Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008097.1 Hibiscus syriacus cultivar Beakdansim tig00110621_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: 3094402
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 9 of 12
Found at i:2191096 original size:51 final size:50
Alignment explanation
Indices: 2190995--2191101 Score: 144
Period size: 51 Copynumber: 2.1 Consensus size: 50
2190985 CATGATCCAT
** *
2190995 GCTATATAAAATTATGTCAGAGTAAAGGTATATTGCGTTACCTGCCCCGC
1 GCTATATAAAATTATGTCAGAGTAAAGGTATAGCGCGTTACCTGACCCGC
* *
2191045 GCTATATAAAATTATGTCGGGAGTAAAGGTATAGCGCGGTT-CCTGATCCGC
1 GCTATATAAAATTATGTC-AGAGTAAAGGTATAGCGC-GTTACCTGACCCGC
2191096 GCTATA
1 GCTATA
2191102 CCCCTACGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
50 18 0.36
51 29 0.58
52 3 0.06
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (50 bp):
GCTATATAAAATTATGTCAGAGTAAAGGTATAGCGCGTTACCTGACCCGC
Found at i:2191236 original size:50 final size:49
Alignment explanation
Indices: 2191113--2191236 Score: 140
Period size: 51 Copynumber: 2.5 Consensus size: 49
2191103 CCCTACGTGG
* * * **
2191113 CGTATAGCGCGCTGCAGGGGCCGCGCTATACCCATGTGGCATCAGCTCAC
1 CGTATAGCGCGATGCAGGGG-CGCGCTATACCCACGTGGCACCAAATCAC
* * * *
2191163 CGTATAGCGCGGTTCAGGAGGCGCGCTATACCCCACGTGGCGCCAAATCAT
1 CGTATAGCGCGATGCAGG-GGCGCGCTATA-CCCACGTGGCACCAAATCAC
2191214 CGTATAGCGCGATGCAGGGGCGC
1 CGTATAGCGCGATGCAGGGGCGC
2191237 ATTTTACTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
50 30 0.48
51 32 0.52
ACGTcount: A:0.19, C:0.31, G:0.32, T:0.17
Consensus pattern (49 bp):
CGTATAGCGCGATGCAGGGGCGCGCTATACCCACGTGGCACCAAATCAC
Found at i:2193022 original size:7 final size:7
Alignment explanation
Indices: 2193001--2193074 Score: 62
Period size: 7 Copynumber: 10.7 Consensus size: 7
2192991 GTTAGATTAC
2193001 ACCCTAA
1 ACCCTAA
*
2193008 A-TCTAA
1 ACCCTAA
2193014 ACCCTAA
1 ACCCTAA
*
2193021 ACCCCAA
1 ACCCTAA
2193028 ATCCC-AA
1 A-CCCTAA
* *
2193035 ATCATAA
1 ACCCTAA
2193042 ACCCTAA
1 ACCCTAA
**
2193049 GTCCTAA
1 ACCCTAA
2193056 ACCCTAA
1 ACCCTAA
*
2193063 ACTCTAA
1 ACCCTAA
2193070 ACCCT
1 ACCCT
2193075 TAATCCGATT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
6 6 0.12
7 42 0.82
8 3 0.06
ACGTcount: A:0.42, C:0.38, G:0.01, T:0.19
Consensus pattern (7 bp):
ACCCTAA
Found at i:2193063 original size:21 final size:21
Alignment explanation
Indices: 2193001--2193070 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
2192991 GTTAGATTAC
2193001 ACCCTAAAT-CTAAACCCTAA
1 ACCCTAAATCCTAAACCCTAA
* * * *
2193021 ACCCCAAATCCCAAATCATAA
1 ACCCTAAATCCTAAACCCTAA
*
2193042 ACCCTAAGTCCTAAACCCTAA
1 ACCCTAAATCCTAAACCCTAA
*
2193063 ACTCTAAA
1 ACCCTAAA
2193071 CCCTTAATCC
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
20 8 0.21
21 30 0.79
ACGTcount: A:0.44, C:0.36, G:0.01, T:0.19
Consensus pattern (21 bp):
ACCCTAAATCCTAAACCCTAA
Found at i:2193069 original size:14 final size:13
Alignment explanation
Indices: 2193001--2193079 Score: 70
Period size: 14 Copynumber: 5.8 Consensus size: 13
2192991 GTTAGATTAC
2193001 ACCCTAAATCTAA
1 ACCCTAAATCTAA
* *
2193014 ACCCTAAACCCCAA
1 ACCCTAAA-TCTAA
2193028 ATCCC-AAATCATAA
1 A-CCCTAAATC-TAA
*
2193042 ACCCTAAGTCCTAA
1 ACCCTAAAT-CTAA
2193056 ACCCTAAACTCTAA
1 ACCCTAAA-TCTAA
*
2193070 ACCCTTAATC
1 ACCCTAAATC
2193080 CGATTATGTG
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
13 14 0.26
14 34 0.64
15 5 0.09
ACGTcount: A:0.42, C:0.37, G:0.01, T:0.20
Consensus pattern (13 bp):
ACCCTAAATCTAA
Found at i:2193070 original size:28 final size:27
Alignment explanation
Indices: 2193001--2193074 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 27
2192991 GTTAGATTAC
2193001 ACCCTAAATCTAAACCCTAAACCCCAA
1 ACCCTAAATCTAAACCCTAAACCCCAA
** *
2193028 ATCCC-AAATCATAAACCCTAAGTCCTAA
1 A-CCCTAAATC-TAAACCCTAAACCCCAA
2193056 ACCCTAAACTCTAAACCCT
1 ACCCTAAA-TCTAAACCCT
2193075 TAATCCGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 9 0.22
28 29 0.73
29 2 0.05
ACGTcount: A:0.42, C:0.38, G:0.01, T:0.19
Consensus pattern (27 bp):
ACCCTAAATCTAAACCCTAAACCCCAA
Found at i:2193209 original size:35 final size:35
Alignment explanation
Indices: 2193169--2193263 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 35
2193159 ACTCTAAACT
* *
2193169 ATAAACCTTAAACCCTAAACCTTAAGT-CATAAATC
1 ATAAACCATAAACCCTAAACCCTAA-TCCATAAATC
* * * *
2193204 CTAAACCCTAAACCCTAAACCCTAATCCCTAAGTC
1 ATAAACCATAAACCCTAAACCCTAATCCATAAATC
2193239 ATAAACCATAAACCCTAAACCCTAA
1 ATAAACCATAAACCCTAAACCCTAA
2193264 ACACTTAATC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
34 1 0.02
35 51 0.98
ACGTcount: A:0.44, C:0.33, G:0.02, T:0.21
Consensus pattern (35 bp):
ATAAACCATAAACCCTAAACCCTAATCCATAAATC
Found at i:2193223 original size:42 final size:42
Alignment explanation
Indices: 2193170--2193265 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
2193160 CTCTAAACTA
* *
2193170 TAAACCTTAAACCCTAAACCTTAAGTCATAAATCC-TAAACCC
1 TAAACCCTAAACCCTAAACCCTAAGTCATAAA-CCATAAACCC
*
2193212 TAAACCCTAAACCCTAATCCCTAAGTCATAAACCATAAACCC
1 TAAACCCTAAACCCTAAACCCTAAGTCATAAACCATAAACCC
2193254 TAAACCCTAAAC
1 TAAACCCTAAAC
2193266 ACTTAATCCA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
41 2 0.04
42 48 0.96
ACGTcount: A:0.44, C:0.33, G:0.02, T:0.21
Consensus pattern (42 bp):
TAAACCCTAAACCCTAAACCCTAAGTCATAAACCATAAACCC
Found at i:2193233 original size:7 final size:7
Alignment explanation
Indices: 2193145--2193265 Score: 98
Period size: 7 Copynumber: 17.3 Consensus size: 7
2193135 GTTAGATTAC
2193145 ACCCTAA
1 ACCCTAA
**
2193152 ATTCTAA
1 ACCCTAA
*
2193159 ACTCTAA
1 ACCCTAA
**
2193166 ACTATAA
1 ACCCTAA
*
2193173 ACCTTAA
1 ACCCTAA
2193180 ACCCTAA
1 ACCCTAA
*
2193187 ACCTTAA
1 ACCCTAA
** *
2193194 GTCATAA
1 ACCCTAA
*
2193201 ATCCTAA
1 ACCCTAA
2193208 ACCCTAA
1 ACCCTAA
2193215 ACCCTAA
1 ACCCTAA
2193222 ACCCTAA
1 ACCCTAA
*
2193229 TCCCTAA
1 ACCCTAA
** *
2193236 GTCATAA
1 ACCCTAA
*
2193243 ACCATAA
1 ACCCTAA
2193250 ACCCTAA
1 ACCCTAA
2193257 ACCCTAA
1 ACCCTAA
2193264 AC
1 AC
2193266 ACTTAATCCA
Statistics
Matches: 93, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 93 1.00
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.22
Consensus pattern (7 bp):
ACCCTAA
Found at i:2194894 original size:23 final size:23
Alignment explanation
Indices: 2194864--2194907 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2194854 TAGGCTAGTG
2194864 GCTTGAATCAAGCTCAATATCAA
1 GCTTGAATCAAGCTCAATATCAA
**
2194887 GCTTGAATTGAGCTCAATATC
1 GCTTGAATCAAGCTCAATATC
2194908 GAGTTCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (23 bp):
GCTTGAATCAAGCTCAATATCAA
Found at i:2194920 original size:12 final size:12
Alignment explanation
Indices: 2194900--2194930 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2194890 TGAATTGAGC
2194900 TCAATATCGAGT
1 TCAATATCGAGT
2194912 TCAATATCGAGT
1 TCAATATCGAGT
*
2194924 TTAATAT
1 TCAATAT
2194931 TTTTTTGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (12 bp):
TCAATATCGAGT
Found at i:2201009 original size:12 final size:13
Alignment explanation
Indices: 2200992--2201020 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2200982 AATATACTGC
2200992 AAAAAAAA-GAAG
1 AAAAAAAAGGAAG
2201004 AAAAAAAAGGAAG
1 AAAAAAAAGGAAG
2201017 AAAA
1 AAAA
2201021 CTATCCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGGAAG
Found at i:2204710 original size:9 final size:9
Alignment explanation
Indices: 2204696--2204729 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2204686 TAAGTAAAAT
2204696 ATTAAATAA
1 ATTAAATAA
2204705 ATTAAAT-A
1 ATTAAATAA
*
2204713 CTTAAATAA
1 ATTAAATAA
2204722 ATTAAATA
1 ATTAAATA
2204730 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:2204728 original size:17 final size:17
Alignment explanation
Indices: 2204692--2204730 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2204682 TATATAAGTA
2204692 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
2204708 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
2204725 AAATAC
1 AAATAC
2204731 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:2204788 original size:10 final size:10
Alignment explanation
Indices: 2204765--2204814 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
2204755 TACTTTAAAC
* *
2204765 AGAGAATATA
1 AGAGAATTTG
*
2204775 AGAGTATTTG
1 AGAGAATTTG
*
2204785 AGAGAAGTTG
1 AGAGAATTTG
*
2204795 AGAGAAATTG
1 AGAGAATTTG
2204805 AGAGAATTTG
1 AGAGAATTTG
2204815 GTGTGATGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:2206967 original size:37 final size:35
Alignment explanation
Indices: 2206896--2206967 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
2206886 TATATTTTTA
* *
2206896 ATTTTGTAAAAAAATTATATAAATATTATGAATTT
1 ATTTTGTAAAAAAAATATATAAATATTATCAATTT
* *
