Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 60 of 343
Found at i:19312374 original size:96 final size:97
Alignment explanation
Indices: 19312197--19312778 Score: 912
Period size: 96 Copynumber: 6.0 Consensus size: 97
19312187 GAAATGATAG
*
19312197 TAAGGCCTAATGGCCGATGTGATGAATGTAAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCG
19312262 ATGTGATGAATGTGAAAGTGTATATATATGTGA
65 ATGTGATGAATGTGAAAGTGTATATATATGTGA
* *
19312295 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATACGTGATAGGGCCTAATGGCCGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGA
*
19312359 TGTGATGAATATGAAAGTGTATATATATGTGA
66 TGTGATGAATGTGAAAGTGTATATATATGTGA
19312391 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG---ATATATATGTGATAAGGCCTAATGGC
19312456 CGATGTGATGAATGTGAAAGTG--TATATATGTGA
63 CGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
19312489 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCG
19312554 ATGTGATGAATGTGAAAGTGTATATATATGTGA
65 ATGTGATGAATGTGAAAGTGTATATATATGTGA
* * *
19312587 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATACGTGATAGGGCCCAATGGCCGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGA
19312651 TGTGATGAATGTGAAAGTG--TATATATGTGA
66 TGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * *
19312681 TAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTG-TATATATGTGACAGGGCCGAGTGGCCAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGA
* *
19312745 CGTGATGGATGTGAAAGTGTATA-A-ATGTGA
66 TGTGATGAATGTGAAAGTGTATATATATGTGA
19312775 TAAG
1 TAAG
19312779 TCCCGAAGGG
Statistics
Matches: 456, Mismatches: 20, Indels: 20
0.92 0.04 0.04
Matches are distributed among these distances:
94 96 0.21
95 1 0.00
96 188 0.41
98 127 0.28
100 44 0.10
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (97 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGA
TGTGATGAATGTGAAAGTGTATATATATGTGA
Found at i:19314872 original size:43 final size:43
Alignment explanation
Indices: 19314815--19314906 Score: 184
Period size: 43 Copynumber: 2.1 Consensus size: 43
19314805 GCATGTGTGG
19314815 GCGGGCAATAAGTGTTCACGGTTGTGAGATTGGCACTAAGTGT
1 GCGGGCAATAAGTGTTCACGGTTGTGAGATTGGCACTAAGTGT
19314858 GCGGGCAATAAGTGTTCACGGTTGTGAGATTGGCACTAAGTGT
1 GCGGGCAATAAGTGTTCACGGTTGTGAGATTGGCACTAAGTGT
19314901 GCGGGC
1 GCGGGC
19314907 TTGAAATGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.22, C:0.15, G:0.37, T:0.26
Consensus pattern (43 bp):
GCGGGCAATAAGTGTTCACGGTTGTGAGATTGGCACTAAGTGT
Found at i:19314923 original size:29 final size:29
Alignment explanation
Indices: 19314888--19314961 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
19314878 GTTGTGAGAT
* *
19314888 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
19314917 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
19314946 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
19314962 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:19315545 original size:40 final size:40
Alignment explanation
Indices: 19315271--19315533 Score: 262
Period size: 40 Copynumber: 6.6 Consensus size: 40
19315261 TTGAATGATG
* * *
19315271 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCT-AGTGA-TATA
* ** * * * *
19315311 TCCGGACTAAGACCCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGA-TATA
19315351 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
* * * * *
19315391 ACCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTT
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
* * **
19315431 TCCGGGCTAAGTTTCGAAGATCATTCGTGCTAGTGAGGTA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
* * *
19315471 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
* *
19315511 TCCGGGCTAGGTCCCGAAGAGCA
1 TCCGGGCTAAGTTCCGAAGAGCA
19315534 ATCATGCTGG
Statistics
Matches: 185, Mismatches: 36, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
40 166 0.90
41 19 0.10
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
Found at i:19318996 original size:47 final size:49
Alignment explanation
Indices: 19318811--19319393 Score: 899
Period size: 49 Copynumber: 12.1 Consensus size: 49
19318801 GAAATGATAG
19318811 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
19318860 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
19318909 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
19318956 T-AGGCCTAATGGCCGATGTGATGAATGT-AAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
19319003 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
19319052 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
19319099 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
19319148 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG------TATATATATGTGA
*
19319203 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
19319250 T-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
19319296 TAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * * *
19319343 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
19319390 TAAG
1 TAAG
19319394 TCCCGAAGGG
Statistics
Matches: 500, Mismatches: 19, Indels: 32
0.91 0.03 0.06
Matches are distributed among these distances:
45 6 0.01
46 72 0.14
47 158 0.32
48 28 0.06
49 187 0.37
55 49 0.10
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (49 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
Found at i:19319072 original size:143 final size:144
Alignment explanation
Indices: 19318813--19319391 Score: 970
Period size: 143 Copynumber: 4.0 Consensus size: 144
19318803 AATGATAGTA
19318813 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
19318878 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
19318943 TGTATATACGTGAT
131 TGTATATACGTGAT
19318957 AGGCCTAATGGCCGATGTGATGAATGT-AAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
19319021 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
19319086 TGTATATACGTGAT
131 TGTATATACGTGAT
19319100 AGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGA
1 A-GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGA
19319165 TGTGATGAATGTGAAAGTGTATATATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
65 TGTGATGAATGTGAAAGTG------TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
19319230 GTGAAAGTGTATATACGTGAT
124 GTGAAAGTGTATATACGTGAT
19319251 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGAT
1 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
* * * * * * * *
19319314 GTGAGGAATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
* *
19319377 TGTATAAATGTGAT
131 TGTATATACGTGAT
19319391 A
1 A
19319392 AGTCCCGAAG
Statistics
Matches: 417, Mismatches: 10, Indels: 20
0.93 0.02 0.04
Matches are distributed among these distances:
140 51 0.12
143 117 0.28
144 53 0.13
145 55 0.13
148 46 0.11
150 33 0.08
151 62 0.15
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (144 bp):
AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATACGTGAT
Found at i:19319202 original size:55 final size:48
Alignment explanation
Indices: 19319192--19319393 Score: 279
Period size: 47 Copynumber: 4.3 Consensus size: 48
19319182 TGTATATATA
19319192 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
*
19319239 TATATACGTGAT-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
*
19319285 TATATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTG-
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
* * * * * * *
19319332 TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG-
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
*
19319379 TATAAATGTGATAAG
1 TATATATGTGATAAG
19319394 TCCCGAAGGG
Statistics
Matches: 140, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
46 45 0.32
47 95 0.68
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (48 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
Found at i:19319297 original size:93 final size:94
Alignment explanation
Indices: 19319192--19319393 Score: 316
Period size: 93 Copynumber: 2.2 Consensus size: 94
19319182 TGTATATATA
* *
19319192 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATA-GGCC
1 TATATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTGTATATACGTGACAGGGCC
* * *
19319256 TAATGGCCGATGTGATGAATGTGAAAGTG
66 GAATGGCCAACGTGATGAATGTGAAAGTG
*
19319285 TATATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTGTATATATGTGACAGGGCC
1 TATATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTGTATATACGTGACAGGGCC
* *
19319350 GAGTGGCCAACGTGATGGATGTGAAAGTG
66 GAATGGCCAACGTGATGAATGTGAAAGTG
*
19319379 TATAAATGTGATAAG
1 TATATATGTGATAAG
19319394 TCCCGAAGGG
Statistics
Matches: 99, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
93 57 0.58
94 42 0.42
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (94 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTGTATATACGTGACAGGGCC
GAATGGCCAACGTGATGAATGTGAAAGTG
Found at i:19326208 original size:42 final size:43
Alignment explanation
Indices: 19326115--19326212 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 43
19326105 TTAACTACAG
* * *
19326115 GGGTCACACGGCCGTGTGGCTAGGCCGTGTAACCTTCGAACTG
1 GGGTCACACGGCCGTGTGCCTAGCCCGTGTAACCTTCGAACTA
* * * *
19326158 GGGACACACGGCCGTGT-CCTTGCCCGTGTGACCTTCTG-AGTA
1 GGGTCACACGGCCGTGTGCCTAGCCCGTGTAACCTTC-GAACTA
19326200 GGGTCACACGGCC
1 GGGTCACACGGCC
19326213 AAACCACACG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 29 0.63
43 17 0.37
ACGTcount: A:0.15, C:0.31, G:0.34, T:0.20
Consensus pattern (43 bp):
GGGTCACACGGCCGTGTGCCTAGCCCGTGTAACCTTCGAACTA
Found at i:19334262 original size:48 final size:48
Alignment explanation
Indices: 19334191--19334287 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
19334181 TTGTGTTAGG
19334191 ACATAAAATTTCTAGTAAAGGGATTAAGGTCGATAAATCTAAAATTGA
1 ACATAAAATTTCTAGTAAAGGGATTAAGGTCGATAAATCTAAAATTGA
19334239 ACATAAAATTTCTAGTAAAGGGATTAAGGTCGATAAATCTAAAATTGA
1 ACATAAAATTTCTAGTAAAGGGATTAAGGTCGATAAATCTAAAATTGA
19334287 A
1 A
19334288 GCCATTGAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.29
Consensus pattern (48 bp):
ACATAAAATTTCTAGTAAAGGGATTAAGGTCGATAAATCTAAAATTGA
Found at i:19341724 original size:12 final size:12
Alignment explanation
Indices: 19341707--19341731 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19341697 ATGTAAGTGA
19341707 TCTTGATGATTT
1 TCTTGATGATTT
19341719 TCTTGATGATTT
1 TCTTGATGATTT
19341731 T
1 T
19341732 TACATTTTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:19342624 original size:50 final size:48
Alignment explanation
