Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397985.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_129.0, 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: 31045
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.24
Warning! 10166 characters in sequence are not A, C, G, or T
Found at i:1398 original size:170 final size:171
Alignment explanation
Indices: 998--1418 Score: 456
Period size: 171 Copynumber: 2.5 Consensus size: 171
988 NNNNNNNNNN
* *
998 TAAAATCAATTATGAGATTATAACACCATTTAAAGAAAGTAATAAGGCTTTTGAAGGAAAGGGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * *
1063 ACAATAAATAA-ACTTTTCTTCTCAATGAATGGCTTTTTCTATATGTCTCCTGTGTTAGGCATTC
66 ACTATAAA-AAGACTTTTCTTCTCAATGAATGACTTTTTCTATACGTCTCCTGAGGTAGACATTC
*********
1127 AATTATAGTCTGTTTTAATGAAGAATGTAAAAANNNNNNNNN
130 AATTATAGTCTGTTTTAATGAAGAATGTAAAAAAATTTAACT
* ** * * *
1169 NAAAATCAATTATGAGATTATAAAACCATTTAAAGTGACTAAAAAGGC-TTTGAAAGGAATGAGT
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTTTTG-AAGGAATGGGT
* * * *
1233 GACTATAAAAAGACTTTTCTTGTCAATGAATGTAC-TTTTCTTTACGTTTCTTGAGGTAGACATT
65 GACTATAAAAAGACTTTTCTTCTCAATGAATG-ACTTTTTCTATACGTCTCCTGAGGTAGACATT
* * *
1297 CAATTATAGTTTGTTTTAACT-AA-AATATTAAAAAATTTAACT
129 CAATTATAGTCTGTTTTAA-TGAAGAATGTAAAAAAATTTAACT
* * **
1339 TAAAATCAATTTTGAGATTACAAAACCATTTAAACCAAGTAATAAGGCTTTTGAAGGAATGGGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTTTTGAAGGAATGGGTG
*
1404 ACTATAAATAGACTT
66 ACTATAAAAAGACTT
1419 NNNNNNNNNN
Statistics
Matches: 205, Mismatches: 40, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
170 79 0.39
171 124 0.60
172 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.34
Consensus pattern (171 bp):
TAAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTTTTGAAGGAATGGGTG
ACTATAAAAAGACTTTTCTTCTCAATGAATGACTTTTTCTATACGTCTCCTGAGGTAGACATTCA
ATTATAGTCTGTTTTAATGAAGAATGTAAAAAAATTTAACT
Found at i:3145 original size:171 final size:167
Alignment explanation
Indices: 2746--3315 Score: 498
Period size: 171 Copynumber: 3.3 Consensus size: 167
2736 NNNNNNNNNN
* * * * * * * *
2746 ACCATTTAAAGTGAGTAATAAGGCTTTTAAAAGAGTGGGTGACTATAAATAAACTTTTGTTGCCA
1 ACCATTTAAAGTAACTAATAAGGCTTTTGAAGGAAT--GAGACTATAAATAGACTTTTCTTGCCA
* * * * *
2811 ATGAATGCTTTTTTC-TCCTTGTGTCATGAGGTAGACATTCAATTGTAATCTGTTTTAACAAAAA
64 ATAAATGCTTTTTTCGT-CATGTTTCTTGAGGTAGACATTCAATTGTAATCTGTTTTAAC-CAAA
* * * *
2875 ATATAAAAAAATTAAACTTCAAATCAAATATAAGATTATAAA
127 ATGTAAAAAAATTAAACTTAAAATTAATTATAAGATTAT-AA
* * * * *
2917 ACCATTTAAAGTTAGC-AACAAGGCTTTTGAAAGGATAAGTGACTATAAATAGACTTTTCTTGTC
1 ACCATTTAAAG-TAACTAATAAGGCTTTTG-AAGGA-ATGAGACTATAAATAGACTTTTCTTGCC
* *
2981 AATAAATGTCTTTTTT-TTCATGTTTCTTGAGATAGACATTCAATTGTAATCTGTTTTAACCAAT
63 AATAAATG-CTTTTTTCGTCATGTTTCTTGAGGTAGACATTCAATTGTAATCTGTTTTAACCAA-
3045 AATGTAAAAAAATTAAACTTAAAATTAATTATAAGATTATAA
126 AATGTAAAAAAATTAAACTTAAAATTAATTATAAGATTATAA
* *********
3087 AGCCATTTAAAGCAACTAATAAGGCTTTTGAAGGAATGAGANNNNNNNNNNGGACTTTTCTTGCC
1 A-CCATTTAAAGTAACTAATAAGGCTTTTGAAGGAATGAGA--CTATAAATAGACTTTTCTTGCC
* * * * *
3152 AATGAATGCTTTTTTCGTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTATTTTAACCAAAA
63 AATAAATGCTTTTTTCGTCATGTTTCTTGAGGTAGACATTCAATTGTAATCTGTTTTAACCAAAA
* * * * * *
3217 CTGCTAACAATAATTGAACATAAAATTAATTTTGAGATAATAGA
128 -TG-TAA-AAAAATTAAACTTAAAATTAATTATAAGATTATA-A
* * * * *
3261 ACCATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTGACAATAAATAGACT
1 ACCATTTAAAGTAACTAATAAGGCTTTTGAAGGAAT--GAGACTATAAATAGACT
3316 NNNNNNNNNN
Statistics
Matches: 319, Mismatches: 63, Indels: 32
0.77 0.15 0.08
Matches are distributed among these distances:
169 4 0.01
170 21 0.07
171 210 0.66
172 16 0.05
173 63 0.20
174 2 0.01
175 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.34
Consensus pattern (167 bp):
ACCATTTAAAGTAACTAATAAGGCTTTTGAAGGAATGAGACTATAAATAGACTTTTCTTGCCAAT
AAATGCTTTTTTCGTCATGTTTCTTGAGGTAGACATTCAATTGTAATCTGTTTTAACCAAAATGT
AAAAAAATTAAACTTAAAATTAATTATAAGATTATAA
Found at i:5284 original size:170 final size:160
Alignment explanation
Indices: 5108--5436 Score: 326
Period size: 170 Copynumber: 2.0 Consensus size: 160
5098 CGAGTAATAG
* *
5108 GGCTTTTGAAA-GAATGAGAGACTATAAATAGAATTTGT-TTTCAAATAACTAAGTTTTTTTACA
1 GGCTTTT-AAAGGAATGAGAAACTATAAAT-GAATTTGTCTTTCAAATAAATAAGTTTTTTTACA
* * *
5171 CG-TTTCTCGAGGTAAGCATTCAATTACAGTATGTTTTAGCAAAAAAT-ATAAAAAAGTT-AACT
64 CGTTTTCT-GAGGCAAGCATTCAATTACAATATGTTTTAACAAAAAATGA-AAAAAA-TTCAACT
* *
5233 TAATATCAATTATAAGTTTATAAAACCATTTAANNNNNNNNNNAA
126 TAAAATCAATTATAAGATTATAAAACCATTTAA----------AA
** * * *
5278 GGCTTTTAAAGGAATGAGAAACTATAAATGGCTTTTTCTTTCAAATAAATGAGTTTTTTTACGCG
1 GGCTTTTAAAGGAATGAGAAACTATAAATGAATTTGTCTTTCAAATAAATAAGTTTTTTTACACG
* ** *
5343 TTTTCTGAGGCAAGCATTCAATTATAATATGTTTTAATGAAAAATGAAAAAAATTCAATTTAAAA
