Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 10 of 297
Found at i:3248137 original size:32 final size:32
Alignment explanation
Indices: 3248101--3248165 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
3248091 ATTAATGTAA
3248101 TTTGTGTTAAGTTATTATTATTACTATTCCTT
1 TTTGTGTTAAGTTATTATTATTACTATTCCTT
*
3248133 TTTGTGTTAAGTTATTATTATTACTATTGCTT
1 TTTGTGTTAAGTTATTATTATTACTATTCCTT
3248165 T
1 T
3248166 CTATGCCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.60
Consensus pattern (32 bp):
TTTGTGTTAAGTTATTATTATTACTATTCCTT
Found at i:3251010 original size:40 final size:40
Alignment explanation
Indices: 3250848--3251010 Score: 188
Period size: 40 Copynumber: 4.1 Consensus size: 40
3250838 GAATTTAACT
** * *
3250848 GGATATAGCT-ACTCGTTCAAATGTCTTCGGGACATAGCCC
1 GGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCC
* *
3250888 GGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
* *
3250928 GGATTTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCC
* *
3250968 GGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 GGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
3251008 GGA
1 GGA
3251011 CATCATTTGA
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
39 4 0.04
40 90 0.86
41 11 0.10
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
Found at i:3263143 original size:21 final size:21
Alignment explanation
Indices: 3263119--3263158 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3263109 GCCTAATATG
*
3263119 TGAATTGGATTGAATTGAGTA
1 TGAATTGGATTAAATTGAGTA
*
3263140 TGAATTGTATTAAATTGAG
1 TGAATTGGATTAAATTGAG
3263159 CTAAATTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (21 bp):
TGAATTGGATTAAATTGAGTA
Found at i:3268436 original size:11 final size:11
Alignment explanation
Indices: 3268420--3268444 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3268410 ATGTAAGCGA
3268420 TTTTGATGATT
1 TTTTGATGATT
3268431 TTTTGATGATT
1 TTTTGATGATT
3268442 TTT
1 TTT
3268445 ACATTTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (11 bp):
TTTTGATGATT
Found at i:3273033 original size:13 final size:13
Alignment explanation
Indices: 3273006--3273059 Score: 101
Period size: 13 Copynumber: 4.2 Consensus size: 13
3272996 GAGTTGATCC
3273006 GTAAATGGA-TTT
1 GTAAATGGATTTT
3273018 GTAAATGGATTTT
1 GTAAATGGATTTT
3273031 GTAAATGGATTTT
1 GTAAATGGATTTT
3273044 GTAAATGGATTTT
1 GTAAATGGATTTT
3273057 GTA
1 GTA
3273060 TGATAGTCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
12 9 0.22
13 32 0.78
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.44
Consensus pattern (13 bp):
GTAAATGGATTTT
Found at i:3275592 original size:12 final size:12
Alignment explanation
Indices: 3275575--3275599 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3275565 ATGTAAGTGA
3275575 TCTTGATGATTT
1 TCTTGATGATTT
3275587 TCTTGATGATTT
1 TCTTGATGATTT
3275599 T
1 T
3275600 TACATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:3276430 original size:44 final size:47
Alignment explanation
Indices: 3276312--3276520 Score: 155
Period size: 47 Copynumber: 4.5 Consensus size: 47
3276302 AGGTGATTTG
*
3276312 TGTGCCAGAGTAAGACATGTCTGGGACATGCATCAGCCTCAACAGAGA
1 TGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCT-AACAGAGA
* ** * * *
3276360 T-AGCCAGTGTAAGATGTGTCTAGGACATGCATC-GGCT-A-AGAGT
1 TGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTAACAGAGA
* * * * *
3276403 TGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCAT-GCATAAA
1 TGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTAACAGAGA
* * *
3276449 TGAGAGCCAGTGTAAGACCATGTCTGAGACATGACATC-GGC--ACAGAGA
1 T--GTGCCAGTGTAAGA-CATGTCTGGGACATG-CATCAGCCTAACAGAGA
*
3276497 TGAGTGCCAGAGTAAGACATGTCT
1 T--GTGCCAGTGTAAGACATGTCT
3276521 AAGGCATGTT
Statistics
Matches: 126, Mismatches: 28, Indels: 15
0.75 0.17 0.09
Matches are distributed among these distances:
43 5 0.04
44 28 0.22
45 2 0.02
46 6 0.05
47 34 0.27
48 32 0.25
49 15 0.12
50 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (47 bp):
TGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTAACAGAGA
Found at i:3276500 original size:48 final size:47
Alignment explanation
Indices: 3276409--3276520 Score: 136
Period size: 48 Copynumber: 2.3 Consensus size: 47
3276399 GAGTTGTGCT
* *
3276409 AGTGTAAGACATGTCTGGGACATGCATCAGCATGCATAAATGAGAGCC
1 AGTGTAAGACATGTCTGAGACATGCATCAGCA-GCAGAAATGAGAGCC
* * *
3276457 AGTGTAAGACCATGTCTGAGACATGACATCGGCA-CAGAGATGAGTGCC
1 AGTGTAAGA-CATGTCTGAGACATG-CATCAGCAGCAGAAATGAGAGCC
*
3276505 AGAGTAAGACATGTCT
1 AGTGTAAGACATGTCT
3276521 AAGGCATGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
47 7 0.12
48 28 0.50
49 14 0.25
50 7 0.12
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.21
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGAGACATGCATCAGCAGCAGAAATGAGAGCC
Found at i:3276671 original size:198 final size:198
Alignment explanation
Indices: 3276322--3276688 Score: 581
Period size: 198 Copynumber: 1.9 Consensus size: 198
3276312 TGTGCCAGAG
*
3276322 TAAGACATGTCTGGGACATGCATCAGCCTCAACAGAGATAGCCAGTGTAAGATGTGTCTAGGACA
1 TAAGACATGTCTGGGACATGCATCAGCCTCAACAGAGATAGCCAGTGTAAAATGTGTCTAGGACA
* * * *
3276387 TGCATCGGCTAAGAGTTGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCATGCATAAATGA
66 CGCATCGGCTAAGAGTTGTCCTAGTGTAAGACATGTCTGAGACATGCATCAGCACGCATAAATGA
3276452 GAGCCAGTGTAAGACCATGTCTGAGACATGACATCGGCACAGAGATGAGTGCCAGAGTAAGACAT
131 GAGCCAGTGTAAGACCATGTCTGAGACATGACATCGGCACAGAGATGAGTGCCAGAGTAAGACAT
3276517 GTC
196 GTC
* * * * *
3276520 TAAGGCATGTTTGGGACATTCATCGGCCTCAACAGAGATAGCCAGTGTAAAATGTGTCTGGGACA
1 TAAGACATGTCTGGGACATGCATCAGCCTCAACAGAGATAGCCAGTGTAAAATGTGTCTAGGACA
* * * *
3276585 CGCATCGGCTAAGAGTTGTCCTATTGTAAGACATGTTTGAGACATGCATCAGCACGTATATATGA
66 CGCATCGGCTAAGAGTTGTCCTAGTGTAAGACATGTCTGAGACATGCATCAGCACGCATAAATGA
* * *
3276650 GAGCCAGTGTAAGACCATGTCTGGGATATGGCATCGGCA
131 GAGCCAGTGTAAGACCATGTCTGAGACATGACATCGGCA
3276689 ATATATACCA
Statistics
Matches: 152, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
198 152 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (198 bp):
TAAGACATGTCTGGGACATGCATCAGCCTCAACAGAGATAGCCAGTGTAAAATGTGTCTAGGACA
CGCATCGGCTAAGAGTTGTCCTAGTGTAAGACATGTCTGAGACATGCATCAGCACGCATAAATGA
GAGCCAGTGTAAGACCATGTCTGAGACATGACATCGGCACAGAGATGAGTGCCAGAGTAAGACAT
GTC
Found at i:3278084 original size:16 final size:16
Alignment explanation
Indices: 3278056--3278126 Score: 79
Period size: 16 Copynumber: 4.4 Consensus size: 16
3278046 GTTTGGTTTA
* *
3278056 CTGTAATGAAATAGGG
1 CTGTAATGGAATAGAG
*
3278072 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
* *
3278088 CTATAATGGAGTAGAG
1 CTGTAATGGAATAGAG
* *
3278104 TTGTACTGGAATAGAG
1 CTGTAATGGAATAGAG
3278120 CTGTAAT
1 CTGTAAT
3278127 CAGTAATTCA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:3278194 original size:44 final size:46
Alignment explanation
Indices: 3278112--3278200 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
3278102 AGTTGTACTG
*
3278112 GAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATGGAATT
1 GAATAGAGCTGTAATCAGTAATTCAATTATTTGGTTGAATGGAATT
*
3278158 GAATAGAGCTGTAAT-AG-AATTC-TTCTATTTGGTTGAATGGAAT
1 GAATAGAGCTGTAATCAGTAATTCAAT-TATTTGGTTGAATGGAAT
3278201 AGATGTTGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 1 0.03
44 22 0.55
45 2 0.05
46 15 0.38
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.37
Consensus pattern (46 bp):
GAATAGAGCTGTAATCAGTAATTCAATTATTTGGTTGAATGGAATT
Found at i:3282708 original size:54 final size:55
Alignment explanation
Indices: 3282505--3282708 Score: 146
Period size: 53 Copynumber: 3.8 Consensus size: 55
3282495 CTCTTTAAAT
* * ** * *
3282505 TTACC-ATCGCCATGTCTTGACAAGGTCTTATGTGGTATCCTTACCTTAT--GAAC
1 TTACCAAT-GCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATCAAAAC
** * * * ** **
3282558 CCACCATTGCCATGCCTTGACATGGTCTTACATGGGATCTTTGCCTTATCGTAGT
1 TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATCAAAAC
* * * * * * * *
3282613 TTATCAACGCCATGTCTTGACATAGTCTTAAATGATTTCCTTGCCTTGT-AAAAC
1 TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATCAAAAC
* *
3282667 TTACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
3282709 AAACCCTACT
Statistics
Matches: 109, Mismatches: 39, Indels: 5
0.71 0.25 0.03
Matches are distributed among these distances:
53 37 0.34
54 35 0.32
55 37 0.34
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (55 bp):
TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATCAAAAC
Found at i:3289682 original size:21 final size:21
Alignment explanation
Indices: 3289619--3289684 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
3289609 TCTTTTATTT
* * *
3289619 ATTATAACTATTATATTATATC
1 ATTATAATTATTATATTTTA-A
*
3289641 ATTATTATTATTATATTTTAA
1 ATTATAATTATTATATTTTAA
3289662 ATTATAATTATTAT-TTCTTAA
1 ATTATAATTATTATATT-TTAA
3289683 AT
1 AT
3289685 ATTAAGTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
20 2 0.05
21 19 0.50
22 17 0.45
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATAATTATTATATTTTAA
Found at i:3296987 original size:68 final size:67
Alignment explanation
Indices: 3296915--3297064 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
3296905 CATCATGTGT
* * * *
3296915 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
3296977 ATGTAG
62 ATGTAG
** * *
3296983 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
3297048 AG
66 AG
3297050 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
3297065 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:3297020 original size:64 final size:64
Alignment explanation
Indices: 3296939--3297122 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
3296929 AGACATTATG
* *
3296939 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
3297003 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
3297068 AA
63 AA
* * * *
3297070 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
3297123 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:3305480 original size:37 final size:37
Alignment explanation
Indices: 3305439--3305519 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
3305429 CTGATGTACT
*
3305439 TCTTTCTGAATTCCTCTTGGAAGAAATCCCAAGTAAC
1 TCTTTCCGAATTCCTCTTGGAAGAAATCCCAAGTAAC
*
3305476 TCTTTCCNAATTCCTCTTGGAAGAAATCCCAAGTAAC
1 TCTTTCCGAATTCCTCTTGGAAGAAATCCCAAGTAAC
3305513 TCTTTCC
1 TCTTTCC
3305520 CTTGGTACCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.33
Consensus pattern (37 bp):
TCTTTCCGAATTCCTCTTGGAAGAAATCCCAAGTAAC
Found at i:3307912 original size:251 final size:251
Alignment explanation
Indices: 3307469--3307968 Score: 957
Period size: 251 Copynumber: 2.0 Consensus size: 251
3307459 TTTAAGCAAT
3307469 TGGACATCATTTATCTTGATTGTAACTTAGTTTAATATGTTGTTATGGAATCTTTAAATCCATAA
1 TGGACATCATTTATCTTGATTGTAACTTAGTTTAATATGTTGTTATGGAATCTTTAAATCCATAA
* *
3307534 AGAGCTAGCCGAATGTGATTTTGTATATAAATTGAAATACTGTATTTGAATTTAATTTGTCAAGG
66 AGAGCTAGCCGAATGTGATTTTGAATATAAATTGAAATACTGTATTTGAATTTAATTTGACAAGG
3307599 TTATATCGTTTAAAAGTTCGTATGATTTATGAGGAATATATGGAATTTTTGTTACATGAATTGTG
131 TTATATCGTTTAAAAGTTCGTATGATTTATGAGGAATATATGGAATTTTTGTTACATGAATTGTG
