Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 24 of 175
Found at i:6396164 original size:29 final size:29
Alignment explanation
Indices: 6396126--6396218 Score: 108
Period size: 23 Copynumber: 3.3 Consensus size: 29
6396116 AATTTAAAAT
*
6396126 TTTTAAAATACTTTTTTAAATTTTTTTAA
1 TTTTAAAATACTTTTTAAAATTTTTTTAA
6396155 TTTTAAAATACTTTTTAAAA----TTT--
1 TTTTAAAATACTTTTTAAAATTTTTTTAA
*
6396178 TTTTAAAATACTTTTTAAAATTTTTTAAAA
1 TTTTAAAATACTTTTTAAAATTTTTT-TAA
6396208 TTTTTAAAATA
1 -TTTTAAAATA
6396219 AAAATAGGCC
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
23 20 0.37
25 3 0.06
27 2 0.04
29 19 0.35
31 10 0.19
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTTAAAATACTTTTTAAAATTTTTTTAA
Found at i:6396186 original size:52 final size:52
Alignment explanation
Indices: 6396072--6396218 Score: 160
Period size: 52 Copynumber: 2.8 Consensus size: 52
6396062 TTTATTTTAA
* *
6396072 TTTTAAAATA-TTTTTAAAATACTTTTTTAAAATTTTT-TAAT-TTTAATTTAAAAT
1 TTTTAAAATACTTTTT-AAA-A-TTTTTTAAAATTTTTAAAATACTT--TTTAAAAT
* *
6396126 TTTTAAAATACTTTTTTAAATTTTTT-TAA-TTTTAAAATACTTTTTAAAATTT
1 TTTTAAAATACTTTTTAAAATTTTTTAAAATTTTTAAAATACTTTTTAAAA--T
6396178 TTTTAAAATACTTTTTAAAATTTTTTAAAATTTTTAAAATA
1 TTTTAAAATACTTTTTAAAATTTTTTAAAATTTTTAAAATA
6396219 AAAATAGGCC
Statistics
Matches: 80, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
50 11 0.14
51 5 0.06
52 34 0.43
53 3 0.04
54 22 0.28
55 5 0.06
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (52 bp):
TTTTAAAATACTTTTTAAAATTTTTTAAAATTTTTAAAATACTTTTTAAAAT
Found at i:6400698 original size:23 final size:23
Alignment explanation
Indices: 6400646--6400699 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
6400636 TTAAAATACT
*
6400646 TTAAAAATATTTTTATTTTTATT
1 TTAAAAATATTTTTATTTTTATA
*
6400669 TTTAAAATATTTTT-TTGTGTT-TA
1 TTAAAAATATTTTTATT-T-TTATA
6400692 TTAAAAAT
1 TTAAAAAT
6400700 TGGGCCGGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 22 0.85
24 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
TTAAAAATATTTTTATTTTTATA
Found at i:6400859 original size:17 final size:18
Alignment explanation
Indices: 6400827--6400861 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
6400817 GATTTTAAAT
*
6400827 TAATTTTTATTATTAATA
1 TAATTTCTATTATTAATA
6400845 TAATTTCTA-TATTAATA
1 TAATTTCTATTATTAATA
6400862 GAAAGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTTCTATTATTAATA
Found at i:6402402 original size:28 final size:29
Alignment explanation
Indices: 6402344--6402400 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
6402334 TTTCTTGTTA
*
6402344 ATTTTGGATTTATTAAATGGTGTATTTTT
1 ATTTTGGATTTATTAAATGGAGTATTTTT
6402373 ATTTGTGGACTTTATT-AAT-GAGTATTTT
1 ATTT-TGGA-TTTATTAAATGGAGTATTTT
6402401 ATATAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 12 0.48
30 7 0.28
31 6 0.24
ACGTcount: A:0.25, C:0.02, G:0.18, T:0.56
Consensus pattern (29 bp):
ATTTTGGATTTATTAAATGGAGTATTTTT
Found at i:6406394 original size:126 final size:124
Alignment explanation
Indices: 6406190--6406541 Score: 535
Period size: 126 Copynumber: 2.8 Consensus size: 124
6406180 TAATTTCGAG
* **
6406190 TTGACATTTCTGATAAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* *
6406255 AAATTGCGCCCTCGTGGACGCGTTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAA--ATTTTT
*
6406316 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAACAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * * * * *
6406381 AAATCGCGGCCTCGT-TAGCGCGCTTTTACTATAGTAGGTCATGTAAGAAATAAATTTTT
66 AAATCGCGCCCTCGTGGA-CGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAAATTTTT
* *
6406440 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
*
6406505 AAATCGCGCCCTCGTGGACGCGCTTTTGTTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
6406542 CATGTTTGGG
Statistics
Matches: 204, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
124 98 0.48
125 2 0.01
126 104 0.51
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAAATTTTT
Found at i:6409771 original size:116 final size:114
Alignment explanation
Indices: 6409573--6409788 Score: 369
Period size: 116 Copynumber: 1.9 Consensus size: 114
6409563 TGATAAATTG
* *
6409573 TATTAAGTCAAAAAAATTTTAATGGTTTGTAAAATTATCAAATTATATAAAATTATTAATTGTTA
1 TATTAAGTCAAAAAAATTTTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTA
6409638 GTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 GTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
* * *
6409687 TATTAAGTCAAAAAATTGTATTAATGATTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
1 TATTAAGTCAAAAAAAT-T-TTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
6409752 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTA
64 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTA
6409789 CGTTAAGGTT
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
114 16 0.17
115 1 0.01
116 78 0.82
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (114 bp):
TATTAAGTCAAAAAAATTTTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTA
GTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
Found at i:6409857 original size:29 final size:29
Alignment explanation
Indices: 6409814--6410250 Score: 612
Period size: 29 Copynumber: 15.4 Consensus size: 29
6409804 TTTTAAGTTA
*
6409814 AGGGTTTAAGGTTTTTAATTAAATTAGGTT
1 AGGG-TTAGGGTTTTTAATTAAATTAGGTT
6409844 AGGGTTAGGGTTTTTAATT-AA--A--TT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
6409868 A-GGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
6409896 AGGGTTAGGG-TTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
6409924 AGGGTTAGGGTTTGTAATT-AA-T---TT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
6409948 A-GGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* * *
6409976 AGGGTTAAGGTTTGTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
6410005 AGGGGTTAGGGTTTTTAATTAAATTAGATT
1 A-GGGTTAGGGTTTTTAATTAAATTAGGTT
*
6410035 AGGGTTAGGATTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* *
6410064 AGGGTTAAGTTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* *
6410093 AGGGTTATGGTTTTTAATTAAATTACGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* * *
6410122 AAGGTTAGGGTTTATAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
6410151 AGGGGTTAGGGTTTTTAATTAAATTAGGTT
1 A-GGGTTAGGGTTTTTAATTAAATTAGGTT
* *
6410181 AGAGTTAGGGTTTTTAATTAAATTTGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
6410210 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
6410239 AGGGTTAGGGTT
1 AGGGTTAGGGTT
6410251 AGGGTTAGGG
Statistics
Matches: 363, Mismatches: 29, Indels: 31
0.86 0.07 0.07
Matches are distributed among these distances:
23 33 0.09
24 10 0.03
25 1 0.00
26 2 0.01
27 1 0.00
28 38 0.10
29 223 0.61
30 55 0.15
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (29 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTT
Found at i:6409892 original size:18 final size:21
Alignment explanation
Indices: 6409847--6409901 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 21
6409837 TTAGGTTAGG
6409847 GTTAGGGTTTTTAATTAAATTA
1 GTTAGGGTTTTTAATTAAA-TA
6409869 GGTTAGGGTTTTTAATTAAATTA
1 -GTTAGGGTTTTTAATTAAA-TA
6409892 GGTTAGGGTT
1 -GTTAGGGTT
6409902 AGGGTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.47
Consensus pattern (21 bp):
GTTAGGGTTTTTAATTAAATA
Found at i:6410054 original size:88 final size:85
Alignment explanation
Indices: 6409814--6410250 Score: 613
Period size: 88 Copynumber: 5.1 Consensus size: 85
6409804 TTTTAAGTTA
6409814 AGGGTTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT-AA--A-TTAGGTTAG
1 AGGG-TTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGTTAGGTTAG
6409875 GGTTTTTAATTAAATTAGGTT
65 GGTTTTTAATTAAATTAGGTT
* *
6409896 AGGGTT-AGGGTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATT-AA-T--TTAGGTTAGG
1 AGGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGTTAGGTTAGG
6409956 GTTTTTAATTAAATTAGGTT
66 GTTTTTAATTAAATTAGGTT
* *
6409976 AGGGTTAAGGTTTGTAATTAATTTAGGTTAGGGGTTAGGGTTTTTAATTAAATTAGATTAGGGTT
1 AGGGTTAAGGTTTTTAATTAAATTAGGTTA-GGGTTAGGGTTTTTAATTAAATTAG-TTA-GGTT
*
6410041 AGGATTTTTAATTAAATTAGGTT
63 AGGGTTTTTAATTAAATTAGGTT
* *
6410064 AGGGTTAAGTTTTTTAATTAAATTAGGTTAGGGTTATGGTTTTTAATTAAATTACGTTAAGGTTA
1 AGGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA-GTT-AGGTTA
* *
6410129 GGGTTTATAATTAATTTAGGTT
64 GGGTTTTTAATTAAATTAGGTT
* * *
6410151 AGGGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTTGGTTAGGGTT
1 A-GGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAA-TTAGTTA-GGTT
6410216 AGGGTTTTTAATTAAATTAGGTT
63 AGGGTTTTTAATTAAATTAGGTT
*
6410239 AGGGTTAGGGTT
1 AGGGTTAAGGTT
6410251 AGGGTTAGGG
Statistics
Matches: 320, Mismatches: 21, Indels: 23
0.88 0.06 0.06
Matches are distributed among these distances:
80 77 0.24
81 22 0.07
82 21 0.07
83 2 0.01
84 1 0.00
87 65 0.20
88 130 0.41
89 2 0.01
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (85 bp):
AGGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGTTAGGTTAGG
GTTTTTAATTAAATTAGGTT
Found at i:6410152 original size:146 final size:145
Alignment explanation
Indices: 6409814--6410250 Score: 630
Period size: 146 Copynumber: 3.1 Consensus size: 145
6409804 TTTTAAGTTA
* *
6409814 AGGGTTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA---A--TTA--GGT
1 AGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTATAATTAATTTAGGTTAGGGGT
*
6409872 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTAATTAAATTAGGTTAGGGTTAGGGTTT
65 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTT
*
6409937 GTAATT-AA-T---TT
130 TTAATTAAATTAGGTT
* *
6409948 A-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTGTAATTAATTTAGGTTAGGGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTATAATTAATTTAGGTTAGGGGTT
