183 Score: 307
Period size: 94 Copynumber: 4.3 Consensus size: 96
23486763 AGGGTAAAAT
* * *
23486773 GCCGATACCATGTCCCAGACATGGTCTTACACTGGCT-T-ATCCATCAA-GTTGATGCCATGTCC
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTCTCAT-C-TCAATGCTGATGCCATGTCC
* * *
23486835 CAGACATGGTCTTACACTGACTATCAAAATCGAG
63 CAGACATGGTCTTACACTAACTCTCATAATCGAG
* * * * * *
23486869 GCCGACGCCGTGTCCCAAACATGGTCTTACACTAGCTCTCATAT-ATCTGTGTCGATGCCATGTC
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTCA-ATG-CT-GATGCCATGTC
* * * *
23486933 TCAAACATGGTCTTACACTAACACCTC-T-ATACG-T
62 CCAGACATGGTCTTACACTAAC-TCTCATAAT-CGAG
* * * * * * *
23486967 GCCGATGCCATGTCCCAAACACGGTCTAACATTA--ACACATCTC-GTAGCTGATG-CATGTCCC
1 GCCGATGCCATGTCCCAGACA-TGTCTTACACTAGCTCTCATCTCAAT-GCTGATGCCATGTCCC
* *
23487028 AGACAT-GTCTTACACTAGCT-TACAT-CTCGAG
64 AGACATGGTCTTACACTAACTCT-CATAATCGAG
*
23487059 GCCGATG-CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAATGCTGATGACATGTCCCAG
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAATGCTGATGCCATGTCCCAG
* ** *
23487123 ACATGGTCTTCCACTGGCTCTCATAAT-GTG
66 ACATGGTCTTACACTAACTCTCATAATCGAG
* *
23487153 GCCGATG-CATTTCCCAGGCATGTCTTACACT
1 GCCGATGCCATGTCCCAGACATGTCTTACACT
23487184 GGCGCACAAA
Statistics
Matches: 250, Mismatches: 44, Indels: 44
0.74 0.13 0.13
Matches are distributed among these distances:
90 10 0.04
91 15 0.06
92 35 0.14
93 27 0.11
94 50 0.20
95 5 0.02
96 39 0.16
97 2 0.01
98 33 0.13
99 32 0.13
100 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (96 bp):
GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAATGCTGATGCCATGTCCCAG
ACATGGTCTTACACTAACTCTCATAATCGAG
Found at i:23493205 original size:2 final size:2
Alignment explanation
Indices: 23493192--23493224 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
23493182 CCAGTTTTAA
*
23493192 TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
23493225 TTGTTTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:23502910 original size:92 final size:92
Alignment explanation
Indices: 23502747--23502915 Score: 230
Period size: 92 Copynumber: 1.8 Consensus size: 92
23502737 CAGTATGAAC
* * * * *
23502747 TGCCAGATCAGATAGTAGTACGTAGCGTAGCCAAGGTACATGCGGTATGGTGCAATGCAATAATT
1 TGCCAGATCAGATAATAGTACGTAGCGTAGCCAACGTACATACGGTACGGTGCAATGCAATAATC
23502812 CACTATACCGATAGGTTGCAGTAAAAT
66 CACTATACCGATAGGTTGCAGTAAAAT
* * * * * *
23502839 TGCCAGTTCAGTTAATAGTATGTAGCGTAGCTAACGTACATATGGTACGGTGCAATGCGATAATC
1 TGCCAGATCAGATAATAGTACGTAGCGTAGCCAACGTACATACGGTACGGTGCAATGCAATAATC
*
23502904 CGCTATACCGAT
66 CACTATACCGAT
23502916 GTGTTGTCAT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
92 65 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (92 bp):
TGCCAGATCAGATAATAGTACGTAGCGTAGCCAACGTACATACGGTACGGTGCAATGCAATAATC
CACTATACCGATAGGTTGCAGTAAAAT
Found at i:23504193 original size:32 final size:34
Alignment explanation
Indices: 23504157--23504221 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
23504147 TAACAGTGGT
*
23504157 ACTGGACCAGAG-CCCTT-TTCAGATTACAATAA
1 ACTGGACCAGAGCCCCTTATTCAGATAACAATAA
* **
23504189 ACTGGGCCTTAGCCCCTTATTCAGATAACAATA
1 ACTGGACCAGAGCCCCTTATTCAGATAACAATA
23504222 TGGCCCATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 9 0.33
33 5 0.19
34 13 0.48
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (34 bp):
ACTGGACCAGAGCCCCTTATTCAGATAACAATAA
Found at i:23506085 original size:25 final size:25
Alignment explanation
Indices: 23506056--23506160 Score: 169
Period size: 25 Copynumber: 4.2 Consensus size: 25
23506046 TGAAATTCCC
23506056 ATCATGGAACATTTACCTAA-CCATT
1 ATCAT-GAACATTTACCTAACCCATT
23506081 ATCATGGAACATTTACCTAACCCATT
1 ATCAT-GAACATTTACCTAACCCATT
23506107 ATCATGAATCATTTACCTAA-CCATT
1 ATCATGAA-CATTTACCTAACCCATT
23506132 ATCATGAACATTTACCTAACCCATT
1 ATCATGAACATTTACCTAACCCATT
23506157 ATCA
1 ATCA
23506161 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
24 11 0.14
25 45 0.58
26 21 0.27
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (25 bp):
ATCATGAACATTTACCTAACCCATT
Found at i:23513157 original size:26 final size:26
Alignment explanation
Indices: 23513125--23513202 Score: 138
Period size: 26 Copynumber: 3.0 Consensus size: 26
23513115 ATTCCCATCC
23513125 TCGAACATTTACCTAACCCATTATCA
1 TCGAACATTTACCTAACCCATTATCA
* *
23513151 TGGAACATTTACCTAACTCATTATCA
1 TCGAACATTTACCTAACCCATTATCA
23513177 TCGAACATTTACCTAACCCATTATCA
1 TCGAACATTTACCTAACCCATTATCA
23513203 ATTTGTATCA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (26 bp):
TCGAACATTTACCTAACCCATTATCA
Found at i:23517799 original size:23 final size:23
Alignment explanation
Indices: 23517718--23517803 Score: 90
Period size: 21 Copynumber: 3.9 Consensus size: 23
23517708 CTAATTAGAG
*
23517718 TACGACACATAAAGTGCCT-AAA
1 TACGACACACAAAGTGCCTGAAA
* *
23517740 -ACGACACACGAGGTGCCTG--A
1 TACGACACACAAAGTGCCTGAAA
* *
23517760 TACGACACACGAGGTGCCTGAAA
1 TACGACACACAAAGTGCCTGAAA
*
23517783 TACGACACATAAAGTGCCTGA
1 TACGACACACAAAGTGCCTGA
23517804 TCGATAAAGC
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.63
23 19 0.35
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (23 bp):
TACGACACACAAAGTGCCTGAAA
Found at i:23518199 original size:15 final size:15
Alignment explanation
Indices: 23518174--23518227 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
23518164 TCATATATAT
23518174 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
23518190 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
23518205 AATAATTTCAATCAA
1 TATAAATTCAATCAA
23518220 TATAAATT
1 TATAAATT
23518228 AAATAAATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 30 0.88
16 4 0.12
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:23519469 original size:5 final size:5
Alignment explanation
Indices: 23519461--23519496 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
23519451 TCTTTAGTTT
23519461 ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
23519497 AATATCTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:23519536 original size:8 final size:8
Alignment explanation
Indices: 23519509--23519547 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
23519499 TATCTTTATT
23519509 ATATAATA
1 ATATAATA
*
23519517 ATAGAATA
1 ATATAATA
23519525 ATATAATA
1 ATATAATA
*
23519533 ATATACTAA
1 ATATAAT-A
