Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_pilon, whole genome shotgun sequence
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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 30
Found at i:5701559 original size:14 final size:14
Alignment explanation
Indices: 5701503--5701559 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
5701493 GAGATTGAGT
*
5701503 TGAATATAAACGAA
1 TGAACATAAACGAA
**
5701517 CAAACATAAACGAA
1 TGAACATAAACGAA
* *
5701531 CGAACATAAATGAA
1 TGAACATAAACGAA
5701545 TGAACATAAACGAA
1 TGAACATAAACGAA
5701559 T
1 T
5701560 AAATAATCGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (14 bp):
TGAACATAAACGAA
Found at i:5707745 original size:14 final size:14
Alignment explanation
Indices: 5707726--5707752 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5707716 AAGTAAAAAT
5707726 ATAATAATAATAAA
1 ATAATAATAATAAA
5707740 ATAATAATAATAA
1 ATAATAATAATAA
5707753 TGTCAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAATAATAATAAA
Found at i:5707746 original size:17 final size:16
Alignment explanation
Indices: 5707721--5707753 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
5707711 TTTTTAAGTA
5707721 AAAATATAATAATAAT
1 AAAATATAATAATAAT
5707737 AAAATAATAATAATAAT
1 AAAAT-ATAATAATAAT
5707754 GTCAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATATAATAATAAT
Found at i:5711624 original size:35 final size:34
Alignment explanation
Indices: 5711571--5711660 Score: 130
Period size: 35 Copynumber: 2.7 Consensus size: 34
5711561 ATTTTTAGAA
*
5711571 AAAAACTATATATTTATGTTTTCAAAAATCATTT
1 AAAAACTATATATATATGTTTTCAAAAATCATTT
**
5711605 AAAAACTATATACTATATGTTTTCAAAAATGTTTT
1 AAAAACTATATA-TATATGTTTTCAAAAATCATTT
5711640 AAAAACTATAT-T-TATGTTTTC
1 AAAAACTATATATATATGTTTTC
5711661 CTTTCATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
32 9 0.17
33 1 0.02
34 12 0.23
35 30 0.58
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (34 bp):
AAAAACTATATATATATGTTTTCAAAAATCATTT
Found at i:5711713 original size:93 final size:93
Alignment explanation
Indices: 5711586--5711772 Score: 349
Period size: 93 Copynumber: 2.0 Consensus size: 93
5711576 CTATATATTT
5711586 ATGTTTTCAAAAATCATTTAAAAACTATATACTATATGTTTTCAAAAATGTTTT-AAAAACTATA
1 ATGTTTTCAAAAATCATTTAAAAACTATATACTATATGTTTTCAAAAATGTTTTAAAAAACTATA
5711650 TTTATGTTTTCCTTTCATTTTGGGTTTG
66 TTTATGTTTTCCTTTCATTTTGGGTTTG
5711678 ATGTTTTCAAAAATCATTTTAAAAACTATATACTATATGTTTTCAAAAATGTTTTAAAAAAACTA
1 ATGTTTTCAAAAATCA-TTTAAAAACTATATACTATATGTTTTCAAAAATGTTTT-AAAAAACTA
5711743 TATTTATGTTTTCCTTTCATTTTGGGTTTG
64 TATTTATGTTTTCCTTTCATTTTGGGTTTG
5711773 TTTTTGAAAC
Statistics
Matches: 92, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
92 16 0.17
93 38 0.41
95 38 0.41
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.48
Consensus pattern (93 bp):
ATGTTTTCAAAAATCATTTAAAAACTATATACTATATGTTTTCAAAAATGTTTTAAAAAACTATA
TTTATGTTTTCCTTTCATTTTGGGTTTG
Found at i:5712918 original size:48 final size:49
Alignment explanation
Indices: 5712765--5713176 Score: 373
Period size: 49 Copynumber: 8.2 Consensus size: 49
5712755 TTAAATGTCT
* * *
5712765 AACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGACGACA
1 AACGGTGCATTTTTGGCAGAAAGGTGTCACTAATGCAAGTTAGATGACA
* * * * *
5712814 AATGGTGCATTTTTGGCAGAAATGTGTCACTAATGCAAGTTAAATGTCT
1 AACGGTGCATTTTTGGCAGAAAGGTGTCACTAATGCAAGTTAGATGACA
* * *
5712863 AACGGTGCA-TTCTAGCATAAAGGTGTCACTAATGCAAGTTAGATGACA
1 AACGGTGCATTTTTGGCAGAAAGGTGTCACTAATGCAAGTTAGATGACA
* * * * * * * *
5712911 AATGGTGCATTTTTTTGCAGAAATGAGCCACTAATGCAAGTTAAATGTCT
1 AACGGTGCA-TTTTTGGCAGAAAGGTGTCACTAATGCAAGTTAGATGACA
* *
5712961 AACGGTGCA-TTATGGCAGAAAGGTGTCACTAATGCAAGTTAGATGAAAAGTTAAATGTCT
1 AACGGTGCATTTTTGGCAGAAAGGTGTCACTAATGCAAGTTAGAT-----G----A---CA
* * *
5713021 AACGGTGCATTTTTGGTAGAAATGTGCCACTAATGCAAGTTAGATGACA
1 AACGGTGCATTTTTGGCAGAAAGGTGTCACTAATGCAAGTTAGATGACA
* * * * * * *
5713070 AATGGTGCATTTTTTGTAGAAAGGTGCCACTAATGCAAGTTAAATGCCT
1 AACGGTGCATTTTTGGCAGAAAGGTGTCACTAATGCAAGTTAGATGACA
* *
5713119 AACGGTGCATTTTT-GTAGAAAGGTGTCACTAATGCAAGTTAAAT-ACA
1 AACGGTGCATTTTTGGCAGAAAGGTGTCACTAATGCAAGTTAGATGACA
*
5713166 AACAGTGCATT
1 AACGGTGCATT
5713177 AACGGCATAA
Statistics
Matches: 298, Mismatches: 50, Indels: 32
0.78 0.13 0.08
Matches are distributed among these distances:
47 11 0.04
48 98 0.33
49 106 0.36
50 38 0.13
52 1 0.00
53 1 0.00
56 1 0.00
60 11 0.04
61 31 0.10
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (49 bp):
AACGGTGCATTTTTGGCAGAAAGGTGTCACTAATGCAAGTTAGATGACA
Found at i:5712935 original size:98 final size:98
Alignment explanation
Indices: 5712752--5713162 Score: 450
Period size: 98 Copynumber: 4.1 Consensus size: 98
5712742 GTTAGATGAA
* *
5712752 AAGTTAAATGTCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGACGACAAAT
1 AAGTTAAATGTCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGACAAAT
*
5712817 GGTGCATTTTTGGCAGAAATGTGTCACTAATGC
66 GGTGCATTTTTGGCAGAAATGTGCCACTAATGC
* * * *
5712850 AAGTTAAATGTCTAACGGTGCA-TTCTAGCATAAAGGTGTCACTAATGCAAGTTAGATGACAAAT
1 AAGTTAAATGTCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGACAAAT
* *
5712914 GGTGCATTTTTTTGCAGAAATGAGCCACTAATGC
66 GGTGCA-TTTTTGGCAGAAATGTGCCACTAATGC
* *
5712948 AAGTTAAATGTCTAACGGTGCA-TTATGGCAGAAAGGTGTCACTAATGCAAGTTAGATGAAAAGT
1 AAGTTAAATGTCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATG---A--
* *
5713012 TAAATGTCTAACGGTGCATTTTTGGTAGAAATGTGCCACTAATGC
61 CAAA----T---GGTGCATTTTTGGCAGAAATGTGCCACTAATGC
* * * * * * * * * *
5713057 AAGTTAGATGACAAATGGTGCATTTTTTGTAGAAAGGTGCCACTAATGCAAGTTAAATGCCTAAC
1 AAGTTAAATGTCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGACAAAT
* * *
5713122 GGTGCATTTTT-GTAGAAAGGTGTCACTAATGC
66 GGTGCATTTTTGGCAGAAATGTGCCACTAATGC
5713154 AAGTTAAAT
1 AAGTTAAAT
5713163 ACAAACAGTG
Statistics
Matches: 267, Mismatches: 32, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
97 69 0.26
98 112 0.42
101 1 0.00
103 3 0.01
105 2 0.01
107 1 0.00
109 42 0.16
110 37 0.14
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (98 bp):
AAGTTAAATGTCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGACAAAT
GGTGCATTTTTGGCAGAAATGTGCCACTAATGC
Found at i:5713066 original size:61 final size:60
Alignment explanation
Indices: 5712948--5713067 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 60
5712938 CCACTAATGC
*
5712948 AAGTTAAATGTCTAACGGTGCATTATGGCAGAAAGGTGTCACTAATGCAAGTTAGATGAA
1 AAGTTAAATGTCTAACGGTGCATTATGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAA
* * *
5713008 AAGTTAAATGTCTAACGGTGCATTTTTGGTAGAAATGTGCCACTAATGCAAGTTAGATGA
1 AAGTTAAATGTCTAACGGTGCA-TTATGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
5713068 CAAATGGTGC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
60 22 0.40
61 33 0.60
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (60 bp):
AAGTTAAATGTCTAACGGTGCATTATGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAA
Found at i:5713107 original size:110 final size:110
Alignment explanation
Indices: 5712914--5713111 Score: 281
Period size: 109 Copynumber: 1.8 Consensus size: 110
5712904 GATGACAAAT
* * *
5712914 GGTGCATTTTTTTGCAGAAATGAGCCACTAATGCAAGTTAAATGTCTAACGGTGCATTATGGCAG
1 GGTGCATTTTTTGGCAGAAATGAGCCACTAATGCAAGTTAAATGACAAACGGTGCATTATGGCAG
*
5712979 AAAGGTGTCACTAATGCAAGTTAGATGAAAAGTTAAATGTCTAAC
66 AAAGGTGCCACTAATGCAAGTTAGATGAAAAGTTAAATGTCTAAC
* * * * * * *
5713024 GGTGCA-TTTTTGGTAGAAATGTGCCACTAATGCAAGTTAGATGACAAATGGTGCATTTTTTGTA
1 GGTGCATTTTTTGGCAGAAATGAGCCACTAATGCAAGTTAAATGACAAACGGTGCA-TTATGGCA
5713088 GAAAGGTGCCACTAATGCAAGTTA
65 GAAAGGTGCCACTAATGCAAGTTA
5713112 AATGCCTAAC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
109 42 0.55
110 34 0.45
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (110 bp):
GGTGCATTTTTTGGCAGAAATGAGCCACTAATGCAAGTTAAATGACAAACGGTGCATTATGGCAG
AAAGGTGCCACTAATGCAAGTTAGATGAAAAGTTAAATGTCTAAC
Found at i:5713139 original size:158 final size:158
Alignment explanation
Indices: 5712850--5713159 Score: 487
Period size: 158 Copynumber: 2.0 Consensus size: 158
5712840 TCACTAATGC
* *
5712850 AAGTTAAATGTCTAACGGTGCATTCTAGCATAAAGGTGTCACTAATGCAAGTTAGATGACAAATG
1 AAGTTAAATGTCTAACGGTGCATTCTAGCAGAAAGGTGCCACTAATGCAAGTTAGATGACAAATG
* *
5712915 GTGCATTTTTTTGCAGAAATGAGCCACTAATGCAAGTTAAATGTCTAACGGTGCATTATGGCAGA
66 GTGCATTTTTTTGCAGAAAGGAGCCACTAATGCAAGTTAAATGCCTAACGGTGCATTATGGCAGA
5712980 AAGGTGTCACTAATGCAAGTTAGATGAA
131 AAGGTGTCACTAATGCAAGTTAGATGAA
* * * *
5713008 AAGTTAAATGTCTAACGGTGCATTTTTGGTAGAAATGTGCCACTAATGCAAGTTAGATGACAAAT
1 AAGTTAAATGTCTAACGGTGCA-TTCTAGCAGAAAGGTGCCACTAATGCAAGTTAGATGACAAAT
* * * * *
5713073 GGTGCA-TTTTTTGTAGAAAGGTGCCACTAATGCAAGTTAAATGCCTAACGGTGCATTTTTGTAG
65 GGTGCATTTTTTTGCAGAAAGGAGCCACTAATGCAAGTTAAATGCCTAACGGTGCATTATGGCAG
5713137 AAAGGTGTCACTAATGCAAGTTA
130 AAAGGTGTCACTAATGCAAGTTA
5713160 AATACAAACA
Statistics
Matches: 138, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
158 96 0.70
159 42 0.30
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (158 bp):
AAGTTAAATGTCTAACGGTGCATTCTAGCAGAAAGGTGCCACTAATGCAAGTTAGATGACAAATG
GTGCATTTTTTTGCAGAAAGGAGCCACTAATGCAAGTTAAATGCCTAACGGTGCATTATGGCAGA
AAGGTGTCACTAATGCAAGTTAGATGAA
Found at i:5713190 original size:97 final size:98
Alignment explanation
Indices: 5713008--5713197 Score: 251
Period size: 97 Copynumber: 1.9 Consensus size: 98
5712998 GTTAGATGAA
* * * *
5713008 AAGTTAAATGTCTAACGGTGCATTTTTGGTAGAAATGTGCCACTAATGCAAGTTAGATGACAAAT
1 AAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAC
* ****
5713073 GGTGCATTTTTTGTAGAAAGGTGCCACTAATGC
66 AGTGCATTAACGGTAGAAAGGTGCCACTAATGC
*
5713106 AAGTTAAATGCCTAACGGTGCATTTTT-GTAGAAAGGTGTCACTAATGCAAGTTAAAT-ACAAAC
1 AAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAC
5713169 AGTGCATTAACGGCATA-AAAGGTGCCACT
66 AGTGCATTAACGG--TAGAAAGGTGCCACT
5713198 CATAGTATTT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
96 13 0.16
97 39 0.49
98 28 0.35
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (98 bp):
AAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAC
AGTGCATTAACGGTAGAAAGGTGCCACTAATGC
Found at i:5717214 original size:24 final size:25
Alignment explanation
Indices: 5717182--5717229 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
5717172 CTTCGGAATA
* *
5717182 ATTTCTAAGTGGCACTTCTGTGCAT
1 ATTTCTAAGCGGCACTTCGGTGCAT
*
5717207 ATTT-TAAGCGGGACTTCGGTGCA
1 ATTTCTAAGCGGCACTTCGGTGCA
5717230 ATTCTATATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (25 bp):
ATTTCTAAGCGGCACTTCGGTGCAT
Found at i:5724147 original size:157 final size:156