* * *
6410012 AGGGTTTTTAATTAAATTAGATTAGGGTTAGGATTTTTAATTAAATTAGGTTAGGGTTAAGTTTT
66 AGGGTTTTTAATTAAATTAGGTTAGGGTTAGG-TTTTTAATTAAATTAGGTTAGGGTTAGGGTTT
6410077 TTAATTAAATTAGGTT
130 TTAATTAAATTAGGTT
* * *
6410093 AGGGTTATGGTTTTTAATTAAATTACGTTAAGGTTAGGGTTTATAATTAATTTAGGTTAGGGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTATAATTAATTTAGGTTAGGGGTT
* *
6410158 AGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTTGGTTAGGGTTAGGGTTT
66 AGGGTTTTTAATTAAATTAGGTTAGGGTTA-GGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTT
6410223 TTAATTAAATTAGGTT
130 TTAATTAAATTAGGTT
6410239 AGGGTTAGGGTT
1 AGGGTTAGGGTT
6410251 AGGGTTAGGG
Statistics
Matches: 269, Mismatches: 19, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
132 43 0.16
133 2 0.01
134 1 0.00
135 1 0.00
137 3 0.01
139 35 0.13
140 34 0.13
141 2 0.01
142 1 0.00
145 3 0.01
146 142 0.53
147 2 0.01
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (145 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTATAATTAATTTAGGTTAGGGGTT
AGGGTTTTTAATTAAATTAGGTTAGGGTTAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTT
TAATTAAATTAGGTT
Found at i:6410157 original size:117 final size:114
Alignment explanation
Indices: 6409814--6410250 Score: 608
Period size: 117 Copynumber: 3.9 Consensus size: 114
6409804 TTTTAAGTTA
*
6409814 AGGGTTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTA--G--
1 AGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
6409875 -GGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTAATTAAATTAGGTT
65 AGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTAATTAAATTAGGTT
*
6409924 AGGGTTAGGGTTTGTAATT-AA-T---TTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT-
* * *
6409983 AGGTTTGTAATTAATTTAGGTTAGGGGTTAGGGTTTTTAATTAAATTAGATT
65 AGGTTTTTAATTAAATTAGGTTA-GGGTTAGGG-TTTTAATTAAATTAGGTT
* * *
6410035 AGGGTTAGGATTTTTAATTAAATTAGGTTAGGGTTAAGTTTTTTAATTAAATTAGGTTAGGGTTA
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA
* * *
6410100 TGGTTTTTAATTAAATTACGTTAAGGTTAGGGTTTATAATTAATTTAGGTT
66 -GGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTT-TAATTAAATTAGGTT
* *
6410151 AGGGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTTGGTTAGGGTT
1 A-GGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
6410216 AGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT
65 A-GGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT
6410251 AGGGTTAGGG
Statistics
Matches: 287, Mismatches: 23, Indels: 27
0.85 0.07 0.08
Matches are distributed among these distances:
103 28 0.10
104 3 0.01
105 1 0.00
107 1 0.00
108 2 0.01
109 33 0.11
110 13 0.05
111 34 0.12
112 2 0.01
113 1 0.00
115 3 0.01
116 26 0.09
117 140 0.49
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (114 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA
GGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTAATTAAATTAGGTT
Found at i:6410246 original size:6 final size:6
Alignment explanation
Indices: 6410235--6410262 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6410225 AATTAAATTA
6410235 GGTTAG GGTTAG GGTTAG GGTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTTAG GGTT
6410263 TTTAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.50, T:0.36
Consensus pattern (6 bp):
GGTTAG
Found at i:6410251 original size:41 final size:42
Alignment explanation
Indices: 6410206--6410293 Score: 160
Period size: 41 Copynumber: 2.1 Consensus size: 42
6410196 AATTAAATTT
6410206 GGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAG
1 GGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAG
*
6410247 GGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTTAG
1 GGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAG
6410289 GGTTA
1 GGTTA
6410294 AATTAGATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 36 0.80
42 9 0.20
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.43
Consensus pattern (42 bp):
GGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAG
Found at i:6410386 original size:44 final size:45
Alignment explanation
Indices: 6410318--6410404 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 45
6410308 TTTTATTACA
*
6410318 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
* *
6410363 TCAAA-AAATTTCTATTTTTTTACATAAAATAATATCAAAATA
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATA
6410405 TTCAAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 34 0.87
45 5 0.13
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (45 bp):
TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:6410850 original size:18 final size:18
Alignment explanation
Indices: 6410827--6410861 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6410817 CGGAAAAAGA
*
6410827 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
6410845 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
6410862 AAACGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:6416459 original size:17 final size:17
Alignment explanation
Indices: 6416438--6416488 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
6416428 TTATTATATT
*
6416438 ATTAATAAAATTTAATT
1 ATTAATAAAATTTAATA
*
6416455 TTTAA-AAATATTTAA-A
1 ATTAATAAA-ATTTAATA
6416471 ATTAATAAAATATTAATA
1 ATTAATAAAAT-TTAATA
6416489 TAAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
16 9 0.33
17 17 0.63
18 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTAATAAAATTTAATA
Found at i:6416589 original size:13 final size:14
Alignment explanation
Indices: 6416548--6416613 Score: 64
Period size: 13 Copynumber: 4.6 Consensus size: 14
6416538 ATATATAATC
6416548 AAATAATAAATTATT
1 AAATAATAAATT-TT
**
6416563 AACATAATTTATTTT
1 AA-ATAATAAATTTT
6416578 -AATAATAAATTTT
1 AAATAATAAATTTT
6416591 AAAAATAATAAA-TTT
1 --AAATAATAAATTTT
6416606 AAATAATA
1 AAATAATA
6416614 TTCTTCATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 18 0.42
14 1 0.02
15 7 0.16
16 17 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATAATAAATTTT
Found at i:6416598 original size:29 final size:29
Alignment explanation
Indices: 6416548--6416613 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
6416538 ATATATAATC
* **
6416548 AAATAATAAATTATTAACATAATTTATTT
1 AAATAATAAATTATTAAAATAATAAATTT
*
6416577 TAATAATAAATT-TTAAAAATAATAAATTT
1 AAATAATAAATTATT-AAAATAATAAATTT
6416606 AAATAATA
1 AAATAATA
6416614 TTCTTCATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.06
29 29 0.94
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
AAATAATAAATTATTAAAATAATAAATTT
Found at i:6416613 original size:16 final size:17
Alignment explanation
Indices: 6416577--6416613 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
6416567 TAATTTATTT
6416577 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
6416594 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
6416609 TAATA
1 TAATA
6416614 TTCTTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:6416667 original size:15 final size:15
Alignment explanation
Indices: 6416638--6416703 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 15
6416628 TTGAAAAGTA
*
6416638 TTTAAT-ATTAATAT
1 TTTAATAATAAATAT
6416652 TTTAATAATAAATATT
1 TTTAATAATAAATA-T
*
6416668 TATTACAATTATAAATAT
1 T-TT--AATAATAAATAT
* *
6416686 ATTAATAATAAATGT
1 TTTAATAATAAATAT
6416701 TTT
1 TTT
6416704 GTAGTATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 6 0.15
15 18 0.44
16 2 0.05
17 4 0.10
18 1 0.02
19 10 0.24
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (15 bp):
TTTAATAATAAATAT
Found at i:6419913 original size:22 final size:22
Alignment explanation
Indices: 6419888--6419930 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
6419878 TACTCAAACA
6419888 ATAACAACAAAAT-AGTAGCAAT
1 ATAACAACAAAATGA-TAGCAAT
* *
6419910 ATAATAACGAAATGATAGCAA
1 ATAACAACAAAATGATAGCAA
6419931 AACAATGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATGATAGCAAT
Found at i:6419973 original size:21 final size:22
Alignment explanation
Indices: 6419926--6419973 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
6419916 ACGAAATGAT
**
6419926 AGCAAAACAATGAAAAAACAGT
1 AGCAAAACAATGAAAAAACAAC
* *
6419948 GGCAAAACAAT-AAAAAATAAC
1 AGCAAAACAATGAAAAAACAAC
6419969 AGCAA
1 AGCAA
6419974 TTTTTTTCTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.65, C:0.15, G:0.12, T:0.08
Consensus pattern (22 bp):
AGCAAAACAATGAAAAAACAAC
Found at i:6425460 original size:16 final size:16
Alignment explanation
Indices: 6425436--6425468 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6425426 TGTATTGGGT
*
6425436 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
6425452 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
6425468 T
1 T
6425469 AGCAAATCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:6425513 original size:45 final size:44
Alignment explanation
Indices: 6425447--6425541 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 44
6425437 GGATTAGAGG
* *
6425447 TGTAATGGAATAGAGGTGTAATAGCAAATCAGCTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACAG-TGTTTGGTTGAA
* *
6425492 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACAGTGTTTGGTTGAA
6425536 TGTAAT
1 TGTAAT
6425542 AGAGGTGTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 18 0.39
45 28 0.61
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACAGTGTTTGGTTGAA
Found at i:6425724 original size:18 final size:17
Alignment explanation
Indices: 6425703--6425737 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6425693 TTATTATTTA
*
6425703 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
6425721 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
6425738 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:6425731 original size:28 final size:27
Alignment explanation
