Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 22 of 172
Found at i:5382235 original size:13 final size:13
Alignment explanation
Indices: 5382217--5382243 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5382207 TAGTTCAATT
5382217 CTTCACTAGAAAA
1 CTTCACTAGAAAA
5382230 CTTCACTAGAAAA
1 CTTCACTAGAAAA
5382243 C
1 C
5382244 AAATATCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.22
Consensus pattern (13 bp):
CTTCACTAGAAAA
Found at i:5384194 original size:4 final size:4
Alignment explanation
Indices: 5384185--5384228 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
5384175 AGACTTAAAA
*
5384185 TATG TATG TATG TATG TATG TATG TATG TAT- T-TA TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
5384229 AAAATTATGG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
2 1 0.03
3 2 0.05
4 34 0.92
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:5384693 original size:3 final size:3
Alignment explanation
Indices: 5384685--5384738 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
5384675 ATTACAAGAT
*
5384685 TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5384731 TAG TAA TA
1 TAA TAA TA
5384739 GTAAACTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5385746 original size:18 final size:18
Alignment explanation
Indices: 5385723--5385769 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
5385713 GCTTAGGATA
*
5385723 GTTTGGGCTTATTTAATG
1 GTTTGGGCCTATTTAATG
* *
5385741 GTTTGGGCCTGTTTATTG
1 GTTTGGGCCTATTTAATG
5385759 GTTTGGGCCTA
1 GTTTGGGCCTA
5385770 GGCATATTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.11, C:0.11, G:0.32, T:0.47
Consensus pattern (18 bp):
GTTTGGGCCTATTTAATG
Found at i:5385895 original size:16 final size:16
Alignment explanation
Indices: 5385874--5385930 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
5385864 TAAGCCTCAA
5385874 CTTCTTCGGTGCTTTT
1 CTTCTTCGGTGCTTTT
* **
5385890 CTTCTTCAAGTAGCCTCGT
1 CTTCTTC-GGT-G-CTTTT
5385909 -TTCTTCGGTGCTTTT
1 CTTCTTCGGTGCTTTT
5385924 CTTCTTC
1 CTTCTTC
5385931 AACTAGTGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
15 3 0.10
16 14 0.45
17 4 0.13
18 7 0.23
19 3 0.10
ACGTcount: A:0.05, C:0.28, G:0.16, T:0.51
Consensus pattern (16 bp):
CTTCTTCGGTGCTTTT
Found at i:5386277 original size:128 final size:129
Alignment explanation
Indices: 5386100--5386347 Score: 383
Period size: 128 Copynumber: 1.9 Consensus size: 129
5386090 AAATCTTGAC
* * *
5386100 GCGATCTGCTCTACTGCAACTTCAGAGAGATGAGATCTGTGGTTTTAATCCACTCCACTGCAACT
1 GCGATCTGCCCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTCTAATCCACTCCACTGCAACT
* * *
5386165 TCAAGGAGATAGGATTATTTCCTTCT-TTCTATTCCACTGCAACTTCAGGGGGATAAGACTAAAT
66 TCAAGGAGATAGGATTATTTCCTT-TAATCTACTCCACTGCAACTTCAGGGAGATAAGACTAAAT
* *
5386229 GCGATCTGCCCT-CTGCCACTTCAGAGAGATAAGATCTGTGGTTCTAATCCGCTCCACTGCAACT
1 GCGATCTGCCCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTCTAATCCACTCCACTGCAACT
* *
5386293 TCAGGGAGATAGGATTATTTGCTTTAATCTACTCCACTGCAACTTCAGGGAGATA
66 TCAAGGAGATAGGATTATTTCCTTTAATCTACTCCACTGCAACTTCAGGGAGATA
5386348 GGATTATTTT
Statistics
Matches: 108, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
127 1 0.01
128 96 0.89
129 11 0.10
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (129 bp):
GCGATCTGCCCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTCTAATCCACTCCACTGCAACT
TCAAGGAGATAGGATTATTTCCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGACTAAAT
Found at i:5386389 original size:44 final size:44
Alignment explanation
Indices: 5386103--5386390 Score: 198
Period size: 44 Copynumber: 6.6 Consensus size: 44
5386093 TCTTGACGCG
* * * * *
5386103 ATCTGCTCTACTGCAACTTCAGAGAGAT-GAGATCT-GTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAG-GAT-TATTTGCTTTA
** * *
5386147 ATCCACTCCACTGCAACTTCAAGGAGATAGGATTATTTCCTTCT-
1 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTTGCTT-TA
* ** * * * ** *
5386191 TTCTATTCCACTGCAACTTCAGGGGGATAAGACTAAATGC---G
1 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTTGCTTTA
* * * * * * *
5386232 ATCTGC-CCTCTGCCACTTCAGAGAGATAAGA-TCTGTGGTTCTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTTGCTT-TA
*
5386275 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTTGCTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTTGCTTTA
* *
5386319 ATCTACTCCACTGCAACTTCAGGGAGATAGGATTATTTTCTTCT-
1 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTTGCTT-TA
* *
5386363 GTCTGCTCCACTGCAACTTCAAGGAGAT
1 ATCTGCTCCACTGCAACTTCAGGGAGAT
5386391 CAGACTTGTA
Statistics
Matches: 188, Mismatches: 45, Indels: 22
0.74 0.18 0.09
Matches are distributed among these distances:
39 3 0.02
40 21 0.11
41 3 0.02
43 6 0.03
44 146 0.78
45 9 0.05
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTTGCTTTA
Found at i:5386483 original size:44 final size:44
Alignment explanation
Indices: 5386401--5386930 Score: 586
Period size: 44 Copynumber: 12.0 Consensus size: 44
5386391 CAGACTTGTA
* * *** * * *
5386401 TCTTTGATCTACTTCACCACCAATATGGGAAAACAAGATCTACTA
1 TCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTT
* *
5386446 TCTTTGATCTACTTCATGCCAATACATGAAGACAAGATC--CTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * *
5386488 TCTTTGATCTACTTCATGCCAATACATGAAGACAAGATTTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * *
5386532 TCTTCGATCTACTTCACGCCAATACATGAAGATAAAATCTACTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * *
5386576 TCTTCAATCTACTTCA--CCACTAGTATGGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCACGCCAATA-CAT--GAAGACAAGATCTGCTT
* *
5386621 TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* **
5386665 TCTTCGATCTACTTCACGGCAATACATGAAGACAAGATCTATTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
*
5386709 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
*
5386753 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * *** * *
5386797 TCTTCGATCTACTCTGC-CACCAGTATGGGAAGACAAGATATGCTA
1 TCTTCGATCTACT-T-CACGCCAATACATGAAGACAAGATCTGCTT
* * * * *
5386842 TCTTCGATCTACTTCACGCTAATACATGAGGACAATATTTGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
*
5386886 TCTTCGATCTACTTTGC-CACCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTAC-TT-CACGCCAATACATGAAGACAAGATCTGCTT
5386931 CTTTTTAACC
Statistics
Matches: 413, Mismatches: 60, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
42 45 0.11
43 3 0.01
44 253 0.61
45 103 0.25
46 4 0.01
47 5 0.01
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (44 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
Found at i:5386772 original size:221 final size:219
Alignment explanation
Indices: 5386399--5386926 Score: 702
Period size: 221 Copynumber: 2.4 Consensus size: 219
5386389 ATCAGACTTG
* * *** * ** * * *
5386399 TATCTTTGATCTACTTCACCACCAATATGGGAAAACAAGATCTACTATCTTTGATCTACTTCATG
1 TATCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCACG
* * *
5386464 CCAATACATGAAGACAAGATC-CTTTCTTTGATCTACTTCATGCCAATACATGAAGACAAGATTT
65 -CAATACATGAAGACAAGATCTCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
* *
5386528 GCTTTCTTCGATCTACTTCACGCCAATACATGAAGATAAAATCTACTTTCTTCAATCTACT-TCA
129 GCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAAATCTACTTTCTTCAATCTACTCT-A
* *
5386592 CCACTAGTATGGGAAGACAAGATCTGC
193 CCACCAGTATGGGAAGACAAGATATGC
*
5386619 TATCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCACGG
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCAC-G
*
5386684 CAATACATGAAGACAAGATCTATTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
65 CAATACATGAAGACAAGATCT-CTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
* * * * *
5386749 GCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTCTGC
129 GCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAAATCTACTTTCTTCAATCTACTCTAC
5386814 CACCAGTATGGGAAGACAAGATATGC
194 CACCAGTATGGGAAGACAAGATATGC
* * * *
5386840 TATCTTCGATCTACTTCACGCTAATACATGAGGACAATATTTGTTTTCTTCGATCTACTTTGCCA
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTAC-TT--CA
5386905 C-CAATACATGAAGACAAGATCT
63 CGCAATACATGAAGACAAGATCT
5386927 GCTTCTTTTT
Statistics
Matches: 271, Mismatches: 30, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
219 54 0.20
220 18 0.07
221 172 0.63
222 24 0.09
224 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (219 bp):
TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCACGC
AATACATGAAGACAAGATCTCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
TATCTTCGATCTACTTCACGCCAATACATGAAGACAAAATCTACTTTCTTCAATCTACTCTACCA
CCAGTATGGGAAGACAAGATATGC
Found at i:5386933 original size:133 final size:131
Alignment explanation
Indices: 5386401--5386930 Score: 568
Period size: 133 Copynumber: 4.0 Consensus size: 131
5386391 CAGACTTGTA
* ** * * *
5386401 TCTTTGATCTACTTCACCACCAATATGGGAAAACAAGATCTACTATCTTTGATCTACTTCATGCC
1 TCTTCGATCTACTT--CCACCAATACAGGAAGACAAGATCTACTATCTTCGATCTACTTCACGCC
* * ** *
5386466 AATACATGAAGACAAGATC--CTTTCTTTGATCTACTTCATGCCAATACATGAAGACAAGATTTG
64 AATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTG
5386529 CTT
129 CTT
* * * * * *
5386532 TCTTCGATCTACTTCACGCCAATACATGAAGATAAAATCTACTTTCTTCAATCTACTTCA--CCA
1 TCTTCGATCTACTTC-CACCAATACAGGAAGACAAGATCTACTATCTTCGATCTACTTCACGCCA
* * * *
5386595 CTAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATC
65 ATA-CAT--GAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACATGAAGACAAGATC
*
5386660 TGTTT
127 TGCTT
* * *
5386665 TCTTCGATCTACTT-CACGGCAATACATGAAGACAAGATCTATTTTCTTCGATCTACTTCACGCC
1 TCTTCGATCTACTTCCAC--CAATACAGGAAGACAAGATCTACTATCTTCGATCTACTTCACGCC
* *
5386729 AATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
64 AATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTG
5386794 CTT
129 CTT
* ** * * *
5386797 TCTTCGATCTACTCTGCCACCAGTATGGGAAGACAAGATATGCTATCTTCGATCTACTTCACGCT
1 TCTTCGATCTACT-T-CCACCAATACAGGAAGACAAGATCTACTATCTTCGATCTACTTCACGCC
* * * * *
5386862 AATACATGAGGACAATATTTGTTTTCTTCGATCTACTTTGC-CACCAATACATGAAGACAAGATC
64 AATACATGAAGACAAGATCTGCTATCTTCGATCTAC-TT-CACACCAATACATGAAGACAAGATC
5386926 TGCTT
127 TGCTT
5386931 CTTTTTAACC
Statistics
Matches: 339, Mismatches: 45, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
128 5 0.01
129 3 0.01
130 34 0.10
131 27 0.08
132 71 0.21
133 159 0.47
134 31 0.09
135 9 0.03
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (131 bp):
TCTTCGATCTACTTCCACCAATACAGGAAGACAAGATCTACTATCTTCGATCTACTTCACGCCAA
TACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCT
T
Found at i:5388184 original size:7 final size:7
Alignment explanation
Indices: 5388166--5388208 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
5388156 TCCATTTTAC
5388166 TTTTCTAT
1 TTTTC-AT
*
5388174 TTTTCAG
1 TTTTCAT
5388181 TTTTCA-
1 TTTTCAT
5388187 TTTTCACT
1 TTTTCA-T
5388195 TTTTCAT
1 TTTTCAT
5388202 TTTTCAT
1 TTTTCAT
5388209 CTAATCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
6 6 0.19
7 15 0.47
8 11 0.34
ACGTcount: A:0.14, C:0.16, G:0.02, T:0.67
Consensus pattern (7 bp):
TTTTCAT
Found at i:5388189 original size:14 final size:15
Alignment explanation
Indices: 5388166--5388207 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5388156 TCCATTTTAC
5388166 TTTTCTATTTTTCA-G
1 TTTTC-ATTTTTCACG
*
5388181 TTTTCA-TTTTCACT
1 TTTTCATTTTTCACG
5388195 TTTTCATTTTTCA
1 TTTTCATTTTTCA
5388208 TCTAATCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 6 0.25
14 7 0.29
15 11 0.46
ACGTcount: A:0.14, C:0.17, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTCATTTTTCACG
Found at i:5388827 original size:18 final size:18
Alignment explanation
Indices: 5388804--5388848 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5388794 GCTTAGGATA
*
5388804 GTTTGGGCTTGTTTAATG
1 GTTTGGGCCTGTTTAATG
*
5388822 GTTTGGGCCTGTTTATTG
1 GTTTGGGCCTGTTTAATG
5388840 GTTTGGGCC
1 GTTTGGGCC
5388849 CTGGCCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.07, C:0.11, G:0.36, T:0.47
Consensus pattern (18 bp):
GTTTGGGCCTGTTTAATG
Found at i:5390051 original size:23 final size:22
Alignment explanation
Indices: 5389999--5390051 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
5389989 GAATTGATTA
5389999 AATTGTATTTTATAATTATTAAT
1 AATT-TATTTTATAATTATTAAT
* * *
5390022 ATTTTTATTTTATGATTTTTTAAT
1 A-ATTTATTTTAT-AATTATTAAT
5390046 AATTTA
1 AATTTA
5390052 CTTGATTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
AATTTATTTTATAATTATTAAT
Found at i:5391501 original size:112 final size:110
Alignment explanation
Indices: 5391307--5392092 Score: 657
Period size: 112 Copynumber: 7.3 Consensus size: 110
5391297 GAAAAAAAAA
* * *
5391307 TTTGGTGGTAGCCTGGCAATAGCCGGCACCACCTTTATGTAAAAAAAA------TTACATTTTGG
1 TTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAAAATTTTTTTTACATTTTGG
* *
5391366 GCTATCATTGGCTGACAACAGTATACGAAAAAATTTAAAAAAATATT
66 GCTATCATTGGC-GGCACCAGTATACGAAAAAA-TTAAAAAAATATT
* * * * *
5391413 TTTGTTGGTGGCTTGCCAATGGCCGCCACCACCGTTATGTAAAAAAAGA-TTTTTTTACATCTTG
1 TTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAAA-ATTTTTTTTACATTTTG
*
5391477 GGCTATCATTGGACGGCACTAGTATACGAAAAAA-TAAAAAAA-A--
65 GGCTATCATTGG-CGGCACCAGTATACGAAAAAATTAAAAAAATATT