66 TTTTCTGAGGCAAGCATTCAATTACAATATGTTTTAACAAAAAATGAAAAAAATTCAACTTAAAA
* *
5408 TCAATTATGAGATTATGAAACCATTTAAA
131 TCAATTATAAGATTATAAAACCATTTAAA
5437 NNNNNNNNNN
Statistics
Matches: 136, Mismatches: 18, Indels: 20
0.78 0.10 0.11
Matches are distributed among these distances:
160 1 0.01
169 10 0.07
170 119 0.88
171 6 0.04
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.35
Consensus pattern (160 bp):
GGCTTTTAAAGGAATGAGAAACTATAAATGAATTTGTCTTTCAAATAAATAAGTTTTTTTACACG
TTTTCTGAGGCAAGCATTCAATTACAATATGTTTTAACAAAAAATGAAAAAAATTCAACTTAAAA
TCAATTATAAGATTATAAAACCATTTAAAA
Found at i:10884 original size:171 final size:168
Alignment explanation
Indices: 9408--12564 Score: 2063
Period size: 170 Copynumber: 18.5 Consensus size: 168
9398 TTCTCGAGAC
* * * * ** *
9408 AGACATTTAATTGTAGTTTGTTTTAACCAAATATGATGAAAAAACAGAACATAAAATCAATTTTG
1 AGACATTCAATTATAGTTTGTTTTAACCAAAAATG-TAAAAAAATTGAACTTAAAATCAATTTTG
** * * * *
9473 AGAGAATAAAACTATTTAAAGTGAGTTATAAGGGTTTTGAAGGAAT-GCGAGACTATAAATGAGC
65 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAG-GAGACTATAAATG-GA
** * *
9537 TTTGCTTGTCAATGAATG-CTTTTTTTCACGTTTCCCAAGGT
128 TTTTTTTTTCAATGAATGCCTTTTTTTCACGTTT-CTAAGGT
* * ** * * *
9578 AAACATTCAATTATAGTTTGTCTTAGTCAAAAATGTAAAAATAATTGAACATAAATTTAATTTTG
1 AGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAA-AATTGAACTTAAAATCAATTTTG
* * * * *
9643 AGATAAT-AAACCTATTTAAAATGGGTAATAAAGCTTTTAAAGGAATA-GATGACTATAAATGGA
65 AGATTATAAAACC-ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGA-GACTATAAATGGA
* * * ** * * *
9706 CTTTTCTTTTAAATAAATGGGTTGTTTACACATTTCTAGAGGT
128 -TTTTTTTTTCAATGAATGCCTTTTTTTCACGTTTCTA-AGGT
* * *
9749 AGACATT-AAAT-TAGTCTT-TTTTAA-CAAAAATGT-AAAAAATTCAACTTAAAATCAATTATG
1 AGACATTCAATTATAGT-TTGTTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTTTG
* * * ** * * * * *
9809 AGATTACAAAACCCTGTAAAACGAGTAATAAGACTTTTGAAAGAATGGGAGACTATAAATGAACT
65 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGATT
* * * ** * *
9874 TTTCTTCCAAATAAATGAGTTTTTCTACACGTTTCTTAAGGC
130 TTTTTTTC-AATGAATGCCTTTTT-TTCACGTTTC-TAAGGT
*** * ** * *** *
9916 AGGTTTTCAATTACAGTTTGTTTTAATAAAAAATAT-AAAAAAGCCAACTTAAAATCAATTATGA
1 AGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTTTGA
* * * * * * **
9980 GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGGCTATAAATAAACTT
66 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGA-TT
** *** * *
10045 TTTTTACCAATGAATGCCTTTTCCCCTACGTGTCATGAGGT
130 TTTTTTTCAATGAATGCCTTTTTTTC-ACGTTTC-TAAGGT
* *** * * * * **
10086 AGACATTCAATTGTAACCTGTTTTAACCAAAATTGTAAAAAAAATGATCTTGAAATCAAAATTGA
1 AGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTTTGA
* * * *
10151 GATTATAAAACCATTTAAAGTGAGTAA-AAGGCTTTTAAAGGAATAAGTGACTATAAGTGGACTT
66 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGA-TT
* * * * * * *
10215 TTCTTATCATTAAATGTCTTTTTCTTCACATTTCTCTAGGT
130 TTTTTTTCAATGAATGCCTTTTT-TTCACGTTTCT-AAGGT
* * * * * *
10256 AGACATTCAATTATAATCTGTTTTAACCAATAATGTAAAAAAATTAAACCTAAAATCAATTATGA
1 AGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTTTGA
* ** * * *
10321 CATTATAAGGCCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGAGACTATAAATGGACTT
66 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGA-TT
* ** * * *
10386 TTCTTACCAATGAATGCCTTTTTTTCTTTATGTTTCTTGAGGC
130 TTTTTTTCAATGAATGCCTTTTTTTC---ACGTTTC-TAAGGT
* * * * * * * *
10429 AAACACTCAAATATAGTCTGTTTTAACAAAAAATATTAAAAAAACTGAACATAAAA-CGAATTTT
1 AGACATTCAATTATAGTTTGTTTTAACCAAAAAT-GTAAAAAAATTGAACTTAAAATC-AATTTT
* * * * * * *
10493 GAGATGATAAAACTATTTACACTCAGTAATAAGACTTTTGAAGGTATAGGAGACTATAAATGGAC
64 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGA-
* * * * **
10558 ATTTGTTGTCAATGAATGCTTTTTTCTTCATATTTCTTAAGGT
128 TTTTTTTTTCAATGAATGCCTTTTT-TTCACGTTTC-TAAGGT
* * *
10601 AGACATTCAATTATAGTTT-TTCTTAACTAAAAATATAAAACAAAATTGAACATAAAATCAATTT
1 AGACATTCAATTATAGTTTGTT-TTAACCAAAAATGT-AAA-AAAATTGAACTTAAAATCAATTT
* * * *
10665 TGAGATAATAAAACCATTTAAAGTGAGTAATAATGCTTTTCAAGGAATAGGAGACTATAAATAGA
63 TGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGA
* * *
10730 TTTCTTTTTTCTAATGAATGCCTTGTTTTCATGTTTCTAGATGT
128 TTT-TTTTTTC-AATGAATGCCTTTTTTTCACGTTTCTA-AGGT
* *** *
10774 AGACATTCAATTATAATTTGTTTTAGTTAAAAGAT-TAAAAAAATTAAACTTAAAATCAATTTTG
1 AGACATTCAATTATAGTTTGTTTTAACCAAAA-ATGTAAAAAAATTGAACTTAAAATCAATTTTG
* * * * * *
10838 AGATTATAAAACAATTTAGAGTGAGCAATAACGCTTTTGAAGGAATAAGTA-ATTATAAATGGAC
65 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-AGGAGACTATAAATGGA-
* * * * * * *
10902 TTTTCTTGTCAGTAAATGCATTTTTCCTCATGTTTCTCAAGGT
128 TTTTTTTTTCAATGAATGCCTTTTT-TTCACGTTTCT-AAGGT
* * * * *
10945 CGACATTCAATTATAATCTGTTTTAACCAATAATGTAAAAAAATTGAACTTAAAATCAATTATGA
1 AGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTTTGA
* * * * *
