Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 18 of 332
Found at i:5216406 original size:143 final size:141
Alignment explanation
Indices: 5216150--5216460 Score: 469
Period size: 143 Copynumber: 2.2 Consensus size: 141
5216140 CCCTTCGGGA
* * * * *
5216150 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
*
5216215 TTTCACATTCATCATATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACATC
*
5216280 GGCTATTAGGC
131 GGCCATTAGGC
* * *
5216291 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCAC--ATATATAC
* * *
5216356 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACA
5216421 TCGGCCATTAGGC
129 TCGGCCATTAGGC
* *
5216434 CTTATCACATATATATACATTCACATC
1 CTTATCACATATATACACTTTCACATC
5216461 ACAATTATCC
Statistics
Matches: 152, Mismatches: 16, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
141 47 0.31
143 105 0.69
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:5220682 original size:40 final size:40
Alignment explanation
Indices: 5220603--5220779 Score: 200
Period size: 40 Copynumber: 4.5 Consensus size: 40
5220593 CGGATGATAA
* * * *
5220603 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATTATAT
* * * * *
5220643 CCAGGCTATGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATTATAT
* *
5220683 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATTATAT
5220723 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATTATAT
5220763 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
5220780 ATACTTGGGT
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 15 0.13
40 99 0.85
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATTATAT
Found at i:5220741 original size:80 final size:80
Alignment explanation
Indices: 5220603--5220779 Score: 234
Period size: 80 Copynumber: 2.2 Consensus size: 80
5220593 CGGATGATAA
* * * * *
5220603 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCAGGCTATGTCCCGAAGGCATTTA
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTACTATATCCAGGCTAAGACCCGAAGGCATTTA
*
5220668 TGCTAG-TGATTATAT
66 TGCGAGTTG-TTATAT
* * *
5220683 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTACTATATCCAGGCTAAGACCCGAAGGCATTTA
5220748 TGCGAGTTGTTATAT
66 TGCGAGTTGTTATAT
5220763 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
5220780 ATACTTGGGT
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
78 1 0.01
79 13 0.15
80 70 0.81
81 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTACTATATCCAGGCTAAGACCCGAAGGCATTTA
TGCGAGTTGTTATAT
Found at i:5221048 original size:22 final size:22
Alignment explanation
Indices: 5221008--5221049 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5220998 GAATGTGCAT
*
5221008 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
5221030 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
5221050 TCAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:5223021 original size:17 final size:18
Alignment explanation
Indices: 5222999--5223034 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5222989 ATAAAATAAG
*
5222999 TTTTATTCTAT-TTAATC
1 TTTTATTATATATTAATC
5223016 TTTTATTATATATTAATC
1 TTTTATTATATATTAATC
5223034 T
1 T
5223035 ATTCACTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATTATATATTAATC
Found at i:5230984 original size:62 final size:62
Alignment explanation
Indices: 5230918--5231048 Score: 192
Period size: 62 Copynumber: 2.1 Consensus size: 62
5230908 CTTTTAAATT
* *
5230918 TTAATCAATTTACTTTATTTCTCTTTATCTCATTCCGGACAGAGATAATTTAAAAAAAAAAA
1 TTAATCAATTTACTTTATTTCTCTTCATCTCATTCCAGACAGAGATAATTTAAAAAAAAAAA
* * ***
5230980 TTAATCAATTTGCTTTATTTCTCTTCATCTCATTCCAGACAGGGATAATTTTTTAAAAAAAA
1 TTAATCAATTTACTTTATTTCTCTTCATCTCATTCCAGACAGAGATAATTTAAAAAAAAAAA
5231042 TT-ATCAA
1 TTAATCAA
5231049 CATATTTTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
61 5 0.08
62 57 0.92
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.40
Consensus pattern (62 bp):
TTAATCAATTTACTTTATTTCTCTTCATCTCATTCCAGACAGAGATAATTTAAAAAAAAAAA
Found at i:5233083 original size:4 final size:4
Alignment explanation
Indices: 5233074--5233103 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
5233064 TTCATTTATC
5233074 AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
5233104 GATTGCTGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:5239329 original size:18 final size:18
Alignment explanation
Indices: 5239314--5239360 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
5239304 GTCATCCATG
5239314 TATCCTCCACCATCCACA
1 TATCCTCCACCATCCACA
*
5239332 TATCCTCCACC-TCCTGCA
1 TATCCTCCACCATCC-ACA
*
5239350 TACCCTCCACC
1 TATCCTCCACC
5239361 TCCCTTGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.21, C:0.53, G:0.02, T:0.23
Consensus pattern (18 bp):
TATCCTCCACCATCCACA
Found at i:5243300 original size:19 final size:17
Alignment explanation
Indices: 5243266--5243301 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
5243256 CTAAAATAGT
5243266 AATAAAATTAACAATAA
1 AATAAAATTAACAATAA
5243283 AATAAGAATTATACAATAA
1 AATAA-AATTA-ACAATAA
5243302 CAACAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.25
Consensus pattern (17 bp):
AATAAAATTAACAATAA
Found at i:5245726 original size:13 final size:13
Alignment explanation
Indices: 5245708--5245732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5245698 GGCACCAAAT
5245708 TTTTTATTTTTTA
1 TTTTTATTTTTTA
5245721 TTTTTATTTTTT
1 TTTTTATTTTTT
5245733 TGGTACCACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:5249003 original size:40 final size:40
Alignment explanation
Indices: 5248958--5249270 Score: 283
Period size: 40 Copynumber: 7.7 Consensus size: 40
5248948 GTTTTAGTCT
*
5248958 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCC
* * * *
5248998 ACTCCACTACTGCTTAGGG-GAATAAGATCTGTGGT-TCTATCT
1 GCTCCACTACTGCTTAGGGAG-ATAAGA-CT-TGATGT-GATCC
* * * * * *
5249040 GCTCCACTATTGCTTGGGGAGGTAAGACTTGAAGCGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCC
* * *
5249080 GCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTTTG-TCC
1 GCTCCACTACTGCTTAGGGAGATAAGA-CT-T-GATGTGATCC
* *
5249122 GCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCC
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCC
* * * *
5249162 GCTCCATTATTGCTTAGGGAGATAAGATCTGTGGTTTTG-TCC
1 GCTCCACTACTGCTTAGGGAGATAAGA-CT-T-GATGTGATCC
* * **
5249204 GCTCCGCTACTACTTAGGGAGATAAGACTTGATACGATCC
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCC
*
5249244 GCTCCACTATTGCTTAGGGAGATAAGA
1 GCTCCACTACTGCTTAGGGAGATAAGA
5249271 TCTGTGGTTT
Statistics
Matches: 220, Mismatches: 39, Indels: 28
0.77 0.14 0.10
Matches are distributed among these distances:
39 7 0.03
40 111 0.50
41 13 0.06
42 83 0.38
43 6 0.03
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (40 bp):
GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCC
Found at i:5249043 original size:82 final size:82
Alignment explanation
Indices: 5248939--5249281 Score: 481
Period size: 82 Copynumber: 4.2 Consensus size: 82
5248929 CATGGGGATG
* * * **
5248939 AGATTTGTGGTTTTAGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTACTCCA
1 AGATCTGTGGTTTTA-TCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCA
*
5249004 CTACTGCTTAGGG-GAATA
65 CTATTGCTTAGGGAG-ATA
* * * * * * *
5249022 AGATCTGTGGTTCTATCTGCTCCACTATTGCTTGGGGAGGTAAGACTTGAAGCGATCTGCTCCAC
1 AGATCTGTGGTTTTATCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
5249087 TATTGCTTAGGGAGATA
66 TATTGCTTAGGGAGATA
* * *
5249104 AGATCTGTGGTTTTGTCCGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAT
1 AGATCTGTGGTTTTATCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
5249169 TATTGCTTAGGGAGATA
66 TATTGCTTAGGGAGATA
* * * *
5249186 AGATCTGTGGTTTTGTCCGCTCCGCTACTACTTAGGGAGATAAGACTTGATACGATCCGCTCCAC
1 AGATCTGTGGTTTTATCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
5249251 TATTGCTTAGGGAGATA
66 TATTGCTTAGGGAGATA
5249268 AGATCTGTGGTTTT
1 AGATCTGTGGTTTT
5249282 CACTCTATTC
Statistics
Matches: 237, Mismatches: 22, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
82 223 0.94
83 14 0.06
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (82 bp):
AGATCTGTGGTTTTATCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
TATTGCTTAGGGAGATA
Found at i:5249591 original size:44 final size:44
Alignment explanation
Indices: 5249442--5249956 Score: 470
Period size: 44 Copynumber: 11.7 Consensus size: 44
5249432 CAAATACAGG
* * * * *
5249442 GACAAAATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAA
1 GACAAGATCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAA
* * * *
5249487 GACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAA
1 GACAAGATCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAA
* * *
5249532 GACAAGATCTG-TATCTTGGATCCACTTCCTATCAATATAGGAA
1 GACAAGATCTGCTATCTTCGATCTACTTCCTACCAATATAGGAA
* * * * * *
5249575 GATAGGACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAA
1 GACAAGATCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAA
* * * *
5249619 GACAAGATCTGCTTTCTGCGATCTACTTCGCCCACCAATATGGGAA
1 GACAAGATCTGCTATCTTCGATCTACTT--CCTACCAATATAGGAA
* *
5249665 GACAAGATCTGC-ATCGTCGATCCACTTCCTACCAATATAGGAA
1 GACAAGATCTGCTATCTTCGATCTACTTCCTACCAATATAGGAA
** * * * *
5249708 GACCGGACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAA
1 GACAAGATCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAA
* * * *
5249752 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAA-ATGGGAA
1 GACAAGATCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAA
*
5249796 GACAAGATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAA
1 GACAAGATCTGCTATCTTCGATCTACTTCCTACCAATATAGGAA
* * * * * *
5249839 GATAGGATCTGCTACCTTCGATCTACTTCAC-GCCAATACATGAA
1 GACAAGATCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAA
* * * *
5249883 GATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATAGGAA
1 GACAAGATCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAA
* *
5249928 GACAAGATCTGCAATCTTCAATCTA-TTCC
1 GACAAGATCTGCTATCTTCGATCTACTTCC
5249957 ACTGCCAAAT
Statistics
Matches: 383, Mismatches: 75, Indels: 26
0.79 0.15 0.05
Matches are distributed among these distances:
42 6 0.02
43 72 0.19
44 179 0.47
45 104 0.27
46 22 0.06
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (44 bp):
GACAAGATCTGCTATCTTCGATCTACTTCCTACCAATATAGGAA
Found at i:5249661 original size:133 final size:132
Alignment explanation
Indices: 5249450--5249946 Score: 789
Period size: 133 Copynumber: 3.8 Consensus size: 132
5249440 GGGACAAAAT
* * * *** *
5249450 CTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTTCTTCGATCTACTT
1 CTGCTATCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTT
* * * * *
5249515 CACCACCAGTATGGGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATAG
65 CGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAG
5249580 GAC
130 GAC
5249583 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
* **
5249648 GCCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGACCG
66 G-CCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAG
5249713 GAC
130 GAC
5249716 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
5249781 GCCACCAA-ATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGG
*
5249845 AT
131 AC
* *
5249847 CTGCTACCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
*
5249912 GCCACCAATATAGGAAGACAAGATCTGCAATCTTC
66 GCCACCAATATGGGAAGACAAGATCTGC-ATCTTC
5249947 AATCTATTCC
Statistics
Matches: 339, Mismatches: 22, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
131 125 0.37
132 62 0.18
133 152 0.45
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (132 bp):
CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
GCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGG
AC
Found at i:5249776 original size:177 final size:177
Alignment explanation
Indices: 5249442--5249944 Score: 437
Period size: 177 Copynumber: 2.8 Consensus size: 177
5249432 CAAATACAGG
* * * *
5249442 GACAAAATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTTCTTCG
1 GACAAAATCTGCTTTCTGCGATCTACTTCACCACCAATATGGGAAGACAAGATCTGCTATCGTCG
* * * * * * *
5249507 ATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAG
66 ATCCACTTCACCACCAATATAGGAAGACAAGACCTGTATCTTCGATCCACTTCCTACCAATACAG
* * *
5249572 GAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAA
131 GAAGACAAGACCTGCTATCTGCGATCTACTTCACGCCAATACATGAA
* *
5249619 GACAAGATCTGCTTTCTGCGATCTACTTCGCCCACCAATATGGGAAGACAAGATCTGC-ATCGTC
1 GACAAAATCTGCTTTCTGCGATCTACTTC-ACCACCAATATGGGAAGACAAGATCTGCTATCGTC
* ** * *
5249683 GATCCACTTC-CTACCAATATAGGAAGACCGGACCTGCTATCTTCGATCTACTTCAC-GCCAATA
65 GATCCACTTCACCACCAATATAGGAAGACAAGACCTG-TATCTTCGATCCACTTC-CTACCAATA
* * * ** *
5249746 CATGAAGACAAGATCTGCTTTCTGCGATCTACTT--CGCCACCAAATGGGAA
128 CAGGAAGACAAGACCTGCTATCTGCGATCTACTTCACGCCAATACAT--GAA
* * * * * * * * * *
5249796 GACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGATAGGATCTGCTACCTTCG
1 GACAAAATCTGCTTTCTGCGATCTACTTCACCACCAATATGGGAAGACAAGATCTGCTATCGTCG
* * * * * * * * * * *
5249859 ATCTACTTCA-CGCCAATACATGAAGATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
66 ATCCACTTCACCACCAATATAGGAAGACAAGACCTG-TATCTTCGATCCACTTC-CTACCAATAC
* *
5249923 AGGAAGACAAGATCTGCAATCT
129 AGGAAGACAAGACCTGCTATCT
5249945 TCAATCTATT
Statistics
Matches: 265, Mismatches: 53, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
174 23 0.09
175 55 0.21
176 58 0.22
177 102 0.38
178 27 0.10
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (177 bp):
GACAAAATCTGCTTTCTGCGATCTACTTCACCACCAATATGGGAAGACAAGATCTGCTATCGTCG
ATCCACTTCACCACCAATATAGGAAGACAAGACCTGTATCTTCGATCCACTTCCTACCAATACAG
GAAGACAAGACCTGCTATCTGCGATCTACTTCACGCCAATACATGAA
Found at i:5249823 original size:87 final size:88
Alignment explanation
Indices: 5249442--5249952 Score: 428
Period size: 89 Copynumber: 5.8 Consensus size: 88
5249432 CAAATACAGG
* * * * * * *
5249442 GACAAAATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTTCTTCG
1 GACAAGATCTGCTATCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGATCTGCTATCTTCG
* *
5249507 ATCTACTTCACCACCAGTATGGGAA
65 ATCTACTTCGCCACCA-AATGGGAA
* * * * *
5249532 GACAAGATCTG-TATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGA
1 GACAAGATCTGCTATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCTGCTATCTTCGA
** *
5249596 TCTACTTCACGCCAATACAT--GAA
66 TCTACTT--CGCCACCAAATGGGAA
* * * * * *
5249619 GACAAGATCTGCTTTCTGCGATCTACTTCGCCCACCAATATGGGAAGACAAGATCTGC-ATCGTC
1 GACAAGATCTGCTATCTTCGATCCACTT--CCTACCAATATAGGAAGACAAGATCTGCTATCTTC
* * *
5249683 GATCCACTTC-CTACCAATATAGGAA
64 GATCTACTTCGCCACCAA-ATGGGAA
** * * * * * * *
5249708 GACCGGACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTTTCTGCG
1 GACAAGATCTGCTATCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGATCTGCTATCTTCG
5249772 ATCTACTTCGCCACCAAATGGGAA
65 ATCTACTTCGCCACCAAATGGGAA
* * *
5249796 GACAAGATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGA
1 GACAAGATCTGCTATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCTGCTATCTTCGA
** *
5249860 TCTACTTCACGCCAATACAT--GAA
66 TCTACTT--CGCCACCAAATGGGAA
* * * * * * *
5249883 GATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCAATCTTCA
1 GACAAGATCTGCTATCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGATCTGCTATCTTCG
5249948 ATCTA
65 ATCTA
5249953 TTCCACTGCC
Statistics
Matches: 333, Mismatches: 72, Indels: 33
0.76 0.16 0.08
Matches are distributed among these distances:
86 4 0.01
87 101 0.30
88 88 0.26
89 103 0.31
90 37 0.11
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (88 bp):
GACAAGATCTGCTATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCTGCTATCTTCGA
TCTACTTCGCCACCAAATGGGAA
Found at i:5250083 original size:136 final size:134
Alignment explanation
Indices: 5249901--5250217 Score: 478
Period size: 136 Copynumber: 2.4 Consensus size: 134
5249891 CTGCTTTCTG
* ** * *
5249901 CGATCTACTTCGCCACC-AATATAGGAAGACAAGATCTGCAATCTTCAATCTATTCCACTGCCAA
1 CGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAA
*
5249965 ATACAGTGAGATAGAGTTATCGACTTCAATCTACTCCACTGTAGTCACAGGGAGGTAAAATCTGC
66 ATACAGGGAGATAGAGTTATCGACTTCAATCTACTCCACTGTAGT--CAGGGAGGTAAAATCTGC
5250030 CATCTT
129 CATCTT
*
5250036 CGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAG
1 CGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAA
* * * *
5250101 ATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTTGTCAGGGAGGTAAAATTTGCCA
66 ATACAGGGAGATAGAGTTATCGACTTCAATCTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCA
5250166 TCTT
131 TCTT
*
5250170 CGATCTGCTTCGCTGCCAAATACAGGAAAG-AAGATCTG-ATATCTTCAA
1 CGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCA-ATCTTCAA
5250218 CCAGCTCTGC
Statistics
Matches: 168, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
132 1 0.01
133 16 0.10
134 52 0.31
135 14 0.08
136 85 0.51
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (134 bp):
CGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAA
ATACAGGGAGATAGAGTTATCGACTTCAATCTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCA
TCTT
Found at i:5250098 original size:46 final size:46
Alignment explanation
Indices: 5249382--5250107 Score: 161
Period size: 44 Copynumber: 16.3 Consensus size: 46
5249372 ATCTGCTTCG
* * *
5249382 CTGCCCAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCA
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTATTCCA
* * ** *
5249428 CTGTCAAATACAGG--GACAAAATCTGCTTTCTTCGATCTACTT-CA
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTA-TTCCA
** * ** ** *
5249472 CCACC-AGTATGGGAAGACAAGATCTGCTTTCTTCGATCTACTT-CA
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTA-TTCCA
** * ** * ** *
5249517 CCACC-AGTATGGGAAGACAAGATCTG-TATCTTGGATCCACTTCCTA
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTA-TTCC-A
* * * * * *
5249563 -T--C-AATATAGGAAGATAGGACCTGCTATCTTCGATCTACTT-CA
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTA-TTCCA
* ** * *
5249605 C-GCC-AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGC-
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTA-TTC-CA
** ** * * *
5249650 CCACC-AATATGGGAAGACAAGATCTGC-ATCGTCGATCCACTT-C-
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTA-TTCCA
* * ** * * *
5249693 CTACC-AATATAGGAAGACCGGACCTGCTATCTTCGATCTACTT-CA
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTA-TTCCA
* ** * *
5249738 C-GCC-AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGC-
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTA-TTC-CA
* * * *
5249783 C-ACCAAAT--GGGAAGACAAGATCTGC-ATCTTCGATCCACTT-C-
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTA-TTCCA
* * * * * * *
5249824 CTACC-AATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT-CA
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTA-TTCCA
* * ** * *
5249869 C-GCC-AATACATGAAGATAAGATCTGCTTTCTGCGATCTACTTCGC-
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTA-TTC-CA
* *
5249914 C-ACC-AATATAGGAAGACAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTATTCCA
* * * * *
5249958 CTGCCAAATACAGTG-AGATAGAGTTAT-CGA-CTTCAATCTACTCCA
1 CTGCCAAATACAG-GAAGACA-AGATCTGCAATCTTCAATCTATTCCA
* * * ** * * * * *
5250003 CTG--TAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT-CG
1 CTGCCAAAT-ACAGGAAGACAAGATCTGCAATCTTCAATCT-ATTCCA
*
5250048 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTATTCCA
*
5250094 CTGCCAGATACAGG
1 CTGCCAAATACAGG
5250108 GAGATAGAGT
Statistics
Matches: 533, Mismatches: 110, Indels: 74
0.74 0.15 0.10
Matches are distributed among these distances:
