Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398090.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1397.0, 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: 30332
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.25
Warning! 10662 characters in sequence are not A, C, G, or T
Found at i:10955 original size:171 final size:169
Alignment explanation
Indices: 10487--11316 Score: 482
Period size: 171 Copynumber: 4.8 Consensus size: 169
10477 NNNNNNNNAA
*
10487 GTTCAATTTTTTTTTACATTTTTTG-TTAAAACAGATTATAATTGAATGTCTATC-TC-ATGAAC
1 GTTCAA-TTTTTTTTAC--TTTTTGATTAAAACAGATTATAATTGAATGTCTA-CATCGA-GAAA
* * * * * * ******
10549 CATGAAGAGAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTCTTTCATTCCTTTANNNNNN
61 CGTGAAGAAAAAGGTATTCATTGAC-A-AAAAGTTCATTTATAGTCTCTCATTCCTTCAAAAGCC
**** ** * * * * *
10614 NNNNTACTCGTTTTAAATGGTTTTATAATATCAAAATTGATTTTAA
124 TTATTACTCACTTTAAATAGTTTTATAATCTCCAAATTAATTTTAT
* * * * * *
10660 ATTTAATTCTTTTTACATTTTTTG-TTAAAACAAATTATAATT-AATGTCTACCTC-ATGAAACA
1 GTTCAATTTTTTTTAC--TTTTTGATTAAAACAGATTATAATTGAATGTCTACATCGA-GAAACG
* * **********
10722 TGAA-AAGAAAGGCATTCATTGGCAAGAAAAG-TCTATTTATAGTCANNNNNNNNNNT-AAAAGC
63 TGAAGAA-AAAGGTATTCATTGAC-A-AAAAGTTC-ATTTATAGTC-TCTCATTCCTTCAAAAGC
* * *
10784 CTTATTACTCACTTTAAATTGTTTTATAATCTCCAAATTCATTTTAA
123 CTTATTACTCACTTTAAATAGTTTTATAATCTCCAAATTAATTTTAT
* * * ** *
10831 GTTCAAATTTGTTTACTGTTTTGATTAAAACAGATTATAATTGAATGTCTACGTTAAGAAACGTA
1 GTTCAATTTTTTTTACT-TTTTGATTAAAACAGATTATAATTGAATGTCTACATCGAGAAACGTG
* * * * *
10896 AAGAAAAAGGCATTCATTGACAAGAAAG-TCTGTTTATAGTCTCCCGTTCCTTCAAAAGCCTTAN
65 AAGAAAAAGGTATTCATTGACAA-AAAGTTC-ATTTATAGTCTCTCATTCCTTCAAAAGCCTTAT
********* * * *
10960 NNNNNNNNNTAAATGGTTTTATACTCT-CATAATTGATTTTAT
128 TACTCACTTTAAATAGTTTTATAATCTCCA-AATTAATTTTAT
* * * *
11002 GTTGAATTTTTTTTACATTATTGATTAAAACAGATTAT-ATTGACTGTCTACATCGAGAAACATG
1 GTTCAATTTTTTTTAC-TTTTTGATTAAAACAGATTATAATTGAATGTCTACATCGAGAAACGTG
* * ** * *
11066 AAGAAAATGGTATTTATTAGTA-AAAATAGTTCATTTATAGTCAATCATTCCTTTAAAAGTCTTA
65 AAGAAAAAGGTATTCATT-G-ACAAAA-AGTTCATTTATAGTCTCTCATTCCTTCAAAAGCCTTA
* * *
11130 TTTAC-CAATTTTAAATAGTTTTATTATCTCAAAATTAATTTTAT
127 -TTACTC-ACTTTAAATAGTTTTATAATCTCCAAATTAATTTTAT
* * * * * * * *
11174 GTTTAATTTTTTTTAATTTTTGGTGAAGACAAACTATAATTGAATGTCTACCTCGAGAAACGTGA
1 GTTCAATTTTTTTTACTTTTTGATTAAAACAGATTATAATTGAATGTCTACATCGAGAAACGTGA
* * * *
11239 AGAAAAAAGTATTCACTGACAAAAAAAGTTCATTTATAGACTCTTATTCCTTCAAAAGCCTTATT
66 AGAAAAAGGTATTCATTGAC--AAAAAGTTCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATT
11304 ACTCACTTTAAAT
129 ACTCACTTTAAAT
11317 GGTTNNNNNN
Statistics
Matches: 508, Mismatches: 124, Indels: 52
0.74 0.18 0.08
Matches are distributed among these distances:
169 1 0.00
170 51 0.10
171 263 0.52
172 181 0.36
173 12 0.02
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.39
Consensus pattern (169 bp):
GTTCAATTTTTTTTACTTTTTGATTAAAACAGATTATAATTGAATGTCTACATCGAGAAACGTGA
AGAAAAAGGTATTCATTGACAAAAAGTTCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTAC
TCACTTTAAATAGTTTTATAATCTCCAAATTAATTTTAT
Found at i:11290 original size:172 final size:172
Alignment explanation
Indices: 10969--11303 Score: 397
Period size: 172 Copynumber: 1.9 Consensus size: 172
10959 NNNNNNNNNN
* * * *
10969 TAAATGGTTTTATACTCTCATAATTGATTTTATGTTGAATTTTTTTTACATTATTGATTAAAACA
1 TAAATAGTTTTATACTCTCAAAATTAATTTTATGTTGAATTTTTTTTACATTATTGATGAAAACA
* * * ** * * * *
11034 GATTATATTGACTGTCTACATCGAGAAACATGAAGAAAATGGTATTTATTAGTAAAAATAGTTCA
66 AACTATATTGAATGTCTACATCGAGAAACATGAAGAAAAAAGTATTCATGAGCAAAAAAAGTTCA
* * *
11099 TTTATAGTCAATCATTCCTTTAAAAGTCTTATTTACCAATTT
131 TTTATAGACAATCATTCCTTCAAAAGCCTTATTTACCAATTT
* * * *
11141 TAAATAGTTTTATTA-TCTCAAAATTAATTTTATGTTTAATTTTTTTTA-ATTTTTGGTGAAGAC
1 TAAATAGTTTTA-TACTCTCAAAATTAATTTTATGTTGAATTTTTTTTACATTATTGATGAAAAC
* *
11204 AAACTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAAAGTATTCACTGA-CAAAAAAAGT
65 AAACTAT-ATTGAATGTCTACATCGAGAAACATGAAGAAAAAAGTATTCA-TGAGCAAAAAAAGT
** *
11268 TCATTTATAGACTCTTATTCCTTCAAAAGCCTTATT
128 TCATTTATAGACAATCATTCCTTCAAAAGCCTTATT
11304 ACTCACTTTA
Statistics
Matches: 135, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
171 16 0.12
172 115 0.85
173 4 0.03
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (172 bp):
TAAATAGTTTTATACTCTCAAAATTAATTTTATGTTGAATTTTTTTTACATTATTGATGAAAACA
AACTATATTGAATGTCTACATCGAGAAACATGAAGAAAAAAGTATTCATGAGCAAAAAAAGTTCA
TTTATAGACAATCATTCCTTCAAAAGCCTTATTTACCAATTT
Found at i:12645 original size:172 final size:171
Alignment explanation
Indices: 12046--13031 Score: 750
Period size: 172 Copynumber: 5.7 Consensus size: 171
12036 NNNNNNNNNN
* * * * *
12046 TTTTTTACTTTTTTGATTAAAACAGATTATAATTGAATATCTACGTCAAGAAACGTGAAGATAAA
1 TTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATATCTACCTCAAGAAACGTGAAGAAAAA
** * *
12111 GGCATTCATTGACAAG-AAAGTTTGTTTATATTC-TCTCATTCCTTGAAAAGCCTTATTACTCAC
66 GGCATTCATTGACAAGAAAAGTTCATTTATAGTCATC-CATTCCTTCAAAAGCCTTATTACTCAC
* * *
12174 TTTAAATGGTTTTA-TACTCATAATTGATTTTAAGTTGAATT
