Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399855.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_309.1, 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: 13553
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.30
Warning! 2148 characters in sequence are not A, C, G, or T
Found at i:392 original size:169 final size:170
Alignment explanation
Indices: 1--804 Score: 653
Period size: 169 Copynumber: 4.7 Consensus size: 170
* * *
1 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACA-ATAAATAAACTTTTCTTGC
1 AACCATTTAAATCGAGTAATAAGGCTTTTAAAGGAATGGGAGA-ATATAAATAGACTTTTCTT-C
* * * ** * * * * * *
65 -CAATGAAAGCCTTTTTC-CTTAC-TGTTCTTGAGGTAGACATTCAATTATAATTTATCTTAACC
64 ACAATGAATGCATTTTTCTC-CACGT-TTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAATC
* * * *
127 AAATAT-CTAAAAAAAATTGAACTTAAAATCGATTTTGAGATTATAA
127 AAAAATGC---AAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * * *
173 AACCATTTGAAGT-GAGTAATAAGGCTTTTGAAGGAATAGGTA-ACTATAAATAGACTTTTATTC
1 AACCATTT-AAATCGAGTAATAAGGCTTTTAAAGGAAT-GGGAGAATATAAATAGACTTTTCTTC
*
236 ACAATGAATGCATTTTTCTCCATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAATCAA
64 ACAATGAATGCATTTTTCTCCACGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAATCAA
* * *
301 GAATGCAAACAAATTCAACATAAAATTAATTATGAGA-T-TAA
129 AAATGCAAA-AAATTCAACTTAAAATCAATTATGAGATTATAA
* *
342 AACCATTTAAATCGAGTAATAAGGCTTTTAAAGGAATGAGAGAATATAAAT-GAACATTTCTTC-
1 AACCATTTAAATCGAGTAATAAGGCTTTTAAAGGAATGGGAGAATATAAATAG-ACTTTTCTTCA
* ** * * * **
405 CAAATAAATGGGTTTTTCTACACGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAAGGAA
65 C-AATGAATGCATTTTTCTCCACGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAATCAA
** * * **********
470 AAATATAAAAAATTCAACTGAAACTCAATTANNNNNNNNNNA
129 AAATGCAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * * *
512 AACCATTTAAAGCGAGTAATAAGGATTTTAAATGAATGGGTGACTATAAATAGACTTTTC-TCAC
1 AACCATTTAAATCGAGTAATAAGGCTTTTAAAGGAATGGGAGAATATAAATAGACTTTTCTTCA-
* *
576 CAATGAATGCATTTTTCTTCCA-GTTTCTCAAAGCAGACATTCAATTATA----GTTTTAAACAA
65 CAATGAATGCATTTTTC-TCCACGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAATCAA
* * *
636 AAATGTGAAAAAA-ACAAACTTAAAATCAATTATAAGATTATAA
129 AAATG-CAAAAAATTC-AACTTAAAATCAATTATGAGATTATAA
* * * *
679 AACTATTTAAAGT-GAGTAATAACGCTTCTTGAAA-GAAAGGGAGACTATAAATAGACTTTTCTT
1 AACCATTTAAA-TCGAGTAATAAGGCTT-TT-AAAGGAATGGGAGAATATAAATAGACTTTTCTT
* * *
742 CTA-AATAAATG-AGTTTTTCTACACGTTTCTCAAGGGAGACATTCAATTATAGTCTGTTTTAAT
63 C-ACAATGAATGCA-TTTTTCTCCACGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAAT
805 GAAAGAATAG
Statistics
Matches: 503, Mismatches: 98, Indels: 62
0.76 0.15 0.09
Matches are distributed among these distances:
166 14 0.03
167 47 0.09
168 90 0.18
169 117 0.23
170 94 0.19
171 28 0.06
172 105 0.21
173 8 0.02
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (170 bp):
AACCATTTAAATCGAGTAATAAGGCTTTTAAAGGAATGGGAGAATATAAATAGACTTTTCTTCAC
AATGAATGCATTTTTCTCCACGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAATCAAAA
ATGCAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
Found at i:623 original size:339 final size:329
Alignment explanation
Indices: 170--813 Score: 779
Period size: 339 Copynumber: 1.9 Consensus size: 329
160 TTTGAGATTA
* * * * *
170 TAAAACCATTTGAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTAACTATAAATAGACTTTTATT
1 TAAAACCATTTAAAGCGAGTAATAAGGATTTTAAAGGAATAGGTAACTATAAATAGACTTTTACT
* *
235 CACAATGAATGCATTTTTCTCCATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAATCA
66 CACAATGAATGCATTTTTCTCCATGTTTCTCAAAGCAGACATTCAATTATA----GTTTTAAACA
* * * *
300 AGAATG-CAAACAAATTC-AACATAAAATTAATTATGAGA-T-TAAAACCATTTAAA-TCGAGTA
127 AAAATGTCAAA-AAA-ACAAACATAAAATCAATTATAAGATTATAAAACCATTTAAAGT-GAGTA
* * *
360 ATAAGGCTT-TT-AAAGGAATGAGAGAATATAAAT-GAACATTTCTTCCAAATAAATGGGTTTTT
189 ATAACGCTTCTTGAAA-GAAAGAGAGAATATAAATAG-ACATTTCTTCCAAATAAATGAGTTTTT
* *
422 CTACACGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAAGGAAA-AATATAAAAAATTCA
252 CTACACGTTTCTCAAGGGAGACATTCAATTATAGTCTGTTTTAAGGAAAGAATATAAAAAATTCA
486 ACTGAAACTCAAT
317 ACTGAAACTCAAT
* * *
499 TANNNNNNNNNNAAACCATTTAAAGCGAGTAATAAGGATTTTAAATGAATGGGTGACTATAAATA
1 TA----------AAACCATTTAAAGCGAGTAATAAGGATTTTAAAGGAATAGGTAACTATAAATA
564 GACTTTT-CTCACCAATGAATGCATTTTTCTTCCA-GTTTCTCAAAGCAGACATTCAATTATAGT
56 GACTTTTACTCA-CAATGAATGCATTTTTC-TCCATGTTTCTCAAAGCAGACATTCAATTATAGT
* * *
627 TTTAAACAAAAATGTGAAAAAAACAAACTTAAAATCAATTATAAGATTATAAAACTATTTAAAGT
119 TTTAAACAAAAATGTCAAAAAAACAAACATAAAATCAATTATAAGATTATAAAACCATTTAAAGT
* * * *
692 GAGTAATAACGCTTCTTGAAAGAAAGGGAGACTATAAATAGACTTTTCTTCTAAATAAATGAGTT
184 GAGTAATAACGCTTCTTGAAAGAAAGAGAGAATATAAATAGACATTTCTTCCAAATAAATGAGTT
*
757 TTTCTACACGTTTCTCAAGGGAGACATTCAATTATAGTCTGTTTTAATGAAAGAATA
249 TTTCTACACGTTTCTCAAGGGAGACATTCAATTATAGTCTGTTTTAAGGAAAGAATA
814 GATGAGAAAT
Statistics
Matches: 267, Mismatches: 27, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
329 2 0.01
334 1 0.00
335 35 0.13
336 4 0.01
337 26 0.10
338 91 0.34
339 104 0.39
340 4 0.01
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.32
Consensus pattern (329 bp):
TAAAACCATTTAAAGCGAGTAATAAGGATTTTAAAGGAATAGGTAACTATAAATAGACTTTTACT
CACAATGAATGCATTTTTCTCCATGTTTCTCAAAGCAGACATTCAATTATAGTTTTAAACAAAAA
TGTCAAAAAAACAAACATAAAATCAATTATAAGATTATAAAACCATTTAAAGTGAGTAATAACGC
TTCTTGAAAGAAAGAGAGAATATAAATAGACATTTCTTCCAAATAAATGAGTTTTTCTACACGTT
TCTCAAGGGAGACATTCAATTATAGTCTGTTTTAAGGAAAGAATATAAAAAATTCAACTGAAACT
CAAT
Found at i:1375 original size:170 final size:172
Alignment explanation
Indices: 849--2007 Score: 919
Period size: 170 Copynumber: 6.8 Consensus size: 172
839 ATAAGCGACA
** * * * *
849 ATAAAT-GATCTTTTCTTATCAATTAATGCCTTTTTCTTCATGTTTCTCGACGTAGACATTCAAT
1 ATAAATGGA-CTTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* * * * * * * *
913 TATAATTTTTTTTAACCAAAAAAGTAAAAAAAATTGAAATTAAAATTAATTTTGAGATTATAAAA
65 TATAGTCTGTTTTAACTAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAA
** *** *
978 C-TATTTAAAGTAAGTAATAAGGCTTTTAAAGGAATGGGTGACA
130 CAT-TTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGAAAGACT
* * * * * **
1021 AAAAATAGACTTTTGTTGCCAATGAATGCTTTTTTCTTCACATTTCTCAAGGTAG-CATTCAATT
1 ATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATT
* * * * * * * *
1085 ATAGTCTTTTTTGA-TAAAAAATATAAAACAAATTGAACATCAAATCAATTTTGAGATAATAAAA
66 ATAGTCTGTTTTAACT-AAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAA
* * * *
1149 TCA-GTTAAACCGAGTAATAAGGCTTTTGAAGGAATGAGAGACT
130 -CATTTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGAAAGACT
* *
1192 GTAAATGGACTTTTCTTGCCAATGAACACCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATT
1 ATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATT
* ** * *
1257 ATAGTCTGTTTTAA-TGAAAATGT-AAAGGAATTCAACTTAAAATCAATTACGAGATTATAAAAC
66 ATAGTCTGTTTTAACTAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAAC
*
1320 ATTTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGAAAGGCT
131 ATTTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGAAAGACT
* * * * * * * **
1362 ATAAATTGACTTTTCTT-CTAAATAAATTA-GTTTTTCTACATGTCTTATGAA-ACAGACATTCA
1 ATAAATGGACTTTTCTTGC-CAATGAA-TACCTTTTTCTTCATGT-TTCTCAAGGTAGACATTCA
* * * * * * **
1424 ATTATAGTCTGTTTAAACAAAAAATG--CAAAAAATTCAACTTCAGATCAATTACAAGATTATAA
63 ATTATAGTCTGTTTTAACTAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAA
* ***
1487 AA-AGTTTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACT
128 AACA-TTTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGAAAGACT
* * * *
1532 ATAAATGGACTTTTCTTAG-TAATGAATACCTTTTTCTTCATGTTTCAT-GAGTTAGTCATTCAA
1 ATAAATGGACTTTTCTT-GCCAATGAATACCTTTTTCTTCATGTTTC-TCAAGGTAGACATTCAA
* * * * * *
1595 TTATAATATATTTTAACTAAAAA--TAAAAAAAATTGAACATAAAATCAATTTTGAGATAATAAA
64 TTATAGTCTGTTTTAACTAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAA
* * * * **
1658 ATCA-CTTAAAGTGAGTAATAAAGCTTTTGAAA-AAAT-AGGTGACT
129 A-CATTTTAAAGCGAGTAATAAGGCTTTT-AAAGGAATGA-AAGACT
** * * ** * * *
1702 ATAAATGGACTTTTCTTGTTAATGAATGA-CTTTTACTTGACATTTCAT-GAGGAACACATTCAA
1 ATAAATGGACTTTTCTTGCCAATGAAT-ACCTTTTTCTTCATGTTTC-TCAAGGTAGACATTCAA
** * * * *
1765 TTATAACCTGTTTTAACTAAAAATGTTGAAAGAAATTGAACTTAAAATCAACTATAAGATTATAA
64 TTATAGTCTGTTTTAACTAAAAATG-TAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAA
* ** * * * *
1830 AGCCGTTTAAAGTGAGTAATAATGCTTTTGAAGGAATGAAAGAGT
128 AACATTTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGAAAGACT
* * * * * *
1875 ATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAGATATTTAATT
1 ATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATT
* * * * * *
1940 ATAGTCTATTTTAA-TCAAAAATCTAAAAAAAA-TGAA-TATAAAAGCAATTTTAAGATAATAAA
66 ATAGTCTGTTTTAACT-AAAAATGTAAAAAAAATTGAACT-TAAAATCAATTATGAGATTATAAA
2002 ACATTT
129 ACATTT
2008 AATTATAAAC
Statistics
Matches: 789, Mismatches: 164, Indels: 69
0.77 0.16 0.07
Matches are distributed among these distances:
169 10 0.01
170 385 0.49
171 186 0.24
172 78 0.10
173 129 0.16
174 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (172 bp):
ATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATT
ATAGTCTGTTTTAACTAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAAC
ATTTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGAAAGACT
Found at i:2023 original size:72 final size:72
Alignment explanation
Indices: 1931--2082 Score: 175
Period size: 72 Copynumber: 2.1 Consensus size: 72
1921 TCAAGGTAGA
** *
1931 TATTTAATTATAGTCTATTTTAATC-AAAAATCTAAAAAAAATGAATA-TAAAAGCAATTTTAAG
1 TATTTAATTATAAACTATTTT-ACCGAAAAA-CTAAAAAAAATGAA-ACTAAAAGCAATTTTAAG
1994 ATAATAAAAC
63 ATAATAAAAC
* * * *
2004 -ATTTAATTATAAACTATTTTACCGAAAAAGTAAAAAAAATTAAACCTAAAATCAATTTTGAGAT
1 TATTTAATTATAAACTATTTTACCGAAAAACTAAAAAAAATGAAA-CTAAAAGCAATTTTAAGAT
*
2068 TATAAAAC
65 AATAAAAC
2076 TATTTAA
1 TATTTAA
2083 AGTGAGTAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
70 1 0.01
71 14 0.21
72 46 0.69
73 6 0.09
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (72 bp):
TATTTAATTATAAACTATTTTACCGAAAAACTAAAAAAAATGAAACTAAAAGCAATTTTAAGATA
ATAAAAC
Found at i:2329 original size:172 final size:171
Alignment explanation
Indices: 2002--3412 Score: 1319
Period size: 172 Copynumber: 8.2 Consensus size: 171
1992 AGATAATAAA
* ** * * *
2002 ACATTTAATTATAAACTATTTT-ACCGAAAAA-GTAAAAAAAATTAAACCTAAAATCAATTTTGA
1 ACATTCAATTATAGTCTGTTTTAACC-AAAAATGT-AAAAAAATTGAACTTAAAATCAATTTTGA
* * *
2065 GATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTT
64 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTT
* * * *
2130 TTCTTGTCAATGAATGCCTTATTCTTCACGTTTCACGAGGTAG
129 TTCTTGTCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAG
* * * *
2173 ACATTCAATTATATTCTGTTTTAGCCAAAAATGTAAGAAAAATTAAAGTTAAAATCAATTTTGAG
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAA-AAAAATTGAACTTAAAATCAATTTTGAG
** * * *** * **
2238 ATTATAAAATTATTCAAAGTGAGTAATAAAGCTTTTGAAGGAATGAACGACTACAAATAAACTTT
65 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTT
** * * *
2303 TCTTACCAATGAATGTATTTTTCTTCACGTTTCTTAAGGGAG
130 TCTTGTCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAG
* * * * *
2345 ACATTCAATTATTA-TTTGTTTTAACTAAAAATGT-AAAAGATTCG-ATTTAAAATCAATTATGA
1 ACATTCAATTA-TAGTCTGTTTTAACCAAAAATGTAAAAAAATT-GAACTTAAAATCAATTTTGA
* * * * * * *
2407 GACTATAAAGCCATTTAAAGCGAATAATAAGGGTTTTGAAGGAATGGGAGACTATAAATAGACTT
64 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTT
* * * * * *
2472 TTTTTATCAATAAATGT-TGTTT-TTCACCTTTCTCAAGGCAG
129 TTCTTGTCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAG
* * ** * * *
2513 ACACTCAATTATAGTCTATTTTAATGAAAAATGT-TAAAAATAT-AACTTAAAGTCAATTATGAG
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAT-TGAACTTAAAATCAATTTTGAG
* * * *
2576 ATTATAAAACCATTTAAAGTAAGTGATAAGGCTTTTGAAGGAATCGGTGACTACAAATGGACTTT
65 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTT
* * * *
2641 TCTTGTCAATCAAT-TCTTTTTTCTTCATGTTTTTTAAGGT-G
130 TCTTGTCAATGAATGTC-TTTTTCTTCACGTTTCTCAAGGTAG
* * * * * *
2682 TACATTCCATTATAGGCTGTTTTAACCAAAATTGTAAAGGAAATTGAACTTTAAATTAATTTTGA
1 -ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA-AAAATTGAACTTAAAATCAATTTTGA
* * * * * * * * *
2747 GTTTATAAAATCATTTAAAGAGTGTAATAAGGCTTTTAAAAGATTGGGTAACTATAAATAGACTT
64 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTT
* * * * *
2812 TTCTTGCCATTGAATGCCTTTTTCTTCACGTTTCTCTATGTAG
129 TTCTTGTCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAG
* * * *
2855 ACATTCAATTATAATTTGTTTTAACCAAAAATGTAGAAAAAATTGAACATAAAATCAATTTTGAT