41 5 0.01
42 4 0.01
43 79 0.15
44 206 0.39
45 139 0.26
46 93 0.17
47 7 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (46 bp):
CTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCTATTCCA
Found at i:5250270 original size:86 final size:86
Alignment explanation
Indices: 5250166--5250514 Score: 549
Period size: 86 Copynumber: 4.1 Consensus size: 86
5250156 AAATTTGCCA
* * * *
5250166 TCTTCGATCTGCTTCGCTGCCAAATACAGGAAAG-AAGATCTGATATCTTCAACCAGCTCTGCTA
1 TCTTCGATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTA
5250230 CAAACGAGAGAGGCAAGGTTTG
65 CAAACGAGAGAGGCAAGGTTTG
* *
5250252 TCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
5250317 AAACGAGA-ATGGCAAGGTTTG
66 AAACGAGAGA-GGCAAGGTTTG
*
5250338 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
*
5250403 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
* *
5250424 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAACTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
* * *
5250489 GACCGAGAGAGGCAAGGTTTA
66 AAACGAGAGAGGCAAGGTTTG
5250510 TCTTC
1 TCTTC
5250515 AATTTTTACT
Statistics
Matches: 245, Mismatches: 15, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
85 10 0.04
86 235 0.96
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (86 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
AAACGAGAGAGGCAAGGTTTG
Found at i:5250460 original size:42 final size:42
Alignment explanation
Indices: 5250240--5250460 Score: 116
Period size: 42 Copynumber: 5.2 Consensus size: 42
5250230 CAAACGAGAG
*
5250240 AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAGTGCAGGA
1 AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
* * * * * * * *
5250282 AGGCAAGATCTGCTATCTTCAACCAGC-TCTACT-ACAA-AC-GAGA
1 AGGCAAGGT-T--TGTCTTCGATCTGCTTC-GCTGTCAATGCAG-GA
5250325 ATGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
1 A-GGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
* * * * * * * *
5250368 AGGCAAGATCTGCTATCTTCAACCAGC-TCTACT-ACAA-AC-GAGA
1 AGGCAAGGT-T--TGTCTTCGATCTGCTTC-GCTGTCAATGCAG-GA
*
5250411 GTGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
5250454 AGGCAAG
1 AGGCAAG
5250461 ATCTGATAAC
Statistics
Matches: 124, Mismatches: 35, Indels: 40
0.62 0.18 0.20
Matches are distributed among these distances:
41 24 0.19
42 33 0.27
43 18 0.15
44 25 0.20
45 24 0.19
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.27
Consensus pattern (42 bp):
AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
Found at i:5254674 original size:19 final size:20
Alignment explanation
Indices: 5254650--5254693 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
5254640 CGTGAAAGTC
* *
5254650 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
5254669 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
5254689 -AATGC
1 TAATGC
5254694 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:5261662 original size:16 final size:16
Alignment explanation
Indices: 5261638--5261676 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5261628 GATTTTTTTG
*
5261638 TATTTTTTATGTTTAAT
1 TATTTTTAAT-TTTAAT
*
5261655 TATTTTTAATTTTATT
1 TATTTTTAATTTTAAT
5261671 TATTTT
1 TATTTT
5261677 ATTAATTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TATTTTTAATTTTAAT
Found at i:5264224 original size:2 final size:2
Alignment explanation
Indices: 5264217--5264254 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5264207 AGAATCTTAT
5264217 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5264255 ATCATTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5269768 original size:81 final size:81
Alignment explanation
Indices: 5269633--5269795 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
5269623 CAAGTCCCTT
5269633 GCTTAAAATATTATCCACTATCTACTTTACAAATCTTACTTTCCACTATTAGATTTTACAATGAC
1 GCTTAAAATATTATCCACTATCTACTTTACAAATCTTACTTTCCACTATTAGATTTTACAATGAC
5269698 AAACCCTTGTAATTTG
66 AAACCCTTGTAATTTG
5269714 GCTTAAAATATTATCCACTATCTACTTTACAAATCTTACTTTCCACTATTAGATTTTACAATGAC
1 GCTTAAAATATTATCCACTATCTACTTTACAAATCTTACTTTCCACTATTAGATTTTACAATGAC
5269779 AAACCCTTGTAATTTG
66 AAACCCTTGTAATTTG
5269795 G
1 G
5269796 ACCGGAGTCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (81 bp):
GCTTAAAATATTATCCACTATCTACTTTACAAATCTTACTTTCCACTATTAGATTTTACAATGAC
AAACCCTTGTAATTTG
Found at i:5280319 original size:18 final size:17
Alignment explanation
Indices: 5280298--5280348 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
5280288 AGAGTTTTAA
5280298 AAATATTTATAAAATTT
1 AAATATTTATAAAATTT
*
5280315 GAAATTTTTATAAATATATT
1 -AAATATTTATAAA-AT-TT
5280335 AAA-ATTTA-AAAATT
1 AAATATTTATAAAATT
5280349 ATTTTGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 1 0.03
16 2 0.07
17 3 0.10
18 16 0.55
19 5 0.17
20 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
AAATATTTATAAAATTT
Found at i:5280348 original size:28 final size:28
Alignment explanation
Indices: 5280292--5280345 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
5280282 ATTTTTAGAG
* *
5280292 TTTTAAAAATATTTATAAAATTTGAAAT
1 TTTTAAAAATATATATAAAATTTAAAAT
*
5280320 TTTTATAAATATAT-TAAAATTTAAAA
1 TTTTAAAAATATATATAAAATTTAAAA
5280346 ATTATTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
TTTTAAAAATATATATAAAATTTAAAAT
Found at i:5280772 original size:3 final size:3
Alignment explanation
Indices: 5280764--5280797 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
5280754 TCTGATTTTT
5280764 ATA ATA ATA ATA ATA ATA ATAA ATAA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT-A AT-A ATA ATA AT
5280798 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 23 0.77
4 7 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5286932 original size:54 final size:53
Alignment explanation
Indices: 5286765--5287068 Score: 200
Period size: 54 Copynumber: 5.7 Consensus size: 53
5286755 TACGGGTTGT
*** * * * * *
5286765 TGATTTACGATGGCGACCTCCTATTTACGAGATTTTAAGAATTTATAGTTCAC
1 TGATTTACGATCATGACCTTCTACTTACAAGATTTCAAGAATTTATGGTTCAC
* ** * * *
5286818 TAATTTACGATTTTCACCTTCTACTTACAAGATTTTAAGAATAT-TGCGATTCAC
1 TGATTTACGATCATGACCTTCTACTTACAAGATTTCAAGAATTTATG-G-TTCAC
** * * * *
5286872 CCATTTACGATTATGACCTTTTACTTACAAGATTTCAAGATTCTTATGGTTCGC
1 TGATTTACGATCATGACCTTCTACTTACAAGATTTCAAGAAT-TTATGGTTCAC
* ** * * * ***
5286926 TGATTTACAATCACAACCTTCTATTTACAAGATTTCAAAGATTTTACGGTTGGT
1 TGATTTACGATCATGACCTTCTACTTACAAGATTTC-AAGAATTTATGGTTCAC
* * *
5286980 TGATTTACGATCGTGACCTTCTACTTATAAGA-TTCTAAGAATCTTATGATTCA-
1 TGATTTACGATCATGACCTTCTACTTACAAGATTTC-AAGAAT-TTATGGTTCAC
*** *
5287033 TCGATTTACGATCGCAACCATCTACTTACAAGATTT
1 T-GATTTACGATCATGACCTTCTACTTACAAGATTT
5287069 TCAGAATCTT
Statistics
Matches: 197, Mismatches: 46, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
52 1 0.01
53 45 0.23
54 139 0.71
55 10 0.05
56 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (53 bp):
TGATTTACGATCATGACCTTCTACTTACAAGATTTCAAGAATTTATGGTTCAC
Found at i:5286986 original size:108 final size:108
Alignment explanation
Indices: 5286874--5287068 Score: 259
Period size: 108 Copynumber: 1.8 Consensus size: 108
5286864 CGATTCACCC
* * * * *
5286874 ATTTACGATTATGACCTTTTACTTACAAGATT-TCAAGATTCTTATGGTTC-GCTGATTTACAAT
1 ATTTACGATCATGACCTTCTACTTACAAGATTCT-AAGAATCTTATGATTCATC-GATTTACAAT
* *
5286937 CACAACCTTCTATTTACAAGATTTCAAAGATTTTACGGTTGGTTG
64 CACAACCATCTACTTACAAGATTTCAAAGATTTTACGGTTGGTTG
* * * *
5286982 ATTTACGATCGTGACCTTCTACTTATAAGATTCTAAGAATCTTATGATTCATCGATTTACGATCG
1 ATTTACGATCATGACCTTCTACTTACAAGATTCTAAGAATCTTATGATTCATCGATTTACAATCA
5287047 CAACCATCTACTTACAAGATTT
66 CAACCATCTACTTACAAGATTT
5287069 TCAGAATCTT
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
108 72 0.97
109 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (108 bp):
ATTTACGATCATGACCTTCTACTTACAAGATTCTAAGAATCTTATGATTCATCGATTTACAATCA
CAACCATCTACTTACAAGATTTCAAAGATTTTACGGTTGGTTG
Found at i:5287075 original size:54 final size:54
Alignment explanation
Indices: 5286833--5287176 Score: 218
Period size: 54 Copynumber: 6.4 Consensus size: 54
5286823 TACGATTTTC
* * ** * * ****
5286833 ACCTTCTACTTACAAGATTTTAAGAATATTGCGATTCACCCATTTACGATTATG
1 ACCTTCTACTTACAAGATTTTCAGAATCTTATGATTCATCGATTTACGATCGCA
* * * * * *
5286887 ACCTTTTACTTACAAGA-TTTCAAGATTCTTATGGTTC-GCTGATTTACAATCACA
1 ACCTTCTACTTACAAGATTTTC-AGAATCTTATGATTCATC-GATTTACGATCGCA
* * * * * ** * **
5286941 ACCTTCTATTTACAAGA-TTTCAAAGATTTTACGGTTGGTTGATTTACGATCGTG
1 ACCTTCTACTTACAAGATTTTCAGA-ATCTTATGATTCATCGATTTACGATCGCA
* * *
5286995 ACCTTCTACTTATAAGATTCTAAGAATCTTATGATTCATCGATTTACGATCGCA
1 ACCTTCTACTTACAAGATTTTCAGAATCTTATGATTCATCGATTTACGATCGCA
* * * *
5287049 ACCATCTACTTACAAGATTTTCAGAATCTTATAATTCTTCGATTTACGATCGCG
1 ACCTTCTACTTACAAGATTTTCAGAATCTTATGATTCATCGATTTACGATCGCA
* * * *
5287103 A-CTTCCTACTTATAAGATCTT-AGAAT-TT-CGCAGTTCATTGATTT-CAGATCGCA
1 ACCTT-CTACTTACAAGATTTTCAGAATCTTATG-A-TTCATCGATTTAC-GATCGCA
* *
5287156 ACCTTTTACTTACAATATTTT
1 ACCTTCTACTTACAAGATTTT
5287177 AAAAATCTCG
Statistics
Matches: 222, Mismatches: 58, Indels: 21
0.74 0.19 0.07
Matches are distributed among these distances:
52 4 0.02
53 41 0.18
54 173 0.78
55 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (54 bp):
ACCTTCTACTTACAAGATTTTCAGAATCTTATGATTCATCGATTTACGATCGCA
Found at i:5287176 original size:107 final size:108
Alignment explanation
Indices: 5286981--5287176 Score: 258
Period size: 107 Copynumber: 1.8 Consensus size: 108
5286971 ACGGTTGGTT
* *
5286981 GATTTACGATCGTGACCTTCTACTTATAAGATTCTAAGAATCTTATGATTCATCGATTTACGATC
1 GATTTACGATCGCGACCTTCTACTTATAAGATTCTAAGAATCTTACGATTCATCGATTTACGATC
5287046 GCAACCATCTACTTACAAGATTTTCAGAATCTTATAATTCTTC
66 GCAACCATCTACTTACAAGATTTTCAGAATCTTATAATTCTTC
* *
5287089 GATTTACGATCGCGA-CTTCCTACTTATAAGA-TCTTAGAAT-TT-CGCAGTTCATTGATTT-CA