* *
5391520 TTTGGTGGTGGCTTGCAAATGGCCGGCACCACCTTTATGTAAAAAAAATATTTTTTTTACATTTT
1 TTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGT-AAAAAAA-ATTTTTTTTACATTTT
* * * * * *
5391585 GGGCTGTCATTAGCTGGCACCAATATATG--AAAA--AAAAAATTTTT
64 GGGCTATCATTGGC-GGCACCAGTATACGAAAAAATTAAAAAAATATT
* * * *
5391629 TTTGGTGGTGGCCTGGCAATGGTCAGCACCACCTTTATGTAAAAAAAA----ATTTACATTTTGG
1 TTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAAAATTTTTTTTACATTTTGG
* *
5391690 GCTATCTTTAGCCGGCACCAGTATACGAAAAAATTTTTTAAAAAAAT-TGT
66 GCTATCATT-GGCGGCACCAGTATACGAAAAAA----TTAAAAAAATAT-T
* * *
5391740 TTTGTTGGTGGCCTGCCAATGGCCGGTACCACCATTATGTAAAAAATAATTTTTTTTTACATTTT
1 TTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAA-AA-TTTTTTTTACATTTT
* * ** *
5391805 GGGCTGTCATTGGCCTGCACCAGTATACGAAAAAATT-AAAATTTTTT
64 GGGCTATCATTGG-CGGCACCAGTATACGAAAAAATTAAAAAAATATT
* *
5391852 TTTGATGGTGGCCTGCCAATGGCCGGCACCACCTTTATGT-AAAAAAA------TTACATTTTGA
1 TTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAAAATTTTTTTTACATTTTGG
* * * * * * * *
5391910 ACTGTCATTGACTGGCACCAGAATACGAAAAAGTT---CAATTTTT
66 GCTATCATTGGC-GGCACCAGTATACGAAAAAATTAAAAAAATATT
* * *****
5391953 TTTTGTGGTGCCCTGCCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTATTTTTTACATTTT
1 TTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAA-AAAAATT-TTTTTTACATTTT
* * *
5392018 GGGCTGTCATTGGCCGGCACCAGTATACAAAAAAAATTAAAAAAA-A-A
64 GGGCTATCATTGG-CGGCACCAGTATAC-GAAAAAATTAAAAAAATATT
**
5392065 TTTGGTGGTGGTTTGCCAATGGCCGGCA
1 TTTGGTGGTGGCCTGCCAATGGCCGGCA
5392093 TCAAATTTAT
Statistics
Matches: 551, Mismatches: 83, Indels: 86
0.77 0.12 0.12
Matches are distributed among these distances:
101 43 0.08
102 3 0.01
103 69 0.13
104 1 0.00
105 4 0.01
106 46 0.08
107 42 0.08
108 16 0.03
109 71 0.13
110 42 0.08
111 61 0.11
112 107 0.19
113 4 0.01
114 2 0.00
116 1 0.00
117 39 0.07
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (110 bp):
TTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAAAATTTTTTTTACATTTTGG
GCTATCATTGGCGGCACCAGTATACGAAAAAATTAAAAAAATATT
Found at i:5391800 original size:220 final size:211
Alignment explanation
Indices: 5391311--5392053 Score: 692
Period size: 220 Copynumber: 3.5 Consensus size: 211
5391301 AAAAAATTTG
* * *
5391311 GTGGTAGCCTGGCAATAGCCGGCACCACCTTTATGTAAAAAA-AA-------TTACATTTTGGGC
1 GTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAATAATTTTTTTTTACATTTTGGGC
* * * * * * *
5391368 TATCATTGGCTGACAACAGTATACGAAAAAATTTAAAAAAATATTTTTGTTGGTGGCTTGCCAAT
66 TGTCATTGGCTGGCACCAGTATA-G--AAAA---AAAAAATTTTTTTTGATGGTGGCCTGCCAAT
* * * * * *
5391433 GGCCGCCACCACCGTTATGTAAAAAAAGATTTTTTTACATCTTGGGCTATCATTGGACGGCACTA
125 GGCAG-CACCACCTTTATGTAAAAAAA-A---ATTTACATTTTGGGCTATCATT-GCCGGCACCA
* *
5391498 GTATACGAAAAAA-TAAAAAAA-ATTTG
184 GTATACGAAAAAATTAAAAAAATTTTTT
* *
5391524 GTGGTGGCTTGCAAATGGCCGGCACCACCTTTATGTAAAAAA-AATATTTTTTTTACATTTTGGG
1 GTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAATAAT-TTTTTTTTACATTTTGGG
* * * *
5391588 CTGTCATTAGCTGGCACCAATATATGAAAAAAAAAATTTTTTTTGGTGGTGGCCTGGCAATGGTC
65 CTGTCATTGGCTGGCACCAGTATA-GAAAAAAAAAATTTTTTTTGATGGTGGCCTGCCAATGG-C
*
5391653 AGCACCACCTTTATGTAAAAAAAAATTTACATTTTGGGCTATCTTTAGCCGGCACCAGTATACGA
128 AGCACCACCTTTATGTAAAAAAAAATTTACATTTTGGGCTATCATT-GCCGGCACCAGTATACGA
5391718 AAAAATTTTTTAAAAAAATTGTTTT
192 AAAAA----TTAAAAAAATT-TTTT
* *
5391743 GTTGGTGGCCTGCCAATGGCCGGTACCACCATTATGTAAAAAATAATTTTTTTTTACATTTTGGG
1 G-TGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAATAATTTTTTTTTACATTTTGGG
5391808 CTGTCATTGGCCT-GCACCAGTATACGAAAAAATTAAAATTTTTTTTTGATGGTGGCCTGCCAAT
65 CTGTCATTGG-CTGGCACCAGTATA-GAAAAAA--AAAA-TTTTTTTTGATGGTGGCCTGCCAAT
* ** * * *
5391872 GGCCGGCACCACCTTTATGT--AAAAAAA-TTACATTTTGAACTGTCATTGACTGGCACCAGAAT
125 GG-CAGCACCACCTTTATGTAAAAAAAAATTTACATTTTGGGCTATCATTG-CCGGCACCAGTAT
* * ***
5391934 ACGAAAAAGTT-CAATTTTTTTTT
188 ACGAAAAAATTAAAAAAATTTTTT
* ** **
5391957 GTGGTGCCCTGCCAATGGCCGGCACCACCTTTATGT-AAATTTTTTTTATTTTTTACATTTTGGG
1 GTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAATAATTT-TTTTTTACATTTTGGG
* *
5392021 CTGTCATTGGCCGGCACCAGTATACAAAAAAAA
65 CTGTCATTGGCTGGCACCAGTATAGAAAAAAAA
5392054 TTAAAAAAAA
Statistics
Matches: 448, Mismatches: 57, Indels: 53
0.80 0.10 0.09
Matches are distributed among these distances:
210 2 0.00
212 54 0.12
213 108 0.24
214 5 0.01
215 5 0.01
216 50 0.11
217 10 0.02
219 9 0.02
220 116 0.26
221 44 0.10
222 4 0.01
223 41 0.09
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (211 bp):
GTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAATAATTTTTTTTTACATTTTGGGC
TGTCATTGGCTGGCACCAGTATAGAAAAAAAAAATTTTTTTTGATGGTGGCCTGCCAATGGCAGC
ACCACCTTTATGTAAAAAAAAATTTACATTTTGGGCTATCATTGCCGGCACCAGTATACGAAAAA
ATTAAAAAAATTTTTT
Found at i:5391881 original size:56 final size:56
Alignment explanation
Indices: 5391700--5391882 Score: 138
Period size: 56 Copynumber: 3.2 Consensus size: 56
5391690 GCTATCTTTA
** * *
5391700 GCCGGCACCAGTATACGAAAAAATTTTTTAAAAAAATTGTTTTGTTGGTGGCCTGCCAATG
1 GCCGGCACCAGTATACGAAAAAA----TT-AAAATTTTTTTTTGATGGTGGCCTGCCAATG
* ** * * ** * * *
5391761 GCCGGTACCACCATTATGTAAAAAA-T--AATTTTTTTTTACATTTTGGGCTGTCATTG
1 GCCGGCACCAGTA-TACG-AAAAAATTAAAATTTTTTTTT-GATGGTGGCCTGCCAATG
*
5391817 GCCTGCACCAGTATACGAAAAAATTAAAATTTTTTTTTGATGGTGGCCTGCCAATG
1 GCCGGCACCAGTATACGAAAAAATTAAAATTTTTTTTTGATGGTGGCCTGCCAATG
5391873 GCCGGCACCA
1 GCCGGCACCA
5391883 CCTTTATGTA
Statistics
Matches: 90, Mismatches: 26, Indels: 17
0.68 0.20 0.13
Matches are distributed among these distances:
54 6 0.07
55 12 0.13
56 41 0.46
57 11 0.12
58 1 0.01
61 10 0.11
62 3 0.03
63 6 0.07
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (56 bp):
GCCGGCACCAGTATACGAAAAAATTAAAATTTTTTTTTGATGGTGGCCTGCCAATG
Found at i:5391994 original size:101 final size:103
Alignment explanation
Indices: 5391318--5391995 Score: 363
Period size: 109 Copynumber: 6.3 Consensus size: 103
5391308 TTGGTGGTAG
* * ** *
5391318 CCTGGCAATAGCCGGCACCACCTTTATGTAAAAAAAATTACATTTTGGGCTATCATTGG-CTGAC
1 CCTGCCAATGGCCGGCACCACCTTTATGT-AAAAAAATTACATTTTGAACTGTCATTGGACTG-C
* * ** * * *
5391382 AACAGTATACGAAAAAATTTAAAAAAATATTTTTGTTGGTGG
64 ACCAGAATACGAAAAAA-TT-AAAATTTTTTTTTGATGGTGC
* * * * ** *
5391424 CTTGCCAATGGCCGCCACCACCGTTATGTAAAAAAAGATTTTTTTACATCTTGGGCTATCATTGG
1 CCTGCCAATGGCCGGCACCACCTTTATGT-AAAAAA-A-----TTACATTTTGAACTGTCATTGG
* * * **** * *
5391489 ACGGCACTAGTATACGAAAAAA-TAAAA--AAAATTTGGTGGTGG
59 ACTGCACCAGAATACGAAAAAATTAAAATTTTTTTTTGATGGTGC
* * **
5391531 CTTGCAAATGGCCGGCACCACCTTTATGTAAAAAAAATATTTTTTTTACATTTTGGGCTGTCATT
1 CCTGCCAATGGCCGGCACCACCTTTATGT--AAAAAA-A------TTACATTTTGAACTGTCATT
* * * *
5391596 AG-CTGGCACCA-ATATATGAAAAAA--AAAA-TTTTTTTTGGTGGTGG
57 GGACT-GCACCAGA-ATACGAAAAAATTAAAATTTTTTTTTGATGGTGC
* * * ** * * * * *
5391640 CCTGGCAATGGTCAGCACCACCTTTATGTAAAAAAAAATTTACATTTTGGGCTATCTTTAGCCGG
1 CCTGCCAATGGCCGGCACCACCTTTATGT--AAAAAAA-TTACATTTTGAACTGTCATTGGACTG
* ** * * *
5391705 CACCAGTATACGAAAAAATTTTTTAAAAAAATTGTTTTGTTGGTGG
63 CACCAGAATACGAAAAAA----TT-AAAATTTTTTTTTGATGGTGC
* * **
5391751 CCTGCCAATGGCCGGTACCACCATTATGTAAAAAATAATTTTTTTTTACATTTTGGGCTGTCATT
1 CCTGCCAATGGCCGGCACCACCTTTATGT-AAAAA-AA-------TTACATTTTGAACTGTCATT
* * *
5391816 GGCCTGCACCAGTATACGAAAAAATTAAAATTTTTTTTTGATGGTGG
57 GGACTGCACCAGAATACGAAAAAATTAAAATTTTTTTTTGATGGTGC
5391863 CCTGCCAATGGCCGGCACCACCTTTATGTAAAAAAATTACATTTTGAACTGTCATT-GACTGGCA
1 CCTGCCAATGGCCGGCACCACCTTTATGTAAAAAAATTACATTTTGAACTGTCATTGGACT-GCA
* *
5391927 CCAGAATACGAAAAAGTT-CAATTTTTTTTTG-TGGTGC
65 CCAGAATACGAAAAAATTAAAATTTTTTTTTGATGGTGC
5391964 CCTGCCAATGGCCGGCACCACCTTTATGTAAA
1 CCTGCCAATGGCCGGCACCACCTTTATGTAAA
5391996 TTTTTTTTAT
Statistics
Matches: 479, Mismatches: 63, Indels: 65
0.79 0.10 0.11
Matches are distributed among these distances:
101 37 0.08
102 15 0.03
103 74 0.15
104 1 0.00
106 31 0.06
107 38 0.08
108 14 0.03
109 86 0.18
110 13 0.03
111 44 0.09
112 81 0.17
113 4 0.01
117 41 0.09
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (103 bp):
CCTGCCAATGGCCGGCACCACCTTTATGTAAAAAAATTACATTTTGAACTGTCATTGGACTGCAC
CAGAATACGAAAAAATTAAAATTTTTTTTTGATGGTGC
Found at i:5392008 original size:101 final size:103
Alignment explanation
Indices: 5391739--5392008 Score: 285
Period size: 101 Copynumber: 2.6 Consensus size: 103
5391729 AAAAAAATTG
* * *
5391739 TTTTGTTGGTGGCCTGCCAATGGCCGGTACCACCATTATGTAAAAAATAATTTTTTTTTACATTT
1 TTTTGATGGTGGCCTGCCAATGGCCGGCACCACCTTTATGT-----A-AA-TTTTTTTT--ATTT
** * *
5391804 TGGGCTGTCATTGGCCTGCACCAGTATACGAAAAAATTAAAATTTTT
57 TGAACTGTCATTGGACTGCACCAGAATACGAAAAAATTAAAATTTTT
**** **
5391851 TTTTGATGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAAATTACATTTTGAACTGTC
1 TTTTGATGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTATTTTGAACTGTC
* *
5391916 ATT-GACTGGCACCAGAATACGAAAAAGTT-CAATTTTT
66 ATTGGACT-GCACCAGAATACGAAAAAATTAAAATTTTT
*
5391953 TTTTG-TGGTGCCCTGCCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTATTTT
1 TTTTGATGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTATTTT
5392009 TTACATTTTG
Statistics
Matches: 135, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
101 44 0.33
102 15 0.11
103 33 0.24
105 2 0.01
106 2 0.01
107 1 0.01
112 38 0.28
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (103 bp):
TTTTGATGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTATTTTGAACTGTC
ATTGGACTGCACCAGAATACGAAAAAATTAAAATTTTT
Found at i:5392762 original size:51 final size:51
Alignment explanation
Indices: 5392694--5392792 Score: 173
Period size: 51 Copynumber: 1.9 Consensus size: 51
5392684 TTTTTCCTGT
*
5392694 TAATTTTTACTTAATTTAAAATTATTCTGTAAATATTTCTTTTATTTTAAA
1 TAATTTTTAATTAATTTAAAATTATTCTGTAAATATTTCTTTTATTTTAAA
5392745 TAATTATTTAATT-ATTTAAAATTATTCTGTAAATATTTCTTTTATTTT
1 TAATT-TTTAATTAATTTAAAATTATTCTGTAAATATTTCTTTTATTTT
5392793 TTCCTGTTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 40 0.87
52 6 0.13
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (51 bp):
TAATTTTTAATTAATTTAAAATTATTCTGTAAATATTTCTTTTATTTTAAA
Found at i:5393795 original size:110 final size:110
Alignment explanation
Indices: 5393609--5393929 Score: 408
Period size: 107 Copynumber: 2.9 Consensus size: 110
5393599 GTAAAAAAAA
**
5393609 TTACATAAAGGTGGTG-TCGGGAATTGGCAGGCCACCACCAAAATTTTTTTTCAATTTTTTCGTA
1 TTACATAAAGGTGGTGCT-GGCCATTGGCAGGCCACCA-CAAAATTTTTTTT-AATTTTTTCGTA
*
5393673 TACTGGTGCCGGCCAATGACAACCCAAAATGTAAAAAAAAATTCTTTTT
63 TACTGGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAAATT-TTTTT
5393722 TTACATAAAGGTGGTGCTGGCCATTGGCAGGCCACCAC-AAATTTTTTTTAATTTTTTCGTATAC
1 TTACATAAAGGTGGTGCTGGCCATTGGCAGGCCACCACAAAATTTTTTTTAATTTTTTCGTATAC
*
5393786 TGGTGCCGGCCAATGACAGCCCATAATGT-------AATTTTTTT
66 TGGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAAATTTTTTT
* * * *
5393824 TTACATAAAGGTGGTGCCGGCCATTGTCAGGCCACCACAAAAATAATTTTTTTTAAATTTATCGT
1 TTACATAAAGGTGGTGCTGGCCATTGGCAGGCCACCAC---AA-AATTTTTTTTAATTTTTTCGT
* * *
5393889 ATACTAGTGCTGGCCAATGATAGCCCAAAATGTAAAAAAAA
62 ATACTGGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAA
5393930 TTACTTAAAG
Statistics
Matches: 183, Mismatches: 12, Indels: 25
0.83 0.05 0.11
Matches are distributed among these distances:
102 41 0.22
103 4 0.02
106 1 0.01
107 48 0.26
110 42 0.23
111 11 0.06
112 1 0.01
113 33 0.18
114 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (110 bp):
TTACATAAAGGTGGTGCTGGCCATTGGCAGGCCACCACAAAATTTTTTTTAATTTTTTCGTATAC
TGGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAAATTTTTTT
Found at i:5393823 original size:102 final size:104
Alignment explanation
Indices: 5393548--5393988 Score: 415
Period size: 102 Copynumber: 4.2 Consensus size: 104
5393538 CCACCGGGAT
* * * * * ******
5393548 TTTTTTTTATTTTTTTTCGTATACTAGTGCCAGCCAATGGCAGCACAAAATGTAA-AAAAAATTA
1 TTTTTTTTA-ATTTTTTCGTATACTGGTGCCGGCCAATGACAGCCCAAAATGTAATTTTTTTTTA
* **
5393612 CATAAAGGTGGTGTCGGGAATTGGCAGGCCACCACCAAAA
65 CATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAA
*
5393652 TTTTTTTTCAATTTTTTCGTATACTGGTGCCGGCCAATGACAACCCAAAATGTAAAAAAAAATTC
1 TTTTTTTT-AATTTTTTCGTATACTGGTGCCGGCCAATGACAGCCCAAAATGT-------AATT-
*
5393717 TTTTTTTACATAAAGGTGGTGCTGGCCATTGGCAGGCCACCA-C-AAA
57 TTTTTTTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAA
*
5393763 TTTTTTTTAATTTTTTCGTATACTGGTGCCGGCCAATGACAGCCCATAATGTAATTTTTTTTTAC
1 TTTTTTTTAATTTTTTCGTATACTGGTGCCGGCCAATGACAGCCCAAAATGTAATTTTTTTTTAC
* *
5393828 ATAAAGGTGGTGCCGGCCATTGTCAGGCCACCACAAAAATAA
66 ATAAAGGTGGTGCCGGCCATTGGCAGGCCACCAC--CAA-AA
* * * * * ******
5393870 TTTTTTTTAAATTTATCGTATACTAGTGCTGGCCAATGATAGCCCAAAATGTAA-AAAAAATTAC
1 TTTTTTTTAATTTTTTCGTATACTGGTGCCGGCCAATGACAGCCCAAAATGTAATTTTTTTTTAC
* * * *
5393934 TTAAAGGTGGTGCCGGCTATTGGCAAGCCACCACC-ATA
66 ATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAA
*
5393972 TTTTTTTTATTTTTTTC
1 TTTTTTTTAATTTTTTC
5393989 TTTATTGGTA
Statistics
Matches: 280, Mismatches: 42, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
102 55 0.20
103 5 0.02
104 45 0.16
105 1 0.00
106 35 0.12
107 50 0.18
110 42 0.15
111 13 0.05
112 1 0.00
113 33 0.12
