Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 185 of 199
Found at i:53947939 original size:28 final size:27
Alignment explanation
Indices: 53947905--53947975 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 27
53947895 TAGTAATAAT
53947905 AAAATTATATTT-TCTTTTAATAAA-TATA
1 AAAATTA-ATTTAT-TTTTAA-AAATTATA
53947933 AAAATTAATTTAATTTTTAAAAATTATA
1 AAAATTAATTT-ATTTTTAAAAATTATA
*
53947961 AAAATATAAATTATT
1 AAAAT-TAATTTATT
53947976 AAAATAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 7 0.18
28 25 0.66
29 6 0.16
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
AAAATTAATTTATTTTTAAAAATTATA
Found at i:53947971 original size:15 final size:17
Alignment explanation
Indices: 53947952--53947992 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
53947942 TTAATTTTTA
53947952 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
53947968 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
53947984 AAAATTATA
1 AAAATTATA
53947993 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:53969615 original size:2 final size:2
Alignment explanation
Indices: 53969610--53969637 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53969600 AAGTACATAA
53969610 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53969638 GTTTTTGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53970431 original size:41 final size:39
Alignment explanation
Indices: 53970386--53970532 Score: 147
Period size: 41 Copynumber: 3.6 Consensus size: 39
53970376 GGTTCTGTAC
53970386 CTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAA-TAATTCAGACTTTA-GT
*
53970427 CTAGCAGGCTTAATGCCGGTG-ATACATTTCAGACTATATGT
1 CTAGCAGGCTTAATGCCGGTGAATA-A-TTCAGACTTTA-GT
* * *
53970468 CTAGCAGGC-TAAGTGCCGGTGTACTAAATCAGGCTTT-GAT
1 CTAGCAGGCTTAA-TGCCGGTG-AATAATTCAGACTTTAG-T
*
53970508 CCTAGCAGGCTAAATGCCGGTGAAT
1 -CTAGCAGGCTTAATGCCGGTGAAT
53970533 CTGTTTAAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 17
0.78 0.07 0.15
Matches are distributed among these distances:
39 3 0.03
40 8 0.09
41 74 0.82
42 3 0.03
43 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (39 bp):
CTAGCAGGCTTAATGCCGGTGAATAATTCAGACTTTAGT
Found at i:53976059 original size:30 final size:31
Alignment explanation
Indices: 53976016--53976082 Score: 111
Period size: 30 Copynumber: 2.2 Consensus size: 31
53976006 TTTCTTATGC
*
53976016 CAATATTTCGATACCCATATCTTTGACTTTT
1 CAATAATTCGATACCCATATCTTTGACTTTT
53976047 CAATAATT-GATACCCATATCTTTGACTTTT
1 CAATAATTCGATACCCATATCTTTGACTTTT
53976077 C-ATAAT
1 CAATAAT
53976083 ATAGATGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 5 0.14
30 23 0.66
31 7 0.20
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (31 bp):
CAATAATTCGATACCCATATCTTTGACTTTT
Found at i:53979031 original size:70 final size:67
Alignment explanation
Indices: 53978933--53979219 Score: 321
Period size: 70 Copynumber: 4.2 Consensus size: 67
53978923 AAGCACTTGA
* *
53978933 AAAAGTAAAAGAATAAATAAATATATAAATTGATAAATCAAATATAAATAATATTGAATTTAAAT
1 AAAAGTAAAAGAA-AAATAAATA-ATAAATAGATAAAACAAATATAAATAATATT-AATTTAAAT
*
53978998 GTTTT
63 ATTTT
* * * **
53979003 AAAAGTAAAAGAACAAATAAGTGAATAAATAGATAAAACAAATATAAACAATATTAAATGTAAGC
1 AAAAGTAAAAGAA-AAATAAAT-AATAAATAGATAAAACAAATATAAATAATATT-AATTTAAAT
*
53979068 ATTTA
63 ATTTT
* * *
53979073 AAAAGTAAAAGAATAAT-AA-AA-AAATAGATAAAATAAATATACATAATATTCAATTTAAATAT
1 AAAAGTAAAAGAAAAATAAATAATAAATAGATAAAACAAATATAAATAATATT-AATTTAAATAT
53979135 TTT
65 TTT
** *
53979138 AAAAGTAAAAGAATGATAAATAAATAAATTGATAAAACAAATATAAATAATATTACATTTAAATA
1 AAAAGTAAAAGAAAAATAAAT-AATAAATAGATAAAACAAATATAAATAATATTA-ATTTAAATA
53979203 -TTT
64 TTTT
53979206 AAAAGATAAAAGAA
1 AAAAG-TAAAAGAA
53979220 TAATGAACAA
Statistics
Matches: 185, Mismatches: 25, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
65 52 0.28
66 4 0.02
68 12 0.06
69 46 0.25
70 70 0.38
71 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (67 bp):
AAAAGTAAAAGAAAAATAAATAATAAATAGATAAAACAAATATAAATAATATTAATTTAAATATT
TT
Found at i:53979188 original size:69 final size:69
Alignment explanation
Indices: 53978933--53979354 Score: 367
Period size: 69 Copynumber: 6.3 Consensus size: 69
53978923 AAGCACTTGA
* * * *
53978933 AAAAGTAAAAGAATAAATAAATATATAAATTGATAAATCAAATATAAATAATATTGAATTTAAAT
1 AAAAGTAAAAGAAT-AATAAATAAATAAATAGATAAAACAAATATAAATAATATTAAATTTAAAT
*
53978998 GTTTT
65 ATTTT
* * * * * **
53979003 AAAAGTAAAAGAACAAATAAGTGAATAAATAGATAAAACAAATATAAACAATATTAAATGTAAGC
1 AAAAGTAAAAGAA-TAATAAATAAATAAATAGATAAAACAAATATAAATAATATTAAATTTAAAT
*
53979068 ATTTA
65 ATTTT
* * *
53979073 AAAAGTAAAAGAATAAT--A-AAA-AAATAGATAAAATAAATATACATAATATTCAATTTAAATA
1 AAAAGTAAAAGAATAATAAATAAATAAATAGATAAAACAAATATAAATAATATTAAATTTAAATA
53979134 TTTT
66 TTTT
* * *
53979138 AAAAGTAAAAGAATGATAAATAAATAAATTGATAAAACAAATATAAATAATATTACATTTAAATA
1 AAAAGTAAAAGAATAATAAATAAATAAATAGATAAAACAAATATAAATAATATTAAATTTAAATA
53979203 -TTT
66 TTTT
* * * * * * * * **
53979206 AAAAGATAAAAGAATAATGAACAAATAAGTAAATATAATAGATATGAATAATATTAAATTTAGGT
1 AAAAG-TAAAAGAATAATAAATAAATAAATAGATAAAACAAATATAAATAATATTAAATTTAAAT
53979271 A-TTT
65 ATTTT
* ** *
53979275 -AAA--AAAAG---AAT-GATAAAT--AT--ATAAAACAAATATAAATAATATTAGCTTTAGATA
1 AAAAGTAAAAGAATAATAAATAAATAAATAGATAAAACAAATATAAATAATATTAAATTTAAATA
*
53979329 TTTA
66 TTTT
* *
53979333 AAAAAT-GAAGAATAATAAATAA
1 AAAAGTAAAAGAATAATAAATAA
53979355 GTTAACATAT
Statistics
Matches: 282, Mismatches: 56, Indels: 34
0.76 0.15 0.09
Matches are distributed among these distances:
57 27 0.10
58 2 0.01
59 4 0.01
60 3 0.01
61 5 0.02
62 3 0.01
63 3 0.01
64 4 0.01
65 57 0.20
66 2 0.01
67 1 0.00
68 14 0.05
69 88 0.31
70 69 0.24
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (69 bp):
AAAAGTAAAAGAATAATAAATAAATAAATAGATAAAACAAATATAAATAATATTAAATTTAAATA
TTTT
Found at i:53979219 original size:134 final size:135
Alignment explanation
Indices: 53978933--53979351 Score: 381
Period size: 134 Copynumber: 3.2 Consensus size: 135
53978923 AAGCACTTGA
* * *
53978933 AAAAG-TAAAAGAATAAATAAATATATAAATTGAT-AAATCAAATATAAATAATATTGAATTTAA
1 AAAAGATAAAAGAAT-AATAAACA-A-AAATAGATAAAAT-AAATAT-AATAATATTAAATTTAA
* ** * * * * *
53978996 ATGTTTTAAAAGTAAAAGAACAAATAAGTGAATAAATAGATAAAACAAATATAAACAATATTAAA
61 ATATTTTAAAAGTAAAAGAA-TGATAAATAAATAAATTGATAAAACAAATATAAATAATATTACA
* **
53979061 TGTAAGCATTT
125 TTTAAATATTT
*
53979072 AAAA-AGTAAAAGAATAAT-AA-AAAAATAGATAAAATAAATATACATAATATTCAATTTAAATA
1 AAAAGA-TAAAAGAATAATAAACAAAAATAGATAAAATAAATATA-ATAATATTAAATTTAAATA
53979134 TTTTAAAAGTAAAAGAATGATAAATAAATAAATTGATAAAACAAATATAAATAATATTACATTTA
64 TTTTAAAAGTAAAAGAATGATAAATAAATAAATTGATAAAACAAATATAAATAATATTACATTTA
53979199 AATATTT
129 AATATTT
* * * * **
53979206 AAAAGATAAAAGAATAATGAACAAATAAGTAAATATAATAGATATGAATAATATTAAATTTAGGT
1 AAAAGATAAAAGAATAATAAACAAA-AA-TAGATAAAATAAATAT-AATAATATTAAATTTAAAT
53979271 A-TTT-AAA--AAAAGAATG----ATAAAT--A-T-ATAAAACAAATATAAATAATATTAGC-TT
63 ATTTTAAAAGTAAAAGAATGATAAATAAATAAATTGATAAAACAAATATAAATAATATTA-CATT
*
53979323 TAGATATTT
127 TAAATATTT
* *
53979332 AAAAAAT-GAAGAATAATAAA
1 AAAAGATAAAAGAATAATAAA
53979352 TAAGTTAACA
Statistics
Matches: 246, Mismatches: 23, Indels: 36
0.81 0.08 0.12
Matches are distributed among these distances:
125 11 0.04
126 40 0.16
127 2 0.01
128 1 0.00
130 6 0.02
134 71 0.29
135 50 0.20
136 11 0.04
137 6 0.02
138 31 0.13
139 8 0.03
140 9 0.04
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (135 bp):
AAAAGATAAAAGAATAATAAACAAAAATAGATAAAATAAATATAATAATATTAAATTTAAATATT
TTAAAAGTAAAAGAATGATAAATAAATAAATTGATAAAACAAATATAAATAATATTACATTTAAA
TATTT
Found at i:53979371 original size:57 final size:57
Alignment explanation
Indices: 53979247--53979354 Score: 139
Period size: 57 Copynumber: 1.9 Consensus size: 57
53979237 AATATAATAG
* * *
53979247 ATATGAATAATATTAAATTTAGGTATTTAAAAAAAGAATGATAAATATATAAAACAA
1 ATATAAATAATATTAAATTTAGATATTTAAAAAAAGAATGATAAATAAATAAAACAA
** *
53979304 ATATAAATAATATTAGCTTTAGATATTTAAAAAATGAA-GA-ATAATAAATAA
1 ATATAAATAATATTAAATTTAGATATTTAAAAAAAGAATGATA-AATAAATAA
53979355 GTTAACATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
55 1 0.02
56 10 0.23
57 33 0.75
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.32
Consensus pattern (57 bp):
ATATAAATAATATTAAATTTAGATATTTAAAAAAAGAATGATAAATAAATAAAACAA
Found at i:53983782 original size:9 final size:9
Alignment explanation
Indices: 53983745--53983790 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
53983735 GGTTGCAAAA
53983745 AGGACGATG
1 AGGACGATG
*
53983754 ACGACGATG
1 AGGACGATG
*
53983763 ACGACGATG
1 AGGACGATG
53983772 AGGACGATG
1 AGGACGATG
*
53983781 AGGATGATG
1 AGGACGATG
53983790 A
1 A
53983791 TGTTTCTTCG
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:0.35, C:0.13, G:0.39, T:0.13
Consensus pattern (9 bp):
AGGACGATG
Found at i:53985522 original size:13 final size:13
