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 14 of 290
Found at i:4890115 original size:14 final size:14
Alignment explanation
Indices: 4890096--4890125 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4890086 TAAGAAAGGA
4890096 GGCATGACTATTGT
1 GGCATGACTATTGT
*
4890110 GGCATGACTGTTGT
1 GGCATGACTATTGT
4890124 GG
1 GG
4890126 TTAATGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.13, G:0.37, T:0.33
Consensus pattern (14 bp):
GGCATGACTATTGT
Found at i:4894222 original size:18 final size:17
Alignment explanation
Indices: 4894201--4894258 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 17
4894191 TCAATATATG
4894201 TTTTATTCATTATATTAT
1 TTTTATT-ATTATATTAT
*
4894219 TTTTATTATATATATTAA
1 TTTTATTAT-TATATTAT
*
4894237 TTGTATTATT-TATTAT
1 TTTTATTATTATATTAT
*
4894253 TATTAT
1 TTTTAT
4894259 GTACATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 9 0.26
17 3 0.09
18 22 0.65
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTTATTATTATATTAT
Found at i:4895956 original size:46 final size:46
Alignment explanation
Indices: 4895904--4896077 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
4895894 TTTGGGCATT
*
4895904 CGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
* * * *
4895950 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G--TC
* *
4895997 C-AAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAAGCC
1 CGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
*
4896043 CGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4896078 GCAGGTTACA
Statistics
Matches: 105, Mismatches: 12, Indels: 22
0.76 0.09 0.16
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 59 0.56
47 27 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
Found at i:4896008 original size:93 final size:93
Alignment explanation
Indices: 4895898--4896070 Score: 303
Period size: 93 Copynumber: 1.9 Consensus size: 93
4895888 CGGATATTTG
* * *
4895898 GGCATTCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAAGCCCGAACTCGTTGAG
4895963 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
4895991 GGCATTC-AAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAAGCCCGAACTCGTTGA
1 GGCATTCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAAGCCCGAACTCGTTGA
4896055 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAGTTCG
4896071 CTTATGGGCA
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GGCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAAGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:4899430 original size:3 final size:3
Alignment explanation
Indices: 4899419--4899451 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
4899409 CTTCTTTTTC
4899419 TTA TCTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TT
4899452 TGTTTATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4901156 original size:23 final size:23
Alignment explanation
Indices: 4901130--4901173 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4901120 TTATTTTCAC
* *
4901130 TTTGTTTTTCTTTTTCTTTTTCT
1 TTTGTTTTTATTTTTATTTTTCT
4901153 TTTGTTTTTATTTTTATTTTT
1 TTTGTTTTTATTTTTATTTTT
4901174 ATTTCTCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.84
Consensus pattern (23 bp):
TTTGTTTTTATTTTTATTTTTCT
Found at i:4909817 original size:28 final size:29
Alignment explanation
Indices: 4909772--4909826 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
4909762 CAAAAAGTAT
*
4909772 TTTATGTATATATTTATT-ATTTAAATGG
1 TTTATGTATATATTTATTGATTAAAATGG
*
4909800 TTTATTTATAT-TTATATTGATTAAAAT
1 TTTATGTATATATT-TATTGATTAAAAT
4909827 ACAATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 14 0.61
29 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (29 bp):
TTTATGTATATATTTATTGATTAAAATGG
Found at i:4910243 original size:29 final size:28
Alignment explanation
Indices: 4910185--4910263 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 28
4910175 TAAAGTTCAG
* *
4910185 GGATTAGTGGG-TAAAGGTTAAGGGTTAT
1 GGATTA-TGGGTTTAAGGTTAAGGGTCAT
4910213 GGATTATGGGTTTAAGGATTAAGGGTCAT
1 GGATTATGGGTTTAAGG-TTAAGGGTCAT
*
4910242 GGGTTATGGGTTTAATGGTTAA
1 GGATTATGGGTTTAA-GGTTAA
4910264 AGGGATATGG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 4 0.09
28 11 0.24
29 28 0.62
30 2 0.04
ACGTcount: A:0.27, C:0.01, G:0.37, T:0.35
Consensus pattern (28 bp):
GGATTATGGGTTTAAGGTTAAGGGTCAT
Found at i:4910750 original size:26 final size:27
Alignment explanation
Indices: 4910677--4910751 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 27
4910667 AATAATTTAA
4910677 AATTTTAAAGATTTCAAA-TTTAGAAT
1 AATTTTAAAGATTTCAAATTTTAGAAT
* *
4910703 AAATTTCAAGATTTCAAATTTTA-AAT
1 AATTTTAAAGATTTCAAATTTTAGAAT
*
4910729 AATTTTAAATATTTCAAATTTTA
1 AATTTTAAAGATTTCAAATTTTA
4910752 TCTAATTCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 39 0.91
27 4 0.09
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (27 bp):
AATTTTAAAGATTTCAAATTTTAGAAT
Found at i:4910884 original size:18 final size:18
Alignment explanation
Indices: 4910863--4910897 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4910853 TATAGTTGAT
*
4910863 TTTTTTAATT-TATATTA
1 TTTTTAAATTATATATTA
4910880 TTTTTAAATTATATATTA
1 TTTTTAAATTATATATTA
4910898 AATAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTAAATTATATATTA
Found at i:4911369 original size:14 final size:13
Alignment explanation
Indices: 4911332--4911365 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
4911322 CCTTAAGTGT
4911332 TTTTCCCCTAAAA
1 TTTTCCCCTAAAA
*
4911345 CTTTCCCCTAAAA
1 TTTTCCCCTAAAA
4911358 TTTTCCCC
1 TTTTCCCC
4911366 CTAACCCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.38, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTTCCCCTAAAA
Found at i:4915018 original size:9 final size:9
Alignment explanation
Indices: 4915004--4915120 Score: 108
Period size: 9 Copynumber: 12.3 Consensus size: 9
4914994 CTTAAAGAAA
4915004 TTACATAAC
1 TTACATAAC
4915013 TTACATAAC
1 TTACATAAC
* *
4915022 TCATATAAC
1 TTACATAAC
*
4915031 TTACATAAT
1 TTACATAAC
4915040 TTACATAACAAC
1 TTACAT---AAC
4915052 TTACATAAC
1 TTACATAAC
*
4915061 TCACATAAC
1 TTACATAAC
*
4915070 TTACATAAT
1 TTACATAAC
*
4915079 TTACATATC
1 TTACATAAC
*
4915088 TCACATAAC
1 TTACATAAC
*
4915097 ATACATAACAAC
1 TTACAT---AAC
4915109 TTACATAAC
1 TTACATAAC
4915118 TTA
1 TTA
4915121 ACTAATACAT
Statistics
Matches: 86, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
9 70 0.81
12 16 0.19
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.32
Consensus pattern (9 bp):
TTACATAAC
Found at i:4915062 original size:39 final size:39
Alignment explanation
Indices: 4915010--4915085 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
4915000 GAAATTACAT
*
4915010 AACTTACATAACTCATATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
4915049 AACTTACATAACTCACATAACTTACATAATTTACATA
1 AACTTACATAACTCACATAACTTACATAATTTACATA
4915086 TCTCACATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:4915083 original size:48 final size:49
Alignment explanation
Indices: 4915004--4915120 Score: 141
Period size: 48 Copynumber: 2.4 Consensus size: 49
4914994 CTTAAAGAAA
* * *
4915004 TTACATAACTTACATAACTCATATAACTTACATAAT-TTACATAACA-AC
1 TTACATAACTTACATAACTTACATAACTTACAT-ATCTCACATAACATAC
* *
4915052 TTACATAACTCACATAACTTACATAATTTACATATCTCACATAACATAC
1 TTACATAACTTACATAACTTACATAACTTACATATCTCACATAACATAC
* *
4915101 ATA-ACAACTTACATAACTTA
1 TTACATAACTTACATAACTTA
4915121 ACTAATACAT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 2 0.03
48 53 0.90
49 4 0.07
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.32
Consensus pattern (49 bp):
TTACATAACTTACATAACTTACATAACTTACATATCTCACATAACATAC
Found at i:4915094 original size:57 final size:57
Alignment explanation
Indices: 4915006--4915118 Score: 163
Period size: 57 Copynumber: 2.0 Consensus size: 57
4914996 TAAAGAAATT
* * **
4915006 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAACATACATAACAACTTACATAACTC
* * *
4915063 ACATAACTTACATAATTTACATATCTCACATAACATACATAACAACTTACATAACT
1 ACATAACTTACATAACTCACATAACTCACATAACATACATAACAACTTACATAACT
4915119 TAACTAATAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAACATACATAACAACTTACATAACTC
Found at i:4920719 original size:15 final size:16
Alignment explanation
Indices: 4920694--4920723 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4920684 GCAACAACTT
4920694 AGAGCGGAGGCAGCAA
1 AGAGCGGAGGCAGCAA
4920710 AGAG-GGAGGCAGCA
1 AGAGCGGAGGCAGCA