Alignment explanation
Indices: 5723902--5724300 Score: 521
Period size: 156 Copynumber: 2.5 Consensus size: 156
5723892 CATGATTTCA
* * *
5723902 TTATTTCTTCAATTCCTCATTTATTTTTAGGTCTATTTCTTACCAAATTTGAACCACATG-TTAT
1 TTATTTCTTCAATTCGTCATTTA-TTTTAAGTC-ATTT-TTACCAAATTTGAACCACATGCTCA-
* * * * * *
5723966 TAAACCATAGTATAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAATTTTTTTTATTTTT
62 TAAACCATAATAGAATACACGTGTACTTTCAATACCTCTTTCTGATAACAA-ATTTTTTATTTTT
*
5724031 CAATTTAGTCCTTCAATTTTTCATAATCTCC
126 CAATTAAGTCCTTCAATTTTTCATAATCTCC
* * *
5724062 TTATTTCTTCAATTCGTCATTTATTTTAAGTCATTTTTATCAAATTTGAGCCACATGCTCCTAAA
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCATTTTTACCAAATTTGAACCACATGCTCATAAA
5724127 CCATAATAGAATACACGTGTACTTTCAATACCTCTTTCTGATAACAAATTTTTTATTTTTCAATT
66 CCATAATAGAATACACGTGTACTTTCAATACCTCTTTCTGATAACAAATTTTTTATTTTTCAATT
5724192 AAGTCCTTCAATTTTTCATAATCTCC
131 AAGTCCTTCAATTTTTCATAATCTCC
* * * * * *
5724218 TTGTTCCTTCAATTTGTGATCTATTTTAAGTCACTTTGTTTTACCAAACTTGAACCACATGCTCA
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCA---T-TTTTACCAAATTTGAACCACATGCTCA
* *
5724283 TATACCACAATAGAATAC
62 TAAACCATAATAGAATAC
5724301 TTATGTAACT
Statistics
Matches: 210, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
156 70 0.33
157 65 0.31
158 5 0.02
159 9 0.04
160 61 0.29
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.45
Consensus pattern (156 bp):
TTATTTCTTCAATTCGTCATTTATTTTAAGTCATTTTTACCAAATTTGAACCACATGCTCATAAA
CCATAATAGAATACACGTGTACTTTCAATACCTCTTTCTGATAACAAATTTTTTATTTTTCAATT
AAGTCCTTCAATTTTTCATAATCTCC
Found at i:5725934 original size:63 final size:63
Alignment explanation
Indices: 5725835--5725967 Score: 257
Period size: 63 Copynumber: 2.1 Consensus size: 63
5725825 TTTCTTTAGT
5725835 TGAATATGAGCTTGTTACTGTTCCTGATCAGGGTATGAATTAGGGGCTGATCTTATGAGTAAA
1 TGAATATGAGCTTGTTACTGTTCCTGATCAGGGTATGAATTAGGGGCTGATCTTATGAGTAAA
*
5725898 TGAATATGAGCTTGTTACTGTTCCTGATCAGGGTATGAATTAGGGGCTGATCTTATGAGTGAA
1 TGAATATGAGCTTGTTACTGTTCCTGATCAGGGTATGAATTAGGGGCTGATCTTATGAGTAAA
5725961 TGAATAT
1 TGAATAT
5725968 ATATATATAG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 69 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (63 bp):
TGAATATGAGCTTGTTACTGTTCCTGATCAGGGTATGAATTAGGGGCTGATCTTATGAGTAAA
Found at i:5732614 original size:25 final size:25
Alignment explanation
Indices: 5732586--5732708 Score: 76
Period size: 25 Copynumber: 4.8 Consensus size: 25
5732576 AATAATAAAC
* *
5732586 AAAACATAAAAAAAGATAAATAAGTA
1 AAAACATAAAAAAACA-AAATAAATA
*
5732612 AAAACA-AGAATAAACAAAATAAAT-
1 AAAACATA-AAAAAACAAAATAAATA
*
5732636 AAAACGATAAAAAAA-AACAATACA-A
1 AAAAC-ATAAAAAAACAA-AATAAATA
* *
5732661 AACA-ATACAAAAATACAAAATAAAAA
1 AAAACATA-AAAAA-ACAAAATAAATA
5732687 AAAACATGAAACAAAAACAAAA
1 AAAACAT--AA-AAAAACAAAA
5732709 CAAAAACAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 24
0.70 0.07 0.22
Matches are distributed among these distances:
23 3 0.04
24 12 0.16
25 28 0.37
26 19 0.25
27 2 0.03
28 7 0.09
29 5 0.07
ACGTcount: A:0.76, C:0.10, G:0.04, T:0.11
Consensus pattern (25 bp):
AAAACATAAAAAAACAAAATAAATA
Found at i:5732662 original size:10 final size:10
Alignment explanation
Indices: 5732649--5732680 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5732639 ACGATAAAAA
5732649 AAAACAATAC
1 AAAACAATAC
5732659 AAAACAATAC
1 AAAACAATAC
5732669 -AAA-AATAC
1 AAAACAATAC
5732677 AAAA
1 AAAA
5732681 TAAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 5 0.24
9 6 0.29
10 10 0.48
ACGTcount: A:0.75, C:0.16, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAACAATAC
Found at i:5732685 original size:23 final size:23
Alignment explanation
Indices: 5732632--5732685 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5732622 TAAACAAAAT
*
5732632 AAATAAAACGATAAAAAAAAACA
1 AAATAAAACAATAAAAAAAAACA
* * * *
5732655 ATACAAAACAATACAAAAATACA
1 AAATAAAACAATAAAAAAAAACA
5732678 AAATAAAA
1 AAATAAAA
5732686 AAAAACATGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.76, C:0.11, G:0.02, T:0.11
Consensus pattern (23 bp):
AAATAAAACAATAAAAAAAAACA
Found at i:5733075 original size:21 final size:21
Alignment explanation
Indices: 5733051--5733145 Score: 95
Period size: 21 Copynumber: 4.6 Consensus size: 21
5733041 TATCGCAAAT
*
5733051 TCGCGTTGCGGTAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
5733072 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*** *
5733093 TCGCGTTGCGAT--TTTCCAT
1 TCGCGTTGCGATAATTGAAAA
* *
5733112 TGCGCTTTGCGATAGTTGAAAA
1 T-CGCGTTGCGATAATTGAAAA
5733134 TCGCGTTGCGAT
1 TCGCGTTGCGAT
5733146 TTTCCAGTTC
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
19 4 0.07
20 10 0.17
21 41 0.69
22 4 0.07
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:5733127 original size:41 final size:41
Alignment explanation
Indices: 5733072--5733168 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
5733062 TAATTGAAAA
5733072 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCA-T
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
*
5733112 TGCGCTTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
1 T-CGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
5733154 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
5733169 CTACAGTTGT
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
40 1 0.02
41 50 0.94
42 2 0.04
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.35
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
Found at i:5733159 original size:20 final size:19
Alignment explanation
Indices: 5733093--5733165 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
5733083 TAGTTGAAAA
5733093 TCGCGTTGCGATTTTCCAT
1 TCGCGTTGCGATTTTCCAT
* *** *
5733112 TGCGCTTTGCGATAGTTGAAAA
1 T-CGCGTTGCGAT--TTTCCAT
5733134 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCA-T
5733154 TCGCGTTGCGAT
1 TCGCGTTGCGAT
5733166 AGTCTACAGT
Statistics
Matches: 40, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
19 4 0.10
20 22 0.55
21 10 0.25
22 4 0.10
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCCAT
Found at i:5733310 original size:6 final size:6
Alignment explanation
Indices: 5733299--5733333 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
5733289 GACATGTATT
5733299 ACCACG ACCACG ACCACG ACCACG ACC-CG A-CACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
5733334 GACGGACAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 1 0.04
5 6 0.21
6 21 0.75
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:5733850 original size:6 final size:6
Alignment explanation
Indices: 5733821--5733880 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
5733811 TCTCGTCTCG
*
5733821 GGTCG- GGTCG- GGTCG- GGTCAT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
5733866 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
5733881 AATACGTGTC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
5 14 0.27
6 38 0.73
ACGTcount: A:0.02, C:0.17, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:5733990 original size:22 final size:22
Alignment explanation
Indices: 5733958--5734056 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 22
5733948 CTTTTTTTTA
*
5733958 ACTATCGCAACGATAACTGTAG
1 ACTATCGCAACGACAACTGTAG
* *
5733980 ACTTTCGCAACAACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
* * *
5734002 ACTATAGCAACGCGCGAAATG--G
1 ACTATCGCAACG-AC-AACTGTAG
** *
5734024 AAAATCGCAACGAC-ATTGTAG
1 ACTATCGCAACGACAACTGTAG
5734045 ACTATCGCAACG
1 ACTATCGCAACG
5734057 CGAAATGGAA
Statistics
Matches: 58, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
19 3 0.05
21 12 0.21
22 38 0.66
23 1 0.02
24 4 0.07
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (22 bp):
ACTATCGCAACGACAACTGTAG
Found at i:5734071 original size:41 final size:42
Alignment explanation
Indices: 5733997--5734076 Score: 135
Period size: 41 Copynumber: 1.9 Consensus size: 42
5733987 CAACAACAAC
5733997 TGTAGACTATAGCAACGCGCGAAATGGAAAATCGCAACGACAT
1 TGTAGACTATAGCAAC-CGCGAAATGGAAAATCGCAACGACAT
*
5734040 TGTAGACTATCGCAA-CGCGAAATGGAAAATCGCAACG
1 TGTAGACTATAGCAACCGCGAAATGGAAAATCGCAACG
5734077 CGAAATGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
41 22 0.61
43 14 0.39
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (42 bp):
TGTAGACTATAGCAACCGCGAAATGGAAAATCGCAACGACAT
Found at i:5734073 original size:20 final size:20
Alignment explanation
Indices: 5734048--5734165 Score: 110
Period size: 20 Copynumber: 5.8 Consensus size: 20
5734038 ATTGTAGACT
5734048 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
5734068 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*** ** *
5734088 ATCGCAACGCGGTTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
** ** *
5734109 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
5734130 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
5734150 ATCGCAACGCAAAATG
1 ATCGCAACGCGAAATG
5734166 CAACGTGAAT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 49 0.58
21 35 0.42
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:5734089 original size:61 final size:62
Alignment explanation
Indices: 5734014--5734159 Score: 190
Period size: 61 Copynumber: 2.4 Consensus size: 62
5734004 TATAGCAACG
*
5734014 CGCGAAATGGAAAATCGCAACGAC-ATTGT-AGACTATCGCAACGCGAAATGGAA-AATCGCAA
1 CGCGAAATGGAAAATCGCAACG-CGATTGTCA-ACTATCGCAACGCGAAATGCAACAATCGCAA
* * ** * *
5734075 CGCGAAATGGAAAATCGCAACGCGGTTTTCAACTATCGCAACGCGATTTTCAACTATCGCAA
1 CGCGAAATGGAAAATCGCAACGCGATTGTCAACTATCGCAACGCGAAATGCAACAATCGCAA
5734137 CGCGAAATGGAAAATCGCAACGC
1 CGCGAAATGGAAAATCGCAACGC
5734160 AAAATGCAAC
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
60 1 0.01
61 43 0.57
62 31 0.41
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (62 bp):
CGCGAAATGGAAAATCGCAACGCGATTGTCAACTATCGCAACGCGAAATGCAACAATCGCAA
Found at i:5734114 original size:21 final size:21
Alignment explanation
Indices: 5734088--5734141 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
5734078 GAAATGGAAA
*
5734088 ATCGCAACGCGGTTTTCAACT
1 ATCGCAACGCGATTTTCAACT
5734109 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
5734130 ATCGCAACGCGA
1 ATCGCAACGCGA
5734142 AATGGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:5734154 original size:41 final size:40
Alignment explanation
Indices: 5734014--5734159 Score: 134
Period size: 41 Copynumber: 3.6 Consensus size: 40
5734004 TATAGCAACG
*
5734014 CGCGAAATGGAAAATCGCAACGAC-ATTGTAGACTATCGCAA
1 CGCGAAATGGAAAATCGCAACG-CGATTTTA-ACTATCGCAA
* ** *