Alignment explanation
Indices: 53985504--53985528 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53985494 TTTGTTTGTT
53985504 TTGGGCTTGTAAG
1 TTGGGCTTGTAAG
53985517 TTGGGCTTGTAA
1 TTGGGCTTGTAA
53985529 TATTTGGTCT
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:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (13 bp):
TTGGGCTTGTAAG
Found at i:53985978 original size:96 final size:96
Alignment explanation
Indices: 53985868--53986099 Score: 277
Period size: 96 Copynumber: 2.4 Consensus size: 96
53985858 TGTTATCTTC
* * * * *
53985868 AATCTACTACACTGCAACTCCATGGAAATAAGATTCGCT-ATCTTCAATCTGCTCCACTAAAACT
1 AATCTATTCCACTGCAACTCCAGGGAAATAAGATT-GATAATATTCAATCTGCTCCACTAAAACT
* *
53985932 TTAGGGAGATAAAATTTGTAACTTGTAGCTTT
65 TCAGGGAGATAAAATTTATAACTTGTAGCTTT
* * * * **
53985964 AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTATAATATTCAATTTGCTCCACTGTAACTT
1 AATCTATTCCACTGCAACTCCAGGGAAATAAGATTGATAATATTCAATCTGCTCCACTAAAACTT
*
53986029 CAGGGAGATAAGATTTATAACTTGTAGCTTT
66 CAGGGAGATAAAATTTATAACTTGTAGCTTT
* ** * *
53986060 AATCTATTCCACTACAACTTGAGGGAAATAAAATTTATAA
1 AATCTATTCCACTGCAACTCCAGGGAAATAAGATTGATAA
53986100 CTTGTAGCTT
Statistics
Matches: 117, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
95 1 0.01
96 116 0.99
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (96 bp):
AATCTATTCCACTGCAACTCCAGGGAAATAAGATTGATAATATTCAATCTGCTCCACTAAAACTT
CAGGGAGATAAAATTTATAACTTGTAGCTTT
Found at i:53985989 original size:51 final size:51
Alignment explanation
Indices: 53985913--53986241 Score: 270
Period size: 51 Copynumber: 6.7 Consensus size: 51
53985903 CGCTATCTTC
* * * * * *
53985913 AATCTGCTCCACTAAAACTTTAGGGAGATAAAATTTGTAACTTGTAGCTTT
1 AATCTGTTCCACTACAACTTCAGGGAAATAAGATTTATAACTTGTAGCTTT
* *
53985964 AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTATAA----TA--TTC
1 AATCTGTTCCACTACAACTTCAGGGAAATAAGATTTATAACTTGTAGCTTT
* * ** *
53986009 AATTTGCTCCACTGTAACTTCAGGGAGATAAGATTTATAACTTGTAGCTTT
1 AATCTGTTCCACTACAACTTCAGGGAAATAAGATTTATAACTTGTAGCTTT
* * *
53986060 AATCTATTCCACTACAACTTGAGGGAAATAAAATTTATAACTTGTAGCTTT
1 AATCTGTTCCACTACAACTTCAGGGAAATAAGATTTATAACTTGTAGCTTT
* * * ** * *
53986111 AATCTATTCCACTACAACTTCAAGAAAATAAGA--T-TCGC-TATA--TTC
1 AATCTGTTCCACTACAACTTCAGGGAAATAAGATTTATAACTTGTAGCTTT
* * * * * *
53986156 AAACTGCTCCAATGCAACTTTA-GGAAGATAAGATTTGTAACTTGTAGCTTT
1 AATCTGTTCCACTACAACTTCAGGGAA-ATAAGATTTATAACTTGTAGCTTT
* * *
53986207 AATCTATTCCACTATAACTTCAGAGAAATAAGATT
1 AATCTGTTCCACTACAACTTCAGGGAAATAAGATT
53986242 CGCATCTTCA
Statistics
Matches: 216, Mismatches: 48, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
44 3 0.01
45 62 0.29
47 6 0.03
48 4 0.02
49 6 0.03
51 132 0.61
52 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (51 bp):
AATCTGTTCCACTACAACTTCAGGGAAATAAGATTTATAACTTGTAGCTTT
Found at i:53986112 original size:147 final size:147
Alignment explanation
Indices: 53985762--53986237 Score: 441
Period size: 147 Copynumber: 3.3 Consensus size: 147
53985752 GGTATAGGAA
* * * ** * * * *
53985762 TTGTCGCTTTAATCTGTTCTACTGCAACTTTAGAGAGATAAAATTTATAACTCGTAGCTTTAATC
1 TTGTAGCTTTAATCTATTCCACTAAAACTTCAGGGAAATAAAATTTATAACTTGTAGCTTTAATC
* ** * * * * * * * * *
53985827 TGTTTTACTACAAC-TCTAGAAAAATAAGATTTGTTATCTTCAATCTACTACACTGCAACTCCAT
66 TATTCCACTACAACTTCAAG-AAAATAAGATTCGATATATTCAAACTGCTCCAATGCAACTTCA-
53985891 GGAA-ATAAGA--T-T--C
129 GGAAGATAAGATTTATAAC
* * ** * * *
53985904 --GCTATCTTCAATCTGCTCCACTAAAACTTTAGGGAGATAAAATTTGTAACTTGTAGCTTTAAT
1 TTG-TAGCTTTAATCTATTCCACTAAAACTTCAGGGAAATAAAATTTATAACTTGTAGCTTTAAT
* * * * * ** * *
53985967 CTGTTCCACTGCAACTTCAGGGAAATAAGATT-TATAATATTCAATTTGCTCCACTGTAACTTCA
65 CTATTCCACTACAACTTCAAGAAAATAAGATTCGAT-ATATTCAAACTGCTCCAATGCAACTTCA
*
53986031 GGGAGATAAGATTTATAAC
129 GGAAGATAAGATTTATAAC
* *
53986050 TTGTAGCTTTAATCTATTCCACTACAACTTGAGGGAAATAAAATTTATAACTTGTAGCTTTAATC
1 TTGTAGCTTTAATCTATTCCACTAAAACTTCAGGGAAATAAAATTTATAACTTGTAGCTTTAATC
* *
53986115 TATTCCACTACAACTTCAAGAAAATAAGATTCGCTATATTCAAACTGCTCCAATGCAACTTTAGG
66 TATTCCACTACAACTTCAAGAAAATAAGATTCGATATATTCAAACTGCTCCAATGCAACTTCAGG
*
53986180 AAGATAAGATTTGTAAC
131 AAGATAAGATTTATAAC
* *
53986197 TTGTAGCTTTAATCTATTCCACTATAACTTCAGAGAAATAA
1 TTGTAGCTTTAATCTATTCCACTAAAACTTCAGGGAAATAA
53986238 GATTCGCATC
Statistics
Matches: 273, Mismatches: 49, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
140 5 0.02
141 101 0.37
142 3 0.01
143 1 0.00
144 1 0.00
146 1 0.00
147 159 0.58
148 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (147 bp):
TTGTAGCTTTAATCTATTCCACTAAAACTTCAGGGAAATAAAATTTATAACTTGTAGCTTTAATC
TATTCCACTACAACTTCAAGAAAATAAGATTCGATATATTCAAACTGCTCCAATGCAACTTCAGG
AAGATAAGATTTATAAC
Found at i:53986174 original size:96 final size:95
Alignment explanation
Indices: 53986074--53986286 Score: 295
Period size: 96 Copynumber: 2.2 Consensus size: 95
53986064 TATTCCACTA
* *
53986074 CAACTTGAGGGAAATAAAATTTATAACTTGTAGCTTTAATCTATTCCACTACAACTTCA-AGAAA
1 CAACTTCAGGGAAATAAGATTTATAACTTGTAGCTTTAATCTATTCCACTACAACTTCAGAG-AA
53986138 ATAAGATTCGCTATATTCAAACTGCTCCAATG
65 ATAAGATTCGC-ATATTCAAACTGCTCCAATG
* * *
53986170 CAACTTTA-GGAAGATAAGATTTGTAACTTGTAGCTTTAATCTATTCCACTATAACTTCAGAGAA
1 CAACTTCAGGGAA-ATAAGATTTATAACTTGTAGCTTTAATCTATTCCACTACAACTTCAGAGAA
* * *
53986234 ATAAGATTCGCATCTTCAATCTGCTCCACTG
65 ATAAGATTCGCATATTCAAACTGCTCCAATG
* *
53986265 CAAGTTCAGGGAGATAAGATTT
1 CAACTTCAGGGAAATAAGATTT
53986287 GTATATGTTA
Statistics
Matches: 104, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
95 36 0.35
96 66 0.63
97 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (95 bp):
CAACTTCAGGGAAATAAGATTTATAACTTGTAGCTTTAATCTATTCCACTACAACTTCAGAGAAA
TAAGATTCGCATATTCAAACTGCTCCAATG
Found at i:53992096 original size:9 final size:9
Alignment explanation
Indices: 53992082--53992166 Score: 125
Period size: 9 Copynumber: 9.4 Consensus size: 9
53992072 TTTGGTTAAA
53992082 AATTAACCG
1 AATTAACCG
53992091 AATTAACCG
1 AATTAACCG
53992100 AATTAACCG
1 AATTAACCG
*
53992109 AATTACCCG
1 AATTAACCG
*
53992118 AATTACCCG
1 AATTAACCG
53992127 AATTAACCG
1 AATTAACCG
*
53992136 AATTACCCG
1 AATTAACCG
*
53992145 AATTAACCA
1 AATTAACCG
*
53992154 AATTAACCA
1 AATTAACCG
53992163 AATT
1 AATT
53992167 GAATCACTAC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 71 1.00
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:53993025 original size:28 final size:29
Alignment explanation
Indices: 53992994--53993049 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
53992984 TTTGATTCCT
*
53992994 TTTAATAGTTCAAGGACTAA-TTGATCAA
1 TTTAATAGTACAAGGACTAATTTGATCAA
* *
53993022 TTTAATAGTAGAGGGACTAATTTGATCA
1 TTTAATAGTACAAGGACTAATTTGATCA
53993050 TGTATCTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (29 bp):
TTTAATAGTACAAGGACTAATTTGATCAA
Found at i:53999509 original size:31 final size:32
Alignment explanation
Indices: 53999471--53999536 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
53999461 TGTAGAGTCC
* * *
53999471 AAAAATTTTTTT-ACCAACTTTTATGAGACCT
1 AAAAATTTTTTTCACCAACTTGTAAGAAACCT
*
53999502 AAAAATTTTTTTCTCCAACTTGTAAGAAACCT
1 AAAAATTTTTTTCACCAACTTGTAAGAAACCT
53999534 AAA
1 AAA
53999537 CCCCCATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (32 bp):
AAAAATTTTTTTCACCAACTTGTAAGAAACCT
Found at i:54003677 original size:25 final size:25
Alignment explanation
Indices: 54003643--54003690 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
54003633 TCAATGGGGC
*
54003643 CTGCTAAACACAGTCTGCACAAAGT
1 CTGCCAAACACAGTCTGCACAAAGT
54003668 CTGCCAAACACAGTCTGCACAAA
1 CTGCCAAACACAGTCTGCACAAA
54003691 TGTCAACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.31, G:0.15, T:0.17
Consensus pattern (25 bp):
CTGCCAAACACAGTCTGCACAAAGT
Found at i:54007680 original size:27 final size:26
Alignment explanation
Indices: 54007650--54007716 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
54007640 AAACTCACCC
54007650 ATATTATTTTTTAAAAATATTTATATT
1 ATATTATTTTTTAAAAAT-TTTATATT
* * * *
54007677 ATATTAATATTTAATAATTTTTTATT
1 ATATTATTTTTTAAAAATTTTATATT
54007703 -TATTGAATTTTTTA
1 ATATT--ATTTTTTA
54007717 TATAATCATC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 4 0.12
26 7 0.22
27 21 0.66
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (26 bp):
ATATTATTTTTTAAAAATTTTATATT
Found at i:54007704 original size:15 final size:16
Alignment explanation
Indices: 54007684--54007722 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
54007674 ATTATATTAA
54007684 TATTTAAT-AATTTTT
1 TATTTAATGAATTTTT
*
54007699 TATTTATTGAATTTTT
1 TATTTAATGAATTTTT
*
54007715 TATATAAT
1 TATTTAAT
54007723 CATCTTAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TATTTAATGAATTTTT
Found at i:54009185 original size:2 final size:2
Alignment explanation
