Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 162 of 362
Found at i:53385233 original size:25 final size:25
Alignment explanation
Indices: 53385205--53385273 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
53385195 TTTTCTTTTC
*
53385205 TTTTCTTTTTCTTTTTTAAATTAGA
1 TTTTCTTTTTCTTTTTTAAAGTAGA
*
53385230 TTTTCTCTTTTC-TTTTTAGAGTAGA
1 TTTTCT-TTTTCTTTTTTAAAGTAGA
* *
53385255 TATTCTTTTTGTTGTTTTA
1 TTTTCTTTTTCTT-TTTTA
53385274 TATTTTTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 4 0.11
25 23 0.62
26 10 0.27
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.67
Consensus pattern (25 bp):
TTTTCTTTTTCTTTTTTAAAGTAGA
Found at i:53389021 original size:37 final size:37
Alignment explanation
Indices: 53388971--53389049 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
53388961 TTATTACGAA
* * * *
53388971 GTCTTACCCGGACATAATCTCCACTCGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
53389008 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
53389045 GTCTT
1 GTCTT
53389050 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:53389318 original size:47 final size:47
Alignment explanation
Indices: 53389168--53389639 Score: 667
Period size: 47 Copynumber: 10.2 Consensus size: 47
53389158 CCCTTCGGGA
* * * * * * *
53389168 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
53389215 CCTGTCACATATATACACTTTCACATTCA-CACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53389261 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53389308 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53389355 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53389402 CTTATAACATATATACACTTT--CA--CAT--CA---GCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53389440 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53389487 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
*
53389535 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53389582 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53389629 CTTATCGACAT
1 CTTATC-ACAT
53389640 CATACCTTAT
Statistics
Matches: 389, Mismatches: 24, Indels: 23
0.89 0.06 0.05
Matches are distributed among these distances:
38 29 0.07
40 2 0.01
41 2 0.01
42 3 0.01
43 3 0.01
44 2 0.01
45 2 0.01
46 39 0.10
47 258 0.66
48 49 0.13
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:53389379 original size:38 final size:38
Alignment explanation
Indices: 53389337--53389465 Score: 150
Period size: 38 Copynumber: 3.2 Consensus size: 38
53389327 TTCACATTCA
53389337 TCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATT
1 TCACATCGGCTATTAGGCCTTATCACATATAT--A----CAC-TT
*
53389382 CATCACATCGGCTATTAGGCCTTATAACATATATACACTT
1 --TCACATCGGCTATTAGGCCTTATCACATATATACACTT
* *
53389422 TCACATCAGCTATTAGGCCTTATCACACATATACACTT
1 TCACATCGGCTATTAGGCCTTATCACATATATACACTT
53389460 TCACAT
1 TCACAT
53389466 TCATCACATC
Statistics
Matches: 78, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
38 41 0.53
40 2 0.03
41 3 0.04
45 1 0.01
47 31 0.40
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (38 bp):
TCACATCGGCTATTAGGCCTTATCACATATATACACTT
Found at i:53389437 original size:85 final size:85
Alignment explanation
Indices: 53389337--53389607 Score: 380
Period size: 85 Copynumber: 3.1 Consensus size: 85
53389327 TTCACATTCA
* *
53389337 TCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 TCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
53389402 CTTATAACATATATACACTT
66 CTTATAACATATATACACTT
* *
53389422 TCACATCAGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 TCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53389487 CTTATCACACATATACACTTTCACATT
66 CTTAT-A-ACATAT--A--TACAC-TT
*
53389514 CATCACATCGGCCATTTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTA
1 --TCACATCGGCTA-TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTA
* *
53389579 GGCCTTATCACACATATACACTT
63 GGCCTTATAACATATATACACTT
53389602 TCACAT
1 TCACAT
53389608 TCATCACATC
Statistics
Matches: 165, Mismatches: 11, Indels: 19
0.85 0.06 0.10
Matches are distributed among these distances:
85 66 0.40
86 7 0.04
87 6 0.04
88 2 0.01
89 5 0.03
91 5 0.03
92 2 0.01
93 5 0.03
94 10 0.06
95 57 0.35
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (85 bp):
TCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
CTTATAACATATATACACTT
Found at i:53389462 original size:132 final size:132
Alignment explanation
Indices: 53389290--53389717 Score: 532
Period size: 132 Copynumber: 3.0 Consensus size: 132
53389280 TTCACATTCA
* *
53389290 TCACATCGGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 TCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
53389355 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATAACATATATACAC
66 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATAACATATATACAC
53389420 TT
131 TT
* * * *
53389422 TCACATCAGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 TCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
53389487 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTTAGGCCTTATCACACATATACA
66 CTTATCACATATATACACTTTCACATTCATCACATCGGCTA-TTAGGCCTTAT-A-ACATAT--A
*
53389552 CTTTCACATT
126 --TACAC-TT
53389562 CATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAG
1 --TCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTA-
53389627 GCCTTATCGACATCATACCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
63 G-------G--------CCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
53389692 CTTATCACATATATACACTT
113 CTTATAACATATATACACTT
53389712 TCACAT
1 TCACAT
53389718 TCATCACATC
Statistics
Matches: 253, Mismatches: 17, Indels: 36
0.83 0.06 0.12
Matches are distributed among these distances:
132 98 0.39
133 11 0.04
134 1 0.00
135 6 0.02
137 1 0.00
139 4 0.02
140 2 0.01
142 58 0.23
143 1 0.00
148 6 0.02
150 3 0.01
151 4 0.02
153 1 0.00
155 6 0.02
157 11 0.04
158 40 0.16
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (132 bp):
TCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATAACATATATACAC
TT
Found at i:53389545 original size:95 final size:94
Alignment explanation
Indices: 53389422--53389643 Score: 381
Period size: 95 Copynumber: 2.3 Consensus size: 94
53389412 ATATACACTT
* * *
53389422 TCACATCAGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 TCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
53389487 CTTATCACACATATACACTTTCACATTCA
66 CTTATCACACATATACACTTTCACATTCA
53389516 TCACATCGGCCATTTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGG
1 TCACATCGGCCA-TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGG
53389581 CCTTATCACACATATACACTTTCACATTCA
65 CCTTATCACACATATACACTTTCACATTCA
*
53389611 TCACATCGGCTATTAGGCCTTATCGACATCATA
1 TCACATCGGCCATTAGGCCTTATC-ACA-CATA
53389644 CCTTATCACA
Statistics
Matches: 121, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
94 22 0.18
95 95 0.79
96 4 0.03
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (94 bp):
TCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
CTTATCACACATATACACTTTCACATTCA
Found at i:53389615 original size:227 final size:225
Alignment explanation
Indices: 53389219--53389633 Score: 740
Period size: 227 Copynumber: 1.8 Consensus size: 225
53389209 CTCGGCCCTG
* *
53389219 TCACATATATACACTTTCACATTCACACATCGACCATTAGGCCTTATCACATATATACACTTTCA
1 TCACACATATACACTTTCACATTCACACATCGACCATTAGGCCTTATCACACATATACACTTTCA
* * *
53389284 CATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCTA
66 CATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCA
*
53389349 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATAACATAT
131 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATAACATAT
53389414 ATACACTTTCACATCAGCTATTAGGCCTTA
196 ATACACTTTCACATCAGCTATTAGGCCTTA
* *
53389444 TCACACATATACACTTTCACATTCATCACATCGGCCATTTGGCCTTATCACACATATACACTTTC
1 TCACACATATACACTTTCACATTCA-CACATCGACCATTAGGCCTTATCACACATATACACTTTC
53389509 ACATTCATCACATCGGCCATTTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGC
65 ACATTCATCACATCGGCCA-TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGC
53389574 CATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTAT
129 CATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTAT
53389634 CGACATCATA
Statistics
Matches: 180, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
225 24 0.13
226 55 0.31
227 101 0.56
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (225 bp):
TCACACATATACACTTTCACATTCACACATCGACCATTAGGCCTTATCACACATATACACTTTCA
CATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCA
TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATAACATAT
ATACACTTTCACATCAGCTATTAGGCCTTA
Found at i:53389659 original size:110 final size:110
Alignment explanation
Indices: 53389534--53389742 Score: 382
Period size: 110 Copynumber: 1.9 Consensus size: 110
53389524 GCCATTTAGG
53389534 CCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACA
1 CCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACA
*
53389599 CTTTCACATTCATCACATCGGCTATTAGGCCTTATCGACATCATA
66 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCGACATCATA
* * *
53389644 CCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACA
1 CCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACA
53389709 CTTTCACATTCATCACATCGGCCATTAGGCCTTA
66 CTTTCACATTCATCACATCGGCCATTAGGCCTTA
53389743 CTATCATTTC
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 95 1.00
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (110 bp):
CCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACA
CTTTCACATTCATCACATCGGCCATTAGGCCTTATCGACATCATA
Found at i:53389697 original size:47 final size:47
Alignment explanation
Indices: 53389644--53389742 Score: 189
Period size: 47 Copynumber: 2.1 Consensus size: 47
53389634 CGACATCATA
*
53389644 CCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGG
1 CCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG
53389691 CCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG
1 CCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG
53389738 CCTTA
1 CCTTA
53389743 CTATCATTTC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG
Found at i:53389717 original size:63 final size:63
Alignment explanation
Indices: 53389581--53389701 Score: 226
Period size: 63 Copynumber: 1.9 Consensus size: 63
53389571 GGCCATTAGG
*
53389581 CCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCGACATCATA
1 CCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCGACATCATA
53389644 CCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATC-ACAT
1 CCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCGACAT
53389702 ATATACACTT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 4 0.07
63 53 0.93
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (63 bp):
CCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCGACATCATA
Found at i:53393213 original size:40 final size:38
Alignment explanation
Indices: 53393160--53393299 Score: 118
Period size: 40 Copynumber: 3.5 Consensus size: 38
53393150 CATGATTGCT
* * *
53393160 CTTCGGGATTTAGCACGGATATATCACTAGCACGAATGC
1 CTTCGGAACTTAGCCCGGATATATCACTAGCAC-AATGC
* * *
53393199 TCTTCGGAACTTAGCCCGGATTTAGTAACTCGCCACCAATGC
1 -CTTCGGAACTTAGCCCGGATATA-TCACTAG-CA-CAATGC
* * * *
53393241 CTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAAGC
1 CTTCGGAACTTAGCCCGGATAT-ATCAC-TAGCACAATGC
*
53393281 CTTCGGGACTTAGCCCGGA
1 CTTCGGAACTTAGCCCGGA
53393300 CATCATTCGA
Statistics
Matches: 79, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
40 40 0.51
41 29 0.37
42 9 0.11
43 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (38 bp):
CTTCGGAACTTAGCCCGGATATATCACTAGCACAATGC
Found at i:53393645 original size:29 final size:29
Alignment explanation
Indices: 53393606--53393684 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
53393596 CTTAATAATC
*
53393606 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
53393636 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
53393665 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
53393685 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:53393727 original size:43 final size:43
Alignment explanation
Indices: 53393666--53393768 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
53393656 TGCATTTCAA
53393666 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
53393709 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
53393752 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
53393769 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:53395669 original size:37 final size:37
Alignment explanation
Indices: 53395619--53395697 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
53395609 TTATTACGAA
* * *
53395619 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
53395656 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
53395693 GTCTT
1 GTCTT
53395698 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:53396107 original size:47 final size:47
Alignment explanation
Indices: 53395816--53396344 Score: 783
Period size: 48 Copynumber: 11.1 Consensus size: 47
53395806 CCCTTCGGGA
* * * * * * * *
53395816 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGCC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53395863 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53395909 CTTATCACATATATACACTTTCACATTCATCATCAGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACA-T--TCATCA-CATCGGCCATTAGGC
* *
53395960 CTTATTACATATATACACTTTCACATTCATCACATCGCGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCG-GCCATTAGGC
*
53396008 CTTATCACATATATACACTTTCACATTCATTCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCA-TCACATCGGCCATTAGGC
*
53396056 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53396103 CTTATCACACATTATACACTTTCACATTCATCACATCGGCATATTAGGC
1 CTTATCACATA-TATACACTTTCACATTCATCACATCGGC-CATTAGGC
*
53396152 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53396199 CTTATCACACATATACACTTTCACATTCATCACAATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCAC-ATCGGCCATTAGGC
*
53396247 CTTATCACACATATACACTTTCACATTCATCACATCGG-CATTTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
53396294 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53396341 CTTA
1 CTTA
53396345 CTATCATTTC
Statistics
Matches: 452, Mismatches: 18, Indels: 24
0.91 0.04 0.05
Matches are distributed among these distances:
46 37 0.08
47 156 0.35
48 187 0.41
49 30 0.07
50 3 0.01
51 39 0.09
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:53396231 original size:25 final size:25
Alignment explanation
Indices: 53396202--53396280 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
53396192 ATTAGGCCTT
53396202 ATCACACATATACACTTTCACATTC
1 ATCACACATATACACTTTCACATTC
*** * *
53396227 ATCACA-ATCGGC-CATT-AGGCCTT-
1 ATCACACATATACACTTTCA--CATTC
53396250 ATCACACATATACACTTTCACATTC
1 ATCACACATATACACTTTCACATTC
53396275 ATCACA
1 ATCACA
53396281 TCGGCATTTA
Statistics
Matches: 38, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
22 1 0.03
23 9 0.24
24 12 0.32
25 15 0.39
26 1 0.03
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.29
Consensus pattern (25 bp):
ATCACACATATACACTTTCACATTC
Found at i:53404332 original size:20 final size:20
Alignment explanation
Indices: 53404311--53404383 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
53404301 CTTTGTTATC
*
53404311 TGAGCTCATGAGTTGTGGTC
1 TGAGCTCATGAGTTGTGGTA
* * *
53404331 TGAGCTAATGAAATATGTGATA
1 TGAGCTCATG-AGT-TGTGGTA
* *
53404353 TAAACTCATGAGTTGTGGTA
1 TGAGCTCATGAGTTGTGGTA
*
53404373 TGAGTTCATGA
1 TGAGCTCATGA
53404384 TATATGTGAC
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
20 23 0.59
21 4 0.10
22 12 0.31
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (20 bp):
TGAGCTCATGAGTTGTGGTA
Found at i:53408730 original size:40 final size:40
Alignment explanation
Indices: 53408686--53408773 Score: 176
Period size: 40 Copynumber: 2.2 Consensus size: 40
53408676 AAGTTTTTGC
53408686 ACACGGGCTAAGACACGGGCGTGTCCTGGCCGTGTGAAGG
1 ACACGGGCTAAGACACGGGCGTGTCCTGGCCGTGTGAAGG
53408726 ACACGGGCTAAGACACGGGCGTGTCCTGGCCGTGTGAAGG
1 ACACGGGCTAAGACACGGGCGTGTCCTGGCCGTGTGAAGG
53408766 ACACGGGC
1 ACACGGGC
53408774 CTGAGATACG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.20, C:0.26, G:0.40, T:0.14
Consensus pattern (40 bp):
ACACGGGCTAAGACACGGGCGTGTCCTGGCCGTGTGAAGG
Found at i:53415477 original size:27 final size:27
Alignment explanation
Indices: 53415447--53415513 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 27
53415437 ATATTTTATA
53415447 ATTATTTAATTAGATAA-ATATTATTTT
1 ATTATTT-ATTAGATAATATATTATTTT
*
53415474 ATTAATATT-TTA-ATAATATATTTTTTT
1 ATT-AT-TTATTAGATAATATATTATTTT
53415501 ATTATTTTATTAG
1 ATTA-TTTATTAG
53415514 TATATAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
26 7 0.21
27 22 0.67
28 2 0.06
29 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (27 bp):
ATTATTTATTAGATAATATATTATTTT
Found at i:53415495 original size:24 final size:24
Alignment explanation
Indices: 53415463--53415518 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
53415453 TAATTAGATA
53415463 AATATTATTTTATTAATATTTTAAT
1 AATA-TATTTTATTAATATTTTAAT
* * *
53415488 AATATATTTTTTTATTATTTTATT
1 AATATATTTTATTAATATTTTAAT
*
53415512 AGTATAT
1 AATATAT
53415519 AAAGAAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
AATATATTTTATTAATATTTTAAT
Found at i:53417642 original size:46 final size:46
Alignment explanation
Indices: 53417590--53417816 Score: 312
Period size: 46 Copynumber: 4.9 Consensus size: 46
53417580 GTGTGCTCTC
* *
53417590 TGATATGAAATGTGTAAGACCATGGTTGGAAGATACCATGGCAACT
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA
* *
53417636 TGATATGAAATGTGAAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA
*
53417682 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA
** **
53417728 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGATAACA
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * *
53417774 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
53417817 TTATGTCAAA
Statistics
Matches: 163, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 162 0.99
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (46 bp):
TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:53427130 original size:42 final size:43
Alignment explanation
Indices: 53427040--53427174 Score: 150
Period size: 44 Copynumber: 3.2 Consensus size: 43
53427030 TCCACGTGGC
* * * *
53427040 CTTACATGTAATCAAATATCGATGCCACTGTCCC-GACAGGGT
1 CTTACACGAAATCAAATATCGATGCCAATGTCCCAGACATGGT
* *
53427082 ATTACACGAAATCATATA-CGATGCCAATGTCCCAGACATGGT
1 CTTACACGAAATCAAATATCGATGCCAATGTCCCAGACATGGT
* * *
53427124 CTTACACGTAAATCACAA-ATCGATGCCAACGTCCCAAACGTGGT
1 CTTACACG-AAATCA-AATATCGATGCCAATGTCCCAGACATGGT
53427168 CTTACAC
1 CTTACAC
53427175 AATAACACAT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
41 14 0.18
42 28 0.36
43 7 0.09
44 29 0.37
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (43 bp):
CTTACACGAAATCAAATATCGATGCCAATGTCCCAGACATGGT
Found at i:53433150 original size:43 final size:43
Alignment explanation
Indices: 53433102--53433271 Score: 166
Period size: 43 Copynumber: 4.0 Consensus size: 43
53433092 GTTACCGAGA
53433102 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * *
53433145 TGTGATTACGTGTAAGACCATGTCTGGGACATTGACATTGCTAA
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTG-TAT
* *** * * **
53433189 T-CGATTTTGTGTAAGACCCTGTCTGGGACAGTGGCA-TCAAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * * *
53433230 ATGTGATAACATGTAAGACCATATTTGGGATA-TGGCATTGTA
1 -TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA
53433272 CAAGCGATAT
Statistics
Matches: 100, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
41 1 0.01
42 7 0.07
43 89 0.89
44 3 0.03
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:53439663 original size:27 final size:26
Alignment explanation
Indices: 53439605--53439715 Score: 141
Period size: 27 Copynumber: 4.2 Consensus size: 26
53439595 AACAAGGCTG
* *
53439605 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
53439631 CTAGAACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAAT-GTGGCAGAGCCA
*
53439658 CCAGAACAGATGTATGTGGCAGAGCCA
1 CCAGAACAGAT-AATGTGGCAGAGCCA
* *
53439685 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
53439712 CCAG
1 CCAG
53439716 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 14 0.19
27 58 0.78
28 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:53441155 original size:24 final size:24
Alignment explanation
Indices: 53441127--53441176 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
53441117 CAACACTGTC
53441127 CTCCCTAATCAGCTCCTAAATCCT
1 CTCCCTAATCAGCTCCTAAATCCT
*
53441151 CTCCCTTATCAGCTCCTAAATCCT
1 CTCCCTAATCAGCTCCTAAATCCT
53441175 CT
1 CT
53441177 TCTGACAGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.42, G:0.04, T:0.32
Consensus pattern (24 bp):
CTCCCTAATCAGCTCCTAAATCCT
Found at i:53447462 original size:27 final size:26
Alignment explanation
Indices: 53447406--53447517 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
53447396 CAGCAAGGCT
* *
53447406 ACCAGAACAGATAATGTGACAGAGTC
1 ACCAGAACAGATAATGTGGCAGAGCC
*
53447432 ACCAGTACAGATAATCGTGGCAGAGCC
1 ACCAGAACAGATAAT-GTGGCAGAGCC
*
53447459 ACCAGAATAGATATATGTGGCAGAGCC
1 ACCAGAACAGATA-ATGTGGCAGAGCC
* * *
53447486 ACCAGATCAGATAATTTTGGCATAGCC
1 ACCAGAACAGATAA-TGTGGCAGAGCC
53447513 ACCAG
1 ACCAG
53447518 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 15 0.20
27 57 0.77
28 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
ACCAGAACAGATAATGTGGCAGAGCC
Found at i:53448959 original size:24 final size:24
Alignment explanation
Indices: 53448930--53448981 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
53448920 CAACACTATC
*
53448930 CTCCCTTATCAGTTCCTAAATCCT
1 CTCCCTTATCAGCTCCTAAATCCT
53448954 CTCCCTTATCAGCTCCTAAATCCT
1 CTCCCTTATCAGCTCCTAAATCCT
53448978 CTCC
1 CTCC
53448982 TGACAGACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.42, G:0.04, T:0.35
Consensus pattern (24 bp):
CTCCCTTATCAGCTCCTAAATCCT
Found at i:53454517 original size:48 final size:47
Alignment explanation
Indices: 53454399--53454635 Score: 287
Period size: 48 Copynumber: 4.9 Consensus size: 47
53454389 AAAAGGGTAA
* ** *
53454399 AATGCCGATGCCATGTCCCGGACATGGTCTTACACTAGCTC-TATACATC
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACT-GCTCACATA-A-C
* *
53454448 AGTGCCGATGCCATGTCCCAAACATGGTCTTACACTGCCTCACATAAC
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTG-CTCACATAAC
* **
53454496 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCGCATATT
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACT-GCTCACATAAC
* * *
53454544 GATGCCGATGCCATGTTCCAGACATGGTCTTACACTAGCTCTCATAAC
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACT-GCTCACATAAC
*
53454592 AATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACA
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACT-GCTCACA
53454636 CATAACCCTA
Statistics
Matches: 165, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
48 124 0.75
49 38 0.23
50 3 0.02
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (47 bp):
AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGCTCACATAAC
Found at i:53454590 original size:96 final size:97
Alignment explanation
Indices: 53454399--53454632 Score: 330
Period size: 96 Copynumber: 2.4 Consensus size: 97
53454389 AAAAGGGTAA
* ** * *
53454399 AATGCCGATGCCATGTCCCGGACATGGTCTTACACTAGCTCTATACATCAGTGCCGATGCCATGT
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCCATACATCAGTGCCGATGCCATGT
53454464 CCCAAACATGGTCTTACACTGCCTCACATAAC
66 CCCAAACATGGTCTTACACTGCCTCACATAAC
* *
53454496 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCGCATA-TTGA-TGCCGATGCCATG
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTC-CATACATCAGTGCCGATGCCATG
* * *
53454559 TTCCAGACATGGTCTTACACTAG-CTCTCATAAC
65 TCCCAAACATGGTCTTACACT-GCCTCACATAAC
*
53454592 AATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTC
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTC
53454633 ACACATAACC
Statistics
Matches: 124, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
96 81 0.65
97 40 0.32
98 3 0.02
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (97 bp):
AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCCATACATCAGTGCCGATGCCATGT
CCCAAACATGGTCTTACACTGCCTCACATAAC
Found at i:53469396 original size:2 final size:2
Alignment explanation
Indices: 53469389--53469431 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
53469379 TCACTATAAG
53469389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53469431 A
1 A
53469432 AAGAATGAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53469743 original size:20 final size:20
Alignment explanation
Indices: 53469720--53469761 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
53469710 AGAAGTTAGC
*
53469720 TAGCTGTTAAGTAAAGTAGT
1 TAGCTATTAAGTAAAGTAGT
* *
53469740 TAGCTATTAGGTGAAGTAGT
1 TAGCTATTAAGTAAAGTAGT
53469760 TA
1 TA
53469762 CTTCTAGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (20 bp):
TAGCTATTAAGTAAAGTAGT
Found at i:53484720 original size:23 final size:23
Alignment explanation
Indices: 53484691--53484768 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
53484681 CTGATGAGCA
53484691 GTAAGCTTTATCGAGCTGAAACG
1 GTAAGCTTTATCGAGCTGAAACG
** * *
53484714 GTAAGCTCCATTGAGCTG-AACA
1 GTAAGCTTTATCGAGCTGAAACG
*
53484736 GTAAACTCTTA-CGAGCTGATATATCG
1 GTAAGCT-TTATCGAGCTGA-A-A-CG
53484762 GTAAGCT
1 GTAAGCT
53484769 CATACGAGCT
Statistics
Matches: 40, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
22 15 0.38
23 16 0.40
24 1 0.03
25 1 0.03
26 7 0.17
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (23 bp):
GTAAGCTTTATCGAGCTGAAACG
Found at i:53484778 original size:48 final size:45
Alignment explanation
Indices: 53484689--53484779 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 45
53484679 AGCTGATGAG
* *
53484689 CAGTAAGCTTTATCGAGCTGAAACGGTAAGCTCCATTGAGCTGAA
1 CAGTAAACTTTATCGAGCTGAAACGGTAAGCTCCATCGAGCTGAA
53484734 CAGTAAACTCTTA-CGAGCTGATATATCGGTAAGCT-CATACGAGCTG
1 CAGTAAACT-TTATCGAGCTGA-A-A-CGGTAAGCTCCAT-CGAGCTG
53484780 TGGTGAGTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
45 16 0.41
46 4 0.10
47 4 0.10
48 15 0.38
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (45 bp):
CAGTAAACTTTATCGAGCTGAAACGGTAAGCTCCATCGAGCTGAA
Found at i:53485683 original size:19 final size:20
Alignment explanation
Indices: 53485657--53485706 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
53485647 TTTATTTTAT
53485657 TATAATTATGATTTTAAACA
1 TATAATTATGATTTTAAACA
** * *
53485677 T-TAATTACCATTTTAACCT
1 TATAATTATGATTTTAAACA
53485696 TATAATTATGA
1 TATAATTATGA
53485707 CTTATAAATC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (20 bp):
TATAATTATGATTTTAAACA
Found at i:53497466 original size:48 final size:49
Alignment explanation
Indices: 53497368--53497592 Score: 161
Period size: 48 Copynumber: 4.6 Consensus size: 49
53497358 TAGGGTGCCA
* * * * *
53497368 ATGCCATATCCCAGACATGGTCTTACATTGGGC--TCATATC-TCAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGACTATCATATCGT--AGCCG
*
53497416 ATGCCATGTCCCAGACATGGTCTTACACT-GACTATCATTTCGTAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGACTATCATATCGTAGCCG
* *
53497464 ATG-TATGTCCCA-AGCAT-GTCTTACACTAGCACTTGTC-TCGATGCCG-ATGCCG
1 ATGCCATGTCCCAGA-CATGGTCTTACACTAG-AC-TATCAT--AT--CGTA-GCCG
* * *
53497516 ATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTTATAAT-GTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGACTATCAT-ATCGTAGCCG
53497564 ATG-CATGTCCCAGACAT-GTCTTACACTAG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG
53497593 CCCACAACAA
Statistics
Matches: 147, Mismatches: 13, Indels: 36
0.75 0.07 0.18
Matches are distributed among these distances:
46 23 0.16
47 28 0.19
48 45 0.31
49 9 0.06
50 2 0.01
51 5 0.03
52 11 0.07
53 11 0.07
54 13 0.09
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGACTATCATATCGTAGCCG
Found at i:53497564 original size:100 final size:100
Alignment explanation
Indices: 53497414--53497593 Score: 267
Period size: 100 Copynumber: 1.8 Consensus size: 100
53497404 TATCTCAAGT
* *
53497414 CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATTTCGTAGCCGATGTATGTCCCA-AG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATATCGTAGCCGATGCATGTCCCAGA-
53497478 CATGTCTTACACTAGCACTTGTCTCGATGCCGATGC
65 CATGTCTTACACTAGCACTTGTCTCGATGCCGATGC
* * *
53497514 CGATGCCATGTCCCAGACATGGTCTTACACT-AGCTCTTATAAT-GTGGCCGATGCATGTCCCAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGA-CTATCAT-ATCGTAGCCGATGCATGTCCCAG
53497577 ACATGTCTTACACTAGC
64 ACATGTCTTACACTAGC
53497594 CCACAACAAC
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 69 0.96
101 2 0.03
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (100 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATATCGTAGCCGATGCATGTCCCAGAC
ATGTCTTACACTAGCACTTGTCTCGATGCCGATGC
Found at i:53498017 original size:30 final size:30
Alignment explanation
Indices: 53497936--53498019 Score: 150
Period size: 30 Copynumber: 2.8 Consensus size: 30
53497926 CATCTTCGGT
*
53497936 AAAATGACCATTTTGCCCCTAAACTTTGAC
1 AAAATGACCATTTTGCCCCTAGACTTTGAC
53497966 AAAATGACCATTTTGCCCCTAGACTTTGAC
1 AAAATGACCATTTTGCCCCTAGACTTTGAC
*
53497996 AAAATGACCATTTTACCCCTAGAC
1 AAAATGACCATTTTGCCCCTAGAC
53498020 CCGAAAATTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (30 bp):
AAAATGACCATTTTGCCCCTAGACTTTGAC
Found at i:53498959 original size:22 final size:22
Alignment explanation
Indices: 53498903--53498963 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
53498893 TTTTGTAAGT
53498903 TTTGGTGCTA-TTTTGGTGTTC
1 TTTGGTGCTATTTTTGGTGTTC
* * *
53498924 TTGGTGATGCTATTTTTTGTGTTG
1 TT--TGGTGCTATTTTTGGTGTTC
53498948 TTTGGTGCTATTTTTG
1 TTTGGTGCTATTTTTG
53498964 TGGAGTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.06
22 12 0.38
23 7 0.22
24 11 0.34
ACGTcount: A:0.07, C:0.07, G:0.28, T:0.59
Consensus pattern (22 bp):
TTTGGTGCTATTTTTGGTGTTC
Found at i:53498971 original size:21 final size:22
Alignment explanation
Indices: 53498931--53498971 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
53498921 TTCTTGGTGA
**
53498931 TGCTATTTTTTGTGTTGTTTGG
1 TGCTATTTTTTGTGGAGTTTGG
53498953 TGCTA-TTTTTGTGGAGTTT
1 TGCTATTTTTTGTGGAGTTT
53498972 TTATGCCGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.07, C:0.05, G:0.27, T:0.61
Consensus pattern (22 bp):
TGCTATTTTTTGTGGAGTTTGG
Found at i:53498994 original size:11 final size:11
Alignment explanation
Indices: 53498980--53499004 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53498970 TTTTATGCCG
53498980 TTTGGTGTTGT
1 TTTGGTGTTGT
53498991 TTTGGTGTTGT
1 TTTGGTGTTGT
53499002 TTT
1 TTT
53499005 TATACTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (11 bp):
TTTGGTGTTGT
Found at i:53499288 original size:15 final size:15
Alignment explanation
Indices: 53499265--53499295 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53499255 ATAATAGAAC
53499265 TAAAAGTACAGCTTT
1 TAAAAGTACAGCTTT
*
53499280 TAAAGGTACAGCTTT
1 TAAAAGTACAGCTTT
53499295 T
1 T
53499296 TCTAATATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (15 bp):
TAAAAGTACAGCTTT
Found at i:53503821 original size:16 final size:16
Alignment explanation
Indices: 53503800--53503830 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53503790 CAGATTTCAG
53503800 AAAAGAAAAGAAAAAA
1 AAAAGAAAAGAAAAAA
*
53503816 AAAAGAAAGGAAAAA
1 AAAAGAAAAGAAAAA
53503831 CCCATAAGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAA
Found at i:53505391 original size:20 final size:20
Alignment explanation
Indices: 53505354--53505391 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53505344 AATAAATTTT
*
53505354 TTTATATTTTAGATAAAACA
1 TTTATATTTTAGAAAAAACA
53505374 TTTATAATTTTA-AAAAAA
1 TTTAT-ATTTTAGAAAAAA
53505392 TAAAAACTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
TTTATATTTTAGAAAAAACA
Found at i:53513113 original size:12 final size:12
Alignment explanation
Indices: 53513096--53513125 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
53513086 CCTCACACGC
53513096 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
53513108 CCGTGTGCTAGG
1 CCGTGTGCCAGG
53513120 CCGTGT
1 CCGTGT
53513126 AACAACCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:53516878 original size:61 final size:61
Alignment explanation
Indices: 53516803--53517184 Score: 426
Period size: 61 Copynumber: 6.3 Consensus size: 61
53516793 TACTCTTCAT
* * *
53516803 AAAGGCTATCCTTTACATTTAGTACTCACCATAAAGGCTTTCTTATCTAGAGTTGTTCCAC
1 AAAGGCTATCCTTTACATTTAGTACTCACCACAAAGGCTTTCCTATCTAGAGTTGTGCCAC
* * * * *
53516864 AAAGGCTATCCTTTACATTTAGTACT-AGCCACAAAGGCTTTCCTGTCGAGATTTATGCCTC
1 AAAGGCTATCCTTTACATTTAGTACTCA-CCACAAAGGCTTTCCTATCTAGAGTTGTGCCAC
* * * * * * * * * *
53516925 AAAGGCTGTCCTTTACATTAAGTACTCGCTACAAAGGCTTTCTTGTATAGATTTGTACCTC
1 AAAGGCTATCCTTTACATTTAGTACTCACCACAAAGGCTTTCCTATCTAGAGTTGTGCCAC
* * * * * *
53516986 AAAGGCTATCCTTTACGTTCAGTACT-AGCCACAAAGGCTTTCTTATCCAAATTTGTGCCAC
1 AAAGGCTATCCTTTACATTTAGTACTCA-CCACAAAGGCTTTCCTATCTAGAGTTGTGCCAC
* * * * *
53517047 GAAGGCTATCCTTTACATTCAGTACTCGCCGCAAAGGCTTTCCTATCTAGAGTTGTGCCTC
1 AAAGGCTATCCTTTACATTTAGTACTCACCACAAAGGCTTTCCTATCTAGAGTTGTGCCAC
* * ** *
53517108 AAAGGTTATCCTTTACATTTAGTATTTGCCACAAAGGCTTTCCTATCTAGAGTTGTACCAC
1 AAAGGCTATCCTTTACATTTAGTACTCACCACAAAGGCTTTCCTATCTAGAGTTGTGCCAC
53517169 AAAGGCTATCCTTTAC
1 AAAGGCTATCCTTTAC
53517185 TGGTGTTTCG
Statistics
Matches: 271, Mismatches: 46, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
60 1 0.00
61 270 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (61 bp):
AAAGGCTATCCTTTACATTTAGTACTCACCACAAAGGCTTTCCTATCTAGAGTTGTGCCAC
Found at i:53516951 original size:122 final size:122
Alignment explanation
Indices: 53516803--53517184 Score: 503
Period size: 122 Copynumber: 3.1 Consensus size: 122