Indices: 19342560--19342837 Score: 295
Period size: 50 Copynumber: 5.6 Consensus size: 48
19342550 GAGACATGTC
* *
19342560 AGTGTAAGATCATGTCTGGGACATGGCATAAGCATGGATATGCAAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATGGATATG--AGAGCT
* * *
19342610 AGTGTAAGACCATGTCTGGGACATGGAATCAGCACGTAAGTATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATG-GA-TATGAGAGCT
* * * * * * *
19342660 AGTGTAAGACCATGTCTAGGACATGGCATCGGCTTCGATGAGGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATGGAT-ATGAGAGCT
* * *
19342709 AGTGTAAGACCATGTCTGGGACATGGAATCAGCACGTAAGTATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATG-GA-TATGAGAGCT
* * * * * *
19342759 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGATGAGGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATGGAT-ATGAGAGCT
19342808 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
19342838 GGCAACTTAA
Statistics
Matches: 188, Mismatches: 34, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
48 2 0.01
49 74 0.39
50 106 0.56
51 2 0.01
52 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCATGGATATGAGAGCT
Found at i:19342724 original size:149 final size:142
Alignment explanation
Indices: 19342418--19342840 Score: 455
Period size: 149 Copynumber: 2.9 Consensus size: 142
19342408 GTAATTTGTG
* * * * * * *
19342418 TGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACG-AGTGCCAGTGTAAGA-TA
1 TGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATGGATATGCAGAGCTAGTGTAAGACCA
* * * *
19342481 TGTCCGGGACAT-GCATCGGCCTTTAGATGTAAGCTAGTGTAAGA-CATGCCTGGGACAT-GCAT
66 TGTCTGGGACATGGCATCGGCCGTAAGATG-AAGCTAGTGTAAGACCATGTCTGGGACATGGCAT
19342543 CGGCTACGAGACA
130 CGGCTACGAGACA
* * *
19342556 TGTCAGTGTAAGATCATGTCTGGGACATGGCATAAGCATGGATATGCAAGAGCTAGTGTAAGACC
1 TGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATGGATATGC-AGAGCTAGTGTAAGACC
* * *
19342621 ATGTCTGGGACATGGAATCAGCACGTAAGTATGAGAGCTAGTGTAAGACCATGTCTAGGACATGG
65 ATGTCTGGGACATGGCATCGGC-CGTAAG-ATGA-AGCTAGTGTAAGACCATGTCTGGGACATGG
* *
19342686 CATCGGCTTCGATGAGGA
127 CATCGGCTACGA-GA-CA
* * *
19342704 TAGCCAGTGTAAGACCATGTCTGGGACATGGAATCAGCACGTAAGTATG-AGAGCTAGTGTAAGA
1 T-GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATG-GA-TATGCAGAGCTAGTGTAAGA
* * *
19342768 CCATGTCTGGGACATGGCATCGGCTTCG-ATGAGGATAGCCAGTGTAAGACCATGTCTGGGACAT
63 CCATGTCTGGGACATGGCATCGGC--CGTAAGATGA-AGCTAGTGTAAGACCATGTCTGGGACAT
19342832 GGCATCGGC
125 GGCATCGGC
19342841 AACTTAACCC
Statistics
Matches: 237, Mismatches: 33, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
138 39 0.16
140 13 0.05
141 12 0.05
142 6 0.03
143 5 0.02
144 16 0.07
145 12 0.05
146 12 0.05
147 2 0.01
148 40 0.17
149 73 0.31
150 3 0.01
151 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.23
Consensus pattern (142 bp):
TGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATGGATATGCAGAGCTAGTGTAAGACCA
TGTCTGGGACATGGCATCGGCCGTAAGATGAAGCTAGTGTAAGACCATGTCTGGGACATGGCATC
GGCTACGAGACA
Found at i:19342735 original size:99 final size:99
Alignment explanation
Indices: 19342610--19342833 Score: 439
Period size: 99 Copynumber: 2.3 Consensus size: 99
19342600 TGCAAGAGCT
19342610 AGTGTAAGACCATGTCTGGGACATGGAATCAGCACGTAAGTATGAGAGCTAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGAATCAGCACGTAAGTATGAGAGCTAGTGTAAGACCATGT
19342675 CTAGGACATGGCATCGGCTTCGATGAGGATAGCC
66 CTAGGACATGGCATCGGCTTCGATGAGGATAGCC
19342709 AGTGTAAGACCATGTCTGGGACATGGAATCAGCACGTAAGTATGAGAGCTAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGAATCAGCACGTAAGTATGAGAGCTAGTGTAAGACCATGT
*
19342774 CTGGGACATGGCATCGGCTTCGATGAGGATAGCC
66 CTAGGACATGGCATCGGCTTCGATGAGGATAGCC
19342808 AGTGTAAGACCATGTCTGGGACATGG
1 AGTGTAAGACCATGTCTGGGACATGG
19342834 CATCGGCAAC
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 124 1.00
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (99 bp):
AGTGTAAGACCATGTCTGGGACATGGAATCAGCACGTAAGTATGAGAGCTAGTGTAAGACCATGT
CTAGGACATGGCATCGGCTTCGATGAGGATAGCC
Found at i:19355223 original size:47 final size:47
Alignment explanation
Indices: 19355164--19355293 Score: 156
Period size: 47 Copynumber: 2.8 Consensus size: 47
19355154 GTGTGAATAA
* * * *
19355164 TACCTTGATTTGGCTATGAG-CAGGGGTATAGGTACTCTGGGATAAGT
1 TACCTTGATTTGGCTACGAGCCA-GGGTATAGGTACTCCGAGATAAAT
* * *
19355211 TATCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCGAGATAAAT
1 TACCTTGATTTGGCTACGAGCCAGGGTATAGGTACTCCGAGATAAAT
*
19355258 TACCTTGATTTGGCTAC-AGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACGA-GCCAGGGTATAGGTACT
19355294 TATCAATTGA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
47 70 0.97
48 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGAGCCAGGGTATAGGTACTCCGAGATAAAT
Found at i:19360892 original size:15 final size:15
Alignment explanation
Indices: 19360847--19360895 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
19360837 ACACCAAGGG
*
19360847 ACACACGGCTGTGTA
1 ACACACGGCTGTGTC
*
19360862 ACATCACTG-TGTGTC
1 ACA-CACGGCTGTGTC
*
19360877 ACACACGGCTGAGTC
1 ACACACGGCTGTGTC
19360892 ACAC
1 ACAC
19360896 GCCTGTGTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 4 0.14
15 20 0.71
16 4 0.14
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (15 bp):
ACACACGGCTGTGTC
Found at i:19367318 original size:17 final size:17
Alignment explanation
Indices: 19367296--19367328 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19367286 GTTAATAATA
19367296 GTTAACAGAATTGGATG
1 GTTAACAGAATTGGATG
*
19367313 GTTAACATAATTGGAT
1 GTTAACAGAATTGGAT
19367329 AAAAATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (17 bp):
GTTAACAGAATTGGATG
Found at i:19384710 original size:18 final size:18
Alignment explanation
Indices: 19384687--19384779 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
19384677 CCCAATTACT
*
19384687 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* *
19384705 GTATACATGAATAGTGCC
1 GTATACGTGAATAGTACC
*
19384723 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* * *
19384741 GTATACGTAAATAGTGCT
1 GTATACGTGAATAGTACC
19384759 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
19384777 GTA
1 GTA
19384780 AACGGTCGTA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:19384739 original size:36 final size:36
Alignment explanation
Indices: 19384688--19384779 Score: 139
Period size: 36 Copynumber: 2.6 Consensus size: 36
19384678 CCAATTACTG
* *
19384688 TATACGTGAACAGTACCGTATACATGAATAGTGCCA
1 TATACGTGAATAGTACCGTATACATAAATAGTGCCA
* **
19384724 TATACGTGAATAGTACCGTATACGTAAATAGTGCTG
1 TATACGTGAATAGTACCGTATACATAAATAGTGCCA
19384760 TATACGTGAATAGTACCGTA
1 TATACGTGAATAGTACCGTA
19384780 AACGGTCGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (36 bp):
TATACGTGAATAGTACCGTATACATAAATAGTGCCA
Found at i:19386672 original size:33 final size:33
Alignment explanation
Indices: 19386634--19386701 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
19386624 GTCTTACTAT
19386634 TTCAGTTAATATAAAGTTAACCACCCTATTAAG
1 TTCAGTTAATATAAAGTTAACCACCCTATTAAG
*
19386667 TTCAGTTAATATAAAGTTAACCACCCTGTTAAG
1 TTCAGTTAATATAAAGTTAACCACCCTATTAAG
19386700 TT
1 TT
19386702 TTAGATTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (33 bp):
TTCAGTTAATATAAAGTTAACCACCCTATTAAG
Found at i:19390164 original size:29 final size:29
Alignment explanation
Indices: 19390101--19390182 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
19390091 TATTGTTTTA
19390101 GAAAAAATAAATTTGACAAGATGGGATAT
1 GAAAAAATAAATTTGACAAGATGGGATAT
* ** * * *
19390130 GCAAAAATAAATTTGACGTGATGTGTTCT
1 GAAAAAATAAATTTGACAAGATGGGATAT
* * *
19390159 GAAAAAATTATTTTGATAAGATGG
1 GAAAAAATAAATTTGACAAGATGG
19390183 ATTTTATTTT
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (29 bp):
GAAAAAATAAATTTGACAAGATGGGATAT
Found at i:19400006 original size:14 final size:14
Alignment explanation
Indices: 19399983--19400012 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19399973 TTGAAAATAT
19399983 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
19399997 GTTGATTTGGATTG
1 GTTGAATTGGATTG
19400011 GT
1 GT
19400013 CTCGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:19402312 original size:37 final size:37
Alignment explanation
Indices: 19402262--19402406 Score: 227
Period size: 37 Copynumber: 3.9 Consensus size: 37
19402252 ACCTTTAGCT
* * * *
19402262 CGGACGAAATCTCCATACGAAGTTATCGGGTCTTACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
19402299 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
*
19402336 CGGGCAAAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
* *
19402373 CGGACATACTCTCCACACGTAGTCATCGGGTCTT
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTT
19402407 TAGAGCTCGG
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 100 1.00
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (37 bp):
CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
Found at i:19402596 original size:47 final size:47
Alignment explanation
Indices: 19402525--19402932 Score: 672
Period size: 47 Copynumber: 8.6 Consensus size: 47
19402515 CCCTTCGGGA
* * * * * *
19402525 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19402572 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19402619 CTTACCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19402666 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19402713 CTTATCACATATATACACTTTCACATTCATCACATCGACTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19402760 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
19402807 CTTATCACATATATACACTTTCACATTCATCACATCGGTTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19402854 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19402901 CTTATCACATATATATATGCTTTCACATTCAT
1 CTTATCACATATATACA--CTTTCACATTCAT
19402933 TCAAATATAC
Statistics
Matches: 342, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
47 329 0.96
49 13 0.04
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:19434642 original size:3 final size:3
Alignment explanation
Indices: 19434636--19434872 Score: 68
Period size: 3 Copynumber: 80.0 Consensus size: 3
19434626 TTAGAACGTA
* * *
19434636 TAT TAT TAT TAT TAAT GTAT CAT TGT TAT TTT CTAT T-T TAT TAT TACT
1 TAT TAT TAT TAT T-AT -TAT TAT TAT TAT TAT -TAT TAT TAT TAT TA-T
* * *
19434684 T-T TAT TAC TAT TGT T-T CTAT TAT TAT TAT T-T TCAT TACT T-C TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT T-AT TA-T TAT TAT
* * * * * *
19434728 TAT TAT TAT CAT TAT TTT CTAT TAT CAT TAA TA- TGT TGT T-T GT-T