3307664 TATGAGACAACATTATAATAGTGATATTCGGGCTTTAAGCCTAGCAAGCTTTATGC
196 TATGAGACAACATTATAATAGTGATATTCGGGCTTTAAGCCTAGCAAGCTTTATGC
3307720 TGGACATCATTTATCTTGATTGTAACTTAGTTTAATATGTTGTTATGGAATCTTTAAATCCATAA
1 TGGACATCATTTATCTTGATTGTAACTTAGTTTAATATGTTGTTATGGAATCTTTAAATCCATAA
3307785 AGAGCTAGCCGAATGT-ATTTGTGAATATAAATTGAAATACTGTATTTGAATTTAATTTGACAAG
66 AGAGCTAGCCGAATGTGATTT-TGAATATAAATTGAAATACTGTATTTGAATTTAATTTGACAAG
3307849 GTTATATCGTTTAAAAGTTCGTATGATTTATGAGGAATATATGGAATTTTTGTTACATGAATTGT
130 GTTATATCGTTTAAAAGTTCGTATGATTTATGAGGAATATATGGAATTTTTGTTACATGAATTGT
*
3307914 GTATGAGACAACATTATAATAGTGATATTCGGGCTTTGAGCCTAGCAAGCTTTAT
195 GTATGAGACAACATTATAATAGTGATATTCGGGCTTTAAGCCTAGCAAGCTTTAT
3307969 ACCGGTGAAT
Statistics
Matches: 245, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
250 4 0.02
251 241 0.98
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.40
Consensus pattern (251 bp):
TGGACATCATTTATCTTGATTGTAACTTAGTTTAATATGTTGTTATGGAATCTTTAAATCCATAA
AGAGCTAGCCGAATGTGATTTTGAATATAAATTGAAATACTGTATTTGAATTTAATTTGACAAGG
TTATATCGTTTAAAAGTTCGTATGATTTATGAGGAATATATGGAATTTTTGTTACATGAATTGTG
TATGAGACAACATTATAATAGTGATATTCGGGCTTTAAGCCTAGCAAGCTTTATGC
Found at i:3308310 original size:21 final size:21
Alignment explanation
Indices: 3308269--3308311 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3308259 ACATAATCCA
*
3308269 ATATATATAAAAAAATTATAT
1 ATATATATAAAAAAATCATAT
*
3308290 ATATATATATACAAAA-CATAT
1 ATATATATA-AAAAAATCATAT
3308311 A
1 A
3308312 ATGAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
ATATATATAAAAAAATCATAT
Found at i:3310262 original size:43 final size:43
Alignment explanation
Indices: 3310181--3310266 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
3310171 AAATCGTACA
* **
3310181 ATGCCAACGTCCCAGACATGGTCTTACATGTAGTCACATATCG
1 ATGCCAACGTCCCAGACAGGGTCTTACATGTAAACACATATCG
3310224 ATGCC-ACTGTCCCAGACAGGGTCTTAC-TCGTAAACACATATCG
1 ATGCCAAC-GTCCCAGACAGGGTCTTACAT-GTAAACACATATCG
3310267 GAGTCACATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 3 0.08
43 35 0.92
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACATGTAAACACATATCG
Found at i:3312567 original size:35 final size:35
Alignment explanation
Indices: 3312516--3312684 Score: 185
Period size: 35 Copynumber: 4.8 Consensus size: 35
3312506 AGGTAAGTAT
* *
3312516 ATGTGAGGTTACATTGAACTTGTATATTCGGCTGC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGCTAC
*
3312551 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGCTAC
* * * *
3312586 ATGTGAGATTATATTGAATTTGTATATTCGGCCAT
1 ATGTGAGGTTATATTGAACTTGTATATTCGGCTAC
* * * * * * *
3312621 ATGAGATGTTTTATTGAACTTGAACATTAGGTTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGCTAC
* * *
3312656 ATGTGATGATATATTGAACTTATATATTC
1 ATGTGAGGTTATATTGAACTTGTATATTC
3312685 AGTATAATGA
Statistics
Matches: 108, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 108 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.41
Consensus pattern (35 bp):
ATGTGAGGTTATATTGAACTTGTATATTCGGCTAC
Found at i:3312609 original size:70 final size:69
Alignment explanation
Indices: 3312516--3312684 Score: 207
Period size: 70 Copynumber: 2.4 Consensus size: 69
3312506 AGGTAAGTAT
* * * * * *
3312516 ATGTGAGGTTACATTGAACTTGTATATTCGGCTGCATGTGAG-GTTATATTGAACTTGTATATTC
1 ATGTGAGATTATATTGAACTTGTATATTCGGC--CATATGAGAGTTATATTGAACTTGAACATTA
3312580 GGTTAC
64 GGTTAC
* *
3312586 ATGTGAGATTATATTGAATTTGTATATTCGGCCATATGAGATGTTTTATTGAACTTGAACATTAG
1 ATGTGAGATTATATTGAACTTGTATATTCGGCCATATGAGA-GTTATATTGAACTTGAACATTAG
3312651 GTTAC
65 GTTAC
*
3312656 ATGTGATGA-TATATTGAACTTATATATTC
1 ATGTGA-GATTATATTGAACTTGTATATTC
3312685 AGTATAATGA
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
68 7 0.08
70 77 0.90
71 2 0.02
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.41
Consensus pattern (69 bp):
ATGTGAGATTATATTGAACTTGTATATTCGGCCATATGAGAGTTATATTGAACTTGAACATTAGG
TTAC
Found at i:3317472 original size:27 final size:26
Alignment explanation
Indices: 3317433--3317513 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 26
3317423 AGCATGGCTG
* *
3317433 CCAGAACTGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGACAGAGCCA
*
3317459 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGACAGAGCCA
* * *
3317486 CCAGAATCAGATAATGTGGCAAAGCCA
1 CCAGAA-CAGATATTGTGACAGAGCCA
3317513 C
1 C
3317514 TTAACAGAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 6 0.12
27 42 0.88
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGAGCCA
Found at i:3318024 original size:27 final size:28
Alignment explanation
Indices: 3317962--3318025 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
3317952 CATTCACTTG
*
3317962 CCCACAAGGGCAAAACAGTCATTTAACA
1 CCCACAAGGGCAAAACAGTAATTTAACA
* ** *
3317990 CCC-TAAGGGCAAAATGGTAATTTTAC-
1 CCCACAAGGGCAAAACAGTAATTTAACA
3318016 CCCACAAGGG
1 CCCACAAGGG
3318026 TATCTCGGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.10
27 23 0.79
28 3 0.10
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.17
Consensus pattern (28 bp):
CCCACAAGGGCAAAACAGTAATTTAACA
Found at i:3318035 original size:27 final size:27
Alignment explanation
Indices: 3318005--3318389 Score: 536
Period size: 27 Copynumber: 14.3 Consensus size: 27
3317995 AGGGCAAAAT
* * * *
3318005 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
3318032 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** * *
3318059 ATTAATTCTACCCCATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
3318086 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
3318113 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
3318140 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
3318167 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
3318194 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
3318221 GGTAATTCTACCTTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
3318248 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
3318275 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
3318302 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
3318329 GGTAATTCTACCCTATAGTGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
3318356 AGTAATTCTACCCTAAAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
3318383 AGTAATT
1 GGTAATT
3318390 TTACAAATCG
Statistics
Matches: 320, Mismatches: 38, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 320 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:3318406 original size:27 final size:27
Alignment explanation
Indices: 3318373--3318552 Score: 172
Period size: 27 Copynumber: 6.7 Consensus size: 27
3318363 CTACCCTAAA
3318373 AGGGTATTTCAGTAATTTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
*
3318400 AGTGTATTTCAGTAATTTTACAAA-CTG
1 AGGGTATTTCAGTAATTTTACAAATC-G
* **
3318427 AGGGTATTTCGGTAATTTTACAAATTA
1 AGGGTATTTCAGTAATTTTACAAATCG
*
3318454 AGGGTATTTTAGTAATTTTAC-AATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* * * *
3318480 ACGATATTTC-GATAATTTTATAAACCG
1 AGGGTATTTCAG-TAATTTTACAAATCG
* * *
3318507 GGGGTACTTT-GGTAATTTTACAACT-G
1 AGGGTA-TTTCAGTAATTTTACAAATCG
* *
3318533 GGGGTATTTTAGTAATTTTA
1 AGGGTATTTCAGTAATTTTA
3318553 GTAAACTAAA
Statistics
Matches: 125, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
25 4 0.03
26 35 0.28
27 82 0.66
28 4 0.03
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTACAAATCG
Found at i:3318407 original size:54 final size:53
Alignment explanation
Indices: 3318022--3318470 Score: 501
Period size: 54 Copynumber: 8.3 Consensus size: 53
3318012 TTACCCCACA
* * **
3318022 AGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCATTAATTCTACCCCATA-
1 AGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTA--CCATAC
* *
3318076 GGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTAC
1 AGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCATAC
*
3318129 AGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTAC
1 A-GGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCATAC
*
3318183 AGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTAC
1 A-GGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCATAC
* * *
3318237 AGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTAC
1 A-GGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCATAC
* * * *
3318291 AAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTAT
1 -AGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCATAC
* * * * * *
3318345 AGTGGTATTTTAGTAATTCTACCCTAAAAGGGTATTTCAGTAATTTTA-CAAATC
1 AG-GGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCATA-C
* * ** * * *
3318399 GAGTGTATTTCAGTAATTTTA-CAAACTGAGGGTATTTCGGTAATTTTACAAATTA-
1 -AGGGTATTTCAGTAATTCTACCCTACAG-GGGTATTTCGGTAATTCTAC-CA-TAC
*
3318454 AGGGTATTTTAGTAATT
1 AGGGTATTTCAGTAATT
3318471 TTACAATCGA
Statistics
Matches: 349, Mismatches: 36, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
52 4 0.01
53 6 0.02
54 334 0.96
55 3 0.01
56 1 0.00
57 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (53 bp):
AGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCATAC
Found at i:3318433 original size:81 final size:79
Alignment explanation
Indices: 3318348--3318552 Score: 200
Period size: 80 Copynumber: 2.6 Consensus size: 79
3318338 ACCCTATAGT
* * *
3318348 GGTATTTTAGTAATTCTACCCTAA-AAGGGTATTTCAGTAATTTTACAAATCGA-GTGTATTTC-
1 GGTATTTTGGTAATTCTA--CAAATAAGGGTATTTCAGTAATTTTAC-AATCGACG-ATATTTCG
*
3318410 AGTAATTTTACAAACTGAG
62 A-TAATTTTACAAACCGAG
* * *
3318429 GGTATTTCGGTAATTTTACAAATTAAGGGTATTTTAGTAATTTTACAATCGACGATATTTCGATA
1 GGTATTTTGGTAATTCTACAAA-TAAGGGTATTTCAGTAATTTTACAATCGACGATATTTCGATA
* *
3318494 ATTTTATAAACCGGG
65 ATTTTACAAACCGAG
* * * ** *
3318509 GGTACTTTGGTAATTTTACAACTGGGGGTATTTTAGTAATTTTA
1 GGTATTTTGGTAATTCTACAAATAAGGGTATTTCAGTAATTTTA
3318553 GTAAACTAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
79 23 0.22
80 45 0.42
81 38 0.36
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.40
Consensus pattern (79 bp):
GGTATTTTGGTAATTCTACAAATAAGGGTATTTCAGTAATTTTACAATCGACGATATTTCGATAA
TTTTACAAACCGAG
Found at i:3318471 original size:54 final size:54
Alignment explanation
Indices: 3318373--3318552 Score: 195
Period size: 53 Copynumber: 3.4 Consensus size: 54
3318363 CTACCCTAAA
* *
3318373 AGGGTATTTCAGTAATTTTACAAATCGAGTGTATTTCAGTAATTTTACAAACTG
1 AGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTTAGTAATTTTACAAACTG
* ** *
3318427 AGGGTATTTCGGTAATTTTACAAATTAAGGGTATTTTAGTAATTTTACAATC-G
1 AGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTTAGTAATTTTACAAACTG
* * * * * * *
3318480 ACGATATTTC-GATAATTTTATAAACCGGGGGTACTTTGGTAATTTTAC-AACTG
1 AGGGTATTTCAG-TAATTTTACAAATCGAGGGTATTTTAGTAATTTTACAAACTG
* *
3318533 GGGGTATTTTAGTAATTTTA
1 AGGGTATTTCAGTAATTTTA
3318553 GTAAACTAAA
Statistics
Matches: 103, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
52 3 0.03
53 53 0.51
54 47 0.46
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (54 bp):
AGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTTAGTAATTTTACAAACTG
Found at i:3320302 original size:39 final size:39
Alignment explanation
Indices: 3320250--3320342 Score: 159