Indices: 6425661--6425733 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
6425651 TTTATTATCA
*
6425661 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
6425689 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
6425716 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
6425734 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:6425865 original size:16 final size:17
Alignment explanation
Indices: 6425839--6425880 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
6425829 AAACATAATT
6425839 ATTATAAATATAT-TTTA
1 ATTA-AAATATATATTTA
6425856 ATTAAAATATATAATTTA
1 ATTAAAATATAT-ATTTA
6425874 A-TAAAAT
1 ATTAAAAT
6425881 TCTTAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 10 0.43
18 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTAAAATATATATTTA
Found at i:6425873 original size:18 final size:17
Alignment explanation
Indices: 6425846--6425880 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6425836 ATTATTATAA
*
6425846 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
6425864 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
6425881 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:6425886 original size:143 final size:147
Alignment explanation
Indices: 6425622--6425892 Score: 478
Period size: 143 Copynumber: 1.9 Consensus size: 147
6425612 ATGATTATTG
6425622 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
6425687 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
6425752 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
6425771 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
6425833 ATAATTATTA-TAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
6425893 ATATTCTTAT
Statistics
Matches: 120, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
143 49 0.41
144 42 0.35
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:6426068 original size:17 final size:16
Alignment explanation
Indices: 6426046--6426092 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
6426036 ACTCAAATCA
6426046 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
6426063 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
6426077 TAAATATATGATTTAA
1 T-AATATATGATTTAA
6426093 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:6426093 original size:17 final size:17
Alignment explanation
Indices: 6426065--6426098 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6426055 ATTATAACTA
*
6426065 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
6426082 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
6426099 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:6426241 original size:93 final size:91
Alignment explanation
Indices: 6426131--6426324 Score: 284
Period size: 92 Copynumber: 2.1 Consensus size: 91
6426121 GATTATAGTT
* *
6426131 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTA-ATATAATTAT-ATAATAATATATAATTTC
* *
6426194 ATAAAATTCTTGATAATAAAAATTTTCTTA
63 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
6426224 TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAGTGATATATAATTTCATA
1 TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAATAATATATAATTTCATA
6426289 AAATTCTTAATAATAAAATGTTCTTA
66 AAATTCTTAATAATAAAATGTTCTTA
6426315 TATGAATTTA
1 TATGAATTTA
6426325 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
91 21 0.23
92 40 0.43
93 29 0.31
94 3 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (91 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAATAATATATAATTTCATA
AAATTCTTAATAATAAAATGTTCTTA
Found at i:6427741 original size:11 final size:11
Alignment explanation
Indices: 6427727--6427753 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6427717 AAAAATAAAT
6427727 ACAAAAGTTTC
1 ACAAAAGTTTC
6427738 ACAAAAGTTTC
1 ACAAAAGTTTC
6427749 ACAAA
1 ACAAA
6427754 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:6438358 original size:32 final size:32
Alignment explanation
Indices: 6438317--6438381 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
6438307 GCCTTGGGAG
6438317 TATGCTTTAGAACCCAAGTTTGATTCCTAAGT
1 TATGCTTTAGAACCCAAGTTTGATTCCTAAGT
6438349 TATGCTTTAGAACCCAAGTTTGATTCCTAAGT
1 TATGCTTTAGAACCCAAGTTTGATTCCTAAGT
6438381 T
1 T
6438382 TCAGATTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (32 bp):
TATGCTTTAGAACCCAAGTTTGATTCCTAAGT
Found at i:6439657 original size:11 final size:11
Alignment explanation
Indices: 6439622--6439658 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
6439612 CGTTTATGAT
6439622 TATGATATGTA
1 TATGATATGTA
**
6439633 TAAAATATGTA
1 TATGATATGTA
6439644 TATGATATGTA
1 TATGATATGTA
6439655 TATG
1 TATG
6439659 TGTGGGGTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (11 bp):
TATGATATGTA
Found at i:6444148 original size:3 final size:3
Alignment explanation
Indices: 6444140--6444171 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
6444130 TAAACAAAGC
*
6444140 TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
6444172 CATATATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:6447539 original size:2 final size:2
Alignment explanation
Indices: 6447532--6447558 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6447522 TTTTTGAGAT
6447532 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
6447559 TGTTCTAGTT
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:6462065 original size:17 final size:17
Alignment explanation
Indices: 6462034--6462071 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 17
6462024 TAATAAATAA
6462034 TAAAATATTTTAAATT-
1 TAAAATATTTTAAATTC
6462050 TAAAATATTTTAAAATTC
1 TAAAATATTTT-AAATTC
6462068 TAAA
1 TAAA
6462072 TAAAATGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.55
17 5 0.25
18 4 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAATATTTTAAATTC
Found at i:6464942 original size:20 final size:20
Alignment explanation
Indices: 6464917--6464956 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6464907 CATAAAATGA
*
6464917 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
6464937 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
6464957 GGAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:6478326 original size:21 final size:22
Alignment explanation
Indices: 6478297--6478343 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
6478287 CAGAAGGAGT
*
6478297 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
6478319 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
6478340 GAGT
1 GAGT
6478344 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:6491811 original size:72 final size:72
Alignment explanation
Indices: 6491693--6491833 Score: 221
Period size: 72 Copynumber: 2.0 Consensus size: 72
6491683 AGGAACTAAG
* *
6491693 GGAGGCAACAGAGTAAACATATTGAATGTTAAGTAAATCCACATGAAATTTACTTAACTTACCTT
1 GGAGGCAACAGAGTAAACATATTAAACGTTAAGTAAATCCACATGAAATTTACTTAACTTACCTT
6491758 AACAAAT
66 AACAAAT
* * *
6491765 GGAGGCAACGGAGTAAACATATTAAACGCTT-AGTAAGTCCATATGAAATTTACTTAACTTACCT
1 GGAGGCAACAGAGTAAACATATTAAACG-TTAAGTAAATCCACATGAAATTTACTTAACTTACCT
6491829 TAACA
65 TAACA
6491834 TTACAACAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 61 0.97
73 2 0.03
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (72 bp):
GGAGGCAACAGAGTAAACATATTAAACGTTAAGTAAATCCACATGAAATTTACTTAACTTACCTT
AACAAAT
Found at i:6495242 original size:5 final size:5
Alignment explanation
Indices: 6495226--6495257 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
6495216 ATAGATATAG
6495226 ATAAA GATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA -ATAAA ATAAA ATAAA ATAAA ATAAA A
6495258 ATCTATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:6495810 original size:13 final size:13
Alignment explanation
Indices: 6495794--6495819 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6495784 ATATAACCCC
6495794 TAAAAATAAAAAA
1 TAAAAATAAAAAA
6495807 TAAAAATAAAAAA
1 TAAAAATAAAAAA
6495820 GAGAGAAAAT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:6510446 original size:260 final size:260
Alignment explanation
Indices: 6509985--6510507 Score: 1028
Period size: 260 Copynumber: 2.0 Consensus size: 260
6509975 TCTAATGGTG
6509985 CATTTGGGAGGACTGGGGAAGTGATGGGATATGTGACAATGAAGTTCATGGATTGCTGGTACAAG
1 CATTTGGGAGGACTGGGGAAGTGATGGGATATGTGACAATGAAGTTCATGGATTGCTGGTACAAG
6510050 TGAAAATCAGACTTTAAGAAGTTCAGAATGGATCAAGTCTTGTGTATTTCAGATATTACTAGAAT
66 TGAAAATCAGACTTTAAGAAGTTCAGAATGGATCAAGTCTTGTGTATTTCAGATATTACTAGAAT
*
6510115 TGAAGGGTTTTATAGCTTACTGAATTGTTTTCCATTTATAACTTCAAAGGACATTTATGTTCTTG
131 TGAAGGGTTTTATAGCTTACTGAATTGTTTTCCATTTATAACTTCAAAGGACATTTACGTTCTTG
6510180 GTAGCTTTTGAACATATTCTACGATGTGGAAAACATTTGGAATGTTCTTCAAAACTAGATATTTA
196 GTAGCTTTTGAACATATTCTACGATGTGGAAAACATTTGGAATGTTCTTCAAAACTAGATATTTA
*
6510245 CATTTGGGAGGACTGGGGAAGTGATGGGATATGTGATAATGAAGTTCATGGATTGCTGGTACAAG
1 CATTTGGGAGGACTGGGGAAGTGATGGGATATGTGACAATGAAGTTCATGGATTGCTGGTACAAG
6510310 TGAAAATCAGACTTTAAGAAGTTCAGAATGGATCAAGTCTTGTGTATTTCAGATATTACTAGAAT
66 TGAAAATCAGACTTTAAGAAGTTCAGAATGGATCAAGTCTTGTGTATTTCAGATATTACTAGAAT
6510375 TGAAGGGTTTTATAGCTTACTGAATTGTTTTCCATTTATAACTTCAAAGGACATTTACGTTCTTG
131 TGAAGGGTTTTATAGCTTACTGAATTGTTTTCCATTTATAACTTCAAAGGACATTTACGTTCTTG
6510440 GTAGCTTTTGAACATATTCTACGATGTGGAAAACATTTGGAATGTTCTTCAAAACTAGATATTTA
196 GTAGCTTTTGAACATATTCTACGATGTGGAAAACATTTGGAATGTTCTTCAAAACTAGATATTTA
6510505 CAT
1 CAT
6510508 GGTGATCCTG
Statistics
Matches: 261, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
260 261 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.35
Consensus pattern (260 bp):
CATTTGGGAGGACTGGGGAAGTGATGGGATATGTGACAATGAAGTTCATGGATTGCTGGTACAAG
TGAAAATCAGACTTTAAGAAGTTCAGAATGGATCAAGTCTTGTGTATTTCAGATATTACTAGAAT
TGAAGGGTTTTATAGCTTACTGAATTGTTTTCCATTTATAACTTCAAAGGACATTTACGTTCTTG