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (104 bp):
TTTTTTTTAATTTTTTCGTATACTGGTGCCGGCCAATGACAGCCCAAAATGTAATTTTTTTTTAC
ATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAA
Found at i:5393871 original size:53 final size:53
Alignment explanation
Indices: 5393706--5393877 Score: 140
Period size: 53 Copynumber: 3.3 Consensus size: 53
5393696 CCAAAATGTA
* * *
5393706 AAAAAAAATTCTTTTTTTACATAAAGGTGGTGCTGGCCATTGGCAGGCCACCAC
1 AAAAATAATT-TTTTTTTACATAAAGGTGGTGCCGGCCATTGACAGGCCACCAC
* ** * * * * *
5393760 -AAATTTTTTTTAATTTTTTCGTATA-CTGGTGCCGGCCAATGACA-G-C-CCA-
1 AAAAATAATTTT--TTTTTACATAAAGGTGGTGCCGGCCATTGACAGGCCACCAC
* ** *
5393809 TAATGTAATTTTTTTTTACATAAAGGTGGTGCCGGCCATTGTCAGGCCACCAC
1 AAAAATAATTTTTTTTTACATAAAGGTGGTGCCGGCCATTGACAGGCCACCAC
5393862 AAAAATAATTTTTTTT
1 AAAAATAATTTTTTTT
5393878 AAATTTATCG
Statistics
Matches: 86, Mismatches: 24, Indels: 17
0.68 0.19 0.13
Matches are distributed among these distances:
48 9 0.10
49 16 0.19
50 11 0.13
51 2 0.02
52 6 0.07
53 33 0.38
54 9 0.10
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (53 bp):
AAAAATAATTTTTTTTTACATAAAGGTGGTGCCGGCCATTGACAGGCCACCAC
Found at i:5395060 original size:26 final size:24
Alignment explanation
Indices: 5395031--5395121 Score: 96
Period size: 25 Copynumber: 3.7 Consensus size: 24
5395021 TCACGTATGG
5395031 TTTTTACATAATATATATATGCATT
1 TTTTTACAT-ATATATATATGCATT
* *
5395056 TTTTT-CATATAGTACATACGCATAT
1 TTTTTACATATA-TATATATGCAT-T
* *
5395081 TTTTTATATATAATATATATGCATA
1 TTTTTACATAT-ATATATATGCATT
5395106 TTTTTA-ATATATATAT
1 TTTTTACATATATATAT
5395122 TTTTAAGCTT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
23 9 0.16
24 16 0.29
25 17 0.30
26 13 0.23
27 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTTTACATATATATATATGCATT
Found at i:5395064 original size:24 final size:23
Alignment explanation
Indices: 5395031--5395121 Score: 83
Period size: 24 Copynumber: 3.7 Consensus size: 23
5395021 TCACGTATGG
*
5395031 TTTTTACATAATATATATATGCAT
1 TTTTTTCAT-ATATATATATGCAT
* *
5395055 TTTTTTCATATAGTACATACGCAT
1 TTTTTTCATATA-TATATATGCAT
*
5395079 ATTTTTTATATATAATATATATGCAT
1 -TTTTTT-CATAT-ATATATATGCAT
* *
5395105 ATTTTTAATATATATAT
1 TTTTTTCATATATATAT
5395122 TTTTAAGCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
23 9 0.16
24 21 0.38
25 11 0.20
26 13 0.24
27 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTTTTCATATATATATATGCAT
Found at i:5401696 original size:132 final size:132
Alignment explanation
Indices: 5401429--5402628 Score: 1737
Period size: 132 Copynumber: 9.2 Consensus size: 132
5401419 GGAGCAGTTT
* *
5401429 GATGGCAGATTTTACCTCCCTGAGGTTACAGTAGAGTACATTGAAGCCAGTAATTCTA--TCTCC
1 GATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTC-CC
* * * * * *
5401492 TGGGCAGCAGTGGAATAGATGGAATATTACAGATCTTATCTCCTTAAGAAGTAGTGGAGCAGATC
65 TGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATC
*
5401557 GAA
130 AAA
* * * **
5401560 GATGGCGGATTTTAACTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTAAC
1 GATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCC
* * * * * * *
5401624 TGGGCAGCAGTAGAATAAATTGAATATTAT-AGATCTTATCTACCTAAGCAATAGTGGAGCAGGT
65 TGGGCAGCAGTGGAATAGATTGAAGATT-TCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGAT
5401688 CAAA
129 CAAA
* *
5401692 GATGGCGGATTTTACCTCTCTGTGGTTACAGTGGAGTACATTGAAGCCAGT-A----A-TT--CT
1 GATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
* * * *
5401749 GGGCAGCAGCGGAATAGATTGAAGATTTTAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGGTCA
66 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
5401814 AA
131 AA
*
5401816 GATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCTT
1 GATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
* * * *
5401881 GGGCATCAGTGGAATAGATTGAAGATTTCAGATATAGTCTCCCTAAGCAGTAGTGAAGCAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
5401946 AA
131 AA
* * *
5401948 TATGGTAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCT
1 GATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
* * * *
5402013 AGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTTCCTAAGCAGTAGTGGAGCAGGTCA
66 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
5402078 AA
131 AA
* *
5402080 GATAGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCT
1 GATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
**
5402145 GGGCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
5402210 AA
131 AA
* *
5402212 GATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
1 GATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
* *
5402277 GGGCATCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
5402342 AA
131 AA
* *
5402344 GATGG-TGAATTTTACCTCCCTTTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
1 GATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
* * *
5402408 TAGACAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCGGTAGTGGAGCAGATC
65 TGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATC
5402473 AAA
130 AAA
* *
5402476 GATGG-TGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAATCCAGTAATTCTACTTCCC
1 GATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC
* *
5402540 T-GGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGGTC
65 TGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATC
5402604 AAA
130 AAA
*
5402607 GATGACAGATTTTACCTCCCTG
1 GATGGCAGATTTTACCTCCCTG
5402629 AAGTTGCAAT
Statistics
Matches: 972, Mismatches: 83, Indels: 28
0.90 0.08 0.03
Matches are distributed among these distances:
123 1 0.00
124 108 0.11
125 1 0.00
126 1 0.00
127 2 0.00
129 1 0.00
130 2 0.00
131 137 0.14
132 718 0.74
133 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
GATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
AA
Found at i:5404102 original size:26 final size:23
Alignment explanation
Indices: 5404079--5404169 Score: 85
Period size: 24 Copynumber: 3.7 Consensus size: 23
5404069 TCACGCATGG
5404079 TTTTTACATAATATATATATGCAT
1 TTTTTACAT-ATATATATATGCAT
* * *
5404103 TTTTTTCATATAGTACATACGCATAT
1 TTTTTACATATA-TATATATGC--AT
*
5404129 TTTTTATATATAATATATATGCAT
1 TTTTTACATAT-ATATATATGCAT
5404153 ATTTTTA-ATATATATAT
1 -TTTTTACATATATATAT
5404170 TTTTAAGCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
23 9 0.16
24 21 0.38
25 6 0.11
26 18 0.33
27 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTTTACATATATATATATGCAT
Found at i:5405790 original size:14 final size:13
Alignment explanation
Indices: 5405767--5405792 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5405757 GGCCACCACC
5405767 AAAAAATTTTTTT
1 AAAAAATTTTTTT
5405780 AAAAAATTTTTTT
1 AAAAAATTTTTTT
5405793 CGTATACTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAAAATTTTTTT
Found at i:5405792 original size:168 final size:167
Alignment explanation
Indices: 5405576--5405881 Score: 454
Period size: 168 Copynumber: 1.8 Consensus size: 167
5405566 ATAAAGGTGG
* * * *
5405576 TGCCGGCCATTGACAAGGCACCACAAAAATTTTTTTTAAAATTTTTTTTCCTATATTGGTGCCGA
1 TGCCGGCCATTGACAAGGCACCACAAAAATTTTTTTAAAAAATTTTTTTCCTATACTGGTACCGA
* * *
5405641 CCAATAACATCCTAAAATGTAACAAAAAAATT-ACATAAAGGTGGTGCCGGCCATTGGCAGGCCA
66 CCAATAACAGCCCAAAATGTAAAAAAAAAATTAACATAAAGGTGGTGCCGGCCATTGGCAGGCCA
5405705 CCACCAAATTTTTTTTTAAAATTTTTTCGTATACTGA
131 CCACCAAATTTTTTTTTAAAATTTTTTCGTATACTGA
* *
5405742 TGCCGGCCATTG-CCAGGCCACCACCAAAAAATTTTTTTAAAAAATTTTTTTCGTATACTGGTAC
1 TGCCGGCCATTGACAAGG-CACCA-C-AAAAATTTTTTTAAAAAATTTTTTTCCTATACTGGTAC
* * * *
5405806 CGGCCAATGATAGCCCAAAATGTAAAAAAAAAATTAACATAAAGGTGGTGCCGTCCATTGGCAGG
63 CGACCAATAACAGCCCAAAATGTAAAAAAAAAATTAACATAAAGGTGGTGCCGGCCATTGGCAGG
5405871 CCACCACCAAA
128 CCACCACCAAA
5405882 AAAATTTTTA
Statistics
Matches: 123, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
165 4 0.03
166 17 0.14
167 1 0.01
168 62 0.50
169 39 0.32
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (167 bp):
TGCCGGCCATTGACAAGGCACCACAAAAATTTTTTTAAAAAATTTTTTTCCTATACTGGTACCGA
CCAATAACAGCCCAAAATGTAAAAAAAAAATTAACATAAAGGTGGTGCCGGCCATTGGCAGGCCA
CCACCAAATTTTTTTTTAAAATTTTTTCGTATACTGA
Found at i:5405809 original size:61 final size:57
Alignment explanation
Indices: 5405682--5405811 Score: 179
Period size: 57 Copynumber: 2.2 Consensus size: 57
5405672 TACATAAAGG
* **
5405682 TGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTAAAATTTTTTCGTATAC
1 TGGTGCCGGCCATTGCCAGGCCACCACCAAATTTTTTTAAAAAATTTTTTCGTATAC
*
5405739 TGATGCCGGCCATTGCCAGGCCACCACCAAAAAATTTTTTTAAAAAATTTTTTTCGTATAC
1 TGGTGCCGGCCATTGCCAGGCCACCACC---AAATTTTTTTAAAAAA-TTTTTTCGTATAC
*
5405800 TGGTACCGGCCA
1 TGGTGCCGGCCA
5405812 ATGATAGCCC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
57 26 0.41
60 14 0.22
61 23 0.37
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (57 bp):
TGGTGCCGGCCATTGCCAGGCCACCACCAAATTTTTTTAAAAAATTTTTTCGTATAC
Found at i:5405948 original size:169 final size:165
Alignment explanation
Indices: 5405594--5405935 Score: 402
Period size: 168 Copynumber: 2.0 Consensus size: 165
5405584 ATTGACAAGG
* * * * *
5405594 CACCACAAAAATTTTTTTTAAAATTTTTTTTCCTATATTGGTGCCGACCAATAACATCCTAAAAT
1 CACCA-AAAAATTTTTTTTAAAAATTTTTTTCCTATACTGGTACCGACCAATAACAGCCCAAAAT
* ****
5405659 GTAACAAAAAAATTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTAA
65 GTAAAAAAAAAATTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAAAATTTTTAA
* * *
5405724 AATTTTTTCGTATACTGATGCCGGCCATTGCCAGGCCAC
130 AATTTTTTCGTATACTGATGCCGGCAAATG-CA-G-CAA
* * * * *
5405763 CACCAAAAAATTTTTTTAAAAAATTTTTTTCGTATACTGGTACCGGCCAATGATAGCCCAAAATG
1 CACCAAAAAATTTTTTTTAAAAATTTTTTTCCTATACTGGTACCGACCAATAACAGCCCAAAATG
*
5405828 TAAAAAAAAAATTAACATAAAGGTGGTGCCGTCCATTGGCAGGCCACCACCAAAAAAATTTTTAA
66 TAAAAAAAAAATT-ACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAAAATTTTTAA
* * *
5405893 ATTTTTTTTTCGTATACTGGTGCTGGCAAATG-A-CAA
130 A--ATTTTTTCGTATACTGATGCCGGCAAATGCAGCAA
5405929 C-CCAAAA
1 CACCAAAA
5405936 TGTAATTTTT
Statistics
Matches: 148, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
165 6 0.04
166 3 0.02
168 62 0.42
169 53 0.36
171 24 0.16
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.30
Consensus pattern (165 bp):
CACCAAAAAATTTTTTTTAAAAATTTTTTTCCTATACTGGTACCGACCAATAACAGCCCAAAATG
TAAAAAAAAAATTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAAAATTTTTAAA
ATTTTTTCGTATACTGATGCCGGCAAATGCAGCAA
Found at i:5410953 original size:19 final size:19
Alignment explanation
Indices: 5410907--5410944 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5410897 CTCTCTCAAC
**
5410907 AAAAAATTAAAAAAATTCA
1 AAAAAATTTGAAAAATTCA
5410926 AAAAAATTTGAAAAATTCA
1 AAAAAATTTGAAAAATTCA
5410945 CAATAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (19 bp):
AAAAAATTTGAAAAATTCA
Found at i:5424042 original size:14 final size:14
Alignment explanation
Indices: 5424023--5424049 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5424013 GTAAAAAATT
5424023 TGTATAATTTATTA
1 TGTATAATTTATTA
5424037 TGTATAATTTATT
1 TGTATAATTTATT
5424050 GCACCTATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TGTATAATTTATTA
Found at i:5425197 original size:5 final size:5
Alignment explanation
Indices: 5425189--5425218 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
5425179 ACTTTATCTA
5425189 TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
5425219 ATTTCACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:5425919 original size:5 final size:5
Alignment explanation
Indices: 5425911--5425941 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
5425901 ACTTTATCTA
5425911 TATAT TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT T
5425942 TCACATGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:5426462 original size:720 final size:722
Alignment explanation
Indices: 5425082--5426496 Score: 2807
Period size: 720 Copynumber: 2.0 Consensus size: 722
5425072 TTAAATTCGT
5425082 GTTTTTAAATAAAGACAAAAGTAAATAGTTAACTGATTATTTTATAACTTTTCGAAATTGAGAAT
1 GTTTTTAAATAAAGACAAAAGTAAATAGTTAACTGATTATTTTATAACTTTTCGAAATTGAGAAT
5425147 AAAGAAATCCATAGTTGGGTCACAACTAATTTACTTTATCTATATATTATATTATATTATATTAT
66 AAAGAAATCCATAGTTGGGTCACAACTAATTTACTTTATCTATATATTATATTATATTATATTAT
5425212 ATTATATATTTCACATGTAAAAGAACCTTATTTGCTAAAAGTCTTTTTTTTGTCCTTATCGGTCC
131 ATTATATATTTCACATGTAAAAGAACCTTATTTGCTAAAAGTCTTTTTTTTGTCCTTATCGGTCC
5425277 CTCTATTAGGGGTATAAATGAGATTCCAAAAAAAATTTGAATTTGACTCAGTAATTATTGAGCTG
196 CTCTATTAGGGGTATAAATGAGATTCCAAAAAAAATTTGAATTTGACTCAGTAATTATTGAGCTG
5425342 AGCTCAAACTATCGATCAAGCAAAATTCGAGCTTAATAATACTTAACTTGAATAACTTGTGAGTC
261 AGCTCAAACTATCGATCAAGCAAAATTCGAGCTTAATAATACTTAACTTGAATAACTTGTGAGTC
5425407 TTAATGAGCTTTTCATATTTTTATATTATTAAGTTATATATTTCTCTTAATTCTCAAGTCGAGCT
326 TTAATGAGCTTTTCATATTTTTATATTATTAAGTTATATATTTCTCTTAATTCTCAAGTCGAGCT
5425472 CAAGTTCAAGTAGCTCAATTATATCTCAAGTGAGTTCGAACATAAAAATAAATATTAAATTAAAC
391 CAAGTTCAAGTAGCTCAATTATATCTCAAGTGAGTTCGAACATAAAAATAAATATTAAATTAAAC
5425537 TTAAACGAAATATCGAATTCTAAATTTTAAGTCGAACTTAACAATATTCAAACTCGACTCTACAA
456 TTAAACGAAATATCGAATTCTAAATTTTAAGTCGAACTTAACAATATTCAAACTCGACTCTACAA
5425602 GCTAATTTGTATAGCAAGTATCTGTCGCCGTAAAAGGTGCAATGCACCCCATTTGCTCTCATGAC