Indices: 54009178--54009203 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54009168 GCATGGTCTT
54009178 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
54009204 AATGCTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54009349 original size:33 final size:33
Alignment explanation
Indices: 54009306--54009373 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
54009296 AACTTTTTCG
54009306 GACATATTTTTTTTC-AATTCGGTACCTAAACTT
1 GACA-ATTTTTTTTCTAATTCGGTACCTAAACTT
* *
54009339 GACATTTTTTTTTCTAATTTGGTACCTAAACTT
1 GACAATTTTTTTTCTAATTCGGTACCTAAACTT
54009372 GA
1 GA
54009374 TAGTTTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 9 0.28
33 23 0.72
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.47
Consensus pattern (33 bp):
GACAATTTTTTTTCTAATTCGGTACCTAAACTT
Found at i:54016486 original size:40 final size:40
Alignment explanation
Indices: 54016415--54016491 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
54016405 TCCACGGCAT
* *
54016415 CTCTATACTTATGCTTAGCTAAAAATGTATGTTTGTACAC
1 CTCTATACTTATGCTTAGCTAAAAATATATGTATGTACAC
*
54016455 CTCTGTACTTATGCTTAGCTAAAGAA-ATATGTATGTA
1 CTCTATACTTATGCTTAGCTAAA-AATATATGTATGTA
54016492 TGTGTATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (40 bp):
CTCTATACTTATGCTTAGCTAAAAATATATGTATGTACAC
Found at i:54019486 original size:15 final size:15
Alignment explanation
Indices: 54019466--54019495 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54019456 TATTGGGAAG
54019466 GTCATGCTCTATTTC
1 GTCATGCTCTATTTC
54019481 GTCATGCTCTATTTC
1 GTCATGCTCTATTTC
54019496 ATGCTCGAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.13, T:0.47
Consensus pattern (15 bp):
GTCATGCTCTATTTC
Found at i:54022969 original size:24 final size:24
Alignment explanation
Indices: 54022942--54022995 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
54022932 AATCAAAGTC
* *
54022942 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
54022966 AAATTTATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
54022990 AAATAT
1 AAATAT
54022996 TCTAGAAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:54027387 original size:24 final size:24
Alignment explanation
Indices: 54027360--54027411 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54027350 AATCAAAGTC
* *
54027360 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
54027384 AAATATGTTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
54027408 AAAT
1 AAAT
54027412 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:54032031 original size:20 final size:20
Alignment explanation
Indices: 54032008--54032045 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54031998 CACTTTGCCC
54032008 CCTTAAAAATGATAAATAAT
1 CCTTAAAAATGATAAATAAT
* *
54032028 CCTTTAAAATTATAAATA
1 CCTTAAAAATGATAAATA
54032046 TATCAGCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
CCTTAAAAATGATAAATAAT
Found at i:54039988 original size:41 final size:41
Alignment explanation
Indices: 54039938--54040122 Score: 134
Period size: 41 Copynumber: 4.6 Consensus size: 41
54039928 TAAACTTTTC
* *
54039938 ATCCCAAGTATGATGCTTCTAAGTATAAGTTTAAATTGTTA
1 ATCCAAAGTATGATGCTTCTAAGCATAAGTTTAAATTGTTA
* ** * *
54039979 ATCCAAAGTATGATGCTTTTAAGCA-AGAGCATGATTTGTTA
1 ATCCAAAGTATGATGCTTCTAAGCATA-AGTTTAAATTGTTA
** * ** * * *
54040020 GCCCCAA--A--ATGC--AAAAGGCACAAGCTTAAAATT-TTC
1 ATCCAAAGTATGATGCTTCTAA-GCATAAG-TTTAAATTGTTA
*
54040056 ATCCAAAGTATGATGCTTCTAAGTATAAGTTTAAATTGTTA
1 ATCCAAAGTATGATGCTTCTAAGCATAAGTTTAAATTGTTA
*
54040097 ATCCAAAATATGATGCTTCTAAGCAT
1 ATCCAAAGTATGATGCTTCTAAGCAT
54040123 GAGGATGATT
Statistics
Matches: 104, Mismatches: 29, Indels: 22
0.67 0.19 0.14
Matches are distributed among these distances:
35 2 0.02
36 11 0.11
37 8 0.08
38 1 0.01
39 1 0.01
40 12 0.12
41 67 0.64
42 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (41 bp):
ATCCAAAGTATGATGCTTCTAAGCATAAGTTTAAATTGTTA
Found at i:54040131 original size:118 final size:118
Alignment explanation
Indices: 54039917--54040154 Score: 413
Period size: 118 Copynumber: 2.0 Consensus size: 118
54039907 CAACACTCTT
* *
54039917 AGGCACAAGCTTAAACTTTTCATCCCAAGTATGATGCTTCTAAGTATAAGTTTAAATTGTTAATC
1 AGGCACAAGCTTAAAATTTTCATCCAAAGTATGATGCTTCTAAGTATAAGTTTAAATTGTTAATC
* *
54039982 CAAAGTATGATGCTTTTAAGCAAGAGCATGATTTGTTAGCCCCAAAATGCAAA
66 CAAAATATGATGCTTCTAAGCAAGAGCATGATTTGTTAGCCCCAAAATGCAAA
54040035 AGGCACAAGCTTAAAATTTTCATCCAAAGTATGATGCTTCTAAGTATAAGTTTAAATTGTTAATC
1 AGGCACAAGCTTAAAATTTTCATCCAAAGTATGATGCTTCTAAGTATAAGTTTAAATTGTTAATC
* * *
54040100 CAAAATATGATGCTTCTAAGCATGAGGATGATTTGTTCGCCCCAAAATGCAAA
66 CAAAATATGATGCTTCTAAGCAAGAGCATGATTTGTTAGCCCCAAAATGCAAA
54040153 AG
1 AG
54040155 TGCATGAGCG
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 113 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (118 bp):
AGGCACAAGCTTAAAATTTTCATCCAAAGTATGATGCTTCTAAGTATAAGTTTAAATTGTTAATC
CAAAATATGATGCTTCTAAGCAAGAGCATGATTTGTTAGCCCCAAAATGCAAA
Found at i:54059084 original size:11 final size:11
Alignment explanation
Indices: 54059070--54059106 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
54059060 TACAATATTC
*
54059070 AAATAATAATA
1 AAATAATAGTA
54059081 AAATAATAGTA
1 AAATAATAGTA
*
54059092 ATATAATAGTA
1 AAATAATAGTA
54059103 AAAT
1 AAAT
54059107 GGTAGCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (11 bp):
AAATAATAGTA
Found at i:54072837 original size:43 final size:43
Alignment explanation
Indices: 54072789--54072934 Score: 188
Period size: 43 Copynumber: 3.4 Consensus size: 43
54072779 GTTTATGTGG
* *
54072789 AGAAGCGCTGCTAAAGATCATGTTCTTTAATGGCGTTTTTAGT
1 AGAAGCGCCGCTAAAGATCATGTTCTTTAGTGGCGTTTTTAGT
* * *
54072832 AGAAGCGCCGCTAAAGATCATGTTATTTAGCGACGTTTTTACG-
1 AGAAGCGCCGCTAAAGATCATGTTCTTTAGTGGCGTTTTTA-GT
* *
54072875 AGATGCGCCGCTAAA-AGTCATGTTCTATAGTGGCGTTTTTAGT
1 AGAAGCGCCGCTAAAGA-TCATGTTCTTTAGTGGCGTTTTTAGT
*
54072918 AGAAGCGTCGCTAAAGA
1 AGAAGCGCCGCTAAAGA
54072935 CCATATCAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
42 2 0.02
43 83 0.95
44 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (43 bp):
AGAAGCGCCGCTAAAGATCATGTTCTTTAGTGGCGTTTTTAGT
Found at i:54075254 original size:41 final size:41
Alignment explanation
Indices: 54075200--54075304 Score: 147
Period size: 41 Copynumber: 2.5 Consensus size: 41
54075190 AAAATTTTTT
*
54075200 ATTTTTTTAAATTTTAAAATACTTTTAAAATATTTTTTTTAA
1 ATTTTTTT-AATTTTAAAATACTTTTAAAATAATTTTTTTAA
* *
54075242 ATTTTTTTAATTTTAAAATATTTTTAAAATAATTTTTTTAT
1 ATTTTTTTAATTTTAAAATACTTTTAAAATAATTTTTTTAA
*
54075283 TTTTGTTTTAATTTTTAAAATA
1 ATTT-TTTTAA-TTTTAAAATA
54075305 AAATTTTGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
41 33 0.58
42 14 0.25
43 10 0.18
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (41 bp):
ATTTTTTTAATTTTAAAATACTTTTAAAATAATTTTTTTAA
Found at i:54075260 original size:17 final size:17
Alignment explanation
Indices: 54075222--54075268 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
54075212 TTTAAAATAC
54075222 TTTTAAAATA-TTTT--
1 TTTTAAAATATTTTTAA
*
54075236 TTTT-AAATTTTTTTAA
1 TTTTAAAATATTTTTAA
54075252 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
54075269 AATAATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 4 0.15
14 8 0.30
16 4 0.15
17 11 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:54075278 original size:30 final size:29
Alignment explanation
Indices: 54075222--54075286 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 29
54075212 TTTAAAATAC
*
54075222 TTTTAAAATATTTTTTTTAAATTTTTTTAA
1 TTTTAAAATA-TTTTTTAAAATTTTTTTAA
* *
54075252 TTTTAAAATATTTTTAAAATAATTTTTTTAT
1 TTTTAAAATATTTTT-TAA-AATTTTTTTAA
54075283 TTTT
1 TTTT
54075287 GTTTTAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 5 0.17
30 11 0.37
31 14 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTAAAATATTTTTTAAAATTTTTTTAA
Found at i:54076638 original size:2 final size:2
Alignment explanation
Indices: 54076631--54076681 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
54076621 TGTACACGTG
54076631 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54076673 TA TA T- TA TA
1 TA TA TA TA TA
54076682 AGACATAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54076899 original size:25 final size:23
Alignment explanation
Indices: 54076861--54076918 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
54076851 GTAAATTAAT
54076861 TATAGTATAAAAAAACATAAATATA
1 TATAGTATAAAAAAA-ATAAA-ATA
54076886 TATA-TATAAGAAAAAATAAAATA
1 TATAGTATAA-AAAAAATAAAATA
*
54076909 TAAAG-ATAAA
1 TATAGTATAAA
54076919 TTTAATAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 1 0.03
23 10 0.33
24 10 0.33
25 9 0.30
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (23 bp):
TATAGTATAAAAAAAATAAAATA
Found at i:54076981 original size:2 final size:2
Alignment explanation