23519542 ATATAA
1 ATATAA
23519548 AAAAAATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (8 bp):
ATATAATA
Found at i:23524296 original size:34 final size:34
Alignment explanation
Indices: 23524253--23524320 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
23524243 CTCATTCTTG
23524253 TCATTAATTGAATGAAAATAAGATTTAAGTCAAA
1 TCATTAATTGAATGAAAATAAGATTTAAGTCAAA
23524287 TCATTAATTGAATGAAAATAAGATTTAAGTCAAA
1 TCATTAATTGAATGAAAATAAGATTTAAGTCAAA
23524321 AGATTAGGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (34 bp):
TCATTAATTGAATGAAAATAAGATTTAAGTCAAA
Found at i:23526641 original size:25 final size:26
Alignment explanation
Indices: 23526592--23526683 Score: 84
Period size: 26 Copynumber: 3.6 Consensus size: 26
23526582 TTATTATTTG
* * *
23526592 AAAATTATAAAAAAAATCTAAAAATT
1 AAAATTATAAAAAATATATTAAAATT
*
23526618 AAAATTATAAAAAGT-T-TTATAAA-T
1 AAAATTATAAAAAATATATTA-AAATT
*
23526642 AAAA-AATAAAAAATATATTAAAATTT
1 AAAATTATAAAAAATATATTAAAA-TT
23526668 AAAATTATATAAAAAT
1 AAAATTATA-AAAAAT
23526684 TAATAATATT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
23 8 0.15
24 11 0.21
25 7 0.13
26 18 0.34
27 3 0.06
28 6 0.11
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (26 bp):
AAAATTATAAAAAATATATTAAAATT
Found at i:23526664 original size:18 final size:18
Alignment explanation
Indices: 23526643--23526702 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 18
23526633 TTTATAAATA
23526643 AAAAATAAAAAATATATT
1 AAAAATAAAAAATATATT
* * *
23526661 AAAATTTAAAATTATA-T
1 AAAAATAAAAAATATATT
* * *
23526678 AAAAATTAATAATATTTT
1 AAAAATAAAAAATATATT
*
23526696 AATAATA
1 AAAAATA
23526703 TTAAGTAAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAATAAAAAATATATT
Found at i:23529724 original size:21 final size:21
Alignment explanation
Indices: 23529675--23529715 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23529665 TATGAGATTT
* *
23529675 AATGATTGCTGATAGATTATA
1 AATGTTTGATGATAGATTATA
23529696 AATGTTTGATGATAG-TTATA
1 AATGTTTGATGATAGATTATA
23529716 CAAGTTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (21 bp):
AATGTTTGATGATAGATTATA
Found at i:23532870 original size:9 final size:9
Alignment explanation
Indices: 23532856--23532892 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
23532846 TATAGTCTGA
23532856 TATTCGAAT
1 TATTCGAAT
23532865 TATTCGAAT
1 TATTCGAAT
* *
23532874 CATTCGAGT
1 TATTCGAAT
23532883 TATTCGAAT
1 TATTCGAAT
23532892 T
1 T
23532893 TGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (9 bp):
TATTCGAAT
Found at i:23532969 original size:18 final size:18
Alignment explanation
Indices: 23532943--23532977 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23532933 ATTCAAGTTG
*
23532943 ACTCGAATAACTTGATTA
1 ACTCGAATAACTCGATTA
*
23532961 ACTCTAATAACTCGATT
1 ACTCGAATAACTCGATT
23532978 CGTTTAATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (18 bp):
ACTCGAATAACTCGATTA
Found at i:23536743 original size:36 final size:36
Alignment explanation
Indices: 23536665--23536749 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 36
23536655 AATAGTAAGT
* *
23536665 TGTGCCAAACACTAGTTGGTAAAACCGAAAAATAGA
1 TGTGCCCAACACTAGTTAGTAAAACCGAAAAATAGA
* * * * *
23536701 TGTGCCCAACACTTGTTAGTATAACCGACAAATGGG
1 TGTGCCCAACACTAGTTAGTAAAACCGAAAAATAGA
*
23536737 TGTGCCCAGCACT
1 TGTGCCCAACACT
23536750 CCCGATACGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (36 bp):
TGTGCCCAACACTAGTTAGTAAAACCGAAAAATAGA
Found at i:23537491 original size:51 final size:51
Alignment explanation
Indices: 23537415--23537518 Score: 183
Period size: 51 Copynumber: 2.0 Consensus size: 51
23537405 TATTATTTGG
*
23537415 ATGCCCCTATACTTTTTCATTTTATTCAATTTAGTCCCTAAAATCAAAACT
1 ATGCCCCTATACTTTTTCATTTTATTCAATTTAGTCCCTAAAATAAAAACT
23537466 ATGCCCCTATACTTTTGT-ATTTTATTCAATTTAGTCCCTAAAATAAAAACT
1 ATGCCCCTATACTTTT-TCATTTTATTCAATTTAGTCCCTAAAATAAAAACT
23537517 AT
1 AT
23537519 CATAGTTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 50 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (51 bp):
ATGCCCCTATACTTTTTCATTTTATTCAATTTAGTCCCTAAAATAAAAACT
Found at i:23540862 original size:19 final size:20
Alignment explanation
Indices: 23540838--23540875 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23540828 ACTTTTTTCA
*
23540838 TTTTACTT-TCTCTCAAAAC
1 TTTTACTTCTCCCTCAAAAC
23540857 TTTTACTTCTCCCTCAAAA
1 TTTTACTTCTCCCTCAAAA
23540876 AATTTAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTACTTCTCCCTCAAAAC
Found at i:23540877 original size:75 final size:74
Alignment explanation
Indices: 23540772--23540940 Score: 225
Period size: 74 Copynumber: 2.3 Consensus size: 74
23540762 CCTCAACCCC
* * * *
23540772 CTCTCAAACCCTTTTACTT-TCCCCTAAAAAATTTTACTTCTCCCCAAACTCTCAAAACTTTTTT
1 CTCTCAAA-ACTTTTACTTCTCCCCTAAAAAA-TTTAATTCTCCCCAAACCCCCAAAACTTTTTT
23540836 CATTTTACTTT
64 CATTTTACTTT
* *
23540847 CTCTCAAAACTTTTACTTCT-CCCTCAAAAAATTTAATTCTCTCCAAACCCCCAAAACTTTTTTT
1 CTCTCAAAACTTTTACTTCTCCCCT-AAAAAATTTAATTCTCCCCAAACCCCCAAAACTTTTTTC
23540911 ATTTTACTTT
65 ATTTTACTTT
*
23540921 CCCTCTAAAACTTTTACTTC
1 CTCTC-AAAACTTTTACTTC
23540941 CCCAAACTTC
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
74 55 0.65
75 29 0.35
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.42
Consensus pattern (74 bp):
CTCTCAAAACTTTTACTTCTCCCCTAAAAAATTTAATTCTCCCCAAACCCCCAAAACTTTTTTCA
TTTTACTTT
Found at i:23540881 original size:20 final size:20
Alignment explanation
Indices: 23540839--23540887 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
23540829 CTTTTTTCAT
* **
23540839 TTTACTT-TCTCTCAAAACT
1 TTTACTTCTCCCTCAAAAAA
23540858 TTTACTTCTCCCTCAAAAAA
1 TTTACTTCTCCCTCAAAAAA
*
23540878 TTTAATTCTC
1 TTTACTTCTC
23540888 TCCAAACCCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTACTTCTCCCTCAAAAAA
Found at i:23542425 original size:5 final size:5
Alignment explanation
Indices: 23542415--23542444 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
23542405 GCTCTCAGAG
23542415 TCTCC TCTCC TCTCC TCTCC TCTCC TCTCC
1 TCTCC TCTCC TCTCC TCTCC TCTCC TCTCC
23542445 CTGCCTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
TCTCC
Found at i:23542969 original size:11 final size:11
Alignment explanation
Indices: 23542945--23542991 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
