Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397396.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1062.0, whole genome shotgun sequence
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: 25985
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.30
Warning! 4932 characters in sequence are not A, C, G, or T
Found at i:1933 original size:171 final size:171
Alignment explanation
Indices: 1395--1886 Score: 521
Period size: 171 Copynumber: 2.9 Consensus size: 171
1385 NNNNNNNGTC
* * * * * * * *
1395 ACCCATGCCTTTGAAAGTCTTATTACTCGCTTTAAATAGTTTTATAATCTCTTCATTGATTTCAA
1 ACCCATGCCTTCGAAAGCCTTATTACTTGCCTTAAATAGTTTTAAAATCTCGTAATTGATTTTAA
* * * ** * * * *
1460 GCTAAATTTTTTTACATTTTTAATTAAGACAAATCATAATTGAATGTTTG-CTTATGGAAA-GCT
66 CCTGAATTTTTGTACATTTTTGGTTAAAACATATAATAATTGAATGTCTGCCTTA-GGAAACG-T
* ** * * *
1523 GAAGAAAAAGCCATTCATTGGCAACAAAAGTTCATA--TATAG-T
129 GAAAAAAAAGATATCCATTGGCTAGAAAA-TT-ATATTTATAGCT
* * * * * * * * *
1565 CATCTACGCCTTCAAAAGCCTTATTAGTTGCCTGAAATATTTTTAGAATCTCGTAATTAATTTTA
1 -ACCCATGCCTTCGAAAGCCTTATTACTTGCCTTAAATAGTTTTAAAATCTCGTAATTGATTTTA
* *
1630 ACCTGAATTTTTGTATATTTTTGGTTAAAACATATAATATTTGAATGTCTGCCTTAGGAAACGTG
65 ACCTGAATTTTTGTACATTTTTGGTTAAAACATATAATAATTGAATGTCTGCCTTAGGAAACGTG
* *
1695 AAGAAAAATATATCCATTGGCTAGAAAATTATATTTATAGCT
130 AAAAAAAAGATATCCATTGGCTAGAAAATTATATTTATAGCT
*
1737 ATCCATGCCTTCGAAAGCCTTATTACTTGCCTTAAATAGTTTTAAAATCTCGTAATTGATTTTAA
1 ACCCATGCCTTCGAAAGCCTTATTACTTGCCTTAAATAGTTTTAAAATCTCGTAATTGATTTTAA
* *
1802 CTTGAATTTTTGTACATTTTTGGTTAAAAC-TGATAATAATTGAATGTTTGCCTTAGGAAACAG-
66 CCTGAATTTTTGTACATTTTTGGTTAAAACAT-ATAATAATTGAATGTCTGCCTTAGGAAAC-GT
1865 GAAAAAAAAGATATCCATTGGC
129 GAAAAAAAAGATATCCATTGGC
1887 ANNNNNNNNN
Statistics
Matches: 267, Mismatches: 47, Indels: 14
0.81 0.14 0.04
Matches are distributed among these distances:
169 3 0.01
170 3 0.01
171 254 0.95
172 7 0.03
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (171 bp):
ACCCATGCCTTCGAAAGCCTTATTACTTGCCTTAAATAGTTTTAAAATCTCGTAATTGATTTTAA
CCTGAATTTTTGTACATTTTTGGTTAAAACATATAATAATTGAATGTCTGCCTTAGGAAACGTGA
AAAAAAAGATATCCATTGGCTAGAAAATTATATTTATAGCT
Found at i:2122 original size:171 final size:169
Alignment explanation
Indices: 1633--2431 Score: 441
Period size: 171 Copynumber: 4.7 Consensus size: 169
1623 AATTTTAACC
** * * ** * * * *
1633 TGAATTTTTGTATATTTTTGGTTAAAACATATAAT-ATTTGAATGTCTGCCTTAGGAAACGTGAA
1 TGAATTTTT-TATATTTTTTATTAAAACAGATTATAATTT-AATGTCTATCTCAAGAAACATAAA
* * * * *
1697 GAAAAATATATCCATTGGCTAGAAAA-TTATATTTATAG-CTATCCATGCCTTCGAAAGCCTTAT
64 AAAAAAGATATCCATT-GCAAGAAAAGTTA-ATTTATAGTC-ACCCATACCTTCGAAAGCCTTAT
* * * * * * *
1760 TACTTGC-CT-TAAATAGTTTTAAAATCTCGTAATTGATTTTAACT
126 GAC-T-CACTATAAATGGTTTTATAATGTCATAATTGACTTTAAAT
* ** * * * * ** * * **
1804 TGAATTTTTGTACATTTTTGGTTAAAACTGATAATAATTGAATGTTTGCCTTAGGAAACAGGAAA
1 TGAATTTTT-TATATTTTTTATTAAAACAGATTATAATTTAATGTCTATCTCAAGAAACATAAAA
********** * ** * * *
1869 AAAAAGATATCCATTGGCANNNNNNNNNNATTTATAGTTACCCATGTCTTTGGAAGCCTTATTAC
65 AAAAAGATATCCATT-GCAAGAAAAGTTAATTTATAGTCACCCATACCTTCGAAAGCCTTATGAC
* * * * *
1934 -CGCGT-TAAATAGTTTTATAATGTCATAATTGATTTTGAGT
129 TCAC-TATAAATGGTTTTATAATGTCATAATTGACTTTAAAT
* * * *
1974 TAAATTTATTAATATTTTTTATTAAACCAGATTATAATTTAATGTGTATCTCAAGAAACATAAAA
1 TGAATTT-TTTATATTTTTTATTAAAACAGATTATAATTTAATGTCTATCTCAAGAAACAT-AAA
*
2039 AAAAAAGATATCCATTAGCAAGAAAAGTTAATTTATAGTCACCCATTCCTTCGAAAGCCTTATGA
64 AAAAAAGATATCCATT-GCAAGAAAAGTTAATTTATAGTCACCCATACCTTCGAAAGCCTTATGA
* * **********
2104 GTTACTAT-AATGGTTTTATAATGTCATAATTNNNNNNNNNN
128 CTCACTATAAATGGTTTTATAATGTCATAATTGACTTTAAAT
* * ** * ** * *
2145 TGAATTGTTTTATATTTTTTATTAAAATAGATTATAATTAAATACCTAACTTGAGAAACGTGAAA
1 TGAATT-TTTTATATTTTTTATTAAAACAGATTATAATTTAATGTCTATCTCAAGAAACATAAAA
* * * * * *
2210 AAAAAGATATCTATTGACAAGAAAACTTTATTTATAGTCACACATGCCTTCGAAAGCCTTATTAC
65 AAAAAGATATCCATTG-CAAGAAAAGTTAATTTATAGTCACCCATACCTTCGAAAGCCTTATGAC
* * * * *
2275 TCGCTCTAAATGTTTTTATAATCTGAT-ATTGACTTTAAAT
129 TCACTATAAATGGTTTTATAATGTCATAATTGACTTTAAAT
** * * *
2315 TGAATTTGTTTGCATTTTTTATTAAAACAGATTATAATTTAATGTCTGTCTCTAGAAACATGATA
1 TGAATTT-TTTATATTTTTTATTAAAACAGATTATAATTTAATGTCTATCTCAAGAAACAT-AAA
* *
2380 AAAAAAGATATTCATTGGTAAGAAAAG--AATACTTATAGTCACCCATACCTTC
64 AAAAAAGATATCCATT-GCAAGAAAAGTTAAT--TTATAGTCACCCATACCTTC
2432 ANNNNNNNNN
Statistics
Matches: 479, Mismatches: 132, Indels: 34
0.74 0.20 0.05
Matches are distributed among these distances:
168 1 0.00
169 5 0.01
170 188 0.39
171 278 0.58
172 7 0.01
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.37
Consensus pattern (169 bp):
TGAATTTTTTATATTTTTTATTAAAACAGATTATAATTTAATGTCTATCTCAAGAAACATAAAAA
AAAAGATATCCATTGCAAGAAAAGTTAATTTATAGTCACCCATACCTTCGAAAGCCTTATGACTC
ACTATAAATGGTTTTATAATGTCATAATTGACTTTAAAT
Found at i:4901 original size:171 final size:171
Alignment explanation
Indices: 4457--4905 Score: 411
Period size: 171 Copynumber: 2.6 Consensus size: 171
4447 AATTTAACTC
* * * * * * *** *
4457 AAAATCAATTATGACATTATAAAACTATTTAACGCGAGTAATAAGGCTTCCAAAGACATGGATAA
1 AAAATCAATTACGAGATTCTAAAACTATTTAAGGCGAATAATAAGACTTTTGAAGGCATGGATAA
* * * * * * * * * * *
4522 CTATAAGTATATTTTTCCTGTCAATGGATATCTTTTTTTTC-CTATTTCCCAACGCAAACATTCA
66 CTATAAATATACTTTTCTTGCCAATGAATAGCTTTTTCTTCAC-GTTTCCTAAGGCAGACATTCA
* *
4586 ATTATTATATGTTTTAACCAAAAATGTACAAAAATTCAAGTT
130 ATTATTATATGTTTTAACAAAAAATATACAAAAATTCAAGTT
* * *
4628 AAAATCAATTACGATATTCTAAAACTATTTAAGGCGAGTAATAAGACTTTTGAAGGTATGGATAA
1 AAAATCAATTACGAGATTCTAAAACTATTTAAGGCGAATAATAAGACTTTTGAAGGCATGGATAA
********** * *
4693 CTATAAATATANNNNNNNNNNCAATGGATATCTTTTTCTTCACGTTTCCTAAGGCAGACATTCAA
66 CTATAAATATACTTTTCTTGCCAATGAATAGCTTTTTCTTCACGTTTCCTAAGGCAGACATTCAA
* *
4758 TTATTATATGTTTTAATAAAAAATATATAAAAATTCAAGTT
131 TTATTATATGTTTTAACAAAAAATATACAAAAATTCAAGTT
* * * *
4799 AAAATTAATTACGAGATTCTAAAAAC-ATTTTAGGC-ATATAATAAGGCTTTTGAAGGCGTGGAT
1 AAAATCAATTACGAGATTCT-AAAACTATTTAAGGCGA-ATAATAAGACTTTTGAAGGCATGGAT
* * *
4862 GACTATATATGA-ACTTTTCTTGCCAATGAATGGCTTTTTCTTCA
64 AACTATAAAT-ATACTTTTCTTGCCAATGAATAGCTTTTTCTTCA
4906 GCTTTCNNNN
Statistics
Matches: 222, Mismatches: 52, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
170 1 0.00
171 214 0.96
172 7 0.03
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.35
Consensus pattern (171 bp):
AAAATCAATTACGAGATTCTAAAACTATTTAAGGCGAATAATAAGACTTTTGAAGGCATGGATAA
CTATAAATATACTTTTCTTGCCAATGAATAGCTTTTTCTTCACGTTTCCTAAGGCAGACATTCAA
TTATTATATGTTTTAACAAAAAATATACAAAAATTCAAGTT
Found at i:5757 original size:171 final size:171
Alignment explanation
Indices: 5447--5759 Score: 367
Period size: 171 Copynumber: 1.8 Consensus size: 171
5437 TTAAATTATA
* * * ** *
5447 ATCTGTTGGAATAAAAATTATATAAAAACTCAACTTAAAATTAATTATGATGTTATAAAATCATT
1 ATCTGTTGGAATAAAAAATATAAAAAAACTCAACTTAAAATAAATTACAAGGTTATAAAATCATT
* ********** *
5512 TAAACCAAGTAATAAGGCTTTCAAACACATGGGTGACTATAAATGGACNNNNNNNNNNAATGAAT
66 TAAACCAAGTAATAAGCCTTTCAAACACATGGGTGACTATAAATGGACTTTTCCTAGCAATGAAC
*
5577 GATTTTTTCTTCTCGTTTTTCAATACAGACATTCATATATT
131 GACTTTTTCTTCTCGTTTTTCAATACAGACATTCATATATT
** *
5618 ATCTGTTTTAATAAAAAATATAAAAAAACTCAACTTAAAATAAATTACAAGGTTATAAAATTATT
1 ATCTGTTGGAATAAAAAATATAAAAAAACTCAACTTAAAATAAATTACAAGGTTATAAAATCATT
* * **
5683 TAAACCGAG-AGATAAGCCTTTGAAACGTATGGGTGACTATAAATGGACTTTTCCTAGCAATGAA
66 TAAACCAAGTA-ATAAGCCTTTCAAACACATGGGTGACTATAAATGGACTTTTCCTAGCAATGAA
*
5747 CGGCTTTTTCTTC
130 CGACTTTTTCTTC