521 GCTAATTTGTATAGCAAGTATCTGTCGCCGTAAAAGGTGCAATGCACCCCATTTGCTCTCATGAC
5425667 ATCTTCTTTCCTAATTCAATGTACAGTAGAAATTTCCAAGGAAGATTTGCAAAGAAAAACGATAA
586 ATCTTCTTTCCTAATTCAATGTACAGTAGAAATTTCCAAGGAAGATTTGCAAAGAAAAACGATAA
5425732 TCTGAACTGTAAGACCCAAATTTTGCCCGGGCCCAATGCCAATACTTTTCGAAATAAAGACAAAA
651 TCTGAACTGTAAGACCCAAATTTTGCCCGGGCCCAATGCCAATACTTTTCGAAATAAAGACAAAA
5425797 GTAAATA
716 GTAAATA
5425804 GTTTTTAAATAAAGACAAAAGTAAATAGTTAACTGATTATTTTATAACTTTTCGAAATTGAGAAT
1 GTTTTTAAATAAAGACAAAAGTAAATAGTTAACTGATTATTTTATAACTTTTCGAAATTGAGAAT
5425869 AAAGAAATCCATAGTTGGGTCACAACTAATTTACTTTATCTATATATTATATTATATTATATTAT
66 AAAGAAATCCATAGTTGGGTCACAACTAATTTACTTTATCTATATATTATATTATATTATATTAT
5425934 A-T-TATATTTCACATGTAAAAGAACCTTATTTGCTAAAAGTCTTTTTTTTGTCCTTATCGGTCC
131 ATTATATATTTCACATGTAAAAGAACCTTATTTGCTAAAAGTCTTTTTTTTGTCCTTATCGGTCC
5425997 CTCTATTAGGGGTATAAATGAGATTCCAAAAAAAATTTGAATTTGACTCAGTAATTATTGAGCTG
196 CTCTATTAGGGGTATAAATGAGATTCCAAAAAAAATTTGAATTTGACTCAGTAATTATTGAGCTG
5426062 AGCTCAAACTATCGATCAAGCAAAATTCGAGCTTAATAATACTTAACTTGAATAACTTGTGAGTC
261 AGCTCAAACTATCGATCAAGCAAAATTCGAGCTTAATAATACTTAACTTGAATAACTTGTGAGTC
5426127 TTAATGAGCTTTTCATATTTTTATATTATTAAGTTATATATTTCTCTTAATTCTCAAGTCGAGCT
326 TTAATGAGCTTTTCATATTTTTATATTATTAAGTTATATATTTCTCTTAATTCTCAAGTCGAGCT
*
5426192 CAAGTTCAAGTAGCTCAATTATATCTCAAGTGAGTTCGAACATAAAAATAAATATTAAATTGAAC
391 CAAGTTCAAGTAGCTCAATTATATCTCAAGTGAGTTCGAACATAAAAATAAATATTAAATTAAAC
5426257 TTAAACGAAATATCGAATTCTAAATTTTAAGTCGAACTTAACAATATTCAAACTCGACTCTACAA
456 TTAAACGAAATATCGAATTCTAAATTTTAAGTCGAACTTAACAATATTCAAACTCGACTCTACAA
5426322 GCTAATTTGTATAGCAAGTATCTGTCGCCGTAAAAGGTGCAATGCACCCCATTTGCTCTCATGAC
521 GCTAATTTGTATAGCAAGTATCTGTCGCCGTAAAAGGTGCAATGCACCCCATTTGCTCTCATGAC
5426387 ATCTTCTTTCCTAATTCAATGTACAGTAGAAATTTCCAAGGAAGATTTGCAAAGAAAAACGATAA
586 ATCTTCTTTCCTAATTCAATGTACAGTAGAAATTTCCAAGGAAGATTTGCAAAGAAAAACGATAA
5426452 TCTGAACTGTAAGACCCAAATTTTGCCCGGGCCCAATGCCAATAC
651 TCTGAACTGTAAGACCCAAATTTTGCCCGGGCCCAATGCCAATAC
5426497 CAAAATAAAC
Statistics
Matches: 692, Mismatches: 1, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
720 560 0.81
721 1 0.00
722 131 0.19
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (722 bp):
GTTTTTAAATAAAGACAAAAGTAAATAGTTAACTGATTATTTTATAACTTTTCGAAATTGAGAAT
AAAGAAATCCATAGTTGGGTCACAACTAATTTACTTTATCTATATATTATATTATATTATATTAT
ATTATATATTTCACATGTAAAAGAACCTTATTTGCTAAAAGTCTTTTTTTTGTCCTTATCGGTCC
CTCTATTAGGGGTATAAATGAGATTCCAAAAAAAATTTGAATTTGACTCAGTAATTATTGAGCTG
AGCTCAAACTATCGATCAAGCAAAATTCGAGCTTAATAATACTTAACTTGAATAACTTGTGAGTC
TTAATGAGCTTTTCATATTTTTATATTATTAAGTTATATATTTCTCTTAATTCTCAAGTCGAGCT
CAAGTTCAAGTAGCTCAATTATATCTCAAGTGAGTTCGAACATAAAAATAAATATTAAATTAAAC
TTAAACGAAATATCGAATTCTAAATTTTAAGTCGAACTTAACAATATTCAAACTCGACTCTACAA
GCTAATTTGTATAGCAAGTATCTGTCGCCGTAAAAGGTGCAATGCACCCCATTTGCTCTCATGAC
ATCTTCTTTCCTAATTCAATGTACAGTAGAAATTTCCAAGGAAGATTTGCAAAGAAAAACGATAA
TCTGAACTGTAAGACCCAAATTTTGCCCGGGCCCAATGCCAATACTTTTCGAAATAAAGACAAAA
GTAAATA
Found at i:5428212 original size:18 final size:19
Alignment explanation
Indices: 5428184--5428231 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
5428174 ATATACCTAC
5428184 ATAGTTTTTTTTGTATTTT
1 ATAGTTTTTTTTGTATTTT
5428203 ATAGTTTTTTTTGTATTTT
1 ATAGTTTTTTTTGTATTTT
*
5428222 A-AATTTTTTT
1 ATAGTTTTTTT
5428232 AAATTCATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (19 bp):
ATAGTTTTTTTTGTATTTT
Found at i:5428406 original size:21 final size:21
Alignment explanation
Indices: 5428372--5428422 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
5428362 TTTATCTACA
* *
5428372 TGTTATTGTATATAATTGATTT
1 TGTTATTTTGTAT-ATTGATTT
*
5428394 T-TTATTTTGTATATTTATTT
1 TGTTATTTTGTATATTGATTT
5428414 TGTTATTTT
1 TGTTATTTT
5428423 TACTCGTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 8 0.32
21 16 0.64
22 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.69
Consensus pattern (21 bp):
TGTTATTTTGTATATTGATTT
Found at i:5428436 original size:15 final size:15
Alignment explanation
Indices: 5428416--5428449 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5428406 ATTTATTTTG
*
5428416 TTATTTTTACTCGTA
1 TTATTTTTACTCGCA
5428431 TTATTTTTACTCGCA
1 TTATTTTTACTCGCA
5428446 TTAT
1 TTAT
5428450 CGTAATTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.59
Consensus pattern (15 bp):
TTATTTTTACTCGCA
Found at i:5431176 original size:23 final size:24
Alignment explanation
Indices: 5431146--5431194 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
5431136 TTGAATCGTA
*
5431146 TTTTATAA-TTGTTAATATTTTAT
1 TTTTATAACTTGTTAATAATTTAT
*
5431169 TTTTATAACTTTTTAATAATTTAT
1 TTTTATAACTTGTTAATAATTTAT
5431193 TT
1 TT
5431195 GATTTGCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTATAACTTGTTAATAATTTAT
Found at i:5436286 original size:3 final size:3
Alignment explanation
Indices: 5436278--5436308 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5436268 TTGGTTTCTT
5436278 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5436309 ACTTTTATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5440422 original size:21 final size:20
Alignment explanation
Indices: 5440392--5440430 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5440382 ATATAAGTTT
*
5440392 AAAATAATTAAAATAATATC
1 AAAATAATTAAAAAAATATC
5440412 AAAATTAATTAAAAAAATA
1 AAAA-TAATTAAAAAAATA
5440431 AAACAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATAATTAAAAAAATATC
Found at i:5442307 original size:44 final size:44
Alignment explanation
Indices: 5442259--5442706 Score: 209
Period size: 44 Copynumber: 10.2 Consensus size: 44
5442249 TATCTTGGAA
* * *
5442259 AGATAAGATTTTCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * * *
5442303 AGATAAGATCTACAATCTTCAACCTTCTCCTCTGCTGCTTAGAG
1 AGATAAGATTTGCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * *
5442347 AGACAATG-CTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGCAGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
** * * *
5442391 AGATAAGATTTGTTGGCTTCGATCTGCTCCACTACTGTTTAGGG
1 AGATAAGATTTGCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * *
5442435 AGATAAGATTTACAAACTTCAACCTTCTCCACTGCTGCTTAGGG
1 AGATAAGATTTGCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** ** * * *
5442479 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCAGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
5442523 AGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * ** *
5442567 AGATAAGATCTACAATCTTCAACCT--TTAAGCTGCTGCTTAGGG
1 AGATAAGATTTGCAGTCTTCAATCTGCTCCA-CTACTGCTTAGGG
* ** * * *
5442610 AGATAAGGTTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCAGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * * *
5442654 ACATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGTTTAGGG
1 AGATAAGATTTGCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
5442698 AGATAAGAT
1 AGATAAGAT
5442707 CTACAATTTT
Statistics
Matches: 285, Mismatches: 96, Indels: 46
0.67 0.22 0.11
Matches are distributed among these distances:
42 20 0.07
43 40 0.14
44 200 0.70
45 12 0.04
46 12 0.04
47 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (44 bp):
AGATAAGATTTGCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:5442735 original size:263 final size:264
Alignment explanation
Indices: 5442213--5442805 Score: 983
Period size: 263 Copynumber: 2.2 Consensus size: 264
5442203 GCAACTTCGT
* * *
5442213 GGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCTACTATCTTGGAAAGATAAGATTTTCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
***
5442278 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCTCTGCTGCTT
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTAAGCTGCTGCTT
* * **
5442343 AGAGAGACAATGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTTGGC
131 AGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAACATAAGATTTGCCGGC
*
5442408 TTCGATCTGCTCCACTACTGTTTAGGGAGATAAGATTTACAAACTTCAACCTTCTCCACTGCTGC
196 TTCGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAAACTTCAACCTTCTCCACTGCTGC
*
5442473 TTAG
261 TCAG
5442477 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
5442542 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTT-TAAGCTGCTGCTT
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTAAGCTGCTGCTT
* * * *
5442606 AGGGAGATAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAACATAAGATTTGCCGTC
131 AGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAACATAAGATTTGCCGGC
** *
5442671 TTCGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGC
196 TTCGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAAACTTCAACCTTCTCCACTGCTGC
5442736 TCAG
261 TCAG
*
5442740 GGAGACAAGGCTTTGG-GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCT
1 GGAGACAAGGC-TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCT
5442804 TC
65 TC
5442806 AGTCTGCCTC
Statistics
Matches: 308, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
263 191 0.62
264 117 0.38
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (264 bp):
GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTAAGCTGCTGCTT
AGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAACATAAGATTTGCCGGC
TTCGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAAACTTCAACCTTCTCCACTGCTGC
TCAG
Found at i:5442812 original size:132 final size:132
Alignment explanation
Indices: 5442213--5442805 Score: 965
Period size: 132 Copynumber: 4.5 Consensus size: 132
5442203 GCAACTTCGT
* * *
5442213 GGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCTACTATCTTGGAAAGATAAGATTTTCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
*
5442278 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCTCTGCTGCTT
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
5442343 AG
131 AG
* * ** *
5442345 AGAGACAATGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTTGGCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
* * * *
5442410 CGATCTGCTCCACTACTGTTTAGGGAGATAAGATTTACAAACTTCAACCTTCTCCACTGCTGCTT
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
5442475 AG
131 AG
5442477 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
**
5442542 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTT-TAAGCTGCTGCTT
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
5442606 AG
131 AG
* * *
5442608 GGAGATAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAACATAAGATTTGCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
* * *
5442673 CGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTC
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
5442738 AG
131 AG
*
5442740 GGAGACAAGGCTTTGG-GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCT
1 GGAGACAAGGC-TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCT
5442804 TC
65 TC
5442806 AGTCTGCCTC
Statistics
Matches: 424, Mismatches: 35, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
131 123 0.29
132 297 0.70
133 4 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (132 bp):
GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
AG
Found at i:5453897 original size:21 final size:20
Alignment explanation
Indices: 5453859--5453899 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5453849 ATAAAAATAT
5453859 ATAAGTTTAAAATAATTAAA
1 ATAAGTTTAAAATAATTAAA
5453879 ATAA-TTTCAAAATTAATTAAA
1 ATAAGTTT-AAAA-TAATTAAA
5453900 TAAATAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 8 0.42
21 8 0.42
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
ATAAGTTTAAAATAATTAAA
Found at i:5456016 original size:132 final size:132
Alignment explanation
Indices: 5455773--5456496 Score: 1213
Period size: 132 Copynumber: 5.5 Consensus size: 132
5455763 GCAATTTCAT
* * **
5455773 GGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCTACTATCTTATAAAGATAAGATTTGCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
5455838 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
5455903 AG
131 AG
* * * *
5455905 AGAGGCAAGGCTTGGTGGCTTAAATCTGCTTCCAACTATCTTGGAAATATAAGATTTGCCAG-CT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCC-GTCT
* * *
5455969 TCGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCTGCTGCTGCT
65 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCT
5456034 TAG
130 TAG
5456037 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
**
5456102 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTT-TAAGCTGCTGCTT
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
5456166 AG
131 AG
* *
5456168 GGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCCTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
* *
5456233 CGATCTTCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
5456298 AG
131 AG
5456300 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
* * *
5456365 CGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTC
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
5456430 A-
131 AG
*
5456431 GGAGACAAGGCTTTGG-GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCT
1 GGAGACAAGGC-TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCT
5456495 TC
65 TC
5456497 AGTCTGCCTC
Statistics