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * * * * *
19434772 TAT TAT TAT TAT TAT TAT TAA CAC TAT TAT CAT CAT TA- TAT T-T AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
19434818 T-T T-T TAAA TAT TAT TAC CAT TA- TAT TTT TTT TAT TAT TAC TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
19434861 TAT TTT TAT TAT
1 TAT TAT TAT TAT
19434873 CTGTCCTATT
Statistics
Matches: 173, Mismatches: 40, Indels: 42
0.68 0.16 0.16
Matches are distributed among these distances:
2 20 0.12
3 136 0.79
4 16 0.09
5 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:19434735 original size:30 final size:30
Alignment explanation
Indices: 19434636--19434751 Score: 87
Period size: 30 Copynumber: 3.8 Consensus size: 30
19434626 TTAGAACGTA
* ** *
19434636 TATTATTATTATTAATGTATCATTGTTATTTT
1 TATTATTATTATT-AT-TTTCATTACTATTAT
*
19434668 CTATT-TTATTATTACTTTT-ATTACTATTGT
1 -TATTATTATTATTA-TTTTCATTACTATTAT
19434698 T-TCTATTATTATTATTTTCATTACT-TCTAT
1 TAT-TATTATTATTATTTTCATTACTAT-TAT
*
19434728 TATTATTATCATTATTTTCTATTA
1 TATTATTATTATTATTTTC-ATTA
19434752 TCATTAATAT
Statistics
Matches: 70, Mismatches: 6, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
28 1 0.01
29 7 0.10
30 41 0.59
31 8 0.11
32 9 0.13
33 4 0.06
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.63
Consensus pattern (30 bp):
TATTATTATTATTATTTTCATTACTATTAT
Found at i:19436800 original size:19 final size:19
Alignment explanation
Indices: 19436776--19436821 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
19436766 CATTCTTTCT
*
19436776 TTTGCATT-CATTCCATGCA
1 TTTGCATTGCATTACAT-CA
*
19436795 TTTGCATTGCATTACATTA
1 TTTGCATTGCATTACATCA
19436814 TTTGCATT
1 TTTGCATT
19436822 AGATTTTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.48
Consensus pattern (19 bp):
TTTGCATTGCATTACATCA
Found at i:19447542 original size:27 final size:28
Alignment explanation
Indices: 19447457--19447554 Score: 171
Period size: 28 Copynumber: 3.5 Consensus size: 28
19447447 TAAATTGTAC
19447457 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
19447485 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
19447513 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
19447540 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19447555 GACTTAATAT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 23 0.34
28 45 0.66
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:19447565 original size:27 final size:27
Alignment explanation
Indices: 19447457--19447567 Score: 107
Period size: 28 Copynumber: 4.0 Consensus size: 27
19447447 TAAATTGTAC
* * *
19447457 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* * *
19447485 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
19447513 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
19447540 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
19447567 A
1 A
19447568 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 29 0.38
28 48 0.62
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:19455641 original size:27 final size:28
Alignment explanation
Indices: 19455556--19455653 Score: 171
Period size: 28 Copynumber: 3.5 Consensus size: 28
19455546 TAAATTGTAC
19455556 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
19455584 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
19455612 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
19455639 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19455654 GACTTAATAT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 23 0.34
28 45 0.66
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:19455664 original size:27 final size:27
Alignment explanation
Indices: 19455556--19455666 Score: 107
Period size: 28 Copynumber: 4.0 Consensus size: 27
19455546 TAAATTGTAC
* * *
19455556 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* * *
19455584 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
19455612 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
19455639 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
19455666 A
1 A
19455667 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 29 0.38
28 48 0.62
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:19457435 original size:46 final size:46
Alignment explanation
Indices: 19457348--19457435 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
19457338 TGAAGAAGCA
*
19457348 ACAAATCCTATACCCCTGAGTTGCAGTGGGATAAATTGAAGATGGT
1 ACAAATCCTATACCCCTGAGTTGCAGTGGGATAAATAGAAGATGGT
* **
19457394 ACAAATCCTATACCCCTTAGTTGCAGTGGGATGGATAGAAGA
1 ACAAATCCTATACCCCTGAGTTGCAGTGGGATAAATAGAAGA
19457436 AACCACAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (46 bp):
ACAAATCCTATACCCCTGAGTTGCAGTGGGATAAATAGAAGATGGT
Found at i:19457444 original size:46 final size:46
Alignment explanation
Indices: 19457339--19457445 Score: 133
Period size: 46 Copynumber: 2.3 Consensus size: 46
19457329 TCAATTGATT
*
19457339 GAAGAAGCAACAAATCCTATACCCCTGAGTTGCAGTGGGATAAATT
1 GAAGAAGCAACAAATCCTATACCCCTGAGTTGCAGTGGGATAAATA
* ** * **
19457385 GAAGATGGTACAAATCCTATACCCCTTAGTTGCAGTGGGATGGATA
1 GAAGAAGCAACAAATCCTATACCCCTGAGTTGCAGTGGGATAAATA
* *
19457431 GAAGAAACCACAAAT
1 GAAGAAGCAACAAAT
19457446 TTTATCTCAT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (46 bp):
GAAGAAGCAACAAATCCTATACCCCTGAGTTGCAGTGGGATAAATA
Found at i:19457878 original size:44 final size:44
Alignment explanation
Indices: 19457830--19457947 Score: 130
Period size: 44 Copynumber: 2.7 Consensus size: 44
19457820 GATGGAAAAT
* * * * * *
19457830 CTTATCTCTATGTAGTGGCAATGGAGCAGATTTAAGCCACCAGC
1 CTTATCTCTCTGAAGTTGCAATGGAGCAGATTCAAGACACAAGC
* * * *
19457874 CTTATCTAC-CTGAAGTTGCAGTGGAGCAGGTTCAAGATACAAGT
1 CTTATCT-CTCTGAAGTTGCAATGGAGCAGATTCAAGACACAAGC
19457918 CTTATCTCTCTGAAGTTGCAATGGAGCAGA
1 CTTATCTCTCTGAAGTTGCAATGGAGCAGA
19457948 CTGAAAATTA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
43 1 0.02
44 58 0.97
45 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (44 bp):
CTTATCTCTCTGAAGTTGCAATGGAGCAGATTCAAGACACAAGC
Found at i:19457939 original size:88 final size:88
Alignment explanation
Indices: 19457786--19458079 Score: 281
Period size: 88 Copynumber: 3.3 Consensus size: 88
19457776 ATTCACAGAT
** * * *
19457786 CTTATCTCCCTAAGCAGTAGTGGAGCA-AATCAAAGATGGAAAATCTTATCTCTATGTAGTGGCA
1 CTTATCTCCCTAAGTTGCAGTGGAGCAGGATCGAAGAT-GAAAATCTTATCTCTATGTAGTGGCA
19457850 ATGGAGCAGATTTAAGCCACCAGC
65 ATGGAGCAGATTTAAGCCACCAGC
* * * * * *
19457874 CTTATCTACCTGAAGTTGCAGTGGAGCAGGTTC-AAGAT-ACAAGTCTTATCTCTCTGAAGTTGC
1 CTTATCTCCCT-AAGTTGCAGTGGAGCAGGATCGAAGATGA-AAATCTTATCTCTATGTAGTGGC
** *** * **
19457937 AATGGAGCAGACTGAAAATTACAAAT
64 AATGGAGCAGA-TTTAAGCCACCAGC
**** *
19457963 CTTATCTCCCTAAGCAATAGTGGAGCA-GATCGAAGATGGAAAATCTTATCTCTATGTAGCGGCA
1 CTTATCTCCCTAAGTTGCAGTGGAGCAGGATCGAAGAT-GAAAATCTTATCTCTATGTAGTGGCA
*
19458027 ATGGAGCAAATTTAAGCCACCAGC
65 ATGGAGCAGATTTAAGCCACCAGC
19458051 CTTATCTCCCTAAAGTTGCAGTGGAGCAG
1 CTTATCTCCCT-AAGTTGCAGTGGAGCAG
19458080 ACTGAAAATT
Statistics
Matches: 155, Mismatches: 42, Indels: 16
0.73 0.20 0.08
Matches are distributed among these distances:
87 4 0.03
88 74 0.48
89 74 0.48
90 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (88 bp):
CTTATCTCCCTAAGTTGCAGTGGAGCAGGATCGAAGATGAAAATCTTATCTCTATGTAGTGGCAA
TGGAGCAGATTTAAGCCACCAGC
Found at i:19458122 original size:177 final size:178
Alignment explanation
Indices: 19457775--19458124 Score: 497
Period size: 177 Copynumber: 2.0 Consensus size: 178
19457765 AACATCGGTG
* *
19457775 AATTCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGAAAATCTTATCTCTA
1 AATTCACAAATCTTATCTCCCTAAGCAATAGTGGAGCAAATCAAAGATGGAAAATCTTATCTCTA
* * * **
19457840 TGTAGTGGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTACCTGAAGTTGCAGTGGAGCAGGT
66 TGTAGCGGCAATGGAGCAAATTTAAGCCACCAGCCTTATCTACCTAAAGTTGCAGTGGAGCAGAC
* * **
19457905 TCAAGATACAAGTCTTATCTCTCTGAAGTTGCAATGGAGCAGACTGAA
131 TCAAAATACAAGTCTTATCTCCCTGAAGCAGCAATGGAGCAGACTGAA
* *
19457953 AATT-ACAAATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGAAAATCTTATCTCTA
1 AATTCACAAATCTTATCTCCCTAAGCAATAGTGGAGCAAATCAAAGATGGAAAATCTTATCTCTA
*
19458017 TGTAGCGGCAATGGAGCAAATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGCAGTGGAGCAGAC
66 TGTAGCGGCAATGGAGCAAATTTAAGCCACCAGCCTTATCTACCTAAAGTTGCAGTGGAGCAGAC
* *** * *
19458082 TGAAAATTGTAGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGA
131 TCAAAATACAAG-TCTTATCTCCCTGAAGCAGCAATGGAGCAGA
19458125 TCGAAGACGA
Statistics
Matches: 151, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
177 136 0.90
178 15 0.10
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (178 bp):
AATTCACAAATCTTATCTCCCTAAGCAATAGTGGAGCAAATCAAAGATGGAAAATCTTATCTCTA
TGTAGCGGCAATGGAGCAAATTTAAGCCACCAGCCTTATCTACCTAAAGTTGCAGTGGAGCAGAC
TCAAAATACAAGTCTTATCTCCCTGAAGCAGCAATGGAGCAGACTGAA
Found at i:19458142 original size:44 final size:44
Alignment explanation
Indices: 19458094--19458278 Score: 124
Period size: 44 Copynumber: 4.2 Consensus size: 44
19458084 AAAATTGTAG
* *
19458094 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATAA
1 ATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACAATAA
* * * ** * *
19458138 ATCTTATCTCCATGTAGC-GACAATGGAGCAGATTTAAGCCACT-A
1 ATCTTATCTCCCT-AAGCAG-CAGTGGAGCAGATCGAAGACAATAA
** * * ** * *
19458182 GCCTTATCTCCCTGAGCAGCAGTGGAGCAG-GCTGAAGATTACAG
1 ATCTTATCTCCCTAAGCAGCAGTGGAGCAGATC-GAAGACAATAA
** * *
19458226 ATCTTATCTCCCTAAGCAGTGGTGGATCAGATCGAAGACAATGA
1 ATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACAATAA
*
19458270 ATCTCATCT
1 ATCTTATCT
19458279 TCCCGAGGTA
Statistics
Matches: 99, Mismatches: 36, Indels: 12
0.67 0.24 0.08
Matches are distributed among these distances:
43 16 0.16
44 63 0.64
45 20 0.20
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACAATAA
Found at i:19458191 original size:177 final size:176
Alignment explanation
Indices: 19457784--19458170 Score: 382
Period size: 177 Copynumber: 2.2 Consensus size: 176
19457774 GAATTCACAG
* ** * * * ** * *
19457784 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGAAAATCTTATCTCTATGTAGTGGC
1 ATCTTATCTCCATAAGCAACAATGGAGCAGATCGAAGA-CCAAAACCTTATCTCTATGTAGCGGC
* * ** *
19457849 AATGGAGCAGATTTAAGCCACCAGCCTTATCTACCTGAAGTTGCAGTGGAGCAGGTTCAAGATAC
65 AATGGAGCAAATTTAAGCCACCAGCCTTATCTACCTAAAGTTGCAGTGGAGCAGACTCAAAATAC
* ** **
19457914 AAGTCTTATCTCTCTGAAGTTGCAATGGAGCAGACTGAAAATTACAA
130 AAGTCTTATCTCCCTGAAGCAGCAATGGAGCAGACTGAAAACGACAA