5760 ATATTTGCTA
Statistics
Matches: 114, Mismatches: 27, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
170 1 0.01
171 113 0.99
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.33
Consensus pattern (171 bp):
ATCTGTTGGAATAAAAAATATAAAAAAACTCAACTTAAAATAAATTACAAGGTTATAAAATCATT
TAAACCAAGTAATAAGCCTTTCAAACACATGGGTGACTATAAATGGACTTTTCCTAGCAATGAAC
GACTTTTTCTTCTCGTTTTTCAATACAGACATTCATATATT
Found at i:6163 original size:171 final size:171
Alignment explanation
Indices: 5985--6519 Score: 437
Period size: 171 Copynumber: 3.1 Consensus size: 171
5975 NNNNNNNNNC
* * * * *
5985 AAATTCAATTTAAAGTCAATTATCATATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCAAA
1 AAATTCAACTCAAAATCAATTATAACATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCAAA
* *
6050 GGTATGAGTGACTATAAATAGACTTTTCTTCTAATAGATATCTTTTTTCTTCACGTTTCTTGAGG
66 GGTATGGGTGACTATAAATAGACTTTTCTTCTAATAGATATCTTTTTTCTTCACGTTTCTCGAGG
6115 TAGATA-ATT-AATTATAATCTATTTTAATAAACAACATA-AAA-
131 TA-A-ACATTCAATTATAATCTATTTTAA-AAACAA-ATATAAAT
* * * * * ** *
6156 CAATTCAACTCAAAATCAATTATGACATTATAAAATCA-TTAAAGTGACTCTTAAGGCTTTCGAA
1 AAATTCAACTCAAAATCAATTATAACATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCAAA
* ********** * * * * *
6220 GGCATGGGTGANNNNNNNNNNACTTTTCTTGTCAATGGATATCTTTTTTTTTTATGTTTCTCGAG
66 GGTATGGGTGACTATAAATAGACTTTTCTTCT-AATAGATATCTTTTTTCTTCACGTTTCTCGAG
*
6285 GTAAACATTCAATTATAATCTATTTTAACAACAAATATAAAT
130 GTAAACATTCAATTATAATCTATTTTAAAAACAAATATAAAT
* ** *
6327 AAATTTAACTCAAAATCAATTATAACATTAT-AAAACTATTTACCGCGAGTAATAAGGCTTCCAA
1 AAATTCAACTCAAAATCAATTATAACATTATAAAAAC-ATTTAAAGCGAGTAATAAGGCTTTCAA
* * * * *
6391 AGATATGGGTAACTATAAATATATTTTTCTTGCCAATAGATATCTTTTTGTTCTT-A--TTTC-C
65 AGGTATGGGTGACTATAAATAGACTTTTCTT-CTAATAGATATC-TTTT-TTCTTCACGTTTCTC
* * * * * *
6452 TAAGGCAAACATTCAATTATTATCTGTTTTAACAAA-ATATTTATAA-
127 -GAGGTAAACATTCAATTATAATCTATTTTAA-AAACAAATATA-AAT
* *
6498 AAATTCAAGTTAAAATCAATTA
1 AAATTCAACTCAAAATCAATTA
6520 CNNNNNNNNN
Statistics
Matches: 280, Mismatches: 71, Indels: 26
0.74 0.19 0.07
Matches are distributed among these distances:
169 4 0.01
170 57 0.20
171 163 0.58
172 47 0.17
173 5 0.02
174 4 0.01
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.37
Consensus pattern (171 bp):
AAATTCAACTCAAAATCAATTATAACATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCAAA
GGTATGGGTGACTATAAATAGACTTTTCTTCTAATAGATATCTTTTTTCTTCACGTTTCTCGAGG
TAAACATTCAATTATAATCTATTTTAAAAACAAATATAAAT
Found at i:6537 original size:171 final size:161
Alignment explanation
Indices: 6360--6691 Score: 385
Period size: 171 Copynumber: 2.0 Consensus size: 161
6350 AACATTATAA
* * * * *
6360 AACTATTTACCGCGAGTAATAAGGCTTCCAAAGATATGGGTAACTATAAATATATTTTTCTTGCC
1 AACTATTTAACGCGAGTAATAAGGCTTCCAAAGATATGGATAAATATAAATATACTTTTCTAGCC
* * * * * *
6425 AATAGATATCTTTTTGTTCTTATTTCCTAAGGCAAACATTCAATTATTATCTGTTTTAACAAAAT
66 AATAGATATCTTTTTCTTCATATATCCCAAGGCAAACATTCAATTATTATCTATTTTAACAAAAA
* *
6490 ATTTATAAAAATTCAAGTTAAAATCAATTAC
131 ATGTACAAAAATTCAAGTTAAAATCAATTAC
* * * *
6521 NNNNNNNNNNAACTATTTAAGGCGAGTAATAAGGCTTGCGAAGGTATGGATAAATATAAATATAC
1 ----------AACTATTTAACGCGAGTAATAAGGCTTCCAAAGATATGGATAAATATAAATATAC
* *
6586 TTTTCTAGCCAATGGATATCTTTTTCTTCATGTATCCCAAGGCAAACATTCAATTATTATCTATT
56 TTTTCTAGCCAATAGATATCTTTTTCTTCATATATCCCAAGGCAAACATTCAATTATTATCTATT
* *
6651 TTAATAAAAAATGTACAAAAATTCAAGTTAAAATTAATTAC
121 TTAACAAAAAATGTACAAAAATTCAAGTTAAAATCAATTAC
6692 GAGACTCTAA
Statistics
Matches: 140, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
171 140 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.36
Consensus pattern (161 bp):
AACTATTTAACGCGAGTAATAAGGCTTCCAAAGATATGGATAAATATAAATATACTTTTCTAGCC
AATAGATATCTTTTTCTTCATATATCCCAAGGCAAACATTCAATTATTATCTATTTTAACAAAAA
ATGTACAAAAATTCAAGTTAAAATCAATTAC
Found at i:7593 original size:127 final size:127
Alignment explanation
Indices: 7356--7599 Score: 276
Period size: 127 Copynumber: 1.9 Consensus size: 127
7346 CATTGGCTAG
*
7356 AAAAGTATATTTATAGTTATCCATACCTTCGCAAGCCTTATTACTCGCCTTAAATAATTTTAGAA
1 AAAAGTATATTTATAGTTACCCATACCTTCGCAAGCCTTATTACTCGCCTTAAATAATTTTAGAA
* * * *
7421 TCTCGTAATTGATTTTAACTTGAATTTTTGTAAATATTTTGTTAAAACAGATATATTTTGTT
66 TCTCATAATTGATTTTAACTTGAATTTATATAAATATTTTATTAAAACAGATATATTTTGTT
** * * * * **
7483 AAAA-TATATTTATAGTTACCCAATGTCTTTGGAAGCCTTATTACTCGCGTTAAATAGTTTTCTA
1 AAAAGTATATTTATAGTTACCC-ATACCTTCGCAAGCCTTATTACTCGCCTTAAATAATTTTAGA
* * * * * * *
7547 ATGTTATAATTGATTTTGAGTT-ACATTTATATATATTTTTTATTAAAATAGAT
65 ATCTCATAATTGATTTTAACTTGA-ATTTATATAAATATTTTATTAAAACAGAT
7600 TATAATTGAA
Statistics
Matches: 95, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
126 17 0.18
127 78 0.82
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (127 bp):
AAAAGTATATTTATAGTTACCCATACCTTCGCAAGCCTTATTACTCGCCTTAAATAATTTTAGAA
TCTCATAATTGATTTTAACTTGAATTTATATAAATATTTTATTAAAACAGATATATTTTGTT
Found at i:10769 original size:170 final size:160
Alignment explanation
Indices: 10456--10772 Score: 318
Period size: 169 Copynumber: 1.9 Consensus size: 160
10446 NNNNNNNNNN
* * *
10456 TTTTTATTAAAATAGATTATAATTTAATGTCTATCTCGAGAAATGTAAAAAAAAAGATATCCATT
1 TTTTTATTAAAATAGATTATAATTAAATATCTATCTCGAGAAACGTAAAAAAAAAGATATCCATT
* * * * *
10521 AGTAAGAAAAGTTAATTTATAGTCACCCATTCCTTCGAAAGCCTTATGAGTCACTTTAGTAGTTT
66 AGCAAGAAAAGTTAATTTAAAGTCACCCATGCCTTCGAAAGCCTTATGACTCACTTTAATAGTTT
* *
10586 TATAATGTCATAATTGATTTTGAGTTGAAT
131 TACAATCTCATAATTGATTTTGAGTTGAAT
* *
10616 TNNNNNNNNNNTTTTATTAAAATAGATTATAATTAAATATCTATCTTGAGAAACGT-GAAAAAAA
1 T----------TTTTATTAAAATAGATTATAATTAAATATCTATCTCGAGAAACGTAAAAAAAAA
* * * * *
10680 GATATCTATT-GACAAGAAAAGTCT-ATTTAAAGTCACTCATGCCTTCGAAAGCTTTATTACTCG
56 GATATCCATTAG-CAAGAAAAGT-TAATTTAAAGTCACCCATGCCTTCGAAAGCCTTATGACTCA
*
10743 TTTTAA-ATGATTTTACAATCTCATAATTGA
119 CTTTAATA-G-TTTTACAATCTCATAATTGA
10773 CTTTAAATAA
Statistics
Matches: 125, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
160 1 0.01
168 2 0.02
169 62 0.50
170 60 0.48
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.37
Consensus pattern (160 bp):
TTTTTATTAAAATAGATTATAATTAAATATCTATCTCGAGAAACGTAAAAAAAAAGATATCCATT
AGCAAGAAAAGTTAATTTAAAGTCACCCATGCCTTCGAAAGCCTTATGACTCACTTTAATAGTTT
TACAATCTCATAATTGATTTTGAGTTGAAT
Found at i:10951 original size:171 final size:161
Alignment explanation
Indices: 10733--11042 Score: 320
Period size: 171 Copynumber: 1.9 Consensus size: 161
10723 TTCGAAAGCT
* * * * *
10733 TTATTACTCGTTTTAAATGATTTTACAATCTCATAATTGACTTTAAATAAGATTTGTTT-GCATT
1 TTATTACTCGCTTAAAATAATTTTACAATCTCATAAATGACTTTAAATAAGATTT-TTTCACATT
* * * * * *
10797 TTTTATTAAAACAGATTATAATTTAATGTCTGTCTC-AGGAAACATGAAAAAAAAGATATTCATT
65 TTTAAGTAAAACAGATAATAATTGAATGTCTGTCTCGA-CAAACATGAAAAAAAAGACATTCATT
* *
10861 GGTATGAAAAGAATACTTATAGTCACCCNNNNNNNNNNAAGAC
129 GCTAGGAAAAGAATACTTATAGTCACCC----------AAGAC
* * *
10904 TTATTACTCGCTTAAAATAATTTTATC-ATCTCATAAATGATTTTAAATTATATTTTTTCACATT
1 TTATTACTCGCTTAAAATAATTTTA-CAATCTCATAAATGACTTTAAATAAGATTTTTTCACATT
* *
10968 TTTAAGTAAAACAGATAATAATTGAATGTCTGTCTCGACAAACATGAAGAAAAAGCCATTCATTG
65 TTTAAGTAAAACAGATAATAATTGAATGTCTGTCTCGACAAACATGAAAAAAAAGACATTCATTG
11033 CTAGGAAAAG
130 CTAGGAAAAG
11043 TCCATTTATA
Statistics
Matches: 118, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
170 3 0.03
171 113 0.96
172 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.36
Consensus pattern (161 bp):