2206931 ATTTTTTAAAAGAAAATATATAAATATTTTACAATTT
1 ATTTTGTAAAA-AAAATATATAAATATTAT-CAATTT
2206968 GTAATATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 10 0.32
36 16 0.52
37 5 0.16
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (35 bp):
ATTTTGTAAAAAAAATATATAAATATTATCAATTT
Found at i:2207138 original size:20 final size:20
Alignment explanation
Indices: 2207113--2207150 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2207103 ATCTAATTTC
2207113 CTGATAATCTTT-TATTCCCA
1 CTGATAAT-TTTATATTCCCA
2207133 CTGATAATTTTATATTCC
1 CTGATAATTTTATATTCC
2207151 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.47
Consensus pattern (20 bp):
CTGATAATTTTATATTCCCA
Found at i:2208177 original size:44 final size:44
Alignment explanation
Indices: 2208121--2208205 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
2208111 ATTAAAAATA
* * *
2208121 TAATATTTTATGTTA-ATTATAATTTAAAATACTATTTTTTTTCT
1 TAATATTTTATGTTATATT-CAATCTAAAATACTATATTTTTTCT
*
2208165 TAATATTTTATGTTATATTCAATCTAAAATATTATATTTTT
1 TAATATTTTATGTTATATTCAATCTAAAATACTATATTTTT
2208206 AGCTGCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 33 0.92
45 3 0.08
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (44 bp):
TAATATTTTATGTTATATTCAATCTAAAATACTATATTTTTTCT
Found at i:2209577 original size:29 final size:29
Alignment explanation
Indices: 2209535--2209591 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
2209525 AGTATTGGCC
*
2209535 GTAGGTCGCCATGCATTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
2209564 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
2209592 ACCCTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.33, G:0.32, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:2209683 original size:29 final size:29
Alignment explanation
Indices: 2209650--2209733 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 29
2209640 TCCCAACACA
*
2209650 TAGGTCGCCATGCCCTCCGGGCGATCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
2209679 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
* * *
2209708 TA-GTTGCCATACACTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
2209734 ACCCTCGCTC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 21 0.41
29 30 0.59
ACGTcount: A:0.13, C:0.36, G:0.29, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:2209786 original size:33 final size:33
Alignment explanation
Indices: 2209749--2209854 Score: 130
Period size: 33 Copynumber: 3.3 Consensus size: 33
2209739 CGCTCGGCTT
*
2209749 CCCTCGGAT-TCCCTCGCATAGCTCGTTCGGTTG
1 CCCTCGGATGT-CCTCGCATAGCTCGTTCGGATG
*
2209782 CCCTCGGATGTCCTCGCATAGCTCGTTTGGATG
1 CCCTCGGATGTCCTCGCATAGCTCGTTCGGATG
* *
2209815 GCCTCGGATGTCCTCGGAT-GCTC--TCGGATG
1 CCCTCGGATGTCCTCGCATAGCTCGTTCGGATG
*
2209845 CTCTCGGATG
1 CCCTCGGATG
2209855 CTCTCGGATG
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
30 14 0.22
32 4 0.06
33 46 0.71
34 1 0.02
ACGTcount: A:0.10, C:0.32, G:0.28, T:0.29
Consensus pattern (33 bp):
CCCTCGGATGTCCTCGCATAGCTCGTTCGGATG
Found at i:2209829 original size:10 final size:10
Alignment explanation
Indices: 2209817--2209873 Score: 82
Period size: 10 Copynumber: 5.7 Consensus size: 10
2209807 TTTGGATGGC
2209817 CTCGGATG-T
1 CTCGGATGCT
2209826 CCTCGGATGCT
1 -CTCGGATGCT
2209837 CTCGGATGCT
1 CTCGGATGCT
2209847 CTCGGATGCT
1 CTCGGATGCT
2209857 CTCGGATGAC-
1 CTCGGATG-CT
2209867 CTCGGAT
1 CTCGGAT
2209874 ACCCAGCGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
10 43 0.96
11 2 0.04
ACGTcount: A:0.12, C:0.30, G:0.30, T:0.28
Consensus pattern (10 bp):
CTCGGATGCT
Found at i:2209851 original size:30 final size:29
Alignment explanation
Indices: 2209783--2209873 Score: 87
Period size: 30 Copynumber: 3.0 Consensus size: 29
2209773 GTTCGGTTGC
* *
2209783 CCTCGGATGTCCTCGCATAGCTCGTTTGGATGG
1 CCTCGGATGTCCTCGGAT-GCTC--TCGGAT-G
2209816 CCTCGGATGTCCTCGGATGCTCTCGGATG
1 CCTCGGATGTCCTCGGATGCTCTCGGATG
2209845 CTCTCGGATG-CTCTCGGATGAC-CTCGGAT
1 C-CTCGGATGTC-CTCGGATG-CTCTCGGAT
2209874 ACCCAGCGTG
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
29 3 0.06
30 28 0.53
31 1 0.02
32 4 0.08
33 17 0.32
ACGTcount: A:0.12, C:0.30, G:0.30, T:0.29
Consensus pattern (29 bp):
CCTCGGATGTCCTCGGATGCTCTCGGATG
Found at i:2213236 original size:60 final size:60
Alignment explanation
Indices: 2213128--2213299 Score: 192
Period size: 60 Copynumber: 2.9 Consensus size: 60
2213118 TTGAAATATA
** * * *
2213128 CATCCTCAAATTAT--GGCTTATTTTAAATTAATTCCTAAACTTTTGAACATTTTAATTT
1 CATCCTCAAATTATCAACCTTATTCTAAATTAATCCCCAAACTTTTGAACATTTTAATTT
* * * * *
2213186 CATCC-CTAAATTAT-GA-CTTCCATTCTGAATTGATTCTCAAACTTTTGAACATTTTAATTT
1 CATCCTC-AAATTATCAACCTT--ATTCTAAATTAATCCCCAAACTTTTGAACATTTTAATTT
2213246 CATCCTCAAATTATCAACCTTATTCTAAATTAATCCCCAAACTTTTGAACATTT
1 CATCCTCAAATTATCAACCTTATTCTAAATTAATCCCCAAACTTTTGAACATTT
2213300 CAGTAATATA
Statistics
Matches: 96, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
57 1 0.01
58 15 0.16
60 75 0.78
61 2 0.02
62 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (60 bp):
CATCCTCAAATTATCAACCTTATTCTAAATTAATCCCCAAACTTTTGAACATTTTAATTT
Found at i:2215204 original size:6 final size:6
Alignment explanation
Indices: 2215142--2215186 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
2215132 GAGAATGAAA
2215142 GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG GAG
1 GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG GAG
2215187 GAGAAAGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (6 bp):
GAGAAG
Found at i:2215204 original size:12 final size:12
Alignment explanation
Indices: 2215138--2215203 Score: 75
Period size: 12 Copynumber: 5.8 Consensus size: 12
2215128 CAAAGAGAAT
2215138 GAAAGAGAAGGA
1 GAAAGAGAAGGA
*
2215150 GAAGGAGAAGGA
1 GAAAGAGAAGGA
*
2215162 GAAGGAGAAGGA
1 GAAAGAGAAGGA
*
2215174 GAAGGAGAAGGA
1 GAAAGAGAAGGA
*
2215186 G---GAGAAAGA
1 GAAAGAGAAGGA
2215195 GAAAGAGAA
1 GAAAGAGAA
2215204 AAAGAGATGA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
9 8 0.16
12 41 0.84
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (12 bp):
GAAAGAGAAGGA
Found at i:2216607 original size:18 final size:19
Alignment explanation
Indices: 2216584--2216626 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
2216574 CAGTAATCCT
2216584 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
*
2216602 ATTCCCACTGGTAATCTTAT
1 ATT-CCACTGGTAATCTTAC
2216622 ATTCC
1 ATTCC
2216627 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:2216614 original size:20 final size:20
Alignment explanation
Indices: 2216589--2216626 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2216579 ATCCTATTCC
2216589 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
2216609 CTGGTAATCTTATATTCC
1 CTGGTAATCTTACATTCC
2216627 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2217174 original size:24 final size:25
Alignment explanation
Indices: 2217130--2217178 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
2217120 ATTTTTTTAA
2217130 TTTTTATGCTTTTATGACACGGTTTTT
1 TTTTTATGCTTTTAT-ACAC-GTTTTT
2217157 TTTTTAT-CTTTTAT-CACGTTTT
1 TTTTTATGCTTTTATACACGTTTT
2217179 CGGTCATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 5 0.23
24 3 0.14
26 7 0.32
27 7 0.32
ACGTcount: A:0.14, C:0.12, G:0.10, T:0.63
Consensus pattern (25 bp):
TTTTTATGCTTTTATACACGTTTTT
Found at i:2221207 original size:18 final size:19
Alignment explanation
Indices: 2221165--2221208 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2221155 ATATTTGATT
* *
2221165 TTATTTATAATTTTTTACA
1 TTATTTATAATTTTTAAAA
2221184 TCTATTTATAA-TTTTAAAA
1 T-TATTTATAATTTTTAAAA
2221203 TTATTT
1 TTATTT
2221209 TATATGTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTTATAATTTTTAAAA
Found at i:2223075 original size:20 final size:19
Alignment explanation
Indices: 2223050--2223099 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2223040 ATCATAATTG
*
2223050 ATCATTGATTTTGACAAAAA
1 ATCATT-ATTTTAACAAAAA
* *
2223070 ATCATTTTTTTAATAAAAA
1 ATCATTATTTTAACAAAAA
2223089 ATCA-TATTTTA
1 ATCATTATTTTA
2223100 TATTTTTCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 6 0.23
19 14 0.54
20 6 0.23
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (19 bp):
ATCATTATTTTAACAAAAA
Found at i:2226035 original size:21 final size:21
Alignment explanation
Indices: 2225993--2226035 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2225983 TTTTTGGGTT
* * *
2225993 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
2226014 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
2226035 A
1 A
2226036 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:2226085 original size:61 final size:61
Alignment explanation
Indices: 2226015--2226130 Score: 196
Period size: 61 Copynumber: 1.9 Consensus size: 61
2226005 ACCCATTCAA
*