* * * ** *
19457961 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGAAAATCTTATCTCTATGTAGCGGC
1 ATCTTATCTCCATAAGCAACAATGGAGCAGATCGAAGA-CCAAAACCTTATCTCTATGTAGCGGC
* * **
19458026 AATGGAGCAAATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAAATTG
65 AATGGAGCAAATTTAAGCCACCAGCCTTATCTACCTAAAGTTGCAGTGGAGCAGACTCAAAATAC
* * * * *
19458091 TAGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGA-TCGAAGACGATAA
130 AAG-TCTTATCTCCCTGAAGCAGCAATGGAGCAGACT-GAAAACGACAA
* *
19458138 ATCTTATCTCCATGTAGCGACAATGGAGCAGAT
1 ATCTTATCTCCAT-AAGCAACAATGGAGCAGAT
19458171 TTAAGCCACT
Statistics
Matches: 179, Mismatches: 28, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
176 1 0.01
177 152 0.85
178 26 0.15
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (176 bp):
ATCTTATCTCCATAAGCAACAATGGAGCAGATCGAAGACCAAAACCTTATCTCTATGTAGCGGCA
ATGGAGCAAATTTAAGCCACCAGCCTTATCTACCTAAAGTTGCAGTGGAGCAGACTCAAAATACA
AGTCTTATCTCCCTGAAGCAGCAATGGAGCAGACTGAAAACGACAA
Found at i:19458264 original size:132 final size:131
Alignment explanation
Indices: 19457939--19458640 Score: 765
Period size: 132 Copynumber: 5.3 Consensus size: 131
19457929 GAAGTTGCAA
* * * * *
19457939 TGGAGCAGACTGAAAATTACAAATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGA-
1 TGGAGCAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CGAT
* * * * * * *
19458003 AAATCTTATCT-CT-ATGTAG-CGGCAATGGAGCAAATTTAAGCCACCAGCCTTATCTCCCTAAA
65 GAATCTTATCTCCTGAGGTAGTAGG----GAAGCAGATTTAAGCCACTAGCCTTATCTCCCT-GA
**
19458065 GTTGCAG
125 GCAGCAG
* * ** *
19458072 TGGAGCAGACTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATA
1 TGGAGCAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATG
** *
19458137 AATCTTATCTCCATGTAGCG-ACAATGG-AGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCA
66 AATCTTATCTCC-TG-AG-GTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCA
19458200 GCAG
128 GCAG
* * *
19458204 TGGAGCAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTGGTGGATCAGATCGAAGACAATG
1 TGGAGCAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATG
* * * * * * *
19458269 AATCTCATCTTCCCGAGGTAGTAGGGAAGTAGATTTAAGCCACTAGCCTTAACTCTCTGAGTAGT
66 AATCTTATC-TCCTGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCAGC
19458334 AG
130 AG
** * * *
19458336 T-GAGCAGGCTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAATGGAGTAGATCGAAGACGGTG
1 TGGAGCAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATG
* *
19458400 AATCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCAAC
66 AATCTTATC-TCCTGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCAGC
19458465 AG
130 AG
* * * * *
19458467 TGGAGCTGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGCAGTGGAACAGATCGAAGA-TAGC
1 TGGAGCAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGA-T
* * * *
19458531 GAATCTTATTTTCCTGGGGTAGTAGGGAAGCAGATTTAAGCCACTAGCTTTATCTCTCTGAGCAG
65 GAATCTTA-TCTCCTGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCAG
19458596 CAG
129 CAG
* **
19458599 T-GAGCAGGCCGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
1 TGGAGCAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTA
19458641 ACAGAGTAGA
Statistics
Matches: 488, Mismatches: 68, Indels: 28
0.84 0.12 0.05
Matches are distributed among these distances:
130 1 0.00
131 158 0.32
132 222 0.45
133 100 0.20
134 2 0.00
135 1 0.00
137 2 0.00
138 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (131 bp):
TGGAGCAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATG
AATCTTATCTCCTGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCAGCA
G
Found at i:19458433 original size:263 final size:263
Alignment explanation
Indices: 19458031--19458656 Score: 871
Period size: 263 Copynumber: 2.4 Consensus size: 263
19458021 GCGGCAATGG
* * * * * * *
19458031 AGCAAATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAAATTGTAGAT
1 AGCAGATTTAAGCCACTAGCCTTATCTCTCT-GAGTAGCAGT-GAGCAGGCTGAAGATTGTAGAT
* * *
19458096 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATAAATCTTATCTCCATGTAGCGACAA
64 CTTATCTCCCTAAGCAGTAATGGAGTAGATCGAAGACGATAAATCTTATCTCCACGTAGCGACAA
* *
19458161 TGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCAGCAGTGGAGCAGGCTGAAGATTACAG
129 GGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCAACAGTGGAGCAGGCTGAAGATTACAG
** * *
19458226 ATCTTATCTCCCTAAGCAGTGGTGGATCAGATCGAAGACAATGAATCTCATCTTCCCGAGGTAGT
194 ATCTTATCTCCCTAAGCAGCAGTGGAACAGATCGAAGACAACGAATCTCATCTTCCCGAGGTAGT
19458291 AGGGA
259 AGGGA
* * *
19458296 AGTAGATTTAAGCCACTAGCCTTAACTCTCTGAGTAGTAGTGAGCAGGCTGAAGATTGTAGATCT
1 AGCAGATTTAAGCCACTAGCCTTATCTCTCTGAGTAGCAGTGAGCAGGCTGAAGATTGTAGATCT
* * **
19458361 TATCTCCCTAAGCAGTAATGGAGTAGATCGAAGACGGTGAATCTTATCTTCC-CG-AG-GTAGTA
66 TATCTCCCTAAGCAGTAATGGAGTAGATCGAAGACGATAAATCTTATC-TCCACGTAGCG-ACAA
*
19458423 GGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCAACAGTGGAGCTGGCTGAAGATTACA
129 GGG-AGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCAACAGTGGAGCAGGCTGAAGATTACA
* * * * * *
19458488 GATCTTATCTCCCTAAGCAGCAGTGGAACAGATCGAAGATAGCGAATCTTATTTTCCTGGGGTAG
193 GATCTTATCTCCCTAAGCAGCAGTGGAACAGATCGAAGACAACGAATCTCATCTTCCCGAGGTAG
19458553 TAGGGA
258 TAGGGA
* * *
19458559 AGCAGATTTAAGCCACTAGCTTTATCTCTCTGAGCAGCAGTGAGCAGGCCGAAGATTGTAGATCT
1 AGCAGATTTAAGCCACTAGCCTTATCTCTCTGAGTAGCAGTGAGCAGGCTGAAGATTGTAGATCT
**
19458624 TATCTCCCTAAGCAGTAACAGAGTAGATCGAAG
66 TATCTCCCTAAGCAGTAATGGAGTAGATCGAAG
19458657 CTAAAAATCT
Statistics
Matches: 320, Mismatches: 38, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
261 1 0.00
262 6 0.02
263 277 0.87
264 10 0.03
265 26 0.08
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (263 bp):
AGCAGATTTAAGCCACTAGCCTTATCTCTCTGAGTAGCAGTGAGCAGGCTGAAGATTGTAGATCT
TATCTCCCTAAGCAGTAATGGAGTAGATCGAAGACGATAAATCTTATCTCCACGTAGCGACAAGG
GAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCAACAGTGGAGCAGGCTGAAGATTACAGAT
CTTATCTCCCTAAGCAGCAGTGGAACAGATCGAAGACAACGAATCTCATCTTCCCGAGGTAGTAG
GGA
Found at i:19458951 original size:13 final size:13
Alignment explanation
Indices: 19458915--19458963 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
19458905 GTCCAATTAA
19458915 CACCCCACTAAAC
1 CACCCCACTAAAC
* * *
19458928 TA-ACTACTAAAC
1 CACCCCACTAAAC
19458940 CACCCCACTAAAC
1 CACCCCACTAAAC
*
19458953 CACCCTACTAA
1 CACCCCACTAA
19458964 CTCCATCACC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.41, C:0.45, G:0.00, T:0.14
Consensus pattern (13 bp):
CACCCCACTAAAC
Found at i:19459404 original size:3 final size:3
Alignment explanation
Indices: 19459396--19459859 Score: 88
Period size: 3 Copynumber: 154.3 Consensus size: 3
19459386 GGGGAGAGTG
*
19459396 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA CTT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* * * * * * *
19459441 CTG TTA TT- CTA TATA CTA TTA CTG TT- TTC TT- TT- TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * *
19459483 GTA GTA GTAA CGTA ATA GTA TTT TTA TTA TT- TTA TTA TTA TTT TTA
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
19459529 CCTTT TTA TTA CTA TTA TTA TTAA CCTA CTA TTA TTA TTT TTA TTA ATA
1 --TTA TTA TTA TTA TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TTA
** * * * ** *
19459578 -TA GCA TTA TT- TTC TT- TTT TTA -TA TTG TTA TTA TTA TTA GCA CGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * *
19459623 -TA TTA TTA TTAA TGTA TCA TTG TTA TTT TCTA TT- TTA TTA TTA CTT-
1 TTA TTA TTA TT-A T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA -TTA
* * *
19459669 TTA TTA CTA TTG TT- TCTA TTA TTA TTA TT- TTCA TTA CTT- TCA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TT-A TTA -TTA TTA TTA
* * * * *
19459714 TTA TTA TCA TTA TTT TCTA TTA TCA TTA ATA TGTCG TT- TGT- TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-T-A TTA T-TA TTA TTA
* ** * * * *
19459761 TTA CTA TTA TTA TTA ACA CTA TTA TCA TCA TTA -TA TTTA CTT- TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA
* ** * * * *
19459806 TTA ATA TTA TTA CCA TTA -TA TTT TTT TTA TTA TTA TTA CTA TTA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19459853 TTA TTA T
1 TTA TTA T
19459860 CCGTCCTATT
Statistics
Matches: 335, Mismatches: 87, Indels: 78
0.67 0.17 0.16
Matches are distributed among these distances:
2 37 0.11
3 263 0.79
4 30 0.09
5 5 0.01
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:19459526 original size:20 final size:20
Alignment explanation
Indices: 19459501--19459574 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
19459491 AACGTAATAG
19459501 TATTTTTATTATTTTATTAT
1 TATTTTTATTATTTTATTAT
* *
19459521 TATTTTTACCT-TTTTATTAC
1 TATTTTTA-TTATTTTATTAT
* **
19459541 TATTATTATTAACCTACTATTAT
1 TATTTTTATT-A--TTTTATTAT
19459564 TATTTTTATTA
1 TATTTTTATTA
19459575 ATATAGCATT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 1 0.02
20 23 0.56
21 1 0.02
22 1 0.02
23 15 0.37
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTTTATTATTTTATTAT
Found at i:19459839 original size:26 final size:25
Alignment explanation
Indices: 19459801--19459854 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
19459791 TTATATTTAC
19459801 TTTTTTTAATATTATTACCATTATAT
1 TTTTTTTAATATTATTACCATTAT-T
* *
19459827 TTTTTTTATTATTATTACTATTATT
1 TTTTTTTAATATTATTACCATTATT
19459852 TTT
1 TTT
19459855 ATTATCCGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTTTTAATATTATTACCATTATT
Found at i:19459978 original size:23 final size:23
Alignment explanation
Indices: 19459952--19459996 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
19459942 ATTCGAATTT
* *
19459952 TCTATGTTATTTCATTTTTTATC
1 TCTATATTATTTCATTTATTATC
*
19459975 TCTATATTATTTTATTTATTAT
1 TCTATATTATTTCATTTATTAT
19459997 TATCTTTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (23 bp):
TCTATATTATTTCATTTATTATC
Found at i:19463511 original size:24 final size:24
Alignment explanation
Indices: 19463479--19463527 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
19463469 CAAAGATTGC
*
19463479 GGAGATGTTTGCATCACCCACAAG
1 GGAGATGTTTGAATCACCCACAAG
* * *
19463503 GGAGGTGTTTGAATCCCCCATAAG
1 GGAGATGTTTGAATCACCCACAAG
19463527 G
1 G
19463528 TGATGGGGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (24 bp):
GGAGATGTTTGAATCACCCACAAG
Found at i:19466071 original size:39 final size:40
Alignment explanation
Indices: 19466003--19466092 Score: 121
Period size: 39 Copynumber: 2.2 Consensus size: 40
19465993 TAAAATGTAT
* *
19466003 TTATATTAAAAAACTCTACCATAATTATAATAAATGTTTTA
