Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 129 of 318
Found at i:40000140 original size:20 final size:17
Alignment explanation
Indices: 40000095--40000131 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
40000085 TTTAGTTTAG
40000095 TGATAAAATTAATAGAA
1 TGATAAAATTAATAGAA
*
40000112 TGATAAAATTAATAGCA
1 TGATAAAATTAATAGAA
40000129 TGA
1 TGA
40000132 GTTTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.30
Consensus pattern (17 bp):
TGATAAAATTAATAGAA
Found at i:40005192 original size:23 final size:22
Alignment explanation
Indices: 40005166--40005219 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
40005156 TGTATACGCG
40005166 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATA-ATACTAA
* *
40005189 TACATAATAATAATAATAGTAA
1 TACATAATAAAAATAATACTAA
40005211 TAC-TAATAA
1 TACATAATAA
40005220 TACTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (22 bp):
TACATAATAAAAATAATACTAA
Found at i:40005200 original size:3 final size:3
Alignment explanation
Indices: 40005169--40005239 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
40005159 ATACGCGTAC
* * * *
40005169 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
40005216 ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
40005240 CAGGATATTT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:40005721 original size:13 final size:12
Alignment explanation
Indices: 40005703--40005738 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
40005693 AAGAAAAAAA
40005703 GAAGAGAGAGAGG
1 GAAGAGAGA-AGG
40005716 GAAGAGAGAAGG
1 GAAGAGAGAAGG
40005728 G-AGAGAGAAGG
1 GAAGAGAGAAGG
40005739 AGGGGGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.43
12 4 0.17
13 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:40006240 original size:8 final size:8
Alignment explanation
Indices: 40006227--40006251 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
40006217 GGTGTTCGGC
40006227 GCAAGTGG
1 GCAAGTGG
40006235 GCAAGTGG
1 GCAAGTGG
40006243 GCAAGTGG
1 GCAAGTGG
40006251 G
1 G
40006252 GGGTAGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.52, T:0.12
Consensus pattern (8 bp):
GCAAGTGG
Found at i:40006761 original size:44 final size:44
Alignment explanation
Indices: 40006713--40007218 Score: 130
Period size: 44 Copynumber: 11.2 Consensus size: 44
40006703 AACTTCAGAG
* *
40006713 AGATAAGATCATTTAT-TTTAATCCACTCCACTGTAATCTCAGGC
1 AGATAAGATCA-CTATCTTCAATCCACTCCACTGTAATCTCAGGC
* * * * *
40006757 AGATAGGATTACTATCTTCAATCTACTCCGCTGTAATCTCAGGG
1 AGATAAGATCACTATCTTCAATCCACTCCACTGTAATCTCAGGC
* * ** *** *
40006801 AGATAAGATCTGA-AATTTTTCGGTCTGTTCCACTGTAATCTCAGGG
1 AGATAAGATC--ACTA-TCTTCAATCCACTCCACTGTAATCTCAGGC
* ** *
40006847 AGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAA-CTTCAGAG-
1 AGATAAGATCACTATCTTCAATC---------C-ACTCCACTGTAATC-TCAG-GC
* *
40006901 AGATAAGATC-CTTTAT-TTTAATCCGCTCCACTGTAA-CTTCAGAG-
1 AGATAAGATCAC--TATCTTCAATCCACTCCACTGTAATC-TCAG-GC
* * * * * *
40006945 AGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGG
1 AGATAAGATCACTATCTTCAATCCACTCCACTGTAATCTCAGGC
* ** * *
40006989 AGATAAGATTACTATGGCTTCAATCTGCTCCACTGTAACCTCAGGG
1 AGATAAGATCACTAT--CTTCAATCCACTCCACTGTAATCTCAGGC
* ** * * *
40007035 AGATAAGATCTGA-AATTCTTCGGTCTACTCCACTGTAACCTCAGGG
1 AGATAAGATC--ACTA-TCTTCAATCCACTCCACTGTAATCTCAGGC
* * * * **
40007081 TGATAAGA-C-CTGA--TACGATCTACT-CTGTGTAA-CTTCAGAG-
1 AGATAAGATCACT-ATCTTCAATCCACTCCACTGTAATC-TCAG-GC
* * *
40007121 AGATAAGATC-CTTTAT-TTTAATCCGCTCCACTGTAATCTCAGGG
1 AGATAAGATCAC--TATCTTCAATCCACTCCACTGTAATCTCAGGC
* * * * ** *
40007165 AGATAGGATTACTAGCTTCAATCTACTCCGTTGTAATCTCAGGG
1 AGATAAGATCACTATCTTCAATCCACTCCACTGTAATCTCAGGC
40007209 AGATAAGATC
1 AGATAAGATC
40007219 TGAAATTCTT
Statistics
Matches: 348, Mismatches: 73, Indels: 82
0.69 0.15 0.16
Matches are distributed among these distances:
39 1 0.00
40 17 0.05
41 12 0.03
42 1 0.00
43 16 0.05
44 155 0.45
45 7 0.02
46 103 0.30
47 1 0.00
48 2 0.01
53 2 0.01
54 29 0.08
55 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (44 bp):
AGATAAGATCACTATCTTCAATCCACTCCACTGTAATCTCAGGC
Found at i:40006804 original size:88 final size:87
Alignment explanation
Indices: 40006689--40006997 Score: 259
Period size: 88 Copynumber: 3.4 Consensus size: 87
40006679 GTCTGCTGTG
* *
40006689 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTGTAATCTCA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCA
*
40006754 GGCAGATAGGATTACTATCTTCA
66 GG-AGATAGGATTACTAGCTTCA
* * * *** * *
40006777 ATCTACTCCGCTGTAA-TCTCAGGGAGATAAGATCTGAAATT-TTTCGGTCTGTTCCACTGTAAT
1 ATCTACTCCACTGTAACT-TCAGAGAGATAAGATC---ATTTATTTTAATCCGCTCCACTGTAAT
* *
40006840 CTCAGGGAGATAAGATCT-CTGGCTTCA
62 CTCA-GGAGATAGGAT-TACTAGCTTCA
*
40006867 ATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCAC
1 ATC-----T-A-CT-C-C-ACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCAC
40006932 TGTAA-CTTCAGAGAGATAGGATTACTAGCTTCA
56 TGTAATC-TCAG-GAGATAGGATTACTAGCTTCA
* *
40006965 ATCTACTCCGCTGTAA-TCTCAGGGAGATAAGAT
1 ATCTACTCCACTGTAACT-TCAGAGAGATAAGAT
40006998 TACTATGGCT
Statistics
Matches: 173, Mismatches: 26, Indels: 44
0.71 0.11 0.18
Matches are distributed among these distances:
87 2 0.01
88 49 0.28
89 1 0.01
90 39 0.23
91 8 0.05
92 1 0.01
93 1 0.01
95 1 0.01
96 1 0.01
97 7 0.04
98 40 0.23
99 1 0.01
100 21 0.12
101 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (87 bp):
ATCTACTCCACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCA
GGAGATAGGATTACTAGCTTCA
Found at i:40006953 original size:188 final size:187
Alignment explanation
Indices: 40006656--40007045 Score: 572
Period size: 188 Copynumber: 2.1 Consensus size: 187
40006646 CTAACTGCTT
* *** *
40006656 AGGGAGATAAGATCTGTGGTTTTGTCTGCTGTGATCTACTCTACTGTAACTTCAGAGAGATAAGA
1 AGGGAGATAAGATCTCTGGTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGA
*
40006721 TCATTTATTTTAATCCACTCCACTGTAATCTCAGGCAGATAGGATTACTATCTTCAATCTACTCC
66 TCATTTATTTTAATCCACTCCACTGTAATCTCAGGCAGATAGGATTACTAGCTTCAATCTACTCC
** ** * *
40006786 GCTGTAATCTCAGGGAGATAAGATCTGA-AAT-TTTTCGGTCTGTTCCACTGTAATCTC
131 GCTGTAATCTCAGGGAGATAAGAT-T-ACAATGGCTTCAATCTGCTCCACTGTAACCTC
40006843 AGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAG
1 AGGGAGATAAGATCTCTGG-TTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAG
* *
40006908 ATCCTTTATTTTAATCCGCTCCACTGTAA-CTTCAGAG-AGATAGGATTACTAGCTTCAATCTAC
65 ATCATTTATTTTAATCCACTCCACTGTAATC-TCAG-GCAGATAGGATTACTAGCTTCAATCTAC
*
40006971 TCCGCTGTAATCTCAGGGAGATAAGATTACTATGGCTTCAATCTGCTCCACTGTAACCTC
128 TCCGCTGTAATCTCAGGGAGATAAGATTACAATGGCTTCAATCTGCTCCACTGTAACCTC
40007031 AGGGAGATAAGATCT
1 AGGGAGATAAGATCT
40007046 GAAATTCTTC
Statistics
Matches: 183, Mismatches: 15, Indels: 9
0.88 0.07 0.04
Matches are distributed among these distances:
186 1 0.01
187 22 0.12
188 159 0.87
189 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (187 bp):
AGGGAGATAAGATCTCTGGTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGA
TCATTTATTTTAATCCACTCCACTGTAATCTCAGGCAGATAGGATTACTAGCTTCAATCTACTCC
GCTGTAATCTCAGGGAGATAAGATTACAATGGCTTCAATCTGCTCCACTGTAACCTC
Found at i:40007025 original size:46 final size:45
Alignment explanation
Indices: 40006926--40007262 Score: 212
Period size: 46 Copynumber: 7.6 Consensus size: 45
40006916 TTTTAATCCG
* *
40006926 CTCCACTGTAA-CTTCAGAGAGATAGGATTACTA-GCTTCAATCTA
1 CTCCACTGTAATC-TCAGGGAGATAAGATTACTATGCTTCAATCTA
* *
40006970 CTCCGCTGTAATCTCAGGGAGATAAGATTACTATGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTAT-GCTTCAATCTA
* * * **
40007016 CTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTCGGTCTA
1 CTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTATGCTTCAATCTA
* * * * * *
40007062 CTCCACTGTAACCTCAGGGTGATAAG---AC-CTGATACGATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTATGCTTCAATCTA
** * * * ** * **
40007103 CT-CTGTGTAA-CTTCAGAGAGATAAGA-TCCTTTATTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATTACTATGCTTCAATCTA
*
40007146 CTCCACTGTAATCTCAGGGAGATAGGATTACTA-GCTTCAATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTATGCTTCAATCTA
** * * *** *
40007190 CTCCGTTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTATGCTTCAATCTA
*
40007236 TTCCACTGTAATCTCAGGGAGATAAGA
1 CTCCACTGTAATCTCAGGGAGATAAGA
40007263 CCTGTATAAT
Statistics
Matches: 224, Mismatches: 53, Indels: 30
0.73 0.17 0.10
Matches are distributed among these distances:
39 1 0.00
40 17 0.08
41 11 0.05
42 1 0.00
43 7 0.03
44 77 0.34
45 7 0.03
46 99 0.44
47 3 0.01
48 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (45 bp):
CTCCACTGTAATCTCAGGGAGATAAGATTACTATGCTTCAATCTA
Found at i:40018760 original size:23 final size:22
Alignment explanation
Indices: 40018734--40018787 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
40018724 TGTATACGCG
40018734 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATA-ATACTAA
* *
40018757 TACATAATAATAATAATAGTAA
1 TACATAATAAAAATAATACTAA
40018779 TAC-TAATAA
1 TACATAATAA
40018788 TACTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (22 bp):
TACATAATAAAAATAATACTAA
Found at i:40018768 original size:3 final size:3
Alignment explanation
Indices: 40018737--40018807 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
40018727 ATACGCGTAC
* * * *
40018737 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
40018784 ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
40018808 CGAGGATATT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:40019291 original size:13 final size:12
Alignment explanation
Indices: 40019273--40019308 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
40019263 AGAAAAAAAA
40019273 GAAGAGAGAGAGG
1 GAAGAGAGA-AGG
40019286 GAAGAGAGAAGG
1 GAAGAGAGAAGG
40019298 G-AGAGAGAAGG
1 GAAGAGAGAAGG
40019309 AAGGGGGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.43
12 4 0.17
13 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:40019301 original size:22 final size:22
Alignment explanation
Indices: 40019276--40019320 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
40019266 AAAAAAAGAA
*
40019276 GAGAGAGAGGGAAGAGAGAAGG
1 GAGAGAGAAGGAAGAGAGAAGG
* *
40019298 GAGAGAGAAGGAAGGGGGAAGG
1 GAGAGAGAAGGAAGAGAGAAGG
40019320 G
1 G
40019321 GAATCCGGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (22 bp):
GAGAGAGAAGGAAGAGAGAAGG
Found at i:40019810 original size:8 final size:8
Alignment explanation
Indices: 40019797--40019821 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
40019787 GGTGTTCGGC
40019797 GCAAGTGG
1 GCAAGTGG
40019805 GCAAGTGG
1 GCAAGTGG
40019813 GCAAGTGG
1 GCAAGTGG
40019821 G
1 G
40019822 GGTAGGTGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.52, T:0.12
Consensus pattern (8 bp):
GCAAGTGG
Found at i:40020589 original size:254 final size:254
Alignment explanation
Indices: 40020140--40020656 Score: 980
Period size: 254 Copynumber: 2.0 Consensus size: 254
40020130 AAATAATTAA
40020140 AAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTAAATTAACTATCCA
1 AAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTAAATTAACTATCCA
*
40020205 ATTAACAAAATTAAGGGATCGAACTTTAATTAACTTTTATTATAATATCGTAAATATTAAAATAA
66 ATTAACAAAATTAAGGGATCGAACTTTAATTAACTTTTATTATAATATCATAAATATTAAAATAA
40020270 TAATATTTACGAACTCAAACATTAAAAATGGGGTTCCGAAATAGCCATTTTCAACACCACTGAAA
131 TAATATTTACGAACTCAAACATTAAAAATGGGGTTCCGAAATAGCCATTTTCAACACCACTGAAA
*
40020335 ACGGGTTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAATAGAACCAAG
196 ACGGATTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAATAGAACCAAG
*
40020394 AAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTTAATTAACTATCCA
1 AAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTAAATTAACTATCCA
*
40020459 ATTAACAAAATTAAGGGATTGAACTTTAATTAACTTTTATTATAATATCATAAATATTAAAATAA
66 ATTAACAAAATTAAGGGATCGAACTTTAATTAACTTTTATTATAATATCATAAATATTAAAATAA
*
40020524 TAATATTTACGAACTCAAACATTAAAAATGGGGTTCCGTAATAGCCATTTTCAACACCACTGAAA
131 TAATATTTACGAACTCAAACATTAAAAATGGGGTTCCGAAATAGCCATTTTCAACACCACTGAAA
*
40020589 ATGGATTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAATAGAACCAAG
196 ACGGATTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAATAGAACCAAG
40020648 AAATCAATA
1 AAATCAATA
40020657 CAGTCAATAT
Statistics
Matches: 257, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
254 257 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (254 bp):
AAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTAAATTAACTATCCA
ATTAACAAAATTAAGGGATCGAACTTTAATTAACTTTTATTATAATATCATAAATATTAAAATAA
TAATATTTACGAACTCAAACATTAAAAATGGGGTTCCGAAATAGCCATTTTCAACACCACTGAAA
ACGGATTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAATAGAACCAAG
Found at i:40021755 original size:254 final size:254
Alignment explanation
Indices: 40021306--40021822 Score: 962
Period size: 254 Copynumber: 2.0 Consensus size: 254
40021296 AAATAATTAA
*
40021306 AAATCAACAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTAAATTAACTATCCA
1 AAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTAAATTAACTATCCA
40021371 ATTAACAAAATTAAGGGATCGAACTTTAATTAACTTTTATTATAATATCGTAAATATTAAAATAA
66 ATTAACAAAATTAAGGGATCGAACTTTAATTAACTTTTATTATAATATCGTAAATATTAAAATAA
40021436 TAATATTTACGAACTCAAACATTAAAAATGGGGTTCCAAAATAGCCATTTTCAACACCACTGAAA
131 TAATATTTACGAACTCAAACATTAAAAATGGGGTTCCAAAATAGCCATTTTCAACACCACTGAAA
* *
40021501 ACGGGTTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAATAGAACCAAG
196 ACGGATTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAACAGAACCAAG
*
40021560 AAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTTAATTAACTATCCA
1 AAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTAAATTAACTATCCA
*
40021625 ATTAACAAAATTAAGGGATTGAACTTTAATTAACTTTTATTATAATATCGTAAATATTAAAATAA
66 ATTAACAAAATTAAGGGATCGAACTTTAATTAACTTTTATTATAATATCGTAAATATTAAAATAA
**
40021690 TAATATTTACGAACTCAAACATTAAAAATGGGGTTCCGTAATAGCCATTTTCAACACCACTGAAA
131 TAATATTTACGAACTCAAACATTAAAAATGGGGTTCCAAAATAGCCATTTTCAACACCACTGAAA
*
40021755 ATGGATTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAACAGAACCAAG
196 ACGGATTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAACAGAACCAAG
40021814 AAATCAATA
1 AAATCAATA
40021823 CAGTCAATAT
Statistics
Matches: 255, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
254 255 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.35
Consensus pattern (254 bp):
AAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTAAATTAACTATCCA
ATTAACAAAATTAAGGGATCGAACTTTAATTAACTTTTATTATAATATCGTAAATATTAAAATAA
TAATATTTACGAACTCAAACATTAAAAATGGGGTTCCAAAATAGCCATTTTCAACACCACTGAAA
ACGGATTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAACAGAACCAAG
Found at i:40023572 original size:142 final size:143
Alignment explanation
Indices: 40023403--40023680 Score: 459
Period size: 142 Copynumber: 2.0 Consensus size: 143
40023393 TAAATGACTG
* *
40023403 TCATCATTATCATCCATTATCTCATAAGAAACAATGAGTCAATAACCATTTAGGTCCCTTGGTTA
1 TCATCATTATCATCCACTATCTCATAAGAAACAATGAGTCAATAACCATTTAGGTCCCTTGATTA
* *
40023468 ATTACCAATTAGGTCATCAAACATTTTCCAATATAAAATTCAATAGCAATTGGAC-TTTACAATT
66 AATACCAATTAGGTCATCAAACATTTTCCAATATAAAATTCAATAACAATTGGACTTTTACAATT
40023532 TAGTCTCTAACTA
131 TAGTCTCTAACTA
* * *
40023545 TCATCATTATCATCCACTATCTTATAAGGAACAATGAGTTAATAACCATTTAGGTCCCTTGATTA
1 TCATCATTATCATCCACTATCTCATAAGAAACAATGAGTCAATAACCATTTAGGTCCCTTGATTA
* * *
40023610 AATACCAATTAGGTCATCAAGCATTTTCCACTATAAAATTTAATAACAATTGGACTTTTACAATT
66 AATACCAATTAGGTCATCAAACATTTTCCAATATAAAATTCAATAACAATTGGACTTTTACAATT
40023675 TAGTCT
131 TAGTCT
40023681 TTAAACTTTA
Statistics
Matches: 125, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
142 110 0.88
143 15 0.12
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (143 bp):
TCATCATTATCATCCACTATCTCATAAGAAACAATGAGTCAATAACCATTTAGGTCCCTTGATTA
AATACCAATTAGGTCATCAAACATTTTCCAATATAAAATTCAATAACAATTGGACTTTTACAATT
TAGTCTCTAACTA
Found at i:40026105 original size:14 final size:14
Alignment explanation
Indices: 40026086--40026112 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40026076 TTAGTGTAAG
40026086 AAAATAAATCCTTT
1 AAAATAAATCCTTT
40026100 AAAATAAATCCTT
1 AAAATAAATCCTT
40026113 GTTGTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATAAATCCTTT
Found at i:40028636 original size:21 final size:21
Alignment explanation
Indices: 40028610--40028658 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
40028600 CTAAAACATT
*
40028610 GGCATGTCCCATAGCCACACG
1 GGCATGTCCCATAGCCACACA
* *
40028631 GGCATGTCCCTTGGCCACACA
1 GGCATGTCCCATAGCCACACA
40028652 GGCATGT
1 GGCATGT
40028659 GACCCCTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.35, G:0.27, T:0.18
Consensus pattern (21 bp):
GGCATGTCCCATAGCCACACA
Found at i:40033254 original size:111 final size:112
Alignment explanation
Indices: 40033053--40033264 Score: 261
Period size: 111 Copynumber: 1.9 Consensus size: 112
40033043 TAAGAATGTA
* * *
40033053 TTGGGCTGAGTAAGCGGGGTGGGGTGCTTGGTTGTCATCTCTTTTCGAGTCAAAAGGTTCAATAT
1 TTGGGCTGAGTAAGCGGGGTGGGGTGCTTCGTTGTCATCTCTCTTCGAGTCAAAACGTTCAATAT
* * * * * *
40033118 GTTATTAAGAATAAAACATATATAAATATAA-TAAATTAGGAGTATG
66 ATTATTAAGAAAAAAAAAAAAATAAAAATAAGTAAATTAGGAGTATG
* *
40033164 TTGGGCTGAGTAA-CTGGGGTGGGGTGCTTCGTTGTCATTTCTCTTCGCA-TCAAAACGTTTAAT
1 TTGGGCTGAGTAAGC-GGGGTGGGGTGCTTCGTTGTCATCTCTCTTCG-AGTCAAAACGTTCAAT
*
40033227 ATATTCTTAA-AAAAAGAAAAAAAATAAAAATAAGTAAA
64 ATATTATTAAGAAAAA-AAAAAAAATAAAAATAAGTAAA
40033265 AAATAATAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
110 5 0.06
111 75 0.88
112 5 0.06
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (112 bp):
TTGGGCTGAGTAAGCGGGGTGGGGTGCTTCGTTGTCATCTCTCTTCGAGTCAAAACGTTCAATAT
ATTATTAAGAAAAAAAAAAAAATAAAAATAAGTAAATTAGGAGTATG
Found at i:40033256 original size:17 final size:20
Alignment explanation
Indices: 40033234--40033273 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
40033224 AATATATTCT
40033234 TAAAAA-AAG-AAAAAA-AA
1 TAAAAATAAGTAAAAAATAA
40033251 TAAAAATAAGTAAAAAATAA
1 TAAAAATAAGTAAAAAATAA
40033271 TAA
1 TAA
40033274 TAAAGAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 3 0.15
19 6 0.30
20 5 0.25
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (20 bp):
TAAAAATAAGTAAAAAATAA
Found at i:40034636 original size:21 final size:20
Alignment explanation
Indices: 40034612--40034651 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40034602 AATTATGTTT
* *
40034612 ATTTTTACAATTTCAATTTCA
1 ATTTATACAATGTC-ATTTCA
40034633 ATTTATACAATGTCATTTC
1 ATTTATACAATGTCATTTC
40034652 GTCCATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.50
Consensus pattern (20 bp):
ATTTATACAATGTCATTTCA
Found at i:40035069 original size:28 final size:28
Alignment explanation
Indices: 40035029--40035083 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
40035019 ATTCCAATGA
40035029 TTACGTATTGGAGAAGAACTAAATCTTT
1 TTACGTATTGGAGAAGAACTAAATCTTT
40035057 TTACGTATTGGAGAAGAACTAAATCTT
1 TTACGTATTGGAGAAGAACTAAATCTT
40035084 GCTAAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (28 bp):
TTACGTATTGGAGAAGAACTAAATCTTT
Found at i:40036414 original size:26 final size:26
Alignment explanation
Indices: 40036378--40036487 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
40036368 TGATACAAAT
*
40036378 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
40036404 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
40036430 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
40036456 TGATAATGGGTTAGGTAAATATTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
40036482 TGATAA
1 TGATAA
40036488 GAATTTCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:40038147 original size:27 final size:27
Alignment explanation
Indices: 40038106--40038245 Score: 183
Period size: 27 Copynumber: 5.2 Consensus size: 27
40038096 GAGGAAGCGT
*
40038106 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
40038133 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
40038160 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
40038187 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
40038215 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
40038241 TCTGG
1 TCTGG
40038246 CAGCCATGCT
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
26 5 0.05
27 82 0.80
28 15 0.15
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:40038191 original size:54 final size:55
Alignment explanation
Indices: 40038106--40038245 Score: 203
Period size: 54 Copynumber: 2.6 Consensus size: 55
40038096 GAGGAAGCGT
* * *
40038106 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
40038160 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
40038215 TCTGGTGACTCTGTCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
40038246 CAGCCATGCT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 60 0.77
55 18 0.23
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
Found at i:40049870 original size:54 final size:54
Alignment explanation
Indices: 40049795--40049904 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
40049785 TCCATTTCCT
40049795 AAGACTAAAAGCAGGCCTCTACCTTCTATGGGTAGAAAAACACAAGCTTCCTAA
1 AAGACTAAAAGCAGGCCTCTACCTTCTATGGGTAGAAAAACACAAGCTTCCTAA
40049849 AAGACTAAAAGCAGGCCTCTACCTTCTATGGGTAGAAAAACACAAGCTTCCTAA
1 AAGACTAAAAGCAGGCCTCTACCTTCTATGGGTAGAAAAACACAAGCTTCCTAA
40049903 AA
1 AA
40049905 ATAACTTTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (54 bp):
AAGACTAAAAGCAGGCCTCTACCTTCTATGGGTAGAAAAACACAAGCTTCCTAA
Found at i:40054600 original size:30 final size:30
Alignment explanation
Indices: 40054561--40054627 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
40054551 CGTTCAAAAA
* *
40054561 CTTGAGAAGACCCGATATCT-AGTTCAGGAG
1 CTTGGGAAGACCCGATATCTCA-CTCAGGAG
* *
40054591 CTTGGGAAGACTCGATATCTCACTCAGGAT
1 CTTGGGAAGACCCGATATCTCACTCAGGAG
40054621 CTTGGGA
1 CTTGGGA
40054628 TTGAGAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (30 bp):
CTTGGGAAGACCCGATATCTCACTCAGGAG
Found at i:40054674 original size:30 final size:29