1 GATTTACGATCGCGACCTT-CTACTTATAAGATTCTAAGAATCTTACG-A-TTCATCGATTTAC-
* * *
5287149 GATCGCAACCTTTTACTTACAATATTTT
62 GATCGCAACCATCTACTTACAAGATTTT
5287177 AAAAATCTCG
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
105 1 0.01
106 4 0.05
107 46 0.60
108 26 0.34
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (108 bp):
GATTTACGATCGCGACCTTCTACTTATAAGATTCTAAGAATCTTACGATTCATCGATTTACGATC
GCAACCATCTACTTACAAGATTTTCAGAATCTTATAATTCTTC
Found at i:5287400 original size:55 final size:55
Alignment explanation
Indices: 5287301--5287476 Score: 167
Period size: 55 Copynumber: 3.2 Consensus size: 55
5287291 TGTAGTTCGT
* * * * * *
5287301 CAATTTCAGATCACAAC-TTTTTAATTGACAAGATCCTT-AAAATCTCATAGTTCAC
1 CAATTTTAGATCACAACATTTTAAATT-ACAATAT-TTTCAGAATCTCACAGTTCAC
* * * * *
5287356 CGATTTTATATCACAACCTTTTAAATTACAATATTTTCATAATCTCACAGTTCGC
1 CAATTTTAGATCACAACATTTTAAATTACAATATTTTCAGAATCTCACAGTTCAC
* * * * * *
5287411 TAATTTTAGATCGCGACATTTTAACTTACAATATTTTCAGAATCTCGCAATTCAC
1 CAATTTTAGATCACAACATTTTAAATTACAATATTTTCAGAATCTCACAGTTCAC
5287466 CAATTTTAGAT
1 CAATTTTAGAT
5287477 TGTAAACTTT
Statistics
Matches: 98, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
54 2 0.02
55 88 0.90
56 8 0.08
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.38
Consensus pattern (55 bp):
CAATTTTAGATCACAACATTTTAAATTACAATATTTTCAGAATCTCACAGTTCAC
Found at i:5287488 original size:55 final size:54
Alignment explanation
Indices: 5287341--5287494 Score: 148
Period size: 55 Copynumber: 2.8 Consensus size: 54
5287331 AGATCCTTAA
* * * * * *
5287341 AATCTCATAGTTCACCGATTTTATATC-ACAACCTTTTAAATTACAATATTTTCAT
1 AATCTCACAATTCACCAATTTTAGATCGA-AA-CTTTTAACTTACAATATTTTCAG
* * * **
5287396 AATCTCACAGTTCGCTAATTTTAGATCGCGACATTTTAACTTACAATATTTTCAG
1 AATCTCACAATTCACCAATTTTAGATCGAAAC-TTTTAACTTACAATATTTTCAG
* *
5287451 AATCTCGCAATTCACCAATTTTAGATTGTAAACTTTTAACTTAC
1 AATCTCACAATTCACCAATTTTAGATCG-AAACTTTTAACTTAC
5287495 CAAGTTTTCA
Statistics
Matches: 80, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
54 1 0.01
55 77 0.96
56 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (54 bp):
AATCTCACAATTCACCAATTTTAGATCGAAACTTTTAACTTACAATATTTTCAG
Found at i:5287581 original size:54 final size:54
Alignment explanation
Indices: 5287481--5287613 Score: 133
Period size: 54 Copynumber: 2.4 Consensus size: 54
5287471 TTAGATTGTA
* * * **
5287481 AACTTTTAACTTACCAAG-TTTTCATAATCTTGTGGTTCGTCAATTTCTTATCGC
1 AACTTTTAACTTA-CAAGATTTTCAAAATCTTGGGGTTAGTCAATTTCAAATCGC
* ** *
5287535 AACTTTTAACTTACAAGATTTTCAAAATTTTGGGGTTAGTTGATTTCAAATCTC
1 AACTTTTAACTTACAAGATTTTCAAAATCTTGGGGTTAGTCAATTTCAAATCGC
* * *
5287589 AACTTTTTAATTTATAATATTTTCA
1 AAC-TTTTAACTTACAAGATTTTCA
5287614 GGGTCTTGCA
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
53 4 0.06
54 43 0.66
55 18 0.28
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (54 bp):
AACTTTTAACTTACAAGATTTTCAAAATCTTGGGGTTAGTCAATTTCAAATCGC
Found at i:5292294 original size:24 final size:26
Alignment explanation
Indices: 5292246--5292294 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
5292236 GTTTTAATTT
* *
5292246 TTTTAATTTTTTATAAAATTTATTAA
1 TTTTAATTTTATATAAAATTAATTAA
5292272 TTTTAATTTTAT-TAAAA-TAATTA
1 TTTTAATTTTATATAAAATTAATTA
5292295 GTTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTAATTTTATATAAAATTAATTAA
Found at i:5294268 original size:56 final size:54
Alignment explanation
Indices: 5294117--5294268 Score: 189
Period size: 56 Copynumber: 2.8 Consensus size: 54
5294107 ATAATTTAGG
** * *
5294117 TGCACCTACCTTATTGGCAAACTGTGTTGGTGGCTAGGTAAACAAATATATATA
1 TGCACCTACCTTGCTGGCGAACTGTGTTGGTGGATAGGTAAACAAATATATATA
* * * * *
5294171 TGCACATACCTTGCTAGTGAACTGTG-TGGTCGACTAAGTAAACAAATATATATATA
1 TGCACCTACCTTGCTGGCGAACTGTGTTGGTGGA-TAGGTAAAC-AA-ATATATATA
5294227 TGCACCTACCTTGCTGGCGAACTGTGTTGGTGGATAGGTAAA
1 TGCACCTACCTTGCTGGCGAACTGTGTTGGTGGATAGGTAAA
5294269 ATTTATTTGC
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
53 5 0.06
54 28 0.35
55 2 0.03
56 39 0.49
57 6 0.08
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (54 bp):
TGCACCTACCTTGCTGGCGAACTGTGTTGGTGGATAGGTAAACAAATATATATA
Found at i:5297072 original size:22 final size:19
Alignment explanation
Indices: 5297030--5297074 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 19
5297020 TTTATATTTT
5297030 ATTATTTTTAAATAAAAAA
1 ATTATTTTTAAATAAAAAA
5297049 ATTATTTTATAAATCAAAATAA
1 ATTATTTT-TAAAT-AAAA-AA
5297071 ATTA
1 ATTA
5297075 AACCCGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.35
20 5 0.22
21 4 0.17
22 6 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTATTTTTAAATAAAAAA
Found at i:5300189 original size:22 final size:22
Alignment explanation
Indices: 5300164--5300213 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
5300154 ATTGTTTTTC
*
5300164 ATTATTTTGCTATCATTTCATT
1 ATTATTTTACTATCATTTCATT
* * *
5300186 ATTATATTACTATTATTTTATT
1 ATTATTTTACTATCATTTCATT
5300208 ATTATT
1 ATTATT
5300214 ATTATTATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTATTTTACTATCATTTCATT
Found at i:5300202 original size:3 final size:3
Alignment explanation
Indices: 5300183--5300222 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
5300173 CTATCATTTC
*
5300183 ATT ATT A-T ATT ACT ATT ATT -TT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5300223 TGGATATTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5300202 original size:14 final size:14
Alignment explanation
Indices: 5300183--5300218 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5300173 CTATCATTTC
5300183 ATTATTATATTACT
1 ATTATTATATTACT
* *
5300197 ATTATTTTATTATT
1 ATTATTATATTACT
5300211 ATTATTAT
1 ATTATTAT
5300219 TATTTGGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTATATTACT
Found at i:5304040 original size:15 final size:15
Alignment explanation
Indices: 5304018--5304059 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
5304008 TACTCATCAT
5304018 CTATTATGTAATGCCA
1 CTATTATG-AATGCCA
*
5304034 C-ATTATGAATTCCA
1 CTATTATGAATGCCA
*
5304048 CTATTACGAATG
1 CTATTATGAATG
5304060 ATCCTACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 7 0.32
15 14 0.64
16 1 0.05
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (15 bp):
CTATTATGAATGCCA
Found at i:5308909 original size:22 final size:24
Alignment explanation
Indices: 5308858--5308918 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 24
5308848 AAGTATTTAA
*
5308858 ATTAAAATATAATTTTTAGAATAG
1 ATTAAATTATAATTTTTAGAATAG
*
5308882 -TAAAATTATAATTTTTA-AA-AG
1 ATTAAATTATAATTTTTAGAATAG
*
5308903 ATTAAATTAAAATTTT
1 ATTAAATTATAATTTT
5308919 ATCATTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 15 0.47
23 15 0.47
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (24 bp):
ATTAAATTATAATTTTTAGAATAG
Found at i:5313734 original size:7 final size:7
Alignment explanation
Indices: 5313722--5313752 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
5313712 CTTTTAAATC
5313722 ATATATT
1 ATATATT
5313729 ATATATT
1 ATATATT
5313736 ATATATT
1 ATATATT
5313743 ATATATT
1 ATATATT
5313750 ATA
1 ATA
5313753 CATTTATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATATATT
Found at i:5316291 original size:20 final size:22
Alignment explanation
Indices: 5316266--5316307 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5316256 CCATTGTTGA
5316266 GAAATTGA-A-AAATCAAGCTT
1 GAAATTGATAGAAATCAAGCTT
*
5316286 GAAATTGATAGAAATTAAGCTT
1 GAAATTGATAGAAATCAAGCTT
5316308 AGCTTATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.29
Consensus pattern (22 bp):
GAAATTGATAGAAATCAAGCTT
Found at i:5318708 original size:22 final size:24
Alignment explanation
Indices: 5318682--5318734 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
5318672 ACTTTACAAT
*
5318682 TATTTTTAT-TTAATTTAATTATA
1 TATTTTTATAATAATTTAATTATA
*
5318705 -ATTTTTATAATATTTTAATTATA
1 TATTTTTATAATAATTTAATTATA
5318728 TATTTTT
1 TATTTTT
5318735 TTATAAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.31
23 12 0.46
24 6 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TATTTTTATAATAATTTAATTATA
Found at i:5318729 original size:25 final size:27
Alignment explanation
Indices: 5318697--5318757 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
5318687 TTATTTAATT
*
5318697 TAAT-TATA-ATTTTTATAATATTTTA
1 TAATATATATATTTTTATAAGATTTTA
* *
5318722 -ATTATATATTTTTTTATAAGATTTTA
1 TAATATATATATTTTTATAAGATTTTA
5318748 TAATATATAT
1 TAATATATAT
5318758 TTCATTTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 2 0.07
25 4 0.14
26 15 0.52
27 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
TAATATATATATTTTTATAAGATTTTA
Found at i:5318771 original size:26 final size:26
Alignment explanation
Indices: 5318709--5318772 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
5318699 ATTATAATTT
* * **
5318709 TTATAATATTTTAATTATATATTTTT
1 TTATAACATTTTAAATATATATTTCA
*
5318735 TTATAAGATTTTATAATATATATTTCA
1 TTATAACATTTTA-AATATATATTTCA
5318762 TT-TAACATTTT
1 TTATAACATTTT
5318773 GAAGTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 20 0.62
27 12 0.38
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (26 bp):
TTATAACATTTTAAATATATATTTCA
Found at i:5320428 original size:31 final size:32
Alignment explanation
Indices: 5320370--5320434 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
5320360 AATTTATATT
**
5320370 TTATGTATTATTATATTAAGTTATTT-AAATA
1 TTATGTATTATTATATTAAAATATTTAAAATA
*
5320401 TTATTTATTATTATATTTAAAAT-TTTAAAATA
1 TTATGTATTATTATA-TTAAAATATTTAAAATA
5320433 TT
1 TT
5320435 TCATGTGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 17 0.59
32 12 0.41
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (32 bp):
TTATGTATTATTATATTAAAATATTTAAAATA
Found at i:5320544 original size:61 final size:63
Alignment explanation