23542935 GAAACAGGTA
*
23542945 TTATATTTCAT
1 TTATATTTTAT
*
23542956 TTATATTTTTT
1 TTATATTTTAT
23542967 TTAATAGTTTTAT
1 TT-ATA-TTTTAT
23542980 TTA-ATTTTAT
1 TTATATTTTAT
23542990 TT
1 TT
23542992 TGAAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 8 0.26
11 12 0.39
12 4 0.13
13 7 0.23
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (11 bp):
TTATATTTTAT
Found at i:23543376 original size:16 final size:16
Alignment explanation
Indices: 23543355--23543386 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
23543345 TCATGAAGTC
23543355 GAATTGGCAATAAAGA
1 GAATTGGCAATAAAGA
23543371 GAATTGGCAATAAAGA
1 GAATTGGCAATAAAGA
23543387 AAGAAGTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (16 bp):
GAATTGGCAATAAAGA
Found at i:23547240 original size:15 final size:15
Alignment explanation
Indices: 23547216--23547254 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
23547206 GCCCGTGAGT
23547216 GAAGGAGAAGAAAAA
1 GAAGGAGAAGAAAAA
* *
23547231 GAATGAGAAGAAGAA
1 GAAGGAGAAGAAAAA
23547246 GAAGGAGAA
1 GAAGGAGAA
23547255 TGAGAGGGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.03
Consensus pattern (15 bp):
GAAGGAGAAGAAAAA
Found at i:23547240 original size:21 final size:21
Alignment explanation
Indices: 23547216--23547259 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
23547206 GCCCGTGAGT
*
23547216 GAAGGAGAAGAAAAAGAATGA
1 GAAGAAGAAGAAAAAGAATGA
**
23547237 GAAGAAGAAGAAGGAGAATGA
1 GAAGAAGAAGAAAAAGAATGA
23547258 GA
1 GA
23547260 GGGCGGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.36, T:0.05
Consensus pattern (21 bp):
GAAGAAGAAGAAAAAGAATGA
Found at i:23547274 original size:5 final size:5
Alignment explanation
Indices: 23547264--23547289 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
23547254 ATGAGAGGGC
23547264 GGGAA GGGAA GGGAA GGGAA GGGAA G
1 GGGAA GGGAA GGGAA GGGAA GGGAA G
23547290 AGAAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (5 bp):
GGGAA
Found at i:23549374 original size:14 final size:14
Alignment explanation
Indices: 23549355--23549383 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
23549345 GACAAATTCT
23549355 TTATAATGATACTA
1 TTATAATGATACTA
23549369 TTATAATGATACTA
1 TTATAATGATACTA
23549383 T
1 T
23549384 ATTTACCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTATAATGATACTA
Found at i:23550241 original size:33 final size:33
Alignment explanation
Indices: 23550199--23550290 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 33
23550189 TCTTTGGGTT
* * *
23550199 GTATCCACCGTAGTACAGCACTTCT-TCCGACCC
1 GTATCCACCGCAGTACAACACTCCTCTCCGA-CC
*
23550232 GTATCCACCGCAGTACAACACTCCTCTCGGACC
1 GTATCCACCGCAGTACAACACTCCTCTCCGACC
** **
23550265 GTATCCACTACAGTACTTCACTCCTC
1 GTATCCACCGCAGTACAACACTCCTC
23550291 CTGGGTCGTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
33 46 0.92
34 4 0.08
ACGTcount: A:0.23, C:0.40, G:0.13, T:0.24
Consensus pattern (33 bp):
GTATCCACCGCAGTACAACACTCCTCTCCGACC
Found at i:23555258 original size:15 final size:17
Alignment explanation
Indices: 23555238--23555269 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
23555228 CCCTCTCTAT
23555238 TCTTTTT-GTTG-TTTC
1 TCTTTTTAGTTGCTTTC
23555253 TCTTTTTAGTTGCTTTC
1 TCTTTTTAGTTGCTTTC
23555270 AGCCGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.03, C:0.16, G:0.12, T:0.69
Consensus pattern (17 bp):
TCTTTTTAGTTGCTTTC
Found at i:23560350 original size:32 final size:32
Alignment explanation
Indices: 23560311--23560376 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
23560301 ATCATAAGAA
23560311 GTAGGATCCGTATATATTTGTCATATAATCAG
1 GTAGGATCCGTATATATTTGTCATATAATCAG
23560343 GTAGGATCCGTATATATTTGTCATATAATCAG
1 GTAGGATCCGTATATATTTGTCATATAATCAG
23560375 GT
1 GT
23560377 CTCATCCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (32 bp):
GTAGGATCCGTATATATTTGTCATATAATCAG
Found at i:23561924 original size:27 final size:27
Alignment explanation
Indices: 23561881--23561932 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
23561871 GATAATAGTC
* *
23561881 CATTTCTAGCAAAATCAAATTTATTGT
1 CATTTCTAACAAAATCAAATATATTGT
*
23561908 CATTTCTAACAATATCAAATATATT
1 CATTTCTAACAAAATCAAATATATT
23561933 AAAATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.40
Consensus pattern (27 bp):
CATTTCTAACAAAATCAAATATATTGT
Found at i:23561939 original size:27 final size:27
Alignment explanation
Indices: 23561882--23561939 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
23561872 ATAATAGTCC
* * ***
23561882 ATTTCTAGCAAAATCAAATTTATTGTC
1 ATTTCTAACAAAATCAAATATATTAAA
*
23561909 ATTTCTAACAATATCAAATATATTAAA
1 ATTTCTAACAAAATCAAATATATTAAA
23561936 ATTT
1 ATTT
23561940 TTTATAAGAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.41
Consensus pattern (27 bp):
ATTTCTAACAAAATCAAATATATTAAA
Found at i:23563358 original size:21 final size:21
Alignment explanation
Indices: 23563332--23563371 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
23563322 ATATAATTAT
23563332 AAAA-TTACACTTTCATTTTCA
1 AAAATTTACA-TTTCATTTTCA
*
23563353 AAAATTTATATTTCATTTT
1 AAAATTTACATTTCATTTT
23563372 TACTCTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (21 bp):
AAAATTTACATTTCATTTTCA
Found at i:23566350 original size:15 final size:15
Alignment explanation
Indices: 23566332--23566360 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
23566322 TTATTTTTAA
23566332 TATATATATTTGAAG
1 TATATATATTTGAAG
23566347 TATATATATTTGAA
1 TATATATATTTGAA
23566361 AATATTTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
TATATATATTTGAAG
Found at i:23571629 original size:16 final size:16
Alignment explanation
Indices: 23571610--23571640 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23571600 CTTCTTCACT
23571610 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
23571626 TACTTACTTACTTAA
1 TACTCACTTACTTAA
23571641 TCAAATTTAT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:23571646 original size:20 final size:20
Alignment explanation
Indices: 23571607--23571646 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
23571597 AAACTTCTTC
* *
23571607 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
23571627 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
23571647 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:23571766 original size:5 final size:5