5734055 CGCGAAATGGAAAATCGCAACGCGAAATGGAA-AATCGCAA
1 CGCGAAATGGAAAATCGCAACGCG-ATTTTAACTATCGCAA
*** ** *
5734095 CGCGGTTTTCAACTATCGCAACGCGATTTTCAACTATCGCAA
1 CGCGAAATGGAA-AATCGCAACGCGATTTT-AACTATCGCAA
5734137 CGCGAAATGGAAAATCGCAACGC
1 CGCGAAATGGAAAATCGCAACGC
5734160 AAAATGCAAC
Statistics
Matches: 81, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
40 17 0.21
41 46 0.57
42 18 0.22
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (40 bp):
CGCGAAATGGAAAATCGCAACGCGATTTTAACTATCGCAA
Found at i:5736507 original size:121 final size:120
Alignment explanation
Indices: 5736154--5736557 Score: 506
Period size: 121 Copynumber: 3.3 Consensus size: 120
5736144 CACTCCTTCT
* * *
5736154 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATTGATGCTGCTTGTGGGCA
1 TTGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAG--T-A-GTTGCTTGTGGGCA
* *
5736219 TTATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCC
62 TGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCC
* * * * * * *
5736278 TTGAA-TGGATATCCTTCGTCGTAAAGTTGAAATCCAAGTATTGTGT-GTTGCTGGTGGACACGA
1 TTGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAA-TCTTGAGTAGTTGCTTGTGGGCATGA
* ** * *
5736341 TATCCTTCGTTGCAAAGTTAAAATCGTGGATGGCCCCTTCGTTGTGAATTTGAGCC
65 TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCC
* * * *
5736397 TTGAATTAGATATCCTTCATCGTGAAGTTGAAATCTAATCTTGAGTAAGTTGGTTATGGGCATGA
1 TTGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGT-AGTTGCTTGTGGGCATGA
*
5736462 TATCCTTCGTCGTGAAGTTGAAATTGTGGATGGCCCCTTCGTTGTGAAGTTGAGCC
65 TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCC
* * * *
5736518 TGGAATGAGAGATCCTTCGTCGTTAAGTTGAAATCCAATC
1 TTGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATC
5736558 AAATTGTGTC
Statistics
Matches: 238, Mismatches: 38, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
119 73 0.31
120 28 0.12
121 96 0.40
122 1 0.00
123 31 0.13
124 9 0.04
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (120 bp):
TTGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAGTTGCTTGTGGGCATGAT
ATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCC
Found at i:5736601 original size:240 final size:242
Alignment explanation
Indices: 5736154--5736604 Score: 599
Period size: 240 Copynumber: 1.9 Consensus size: 242
5736144 CACTCCTTCT
* * * *
5736154 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATTGATGCTGCTTGTGGGCA
1 TTGAATTAGATATCCTTCATCGTGAAGTTGAAATCCAATCTAGAGA-TGAAGCTGCTTATGGGCA
* *
5736219 TTATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAAT
65 TGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTGGAAT
* * * * *
5736284 GGATATCCTTCGTCGTAAAGTTGAAATCCAAGTATTGTGTGTTGCTGGTGGACACGATATCCTTC
130 GGAGATCCTTCGTCGTAAAGTTGAAATCCAAGTAATGTGTGTCGCTGGTGGACACAATATCCTCC
**
5736349 GTTGCAAAGTTAAAATCGTGGATGGCCCCTTCGTTGTGAATTTGAGCC
195 ACTGCAAAGTTAAAATCGTGGATGGCCCCTTCGTTGTGAATTTGAGCC
* * * *
5736397 TTGAATTAGATATCCTTCATCGTGAAGTTGAAATCTAATCTTGAG-T-AAGTTGGTTATGGGCAT
1 TTGAATTAGATATCCTTCATCGTGAAGTTGAAATCCAATCTAGAGATGAAGCTGCTTATGGGCAT
* *
5736460 GATATCCTTCGTCGTGAAGTTGAAATTGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTGGAATG
66 GATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTGGAATG
* * *
5736525 AGAGATCCTTCGTCGTTAAGTTGAAATCCAA-TCAAAT-TGTGTCGCT-TTGAGTC-CAATATCC
131 -GAGATCCTTCGTCGTAAAGTTGAAATCCAAGT--AATGTGTGTCGCTGGTG-GACACAATATCC
**
5736586 TCCACTGTGAAGTTAAAAT
192 TCCACTGCAAAGTTAAAAT
5736605 TGACTCTAGC
Statistics
Matches: 180, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
240 98 0.54
241 39 0.22
242 2 0.01
243 41 0.23
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (242 bp):
TTGAATTAGATATCCTTCATCGTGAAGTTGAAATCCAATCTAGAGATGAAGCTGCTTATGGGCAT
GATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTGGAATG
GAGATCCTTCGTCGTAAAGTTGAAATCCAAGTAATGTGTGTCGCTGGTGGACACAATATCCTCCA
CTGCAAAGTTAAAATCGTGGATGGCCCCTTCGTTGTGAATTTGAGCC
Found at i:5737480 original size:11 final size:11
Alignment explanation
Indices: 5737459--5737489 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
5737449 CTAAACGTTT
5737459 TTCTCTTTTTTG
1 TTCT-TTTTTTG
5737471 TTCTTTTTTTG
1 TTCTTTTTTTG
5737482 TTCTTTTT
1 TTCTTTTT
5737490 CTTCTTCGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (11 bp):
TTCTTTTTTTG
Found at i:5741464 original size:3 final size:3
Alignment explanation
Indices: 5741456--5741527 Score: 137
Period size: 3 Copynumber: 24.3 Consensus size: 3
5741446 GAGACTATCA
5741456 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5741503 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
5741528 TACAAAATAA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 66 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5742687 original size:2 final size:2
Alignment explanation
Indices: 5742680--5742707 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5742670 ACACATTAAG
5742680 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5742708 GAAAAATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5743616 original size:16 final size:15
Alignment explanation
Indices: 5743595--5743626 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
5743585 TTCTTTCAAT
5743595 TTATTTTATTTATTTA
1 TTATTTTATTT-TTTA
5743611 TTATTTTATTTTTTA
1 TTATTTTATTTTTTA
5743626 T
1 T
5743627 AGCCTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTATTTTATTTTTTA
Found at i:5744672 original size:22 final size:22
Alignment explanation
Indices: 5744626--5744681 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
5744616 GCATACATGC
*
5744626 ATTTGCATTTTATTTGTGTTAT
1 ATTTGCATTTTATTTGTATTAT
5744648 ATTTGCATTATTATATT-TATT-T
1 ATTTGCATT-TTAT-TTGTATTAT
5744670 ATTTAGCATTTT
1 ATTT-GCATTTT
5744682 TTGCATTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 16 0.53
23 12 0.40
24 2 0.07
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.62
Consensus pattern (22 bp):
ATTTGCATTTTATTTGTATTAT
Found at i:5752749 original size:40 final size:39
Alignment explanation
Indices: 5752632--5752750 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 39
5752622 ATATTTTAGG
5752632 AAACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAA
1 AAACATCATCCTTAG--AACCAGA-GTCCTCATCACGAA-GAA
* ** * *
5752675 CAATGTCATCCACT-GATA--AGAATCCTCATCACGAAGAA
1 AAACATCATCC-TTAGA-ACCAGAGTCCTCATCACGAAGAA
5752713 AAACATCATCCTTAGAACCAGATGTCCTCATCACGAAG
1 AAACATCATCCTTAGAACCAGA-GTCCTCATCACGAAG
5752751 GAACCGTGTT
Statistics
Matches: 60, Mismatches: 10, Indels: 15
0.71 0.12 0.18
Matches are distributed among these distances:
37 2 0.03
38 13 0.22
39 16 0.27
40 17 0.28
41 1 0.02
42 1 0.02
43 9 0.15
44 1 0.02
ACGTcount: A:0.39, C:0.28, G:0.13, T:0.20
Consensus pattern (39 bp):
AAACATCATCCTTAGAACCAGAGTCCTCATCACGAAGAA
Found at i:5752894 original size:137 final size:137
Alignment explanation
Indices: 5752651--5753501 Score: 1284
Period size: 137 Copynumber: 6.2 Consensus size: 137
5752641 CCTTAGATAA
*
5752651 CCAGACGTCCTCATCACGAAGGAACAATGTCATCCA-CTGATAAGAA-TCCTCATCACGAA-GAA
1 CCAGACGTCCTCATCACGAAGGAACAATGTCATCCATC-GATCAGAACTCCTCATCACGAAGGAA
* * *
5752713 AAACATCATCCTTAG--AACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTTAAATATCTTT
65 CAACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
5752776 AAAGATGG
130 AAAGATGG
** * * * * *
5752784 CCAGACGTCCTCATCGTGAAGAAACAATGGCATCTATCGATCAGAACTCCTCATCACAAATGAAC
1 CCAGACGTCCTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGAAGGAAC
*
5752849 AACATCATCCTTAGATAATCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
66 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
5752914 AAGATGG
131 AAGATGG
*
5752921 CCAGACGTCCTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGAAGGAGC
1 CCAGACGTCCTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGAAGGAAC
* *
5752986 AACATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
66 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
5753051 AAGATGG
131 AAGATGG
*
5753058 CCAGACGTCCTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGAAGGAGC
1 CCAGACGTCCTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGAAGGAAC
* * * *
5753123 AACATCATCCTTAGATAGCCAGATGTCCTCGTTACGAAGGAACCGTGTTATCTCAAATATCTTTA
66 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
*
5753188 AAGATGT
131 AAGATGG
* * *
5753195 CCAGACGTTCTCATCACGAAGGAACAATGTCATCCACCAATCAGAACTCCTCATCACGAAGGAAC
1 CCAGACGTCCTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGAAGGAAC
* *
5753260 AACATCATCCTTAGATAACCATACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTATA
66 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
5753325 AAGATGG
131 AAGATGG
* * * * *
5753332 CTAGACGTCCTCATCACGAAGGAACAATGTCATCCA-CTGACCAGAATTCCTCATCACGTATGAG
1 CCAGACGTCCTCATCACGAAGGAACAATGTCATCCATC-GATCAGAACTCCTCATCACGAAGGA-
* * * * *
5753396 TCGA-GTCATCCTCAGATAACCAGACGTCCTCATCATGAAGGAACCGTGTTATCTCAAATATCTT
64 ACAACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTT
*
5753460 CAAAGATGG
129 TAAAGATGG
*
5753469 TCAGACGTCCTCATCACGAAGGAACAATGTCAT
1 CCAGACGTCCTCATCACGAAGGAACAATGTCAT
5753502 ACAACAGTTG
Statistics
Matches: 658, Mismatches: 53, Indels: 10
0.91 0.07 0.01
Matches are distributed among these distances:
133 38 0.06
134 13 0.02
135 17 0.03
136 1 0.00
137 587 0.89
138 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (137 bp):
CCAGACGTCCTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGAAGGAAC
AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
AAGATGG
Found at i:5752983 original size:40 final size:41
Alignment explanation
Indices: 5752928--5753028 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 41
5752918 TGGCCAGACG
** *
5752928 TCCTCATCACGAAGGAACAATGTCATCCATCGAT-CAGAAC
1 TCCTCATCACGAAGGAACAACATCATCCATAGATACAGAAC
* * **
5752968 TCCTCATCACGAAGGAGCAACATCATCCTTAGATAGCCAGATG
1 TCCTCATCACGAAGGAACAACATCATCCATAGATA--CAGAAC
5753011 TCCTCATCACGAAGGAAC
1 TCCTCATCACGAAGGAAC
5753029 CGTGTTATCT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 29 0.58
43 21 0.42
ACGTcount: A:0.34, C:0.30, G:0.17, T:0.20
Consensus pattern (41 bp):
TCCTCATCACGAAGGAACAACATCATCCATAGATACAGAAC
Found at i:5753668 original size:3 final size:3
Alignment explanation
Indices: 5753660--5753749 Score: 155
Period size: 3 Copynumber: 29.7 Consensus size: 3
5753650 CGTCCAAGAC
5753660 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TA-T TAT
5753707 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5753750 CAAAATAAAT
Statistics
Matches: 84, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.02