53516793 TACTCTTCAT
* * * * *
53516803 AAAGGCTATCCTTTACATTTAGTACTCACCATAAAGGCTTTCTTATCTAGAGTTGTTCCACAAAG
1 AAAGGCTATCCTTTACATTAAGTACTCGCCACAAAGGCTTTCTTATCTAGAGTTGTACCTCAAAG
* * * *
53516868 GCTATCCTTTACATTTAGTACTAGCCACAAAGGCTTTCCTGTCGAGATTTATGCCTC
66 GCTATCCTTTACATTTAGTACTAGCCACAAAGGCTTTCCTATCCAGATTTGTGCCAC
* * * * *
53516925 AAAGGCTGTCCTTTACATTAAGTACTCGCTACAAAGGCTTTCTTGTATAGATTTGTACCTCAAAG
1 AAAGGCTATCCTTTACATTAAGTACTCGCCACAAAGGCTTTCTTATCTAGAGTTGTACCTCAAAG
* * * *
53516990 GCTATCCTTTACGTTCAGTACTAGCCACAAAGGCTTTCTTATCCAAATTTGTGCCAC
66 GCTATCCTTTACATTTAGTACTAGCCACAAAGGCTTTCCTATCCAGATTTGTGCCAC
* * * * *
53517047 GAAGGCTATCCTTTACATTCAGTACTCGCCGCAAAGGCTTTCCTATCTAGAGTTGTGCCTCAAAG
1 AAAGGCTATCCTTTACATTAAGTACTCGCCACAAAGGCTTTCTTATCTAGAGTTGTACCTCAAAG
* * * * * *
53517112 GTTATCCTTTACATTTAGTATTTGCCACAAAGGCTTTCCTATCTAGAGTTGTACCAC
66 GCTATCCTTTACATTTAGTACTAGCCACAAAGGCTTTCCTATCCAGATTTGTGCCAC
53517169 AAAGGCTATCCTTTAC
1 AAAGGCTATCCTTTAC
53517185 TGGTGTTTCG
Statistics
Matches: 221, Mismatches: 39, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
122 221 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (122 bp):
AAAGGCTATCCTTTACATTAAGTACTCGCCACAAAGGCTTTCTTATCTAGAGTTGTACCTCAAAG
GCTATCCTTTACATTTAGTACTAGCCACAAAGGCTTTCCTATCCAGATTTGTGCCAC
Found at i:53517027 original size:183 final size:183
Alignment explanation
Indices: 53516803--53517184 Score: 514
Period size: 183 Copynumber: 2.1 Consensus size: 183
53516793 TACTCTTCAT
* * * * *
53516803 AAAGGCTATCCTTTACATTTAGTACTCACCATAAAGGCTTTCTTATCTAGAGTTGTTCCACAAAG
1 AAAGGCTATCCTTTACATTCAGTACTCACCACAAAGGCTTTCTTATCCAAAGTTGTGCCACAAAG
* * * *
53516868 GCTATCCTTTACATTTAGTACTAGCCACAAAGGCTTTCCTGTCGAGATTTATGCCTCAAAGGCTG
66 GCTATCCTTTACATTCAGTACTAGCCACAAAGGCTTTCCTATCGAGAGTTATGCCTCAAAGGCTA
* * * * *
53516933 TCCTTTACATTAAGTACTCGCTACAAAGGCTTTCTTGTATAGATTTGTACCTC
131 TCCTTTACATTAAGTACTCGCCACAAAGGCTTTCCTATATAGAGTTGTACCAC
* * *
53516986 AAAGGCTATCCTTTACGTTCAGTACT-AGCCACAAAGGCTTTCTTATCCAAATTTGTGCCACGAA
1 AAAGGCTATCCTTTACATTCAGTACTCA-CCACAAAGGCTTTCTTATCCAAAGTTGTGCCACAAA
* * * * *
53517050 GGCTATCCTTTACATTCAGTACTCGCCGCAAAGGCTTTCCTATCTAGAGTTGTGCCTCAAAGGTT
65 GGCTATCCTTTACATTCAGTACTAGCCACAAAGGCTTTCCTATCGAGAGTTATGCCTCAAAGGCT
* * * *
53517115 ATCCTTTACATTTAGTATTTGCCACAAAGGCTTTCCTATCTAGAGTTGTACCAC
130 ATCCTTTACATTAAGTACTCGCCACAAAGGCTTTCCTATATAGAGTTGTACCAC
53517169 AAAGGCTATCCTTTAC
1 AAAGGCTATCCTTTAC
53517185 TGGTGTTTCG
Statistics
Matches: 172, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
182 1 0.01
183 171 0.99
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (183 bp):
AAAGGCTATCCTTTACATTCAGTACTCACCACAAAGGCTTTCTTATCCAAAGTTGTGCCACAAAG
GCTATCCTTTACATTCAGTACTAGCCACAAAGGCTTTCCTATCGAGAGTTATGCCTCAAAGGCTA
TCCTTTACATTAAGTACTCGCCACAAAGGCTTTCCTATATAGAGTTGTACCAC
Found at i:53517111 original size:29 final size:29
Alignment explanation
Indices: 53517078--53517180 Score: 100
Period size: 29 Copynumber: 3.4 Consensus size: 29
53517068 GTACTCGCCG
*
53517078 CAAAGGCTTTCCTATCTAGAGTTGTGCCT
1 CAAAGGCTTTCCTATCTAGAGTTGTGCCA
* ** *
53517107 CAAAGG-TTATCCTTTACATTTAGTATTTGCCA
1 CAAAGGCTT-TCCTAT-C-TAGAGT-TGTGCCA
*
53517139 CAAAGGCTTTCCTATCTAGAGTTGTACCA
1 CAAAGGCTTTCCTATCTAGAGTTGTGCCA
*
53517168 CAAAGGCTATCCT
1 CAAAGGCTTTCCT
53517181 TTACTGGTGT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
28 2 0.03
29 28 0.48
30 5 0.09
31 5 0.09
32 16 0.28
33 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (29 bp):
CAAAGGCTTTCCTATCTAGAGTTGTGCCA
Found at i:53517400 original size:53 final size:53
Alignment explanation
Indices: 53517294--53517428 Score: 134
Period size: 53 Copynumber: 2.6 Consensus size: 53
53517284 CCTTGATTTT
* * * **
53517294 TTCC-ATATGATGTCATAACCCATTTGTTACAGTTTTACATAATATTTTATTC
1 TTCCTATATGATGTCATAACCCACTAGTTACAGTCTTACATAATATGGTATTC
* * *
53517346 TTCCTATATGATGTCATAACCCACCAGTTAC-GATCTTACATGATATGGTCTTC
1 TTCCTATATGATGTCATAACCCACTAGTTACAG-TCTTACATAATATGGTATTC
*
53517399 TT-CTCATATGAT-TCCATAAGCCACTAGTTA
1 TTCCT-ATATGATGT-CATAACCCACTAGTTA
53517429 TGGTCTTAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
52 8 0.12
53 61 0.88
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.40
Consensus pattern (53 bp):
TTCCTATATGATGTCATAACCCACTAGTTACAGTCTTACATAATATGGTATTC
Found at i:53525500 original size:21 final size:20
Alignment explanation
Indices: 53525470--53525514 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
53525460 ATAGTTGAAA
**
53525470 AAAAAATTAATACTTTGTTTT
1 AAAAAATTAA-ACTTTCCTTT
*
53525491 AAAAATTTAAACTTTCCTTT
1 AAAAAATTAAACTTTCCTTT
53525511 AAAA
1 AAAA
53525515 TGACTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (20 bp):
AAAAAATTAAACTTTCCTTT
Found at i:53525740 original size:18 final size:18
Alignment explanation
Indices: 53525716--53525751 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
53525706 GTCTATGGCA
*
53525716 AAAAAAAAAAAGATAGAAG
1 AAAAAAAAGAA-ATAGAAG
53525735 AAAAAAAAGAAATAGAA
1 AAAAAAAAGAAATAGAA
53525752 TGCTTGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAAAAAGAAATAGAAG
Found at i:53526415 original size:42 final size:42
Alignment explanation
Indices: 53526363--53526834 Score: 615
Period size: 42 Copynumber: 11.3 Consensus size: 42
53526353 CTTCATATAC
* * * * *
53526363 AATGAAATGAAAAGTAAATGGACCTCCACTCCAGAGCCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
*
53526405 AATGCAATGAAAAGTAAACGGACCTCCACACCTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * **
53526447 AATGCAATGAAAAGTCAATAGACCTCCACACCTGGATCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * *
53526489 AATGCAATGAATAGTGAAT-GAACTCCACACCTGAGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * * *
53526530 AATGTAATGAAAAGCAAGTGGACCTCCACATCTGGGCCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
*
53526572 AATGCAATGAAAAGTAAATGGACCTCTACACCTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * *
53526614 AATGCAATGAAAAGTTAATGGAACTCTACACCTAGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * *
53526656 AATGCAATAAAAAGTAAATGGATCTCCACACATGTGCC-CTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTC-TA
*
53526698 AATGCAATGAAAAGTAAATGGAACTCCACACCTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
53526740 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * **
53526782 AATGCAATAAAAAGTAAATGGACCTCTAGGCCTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
*
53526824 AATGTAATGAA
1 AATGCAATGAA
53526835 TGTTTTCCTT
Statistics
Matches: 374, Mismatches: 53, Indels: 6
0.86 0.12 0.01
Matches are distributed among these distances:
41 33 0.09
42 340 0.91
43 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (42 bp):
AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
Found at i:53528811 original size:40 final size:40
Alignment explanation
Indices: 53528756--53528947 Score: 305
Period size: 40 Copynumber: 4.8 Consensus size: 40
53528746 CGGATGATAA
*
53528756 CCGGGCTAAGTCCCGAAGGCATTTATGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
* *
53528796 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
53528836 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
* *
53528876 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCA-AAT
* *
53528916 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
53528948 AGCTATATCC
Statistics
Matches: 141, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 139 0.99
41 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
Found at i:53535375 original size:14 final size:15
Alignment explanation
Indices: 53535349--53535382 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
53535339 GAAAATAAAG
53535349 AAGAAGCAAAAAGAA
1 AAGAAGCAAAAAGAA
*
53535364 TAGAAG-AAAAAGAA
1 AAGAAGCAAAAAGAA
53535378 AAGAA
1 AAGAA
53535383 AAGTGAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.03
Consensus pattern (15 bp):
AAGAAGCAAAAAGAA
Found at i:53535788 original size:47 final size:48
Alignment explanation
Indices: 53535730--53535861 Score: 203
Period size: 47 Copynumber: 2.8 Consensus size: 48
53535720 CACAATCGAT
*
53535730 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCTC-A
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCTA
* * *
53535777 GAGTACATATACCATGGCCCGTAGCCAAATCAAGGTAACTCCTCTCTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCTA
* *
53535825 AAATACCTATACCATAGCCCGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
53535862 TCATTCGCAC
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
47 42 0.55
48 34 0.45
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCTA
Found at i:53540500 original size:7 final size:7
Alignment explanation
Indices: 53540466--53540511 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
53540456 AAGAGAATGA
*
53540466 ATGAGGA
1 ATGAGGG
53540473 ATGAGGG
1 ATGAGGG
*
53540480 ATGAGTG
1 ATGAGGG
*
53540487 ATTAGGG
1 ATGAGGG
*
53540494 ATAAGGG
1 ATGAGGG
53540501 ATGAGGG
1 ATGAGGG
53540508 ATGA
1 ATGA
53540512 TTAGAAATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.46, T:0.20
Consensus pattern (7 bp):
ATGAGGG
Found at i:53544714 original size:27 final size:27
Alignment explanation
Indices: 53544681--53544885 Score: 252
Period size: 27 Copynumber: 7.6 Consensus size: 27
53544671 TAAATTGTAC
53544681 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
53544708 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
53544735 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
53544761 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
53544789 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
53544817 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
53544844 AGCACTAAGTGTGCGAGTTGA-TGATAT
1 AGCACTAAGTGTGCGATTTGACT-ATGT
*
53544871 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
53544886 GACTCAATAT
Statistics
Matches: 155, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
26 1 0.01
27 131 0.85
28 23 0.15
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:53555497 original size:27 final size:28
Alignment explanation
Indices: 53555466--53555543 Score: 124
Period size: 27 Copynumber: 2.9 Consensus size: 28
53555456 AATCTCATAT
* *
53555466 CTGTAGGCTAGAATTACTGAAATATC-C
1 CTGTAGGGTAGAATTACTGAAATAGCTC
53555493 CTGTAGGGTAGAATTACTGAAAT-GCTC
1 CTGTAGGGTAGAATTACTGAAATAGCTC
53555520 CTGTAGGGTAGAATTACTGAAATA
1 CTGTAGGGTAGAATTACTGAAATA
53555544 CCCATGGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 1 0.02
27 46 0.98
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (28 bp):
CTGTAGGGTAGAATTACTGAAATAGCTC
Found at i:53555561 original size:27 final size:27
Alignment explanation
Indices: 53555531--53555615 Score: 111
Period size: 27 Copynumber: 3.2 Consensus size: 27
53555521 TGTAGGGTAG
53555531 AATTACTGAAATACCCATGGTTTACAA
1 AATTACTGAAATACCCATGGTTTACAA
*
53555558 AATTACTG-AATACCCTTGGTTTACAA
1 AATTACTGAAATACCCATGGTTTACAA
* **
53555584 AATTAGC-AAAATACCCATGGTTTGTAA
1 AATTA-CTGAAATACCCATGGTTTACAA
53555611 AATTA
1 AATTA
53555616 ACAAAATACC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
26 22 0.43
27 29 0.57
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (27 bp):
AATTACTGAAATACCCATGGTTTACAA
Found at i:53555620 original size:27 final size:26
Alignment explanation
Indices: 53555582--53555881 Score: 174
Period size: 27 Copynumber: 11.0 Consensus size: 26