4920724 GCTGCAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.17, G:0.47, T:0.00
Consensus pattern (16 bp):
AGAGCGGAGGCAGCAA
Found at i:4920998 original size:33 final size:33
Alignment explanation
Indices: 4920961--4921040 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 33
4920951 AGAATTAATT
* *
4920961 TTTTTGGTTGTATTTTTTATGCTAAATTTGCTG
1 TTTTTGGTTGCATTTTTTATACTAAATTTGCTG
* * *
4920994 TTTTTGGCTGCA--TTTTATACTATATTTGTTG
1 TTTTTGGTTGCATTTTTTATACTAAATTTGCTG
* *
4921025 TATTTGGTTGGATTTT
1 TTTTTGGTTGCATTTT
4921041 AATGCAGGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
31 25 0.68
33 12 0.32
ACGTcount: A:0.15, C:0.06, G:0.19, T:0.60
Consensus pattern (33 bp):
TTTTTGGTTGCATTTTTTATACTAAATTTGCTG
Found at i:4921141 original size:43 final size:42
Alignment explanation
Indices: 4921118--4921277 Score: 194
Period size: 43 Copynumber: 3.7 Consensus size: 42
4921108 GAAAAAGCGT
*
4921118 CGCTAAAAGCCTTGACTTTTAGCGGCGCTTCTCCCACAAACGC
1 CGCTAAAAGCCTTGACTTTTAGCGGCG-TTTTCCCACAAACGC
* * * *
4921161 CGCTAAAATCCTTGACTTTTAGCGACGCTTTTCCTACAAACGT
1 CGCTAAAAGCCTTGACTTTTAGCGGCG-TTTTCCCACAAACGC
* * * *
4921204 CACTAAAAGTCTTGACTTTTAGCAGCGCTTTTCCCATAAACGC
1 CGCTAAAAGCCTTGACTTTTAGCGGCG-TTTTCCCACAAACGC
* *
4921247 CGCTAAAATCCTTGACTTTTAGCGACGTTTT
1 CGCTAAAAGCCTTGACTTTTAGCGGCGTTTT
4921278 TTTCAATAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 4 0.04
43 95 0.96
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.31
Consensus pattern (42 bp):
CGCTAAAAGCCTTGACTTTTAGCGGCGTTTTCCCACAAACGC
Found at i:4921232 original size:86 final size:86
Alignment explanation
Indices: 4921115--4921278 Score: 274
Period size: 86 Copynumber: 1.9 Consensus size: 86
4921105 GTAGAAAAAG
* *
4921115 CGTCGCTAAAAGCCTTGACTTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAATCCTTGACTTT
1 CGTCACTAAAAGCCTTGACTTTTAGCAGCGCTTCTCCCACAAACGCCGCTAAAATCCTTGACTTT
4921180 TAGCGACGCTTTTCCTACAAA
66 TAGCGACGCTTTTCCTACAAA
* * *
4921201 CGTCACTAAAAGTCTTGACTTTTAGCAGCGCTTTTCCCATAAACGCCGCTAAAATCCTTGACTTT
1 CGTCACTAAAAGCCTTGACTTTTAGCAGCGCTTCTCCCACAAACGCCGCTAAAATCCTTGACTTT
*
4921266 TAGCGACGTTTTT
66 TAGCGACGCTTTT
4921279 TTCAATAAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 72 1.00
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (86 bp):
CGTCACTAAAAGCCTTGACTTTTAGCAGCGCTTCTCCCACAAACGCCGCTAAAATCCTTGACTTT
TAGCGACGCTTTTCCTACAAA
Found at i:4921299 original size:44 final size:43
Alignment explanation
Indices: 4921122--4921299 Score: 171
Period size: 43 Copynumber: 4.1 Consensus size: 43
4921112 AAGCGTCGCT
* * * * * * *
4921122 AAAAGCCTTGACTTTTAGCGGCGCTTCTCCCACAAACGCCGCT
1 AAAATCCTTGACTTTTAGCGACGCTTTTCCAATAAACGCCACA
* * *
4921165 AAAATCCTTGACTTTTAGCGACGCTTTTCCTACAAACGTCACTA
1 AAAATCCTTGACTTTTAGCGACGCTTTTCCAATAAACGCCAC-A
* * * *
4921209 AAAGT-CTTGACTTTTAGC-AGCGCTTTTCCCATAAACGCCGCT
1 AAAATCCTTGACTTTTAGCGA-CGCTTTTCCAATAAACGCCACA
* *
4921251 AAAATCCTTGACTTTTAGCGACGTTTTTTTCAATAAACGCCACA
1 AAAATCCTTGACTTTTAGCGACG-CTTTTCCAATAAACGCCACA
4921295 AAAAT
1 AAAAT
4921300 TTGTGGCATT
Statistics
Matches: 111, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
42 5 0.05
43 81 0.73
44 25 0.23
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.30
Consensus pattern (43 bp):
AAAATCCTTGACTTTTAGCGACGCTTTTCCAATAAACGCCACA
Found at i:4928389 original size:37 final size:39
Alignment explanation
Indices: 4928342--4928416 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 39
4928332 TATGTGAAAA
* *
4928342 TTAAATTTTACA-ATTTTTACAATTTAGT-CTATAAAATT
1 TTAAATTTTACATAGTTTTACAATTCAGTCCTA-AAAATT
4928380 TTAAA-TTTACATAGTTTTACAATTCAGTCCTAAAAAT
1 TTAAATTTTACATAGTTTTACAATTCAGTCCTAAAAAT
4928417 CAGATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 6 0.18
38 24 0.73
39 3 0.09
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (39 bp):
TTAAATTTTACATAGTTTTACAATTCAGTCCTAAAAATT
Found at i:4930800 original size:20 final size:21
Alignment explanation
Indices: 4930777--4930825 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
4930767 AATTATATTG
*
4930777 AATTGAAAAAAAATAT-AGTT
1 AATTGAAAAAAAATATGAATT
**
4930797 AATT-AATTAAAATATGAATT
1 AATTGAAAAAAAATATGAATT
4930817 AATTGAAAA
1 AATTGAAAA
4930826 CTGAAAAGTG
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
19 9 0.41
20 11 0.50
21 2 0.09
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (21 bp):
AATTGAAAAAAAATATGAATT
Found at i:4931011 original size:6 final size:6
Alignment explanation
Indices: 4931000--4931027 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4930990 TGTCAGATAT
4931000 TGTTAC TGTTAC TGTTAC TGTTAC TGTT
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTT
4931028 CCGGATTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.54
Consensus pattern (6 bp):
TGTTAC
Found at i:4931464 original size:18 final size:18
Alignment explanation
Indices: 4931191--4931468 Score: 182
Period size: 18 Copynumber: 15.1 Consensus size: 18
4931181 AAAGGTATAA
*
4931191 AATAACTGATTATTACTG
1 AATAACTGATTGTTACTG
* * * *
4931209 AATAATTGACTATTACCG
1 AATAACTGATTGTTACTG
* *
4931227 AATAAGTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
4931245 AATAACTGAATATTACTG
1 AATAACTGATTGTTACTG
* **
4931263 AATAATTGATCATTACTG
1 AATAACTGATTGTTACTG
* * *
4931281 AATAATTGATTGTCATTG
1 AATAACTGATTGTTACTG
* *
4931299 AATGACTGACTGTTACTG
1 AATAACTGATTGTTACTG
*
4931317 AATAACTTAATTGTTACTG
1 AATAAC-TGATTGTTACTG
*
4931336 AATATCTGATT-TTACTG
1 AATAACTGATTGTTACTG
* *
4931353 AATAATTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
4931371 GATAACCGATCAATTGATCGATACTG
1 AATAA-C--T-GATTG-T---TACTG
* * *
4931397 AATAACTGGTTATTATTG
1 AATAACTGATTGTTACTG
* *
4931415 AATAATTGATTGTTACCG
1 AATAACTGATTGTTACTG
*
4931433 AATAACTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
4931451 AATAAATAATTGTT-CTG
1 AATAACTGATTGTTACTG
4931468 A
1 A
4931469 GTGTTAATGA
Statistics
Matches: 201, Mismatches: 49, Indels: 21
0.74 0.18 0.08
Matches are distributed among these distances:
17 18 0.09
18 149 0.74
19 15 0.07
21 2 0.01
22 5 0.02
23 2 0.01
25 1 0.00
26 9 0.04
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (18 bp):
AATAACTGATTGTTACTG
Found at i:4932656 original size:13 final size:12
Alignment explanation
Indices: 4932638--4932676 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
4932628 TTTCTTCCAA
4932638 TTTTATAACTTTT
1 TTTTATAA-TTTT
4932651 TTTTATAAATTTT
1 TTTTAT-AATTTT
*
4932664 GTTTATAATTTT
1 TTTTATAATTTT
4932676 T
1 T
4932677 ATGATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 15 0.65
14 2 0.09
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTTATAATTTT
Found at i:4933376 original size:30 final size:31
Alignment explanation
Indices: 4933342--4933404 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
4933332 TAAATTTGAA
4933342 AATATCAAGATATT-TAAATATTAATA-TATT
1 AATATCAA-ATATTATAAATATTAATATTATT
* *
4933372 AATATCAAATATTATAATTTTTAATATTATT
1 AATATCAAATATTATAAATATTAATATTATT
4933403 AA
1 AA
4933405 ACATATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.17
30 18 0.62
31 6 0.21
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (31 bp):
AATATCAAATATTATAAATATTAATATTATT
Found at i:4940095 original size:14 final size:14
Alignment explanation
Indices: 4940076--4940107 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4940066 ATTATCATGG
4940076 AAGGATTTTCACAT
1 AAGGATTTTCACAT
4940090 AAGGATTTTCACAT
1 AAGGATTTTCACAT
4940104 AAGG
1 AAGG
4940108 CAAGGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (14 bp):
AAGGATTTTCACAT
Found at i:4948927 original size:24 final size:24
Alignment explanation
Indices: 4948900--4948948 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
4948890 CGGAAGAGGA
4948900 GAGTTTTCGAT-GATATTGGCTGAG
1 GAGTTTTC-ATAGATATTGGCTGAG
* *
4948924 GAGTTTTCATAGTTTTTGGCTGAG
1 GAGTTTTCATAGATATTGGCTGAG
4948948 G
1 G
4948949 GATTTTGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.18, C:0.08, G:0.33, T:0.41
Consensus pattern (24 bp):
GAGTTTTCATAGATATTGGCTGAG
Found at i:4955213 original size:17 final size:18
Alignment explanation
Indices: 4955179--4955214 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
4955169 TCATTGAAGT
4955179 TAATTTTATAAGTTTTAA
1 TAATTTTATAAGTTTTAA
*
4955197 TAATTTT-TAATTTTTAA
1 TAATTTTATAAGTTTTAA
4955214 T
1 T
4955215 TTTTATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TAATTTTATAAGTTTTAA
Found at i:4956907 original size:33 final size:35
Alignment explanation
Indices: 4956827--4956909 Score: 98
