Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 38 of 325
Found at i:11357423 original size:11 final size:12
Alignment explanation
Indices: 11357388--11357443 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 12
11357378 TTATGTTTCA
11357388 TATTAT-TATAT
1 TATTATATATAT
*
11357399 TATT-TATTTAT
1 TATTATATATAT
11357410 TATTATATAT-T
1 TATTATATATAT
* *
11357421 TATTATGTA-AA
1 TATTATATATAT
11357432 TA-TATATATAT
1 TATTATATATAT
11357443 T
1 T
11357444 TTTAAGCGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
10 6 0.17
11 25 0.71
12 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (12 bp):
TATTATATATAT
Found at i:11357436 original size:17 final size:14
Alignment explanation
Indices: 11357396--11357426 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11357386 CATATTATTA
*
11357396 TATTATTTATTTAT
1 TATTATATATTTAT
11357410 TATTATATATTTAT
1 TATTATATATTTAT
11357424 TAT
1 TAT
11357427 GTAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATATATTTAT
Found at i:11358112 original size:126 final size:126
Alignment explanation
Indices: 11357887--11358130 Score: 434
Period size: 126 Copynumber: 1.9 Consensus size: 126
11357877 CATTGATCTT
* *
11357887 CTCTCAAAATTTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTA
1 CTCTCAAAAATTTTCAAAATAAAGGCAATGTTCAGTATTTAAAGAATTCGAAGAATCGTGCCCTA
* * *
11357952 ATGTATTGGGTTTCGTTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCA
66 ACGTACTGGGTTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCA
11358013 CTCTCAAAAATTTTCAAAATAAAGGCAATGTTCAGTATTTAAAGAATTCGAAGAATCGTGCCCTA
1 CTCTCAAAAATTTTCAAAATAAAGGCAATGTTCAGTATTTAAAGAATTCGAAGAATCGTGCCCTA
*
11358078 ACGTACTGGGTTTCGCTTTCTTTGTTTGTTTTGAATATTCGAATATCCTCTTA
66 ACGTACTGGGTTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTA
11358131 AGGCTAAAAC
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 112 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (126 bp):
CTCTCAAAAATTTTCAAAATAAAGGCAATGTTCAGTATTTAAAGAATTCGAAGAATCGTGCCCTA
ACGTACTGGGTTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCA
Found at i:11358729 original size:35 final size:35
Alignment explanation
Indices: 11358686--11358760 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
11358676 TACAATCCTT
*
11358686 TTAC-TGCATTCATTTTGGTTCAAGTCCCCTTGCA
1 TTACATGCATTCATTTTAGTTCAAGTCCCCTTGCA
*
11358720 TTACATGCATTCATTTTAGTTTAAGTCCCCTTGCA
1 TTACATGCATTCATTTTAGTTCAAGTCCCCTTGCA
11358755 TTACAT
1 TTACAT
11358761 ATTGCATGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 4 0.11
35 34 0.89
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (35 bp):
TTACATGCATTCATTTTAGTTCAAGTCCCCTTGCA
Found at i:11368458 original size:64 final size:64
Alignment explanation
Indices: 11368344--11368470 Score: 193
Period size: 64 Copynumber: 2.0 Consensus size: 64
11368334 CATTCATAGT
*
11368344 ACATCTAGTTAGGAGCATTTGATTCATCTTGATCATAGCATCCTAATTATTTGACATAAGCATC
1 ACATCTAGCTAGGAGCATTTGATTCATCTTGATCATAGCATCCTAATTATTTGACATAAGCATC
* * * *
11368408 ACATTTAGCTAGGAGCATTTGGATT-ATTTTGATCATAGCATCCTAGTTATTTGGCATAAGCAT
1 ACATCTAGCTAGGAGCATTT-GATTCATCTTGATCATAGCATCCTAATTATTTGACATAAGCAT
11368471 AGATACAGGA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 53 0.93
65 4 0.07
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (64 bp):
ACATCTAGCTAGGAGCATTTGATTCATCTTGATCATAGCATCCTAATTATTTGACATAAGCATC
Found at i:11368786 original size:45 final size:44
Alignment explanation
Indices: 11368669--11369657 Score: 309
Period size: 45 Copynumber: 22.2 Consensus size: 44
11368659 GGAGATACAG
* *
11368669 GTCTTATCTTCCTGAAGTTGCAG-GAAGCAGACTGAAAAGTTAC-A
1 GTCTTATC-TCCTGAAGTTGCAGTGGAGCAGACTGAAAA-TGACAA
* * ***
11368713 GATCTTATCTCTATGTACCGGCTA-TGGAGCAGA-TCGAAAATGACAA
1 G-TCTTATCTC-CTGAAGTTGC-AGTGGAGCAGACT-GAAAATGACAA
11368759 GTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGACA-G-CAA
1 GTCTTATCTCC-TGAAGTTGCAGTGGAGCAGACTGAA-A-ATGACAA
* * *
11368804 GTCTTATCTTCCTGAAGTTGTAG-GAAGCAGACT-AAAAGTTAC-A
1 GTCTTATC-TCCTGAAGTTGCAGTGGAGCAGACTGAAAA-TGACAA
* * * * *
11368847 GATCTTATCTCCATGTA-TCGGCTA-TGGAGTAGA-TCGGAAATGGCAA
1 G-TCTTATCTCC-TGAAGT-TGC-AGTGGAGCAGACT-GAAAATGACAA
*
11368893 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AGCAA
1 GTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTGAAAATGA-CAA
* * *
11368938 GTCTTATCTTCCTGAAGTTGCAG-GAAGCAGACTAAAAATTTAC-A
1 GTCTTATC-TCCTGAAGTTGCAGTGGAGCAGACTGAAAA-TGACAA
* * * * * **
11368982 GATTTTATCTCCATGTA-TCGGCTA-TGGAGTAGA-TCAAAAATGATGA
1 G-TCTTATCTCC-TGAAGT-TGC-AGTGGAGCAGACT-GAAAATGACAA
11369028 GTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAAAT-AGCAA
1 GTCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTGAAAATGA-CAA
* *
11369073 GTCTTA-CTTCCTGAAGTTGCA--GGA--AGCCT-AAAATTAC-A
1 GTCTTATC-TCCTGAAGTTGCAGTGGAGCAGACTGAAAATGACAA
* * * * *
11369111 GATCTTATCTCCATGTA-TCGGCTA-TGGAGCAGA-TAAAAAATGGCGA
1 G-TCTTATCTCC-TGAAGT-TGC-AGTGGAGCAGACT-GAAAATGACAA
* *** *** *
11369157 GTCTTATCT-CT-ATGTATCGGCTA-TGGAGCAGA-TTTTAGCCACTA
1 GTCTTATCTCCTGAAGT-T--GC-AGTGGAGCAGACTGAAAATGACAA
* * * *
11369201 GTCTTATCTTCCTGAAGTTGCA-AGAAGCAGACTGAAAATTTA-TA
1 GTCTTATC-TCCTGAAGTTGCAGTGGAGCAGACTGAAAA-TGACAA
*
11369245 GATCTTATCTCCAT-ATA-TCGACTA-TGGAGCAGA-TCGAAAATGACAA
1 G-TCTTATCTCC-TGA-AGTTG-C-AGTGGAGCAGACT-GAAAATGACAA
* *
11369291 GTCTTATCTCTCTGAAGTTGTAGTGGAGCAGACTGAAGAT-AGCAA
1 GTCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTGAAAATGA-CAA
* * *
11369336 GTCTTATCTTCCTGAAGTTGCAG-GAAGTAGACTG-AAATTAC-A
1 GTCTTATC-TCCTGAAGTTGCAGTGGAGCAGACTGAAAATGACAA
* * * * * ****
11369378 GATCTCATCTCCATGTA-TCGGCTA-TGGAGCAGATTAAAAATGGTGG
1 G-TCTTATCTCC-TGAAGT-TGC-AGTGGAGCAGACTGAAAATGACAA
* * *** ** **
11369424 GTCTTATCTCCATGTA-TCGGCTA-TGGAGCAGA-TTTCAACCACTG
1 GTCTTATCTCC-TGAAGT-TGC-AGTGGAGCAGACTGAAAATGACAA
* * *
11369468 GCCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGAT-AGCAA
1 GTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTGAAAATGA-CAA
* * *
11369513 GCCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AGTAA
1 GTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTGAAAATGA-CAA
* *
11369558 GTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGAT-AGCAA
1 GTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTGAAAATGA-CAA
* * * * *
11369603 GTCTTATCTTCTTGAAGTTGTAG-GAAGTAGACTGAAAATTACAA
1 GTCTTATC-TCCTGAAGTTGCAGTGGAGCAGACTGAAAATGACAA
*
11369647 ATCTTATCTCC
1 GTCTTATCTCC
11369658 ATGTATCAGC
Statistics
Matches: 723, Mismatches: 129, Indels: 187
0.70 0.12 0.18
Matches are distributed among these distances:
38 2 0.00
39 15 0.02
40 11 0.02
41 2 0.00
42 13 0.02
43 37 0.05
44 155 0.21
45 406 0.56
46 78 0.11
47 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
GTCTTATCTCCTGAAGTTGCAGTGGAGCAGACTGAAAATGACAA
Found at i:11368863 original size:134 final size:134
Alignment explanation
Indices: 11368583--11369726 Score: 1106
Period size: 134 Copynumber: 8.6 Consensus size: 134
11368573 AAATGGTGGG
* ** *** * *
11368583 TCTTATCTCCATGTATCGGCTATGGAGTAGAT-TTAAGCCACCAGCCTTATCT-CTGTGAAGTTG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGACAAGTCTTATCTCCT-TGAAGTTG
* ** * *
11368646 CAG-AGAGCAGGTTGGAGATA-CAGGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAAGT
65 CAGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAA-T
11368709 TACAGA
129 TACAGA
* *
11368715 TCTTATCTCTATGTACCGGCTATGGAGCAGATCGAAAATGACAAGTCTTATCTCCTTGAAGTTGC
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGACAAGTCTTATCTCCTTGAAGTTGC
* *
11368780 AGTGGAGCAGACTGAAGACAGCAAGTCTTATCTTCCTGAAGTTGTAGGAAGCAGACT-AAAAGTT
66 AGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAA-TT
11368844 ACAGA
130 ACAGA
* * * *
11368849 TCTTATCTCCATGTATCGGCTATGGAGTAGATCGGAAATGGCAAGTCTTATCTCCCTGAAGTTGC
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGACAAGTCTTATCTCCTTGAAGTTGC
*
11368914 AGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTAAAAATTT
66 AGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAA-TT
11368979 ACAGA
130 ACAGA
* * * **
11368984 TTTTATCTCCATGTATCGGCTATGGAGTAGATCAAAAATGATGAGTCTTATCT-CTCTGAAGTTG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGACAAGTCTTATCTCCT-TGAAGTTG
*
11369048 CAGTGGAGCAGACTGAAAATAGCAAGTCTTA-CTTCCTGAAGTTGCAGGAAGC---CT-AAAATT
65 CAGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATT
11369108 ACAGA
130 ACAGA
** * * * *
11369113 TCTTATCTCCATGTATCGGCTATGGAGCAGATAAAAAATGGCGAGTCTTATCT-CTATGTA-TCG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGACAAGTCTTATCTCCT-TGAAGT-T
* ** ** * *
11369176 GCTA-TGGAGCAGATTTTAGCCA-CTAGTCTTATCTTCCTGAAGTTGCAAGAAGCAGACTGAAAA
64 GC-AGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAA
*
11369239 TTTATAGA
128 -TTACAGA
* *
11369247 TCTTATCTCCATATATCGACTATGGAGCAGATCGAAAATGACAAGTCTTATCT-CTCTGAAGTTG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGACAAGTCTTATCTCCT-TGAAGTTG
* *
11369311 TAGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTG-AAATT
65 CAGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATT
11369375 ACAGA
130 ACAGA
* ** **** * * *
11369380 TCTCATCTCCATGTATCGGCTATGGAGCAGATTAAAAATGGTGGGTCTTATCTCCATGTA-TCGG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGACAAGTCTTATCTCCTTGAAGT-TG
* * ** ** * * * * *
11369444 CTA-TGGAGCAGATTTCAA-CCA-CTGGCCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAG
65 C-AGTGGAGCAGA-CTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAG-GAAGCAGACTGAAA
11369506 A-TAGCA-A
127 ATTA-CAGA
* * * * * * *
11369513 GCCTTATCTCCCTGAAGT-TGC-AGTGGAGCAGA-CTGAAGAT-AGTAAGTCTTATCTCCCTGAA
1 -TCTTATCTCCATGTA-TCGGCTA-TGGAGCAGATC-GAAAATGA-CAAGTCTTATCTCCTTGAA
* * * *
11369574 GTTACAGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCTTGAAGTTGTAGGAAGTAGACTGAA
61 GTTGCAGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAA
*
11369639 AATTACAAA
126 AATTACAGA
* * ** ** *
11369648 TCTTATCTCCATGTATCAGCTATTGAGCAGATCTCAGCT-ACTAGTCTTATCTTCC-TGAAGTTG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGACAAGTCTTATC-TCCTTGAAGTTG
*
11369711 CAG-GAAGCAGACTGAA
65 CAGTGGAGCAGACTGAA
11369727 AAGTTACAGA
Statistics
Matches: 837, Mismatches: 136, Indels: 78
0.80 0.13 0.07
Matches are distributed among these distances:
128 9 0.01
129 94 0.11
130 5 0.01
131 2 0.00
132 65 0.08
133 130 0.16
134 341 0.41
135 191 0.23
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (134 bp):
TCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGACAAGTCTTATCTCCTTGAAGTTGC
AGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTA
CAGA
Found at i:11369294 original size:398 final size:397
Alignment explanation
Indices: 11368583--11369726 Score: 1124
Period size: 398 Copynumber: 2.9 Consensus size: 397
11368573 AAATGGTGGG
** *** ** * *
11368583 TCTTATCTCCATGTATCGGCTATGGAGTAGATTTAAGCCACCAGCCTTATCTCTGTGAAGTTGCA
1 TCTTATCTCCATGTATCGGCTATGGAGTAGATAAAAATGATGAGTCTTATCTCTCTGAAGTTGCA
** * * *
11368648 GAGAGCAGGTTGGAGATACAGGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAAGTTACA
66 GAGAGCAGACTGAAAATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGC--ACTGAAAAGTTACA
* ** *
11368713 GATCTTATCTCTATGTACCGGCTATGGAGCAGATCGAAAATGACAAGTCTTATCTCCTTGAAGTT
129 GATCTTATCTCCATGTACCGGCTATGGAGCAGATAAAAAATGACAAGTCTTATCTCCTTGAAGTG
* *
11368778 GCAGTGGAGCAGACTGAAGACAGCAAGTCTTATCTTCCTGAAGTTGTAGGAAGCAGACTAAAAGT
194 GCAGTGGAGCAGACTGAAGACAGCAAGTCTTATCTTCCTGAAGTTGCAAGAAGCAGACTAAAAGT
* * * * *
11368843 TACAGATCTTATCTCCATGTATCGGCTATGGAGTAGATCGGAAATGGCAAGTCTTATCTCCCTGA
259 TACAGATCTTATCTCCATATATCGACTATGGAGCAGATCGAAAATGACAAGTCTTATCTCCCTGA
11368908 AGTTGCAGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTAA
324 AGTTGCAGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACT-A
11368973 AAATTTACAGA
