Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 158 of 187
Found at i:46685373 original size:23 final size:23
Alignment explanation
Indices: 46685333--46685377 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
46685323 TGACAGCAAG
*
46685333 AAAAATTTGTTATTTCCAAAATA
1 AAAAATTTGTTATGTCCAAAATA
46685356 AAAAATTTG-TATCGTCCAAAAT
1 AAAAATTTGTTAT-GTCCAAAAT
46685378 GAGAGTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.36
Consensus pattern (23 bp):
AAAAATTTGTTATGTCCAAAATA
Found at i:46689466 original size:16 final size:17
Alignment explanation
Indices: 46689445--46689477 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46689435 AAGGATCATG
46689445 ACAGAT-TTAGATTTTT
1 ACAGATATTAGATTTTT
*
46689461 ACAGATATTCGATTTTT
1 ACAGATATTAGATTTTT
46689478 TATGAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.48
Consensus pattern (17 bp):
ACAGATATTAGATTTTT
Found at i:46690244 original size:43 final size:43
Alignment explanation
Indices: 46690183--46690268 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
46690173 AGCAAAGAGA
46690183 TATAAAAATTTCCAGTTCTAAAAGGTATACTTTTACATCGTAT
1 TATAAAAATTTCCAGTTCTAAAAGGTATACTTTTACATCGTAT
46690226 TATAAAAATTTCCAGTTCTAAAAGGTATACTTTTACATCGTAT
1 TATAAAAATTTCCAGTTCTAAAAGGTATACTTTTACATCGTAT
46690269 ACATATAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (43 bp):
TATAAAAATTTCCAGTTCTAAAAGGTATACTTTTACATCGTAT
Found at i:46691443 original size:26 final size:25
Alignment explanation
Indices: 46691399--46691452 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
46691389 GCATAACCTT
* *
46691399 TTTATTTTCTTATATCATT-TATTTA
1 TTTATTTTCTAATAGCATTAT-TTTA
46691424 TTTATTATTCTAATAGCATTATTTTA
1 TTTATT-TTCTAATAGCATTATTTTA
46691450 TTT
1 TTT
46691453 TTTACCCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 18 0.72
27 1 0.04
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTATTTTCTAATAGCATTATTTTA
Found at i:46705342 original size:50 final size:51
Alignment explanation
Indices: 46705284--46705411 Score: 172
Period size: 50 Copynumber: 2.5 Consensus size: 51
46705274 TCCTATACCT
*
46705284 CTAAAGTTGCAGTGGGTCAGATTGAAGTC-ACCATAGCGAATCTTATTTCC
1 CTAAAGTTGCAGTGGGTCAGATTGAAGTCTACCATAGCGAATCTTATCTCC
* * *
46705334 CTAAAGTTGCAGTGGATCAGATTGAA-TCTACCATAGTGGATCTTATCTCC
1 CTAAAGTTGCAGTGGGTCAGATTGAAGTCTACCATAGCGAATCTTATCTCC
* *
46705384 CTGAAGTTGCAGTGAAG-CAGATTGAAGT
1 CTAAAGTTGCAGTG-GGTCAGATTGAAGT
46705412 AGCAAATCTT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
49 2 0.03
50 65 0.96
51 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (51 bp):
CTAAAGTTGCAGTGGGTCAGATTGAAGTCTACCATAGCGAATCTTATCTCC
Found at i:46706119 original size:5 final size:6
Alignment explanation
Indices: 46706097--46706128 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
46706087 ATAGAAGCAG
46706097 AAAAAGT AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAA-T AAAAAT AAAAAT AAAAAT AAAAAT A
46706129 TTTGTAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:46706728 original size:21 final size:21
Alignment explanation
Indices: 46706702--46706758 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
46706692 AATTATATGT
46706702 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
*
46706723 TCTAAGATTGCATATATCATA
1 TCTAAGATTGTATATATCATA
46706744 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
46706759 CCTCGAAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:46707224 original size:132 final size:132
Alignment explanation
Indices: 46706987--46707931 Score: 1448
Period size: 132 Copynumber: 7.2 Consensus size: 132
46706977 CACTGCAACT
* * ** *
46706987 TCAGGGAGATAAGACTTACTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTT-ATC
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCT-
*
46707051 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGC
65 GTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGC
46707116 TGC
130 TGC
* *
46707119 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAATATTTGCTA
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCTG
* * * * * *
46707184 TCTTTGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTATTCCACTGCT
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCT
46707249 GC
131 GC
* *
46707251 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACCATCTTGGAAAGATAAGATTTGCCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCTG
* *
46707316 TCTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCT
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCT
*
46707381 GT
131 GC
* *
46707383 TTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCTG
** ** * *
46707448 TTCTT-GATCTATTCCACTACTGCTTAGGGAGATAAGATCTACGATCCTCAACCTACTCCGCTGT
66 -TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGC
46707512 TGC
130 TGC
* *
46707515 TCAGGGAGACAAGGTTTGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTG-TC
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCT-
* *
46707579 GTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTATAATCTTCAACCTTCTCCGCTGC
65 GTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGC
46707644 TGC
130 TGC
* * *
46707647 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTACCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCTG
* * *
46707712 TTTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAAGT-TTCAACCTACTCCGCTGC
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAA-TCTTCAACCTACTCCGCTGC
46707776 TGC
130 TGC
* * *
46707779 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAATATTTACCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCTG
* *
46707844 TCTTCGATCTGCTCCACTACTGCTTAGGGACATAAGATCTATAATCTTCAACCTTCTCCGCTGCT
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCT
46707909 GC
131 GC
46707911 TCAGGGAGACAAGGCTTGGTG
1 TCAGGGAGACAAGGCTTGGTG
46707932 TTTCACCGGT
Statistics
Matches: 743, Mismatches: 63, Indels: 14
0.91 0.08 0.02
Matches are distributed among these distances:
131 5 0.01
132 732 0.99
133 6 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (132 bp):
TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCTG
TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCT
GC
Found at i:46707614 original size:44 final size:44
Alignment explanation
Indices: 46707037--46707881 Score: 166
Period size: 44 Copynumber: 19.2 Consensus size: 44
46707027 TATCTTGGAA
* * *
46707037 AGATAAGATTTATCATCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * *
46707081 AGATAAGATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
46707125 AGACAAGGCTTGGT-GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * ** *
46707169 AGATAATATTTG-CTATCTTTGATCTGTTCCACTACTGCTTAGGG
1 AGATAAGATTTGTC-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * ** ** * *
46707213 AGATAAGATCT-ACAATCTTCAGCCTATTCCACTGCTGCTCAGGG
1 AGATAAGATTTGTC-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
46707257 AGACAAGGCTTGGT-GGCTTAAATCTGCTTCCCACCA-T-CTT-GGAA
1 AGATAA-GATTTGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
46707301 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTACTTAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * *
46707345 AGATAAGATCTATAATCTTCAACCTACTCCGCTGCTGTTTAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
46707389 AGACAAGGCTTGGT-GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * **
46707433 AGATAAGATTTGCCGTTCTT-GATCTATTCCACTACTGCTTAGGG
1 AGATAAGATTTGTCG-TCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * ** *
46707477 AGATAAGATCT-ACGATCCTCAACCTACTCCGCTGTTGCTCAGGG
1 AGATAAGATTTGTCG-TCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
46707521 AGACAAGGTTTGGT-GGCTTAAATCTACTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTT-GTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
46707565 AGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * ** * * * * *
46707609 AGATAAAATCTATAATCTTCAACCTTCTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
46707653 AGACAAGGCTTGGT-GGCTTAAATCTACTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
** * **
46707697 AGATAAGATTTACCGTTTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
46707741 AGATAAGATCT-ACAAGT-TTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGTC--GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
46707785 AGACAAGGCTTGGT-GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* ** *
46707829 AGATAATATTTACCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
*
46707873 ACATAAGAT
1 AGATAAGAT
46707882 CTATAATCTT
Statistics
Matches: 542, Mismatches: 201, Indels: 116
0.63 0.23 0.14
Matches are distributed among these distances:
42 35 0.06
43 49 0.09
44 392 0.72
45 42 0.08
46 24 0.04
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (44 bp):
AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:46709179 original size:6 final size:6
Alignment explanation
Indices: 46709168--46709195 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
46709158 GGCCTCTCCA
46709168 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
46709196 ATCACTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:46709226 original size:21 final size:22
Alignment explanation
Indices: 46709178--46709219 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
46709168 TTTTCTTTTT
46709178 CTTTTTCTTTTTCTTTTTATCA
1 CTTTTTCTTTTTCTTTTTATCA
46709200 CTTTTTCTTCTTT-TTTTTAT
1 CTTTTTCTT-TTTCTTTTTAT
46709220 ATATTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (22 bp):
CTTTTTCTTTTTCTTTTTATCA
Found at i:46712765 original size:23 final size:23
Alignment explanation
Indices: 46712733--46712795 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 23
46712723 TATGTATACT
*
46712733 AAAATAAATATATACATATAGATA
1 AAAAT-AATATATACATATAAATA
46712757 AAAATAATA-ATTACATATAAATA
1 AAAATAATATA-TACATATAAATA
*
46712780 AATAATTATATTATAC
1 AA-AATAATA-TATAC
46712796 TGCAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 1 0.03
23 17 0.52
24 11 0.33
25 3 0.09
26 1 0.03
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAATAATATATACATATAAATA
Found at i:46713303 original size:22 final size:22
Alignment explanation