Matches: 558, Mismatches: 30, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
131 187 0.34
132 370 0.66
133 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (132 bp):
GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
AG
Found at i:5456277 original size:263 final size:264
Alignment explanation
Indices: 5455773--5456496 Score: 1229
Period size: 263 Copynumber: 2.8 Consensus size: 264
5455763 GCAATTTCAT
* * **
5455773 GGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCTACTATCTTATAAAGATAAGATTTGCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
5455838 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
* * * * *
5455903 AGAGAGGCAAGGCTTGGTGGCTTAAATCTGCTTCCAACTATCTTGGAAATATAAGATTTGCCAGC
131 AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATC
* * *
5455968 TTCGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCTGCTGCTGC
196 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGC
*
5456033 TTAG
261 TCAG
5456037 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
**
5456102 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTT-TAAGCTGCTGCTT
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
* *
5456166 AGGGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCCTC
131 AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATC
*
5456231 TTCGATCTTCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGC
196 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGC
5456296 TCAG
261 TCAG
5456300 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
* * *
5456365 CGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTC
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
5456430 A-GGAGACAAGGCTTTGG-GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCAT
131 AGGGAGACAAGGC-TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCAT
5456493 CTTC
195 CTTC
5456497 AGTCTGCCTC
Statistics
Matches: 433, Mismatches: 25, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
263 306 0.71
264 127 0.29
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (264 bp):
GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTT
AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATC
TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGC
TCAG
Found at i:5461668 original size:17 final size:17
Alignment explanation
Indices: 5461635--5461668 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5461625 CGCGCCATTC
5461635 TCTATTCCTGCCTTTTT
1 TCTATTCCTGCCTTTTT
*
5461652 TCTATCTCCTTCCTTTT
1 TCTAT-TCCTGCCTTTT
5461669 CTGTCCTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.06, C:0.32, G:0.03, T:0.59
Consensus pattern (17 bp):
TCTATTCCTGCCTTTTT
Found at i:5472257 original size:21 final size:21
Alignment explanation
Indices: 5472223--5472268 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5472213 CTAAGATATG
*
5472223 AATTGGATTGAATTGAATG-TA
1 AATTGGATTAAATTG-ATGTTA
*
5472244 AATTGTATTAAATTGATGTTA
1 AATTGGATTAAATTGATGTTA
5472265 AATT
1 AATT
5472269 CATTCATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.43
Consensus pattern (21 bp):
AATTGGATTAAATTGATGTTA
Found at i:5473914 original size:63 final size:63
Alignment explanation
Indices: 5473802--5473939 Score: 172
Period size: 63 Copynumber: 2.2 Consensus size: 63
5473792 GGTGTCTAAT
* * * * * *
5473802 ATGATTGTG-AGTGCTATGGTGCTTGTGTAAAATAAATTGGTGTTGAAGGTGTT-GATGCAGGGA
1 ATGATTGTGCA-TGCTATGGTACTTGTGTAAAATAAACTGGAGCTAAAGGTGTTAAAT-CAGGGA
* *
5473865 ATGATTGTGCATGCTATGGTATTTGTGTAAAATAAACTGGAGCTAAAGGTGTTAAATCGGGGA
1 ATGATTGTGCATGCTATGGTACTTGTGTAAAATAAACTGGAGCTAAAGGTGTTAAATCAGGGA
5473928 ATGATTGTGCAT
1 ATGATTGTGCAT
5473940 ATTGTGATGC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
63 62 0.95
64 3 0.05
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.34
Consensus pattern (63 bp):
ATGATTGTGCATGCTATGGTACTTGTGTAAAATAAACTGGAGCTAAAGGTGTTAAATCAGGGA
Found at i:5473954 original size:63 final size:63
Alignment explanation
Indices: 5473802--5473963 Score: 157
Period size: 63 Copynumber: 2.6 Consensus size: 63
5473792 GGTGTCTAAT
* * * * * * *
5473802 ATGATTGTG-AGTGCTATGGTGCTTGTGTAAAATAAATTGGTGTTGAAGGTGTTGATGCAGGGA
1 ATGATTGTGCA-TACTATGATGCTTGTGTAAAATAAACTGGAGCTAAAGGTGTTAATGCAGGGA
* * ** *
5473865 ATGATTGTGCATGCTATGGTATTTGTGTAAAATAAACTGGAGCTAAAGGTGTTAAAT-CGGGGA
1 ATGATTGTGCATACTATGATGCTTGTGTAAAATAAACTGGAGCTAAAGGTGTT-AATGCAGGGA
* * *
5473928 ATGATTGTGCATATTGTGATGCTTGTGTCAAATAAA
1 ATGATTGTGCATACTATGATGCTTGTGTAAAATAAA
5473964 ATGGGTTAGG
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
63 79 0.96
64 3 0.04
ACGTcount: A:0.29, C:0.07, G:0.30, T:0.35
Consensus pattern (63 bp):
ATGATTGTGCATACTATGATGCTTGTGTAAAATAAACTGGAGCTAAAGGTGTTAATGCAGGGA
Found at i:5475724 original size:7 final size:7
Alignment explanation
Indices: 5475700--5475804 Score: 93
Period size: 7 Copynumber: 15.0 Consensus size: 7
5475690 TTAAAAAAGT
5475700 AATTGAG
1 AATTGAG
*
5475707 AAATGAG
1 AATTGAG
*
5475714 AATTGAT
1 AATTGAG
*
5475721 AATTAAG
1 AATTGAG
5475728 AATTGAG
1 AATTGAG
*
5475735 GATTGAG
1 AATTGAG
*
5475742 GATTGAG
1 AATTGAG
*
5475749 GATTGAG
1 AATTGAG
* *
5475756 AAATGAA
1 AATTGAG
5475763 AATTGAG
1 AATTGAG
*
5475770 GATTGAG
1 AATTGAG
*
5475777 AATTTAG
1 AATTGAG
*
5475784 GATTGAG
1 AATTGAG
*
5475791 GATTGAG
1 AATTGAG
*
5475798 TATTGAG
1 AATTGAG
5475805 TTAAAAAGAA
Statistics
Matches: 80, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 80 1.00
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (7 bp):
AATTGAG
Found at i:5490581 original size:16 final size:18
Alignment explanation
Indices: 5490549--5490583 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
5490539 CATAATTAAA
5490549 TTAATTTATATAAATATT
1 TTAATTTATATAAATATT
5490567 TTAATTT-TA-AAATATT
1 TTAATTTATATAAATATT
5490583 T
1 T
5490584 AAGTAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 2 0.12
18 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAATTTATATAAATATT
Found at i:5493549 original size:72 final size:72
Alignment explanation
Indices: 5493377--5493538 Score: 245
Period size: 72 Copynumber: 2.2 Consensus size: 72
5493367 GAAGAGTTTG
** * *
5493377 AAACAGTTGGACCTATCCAATAACCAAATTCTTGGTCCTATTCCTTCTACCTTGGGCAACTTAAC
1 AAACAGTTGGACCTATCCAATAACCAAATTAGTGGTCCTATCCCTTCTACCTTGGGCAAATTAAC
5493442 CAATTTA
66 CAATTTA
* *
5493449 AAA-ATGTTGAACCTATCCAAAAACCAAATTAGTGGTCCTATCCCTTCTACCTTGGGCAAATTAA
1 AAACA-GTTGGACCTATCCAATAACCAAATTAGTGGTCCTATCCCTTCTACCTTGGGCAAATTAA
5493513 CCAATTTA
65 CCAATTTA
*
5493521 AAACAGTTGGACTTATCC
1 AAACAGTTGGACCTATCC
5493539 TTTAATCAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
71 1 0.01
72 78 0.98
73 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (72 bp):
AAACAGTTGGACCTATCCAATAACCAAATTAGTGGTCCTATCCCTTCTACCTTGGGCAAATTAAC
CAATTTA
Found at i:5493567 original size:72 final size:72
Alignment explanation
Indices: 5493382--5493576 Score: 178
Period size: 72 Copynumber: 2.7 Consensus size: 72
5493372 GTTTGAAACA
* * * * * *
5493382 GTTGGACCTATCCAATAACCAAATTC-TTGGTCCTATTCCTTCTACCTTGGGCAACTTAACCAAT
1 GTTGAACCTATCCAAAAACCAAA-TCACTGGGCCAATTCCTTCTACCTTGGGCAAATTAACCAAT
5493446 TTAAAAAT
65 TTAAAAAT
* * * * *
5493454 GTTGAACCTATCCAAAAACCAAATTAGTGGTCCTATCCCTTCTACCTTGGGCAAATTAACCAATT
1 GTTGAACCTATCCAAAAACCAAATCACTGGGCCAATTCCTTCTACCTTGGGCAAATTAACCAATT
5493519 TAAAACA-
66 TAAAA-AT
* * *** * * * *
5493526 GTTGGACTTATCCTTTAATCAAATCACTGGGGCAATTCCTTCAACTTTGGG
1 GTTGAACCTATCCAAAAACCAAATCACTGGGCCAATTCCTTCTACCTTGGG
5493577 TCGCTTAACC
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
71 1 0.01
72 99 0.98
73 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (72 bp):
GTTGAACCTATCCAAAAACCAAATCACTGGGCCAATTCCTTCTACCTTGGGCAAATTAACCAATT
TAAAAAT
Found at i:5499578 original size:16 final size:17
Alignment explanation
Indices: 5499548--5499588 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5499538 ATAGGTTCAA
5499548 TTATTAAATTATTTA-TT
1 TTATT-AATTATTTACTT
*
5499565 TTATTAATTGTTTACTT
1 TTATTAATTATTTACTT
5499582 TT-TTAAT
1 TTATTAAT
5499589 AATTATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
TTATTAATTATTTACTT
Found at i:5500648 original size:24 final size:24
Alignment explanation
Indices: 5500620--5500668 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5500610 CATGCATTCC
5500620 ATAGCACCTCAAATGGGTGCCACG
1 ATAGCACCTCAAATGGGTGCCACG
*
5500644 ATAGCACCTCAAATGGGTGTCACG
1 ATAGCACCTCAAATGGGTGCCACG
5500668 A
1 A
5500669 CACGCCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (24 bp):
ATAGCACCTCAAATGGGTGCCACG
Found at i:5501887 original size:10 final size:9
Alignment explanation
Indices: 5501862--5502007 Score: 53
Period size: 10 Copynumber: 15.0 Consensus size: 9
5501852 ATGATAACAA
*
5501862 ATAAAAATCA
1 ATAAAAAT-T
*
5501872 ATAAAAGTT
1 ATAAAAATT
5501881 ATAAAAATT
1 ATAAAAATT
**
5501890 ATTAAATTTT
1 A-TAAAAATT
5501900 ATTAAAAA-T
1 A-TAAAAATT
5501909 ATAAAAAATT
1 AT-AAAAATT
**
5501919 ATTTAAATTTT
1 A--TAAAAATT
*
5501930 AGTAACAATT
1 A-TAAAAATT
*
5501940 AGAAAAAATT
1 A-TAAAAATT
5501950 ATAAAAATCT
1 ATAAAAAT-T
5501960 -TAAAAAATT
1 AT-AAAAATT
*
5501969 ATAGAATATAT
1 ATA-AAAAT-T
* *
5501980 AGAAATAAAT
1 ATAAA-AATT
5501990 ATAAAAATT
1 ATAAAAATT
*
5501999 ATAAGAATT
1 ATAAAAATT
5502008 CAAGGTAGTT
Statistics
Matches: 102, Mismatches: 23, Indels: 23
0.69 0.16 0.16
Matches are distributed among these distances:
8 1 0.01
9 36 0.35
10 54 0.53
11 10 0.10
12 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:5501927 original size:30 final size:31
Alignment explanation
Indices: 5501883--5501951 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
5501873 TAAAAGTTAT
* *
5501883 AAAAATTA-TTAAATTTTATTAA-AAATATA
1 AAAAATTATTTAAATTTTAGTAACAAATAGA
*
5501912 AAAAATTATTTAAATTTTAGTAACAATTAGA
1 AAAAATTATTTAAATTTTAGTAACAAATAGA
5501943 AAAAATTAT
1 AAAAATTAT
5501952 AAAAATCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 8 0.23
30 13 0.37
31 14 0.40
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (31 bp):
AAAAATTATTTAAATTTTAGTAACAAATAGA
Found at i:5501945 original size:29 final size:29
Alignment explanation
Indices: 5501883--5501951 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
5501873 TAAAAGTTAT
*
5501883 AAAAATTATTAAATTTTATTAAAAATATA
1 AAAAATTATTAAATTTTAGTAAAAATATA
* *
5501912 AAAAATTATTTAAATTTTAGTAACAATTAGA
1 AAAAATTA-TTAAATTTTAGTAA-AAATATA
5501943 AAAAATTAT
1 AAAAATTAT
5501952 AAAAATCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 8 0.23
30 14 0.40
31 13 0.37
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAAATTATTAAATTTTAGTAAAAATATA
Found at i:5502670 original size:40 final size:40
Alignment explanation
Indices: 5502626--5502701 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
5502616 ATTTGGAGAA
* * *
5502626 AAAACGCTGCTAAAAATCAAGTATTAGCGGCGCTTTAAAT
1 AAAACGCCGCTAAAAACCAAGCATTAGCGGCGCTTTAAAT
* *
5502666 AAAACGCCGCTAAAGACCGAGCATTAGCGGCGCTTT
1 AAAACGCCGCTAAAAACCAAGCATTAGCGGCGCTTT
5502702 CCTAAAAGCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (40 bp):
AAAACGCCGCTAAAAACCAAGCATTAGCGGCGCTTTAAAT
Found at i:5502727 original size:39 final size:40
Alignment explanation
Indices: 5502648--5502731 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
5502638 AAAATCAAGT
* *
5502648 ATTAGCGGCGCTTTAAATAAAACGCCGCTAAAGACCGAGC
1 ATTAGCGGCGCTTTAAATAAAACGCCGCCAAAGAACGAGC
** *
5502688 ATTAGCGGCGCTTT-CCTAAAAGCGCCGCCAAA-AATGAGC
1 ATTAGCGGCGCTTTAAATAAAA-CGCCGCCAAAGAACGAGC
5502727 ATTAG
1 ATTAG
5502732 TGGCATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
39 15 0.39
40 23 0.61
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (40 bp):
ATTAGCGGCGCTTTAAATAAAACGCCGCCAAAGAACGAGC
Found at i:5502855 original size:41 final size:41
Alignment explanation
Indices: 5502800--5503068 Score: 405
Period size: 41 Copynumber: 6.6 Consensus size: 41
5502790 TTTCGGGGCT
* * *
5502800 TTTAGCGGCGTTTTTGAAAAAGCGACGCTAATGCTC-GGAGC
1 TTTAGCGGCGTTTTTGACAAAGCGCCGCTAATGCTCAGG-CC
* *
5502841 TTTAGCGGCATTTTTGACAAAGCGCTGCTAATGCTCAGGCC
1 TTTAGCGGCGTTTTTGACAAAGCGCCGCTAATGCTCAGGCC
* *
5502882 TTTAGCGGCGTTTTTGACGAAGCGCCGCTAATACTCAGGCC
1 TTTAGCGGCGTTTTTGACAAAGCGCCGCTAATGCTCAGGCC
* *
5502923 TTTAGCGGCGTTTTTGACGAAGCACCGCTAATGCTCAGGCC
1 TTTAGCGGCGTTTTTGACAAAGCGCCGCTAATGCTCAGGCC
* *
5502964 TTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGGCC
1 TTTAGCGGCGTTTTTGACAAAGCGCCGCTAATGCTCAGGCC
*
5503005 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGCC
1 TTTAGCGGCGTTTTTGACAAAGCGCCGCTAATGCTCAGGCC
*
5503046 TTTAGCGGCGTTTTTGAAAAAGC
1 TTTAGCGGCGTTTTTGACAAAGC
5503069 ACCCCTAAAA
Statistics
Matches: 210, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
41 208 0.99
42 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGACAAAGCGCCGCTAATGCTCAGGCC
Found at i:5503546 original size:13 final size:13
Alignment explanation
Indices: 5503511--5503560 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
5503501 AGGGTTGTGA
5503511 TTTAGGGGTTAAGGG
1 TTTA-GGGTT-AGGG
5503526 -TTAGGGGTTAGGG
1 TTTA-GGGTTAGGG
5503539 ATTT-GGGTTAGGG
1 -TTTAGGGTTAGGG
5503552 TTTAGGGTT
1 TTTAGGGTT
5503561 TAGATTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.09