Period size: 39 Copynumber: 2.4 Consensus size: 39
3320240 AACTTTAAGC
*
3320250 CCGGATATATTTCCAGCACATAACCTGCGGACCTCAAGT
1 CCGGATATGTTTCCAGCACATAACCTGCGGACCTCAAGT
* *
3320289 CCGGATATGTTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATGTTTCCAGCACATAACCTGCGGACCTCAAGT
3320328 CCGGATATGTTTCCA
1 CCGGATATGTTTCCA
3320343 AGTATCATGC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.25
Consensus pattern (39 bp):
CCGGATATGTTTCCAGCACATAACCTGCGGACCTCAAGT
Found at i:3324031 original size:20 final size:20
Alignment explanation
Indices: 3324003--3324043 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3323993 CGGGTCTATA
*
3324003 ATCGGTACGAAGCCCACAAT
1 ATCGATACGAAGCCCACAAT
3324023 ATCGATACGAAGCCCACAAT
1 ATCGATACGAAGCCCACAAT
3324043 A
1 A
3324044 ACGGCACACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.29, G:0.17, T:0.15
Consensus pattern (20 bp):
ATCGATACGAAGCCCACAAT
Found at i:3324126 original size:20 final size:20
Alignment explanation
Indices: 3324101--3324141 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3324091 CGGGTCTATA
*
3324101 ATCGATACGAAGCCTACAAT
1 ATCGATACGAAGCCCACAAT
3324121 ATCGATACGAAGCCCACAAT
1 ATCGATACGAAGCCCACAAT
3324141 A
1 A
3324142 ATGGCGCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.27, G:0.15, T:0.17
Consensus pattern (20 bp):
ATCGATACGAAGCCCACAAT
Found at i:3324152 original size:98 final size:98
Alignment explanation
Indices: 3323981--3324219 Score: 379
Period size: 98 Copynumber: 2.4 Consensus size: 98
3323971 CGTGGCACAA
* *
3323981 AGCCATCGATAACGGGTCTATAATCGGTACGAAGCCCACAATATCGATACGAAGCCCACAATAAC
1 AGCCATTGATAACGGGTCTATAATCGGTACGAAGCCTACAATATCGATACGAAGCCCACAATAAC
* *
3324046 GGCACACAGCCTTCGGTAACATGATCGGCAATC
66 GGCACACAGCCTTCGGTAACACGATCGACAATC
* *
3324079 AGCCATTGATAACGGGTCTATAATCGATACGAAGCCTACAATATCGATACGAAGCCCACAATAAT
1 AGCCATTGATAACGGGTCTATAATCGGTACGAAGCCTACAATATCGATACGAAGCCCACAATAAC
* * *
3324144 GGCGCACAGCTTTCGGTAACACGATCGACACTC
66 GGCACACAGCCTTCGGTAACACGATCGACAATC
* *
3324177 AGCCATTGATAACGGGTCTATAATCGGCACCAAGCCTACAATA
1 AGCCATTGATAACGGGTCTATAATCGGTACGAAGCCTACAATA
3324220 ACGACACACA
Statistics
Matches: 129, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 129 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (98 bp):
AGCCATTGATAACGGGTCTATAATCGGTACGAAGCCTACAATATCGATACGAAGCCCACAATAAC
GGCACACAGCCTTCGGTAACACGATCGACAATC
Found at i:3324606 original size:27 final size:27
Alignment explanation
Indices: 3324576--3324879 Score: 331
Period size: 27 Copynumber: 11.3 Consensus size: 27
3324566 GGGGCAAAAT
* * * *
3324576 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
3324603 GGTAATTCTACTCC-ATAGGGGTATTTC
1 GGTAATTCTAC-CCTACAGGGGTATTTC
** * *
3324630 AATAATTCTACCCCATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
3324657 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
3324684 GATAATTCTACCTTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
3324711 AGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
3324738 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
3324765 GGTAGTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
3324792 TGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * ** *
3324819 TGTAATTCTACCCTATACTGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
3324846 AGTAATTCTACGCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
3324873 AGTAATT
1 GGTAATT
3324880 TTATAAATCG
Statistics
Matches: 242, Mismatches: 33, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
26 2 0.01
27 238 0.98
28 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:3324893 original size:27 final size:27
Alignment explanation
Indices: 3324863--3325040 Score: 118
Period size: 27 Copynumber: 6.7 Consensus size: 27
3324853 CTACGCTACA
3324863 AGGGTATTTCAGTAATTTTATAAATCG
1 AGGGTATTTCAGTAATTTTATAAATCG
* *
3324890 AGGGCATTTCAGTAATTTTGCAT-ACT-G
1 AGGGTATTTCAGTAATTTT--ATAAATCG
* * * * *
3324917 AGGGTATGTCGGTAATTTTACAAGTCA
1 AGGGTATTTCAGTAATTTTATAAATCG
*
3324944 AGGGTATTTTAGTAATTTTA-AAATCG
1 AGGGTATTTCAGTAATTTTATAAATCG
* * *
3324970 ACGGTATTT-TGATAATTTTATAAACCG
1 AGGGTATTTCAG-TAATTTTATAAATCG
* * *
3324997 -GGTGTACTTT-GGTAATTTTACAACT-G
1 AGG-GTA-TTTCAGTAATTTTATAAATCG
* *
3325023 GGGGTATTTTAGTAATTT
1 AGGGTATTTCAGTAATTT
3325041 CAGTAAACTA
Statistics
Matches: 119, Mismatches: 22, Indels: 21
0.73 0.14 0.13
Matches are distributed among these distances:
25 5 0.04
26 34 0.29
27 72 0.61
28 6 0.05
29 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTATAAATCG
Found at i:3327238 original size:27 final size:26
Alignment explanation
Indices: 3327199--3327279 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
3327189 AGCATGGTTG
* *
3327199 CCAGAACTGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGACAGAGCCA
* *
3327225 CCAGATACAGATATTGGGGCAGAGCCA
1 CCAGA-ACAGATATTGTGACAGAGCCA
* * *
3327252 CCAGAATCAGATAATGTGGCAAAGCCA
1 CCAGAA-CAGATATTGTGACAGAGCCA
3327279 C
1 C
3327280 TTAACAGAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
26 6 0.13
27 40 0.87
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGAGCCA
Found at i:3327472 original size:98 final size:98
Alignment explanation
Indices: 3327301--3327539 Score: 343
Period size: 98 Copynumber: 2.4 Consensus size: 98
3327291 CGTGGCACAA
* * * * *
3327301 AGCCATCGATAACAGGTCTATAATCGGCACGAAGCCCACAATATCGATACGAAGCCCACAGTGAC
1 AGCCATTGATAACGGGTCTATAATCGGCACGAAGCCTACAATATCGATACGAAGCCCACAATAAC
* *
3327366 GGCACACAGCCTTCTGTAACATGATCGGAACTC
66 GGCACACAGCCTTCGGTAACACGATCGGAACTC
* *
3327399 AGCCATTGGTAACGGGTCTATAATCGGCACGAAGCCTACAATATCGATACGAAGCCCACAATAAT
1 AGCCATTGATAACGGGTCTATAATCGGCACGAAGCCTACAATATCGATACGAAGCCCACAATAAC
* *
3327464 GGCGCACAGCCTTCGGTAACACGATCGGCACTC
66 GGCACACAGCCTTCGGTAACACGATCGGAACTC
* * * *
3327497 AGCCATTGATAACGTGTCTATAATCAGCACCAAGCCTTCAATA
1 AGCCATTGATAACGGGTCTATAATCGGCACGAAGCCTACAATA
3327540 ACGGCACACA
Statistics
Matches: 125, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 125 1.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.19
Consensus pattern (98 bp):
AGCCATTGATAACGGGTCTATAATCGGCACGAAGCCTACAATATCGATACGAAGCCCACAATAAC
GGCACACAGCCTTCGGTAACACGATCGGAACTC
Found at i:3327927 original size:27 final size:27
Alignment explanation
Indices: 3327897--3328118 Score: 286
Period size: 27 Copynumber: 8.2 Consensus size: 27
3327887 GGGCAAAATG
* *
3327897 GTAATTTTACCCCACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
*
3327924 GTAATTCTACCCTAC-AGCGGTATTTCG
1 GTAATTCTACCCTACAAG-GGTATTTCA
* * *
3327951 GTAATTCTACCTTACAGGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
3327978 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
3328005 GTATTTCTACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
*
3328032 GTAATTCTACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
3328059 GTAATTCTACCCTA-TAGTGGTATTTTA
1 GTAATTCTACCCTACAAG-GGTATTTCA
*
3328086 GTAATTCTACCCTACAAGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCA
3328113 GTAATT
1 GTAATT
3328119 TTATAAATCG
Statistics
Matches: 174, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
26 4 0.02
27 167 0.96
28 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.37
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:3328133 original size:81 final size:81
Alignment explanation
Indices: 3327897--3328145 Score: 259
Period size: 81 Copynumber: 3.1 Consensus size: 81
3327887 GGGCAAAATG
* * * * *
3327897 GTAATTTTACCCCACAAGGGTATTTCAGTAATTCTACCCTAC-AGCGGTATTTCGGTAATTCTAC
1 GTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAG-GGTATTTCAGTAATTCTAA
** * *
3327961 CTTACAGGGGTATTTTA
65 AATACAAGGGTATTTCA
* * * **
3327978 GTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACC
1 GTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTAAA
* *
3328043 CTACAAGGGTATTTCG
66 ATACAAGGGTATTTCA
* * * * *
3328059 GTAATTCTACCCTATAGTGGTATTTTAGTAATTCTACCCTACAAGGGTATTTTAGTAATTTTATA
1 GTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTA-A
*
3328124 AAT-CGAGGGTATTTCA
65 AATACAAGGGTATTTCA
*
3328140 ATAATT
1 GTAATT
3328146 TTGCAAACTG
Statistics
Matches: 143, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
81 140 0.98
82 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (81 bp):
GTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTAAA
ATACAAGGGTATTTCA
Found at i:3328135 original size:54 final size:54
Alignment explanation
Indices: 3327913--3328145 Score: 253
Period size: 54 Copynumber: 4.3 Consensus size: 54
3327903 TTACCCCACA
3327913 AGGGTATTTCAGTAATTCTACCCTAC-AGCGGTATTTCGGTAATTCTAC-CT-TAC
1 AGGGTATTTCAGTAATTCTACCCTACAAG-GGTATTTCGGTAATTCTACTCTAT-C
* * * *
3327966 AGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTA-C
1 A-GGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACTCTATC
* *
3328020 AAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTAT-
1 -AGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACTCTATC
* ** * **
3328074 AGTGGTATTTTAGTAATTCTACCCTACAAGGGTATTTTAGTAATTTTA-TAAATC
1 AG-GGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACTCTATC
*
3328128 GAGGGTATTTCAATAATT
1 -AGGGTATTTCAGTAATT
3328146 TTGCAAACTG
Statistics
Matches: 154, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
53 5 0.03
54 143 0.93
55 6 0.04
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (54 bp):
AGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACTCTATC
Found at i:3328215 original size:26 final size:27
Alignment explanation
Indices: 3328102--3328281 Score: 158
Period size: 27 Copynumber: 6.7 Consensus size: 27
3328092 CTACCCTACA
* *
3328102 AGGGTATTTTAGTAATTTTATAAATC-G
1 AGGGTATTTCAGTAATTTTA-CAATCTG
* * *
3328129 AGGGTATTTCAATAATTTTGCAAACTG
1 AGGGTATTTCAGTAATTTTACAATCTG
3328156 AGGGTATTTC-GATAATTTTACAAATC-G
1 AGGGTATTTCAG-TAATTTTAC-AATCTG
*
3328183 AGCGTATTTCAGTAATTTTACAATC-G
1 AGGGTATTTCAGTAATTTTACAATCTG
* * *
3328209 ACGGTATTTC-GATAATTTTATAAACTG
1 AGGGTATTTCAG-TAATTTTACAATCTG
* *
3328236 GGGGTACTTT-GGTAATTTTACAA-CTG
1 AGGGTA-TTTCAGTAATTTTACAATCTG
*
3328262 GGGGTATTTCAGTAATTTTA
1 AGGGTATTTCAGTAATTTTA
3328282 GTAAACTAAA
Statistics
Matches: 127, Mismatches: 17, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
25 4 0.03
26 45 0.35
27 70 0.55
28 8 0.06
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTACAATCTG
Found at i:3328251 original size:53 final size:54
Alignment explanation
Indices: 3328114--3328288 Score: 173
Period size: 53 Copynumber: 3.3 Consensus size: 54
3328104 GGTATTTTAG
* * * *
3328114 TAATTTTATAAA-TCGAGGGTATTTCAATAATTTTGCAAACTGAGGGTATTTCGA
1 TAATTTTATAAACTCGAGCGTATTTCAGTAATTTTAC-AACTGACGGTATTTCGA
*
3328168 TAATTTTACAAA-TCGAGCGTATTTCAGTAATTTTACAA-TCGACGGTATTTCGA
1 TAATTTTATAAACTCGAGCGTATTTCAGTAATTTTACAACT-GACGGTATTTCGA
* * * **
3328221 TAATTTTATAAACT-GGGGGTACTTT-GGTAATTTTACAACTGGGGGTATTTC-A
1 TAATTTTATAAACTCGAGCGTA-TTTCAGTAATTTTACAACTGACGGTATTTCGA
3328273 GTAATTTTAGTAAACT
1 -TAATTTTA-TAAACT
3328289 AAAGTATTCT
Statistics
Matches: 104, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
52 2 0.02
53 59 0.57
54 43 0.41
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.39