GTAGCTTTTGAACATATTCTACGATGTGGAAAACATTTGGAATGTTCTTCAAAACTAGATATTTA
Found at i:6514502 original size:2 final size:2
Alignment explanation
Indices: 6514495--6514527 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6514485 TTAATCAAGG
6514495 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
6514528 TTGGTGATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6515749 original size:16 final size:16
Alignment explanation
Indices: 6515728--6515758 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6515718 AAATAATATA
6515728 TATTTTTTTAGAAAGC
1 TATTTTTTTAGAAAGC
*
6515744 TATTTTTTTATAAAG
1 TATTTTTTTAGAAAG
6515759 AAGTTAAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (16 bp):
TATTTTTTTAGAAAGC
Found at i:6515806 original size:21 final size:21
Alignment explanation
Indices: 6515777--6515816 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6515767 ATAAGAAAAC
6515777 AAAACTATAACATTTTTATGA
1 AAAACTATAACATTTTTATGA
* **
6515798 AAAAGTATATTATTTTTAT
1 AAAACTATAACATTTTTAT
6515817 AATATATAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (21 bp):
AAAACTATAACATTTTTATGA
Found at i:6516002 original size:28 final size:26
Alignment explanation
Indices: 6515959--6516011 Score: 61
Period size: 28 Copynumber: 2.0 Consensus size: 26
6515949 ACCATTTGAA
*
6515959 TTTTTTTTAGAATTTACATAATATAC
1 TTTTTTTTAGAATTTACAAAATATAC
* *
6515985 TTTTTTGTTATAACTTTATAAAATATA
1 TTTTTT-TTAGAA-TTTACAAAATATA
6516012 TAAATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 6 0.27
27 5 0.23
28 11 0.50
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.55
Consensus pattern (26 bp):
TTTTTTTTAGAATTTACAAAATATAC
Found at i:6516563 original size:34 final size:34
Alignment explanation
Indices: 6516525--6516642 Score: 148
Period size: 34 Copynumber: 3.5 Consensus size: 34
6516515 TTTGAAAAAA
* **
6516525 TAAATTAGGGTTTAGAATTTTTAA-AAAATTTAAT
1 TAAATTAAGGTTTAGGGTTTTTAAGAAAA-TTAAT
* * *
6516559 TAAATTAAGTTTTAGGGGTTTTAAGTAAATTAAT
1 TAAATTAAGGTTTAGGGTTTTTAAGAAAATTAAT
*
6516593 TAAAATAAGGTTTAGGGTTTTTAAGAAAATTAAT
1 TAAATTAAGGTTTAGGGTTTTTAAGAAAATTAAT
*
6516627 TAAATTAGGGTTTAGG
1 TAAATTAAGGTTTAGG
6516643 TTTAAAAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
34 68 0.96
35 3 0.04
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.42
Consensus pattern (34 bp):
TAAATTAAGGTTTAGGGTTTTTAAGAAAATTAAT
Found at i:6517092 original size:127 final size:126
Alignment explanation
Indices: 6516742--6517268 Score: 696
Period size: 126 Copynumber: 4.2 Consensus size: 126
6516732 GATTTTGTTT
* * * * * *
6516742 TCTTTTTCTACAGTAGTTTCTGAAAAATTAATTTTGAGAAGATACTTCTGAAAAGATAATGTCAA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGATAGTTCTGAAAAAATAGTGTCAA
* * * * * *
6516807 ACACGCTTTAAACAGGATGTACTATCAGCAAAAGTACTAAAAAAAGCTCCCACGTGGACGC
66 AAACGCTTCAAACAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTTCCACGTGGACGC
* * * * *
6516868 TCTTTTTCTATAGTAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTTTGAAAAAATAGTGTCAA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGATAGTTCTGAAAAAATAGTGTCAA
* * * *
6516933 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTTCCATGTGGATGC
66 AAACGCTTCAAACAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTTCCACGTGGACGC
*
6516994 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGATGGTTCTGAAAAAAATAGTGTCA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGATAGTTCTG-AAAAAATAGTGTCA
* * * * * *
6517059 AAAACGCTTCAAACAGGATACACTGTCAACAAAATTACTGAAAAAAGC-TCCTACATGAATGC
65 AAAACGCTTCAAACAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTTCC-ACGTGGACGC
* * * *
6517121 TCTTTTTCTACAGTAGATCCTGAAAAAATAATTTAGAGAAGATGGTTCTGAAGAAATAGTGTTAA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGATAGTTCTGAAAAAATAGTGTCAA
* * *
6517186 AAACGCTTCAAGCAGGATGCACTATTAGCAAAATTACTGAAAAAAGCTTCCAGGTGGACGC
66 AAACGCTTCAAACAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTTCCACGTGGACGC
* *
6517247 ACTTTTTCTAAAGTAGTTCCTG
1 TCTTTTTCTACAGTAGTTCCTG
6517269 CTTGGCCTTA
Statistics
Matches: 352, Mismatches: 46, Indels: 6
0.87 0.11 0.01
Matches are distributed among these distances:
126 234 0.66
127 118 0.34
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (126 bp):
TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGATAGTTCTGAAAAAATAGTGTCAA
AAACGCTTCAAACAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTTCCACGTGGACGC
Found at i:6517190 original size:253 final size:252
Alignment explanation
Indices: 6516742--6517268 Score: 739
Period size: 253 Copynumber: 2.1 Consensus size: 252
6516732 GATTTTGTTT
* * * *
6516742 TCTTTTTCTACAGTAGTTTCTGAAAAATTAATTTTGAGAAGATACTTCTGAAAAGATAATGTCAA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGATACTTCTGAAAAAATAATGTCAA
* * ** * * *
6516807 ACACGCTTTAAACAGGATGTACTATCAGCAAAAGTACTAAAAAAAGCTCCCACGTGGACGCTCTT
66 AAACGCTTCAAACAGGATACACTATCAACAAAAGTACTAAAAAAAGCTCCCACATGAACGCTCTT
* * * * *
6516872 TTTCTATAGTAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTTTGAAAAAATAGTGTCAAAAAC
131 TTTCTACAGTAGATCCTGAAAAAATAATTTAGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAAC
* * *
6516937 GCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTTCCATGTGGATGC
196 GCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTTCCAGGTGGACGC
** *
6516994 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGATGGTTCTGAAAAAAATAGTGTCA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGATACTTCTG-AAAAAATAATGTCA
* * * * *
6517059 AAAACGCTTCAAACAGGATACACTGTCAACAAAATTACTGAAAAAAGCTCCTACATGAATGCTCT
65 AAAACGCTTCAAACAGGATACACTATCAACAAAAGTACTAAAAAAAGCTCCCACATGAACGCTCT
** * *
6517124 TTTTCTACAGTAGATCCTGAAAAAATAATTTAGAGAAGATGGTTCTGAAGAAATAGTGTTAAAAA
130 TTTTCTACAGTAGATCCTGAAAAAATAATTTAGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAA
*
6517189 CGCTTCAAGCAGGATGCACTATTAGCAAAATTACTGAAAAAAGCTTCCAGGTGGACGC
195 CGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTTCCAGGTGGACGC
* *
6517247 ACTTTTTCTAAAGTAGTTCCTG
1 TCTTTTTCTACAGTAGTTCCTG
6517269 CTTGGCCTTA
Statistics
Matches: 240, Mismatches: 34, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
252 45 0.19
253 195 0.81
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (252 bp):
TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGATACTTCTGAAAAAATAATGTCAA
AAACGCTTCAAACAGGATACACTATCAACAAAAGTACTAAAAAAAGCTCCCACATGAACGCTCTT
TTTCTACAGTAGATCCTGAAAAAATAATTTAGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAAC
GCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTTCCAGGTGGACGC
Found at i:6519246 original size:21 final size:21
Alignment explanation
Indices: 6519219--6519275 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
6519209 CTTCAGTTTC
6519219 ACCCTTATGGGTTTCCGTTCA
1 ACCCTTATGGGTTTCCGTTCA
* * *
6519240 ACTCTTATGAGCTTCCGTTCA
1 ACCCTTATGGGTTTCCGTTCA
6519261 ACCCTTATGGGTTTC
1 ACCCTTATGGGTTTC
6519276 TGTTTAGCAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.28, G:0.18, T:0.39
Consensus pattern (21 bp):
ACCCTTATGGGTTTCCGTTCA
Found at i:6519289 original size:42 final size:42
Alignment explanation
Indices: 6519155--6519290 Score: 159
Period size: 42 Copynumber: 3.2 Consensus size: 42
6519145 CTTTCCATTT
* * *
6519155 AGCTCTCATGAGCTTCAGTTTAACCC-TATTGGGTTTTTGTTC
1 AGCTCTTATGAGCTTCAGTTCAACCCTTA-TGGGTTTCTGTTC
* *
6519197 AGCTCTTTTGAGCTTCAGTTTC-ACCCTTATGGGTTTCCGTTC
1 AGCTCTTATGAGCTTCAG-TTCAACCCTTATGGGTTTCTGTTC
* * *
6519239 AACTCTTATGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTT
1 AGCTCTTATGAGCTTCAGTTCAACCCTTATGGGTTTCTGTTC
*
6519281 AGCACTTATG
1 AGCTCTTATG
6519291 TTCTTCTGTG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
41 3 0.04
42 72 0.91
43 4 0.05
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (42 bp):
AGCTCTTATGAGCTTCAGTTCAACCCTTATGGGTTTCTGTTC
Found at i:6523559 original size:18 final size:18
Alignment explanation
Indices: 6523533--6523578 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
6523523 GACTGGAAAA
* * *
6523533 AGGAAACATATAAGTGTT
1 AGGATACATATAAGGGCT
6523551 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
6523569 AGGATACATA
1 AGGATACATA
6523579 CTGGCATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.24
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:6526611 original size:21 final size:22
Alignment explanation
Indices: 6526581--6526650 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
6526571 CGACCCGAAT
*
6526581 TATATATTAAATATATATTTTT
1 TATATATTAAATATATATTTTA
* *
6526603 TAT-TTTTAATCAAATATATTTTA
1 TATATATTAA--ATATATATTTTA
*
6526626 TATATATTAAATATATATTTAA
1 TATATATTAAATATATATTTTA
6526648 TAT
1 TAT
6526651 GGGTCGGGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 5 0.13
22 16 0.41
23 13 0.33
24 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATATTAAATATATATTTTA
Found at i:6526632 original size:11 final size:11
Alignment explanation
Indices: 6526616--6526650 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
6526606 TTTTAATCAA
*
6526616 ATATATTTTAT
1 ATATATTTAAT
*
6526627 ATATATTAAAT
1 ATATATTTAAT
6526638 ATATATTTAAT
1 ATATATTTAAT
6526649 AT
1 AT
6526651 GGGTCGGGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATATATTTAAT
Found at i:6536307 original size:365 final size:365
Alignment explanation
Indices: 6535637--6536366 Score: 1442
Period size: 365 Copynumber: 2.0 Consensus size: 365
6535627 TCATAATTAA
6535637 TATAATTTAATAAATAATGTTAAAAGTACAATGGTTTGATACACGGTCCAAAATGCCTCTTCAAC
1 TATAATTTAATAAATAATGTTAAAAGTACAATGGTTTGATACACGGTCCAAAATGCCTCTTCAAC
6535702 CTCAACTTTCTGTAGGTAAGAGAATACCTGCTGGACGTGACAATCGCAGAGGTACAAAATAGAAT
66 CTCAACTTTCTGTAGGTAAGAGAATACCTGCTGGACGTGACAATCGCAGAGGTACAAAATAGAAT
6535767 GAAGCAAGACGACCTAAAATAATGCTCTAATAAATTACCTCAGAGCCCACAAACTTTTCCGGCTG