TTATTACTCGCTTAAAATAATTTTACAATCTCATAAATGACTTTAAATAAGATTTTTTCACATTT
TTAAGTAAAACAGATAATAATTGAATGTCTGTCTCGACAAACATGAAAAAAAAGACATTCATTGC
TAGGAAAAGAATACTTATAGTCACCCAAGAC
Found at i:13281 original size:172 final size:169
Alignment explanation
Indices: 12745--13307 Score: 577
Period size: 171 Copynumber: 3.3 Consensus size: 169
12735 NNNNNNNNNN
* * *
12745 TAGTCACTCATGCCTTTAAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATAG-G
1 TAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTGAC
* * * *
12809 TTTAAGTTGAATTTTTTTACATTTTTATTAAAACAGATTATAATTGAATATCTGT-C-TCGAGAA
66 TTTAAGTAGAATTTTTTTACATTTTTATAAAAACAGATTATAATTGAATGTCT-TCCTTAGA-AA
* *
12872 ACTTAAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTA
129 AC-TGAAGAAAAAGATATCCATTGGCAAGAAAAGTCAATTTA
* * *
12914 TAGTCACTCATGCGTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAA-CTTCCTAATTGA
1 TAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTATAATC-TCATAATTGA
* * ********* * *
12978 TTTTAAGTTA-AATTTTTTTATATTTNNNNNNNNNNCAGATTATAATTGAATGTCTACCTCAAGA
65 CTTTAAG-TAGAATTTTTTTACATTT-TTATAAAAACAGATTATAATTGAATGTCTTCCT-TAGA
* * *
13042 AATCTGAAGAAAAAGATATCCATTGGTACGAAAAGTCAATTTA
127 AAACTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCAATTTA
* ** *
13085 TAGTCACCCACACC-TCTAAAAGCCTTATTACTCGCTTTTAAA-GTTTTTATAATCTCATAATTG
1 TAGTCACTCATGCCTTC-AAAAGCCTTATTACTCGC-TTTAAATGATTTTATAATCTCATAATTG
* * *
13148 ACTTTAAGTAGAATTTTTTTACATTTTTTATGAAAAAAAGATTATAATTGAATGCCTTCCTTGGA
64 ACTTTAAGTAGAATTTTTTTACA-TTTTTAT-AAAAACAGATTATAATTGAATGTCTTCCTTAGA
* * * *
13213 AAACATGAAGAAAAAGATATTCTTTGGCAAGAAAAGTCTACTTA
127 AAAC-TGAAGAAAAAGATATCCATTGGCAAGAAAAGTCAATTTA
*
13257 TAGTCAC-CAATGCCTTCGAAAGCCTTATTACTCGCTTTAAAT-AGTTTTATA
1 TAGTCACTC-ATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGA-TTTTATA
13308 NNNNNNNNNN
Statistics
Matches: 316, Mismatches: 60, Indels: 33
0.77 0.15 0.08
Matches are distributed among these distances:
168 1 0.00
169 56 0.18
170 24 0.08
171 130 0.41
172 101 0.32
173 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (169 bp):
TAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTGAC
TTTAAGTAGAATTTTTTTACATTTTTATAAAAACAGATTATAATTGAATGTCTTCCTTAGAAAAC
TGAAGAAAAAGATATCCATTGGCAAGAAAAGTCAATTTA
Found at i:13666 original size:170 final size:171
Alignment explanation
Indices: 13368--13816 Score: 431
Period size: 170 Copynumber: 2.6 Consensus size: 171
13358 NNTTTTTGGG
** * *
13368 TAAAACAGATAATAATTGAATGTTTGTCTTGACAAACATGAAGAAAAAGCCT-TTCATTGGCAAC
1 TAAAACAGATAATAATTGAATGTTTACCTTAAGAAACATGAAGAAAAAG-CTATTCATTGGCAAC
* * * * * * *
13432 AAAAATTCATTTATAGTCACCCATGCGTTTGAAAGCCTTATTACTTGGTTTAAATGATTTTATAA
65 AAAAGTCCATTTACAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAA
* *
13497 CCTCATAATTCATTAT-AAGTTAAAGTTTTTA-ACATTTTTGAT
130 CCTCATAATT-ATTATCAAGCT-AAGTTTTTACACATTTTTAAT
* * * * * *
13539 TAAAACAGATAATAATTGAATGTCTACCTCAAGAAACGTGAAG-AAAAGGTATCCATTGGCAATA
1 TAAAACAGATAATAATTGAATGTTTACCTTAAGAAACATGAAGAAAAAGCTATTCATTGGCAACA
* * * *
13603 AAAGTCCATTTACAGTTATCGATGCCTTCGAAAGCCTTATTACTCGCTTT-AATTAGTTTTATAA
66 AAAGTCCATTTACAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGA-TTTTATAA
* * * * * *
13667 TCTCATAATTTTTGTCAAGCTGATTTTTTACCCATTTTTAAT
130 CCTCATAATTATTATCAAGCTAAGTTTTTACACATTTTTAAT
* * * * * * *
13709 TAAAACAAATAATAACTGAATGTTTACCTTAGGAAACTTGAGGAAAAAGCCATTCATTGGCAAGA
1 TAAAACAGATAATAATTGAATGTTTACCTTAAGAAACATGAAGAAAAAGCTATTCATTGGCAACA
** * * * * * *
13774 AAAGTATATTTATAGTTACCCTTGCCTTCAAAAGTCTTTTTAC
66 AAAGTCCATTTACAGTCACCCATGCCTTCGAAAGCCTTATTAC
13817 GTGCCTAAAA
Statistics
Matches: 224, Mismatches: 49, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
169 15 0.07
170 122 0.54
171 87 0.39
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (171 bp):
TAAAACAGATAATAATTGAATGTTTACCTTAAGAAACATGAAGAAAAAGCTATTCATTGGCAACA
AAAGTCCATTTACAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAAC
CTCATAATTATTATCAAGCTAAGTTTTTACACATTTTTAAT
Found at i:14251 original size:171 final size:170
Alignment explanation
Indices: 13950--14647 Score: 585
Period size: 171 Copynumber: 4.1 Consensus size: 170
13940 NNNNNNNNNN
* * * * *
13950 CTTATTACTCGCTTTAAATAGTTTTATAATCTCATAAATAATTTTAAGTTGAA-TCTGTTATATT
1 CTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATT
* * * * * *
14014 TTTGGGTAAAACAGTTAATAATTGAATGTTTGTCTTGA-CAAACATGAAGAAAAAGTGATTCATT
66 TTTGGTTAAAACAGATAATAATTGAATGTTTG-CCTGAGGAAACGTGAAG-AAAAGCGATTCATT
* * * ***
14078 GACAACAAAAATCCATTTATAGTCACCTATGCGTTTGCAAGC
129 GACAAGAAAAATCCATTTATAGTCACCCATGCCTTCAAAAGC
* * * * *
14120 CTTATTACTTGGTTTAAAT-GATTTTATAACCTCATAATTGATTATAAGTTGAATTTTTTTATAT
1 CTTATTACTCGCTTTAAATAG-TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACAT
* *
14184 TTTTGGTTAAAACAGATAATAAATGAATGTCTGCCTCGA-GAAACGTGAAGAAAAG-GATATCCA
65 TTTTGGTTAAAACAGATAATAATTGAATGTTTGCCT-GAGGAAACGTGAAGAAAAGCGAT-T-CA
* * * * *
14247 TTGACAA-AAAAAGTCAATTTATAGTTATCGATGCCTTCGAAAGC
127 TTGACAAGAAAAA-TCCATTTATAGTCACCCATGCCTTCAAAAGC
* * * *
14291 CTTACTACTCGCTTTAAATAGTTTTATAATCTCATAATT-TTTTTCAAGCTG-ATTTTTTACACA
1 CTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTT-AAGTTGAATTTTTT-TACA
** * * * * * *
14354 TTTTTAATTAAAACAAATAATAACTGAATGTTTGCCTTAGGAAACTTGAGAAAAAAGCCATTCAT
64 TTTTTGGTTAAAACAGATAATAATTGAATGTTTGCCTGAGGAAACGTGA-AGAAAAGCGATTCAT
*
14419 TGGCAAGAGAAGAAT--ATTTATAGTCACCCATGCCTTCAAAAGC
128 TGACAAGA-AA-AATCCATTTATAGTCACCCATGCCTTCAAAAGC
* * * * ** * * *
14462 CTTTTTACGT-GCCTAAAAT-GTATTTTAGAATCTTGTAATTGATGTTAACTTGAATTTTTGTAC
1 CTTATTAC-TCGCTTTAAATAG--TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAC
* * * * * * *
14525 ATTTTTGGCTAAAATAGATAGTAATTGAATGTTTACCTTAGGAAATGTGAAGAAAA-AGATATCC
63 ATTTTTGGTTAAAACAGATAATAATTGAATGTTTGCCTGAGGAAACGTGAAGAAAAGCGAT-T-C
* * * * *
14589 GTTGACAAGAAAAGTCCATTTATAGTTACCCATTCCTTTAAAAGC
126 ATTGACAAGAAAAATCCATTTATAGTCACCCATGCCTTCAAAAGC
14634 CTTATTACTCGCTT
1 CTTATTACTCGCTT
14648 NNNNNNNNNN
Statistics
Matches: 424, Mismatches: 79, Indels: 48
0.77 0.14 0.09
Matches are distributed among these distances:
169 4 0.01
170 74 0.17
171 215 0.51
172 115 0.27
173 14 0.03
174 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (170 bp):
CTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATT
TTTGGTTAAAACAGATAATAATTGAATGTTTGCCTGAGGAAACGTGAAGAAAAGCGATTCATTGA
CAAGAAAAATCCATTTATAGTCACCCATGCCTTCAAAAGC
Found at i:15689 original size:171 final size:171
Alignment explanation
Indices: 15316--16370 Score: 611
Period size: 171 Copynumber: 6.2 Consensus size: 171
15306 NNNNNNNNNN
* * * * * *
15316 AAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTC-TTCTAATAGATAT
1 AAGCGAATAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTTCCAATGGATAT
* * * * * * * * * * ** *
15380 CTTTTTTTTTACGTTTCTCGAGATAGATATTTAATTATAATCTATTTTAATAAAAAATATAAAAA
66 CTTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAA
* * * ** **
15445 AATTCAAGTTAAAATTTGTTATGAGATTATAAAAATATTTA
131 AATTCAACTTTAAACTAATTATGAGATTATAAAACCATTTA
* ********** * *
15486 AAGCGAGTANNNNNNNNNNCGAAGGCATGGGTGACTATAAATGGACTTTTGTTTCCAATGGATAT
1 AAGCGAATAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTTCCAATGGATAT
* * * * *
15551 TTTTTTCTTCATGTTTCTCAAGGTAGATATTCACTTATAATATGTTTTAA-TAGAAAATGTAAAA
66 CTTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAATATGTTTTAACCA-AAAATGTAAAA
*
15615 AAATTCAACTTTAAACTAATTATGAGGTTATAAAACCATTTA
130 AAATTCAACTTTAAACTAATTATGAGATTATAAAACCATTTA