3 77 0.92
4 4 0.05
5 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5761237 original size:12 final size:13
Alignment explanation
Indices: 5761201--5761237 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
5761191 CCATTAAAAA
5761201 CAGGTTTGGAGCT
1 CAGGTTTGGAGCT
5761214 CAGGTTTGGAGCT
1 CAGGTTTGGAGCT
*
5761227 C-GGTTTAGAGC
1 CAGGTTTGGAGC
5761238 CTTAGATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.16, C:0.16, G:0.38, T:0.30
Consensus pattern (13 bp):
CAGGTTTGGAGCT
Found at i:5761809 original size:16 final size:16
Alignment explanation
Indices: 5761785--5761883 Score: 60
Period size: 16 Copynumber: 6.1 Consensus size: 16
5761775 GAGTCGAATT
* *
5761785 AAAACATAAATAATAA
1 AAAAGATAAAAAATAA
* *
5761801 AAAAGATAACTAAGTAAA
1 AAAAGATAA-AAAAT-AA
5761819 AAAAGAATAAACAAATAA
1 AAAAG-ATAAA-AAATAA
* *
5761837 AAATGAT-AAAAA-AC
1 AAAAGATAAAAAATAA
* *
5761851 AAAACA-AAACAATAA
1 AAAAGATAAAAAATAA
*
5761866 AAAAAATAAAAAATAA
1 AAAAGATAAAAAATAA
5761882 AA
1 AA
5761884 CAAACTGAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
14 9 0.15
15 9 0.15
16 20 0.32
17 4 0.06
18 13 0.21
19 7 0.11
ACGTcount: A:0.77, C:0.06, G:0.04, T:0.13
Consensus pattern (16 bp):
AAAAGATAAAAAATAA
Found at i:5761859 original size:20 final size:20
Alignment explanation
Indices: 5761827--5761877 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
5761817 AAAAAAGAAT
**
5761827 AAACAAATAAAAATGATAAA
1 AAACAAATAAAAACAATAAA
5761847 AAACAAA-ACAAAACAAT-AA
1 AAACAAATA-AAAACAATAAA
5761866 AAA-AAATAAAAA
1 AAACAAATAAAAA
5761878 ATAAAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 7 0.26
19 7 0.26
20 13 0.48
ACGTcount: A:0.80, C:0.08, G:0.02, T:0.10
Consensus pattern (20 bp):
AAACAAATAAAAACAATAAA
Found at i:5761864 original size:29 final size:30
Alignment explanation
Indices: 5761827--5761887 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
5761817 AAAAAAGAAT
**
5761827 AAACAAATAAAAATGATAAAAAACAAAACA
1 AAACAAATAAAAAAAATAAAAAACAAAACA
*
5761857 AAAC-AATAAAAAAAATAAAAAATAAAACA
1 AAACAAATAAAAAAAATAAAAAACAAAACA
5761886 AA
1 AA
5761888 CTGAAACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.80, C:0.08, G:0.02, T:0.10
Consensus pattern (30 bp):
AAACAAATAAAAAAAATAAAAAACAAAACA
Found at i:5761946 original size:18 final size:17
Alignment explanation
Indices: 5761923--5761979 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
5761913 TAATGGAATT
5761923 AAATAAAACATAG-ATAAA
1 AAATAAAA-A-AGAATAAA
5761941 AAATAAAAAAGAATAAA
1 AAATAAAAAAGAATAAA
5761958 AAA-AAATAAA-AATAAA
1 AAATAAA-AAAGAATAAA
5761974 GAAATA
1 -AAATA
5761980 CAATACATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
16 11 0.31
17 15 0.43
18 9 0.26
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (17 bp):
AAATAAAAAAGAATAAA
Found at i:5761958 original size:9 final size:10
Alignment explanation
Indices: 5761938--5761969 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
5761928 AAACATAGAT
5761938 AAAAAATAAA
1 AAAAAATAAA
*
5761948 AAAGAATAAA
1 AAAAAATAAA
5761958 AAAAAATAAA
1 AAAAAATAAA
5761968 AA
1 AA
5761970 TAAAGAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:5761984 original size:19 final size:18
Alignment explanation
Indices: 5761936--5761984 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
5761926 TAAAACATAG
5761936 ATAAAAAATAAA-AAAGA
1 ATAAAAAATAAATAAAGA
5761953 ATAAAAAA-AAATAAA-A
1 ATAAAAAATAAATAAAGA
5761969 ATAAAGAAATACAATA
1 ATAAA-AAATA-AATA
5761985 CATGTATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 9 0.32
17 14 0.50
18 1 0.04
19 4 0.14
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (18 bp):
ATAAAAAATAAATAAAGA
Found at i:5762059 original size:2 final size:2
Alignment explanation
Indices: 5762054--5762087 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5762044 GTTAAAATAG
*
5762054 AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5762088 CTATGTACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5762118 original size:10 final size:10
Alignment explanation
Indices: 5762103--5762140 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
5762093 TACATATGAA
*
5762103 AAATATAAGT
1 AAATATAAAT
5762113 AAATATAAAT
1 AAATATAAAT
5762123 AAA-ATAAAT
1 AAATATAAAT
*
5762132 AAAAATAAA
1 AAATATAAA
5762141 ATATTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (10 bp):
AAATATAAAT
Found at i:5762132 original size:15 final size:15
Alignment explanation
Indices: 5762101--5762143 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
5762091 TGTACATATG
*
5762101 AAAAATATAAGTAAAT
1 AAAAATA-AAATAAAT
*
5762117 ATAAATAAAATAAAT
1 AAAAATAAAATAAAT
5762132 AAAAATAAAATA
1 AAAAATAAAATA
5762144 TTAATTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:5764901 original size:21 final size:21
Alignment explanation
Indices: 5764876--5764955 Score: 124
Period size: 21 Copynumber: 3.8 Consensus size: 21
5764866 GTCCGAGTTA
*
5764876 CCCGCGACGGCCGCAATAGCG
1 CCCGCGACAGCCGCAATAGCG
*
5764897 TCCGCGACAGCCGCAATAGCG
1 CCCGCGACAGCCGCAATAGCG
5764918 CCCGCGACAGCCGCAATAGCG
1 CCCGCGACAGCCGCAATAGCG
* *
5764939 CCCGCGACGGTCGCAAT
1 CCCGCGACAGCCGCAAT
5764956 CACGGTAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.21, C:0.41, G:0.30, T:0.07
Consensus pattern (21 bp):
CCCGCGACAGCCGCAATAGCG
Found at i:5770280 original size:21 final size:20
Alignment explanation
Indices: 5770255--5770299 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5770245 TAGTTGAGTT
5770255 TTCTGTTACAAGTTGTTATGC
1 TTCTGTT-CAAGTTGTTATGC
* *
5770276 TTCTGTTTAAGTTGTTATGG
1 TTCTGTTCAAGTTGTTATGC
5770296 TTCT
1 TTCT
5770300 ATTTCAGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.53
Consensus pattern (20 bp):
TTCTGTTCAAGTTGTTATGC
Found at i:5770308 original size:20 final size:20
Alignment explanation
Indices: 5770264--5770308 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5770254 TTTCTGTTAC
*
5770264 AAGTTGTTATGCTTCTGTTT
1 AAGTTGTTATGCTTCTATTT
*
5770284 AAGTTGTTATGGTTCTATTT
1 AAGTTGTTATGCTTCTATTT
*
5770304 CAGTT
1 AAGTT
5770309 CAGTTGAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.20, T:0.53
Consensus pattern (20 bp):
AAGTTGTTATGCTTCTATTT
Found at i:5776025 original size:17 final size:17
Alignment explanation
Indices: 5775989--5776022 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5775979 ATAGAGGTAC
*
5775989 TTTTTTTTTAATTTTAA
1 TTTTTTTTTAATTGTAA
5776006 TTTTTTATTTAATTGTA
1 TTTTTT-TTTAATTGTA
5776023 TTTATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTTTTTAATTGTAA
Found at i:5784448 original size:23 final size:22
Alignment explanation
Indices: 5784413--5784482 Score: 77
Period size: 23 Copynumber: 3.1 Consensus size: 22
5784403 ACAAACGTGC
*
5784413 CACAAAGACAGAGATAAATGTG
1 CACAAAGGCAGAGATAAATGTG
* *
5784435 TCACAAAGGTAGAGATAAACGTG
1 -CACAAAGGCAGAGATAAATGTG
* *
5784458 CAACACAGGCCGAGATAAATGTG
1 C-ACAAAGGCAGAGATAAATGTG
5784481 CA
1 CA
5784483 ACACATAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
22 2 0.05
23 37 0.95
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.14
Consensus pattern (22 bp):
CACAAAGGCAGAGATAAATGTG
Found at i:5784483 original size:23 final size:23
Alignment explanation
Indices: 5784421--5784487 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
5784411 GCCACAAAGA
*
5784421 CAGAGATAAATGTGTC-ACAAAGG
1 CAGAGATAAATGTG-CAACACAGG
* *
5784444 TAGAGATAAACGTGCAACACAGG
1 CAGAGATAAATGTGCAACACAGG
*
5784467 CCGAGATAAATGTGCAACACA
1 CAGAGATAAATGTGCAACACA
5784488 TAATTATTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (23 bp):
CAGAGATAAATGTGCAACACAGG
Found at i:5785855 original size:21 final size:22
Alignment explanation
Indices: 5785815--5785870 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
5785805 TAATTATTAA
*
5785815 AATATTTAAAATACATTTAT-T
1 AATATTTATAATACATTTATAT
5785836 AATATTTATAATA-ATATTATAT
1 AATATTTATAATACAT-TTATAT
* *
5785858 TATATTTTTAATA
1 AATATTTATAATA
5785871 TTATAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.07
21 16 0.53
22 12 0.40
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTTATAATACATTTATAT
Found at i:5785891 original size:31 final size:32
Alignment explanation
Indices: 5785829--5785904 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
5785819 TTTAAAATAC
*
5785829 ATTTATTAATATTTATAATAATATTATATTAT
1 ATTTATTAATATTTATAATAATATCATATTAT
5785861 ATTT-TTAATA-TTATAATAAATAATCA-ATTAT
1 ATTTATTAATATTTATAAT-AAT-ATCATATTAT
*
5785892 ATTATAATAATAT
1 ATT-TATTAATAT
5785905 AAGCTATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 7 0.19
31 17 0.46
32 8 0.22
33 5 0.14
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTTATTAATATTTATAATAATATCATATTAT
Found at i:5785896 original size:22 final size:23
Alignment explanation
Indices: 5785868--5785917 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
5785858 TATATTTTTA
*
5785868 ATATTATAATAA-ATAATCAATT
1 ATATTATAATAATATAAGCAATT
*
5785890 ATATTATAATAATATAAGCTATT
1 ATATTATAATAATATAAGCAATT
5785913 ATATT
1 ATATT
5785918 TTTTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
ATATTATAATAATATAAGCAATT
Found at i:5786019 original size:19 final size:18
Alignment explanation
Indices: 5785995--5786063 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
5785985 ATATTATTAA
5785995 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
5786014 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
5786032 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
5786054 ATT-TTAATAA
1 ATTATTAATAA
5786064 AGATATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:5786038 original size:27 final size:27
Alignment explanation
Indices: 5785958--5786043 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
5785948 AATAAAATTT
* *
5785958 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
5785985 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
5786012 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
5786041 ATA
1 ATA
5786044 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:5786084 original size:23 final size:23
Alignment explanation
Indices: 5786058--5786102 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5786048 AATAATATTT
5786058 TAATAAAGATATATAAAATATAC
1 TAATAAAGATATATAAAATATAC
* * * *
5786081 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATATAAAATATA
5786103 ATATAACACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TAATAAAGATATATAAAATATAC
Found at i:5786239 original size:28 final size:27
Alignment explanation
Indices: 5786208--5786295 Score: 71