1 TTATATTAAAAAACTCTA-CATAAATATAATAAATATTTTA
19466044 TTATATTAAAAAACAT-TA-ATAAATATAATAAATATTTTA
1 TTATATTAAAAAAC-TCTACATAAATATAATAAATATTTTA
*
19466083 TTTTATTAAA
1 TTATATTAAA
19466093 TATAAATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
39 28 0.62
41 16 0.36
42 1 0.02
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (40 bp):
TTATATTAAAAAACTCTACATAAATATAATAAATATTTTA
Found at i:19467673 original size:37 final size:37
Alignment explanation
Indices: 19467591--19467681 Score: 119
Period size: 37 Copynumber: 2.5 Consensus size: 37
19467581 ACACAGCTAA
* *
19467591 CCTCTCAAGTCACTTAGTCGAGTAGAAACACTGGTAG
1 CCTCTTAAGTCACTTAGTCGAGTAGAAACACTAGTAG
* * * *
19467628 CTTATTAAGTCACTTAGTCGAGTAGAAATACTATTAG
1 CCTCTTAAGTCACTTAGTCGAGTAGAAACACTAGTAG
*
19467665 CCTCTTAAGTAACTTAG
1 CCTCTTAAGTCACTTAG
19467682 CTAAATATCA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (37 bp):
CCTCTTAAGTCACTTAGTCGAGTAGAAACACTAGTAG
Found at i:19468764 original size:19 final size:20
Alignment explanation
Indices: 19468740--19468777 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
19468730 AAATCATACT
19468740 TTATAATAATT-AATTGTAA
1 TTATAATAATTCAATTGTAA
*
19468759 TTATAATTATTCAATTGTA
1 TTATAATAATTCAATTGTA
19468778 TTCTTTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
TTATAATAATTCAATTGTAA
Found at i:19471363 original size:270 final size:263
Alignment explanation
Indices: 19470753--19471474 Score: 893
Period size: 270 Copynumber: 2.7 Consensus size: 263
19470743 CCCACTTCTA
* * * * * *
19470753 AGAATCAGCCGTTGTGCCTTCACAAATTATTGT-GAAGCTTAGAAATTCACTTTGGGTAGCCAAT
1 AGAATCTGCCATTGTGCATTCACAAATTATT-TAAAAGCTTAGAAATTCACATTGGGTAGCCTAT
* * * * * * *
19470817 TACAACTCTTCCCTATCAAATTCCCATCAAAGGTAAGAGCATAAAGCACAACGGAACCAATAAAT
65 GACAACTCTTCCCTATCAAATCCCCATCAAAGGTAAGGGCAT-AAGCACAATGGAAGCAGTAACT
* * *
19470882 CCTACTTCAGAAAATCTGTCACAGTGCATTCACAAA-TCATTGAAAACCATATTAGGAATTTATA
129 CCTACTTCAGAAAACCTGCCACAGTGCATTCACAAATTCATTGAAAAGC--A-TAGGAATTTATA
* * *
19470946 GTCTATTACGGTTCTTCCCTATCAAATCTCCACCTAATGAAAATGTGTAAAAGCACAGAAAATCC
191 GTCTATCACAGTTCTTCCCTATCAAATCTCCACCTAATGAAAAGGTGTAAAAGCACAGAAAATCC
* **
19471011 TACTTTCG
256 CACTACCG
* * * *
19471019 AGAATCTGACATTGTGCTTTCACAAATTATTGAAAAGCTTATG-AATTCACATTGGGTAACCTAT
1 AGAATCTGCCATTGTGCATTCACAAATTATTTAAAAGCTTA-GAAATTCACATTGGGTAGCCTAT
*
19471083 GACAACTCTTCCCTATCAAATCCCCATCAAAGGTAAGGGCATAAGCACAATGGAAGCAGCAACTC
65 GACAACTCTTCCCTATCAAATCCCCATCAAAGGTAAGGGCATAAGCACAATGGAAGCAGTAACTC
* * *
19471148 CTAATTCAGAAAACCTGCCATAGTGCATTCACAAATTC-TTGAAAAGCATAGGAATTTATAGTTT
130 CTACTTCAGAAAACCTGCCACAGTGCATTCACAAATTCATTGAAAAGCATAGGAATTTATAGTCT
* *
19471212 ATCACAGTTCTTCCCTATCAAATCTCCATCT-ATGGCAAAGGTGT-AAAGCACAATCGAACTATT
195 ATCACAGTTCTTCCCTATCAAATCTCCACCTAAT-GAAAAGGTGTAAAAGCAC-A--G----A--
19471275 AAATCCCACTACCG
250 AAATCCCACTACCG
* * * *
19471289 AGAATCTGCCATTGTGCAGTCACAAATTATTTAAAAGGTTAGAAATTGACATTGGGTAGCTTATG
1 AGAATCTGCCATTGTGCATTCACAAATTATTTAAAAGCTTAGAAATTCACATTGGGTAGCCTATG
*
19471354 ACTACTCTTCCCTATCAAATCCCCATCAAAGGTAAGGGCATAAGCACAATGGAAGCAGTAACTCC
66 ACAACTCTTCCCTATCAAATCCCCATCAAAGGTAAGGGCATAAGCACAATGGAAGCAGTAACTCC
* *
19471419 TACTTCAGAAAACCTGCCAGAGTGCATTCAC--ATTCATTGAAAAGTATAGGAATTTA
131 TACTTCAGAAAACCTGCCACAGTGCATTCACAAATTCATTGAAAAGCATAGGAATTTA
19471475 CATTGTGTAG
Statistics
Matches: 397, Mismatches: 44, Indels: 27
0.85 0.09 0.06
Matches are distributed among these distances:
261 9 0.02
262 52 0.13
263 1 0.00
264 1 0.00
265 57 0.14
266 93 0.23
267 1 0.00
268 5 0.01
269 20 0.05
270 158 0.40
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (263 bp):
AGAATCTGCCATTGTGCATTCACAAATTATTTAAAAGCTTAGAAATTCACATTGGGTAGCCTATG
ACAACTCTTCCCTATCAAATCCCCATCAAAGGTAAGGGCATAAGCACAATGGAAGCAGTAACTCC
TACTTCAGAAAACCTGCCACAGTGCATTCACAAATTCATTGAAAAGCATAGGAATTTATAGTCTA
TCACAGTTCTTCCCTATCAAATCTCCACCTAATGAAAAGGTGTAAAAGCACAGAAAATCCCACTA
CCG
Found at i:19471495 original size:137 final size:137
Alignment explanation
Indices: 19471032--19471524 Score: 476
Period size: 138 Copynumber: 3.6 Consensus size: 137
19471022 ATCTGACATT
* * * * *
19471032 GTGCTTTCACAAATT-ATTGAAAAGCTTATGAATTCACATTGGGTAACCTATGACAACTCTTCCC
1 GTGCATTCAC-AATTCATTGAAAAG-TTAGGAATTTACATTGGGTAGCCTATGACTACTCTTCCC
* *
19471096 TATCAAATCCCCATCAAAGGTAAGGGCATAAGCACAATGGAAGCAGCAACTCCTAATTCAGAAAA
64 TATCAAATCCCCATCAAAGGTAAGGGCATAAGCACAATGGAAGCAGTAACTCCTACTTCAGAAAA
19471161 CCTGCCATA
129 CCTGCCATA
* * *
19471170 GTGCATTCACAAATTC-TTGAAAAGCATAGGAATTTATAGTT---TATCAC-A-G--T--TCTTC
1 GTGCATTCAC-AATTCATTGAAAAG-TTAGGAATTTACA-TTGGGTAGC-CTATGACTACTCTTC
* * * * * * * * * * *
19471225 CCTATCAAATCTCCATCTATGGCAAAGGTGTA-AAGCACAATCGAA-CTATTAAATCCCACTACC
62 CCTATCAAATCCCCATCAAAGG-TAAGG-GCATAAGCACAATGGAAGC-AGTAACTCCTACTTCA
* * *
19471288 GAGAATCTGCCATT
124 GAAAACCTGCCATA
* * * * *
19471302 GTGCAGTCACAAATT-ATTTAAAAGGTTAGAAATTGACATTGGGTAGCTTATGACTACTCTTCCC
1 GTGCATTCAC-AATTCATTGAAAA-GTTAGGAATTTACATTGGGTAGCCTATGACTACTCTTCCC
19471366 TATCAAATCCCCATCAAAGGTAAGGGCATAAGCACAATGGAAGCAGTAACTCCTACTTCAGAAAA
64 TATCAAATCCCCATCAAAGGTAAGGGCATAAGCACAATGGAAGCAGTAACTCCTACTTCAGAAAA
*
19471431 CCTGCCAGA
129 CCTGCCATA
*
19471440 GTGCATTCAC-ATTCATTGAAAAGTATAGGAATTTACATTGTGTAGCCTATGACTACTCTTCCCT
1 GTGCATTCACAATTCATTGAAAAGT-TAGGAATTTACATTGGGTAGCCTATGACTACTCTTCCCT
* *
19471504 ATCAGATCCCCATCTAAGGTA
65 ATCAAATCCCCATCAAAGGTA
19471525 TAGGCTTAAA
Statistics
Matches: 280, Mismatches: 54, Indels: 43
0.74 0.14 0.11
Matches are distributed among these distances:
131 27 0.10
132 65 0.23
133 3 0.01
134 4 0.01
135 2 0.01
136 9 0.03
137 65 0.23
138 78 0.28
139 27 0.10
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (137 bp):
GTGCATTCACAATTCATTGAAAAGTTAGGAATTTACATTGGGTAGCCTATGACTACTCTTCCCTA
TCAAATCCCCATCAAAGGTAAGGGCATAAGCACAATGGAAGCAGTAACTCCTACTTCAGAAAACC
TGCCATA
Found at i:19473344 original size:10 final size:10
Alignment explanation
Indices: 19473331--19473360 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
19473321 TTTTTTTATT
19473331 TTTTTATAAA
1 TTTTTATAAA
19473341 TTTTTATAAA
1 TTTTTATAAA
*
19473351 TTTTTTTAAA
1 TTTTTATAAA
19473361 AAATAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTTATAAA
Found at i:19479649 original size:9 final size:9
Alignment explanation
Indices: 19479635--19479667 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
19479625 ATTTTACAAT
19479635 TTGAATAAC
1 TTGAATAAC
*
19479644 TTGAATAAT
1 TTGAATAAC
19479653 TTGAATAAC
1 TTGAATAAC
19479662 TTGAAT
1 TTGAAT
19479668 GGCAAACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (9 bp):
TTGAATAAC
Found at i:19479653 original size:18 final size:18
Alignment explanation
Indices: 19479632--19479667 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19479622 TTAATTTTAC
19479632 AATTTGAATAACTTGAAT
1 AATTTGAATAACTTGAAT
19479650 AATTTGAATAACTTGAAT
1 AATTTGAATAACTTGAAT
19479668 GGCAAACTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
AATTTGAATAACTTGAAT
Found at i:19481891 original size:15 final size:17
Alignment explanation
Indices: 19481859--19481892 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
19481849 AAATTTATCA
19481859 ATTTTATTAAAAATAAT
1 ATTTTATTAAAAATAAT
19481876 ATTTT-TTAAAAA-AAT
1 ATTTTATTAAAAATAAT
19481891 AT
1 AT
19481893 AAAAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTTATTAAAAATAAT
Found at i:19481939 original size:14 final size:13
Alignment explanation
Indices: 19481920--19481949 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
19481910 GTATATGTGA
19481920 AAAAAAATAAAAAT
1 AAAAAAAT-AAAAT
19481934 AAAAAAATAAAAT
1 AAAAAAATAAAAT
19481947 AAA
1 AAA
19481950 GAACACACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:19486421 original size:46 final size:46
Alignment explanation
Indices: 19486346--19486603 Score: 358
Period size: 46 Copynumber: 5.6 Consensus size: 46
19486336 TGATGTCATA
* * *
19486346 TATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACTC-ATTTCATGTCATGTTGCCATGG
* **
19486392 TATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACTCA-TTTCATGTCATGTTGCCATGG
19486439 TATCTTTCAACCATGGTCTTACTCATTTCATGTCA-GATTGCCATGG
1 TATCTTTCAACCATGGTCTTACTCATTTCATGTCATG-TTGCCATGG
* * *
19486485 TATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGG
* * *
19486531 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGG
*
19486577 TATCTTTCAACCATGGTCTTACACATT
1 TATCTTTCAACCATGGTCTTACTCATT
19486604 CCATATCAGA
Statistics
Matches: 195, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
45 1 0.01
46 154 0.79
47 40 0.21
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
TATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGG
Found at i:19490381 original size:24 final size:25
Alignment explanation
Indices: 19490354--19490411 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
19490344 AACCCTAAAC
*
19490354 CATTACTGGAA-CAGGGTTAC-AGAG
1 CATTACTCGAATCAGGGTTACGA-AG
19490378 CATTA-TCGAATCAGGGTTACGAAG
1 CATTACTCGAATCAGGGTTACGAAG
19490402 CATTAC-CGAA
1 CATTACTCGAA
19490412 CTTTCAGACA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 4 0.13
24 25 0.83
25 1 0.03
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.22
Consensus pattern (25 bp):
CATTACTCGAATCAGGGTTACGAAG
Found at i:19491754 original size:21 final size:21
Alignment explanation
Indices: 19491728--19491769 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
19491718 TCAATTTTCA
19491728 ATCAATATACATTCAAATATT
1 ATCAATATACATTCAAATATT
19491749 ATCAATATACATTCAAATATT
1 ATCAATATACATTCAAATATT
19491770 CACATAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (21 bp):
ATCAATATACATTCAAATATT
Found at i:19496192 original size:69 final size:69
Alignment explanation
Indices: 19496097--19496232 Score: 202
Period size: 69 Copynumber: 2.0 Consensus size: 69
19496087 AACATAGAGG
* ** *
19496097 TGCTCTGTCATAAAATCGAGATAGTTTTCTTTATTTCT-TCGGTTCTAGATGCGGTGTCGCAACA
1 TGCTCTGTCACAAAATCGAGATAGTTTTCTCAATTTCTCT-GATTCTAGATGCGGTGTCGCAACA
19496161 CGGCA
65 CGGCA
* *
19496166 TGCTCTGTCACAAAATCGAGATAGTTTTCTCAATTTCTCTGATTCTGGATGCGGTGTTGCAACAC
1 TGCTCTGTCACAAAATCGAGATAGTTTTCTCAATTTCTCTGATTCTAGATGCGGTGTCGCAACAC
19496231 GG
66 GG
19496233 AGATGCCGTG
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
69 59 0.98
70 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (69 bp):
TGCTCTGTCACAAAATCGAGATAGTTTTCTCAATTTCTCTGATTCTAGATGCGGTGTCGCAACAC
GGCA
Found at i:19500517 original size:22 final size:21