* * * *
15657 AAGCGAATAATAAGGCTTTTAAAAGAATGGGTGACTGTAAATGGACTTTTCTTGT-CAATGGATA
1 AAGCGAATAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTT-TCCAATGGATA
* ** **
15721 TATTTTTCTTCACAT-TTTCT-AAGGTAAACATTCAATTAT--TATCAATTTAGGCAAAAATGTA
65 TCTTTTTCTT--CATGTTTCTCAAGGTAAACATTCAATTATAATAT-GTTTTAACCAAAAATGTA
* * ** * * *
15782 CAAAAATTCAA-GTT-AACATCAATTACAAGATTCTAAAAAACATTTT
127 AAAAAATTCAACTTTAAAC-T-AATTATGAGATTAT-AAAACCATTTA
* ** *** * *
15828 AGGCACGAA-AA-AAGGCTTTTGAAGGCAT-GGTGACTATAAATATTCTTTTCTTGCCAATGAAT
1 AAG--CGAATAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTTCCAATGGAT
** * * * * * **
15890 GGCTTTTTCCTCAGGTTT-TCTAAGGCAAACATTCAGTTATTATTAT-TTTTAATTAAAAATGTG
64 ATCTTTTTCTTCATGTTTCTC-AAGGTAAACATTCAATTA-TAATATGTTTTAACCAAAAATGT-
* * * * *
15953 TAAAAAA-TCAGCTTGAAA-AACATTATGAGATTATAAAACTATTTA
126 AAAAAAATTCAACTTTAAACTA-ATTATGAGATTATAAAACCATTTA
* * * * * *
15998 AAGCGAGTAATAAGGCTTTCGAAGGCATCGATAACTATAAATGGACTTTTTTTTGCCAATGGATA
1 AAGCGAATAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTT-CCAATGGATA
* * * * * * * *
16063 TCCTTTTCTTCACGTTTCTCAGGGTAGACATTCATTTATTATCTGTTTGAACCAAAAATGTAAAA
65 TCTTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAATATGTTTTAACCAAAAATGTAAAA
* * * *
16128 AAATTTAAC-TTATAATTAATTATGAGGTTATAAAATCATTTA
130 AAATTCAACTTTA-AACTAATTATGAGATTATAAAACCATTTA
* * * * * *
16170 AA-CTAAGTAATAAGGCTTTCAAACGCATGGATGACTATAAATGGATTTTTGTTGT-CAATGCAT
1 AAGCGAA-TAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTT-TCCAATGGAT
** * * ** ********** * *
16233 GGCTATTTCTTCATGTTTGTCAAGACAAACATTCAATTNNNNNNNNNNTTACCCAAAAATAT-AA
64 ATCTTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAATATGTTTTAACCAAAAATGTAAA
* * * * *
16297 AAAATTCAACTTAAAATTATTTATAAGATTATAAAACTATTTA
129 AAAATTCAACTTTAAACTAATTATGAGATTATAAAACCATTTA
* **
16340 AAGCGAGTAATAAGGCTTTTGAAGGCATGGG
1 AAGCGAATAATAAGGCTTTCAAAGGCATGGG
16371 NNNNNNNNNN
Statistics
Matches: 668, Mismatches: 181, Indels: 72
0.73 0.20 0.08
Matches are distributed among these distances:
168 9 0.01
169 11 0.02
170 205 0.31
171 297 0.44
172 130 0.19
173 16 0.02
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.36
Consensus pattern (171 bp):
AAGCGAATAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTTCCAATGGATAT
CTTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAA
AATTCAACTTTAAACTAATTATGAGATTATAAAACCATTTA
Found at i:18112 original size:171 final size:171
Alignment explanation
Indices: 16873--21656 Score: 2800
Period size: 171 Copynumber: 28.0 Consensus size: 171
16863 NNNNNNNNNN
* * * * * * *
16873 AAAATCATTTATGAGATGATAAAATCATTTTAAGCGAGTAATAAGGCTTTTGAATGTATGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* *** * * * * ** * *
16938 CTATAAGTATTCTTTTCTTACCAATGAATATCTTTTTTTTCATGTTTC-CTGAGACAGGCATTAA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTC-AAGGTAGACATTCA
* *********** *
17002 ATTATAATCTGTTTTAATAANNNNNNNNNNCAAATTCAATTT
130 ATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * ** **
17044 AAAGTCAATTATCAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTC-AAGGGCATAAGTG
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAA-GGCATGGGTG
* * * *** * *
17108 ACTATAAATAGACTTTTCTT-CTAAT-AGATATCTTTTTAATT-A--TAAATAGACAGGTAGATA
65 ACTATAAATGGACTTTTCTTGCCAATGA-ATATCTTTTT-CTTCACGTTTCT-CA-AGGTAGACA
* * * * * *
17168 TTTAATTATAATCTATTTTTAATAAAAAATATAAAACAATTCAACTC
126 TTCAATTATTATCT-GTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * * * * * * * *
17215 AAAATTATTTATGACATTATAAAACCA-TTCAAGTGACTCATAAGGCTTTCGAAAGCATGGGTAA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
** ** * * * *
17279 CTATAAATTAACTTTTCTTGTTAATGGATATCTTTTTTTTTTTACGTTTCTCAAGGTAAACATTC
66 CTATAAATGGACTTTTCTTGCCAATGAATATC--TTTTTCTTCACGTTTCTCAAGGTAGACATTC
* * *********** * *
17344 AATTATAATCTATTTTAATAANNNNNNNNNNTAAATTTAACTC
129 AATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * * ** * * * *
17387 AAAATCAATTATGACATTATAAAACTATTTAACGTAAGTAATAAGGCTTCCAAAGACATGGGTAA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
** * * * * ** * *
17452 CTATAAATATATTTTTCTTACCAATGGATATCTTTTTGTTCTTGTTTC-CGAAGGCAAACATTCA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTC-AAGGTAGACATTCA
* * * * *
17516 ATTATTATTTTTTTTAACAAAAAATGTACAAAAATTCAAGTT
130 ATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
** * * * ********** * * *
17558 AAAATCAATTACAAGATTCTAAAACTATTTAAGGCGAGTAATANNNNNNNNNNAGGTATGGATAA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
** ** * * * *
17623 CTATAAATATACTTTTCTACCCAATGGATATCTTTTTCTTCATGTTTCCCAAGGCAGACATTCAA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
* * *
17688 TTATTATCTGTTTTAATAAAAAAAGTATAAAAATTCAAGTT
131 TTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * * * * ********** * ** *
17729 AAAATTAATTACGAGACTCTAAAAACATTNNNNNNNNNNAATAAGGCTTTTGAAGGTGTGGATGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * * ** * * *
17794 CTATATATGGACTTTTCATACCAATGAATGGCTTTTTCTTCA-GCTTTC-CATAAGCAAACATTC
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACG-TTTCTCA-AGGTAGACATTC
* * * * * *
17857 AATTATTAT-TATTTTTAATTAAAAATATAAAACAATTTAGCTT
129 AATTATTATCT-GTTTTAATAAAAAATGTAAAAAAATTCAACTT
* ********** * * *
17900 GAAATCAATTATGAGATTATNNNNNNNNNNAAAGCGAGTAATAAGACTTTCAAAGGCATGAGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * * * * *
17965 CTGTAAATGGGCTTTTCTTGCTAATGAATATCTTTTTCTTCACATTTCTCAAGATAAACATTCAA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
* * * * *
18030 TTATAATCTGTTTTAACAAAAAACGTAAAAAAAATCAACCT
131 TTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * * *
18071 AAAATCAAATATGAGATTATAAAGCCATTGAAAGTGAGTAATAAGGCTTTCGAAGGCATGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * **
18136 CTATAAATAGACTTTTCTTGTCAAT-AGATATCTTTTTCTTTGCGTTTCTCAAGGTAGACATTCA
66 CTATAAATGGACTTTTCTTGCCAATGA-ATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
* * * * *
18200 ATTATAATCTATTTTAATAAAAAATATAAAAAAAAGTCAACTG
130 ATTATTATCTGTTTTAATAAAAAATGT-AAAAAAATTCAACTT
* ** * * * ** * * * *
18243 AAAATCAATTATTAGGCTATGAAATCATATAAAATGAGTAATAAGGCTTTCGAAGGTATAGGCGG
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * * **
18308 CTATAAATAGACTTTTCTTGCCAATGGATATCTCTTTCTTCACGTTTCTTGAGGTAGACATTCAA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
* * * *
18373 TTGTTATCTGTTTTAATAAAAAATATAAAAAAATTTAACTC
131 TTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * ********** *
18414 AAAATTAATTATGAGATTATAAAACCATTTAATGCGAGTAATAAGGCNNNNNNNNNNATGTGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * * * * *
18479 CTATAAATGGACTTTTCTTGCTAATGGATATCTTTTTCTTAATGTTT-TCCAAGGCAAACATTCA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCT-CAAGGTAGACATTCA
* * * * * *
18543 ATTATTGTCTATTTT-A-AAAAAATATATAAAAATTGAAGTT
130 ATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
** * ** ** * * **
18583 AAAATCAATTACAAGATTCTAAAAATAATTTAGGTGCCA--AATATGGCTTTTAAAGGCATGGGT
1 AAAATCAATTATGAGATTAT-AAAACCATTTA-AAGCGAGTAATAAGGCTTTCGAAGGCATGGGT
* * * * *
18646 GATTATAAATAGACTTTTCTTGCTC-ATGAATATCTTTTTCTTCATGTTTCTCAAGGCAGATATT
64 GACTATAAATGGACTTTTCTTGC-CAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGACATT
* ** *
18710 CAATTATTATCTATTTTAATCCAAAATGTTAAAAAATTCAACTT
128 CAATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * * * *
18754 AAAATCAATTATGAGATTATAAAAACATTTAAGGTGAGTAATAAGGCTTTTGAAGGCATAGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * * * * * *
18819 CTATAAACGGAGTTTTCTTACCAATGAATATCTTTTTCTTCATGTTTCTCAATGTAGACATACAG
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
** * * * *
18884 TTACAATCAGTGTTAATAAAAAATATAAAAAAACTCAACTT
131 TTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
** * * * *
18925 AAAATCAATTATGA-AGTTATTGAATCATTTAAACCGAGCAATAAGGCTTTCGAATGCATGGGTG
1 AAAATCAATTATGAGA-TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTG
* ** * * * * **
18989 ACTATAAATGGACTTTTCCTAACAATGACTGATTTTTTTCTTCACGTCTGCT-GAGACAGACATT
65 ACTATAAATGGACTTTTCTTGCCAATGAAT-ATCTTTTTCTTCACGT-TTCTCAAGGTAGACATT
*** *
19053 CAATTATTATCTGTTTTAACCTAAAATGTAAAAACATTCAACTT
128 CAATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
*** ** ********** * *
19097 AAAATTTGTTATGAGATTATAAAAATATTTAANNNNNNNNNNAAGGCTTTCAAAGGCATGGGTAA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * * * * *
19162 CTATAAATGGACTTTTGTTTCCAATGGATAT-TTATTTCTTCATGTTTCTCAAGGCAGATATTCA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTT-TTTCTTCACGTTTCTCAAGGTAGACATTCA
* * * ** *
19226 CTTATAATATGTTTTAATAGCAAATGTAAAAAAATTCAACTC
130 ATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * ********** **
19268 AAAACCAATTATGAGGTTATAAAACCATTTAAAGCGAGTAATANNNNNNNNNNAGAAATGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * * * * *
19333 CTATAAATGGACTTTCCTTGTCAATGGATATCTTTTTCTTCACATTTC-CTAAGGTAAAGATTCA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTC-AAGGTAGACATTCA
* ** * * *
19397 ATTATTATCTATTTTACCAAAAAATGTACAAAAATTTAAGTT
130 ATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * ** * ********** * * * *
19439 TACATCAATTACAAGATTCTAAAANNNNNNNNNNC-ACGTAAAAAGACTTTTGAAGGCATGTGTG
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGA-GTAATAAGGCTTTCGAAGGCATGGGTG
** * * * * *
19503 ACTATAAATATACTTTTCTTGCCAATGAATAGCTTTTTCCTCAGGTTTCAT-AAGGCAAACATTC
65 ACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTC-TCAAGGTAGACATTC
* * * * **
19567 AGTTATTATTTGTTTTAATTAAAAATGTATAAAAATTCAGGTT
129 AATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* ********** *** *
19610 GAAAA--AATTATGAGATTATAAAACTATNNNNNNNNNNTAATAAGGCTTTCGAAGGCATCAATA
1 -AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTG
* * *
19673 ACTATAAATGGACTTTTTTTGCCAATGGATATCCTTTTT-TTCACGTTTCTCGAGGTAGACATTC
65 ACTATAAATGGACTTTTCTTGCCAATGAATAT-CTTTTTCTTCACGTTTCTCAAGGTAGACATTC
* * **
19737 ATTTATTATCTATTTTAACCAAAAATGTAAAAAAATTCAACTT
129 AATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * * * *** * *
19780 ATAATTAATTATGAGGTTATAAAATCATTTAAATTAAGTAATAAGGCTTTCAAACGCATGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * ** ** * * ** *
19845 TTATAAATGGA-TTTTGTTGCCAATGAATGGCTTTTTCTTCATTTTTGTTAAGACAAACATTCAA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
* * *
19909 TTATTATCTGTGTTT-CTCAAAAATAT-AAAAAATTCAACTT
131 TTATTATCTGT-TTTAATAAAAAATGTAAAAAAATTCAACTT
* * ********************
19949 AAAATCATTTATGAGATTATAAAACTATTTANNNNNNNNNNNNNNNNNNNNGAAGGCATGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * * * * *
20014 CTATAAGTAGACTTTTCTTGCCAAAGAATATCTTTTTCTTCATGTTT-TCTAAGGAAGGCATTCA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTC-AAGGTAGACATTCA
* * * * *
20078 ATTATAATCTCTTTTAATAAAAAATATAAAAAAATTCTATTT
130 ATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* ** * **
20120 AAAGTCAATTATGAGATTAT-AAA-CACTTTAACAGTTAGTAATAAGGCTTT-TAGAGGTGTGGG
1 AAAATCAATTATGAGATTATAAAACCA-TTTAA-AGCGAGTAATAAGGCTTTCGA-AGGCATGGG
** * * * ** * *
20182 TGACTATAAATTAACTTTTCGTACCAATGGATATCTTTTTCTTCATATTTCTCGAGATAGACATT
63 TGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGACATT
* * * *
20247 TAATTATAATCTGTTTTAATAAAAAATGTGAAAAAATTTAACTT
128 CAATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * *** * *********
20291 AAAATCAATTAGGAGGTTATAAATTAATTTAAAGCGAGTAATAAGGCTTCCGAAGGNNNNNNNNN
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * * * * ** ** *
20356 NTATAAATGGACTTTTCTTGCCAATGGATAT-ATTTTCTTTAAGTTTCTTGAGACAGATATTCAA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
*
20420 TTATAATCTGTTTTAA-AAAAAATGTAAAAAAATTCAACTT
131 TTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * *
20460 AAAACCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGTATGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * * *
20525 CTATAAATGGACTTTTCTTGCCAATGGATATCATTTTCTTCACATTT-TCCAAGGTAAACATTCA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCT-CAAGGTAGACATTCA
* ** *
20589 ATTATTAGCTGTTTTAATAAAAAATGTGCAAAAATTCAAGTT
130 ATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
** * * * * * * * **
20631 AAAATCAATTACCAGATTCTAAAAACATTTTAGGTGCGTAAAAAGGCTTCTC-AAGGCATTAGTG
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT-TCGAAGGCATGGGTG
* * * * * * * * * * * *
20695 ACTATAAATGTACTTTTCTTACCAATGAATAGCTTTTCCTTTAGGGTTCCCTAGGCAAACATTTA
65 ACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
* * * * * * *
20760 GTTATTATTTGTTTTAATTAAAAATATGAAAAAATTTAGCTT
130 ATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * * * * ***
20802 GAAATCAATTATGAGAATATATAACCATTTAAAGCGAGTAATAAGGCCTTCGAAGCCATCAATGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* ********** *
20867 CTATAAATGGACTTTTATTNNNNNNNNNNATCTTTTTCTTCACGTTTCTCAAGGTCGACATTCAA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
* * *
20932 TTATTATCTATTCTAACT-AAAAATATAAAAAAATTCAACTT
131 TTATTATCTGTTTTAA-TAAAAAATGTAAAAAAATTCAACTT
* * * * * * * *
20973 CAAATCAACTATGAGGTTATAAAATCATTTAAATCGAGTAATAAGGCTTTCAAACGTATGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* ** * * ** *
21038 CTATAAATGGACTTTTGTTGCCAATGAATGGCTTTCTCTTCACGTTTGTCGAA-ACAAACATTCA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTC-AAGGTAGACATTCA
* *** * *
21102 ATTATTATCTGTTTCACCCAAAAA--TATAAAAATTAAACTT
130 ATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
* * * * * * * *
21142 AAAATCATTTATGAGATTGTAAAACTATTTAAAACGAGCAATAAAGCTTTTGAAGGCATTGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * * *********** *
21207 CTATAAGTAGACTTTTCTTGCCAAAGAATATCTTTTTCTTTNNNNNNNNNNAGGTAGGCATTCAA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
* * *
21272 TTATAATCCGTTTTAATAAAAAATGTAAAAAAAATT-TACTT
131 TTATTATCTGTTTTAATAAAAAATGT-AAAAAAATTCAACTT
* * ** * * * * *
21313 CAAGTCAATTATGAGATTATAAAAATATTTAAAGTGAGTAATAAGGATTTTGAAGGCGTGGCTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
** * * * **********
21378 CTATAAATCAACTTTTCATGTCAATGAATATCTTTTTCTTCACATTTNNNNNNNNNNACATTCAA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
* * *
21443 TTATAATTTGTTTTAATAAAAAATATAAAACAAATTCAACTT
131 TTATTATCTGTTTTAATAAAAAATGTAAAA-AAATTCAACTT
* * * * * * *
21485 AAAACCAATAATGAGATTACACAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGTATGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
* * * * * * *
21550 CTATAAATGTATTTTTTTTACTAATGAATATCTTTATCTTCACGTTTCATGAA-GTAGACATTCA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTC-TCAAGGTAGACATTCA
* * *
21614 ATTATAATCTGTTTTAATAAAAAATATAAAACAATTCAACTT
130 ATTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
21656 A
1 A
21657 NNNNNNNNNN
Statistics
Matches: 3461, Mismatches: 1069, Indels: 166
0.74 0.23 0.04
Matches are distributed among these distances:
168 2 0.00
169 418 0.12
170 436 0.13
171 2050 0.59
172 467 0.13
173 85 0.02
174 1 0.00
175 2 0.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.35