388 AAA-TTACAGA
*
11368984 TTTTATCTCCATGTATCGGCTATGGAGTAGATCAAAAATGATGAGTCTTATCTCTCTGAAGTTGC
1 TCTTATCTCCATGTATCGGCTATGGAGTAGAT-AAAAATGATGAGTCTTATCTCTCTGAAGTTGC
*
11369049 AGTGGAGCAGACTGAAAATAGCAAGTCTTA-CTTCCTGAAGTTGCAGGAAGC-CT-AAAA-TTAC
65 AG-AGAGCAGACTGAAAATA-CAAGTCTTATCTTCCTGAAGTTGCAGGAAGCACTGAAAAGTTAC
* * * *
11369110 AGATCTTATCTCCATGTATCGGCTATGGAGCAGATAAAAAATGGCGAGTCTTATCT-CTATGTA-
128 AGATCTTATCTCCATGTACCGGCTATGGAGCAGATAAAAAATGACAAGTCTTATCTCCT-TGAAG
* ** * *
11369173 TCGGCTA-TGGAGCAGATTTTAGCCA-CTAGTCTTATCTTCCTGAAGTTGCAAGAAGCAGACTGA
192 T-GGC-AGTGGAGCAGACTGAAGACAGCAAGTCTTATCTTCCTGAAGTTGCAAGAAGCAGACT-A
* *
11369236 AAATTTATAGATCTTATCTCCATATATCGACTATGGAGCAGATCGAAAATGACAAGTCTTATCTC
254 AAAGTTACAGATCTTATCTCCATATATCGACTATGGAGCAGATCGAAAATGACAAGTCTTATCTC
* * *
11369301 TCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAG
319 CCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAG
*
11369366 ACTGAAATTACAGA
384 ACTAAAATTACAGA
* * * * * *
11369380 TCTCATCTCCATGTATCGGCTATGGAGCAGATTAAAAATGGTGGGTCTTATCTC-CATGTA-TCG
1 TCTTATCTCCATGTATCGGCTATGGAGTAGA-TAAAAATGATGAGTCTTATCTCTC-TGAAGT-T
* ** ** ** * * * *
11369443 GCTATG-GAGCAGATTTCAACCACTGGCCTTATCTCCCTGAAGTTACAGTGGAGCAGACTG--AA
63 GC-A-GAGAGCAGACTGAAAATACAAGTCTTATCTTCCTGAAGTTGCAG-GAAGC--ACTGAAAA
* * * * *** * * *
11369505 GATAGCA-AGCCTTATCTCCCTGAAGTTGC-AGTGGAGCAGACT-GAAGAT-AGTAAGTCTTATC
123 GTTA-CAGA-TCTTATCTCCATGTACCGGCTA-TGGAGCAGA-TAAAAAATGA-CAAGTCTTATC
* ** * * * * *
11369566 TCCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCTTGAAGTTGTAGGAAGT
183 TCCTTGAAGTGGCAGTGGAGCAGACTGAAGACAGCAAGTCTTATCTTCCTGAAGTTGCAAGAAGC
* * * ** ** *
11369631 AGACTGAAAA-TTACAAATCTTATCTCCATGTATC-AGCTATTGAGCAGATCTCAGCT-ACTAGT
248 AGACT-AAAAGTTACAGATCTTATCTCCATATATCGA-CTATGGAGCAGATCGAAAATGACAAGT
* *
11369693 CTTATCTTCCTGAAGTTGCAG-GAAGCAGACTGAA
311 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA
11369727 AAGTTACAGA
Statistics
Matches: 615, Mismatches: 99, Indels: 60
0.79 0.13 0.08
Matches are distributed among these distances:
395 8 0.01
396 84 0.14
397 45 0.07
398 198 0.32
399 19 0.03
400 33 0.05
401 123 0.20
402 64 0.10
403 33 0.05
404 8 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (397 bp):
TCTTATCTCCATGTATCGGCTATGGAGTAGATAAAAATGATGAGTCTTATCTCTCTGAAGTTGCA
GAGAGCAGACTGAAAATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGCACTGAAAAGTTACAGA
TCTTATCTCCATGTACCGGCTATGGAGCAGATAAAAAATGACAAGTCTTATCTCCTTGAAGTGGC
AGTGGAGCAGACTGAAGACAGCAAGTCTTATCTTCCTGAAGTTGCAAGAAGCAGACTAAAAGTTA
CAGATCTTATCTCCATATATCGACTATGGAGCAGATCGAAAATGACAAGTCTTATCTCCCTGAAG
TTGCAGTGGAGCAGACTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTAAAA
TTACAGA
Found at i:11369485 original size:267 final size:267
Alignment explanation
Indices: 11368669--11369679 Score: 1244
Period size: 267 Copynumber: 3.8 Consensus size: 267
11368659 GGAGATACAG
* * * *
11368669 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAAGTTACAGATCTTATCTCTATGTACCGG
1 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTTACAGATCTTATCTCCATATATCGG
11368734 CTATGGAGCAGATCGAAAATGACAAGTCTTATCTC-CTTGAAGTTGCAGTGGAGCAGACTGAAGA
66 CTATGGAGCAGATCGAAAATGACAAGTCTTATCTCTC-TGAAGTTGCAGTGGAGCAGACTGAAGA
* * *
11368798 CAGCAAGTCTTATCTTCCTGAAGTTGTAGGAAGCAGACTAAAAGTTACAGATCTTATCTCCATGT
130 TAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTAAAA-TTACAGATCTTATCTCCATGT
* *** * * * *
11368863 ATCGGCTATGGAGTAGATCGGAAATGGCAAGTCTTATCTCCCTGAAGT-TGC-AGTGGAGCAGA-
194 ATCGGCTATGGAGCAGATAAAAAATGGCGAGTCTTATCTCCATGTA-TCGGCTA-TGGAGCAGAT
* * ** *
11368925 CTGAAGATAGCAA
257 TTCAA-CCA-CTA
* * *
11368938 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTAAAAATTTACAGATTTTATCTCCATGTATCGG
1 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTTACAGATCTTATCTCCATATATCGG
* * ** *
11369003 CTATGGAGTAGATCAAAAATGATGAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAAAT
66 CTATGGAGCAGATCGAAAATGACAAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGAT
*
11369068 AGCAAGTCTTA-CTTCCTGAAGTTGCAGG-A--AGCCTAAAATTACAGATCTTATCTCCATGTAT
131 AGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTAAAATTACAGATCTTATCTCCATGTAT
* *
11369129 CGGCTATGGAGCAGATAAAAAATGGCGAGTCTTATCTCTATGTATCGGCTATGGAGCAGATTTTA
196 CGGCTATGGAGCAGATAAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTCA
*
11369194 GCCACTA
261 ACCACTA
* * *
11369201 GTCTTATCTTCCTGAAGTTGCAAGAAGCAGACTGAAAATTTATAGATCTTATCTCCATATATCGA
1 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTTACAGATCTTATCTCCATATATCGG
*
11369266 CTATGGAGCAGATCGAAAATGACAAGTCTTATCTCTCTGAAGTTGTAGTGGAGCAGACTGAAGAT
66 CTATGGAGCAGATCGAAAATGACAAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGAT
* *
11369331 AGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTGAAATTACAGATCTCATCTCCATGTAT
131 AGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTAAAATTACAGATCTTATCTCCATGTAT
* * *
11369396 CGGCTATGGAGCAGATTAAAAATGGTGGGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTCA
196 CGGCTATGGAGCAGATAAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTCA
*
11369461 ACCACTG
261 ACCACTA
* * * * * * *
11369468 GCCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGA--TAGCA-AGCCTTATCTCCCTGA-A
1 GTCTTATCTTCCTGAAGTTGCAG-GAAGCAGACTGAAAATTTA-CAGA-TCTTATCTCCAT-ATA
* * * * *
11369529 GT-TGC-AGTGGAGCAGA-CTGAAGAT-AGTAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGA
62 -TCGGCTA-TGGAGCAGATC-GAAAATGA-CAAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGA
* * *
11369590 CTGAAGATAGCAAGTCTTATCTTCTTGAAGTTGTAGGAAGTAGACTGAAAATTACAAATCTTATC
123 CTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAGACT-AAAATTACAGATCTTATC
* *
11369655 TCCATGTATCAGCTATTGAGCAGAT
187 TCCATGTATCGGCTATGGAGCAGAT
11369680 CTCAGCTACT
Statistics
Matches: 652, Mismatches: 73, Indels: 35
0.86 0.10 0.05
Matches are distributed among these distances:
263 132 0.20
264 88 0.13
265 12 0.02
266 6 0.01
267 216 0.33
268 69 0.11
269 128 0.20
270 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (267 bp):
GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTTACAGATCTTATCTCCATATATCGG
CTATGGAGCAGATCGAAAATGACAAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGAT
AGCAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTAAAATTACAGATCTTATCTCCATGTAT
CGGCTATGGAGCAGATAAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTCA
ACCACTA
Found at i:11369743 original size:45 final size:45
Alignment explanation
Indices: 11369515--11369744 Score: 119
Period size: 45 Copynumber: 5.2 Consensus size: 45
11369505 GATAGCAAGC
* *
11369515 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG-TA-AG-T
1 CTTATCTTCCTGAAGTTGCAG-GAAGCAGACTGAA-A-AGTTACAGAT
* * * *
11369560 CTTATCTCCCTGAAGTTACAGTGGAGCAGACTG--AAGATAGCA-AGT
1 CTTATCTTCCTGAAGTTGCAG-GAAGCAGACTGAAAAGTTA-CAGA-T
* * * *
11369605 CTTATCTTCTTGAAGTTGTAGGAAGTAGACTGAAAA-TTACAAAT
1 CTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAAGTTACAGAT
* * * * *
11369649 CTTATC-TCCATGTA-TCAGCTATTG-AGCAGATCT---CAGCTACTAG-T
1 CTTATCTTCC-TGAAGT-TGC-A-GGAAGCAGA-CTGAAAAGTTAC-AGAT
11369693 CTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAAGTTACAGAT
1 CTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAAGTTACAGAT
11369738 CTTATCT
1 CTTATCT
11369745 CCATGTATCG
Statistics
Matches: 141, Mismatches: 22, Indels: 44
0.68 0.11 0.21
Matches are distributed among these distances:
41 2 0.01
42 6 0.04
43 11 0.08
44 40 0.28
45 77 0.55
46 5 0.04
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (45 bp):
CTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAAGTTACAGAT
Found at i:11369759 original size:89 final size:88
Alignment explanation
Indices: 11369602--11369768 Score: 271
Period size: 88 Copynumber: 1.9 Consensus size: 88
11369592 GAAGATAGCA
* * *
11369602 AGTCTTATCTTCTTGAAGTTGTAGGAAGTAGACTGAAAATTACAAATCTTATCTCCATGTATCAG
1 AGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTACAAATCTTATCTCCATGTATCAG
*
11369667 CTATTGAGCAGATCTCAGCTACT
66 CTATGGAGCAGATCTCAGCTACT
* *
11369690 AGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAAGTTACAGATCTTATCTCCATGTATCG
1 AGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAA-TTACAAATCTTATCTCCATGTATCA
11369755 GCTATGGAGCAGAT
65 GCTATGGAGCAGAT
11369769 TTTAGCCACC
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
88 36 0.50
89 36 0.50
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (88 bp):
AGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTACAAATCTTATCTCCATGTATCAG
CTATGGAGCAGATCTCAGCTACT
Found at i:11369798 original size:89 final size:88
Alignment explanation
Indices: 11369617--11369801 Score: 244
Period size: 89 Copynumber: 2.1 Consensus size: 88
11369607 TATCTTCTTG
* * *
11369617 AAGTTGTAGGAAGTAGACTGAAAATTACAAATCTTATCTCCATGTATCAGCTATTGAGCAGATCT
1 AAGTTGCAGGAAGCAGACTGAAAATTACAAATCTTATCTCCATGTATCAGCTATGGAGCAGATCT
* * ** * *
11369682 CAGCTACTAGTCTTATCTTCCTG
66 CAGCCACCAACCTTATCTCCCTA
* * *
11369705 AAGTTGCAGGAAGCAGACTGAAAAGTTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATT
1 AAGTTGCAGGAAGCAGACTGAAAA-TTACAAATCTTATCTCCATGTATCAGCTATGGAGCAGATC
*
11369770 TTAGCCACCAACCTTATCTCCCTA
65 TCAGCCACCAACCTTATCTCCCTA
11369794 AAGTTGCA
1 AAGTTGCA
11369802 ATGGAGCAGG
Statistics
Matches: 83, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
88 22 0.27
89 61 0.73
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (88 bp):
AAGTTGCAGGAAGCAGACTGAAAATTACAAATCTTATCTCCATGTATCAGCTATGGAGCAGATCT
CAGCCACCAACCTTATCTCCCTA
Found at i:11372106 original size:125 final size:126
Alignment explanation
Indices: 11371703--11372146 Score: 484
Period size: 132 Copynumber: 3.5 Consensus size: 126
11371693 AACATAAGGA
* * *
11371703 AATATCTCGTATTTGGGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGTTCTTTTCATT
1 AATATTTCGTATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGAT-TTTTCATT
* * ** *
11371768 CGACTAAAATACGGAATATCCTTTGGAAATTTCGTCCATATTTTTTTTAAAAAAATTAAAATGAG
65 CGACTAAAATATGGAATATCCTTTTGAAATTTCGTCC--ACGTTTTCT---AAAATTAAAATGAG
11371833 GC
125 GC
* * * *
11371835 AATATTTCGTATTTGGGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGATTTCGTTTTTTTCGTT
1 AATATTTCGTATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCG-ATTTTTCATT
* *
11371900 CGACTAAAATATGGAATATCCTTTTTTGAAATTTTCATCCACGTTTTCTTAAAA-TAAAACGAGG
65 CGACTAAAATATGGAATATCC--TTTTGAAA-TTTCGTCCACGTTTTC-TAAAATTAAAATGAGG
11371964 C
126 C
** * * * *
11371965 AATATTTCGTGCTT-GGAAGTTTG-GGGAGTCGTGCCCAATCGTGCTGGGCTTCAATTTTCCATT
1 AATATTTCGTATTTGGGAAGTTTGAGAGA-TCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATT
** * *
11372028 CGACTAAAATATAAAATATCCTTTTGAAGTTTCGTCCACGTTTTCTGAAATTAAAATGAGGC
65 CGACTAAAATATGGAATATCCTTTTGAAATTTCGTCCACGTTTTCTAAAATTAAAATGAGGC
* * * *
11372090 AATGTTTCGTATTT-GGATA-TTCGATAAATCGTGCCCAATCGTGCTGGGTTTCGATTT
1 AATATTTCGTATTTGGGA-AGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTT
11372147 ACCGTTTGGG
Statistics
Matches: 268, Mismatches: 35, Indels: 25
0.82 0.11 0.08
Matches are distributed among these distances:
124 4 0.01
125 69 0.26
126 9 0.03
128 29 0.11
129 30 0.11
130 22 0.08
131 4 0.01
132 79 0.29
133 7 0.03
134 8 0.03
135 7 0.03
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (126 bp):
AATATTTCGTATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATTC
GACTAAAATATGGAATATCCTTTTGAAATTTCGTCCACGTTTTCTAAAATTAAAATGAGGC
Found at i:11372694 original size:24 final size:24
Alignment explanation
Indices: 11372666--11372717 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
11372656 TTAACAAGTC
* *
11372666 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
11372690 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
11372714 AAAT
1 AAAT