Alignment explanation
Indices: 23571756--23571783 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
23571746 TATAACTCGT
23571756 CTTAC CTTAC CTTAC CTTAC CTTAC CTT
1 CTTAC CTTAC CTTAC CTTAC CTTAC CTT
23571784 GATATTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.39, G:0.00, T:0.43
Consensus pattern (5 bp):
CTTAC
Found at i:23571916 original size:49 final size:51
Alignment explanation
Indices: 23571842--23572096 Score: 203
Period size: 55 Copynumber: 4.8 Consensus size: 51
23571832 ACGTGGGTAC
* *
23571842 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCCTT-TT-TAAA
1 CTTACCATTGCCATGACTTGACATGGTCTTACATGGTATCCTTCTTATAAA
* *
23571891 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
1 CTTACCATTGCCATGACTTGACATGGTCTTACATGGTATCCTT--CTTATAAA
* * * * *
23571944 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCATTGCCATGACTTGACATGGTCTTACATGGTATCC-TT--CTTATA--AA
* * * * * * * * *
23571999 CTTATCAATGTCATGTCTTGACGTGGTCTTACATGATTTCCTTGCCTGAGAAA
1 CTTACCATTGCCATGACTTGACATGGTCTTACATGGTATCCTT--CTTATAAA
*
23572052 CCTTACCAATTGCCATGCCTT-AGCATGGTCTTACATGGTATCCTT
1 -CTTACC-ATTGCCATGACTTGA-CATGGTCTTACATGGTATCCTT
23572097 AAACCCTAAT
Statistics
Matches: 167, Mismatches: 28, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
49 40 0.24
52 4 0.02
53 47 0.28
54 6 0.04
55 68 0.41
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (51 bp):
CTTACCATTGCCATGACTTGACATGGTCTTACATGGTATCCTTCTTATAAA
Found at i:23576961 original size:13 final size:14
Alignment explanation
Indices: 23576943--23576975 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
23576933 GGGCCTCATG
23576943 TTTTTG-TCATGTA
1 TTTTTGATCATGTA
23576956 TTTTTGTATCATGTA
1 TTTTTG-ATCATGTA
23576971 TTTTT
1 TTTTT
23576976 ATACCATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
15 12 0.67
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.67
Consensus pattern (14 bp):
TTTTTGATCATGTA
Found at i:23577778 original size:131 final size:127
Alignment explanation
Indices: 23577562--23577992 Score: 389
Period size: 131 Copynumber: 3.3 Consensus size: 127
23577552 AGATTTGATA
* * ** * * * *
23577562 TTTGGCAA-TCGTGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCTCGTTTACTTAAAATAAT
1 TTTGGCAATTCG-GGAATCATGCCCTATCGTGCTGGGTTGTGACTTCTCGTTTGCTCAAAACAAT
* * * * * * *
23577626 CAAATATCCCTCCAAAATTTCACGCATGTCTTCTAAAAATCATTTAAAACGAAGCCAATATTCGG
65 CGAATATCCCTTC-AAGTTTCACTCATGT-TTCTAAAAATCCTTTAAAACGAAG--AATGTTCGA
23577691 TG
126 TG
* *
23577693 ATTGACAATTCGGGAATCATGCCCTATCGTGCTGGGTTGTGACTTCTCGTTTGCTCAAAACAATC
1 TTTGGCAATTCGGGAATCATGCCCTATCGTGCTGGGTTGTGACTTCTCGTTTGCTCAAAACAATC
* * * * * * *
23577758 GAATATTCCTTTAGGTTTTCACTCATGTTTATTAAAAATCCTTCAAAACAAAGGATGTTCGATG
66 GAATATCCCTTCAAG-TTTCACTCATGTTT-CTAAAAATCCTTTAAAACGAAGAATGTTCGATG
* * * * * * * * *
23577822 TTTGGCGATTTGAGAATCGTGCCCTATCGTGCTGGGTTGTG-CTTTTTCATTCGCCCTAAACAAT
1 TTTGGCAATTCGGGAATCATGCCCTATCGTGCTGGGTTGTGAC-TTCTCGTTTGCTCAAAACAAT
* * * *
23577886 CGAAGATCCCTTCGAAGTTTCATTCACGTTTTCTAAAAACCCTTTAAAACGAAAGAAGTGTTCGA
65 CGAATATCCCTTC-AAGTTTCACTCATG-TTTCTAAAAATCCTTTAAAACG-AAGAA-TGTTCGA
23577951 TG
126 TG
*
23577953 TTTGGCAATTCGGGGAATAATGCCCTATCGTGCTGGGTTG
1 TTTGGCAATTC-GGGAATCATGCCCTATCGTGCTGGGTTG
23577993 CAATCTCCTG
Statistics
Matches: 240, Mismatches: 51, Indels: 17
0.78 0.17 0.06
Matches are distributed among these distances:
128 1 0.00
129 93 0.39
130 12 0.05
131 106 0.44
132 28 0.12
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (127 bp):
TTTGGCAATTCGGGAATCATGCCCTATCGTGCTGGGTTGTGACTTCTCGTTTGCTCAAAACAATC
GAATATCCCTTCAAGTTTCACTCATGTTTCTAAAAATCCTTTAAAACGAAGAATGTTCGATG
Found at i:23577883 original size:129 final size:132
Alignment explanation
Indices: 23577698--23577992 Score: 343
Period size: 129 Copynumber: 2.3 Consensus size: 132
23577688 CGGTGATTGA
* * * *
23577698 CAATTCGG-GAATCATGCCCTATCGTGCTGGGTTGTGACTTCTCGTTTGCTCAAAACAATCGAAT
1 CAATTCGGAGAATCATGCCCTATCGTGCTGGGTTGTGACTTCTCATTCGCCCAAAACAATCGAAG
* * * * * *
23577762 ATTCCTT-TAGGTTTTCACTCATGTTTAT-TAAAAATCCTTCAAAAC-AAAGGA-TGTTCGATGT
66 ATCCCTTCGAAG-TTTCACTCACGTTT-TCTAAAAACCCTTCAAAACGAAAGAAGTGTTCGATGT
23577823 TTGG
129 TTGG
* * * * *
23577827 CGATT-TGAGAATCGTGCCCTATCGTGCTGGGTTGTG-CTTTTTCATTCGCCCTAAACAATCGAA
1 CAATTCGGAGAATCATGCCCTATCGTGCTGGGTTGTGAC-TTCTCATTCGCCCAAAACAATCGAA
* *
23577890 GATCCCTTCGAAGTTTCATTCACGTTTTCTAAAAACCCTTTAAAACGAAAGAAGTGTTCGATGTT
65 GATCCCTTCGAAGTTTCACTCACGTTTTCTAAAAACCCTTCAAAACGAAAGAAGTGTTCGATGTT
23577955 TGG
130 TGG
* *
23577958 CAATTCGGGGAATAATGCCCTATCGTGCTGGGTTG
1 CAATTCGGAGAATCATGCCCTATCGTGCTGGGTTG
23577993 CAATCTCCTG
Statistics
Matches: 137, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
128 3 0.02
129 84 0.61
130 7 0.05
131 18 0.13
132 25 0.18
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (132 bp):
CAATTCGGAGAATCATGCCCTATCGTGCTGGGTTGTGACTTCTCATTCGCCCAAAACAATCGAAG
ATCCCTTCGAAGTTTCACTCACGTTTTCTAAAAACCCTTCAAAACGAAAGAAGTGTTCGATGTTT
GG
Found at i:23591178 original size:30 final size:30
Alignment explanation
Indices: 23591144--23591213 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
23591134 ACCATCTCGC
23591144 ATGCGAACCCCCTTGCATGT-GAACCTCTAT
1 ATGCGAACCCCCTTGCATGTGGAACC-CTAT
*
23591174 ATGCGAAACCCCTTGCATGTGGAACCCTAT
1 ATGCGAACCCCCTTGCATGTGGAACCCTAT
*
23591204 ATACGAACCC
1 ATGCGAACCC
23591214 ATTTATATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 31 0.86
31 5 0.14
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (30 bp):
ATGCGAACCCCCTTGCATGTGGAACCCTAT
Found at i:23591284 original size:27 final size:28
Alignment explanation
Indices: 23591225--23591285 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
23591215 TTTATATGTG
**
23591225 AAACCCCTATAGGTGAGCCCCTGCACGC
1 AAACCCCTATAGGTGAGCCCCTAAACGC
* * *
23591253 GAACCCCTATA-GTGAGCCCTTAAATGC
1 AAACCCCTATAGGTGAGCCCCTAAACGC
23591280 AAACCC
1 AAACCC
23591286 ATGTATGCGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.30, C:0.36, G:0.18, T:0.16
Consensus pattern (28 bp):
AAACCCCTATAGGTGAGCCCCTAAACGC
Found at i:23591604 original size:23 final size:21
Alignment explanation
Indices: 23591569--23591627 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
23591559 GAACCCAATA
* *