11010 GATTATAAAGCCATTTAAAGTGAGAAATAAGGTTTTTGAAGGAAT-GAGAGACAATAAATAGACT
66 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAG-GAGACTATAAATGGA-T
* ** * * * * * **
11074 TTTCTTGCCAAAGAATACATTTTTCTTCATGTTTCTCGAGAC
129 TTTTTTTTCAATGAATGCCTTTTT-TTCACGTTTCT-AAGGT
* * * * ** * *
11116 AAACATTTAATTGTAGTCTAATTTAACCAAAAATGTTAAAAAAACTGAACATAAAATCAATTTTG
1 AGACATTCAATTATAGTTTGTTTTAACCAAAAATG-TAAAAAAATTGAACTTAAAATCAATTTTG
* *
11181 AGATAATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GTGAGACTATAAATGGAC
65 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAG-GAGACTATAAATGGA-
* * * * *
11245 TTTTTTTGTCAATGAATACTTTTTTATTCATGTTTCTCAAAGT
128 TTTTTTTTTCAATGAATGCCTTTTT-TTCACGTTTCT-AAGGT
* * * * *
11288 AGACATTCAATTATAGTTTGTCTTAACTAAAAATATAAAAATAATTGCACATAAAATCAATTTTG
1 AGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAA-AATTGAACTTAAAATCAATTTTG
* * * * *
11353 AGATAATAAAACCATTTTAAA-TGGGTAATAAGGCTTTTGAAGGAATAGGTGACTAGAAATGGAC
65 AGATTATAAAACCA-TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGAT
* * * *
11417 TTTTATTGCTATGGAATGCTTGTTTTTTCACGTTTCATAAGGT
129 TTTTTTTTCAAT-GAATGCCT-TTTTTTCACGTTTC-TAAGGT
* * * ** * * * *
11460 GGACATTCAATTATTGTCTGTTTTAATGAAAAATATAAAAAAATTCAACTTAAAATGAATTATGA
1 AGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTTTGA
* * * * * * *
11525 GATTATAAAACTATTTAAAGTGAGGAATAAGTCTTTTGAAGTAATGGGAGACTATAAATAGAGTT
66 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGATTT
* ** * * *
11590 TTCTTTCATAT-AATTGAGTTTTTCTACACGTTTCCTAAAGC
131 TTTTTTCA-ATGAA-TGCCTTTTT-TTCACGTTT-CTAAGGT
** * * * *
11631 A-AGCATTCAATTATAGAATGTTTTAA-TAGAAAATAT-AAAAAATTTAACTTAAAATCAATTAT
1 AGA-CATTCAATTATAGTTTGTTTTAACCA-AAAATGTAAAAAAATTGAACTTAAAATCAATTTT
* * * * *
11693 GAGATTATGAAACCATTTAAAGTGAGTAATAAGACTTTTGAAAGAATGGGAGACTATAAATGAAT
64 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGAT
* * ** * *
11758 TTTTTTCTCAAATAAATGGGTTTTTTACACGTTTCTAAGAT
129 TTTTTTTTC-AATGAATGCCTTTTTTTCACGTTTCTAAGGT
* * * *
11799 AGGCATTCAATTATAGTCTT-TTTTAACAAAAAAATGT-AAAAAATTCAACTTAAAATCAATTAT
1 AGACATTCAATTATAGT-TTGTTTTAAC-CAAAAATGTAAAAAAATTGAACTTAAAATCAATTTT
* * * ** * *
11862 GAAATGATAAAACCCTTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGAC
64 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGA-
* * * * *** * * * *
11927 TTTTCTTCTAAATAAATTAGTTTTTTCACACATTTCCCAAGGC
128 TTTTTTTTTCAATGAATGCCTTTTTT-TCACGTTT-CTAAGGT
* *** * * * *
11970 A-AGCATTCAATTACACACTGTTTTAACAAAAAATG-AAAAAAAGTCAACTTAAAATCAATTATG
1 AGA-CATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTTTG
* * * * *
12033 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTCTGAAGGAATGGGCAG-CTATAAGTAGAC
65 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGG-AGACTATAAATGGA-
* ** * ** * *
12097 TTTTCTTACCAGTGAATGCCTTTTTCCCTACGTGTCATGAGGT
128 TTTTTTTTTCAATGAATGCCTTTTTTTC-ACGTTTC-TAAGGT
* * * * * **
12140 AGACATTCAATTATAATCTATTTTAACCAAAAATGTAAAAAAAAAT-AACATAAAATCAAAATTG
1 AGACATTCAATTATAGTTTGTTTTAACCAAAAATGT-AAAAAAATTGAACTTAAAATCAATTTTG
* * * * * *********
12204 AGATTATAAAACTAATTAAAGTGAGTAATAAAGCTTTTGAAGGAATAAGTGACTANNNNNNNNNN
65 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTA-TAAATGGAT
* ** * * * * **
12269 TTTCTTGCCAATAAATGTCTTTTTCTTCATGTTTCCCAAAAT
129 TTTTTTTTCAATGAATGCCTTTTT-TTCACGTTT-CTAAGGT
* * * * * ***********
12311 AGACATTCAATTATAATCTG-TTTAACTAATAATGTAAAAAAATT-AAATCTNNNNNNNNNNATG
1 AGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTGAACT-TAAAATCAATTTTG
* ** * * * *
12374 AGATTATAAAGCCATTTAAAAAGTGTAATAAGACTTTTGAAGGAATAAGAGACTATAAATGGACT
65 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGATT
* * ** *
12439 TTTCTTACTAATGAATGTTTTTTTTTCTTCATGTTTCTCAAGGT
130 TTTTTTTC-AATGAATG--CCTTTTT-TTCACGTTTCT-AAGGT
* * * * *
12483 AGTCATTCAATTATAGTCTGTTTTAATCAAAAATATTAAAAAAATTGAACATAAAATCAATTTTG
1 AGACATTCAATTATAGTTTGTTTTAACCAAAAAT-GTAAAAAAATTGAACTTAAAATCAATTTTG
* *
12548 AGATAATAAAACTATTT
65 AGATTATAAAACCATTT
12565 NNNNNNNNNN
Statistics
Matches: 2371, Mismatches: 526, Indels: 176
0.77 0.17 0.06
Matches are distributed among these distances:
165 5 0.00
166 73 0.03
167 27 0.01
168 40 0.02
169 158 0.07
170 730 0.31
171 643 0.27
172 372 0.16
173 178 0.08
174 140 0.06
175 5 0.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (168 bp):
AGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAAAAATTGAACTTAAAATCAATTTTGA
GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGATTT
TTTTTTCAATGAATGCCTTTTTTTCACGTTTCTAAGGT
Found at i:11482 original size:515 final size:507
Alignment explanation
Indices: 9409--12564 Score: 2316
Period size: 515 Copynumber: 6.2 Consensus size: 507
9399 TCTCGAGACA
* * * * * * ** * *
9409 GACATTTAATTGTAGTTTGTTTTAACCAAATATGATGAAAAAACAGAACATAAAATCAATTTTGA