Alignment explanation
Indices: 19500491--19500532 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19500481 TAATTTAAGT
*
19500491 GGATAATATTTTTTTAAAAAAA
1 GGAT-ATACTTTTTTAAAAAAA
*
19500513 GGATATACTTTTTTACAAAA
1 GGATATACTTTTTTAAAAAA
19500533 GAGTAACTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (21 bp):
GGATATACTTTTTTAAAAAAA
Found at i:19501881 original size:14 final size:14
Alignment explanation
Indices: 19501864--19501930 Score: 66
Period size: 14 Copynumber: 4.8 Consensus size: 14
19501854 TTTTCAATCC
*
19501864 TCAATCTTCAATCT
1 TCAATCTTCAATTT
**
19501878 TCAATCCCCAATTT
1 TCAATCTTCAATTT
*
19501892 TCAAT-TTTATATTT
1 TCAATCTTCA-ATTT
19501906 TCAATCTTCAAATTT
1 TCAATCTTC-AATTT
19501921 TCAAT-TTCAA
1 TCAATCTTCAA
19501931 ATTTGTAATC
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
13 3 0.07
14 28 0.65
15 11 0.26
16 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.46
Consensus pattern (14 bp):
TCAATCTTCAATTT
Found at i:19501882 original size:21 final size:21
Alignment explanation
Indices: 19501856--19501896 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19501846 ATCCTAAATT
*
19501856 TTCAATCCTCAATCTTCAATC
1 TTCAATCCCCAATCTTCAATC
*
19501877 TTCAATCCCCAATTTTCAAT
1 TTCAATCCCCAATCTTCAAT
19501897 TTTATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (21 bp):
TTCAATCCCCAATCTTCAATC
Found at i:19501896 original size:7 final size:7
Alignment explanation
Indices: 19501852--19501927 Score: 55
Period size: 7 Copynumber: 10.7 Consensus size: 7
19501842 TTCCATCCTA
19501852 AATTTTC
1 AATTTTC
**
19501859 AATCCTC
1 AATTTTC
*
19501866 AATCTTC
1 AATTTTC
*
19501873 AATCTTC
1 AATTTTC
***
19501880 AATCCCC
1 AATTTTC
19501887 AATTTTC
1 AATTTTC
19501894 AATTTT-
1 AATTTTC
19501900 ATATTTTC
1 A-ATTTTC
*
19501908 AATCTTC
1 AATTTTC
19501915 AAATTTTC
1 -AATTTTC
19501923 AATTT
1 AATTT
19501928 CAAATTTGTA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
6 1 0.02
7 48 0.86
8 7 0.12
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.47
Consensus pattern (7 bp):
AATTTTC
Found at i:19501931 original size:14 final size:14
Alignment explanation
Indices: 19501887--19501934 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
19501877 TTCAATCCCC
*
19501887 AATTTTCAATTTTA
1 AATTTTCAATTTCA
*
19501901 TATTTTCAATCTTCA
1 AATTTTCAAT-TTCA
19501916 AATTTTCAATTTCA
1 AATTTTCAATTTCA
19501930 AATTT
1 AATTT
19501935 GTAATCCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.54
Consensus pattern (14 bp):
AATTTTCAATTTCA
Found at i:19503214 original size:17 final size:18
Alignment explanation
Indices: 19503183--19503217 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19503173 AAAAAAAATT
19503183 AAATTCAAAATATTTATA
1 AAATTCAAAATATTTATA
*
19503201 AAATTCCAAA-ATTTATA
1 AAATTCAAAATATTTATA
19503218 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTCAAAATATTTATA
Found at i:19503403 original size:16 final size:16
Alignment explanation
Indices: 19503384--19503414 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19503374 TTAAAAAAGT
19503384 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
19503400 TTTCAAATTTATATG
1 TTTCAAATATATATG
19503415 CTCTAATATG
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:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:19506137 original size:12 final size:12
Alignment explanation
Indices: 19506120--19506144 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19506110 CTAATGATAA
19506120 TTTTTTTTACTT
1 TTTTTTTTACTT
19506132 TTTTTTTTACTT
1 TTTTTTTTACTT
19506144 T
1 T
19506145 CACCTCATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTACTT
Found at i:19515226 original size:22 final size:23
Alignment explanation
Indices: 19515201--19515246 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
19515191 AGCATTTATT
19515201 TATTTTTTAT-ATTTTTTAAAAA
1 TATTTTTTATAATTTTTTAAAAA
*
19515223 TATTTTTTATAATTTTTTGAAAA
1 TATTTTTTATAATTTTTTAAAAA
19515246 T
1 T
19515247 TTAAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TATTTTTTATAATTTTTTAAAAA
Found at i:19520003 original size:21 final size:22
Alignment explanation
Indices: 19519974--19520020 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
19519964 CAGAAGGAGT
*
19519974 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
19519996 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
19520017 GAGT
1 GAGT
19520021 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:19524668 original size:17 final size:19
Alignment explanation
Indices: 19524634--19524671 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
19524624 GATAATATTA
*
19524634 TAAATATAAATATTTAAAT
1 TAAATATAAATATATAAAT
19524653 TAAATA-AAATA-ATAAAT
1 TAAATATAAATATATAAAT
19524670 TA
1 TA
19524672 TCTGATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 5 0.28
19 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATATAAATATATAAAT
Found at i:19525127 original size:20 final size:20
Alignment explanation
Indices: 19525104--19525156 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
19525094 TTAAGTTGAA
19525104 TTTTGAAGAATTAAATGTTT
1 TTTTGAAGAATTAAATGTTT
* *
19525124 TTTTAAGTAAGACTTAAATTTTT
1 TTTT--G-AAGAATTAAATGTTT
*
19525147 TTTTAAAGAA
1 TTTTGAAGAA
19525157 AATGAAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
20 8 0.31
22 1 0.04
23 17 0.65
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (20 bp):
TTTTGAAGAATTAAATGTTT
Found at i:19525135 original size:23 final size:23
Alignment explanation
Indices: 19525109--19525152 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19525099 TTGAATTTTG
19525109 AAGAATTAAATGTTTTTTTAAGT
1 AAGAATTAAATGTTTTTTTAAGT
* *
19525132 AAGACTTAAATTTTTTTTTAA
1 AAGAATTAAATGTTTTTTTAA
19525153 AGAAAATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (23 bp):
AAGAATTAAATGTTTTTTTAAGT
Found at i:19525290 original size:5 final size:5
Alignment explanation
Indices: 19525221--19525289 Score: 129
Period size: 5 Copynumber: 13.8 Consensus size: 5
19525211 TGTAACTTGC
19525221 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
*
19525271 TATAT TATAT TATAG TATA
1 TATAT TATAT TATAT TATA
19525290 GGGTAGATGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 63 1.00
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:19526100 original size:26 final size:26
Alignment explanation
Indices: 19526071--19526120 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
19526061 TTATGAGTAG
19526071 AAATAAGTAT-AGTATTTTATATTTCC
1 AAAT-AGTATGAGTATTTTATATTTCC
* *
19526097 AAATATTATGATTATTTTATATTT
1 AAATAGTATGAGTATTTTATATTT
19526121 GATACTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (26 bp):
AAATAGTATGAGTATTTTATATTTCC
Found at i:19538688 original size:13 final size:13
Alignment explanation
Indices: 19538670--19538724 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
19538660 CTAGTTTGGC
19538670 AATGCTTTTGAAA
1 AATGCTTTTGAAA
* *
19538683 AATGCTGTGGAAA
1 AATGCTTTTGAAA
* * *
19538696 AGTACTTTTGAGA
1 AATGCTTTTGAAA
*
19538709 AGTGCTTTTGAAA
1 AATGCTTTTGAAA
19538722 AAT
1 AAT
19538725 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (13 bp):
AATGCTTTTGAAA
Found at i:19540479 original size:23 final size:24
Alignment explanation
Indices: 19540428--19540511 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 24
19540418 TTAGCTCGTA
* * *
19540428 AGAGTTTACTGTTTTCAGCTCATT
1 AGAGCTTACCGTTTTCAGCTCAAT
*
19540452 GGAGCTTACCGTTTT-AGCTCAAT
1 AGAGCTTACCGTTTTCAGCTCAAT
* * **
19540475 AGAGCTTACTGTTCATCAGCTCAGG
1 AGAGCTTACCGTT-TTCAGCTCAAT
19540500 AGGAGCTTACCG
1 A-GAGCTTACCG
19540512 ATTATAGCTC
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
23 18 0.38
24 13 0.28
25 7 0.15
26 9 0.19
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (24 bp):
AGAGCTTACCGTTTTCAGCTCAAT
Found at i:19540520 original size:25 final size:24
Alignment explanation
Indices: 19540452--19540521 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
19540442 TCAGCTCATT
* *
19540452 GGAGCTTACCGTTTTAGCTCAATA
1 GGAGCTTACCGTTATAGCTCAAGA
* *
19540476 -GAGCTTACTGTTCATCAGCTCAGGA
1 GGAGCTTACCGTT-AT-AGCTCAAGA
19540501 GGAGCTTACCGATTATAGCTC
1 GGAGCTTACCG-TTATAGCTC
19540522 GAAAGAGCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 11 0.30
24 1 0.03
25 12 0.32
26 11 0.30
27 2 0.05
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (24 bp):
GGAGCTTACCGTTATAGCTCAAGA
Found at i:19540529 original size:50 final size:48
Alignment explanation
Indices: 19540404--19540529 Score: 130
Period size: 50 Copynumber: 2.6 Consensus size: 48
19540394 AGCTCATATC
* * * * **
19540404 AGCTTACCAATATATTAGCTCGTAAGAGTTTACTGTTTTCAGCTCATTGG
1 AGCTTACCGAT-TA-TAGCTCGAAAGAGCTTACTGTTATCAGCTCAGAGG
*
19540454 AGCTTACCG-TTTTAGCTC-AATAGAGCTTACTGTTCATCAGCTCAGGAGG
1 AGCTTACCGATTATAGCTCGAA-AGAGCTTACTGTT-ATCAGCTCA-GAGG
19540503 AGCTTACCGATTATAGCTCGAAAGAGC
1 AGCTTACCGATTATAGCTCGAAAGAGC
19540530 ATAAATGATA
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
46 1 0.02
47 18 0.29
48 9 0.14
49 12 0.19
50 21 0.33
51 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (48 bp):
AGCTTACCGATTATAGCTCGAAAGAGCTTACTGTTATCAGCTCAGAGG
Found at i:19546739 original size:51 final size:49
Alignment explanation
Indices: 19546651--19546764 Score: 192
Period size: 51 Copynumber: 2.3 Consensus size: 49
19546641 ACTTGTTAAA
*
19546651 TTGATTAAATAATTAAGTGTTATCAATTATGATCATTCATCAATAGGTT
1 TTGATTAAATAATTAAGTGTTATCAATTATGACCATTCATCAATAGGTT
*
19546700 TTGATTAAATAACTTAAGTGTTAATCAATTTTGACCATTCATCAATAGGTT
1 TTGATTAAATAA-TTAAGTGTT-ATCAATTATGACCATTCATCAATAGGTT
19546751 TTGATTAAATAATT
1 TTGATTAAATAATT
19546765 TTGTTAAAAG
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
49 12 0.20
50 11 0.18
51 38 0.62
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (49 bp):
TTGATTAAATAATTAAGTGTTATCAATTATGACCATTCATCAATAGGTT
Found at i:19550822 original size:63 final size:64
Alignment explanation
Indices: 19550717--19550845 Score: 170
Period size: 63 Copynumber: 2.0 Consensus size: 64
19550707 CATTAAGAGC
* * * * * *
19550717 CATATATCGGGACACTCATAAAGAGCTGCGGTATGTCTGCAATACATACAAGATCAATACC-AT
1 CATATAACAGGACACTCACAAAGAGCTGCAGTATATCCGCAATACATACAAGATCAATACCGAT
* * *
19550780 CATATAACAGGACGCTCACAAAGAGCTGCAGTATATCCGCAATACATGCAAGATCGATACCGAT
1 CATATAACAGGACACTCACAAAGAGCTGCAGTATATCCGCAATACATACAAGATCAATACCGAT
19550844 CA
1 CA
19550846 AGATGCTCGC
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
63 52 0.93
64 4 0.07