Period size: 33 Copynumber: 2.4 Consensus size: 35
4956817 AGCAGAGCTC
4956827 CTACTTATGCTTCTCCTAGAAGATCTTACAGGACTT
1 CTACTTATGCTTCTCC-AGAAGATCTTACAGGACTT
** * *
4956863 CCGCTAATGCTTCTCC-G-AGATCTTGCAGGACTT
1 CTACTTATGCTTCTCCAGAAGATCTTACAGGACTT
*
4956896 CTACTTGTGCTTCT
1 CTACTTATGCTTCT
4956910 TTTTGAAAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
33 25 0.64
34 1 0.03
36 13 0.33
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (35 bp):
CTACTTATGCTTCTCCAGAAGATCTTACAGGACTT
Found at i:4960899 original size:84 final size:84
Alignment explanation
Indices: 4960755--4960924 Score: 243
Period size: 84 Copynumber: 2.0 Consensus size: 84
4960745 AAAGCATGTG
* * * *
4960755 CATAACACAAATACTACAACGTTTAAAACATTTCCATGAAATGATTGAATTTTAATATATTAAAA
1 CATAACACAAATACGACAACGTTCAAAACATTTCCATGAAATAATTGAATTTTAAAATATTAAAA
*
4960820 GAAAGGAGAATCCTGTACC
66 GAAAGGAGAATCCTGCACC
* * *
4960839 CATAACACAAATAGGAC-ACTGTTCAAATCATTTCCATGAAATAATTGGATTTTAAAATATTAAA
1 CATAACACAAATACGACAAC-GTTCAAAACATTTCCATGAAATAATTGAATTTTAAAATATTAAA
*
4960903 AGAAAGGAGAATCTTGCACC
65 AGAAAGGAGAATCCTGCACC
4960923 CA
1 CA
4960925 CTCTTCATTA
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
83 2 0.03
84 74 0.97
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.28
Consensus pattern (84 bp):
CATAACACAAATACGACAACGTTCAAAACATTTCCATGAAATAATTGAATTTTAAAATATTAAAA
GAAAGGAGAATCCTGCACC
Found at i:4967065 original size:36 final size:35
Alignment explanation
Indices: 4967018--4967129 Score: 102
Period size: 36 Copynumber: 3.2 Consensus size: 35
4967008 CTCCTACTTA
4967018 TGCTTCTCCTAGAAGATCTTACAGGACTTCTGCTAG
1 TGCTTCTCCTA-AAGATCTTACAGGACTTCTGCTAG
* ** * *
4967054 TGCTTCTCCT--AGACCTTATGGGGCTTCTGCTAA
1 TGCTTCTCCTAAAGATCTTACAGGACTTCTGCTAG
* * * * *
4967087 TGCTTCTCCGAAAAGATCTTGCAGGACTTTTACTTG
1 TGCTTCTCC-TAAAGATCTTACAGGACTTCTGCTAG
4967123 TGCTTCT
1 TGCTTCT
4967130 TTTTGAAAGT
Statistics
Matches: 58, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
33 27 0.47
36 31 0.53
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.37
Consensus pattern (35 bp):
TGCTTCTCCTAAAGATCTTACAGGACTTCTGCTAG
Found at i:4992874 original size:23 final size:23
Alignment explanation
Indices: 4992827--4992871 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
4992817 TTCTTTTATC
4992827 TTTTCACTATTCAATTTCCTTTG
1 TTTTCACTATTCAATTTCCTTTG
*
4992850 TTTTCA-TATTCGATTT-CTTTG
1 TTTTCACTATTCAATTTCCTTTG
4992871 T
1 T
4992872 GTTAGATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 9 0.43
23 6 0.29
ACGTcount: A:0.16, C:0.18, G:0.07, T:0.60
Consensus pattern (23 bp):
TTTTCACTATTCAATTTCCTTTG
Found at i:4993416 original size:19 final size:19
Alignment explanation
Indices: 4993374--4993416 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4993364 TCCATTTATT
*
4993374 TTTAATTCATTTTATTCTA
1 TTTAATTCATTTTATACTA
*
4993393 GTTAATT-ATTTTTATACTA
1 TTTAATTCA-TTTTATACTA
4993412 TTTAA
1 TTTAA
4993417 GATTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTAATTCATTTTATACTA
Found at i:4997919 original size:23 final size:23
Alignment explanation
Indices: 4997859--4997922 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
4997849 ATAATATTTG
*
4997859 AAATTTACAATTTTGGATTAATCT
1 AAATTTA-AATTTTGGATGAATCT
*
4997883 AAATTT-ATTATTTGGATAGAAT-T
1 AAATTTAAAT-TTTGGAT-GAATCT
4997906 AAATTTAAATTTTGGAT
1 AAATTTAAATTTTGGAT
4997923 TTTAATCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 2 0.06
23 21 0.62
24 11 0.32
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (23 bp):
AAATTTAAATTTTGGATGAATCT
Found at i:5000477 original size:38 final size:39
Alignment explanation
Indices: 5000393--5000527 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
5000383 ACCAATATGG
*
5000393 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
5000432 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
5000470 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
5000511 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
5000528 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:5011117 original size:28 final size:28
Alignment explanation
Indices: 5011077--5011132 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
5011067 AAAATATAGG
5011077 GACTAGAAAAGAAGAAATTTTCTTCATT
1 GACTAGAAAAGAAGAAATTTTCTTCATT
5011105 GACTAGAAAAGAAGAAATTTTCTTCATT
1 GACTAGAAAAGAAGAAATTTTCTTCATT
5011133 CTGGCAGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (28 bp):
GACTAGAAAAGAAGAAATTTTCTTCATT
Found at i:5017699 original size:5 final size:5
Alignment explanation
Indices: 5017689--5017720 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
5017679 AGGTTATCAA
5017689 GCTAG GCTAG GCTAG GCTAG GCTAG GCTAG GC
1 GCTAG GCTAG GCTAG GCTAG GCTAG GCTAG GC
5017721 ATAAAAGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.22, G:0.41, T:0.19
Consensus pattern (5 bp):
GCTAG
Found at i:5020411 original size:42 final size:42
Alignment explanation
Indices: 5020363--5020447 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
5020353 CATGAGTACC
5020363 TAAATTGCAAGCTTTTTATGTTAAGAGCCTGAAATAAAAACA
1 TAAATTGCAAGCTTTTTATGTTAAGAGCCTGAAATAAAAACA
5020405 TAAATTGCAAGCTTTTTATGTTAAGAGCCTGAAATAAAAACA
1 TAAATTGCAAGCTTTTTATGTTAAGAGCCTGAAATAAAAACA
5020447 T
1 T
5020448 TTAATAGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (42 bp):
TAAATTGCAAGCTTTTTATGTTAAGAGCCTGAAATAAAAACA
Found at i:5027174 original size:188 final size:188
Alignment explanation
Indices: 5026852--5027201 Score: 477
Period size: 188 Copynumber: 1.9 Consensus size: 188
5026842 AAATGAAGAA
* * * ** *
5026852 GGTTTAAGGAACGCCCACAAACTACATTTAAGTTAGAAATTTAGTAACTCGGGCTTAAGCACCAA
1 GGTTCAAGGAACGCCCACAAACTACATTTAAGTTAGAAATTTAGCAACCCAAGCGTAAGCACCAA
** * * *
5026917 TGCATGCAGGAAGCATCTCAAAGTAAAGAAAAAAGCTAGAAGTCTGAACAGCATACAGAGGCAAT
66 TGCAAACAAGAAGCATCTCAAAGTAAAGAAAAAAGCTACAAGTCAGAACAGCATACAGAGGCAAT
*
5026982 TAACCTAATTTATGCAAAAGTACCACATGAAGATAGAAATACCAGTGTTGCTATCTTG
131 TAACCTAATTTATGCAAAAATACCACATGAAGATAGAAATACCAGTGTTGCTATCTTG
* * * * **
5027040 GGTTCAAGGAACTCCCACAAACTACATTTCAGTTATAAATTTAGCAACCCAAGCGTAAGTACCGG
1 GGTTCAAGGAACGCCCACAAACTACATTTAAGTTAGAAATTTAGCAACCCAAGCGTAAGCACCAA
* * * *
5027105 TGCAAACAAGCAGCATCTCAAAGTAAGGCAAAAAGCTACAAGTCCAG-GCAGCATACAGAGGCAA
66 TGCAAACAAGAAGCATCTCAAAGTAAAGAAAAAAGCTACAAGT-CAGAACAGCATACAGAGGCAA
*
5027169 TTAACCTAATTTATGCAAAAATCCCACATGAAG
130 TTAACCTAATTTATGCAAAAATACCACATGAAG
5027202 GCAGGAAATG
Statistics
Matches: 138, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
188 136 0.99
189 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (188 bp):
GGTTCAAGGAACGCCCACAAACTACATTTAAGTTAGAAATTTAGCAACCCAAGCGTAAGCACCAA
TGCAAACAAGAAGCATCTCAAAGTAAAGAAAAAAGCTACAAGTCAGAACAGCATACAGAGGCAAT
TAACCTAATTTATGCAAAAATACCACATGAAGATAGAAATACCAGTGTTGCTATCTTG
Found at i:5031373 original size:22 final size:22
Alignment explanation
Indices: 5031347--5031391 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5031337 GTAAGTTAGT
5031347 ATCAATAGGCAGAAGAAGATCA
1 ATCAATAGGCAGAAGAAGATCA
5031369 ATCAATAGGCAGAAGAAGATCA
1 ATCAATAGGCAGAAGAAGATCA
5031391 A
1 A
5031392 GGGTCCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.13, G:0.22, T:0.13
Consensus pattern (22 bp):
ATCAATAGGCAGAAGAAGATCA
Found at i:5038336 original size:21 final size:21
Alignment explanation
Indices: 5038297--5038336 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5038287 ATCAACAATA
**
5038297 TAAAATAAATAAATTAATGAC
1 TAAAATAAATAAACAAATGAC
5038318 TAAAATAAATAAACAAATG
1 TAAAATAAATAAACAAATG
5038337 CATGGAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (21 bp):
TAAAATAAATAAACAAATGAC
Found at i:5040834 original size:21 final size:20
Alignment explanation
Indices: 5040803--5040844 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
5040793 TTTTGGACCC
5040803 TTGATTTCTTCTGCCTATGA
1 TTGATTTCTTCTGCCTATGA
*
5040823 TTGATCTTCTTCTGCCTTTGA
1 TTGAT-TTCTTCTGCCTATGA
5040844 T
1 T
5040845 ACTAACTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.12, C:0.21, G:0.14, T:0.52
Consensus pattern (20 bp):
TTGATTTCTTCTGCCTATGA
Found at i:5058022 original size:14 final size:14
Alignment explanation
Indices: 5057996--5058032 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
5057986 ACTAAAAATA
5057996 CTATAAA-CATTTT
1 CTATAAATCATTTT
*
5058009 TTATAAATCATTTT
1 CTATAAATCATTTT
5058023 CTATAAATCA
1 CTATAAATCA
5058033 AATACACCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.46