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTA-AAAAAATTGAACTTAAAATCAATTTTGAG
* ** * * * *
2920 ATAATAAAA-CATTTTAAAAAGAGTAATAAGGCTCTAGAAAGAATGGGAGACTATAAATGGACTT
65 ATTATAAAACCA-TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTT
* ** *
2984 TTCTCGTCAATGAATACCCTTTTT-ATCATC-TTTCTCAAGGTAG
129 TTCTTGTCAATGAAT-GTCTTTTTCTTCA-CGTTTCTCAAGGTAG
* * * *
3027 ACATTCAAATATAGTATGTTTTAACTAAAAATGTAAAAAAGAATTGAACATAAAATCAATTTTGA
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGT-AAAAA-AATTGAACTTAAAATCAATTTTGA
* * * * *
3092 GAGTATAAAGCTATTTAAAGTGAGTAATAAGGCTTTTTAAGAAATGGGTGACTATAAATGGACTT
64 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTT
* * * **
3157 TTCTTGAT-AATGAATATTTTTTTCTTCACGTTTCACGTGGTAG
129 TTCTTG-TCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAG
* * * * * * *
3200 ATATTTAATTATAATCTGTTTTAACAAAAAAATATAAAAAAATTGAACTTAAAATTAATTTTGGG
1 ACATTCAATTATAGTCTGTTTTAAC-CAAAAATGTAAAAAAATTGAACTTAAAATCAATTTTGAG
* * *
3265 ATTATAAAATCATTTAAAGGGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTC
65 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTT-
* * * * * *
3330 TT-TTG-CTAATGAATGCCTTGTTCCTAACGTTTCTCAACGTAT
129 TTCTTGTC-AATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAG
* * *
3372 ACATTCAATTATACTCTGTTCTAACTAAGAAA-GTAAAAAAA
1 ACATTCAATTATAGTCTGTTTTAACCAA-AAATGTAAAAAAA
3413 NNNNNNNNNN
Statistics
Matches: 1003, Mismatches: 205, Indels: 64
0.79 0.16 0.05
Matches are distributed among these distances:
167 3 0.00
168 129 0.13
169 10 0.01
170 126 0.13
171 40 0.04
172 545 0.54
173 141 0.14
174 9 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (171 bp):
ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTTTGAGA
TTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT
CTTGTCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAG
Found at i:2424 original size:415 final size:415
Alignment explanation
Indices: 1588--2356 Score: 1032
Period size: 415 Copynumber: 1.9 Consensus size: 415
1578 ATGAGTTAGT
* * *
1588 CATTCAATTATAATATATTTTAACTAAAAATAAAAAAAATTGAACATAAAATCAATTTTGAGATA
1 CATTTAATTATAATATATTTTAACGAAAAATAAAAAAAATTAAACATAAAATCAATTTTGAGATA
1653 ATAAAATCACTTAAAGTGAGTAATAAAGCTTTTGAAAAAATAGGTGACTATAAATGGACTTTTCT
66 ATAAAATCACTTAAAGTGAGTAATAAAGCTTTTGAAAAAATAGGTGACTATAAATGGACTTTTCT
* * * *
1718 TGTTAATGAATGACTTTTACTTGACATTTCATGAGGAACACATTCAATTATAACCTGTTTTAACT
131 TGTCAATGAATGACTTTTACTTCACATTTCACGAGGAACACATTCAATTATAACCTGTTTTAACC
* * * * *
1783 AAAAATGTTGAAAGAAATTGAACTTAAAATCAACTATAAGATTATAAAGCCGTTTAAAGTGAGTA
196 AAAAATGTTGAAAAAAATTAAACTTAAAATCAACTATAAGATTATAAAACCATTCAAAGTGAGTA
* * * **
1848 ATAATGCTTTTGAAGGAATGAAAGAGTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTT
261 ATAAAGCTTTTGAAGGAATGAAAGACTACAAATAAACTTTTCTTACCAATGAATGCTTTTTTCTT
* * *
1913 CACGTTTCTCAAGGTAGATATTTAATTATAGTCTATTTTAATCAAAAATCTAAAAAAAATGAATA
326 CACGTTTCTCAAGGGAGACATTCAATTATAGTCTATTTTAATCAAAAATCTAAAAAAAATGAATA
*
1978 TAAAAGCAATTTTAAGATAATAAAA
391 TAAAAGCAATTATAAGATAATAAAA
* *
2003 CATTTAATTATAA-ACTATTTTACCGAAAAAGTAAAAAAAATTAAACCTAAAATCAATTTTGAGA
1 CATTTAATTATAATA-TATTTTAACGAAAAA-TAAAAAAAATTAAACATAAAATCAATTTTGAGA
* * * *
2067 TTATAAAA-CTATTTAAAGTGAGTAATAAGGCTTTT-AAAGGAAT-GAGTGACTATAAATGGACT
64 TAATAAAATC-ACTTAAAGTGAGTAATAAAGCTTTTGAAA-AAATAG-GTGACTATAAATGGACT
* * * * **
2129 TTTCTTGTCAATGAATGCCTTATT-CTTCACGTTTCACGAGGTAGACATTCAATTATATTCTGTT
126 TTTCTTGTCAATGAATGACTT-TTACTTCACATTTCACGAGGAACACATTCAATTATAACCTGTT
* * * * * **
2193 TTAGCCAAAAATG-T-AAGAAAAATTAAAGTTAAAATCAATTTTGAGATTATAAAATTATTCAAA
190 TTAACCAAAAATGTTGAA-AAAAATTAAACTTAAAATCAACTATAAGATTATAAAACCATTCAAA
*
2256 GTGAGTAATAAAGCTTTTGAAGGAATGAACGACTACAAATAAACTTTTCTTACCAATGAATG-TA
254 GTGAGTAATAAAGCTTTTGAAGGAATGAAAGACTACAAATAAACTTTTCTTACCAATGAATGCT-
*
2320 TTTTTCTTCACGTTTCTTAAGGGAGACATTCAATTAT
318 TTTTTCTTCACGTTTCTCAAGGGAGACATTCAATTAT
2357 TATTTGTTTT
Statistics
Matches: 305, Mismatches: 41, Indels: 16
0.84 0.11 0.04
Matches are distributed among these distances:
414 4 0.01
415 155 0.51
416 144 0.47
417 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (415 bp):
CATTTAATTATAATATATTTTAACGAAAAATAAAAAAAATTAAACATAAAATCAATTTTGAGATA
ATAAAATCACTTAAAGTGAGTAATAAAGCTTTTGAAAAAATAGGTGACTATAAATGGACTTTTCT
TGTCAATGAATGACTTTTACTTCACATTTCACGAGGAACACATTCAATTATAACCTGTTTTAACC
AAAAATGTTGAAAAAAATTAAACTTAAAATCAACTATAAGATTATAAAACCATTCAAAGTGAGTA
ATAAAGCTTTTGAAGGAATGAAAGACTACAAATAAACTTTTCTTACCAATGAATGCTTTTTTCTT
CACGTTTCTCAAGGGAGACATTCAATTATAGTCTATTTTAATCAAAAATCTAAAAAAAATGAATA
TAAAAGCAATTATAAGATAATAAAA
Found at i:5127 original size:171 final size:171
Alignment explanation
Indices: 3815--5583 Score: 1145
Period size: 170 Copynumber: 10.3 Consensus size: 171
3805 NNNNNNNNNN
* * * * * * *
3815 GTAGACATTCAATTATAGTCTGCTATAACTAAAAATTTAAAAAATTTTAACTTAAAATCGATTAT
1 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAATCAATTAT
* * * ********** *
3880 GAGATTATAAAACCATTTCAAGTAAGTAATAAGGCTTTTGAAAGAATGGGTNNNNNNNNNNGAAC
66 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
** * * *
3945 TTTTCTTGC-CAATGAATGTATTTTTCTTTAAGTTTCTCAAG
131 TTTTCTT-CACAATGAATACATTTTTCTTCACGTTTCTTAAG
********** * * * *
3986 GTAGACATTCAATTANNNNNNNNNNTGACCAAAAATATAAAAAAATTCAGCTTAAAATTAATTAT
1 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAATCAATTAT
* * * * *
4051 GAGATTATAAAACTATTTAATGGGAGTAATAAGGCTTTTGAAGAAATGAGAT-ACTATAAATGGA
66 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATG-GGTGACTATAAATGGA
* * * * *** *
4115 TTTTTTTTCAAAATAAATGGGTTTTTCTAT-GCGTTTCTCTAAG
130 CTTTTCTTCACAATGAATACATTTTTCT-TCACGTTTCT-TAAG
** ** * * *
4158 G-AGGTATTCAATTATAGTCTGTTTTAATGAAAAAT-GAGAAAAATTAAATTTAAAATCAATTAT
1 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAATCAATTAT
* * * ********** * *
4221 AATATTATAAAATCATTTAAANNNNNNNNNNAGGCTTTTGAAGGAATGAGTGACTATAAATGAAC
66 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
* * * *** ** *
4286 CTTTCTTGC-CAATTAATGTC-TTTTTCTTTGTGTTTCTCGAT
131 TTTTCTT-CACAATGAAT-ACATTTTTCTTCACGTTTCTTAAG
* * * ****
4327 GT-GACATTCAATTATAATCTATTTTAACTAAAAA-ATTAAAAAACATTAAAC-TAAATATGNNN
1 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATA-TAAAAAA-ATTAAACTTAAA-ATCAAT
********** * * * *
4389 NNNNNNNNNNTAAAACCATTTAAAGTGAGTAATAATGCTTTAGAAGGAATAGGTGACTATAAATA