Indices: 54076970--54077043 Score: 141
Period size: 2 Copynumber: 37.5 Consensus size: 2
54076960 TATGTGCGTG
54076970 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54077011 TA TA TA 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 TA TA TA T
54077044 GAAAAATGTA
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 70 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54077410 original size:3 final size:3
Alignment explanation
Indices: 54077402--54077481 Score: 67
Period size: 3 Copynumber: 26.7 Consensus size: 3
54077392 AAGTAATTAA
* *
54077402 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAAT AAT AAA AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A-AT
* * *
54077449 GAT AAT -AC AAT AA- AAT AAT GAAG AA- AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
54077482 AAATGCTAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
2 5 0.08
3 51 0.82
4 6 0.10
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:54080900 original size:24 final size:24
Alignment explanation
Indices: 54080868--54080937 Score: 59
Period size: 25 Copynumber: 2.9 Consensus size: 24
54080858 TAGCTCAGAA
*
54080868 GAGCGTCCCGTTATTAGCTCTCAT
1 GAGCTTCCCGTTATTAGCTCTCAT
* * * * *
54080892 TAGCTTCCCATTATATGGTTCTTAT
1 GAGCTTCCCGTTAT-TAGCTCTCAT
* *
54080917 GAGCTTCCCGATAATAGCTCT
1 GAGCTTCCCGTTATTAGCTCT
54080938 TCAAAGCATC
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (24 bp):
GAGCTTCCCGTTATTAGCTCTCAT
Found at i:54081254 original size:21 final size:22
Alignment explanation
Indices: 54081228--54081272 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
54081218 GTTCATATAT
54081228 GTTTATGTACAT-GAAATTAAA
1 GTTTATGTACATGGAAATTAAA
*
54081249 GTTTATGTACATGGAAGTTAAA
1 GTTTATGTACATGGAAATTAAA
54081271 GT
1 GT
54081273 GAACCATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (22 bp):
GTTTATGTACATGGAAATTAAA
Found at i:54085004 original size:3 final size:3
Alignment explanation
Indices: 54084989--54085138 Score: 192
Period size: 3 Copynumber: 50.0 Consensus size: 3
54084979 TTTAAGATTT
* * * *
54084989 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
54085037 TCA TCA TCA TCA TCA TCA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
54085085 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54085133 TTA TTA
1 TTA TTA
54085139 AATTGTTTTA
Statistics
Matches: 139, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 139 1.00
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:54094207 original size:24 final size:24
Alignment explanation
Indices: 54094175--54094222 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
54094165 TAGCCTATGT
* * *
54094175 CGGGTAGCTCTGAAGAGTACTTAA
1 CGGGAAGCTCCGAAGAGCACTTAA
54094199 CGGGAAGCTCCGAAGAGCACTTAA
1 CGGGAAGCTCCGAAGAGCACTTAA
54094223 TCAAAGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (24 bp):
CGGGAAGCTCCGAAGAGCACTTAA
Found at i:54095990 original size:14 final size:14
Alignment explanation
Indices: 54095971--54095999 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54095961 CATACTCTGC
54095971 CTCTGGATAACAGG
1 CTCTGGATAACAGG
54095985 CTCTGGATAACAGG
1 CTCTGGATAACAGG
54095999 C
1 C
54096000 AATCATCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (14 bp):
CTCTGGATAACAGG
Found at i:54100424 original size:79 final size:79
Alignment explanation
Indices: 54100283--54100457 Score: 323
Period size: 79 Copynumber: 2.2 Consensus size: 79
54100273 ATCAAATATG
* *
54100283 TTAGTTATTCATTTCATGTAAATATCAATAACAAAGATGAGCTCATCAAATACCAAGTTCCATGC
1 TTAGATATTGATTTCATGTAAATATCAATAACAAAGATGAGCTCATCAAATACCAAGTTCCATGC
54100348 ATTTCATGTATTTT
66 ATTTCATGTATTTT
54100362 TTAGATATTGATTTCATGTAAATATCAATAACAAAGATGAGCTCATCAAATACCAAGTTCCATGC
1 TTAGATATTGATTTCATGTAAATATCAATAACAAAGATGAGCTCATCAAATACCAAGTTCCATGC
54100427 ATTTCATGTATTTT
66 ATTTCATGTATTTT
*
54100441 TCAGATATTGATTTCAT
1 TTAGATATTGATTTCAT
54100458 TTTGATTTTC
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 93 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (79 bp):
TTAGATATTGATTTCATGTAAATATCAATAACAAAGATGAGCTCATCAAATACCAAGTTCCATGC
ATTTCATGTATTTT
Found at i:54104321 original size:18 final size:17
Alignment explanation
Indices: 54104288--54104321 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54104278 TCTTTTAAGA
*
54104288 ATTAAAAAAAATATATC
1 ATTAAAAAAAAAATATC
54104305 ATTAAAAAATAAAATAT
1 ATTAAAAAA-AAAATAT
54104322 AATTTTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTAAAAAAAAAATATC
Found at i:54111401 original size:2 final size:2
Alignment explanation
Indices: 54111394--54111424 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54111384 TTCCTACATT
54111394 TA TA 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 TA TA T
54111425 GTCTTTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54124250 original size:5 final size:5
Alignment explanation
Indices: 54124240--54124272 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
54124230 AAAACTCATA
54124240 AAAAT AAAAT AAAAT AAAAT AAAAT AAATAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AA
54124273 CTAGTCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:54125440 original size:23 final size:25
Alignment explanation
Indices: 54125410--54125460 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
54125400 TAGAATTTTT
*
54125410 TTTATATTA-TAAA-GTTAAAAAAA
1 TTTATATTATTAAATCTTAAAAAAA
54125433 TTTATATTATTTAAATCTTAAAAAAA
1 TTTATATTA-TTAAATCTTAAAAAAA
54125459 TT
1 TT
54125461 CTGAAGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
25 4 0.17
26 11 0.46
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTATATTATTAAATCTTAAAAAAA
Found at i:54129074 original size:22 final size:22
Alignment explanation
Indices: 54129029--54129074 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
54129019 AAGGTTCAAC
* *
54129029 AATTTATATGGATAAATTTTAT
1 AATTTATATGAATAAATTTAAT
54129051 AATTTATATGTAATAAA-TTAAT
1 AATTTATATG-AATAAATTTAAT
54129073 AA
1 AA
54129075 AATAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (22 bp):
AATTTATATGAATAAATTTAAT
Found at i:54129610 original size:11 final size:11
Alignment explanation
Indices: 54129594--54129618 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54129584 GTTGTGTTTA
54129594 TTTTTGTTTTT
1 TTTTTGTTTTT
54129605 TTTTTGTTTTT
1 TTTTTGTTTTT
54129616 TTT
1 TTT
54129619 ATGGATTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:54139030 original size:35 final size:35
Alignment explanation
Indices: 54138983--54139059 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 35
54138973 TGTTAGCGTT
54138983 GTTTACTCTGGATTTGTTCTTCTAATTGAATCGAA
1 GTTTACTCTGGATTTGTTCTTCTAATTGAATCGAA
*
54139018 GTTTACTTTGGATTTGTTCTTCTAATTGAATCGAA
1 GTTTACTCTGGATTTGTTCTTCTAATTGAATCGAA
*
54139053 GCTTACT
1 GTTTACT
54139060 GATGATGTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (35 bp):
GTTTACTCTGGATTTGTTCTTCTAATTGAATCGAA
Found at i:54142354 original size:48 final size:48
Alignment explanation
Indices: 54142282--54142377 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
54142272 AGCAGAGGAT
54142282 AGCTGAGATTCCTTCTCCGACTAACGAC-TCTTCAAGGACAGCATATGG
1 AGCTGAGATTCCTTCTCCGACTAACG-CTTCTTCAAGGACAGCATATGG
*
54142330 AGCTGAGATTCCTTCTCCGGCTAACGCTTCTTCAAGGACAGCATATGG
1 AGCTGAGATTCCTTCTCCGACTAACGCTTCTTCAAGGACAGCATATGG
54142378 TTTCAGCTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 1 0.02
48 45 0.98
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (48 bp):
AGCTGAGATTCCTTCTCCGACTAACGCTTCTTCAAGGACAGCATATGG
Found at i:54143193 original size:24 final size:24
Alignment explanation
Indices: 54143146--54143193 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
54143136 GATGACTGTG
* *
54143146 ATTAAACCTTAACTGCCAACTACA
1 ATTAAACATTAACAGCCAACTACA
54143170 ATTAAACATTAACCAGCCAA-TACA
1 ATTAAACATTAA-CAGCCAACTACA
54143194 TGGACCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.46, C:0.27, G:0.04, T:0.23
Consensus pattern (24 bp):
ATTAAACATTAACAGCCAACTACA
Found at i:54151423 original size:25 final size:25
Alignment explanation
Indices: 54151389--54151438 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
54151379 TGGCTGGTGG
*
54151389 TGCAGCATGCTGGCTC-ACTTCATCA
1 TGCAGCATGCTAGC-CAACTTCATCA
54151414 TGCAGCATGCTAGCCAACTTCATCA
1 TGCAGCATGCTAGCCAACTTCATCA
54151439 GGATCCCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (25 bp):
TGCAGCATGCTAGCCAACTTCATCA
Found at i:54152230 original size:26 final size:26
Alignment explanation
Indices: 54152194--54152247 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
54152184 TTCTATCGAG
54152194 AATTCTCATTTTGCGAGAGTTAGGCT
1 AATTCTCATTTTGCGAGAGTTAGGCT
54152220 AATTCTCATTTTGCGAGAGTTAGGCT
1 AATTCTCATTTTGCGAGAGTTAGGCT
54152246 AA
1 AA
54152248 CTTAAACTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (26 bp):
