Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 22 of 196
Found at i:6315945 original size:43 final size:43
Alignment explanation
Indices: 6315817--6317048 Score: 1123
Period size: 43 Copynumber: 28.4 Consensus size: 43
6315807 TCAAATTATA
*
6315817 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAAGGGTTAAGGAT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG-T-----T
*
6315866 TTTAAAGTTAAGGGTCTAGGGTTTTAAAGTTAAGGGTTTAGGGTT
1 TTT-AAGTTAAGGGT-TAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
6315911 TTTAGGTTAAGGGTTAGGGTTTTTAGGTTTAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
6315954 TTTAATTTAAGGGTTATGGTTTTTAAGTTAAAGGTCTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
6315997 TTAAAGTTAAGGGTCTATGGTTTTAAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGT-TAGGGTTTTTAAGTTAAGGGTTTAGGGTT
*
6316040 TTTAGGTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
6316083 TTTAAGTTAAGGGTTTATGGTTTTAAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * * *
6316127 TTAAAGTTAAGGTTTAAGGTTTTTAGGTTAAGGG-TTATGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
6316169 TTTAGGTTAAGGTTTAGGGTTTTTAATTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
6316211 TTTAAGTTAAAGTTTAGGGTTTTCAGGTTAAGGG-TTAGGGTTTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG--TT
* * * * * *
6316255 TAGGTTAAGGTTTAGGGTTTAGGGTTTTTAATTTAA-TGATTATGATT
1 T---TTAA-GTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
6316302 TTTAAGTTAAGCGTTTAGGGTTTTTAAGTTAAGGGTCTAAGGTT
1 TTTAAGTTAAG-GGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
6316346 TTAAAGTTAAGGTTTAGGGTTTTCAGGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * * *
6316388 TTTAGGTTAAATGTTTAGGG-TTTTAATTTAAGGG-TTAAGGTT
1 TTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
6316430 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
6316474 TTAAAGTTAAGGTTTATGGTTTTTAGGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
6316516 TTTAGGTTAAGGGTTTAAGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
** * ** *
6316560 TAAAAGTTAAGGTTTAGGGTTTTTGGGTTAAGAG-TTAGGG-T
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
6316601 TTTAGGTTAAGGGTTTAGGGTTTTTAATTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
6316644 TTTAAGTTAAGGGTTTATGGTTTCTAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
** * * *
6316688 TAAAAGTTAAAGTTTAGGGTTTTTAGGTTAAGGG-TTAGGG-T
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* ** * * * *
6316729 TTTATGTTAAAGATTTAGGGTTTTAAATTTAA-GGATTAGTGTT
1 TTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
6316772 TTTAAGTTAAGGGTTTAGGG-TTTTAAGTTAAGGGTCTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * * * * *
6316815 TTAAACTTAAGGGTTATGGTTTTTAGGTTTAGGGGTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
6316858 TTTAATTTAAGGGTTTATGGTTTTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
6316902 TTTAATTTAAAAGTTTAGGGTTTTTTAAGTTAAGGGTTTAAGG-T
1 TTTAAGTT-AAGGGTTAGGG-TTTTTAAGTTAAGGGTTTAGGGTT
* * *
6316946 TTTAAGGTTAAGGGTTAAGGTTTTTAGGTTAAGGGGTTAGGGTT
1 TTTAA-GTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
6316990 TTAAAGTTAATGGTTAGGGTTTTTAGGTTAATGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
6317033 TTAAAGTTAAAGGTTA
1 TTTAAGTTAAGGGTTA
6317049 ATGAGTTAGG
Statistics
Matches: 974, Mismatches: 174, Indels: 76
0.80 0.14 0.06
Matches are distributed among these distances:
41 21 0.02
42 210 0.22
43 466 0.48
44 176 0.18
45 29 0.03
47 7 0.01
48 6 0.01
49 22 0.02
50 12 0.01
51 25 0.03
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.45
Consensus pattern (43 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
Found at i:6316290 original size:28 final size:27
Alignment explanation
Indices: 6316235--6316290 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
6316225 TAGGGTTTTC
*
6316235 AGGTTAAGGGTTAGGGTTTTTAGGTTA
1 AGGTTAAGGGTTAGGGTTTTTAAGTTA
* *
6316262 AGGTTTAGGGTTTAGGGTTTTTAATTTA
1 AGGTTAAGGG-TTAGGGTTTTTAAGTTA
6316290 A
1 A
6316291 TGATTATGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (27 bp):
AGGTTAAGGGTTAGGGTTTTTAAGTTA
Found at i:6316307 original size:128 final size:127
Alignment explanation
Indices: 6315817--6317034 Score: 782
Period size: 128 Copynumber: 9.3 Consensus size: 127
6315807 TCAAATTATA
* * *
6315817 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAAGGG--TTAAGGATTTTAAAGTTAAGGG
1 TTTAAGTTAAGGTTTAGGGTTTTAAAGTTAAGGGTT-AGGGTTTTTAGG---TT-AAGTT-AGGG
* * * * * * *
6315880 TCTAGGGTTTTAAAGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTTAGGGTTTTTAGGTTTAGGG
60 TTTAAGGTTTTTAAGTTAAGGG-TTATGG--TTTA--TTAAGGTTTAGGGTTTTTAAGTTAAGGG
*
6315945 TTTATGGTT
120 -TTAGGGTT
* * * * * *
6315954 TTTAATTTAAGGGTTATGGTTTTTAAGTTAAAGGTCTAGGG-TTTTA----AAGTTAAGGGTCTA
1 TTTAAGTTAAGGTTTAGGGTTTTAAAGTTAAGGGT-TAGGGTTTTTAGGTTAAGTT-AGGGTTTA
* * *
6316014 TGGTTTTAAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAG
64 AGGTTTTTAAGTTAAGGGTTATGG--TTTA--TTAA-GGTTTAGGGTTTTTAAGTTAAGGGTTAG
6316079 GGTT
124 GGTT
* * *
6316083 TTTAAGTTAAGGGTTTATGGTTTTAAAGTTAAGGGTCTATGG-TTTTA----AAGTTAAGGTTTA
1 TTTAAGTTAA-GGTTTAGGGTTTTAAAGTTAAGGGT-TAGGGTTTTTAGGTTAAGTTAGGGTTTA
* *
6316143 AGGTTTTTAGGTTAAGGGTTATGGTTTTTAGGTTAAGGTTTAGGGTTTTTAATTTAAGGGTTAGG
64 AGGTTTTTAAGTTAAGGGTTATGG--TTTA--TTAAGGTTTAGGGTTTTTAAGTTAAGGGTTAGG
6316208 GTT
125 GTT
* * *
6316211 TTTAAGTTAAAGTTTAGGGTTTTCAGGTTAAGGGTTAGGGTTTTTAGGTTAAGGTTTAGGGTTTA
1 TTTAAGTTAAGGTTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTTAGGTTAA-G-TTAGGGTTTA
* * * * *
6316276 GGGTTTTTAATTTAATGATTATGATTTTTAAGTTAAGCGTTTAGGGTTTTTAAGTTAAGGGTCTA
64 AGGTTTTTAAGTTAAGGGTTATG--GTTT-A-TTAAG-GTTTAGGGTTTTTAAGTTAAGGGT-TA
*
6316341 AGGTT
123 GGGTT
* * * *
6316346 TTAAAGTTAAGGTTTAGGGTTTTCAGGTTAAGGGTTAGGGTTTTTAGGTTAA---A-TGTTT-AG
1 TTTAAGTTAAGGTTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTTAGGTTAAGTTAGGGTTTAAG
* * * *
6316406 GGTTTTAATTTAAGGGTTAAGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTCTATG
66 GTTTTTAAGTTAAGGGTTATGG--TTT-A-TTAA-GGTTTAGGGTTTTTAAGTTAAGGGT-TAGG
6316471 GTT
125 GTT
* * * *
6316474 TTAAAGTTAAGGTTTATGGTTTTTAGGTTAAGGGTTAGGGTTTTTAGGTT-A---AGGGTTTAAG
1 TTTAAGTTAAGGTTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTTAGGTTAAGTTAGGGTTTAAG
* ** *
6316535 GTTTTTAAGTTAAGGGTTTAGGGTTTAAAAGTTAAGGTTTAGGGTTTTTGGGTTAAGAGTTAGGG
66 GTTTTTAAGTTAAGGG-TTATGGTTT---A-TTAAGGTTTAGGGTTTTTAAGTTAAGGGTTAGGG
6316600 -T
126 TT
* * * * *
6316601 TTTAGGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTAGGGTTTTTAAGTT-A---AGGGTTTAT
1 TTTAAGTTAA-GGTTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTTAGGTTAAGTTAGGGTTTAA
* * *
6316662 GGTTTCTAAGTTAAGGGTCTATGGTTTAAAAGTTAAAGTTTAGGGTTTTTAGGTTAAGGGTTAGG
65 GGTTTTTAAGTTAAGGGT-TATGGTTT---A-TTAAGGTTTAGGGTTTTTAAGTTAAGGGTTAGG
6316727 G-T
125 GTT
* * * * * *
6316729 TTTATGTTAAAGATTTAGGGTTTTAAATTTAAGGATTAGTGTTTTTAAGTT-A---AGGGTTT-A
1 TTTAAGTT-AAGGTTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTTAGGTTAAGTTAGGGTTTAA
* * * * * * *
6316789 GGGTTTTAAGTTAAGGGTCTAAGGTTTTAAACTTAAGGGTTATGGTTTTTAGGTTTAGGGGTTAT
65 GGTTTTTAAGTTAAGGGT-TATGG-TTT--A-TTAAGGTTTAGGGTTTTTAAG-TTAAGGGTTAG
6316854 GGTT
124 GGTT
* * * * ** *
6316858 TTTAATTTAAGGGTTTATGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTTAA---A-AGTTTA
1 TTTAAGTTAA-GGTTTAGGGTTTTAAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGTTAGGGTTTA
* * * * *
6316919 GGGTTTTTTAAGTTAAGGGTTTAAGGTTTTAAGGTTAAGGGTTAAGGTTTTTAGGTTAAGGGGTT
64 AGG-TTTTTAAGTTAAGGG-TTATGG-TTT-A--TTAAGGTTTAGGGTTTTTAAGTTAA-GGGTT
6316984 AGGGTT
122 AGGGTT
* * * *
6316990 TTAAAGTTAATGG-TTAGGGTTTTTAGGTTAATGGTTTAGGGTTTT
1 TTTAAGTTAA-GGTTTAGGGTTTTAAAGTTAA-GGGTTAGGGTTTT
6317035 AAAGTTAAAG
Statistics
Matches: 938, Mismatches: 104, Indels: 84
0.83 0.09 0.07
Matches are distributed among these distances:
126 4 0.00
127 80 0.09
128 331 0.35
129 144 0.15
130 120 0.13
131 36 0.04
132 66 0.07
133 37 0.04
134 24 0.03
135 56 0.06
137 36 0.04
138 4 0.00
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.45
Consensus pattern (127 bp):
TTTAAGTTAAGGTTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTTAGGTTAAGTTAGGGTTTAAG
GTTTTTAAGTTAAGGGTTATGGTTTATTAAGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
Found at i:6317356 original size:21 final size:21
Alignment explanation
Indices: 6317331--6317393 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
6317321 TCCAGCTTTT
*
6317331 GGCGGCGATTATAGTTCTTCC
1 GGCGGCGATTATGGTTCTTCC
* *
6317352 GGCGGCGGTTGTGGTTCTTCC
1 GGCGGCGATTATGGTTCTTCC
* *
6317373 GGCGGGGATTCTGGTTCTTCC
1 GGCGGCGATTATGGTTCTTCC
6317394 AGTAGGGCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.06, C:0.24, G:0.37, T:0.33
Consensus pattern (21 bp):
GGCGGCGATTATGGTTCTTCC
Found at i:6317676 original size:18 final size:18
Alignment explanation
Indices: 6317650--6317692 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
6317640 GACTCGAAAA
* *
6317650 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
6317668 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
6317686 AGGAAAC
1 AGGAAAC
6317693 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:6318504 original size:20 final size:20
Alignment explanation
Indices: 6318467--6318504 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6318457 TTTATTTTTA
*
6318467 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
6318487 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
6318505 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:6326050 original size:104 final size:104
Alignment explanation