Consensus pattern (171 bp):
AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGA
CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
TTATTATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
Found at i:20589 original size:511 final size:506
Alignment explanation
Indices: 17930--21656 Score: 1835
Period size: 511 Copynumber: 7.3 Consensus size: 506
17920 NNNNNNNNNN
* * * * * *
17930 AAAGCGAGTAATAAGACTTTCAAAGGCATGAGTGACTGTAAATGGGCTTTTCTTGCTAATGAATA
1 AAAGCGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATA
* * * * **
17995 TCTTTTTCTTCAC-ATTTCTCAAGATAAACATTCAATTATAATCTGTTTTAACAAAAAACGTAAA
66 TCTTTATCTTCACGTTTTC-CAAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAA
* * * * * *
18059 AAAAATCAACCTAAAATCAAATATGAGATTATAAAGCCATTGAAAGTGAGTAATAAGGC-TTTCG
130 AAAATTCAACTTAAAATCAATTATGAGATTATAAA-ACATTTAAAGT-AGTAATAAGGCTTTTAG
* ** * *
18123 AAGGCATGGGTGACTATAAA-TAGACTTTTCTTGTCAAT-AGATATCTTTTTCTTT-GCGTTTCT
193 -AGGCATTGGTGACTATAAATTA-ACTTTTCTTACCAATGA-ATATCTTTTTCTTTAGAG-TTCC
* * * * * * * *
18185 CAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAAAGTCAACTGAAAATCA
254 CGAGGTAGACATTTAATTATAATCTGTTTTAATAAAAAATGT-GAAAAAATTTAACTTAAAATCA
* ** ** * ** * ** *
18250 ATTATTAGGCTATGAAATCATATAAAATGAGTAATAAGGCTTTCGAAGGTAT-AGGCGGCTATAA
318 ATTATGAGATTAT-AAAAAATTTAAAGCGAGTAATAAGGC-TTCGAAGGCATCA-ATGACTATAA
* * * * * * *
18314 ATAGACTTTTCTTGCCAATGGATATCTCTTTCTTCACGTTTCTTGAGGTA-GACATTCAATTGTT
380 ATGGACTTTTCTTGCCAATGAATAT-T-TTTCTTCAAGTTTC-TCAAG-ACGACATTCAATTATA
* * * **
18378 ATCTGTTTTAATAAAAAATATAAAAAAATTTAACTCAAAATTAATTATGAGATTATAAAACCATT
441 ATCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAACCAATTATGAGATTATAAAACCATT
18443 T
506 T
* ********** * * *
18444 AATGCGAGTAATAAGGCNNNNNNNNNNATGTGTGACTATAAATGGACTTTTCTTGCTAATGGATA
1 AAAGCGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATA
* * * * ** * *
18509 TCTTTTTCTTAATGTTTTCCAAGGCAAACATTCAATTATTGTCTATTTT-A-AAAAAATATATAA
66 TCTTTATCTTCACGTTTTCCAAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAA
* * ** * * * * *
18572 AAATTGAAGTTAAAATCAATTACAAGATTCTAAAA-ATAATTTAGGT-GCCAAATATGGCTTTTA
131 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAT--TTAAAGTAG--TAATAAGGCTTTTA
* * * * * * *
18635 AAGGCATGGGTGATTATAAA-TAGACTTTTCTTGCTC-ATGAATATCTTTTTCTTCATG-TTTCT
192 GAGGCATTGGTGACTATAAATTA-ACTTTTCTTAC-CAATGAATATCTTTTTCTTTA-GAGTTCC
* * * * * * ** * *
18697 CAAGGCAGATATTCAATTATTATCTATTTTAATCCAAAATGTTAAAAAATTCAACTTAAAATCAA
254 CGAGGTAGACATTTAATTATAATCTGTTTTAATAAAAAATGTGAAAAAATTTAACTTAAAATCAA
* * * *
18762 TTATGAGATTATAAAAACATTTAAGGTGAGTAATAAGGCTTTTGAAGGCAT-AGGTGACTATAAA
319 TTATGAGATTATAAAAA-ATTTAAAGCGAGTAATAAGGC-TTCGAAGGCATCA-ATGACTATAAA
* * * * * * *
18826 CGGAGTTTTCTTACCAATGAATATCTTTTTCTTCATGTTTCTCAATGTA-GACATACAGTTACAA
381 TGGACTTTTCTTGCCAATGAATA--TTTTTCTTCAAGTTTCTCAA-G-ACGACATTCAATTATAA
* * * * * ** *
18890 TCAGTGTTAATAAAAAATATAAAAAAACTCAACTTAAAATCAATTATGA-AGTTATTGAATCATT
442 TCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAACCAATTATGAGA-TTATAAAACCATT
18954 T
506 T
* * * * * * ** *
18955 AAACCGAGCAATAAGGCTTTCGAATGCATGGGTGACTATAAATGGACTTTTCCTAACAATGACTG
1 AAAGCGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT-
* * * * ** ** * * *** *
19020 ATTTTTTTCTTCACGTCTGCTGAGACAGACATTCAATTATTATCTGTTTTAACCTAAAATGTAAA
65 ATCTTTATCTTCACGTTTTCCAAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAA
* *** * ********* * *
19085 AACATTCAACTTAAAATTTGTTATGAGATTATAAAAATATTTAANNNNNNNNNNAAGGCTTTCAA
130 AAAATTCAACTTAAAATCAATTATGAGATTAT-AAAACATTTAA-AGTAGTAATAAGGCTTTTAG
* * ** * * * * * * *
19150 AGGCATGGGTAACTATAAATGGACTTTTGTTTCCAATGGATAT-TTATTTCTTCATG-TTTCTCA
193 AGGCATTGGTGACTATAAATTAACTTTTCTTACCAATGAATATCTT-TTTCTTTA-GAGTTCCCG
* * * * * ** * * * *
19213 AGGCAGATATTCACTTATAATATGTTTTAATAGCAAATGTAAAAAAATTCAACTCAAAACCAATT
256 AGGTAGACATTTAATTATAATCTGTTTTAATAAAAAATGTGAAAAAATTTAACTTAAAATCAATT
* * ********* ** ***
19278 ATGAGGTTATAAAACCATTTAAAGCGAGTAATANNNNNNNNNNAGAAATGGGTGACTATAAATGG
321 ATGAGATTATAAAA-AATTTAAAGCGAGTAATA-AGGCTTCGAAGGCATCAATGACTATAAATGG
* * * * * *
19343 ACTTTCCTTGTCAATGGATATCTTTTTCTTCACA-TTTC-CTAAGGTA-AAGATTCAATTATTAT
384 ACTTTTCTTGCCAAT-GA-ATATTTTTCTTCA-AGTTTCTC-AA-G-ACGACATTCAATTATAAT
* * * * * * * * * ** * ******
19405 CTATTTTACCAAAAAATGTACAAAAATTTAAGTTTACATCAATTACAAGATTCTAAAANNNNNN
443 CTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAACCAATTATGAGATTATAAAACCATTT
**** * * ** * * **
19469 NNNNC-ACGTAAAAAGACTTTTGAAGGCATGTGTGACTATAAATATACTTTTCTTGCCAATGAAT
1 AAAGCGA-GTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * * * * * * * * * *
19533 AGCTTTTTCCTCA-GGTTTCATAAGGCAAACATTCAGTTATTATTTGTTTTAATTAAAAATGTAT
65 ATCTTTATCTTCACGTTTTC-CAAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAA
** *********
19597 AAAAATTCAGGTTGAAAA--AATTATGAGATTATAAAACTATNNNNNNNNNNTAATAAGGC-TTT
129 AAAAATTCAACTT-AAAATCAATTATGAGATTATAAAAC-AT-TTAAAGTAGTAATAAGGCTTTT
* *** * ** * * * * *
19659 CGAAGGCATCAATAACTATAAATGGACTTTTTTTGCCAATGGATATCCTTTTT-TTCACG-TTTC
191 AG-AGGCATTGGTGACTATAAATTAACTTTTCTTACCAATGAATAT-CTTTTTCTTTA-GAGTTC
* * * * * ** * * * *
19722 TCGAGGTAGACATTCATTTATTATCTATTTTAACCAAAAATGTAAAAAAATTCAACTTATAATTA
253 CCGAGGTAGACATTTAATTATAATCTGTTTTAATAAAAAATGTGAAAAAATTTAACTTAAAATCA
* * *** * * *** *
19787 ATTATGAGGTTATAAAATCATTTAAATTAAGTAATAAGGCTTTCAAACGCATGGGTGATTATAAA
318 ATTATGAGATTATAAAA-AATTTAAAGCGAGTAATAAGGC-TTCGAAGGCATCAATGACTATAAA
* * ** * * * *
19852 TGGA-TTTTGTTGCCAATGAATGGCTTTTTCTTCATTTTTGTTAAGACAAACATTCAATTATTAT
381 TGGACTTTTCTTGCCAATGAAT--ATTTTTCTTCAAGTTTCTCAAGAC-GACATTCAATTATAAT
** * * *
19916 CTGTGTTTCTC-AAAAATAT-AAAAAATTCAACTTAAAATCATTTATGAGATTATAAAACTATTT
443 CTGT-TTTAACAAAAAATATAAAAAAATTCAACTTAAAACCAATTATGAGATTATAAAACCATTT
********************* * * * *
19979 ANNNNNNNNNNNNNNNNNNNNGAAGGCATGGGTGACTATAAGTAGACTTTTCTTGCCAAAGAATA
1 AAAGCGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATA
* * * * *
20044 TCTTTTTCTTCATGTTTTCTAAGG-AAGGCATTCAATTATAATCTCTTTTAATAAAAAATATAAA
66 TCTTTATCTTCACGTTTTCCAAGGTAA-ACATTCAATTATAATCTGTTTTAATAAAAAATATAAA
* * *
20108 AAAATTCTATTTAAAGTCAATTATGAGATTAT-AAACACTTTAACAGTTAGTAATAAGGCTTTTA
130 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACA-TTTAA-AG-TAGTAATAAGGCTTTTA
** * * * * * * *
20172 GAGGTGTGGGTGACTATAAATTAACTTTTCGTACCAATGGATATCTTTTTCTTCATATTTCTCGA
192 GAGGCATTGGTGACTATAAATTAACTTTTCTTACCAATGAATATCTTTTTCTTTAGAGTTCCCGA
*
20237 GATAGACATTTAATTATAATCTGTTTTAATAAAAAATGTGAAAAAATTTAACTTAAAATCAATTA
257 GGTAGACATTTAATTATAATCTGTTTTAATAAAAAATGTGAAAAAATTTAACTTAAAATCAATTA
* * * **********
20302 GGAGGTTATAAATTAATTTAAAGCGAGTAATAAGGCTTCCGAAGGNNNNNNNNNNTATAAATGGA
322 TGAGATTATAAA-AAATTTAAAGCGAGTAATAAGGCTT-CGAAGGCATCAATGACTATAAATGGA
* * ** *
20367 CTTTTCTTGCCAATGGATATATTTTCTTTAAGTTTCTTGAGACAGATATTCAATTATAATCTGTT
385 CTTTTCTTGCCAATGAATAT-TTTTCTTCAAGTTTCTCAAGAC-GACATTCAATTATAATCTGTT
*
20432 TTAA-AAAAAATGTAAAAAAATTCAACTTAAAACCAATTATGAGATTATAAAACCATTT
448 TTAACAAAAAATATAAAAAAATTCAACTTAAAACCAATTATGAGATTATAAAACCATTT
*
20490 AAAGCGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATA
1 AAAGCGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATA
* * * * **
20555 TCATTT-TCTTCACATTTTCCAAGGTAAACATTCAATTATTAGCTGTTTTAATAAAAAATGTGCA
66 TC-TTTATCTTCACGTTTTCCAAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAA
* ** * * * * * *