AATTCTCATTTTGCGAGAGTTAGGCT
Found at i:54153349 original size:22 final size:22
Alignment explanation
Indices: 54153297--54153349 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
54153287 CTTTATCTGT
** *
54153297 GGTTTTTTATCCTCTTCGGAGA
1 GGTTTTTCCTCCTCATCGGAGA
54153319 GGTTTTTCCTCCTCATCGGAGA
1 GGTTTTTCCTCCTCATCGGAGA
54153341 GGTTTTTCC
1 GGTTTTTCC
54153350 ATGTAAAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (22 bp):
GGTTTTTCCTCCTCATCGGAGA
Found at i:54155346 original size:11 final size:11
Alignment explanation
Indices: 54155332--54155376 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
54155322 AGATAAATAT
54155332 TATTTTATTAA
1 TATTTTATTAA
*
54155343 TATTTTCATGAGA
1 TATTTT-ATTA-A
*
54155356 TATTTTACTAA
1 TATTTTATTAA
54155367 TATTTTATTA
1 TATTTTATTA
54155377 TAAATAGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 16 0.57
12 5 0.18
13 7 0.25
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:54157041 original size:26 final size:26
Alignment explanation
Indices: 54157011--54157076 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 26
54157001 CCGGAGCTCT
*
54157011 TGATTAAAGGCTCTTCATGAGCTTCC
1 TGATTAAAGGCTCTTCATGAACTTCC
* * **
54157037 TGATTAAAAGTTCTTTGTGAACTTCC
1 TGATTAAAGGCTCTTCATGAACTTCC
*
54157063 TGATT-ATGGCTCTT
1 TGATTAAAGGCTCTT
54157077 TTAAGCTTCC
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
25 6 0.19
26 26 0.81
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (26 bp):
TGATTAAAGGCTCTTCATGAACTTCC
Found at i:54168701 original size:5 final size:5
Alignment explanation
Indices: 54168691--54168724 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
54168681 CTTTTGGTTC
54168691 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
54168725 ATTAAAAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:54191510 original size:29 final size:30
Alignment explanation
Indices: 54191446--54191510 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
54191436 TATATAAACG
*
54191446 TATATAGAATTGAATCAAATTAAAATTACA
1 TATATAGAATTGAATCAAATCAAAATTACA
* *
54191476 CATATAGAATTGCA-CAAAATCAAAATT-CA
1 TATATAGAATTGAATC-AAATCAAAATTACA
54191505 TATATA
1 TATATA
54191511 ATATCGCAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (30 bp):
TATATAGAATTGAATCAAATCAAAATTACA
Found at i:54192607 original size:22 final size:21
Alignment explanation
Indices: 54192560--54192607 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
54192550 TATTAATTTT
* *
54192560 TATTTTTTAAATTTTATTTAA
1 TATTTTTTAAATTTCATATAA
54192581 TATTTTTATAAATTTCA-ATAA
1 TATTTTT-TAAATTTCATATAA
54192602 TGATTT
1 T-ATTT
54192608 ATACATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTTTTTAAATTTCATATAA
Found at i:54193288 original size:9 final size:8
Alignment explanation
Indices: 54193240--54193288 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
54193230 TATTTCATGC
54193240 AATTTTTT
1 AATTTTTT
*
54193248 AACTTTTT
1 AATTTTTT
54193256 -ATTTTTT
1 AATTTTTT
**
54193263 AATTTGAT
1 AATTTTTT
54193271 AATTTTTT
1 AATTTTTT
54193279 AATATTTTT
1 AAT-TTTTT
54193288 A
1 A
54193289 TAAAATTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
7 6 0.18
8 21 0.64
9 6 0.18
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (8 bp):
AATTTTTT
Found at i:54193675 original size:23 final size:24
Alignment explanation
Indices: 54193649--54193693 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
54193639 TTAGTCTTTT
*
54193649 TTAAAAAATGATGAAA-TTATAAA
1 TTAAAAAATGATAAAACTTATAAA
* *
54193672 TTAATATATGATAAAACTTATA
1 TTAAAAAATGATAAAACTTATA
54193694 TCTTGACCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (24 bp):
TTAAAAAATGATAAAACTTATAAA
Found at i:54194778 original size:15 final size:15
Alignment explanation
Indices: 54194758--54194786 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54194748 TTAAAGAAAA
54194758 ATGAATATTGTAAAG
1 ATGAATATTGTAAAG
54194773 ATGAATATTGTAAA
1 ATGAATATTGTAAA
54194787 AATATTGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (15 bp):
ATGAATATTGTAAAG
Found at i:54195465 original size:8 final size:9
Alignment explanation
Indices: 54195438--54195475 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
54195428 GTTTCCCATG
*
54195438 TTAGAATTT
1 TTAGGATTT
*
54195447 TTAGGGTTT
1 TTAGGATTT
54195456 TTAGGATTT
1 TTAGGATTT
54195465 TTAGGATTT
1 TTAGGATTT
54195474 TT
1 TT
54195476 GGAGAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.58
Consensus pattern (9 bp):
TTAGGATTT
Found at i:54195894 original size:127 final size:125
Alignment explanation
Indices: 54195588--54196160 Score: 742
Period size: 127 Copynumber: 4.6 Consensus size: 125
54195578 TAAGATAAAA
* * * * * * * * * * *
54195588 TCAAAGCAAGATGATTTATTAGAAGGATTTTTGAAGTCGTGCCCACGTGTACGCGTTTTTGCTAT
1 TCAAA-CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCTACGTGGACGCGCTTTTGCTAC
**
54195653 AGTAGGTATTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGT-TAAAAAAACGCT
65 AGTAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAAACGCT
* * * * *
54195714 TTAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCT-CGTGAACGCGCTTTTACTAC
1 TCAAACAGGATGCTTTATGAGAAGAATTTGTGAAATCGC-GCCTACGTGGACGCGCTTTTGCTAC
* *
54195778 AGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTTAAAAAACGCT
65 AGTAGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAG-TATAAAAAACGCT
54195841 TCAAACAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCTACGTGGACGCGCTTTTGCTACA
1 TCAAACAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCTACGTGGACGCGCTTTTGCTACA
* *
54195906 GTAGGTCCTGAAAAAATAATTTCGAGTTGATGTTTCTGAGCAAATAGTATAAAATAACGCT
66 GTAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAA-AACGCT
*
54195967 GCAAACAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCCT-CGTGGACGCGCTTTTGCT
1 TCAAACAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCG--CCTACGTGGACGCGCTTTTGCT
* * * * *
54196030 ACAGTAGGTCCTAGAAAAATAATTTCAACTTGACGTTTCTGAGCAAATAGTAT-AAAATCACT
63 ACAGTAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCT
* * * *
54196092 TCTAGCAGGATGCTTTATGAGAAGAATTTGTGAAATTGCGCCCACGTGGACGCGCTTTTGCTACA
1 TCAAACAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCTACGTGGACGCGCTTTTGCTACA
54196157 GTAG
66 GTAG
54196161 CATGTTTGGG
Statistics
Matches: 396, Mismatches: 40, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
123 2 0.01
124 27 0.07
125 97 0.24
126 120 0.30
127 146 0.37
128 4 0.01
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (125 bp):
TCAAACAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCTACGTGGACGCGCTTTTGCTACA
GTAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCT
Found at i:54197675 original size:20 final size:20
Alignment explanation
Indices: 54197638--54197675 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54197628 TTTATTTTTA
*
54197638 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
54197658 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
54197676 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:54198656 original size:51 final size:51
Alignment explanation
Indices: 54198601--54198700 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
54198591 AATTATTTAA
*
54198601 AAATAGGGATTTAAGAGAAATTTAAGAA-GAACTTGAGAGTAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTT-AGAAGGAACTTGAGAGCAAATTGAGATT
* * * *
54198652 AAATATGGATTTGAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGA
54198701 GGAAATTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 3 0.07
51 40 0.93
ACGTcount: A:0.45, C:0.02, G:0.26, T:0.27
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGATT
Found at i:54198674 original size:11 final size:11
Alignment explanation
Indices: 54198660--54198714 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
54198650 TTAAATATGG
54198660 ATTTGAGAGAA
1 ATTTGAGAGAA
*
54198671 ATTTG-GAAGGA
1 ATTTGAG-AGAA
54198682 ATTTGAGAGCAA
1 ATTTGAGAG-AA
54198694 A-TTGAGAGGAA
1 ATTTGAGA-GAA
54198705 ATTTGAGAGA
1 ATTTGAGAGA
54198715 GGGTTAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 1 0.03
11 26 0.70
12 10 0.27
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:54198707 original size:23 final size:22
Alignment explanation
Indices: 54198660--54198714 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
54198650 TTAAATATGG
54198660 ATTTGAGAGAAATTTGGAAGGA
1 ATTTGAGAGAAATTTGGAAGGA
54198682 ATTTGAGAGCAAA-TT-GAGAGGAA
1 ATTTGAGAG-AAATTTGGA-AGG-A
54198705 ATTTGAGAGA
1 ATTTGAGAGA
54198715 GGGTTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.07
22 15 0.50
23 13 0.43
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.25
Consensus pattern (22 bp):
ATTTGAGAGAAATTTGGAAGGA
Found at i:54200167 original size:27 final size:27
Alignment explanation