131 GAAGCAAGACGACCTAAAATAATGCTCTAATAAATTACCTCAGAGCCCACAAACTTTTCCGGCTG
*
6535832 ACAACGATGCAGCACTTTGACATCTAGTCCAAAATAATTATTCCATAAGTTGAACAACAAGCTCA
196 ACAACGATGCAACACTTTGACATCTAGTCCAAAATAATTATTCCATAAGTTGAACAACAAGCTCA
6535897 CAAGCACTTTAAAATTCGCAGCAGCCAATTCAACTCTCCAAACTCTAGATTTCCTCTCCATTATC
261 CAAGCACTTTAAAATTCGCAGCAGCCAATTCAACTCTCCAAACTCTAGATTTCCTCTCCATTATC
6535962 GAGAACCAGCTGCAAGAAGTGATCTTTCCACTCAAACAGG
326 GAGAACCAGCTGCAAGAAGTGATCTTTCCACTCAAACAGG
6536002 TATAATTTAATAAATAATGTTAAAAGTACAATGGTTTGATACACGGTCCAAAATGCCTCTTCAAC
1 TATAATTTAATAAATAATGTTAAAAGTACAATGGTTTGATACACGGTCCAAAATGCCTCTTCAAC
6536067 CTCAACTTTCTGTAGGTAAGAGAATACCTGCTGGACGTGACAATCGCAGAGGTACAAAATAGAAT
66 CTCAACTTTCTGTAGGTAAGAGAATACCTGCTGGACGTGACAATCGCAGAGGTACAAAATAGAAT
6536132 GAAGCAAGACGACCTAAAATAATGCTCTAATAAATTACCTCAGAGCCCACAAACTTTTCCGGCTG
131 GAAGCAAGACGACCTAAAATAATGCTCTAATAAATTACCTCAGAGCCCACAAACTTTTCCGGCTG
*
6536197 ACAACGATGCAACACTTTGACATCTAGTCCAAAATAATTATTCCATAAGTTGAACAAGAAGCTCA
196 ACAACGATGCAACACTTTGACATCTAGTCCAAAATAATTATTCCATAAGTTGAACAACAAGCTCA
6536262 CAAGCACTTTAAAATTCGCAGCAGCCAATTCAACTCTCCAAACTCTAGATTTCCTCTCCATTATC
261 CAAGCACTTTAAAATTCGCAGCAGCCAATTCAACTCTCCAAACTCTAGATTTCCTCTCCATTATC
6536327 GAGAACCAGCTGCAAGAAGTGATCTTTCCACTCAAACAGG
326 GAGAACCAGCTGCAAGAAGTGATCTTTCCACTCAAACAGG
6536367 CCCGCGAAAG
Statistics
Matches: 363, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
365 363 1.00
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (365 bp):
TATAATTTAATAAATAATGTTAAAAGTACAATGGTTTGATACACGGTCCAAAATGCCTCTTCAAC
CTCAACTTTCTGTAGGTAAGAGAATACCTGCTGGACGTGACAATCGCAGAGGTACAAAATAGAAT
GAAGCAAGACGACCTAAAATAATGCTCTAATAAATTACCTCAGAGCCCACAAACTTTTCCGGCTG
ACAACGATGCAACACTTTGACATCTAGTCCAAAATAATTATTCCATAAGTTGAACAACAAGCTCA
CAAGCACTTTAAAATTCGCAGCAGCCAATTCAACTCTCCAAACTCTAGATTTCCTCTCCATTATC
GAGAACCAGCTGCAAGAAGTGATCTTTCCACTCAAACAGG
Found at i:6542915 original size:6 final size:6
Alignment explanation
Indices: 6542904--6542928 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6542894 TGTGGGTGAT
6542904 TGATGG TGATGG TGATGG TGATGG T
1 TGATGG TGATGG TGATGG TGATGG T
6542929 CTTCTTGCCT
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:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (6 bp):
TGATGG
Found at i:6544856 original size:9 final size:8
Alignment explanation
Indices: 6544841--6544865 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6544831 TATGGTTTGA
6544841 ATTTTTTT
1 ATTTTTTT
6544849 ATTTTTTT
1 ATTTTTTT
6544857 ATTTTTTT
1 ATTTTTTT
6544865 A
1 A
6544866 ATGGGATGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
ATTTTTTT
Found at i:6548280 original size:13 final size:13
Alignment explanation
Indices: 6548262--6548303 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
6548252 AATTTCAAAT
6548262 TATTTAGTGATAA
1 TATTTAGTGATAA
*
6548275 TATTTA--GA-AT
1 TATTTAGTGATAA
6548285 TATTTAGTGATAA
1 TATTTAGTGATAA
6548298 TATTTA
1 TATTTA
6548304 AGAACGATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
12 2 0.08
13 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:6548285 original size:23 final size:23
Alignment explanation
Indices: 6548259--6548303 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
6548249 TTAAATTTCA
6548259 AATTATTTAGTGATAATATTTAG
1 AATTATTTAGTGATAATATTTAG
6548282 AATTATTTAGTGATAATATTTA
1 AATTATTTAGTGATAATATTTA
6548304 AGAACGATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (23 bp):
AATTATTTAGTGATAATATTTAG
Found at i:6557090 original size:12 final size:12
Alignment explanation
Indices: 6557073--6557098 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6557063 TGTGTTGTTG
6557073 ATTATGGAGAGC
1 ATTATGGAGAGC
6557085 ATTATGGAGAGC
1 ATTATGGAGAGC
6557097 AT
1 AT
6557099 ATCTTCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (12 bp):
ATTATGGAGAGC
Found at i:6563889 original size:28 final size:28
Alignment explanation
Indices: 6563849--6563974 Score: 218
Period size: 28 Copynumber: 4.5 Consensus size: 28
6563839 TAAATTGTAC
6563849 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
6563877 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
6563905 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
* *
6563933 AGCACTAAGTGTGCAAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
6563960 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6563975 GACTTAATAT
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 22 0.23
28 72 0.77
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:6565892 original size:49 final size:49
Alignment explanation
Indices: 6565820--6565919 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
6565810 ATATAGAGTT
6565820 AAAACAAAAACTTAGTCTGGAAACCATATTATGAGCTGGGCTCGTCATG
1 AAAACAAAAACTTAGTCTGGAAACCATATTATGAGCTGGGCTCGTCATG
6565869 AAAACAAAAACTTAGTCTGGAAACCATATTATGAGCTGGGCTCGTCATG
1 AAAACAAAAACTTAGTCTGGAAACCATATTATGAGCTGGGCTCGTCATG
6565918 AA
1 AA
6565920 GGTGCGAGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (49 bp):
AAAACAAAAACTTAGTCTGGAAACCATATTATGAGCTGGGCTCGTCATG
Found at i:6570145 original size:25 final size:25
Alignment explanation
Indices: 6570117--6570164 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
6570107 TTACTGATAC
* *
6570117 TCAGCTCGCATGAGCTTGCCGTTAT
1 TCAGCTCGCAGGAGCTTACCGTTAT
*
6570142 TCAGCTCGGAGGAGCTTACCGTT
1 TCAGCTCGCAGGAGCTTACCGTT
6570165 TATAGCTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (25 bp):
TCAGCTCGCAGGAGCTTACCGTTAT
Found at i:6582702 original size:41 final size:41
Alignment explanation
Indices: 6582536--6582691 Score: 285
Period size: 41 Copynumber: 3.8 Consensus size: 41
6582526 TTTATCGTTA
* *
6582536 GTGACATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
6582577 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
6582618 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
6582659 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
6582692 AAGAGCCGGT
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 112 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:6582962 original size:33 final size:32
Alignment explanation
Indices: 6582906--6582969 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
6582896 ATAGATATGT
6582906 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
6582938 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
6582970 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:6582986 original size:33 final size:33
Alignment explanation
Indices: 6582913--6582986 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
6582903 TGTATATATA
* * **
6582913 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
6582945 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
6582978 TGTATGTAT
1 TATATGTAT
6582987 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:6593118 original size:6 final size:6
Alignment explanation
Indices: 6593102--6593131 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
6593092 TCAAGTCTCA
*
6593102 ATTTTT CTTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
6593132 GATGTAGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:6594663 original size:31 final size:31
Alignment explanation
Indices: 6594627--6594685 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
6594617 AACTTTAATT
* *
6594627 CTTATACTTTTCGAATTTGTCAATTTTAGTC
1 CTTATACTTTTCAAATTTGTAAATTTTAGTC
6594658 CTTATACTTTTCAAATTTGTAAATTTTA
1 CTTATACTTTTCAAATTTGTAAATTTTA
6594686 ATGCTAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.53
Consensus pattern (31 bp):
CTTATACTTTTCAAATTTGTAAATTTTAGTC
Found at i:6598431 original size:3 final size:3
Alignment explanation
Indices: 6598425--6598469 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
6598415 TTTTAACTGT
6598425 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6598470 AACATTCATG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6598657 original size:11 final size:11
Alignment explanation
Indices: 6598641--6598667 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6598631 TATACATATA
6598641 TTTTTTTCCTT
1 TTTTTTTCCTT
6598652 TTTTTTTCCTT
1 TTTTTTTCCTT
6598663 TTTTT
1 TTTTT
6598668 AAAAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTCCTT
Found at i:6610665 original size:45 final size:46
Alignment explanation
Indices: 6610533--6610668 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 46
6610523 GTTGAAAAGC
*
6610533 AGCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAA-GAA
1 AGCAAATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAA
* * * *** * *** * *
6610578 AGTAGATCTTGTCTTCATGTACCGG-CATGAAGTAGATCAAAGGTA
1 AGCAAATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAA
6610623 A-CAAATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAA
1 AGCAAATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAA
6610668 A
1 A
6610669 AAGCAGATCT
Statistics
Matches: 66, Mismatches: 23, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
44 28 0.42
45 38 0.58
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (46 bp):
AGCAAATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAA
Found at i:6610730 original size:92 final size:89
Alignment explanation
Indices: 6610542--6610714 Score: 265
Period size: 92 Copynumber: 1.9 Consensus size: 89
6610532 CAGCAGATCT
*
6610542 TGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTACCGGCATG
1 TGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTGTCTTCATGTACCGGCATG
** *
6610607 AAGTAGATCAAAGGTAACAAATCT
66 AAGTAGATCAAAGACAACAAATCC
*
6610631 TGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAAAAAGCAGATCTTGTCTTCATGTACTGGC
1 TGCCTTCCCATACTGGTGGCGAAGCAGATCAAA-G--AAAGCAGATCTTGTCTTCATGTACCGGC
*
6610696 GTGAAGTAGATCAAAGACA
63 ATGAAGTAGATCAAAGACA
6610715 TCAGGTCCTG