Consensus pattern (14 bp):
CTATAAATCATTTT
Found at i:5060162 original size:30 final size:28
Alignment explanation
Indices: 5060113--5060169 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
5060103 GACATGTGAC
5060113 AAAAATTTAAAAATACAAATAAAAATAA
1 AAAAATTTAAAAATACAAATAAAAATAA
* *
5060141 AAAATATTTAAAATTTACAAATATAAATA
1 AAAA-ATTTAAAA-ATACAAATAAAAATA
5060170 TATAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 8 0.32
30 13 0.52
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAAATTTAAAAATACAAATAAAAATAA
Found at i:5060611 original size:23 final size:24
Alignment explanation
Indices: 5060576--5060620 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
5060566 AGTTTATTTT
5060576 TCATAAATAAATTCTA-TTTTTCG
1 TCATAAATAAATTCTAGTTTTTCG
* * *
5060599 TCATAACTTAATTTTAGTTTTT
1 TCATAAATAAATTCTAGTTTTT
5060621 TACCCATAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.53
Consensus pattern (24 bp):
TCATAAATAAATTCTAGTTTTTCG
Found at i:5062910 original size:3 final size:3
Alignment explanation
Indices: 5062902--5062931 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5062892 TCTTATTGCC
*
5062902 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5062932 ATATAGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5062919 original size:12 final size:12
Alignment explanation
Indices: 5062883--5062931 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
5062873 ATTTTCACTG
*
5062883 TTATTGTTA-TC
1 TTATTGTTATTA
*
5062894 TTATTGCCTATTA
1 TTATTG-TTATTA
5062907 TTATTGTTATTA
1 TTATTGTTATTA
*
5062919 TTATTATTATTA
1 TTATTGTTATTA
5062931 T
1 T
5062932 ATATAGTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 6 0.19
12 19 0.59
13 7 0.22
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.63
Consensus pattern (12 bp):
TTATTGTTATTA
Found at i:5063047 original size:26 final size:25
Alignment explanation
Indices: 5063017--5063080 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
5063007 CTTTGTTTCA
5063017 TTTTTATTTATTTT-TACCTAT-TATT
1 TTTTTATTTATTTTGT-CCT-TCTATT
* *
5063042 CTTTTTTTTTGTTTTGTCCTTCTATT
1 -TTTTTATTTATTTTGTCCTTCTATT
*
5063068 TATTTATTTATTT
1 TTTTTATTTATTT
5063081 ATTTTGCTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 11 0.35
26 19 0.61
27 1 0.03
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.73
Consensus pattern (25 bp):
TTTTTATTTATTTTGTCCTTCTATT
Found at i:5065487 original size:3 final size:3
Alignment explanation
Indices: 5065479--5065508 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5065469 ACTTGTAATA
5065479 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5065509 GCACGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5065707 original size:10 final size:10
Alignment explanation
Indices: 5065689--5065719 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5065679 ATCTTACTAA
*
5065689 TATAATATTT
1 TATATTATTT
5065699 TATATTATTT
1 TATATTATTT
5065709 TATATTATTT
1 TATATTATTT
5065719 T
1 T
5065720 GTATAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATATTATTT
Found at i:5069621 original size:24 final size:22
Alignment explanation
Indices: 5069594--5069651 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
5069584 AATTTTAATA
*
5069594 TTTATTTATATGGTTTTAATCCTT
1 TTTATTTATAT--TTTTAATCATT
*
5069618 TTTAATTATTATTTTTAATCATT
1 TTTATTTA-TATTTTTAATCATT
5069641 TTTATATTATA
1 TTTAT-TTATA
5069652 AATATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 16 0.55
24 10 0.34
25 3 0.10
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (22 bp):
TTTATTTATATTTTTAATCATT
Found at i:5079544 original size:25 final size:25
Alignment explanation
Indices: 5079515--5079563 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5079505 TTAAGACTCC
*
5079515 CGAGAATGATGTTGCTCGACTCTAA
1 CGAGAATGATATTGCTCGACTCTAA
5079540 CGAGAATGATATTGCTCGACTCTA
1 CGAGAATGATATTGCTCGACTCTA
5079564 TCAAGCGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (25 bp):
CGAGAATGATATTGCTCGACTCTAA
Found at i:5081021 original size:13 final size:13
Alignment explanation
Indices: 5081003--5081029 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5080993 AGAATCAAGA
5081003 ATTAAAGAAATTG
1 ATTAAAGAAATTG
5081016 ATTAAAGAAATTG
1 ATTAAAGAAATTG
5081029 A
1 A
5081030 GAAAAAATAT
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:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (13 bp):
ATTAAAGAAATTG
Found at i:5084890 original size:63 final size:63
Alignment explanation
Indices: 5084791--5085039 Score: 435
Period size: 63 Copynumber: 4.0 Consensus size: 63
5084781 GCAAACAGCA
* * * *
5084791 AATACAGAACCTTCTCGTTTATTTGATGACCTCTTACTGTGCAGATGGTTCCTTTCTCTCTTT
1 AATACAGAACCTTCTGGTTTGTTTGATGACCTCTTACTGTGCATATGGTTCCTTTCTCTCATT
*
5084854 AATACAGAACCTTCTGATTTGTTTGATGACCTCTTACTGTGCATATGGTTCCTTTCTCTCATT
1 AATACAGAACCTTCTGGTTTGTTTGATGACCTCTTACTGTGCATATGGTTCCTTTCTCTCATT
5084917 AATACAGAACCTTCTGGTTTGTTTGATGACCTCTTACTGTGCATATGGTTCCTTTCTCTCATT
1 AATACAGAACCTTCTGGTTTGTTTGATGACCTCTTACTGTGCATATGGTTCCTTTCTCTCATT
* *
5084980 AATACAGAACCTTCTGGTTTGTTTGATGACCTCTTACTGTGCATAAGGTTCCTTTGTCTC
1 AATACAGAACCTTCTGGTTTGTTTGATGACCTCTTACTGTGCATATGGTTCCTTTCTCTC
5085040 TTTCTATTAT
Statistics
Matches: 178, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 178 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (63 bp):
AATACAGAACCTTCTGGTTTGTTTGATGACCTCTTACTGTGCATATGGTTCCTTTCTCTCATT
Found at i:5095779 original size:17 final size:18
Alignment explanation
Indices: 5095745--5095790 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
5095735 CCGTTATGTC
5095745 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
5095760 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
5095777 CGCGACCGCGACCG
1 CGCGACCGCGACCG
5095791 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:5097476 original size:16 final size:16
Alignment explanation
Indices: 5097451--5097481 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5097441 AAAAATATAT
5097451 ATTTTCAATTTTTAAA
1 ATTTTCAATTTTTAAA
*
5097467 ATTTTTAATTTTTAA
1 ATTTTCAATTTTTAA
5097482 GAACCAAGAC
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:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTCAATTTTTAAA
Found at i:5108760 original size:17 final size:17
Alignment explanation
Indices: 5108738--5108773 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5108728 GAAACAGTGA
5108738 AAGGCGAAAACTAGAAG
1 AAGGCGAAAACTAGAAG
5108755 AAGGCGAAAACTAGAAG
1 AAGGCGAAAACTAGAAG
5108772 AA
1 AA
5108774 AACACTCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.11, G:0.28, T:0.06
Consensus pattern (17 bp):
AAGGCGAAAACTAGAAG
Found at i:5112457 original size:52 final size:52
Alignment explanation
Indices: 5112379--5112482 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
5112369 AGAATAAAGG
5112379 GATCAATATAGCTGACAAGATGTCTATGGAACTTTATCTCTCTCATTTTCTT
1 GATCAATATAGCTGACAAGATGTCTATGGAACTTTATCTCTCTCATTTTCTT
5112431 GATCAATATAGCTGACAAGATGTCTATGGAACTTTATCTCTCTCATTTTCTT
1 GATCAATATAGCTGACAAGATGTCTATGGAACTTTATCTCTCTCATTTTCTT
5112483 CTGTAAATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (52 bp):
GATCAATATAGCTGACAAGATGTCTATGGAACTTTATCTCTCTCATTTTCTT
Found at i:5115008 original size:18 final size:18
Alignment explanation
Indices: 5114985--5115026 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5114975 TATTTTGTTA
5114985 AAAATTA-AATATATAATT
1 AAAATTACAATA-ATAATT
*
5115003 AAAATTACAATAATATTT
1 AAAATTACAATAATAATT
5115021 AAAATT
1 AAAATT
5115027 TAAAAAGCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTACAATAATAATT
Found at i:5116062 original size:14 final size:13
Alignment explanation
Indices: 5116047--5116107 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
5116037 ATACACATCA
5116047 AAATATAAAAATC
1 AAATATAAAAATC
* * *
5116060 AAACATACAAATA
1 AAATATAAAAATC
5116073 AAATATAAAAAATC
1 AAATAT-AAAAATC
5116087 --ATATAAAAAT-
1 AAATATAAAAATC
5116097 AAATATAAAAA
1 AAATATAAAAA
5116108 AATAAAATCA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
11 6 0.15
12 13 0.33
13 15 0.38
14 5 0.13
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATATAAAAATC
Found at i:5116364 original size:25 final size:25
Alignment explanation
Indices: 5116332--5116381 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5116322 GCTGAACTTT
*
5116332 TTACAACTCAATGATGATTCAATAC
1 TTACAACTCAATGATGATCCAATAC
* *
5116357 TTACAACTCAGTGGTGATCCAATAC
1 TTACAACTCAATGATGATCCAATAC