Indices: 5320364--5320544 Score: 156
Period size: 61 Copynumber: 2.9 Consensus size: 63
5320354 TAGATTAATT
* * * * * *
5320364 TATATTTTATGTATTATTATA-TTAAGTTATTTAAATATTATTTATTATTATATTTAAAATTTTA
1 TATATTTTATGTGTAATTATATTTAAATTAATTAAATATTATTTA-AATTA-ATTTAAAA-TATA
5320428 A
63 A
* * * * * * * *
5320429 AATATTTCATGTGTAATTAAATTTATAAATAATTTATTAATT-TTAAAAGT-ATTTAAAA-AT-A
1 TATATTTTATGTGTAATTATATTTA-AATTAATTAAAT-ATTATTTAAATTAATTTAAAATATAA
5320490 TATATTTTATGTGTAATTATATTTAAATTAATTAAATATTATTTAAATTAATTTA
1 TATATTTTATGTGTAATTATATTTAAATTAATTAAATATTATTTAAATTAATTTA
5320545 TTTTTAATTT
Statistics
Matches: 89, Mismatches: 22, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
59 3 0.03
60 15 0.17
61 28 0.31
62 1 0.01
64 8 0.09
65 16 0.18
66 5 0.06
67 10 0.11
68 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (63 bp):
TATATTTTATGTGTAATTATATTTAAATTAATTAAATATTATTTAAATTAATTTAAAATATAA
Found at i:5322150 original size:61 final size:61
Alignment explanation
Indices: 5322078--5322206 Score: 152
Period size: 61 Copynumber: 2.1 Consensus size: 61
5322068 ACCCAAAATA
* * ** * *
5322078 TAAAATATTCAACAAATTTAATCTTCAATGTTTATAAAAATTATCT-ATTTAGTTTTAATTTT
1 TAAAA-ATTCAACAAATTTAACCATCAAAATTTACAAAAATTAT-TGATTTAGTTCTAATTTT
* * *
5322140 TAAAAATTCAATAAATTTAGCCATCAAAATTTACAAAATTTATTGATTTAGTTCTAATTTT
1 TAAAAATTCAACAAATTTAACCATCAAAATTTACAAAAATTATTGATTTAGTTCTAATTTT
5322201 TAAAAA
1 TAAAAA
5322207 ATTAATACTT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
60 1 0.02
61 51 0.89
62 5 0.09
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (61 bp):
TAAAAATTCAACAAATTTAACCATCAAAATTTACAAAAATTATTGATTTAGTTCTAATTTT
Found at i:5325880 original size:24 final size:24
Alignment explanation
Indices: 5325848--5325894 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
5325838 AACCTAGAGT
5325848 TAGTTGTTCTTACTCTCGAAAGAA
1 TAGTTGTTCTTACTCTCGAAAGAA
5325872 TAGTTGTTCTTACTCTCGAAAGA
1 TAGTTGTTCTTACTCTCGAAAGA
5325895 GATATTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
TAGTTGTTCTTACTCTCGAAAGAA
Found at i:5340484 original size:17 final size:17
Alignment explanation
Indices: 5340459--5340492 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5340449 CACATGCATC
*
5340459 ATCTTCATGCAAATTAA
1 ATCTCCATGCAAATTAA
5340476 ATCTCCATGCAAATTAA
1 ATCTCCATGCAAATTAA
5340493 CATACTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (17 bp):
ATCTCCATGCAAATTAA
Found at i:5350967 original size:13 final size:14
Alignment explanation
Indices: 5350949--5350977 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5350939 CTTTTTTATC
5350949 TAAATTTAT-TTTT
1 TAAATTTATATTTT
5350962 TAAATTTATATTTT
1 TAAATTTATATTTT
5350976 TA
1 TA
5350978 TCTAAATCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TAAATTTATATTTT
Found at i:5351941 original size:25 final size:25
Alignment explanation
Indices: 5351913--5351965 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
5351903 GACATGTGAC
*
5351913 AAACATAAATTA-ATAAAATTAATAA
1 AAACATAAAATATAT-AAATTAATAA
*
5351938 AAACTTAAAATATATAAATTAATAA
1 AAACATAAAATATATAAATTAATAA
5351963 AAA
1 AAA
5351966 AAAAGTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (25 bp):
AAACATAAAATATATAAATTAATAA
Found at i:5352812 original size:8 final size:8
Alignment explanation
Indices: 5352811--5352842 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
5352801 TTTATAAATT
*
5352811 TATAAAAA
1 TATATAAA
5352819 TATATAAA
1 TATATAAA
5352827 TATATAAA
1 TATATAAA
5352835 TATATAAA
1 TATATAAA
5352843 AGGACTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
TATATAAA
Found at i:5352826 original size:18 final size:18
Alignment explanation
Indices: 5352803--5352840 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5352793 TTTTAGATTT
*
5352803 TATAAATTTATAAAAATA
1 TATAAATATATAAAAATA
*
5352821 TATAAATATATAAATATA
1 TATAAATATATAAAAATA
5352839 TA
1 TA
5352841 AAAGGACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATAAATATATAAAAATA
Found at i:5364686 original size:3 final size:3
Alignment explanation
Indices: 5364680--5364711 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5364670 TGCCATCATC
5364680 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5364712 CCTAATGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5364948 original size:17 final size:17
Alignment explanation
Indices: 5364901--5364969 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 17
5364891 TTTTCCCATA
5364901 AAAATAATAAAAA-ATT
1 AAAATAATAAAAATATT
*
5364917 ATAAAT-ATCAGAAAATATC
1 A-AAATAAT-A-AAAATATT
5364936 AAAATAATAAAAATGATT
1 AAAATAATAAAAAT-ATT
5364954 AAATATAA-AAAAATAT
1 AAA-ATAATAAAAATAT
5364970 GAATATTGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
16 3 0.07
17 12 0.27
18 20 0.45
19 9 0.20
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATAATAAAAATATT
Found at i:5364957 original size:35 final size:35
Alignment explanation
Indices: 5364901--5364969 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
5364891 TTTTCCCATA
* * *
5364901 AAAATAATAAAAAATTATAAATATCAGAAAATATC
1 AAAATAATAAAAAATGATAAATATAAAAAAATATC
5364936 AAAATAAT-AAAAATGATTAAATATAAAAAAATAT
1 AAAATAATAAAAAATGA-TAAATATAAAAAAATAT
5364970 GAATATTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 7 0.23
35 23 0.77
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (35 bp):
AAAATAATAAAAAATGATAAATATAAAAAAATATC
Found at i:5364974 original size:16 final size:16
Alignment explanation
Indices: 5364902--5364975 Score: 60
Period size: 16 Copynumber: 4.4 Consensus size: 16
5364892 TTTCCCATAA
*
5364902 AAATAATAAAAAATTAT
1 AAAT-ATAAAAAAATAT
* *
5364919 AAATATCAGAAAATAT
1 AAATATAAAAAAATAT
5364935 CAAA-ATAATAAAAATGATT
1 -AAATATAA-AAAAAT-A-T
5364954 AAATATAAAAAAATAT
1 AAATATAAAAAAATAT
*
5364970 GAATAT
1 AAATAT
5364976 TGATTTAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
16 18 0.39
17 13 0.28
18 10 0.22
19 5 0.11
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (16 bp):
AAATATAAAAAAATAT
Found at i:5365027 original size:19 final size:20
Alignment explanation
Indices: 5365004--5365078 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 20
5364994 ATTATAAAAA
5365004 TAAAATTCTAATAAAAATA-
1 TAAAATTCTAATAAAAATAT
5365023 TAAAA-T-TAATAAAATATATT
1 TAAAATTCTAATAAAA-ATA-T
* *
5365043 TAAAATTTTATAAAAAAATAT
1 TAAAATTCTA-ATAAAAATAT
*
5365064 TAATATTCT-ATAAAA
1 TAAAATTCTAATAAAA
5365079 TCATAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
17 8 0.17
18 4 0.09
19 10 0.22
20 5 0.11
21 9 0.20
22 5 0.11
23 5 0.11
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAATTCTAATAAAAATAT
Found at i:5365049 original size:20 final size:17
Alignment explanation
Indices: 5364928--5365040 Score: 65
Period size: 17 Copynumber: 6.5 Consensus size: 17
5364918 TAAATATCAG
5364928 AAAATATCAAAA-TAATA
1 AAAATAT-AAAATTAATA
*
5364945 AAAATGATTAAATATAA-A
1 AAAAT-ATAAAAT-TAATA
* *
5364963 AAAATATGAATATTGATTTA
1 AAAATAT-AAAATT-A-ATA
**
5364983 AAGTTATAAATATT-ATA
1 AAAATATAAA-ATTAATA
*
5365000 AAAATA-AAATTCTAATA
1 AAAATATAAAAT-TAATA
5365017 AAAATATAAAATTAAT-
1 AAAATATAAAATTAATA
5365033 AAAATATA
1 AAAATATA
5365041 TTTAAAATTT
Statistics
Matches: 73, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
15 1 0.01
16 12 0.16
17 30 0.41
18 16 0.22
19 5 0.07
20 9 0.12
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (17 bp):
AAAATATAAAATTAATA
Found at i:5365057 original size:21 final size:22
Alignment explanation
Indices: 5365018--5365079 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
5365008 ATTCTAATAA
*
5365018 AAATA-TAAAA-TTAATAAAAT
1 AAATATTAAAATTTTATAAAAT
*
5365038 ATAT-TTAAAATTTTATAAAA-
1 AAATATTAAAATTTTATAAAAT
* *
5365058 AAATATTAATATTCTATAAAAT
1 AAATATTAAAATTTTATAAAAT
5365080 CATAAAAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
20 11 0.33
21 22 0.67
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATATTAAAATTTTATAAAAT
Found at i:5365104 original size:26 final size:29
Alignment explanation
Indices: 5365052--5365116 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 29
5365042 TTAAAATTTT
*
5365052 ATAAAAAAATATTAATATTCTATAAAATC
1 ATAAAAAAATATTAATATTATATAAAATC
* *
5365081 ATAAAAAAGTATTAA-A-TATA-AAAATT
1 ATAAAAAAATATTAATATTATATAAAATC
5365107 ATAAAAAAAT
1 ATAAAAAAAT
5365117 CATAAAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 14 0.44
27 3 0.09
28 1 0.03
29 14 0.44
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (29 bp):
ATAAAAAAATATTAATATTATATAAAATC
Found at i:5365662 original size:12 final size:12
Alignment explanation
Indices: 5365645--5365677 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
5365635 CTGCCTGCCC
5365645 ATATTAATTTTT
1 ATATTAATTTTT
5365657 ATATT-ATTTTT
1 ATATTAATTTTT
5365668 ATA-TAATTTT
1 ATATTAATTTT
5365678 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:5365896 original size:22 final size:22
Alignment explanation
Indices: 5365871--5365920 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
5365861 CAATAACAAC
*
5365871 AAAATAGTAGCAACATAA-TAG
1 AAAATAGTAGCAAAATAAGTAG
*
5365892 TAAAATGGTAGCAAAATAAGTAG
1 -AAAATAGTAGCAAAATAAGTAG
5365915 AAAATA
1 AAAATA
5365921 ACAAGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.20
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGTAG
Found at i:5366177 original size:9 final size:9
Alignment explanation
Indices: 5366165--5366282 Score: 52
Period size: 9 Copynumber: 13.1 Consensus size: 9
5366155 TTATGTTTTT
5366165 TTTTTATAA
1 TTTTTATAA
5366174 TTTTTATAA
1 TTTTTATAA
* *
5366183 GTTATATAA
1 TTTTTATAA
*
5366192 TTTTAAATATA
1 TTTT-TATA-A
*
5366203 TTTTT-TAT
1 TTTTTATAA
5366211 TTTTTA-AGA
1 TTTTTATA-A
* *
5366220 CTTCTAATACA
1 -TTTTTATA-A
5366231 TTTTT-TAA
1 TTTTTATAA
*
5366239 GTTTTACTAA