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
89 33 0.43
90 1 0.01
92 42 0.55
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (89 bp):
TGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTGTCTTCATGTACCGGCATG
AAGTAGATCAAAGACAACAAATCC
Found at i:6612500 original size:3 final size:3
Alignment explanation
Indices: 6612494--6612526 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
6612484 TTTTAACTAT
6612494 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6612527 AACATTCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:6619609 original size:3 final size:3
Alignment explanation
Indices: 6619497--6619590 Score: 86
Period size: 3 Copynumber: 30.7 Consensus size: 3
6619487 ATATTATCAG
* * *
6619497 AAT AAT AAT GAAT AAAT AA- AAG AAA AAT AA- AACT AAT AAT GAT CAAT
1 AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT -AAT
*
6619544 AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT GAA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
6619589 AA
1 AA
6619591 AGTAATTAAC
Statistics
Matches: 77, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
2 6 0.08
3 59 0.77
4 12 0.16
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:6627578 original size:29 final size:29
Alignment explanation
Indices: 6627546--6627604 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
6627536 GTGCGTTCTG
6627546 CTTGATAGAATATGAAGAACTTATTTTAT
1 CTTGATAGAATATGAAGAACTTATTTTAT
6627575 CTTGATAGAATATGAAGAACTTATTTTAT
1 CTTGATAGAATATGAAGAACTTATTTTAT
6627604 C
1 C
6627605 ATTTTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (29 bp):
CTTGATAGAATATGAAGAACTTATTTTAT
Found at i:6636162 original size:30 final size:30
Alignment explanation
Indices: 6636117--6636297 Score: 253
Period size: 30 Copynumber: 6.1 Consensus size: 30
6636107 ATAGAAACTA
*
6636117 ATATCAGTTAACTGATTCTTAGGAAATTAGG
1 ATATCAATT-ACTGATTCTTAGGAAATTAGG
* *
6636148 ATATCAATTACTGATTTTTAGGAAAACTA--
1 ATATCAATTACTGATTCTTAGG-AAATTAGG
*
6636177 ATATCAGTTACTGATTCTTAGGAAATTAGG
1 ATATCAATTACTGATTCTTAGGAAATTAGG
*
6636207 ATATCAATTACTGATTCTTAGGAAAACTA--
1 ATATCAATTACTGATTCTTAGG-AAATTAGG
*
6636236 ATATCAGTTACTGATTCTTAGGAAATTAGG
1 ATATCAATTACTGATTCTTAGGAAATTAGG
6636266 ATATCAATTACTGATTCTTAGGAAATTAGG
1 ATATCAATTACTGATTCTTAGGAAATTAGG
6636296 AT
1 AT
6636298 TTATTTCCTT
Statistics
Matches: 133, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
28 10 0.08
29 41 0.31
30 64 0.48
31 18 0.14
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (30 bp):
ATATCAATTACTGATTCTTAGGAAATTAGG
Found at i:6636204 original size:59 final size:59
Alignment explanation
Indices: 6636111--6636290 Score: 342
Period size: 59 Copynumber: 3.0 Consensus size: 59
6636101 TTGTAAATAG
*
6636111 AAACTAATATCAGTTAACTGATTCTTAGGAAATTAGGATATCAATTACTGATTTTTAGGA
1 AAACTAATATCAGTT-ACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
6636171 AAACTAATATCAGTTACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
1 AAACTAATATCAGTTACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
6636230 AAACTAATATCAGTTACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
1 AAACTAATATCAGTTACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
6636289 AA
1 AA
6636291 TTAGGATTTA
Statistics
Matches: 119, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
59 104 0.87
60 15 0.13
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (59 bp):
AAACTAATATCAGTTACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
Found at i:6636278 original size:89 final size:89
Alignment explanation
Indices: 6636117--6636297 Score: 251
Period size: 89 Copynumber: 2.0 Consensus size: 89
6636107 ATAGAAACTA
* * *
6636117 ATATCAGTTAACTGATTCTTAGGAAATTAGGATATCAATTACTGATTTTTAGGAAAACTAATATC
1 ATATCAATTAACTGATTCTTAGGAAACTA-GATATCAATTACTGATTCTTAGGAAAACTAATATC
*
6636182 AGTTACTGATTCTTAGGAAATTAGG
65 AATTACTGATTCTTAGGAAATTAGG
* *
6636207 ATATCAATT-ACTGATTCTTAGGAAAACTA-ATATCAGTTACTGATTCTTAGG-AAATTAGGATA
1 ATATCAATTAACTGATTCTTAGG-AAACTAGATATCAATTACTGATTCTTAGGAAAACTA--ATA
6636269 TCAATTACTGATTCTTAGGAAATTAGG
63 TCAATTACTGATTCTTAGGAAATTAGG
6636296 AT
1 AT
6636298 TTATTTCCTT
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
87 5 0.06
88 20 0.24
89 44 0.54
90 13 0.16
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (89 bp):
ATATCAATTAACTGATTCTTAGGAAACTAGATATCAATTACTGATTCTTAGGAAAACTAATATCA
ATTACTGATTCTTAGGAAATTAGG
Found at i:6643753 original size:17 final size:17
Alignment explanation
Indices: 6643726--6643758 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6643716 GTATTTTTTA
6643726 TGAATTGTG-AATAAAG
1 TGAATTGTGAAATAAAG
6643742 TGAATATGTGAAATAAA
1 TGAAT-TGTGAAATAAA
6643759 AATATAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.30
Consensus pattern (17 bp):
TGAATTGTGAAATAAAG
Found at i:6649521 original size:12 final size:12
Alignment explanation
Indices: 6649501--6649531 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6649491 CTCCAGTTTT
*
6649501 CACATGGCCTAG
1 CACACGGCCTAG
6649513 CACACGGCCTAG
1 CACACGGCCTAG
6649525 CACACGG
1 CACACGG
6649532 GTGTGTGGTT
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:0.26, C:0.39, G:0.26, T:0.10
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:6650609 original size:21 final size:21
Alignment explanation
Indices: 6650557--6650632 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
6650547 CAGTAAACGG
*
6650557 CACAT-AAGTGCCTGAAACGA
1 CACATAAAGTGCCTGATACGA
** * *
6650577 CACACGAGGTGCCTGATATGA
1 CACATAAAGTGCCTGATACGA
6650598 CACATAAAGTGCCTGATGTACGA
1 CACATAAAGTGCCTGA--TACGA
6650621 CACATAAAGTGC
1 CACATAAAGTGC
6650633 TTAATCGGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
20 4 0.09
21 25 0.56
23 16 0.36
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (21 bp):
CACATAAAGTGCCTGATACGA
Found at i:6650996 original size:16 final size:16
Alignment explanation
Indices: 6650970--6651009 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
6650960 TTAATAATAA
*
6650970 TACTTATCTTA-TATT
1 TACTTACCTTATTATT
6650985 TCACTTACCTTATTATT
1 T-ACTTACCTTATTATT
6651002 TACTTACC
1 TACTTACC
6651010 ATACACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.73
17 5 0.23
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.53
Consensus pattern (16 bp):
TACTTACCTTATTATT
Found at i:6651441 original size:5 final size:5
Alignment explanation
Indices: 6651431--6651516 Score: 172
Period size: 5 Copynumber: 17.2 Consensus size: 5
6651421 TTATTTTTAC
6651431 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6651481 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
6651517 AATTTAAAAC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 81 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:6655723 original size:29 final size:29
Alignment explanation
Indices: 6655675--6655732 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
6655665 TTAATCAATT
6655675 CTAATCAATAATTCTATCAA-ATAAACCC
1 CTAATCAATAATTCTATCAACATAAACCC
* *
6655703 CTAATTCAATCATTC-ATTCAACATGAACCC
1 CTAA-TCAATAATTCTA-TCAACATAAACCC
6655733 TACTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 5 0.20
29 13 0.52
30 7 0.28
ACGTcount: A:0.41, C:0.28, G:0.02, T:0.29
Consensus pattern (29 bp):
CTAATCAATAATTCTATCAACATAAACCC
Found at i:6656331 original size:32 final size:33
Alignment explanation
Indices: 6656288--6656360 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
6656278 TATTTATCAT
* *
6656288 ATAAAAAATC-TTTTACTAATTA-ATAATAAATA
1 ATAAAATATCTTTTTACTAAATATAT-ATAAATA
6656320 ATAAAATATCTTTTTACTAAATATATATAAATA
1 ATAAAATATCTTTTTACTAAATATATATAAATA
6656353 ATACAAAT
1 ATA-AAAT
6656361 GTACTTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 9 0.25
33 21 0.58
34 6 0.17
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (33 bp):
ATAAAATATCTTTTTACTAAATATATATAAATA
Found at i:6663390 original size:18 final size:20
Alignment explanation
Indices: 6663359--6663396 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
6663349 TAAATCAGAA
6663359 ATAAATAAATAAACAAAAAT
1 ATAAATAAATAAACAAAAAT
6663379 ATAAAT-AA-AAACAAAAAT
1 ATAAATAAATAAACAAAAAT
6663397 TATTAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
ATAAATAAATAAACAAAAAT
Found at i:6663467 original size:15 final size:15
Alignment explanation
Indices: 6663443--6663478 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6663433 ATCAATACGG
*
6663443 CCCAACTAGCCTAAA
1 CCCAATTAGCCTAAA
*
6663458 CCCAATTAGCCTAAG
1 CCCAATTAGCCTAAA
6663473 CCCAAT
1 CCCAAT
6663479 ACCCTAGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.39, G:0.08, T:0.17
Consensus pattern (15 bp):
CCCAATTAGCCTAAA
Found at i:6680512 original size:16 final size:17
Alignment explanation
Indices: 6680481--6680513 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6680471 TAGCATTTCA
*
6680481 TAACTAAACAACATTTT
1 TAACCAAACAACATTTT
6680498 TAACCAAAC-ACATTTT
1 TAACCAAACAACATTTT
6680514 ACTTGCTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
TAACCAAACAACATTTT
Found at i:6681404 original size:40 final size:41
Alignment explanation
Indices: 6681257--6681434 Score: 134
Period size: 40 Copynumber: 4.4 Consensus size: 41
6681247 ACTTAATTTT
* * *
6681257 TCGCACACTAAATGCCATCGAATAGCCGAAGTTATT-A-TAA
1 TCGCACACTAAGTGCCAT-AAATAGCCGAAGCTATTCACTAA
** * * * *
6681297 TCTCGCACACTAAGTGCTTTACATA-CCTAAAGCTATCTCAGT-C
1 --TCGCACACTAAGTGCCATAAATAGCC-GAAGCTAT-TCACTAA
* * *
6681340 TCGCACACTAAGTGTCGTATATAGCCGAAGCTATTC-CTAA
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATTCACTAA
* * *
6681380 TCGCACACTAAGTGCCATAAATAGCCGAAGTTA-TCTCGAA
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATTCACTAA
6681420 TCGCACACTAAGTGC
1 TCGCACACTAAGTGC
6681435 TAAACATAGT
Statistics