11372718 CTTTTGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:11387910 original size:18 final size:17
Alignment explanation
Indices: 11387868--11387910 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
11387858 TTTTTTAGTT
*
11387868 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
11387885 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
11387903 TATAATTT
1 TATAATTT
11387911 AGAACACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:11388803 original size:21 final size:21
Alignment explanation
Indices: 11388759--11388803 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11388749 AAAAAACTAT
* **
11388759 AAATTTGTAAAAACATTATTA
1 AAATTTATAAAAACATTAAAA
*
11388780 AAATTTATAAAAATATTAAAA
1 AAATTTATAAAAACATTAAAA
11388801 AAA
1 AAA
11388804 GTTCAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AAATTTATAAAAACATTAAAA
Found at i:11388828 original size:12 final size:11
Alignment explanation
Indices: 11388797--11388825 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
11388787 TAAAAATATT
11388797 AAAAAAAGTTC
1 AAAAAAAGTTC
11388808 AAAAAAAGTTC
1 AAAAAAAGTTC
11388819 AAAAAAA
1 AAAAAAA
11388826 AGTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAAAAAGTTC
Found at i:11389312 original size:12 final size:13
Alignment explanation
Indices: 11389283--11389317 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
11389273 TAAAACATTA
*
11389283 ATTATAAATTTTT
1 ATTATATATTTTT
11389296 ATTATATATTTTT
1 ATTATATATTTTT
11389309 -TTATATATT
1 ATTATATATT
11389318 GCCTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATTATATATTTTT
Found at i:11389947 original size:19 final size:20
Alignment explanation
Indices: 11389910--11389969 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 20
11389900 TTATTTAACA
* *
11389910 TTTTTATCAATTTTAATAATT
1 TTTTTA-CAAATTTAATAAAT
11389931 TTTTTACAAATTT-ATAAAT
1 TTTTTACAAATTTAATAAAT
*
11389950 TTTTTA-AAAATTAA-AAAT
1 TTTTTACAAATTTAATAAAT
11389968 TT
1 TT
11389970 AAAAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 11 0.31
19 12 0.34
20 6 0.17
21 6 0.17
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTACAAATTTAATAAAT
Found at i:11389967 original size:18 final size:19
Alignment explanation
Indices: 11389930--11389969 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
11389920 TTTTAATAAT
* *
11389930 TTTTTTACAAATTTATAAA
1 TTTTTTACAAAATTAAAAA
11389949 TTTTTTA-AAAATTAAAAA
1 TTTTTTACAAAATTAAAAA
11389967 TTT
1 TTT
11389970 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTTTACAAAATTAAAAA
Found at i:11393182 original size:101 final size:101
Alignment explanation
Indices: 11393007--11393210 Score: 381
Period size: 101 Copynumber: 2.0 Consensus size: 101
11392997 CTCTCTGCTG
11393007 ATACATGTCTGCGTATTTGTTGCCTCTCAATATTCAACAAGTAAATGGTTGCAATGTGATGCTAT
1 ATACATGTCTGCGTATTTGTTGCCTCTCAATATTCAACAAGTAAATGGTTGCAATGTGATGCTAT
* *
11393072 CTGTACTTACATTAAATGAGTTCGGTTCACAAGTAA
66 CTATACTTACATTAAATGAGTTCGGGTCACAAGTAA
*
11393108 ATACATGTCTGCGTATTTGTTGCCTCTCAATATTCAACAAGTAGATGGTTGCAATGTGATGCTAT
1 ATACATGTCTGCGTATTTGTTGCCTCTCAATATTCAACAAGTAAATGGTTGCAATGTGATGCTAT
11393173 CTATACTTACATTAAATGAGTTCGGGTCACAAGTAA
66 CTATACTTACATTAAATGAGTTCGGGTCACAAGTAA
11393209 AT
1 AT
11393211 TAGTCAGTAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (101 bp):
ATACATGTCTGCGTATTTGTTGCCTCTCAATATTCAACAAGTAAATGGTTGCAATGTGATGCTAT
CTATACTTACATTAAATGAGTTCGGGTCACAAGTAA
Found at i:11394251 original size:12 final size:13
Alignment explanation
Indices: 11394234--11394265 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
11394224 TGGTATTAAT
11394234 TGTAATTTA-TGA
1 TGTAATTTATTGA
11394246 TGTAATTTATTGA
1 TGTAATTTATTGA
11394259 TGTAATT
1 TGTAATT
11394266 AAATTAGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (13 bp):
TGTAATTTATTGA
Found at i:11397926 original size:14 final size:14
Alignment explanation
Indices: 11397907--11397933 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11397897 ACCCATGCAA
11397907 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
11397921 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
11397934 ATCCCCAGAT
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:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:11398917 original size:29 final size:30
Alignment explanation
Indices: 11398856--11398922 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
11398846 CTAAACTTAT
*
11398856 TTTTTAAA-ATAATTTTATATATTTAATTT
1 TTTTTAAATATAATTTTATATATTTAATTA
11398885 TTTTTAAATATCATATTTT-TATA-TT-ATTA
1 TTTTTAAATAT-A-ATTTTATATATTTAATTA
*
11398914 TTTTGAAAT
1 TTTTTAAAT
11398923 TAAAAGTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 19 0.58
30 4 0.12
31 5 0.15
32 5 0.15
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTTTAAATATAATTTTATATATTTAATTA
Found at i:11410604 original size:16 final size:17
Alignment explanation
Indices: 11410583--11410619 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
11410573 CATGTTAGCT
11410583 AAAATAAAAA-ATTCAA
1 AAAATAAAAATATTCAA
11410599 AAAATAAAAATTATTCAA
1 AAAATAAAAA-TATTCAA
11410617 AAA
1 AAA
11410620 TTTTAAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAATAAAAATATTCAA
Found at i:11411235 original size:10 final size:9
Alignment explanation
Indices: 11411175--11411267 Score: 71
Period size: 9 Copynumber: 9.6 Consensus size: 9
11411165 GTGTTGTAAC
*
11411175 TTTTATGAT
1 TTTTATAAT
11411184 TTTTATAAT
1 TTTTATAAT
*
11411193 TTTTAAATAT
1 TTTTATA-AT
11411203 TTTTA-AAT
1 TTTTATAAT
*
11411211 CATATTATAAGT
1 --TTTTATAA-T
*
11411223 TTTGATAAT
1 TTTTATAAT
11411232 TTTTATAAATTT
1 TTTTAT-AA--T
11411244 TTTTATAAT
1 TTTTATAAT
11411253 TTTTATAAAT
1 TTTTAT-AAT
11411263 TTTTA
1 TTTTA
11411268 AATACTAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
8 2 0.03
9 28 0.41
10 27 0.39
11 4 0.06
12 8 0.12
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:11411251 original size:21 final size:21
Alignment explanation
Indices: 11411222--11411266 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
11411212 ATATTATAAG
11411222 TTTTGATAATTTTTATAAATT
1 TTTTGATAATTTTTATAAATT
*
11411243 TTTTTATAATTTTTATAAATT
1 TTTTGATAATTTTTATAAATT
11411264 TTT
1 TTT
11411267 AAATACTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTGATAATTTTTATAAATT
Found at i:11414734 original size:33 final size:33
Alignment explanation
Indices: 11414692--11414767 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
11414682 CCTATACTAG
11414692 TGTCTTCGTCATCGAATCTAGTCCCTTTACCAA
1 TGTCTTCGTCATCGAATCTAGTCCCTTTACCAA
*
11414725 TGTCTTCGTCATCGAATCTTGTCCCTTTACCAA
1 TGTCTTCGTCATCGAATCTAGTCCCTTTACCAA
11414758 TGTCTTCGTC
1 TGTCTTCGTC
11414768 TTCTGATCCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.17, C:0.30, G:0.13, T:0.39
Consensus pattern (33 bp):
TGTCTTCGTCATCGAATCTAGTCCCTTTACCAA
Found at i:11415514 original size:12 final size:12
Alignment explanation
Indices: 11415497--11415523 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11415487 AAAATCTAGA
11415497 AATATATATTGT
1 AATATATATTGT
11415509 AATATATATTGT
1 AATATATATTGT
11415521 AAT
1 AAT
11415524 CTTGCTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
AATATATATTGT
Found at i:11418473 original size:3 final size:3
Alignment explanation
Indices: 11418467--11418493 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11418457 TTTTTTTGTT
11418467 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
11418494 CAGAAGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:11430402 original size:61 final size:60
Alignment explanation
Indices: 11430289--11430427 Score: 169
Period size: 61 Copynumber: 2.3 Consensus size: 60
11430279 TAAATGTTGA
*
11430289 ATTTGTATTAATATTATAATTATTTAACTTTATTTTTTTAACTAATTAATATTTAGATACT
1 ATTTGTATTAATATTATAATTATTTAACTTTA-TTTTTTAACTAACTAATATTTAGATACT
* *
11430350 ATTTGTACTTATATATTGTAATTA-TTAACCTTTA-TTTTT-ACTAAACTAATATTTAGATATT
1 ATTTGTA-TTA-ATATTATAATTATTTAA-CTTTATTTTTTAACT-AACTAATATTTAGATACT
11430411 ATTTTGTATTAAT-TTAT
1 A-TTTGTATTAATATTAT
11430428 CGAATTAAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
59 3 0.04
60 5 0.07
61 32 0.46
62 13 0.19
63 16 0.23
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (60 bp):
ATTTGTATTAATATTATAATTATTTAACTTTATTTTTTAACTAACTAATATTTAGATACT
Found at i:11432177 original size:19 final size:19
Alignment explanation
Indices: 11432153--11432190 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
11432143 GTAATTGAAC
*
11432153 TTGAAAATTGGACCTGAGA
1 TTGAAAATTGGACCCGAGA
11432172 TTGAAAATTGGACCCGAGA
1 TTGAAAATTGGACCCGAGA
11432191 ACCAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (19 bp):
TTGAAAATTGGACCCGAGA
Found at i:11435746 original size:37 final size:37
Alignment explanation
Indices: 11435700--11435780 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
11435690 TAGTATTTTA
*
11435700 TTAAT-TTTATAGTAATA-TG-ATATATTTTAATTTAAT
1 TTAATATTTATAGTAATATTGAAAATATTTT-A-TTAAT
* *
11435736 TTAATATTTATATTTATATTGAAAATATTTTATTAAT
1 TTAATATTTATAGTAATATTGAAAATATTTTATTAAT
11435773 TTAATATT
1 TTAATATT
11435781 AATGTGATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
36 5 0.13
37 23 0.59
38 3 0.08
39 8 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (37 bp):
TTAATATTTATAGTAATATTGAAAATATTTTATTAAT
Found at i:11447638 original size:20 final size:20
Alignment explanation
Indices: 11447598--11447652 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
11447588 ATTAGATCAT
**
11447598 AAACCTTAAACCACAAAACCC
1 AAACCTTAAA-CATTAAACCC
11447619 AAACCTTAAACATTAAACCC
1 AAACCTTAAACATTAAACCC
* *
11447639 TAACCTCAAACATT
1 AAACCTTAAACATT
11447653 GAATCTTGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (20 bp):
AAACCTTAAACATTAAACCC
Found at i:11447680 original size:20 final size:19
Alignment explanation
Indices: 11447657--11447702 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
11447647 AACATTGAAT
*
11447657 CTTGGATCGAAACCTCAAAC
1 CTTGAATCGAAACC-CAAAC
*
11447677 CTTGAATCTAAACCCAAAC
1 CTTGAATCGAAACCCAAAC
*
11447696 CTCGAAT
1 CTTGAAT
11447703 AGTTCAGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.22
Consensus pattern (19 bp):
CTTGAATCGAAACCCAAAC
Found at i:11448091 original size:44 final size:44
Alignment explanation
Indices: 11448039--11448122 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
11448029 AATATTACTA
* * *
11448039 AATTCACATTT-AAAAATAATTATAATTTAATAAAAGTTGAAAT
1 AATTCACATTTAAAAAATAAATATAAGTTAAAAAAAGTTGAAAT
*
11448082 AATTACACATTTAAAAAATAAATATTAGTTAAAAAAAGTTG
1 AATT-CACATTTAAAAAATAAATATAAGTTAAAAAAAGTTG
11448123 TGATAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 4 0.11
44 7 0.20
45 24 0.69
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.35
Consensus pattern (44 bp):
AATTCACATTTAAAAAATAAATATAAGTTAAAAAAAGTTGAAAT
Found at i:11449486 original size:19 final size:19
Alignment explanation
Indices: 11449462--11449500 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
11449452 GTTAATTTTG
11449462 TTATTATTTTAAAGGCATT
1 TTATTATTTTAAAGGCATT
*
11449481 TTATTATTTTAGAGGCATT
1 TTATTATTTTAAAGGCATT
11449500 T
1 T
11449501 GCTTGCTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.13, T:0.54
Consensus pattern (19 bp):
TTATTATTTTAAAGGCATT
Found at i:11457489 original size:19 final size:19
Alignment explanation
Indices: 11457465--11457502 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
11457455 GCATTTAACT
11457465 TCTAAAAAATAGAGAAATA
1 TCTAAAAAATAGAGAAATA
11457484 TCTAAAAAATAGAGAAATA
1 TCTAAAAAATAGAGAAATA
11457503 AATGTAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.05, G:0.11, T:0.21
Consensus pattern (19 bp):
TCTAAAAAATAGAGAAATA
Found at i:11458128 original size:42 final size:42