53555572 CTTGGTTTAC
* *
53555582 AAAATTAGCAAAATACCCATGGTTTGT
1 AAAATTATCAAAATACCC-TGATTTGT
*
53555609 AAAATTAACAAAATACCTCTGATTTGT
1 AAAATTATCAAAATACC-CTGATTTGT
* * * * *
53555636 GAAATTATTAAAATACCTTCGACTTAT
1 AAAATTATCAAAATACCCT-GATTTGT
* *
53555663 AAAATTACCAAAATACCCTCGACTTGT
1 AAAATTATCAAAATACCCT-GATTTGT
* *
53555690 AAAATTATCGAAATACCCTCGATTTTT
1 AAAATTATCAAAATACCCT-GATTTGT
*
53555717 AAAATTATCAAAATACCCCTGATTTGG
1 AAAATTATCAAAATA-CCCTGATTTGT
* * * * *
53555744 AAAATTACCGAAATATCCTTAATTTGG
1 AAAATTATCAAAATA-CCCTGATTTGT
* * **
53555771 AAGATTAT-AGAAATACCCCTAATTTAC
1 AAAATTATCA-AAATA-CCCTGATTTGT
* **
53555798 AAAATTA-CAGAAATAACCTTGACTTTCA
1 AAAATTATCA-AAAT-ACCCTGA-TTTGT
* *
53555826 AAAATTA-CAAAAAATACCATTGGTTTGT
1 AAAATTATC--AAAATACC-CTGATTTGT
* *
53555854 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTATCAAAATACCC-TGATTTGT
53555881 A
1 A
53555882 GATTTACCAA
Statistics
Matches: 220, Mismatches: 41, Indels: 24
0.77 0.14 0.08
Matches are distributed among these distances:
26 1 0.00
27 180 0.82
28 30 0.14
29 8 0.04
30 1 0.00
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (26 bp):
AAAATTATCAAAATACCCTGATTTGT
Found at i:53555675 original size:81 final size:81
Alignment explanation
Indices: 53555582--53555733 Score: 200
Period size: 81 Copynumber: 1.9 Consensus size: 81
53555572 CTTGGTTTAC
* ** * *
53555582 AAAATTAGCAAAATACCCAT-GGTTTGTAAAATTAACAAAATA-CCTCTGATTTGTGAAATTATT
1 AAAATTACCAAAATACCC-TCGACTTGTAAAATTAACAAAATACCCTC-GATTTGTAAAATTATC
53555645 AAAATACCTTCGACTTAT
64 AAAATACCTTCGACTTAT
* * *
53555663 AAAATTACCAAAATACCCTCGACTTGTAAAATTATCGAAATACCCTCGATTTTTAAAATTATCAA
1 AAAATTACCAAAATACCCTCGACTTGTAAAATTAACAAAATACCCTCGATTTGTAAAATTATCAA
53555728 AATACC
66 AATACC
53555734 CCTGATTTGG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 1 0.02
81 56 0.92
82 4 0.07
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.32
Consensus pattern (81 bp):
AAAATTACCAAAATACCCTCGACTTGTAAAATTAACAAAATACCCTCGATTTGTAAAATTATCAA
AATACCTTCGACTTAT
Found at i:53555888 original size:27 final size:27
Alignment explanation
Indices: 53555566--53555901 Score: 119
Period size: 27 Copynumber: 12.4 Consensus size: 27
53555556 AAAATTACTG
* ** *
53555566 AATACCCTTGGTTTACAAAATTAGCAA
1 AATACCATTGGTTTGTAAAATTACCAA
*
53555593 AATACCCA-TGGTTTGTAAAATTAACAA
1 AATA-CCATTGGTTTGTAAAATTACCAA
* * **
53555620 AATACC-TCTGATTTGTGAAATTATTAA
1 AATACCAT-TGGTTTGTAAAATTACCAA
** *
53555647 AATACC-TTCGACTTATAAAATTACCAA
1 AATACCATT-GGTTTGTAAAATTACCAA
* * ** * *
53555674 AATACCCTCGACTTGTAAAATTATCGA
1 AATACCATTGGTTTGTAAAATTACCAA
* * * * *
53555701 AATACCCTCGATTTTTAAAATTATCAA
1 AATACCATTGGTTTGTAAAATTACCAA
** * * *
53555728 AATACCCCTGATTTGGAAAATTACCGA
1 AATACCATTGGTTTGTAAAATTACCAA
** * * *
53555755 AATATCC-TTAATTTGGAAGATTA-TAGA
1 AATA-CCATTGGTTTGTAAAATTACCA-A
** ** **
53555782 AATACCCCTAATTTACAAAATTA-CAGA
1 AATACCATTGGTTTGTAAAATTACCA-A
* ** *
53555809 AATAACC-TTGACTTTCAAAAATTACAAAA
1 AAT-ACCATTG-GTTTGTAAAATTAC-CAA
53555838 AATACCATTGGTTTGTAAAATTACCAA
1 AATACCATTGGTTTGTAAAATTACCAA
* * *
53555865 AATACCCTTGGTTTGTAGATTTACCAA
1 AATACCATTGGTTTGTAAAATTACCAA
*
53555892 AACACCATTG
1 AATACCATTG
53555902 TAGGGTGAAA
Statistics
Matches: 245, Mismatches: 51, Indels: 26
0.76 0.16 0.08
Matches are distributed among these distances:
26 5 0.02
27 200 0.82
28 32 0.13
29 7 0.03
30 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.32
Consensus pattern (27 bp):
AATACCATTGGTTTGTAAAATTACCAA
Found at i:53556196 original size:41 final size:41
Alignment explanation
Indices: 53556139--53556220 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
53556129 GGAGGAAGAA
*
53556139 ATTAAGGATCGCATGGTTGCTTGACAACCGTTGATCCACCG
1 ATTAAGGATCGCATGGTTGCTTGACAACCGTGGATCCACCG
*
53556180 ATTAAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
1 ATTAAGGATCGCATGGTTGCTTGACAACCGTGGATCCACCG
53556221 GTGGCTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (41 bp):
ATTAAGGATCGCATGGTTGCTTGACAACCGTGGATCCACCG
Found at i:53556394 original size:22 final size:22
Alignment explanation
Indices: 53556366--53556426 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
53556356 ATTATTCTGA
*
53556366 ATATGGCTTTGCGCCAACCTAC
1 ATATGGCTCTGCGCCAACCTAC
*
53556388 ATATGGCTCTGTGCCAACCTGA-
1 ATATGGCTCTGCGCCAACCT-AC
* *
53556410 TTATGGCTCTGTGCCAA
1 ATATGGCTCTGCGCCAA
53556427 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (22 bp):
ATATGGCTCTGCGCCAACCTAC
Found at i:53558053 original size:69 final size:69
Alignment explanation
Indices: 53557942--53558123 Score: 269
Period size: 69 Copynumber: 2.6 Consensus size: 69
53557932 GAATCTATTG
53557942 GCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTTGGCTACAATAT-AGTGGTAG
1 GCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTTGGCTAC-ATATCAGTGGTAG
53558006 CTTCA
65 CTTCA
*
53558011 GCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTTGGCTACATCTCAGTGGTAGC
1 GCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTTGGCTACATATCAGTGGTAGC
*
53558076 TTCG
66 TTCA
* * ** *
53558080 GCTACAGT-ACAATGGTAGCTTCGGCTACGTTACAGTGATAGCTT
1 GCTACA-TCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTT
53558124 CAGCTATATT
Statistics
Matches: 104, Mismatches: 7, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
68 3 0.03
69 100 0.96
70 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (69 bp):
GCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTTGGCTACATATCAGTGGTAGC
TTCA
Found at i:53558135 original size:23 final size:23
Alignment explanation
Indices: 53557941--53558136 Score: 227
Period size: 23 Copynumber: 8.5 Consensus size: 23
53557931 GGAATCTATT
53557941 GGCTACATCT-CAGTGGTAGCTTC
1 GGCTACAT-TACAGTGGTAGCTTC
* *
53557964 GGCTACAATACAGTGGTAGCTTT
1 GGCTACATTACAGTGGTAGCTTC
* *
53557987 GGCTACAATATAGTGGTAGCTTC
1 GGCTACATTACAGTGGTAGCTTC
*
53558010 AGCTACATCT-CAGTGGTAGCTTC
1 GGCTACAT-TACAGTGGTAGCTTC
* *
53558033 GGCTACAATACAGTGGTAGCTTT
1 GGCTACATTACAGTGGTAGCTTC
53558056 GGCTACATCT-CAGTGGTAGCTTC
1 GGCTACAT-TACAGTGGTAGCTTC
* *
53558079 GGCTACAGTACAATGGTAGCTTC
1 GGCTACATTACAGTGGTAGCTTC
* *
53558102 GGCTACGTTACAGTGATAGCTTC
1 GGCTACATTACAGTGGTAGCTTC
* *
53558125 AGCTATATTACA
1 GGCTACATTACA
53558137 ATGTGGCACT
Statistics
Matches: 147, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
22 3 0.02
23 142 0.97
24 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (23 bp):
GGCTACATTACAGTGGTAGCTTC
Found at i:53560988 original size:8 final size:8
Alignment explanation
Indices: 53560977--53561011 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
53560967 AACGAATGGA
*
53560977 TGAATGCT
1 TGAATGAT
53560985 TGAATGAT
1 TGAATGAT
53560993 TGAATGAT
1 TGAATGAT
53561001 TGAATGAT
1 TGAATGAT
53561009 TGA
1 TGA
53561012 TTGAAATTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (8 bp):
TGAATGAT
Found at i:53560989 original size:16 final size:17
Alignment explanation
Indices: 53560970--53561011 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
53560960 ATGAGTGAAC
*
53560970 GAATGGA-TGAATGCTT
1 GAATGGATTGAATGATT
53560986 GAAT-GATTGAATGATT
1 GAATGGATTGAATGATT
53561002 GAAT-GATTGA
1 GAATGGATTGA
53561012 TTGAAATTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (17 bp):
GAATGGATTGAATGATT
Found at i:53565644 original size:33 final size:34
Alignment explanation
Indices: 53565598--53565668 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 34
53565588 ACAGTGCATG
* * *
53565598 CAGTAACAGTCT-GGACTTGAGCCCTATTCAGTAT
1 CAGTAACAATCTGGGACTT-AGCCCTATACAGTAA
*
53565632 CAGT-ACAATCTGGGCCTTAGCCCTATACAGTAA
1 CAGTAACAATCTGGGACTTAGCCCTATACAGTAA
53565665 CAGT
1 CAGT
53565669 GTGGCCCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 23 0.72
34 9 0.28
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (34 bp):
CAGTAACAATCTGGGACTTAGCCCTATACAGTAA
Found at i:53566065 original size:26 final size:27
Alignment explanation
Indices: 53566032--53566165 Score: 82
Period size: 27 Copynumber: 5.0 Consensus size: 27
53566022 TCATACAGAA
53566032 CATA-AGGGCATAATC-GTCATTTTAC
1 CATACAGGGCATAATCGGTCATTTTAC
* *
53566057 CATACAGGG-GTATTACGGTCATTTTAC
1 CATACAGGGCATAAT-CGGTCATTTTAC
* * *
53566084 CCTTCAGGGACATGA-CGGTCATTTTAC
1 CATACAGGG-CATAATCGGTCATTTTAC
* * * *
53566111 CCTACAGGG-GTATTACGGTTATTTTAC
1 CATACAGGGCATAAT-CGGTCATTTTAC
* * *
53566138 CCTACAGGG-GTATTACGGTCATTTTAC
1 CATACAGGGCATAAT-CGGTCATTTTAC
53566165 C
1 C
53566166 CTATAGGGGT
Statistics
Matches: 89, Mismatches: 13, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
25 8 0.09
26 5 0.06
27 75 0.84
29 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (27 bp):
CATACAGGGCATAATCGGTCATTTTAC
Found at i:53566077 original size:27 final size:27
Alignment explanation
Indices: 53566047--53566219 Score: 229
Period size: 27 Copynumber: 6.4 Consensus size: 27
53566037 GGGCATAATC
*
53566047 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* ** *
53566074 GTCATTTTACCCTTCAGGGACATGACG
1 GTCATTTTACCCTACAGGGGTATTACG
53566101 GTCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
*
53566128 GTTATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
*
53566155 GTCATTTTACCCTATAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* * * * *
53566182 GCCATTTTATCCTAAAGGGGCATTACA
1 GTCATTTTACCCTACAGGGGTATTACG
*
53566209 GTTATTTTACC
1 GTCATTTTACC
53566220 TATTTTGAGG
Statistics
Matches: 126, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 126 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTACG
Found at i:53570033 original size:10 final size:10
Alignment explanation
Indices: 53570004--53570039 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
53569994 AATGGACATG
53570004 AAAATAAATA
1 AAAATAAATA
53570014 AAAATGAAATA
1 AAAAT-AAATA
*
53570025 AGAATAAATA
1 AAAATAAATA
53570035 AAAAT
1 AAAAT
53570040 TATACAAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (10 bp):
AAAATAAATA
Found at i:53570220 original size:24 final size:24
Alignment explanation
Indices: 53570191--53570238 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
53570181 TTCCTAGAAG
* *
53570191 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
53570215 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
53570239 GTAATATTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:53572844 original size:79 final size:79
Alignment explanation
Indices: 53572733--53572956 Score: 292
Period size: 79 Copynumber: 2.8 Consensus size: 79
53572723 GCTACTCGTT
* * *
53572733 CAAATGCCTTCGGGACATAGCCCGGCTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
53572798 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
*
53572813 CAAATGCCTTCGGGCTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
53572876 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * * *
53572891 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
53572955 GA
64 GA
53572957 CATCATTCAA
Statistics
Matches: 127, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
78 36 0.28
79 57 0.45
80 34 0.27
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:53572850 original size:39 final size:40
Alignment explanation
Indices: 53572733--53572956 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
53572723 GCTACTCGTT
* *
53572733 CAAATGCCTTCGGGACATAGCCCGG-CTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