Alignment explanation
Indices: 40054574--40054693 Score: 87
Period size: 30 Copynumber: 3.8 Consensus size: 29
40054564 GAGAAGACCC
*
40054574 GATATCTAGTTCAGGAGCTTGGGAAGACTC
1 GATATCTA-TTCAGGAGCTTGGGAAGACTA
* * *
40054604 GATATCTCACTCAGGATCTTGGGATTGAGAAGATAA
1 GATATCT-ATTCAGGAGCTTGGGA---AG-A-CT-A
*
40054640 GATATCTCATTCAGGAGCTTGGGAAGACTT
1 GATATCT-ATTCAGGAGCTTGGGAAGACTA
* *
40054670 GATATCGTGTTCAAGAGCTTGGGA
1 GATATC-TATTCAGGAGCTTGGGA
40054694 TGGAGAAGAC
Statistics
Matches: 72, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
30 40 0.56
31 3 0.04
32 1 0.01
33 4 0.06
34 1 0.01
35 1 0.01
36 22 0.31
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (29 bp):
GATATCTATTCAGGAGCTTGGGAAGACTA
Found at i:40054691 original size:66 final size:66
Alignment explanation
Indices: 40054574--40054732 Score: 178
Period size: 66 Copynumber: 2.4 Consensus size: 66
40054564 GAGAAGACCC
* * *
40054574 GATATCTAGTTCAGGAGCTTGGGAAGACTCGATATCTCACTCAGGATCTTGGGATTGAGAAGATA
1 GATATCTAGTTCAGGAGCTTGGGAAGACTCGATATCTCACTCAAGAGCTTGGGATGGAGAAGATA
40054639 A
66 A
* **
40054640 GATATCTCA-TTCAGGAGCTTGGGAAGACTTGATATCGT-GTTCAAGAGCTTGGGATGGAGAAGA
1 GATATCT-AGTTCAGGAGCTTGGGAAGACTCGATATC-TCACTCAAGAGCTTGGGATGGAGAAGA
***
40054703 CCT
64 TAA
* * *
40054706 GATATCTTGTTTAGGAGTTTGGGAAGA
1 GATATCTAGTTCAGGAGCTTGGGAAGA
40054733 TCCGGTGTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
66 76 0.97
67 2 0.03
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.29
Consensus pattern (66 bp):
GATATCTAGTTCAGGAGCTTGGGAAGACTCGATATCTCACTCAAGAGCTTGGGATGGAGAAGATA
A
Found at i:40060013 original size:131 final size:131
Alignment explanation
Indices: 40059768--40060015 Score: 329
Period size: 131 Copynumber: 1.9 Consensus size: 131
40059758 AAAACGAAGG
* * *
40059768 CAATACTCGGTGTTTGATAATTCGAGAATCATGCCTTATCGTGCTGGGTTGTGATTTCTCGTTTG
1 CAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAACGTACTGGGTTGTGATTTCTCGTTTG
* * ** * ** *
40059833 TTCAAAACAATCGAATATTCCTTTAGGTTTTTACTCGTGTTTATTAAAAACCTTCCAAAATGAAT
66 TTCAAAACAATCGAAGATTCCTTGAGAATTTCACTCACGTTTATAAAAAACCTTCCAAAATGAAT
40059898 A
131 A
* * * *
40059899 CAATACTCGGTGTTTGATAATTCGGGAATCGTGCCCTAACGTATTGGGTTGTGATTTCTCGTTTT
1 CAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAACGTACTGGGTTGTGATTTCTCGTTTG
40059964 TTCAAAACAATCGAAGATTCCTTCGA-AATTTCACTCACGTTT-TCAAAAAACC
66 TTCAAAACAATCGAAGATTCCTT-GAGAATTTCACTCACGTTTAT-AAAAAACC
40060016 CCTTAAAACG
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
130 1 0.01
131 98 0.98
132 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (131 bp):
CAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAACGTACTGGGTTGTGATTTCTCGTTTG
TTCAAAACAATCGAAGATTCCTTGAGAATTTCACTCACGTTTATAAAAAACCTTCCAAAATGAAT
A
Found at i:40061446 original size:19 final size:18
Alignment explanation
Indices: 40061424--40061483 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
40061414 ATCCCATGCA
40061424 TTTGCATTGCATTGCATC
1 TTTGCATTGCATTGCATC
40061442 -TT---TTGCATTGCATC
1 TTTGCATTGCATTGCATC
*
40061456 TTTTACATTGCATTGCATC
1 -TTTGCATTGCATTGCATC
40061475 ATTTGCATT
1 -TTTGCATT
40061484 AGATTTTCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 12 0.34
16 2 0.06
17 2 0.06
19 19 0.54
ACGTcount: A:0.18, C:0.20, G:0.13, T:0.48
Consensus pattern (18 bp):
TTTGCATTGCATTGCATC
Found at i:40061483 original size:14 final size:14
Alignment explanation
Indices: 40061430--40061468 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
40061420 TGCATTTGCA
40061430 TTGCATTGCATCTT
1 TTGCATTGCATCTT
40061444 TTGCATTGCATCTT
1 TTGCATTGCATCTT
*
40061458 TTACATTGCAT
1 TTGCATTGCAT
40061469 TGCATCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.49
Consensus pattern (14 bp):
TTGCATTGCATCTT
Found at i:40065170 original size:64 final size:64
Alignment explanation
Indices: 40065094--40065281 Score: 286
Period size: 64 Copynumber: 2.9 Consensus size: 64
40065084 TCATTCATAA
* * * *
40065094 CACATCTAGTTAGGAGCATTTGATTCATGTCGATTATAACATTCTAATTATTTGAGATAAACAT
1 CACATCTAGTTAGGAACATTTGATTCATGTCGATCATAGCATTCTAATTATTTGACATAAACAT
*
40065158 CACATCTAGTTAGGAACATTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACAT
1 CACATCTAGTTAGGAACATTTGATTCATGTCGATCATAGCATTCTAATTATTTGACATAAACAT
* ** * *
40065222 CACATCTAGTTAGGAACAATTGATTCATGTTAATCATAGCATCCTAATTATTTGGCATAA
1 CACATCTAGTTAGGAACATTTGATTCATGTCGATCATAGCATTCTAATTATTTGACATAA
40065282 GCATAGGCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 113 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (64 bp):
CACATCTAGTTAGGAACATTTGATTCATGTCGATCATAGCATTCTAATTATTTGACATAAACAT
Found at i:40065537 original size:131 final size:131
Alignment explanation
Indices: 40065303--40066104 Score: 1102
Period size: 131 Copynumber: 6.0 Consensus size: 131
40065293 TGAAACAGAA
* * * **
40065303 TGTAGATATTATCTCCTTGAAGTTGCAGTGGGGCAAATTGAAGACGACGAATCTTGGCTTCCTGA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCAAAGACGACGAATCTTGGCTTCCTGA
* * *
40065368 AGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGATGAAGA
66 AGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAAGA
40065433 T
131 T
40065434 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCAAAGACGACGAATCTTGGCTTCCTGA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCAAAGACGACGAATCTTGGCTTCCTGA
* * *
40065499 AGTTGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGTTGAATA
66 AGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAAGA
40065564 T
131 T
* *
40065565 TGTAGATCTTGTCTCTCTGAAGTTGCAGTGGGGCAAATCGAAGAGGAAAATTGAAGAGGACGAAT
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATC----------A---AAGACGACGAAT
*
40065630 CTTGGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGG
53 CTTGGCTTCCTGAAGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGG
*
40065695 AGTAGGCTGAATAT
118 AGTAGGCTGAAGAT
* * * * *
40065709 TGCAGATCTTGTCTCCCTGAAGTTACAGTGGGGCAAATCGAAGATGATGAATCTTGGCTTCCTGA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCAAAGACGACGAATCTTGGCTTCCTGA
*
40065774 AGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAATA
66 AGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAAGA
40065839 T
131 T
* * * * *
40065840 TGTAGATCTTGTCTCCCTGAAGCTACAGTGGGGCAAATCGAAA-ATGATGAATCTTGGCTTCCTA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATC-AAAGACGACGAATCTTGGCTTCCTG
* * * *
40065904 AAGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGTTCCCTAAAGTTGTAGTGGAGTAGGCCGAAG
65 AAGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAAG
40065969 AT
130 AT
* * *
40065971 TGTAGATCTTGTCTCCTTGAAGTTGCAGTGGGGCAAATCGAAGACGACAAATCTTGGCTTCCTGA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCAAAGACGACGAATCTTGGCTTCCTGA
* * * * **
40066036 AGTTGTAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAATGTTGTAGTGGAGTAGGCTGAA
66 AGATGCAGTGAAGCAGATTTAAGCTA--GTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAA
40066101 GAT
129 GAT
40066104 T
1 T
40066105 ACAGACCTTG
Statistics
Matches: 610, Mismatches: 44, Indels: 32
0.89 0.06 0.05
Matches are distributed among these distances:
130 2 0.00
131 443 0.73
132 2 0.00
133 37 0.06
141 1 0.00
144 125 0.20
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (131 bp):
TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCAAAGACGACGAATCTTGGCTTCCTGA
AGATGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAAGA
T
Found at i:40065828 original size:275 final size:268
Alignment explanation
Indices: 40065337--40066100 Score: 1162
Period size: 275 Copynumber: 2.8 Consensus size: 268
40065327 GCAGTGGGGC
40065337 AAATTGAAGACGACGAATCTTGGCTTCCTGAAGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGC
1 AAATTGAAGA-GACGAATCTTGGCTTCCTGAAGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGC
*
40065402 TCCCTAAAGTTGTAGTGGAGTAGGATGAAGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGG
65 TCCCTAAAGTTGTAGTGGAGTAGGCTGAAGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGG
*
40065467 CAAATCAAAGACGACGAATCTTGGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCTAGTCCTAG
130 CAAATCGAAGACGACGAATCTTGGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCTAGTCCTAG
* * * *
40065532 CTCCCTAAAATTGTAGTGGAGTAGGTTGAATATTGTAGATCTTGTCTCTCTGAAGTTGCAGTGGG
195 CTCCCTAAAATTGTAGTGGAGTAGGCTGAATATTGTAGATCTTGTCTCCCTGAAGCTACAGTGGG
40065597 GCAAATCGAAGAGGA
260 GCAAATC------GA
* *
40065612 AAATTGAAGAGGACGAATCTTGGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCTAGTCCTAGC
1 AAATTGAAGA-GACGAATCTTGGCTTCCTGAAGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGC
* * * *
40065677 TCCCTAAAATTGTAGTGGAGTAGGCTGAATATTGCAGATCTTGTCTCCCTGAAGTTACAGTGGGG
65 TCCCTAAAGTTGTAGTGGAGTAGGCTGAAGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGG
* * *
40065742 CAAATCGAAGATGATGAATCTTGGCTTCCTGAAGATGCAGTGAAGCAGATTTAAGCTAGTCCTAG
130 CAAATCGAAGACGACGAATCTTGGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCTAGTCCTAG
40065807 CTCCCTAAAATTGTAGTGGAGTAGGCTGAATATTGTAGATCTTGTCTCCCTGAAGCTACAGTGGG
195 CTCCCTAAAATTGTAGTGGAGTAGGCTGAATATTGTAGATCTTGTCTCCCTGAAGCTACAGTGGG
40065872 GCAAATCGA
260 GCAAATCGA
* * *
40065881 AAA-T-----GATGAATCTTGGCTTCCTAAAGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGTT
1 AAATTGAAGAGACGAATCTTGGCTTCCTGAAGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGCT
* *
40065940 CCCTAAAGTTGTAGTGGAGTAGGCCGAAGATTGTAGATCTTGTCTCCTTGAAGTTGCAGTGGGGC
66 CCCTAAAGTTGTAGTGGAGTAGGCTGAAGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGC
* * * *
40066005 AAATCGAAGACGACAAATCTTGGCTTCCTGAAGTTGTAGTGAAGCAGATTTAAGCCACCATCCTA
131 AAATCGAAGACGACGAATCTTGGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCTA--GTCCTA
**
40066070 GCTCCCTAATGTTGTAGTGGAGTAGGCTGAA
194 GCTCCCTAAAATTGTAGTGGAGTAGGCTGAA
40066101 GATTACAGAC
Statistics
Matches: 451, Mismatches: 36, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
262 160 0.35
264 34 0.08
268 1 0.00
269 5 0.01
275 251 0.56
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (268 bp):
AAATTGAAGAGACGAATCTTGGCTTCCTGAAGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGCT
CCCTAAAGTTGTAGTGGAGTAGGCTGAAGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGC
AAATCGAAGACGACGAATCTTGGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCTAGTCCTAGC
TCCCTAAAATTGTAGTGGAGTAGGCTGAATATTGTAGATCTTGTCTCCCTGAAGCTACAGTGGGG
CAAATCGA
Found at i:40069284 original size:131 final size:131
Alignment explanation
Indices: 40069133--40069376 Score: 364
Period size: 131 Copynumber: 1.9 Consensus size: 131
40069123 GTTTCACAAC
* * *
40069133 TATTAAAAATTCTTTCAAACGAAGGCAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTATC
1 TATTAAAAATCCTTTCAAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAAC
*
40069198 GTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAATATTCCTTTAGGTTTTCACTCGTGT
66 GTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAAGATTCCTTTAGGTTTTCACTCGTGT
40069263 T
131 T
* * * *