5116382 ATTTTAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (25 bp):
TTACAACTCAATGATGATCCAATAC
Found at i:5116456 original size:15 final size:15
Alignment explanation
Indices: 5116436--5116466 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5116426 TCAGATACAA
5116436 ATATATTTATATAAT
1 ATATATTTATATAAT
*
5116451 ATATATTTATGTAAT
1 ATATATTTATATAAT
5116466 A
1 A
5116467 ATTCGAGAAG
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:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATATATTTATATAAT
Found at i:5117918 original size:60 final size:62
Alignment explanation
Indices: 5117834--5117966 Score: 200
Period size: 60 Copynumber: 2.2 Consensus size: 62
5117824 ATACTAAACT
* * *
5117834 AAACAC-AACAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTA-C
1 AAACACAAAAAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTATA
*
5117894 AAACACAAAAAATTT-TAACATAATCCTAATTTACTAATAAATTAATTTTAAAATAATTATA
1 AAACACAAAAAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTATA
*
5117955 AAAAACAAAAAA
1 AAACACAAAAAA
5117967 AATTACATTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
60 48 0.73
61 18 0.27
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.32
Consensus pattern (62 bp):
AAACACAAAAAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTATA
Found at i:5119942 original size:4 final size:4
Alignment explanation
Indices: 5119933--5119958 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5119923 GCCTCTGCTA
5119933 TATC TATC TATC TATC TATC TATC TA
1 TATC TATC TATC TATC TATC TATC TA
5119959 ATAATTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:5121549 original size:22 final size:23
Alignment explanation
Indices: 5121511--5121562 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
5121501 ATACAAGTAG
*
5121511 AATA-ATATGGAATCAA-TAATAA
1 AATATATATGGAAACAATTAAT-A
5121533 AATATATAT-GAAACAATTAATA
1 AATATATATGGAAACAATTAATA
*
5121555 CATATATA
1 AATATATA
5121563 AAAATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (23 bp):
AATATATATGGAAACAATTAATA
Found at i:5121717 original size:3 final size:3
Alignment explanation
Indices: 5121709--5121814 Score: 62
Period size: 3 Copynumber: 36.7 Consensus size: 3
5121699 ACGAACTATT
* *
5121709 ATA ATA ATA A-A AT- ATA ATGA ATA ATA TTA GTA ATA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
5121752 TTA ACTA TTA ACA GTA A-A GT- ATA ATA A-A ATA GTA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
5121795 ATA ATA ATA CTA AAA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
5121815 TAATTTTATG
Statistics
Matches: 76, Mismatches: 19, Indels: 16
0.68 0.17 0.14
Matches are distributed among these distances:
2 10 0.13
3 61 0.80
4 5 0.07
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5123246 original size:44 final size:44
Alignment explanation
Indices: 5123198--5123388 Score: 187
Period size: 44 Copynumber: 4.3 Consensus size: 44
5123188 ATCTGCTCCA
5123198 CTATTGCTTAGGGAGATAAGATCTGTAATCTTCAGCTTGTTACC
1 CTATTGCTTAGGGAGATAAGATCTGTAATCTTCAGCTTGTTACC
* * *
5123242 CTATTGCTTAGGGAGTTAA-AGCCTGCAATCTTCAGCTTGTTACC
1 CTATTGCTTAGGGAGATAAGA-TCTGTAATCTTCAGCTTGTTACC
* * * **
5123286 CTATTGCTTAGGGAGTTAAAGCCTACTGT--T-TTC-GATT-TGCCCC
1 CTATTGCTTAGGGAGAT-AAG-AT-CTGTAATCTTCAGCTTGT-TACC
* * *
5123329 ACTATTGCTTAGGGAGATAAGATCTGTAATTTTTAACTTGTTACC
1 -CTATTGCTTAGGGAGATAAGATCTGTAATCTTCAGCTTGTTACC
5123374 CTATTGCTTAGGGAG
1 CTATTGCTTAGGGAG
5123389 TTAAAGCCTG
Statistics
Matches: 119, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
41 4 0.03
42 2 0.02
43 10 0.08
44 92 0.77
45 7 0.06
46 1 0.01
47 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (44 bp):
CTATTGCTTAGGGAGATAAGATCTGTAATCTTCAGCTTGTTACC
Found at i:5124027 original size:17 final size:18
Alignment explanation
Indices: 5124001--5124052 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
5123991 AAAAATTTAT
5124001 ATAAATATA-TTAAATATA
1 ATAAATATATTTAAAT-TA
5124019 ATAAA-ATATTTAAATTA
1 ATAAATATATTTAAATTA
*
5124036 ATTAATGATATTATAAA
1 ATAAAT-ATATT-TAAA
5124053 AATTGAGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 9 0.31
18 11 0.38
19 5 0.17
20 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATAAATATATTTAAATTA
Found at i:5124273 original size:31 final size:31
Alignment explanation
Indices: 5124238--5124298 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
5124228 AATTAATTAG
*
5124238 ATCAACAATTTTATTTA-AAATCAATCACTAT
1 ATCAACAATTTTA-ATAGAAATCAATCACTAT
* *
5124269 ATCAATAATTTTAATAGGAATCAATCACTA
1 ATCAACAATTTTAATAGAAATCAATCACTA
5124299 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (31 bp):
ATCAACAATTTTAATAGAAATCAATCACTAT
Found at i:5125168 original size:22 final size:22
Alignment explanation
Indices: 5125143--5125186 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5125133 TAGTCTTATA
5125143 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
5125165 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
5125187 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:5125231 original size:15 final size:16
Alignment explanation
Indices: 5125210--5125245 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
5125200 AATTTTATTT
5125210 TAATAATAAATTTAAA
1 TAATAATAAATTTAAA
*
5125226 -AATAATAATTTTAAA
1 TAATAATAAATTTAAA
5125241 TAATA
1 TAATA
5125246 TTATTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAATAAATTTAAA
Found at i:5125298 original size:15 final size:15
Alignment explanation
Indices: 5125278--5125333 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
5125268 GTTCAATATT
5125278 AATATTTTAATAATA
1 AATATTTTAATAATA
*
5125293 AATATTTATTATAATTATA
1 AATA--T-TT-TAATAATA
*
5125312 AATATATTAATAATA
1 AATATTTTAATAATA
5125327 AAT-TTTT
1 AATATTTT
5125334 TGTAGTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
14 3 0.09
15 14 0.42
16 1 0.03
17 2 0.06
18 2 0.06
19 11 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:5125307 original size:19 final size:19
Alignment explanation
Indices: 5125280--5125316 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5125270 TCAATATTAA
*
5125280 TATTTTAATAATAAATATT
1 TATTATAATAATAAATATT
*
5125299 TATTATAATTATAAATAT
1 TATTATAATAATAAATAT
5125317 ATTAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATAATAATAAATATT
Found at i:5129792 original size:15 final size:15
Alignment explanation
Indices: 5129772--5129821 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
5129762 AGAACATGTT
*
5129772 AACGTAAGTGACTAA
1 AACGTAAGTGATTAA
*
5129787 AACGTAA-T-ATTCA
1 AACGTAAGTGATTAA
5129800 AACGTAAGTGATTAA
1 AACGTAAGTGATTAA
*
5129815 AATGTAA
1 AACGTAA
5129822 CATGAGGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 10 0.34
14 2 0.07
15 17 0.59
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (15 bp):
AACGTAAGTGATTAA
Found at i:5130989 original size:23 final size:21
Alignment explanation
Indices: 5130959--5131006 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
5130949 TTATAAAATT
5130959 AAATT-AAATTATGAAAACTATA
1 AAATTAAAATTAT-AAAACTA-A
*
5130981 AAATATAAAATTCTAAAACTAA
1 AAAT-TAAAATTATAAAACTAA
5131003 AAAT
1 AAAT
5131007 GATTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 9 0.39
23 8 0.35
24 6 0.26
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.29
Consensus pattern (21 bp):
AAATTAAAATTATAAAACTAA
Found at i:5131856 original size:7 final size:7
Alignment explanation
Indices: 5131844--5131898 Score: 110
Period size: 7 Copynumber: 7.9 Consensus size: 7
5131834 CTTGAGTGCT
5131844 CAAAATA
1 CAAAATA
5131851 CAAAATA
1 CAAAATA
5131858 CAAAATA
1 CAAAATA
5131865 CAAAATA
1 CAAAATA
5131872 CAAAATA
1 CAAAATA
5131879 CAAAATA
1 CAAAATA
5131886 CAAAATA
1 CAAAATA
5131893 CAAAAT
1 CAAAAT
5131899 CAATATATAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (7 bp):
CAAAATA
Found at i:5135797 original size:7 final size:6
Alignment explanation
Indices: 5135768--5135803 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
5135758 TTTCTTTCAT
*
5135768 TTTTCTG TTTTTG TTTTTG TTTTTG TTTTTA TTTTT
1 TTTT-TG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
5135804 TATTTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.03, C:0.03, G:0.11, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:5139464 original size:17 final size:18
Alignment explanation
Indices: 5139442--5139475 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5139432 TATAGTATAG
5139442 ATAATT-AAATATGATAT
1 ATAATTAAAATATGATAT
5139459 ATAATTAAAATATGATA