2226015 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTAGAGGGGAACCCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCCCCAGG
* * *
2226076 GGGGAACCGATACCCCCTCAATGGATATGAAATTCCAGAATGCTAGAGGGGAACC
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACC
2226131 GATACCCCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.16
Consensus pattern (61 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCCCCAGG
Found at i:2226838 original size:23 final size:23
Alignment explanation
Indices: 2226771--2226830 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
2226761 ATCATTATAT
*
2226771 GGCACTACGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
2226794 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
2226817 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
2226831 TTTATACGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:2232909 original size:21 final size:21
Alignment explanation
Indices: 2232867--2232909 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2232857 TTTCTGGGTT
* * *
2232867 AGGGGAAGCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
2232888 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
2232909 A
1 A
2232910 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.28, T:0.12
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:2232967 original size:67 final size:67
Alignment explanation
Indices: 2232889--2233018 Score: 206
Period size: 67 Copynumber: 1.9 Consensus size: 67
2232879 ACCCATTCAA
* * *
2232889 GGGGAACCGATACCCCCTCAACGAATATGAATTTCTAGAATACTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCA
2232954 TG
66 TG
* * *
2232956 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATGCTAGAGGGGAACCGATTCCCC
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCC
2233019 TATGAGAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.18
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCA
TG
Found at i:2233698 original size:23 final size:23
Alignment explanation
Indices: 2233631--2233690 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
2233621 ATCATTATAT
*
2233631 GGCACTACGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
2233654 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
2233677 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
2233691 TTTATACGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:2235651 original size:36 final size:35
Alignment explanation
Indices: 2235610--2235738 Score: 179
Period size: 36 Copynumber: 3.6 Consensus size: 35
2235600 AGAAAGAAAT
2235610 GAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAG
1 GAAGCATCAGCACTTTCGATTC-AAGTGAACGGAAG
* * *
2235646 GAAGCATCGGCACTTTCGATTCAAGAAGAACGAAAG
1 GAAGCATCAGCACTTTCGATTCAAG-TGAACGGAAG
*
2235682 GAAGCA-CCGACACTTTCGATTCAAGTGAACGGAAG
1 GAAGCATCAG-CACTTTCGATTCAAGTGAACGGAAG
*
2235717 GAAGCGTCAGCACTTTCGATTC
1 GAAGCATCAGCACTTTCGATTC
2235739 GGTTGTTCAT
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
35 30 0.37
36 52 0.63
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (35 bp):
GAAGCATCAGCACTTTCGATTCAAGTGAACGGAAG
Found at i:2235735 original size:71 final size:72
Alignment explanation
Indices: 2235596--2235738 Score: 218
Period size: 71 Copynumber: 2.0 Consensus size: 72
2235586 GAAGGTGAAT
* * *
2235596 AAGAAGAAAGAAATGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTT
1 AAGAAGAAAGAAAGGAAGCACCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCAGCACTT
2235661 TCGATTC
66 TCGATTC
* *
2235668 AAGAAGAACGAAAGGAAGCACC-GACACTTTCGATTC-AAGTGAACGGAAGGAAGCGTCAGCACT
1 AAGAAGAAAGAAAGGAAGCACCAG-CACTTTCGATTCAAAGTGAACGGAAGGAAGCATCAGCACT
2235731 TTCGATTC
65 TTCGATTC
2235739 GGTTGTTCAT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 34 0.52
72 31 0.48
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (72 bp):
AAGAAGAAAGAAAGGAAGCACCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCAGCACTT
TCGATTC
Found at i:2236475 original size:13 final size:13
Alignment explanation
Indices: 2236453--2236489 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2236443 TTCATATATA
2236453 TAAA-TATTTGAG
1 TAAATTATTTGAG
2236465 TAAATTATTTGAG
1 TAAATTATTTGAG
*
2236478 CAAATTATTTGA
1 TAAATTATTTGA
2236490 ATATCAAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.43
Consensus pattern (13 bp):
TAAATTATTTGAG
Found at i:2238864 original size:13 final size:13
Alignment explanation
Indices: 2238842--2238878 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2238832 TTCATATATA
2238842 TAAA-TATTTGAG
1 TAAATTATTTGAG
2238854 TAAATTATTTGAG
1 TAAATTATTTGAG
*
2238867 CAAATTATTTGA
1 TAAATTATTTGA
2238879 ATATCAAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.43
Consensus pattern (13 bp):
TAAATTATTTGAG
Found at i:2239786 original size:28 final size:29
Alignment explanation
Indices: 2239746--2239807 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 29
2239736 GTCGGGTTTT
2239746 TTTTTAAAAAAATCGGGATCGGGTC-GGA
1 TTTTTAAAAAAATCGGGATCGGGTCTGGA
* *
2239774 TTTTTAAAAAAATCGGGTTCGGGTCTGGT
1 TTTTTAAAAAAATCGGGATCGGGTCTGGA
2239803 TTTTT
1 TTTTT
2239808 TAAGTTTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 24 0.77
29 7 0.23
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.39
Consensus pattern (29 bp):
TTTTTAAAAAAATCGGGATCGGGTCTGGA
Found at i:2239822 original size:28 final size:28
Alignment explanation
Indices: 2239791--2239876 Score: 147
Period size: 28 Copynumber: 3.1 Consensus size: 28
2239781 AAAAATCGGG
* *
2239791 TTCGGGTCTGGTTTTTTTAAGTTTGATA
1 TTCGGGTCGGGTTTTTTTAAGTGTGATA
2239819 TTCGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTTAAGTGTGATA
2239847 TTCGGGTCGGGTTTTTTT-AGTGTGATA
1 TTCGGGTCGGGTTTTTTTAAGTGTGATA
2239874 TTC
1 TTC
2239877 AGGTGGGATT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
27 12 0.21
28 44 0.79
ACGTcount: A:0.13, C:0.08, G:0.29, T:0.50
Consensus pattern (28 bp):
TTCGGGTCGGGTTTTTTTAAGTGTGATA
Found at i:2240481 original size:16 final size:16
Alignment explanation
Indices: 2240460--2240510 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2240450 TCAGATTTAG
2240460 ATTCCAATTCCCTCAT
1 ATTCCAATTCCCTCAT
* *
2240476 ATTCCAATTCCTTCACAG
1 ATTCCAATTCC--CTCAT
*
2240494 ATTTCAATTCCCTCAT
1 ATTCCAATTCCCTCAT
2240510 A
1 A
2240511 AACATTCCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 15 0.54
18 13 0.46
ACGTcount: A:0.27, C:0.33, G:0.02, T:0.37
Consensus pattern (16 bp):
ATTCCAATTCCCTCAT
Found at i:2244103 original size:2 final size:2
Alignment explanation
Indices: 2244096--2244121 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2244086 TAGCTACGTT
2244096 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2244122 CAAGAAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2244598 original size:3 final size:3
Alignment explanation
Indices: 2244576--2244640 Score: 76
Period size: 3 Copynumber: 21.7 Consensus size: 3
2244566 TCGTCCCCAA
* * * * * *
2244576 TAT TAT TAG TAT AAT GAT TAT TAT TAT AAT GAC TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2244624 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
2244641 AATAATAATT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:2246607 original size:22 final size:22
Alignment explanation
Indices: 2246565--2246608 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2246555 GGTTAAACGC
*
2246565 AAATAATTTTTTTTATCTTTTA
1 AAATAATTTTTTTAATCTTTTA
* *
2246587 AAATCATTTTTCTTAATTTTTT
1 AAATAATTTTT-TTAATCTTTT
2246609 TTAAAATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (22 bp):
AAATAATTTTTTTAATCTTTTA
Found at i:2247848 original size:2 final size:2
Alignment explanation
Indices: 2247843--2247873 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2247833 ATTATTGGTA
2247843 AT AT AT 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 AT AT AT A
2247874 CTACATATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2248506 original size:23 final size:24
Alignment explanation
Indices: 2248446--2248498 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2248436 TATATGTATC
* *
2248446 TTATATAATAGAATATTCATATTA
1 TTATATTATATAATATTCATATTA
*
2248470 TTATATTATGTAATA-TCATATTA
1 TTATATTATATAATATTCATATTA
2248493 -TATATT
1 TTATATT
2248499 TTTATAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 6 0.23
23 8 0.31
24 12 0.46
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (24 bp):
TTATATTATATAATATTCATATTA
Found at i:2249577 original size:27 final size:25
Alignment explanation
Indices: 2249539--2249591 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
2249529 CGTATGTTCA
2249539 TTTTTTCAGTTTAATGCCTAACGTT
1 TTTTTTCAGTTTAATGCCTAACGTT
** *
2249564 TTTTGTTCTAGTTTGGTGCCTAATGTT
1 TTTT-TTC-AGTTTAATGCCTAACGTT
2249591 T
1 T
2249592 CATTTCGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 3 0.13