40069264 TATTAAAAA-CCTTTCAAAACGAATACAATACTTGGTGTTTGATAATTCGGGAATCGTGCCCTAA
1 TATTAAAAATCCTTTC-AAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAA
* ** *
40069328 CGTGTTGGGTTGTGATTTCTCATTTTTTCAAAACAATCGAAGATTCCTT
65 CGTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAAGATTCCTT
40069377 CGAAATTTCA
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
130 5 0.05
131 95 0.95
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (131 bp):
TATTAAAAATCCTTTCAAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAAC
GTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAAGATTCCTTTAGGTTTTCACTCGTGT
T
Found at i:40069402 original size:131 final size:130
Alignment explanation
Indices: 40069133--40069405 Score: 343
Period size: 131 Copynumber: 2.1 Consensus size: 130
40069123 GTTTCACAAC
* * *
40069133 TATTAAAAATTCTTTCAAACGAAGGCAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTATC
1 TATTAAAAA-CCTTTCAAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAAC
* * ** **
40069198 GTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAATATTCCTTTAGGTTTTCACTCGTGT
65 GTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAAGATTCCTTGAGAATTTCACTCACGT
40069263 T
130 T
* * * *
40069264 TATTAAAAACCTTTCAAAACGAATACAATACTTGGTGTTTGATAATTCGGGAATCGTGCCCTAAC
1 TATTAAAAACCTTTC-AAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAAC
* ** *
40069329 GTGTTGGGTTGTGATTTCTCATTTTTTCAAAACAATCGAAGATTCCTTCGA-AATTTCACTCACG
65 GTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAAGATTCCTT-GAGAATTTCACTCACG
40069393 TT
129 TT
40069395 T-TCTAAAAACC
1 TAT-TAAAAACC
40069406 CTTGAAAATG
Statistics
Matches: 122, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
130 6 0.05
131 115 0.94
132 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (130 bp):
TATTAAAAACCTTTCAAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAACG
TGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAAGATTCCTTGAGAATTTCACTCACGTT
Found at i:40069442 original size:131 final size:131
Alignment explanation
Indices: 40069149--40069500 Score: 332
Period size: 131 Copynumber: 2.7 Consensus size: 131
40069139 AAATTCTTTC
* * * * * * * **
40069149 AAACGAAGGCAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTATCGTGCTAAGTTGTGATT
1 AAACGAAGACAATACTTGATGCTTGACAATTCGGGAATCGTGCCCTATCGTGCTGGGTTGTGATT
* * ** ** *
40069214 TCTCATTTGTTCAAAACAATCGAATATTCCTTTAGGTTTTCACTCGTGTTTATTAAAAACCTTTC
66 TCTCATTTGTTCAAAACAATCGAAGATTCCTTGAGAATTTCACTCACGTTTATTAAAAACCCTTC
40069279 A
131 A
* * * * * *
40069280 AAACGAATACAATACTTGGTGTTTGATAATTCGGGAATCGTGCCCTAACGTGTTGGGTTGTGATT
1 AAACGAAGACAATACTTGATGCTTGACAATTCGGGAATCGTGCCCTATCGTGCTGGGTTGTGATT
*
40069345 TCTCATTTTTTCAAAACAATCGAAGATTCCTTCGA-AATTTCACTCACGTTT-TCTAAAAACCCT
66 TCTCATTTGTTCAAAACAATCGAAGATTCCTT-GAGAATTTCACTCACGTTTAT-TAAAAACCCT
*
40069408 TGA
129 TCA
* * * * * ***
40069411 AAATGAAGACGATA-TTCGATGCTTGGCAATTCGAGGAATAGTACCCTATCGTGCTGGGTTACAA
1 AAACGAAGACAATACTT-GATGCTTGACAATTCG-GGAATCGTGCCCTATCGTGCTGGGTTGTGA
* * *
40069475 TTTCCCGTTTGTTCAAAATAATCGAA
64 TTTCTCATTTGTTCAAAACAATCGAA
40069501 TATCTCTTCA
Statistics
Matches: 181, Mismatches: 36, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
130 3 0.02
131 132 0.73
132 46 0.25
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (131 bp):
AAACGAAGACAATACTTGATGCTTGACAATTCGGGAATCGTGCCCTATCGTGCTGGGTTGTGATT
TCTCATTTGTTCAAAACAATCGAAGATTCCTTGAGAATTTCACTCACGTTTATTAAAAACCCTTC
A
Found at i:40071870 original size:23 final size:24
Alignment explanation
Indices: 40071838--40071903 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
40071828 AATTAATCTA
*
40071838 AATATAACTTAAAATCTAAATT-T
1 AATAAAACTTAAAATCTAAATTCT
* *
40071861 ACTAATACTTAAAAAATCT-AATTCT
1 AATAAAACTT--AAAATCTAAATTCT
40071886 AATAAAACTTAAAATCTA
1 AATAAAACTTAAAATCTA
40071904 TTTTTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
23 14 0.41
24 4 0.12
25 16 0.47
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (24 bp):
AATAAAACTTAAAATCTAAATTCT
Found at i:40071880 original size:25 final size:25
Alignment explanation
Indices: 40071825--40071899 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
40071815 CGGGTCACTG
*
40071825 AAAAAT-TAA-TCTAAATATAACTT-
1 AAAAATCTAATTCT-AATAAAACTTA
* *
40071848 -AAAATCTAAATT-TACTAATACTTA
1 AAAAATCT-AATTCTAATAAAACTTA
40071872 AAAAATCTAATTCTAATAAAACTTA
1 AAAAATCTAATTCTAATAAAACTTA
40071897 AAA
1 AAA
40071900 TCTATTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
22 5 0.12
23 8 0.20
24 7 0.17
25 21 0.51
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAAATCTAATTCTAATAAAACTTA
Found at i:40076220 original size:5 final size:5
Alignment explanation
Indices: 40076212--40076278 Score: 75
Period size: 5 Copynumber: 13.0 Consensus size: 5
40076202 TAACTAATTT
*
40076212 AATAA AATAA AATAA AATAA AATAA ATTGAA AAT-A AATAAA AATAA AA-ATA
1 AATAA AATAA AATAA AATAA AATAA AAT-AA AATAA AAT-AA AATAA AATA-A
40076263 AATAAA AATAA AATAA
1 AAT-AA AATAA AATAA
40076279 TGTATTCCTA
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
4 5 0.09
5 36 0.67
6 12 0.22
7 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:40076232 original size:15 final size:16
Alignment explanation
Indices: 40076212--40076278 Score: 79
Period size: 16 Copynumber: 4.3 Consensus size: 16
40076202 TAACTAATTT
40076212 AATAAAAT-AAAATAA
1 AATAAAATAAAAATAA
*
40076227 AATAAAAT-AAATTGAA
1 AATAAAATAAAAAT-AA
40076243 AAT-AAATAAAAATAA
1 AATAAAATAAAAATAA
40076258 AA-ATAAATAAAAATAA
1 AATA-AAATAAAAATAA
40076274 AATAA
1 AATAA
40076279 TGTATTCCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
15 20 0.44
16 24 0.53
17 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (16 bp):
AATAAAATAAAAATAA
Found at i:40079638 original size:16 final size:16
Alignment explanation
Indices: 40079619--40079670 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
40079609 TTATTAGGTA
40079619 ATGGGTTTATTTGGGT
1 ATGGGTTTATTTGGGT
*
40079635 ATGGGTTAATTGTGGGT
1 ATGGGTTTATT-TGGGT
40079652 AATGTGG-TTAGTTTGGGT
1 -ATG-GGTTTA-TTTGGGT
40079670 A
1 A
40079671 GGTAAGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 10 0.33
17 6 0.20
18 10 0.33
19 4 0.13
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.44
Consensus pattern (16 bp):
ATGGGTTTATTTGGGT
Found at i:40087770 original size:47 final size:47
Alignment explanation
Indices: 40087716--40088000 Score: 419
Period size: 47 Copynumber: 6.1 Consensus size: 47
40087706 TTAGGATTTT
** * * *
40087716 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
40087763 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
40087810 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40087857 ATGTGATGAATGTGAATATGCACATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
40087904 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
40087951 ATGTGATGAACGTGGAAC-TGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAATGGCCA
40087998 ATG
1 ATG
40088001 CGAAATGTGT
Statistics
Matches: 219, Mismatches: 18, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
47 215 0.98
48 4 0.02
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:40087863 original size:22 final size:22
Alignment explanation
Indices: 40087836--40087910 Score: 80
Period size: 22 Copynumber: 3.3 Consensus size: 22
40087826 CATGCATATG
40087836 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
40087858 TGTGATGAATG-TGAATATGCACATA
1 TGTGAT-AAGGCCGAAT-GGC-CA-A
40087883 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
40087905 TGTGAT
1 TGTGAT
40087911 GAATGTGAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
22 17 0.40
23 7 0.17
24 7 0.17
25 11 0.26
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:40087957 original size:22 final size:22
Alignment explanation
Indices: 40087836--40087957 Score: 72
Period size: 22 Copynumber: 5.3 Consensus size: 22
40087826 CATGCATATG
*
40087836 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCAGAATGGCCAA
* * *
40087858 TGTGATGAATG-TGAATATGCACATA
1 TGTGAT-AAGGCAGAAT-GGC-CA-A
*
40087883 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCAGAATGGCCAA
*
40087905 TGTGATGAATGTG-A-ACAT-GCATATA
1 TGTGAT-AA-G-GCAGA-ATGGC-CA-A
40087930 TGTGATAAGGCAGAATGGCCAA
1 TGTGATAAGGCAGAATGGCCAA
40087952 TGTGAT
1 TGTGAT
40087958 GAACGTGGAA
Statistics
Matches: 77, Mismatches: 9, Indels: 28
0.68 0.08 0.25
Matches are distributed among these distances:
22 25 0.32
23 17 0.22
24 16 0.21
25 19 0.25
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCAGAATGGCCAA
Found at i:40088030 original size:46 final size:46
Alignment explanation
Indices: 40087974--40088156 Score: 285
Period size: 46 Copynumber: 4.0 Consensus size: 46
40087964 GGAACTGTAT
* *
40087974 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
*
40088020 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTTTGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
40088066 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
* * * * **
40088112 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATG
40088157 TGTATATATA
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 127 1.00
ACGTcount: A:0.34, C:0.09, G:0.32, T:0.25
Consensus pattern (46 bp):
ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
Found at i:40089721 original size:21 final size:22
Alignment explanation
Indices: 40089697--40089743 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
40089687 TATTATTTCA
40089697 TATATTATT-TCATA-TATTATT
1 TATATTATTGT-ATATTATTATT
*
40089718 TATATTATTGTATATTTTTATT
1 TATATTATTGTATATTATTATT
40089740 TATA
1 TATA
40089744 AATTTAGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TATATTATTGTATATTATTATT
Found at i:40089722 original size:35 final size:34
Alignment explanation
Indices: 40089609--40089739 Score: 84
Period size: 33 Copynumber: 3.9 Consensus size: 34
40089599 ATTTATCTAT
*
40089609 TATATTA-TTATACATT-TTTA-ATCTT-TA-TCA
1 TATATTATTTATATATTATTTATAT-TTATATTCA
*
40089639 TATATTAATTATATATTATTTATATTTATATT-A
1 TATATTATTTATATATTATTTATATTTATATTCA
* *
40089672 T-TGTTTTTTAGTATATATTATTTCATATATTAT-TTCA
1 TAT-ATTATT--TATATATTATTT-ATAT-TTATATTCA
*
40089709 TATATTA-TT-TATATTATTGTATATTTTTATT
1 TATATTATTTATATATTATT-TATATTTATATT
40089740 TATAAATTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 25
0.71 0.06 0.22
Matches are distributed among these distances:
30 7 0.09
31 8 0.10
32 10 0.12
33 24 0.30
34 3 0.04
35 12 0.15
36 7 0.09
37 8 0.10
38 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (34 bp):
TATATTATTTATATATTATTTATATTTATATTCA
Found at i:40089726 original size:12 final size:11
Alignment explanation
Indices: 40089638--40089743 Score: 76
Period size: 12 Copynumber: 9.3 Consensus size: 11
40089628 AATCTTTATC
*
40089638 ATATATTAATT
1 ATATATTATTT
40089649 ATATATTATTT
1 ATATATTATTT
40089660 ATAT-TTATATT
1 ATATATTAT-TT
* *
40089671 AT-TGTTTTTTAGT
1 ATAT-ATTATT--T
40089684 ATATATTATTT
1 ATATATTATTT
40089695 CATATATTATTT