1 ATAATTAAAATATGATA
5139476 CAAAGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
ATAATTAAAATATGATAT
Found at i:5141829 original size:31 final size:29
Alignment explanation
Indices: 5141777--5141840 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 29
5141767 ACTTAAAAGG
*
5141777 AAAAAATTTAATAACCTAATAAATTGAAT
1 AAAAAATTTAATAACCTAATAAATTAAAT
*
5141806 AAAAAATTATGAATAA-CTCAATAATTTAAAT
1 AAAAAATT-T-AATAACCT-AATAAATTAAAT
5141837 AAAA
1 AAAA
5141841 TTTTTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.27
30 3 0.10
31 19 0.63
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAAAATTTAATAACCTAATAAATTAAAT
Found at i:5152016 original size:38 final size:38
Alignment explanation
Indices: 5151950--5152022 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
5151940 ACCAGAATGG
*
5151950 CACCCAGTGCCTCATCGGATAGTTCGAAGCAAAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGCAAAGTTGA
* * *
5151988 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAAAGT
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGCAAAGT
5152023 GGTGCCCAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 27 0.90
39 3 0.10
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGCAAAGTTGA
Found at i:5152901 original size:10 final size:10
Alignment explanation
Indices: 5152886--5152910 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5152876 TTATCACATA
5152886 AAAATTTTAT
1 AAAATTTTAT
5152896 AAAATTTTAT
1 AAAATTTTAT
5152906 AAAAT
1 AAAAT
5152911 AATTATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AAAATTTTAT
Found at i:5153315 original size:15 final size:16
Alignment explanation
Indices: 5153297--5153329 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5153287 ATTACAATTG
5153297 TACAAATATA-ATTTT
1 TACAAATATATATTTT
*
5153312 TACACATATATATTTT
1 TACAAATATATATTTT
5153328 TA
1 TA
5153330 TTGCCATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
TACAAATATATATTTT
Found at i:5154644 original size:43 final size:43
Alignment explanation
Indices: 5154595--5154754 Score: 199
Period size: 43 Copynumber: 3.9 Consensus size: 43
5154585 GGCGTTTATT
*
5154595 AAAAAAAAGCACCGCTAAAAGTCATGGCCTTTAGCGGCGTTTG
1 AAAAAAAAGCACCGCTAAAAGTCATGGCCTTTAGCGGCATTTG
* *
5154638 AAAAAAAAGCGCTGCTAAAAGTCATGGCCTTTAGCGGCATTTG
1 AAAAAAAAGCACCGCTAAAAGTCATGGCCTTTAGCGGCATTTG
* *
5154681 AAGAAAAA--A-CGCT----GTCGTGGCCTTTAGCGGCATTTG
1 AAAAAAAAGCACCGCTAAAAGTCATGGCCTTTAGCGGCATTTG
* * *
5154717 AAGAAAAAGCGCCGCTAAAAGTCGTGGCCTTTAGCGGC
1 AAAAAAAAGCACCGCTAAAAGTCATGGCCTTTAGCGGC
5154755 GCTTTTTCAT
Statistics
Matches: 102, Mismatches: 8, Indels: 14
0.82 0.06 0.11
Matches are distributed among these distances:
36 30 0.29
39 4 0.04
40 3 0.03
43 65 0.64
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (43 bp):
AAAAAAAAGCACCGCTAAAAGTCATGGCCTTTAGCGGCATTTG
Found at i:5154889 original size:31 final size:30
Alignment explanation
Indices: 5154854--5154919 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
5154844 CTTCCTGCAT
5154854 TAAAATCCAACC-AAATACAACAAATATAGCA
1 TAAAATCCAACCAAAATAC--CAAATATAGCA
* * *
5154885 TAAAATGCAGCCAAAATACCAAATTTAGCA
1 TAAAATCCAACCAAAATACCAAATATAGCA
5154915 TAAAA
1 TAAAA
5154920 AAATACAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 15 0.48
31 10 0.32
32 6 0.19
ACGTcount: A:0.56, C:0.20, G:0.06, T:0.18
Consensus pattern (30 bp):
TAAAATCCAACCAAAATACCAAATATAGCA
Found at i:5155222 original size:24 final size:21
Alignment explanation
Indices: 5155155--5155216 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
5155145 TTCCTATGCT
5155155 CTGCCTCCCTCGCTGCTGCCG
1 CTGCCTCCCTCGCTGCTGCCG
*
5155176 TTGCCTCCCTCGCTGCTGCCG
1 CTGCCTCCCTCGCTGCTGCCG
*
5155197 CTGCCTCCCTCTCTGCTGCC
1 CTGCCTCCCTCGCTGCTGCC
5155217 TCCGCTCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.00, C:0.52, G:0.21, T:0.27
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCTGCCG
Found at i:5155653 original size:13 final size:14
Alignment explanation
Indices: 5155628--5155656 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5155618 TGATGAATTG
5155628 AATTAAACAATTAT
1 AATTAAACAATTAT
5155642 AATTAAAC-ATTAT
1 AATTAAACAATTAT
5155655 AA
1 AA
5155657 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:5155860 original size:16 final size:17
Alignment explanation
Indices: 5155823--5155861 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
5155813 AAAATATTAT
*
5155823 TTAATATTAGAAAGTTA
1 TTAATATTAGAAAGTAA
*
5155840 TTAATATTTGAAAG-AA
1 TTAATATTAGAAAGTAA
5155856 TTAATA
1 TTAATA
5155862 AAATTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (17 bp):
TTAATATTAGAAAGTAA
Found at i:5160859 original size:9 final size:9
Alignment explanation
Indices: 5160845--5161033 Score: 100
Period size: 9 Copynumber: 20.6 Consensus size: 9
5160835 TATTTAAGTA
5160845 TTATGTAAG
1 TTATGTAAG
5160854 TTATGTAAG
1 TTATGTAAG
5160863 TTATG-ATA-
1 TTATGTA-AG
* *
5160871 TGAT-TATAT
1 TTATGTA-AG
*
5160880 TTATGTAAA
1 TTATGTAAG
* *
5160889 TTATAT-AT
1 TTATGTAAG
*
5160897 TTATCTAAG
1 TTATGTAAG
*
5160906 TTATATAAG
1 TTATGTAAG
5160915 TTATGTAAG
1 TTATGTAAG
*
5160924 TTATGTAAA
1 TTATGTAAG
*
5160933 TTATGATATAAAA
1 TTATG---T-AAG
*
5160946 TATATTTAAG
1 T-TATGTAAG
5160956 TATTATGTAAG
1 --TTATGTAAG
5160967 TTATGTAAG
1 TTATGTAAG
* *
5160976 TTATAT-AT
1 TTATGTAAG
*
5160984 TTATCTAAG
1 TTATGTAAG
*
5160993 TTATATAAG
1 TTATGTAAG
*
5161002 TTATGTATG
1 TTATGTAAG
*
5161011 TTTTGTAAG
1 TTATGTAAG
* *
5161020 TTATATAAA
1 TTATGTAAG
5161029 TTATG
1 TTATG
5161034 ATATCAAATA
Statistics
Matches: 141, Mismatches: 26, Indels: 26
0.73 0.13 0.13
Matches are distributed among these distances:
8 19 0.13
9 101 0.72
10 4 0.03
11 8 0.06
12 2 0.01
13 4 0.03
14 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:5160895 original size:17 final size:17
Alignment explanation
Indices: 5160875--5160999 Score: 85
Period size: 17 Copynumber: 7.2 Consensus size: 17
5160865 ATGATATGAT
*
5160875 TATATTTATGTAAATTA
1 TATATTTATGTAAGTTA
*
5160892 TATATTTATCTAAGTTA
1 TATATTTATGTAAGTTA
*
5160909 TATAAGTTATGTAAGTTA
1 TAT-ATTTATGTAAGTTA
* * **
5160927 TGTAAATTATGATATA-AAA
1 TAT-ATTTATG-TA-AGTTA
*
5160946 TATATTTAAGT-A-TTA
1 TATATTTATGTAAGTTA
* *
5160961 TGTAAGTTATGTAAGTTA
1 TAT-ATTTATGTAAGTTA
*
5160979 TATATTTATCTAAGTTA
1 TATATTTATGTAAGTTA
5160996 TATA
1 TATA
5161000 AGTTATGTAT
Statistics
Matches: 83, Mismatches: 19, Indels: 12
0.73 0.17 0.11
Matches are distributed among these distances:
15 4 0.05
16 6 0.07
17 36 0.43
18 31 0.37
19 5 0.06
20 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (17 bp):
TATATTTATGTAAGTTA
Found at i:5160906 original size:43 final size:43
Alignment explanation
Indices: 5160821--5160909 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
5160811 ACTAGTTATG
* *
5160821 TATGATATGATATATATTTAAGTATTATGTAAGTTATGTAAGT
1 TATGATATGATATATATTTAAGTATTATATAAGTTATCTAAGT
* *
5160864 TATGATATGAT-TATATTTATGTAAATTATAT-ATTTATCTAAGT
1 TATGATATGATATATATTTAAGT--ATTATATAAGTTATCTAAGT
5160907 TAT
1 TAT
5160910 ATAAGTTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
42 10 0.25
43 24 0.60
44 6 0.15
ACGTcount: A:0.37, C:0.01, G:0.12, T:0.49
Consensus pattern (43 bp):
TATGATATGATATATATTTAAGTATTATATAAGTTATCTAAGT
Found at i:5160974 original size:87 final size:90
Alignment explanation
Indices: 5160880--5161064 Score: 259
Period size: 96 Copynumber: 2.0 Consensus size: 90
5160870 ATGATTATAT
*
5160880 TTATGTAAATTATATATTTATCTAAGTTATATAAG-T-TA-TGTAAGTTATGTAAATTATGATAT
1 TTATGTAAATTATATATTTATCTAAGTTATATAAGTTGTATTGTAAGTTATATAAATTATGATAT
5160942 AAAATATATTTAAGTATTATGTAAG
66 AAAATATATTTAAGTATTATGTAAG
*
5160967 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTATGTTTTGTAAGTTATATAAATTA
1 TTATGTAAATTATATATTTATCTAAGTTATATAAG-T-TGTA----TTGTAAGTTATATAAATTA
* *
5161032 TGATATCAAATATATTTATGTATTATGTAAG
60 TGATATAAAATATATTTAAGTATTATGTAAG
5161063 TT
1 TT
5161065 TTTTATTTCA
Statistics
Matches: 85, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
87 34 0.40
90 1 0.01
91 2 0.02
96 48 0.56
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (90 bp):
TTATGTAAATTATATATTTATCTAAGTTATATAAGTTGTATTGTAAGTTATATAAATTATGATAT
AAAATATATTTAAGTATTATGTAAG
Found at i:5160992 original size:26 final size:27
Alignment explanation
Indices: 5160845--5161037 Score: 117
Period size: 26 Copynumber: 7.0 Consensus size: 27
5160835 TATTTAAGTA
*
5160845 TTATGTAAGTTATGTAAGTTATGATATG
1 TTATGTAAGTTATATAAGTTAT-ATATG
* * *