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (64 bp):
CATATAACAGGACACTCACAAAGAGCTGCAGTATATCCGCAATACATACAAGATCAATACCGAT
Found at i:19557643 original size:47 final size:47
Alignment explanation
Indices: 19557534--19557644 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
19557524 CCGGGATAAG
* * * *
19557534 CACATAGTGCTTCATCGGAATAAATTCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
19557581 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
19557628 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
19557645 ACTCAATGTC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 1 0.02
47 50 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:19572737 original size:27 final size:26
Alignment explanation
Indices: 19572707--19572782 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 26
19572697 ACTCTCTGTG
19572707 CAAAAG-AGCAAGCCAACAAGTGTAAGC
1 CAAAAGTA-CAAGCCAA-AAGTGTAAGC
* *
19572734 CAAAAGTAAAAGTCAAAAAGTGTAAGC
1 CAAAAGTACAAG-CCAAAAGTGTAAGC
*
19572761 CAAAAGTACAAGCTAAAAGTGT
1 CAAAAGTACAAGCCAAAAGTGT
19572783 GAGCTAACAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
26 9 0.21
27 30 0.70
28 4 0.09
ACGTcount: A:0.51, C:0.16, G:0.20, T:0.13
Consensus pattern (26 bp):
CAAAAGTACAAGCCAAAAGTGTAAGC
Found at i:19572765 original size:13 final size:13
Alignment explanation
Indices: 19572716--19572782 Score: 62
Period size: 13 Copynumber: 5.0 Consensus size: 13
19572706 GCAAAAGAGC
19572716 AAGCCAACAAGTGT
1 AAGCCAA-AAGTGT
**
19572730 AAGCCAAAAGTAA
1 AAGCCAAAAGTGT
*
19572743 AAGTCAAAAAGTGT
1 AAG-CCAAAAGTGT
**
19572757 AAGCCAAAAGTAC
1 AAGCCAAAAGTGT
*
19572770 AAGCTAAAAGTGT
1 AAGCCAAAAGTGT
19572783 GAGCTAACAA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
13 24 0.59
14 17 0.41
ACGTcount: A:0.51, C:0.15, G:0.19, T:0.15
Consensus pattern (13 bp):
AAGCCAAAAGTGT
Found at i:19577585 original size:18 final size:18
Alignment explanation
Indices: 19577572--19577645 Score: 89
Period size: 18 Copynumber: 4.1 Consensus size: 18
19577562 TGAAAAAGTC
19577572 TAGAAAAATAAAAATAAA
1 TAGAAAAATAAAAATAAA
19577590 TAGAAAAATAAAAATAAGA
1 TAGAAAAATAAAAATAA-A
*
19577609 -ACTAAAAATAAAAAT-AA
1 TA-GAAAAATAAAAATAAA
*
19577626 GAGAAAATATAAAAATAAA
1 TAGAAAA-ATAAAAATAAA
19577645 T
1 T
19577646 GGATTCAATG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
17 5 0.10
18 28 0.58
19 15 0.31
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (18 bp):
TAGAAAAATAAAAATAAA
Found at i:19577586 original size:6 final size:6
Alignment explanation
Indices: 19577575--19577644 Score: 70
Period size: 6 Copynumber: 11.5 Consensus size: 6
19577565 AAAAGTCTAG
* * *
19577575 AAAAAT AAAAAT AAATAG AAAAAT AAAAAT AAGAACT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT AAAAAT AAAAAT
* *
19577624 AAGAGA- AAATAT AAAAAT AAA
1 AA-AAAT AAAAAT AAAAAT AAA
19577645 TGGATTCAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
5 2 0.04
6 43 0.83
7 7 0.13
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:19579315 original size:21 final size:21
Alignment explanation
Indices: 19579286--19579342 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
19579276 AATAACAGAC
*
19579286 AAATGAATAAAAGTAATAAAT-
1 AAATAAATAAAAG-AATAAATA
*
19579307 AAATAAAT-AAAGATTAAATA
1 AAATAAATAAAAGAATAAATA
19579327 AAATAAA-ATAAAGAAT
1 AAATAAATA-AAAGAAT
19579343 GGGTAAAGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 6 0.20
20 11 0.37
21 13 0.43
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (21 bp):
AAATAAATAAAAGAATAAATA
Found at i:19582788 original size:20 final size:20
Alignment explanation
Indices: 19582763--19582803 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
19582753 AGCAGGAGCA
19582763 TTACATAATTCAAAAGTTAT
1 TTACATAATTCAAAAGTTAT
19582783 TTACATAATTCAAAAGTTAT
1 TTACATAATTCAAAAGTTAT
19582803 T
1 T
19582804 CTTCGGTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (20 bp):
TTACATAATTCAAAAGTTAT
Found at i:19586420 original size:33 final size:33
Alignment explanation
Indices: 19586374--19586517 Score: 170
Period size: 33 Copynumber: 4.4 Consensus size: 33
19586364 CTTTCTGAGT
*
19586374 GGTACACACAAAGTATATCTTTCCTTTTCATAA
1 GGTACACACAAAGTATACCTTTCCTTTTCATAA
* *
19586407 GGTATACACAAAGTATACCTTTCCTTTTCATAT
1 GGTACACACAAAGTATACCTTTCCTTTTCATAA
*
19586440 GGTATACACAAAGTATACCTTTCCTTTTC--AA
1 GGTACACACAAAGTATACCTTTCCTTTTCATAA
* * **
19586471 GTGTACACACAAAGTGTACATAACCTTTTC--AA
1 G-GTACACACAAAGTATACCTTTCCTTTTCATAA
19586503 GTGTACACACAAAGT
1 G-GTACACACAAAGT
19586518 GTACATAACC
Statistics
Matches: 101, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
31 2 0.02
32 40 0.40
33 59 0.58
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (33 bp):
GGTACACACAAAGTATACCTTTCCTTTTCATAA
Found at i:19586498 original size:32 final size:32
Alignment explanation
Indices: 19586462--19586566 Score: 149
Period size: 32 Copynumber: 3.2 Consensus size: 32
19586452 GTATACCTTT
19586462 CCTTTTCAAGTGTACACACAAAGTGTACATAA
1 CCTTTTCAAGTGTACACACAAAGTGTACATAA
19586494 CCTTTTCAAGTGTACACACAAAGTGTACATAA
1 CCTTTTCAAGTGTACACACAAAGTGTACATAA
* * * *
19586526 CCTTTTCATGTGGTATACATAAAG-GATACCTAA
1 CCTTTTCAAGT-GTACACACAAAGTG-TACATAA
19586559 CCTTTTCA
1 CCTTTTCA
19586567 CATTCGATAG
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
32 43 0.64
33 24 0.36
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.31
Consensus pattern (32 bp):
CCTTTTCAAGTGTACACACAAAGTGTACATAA
Found at i:19586565 original size:33 final size:33
Alignment explanation
Indices: 19586372--19586566 Score: 155
Period size: 33 Copynumber: 6.0 Consensus size: 33
19586362 TTCTTTCTGA
* * * **
19586372 GTGGTACACACAAAGTATATCTTTCCTTTTCAT
1 GTGGTATACACAAAGGATACCTAACCTTTTCAT
** * **
19586405 AAGGTATACACAAAGTATACCTTTCCTTTTCAT
1 GTGGTATACACAAAGGATACCTAACCTTTTCAT
* * ** *
19586438 ATGGTATACACAAAGTATACCTTTCCTTTTCAA
1 GTGGTATACACAAAGGATACCTAACCTTTTCAT
* * *
19586471 GT-GTACACACAAAGTG-TACATAACCTTTTCAA
1 GTGGTATACACAAAG-GATACCTAACCTTTTCAT
* *
19586503 GT-GTACACACAAAGTG-TACATAACCTTTTCAT
1 GTGGTATACACAAAG-GATACCTAACCTTTTCAT
*
19586535 GTGGTATACATAAAGGATACCTAACCTTTTCA
1 GTGGTATACACAAAGGATACCTAACCTTTTCA
19586567 CATTCGATAG
Statistics
Matches: 143, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
32 58 0.41
33 85 0.59
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (33 bp):
GTGGTATACACAAAGGATACCTAACCTTTTCAT
Found at i:19586601 original size:29 final size:29
Alignment explanation
Indices: 19586559--19586686 Score: 186
Period size: 29 Copynumber: 4.4 Consensus size: 29
19586549 GGATACCTAA
*
19586559 CCTTTTCACATTCGATAGCCAAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
19586588 CCTTTTCACATTCGATAGCCGAAGCTATCC
1 CCTTTTCACATTCGATAGCCGAAGCTAT-C
* * *
19586618 CCTTTTTAAATTCGATAGACGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
*
19586647 CCTTTTCACATTCTATAGCCGTAA-CTATC
1 CCTTTTCACATTCGATAGCCG-AAGCTATC
19586676 CCTTTTCACAT
1 CCTTTTCACAT
19586687 GGTACAGATA
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
29 61 0.69
30 28 0.31
ACGTcount: A:0.26, C:0.30, G:0.10, T:0.34
Consensus pattern (29 bp):
CCTTTTCACATTCGATAGCCGAAGCTATC
Found at i:19586631 original size:59 final size:58
Alignment explanation
Indices: 19586559--19586683 Score: 180
Period size: 59 Copynumber: 2.1 Consensus size: 58
19586549 GGATACCTAA
* *
19586559 CCTTTTCACATTCGATAGCCAAAGCTATCCCTTTTCACATTCGATAGCCG-AAGCTATCC
1 CCTTTTCAAATTCGATAGACAAAGCTATCCCTTTTCACATTCGATAGCCGTAA-CTAT-C
* * *
19586618 CCTTTTTAAATTCGATAGACGAAGCTATCCCTTTTCACATTCTATAGCCGTAACTATC
1 CCTTTTCAAATTCGATAGACAAAGCTATCCCTTTTCACATTCGATAGCCGTAACTATC
19586676 CCTTTTCA
1 CCTTTTCA
19586684 CATGGTACAG
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 8 0.14
59 49 0.83
60 2 0.03
ACGTcount: A:0.26, C:0.30, G:0.10, T:0.34
Consensus pattern (58 bp):
CCTTTTCAAATTCGATAGACAAAGCTATCCCTTTTCACATTCGATAGCCGTAACTATC
Found at i:19588524 original size:35 final size:35
Alignment explanation
Indices: 19588485--19588554 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
19588475 GAATAGTGTT
*
19588485 AGGTTTAAGTTCAAAATTATTTGCAGCAATAGCAC
1 AGGTTTAAGTTCAAAATTATTTGCAACAATAGCAC
19588520 AGGTTTAAGTTCAAAATTATTTGCAACAATAGCAC
1 AGGTTTAAGTTCAAAATTATTTGCAACAATAGCAC
19588555 GTCTAACAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (35 bp):
AGGTTTAAGTTCAAAATTATTTGCAACAATAGCAC
Found at i:19596482 original size:42 final size:41
Alignment explanation
Indices: 19596436--19596564 Score: 152
Period size: 42 Copynumber: 3.1 Consensus size: 41
19596426 GAGCTAAATA
19596436 GAAACCCATAAGGGTTAAACGAAAGCTCGTAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAAC-AAAGCTCGTAAGAGCTGAACG
* * *
19596478 GAAACCCATAAAGGTTAAACAGAAGCTC-AAAGAGCTGAACA
1 GAAACCCATAAGGGTTAAACA-AAGCTCGTAAGAGCTGAACG
* * * * *
19596519 GACACTCATATGAGTTAAACAAAAGCTCGTAATAGCTGAACG
1 GAAACCCATAAGGGTTAAAC-AAAGCTCGTAAGAGCTGAACG
19596561 GAAA
1 GAAA
19596565 GTAAACATGA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 33 0.46
42 39 0.54
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.16
Consensus pattern (41 bp):
GAAACCCATAAGGGTTAAACAAAGCTCGTAAGAGCTGAACG
Found at i:19597056 original size:18 final size:20
Alignment explanation
Indices: 19597015--19597064 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
19597005 AATTTAGTCC
19597015 TTAACTAATTAATCTTATCAAA
1 TTAACTAATT--TCTTATCAAA
19597037 TTAACTAATTT-TTATC-AA
1 TTAACTAATTTCTTATCAAA
19597055 TTAA-TAATTT
1 TTAACTAATTT
19597065 ATCTAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.21
18 6 0.21
19 5 0.18
20 1 0.04
22 10 0.36
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAACTAATTTCTTATCAAA
Found at i:19600043 original size:23 final size:24
Alignment explanation
Indices: 19600017--19600063 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
19600007 TTCTAACCAA
19600017 GCACAC-TCAAATTTATTTTCTTT
1 GCACACTTCAAATTTATTTTCTTT
19600040 GCACACTTCAAATTTATTTTCTTT
1 GCACACTTCAAATTTATTTTCTTT
19600064 TCACTTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.26, C:0.21, G:0.04, T:0.49
Consensus pattern (24 bp):
GCACACTTCAAATTTATTTTCTTT
Found at i:19607370 original size:3 final size:3
Alignment explanation
Indices: 19607364--19607390 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
19607354 TCTTCTTTTT
19607364 GTG GTG GTG GTG GTG GTG GTG GTG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG
19607391 ATTGGTGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GTG