Alignment explanation
Indices: 11458081--11458160 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
11458071 TATTCAACTC
11458081 GAAAAAGAAAGATTTGAATTTAACCTGAAAAGAAGACAAGTT
1 GAAAAAGAAAGATTTGAATTTAACCTGAAAAGAAGACAAGTT
11458123 GAAAAAGAAAGATTTGAATTTAACCTGAAAAGAAGACA
1 GAAAAAGAAAGATTTGAATTTAACCTGAAAAGAAGACA
11458161 CCAAATAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.54, C:0.07, G:0.19, T:0.20
Consensus pattern (42 bp):
GAAAAAGAAAGATTTGAATTTAACCTGAAAAGAAGACAAGTT
Found at i:11464058 original size:39 final size:39
Alignment explanation
Indices: 11464015--11464119 Score: 174
Period size: 39 Copynumber: 2.7 Consensus size: 39
11464005 ATCATGATCT
** *
11464015 GAAGCCCGAAATCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
*
11464054 GAAGCCCGGAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
11464093 GAAGCCCGAAGGCTAACTGAAGCACAT
1 GAAGCCCGAAGGCTAACTGAAGCACAT
11464120 CAGAGCTGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.37, C:0.24, G:0.26, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:11464097 original size:21 final size:21
Alignment explanation
Indices: 11464033--11464097 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
11464023 AAATCTAGCT
11464033 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
*** *
11464054 GAAGC-CCGGAG-GCT-AACT
1 GAAGCACATAAGTGCTAAACG
11464072 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
11464093 GAAGC
1 GAAGC
11464098 CCGAAGGCTA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 6 0.18
21 13 0.39
ACGTcount: A:0.38, C:0.22, G:0.28, T:0.12
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACG
Found at i:11469193 original size:20 final size:20
Alignment explanation
Indices: 11469170--11469209 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11469160 CCTTGAAAAA
11469170 GGTACCGATA-CTTTATGATT
1 GGTACCGATACCTTTA-GATT
*
11469190 GGTATCGATACCTTTAGATT
1 GGTACCGATACCTTTAGATT
11469210 TAATTCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (20 bp):
GGTACCGATACCTTTAGATT
Found at i:11471672 original size:2 final size:2
Alignment explanation
Indices: 11471667--11471692 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11471657 TGTGTGGAAA
11471667 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
11471693 CATCCATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:11484808 original size:33 final size:33
Alignment explanation
Indices: 11484763--11484835 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
11484753 AACCTCAGCT
* * *
11484763 ATTTTGGTCGTGT-GGGCCACACGGGCAAGGCCA
1 ATTTGGGTCGTGTAGGCCCACACAGGCAA-GCCA
*
11484796 ATTTGGGTCGTGTATGCCCACACAGGCAAGCCA
1 ATTTGGGTCGTGTAGGCCCACACAGGCAAGCCA
*
11484829 TTTTGGG
1 ATTTGGG
11484836 GATGTGTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 22 0.65
34 12 0.35
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.25
Consensus pattern (33 bp):
ATTTGGGTCGTGTAGGCCCACACAGGCAAGCCA
Found at i:11491146 original size:21 final size:21
Alignment explanation
Indices: 11491122--11491207 Score: 73
Period size: 21 Copynumber: 4.1 Consensus size: 21
11491112 ATGAGGGTTA
11491122 AACGGAAACTCATAAGAGCTG
1 AACGGAAACTCATAAGAGCTG
* * *
11491143 AACGGAAACCCATAAGAGTTA
1 AACGGAAACTCATAAGAGCTG
** * * *
11491164 AATAGAAGCTTAAAAGAGCTG
1 AACGGAAACTCATAAGAGCTG
* * *
11491185 AATGGAAACTCATATGAGATG
1 AACGGAAACTCATAAGAGCTG
11491206 AA
1 AA
11491208 TAGAAGCTTG
Statistics
Matches: 48, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.17
Consensus pattern (21 bp):
AACGGAAACTCATAAGAGCTG
Found at i:11491152 original size:42 final size:42
Alignment explanation
Indices: 11491091--11491198 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 42
11491081 ACAGAAGCAT
* * * * * *
11491091 ATAAGTGCTAAACAGAAACCCATGAGGGTTAAACGGAAACTC
1 ATAAGAGCTGAACGGAAACCCATAAGAGTTAAACAGAAACTC
* * *
11491133 ATAAGAGCTGAACGGAAACCCATAAGAGTTAAATAGAAGCTT
1 ATAAGAGCTGAACGGAAACCCATAAGAGTTAAACAGAAACTC
* * *
11491175 AAAAGAGCTGAATGGAAACTCATA
1 ATAAGAGCTGAACGGAAACCCATA
11491199 TGAGATGAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (42 bp):
ATAAGAGCTGAACGGAAACCCATAAGAGTTAAACAGAAACTC
Found at i:11491210 original size:42 final size:42
Alignment explanation
Indices: 11491135--11491234 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
11491125 GGAAACTCAT
*
11491135 AAGAGCTGAACGGAAACCCATAAGAGTTAAATAGAAGCTTAA
1 AAGAGCTGAACGGAAACCCATAAGAGATAAATAGAAGCTTAA
* * * * **
11491177 AAGAGCTGAATGGAAACTCATATGAGATGAATAGAAGCTTGT
1 AAGAGCTGAACGGAAACCCATAAGAGATAAATAGAAGCTTAA
* *
11491219 GAGAGCTAAACGGAAA
1 AAGAGCTGAACGGAAA
11491235 GTAAACATGA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.45, C:0.12, G:0.25, T:0.18
Consensus pattern (42 bp):
AAGAGCTGAACGGAAACCCATAAGAGATAAATAGAAGCTTAA
Found at i:11499740 original size:14 final size:14
Alignment explanation
Indices: 11499721--11499750 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11499711 AGGTTAAAAA
11499721 TTAATAAGAATTGG
1 TTAATAAGAATTGG
11499735 TTAATAAGAATTGG
1 TTAATAAGAATTGG
11499749 TT
1 TT
11499751 TCATTTACAA
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:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (14 bp):
TTAATAAGAATTGG
Found at i:11506357 original size:35 final size:35
Alignment explanation
Indices: 11506318--11506389 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 35
11506308 CATCTCCGGA
* *
11506318 GCTTGGCAAATATGGAAAGTAATCTTCAAAGATAT
1 GCTTGGAAAATATGGAAAGGAATCTTCAAAGATAT
* * *
11506353 GCTTGGAAAATATGGAAGGGGATTTTCAAAGATAT
1 GCTTGGAAAATATGGAAAGGAATCTTCAAAGATAT
11506388 GC
1 GC
11506390 GATCCTAGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (35 bp):
GCTTGGAAAATATGGAAAGGAATCTTCAAAGATAT
Found at i:11506607 original size:12 final size:12
Alignment explanation
Indices: 11506590--11506622 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
11506580 CATTCACTCA
11506590 AACTTTTCTCTC
1 AACTTTTCTCTC
11506602 AACTTTTCTCTC
1 AACTTTTCTCTC
*
11506614 AACTGTTCT
1 AACTTTTCT
11506623 TATTTTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.30, G:0.03, T:0.48
Consensus pattern (12 bp):
AACTTTTCTCTC
Found at i:11507414 original size:16 final size:16
Alignment explanation
Indices: 11507383--11507447 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
11507373 AACATTTTAC
*
11507383 AAAATAGTATAAAAAAT
1 AAAATACTA-AAAAAAT
11507400 AAAATACTAAAAAAAT
1 AAAATACTAAAAAAAT
*** * *
11507416 ATCTTAATGAAAAAAT
1 AAAATACTAAAAAAAT
*
11507432 AAAATACGAAAAAAAT
1 AAAATACTAAAAAAAT
11507448 TTTTTTGGGG
Statistics
Matches: 36, Mismatches: 12, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
16 28 0.78
17 8 0.22
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.22
Consensus pattern (16 bp):
AAAATACTAAAAAAAT
Found at i:11507841 original size:152 final size:149
Alignment explanation
Indices: 11507480--11508256 Score: 1073
Period size: 147 Copynumber: 5.2 Consensus size: 149
11507470 GCGAGTTTTT
11507480 TACTAAAATAATAT-AAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCCAAAAATT
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCCAAAAA-T
* * * * *
11507544 TAAAAAATA-CAAACAAAGGGTCAAAATTAGGGTTATTTACTAAATT-A-ATAAAAATACTAAAA
65 AAAAAAATACCAAA-AAAGTGTCAAAATTAGGGTTATTTATTAAATTAATATAAAAACACTTAAA
11507606 TAATACATTTGAAACATTTATG
129 TAATACATTTGAAACA-TTATG
* **
11507628 TACTAAAATAATAT---AAA-AAAATACGAAAATAGTATATTTTAAAAAATAAAATCTGAAAATA
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCCAAAAATA
*
11507689 AAAAAATACCAAAAAAGTGTCAAAATTAGGGTTATTTGTTAAATTAATATAAAAACACTTAAATA
66 AAAAAATACCAAAAAAGTGTCAAAATTAGGGTTATTTATTAAATTAATATAAAAACACTTAAATA
11507754 ATACATTTGAAACATTATG
131 ATACATTTGAAACATTATG
* * * *
11507773 TGCTAAAATAATATATAAAAAAATAAAATACGAAAATAGTATATTTCAAAAAATAAAATCTAAAA
1 TACTAAAAT-A-ATAT-AAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCCAAAA
*
11507838 ATAAAAAAATACCAACAAAGTGTCAAAATTAGGGTTATTTATTAAATTAATATAAAAAAACACTT
63 ATAAAAAAATACCAAAAAAGTGTCAAAATTAGGGTTATTTATTAAATTAATAT--AAAAACACTT
11507903 AAATAATACATTTGAAACATTATG
126 AAATAATACATTTGAAACATTATG
*
11507927 TACTAAAATAATAT---AAA-AAAA-ACGAAAATAATATATTTTAAAAAATAAAATCCGAAAATA
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCCAAAAAT-
* * * * *
11507987 AAAAAAATACCAACAGAGTGTCAAAATCATGGTTATTTATTAAATTAATA-AAAAA-AATTAAAT
65 AAAAAAATACCAAAAAAGTGTCAAAATTAGGGTTATTTATTAAATTAATATAAAAACACTTAAAT
* *
11508050 AATATATTTGAAATATTATG
130 AATACATTTGAAACATTATG
11508070 TACTAAAATAATATAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCCAAAAATA
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCCAAAAATA
* * *
11508135 AAAAAATA-CAAATAAAGTATCAAAATCATGGTTATTTATTAAATTAATATAAAAAACACTTAAA
66 AAAAAATACCAAA-AAAGTGTCAAAATTAGGGTTATTTATTAAATTAATAT-AAAAACACTTAAA
* * *
11508199 TAATATATTTAAAATATTATG
129 TAATACATTTGAAACATTATG
*
11508220 TACCAAAATAATATAAAAAAATAAAATACGAAAATAA
1 TACTAAAATAATAT-AAAAAATAAAATACGAAAATAA
11508257 AAAAATATCA
Statistics
Matches: 574, Mismatches: 32, Indels: 43
0.88 0.05 0.07
Matches are distributed among these distances:
143 39 0.07
144 43 0.07
145 57 0.10
146 73 0.13
147 102 0.18
148 54 0.09
149 5 0.01
150 39 0.07
151 25 0.04
152 94 0.16
153 1 0.00
154 42 0.07
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29
Consensus pattern (149 bp):
TACTAAAATAATATAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCCAAAAATA
AAAAAATACCAAAAAAGTGTCAAAATTAGGGTTATTTATTAAATTAATATAAAAACACTTAAATA
ATACATTTGAAACATTATG
Found at i:11510591 original size:33 final size:33
Alignment explanation
Indices: 11510554--11510627 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
11510544 CCCATATTCG
** * *
11510554 CCGCAGTATAGCACTACCTTCGGCCTGTATCCA
1 CCGCAGTATAGCACTACCCCCAGCCCGTATCCA
11510587 CCGCAGTATAGCACTACCCCCAGCCCGTATCCA
1 CCGCAGTATAGCACTACCCCCAGCCCGTATCCA
11510620 CCGCAGTA
1 CCGCAGTA
11510628 CTCCACTCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.23, C:0.41, G:0.18, T:0.19
Consensus pattern (33 bp):
CCGCAGTATAGCACTACCCCCAGCCCGTATCCA
Found at i:11511067 original size:18 final size:18
Alignment explanation
Indices: 11511044--11511131 Score: 81
Period size: 18 Copynumber: 4.8 Consensus size: 18
11511034 ATACATTACA
11511044 ACATTAATCTAATTAAAC
1 ACATTAATCTAATTAAAC
**
11511062 ACATTAATCTAATTGGA-
1 ACATTAATCTAATTAAAC
*
11511079 ACATTAAT-TAAATTCATTAC
1 ACATTAATCT-AATT-A-AAC
* *
11511099 AACATAAATCTAATTAAAT
1 -ACATTAATCTAATTAAAC
11511118 ACATTAATCTAATT
1 ACATTAATCTAATT
11511132 GGAACATTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
16 1 0.02
17 12 0.21
18 28 0.50
19 2 0.04
20 1 0.02
21 11 0.20
22 1 0.02
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (18 bp):
ACATTAATCTAATTAAAC
Found at i:11511067 original size:26 final size:26
Alignment explanation
Indices: 11511031--11511169 Score: 97
Period size: 26 Copynumber: 5.0 Consensus size: 26
11511021 GAACAAACTC
11511031 TAAATACATTACAACATTAATCTAAT
1 TAAATACATTACAACATTAATCTAAT
* *
11511057 TAAACACATTA-ATCTAATTGGAA-CATTAAT
1 TAAATACATTACAAC--ATT--AATC--TAAT
* *
11511087 TAAATTCATTACAACATAAATCTAAT
1 TAAATACATTACAACATTAATCTAAT
*
11511113 TAAATACATTA-ATCTAATTGGAA-CATTAAT
1 TAAATACATTACAAC--ATT--AATC--TAAT
11511143 TAAATACATTACAACATTAATCTAAT
1 TAAATACATTACAACATTAATCTAAT
11511169 T
1 T
11511170 GGAACAAACT
Statistics
Matches: 87, Mismatches: 10, Indels: 32
0.67 0.08 0.25
Matches are distributed among these distances:
25 4 0.05
26 29 0.33
27 9 0.10
28 4 0.05
29 9 0.10
30 28 0.32
31 4 0.05
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35
Consensus pattern (26 bp):
TAAATACATTACAACATTAATCTAAT
Found at i:11511089 original size:30 final size:30
Alignment explanation
Indices: 11511053--11511153 Score: 115