20619 AAAATTCAAGTTAAAATCAATTACCAGATTCTAAAAACATTTTAGGTGCGTAAAAAGGCTTCTCA
130 AAAATTCAACTTAAAATCAATTATGAGATTAT-AAAACATTTAAAGT-AGTAATAAGGCTT-TTA
* * * * *
20684 -AGGCATTAGTGACTATAAATGT-ACTTTTCTTACCAATGAATAGCTTTTCCTTTAGGGTTCCCT
192 GAGGCATTGGTGACTATAAAT-TAACTTTTCTTACCAATGAATATCTTTTTCTTTAGAGTTCCCG
* * * * * * * * *
20747 AGGCAAACATTTAGTTATTATTTGTTTTAATTAAAAATATGAAAAAATTTAGCTTGAAATCAATT
256 AGGTAGACATTTAATTATAATCTGTTTTAATAAAAAATGTGAAAAAATTTAACTTAAAATCAATT
* ** *
20812 ATGAGAATATATAACCATTTAAAGCGAGTAATAAGGCCTTCGAAGCCATCAATGACTATAAATGG
321 ATGAGATTATA-AAAAATTTAAAGCGAGTAATAAGG-CTTCGAAGGCATCAATGACTATAAATGG
* ******** * * * * *
20877 ACTTTTATTNNNNNNNNNNATCTTTTTCTTCACGTTTCTCAAGGTCGACATTCAATTATTATCTA
384 ACTTTTCTT--GCCAATGAATATTTTTCTTCAAGTTTCTCAA-GACGACATTCAATTATAATCTG
* * * * * * *
20942 TTCTAACTAAAAATATAAAAAAATTCAACTTCAAATCAACTATGAGGTTATAAAATCATTT
446 TTTTAACAAAAAATATAAAAAAATTCAACTTAAAACCAATTATGAGATTATAAAACCATTT
* * * *
21003 AAATCGAGTAATAAGGCTTTCAAACGTATGGGTGACTATAAATGGACTTTTGTTGCCAATGAATG
1 AAAGCGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATA
* * * ** * * ***
21068 GCTTTCTCTTCACGTTTGTCGAA-ACAAACATTCAATTATTATCTGTTTCACCCAAAAATAT--A
66 TCTTTATCTTCACGTTT-TCCAAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAA
* * * * *
21130 AAAATTAAACTTAAAATCATTTATGAGATTGTAAAACTATTTAAAACG-AGCAATAAAGCTTTT-
130 AAAATTCAACTTAAAATCAATTATGAGATTATAAAAC-ATTT-AAA-GTAGTAATAAGGCTTTTA
* * * *********
21193 GAAGGCATTGGTGACTAT-AAGTAGACTTTTCTTGCCAAAGAATATCTTTTTCTTTNNNNNNNNN
192 G-AGGCATTGGTGACTATAAATTA-ACTTTTCTTACCAATGAATATCTTTTTCTTTAGAGTTCCC
* * * * * * *
21257 NAGGTAGGCATTCAATTATAATCCGTTTTAATAAAAAATGTAAAAAAAATTT-ACTTCAAGTCAA
255 GAGGTAGACATTTAATTATAATCTGTTTTAATAAAAAATGT-GAAAAAATTTAACTTAAAATCAA
* * * * ***
21321 TTATGAGATTATAAAAATATTTAAAGTGAGTAATAAGGATTTTGAAGGCGTGGCTGACTATAAAT
319 TTATGAGATTATAAAAA-ATTTAAAGCGAGTAATAAGG-CTTCGAAGGCATCAATGACTATAAAT
** * * *********
21386 CAACTTTTCATGTCAATGAATATCTTTTTCTTCACA-TTTNNNNNNNNNNACATTCAATTATAAT
382 GGACTTTTCTTGCCAATGAATA--TTTTTCTTCA-AGTTT-CTCAAGACGACATTCAATTATAAT
* * * * *
21450 TTGTTTTAATAAAAAATATAAAACAAATTCAACTTAAAACCAATAATGAGATTACACAACCATTT
443 CTGTTTTAACAAAAAATATAAAA-AAATTCAACTTAAAACCAATTATGAGATTATAAAACCATTT
* ** * * * * *
21515 AAAGCAAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGTATTTTTTTTACTAATGAATA
1 AAAGCGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATA
* *
21580 TCTTTATCTTCACG-TTT-CATGAAGTAGACATTCAATTATAATCTGTTTTAATAAAAAATATAA
66 TCTTTATCTTCACGTTTTCCA--AGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAA
*
21643 AACAATTCAACTTA
129 AAAAATTCAACTTA
21657 NNNNNNNNNN
Statistics
Matches: 2437, Mismatches: 676, Indels: 200
0.74 0.20 0.06
Matches are distributed among these distances:
509 13 0.01
510 173 0.07
511 1014 0.42
512 566 0.23
513 230 0.09
514 426 0.17
515 11 0.00
516 4 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (506 bp):
AAAGCGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATA
TCTTTATCTTCACGTTTTCCAAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAA
AAATTCAACTTAAAATCAATTATGAGATTATAAAACATTTAAAGTAGTAATAAGGCTTTTAGAGG
CATTGGTGACTATAAATTAACTTTTCTTACCAATGAATATCTTTTTCTTTAGAGTTCCCGAGGTA
GACATTTAATTATAATCTGTTTTAATAAAAAATGTGAAAAAATTTAACTTAAAATCAATTATGAG
ATTATAAAAAATTTAAAGCGAGTAATAAGGCTTCGAAGGCATCAATGACTATAAATGGACTTTTC
TTGCCAATGAATATTTTTCTTCAAGTTTCTCAAGACGACATTCAATTATAATCTGTTTTAACAAA
AAATATAAAAAAATTCAACTTAAAACCAATTATGAGATTATAAAACCATTT
Found at i:22109 original size:172 final size:162
Alignment explanation
Indices: 21898--22228 Score: 373
Period size: 172 Copynumber: 2.0 Consensus size: 162
21888 AATTTAAATC
* *
21898 AAAATCAATTATGAGGTTATAAAATCATTTAAAGTGAGTAAT-AAGGTTTTCAAAGGCATAAGTG
1 AAAATCAATTATGAGATTATAAAAACATTTAAAGTGAGTAATAAAGG-TTTCAAAGGCATAAGTG
* * *
21962 ACTATAAATGGACTTTTCTTGCTAATGGATAT--TTTTTACTTCAAGTATCTCGA-GCAAGACAT
65 ACTATAAATGAACTTTTCTTACTAATGGATATACTTTTCA-TT-AAGTATCTCGAGGC-AGACAT
22024 TCAATTATAATATGTTTTAATAAAAAATATAAAAAA
127 TCAATTATAATATGTTTTAATAAAAAATATAAAAAA
* *
22060 ANNNNNNNNNNAAATCAATTATGAGATTATAAAAACATTTAAGGTGAGTAATAAAGGTTTCGAAG
1 A----------AAATCAATTATGAGATTATAAAAACATTTAAAGTGAGTAATAAAGGTTTCAAAG
* * * * *
22125 GCATAGGTGACTATAAATGAACTTTTCTTACTAATGGATATACTTTTCATTACGTTTTTTGAGGC
56 GCATAAGTGACTATAAATGAACTTTTCTTACTAATGGATATACTTTTCATTAAGTATCTCGAGGC
* * *
22190 AGACATTCAGTTATAATCTGTTTTAATAAAAAATGTAAA
121 AGACATTCAATTATAATATGTTTTAATAAAAAATATAAA
22229 NNNNNNNNNN
Statistics
Matches: 140, Mismatches: 15, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
162 1 0.01
172 126 0.90
173 8 0.06
174 5 0.04
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.34
Consensus pattern (162 bp):
AAAATCAATTATGAGATTATAAAAACATTTAAAGTGAGTAATAAAGGTTTCAAAGGCATAAGTGA
CTATAAATGAACTTTTCTTACTAATGGATATACTTTTCATTAAGTATCTCGAGGCAGACATTCAA
TTATAATATGTTTTAATAAAAAATATAAAAAA
Found at i:24583 original size:170 final size:170
Alignment explanation
Indices: 22930--25140 Score: 1248
Period size: 171 Copynumber: 13.0 Consensus size: 170
22920 NNNNNNNAGG
* ** * * * *
22930 TTATAAAATA-ATTTAAACCGAGTAATAAGGCTTTCAAACGCGT-AGGTGACTATAAATCGATTT
1 TTATAAAA-ACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGA-GTGACTATAAATGGACTT
* ** ** * ** * *
22993 TTGTTGCCAATGAATGGCTTTTTCTTCATATTT-GTCAAGAAAAACATTCAATTATTATCTGTTT
64 TTCTTGCCAATGAATATCTTTTTCTTCACGTTTCCT-AAGGTAGACATTCAATTATAATCTGTTT
* *** * *
23057 CACCCAAAAATATAAAAAATTAAACTTAAAATCATTTATGAGA
128 TAATAAAAAATATAAAAAATTTAACTTAAAATCAATTATGAGA
* * * * * **
23100 TTAT-AAAACTAATTAAAACGAGCAATAAGACTTTTGAAGGCATGAGTGACTATAAGTAAACTTT
1 TTATAAAAAC-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTT
* * * * * * * * *
23164 TCTTGTCAAAGAATATCTTTTTTTTTACATTTCCCATGGTAGGCATTCAATTATAATATGTTTTA
65 TCTTGCCAATGAATATCTTTTTCTTCACGTTTCCTAAGGTAGACATTCAATTATAATCTGTTTTA
***********
23229 ATAAAAAATATAAAAAATNNNNNNNNNNGTCAATTATGAGA
130 ATAAAAAATATAAAAAATTTAACTTAAAATCAATTATGAGA
* * **
23270 TTATAAAAACTTTTAAAGCGAGTAATTAGGCTTTT-AGAGG--TGTAGGTGACTATAAATTAACT
1 TTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGA-AGGCATG-A-GTGACTATAAATGGACT
* * * * * *
23332 TTTCGTGCCAAGGGATATTTTTTTTCTTCACATTTCTTAAGGTAGACATTCAATTATAATCTGTT
63 TTTCTTGCCAATGAATA-TCTTTTTCTTCACGTTTCCTAAGGTAGACATTCAATTATAATCTGTT
* * * * * *
23397 TTAATAAGAAATGTAAAAGAATTCAACTTAAAATCCATTAGGAGG
127 TTAATAAAAAATATAAAA-AATTTAACTTAAAATCAATTATGAGA
* * **********
23442 TTATAAAATCATTTAAAGCAAGTAATAAGGCTNNNNNNNNNNT-AGGTGACTATAAATGGACTTT
1 TTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGA-GTGACTATAAATGGACTTT
* * * * ** *
23506 TCTTGCTAATGGATATCTTTCTCTTTACGTTTCCTAAGGTAGATTTTCAATTATTATCTGTTTTA
65 TCTTGCCAATGAATATCTTTTTCTTCACGTTTCCTAAGGTAGACATTCAATTATAATCTGTTTTA
* * **
23571 AGT-AAAAATCTACAAAAA-TTCACGTTAAAATCAATTACAAGA
130 A-TAAAAAATATA-AAAAATTTAAC-TTAAAATCAATTATGAGA
* * * * * * *
23613 TTCTAAAAATATTTTAGGC-ACATAATAAGCCTTTCGAAGGCATGAGTGACTATAAATGGACTTT
1 TTATAAAAACATTTAAAGCGA-GTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTT
* * * * * * * ** * *
23677 TCTTACCAACGGATATATTTTTCTTTAGGTTT-CTCGAGACAGATATTCACTTATAATCTGTTTT
65 TCTTGCCAATGAATATCTTTTTCTTCACGTTTCCT-AAGGTAGACATTCAATTATAATCTGTTTT
* *
23741 AATAAAAAATATAAAAAAATTTCAAATTAAAACCAATTATGAGA
129 AATAAAAAATAT-AAAAAATTT-AACTTAAAATCAATTATGAGA
* ** *
23785 TTAT-AAAACTATTTAAAGCGAGTAATAAGGATTTCAAAGCCATGAGTGACTATAAATGGACTTT
1 TTATAAAAAC-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTT
* * * * * * * *