63 TATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
* *
4454 GACTTTTTCCTGC-CAATGAATACATTTTTCTTCATGTTTCTTAAG
128 GAC-TTTT-CTTCACAATGAATACATTTTTCTTCACGTTTCTTAAG
* * * * *
4499 GTAGATATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAAAAATTAAACTTTAAATCAAT
1 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAA--T-ATAAAAAAATTAAACTTAAAATCAAT
** *************
4564 TATGAGATTATAAAACCATTTAAACCGAGTAATAAGGCTTNNNNNNNNNNNNNTGACTATAAATG
63 TATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
** * * * *
4629 GACTTTTCTTGTCAATAAATACTTTTTTCTTCGCGTTTCTCAAG
128 GACTTTTCTTCACAATGAATACATTTTTCTTCACGTTTCTTAAG
* * ** * ** *
4673 GTAGACATTCAATTATACTCTATTTTAATAAAAAATAT-AAAAAATTTAGTTTAAAATGAATTAT
1 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAATCAATTAT
* * * * * **
4737 GAGTTTATAAAAGCATTTAAAGTAAGTAATAAGGCTTTTGAAAGAATGGATGACTATAAATAAAC
66 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
* * *
4802 TTTTCTT-ATCAATGAATGTC-TTTTTTTTC-CTGTTTCTTGAG
131 TTTTCTTCA-CAATGAAT-ACATTTTTCTTCAC-GTTTCTTAAG
* * * * * *
4843 GTAGATATTCCATTATAATATGTTTTAACCAAAAATCTAAAAAAAAATTAAACTTAAAATTAATT
1 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAA--TATAAAAAAATTAAACTTAAAATCAATT
* * * * * * * *
4908 TTGAGATTGTAAAAGCATTTGAAGTGAGGAATAAGGCTTTTAAAGGAATGGGTGTCTATATATGG
64 ATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* * * *
4973 ATTTTTCTTGAAAATGAATACATTTTTCTTCACATTTCTTAAG
129 ACTTTTCTTCACAATGAATACATTTTTCTTCACGTTTCTTAAG
* * *
5016 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAGTTAT
1 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAATCAATTAT
* * * * *
5081 GAGATTATTAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGAC
66 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
* *** * * * *
5146 TTTTCTTC-CAAATAAATGGGTTTTTCTACATGTTTCTCACG
131 TTTTCTTCAC-AATGAATACATTTTTCTTCACGTTTCTTAAG
* * * **
5187 GCAGGCATTAAATTATAGTCTGTTTTAATGAAAAATAT-AAAAAATTAAACTTAAAATCAATTAT
1 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAATCAATTAT
* * * ** * * *
5251 GACATTACAAAACCATTCAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTGTAAA-GGAC
66 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
* * * *
5315 TTTTC-TCACCAATGAATGCTTTTTTCTTCAAGTTTCTCAAG
131 TTTTCTTCA-CAATGAATACATTTTTCTTCACGTTTCTTAAG
* * * * * *
5356 GTAAACATTGAATTATAGTTTGTTTTAACTAAAAATATAAAAAAATTTATCTTAAAATCAATTAT
1 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAATCAATTAT
* * * ** * *
5421 GAGATTATAAAACTATTTAAAGTGAGTGATAAGGTTTTTGAAGGAAT-AATCGACTACAAATAGA
66 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT-GACTATAAATGGA
* * * *
5485 CTTTTCTTCAAAATAAATGA-GTTTTTCTACACGTTTCTTGAAG
130 CTTTTCTTCACAATGAAT-ACATTTTTCTTCACGTTTCTT-AAG
** * **
5528 G-ACCCATTCAATTATAGCCTGTTTTAATGAAAAATA-AAAAAAATTAAACTTAAAAT
1 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAAT
5584 TATAAAAAAA
Statistics
Matches: 1207, Mismatches: 350, Indels: 83
0.74 0.21 0.05
Matches are distributed among these distances:
168 2 0.00
169 97 0.08
170 388 0.32
171 382 0.32
172 47 0.04
173 168 0.14
174 63 0.05
175 50 0.04
176 9 0.01
177 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.35
Consensus pattern (171 bp):
GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAATCAATTAT
GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
TTTTCTTCACAATGAATACATTTTTCTTCACGTTTCTTAAG
Found at i:5428 original size:340 final size:341
Alignment explanation
Indices: 3821--5583 Score: 1307
Period size: 340 Copynumber: 5.2 Consensus size: 341
3811 NNNNGTAGAC
* * ** * * *
3821 ATTCAATTATAGTCTGCTATAACT-AAAAATTTAAAAAATTTTAACTTAAAATCGATTATGAGAT
1 ATTCAATTATAGTCTGTTTTAA-TGAAAAATAAAAAAAAATTAAACTTAAAATCAATTATGAGAT
* ** * * ********** *
3885 TATAAAACCATTTCAAGTAAGTAATAAGGCTTTTGAAAGAATGGGTNNNNNNNNNNGAACTTTTC
65 TATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTC
* * * ********** *
3950 TTGCCAATGAAT-GTATTTTTCTTTAAGTTTCTCAAGGTAGACATTCAATTANNNNNNNNNNTGA
130 TTACCAATGAATACT-TTTTTCTTCAAGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAA
* * * * *
4014 CCAAAAATATAAAAAAATTCAGCTTAAAATTAATTATGAGATTATAAAACTATTTAATGGGAGTA
194 CTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTA
* * * * * *
4079 ATAAGGCTTTTGAAGAAAT-GAGATACTATAAATGGATTTTTTTTCAAAATAAATGGGTTTTTCT
259 ATAAGGCTTTTGAAGGAATAG-GAGACTATAAATAGACTTTTCTTCCAAATAAATGGGTTTTTCT
*** *
4143 ATGCGTTTCTCTAAGGAGGT
323 ACATGTTTCTC-AAGGAGAT
* * * * *
4163 ATTCAATTATAGTCTGTTTTAATGAAAAAT-GAGAAAAATTAAATTTAAAATCAATTATAATATT
1 ATTCAATTATAGTCTGTTTTAATGAAAAATAAAAAAAAATTAAACTTAAAATCAATTATGAGATT
* ********** * *
4227 ATAAAATCATTTAAANNNNNNNNNNAGGCTTTTGAAGGAATGAGTGACTATAAATGAACCTTTCT
66 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCT
* * * *** * * *
4292 TGCCAATTAAT-GTCTTTTTCTTTGTGTTTCTCGATGT-GACATTCAATTATAATCTATTTTAAC
131 TACCAATGAATACT-TTTTTCTTCAAGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAAC
* ************** *
4355 TAAAAA-ATTAAAAAACATTAAAC-TAAATATGNNNNNNNNNNNNNTAAAACCATTTAAAGTGAG
195 TAAAAATA-TAAAAAA-ATTCAACTTAAA-ATCAATTATGAGATTATAAAACTATTTAAAGTGAG
* * * * * ***
4418 TAATAATGCTTTAGAAGGAATAGGTGACTATAAATAGACTTTTTCCTGCC-AATGAATACATTTT
257 TAATAAGGCTTTTGAAGGAATAGGAGACTATAAATAGAC-TTTT-CTTCCAAATAAATGGGTTTT
* *
4482 TCTTCATGTTTCTTAAGGTAGAT
320 TCTACATGTTTCTCAAGG-AGAT
* *
4505 ATTCAATTATAATCTGTTTTAACT-AAAAATGTAAAAAAAAAATTAAACTTTAAATCAATTATGA
1 ATTCAATTATAGTCTGTTTTAA-TGAAAAA--T-AAAAAAAAATTAAACTTAAAATCAATTATGA
* *************
4569 GATTATAAAACCATTTAAACCGAGTAATAAGGCTTNNNNNNNNNNNNNTGACTATAAATGGACTT
62 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTT
** * ** *
4634 TTCTTGTCAATAAATACTTTTTTCTTCGCGTTTCTCAAGGTAGACATTCAATTATACTCTATTTT
127 TTCTTACCAATGAATACTTTTTTCTTCAAGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTT
* ** * * *
4699 AA-TAAAAA-ATATAAAAAATTTAGTTTAAAATGAATTATGAGTTTATAAAAGC-ATTTAAAGTA
192 AACTAAAAATATA-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-CTATTTAAAGTG
* * * * **
4761 AGTAATAAGGCTTTTGAAAGAAT-GGATGACTATAAATAAACTTTTCTTATC-AATGAATGTCTT
255 AGTAATAAGGCTTTTGAAGGAATAGGA-GACTATAAATAGACTTTTCTT-CCAAATAAATGGGTT
* * * **
4824 TTTTTTCCTGTTTCTTGAGGTAGAT
318 TTTCTACATGTTTCTCAAGG-AGAT
* * * ** * *
4849 ATTCCATTATAATATGTTTTAACCAAAAATCTAAAAAAAAATTAAACTTAAAATTAATTTTGAGA