Indices: 6325869--6326229 Score: 582
Period size: 104 Copynumber: 3.5 Consensus size: 104
6325859 CGGTAGATCC
*
6325869 CGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACA
1 CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACA
6325934 TAGCAACCCCCTTTTTCATTTCAAAGATACGGTGGATAT
66 TAGCAACCCCCTTTTTCATTTCAAAGATACGGTGGATAT
* * * *
6325973 TGCACTTAGCATCACCAATGAATCAGGGAATCAGCACTTAGTAACCCCTCGGGGGAATCAGCACA
1 CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACA
*
6326038 TAGCAACCCCC-TTTTCATTTCAAAGATACGATGGATAT
66 TAGCAACCCCCTTTTTCATTTCAAAGATACGGTGGATAT
6326076 CGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCAC
1 CGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCAC
** *
6326141 ATAGCAACCCCCTTTCACATTTCAAAGATATGGTGGATCA-
65 ATAGCAACCCCCTTTTTCATTTCAAAGATACGGTGGAT-AT
* **
6326181 CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
6326230 TTTATATACA
Statistics
Matches: 237, Mismatches: 17, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
103 44 0.19
104 152 0.64
105 40 0.17
106 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (104 bp):
CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACA
TAGCAACCCCCTTTTTCATTTCAAAGATACGGTGGATAT
Found at i:6332191 original size:15 final size:15
Alignment explanation
Indices: 6332173--6332217 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
6332163 AATATATATA
*
6332173 TCAATTCCATCCAAT
1 TCAATTCAATCCAAT
6332188 TCAATTCAATCCAAT
1 TCAATTCAATCCAAT
*
6332203 TCAATTCAATTCAAT
1 TCAATTCAATCCAAT
6332218 AATCAATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.36
Consensus pattern (15 bp):
TCAATTCAATCCAAT
Found at i:6332194 original size:5 final size:5
Alignment explanation
Indices: 6332173--6332217 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
6332163 AATATATATA
* * *
6332173 TCAAT TCCAT CCAAT TCAAT TCAAT CCAAT TCAAT TCAAT TCAAT
1 TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT
6332218 AATCAATACA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.36
Consensus pattern (5 bp):
TCAAT
Found at i:6333522 original size:37 final size:37
Alignment explanation
Indices: 6333481--6333823 Score: 377
Period size: 37 Copynumber: 9.2 Consensus size: 37
6333471 TTGAACAACT
* * * **
6333481 TTCAGTATATTCAATAGACATTGCTCTTTTGAGCATG
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCACA
* *
6333518 TTCAGTATAATTAGTAGATATTGCT-TGTTTGAGCAACT
1 TTCAGTATAATCAGTAGATATTGCTCT-TTTGAGC-ACA
* *
6333556 TTCAATATAATCAGTAGATATTGCTCTTTTAAGCACA
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCACA
* *
6333593 TTTAGTATAATCAGTAGATATTGCT-TATTTGAGCAACT
1 TTCAGTATAATCAGTAGATATTGCTCT-TTTGAGC-ACA
* * ** *
6333631 TTCAGTATAATCAATAGACATTATTCTTTTGAGCACG
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCACA
* *
6333668 TTCAATATAATCAGTAGATATTGCTCGTTTGAGCA-A
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCACA
* *
6333704 CTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACG
1 -TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCACA
* * * *
6333742 TCCAATATAATCAGAAGATATTGCTCGTTTGAGCACA
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCACA
* * *
6333779 TTCAGTATAATAAGTAGATATTGCTCATTTGAGCATA
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCACA
6333816 TTCAGTAT
1 TTCAGTAT
6333824 TTAATCGATT
Statistics
Matches: 255, Mismatches: 43, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
36 2 0.01
37 192 0.75
38 59 0.23
39 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (37 bp):
TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCACA
Found at i:6333600 original size:75 final size:75
Alignment explanation
Indices: 6333467--6333823 Score: 466
Period size: 75 Copynumber: 4.8 Consensus size: 75
6333457 ACAATATCGT
* * * * *
6333467 TCGTTTGAACAACTTTCAGTATATTCAATAGACATTGCTCTTTTGAGCATGTTCAGTATAATTAG
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
6333532 TAGATATTGC
66 TAGATATTGC
* * * * * *
6333542 TTGTTTGAGCAACTTTCAATATAATCAGTAGATATTGCTCTTTTAAGCACATTTAGTATAATCAG
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
6333607 TAGATATTGC
66 TAGATATTGC
** * ** *
6333617 TTATTTGAGCAACTTTCAGTATAATCAATAGACATTATTCTTTTGAGCACGTTCAATATAATCAG
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
6333682 TAGATATTGC
66 TAGATATTGC
* *
6333692 TCGTTTGAGCAAC-TTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTCCAATATAATCAG
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
*
6333756 AAGATATTGC
66 TAGATATTGC
* * * * **
6333766 TCGTTTGAGC-ACATTCAGTATAATAAGTAGATATTGCTCATTTGAGCATATTCAGTAT
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTAT
6333824 TTAATCGATT
Statistics
Matches: 246, Mismatches: 35, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
73 2 0.01
74 104 0.42
75 140 0.57
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (75 bp):
TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
TAGATATTGC
Found at i:6337681 original size:62 final size:59
Alignment explanation
Indices: 6337612--6337728 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
6337602 AGTGATTATC
* * * * *
6337612 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-TA-ATAAACATTATATTAATTTAATAAGAT
6337674 TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATA
6337729 TTAAAGTCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
60 2 0.04
61 1 0.02
62 27 0.54
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATAAGAT
Found at i:6341138 original size:45 final size:45
Alignment explanation
Indices: 6341069--6341169 Score: 148
Period size: 45 Copynumber: 2.2 Consensus size: 45
6341059 GATGTGTTCG
* * *
6341069 TATAACAGGTTTGGATATCGTAAATGAGCTTACACACGTCCAACC
1 TATAACAGATCTGGATATCATAAATGAGCTTACACACGTCCAACC
* * *
6341114 TATAACAGATCTGGATATCATAAATGGGCTTGCACATGTCCAACC
1 TATAACAGATCTGGATATCATAAATGAGCTTACACACGTCCAACC
6341159 TATAACAGATC
1 TATAACAGATC
6341170 ACTCTTATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (45 bp):
TATAACAGATCTGGATATCATAAATGAGCTTACACACGTCCAACC
Found at i:6341786 original size:25 final size:25
Alignment explanation
Indices: 6341747--6341803 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
6341737 TGCAAATTTT
6341747 TTAAGAATTACAAAAAGTTAT-AAAAA
1 TTAA-AATTAC-AAAAGTTATCAAAAA
* *
6341773 TTAAAATTATAAAATTTATCAAAAA
1 TTAAAATTACAAAAGTTATCAAAAA
*
6341798 TAAAAA
1 TTAAAA
6341804 ATGTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 8 0.30
25 15 0.56
26 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (25 bp):
TTAAAATTACAAAAGTTATCAAAAA
Found at i:6341816 original size:20 final size:20
Alignment explanation
Indices: 6341787--6341854 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
6341777 AATTATAAAA
*
6341787 TTTATCAAAAATAAAAAATG
1 TTTATAAAAAATAAAAAATG
* *
6341807 TTTATAAAAAAT---TAATA
1 TTTATAAAAAATAAAAAATG
6341824 TTT-TAAAAAATAAAAAATG
1 TTTATAAAAAATAAAAAATG
6341843 TTTATAAAAAAT
1 TTTATAAAAAAT
6341855 TAATATTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
16 8 0.21
17 6 0.15
19 6 0.15
20 19 0.49
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (20 bp):
TTTATAAAAAATAAAAAATG
Found at i:6341832 original size:16 final size:16
Alignment explanation
Indices: 6341811--6341870 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 16
6341801 AAAATGTTTA
6341811 TAAAAAATTAATATTT
1 TAAAAAATTAATATTT
* *
6341827 TAAAAAATAAAAAATGTTT
1 TAAAAAAT---TAATATTT
6341846 ATAAAAAATTAATATTT
1 -TAAAAAATTAATATTT
6341863 TAAAAAAT
1 TAAAAAAT
6341871 AAAATAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
16 16 0.44
17 6 0.17
19 6 0.17
20 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
TAAAAAATTAATATTT
Found at i:6341839 original size:35 final size:36
Alignment explanation
Indices: 6341793--6341874 Score: 164
Period size: 36 Copynumber: 2.3 Consensus size: 36
6341783 AAAATTTATC
6341793 AAAAATAAAAAATGTTTATAAAAAATTAATATTTTA
1 AAAAATAAAAAATGTTTATAAAAAATTAATATTTTA
6341829 AAAAATAAAAAATGTTTATAAAAAATTAATATTTTA
1 AAAAATAAAAAATGTTTATAAAAAATTAATATTTTA
6341865 AAAAATAAAA
1 AAAAATAAAA
6341875 TAAATATAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (36 bp):
AAAAATAAAAAATGTTTATAAAAAATTAATATTTTA
Found at i:6341876 original size:17 final size:17
Alignment explanation
Indices: 6341801--6341876 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 17
6341791 TCAAAAATAA
*
6341801 AAAATGTTTATAAAAAAT
1 AAAATATTT-TAAAAAAT
*
6341819 -TAATATTTTAAAAAAT
1 AAAATATTTTAAAAAAT
*
6341835 AAAAAATGTTTATAAAAA-
1 AAAATAT-TTTA-AAAAAT
*
6341853 ATTAATATTTTAAAAAAT
1 A-AAATATTTTAAAAAAT
6341871 AAAATA
1 AAAATA
6341877 AATATAAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
16 8 0.17
17 19 0.41
18 10 0.22
19 9 0.20
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
AAAATATTTTAAAAAAT
Found at i:6342647 original size:21 final size:21
Alignment explanation
Indices: 6342621--6342660 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
6342611 AATAAATACC
6342621 AAAAATTTATTTTAAAAATTA
1 AAAAATTTATTTTAAAAATTA
6342642 AAAAATTTATTTTAAAAAT
1 AAAAATTTATTTTAAAAAT
6342661 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAATTTATTTTAAAAATTA
Found at i:6343056 original size:3 final size:3
Alignment explanation
Indices: 6343048--6343074 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6343038 CATTTTAACC
6343048 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
6343075 TAAAGTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6349819 original size:39 final size:43
Alignment explanation
Indices: 6349720--6349826 Score: 134
Period size: 39 Copynumber: 2.5 Consensus size: 43
6349710 GGTTCGCTGT