23591569 TGTATGTGTGAACCCTACATG
1 TGTATATGCGAACCCTACATG
*
23591590 TTGTGATATGCGAACCCTATATG
1 -TGT-ATATGCGAACCCTACATG
*
23591613 TGTATATGCAAACCC
1 TGTATATGCGAACCC
23591628 ATATGTGCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 11 0.34
22 6 0.19
23 15 0.47
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (21 bp):
TGTATATGCGAACCCTACATG
Found at i:23591631 original size:20 final size:20
Alignment explanation
Indices: 23591591--23591634 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
23591581 CCCTACATGT
*
23591591 TGTGATATGCGAACCCTATA
1 TGTGATATGCAAACCCTATA
23591611 TGTGTATATGCAAACCC-ATA
1 TGTG-ATATGCAAACCCTATA
23591631 TGTG
1 TGTG
23591635 CGAATCCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (20 bp):
TGTGATATGCAAACCCTATA
Found at i:23592343 original size:48 final size:48
Alignment explanation
Indices: 23592272--23592367 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
23592262 CAAGATCACT
*
23592272 TCGATGATCAATGTAACACCTTCGACTTAGCTGAAACTCTTAGGCCGG
1 TCGATAATCAATGTAACACCTTCGACTTAGCTGAAACTCTTAGGCCGG
*
23592320 TCGATAATCAATGTAACGCCTTCGACTTAGCTGAAACTCTTAGGCCGG
1 TCGATAATCAATGTAACACCTTCGACTTAGCTGAAACTCTTAGGCCGG
23592368 GTCGGGAGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (48 bp):
TCGATAATCAATGTAACACCTTCGACTTAGCTGAAACTCTTAGGCCGG
Found at i:23598695 original size:13 final size:13
Alignment explanation
Indices: 23598679--23598714 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
23598669 CAATGCTTTT
23598679 GAAAAGTGCTGCA
1 GAAAAGTGCTGCA
*
23598692 GAAAAGTGCTGGA
1 GAAAAGTGCTGCA
23598705 GAAAAGTGCT
1 GAAAAGTGCT
23598715 CTTGAGAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.33, T:0.17
Consensus pattern (13 bp):
GAAAAGTGCTGCA
Found at i:23598724 original size:13 final size:13
Alignment explanation
Indices: 23598708--23598737 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
23598698 TGCTGGAGAA
23598708 AAGTGCTCTTGAG
1 AAGTGCTCTTGAG
*
23598721 AAGTGCTTTTGAG
1 AAGTGCTCTTGAG
23598734 AAGT
1 AAGT
23598738 ACTTTTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.10, G:0.30, T:0.33
Consensus pattern (13 bp):
AAGTGCTCTTGAG
Found at i:23598742 original size:13 final size:13
Alignment explanation
Indices: 23598716--23598745 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
23598706 AAAAGTGCTC
*
23598716 TTGAGAAGTGCTT
1 TTGAGAAGTACTT
23598729 TTGAGAAGTACTT
1 TTGAGAAGTACTT
23598742 TTGA
1 TTGA
23598746 AAAATTTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.40
Consensus pattern (13 bp):
TTGAGAAGTACTT
Found at i:23609362 original size:3 final size:3
Alignment explanation
Indices: 23609354--23609590 Score: 112
Period size: 3 Copynumber: 77.3 Consensus size: 3
23609344 CTATTTTACC
* * *
23609354 ATT ATT ATT ATT ATT ATT ATT ATT -TGT ATC CTT ATT AAT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT
* ** * * *
23609398 ATT ATC ATT -TCCT CCT ATT ATT ATT AACCT ATT ATT ATT CTT ATT AGT
1 ATT ATT ATT AT--T ATT ATT ATT ATT -A-TT ATT ATT ATT ATT ATT ATT
*
23609446 A-T ATT ATT ATT -TCCT ATT CTT -TAT ATT ATT ATT ATT ATT ATT CATGT
1 ATT ATT ATT ATT AT--T ATT ATT AT-T ATT ATT ATT ATT ATT ATT -AT-T
* * * * * *
23609493 ATAT ATT ATT ATT GTT ATT ATT GTT ATT ATT AAT ATT CTT ATC GTT
1 AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
23609539 ACT ATT ATT TTT ATT CCTT -TT ATT AGTT ATT ATC AAT A-T ATT ATT
1 ATT ATT ATT ATT ATT -ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
23609584 ATT ATT A
1 ATT ATT A
23609591 CCACTGTATT
Statistics
Matches: 177, Mismatches: 37, Indels: 40
0.70 0.15 0.16
Matches are distributed among these distances:
2 12 0.07
3 144 0.81
4 18 0.10
5 3 0.02
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:23609969 original size:14 final size:14
Alignment explanation
Indices: 23609920--23609971 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
23609910 TAATTTCAAA
23609920 TATTT-TTTTAGCT
1 TATTTATTTTAGCT
*
23609933 TATTTATTATT-TCT
1 TATTTATT-TTAGCT
*
23609947 TTTTTATTTTAGCT
1 TATTTATTTTAGCT
*
23609961 TATTCATTTTA
1 TATTTATTTTA
23609972 CCCATTTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 7 0.23
14 22 0.71
15 2 0.06
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.69
Consensus pattern (14 bp):
TATTTATTTTAGCT
Found at i:23612108 original size:27 final size:27
Alignment explanation
Indices: 23612061--23612116 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
23612051 TAAATTAGAA
* *
23612061 AAAAAATTAAATATAATTTTTAATATT
1 AAAAAATTAAATATAAGTTTTAACATT
* *
23612088 AAAAAATTGAATTTAAGTTTTAACATT
1 AAAAAATTAAATATAAGTTTTAACATT
23612115 AA
1 AA
23612117 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (27 bp):
AAAAAATTAAATATAAGTTTTAACATT
Found at i:23613005 original size:23 final size:22
Alignment explanation
Indices: 23612979--23613024 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
23612969 TGTATATATC
23612979 TTTTAAAGATTATGCAATATACT
1 TTTTAAAGATTATGCAAT-TACT
** *
23613002 TTTTAATTATTGTGCAATTACT
1 TTTTAAAGATTATGCAATTACT
23613024 T
1 T
23613025 AATTATGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (22 bp):
TTTTAAAGATTATGCAATTACT
Found at i:23613131 original size:75 final size:75
Alignment explanation
Indices: 23613041--23613192 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 75
23613031 GATTTGAAAG
*
23613041 AATGTTACGAAATAAAATATTTTATTGAATAAAAATATCAATTTAGCCCCTGTACGTTATATGAG
1 AATGTTACGAAATAAAATATTTTATTGAATAAAAATATCAATTTAGCCCCTGTACATTATATGAG
23613106 TGAGCAAAAC
66 TGAGCAAAAC
*
23613116 AATGTTACGAAATAAAATATTTTATTGAATAAAAATATCAATTTAGCCCTTGTACATTATATGAG
1 AATGTTACGAAATAAAATATTTTATTGAATAAAAATATCAATTTAGCCCCTGTACATTATATGAG
23613181 TGAGCAAAAC
66 TGAGCAAAAC
23613191 AA
1 AA
23613193 CACTTCCATT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.32
Consensus pattern (75 bp):
AATGTTACGAAATAAAATATTTTATTGAATAAAAATATCAATTTAGCCCCTGTACATTATATGAG
TGAGCAAAAC
Found at i:23613649 original size:21 final size:24
Alignment explanation
Indices: 23613605--23613657 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 24
23613595 ACTTATATAT
*
23613605 ATATATATATTTATAATATTTAAA
1 ATATTTATATTTATAATATTTAAA
23613629 ATATTTAT-TTTA-AAT-TTTAAA
1 ATATTTATATTTATAATATTTAAA
23613650 ATGATTTA
1 AT-ATTTA