Consensus pattern (54 bp):
TAATTTTATAAACTCGAGCGTATTTCAGTAATTTTACAACTGACGGTATTTCGA
Found at i:3332794 original size:35 final size:35
Alignment explanation
Indices: 3332752--3332960 Score: 220
Period size: 35 Copynumber: 6.0 Consensus size: 35
3332742 ATAGGTAAGG
3332752 ACATGTGAGGTTATATTGAACTTGTATATTCGGCT
1 ACATGTGAGGTTATATTGAACTTGTATATTCGGCT
* * * **
3332787 GCATGTGAGGTTATATTGAACTTGTGTATTTGATT
1 ACATGTGAGGTTATATTGAACTTGTATATTCGGCT
* * *
3332822 ACATGTGAGCTTATATTGAACTTGTATATCCGGTT
1 ACATGTGAGGTTATATTGAACTTGTATATTCGGCT
* * *
3332857 ACATGTGAGATTATATTGAATTTGTATATTCGGCC
1 ACATGTGAGGTTATATTGAACTTGTATATTCGGCT
* * * * * * * *
3332892 ATATGAGATGTTTTATTGAACTTGAACATTAGGTT
1 ACATGTGAGGTTATATTGAACTTGTATATTCGGCT
* * *
3332927 ACATGTGATGATATATTGAACTTATATATTCGGC
1 ACATGTGAGGTTATATTGAACTTGTATATTCGGC
3332961 CATATGAAAT
Statistics
Matches: 138, Mismatches: 36, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 138 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (35 bp):
ACATGTGAGGTTATATTGAACTTGTATATTCGGCT
Found at i:3332909 original size:105 final size:104
Alignment explanation
Indices: 3332752--3332955 Score: 259
Period size: 105 Copynumber: 1.9 Consensus size: 104
3332742 ATAGGTAAGG
* * ***
3332752 ACATGTGAGGTTATATTGAACTTGTATATTCGGCTGCATGTGAGGTTATATTGAACTTGTGTATT
1 ACATGTGAGATTATATTGAACTTGTATATTCGGC-GCATATGAGGTTATATTGAACTTGAACATT
* * *
3332817 TGATTACATGTGA-GCTTATATTGAACTTGTATATCCGGTT
65 AGATTACATGTGATG-ATATATTGAACTTATATATCCGGTT
* *
3332857 ACATGTGAGATTATATTGAATTTGTATATTCGGC-CATATGAGATGTTTTATTGAACTTGAACAT
1 ACATGTGAGATTATATTGAACTTGTATATTCGGCGCATATGAG--GTTATATTGAACTTGAACAT
*
3332921 TAGGTTACATGTGATGATATATTGAACTTATATAT
64 TAGATTACATGTGATGATATATTGAACTTATATAT
3332956 TCGGCCATAT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
103 7 0.08
105 77 0.91
106 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (104 bp):
ACATGTGAGATTATATTGAACTTGTATATTCGGCGCATATGAGGTTATATTGAACTTGAACATTA
GATTACATGTGATGATATATTGAACTTATATATCCGGTT
Found at i:3345642 original size:48 final size:48
Alignment explanation
Indices: 3345525--3345799 Score: 374
Period size: 48 Copynumber: 5.8 Consensus size: 48
3345515 ACCGTGCTGA
* * *
3345525 ATGTGCCTGTGTAAGACCGTGTCTGCGACATGGAATCGGCGATGA-AT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* * * *
3345572 ATGTACCTGTGTAAGACTATGTCTAGGACATGGCATCAGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* *
3345620 GTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* * *
3345668 ATGTGCATGTGCAAGACCATGTCTAGGACATGGCATCGGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
** *
3345716 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAAC-AGTGATGT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGA-TGATAT
* *
3345764 ATGTGCCCGTGTAAGACTATGTCTGGGACATGGCAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCAT
3345800 TGGTACTTTA
Statistics
Matches: 200, Mismatches: 26, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
47 39 0.19
48 161 0.81
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (48 bp):
ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
Found at i:3353855 original size:48 final size:48
Alignment explanation
Indices: 3353782--3354153 Score: 545
Period size: 48 Copynumber: 7.8 Consensus size: 48
3353772 ACCGTGCTGA
* *
3353782 ATGTGCCTGTGTAAGACCATATCTGGGACATGGCATCGGCGATGATAT
1 ATGTGCATGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
3353830 ATGTGCATGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
1 ATGTGCATGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* ** *
3353878 GTGTGCCA-GTGTAAGACCATGTCTAAGACATGGCATCGGTGATGATAT
1 ATGTG-CATGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
*
3353926 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
1 ATGTGCATGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
*
3353974 GTGTGCCA-GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
1 ATGTG-CATGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
*
3354022 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
1 ATGTGCATGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* * *
3354070 ATGTGCCTTTGTAAGACCATGTCTGGGACATGGCATCAGCGATG--AT
1 ATGTGCATGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* * *
3354116 ATGTGGATTCATGTAAGACCATGTCGGGGACATGGCAT
1 ATGTGCA-T-GTGTAAGACCATGTCTGGGACATGGCAT
3354154 AGGTACTTTA
Statistics
Matches: 297, Mismatches: 21, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
46 7 0.02
47 3 0.01
48 284 0.96
49 3 0.01
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (48 bp):
ATGTGCATGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
Found at i:3354042 original size:144 final size:143
Alignment explanation
Indices: 3353782--3354153 Score: 602
Period size: 144 Copynumber: 2.6 Consensus size: 143
3353772 ACCGTGCTGA
* *
3353782 ATGTGCCTGTGTAAGACCATATCTGGGACATGGCATCGGCGATGATATATGTGCATGTGTAAGAC
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATGTGTGCA-GTGTAAGAC
*
3353847 CATGTCTGGGACATGGCATCGGCGATGATATGTGTGCCAGTGTAAGACCATGTCTAAGACATGGC
65 CATGTCTGGGACATGGCATCGGCGATGATATATGTGCCAGTGTAAGACCATGTCTAAGACATGGC
*
3353912 ATCGGTGATGATAT
130 ATCGGCGATGATAT
3353926 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATGTGTGCCAGTGTAAGAC
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATGTGTG-CAGTGTAAGAC
* **
3353991 CATGTCTGGGACATGGCATCGGCGATGATATATGTGCCTGTGTAAGACCATGTCTGGGACATGGC
65 CATGTCTGGGACATGGCATCGGCGATGATATATGTGCCAGTGTAAGACCATGTCTAAGACATGGC
3354056 ATCGGCGATGATAT
130 ATCGGCGATGATAT
* * *
3354070 ATGTGCCTTTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATATGTGGATTCA-TGTAAGA
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATGT-G-TGCAGTGTAAGA
*
3354134 CCATGTCGGGGACATGGCAT
64 CCATGTCTGGGACATGGCAT
3354154 AGGTACTTTA
Statistics
Matches: 214, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
144 208 0.97
145 5 0.02
146 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (143 bp):
ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATGTGTGCAGTGTAAGACC
ATGTCTGGGACATGGCATCGGCGATGATATATGTGCCAGTGTAAGACCATGTCTAAGACATGGCA
TCGGCGATGATAT
Found at i:3355867 original size:18 final size:19
Alignment explanation
Indices: 3355824--3355873 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 19
3355814 TTAAATTTTA
*
3355824 TTATTTAATTATT--TAAT
1 TTATTAAATTATTAATAAT
3355841 TTATTAAATTATTAATAAT
1 TTATTAAATTATTAATAAT
*
3355860 TT-TTAAATTTTTAA
1 TTATTAAATTATTAA
3355874 GAAAATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 12 0.41
18 11 0.38
19 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTAAATTATTAATAAT
Found at i:3361613 original size:25 final size:25
Alignment explanation
Indices: 3361585--3361634 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3361575 GAAAAATACT
*
3361585 TTAAAAATTCATGGGAAATGGCTTA
1 TTAAAAATTCATGGGAAATGCCTTA
*
3361610 TTAAAAATTCATGTGAAATGCCTTA
1 TTAAAAATTCATGGGAAATGCCTTA
3361635 CCCCACATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (25 bp):
TTAAAAATTCATGGGAAATGCCTTA
Found at i:3362305 original size:7 final size:7
Alignment explanation
Indices: 3362290--3362358 Score: 75
Period size: 7 Copynumber: 9.3 Consensus size: 7
3362280 AAGGCAACAG
*
3362290 TAAAACC
1 TAAACCC
3362297 TAAACCC
1 TAAACCC
*
3362304 TAAAACC
1 TAAACCC
3362311 TAAAACCC
1 T-AAACCC
*
3362319 TAAAACAC
1 T-AAACCC
3362327 TAAAACCC
1 T-AAACCC
3362335 TAAAACCC
1 T-AAACCC
3362343 TAAACCC
1 TAAACCC
3362350 TAAACCC
1 TAAACCC
3362357 TA
1 TA
3362359 GACATGCTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
7 28 0.50
8 28 0.50
ACGTcount: A:0.51, C:0.35, G:0.00, T:0.14
Consensus pattern (7 bp):
TAAACCC
Found at i:3362318 original size:15 final size:15
Alignment explanation
Indices: 3362290--3362358 Score: 97
Period size: 15 Copynumber: 4.6 Consensus size: 15
3362280 AAGGCAACAG
3362290 TAAAACCT-AAACCC
1 TAAAACCTAAAACCC
3362304 TAAAACCTAAAACCC
1 TAAAACCTAAAACCC
3362319 TAAAACACTAAAACCC
1 TAAAAC-CTAAAACCC
3362335 TAAAACCCT-AAACCC
1 TAAAA-CCTAAAACCC
*
3362350 TAAACCCTA
1 TAAAACCTA
3362359 GACATGCTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
14 11 0.22
15 22 0.44
16 16 0.32
17 1 0.02
ACGTcount: A:0.51, C:0.35, G:0.00, T:0.14
Consensus pattern (15 bp):
TAAAACCTAAAACCC
Found at i:3362320 original size:8 final size:8
Alignment explanation
Indices: 3362290--3362358 Score: 94
Period size: 8 Copynumber: 9.2 Consensus size: 8
3362280 AAGGCAACAG
3362290 TAAAA-CC
1 TAAAACCC
3362297 T-AAACCC
1 TAAAACCC
3362304 TAAAA-CC
1 TAAAACCC
3362311 TAAAACCC
1 TAAAACCC
*
3362319 TAAAACAC
1 TAAAACCC
3362327 TAAAACCC
1 TAAAACCC
3362335 TAAAACCC
1 TAAAACCC
3362343 T-AAACCC
1 TAAAACCC
3362350 T-AAACCC
1 TAAAACCC
3362357 TA
1 TA
3362359 GACATGCTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
6 3 0.05
7 25 0.45
8 28 0.50
ACGTcount: A:0.51, C:0.35, G:0.00, T:0.14
Consensus pattern (8 bp):
TAAAACCC
Found at i:3363685 original size:25 final size:25
Alignment explanation
Indices: 3363657--3363706 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3363647 GAAACATACT
*
3363657 TTAAAAATTCATGGGAAATGGCTTA
1 TTAAAAATTCATGGGAAATGCCTTA
*
3363682 TTAAAAATTCATGTGAAATGCCTTA
1 TTAAAAATTCATGGGAAATGCCTTA
3363707 CCCCCCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (25 bp):
TTAAAAATTCATGGGAAATGCCTTA
Found at i:3365135 original size:27 final size:28
Alignment explanation
Indices: 3365103--3365345 Score: 252
Period size: 27 Copynumber: 9.0 Consensus size: 28
3365093 AAGTACTCCT
*
3365103 GATTTATAGAATTACTGTTTTACCCTTA
1 GATTTACAGAATTACTGTTTTACCCTTA
* *
3365131 G-TTTACAGAATTACTATTTTACCC-TC
1 GATTTACAGAATTACTGTTTTACCCTTA
*
3365157 GATTTATAGAATTACTGTTTTACCCTTA
1 GATTTACAGAATTACTGTTTTACCCTTA
*
3365185 G-TTTACAGAATTACTGTTTTACCCTCA
1 GATTTACAGAATTACTGTTTTACCCTTA
* * *
3365212 -ATTTATAGAATTACCGTTTTA-CCTTC
1 GATTTACAGAATTACTGTTTTACCCTTA
** * *
3365238 GATTTGTAAAATTACCGTTTTACCCTT-
1 GATTTACAGAATTACTGTTTTACCCTTA
* *
3365265 GATTTACAGAATTACTGGTTTACCCTCA
1 GATTTACAGAATTACTGTTTTACCCTTA
* * *
3365293 G-TTTACAAAATTA-TCGTTCTACCC-TC
1 GATTTACAGAATTACT-GTTTTACCCTTA
*
3365319 GATTTACAGAATTACCGTTTTACCCTT
1 GATTTACAGAATTACTGTTTTACCCTT
3365346 GACTGTGAAA
Statistics
Matches: 177, Mismatches: 28, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
26 7 0.04
27 161 0.91
28 9 0.05
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.42
Consensus pattern (28 bp):
GATTTACAGAATTACTGTTTTACCCTTA
Found at i:3365161 original size:54 final size:54
Alignment explanation
Indices: 3365103--3365345 Score: 310
Period size: 54 Copynumber: 4.5 Consensus size: 54
3365093 AAGTACTCCT
* *
3365103 GATTTATAGAATTACTGTTTTACCCTTAGTTTACAGAATTACTATTTTACCCTC
1 GATTTATAGAATTACTGTTTTACCCTTAGTTTACAAAATTACTGTTTTACCCTC
*
3365157 GATTTATAGAATTACTGTTTTACCCTTAGTTTACAGAATTACTGTTTTACCCTC
1 GATTTATAGAATTACTGTTTTACCCTTAGTTTACAAAATTACTGTTTTACCCTC
* * * ** * *
3365211 AATTTATAGAATTACCGTTTTA-CCTTCGATTTGTAAAATTACCGTTTTACCCTT
1 GATTTATAGAATTACTGTTTTACCCTTAG-TTTACAAAATTACTGTTTTACCCTC
* * * *
3365265 GATTTACAGAATTACTGGTTTACCCTCAGTTTACAAAATTA-TCGTTCTACCCTC
1 GATTTATAGAATTACTGTTTTACCCTTAGTTTACAAAATTACT-GTTTTACCCTC