6349720 AATGGAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTGAATGC
1 AATGGAATAGAGGCGTAATAGCAATTCAATTGTTTGGTT--ATGC
* *
6349765 AATGGAATAGAGGCGTAATAG-TATTC-TTGTGTTTGG-T-TG-
1 AATGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTATGC
6349804 AATGGAATAGAGGCGTAATAGCA
1 AATGGAATAGAGGCGTAATAGCA
6349827 TAAGAAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
39 21 0.37
40 2 0.04
43 2 0.04
44 11 0.19
45 21 0.37
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.31
Consensus pattern (43 bp):
AATGGAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTATGC
Found at i:6349944 original size:21 final size:20
Alignment explanation
Indices: 6349920--6350006 Score: 53
Period size: 19 Copynumber: 4.5 Consensus size: 20
6349910 AATAAGATTA
6349920 TTAATATAAATAATAAATAAT
1 TTAATATAAATAA-AAATAAT
* *
6349941 TTAATAATAATTTAAAATAA-
1 TTAAT-ATAAATAAAAATAAT
* *
6349961 TT-AT-T-ATTAAATATAAT
1 TTAATATAAATAAAAATAAT
*
6349978 TTAATA-AAA-AATATATAAT
1 TTAATATAAATAA-AAATAAT
6349997 TTAATA-AAAT
1 TTAATATAAAT
6350007 TCTTAATATA
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
16 9 0.17
17 3 0.06
18 4 0.07
19 19 0.35
20 2 0.04
21 11 0.20
22 6 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATATAAATAAAAATAAT
Found at i:6349949 original size:11 final size:11
Alignment explanation
Indices: 6349930--6349962 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
6349920 TTAATATAAA
6349930 TAATAAATAATT
1 TAAT-AATAATT
6349942 TAATAATAATT
1 TAATAATAATT
6349953 TAA-AATAATT
1 TAATAATAATT
6349963 ATTATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 10 0.48
12 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATAATAATT
Found at i:6349983 original size:24 final size:21
Alignment explanation
Indices: 6349907--6350019 Score: 79
Period size: 21 Copynumber: 5.1 Consensus size: 21
6349897 GTTATTAAAT
6349907 TTTAATAAGATTATTAATATAA
1 TTTAATAA-ATTATTAATATAA
* *
6349929 -ATAATAAATAATTTAATAATAA
1 TTTAATAAATTA-TTAAT-ATAA
6349951 TTTAAAATAATTATTATTAAATATAA
1 TTT--AATAA--ATTATT-AATATAA
* *
6349977 TTTAATAAA-AAAT-ATATAA
1 TTTAATAAATTATTAATATAA
*
6349996 TTTAATAAAATTCTTAATATAA
1 TTTAAT-AAATTATTAATATAA
6350018 TT
1 TT
6350020 ATTCTTATAT
Statistics
Matches: 71, Mismatches: 9, Indels: 22
0.70 0.09 0.22
Matches are distributed among these distances:
19 12 0.17
20 6 0.08
21 14 0.20
22 13 0.18
23 1 0.01
24 5 0.07
25 5 0.07
26 9 0.13
27 6 0.08
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (21 bp):
TTTAATAAATTATTAATATAA
Found at i:6349986 original size:29 final size:28
Alignment explanation
Indices: 6349953--6350043 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 28
6349943 AATAATAATT
6349953 TAAAATAATTATTATTAAATATAATTTAA
1 TAAAATAATTATTATTAAATATAATTT-A
* * *
6349982 TAAAA-AATATATAATTTAATAAAATTCT-
1 TAAAATAAT-TATTATTAAATATAATT-TA
* * *
6350010 TAATATAATTATTCTTATAT-TAATTTA
1 TAAAATAATTATTATTAAATATAATTTA
6350037 CTAAAAT
1 -TAAAAT
6350044 CATAATATAT
Statistics
Matches: 47, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
26 1 0.02
27 4 0.09
28 19 0.40
29 22 0.47
30 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
TAAAATAATTATTATTAAATATAATTTA
Found at i:6349996 original size:56 final size:57
Alignment explanation
Indices: 6349920--6350048 Score: 156
Period size: 56 Copynumber: 2.3 Consensus size: 57
6349910 AATAAGATTA
6349920 TTAATATAAATAATAAATAATTTAATAATAA-T-TTAAAATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAATAATTTAATAA-AATTCTTAAAATAATTATTATTAAAT-TAAT
* * * *
6349978 TTAATAAAA-AATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATTAAT
1 TTAATAAAATAATAAATAATTTAATAAAATTCTTAAAATAATTATTATTAAATTAAT
* *
6350034 TTACTAAAATCATAA
1 TTAATAAAATAATAA
6350049 TATATAATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
55 2 0.03
56 29 0.48
57 24 0.39
58 6 0.10
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (57 bp):
TTAATAAAATAATAAATAATTTAATAAAATTCTTAAAATAATTATTATTAAATTAAT
Found at i:6350470 original size:77 final size:77
Alignment explanation
Indices: 6350343--6350504 Score: 315
Period size: 77 Copynumber: 2.1 Consensus size: 77
6350333 ATTTTTTGTC
6350343 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATATTTGAACTTGAAATATATAAAATT
1 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATATTTGAACTTGAAATATATAAAATT
6350408 TTATTGACATAA
66 TTATTGACATAA
*
6350420 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
1 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATATTTGAACTTGAAATATATAAAATT
6350485 TTATTGACATAA
66 TTATTGACATAA
6350497 CACTTTAA
1 CACTTTAA
6350505 GATTGTCTCA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 84 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.41
Consensus pattern (77 bp):
CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATATTTGAACTTGAAATATATAAAATT
TTATTGACATAA
Found at i:6365531 original size:21 final size:21
Alignment explanation
Indices: 6365506--6365552 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
6365496 AAAAAATAAA
6365506 ATATTAAAA-ATATATTATTTT
1 ATATTAAAATATATA-TATTTT
* *
6365527 ATATTAATATTTATATATTTT
1 ATATTAAAATATATATATTTT
6365548 ATATT
1 ATATT
6365553 TAAACTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTAAAATATATATATTTT
Found at i:6365850 original size:20 final size:21
Alignment explanation
Indices: 6365808--6365851 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
6365798 GTATGTTTTA
* *
6365808 ATATTTACATTGTAATACTAT
1 ATATTTAAATTGTAATACAAT
*
6365829 ATATTTAAATT-TTATACAAT
1 ATATTTAAATTGTAATACAAT
6365849 ATA
1 ATA
6365852 AAATACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATTTAAATTGTAATACAAT
Found at i:6368629 original size:16 final size:16
Alignment explanation
Indices: 6368608--6368640 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6368598 AGAGGTAAAG
6368608 TTGTTACACTACTTCA
1 TTGTTACACTACTTCA
6368624 TTGTTACACTACTTCA
1 TTGTTACACTACTTCA
6368640 T
1 T
6368641 AAAAACTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (16 bp):
TTGTTACACTACTTCA
Found at i:6386034 original size:11 final size:11
Alignment explanation
Indices: 6386011--6386048 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
6386001 GTAAGATGGC
6386011 TTTTCTT-TCT
1 TTTTCTTCTCT
6386021 TTTTCTTCTCT
1 TTTTCTTCTCT
*
6386032 TTTTTTTCT-T
1 TTTTCTTCTCT
6386042 TTTTCTT
1 TTTTCTT
6386049 TTTTCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 14 0.56
11 11 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTCTTCTCT
Found at i:6386044 original size:21 final size:20
Alignment explanation
Indices: 6386010--6386061 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
6386000 GGTAAGATGG
*
6386010 CTTTTCTTTC-TTTTTCTTCT
1 CTTTTTTTTCTTTTTTCTT-T
6386030 CTTTTTTTTCTTTTTTCTTT
1 CTTTTTTTTCTTTTTTCTTT
*
6386050 TTTCTTTTTTCT
1 CTT-TTTTTTCT
6386062 GTAGTTGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (20 bp):
CTTTTTTTTCTTTTTTCTTT
Found at i:6386045 original size:7 final size:7
Alignment explanation
Indices: 6386016--6386061 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
6386006 ATGGCTTTTC
6386016 TTTC-TT
1 TTTCTTT
6386022 TTTCTTCT
1 TTTCTT-T
*
6386030 CTT-TTT
1 TTTCTTT
6386036 TTTCTTT
1 TTTCTTT
6386043 TTTCTTT
1 TTTCTTT
6386050 TTTCTTT
1 TTTCTTT
6386057 TTTCT
1 TTTCT
6386062 GTAGTTGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 7 0.20
7 25 0.71
8 3 0.09
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTCTTT
Found at i:6388393 original size:12 final size:12
Alignment explanation
Indices: 6388376--6388405 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6388366 ACAAAATTCG
6388376 AATTTAATTTCC
1 AATTTAATTTCC
*
6388388 AATTTAATTTCT
1 AATTTAATTTCC
6388400 AATTTA
1 AATTTA
6388406 TTTATGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:6393482 original size:12 final size:12
Alignment explanation
Indices: 6393465--6393497 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
6393455 ACAAAATCCG
6393465 AATTTAATTTCC
1 AATTTAATTTCC
*
6393477 AATTTAATTTCT
1 AATTTAATTTCC
6393489 AATTTAATT
1 AATTTAATT
6393498 AATTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:6393921 original size:6 final size:6
Alignment explanation
Indices: 6393910--6393934 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6393900 GCTTTTTTAT
6393910 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
6393935 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:6393945 original size:6 final size:6
Alignment explanation
Indices: 6393936--6393960 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6393926 TATTAATATA
6393936 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
6393961 TTATTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:6394254 original size:30 final size:29
Alignment explanation
Indices: 6394191--6394254 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
6394181 TAATCTTGTT
* *
6394191 TAGTTGGATGACCAATTTAAAAAAATTCA
1 TAGTTGGATGACAAATTTAAAAAAATCCA
* * *
6394220 TAGTTGGGTGACAAATTTGAGACAAATCCA
1 TAGTTGGATGACAAATTT-AAAAAAATCCA
6394250 TAGTT
1 TAGTT
6394255 AGGTAATCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (29 bp):
TAGTTGGATGACAAATTTAAAAAAATCCA
Found at i:6394905 original size:13 final size:13
Alignment explanation
Indices: 6394887--6394912 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6394877 CATGCAAGAC
6394887 AACGTGGTTGAGA
1 AACGTGGTTGAGA
6394900 AACGTGGTTGAGA
1 AACGTGGTTGAGA
6394913 GCAAGGCAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.38, T:0.23
Consensus pattern (13 bp):
AACGTGGTTGAGA
Found at i:6395726 original size:18 final size:18
Alignment explanation