1 GACATTCAATTATAGTCTGTTTTAACAAAAAATG-TAAAAAAACTCAACTTAAAATCAATTATGA
** * * *
9474 GAGAATAAAACTATTTAAAGTGAGTTATAAGGGTTTTGAAGGAATGCGAGACTATAAAT-GAGCT
65 GATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGA-CT
* * * * * * *
9538 TTGCTTGTCAATGAATGCTTTTT-TTCACGTTTCCCAAGGTAAACATTCAATTATAGTTTGTCTT
129 TTTCTTGCCAATGAATGCTTTTTCTTCACGTTTCTCGAGGTAAACATTCAATTATAGTCTATTTT
** * * *
9602 AGTCAAAAATG-TAAAAATAATTGAACATAAATTTAATTTTGAGATAAT-AAACCTATTTAAAAT
194 AACCAAAAATGTTAAAAA-AATTGAACATAAAATCAATTTTGAGATAATAAAACC-ATTTAAAGT
* * * *
9665 GGGTAATAAAGCTTTTAAAGGAAT-AGATGACTATAAATGGACTTTTCTTTTAAATAAATGGGTT
257 GAGTAATAAGGCTTTTGAAGGAATGAGA-GACTATAAATGGACTTTT-TTTTCAATAAAT-GGTT
* * * * *
9729 GTTTA--CACATTTCTAGAGGTAGACATT-AAAT-TAGTCTT-TTTTAACAAAAATGT-AAAAAA
319 TTTTATTCACGTTTCTA-AAGTAGACATTCAATTATAGT-TTGTTTTAACAAAAATATAAAAAAA
* * * * * *
9788 TTCAACTTAAAATCAATTATGAGATTACAAAACCCTGTAAAACGAGTAATAAGACTTTTGAAAGA
382 TTC-ACTTAAAATCAATTATGAGATTATAAAACCATTTTAAA-GAGTAATAAGGCTTTTGAAGGA
* * *
9853 ATGGGAGACTATAAATGAACTTTTCTTCCAAATAAATG--AGTTTTTCTACACGTTTCTTAAGG-
445 ATGGGAGACTATAAATGGACTTTTCTTCC-TATAAATGCTTGTTTTT-T-CACGTTTCTTAAGGT
9915 C
507 C
*** * * * * *
9916 AGGTTTTCAATTACAGTTTGTTTTAATAAAAAATATAAAAAAGC-CAACTTAAAATCAATTATGA
1 -GACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAACTCAACTTAAAATCAATTATGA
* * * * *
9980 GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGGCTATAAATAAACTT
65 GATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTT
* * * ** * * * ** *
10045 TTTTTACCAATGAATGCCTTTTCCCCTACGTGTCAT-GAGGTAGACATTCAATTGTAACCTGTTT
130 TTCTTGCCAATGAATGCTTTTTCTTC-ACGTTTC-TCGAGGTAAACATTCAATTATAGTCTATTT
* * * * * ** *
10109 TAACCAAAATTG-TAAAAAAAATGATCTTGAAATCAAAATTGAGATTATAAAACCATTTAAAGTG
193 TAACCAAAAATGTTAAAAAAATTGAACATAAAATCAATTTTGAGATAATAAAACCATTTAAAGTG
* * * * * *
10173 AGTAA-AAGGCTTTTAAAGGAATAAGTGACTATAAGTGGACTTTTCTTATCATTAAAT-GTCTTT
258 AGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTT-TTTTCAATAAATGGT-TTT
* * * * * * * *
10236 TTCTTCACATTTCTCTAGGTAGACATTCAATTATAATCTGTTTTAACCAATAATGTAAAAAAATT
321 TTATTCACGTTTCT-AAAGTAGACATTCAATTATAGTTTGTTTTAA-CAAAAATATAAAAAAATT
* * * ** *
10301 AAACCTAAAATCAATTATGACATTATAAGGCCA-TTTAAAGCGAGTAATAAGGCTTTTGAAAGAA
384 -CACTTAAAATCAATTATGAGATTATAAAACCATTTTAAA--GAGTAATAAGGCTTTTGAAGGAA
* * * * * *
10365 TGGGAGACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTTTCTTTATGTTTCTTGAGG-C
446 TGGGAGACTATAAATGGACTTTTCTT-CCTATAAATG-CTTGTTTT-TTCACGTTTCTTAAGGTC
* * * * * * *
10429 AAACACTCAAATATAGTCTGTTTTAACAAAAAATATTAAAAAAACTGAACATAAAA-CGAATTTT
1 -GACATTCAATTATAGTCTGTTTTAACAAAAAAT-GTAAAAAAACTCAACTTAAAATC-AATTAT
* * * * * * * *
10493 GAGATGATAAAACTATTTACACTCAGTAATAAGACTTTTGAAGGTATAGGAGACTATAAATGGAC
63 GAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGAC
* * * ** ** * *
10558 ATTTGTTGTCAATGAATGCTTTTTTCTTCATATTTCTTAAGGTAGACATTCAATTATAGT-TTTT
128 TTTTCTTGCCAATGAATGC-TTTTTCTTCACGTTTCTCGAGGTAAACATTCAATTATAGTCTATT
* * *
10622 CTTAACTAAAAATATAAAACAAAATTGAACATAAAATCAATTTTGAGATAATAAAACCATTTAAA
192 -TTAACCAAAAATGTTAAA-AAAATTGAACATAAAATCAATTTTGAGATAATAAAACCATTTAAA
* * * * * *
10687 GTGAGTAATAATGCTTTTCAAGGAAT-AGGAGACTATAAATAGATTTCTTTTTTCTAATGAATGC
255 GTGAGTAATAAGGCTTTTGAAGGAATGA-GAGACTATAAATGGACTT-TTTTTTC-AATAAATGG
* * * * * **
10751 CTTGTT-TTCATGTTTCTAGATGTAGACATTCAATTATAATTTGTTTTAGTTAAAAGAT-TAAAA
317 TTTTTTATTCACGTTTCTA-AAGTAGACATTCAATTATAGTTTGTTTTA-ACAAAA-ATATAAAA
* * * * * *
10814 AAATTAAACTTAAAATCAATTTTGAGATTATAAAA-CAATTTAGAGTGAGCAATAACGCTTTTGA
379 AAATT-CACTTAAAATCAATTATGAGATTATAAAACCATTTTA-A-AGAGTAATAAGGCTTTTGA
* * * * ** * *
10878 AGGAATAAGTA-ATTATAAATGGACTTTTCTT-GTCAGTAAATGCATT-TTTCCTCATGTTTCTC
441 AGGAAT-GGGAGACTATAAATGGACTTTTCTTCCT-A-TAAATGC-TTGTTTTTTCACGTTTCTT
10940 AAGGTC
502 AAGGTC
* * * * *
10946 GACATTCAATTATAATCTGTTTTAACCAATAATGTAAAAAAATTGAACTTAAAATCAATTATGAG
1 GACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAACTCAACTTAAAATCAATTATGAG
* * * * * *
11011 ATTATAAAGCCATTTAAAGTGAGAAATAAGGTTTTTGAAGGAATGAGAGACAATAAATAGACTTT
66 ATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTT
* * * ** * * *
11076 TCTTGCCAAAGAATACATTTTTCTTCATGTTTCTCGAGACAAACATTTAATTGTAGTCTAATTTA
131 TCTTGCCAATGAATGC-TTTTTCTTCACGTTTCTCGAGGTAAACATTCAATTATAGTCTATTTTA
* *
11141 ACCAAAAATGTTAAAAAAACTGAACATAAAATCAATTTTGAGATAATAAAACTATTTAAAGTGAG
195 ACCAAAAATGTTAAAAAAATTGAACATAAAATCAATTTTGAGATAATAAAACCATTTAAAGTGAG
* * **
11206 TAATAAGGCTTTTGAAGGAATGTGAGACTATAAATGGACTTTTTTTGTCAATGAATACTTTTTTA
260 TAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTTTT-TCAATAAATGGTTTTTTA
* *
11271 TTCATGTTTCTCAAAGTAGACATTCAATTATAGTTTGTCTTAACTAAAAATATAAAAATAATTGC
324 TTCACGTTTCT-AAAGTAGACATTCAATTATAGTTTGTTTTAAC-AAAAATATAAAAA-AATT-C
* * * * *
11336 ACATAAAATCAATTTTGAGATAATAAAACCATTTTAAATGGGTAATAAGGCTTTTGAAGGAATAG