27 16 0.70
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.55
Consensus pattern (25 bp):
TTTTTTCAGTTTAATGCCTAACGTT
Found at i:2249730 original size:15 final size:16
Alignment explanation
Indices: 2249700--2249733 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2249690 CTGATTTTTA
*
2249700 AAAATAAAAATTAATT
1 AAAATAAAAATAAATT
2249716 AAAATAAAAA-AAATT
1 AAAATAAAAATAAATT
2249731 AAA
1 AAA
2249734 CTTTATTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAAAAATAAATT
Found at i:2252007 original size:25 final size:25
Alignment explanation
Indices: 2251959--2252007 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2251949 AAATTCATAA
*
2251959 AATTTTAGAAAAAATAAACTTAAAG
1 AATTTTAGAAAAAATAAACATAAAG
*
2251984 AATTTTATAGAAAAATAAA-ATAAA
1 AATTTTAGA-AAAAATAAACATAAA
2252008 TTACCTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (25 bp):
AATTTTAGAAAAAATAAACATAAAG
Found at i:2253233 original size:21 final size:21
Alignment explanation
Indices: 2253207--2253248 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2253197 ATAATTTACA
*
2253207 ATTTTTAATAATTAATCGATTG
1 ATTTTAAAT-ATTAATCGATTG
*
2253229 ATTTTAAATTTTAATCGATT
1 ATTTTAAATATTAATCGATT
2253249 TTCTTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (21 bp):
ATTTTAAATATTAATCGATTG
Found at i:2253384 original size:28 final size:27
Alignment explanation
Indices: 2253353--2253406 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
2253343 GTATTCTAAT
2253353 ATAAAT-ATTTATATTTATATTTAAAAAA
1 ATAAATAATTTA-ATTTA-ATTTAAAAAA
2253381 ATAAATAATTTAATTTAATTTAAAAA
1 ATAAATAATTTAATTTAATTTAAAAA
2253407 TTTTTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 9 0.36
28 11 0.44
29 5 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
ATAAATAATTTAATTTAATTTAAAAAA
Found at i:2256533 original size:84 final size:83
Alignment explanation
Indices: 2256385--2256546 Score: 222
Period size: 84 Copynumber: 1.9 Consensus size: 83
2256375 ATATTTGGTT
* *
2256385 ATGTCACATGTTTCATTTATCGGATAAAAATTGGTTGTCTTTTTTGTCTTTGTCCTATTCTTGTT
1 ATGTCACATGTTTCATTTATC-GATAAAAATTGATTGTCTTTTTTGTCTTTGTCATATTCTTGTT
2256450 AACACAAGAATGTTTGTTA
65 AACACAAGAATGTTTGTTA
*
2256469 ATGTTACATGTTTCATTTATC-ATACAAAATTTGATTGTCTTTTTCT-TCTTTGTCATA-TCATT
1 ATGTCACATGTTTCATTTATCGATA-AAAA-TTGATTGTCTTTTT-TGTCTTTGTCATATTC-TT
*
2256531 GTTAACATAAGAATGT
62 GTTAACACAAGAATGT
2256547 GCAAATAAGG
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
82 3 0.04
83 6 0.09
84 60 0.86
85 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (83 bp):
ATGTCACATGTTTCATTTATCGATAAAAATTGATTGTCTTTTTTGTCTTTGTCATATTCTTGTTA
ACACAAGAATGTTTGTTA
Found at i:2256612 original size:3 final size:3
Alignment explanation
Indices: 2256604--2256659 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
2256594 ATATTTTAAA
* * * *
2256604 TAT TAT TAT TAG TAT TAT TAT TAT TAT TAA TAT TAA TAT T-T TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2256651 TAAT TAT TA
1 T-AT TAT TA
2256660 CCTAACCTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2256704 original size:33 final size:33
Alignment explanation
Indices: 2256666--2256754 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 33
2256656 ATTACCTAAC
* ** *
2256666 CTAAAAACTGACTACCTATTAAATAATCATTCA
1 CTAAAAACTCACTACCTATTAAATAAAAATCCA
* *
2256699 CTAAAAACCCACTACCCATTAAATAAAAATCCA
1 CTAAAAACTCACTACCTATTAAATAAAAATCCA
* *
2256732 CTAAAAACTTACTAACTATTAAA
1 CTAAAAACTCACTACCTATTAAA
2256755 CAAAGAAAGC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (33 bp):
CTAAAAACTCACTACCTATTAAATAAAAATCCA
Found at i:2261445 original size:44 final size:44
Alignment explanation
Indices: 2261397--2261489 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 44
2261387 AAGTCTCTAA
2261397 ACTCTCTCCCTTCTCCTACCACTTGTCACCACCTAGTCACCTAC
1 ACTCTCTCCCTTCTCCTACCACTTGTCACCACCTAGTCACCTAC
*
2261441 ACTCTCTCCCTTCTCCTACCACTTGTCACCACCTAGTCATCTAC
1 ACTCTCTCCCTTCTCCTACCACTTGTCACCACCTAGTCACCTAC
2261485 ACTCT
1 ACTCT
2261490 TCAAACATCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.18, C:0.46, G:0.04, T:0.31
Consensus pattern (44 bp):
ACTCTCTCCCTTCTCCTACCACTTGTCACCACCTAGTCACCTAC
Found at i:2265527 original size:20 final size:20
Alignment explanation
Indices: 2265502--2265639 Score: 141
Period size: 20 Copynumber: 6.8 Consensus size: 20
2265492 ATTCGTGTTG
2265502 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
2265522 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** *
2265543 AAAATCGCGTTGAGATTTTC
1 CATTTCGCGTTGCGATTTTC
*
2265563 CATTTCGCGTTGCAATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
2265583 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* **
2265604 AAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
*
2265624 TATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
2265640 AGTCTACAGT
Statistics
Matches: 92, Mismatches: 24, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
20 63 0.68
21 29 0.32
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:2265569 original size:61 final size:61
Alignment explanation
Indices: 2265502--2265639 Score: 249
Period size: 61 Copynumber: 2.3 Consensus size: 61
2265492 ATTCGTGTTG
2265502 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGAGATTTTC
1 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGAGATTTTC
* *
2265563 CATTTCGCGTTGCAATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGAGATTTTC
*
2265624 TATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
2265640 AGTCTACAGT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 73 1.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.40
Consensus pattern (61 bp):
CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGAGATTTTC
Found at i:2265659 original size:22 final size:22
Alignment explanation
Indices: 2265631--2265702 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
2265621 TTCTATTTCG
2265631 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
** * *
2265653 CGTTGCGATTTTCCA-AATT-T
1 CGTTGCGATAGTCTACAGTTGT
*
2265673 -GTTGTGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
2265694 CGTTGCGAT
1 CGTTGCGAT
2265703 TTTCCAAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 10 0.27
20 4 0.11
21 4 0.11
22 19 0.51
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:2265682 original size:41 final size:41
Alignment explanation
Indices: 2265631--2265724 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2265621 TTCTATTTCG
2265631 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
* *
2265672 TGTTGTGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
2265713 CGTTGCGATAGT
1 CGTTGCGATAGT
2265725 TAAAAAAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:2265717 original size:19 final size:19
Alignment explanation
Indices: 2265652--2265721 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
2265642 TCTACAGTTG
2265652 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * * * **
2265671 TTGTTGTGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
2265692 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
2265712 TCGTTGCGAT
1 TCGTTGCGAT
2265722 AGTTAAAAAA
Statistics
Matches: 36, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
19 18 0.50
20 5 0.14
21 5 0.14
22 8 0.22
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:2266506 original size:22 final size:22
Alignment explanation
Indices: 2266480--2266532 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
2266470 GATTTGAAAA
2266480 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
2266502 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
2266524 ATCGCAACG
1 ATCGCAACG
2266533 CGAAATGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:2266549 original size:20 final size:20
Alignment explanation
Indices: 2266524--2266636 Score: 136
Period size: 20 Copynumber: 5.6 Consensus size: 20
2266514 ACTGTAGACT
*
2266524 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
* ** * **
2266544 ATCGCAACGTGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
*
2266565 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
2266585 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
2266605 ATCGCAATGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
2266625 ATCGCAACGCGA
1 ATCGCAACGCGA
2266637 TTTTCAACTA
Statistics
Matches: 75, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
20 62 0.83
21 13 0.17
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:2266570 original size:41 final size:41
Alignment explanation
Indices: 2266521--2266658 Score: 197
Period size: 41 Copynumber: 3.4 Consensus size: 41
2266511 ACAACTGTAG
*
2266521 ACTATCGCAACGCGAAATGGAAAATCGCAACGTGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