1 TTTTTA-TAA
5366249 -TTTTAT--
1 TTTTTATAA
5366255 TTTTTATAA
1 TTTTTATAA
5366264 TTTTT-TATA
1 TTTTTATA-A
*
5366273 TTTCTATAA
1 TTTTTATAA
5366282 T
1 T
5366283 ATTACAAGTT
Statistics
Matches: 81, Mismatches: 15, Indels: 26
0.66 0.12 0.21
Matches are distributed among these distances:
7 6 0.07
8 14 0.17
9 39 0.48
10 15 0.19
11 7 0.09
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:5367525 original size:16 final size:15
Alignment explanation
Indices: 5367482--5367525 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5367472 TAATAATGGT
*
5367482 AAATTTTAATTTTTA
1 AAATTTTAATATTTA
*
5367497 AAATTTTATTATTTA
1 AAATTTTAATATTTA
*
5367512 ATAATTTGAATATT
1 A-AATTTTAATATT
5367526 ATTAATATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
AAATTTTAATATTTA
Found at i:5374633 original size:69 final size:69
Alignment explanation
Indices: 5374522--5374660 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
5374512 GATAGGAAAA
*
5374522 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTTGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
5374587 GCTG
66 GCTG
5374591 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
5374656 GCTG
66 GCTG
5374660 A
1 A
5374661 TAGAGTCTTG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.28
Consensus pattern (69 bp):
ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
GCTG
Found at i:5380888 original size:3 final size:3
Alignment explanation
Indices: 5380880--5380914 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5380870 TATCAAAATG
5380880 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5380915 ATTAGCTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5388078 original size:10 final size:12
Alignment explanation
Indices: 5388058--5388100 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
5388048 ACAAAGCGAA
5388058 GAAAAAGAAA-T
1 GAAAAAGAAATT
5388069 GAAAAA-AAATT
1 GAAAAAGAAATT
*
5388080 GAAAAAGAACTT
1 GAAAAAGAAATT
*
5388092 GAAGAAGAA
1 GAAAAAGAA
5388101 GAACCAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 3 0.11
11 13 0.46
12 12 0.43
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.12
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:5390497 original size:28 final size:27
Alignment explanation
Indices: 5390466--5390530 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 27
5390456 TTTATTTCAC
*
5390466 TATTATTTA-T-TAATGTTTTTTATCATTT
1 TATTATTTATTGTAAT-TATTTTAT--TTT
5390494 TATTATTATATTGTAATTATTTTATTTT
1 TATTATT-TATTGTAATTATTTTATTTT
5390522 TATTATTTA
1 TATTATTTA
5390531 AATATTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 2 0.06
28 17 0.52
29 2 0.06
30 8 0.24
31 4 0.12
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.68
Consensus pattern (27 bp):
TATTATTTATTGTAATTATTTTATTTT
Found at i:5390526 original size:14 final size:14
Alignment explanation
Indices: 5390491--5390529 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5390481 TTTTTTATCA
*
5390491 TTTTATTATTATAT
1 TTTTATTATTTTAT
* *
5390505 TGTAATTATTTTAT
1 TTTTATTATTTTAT
5390519 TTTTATTATTT
1 TTTTATTATTT
5390530 AAATATTATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTTATTATTTTAT
Found at i:5390536 original size:22 final size:22
Alignment explanation
Indices: 5390490--5390536 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5390480 GTTTTTTATC
*
5390490 ATTTTATTATTATATTGTAATT
1 ATTTTATTATTATATTGTAAAT
*
5390512 ATTTTATTTTTATTATT-TAAAT
1 ATTTTATTATTA-TATTGTAAAT
5390534 ATT
1 ATT
5390537 ATATAATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTTTATTATTATATTGTAAAT
Found at i:5392170 original size:13 final size:12
Alignment explanation
Indices: 5392146--5392179 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
5392136 TGTTTAATTA
5392146 TATTAAGATAAT
1 TATTAAGATAAT
5392158 TATTAAGGATAAT
1 TATTAA-GATAAT
*
5392171 TATTTAGAT
1 TATTAAGAT
5392180 TTAAATTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (12 bp):
TATTAAGATAAT
Found at i:5392206 original size:10 final size:10
Alignment explanation
Indices: 5392191--5392242 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
5392181 TAAATTTAGG
5392191 ATTTATTTTT
1 ATTTATTTTT
*
5392201 ATTTATCTTT
1 ATTTATTTTT
* *
5392211 AATTATCTTT
1 ATTTATTTTT
*
5392221 ATTTATTTGT
1 ATTTATTTTT
5392231 ATTTATCTTTT
1 ATTTAT-TTTT
5392242 A
1 A
5392243 GAATTTAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
10 31 0.89
11 4 0.11
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:5396228 original size:39 final size:39
Alignment explanation
Indices: 5396156--5396242 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
5396146 GACTTAATGT
*
5396156 CTAGCAGGCTTCGTGCCAGTGATAAATTCAGGTTTATAC
1 CTAGCAGGCCTCGTGCCAGTGATAAATTCAGGTTTATAC
* * * *
5396195 CTAGTAGGCCTCGTGCCGGTGATAAGTTTAGGTTTATAC
1 CTAGCAGGCCTCGTGCCAGTGATAAATTCAGGTTTATAC
5396234 CTAGCAGGC
1 CTAGCAGGC
5396243 TAATTGCCGG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (39 bp):
CTAGCAGGCCTCGTGCCAGTGATAAATTCAGGTTTATAC
Found at i:5396251 original size:39 final size:39
Alignment explanation
Indices: 5396156--5396255 Score: 112
Period size: 39 Copynumber: 2.6 Consensus size: 39
5396146 GACTTAATGT
* * *
5396156 CTAGCAGGCTTCGTGCCAGTGATAAATTCAGGTTTATAC
1 CTAGCAGGCCTAGTGCCGGTGATAAATTCAGGTTTATAC
* * * *
5396195 CTAGTAGGCCTCGTGCCGGTGATAAGTTTAGGTTTATAC
1 CTAGCAGGCCTAGTGCCGGTGATAAATTCAGGTTTATAC
*
5396234 CTAGCAGG-CTAATTGCCGGTGA
1 CTAGCAGGCCT-AGTGCCGGTGA
5396256 AATAATAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 2 0.04
39 50 0.96
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (39 bp):
CTAGCAGGCCTAGTGCCGGTGATAAATTCAGGTTTATAC
Found at i:5399252 original size:5 final size:5
Alignment explanation
Indices: 5399242--5399319 Score: 63
Period size: 5 Copynumber: 15.4 Consensus size: 5
5399232 GTAACCCAAT
* *
5399242 TTTTA TTTTA TTTT- TATTTA TTTTA TTTATTA TTTTA TTTTG TTTTC
1 TTTTA TTTTA TTTTA T-TTTA TTTTA -TT-TTA TTTTA TTTTA TTTTA
* *
5399289 TTTT- TTATT- TATTA CTTTA TTTTA TTTTA TT
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TT
5399320 ATTTATTAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
4 5 0.08
5 48 0.79
6 5 0.08
7 3 0.05
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:5399263 original size:4 final size:4
Alignment explanation
Indices: 5399254--5399335 Score: 50
Period size: 4 Copynumber: 20.8 Consensus size: 4
5399244 TTATTTTATT
* *
5399254 TTTA TTTA TTTTA TTTA -TTA TTTTA TTT- TGT- TTTC TTT- TTTA TTTA
1 TTTA TTTA -TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
5399300 -TTA CTTTA TTTTA TTT- TATTA TTTA TTAA TTTA TTT
1 TTTA -TTTA -TTTA TTTA T-TTA TTTA TTTA TTTA TTT
5399336 GGATATTAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
3 14 0.22
4 35 0.55
5 15 0.23
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:5399307 original size:29 final size:29
Alignment explanation
Indices: 5399243--5399326 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 29
5399233 TAACCCAATT
*
5399243 TTTATTTTATTTTTATTTATTTTATTTATTAT
1 TTTATTTTA-TTTTA-TT-TTTTATTTATTAC
* *
5399275 TTTATTTTGTTTTCTTTTTTATTTATTAC
1 TTTATTTTATTTTATTTTTTATTTATTAC
*
5399304 TTTATTTTATTTTATTATTTATT
1 TTTATTTTATTTTATTTTTTATT
5399327 AATTTATTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 32 0.70
30 2 0.04
31 4 0.09
32 8 0.17
ACGTcount: A:0.19, C:0.02, G:0.01, T:0.77
Consensus pattern (29 bp):
TTTATTTTATTTTATTTTTTATTTATTAC
Found at i:5399321 original size:25 final size:23
Alignment explanation
Indices: 5399249--5399335 Score: 90
Period size: 25 Copynumber: 3.7 Consensus size: 23
5399239 AATTTTTATT
5399249 TTATTTTTATTTATTTTA-TTTA
1 TTATTTTTATTTATTTTATTTTA
* *
5399271 TTA-TTTTATTTTGTTTTCTTTT-
1 TTATTTTTA-TTTATTTTATTTTA
5399293 TTATTTATTACTTTATTTTATTTTA
1 TTATTT-TTA-TTTATTTTATTTTA
5399318 TTATTTATTAATTTATTT
1 TTATTT-TT-ATTTATTT
5399336 GGATATTAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
21 5 0.09
22 13 0.24
23 5 0.09
24 14 0.26
25 16 0.30
26 1 0.02
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.76
Consensus pattern (23 bp):
TTATTTTTATTTATTTTATTTTA
Found at i:5400509 original size:96 final size:97
Alignment explanation
Indices: 5400345--5400526 Score: 294
Period size: 96 Copynumber: 1.9 Consensus size: 97
5400335 TTTAAGAATG
*
5400345 TGTTGGGCTAAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGAT
1 TGTTGGGCTAAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAAT
*
5400410 ATATTCTTAAG-AAAAATAAAAATTAGGAGTA
66 ATATTCCTAAGTAAAAATAAAAATTAGGAGTA
* * * *
5400441 TGTTGGGCTGAGTAACCGGGGTGGGGTGTTTGGCTGTCGTCTCTCTTCGCGTCAAAAGGTTCAAT
1 TGTTGGGCTAAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAAT
*
5400506 ATATTCCTAAGTAAAACTAAA
66 ATATTCCTAAGTAAAAATAAA
5400527 TAAATTAAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
96 70 0.90
97 8 0.10
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (97 bp):
TGTTGGGCTAAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAAT
ATATTCCTAAGTAAAAATAAAAATTAGGAGTA
Found at i:5401180 original size:10 final size:10
Alignment explanation
Indices: 5401167--5401209 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
5401157 AGAATTTCTT
5401167 TTTATTTATC
1 TTTATTTATC
*
5401177 TTTAATTATC
1 TTTATTTATC
5401187 TTTATTTAT-
1 TTTATTTATC
5401196 TTGTATTTATC
1 TT-TATTTATC
5401207 TTT
1 TTT
5401210 TAGAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 2 0.07
10 25 0.86
11 2 0.07
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTATTTATC
Found at i:5413423 original size:19 final size:20
Alignment explanation
Indices: 5413393--5413439 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
5413383 TATAATAATA
*
5413393 AAACAAATAAATA-AAAGAAG
1 AAACAAAGAAATAGAAA-AAG
5413413 AAA-AAAGAAATAGAAAAAG