Period size: 30 Copynumber: 3.5 Consensus size: 30
11511043 AACATTAATC
*
11511053 TAATTAAACACATTAATCTAATTGGAACAT
1 TAATTAAATACATTAATCTAATTGGAACAT
* *
11511083 TAATTAAATTCATT-A-C-AACAT--AA-AT
1 TAATTAAATACATTAATCTAA-TTGGAACAT
11511108 CTAATTAAATACATTAATCTAATTGGAACAT
1 -TAATTAAATACATTAATCTAATTGGAACAT
11511139 TAATTAAATACATTA
1 TAATTAAATACATTA
11511154 CAACATTAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
25 2 0.03
26 15 0.26
27 3 0.05
28 4 0.07
29 3 0.05
30 29 0.50
31 2 0.03
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.36
Consensus pattern (30 bp):
TAATTAAATACATTAATCTAATTGGAACAT
Found at i:11511102 original size:56 final size:56
Alignment explanation
Indices: 11511031--11511169 Score: 251
Period size: 56 Copynumber: 2.5 Consensus size: 56
11511021 GAACAAACTC
11511031 TAAATACATTACAACATTAATCTAATTAAACACATTAATCTAATTGGAACATTAAT
1 TAAATACATTACAACATTAATCTAATTAAACACATTAATCTAATTGGAACATTAAT
* * *
11511087 TAAATTCATTACAACATAAATCTAATTAAATACATTAATCTAATTGGAACATTAAT
1 TAAATACATTACAACATTAATCTAATTAAACACATTAATCTAATTGGAACATTAAT
11511143 TAAATACATTACAACATTAATCTAATT
1 TAAATACATTACAACATTAATCTAATT
11511170 GGAACAAACT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 78 1.00
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35
Consensus pattern (56 bp):
TAAATACATTACAACATTAATCTAATTAAACACATTAATCTAATTGGAACATTAAT
Found at i:11515715 original size:19 final size:19
Alignment explanation
Indices: 11515691--11515788 Score: 155
Period size: 19 Copynumber: 5.2 Consensus size: 19
11515681 AATCTTTAAG
11515691 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11515710 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11515729 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11515746 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
11515765 GATGTGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
11515786 GAT
1 GAT
11515789 CTTGTAATCT
Statistics
Matches: 74, Mismatches: 1, Indels: 6
0.91 0.01 0.07
Matches are distributed among these distances:
17 17 0.23
19 48 0.65
21 9 0.12
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:11515721 original size:36 final size:35
Alignment explanation
Indices: 11515681--11515766 Score: 115
Period size: 36 Copynumber: 2.4 Consensus size: 35
11515671 ATGGAAATAT
11515681 AATCTTTAAGGATATG-CAATCTTAGATATGATATGC
1 AATCTTT-A-GATATGACAATCTTAGATATGATATGC
11515717 AATC-TTAGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAGATATG--ACAATCTTAGATATGATATGC
11515753 AATC-TTAGATATGA
1 AATCTTTAGATATGA
11515767 TGTGCAATCT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
33 6 0.13
34 2 0.04
35 2 0.04
36 37 0.79
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (35 bp):
AATCTTTAGATATGACAATCTTAGATATGATATGC
Found at i:11515767 original size:36 final size:36
Alignment explanation
Indices: 11515697--11515767 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
11515687 TAAGGATATG
11515697 CAATCTTAGATATGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGATA
11515733 CAATCTTAGATATGATATGCAATCTTAGATATGAT
1 CAATCTTAGATATGATATGCAATCTTAGATATGAT
11515768 GTGCAATCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (36 bp):
CAATCTTAGATATGATATGCAATCTTAGATATGATA
Found at i:11516720 original size:25 final size:25
Alignment explanation
Indices: 11516692--11516743 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
11516682 ATTAATTACT
* *
11516692 TATTTTATACTTATAT-TTATATATA
1 TATTATATA-TTATATATTATAAATA
*
11516717 TATTATATATTATTTATTATAAATA
1 TATTATATATTATATATTATAAATA
11516742 TA
1 TA
11516744 AATTCTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTATATATTATATATTATAAATA
Found at i:11516881 original size:18 final size:20
Alignment explanation
Indices: 11516831--11516895 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 20
11516821 TTTTATAAAT
* * *
11516831 TTTTGTTATTATATATTATA
1 TTTTATTATTAAATATCATA
11516851 TATTGTA-TATTAAATA-C-TA
1 T-TT-TATTATTAAATATCATA
11516870 TTTTATTATTAAATATCATA
1 TTTTATTATTAAATATCATA
11516890 TTTTAT
1 TTTTAT
11516896 GTGTATTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
17 2 0.05
18 11 0.30
19 4 0.11
20 9 0.24
21 10 0.27
22 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTTATTATTAAATATCATA
Found at i:11518185 original size:46 final size:46
Alignment explanation
Indices: 11518134--11518458 Score: 375
Period size: 46 Copynumber: 7.0 Consensus size: 46
11518124 GTGTGCTCTC
* * *
11518134 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATAGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* *
11518180 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * *
11518226 TAATATGAAATGTGTAAGACCGTGGTTGGAAGATACCATGGTAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * *
11518272 TGATA-GAAAATGAATAAAACCATGGTTGAAAGATACCATGGCAGCG
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* *
11518318 TGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
*** * *
11518364 TGACGGGAAAATGAATAAGAACATGGTTGAAAGATACCATGGCAACA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * *
11518411 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
11518457 TG
1 TG
11518459 TCAAAGATAA
Statistics
Matches: 247, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
45 1 0.00
46 203 0.82
47 43 0.17
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:11518411 original size:24 final size:24
Alignment explanation
Indices: 11518338--11518412 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
11518328 TGAATAAGAC
11518338 CATGGTTGAAAGATACCATGGCAA
1 CATGGTTGAAAGATACCATGGCAA
* *
11518362 CATGACG-GGAAA-ATGA--ATAAG-AA
1 CATG--GTTGAAAGAT-ACCAT-GGCAA
11518385 CATGGTTGAAAGATACCATGGCAA
1 CATGGTTGAAAGATACCATGGCAA
11518409 CATG
1 CATG
11518413 ACAGAAAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 18
0.63 0.07 0.30
Matches are distributed among these distances:
21 1 0.03
22 5 0.13
23 11 0.29
24 15 0.39
25 5 0.13
26 1 0.03
ACGTcount: A:0.41, C:0.15, G:0.25, T:0.19
Consensus pattern (24 bp):
CATGGTTGAAAGATACCATGGCAA
Found at i:11518758 original size:16 final size:17
Alignment explanation
Indices: 11518739--11518771 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11518729 ATGATGGAGT
11518739 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
11518755 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
11518772 TATACTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:11520910 original size:18 final size:18
Alignment explanation
Indices: 11520889--11520964 Score: 61
Period size: 18 Copynumber: 4.3 Consensus size: 18
11520879 AACCTAAAAC
11520889 ACATATAACAAATAAATT
1 ACATATAACAAATAAATT
11520907 ACATA-AA-AGAATAAA--
1 ACATATAACA-AATAAATT
* * **
11520922 ACATCTAATCAACCTAAAAC
1 ACATATAA-CAA-ATAAATT
11520942 ACATATAACAAATAAATT
1 ACATATAACAAATAAATT
11520960 ACATA
1 ACATA
11520965 AAAGAATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
15 4 0.09
16 3 0.07
17 9 0.20
18 19 0.42
19 3 0.07
20 7 0.16
ACGTcount: A:0.61, C:0.16, G:0.01, T:0.22
Consensus pattern (18 bp):
ACATATAACAAATAAATT
Found at i:11520929 original size:53 final size:53
Alignment explanation
Indices: 11520871--11520978 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
11520861 TATAAATATT
11520871 ATCTAATCAACCTAAAACACATATAACAAATAAATTACATAAAAGAATAAAAC
1 ATCTAATCAACCTAAAACACATATAACAAATAAATTACATAAAAGAATAAAAC
11520924 ATCTAATCAACCTAAAACACATATAACAAATAAATTACATAAAAGAATAAAAC
1 ATCTAATCAACCTAAAACACATATAACAAATAAATTACATAAAAGAATAAAAC
11520977 AT
1 AT
11520979 TCTTTACATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.60, C:0.17, G:0.02, T:0.21
Consensus pattern (53 bp):
ATCTAATCAACCTAAAACACATATAACAAATAAATTACATAAAAGAATAAAAC
Found at i:11521134 original size:16 final size:16
Alignment explanation
Indices: 11521113--11521145 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11521103 TAGTTTTTTT
11521113 ACTAACAATAATAATA
1 ACTAACAATAATAATA
*
11521129 ACTAACAATAATGATA
1 ACTAACAATAATAATA
11521145 A
1 A
11521146 GGGTTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.12, G:0.03, T:0.24
Consensus pattern (16 bp):
ACTAACAATAATAATA
Found at i:11521165 original size:26 final size:26
Alignment explanation
Indices: 11521129--11521220 Score: 150
Period size: 26 Copynumber: 3.6 Consensus size: 26
11521119 AATAATAATA
*
11521129 ACTAACAATAATGATAAGGGTTTTTT
1 ACTAACAATAATAATAAGGGTTTTTT
*
11521155 ACTAACAATAATAATAAGGATTTTTT
1 ACTAACAATAATAATAAGGGTTTTTT
11521181 ACTAACAATAATAATAA-GGTTTTTT
1 ACTAACAATAATAATAAGGGTTTTTT
*
11521206 ACTAATAATAATAAT
1 ACTAACAATAATAAT
11521221 TACTAACAAC
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 21 0.34
26 41 0.66
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.38
Consensus pattern (26 bp):
ACTAACAATAATAATAAGGGTTTTTT
Found at i:11522325 original size:18 final size:18
Alignment explanation
Indices: 11522302--11522374 Score: 76
Period size: 18 Copynumber: 3.9 Consensus size: 18
11522292 TTTATTTTTT
11522302 TTACTATTATTTATATTA
1 TTACTATTATTTATATTA
*
11522320 TTACTATTATTTCTCATGTA
1 TTACTATTATTTAT-AT-TA
*
11522340 TATATTATTATTTATATTA
1 T-TACTATTATTTATATTA
*
11522359 TTATTA-TATTATATAT
1 TTACTATTATT-TATAT
11522375 ACCCTCTCCA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
17 4 0.08
18 23 0.48
19 5 0.10
20 5 0.10
21 11 0.23
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.60
Consensus pattern (18 bp):
TTACTATTATTTATATTA
Found at i:11522450 original size:3 final size:3
Alignment explanation
Indices: 11522442--11522518 Score: 95
Period size: 3 Copynumber: 25.0 Consensus size: 3
11522432 TATTTCTGAC
*
11522442 TAT TAT TAT TA- TAT ATAT GTAT GTAT TAT TGT T-T GTAT TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT -TAT -TAT TAT TAT TAT -TAT TAT TAT TAT
11522489 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11522519 CACCCCTATT
Statistics
Matches: 68, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
2 3 0.04
3 54 0.79
4 11 0.16
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:11527744 original size:12 final size:12
Alignment explanation
Indices: 11527710--11527792 Score: 69
Period size: 12 Copynumber: 6.6 Consensus size: 12
11527700 TTTATTTTTT
*
11527710 TTTATTTTATTA
1 TTTATATTATTA
* *
11527722 TTTTTACTATTA
1 TTTATATTATTA
11527734 TTTATATTATTA
1 TTTATATTATTA
* *
11527746 CTATTAT-TTCTCA
1 -T-TTATATTATTA
11527759 TGTATATATTATTA
1 T-T-TATATTATTA
11527773 TTTATATTATTA
1 TTTATATTATTA
11527785 TATTATAT
1 T-TTATAT
11527793 ATACCCTCTC
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
12 32 0.57
13 15 0.27
14 9 0.16
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:11527795 original size:9 final size:9
Alignment explanation
Indices: 11527715--11527795 Score: 60
Period size: 9 Copynumber: 8.7 Consensus size: 9
11527705 TTTTTTTTAT
11527715 TTTATTATT-
1 TTTA-TATTA
11527724 TTTACTATTA
1 TTTA-TATTA
11527734 TTTATATTA
1 TTTATATTA
11527743 -TTACTATTA
1 TTTA-TATTA
*
11527752 TTTCTCATGTA
1 TTTAT-AT-TA
*
11527763 TATATTATTA
1 TTTA-TATTA
11527773 TTTATATTA
1 TTTATATTA
11527782 -TTATATTA
1 TTTATATTA
*
11527790 TATATA
1 TTTATA
11527796 CCCTCTCCAT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
8 11 0.19
9 28 0.47
10 13 0.22
11 6 0.10
12 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTATATTA
Found at i:11528205 original size:123 final size:118
Alignment explanation
Indices: 11527987--11528207 Score: 284
Period size: 123 Copynumber: 1.8 Consensus size: 118
11527977 TTATTTTTGC
* *
11527987 TATTACTATTATTATTATTATATTAGTGTATATTTTTATGTATATATATATTATATATAGTATTG
1 TATTACTATTATTATTATTATATTAGTGTATATTTCTATGTATATATATATTATATATAGTATAG
* *
11528052 TTTTTTATTACTTTAATTTAATATTTTTATTATATTTGCTTTTTGTATTTCTA
66 TTTATTATTACTTTAATTTAATATTATTATTATATTTGCTTTTTGTATTTCTA