Indices: 6395699--6395733 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6395689 AGCACCAAAG
6395699 CTTTCATCCTCCTCCTCA
1 CTTTCATCCTCCTCCTCA
* *
6395717 CTTTCTTCCTCTTCCTC
1 CTTTCATCCTCCTCCTC
6395734 TTCTTCATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.49, G:0.00, T:0.46
Consensus pattern (18 bp):
CTTTCATCCTCCTCCTCA
Found at i:6400624 original size:14 final size:16
Alignment explanation
Indices: 6400605--6400636 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
6400595 CCAATATTTT
6400605 ATTTTT-TAAAAT-TA
1 ATTTTTATAAAATATA
6400619 ATTTTTATAAAATATA
1 ATTTTTATAAAATATA
6400635 AT
1 AT
6400637 GCACTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTTATAAAATATA
Found at i:6401179 original size:21 final size:21
Alignment explanation
Indices: 6401114--6401184 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
6401104 GTTTTTAGGG
6401114 TTAAGGTTTTGTTAAAATAAT
1 TTAAGGTTTTGTTAAAATAAT
** ** *
6401135 TTGGGGTTAGGTT--TATAAGGT
1 TTAAGGTTTTGTTAAAATAA--T
6401156 TTAAGGTTTTGTTAAAATAAT
1 TTAAGGTTTTGTTAAAATAAT
6401177 TTAAGGTT
1 TTAAGGTT
6401185 CTTGGTTTTA
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
19 4 0.11
21 28 0.78
23 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (21 bp):
TTAAGGTTTTGTTAAAATAAT
Found at i:6401334 original size:34 final size:33
Alignment explanation
Indices: 6401229--6401334 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
6401219 TTTAGTGTTC
* *
6401229 TTTTTT-AAAAATTAATTAAATTAGGGTTTAGG
1 TTTTTTAAAAAATTAATTAAATTTGGGTTTAGT
** *
6401261 AGTTTTAAATTAATTAATTAAATTTGGGTTTAGT
1 TTTTTTAAA-AAATTAATTAAATTTGGGTTTAGT
*
6401295 GTTTTTAAGAAAATTAATTAAATTTGGGTTTAGT
1 TTTTTTAA-AAAATTAATTAAATTTGGGTTTAGT
6401329 TTTTTT
1 TTTTTT
6401335 TAAAGGCATA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 4 0.06
33 2 0.03
34 55 0.89
35 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (33 bp):
TTTTTTAAAAAATTAATTAAATTTGGGTTTAGT
Found at i:6403442 original size:125 final size:127
Alignment explanation
Indices: 6403220--6403739 Score: 737
Period size: 126 Copynumber: 4.1 Consensus size: 127
6403210 GATTTTAGTT
* * * * * * *
6403220 TTTTTCTACGGTAGTTCCTGAAAAAATAATTTTGAGAAGATGATTCTCAACAAATAGTCTTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
* *
6403285 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACT-AAAAAAACTCCCACGTGGA-AGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACA-CTC
* * * *
6403345 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTAAGAAGACGGTTCTAAATAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
* * *
6403410 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCTACGTGGACACTT
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACACTC
* *
6403471 TTTTTCTACAGTAGTTCGTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
* * * * *
6403536 ACCCTTCAAGTAGGATGCACTGTCAACAAAATTGA-AGAAAAAAGCTCCTACGTGGACACTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACACTC
* *
6403597 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGTTTCTGAATAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
*
6403662 ACACTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGACACTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACACTC
* *
6403723 TTTTTTTACAGCAGTTC
1 TTTTTCTACAGTAGTTC
6403740 ATGTTTGGCC
Statistics
Matches: 354, Mismatches: 37, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
125 89 0.25
126 264 0.75
127 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (127 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACACTC
Found at i:6403931 original size:28 final size:28
Alignment explanation
Indices: 6403900--6403961 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
6403890 CGGCGTTATT
* *
6403900 TTTTTATCGGAGAATACAACGCGAATAA
1 TTTTTATCAGAGAACACAACGCGAATAA
*
6403928 TTTTTATCAGAGAACACAACGCGAATTA
1 TTTTTATCAGAGAACACAACGCGAATAA
6403956 TTTTTA
1 TTTTTA
6403962 ACTAGACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (28 bp):
TTTTTATCAGAGAACACAACGCGAATAA
Found at i:6406344 original size:20 final size:20
Alignment explanation
Indices: 6406319--6406356 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
6406309 ACAACCTATG
6406319 GTGTACACCTGATAAATATC
1 GTGTACACCTGATAAATATC
6406339 GTGTACACCTGATAAATA
1 GTGTACACCTGATAAATA
6406357 AGACTTGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (20 bp):
GTGTACACCTGATAAATATC
Found at i:6407273 original size:18 final size:18
Alignment explanation
Indices: 6407242--6407285 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
6407232 GACTGGAAAA
* *
6407242 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
* *
6407260 ATGATACATGTAAGGGCT
1 AGGATACATATAAGGGCT
6407278 AGGATACA
1 AGGATACA
6407286 CACCTGGCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.27, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:6409064 original size:30 final size:30
Alignment explanation
Indices: 6409030--6409098 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
6409020 ATTAATTAAA
6409030 GAGAGTTTTGAGAAATTTAAGGAGAAATTT
1 GAGAGTTTTGAGAAATTTAAGGAGAAATTT
* *
6409060 GAGAGCTTTGAGAAATTTAGGGAGAAATTT
1 GAGAGTTTTGAGAAATTTAAGGAGAAATTT
*
6409090 GAAAGTTTT
1 GAGAGTTTT
6409099 TTTGCTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.38, C:0.01, G:0.28, T:0.33
Consensus pattern (30 bp):
GAGAGTTTTGAGAAATTTAAGGAGAAATTT
Found at i:6410172 original size:20 final size:20
Alignment explanation
Indices: 6410149--6410210 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
6410139 TATTTTTCTA
6410149 GATTAGTTCAGATTTAAATT
1 GATTAGTTCAGATTTAAATT
** *** *
6410169 GATT--TTCTTATTTTTCTA
1 GATTAGTTCAGATTTAAATT
6410187 GATTAGTTCAGATTTAAATT
1 GATTAGTTCAGATTTAAATT
6410207 GATT
1 GATT
6410211 TTTATACATT
Statistics
Matches: 28, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
18 12 0.43
20 16 0.57
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (20 bp):
GATTAGTTCAGATTTAAATT
Found at i:6410188 original size:38 final size:38
Alignment explanation
Indices: 6410137--6410212 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
6410127 ATTATATGTG
6410137 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
1 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
6410175 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
1 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
6410213 TATACATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (38 bp):
CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
Found at i:6410520 original size:16 final size:16
Alignment explanation
Indices: 6410491--6410523 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6410481 AAAGATTTTT
6410491 AATTATATTCTAATTA
1 AATTATATTCTAATTA
6410507 AATTGATATT-TAATTA
1 AATT-ATATTCTAATTA
6410523 A
1 A
6410524 CTCGTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
AATTATATTCTAATTA
Found at i:6423261 original size:3 final size:3
Alignment explanation
Indices: 6423253--6423289 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
6423243 AATGATTTTG
6423253 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6423290 GAAATAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:6424562 original size:49 final size:49
Alignment explanation
Indices: 6424493--6424638 Score: 220
Period size: 49 Copynumber: 3.0 Consensus size: 49
6424483 TTCGTTTTCT
* * * *
6424493 CGATACCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
* *
6424542 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACTTAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
*
6424591 CGATGCCATATCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACA-AATCACAT
6424639 GTTCACATGT
Statistics
Matches: 87, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
49 81 0.93
50 6 0.07
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (49 bp):
CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
Found at i:6425630 original size:37 final size:37
Alignment explanation
Indices: 6425565--6425673 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
6425555 TACGTATGAT
* *
6425565 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
6425600 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
6425637 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
6425674 TAAAGCTATC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 10 0.14
36 3 0.04
37 56 0.81
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:6425690 original size:46 final size:46
Alignment explanation
Indices: 6425637--6425896 Score: 252
Period size: 52 Copynumber: 5.6 Consensus size: 46
6425627 TAAGTGTAGC
* *
6425637 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
6425683 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAA-CTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCC-AAAGCTAT
* *
6425735 CACTTATCACTTTGTCTCTTGATCAGATAA--GT----ATAGC---
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* * *
6425772 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
*
6425818 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
*
6425870 CACCTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
6425897 AGTACTCAAA
Statistics
Matches: 181, Mismatches: 10, Indels: 46
0.76 0.04 0.19
Matches are distributed among these distances:
37 30 0.17
39 3 0.02
40 1 0.01
43 3 0.02
44 2 0.01
46 54 0.30
48 1 0.01
49 2 0.01
50 1 0.01
52 81 0.45
53 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
Found at i:6425777 original size:37 final size:37
Alignment explanation
Indices: 6425735--6425809 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
6425725 CCGAAACTAT