5160873 --AT-TATATTTATGTAAATTATATAT-
1 TTATGTA-AGTTATATAAGTTATATATG
* * *
5160897 TTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATATATG
* * * *
5160924 TTATGTAAATTATGATATAAAATATATTTAAGTA
1 TTATGT-AAGT-T-ATAT-AAGT-TATAT-A-TG
*
5160958 TTATGTAAGTTATGTAAGTTATATAT-
1 TTATGTAAGTTATATAAGTTATATATG
* *
5160984 TTATCTAAGTTATATAAGTTATGTATG
1 TTATGTAAGTTATATAAGTTATATATG
* *
5161011 TTTTGTAAGTTATATAAATTATGATAT
1 TTATGTAAGTTATATAAGTTAT-ATAT
5161038 CAAATATATT
Statistics
Matches: 127, Mismatches: 24, Indels: 28
0.71 0.13 0.16
Matches are distributed among these distances:
25 6 0.05
26 54 0.43
27 27 0.21
28 7 0.06
29 5 0.04
30 7 0.06
31 6 0.05
32 5 0.04
33 4 0.03
34 6 0.05
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (27 bp):
TTATGTAAGTTATATAAGTTATATATG
Found at i:5161059 original size:48 final size:49
Alignment explanation
Indices: 5160915--5161060 Score: 144
Period size: 48 Copynumber: 3.0 Consensus size: 49
5160905 GTTATATAAG
*
5160915 TTATGTAAGTTATGTAAATTATGATATAAAATATATTTAAGTATTATGTAA
1 TTATGTAAGTTATATAAATTATGATAT-AAATATATTTAAGTATTATGT-A
* * *
5160966 GTTATGTAAGTTATAT--ATT-T-ATCTAAGT-TATATAAGTTATGTATGT-
1 -TTATGTAAGTTATATAAATTATGATATAAATATATTTAAG-TAT-TATGTA
*
5161012 TT-TGTAAGTTATATAAATTATGATATCAAATATATTTATGTATTATGTA
1 TTATGTAAGTTATATAAATTATGATAT-AAATATATTTAAGTATTATGTA
5161061 AGTTTTTTAT
Statistics
Matches: 77, Mismatches: 8, Indels: 21
0.73 0.08 0.20
Matches are distributed among these distances:
44 12 0.16
45 2 0.03
46 10 0.13
47 7 0.09
48 16 0.21
49 7 0.09
50 9 0.12
52 14 0.18
ACGTcount: A:0.38, C:0.01, G:0.12, T:0.48
Consensus pattern (49 bp):
TTATGTAAGTTATATAAATTATGATATAAATATATTTAAGTATTATGTA
Found at i:5161072 original size:87 final size:87
Alignment explanation
Indices: 5160880--5161064 Score: 234
Period size: 87 Copynumber: 2.1 Consensus size: 87
5160870 ATGATTATAT
*
5160880 TTATGTAAATTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAAA
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAAA
** *
5160945 ATATATTTAAGTATTATGTAAG
66 ATATATCAAAATATTATGTAAG
* * *
5160967 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTATGTTTTGTAAGTTAT-ATA-AAT
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAA-
*
5161030 TATGATATCAAATATATTTATGT-A-
65 AAT-ATATCAAA-ATA-TTATGTAAG
5161054 TTATGTAAGTT
1 TTATGTAAGTT
5161065 TTTTATTTCA
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
85 2 0.02
86 5 0.06
87 70 0.81
88 3 0.03
89 6 0.07
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (87 bp):
TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAAA
ATATATCAAAATATTATGTAAG
Found at i:5161158 original size:15 final size:15
Alignment explanation
Indices: 5161138--5161193 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
5161128 AAGTAGCGGG
5161138 ATTAAATAATATTTA
1 ATTAAATAATATTTA
5161153 ATTAAATAATATTT-
1 ATTAAATAATATTTA
5161167 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
*
5161182 ATTAAGTAATAT
1 ATTAAATAATAT
5161194 ACATGTCGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.46
16 5 0.14
17 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:5162653 original size:14 final size:13
Alignment explanation
Indices: 5162634--5162663 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
5162624 CAATATAATT
5162634 TTACTTCATATATA
1 TTACTTCATATA-A
5162648 TTACTTCATATAA
1 TTACTTCATATAA
5162661 TTA
1 TTA
5162664 TTATAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (13 bp):
TTACTTCATATAA
Found at i:5164389 original size:15 final size:16
Alignment explanation
Indices: 5164369--5164398 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5164359 AAAGGTTATA
5164369 CACTG-AAAACTCATG
1 CACTGAAAAACTCATG
5164384 CACTGAAAAACTCAT
1 CACTGAAAAACTCAT
5164399 TCATAACTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (16 bp):
CACTGAAAAACTCATG
Found at i:5166399 original size:16 final size:16
Alignment explanation
Indices: 5166380--5166414 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5166370 ATTATTTAAT
5166380 ATATAAATAAAAAACA
1 ATATAAATAAAAAACA
*
5166396 ATATAAATTAAAAACA
1 ATATAAATAAAAAACA
5166412 ATA
1 ATA
5166415 AGTTATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
ATATAAATAAAAAACA
Found at i:5166463 original size:26 final size:28
Alignment explanation
Indices: 5166434--5166498 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
5166424 GCCAAAAAAC
*
5166434 TTTAATTTTAT-TTTAAAT-AATAGTAT
1 TTTAATTTTATATTTAAATAAATAATAT
*
5166460 TTTAATTATT-TATTTAAATAAATAATTT
1 TTTAATT-TTATATTTAAATAAATAATAT
*
5166488 TTTAAATTTAT
1 TTTAATTTTAT
5166499 CTAATATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 8 0.25
27 11 0.34
28 13 0.41
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTAATTTTATATTTAAATAAATAATAT
Found at i:5166815 original size:73 final size:73
Alignment explanation
Indices: 5166719--5166886 Score: 171
Period size: 73 Copynumber: 2.3 Consensus size: 73
5166709 ATCCCATTAA
* * * *
5166719 CCCTTAAACCCCTAAACCCTAAACTATTAACCCTTAATCCCTAAAATTTAAACACTAAACCTTAA
1 CCCTTAAACCCCTAAACCCTAAACCATAAACCCTTAATCCATAAAATTTAAACACTAAACCCTAA
*
5166784 ACAATGTC
66 ACAATATC
* * * **
5166792 CCCTT-AACTCCC-AAACCCATAAACCCTAAACCCTTAATCCATAGACTTTGTACACTAAACCCT
1 CCCTTAAAC-CCCTAAACCC-TAAACCATAAACCCTTAATCCATAAAATTTAAACACTAAACCCT
*
5166855 AAACTATATC
64 AAACAATATC
* *
5166865 CCC-TCAACCCCTTAACTCCTAA
1 CCCTTAAACCCCTAAAC-CCTAA
5166887 CCTTTGACCC
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
72 13 0.17
73 63 0.81
74 2 0.03
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.25
Consensus pattern (73 bp):
CCCTTAAACCCCTAAACCCTAAACCATAAACCCTTAATCCATAAAATTTAAACACTAAACCCTAA
ACAATATC
Found at i:5167127 original size:18 final size:18
Alignment explanation
Indices: 5167100--5167165 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 18
5167090 ATTAACTTGT
* *
5167100 CATAATCCATAAATCATG
1 CATAAACCATAAACCATG
5167118 CATAAACCATAAACCAT-
1 CATAAACCATAAACCATG
* *
5167135 -ATATACCCTAAACCATG
1 CATAAACCATAAACCATG
*
5167152 CATAAACCTTAAAC
1 CATAAACCATAAAC
5167166 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
16 14 0.35
18 26 0.65
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (18 bp):
CATAAACCATAAACCATG
Found at i:5178470 original size:41 final size:42
Alignment explanation
Indices: 5178364--5178498 Score: 213
Period size: 42 Copynumber: 3.3 Consensus size: 42
5178354 TAGATCTTTA
5178364 GCGGCGTTTTTCCAAAAAGCGCCGCTGAAACTCATATCTATT
1 GCGGCGTTTTTCCAAAAAGCGCCGCTGAAACTCATATCTATT
5178406 GCGGCGTTTTTCCAAAAAGCGCCGCTGAAACTCATATCTATT
1 GCGGCGTTTTTCCAAAAAGCGCCGCTGAAACTCATATCTATT
* *
5178448 GCGGCG-TTTTCTAAAAAGCGCCGCT-AATACTCA-ATCTATA
1 GCGGCGTTTTTCCAAAAAGCGCCGCTGAA-ACTCATATCTATT
*
5178488 GCGGTGTTTTT
1 GCGGCGTTTTT
5178499 GCGCAAGCGC
Statistics
Matches: 88, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
40 13 0.15
41 27 0.31
42 48 0.55
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (42 bp):
GCGGCGTTTTTCCAAAAAGCGCCGCTGAAACTCATATCTATT
Found at i:5178640 original size:41 final size:40
Alignment explanation
Indices: 5178560--5178669 Score: 107
Period size: 41 Copynumber: 2.7 Consensus size: 40
5178550 TTTAATTTTT
* **
5178560 TAGCGGCGTTTCTATAAAAACGCCGCTATAGGCCGACCTA
1 TAGCGGCGTTTCTATAAAAACGCCGCTATACGCAAACCTA
* *
5178600 TAGCGGCGCTTTCTA-AAAAATGCCGCTAATACTCAAACCTA
1 TAGCGGCG-TTTCTATAAAAACGCCGCT-ATACGCAAACCTA
* * *
5178641 TAGCTGCGTTTTTGAT-AAAGCGCCGCTAT
1 TAGCGGCGTTTCT-ATAAAAACGCCGCTAT
5178670 TGCCACTGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
40 25 0.44
41 32 0.56
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.26
Consensus pattern (40 bp):
TAGCGGCGTTTCTATAAAAACGCCGCTATACGCAAACCTA
Found at i:5178741 original size:154 final size:154
Alignment explanation
Indices: 5178443--5178821 Score: 465
Period size: 154 Copynumber: 2.5 Consensus size: 154
5178433 AAACTCATAT
* * * * * ***
5178443 CTATTGCGGCGTTTTCTAAAAAGCGCCGCTAATACTCAATCTATAGCGGTGTTTTTGCGCAAGCG
1 CTATAGCGGCGCTTTCTAAAAAACGCCGCTAATACTCAAACTATAGCGGCGTTTTTGAAAAAGCG
* * ** *
5178508 CCGCTATTGCCAGTGAAGCTCAAAACAAACGACGCTGTTCGATTTAATTTTTTAGCGGCGTTTCT
66 CCGCTATTGCCACTGAAGCTCAAAACAAACGACGCCGTTCGACCTAATCTTTTAGCGGCGTTTCT
5178573 ATAAAAACGCCGCTATAGGCCGAC
131 ATAAAAACGCCGCTATAGGCCGAC
* * *
5178597 CTATAGCGGCGCTTTCTAAAAAATGCCGCTAATACTCAAACCTATAGCTGCGTTTTTGATAAAGC
1 CTATAGCGGCGCTTTCTAAAAAACGCCGCTAATACTCAAA-CTATAGCGGCGTTTTTGAAAAAGC
* * * *
5178662 GCCGCTATTGCCACTGAAGCTCACAATAAACGACGCCGTTCG-CCTAATCTTTTAGTGGCGTTTT