1 -ATATATTATTT
40089707 CATATATTA-TT
1 -ATATATTATTT
40089718 -TATATTATTGT
1 ATATATTATT-T
*
40089729 ATATTTTTATTT
1 ATA-TATTATTT
40089741 ATA
1 ATA
40089744 AATTTAGTAT
Statistics
Matches: 79, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
9 7 0.09
10 6 0.08
11 23 0.29
12 29 0.37
13 13 0.16
14 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (11 bp):
ATATATTATTT
Found at i:40103963 original size:39 final size:39
Alignment explanation
Indices: 40103884--40103974 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 39
40103874 TGCATGGTAT
* * * *
40103884 TGGAAAAATATCCGGACTTGAAGTCCGCAGGCTTTATGC
1 TGGAAAAATATCCAGACTTAAAGTCCGCAGGCATAATGC
*
40103923 TGGAAATATATCCAGACTTAAAGTCCGCAGG-ATAAGTGC
1 TGGAAAAATATCCAGACTTAAAGTCCGCAGGCATAA-TGC
40103962 TGGAAAAATATCC
1 TGGAAAAATATCC
40103975 GGGCTAAGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 2 0.04
39 43 0.96
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (39 bp):
TGGAAAAATATCCAGACTTAAAGTCCGCAGGCATAATGC
Found at i:40104012 original size:39 final size:39
Alignment explanation
Indices: 40103969--40104184 Score: 342
Period size: 39 Copynumber: 5.5 Consensus size: 39
40103959 TGCTGGAAAA
*
40103969 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGTTGGTATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
* *
40104008 ATATCCGGGATAAGTCCTGAAGGCATTCGTGCTGGTATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
**
40104047 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
**
40104086 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGCGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
*
40104125 ATATTCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
40104164 ATATCCGGGCTTAAAGTCCCG
1 ATATCCGGGC-T-AAGTCCCG
40104185 CATGCTTTGT
Statistics
Matches: 162, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 153 0.94
40 1 0.01
41 8 0.05
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.28
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
Found at i:40106153 original size:206 final size:206
Alignment explanation
Indices: 40105821--40106297 Score: 670
Period size: 206 Copynumber: 2.3 Consensus size: 206
40105811 TATACTAAAG
* * * *
40105821 CAAGATCCAAGGTGATTTGGCATCCTTGTGCTTACAAGGACCAAATCAAAGACATAGCTGATTTG
1 CAAGATCCAAGATGATTTGGCATTCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTG
*
40105886 GCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACA
66 GCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTACTGTCAGAGAACA
** * * * *
40105951 AATTGAAGTCTAGCATCTCCA-CTTCAACGG-GTAGTAGATACATAGCAGATCTCACCTTCAGAT
131 AATCAAAGTCTAGCATCTCCATATTCAACGGAG-AGCAGACACATAGCAGATCTAACCTTCAGAT
*
40106014 AATTCCACTGAAA
195 AATTACACTG-AA
40106027 CAAGATCCAAGATGATTTGGCATTCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTG
1 CAAGATCCAAGATGATTTGGCATTCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTG
*
40106092 GCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTACTGTCAGAGAACA
66 GCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTACTGTCAGAGAACA
* * ** * * *
40106157 AATCAAAGTTTGGGGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTCAGATG
131 AATCAAAGTCTAGCATCTCCATATTCAACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATA
* *
40106222 TTTATACTGAA
196 ATTACACTGAA
** * * * *
40106233 GTAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAGGACATGGCAGATTTG
1 CAAGATCCAAGATGATTTGGCATTCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTG
40106298 ACTCTCGGAT
Statistics
Matches: 241, Mismatches: 28, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
206 200 0.83
207 40 0.17
208 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (206 bp):
CAAGATCCAAGATGATTTGGCATTCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTG
GCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTACTGTCAGAGAACA
AATCAAAGTCTAGCATCTCCATATTCAACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATA
ATTACACTGAA
Found at i:40108259 original size:31 final size:31
Alignment explanation
Indices: 40108188--40108259 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
40108178 TTTATTTCAC
40108188 TATATTTATCTATTATATTATTATACATTTT
1 TATATTTATCTATTATATTATTATACATTTT
* *
40108219 TAATCTTTATC-A-TATATTAATTATATATTATT
1 T-ATATTTATCTATTATATT-ATTATACATT-TT
40108251 TATATTTAT
1 TATATTTAT
40108260 ATTATTGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
30 6 0.17
31 18 0.51
32 11 0.31
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (31 bp):
TATATTTATCTATTATATTATTATACATTTT
Found at i:40108312 original size:21 final size:18
Alignment explanation
Indices: 40108288--40108333 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 18
40108278 TATTATTTCA
40108288 TATATTATTAGTTATATTATT
1 TATATTATT-G-TATATT-TT
40108309 TATATTATTGTATATTTT
1 TATATTATTGTATATTTT
40108327 TAT-TTAT
1 TATATTAT
40108334 AAATTTAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.16
18 5 0.20
19 6 0.24
20 1 0.04
21 9 0.36
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (18 bp):
TATATTATTGTATATTTT
Found at i:40108316 original size:9 final size:9
Alignment explanation
Indices: 40108293--40108333 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
40108283 TTTCATATAT
*
40108293 TATTAGTTA
1 TATTATTTA
40108302 TATTATTTA
1 TATTATTTA
40108311 TATTATTGTA
1 TATTATT-TA
40108321 TATT-TTTA
1 TATTATTTA
40108329 T-TTAT
1 TATTAT
40108334 AAATTTAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
7 2 0.07
8 4 0.14
9 17 0.59
10 6 0.21
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (9 bp):
TATTATTTA
Found at i:40111945 original size:5 final size:5
Alignment explanation
Indices: 40111935--40112003 Score: 93
Period size: 5 Copynumber: 13.4 Consensus size: 5
40111925 AATAACCTAA
* * *
40111935 AAAAT AAAAT AAAAT AAACT AAAAT AAACT AAAAT AAACT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
40111985 GAAAAT AAAAAT AAAAT AA
1 -AAAAT -AAAAT AAAAT AA
40112004 TATCTTCCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
5 46 0.82
6 10 0.18
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:40121076 original size:15 final size:15
Alignment explanation
Indices: 40121056--40121085 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40121046 GAATACCTAT
*
40121056 ACCATGGCCCGTAGC
1 ACCATGGACCGTAGC
40121071 ACCATGGACCGTAGC
1 ACCATGGACCGTAGC
40121086 TAAATCAAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.37, G:0.27, T:0.13
Consensus pattern (15 bp):
ACCATGGACCGTAGC
Found at i:40124745 original size:38 final size:38
Alignment explanation
Indices: 40124508--40124746 Score: 277
Period size: 38 Copynumber: 6.3 Consensus size: 38
40124498 AATCTAATGC
* * *
40124508 TATTTGGGCTATGTGCCTAGTAGGCTGTGTGCCGGTGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* **
40124546 TATTCGGGTTGAT-TGCCTAGCAGGCTTTGTGCTAGTGA
1 TATTCGGGCT-ATGTGCCTAGCAGGCTTTGTGCCGGTGA
* * ** *
40124584 TATTCGGGCT-TGTGCCAAGAAAACTTTGTGCCGATGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* *
40124621 TATTCGGGCTGTGTGCCTAGCAGGCTTTGTGCCGGAGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* *
40124659 TATTCGGGCTGTGTGCCTAGCAGGCTTTGTGCTGGTGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* * *
40124697 TATAT-AGGCTATGTGCCTAGTAGGCTGTGTGCCGGTGA
1 TAT-TCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
40124735 TATTCGGGCTAT
1 TATTCGGGCTAT
40124747 TCGGGCTATG
Statistics
Matches: 168, Mismatches: 28, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
36 1 0.01
37 29 0.17
38 135 0.80
39 3 0.02
ACGTcount: A:0.16, C:0.18, G:0.33, T:0.33
Consensus pattern (38 bp):
TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
Found at i:40127225 original size:40 final size:38
Alignment explanation
Indices: 40127181--40127276 Score: 102
Period size: 40 Copynumber: 2.5 Consensus size: 38
40127171 ACGGTACAAT
** * *
40127181 TTGGTGTGTAGGGTTGGATGGGTTGATTTTATCCCCATAC
1 TTGGTGTGTAGGGTTGGATAAGTCGATTCTATCCCC--AC
* *
40127221 TTGGTGTGTAGGGCTGGGTAAGTCGATTCTATCCCCAC
1 TTGGTGTGTAGGGTTGGATAAGTCGATTCTATCCCCAC
* *
40127259 ATGGTGTGTTGGGTTGGA
1 TTGGTGTGTAGGGTTGGA
40127277 CAGAGATGGT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
38 16 0.35
40 30 0.65
ACGTcount: A:0.15, C:0.14, G:0.35, T:0.36
Consensus pattern (38 bp):
TTGGTGTGTAGGGTTGGATAAGTCGATTCTATCCCCAC
Found at i:40129433 original size:27 final size:27
Alignment explanation
Indices: 40129402--40129484 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 27
40129392 AGATATTTTG
*
40129402 ATATTTTATAATTATTTAATTAGATAA
1 ATATTTTATTATTATTTAATTAGATAA
*
40129429 ATATTATT-TTATTA-TTATTTTA-ATAA
1 ATATT-TTATTATTATTTA-ATTAGATAA
*
40129455 GATATTTTATTATTATTTTATTAGTATAA
1 -ATATTTTATTATTATTTAATTAG-ATAA
40129484 A
1 A
40129485 AAGAAAGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
26 9 0.20
27 27 0.60
28 5 0.11
29 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (27 bp):
ATATTTTATTATTATTTAATTAGATAA
Found at i:40129444 original size:11 final size:11
Alignment explanation
Indices: 40129430--40129477 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
40129420 ATTAGATAAA
40129430 TATTATTTTAT
1 TATTATTTTAT
40129441 TATTATTTTAAT
1 TATTATTTT-AT
* *
40129453 AAGATATTTTAT
1 TA-TTATTTTAT
40129465 TATTATTTTAT
1 TATTATTTTAT
40129476 TA
1 TA
40129478 GTATAAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 19 0.61
12 6 0.19
13 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:40131329 original size:46 final size:46
Alignment explanation
Indices: 40131269--40131519 Score: 371
Period size: 46 Copynumber: 5.5 Consensus size: 46
40131259 TTCAGATATG
* * *
40131269 TAAGACCATAGTTGAAAGATACTATGGCAATATGATGA-GAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGA-GAGGAAATGAA
* * *
40131315 TAAGACCATGGTTGAAAGATACCGTGGCAACATGACATGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGAGAGGAAATGAA
* **
40131361 TAAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAACAAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGAGAGGAAATGAA
40131407 TAAGACCATGGTTGAAAGATACCATGGCAACATG-GCAGGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGAG-AGGAAATGAA
* *
40131453 TAAGACCATGGTTGAAAGATACCATGGCAACATGAAAGGAAATAAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGAGAGGAAATGAA
40131499 TAAGACCATGGTTGAAAGATA
1 TAAGACCATGGTTGAAAGATA
40131520 GAAATGAATA
Statistics
Matches: 187, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
45 1 0.01
46 186 0.99
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGAGAGGAAATGAA
Found at i:40131546 original size:29 final size:29
Alignment explanation
Indices: 40131491--40131546 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
40131481 AACATGAAAG
*
40131491 GAAATAAATAAGACCATGGTTGAAAGATA
1 GAAATAAATAAGACCATAGTTGAAAGATA
* * *
40131520 GAAATGAATAAGACCATATTTGGAAGA
1 GAAATAAATAAGACCATAGTTGAAAGA
40131547 CATTATGGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (29 bp):
GAAATAAATAAGACCATAGTTGAAAGATA