Indices: 46713278--46713323 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
46713268 TTCCTCCTCC
46713278 TTTTTTTATTGATTCTCTCCTT
1 TTTTTTTATTGATTCTCTCCTT
46713300 TTTTTTTATTGATTCTCTCCTT
1 TTTTTTTATTGATTCTCTCCTT
46713322 TT
1 TT
46713324 CTACAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.09, C:0.17, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTTTTTATTGATTCTCTCCTT
Found at i:46713489 original size:21 final size:21
Alignment explanation
Indices: 46713431--46713523 Score: 93
Period size: 21 Copynumber: 4.4 Consensus size: 21
46713421 AAATTAAATC
*
46713431 TCTAAGATTACA-AAATCATA
1 TCTAAGATTACATATATCATA
**
46713451 TCTTCTAAGATTGTATATATCATA
1 ---TCTAAGATTACATATATCATA
*
46713475 TCTAATATTACATATATCATA
1 TCTAAGATTACATATATCATA
*
46713496 TCTAAGATTGCATATA--ATA
1 TCTAAGATTACATATATCATA
46713515 TCTAAGATT
1 TCTAAGATT
46713524 GTATATCCTC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 12 0.20
21 32 0.52
23 10 0.16
24 7 0.11
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (21 bp):
TCTAAGATTACATATATCATA
Found at i:46713792 original size:44 final size:44
Alignment explanation
Indices: 46713733--46713817 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
46713723 AGGAATTCGT
*
46713733 GCTTCAATCTACTCCACTGTAACTTCAGG-GAGATAAGACTTATA
1 GCTTCAATCTACTCCACTGCAACTTCAGGAG-GATAAGACTTATA
* * *
46713777 GCTTTAATCTGCTCCACTGCCACTTCAGGAGGATAAGACTT
1 GCTTCAATCTACTCCACTGCAACTTCAGGAGGATAAGACTT
46713818 GCTGGCTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 35 0.97
45 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
GCTTCAATCTACTCCACTGCAACTTCAGGAGGATAAGACTTATA
Found at i:46714314 original size:132 final size:132
Alignment explanation
Indices: 46714077--46714519 Score: 742
Period size: 132 Copynumber: 3.4 Consensus size: 132
46714067 NNNNNNNNNN
*
46714077 ATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGGCTTAAATCTGCT
1 ATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCT
* *
46714142 TCCCACTATCTTGGAAAGATAAGATTTGTCATCTTTGATCTGCTCCACTATTGCTTAGGGAGATA
66 TCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATA
46714207 AG
131 AG
* *
46714209 ATCTACAATCTTCAAGCTACTCCGCAGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCT
1 ATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCT
* *
46714274 TCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTACACTACTGCTTAGGGAGATA
66 TCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATA
46714339 AG
131 AG
*
46714341 ATCTACAATCTTCAACCAACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCT
1 ATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCT
*
46714406 TCCCACTATCTTGGAAAGATAAGATTTGCCTTCTTTGATCTGCTCCACTACTGCTTAGGGAGATA
66 TCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATA
46714471 AG
131 AG
** * * * * *
46714473 ATCTGTAATTTTAAACCTACTCCACTGCTGCTTAGGGAGATAAGGCT
1 ATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCT
46714520 GGAGTCTTTG
Statistics
Matches: 291, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 291 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (132 bp):
ATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCT
TCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATA
AG
Found at i:46714470 original size:44 final size:44
Alignment explanation
Indices: 46714158--46714516 Score: 117
Period size: 44 Copynumber: 8.2 Consensus size: 44
46714148 TATCTTGGAA
* * * *
46714158 AGATAAGATTTGTCATCTTTGATCTGCTCCACTATTGCTTAGGG
1 AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * *
46714202 AGATAAGATCTACAATCTTCAAGCTACTCCGC-AGCTGCTCAGGG
1 AGATAAGATTTGCCTTCTTTAATCTGCTCCACTA-CTGCTTAGGG
* ** * * * *
46714246 AGACAAGGCTTG-GTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCT-TCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * *
46714290 AGATAAGATTTGCCGTCTTTGATCTGCTACACTACTGCTTAGGG
1 AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** * * ** * * *
46714334 AGATAAGATCTACAATCTTCAACCAACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
* ** * * * *
46714378 AGACAAGGCTTG-GTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCT-TCTTTAATCTGC-T-CCACTACTGCTTAGG-G
*
46714422 AGATAAGATTTGCCTTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
* ** * * * *
46714466 AGATAAGATCTGTAATT-TTAAACCTACTCCACTGCTGCTTAGGG
1 AGATAAGATTTG-CCTTCTTTAATCTGCTCCACTACTGCTTAGGG
46714510 AGATAAG
1 AGATAAG
46714517 GCTGGAGTCT
Statistics
Matches: 216, Mismatches: 80, Indels: 38
0.65 0.24 0.11
Matches are distributed among these distances:
42 11 0.05
43 9 0.04
44 177 0.82
45 11 0.05
46 7 0.03
47 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (44 bp):
AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:46714562 original size:88 final size:87
Alignment explanation
Indices: 46714470--46714747 Score: 360
Period size: 88 Copynumber: 3.1 Consensus size: 87
46714460 TTAGGGAGAT
* * ** ** ** *
46714470 AAGATCTGTAATTTTAAACCTACTCCACTGCTGCTTAGGGAGATAAGGCTGGA-GTCTTTGATCT
1 AAGATCTGT-ATTTTTAACCTACTCCGCTGCAACACAGGGAGGCAAGGCT-GATGTCTTCGATCT
*
46714534 GCTTCGCTGTCGGTGTAGGAAGGC
64 GCTTCGCTGTCGGTGCAGGAAGGC
*
46714558 AAGATCTGCTATTTTTAACCTACTCCGCTGCAACACAGGGAGGCAAGGCTGATGTCTTCGATCTA
1 AAGATCTG-TATTTTTAACCTACTCCGCTGCAACACAGGGAGGCAAGGCTGATGTCTTCGATCTG
**
46714623 CTTCGCCATCGGTGCAGGAAGGC
65 CTTCGCTGTCGGTGCAGGAAGGC
* * *
46714646 AAGATCTTCTATTTTTAACCTGCTCCGCTACAACACAGGGAGGCAAGGCTGATGTCTTCGATCTG
1 AAGATC-TGTATTTTTAACCTACTCCGCTGCAACACAGGGAGGCAAGGCTGATGTCTTCGATCTG
46714711 CTTCGCTGTCGGTGCAGGAAGGC
65 CTTCGCTGTCGGTGCAGGAAGGC
46714734 AAGATCTGCTATTT
1 AAGATCTG-TATTT
46714748 CACTAATCTG
Statistics
Matches: 166, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
87 3 0.02
88 161 0.97
89 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (87 bp):
AAGATCTGTATTTTTAACCTACTCCGCTGCAACACAGGGAGGCAAGGCTGATGTCTTCGATCTGC
TTCGCTGTCGGTGCAGGAAGGC
Found at i:46714604 original size:44 final size:43
Alignment explanation
Indices: 46714554--46714692 Score: 102
Period size: 44 Copynumber: 3.2 Consensus size: 43
46714544 CGGTGTAGGA
46714554 AGGCAAGATCTGCTATTTTTAACCTACTCCGCTGCAACACAGGG
1 AGGCAAGATCTGCTATTTTTAACCTACTCCGCT-CAACACAGGG
* * * * ** * * * * *
46714598 AGGCAAG-GCTGATGTCTTCGATCTACTTCGC-CATCGGTGCAGGA
1 AGGCAAGATCTGCTATTTTTAACCTACTCCGCTCAAC---ACAGGG
* *
46714642 AGGCAAGATCTTCTATTTTTAACCTGCTCCGCTACAACACAGGG
1 AGGCAAGATCTGCTATTTTTAACCTACTCCGCT-CAACACAGGG
46714686 AGGCAAG
1 AGGCAAG
46714693 GCTGATGTCT
Statistics
Matches: 65, Mismatches: 24, Indels: 12
0.64 0.24 0.12
Matches are distributed among these distances:
41 3 0.05
43 16 0.25
44 29 0.45
45 14 0.22
47 3 0.05
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (43 bp):
AGGCAAGATCTGCTATTTTTAACCTACTCCGCTCAACACAGGG
Found at i:46722123 original size:23 final size:23
Alignment explanation
Indices: 46722091--46722198 Score: 68
Period size: 23 Copynumber: 4.8 Consensus size: 23
46722081 TATGTATACT
*
46722091 AAAATAAATATATACATATAGATA
1 AAAAT-AATATATACATATAAATA
46722115 AAAATAATA-ATTACATATAAATA
1 AAAATAATATA-TACATATAAATA
* *
46722138 AATAATTATATTATAC-TACAAA-A
1 AA-AATAATA-TATACATATAAATA
* * *
46722161 AATATAAT-TATGCGTAT--ATGA
1 AAAATAATATATACATATAAAT-A
46722182 AAAAT-ATATATACATAT
1 AAAATAATATATACATAT
46722199 TTTTTTTTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
19 1 0.02
20 6 0.09
21 14 0.21
22 5 0.08
23 20 0.30
24 16 0.24
25 3 0.05
26 1 0.02
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAATAATATATACATATAAATA
Found at i:46722800 original size:21 final size:21
Alignment explanation
Indices: 46722774--46722830 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
46722764 AACCATATCT
46722774 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
*
46722795 TCTAAGATTGCATATATCATA
1 TCTAAGATTGTATATATCATA
46722816 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
46722831 CCTTGAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:46723877 original size:8 final size:8
Alignment explanation
Indices: 46723860--46723907 Score: 60
Period size: 8 Copynumber: 5.9 Consensus size: 8
46723850 TAGCATAACC
46723860 TTTTTTAT
1 TTTTTTAT
*
46723868 TTTCTTAT
1 TTTTTTAT
46723876 TTCTTTTAT
1 TT-TTTTAT
46723885 TTTTTTAT
1 TTTTTTAT
*
46723893 TTATTTAT
1 TTTTTTAT
*
46723901 ATTTTTA
1 TTTTTTA
46723908 ATATCATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
8 27 0.79
9 7 0.21
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTAT
Found at i:46723884 original size:17 final size:17
Alignment explanation
Indices: 46723862--46723905 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
46723852 GCATAACCTT
*
46723862 TTTTATTTTCTTATTTC
1 TTTTATTTTCTTATTTA
*
46723879 TTTTATTTTTTTATTTA
1 TTTTATTTTCTTATTTA
46723896 TTTATATTTT
1 TTT-TATTTT
46723906 TAATATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTATTTTCTTATTTA
Found at i:46743416 original size:10 final size:10
Alignment explanation
Indices: 46743375--46743421 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
46743365 TATTTAAATA
46743375 TTTAAATTTC
1 TTTAAATTTC
*
46743385 TTTATATATTC
1 TTTAAAT-TTC
*
46743396 TTTAGAATTTT
1 TTTA-AATTTC
46743407 TTTAAATTT-
1 TTTAAATTTC
46743416 TTTAAA
1 TTTAAA
46743422 AATATAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 6 0.19
10 11 0.34
11 13 0.41
12 2 0.06
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTAAATTTC
Found at i:46743460 original size:19 final size:20
Alignment explanation
Indices: 46743414--46743480 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 20
46743404 TTTTTTAAAT
46743414 TTTTTAAAAATATAAATTTTGAAA
1 TTTTTAAAAAT-T--ATTTTG-AA
*
46743438 TTTTTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTGAA
46743457 -TTTTAAAAATTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
46743476 TTTTT
1 TTTTT
46743481 TTTGTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 8 0.21
19 11 0.28
20 10 0.26
22 1 0.03
24 9 0.23
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:46743936 original size:13 final size:13
Alignment explanation
Indices: 46743918--46743979 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
46743908 ACCAAAAAAA
46743918 TAAAAAAATATTT