130 TTTAAATGGTTTTATTACTCAAAATTGATTTTATGTTCAATT
* * * *
12215 TGTTTTTACATTATTGGTTAAAACATACTATAATTGAATACCTACATCAAGAAACGTGAAGAAAA
1 T-TTTTTACATTTTTGGTTAAAACAGACTATAATTGAATATCTACCTCAAGAAACGTGAAGAAAA
* * ** * * * *
12280 AGGTATTTATTGGTAAGAAAAGTTCATTTATAGTCAGCCATTCTTTCAAAAGTCTTATTTACCCA
65 AGGCATTCATTGACAAGAAAAGTTCATTTATAGTCATCCATTCCTTCAAAAGCCTTA-TTACTCA
* *
12345 TTTTAAATGGTTTTATTATCTCAAAATTGATTTTATGTGCAATT
129 CTTTAAATGGTTTTATTA-CTCAAAATTGATTTTATGTTCAATT
* * * ** **********
12389 GTTTTTACATTTTTGGTTAAAACA-AGCTATAATTAAATGTCTACCTTGANNNNNNNNNNGAAAA
1 TTTTTTACATTTTTGGTTAAAACAGA-CTATAATTGAATATCTACCTCAAGAAACGTGAAGAAAA
* * * *
12453 AAGCATTCATTGACAAGAAAAGTCCATTTATAATC-TCTCATCCCTTCAAAAGCCTTATTACTCA
65 AGGCATTCATTGACAAGAAAAGTTCATTTATAGTCATC-CATTCCTTCAAAAGCCTTATTACTCA
********** *
12517 CTTTNNNNNNNNNNATTACCTCAAAATTGATTTTATGTTTAATT
129 CTTTAAATGGTTTTATTA-CTCAAAATTGATTTTATGTTCAATT
* * *
12561 TTTTTTACATTTTTGGTTAAAACAGACAATAATTGGATGTCTACGCT-AAGAAACGTGAAGAAAA
1 TTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATATCTAC-CTCAAGAAACGTGAAGAAAA
* ** * * *
12625 AGGCATTTATTGGTAAGAAAAGTTCATTTATAGTCATCCATTCTTTCAAAAGCCTTATTACCCAT
65 AGGCATTCATTGACAAGAAAAGTTCATTTATAGTCATCCATTCCTTCAAAAGCCTTATTACTCAC
* ********* *
12690 TTTAAATAGTTTNNNNNNNNNNAAATTGATTTTGTGTTCAATT
130 TTTAAATGGTTT-TATTACTCAAAATTGATTTTATGTTCAATT
* * * * * * *
12733 TTTTTTACATTTTTGGTTAAGACAAACTATAATTAAATGTCTAACTCGAGAAACATGAAGAAAAA
1 TTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATATCTACCTCAAGAAACGTGAAGAAAAA
** * * **
12798 TACATTCATTGACAAAAAAAGTTCATTTATAGTC-TCTCATTCCTTCAAAAGCCTTACTACTTGC
66 GGCATTCATTGACAAGAAAAGTTCATTTATAGTCATC-CATTCCTTCAAAAGCCTTATTACTCAC
********** * * *
12862 TNNNNNNNNNNTTATAATCTCATAATTGATTTTACGTTCAATT
130 TTTAAATGGTTTTATTA-CTCAAAATTGATTTTATGTTCAATT
* ** * * * * *
12905 ATTTTTA-ATTTTTTCATTAAAACAAAATATAATTGAATGTCTACATCAAGAAATGTGAAGAAAA
1 TTTTTTACA-TTTTTGGTTAAAACAGACTATAATTGAATATCTACCTCAAGAAACGTGAAGAAAA
* * * *
12969 AAGCATTCATCGGCAAGAAAAG-TCTATTTATAGTCA-CTCATTCCTTGAAAAGCCTTATTACTC
65 AGGCATTCATTGACAAGAAAAGTTC-ATTTATAGTCATC-CATTCCTTCAAAAGCCTTATTACTC
13032 GCTNNNNNNN
Statistics
Matches: 625, Mismatches: 174, Indels: 33
0.75 0.21 0.04
Matches are distributed among these distances:
169 1 0.00
170 68 0.11
171 37 0.06
172 402 0.64
173 96 0.15
174 21 0.03
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.37
Consensus pattern (171 bp):
TTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATATCTACCTCAAGAAACGTGAAGAAAAA