385 ACTTAAAATCAATTATGAGATTATAAAACCATTTTAAA-GAGTAATAAGGCTTTTGAAGGAATGG
* * * * * * *
11401 GTGACTAGAAATGGACTTTTATTGCTATGGAATGCTTGTTTTTTCACGTTTCATAAGGTG
449 GAGACTATAAATGGACTTTTCTTCCTAT-AAATGCTTGTTTTTTCACGTTTCTTAAGGTC
* ** * * *
11461 GACATTCAATTATTGTCTGTTTTAATGAAAAATATAAAAAAATTCAACTTAAAATGAATTATGAG
1 GACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAACTCAACTTAAAATCAATTATGAG
* * * *
11526 ATTATAAAACTATTTAAAGTGAGGAATAAGTCTTTTGAAGTAATGGGAGACTATAAATAGAGTTT
66 ATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTT
* * * * * * * ** *
11591 TCTT-TCATAT-AATTGAGTTTTTCTACACGTTTC-CTAAAGCAAGCATTCAATTATAGAATGTT
131 TCTTGCCA-ATGAA-TG-CTTTTTCTTCACGTTTCTC-GAGGTAAACATTCAATTATAGTCTATT
* * * * * * *
11653 TTAA-TAGAAAAT-AT-AAAAAATTTAACTTAAAATCAATTATGAGATTATGAAACCATTTAAAG
192 TTAACCA-AAAATGTTAAAAAAATTGAACATAAAATCAATTTTGAGATAATAAAACCATTTAAAG
* * * *
11715 TGAGTAATAAGACTTTTGAAAGAATGGGAGACTATAAAT-GAATTTTTTTCTCAAATAAATGGGT
256 TGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTTTT-TC-AATAAAT-GGT
* * *
11779 TTTTTA--CACGTTTCT-AAGATAGGCATTCAATTATAGTCTT-TTTTAACAAAAAAATGTAAAA
318 TTTTTATTCACGTTTCTAAAG-TAGACATTCAATTATAGT-TTGTTTTAACAAAAATAT-AAAAA
* * *
11840 AATTCAACTTAAAATCAATTATGAAATGATAAAACC-CTTTAAAGCAAGTAATAAGGCTTTTGAA
380 AATTC-ACTTAAAATCAATTATGAGATTATAAAACCATTTTAAAG--AGTAATAAGGCTTTTGAA
* * * **
11904 GGAATGGGAGACTATAAATAGACTTTTCTT-CTAAATAAAT--TAGTTTTTTCACACATTTCCCA
442 GGAATGGGAGACTATAAATGGACTTTTCTTCCT--ATAAATGCTTGTTTTTT--CACGTTTCTTA
11966 AGG-C
503 AGGTC
* * ** *
11970 AAGCATTCAATTACACACTGTTTTAACAAAAAATG-AAAAAAAGTCAACTTAAAATCAATTATGA
1 GA-CATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAACTCAACTTAAAATCAATTATGA
* * * *
12034 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTCTGAAGGAATGGGCAG-CTATAAGTAGACT
65 GATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGG-AGACTATAAATAGACT
* * * * * *
12098 TTTCTTACCAGTGAATGCCTTTTTC-CCTACGTGTCAT-GAGGTAGACATTCAATTATAATCTAT
129 TTTCTTGCCAATGAATG-CTTTTTCTTC-ACGTTTC-TCGAGGTAAACATTCAATTATAGTCTAT
* * ** * * *
12161 TTTAACCAAAAATGTAAAAAAAAAT-AACATAAAATCAAAATTGAGATTATAAAACTAATTAAAG
191 TTTAACCAAAAATGTTAAAAAAATTGAACATAAAATCAATTTTGAGATAATAAAACCATTTAAAG
* * * ********* * **
12225 TGAGTAATAAAGCTTTTGAAGGAATAAGTGACTANNNNNNNNNNTTTCTTGCCAATAAAT-GTCT
256 TGAGTAATAAGGCTTTTGAAGGAATGAGAGACTA-TAAATGGACTTTTTTTTCAATAAATGGT-T
* * * * * * * *
12289 TTTTCTTCATGTTTCCCAAAATAGACATTCAATTATAATCTG-TTTAACTAATAATGTAAAAAAA
319 TTTTATTCACGTTT-CTAAAGTAGACATTCAATTATAGTTTGTTTTAAC-AAAAATATAAAAAAA
* * ********** * * * *
12353 TTAAATCTNNNNNNNNNNATGAGATTATAAAGCCATTTAAAAAGTGTAATAAGACTTTTGAAGGA
382 TTCACT-TAAAATCAATTATGAGATTATAAAACCATTT-TAAAGAGTAATAAGGCTTTTGAAGGA
** * * * * * *
12418 ATAAGAGACTATAAATGGACTTTTCTTACTAATGAATGTTTTTTTTTCTTCATGTTTCTCAAGGT
445 ATGGGAGACTATAAATGGACTTTTCTTCCT-ATAAATG-CTTGTTTT-TTCACGTTTCTTAAGGT
*
12483 A
507 C
* * * * *
12484 GTCATTCAATTATAGTCTGTTTTAATCAAAAATAT-TAAAAAAATTGAACATAAAATCAATTTTG
1 GACATTCAATTATAGTCTGTTTTAA-CAAAAA-ATGTAAAAAAACTCAACTTAAAATCAATTATG
*
12548 AGATAATAAAACTATTT
64 AGATTATAAAACTATTT
12565 NNNNNNNNNN
Statistics
Matches: 2097, Mismatches: 442, Indels: 211
0.76 0.16 0.08
Matches are distributed among these distances:
504 2 0.00
505 4 0.00
506 130 0.06
507 65 0.03
508 87 0.04
509 152 0.07
510 209 0.10
511 209 0.10
512 54 0.03
513 176 0.08
514 180 0.09
515 542 0.26
516 58 0.03
517 55 0.03
518 158 0.08
519 16 0.01
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (507 bp):
GACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAACTCAACTTAAAATCAATTATGAG
ATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTT
TCTTGCCAATGAATGCTTTTTCTTCACGTTTCTCGAGGTAAACATTCAATTATAGTCTATTTTAA
CCAAAAATGTTAAAAAAATTGAACATAAAATCAATTTTGAGATAATAAAACCATTTAAAGTGAGT
AATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTTTTTCAATAAATGGTTTTTTATT
CACGTTTCTAAAGTAGACATTCAATTATAGTTTGTTTTAACAAAAATATAAAAAAATTCACTTAA
AATCAATTATGAGATTATAAAACCATTTTAAAGAGTAATAAGGCTTTTGAAGGAATGGGAGACTA
TAAATGGACTTTTCTTCCTATAAATGCTTGTTTTTTCACGTTTCTTAAGGTC
Found at i:13493 original size:169 final size:170
Alignment explanation
Indices: 13130--13496 Score: 429
Period size: 170 Copynumber: 2.2 Consensus size: 170
13120 NNNNNNNNNN
* * * *
13130 TGAGATTATAAAACCATTTAAAGCAAAG-AATAAGGCTTTTGAAGTAATGGGAGACTATAAATAG
1 TGAGATTATAAAACCATTTAAAGC-GAGTAACAAAGCTTTTGAAGGAATGGGAGACTATAAATAG
*
13194 AGTTTTCTTTCAAATAACTAAGTTTTTCTACACGTTTCCTAAGGCAAGCATTCAATTATAGCATG
65 AGTTTTCTTTCAAATAAATAAGTTTTTCTACACGTTTCCTAAGGCAAGCATTCAATTATAGCATG
* **********
13259 TTTTAACANNNNNNNNNNAAAATTCAACTTAAAATCAATTA
130 TTTTAAAAAAAAATATAAAAAATTCAACTTAAAATCAATTA
**
13300 TGAGATTACGAAACCATTTAAAGCGAGTAACAAAGCTTTTGAAGGAATGGGAGACTATAAATAGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAACAAAGCTTTTGAAGGAATGGGAGACTATAAATAGA