Indices: 54200112--54200170 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
54200102 AGGGAAGCAA
**
54200112 AAAACTAAACCCTAAACTACGAAGAAG
1 AAAACTAAACCCTAAAAGACGAAGAAG
*
54200139 AAAACATAAACCCTAAAAGATGAAG-AG
1 AAAAC-TAAACCCTAAAAGACGAAGAAG
54200166 AAAAC
1 AAAAC
54200171 GGGAAAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.59, C:0.19, G:0.12, T:0.10
Consensus pattern (27 bp):
AAAACTAAACCCTAAAAGACGAAGAAG
Found at i:54200227 original size:47 final size:47
Alignment explanation
Indices: 54200174--54200271 Score: 169
Period size: 47 Copynumber: 2.1 Consensus size: 47
54200164 AGAAAACGGG
* * *
54200174 AAAACTAGGCTAAAGTCTCGTGTCTCGTGTGTTTTCTCTCTGAAGCC
1 AAAACTAAGCTAAAGTCTCGCGTCTCGTGTGTATTCTCTCTGAAGCC
54200221 AAAACTAAGCTAAAGTCTCGCGTCTCGTGTGTATTCTCTCTGAAGCC
1 AAAACTAAGCTAAAGTCTCGCGTCTCGTGTGTATTCTCTCTGAAGCC
54200268 AAAA
1 AAAA
54200272 TTTGGCATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (47 bp):
AAAACTAAGCTAAAGTCTCGCGTCTCGTGTGTATTCTCTCTGAAGCC
Found at i:54200844 original size:10 final size:11
Alignment explanation
Indices: 54200817--54200842 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54200807 TAAAAAAATA
54200817 AAAAATATTTT
1 AAAAATATTTT
54200828 AAAAATATTTT
1 AAAAATATTTT
54200839 AAAA
1 AAAA
54200843 TAAAAAATAT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:54201558 original size:29 final size:28
Alignment explanation
Indices: 54201521--54201575 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
54201511 TACTCACAAA
*
54201521 TTTAAAATTTAAT-TCTTATATTTTTATT
1 TTTAAAATTTAATAT-TTAAATTTTTATT
54201549 TTTAAGAATTTAATATTTAAATTTTTA
1 TTTAA-AATTTAATATTTAAATTTTTA
54201576 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 5 0.21
29 18 0.75
30 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTAAAATTTAATATTTAAATTTTTATT
Found at i:54201867 original size:13 final size:13
Alignment explanation
Indices: 54201849--54201873 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54201839 AATAATATTT
54201849 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
54201862 AAAAAAAGAAAA
1 AAAAAAAGAAAA
54201874 CAGCTGTACG
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:54220801 original size:17 final size:17
Alignment explanation
Indices: 54220770--54220832 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
54220760 AAATTCTTTT
54220770 TAAATCACAAAAATTCAC
1 TAAATCAC-AAAATTCAC
54220788 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAC
* * *
54220805 CAATTCA-AAAATTCTTC
1 TAAATCACAAAATTC-AC
54220822 TAAATTCACAA
1 TAAA-TCACAA
54220833 TTGACCCATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
16 7 0.19
17 17 0.46
18 11 0.30
19 2 0.05
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:54221315 original size:31 final size:31
Alignment explanation
Indices: 54221278--54221336 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
54221268 TTAACGACCA
*
54221278 AATGACTTAAATAAAAACTTTTGAATAGCTC
1 AATGACTTAAATAAAAACTTTCGAATAGCTC
*
54221309 AATGACTTAAATGAAAACTTTCGAATAG
1 AATGACTTAAATAAAAACTTTCGAATAG
54221337 TTTAGTGACC
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:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (31 bp):
AATGACTTAAATAAAAACTTTCGAATAGCTC
Found at i:54235082 original size:2 final size:2
Alignment explanation
Indices: 54235075--54235100 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54235065 TTTATGTTGA
54235075 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
54235101 TCAGCATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54238769 original size:27 final size:28
Alignment explanation
Indices: 54238703--54238769 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
54238693 AACCTTTGCT
54238703 TTTATAATTAATATATTTATATAATTATG
1 TTTA-AATTAATATATTTATATAATTATG
*
54238732 ATTAAAGTTAAT-TATTATAATATAA-TA-G
1 TTTAAA-TTAATATATT-T-ATATAATTATG
54238760 TTTAAATTAA
1 TTTAAATTAA
54238770 AATAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
27 4 0.12
28 12 0.36
29 11 0.33
30 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
TTTAAATTAATATATTTATATAATTATG
Found at i:54252316 original size:18 final size:18
Alignment explanation
Indices: 54252295--54252333 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
54252285 ATTCGGGTAA
54252295 AATTGAAAAAATTCGGTT
1 AATTGAAAAAATTCGGTT
***
54252313 AATTGATCGAATTCGGTT
1 AATTGAAAAAATTCGGTT
54252331 AAT
1 AAT
54252334 CGGTCAGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (18 bp):
AATTGAAAAAATTCGGTT
Found at i:54252667 original size:9 final size:9
Alignment explanation
Indices: 54252653--54252690 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
54252643 GTAGTGATTC
54252653 AATTCGGTT
1 AATTCGGTT
54252662 AATTCGGTT
1 AATTCGGTT
*
54252671 AATTCGGGT
1 AATTCGGTT
54252680 AATTCGGTT
1 AATTCGGTT
54252689 AA
1 AA
54252691 CCGACGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:54254631 original size:67 final size:67
Alignment explanation
Indices: 54254522--54254718 Score: 342
Period size: 67 Copynumber: 2.9 Consensus size: 67
54254512 TTCACTTGTC
* * * *
54254522 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACA
54254587 TCA
66 -CA
54254590 -TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACA
54254654 CA
66 CA
54254656 TTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCA
54254719 TGTATTATTT
Statistics
Matches: 124, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
66 2 0.02
67 122 0.98
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (67 bp):
TTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACA
CA
Found at i:54254728 original size:35 final size:35
Alignment explanation
Indices: 54254522--54254728 Score: 273
Period size: 35 Copynumber: 6.1 Consensus size: 35
54254512 TTCACTTGTC
* *
54254522 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
* * * *
54254557 TTCTGTTGCAGGGAATCTTTCCTGTTCA--CATCA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
54254590 -TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
* *
54254624 TTTTGTTGCAGGGAATCTCTCCTGTTCA--CA-CA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
54254656 TTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
* * *
54254691 TTTTGTTGCAGGGAATCTCTCCTGTTCATGTATTA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
54254726 TTT
1 TTT
54254729 CTTTTTNNNN
Statistics
Matches: 151, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
32 52 0.34
33 6 0.04
34 6 0.04
35 87 0.58
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.42
Consensus pattern (35 bp):
TTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
Found at i:54257564 original size:20 final size:23
Alignment explanation
Indices: 54257529--54257573 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
54257519 GAGCAAATCG
54257529 TTGATTCTATTTCTTTTTTG-AT
1 TTGATTCTATTTCTTTTTTGTAT
54257551 TTGA-TCTA-TTCTTTTTTGTAT
1 TTGATTCTATTTCTTTTTTGTAT
54257572 TT
1 TT
54257574 CTCTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 8 0.36
22 4 0.18
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (23 bp):
TTGATTCTATTTCTTTTTTGTAT
Found at i:54260989 original size:13 final size:13
Alignment explanation
Indices: 54260937--54260989 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
54260927 TTTAAACCAA
54260937 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
** *
54260950 ACTCCTCAAAAGT
1 ACTTTTCAAAAGC
* *
54260963 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
54260976 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
54260989 A
1 A
54260990 TTGCCAAACT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:54264735 original size:16 final size:15
Alignment explanation
Indices: 54264707--54264748 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
54264697 TCTGGAGAGA
*
54264707 AAACAGGAGCAGTA-
1 AAACAAGAGCAGTAC
54264721 AGAACAAGCAGCAGTAC
1 A-AACAAG-AGCAGTAC
54264738 AAACAAGAGCA
1 AAACAAGAGCA
54264749 AAACAAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 9 0.38
16 13 0.54
17 1 0.04
ACGTcount: A:0.52, C:0.19, G:0.24, T:0.05
Consensus pattern (15 bp):
AAACAAGAGCAGTAC
Found at i:54268508 original size:26 final size:27
Alignment explanation
Indices: 54268463--54268514 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
54268453 TAGTTGGTTT
54268463 GTTAAAGAAAGGTTAAAGAAGTTAGTA
1 GTTAAAGAAAGGTTAAAGAAGTTAGTA
* *
54268490 GTTAAAGATA-GTTACAGAAGTTAGT
1 GTTAAAGAAAGGTTAAAGAAGTTAGT
54268515 TAGCAGCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.44, C:0.02, G:0.25, T:0.29
Consensus pattern (27 bp):
GTTAAAGAAAGGTTAAAGAAGTTAGTA
Found at i:54281129 original size:25 final size:25
Alignment explanation
Indices: 54281077--54281129 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
54281067 AGCTCTTCCA
* **