* *
3365319 GATTTACAGAATTACCGTTTTACCCTT
1 GATTTATAGAATTACTGTTTTACCCTT
3365346 GACTGTGAAA
Statistics
Matches: 163, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
53 5 0.03
54 154 0.94
55 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.42
Consensus pattern (54 bp):
GATTTATAGAATTACTGTTTTACCCTTAGTTTACAAAATTACTGTTTTACCCTC
Found at i:3365195 original size:81 final size:81
Alignment explanation
Indices: 3365102--3365347 Score: 334
Period size: 81 Copynumber: 3.0 Consensus size: 81
3365092 AAAGTACTCC
* * *
3365102 TGATTTATAGAATTACTGTTTTACCCTTAGTTTACAGAATTACTATTTTACCCTCGATTTATAGA
1 TGATTTACAGAATTACTGTTTTACCCTCAGTTTACAGAATTACTGTTTTACCCTCGATTTATAGA
*
3365167 ATTACTGTTTTACCCT
66 ATTACCGTTTTACCCT
* * * * * *
3365183 T-AGTTTACAGAATTACTGTTTTACCCTCAATTTATAGAATTACCGTTTTACCTTCGATTTGTAA
1 TGA-TTTACAGAATTACTGTTTTACCCTCAGTTTACAGAATTACTGTTTTACCCTCGATTTATAG
3365247 AATTACCGTTTTACCCT
65 AATTACCGTTTTACCCT
* * * *
3365264 TGATTTACAGAATTACTGGTTTACCCTCAGTTTACAAAATTA-TCGTTCTACCCTCGATTTACAG
1 TGATTTACAGAATTACTGTTTTACCCTCAGTTTACAGAATTACT-GTTTTACCCTCGATTTATAG
3365328 AATTACCGTTTTACCCT
65 AATTACCGTTTTACCCT
3365345 TGA
1 TGA
3365348 CTGTGAAATT
Statistics
Matches: 142, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
80 1 0.01
81 140 0.99
82 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (81 bp):
TGATTTACAGAATTACTGTTTTACCCTCAGTTTACAGAATTACTGTTTTACCCTCGATTTATAGA
ATTACCGTTTTACCCT
Found at i:3365548 original size:27 final size:27
Alignment explanation
Indices: 3365361--3365549 Score: 243
Period size: 27 Copynumber: 7.0 Consensus size: 27
3365351 TGAAATTATT
* *
3365361 GAAATACCCCTGTAGGGTAGAATTTCC
1 GAAATACCCTTGTAGGGTAGAATTACC
* *
3365388 GAAATACCCTTATAGGGTAGAATTACT
1 GAAATACCCTTGTAGGGTAGAATTACC
* *
3365415 GAAATACCCTTATAGGATAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * *
3365442 AAAATACCCCTGTAGGGTAGAATTATC
1 GAAATACCCTTGTAGGGTAGAATTACC
* *
3365469 GAAATACCCTTGTAGGGTAGAAATATC
1 GAAATACCCTTGTAGGGTAGAATTACC
*
3365496 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * *
3365523 GAGATACCCTTGTGGGGTAAAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
3365550 ATTTTGCCCC
Statistics
Matches: 141, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 141 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (27 bp):
GAAATACCCTTGTAGGGTAGAATTACC
Found at i:3365786 original size:27 final size:26
Alignment explanation
Indices: 3365748--3365827 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 26
3365738 CGGAGGAAGC
3365748 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
*
3365775 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* * * *
3365801 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
3365828 ATTGACCAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 9 0.19
27 39 0.81
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:3365950 original size:22 final size:22
Alignment explanation
Indices: 3365918--3365976 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
3365908 CCCGTTATTA
*
3365918 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
3365940 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
3365962 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
3365977 ACTTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:3366335 original size:6 final size:6
Alignment explanation
Indices: 3366326--3366498 Score: 178
Period size: 6 Copynumber: 28.7 Consensus size: 6
3366316 TTGCATTCAC
* *
3366326 ATTCTG ATTCTG ATTCTG -TCACGTA ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT-TC-TG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
3366375 -TTACTA ATACTG ATTCTG ATTCTG ATTCTG ATTCTG -TTAATG ATTCTG
1 ATT-CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG
*
3366423 ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG
*
3366471 ATTCT- ATTACTG ATTTTG ATTCTG ATTC
1 ATTCTG ATT-CTG ATTCTG ATTCTG ATTC
3366499 GCATTTTGGT
Statistics
Matches: 140, Mismatches: 14, Indels: 26
0.78 0.08 0.14
Matches are distributed among these distances:
5 11 0.08
6 118 0.84
7 9 0.06
8 2 0.01
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:3366398 original size:36 final size:36
Alignment explanation
Indices: 3366351--3366475 Score: 214
Period size: 36 Copynumber: 3.5 Consensus size: 36
3366341 CTGTCACGTA
3366351 ATTCTGATTCTGATTCTGATTCTGTTACTAATACTG
1 ATTCTGATTCTGATTCTGATTCTGTTACTAATACTG
* * *
3366387 ATTCTGATTCTGATTCTGATTCTGTTAATGATTCTG
1 ATTCTGATTCTGATTCTGATTCTGTTACTAATACTG
*
3366423 ATTCTGATTCTGATTCTGATTCTGTTACTAATATTG
1 ATTCTGATTCTGATTCTGATTCTGTTACTAATACTG
3366459 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
3366476 ATTACTGATT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 82 1.00
ACGTcount: A:0.21, C:0.15, G:0.14, T:0.50
Consensus pattern (36 bp):
ATTCTGATTCTGATTCTGATTCTGTTACTAATACTG
Found at i:3366497 original size:36 final size:36
Alignment explanation
Indices: 3366351--3366498 Score: 203
Period size: 36 Copynumber: 4.1 Consensus size: 36
3366341 CTGTCACGTA
* *
3366351 ATTCTGATTCTGATTCTGATTCTGTTACTAATACTG
1 ATTCTGATTCTGATTCTGATTCTGTTACTGATTCTG
*
3366387 ATTCTGATTCTGATTCTGATTCTGTTAATGATTCTG
1 ATTCTGATTCTGATTCTGATTCTGTTACTGATTCTG
*
3366423 ATTCTGATTCTGATTCTGATTCTGTTACTAATAT-TG
1 ATTCTGATTCTGATTCTGATTCTGTTACTGAT-TCTG
*
3366459 ATTCTGATTCTGATTCT-ATTACTGATT-TTGATTCTG
1 ATTCTGATTCTGATTCTGATT-CTG-TTACTGATTCTG
3366495 ATTC
1 ATTC
3366499 GCATTTTGGT
Statistics
Matches: 101, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
35 4 0.04
36 94 0.93
37 3 0.03
ACGTcount: A:0.21, C:0.15, G:0.14, T:0.50
Consensus pattern (36 bp):
ATTCTGATTCTGATTCTGATTCTGTTACTGATTCTG
Found at i:3367331 original size:7 final size:7
Alignment explanation
Indices: 3367316--3367369 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
3367306 AAGGCAACAT
*
3367316 TAAAACC
1 TAAACCC
3367323 TAAACCC
1 TAAACCC
*
3367330 TAAAACC
1 TAAACCC
3367337 TAAAACCC
1 T-AAACCC
*
3367345 TAAAACTC
1 T-AAACCC
3367353 TAAAACCC
1 T-AAACCC
3367361 TAAACCC
1 TAAACCC
3367368 TA
1 TA
3367370 GACATGCTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
7 21 0.51
8 20 0.49
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:3367344 original size:15 final size:15
Alignment explanation
Indices: 3367316--3367369 Score: 83
Period size: 15 Copynumber: 3.6 Consensus size: 15
3367306 AAGGCAACAT
3367316 TAAAACCT-AAACCC
1 TAAAACCTAAAACCC
3367330 TAAAACCTAAAACCC
1 TAAAACCTAAAACCC
3367345 TAAAACTCTAAAACCC
1 TAAAAC-CTAAAACCC
*
3367361 TAAACCCTA
1 TAAAACCTA
3367370 GACATGCTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
14 8 0.22
15 15 0.41
16 14 0.38
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAACCTAAAACCC
Found at i:3367346 original size:8 final size:8
Alignment explanation
Indices: 3367316--3367369 Score: 71
Period size: 8 Copynumber: 7.2 Consensus size: 8
3367306 AAGGCAACAT
3367316 TAAAA-CC
1 TAAAACCC
3367323 T-AAACCC
1 TAAAACCC
3367330 TAAAA-CC
1 TAAAACCC
3367337 TAAAACCC
1 TAAAACCC
*
3367345 TAAAACTC
1 TAAAACCC
3367353 TAAAACCC
1 TAAAACCC
3367361 T-AAACCC
1 TAAAACCC
3367368 TA
1 TA
3367370 GACATGCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 3 0.07
7 18 0.44
8 20 0.49
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (8 bp):
TAAAACCC
Found at i:3368693 original size:25 final size:25
Alignment explanation
Indices: 3368665--3368714 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3368655 GAAACATACT
*
3368665 TTAAAAATTCATGGGAAATGGCTTA
1 TTAAAAATTCATGGGAAATGCCTTA
*
3368690 TTAAAAATTCATGTGAAATGCCTTA
1 TTAAAAATTCATGGGAAATGCCTTA
3368715 CCCCCCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (25 bp):
TTAAAAATTCATGGGAAATGCCTTA
Found at i:3370719 original size:25 final size:25
Alignment explanation
Indices: 3370691--3370740 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3370681 GAAACATTCT
*
3370691 TTAAAAATTCATGGGAAATGGCTTA
1 TTAAAAATTCATGGGAAATGCCTTA
*
3370716 TTAAAAATTCATGTGAAATGCCTTA
1 TTAAAAATTCATGGGAAATGCCTTA
3370741 CCCCCCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (25 bp):
TTAAAAATTCATGGGAAATGCCTTA
Found at i:3371415 original size:8 final size:8
Alignment explanation
Indices: 3371395--3371454 Score: 74
Period size: 7 Copynumber: 8.0 Consensus size: 8
3371385 AGGCAACATT
3371395 AAACCCT-
1 AAACCCTA
*
3371402 AAACCTTA
1 AAACCCTA
3371410 AAA-CCTA
1 AAACCCTA
3371417 AAACCCTA
1 AAACCCTA
*
3371425 AAACTCTA
1 AAACCCTA
3371433 AAACCCT-
1 AAACCCTA
3371440 AAACCCT-
1 AAACCCTA
3371447 AAACCCTA
1 AAACCCTA
3371455 GACATCCTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
7 26 0.57
8 20 0.43
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (8 bp):
AAACCCTA
Found at i:3371420 original size:15 final size:15
Alignment explanation
Indices: 3371402--3371454 Score: 72
Period size: 16 Copynumber: 3.5 Consensus size: 15
3371392 ATTAAACCCT
*
3371402 AAACCTTAAAACCTA
1 AAACCCTAAAACCTA
3371417 AAACCCTAAAACTCTA
1 AAACCCTAAAAC-CTA
*
3371433 AAACCCTAAACCCT-
1 AAACCCTAAAACCTA
3371447 AAACCCTA
1 AAACCCTA
3371455 GACATCCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
14 8 0.23
15 13 0.37
16 14 0.40
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (15 bp):
AAACCCTAAAACCTA
Found at i:3371465 original size:23 final size:21
Alignment explanation
Indices: 3371394--3371454 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 21
3371384 AAGGCAACAT
*
3371394 TAAACCCTAAACCTTAAAACC
1 TAAACCCTAAACCCTAAAACC
*
3371415 TAAAACCCTAAAACTCTAAAACCC
1 T-AAACCCT-AAACCCTAAAA-CC
3371439 TAAACCCTAAACCCTA
1 TAAACCCTAAACCCTA
3371455 GACATCCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 1 0.03
22 14 0.41
23 16 0.47
24 3 0.09
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.18
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAAACC
Found at i:3372784 original size:25 final size:25
Alignment explanation
Indices: 3372756--3372805 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3372746 GAAACATACT
*
3372756 TTAAAAATTCATAG-GAAATGGCTTA
1 TTAAAAATTCAT-GTGAAATGCCTTA
3372781 TTAAAAATTCATGTGAAATGCCTTA
1 TTAAAAATTCATGTGAAATGCCTTA
3372806 CCCCCCTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (25 bp):
TTAAAAATTCATGTGAAATGCCTTA
Found at i:3377243 original size:20 final size:20
Alignment explanation
Indices: 3377214--3377252 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3377204 TTTTATGTGA
3377214 AATATATTTGTGACCTAGTG
1 AATATATTTGTGACCTAGTG
* *
3377234 AATATGTTTGTGACTTAGT
1 AATATATTTGTGACCTAGT
3377253 AATGTTCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.44
Consensus pattern (20 bp):
AATATATTTGTGACCTAGTG
Found at i:3382150 original size:37 final size:37
Alignment explanation
Indices: 3382086--3382194 Score: 155
Period size: 37 Copynumber: 2.9 Consensus size: 37
3382076 AGCTCAGACG
* * *
3382086 AAATCTCCACACGAAGTTATCGAGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
3382123 AAATCTCCACACGTAGTCATCGGGTCTTACCCAGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* * *
3382160 TAATCTTCACACGTAGTCATCGGGCCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