65 GCCGCTATTGCCACTGAAGCTCAAAACAAACGACGCCGTTCGACCTAATCTTTTAGCGGCGTTTC
* *
5178726 TATAAAAACGCCGCTATATGTCGAC
130 TATAAAAACGCCGCTATAGGCCGAC
* * * * * * *
5178751 CTATAGCGACACTTCCTTAAAAACGCCGCTAATTCTCGATA-TATAGCGGCGTTTTTGAAAAAAC
1 CTATAGCGGCGCTTTCTAAAAAACGCCGCTAATACTC-AAACTATAGCGGCGTTTTTGAAAAAGC
5178815 GCCGCTA
65 GCCGCTA
5178822 ATACTCAATT
Statistics
Matches: 192, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
153 27 0.14
154 106 0.55
155 59 0.31
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (154 bp):
CTATAGCGGCGCTTTCTAAAAAACGCCGCTAATACTCAAACTATAGCGGCGTTTTTGAAAAAGCG
CCGCTATTGCCACTGAAGCTCAAAACAAACGACGCCGTTCGACCTAATCTTTTAGCGGCGTTTCT
ATAAAAACGCCGCTATAGGCCGAC
Found at i:5185747 original size:21 final size:21
Alignment explanation
Indices: 5185723--5185787 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
5185713 ATAGAAGAGA
5185723 ATCATGATGGATACATCTAAC
1 ATCATGATGGATACATCTAAC
* *
5185744 ATCA--ATGAGATAGAAC-AGA-
1 ATCATGATG-GATACATCTA-AC
5185763 ATCATGATGGATACATCTAAC
1 ATCATGATGGATACATCTAAC
5185784 ATCA
1 ATCA
5185788 ATAAAGGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
19 8 0.24
20 14 0.41
21 12 0.35
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (21 bp):
ATCATGATGGATACATCTAAC
Found at i:5185754 original size:40 final size:40
Alignment explanation
Indices: 5185710--5185789 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
5185700 AAAATGGAGC
*
5185710 GAGATAGAAGAGAATCATGATGGATACATCTAACATCAAT
1 GAGATAGAACAGAATCATGATGGATACATCTAACATCAAT
5185750 GAGATAGAACAGAATCATGATGGATACATCTAACATCAAT
1 GAGATAGAACAGAATCATGATGGATACATCTAACATCAAT
5185790 AAAGGTGATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.23
Consensus pattern (40 bp):
GAGATAGAACAGAATCATGATGGATACATCTAACATCAAT
Found at i:5186567 original size:23 final size:22
Alignment explanation
Indices: 5186532--5186582 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
5186522 AAAATTAAAA
*
5186532 TTTTAATTTTTTTATATATT-TT
1 TTTTAATTTTTTTA-AAATTATT
5186554 TTTTACATTTTTTTAAAATTATT
1 TTTTA-ATTTTTTTAAAATTATT
5186577 TTTTAA
1 TTTTAA
5186583 AAAATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTAATTTTTTTAAAATTATT
Found at i:5186619 original size:61 final size:61
Alignment explanation
Indices: 5186506--5186628 Score: 144
Period size: 61 Copynumber: 2.0 Consensus size: 61
5186496 TTTAAATATC
* * * *
5186506 AAAATTATTATTTAAAAAAATTAAAATTTTAATTTTTTTATATATTTTTTTTACATTTTTTT
1 AAAATTATTATTTAAAAAAATTAAAATTTTAAATATTTTATATAATTATTTTA-ATTTTTTT
* *
5186568 AAAATTATT-TTTTAAAAAATATAAATTTTATAAATATTTTA-A-AATTATTTTAATTTTTTT
1 AAAATTATTATTTAAAAAAAT-TAAAATTT-TAAATATTTTATATAATTATTTTAATTTTTTT
5186628 A
1 A
5186629 TGATTTTTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
60 9 0.17
61 18 0.34
62 17 0.32
63 9 0.17
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (61 bp):
AAAATTATTATTTAAAAAAATTAAAATTTTAAATATTTTATATAATTATTTTAATTTTTTT
Found at i:5191492 original size:15 final size:15
Alignment explanation
Indices: 5191463--5191491 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5191453 CTCGCCCCCC
5191463 CCCCACACCCCAAAA
1 CCCCACACCCCAAAA
5191478 CCCCAC-CCCCAAAA
1 CCCCACACCCCAAAA
5191492 AATAAAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.62, G:0.00, T:0.00
Consensus pattern (15 bp):
CCCCACACCCCAAAA
Found at i:5199235 original size:19 final size:19
Alignment explanation
Indices: 5199211--5199249 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5199201 ACTAAACAAT
5199211 TCATGATTCCATGCTTCAA
1 TCATGATTCCATGCTTCAA
5199230 TCATGATTCCATGCTTCAA
1 TCATGATTCCATGCTTCAA
5199249 T
1 T
5199250 TCACCATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (19 bp):
TCATGATTCCATGCTTCAA
Found at i:5200612 original size:2 final size:2
Alignment explanation
Indices: 5200605--5200630 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5200595 ATTAAAATTA
5200605 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
5200631 GTGTGTGTGT
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:5203545 original size:17 final size:17
Alignment explanation
Indices: 5203523--5203556 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5203513 GTCATATTGT
5203523 AATGGCCCAAATTTGAG
1 AATGGCCCAAATTTGAG
5203540 AATGGCCCAAATTTGAG
1 AATGGCCCAAATTTGAG
5203557 GTTATCGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (17 bp):
AATGGCCCAAATTTGAG
Found at i:5204411 original size:29 final size:30
Alignment explanation
Indices: 5204352--5204409 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5204342 TCCGAGCCTT
*
5204352 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
5204382 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
5204410 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:5204640 original size:13 final size:13
Alignment explanation
Indices: 5204622--5204652 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5204612 TTCCAGCAAC
5204622 TATGAATTTATTT
1 TATGAATTTATTT
5204635 TATGAATTTATTT
1 TATGAATTTATTT
*
5204648 GATGA
1 TATGA
5204653 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:5204825 original size:50 final size:50
Alignment explanation
Indices: 5204750--5204960 Score: 332
Period size: 50 Copynumber: 4.2 Consensus size: 50
5204740 TGGGTAAAGA
5204750 GGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACAT
1 GGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACAT
5204800 GGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACAT
1 GGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACAT
* * *
5204850 GGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACCATGTCTGGGACAT
1 GGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACAT
* * * **
5204900 GGCATGGGCACCAACATGAGAACATCCCATGTAAGACCATGTCTGGGACAT
1 GGCATTGGCACCGAGATGAG-AGGTCCCATGTAAGACCATGTCTGGGACAT
*
5204951 GGCTTTGGCA
1 GGCATTGGCA
5204961 TGTTATTATC
Statistics
Matches: 147, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 113 0.77
51 34 0.23
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
GGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACAT
Found at i:5206881 original size:22 final size:23
Alignment explanation
Indices: 5206856--5206901 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
5206846 CAACCAAATC
5206856 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
5206878 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
5206901 A
1 A
5206902 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:5206907 original size:23 final size:23
Alignment explanation
Indices: 5206863--5206907 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5206853 ATCAATTCAA
*
5206863 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
5206886 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
5206908 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:5213827 original size:43 final size:43
Alignment explanation
Indices: 5213780--5213936 Score: 160
Period size: 43 Copynumber: 3.7 Consensus size: 43
5213770 AGCTCGTACA
* *
5213780 ATGCCAACGTCCCATACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATATCG
* * * *
5213823 ATGCC-ACTGTCCCAAACAG-GGCCTTACCCGAAATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCAAATATCG
* * *
5213865 ATGCCAACGTCCTAGACGTGGTCTCACACGTAAATCATAA-GTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGT-AATCA-AATATCG
*
5213909 ATGTCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
5213937 TGAAAAAACA
Statistics
Matches: 92, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 24 0.26
43 37 0.40
44 30 0.33
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATATCG
Found at i:5217562 original size:92 final size:92
Alignment explanation
Indices: 5217401--5217574 Score: 267
Period size: 92 Copynumber: 1.9 Consensus size: 92
5217391 AATATTAACT
* *
5217401 AAAGATGACATTTTGTACATTGAAATAGCTACAAAGTAATCATTAACCATACCATGATTAACCCA
1 AAAGATGACATTTTGTACATTAAAATAGCTACAAAGTAATCATTAACCATACCATAATTAACCCA
* *
5217466 AACAATAAAGATTTCACCTTTGCATAA
66 AACAACAAAGACTTCACCTTTGCATAA
* * * * *
5217493 AAAGATGTCATTTTGTACATTAAAATAGCTATAAAGTAATCATTAGCCATACTATAATTAACCCT
1 AAAGATGACATTTTGTACATTAAAATAGCTACAAAGTAATCATTAACCATACCATAATTAACCCA
5217558 AACAACAAAGACTTCAC
66 AACAACAAAGACTTCAC
5217575 ATTCACCTAA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 73 1.00
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (92 bp):
AAAGATGACATTTTGTACATTAAAATAGCTACAAAGTAATCATTAACCATACCATAATTAACCCA
AACAACAAAGACTTCACCTTTGCATAA
Done.