* * * *
11528105 TATTATTATTATTATTATTATATAGTAGTGTGTATTTCTAT-TATATACATATATATTTTTATA-
1 TATTACTATTATTATTATTATAT--TAGTGTATATTTCTATGTATAT--ATATAT-TATATATAG
*
11528168 TATAGTATTATTATTTACTTTACTTTAATATTATTATTAT
61 TATAGT-TTATTA-TTACTTTAATTTAATATTATTATTAT
11528208 TATCATTATA
Statistics
Matches: 87, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
118 22 0.25
119 5 0.06
120 14 0.16
121 11 0.13
122 11 0.13
123 24 0.28
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (118 bp):
TATTACTATTATTATTATTATATTAGTGTATATTTCTATGTATATATATATTATATATAGTATAG
TTTATTATTACTTTAATTTAATATTATTATTATATTTGCTTTTTGTATTTCTA
Found at i:11534776 original size:2 final size:2
Alignment explanation
Indices: 11534769--11534801 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11534759 AGTAGCAGTA
11534769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11534802 CAGAACAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11546202 original size:11 final size:12
Alignment explanation
Indices: 11546181--11546209 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
11546171 ATTTGGGTAA
11546181 AAAAAATAAAAT
1 AAAAAATAAAAT
11546193 AAAAAA-AAAAT
1 AAAAAATAAAAT
11546204 AAAAAA
1 AAAAAA
11546210 GACACAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:11551944 original size:16 final size:16
Alignment explanation
Indices: 11551923--11551954 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11551913 AAAAGAAAAG
*
11551923 ATATCTGATTAATGAA
1 ATATCTGATAAATGAA
11551939 ATATCTGATAAATGAA
1 ATATCTGATAAATGAA
11551955 TCGGTAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (16 bp):
ATATCTGATAAATGAA
Found at i:11557151 original size:16 final size:18
Alignment explanation
Indices: 11557124--11557156 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11557114 TTAGGTTAAA
11557124 TTATATAAA-TTTATTTT
1 TTATATAAATTTTATTTT
11557141 TTATA-AAATTTTATTT
1 TTATATAAATTTTATTT
11557157 ATGAAATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATATAAATTTTATTTT
Found at i:11563296 original size:19 final size:19
Alignment explanation
Indices: 11563267--11563312 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
11563257 CCATATATTT
*
11563267 TAAAT-TTATTTAGTTAGA
1 TAAATCTTATTTAGGTAGA
11563285 TAAATCTTATTTAGGTAGA
1 TAAATCTTATTTAGGTAGA
11563304 TAAATCTTA
1 TAAATCTTA
11563313 GAGATATTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (19 bp):
TAAATCTTATTTAGGTAGA
Found at i:11563754 original size:164 final size:164
Alignment explanation
Indices: 11563483--11563812 Score: 642
Period size: 164 Copynumber: 2.0 Consensus size: 164
11563473 CATCTGAGCT
*
11563483 AGGTTAAATCTCTAATAACATCATGGTTAAAACAACCTTCACTGGAGATAAGAGATCCAATAATC
1 AGGTTAAAACTCTAATAACATCATGGTTAAAACAACCTTCACTGGAGATAAGAGATCCAATAATC
11563548 AAACAGAGGAAGAAAGTTCTACCTTTGAAACAACTACCGAGAGTACAATGACTCAAGGGACAAAG
66 AAACAGAGGAAGAAAGTTCTACCTTTGAAACAACTACCGAGAGTACAATGACTCAAGGGACAAAG
11563613 GTGTTTCATCTTTCTTTCCAGCTAACATCTCACA
131 GTGTTTCATCTTTCTTTCCAGCTAACATCTCACA
11563647 AGGTTAAAACTCTAATAACATCATGGTTAAAACAACCTTCACTGGAGATAAGAGATCCAATAATC
1 AGGTTAAAACTCTAATAACATCATGGTTAAAACAACCTTCACTGGAGATAAGAGATCCAATAATC
11563712 AAACAGAGGAAGAAAGTTCTACCTTTGAAACAACTACCGAGAGTACAATGACTCAAGGGACAAAG
66 AAACAGAGGAAGAAAGTTCTACCTTTGAAACAACTACCGAGAGTACAATGACTCAAGGGACAAAG
*
11563777 GTGTTTCATCTTTCTTTTCAGCTAACATCTCACA
131 GTGTTTCATCTTTCTTTCCAGCTAACATCTCACA
11563811 AG
1 AG
11563813 CTGAATGACA
Statistics
Matches: 164, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 164 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (164 bp):
AGGTTAAAACTCTAATAACATCATGGTTAAAACAACCTTCACTGGAGATAAGAGATCCAATAATC
AAACAGAGGAAGAAAGTTCTACCTTTGAAACAACTACCGAGAGTACAATGACTCAAGGGACAAAG
GTGTTTCATCTTTCTTTCCAGCTAACATCTCACA
Found at i:11573599 original size:42 final size:43
Alignment explanation
Indices: 11573506--11573665 Score: 126
Period size: 43 Copynumber: 3.7 Consensus size: 43
11573496 ATATGTGTTA
* * * * * *
11573506 TCGTGTAAGACCACGTCTAGGACGTTGGCATCAATTTGA-GATT
1 TCGTGTAAGACCATGTCTGGGACATTGGAATCGATAT-ATGATT
*
11573549 TACGTGTAAAACCATGTCTGGGACATTGGAATCG-TATATGATT
1 T-CGTGTAAGACCATGTCTGGGACATTGGAATCGATATATGATT
* * * * * *
11573592 TCGTGTAAGACCTTGTCTAGAACAGTGGCATCGATATTTGATT
1 TCGTGTAAGACCATGTCTGGGACATTGGAATCGATATATGATT
* * * * *
11573635 ACATATAAGACCACGTCTGGGACGTTGGAAT
1 TCGTGTAAGACCATGTCTGGGACATTGGAAT
11573666 TTTACGAGCC
Statistics
Matches: 90, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
42 27 0.30
43 37 0.41
44 26 0.29
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (43 bp):
TCGTGTAAGACCATGTCTGGGACATTGGAATCGATATATGATT
Found at i:11587520 original size:18 final size:19
Alignment explanation
Indices: 11587493--11587529 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
11587483 TCACTATCAC
*
11587493 CCACCGTAATC-AATTTGT
1 CCACCATAATCAAATTTGT
11587511 CCACCATAATCAAATTTGT
1 CCACCATAATCAAATTTGT
11587530 TATTAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.32
Consensus pattern (19 bp):
CCACCATAATCAAATTTGT
Found at i:11588780 original size:44 final size:44
Alignment explanation
Indices: 11588683--11588769 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
11588673 AATCTGACCT
* * * *
11588683 ACTGCAACTTCAGAGGTATAGGATATGTTGCTTTAATCCGCTCC
1 ACTGCAACTTCAGGGGGATAGGATATGTAGCTTCAATCCGCTCC
*
11588727 ACTGCAACTTCAGGGGGATAGGAT-TAGTAGCTTCAATCTGCTC
1 ACTGCAACTTCAGGGGGATAGGATAT-GTAGCTTCAATCCGCTC
11588770 TCCTGTAACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
43 1 0.03
44 36 0.97
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (44 bp):
ACTGCAACTTCAGGGGGATAGGATATGTAGCTTCAATCCGCTCC
Found at i:11588808 original size:45 final size:44
Alignment explanation
Indices: 11588757--11588883 Score: 130
Period size: 44 Copynumber: 2.9 Consensus size: 44
11588747 GGATTAGTAG
* * * * * *
11588757 CTTCAATCTGCTCTCCTGTAACTTTAGGGAGATAAGAGTCGCTAT
1 CTTCAATCTGCTCTACTGCAACTATAAGGAGATAAGA-TCGATAA
** *
11588802 CTTCAATCTATTCTACTGCAACTATAAGGAGATAAGATCTATAA
1 CTTCAATCTGCTCTACTGCAACTATAAGGAGATAAGATCGATAA
* *
11588846 CTTCAATCTGCTCTACTGCTACT-TCAAGGAGATGAGAT
1 CTTCAATCTGCTCTACTGCAACTAT-AAGGAGATAAGAT
11588884 TTGTAATTTG
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 1 0.01
44 36 0.53
45 31 0.46
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
CTTCAATCTGCTCTACTGCAACTATAAGGAGATAAGATCGATAA
Found at i:11589030 original size:44 final size:44
Alignment explanation
Indices: 11588950--11589111 Score: 155
Period size: 44 Copynumber: 3.7 Consensus size: 44
11588940 ATCTTCAGAG
* * *
11588950 TGCTCCACTTCAACTTCAGGGAGAAAAGACTT-ATAGCTTTAATC
1 TGCTCTACTGCAACTTCAGAGAGAAAAGA-TTCATAGCTTTAATC
* * *
11588994 TGCTCTACTACAACTTCAGAGAGATAATATTCATAGCTTTAATC
1 TGCTCTACTGCAACTTCAGAGAGAAAAGATTCATAGCTTTAATC
* * * ** * *
11589038 TACTTTACTGTAACTTCAGAGAGAAAAGATTCACTATATTCAGTC
1 TGCTCTACTGCAACTTCAGAGAGAAAAGATTCA-TAGCTTTAATC
* * *
11589083 TGCTCTACTGCAATTTCAGGGAGATAAGA
1 TGCTCTACTGCAACTTCAGAGAGAAAAGA
11589112 CTTGTAATTT
Statistics
Matches: 95, Mismatches: 21, Indels: 3
0.80 0.18 0.03
Matches are distributed among these distances:
43 2 0.02
44 63 0.66
45 30 0.32
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (44 bp):
TGCTCTACTGCAACTTCAGAGAGAAAAGATTCATAGCTTTAATC
Found at i:11590487 original size:46 final size:46
Alignment explanation
Indices: 11590437--11590612 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 46
11590427 TGGTTGAGCA
*
11590437 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*** * * ** *
11590483 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
* *
11590530 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
11590576 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11590613 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
46 72 0.67
47 35 0.33
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:11590593 original size:93 final size:93
Alignment explanation
Indices: 11590434--11590604 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
11590424 GGATGGTTGA
* *
11590434 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
11590499 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * *
11590527 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
11590592 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
11590605 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:11596897 original size:46 final size:46
Alignment explanation
Indices: 11596837--11597107 Score: 400
Period size: 46 Copynumber: 5.9 Consensus size: 46
11596827 TTTAACATGA
* * * * * *
11596837 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
11596883 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
11596929 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
11596975 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATAAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
11597021 TGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
11597067 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
11597108 TAGAGAGCAC
Statistics
Matches: 207, Mismatches: 17, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
45 4 0.02
46 203 0.98
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:11602938 original size:16 final size:17
Alignment explanation
Indices: 11602907--11602939 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11602897 CATAAGTATA
11602907 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
11602924 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
11602940 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:11603285 original size:46 final size:46
Alignment explanation
Indices: 11603225--11603589 Score: 489
Period size: 46 Copynumber: 7.9 Consensus size: 46
11603215 TTTGAAATGA
* * * *
11603225 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCATGT
* * **
11603271 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTACATATCGCGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCATGT
* ***
11603317 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCATGT
* *
11603363 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCATGT
* * ***
11603409 TGCCATGGTATCTTTCAACTATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCATGT
* *
11603455 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCATGT
* * *
11603501 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCATGT
*
11603547 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCA
11603590 GAGAGCACAC
Statistics
Matches: 286, Mismatches: 32, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 3 0.01
46 283 0.99
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCATGT
Found at i:11606085 original size:30 final size:30
Alignment explanation
Indices: 11606018--11606085 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
11606008 CACTCTTAAA
* * *
11606018 ATATTTGCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
11606048 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
11606077 AGTATTTAC
1 A-TATTTAC
11606086 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:11609136 original size:3 final size:3
Alignment explanation
Indices: 11609128--11609380 Score: 132
Period size: 3 Copynumber: 85.0 Consensus size: 3
11609118 GAAGAGAAAT
* * * *
11609128 ATA ATA ATA GTA ATA ATA ATA TTTA ATTA ATTG AT- TTA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA A-TA A-TA ATA ATA ATA ATA ATA
* * * * *
11609174 ATA ATG ATG ATA ATA AAA ATA AT- ACA ATA ATA ATA A-A ATA GAAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * *
11609218 ATA ATA ATA ACA AT- ACA ATA ATA ATA ATA GTA A-A GATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
* * * * * * * *