6425735 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
6425772 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
6425809 C
1 C
6425810 GAAGCTATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
Found at i:6425839 original size:135 final size:135
Alignment explanation
Indices: 6425600--6425896 Score: 513
Period size: 135 Copynumber: 2.2 Consensus size: 135
6425590 TAAGTGTAGC
* *
6425600 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCTTGATCAGAT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCACTTATCACTTTGTCTCTTGATCAGAT
* * *
6425665 AAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAA
66 AAGTATAGCCAAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAA
6425730 ACTAT
131 ACTAT
6425735 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCACTTATCACTTTGTCTCTTGATCAGAT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCACTTATCACTTTGTCTCTTGATCAGAT
*
6425800 AAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAA
66 AAGTATAGCCAAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAA
*
6425865 GCTAT
131 ACTAT
* *
6425870 CACCTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCTCTTGATCAGA
6425897 AGTACTCAAA
Statistics
Matches: 153, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
135 153 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (135 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCACTTATCACTTTGTCTCTTGATCAGAT
AAGTATAGCCAAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAA
ACTAT
Found at i:6429153 original size:17 final size:17
Alignment explanation
Indices: 6429120--6429153 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6429110 TTGTGTTTTG
*
6429120 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
6429137 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
6429154 GTTAGGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:6430154 original size:41 final size:41
Alignment explanation
Indices: 6430092--6430171 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
6430082 TGATCGAATG
*
6430092 TAATACAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAA
1 TAATACAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
*
6430133 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGA
1 TAATACAGACTTTACGTCTAGCAGGCTTAATGCCGGTGA
6430172 TACATTTCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (41 bp):
TAATACAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
Found at i:6430193 original size:41 final size:41
Alignment explanation
Indices: 6430097--6430211 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 41
6430087 GAATGTAATA
* * *
6430097 CAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAATT
1 CAGACTATACGTCTAGCAGGCTTAATGCCGGTGAAACAATT
* * *
6430138 CAGACTTTACGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATACGTCTAGCAGGCTTAATGCCGGTGAAACAATT
* * * * *
6430179 CGGGCTATAGGTCTAGCAGGCTAAAAGCCGGTG
1 CAGACTATACGTCTAGCAGGCTTAATGCCGGTG
6430212 TACTGAATCA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (41 bp):
CAGACTATACGTCTAGCAGGCTTAATGCCGGTGAAACAATT
Found at i:6430577 original size:18 final size:18
Alignment explanation
Indices: 6430554--6430622 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
6430544 TATGATGAAT
6430554 ATGTATATATATATTCGA
1 ATGTATATATATATTCGA
6430572 ATGTATGTATTAGCTATGTATTCGAA
1 ATGTA--TA-TA--TA--TATTCG-A
6430598 TATGTATATATATATTCGA
1 -ATGTATATATATATTCGA
6430617 ATGTAT
1 ATGTAT
6430623 GTATTAGCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 18
0.70 0.00 0.30
Matches are distributed among these distances:
18 11 0.26
19 1 0.02
20 8 0.19
21 2 0.05
22 2 0.05
23 2 0.05
24 2 0.05
25 8 0.19
26 1 0.02
27 5 0.12
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (18 bp):
ATGTATATATATATTCGA
Found at i:6430596 original size:25 final size:25
Alignment explanation
Indices: 6430565--6430639 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
6430555 TGTATATATA
6430565 TATTCGAATGTATGTATTAGCTATG
1 TATTCGAATGTATGTATTAGCTATG
*
6430590 TATTCGAA--TATGTA-TA--TATA
1 TATTCGAATGTATGTATTAGCTATG
6430610 TATTCGAATGTATGTATTAGCTATG
1 TATTCGAATGTATGTATTAGCTATG
6430635 TATTC
1 TATTC
6430640 AGGTATAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
20 11 0.26
22 8 0.19
23 8 0.19
25 16 0.37
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (25 bp):
TATTCGAATGTATGTATTAGCTATG
Found at i:6430599 original size:45 final size:45
Alignment explanation
Indices: 6430550--6430639 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
6430540 TGTATATGAT
6430550 GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
1 GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
6430595 GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
1 GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
6430640 AGGTATAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (45 bp):
GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
Found at i:6430615 original size:20 final size:20
Alignment explanation
Indices: 6430550--6430618 Score: 84
Period size: 20 Copynumber: 3.2 Consensus size: 20
6430540 TGTATATGAT
6430550 GAATATGTATATATATATTC
1 GAATATGTATATATATATTC
*
6430570 GAATGTATGTATTAGCTATGTATTC
1 GAA--TATGTA-TA--TATATATTC
6430595 GAATATGTATATATATATTC
1 GAATATGTATATATATATTC
6430615 GAAT
1 GAAT
6430619 GTATGTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
20 15 0.36
22 8 0.19
23 8 0.19
25 11 0.26
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.43
Consensus pattern (20 bp):
GAATATGTATATATATATTC
Found at i:6434991 original size:37 final size:37
Alignment explanation
Indices: 6434941--6435014 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
6434931 ATGAAAGAAA
6434941 AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
1 AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
*
6434978 AGAATCCATCACATCAGGCTTGAGACAAGATGTTGGT
1 AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
6435015 TAATAAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (37 bp):
AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
Found at i:6436355 original size:14 final size:14
Alignment explanation
Indices: 6436336--6436363 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6436326 ACCCTAGTAG
6436336 TAATTAACAAGAAA
1 TAATTAACAAGAAA
6436350 TAATTAACAAGAAA
1 TAATTAACAAGAAA
6436364 GTCGCTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
TAATTAACAAGAAA
Found at i:6439438 original size:28 final size:27
Alignment explanation
Indices: 6439407--6439462 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
6439397 AACAAATCAT
*
6439407 TAAAAGTA-TTTAAAATGTATAAAAATTA
1 TAAAAATATTTTAAAAT-T-TAAAAATTA
6439435 TAAAAATATTTTTAAAATTTAAAAATTA
1 TAAAAATA-TTTTAAAATTTAAAAATTA
6439463 ATTAAATGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 16 0.64
29 1 0.04
30 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (27 bp):
TAAAAATATTTTAAAATTTAAAAATTA
Found at i:6442014 original size:17 final size:17
Alignment explanation
Indices: 6441989--6442036 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
6441979 TGATGTGTTC
*
6441989 TTCAGTAAAAGAAAGAA
1 TTCAATAAAAGAAAGAA
6442006 TTCAATAAAAGAAAGAA
1 TTCAATAAAAGAAAGAA
*
6442023 TTCGATAAAAGAAA
1 TTCAATAAAAGAAA
6442037 AGTAGGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.60, C:0.06, G:0.15, T:0.19
Consensus pattern (17 bp):
TTCAATAAAAGAAAGAA
Found at i:6443762 original size:13 final size:13
Alignment explanation
Indices: 6443744--6443768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6443734 TGGGTGTATG
6443744 ATGTCCAATTATA
1 ATGTCCAATTATA
6443757 ATGTCCAATTAT
1 ATGTCCAATTAT
6443769 GACGAAACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
ATGTCCAATTATA
Found at i:6448528 original size:38 final size:38
Alignment explanation
Indices: 6448475--6448551 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
6448465 AAATACTAAG
6448475 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
1 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
** * **
6448513 TGATAAATTTGTTTAGTATGCTTGTTTTTAACTCTTAT
1 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
6448551 T
1 T
6448552 TTTGTGATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (38 bp):
TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
Found at i:6450491 original size:17 final size:18
Alignment explanation
Indices: 6450469--6450505 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
6450459 CAAAACTAAG
6450469 GTTCATTTGGTGTT-CAT
1 GTTCATTTGGTGTTCCAT
6450486 GTTCATTTGGTGTTCCAT
1 GTTCATTTGGTGTTCCAT
6450504 GT
1 GT
6450506 CAGGATGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.11, C:0.14, G:0.24, T:0.51
Consensus pattern (18 bp):
GTTCATTTGGTGTTCCAT
Found at i:6461438 original size:77 final size:76
Alignment explanation
Indices: 6461311--6461532 Score: 245
Period size: 77 Copynumber: 2.9 Consensus size: 76
6461301 CAATTCTCCA
* *
6461311 CATGGTATCAAATGTTTTTGGTTCTTTCCTTATAAGTGTTTTTTTTCTGGTCGAACTCTTGCTTC
1 CATGGTATCAGATGTTTTTGGTTCTTT-CTTATAAGTGTTTTTTTTCTGGTCGAAATCTTGCTTC
*
6461376 TCATGTTTAGTC
65 TCATGTTCAGTC
* *
6461388 CATGGTATCAGATGTTTTTGGTT-TTT-TTCCTAAGTGTTTTCTTTTCCTGGTTGAAATCTTGCT
1 CATGGTATCAGATGTTTTTGGTTCTTTCTT-ATAAGTGTTTT-TTTT-CTGGTCGAAATCTTGCT
* *
6461451 TCTCTTGTTCATTC
63 TCTCATGTTCAGTC
* * * *
6461465 CATGGTATCAGAT-TTTTCTGGTTCCTTAC-TATGAAGAGTTTTTTTTCTTGGTCGAATTATTGC
1 CATGGTATCAGATGTTTT-TGGTT-CTTTCTTAT-AAGTGTTTTTTTTC-TGGTCGAAATCTTGC
6461528 TTCTC
62 TTCTC
6461533 CTATTCTATT
Statistics
Matches: 123, Mismatches: 13, Indels: 17
0.80 0.08 0.11