Period size: 24 Copynumber: 3.3 Consensus size: 27
5786198 ATAAAAATAA
5786208 TATTTGAATAATAAATAAATTATTTTAG
1 TATTT-AATAATAAATAAATTATTTTAG
* *
5786236 TATTT--TAA-AAAT-AATAATATTAAG
1 TATTTAATAATAAATAAATTAT-TTTAG
*
5786260 T-TTT-ATAATAAATAATATTATTTATTG
1 TATTTAATAATAAATAA-ATTATTT-TAG
5786287 TATTTAATA
1 TATTTAATA
5786296 TTTGTAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 15
0.70 0.07 0.22
Matches are distributed among these distances:
23 8 0.17
24 12 0.26
25 7 0.15
26 3 0.06
27 6 0.13
28 8 0.17
29 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (27 bp):
TATTTAATAATAAATAAATTATTTTAG
Found at i:5786263 original size:22 final size:22
Alignment explanation
Indices: 5786238--5786279 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5786228 TATTTTAGTA
5786238 TTTTAAAA-ATAATAATATTAAG
1 TTTTAAAATA-AATAATATTAAG
*
5786260 TTTTATAATAAATAATATTA
1 TTTTAAAATAAATAATATTA
5786280 TTTATTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTTTAAAATAAATAATATTAAG
Found at i:5786272 original size:25 final size:26
Alignment explanation
Indices: 5786215--5786281 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
5786205 TAATATTTGA
*
5786215 ATAATAAATAA-ATTATTTTAGTATTT
1 ATAATAAATAATATTA-TTAAGTATTT
*
5786241 -TAA-AAATAATAATATTAAGT-TTT
1 ATAATAAATAATATTATTAAGTATTT
5786264 ATAATAAATAATATTATT
1 ATAATAAATAATATTATT
5786282 TATTGTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
23 3 0.09
24 14 0.40
25 18 0.51
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (26 bp):
ATAATAAATAATATTATTAAGTATTT
Found at i:5788753 original size:246 final size:246
Alignment explanation
Indices: 5788314--5788805 Score: 740
Period size: 246 Copynumber: 2.0 Consensus size: 246
5788304 AACCATGTTT
* *
5788314 TTATTTCAAATATCAGAGTCATACTTTTTATAAACAGCGAAAAACGTTTTTGTACATAGGAAACA
1 TTATTTCAAATATCAGAGTCATACTTTTTATAAACAGCGAAAAACATCTTTGTACATAGGAAACA
* * * *
5788379 CACTAGAGGATCCATATATTTTTCAGATGCACTAGGTAATTATCAAGAAGGAAAATACAACTTCT
66 CACTAGAGGATCCAGATATTTTTCAGAGGCACTAGATAATTATCAAGAAGGAAAATACAACTTAT
* * *
5788444 ACAAGTTGATCGGATTTCAAAAATAATTGCTACAAAATGGGGGTCAATAGCTAAATTATTTAACA
131 ACAAGTTGATCGAATTTCAAAAATAATTGCTACAAAATAGGGGTCAATAGCTAAATGATTTAACA
*
5788509 AGAGCCTTAGAATTTGCTGCTTTGAGGAACGTTTAGGATTTCATTACACTA
196 AGAGCCCTAGAATTTGCTGCTTTGAGGAACGTTTAGGATTTCATTACACTA
*
5788560 TTATTTCAAATATCAGAGTCATACTTTTTATAAACAGCGAAAAATATCTTTGTACATA-GAGAAC
1 TTATTTCAAATATCAGAGTCATACTTTTTATAAACAGCGAAAAACATCTTTGTACATAGGA-AAC
* * * * *
5788624 ATACTAGAGGATTCAGATATTTTTCGGAGGCACTAGATAATTATCAGGAAGGGAAATACAACTTA
65 ACACTAGAGGATCCAGATATTTTTCAGAGGCACTAGATAATTATCAAGAAGGAAAATACAACTTA
* *
5788689 TACAAGTTGATCGAATTTCAGAAAA-AATGTTCTACAAAA-AGGGGTCAGTTA-CTAAATGATTT
130 TACAAGTTGATCGAATTTCA-AAAATAAT-TGCTACAAAATAGGGGTCA-ATAGCTAAATGATTT
* *
5788751 AACCAGATCCCTAGAATTTGCTGCTTTGAGGAACGTTTAGGATTTCATTACACTA
192 AACAAGAGCCCTAGAATTTGCTGCTTTGAGGAACGTTTAGGATTTCATTACACTA
5788806 GAAAGTATTC
Statistics
Matches: 222, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
245 2 0.01
246 205 0.92
247 15 0.07
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (246 bp):
TTATTTCAAATATCAGAGTCATACTTTTTATAAACAGCGAAAAACATCTTTGTACATAGGAAACA
CACTAGAGGATCCAGATATTTTTCAGAGGCACTAGATAATTATCAAGAAGGAAAATACAACTTAT
ACAAGTTGATCGAATTTCAAAAATAATTGCTACAAAATAGGGGTCAATAGCTAAATGATTTAACA
AGAGCCCTAGAATTTGCTGCTTTGAGGAACGTTTAGGATTTCATTACACTA
Found at i:5799081 original size:21 final size:21
Alignment explanation
Indices: 5799057--5799100 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5799047 ACAAACTAAG
5799057 ATTA-AAATTAAATTAAATTAA
1 ATTATAAATT-AATTAAATTAA
* *
5799078 ATTATATATTAATTCAATTAA
1 ATTATAAATTAATTAAATTAA
5799099 AT
1 AT
5799101 CGAATATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTATAAATTAATTAAATTAA
Found at i:5803478 original size:5 final size:5
Alignment explanation
Indices: 5803468--5803501 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
5803458 TAAACCATCG
5803468 AAATA AAATA AAATA AAATA AAATA AAATA AAAT
1 AAATA AAATA AAATA AAATA AAATA AAATA AAAT
5803502 GGCAAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:5805514 original size:21 final size:21
Alignment explanation
Indices: 5805490--5805530 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5805480 TTTCAAATGG
*
5805490 CACCACAATCATGTCAGATGA
1 CACCACAAGCATGTCAGATGA
*
5805511 CACCACAAGCATTTCAGATG
1 CACCACAAGCATGTCAGATG
5805531 TCGCCATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.15, T:0.20
Consensus pattern (21 bp):
CACCACAAGCATGTCAGATGA
Found at i:5814130 original size:6 final size:6
Alignment explanation
Indices: 5814119--5814145 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5814109 CATATACTCA
5814119 ATAATT ATAATT ATAATT ATAATT ATA
1 ATAATT ATAATT ATAATT ATAATT ATA
5814146 TAAGTGAAGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:5814232 original size:11 final size:11
Alignment explanation
Indices: 5814218--5814243 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5814208 CATTTCTCTG
5814218 ATATTTTTCAT
1 ATATTTTTCAT
5814229 ATATTTTTCAT
1 ATATTTTTCAT
5814240 ATAT
1 ATAT
5814244 AATATAATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (11 bp):
ATATTTTTCAT
Found at i:5815169 original size:31 final size:31
Alignment explanation
Indices: 5815130--5815198 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
5815120 AAAGTTCAGA
* *
5815130 TACTAAAACATA-CTAAAAATGATAGTTTAGG
1 TACTAAAACAAATC-AAAAATAATAGTTTAGG
* *
5815161 TATTAAAACAAATCAAAACTAATAGTTTAGG
1 TACTAAAACAAATCAAAAATAATAGTTTAGG
5815192 TACTAAA
1 TACTAAA
5815199 TGCACAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (31 bp):
TACTAAAACAAATCAAAAATAATAGTTTAGG
Found at i:5815643 original size:159 final size:160
Alignment explanation
Indices: 5815354--5815673 Score: 633
Period size: 159 Copynumber: 2.0 Consensus size: 160
5815344 ATGTTTACAT
5815354 TTTTGTTATCAACCAGTTAAATCTTTTGAACATATATTATATTGTAATCACTTTATAAACAATTT
1 TTTTGTTATCAACCAGTTAAATCTTTTGAACATATATTATATTGTAATCACTTTATAAACAATTT
5815419 TAAAAGCATAATCATAAGCACAACTATATTTGGTCTAAAAAATCATCCCATATTCAACTTTTGTA
66 TAAAAGCATAATCATAAGCACAACTATATTTGGTCTAAAAAATCATCCCATATTCAACTTTTGTA
5815484 ACA-TTAATTTAGATTAGTCAATTAATGAA
131 ACATTTAATTTAGATTAGTCAATTAATGAA
5815513 TTTTGTTATCAACCAGTTAAATCTTTTGAACATATATTATATTGTAATCACTTTATAAACAATTT
1 TTTTGTTATCAACCAGTTAAATCTTTTGAACATATATTATATTGTAATCACTTTATAAACAATTT
5815578 TAAAAGCATAATCATAAGCACAACTATATTTGGTCTAAAAAATCATCCCATATTCAACTTTTGTA
66 TAAAAGCATAATCATAAGCACAACTATATTTGGTCTAAAAAATCATCCCATATTCAACTTTTGTA
5815643 ACATTTAATTTAGATTAGTCAATTAATGAA
131 ACATTTAATTTAGATTAGTCAATTAATGAA
5815673 T
1 T
5815674 CAAACACAAA
Statistics
Matches: 160, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
159 133 0.83
160 27 0.17
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (160 bp):
TTTTGTTATCAACCAGTTAAATCTTTTGAACATATATTATATTGTAATCACTTTATAAACAATTT
TAAAAGCATAATCATAAGCACAACTATATTTGGTCTAAAAAATCATCCCATATTCAACTTTTGTA
ACATTTAATTTAGATTAGTCAATTAATGAA
Found at i:5818042 original size:3 final size:3
Alignment explanation
Indices: 5818034--5818061 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5818024 GTATAAACTC
5818034 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5818062 GTTGTTGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5827370 original size:2 final size:2
Alignment explanation
Indices: 5827363--5827404 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
5827353 TTAAATTAAA
* * *
5827363 AT AT AT AT AT AT AT AT AT AT AT AT TT A- AT TT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5827404 A
1 A
5827405 CCCGGCCCGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5827534 original size:19 final size:19
Alignment explanation
Indices: 5827510--5827548 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5827500 AAATCCCGTG
*
5827510 GTTTTTTAAGCGGAGACGA
1 GTTTTTTAAACGGAGACGA
*
5827529 GTTTTTTAAACGGGGACGA
1 GTTTTTTAAACGGAGACGA
5827548 G
1 G
5827549 ACGAGGGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.10, G:0.33, T:0.31
Consensus pattern (19 bp):
GTTTTTTAAACGGAGACGA
Found at i:5835147 original size:30 final size:30
Alignment explanation
Indices: 5835082--5835156 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 30
5835072 GTTAGTTGAC
*
5835082 ATTTTCATGTATGTTTTATTATTAACGTTTA
1 ATTTT-ATGTATGTTTTATTATTAACGTATA
* *
5835113 ATTTTATGCATGTTTTATTATTAATGTGATA
1 ATTTTATGTATGTTTTATTATTAACGT-ATA
*
5835144 TTTTTATGTATGT
1 ATTTTATGTATGT
5835157 ATGTGACATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 20 0.53
31 18 0.47
ACGTcount: A:0.25, C:0.04, G:0.12, T:0.59
Consensus pattern (30 bp):
ATTTTATGTATGTTTTATTATTAACGTATA
Found at i:5835311 original size:31 final size:31
Alignment explanation
Indices: 5835270--5835329 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
5835260 AATCATACCT
5835270 AATGTATACTTTTTGTTTCATATTAGTACAC
1 AATGTATACTTTTTGTTTCATATTAGTACAC
* *
5835301 AATGTTTACTTTTTGTTTCATTTTAGTAC
1 AATGTATACTTTTTGTTTCATATTAGTAC
5835330 CTAAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (31 bp):
AATGTATACTTTTTGTTTCATATTAGTACAC
Found at i:5837154 original size:15 final size:15
Alignment explanation
Indices: 5837134--5837172 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
5837124 GTTTTTACTC
5837134 AGAGGAAGAAGAGGA
1 AGAGGAAGAAGAGGA
*
5837149 AGAGGAAGACGAGGA
1 AGAGGAAGAAGAGGA
*
5837164 GGAGGAAGA
1 AGAGGAAGA
5837173 TGATAGCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (15 bp):
AGAGGAAGAAGAGGA
Found at i:5839662 original size:17 final size:18
Alignment explanation
Indices: 5839623--5839668 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
5839613 TGTTTCTGAG
5839623 GGAATTAGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
*
5839641 GGAATTAGAATCTGT-CA
1 GGAATTAGAATCTGTGAA
5839658 GGAATTAGAAT
1 GGAATTAGAAT
5839669 TCAATTCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.28
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:5840333 original size:225 final size:228
Alignment explanation
Indices: 5840047--5840518 Score: 738
Period size: 225 Copynumber: 2.1 Consensus size: 228
5840037 ATAAAGTTTC
* * *
5840047 ACCCGACCCGACCCGAATATATGAATTAGAAATCGATCCGAAATAATAAAAAAAATATTTTTATT
1 ACCCGACCCGACCCAAATATATGAATTAGAAACCGACCCGAAATAATAAAAAAAATATTTTTATT
*
5840112 CAATAAAAACAATGACTTAATT-AAAAAATATATATAGAGGGGTATTATTGTAATTATTCCTAAA
66 CAATAAAAACAATGAC-TAATTGAAAAAATATATATAGAGGAGTATTATTGTAATTATTCCTAAA
** *
5840176 TATATAAGGTAAAATTATATAT-TTTTTGGGTCGGGTCGAGTATTTTTCACCCTAAACCCAAACC