3382195 ATATATTTCC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:3382457 original size:98 final size:96
Alignment explanation
Indices: 3382341--3382524 Score: 298
Period size: 98 Copynumber: 1.9 Consensus size: 96
3382331 GCACATCGCC
*
3382341 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTC--ATACATATTTCACATT
*
3382406 -GACCATTCGGCTTTACCACATATGCATATCTCA
64 AG-CCATTCAGCTTTACCACATATGCATATCTCA
* *
3382439 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCGCATTAG
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
3382504 CCATTCAGCTTTACCACATAT
66 CCATTCAGCTTTACCACATAT
3382525 ATACATGTTC
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
96 34 0.42
97 1 0.01
98 46 0.57
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (96 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
CCATTCAGCTTTACCACATATGCATATCTCA
Found at i:3382465 original size:48 final size:48
Alignment explanation
Indices: 3382341--3382525 Score: 291
Period size: 48 Copynumber: 3.8 Consensus size: 48
3382331 GCACATCGCC
*
3382341 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* *
3382391 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
3382439 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
3382487 TACATATTTCGCATTAGCCATTCAGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
3382526 TACATGTTCA
Statistics
Matches: 126, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
48 82 0.65
49 2 0.02
50 42 0.33
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:3382588 original size:47 final size:47
Alignment explanation
Indices: 3382498--3382688 Score: 247
Period size: 47 Copynumber: 4.1 Consensus size: 47
3382488 ACATATTTCG
* * * * * * *
3382498 CATTAGCCATTCAGCTTTACCACATATATACATGTTCATATTCACCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
3382545 CATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
3382592 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * * ** *
3382639 CATTGGTCATTCGGCCTTATCTCATATATACACATTCAAATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
3382686 CAT
1 CAT
3382689 AAAATCCTAA
Statistics
Matches: 127, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 127 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:3392889 original size:28 final size:26
Alignment explanation
Indices: 3392825--3392890 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 26
3392815 AGCAGAACTG
*
3392825 CTAATAACAGTATACGTGGCAAAGTCA
1 CTAAT-ACAGTATACGTGGCAAAGCCA
*
3392852 CCAA-AGCAGTGATTACGTGGCAAAGCCA
1 CTAATA-CAGT-A-TACGTGGCAAAGCCA
3392880 CTAATACAGTA
1 CTAATACAGTA
3392891 CTTCCTCCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
25 1 0.03
26 4 0.12
27 5 0.16
28 21 0.66
29 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (26 bp):
CTAATACAGTATACGTGGCAAAGCCA
Found at i:3397150 original size:46 final size:46
Alignment explanation
Indices: 3397100--3397461 Score: 379
Period size: 46 Copynumber: 7.8 Consensus size: 46
3397090 TGGTTGAGCA
3397100 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3397146 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
3397191 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3397239 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
3397284 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3397332 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
3397377 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3397425 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3397462 GCGGGTTACA
Statistics
Matches: 266, Mismatches: 23, Indels: 54
0.78 0.07 0.16
Matches are distributed among these distances:
42 6 0.02
43 15 0.06
45 9 0.03
46 121 0.45
47 87 0.33
48 9 0.03
50 13 0.05
51 6 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3397256 original size:93 final size:93
Alignment explanation
Indices: 3397097--3397454 Score: 680
Period size: 93 Copynumber: 3.8 Consensus size: 93
3397087 GGATGGTTGA
3397097 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
3397162 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
3397190 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
3397255 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
3397283 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
3397348 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
3397376 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
3397441 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
3397455 CTTATGGGCG
Statistics
Matches: 261, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 261 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:3401609 original size:13 final size:13
Alignment explanation
Indices: 3401591--3401616 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3401581 TTGTTATACG
3401591 AACTTACTAAGCA
1 AACTTACTAAGCA
3401604 AACTTACTAAGCA
1 AACTTACTAAGCA
3401617 TTTGAAATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
AACTTACTAAGCA
Found at i:3403566 original size:35 final size:35
Alignment explanation
Indices: 3403520--3403586 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
3403510 ACAACACTTT
*
3403520 ACCATTTGAAGTAACATTTAGTTTACTCATTTTTC
1 ACCATTTGAAGTAACACTTAGTTTACTCATTTTTC
3403555 ACCATTTGAAGTAACACTTAGTTTACTCATTT
1 ACCATTTGAAGTAACACTTAGTTTACTCATTT
3403587 AAGTTCAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (35 bp):
ACCATTTGAAGTAACACTTAGTTTACTCATTTTTC
Found at i:3409669 original size:22 final size:21
Alignment explanation
Indices: 3409638--3409689 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
3409628 GATGTAAAAG
* *
3409638 AAAAAGTAAATTAAAATTATTT
1 AAAAAATAAATTAAAA-TAATT
3409660 AAAAAATAAAATTAAAATAATT
1 AAAAAAT-AAATTAAAATAATT
3409682 AAAAAATA
1 AAAAAATA
3409690 TACTTCTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 17 0.63
23 9 0.33
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAAATAAATTAAAATAATT
Found at i:3409671 original size:23 final size:22
Alignment explanation
Indices: 3409645--3409689 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3409635 AAGAAAAAGT
*
3409645 AAATTAAAATTATTTAAAAAATA
1 AAATTAAAA-TAATTAAAAAATA
3409668 AAATTAAAATAATTAAAAAATA
1 AAATTAAAATAATTAAAAAATA
3409690 TACTTCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATTAAAATAATTAAAAAATA
Found at i:3413680 original size:3 final size:3
Alignment explanation
Indices: 3413674--3413721 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
3413664 GATGAACACG
3413674 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATGA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
3413720 AT
1 AT
3413722 CTAAAGTTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3413808 original size:23 final size:22
Alignment explanation
Indices: 3413755--3413809 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
3413745 AGTAATAAAC
* *
3413755 AAATAAATAATGGAATAAAATA
1 AAATAAATAAGGGAAAAAAATA
*
3413777 ACAAT-AATAAGGGCAAAAAAATT
1 A-AATAAATAAGGG-AAAAAAATA
3413800 AAATAAATAA
1 AAATAAATAA
3413810 AACGAGCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (22 bp):
AAATAAATAAGGGAAAAAAATA
Found at i:3413910 original size:12 final size:12
Alignment explanation
Indices: 3413895--3413927 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3413885 AATAAATAAA
3413895 TAAATAAAATAT
1 TAAATAAAATAT
*
3413907 TAAAGAAAATAT
1 TAAATAAAATAT
3413919 TAAATAAAA
1 TAAATAAAA
3413928 CATTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (12 bp):
TAAATAAAATAT
Found at i:3415894 original size:119 final size:119
Alignment explanation
Indices: 3415679--3415894 Score: 299
Period size: 119 Copynumber: 1.8 Consensus size: 119
3415669 TGGAGCAGAC
* * * * * * *
3415679 TGAAGATAGCGGATCTTATTTCTCTAAAGTTTCAGTGGAACAAATTAAAGCTATAAAATACAAAT
1 TGAAGATAGCGAATCTTATTTCTCTAAAGTTGCAATAGAACAAATTAAAGCTACAAAACACAAAG
*
3415744 CTGATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGAAAAAAAATTTATCTCTT
66 CTGATCTCCCTGAAGTTGCAGTAGAGAAGATTGAAGAAAAAAAATTTATCTCTT
* * *
3415798 TGAAGATAGCGAATCTTATTTCTCTGAAGTTGCAATAGAACAGATTAAAGCTACAAACCACAAAG
1 TGAAGATAGCGAATCTTATTTCTCTAAAGTTGCAATAGAACAAATTAAAGCTACAAAACACAAAG
* *
3415863 CTTATCTTCCTGAAGTTGCAGT-GAAGAAGATT
66 CTGATCTCCCTGAAGTTGCAGTAG-AGAAGATT
3415895 AAAAATACGA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
118 1 0.01
119 82 0.99
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (119 bp):
TGAAGATAGCGAATCTTATTTCTCTAAAGTTGCAATAGAACAAATTAAAGCTACAAAACACAAAG
CTGATCTCCCTGAAGTTGCAGTAGAGAAGATTGAAGAAAAAAAATTTATCTCTT
Found at i:3415980 original size:45 final size:44
Alignment explanation
Indices: 3415863--3416146 Score: 174
Period size: 44 Copynumber: 6.2 Consensus size: 44
3415853 AACCACAAAG
* * * * * *
3415863 CTTATCTTCCTGAAGTTGCAGTGAAGAAGATTAAAAATACG-AGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-GAAAT
* * * *
3415907 CTCATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAAATAGTAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG-AAAT
* * * *
3415952 CTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGTTACAACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-GA-AA-T
* * **
3415999 TTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGAAAT
* ** ** * *
3416043 CTTATTTCCCTGAAGTTTTAGTGGAATAGATTAAAGCTACAAATTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT---G--A-AGA-TAGAAAT
* * * * *
3416094 CTGATCTCTCTGAAGTTGCAATGGAGTAGATTGAAGAAAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG-AAAT
3416139 CTTATCTC
1 CTTATCTC
3416147 TTTGAAGATA
Statistics
Matches: 183, Mismatches: 44, Indels: 25
0.73 0.17 0.10
Matches are distributed among these distances:
43 1 0.01
44 62 0.34
45 49 0.27
46 3 0.02
47 35 0.19
48 1 0.01
49 1 0.01
50 2 0.01
51 29 0.16
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGAAAT
Found at i:3416084 original size:91 final size:92
Alignment explanation
Indices: 3415910--3416084 Score: 226
Period size: 91 Copynumber: 1.9 Consensus size: 92
3415900 TACGAGTCTC
*
3415910 ATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAAATAGTAAACCTTATCTCCCTGAAGTTGTAGTG
1 ATCTCCCTGAAGTTGCAGTGAAGCAGACTGAAAATAGTAAACCTTATCTCCCTGAAGTTGTAGTG
* * * *
3415975 GAGCAGGTTGAAGTTACAACAAGTTTT
66 GAACAGATTAAAGCTACAACAAGTTTT
* * ** * * *
3416002 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG-CGATCTTATTTCCCTGAAGTTTTAGTG
1 ATCTCCCTGAAGTTGCAGTGAAGCAGACTGAAAATAGTAAACCTTATCTCCCTGAAGTTGTAGTG
*
3416066 GAATAGATTAAAGCTACAA
66 GAACAGATTAAAGCTACAA
3416085 ATTACAAATC
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
91 36 0.51
92 34 0.49
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (92 bp):
ATCTCCCTGAAGTTGCAGTGAAGCAGACTGAAAATAGTAAACCTTATCTCCCTGAAGTTGTAGTG
GAACAGATTAAAGCTACAACAAGTTTT
Found at i:3416151 original size:24 final size:24
Alignment explanation
Indices: 3416124--3416177 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3416114 ATGGAGTAGA
3416124 TTGAAGAAAGCAAATCTTATCTCT
1 TTGAAGAAAGCAAATCTTATCTCT
* * *
3416148 TTGAAGATAGCGAATCTTATTTCT
1 TTGAAGAAAGCAAATCTTATCTCT
*
3416172 CTGAAG
1 TTGAAG
3416178 TTACAGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (24 bp):