Found at i:40131887 original size:17 final size:18
Alignment explanation
Indices: 40131844--40131888 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
40131834 AAATATATGG
40131844 AAATGATAATACATGAAAT
1 AAATGAT-ATACATGAAAT
*
40131863 -ATTGATATA-ATGAAAT
1 AAATGATATACATGAAAT
40131879 AAATGATATA
1 AAATGATATA
40131889 TGCTTATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.56, C:0.02, G:0.11, T:0.31
Consensus pattern (18 bp):
AAATGATATACATGAAAT
Found at i:40137795 original size:38 final size:38
Alignment explanation
Indices: 40137753--40138091 Score: 392
Period size: 38 Copynumber: 8.9 Consensus size: 38
40137743 AATGTAATGT
* * *
40137753 TATTCGGGCTATGTGCCTAGCAGGCTGTATGCCGATGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
*
40137791 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* * *
40137829 TATTCGGGCTATGTACCTAGCAAGCTTTATGCCGGTGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* * *
40137867 TATTTGGGCTTTGTGCCTAGC-GGACTTTGTACCGGTGA
1 TATTCGGGCTATGTGCCTAGCAGG-CTTTGTGCCGGTGA
* **
40137905 TATTCGGGCTGTGTGCCTAGCAAACTTTGTGCCGGTGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* * * * *
40137943 TATTTGGGCTGTGTGCCTAGTAGGCTTTGTGCTGATGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* * *
40137981 TATTCGGGATATGTGCCTAGCACGCTTTGTGCTGGTGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* * * * *
40138019 TATACAGGCTATGTGCCTAGTAGGCTGTGTCCCGGTGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* ** *
40138057 TATTCAGGCTATGTATCTAGCAGGCTGTGTGCCGG
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGG
40138092 GGTTTTTCAA
Statistics
Matches: 255, Mismatches: 44, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
37 1 0.00
38 254 1.00
ACGTcount: A:0.16, C:0.19, G:0.32, T:0.33
Consensus pattern (38 bp):
TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
Found at i:40146027 original size:21 final size:21
Alignment explanation
Indices: 40146001--40146059 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
40145991 GTGTGCCCTT
*
40146001 TCCACACAGGTGTGTAGGGCC
1 TCCACACAGGCGTGTAGGGCC
* * *
40146022 TTCACACGGGCGTGTATGGCC
1 TCCACACAGGCGTGTAGGGCC
**
40146043 TCCACATGGGCGTGTAG
1 TCCACACAGGCGTGTAG
40146060 ACACCTACAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.27, G:0.34, T:0.22
Consensus pattern (21 bp):
TCCACACAGGCGTGTAGGGCC
Found at i:40147827 original size:39 final size:39
Alignment explanation
Indices: 40147784--40147861 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
40147774 TTAGATTATG
40147784 AGGATCATCTTCAAACTTTTTCTTACCAATGTTTCTATC
1 AGGATCATCTTCAAACTTTTTCTTACCAATGTTTCTATC
40147823 AGGATCATCTTCAAACTTTTTCTTACCAATGTTTCTATC
1 AGGATCATCTTCAAACTTTTTCTTACCAATGTTTCTATC
40147862 TTGGAGGGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.44
Consensus pattern (39 bp):
AGGATCATCTTCAAACTTTTTCTTACCAATGTTTCTATC
Found at i:40148022 original size:14 final size:13
Alignment explanation
Indices: 40147999--40148040 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
40147989 TAATATTTGA
40147999 TTTATTATTTTAT
1 TTTATTATTTTAT
40148012 TTTATT-TATTTAT
1 TTTATTAT-TTTAT
*
40148025 TTTAATTGTTTTAT
1 TTT-ATTATTTTAT
40148039 TT
1 TT
40148041 GACTTGGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.04
13 14 0.54
14 10 0.38
15 1 0.04
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTATTATTTTAT
Found at i:40148037 original size:18 final size:18
Alignment explanation
Indices: 40147998--40148040 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
40147988 CTAATATTTG
*
40147998 ATTTA-TTATTTTATTTT
1 ATTTATTTATTTTATTGT
40148015 ATTTATTTATTTTAATTGT
1 ATTTATTTATTTT-ATTGT
40148034 -TTTATTT
1 ATTTATTT
40148041 GACTTGGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 14 0.61
19 4 0.17
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
ATTTATTTATTTTATTGT
Found at i:40148408 original size:16 final size:18
Alignment explanation
Indices: 40148398--40148435 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
40148388 GAAAAATTGC
40148398 AAAAAAT-AAAATATGAA
1 AAAAAATAAAAATATGAA
*
40148415 AAAAAATAAAAAAAT-AA
1 AAAAAATAAAAATATGAA
40148432 AAAA
1 AAAA
40148436 TTTCTATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (18 bp):
AAAAAATAAAAATATGAA
Found at i:40152417 original size:48 final size:48
Alignment explanation
Indices: 40152326--40152427 Score: 150
Period size: 48 Copynumber: 2.1 Consensus size: 48
40152316 CTTACACTAA
*
40152326 ATCACATATCGATGCCAATGCCATATCCCAGATATGCTATTACATGGG
1 ATCACATATCGATGCCAATGCCATATCCCAGACATGCTATTACATGGG
* * * * *
40152374 ATCACATATCGATGCTAATTCCATGTCCCAGACATGGTCTTACATGGG
1 ATCACATATCGATGCCAATGCCATATCCCAGACATGCTATTACATGGG
40152422 ATCACA
1 ATCACA
40152428 CATACCCTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (48 bp):
ATCACATATCGATGCCAATGCCATATCCCAGACATGCTATTACATGGG
Found at i:40153909 original size:93 final size:93
Alignment explanation
Indices: 40153796--40153966 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
40153786 GCCACTAAGT
* *
40153796 GAACTCAGAATCAACTCAACGAGCTCGGGCGTTTGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCAGAATCAACTCAACGAGCTCGGACATTTGCATCCATAAATGAACTCGGACTCAACTCAA
* *
40153861 TGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* * * * *
40153889 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGATTCAACTCAA
1 GAACTCAGAATCAACTCAACGAGCTCGGACATTTGCATCCATAAATGAACTCGGACTCAACTCAA
40153954 CGAGCTCGGATGC
66 CGAGCTCGGATGC
40153967 TCAACCATCC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCAGAATCAACTCAACGAGCTCGGACATTTGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:40153954 original size:46 final size:46
Alignment explanation
Indices: 40153791--40153963 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 46
40153781 AACCCGCCAC
* * * *
40153791 TAAGTGAACTCAGAATCAACTCAACGAGCTCGGGCGTTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
* * * * *
40153837 TAAATGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCATCCA
* * *
40153885 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
*
40153930 TAAGTGAACTCGGATTCAACTCAACGAGCTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
40153964 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 55 0.54
47 28 0.27
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
Found at i:40157722 original size:28 final size:28
Alignment explanation
Indices: 40157684--40157743 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
40157674 GGCATAACTA
40157684 AAAATTCATAATGACTTTACCTTGTTCT
1 AAAATTCATAATGACTTTACCTTGTTCT
40157712 AAAATTCATAATGACTTTACCTTGTTCT
1 AAAATTCATAATGACTTTACCTTGTTCT
40157740 AAAA
1 AAAA
40157744 GAAGTTTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.40
Consensus pattern (28 bp):
AAAATTCATAATGACTTTACCTTGTTCT
Found at i:40162664 original size:52 final size:52
Alignment explanation
Indices: 40162544--40162721 Score: 233
Period size: 51 Copynumber: 3.5 Consensus size: 52
40162534 ACTAGTGACT
40162544 CAAGTGTGGTACTATGTGAAGGCCAC--TTTGAA-AAGAGATAGC-TTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTTTGAAGAA-AGATAGCTTTGGTCA
*
40162593 AAAGTGTGGTACTATGTGAAGGCCACTTTTTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTTTGAAGAAAGATAGCTTTGGTCA
* * * *
40162645 CAAGTGTGGTATTATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTTT-GACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTTTGAAGAAAGATAGCTTTGGTC-A
* *
40162696 CAAGAGTGGTACTATGTGCAGGCCAC
1 CAAGTGTGGTACTATGTGAAGGCCAC
40162722 CGGGTATCCG
Statistics
Matches: 115, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
49 25 0.22
50 2 0.02
51 47 0.41
52 41 0.36
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTTTGAAGAAAGATAGCTTTGGTCA
Found at i:40168542 original size:43 final size:43
Alignment explanation
Indices: 40168445--40168607 Score: 136
Period size: 43 Copynumber: 3.8 Consensus size: 43
40168435 ACCAAGATGT
* * * *
40168445 GATTACATGTAAGACCATGTCTGGGACATTGGTATTGTATTGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAATGC
40168488 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTTAAT-C
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCG-TAATGC
* * * * * **
40168531 GATTTCGTGTAAGA-CACTGCCTGGGACAGTGACATC-TATATAT
1 GATTACATGTAAGACCA-TGTCTGGGACATTGGCATCGTA-ATGC
* * * *
40168574 GATAACCTGTAAGACCATATCTGGGATA-TGGCAT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCAT
40168608 TGTATGAGCT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
41 2 0.02
42 9 0.09
43 82 0.84
44 5 0.05
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAATGC
Found at i:40169586 original size:18 final size:18
Alignment explanation
Indices: 40169563--40169633 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
40169553 AGGACGTGTC
*
40169563 ATTCATTTTCAAAACGTA
1 ATTCATTTTCAAAACGTT
*
40169581 ATTCATTATCACAAA-GTT
1 ATTCATTTTCA-AAACGTT
* *
40169599 ATTC-TCTTCAAAAATGTT
1 ATTCATTTTC-AAAACGTT
*
40169617 ATTAATTTTCAAAACGT
1 ATTCATTTTCAAAACGT
40169634 CACTTATTGC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
17 6 0.14
18 29 0.69
19 7 0.17
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (18 bp):
ATTCATTTTCAAAACGTT
Found at i:40170540 original size:30 final size:30
Alignment explanation
Indices: 40170499--40170557 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
40170489 CCCGTGCAAC
* *
40170499 TAAGCATCAAAACAGTGAAAATGGGCCCAT
1 TAAGCAACAAAACAGTGAAAATAGGCCCAT
*
40170529 TAAGCAACAAAACTGTGAAAATAGGCCCA
1 TAAGCAACAAAACAGTGAAAATAGGCCCA
40170558 CATGCCCGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.15
Consensus pattern (30 bp):
TAAGCAACAAAACAGTGAAAATAGGCCCAT
Found at i:40178024 original size:42 final size:42
Alignment explanation
Indices: 40177959--40178109 Score: 113
Period size: 48 Copynumber: 3.3 Consensus size: 42
40177949 TAGCCCAGCT
* ** *
40177959 ATGGTCTTACACGATGTCTCATATTGATGCCATGTCCCAGAC
1 ATGGTCTTACATGAAATCACATATTGATGCCATGTCCCAGAC
* * *
40178001 ATGGTCTTACATGAAATCACATATCGATGCCAACACCATATCCCAGAT
1 ATGGTCTTACATGAAATCACATATTGATG------CCATGTCCCAGAC
* *
40178049 ATGGTCTTACATGGAATCACATATCGATGCTAATGCCATGTCCCAAAC
1 ATGGTCTTACATGAAATCACATAT---TG---ATGCCATGTCCCAGAC
40178097 ATGGTCTTACATG
1 ATGGTCTTACATG
40178110 GGATCACACA
Statistics
Matches: 85, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
42 24 0.28
48 57 0.67
51 1 0.01
54 3 0.04
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (42 bp):
ATGGTCTTACATGAAATCACATATTGATGCCATGTCCCAGAC
Found at i:40178067 original size:48 final size:48
Alignment explanation
Indices: 40177988--40178117 Score: 188
Period size: 48 Copynumber: 2.7 Consensus size: 48
40177978 CATATTGATG
*
40177988 CCATGTCCCAGACATGGTCTTACATGAAATCACATATCGATGCCAACA
1 CCATGTCCCAGACATGGTCTTACATGGAATCACATATCGATGCCAACA
* * * **
40178036 CCATATCCCAGATATGGTCTTACATGGAATCACATATCGATGCTAATG
1 CCATGTCCCAGACATGGTCTTACATGGAATCACATATCGATGCCAACA
* *
40178084 CCATGTCCCAAACATGGTCTTACATGGGATCACA