53572773 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
53572813 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
53572852 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
53572891 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
53572932 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53572957 CATCATTCAA
Statistics
Matches: 165, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 74 0.45
40 77 0.47
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:53580788 original size:39 final size:40
Alignment explanation
Indices: 53580706--53580927 Score: 278
Period size: 39 Copynumber: 5.7 Consensus size: 40
53580696 GCTACTCGTT
*
53580706 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
53580746 CAAATGCCTTCGGGACTTA-ACCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
53580785 CAAATGCCTTCGGG-CTTAGCCCGGA-TTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
53580823 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
53580862 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
53580903 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53580928 CATCATTCAA
Statistics
Matches: 163, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
38 43 0.26
39 59 0.36
40 50 0.31
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:53580847 original size:77 final size:78
Alignment explanation
Indices: 53580706--53580927 Score: 281
Period size: 77 Copynumber: 2.8 Consensus size: 78
53580696 GCTACTCGTT
* * *
53580706 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTA-ACCGG
1 CAAATGCCTTCGGG-CTTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
53580770 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
53580785 CAAATGCCTTCGGGCTTAGCCCGGAT-TAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGATATAGTA-CTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
53580848 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * *
53580862 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGGATATAGT-AC-TCGCACAAATGCCTTCGGGACTTAGCCCG
53580926 GA
63 GA
53580928 CATCATTCAA
Statistics
Matches: 127, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
76 5 0.04
77 54 0.43
78 21 0.17
79 27 0.21
80 20 0.16
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:53589185 original size:22 final size:22
Alignment explanation
Indices: 53589149--53589190 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53589139 AATACTTAAA
* * *
53589149 AGGGTTTTGATGTTTTAAATAG
1 AGGGTTTTAAGGTTTAAAATAG
53589171 AGGGTTTTAAGGTTTAAAAT
1 AGGGTTTTAAGGTTTAAAAT
53589191 CGATTAGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (22 bp):
AGGGTTTTAAGGTTTAAAATAG
Found at i:53595914 original size:25 final size:25
Alignment explanation
Indices: 53595883--53595932 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
53595873 TAAAAGCTAT
53595883 ATGAATG-CATGAAACAGATAAAAAA
1 ATGAATGACATGAAA-AGATAAAAAA
*
53595908 ATGAATGATCATGAAAATATAAAAA
1 ATGAATGA-CATGAAAAGATAAAAA
53595933 TAAAAGCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 8 0.36
27 7 0.32
ACGTcount: A:0.60, C:0.06, G:0.14, T:0.20
Consensus pattern (25 bp):
ATGAATGACATGAAAAGATAAAAAA
Found at i:53606205 original size:23 final size:24
Alignment explanation
Indices: 53606179--53606229 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
53606169 AGTGTTCTGT
53606179 TATAAGCC-CTCT-CGAGCTTCCCG
1 TATAAGCCTCT-TACGAGCTTCCCG
*
53606202 TATAAGGCTCTTACGAGCTTCCCG
1 TATAAGCCTCTTACGAGCTTCCCG
53606226 -ATAA
1 TATAA
53606230 TAACTCTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (24 bp):
TATAAGCCTCTTACGAGCTTCCCG
Found at i:53606403 original size:24 final size:25
Alignment explanation
Indices: 53606365--53606434 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 25
53606355 AGTGCTCGCT
*
53606365 TGAACCTCCCGATATTGGCTATCTG
1 TGAACTTCCCGATATTGGCTATCTG
* * * *
53606390 -GAGCTTCCCGATA-TGGTTTTTTG
1 TGAACTTCCCGATATTGGCTATCTG
*
53606413 TGAACTTCCCAATATTGGCTAT
1 TGAACTTCCCGATATTGGCTAT
53606435 TATGAGCTTC
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
23 7 0.21
24 22 0.65
25 5 0.15
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (25 bp):
TGAACTTCCCGATATTGGCTATCTG
Found at i:53607836 original size:34 final size:34
Alignment explanation
Indices: 53607785--53607870 Score: 120
Period size: 34 Copynumber: 2.5 Consensus size: 34
53607775 GCAGTGCAAA
* *
53607785 CAGTCTGGGCCTAAGCCC-TTAACAGTAGCAATAT
1 CAGTCTGGGCCTTAGCCCGCT-ACAGTAGCAATAT
* *
53607819 CAGTGTGGGCCTTAGCCCGCTACAGTAGCAGTAT
1 CAGTCTGGGCCTTAGCCCGCTACAGTAGCAATAT
53607853 CAGTCTGGGCCTTAGCCC
1 CAGTCTGGGCCTTAGCCC
53607871 AATTCAGTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 45 0.98
35 1 0.02
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (34 bp):
CAGTCTGGGCCTTAGCCCGCTACAGTAGCAATAT
Found at i:53607879 original size:34 final size:32
Alignment explanation
Indices: 53607785--53607888 Score: 111
Period size: 34 Copynumber: 3.1 Consensus size: 32
53607775 GCAGTGCAAA
* *
53607785 CAGTCTGGGCCTAAGCCCTTAACAGTAGCAATAT
1 CAGTCTGGGCCTTAGCCCTT--CAGTAGCAGTAT
* *
53607819 CAGTGTGGGCCTTAGCCCGCTACAGTAGCAGTAT
1 CAGTCTGGGCCTTAG-CC-CTTCAGTAGCAGTAT
53607853 CAGTCTGGGCCTTAGCCCAATTCAGTA-CAGTAT
1 CAGTCTGGGCCTTAGCCC--TTCAGTAGCAGTAT
53607886 CAG
1 CAG
53607889 AAATGCATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 44 0.73
35 2 0.03
36 2 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (32 bp):
CAGTCTGGGCCTTAGCCCTTCAGTAGCAGTAT
Found at i:53633443 original size:24 final size:25
Alignment explanation
Indices: 53633411--53633458 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
53633401 CCAATGAACT
*
53633411 GGGGAATCA-ACTTAGCAACCCCTC
1 GGGGAATCACACATAGCAACCCCTC
53633435 GGGGAATCAGCACATAGCAACCCC
1 GGGGAATCA-CACATAGCAACCCC
53633459 CTTTCACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
26 12 0.57
ACGTcount: A:0.31, C:0.33, G:0.23, T:0.12
Consensus pattern (25 bp):
GGGGAATCACACATAGCAACCCCTC
Found at i:53633486 original size:101 final size:102
Alignment explanation
Indices: 53633275--53633537 Score: 379
Period size: 101 Copynumber: 2.6 Consensus size: 102
53633265 AACCGTTATT
* * * *
53633275 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCA-CACTTAGCAACCCCTTCGGGGA
** *
53633340 ATCAGCACATAGCAACCCCCTTTTTATTTCAGAGATAC
65 ATCAGCACATAGCAACCCCCTTTACATTTCAAAGATAC
53633378 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCA-ACTTAGCAACCCC-TCGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCACACTTAGCAACCCCTTCGGGGA
53633440 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 ATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATAC
* **
53633479 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCA-CACTTAGCAACCCCTT
53633538 TATGTACAAC
Statistics
Matches: 144, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
100 29 0.20
101 64 0.44
102 2 0.01
103 48 0.33
104 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (102 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCACACTTAGCAACCCCTTCGGGGAA
TCAGCACATAGCAACCCCCTTTACATTTCAAAGATAC
Found at i:53633898 original size:30 final size:29
Alignment explanation
Indices: 53633864--53633928 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
53633854 TAATCCACCA
53633864 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
53633894 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
53633924 CCCAA
1 CCCAA
53633929 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:53633902 original size:31 final size:30
Alignment explanation
Indices: 53633871--53633928 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
53633861 CCACCCAACT
53633871 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
53633901 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
53633929 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:53640939 original size:101 final size:103
Alignment explanation
Indices: 53640760--53641022 Score: 388
Period size: 102 Copynumber: 2.6 Consensus size: 103
53640750 AACCGTTATT
* * * *
53640760 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCA-CACTTAGCAACCCCTCGGGGGA
** *
53640825 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
65 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
53640863 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCA-ACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCACACTTAGCAACCCCTCGGGGGA
53640926 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
53640965 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCA-CACTTAGCAACCCCT
53641023 TTATGTACAA
Statistics
Matches: 145, Mismatches: 10, Indels: 9
0.88 0.06 0.05
Matches are distributed among these distances:
101 43 0.30
102 52 0.36
103 38 0.26
104 12 0.08
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (103 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCACACTTAGCAACCCCTCGGGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:53641384 original size:30 final size:29
Alignment explanation
Indices: 53641350--53641414 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
53641340 TAATCCACCA
53641350 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
53641380 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
53641410 CCCAA
1 CCCAA
53641415 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:53641388 original size:31 final size:30
Alignment explanation
Indices: 53641357--53641414 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
53641347 CCACCCAACT
53641357 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
53641387 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
53641415 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:53647190 original size:47 final size:45
Alignment explanation
Indices: 53647071--53647197 Score: 150
Period size: 46 Copynumber: 2.8 Consensus size: 45
53647061 GGGATATTTG
* *
53647071 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GGATGCGA
* *
53647118 -GCGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGA-GATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGGATG---CGA
*
53647164 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCG
53647198 CTTATGGGCG
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
43 4 0.06
45 2 0.03
46 33 0.47
47 31 0.44
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (45 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGGATGCGA
Found at i:53652258 original size:41 final size:41
Alignment explanation
Indices: 53652213--53652381 Score: 157
Period size: 41 Copynumber: 4.1 Consensus size: 41
53652203 GCACAAACAT
* *
53652213 CCTTCGGAA-TCAAGCCCGATTCTTAGCACTGGCTCAAAAGC
1 CCTTCGGAACT-AAGCCCGATTATGAGCACTGGCTCAAAAGC
* * * *
53652254 CCTTC-GAGACCAAGCTCGGATTA-GACCACTGGCTCAAAGGC
1 CCTTCGGA-ACTAAGC-CCGATTATGAGCACTGGCTCAAAAGC
* * * *
53652295 CCTTCGGAACTAAGTCCGGTTATGA-AACTGGCTCTAAAGC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
* ** *
53652335 CCTTCGAAACTAAGTTCGATTATTAGCACTGGCTCAAAAGC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
53652376 CCTTCG
1 CCTTCG
53652382 AGACCAAGCT
Statistics
Matches: 103, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
40 40 0.39
41 56 0.54
42 7 0.07
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (41 bp):
CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