1 TAAAAAAATATTT
*
46743931 TAAAAAAGTATTT
1 TAAAAAAATATTT
46743944 TAAAATAAAAAAGTATTT
1 T---A-AAAAAA-TATTT
*
46743962 TAAAAATAT-TTT
1 TAAAAAAATATTT
46743974 TAAAAA
1 TAAAAA
46743980 TAAAAATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
12 9 0.22
13 14 0.34
14 5 0.12
15 1 0.02
16 1 0.02
17 5 0.12
18 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
TAAAAAAATATTT
Found at i:46743967 original size:30 final size:32
Alignment explanation
Indices: 46743913--46743995 Score: 109
Period size: 31 Copynumber: 2.6 Consensus size: 32
46743903 TAAACACCAA
46743913 AAAAATAAAAAAATATTTTAAAAAAGTA-TTTT
1 AAAAATAAAAAAATATTTTAAAAAA-TATTTTT
*
46743945 -AAAATAAAAAAGTATTTT-AAAAATATTTTT
1 AAAAATAAAAAAATATTTTAAAAAATATTTTT
*
46743975 AAAAATAAAAATATATATTTA
1 AAAAATAAAAAAATAT-TTTA
46743996 TTATATTCGG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 2 0.05
30 9 0.20
31 30 0.68
32 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (32 bp):
AAAAATAAAAAAATATTTTAAAAAATATTTTT
Found at i:46743969 original size:19 final size:18
Alignment explanation
Indices: 46743931--46743966 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
46743921 AAAAATATTT
46743931 TAAAAAAGTATTTTAAAA
1 TAAAAAAGTATTTTAAAA
46743949 TAAAAAAGTATTTTAAAA
1 TAAAAAAGTATTTTAAAA
46743967 ATATTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
TAAAAAAGTATTTTAAAA
Found at i:46745219 original size:29 final size:31
Alignment explanation
Indices: 46745187--46745244 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
46745177 AAAAAAATTA
*
46745187 TTTTAGCTCTT-CATTTA-ATTTTTTATCCT
1 TTTTAGCTCTTAAATTTATATTTTTTATCCT
*
46745216 TTTTAGTTCTTAAATTTATATTTTTTATC
1 TTTTAGCTCTTAAATTTATATTTTTTATC
46745245 GAATTACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 5 0.20
31 10 0.40
ACGTcount: A:0.21, C:0.12, G:0.03, T:0.64
Consensus pattern (31 bp):
TTTTAGCTCTTAAATTTATATTTTTTATCCT
Found at i:46745365 original size:21 final size:21
Alignment explanation
Indices: 46745335--46745375 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
46745325 ACCTTTTAAC
* *
46745335 ATTTTAAAAATTCAAAAAATT
1 ATTTTAAAAAATAAAAAAATT
*
46745356 ATTTTTAAAAATAAAAAAAT
1 ATTTTAAAAAATAAAAAAAT
46745376 CATCACAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
ATTTTAAAAAATAAAAAAATT
Found at i:46746968 original size:21 final size:21
Alignment explanation
Indices: 46746913--46746968 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
46746903 TTCTCACATC
* *
46746913 AATTTAATATTAAAGAATAAT
1 AATTTAATATAAAACAATAAT
**
46746934 -ATTTTCTATCAAAACAATAAT
1 AATTTAATAT-AAAACAATAAT
46746955 AATTTAATATAAAA
1 AATTTAATATAAAA
46746969 TATCCCTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
20 7 0.26
21 13 0.48
22 7 0.26
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (21 bp):
AATTTAATATAAAACAATAAT
Found at i:46749981 original size:54 final size:54
Alignment explanation
Indices: 46749860--46749992 Score: 194
Period size: 54 Copynumber: 2.5 Consensus size: 54
46749850 GAAGTTGGGA
* ** *
46749860 CACACGGCCGTGTATCAGCCCATGTCTTTGGCTGTGTGTCTCACTGACTTGTAT
1 CACACGGTCGTGTCCCAGCCCATGTCTTTGGCCGTGTGTCTCACTGACTTGTAT
*
46749914 CACACGGTCGTGTCCCAGCCCATGTCTTTTGCCGTGTGTCTCACTGACTTGTAT
1 CACACGGTCGTGTCCCAGCCCATGTCTTTGGCCGTGTGTCTCACTGACTTGTAT
* * *
46749968 CACATGGTCGTGTCGCAGGCCATGT
1 CACACGGTCGTGTCCCAGCCCATGT
46749993 GTCAACCCAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 71 1.00
ACGTcount: A:0.14, C:0.29, G:0.25, T:0.32
Consensus pattern (54 bp):
CACACGGTCGTGTCCCAGCCCATGTCTTTGGCCGTGTGTCTCACTGACTTGTAT
Found at i:46751241 original size:26 final size:26
Alignment explanation
Indices: 46751212--46751264 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
46751202 CGCCAAAAGT
46751212 AAAAATGAAAAGACAAAGCCAATGTA
1 AAAAATGAAAAGACAAAGCCAATGTA
46751238 AAAAATGAAAAGACAAAGCCAATGTA
1 AAAAATGAAAAGACAAAGCCAATGTA
46751264 A
1 A
46751265 CCATTCTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.62, C:0.11, G:0.15, T:0.11
Consensus pattern (26 bp):
AAAAATGAAAAGACAAAGCCAATGTA
Found at i:46752186 original size:26 final size:27
Alignment explanation
Indices: 46752157--46752213 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 27
46752147 AACCTGAAAT
46752157 GCCAAAAGT-AAAAATGAAAAGACAAA
1 GCCAAAAGTAAAAAATGAAAAGACAAA
*
46752183 GCC-AATGTAAAAAATGAAAAGACAAA
1 GCCAAAAGTAAAAAATGAAAAGACAAA
46752209 GCCAA
1 GCCAA
46752214 TGTAACCCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 4 0.14
26 23 0.82
27 1 0.04
ACGTcount: A:0.61, C:0.14, G:0.16, T:0.09
Consensus pattern (27 bp):
GCCAAAAGTAAAAAATGAAAAGACAAA
Found at i:46752214 original size:26 final size:26
Alignment explanation
Indices: 46752166--46752218 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
46752156 TGCCAAAAGT
46752166 AAAAATGAAAAGACAAAGCCAATGTA
1 AAAAATGAAAAGACAAAGCCAATGTA
46752192 AAAAATGAAAAGACAAAGCCAATGTA
1 AAAAATGAAAAGACAAAGCCAATGTA
46752218 A
1 A
46752219 CCCTTCTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.62, C:0.11, G:0.15, T:0.11
Consensus pattern (26 bp):
AAAAATGAAAAGACAAAGCCAATGTA
Found at i:46752997 original size:954 final size:954
Alignment explanation
Indices: 46751149--46753060 Score: 3304
Period size: 954 Copynumber: 2.0 Consensus size: 954
46751139 TGCCTTGAAA
*
46751149 ATATAAAACTGGAATAAAAATTTGTGCCTAAGTGCTTTTATGTTAACCTAAAACGCCAAAAGTAA
1 ATATAAAACTGGAATAAAAAATTGTGCCTAAGTGCTTTTATGTTAACCTAAAACGCCAAAAGTAA
46751214 AAATGAAAAGACAAAGCCAATGTAAAAAATGAAAAGACAAAGCCAATGTAACCATTCTTCTCCAT
66 AAATGAAAAGACAAAGCCAATGTAAAAAATGAAAAGACAAAGCCAATGTAACCATTCTTCTCCAT
46751279 TCTTCTTCTTCTATTGAAAATAAACCCTTGTATCAGCTATGCAAGAGACCTATTTTCTCCCAAAA
131 TCTTCTTCTTCTATTGAAAATAAACCCTTGTATCAGCTATGCAAGAGACCTATTTTCTCCCAAAA
* *
46751344 TCAAACCTTCTAATACCACAGTCTCTTTCAAAATCTCGAGTTCTTCGGGCGAACAAACACCATAA
196 TCAAACCTTCTAATACCACAATCTCTTTCAAAATCTCGAGTTCTTCGGGCGAACAAACACCACAA
* * *
46751409 GGCTCGGACTCTACCTTTCTATCTAACCGCCATGATTGTCATTTCTCTTCTCTTAATTTGTCAGG
261 GGCCCGGACTCTACCTTTCTATCTAACCGCCATGATTATCATTTCTCCTCTCTTAATTTGTCAGG
* * * *
46751474 ATCTCCACCGTCTATGACGCCTCCTCTATCCAGAATCAAATATGCTCGTAACGCTCTCCTTCCTT
326 ATCTCCACCGTATACGACGCCTCCTCTATCCAGAATCAAAGATGCTCGTAACGCCCTCCTTCCTT
* *
46751539 CGCCATCGCATGAGCCACTTTGTTGGCCCCCCTTGGTACATGTTTGAAACTCAAACTTCTGAAGT
391 CGCCATCGCATAAGCCACTTTGTTGGCCCCCCTTGGTACATGCTTGAAACTCAAACTTCTGAAGT
* * * *
46751604 TGTAACCTCTTCCCTTAATTTTTTTAATCAAGTTACTAATACACGATCTATCTTCATCCACAGAG
456 TGTAACATCTCCCCTTAATTTCTTTAATCAAATTACTAATACACGATCTATCTTCATCCACAGAG
* *
46751669 TTCAGTTTACGTATTATGGTTAGCGCATCCCCTTCTATGCATTTGTCTTGAAACCCTATATCTTC
521 TTCAGTTTACGTATTATGGTTAGCGCATCCCCTTCTATGCATATGTCCTGAAACCCTATATCTTC
*
46751734 AGCCATAATAATGGCTTGCAGACACGCCCTTGCCTCGGCCATCACTGGATCTGAAATGTTTTCCC
586 AGCCATAATAATAGCTTGCAGACACGCCCTTGCCTCGGCCATCACTGGATCTGAAATGTTTTCCC
* * * *
46751799 ATGGGTAGGTACAAGCTGCCATTATTAGACCTTCCTTGTTTCATGTTATGATTCCTGACATAGAA
651 ATGAGTAGGTACAAGCTACCATTATTAGACCTTCATTGTTTCATGCTATGATTCCTGACATAGAA
46751864 CATTTTGTTATTTGATTGAATGAAGAGTCAAAATTGATTTTTATGGTGTCATTGTCTGGTGGTTC
716 CATTTTGTTATTTGATTGAATGAAGAGTCAAAATTGATTTTTATGGTGTCATTGTCTGGTGGTTC
* ** * * *
46751929 CCAAACTGAATGTCTAGCATCACATGAGTTCTTTAATCTCTCCTCCATAATAGTTGTTTCTGTAT
781 CCAAAATGAATGTCTAAAATCACATGAGTACTTTAATCTCTCCCCCATAATAGTTGTTTCTGCAT
*
46751994 AGTTGGCCTTAATAAATCCCACAACTTCAGTCACTTGCTCCTGAACACCATCATGATAGAGTTTA
846 AGTAGGCCTTAATAAATCCCACAACTTCAGTCACTTGCTCCTGAACACCATCATGATAGAGTTTA
*
46752059 TTATGATGATACCAAATTGCCCAATATGCGATAGATCTGATTCT
911 TTATGATGATACCAAATTGCCAAATATGCGATAGATCTGATTCT
* *
46752103 ATATAAAACTGGAATAAAAAATTGTGCCTAAGTGCTTTTATGTTAACCTGAAATGCCAAAAGTAA
1 ATATAAAACTGGAATAAAAAATTGTGCCTAAGTGCTTTTATGTTAACCTAAAACGCCAAAAGTAA
* *
46752168 AAATGAAAAGACAAAGCCAATGTAAAAAATGAAAAGACAAAGCCAATGTAACCCTTCTTCTCCCT
66 AAATGAAAAGACAAAGCCAATGTAAAAAATGAAAAGACAAAGCCAATGTAACCATTCTTCTCCAT
*
46752233 TCTTCTTCTTCTATTGAAAATAAACCCTTGTATCAGCTATGCAAGAGACTTATTTTCTCCCAAAA
131 TCTTCTTCTTCTATTGAAAATAAACCCTTGTATCAGCTATGCAAGAGACCTATTTTCTCCCAAAA
* * *
46752298 TCAAACCTTCTAATACCACAATCTCTTTCAAAATCTCGAGTTTTTCGTGCGAATAAACACCACAA
196 TCAAACCTTCTAATACCACAATCTCTTTCAAAATCTCGAGTTCTTCGGGCGAACAAACACCACAA
*
46752363 GGCCC-GAGTTCTACCTTTCTATCTAACCGCCATGATTATCATTTCTCCTCTCTTAATTTGTCAG
261 GGCCCGGA-CTCTACCTTTCTATCTAACCGCCATGATTATCATTTCTCCTCTCTTAATTTGTCAG
* * * *
46752427 GATCTCCACCGTATGCGGCGCCTCCTCTATCCAGAATCGAGGATGCTCGTAACGCCCTCCTTCCT
325 GATCTCCACCGTATACGACGCCTCCTCTATCCAGAATCAAAGATGCTCGTAACGCCCTCCTTCCT
**
46752492 TCGCCATCGCATAAGCCACTTTGTTGGCTTCCCTTGGTACATGCTTGAAACTCAAACTTCTGAAG
390 TCGCCATCGCATAAGCCACTTTGTTGGCCCCCCTTGGTACATGCTTGAAACTCAAACTTCTGAAG
*
46752557 TTGTAACATCTCCCCTTAATTTCTTTAATCAAATTACTAATACACGATCTATCTTCATCCGCAGA
455 TTGTAACATCTCCCCTTAATTTCTTTAATCAAATTACTAATACACGATCTATCTTCATCCACAGA
* *
46752622 GTTCAGTTTATGTATTATGGTTAGCGCATCCCCTTCTATGCATATGTCCTGGAACCCTATATCTT
520 GTTCAGTTTACGTATTATGGTTAGCGCATCCCCTTCTATGCATATGTCCTGAAACCCTATATCTT
*
46752687 CAGCCATAATAATAGCTTGCAGACATGCCCTTGCCTCGGCCATCACTGGATCTGAAATGTTTTCC
585 CAGCCATAATAATAGCTTGCAGACACGCCCTTGCCTCGGCCATCACTGGATCTGAAATGTTTTCC
*
46752752 CATGAGTAGGTACAAGCTACCATTATTAGACCTTCATTGTTTCATGCTATGATTCCTGATATAGA
650 CATGAGTAGGTACAAGCTACCATTATTAGACCTTCATTGTTTCATGCTATGATTCCTGACATAGA
*
46752817 ACATTTTGTTATTTGATTGAATGATGAGTCAAAATTGATTTTTATGGTGTCATTGTCTGGTGGTT
715 ACATTTTGTTATTTGATTGAATGAAGAGTCAAAATTGATTTTTATGGTGTCATTGTCTGGTGGTT
* *
46752882 CCCAAAATGAATGTCTAAAATCATATGAGTACTTTAATCTTTCCCCCATAATAGTTGTTTCTGCA
780 CCCAAAATGAATGTCTAAAATCACATGAGTACTTTAATCTCTCCCCCATAATAGTTGTTTCTGCA
* *
46752947 TAGTAGGCTTTAATAAATCCCACAACTTCAGTCACTTGCTCCTGAACACCATTATGATAGAGTTT
845 TAGTAGGCCTTAATAAATCCCACAACTTCAGTCACTTGCTCCTGAACACCATCATGATAGAGTTT
46753012 ATTATGATGATACCAAATTGCCAAATATGCGATAGATCTGATTCT
910 ATTATGATGATACCAAATTGCCAAATATGCGATAGATCTGATTCT
46753057 ATAT
1 ATAT
46753061 GCTTCAATGC
Statistics
Matches: 901, Mismatches: 56, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
953 2 0.00
954 899 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.33
Consensus pattern (954 bp):
ATATAAAACTGGAATAAAAAATTGTGCCTAAGTGCTTTTATGTTAACCTAAAACGCCAAAAGTAA