* ** * *
13365 -TTTTTTTCTCAAATAAATGGGTTTTT-TACACGTTTCC-AAGGTAGGCATTCAATTATAGTC-T
66 GTTTTCTT-TCAAATAAATAAGTTTTTCTACACGTTTCCTAAGGCAAGCATTCAATTATAG-CAT
*
13426 TTTTTAATAAAAAAATATAAAAAATTCAACTTAAAATCAATTA
129 GTTTTAA-AAAAAAATATAAAAAATTCAACTTAAAATCAATTA
* *
13469 TGAGATGATAAAACCCTTTAAAGCGAGT
1 TGAGATTATAAAACCATTTAAAGCGAGT
13497 NNNNNNNNNN
Statistics
Matches: 165, Mismatches: 28, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
168 26 0.16
169 68 0.41
170 71 0.43
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.32
Consensus pattern (170 bp):
TGAGATTATAAAACCATTTAAAGCGAGTAACAAAGCTTTTGAAGGAATGGGAGACTATAAATAGA
GTTTTCTTTCAAATAAATAAGTTTTTCTACACGTTTCCTAAGGCAAGCATTCAATTATAGCATGT
TTTAAAAAAAAATATAAAAAATTCAACTTAAAATCAATTA
Found at i:15458 original size:170 final size:170
Alignment explanation
Indices: 14842--16187 Score: 1110
Period size: 170 Copynumber: 7.9 Consensus size: 170
14832 TTCTCTTCAT
* ** ** * * *
14842 GTTTCTCAAGGTAGACATTCAATTATAGTTTGCCTTAACCAAAAATGTAAAACAAAATTGAACAT
1 GTTTCTCGAGGTAGACATTCAATTATAGACTGTTTTAACAAAAAATGT--AA-AAAATTCAACTT
* * * * * * * * * *
14907 AAAATCAATTTTAAGATAATAAAACTATTTAAAGTGAGCAATAACGCTTTTCAAGGAATAAGAGA
63 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGA
* * * * ** *
14972 CCATAAATGGATTTTTCTTTCTAATGAATGTCTTTTTCT-TCAT
128 CTATAAATGGACTTTTCTTTCAAATAAATGAATTTTTCTAT-AC
* * * *** * * *
15015 GTTTCTAGATGTAGACATTCAATTACATTTTGTTTTAGTCAAAAAA-GTTAAACAAAATGAACTT
1 GTTTCTCGAGGTAGACATTCAATTATAGACTGTTTTA-ACAAAAAATG-TAAA-AAATTCAACTT
* * * * ** * *
15079 AAAATTAATTTTGAGATTATAAAACCATTTAAAGTGAGAAATAAAACTTTTGAAAGAATGGGTGA
63 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGA
* * * * **
15144 TTATAAATAGACTTTTCTTTTAAATGAATTTATTTTTCT-TCAC
128 CTATAAATGGACTTTTCTTTCAAATAAATGAATTTTTCTAT-AC
* * * * *
15187 GTTTCTTGAGGTAGACAATCAATTATAGTCTCTTTTAACTAAAAATGTAAAACAATTCAACTTAA
1 GTTTCTCGAGGTAGACATTCAATTATAGACTGTTTTAACAAAAAATGTAAAA-AATTCAACTTAA
* * *
15252 AATCAATTATGAGAATATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACT
65 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACT
*
15317 ATAAATGGACTTTGCTTTCAAATAAATGAATTTTTCTATAC
130 ATAAATGGACTTTTCTTTCAAATAAATGAATTTTTCTATAC
* * * *
15358 GTTTCTCGAGGTA-AGCATTTAATTATAGAATGTTTTAACAAAAAATATAAAAAATTCAATTTAA
1 GTTTCTCGAGGTAGA-CATTCAATTATAGACTGTTTTAACAAAAAATGTAAAAAATTCAACTTAA
*
15422 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACT
65 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACT
* * *
15487 ATAAATGGACTTTTCTTCCAAATAAATGAATTTTT-TCACAT
130 ATAAATGGACTTTTCTTTCAAATAAATGAATTTTTCT-ATAC
* * * * * * * * * *
15528 GTTTCCCAAGGCAGGCATTCAATTACAGTCTATTTTAATAAAAAATCTAAAAAAGTCAACTTAAA
1 GTTTCTCGAGGTAGACATTCAATTATAGACTGTTTTAACAAAAAATGTAAAAAATTCAACTTAAA
* * * * *
15593 ATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGC-TTCGAATGAATGGGTGGCTA
66 ATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTA
* * **
15657 TAAATGGACTTCTCTTGTCAAAGAAA-GCCTTTTTCTATAC
131 TAAATGGACTTTTCTT-TCAAATAAATGAATTTTTCTATAC
* * * * *
15697 GTGTCAT-GAGGTAGACATTCAACTGTA-ATCTGTTTTAACAAAAAATGTAACAATAATTGAACA
1 GTTTC-TCGAGGTAGACATTCAATTATAGA-CTGTTTTAACAAAAAATGTAA-AA-AATTCAACT
* ** ** *
15760 TAAAATCAAATT-TGAAAAAATAAAACCATTTAAAATGGGTAATAAGGCTTTTGAAGGAATGAGT
62 TAAAATC-AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGT
* * * * * * * *
15824 GATTATAAATGAACTTTTCTTGCCAATGAATG-CTTGTTT-TTTCAT
126 GACTATAAATGGACTTTTCTTTCAAATAAATGAATT-TTTCTAT-AC
* * * *
15869 GTTTCACAAGGTAGACATTCAATTAT-GATCTGTTTTAATAAAAAATGTAAACAATTCAACTTAA
1 GTTTCTCGAGGTAGACATTCAATTATAGA-CTGTTTTAACAAAAAATGTAAAAAATTCAACTTAA
** * * * *
15933 AATCAATTATCTG-TTTTAAAACCA-TTAAAGCAAGTAATAAGGCTTTTGAACGAAT-AGGAGAC
65 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-GTGAC
* ** * *
15995 TACAAATAAACTTTTC-TTCTAAATAAATGGATTTTT-TCACAC
129 TATAAATGGACTTTTCTTTC-AAATAAATGAATTTTTCT-ATAC
* ** * * * * *
16037 GTTTCTCGAGGCAGGTATTCAATTACA-ATTTGTTTTAATAAAAAATCTAAAAAAGTCAACTTAA
1 GTTTCTCGAGGTAGACATTCAATTATAGA-CTGTTTTAACAAAAAATGTAAAAAATTCAACTTAA
* *** * * * * * *
16101 AATCAATTATGAGATTATAAAACCATTTACATAAAGAAATAAAGTTTTTGAACGAATGGGTGGCT
65 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACT
16166 ATAAATGGACTTTTCTTGTCAA
130 ATAAATGGACTTTTCTT-TCAA
16188 TGAATGCCTT
Statistics
Matches: 947, Mismatches: 193, Indels: 68
0.78 0.16 0.06
Matches are distributed among these distances:
167 3 0.00
168 119 0.13
169 101 0.11
170 269 0.28
171 205 0.22
172 212 0.22
173 31 0.03
174 7 0.01
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (170 bp):
GTTTCTCGAGGTAGACATTCAATTATAGACTGTTTTAACAAAAAATGTAAAAAATTCAACTTAAA
ATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTA
TAAATGGACTTTTCTTTCAAATAAATGAATTTTTCTATAC
Found at i:15500 original size:341 final size:338