Matches are distributed among these distances:
74 2 0.02
75 10 0.08
76 11 0.09
77 67 0.54
78 22 0.18
79 11 0.09
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.51
Consensus pattern (76 bp):
CATGGTATCAGATGTTTTTGGTTCTTTCTTATAAGTGTTTTTTTTCTGGTCGAAATCTTGCTTCT
CATGTTCAGTC
Found at i:6475001 original size:30 final size:30
Alignment explanation
Indices: 6474967--6475026 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
6474957 GCTCGATAAG
6474967 AATCTTAAATATTAATATTGACACTAAGTT
1 AATCTTAAATATTAATATTGACACTAAGTT
* *
6474997 AATCTTAAATATTAATATTGATATTAAGTT
1 AATCTTAAATATTAATATTGACACTAAGTT
6475027 TAAATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (30 bp):
AATCTTAAATATTAATATTGACACTAAGTT
Found at i:6475106 original size:31 final size:27
Alignment explanation
Indices: 6475068--6475129 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 27
6475058 AAATAATCAT
6475068 TCAACTATGATAGTGTTTTTATTTTAGTCA
1 TCAACTAT-A-AGTGTTTTTA-TTTAGTCA
* *
6475098 CTCAACTATAATTTTTTTTATTTAGTCA
1 -TCAACTATAAGTGTTTTTATTTAGTCA
6475126 TCAA
1 TCAA
6475130 AGTTTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.14
28 8 0.28
29 8 0.28
30 1 0.03
31 8 0.28
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (27 bp):
TCAACTATAAGTGTTTTTATTTAGTCA
Found at i:6481033 original size:26 final size:26
Alignment explanation
Indices: 6481002--6481054 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
6480992 CTATATAGTG
6481002 CATCATTAAATTGTTAGAGCTTCCTC
1 CATCATTAAATTGTTAGAGCTTCCTC
6481028 CATCATTAAATTGTTAGAGCTTCCTC
1 CATCATTAAATTGTTAGAGCTTCCTC
6481054 C
1 C
6481055 TTACCATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (26 bp):
CATCATTAAATTGTTAGAGCTTCCTC
Found at i:6481825 original size:56 final size:56
Alignment explanation
Indices: 6481755--6481875 Score: 217
Period size: 56 Copynumber: 2.2 Consensus size: 56
6481745 AAGGGACGAC
*
6481755 AAAAA-GAAAAAGAATAAGGGTTGTTAACAAAAATATGGATAGATGAAAACAAAAG
1 AAAAAGGAAAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAG
*
6481810 AAAAGGGAAAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAG
1 AAAAAGGAAAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAG
6481866 AAAAAGGAAA
1 AAAAAGGAAA
6481876 GAAGCATAGA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
55 4 0.06
56 58 0.94
ACGTcount: A:0.60, C:0.04, G:0.21, T:0.14
Consensus pattern (56 bp):
AAAAAGGAAAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAG
Found at i:6484071 original size:16 final size:16
Alignment explanation
Indices: 6484032--6484096 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 16
6484022 CGTTCGGTTC
*
6484032 ATTGTAATGGAATAGG
1 ATTGTAATGGAATAGA
* * *
6484048 ACTATAATGTAATAGA
1 ATTGTAATGGAATAGA
*
6484064 ATTGTAATGGAATACA
1 ATTGTAATGGAATAGA
** *
6484080 GCTGTAATAGAATAGA
1 ATTGTAATGGAATAGA
6484096 A
1 A
6484097 CTTTAATAAG
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.29
Consensus pattern (16 bp):
ATTGTAATGGAATAGA
Found at i:6484300 original size:26 final size:24
Alignment explanation
Indices: 6484257--6484320 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 24
6484247 TAATTATTGT
* *
6484257 TATTAAAT--TTTAATAAAATTAT
1 TATTAAATAATTTAATAAAAATAA
6484279 TATTAAATATAATTTAATAAAAATAA
1 TATT-AA-ATAATTTAATAAAAATAA
6484305 TATTAAATAATTTAAT
1 TATTAAATAATTTAAT
6484321 CATGTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.11
23 2 0.06
24 12 0.33
25 2 0.06
26 16 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TATTAAATAATTTAATAAAAATAA
Found at i:6484421 original size:21 final size:21
Alignment explanation
Indices: 6484370--6484419 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
6484360 TATATTGCTC
6484370 TAATAAA-ATAGTAAAATATT
1 TAATAAATATAGTAAAATATT
6484390 TAATAAATATAGT-AAAT-TT
1 TAATAAATATAGTAAAATATT
*
6484409 TAATTAATATA
1 TAATAAATATA
6484420 TAAGCTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 12 0.43
20 11 0.39
21 5 0.18
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
TAATAAATATAGTAAAATATT
Found at i:6484967 original size:5 final size:5
Alignment explanation
Indices: 6484957--6484981 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6484947 CGGATTTATT
6484957 TGTGA TGTGA TGTGA TGTGA TGTGA
1 TGTGA TGTGA TGTGA TGTGA TGTGA
6484982 GTAGCATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
TGTGA
Found at i:6485210 original size:16 final size:16
Alignment explanation
Indices: 6485189--6485237 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
6485179 TTCGCTGTAT
*
6485189 TGGAATAGAGGCGTAG
1 TGGAATAGAGGCGTAA
*
6485205 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
* *
6485221 TGAAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
6485237 T
1 T
6485238 AGCAAATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.37, C:0.02, G:0.37, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:6485484 original size:15 final size:15
Alignment explanation
Indices: 6485460--6485502 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
6485450 TTTAAACATA
*
6485460 ATTATTATTAAATAT
1 ATTATAATTAAATAT
6485475 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
6485489 A-TATAATTATAATA
1 ATTATAATTA-AATA
6485503 AAATTCTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 8 0.32
14 5 0.20
15 12 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:6485488 original size:16 final size:16
Alignment explanation
Indices: 6485451--6485492 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
6485441 TTAATCATAT
*
6485451 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
6485467 TT-AAATATATTATAA
1 TTAAAATATATTATAA
6485482 TTAAAATATAT
1 TTAAAATATAT
6485493 AATTATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:6485492 original size:18 final size:18
Alignment explanation
Indices: 6485471--6485506 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
6485461 TTATTATTAA
6485471 ATAT-ATTATAATTAAAAT
1 ATATAATTATAA-TAAAAT
6485489 ATATAATTATAATAAAAT
1 ATATAATTATAATAAAAT
6485507 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATAATTATAATAAAAT
Found at i:6485495 original size:13 final size:14
Alignment explanation
Indices: 6485460--6485502 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
6485450 TTTAAACATA
*
6485460 ATTATTATTAAATAT
1 ATTATAATTAAA-AT
6485475 ATTATAATTAAAAT
1 ATTATAATTAAAAT
*
6485489 A-TATAATTATAAT
1 ATTATAATTAAAAT
6485502 A
1 A
6485503 AAATTCTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTATAATTAAAAT
Found at i:6485613 original size:59 final size:61
Alignment explanation
Indices: 6485454--6485871 Score: 250
Period size: 59 Copynumber: 7.0 Consensus size: 61
6485444 ATCATATTTA
* * *
6485454 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTA-TAATAAAATTCTTAA-T
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGA-TACTAATAAAATTATAAATT
* * * * * *
6485514 AATCA-ATATTCTTATATGAATTTACTGA-AATCATAATATATGATACT-ATAAAA-TATAAATT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAAAATATATGATACTAATAAAATTATAAATT
* * * *
6485575 AACATAATTATTATTAAATATATTATAATTAAAATATATAAT-TTAATAAAATTCTTAA-T
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGATACTAATAAAATTATAAATT
* * * * * * *
6485634 AATCA-ATATTCTTATATGAATTTACTAAAATTATAATATATGATACT-ATAAAA-TATAATTT
1 AA-CATA-ATTATTAT-TAAATATATTATAATTAAAATATATGATACTAATAAAATTATAAATT
* *
6485695 GAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGAT-TTAATAAAATTCATAATAATT
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATGATACTAATAAAATT-AT-A-AATT
* * * * * * * *
6485758 -A-AT-ATTCTTATATGAATTTACTCA-AATCATAATATATGATACT-ATAAAA-GATAATTT
1 AACATAATTATTAT-TAAATATA-TTATAATTAAAATATATGATACTAATAAAATTATAAATT
* * *
6485815 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGAT-TTAATAAAATT-TAAA
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATGATACTAATAAAATTATAAA
6485872 ATAATTATAA
Statistics
Matches: 267, Mismatches: 60, Indels: 63
0.68 0.15 0.16
Matches are distributed among these distances:
57 3 0.01
58 7 0.03
59 91 0.34
60 54 0.20
61 82 0.31
62 25 0.09
63 5 0.02
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (61 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATGATACTAATAAAATTATAAATT
Found at i:6485620 original size:14 final size:15
Alignment explanation
Indices: 6485571--6485622 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
6485561 ATAAAATATA
6485571 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
6485586 TATTAAATATATTAT
1 AATTAAATATATTAT
6485601 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
6485614 AATTTAATA
1 AATTAAATA
6485623 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:6485733 original size:18 final size:17
Alignment explanation
Indices: 6485710--6485746 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
6485700 AATTATTATT
6485710 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
6485726 AAATATATGATTTAATA
1 AAATATATGATTTAATA
6485743 AAAT
1 AAAT
6485747 TCATAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:6485878 original size:120 final size:120
Alignment explanation
Indices: 6485457--6485867 Score: 689
Period size: 120 Copynumber: 3.4 Consensus size: 120
6485447 ATATTTAAAC
6485457 ATAATTATTATTAAATATATTATAATTAAAATATATAATTATAATAAAATTCTTAATAATCAATA
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATT-TAATAAAATTCTTAATAATCAATA
* *
6485522 TTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATT-AA
65 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
6485577 CATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA
1 -ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA
*