AAATGAAAAGACAAAGCCAATGTAAAAAATGAAAAGACAAAGCCAATGTAACCATTCTTCTCCAT
TCTTCTTCTTCTATTGAAAATAAACCCTTGTATCAGCTATGCAAGAGACCTATTTTCTCCCAAAA
TCAAACCTTCTAATACCACAATCTCTTTCAAAATCTCGAGTTCTTCGGGCGAACAAACACCACAA
GGCCCGGACTCTACCTTTCTATCTAACCGCCATGATTATCATTTCTCCTCTCTTAATTTGTCAGG
ATCTCCACCGTATACGACGCCTCCTCTATCCAGAATCAAAGATGCTCGTAACGCCCTCCTTCCTT
CGCCATCGCATAAGCCACTTTGTTGGCCCCCCTTGGTACATGCTTGAAACTCAAACTTCTGAAGT
TGTAACATCTCCCCTTAATTTCTTTAATCAAATTACTAATACACGATCTATCTTCATCCACAGAG
TTCAGTTTACGTATTATGGTTAGCGCATCCCCTTCTATGCATATGTCCTGAAACCCTATATCTTC
AGCCATAATAATAGCTTGCAGACACGCCCTTGCCTCGGCCATCACTGGATCTGAAATGTTTTCCC
ATGAGTAGGTACAAGCTACCATTATTAGACCTTCATTGTTTCATGCTATGATTCCTGACATAGAA
CATTTTGTTATTTGATTGAATGAAGAGTCAAAATTGATTTTTATGGTGTCATTGTCTGGTGGTTC
CCAAAATGAATGTCTAAAATCACATGAGTACTTTAATCTCTCCCCCATAATAGTTGTTTCTGCAT
AGTAGGCCTTAATAAATCCCACAACTTCAGTCACTTGCTCCTGAACACCATCATGATAGAGTTTA
TTATGATGATACCAAATTGCCAAATATGCGATAGATCTGATTCT
Found at i:46759861 original size:24 final size:24
Alignment explanation
Indices: 46759825--46759870 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
46759815 TTTTCAATAA
* *
46759825 TTTATTTAATTAAATTATTATTAT
1 TTTATTGAATTAAATAATTATTAT
* *
46759849 TTTATTGATTTAAGTAATTATT
1 TTTATTGAATTAAATAATTATT
46759871 TACTTTTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
TTTATTGAATTAAATAATTATTAT
Found at i:46783409 original size:19 final size:19
Alignment explanation
Indices: 46783370--46783428 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
46783360 AAATCAAAGC
* *
46783370 AATTTTCAAAATTTGAAAAT
1 AATTTT-AAAAATTCAAAAT
*
46783390 AATTTTTAAAATTCAAAAT
1 AATTTTAAAAATTCAAAAT
46783409 -ATTTATAAAAATTCTAAAAT
1 AATTT-TAAAAATTC-AAAAT
46783429 TTGTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.12
19 18 0.55
20 11 0.33
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTTTAAAAATTCAAAAT
Found at i:46783417 original size:18 final size:21
Alignment explanation
Indices: 46783377--46783428 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
46783367 AGCAATTTTC
*
46783377 AAAATT-TGAAAATAATTT-TT
1 AAAATTCT-AAAATAATTTATA
46783397 AAAATTC-AAAAT-ATTTATA
1 AAAATTCTAAAATAATTTATA
46783416 AAAATTCTAAAAT
1 AAAATTCTAAAAT
46783429 TTGTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 4 0.14
19 13 0.46
20 11 0.39
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAATTCTAAAATAATTTATA
Found at i:46783581 original size:3 final size:3
Alignment explanation
Indices: 46783573--46783605 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
46783563 TACTGAAATA
46783573 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
46783606 GCTTTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:46792401 original size:18 final size:19
Alignment explanation
Indices: 46792378--46792416 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
46792368 CTTGGCCCAT
* *
46792378 TACAGTATCA-ATATTCAG
1 TACAGTAACAGATATACAG
46792396 TACAGTAACAGATATACAG
1 TACAGTAACAGATATACAG
46792415 TA
1 TA
46792417 TCAAATCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (19 bp):
TACAGTAACAGATATACAG
Found at i:46807222 original size:32 final size:32
Alignment explanation
Indices: 46807185--46807267 Score: 112
Period size: 32 Copynumber: 2.6 Consensus size: 32
46807175 TATTGCAATT
*
46807185 AATTTGTTGGATTTTGAAAATATTATGTTTTA
1 AATTTGTTGGATATTGAAAATATTATGTTTTA
**
46807217 AATTTGTTGGATATTGAATTTATTATGTTTTA
1 AATTTGTTGGATATTGAAAATATTATGTTTTA
***
46807249 CGCTTGTTGGATATTGAAA
1 AATTTGTTGGATATTGAAA
46807268 TGATTAGCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (32 bp):
AATTTGTTGGATATTGAAAATATTATGTTTTA
Found at i:46808617 original size:14 final size:15
Alignment explanation
Indices: 46808594--46808633 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
46808584 CCAAAAATAC
**
46808594 AAATTATTTTTTAAA
1 AAATTATTTTAAAAA
46808609 AAA-TATTTTAAAAA
1 AAATTATTTTAAAAA
46808623 AAATTATTTTA
1 AAATTATTTTA
46808634 CTGACAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTATTTTAAAAA
Found at i:46808923 original size:6 final size:6
Alignment explanation
Indices: 46808912--46808938 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
46808902 CTCTCTTTCC
46808912 CTCTGT CTCTGT CTCTGT CTCTGT CTC
1 CTCTGT CTCTGT CTCTGT CTCTGT CTC
46808939 AAGCCTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.37, G:0.15, T:0.48
Consensus pattern (6 bp):
CTCTGT
Found at i:46810814 original size:16 final size:16
Alignment explanation
Indices: 46810795--46810825 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46810785 TATTTTAGAG
46810795 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
46810811 CATATATATTTGAAA
1 CATATAAATTTGAAA
46810826 ACTTTCTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:46811003 original size:18 final size:17
Alignment explanation
Indices: 46810982--46811066 Score: 55
Period size: 18 Copynumber: 4.8 Consensus size: 17
46810972 TTTTTAAAAA
46810982 TTATAAATTTTGGAATTT
1 TTATAAATTTTGG-ATTT
*
46811000 TTATAAAAATTTGGATTT
1 TTAT-AAATTTTGGATTT
* * *
46811018 GTAAAAATTATTTTGATTT
1 TTATAAA-T-TTTGGATTT
**
46811037 TT-TAAATTTTTAAATTT
1 TTATAAA-TTTTGGATTT
*
46811054 TTTTAAATTTTGG
1 TTATAAATTTTGG
46811067 TTGAGAGAGA
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
17 16 0.31
18 19 0.37
19 17 0.33
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (17 bp):
TTATAAATTTTGGATTT
Found at i:46812050 original size:2 final size:2
Alignment explanation
Indices: 46812043--46812071 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46812033 AGATCTTCAT
46812043 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
46812072 GTATTGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:46815438 original size:28 final size:24
Alignment explanation
Indices: 46815384--46815432 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
46815374 TGTGACAAAC
46815384 AAATATTAACTCATTGATTGTCTA
1 AAATATTAACTCATTGATTGTCTA
46815408 AAATATTAACTCATTGATTGTCTA
1 AAATATTAACTCATTGATTGTCTA
46815432 A
1 A
46815433 GTAAAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (24 bp):
AAATATTAACTCATTGATTGTCTA
Found at i:46821456 original size:3 final size:3
Alignment explanation
Indices: 46821448--46821473 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
46821438 AAATGAAACT
46821448 ACC ACC ACC ACC ACC ACC ACC ACC AC
1 ACC ACC ACC ACC ACC ACC ACC ACC AC
46821474 TTCATCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:46832333 original size:45 final size:46
Alignment explanation
Indices: 46832279--46832389 Score: 197
Period size: 46 Copynumber: 2.4 Consensus size: 46
46832269 ATCACTTGTC
*
46832279 CTTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTACCA
1 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
*
46832324 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTATCA
1 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
46832370 CTTGATCAGATAAGTGTAGC
1 CTTGATCAGATAAGTGTAGC
46832390 CACTTATCAC
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 21 0.33
46 42 0.67
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (46 bp):
CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
Found at i:46832372 original size:46 final size:45
Alignment explanation
Indices: 46832266--46832499 Score: 243
Period size: 37 Copynumber: 5.6 Consensus size: 45
46832256 CATATGACCT
*
46832266 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
46832309 CTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
46832355 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
46832392 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
** *
46832429 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAACTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
46832475 CTTATCACTTTGTCACTTGATCAGA
1 CTTATCACTTTGTCACTTGATCAGA
46832500 AGTACTCAAA
Statistics
Matches: 169, Mismatches: 9, Indels: 23
0.84 0.04 0.11
Matches are distributed among these distances:
37 64 0.38
39 2 0.01
40 3 0.02
41 1 0.01
42 1 0.01
43 10 0.06
44 5 0.03
45 21 0.12
46 62 0.37
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:46836151 original size:51 final size:51
Alignment explanation
Indices: 46836035--46836301 Score: 437
Period size: 51 Copynumber: 5.3 Consensus size: 51
46836025 CTTACGAATG
* * *
46836035 ATCACTTATCACTTGTCCCTGATTAGATAAGTGTAGCTAAA-CTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
46836085 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
46836136 ATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * * *
46836187 ATCACTTGTCACTTTTCATTGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
46836238 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACTACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
46836289 ATCACTTGTCACT
1 ATCACTTGTCACT
46836302 GATCAGAAGT
Statistics
Matches: 200, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
50 38 0.19
51 162 0.81
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.33
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:46836784 original size:31 final size:31
Alignment explanation
Indices: 46836749--46836811 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
46836739 ACTTACCAAC
46836749 ATGTGTTAATTCATAAACCATTCATAACATT
1 ATGTGTTAATTCATAAACCATTCATAACATT
46836780 ATGTGTTAATTCATAAACCATTCATAACATT
1 ATGTGTTAATTCATAAACCATTCATAACATT
46836811 A
1 A
46836812 CTTCAAGCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (31 bp):
ATGTGTTAATTCATAAACCATTCATAACATT
Found at i:46841822 original size:23 final size:25
Alignment explanation
Indices: 46841784--46841829 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
46841774 CAAAAAAATT
46841784 AAATATATATA-TTTTTTATTTTTA
1 AAATATATATAGTTTTTTATTTTTA
46841808 AAATATA-ATAGTTTTTTATTTT
1 AAATATATATAGTTTTTTATTTT
46841830 AAGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
AAATATATATAGTTTTTTATTTTTA
Found at i:46842041 original size:16 final size:16
Alignment explanation
Indices: 46842020--46842061 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
46842010 AATAATTTGA
*
46842020 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
46842036 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