1 ATTCAATTATAGTCTGTTTTAATGAAAAA--TAAAAAAAAATTAAACTTAAAATCAATTATGAGA
* * * * * * * * * *
4914 TTGTAAAAGCATTTGAAGTGAGGAATAAGGCTTTTAAAGGAATGGGTGTCTATATATGGATTTTT
64 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTT
* * * *
4979 CTTGA-AAATGAATACATTTTTCTTCACA-TTTCTTAAGGTAGACATTCAATTATAGTCTGTTTT
129 CTT-ACCAATGAATACTTTTTTCTTCA-AGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTT
* * * * * *
5042 AACCAAAAATGTAAAAAAATTCAACTTAAAATCAGTTATGAGATTATTAAACAATTTAAAGCGAG
192 AACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAG
*
5107 TAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTCCAAATAAATGGGTTTTTC
257 TAATAAGGCTTTTGAAGGAATAGGAGACTATAAATAGACTTTTCTTCCAAATAAATGGGTTTTTC
* **
5172 TACATGTTTCTCACGGCAGGC
322 TACATGTTTCTCAAGG-AGAT
* * *
5193 ATTAAATTATAGTCTGTTTTAATGAAAAAT-ATAAAAAATTAAACTTAAAATCAATTATGACATT
1 ATTCAATTATAGTCTGTTTTAATGAAAAATAAAAAAAAATTAAACTTAAAATCAATTATGAGATT
* * * * *
5257 ACAAAACCATTCAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTGTAAA-GGACTTTTCT
66 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCT
* * * * * *
5321 CACCAATGAATGCTTTTTTCTTCAAGTTTCTCAAGGTAAACATTGAATTATAGTTTGTTTTAACT
131 TACCAATGAATACTTTTTTCTTCAAGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACT
* * *
5386 AAAAATATAAAAAAATTTATCTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTGAT
196 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAAT
* *** * * *
5451 AAGGTTTTTGAAGGAATAATCGACTACAAATAGACTTTTCTTCAAAATAAATGAGTTTTTCTACA
261 AAGGCTTTTGAAGGAATAGGAGACTATAAATAGACTTTTCTTCCAAATAAATGGGTTTTTCTACA
* * ***
5516 CGTTTCTTGAAGGACCC
326 TGTTTC-TCAAGGAGAT
*
5533 ATTCAATTATAGCCTGTTTTAATGAAAAAT-AAAAAAAATTAAACTTAAAAT
1 ATTCAATTATAGTCTGTTTTAATGAAAAATAAAAAAAAATTAAACTTAAAAT
5584 TATAAAAAAA
Statistics
Matches: 1104, Mismatches: 286, Indels: 64
0.76 0.20 0.04
Matches are distributed among these distances:
339 3 0.00
340 261 0.24
341 229 0.21
342 80 0.07
343 134 0.12
344 199 0.18
345 61 0.06
346 112 0.10
347 25 0.02
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.35
Consensus pattern (341 bp):
ATTCAATTATAGTCTGTTTTAATGAAAAATAAAAAAAAATTAAACTTAAAATCAATTATGAGATT
ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCT
TACCAATGAATACTTTTTTCTTCAAGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACT
AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAAT
AAGGCTTTTGAAGGAATAGGAGACTATAAATAGACTTTTCTTCCAAATAAATGGGTTTTTCTACA
TGTTTCTCAAGGAGAT
Found at i:5584 original size:12 final size:12
Alignment explanation
Indices: 5567--5608 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
5557 AAAAATAAAA
5567 AAAATTAAACTT
1 AAAATTAAACTT
*
5579 AAAATTATAA--A
1 AAAATTA-AACTT
5590 AAAATTAAACTT
1 AAAATTAAACTT
5602 AAAATTA
1 AAAATTA
5609 TAAAACTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 2 0.08
11 7 0.28
12 14 0.56
13 2 0.08
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAACTT
Found at i:5594 original size:23 final size:23
Alignment explanation
Indices: 5564--5613 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
5554 ATGAAAAATA
5564 AAAAAAATTAAACTTAAAATTAT
1 AAAAAAATTAAACTTAAAATTAT
5587 AAAAAAATTAAACTTAAAATTAT
1 AAAAAAATTAAACTTAAAATTAT
5610 AAAA
1 AAAA
5614 CTATTTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAAAATTAAACTTAAAATTAT
Found at i:5945 original size:171 final size:168
Alignment explanation
Indices: 5619--7667 Score: 1500
Period size: 171 Copynumber: 12.1 Consensus size: 168
5609 TAAAACTATT
* * * * *
5619 TAAAGTGGACTTTTCTTACCAATGAAT-GCTTTTTACTTCACGTTTCTC-AAGTAAACATTTAAT
1 TAAA-TGGACTTTTCTTGCCAATGAATACCTTTTT-CTTCACGTTTCTCGAGGTAGACATTCAAT
* * * ** *
5682 TATAGTCTGTTCTAGTCAAAAATGTAAAAAAATTCAACTTAAAATCGCTTATCAGATTATAAAAC
64 TATAGTCTGTTTTAAT-AAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-
* * * *
5747 CT-TTTAAAGTGAGTACTAAGGCTTTTGAAGGAATGGTTGGCTA
126 CTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGG-AGACTA
* * * *
5790 TAAATGGACTTTTCTTACCAATGAATACCTTTTCCTTCATGTTTCTCGAGGTAGACATTCAAGTA
1 TAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTA
* * * * *
5855 TAATCTGTTTTAATGAAAACTATAAAAATATTCAACTTAAAATGAATTATAAGATCATAAAACTA
66 TAGTCTGTTTTAAT-AAAAATATAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * *
5920 TTTAAAGCGAGTAATAAGACTTTTGAAGGACTAAGAGACTA
129 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGAGACTA
* ** * * * *
5961 TAAATGGACTTTTCTT-CCAAATAAATAGGTTTTTCTACACGTTTCCCGAAGAAGGAC-TTCAAT
1 TAAATGGACTTTTCTTGCC-AATGAATACCTTTTTCTTCACGTTTCTCGAGGTA-GACATTCAAT
* * *
6024 TATAGTCTGTTTTATTGAAAAATATAAAAAATTTAA-TTAAAAATCAATTATGAAATTATAAAAC
64 TATAGTCTGTTTTAAT-AAAAATATAAAAAATTCAACTT-AAAATCAATTATGAGATTATAAAAC
* *
6088 TATTTAAACCGAGTAATAAGGCTTTTGAAAGAATGGATGACTA
127 TATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGA-GACTA
* * *
6131 TAAATGGACTTTTCTTGCCAATG-A-A----TTT-AT--C-TTT-T-GAGGAAGATATTCAATTA
1 TAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTA
* * *
6184 TAGTCTGTTTTAACTAAAAATATAAAAAAATTAAACATAAAATCAATTATGAGATTATAAAACAA
66 TAGTCTGTTTTAA-TAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* *
6249 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTA
129 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG-GAGACTA
* * * *
6290 TAAGTAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCAT-GAGGTAGACATTCAATT
1 TAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCACGTTTC-TCGAGGTAGACATTCAATT
* * * * **
6354 ATAATCTATTTTAAGCAAAAATACAAAAAA-AAAATGCTTAAAATCAATT-TGGAGATTATAAAA
65 ATAGTCTGTTTTAA-TAAAAATATAAAAAATTCAA--CTTAAAATCAATTAT-GAGATTATAAAA
* *
6417 -TCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTA
126 CT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGAGACTA
* * ** *
6461 TAAATGGACTTTTCTTGCCAATGGATACCTTTTTCTTCATGGCTCTTGAGGTAGACATTCAATTA
1 TAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTA
* * * * *
6526 TAGTTTTTTTTAATCAAAAATGA-AAAAAATTTAATTTAAAATCAATTATGAGATTATAAAACCA
66 TAGTCTGTTTTAAT-AAAAAT-ATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * * * * *
6590 TTCAAAGCAAATTATAAGGGTTTTGAAAGAATGAGAGACTA
129 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG-GAGACTA
* * * * * * * * *
6631 TAAATTGACTTTTCTTACCACTGAATGCTTTTTTCTTCACGTTTCTCGAGATACACTTTCAATTC