6485642 TTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAATATAATTTGAA
65 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * * *
6485698 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCATAATAATTAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
* *
6485763 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * *
6485818 ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
6485868 TAAAATAATT
Statistics
Matches: 278, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
120 236 0.85
121 42 0.15
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
Found at i:6485937 original size:26 final size:28
Alignment explanation
Indices: 6485908--6485968 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
6485898 TATGAATTTG
*
6485908 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
6485934 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
6485962 TAAAATT
1 TATAATT
6485969 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:6486059 original size:90 final size:91
Alignment explanation
Indices: 6485883--6486089 Score: 308
Period size: 91 Copynumber: 2.3 Consensus size: 91
6485873 TAATTATAAC
* * * * * * *
6485883 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATCATAATCAAATATAATTTAATAAT
*
6485948 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTAA
6485974 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATCA-AATCAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATCATAATCAAATATAATTTAATAAT
*
6486038 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
6486064 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
6486090 CTAAAATCAA
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
90 46 0.44
91 59 0.56
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATCATAATCAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:6486682 original size:14 final size:15
Alignment explanation
Indices: 6486660--6486736 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
6486650 CAATCAAACA
6486660 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
6486674 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
6486689 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
6486709 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
6486723 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
6486737 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:6486701 original size:20 final size:20
Alignment explanation
Indices: 6486676--6486715 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6486666 AATATTTTCC
*
6486676 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
6486696 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
6486716 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:6486721 original size:34 final size:35
Alignment explanation
Indices: 6486664--6486730 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
6486654 CAAACACCAG
*
6486664 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
6486699 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
6486731 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:6490145 original size:41 final size:41
Alignment explanation
Indices: 6490095--6490434 Score: 527
Period size: 41 Copynumber: 8.3 Consensus size: 41
6490085 AATTCATCAT
* *
6490095 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
6490136 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
6490177 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
6490218 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
6490259 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
6490300 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
6490341 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
6490382 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
6490423 ATTCATATCACC
1 ATTCAGATCACC
6490435 AATTCCAAAC
Statistics
Matches: 270, Mismatches: 29, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 270 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
Found at i:6490238 original size:82 final size:82
Alignment explanation
Indices: 6490101--6490434 Score: 668
Period size: 82 Copynumber: 4.1 Consensus size: 82
6490091 TCATATTCGG
6490101 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
6490166 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
6490183 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
6490248 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
6490265 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
6490330 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
6490347 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
6490412 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
6490429 ATCACC
1 ATCACC
6490435 AATTCCAAAC
Statistics
Matches: 252, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 252 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.29
Consensus pattern (82 bp):
ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
TTTATAACCTGATTCAT
Found at i:6496399 original size:41 final size:41
Alignment explanation
Indices: 6496342--6496441 Score: 155
Period size: 41 Copynumber: 2.4 Consensus size: 41
6496332 TTTAACATAT
* *
6496342 TCACCGGCACTTAGCCTGCTAGGCTAATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTAACAACCTGATTCAGA
* *
6496383 TCACCGGCACTTAGCCTGCTAGGTTTACAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTAACAACCTGATTCAGA
*
6496424 TCACCCGCACTTAGCCTG
1 TCACCGGCACTTAGCCTG
6496442 TTAGATTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTAACAACCTGATTCAGA
Found at i:6504156 original size:41 final size:41
Alignment explanation
Indices: 6504099--6504202 Score: 145
Period size: 41 Copynumber: 2.5 Consensus size: 41
6504089 TTTAACATAT
* * *
6504099 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTACAACCTAATTCAGA
*
6504140 TCACCGGCACTTAGCCTGCTAGGTTTACAACCTAATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTACAACCTAATTCAGA
* * *
6504181 TCACCCGTACTTAGCTTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
6504203 ATTTATGGTC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTACAACCTAATTCAGA
Found at i:6504803 original size:21 final size:22
Alignment explanation
Indices: 6504760--6504805 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
6504750 TACACAAAAA
*
6504760 TAGACTTTTCGCGGCGCTTTTT
1 TAGACCTTTCGCGGCGCTTTTT
*
6504782 TAGACCTTTGGCGGCG-TTTTT
1 TAGACCTTTCGCGGCGCTTTTT
6504803 TAG
1 TAG
6504806 CGCCGCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.11, C:0.20, G:0.26, T:0.43
Consensus pattern (22 bp):
TAGACCTTTCGCGGCGCTTTTT
Found at i:6504993 original size:85 final size:84
Alignment explanation
Indices: 6504895--6505124 Score: 313
Period size: 85 Copynumber: 2.7 Consensus size: 84
6504885 GTTTTCAGAA
6504895 ACAAACGCCGCTAAAGAACAAAACCTTTAGCGGCGATTTTCCCACAAACGCCGCTAAAGACCATG
1 ACAAACGCCGCTAAAGAACAAAACCTTTAGCGGCGATTTTCCCACAAACGCCGCTAAAGA-CAT-
6504960 ACCTTTAGCGACGCTTTT-CC
64 ACCTTTAGCGACGCTTTTCCC
* * ** **
6504980 ACAAATGCCGCTAAAGACCATGACCTTTAGTAGC-ACTTTTCCCACAAACGCCGCTAAAGACATA
1 ACAAACGCCGCTAAAGAACAAAACCTTTAGCGGCGA-TTTTCCCACAAACGCCGCTAAAGACATA
6505044 CCTTTAGCGACGCTTTTCCCC
65 CCTTTAGCGACGCTTTT-CCC
* *
6505065 ACAAACGCCGCTAAAG-ACAAATACCTTTAGCGGCGCTTTTCCCCACAAACGCCACTAAAG
1 ACAAACGCCGCTAAAGAACAAA-ACCTTTAGCGGCGATTTT-CCCACAAACGCCGCTAAAG
6505125 GCAAATACCT
Statistics
Matches: 125, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
83 18 0.14
84 6 0.05
85 83 0.66
86 18 0.14
ACGTcount: A:0.32, C:0.33, G:0.15, T:0.20
Consensus pattern (84 bp):
ACAAACGCCGCTAAAGAACAAAACCTTTAGCGGCGATTTTCCCACAAACGCCGCTAAAGACATAC
CTTTAGCGACGCTTTTCCC
Found at i:6504995 original size:42 final size:42
Alignment explanation
Indices: 6504895--6505124 Score: 286
Period size: 42 Copynumber: 5.4 Consensus size: 42
6504885 GTTTTCAGAA
* * * *
6504895 ACAAACGCCGCTAAAGAACAAAACCTTTAGCGGCGATTTTCCC
1 ACAAACGCCGCTAAAG-ACCATACCTTTAGCGACGCTTTTCCC
6504938 ACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTT-CC
1 ACAAACGCCGCTAAAGACCAT-ACCTTTAGCGACGCTTTTCCC
* * *
6504980 ACAAATGCCGCTAAAGACCATGACCTTTAG-TAGCACTTTTCCC
1 ACAAACGCCGCTAAAGACCAT-ACCTTTAGCGA-CGCTTTTCCC
6505023 ACAAACGCCGCTAAAGA-CATACCTTTAGCGACGCTTTTCCCC
1 ACAAACGCCGCTAAAGACCATACCTTTAGCGACGCTTTT-CCC
* *
6505065 ACAAACGCCGCTAAAGACAAATACCTTTAGCGGCGCTTTTCCCC
1 ACAAACGCCGCTAAAGAC-CATACCTTTAGCGACGCTTTT-CCC
*
6505109 ACAAACGCCACTAAAG
1 ACAAACGCCGCTAAAG
6505125 GCAAATACCT
Statistics
Matches: 167, Mismatches: 13, Indels: 13
0.87 0.07 0.07
Matches are distributed among these distances:
41 15 0.09
42 64 0.38
43 50 0.30
44 38 0.23
ACGTcount: A:0.32, C:0.33, G:0.15, T:0.20
Consensus pattern (42 bp):
ACAAACGCCGCTAAAGACCATACCTTTAGCGACGCTTTTCCC
Found at i:6508407 original size:10 final size:11
Alignment explanation
Indices: 6508381--6508406 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6508371 AAAATCTGTC
6508381 AAAAATAGGAT
1 AAAAATAGGAT
6508392 AAAAATAGGAT
1 AAAAATAGGAT
6508403 AAAA
1 AAAA
6508407 TTCCTTAAAT
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:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (11 bp):
AAAAATAGGAT
Found at i:6510348 original size:15 final size:14
Alignment explanation
Indices: 6510307--6510344 Score: 53
Period size: 12 Copynumber: 2.8 Consensus size: 14
6510297 AATTTAAACC
6510307 CTAAACCCTAA-CT
1 CTAAACCCTAATCT
6510320 C-AAACCCTGAATCT
1 CTAAACCCT-AATCT
6510334 CTAAACCCTAA
1 CTAAACCCTAA
6510345 ATCTATAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 5 0.23
15 7 0.32
ACGTcount: A:0.39, C:0.37, G:0.03, T:0.21
Consensus pattern (14 bp):
CTAAACCCTAATCT