Matches: 109, Mismatches: 20, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
39 3 0.03
40 51 0.47
41 35 0.32
42 18 0.17
43 1 0.01
44 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (41 bp):
TCGCACACTAAGTGCCATAAATAGCCGAAGCTATTCACTAA
Found at i:6684360 original size:9 final size:9
Alignment explanation
Indices: 6684341--6684386 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
6684331 TGAGTTTTCA
*
6684341 AATTTGAAT
1 AATTCGAAT
*
6684350 AACTCGAAT
1 AATTCGAAT
6684359 AATTCGAAT
1 AATTCGAAT
6684368 AATTCGAAT
1 AATTCGAAT
6684377 AATTCGAAT
1 AATTCGAAT
6684386 A
1 A
6684387 TCAAACTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:6684448 original size:21 final size:21
Alignment explanation
Indices: 6684422--6684463 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6684412 ACCCCAAACT
*
6684422 CTCAAACCGTTTTACTT-TTCC
1 CTCAAAAC-TTTTACTTCTTCC
6684443 CTCAAAACTTTTACTTCTTCC
1 CTCAAAACTTTTACTTCTTCC
6684464 TACTTTCCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.21, C:0.33, G:0.02, T:0.43
Consensus pattern (21 bp):
CTCAAAACTTTTACTTCTTCC
Found at i:6686043 original size:21 final size:23
Alignment explanation
Indices: 6686019--6686066 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
6686009 TCTAAATTTT
*
6686019 AAAATT-TTAAAAATGAAAA-AC
1 AAAATTCTTAAAAATAAAAATAC
6686040 AAAATTCTTAAAAATAAAAATAC
1 AAAATTCTTAAAAATAAAAATAC
6686063 AAAA
1 AAAA
6686067 CTAAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 6 0.25
22 12 0.50
23 6 0.25
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (23 bp):
AAAATTCTTAAAAATAAAAATAC
Found at i:6687470 original size:43 final size:42
Alignment explanation
Indices: 6687422--6687513 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 42
6687412 TTTTAGAAAT
* *
6687422 AAACGCCGCTA-ATGATCAGGACATTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTATA-GATCAAGACATTTAGCGGCGC-TTTCCCAC
* *
6687465 AAACGCTGCTATAGATCAAGACTTTTAGCGGCGCTTTCCCAC
1 AAACGCCGCTATAGATCAAGACATTTAGCGGCGCTTTCCCAC
6687507 AAACGCC
1 AAACGCC
6687514 ACTTCGTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 13 0.30
43 29 0.67
44 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (42 bp):
AAACGCCGCTATAGATCAAGACATTTAGCGGCGCTTTCCCAC
Found at i:6687731 original size:42 final size:43
Alignment explanation
Indices: 6687613--6687765 Score: 236
Period size: 43 Copynumber: 3.6 Consensus size: 43
6687603 TACTCAATGT
* *
6687613 CGCTTTTCCCACAAACGCCACTATAGATCAGGACCTTTAGCGG
1 CGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGA
* *
6687656 CGCTTTTTCCACAAATGCCGCTATAGATCAGGACCTTTAGCGA
1 CGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGA
*
6687699 CGCTTTTCCCACAAACGCCGCTA-AGATTAGGACCTTTAGCGA
1 CGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGA
* *
6687741 CACTTTTCCCACAAACGTCGCTATA
1 CGCTTTTCCCACAAACGCCGCTATA
6687766 AATTATAACT
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 39 0.39
43 61 0.61
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (43 bp):
CGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGA
Found at i:6687780 original size:85 final size:86
Alignment explanation
Indices: 6687613--6687790 Score: 232
Period size: 85 Copynumber: 2.1 Consensus size: 86
6687603 TACTCAATGT
* * * *
6687613 CGCTTTTCCCACAAACGCCACTATAGATCAGGACCTTTAGCGGCGCTTTTTCCACAAATGCCGCT
1 CGCTTTTCCCACAAACGCCACTATAGATCAGGACCTTTAGCGACACTTTTCCCACAAACGCCGCT
* *
6687678 ATAGATCAGGACCTTTAGCGA
66 ATAAATCAGAACCTTTAGCGA
* * *
6687699 CGCTTTTCCCACAAACGCCGCTA-AGATTAGGACCTTTAGCGACACTTTTCCCACAAACGTCGCT
1 CGCTTTTCCCACAAACGCCACTATAGATCAGGACCTTTAGCGACACTTTTCCCACAAACGCCGCT
* * * *
6687763 ATAAATTATAACTTTTAGCGG
66 ATAAATCAGAACCTTTAGCGA
6687784 CGCTTTT
1 CGCTTTT
6687791 TTCAGCTAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
85 57 0.72
86 22 0.28
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (86 bp):
CGCTTTTCCCACAAACGCCACTATAGATCAGGACCTTTAGCGACACTTTTCCCACAAACGCCGCT
ATAAATCAGAACCTTTAGCGA
Found at i:6691435 original size:22 final size:21
Alignment explanation
Indices: 6691373--6691436 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
6691363 CTTAAGTACT
* * *
6691373 AAATTAAAAAAATCAAACACC
1 AAATTAAAAAAATAAAATAAC
**
6691394 AAATTAAAAAAATTTTAATAAC
1 AAATTAAAAAAA-TAAAATAAC
6691416 AAATTAGAAAAAATAAAATAA
1 AAATTA-AAAAAATAAAATAA
6691437 TTAAAAGTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 12 0.34
22 17 0.49
23 6 0.17
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.22
Consensus pattern (21 bp):
AAATTAAAAAAATAAAATAAC
Found at i:6691612 original size:5 final size:5
Alignment explanation
Indices: 6691602--6691628 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6691592 ATAATTATTT
6691602 TTATA TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TT
6691629 GATTGGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:6694197 original size:7 final size:7
Alignment explanation
Indices: 6694187--6694238 Score: 79
Period size: 7 Copynumber: 7.6 Consensus size: 7
6694177 CACTAACTCT
6694187 TAACCCC
1 TAACCCC
6694194 TAACCCC
1 TAACCCC
6694201 TAACCCC
1 TAACCCC
*
6694208 AAACCCC
1 TAACCCC
6694215 TAACCCC
1 TAACCCC
6694222 TAA-CCC
1 TAACCCC
*
6694228 TAACCCA
1 TAACCCC
6694235 TAAC
1 TAAC
6694239 TACTAACCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
6 6 0.15
7 35 0.85
ACGTcount: A:0.35, C:0.52, G:0.00, T:0.13
Consensus pattern (7 bp):
TAACCCC
Found at i:6694315 original size:7 final size:7
Alignment explanation
Indices: 6694290--6694341 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 7
6694280 ACTAATTAAT
*
6694290 CTAAACC
1 CTAACCC
6694297 CTAA-CC
1 CTAACCC
* *
6694303 CAAATCC
1 CTAACCC
*
6694310 CTAATCC
1 CTAACCC
6694317 CTAACCC
1 CTAACCC
6694324 CTAACCC
1 CTAACCC
6694331 CTAACCC
1 CTAACCC
6694338 CTAA
1 CTAA
6694342 ATCACAACCC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
6 5 0.12
7 36 0.88
ACGTcount: A:0.35, C:0.48, G:0.00, T:0.17
Consensus pattern (7 bp):
CTAACCC
Found at i:6694859 original size:41 final size:41
Alignment explanation
Indices: 6694780--6694930 Score: 205
Period size: 41 Copynumber: 3.7 Consensus size: 41
6694770 AAACGTTTTT
* *
6694780 GCGGTGCTTTTTCAAAAACGCCGCTAAAGCCCTA-AGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCC-AGAGCATTA
* **
6694821 GCGGCGCTTCTTGGAAAACGCCGCTAAAACCCAGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCAGAGCATTA
* * * *
6694862 GTGGCGCTTTTTCAAAAACACCGCTAAAAGCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCAGAGCATTA
6694903 GCGGCGCTTTTTCAAAAACGCCGCTAAA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAA
6694931 GCCCCGAAAG
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
40 1 0.01
41 94 0.99
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCAGAGCATTA
Found at i:6695060 original size:40 final size:40
Alignment explanation
Indices: 6694970--6695103 Score: 126
Period size: 40 Copynumber: 3.4 Consensus size: 40
6694960 GGCTTAGGTT
* ** * * *
6694970 TTTAGCGGCGTTTTTCAAAAAAACGCCGCTAATGC-TCATT
1 TTTAGCGGCGTTTTAC-TGAAAGCGCCGCTAATGCTTGATC
* * * *
6695010 TTTGGTGGCGTTTTCCTGAAAGCGCCGCTAATGCTTGGTC
1 TTTAGCGGCGTTTTACTGAAAGCGCCGCTAATGCTTGATC
* * *
6695050 TTTAGCGGCGTTTTATTTAAAGCGCCGCTAATGCTTGATT
1 TTTAGCGGCGTTTTACTGAAAGCGCCGCTAATGCTTGATC
*
6695090 TTTAGCGGTGTTTT
1 TTTAGCGGCGTTTT
6695104 TTATCCAAAC
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
39 15 0.20
40 61 0.80
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (40 bp):
TTTAGCGGCGTTTTACTGAAAGCGCCGCTAATGCTTGATC
Found at i:6696250 original size:20 final size:21
Alignment explanation
Indices: 6696225--6696270 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
6696215 GAGCAAGTAT
6696225 AAAAAAATTGAGAAAATA-CA
1 AAAAAAATTGAGAAAATACCA
*
6696245 AAAAAAATTGAGAAGATACCA
1 AAAAAAATTGAGAAAATACCA
6696266 AAAAA
1 AAAAA
6696271 TGTGAGGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.70, C:0.07, G:0.11, T:0.13
Consensus pattern (21 bp):
AAAAAAATTGAGAAAATACCA
Found at i:6696385 original size:20 final size:20
Alignment explanation
Indices: 6696362--6696418 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
6696352 AAGTGAATAT
6696362 ACCAAAAAAAATGAGGACAA
1 ACCAAAAAAAATGAGGACAA
* * * *
6696382 ACCAATAAACATGAGGAGAT
1 ACCAAAAAAAATGAGGACAA
6696402 ACCAAAAAAATATGAGG
1 ACCAAAAAAA-ATGAGG
6696419 GAATATAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 24 0.80
21 6 0.20
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.11
Consensus pattern (20 bp):
ACCAAAAAAAATGAGGACAA
Found at i:6696418 original size:21 final size:21
Alignment explanation
Indices: 6696360--6696438 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 21
6696350 AAAAGTGAAT
*
6696360 ATACCAAAAAAA-ATGAGGAC
1 ATACCAAAAAAATATGAGGAG
* * *
6696380 AAACC-AATAAACATGAGGAG
1 ATACCAAAAAAATATGAGGAG
6696400 ATACCAAAAAAATATGAGG-G
1 ATACCAAAAAAATATGAGGAG
**
6696420 AATATAAAAAAAATATGAG
1 -ATACCAAAAAAATATGAG
6696439 ATGTGCCAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.10
20 16 0.33
21 27 0.56
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.14
Consensus pattern (21 bp):
ATACCAAAAAAATATGAGGAG
Found at i:6697402 original size:17 final size:17
Alignment explanation
Indices: 6697359--6697404 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
6697349 GCTTTTAAAG
*
6697359 ATATC-AAAATTATAAA
1 ATATCAAAAATTAGAAA
*
6697375 ATTAT-ATAAATTAGAAA
1 A-TATCAAAAATTAGAAA
6697392 ATATCAAAAATTA
1 ATATCAAAAATTA
6697405 TGAGAGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (17 bp):
ATATCAAAAATTAGAAA
Found at i:6699702 original size:18 final size:18
Alignment explanation
Indices: 6699677--6699720 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
6699667 GCTTGTAGAC
*
6699677 GATGGTTGGTCTGTGGAT
1 GATGGTTGGCCTGTGGAT