1 TAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTA
* * * * * * * * *
6696 TAATCTGTTTCAACTAAACAGGTAAAAAAAATTGAACTTAAAATCAATTTTGA-ATTATAGATCA
66 TAGTCTGTTTTAA-TAAA-A-ATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACT
* * * * * * *
6760 ATCTAAAGTGAGTAATAAGTCTTTTAAAGGAATAGAAAATTA
128 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGAGACTA
* ** * * * * *
6802 TAAATGGACTTTTCTTGCTAATGAA-AGAATTTTTCTTCATGTTTCTCAAGGTAAAAATTCAAGT
1 TAAATGGACTTTTCTTGCCAATGAATA-CCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATT
* *
6866 ATAGTCTATTTTAGATAAATATATAAAAATATTCAACTTAAAATCAATTATGAGATTATAAAA-T
65 ATAGTCTGTTTTA-ATAAAAATATAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAACT
* * * *
6930 CATTTAAAGCCAATAATAAGGCTTTTGAAGCAATGAAAGACTA
128 -ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG-GAGACTA
* **** * * * ***
6973 TAAATGGACTTTTCTT-CCAAATAAATGGAGTTTTCTACTCA-TTTTC-CAAGGCAGGTGTTCAA
1 TAAATGGACTTTTCTTGCC-AATGAATACCTTTTTCT--TCACGTTTCTCGAGGTAGACATTCAA
* *
7035 TTATAGTCTATTTTAATAAAAATATAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACT
63 TTATAGTCTGTTTTAATAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACT
**********
7100 NNNNNNNNNNAGTAATAAGGCTTTTGAAGGAATAGGAGACTA
128 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGAGACTA
* * * * * * *
7142 TATATGGACTTTTCTTGCTAATGAATGCCTTTTTCTTTACGTTTCTTGAAGTAAACATTCAATTA
1 TAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTA
** *
7207 TAGTCTGTTTTAACTAAAAATGGAAAGAAATTCAACTTAAAATCAATTATGAGATTATAAAACTT
66 TAGTCTGTTTTAA-TAAAAATATAAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
********** * * *
7272 TTTNNNNNNNNNNATAAGGCTTTTAAAGGAATGAAAAACTA
129 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG-GAGACTA
* * * * * *
7313 TAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCGCGTTTCTTGAAGTAGATATTCAATTA
1 TAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTA
* * * * * * * ********** *
7378 TAATTTATTTTAACTAATAATGTAAAAAAAAATTGAACCTAAAATCAANNNNNNNNNNATAAAAT
66 TAGTCTGTTTTAA-TAA-AA-AT-ATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* * *
7443 TATTTAAAGCGAGTAATAAGACTTTTGAAGTAATAAGAGACTA
127 TATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGAGACTA
* ** * * * *
7486 GAAATGGACTTTTCTTGTAAATGAATGCTTTTTTCTTCACGTTTCTTGAGGTCA-ACATTCAGTT
1 TAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCACGTTTCTCGAGGT-AGACATTCAATT
* * * * * * *
7550 ATAATTTCTTTATCAA-AAAATATAAAAAAAAATTTAACTTAAAA-CAATTATGAGACTGTAAAA
65 ATAGTCTGTTT-T-AATAAAA-AT-ATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* * * * * *
7613 CCT-TTTAAAGTGAGTACTAAAGCTTTTAAAAGAATGGGTGACTA
126 -CTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGAGACTA
*
7657 TAAATGCACTT
1 TAAATGGACTT
7668 NNNNNNNNNN
Statistics
Matches: 1498, Mismatches: 310, Indels: 140
0.77 0.16 0.07
Matches are distributed among these distances:
157 2 0.00
158 33 0.02
159 92 0.06
160 6 0.00
161 1 0.00
164 3 0.00
165 3 0.00
166 1 0.00
167 2 0.00
168 6 0.00
169 129 0.09
170 301 0.20
171 727 0.49
172 66 0.04
173 119 0.08
174 5 0.00
175 2 0.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.35
Consensus pattern (168 bp):
TAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTA
TAGTCTGTTTTAATAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATT
TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGAGACTA
Found at i:6658 original size:341 final size:336
Alignment explanation
Indices: 5619--7667 Score: 1471
Period size: 341 Copynumber: 6.0 Consensus size: 336
5609 TAAAACTATT
* * * *
5619 TAAAGTGGACTTTTCTTACCAATGAATGCTTTTTACTTCACGTTTCTCAAGTAAACATTTAATTA
1 TAAA-TGGACTTTTCTT-CCAATGAATGCTTTTTTCTTCACGTTTCTGAAGTAGACATTCAATTA
* * * * * ** *
5684 TAGTCTGTTCT-AGTCAAAAATGTAAAAAAATTCAA-CTTAAAATCGCTTATCAGATTATAAAAC
64 TAATCTATTTTAAG-CAAAAATATAAAAAAA--AAATCTTAAAATCAATTATGAGATTATAAAA-
* * * * *
5747 CTTTTAAAGTGAGTACTAAGGCTTTTGAAGGAATGGTTGGCTATAAATGGACTTTTCTTACCAAT
125 CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTCTTGCCAAT
* * * * * *
5812 GAATACCTTTTCCTTCATGTTTCTCGAGGTAGACATTCAAGTATAATCTGTTTTAATGAAAACTA
190 GGATACCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAA--A
* * * * * * *
5877 TAAAAATATTCAACTTAAAATGAATTATAAGATCATAAAACTATTTAAAGCGAGTAATAAGACTT
253 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAATAATAAGGCTT
* * *
5942 TTGAAGGACTAAGAGACTA
318 TTGAAAGAATGAGAGACTA
* * * * *
5961 TAAATGGACTTTTCTTCCAAATAAATAG-GTTTTTCTACACGTTTCCCGAAGAAGGAC-TTCAAT
1 TAAATGGACTTTTCTTCC-AATGAAT-GCTTTTTTCTTCACGTTT-CTGAAGTA-GACATTCAAT
* * * ** * *
6024 TATAGTCTGTTTTATTG-AAAAATATAAAAAATTTAAT-TAAAAATCAATTATGAAATTATAAAA
62 TATAATCTATTTTA-AGCAAAAATATAAAAAA-AAAATCTTAAAATCAATTATGAGATTATAAAA
** *
6087 CTATTTAAACCGAGTAATAAGGCTTTTGAAAGAATGGATGACTATAAATGGACTTTTCTTGCCAA
125 C-ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTCTTGCCAA
* * * *
6152 T-GA-A------T-TT-AT-CTT-TTGAGGAAGATATTCAATTATAGTCTGTTTTAACTAAAAAT
189 TGGATACCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAA-TCAAAA-
* * * * *
6205 ATAAAAAAATTAAACATAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCT
252 ATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAATAATAAGGCT
* *
6270 TTTGAAGGAATGAGTGACTA
317 TTTGAAAGAATGAGAGACTA
* * *
6290 TAAGTAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCATGAGGTAGACATTCAATTA
1 TAAATGGACTTTTCTT-CCAATGAATGCTTTTTTCTTCACGTTTC-TGAAGTAGACATTCAATTA
*
6355 TAATCTATTTTAAGCAAAAATACAAAAAAAAAATGCTTAAAATCAATT-TGGAGATTATAAAATC
64 TAATCTATTTTAAGCAAAAATATAAAAAAAAAAT-CTTAAAATCAATTAT-GAGATTATAAAA-C
*
6419 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATG
126 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTCTTGCCAATG
** * *
6484 GATACCTTTTTCTTCATGGCTCTTGAGGTAGACATTCAATTATAGTTTTTTTTAATCAAAAATGA
191 GATACCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAAT-A
* * * * * *
6549 AAAAAATTTAATTTAAAATCAATTATGAGATTATAAAACCATTCAAAGCAAATTATAAGGGTTTT
255 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAATAATAAGGCTTTT
6614 GAAAGAATGAGAGACTA
320 GAAAGAATGAGAGACTA
* * * *
6631 TAAATTGACTTTTCTTACCACTGAATGCTTTTTTCTTCACGTTTCTCG-AGATACACTTTCAATT
1 TAAATGGACTTTTCTT-CCAATGAATGCTTTTTTCTTCACGTTTCT-GAAG-TAGACATTCAATT
* * * * ** * *
6695 CTAATCTGTTTCAA-CTAAACAGGTAAAAAAAATTGAA-CTTAAAATCAATTTTGA-ATTATAGA