54281077 AGCCATATAACGGGAAGCTCATGTG
1 AGCCATATAACAGGAAGCTCATAAG
*
54281102 AGCCATGTAACAGGAAGCTCATAAG
1 AGCCATATAACAGGAAGCTCATAAG
54281127 AGC
1 AGC
54281130 TATAATCGCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (25 bp):
AGCCATATAACAGGAAGCTCATAAG
Found at i:54281292 original size:24 final size:25
Alignment explanation
Indices: 54281233--54281295 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 25
54281223 CAAGAACCAT
* *
54281233 ATAACGGGAAGCTCGTGAGAGCCAA
1 ATAACGGGATGCTCATGAGAGCCAA
* ** *
54281258 ATATCAAGATGCTCATGAGAG-CTA
1 ATAACGGGATGCTCATGAGAGCCAA
54281282 ATAACGGGATGCTC
1 ATAACGGGATGCTC
54281296 TTTCGAGCTA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (25 bp):
ATAACGGGATGCTCATGAGAGCCAA
Found at i:54283709 original size:18 final size:16
Alignment explanation
Indices: 54283667--54283709 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
54283657 TGTCGTTCGT
54283667 TTTCAAAATATTATTCA
1 TTTC-AAATATTATTCA
54283684 TTTACAAATCATTATTCAA
1 TTT-CAAAT-ATTATTC-A
54283703 TTTCAAA
1 TTTCAAA
54283710 ACGTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCAAATATTATTCA
Found at i:54290510 original size:20 final size:19
Alignment explanation
Indices: 54290476--54290530 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
54290466 ATATATTAAT
54290476 TTAAA-AAAT-TATAAAAA
1 TTAAATAAATATATAAAAA
54290493 -TAGAATTAAATATATAAAAA
1 TTA-AA-TAAATATATAAAAA
*
54290513 TTAAATATATATATAAAA
1 TTAAATAAATATATAAAA
54290531 TAAAGTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 2 0.06
17 2 0.06
19 16 0.50
20 10 0.31
21 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
TTAAATAAATATATAAAAA
Found at i:54290516 original size:15 final size:15
Alignment explanation
Indices: 54290496--54290545 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
54290486 ATAAAAATAG
54290496 AATTAAATATATAAA
1 AATTAAATATATAAA
54290511 AATTAAATATATATATA
1 AATTAAATATATA-A-A
*
54290528 AAATAAAGTATA-AAA
1 AATTAAA-TATATAAA
54290543 AAT
1 AAT
54290546 AAAAATTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 16 0.53
16 2 0.07
17 8 0.27
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (15 bp):
AATTAAATATATAAA
Found at i:54290534 original size:17 final size:18
Alignment explanation
Indices: 54290502--54290539 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
54290492 ATAGAATTAA
54290502 ATATATAAAAATTAAA-T
1 ATATATAAAAATTAAAGT
54290519 ATATATATAAAA-TAAAGT
1 ATATATA-AAAATTAAAGT
54290537 ATA
1 ATA
54290540 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
ATATATAAAAATTAAAGT
Found at i:54294812 original size:8 final size:8
Alignment explanation
Indices: 54294799--54294882 Score: 57
Period size: 9 Copynumber: 10.0 Consensus size: 8
54294789 AAATGAATAA
54294799 AAAATTAT
1 AAAATTAT
54294807 AAAA-T-T
1 AAAATTAT
*
54294813 AAACTTATT
1 AAAATTA-T
54294822 AAAATTAT
1 AAAATTAT
54294830 AAAAATTTAT
1 -AAAA-TTAT
* *
54294840 GAACATTAC
1 -AAAATTAT
54294849 AAAA-TAT
1 AAAATTAT
54294856 AAAAATTAT
1 -AAAATTAT
54294865 AAAATTAAT
1 AAAATT-AT
54294874 AAAACTTAT
1 AAAA-TTAT
54294883 TCAAAACATC
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
6 4 0.07
7 4 0.07
8 18 0.30
9 25 0.42
10 9 0.15
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.35
Consensus pattern (8 bp):
AAAATTAT
Found at i:54298169 original size:22 final size:22
Alignment explanation
Indices: 54298151--54298192 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
54298141 CTACAATTTC
54298151 AAAAAAACCAAACATCAATATT
1 AAAAAAACCAAACATCAATATT
* * *
54298173 AATAAAATCAAACATTAATA
1 AAAAAAACCAAACATCAATA
54298193 AGTAAGTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAAAAACCAAACATCAATATT
Found at i:54299598 original size:14 final size:15
Alignment explanation
Indices: 54299565--54299605 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
54299555 ATAAATTAGA
54299565 ATAAT-TATA-ATTT
1 ATAATATATATATTT
54299578 ATAATATATATATTT
1 ATAATATATATATTT
54299593 AT-ATATATATATT
1 ATAATATATATATT
54299606 CAAAGGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.19
14 15 0.58
15 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATAATATATATATTT
Found at i:54299940 original size:30 final size:29
Alignment explanation
Indices: 54299906--54299964 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
54299896 AACCTAAAAT
* *
54299906 TAATTAAAATAAAATTTAATATAAATTTTA
1 TAATTAAAATAAAATTAAAAAT-AATTTTA
* *
54299936 TAATTTAAATTAAATTAAAAATAATTTTA
1 TAATTAAAATAAAATTAAAAATAATTTTA
54299965 AGAAGAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TAATTAAAATAAAATTAAAAATAATTTTA
Found at i:54317892 original size:23 final size:23
Alignment explanation
Indices: 54317865--54317986 Score: 172
Period size: 23 Copynumber: 5.3 Consensus size: 23
54317855 AGTGTTATTG
*
54317865 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
54317888 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
54317911 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
54317934 TTCAGTGGTAGCTTCGACAACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
54317957 AACAGTGGTAGGTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
54317980 ATCAGTG
1 ATCAGTG
54317987 TTGCACTTAT
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 85 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:54317920 original size:46 final size:46
Alignment explanation
Indices: 54317867--54317986 Score: 195
Period size: 46 Copynumber: 2.6 Consensus size: 46
54317857 TGTTATTGAT
* * *
54317867 CAGTGGTAGCTTCGGCTACGTTTCAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGACAACATAA
54317913 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGACAACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGACAACATAA
* *
54317959 CAGTGGTAGGTTCGGCTACATATCAGTG
1 CAGTGGTAGCTTCGGCTACATTTCAGTG
54317987 TTGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGACAACATAA
Found at i:54320883 original size:24 final size:25
Alignment explanation
Indices: 54320846--54320893 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
54320836 TAATACTGTC
54320846 CAAAAAATAAATAAATTA-ATTAAT
1 CAAAAAATAAATAAATTACATTAAT
* * *
54320870 CAAAATATATATAATTTACATTAA
1 CAAAAAATAAATAAATTACATTAA
54320894 ATGAATTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (25 bp):
CAAAAAATAAATAAATTACATTAAT
Found at i:54323625 original size:21 final size:22
Alignment explanation
Indices: 54323601--54323651 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
54323591 GTAACAACAT
*
54323601 TAATTAAAT-ATTTTTTAATTA
1 TAATTAAATAAATTTTTAATTA
54323622 TAATTAAATAAAATTTTTAATTA
1 TAATTAAAT-AAATTTTTAATTA
54323645 TAATTAA
1 TAATTAA
54323652 TTGAGATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 9 0.33
23 18 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATTAAATAAATTTTTAATTA
Found at i:54331764 original size:15 final size:16
Alignment explanation
Indices: 54331738--54331768 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
54331728 GTTTGGATTA
54331738 ATTTTGAATTTGAGTC
1 ATTTTGAATTTGAGTC
54331754 ATTTT-AATTTGAGTC
1 ATTTTGAATTTGAGTC
54331769 TTTGGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (16 bp):
ATTTTGAATTTGAGTC
Found at i:54333388 original size:23 final size:22
Alignment explanation
Indices: 54333339--54333394 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
54333329 AATCTCTTTT
* *
54333339 AAAATTTTAAAAATTATGTTAA
1 AAAATTATAAAAAATATGTTAA
54333361 AAAATTATAAAAAATA-GTTATA
1 AAAATTATAAAAAATATGTTA-A
54333383 AGAAATTATAAA
1 A-AAATTATAAA
54333395 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 4 0.13
22 16 0.53
23 10 0.33
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (22 bp):
AAAATTATAAAAAATATGTTAA
Found at i:54334285 original size:18 final size:19
Alignment explanation
Indices: 54334244--54334287 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
54334234 TACGGTACGC
54334244 TTCTTTTC--TTCTCACAT
1 TTCTTTTCTTTTCTCACAT
54334261 TTCTTTTCTTTTCTC-CAT
1 TTCTTTTCTTTTCTCACAT
*
54334279 TTTTTTTCT
1 TTCTTTTCT
54334288 CCAGATTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 8 0.33
18 11 0.46
19 5 0.21
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (19 bp):
TTCTTTTCTTTTCTCACAT
Found at i:54334387 original size:17 final size:17
Alignment explanation
Indices: 54334361--54334394 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54334351 GTAAAATCGA
54334361 TTTTGATTTTGATTTTG
1 TTTTGATTTTGATTTTG
* *
54334378 TTTTGCTTTTGCTTTTG
1 TTTTGATTTTGATTTTG
54334395 CTCAAATTTG
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:0.06, C:0.06, G:0.18, T:0.71
Consensus pattern (17 bp):
TTTTGATTTTGATTTTG
Found at i:54337232 original size:15 final size:15
Alignment explanation
Indices: 54337208--54337248 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