130 TATATAAGGTAAAATTATATATATTTTCAGGTCGGGTCAAGTATTTTTCACCCTAAACCCAAACC
5840240 CGACCCGACCCGAATATCACACTTA-AAAAAACG
195 CGACCCGACCCGAATATCACACTTATAAAAAACG
*
5840273 A-CCGACCCGACCCAAATATATGAATTAGAAACCCGACCCGAAATAAT-AAAAAATTATTTTTAT
1 ACCCGACCCGACCCAAATATATGAATTAGAAA-CCGACCCGAAATAATAAAAAAAATATTTTTAT
* * * *
5840336 TCAATAAAAATAGTGACTAATTGAAAAAATGTATATAGAGGAGTATTATTGTAATTATTTCTAAA
65 TCAATAAAAACAATGACTAATTGAAAAAATATATATAGAGGAGTATTATTGTAATTATTCCTAAA
* *
5840401 TATATAAGGTAAAATTATATATATTTTCAGGTCGGGTCAAGTATTTTTCACCCTAAACCCGAACT
130 TATATAAGGTAAAATTATATATATTTTCAGGTCGGGTCAAGTATTTTTCACCCTAAACCCAAACC
*
5840466 CGACCCGACCCGAATATCACACTTATAAAAACCG
195 CGACCCGACCCGAATATCACACTTATAAAAAACG
* *
5840500 ACCCGACCTGACCAAAATA
1 ACCCGACCCGACCCAAATA
5840519 AAGTTTCACC
Statistics
Matches: 224, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
224 5 0.02
225 120 0.54
226 76 0.34
227 8 0.04
228 15 0.07
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.28
Consensus pattern (228 bp):
ACCCGACCCGACCCAAATATATGAATTAGAAACCGACCCGAAATAATAAAAAAAATATTTTTATT
CAATAAAAACAATGACTAATTGAAAAAATATATATAGAGGAGTATTATTGTAATTATTCCTAAAT
ATATAAGGTAAAATTATATATATTTTCAGGTCGGGTCAAGTATTTTTCACCCTAAACCCAAACCC
GACCCGACCCGAATATCACACTTATAAAAAACG
Found at i:5840893 original size:15 final size:15
Alignment explanation
Indices: 5840875--5840923 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
5840865 AGATTATTTA
*
5840875 AAAATTATTTTATGT
1 AAAATTATTTTATAT
* * *
5840890 AAAATGA-ATTATCT
1 AAAATTATTTTATAT
5840904 AAAATTATTTTATAT
1 AAAATTATTTTATAT
5840919 AAAAT
1 AAAAT
5840924 AAATTATATT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (15 bp):
AAAATTATTTTATAT
Found at i:5840907 original size:29 final size:29
Alignment explanation
Indices: 5840853--5840930 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
5840843 ATGCCATTGG
*
5840853 TTTTATG-AAAATAGATTATTTAAAAATTA
1 TTTTATGTAAAATA-ATTATCTAAAAATTA
5840882 TTTTATGTAAAATGAATTATCT-AAAATTA
1 TTTTATGTAAAAT-AATTATCTAAAAATTA
*
5840911 TTTTATATAAAATAAATTAT
1 TTTTATGTAAAAT-AATTAT
5840931 ATTTTTTGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 32 0.73
30 11 0.25
31 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTTATGTAAAATAATTATCTAAAAATTA
Found at i:5840956 original size:13 final size:14
Alignment explanation
Indices: 5840929--5840963 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5840919 AAAATAAATT
*
5840929 ATATTTTTTGAAAA
1 ATATTTTTCGAAAA
5840943 ATATTTTTCGAAAA
1 ATATTTTTCGAAAA
*
5840957 TTATTTT
1 ATATTTT
5840964 ACGGTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (14 bp):
ATATTTTTCGAAAA
Found at i:5841231 original size:30 final size:27
Alignment explanation
Indices: 5841197--5841258 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 27
5841187 CCCTAATTTT
*
5841197 AATTATTAGTATT-TTATTAACATAATACTA
1 AATTATTA-TATTAATATTAA-AT-ATA-TA
5841227 AATTATTATATTAATATTAAATATATA
1 AATTATTATATTAATATTAAATATATA
5841254 AATTA
1 AATTA
5841259 ATATTATTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.23
28 3 0.10
29 6 0.20
30 14 0.47
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (27 bp):
AATTATTATATTAATATTAAATATATA
Found at i:5841241 original size:19 final size:19
Alignment explanation
Indices: 5841219--5841261 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5841209 TTTATTAACA
*
5841219 TAATACTAAAT-TATTATAT
1 TAATACTAAATATA-TAAAT
*
5841238 TAATATTAAATATATAAAT
1 TAATACTAAATATATAAAT
5841257 TAATA
1 TAATA
5841262 TTATTCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATACTAAATATATAAAT
Found at i:5841300 original size:22 final size:22
Alignment explanation
Indices: 5841238--5841308 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 22
5841228 ATTATTATAT
* *
5841238 TAATATTAAATATATAAATTAA
1 TAATATTATATTTATAAATTAA
* * *
5841260 TATTATTCATTATTAATAATTTAA
1 TAATATT-A-TATTTATAAATTAA
5841284 TAATATTATATTTATAAA--AA
1 TAATATTATATTTATAAATTAA
5841304 TAATA
1 TAATA
5841309 GATAATGTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
20 7 0.18
22 14 0.36
23 2 0.05
24 16 0.41
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATATTATATTTATAAATTAA
Found at i:5849495 original size:2 final size:2
Alignment explanation
Indices: 5849490--5849545 Score: 89
Period size: 2 Copynumber: 28.5 Consensus size: 2
5849480 AGTTACTAAT
5849490 TA TA TA TCA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5849532 TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA T
5849546 TCTATTATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.04
2 48 0.94
3 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5850976 original size:21 final size:18
Alignment explanation
Indices: 5850950--5850998 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 18
5850940 TTTATTATCC
5850950 TTTTATTTTCTTATATCATAT
1 TTTTATTTTCTT-T-T-ATAT
5850971 TTTTATTTTCTTTTATAT
1 TTTTATTTTCTTTTATAT
5850989 TTTTATTTTC
1 TTTTATTTTC
5850999 AATAAATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.50
19 1 0.04
20 1 0.04
21 12 0.43
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTATTTTCTTTTATAT
Found at i:5850985 original size:31 final size:33
Alignment explanation
Indices: 5850934--5850994 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
5850924 TCGACTGTCA
5850934 ATATTCTTTATTATCCTTTTAT-TTTCTTATATC
1 ATATTCTTTATTATCCTTTTATATTT-TTATATC
*
5850967 ATATT-TTTATT-TTCTTTTATATTTTTAT
1 ATATTCTTTATTATCCTTTTATATTTTTAT
5850995 TTTCAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 12 0.46
32 9 0.35
33 5 0.19
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (33 bp):
ATATTCTTTATTATCCTTTTATATTTTTATATC
Found at i:5851049 original size:23 final size:23
Alignment explanation
Indices: 5851005--5851047 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5850995 TTTCAATAAA
5851005 TATGTCTGTATGACACGTTTTCT
1 TATGTCTGTATGACACGTTTTCT
* *
5851028 TATGTCT-TTTGACATGTTTT
1 TATGTCTGTATGACACGTTTT
5851048 TCGATCGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.53
Consensus pattern (23 bp):
TATGTCTGTATGACACGTTTTCT
Found at i:5852137 original size:21 final size:21
Alignment explanation
Indices: 5852113--5852162 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
5852103 GTTTTAATTT
*
5852113 TTAAAATTTAGTGTCAATGAA
1 TTAAAATTTAGAGTCAATGAA
5852134 TTAAAATTTAGAGTCAATGAA
1 TTAAAATTTAGAGTCAATGAA
5852155 TTAAAATT
1 TTAAAATT
5852163 CTGAATTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (21 bp):
TTAAAATTTAGAGTCAATGAA
Found at i:5857014 original size:16 final size:16
Alignment explanation
Indices: 5856993--5857031 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
5856983 GAGGAGTGGA
5856993 AAGATCCCCTGAATCC
1 AAGATCCCCTGAATCC
5857009 AAGATCCCCTGAATCC
1 AAGATCCCCTGAATCC
5857025 AAGATCC
1 AAGATCC
5857032 ATGATTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.36, G:0.13, T:0.18
Consensus pattern (16 bp):
AAGATCCCCTGAATCC
Found at i:5860155 original size:56 final size:55
Alignment explanation
Indices: 5860077--5860268 Score: 249
Period size: 56 Copynumber: 3.4 Consensus size: 55
5860067 CCAAAAAAAG
* *
5860077 GGGCCCCAAAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCATAAAAATA
1 GGGCCCCAAAATTGAGTATATCTATCAGTTGTTGCCATTAAAAAGCATAAAAATA
* * * * *
5860132 GGTGCCTCAAAATTGAGTATATCTATCAGTTATTACCATTAAGAATCATAAAAATA
1 GG-GCCCCAAAATTGAGTATATCTATCAGTTGTTGCCATTAAAAAGCATAAAAATA
* * *
5860188 GAGGCCCCGAAATTGAGTATATGTATCAGCTGTTGCCATTAAAAAGCATAAAAATA
1 G-GGCCCCAAAATTGAGTATATCTATCAGTTGTTGCCATTAAAAAGCATAAAAATA
* *
5860244 GGAGCCCCGAAATTGAATATATCTA
1 GG-GCCCCAAAATTGAGTATATCTA
5860269 GAAAATATAG
Statistics
Matches: 118, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
55 3 0.03
56 114 0.97
57 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (55 bp):
GGGCCCCAAAATTGAGTATATCTATCAGTTGTTGCCATTAAAAAGCATAAAAATA
Found at i:5861432 original size:56 final size:56
Alignment explanation
Indices: 5861346--5861545 Score: 276
Period size: 56 Copynumber: 3.6 Consensus size: 56
5861336 CAGGTCCCCC
* * *
5861346 AAAAAAAGGGCCCCCAAAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCAT
1 AAAAATAGGGGCCCCAAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
* *
5861402 AAAAATAGGGGCCTCAAAATCGAGTATATCTAT-AGGTTGTTGCCATTAAGAATCAT
1 AAAAATAGGGGCCCCAAAATCGAGTATATCTATCA-GTTGTTGCCATTAAGAAGCAT
* * * * *
5861458 AAAAATAGAGGCCCCGAAATTGAGTATATGTATCAGTTGTTTCCATTAAGAAGCAT
1 AAAAATAGGGGCCCCAAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
* *
5861514 AAAAATAGGGGCCCCGAAATCGAATATATCTA
1 AAAAATAGGGGCCCCAAAATCGAGTATATCTA
5861546 GAAAATATGG
Statistics
Matches: 126, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
55 1 0.01
56 124 0.98
57 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (56 bp):
AAAAATAGGGGCCCCAAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
Found at i:5862695 original size:56 final size:56
Alignment explanation
Indices: 5862625--5862807 Score: 269
Period size: 56 Copynumber: 3.3 Consensus size: 56
5862615 AAGAGTCCCG
* *
5862625 AAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCATAAAAATAGGGGCCTCA
1 AAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCATAAAAATAGGGGCCCCA
* * *
5862681 AAATCGAGTATATCTATCAATTGTTGCCATTAAGAATCATAAAAATAGAGGCCCCA
1 AAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCATAAAAATAGGGGCCCCA
* * * *
5862737 AAATTGAGTATATGTATCAGTTATTGTCATTAAGAAGCATAAAAATA-GGGCCCCA
1 AAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCATAAAAATAGGGGCCCCA
*
5862792 AAATCGAATATATCTA
1 AAATCGAGTATATCTA
5862808 AAAAATATGG
Statistics
Matches: 112, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
55 20 0.18
56 92 0.82
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (56 bp):
AAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCATAAAAATAGGGGCCCCA
Found at i:5864149 original size:19 final size:20
Alignment explanation
Indices: 5864113--5864150 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5864103 CAGGTAAATT
* *
5864113 AAATCAATTTTTATAAAAAC
1 AAATCAATTTATAGAAAAAC
5864133 AAAT-AATTTATAGAAAAA
1 AAATCAATTTATAGAAAAA
5864151 ATCGATTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (20 bp):
AAATCAATTTATAGAAAAAC
Found at i:5868987 original size:106 final size:105
Alignment explanation
Indices: 5868802--5869921 Score: 1570
Period size: 106 Copynumber: 11.1 Consensus size: 105
5868792 GTATTGTTCC
* ** * * * *
5868802 GAGTCCAATATCCTCCGCCGTGAAATTGAAATTGGCTCTGGAACTG-GAAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTT-TTTATTGACA
* *