23613658 ATTGATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 8 0.30
22 8 0.30
23 4 0.15
24 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATATTTATATTTATAATATTTAAA
Found at i:23614984 original size:17 final size:17
Alignment explanation
Indices: 23614959--23615017 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
23614949 TCAATATGAC
*
23614959 TAAACAATATAATAATA
1 TAAATAATATAATAATA
*
23614976 TAAATAATATAA-AATG
1 TAAATAATATAATAATA
*
23614992 TGAAATTTAATTTAATAATA
1 T-AAA--TAATATAATAATA
23615012 TAAATA
1 TAAATA
23615018 GTAGATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.12
17 16 0.47
19 10 0.29
20 4 0.12
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAATAATATAATAATA
Found at i:23615586 original size:9 final size:9
Alignment explanation
Indices: 23615572--23615604 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
23615562 ATTCGAGTTG
23615572 ACTCGAATA
1 ACTCGAATA
*
23615581 ACTCGATTA
1 ACTCGAATA
23615590 ACTCGAATA
1 ACTCGAATA
23615599 ACTCGA
1 ACTCGA
23615605 TTTGTTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (9 bp):
ACTCGAATA
Found at i:23615595 original size:18 final size:18
Alignment explanation
Indices: 23615572--23615606 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
23615562 ATTCGAGTTG
23615572 ACTCGAATAACTCGATTA
1 ACTCGAATAACTCGATTA
23615590 ACTCGAATAACTCGATT
1 ACTCGAATAACTCGATT
23615607 TGTTTAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (18 bp):
ACTCGAATAACTCGATTA
Found at i:23625380 original size:44 final size:46
Alignment explanation
Indices: 23625320--23625488 Score: 132
Period size: 46 Copynumber: 3.7 Consensus size: 46
23625310 TATGCATGTT
*
23625320 GATGCATGTCCCAGACATGTCTTACACTAGCACAACCCT-T-A-GCC
1 GATGCATGTCCTAGACATGTCTTACACTAGC-CAACCCTGTCAGGCC
* * * * * *
23625364 GATGCGTGTCCTAGACACGTCTTACACTGGCTATCTCTGTCGAGGCC
1 GATGCATGTCCTAGACATGTCTTACACTAGCCAACCCTGTC-AGGCC
* * * *** *
23625411 GATGCATGTCCTAGACATGTCTTACTCT-GGC-ACTCATAAAATGGCT
1 GATGCATGTCCTAGACATGTCTTACACTAGCCAAC-CCTGTCA-GGCC
*
23625457 GAAGCATGTCCTAGACATGTCTTACACTAGCC
1 GATGCATGTCCTAGACATGTCTTACACTAGCC
23625489 CTTATCTGGA
Statistics
Matches: 96, Mismatches: 22, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
43 4 0.04
44 28 0.29
45 2 0.02
46 32 0.33
47 30 0.31
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (46 bp):
GATGCATGTCCTAGACATGTCTTACACTAGCCAACCCTGTCAGGCC
Found at i:23625567 original size:94 final size:92
Alignment explanation
Indices: 23625408--23625578 Score: 236
Period size: 94 Copynumber: 1.8 Consensus size: 92
23625398 CTCTGTCGAG
* * ** *
23625408 GCCGATGCATGTCCTAGACATGTCTTACTCTGGCACTCATAAAATGGCTGAAGCATGTCCTAGAC
1 GCCGATGCATGTCCCAGACATGTCTTACTCTGGCACTCATAAAACGGCCAAAGCATGTCCCAGAC
23625473 ATGTCTTACACTAGCCCTTATCTGGAT
66 ATGTCTTACACTAGCCCTTATCTGGAT
* **
23625500 GCCGATGCCATGTCCCAGACATGGTCTTA-TACTGGCTCTCATAGTACGGCCAAAGCATGTCCCA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACT-CTGGCACTCATAAAACGGCCAAAGCATGTCCCA
23625564 GACATGTCTTACACT
63 GACATGTCTTACACT
23625579 GGCGCACAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
92 7 0.10
93 14 0.21
94 47 0.69
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCTTACTCTGGCACTCATAAAACGGCCAAAGCATGTCCCAGAC
ATGTCTTACACTAGCCCTTATCTGGAT
Found at i:23625967 original size:30 final size:30
Alignment explanation
Indices: 23625922--23625981 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
23625912 ATTCACAACT
* * *
23625922 TTGGTAAAATAACCATTTTGCCCTTATGCC
1 TTGGCAAAATAACCATTTTACCCCTATGCC
*
23625952 TTGGCAAAATGACCATTTTACCCCTATGCC
1 TTGGCAAAATAACCATTTTACCCCTATGCC
23625982 CGAAAATTAA
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:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (30 bp):
TTGGCAAAATAACCATTTTACCCCTATGCC
Found at i:23629385 original size:47 final size:46
Alignment explanation
Indices: 23629265--23629446 Score: 183
Period size: 47 Copynumber: 3.9 Consensus size: 46
23629255 ATAATTTCAC
*
23629265 CCATAATGAACTCGGAACGCAACTCAACGAGCTTAGG-TGCTCACAT
1 CCATAATGAACTCGGAACGCAACTCAACGAG-TTCGGATGCTCACAT
* * * **
23629311 CCATAATGAACTCGGAACACAATTCAACAAGTTCGGATGCTTGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTCACAT
* *
23629357 CCATAAGTGAAC-CTGTAACGCAACTCAACGAGTTCGGATGCCTCATAAT
1 CCATAA-TGAACTC-GGAACGCAACTCAACGAGTTCGGATG-CTCA-CAT
* * * *
23629406 TC-TCACGAACTCGGAACGTAACTCAACGAGTTCGGAT-CTCA
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTCA
23629447 ATTTCCTAGT
Statistics
Matches: 112, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
45 8 0.07
46 42 0.38
47 54 0.48
48 5 0.04
49 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTCACAT
Found at i:23637033 original size:93 final size:92
Alignment explanation
Indices: 23636855--23637034 Score: 279
Period size: 93 Copynumber: 1.9 Consensus size: 92
23636845 CCACTTCTCC
* * * *
23636855 TGGAAGATACAGTCTAGATTTGGGTGTTCCTTTTTCCCCTTTTTTCCAATATGCTATACAGCCAG
1 TGGAAGATAAAATCTAGATTTGGGTGTTCCTTTTTCCCCTTTTTTCCAATATGCAACACAGCCAG
* *
23636920 TTTATAAAGAATTATCTAATCCCCTAT
66 TATATAAAGAAATATCTAATCCCCTAT
* *
23636947 TGGAAGATAAAATCTAGATTTGGGTGTTCTTTTTTCCCCTTTTTTTCCATTATGCAACACAGCCA
1 TGGAAGATAAAATCTAGATTTGGGTGTTCCTTTTTCCCC-TTTTTTCCAATATGCAACACAGCCA
23637012 GTATATAAAGAAATATCTAATCC
65 GTATATAAAGAAATATCTAATCC
23637035 TCAACTTTGT
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 36 0.46
93 43 0.54
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (92 bp):
TGGAAGATAAAATCTAGATTTGGGTGTTCCTTTTTCCCCTTTTTTCCAATATGCAACACAGCCAG
TATATAAAGAAATATCTAATCCCCTAT
Found at i:23637650 original size:174 final size:174
Alignment explanation
Indices: 23637360--23637709 Score: 682
Period size: 174 Copynumber: 2.0 Consensus size: 174
23637350 GCCTATAGCA
23637360 TTACTACTGCAGGTAATAATCTATTTTATGCTTACATTACATATGTTTCATAAATATATGAAGAG
1 TTACTACTGCAGGTAATAATCTATTTTATGCTTACATTACATATGTTTCATAAATATATGAAGAG
23637425 GTAAAAGGAAGTTGATATGATATGAATGTATCGGGCAGTAATCCCTATTTGAGTGGCTTAGTAAG
66 GTAAAAGGAAGTTGATATGATATGAATGTATCGGGCAGTAATCCCTATTTGAGTGGCTTAGTAAG
23637490 CATCTTTCCTCATGGTCTTTGTTTCAGCATATGAGTAAACTGTC
131 CATCTTTCCTCATGGTCTTTGTTTCAGCATATGAGTAAACTGTC
* *
23637534 TTACTACTGCAGGTAATAATGTATTTTATGCTTACATTACGTATGTTTCATAAATATATGAAGAG
1 TTACTACTGCAGGTAATAATCTATTTTATGCTTACATTACATATGTTTCATAAATATATGAAGAG