63 ATAATCTATTTTAAGC-AAAAATATAAAAAAAA---AATCTTAAAATCAATTATGAGATTATAAA
* * * * * ** * *
6757 TCAATCTAAAGTGAGTAATAAGTCTTTTAAAGGAATAGAAAATTATAAATGGACTTTTCTTGCTA
124 AC-ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTCTTGCCA
* ** ** * * * *
6822 AT-GAAAGAATTTTTCTTCATGTTTCTCAAGGTAAAAATTCAAGTATAGTCTATTTTAGAT-AAA
188 ATGGATA-CCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTA-ATCAAA
* * *
6885 TATATAAAAATATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCCAATAATAAG
251 -A-ATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAATAATAAG
*
6950 GCTTTTG-AAGCAATGAAAGACTA
314 GCTTTTGAAAG-AATGAGAGACTA
* *** * * * ***
6973 TAAATGGACTTTTCTTCCAAATAAATGGAGTTTTCTACTCA-TTTTC-CAAGGCAGGTGTTCAAT
1 TAAATGGACTTTTCTTCC-AATGAATGCTTTTTTCT--TCACGTTTCTGAA-GTAGACATTCAAT
* * ** *
7036 TATAGTCTATTTTAA-TAAAAATATAAAAAATTCAA-CTTAAAATTAATTATGAGATTATAAAAC
62 TATAATCTATTTTAAGCAAAAATATAAAAAA-AAAATCTTAAAATCAATTATGAGATTATAAAAC
******** * *
7099 -TNNNNNNNNNNAGTAATAAGGCTTTTGAAGGAATAGGA-GACTATATATGGACTTTTCTTGCTA
126 AT--TTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GGATGACTATAAATGGACTTTTCTTGCCA
* * * * * *
7162 ATGAATGCCTTTTTCTTTACGTTTCTTGAAGTAAACATTCAATTATAGTCTGTTTTAA-CTAAAA
188 ATGGATACCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATC-AAAA
* ** **********
7226 ATGGAAAGAAATTCAACTTAAAATCAATTATGAGATTATAAAACTTTTTNNNNNNNNNNATAAGG
252 AT--AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAATAATAAGG
* *
7291 CTTTT-AAAGGAATGAAAAACTA
315 CTTTTGAAA-GAATGAGAGACTA
* *
7313 TAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCGCGTTTCTTGAAGTAGATATTCAATTA
1 TAAATGGACTTTTCTT-CCAATGAATGCTTTTTTCTTCACGTTTC-TGAAGTAGACATTCAATTA
* * * * * **********
7378 TAATTTATTTTAA-CTAATAATGTAAAAAAAAATTGAACCTAAAATCAANNNNNNNNNNATAAAA
64 TAATCTATTTTAAGC-AAAAATATAAAAAAAAA---ATCTTAAAATCAATTATGAGATTATAAAA
* * * * * * **
7442 TTATTTAAAGCGAGTAATAAGACTTTTGAAGTAATAAGA-GACTAGAAATGGACTTTTCTTGTAA
125 -CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GGATGACTATAAATGGACTTTTCTTGCCA
* * * * * *
7506 ATGAATGCTTTTTTCTTCACGTTTCTTGAGGTCA-ACATTCAGTTATAAT-T-TCTTT-ATCAAA
188 ATGGATACCTTTTTCTTCATGTTTCTTGAGGT-AGACATTCAATTATAGTCTGT-TTTAATC--A
* * * * * * *
7567 AAATATAAAAAAAAATTTAACTTAAAA-CAATTATGAGACTGTAAAACCTTTTAAAGTGAGTACT
249 AAA-AT--AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAATAAT
* * * *
7631 AAAGCTTTTAAAAGAATGGGTGACTA
311 AAGGCTTTTGAAAGAATGAGAGACTA
*
7657 TAAATGCACTT
1 TAAATGGACTT
7668 NNNNNNNNNN
Statistics
Matches: 1350, Mismatches: 278, Indels: 156
0.76 0.16 0.09
Matches are distributed among these distances:
328 9 0.01
329 172 0.13
330 91 0.07
331 5 0.00
332 3 0.00
338 6 0.00
339 26 0.02
340 228 0.17
341 403 0.30
342 205 0.15
343 16 0.01
344 162 0.12
345 23 0.02
346 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.35
Consensus pattern (336 bp):
TAAATGGACTTTTCTTCCAATGAATGCTTTTTTCTTCACGTTTCTGAAGTAGACATTCAATTATA
ATCTATTTTAAGCAAAAATATAAAAAAAAAATCTTAAAATCAATTATGAGATTATAAAACATTTA
AAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTCTTGCCAATGGATAC
CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAATAAAAAAA
TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAATAATAAGGCTTTTGAAAGA
ATGAGAGACTA
Found at i:7036 original size:512 final size:511
Alignment explanation
Indices: 6176--7390 Score: 1162
Period size: 512 Copynumber: 2.4 Consensus size: 511
6166 GAGGAAGATA
* *
6176 TTCAATTATAGTCTGTTTTAACTAAAAATATAAAAAAATTAAACATAAAATCAATTATGAGATTA
1 TTCAATTATAATCTGTTTCAACTAAAAATATAAAAAAATTAAACATAAAATCAATTATGAGATTA
* * ** *
6241 TAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAGTAGACTTTTCTT
66 TAAAACAATCTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGAAACTATAAATAGACTTTTCTT
* ** * * * *
6306 GCCAATGAATGCTTTTTTCTTCACGTTTCATGAGGTAGACATTCAATTATAATCTATTTTAAGCA
131 GCCAATGAAAGAATTTTTCTTCACGTTTCATAAGGTAAAAATTCAAGTATAATCTATTTTAAGCA
* ** *
6371 AAAATACAAAAAAAAAATGCTTAAAATCAATTTGGAGATTATAAAATCATTTAAAGTGAGTAATA
196 AAAATACAAAAAAAAAATACTTAAAATCAATTTGGAGATTATAAAATCATTTAAAGCCAATAATA
* *** ** **
6436 AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATACCTTTTTCTTCAT
261 AGGCTTTTGAAGCAATGAAAGACTATAAATGGACTTTTCTTGCCAATAAATACAGTTTTCTTCAT
** * * * * *
6501 GGCTCTTGAGGTAGACATTCAATTATAGTTTTTTTTAATCAAAAATGA-AAAAAATTTAATTTAA
326 GGCTCTCAAGGCAGACATTCAATTATAGTCTATTTTAAT-AAAAAT-ATAAAAAATTCAACTTAA
6565 AATCAATTATGAGATTATAAAACCATTCAAAGCAAATTATAAGGGTTTTGAAAGAATGAGAGACT
389 AATCAATTATGAGATTATAAAACCATTCAAAGCAAATTATAAGGGTTTTGAAAGAATGAGAGACT
6630 ATAAATTGACTTTTCTTACCACTGAATGCTTTTTTCTTCACGTTTCTCGAGATACACT
454 ATAAATTGACTTTTCTTACCACTGAATGCTTTTTTCTTCACGTTTCTCGAGATACACT
* * * * *
6688 TTCAATTCTAATCTGTTTCAACTAAACAGGTA-AAAAAAATTGAACTTAAAATCAATTTTGA-AT
1 TTCAATTATAATCTGTTTCAACTAAA-A-ATATAAAAAAATTAAACATAAAATCAATTATGAGAT
* * * * *
6751 TATAGATCAATCTAAAGTGAGTAATAAGTCTTTTAAAGGAAT-AGAAAATTATAAATGGACTTTT
64 TATAAAACAATCTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAG-AAACTATAAATAGACTTTT
* * *
6815 CTTGCTAATGAAAGAATTTTTCTTCATGTTTC-TCAAGGTAAAAATTCAAGTATAGTCTATTTT-
128 CTTGCCAATGAAAGAATTTTTCTTCACGTTTCAT-AAGGTAAAAATTCAAGTATAATCTATTTTA
* * * * *
6878 AG-ATAAATATATAAAAATATTCAACTTAAAATCAATTAT-GAGATTATAAAATCATTTAAAGCC
192 AGCAAAAATACAAAAAAAAAAT--ACTTAAAATCAATT-TGGAGATTATAAAATCATTTAAAGCC
**
6941 AATAATAAGGCTTTTGAAGCAATGAAAGACTATAAATGGACTTTTCTT-CCAAATAAATGGAGTT
254 AATAATAAGGCTTTTGAAGCAATGAAAGACTATAAATGGACTTTTCTTGCC-AATAAATACAGTT
** ***
7005 TTCTACTCAT-TTTC-CAAGGCAGGTGTTCAATTATAGTCTATTTTAATAAAAATATAAAAAATT
318 TTCT--TCATGGCTCTCAAGGCAGACATTCAATTATAGTCTATTTTAATAAAAATATAAAAAATT
* *********** * * * *
7068 CAACTTAAAATTAATTATGAGATTATAAAACTNNNNNNNNNNAGTAATAAGGCTTTTGAAGGAAT
381 CAACTTAAAATCAATTATGAGATTATAAAACCATTCAAAGCAAATTATAAGGGTTTTGAAAGAAT
* * * * * * * * *
7133 -AGGAGACTATATATGGACTTTTCTTGCTAATGAATGCCTTTTTCTTTACGTTTCTTGA-AGTAA
446 GA-GAGACTATAAATTGACTTTTCTTACCACTGAATGCTTTTTTCTTCACGTTTCTCGAGA-TAC
*
7196 ACA
509 ACT
* * ** * * *
7199 TTCAATTATAGTCTGTTTTAACTAAAAATGGAAAGAAATTCAACTTAAAATCAATTATGAGATTA
1 TTCAATTATAATCTGTTTCAACTAAAAATATAAAAAAATTAAACATAAAATCAATTATGAGATTA
** * ********** * *
7264 TAAAACTTTTTNNNNNNNNNNATAAGGCTTTTAAAGGAATGAAAAACTATAAATGGACTTTTCTT
66 TAAAACAATCTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGAAACTATAAATAGACTTTTCTT
* ** * * * * * *
7329 GCCAATGAATGCTTTTTTCTTCGCGTTTCTTGAA-GTAGATATTCAATTATAATTTATTTTAA
131 GCCAATGAAAGAATTTTTCTTCACGTTTCAT-AAGGTAAAAATTCAAGTATAATCTATTTTAA
7391 CTAATAATGT
Statistics
Matches: 563, Mismatches: 122, Indels: 36
0.78 0.17 0.05
Matches are distributed among these distances:
509 1 0.00
510 44 0.08
511 236 0.42
512 246 0.44
513 30 0.05
514 6 0.01
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (511 bp):
TTCAATTATAATCTGTTTCAACTAAAAATATAAAAAAATTAAACATAAAATCAATTATGAGATTA
TAAAACAATCTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGAAACTATAAATAGACTTTTCTT
GCCAATGAAAGAATTTTTCTTCACGTTTCATAAGGTAAAAATTCAAGTATAATCTATTTTAAGCA
AAAATACAAAAAAAAAATACTTAAAATCAATTTGGAGATTATAAAATCATTTAAAGCCAATAATA
AGGCTTTTGAAGCAATGAAAGACTATAAATGGACTTTTCTTGCCAATAAATACAGTTTTCTTCAT
GGCTCTCAAGGCAGACATTCAATTATAGTCTATTTTAATAAAAATATAAAAAATTCAACTTAAAA
TCAATTATGAGATTATAAAACCATTCAAAGCAAATTATAAGGGTTTTGAAAGAATGAGAGACTAT
AAATTGACTTTTCTTACCACTGAATGCTTTTTTCTTCACGTTTCTCGAGATACACT
Found at i:11400 original size:171 final size:170
Alignment explanation
Indices: 10938--11441 Score: 451
Period size: 172 Copynumber: 2.9 Consensus size: 170
10928 NNNNNNNTGT
* * * *
10938 AAAACAATTCAACTTAAAATAAGTTATGAGATTACAAAACCTTTTAAAGCGAATACTATAGCTTT
1 AAAAAAATTCAACTTAAAATAAGTTATGAGATTACAAAACCTTTTAAAGCGAGTA-AAAAGCTTT
* * * * *
11003 TGAAA-AAATGGATGACTATAAATGGATTTTTCTTGCCAATGAATGCCCTTTTCTTTGTGTTTCT
65 TGAAAGAATTGG-CGACTATAAATGGACTTTTCTTGCCAATGAATG-CATTTTCTTTATGTTTCT
*
11067 CAAGGTAGACATTCAATTATAATATGTTTTAAGGAAAAACATA
128 TAAGGTAGACATTCAATTATAATATGTTTTAAGGAAAAACATA
* * * *
11110 AAAAAAATTGAACTTAAAATCAA-TTTTGAGATTAGAAAA-CTATTTAAAGCAAGTAATAAAGCT
1 AAAAAAATTCAACTTAAAAT-AAGTTATGAGATTACAAAACCT-TTTAAAGCGAGTAA-AAAGCT
* * ** * * * *
11173 TTTG-AAGAAATCGACGACTATAAATACACCTTTCTTGCCAGTGAATGCTTTTTTCTTTACGTTT
63 TTTGAAAG-AATTGGCGACTATAAATGGACTTTTCTTGCCAATGAATGC-ATTTTCTTTATGTTT
* * ********** *
11237 CTTAAGGTAGACATTCAATTATAGTTTGTTNNNNNNNNNNATAT-
126 CTTAAGGTAGACATTCAATTATAATATGTTTTAAGGAAAAACATA
* * *
11281 AAAAATATTCAACTTAAAATTAGTTATGAGATTATAAAACCTTTTAAAGCGAGTAAAAAGGCTTT
1 AAAAAAATTCAACTTAAAATAAGTTATGAGATTACAAAACCTTTTAAAGCGAGTAAAAA-GCTTT
* * *** * *
11346 TGAAAGAATTGGCGATTATAAATGGACTTTTCCTATAAATGAATGTCATTTTCTTCATATTTCTT
65 TGAAAGAATTGGCGACTATAAATGGACTTTTCTTGCCAATGAATG-CATTTTCTTTATGTTTCTT
* * *
11411 GAGGTAGACATTCAATTATAATCTTTTTTAA
129 AAGGTAGACATTCAATTATAATATGTTTTAA
11442 CAATAAATGT
Statistics
Matches: 258, Mismatches: 63, Indels: 23
0.75 0.18 0.07
Matches are distributed among these distances:
170 4 0.02
171 122 0.47
172 127 0.49
173 5 0.02
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (170 bp):
AAAAAAATTCAACTTAAAATAAGTTATGAGATTACAAAACCTTTTAAAGCGAGTAAAAAGCTTTT
GAAAGAATTGGCGACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTCTTTATGTTTCTTAA
GGTAGACATTCAATTATAATATGTTTTAAGGAAAAACATA
Found at i:12681 original size:170 final size:170
Alignment explanation
Indices: 12490--13553 Score: 706
Period size: 170 Copynumber: 6.2 Consensus size: 170
12480 NNNNNNNNNN
* * * ** * *
12490 TGGACTTTCCTTACAAATAAATAGAATTTTCTACATGTTTCCTAAGATAGGCATTCAATTATAAT
1 TGGACTTTTCTTACCAATGAATAGTTTTTTCTTCATGTTTCCTAAGATAGACATTCAATTATAAT
* * *
12555 CTGTTTTAAACAAAAATATAAAAAATTCAATTTAAAATCAATTTTGAGATTATAAAACAATTTAA
66 CTGTTTTAACCAAAAATATAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAA
*
12620 AGCGAGTTATTAAGCTTTTAAAGGAATAGGCGACTCTAAA
131 AGCGAGTTATTAAGCTTTTAAAGGAATAGGCGACTATAAA
* * * * * * *
12660 TGGACTTTTTTTGCCAATAAATA-TCTTTTT-TTTACGTTTTAC-AAGGTAGACATTCAATTATA
1 TGGACTTTTCTTACCAATGAATAGT-TTTTTCTTCATG-TTTCCTAAGATAGACATTCAATTATA
* * * * * * *
12722 AACTGTTTTTACCAAAAATATAAAAATATTGAACTTAAAATCATTTTTAAAATTATAAAACTATT
64 ATCTGTTTTAACCAAAAATATAAAAA-ATTCAACTTAAAATCAATTTTGAGATTATAAAACCATT
* *
12787 TAAAGCGAG-TAATAAGGCTTTTAAAGGAAT-GTGCGAATATAAA
128 TAAAGCGAGTTATTAA-GCTTTTAAAGGAATAG-GCGACTATAAA
* * * *
12830 TGGACTTTTCTTGCTAATGAAT-GTCTTTTGCTTCACG-TTCTCTAAG-TAGACATTCAATTATA
1 TGGACTTTTCTTACCAATGAATAGT-TTTTTCTTCATGTTTC-CTAAGATAGACATTCAATTATA
* * * *
12892 ATCTAG-TTTAACCAATAAT-TGAAAGCAAAACTT-AACCTAAAATCAATTATGACATTATAAAA
64 ATCT-GTTTTAACCAAAAATAT--AA--AAAA-TTCAACTTAAAATCAATTTTGAGATTATAAAA
* ********** * *
12954 CTATTTAAAGCGNNNNNNNNNNCTTTTGAAGGAATAGGAGACTATAAA
123 CCATTTAAAGCGAGTTATTAAGCTTTTAAAGGAATAGGCGACTATAAA
* * * * ** *
13002 TGGACTTTTCTCACCAATGAAT-GCTTTTTTCTTGATGTTTCTTGAGGCAGACATTCAATTATAC
1 TGGACTTTTCTTACCAATGAATAG-TTTTTTCTTCATGTTTCCTAAGATAGACATTCAATTATAA
* * * * * *
13066 TCTGTTTTAACCAAAAATGTAAAAACTTCAA-TAAAAAATCAATTATGAGATTAAAAAACCACTT
65 TCTGTTTTAACCAAAAATATAAAAAATTCAACT-TAAAATCAATTTTGAGATTATAAAACCATTT
* * * * * ***
13130 AAAGCAAATTGTTATGCTTTTAAAAGAATAAATGACTATAAA
129 AAAGCGAGTTATTAAGCTTTTAAAGGAATAGGCGACTATAAA
* * * *
13172 CGGACTTTTCTTATCAATGAATA-TCTTTTTCTTTATGTTTCAC-GAGATAGACATTCAATTATA
1 TGGACTTTTCTTACCAATGAATAGT-TTTTTCTTCATGTTTC-CTAAGATAGACATTCAATTATA
* * * *
13235 ATCTATTTTAACCCAAAATATAAAAAAATTAAACTTAAAATCAAATTTGAGATTAT-AAACCATT
64 ATCTGTTTTAACCAAAAATAT-AAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATT
* * * *********** *
13299 TAAAGTGAGTAATAAAGCTTNNNNNNNNNNGGGTGACTATAAA
128 TAAAGCGAGTTATTAAGCTTTTAAAGGAATAGGCGACTATAAA
* ** * * * * *
13342 TGGACTTTTTTTTGTCAATGAAT-GCCTTTTTCTTCATGTTTCTTAAGGTAGACATTTAATCATA
1 TGGAC-TTTTCTTACCAATGAATAG-TTTTTTCTTCATGTTTCCTAAGATAGACATTCAATTATA
* * * **********
13406 ATATGTTTTACCCAAAAATGTAAAAAAATTCAACTTAAAATNNNNNNNNNNATTATAAAACCATT
64 ATCTGTTTTAACCAAAAATAT-AAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATT
* ** * * * *
13471 TAAAGTGAGCAATAAAGCTTTTGAAGGATTAGGAGACTATAAA
128 TAAAGCGAGTTATTAAGCTTTTAAAGGAATAGGCGACTATAAA
* *
13514 TAGACTTTTCTTGCCAATGAAT-GCTTTTTTCTTCATGTTT
1 TGGACTTTTCTTACCAATGAATAG-TTTTTTCTTCATGTTT
Statistics
Matches: 695, Mismatches: 165, Indels: 67
0.75 0.18 0.07
Matches are distributed among these distances:
169 56 0.08
170 307 0.44
171 155 0.22
172 136 0.20
173 40 0.06
174 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.36
Consensus pattern (170 bp):
TGGACTTTTCTTACCAATGAATAGTTTTTTCTTCATGTTTCCTAAGATAGACATTCAATTATAAT
CTGTTTTAACCAAAAATATAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAA
AGCGAGTTATTAAGCTTTTAAAGGAATAGGCGACTATAAA
Done.