11609262 ATA AGA ATG ATA AGA ATA CTA CTA CTA CTA CTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
11609310 ATA ATA ATA GTA ATA ATA ATA ATA A-A ATTA ATTA ATT A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA A-TA ATA ATA ATA ATA
*
11609355 A-A ATTA ATTA AT- TTA ATA ATA A-A ATA
1 ATA A-TA A-TA ATA ATA ATA ATA ATA ATA
11609381 GCCGAAATAA
Statistics
Matches: 196, Mismatches: 37, Indels: 34
0.73 0.14 0.13
Matches are distributed among these distances:
2 16 0.08
3 157 0.80
4 23 0.12
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11609194 original size:26 final size:26
Alignment explanation
Indices: 11609165--11609223 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
11609155 TAATTGATTT
* * *
11609165 AATAATATAATAATGATGATAATA-AA
1 AATAATACAATAATAAT-AAAATAGAA
11609191 AATAATACAATAATAATAAAATAGAA
1 AATAATACAATAATAATAAAATAGAA
11609217 AATAATA
1 AATAATA
11609224 ATAACAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (26 bp):
AATAATACAATAATAATAAAATAGAA
Found at i:11609257 original size:35 final size:35
Alignment explanation
Indices: 11609165--11609262 Score: 103
Period size: 35 Copynumber: 2.8 Consensus size: 35
11609155 TAATTGATTT
* * * * *
11609165 AATAAT-ATAATAATGATGATAATAAAAATAATAC
1 AATAATAATAATAGTAAAGATAATAATAACAATAC
11609199 AATAATAATAAAATAG-AAA-ATAATAATAACAATAC
1 AATAATAAT--AATAGTAAAGATAATAATAACAATAC
*
11609234 AATAATAATAATAGTAAAGATAATGATAA
1 AATAATAATAATAGTAAAGATAATAATAA
11609263 TAAGAATGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
33 5 0.09
34 9 0.17
35 34 0.64
36 1 0.02
37 4 0.08
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (35 bp):
AATAATAATAATAGTAAAGATAATAATAACAATAC
Found at i:11612391 original size:13 final size:13
Alignment explanation
Indices: 11612375--11612399 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11612365 TGTTTTAAAA
11612375 TTTTTAATTAATG
1 TTTTTAATTAATG
11612388 TTTTTAATTAAT
1 TTTTTAATTAAT
11612400 AAATATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:11612889 original size:20 final size:20
Alignment explanation
Indices: 11612857--11612894 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11612847 TAAGAAATAA
*
11612857 TATTTTTATTATATAATACC
1 TATTTTTATTATAAAATACC
11612877 TATTATTTA-TATAAAATA
1 TATT-TTTATTATAAAATA
11612895 AAAAGAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTTTTATTATAAAATACC
Found at i:11614167 original size:16 final size:16
Alignment explanation
Indices: 11614146--11614180 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11614136 TTACTAAGCA
11614146 TTTAATGTTTACTTTG
1 TTTAATGTTTACTTTG
* *
11614162 TTTAATTTTTCCTTTG
1 TTTAATGTTTACTTTG
11614178 TTT
1 TTT
11614181 TATAGTGCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.69
Consensus pattern (16 bp):
TTTAATGTTTACTTTG
Found at i:11614891 original size:126 final size:126
Alignment explanation
Indices: 11614689--11614945 Score: 361
Period size: 126 Copynumber: 2.0 Consensus size: 126
11614679 ATACTGGTGC
* * * * *
11614689 GTGTCTCAACCGTGTGTGACACACGGCCATGCGCATGGGCGTGTGGTTTGGCTATGTGTCCCTTG
1 GTGTCTCAACCGTGTGTGACACACGACCATGCGCACGGGCATGTGGTTTGGCTATATGTCACTTG
* * * * *
11614754 CATTTTAAAATTTGAGAAACATAATGCTTAGAATTAAGCACACCGGCAGAGACACGGGCGT
66 CATCTTAAAATTTAAGAAACAGAATGCTCAAAATTAAGCACACCGGCAGAGACACGGGCGT
* * * *
11614815 GTGTCTCAACTGTGTGTGACACACGACCATGCGTACGGGCATGTGGTTTGGTTGTATGTCACTTG
1 GTGTCTCAACCGTGTGTGACACACGACCATGCGCACGGGCATGTGGTTTGGCTATATGTCACTTG
* * *
11614880 CATCTTAAAATTTAAGAAACAGAATGCTCAAAATTGAGCATACGGGCAGAGACACGGGCGT
66 CATCTTAAAATTTAAGAAACAGAATGCTCAAAATTAAGCACACCGGCAGAGACACGGGCGT
11614941 GTGTC
1 GTGTC
11614946 CTGGCCGTGT
Statistics
Matches: 114, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
126 114 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (126 bp):
GTGTCTCAACCGTGTGTGACACACGACCATGCGCACGGGCATGTGGTTTGGCTATATGTCACTTG
CATCTTAAAATTTAAGAAACAGAATGCTCAAAATTAAGCACACCGGCAGAGACACGGGCGT
Found at i:11620037 original size:26 final size:25
Alignment explanation
Indices: 11620003--11620051 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
11619993 ATAAATAAAT
* *
11620003 AAAATTAAATTAAACAAAAGAAATGA
1 AAAACTAAATAAAACAAAA-AAATGA
11620029 AAAACTAAATAAAACAAAAAAAT
1 AAAACTAAATAAAACAAAAAAAT
11620052 CATATGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.16
Consensus pattern (25 bp):
AAAACTAAATAAAACAAAAAAATGA
Found at i:11621934 original size:30 final size:29
Alignment explanation
Indices: 11621900--11621963 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
11621890 TTAATAAAGG
*
11621900 TAAAATTACGCTTTAATCTTCTT-AAAATTA
1 TAAAATT-CGATTTAATCTT-TTAAAAATTA
*
11621930 TAAAAATTTGATTTAATCTTTTAAAAATTA
1 T-AAAATTCGATTTAATCTTTTAAAAATTA
11621960 TAAA
1 TAAA
11621964 TATATAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
29 5 0.17
30 19 0.63
31 6 0.20
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (29 bp):
TAAAATTCGATTTAATCTTTTAAAAATTA
Found at i:11623593 original size:29 final size:29
Alignment explanation
Indices: 11623560--11623618 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
11623550 GAGACTTGTT
* *
11623560 AGGCACCGCCCAGGTAGAGGGATGCTGTC
1 AGGCAACGCCCAGGTAGAGGGACGCTGTC
* *
11623589 AGGCAATGCCCAGGTGGAGGGACGCTGTC
1 AGGCAACGCCCAGGTAGAGGGACGCTGTC
11623618 A
1 A
11623619 AGCGACATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.25, G:0.39, T:0.14
Consensus pattern (29 bp):
AGGCAACGCCCAGGTAGAGGGACGCTGTC
Found at i:11624986 original size:43 final size:43
Alignment explanation
Indices: 11624864--11625013 Score: 173
Period size: 44 Copynumber: 3.5 Consensus size: 43
11624854 ATGTGTTTTT
*
11624864 ATGTAAGACCACGTATGGGAC-GTTGGCATCGA-ATTATGATTTAC
1 ATGTAAGACCACGTTTGGGACAG-TGGCATCGATATT-TGATTT-C
* * *
11624908 GTGTAAGACCACGTTTGAGACA-TCGGCATC-TTATTTGATTTC
1 ATGTAAGACCACGTTTGGGACAGT-GGCATCGATATTTGATTTC
* *
11624950 ATGTAAGACCATGTTTGGGACAGTGGCATCGATATTTGATTAC
1 ATGTAAGACCACGTTTGGGACAGTGGCATCGATATTTGATTTC
11624993 ATGTAAGACCACGTTTTGGGA
1 ATGTAAGACCACG-TTTGGGA
11625014 TGTTGGCATT
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
42 26 0.29
43 30 0.33
44 34 0.38
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (43 bp):
ATGTAAGACCACGTTTGGGACAGTGGCATCGATATTTGATTTC
Found at i:11637150 original size:24 final size:24
Alignment explanation
Indices: 11637097--11637208 Score: 152
Period size: 24 Copynumber: 4.7 Consensus size: 24
11637087 GATTCAACTC
* * * *
11637097 CGCACACATAGTGCCAAATAATTC
1 CGCACACATAGTGCCATACAAATA
* * *
11637121 CACACACATAGTGCCTTACATATA
1 CGCACACATAGTGCCATACAAATA
11637145 CGCACACATAGTGCCATACAAATA
1 CGCACACATAGTGCCATACAAATA
*
11637169 CGCTCACATAGTGCCATACAAATA
1 CGCACACATAGTGCCATACAAATA
11637193 CGCACACATAGTGCCA
1 CGCACACATAGTGCCA
11637209 CTTAAATCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (24 bp):
CGCACACATAGTGCCATACAAATA
Found at i:11643991 original size:10 final size:10
Alignment explanation
Indices: 11643976--11644006 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
11643966 CTTTGGTTCT
11643976 TATTCTTTTC
1 TATTCTTTTC
*
11643986 TATTCTATTC
1 TATTCTTTTC
11643996 TATTCTTTTC
1 TATTCTTTTC
11644006 T
1 T
11644007 TTTTTAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTCTTTTC
Found at i:11648644 original size:51 final size:51
Alignment explanation
Indices: 11648589--11649144 Score: 260
Period size: 51 Copynumber: 11.5 Consensus size: 51
11648579 ATCTACTCCG
* * *
11648589 CTGCAACTTTAGGAAGATAAGGTTTGTAACTTGTAACTTTAATCTGTTCCA
1 CTGCAACTTCAGGAAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
* * * *
11648640 CTGCAACTTCAGAGAA-ATAAGATTTG---C---TATCTTCAATCCGCTCCA
1 CTGCAACTTCAG-GAAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
* * * * *
11648685 CTGCAACTTTAGGGAGATAAGATTTATAACTTGTAGCTTTAATATGTTCTA
1 CTGCAACTTCAGGAAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
* * * * * *
11648736 CTGCAACTTCAGGAAAATAAGATTCG---C---TATCTTCAATTTGCTCCA
1 CTGCAACTTCAGGAAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
* * * *
11648781 CTGCAGCATCAGGGAGATAAGATTTATAACTTGTAGCTTTAATCTGTTCCA
1 CTGCAACTTCAGGAAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
* * * * * **
11648832 CTGCAACTTTAGG-GGAGTAAGATTCG---C---TATCTTCAATCTACTCCA
1 CTGCAACTTCAGGAAGA-TAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
* * * *
11648877 CTGCAACATCATGG-AGATAAGA--T-TCACTATCT-GC---AATCTGCTCCA
1 CTGCAACTTCA-GGAAGATAAGATTTGTAACT-TGTAGCTTTAATCTGTTCCA
* *
11648922 CTGCAACATCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
1 CTGCAACTTCAGGAAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
* * * * * * **
11648973 CTGTAACTTTAGGGAGATAAGACTTGCT-A-TGGTAGATTTAATCT-AACCTA
1 CTGCAACTTCAGGAAGATAAGATTTG-TAACTTGTAGCTTTAATCTGTTCC-A
* * *
11649023 CTGCAACTTCA--AAGGTATAAGA-CT-T-A-TCGT---TTCAATCTGCTT-CA
1 CTGCAACTTCAGGAA-G-ATAAGATTTGTAACTTGTAGCTTTAATCTG-TTCCA
* * * *
11649067 CTGCAACTTTAGGAAGATAAGATTTATAGCTTGTAGCTTTAATTTGTTCCA
1 CTGCAACTTCAGGAAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
* *
11649118 CTGTAACTTCAGGGAA-ATAAAATTTGT
1 CTGCAACTTCA-GGAAGATAAGATTTGT
11649145 TATCTTTAAT
Statistics
Matches: 377, Mismatches: 80, Indels: 96
0.68 0.14 0.17
Matches are distributed among these distances:
44 28 0.07
45 128 0.34
46 7 0.02
47 8 0.02
48 16 0.04
49 5 0.01
50 33 0.09
51 144 0.38
52 8 0.02
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (51 bp):
CTGCAACTTCAGGAAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
Found at i:11648689 original size:96 final size:96
Alignment explanation
Indices: 11648575--11649304 Score: 567
Period size: 96 Copynumber: 7.7 Consensus size: 96
11648565 GAATTGTAGT
* * * * * *
11648575 TTCAATCTACTCCGCTGCAACTTTAGGAAGATAAGGTTTGTAACTTGTAACTTTAATCTGTTCCA
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTGTAGCTTTAATCTGTTCCA
*
11648640 CTGCAACTTCAGAGAAATAAGATTTGCTATC
66 CTGCAACTTCAGGGAAATAAGATTTGCTATC
* * *
11648671 TTCAATCCGCTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTGTAGCTTTAATATGTTCTA
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTGTAGCTTTAATCTGTTCCA
* *
11648736 CTGCAACTTCAGGAAAATAAGATTCGCTATC
66 CTGCAACTTCAGGGAAATAAGATTTGCTATC
* * * *
11648767 TTCAATTTGCTCCACTGCAGCATCAGGGAGATAAGATTTATAACTTGTAGCTTTAATCTGTTCCA
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTGTAGCTTTAATCTGTTCCA
* * * *
11648832 CTGCAACTTTAGGGGAGTAAGATTCGCTATC
66 CTGCAACTTCAGGGAAATAAGATTTGCTATC
* * * * * * *
11648863 TTCAATCTACTCCACTGCAACATCATGGAGATAAGA--T-TCACTATCT-GC---AATCTGCTCC
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTATAACT-TGTAGCTTTAATCTGTTCC
* * *
11648921 ACTGCAACATCAGGGAGATAAGATTTGTAACTTGTAGC
65 ACTGCAACTTCAGGGAAATAAGATTTG---C---TATC
* * * ** * * **
11648959 TTTAATCTGTTCCACTGTAACTTTAGGGAGATAAGACTTGCT-A-TGGTAGATTTAATCT-AACC
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGA-TTTATAACTTGTAGCTTTAATCTGTTCC
* * *
11649021 TACTGCAACTTCAAAGG-TATAAGA-CT--TATC
65 -ACTGCAACTTC-AGGGAAATAAGATTTGCTATC
* * * *
11649051 GTTTCAATCTGCTTCACTGCAACTTTAGGAAGATAAGATTTATAGCTTGTAGCTTTAATTTGTTC
1 --TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTGTAGCTTTAATCTGTTC
* * *
11649116 CACTGTAACTTCAGGGAAATAAAATTTGTTATC
64 CACTGCAACTTCAGGGAAATAAGATTTGCTATC
* * * * * * *
11649149 TTTAATCTACTCCACTGCAGCTTCAGGGAGAT--GA--GAT---TTGTAGCTTTAATCCGCTCCA
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTGTAGCTTTAATCTGTTCCA
*
11649207 CTGCAACTTCAGGGAGAT-A-ATGTT-C--TC
66 CTGCAACTTCAGGGAAATAAGAT-TTGCTATC
* * * * * * ** *
11649234 TTTAATCTGCTCCACTGTATCTTCAGAGAGATAAGATTTGTAACTTGTAGCTTTAGCCTATTCCA
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTGTAGCTTTAATCTGTTCCA
11649299 CTGCAA
66 CTGCAA
11649305 TGTAGCACCC
Statistics
Matches: 503, Mismatches: 97, Indels: 72
0.75 0.14 0.11