54337198 AAGCTCTGTG
54337208 ATAT-TTTAATTATA
1 ATATATTTAATTATA
*
54337222 ATATATTTAATAATA
1 ATATATTTAATTATA
54337237 AT-TATGTTAATT
1 ATATAT-TTAATT
54337249 TATATTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATATTTAATTATA
Found at i:54337329 original size:59 final size:59
Alignment explanation
Indices: 54337266--54337449 Score: 166
Period size: 59 Copynumber: 3.1 Consensus size: 59
54337256 TATAGTATCA
54337266 TATATTATGATTTGAGTAAATTCATATAATAATATTGATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTGAGTAAATTCATATAATAATATTGATTATTAAGAATTTTATTAAAT
* * * * * *
54337325 TATA-TAT--TTTAATTATAATAT-ATTTAATAATAATT-ATGTTAATTTA-TATTTTA-TAGTA
1 TATATTATGATTTGAGTA-AAT-TCATATAATAAT-ATTGA--TT-ATTAAGAATTTTATTA-AA
54337383 T
59 T
* *
54337384 CATATATTATGATTTGAGTAATTTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTGAGTAAATTCATATAATAATATTGATTATTAAGAATTTTATTAAAT
54337445 TATAT
1 TATAT
54337450 ATTTTAATTA
Statistics
Matches: 95, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
56 6 0.06
57 13 0.14
58 9 0.09
59 19 0.20
60 8 0.08
61 14 0.15
62 9 0.09
63 11 0.12
64 6 0.06
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (59 bp):
TATATTATGATTTGAGTAAATTCATATAATAATATTGATTATTAAGAATTTTATTAAAT
Found at i:54337330 original size:61 final size:61
Alignment explanation
Indices: 54337265--54337452 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
54337255 TTATAGTATC
54337265 ATATATTATGATTTGAGTAAATTCATATAATAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAATAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * * * *
54337326 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAATTTA-TATTTTA-TAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAATAATAT-TGATT-ATTAAGAATTTTATTA-AATT
* *
54337385 ATATATTATGATTTGAGTAATTTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAATAATATTGATTATTAAGAATTTTATTAAATT
54337446 ATATATT
1 ATATATT
54337453 TTAATTATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 28 0.29
60 27 0.28
61 36 0.37
62 3 0.03
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAATAATATTGATTATTAAGAATTTTATTAAATT
Found at i:54337352 original size:15 final size:15
Alignment explanation
Indices: 54337317--54337368 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
54337307 TTAAGAATTT
*
54337317 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54337331 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54337345 TATTTAATAATAAT-
1 TATTTAATTATAATA
54337359 TATGTTAATT
1 TAT-TTAATT
54337369 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54337421 original size:120 final size:120
Alignment explanation
Indices: 54337208--54337484 Score: 536
Period size: 120 Copynumber: 2.3 Consensus size: 120
54337198 AAGCTCTGTG
54337208 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA
1 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA
*
54337273 TGATTTGAGTAAATTCATATAATAATATTGATTATTAAGAATTTTATTAAATTAT
66 TGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT
54337328 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA
1 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA
*
54337393 TGATTTGAGTAATTTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT
66 TGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT
54337448 ATATTTTAATTATAATATATTTAATAATAATTATGTT
1 ATATTTTAATTATAATATATTTAATAATAATTATGTT
54337485 TAAATATGAT
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 155 1.00
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (120 bp):
ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA
TGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT
Found at i:54337467 original size:16 final size:16
Alignment explanation
Indices: 54337446--54337487 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
54337436 TTATTAAATT
*
54337446 ATATATTTTAATTATA
1 ATATATTTTAATAATA
54337462 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
54337477 AT-TATGTTTAA
1 ATATAT-TTTAA
54337488 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:54337472 original size:15 final size:15
Alignment explanation
Indices: 54337437--54337478 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54337427 TTAAGAATTT
*
54337437 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54337451 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54337465 TATTTAATAATAAT
1 TATTTAATTATAAT
54337479 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54337658 original size:39 final size:40
Alignment explanation
Indices: 54337615--54337719 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
54337605 TTCCATTATG
54337615 CTATTACACCTCTATTCCATTCAACCAAACACAAGATT-A
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTCA
* *** *
54337654 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTCG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTCA
54337699 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
54337720 ACACTTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 19 0.35
45 15 0.28
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.33
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTCA
Found at i:54337713 original size:45 final size:44
Alignment explanation
Indices: 54337613--54337722 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
54337603 TTTTCCATTA
54337613 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
54337652 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
54337696 TCGCTATTACACCTCTATTCCATTACA
1 T-GCTATTACACCTCTATTCCATTACA
54337723 CTTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 18 0.31
45 23 0.40
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:54337834 original size:9 final size:9
Alignment explanation
Indices: 54337816--54337847 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
54337806 TAAATTTATA
54337816 AATT-TATT
1 AATTGTATT
54337824 AATTGTATT
1 AATTGTATT
54337833 AATTGTATT
1 AATTGTATT
54337842 AATTGT
1 AATTGT
54337848 TGTAACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (9 bp):
AATTGTATT
Found at i:54346473 original size:19 final size:20
Alignment explanation
Indices: 54346431--54346473 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
54346421 TAATATACTG
*
54346431 TTTAATATTTAAATTTGACA
1 TTTAATATTTAAATTTAACA
*
54346451 -TTAATA-TTAAATTTAATA
1 TTTAATATTTAAATTTAACA
54346469 TTTAA
1 TTTAA
54346474 ATCAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTAATATTTAAATTTAACA
Found at i:54353115 original size:3 final size:3
Alignment explanation
Indices: 54353107--54353134 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54353097 CTTCATCTTC
54353107 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
54353135 GTTTCCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:54354899 original size:15 final size:16
Alignment explanation
Indices: 54354855--54355118 Score: 88
Period size: 15 Copynumber: 17.1 Consensus size: 16
54354845 TGTGACCTGC
54354855 CTTCATGTAAATGCAG
1 CTTCATGTAAATGCAG
* * *
54354871 C-TCGTGCAATTGCA-
1 CTTCATGTAAATGCAG
54354885 CTTCATGTAAATGCAG
1 CTTCATGTAAATGCAG
* *
54354901 C-TCATGCAACTGCA-
1 CTTCATGTAAATGCAG
* * *
54354915 ATCCGTGTAAATGCAG
1 CTTCATGTAAATGCAG
* ** *
54354931 C-TCGTGCGACTGCA-
1 CTTCATGTAAATGCAG
* * *
54354945 ATCCGTGTAAATGCAG
1 CTTCATGTAAATGCAG
* * *
54354961 C-TCGTGCAACTGCA-
1 CTTCATGTAAATGCAG
* * *
54354975 ATCCGTGTAAATGCAG
1 CTTCATGTAAATGCAG
* * *
54354991 C-TCATGTGACTGTAG
1 CTTCATGTAAATGCAG
54355006 -TTCATGTAAATGCAG
1 CTTCATGTAAATGCAG
* * *
54355021 CAGTTTATGTGACTGCAG
1 C--TTCATGTAAATGCAG
54355039 -TTCATGTAAATGCAG
1 CTTCATGTAAATGCAG
* * *
54355054 C-ACATGCAACTGCAG
1 CTTCATGTAAATGCAG
54355069 -TTCATGTAAATGCAG
1 CTTCATGTAAATGCAG
* ** *
54355084 CAGTTTATGCGACTGCAG
1 C--TTCATGTAAATGCAG
54355102 -TTCATGTAAATGCAG
1 CTTCATGTAAATGCAG
54355117 CT
1 CT
54355119 CGTGTGACTG
Statistics
Matches: 170, Mismatches: 60, Indels: 36
0.64 0.23 0.14
Matches are distributed among these distances:
14 1 0.01
15 143 0.84
16 3 0.02
18 23 0.14
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (16 bp):
CTTCATGTAAATGCAG
Found at i:54355041 original size:33 final size:33
Alignment explanation
Indices: 54354998--54355117 Score: 183
Period size: 33 Copynumber: 3.7 Consensus size: 33
54354988 CAGCTCATGT
* *
54354998 GACTGTAGTTCATGTAAATGCAGCAGTTTATGT
1 GACTGCAGTTCATGTAAATGCAGCAGTTTATGC
*
54355031 GACTGCAGTTCATGTAAATGCAGCA---CATGC
1 GACTGCAGTTCATGTAAATGCAGCAGTTTATGC
*
54355061 AACTGCAGTTCATGTAAATGCAGCAGTTTATGC
1 GACTGCAGTTCATGTAAATGCAGCAGTTTATGC
54355094 GACTGCAGTTCATGTAAATGCAGC
1 GACTGCAGTTCATGTAAATGCAGC
54355118 TCGTGTGACT
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
30 27 0.35
33 51 0.65
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (33 bp):
GACTGCAGTTCATGTAAATGCAGCAGTTTATGC
Done.