Found at i:53652382 original size:41 final size:41
Alignment explanation
Indices: 53652237--53652382 Score: 170
Period size: 41 Copynumber: 3.6 Consensus size: 41
53652227 CCCGATTCTT
* * *
53652237 AGCACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGATTA-G
1 AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTTC-GATTATG
* * * * *
53652278 ACCACTGGCTCAAAGGCCCTTCGGAACTAAGTCCGGTTATG
1 AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGATTATG
* * *
53652319 A-AACTGGCTCTAAAGCCCTTCGAAACTAAGTTCGATTATT
1 AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGATTATG
53652359 AGCACTGGCTCAAAAGCCCTTCGA
1 AGCACTGGCTCAAAAGCCCTTCGA
53652383 GACCAAGCTC
Statistics
Matches: 86, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 37 0.43
41 49 0.57
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (41 bp):
AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGATTATG
Found at i:53659390 original size:41 final size:41
Alignment explanation
Indices: 53659345--53659512 Score: 148
Period size: 40 Copynumber: 4.1 Consensus size: 41
53659335 GCACAAACAT
* *
53659345 CCTTCGGAA-TCAAGCCCGATTCTTAGCACTGGCTCAAAAGC
1 CCTTCGGAACT-AAGCCCGATTATGAGCACTGGCTCAAAAGC
* * * *
53659386 CCTTC-GAGACCAAGCTCAGATTA-GACCACTGGCTCAAAGGC
1 CCTTCGGA-ACTAAGC-CCGATTATGAGCACTGGCTCAAAAGC
* * * *
53659427 CCTTCGGAACTAAGTCCGGTTATGA-CACTGGCTCTAAATC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
** * *
53659467 CCTTC-GAACTAAGTTCGGTTATTAGCACTGGCTCAAAAGC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
53659507 CCTTCG
1 CCTTCG
53659513 AGACCAAGCT
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
39 17 0.17
40 42 0.41
41 37 0.36
42 7 0.07
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (41 bp):
CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
Found at i:53659513 original size:40 final size:40
Alignment explanation
Indices: 53659367--53659513 Score: 165
Period size: 40 Copynumber: 3.6 Consensus size: 40
53659357 AGCCCGATTC
* * *
53659367 TTAGCACTGGCTCAAAAGCCCTTCGAGACCAAGCTCAG--A
1 TTAGCACTGGCTCAAAAGCCCTTCGA-ACTAAGTTCGGTTA
* *
53659406 TTAGACCACTGGCTCAAAGGCCCTTCGGAACTAAGTCCGGTTA
1 TTAG--CACTGGCTCAAAAGCCCTTC-GAACTAAGTTCGGTTA
* * *
53659449 TGA-CACTGGCTCTAAATCCCTTCGAACTAAGTTCGGTTA
1 TTAGCACTGGCTCAAAAGCCCTTCGAACTAAGTTCGGTTA
53659488 TTAGCACTGGCTCAAAAGCCCTTCGA
1 TTAGCACTGGCTCAAAAGCCCTTCGA
53659514 GACCAAGCTC
Statistics
Matches: 89, Mismatches: 13, Indels: 11
0.79 0.12 0.10
Matches are distributed among these distances:
39 21 0.24
40 37 0.42
41 26 0.29
42 2 0.02
43 3 0.03
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
TTAGCACTGGCTCAAAAGCCCTTCGAACTAAGTTCGGTTA
Found at i:53661902 original size:275 final size:275
Alignment explanation
Indices: 53661411--53661968 Score: 1107
Period size: 275 Copynumber: 2.0 Consensus size: 275
53661401 CGTCGAAGCA
53661411 TCGAAACATGAAAAACATTGTGAATCTTTTCGAGATCAGGGGGTAAAATCAATCTATATGCCACT
1 TCGAAACATGAAAAACATTGTGAATCTTTTCGAGATCAGGGGGTAAAATCAATCTATATGCCACT
53661476 GGACCAACTCGTTCGGATATTTCATACGGCCCTATGAACCTCGGACTCAGTTTGCCATTACGGCC
66 GGACCAACTCGTTCGGATATTTCATACGGCCCTATGAACCTCGGACTCAGTTTGCCATTACGGCC
53661541 AAATCTGAGTATCTTTTTCCAAGGTGAAACTTTAAGAAACACTTTGTCTCCCACCTGATACTCAA
131 AAATCTGAGTATCTTTTTCCAAGGTGAAACTTTAAGAAACACTTTGTCTCCCACCTGATACTCAA
53661606 TATCTCTTCGTTTTAAATCCGCGTACGACTTCTGACCCTCAAACAATCGTCATCATCAATTTGAA
196 TATCTCTTCGTTTTAAATCCGCGTACGACTTCTGACCCTCAAACAATCGTCATCATCAATTTGAA
*
53661671 ACTCTAATTCCTTAT
261 ACTCTAATTCCCTAT
53661686 TCGAAACATGAAAAACATTGTGAATCTTTTCGAGATCAGGGGGTAAAATCAATCTATATGCCACT
1 TCGAAACATGAAAAACATTGTGAATCTTTTCGAGATCAGGGGGTAAAATCAATCTATATGCCACT
53661751 GGACCAACTCGTTCGGATATTTCATACGGCCCTATGAACCTCGGACTCAGTTTGCCATTACGGCC
66 GGACCAACTCGTTCGGATATTTCATACGGCCCTATGAACCTCGGACTCAGTTTGCCATTACGGCC
53661816 AAATCTGAGTATCTTTTTCCAAGGTGAAACTTTAAGAAACACTTTGTCTCCCACCTGATACTCAA
131 AAATCTGAGTATCTTTTTCCAAGGTGAAACTTTAAGAAACACTTTGTCTCCCACCTGATACTCAA
53661881 TATCTCTTCGTTTTAAATCCGCGTACGACTTCTGACCCTCAAACAATCGTCATCATCAATTTGAA
196 TATCTCTTCGTTTTAAATCCGCGTACGACTTCTGACCCTCAAACAATCGTCATCATCAATTTGAA
53661946 ACTCTAATTCCCTAT
261 ACTCTAATTCCCTAT
53661961 TCGAAACA
1 TCGAAACA
53661969 CATTCAGCCT
Statistics
Matches: 282, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
275 282 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (275 bp):
TCGAAACATGAAAAACATTGTGAATCTTTTCGAGATCAGGGGGTAAAATCAATCTATATGCCACT
GGACCAACTCGTTCGGATATTTCATACGGCCCTATGAACCTCGGACTCAGTTTGCCATTACGGCC
AAATCTGAGTATCTTTTTCCAAGGTGAAACTTTAAGAAACACTTTGTCTCCCACCTGATACTCAA
TATCTCTTCGTTTTAAATCCGCGTACGACTTCTGACCCTCAAACAATCGTCATCATCAATTTGAA
ACTCTAATTCCCTAT
Found at i:53666866 original size:40 final size:41
Alignment explanation
Indices: 53666752--53666919 Score: 157
Period size: 40 Copynumber: 4.1 Consensus size: 41
53666742 GCACAAACAT
* * *
53666752 CCTTCGGAA-TCAAGCCCGATTCTTAGCACTGGCTCAAAAGC
1 CCTTCGGAACT-AAGTCCGATTATGAGCACTGGCTCAAAAGC
* * * *
53666793 CCTTC-GAGACCAAGCTCAGATTA-GACCACTGGCTCAAAGGC
1 CCTTCGGA-ACTAAG-TCCGATTATGAGCACTGGCTCAAAAGC
* *
53666834 CCTTCGGAACTAAGTCCGATTATGA-CACTGGCTCTAAATC
1 CCTTCGGAACTAAGTCCGATTATGAGCACTGGCTCAAAAGC
* * * *
53666874 CCTTC-GAACTAAGTTCGGTTATTAGCACTGGTTCAAAAGC
1 CCTTCGGAACTAAGTCCGATTATGAGCACTGGCTCAAAAGC
53666914 CCTTCG
1 CCTTCG
53666920 AGACCAAGCT
Statistics
Matches: 102, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
39 16 0.16
40 43 0.42
41 36 0.35
42 7 0.07
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (41 bp):
CCTTCGGAACTAAGTCCGATTATGAGCACTGGCTCAAAAGC
Found at i:53670590 original size:53 final size:53
Alignment explanation
Indices: 53670510--53670615 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
53670500 GAAAATTTAG
53670510 AAAATTTTTCAAAATACAAAGGACACACACCTGTATGGCCCGGTTGTGTGTCT
1 AAAATTTTTCAAAATACAAAGGACACACACCTGTATGGCCCGGTTGTGTGTCT
* * *
53670563 AAAATTTTTCAAAATACAAGGGACACACGCCTGTGTGGCCCGGTTGTGTGTCT
1 AAAATTTTTCAAAATACAAAGGACACACACCTGTATGGCCCGGTTGTGTGTCT
53670616 CACACGGCCA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (53 bp):
AAAATTTTTCAAAATACAAAGGACACACACCTGTATGGCCCGGTTGTGTGTCT
Found at i:53678716 original size:47 final size:47
Alignment explanation
Indices: 53678647--53679098 Score: 679
Period size: 47 Copynumber: 9.6 Consensus size: 47
53678637 TGATAGTATA
53678647 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
53678694 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGCTG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
53678741 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
53678790 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
53678837 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
53678884 AATGTAAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
53678931 AATGTGAAAGTGTATATATGTGCTAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * **
53678978 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACATGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * **
53679025 GATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACATGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
53679072 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
53679099 TCCCGAAGGG
Statistics
Matches: 382, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 338 0.88
49 44 0.12
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:53680837 original size:40 final size:40
Alignment explanation
Indices: 53680514--53680825 Score: 489
Period size: 40 Copynumber: 7.8 Consensus size: 40
53680504 GAGAATTGAG
53680514 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
53680554 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
53680594 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCATGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
53680634 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
53680674 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
53680714 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCATGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * **
53680754 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * *
53680794 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
53680826 ATCATGCTGG
Statistics
Matches: 252, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 252 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:53680877 original size:21 final size:22
Alignment explanation
Indices: 53680853--53680893 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
53680843 ATTCGGCCTT
53680853 CGTGCCTAGTAGG-CTTCGTGC
1 CGTGCCTAGTAGGCCTTCGTGC
53680874 CGTGCCTAGTAGGCCTTCGT
1 CGTGCCTAGTAGGCCTTCGT
53680894 TGCACGGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.10, C:0.29, G:0.32, T:0.29
Consensus pattern (22 bp):
CGTGCCTAGTAGGCCTTCGTGC
Found at i:53684933 original size:47 final size:47
Alignment explanation
Indices: 53684879--53685331 Score: 737
Period size: 47 Copynumber: 9.6 Consensus size: 47
53684869 TATTTGAATA
53684879 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
53684926 AATGTGAAAGTGTATATATGTGATAAGG-CTGAATGGCCAATGTGCTG
1 AATGTGAAAGTGTATATATGTGATAAGGCCT-AATGGCCGATGTGATG
53684973 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
53685022 AATGTGAAAGTGTATTATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTA-TATATGTGATAAGGCCTAATGGCCGATGTGATG
53685070 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
53685117 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
53685164 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
53685211 AATGTGAAAGTGTATATATGTGATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * **
53685258 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACATGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
53685305 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
53685332 TCCCGAAGGG
Statistics
Matches: 386, Mismatches: 15, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
46 2 0.01
47 294 0.76
48 46 0.12
49 42 0.11
50 2 0.01
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:53689843 original size:27 final size:27
Alignment explanation
Indices: 53689805--53689927 Score: 124
Period size: 27 Copynumber: 4.6 Consensus size: 27
53689795 AACAATACAT
*
53689805 CACATAGGGGCAAAATCATCATTTTAC
1 CACATAAGGGCAAAATCATCATTTTAC
* * *
53689832 CACACAAGGGCAAAATCGTCATTTTAA
1 CACATAAGGGCAAAATCATCATTTTAC
* *
53689859 CACATAAGGGCAAAA-GAGTCATTTTTC
1 CACATAAGGGCAAAATCA-TCATTTTAC
* * * *
53689886 CACATAAGGGAAAAACCGTCATTTTAT
1 CACATAAGGGCAAAATCATCATTTTAC
*
53689913 CACAT-AGAGCAAAAT
1 CACATAAGGGCAAAAT
53689928 TGTAACACCC
Statistics
Matches: 77, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
26 7 0.09
27 70 0.91
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (27 bp):
CACATAAGGGCAAAATCATCATTTTAC
Found at i:53689871 original size:54 final size:55
Alignment explanation
Indices: 53689805--53689927 Score: 153
Period size: 54 Copynumber: 2.3 Consensus size: 55
53689795 AACAATACAT
* * *
53689805 CACATAGGGGCAAAATCA-TCATTTTACCACACAAGGGCAAAATCGTCATTTTAA
1 CACATAAGGGCAAAATCAGTCATTTTACCACACAAGGGAAAAACCGTCATTTTAA
* * * *
53689859 CACATAAGGGCAAAA-GAGTCATTTTTCCACATAAGGGAAAAACCGTCATTTTAT
1 CACATAAGGGCAAAATCAGTCATTTTACCACACAAGGGAAAAACCGTCATTTTAA
*
53689913 CACAT-AGAGCAAAAT
1 CACATAAGGGCAAAAT
53689928 TGTAACACCC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