Alignment explanation
Indices: 14837--16192 Score: 1276
Period size: 341 Copynumber: 4.0 Consensus size: 338
14827 TGCTTTTCTC
* * * **
14837 TTCATGTTTCTCAAGGTAGACATTCAATTATAGTTTGC-CTTAACCAAAAATGTAAAACAAAATT
1 TTCACGTTTCTCAAGGTAGACATTCAATTATAGTCT-CTTTTAATAAAAAATGTAAAAC--AATT
* * * * * * * * *
14901 GAACATAAAATCAATTTTAAGATAATAAAACTATTTAAAGTGAGCAATAACGCTTTTCAAGGAAT
63 CAACTTAAAATCAATTATGAGAT-ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT
* * * * * ** * * *
14966 AAGAGACCATAAATGGATTTTTCTTTCTAATGAATGTCTTTTTCT-TCATGTTTCTAGATGTAGA
127 GAGAGACTATAAATGGACTTTTCTTTCAAATAAATGAATTTTTCTAT-ACGTTTCTCGAGGTAGA
* * * * * *
15030 CATTCAATTACATTTTGTTTTAGTCAAAAAAGTTAAACAAAATGAACTTAAAATTAATTTTGAGA
191 CATTCAATTACAATTTGTTTTA-ACAAAAAA-TTAAA-AAATTCAACTTAAAATCAATTATGAGA
* * * *
15095 TTATAAAACCATTTAAAGTGAGAAATAAAACTTTTGAAAGAATGGGTGATTATAAATAGACTTTT
253 TTATAAAACCATTTAAAGTGAGAAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT
**
15160 CTTTTAAATGAATTTATTTTT
318 CTTGCAAATGAATTTATTTTT
** *
15181 CTTCACGTTTCTTGAGGTAGACAATCAATTATAGTCTCTTTTAACT-AAAAATGTAAAACAATTC
1 -TTCACGTTTCTCAAGGTAGACATTCAATTATAGTCTCTTTTAA-TAAAAAATGTAAAACAATTC
*
15245 AACTTAAAATCAATTATGAGAATATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG
64 AACTTAAAATCAATTATGAG-ATATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG
*
15310 AGAGACTATAAATGGACTTTGCTTTCAAATAAATGAATTTTTCTATACGTTTCTCGAGGTA-AGC
128 AGAGACTATAAATGGACTTTTCTTTCAAATAAATGAATTTTTCTATACGTTTCTCGAGGTAGA-C
* * * *
15374 ATTTAATTATAGA-ATGTTTTAACAAAAAATATAAAAAATTCAATTTAAAATCAATTATGAGATT
192 ATTCAATTACA-ATTTGTTTTAACAAAAAAT-TAAAAAATTCAACTTAAAATCAATTATGAGATT
* * *
15438 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT
255 ATAAAACCATTTAAAGTGAGAAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT
* * * *
15503 TCCAAAT-AAATGAATTTT
320 TGCAAATGAATTTATTTTT
* * * * * * *
15521 TTCACATGTTTCCCAAGGCAGGCATTCAATTACAGTCTATTTTAATAAAAAATCTAAAA-AAGTC
1 TTCAC--GTTTCTCAAGGTAGACATTCAATTATAGTCTCTTTTAATAAAAAATGTAAAACAATTC
* * *
15585 AACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGC-TTCGAATGAATG
64 AACTTAAAATCAATTATGAGA-TATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG
* * * * * ** *
15649 GGTGGCTATAAATGGACTTCTCTTGTCAAAGAAA-GCCTTTTTCTATACGTGTCAT-GAGGTAGA
128 AGAGACTATAAATGGACTTTTCTT-TCAAATAAATGAATTTTTCTATACGTTTC-TCGAGGTAGA
* ** * * * *
15712 CATTCAACTGTAATCTGTTTTAACAAAAAATGTAACAATAATTGAACATAAAATCAAATT-TGAA
191 CATTCAATTACAATTTGTTTTAACAAAAAAT-TAA-AA-AATTCAACTTAAAATC-AATTATGAG
** * * * * * * *
15776 AAAATAAAACCATTTAAAATGGGTAATAAGGCTTTTGAAGGAATGAGTGATTATAAATGAACTTT
252 ATTATAAAACCATTTAAAGTGAGAAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTT
* *
15841 TCTTGCCAATGAATGCTT-GTTTT
317 TCTTGCAAATGAAT--TTATTTTT
* * *
15864 TTCATGTTTCACAAGGTAGACATTCAATTAT-GATCTGTTTTAATAAAAAATGT-AAACAATTCA
1 TTCACGTTTCTCAAGGTAGACATTCAATTATAG-TCTCTTTTAATAAAAAATGTAAAACAATTCA
** * * * *
15927 ACTTAAAATCAATTATCTGTTTTAAAACCA-TTAAAGCAAGTAATAAGGCTTTTGAACGAAT-AG
65 ACTTAAAATCAATTATGAGATATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-
* ** * * * **
15990 GAGACTACAAATAAACTTTTC-TTCTAAATAAATGGATTTTT-TCACACGTTTCTCGAGGCAGGT
129 GAGACTATAAATGGACTTTTCTTTC-AAATAAATGAATTTTTCT-ATACGTTTCTCGAGGTAGAC
* *
16053 ATTCAATTACAATTTGTTTTAATAAAAAATCTAAAAAAGTCAACTTAAAATCAATTATGAGATTA
192 ATTCAATTACAATTTGTTTTAACAAAAAAT-TAAAAAATTCAACTTAAAATCAATTATGAGATTA
* * * * *
16118 TAAAACCATTTACA-TAAAGAAATAAAGTTTTTGAACGAATGGGTGGCTATAAATGGACTTTTCT
256 TAAAACCATTTAAAGT-GAGAAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT
16182 TGTC-AATGAAT
320 TG-CAAATGAAT
16193 GCCTTTTNNN
Statistics
Matches: 832, Mismatches: 147, Indels: 71
0.79 0.14 0.07
Matches are distributed among these distances:
337 5 0.01
338 81 0.10
339 115 0.14
340 157 0.19
341 271 0.33
342 18 0.02
343 132 0.16
344 5 0.01
345 48 0.06
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (338 bp):
TTCACGTTTCTCAAGGTAGACATTCAATTATAGTCTCTTTTAATAAAAAATGTAAAACAATTCAA
CTTAAAATCAATTATGAGATATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGA
GACTATAAATGGACTTTTCTTTCAAATAAATGAATTTTTCTATACGTTTCTCGAGGTAGACATTC
AATTACAATTTGTTTTAACAAAAAATTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
CCATTTAAAGTGAGAAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCAAA
TGAATTTATTTTT
Found at i:19233 original size:173 final size:172
Alignment explanation
Indices: 19046--19380 Score: 372
Period size: 173 Copynumber: 1.9 Consensus size: 172
19036 GAGAGACTAC
* * * *
19046 AAATGGACTTTTCTTGT-AAATGAAAG-CTTTTCTCTTCATGTTTCTCGAGGTAAACATTCGATT
1 AAATGGACTTTTCTT-TCAAATGAAAGCCTTTT-TCCTCACGTTTCTAGAGGTAAACATTCAATT
* * *
19109 ATAGTTTGTCTTAACCAAAAAAGTAAAACAAAATTGAACATAAAATCAATTTCAAGACAATAAAA
64 ACAATCTGTCTTAACCAAAAAAGTAAAACAAAA-TGAACATAAAATCAATTTCAAGACAATAAAA
*