Matches are distributed among these distances:
85 30 0.06
87 4 0.01
88 3 0.01
89 35 0.07
90 30 0.06
92 27 0.05
93 10 0.02
94 39 0.08
95 27 0.05
96 262 0.52
97 1 0.00
98 6 0.01
99 1 0.00
100 4 0.01
101 21 0.04
102 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (96 bp):
TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTGTAGCTTTAATCTGTTCCA
CTGCAACTTCAGGGAAATAAGATTTGCTATC
Found at i:11648897 original size:141 final size:139
Alignment explanation
Indices: 11648735--11649226 Score: 503
Period size: 141 Copynumber: 3.5 Consensus size: 139
11648725 AATATGTTCT
* * *
11648735 ACTGCAACTTCAGGAAAATAAGATTCGCTATCTTCAATTTGCTCCACTGCAGCATCAGGGAGATA
1 ACTGCAACTTCAGG-AGATAAGATTCGCTATCTTCAATCTGCTCCACTGCAACATCAGGGAGATA
*
11648800 AGATTTATAACTTGTAGCTTTAATCTGTTCCACTGCAACTTTAGGGGAGTAAGATTCGCTATCTT
65 AGATTTATAACTTGTAGCTTTAATCTGTTCCACTGTAACTTTAGGGGAGTAAGATT-GCTATCTT
*
11648865 CAATCTACTCC
129 TAATCTACTCC
* * *
11648876 ACTGCAACATCATGGAGATAAGATTCACTATCTGCAATCTGCTCCACTGCAACATCAGGGAGATA
1 ACTGCAACTTCA-GGAGATAAGATTCGCTATCTTCAATCTGCTCCACTGCAACATCAGGGAGATA
*
11648941 AGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGTAACTTTA-GGGAGATAAGACTTGCTATGG
65 AGATTTATAACTTGTAGCTTTAATCTGTTCCACTGTAACTTTAGGGGAG-TAAGA-TTGCTA---
* *
11649005 TAGATTTAATCTAAC-CT
125 T--CTTTAATCT-ACTCC
* * * * * *
11649022 ACTGCAACTTCAAAGG-TATAAGA--C-TTATCGTTTCAATCTGCTTCACTGCAACTTTAGGAAG
1 ACTGCAACTTC--AGGAGATAAGATTCGCTATC--TTCAATCTGCTCCACTGCAACATCAGGGAG
* * * * * * *
11649083 ATAAGATTTATAGCTTGTAGCTTTAATTTGTTCCACTGTAACTTCAGGGAAATAAAATTTGTTAT
62 ATAAGATTTATAACTTGTAGCTTTAATCTGTTCCACTGTAACTTTAGGGGAGTAAGA-TTGCTAT
11649148 CTTTAATCTACTCC
126 CTTTAATCTACTCC
* * * * * * *
11649162 ACTGCAGCTTCAGGGAGATGAGATTTG-TAGCTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
1 ACTGCAACTTCA-GGAGATAAGATTCGCTATCTTCAATCTGCTCCACTGCAACATCAGGGAGATA
11649226 A
65 A
11649227 TGTTCTCTTT
Statistics
Matches: 291, Mismatches: 40, Indels: 41
0.78 0.11 0.11
Matches are distributed among these distances:
138 1 0.00
139 4 0.01
140 58 0.20
141 106 0.36
142 8 0.03
143 4 0.01
144 2 0.01
145 76 0.26
146 27 0.09
147 4 0.01
148 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (139 bp):
ACTGCAACTTCAGGAGATAAGATTCGCTATCTTCAATCTGCTCCACTGCAACATCAGGGAGATAA
GATTTATAACTTGTAGCTTTAATCTGTTCCACTGTAACTTTAGGGGAGTAAGATTGCTATCTTTA
ATCTACTCC
Found at i:11649211 original size:44 final size:44
Alignment explanation
Indices: 11648619--11649275 Score: 313
Period size: 45 Copynumber: 14.1 Consensus size: 44
11648609 GGTTTGTAAC
* * * *
11648619 TTGTAACTTTAATCTGTTCCACTGCAACTTCAGAGAAATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
11648663 TTGCTATCTTCAATCCGCTCCACTGCAACTTTAGGGAGATAAGATTTAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG----AT
* * * * *
11648712 AACTTGTAGCTTTAATATGTTCTACTGCAACTTCAGGAAAATAAGAT
1 ---TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * * *
11648759 TCGCTATCTTCAATTTGCTCCACTGCAGCATCAGGGAGATAAGATTTAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG----AT
* *
11648808 AACTTGTAGCTTTAATCTGTTCCACTGCAACTTTAGGG-GAGTAAGAT
1 ---TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGA-TAAGAT
* * * * * *
11648855 TCGCTATCTTCAATCTACTCCACTGCAACATCATGGAGATAAGAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
** * ** *
11648900 TCACTATCTGCAATCTGCTCCACTGCAACATCAGGGAGATAAGATTTGT
1 T-TGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA----T
* * *
11648949 AACTTGTAGCTTTAATCTGTTCCACTGTAACTTTAGGGAGATAAGACTT
1 ---TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T
* * * * * *
11648998 GCTATGGTAGATTTAATCTAAC-CTACTGCAACTTCAAAGG-TATAAGAC
1 --T-T-GTAGCTTTAATCT-GCTCCACTGCAACTTC-AGGGAGATAAGAT
* * * * *
11649046 TTATCG-TTTCAATCTGCTTCACTGCAACTTTAGGAAGATAAGATTTAT
1 TTGTAGCTTT-AATCTGCTCCACTGCAACTTCAGGGAGATAAG----AT
* * * * *
11649094 AGCTTGTAGCTTTAATTTGTTCCACTGTAACTTCAGGGAAATAAAAT
1 ---TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
11649141 TTGTTATCTTTAATCTACTCCACTGCAGCTTCAGGGAGATGAGAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*
11649186 TTGTAGCTTTAATCCGCTCCACTGCAACTTCAGGGAGAT-A-AT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
11649228 GTTCT--CTTTAATCTGCTCCACTGTATCTTCAGAGAGATAAGAT
1 -TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
11649271 TTGTA
1 TTGTA
11649276 ACTTGTAGCT
Statistics
Matches: 459, Mismatches: 107, Indels: 95
0.69 0.16 0.14
Matches are distributed among these distances:
41 29 0.06
42 6 0.01
43 12 0.03
44 64 0.14
45 167 0.36
46 3 0.01
47 6 0.01
48 3 0.01
49 7 0.02
50 30 0.07
51 123 0.27
52 9 0.02
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (44 bp):
TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
Found at i:11649271 original size:85 final size:87
Alignment explanation
Indices: 11649097--11649275 Score: 227
Period size: 85 Copynumber: 2.1 Consensus size: 87
11649087 GATTTATAGC
** * *
11649097 TTGTAGCTTTAATTTGTTCCACTGTAACTTCAGGGAAATAAAATTTGTTATCTTTAATCTACTCC
1 TTGTAGCTTTAATCCGCTCCACTGCAACTTCAGGGAAAT-AAA-TTGTTATCTTTAATCTACTCC
* *
11649162 ACTGCAGCTTCAGGGAGATGAGAT
64 ACTGCAGCTTCAGAGAGATAAGAT
* * *
11649186 TTGTAGCTTTAATCCGCTCCACTGCAACTTCAGGGAGAT-AA-TGTTCTCTTTAATCTGCTCCAC
1 TTGTAGCTTTAATCCGCTCCACTGCAACTTCAGGGAAATAAATTGTTATCTTTAATCTACTCCAC
* *
11649249 TGTATCTTCAGAGAGATAAGAT
66 TGCAGCTTCAGAGAGATAAGAT
11649271 TTGTA
1 TTGTA
11649276 ACTTGTAGCT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
85 43 0.54
87 2 0.03
89 34 0.43
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (87 bp):
TTGTAGCTTTAATCCGCTCCACTGCAACTTCAGGGAAATAAATTGTTATCTTTAATCTACTCCAC
TGCAGCTTCAGAGAGATAAGAT
Found at i:11652378 original size:44 final size:44
Alignment explanation
Indices: 11652296--11652571 Score: 155
Period size: 44 Copynumber: 6.4 Consensus size: 44
11652286 CGTTACATGC
* * *
11652296 AACTTCAGAGAGAT-A-A-TGGTAGATTTAATCTGAC-CCACTAA
1 AACTTCAGAGAGATAAGATTTGTAGCTTCAATCTG-CTCCACTAA
* * **
11652337 AACTTCAGAGATATAAGATTTGTCGCTTCAATCTGCTCCACTGT
1 AACTTCAGAGAGATAAGATTTGTAGCTTCAATCTGCTCCACTAA
* * * *
11652381 AACTTTAGGGAGATAAGATTTGTAGCTTCAACCTGCTCCACTAC
1 AACTTCAGAGAGATAAGATTTGTAGCTTCAATCTGCTCCACTAA
* * * * *
11652425 AACTTCA-AGGAGATAAG--GT-TA-CTTTAATCTGATCCATTGCA
1 AACTTCAGA-GAGATAAGATTTGTAGCTTCAATCTGCTCCACT-AA
** * * *
11652466 CCCTT-AG-GAAGATAAGATTTGTAACTTCAATCTACTCCACTAC
1 AACTTCAGAG-AGATAAGATTTGTAGCTTCAATCTGCTCCACTAA
* * * ** *
11652509 AACTTTA-AGGAGATAAGGTTTGT-GACTTTAATCTATTCCACTAC
1 AACTTCAGA-GAGATAAGATTTGTAG-CTTCAATCTGCTCCACTAA
*
11652553 AACTTCAGGGAGATAAGAT
1 AACTTCAGAGAGATAAGAT
11652572 CTGCCACGAT
Statistics
Matches: 177, Mismatches: 41, Indels: 31
0.71 0.16 0.12
Matches are distributed among these distances:
39 1 0.01
40 21 0.12
41 18 0.10
42 3 0.02
43 7 0.04
44 126 0.71
45 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (44 bp):
AACTTCAGAGAGATAAGATTTGTAGCTTCAATCTGCTCCACTAA
Found at i:11666797 original size:25 final size:23
Alignment explanation
Indices: 11666753--11666809 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
11666743 TGGTATTATG
* *
11666753 ATCATTATTGTTATCCTTATTACTC
1 ATCATTATTATTATACTTA-TA-TC
*
11666778 ATCATTATTATTATAGTTATATC
1 ATCATTATTATTATACTTATATC
11666801 ATTCATTAT
1 A-TCATTAT
11666810 GCATTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.11
24 9 0.32
25 16 0.57
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.53
Consensus pattern (23 bp):
ATCATTATTATTATACTTATATC
Found at i:11668463 original size:24 final size:24
Alignment explanation
Indices: 11668434--11668487 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
11668424 AATTAAGTAT
11668434 AAAATATAATTTT-ATTATTTGATA
1 AAAATATAATTTTGATTATTT-ATA
*
11668458 AAAATA-AATTTTGATTATTTTTA
1 AAAATATAATTTTGATTATTTATA
11668481 AAAATAT
1 AAAATAT
11668488 TCATTTCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAAATATAATTTTGATTATTTATA
Found at i:11677961 original size:25 final size:25
Alignment explanation
Indices: 11677933--11677985 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
11677923 TTAAAATTTC
11677933 ATAAGAGAACAAATCTAATATGCAA
1 ATAAGAGAACAAATCTAATATGCAA
* *
11677958 ATAAGGGAACAAATTTAATATGCAA
1 ATAAGAGAACAAATCTAATATGCAA
11677983 ATA
1 ATA
11677986 GATCAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (25 bp):
ATAAGAGAACAAATCTAATATGCAA
Found at i:11679188 original size:17 final size:14
Alignment explanation
Indices: 11679144--11679179 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
11679134 AACTTGAATC
*
11679144 ATTA-ATTAACTTT
1 ATTATATTAAATTT
11679157 ATTATATTAAATTT
1 ATTATATTAAATTT
11679171 ATTATATTA
1 ATTATATTA
11679180 CAAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATATTAAATTT
Found at i:11679249 original size:17 final size:18
Alignment explanation
Indices: 11679223--11679256 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11679213 TCTTTAATTT
*
11679223 TTTTTAAAAAATTTATAA
1 TTTTTAAAAAATATATAA
11679241 TTTTT-AAAAATATATA
1 TTTTTAAAAAATATATA
11679257 TTGAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTAAAAAATATATAA
Found at i:11679297 original size:19 final size:19
Alignment explanation
Indices: 11679224--11679298 Score: 57
Period size: 18 Copynumber: 3.9 Consensus size: 19
11679214 CTTTAATTTT
*
11679224 TTTTAAAAA--ATTTATAAT
1 TTTTAAAAATTATTT-TAAA
*
11679242 TTTTAAAAATATATATTGAAA
1 TTTTAAAAAT-TAT-TTTAAA
* *
11679263 TTTTTATAAAGT-TTTTAAA
1 -TTTTAAAAATTATTTTAAA
11679282 TTTTAAAAATTATTTTA
1 TTTTAAAAATTATTTTA
11679299 TTTTATTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
18 18 0.41
19 10 0.23
20 1 0.02
21 5 0.11
22 10 0.23
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:11679946 original size:24 final size:25
Alignment explanation
Indices: 11679914--11679972 Score: 86
Period size: 24 Copynumber: 2.4 Consensus size: 25
11679904 TAATAAATAA
*
11679914 TTAATATTAATTACT-TAGAATTAT
1 TTAAAATTAATTACTATAGAATTAT
*
11679938 TTAAAATTAA-TATTATAGAATTAT
1 TTAAAATTAATTACTATAGAATTAT
11679962 TTAAAATTAAT
1 TTAAAATTAAT
11679973 ATTATATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (25 bp):
TTAAAATTAATTACTATAGAATTAT
Found at i:11679973 original size:24 final size:24
Alignment explanation
Indices: 11679929--11679978 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
11679919 ATTAATTACT
11679929 TAGAATTATTTAAAATTAATATTA
1 TAGAATTATTTAAAATTAATATTA
11679953 TAGAATTATTTAAAATTAATATTA
1 TAGAATTATTTAAAATTAATATTA
11679977 TA
1 TA
11679979 TATTAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
TAGAATTATTTAAAATTAATATTA
Found at i:11680184 original size:13 final size:13
Alignment explanation
Indices: 11680168--11680233 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
11680158 TTTAAATTAA
11680168 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
11680181 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
* * *
11680194 ACTTTTTTACAA-T
1 AC-TTTTCAAAAGC
11680207 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
11680220 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
11680233 A
1 A
11680234 TTGCCAAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 7 0.16
13 30 0.68
14 7 0.16
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:11680197 original size:26 final size:26
Alignment explanation
Indices: 11680168--11680233 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
11680158 TTTAAATTAA
* *
11680168 ACTTTTCAAAAGCACTTTTCAAAAGT
1 ACTTTTTAAAAGCACTTTTCAAAAGC
* *
11680194 ACTTTTTTACAA-TACTTTTCAAAAGC
1 AC-TTTTTAAAAGCACTTTTCAAAAGC
11680220 ACTTTTTAAAAGCA
1 ACTTTTTAAAAGCA
11680234 TTGCCAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 8 0.25
26 17 0.53
27 7 0.22
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (26 bp):
ACTTTTTAAAAGCACTTTTCAAAAGC
Done.