TTGAAGAAAGCAAATCTTATCTCT
Found at i:3416288 original size:351 final size:351
Alignment explanation
Indices: 3415636--3416338 Score: 1093
Period size: 351 Copynumber: 2.0 Consensus size: 351
3415626 GGTGGGTATT
3415636 GTTACAACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGGATCTTATTTC
1 GTTACAACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGGATCTTATTTC
* * *
3415701 TCTAAAGTTTCAGTGGAACAAATTAAAGCTATAAAATACAAATCTGATCTCCCTGAAGTTGCAGT
66 CCTAAAGTTTCAGTGGAACAAATTAAAGCTACAAAATACAAATCTGATCTCCCTGAAGTTGCAAT
*
3415766 AGAGTAGATTGAAGAAAAAAAATTTATCTCTTTGAAGATAGCGAATCTTATTTCTCTGAAGTTGC
131 AGAGTAGATTGAAGAAAAAAAATTTATCTCTTTGAAGATAGCGAATCTTATTTCTCTGAAGTTAC
*
3415831 AATAGAACAGATTAAAGCTACAAACCACAAAGCTTATCTTCCTGAAGTTGCAGTGAAGAAGATTA
196 AATAGAACAGATTAAAGCTACAAACCACAAAGCTTATCTTCCTAAAGTTGCAGTGAAGAAGATTA
* * * * *
3415896 AAAATACGAGTCTCATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAAATAGTAAACCTTATCTCC
261 AAAATACAAGTCTCATCTCCCTAAAGTTACAATGAAGCAGATTGAAAATAGCAAACCTTATCTCC
* *
3415961 CTGAAGTTGTAGTGGAGCAGGTTGAA
326 CTGAAGTTGTAGTGCAGCAGATTGAA
* *
3415987 GTTACAACAAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGC-GATCTTATTTC
1 GTTACAACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGGATCTTATTTC
* * * * * *
3416051 CCTGAAGTTTTAGTGGAATAGATTAAAGCTACAAATTACAAATCTGATCTCTCTGAAGTTGCAAT
66 CCTAAAGTTTCAGTGGAACAAATTAAAGCTACAAAATACAAATCTGATCTCCCTGAAGTTGCAAT
* **
3416116 GGAGTAGATTGAAGAAAGCAAATCTTATCTCTTTGAAGATAGCGAATCTTATTTCTCTGAAGTTA
131 AGAGTAGATTGAAGAAAAAAAAT-TTATCTCTTTGAAGATAGCGAATCTTATTTCTCTGAAGTTA
* * ** * *
3416181 CAGTGGAACAGATTAAAGCTACAAACCACAAATTTTATCTTCCTAAAGTTGTAGTGAAGACGATT
195 CAATAGAACAGATTAAAGCTACAAACCACAAAGCTTATCTTCCTAAAGTTGCAGTGAAGAAGATT
* * * *
3416246 GAAGATACAAGTCTCATCTCCCTAAAGTTATAATGGAGCAGATTGAAAATAGCAAACCTTATCTC
260 AAAAATACAAGTCTCATCTCCCTAAAGTTACAATGAAGCAGATTGAAAATAGCAAACCTTATCTC
3416311 CCTGAAGTTGTAGTGCAGCAGATTGAA
325 CCTGAAGTTGTAGTGCAGCAGATTGAA
3416338 G
1 G
3416339 CGACAAATCT
Statistics
Matches: 318, Mismatches: 33, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
350 87 0.27
351 231 0.73
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (351 bp):
GTTACAACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGGATCTTATTTC
CCTAAAGTTTCAGTGGAACAAATTAAAGCTACAAAATACAAATCTGATCTCCCTGAAGTTGCAAT
AGAGTAGATTGAAGAAAAAAAATTTATCTCTTTGAAGATAGCGAATCTTATTTCTCTGAAGTTAC
AATAGAACAGATTAAAGCTACAAACCACAAAGCTTATCTTCCTAAAGTTGCAGTGAAGAAGATTA
AAAATACAAGTCTCATCTCCCTAAAGTTACAATGAAGCAGATTGAAAATAGCAAACCTTATCTCC
CTGAAGTTGTAGTGCAGCAGATTGAA
Found at i:3416290 original size:44 final size:45
Alignment explanation
Indices: 3416242--3416338 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
3416232 TAGTGAAGAC
** *
3416242 GATTGAAGATA-CAAGTCTCATCTCCCTAAAGTTATAATGGAGCA
1 GATTGAAGATAGCAAACCTCATCTCCCTAAAGTTATAATGCAGCA
* * * * *
3416286 GATTGAAAATAGCAAACCTTATCTCCCTGAAGTTGTAGTGCAGCA
1 GATTGAAGATAGCAAACCTCATCTCCCTAAAGTTATAATGCAGCA
3416331 GATTGAAG
1 GATTGAAG
3416339 CGACAAATCT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
44 10 0.23
45 33 0.77
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (45 bp):
GATTGAAGATAGCAAACCTCATCTCCCTAAAGTTATAATGCAGCA
Found at i:3416335 original size:89 final size:89
Alignment explanation
Indices: 3416215--3416746 Score: 360
Period size: 89 Copynumber: 5.9 Consensus size: 89
3416205 ACCACAAATT
* * * * * * * *
3416215 TTATCTTCCTAAAGTTGTAGTGAAG-ACGATTGAAGATACAAGTCTCATCTCCCTAAAGTTATAA
1 TTATCTCCCTGAAGTTGCAGTGCAGCA-GATTGAAGCTACAAATCTCATCTCCCTAAAGTTACAG
3416279 TGGAGCAGATTGAAAATAGCAAACC
65 TGGAGCAGATTGAAAATAGCAAACC
* * * * *
3416304 TTATCTCCCTGAAGTTGTAGTGCAGCAGATTGAAGCGACAAATCTTATAC-CTCTGAAGTTACAG
1 TTATCTCCCTGAAGTTGCAGTGCAGCAGATTGAAGCTACAAATCTCAT-CTCCCTAAAGTTACAG
* * ***
3416368 TGG-GTCGGATTAAATCCACTATAGCAAGTA
65 TGGAG-CAGATTGAA---A--ATAGCAAACC
* ** * *
3416398 TTATCTCCCTGAAGTTACAGTAG-AATAGACTAAAGCTACGAGCTACAAATCTTATCTCCCTAAA
1 TTATCTCCCTGAAGTTGCAGT-GCAGCAGA-T--TG--A--AGCTACAAATCTCATCTCCCTAAA
** * ** *
3416462 GTTAGTGTAGAATAGATTGAAAATAGCAAACT
58 GTTACAGTGGAGCAGATTGAAAATAGCAAACC
* * * * * *
3416494 TTATCTCCCTGAAGTTGCAATGGAGCA-AGTTGAAGGTACAAGTCTCATCTCCCTGAAGTTGCAG
1 TTATCTCCCTGAAGTTGCAGTGCAGCAGA-TTGAAGCTACAAATCTCATCTCCCTAAAGTTACAG
* * * *
3416558 TGGAGCATATCGAATATAGCAAATC
65 TGGAGCAGATTGAAAATAGCAAACC
* * * * * *
3416583 TTATCTCCTTGAAGTTACAGTAG-AGCAAATTGAAGCCACTAATCTTATCTCCCTAAAGTTACAG
1 TTATCTCCCTGAAGTTGCAGT-GCAGCAGATTGAAGCTACAAATCTCATCTCCCTAAAGTTACAG
* *
3416647 TGGAGTAGA-TGAAAACCA-CAAACC
65 TGGAGCAGATTGAAAA-TAGCAAACC
* * * * * *
3416671 TTATCTCCCTGAAGTTGCAGTGGAGTAGGTTGAAGTTACAAATCTCATCTCCCTGAGGTTACAGT
1 TTATCTCCCTGAAGTTGCAGTGCAGCAGATTGAAGCTACAAATCTCATCTCCCTAAAGTTACAGT
3416736 GGAGCAGATTG
66 GGAGCAGATTG
3416747 TAGATGCGAG
Statistics
Matches: 336, Mismatches: 83, Indels: 48
0.72 0.18 0.10
Matches are distributed among these distances:
87 1 0.00
88 69 0.21
89 160 0.48
90 4 0.01
91 1 0.00
92 1 0.00
93 1 0.00
94 30 0.09
95 5 0.01
96 28 0.08
97 1 0.00
98 1 0.00
99 1 0.00
100 1 0.00
101 32 0.10
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (89 bp):
TTATCTCCCTGAAGTTGCAGTGCAGCAGATTGAAGCTACAAATCTCATCTCCCTAAAGTTACAGT
GGAGCAGATTGAAAATAGCAAACC
Found at i:3416549 original size:44 final size:44
Alignment explanation
Indices: 3416438--3416741 Score: 231
Period size: 44 Copynumber: 6.9 Consensus size: 44
3416428 TAAAGCTACG
* * *
3416438 AGCTACAAATCTTATCTCCCTAAAGTT--AGTGTAGAATAGATTGA
1 AGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCA-AG-TTGA
** * *
3416482 AAATAGCAAA-CTTTATCTCCCTGAAGTTGCAATGGAGCAAGTTGA
1 AGCTA-CAAATC-TTATCTCCCTGAAGTTACAGTGGAGCAAGTTGA
* * * * *
3416527 AGGTACAAGTCTCATCTCCCTGAAGTTGCAGTGGAGCATA-TCGA
1 AGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCA-AGTTGA
** * * *
3416571 ATATAGCAAATCTTATCTCCTTGAAGTTACAGTAGAGCAAATTGA
1 AGCTA-CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAAGTTGA
* * * * *
3416616 AGCCACTAATCTTATCTCCCTAAAGTTACAGTGGAG-TAGATGAA
1 AGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAAGTTG-A
* * * * * *
3416660 AACCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGTAGGTTGA
1 AGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAAGTTGA
* * *
3416704 AGTTACAAATCTCATCTCCCTGAGGTTACAGTGGAGCA
1 AGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCA
3416742 GATTGTAGAT
Statistics
Matches: 204, Mismatches: 46, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
43 3 0.01
44 129 0.63
45 64 0.31
46 2 0.01
47 6 0.03
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
AGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAAGTTGA
Found at i:3418680 original size:79 final size:79
Alignment explanation
Indices: 3418593--3418773 Score: 299
Period size: 79 Copynumber: 2.3 Consensus size: 79
3418583 ATTTTTTTTG
*
3418593 CCCTTATTATTGTTATTTTATTCCATTATTTATTTGTTTATTACTTTTTATGTGCTTTCAAAATT
1 CCCTTATTATTGTTATTTTATTCCATTATTTATTTGTTTATTACTTTTTATGTACTTTCAAAATT
3418658 TAGATTATTCATTA
66 TAGATTATTCATTA
*
3418672 CCCTTATTATTGTTATTTTATTCCATTATTTATTTGTTTATTACTTTTTATGTACTTTCAAACTT
1 CCCTTATTATTGTTATTTTATTCCATTATTTATTTGTTTATTACTTTTTATGTACTTTCAAAATT
3418737 TAGATTATTCATTA
66 TAGATTATTCATTA
*** *
3418751 TTATTATTATTATTATTATTATT
1 CCCTTATTATTGTTATT-TTATT
3418774 ATTATTATTA
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 90 0.95
80 5 0.05
ACGTcount: A:0.25, C:0.10, G:0.05, T:0.60
Consensus pattern (79 bp):
CCCTTATTATTGTTATTTTATTCCATTATTTATTTGTTTATTACTTTTTATGTACTTTCAAAATT
TAGATTATTCATTA
Found at i:3418830 original size:3 final size:3
Alignment explanation
Indices: 3418740--3418810 Score: 126
Period size: 3 Copynumber: 23.7 Consensus size: 3
3418730 CAAACTTTAG
3418740 ATT ATT CATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3418786 ATT ATT ATT ATT ATT ATT A-T ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
3418811 CGTGTTCATC
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 61 0.92
4 3 0.05
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3418845 original size:29 final size:28
Alignment explanation
Indices: 3418792--3418874 Score: 73
Period size: 28 Copynumber: 2.9 Consensus size: 28
3418782 TATTATTATT
* * *
3418792 ATTATTATTATTATATTATCGTGTTCATC
1 ATTATTATTACTATATTATCATGTT-AAC
3418821 ATTATTATTACTAT-TTATGCATGTTAAC
1 ATTATTATTACTATATTAT-CATGTTAAC
*
3418849 ATTATGATTCACTA-A-TATCATTGTTA
1 ATTATTATT-ACTATATTATCA-TGTTA
3418875 TATATGTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
27 2 0.04
28 22 0.48
29 22 0.48
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (28 bp):
ATTATTATTACTATATTATCATGTTAAC
Found at i:3424091 original size:93 final size:93
Alignment explanation
Indices: 3423898--3424104 Score: 222
Period size: 93 Copynumber: 2.2 Consensus size: 93
3423888 TGATTTGTGT
** * * * * *
3423898 GCCAGTGTAAGACATGTCTGGGACATGCTTCGGCCACATTATGAGAGCCAGTGTAAGCCATGTCT
1 GCCAGTGTAAGACATGTCTGGGACATAATTCAGCCACATTATAAGAGCCAGAGTAAGACATGTCC
*
3423963 GAGACATGGCATCGGCATCCAGACGAGG
66 GAGACATGGCATCGACATCCAGACGAGG
* * * *
3423991 GCTAGTGTAAGACATGTTTGGGACATAATTCAGCCATATTATAAGTGCCAGAGTAAGACATGTCC
1 GCCAGTGTAAGACATGTCTGGGACATAATTCAGCCACATTATAAGAGCCAGAGTAAGACATGTCC
* * *
3424056 GGGACAT-GCATTGACCT-C-GACAGAGG
66 GAGACATGGCATCGACATCCAGAC-GAGG
*
3424082 TAGCCAGTGTAAGACGTGTCTGG
1 --GCCAGTGTAAGACATGTCTGG
3424105 AACACGCATT
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
90 3 0.03
91 5 0.05
92 7 0.08
93 78 0.84
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (93 bp):
GCCAGTGTAAGACATGTCTGGGACATAATTCAGCCACATTATAAGAGCCAGAGTAAGACATGTCC
GAGACATGGCATCGACATCCAGACGAGG
Found at i:3428730 original size:24 final size:24
Alignment explanation
Indices: 3428698--3428746 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
3428688 ATTCTCTCTC
3428698 TTAAGGTTAGGGTTTTTATTT-TTA
1 TTAAGGTTAGGGTTTTT-TTTATTA
3428722 TTAAGGTTAGGGTTTTTTTTATTA
1 TTAAGGTTAGGGTTTTTTTTATTA
3428746 T
1 T
3428747 GGTTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.59
Consensus pattern (24 bp):
TTAAGGTTAGGGTTTTTTTTATTA
Found at i:3428742 original size:21 final size:23
Alignment explanation
Indices: 3428698--3428750 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 23
3428688 ATTCTCTCTC
3428698 TTAAGGTTAGGGTTTTTATTTTTA
1 TTAAGGTTAGGG-TTTTATTTTTA
3428722 TTAAGGTTAGGG-TTT-TTTTTA
1 TTAAGGTTAGGGTTTTATTTTTA
*
3428743 TTATGGTT
1 TTAAGGTT
3428751 TTTATTTACG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 13 0.46
22 3 0.11
24 12 0.43
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (23 bp):
TTAAGGTTAGGGTTTTATTTTTA
Found at i:3436017 original size:9 final size:9
Alignment explanation
Indices: 3436005--3436058 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
3435995 ATGAGAGAGA
*
3436005 TGAGAGACT
1 TGAGAGATT
*
3436014 TGAGAGGGTT
1 TGAGA-GATT
3436024 TGAGAGAATT
1 TGAGAG-ATT
*
3436034 TGAGAGAAT
1 TGAGAGATT
*
3436043 TGAGAGAGT
1 TGAGAGATT
3436052 TGAGAGA
1 TGAGAGA
3436059 AGGATGTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
9 23 0.61
10 15 0.39
ACGTcount: A:0.35, C:0.02, G:0.39, T:0.24
Consensus pattern (9 bp):