Found at i:19608683 original size:35 final size:35
Alignment explanation
Indices: 19608637--19608708 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
19608627 ACATTTGGTG
19608637 ATTGAGAAACTAACTTCTAGGATATCAAGAAATAA
1 ATTGAGAAACTAACTTCTAGGATATCAAGAAATAA
19608672 ATTGAGAAACTAACTTCTAGGATATCAAGAAATAA
1 ATTGAGAAACTAACTTCTAGGATATCAAGAAATAA
19608707 AT
1 AT
19608709 AAATTAGACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (35 bp):
ATTGAGAAACTAACTTCTAGGATATCAAGAAATAA
Found at i:19619796 original size:19 final size:20
Alignment explanation
Indices: 19619772--19619813 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
19619762 AACCCAACTC
*
19619772 AATTAATTA-TCAAATATAA
1 AATTAAGTACTCAAATATAA
*
19619791 AATTAAGTACTCAAATGTAA
1 AATTAAGTACTCAAATATAA
19619811 AAT
1 AAT
19619814 AACCCAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (20 bp):
AATTAAGTACTCAAATATAA
Found at i:19622987 original size:12 final size:14
Alignment explanation
Indices: 19622959--19622990 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
19622949 ATAAAATAAA
19622959 AAGATATTGATATT
1 AAGATATTGATATT
19622973 AAGAT-TTGA-ATT
1 AAGATATTGATATT
19622985 AAGATA
1 AAGATA
19622991 AATGCATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.47
13 4 0.24
14 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (14 bp):
AAGATATTGATATT
Found at i:19626476 original size:12 final size:12
Alignment explanation
Indices: 19626459--19626484 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19626449 CAACAAGGGA
19626459 AACAAAAAAAAT
1 AACAAAAAAAAT
19626471 AACAAAAAAAAT
1 AACAAAAAAAAT
19626483 AA
1 AA
19626485 AACCACAAAA
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:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AACAAAAAAAAT
Found at i:19629025 original size:27 final size:27
Alignment explanation
Indices: 19628995--19629048 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
19628985 AACAACCAAG
19628995 AAGCGAAACAATACCCAAGAAAGAATT
1 AAGCGAAACAATACCCAAGAAAGAATT
19629022 AAGCGAAACAATACCCAAGAAAGAATT
1 AAGCGAAACAATACCCAAGAAAGAATT
19629049 CACCTAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.19, G:0.15, T:0.11
Consensus pattern (27 bp):
AAGCGAAACAATACCCAAGAAAGAATT
Found at i:19631339 original size:28 final size:28
Alignment explanation
Indices: 19631307--19631363 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
19631297 AATATTTTAT
* *
19631307 CATTACAATATGATCGTTGGAATATGGC
1 CATTACAAAATGATCGTTGAAATATGGC
* * *
19631335 CATTATAAAATGATTGTTGAAATTTGGC
1 CATTACAAAATGATCGTTGAAATATGGC
19631363 C
1 C
19631364 GCTGTAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (28 bp):
CATTACAAAATGATCGTTGAAATATGGC
Found at i:19631915 original size:38 final size:38
Alignment explanation
Indices: 19631870--19631953 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
19631860 CTTGGTTTAT
* *
19631870 TTTCTAATAAGCGGTAACGAATTTATTTTACAATCTTA
1 TTTCTAATAAGCGCTAACAAATTTATTTTACAATCTTA
*
19631908 TTTCTAATAAGTGCTAACAAATTTATTTTACAATCTTA
1 TTTCTAATAAGCGCTAACAAATTTATTTTACAATCTTA
*
19631946 TTTTTAAT
1 TTTCTAAT
19631954 TTCAACGGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (38 bp):
TTTCTAATAAGCGCTAACAAATTTATTTTACAATCTTA
Found at i:19633123 original size:23 final size:24
Alignment explanation
Indices: 19633078--19633127 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
19633068 ACGTGTTTAT
19633078 TTTTTAAAATTTTAAAATAATATA
1 TTTTTAAAATTTTAAAATAATATA
19633102 TTTTTAAAATTTTAAAAT-ATATA
1 TTTTTAAAATTTTAAAATAATATA
19633125 TTT
1 TTT
19633128 ACTAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTTAAAATTTTAAAATAATATA
Found at i:19633796 original size:30 final size:32
Alignment explanation
Indices: 19633760--19633836 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 32
19633750 TTAATATACC
*
19633760 ATCATATTAATTAATATT-ACT-TTTATTATT
1 ATCATATTAATTAATATTAACTAATTATTATT
19633790 ATCATA-TAA-TAATATTAACTAATTATTATT
1 ATCATATTAATTAATATTAACTAATTATTATT
* *
19633820 TTAATATTAATTTAATA
1 ATCATATTAA-TTAATA
19633837 ATATATTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 7 0.18
29 6 0.15
30 18 0.46
31 3 0.08
33 5 0.13
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (32 bp):
ATCATATTAATTAATATTAACTAATTATTATT
Found at i:19633807 original size:38 final size:36
Alignment explanation
Indices: 19633749--19633840 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 36
19633739 TTAATTTCAC
* * *
19633749 ATTAATATACCATCATATTAATTAA-TATTACTTTTATT
1 ATTAATATA--ATAATATTAACTAATTATTA-TTTTAAT
19633787 ATTATCATATAATAATATTAACTAATTATTATTTTAAT
1 ATTA--ATATAATAATATTAACTAATTATTATTTTAAT
*
19633825 ATTAATTTAATAATAT
1 ATTAATATAATAATAT
19633841 ATTGAACAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
36 11 0.23
38 26 0.55
39 5 0.11
40 5 0.11
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (36 bp):
ATTAATATAATAATATTAACTAATTATTATTTTAAT
Found at i:19637498 original size:21 final size:24
Alignment explanation
Indices: 19637467--19637509 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
19637457 CGATTAATAG
19637467 GGGAGGGGAAGGA-A-TGGGAGAA
1 GGGAGGGGAAGGAGACTGGGAGAA
19637489 GGGA-GGGAAGGAGACTGGGAG
1 GGGAGGGGAAGGAGACTGGGAG
19637510 TGCAGTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 5 0.26
23 6 0.32
ACGTcount: A:0.33, C:0.02, G:0.60, T:0.05
Consensus pattern (24 bp):
GGGAGGGGAAGGAGACTGGGAGAA
Found at i:19642697 original size:31 final size:30
Alignment explanation
Indices: 19642629--19642695 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
19642619 AGTAGTTTAT
*
19642629 ATTTTTATAATTTTTAAAAGATTAAATTAA
1 ATTTTTATAATTTTTAAAAGATTAAATGAA
* * *
19642659 ATTTTTATCATTTTTAAGGAGATTAAAATGCA
1 ATTTTTATAATTTTTAA-AAGATT-AAATGAA
19642691 ATTTT
1 ATTTT
19642696 ATTATTACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 16 0.52
31 5 0.16
32 10 0.32
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.49
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAAGATTAAATGAA
Found at i:19643609 original size:19 final size:19
Alignment explanation
Indices: 19643580--19643620 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
19643570 CTATATGAAC
*
19643580 AAATAATTTAAAATTAATAA
1 AAATAATTTAAAAATAA-AA
19643600 AAAT-ATTTAAAAATAAAA
1 AAATAATTTAAAAATAAAA
19643618 AAA
1 AAA
19643621 CCATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 11 0.55
20 4 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATAATTTAAAAATAAAA
Found at i:19645952 original size:5 final size:5
Alignment explanation
Indices: 19645944--19645981 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
19645934 TTCAGTTGCA
19645944 ATATT ATATT ATATTT ATATT ATATT ATATT ATATT AT
1 ATATT ATATT ATA-TT ATATT ATATT ATATT ATATT AT
19645982 GGGCAACTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATATT
Found at i:19649419 original size:17 final size:17
Alignment explanation
Indices: 19649386--19649428 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
19649376 TTATTTATTT
19649386 AATTAATTTACTTAATTA
1 AATTAATTTAC-TAATTA
19649404 AATTAATTTCAC-AATTA
1 AATTAATTT-ACTAATTA
19649421 AA-TAATTT
1 AATTAATTT
19649429 TTAACACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.25
17 7 0.29
18 9 0.38
19 2 0.08
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAATTTACTAATTA
Found at i:19656510 original size:5 final size:5
Alignment explanation
Indices: 19656500--19656525 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19656490 TTACTCTTTG
19656500 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
19656526 TGCTTAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:19658673 original size:11 final size:11
Alignment explanation
Indices: 19658659--19658687 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
19658649 GTCAACTGGG
19658659 AACCAACTAGC
1 AACCAACTAGC
19658670 AACCAACTAGC
1 AACCAACTAGC
19658681 AA-CAACT
1 AACCAACT
19658688 CAATTAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.48, C:0.34, G:0.07, T:0.10
Consensus pattern (11 bp):
AACCAACTAGC
Found at i:19660368 original size:24 final size:25
Alignment explanation
Indices: 19660324--19660387 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
19660314 TTTTATATTT
*
19660324 AATAAAATAATT-TTTTCAATATAAA
1 AATAAAAT-ATTATTCTCAATATAAA
*
19660349 AATAAAATATTATTCT-AATATTAA
1 AATAAAATATTATTCTCAATATAAA
*
19660373 TATAAAAATATTATT
1 AAT-AAAATATTATT
19660388 TTTAATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.35
25 22 0.65
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (25 bp):
AATAAAATATTATTCTCAATATAAA
Found at i:19661223 original size:3 final size:3
Alignment explanation
Indices: 19661215--19661243 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19661205 ATTGCCCTCT
19661215 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19661244 GTTTTATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19666323 original size:23 final size:24
Alignment explanation
Indices: 19666276--19666323 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
19666266 AAGCCTAAAC
* * *
19666276 CAAAACCCTATCAGCCTAAATTAT
1 CAAAACCCTATAAGCCCAAACTAT
19666300 CAAAACCCTA-AAGCCCAAACTAT
1 CAAAACCCTATAAGCCCAAACTAT
19666323 C
1 C
19666324 TTAAACATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.44, C:0.33, G:0.04, T:0.19
Consensus pattern (24 bp):
CAAAACCCTATAAGCCCAAACTAT
Found at i:19667827 original size:49 final size:48
Alignment explanation
Indices: 19667733--19667829 Score: 133
Period size: 49 Copynumber: 2.0 Consensus size: 48
19667723 TTTATGATTT
* * *
19667733 TTTATATACATTATTTATTCTAAAATTTTACATATTATTTATTTTAAA
1 TTTATATACATTATGTAGTCTAAAATTATACATATTATTTATTTTAAA
*
19667781 TTTATATACATTATGTAGT-TAAACTATTATATATATTATTTATTTTAAA
1 TTTATATACATTATGTAGTCTAAA--ATTATACATATTATTTATTTTAAA
19667830 CCCTCTTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 4 0.09
48 17 0.40
49 22 0.51
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (48 bp):
TTTATATACATTATGTAGTCTAAAATTATACATATTATTTATTTTAAA
Found at i:19672058 original size:19 final size:20
Alignment explanation
Indices: 19672031--19672073 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
19672021 TCTTTTTGCA
* *
19672031 TTCATTCATTTGCATTACAT
1 TTCATTCATATGCATTAAAT
19672051 TTCA-TCATATGCATTAAAT
1 TTCATTCATATGCATTAAAT
19672070 TTCA
1 TTCA
19672074 CGAAAAGACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (20 bp):
TTCATTCATATGCATTAAAT
Done.