Found at i:6510402 original size:34 final size:34
Alignment explanation
Indices: 6510359--6510450 Score: 103
Period size: 34 Copynumber: 2.7 Consensus size: 34
6510349 ATAACTCTTA
* **
6510359 AACCTTAACCCCTAACCCCTAGCCCTTAAATCCC
1 AACCCTAACCCCTAACCCCTAAACCTTAAATCCC
* *
6510393 AACCCTAACCCTTAGCCCCTAAACCTTAAATCCC
1 AACCCTAACCCCTAACCCCTAAACCTTAAATCCC
* * *
6510427 AACCCTTAAACCATAATCCCTAAA
1 AACCC-TAACCCCTAACCCCTAAA
6510451 TTCATACTCC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
34 34 0.71
35 14 0.29
ACGTcount: A:0.35, C:0.42, G:0.02, T:0.21
Consensus pattern (34 bp):
AACCCTAACCCCTAACCCCTAAACCTTAAATCCC
Found at i:6510906 original size:41 final size:41
Alignment explanation
Indices: 6510849--6511042 Score: 329
Period size: 41 Copynumber: 4.8 Consensus size: 41
6510839 AAATGTTTTT
6510849 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTA
* * *
6510890 GCGGCGCTTCTTCAAAAATGCCACTAAAGGCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTA
6510931 GCGGCGCTTCTTCAAAAACGCCGCT--AGGCCAGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTA
*
6510970 GCGGCGCTTCCTCAAAAACGCCGCTAAAGGCCAGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTA
*
6511011 GCGGCGCTTCCTCAAAAACGCCGCTAAAGGCC
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCC
6511043 CCAAAAACTC
Statistics
Matches: 144, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
39 37 0.26
41 107 0.74
ACGTcount: A:0.28, C:0.31, G:0.24, T:0.16
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTA
Found at i:6510985 original size:80 final size:80
Alignment explanation
Indices: 6510849--6511036 Score: 313
Period size: 80 Copynumber: 2.3 Consensus size: 80
6510839 AAATGTTTTT
* *
6510849 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAATGCCAC
1 GCGGCGCTTCTTCAAAAACGCCGCT--AGGCCAGAGCATTAGCGGCGCTTCCTCAAAAACGCCAC
*
6510914 TAAAGGCCCGAGCATTA
64 TAAAGGCCAGAGCATTA
*
6510931 GCGGCGCTTCTTCAAAAACGCCGCTAGGCCAGAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAGGCCAGAGCATTAGCGGCGCTTCCTCAAAAACGCCACTA
6510996 AAGGCCAGAGCATTA
66 AAGGCCAGAGCATTA
*
6511011 GCGGCGCTTCCTCAAAAACGCCGCTA
1 GCGGCGCTTCTTCAAAAACGCCGCTA
6511037 AAGGCCCCAA
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
80 76 0.75
82 25 0.25
ACGTcount: A:0.28, C:0.31, G:0.24, T:0.17
Consensus pattern (80 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAGGCCAGAGCATTAGCGGCGCTTCCTCAAAAACGCCACTA
AAGGCCAGAGCATTA
Found at i:6518123 original size:27 final size:27
Alignment explanation
Indices: 6518093--6518147 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
6518083 GGATGCTAAG
6518093 TATGATCATTTTGGATAAGTATTTTGC
1 TATGATCATTTTGGATAAGTATTTTGC
*
6518120 TATGATCGTTTTGGATAAGTATTTTGC
1 TATGATCATTTTGGATAAGTATTTTGC
6518147 T
1 T
6518148 TGGTACGAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (27 bp):
TATGATCATTTTGGATAAGTATTTTGC
Found at i:6520505 original size:80 final size:80
Alignment explanation
Indices: 6520421--6520576 Score: 249
Period size: 80 Copynumber: 1.9 Consensus size: 80
6520411 TTGATGTCTC
* ** *
6520421 AAATCTGTATCAAAAAAGGGTGAGAGTTTTTTTTTGGAGTTCCAATGCAATGCCATAAATAACTA
1 AAATCTATATCAAAAAAGGGTGAGAACTTTTTTTTGGAGTTCCAATGCAATGCCATAAAGAACTA
6520486 CTCTTGATAATTTCT
66 CTCTTGATAATTTCT
* * *
6520501 AAATCTATATCAAAAACGGGTGAGAACTTTTTTTTGGAGTTCTAATGCAATGCCATCAAGAACTA
1 AAATCTATATCAAAAAAGGGTGAGAACTTTTTTTTGGAGTTCCAATGCAATGCCATAAAGAACTA
6520566 CTCTTGATAAT
66 CTCTTGATAAT
6520577 GATGTTTGGA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (80 bp):
AAATCTATATCAAAAAAGGGTGAGAACTTTTTTTTGGAGTTCCAATGCAATGCCATAAAGAACTA
CTCTTGATAATTTCT
Found at i:6521072 original size:14 final size:14
Alignment explanation
Indices: 6521053--6521090 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
6521043 CTTTCCTTTG
6521053 TTTTTCTGTTT-CTC
1 TTTTTCT-TTTCCTC
6521067 TTTTTCTTTTCCTC
1 TTTTTCTTTTCCTC
6521081 TTTATTCTTT
1 TTT-TTCTTT
6521091 ATTGTATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 13 0.59
15 6 0.27
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTTCTTTTCCTC
Found at i:6526720 original size:43 final size:42
Alignment explanation
Indices: 6526673--6526771 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 42
6526663 TCCCAGACGT
* * *
6526673 GGTCTTACATGTAATTA-ATTATCGATGCCACTGTCCCAAACAG
1 GGTCTTACACGTAATTATA-TA-CGACGCCAATGTCCCAAACAG
* * *
6526716 GGTCTTATACGTAATTATATACGACGCCAATGTCCCAGACAT
1 GGTCTTACACGTAATTATATACGACGCCAATGTCCCAAACAG
6526758 GGTCTTACACGTAA
1 GGTCTTACACGTAA
6526772 ATCTCAAATC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 30 0.62
43 17 0.35
44 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (42 bp):
GGTCTTACACGTAATTATATACGACGCCAATGTCCCAAACAG
Found at i:6526763 original size:42 final size:41
Alignment explanation
Indices: 6526663--6526812 Score: 140
Period size: 44 Copynumber: 3.5 Consensus size: 41
6526653 AATGCCAACA
* * * *
6526663 TCCCAGACGTGGTCTTACATGTAATTAATTATCGATGCCACTG
1 TCCCAGACATGGTCTTACACGTAATTAA-TA-CGACGCCAATG
* * *
6526706 TCCCAAACAGGGTCTTATACGTAATTATATACGACGCCAATG
1 TCCCAGACATGGTCTTACACGTAATTA-ATACGACGCCAATG
* *
6526748 TCCCAGACATGGTCTTACACGTAAATCTCAA-ATCGAGGCCAACG
1 TCCCAGACATGGTCTTACACGT-AAT-T-AATA-CGACGCCAATG
*
6526792 TCCTAGACATGGTCTTACACG
1 TCCCAGACATGGTCTTACACG
6526813 ATGTCACATT
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
42 28 0.31
43 28 0.31
44 32 0.36
45 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (41 bp):
TCCCAGACATGGTCTTACACGTAATTAATACGACGCCAATG
Found at i:6527788 original size:15 final size:15
Alignment explanation
Indices: 6527768--6527798 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6527758 ATAAATTAAA
6527768 AGGTATAATTTCAAC
1 AGGTATAATTTCAAC
6527783 AGGTATAATTTCAAC
1 AGGTATAATTTCAAC
6527798 A
1 A
6527799 AAAGGCCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (15 bp):
AGGTATAATTTCAAC
Found at i:6532562 original size:106 final size:108
Alignment explanation
Indices: 6532367--6532570 Score: 315
Period size: 106 Copynumber: 1.9 Consensus size: 108
6532357 TGGATTAAGA
*
6532367 TTTAAGAGAATATTTGGCTATTTGGTCAAACGAAAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAGAGAATATTTGGCTATTTGGTCAAACGAAAAAAATCGAAACCCAACACATTAGGGCACGT
*
6532432 TTCCTCGAATTTCCAAACGCAAAATATTGCCTTACTCTGAAAT
66 TTCCTCGAATTCCCAAACGCAAAATATTGCCTTACTCTGAAAT
* * *
6532475 TTTAA-AGGATATTTGGCTATTTGGTCGAATG-AAAAAATCGAAACCCAACACATTAGGGCACGC
1 TTTAAGAGAATATTTGGCTATTTGGTCAAACGAAAAAAATCGAAACCCAACACATTAGGGCACG-
* *
6532538 TTT-CTCGAATTCCCAAATGTAAAATATTGCCTT
65 TTTCCTCGAATTCCCAAACGCAAAATATTGCCTT
6532571 TATTATTTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
106 57 0.65
107 26 0.30
108 5 0.06
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (108 bp):
TTTAAGAGAATATTTGGCTATTTGGTCAAACGAAAAAAATCGAAACCCAACACATTAGGGCACGT
TTCCTCGAATTCCCAAACGCAAAATATTGCCTTACTCTGAAAT
Found at i:6533625 original size:12 final size:12
Alignment explanation
Indices: 6533587--6533625 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
6533577 GAAATATATA
*
6533587 AATAATATCAAT
1 AATAATATTAAT
*
6533599 AATAATAGTAAT
1 AATAATATTAAT
*
6533611 AATAATATTATT
1 AATAATATTAAT
6533623 AAT
1 AAT
6533626 TAATTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:6539902 original size:19 final size:19
Alignment explanation
Indices: 6539878--6539916 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6539868 AAAGGAAGAG
6539878 ATAGTTAATTCATTTTCCA
1 ATAGTTAATTCATTTTCCA
6539897 ATAGTTAATTCATTTTCCA
1 ATAGTTAATTCATTTTCCA
6539916 A
1 A
6539917 AGAAGAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (19 bp):
ATAGTTAATTCATTTTCCA
Found at i:6546323 original size:13 final size:13
Alignment explanation
Indices: 6546305--6546329 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6546295 ATTTCTGGTC
6546305 TTTACTCAAGTTT
1 TTTACTCAAGTTT
6546318 TTTACTCAAGTT
1 TTTACTCAAGTT
6546330 CTTAAGCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTACTCAAGTTT
Found at i:6546461 original size:31 final size:31
Alignment explanation
Indices: 6546426--6546486 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
6546416 TTTCAACAAT
6546426 TTGATATCAAGAGCTTATTTCTTAGTGGACA
1 TTGATATCAAGAGCTTATTTCTTAGTGGACA
6546457 TTGATATCAAGAGCTTATTTCTTAGTGGAC
1 TTGATATCAAGAGCTTATTTCTTAGTGGAC
6546487 CTGTCATTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (31 bp):
TTGATATCAAGAGCTTATTTCTTAGTGGACA
Found at i:6550837 original size:13 final size:13
Alignment explanation
Indices: 6550819--6550843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6550809 ATTTCTGGTC
6550819 TTTACTCAAGTTT
1 TTTACTCAAGTTT
6550832 TTTACTCAAGTT
1 TTTACTCAAGTT
6550844 CTTAAGCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTACTCAAGTTT
Found at i:6557538 original size:22 final size:22
Alignment explanation
Indices: 6557513--6557566 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
6557503 TTGTTTTTAA
* *
6557513 AAAATTAT-TTAATTTTAATTAT
1 AAAATTATATAAATATTAA-TAT
*
6557535 AAAAGTATATAAATATTAATAT
1 AAAATTATATAAATATTAATAT
*
6557557 AACATTATAT
1 AAAATTATAT
6557567 TTTTTAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAATTATATAAATATTAATAT
Found at i:6557685 original size:29 final size:28
Alignment explanation
Indices: 6557627--6557685 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
6557617 ATGTAAAATT
* * **
6557627 ATATTAATATTAATCTTTTATTATGTTA
1 ATATTAAAATTAATATTTTATTATACTA
*
6557655 ATATTAAAATTATATATTTTATTTTACTA
1 ATATTAAAATTA-ATATTTTATTATACTA
6557684 AT
1 AT
6557686 TATCATATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATTAAAATTAATATTTTATTATACTA
Done.