** *
2266562 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA-AATGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
** * *
2266602 AAAATCGCAATGCGAAATGAAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
2266643 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
2266659 TTTGCGATAC
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 33 0.40
41 49 0.60
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:2267821 original size:17 final size:18
Alignment explanation
Indices: 2267801--2267834 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2267791 ATTATATTAA
2267801 TAAAATA-TTAAATAAAG
1 TAAAATACTTAAATAAAG
2267818 TAAAATACTTAAATAAA
1 TAAAATACTTAAATAAA
2267835 TTATATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
TAAAATACTTAAATAAAG
Found at i:2270687 original size:6 final size:6
Alignment explanation
Indices: 2270678--2270756 Score: 68
Period size: 6 Copynumber: 12.5 Consensus size: 6
2270668 CATCTCTCTC
* ** *
2270678 TCCCAA TCCCAA TCCCAA TCCCAT TCCCTC TCCCACAA TCCCAA TCCCAT
1 TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA T-CC-CAA TCCCAA TCCCAA
**
2270728 TCCCTC TCCCACAA TCCCAA TCCCAA TCC
1 TCCCAA T-CC-CAA TCCCAA TCCCAA TCC
2270757 TAAACCTAAC
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
6 47 0.80
7 8 0.14
8 4 0.07
ACGTcount: A:0.25, C:0.53, G:0.00, T:0.22
Consensus pattern (6 bp):
TCCCAA
Found at i:2270709 original size:32 final size:31
Alignment explanation
Indices: 2270673--2270756 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 31
2270663 TCCCACATCT
2270673 CTCTCTCCCAATCCCAATCCCAATCCCATTC
1 CTCTCTCCCAATCCCAATCCCAATCCCATTC
2270704 C-CTCTCCC-A---CAATCCCAATCCCATTC
1 CTCTCTCCCAATCCCAATCCCAATCCCATTC
2270730 C-CTCTCCCACAATCCCAATCCCAATCC
1 CTCTCT-CC-CAATCCCAATCCCAATCC
2270757 TAAACCTAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
26 22 0.47
27 2 0.04
28 1 0.02
29 2 0.04
30 7 0.15
31 1 0.02
32 12 0.26
ACGTcount: A:0.24, C:0.54, G:0.00, T:0.23
Consensus pattern (31 bp):
CTCTCTCCCAATCCCAATCCCAATCCCATTC
Found at i:2270721 original size:26 final size:26
Alignment explanation
Indices: 2270687--2270752 Score: 132
Period size: 26 Copynumber: 2.5 Consensus size: 26
2270677 CTCCCAATCC
2270687 CAATCCCAATCCCATTCCCTCTCCCA
1 CAATCCCAATCCCATTCCCTCTCCCA
2270713 CAATCCCAATCCCATTCCCTCTCCCA
1 CAATCCCAATCCCATTCCCTCTCCCA
2270739 CAATCCCAATCCCA
1 CAATCCCAATCCCA
2270753 ATCCTAAACC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.26, C:0.53, G:0.00, T:0.21
Consensus pattern (26 bp):
CAATCCCAATCCCATTCCCTCTCCCA
Found at i:2316253 original size:30 final size:30
Alignment explanation
Indices: 2316219--2316279 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
2316209 TTCGATATAA
*
2316219 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
2316249 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
2316279 C
1 C
2316280 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:2322393 original size:23 final size:21
Alignment explanation
Indices: 2322340--2322402 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
2322330 TTTTGGTGCA
*
2322340 GAGGGAATCGATTCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
2322361 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
2322382 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
2322403 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:2322410 original size:21 final size:21
Alignment explanation
Indices: 2322342--2322423 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
2322332 TTGGTGCAGA
* *
2322342 GGGAATCGATTCCCCCC-CTG
1 GGGAACCGATTCCCCCCACAG
*
2322362 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
2322386 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
2322407 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
2322424 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.02
21 32 0.64
23 16 0.32
24 1 0.02
ACGTcount: A:0.22, C:0.38, G:0.24, T:0.16
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:2324866 original size:30 final size:30
Alignment explanation
Indices: 2324832--2324892 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
2324822 TTCGATATAA
*
2324832 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
2324862 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
2324892 C
1 C
2324893 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:2340862 original size:4 final size:4
Alignment explanation
Indices: 2340855--2340905 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
2340845 CTACCATCAC
2340855 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
2340903 AAA
1 AAA
2340906 AGAAGACCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:2341997 original size:19 final size:21
Alignment explanation
Indices: 2341973--2342020 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2341963 ATATACGTTT
**
2341973 TATGAACAGT-AA-AATACGG
1 TATGAACAGTGAACAATACCA
2341992 TATGAACAGTGAACAATACCA
1 TATGAACAGTGAACAATACCA
2342013 TATGAACA
1 TATGAACA
2342021 ATAATGAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.40
20 2 0.08
21 13 0.52
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.21
Consensus pattern (21 bp):
TATGAACAGTGAACAATACCA
Found at i:2342029 original size:10 final size:10
Alignment explanation
Indices: 2342014--2342040 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2342004 ACAATACCAT
2342014 ATGAACAATA
1 ATGAACAATA
2342024 ATGAACAATA
1 ATGAACAATA
2342034 ATGAACA
1 ATGAACA
2342041 GTACCGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (10 bp):
ATGAACAATA
Found at i:2342126 original size:21 final size:21
Alignment explanation
Indices: 2342099--2342172 Score: 130
Period size: 21 Copynumber: 3.5 Consensus size: 21
2342089 GAACTGATTC
*
2342099 CCCTGCTACAGGGAATTGATA
1 CCCTGCTACAGGGAATCGATA
*
2342120 CCTTGCTACAGGGAATCGATA
1 CCCTGCTACAGGGAATCGATA
2342141 CCCTGCTACAGGGAATCGATA
1 CCCTGCTACAGGGAATCGATA
2342162 CCCTGCTACAG
1 CCCTGCTACAG
2342173 TAACTTTCAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (21 bp):
CCCTGCTACAGGGAATCGATA
Found at i:2345640 original size:28 final size:28
Alignment explanation
Indices: 2345598--2345665 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
2345588 CAGGTCAAAC
*
2345598 TGAGTCAACTCGACCAAGTTAACCCAAT
1 TGAGTCAACTTGACCAAGTTAACCCAAT
2345626 TGAGTCAACTTGACCAAGTTAACCCAAT
1 TGAGTCAACTTGACCAAGTTAACCCAAT
2345654 TGAGTCAACTTG
1 TGAGTCAACTTG
2345666 TTAACTTTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (28 bp):
TGAGTCAACTTGACCAAGTTAACCCAAT
Found at i:2348045 original size:22 final size:22
Alignment explanation
Indices: 2347985--2348047 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
2347975 ATTATACTTT
* * *
2347985 ATGAATAGTACCGTAAACAGTA
1 ATGAATAGTACTGTGAACAATA
*
2348007 ATGAATAGTGCTGTGAACAATA
1 ATGAATAGTACTGTGAACAATA
*
2348029 ATGAATAGTACTATGAACA
1 ATGAATAGTACTGTGAACA
2348048 GTACCAATGC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.25
Consensus pattern (22 bp):
ATGAATAGTACTGTGAACAATA
Found at i:2348113 original size:21 final size:21
Alignment explanation
Indices: 2348084--2348125 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2348074 TGATACAGGG
2348084 GTATCGATACCCTGCTACAGT
1 GTATCGATACCCTGCTACAGT
* *
2348105 GTATTGATACCCTGTTACAGT
1 GTATCGATACCCTGCTACAGT
2348126 AATTTCGGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (21 bp):
GTATCGATACCCTGCTACAGT
Found at i:2348801 original size:15 final size:15
Alignment explanation
Indices: 2348781--2348809 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2348771 ATTTTTCATA
2348781 ACATATCACATATAC
1 ACATATCACATATAC
2348796 ACATATCACATATA
1 ACATATCACATATA
2348810 ATATATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (15 bp):
ACATATCACATATAC
Found at i:2348981 original size:31 final size:31
Alignment explanation
Indices: 2348943--2349052 Score: 118
Period size: 31 Copynumber: 3.5 Consensus size: 31
2348933 TCCATATGTT
* *
2348943 CCGAAGAACATAGGTAAA-AGGACTATTTATC
1 CCGAAGAACATAGGTAAACAGGTCTATAT-TC
*
2348974 CCGAAGAACATAGGTAAACA-GTCCATATGTC
1 CCGAAGAACATAGGTAAACAGGTCTATAT-TC
* * *
2349005 CTGAAGAACATAGGTAAACAGTTC-ATATGTT
1 CCGAAGAACATAGGTAAACAGGTCTATAT-TC
2349036 CCGAAGAACATAGGTAA
1 CCGAAGAACATAGGTAA
2349053 CCATCGACTC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
31 66 0.96
32 3 0.04
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGGTCTATATTC
Found at i:2349040 original size:62 final size:62
Alignment explanation
Indices: 2348930--2349052 Score: 171
Period size: 62 Copynumber: 2.0 Consensus size: 62
2348920 CTTGAATGAC
*
2348930 CAGTCCATATGTTCCGAAGAACATAGGTAAAAGGACTATTTATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAAAGGACTATGTATCCCGAAGAACATAGGTAAA