46842052 TAGTTTTAAT
1 TAATTTTAAT
46842062 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:46842045 original size:22 final size:22
Alignment explanation
Indices: 46842035--46842096 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
46842025 TTACTAACAA
* * *
46842035 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
46842057 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
46842079 TTAATTTTAATTAAAAAT
1 TTAATTTTAATAAAAAAT
46842097 GGGTAGGGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:46845835 original size:25 final size:25
Alignment explanation
Indices: 46845807--46845854 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
46845797 AAAAATACAT
46845807 AAAA-TTGAAAAATAAAAAAGAAATG
1 AAAATTTGAAAAAT-AAAAAGAAATG
* *
46845832 AAAATTTTAAAAATAGAAAGAAA
1 AAAATTTGAAAAATAAAAAGAAA
46845855 AAATAAGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (25 bp):
AAAATTTGAAAAATAAAAAGAAATG
Found at i:46847447 original size:23 final size:23
Alignment explanation
Indices: 46847351--46847441 Score: 146
Period size: 23 Copynumber: 4.0 Consensus size: 23
46847341 GTAAATTGAT
* **
46847351 CAGTGGTAGCTTCGGCTACGTTT
1 CAGTGGTAGCTTCGGCTACATAA
46847374 CAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
*
46847397 CAGTGGTAGCTTCGGTTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
46847420 CAGTGGTAGCTTCGGCTACATA
1 CAGTGGTAGCTTCGGCTACATA
46847442 TGAGTGTTGC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (23 bp):
CAGTGGTAGCTTCGGCTACATAA
Found at i:46849267 original size:73 final size:71
Alignment explanation
Indices: 46849180--46849317 Score: 231
Period size: 73 Copynumber: 1.9 Consensus size: 71
46849170 AAAAAAGGGA
* * *
46849180 TTTAACTAATAAAAATAATGGTTTGCAGCTTTAAGAACCAAATTAAACTAAAAAAATCCTTCTAA
1 TTTAACTAATAAAAATAATGATTTGCAACTTTAAAAACCAAATTAAACT-AAAAAATCCTTC-AA
46849245 ATATGGGG
64 ATATGGGG
46849253 TTTAACTAATAAAAATAATGATTTGCAACTTTAAAAACCAAATTAAACTAAAAAATCCTTCAAAT
1 TTTAACTAATAAAAATAATGATTTGCAACTTTAAAAACCAAATTAAACTAAAAAATCCTTCAAAT
46849318 TTCAATATTT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
71 4 0.06
72 12 0.19
73 46 0.74
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30
Consensus pattern (71 bp):
TTTAACTAATAAAAATAATGATTTGCAACTTTAAAAACCAAATTAAACTAAAAAATCCTTCAAAT
ATGGGG
Found at i:46864204 original size:211 final size:211
Alignment explanation
Indices: 46863840--46864222 Score: 730
Period size: 211 Copynumber: 1.8 Consensus size: 211
46863830 TATTCTGCTA
* *
46863840 ATCTGATAATTATCAATATTATTTTCCTTATTTCATTATAGTAGTTTTAATTTATATAGATTTTT
1 ATCTGATAATTATCAATATTATTTTCCTTATTTCATTATAGTAGTTTTAATTTATATAAACTTTT
46863905 GTCATATACCTATTTGACACGGATTCAAATTGTGCGACTCTCATCCCCACTTTCAATATCGTGTA
66 GTCATATACCTATTTGACACGGATTCAAATTGTGCGACTCTCATCCCCACTTTCAATATCGTGTA
*
46863970 AAAAATCAGTGCTTAATATCAATAATTGCTTTGAAATAATACTATTTGACACGAATTCATTATAC
131 AAAAATCAGTACTTAATATCAATAATTGCTTTGAAATAATACTATTTGACACGAATTCATTATAC
46864035 TATTTGAAATAATACT
196 TATTTGAAATAATACT
46864051 ATCTGATAATTATCAATATTATTTTCCTTATTTCATTATAGTAGTTTTAATTTATATAAACTTTT
1 ATCTGATAATTATCAATATTATTTTCCTTATTTCATTATAGTAGTTTTAATTTATATAAACTTTT
*
46864116 GTCATATACCTATTTGACACGGATTCAAATTGTGCGACTCTCATCTCCACTTTCAATATCGTGTA
66 GTCATATACCTATTTGACACGGATTCAAATTGTGCGACTCTCATCCCCACTTTCAATATCGTGTA
46864181 AAAAATCAGTACTTAATATCAATAATTGCTTTGAAATAATAC
131 AAAAATCAGTACTTAATATCAATAATTGCTTTGAAATAATAC
46864223 AAATCCAAAC
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
211 168 1.00
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (211 bp):
ATCTGATAATTATCAATATTATTTTCCTTATTTCATTATAGTAGTTTTAATTTATATAAACTTTT
GTCATATACCTATTTGACACGGATTCAAATTGTGCGACTCTCATCCCCACTTTCAATATCGTGTA
AAAAATCAGTACTTAATATCAATAATTGCTTTGAAATAATACTATTTGACACGAATTCATTATAC
TATTTGAAATAATACT
Found at i:46871272 original size:41 final size:41
Alignment explanation
Indices: 46871215--46871321 Score: 191
Period size: 41 Copynumber: 2.6 Consensus size: 41
46871205 TTTTTATTTT
46871215 AAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATT-A
1 AAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
46871255 AAAAAATTAAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAAATT-AAAAAAAGTATTTTAAAAATATTTTAAAATTAA
46871297 AAAAAATTAAAAAAA-TATTTTAAAA
1 AAAAAATTAAAAAAAGTATTTTAAAA
46871322 TTAAAAAAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
40 18 0.28
41 38 0.58
42 9 0.14
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (41 bp):
AAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
Found at i:46871298 original size:29 final size:29
Alignment explanation
Indices: 46871278--46871338 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
46871268 AAAGTATTTT
46871278 AAAAATATTTTAAAATTAAAAAAAATTAA
1 AAAAATATTTTAAAATTAAAAAAAATTAA
46871307 AAAAATATTTTAAAATT-AAAAAAATTAA
1 AAAAATATTTTAAAATTAAAAAAAATTAA
46871335 AAAA
1 AAAA
46871339 GTATGTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (29 bp):
AAAAATATTTTAAAATTAAAAAAAATTAA
Found at i:46871321 original size:11 final size:11
Alignment explanation
Indices: 46871209--46871292 Score: 54
Period size: 12 Copynumber: 7.9 Consensus size: 11
46871199 GGCCCATTTT
46871209 TATTTTAAAAA
1 TATTTTAAAAA
**
46871220 -ATTAAAAAAA
1 TATTTTAAAAA
46871230 GTATTTTAAAAA
1 -TATTTTAAAAA
46871242 TATTTT--AAA
1 TATTTTAAAAA
46871251 -A--TTAAAAA
1 TATTTTAAAAA
* **
46871259 AATTAAAAAAAA
1 TATT-TTAAAAA
46871271 GTATTTTAAAAA
1 -TATTTTAAAAA
46871283 TATTTTAAAA
1 TATTTTAAAA
46871293 TTAAAAAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 18
0.67 0.11 0.22
Matches are distributed among these distances:
6 2 0.04
8 4 0.07
9 4 0.07
10 8 0.15
11 16 0.29
12 18 0.33
13 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:46871349 original size:28 final size:29
Alignment explanation
Indices: 46871278--46871349 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 29
46871268 AAAGTATTTT
* *
46871278 AAAAATATTTTAAAATTAAAAAAAATTAA
1 AAAAATATGTAAAAATTAAAAAAAATTAA
* *
46871307 AAAAATATTTTAAAATT-AAAAAAATTAA
1 AAAAATATGTAAAAATTAAAAAAAATTAA
*
46871335 AAAAGTATGTAAAAA
1 AAAAATATGTAAAAA
46871350 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 23 0.57
29 17 0.43
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (29 bp):
AAAAATATGTAAAAATTAAAAAAAATTAA
Found at i:46871350 original size:29 final size:29
Alignment explanation
Indices: 46871255--46871351 Score: 88
Period size: 29 Copynumber: 3.2 Consensus size: 29
46871245 TTTAAAATTA
**
46871255 AAAAAATTAAAAAAAAGTATTTTAAAAATATT
1 AAAAAATT-AAAAAAA--ATTAAAAAAATATT
**
46871287 TTAAAATTAAAAAAAATTAAAAAAATATT
1 AAAAAATTAAAAAAAATTAAAAAAATATT
** *
46871316 TTAAAATT-AAAAAAATTAAAAAAGTATGT
1 AAAAAATTAAAAAAAATTAAAAAAATAT-T
46871345 AAAAAAT
1 AAAAAAT
46871352 ATTTTAAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
28 18 0.32
29 26 0.46
31 7 0.12
32 6 0.11
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAAAATTAAAAAAAATTAAAAAAATATT
Found at i:46871367 original size:20 final size:20
Alignment explanation
Indices: 46871306--46871372 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
46871296 AAAAAAATTA
46871306 AAAAAATATTTTAAAA--TT
1 AAAAAATATTTTAAAATTTT
** *
46871324 AAAAAA-ATTAAAAAAGTATGT
1 AAAAAATATTTTAAAA-T-TTT
46871345 AAAAAATATTTTAAAATTTT
1 AAAAAATATTTTAAAATTTT
46871365 AAAAAATA
1 AAAAAATA
46871373 AATATATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
17 7 0.18
18 6 0.16
20 10 0.26
21 8 0.21
22 7 0.18
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAAATATTTTAAAATTTT
Found at i:46871705 original size:23 final size:24
Alignment explanation
Indices: 46871679--46871729 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
46871669 TTTCCTGGTG
*
46871679 TTTTGATGTTGTTTTT-CTATTAT
1 TTTTGATGGTGTTTTTGCTATTAT
* *
46871702 TTTTGCTGGTGTTTTTGCTGTTAT
1 TTTTGATGGTGTTTTTGCTATTAT
46871726 TTTT
1 TTTT
46871730 ACTGCCGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.69
Consensus pattern (24 bp):
TTTTGATGGTGTTTTTGCTATTAT
Found at i:46871728 original size:12 final size:12
Alignment explanation
Indices: 46871679--46871729 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
46871669 TTTCCTGGTG
* *
46871679 TTTTGATGTTGT
1 TTTTGCTGTTAT
*
46871691 TTTT-CTATTAT
1 TTTTGCTGTTAT
* *
46871702 TTTTGCTGGTGT
1 TTTTGCTGTTAT
46871714 TTTTGCTGTTAT
1 TTTTGCTGTTAT
46871726 TTTT
1 TTTT
46871730 ACTGCCGTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
11 8 0.27
12 22 0.73
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.69
Consensus pattern (12 bp):
TTTTGCTGTTAT
Found at i:46871739 original size:24 final size:24
Alignment explanation
Indices: 46871689--46871747 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
46871679 TTTTGATGTT
* * **
46871689 GTTTTT-CTATTATTTTTGCTGGT
1 GTTTTTGCTGTTATTTTTACTGCC
46871712 GTTTTTGCTGTTATTTTTACTGCC
1 GTTTTTGCTGTTATTTTTACTGCC
*
46871736 GTTTTTGTTGTT
1 GTTTTTGCTGTT
46871748 TGGGTGTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 6 0.20
24 24 0.80
ACGTcount: A:0.07, C:0.10, G:0.19, T:0.64
Consensus pattern (24 bp):
GTTTTTGCTGTTATTTTTACTGCC
Found at i:46874514 original size:19 final size:18
Alignment explanation
Indices: 46874490--46874533 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
46874480 TAAAAAATTT
* * *
46874490 AAAAAATATATAATTTAG
1 AAAAAAAATATAAATTAC
*
46874508 AAAAAAAATCTAAATTAC
1 AAAAAAAATATAAATTAC
46874526 AAAAAAAA
1 AAAAAAAA
46874534 ATTATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (18 bp):
AAAAAAAATATAAATTAC
Found at i:46874541 original size:20 final size:19
Alignment explanation
Indices: 46874490--46874541 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
46874480 TAAAAAATTT
* *
46874490 AAAAAATATATAATTTAGAA
1 AAAAAAT-TATAAATTAAAA
*
46874510 AAAAAA-TCTAAATTACAAA
1 AAAAAATTATAAATTA-AAA
46874529 AAAAAATTATAAA
1 AAAAAATTATAAA
46874542 AATTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.27
19 8 0.31
20 11 0.42
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (19 bp):
AAAAAATTATAAATTAAAA
Found at i:46875310 original size:18 final size:18
Alignment explanation
Indices: 46875287--46875344 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