13 18 0.56
14 9 0.28
15 2 0.06
ACGTcount: A:0.16, C:0.00, G:0.46, T:0.38
Consensus pattern (13 bp):
TTTAGGGTTAGGG
Found at i:5503621 original size:14 final size:14
Alignment explanation
Indices: 5503602--5503675 Score: 67
Period size: 14 Copynumber: 5.3 Consensus size: 14
5503592 TAAATAAGGT
*
5503602 TTAGGGGTTAGTAG
1 TTAGGGGTTAGGAG
*
5503616 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGAG
* *
5503630 TTTGGGGTTAGGGG
1 TTAGGGGTTAGGAG
* * *
5503644 TTGGGGGTTGGGGG
1 TTAGGGGTTAGGAG
* *
5503658 TTAGAGGTTAAGAG
1 TTAGGGGTTAGGAG
5503672 TTAG
1 TTAG
5503676 TGATTTAAGG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 50 1.00
ACGTcount: A:0.16, C:0.00, G:0.51, T:0.32
Consensus pattern (14 bp):
TTAGGGGTTAGGAG
Found at i:5503625 original size:7 final size:7
Alignment explanation
Indices: 5503602--5503667 Score: 78
Period size: 7 Copynumber: 9.4 Consensus size: 7
5503592 TAAATAAGGT
5503602 TTAGGGG
1 TTAGGGG
**
5503609 TTAGTAG
1 TTAGGGG
5503616 TTAGGGG
1 TTAGGGG
5503623 TTAGGGG
1 TTAGGGG
*
5503630 TTTGGGG
1 TTAGGGG
5503637 TTAGGGG
1 TTAGGGG
*
5503644 TTGGGGG
1 TTAGGGG
*
5503651 TTGGGGG
1 TTAGGGG
*
5503658 TTAGAGG
1 TTAGGGG
5503665 TTA
1 TTA
5503668 AGAGTTAGTG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.14, C:0.00, G:0.53, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:5508252 original size:42 final size:42
Alignment explanation
Indices: 5508206--5508347 Score: 185
Period size: 43 Copynumber: 3.3 Consensus size: 42
5508196 TTTTTCCTAG
* * * *
5508206 AAGCGTCGCTAAAGGTTTGTTCTTTAGCGGTGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTGTGGTCTTTAGCGGCGTTTGTGGGAA
* *
5508248 AAGCGCCGCTAAAGGCCGTGGTCTTTAGCGGCGTTTGTAGGAA
1 AAGCGCCGCTAAAGG-TGTGGTCTTTAGCGGCGTTTGTGGGAA
* *
5508291 AAGCGCCGCTAAAGGTCGTGGTCTTTAGCAGCGTTTGTGGGCA
1 AAGCGCCGCTAAAGGT-GTGGTCTTTAGCGGCGTTTGTGGGAA
*
5508334 AAGCGCCACTAAAG
1 AAGCGCCGCTAAAG
5508348 ATCATGCGCC
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 14 0.16
43 73 0.84
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (42 bp):
AAGCGCCGCTAAAGGTGTGGTCTTTAGCGGCGTTTGTGGGAA
Found at i:5508284 original size:43 final size:43
Alignment explanation
Indices: 5508226--5508347 Score: 190
Period size: 43 Copynumber: 2.8 Consensus size: 43
5508216 AAAGGTTTGT
*
5508226 TCTTTAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGGCCGTGG
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCGTGG
* *
5508269 TCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCGTGG
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCGTGG
* * *
5508312 TCTTTAGCAGCGTTTGTGGGCAAAGCGCCACTAAAG
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
5508348 ATCATGCGCC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 72 1.00
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCGTGG
Found at i:5515383 original size:7 final size:7
Alignment explanation
Indices: 5515371--5515452 Score: 83
Period size: 7 Copynumber: 11.7 Consensus size: 7
5515361 TAAAAAAATT
5515371 AATTGAG
1 AATTGAG
5515378 AATTGAG
1 AATTGAG
*
5515385 AATTAAG
1 AATTGAG
5515392 AATTGAG
1 AATTGAG
*
5515399 GATTGAG
1 AATTGAG
*
5515406 GATTGAG
1 AATTGAG
*
5515413 GATTGAG
1 AATTGAG
*
5515420 GATTGAG
1 AATTGAG
* *
5515427 AAATGAA
1 AATTGAG
5515434 AATTGAG
1 AATTGAG
*
5515441 GATTGAG
1 AATTGAG
*
5515448 TATTG
1 AATTG
5515453 TGTTGAAAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 65 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (7 bp):
AATTGAG
Found at i:5515397 original size:21 final size:21
Alignment explanation
Indices: 5515371--5515447 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
5515361 TAAAAAAATT
*
5515371 AATTGAGAATTGAGAATTAAG
1 AATTGAGGATTGAGAATTAAG
* *
5515392 AATTGAGGATTGAGGATTGAG
1 AATTGAGGATTGAGAATTAAG
* *
5515413 GATTGAGGATTGAGAAATGAA-
1 AATTGAGGATTGAG-AATTAAG
5515434 AATTGAGGATTGAG
1 AATTGAGGATTGAG
5515448 TATTGTGTTG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 44 0.94
22 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.27
Consensus pattern (21 bp):
AATTGAGGATTGAGAATTAAG
Found at i:5516079 original size:17 final size:19
Alignment explanation
Indices: 5516050--5516087 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5516040 ATACAAAATT
5516050 AACCCTCAGCCC-AAACTA
1 AACCCTCAGCCCAAAACTA
5516068 AACCCT-AGCCCAAAACTA
1 AACCCTCAGCCCAAAACTA
5516086 AA
1 AA
5516088 AACTTTTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.45, C:0.39, G:0.05, T:0.11
Consensus pattern (19 bp):
AACCCTCAGCCCAAAACTA
Found at i:5517474 original size:20 final size:20
Alignment explanation
Indices: 5517449--5517494 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
5517439 GAGCATTTCA
*
5517449 TATTATTTATTTTAAATCT-T
1 TATTATTTACTTTAAAT-TGT
5517469 TATTATTTACTTTAAATTGT
1 TATTATTTACTTTAAATTGT
5517489 TATTAT
1 TATTAT
5517495 GTGATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (20 bp):
TATTATTTACTTTAAATTGT
Found at i:5522023 original size:16 final size:16
Alignment explanation
Indices: 5521998--5522039 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
5521988 AATATTTCAA
5521998 AAAAAT-AAAAAAATG
1 AAAAATGAAAAAAATG
**
5522013 AAAAATGAAAATGATG
1 AAAAATGAAAAAAATG
*
5522029 AAAAAAGAAAA
1 AAAAATGAAAA
5522040 GAAAAAGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAAATGAAAAAAATG
Found at i:5522039 original size:22 final size:20
Alignment explanation
Indices: 5522014--5522061 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
5522004 AAAAAAATGA
*
5522014 AAAATGAAAATGATGAAAAAAG
1 AAAA-GAAAAAGA-GAAAAAAG
5522036 AAAAGAAAAAGAGAAGGAAAAG
1 AAAAGAAAAAGAGAA--AAAAG
5522058 AAAA
1 AAAA
5522062 AGGAGAGGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 3 0.13
21 7 0.30
22 13 0.57
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (20 bp):
AAAAGAAAAAGAGAAAAAAG
Found at i:5522210 original size:42 final size:41
Alignment explanation
Indices: 5522140--5522258 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 41
5522130 AAAAGGACAT
* *
5522140 CTCAAATGTTGATCAGAATGGGGCATGAGGTGATTAGAGTAG
1 CTCAAAT-TTGATCAAAATGGGGCATGAGGTGATCAGAGTAG
* * *
5522182 CTCAAATTTCGATCAAAATTGGGTATGAGGTGATCAGGGTAG
1 CTCAAATTT-GATCAAAATGGGGCATGAGGTGATCAGAGTAG
* * * *
5522224 CTCAAATTTTGATCAGATTAGGGCATGTGGTGATC
1 CTCAAA-TTTGATCAAAATGGGGCATGAGGTGATC
5522259 TTGTTGTACC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.03
42 60 0.92
43 3 0.05
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (41 bp):
CTCAAATTTGATCAAAATGGGGCATGAGGTGATCAGAGTAG
Found at i:5523448 original size:44 final size:44
Alignment explanation
Indices: 5523393--5523599 Score: 170
Period size: 44 Copynumber: 4.7 Consensus size: 44
5523383 AAGCCACCAG
* * * *
5523393 TCCTATCTCCCTAAGTAGCAGTGGAGTAGGTTGAAGATTGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGA
* ** *
5523437 TCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT-GAA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAG-A
* * * *****
5523481 TCTTATCTTCCC-AAGGTAGTAG-GGAAGCAGATTTAAGCCACCAG-
1 TCCTATC-TCCCTAA-GCAGTAGTGG-AGCAGATTGAAGATTGTAGA
* * *
5523525 TCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGA
*
5523569 TCCTGTCTCCCTAAGCAGTAGTGGAGCAGAT
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGAT
5523600 CAAAGACGGT
Statistics
Matches: 122, Mismatches: 33, Indels: 16
0.71 0.19 0.09
Matches are distributed among these distances:
43 21 0.17
44 80 0.66
45 20 0.16
46 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (44 bp):
TCCTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGA
Found at i:5523580 original size:132 final size:132
Alignment explanation
Indices: 5523338--5523867 Score: 825
Period size: 132 Copynumber: 4.0 Consensus size: 132
5523328 TGGATTGAAG
*
5523338 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGAAAGCAGATTTAAGCCACCAGTCCTATCTCC
1 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCC
*
5523403 CTAAGTAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGAT
66 CTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGAT
5523468 CA
131 CA
*
5523470 AAGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCC
1 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCC
5523535 CTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGAT
66 CTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGAT
5523600 CA
131 CA
* *
5523602 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCATATTTAAGCCACCAGTCCTATCTTC
1 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCC
* * * * *
5523667 CTGAGCAGCAGTGGAGTAGGTTAAAGATTGTAGATTCTGTCTCCCT-A--AGTAGTAGAACAGAT
66 CTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGAT
5523729 CA
131 CA
* * * * * * *
5523731 TAGATGGTGAATCTTATCTTCCCAGGGTAGTAGGGAAGCAAATTTAAACCACTAGTCTTATCTCC
1 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCC
* * * *
5523796 CTAAGCAGTAGTGGAGTAGGTT-AATGATTGTAGATCCTGTCTCTCTAAGTAGTAGCGGAGCAGA
66 CTAAGCAGCAGTGGAGTAGGTTGAA-GATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGA
*
5523860 TCG
130 TCA
5523863 AAGAC
1 AAGAC
5523868 ATCGAACCTT
Statistics
Matches: 365, Mismatches: 29, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
128 2 0.01
129 111 0.30
130 1 0.00
131 1 0.00
132 250 0.68
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (132 bp):
AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCC
CTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGAT
CA
Found at i:5523858 original size:261 final size:263
Alignment explanation
Indices: 5523338--5523867 Score: 841
Period size: 261 Copynumber: 2.0 Consensus size: 263
5523328 TGGATTGAAG
5523338 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGAAAGCAGATTTAAGCCACCAGTCCTATCTCC
1 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGAAAGCAGATTTAAGCCACCAGTCCTATCTCC
* * * *
5523403 CTAAGTAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGAT
66 CTAAGCAGCAGTGGAGTAGGTTAAAGATTGTAGATCCTGTCTCCCTAA-CAGTAGTAGAACAGAT
* *
5523468 CAAAGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCT
130 CAAAGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAACCACCAGTCCTATCT
*
5523533 CCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAG
195 CCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAG
5523598 ATCA
260 ATCA
* * *
5523602 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCATATTTAAGCCACCAGTCCTATCTTC
1 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGAAAGCAGATTTAAGCCACCAGTCCTATCTCC
* *
5523667 CTGAGCAGCAGTGGAGTAGGTTAAAGATTGTAGATTCTGTCTCCCT-A-AGTAGTAGAACAGATC
66 CTAAGCAGCAGTGGAGTAGGTTAAAGATTGTAGATCCTGTCTCCCTAACAGTAGTAGAACAGATC
* * * *
5523730 ATAGATGGTGAATCTTATCTTCCCAGGGTAGTAGGGAAGCAAATTTAAACCACTAGTCTTATCTC
131 AAAGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAACCACCAGTCCTATCTC
* * *
5523795 CCTAAGCAGTAGTGGAGTAGGTT-AATGATTGTAGATCCTGTCTCTCTAAGTAGTAGCGGAGCAG
196 CCTAAGCAGCAGTGGAGTAGGTTGAA-GATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAG
*
5523859 ATCG
260 ATCA
5523863 AAGAC
1 AAGAC
5523868 ATCGAACCTT
Statistics
Matches: 245, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
260 2 0.01
261 138 0.56
263 1 0.00
264 104 0.42
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (263 bp):
AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGAAAGCAGATTTAAGCCACCAGTCCTATCTCC
CTAAGCAGCAGTGGAGTAGGTTAAAGATTGTAGATCCTGTCTCCCTAACAGTAGTAGAACAGATC
AAAGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAACCACCAGTCCTATCTC
CCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAGA
TCA
Found at i:5523971 original size:21 final size:21
Alignment explanation
Indices: 5523945--5523984 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5523935 CTGGCATTGT
5523945 AGTGGAATAGATTAAAGCTGA
1 AGTGGAATAGATTAAAGCTGA
* *
5523966 AGTGGAGTGGATTAAAGCT
1 AGTGGAATAGATTAAAGCT
5523985 AAAGGCAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.33, T:0.25
Consensus pattern (21 bp):
AGTGGAATAGATTAAAGCTGA
Found at i:5525827 original size:23 final size:23
Alignment explanation
Indices: 5525796--5525839 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5525786 TTTATGTTAA
* *
5525796 ATTTTATATTGTTAATTTTAAGC
1 ATTTCATATTATTAATTTTAAGC
*
5525819 ATTTCATATTATTCATTTTAA
1 ATTTCATATTATTAATTTTAA
5525840 ATCTTTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.57
Consensus pattern (23 bp):
ATTTCATATTATTAATTTTAAGC
Found at i:5530840 original size:62 final size:62
Alignment explanation
Indices: 5530764--5530891 Score: 222
Period size: 63 Copynumber: 2.1 Consensus size: 62
5530754 AATTTAGCCT
* *
5530764 TATTTAATT-TTTTTTATAGTAGAGGGATTAATTTGATTAAGTTCTAGTGGGACTCTCAGGTA
1 TATTTAATTATTTTTAATAGTAGAGAGATTAATTTGATTAAGTTCTAGTGGGACTCT-AGGTA
5530826 TATTTAATTATTTTTAATAGTAGAGAGATTAATTTGATTAAGTTCTAGTGGGACTCTAGGTA
1 TATTTAATTATTTTTAATAGTAGAGAGATTAATTTGATTAAGTTCTAGTGGGACTCTAGGTA
5530888 TATT
1 TATT
5530892 CATTCGTATA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
62 18 0.29
63 45 0.71
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (62 bp):
TATTTAATTATTTTTAATAGTAGAGAGATTAATTTGATTAAGTTCTAGTGGGACTCTAGGTA