53 9 0.15
54 50 0.85
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (55 bp):
CACATAAGGGCAAAATCAGTCATTTTACCACACAAGGGAAAAACCGTCATTTTAA
Found at i:53690955 original size:26 final size:26
Alignment explanation
Indices: 53690871--53691006 Score: 181
Period size: 26 Copynumber: 5.3 Consensus size: 26
53690861 TTGGAGGCCT
53690871 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
53690895 AGCCCTTTTCGGTAAACTGGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
*
53690920 AGCCCTTTTCAATAAATTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
53690946 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
53690972 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
53690998 AGTCCTTTT
1 AGCCCTTTT
53691007 GCACTTCCTC
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
23 5 0.05
24 5 0.05
25 32 0.33
26 56 0.57
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:53690996 original size:52 final size:51
Alignment explanation
Indices: 53690871--53691006 Score: 215
Period size: 52 Copynumber: 2.7 Consensus size: 51
53690861 TTGGAGGCCT
53690871 AGCCTCTTTT-AAT-AACTGGGGCA-AAGCCCTTTTCGGTAAACTGGGGCAA
1 AGCC-CTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAA
*
53690920 AGCCCTTTTCAATAAATTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCA-A
*
53690972 AGCCCTTTTCAATAAACTGGGGCATAAGTCCTTTT
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
53691007 GCACTTCCTC
Statistics
Matches: 80, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
48 5 0.06
49 7 0.09
50 9 0.11
51 25 0.31
52 34 0.43
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (51 bp):
AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAA
Found at i:53691101 original size:40 final size:40
Alignment explanation
Indices: 53691056--53691140 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
53691046 TTATGAATAC
53691056 ATCATGTGCATTTCATACATATCATGTGCATATCATA-CA
1 ATCATGTGCATTTCATACATATCATGTGCATATCATATCA
* *
53691095 TATCATGTGCATTTTATACATATCATGTGTATATCATATCA
1 -ATCATGTGCATTTCATACATATCATGTGCATATCATATCA
53691136 ATCAT
1 ATCAT
53691141 AGCCCACGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 40 0.95
41 2 0.05
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (40 bp):
ATCATGTGCATTTCATACATATCATGTGCATATCATATCA
Found at i:53691140 original size:20 final size:20
Alignment explanation
Indices: 53691056--53691132 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 20
53691046 TTATGAATAC
*
53691056 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
53691076 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
53691096 ATCATGTGCATTTTATACAT
1 ATCATGTGCATATCATACAT
*
53691116 ATCATGTGTATATCATA
1 ATCATGTGCATATCATA
53691133 TCAATCATAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.40
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:53691197 original size:25 final size:25
Alignment explanation
Indices: 53691169--53691216 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53691159 ATAATTAAAC
* * *
53691169 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
53691194 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
53691217 CATACTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:53692945 original size:27 final size:26
Alignment explanation
Indices: 53692905--53692999 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 26
53692895 GATGTTACAA
*
53692905 AAATCGCCATTTTAACACATAAGGGC
1 AAATCGTCATTTTAACACATAAGGGC
*
53692931 AAGATCGTCATTTTAACATATAAGGGC
1 AA-ATCGTCATTTTAACACATAAGGGC
* **
53692958 AAAATAGTCATTTTGCCACATAAGGGC
1 -AAATCGTCATTTTAACACATAAGGGC
*
53692985 AAAACTGTCATTTTA
1 AAATC-GTCATTTTA
53693000 TCTTATAGGC
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
26 5 0.09
27 50 0.88
28 2 0.04
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (26 bp):
AAATCGTCATTTTAACACATAAGGGC
Found at i:53693021 original size:27 final size:27
Alignment explanation
Indices: 53692991--53693052 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
53692981 GGGCAAAACT
*
53692991 GTCATTTTATCTTATAGGCGTAT-TACA
1 GTCATTTTACCTTATAGGCGTATCT-CA
*
53693018 GTCATTTTACCTTATAGGGGTATCTCA
1 GTCATTTTACCTTATAGGCGTATCTCA
53693045 GTCATTTT
1 GTCATTTT
53693053 CAAGTAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCTTATAGGCGTATCTCA
Found at i:53693472 original size:24 final size:24
Alignment explanation
Indices: 53693437--53693482 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
53693427 TCAACAACCC
53693437 ACTTTTCAGCTTTTCAGCCTTTTG
1 ACTTTTCAGCTTTTCAGCCTTTTG
*
53693461 ACTTTTCGGCTTTTCAGCCTTT
1 ACTTTTCAGCTTTTCAGCCTTT
53693483 GTAGTTTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.11, C:0.26, G:0.13, T:0.50
Consensus pattern (24 bp):
ACTTTTCAGCTTTTCAGCCTTTTG
Found at i:53708896 original size:8 final size:8
Alignment explanation
Indices: 53708883--53708907 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53708873 TGCATAAGGC
53708883 TTTTGTTA
1 TTTTGTTA
53708891 TTTTGTTA
1 TTTTGTTA
53708899 TTTTGTTA
1 TTTTGTTA
53708907 T
1 T
53708908 ATGTGTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (8 bp):
TTTTGTTA
Found at i:53710218 original size:20 final size:21
Alignment explanation
Indices: 53710180--53710218 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
53710170 CTAAGCAATT
*
53710180 TTTAGGGCCTCAAAGGCTTGA
1 TTTAGGGACTCAAAGGCTTGA
*
53710201 TTTAGGGAC-CAAATGCTT
1 TTTAGGGACTCAAAGGCTT
53710219 ATATTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (21 bp):
TTTAGGGACTCAAAGGCTTGA
Found at i:53715082 original size:40 final size:40
Alignment explanation
Indices: 53715045--53715160 Score: 162
Period size: 40 Copynumber: 2.9 Consensus size: 40
53715035 GGATATAGCT
* ** *
53715045 ACTCGCTCAAATGCCTTCTAGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
53715085 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGATT-TGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
53715125 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
53715161 CATCCGAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.03
40 63 0.94
41 2 0.03
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:53720101 original size:48 final size:48
Alignment explanation
Indices: 53719990--53720365 Score: 535
Period size: 48 Copynumber: 7.8 Consensus size: 48
53719980 ATGAGATTCC
* * *
53719990 GTGTAAGACCATGTCTGGGACATGGCATTGG-AATCTGAGATATGTGCCTA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGA--TGATATATGTGCC-A
* *
53720040 -TGTAAGACCATGTCTGGGACATGGCATCGGCGATAATGTATGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCA
* *
53720087 GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAAATTTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCA
* * * *
53720135 GTGTAAGACCATGTATGGGACACGGCATCGGCGATAATGTATGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCA
*
53720183 GTGTAAGACCATGTCTGGGACATGGCATCGGCAATGAT-TATGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCA
* *
53720230 ATGTAAGACCATGTAC-GGGACATGGCATCGACGATGATATATGTGCCA
1 GTGTAAGACCATGT-CTGGGACATGGCATCGGCGATGATATATGTGCCA
* *
53720278 GTGTAAGACCATGTCTGGGACATGGCATCAGTGATGATATATGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCA
*
53720326 GTGTAAGACCATGTCAGGGACATGGCATCGGCGATGATAT
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
53720366 GTGGATTCAT
Statistics
Matches: 292, Mismatches: 29, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
47 44 0.15
48 218 0.75
49 29 0.10
50 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCA
Found at i:53720316 original size:191 final size:192
Alignment explanation
Indices: 53719990--53720360 Score: 579
Period size: 191 Copynumber: 1.9 Consensus size: 192
53719980 ATGAGATTCC
* *
53719990 GTGTAAGACCATGTCTGGGACATGGCATTGGAATCTGAGATATGTGCCTATGTAAGACCATGTCT
1 GTGTAAGACCATGTCTGGGACATGGCATCGGAA-CTGAGATATGTGCCAATGTAAGACCATGTCT
* * *
53720055 GGGACATGGCATCGGCGATAATGTATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCG
65 GGGACATGGCATCGACGATAATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCG
*
53720120 ATGATAAATTTGCCAGTGTAAGACCATGT-ATGGGACACGGCATCGGCGATAATGTATGTGCCA
130 ATGATAAATGTGCCAGTGTAAGACCATGTCA-GGGACACGGCATCGGCGATAATGTATGTGCCA
*
53720183 GTGTAAGACCATGTCTGGGACATGGCATCGGCAA-TGA-TTATGTGCCAATGTAAGACCATGTAC
1 GTGTAAGACCATGTCTGGGACATGGCATCGG-AACTGAGATATGTGCCAATGTAAGACCATGT-C
* *
53720246 -GGGACATGGCATCGACGATGATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGT
64 TGGGACATGGCATCGACGATAATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGC
* *
53720310 GATGATATATGTGCCAGTGTAAGACCATGTCAGGGACATGGCATCGGCGAT
129 GATGATAAATGTGCCAGTGTAAGACCATGTCAGGGACACGGCATCGGCGAT
53720361 GATATGTGGA
Statistics
Matches: 164, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
191 127 0.77
192 5 0.03
193 30 0.18
194 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (192 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGAACTGAGATATGTGCCAATGTAAGACCATGTCTG
GGACATGGCATCGACGATAATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCGA
TGATAAATGTGCCAGTGTAAGACCATGTCAGGGACACGGCATCGGCGATAATGTATGTGCCA
Found at i:53720383 original size:191 final size:191
Alignment explanation
Indices: 53719993--53720401 Score: 562
Period size: 191 Copynumber: 2.1 Consensus size: 191
53719983 AGATTCCGTG
* *
53719993 TAAGACCATGTCTGGGACATGGCATTGGAATCTGAGATATGTGCCTATGTAAGACCATGTCTGGG
1 TAAGACCATGTCTGGGACATGGCATCGGAA-CTGAGATATGTGCCAATGTAAGACCATGTCTGGG
* * *
53720058 ACATGGCATCGGCGATAATGTATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
65 ACATGGCATCGACGATAATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCGATG
* *
53720123 ATAAATTTGCCAGTGTAAGACCATGTATGGGACACGGCATCGGCGATAATGTATGTGCCAGTG
130 ATAAATGTGCCAGTGTAAGACCATGTATGGGACACGGCATCGGCGATAATGTATGT-CCAGTA
*
53720186 TAAGACCATGTCTGGGACATGGCATCGGCAA-TGA-TTATGTGCCAATGTAAGACCATGTAC-GG
1 TAAGACCATGTCTGGGACATGGCATCGG-AACTGAGATATGTGCCAATGTAAGACCATGT-CTGG
* *
53720248 GACATGGCATCGACGATGATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGTGAT
64 GACATGGCATCGACGATAATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCGAT
* *
53720313 GATATATGTGCCAGTGTAAGACCATGTCA-GGGACATGGCATCGGCGATGATATGTGGAT-T-CA
129 GATAAATGTGCCAGTGTAAGACCATGT-ATGGGACACGGCATCGGCGAT-A-ATGT--ATGTCCA
53720375 -TA
189 GTA
* *
53720377 TAAGACCATGTCGGGGACATAGCAT
1 TAAGACCATGTCTGGGACATGGCAT
53720402 TGGTACTTTA
Statistics
Matches: 195, Mismatches: 14, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
191 151 0.77
192 8 0.04
193 31 0.16
194 3 0.02
195 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (191 bp):
TAAGACCATGTCTGGGACATGGCATCGGAACTGAGATATGTGCCAATGTAAGACCATGTCTGGGA
CATGGCATCGACGATAATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCGATGA
TAAATGTGCCAGTGTAAGACCATGTATGGGACACGGCATCGGCGATAATGTATGTCCAGTA
Found at i:53750840 original size:18 final size:20
Alignment explanation
Indices: 53750802--53750841 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
53750792 CTCTCCGCGT
53750802 CACACGCCCGTGCTCGCCAC
1 CACACGCCCGTGCTCGCCAC
*
53750822 CACATGCCCGTG-T-GCCAC
1 CACACGCCCGTGCTCGCCAC
53750840 CA
1 CA
53750842 TACAACAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 1 0.05
20 11 0.58
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.12
Consensus pattern (20 bp):
CACACGCCCGTGCTCGCCAC
Done.