23849 TCTTACTAAT-AGACATCTTTTTCTTCACGTTTTC-AAGATAAATATTCAATTATTATCTGTTTT
65 TCTTGCCAATGA-ATATCTTTTTCTTCACGTTTCCTAAGGTAGACATTCAATTATAATCTGTTTT
*********** * * **
23912 AACCNNNNNNNNNNAAAAATTCAAGTTAAAATCAATTACAAGA
129 AA-TAAAAAATATAAAAAATTTAACTTAAAATCAATTATGAGA
* * * * * * * ** *
23955 TTCTAAAAACATTTTAGGCGCGTAAAAAGGCTTTTCAAGGCATGGGTGACTATAAATATATTTTT
1 TTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTTT
* ** * * * * * * *
24020 CTTGTCAATGAATGGCTTTTTCTTTAGGATTTCCT-AGGCAAACATTCAGTTATTATTTGTTTTA
66 CTTGCCAATGAATATCTTTTTCTTCACG-TTTCCTAAGGTAGACATTCAATTATAATCTGTTTTA
** * * * * *
24084 ATTTAAAATGTGAAAACATTCAGCTTGAAATCAATTATGAGA
130 ATAAAAAATAT-AAAAAATTTAACTTAAAATCAATTATGAGA
********** * * * * *
24126 TNNNNNNNNNNTTTAAAGCGAGTAATAAGGCTTTCGAAGACATCAATGATTATAAATGGACTTTT
1 TTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTTT
* * * * * * * *
24191 ATTGCCAATGGATATCTTTTTCTTCATGTTTCTTGAGATAAACATTCAATTATTATCTGTTTTNN
66 CTTGCCAATGAATATCTTTTTCTTCACGTTTCCTAAGGTAGACATTCAATTATAATCTGTTTT--
******** * * * *
24256 NNNNNNNNATA-AAAAAATTCAACTTAAAATTAACTATGAGG
129 AATAAAAAATATAAAAAATTTAACTTAAAATCAATTATGAGA
** * * * * ** *
24297 TTATAAAATTATTTAAATCGAGTAATAAGACTTTCGAACGTGTGGGTGACTATAAATGGACTTTT
1 TTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTTT
* * * * * ** * * * * *
24362 GTTGCCAATGAATAGCTTTCTCTTCACGTTTGTCGAA-ACAAACAATCAATTATTATCTATTTCA
66 CTTGCCAATGAATATCTTTTTCTTCACGTTT-CCTAAGGTAGACATTCAATTATAATCTGTTTTA
*** * *
24426 CCCAAAAATATAAAAAATTTAACTTAAAATCATTTATGATA
130 ATAAAAAATATAAAAAATTTAACTTAAAATCAATTATGAGA
* * * * * *
24467 TTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTAAAGGCATGAGTGATTATAAGTAGACTTTT
1 TTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTTT
* * *
24532 CTTGCCAATGAATATCTTTTTCTTCCCGTTTCCTAAGGTAGGCATTCAATTATAATCTGGTTTAA
66 CTTGCCAATGAATATCTTTTTCTTCACGTTTCCTAAGGTAGACATTCAATTATAATCTGTTTTAA
*
24597 TAAAAAATATAAAAAAAATTT-ACTTAAAGTCAATTATGAGA
131 TAAAAAATAT--AAAAAATTTAACTTAAAATCAATTATGAGA
* * * ** * *
24638 ATATAAAAACATTTAAAGTGAGTAATAAGGCTTTTGGAGGTGTGGGTGACTATAAATCGACTTTT
1 TTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTTT
* * * * * * * * * * *
24703 CATGCCAATGGATATATTTTTCTTTATGTTTCTTGACGTAAACA-TCTAATTATAATCTATTTTT
66 CTTGCCAATGAATATCTTTTTCTTCACGTTTCCTAAGGTAGACATTC-AATTATAATCTGTTTTA
* *
24767 A-AAAAAATATAAAAAAATTTAACTTAAAACCAATTATAAGA
130 ATAAAAAATAT-AAAAAATTTAACTTAAAATCAATTATGAGA
* * * ********** * *
24808 TTACACAACCATNNNNNNNNNNTAATAAGGCTTTTGAAGACATGGGTGACTATAAATGGACTTTT
1 TTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTTT
* ** * * * * ***
24873 CTTGCCAAT-AGATATCTTTATCTTCATATTTCATGAGGCAGACATTCAATTATAATCTATTNNN
66 CTTGCCAATGA-ATATCTTTTTCTTCACGTTTCCTAAGGTAGACATTCAATTATAATCTGTTTTA
*******
24937 NNNNNNNATATTAAAAAATTTAACTTAAAA-CAATTATGAGA
130 ATAAAAAATA-TAAAAAATTTAACTTAAAATCAATTATGAGA
** * * * *
24978 TTATAAAATTATTTAAAGTGAGTAATAAGGCTTTCGAAGGCATGGGTGTCTATAAATGGACTTTT
1 TTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTTT
* * * * * * *
25043 CTTACCAATTG-ATATCTTTTTCTTCACGCTTCTTCAGGAAGACGTTCAATTATAATCTATTTTA
66 CTTGCCAA-TGAATATCTTTTTCTTCACGTTTCCTAAGGTAGACATTCAATTATAATCTGTTTTA
* * *
25107 ATAAAAAACATAAAAAATTCAAATTAAAATCAAT
130 ATAAAAAATATAAAAAATTTAACTTAAAATCAAT
25141 NNNNNNNNNN
Statistics
Matches: 1522, Mismatches: 469, Indels: 100
0.73 0.22 0.05
Matches are distributed among these distances:
168 3 0.00
169 38 0.02
170 625 0.41
171 673 0.44
172 177 0.12
173 5 0.00
174 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.36
Consensus pattern (170 bp):
TTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTTT
CTTGCCAATGAATATCTTTTTCTTCACGTTTCCTAAGGTAGACATTCAATTATAATCTGTTTTAA
TAAAAAATATAAAAAATTTAACTTAAAATCAATTATGAGA
Found at i:24872 original size:341 final size:330
Alignment explanation
Indices: 24489--25140 Score: 650
Period size: 340 Copynumber: 1.9 Consensus size: 330
24479 TTAAAGCAAG
* * * *
24489 TAATAAGGCTTTTAAAGGCATGAGTGATTATAAGTAGACTTTTCTTGCCAAT-GAATATCTTTTT
1 TAATAAGGCTTTTAAAGACATGAGTGACTATAAATAGACTTTTCTTGCCAATAG-ATATCTTTAT
* * * * * *
24553 CTTCCCGTTTCCTAAGGTAGGCATTCAATTATAATCTGGTT-TAATAAAAAATATAAAAAAAATT
65 CTTCACATTTCATAAGGCAGACATTCAATTATAATCT-ATTATAATAAAAAATAT-AAAAAAATT
* * * **
24617 T-ACTTAAAGTCAATTATGAGAATATAAAAACATTTAAAGTGAGTAATAAGGCTTTTGGAGGTGT
128 TAACTTAAA-ACAATTATGAGAATATAAAAACATTTAAAGTGAGTAATAAGGCTTTCGAAGGCAT
* * * * * *
24681 GGGTGACTATAAATCGACTTTTCATGCCAATGGATATATTTTTCTTTATGTTTCTTGACGTAA-A
192 GGGTGACTATAAATCGACTTTTCATACCAATGGATATATTTTTCTTCACGCTTCTTCA-GGAAGA
* * * *
24745 CA-TCTAATTATAATCTATTTTTA-AAAAAATATAAAAAAATTTAACTTAAAACCAATTATAAGA
256 CATTC-AATTATAATCTATTTTAATAAAAAACAT-AAAAAATTCAAATTAAAACCAATTATAAGA
24808 TTACACAACCAT
319 TTACACAACCAT
* * *
24820 NNNNNNNNNNTAATAAGGCTTTTGAAGACATGGGTGACTATAAATGGACTTTTCTTGCCAATAGA
1 ----------TAATAAGGCTTTTAAAGACATGAGTGACTATAAATAGACTTTTCTTGCCAATAGA
* * ********** *
24885 TATCTTTATCTTCATATTTCATGAGGCAGACATTCAATTATAATCTATTNNNNNNNNNNATATTA
56 TATCTTTATCTTCACATTTCATAAGGCAGACATTCAATTATAATCTATTATAATAAAAAATATAA
* **
24950 AAAAATTTAACTTAAAACAATTATGAGATTATAAAATTATTTAAAGTGAGTAATAAGGCTTTCGA
121 AAAAATTTAACTTAAAACAATTATGAGAATATAAAAACATTTAAAGTGAGTAATAAGGCTTTCGA
* * * * *
25015 AGGCATGGGTGTCTATAAATGGACTTTTCTTACCAATTGATATCTTTTTCTTCACGCTTCTTCAG
186 AGGCATGGGTGACTATAAATCGACTTTTCATACCAATGGATATATTTTTCTTCACGCTTCTTCAG
* *
25080 GAAGACGTTCAATTATAATCTATTTTAATAAAAAACATAAAAAATTCAAATTAAAATCAAT
251 GAAGACATTCAATTATAATCTATTTTAATAAAAAACATAAAAAATTCAAATTAAAACCAAT
25141 NNNNNNNNNN
Statistics
Matches: 255, Mismatches: 50, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
339 3 0.01
340 145 0.57
341 106 0.42
342 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.36
Consensus pattern (330 bp):
TAATAAGGCTTTTAAAGACATGAGTGACTATAAATAGACTTTTCTTGCCAATAGATATCTTTATC
TTCACATTTCATAAGGCAGACATTCAATTATAATCTATTATAATAAAAAATATAAAAAAATTTAA
CTTAAAACAATTATGAGAATATAAAAACATTTAAAGTGAGTAATAAGGCTTTCGAAGGCATGGGT
GACTATAAATCGACTTTTCATACCAATGGATATATTTTTCTTCACGCTTCTTCAGGAAGACATTC
AATTATAATCTATTTTAATAAAAAACATAAAAAATTCAAATTAAAACCAATTATAAGATTACACA
ACCAT
Found at i:25965 original size:171 final size:171
Alignment explanation
Indices: 25666--25981 Score: 379
Period size: 171 Copynumber: 1.8 Consensus size: 171
25656 GTGTTAATAA
* * * *
25666 AAAATCAATTATGAGGTTATAAAATCATTTAAACTGAGCAATAAGGCTTTCGAATGCATGAGTAA
1 AAAATCAATTATGAGATTATAAAATCATTTAAACTAAGCAATAAAGCTTTCGAAGGCATGAGTAA
* * ** *
25731 CTATAAATGGACTTTTCCTAGCAATGAATGGCTTTTTCTTCTTGTTTGCCATGACAGACATTCAA
66 CTATAAATAGACTTTTCCTAGCAATGAATAGCTTTTTCTTCACGTTTGCCATGACAAACATTCAA
* *
25796 TTATTATCTGTTTTACTAAAAAATGTAAAAAAAATCAACTT
131 TTATAATCTATTTTACTAAAAAATGTAAAAAAAATCAACTT
* * * * *
25837 AAAATCATTTATGAGATTATAAAATCATTTAAAAC-AAGTAATAAAGCTTTTGAAGGCATGGGTG
1 AAAATCAATTATGAGATTATAAAATCATTT-AAACTAAGCAATAAAGCTTTCGAAGGCATGAGTA
* * ** *
25901 ACTATAAGTAGACTTTT-CTTGTCAATGAATATTTTTTTCTTCACGTTT-CTCGA-GATAAACAT
65 ACTATAAATAGACTTTTCCTAG-CAATGAATAGCTTTTTCTTCACGTTTGC-C-ATGACAAACAT
25963 TCAATTATAATCTATTTTA
127 TCAATTATAATCTATTTTA
25982 ATAA
Statistics
Matches: 120, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
170 4 0.03
171 111 0.93
172 5 0.04
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (171 bp):
AAAATCAATTATGAGATTATAAAATCATTTAAACTAAGCAATAAAGCTTTCGAAGGCATGAGTAA
CTATAAATAGACTTTTCCTAGCAATGAATAGCTTTTTCTTCACGTTTGCCATGACAAACATTCAA
TTATAATCTATTTTACTAAAAAATGTAAAAAAAATCAACTT
Done.