*
6699695 GGTGGTTGGCCTGTGGAT
1 GATGGTTGGCCTGTGGAT
6699713 GATGGTTG
1 GATGGTTG
6699721 TGGAGGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.09, C:0.07, G:0.48, T:0.36
Consensus pattern (18 bp):
GATGGTTGGCCTGTGGAT
Found at i:6702612 original size:30 final size:30
Alignment explanation
Indices: 6702578--6702675 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
6702568 AAAAATGTAG
6702578 TTTTTAAAGGATTAAATTAAAATTTTATCC
1 TTTTTAAAGGATTAAATTAAAATTTTATCC
* * * **
6702608 TTTTTAAAGGGGTCAAAGTGTAATTTTAT-C
1 TTTTTAAA-GGATTAAATTAAAATTTTATCC
* *** *
6702638 TTTTTTAATTTTTAATTTTAAAATTTTATCC
1 TTTTTAAAGGATTAA-ATTAAAATTTTATCC
6702669 TTTTTAA
1 TTTTTAA
6702676 GGGGGTGGGG
Statistics
Matches: 50, Mismatches: 15, Indels: 5
0.71 0.21 0.07
Matches are distributed among these distances:
29 3 0.06
30 25 0.50
31 22 0.44
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (30 bp):
TTTTTAAAGGATTAAATTAAAATTTTATCC
Found at i:6705004 original size:115 final size:114
Alignment explanation
Indices: 6704542--6705391 Score: 1362
Period size: 114 Copynumber: 7.4 Consensus size: 114
6704532 GTTTACTTGT
*
6704542 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCATTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* * *
6704607 GCTTATGAAAAAACGCCGCTAAAGCACATAATTAGCGACGCCTT-TATAA
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATA-AA
* * *
6704656 AAGCGCCGCAAAATATCTTAACCAAAATGCAGTGCTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* *** *
6704721 GCTTATG-AAAAACGCCACTAAAGCACGGAATTAGCAGCGCATTATAAA
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAA
* *
6704769 AAGCGCCGTAAAATATCTTAACCAAAACGCAGCATTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* *
6704834 GCTTATGAAAAAATGCCGCTAAAGCACAGCATTAGCGGCGCATTATAAA
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAA
6704883 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTTAGAATTAGTGG
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATA-TTAGAATTAGTGG
* * *
6704948 CGCTTATGAGAAAACGTCGCTAAAGCACATCATTAGCGGAGCATTATAAA
65 CGCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAA
* *
6704998 AAGCGCCGCAAAATATCTTAACCAAAATGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* * *
6705063 GCTTATGAGAAAACGCCGCTAAAGCACATCATTTGCGGCGTATTATAAA
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAA
*
6705112 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTTAAAATTAGTGG
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATA-TTAGAATTAGTGG
* * *
6705177 CGCTTATGAAAAAATGCCACTAAAGCACATCATTAGCGGCGTATTATAAA
65 CGCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAA
* * *
6705227 AAGCGCCGCAAAATATCTTAACCAGAACGCAGCGTTTTGTCTTGATGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* *
6705292 GCTTATGAGAAAATGCCGCTAAAGCACATCATTAGCGGCGCATTATAAA
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAA
6705341 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATA
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATA
6705392 GAGCCCATAG
Statistics
Matches: 682, Mismatches: 50, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
113 99 0.15
114 370 0.54
115 213 0.31
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (114 bp):
AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAA
Found at i:6705083 original size:229 final size:228
Alignment explanation
Indices: 6704542--6705391 Score: 1380
Period size: 229 Copynumber: 3.7 Consensus size: 228
6704532 GTTTACTTGT
6704542 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCATTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCATTTGGTCTTGAGGTATATTAGAATTAGTGGC
* * *
6704607 GCTTATGAAAAAACGCCGCTAAAGCACATAATTAGCGACGCCTT-TATAAAAGCGCCGCAAAATA
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATA-AAAAGCGCCGCAAAATA
* * *
6704671 TCTTAACCAAAATGCAGTGCTTGGTCTTGAGGTATA-TTAGAATTAGTGGCGCTTATGAAAAACG
130 TCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTTAGAATTAGTGGCGCTTATGAAAAACG
*** *
6704735 CCACTAAAGCACGGAATTAGCAGCGCATTATAAA
195 CCACTAAAGCACATCATTAGCGGCGCATTATAAA
*
6704769 AAGCGCCGTAAAATATCTTAACCAAAACGCAGCATTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCATTTGGTCTTGAGGTATATTAGAATTAGTGGC
* *
6704834 GCTTATGAAAAAATGCCGCTAAAGCACAGCATTAGCGGCGCATTATAAAAAGCGCCGCAAAATAT
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAAAAGCGCCGCAAAATAT
6704899 CTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTTAGAATTAGTGGCGCTTATGAGAAAACG
131 CTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTTAGAATTAGTGGCGCTTATGA-AAAACG
* * *
6704964 TCGCTAAAGCACATCATTAGCGGAGCATTATAAA
195 CCACTAAAGCACATCATTAGCGGCGCATTATAAA
* * *
6704998 AAGCGCCGCAAAATATCTTAACCAAAATGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCATTTGGTCTTGAGGTATATTAGAATTAGTGGC
* * *
6705063 GCTTATGAGAAAACGCCGCTAAAGCACATCATTTGCGGCGTATTATAAAAAGCGCCGCAAAATAT
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAAAAGCGCCGCAAAATAT
* *
6705128 CTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTTAAAATTAGTGGCGCTTATGAAAAAATG
131 CTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTTAGAATTAGTGGCGCTTATG-AAAAACG
*
6705193 CCACTAAAGCACATCATTAGCGGCGTATTATAAA
195 CCACTAAAGCACATCATTAGCGGCGCATTATAAA
* * * *
6705227 AAGCGCCGCAAAATATCTTAACCAGAACGCAGCGTTTTGTCTTGATGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCATTTGGTCTTGAGGTATATTAGAATTAGTGGC
* *
6705292 GCTTATGAGAAAATGCCGCTAAAGCACATCATTAGCGGCGCATTATAAAAAGCGCCGCAAAATAT
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAAAAGCGCCGCAAAATAT
6705357 CTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATA
131 CTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATA
6705392 GAGCCCATAG
Statistics
Matches: 582, Mismatches: 37, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
227 153 0.26
228 24 0.04
229 404 0.69
230 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (228 bp):
AAGCGCCGCAAAATATCTTAACCAAAACGCAGCATTTGGTCTTGAGGTATATTAGAATTAGTGGC
GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAAAAGCGCCGCAAAATAT
CTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTTAGAATTAGTGGCGCTTATGAAAAACGC
CACTAAAGCACATCATTAGCGGCGCATTATAAA
Found at i:6706132 original size:21 final size:22
Alignment explanation
Indices: 6706100--6706142 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
6706090 TTGTTGTTTG
*
6706100 TGGTTTACGGGTTTAATATTTA
1 TGGTTTACGGGTTTAAGATTTA
6706122 TGGTTTA-GGGTTTAAGATTTA
1 TGGTTTACGGGTTTAAGATTTA
6706143 GGATTAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.23, C:0.02, G:0.26, T:0.49
Consensus pattern (22 bp):
TGGTTTACGGGTTTAAGATTTA
Found at i:6706248 original size:7 final size:7
Alignment explanation
Indices: 6706238--6706269 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
6706228 AAGTTTTACA
6706238 GTTTGGG
1 GTTTGGG
6706245 GTTTGGG
1 GTTTGGG
*
6706252 GTTTAGG
1 GTTTGGG
6706259 GTTTGGG
1 GTTTGGG
6706266 GTTT
1 GTTT
6706270 AAGATTTACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.03, C:0.00, G:0.50, T:0.47
Consensus pattern (7 bp):
GTTTGGG
Found at i:6706282 original size:21 final size:21
Alignment explanation
Indices: 6706223--6706282 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
6706213 ACGGGTTCAA
* *
6706223 GGTTTAAGTTTTACAGTTTGG
1 GGTTTAAGATTTACGGTTTGG
** * *
6706244 GGTTTGGGGTTTAGGGTTTGG
1 GGTTTAAGATTTACGGTTTGG
6706265 GGTTTAAGATTTACGGTT
1 GGTTTAAGATTTACGGTT
6706283 AAGGCTTACA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.15, C:0.03, G:0.37, T:0.45
Consensus pattern (21 bp):
GGTTTAAGATTTACGGTTTGG
Found at i:6706428 original size:15 final size:16
Alignment explanation
Indices: 6706408--6706441 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
6706398 TATTTTAGAC
*
6706408 TATAAATGTAAA-TAA
1 TATAAATATAAATTAA
6706423 TATAAATATAAATTAA
1 TATAAATATAAATTAA
6706439 TAT
1 TAT
6706442 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
TATAAATATAAATTAA
Found at i:6706682 original size:21 final size:20
Alignment explanation
Indices: 6706642--6706679 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6706632 AATATATTGA
*
6706642 TGTATTTATTTTTTAAAATG
1 TGTAATTATTTTTTAAAATG
6706662 TGTAATTATTTTTTAAAA
1 TGTAATTATTTTTTAAAA
6706680 ATGCATTACT
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:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
TGTAATTATTTTTTAAAATG
Found at i:6707003 original size:23 final size:23
Alignment explanation
Indices: 6706977--6707025 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
6706967 TAAGTTTTAC
**
6706977 ATAAATGGTGTTGTTTTTTATAT
1 ATAAATGGTGGCGTTTTTTATAT
* *
6707000 ATAAGTTGTGGCGTTTTTTATAT
1 ATAAATGGTGGCGTTTTTTATAT
6707023 ATA
1 ATA
6707026 CGTTTTACCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.02, G:0.18, T:0.53
Consensus pattern (23 bp):
ATAAATGGTGGCGTTTTTTATAT
Found at i:6707237 original size:13 final size:12
Alignment explanation
Indices: 6707199--6707238 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
6707189 AGCCAAAAAT
*
6707199 CCCTCAGTTTTC
1 CCCTCAATTTTC
*
6707211 CCCTCAAATTTC
1 CCCTCAATTTTC
6707223 CCCTCCAATTTTC
1 CCCT-CAATTTTC
6707236 CCC
1 CCC
6707239 AAAATTCCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.15, C:0.47, G:0.03, T:0.35
Consensus pattern (12 bp):
CCCTCAATTTTC
Found at i:6708378 original size:26 final size:26
Alignment explanation
Indices: 6708342--6708400 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
6708332 CTCGTTGCAT
*
6708342 AATAATTCTTACTCTATAGCTTATCA
1 AATAATTCTTACTCTATAGCTTATAA
6708368 AATAATTCTTACTCTATAGCTTATAA
1 AATAATTCTTACTCTATAGCTTATAA
6708394 AATAATT
1 AATAATT
6708401 AAATTGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.39, C:0.15, G:0.03, T:0.42
Consensus pattern (26 bp):
AATAATTCTTACTCTATAGCTTATAA
Done.