1 AAACAAAGAAATAGAAAAAG
5413432 AAACAAAG
1 AAACAAAG
5413440 CAAACCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.77, C:0.04, G:0.13, T:0.06
Consensus pattern (20 bp):
AAACAAAGAAATAGAAAAAG
Found at i:5413474 original size:20 final size:19
Alignment explanation
Indices: 5413451--5413493 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
5413441 AAACCCAAAG
* *
5413451 GAAACAAAACGGGAAAGAAA
1 GAAACAAAAAGAGAAAG-AA
*
5413471 GAAAGAAAAAGAGAAAGAA
1 GAAACAAAAAGAGAAAGAA
5413490 GAAA
1 GAAA
5413494 TAAAGCCAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.70, C:0.05, G:0.26, T:0.00
Consensus pattern (19 bp):
GAAACAAAAAGAGAAAGAA
Found at i:5414448 original size:41 final size:38
Alignment explanation
Indices: 5414360--5414466 Score: 119
Period size: 41 Copynumber: 2.8 Consensus size: 38
5414350 TGACTTCGAG
* *
5414360 TCGATGAGGCACTGAGTG-CTAATTTACT-TTGGTTTAA
1 TCGATGAGACACTGGGTGTC-AATTTACTATTGGTTTAA
* *
5414397 TCAATGAGACACTGGGTGTCAATTTACTACTTCGGATTTAT
1 TCGATGAGACACTGGGTGTCAATTTACTA-TT-GG-TTTAA
*
5414438 TCGATGAGACATTGGGTGTCAATTTACTA
1 TCGATGAGACACTGGGTGTCAATTTACTA
5414467 GTTTGAATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
37 23 0.39
38 1 0.02
39 2 0.03
40 2 0.03
41 31 0.53
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (38 bp):
TCGATGAGACACTGGGTGTCAATTTACTATTGGTTTAA
Found at i:5414495 original size:40 final size:41
Alignment explanation
Indices: 5414397--5414495 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
5414387 TTTGGTTTAA
* *
5414397 TCAATGAGACACTGGGTGTCAATTTACTACTTCGGATTTAT
1 TCAATGAGACACCGGGTGTCAATTTACTACTTCGGAATTAT
* ** * *
5414438 TCGATGAGACATTGGGTGTCAATTTACTAGTT-TGAATTAT
1 TCAATGAGACACCGGGTGTCAATTTACTACTTCGGAATTAT
**
5414478 TCAATGAGGTACCGGGTG
1 TCAATGAGACACCGGGTG
5414496 CCAAACTGGT
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 19 0.40
41 29 0.60
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.35
Consensus pattern (41 bp):
TCAATGAGACACCGGGTGTCAATTTACTACTTCGGAATTAT
Found at i:5414738 original size:16 final size:16
Alignment explanation
Indices: 5414687--5414738 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
5414677 TTATATACTC
*
5414687 ATGAATTGAGTATGGT
1 ATGAATTGAGTATTGT
* *
5414703 ATGAAATGATGTATT-C
1 ATGAATTGA-GTATTGT
5414719 ATGAATTGAGTATTGT
1 ATGAATTGAGTATTGT
5414735 ATGA
1 ATGA
5414739 CTGATGCCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 5 0.17
16 20 0.69
17 4 0.14
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (16 bp):
ATGAATTGAGTATTGT
Found at i:5424023 original size:29 final size:28
Alignment explanation
Indices: 5423965--5424023 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
5423955 CTTTTTACAC
* *
5423965 AAATAATATAAAAAAAATTAATTATAAA
1 AAATAATATAAAAAAAAATAATTACAAA
*
5423993 AAAT-ATATAAAAAACATAATAATTACGAA
1 AAATAATATAAAAAA-A-AATAATTACAAA
5424022 AA
1 AA
5424024 TAAACATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 10 0.38
28 5 0.19
29 11 0.42
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.25
Consensus pattern (28 bp):
AAATAATATAAAAAAAAATAATTACAAA
Found at i:5424867 original size:28 final size:28
Alignment explanation
Indices: 5424822--5424875 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5424812 CAAATGCCTA
*
5424822 TTTTTGTAATTATTTTATTTTCTATACC
1 TTTTTGTAATTATATTATTTTCTATACC
*
5424850 TTTTTCGTAATTA-ATTATTTTTTATA
1 TTTTT-GTAATTATATTATTTTCTATA
5424876 TTATTTGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (28 bp):
TTTTTGTAATTATATTATTTTCTATACC
Found at i:5424871 original size:29 final size:27
Alignment explanation
Indices: 5424822--5424875 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 27
5424812 CAAATGCCTA
*
5424822 TTTTTGTAATTATTTTATTTTCTATACC
1 TTTTTGTAATTATTATATTTT-TATACC
5424850 TTTTTCGTAATTAATTAT-TTTTTATA
1 TTTTT-GTAATT-ATTATATTTTTATA
5424876 TTATTTGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 9 0.39
29 10 0.43
30 4 0.17
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (27 bp):
TTTTTGTAATTATTATATTTTTATACC
Found at i:5428784 original size:25 final size:24
Alignment explanation
Indices: 5428729--5428785 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
5428719 AATGTTCATA
5428729 CGAGCACATAAACGAGAAACTCTGT
1 CGAGC-CATAAACGAGAAACTCTGT
* *
5428754 CAAGCCATATAACGAGAAGCTCATGT
1 CGAGCCATA-AACGAGAAACTC-TGT
5428780 -GAGCCA
1 CGAGCCA
5428786 ATATCAGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 4 0.15
25 20 0.74
26 3 0.11
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.16
Consensus pattern (24 bp):
CGAGCCATAAACGAGAAACTCTGT
Found at i:5428831 original size:24 final size:24
Alignment explanation
Indices: 5428769--5428833 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
5428759 CATATAACGA
**
5428769 GAAGCTCATGTGAGCCAATATCAG
1 GAAGCTCATAAGAGCCAATATCAG
* * *
5428793 GAAGTTCA-AGCGAGCCAATATCTG
1 GAAGCTCATA-AGAGCCAATATCAG
5428817 GAAGCTCATAAGAGCCA
1 GAAGCTCATAAGAGCCA
5428834 TAACGGGAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 32 0.97
25 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (24 bp):
GAAGCTCATAAGAGCCAATATCAG
Found at i:5431473 original size:7 final size:7
Alignment explanation
Indices: 5431457--5431495 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
5431447 CAAACTCATA
*
5431457 CAAAGAT
1 CAAAGCT
5431464 CAAAGCT
1 CAAAGCT
5431471 CAAAGCT
1 CAAAGCT
5431478 CAAAGCT
1 CAAAGCT
5431485 CAAAGCT
1 CAAAGCT
5431492 CAAA
1 CAAA
5431496 TTTTGAAGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.49, C:0.26, G:0.13, T:0.13
Consensus pattern (7 bp):
CAAAGCT
Found at i:5432822 original size:20 final size:19
Alignment explanation
Indices: 5432799--5432859 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
5432789 TTATAAATAA
5432799 TATATTAATTATTTAAAAT
1 TATATTAATTATTTAAAAT
* *
5432818 GTATATT--TTATGTATAAT
1 -TATATTAATTATTTAAAAT
*
5432836 TATATTAAGCTATTTAAATAT
1 TATATTAA-TTATTTAAA-AT
5432857 TAT
1 TAT
5432860 CTAAATTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
17 6 0.19
18 9 0.28
20 12 0.38
21 5 0.16
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (19 bp):
TATATTAATTATTTAAAAT
Found at i:5436079 original size:3 final size:3
Alignment explanation
Indices: 5436066--5436097 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5436056 CAGAGATGGA
*
5436066 GCT GTT GCT GCT GCT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
5436098 AAGTGTAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
GCT
Found at i:5444865 original size:47 final size:47
Alignment explanation
Indices: 5444801--5444911 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
5444791 GACATTGAGT
* *
5444801 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATCTTAAAGTTCCGGATTTGTTC
* * *
5444848 CGATGAAGTACTTTGTGTACTATAATCTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATCTTAAAGTTCCGGATTTGTTC
5444895 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
5444912 CTTATCCCGG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 51 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATCTTAAAGTTCCGGATTTGTTC
Found at i:5446607 original size:18 final size:18
Alignment explanation
Indices: 5446555--5446607 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 18
5446545 ATCAACAAAT
* * *
5446555 AATTTTAAATATGTAGAA
1 AATTTAAAATATATATAA
5446573 ATATTTAAAA-ATA-ATAA
1 A-ATTTAAAATATATATAA
5446590 AATTTAAAATATATATAA
1 AATTTAAAATATATATAA
5446608 TGTATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 8 0.28
17 7 0.24
18 7 0.24
19 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (18 bp):
AATTTAAAATATATATAA
Found at i:5447405 original size:24 final size:24
Alignment explanation
Indices: 5447378--5447429 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
5447368 TAAAACTAAT
5447378 TAAAAAGATAAAATGATTTCCCCA
1 TAAAAAGATAAAATGATTTCCCCA
**
5447402 TAAAGTGATAAAATGATTTCCCCA
1 TAAAAAGATAAAATGATTTCCCCA
5447426 TAAA
1 TAAA
5447430 GTCCCAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (24 bp):
TAAAAAGATAAAATGATTTCCCCA
Found at i:5447430 original size:24 final size:24
Alignment explanation
Indices: 5447384--5447431 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5447374 TAATTAAAAA
5447384 GATAAAATGATTTCCCCATAAAGT
1 GATAAAATGATTTCCCCATAAAGT
5447408 GATAAAATGATTTCCCCATAAAGT
1 GATAAAATGATTTCCCCATAAAGT
5447432 CCCAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (24 bp):
GATAAAATGATTTCCCCATAAAGT
Found at i:5447489 original size:21 final size:19
Alignment explanation
Indices: 5447465--5447507 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
5447455 CTTTTTATTG
*
5447465 AAAATTTAAAAATAAATCTA
1 AAAAATTAAAAATAAAT-TA
*
5447485 AAAAATTGAAAATAAATTA
1 AAAAATTAAAAATAAATTA
5447504 AAAA
1 AAAA
5447508 GATAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATTAAAAATAAATTA
Found at i:5451816 original size:11 final size:11
Alignment explanation
Indices: 5451802--5451826 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5451792 GAAAAGAATG
5451802 GAAAAAAAAAA
1 GAAAAAAAAAA
5451813 GAAAAAAAAAA
1 GAAAAAAAAAA
5451824 GAA
1 GAA
5451827 GGAAAGTTGA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:5452524 original size:25 final size:24
Alignment explanation
Indices: 5452494--5452543 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
5452484 AAATAAAAAA
* *
5452494 ATTTTAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
5452520 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
5452544 TAAAACAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:5458851 original size:25 final size:25
Alignment explanation
Indices: 5458805--5458852 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5458795 AATTTTATAC
* * *