23637599 GTAAAAGGAAGTTGATATGATATGAATGTATCGGGCAGTAATCCCTATTTGAGTGGCTTAGTAAG
66 GTAAAAGGAAGTTGATATGATATGAATGTATCGGGCAGTAATCCCTATTTGAGTGGCTTAGTAAG
23637664 CATCTTTCCTCATGGTCTTTGTTTCAGCATATGAGTAAACTGTC
131 CATCTTTCCTCATGGTCTTTGTTTCAGCATATGAGTAAACTGTC
23637708 TT
1 TT
23637710 TCTATCACTT
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.37
Consensus pattern (174 bp):
TTACTACTGCAGGTAATAATCTATTTTATGCTTACATTACATATGTTTCATAAATATATGAAGAG
GTAAAAGGAAGTTGATATGATATGAATGTATCGGGCAGTAATCCCTATTTGAGTGGCTTAGTAAG
CATCTTTCCTCATGGTCTTTGTTTCAGCATATGAGTAAACTGTC
Found at i:23642143 original size:26 final size:25
Alignment explanation
Indices: 23642114--23642162 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
23642104 TTATATCAAT
*
23642114 TTTAAAAAATTATAAAATATAAAAAA
1 TTTAAAAAAGTATAAAA-ATAAAAAA
*
23642140 TTTAGAAAAGTATAAAAATAAAA
1 TTTAAAAAAGTATAAAAATAAAA
23642163 TTATAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (25 bp):
TTTAAAAAAGTATAAAAATAAAAAA
Found at i:23642148 original size:18 final size:18
Alignment explanation
Indices: 23642116--23642157 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
23642106 ATATCAATTT
*
23642116 TAAAAAATTATAAAA-TA
1 TAAAAAATTAGAAAAGTA
23642133 TAAAAAATTTAGAAAAGTA
1 TAAAAAA-TTAGAAAAGTA
23642152 TAAAAA
1 TAAAAA
23642158 TAAAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 7 0.32
19 8 0.36
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
TAAAAAATTAGAAAAGTA
Found at i:23642158 original size:18 final size:17
Alignment explanation
Indices: 23642116--23642158 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
23642106 ATATCAATTT
* *
23642116 TAAAAAATTATAAAATA
1 TAAAAATTTAGAAAATA
23642133 TAAAAAATTTAGAAAAGTA
1 T-AAAAATTTAGAAAA-TA
23642152 TAAAAAT
1 TAAAAAT
23642159 AAAATTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 18 0.82
19 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (17 bp):
TAAAAATTTAGAAAATA
Found at i:23642167 original size:14 final size:15
Alignment explanation
Indices: 23642145--23642177 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23642135 AAAAATTTAG
23642145 AAAAGTAT-AAAAAT
1 AAAAGTATAAAAAAT
*
23642159 AAAATTATAAAAAAT
1 AAAAGTATAAAAAAT
23642174 AAAA
1 AAAA
23642178 AATCATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAAGTATAAAAAAT
Found at i:23642178 original size:22 final size:23
Alignment explanation
Indices: 23642114--23642180 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 23
23642104 TTATATCAAT
23642114 TTTA-AAAAATTATAAAATATAAAAAA
1 TTTAGAAAAA-TATAAAA-AT--AAAA
*
23642140 TTTAGAAAAGTATAAAAATAAAA
1 TTTAGAAAAATATAAAAATAAAA
23642163 TTATA-AAAAATA-AAAAAT
1 TT-TAGAAAAATATAAAAAT
23642181 CATTAATTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 6 0.16
23 12 0.32
24 2 0.05
25 2 0.05
26 11 0.30
27 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (23 bp):
TTTAGAAAAATATAAAAATAAAA
Found at i:23649844 original size:19 final size:19
Alignment explanation
Indices: 23649816--23649855 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
23649806 TACAAAGCGA
23649816 ATGCTAGCACACGAA-GTGC
1 ATGCTAGCACAC-AAGGTGC
*
23649835 ATGCTGGCACACAAGGTGC
1 ATGCTAGCACACAAGGTGC
23649854 AT
1 AT
23649856 CTTGGTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.17
Consensus pattern (19 bp):
ATGCTAGCACACAAGGTGC
Found at i:23650191 original size:18 final size:18
Alignment explanation
Indices: 23650168--23650204 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
23650158 GTATATTTAT
23650168 CTAATTAACACATATAGG
1 CTAATTAACACATATAGG
23650186 CTAATTAACACATATAGG
1 CTAATTAACACATATAGG
23650204 C
1 C
23650205 AAGCACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (18 bp):
CTAATTAACACATATAGG
Found at i:23653209 original size:43 final size:43
Alignment explanation
Indices: 23653141--23653310 Score: 170
Period size: 43 Copynumber: 4.0 Consensus size: 43
23653131 AACTCGTACA
*
23653141 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAAATATCG
* *
23653184 ATGCC-ACTGTCCCAGACAG-GATCTTACATAAAATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAATCAAATATCG
* * * ** *
23653226 ATGCCGATGTCCTAGATATGGTCTTACACGTAAAT-ATCAA-ATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATG-AAATCA--AATATCG
*
23653270 ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCACATAT
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAAATAT
23653311 TGGAAATCCT
Statistics
Matches: 100, Mismatches: 17, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
42 26 0.26
43 44 0.44
44 30 0.30
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAAATATCG
Found at i:23655329 original size:17 final size:18
Alignment explanation
Indices: 23655309--23655342 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
23655299 AAAATTAATT
*
23655309 AAAATTAAAAA-ATAAAG
1 AAAATAAAAAAGATAAAG
23655326 AAAATAAAAAAGATAAA
1 AAAATAAAAAAGATAAA
23655343 ATAATTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (18 bp):
AAAATAAAAAAGATAAAG
Found at i:23655412 original size:115 final size:115
Alignment explanation
Indices: 23655190--23655427 Score: 268
Period size: 115 Copynumber: 2.0 Consensus size: 115
23655180 AAAAAACTGA
* ** * *
23655190 AATTAAATCTAAAAAATAAAAACATAAAGAAATTTAAATTAGTTTTTCCTATAAAAATTCAGATA
1 AATTAAATCTAAAAAATAAAAAAATAAAGAAAGATAAAATAATTTTTCCTATAAAAATTCAGATA
* * *
23655255 ATTTCTAGTAAAATCTCATGTTTTTTCTTTTTACTGGAAAAACTAAAATT
66 ATTTCTAGTAAAATCTAATGTTTTTTCCTTTTACTAGAAAAACTAAAATT
* * *
23655305 AATTAAAAT-TAAAAAATAAAGAAAATAAA-AAAGATAAAATAATTTTTCTTATAAAAATTGAGG
1 AATT-AAATCTAAAAAATAAA-AAAATAAAGAAAGATAAAATAATTTTTCCTATAAAAATTCAGA
* *
23655368 TAATTTCTA-TAAAATCTTAATTTTTTTTTCCTTTTA-TAAGAAAACAACTGAAATT
64 TAATTTCTAGTAAAATC-TAA-TGTTTTTTCCTTTTACT-AG-AAA-AACTAAAATT
23655423 AATTA
1 AATTA
23655428 TAAAAAATTA
Statistics
Matches: 103, Mismatches: 13, Indels: 12
0.80 0.10 0.09
Matches are distributed among these distances:
114 7 0.07
115 54 0.52
116 25 0.24
117 4 0.04
118 13 0.13
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.38
Consensus pattern (115 bp):
AATTAAATCTAAAAAATAAAAAAATAAAGAAAGATAAAATAATTTTTCCTATAAAAATTCAGATA
ATTTCTAGTAAAATCTAATGTTTTTTCCTTTTACTAGAAAAACTAAAATT
Found at i:23663010 original size:30 final size:31
Alignment explanation