GGCATTCATTGACAAGAAAAGTTCATTTATAGTCATCCATTCCTTCAAAAGCCTTATTACTCACT
TTAAATGGTTTTATTACTCAAAATTGATTTTATGTTCAATT
Found at i:12891 original size:344 final size:334
Alignment explanation
Indices: 12047--13029 Score: 837
Period size: 344 Copynumber: 2.9 Consensus size: 334
12037 NNNNNNNNNT
* * * * * * * * *
12047 TTTTTACTTTTTTGATTAAAACAGATTATAATTGAATATCT-ACGTCAAGAAACGTGAAGATAAA
1 TTTTTACATTTTTGGTTAAAACAAACTATAATTAAATGTCTAAC-TCGAGAAACATGAAGAAAAA
* * *** * * * *
12111 GGCATTCATTGAC-AAGAAAGTTTGTTTATATTCTCTCATTCCTTGAAAAGCCTTATTACTCACT
65 AGCATTCATTGACAAAAAAAGTCCATTTATAATCTCTCATCCCTTCAAAAGCCTTACTACTCAC-
* * *
12175 TTAAATGGTTTTATA-CTCATAATTGATTTTAAGTTGAATTTGTTTTTACATTATTGGTTAAAAC
129 TT---T--TTATA-ACCTCATAATTGATTTTAAGTTCAATTT-TTTTTACATTTTTGGTTAAAAC
* ** *
12239 ATACTATAATTGAATACCTACATCAAGAAACGTGAAGAAAAAGGTATTTATTGGTAAGAAAAGTT
187 A-ACAATAATTGAATGTCTACATCAAGAAACGTGAAGAAAAAGGCATTTATTGGTAAGAAAAGTT
* *
12304 CATTTATAGTCAGCCATTCTTTCAAAAGTCTTATTTACCCATTTTAAATGGTTTTATTATCTCAA
251 CATTTATAGTCA-CCATTCTTTCAAAAGCCTTA-TTACCCATTTTAAATAGTTTTATTATCTCAA
12369 AATTGATTTTATGTGCAATTG
314 AATTGATTTTATGTGCAATTG
* * * **********
12390 TTTTTACATTTTTGGTTAAAACAAGCTATAATTAAATGTCTACCTTGANNNNNNNNNNGAAAAAA
1 TTTTTACATTTTTGGTTAAAACAAACTATAATTAAATGTCTAACTCGAGAAACATGAAGAAAAAA
* *
12455 GCATTCATTGACAAGAAAAGTCCATTTATAATCTCTCATCCCTTCAAAAGCCTTATTACTCACTT
66 GCATTCATTGACAAAAAAAGTCCATTTATAATCTCTCATCCCTTCAAAAGCCTTACTACTCACTT
** * * * *
12520 TNNNNNNNNNNATTACCTCAAAATTGATTTTATGTTTAATTTTTTTTACATTTTTGGTTAAAACA
131 T--------TTATAACCTCATAATTGATTTTAAGTTCAATTTTTTTTACATTTTTGGTTAAAACA
* *
12585 GACAATAATTGGATGTCTAC-GCTAAGAAACGTGAAGAAAAAGGCATTTATTGGTAAGAAAAGTT
188 -ACAATAATTGAATGTCTACATC-AAGAAACGTGAAGAAAAAGGCATTTATTGGTAAGAAAAGTT
**********
12649 CATTTATAGTCATCCATTCTTTCAAAAGCCTTATTACCCATTTTAAATAGTTTNNNNNNNNNNAA
251 CATTTATAGTCA-CCATTCTTTCAAAAGCCTTATTACCCATTTTAAATAGTTTTATTATCTCAAA
* * *
12714 ATTGATTTTGTGTTCAATTT
315 ATTGATTTTATGTGCAATTG
*
12734 TTTTTACATTTTTGGTTAAGACAAACTATAATTAAATGTCTAACTCGAGAAACATGAAGAAAAAT
1 TTTTTACATTTTTGGTTAAAACAAACTATAATTAAATGTCTAACTCGAGAAACATGAAGAAAAA-
* * * **
12799 A-CATTCATTGACAAAAAAAGTTCATTTATAGTCTCTCATTCCTTCAAAAGCCTTACTACTTGCT
65 AGCATTCATTGACAAAAAAAGTCCATTTATAATCTCTCATCCCTTCAAAAGCCTTACTACTCACT
** * * * **
12863 NNNNNNNNNNTTATAATCTCATAATTGATTTTACGTTCAATTATTTTTA-ATTTTTTCATTAAAA
130 --------TTTTATAACCTCATAATTGATTTTAAGTTCAATTTTTTTTACA-TTTTTGGTTAAAA
* * * * * *
12927 CAAAATATAATTGAATGTCTACATCAAGAAATGTGAAGAAAAAAGCATTCATCGGCAAGAAAAG-
186 CAACA-ATAATTGAATGTCTACATCAAGAAACGTGAAGAAAAAGGCATTTATTGGTAAGAAAAGT