**
2348992 CAGTCCATATG-TCCTGAAGAACATAGGTAAACAGTTCATATGT-T-CCGAAGAACATAGGTAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAAA-AGGAC-TATGTATCCCGAAGAACATAGGTAA
2349053 CCATCGACTC
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
61 3 0.05
62 44 0.80
63 4 0.07
64 4 0.07
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAAAGGACTATGTATCCCGAAGAACATAGGTAAA
Found at i:2351206 original size:2 final size:2
Alignment explanation
Indices: 2351195--2351233 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2351185 TCAAACTTCA
2351195 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2351234 TATTTTACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2366704 original size:4 final size:4
Alignment explanation
Indices: 2366695--2366722 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2366685 GGTATTGATC
2366695 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
2366723 TGAGATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:2370172 original size:14 final size:14
Alignment explanation
Indices: 2370153--2370183 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2370143 GTAGAATTCT
2370153 AAATATTTAAATAA
1 AAATATTTAAATAA
*
2370167 AAATATTTATATAA
1 AAATATTTAAATAA
2370181 AAA
1 AAA
2370184 ATCATCGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATATTTAAATAA
Found at i:2370437 original size:24 final size:24
Alignment explanation
Indices: 2370409--2370454 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2370399 AATTTTAATA
2370409 GATTTAACATTATCAATAAAAAAT
1 GATTTAACATTATCAATAAAAAAT
*
2370433 GATTTAACATTATCAATCAAAA
1 GATTTAACATTATCAATAAAAA
2370455 GCATTGGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.33
Consensus pattern (24 bp):
GATTTAACATTATCAATAAAAAAT
Found at i:2378143 original size:7 final size:7
Alignment explanation
Indices: 2378131--2378176 Score: 83
Period size: 7 Copynumber: 6.4 Consensus size: 7
2378121 TGAAATATCT
2378131 CCTAAAC
1 CCTAAAC
2378138 CCTAAAC
1 CCTAAAC
2378145 CCTAAAC
1 CCTAAAC
2378152 CCTAAAC
1 CCTAAAC
2378159 CCTAAAAC
1 CCT-AAAC
2378167 CCTAAAC
1 CCTAAAC
2378174 CCT
1 CCT
2378177 GTGAAGTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 31 0.82
8 7 0.18
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.15
Consensus pattern (7 bp):
CCTAAAC
Found at i:2382242 original size:118 final size:117
Alignment explanation
Indices: 2382095--2382327 Score: 403
Period size: 118 Copynumber: 2.0 Consensus size: 117
2382085 CTACAATAAT
* * *
2382095 AACAACGAAATTGACTCGAGTCTCAAAGTCACAAAATAATAACAATATTAAAAATAAACACAGAA
1 AACAACAAAATTGACTCAAGTCTCAAAGTCACAAAATAATAAAAATATTAAAAATAAACACAGAA
2382160 TCAAAAGAAATTAATAATATTTTAAAAAAATACCCAAGTCTTGAAATTTTGAC
66 TCAAAAGAAATTAATAATA-TTTAAAAAAATACCCAAGTCTTGAAATTTTGAC
* *
2382213 AACAACAAAATTGACTCAAGTCTCGAAGTCACAAAATAATAAAAATATTAATAATAAACACAGAA
1 AACAACAAAATTGACTCAAGTCTCAAAGTCACAAAATAATAAAAATATTAAAAATAAACACAGAA
*
2382278 TCAAAAGAAATTAATAATATTTAAAAAAATACCCAAGTCTTTAAATTTTG
66 TCAAAAGAAATTAATAATATTTAAAAAAATACCCAAGTCTTGAAATTTTG
2382328 TTTATCAAAG
Statistics
Matches: 109, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
117 30 0.28
118 79 0.72
ACGTcount: A:0.53, C:0.14, G:0.08, T:0.25
Consensus pattern (117 bp):
AACAACAAAATTGACTCAAGTCTCAAAGTCACAAAATAATAAAAATATTAAAAATAAACACAGAA
TCAAAAGAAATTAATAATATTTAAAAAAATACCCAAGTCTTGAAATTTTGAC
Found at i:2385909 original size:37 final size:36
Alignment explanation
Indices: 2385859--2386011 Score: 128
Period size: 37 Copynumber: 4.4 Consensus size: 36
2385849 AAGATATTTG
*
2385859 TTGTTTCATGAGAAACGGTCTCAAGGGAGAC-AAGATT
1 TTGTTTCAAGAGAAACGGTCTCAAGGGAGACGAA-A-T
*
2385896 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAAT
1 TTGTTTCAAGAGAAACGGTCTCAAGGGAGACGAAAT
* * *
2385932 TAGTTTCAA-AGAAACAGAT-TC-A---A-A-G-ATT
1 TTGTTTCAAGAGAAAC-GGTCTCAAGGGAGACGAAAT
* * * *
2385960 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAAT
1 TTGTTTCAAGAGAAACGGTCTCAAGGGAGACGAAAT
2385996 TTGTTTCAAGAGAAAC
1 TTGTTTCAAGAGAAAC
2386012 TGCTTCAAAC
Statistics
Matches: 92, Mismatches: 13, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
28 11 0.12
29 8 0.09
30 2 0.02
31 1 0.01
33 1 0.01
34 2 0.02
35 8 0.09
36 27 0.29
37 30 0.33
38 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (36 bp):
TTGTTTCAAGAGAAACGGTCTCAAGGGAGACGAAAT
Found at i:2385996 original size:64 final size:65
Alignment explanation
Indices: 2385890--2386042 Score: 218
Period size: 64 Copynumber: 2.3 Consensus size: 65
2385880 CAAGGGAGAC
* *
2385890 AAGATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTAGTTTCAA-AGAAACAGATTCA
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTAGTTTCAAGAGAAACAGATTCA
* * * *
2385954 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGAGAAACTGCTTCA
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTAGTTTCAAGAGAAACAGATTCA
*
2386019 AACATCTTGTGTTTCAAGGGAAAC
1 AAGAT-TT-TGTTTCAAGGGAAAC
2386043 GTTTTCAAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
64 47 0.59
65 15 0.19
66 2 0.03
67 15 0.19
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (65 bp):
AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTAGTTTCAAGAGAAACAGATTCA
Found at i:2386115 original size:36 final size:36
Alignment explanation
Indices: 2386075--2386143 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
2386065 AGAGAAATCG
* *
2386075 TCTCAAGGGAGACAAAATTTATTCCAAGGGAAACTA
1 TCTCAAGAGAGACAAAATTCATTCCAAGGGAAACTA
*
2386111 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
1 TCTCAAGAGAGACAAAATTCATTCCAAGGGAAA
2386144 TGTTTTCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTCATTCCAAGGGAAACTA
Found at i:2386176 original size:198 final size:201
Alignment explanation
Indices: 2385828--2386211 Score: 476
Period size: 198 Copynumber: 1.9 Consensus size: 201
2385818 GACAGAATTC
* *
2385828 GTTTCAAGGGAAACGATCTCAAAGATATTTGTTGTTTCATGAGAAACGGTCTCAAGGGAGACAAG
1 GTTTCAAGGGAAACGATCTCAAAGATATTTGATGTTTCAAGAGAAACGGTCTCAAGGGAGACAAG
* * * * * *
2385893 ATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTAGTTTCAAAGAAACAGATTCAAAGA
66 AATTTATTCCAAGAGAAACTATCTCAAGAGAGACAAAATTAGTTTCAAAGAAACAGATTCAAAGA
* ** * *
2385958 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGAGAAACTGCTTCAAACA
131 TTATGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGCTTCAAACA
2386023 TCTTGT
196 TCTTGT
* *
2386029 GTTTCAAGGGAAACGTTTTCAAAG-T-TTT-ATGTTTCAAGAGAAATC-GTCTCAAGGGAGACAA
1 GTTTCAAGGGAAACGATCTCAAAGATATTTGATGTTTCAAGAGAAA-CGGTCTCAAGGGAGACAA
* * * *
2386090 -AATTTATTCCAAGGGAAACTATCTCAAGAGAGACAAAATTCA-TTTCAAGGGAAA-TGTTTTCA
65 GAATTTATTCCAAGAGAAACTATCTCAAGAGAGACAAAATT-AGTTTCAA-AGAAACAG-ATTCA
* * * *
2386152 ATGCTTATGTTTCAAGAAAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAACTG
127 AAGATTATGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTG
2386212 TCTCAAGAGA
Statistics
Matches: 156, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
197 40 0.26
198 89 0.57
199 4 0.03
200 1 0.01
201 22 0.14
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (201 bp):
GTTTCAAGGGAAACGATCTCAAAGATATTTGATGTTTCAAGAGAAACGGTCTCAAGGGAGACAAG
AATTTATTCCAAGAGAAACTATCTCAAGAGAGACAAAATTAGTTTCAAAGAAACAGATTCAAAGA
TTATGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGCTTCAAACA
TCTTGT
Found at i:2386181 original size:101 final size:102
Alignment explanation
Indices: 2386030--2386226 Score: 308
Period size: 101 Copynumber: 1.9 Consensus size: 102
2386020 ACATCTTGTG
* *
2386030 TTTCAAGGGAAACGTTTTCAAAGTTTTATGTTTCAAGAGAAATCGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAACGTTTTCAAAGTCTTATGTTTCAAGAAAAATCGTCTCAAGGGAGACAAAATTT
*
2386095 ATTCCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 ATTCCAAGGGAAACTATCTCAAGAGAAACAAAATTCA
* *
2386132 TTTCAAGGGAAATGTTTTCAATG-CTTATGTTTCAAGAAAAA-CTGTCTCAAGGGAGACAAAATT
1 TTTCAAGGGAAACGTTTTCAAAGTCTTATGTTTCAAGAAAAATC-GTCTCAAGGGAGACAAAATT
* *
2386195 TATTTCAAGGGAAACTGTCTCAAGAGAAACAA
65 TATTCCAAGGGAAACTATCTCAAGAGAAACAA
2386227 TGGTGAGCAC
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
100 1 0.01
101 65 0.75
102 21 0.24
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (102 bp):
TTTCAAGGGAAACGTTTTCAAAGTCTTATGTTTCAAGAAAAATCGTCTCAAGGGAGACAAAATTT
ATTCCAAGGGAAACTATCTCAAGAGAAACAAAATTCA
Found at i:2386944 original size:106 final size:106
Alignment explanation
Indices: 2386351--2386919 Score: 942
Period size: 106 Copynumber: 5.4 Consensus size: 106
2386341 GTATTGCTCC
* * * * * * *
2386351 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATCGGTTCT-AGAACTGGGAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AATTGAGAAGTTGTTTGTTGACA
* *
2386415 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2386457 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
2386522 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2386563 GAGTCCAATATCCTTCGTTGTGAAGTTGAATTTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