1 CCATGTCCCAGACATGGTCTTACATGGAATCACA
40178118 CATACCCTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (48 bp):
CCATGTCCCAGACATGGTCTTACATGGAATCACATATCGATGCCAACA
Found at i:40187979 original size:13 final size:14
Alignment explanation
Indices: 40187955--40187984 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
40187945 GGTTGTTTAT
40187955 TAAACTTAATTAAC
1 TAAACTTAATTAAC
40187969 TAAAC-TAATTAAC
1 TAAACTTAATTAAC
40187982 TAA
1 TAA
40187985 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAACTTAATTAAC
Found at i:40192786 original size:66 final size:68
Alignment explanation
Indices: 40192648--40192788 Score: 187
Period size: 66 Copynumber: 2.1 Consensus size: 68
40192638 GTAGCGAGGT
* * *
40192648 TATGGCACTATAGGCATAAGACCATGGTTGGACTATGGCAGTGTATACATGTAAGAACATAACTA
1 TATGGCACTATAGACATAAGACCATGGTTGGACCATGGCAATGTATACATGTAAGAACATAACTA
*
40192713 GGT
66 GGC
* * * * *
40192716 TATGGCACTA-A-ACATAAGACCATGGTTGGACCATGGCAATGTATATATGTATGACCATAGCTG
1 TATGGCACTATAGACATAAGACCATGGTTGGACCATGGCAATGTATACATGTAAGAACATAACTA
40192779 GGC
66 GGC
40192782 TATGGCA
1 TATGGCA
40192789 TTCTAATGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 53 0.83
67 1 0.02
68 10 0.16
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (68 bp):
TATGGCACTATAGACATAAGACCATGGTTGGACCATGGCAATGTATACATGTAAGAACATAACTA
GGC
Found at i:40192839 original size:33 final size:33
Alignment explanation
Indices: 40192757--40192926 Score: 110
Period size: 33 Copynumber: 5.1 Consensus size: 33
40192747 CATGGCAATG
* * * *
40192757 TATATATGTATGACCATAGCTGGGCTATGGCAT
1 TATAGATGTAAGACCATAACTGGGCTATGGCAC
* * *
40192790 TCTA-ATGATAATACCATAACTGGGTTATGGCAC
1 TATAGATG-TAAGACCATAACTGGGCTATGGCAC
* *** * * * *
40192823 TATAGACGTAAGACCATGGTTGGACCATGACAGTG
1 TATAGATGTAAGACCATAACTGGGCTATGGCA--C
*
40192858 TATACATGTAAGACCATAACTGGGCTATGGCA-
1 TATAGATGTAAGACCATAACTGGGCTATGGCAC
* * * *
40192890 TTTTGATGATCAGACCATAACTGGGTTATGGCAC
1 TATAGATG-TAAGACCATAACTGGGCTATGGCAC
40192924 TAT
1 TAT
40192927 GAACATAAAA
Statistics
Matches: 100, Mismatches: 31, Indels: 11
0.70 0.22 0.08
Matches are distributed among these distances:
32 8 0.08
33 64 0.64
34 4 0.04
35 24 0.24
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (33 bp):
TATAGATGTAAGACCATAACTGGGCTATGGCAC
Found at i:40192842 original size:101 final size:100
Alignment explanation
Indices: 40192699--40192943 Score: 339
Period size: 101 Copynumber: 2.4 Consensus size: 100
40192689 TGTATACATG
* * * *
40192699 TAAGAACATAACTAGGTTATGGCACTA-AACATAAGACCATGGTTGGACCATGGCAATGTATATA
1 TAAGACCATAACTGGGTTATGGCACTATAACATAAGACCATGGTTGGACCATGACAATGTATACA
* *
40192763 TGTATGACCATAGCTGGGCTATGGCATTCTAATGA
66 TGTAAGACCATAACTGGGCTATGGCATTCTAATGA
* * *
40192798 TAATACCATAACTGGGTTATGGCACTATAGACGTAAGACCATGGTTGGACCATGACAGTGTATAC
1 TAAGACCATAACTGGGTTATGGCACTATA-ACATAAGACCATGGTTGGACCATGACAATGTATAC
* *
40192863 ATGTAAGACCATAACTGGGCTATGGCATTTTGATGA
65 ATGTAAGACCATAACTGGGCTATGGCATTCTAATGA
* * *
40192899 TCAGACCATAACTGGGTTATGGCACTATGAACATAAAAACATGGT
1 TAAGACCATAACTGGGTTATGGCACTAT-AACATAAGACCATGGT
40192944 AGGGCAATGG
Statistics
Matches: 127, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
99 24 0.19
100 1 0.01
101 101 0.80
102 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (100 bp):
TAAGACCATAACTGGGTTATGGCACTATAACATAAGACCATGGTTGGACCATGACAATGTATACA
TGTAAGACCATAACTGGGCTATGGCATTCTAATGA
Found at i:40201335 original size:12 final size:13
Alignment explanation
Indices: 40201318--40201350 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40201308 ATAAATACCG
*
40201318 AAAATAAAC-TAT
1 AAAATAAACATAA
40201330 AAAATAAACATAA
1 AAAATAAACATAA
40201343 AAAATAAA
1 AAAATAAA
40201351 AACCAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAATAAACATAA
Found at i:40202049 original size:3 final size:3
Alignment explanation
Indices: 40202041--40202066 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40202031 ATGTTTGAGA
40202041 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
40202067 TTGGGAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:40202245 original size:3 final size:3
Alignment explanation
Indices: 40202237--40202264 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40202227 GGCAAGTTGG
40202237 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
40202265 TTTGCCACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:40204328 original size:13 final size:13
Alignment explanation
Indices: 40204310--40204334 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40204300 TAATATATTT
40204310 ATTAATTAAAAAC
1 ATTAATTAAAAAC
40204323 ATTAATTAAAAA
1 ATTAATTAAAAA
40204335 AATGCTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:40204817 original size:41 final size:42
Alignment explanation
Indices: 40204747--40204923 Score: 187
Period size: 43 Copynumber: 4.2 Consensus size: 42
40204737 AAAAAATGCT
* *
40204747 GCTAAAGAACATGACCTTTAACGGTGCTTTCTCCACAAACGCC
1 GCTAAAGAACATGA-CTTTAGCGGCGCTTTCTCCACAAACGCC
** *
40204790 GCTAAAGGTCAT-TCTTTAGCGGCGCTTT-TCCCACAAACGCC
1 GCTAAAGAACATGACTTTAGCGGCGCTTTCT-CCACAAACGCC
* *
40204831 GCTAAAGAACATGACTTTTAGTGGCGCTTTCCCCACAAACGCC
1 GCTAAAGAACATGAC-TTTAGCGGCGCTTTCTCCACAAACGCC
* * * * * *
40204874 GCTAAAGAACATGACATTCAGTGGCACTTTTTCCAAAAACACC
1 GCTAAAGAACATGAC-TTTAGCGGCGCTTTCTCCACAAACGCC
40204917 GCTAAAG
1 GCTAAAG
40204924 CTCATGAAAT
Statistics
Matches: 113, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.01
41 34 0.30
42 1 0.01
43 77 0.68
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.24
Consensus pattern (42 bp):
GCTAAAGAACATGACTTTAGCGGCGCTTTCTCCACAAACGCC
Found at i:40205056 original size:11 final size:11
Alignment explanation
Indices: 40205040--40205068 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
40205030 TATAAAAATT
40205040 TTCTATTAAAA
1 TTCTATTAAAA
40205051 TTCTATTAAAA
1 TTCTATTAAAA
40205062 TTC-ATTA
1 TTCTATTA
40205069 TCAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (11 bp):
TTCTATTAAAA
Found at i:40207450 original size:16 final size:16
Alignment explanation
Indices: 40207429--40207463 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40207419 CAAAAGATAG
* *
40207429 ATATAGGCATTCATAC
1 ATATAGGCAGTCACAC
40207445 ATATAGGCAGTCACAC
1 ATATAGGCAGTCACAC
40207461 ATA
1 ATA
40207464 AAACGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (16 bp):
ATATAGGCAGTCACAC
Found at i:40210339 original size:14 final size:14
Alignment explanation
Indices: 40210309--40210348 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
40210299 TATTAATTAA
*
40210309 TCTAAACCCTAAACC
1 TCTAAACCCT-ACCC
*
40210324 TCTAACCCCTACCC
1 TCTAAACCCTACCC
40210338 TCTAAACCCTA
1 TCTAAACCCTA
40210349 AATCTTAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.23
Consensus pattern (14 bp):
TCTAAACCCTACCC
Found at i:40210474 original size:7 final size:7
Alignment explanation
Indices: 40210462--40210532 Score: 52
Period size: 7 Copynumber: 9.9 Consensus size: 7
40210452 CCCCAACATT
40210462 TAAACCA
1 TAAACCA
40210469 TAAACCA
1 TAAACCA
* *
40210476 TAACCCC
1 TAAACCA
40210483 TAAACCCA
1 TAAA-CCA
*
40210491 TAATCCA
1 TAAACCA
*
40210498 TAAACCT
1 TAAACCA
**
40210505 TAAAATA
1 TAAACCA
*
40210512 TTAACTCA
1 TAAAC-CA
*
40210520 TAAACTA
1 TAAACCA
40210527 TAAACC
1 TAAACC
40210533 CCTAACCCCT
Statistics
Matches: 46, Mismatches: 16, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
7 36 0.78
8 10 0.22
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCA
Found at i:40210493 original size:15 final size:15
Alignment explanation
Indices: 40210466--40210503 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
40210456 AACATTTAAA
40210466 CCATAAA-CCATAAC
1 CCATAAACCCATAAC
* *
40210480 CCCTAAACCCATAAT
1 CCATAAACCCATAAC
40210495 CCATAAACC
1 CCATAAACC
40210504 TTAAAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (15 bp):
CCATAAACCCATAAC
Found at i:40210539 original size:7 final size:7
Alignment explanation
Indices: 40210529--40210580 Score: 59
Period size: 7 Copynumber: 7.3 Consensus size: 7
40210519 ATAAACTATA
40210529 AACCCCT
1 AACCCCT
40210536 AACCCCT
1 AACCCCT
*
40210543 ATCCCCTT
1 AACCCC-T
*
40210551 AACCCTT
1 AACCCCT
40210558 AACCCCT
1 AACCCCT
*
40210565 AACCACT
1 AACCCCT
*
40210572 AACCACT
1 AACCCCT
40210579 AA
1 AA
40210581 ATCTTAAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
7 34 0.87
8 5 0.13
ACGTcount: A:0.33, C:0.48, G:0.00, T:0.19
Consensus pattern (7 bp):
AACCCCT
Found at i:40210567 original size:14 final size:14
Alignment explanation
Indices: 40210529--40210601 Score: 67
Period size: 14 Copynumber: 5.1 Consensus size: 14
40210519 ATAAACTATA
*
40210529 AACCCCTAACCCCT
1 AACCCCTAACCCTT
*
40210543 ATCCCCTTAACCCTT
1 AACCCC-TAACCCTT
40210558 AACCCCTAACCAC-T
1 AACCCCTAACC-CTT
* **
40210572 AACCACTAAATCTT
1 AACCCCTAACCCTT
*
40210586 AAACCCTAACCCTT
1 AACCCCTAACCCTT
40210600 AA
1 AA
40210602 ACACTAAACT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
13 1 0.02
14 32 0.70
15 13 0.28
ACGTcount: A:0.34, C:0.44, G:0.00, T:0.22
Consensus pattern (14 bp):
AACCCCTAACCCTT
Found at i:40210595 original size:28 final size:28
Alignment explanation
Indices: 40210555--40210631 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
40210545 CCCCTTAACC
* *
40210555 CTTAACCCCTAACCAC-TAACCACTAAAT
1 CTTAAACCCTAACC-CTTAAACACTAAAT
40210583 CTTAAACCCTAACCCTTAAACACTAAA-
1 CTTAAACCCTAACCCTTAAACACTAAAT
* *
40210610 CTCATAACCACTAAACCTTAAA
1 CTTA-AACC-CTAACCCTTAAA
40210632 ATATTAACTC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.10
28 27 0.64
29 11 0.26
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (28 bp):
CTTAAACCCTAACCCTTAAACACTAAAT
Found at i:40210602 original size:14 final size:14
Alignment explanation
Indices: 40210527--40210608 Score: 51
Period size: 14 Copynumber: 5.7 Consensus size: 14
40210517 TCATAAACTA
*
40210527 TAAACCCCTAACCCC
1 TAAA-CCCTAACCCT
**
40210542 TATCCCCTTAACCCT
1 TAAACCC-TAACCCT
*
40210557 TAACCCCTAACCAC-
1 TAAACCCTAACC-CT
**
40210571 T-AACCACTAAATCT
1 TAAACC-CTAACCCT
40210585 TAAACCCTAACCCT
1 TAAACCCTAACCCT
*
40210599 TAAACACTAA
1 TAAACCCTAA
40210609 ACTCATAACC
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
13 4 0.08
14 29 0.56
15 19 0.37
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAACCCT
Found at i:40210631 original size:29 final size:30
Alignment explanation
Indices: 40210585--40210661 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
40210575 CACTAAATCT
*
40210585 TAAACC-CTAACCCTTAAACACTA-AACTCA
1 TAAACCACTAAACCTTAAACA-TATAACTCA
40210614 T-AACCACTAAACCTTAAA-ATATTAACTCA
1 TAAACCACTAAACCTTAAACATA-TAACTCA
*
40210643 TAAACCA-TAAACCCTAAAC
1 TAAACCACTAAACCTTAAAC
40210662 CATAATGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
27 2 0.05
28 5 0.12
29 29 0.71
30 5 0.12
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (30 bp):
TAAACCACTAAACCTTAAACATATAACTCA
Found at i:40211070 original size:39 final size:38