46875277 CTAAACATTT
46875287 TTTTTACAATTTTTAATA
1 TTTTTACAATTTTTAATA
***
46875305 TTTTTA-AAAAATTAATGA
1 TTTTTACAATTTTTAAT-A
*
46875323 TTTTCACAATTTTTAATA
1 TTTTTACAATTTTTAATA
46875341 TTTT
1 TTTT
46875345 AAATAGTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
17 7 0.23
18 17 0.55
19 7 0.23
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTTACAATTTTTAATA
Found at i:46875385 original size:22 final size:22
Alignment explanation
Indices: 46875356--46875399 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
46875346 AATAGTTTTA
*
46875356 TTTTTTTTTCAAATTTTTATAAG
1 TTTTTTTTAC-AATTTTTATAAG
*
46875379 TTTTTTTTACATTTTTTATAA
1 TTTTTTTTACAATTTTTATAA
46875400 TGATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTTTTTACAATTTTTATAAG
Found at i:46875449 original size:17 final size:17
Alignment explanation
Indices: 46875408--46875471 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 17
46875398 AATGATATTA
*
46875408 TTAATTTCAACTT-TTTT
1 TTAATTT-ATCTTATTTT
46875425 TTACATTTATCTTATTTT
1 TTA-ATTTATCTTATTTT
*
46875443 TTAATTTATATATATATTT
1 TTAATTTATCT-TAT-TTT
46875462 TATAATTTAT
1 T-TAATTTAT
46875472 ATGTTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
17 14 0.35
18 14 0.35
19 4 0.10
20 8 0.20
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TTAATTTATCTTATTTT
Found at i:46875462 original size:18 final size:18
Alignment explanation
Indices: 46875422--46875473 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
46875412 TTTCAACTTT
*
46875422 TTTTTACATTTATCTTAT-
1 TTTTTA-ATTTATATTATA
46875440 TTTTTAATTTATATATATA
1 TTTTTAATTTATAT-TATA
46875459 TTTTATAATTTATAT
1 TTTT-TAATTTATAT
46875474 GTTTTTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 7 0.23
18 9 0.30
19 4 0.13
20 10 0.33
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTAATTTATATTATA
Found at i:46875480 original size:18 final size:18
Alignment explanation
Indices: 46875421--46875499 Score: 72
Period size: 19 Copynumber: 4.2 Consensus size: 18
46875411 ATTTCAACTT
*
46875421 TTTTTTACATTTATCT-TA
1 TTTTTTA-ATTTATATATA
46875439 TTTTTTAATTTATATATA
1 TTTTTTAATTTATATATA
* *
46875457 TATTTTATAATTTATATGTT
1 T-TTTT-TAATTTATATATA
46875477 TTTTTCTAGA-TTATATATA
1 TTTTT-TA-ATTTATATATA
46875496 TTTT
1 TTTT
46875500 CACGAATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
17 7 0.14
18 10 0.20
19 21 0.41
20 13 0.25
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTTAATTTATATATA
Found at i:46879370 original size:43 final size:45
Alignment explanation
Indices: 46879285--46879370 Score: 104
Period size: 45 Copynumber: 2.0 Consensus size: 45
46879275 AATTATAAGA
* * *
46879285 AATATCATTAAAAAGTTAAAATTAATATTATGAAAATTTATATGC
1 AATATCATTAAAAAATTAAAATTAATATTATCAAAATATATATGC
** *
46879330 AATATCATTAAAAAATTACCA-T-ATATTATCACAATATATAT
1 AATATCATTAAAAAATTAAAATTAATATTATCAAAATATATAT
46879371 ATATCAAGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
43 16 0.46
44 1 0.03
45 18 0.51
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.37
Consensus pattern (45 bp):
AATATCATTAAAAAATTAAAATTAATATTATCAAAATATATATGC
Found at i:46893961 original size:50 final size:52
Alignment explanation
Indices: 46893835--46893966 Score: 146
Period size: 50 Copynumber: 2.6 Consensus size: 52
46893825 ATGAACAAAT
* *
46893835 GAGTTACTTAATGCA-AGACTTAATTTAATGATGCAGACTTAAACTAACATGA
1 GAGTTACATAATGCATA-ACTTTATTTAATGATGCAGACTTAAACTAACATGA
** * * *
46893887 GAGTTACATAATGCATGTCATTATTT-ATGATGCATACTT-AACTAGCATG-
1 GAGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGA
*
46893936 GAAGTTACATAATGCATAACTTTATTAAATG
1 G-AGTTACATAATGCATAACTTTATTTAATG
46893967 CAGAACACAC
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
49 1 0.02
50 30 0.45
51 15 0.23
52 20 0.30
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (52 bp):
GAGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGA
Found at i:46897475 original size:283 final size:282
Alignment explanation
Indices: 46896953--46897517 Score: 1112
Period size: 283 Copynumber: 2.0 Consensus size: 282
46896943 TTATTATATA
46896953 AAGTCTTAAGTTCTTGATATATTAGTGAAGAGAAATAAGTGAAAGTGATGTGAAATATTATAGAG
1 AAGTCTTAAGTTCTTGATATATTAGTGAAGAGAAATAAGTGAAAGTGATGTGAAATATTATAGAG
46897018 AAAGGGAATAAGGAAGTTATAAACTTAGTAATTAACATTTTGCACTAAAACAGTTTGGACAACAG
66 AAAGGGAATAAGGAAGTTATAAACTTAGTAATTAACATTTTGCACTAAAACAGTTTGGACAACAG
46897083 AAGTAGGTTAACTTTGAAAAATCACCATAAATTGTGGAAATGAAATTAGAGGATGAAAAAAATAT
131 AAGTAGGTTAACTTTGAAAAATCACCATAAATTGTGGAAATGAAATTAGAGGATGAAAAAAATAT
46897148 TGAATTAAATCTTACTGAGCCTAGTTTCTCATAGAAGAAACGTTGTAAGTAATGGAATTTTAAAT
196 TGAATTAAATCTTACTGAGCCTAGTTTCTCATAGAAGAAACGTTGTAAGTAATGGAATTTTAAAT
46897213 CATGAGATATAATAGATTTTGT
261 CATGAGATATAATAGATTTTGT
46897235 AAGTCTTAAGTTCTTGATATATTAGTGAAGAGAAATAAGTGAAAGTGATGTGAAATATTATAGAG
1 AAGTCTTAAGTTCTTGATATATTAGTGAAGAGAAATAAGTGAAAGTGATGTGAAATATTATAGAG
46897300 AAAGGGAATAAGGAAGTTATAAACTTAGTAATTAACATTTTGCACTAAAACAGTTTTGGACAACA
66 AAAGGGAATAAGGAAGTTATAAACTTAGTAATTAACATTTTGCACTAAAACAG-TTTGGACAACA
46897365 GAAGTAGGTTAACTTTGAAAAATCACCATAAATTGTGGAAATGAAATTAGAGGATGAAAAAAATA
130 GAAGTAGGTTAACTTTGAAAAATCACCATAAATTGTGGAAATGAAATTAGAGGATGAAAAAAATA
*
46897430 TTTAATTAAATCTTACTGAGCCTAGTTTCTCATAGAAGAAACGTTGTAAGTAATGGAATTTTAAA
195 TTGAATTAAATCTTACTGAGCCTAGTTTCTCATAGAAGAAACGTTGTAAGTAATGGAATTTTAAA
46897495 TCATGAGATATAATAGATTTTGT
260 TCATGAGATATAATAGATTTTGT
46897518 GATATAAGGT
Statistics
Matches: 281, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
282 118 0.42
283 163 0.58
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.31
Consensus pattern (282 bp):
AAGTCTTAAGTTCTTGATATATTAGTGAAGAGAAATAAGTGAAAGTGATGTGAAATATTATAGAG
AAAGGGAATAAGGAAGTTATAAACTTAGTAATTAACATTTTGCACTAAAACAGTTTGGACAACAG
AAGTAGGTTAACTTTGAAAAATCACCATAAATTGTGGAAATGAAATTAGAGGATGAAAAAAATAT
TGAATTAAATCTTACTGAGCCTAGTTTCTCATAGAAGAAACGTTGTAAGTAATGGAATTTTAAAT
CATGAGATATAATAGATTTTGT
Found at i:46899673 original size:20 final size:20
Alignment explanation
Indices: 46899628--46899673 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
46899618 CTATTTCAAA
46899628 AATAATATTAATTTAATAAT
1 AATAATATTAATTTAATAAT
**
46899648 TTTAATATTAAATTTAAT-AT
1 AATAATATT-AATTTAATAAT
46899668 AATAAT
1 AATAAT
46899674 TTTCTTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAATATTAATTTAATAAT
Found at i:46900500 original size:22 final size:22
Alignment explanation
Indices: 46900472--46900514 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
46900462 TTATGTTGTT
46900472 TTGCTACCATTTCATTATTATA
1 TTGCTACCATTTCATTATTATA
* * *
46900494 TTGCTACTATTTTATTGTTAT
1 TTGCTACCATTTCATTATTAT
46900515 TGTATGGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (22 bp):
TTGCTACCATTTCATTATTATA
Found at i:46912829 original size:45 final size:45
Alignment explanation
Indices: 46912765--46912937 Score: 188
Period size: 45 Copynumber: 3.8 Consensus size: 45
46912755 TTGGTTTGAA
* * *
46912765 GGAAATGATTAAGACCATAGTTGAAAGACACTATGGCACTATACC
1 GGAAATGAATAAGACCATAGTTGAAAGACATTATGGCACCATACC
*
46912810 GGAAATAAATAAGACCATAGTTGAAAGACATTATGGCACCATACC
1 GGAAATGAATAAGACCATAGTTGAAAGACATTATGGCACCATACC
* * * * * *
46912855 AGAAACGAGTAAGACTATAGCTGAAAGACATTATGGCACCATGATTC
1 GGAAATGAATAAGACCATAGTTGAAAGACATTATGGCACCAT-A-CC
* * * *
46912902 --TATTGAGTAAGACCATAGTTGAAAGACGTTATGGCA
1 GGAAATGAATAAGACCATAGTTGAAAGACATTATGGCA
46912938 TCACGATTCT
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
45 107 0.98
46 1 0.01
47 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (45 bp):
GGAAATGAATAAGACCATAGTTGAAAGACATTATGGCACCATACC
Found at i:46912946 original size:45 final size:45
Alignment explanation
Indices: 46912860--46912985 Score: 171
Period size: 45 Copynumber: 2.8 Consensus size: 45
46912850 ATACCAGAAA
* * * *
46912860 CGAGTAAGACTATAGCTGAAAGACATTATGGCACCATGATTCTAT
1 CGAGTAAGACCATAGCTGAAAGACGTTATGGCATCACGATTCTAT
* *
46912905 TGAGTAAGACCATAGTTGAAAGACGTTATGGCATCACGATTCTAT
1 CGAGTAAGACCATAGCTGAAAGACGTTATGGCATCACGATTCTAT
* * *
46912950 CGAGTAAGACCATAGCTAAAAGATGCTATGGCATCA
1 CGAGTAAGACCATAGCTGAAAGACGTTATGGCATCA
46912986 TGAACCAAAC
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (45 bp):
CGAGTAAGACCATAGCTGAAAGACGTTATGGCATCACGATTCTAT
Found at i:46913003 original size:45 final size:45
Alignment explanation
Indices: 46912909--46913024 Score: 106
Period size: 45 Copynumber: 2.6 Consensus size: 45
46912899 TTCTATTGAG
* * * ** * * *
46912909 TAAGACCATAGTTGAAAGACGTTATGGCATCACGATTCTATCGAG
1 TAAGACCATAGCTAAAAGACGCTATGGCATCACGAACCAAACGAA
* *
46912954 TAAGACCATAGCTAAAAGATGCTATGGCATCATGAACCAAACGAA
1 TAAGACCATAGCTAAAAGACGCTATGGCATCACGAACCAAACGAA
* * * *
46912999 TAAGACTATAGTTGAAAGACACTATG
1 TAAGACCATAGCTAAAAGACGCTATG
46913025 ACAACACAAG
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (45 bp):
TAAGACCATAGCTAAAAGACGCTATGGCATCACGAACCAAACGAA
Found at i:46927558 original size:20 final size:21
Alignment explanation
Indices: 46927533--46927572 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
46927523 GTGTTTCCCT
*
46927533 TTTTTTTACTT-TTTCGAAAA
1 TTTTTTGACTTATTTCGAAAA
*
46927553 TTTTTTGATTTATTTCGAAA
1 TTTTTTGACTTATTTCGAAA
46927573 TGGTCCTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTTTTGACTTATTTCGAAAA
Found at i:46936772 original size:28 final size:28
Alignment explanation
Indices: 46936740--46936797 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
46936730 CTGTCACACC
*
46936740 AGAAACCGGATTATTAGCAACAAGCCTA
1 AGAAACCAGATTATTAGCAACAAGCCTA
46936768 AGAAACCAGATTATTAGCAACAAGCCTA
1 AGAAACCAGATTATTAGCAACAAGCCTA
46936796 AG
1 AG
46936798 GGACAAAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (28 bp):
AGAAACCAGATTATTAGCAACAAGCCTA
Found at i:46941412 original size:7 final size:7
Alignment explanation
Indices: 46941400--46941444 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
46941390 TATAAAAGCT
46941400 AATATTA
1 AATATTA
46941407 AATATTA
1 AATATTA
46941414 AATATTA
1 AATATTA
46941421 AATATTA
1 AATATTA
* *
46941428 AATCTCA
1 AATATTA
46941435 AAT-TTA
1 AATATTA
46941441 AATA
1 AATA
46941445 AAATATAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (7 bp):