5458805 ATAAACTTTGGTTTTGTGCAATTTT
1 ATAAACTTTGATTTTATCCAATTTT
*
5458830 ATAAATTTTGATTTTATCCAATT
1 ATAAACTTTGATTTTATCCAATT
5458853 CTCACAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.52
Consensus pattern (25 bp):
ATAAACTTTGATTTTATCCAATTTT
Found at i:5459039 original size:29 final size:32
Alignment explanation
Indices: 5458984--5459064 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 32
5458974 ATGGTTTAGC
*
5458984 CTAAATTAAAGTTTCATGTA-GATAA-T-TACA
1 CTAAATTAAAG-TTCATGTATCATAATTATACA
5459014 CTAAATTAAAGTTCATGTATCA-AATTATACA
1 CTAAATTAAAGTTCATGTATCATAATTATACA
* * *
5459045 TTTAATCAAAGTTCATGTAT
1 CTAAATTAAAGTTCATGTAT
5459065 AATTTTAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 10 0.23
30 13 0.30
31 21 0.48
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (32 bp):
CTAAATTAAAGTTCATGTATCATAATTATACA
Found at i:5467177 original size:17 final size:17
Alignment explanation
Indices: 5467155--5467190 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5467145 TCTTAAATTG
5467155 AAGCAAAATTAACAATA
1 AAGCAAAATTAACAATA
5467172 AAGCAAAATTAACAATA
1 AAGCAAAATTAACAATA
5467189 AA
1 AA
5467191 ATAAGAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.11, G:0.06, T:0.17
Consensus pattern (17 bp):
AAGCAAAATTAACAATA
Found at i:5469351 original size:30 final size:30
Alignment explanation
Indices: 5469317--5469424 Score: 76
Period size: 30 Copynumber: 3.4 Consensus size: 30
5469307 CCGATATCTT
5469317 GTTCAGGAGCTTGGGAAGACTCAATATGCC
1 GTTCAGGAGCTTGGGAAGACTCAATATGCC
* * **
5469347 GTTCAAGATCTTGGGATTAAGAAGACTTGATAT-CTC
1 GTTCAGGAGCTT-GG-----GAAGACTCAATATGC-C
*
5469383 GTTCAGGAGCTTAGGAAGACTCAATATTG-C
1 GTTCAGGAGCTTGGGAAGACTCAATA-TGCC
*
5469413 GTTTAGGAGCTT
1 GTTCAGGAGCTT
5469425 AGGATTAAGA
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
30 32 0.54
31 3 0.05
35 2 0.03
36 22 0.37
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (30 bp):
GTTCAGGAGCTTGGGAAGACTCAATATGCC
Found at i:5469406 original size:66 final size:66
Alignment explanation
Indices: 5469300--5469453 Score: 202
Period size: 66 Copynumber: 2.3 Consensus size: 66
5469290 TAAGAACTTG
* * * * *
5469300 AGAAGACCCGATATCTTGTTCAGGAGCTTGGGAAGACTCAATA-TGCCGTTCAAGATCTTGGGAT
1 AGAAGACCTGATATCTCGTTCAGGAGCTTAGGAAGACTCAATATTG-CGTTCAAGAGCTTAGGAT
5469364 TA
65 TA
* * *
5469366 AGAAGACTTGATATCTCGTTCAGGAGCTTAGGAAGACTCAATATTGCGTTTAGGAGCTTAGGATT
1 AGAAGACCTGATATCTCGTTCAGGAGCTTAGGAAGACTCAATATTGCGTTCAAGAGCTTAGGATT
5469431 A
66 A
* *
5469432 AGAAGGCCTGATATCTCATTCA
1 AGAAGACCTGATATCTCGTTCA
5469454 AAAGTTTGGA
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
66 74 0.97
67 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (66 bp):
AGAAGACCTGATATCTCGTTCAGGAGCTTAGGAAGACTCAATATTGCGTTCAAGAGCTTAGGATT
A
Found at i:5476223 original size:5 final size:5
Alignment explanation
Indices: 5476209--5476255 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
5476199 TAACACATAT
* * *
5476209 ATTCA TTTCA ATTCA ATTCA ATTCA A-TCA ACTTTA AATCA ATTCA AT
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA A-TTCA ATTCA ATTCA AT
5476256 AATCAAAGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 4 0.12
5 27 0.79
6 3 0.09
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTCA
Found at i:5477478 original size:14 final size:14
Alignment explanation
Indices: 5477461--5477499 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
5477451 CTTTGAAGGT
5477461 TTACAATTGAGTGA
1 TTACAATTGAGTGA
*
5477475 TTACAATTGAGTGC
1 TTACAATTGAGTGA
*
5477489 TTACAAATGAG
1 TTACAATTGAG
5477500 GGGGAAGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (14 bp):
TTACAATTGAGTGA
Found at i:5494407 original size:104 final size:103
Alignment explanation
Indices: 5494271--5494507 Score: 361
Period size: 104 Copynumber: 2.3 Consensus size: 103
5494261 GTTGTACATA
** * *
5494271 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTAGTGCTAAGTGCGATATCCACCGTATCT
* *
5494336 TTGAAATGTGAA-AGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAA--TAAAGAGGGGGTTGCTATGTGCTGATTCCCCC
*
5494375 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTAGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTAGTGCTAAGTGCGATATCCACCGTATC
5494439 TCTGAAATAAAGAGGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAATAAAGAGGGGGTTGCTATGTGCTGATTCCCCC
*
5494478 AAGGGGTTGCTAAGTGCTGATTCTCCGATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATT
5494508 AAGTGGTGGT
Statistics
Matches: 121, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
102 3 0.02
103 54 0.45
104 64 0.53
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.31
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTAGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATAAAGAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:5496872 original size:15 final size:17
Alignment explanation
Indices: 5496840--5496875 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
5496830 TGTTGAAATA
5496840 AAAT-TATATCTAATTT
1 AAATATATATCTAATTT
5496856 AAATATATAT-TAA-TT
1 AAATATATATCTAATTT
5496871 AAATA
1 AAATA
5496876 GTCCAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 7 0.37
17 5 0.26
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATATATATCTAATTT
Found at i:5509473 original size:45 final size:45
Alignment explanation
Indices: 5509409--5509527 Score: 139
Period size: 45 Copynumber: 2.6 Consensus size: 45
5509399 CAAAGGAGCT
* *
5509409 GGTGGTGGGGTAGCTGGAGGAGGAGTAGCAGGAGGGGGAGAAGCA
1 GGTGGTGGGGTAGCCGGAGGAGGAGAAGCAGGAGGGGGAGAAGCA
* * * ** *
5509454 GGTGGTGGGGTAGCCGGAGGTGGAGAAGCCGGTGGGGGAGTTGCG
1 GGTGGTGGGGTAGCCGGAGGAGGAGAAGCAGGAGGGGGAGAAGCA
* * *
5509499 GGAGGTGGAGTAGCCGGGGGAGGAGAAGC
1 GGTGGTGGGGTAGCCGGAGGAGGAGAAGC
5509528 TGGTGGTGGG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.20, C:0.09, G:0.59, T:0.12
Consensus pattern (45 bp):
GGTGGTGGGGTAGCCGGAGGAGGAGAAGCAGGAGGGGGAGAAGCA
Found at i:5509483 original size:15 final size:15
Alignment explanation
Indices: 5509412--5509515 Score: 82
Period size: 15 Copynumber: 6.9 Consensus size: 15
5509402 AGGAGCTGGT
* *
5509412 GGTGGGGTAGCTGGA
1 GGTGGAGTAGCCGGA
* *
5509427 GGAGGAGTAGCAGGA
1 GGTGGAGTAGCCGGA
* * * *
5509442 GGGGGAGAAGCAGGT
1 GGTGGAGTAGCCGGA
*
5509457 GGTGGGGTAGCCGGA
1 GGTGGAGTAGCCGGA
* *
5509472 GGTGGAGAAGCCGGT
1 GGTGGAGTAGCCGGA
* * *
5509487 GGGGGAGTTGCGGGA
1 GGTGGAGTAGCCGGA
5509502 GGTGGAGTAGCCGG
1 GGTGGAGTAGCCGG
5509516 GGGAGGAGAA
Statistics
Matches: 67, Mismatches: 22, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 67 1.00
ACGTcount: A:0.19, C:0.10, G:0.59, T:0.12
Consensus pattern (15 bp):
GGTGGAGTAGCCGGA
Found at i:5509503 original size:30 final size:30
Alignment explanation
Indices: 5509430--5509523 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 30
5509420 AGCTGGAGGA
* *
5509430 GGAGTAGCAGGAGGGGGAGAAGCAGGTGGTG
1 GGAGTAGCAGGAGGTGGAGAAGCCGGTGG-G
*
5509461 GG-GTAGCCGGAGGTGGAGAAGCCGGTGGG
1 GGAGTAGCAGGAGGTGGAGAAGCCGGTGGG
* * *
5509490 GGAGTTGCGGGAGGTGGAGTAGCCGG-GGG
1 GGAGTAGCAGGAGGTGGAGAAGCCGGTGGG
5509519 AGGAG
1 -GGAG
5509524 AAGCTGGTGG
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
29 6 0.11
30 47 0.85
31 2 0.04
ACGTcount: A:0.20, C:0.10, G:0.60, T:0.11
Consensus pattern (30 bp):
GGAGTAGCAGGAGGTGGAGAAGCCGGTGGG
Found at i:5509629 original size:33 final size:36
Alignment explanation
Indices: 5509562--5509631 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
5509552 GGGAGTCGCT
* *
5509562 GGAGGAGGAGTGGAAACTGGTGGTGGTGATGAAGTA
1 GGAGGAGGAGAGGAAACTGGTGGTCGTGATGAAGTA
*
5509598 GGAGGAGGAGAGGAAGCTGGTGG-CG-GA-GAAGTA
1 GGAGGAGGAGAGGAAACTGGTGGTCGTGATGAAGTA
5509631 G
1 G
5509632 TTGTGGGTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 7 0.23
34 2 0.06
35 1 0.03
36 21 0.68
ACGTcount: A:0.29, C:0.04, G:0.53, T:0.14
Consensus pattern (36 bp):
GGAGGAGGAGAGGAAACTGGTGGTCGTGATGAAGTA
Found at i:5513788 original size:22 final size:21
Alignment explanation
Indices: 5513763--5513803 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5513753 TATGTAACAT
5513763 TATTAATAATTATTTTTTAAAA
1 TATT-ATAATTATTTTTTAAAA
*
5513785 TATTATTATTATTTTTTAA
1 TATTATAATTATTTTTTAA
5513804 TACATGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTATAATTATTTTTTAAAA
Found at i:5514123 original size:25 final size:25
Alignment explanation
Indices: 5514063--5514150 Score: 78
Period size: 26 Copynumber: 3.5 Consensus size: 25
5514053 GTTGTTTTTA
5514063 ATATTATG-ATTATTTCTAGTATA-TAT
1 ATATTATGTA-TATTTCTA--ATACTAT
5514089 ATATTATGTATATACTTCTAATACTAT
1 ATATTATGTATAT--TTCTAATACTAT
*
5514116 ATA-T-TGTATATTTCTAATACCAT
1 ATATTATGTATATTTCTAATACTAT
*
5514139 -TATTATTTATAT
1 ATATTATGTATAT
5514151 GTGTATATGT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
22 2 0.04
23 12 0.22
24 6 0.11
25 7 0.13
26 15 0.28
27 7 0.13
28 5 0.09
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (25 bp):
ATATTATGTATATTTCTAATACTAT
Found at i:5514264 original size:25 final size:24
Alignment explanation
Indices: 5514221--5514347 Score: 83
Period size: 25 Copynumber: 4.8 Consensus size: 24
5514211 GTTGCTAATA
*
5514221 TATATATATCATGTATATATGATTTTT
1 TATATATATTATG--TATAT-ATTTTT
*
5514248 TATATATATTATGTATATATCTTT
1 TATATATATTATGTATATATTTTT
* *
5514272 AATATTATATTATTTATATATTTATGCT
1 TATA-TATATTATGTATATATTT-T--T
* *
5514300 TACATATTATCTTACGTATATATTTTT
1 T--ATA-TATATTATGTATATATTTTT
*
5514327 AATAACTATATTATGTATATA
1 TAT-A-TATATTATGTATATA
5514348 CTATTACTAT
Statistics
Matches: 80, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
24 8 0.10
25 23 0.29
26 15 0.19
27 13 0.16
28 1 0.01
29 1 0.01
30 19 0.24
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.54
Consensus pattern (24 bp):
TATATATATTATGTATATATTTTT
Done.