Found at i:5537896 original size:3 final size:3
Alignment explanation
Indices: 5537888--5537937 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
5537878 GCTATAGTGT
5537888 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5537936 AT
1 AT
5537938 TAGATAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5538815 original size:16 final size:16
Alignment explanation
Indices: 5538794--5538831 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5538784 ATTAGAATTA
*
5538794 ATTAAAAGTAAATTTT
1 ATTAAAAGCAAATTTT
*
5538810 ATTAAATGCAAATTTT
1 ATTAAAAGCAAATTTT
5538826 ATTAAA
1 ATTAAA
5538832 TTGATGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (16 bp):
ATTAAAAGCAAATTTT
Found at i:5539382 original size:25 final size:24
Alignment explanation
Indices: 5539346--5539410 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 24
5539336 TCCCGTTATG
*
5539346 GCTCTTATGAGCTTCTCGATAATTA
1 GCTCTTA-GAGCTTCTCGATAACTA
5539371 GCTCTTCAGAGCTTCTCGATAACTA
1 GCTCTT-AGAGCTTCTCGATAACTA
*
5539396 GCTCTTTTGAGCTTC
1 GCTC-TTAGAGCTTC
5539411 CCATTATATG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
25 33 0.92
26 3 0.08
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (24 bp):
GCTCTTAGAGCTTCTCGATAACTA
Found at i:5540911 original size:25 final size:24
Alignment explanation
Indices: 5540861--5540948 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 24
5540851 GTAACATACA
*
5540861 AAAAATTTTATAATGA-AATATAT
1 AAAAATTTTATAATTATAATATAT
*
5540884 AAATAAATTTTATAATTATAAT-TGT
1 -AA-AAATTTTATAATTATAATATAT
*
5540909 AAAAATTTATATAACTTATTAATCAAAT
1 AAAAATTT-TATAA-TTA-TAAT-ATAT
*
5540937 AAAAAATTTATA
1 AAAAATTTTATA
5540949 TAACATAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
23 6 0.12
24 9 0.17
25 18 0.35
26 7 0.13
27 4 0.08
28 8 0.15
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
AAAAATTTTATAATTATAATATAT
Found at i:5547733 original size:34 final size:34
Alignment explanation
Indices: 5547690--5547839 Score: 144
Period size: 34 Copynumber: 4.4 Consensus size: 34
5547680 AGCAGGGTTG
* *
5547690 AGTAGCACCACGAGATGTAAATTATAATTCTTAA
1 AGTAGCACCACTAAATGTAAATTATAATTCTTAA
* ** * *
5547724 AGTAGCACCACT-ACTG-ATTTTCT-TTTCTTTTTAAA
1 AGTAGCACCACTAAATGTAAATTATAATTC---TT-AA
*
5547759 ATTAGCACCACTAAATGTAAATTATAATTCTTAA
1 AGTAGCACCACTAAATGTAAATTATAATTCTTAA
* * *
5547793 AGTAGCTCCACTAAATGTAAATTATAACTCATAA
1 AGTAGCACCACTAAATGTAAATTATAATTCTTAA
5547827 AGTAGCACCACTA
1 AGTAGCACCACTA
5547840 GTGTTTTTCT
Statistics
Matches: 91, Mismatches: 18, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
31 3 0.03
32 4 0.04
33 2 0.02
34 57 0.63
35 15 0.16
36 3 0.03
37 4 0.04
38 3 0.03
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (34 bp):
AGTAGCACCACTAAATGTAAATTATAATTCTTAA
Found at i:5547872 original size:103 final size:103
Alignment explanation
Indices: 5547690--5547879 Score: 290
Period size: 103 Copynumber: 1.8 Consensus size: 103
5547680 AGCAGGGTTG
* * *
5547690 AGTAGCACCACGAGATGTAAATTATAATTCTTAAAGTAGCACCACTACTGATTTTCTTTTCTTTT
1 AGTAGCACCACGAAATGTAAATTATAACTCATAAAGTAGCACCACTACTGATTTTCTTTTCTTTT
5547755 TAAAATTAGCACCACTAAATGTAAATTATAATTCTTAA
66 TAAAATTAGCACCACTAAATGTAAATTATAATTCTTAA
* * * *
5547793 AGTAGCTCCACTAAATGTAAATTATAACTCATAAAGTAGCACCACTAGTGTTTTTCTTTTCTTTT
1 AGTAGCACCACGAAATGTAAATTATAACTCATAAAGTAGCACCACTACTGATTTTCTTTTCTTTT
** *
5547858 TAAAATTATTACCACTAGATGT
66 TAAAATTAGCACCACTAAATGT
5547880 CAAAATAAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 77 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (103 bp):
AGTAGCACCACGAAATGTAAATTATAACTCATAAAGTAGCACCACTACTGATTTTCTTTTCTTTT
TAAAATTAGCACCACTAAATGTAAATTATAATTCTTAA
Found at i:5551530 original size:41 final size:41
Alignment explanation
Indices: 5551473--5551555 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
5551463 AGCCAGAGAC
* *
5551473 TTAGTCGCGTAAAGAGTTTCTAACCTTTTCCACAAGACGGA
1 TTAGTCGCATAAAGAGTTTCTAACCTTTTCCACAAGAAGGA
5551514 TTAGTCGCATAAAGAGTTTCTAACCTTTTCCACAAGAAGGA
1 TTAGTCGCATAAAGAGTTTCTAACCTTTTCCACAAGAAGGA
5551555 T
1 T
5551556 GGGGTCTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (41 bp):
TTAGTCGCATAAAGAGTTTCTAACCTTTTCCACAAGAAGGA
Found at i:5552422 original size:14 final size:14
Alignment explanation
Indices: 5552405--5552434 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5552395 AGAGGCTGAT
5552405 CTTAAGGTATTCAA
1 CTTAAGGTATTCAA
5552419 CTTAAGGTATTCAA
1 CTTAAGGTATTCAA
5552433 CT
1 CT
5552435 GTAACCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (14 bp):
CTTAAGGTATTCAA
Found at i:5553611 original size:88 final size:89
Alignment explanation
Indices: 5553502--5553673 Score: 265
Period size: 89 Copynumber: 1.9 Consensus size: 89
5553492 AAATTGAAGG
* * * * *
5553502 GGTAGAAAAATAGAAATATGG-AGAATATAAATTTTCTTTCCATGTGTGTGCTTGGTAGGAAAGA
1 GGTAGAAAAATAGAAAGATGGAAAAATATAAATTTTCTTTCCATATGTGTGCTTAGTAGGAAAAA
**
5553566 TGGAAAAATTGAAAGAAAAGAAAA
66 TGGAAAAATCAAAAGAAAAGAAAA
*
5553590 GGTAGAAAAATAGAAAGATGGAAAAATATAAATTTTCTTTTCATATGTGTGCTTAGTAGGAAAAA
1 GGTAGAAAAATAGAAAGATGGAAAAATATAAATTTTCTTTCCATATGTGTGCTTAGTAGGAAAAA
5553655 TGGAAAAATCAAAAGAAAA
66 TGGAAAAATCAAAAGAAAA
5553674 TATATTTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
88 20 0.27
89 55 0.73
ACGTcount: A:0.48, C:0.05, G:0.22, T:0.26
Consensus pattern (89 bp):
GGTAGAAAAATAGAAAGATGGAAAAATATAAATTTTCTTTCCATATGTGTGCTTAGTAGGAAAAA
TGGAAAAATCAAAAGAAAAGAAAA
Found at i:5564705 original size:12 final size:12
Alignment explanation
Indices: 5564688--5564712 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5564678 CATATCAATT
5564688 TAAAAAAATTAA
1 TAAAAAAATTAA
5564700 TAAAAAAATTAA
1 TAAAAAAATTAA
5564712 T
1 T
5564713 TTTTAATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAAAAAATTAA
Found at i:5565380 original size:164 final size:165
Alignment explanation
Indices: 5565093--5565410 Score: 442
Period size: 164 Copynumber: 1.9 Consensus size: 165
5565083 ACGTCAATAT
* * ** *
5565093 TGTAACGGTCAACATTAGTTAAAGGGCCTATTTGGTCAATTTTGTTAGTTAAGTGGCTCAATTGG
1 TGTAACGGTAAACATTAGTCAAAGGGCCTATTTGACCAATTTTATTAGTTAAGTGGCTCAATTGG
* ** **
5565158 GTGCAAAAATTTCGTAGGGGTTTAATTAATTTTTTTGAAAGAGTTTGAGGACCAAAAATACCATT
66 GTGCAAAAAGTTCACAGGGACTTAATTAATTTTTTTGAAAGAGTTTGAGGACCAAAAATACCATT
5565223 AAGCCCTTCTTTAACTATTGATATATCCTTTTCTA
131 AAGCCCTTCTTTAACTATTGATATATCCTTTTCTA
* *
5565258 TGTATCGGTAAACATTAGTCAAAGGGCCTATTTGACCAA-TTTATTAGTTCAGTGGCTCAATTGG
1 TGTAACGGTAAACATTAGTCAAAGGGCCTATTTGACCAATTTTATTAGTTAAGTGGCTCAATTGG
* * * * ** *
5565322 GTGTAAAAAGTTCACAGTGACTTAATTGATTTTTTTTTAAA-AGTTTGCTGAGCAAAAATACCAT
66 GTGCAAAAAGTTCACAGGGACTTAATT-AATTTTTTTGAAAGAGTTTGAGGACCAAAAATACCAT
5565386 TAAGCCCTTCTTTAACTATTGATAT
130 TAAGCCCTTCTTTAACTATTGATAT
5565411 GTCTTTTTTA
Statistics
Matches: 133, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
164 88 0.66
165 45 0.34
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (165 bp):
TGTAACGGTAAACATTAGTCAAAGGGCCTATTTGACCAATTTTATTAGTTAAGTGGCTCAATTGG
GTGCAAAAAGTTCACAGGGACTTAATTAATTTTTTTGAAAGAGTTTGAGGACCAAAAATACCATT
AAGCCCTTCTTTAACTATTGATATATCCTTTTCTA
Found at i:5566745 original size:24 final size:25
Alignment explanation
Indices: 5566698--5566746 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5566688 TTTCTTATTA
* * *
5566698 TTGTATTAAAATAATTTTTATAAAT
1 TTGTATAAAAATAATATCTATAAAT
5566723 TTGTATAAAAATAATATCT-TAAAT
1 TTGTATAAAAATAATATCTATAAAT
5566747 CATGTACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (25 bp):
TTGTATAAAAATAATATCTATAAAT
Found at i:5569454 original size:3 final size:3
Alignment explanation
Indices: 5569446--5569488 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
5569436 TCACATTTTA
* * * *
5569446 TAT TAT TAT CAT TAT TAC TAC TAT TAT TAG TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5569489 TTCATATATC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:5572643 original size:144 final size:144
Alignment explanation
Indices: 5572432--5572735 Score: 396
Period size: 144 Copynumber: 2.1 Consensus size: 144
5572422 TTGTGGAATT
* *
5572432 GTTGGTCCAATCCCTTCTGCTTTGGGTCAGTTATTAAATCTCAAATATTTACGTCTAGGGGGAAA
1 GTTGGTTCAATCCCTTCTGCTTTGGGTCAGTTATTAAATCTCAAATATTTACGTCTAGCGGGAAA
* * *
5572497 CAAAATTAATGGATCTATCCCATTTGAAGTCGGATT-TCTATCAAACTTGACATATTTGTAT-CT
66 CAAAATGAATGGATCTATCCCATCTGAAGTCGGATTCT-TATCAAACTTAACATATTTGTATGC-
5572560 CTACAACAACAAACTG
129 CTACAACAACAAACTG
* ** ** *
5572576 GTTGGTTCAATCCCTTCTGCTTTGGGTCAGTTATTAAATCTCAAATCTTTATTTCTTTCGGGCAA
1 GTTGGTTCAATCCCTTCTGCTTTGGGTCAGTTATTAAATCTCAAATATTTACGTCTAGCGGGAAA
* * * * *
5572641 CAAAATGAATGGATCTATTCCATCTGAAGTTGGATTCTTATCTAACTTAACTTATTTTTATGCCT
66 CAAAATGAATGGATCTATCCCATCTGAAGTCGGATTCTTATCAAACTTAACATATTTGTATGCCT
* *
5572706 CCAACAACAGACTG
131 ACAACAACAAACTG
* *
5572720 GTTGGTTTAATACCTT
1 GTTGGTTCAATCCCTT
5572736 TCTCCTTGTA
Statistics
Matches: 138, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
144 136 0.99
145 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (144 bp):
GTTGGTTCAATCCCTTCTGCTTTGGGTCAGTTATTAAATCTCAAATATTTACGTCTAGCGGGAAA
CAAAATGAATGGATCTATCCCATCTGAAGTCGGATTCTTATCAAACTTAACATATTTGTATGCCT
ACAACAACAAACTG
Found at i:5587769 original size:17 final size:16
Alignment explanation
Indices: 5587747--5587781 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5587737 GTTTAAAAAT
*
5587747 TTTAATTAATAAATTTA
1 TTTAATTAA-AAATCTA
5587764 TTTAATTAAAAATCTA
1 TTTAATTAAAAATCTA
5587780 TT
1 TT
5587782 CACATCCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAATTAAAAATCTA
Found at i:5588307 original size:10 final size:10
Alignment explanation
Indices: 5588289--5588332 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
5588279 CTTCATAGTA
5588289 TTTTTTGAAC
1 TTTTTTGAAC
*
5588299 TTTTATGAAC
1 TTTTTTGAAC
5588309 TTTTTTGAA-
1 TTTTTTGAAC
*
5588318 TTTTTT-AAG
1 TTTTTTGAAC
5588327 TTTTTT
1 TTTTTT
5588333 TTCAACACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
8 2 0.06
9 12 0.39
10 17 0.55
ACGTcount: A:0.20, C:0.05, G:0.09, T:0.66
Consensus pattern (10 bp):
TTTTTTGAAC
Found at i:5588897 original size:3 final size:3
Alignment explanation
Indices: 5588891--5588947 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
5588881 CTTTTTTTAA
5588891 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5588939 AAT AAT AAT
1 AAT AAT AAT
5588948 TGTAATACTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5589187 original size:5 final size:5
Alignment explanation
Indices: 5589179--5589210 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
5589169 AAAGGAAAGA
*
5589179 AAATC AAATC AAATC AAATC GAATC AAATC AA
1 AAATC AAATC AAATC AAATC AAATC AAATC AA
5589211 GCAAATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.59, C:0.19, G:0.03, T:0.19
Consensus pattern (5 bp):
AAATC
Found at i:5590380 original size:35 final size:35
Alignment explanation
Indices: 5590341--5590407 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
5590331 ATTTTAGTAC
*
5590341 ATATAAATATGCATATATATTAATATTTTTAATCA
1 ATATAAATATGAATATATATTAATATTTTTAATCA
* * *
5590376 ATATATATATGAATATATATTTATTTTTTTAA
1 ATATAAATATGAATATATATTAATATTTTTAA
5590408 AAAATGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (35 bp):
ATATAAATATGAATATATATTAATATTTTTAATCA
Found at i:5590662 original size:22 final size:21
Alignment explanation
Indices: 5590636--5590719 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 21
5590626 CATGACATGG
5590636 ATTATTGCTTTATATTTAATTT
1 ATTATTGCTTTATATTT-ATTT
5590658 ATTATTTG-TTTATA-TTATTT
1 ATTA-TTGCTTTATATTTATTT
*
5590678 -TTA-TGCTATTA-ATGTATTT
1 ATTATTGCT-TTATATTTATTT
*
5590697 ATTATTG-TTGA-ATTTA-TT
1 ATTATTGCTTTATATTTATTT
5590715 ATTAT
1 ATTAT
5590720 AGCATTTGTA
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
17 2 0.04
18 9 0.17
19 17 0.32
20 8 0.15
21 4 0.08
22 10 0.19
23 3 0.06
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (21 bp):
ATTATTGCTTTATATTTATTT
Found at i:5603016 original size:44 final size:44
Alignment explanation
Indices: 5602572--5603020 Score: 135
Period size: 44 Copynumber: 10.2 Consensus size: 44
5602562 AAAGTTGTAG
* * * *
5602572 ATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGACGACGA
1 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATTGAAGATGACGA
* * * *
5602616 ATCTTATCTTTCC-AAG--ATAGTGGGAAGCAGATTTAAGCT-ACCA
1 ATCTTATC-TCCCTAAGCAATAGT-GG-AGCAGATTGAAGATGACGA
* * * ** * * *
5602659 AGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTA-G-
1 A-TCTTATCTCCCTAAGCAATAGTGGAGCAGATTGAAGA-TG-ACGA
* ** *
5602704 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGA
1 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATTGAAGATGACGA
* * ** *
5602748 ATCTTATCTTTCC-AAG--ATAGTGGGCAGCAGATTTAAG-CCACCA
1 ATCTTATC-TCCCTAAGCAATAGT-GG-AGCAGATTGAAGATGACGA
* * * ** * * *
5602791 AGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTA-G-
1 A-TCTTATCTCCCTAAGCAATAGTGGAGCAGATTGAAGA-TG-ACGA
* * *
5602836 ATCTTATCTCCCTGAGCAATAGTGGAGCAGATCGAAGATGGCGA
1 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATTGAAGATGACGA
* * * ** *