5868866 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG-CATG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
5868908 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT-TTTATTGACAA
5868973 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5869014 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT-TTTATTGACAA
*
5869079 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5869120 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG----GAAATT-----G--TTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTTTTATTGACAAC
5869174 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5869214 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT-TTTATTGACAA
5869279 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5869320 GAGTCCAATATCCTTCGTTGTGAAGTTGAAGTTGG----GAAATT-----G--TTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTTTTATTGACAAC
5869374 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5869414 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT-TTTATTGACAA
5869479 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5869520 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG----GAAATT-----G--TTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTTTTATTGACAAC
*
5869574 CAGCGGTACCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5869614 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT-TTTATTGACAA
* *** *
5869679 TCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5869720 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG----GAAATT-----G--TTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTTTTATTGACAAC
5869774 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* **
5869814 GAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG------TTGACAGT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTTTTATTGACAAC
*** *
5869873 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTT
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5869913 GAGTCCAAT
1 GAGTCCAAT
5869922 GAGCGGATGT
Statistics
Matches: 929, Mismatches: 38, Indels: 101
0.87 0.04 0.09
Matches are distributed among these distances:
94 338 0.36
97 4 0.00
98 24 0.03
99 50 0.05
102 24 0.03
103 4 0.00
106 483 0.52
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:5869149 original size:43 final size:43
Alignment explanation
Indices: 5869088--5869243 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 43
5869078 ACCAGTGGTC
5869088 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** ***
5869131 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
5869181 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
5869225 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
5869244 ATTGGCTCTG
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
43 40 0.48
44 1 0.01
45 3 0.04
46 7 0.08
48 7 0.08
49 3 0.04
50 1 0.01
51 22 0.26
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:5869213 original size:94 final size:94
Alignment explanation
Indices: 5869052--5869921 Score: 1182
Period size: 94 Copynumber: 8.8 Consensus size: 94
5869042 AAATTGGTTC
* * *
5869052 TGAAATTGAGAAGTTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
5869117 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
5869146 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
5869211 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
5869240 TGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1 TGAAATT-G----G-----GA-AA-TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
5869305 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
54 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
5869346 TGAAGTTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
5869411 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
5869440 TGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1 TGAAATT-G----G-----GA-AA-TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
5869505 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
54 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
5869546 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTACCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
5869611 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
**
5869640 TGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAGTCAGCGGTCCCTTCGTCGTGAAGTTG
1 TGAAATT-G----G-----GA-AA-TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*** *
5869705 AACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGT
54 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
5869746 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
5869811 CTGGAGTTCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
*** ** *
5869840 TGAAATTGGCTCTGAAATTGAGAAGTTGACAGTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGT
1 TGAAATTGG----GAAATTGTTTA-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
** *
5869905 ACTGTCTTGAGTCCAAT
61 GTTGTCTGGAGTCCAAT
5869922 GAGCGGATGT
Statistics
Matches: 705, Mismatches: 30, Indels: 77
0.87 0.04 0.09
Matches are distributed among these distances:
94 355 0.50
95 9 0.01
96 6 0.01
98 8 0.01
99 53 0.08
101 3 0.00
104 6 0.01
105 9 0.01
106 256 0.36
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (94 bp):
TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGT
Found at i:5869290 original size:200 final size:200
Alignment explanation
Indices: 5868946--5869921 Score: 1723
Period size: 200 Copynumber: 4.9 Consensus size: 200
5868936 AAATTGGCTC
* * *
5868946 TGAAATTGAGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
5869011 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGAGAAGTTGTTTATTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
*
5869076 CAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
5869141 GAAGT
196 GAAGT
5869146 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
5869211 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
5869276 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
5869341 GAAGT
196 GAAGT
*
5869346 TGAAGTTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
5869411 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
5869476 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
5869541 GAAGT
196 GAAGT
*
5869546 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTACCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
5869611 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
** *** *
5869676 CAGTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
5869741 GAAGT
196 GAAGT
5869746 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
5869811 CTGGAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA---G----TTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
** *** *
5869869 CAGTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTTGAGTCCAAT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
5869922 GAGCGGATGT
Statistics
Matches: 760, Mismatches: 16, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
193 57 0.08
197 1 0.00
200 702 0.92
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (200 bp):
TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
GAAGT
Found at i:5869349 original size:43 final size:43
Alignment explanation
Indices: 5869288--5869443 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 43
5869278 ACCAGCGGTC
5869288 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** ***
5869331 CCTTCGTTGTGAAGTTGAAGTTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
5869381 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
5869425 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
5869444 ATTGGCTCTG
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
43 40 0.48
44 1 0.01
45 3 0.04
46 7 0.08
48 7 0.08
49 3 0.04
50 1 0.01
51 22 0.26
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:5869549 original size:43 final size:43
Alignment explanation
Indices: 5869488--5869643 Score: 143
Period size: 43 Copynumber: 3.4 Consensus size: 43
5869478 ACCAGCGGTC
5869488 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** *
5869531 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTA-
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA---ATAT
5869582 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
5869625 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
5869644 ATTGGCTCTG
Statistics
Matches: 86, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
42 2 0.02
43 40 0.47
45 3 0.03
46 7 0.08
48 7 0.08
49 3 0.03
51 22 0.26
52 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:5869554 original size:400 final size:400
Alignment explanation
Indices: 5868802--5869921 Score: 1826
Period size: 400 Copynumber: 2.8 Consensus size: 400
5868792 GTATTGTTCC
* ** * * * *
5868802 GAGTCCAATATCCTCCGCCGTGAAATTGAAATTGGCTCTGGAACTG-GAAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTATTGACA
*
5868866 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG-CATGGAGTCCAATATCCTTCGTTGTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTC-TGGAGTCCAATATCCTTCGTTGTG
5868930 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
129 AAGTTGAAATTGG----GAAATT-----G---TTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
*
5868995 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTG
182 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG
*
5869060 AGAAGTTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
247 AGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
*
5869125 CAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTC
312 CAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTACCTTCGTC
5869190 GTGAAGTTGAACTTGCGTTGTCTG
377 GTGAAGTTGAACTTGCGTTGTCTG
5869214 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
5869279 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
*
5869344 GTTGAAGTTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
131 GTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
5869409 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATT
196 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATT
5869474 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
261 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
5869539 GTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTACCTTCGTCGTGAAGTTGAACTT
326 GTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTACCTTCGTCGTGAAGTTGAACTT
5869604 GCGTTGTCTG
391 GCGTTGTCTG
*
5869614 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* ** *
5869679 TCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