TGAGAGATT
Found at i:3436040 original size:29 final size:28
Alignment explanation
Indices: 3436005--3436059 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
3435995 ATGAGAGAGA
* *
3436005 TGAGAGACTTGAGAGGGTTTGAGAGAATT
1 TGAGAGAATTGAGAGAG-TTGAGAGAATT
3436034 TGAGAGAATTGAGAGAGTTGAGAGAA
1 TGAGAGAATTGAGAGAGTTGAGAGAA
3436060 GGATGTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.24
Consensus pattern (28 bp):
TGAGAGAATTGAGAGAGTTGAGAGAATT
Found at i:3437094 original size:18 final size:20
Alignment explanation
Indices: 3437061--3437109 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
3437051 AAATTAGTGA
3437061 TAATTATGTCACACTCTG-AT
1 TAATT-TGTCACACTCTGAAT
3437081 TAATTTGT-ACACTCTGAAT
1 TAATTTGTCACACTCTGAAT
*
3437100 TATTTTGTCA
1 TAATTTGTCA
3437110 TATAACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.31
19 12 0.46
20 6 0.23
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (20 bp):
TAATTTGTCACACTCTGAAT
Found at i:3437599 original size:16 final size:15
Alignment explanation
Indices: 3437578--3437613 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
3437568 TTAGCTAGTA
*
3437578 ATTTATTATATATATT
1 ATTTATTAAATA-ATT
3437594 ATTTATTAAATAATT
1 ATTTATTAAATAATT
3437609 ATTTA
1 ATTTA
3437614 AACTCTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTATTAAATAATT
Found at i:3438295 original size:21 final size:21
Alignment explanation
Indices: 3438271--3438310 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3438261 TAAAAATTGT
3438271 AAAAAATAATAAAAAACTATC
1 AAAAAATAATAAAAAACTATC
*
3438292 AAAAAATTATAAAAAACTA
1 AAAAAATAATAAAAAACTA
3438311 GAAATTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAAAATAATAAAAAACTATC
Found at i:3438313 original size:57 final size:57
Alignment explanation
Indices: 3438252--3438364 Score: 149
Period size: 57 Copynumber: 2.0 Consensus size: 57
3438242 AAAAATATGT
* *
3438252 TAGAATTTTTAAAA-ATTGTAAAAAATAATAAAAAACTATC-AAAAAATTATAAAAAAC
1 TAGAAATTGTAAAATATTGT-AAAAATAAT-AAAAACTATCAAAAAAATTATAAAAAAC
* * *
3438309 TAGAAATTGTAAAATATTGTAAAAATTATAAAAATTATCAAAAAAATTGTAAAAAA
1 TAGAAATTGTAAAATATTGTAAAAATAATAAAAACTATCAAAAAAATTATAAAAAA
3438365 ATAATTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
56 9 0.18
57 35 0.71
58 5 0.10
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (57 bp):
TAGAAATTGTAAAATATTGTAAAAATAATAAAAACTATCAAAAAAATTATAAAAAAC
Found at i:3438332 original size:48 final size:46
Alignment explanation
Indices: 3438264--3438353 Score: 110
Period size: 48 Copynumber: 1.9 Consensus size: 46
3438254 GAATTTTTAA
3438264 AAATTGTAAAAAATAATAAAAAACTATCAAAAAATTAT-AAAAAACTAG
1 AAATTGTAAAAAATAAT-AAAAACTAT--AAAAATTATCAAAAAACTAG
* ** *
3438312 AAATTGTAAAATATTGTAAAAATTATAAAAATTATCAAAAAA
1 AAATTGTAAAAAATAATAAAAACTATAAAAATTATCAAAAAA
3438354 ATTGTAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 9 0.24
46 6 0.16
47 8 0.22
48 14 0.38
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (46 bp):
AAATTGTAAAAAATAATAAAAACTATAAAAATTATCAAAAAACTAG
Found at i:3438351 original size:19 final size:19
Alignment explanation
Indices: 3438261--3438352 Score: 57
Period size: 19 Copynumber: 4.8 Consensus size: 19
3438251 TTAGAATTTT
* * *
3438261 TAAAAATTGTAAAAAATAA
1 TAAAAATTATCAAAAATTA
*
3438280 TAAAAAACTATCAAAAAATTA
1 T-AAAAATTATC-AAAAATTA
* *
3438301 TAAAAA--A-CTAGAAATTG
1 TAAAAATTATC-AAAAATTA
*
3438318 TAAAATATTGT-AAAAATTA
1 TAAAA-ATTATCAAAAATTA
3438337 TAAAAATTATCAAAAA
1 TAAAAATTATCAAAAA
3438353 AATTGTAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
17 12 0.22
18 6 0.11
19 17 0.31
20 12 0.22
21 8 0.15
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (19 bp):
TAAAAATTATCAAAAATTA
Found at i:3438352 original size:11 final size:10
Alignment explanation
Indices: 3438262--3438364 Score: 63
Period size: 10 Copynumber: 10.5 Consensus size: 10
3438252 TAGAATTTTT
*
3438262 AAAAATTGTA
1 AAAAATTATA
*
3438272 AAAAATAATA
1 AAAAATTATA
*
3438282 AAAAACTATCA
1 AAAAATTAT-A
3438293 AAAAATTATA
1 AAAAATTATA
*
3438303 AAAAA--CT-
1 AAAAATTATA
* *
3438310 AGAAATTGTA
1 AAAAATTATA
* *
3438320 AAATATTGT-
1 AAAAATTATA
3438329 AAAAATTAT-
1 AAAAATTATA
3438338 AAAAATTATCAA
1 AAAAATTAT--A
*
3438350 AAAAATTGTA
1 AAAAATTATA
3438360 AAAAA
1 AAAAA
3438365 ATAATTAAAA
Statistics
Matches: 73, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
7 4 0.05
8 1 0.01
9 17 0.23
10 34 0.47
11 9 0.12
12 8 0.11
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (10 bp):
AAAAATTATA
Found at i:3438355 original size:12 final size:11
Alignment explanation
Indices: 3438329--3438400 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
3438319 AAAATATTGT
3438329 AAAAATTAT--
1 AAAAATTATAA
3438338 AAAAATTATCAA
1 AAAAATTAT-AA
*
3438350 AAAAATTGTAA
1 AAAAATTATAA
* *
3438361 AAAAATAATTA
1 AAAAATTATAA
* *
3438372 AAAAACTAAAA
1 AAAAATTATAA
*
3438383 AATAAACTA-AA
1 AA-AAATTATAA
3438394 AAAAATT
1 AAAAATT
3438401 GATGTATCTT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
9 9 0.18
10 4 0.08
11 23 0.46
12 14 0.28
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:3438362 original size:9 final size:9
Alignment explanation
Indices: 3438312--3438363 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
3438302 AAAAAACTAG
3438312 AAATTGTAA
1 AAATTGTAA
3438321 AATATTGTAA
1 AA-ATTGTAA
*
3438331 AAATTATAA
1 AAATTGTAA
*
3438340 AAATTATCAAAA
1 AAATTGT---AA
3438352 AAATTGTAA
1 AAATTGTAA
3438361 AAA
1 AAA
3438364 AATAATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 20 0.54
10 9 0.24
12 8 0.22
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (9 bp):
AAATTGTAA
Found at i:3440056 original size:28 final size:27
Alignment explanation
Indices: 3440011--3440067 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
3440001 TTATGATAAT
3440011 TTGTTTAAAATTACTTAGAT-AATTTA
1 TTGTTTAAAATTACTTAGATAAATTTA
*
3440037 TTGTTTAGATAATTATTTAGATAAATTTA
1 TTGTTTA-A-AATTACTTAGATAAATTTA
3440066 TT
1 TT
3440068 AAGAATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 7 0.26
27 1 0.04
28 11 0.41
29 8 0.30
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.53
Consensus pattern (27 bp):
TTGTTTAAAATTACTTAGATAAATTTA
Found at i:3440273 original size:26 final size:26
Alignment explanation
Indices: 3440224--3440273 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3440214 TATATTTTAA
* *
3440224 ATAATTAAAATATATAATTATTATTT
1 ATAATTAAAATAAATAAGTATTATTT
3440250 ATAATTAAAATAAATTAAGT-TTAT
1 ATAATTAAAATAAA-TAAGTATTAT
3440274 GATTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
ATAATTAAAATAAATAAGTATTATTT
Found at i:3440472 original size:25 final size:23
Alignment explanation
Indices: 3440444--3440493 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
3440434 AAATTATTAG
*
3440444 TAATTATTAAACAATATTATATTTT
1 TAATAATTAAA-AAT-TTATATTTT
* *
3440469 TAATAATTTAAGATTTATATTTT
1 TAATAATTAAAAATTTATATTTT
3440492 TA
1 TA
3440494 TGATATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 11 0.50
24 2 0.09
25 9 0.41
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TAATAATTAAAAATTTATATTTT
Found at i:3449925 original size:10 final size:10
Alignment explanation
Indices: 3449910--3449957 Score: 60
Period size: 10 Copynumber: 4.5 Consensus size: 10
3449900 TGCTTATAAT
3449910 TCATACCAAA
1 TCATACCAAA
3449920 TCATACCAAA
1 TCATACCAAA
3449930 TCATAAGCCAAA
1 TCAT-A-CCAAA
3449942 GTCATACCAAA
1 -TCATACCAAA
*
3449953 ACATA
1 TCATA
3449958 TGTTTCACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 18 0.53
11 6 0.18
12 6 0.18
13 4 0.12
ACGTcount: A:0.50, C:0.27, G:0.04, T:0.19
Consensus pattern (10 bp):
TCATACCAAA
Found at i:3449947 original size:23 final size:22
Alignment explanation
Indices: 3449915--3449957 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3449905 ATAATTCATA
*
3449915 CCAAATCATACCAAATCATAAG
1 CCAAATCATACCAAAACATAAG
3449937 CCAAAGTCATACCAAAACATA
1 CCAAA-TCATACCAAAACATA
3449958 TGTTTCACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.51, C:0.28, G:0.05, T:0.16
Consensus pattern (22 bp):
CCAAATCATACCAAAACATAAG
Found at i:3450393 original size:25 final size:24
Alignment explanation
Indices: 3450365--3450421 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
3450355 AGGACCAACT
*
3450365 TATTCATACAACTTATGGAAAAATA
1 TATTCACACAAC-TATGGAAAAATA
* * *
3450390 TATTCACATATCTATGGCAAAATA
1 TATTCACACAACTATGGAAAAATA
3450414 TATTCACA
1 TATTCACA
3450422 TATTCATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (24 bp):
TATTCACACAACTATGGAAAAATA
Found at i:3450411 original size:24 final size:24
Alignment explanation
Indices: 3450378--3450424 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3450368 TCATACAACT
3450378 TATGGAAAAATATATTCACATATC
1 TATGGAAAAATATATTCACATATC
*
3450402 TATGGCAAAATATATTCACATAT
1 TATGGAAAAATATATTCACATAT
3450425 TCATAAGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.34
Consensus pattern (24 bp):
TATGGAAAAATATATTCACATATC
Found at i:3450704 original size:43 final size:41
Alignment explanation
Indices: 3450647--3450773 Score: 132
Period size: 43 Copynumber: 3.0 Consensus size: 41
3450637 CAATGCCAAC
*
3450647 GTCCCAGACGTGGTCTTACGTATAATCAAATATCGATGCCACT
1 GTCCCAGACATGGTCTTACGTA-AATCAAATATCGATGCCA-T
** *
3450690 GTCTTAGACATGGTCTTACATGAAATCAAATA-CGATGCCGAT
1 GTCCCAGACATGGTCTTACGT-AAATCAAATATCGATGCC-AT
*
3450732 GTCCCAGACATGGTCTTGCACGTAAATCTCAA-ATCGATGCCA
1 GTCCCAGACATGGTCTT--ACGTAAATC-AAATATCGATGCCA
3450774 ACATCCCAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
42 23 0.33
43 34 0.49
44 13 0.19
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (41 bp):
GTCCCAGACATGGTCTTACGTAAATCAAATATCGATGCCAT
Found at i:3450741 original size:42 final size:41
Alignment explanation
Indices: 3450647--3450803 Score: 131
Period size: 43 Copynumber: 3.7 Consensus size: 41
3450637 CAATGCCAAC
*
3450647 GTCCCAGACGTGGTCTT--ACGTATAATCAAATATCGATGCCACT
1 GTCCCAGACATGGTCTTACACG-A-AATCAAATA-CGATGCCA-T
** *
3450690 GTCTTAGACATGGTCTTACATGAAATCAAATACGATGCCGAT
1 GTCCCAGACATGGTCTTACACGAAATCAAATACGATGCC-AT
* *
3450732 GTCCCAGACATGGTCTTGCACGTAAATCTCAAAT-CGATGCCAAC
1 GTCCCAGACATGGTCTTACACG-AAA--TCAAATACGATGCC-AT
* * *
3450776 ATCCCAGACGTGGTTTTACACGAAATCA
1 GTCCCAGACATGGTCTTACACGAAATCA
3450804 CATATTGGAG
Statistics
Matches: 94, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
41 3 0.03
42 26 0.28
43 30 0.32
44 27 0.29
45 8 0.09
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (41 bp):
GTCCCAGACATGGTCTTACACGAAATCAAATACGATGCCAT
Found at i:3461264 original size:43 final size:42
Alignment explanation
Indices: 3461217--3461307 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 42
3461207 TCCTAGACGT
* * *
3461217 GGTCTTACATGTAATCAAATATCGATGCC-ACTGTCCCAGACAG
1 GGTCTTACACGAAATCAAATA-CGATACCGA-TGTCCCAGACAG
*
3461260 GGTCTTACACGAAATCAAATACGATACCGATGTCCCAGACAT
1 GGTCTTACACGAAATCAAATACGATACCGATGTCCCAGACAG
3461302 GGTCTT
1 GGTCTT
3461308 GCACATAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 23 0.53
43 20 0.47
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
GGTCTTACACGAAATCAAATACGATACCGATGTCCCAGACAG
Done.