5602880 ATCTTATCTTTCC-AAG--ATAGTGGGAAGTAGATTTAAG-CCAC-C
1 ATCTTATC-TCCCTAAGCAATAGT-GG-AGCAGATTGAAGATGACGA
* * ** * * * *
5602922 ATGCCTTGTCTCCCTGAGCAGCAGCGAAGAAGGTTGAAGATTGTA-G-
1 AT--CTTATCTCCCTAAGCAATAGTGGAGCAGATTGAAGA-TG-ACGA
*
5602968 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATTAAAGATGACGA
1 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATTGAAGATGACGA
5603012 ATCTTATCT
1 ATCTTATCT
5603021 TTCCAAGATA
Statistics
Matches: 277, Mismatches: 90, Indels: 76
0.63 0.20 0.17
Matches are distributed among these distances:
42 16 0.06
43 32 0.12
44 201 0.73
45 17 0.06
46 8 0.03
47 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAATAGTGGAGCAGATTGAAGATGACGA
Found at i:5603148 original size:44 final size:44
Alignment explanation
Indices: 5603100--5603416 Score: 121
Period size: 44 Copynumber: 7.2 Consensus size: 44
5603090 AAGATTGTTG
5603100 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGCGA
* * ** ** *
5603144 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGTAGATTTAAGCCA-CCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCGAAGATAGCGA
* * * * * ** * * * **
5603187 AGCCTTGTCTCCCTCAGTAGCAGCAGAGAAGTTCGAAGATTGTTA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGCGA
* ** * *
5603232 ATCTTATTTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGCGA
* ** ** *
5603276 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCA-CCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCGAAGATAGCGA
* * * * * * * * * *
5603319 AGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTG-TA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGCGA
*
5603363 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGCGA
5603408 ATCTTATCT
1 ATCTTATCT
5603417 TTCCAAGATA
Statistics
Matches: 186, Mismatches: 69, Indels: 36
0.64 0.24 0.12
Matches are distributed among these distances:
42 8 0.04
43 16 0.09
44 143 0.77
45 15 0.08
46 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGCGA
Found at i:5603587 original size:132 final size:132
Alignment explanation
Indices: 5602522--5603578 Score: 1688
Period size: 132 Copynumber: 8.0 Consensus size: 132
5602512 ACCGGTGAAA
*
5602522 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAA-AGTTGTAGATCTTATCTCCCTA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGA-TTGTAGATCTTATCTCCCTA
* * *
5602586 AACAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
65 AGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
5602651 AGC
130 AGC
*
5602654 TACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* *
5602719 GCAGTAGTGGAGCAGATCAAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGCAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5602784 GC
131 GC
*
5602786 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTGA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* *
5602851 GCAATAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5602916 GC
131 GC
* *
5602918 CACCATGCCTTGTCTCCCTGAGCAGCAGCGAAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* ** *
5602983 GCAATAGTGGAGCAGATTAAAGATGACGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5603048 GC
131 GC
** * * *
5603050 CACCAAGCCTTGTCTCCCCCAGTAGCAGCGGAGAAGTTTGAAGATTGTTGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* *
5603115 GCAGTAGTGGAGCAGATCGAAGATAGCGAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5603180 GC
131 GC
* * * *
5603182 CACCAAGCCTTGTCTCCCTCAGTAGCAGCAGAGAA-GTTCGAAGATTGTTA-ATCTTATTTCCCT
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTT-GAAGATTG-TAGATCTTATCTCCCT
* * *
5603245 AAGCAGTAGTGGAGCAGATCGAAGACGGTGTATCTTATCTTTCCAAGATAGTGGGAAGCAGATTT
64 AAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTT
5603310 AAGC
129 AAGC
5603314 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
5603379 GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTAGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5603444 GC
131 GC
* * * * * * *
5603446 CACCAAGCCTTGTCTCCCTCAGTAGCAGCGGAGAAGTTTGAAGATTATTGATCTTATATCCCTGA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * * *
5603511 GCAGTAGTGGAGCAGATCGAAGACGGTGTATCTTATCTTTCCAAGATAGTGGGAAGCAGATTAAA
66 GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5603576 GC
131 GC
5603578 C
1 C
5603579 GATAAGCCTA
Statistics
Matches: 857, Mismatches: 63, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
131 4 0.00
132 848 0.99
133 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:5604062 original size:5 final size:5
Alignment explanation
Indices: 5604054--5604085 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
5604044 AAAGGAAAGA
*
5604054 AAATC AAATC AAATC AAATC GAATC AAATC AA
1 AAATC AAATC AAATC AAATC AAATC AAATC AA
5604086 GCAAATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.59, C:0.19, G:0.03, T:0.19
Consensus pattern (5 bp):
AAATC
Found at i:5604663 original size:21 final size:21
Alignment explanation
Indices: 5604623--5604664 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5604613 GTGGAGAGAG
5604623 TTTTTTTAAAAAGTATTTTTGT
1 TTTTTTTAAAAAG-ATTTTTGT
5604645 TTTTTTTAAAAA-ATGTTTTG
1 TTTTTTTAAAAAGAT-TTTTG
5604665 AAATGAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 5 0.26
22 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (21 bp):
TTTTTTTAAAAAGATTTTTGT
Found at i:5605277 original size:35 final size:35
Alignment explanation
Indices: 5605196--5605279 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 35
5605186 AACCTATATG
* *
5605196 TATATATTTA-TTTTAGTACATATAAATATGCATA
1 TATATATTTATTTTTAATACATATAAATATGAATA
* *
5605230 TATAT-TAATATTTTTAAT-CAATATATATATGAATA
1 TATATAT-TTATTTTTAATAC-ATATAAATATGAATA
5605265 TATATATTTATTTTT
1 TATATATTTATTTTT
5605280 TTTAAAAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
33 1 0.02
34 8 0.20
35 31 0.76
36 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (35 bp):
TATATATTTATTTTTAATACATATAAATATGAATA
Found at i:5605538 original size:22 final size:21
Alignment explanation
Indices: 5605512--5605595 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 21
5605502 CATGACATGG
5605512 ATTATTGCTTTATATTTAGTTT
1 ATTATTGCTTTATATTTA-TTT
5605534 ATTATTTG-TTTATA-TTATTT
1 ATTA-TTGCTTTATATTTATTT
*
5605554 -TTA-TGCTATTA-ATGTATTT
1 ATTATTGCT-TTATATTTATTT
*
5605573 ATTATTG-TTGA-ATTTA-TT
1 ATTATTGCTTTATATTTATTT
5605591 ATTAT
1 ATTAT
5605596 AGCATTTGTA
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
17 2 0.04
18 9 0.17
19 17 0.32
20 7 0.13
21 5 0.09
22 10 0.19
23 3 0.06
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.63
Consensus pattern (21 bp):
ATTATTGCTTTATATTTATTT
Found at i:5606352 original size:3 final size:3
Alignment explanation
Indices: 5606346--5606373 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5606336 AATGGTTTCG
5606346 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
5606374 TAATAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:5606672 original size:70 final size:67
Alignment explanation
Indices: 5606584--5606718 Score: 164
Period size: 70 Copynumber: 2.0 Consensus size: 67
5606574 ATCCAAATAA
* * ** *
5606584 TAAAAGGCAAAACTACGTCATTTTGATAAATGTTT-ACCTTTTCTAAAGTTAAAAGTCAAAACCA
1 TAAAAGGAAAAACTACGTCATTTCGATAAAT-TTTCA-CTCAT-T-AAGTTAAAAGACAAAACCA
5606648 TTAAGT
62 TTAAGT
* *
5606654 TAAAAGGAAAAATTACGTCGTTTCGATAAATTTTCACTCATTAAGTTAAAAGACAAAACCATTAA
1 TAAAAGGAAAAACTACGTCATTTCGATAAATTTTCACTCATTAAGTTAAAAGACAAAACCATTAA
5606719 ATTGTTTATG
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
67 22 0.39
68 1 0.02
69 6 0.11
70 28 0.49
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (67 bp):
TAAAAGGAAAAACTACGTCATTTCGATAAATTTTCACTCATTAAGTTAAAAGACAAAACCATTAA
GT
Found at i:5608824 original size:20 final size:19
Alignment explanation
Indices: 5608781--5608846 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
5608771 AAATTTATTT
*
5608781 AATATTTTATAAATTTTAAT
1 AATATTTTA-AAATTTTAAA
5608801 AATATTTTAAAATTTTATAA
1 AATATTTTAAAATTTTA-AA
* **
5608821 AATATATT-ATTTTTTAAA
1 AATATTTTAAAATTTTAAA
5608839 AATATTTT
1 AATATTTT
5608847 TTTAATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 9 0.22
19 14 0.35
20 17 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATATTTTAAAATTTTAAA
Found at i:5608834 original size:18 final size:16
Alignment explanation
Indices: 5608813--5608850 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
5608803 TATTTTAAAA
5608813 TTTTATAAAATATATTAT
1 TTTTATAAAA-ATATT-T
5608831 TTTT-TAAAAATATTT
1 TTTTATAAAAATATTT
5608846 TTTTA
1 TTTTA
5608851 ATTTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.26
16 5 0.26
17 5 0.26
18 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTATAAAAATATTT
Found at i:5611199 original size:31 final size:31
Alignment explanation
Indices: 5611164--5611230 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
5611154 ATATACCAAG
* *
5611164 AAATTTGGCAATATATAACCATAAACTAATC
1 AAATTTGGCAATACATAACCATAAACAAATC
* * * *
5611195 AAATTTGGTAATGCATAATCATATACAAATC
1 AAATTTGGCAATACATAACCATAAACAAATC
5611226 AAATT
1 AAATT
5611231 CGGTATCCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (31 bp):
AAATTTGGCAATACATAACCATAAACAAATC
Found at i:5611248 original size:31 final size:31
Alignment explanation
Indices: 5611178--5611253 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
5611168 TTGGCAATAT
* * * *
5611178 ATAACCATAAACTAATCAAATTTGGTAATGC
1 ATAATCATAAACAAATCAAATTCGGTAATCC
*
5611209 ATAATCATATACAAATCAAATTCGGT-ATCC
1 ATAATCATAAACAAATCAAATTCGGTAATCC
*
5611239 TATATTCATAAACAA
1 -ATAATCATAAACAA
5611254 TTTAATTTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
30 3 0.08
31 34 0.92
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (31 bp):
ATAATCATAAACAAATCAAATTCGGTAATCC
Found at i:5611300 original size:31 final size:28
Alignment explanation
Indices: 5611258--5611420 Score: 85
Period size: 31 Copynumber: 5.4 Consensus size: 28
5611248 AAACAATTTA
*
5611258 ATTTCAACAATGTATAACCATATACACATT
1 ATTTCAGCAAT-TATAACCATATACA-ATT
*
5611288 ATTTTCAGCAATGT-TCAACCATATACGAATC
1 A-TTTCAGCAAT-TAT-AACCATATAC-AATT
* * * * *
5611319 AATTCGGAAACTTATATCCATTTACAATTT
1 ATTTCAGCAA-TTATAACCATATACAA-TT
* * *
5611349 AATTTCAACAATTTATAATCATATAAAAATT
1 -ATTTCAGCAA-TTATAACCATAT-ACAATT
* *
5611380 ATTTTCAGCAATTTTCAACCATATACAAATC
1 A-TTTCAGCAATTAT-AACCATATAC-AATT
5611411 ATTTCAGCAA
1 ATTTCAGCAA
5611421 CTTCTGTAGA
Statistics
Matches: 100, Mismatches: 22, Indels: 22
0.69 0.15 0.15
Matches are distributed among these distances:
29 2 0.02
30 32 0.32
31 62 0.62
32 4 0.04
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (28 bp):
ATTTCAGCAATTATAACCATATACAATT
Found at i:5611347 original size:92 final size:92
Alignment explanation
Indices: 5611214--5611459 Score: 294
Period size: 92 Copynumber: 2.7 Consensus size: 92
5611204 AATGCATAAT
* * * * * *
5611214 CATATACAAATCAAATTCGGTATCCTATATTCATAAACAATTTAATTTCAACAATGTATAACCAT
1 CATATACAAATC-AATTCGGAAACTTATATACATATACAATTTAATTTCAACAATATATAACCAT
* *
5611279 ATACACATTATTTTCAGCAATGTTCAAC
65 ATAAAAATTATTTTCAGCAATGTTCAAC
* * * * *
5611307 CATATACGAATCAATTCGGAAACTTATATCCATTTACAATTTAATTTCAACAATTTATAATCATA
1 CATATACAAATCAATTCGGAAACTTATATACATATACAATTTAATTTCAACAATATATAACCATA
*
5611372 TAAAAATTATTTTCAGCAATTTTCAAC
66 TAAAAATTATTTTCAGCAATGTTCAAC
* * * * * * *
5611399 CATATACAAATCATTTCAGCAACTTCTGTAGATATACAATTCAATTTCAACAATATATAAC
1 CATATACAAATCAATTCGGAAACTTATATACATATACAATTTAATTTCAACAATATATAAC
5611460 TATAAACAAT
Statistics
Matches: 129, Mismatches: 24, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
92 118 0.91
93 11 0.09
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.35
Consensus pattern (92 bp):
CATATACAAATCAATTCGGAAACTTATATACATATACAATTTAATTTCAACAATATATAACCATA
TAAAAATTATTTTCAGCAATGTTCAAC
Found at i:5619108 original size:24 final size:24
Alignment explanation
Indices: 5619081--5619129 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5619071 TATCACATAT
5619081 TAAATGAAAAACATA-ATAATAATA
1 TAAATG-AAAACATATATAATAATA
* *
5619105 TAAATGATAATATATATAATAATA
1 TAAATGAAAACATATATAATAATA
5619129 T
1 T
5619130 TAGCAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (24 bp):
TAAATGAAAACATATATAATAATA
Found at i:5619116 original size:12 final size:12
Alignment explanation
Indices: 5619095--5619129 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5619085 TGAAAAACAT
5619095 AATAATAATATA
1 AATAATAATATA
*
5619107 AATGATAATATA
1 AATAATAATATA
*
5619119 TATAATAATAT
1 AATAATAATAT
5619130 TAGCAAAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
AATAATAATATA
Found at i:5622131 original size:24 final size:21
Alignment explanation
Indices: 5622086--5622143 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 21
5622076 AAATTTATAC
5622086 AAATTTAAAAATTATAAAAAA
1 AAATTTAAAAATTATAAAAAA
*
5622107 AAATTGTAAAGAATATATAATAAA
1 AAATT-TAAA-AAT-TATAAAAAA
5622131 AAATTTAAAAATT
1 AAATTTAAAAATT
5622144 TTCTAATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 6 0.18
22 7 0.21
23 7 0.21
24 13 0.39
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (21 bp):
AAATTTAAAAATTATAAAAAA
Done.