5869744 GTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
131 GTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
*
5869809 GTCTGGAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA---G----TT
196 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATT
** *** *
5869867 GACAGTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTTGAGTCCAAT
261 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
5869922 GAGCGGATGT
Statistics
Matches: 679, Mismatches: 27, Indels: 23
0.93 0.04 0.03
Matches are distributed among these distances:
393 51 0.08
397 1 0.00
400 491 0.72
403 1 0.00
408 6 0.01
412 127 0.19
413 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (400 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATT
GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
GTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTACCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTG
Found at i:5877077 original size:16 final size:16
Alignment explanation
Indices: 5877056--5877086 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5877046 AAAAAATTTA
5877056 TTCGTTTATGTTCGTG
1 TTCGTTTATGTTCGTG
5877072 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
5877087 TTATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTG
Found at i:5877316 original size:2 final size:2
Alignment explanation
Indices: 5877309--5877333 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5877299 CAAGACTAGA
5877309 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5877334 GCATTTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5885139 original size:15 final size:16
Alignment explanation
Indices: 5885119--5885149 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5885109 AATGGGCAGT
5885119 AATCCCTGC-AAAAAA
1 AATCCCTGCGAAAAAA
5885134 AATCCCTGCGAAAAAA
1 AATCCCTGCGAAAAAA
5885150 TCTCTGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.26, G:0.10, T:0.13
Consensus pattern (16 bp):
AATCCCTGCGAAAAAA
Found at i:5888054 original size:21 final size:22
Alignment explanation
Indices: 5888015--5888055 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5888005 TTCAATGTAA
* *
5888015 AAAAATATTTCTTTGTATACTC
1 AAAAATATTTATTTATATACTC
5888037 AAAAATA-TTATTTATATAC
1 AAAAATATTTATTTATATAC
5888056 GAACTTAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAAATATTTATTTATATACTC
Found at i:5897306 original size:20 final size:20
Alignment explanation
Indices: 5897278--5897366 Score: 94
Period size: 19 Copynumber: 4.5 Consensus size: 20
5897268 TACTGTCCAT
* * *
5897278 TACTGTTCACATAGTATCGG
1 TACTATTCATATAGTATCAG
*
5897298 TACTATTCATACT-GTATCGG
1 TACTATTCATA-TAGTATCAG
*
5897318 TACTATTCATATAGTA-CAA
1 TACTATTCATATAGTATCAG
*
5897337 TACTATTCATATAGT-GCAG
1 TACTATTCATATAGTATCAG
5897356 TACTATTCATA
1 TACTATTCATA
5897367 AAAAACATTT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
19 30 0.49
20 30 0.49
21 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (20 bp):
TACTATTCATATAGTATCAG
Found at i:5899491 original size:19 final size:19
Alignment explanation
Indices: 5899469--5899542 Score: 51
Period size: 19 Copynumber: 3.6 Consensus size: 19
5899459 ACTTGTGGAT
5899469 TGTTACTTTAGTTGTAATA
1 TGTTACTTTAGTTGTAATA
* *
5899488 TGTTATTTTGATGTATTTGTGGA-A
1 TGTTACTTT-A-G---TTGT-AATA
*
5899512 TGTTACTTTGGTTGTAATA
1 TGTTACTTTAGTTGTAATA
*
5899531 TGTTATTTTAGT
1 TGTTACTTTAGT
5899543 GTATTTATGG
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
18 1 0.02
19 23 0.56
20 1 0.02
21 1 0.02
22 1 0.02
24 13 0.32
25 1 0.02
ACGTcount: A:0.22, C:0.03, G:0.20, T:0.55
Consensus pattern (19 bp):
TGTTACTTTAGTTGTAATA
Found at i:5899564 original size:43 final size:42
Alignment explanation
Indices: 5899437--5899565 Score: 177
Period size: 43 Copynumber: 3.0 Consensus size: 42
5899427 TAAAGTATAA
* * *
5899437 TTGTAATATGTTAGTTTGGTGTACTTGTGGATTGTTACTTTAG
1 TTGTAATATGTTA-TTTTGTGTATTTGTGGATTGTTACTTTGG
*
5899480 TTGTAATATGTTATTTTGATGTATTTGTGGAATGTTACTTTGG
1 TTGTAATATGTTATTTTG-TGTATTTGTGGATTGTTACTTTGG
* *
5899523 TTGTAATATGTTATTTTAGTGTATTTATGGATTATTACTTTGG
1 TTGTAATATGTTATTTT-GTGTATTTGTGGATTGTTACTTTGG
5899566 AGTTTAAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
42 4 0.05
43 72 0.94
44 1 0.01
ACGTcount: A:0.21, C:0.03, G:0.22, T:0.53
Consensus pattern (42 bp):
TTGTAATATGTTATTTTGTGTATTTGTGGATTGTTACTTTGG
Found at i:5901566 original size:20 final size:20
Alignment explanation
Indices: 5901541--5901674 Score: 124
Period size: 20 Copynumber: 6.7 Consensus size: 20
5901531 AATTGGGAAA
* *
5901541 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTAACT
* *
5901561 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTAACT
* * **
5901581 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTA-ACT
* *
5901602 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTAACT
* *
5901622 TTCGCAACGCGATTCTAACT
1 ATCGCAACGCGATACTAACT
* *
5901642 TTCGCAACGCGATTCTAACT
1 ATCGCAACGCGATACTAACT
*
5901662 TTCGCAACGCGAT
1 ATCGCAACGCGAT
5901675 TTACATAGCG
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 84 0.86
21 14 0.14
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTAACT
Found at i:5901587 original size:61 final size:61
Alignment explanation
Indices: 5901538--5901654 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
5901528 GCGAATTGGG
* * * * *
5901538 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTAACTATCGCAACGCGATAATAC
* * *
5901599 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTAACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTAACTATCGCAACGCGAT
5901655 TCTAACTTTC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTAACTATCGCAACGCGATAATAC
Found at i:5902232 original size:19 final size:19
Alignment explanation
Indices: 5902194--5902260 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
5902184 TTCGAGAATG
5902194 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
5902214 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* *
5902233 AAAAACGCAACGCGAAACA
1 AAAATCGCAACGCGAAATA
5902252 AAAATCGCA
1 AAAATCGCA
5902261 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.51, C:0.24, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:5902278 original size:19 final size:19
Alignment explanation
Indices: 5902256--5902459 Score: 203
Period size: 19 Copynumber: 11.1 Consensus size: 19
5902246 GAAACAAAAA
* *
5902256 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
5902275 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5902294 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
5902313 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
5902332 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
5902352 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
5902368 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
5902385 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
5902399 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
5902418 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
5902438 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
5902458 TC
1 TC
5902460 AACCAAAAGA
Statistics
Matches: 156, Mismatches: 16, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
14 20 0.13
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 78 0.50
20 49 0.31
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5902375 original size:58 final size:57
Alignment explanation
Indices: 5902256--5902459 Score: 194
Period size: 58 Copynumber: 3.7 Consensus size: 57
5902246 GAAACAAAAA
* * *
5902256 TCGCATTGCGATTTTTATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTGTCATG
5902313 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATTTCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTTATTTCGC-GTTGCGATTTTCATTTCGCGTTGCGATTGTCATG
* ** * * * *
5902368 T-G-GTCGCGATAGTCATTTCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTGTCATG
* * *
5902418 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATTTC
1 T-CGCGTTGCGATTTTTATT-TCGCGTTGCGATTTTCATTTC
5902460 AACCAAAAGA
Statistics
Matches: 122, Mismatches: 12, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
47 14 0.11
50 4 0.03
52 8 0.07
53 27 0.22
54 11 0.09
55 1 0.01
56 3 0.02
57 22 0.18
58 30 0.25
59 2 0.02
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (57 bp):
TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTGTCATG
Found at i:5902384 original size:33 final size:33
Alignment explanation
Indices: 5902347--5902434 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
5902337 GTTGCGATTT
* *
5902347 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
5902380 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
5902413 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
5902435 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:5902436 original size:20 final size:20
Alignment explanation
Indices: 5902402--5902459 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
5902392 GCGATTCTCT
**
5902402 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
5902422 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
5902442 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
5902460 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:5904447 original size:42 final size:42
Alignment explanation
Indices: 5904387--5904509 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
5904377 GCCCGACTCG
* * *
5904387 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
5904429 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
5904471 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
5904510 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:5904467 original size:21 final size:21
Alignment explanation
Indices: 5904443--5904509 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5904433 TCATTCCTCG
5904443 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
5904464 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
5904485 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
5904506 AGAG
1 AGAG
5904510 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:5905885 original size:14 final size:14
Alignment explanation
Indices: 5905866--5905901 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5905856 ATTGTTTAAT
5905866 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
5905880 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
5905894 TGATTTGT
1 TGATTTGT
5905902 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Done.