19174 -CTATTTAAAGTGAGCAATAACA-CTTTTCAAGGAATAAGAGATCAT
128 TC-ATTTAAAGTGAGAAATAA-AGCTTTTCAAGGAATAAGAGATCAT
* * * * * *
19219 AAATGGATTTTTCTTTCTAATGAATGCCTTTTTCCTCACGTTTCTAGATGTAGACATTCAATTGC
1 AAATGGACTTTTCTTTCAAATGAAAGCCTTTTTCCTCACGTTTCTAGAGGTAAACATTCAATTAC
* ** * * * * ** *
19284 AATCTGTTTTAGTCGAAAAAGTTAAACAAAATGAACTTAAAATCAGTTTTGAGACTATAAAATCA
66 AATCTGTCTTAACCAAAAAAGTAAAACAAAATGAACATAAAATCAATTTCAAGACAATAAAATCA
*
19349 TTTAAAGTGAGAAATAAAGCTTTTGAAGGAAT
131 TTTAAAGTGAGAAATAAAGCTTTTCAAGGAAT
19381 GAGTGATTAN
Statistics
Matches: 133, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
171 1 0.01
172 56 0.42
173 71 0.53
174 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (172 bp):
AAATGGACTTTTCTTTCAAATGAAAGCCTTTTTCCTCACGTTTCTAGAGGTAAACATTCAATTAC
AATCTGTCTTAACCAAAAAAGTAAAACAAAATGAACATAAAATCAATTTCAAGACAATAAAATCA
TTTAAAGTGAGAAATAAAGCTTTTCAAGGAATAAGAGATCAT
Found at i:25053 original size:169 final size:169
Alignment explanation
Indices: 24593--25116 Score: 454
Period size: 169 Copynumber: 3.1 Consensus size: 169
24583 ATTCATTGGC
* * * *
24593 AAGAAAAGTCTATTTATAGTCTTTCACTCCTTCAAAAGCCTTATTACTTGCTTTAAATGG-TTTA
1 AAGAAAAGTCCATTTATAGTTTTTCATTCCTTCAAAAG-CTTATTACTCGCTTTAAATGGTTTTA
* * * **
24657 TAATCTAATAATTAATTTTAAGTTAAAGTTTTTGTATTTTTTCTTAAAACAGGCTATAATT-AAT
65 TAATCTAATAATTGATTTTAAGTTAAAGTTTTTATATTTTTTATTAAAACAAACTATAATTGAA-
* * **********
24721 TTCTTACCTCAGGAAACGTGTAAAAAAACNNNNNNNNNNG-
129 TGCTTACCTCAGGAAACATGTAAAAAAACTCAGTTATTTGA
* * *
24761 AAGAAAAGTCCATTTATAG-TCTTCTATTCTTTCAAAAGCTTTATTACTCGCTTTAAATGGTTTC
1 AAGAAAAGTCCATTTATAGTTTTTC-ATTCCTTCAAAAGC-TTATTACTCGCTTTAAATGGTTTT
* ******** * * *
24825 ATAATCTCATAATTGATTTTANNNNNNNNNNTTTTCATA--TTTCATTAAAACATACTATAATTG
64 ATAATCTAATAATTGATTTTA--AGTTAAAGTTTTTATATTTTTTATTAAAACAAACTATAATTG
* * *
24888 AATGCCTACCTCAGGAAAC-TCGT-AAAAAACTCATTTATTTTA
127 AATGCTTACCTCAGGAAACAT-GTAAAAAAACTCAGTTATTTGA
*
24930 AAGAAAAGTCCATTTATAGTTTTTCATTCCTTCAAAAGTCTTATTACTCGTTTTAAATGGTTTTA
1 AAGAAAAGTCCATTTATAGTTTTTCATTCCTTCAAAAG-CTTATTACTCGCTTTAAATGGTTTTA
* * * * ** *
24995 TAAACTTATAATTGATTTTAGGTTGACTTTTTTATATTTTTTATTAAAGCAAACTATAATTGAAT
65 TAATCTAATAATTGATTTTAAGTTAAAGTTTTTATATTTTTTATTAAAACAAACTATAATTGAAT
* *
25060 GCTTACCTC-GAAAAACATGTAAAAAAACTTAGTTATTTGA
130 GCTTACCTCAG-GAAACATGTAAAAAAACTCAGTTATTTGA
*
25100 AAGAAAAGTCTATTTAT
1 AAGAAAAGTCCATTTAT
25117 NNNNNNNNNN
Statistics
Matches: 281, Mismatches: 60, Indels: 28
0.76 0.16 0.08
Matches are distributed among these distances:
167 11 0.04
168 57 0.20
169 167 0.59
170 40 0.14
171 6 0.02
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.40
Consensus pattern (169 bp):
AAGAAAAGTCCATTTATAGTTTTTCATTCCTTCAAAAGCTTATTACTCGCTTTAAATGGTTTTAT
AATCTAATAATTGATTTTAAGTTAAAGTTTTTATATTTTTTATTAAAACAAACTATAATTGAATG
CTTACCTCAGGAAACATGTAAAAAAACTCAGTTATTTGA
Found at i:26307 original size:169 final size:169
Alignment explanation
Indices: 26131--26479 Score: 375
Period size: 169 Copynumber: 2.1 Consensus size: 169
26121 NNNNNNNNNN
*
26131 AAAACCATTTAAAGCGAGTAAT-AAGACTTTTGAAGGAATGAAAAACTATAAATGGACTTTTATT
1 AAAACCATTTAAAGCGAGTAATAAAGACTTTTGAA-GAATGAAAAACTATAAATGGACTTTT-CT
* * * *
26195 TCAAATA-AATGAGTTTTT-TACGCATTTCCTGAGGTA-GACATTCAATTATAGTATGTTTTAAT
64 TCAAA-ACAATGAGTTTTTCTACACATTTCCTGAGGTAGGAAATT-AATTATAGCATGTTTTAAC
* *
26257 GAAATATGA-AAAAAATGTAACTTAAAATCAATTATAAGATTAT
127 AAAAAAT-ACAAAAAATGTAACTTAAAATCAATTATAAGATTAT
* ********** * *
26300 GAAACCATTTAAAGCGAGTAATANNNNNNNNNNAAGAATGGAAGACTATAAATGGACTTTTCTTC
1 AAAACCATTTAAAGCGAGTAATAAAGACTTTTGAAGAATGAAAAACTATAAATGGACTTTTCTTC
* * * *
26365 AAAACAATGGGTTTTTCTACACGTTTCCTGGGGTAGGAAATTAATTATAGCCTGTTTTAACAAAA
66 AAAACAATGAGTTTTTCTACACATTTCCTGAGGTAGGAAATTAATTATAGCATGTTTTAACAAAA
* * *
26430 AATACAAAAAATTTAACTTAAAATTAATTATCAGATTAT
131 AATACAAAAAATGTAACTTAAAATCAATTATAAGATTAT
26469 AAAACCATTTA
1 AAAACCATTTA
26480 NNNNNNNNNN
Statistics
Matches: 147, Mismatches: 28, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
167 1 0.01
168 17 0.12
169 122 0.83
170 7 0.05
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.32
Consensus pattern (169 bp):
AAAACCATTTAAAGCGAGTAATAAAGACTTTTGAAGAATGAAAAACTATAAATGGACTTTTCTTC
AAAACAATGAGTTTTTCTACACATTTCCTGAGGTAGGAAATTAATTATAGCATGTTTTAACAAAA
AATACAAAAAATGTAACTTAAAATCAATTATAAGATTAT
Found at i:30227 original size:21 final size:23
Alignment explanation
Indices: 30185--30228 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
30175 NNNNNNNNNN
30185 TGAGATAATAAAACTATTTAAAG
1 TGAGATAATAAAACTATTTAAAG
*
30208 TGAG-TAATAAGACT-TTTAAAG
1 TGAGATAATAAAACTATTTAAAG
30229 GAATGGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 9 0.45
23 4 0.20
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.32
Consensus pattern (23 bp):
TGAGATAATAAAACTATTTAAAG
Done.