AATATTA
Found at i:46949034 original size:12 final size:12
Alignment explanation
Indices: 46949005--46949041 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
46948995 TATTTCAATC
46949005 AAAATTTTAT-T
1 AAAATTTTATAT
*
46949016 TAAATTTTATAT
1 AAAATTTTATAT
46949028 AAAATTTTA-AT
1 AAAATTTTATAT
46949039 AAA
1 AAA
46949042 TAATAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AAAATTTTATAT
Found at i:46950445 original size:27 final size:28
Alignment explanation
Indices: 46950400--46950455 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
46950390 GACAAAAAAT
*
46950400 AAAAAATAAAACTGCTTAAAGAAACAAA
1 AAAAAATAAAACTGCTTAAAAAAACAAA
46950428 AAAAAATAAAACTG-TTAAAAAAACAAA
1 AAAAAATAAAACTGCTTAAAAAAACAAA
46950455 A
1 A
46950456 CTGATGGGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.71, C:0.09, G:0.05, T:0.14
Consensus pattern (28 bp):
AAAAAATAAAACTGCTTAAAAAAACAAA
Found at i:46954471 original size:48 final size:48
Alignment explanation
Indices: 46954401--46954502 Score: 150
Period size: 48 Copynumber: 2.1 Consensus size: 48
46954391 TTACGTAATC
* * *
46954401 TAATGTACCTAATTTATATTACAAAGTTTGTTCCAATTTTTAATATTG
1 TAATGTACCTAATTTATATTACAAAATTTGTTCCAAGTTGTAATATTG
** *
46954449 TAATGTATTTAATTTATATTACAAAATTTGTTCCAAGTTGTAATGTTG
1 TAATGTACCTAATTTATATTACAAAATTTGTTCCAAGTTGTAATATTG
46954497 TAATGT
1 TAATGT
46954503 TGCAATTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (48 bp):
TAATGTACCTAATTTATATTACAAAATTTGTTCCAAGTTGTAATATTG
Found at i:46959902 original size:2 final size:2
Alignment explanation
Indices: 46959895--46959940 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
46959885 ACCTACATAA
46959895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46959937 AT AT
1 AT AT
46959941 TAAAATAATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46974266 original size:15 final size:15
Alignment explanation
Indices: 46974246--46974276 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
46974236 GCAATCCATA
46974246 CTTGAAACATTAGGT
1 CTTGAAACATTAGGT
46974261 CTTGAAACATTAGGT
1 CTTGAAACATTAGGT
46974276 C
1 C
46974277 CATCTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (15 bp):
CTTGAAACATTAGGT
Found at i:46975708 original size:15 final size:17
Alignment explanation
Indices: 46975688--46975728 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
46975678 AGAGTCTATT
46975688 TTATTATTTTAA-A-AA
1 TTATTATTTTAATATAA
*
46975703 TTATTAATTTAATTATAA
1 TTATTATTTTAA-TATAA
46975721 TTATTATT
1 TTATTATT
46975729 AAATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 11 0.52
17 1 0.05
18 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTATTTTAATATAA
Found at i:46978900 original size:13 final size:14
Alignment explanation
Indices: 46978877--46978905 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
46978867 AGGGTTTTAG
46978877 TAAAAATATAGATT
1 TAAAAATATAGATT
46978891 TAAAAA-ATAGATT
1 TAAAAATATAGATT
46978904 TA
1 TA
46978906 GATAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (14 bp):
TAAAAATATAGATT
Found at i:46984472 original size:42 final size:42
Alignment explanation
Indices: 46984408--46984491 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
46984398 ATTGAGTCTT
*
46984408 AGCTTAATTAACATGAGCATTTTTGTCAATGCAGGAAGCAAG
1 AGCTTAATTAACATGAGAATTTTTGTCAATGCAGGAAGCAAG
46984450 AGCTTAATTAACATGAGAATTTTTGTCAATGCAGGAAGCAAG
1 AGCTTAATTAACATGAGAATTTTTGTCAATGCAGGAAGCAAG
46984492 GGCGAAGCCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (42 bp):
AGCTTAATTAACATGAGAATTTTTGTCAATGCAGGAAGCAAG
Found at i:46989721 original size:5 final size:6
Alignment explanation
Indices: 46989702--46989749 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
46989692 TCCATGCATC
*
46989702 TTTCTT TTTCTT TTTCTT TTT-AT TTTCTT CCTTCTCTT TTTCTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT --TT-TCTT TTTCTT TTTC
46989750 CTACCTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
5 4 0.11
6 24 0.67
7 2 0.06
8 2 0.06
9 4 0.11
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:46991761 original size:105 final size:101
Alignment explanation
Indices: 46991582--46991775 Score: 271
Period size: 105 Copynumber: 1.9 Consensus size: 101
46991572 GACGGATAAG
* * *
46991582 ACCATGGTTGGACCATGGCAGTGTTTAAATGTAAGACCATAGATGGGCTATGGCATTTTAATGAA
1 ACCATGGTTGGACCATGGCAGTATTTAAATGTAAGACCATAGATGGGCTATAGCATTCTAATGAA
*
46991647 AAGATCATAACTAGGTTATGACACCTTGAATGTAAA
66 AAGACCATAACTAGGTTATGACACCTTGAATGTAAA
* * *
46991683 ACCATGGTTGGACCATGGCAGTATATATACATGTGTAAGACCATAGCTGGGCTATAGCATTCTGA
1 ACCATGGTTGGACCATGGCAGTAT-T-TA-A-ATGTAAGACCATAGATGGGCTATAGCATTCTAA
* *
46991748 TGATAAGACCATAACTGGGTTATGACAC
62 TGAAAAGACCATAACTAGGTTATGACAC
46991776 TACAAATGTA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
101 23 0.29
102 1 0.01
103 2 0.03
104 1 0.01
105 53 0.66
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (101 bp):
ACCATGGTTGGACCATGGCAGTATTTAAATGTAAGACCATAGATGGGCTATAGCATTCTAATGAA
AAGACCATAACTAGGTTATGACACCTTGAATGTAAA
Found at i:46991804 original size:105 final size:105
Alignment explanation
Indices: 46991611--46991807 Score: 261
Period size: 105 Copynumber: 1.9 Consensus size: 105
46991601 AGTGTTTAAA
* * * **
46991611 TGTAAGACCATAGATGGGCTATGGCATTTTAATGAAAAGATCATAACTAGGTTATGACACCTTGA
1 TGTAAGACCATAGATGGGCTATAGCATTCTAATGAAAAGACCATAACTAGGTTATGACACCTCAA
**
46991676 ATGTAAAACCATGGTTGGACCATGGCAGTATATATACATG
66 ATGTAAAACCATGGCAGGACCATGGCAGTATATATACATG
* * * *
46991716 TGTAAGACCATAGCTGGGCTATAGCATTCTGATGATAAGACCATAACTGGGTTATGACA-CTACA
1 TGTAAGACCATAGATGGGCTATAGCATTCTAATGAAAAGACCATAACTAGGTTATGACACCT-CA
* *
46991780 AATGTAAGACCATGGCAGGGCCATGGCA
65 AATGTAAAACCATGGCAGGACCATGGCA
46991808 ATGCATGTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
104 2 0.03
105 76 0.97
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (105 bp):
TGTAAGACCATAGATGGGCTATAGCATTCTAATGAAAAGACCATAACTAGGTTATGACACCTCAA
ATGTAAAACCATGGCAGGACCATGGCAGTATATATACATG
Found at i:46992659 original size:72 final size:72
Alignment explanation
Indices: 46992568--46992725 Score: 244
Period size: 72 Copynumber: 2.2 Consensus size: 72
46992558 GCGTGTAGTC
* * * *
46992568 TGGCCGTGTGGCCCTTGCACCTTAATTTCATAAATTAGTTACCCACACGGCCTGACATACGAGCG
1 TGGCCGTGTGACCCCTGCACCTTAATTTCATAAATTAGTTACCCACACGGCCTGACACACGAGCA
*
46992633 TGTGACT
66 TGTAACT
* * *
46992640 TGGCCGTGTGACCCCTGCACCTTAATTTTATAAATTAGTTACCCACACGGCCTGGCACACGGGCA
1 TGGCCGTGTGACCCCTGCACCTTAATTTCATAAATTAGTTACCCACACGGCCTGACACACGAGCA
46992705 TGTAACT
66 TGTAACT
46992712 TGGCCGTGTGACCC
1 TGGCCGTGTGACCC
46992726 AAGTCAGAGA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 78 1.00
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.27
Consensus pattern (72 bp):
TGGCCGTGTGACCCCTGCACCTTAATTTCATAAATTAGTTACCCACACGGCCTGACACACGAGCA
TGTAACT
Found at i:46997097 original size:51 final size:51
Alignment explanation
Indices: 46997021--46997119 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
46997011 CGTGCAACAT
* *
46997021 CAACATTATCCAATCTATCTGATGTTGCAAAATCACCAGCTTATTCATAAA
1 CAACATTATCCAATCCATCTGATGTTGCAAAATCACCAGCATATTCATAAA
* * *
46997072 CAACATTATCCACTCCATTTGATGTTGTAAAATCACCAGCATATTCAT
1 CAACATTATCCAATCCATCTGATGTTGCAAAATCACCAGCATATTCAT
46997120 CAGCAGCAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (51 bp):
CAACATTATCCAATCCATCTGATGTTGCAAAATCACCAGCATATTCATAAA
Found at i:46997361 original size:33 final size:33
Alignment explanation
Indices: 46997302--46997364 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
46997292 ATCTCCTTCA
* *
46997302 CCATCAGATTCTACCCCTTCATCATCACCCTCC
1 CCATCAGATTCCACCCCTTCAACATCACCCTCC
* *
46997335 CCATCAGCTTCCACCCTTTCAACATCACCC
1 CCATCAGATTCCACCCCTTCAACATCACCC
46997365 CTCAATAGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.22, C:0.49, G:0.03, T:0.25
Consensus pattern (33 bp):
CCATCAGATTCCACCCCTTCAACATCACCCTCC
Found at i:46998147 original size:117 final size:117
Alignment explanation
Indices: 46997975--46998185 Score: 332
Period size: 117 Copynumber: 1.8 Consensus size: 117
46997965 GGTAACAGAA
* * * *
46997975 ATCAACATCATCGGAACCACTGTCGCATCACAAATCGACAAAACAAACCCTACATTATGGCACTA
1 ATCAACAACATCGGAACCACTATCGCATAAAAAATCGACAAAACAAACCCTACATTATGGCACTA
*
46998040 AAATTGCAACAATAAATCACAATTAACCATCTACAATTTTGACAACAGTTTT
66 AAATTGCAACAATAAATCACAAATAACCATCTACAATTTTGACAACAGTTTT
* * *
46998092 ATCAACAACATCGGGACCACTATCGCATAAAAAATCGACAAAACAAACCCTACATTGTGGCACTG
1 ATCAACAACATCGGAACCACTATCGCATAAAAAATCGACAAAACAAACCCTACATTATGGCACTA
* *
46998157 AAATTGTAATAATAAATCACAAATAACCA
66 AAATTGCAACAATAAATCACAAATAACCA
46998186 ACAAATCAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 84 1.00
ACGTcount: A:0.44, C:0.25, G:0.09, T:0.22
Consensus pattern (117 bp):
ATCAACAACATCGGAACCACTATCGCATAAAAAATCGACAAAACAAACCCTACATTATGGCACTA
AAATTGCAACAATAAATCACAAATAACCATCTACAATTTTGACAACAGTTTT
Found at i:46998393 original size:16 final size:16
Alignment explanation
Indices: 46998372--46998416 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
46998362 GAATGCTAAC
*
46998372 GATTTAGAGATTTTAA
1 GATTTAGAGATTTGAA
*
46998388 GATTTAGGGATTTGAA
1 GATTTAGAGATTTGAA
*
46998404 AATTTTAGAGATT
1 GA-TTTAGAGATT
46998417 CAACAAAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (16 bp):
GATTTAGAGATTTGAA
Found at i:47010189 original size:23 final size:22
Alignment explanation
Indices: 47010136--47010194 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
47010126 TAAATATTAG
*
47010136 TTTATTAATATTTTAATTTGAT
1 TTTATTAATATATTAATTTGAT
* *
47010158 TTTTTTAATGATATT-ATTTTAT
1 TTTATTAAT-ATATTAATTTGAT
*
47010180 TGTTATTAATTTATT
1 T-TTATTAATATATT
47010195 TAGTATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTATTAATATATTAATTTGAT
Found at i:47012230 original size:45 final size:45
Alignment explanation
Indices: 47012166--47012338 Score: 172
Period size: 45 Copynumber: 3.9 Consensus size: 45
47012156 TACTGAGTAT
* **
47012166 CATTGATTATAAAGGTGGTTGTTATGTGTTGATTCCACCGGGTAC
1 CATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCGGAAAC
* * * *
47012211 CATTGATTATTAAGGTGGTTGTTATGTGCTGACTCCACTGGAAAT