* *
12991 TCTATTTATAGTCACTCATTCCTTGAAAAGCCTTATTAC
250 TC-ATTTATAGTCAC-CATTCTTTCAAAAGCCTTATTAC
13030 TCGCTNNNNN
Statistics
Matches: 510, Mismatches: 106, Indels: 47
0.77 0.16 0.07
Matches are distributed among these distances:
340 1 0.00
343 61 0.12
344 313 0.61
345 111 0.22
346 24 0.05
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.37
Consensus pattern (334 bp):
TTTTTACATTTTTGGTTAAAACAAACTATAATTAAATGTCTAACTCGAGAAACATGAAGAAAAAA
GCATTCATTGACAAAAAAAGTCCATTTATAATCTCTCATCCCTTCAAAAGCCTTACTACTCACTT
TTTATAACCTCATAATTGATTTTAAGTTCAATTTTTTTTACATTTTTGGTTAAAACAACAATAAT
TGAATGTCTACATCAAGAAACGTGAAGAAAAAGGCATTTATTGGTAAGAAAAGTTCATTTATAGT
CACCATTCTTTCAAAAGCCTTATTACCCATTTTAAATAGTTTTATTATCTCAAAATTGATTTTAT
GTGCAATTG
Found at i:13051 original size:172 final size:160
Alignment explanation
Indices: 12873--13197 Score: 318
Period size: 170 Copynumber: 2.0 Consensus size: 160
12863 NNNNNNNNNN
*
12873 TTATAATCTCATAATTGATTTTACGTTCAATTATTTTTA-ATTTTTTCATTAAAACAAAATATAA
1 TTATAATCTCATAATTGATTTTAAGTTCAATT-TTTTTACA-TTTTTCATTAAAACAAAATATAA
* ** *
12937 TTGAATGTCTACATCAAGAAATGTGAAGAAAAAAGCATTCATCGGCAAGAAAAGTCTATTTATAG
64 TTGAATGTCTACATCGAGAAACATGAAGAAAAAA-CATTCATTGGCAAGAAAAGTCTATTTATAG
* *
13002 TCACTCATTCCTTGAAAAGCCTTATTACTCGCT
128 TCTCTCATTCCTTCAAAAGCCTTATTACTCGCT
* *
13035 NNNNNNNNNNTTATAATCTTATAATTGATTTTAAGTT-AAATTTTTTACATTTTTCATTAAAA-A
1 ----------TTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTACATTTTTCATTAAAACA
* * * * * *
13098 AAACTATAATTGAATGCCTACCTCGAGAAACAT-ATAG-AAAAACTTGTTTATTTGAAAGAAAAG
56 AAA-TATAATTGAATGTCTACATCGAGAAACATGA-AGAAAAAAC--ATTCATTGGCAAGAAAAG
*
13161 TCTATTTATAATCTCTCATTCCTTCAAAAGCCTTATT
117 TCTATTTATAGTCTCTCATTCCTTCAAAAGCCTTATT
13198 NNNNNNNNNN
Statistics
Matches: 132, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
168 1 0.01
169 10 0.08
170 92 0.70
171 4 0.03
172 25 0.19
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.38
Consensus pattern (160 bp):
TTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTACATTTTTCATTAAAACAAAATATAATT
GAATGTCTACATCGAGAAACATGAAGAAAAAACATTCATTGGCAAGAAAAGTCTATTTATAGTCT
CTCATTCCTTCAAAAGCCTTATTACTCGCT
Found at i:14234 original size:169 final size:170
Alignment explanation
Indices: 13845--14312 Score: 571
Period size: 169 Copynumber: 2.7 Consensus size: 170
13835 NNNNNNATTT
* * * *
13845 AAAATCAATTTTGAGAATATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGATGGAATGAGAGA
1 AAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGA
* * * * * *
13910 CTATAAATGGATTTTTCTTGCCAATGAATGCTTTTCTCTTCATGTTTCATAAGGTAGAAATTCAA
66 CTATAAATAGACTTTTCTTGCCAATGAATGCTTTT-TTTTCATGTTTCTTGAGGTAGACATTCAA
* * *
13975 TTATAATCTGTTTTAACAAAAAATGTAAAAAAAATTGAACTT
130 TTATAATATGTTTTAACAAAAAATGT-AAAAAAATTCAACTC
* *** * *
14017 AAAACCAATTTTGAGATTATAAAACCATTTAAATTAAGTAATAAGGCTTCTGAAGGAATGGGTGA
1 AAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGA
* * *
14082 CTATAAATAGACTTTTCTTGCAAATGAATTCTTTTTTTTCATGTTTCTTGAGGTCGACATTCAAT
66 CTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTTTCATGTTTCTTGAGGTAGACATTCAAT
* **
14147 TATAGTATGTTTTTTTC-AAAAATGT-AAAAAATTCAACTC
131 TATAATATG-TTTTAACAAAAAATGTAAAAAAATTCAACTC
* * * *
14186 AAAATCAATTATAAGATTATAAAACCATTTACAGCGAGTAATAAGGCTTTTCAAGGAATGAGTGA
1 AAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGA
* * * ** *
14251 CTATAAAGAGACTTTTCTTACCGATGAATGCTTTTTTCTTCACATTTCTTGATGTAGACATT
66 CTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTT-TTCATGTTTCTTGAGGTAGACATT
14313 NNNNNNNNNN
Statistics
Matches: 250, Mismatches: 44, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
169 99 0.40
170 20 0.08
171 40 0.16
172 91 0.36
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (170 bp):
AAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGA
CTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTTTCATGTTTCTTGAGGTAGACATTCAAT
TATAATATGTTTTAACAAAAAATGTAAAAAAATTCAACTC
Found at i:16292 original size:170 final size:171
Alignment explanation
Indices: 15140--16941 Score: 950
Period size: 170 Copynumber: 10.6 Consensus size: 171
15130 TAAAAAAAAC
* * * * **** * * *
15140 TATAATTGAATGCCTACCTCAGGAAACATGTAGAAAAACTTGTTTATTTGAAAGAAAAGTCTATT
1 TATAATTGAATGTCTACGTCAAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCTATT
* *
15205 TATAATCTCCCATTCCTTCAAAAGCCTTATT-CATCGCTTTAAATGGTTTTATAATCTGATAATT
66 TATAGTCTCCCATTCCTTCAAAAGCCTTATTAC-TCGCTTTAAATGGTTTTATAATCTCATAATT
* * * *
15269 GATTTTAAG-TTGAATTTTTTA-TGTTTTTCAATAAAACAGAC
130 GATTTTAAGTTTGATTTTTTTACT-TTTTTGATTAAAACAGAT
* * ** ** * * ** * * *
15310 TATAATTGAATGTCTGCTTTGAGAAACGCGTAGGAAAATCCATTTATTTGAAAGAAAAGTCTATT
1 TATAATTGAATGTCTACGTCAAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCTATT
* * * * *
15375 TATAGTCACCCATTCCTT-AAAAGGCATTATCACTCACTTTAAATGG-TTTATAATCTCAAAATT
66 TATAGTCTCCCATTCCTTCAAAA-GCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATT
********** *
15438 GATTTTAAGNNNNNNNNNNTTACTTTTTTAATTAAAACAGAT
130 GATTTTAAGTTTGATTTTTTTACTTTTTTGATTAAAACAGAT