Alignment explanation
Indices: 40210972--40211113 Score: 133
Period size: 40 Copynumber: 3.6 Consensus size: 38
40210962 TTTTATGGCT
*
40210972 TTTTTAAAAAACGCCGCTAATGCTCGATCTATAGCGGCG
1 TTTTT-AAAAACGCCGCTAATGCTCGATCTATAGCGGAG
* *
40211011 CTTTTTTAAAAACACCGCTAATGCTCGATCTATAGTGGAG
1 --TTTTTAAAAACGCCGCTAATGCTCGATCTATAGCGGAG
* * * * *
40211051 TTTTTAAAAAGTGCTGCTAATTCTCGATCTGTAGGGGCA-
1 TTTTTAAAAA-CGCCGCTAATGCTCGATCTATAGCGG-AG
*
40211090 TTTTTAAAAAAGCGTCGCTAATGC
1 TTTTT-AAAAA-CGCCGCTAATGC
40211114 CACTAAGCGG
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
38 10 0.12
39 25 0.29
40 45 0.53
41 5 0.06
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (38 bp):
TTTTTAAAAACGCCGCTAATGCTCGATCTATAGCGGAG
Found at i:40211111 original size:40 final size:38
Alignment explanation
Indices: 40210972--40211113 Score: 144
Period size: 39 Copynumber: 3.6 Consensus size: 38
40210962 TTTTATGGCT
*
40210972 TTTTTAAAAAACGCCGCTAATGCTCGATCTATAGCGGCGCT
1 TTTTTAAAAAACG-CGCTAATGCTCGATCTATAG-GG-GCA
*
40211013 TTTTTAAAAACAC-CGCTAATGCTCGATCTATAGTGG-A
1 TTTTTAAAAA-ACGCGCTAATGCTCGATCTATAGGGGCA
** * *
40211050 GTTTTTAAAAAGTGCTGCTAATTCTCGATCTGTAGGGGCA
1 -TTTTTAAAAAACGC-GCTAATGCTCGATCTATAGGGGCA
40211090 TTTTTAAAAAAGCGTCGCTAATGC
1 TTTTTAAAAAA-CG-CGCTAATGC
40211114 CACTAAGCGG
Statistics
Matches: 84, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
38 12 0.14
39 30 0.36
40 29 0.35
41 11 0.13
42 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (38 bp):
TTTTTAAAAAACGCGCTAATGCTCGATCTATAGGGGCA
Found at i:40211225 original size:40 final size:41
Alignment explanation
Indices: 40211164--40211260 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 41
40211154 TTCCAAAAAT
*
40211164 GCCGTTAATGCTAGA-CATATAGCGGC-GCTTTGGTAAAAGC
1 GCCGCTAATGCTAGATCATATAGCGGCAGCTTTGG-AAAAGC
* **
40211204 GCCGCTAATGCTCGATC-TATAGCGGCATTTTTGGAAAAGC
1 GCCGCTAATGCTAGATCATATAGCGGCAGCTTTGGAAAAGC
*
40211244 GCCGCTAATGCTTGATC
1 GCCGCTAATGCTAGATC
40211261 CATAACGGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 44 0.88
41 6 0.12
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.27
Consensus pattern (41 bp):
GCCGCTAATGCTAGATCATATAGCGGCAGCTTTGGAAAAGC
Found at i:40211276 original size:41 final size:41
Alignment explanation
Indices: 40211192--40211275 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 41
40211182 ATAGCGGCGC
* *
40211192 TTTGGTAAAAGCGCCGCTAATGCTCGATCTATAGCGGCATT
1 TTTGGTAAAAGCGCCGCTAATGCTCGATCCATAACGGCATT
* *
40211233 TTTGG-AAAAGCGCCGCTAATGCTTGATCCATAACGGTATT
1 TTTGGTAAAAGCGCCGCTAATGCTCGATCCATAACGGCATT
40211273 TTT
1 TTT
40211276 TATTCAAACG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 34 0.87
41 5 0.13
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (41 bp):
TTTGGTAAAAGCGCCGCTAATGCTCGATCCATAACGGCATT
Found at i:40212593 original size:3 final size:3
Alignment explanation
Indices: 40212566--40212640 Score: 123
Period size: 3 Copynumber: 25.0 Consensus size: 3
40212556 GATGATAATG
* * *
40212566 TAA TAA AAA TAA TAC TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40212614 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
40212641 CGAATAACCT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:40212686 original size:4 final size:4
Alignment explanation
Indices: 40212677--40212712 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
40212667 ATAAAAAGAT
*
40212677 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAC ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
40212713 TGAAATAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:40212750 original size:11 final size:10
Alignment explanation
Indices: 40212734--40212796 Score: 58
Period size: 11 Copynumber: 6.1 Consensus size: 10
40212724 TAATGAGGAC
40212734 AAAAATAAAAT
1 AAAAAT-AAAT
40212745 AAAAATAAAT
1 AAAAATAAAT
40212755 -AAAAT-AAT
1 AAAAATAAAT
**
40212763 AAAAAGGAAT
1 AAAAATAAAT
40212773 AATAAATGAAAT
1 AA-AAAT-AAAT
40212785 AACAAATAAAT
1 AA-AAATAAAT
40212796 A
1 A
40212797 TCAGTAAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 3 0.07
9 9 0.20
10 9 0.20
11 14 0.32
12 9 0.20
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.19
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:40214499 original size:3 final size:3
Alignment explanation
Indices: 40214472--40214531 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
40214462 GATGATAATG
* * *
40214472 TAA TAA AAA TAA TAC TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40214520 TAA TAA TAA TAA
1 TAA TAA TAA TAA
40214532 CGAATAACCT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:40214577 original size:4 final size:4
Alignment explanation
Indices: 40214568--40214599 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
40214558 ATAAAAAGAT
*
40214568 ATAA ATAA ATAA ATAA ATAA ATAA ATAC ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
40214600 TGAAATAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:40214637 original size:11 final size:10
Alignment explanation
Indices: 40214621--40214683 Score: 58
Period size: 11 Copynumber: 6.1 Consensus size: 10
40214611 TAATGAGGAC
40214621 AAAAATAAAAT
1 AAAAAT-AAAT
40214632 AAAAATAAAT
1 AAAAATAAAT
40214642 -AAAAT-AAT
1 AAAAATAAAT
**
40214650 AAAAAGGAAT
1 AAAAATAAAT
40214660 AATAAATGAAAT
1 AA-AAAT-AAAT
40214672 AACAAATAAAT
1 AA-AAATAAAT
40214683 A
1 A
40214684 TCAGTAAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 3 0.07
9 9 0.20
10 9 0.20
11 14 0.32
12 9 0.20
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.19
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:40217229 original size:20 final size:20
Alignment explanation
Indices: 40217201--40217241 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40217191 GCACCATGTC
40217201 ATTGATGACATGGCAAGTTG
1 ATTGATGACATGGCAAGTTG
* *
40217221 ATTGGTGACATGGCATGTTG
1 ATTGATGACATGGCAAGTTG
40217241 A
1 A
40217242 CCATGCATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGATGACATGGCAAGTTG
Found at i:40217390 original size:29 final size:30
Alignment explanation
Indices: 40217335--40217399 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
40217325 AAAATTAGTA
*
40217335 AAAAATATTTAGAAAATTTTAAAATTTATTT
1 AAAAATATTTAGAAAATTGTAAAATTT-TTT
* *
40217366 TAAAATA-TTA-AAAGTTGTAAAATTTTTT
1 AAAAATATTTAGAAAATTGTAAAATTTTTT
40217394 AAAAAT
1 AAAAAT
40217400 TCAAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 8 0.27
29 13 0.43
30 3 0.10
31 6 0.20
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (30 bp):
AAAAATATTTAGAAAATTGTAAAATTTTTT
Found at i:40220494 original size:26 final size:26
Alignment explanation
Indices: 40220464--40220519 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
40220454 AGAAATGCCC
40220464 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
40220490 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40220516 ATCA
1 ATCA
40220520 ATTTTATCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:40221312 original size:19 final size:17
Alignment explanation
Indices: 40221280--40221314 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
40221270 TTAGTGTGAG
40221280 GGTTTTTTAGGGTTTAT
1 GGTTTTTTAGGGTTTAT
40221297 GGTTTTTGTAAGGGTTTA
1 GGTTTTT-T-AGGGTTTA
40221315 GTTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.54
Consensus pattern (17 bp):
GGTTTTTTAGGGTTTAT
Found at i:40221376 original size:16 final size:17
Alignment explanation
Indices: 40221337--40221377 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
40221327 AGGGTGTAAG
40221337 ATTAATTAATTAAATTAA
1 ATTAATTAATTAAA-TAA
40221355 A-T-ATTAATTAAA-AA
1 ATTAATTAATTAAATAA
40221369 ATTAATTAA
1 ATTAATTAA
40221378 ATTTGGGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.14
15 1 0.05
16 15 0.71
17 1 0.05
18 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAATTAATTAAATAA
Found at i:40221712 original size:125 final size:126
Alignment explanation
Indices: 40221483--40221867 Score: 483
Period size: 125 Copynumber: 3.1 Consensus size: 126
40221473 TTTTGGTTTT
* * * * * *
40221483 TTTTTCT-TCAGTAGTATCTGGAAAAAA-AATTTTAAGAAGAAGTTTCTGAAGAAATAGTATCCA
1 TTTTTCTAT-AGTGGTATCT-GAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAA
* * * * *
40221546 AAACGCTTCAAGCAGGATGCACTGTCAACAAAATTACTGAAAAATGCTCTCATGTGGACGCTT
64 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACGTGGACGCTC
40221609 TTTTTCTATAGTGGTATCT-AAGAAAATAATTTTGAGAAGACGTTTCTGGAA-AAATAGTGT-AA
1 TTTTTCTATAGTGGTATCTGAA-AAAATAATTTTGAGAAGACGTTTCT-GAACAAATAGTGTCAA
* * * *
40221671 AAACGCTTTAAGCAGGATGCACTGTCAGGAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTC
64 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACGTGGACGCTC
** * * *
40221734 TTTTGATATAGTGGTATCTGAAAAAATAATTGTGAGATGACCTTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTATAGTGGTATCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAA
* * * *
40221799 ACGCTTCATGCAGTATGCACTTTCAGCAAAATTACTGAAAAAAGCTCACACGTGGATGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACGTGGACGCTC
40221860 TTTTTCTA
1 TTTTTCTA
40221868 CAGTAGTTCC
Statistics
Matches: 224, Mismatches: 28, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
124 5 0.02
125 108 0.48
126 107 0.48
127 4 0.02
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (126 bp):
TTTTTCTATAGTGGTATCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACGTGGACGCTC
Found at i:40224934 original size:56 final size:56
Alignment explanation
Indices: 40224843--40224975 Score: 230
Period size: 56 Copynumber: 2.4 Consensus size: 56
40224833 TTCCTTATTC
* *
40224843 AAAACAACTTTTATTCTATTACAAATATAAAAGAGTAAATTATAATTAAAATACTA
1 AAAATAACTTTTATTTTATTACAAATATAAAAGAGTAAATTATAATTAAAATACTA
* *
40224899 AAAATAACTTTTATTTTATTACAAATATAAAAGAGTAAATTATAATTAAGATATTA
1 AAAATAACTTTTATTTTATTACAAATATAAAAGAGTAAATTATAATTAAAATACTA
40224955 AAAATAACTTTTATTTTATTA
1 AAAATAACTTTTATTTTATTA
40224976 AATGAAAGAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 73 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (56 bp):
AAAATAACTTTTATTTTATTACAAATATAAAAGAGTAAATTATAATTAAAATACTA
Found at i:40225398 original size:18 final size:18
Alignment explanation
Indices: 40225372--40225413 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
40225362 GACTAGAAAA
* *
40225372 AGGAAATATATAAGGGTT
1 AGGATATATATAAGGGCT
40225390 AGGATATATATAAGGGCT
1 AGGATATATATAAGGGCT
40225408 AGGATA
1 AGGATA
40225414 CGCACTTGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.29, T:0.26
Consensus pattern (18 bp):
AGGATATATATAAGGGCT
Found at i:40226040 original size:7 final size:7
Alignment explanation
Indices: 40226030--40226066 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
40226020 TTGTATACAT
40226030 AATACTA
1 AATACTA
40226037 AATACTA
1 AATACTA
40226044 AATACTA
1 AATACTA
*
40226051 AATATTA
1 AATACTA
40226058 AATACTA
1 AATACTA
40226065 AA
1 AA
40226067 CACGAAACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (7 bp):
AATACTA
Done.