1 CATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCGGAAAC
** * * * *
47012256 CATTGAAAATAAAAGTGGTTGCTATGTGCTGATTCCA-CTGAATAT
1 CATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCGGAA-AC
* * *
47012301 AATTGATTATAAGGGTGG-TGCTATGTGCTGA-TCCACCG
1 CATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCG
47012339 TGTAACGGTT
Statistics
Matches: 105, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
43 4 0.04
44 17 0.16
45 84 0.80
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (45 bp):
CATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCGGAAAC
Found at i:47012318 original size:90 final size:88
Alignment explanation
Indices: 47012164--47012336 Score: 213
Period size: 90 Copynumber: 1.9 Consensus size: 88
47012154 TGTACTGAGT
** * * * ** *
47012164 ATCATTGATTATAAAGGTGGTTGTTATGTGTTGATTCCACCGGGTACCATTGATTATTAAGGTGG
1 ATCATTGAAAATAAAAGTGGTTGCTATGTGCTGATTCCACCGAATACAATTGATTATTAAGGTGG
*
47012229 TTGTTATGTGCTGACTCCACTGGAA
66 -TGCTATGTGCTGA-TCCACTGGAA
* *
47012254 ATCATTGAAAATAAAAGTGGTTGCTATGTGCTGATTCCACTGAATATAATTGATTA-TAAGGGTG
1 ATCATTGAAAATAAAAGTGGTTGCTATGTGCTGATTCCACCGAATACAATTGATTATTAA-GGTG
47012318 GTGCTATGTGCTGATCCAC
65 GTGCTATGTGCTGATCCAC
47012337 CGTGTAACGG
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
88 5 0.07
89 15 0.21
90 51 0.72
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (88 bp):
ATCATTGAAAATAAAAGTGGTTGCTATGTGCTGATTCCACCGAATACAATTGATTATTAAGGTGG
TGCTATGTGCTGATCCACTGGAA
Found at i:47018190 original size:15 final size:15
Alignment explanation
Indices: 47018170--47018203 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
47018160 CTAAAAGCTC
*
47018170 TTATTGTGACCATTG
1 TTATTGTCACCATTG
47018185 TTATTGTCACCATTG
1 TTATTGTCACCATTG
47018200 TTAT
1 TTAT
47018204 CGACCAGAGT
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:0.15, T:0.50
Consensus pattern (15 bp):
TTATTGTCACCATTG
Found at i:47018643 original size:19 final size:18
Alignment explanation
Indices: 47018604--47018647 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
47018594 TTTTAAATTT
*
47018604 AAAA-ATTAAAAATCATT
1 AAAATATTAAAAATCATA
*
47018621 AAAATATTATAAAATTATA
1 AAAATATTA-AAAATCATA
47018640 AAAATATT
1 AAAATATT
47018648 TTTAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 4 0.17
19 15 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATATTAAAAATCATA
Found at i:47019152 original size:14 final size:14
Alignment explanation
Indices: 47019133--47019162 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
47019123 TCTAAAATAG
*
47019133 AATTTTTTTATTTT
1 AATTTTTTAATTTT
47019147 AATTTTTTAATTTT
1 AATTTTTTAATTTT
47019161 AA
1 AA
47019163 AATTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
AATTTTTTAATTTT
Found at i:47019236 original size:30 final size:29
Alignment explanation
Indices: 47019180--47019236 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
47019170 AATTAATAAA
*
47019180 AATAAAATTATAATTTAACCTTTAAAAGT
1 AATAAAATTATAATTTAACATTTAAAAGT
* *
47019209 AATAAAATTTTAATTTAATTATTTAAAA
1 AATAAAATTATAATTTAA-CATTTAAAA
47019237 ATTACATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (29 bp):
AATAAAATTATAATTTAACATTTAAAAGT
Found at i:47028053 original size:190 final size:190
Alignment explanation
Indices: 47027730--47028110 Score: 708
Period size: 190 Copynumber: 2.0 Consensus size: 190
47027720 ACTTCCAATC
*
47027730 AGCGAACTTTAGGTAAGCTTCAGAATTGGGTTACTAATCAGATATTCCAACTTTCTTTCTTAACA
1 AGCGAACTTTAGGTAAGCCTCAGAATTGGGTTACTAATCAGATATTCCAACTTTCTTTCTTAACA
47027795 ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTATGATGGCAACGATCCCAGCGTGGAAT
66 ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTATGATGGCAACGATCCCAGCGTGGAAT
47027860 CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAGTG
131 CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAGTG
47027920 AGCGAACTTTAGGTAAGCCTCAGAATTGGGTTACTAATCAGATATTCCAACTTTCTTTCTTAACA
1 AGCGAACTTTAGGTAAGCCTCAGAATTGGGTTACTAATCAGATATTCCAACTTTCTTTCTTAACA
* * *
47027985 ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTGTTATGGCAACGATCCCAGCTTGGAAT
66 ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTATGATGGCAACGATCCCAGCGTGGAAT
* *
47028050 CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAACCCAAACTCTAAAAGTG
131 CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAGTG
47028110 A
1 A
47028111 CGGCAAGAAG
Statistics
Matches: 185, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
190 185 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (190 bp):
AGCGAACTTTAGGTAAGCCTCAGAATTGGGTTACTAATCAGATATTCCAACTTTCTTTCTTAACA
ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTATGATGGCAACGATCCCAGCGTGGAAT
CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAGTG
Found at i:47029474 original size:24 final size:23
Alignment explanation
Indices: 47029441--47029522 Score: 76
Period size: 26 Copynumber: 3.4 Consensus size: 23
47029431 AATTTGGATT
*
47029441 AAAAAAATTTAAGTACCAAA-TTA
1 AAAAAAATTTAA-CACCAAATTTA
*
47029464 AAAAAATATTTAACATCAAATTTAAA
1 AAAAAA-ATTTAACACCAAATTT--A
* *
47029490 AAAAAAACTTAAAAACCAAATTTA
1 AAAAAAA-TTTAACACCAAATTTA
47029514 AAAAAAATT
1 AAAAAAATT
47029523 GTGAAGGTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
23 13 0.27
24 16 0.33
25 1 0.02
26 19 0.39
ACGTcount: A:0.65, C:0.09, G:0.01, T:0.26
Consensus pattern (23 bp):
AAAAAAATTTAACACCAAATTTA
Found at i:47029491 original size:25 final size:26
Alignment explanation
Indices: 47029455--47029521 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
47029445 AAATTTAAGT
* *
47029455 ACCAAA-TT-AAAAAAATA-TTTAAC
1 ACCAAATTTAAAAAAAATACTTAAAA
* *
47029478 ATCAAATTTAAAAAAAAAACTTAAAA
1 ACCAAATTTAAAAAAAATACTTAAAA
47029504 ACCAAATTTAAAAAAAAT
1 ACCAAATTTAAAAAAAAT
47029522 TGTGAAGGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
23 5 0.14
24 2 0.06
25 8 0.23
26 20 0.57
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (26 bp):
ACCAAATTTAAAAAAAATACTTAAAA
Found at i:47031198 original size:14 final size:13
Alignment explanation
Indices: 47031152--47031216 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 13
47031142 TCATAATAAC
47031152 TAATTAATTTAATT
1 TAATT-ATTTAATT
47031166 TAATT-TTTAAACTT
1 TAATTATTT-AA-TT
*
47031180 CAATTATTTAATT
1 TAATTATTTAATT
*
47031193 ATAATTAATTAA-T
1 -TAATTATTTAATT
*
47031206 TAATAATTTAA
1 TAATTATTTAA
47031217 AAAAATTCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
12 12 0.29
13 5 0.12
14 22 0.52
15 3 0.07
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATTATTTAATT
Found at i:47035177 original size:42 final size:42
Alignment explanation
Indices: 47035039--47035193 Score: 143
Period size: 42 Copynumber: 3.7 Consensus size: 42
47035029 CCAAAGGCTG
* ** * * *
47035039 AATAGAAGCTCATGAGAGCTAAATGGAAACCCATAAGGGTTG
1 AATAGAAACTCAAAAGAGCTGAACGGAAACCCATAAGGGTTA
* * ** * *
47035081 AATTGAAGCTCGTAAGAGCTGAACGAAAACTCATAAGGGTTA
1 AATAGAAACTCAAAAGAGCTGAACGGAAACCCATAAGGGTTA
*
47035123 AACA-AAAGCTCAAAAGAGCTGAACGGAAACCCA-ATAGGGTTA
1 AATAGAAA-CTCAAAAGAGCTGAACGGAAACCCATA-AGGGTTA
* *
47035165 AATAGAAACTCAAAAGTGCTGAACAGAAA
1 AATAGAAACTCAAAAGAGCTGAACGGAAA
47035194 GAAAACACGA
Statistics
Matches: 92, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
41 3 0.03
42 86 0.93
43 3 0.03
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (42 bp):
AATAGAAACTCAAAAGAGCTGAACGGAAACCCATAAGGGTTA
Found at i:47035192 original size:21 final size:21
Alignment explanation
Indices: 47035094--47035193 Score: 60
Period size: 21 Copynumber: 4.8 Consensus size: 21
47035084 TGAAGCTCGT
*
47035094 AAGAGCTGAAC-GAAAACTCAT
1 AAGAGCTGAACAG-AAACTCAA
* * *
47035115 AAGGGTTAAACA-AAAGCTCAA
1 AAGAGCTGAACAGAAA-CTCAA
* *
47035136 AAGAGCTGAACGGAAACCCAA
1 AAGAGCTGAACAGAAACTCAA
* * * * *
47035157 TAGGGTTAAATAGAAACTCAA
1 AAGAGCTGAACAGAAACTCAA
*
47035178 AAGTGCTGAACAGAAA
1 AAGAGCTGAACAGAAA
47035194 GAAAACACGA
Statistics
Matches: 55, Mismatches: 21, Indels: 6
0.67 0.26 0.07
Matches are distributed among these distances:
20 3 0.05
21 49 0.89
22 3 0.05
ACGTcount: A:0.49, C:0.16, G:0.21, T:0.14
Consensus pattern (21 bp):
AAGAGCTGAACAGAAACTCAA
Found at i:47035283 original size:24 final size:24
Alignment explanation
Indices: 47035251--47035314 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
47035241 TAATTTGCCA
47035251 TCAATTCATCCTTTGCATATACCG
1 TCAATTCATCCTTTGCATATACCG
* *
47035275 TCAATTCATCCTTTGCATTTACTG
1 TCAATTCATCCTTTGCATATACCG
47035299 TCAATTCATCCTTTGC
1 TCAATTCATCCTTTGC
47035315 CACAGAACGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.22, C:0.28, G:0.08, T:0.42
Consensus pattern (24 bp):
TCAATTCATCCTTTGCATATACCG
Found at i:47037239 original size:10 final size:11
Alignment explanation
Indices: 47037215--47037271 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
47037205 TTATATACTA
47037215 AATAAAATAAT
1 AATAAAATAAT
47037226 AATAAAAT-AT
1 AATAAAATAAT
* *
47037236 AATAAAAAAACA
1 AATAAAATAA-T
*
47037248 AATCAAAATATT
1 AAT-AAAATAAT
*
47037260 AATAAACTAAT
1 AATAAAATAAT
47037271 A
1 A
47037272 TTTATTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
10 9 0.25
11 16 0.44
12 6 0.17
13 5 0.14
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:47037239 original size:21 final size:23
Alignment explanation
Indices: 47037215--47037271 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
47037205 TTATATACTA
47037215 AATAAAATAATAAT-AAAATA-T
1 AATAAAATAATAATCAAAATATT
* *
47037236 AATAAAAAAACAAATCAAAATATT
1 AATAAAATAA-TAATCAAAATATT
*
47037260 AATAAACTAATA
1 AATAAAATAATA
47037272 TTTATTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 9 0.32
22 3 0.11
23 7 0.25
24 9 0.32
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (23 bp):
AATAAAATAATAATCAAAATATT
Found at i:47039627 original size:18 final size:18
Alignment explanation
Indices: 47039604--47039639 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
47039594 TATAAGCATA
47039604 TAATAACAATTTGCACTT
1 TAATAACAATTTGCACTT
47039622 TAATAACAATTTGCACTT
1 TAATAACAATTTGCACTT
47039640 AGCATGGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (18 bp):
TAATAACAATTTGCACTT
Done.