2386628 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2386669 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
2386734 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2386775 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
2386840 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2386881 GAGTCCACTATCCTTCGCTGTGAAGTTGAAATTGGCTCT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
2386920 AGAAGTGGAA
Statistics
Matches: 435, Mismatches: 27, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
106 434 1.00
107 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2398360 original size:29 final size:29
Alignment explanation
Indices: 2398303--2398360 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2398293 GTGTTGATCG
* *
2398303 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGACGACCTAC
* *
2398332 TAGGTCGCCATGTCTTCCCGACGAGCTAC
1 TAGGTCGCCATGCCTTCCCGACGACCTAC
2398361 AAGAGATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.36, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGACGACCTAC
Found at i:2398469 original size:23 final size:23
Alignment explanation
Indices: 2398443--2398487 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2398433 CCAAGGCCAT
2398443 CCGAACGAGCTATGCGAGGGCAA
1 CCGAACGAGCTATGCGAGGGCAA
*
2398466 CCGAGCGAGCTATGCGAGGGCA
1 CCGAACGAGCTATGCGAGGGCA
2398488 TCTGAGGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.27, G:0.38, T:0.09
Consensus pattern (23 bp):
CCGAACGAGCTATGCGAGGGCAA
Found at i:2398500 original size:33 final size:33
Alignment explanation
Indices: 2398457--2398540 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
2398447 ACGAGCTATG
*
2398457 CGAGGGCAACCGAGCGAGCTATGCGAGGGCATC
1 CGAGGGCAACCGAGCGAGCTATGCGAGGGAATC
* *
2398490 TGAGGGCAACCGAGCTAGCTATGCGAGGGAATC
1 CGAGGGCAACCGAGCGAGCTATGCGAGGGAATC
2398523 CGAGGG-AAGCCGAGCGAG
1 CGAGGGCAA-CCGAGCGAG
2398541 GGTAGGTCGC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
32 2 0.04
33 43 0.96
ACGTcount: A:0.26, C:0.24, G:0.40, T:0.10
Consensus pattern (33 bp):
CGAGGGCAACCGAGCGAGCTATGCGAGGGAATC
Found at i:2398577 original size:29 final size:29
Alignment explanation
Indices: 2398544--2398600 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
2398534 GAGCGAGGGT
*
2398544 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
* *
2398573 AGGTCGCTCGGAGGGCATTGCGACCTAC
1 AGGTCGCCCGGAGGGCATGGCGACCTAC
2398601 GGCCAACACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.19, C:0.30, G:0.35, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:2402139 original size:26 final size:26
Alignment explanation
Indices: 2402051--2402129 Score: 158
Period size: 26 Copynumber: 3.0 Consensus size: 26
2402041 TATATATATT
2402051 ATATACCATTTCCTTGATTAGAATTG
1 ATATACCATTTCCTTGATTAGAATTG
2402077 ATATACCATTTCCTTGATTAGAATTG
1 ATATACCATTTCCTTGATTAGAATTG
2402103 ATATACCATTTCCTTGATTAGAATTG
1 ATATACCATTTCCTTGATTAGAATTG
2402129 A
1 A
2402130 CATGGTATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (26 bp):
ATATACCATTTCCTTGATTAGAATTG
Found at i:2406459 original size:36 final size:35
Alignment explanation
Indices: 2406419--2406488 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
2406409 AATGTATTTA
2406419 AAATTGCTT-GAGTTTTCAAA-GTTACTTTTTATCCTG
1 AAATTG-TTCGAGTTTTCAAATGTT-C-TTTTATCCTG
*
2406455 AAATTGTTCGAGTTTTTAAATGTTCTTTTATCCT
1 AAATTGTTCGAGTTTTCAAATGTTCTTTTATCCT
2406489 AATATTTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
35 11 0.35
36 17 0.55
37 3 0.10
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (35 bp):
AAATTGTTCGAGTTTTCAAATGTTCTTTTATCCTG
Found at i:2412524 original size:35 final size:34
Alignment explanation
Indices: 2412439--2412525 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
2412429 AAAATAATTT
* *
2412439 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGA
* *
2412473 TAAATGATAACCAAATTACAATAACTGATATTAAATGA
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGA
2412511 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2412526 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 4 0.09
38 10 0.23
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGA
Found at i:2412769 original size:3 final size:3
Alignment explanation
Indices: 2412763--2412815 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
2412753 ATCACCATCA
* * * * * *
2412763 TCG TCG TCG TCG TCG TCG TCA TTG TCA TCG TCA TCG TAG TCG TCA TCG
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
2412811 TCG TC
1 TCG TC
2412816 CTGAGTAGGT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.09, C:0.30, G:0.25, T:0.36
Consensus pattern (3 bp):
TCG
Found at i:2412778 original size:12 final size:12
Alignment explanation
Indices: 2412758--2412815 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
2412748 TCATCATCAC
*
2412758 CATCATCGTCGT
1 CATCGTCGTCGT
*
2412770 CGTCGTCGTCGT
1 CATCGTCGTCGT
* *
2412782 CATTGTCATCGT
1 CATCGTCGTCGT
*
2412794 CATCGTAGTCGT
1 CATCGTCGTCGT
2412806 CATCGTCGTC
1 CATCGTCGTC
2412816 CTGAGTAGGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.12, C:0.31, G:0.22, T:0.34
Consensus pattern (12 bp):
CATCGTCGTCGT
Found at i:2413694 original size:27 final size:27
Alignment explanation
Indices: 2413653--2413711 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
2413643 ATCTGATGGG
*
2413653 CATCAGGTAAGGGAATGGCGGTGGCGA
1 CATCAGGTAAGGGAAAGGCGGTGGCGA
* * *
2413680 CATCTGGTAATGGAAAGGCGGTGGCGG
1 CATCAGGTAAGGGAAAGGCGGTGGCGA
2413707 CATCA
1 CATCA
2413712 TATATGGATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.17, G:0.41, T:0.17
Consensus pattern (27 bp):
CATCAGGTAAGGGAAAGGCGGTGGCGA
Found at i:2414120 original size:522 final size:522
Alignment explanation
Indices: 2413159--2414144 Score: 1607
Period size: 522 Copynumber: 1.9 Consensus size: 522
2413149 CAACTATGGT
* * *
2413159 ATCTGGTAATGGAAAGACGGTGGTGGCATCATATATGGATGCGGTGGCTGTTGTGAAGGTCATGC
1 ATCTGGTAATGGAAAGACGGTGGCGGCATCATATATGGATGCGGTGGCTGCTATGAAGGTCATGC
* *
2413224 TGGTGCAGCTGAGGATAAACTGAAAGCTCCTGCTCTCCGTCCATGAGTCGGGGGACGATGGTGTT
66 TGGTGCAGCTGAGGATAAACCGAAAGCTCCTGCTCTCCGTCCACGAGTCGGGGGACGATGGTGTT
* * * *
2413289 GTGTCGGTGAATGTCTCTGTCGACGTCACGGAAAGGTCTGCCCTCGTGCATCCTCGGGAAGAAGA
131 GTATCAGTGAATGTCTCTATCGACGTCACGGAAAGGTCTACCCTCGTGCATCCTCGGGAAGAAGA
*
2413354 AACAGTTTCCCGTTACTGTTGAACCACTCATAATAACCGTCAGCAACCATCAAGAGGTCAAGTAA
196 AACAGTTTCCCGTTACTGTTGAACCACTCATAATAACCGACAGCAACCATCAAGAGGTCAAGTAA
* *
2413419 AATAGGTTCTCTACGGGGAAGACGCCGATGTCGATCCTCCCATAACACGACCCACGCATGATGCC
261 AATAGGCTCTCTACGGGGAAGACGCCGATGTCGATCCTCCCACAACACGACCCACGCATGATGCC
* * *
2413484 TCACCAGTCAATCTGTATATGTCTTGCCGCACCTATCTGTGCTATGCAACTCGTCCATATTGCGG
326 TCACCAGCCAATCTGTATATGTCTTGCCGCACCTATCTGTGCTATGCAACTCGTCCATATTACGA
*
2413549 GGTGCTTCCGAAATTGGTTGAAAACAACCAAATTACCGGAGCACGCGATCAGTGGAGTGCCACTC
391 GGTGCTTCCGAAATTGGTTGAAAACAACCAAATTACCAGAGCACGCGATCAGTGGAGTGCCACTC
*
2413614 GACGGTCGCTGGACTGTCACCATCCAAACATCTGATGGGCATCAGGTAAGGGAATGGCGGTGGCG
456 GACGATCGCTGGACTGTCACCATCCAAACATCTGATGGGCATCAGGTAAGGGAATGGCGGTGGCG
2413679 AC
521 AC
* * *
2413681 ATCTGGTAATGGAAAGGCGGTGGCGGCATCATATATGGATGTGGTGGCTGCTATGAAGGTCCTGC
1 ATCTGGTAATGGAAAGACGGTGGCGGCATCATATATGGATGCGGTGGCTGCTATGAAGGTCATGC
* * * *
2413746 TGGTGTAGCTGAGGATGAACCGGAAGCAT-CTGCTCTCCGTCCCCGAGTCGGGGGACGATGGTGT
66 TGGTGCAGCTGAGGATAAACCGAAAGC-TCCTGCTCTCCGTCCACGAGTCGGGGGACGATGGTGT
* *
2413810 TGTATCAGTGAATGTCTCTATCGACGTCGCGGAAAGGTCTACCCTCGTGCATCCTCGGGAAGCAG
130 TGTATCAGTGAATGTCTCTATCGACGTCACGGAAAGGTCTACCCTCGTGCATCCTCGGGAAGAAG
* * * *
2413875 AAAC-GATTTCCCGTTACTGTTGAACCATTCGTAATTACTGACAGCAACCATCAAGAGGTCAAGT
195 AAACAG-TTTCCCGTTACTGTTGAACCACTCATAATAACCGACAGCAACCATCAAGAGGTCAAGT
* * *
2413939 AAAATGGGCTCTCTACGGGGAAGACGCCGGTGTTGATCCTCCCACAACACGACCCACGCATGATG
259 AAAATAGGCTCTCTACGGGGAAGACGCCGATGTCGATCCTCCCACAACACGACCCACGCATGATG
*
2414004 CCTCACCAGCCAATCTGTATATGTCTTGCCGCATCTATCTGTGCTATGCAACTCGTCCATATTAC
324 CCTCACCAGCCAATCTGTATATGTCTTGCCGCACCTATCTGTGCTATGCAACTCGTCCATATTAC
* **
2414069 GAGGTGCTTCCGGAATTGGTTGAAAACAACCAAATTTTCAGAGCACGCGATCAGTGGAGTGCCAC
389 GAGGTGCTTCCGAAATTGGTTGAAAACAACCAAATTACCAGAGCACGCGATCAGTGGAGTGCCAC
2414134 TCGACGATCGC
454 TCGACGATCGC
2414145 ATAACAGATC
Statistics
Matches: 425, Mismatches: 37, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
521 1 0.00
522 423 1.00
523 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (522 bp):
ATCTGGTAATGGAAAGACGGTGGCGGCATCATATATGGATGCGGTGGCTGCTATGAAGGTCATGC
TGGTGCAGCTGAGGATAAACCGAAAGCTCCTGCTCTCCGTCCACGAGTCGGGGGACGATGGTGTT
GTATCAGTGAATGTCTCTATCGACGTCACGGAAAGGTCTACCCTCGTGCATCCTCGGGAAGAAGA
AACAGTTTCCCGTTACTGTTGAACCACTCATAATAACCGACAGCAACCATCAAGAGGTCAAGTAA