**
15480 TATCGTT-AACTGTCTACGTCAAGAAACATGAAGAAAAAG-CATTCATTGGCAAGAAAAGTCTAT
1 TATAATTGAA-TGTCTACGTCAAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCTAT
* * * * *
15543 TTATAGTTTCTCATTCTTTCAAAAGCCTCATTACTCGCTTTAAATAGTTTTAT-ATCTCATAATT
65 TTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATT
** * *
15607 GA--TTAAGTTCAATTATTTTTACTTTTTTGGTTAAAATAGAT
130 GATTTTAAGTTTGATT-TTTTTACTTTTTTGATTAAAACAGAT
* ** * * *
15648 TATAATTGAATGTCTACGTCAACAAAACGGGAAGAAAAAGACATTTATTAGCAAGAAAAGTCCAT
1 TATAATTGAATGTCTACGTCAA-GAAACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCTAT
* * * * *********** * *
15713 TTATAGTCACCAATTTCTTTAAAAGCNNNNNNNNNNACTTTAAATGGTTTTATAATCACAAAATT
65 TTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATT
** * *
15778 GATTTTAAGTTCAATTTTGTTTACTTTTTTGATTGAAACAAAT
130 GATTTTAAGTTTGATTTT-TTTACTTTTTTGATTAAAACAGAT
* * * * ** * *
15821 AATAATTGAATTTCTACG-CTGAGAAACATGAAGAAAATGACATTTGTTGGCAAGAAAAATCCAT
1 TATAATTGAATGTCTACGTC-AAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCTAT
* * * ** * *
15885 TTATAGTCTCTCATTCCTTAAAAAGTCTTATTACTCG-TTTCAAATACTTTTATTATCTCAAAAT
65 TTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTT-AAATGGTTTTATAATCTCATAAT
*********** * * * *
15949 TGATTTGNNNNNNNNNNTTTTTACATTTTAGGTTAAAACAAAT
129 TGATTTTAAGTTTGATTTTTTTACTTTTTTGATTAAAACAGAT
* * * *
15992 TATAATTGAATGTCTATC-TCATGAAACATGAAGAGAAAGACATTCATTGGCAAGAAAAGTCCAA
1 TATAATTGAATGTCTA-CGTCAAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCTAT
* * ********** *
16056 TTATAGTCTCCCATTCCCTCAAAAGCCTTATTACTCACTTTNNNNNNNNNNACAATCTCATAATT
65 TTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATT
*
16121 GATTTTAAGTTTGATTTTTTTACTTTTTTGATTAAAACATAT
130 GATTTTAAGTTTGATTTTTTTACTTTTTTGATTAAAACAGAT
* * * *
16163 TATAATTGAATGTTTACGTGAAGAAACGTGAAGAAAAATG-CATTCATAGGCAA-AAAAGTCTAT
1 TATAATTGAATGTCTACGTCAAGAAACATGAAGAAAAA-GACATTCATTGGCAAGAAAAGTCTAT
* * *
16226 TTATAGTCACTCATTCCTTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATT
65 TTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATT
* * * *
16291 GACTTTAAG-TTGAATTTTTTACATTTTTT-ATTAAAAGAGAC
130 GATTTTAAGTTTGATTTTTTTAC-TTTTTTGATTAAAACAGAT
* * * * * * * * *********** * * *
16332 TATTATTGTATG-CTTGCCTTAGGAACCGTNNNNNNNNNNCCATTTATTTGTAAGAAAAGT-TCA
1 TATAATTGAATGTC-TACGTCAAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCT-A
* * * * **********
16395 TTTATAATATCCCATTCCTTCAAAAGCCTTATTACTCTCCTTAAATGGTTTTANNNNNNNNNNAT
64 TTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAAT
* *