Indices: 23662940--23663010 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 31
23662930 AACCGAACAT
*
23662940 TATTCTAT-TTTTTTAATTCATATATAATTAA
1 TATT-TATATTTTTTAATTCATATAAAATTAA
23662971 T-TTTA-ATTTTTT-ATT-ATATAAAATTAAA
1 TATTTATATTTTTTAATTCATATAAAATT-AA
23662999 TATTTATATTTT
1 TATTTATATTTT
23663011 AAAAAGTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
27 9 0.26
28 6 0.17
29 12 0.34
30 7 0.20
31 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (31 bp):
TATTTATATTTTTTAATTCATATAAAATTAA
Found at i:23664087 original size:62 final size:62
Alignment explanation
Indices: 23664011--23664134 Score: 203
Period size: 62 Copynumber: 2.0 Consensus size: 62
23664001 ATGTTATTTG
*
23664011 AATGAGTAATTAGGTTCAAGTGGTAAATCCATAAAGTCAAGTGGTTTTAGAAAATGAGGTAT
1 AATGAGTAATTAGGTTCAAGTGGTAAATCCATAAAGTCAAGTGATTTTAGAAAATGAGGTAT
* ** *
23664073 AATGAGTAATTAGGTTTAAGTGGTAAATCTTTAAAGTTAAGTGATTTTAGAAAATGAGGTAT
1 AATGAGTAATTAGGTTCAAGTGGTAAATCCATAAAGTCAAGTGATTTTAGAAAATGAGGTAT
23664135 CGAGACCTCG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (62 bp):
AATGAGTAATTAGGTTCAAGTGGTAAATCCATAAAGTCAAGTGATTTTAGAAAATGAGGTAT
Found at i:23682026 original size:28 final size:28
Alignment explanation
Indices: 23681994--23682048 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
23681984 GCAGAGTTTC
23681994 CCTCTTCATTGTTTTACAATATTTTATG
1 CCTCTTCATTGTTTTACAATATTTTATG
23682022 CCTCTTCATTGTTTTACAATATTTTAT
1 CCTCTTCATTGTTTTACAATATTTTAT
23682049 ATATTTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.05, T:0.55
Consensus pattern (28 bp):
CCTCTTCATTGTTTTACAATATTTTATG
Found at i:23684596 original size:29 final size:29
Alignment explanation
Indices: 23684559--23684614 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
23684549 AAGCTTCTTC
23684559 AAAGAATGAAATATTCACAAAAAGGTGTA
1 AAAGAATGAAATATTCACAAAAAGGTGTA
* *
23684588 AAAGCATGAAATATTCATAAAAAGGTG
1 AAAGAATGAAATATTCACAAAAAGGTG
23684615 CAGTAGTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.54, C:0.07, G:0.18, T:0.21
Consensus pattern (29 bp):
AAAGAATGAAATATTCACAAAAAGGTGTA
Found at i:23688595 original size:76 final size:77
Alignment explanation
Indices: 23688468--23688628 Score: 297
Period size: 76 Copynumber: 2.1 Consensus size: 77
23688458 TGATTTTAGA
*
23688468 AATTAGGCTAAAATACTAAATAAGTCCTTCGAAAACAATTAAAAAATCAATTAAGCTCCTTATCT
1 AATTAAGCTAAAATACTAAATAAGTCCTTCGAAAACAATTAAAAAATCAATTAAGCTCCTTATCT
23688533 AAAGGTGCACCC
66 AAAGGTGCACCC
23688545 AATTAAGCT-AAATACTAAATAAGTCCTTCGAAAACAATTAAAAAATCAATTAAGCTCCTTATCT
1 AATTAAGCTAAAATACTAAATAAGTCCTTCGAAAACAATTAAAAAATCAATTAAGCTCCTTATCT
*
23688609 AAAGGTGCACCT
66 AAAGGTGCACCC
23688621 AATTAAGC
1 AATTAAGC
23688629 CTCTTGAATT
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
76 74 0.90
77 8 0.10
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.27
Consensus pattern (77 bp):
AATTAAGCTAAAATACTAAATAAGTCCTTCGAAAACAATTAAAAAATCAATTAAGCTCCTTATCT
AAAGGTGCACCC
Found at i:23697345 original size:16 final size:16
Alignment explanation
Indices: 23697324--23697363 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
23697314 ATGGCTTCTC
23697324 AAGATACAACCAAATA
1 AAGATACAACCAAATA
23697340 AAGATACAACCAAATA
1 AAGATACAACCAAATA
23697356 AAGATACA
1 AAGATACA
23697364 TCCTGAAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.62, C:0.17, G:0.07, T:0.12
Consensus pattern (16 bp):
AAGATACAACCAAATA
Found at i:23701140 original size:41 final size:44
Alignment explanation
Indices: 23701039--23701153 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 44
23701029 TATTGCAAAT
*
23701039 CTTATCGCTCTGAAGTTGCAGTAGAGCAGATTAAAACTATAAAC
1 CTTATCCCTCTGAAGTTGCAGTAGAGCAGATTAAAACTATAAAC
* * **
23701083 CTTATCCCTCTGAAGTTGCAGTAGAGCAGGTTGAAA-T-T-AGT
1 CTTATCCCTCTGAAGTTGCAGTAGAGCAGATTAAAACTATAAAC
*
23701124 CTTATCTCCT-TGAAGTTGCAGTGGAGCAGA
1 CTTATC-CCTCTGAAGTTGCAGTAGAGCAGA
23701154 CTGAAGATAG
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 25 0.40
42 4 0.06
43 1 0.02
44 33 0.52
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (44 bp):
CTTATCCCTCTGAAGTTGCAGTAGAGCAGATTAAAACTATAAAC
Found at i:23701487 original size:44 final size:44
Alignment explanation
Indices: 23701320--23701522 Score: 154
Period size: 44 Copynumber: 4.6 Consensus size: 44
23701310 CATGGCGAAT
* * * * * *
23701320 CTTATCTCCCTGAAGTTGCAGAGGAGCAGATTGAAGCCACTAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAAC
* * * ** * * *
23701364 CTTTTCTCCTTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTA-CAAAC
* * * * * * *
23701409 TTTACCTCTCTGAAGTTGCATTAGAGCAGATTAAAGCTATAAAC
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAAC
* * * **
23701453 CTTATCTCCTTAAAGTTGCAGTGGAGCAGGTTAAAGTTACAAGT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAAC
*
23701497 CTTATCTCCCTGAAGTTGCAGTGGAG
1 CTTATCTCCCTAAAGTTGCAGTGGAG
23701523 TGGATCGACT
Statistics
Matches: 123, Mismatches: 35, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
44 91 0.74
45 32 0.26
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (44 bp):
CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAAC
Found at i:23701948 original size:3 final size:3
Alignment explanation
Indices: 23701940--23701970 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
23701930 ATCTACTTAT
*
23701940 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
23701971 CATTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:23702086 original size:27 final size:26
Alignment explanation
Indices: 23702047--23702118 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 26
23702037 ATTTTATCTG
* *
23702047 TTTATTTACTTATTTTTTAACTTGTTTGT
1 TTTATTT--TTATTTTTTAA-TTATTTAT
*
23702076 TTTATTTTTATTTCTTTTATTATTTAT
1 TTTATTTTTATTT-TTTAATTATTTAT
*
23702103 CTTATTTTTATTTTTT
1 TTTATTTTTATTTTTT
23702119 GCTCTTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 3 0.08
27 24 0.63
28 4 0.11
29 7 0.18
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (26 bp):
TTTATTTTTATTTTTTAATTATTTAT
Found at i:23702927 original size:3 final size:3
Alignment explanation
Indices: 23702921--23702955 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
23702911 GGTTGCGACA
23702921 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
23702956 CTTGTTTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.