AATAGGCTCTCTACGGGGAAGACGCCGATGTCGATCCTCCCACAACACGACCCACGCATGATGCC
TCACCAGCCAATCTGTATATGTCTTGCCGCACCTATCTGTGCTATGCAACTCGTCCATATTACGA
GGTGCTTCCGAAATTGGTTGAAAACAACCAAATTACCAGAGCACGCGATCAGTGGAGTGCCACTC
GACGATCGCTGGACTGTCACCATCCAAACATCTGATGGGCATCAGGTAAGGGAATGGCGGTGGCG
AC
Found at i:2415903 original size:31 final size:31
Alignment explanation
Indices: 2415865--2415989 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
2415855 AGGGTCGAGG
2415865 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
2415896 GTTTACCTATGTTCTTCGTGACATAAGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2415927 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
2415958 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
2415989 G
1 G
2415990 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2416675 original size:21 final size:21
Alignment explanation
Indices: 2416641--2416690 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
2416631 TTGTAGCAGT
* *
2416641 ACTGTAGTAGTGCATCGATGC
1 ACTGTAGCAATGCATCGATGC
*
2416662 ATTGTAGCAATGCATCGATGC
1 ACTGTAGCAATGCATCGATGC
2416683 ACTGTAGC
1 ACTGTAGC
2416691 CATTCAAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (21 bp):
ACTGTAGCAATGCATCGATGC
Found at i:2416730 original size:21 final size:21
Alignment explanation
Indices: 2416704--2416745 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2416694 TCAAAGTTTT
*
2416704 ATGCATCGGTGCACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
2416725 ATGCATCGATGCACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
2416746 CTATAGCAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (21 bp):
ATGCATCGATGCACTGTAGCA
Found at i:2418058 original size:25 final size:25
Alignment explanation
Indices: 2418004--2418055 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
2417994 TTATATTTGC
*
2418004 AAAA-AAATTAAATAAGTAAAATATT
1 AAAATAAATTAAAT-AGCAAAATATT
2418029 -AAATAAATTAAATA-CAAAATATT
1 AAAATAAATTAAATAGCAAAATATT
2418052 AAAA
1 AAAA
2418056 ATATAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
23 8 0.33
24 7 0.29
25 9 0.38
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAATAAATTAAATAGCAAAATATT
Found at i:2418169 original size:16 final size:16
Alignment explanation
Indices: 2418148--2418179 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2418138 GATGGAGGTA
*
2418148 TTTATAGGGAGGTTTG
1 TTTATAGAGAGGTTTG
2418164 TTTATAGAGAGGTTTG
1 TTTATAGAGAGGTTTG
2418180 GGGGTATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (16 bp):
TTTATAGAGAGGTTTG
Found at i:2419476 original size:197 final size:198
Alignment explanation
Indices: 2419262--2419655 Score: 763
Period size: 198 Copynumber: 2.0 Consensus size: 198
2419252 CGACCCGAAT
2419262 ATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTT
1 ATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTT
2419327 TTTCCAACTAAGTCACTG-TTTTATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTGGG
66 TTTCCAACTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTGGG
*
2419391 TTTCTAATTCATATATTCGGGTCGGGTTGGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAA
131 TTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAA
2419456 GTA
196 GTA
*
2419459 ATATATATAATTTTACCTTATATATTTAGGAATAATTATAATAATACCCCTCTATATATAATTTT
1 ATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTT
2419524 TTTCCAACTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTGGG
66 TTTCCAACTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTGGG
2419589 TTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAA
131 TTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAA
2419654 GT
196 GT
2419656 GTGATATTCG
Statistics
Matches: 194, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
197 82 0.42
198 112 0.58
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.45
Consensus pattern (198 bp):
ATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTT
TTTCCAACTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTGGG
TTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAA
GTA
Found at i:2420254 original size:17 final size:17
Alignment explanation
Indices: 2420232--2420272 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
2420222 ATTGAATTCT
2420232 AATTCCTGACAGATTTC
1 AATTCCTGACAGATTTC
*
2420249 AATTCCTGATAGATTTC
1 AATTCCTGACAGATTTC
2420266 AATTCCT
1 AATTCCT
2420273 TCACACATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (17 bp):
AATTCCTGACAGATTTC
Found at i:2421150 original size:268 final size:260
Alignment explanation
Indices: 2420586--2421152 Score: 824
Period size: 268 Copynumber: 2.1 Consensus size: 260
2420576 TATTATTTCG
* *
2420586 GGTCTGGTCGAGTGAAACTTTATTTTGGTCGAGTCGGGTCAGTTTTTTTAAGTGTGATATTCGGG
1 GGTCGGGTCGGGTGAAACTTTATTTTGGTCG-GTCGGGTCAGTTTTTTTAAGTGTGATATTCGGG
* **
2420651 TCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCAAAACTATATATAATTTTACCTTAT
65 TCGGGTCGAGTTCGGGTTTAGGATGAAAAATACCCGACCCAAAAAAATATATAATTTTACCTTAT
*
2420716 ATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTCCAATTAAGTCACTGTTTT
130 ATATTTAGGAATAATTACAATAATACCCCTCTATATATAATATTTTCCAATTAAGTCACTGTTTT
2420781 TATTGAATAAAAATAATTTTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATA
195 TATTGAATAAAAATAATTTTTTTTATTATTTCGGGTCGGGT---GTCGGATTTCTAATTCATATA
*
2420846 TTCG
257 TTCA
* * *
2420850 GGTCGGGTCAGGTGAAATTTTA-TTT--T-GGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGT
1 GGTCGGGTCGGGTGAAACTTTATTTTGGTCGGTCGGGTCAGTTTTTTTAAGTGTGATA-T----T
*
2420911 CGGGTCGGGTCGGGTTCGGGTTTAGGATGAAAAATACCCGACCCGACCCAAAAAATATATAATTT
61 CGGGTCGGGTCGAGTTCGGGTTTAGGATGAAAAATACCCGACCC-A---AAAAAATATATAATTT
*
2420976 TACCTTATATATTTAGGAATAATTACATTAATACCCCTCTATATATATATATTTT-CAATTAAGT
122 TACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATA-ATATTTTCCAATTAAGT
* *
2421040 CATTGTTTTTATTGAATAAAAATAATTTTTTTTATTATTTCGGGTCGGGT-T-GGGTTTCTAATT
186 CACTGTTTTTATTGAATAAAAATAATTTTTTTTATTATTTCGGGTCGGGTGTCGGATTTCTAATT
2421103 CATATATTCA
251 CATATATTCA
2421113 GGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGTCGGGTC
1 GGTCGGGTCGGGTGAAACTTTATTTTGGTC-GGTCGGGTC
2421153 TCGGATGGAG
Statistics
Matches: 272, Mismatches: 16, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
259 26 0.10
260 2 0.01
261 1 0.00
263 43 0.16
264 65 0.24
265 1 0.00
266 1 0.00
268 127 0.47
269 6 0.02
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (260 bp):
GGTCGGGTCGGGTGAAACTTTATTTTGGTCGGTCGGGTCAGTTTTTTTAAGTGTGATATTCGGGT
CGGGTCGAGTTCGGGTTTAGGATGAAAAATACCCGACCCAAAAAAATATATAATTTTACCTTATA
TATTTAGGAATAATTACAATAATACCCCTCTATATATAATATTTTCCAATTAAGTCACTGTTTTT
ATTGAATAAAAATAATTTTTTTTATTATTTCGGGTCGGGTGTCGGATTTCTAATTCATATATTCA
Found at i:2421480 original size:13 final size:13
Alignment explanation
Indices: 2421462--2421488 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2421452 CCAAACAAAA
2421462 TATGAAATTGGAT
1 TATGAAATTGGAT
2421475 TATGAAATTGGAT
1 TATGAAATTGGAT
2421488 T
1 T
2421489 CCAATTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
TATGAAATTGGAT
Found at i:2428253 original size:2 final size:2
Alignment explanation
Indices: 2428246--2428272 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2428236 GGTCTGATAC
2428246 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2428273 GTATGTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2429704 original size:40 final size:40
Alignment explanation
Indices: 2429649--2429735 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 40
2429639 ACCCACCAAT
*
2429649 GGTTCTTGCTTTGATCTTTCATTAGCTCTCAATTGTGAAG
1 GGTTCTTGCCTTGATCTTTCATTAGCTCTCAATTGTGAAG
* *
2429689 GGTTCTTGCCTTGATCTTTCATTAGGTTTCAATTGTGAAG
1 GGTTCTTGCCTTGATCTTTCATTAGCTCTCAATTGTGAAG
*
2429729 GGATCTT
1 GGTTCTT
2429736 AGTATCTTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.45
Consensus pattern (40 bp):
GGTTCTTGCCTTGATCTTTCATTAGCTCTCAATTGTGAAG
Found at i:2430742 original size:33 final size:33
Alignment explanation
Indices: 2430700--2430791 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
2430690 TGGTAAGTTG
2430700 GAAATTTCATCTTGGTTGGTGGCCAACTTATTA
1 GAAATTTCATCTTGGTTGGTGGCCAACTTATTA
*
2430733 GAAATTTCATCTTGATTGGTGGCCAACTTATTA
1 GAAATTTCATCTTGGTTGGTGGCCAACTTATTA
*
2430766 GAAATTTCATCTTAGTTGGTGGCCAA
1 GAAATTTCATCTTGGTTGGTGGCCAA
2430792 ATTTTGAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (33 bp):
GAAATTTCATCTTGGTTGGTGGCCAACTTATTA
Found at i:2437735 original size:16 final size:16
Alignment explanation
Indices: 2437701--2437740 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2437691 TTTACTTCAT
*
2437701 AATGATT-AAGTGCTG
1 AATGATTCAAATGCTG
*
2437716 AATGATTCAAATGTTG
1 AATGATTCAAATGCTG
2437732 AATGATTCA
1 AATGATTCA
2437741 GAGGCTCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (16 bp):
AATGATTCAAATGCTG
Done.