16460 TGATTTTAAG-TTGAATTTTTTATA-TTTTTT-AATAAAACAGAC
129 TGATTTTAAGTTTG-ATTTTTT-TACTTTTTTGATTAAAACAGAT
* * * * * * * * ** * * * *
16502 AATAATTGATTGCCTGCCTTAGGAAACGT-ACAGAAAAACTCATTTATTTAGAAAAAAAAGTGC-
1 TATAATTGAATGTCTACGTCAAGAAACATGA-AGAAAAAGACATTCA-TTGGCAAGAAAAGT-CT
* ** * * * *
16565 ATTTATAGTATCCCATTTTTTCAAAAGCCTCATTAGTCGCTTTAAAAGGTTTTATATTCTCATAA
63 ATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAA
* ** ** * *
16630 TTGATCTTAAG-TACACCTTTTTACATTTTTT-ATGAAAACAGAC
128 TTGATTTTAAGTTTGATTTTTTTAC-TTTTTTGATTAAAACAGAT
** * * * ** * * * *
16673 CGTAATTGAATGTTTGCCTCGTGAAACATGTAA-AAAAA-CCTATTTATTTGG-AAGAAAATTCC
1 TATAATTGAATGTCTACGTCAAGAAACATG-AAGAAAAAGAC-ATTCA-TTGGCAAGAAAAGTCT
* **********
16735 ATTTATAGTCTCTCATTCCTTNNNNNNNNNNATTACTCG-TTTCAAATGGTTTTATAATCTCATA
63 ATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTT-AAATGGTTTTATAATCTCATA
* * * * ** *
16799 ATTGATTTTGAG-TTGAATTTTTTACATTTTTCAAAAAAACAGAC
127 ATTGATTTTAAGTTTGATTTTTTTACTTTTTTGATTAAAACAGAT
* * * * * *
16843 TATAATTGAATGTCTACCTCAAGAAACAT-AAAAAAAATAAATTCATTTGCAAGAAAATTCTATT
1 TATAATTGAATGTCTACGTCAAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCTATT
* *
16907 TATAGTCACTCATTCCTTCAAAAGCCTTATTACTC
66 TATAGTCTCCCATTCCTTCAAAAGCCTTATTACTC
16942 ACTNNNNNNN
Statistics
Matches: 1220, Mismatches: 367, Indels: 91
0.73 0.22 0.05
Matches are distributed among these distances:
167 5 0.00
168 42 0.03
169 220 0.18
170 484 0.40
171 325 0.27
172 94 0.08
173 50 0.04
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.37
Consensus pattern (171 bp):
TATAATTGAATGTCTACGTCAAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCTATT
TATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTG
ATTTTAAGTTTGATTTTTTTACTTTTTTGATTAAAACAGAT
Found at i:18191 original size:168 final size:157
Alignment explanation
Indices: 17803--18285 Score: 353
Period size: 168 Copynumber: 2.9 Consensus size: 157
17793 GTCTACATCA
* * * ** * * * *
17803 AGAAACGTGAAGAAAAAAGTATTTATTGGTAAGAAAAGTTCATTTATAGTCAGTCATTGCTTCAA
1 AGAAACATGAA-AAAAAAGCATTCATTGAAAAGAAAAGTCCATTTATAGTCA-CCATTCCTTAAA
* * * * * * * *
17868 AAGTCTTATTTACCCATTTTAAACAGATTTATTATCTCAAAATTGATTTGATGTTCAATTGTTTT
64 AAGCCTTA-TTACCCACTTTAAATAGTTTTATTACCTCAAAATTAATTTTATCTT--ATT-TTTT
*
17933 TACATTTTTGGTTAACACA-AGCTTTAATTAAATGTCTACTT
125 TACATTTTTGGTTAAAACAGA-C--T-A-TAAA---C-ACTT
* * *
17974 GGAAAAACATGAAAAAAAAGCATTCATTGAAAAGAAAAGTCCATTTATAGTTC-CACATTCTTTC
1 --AGAAACATGAAAAAAAAGCATTCATTGAAAAGAAAAGTCCATTTATAG-TCAC-CATTCCTTA
* * *
18038 AAAAGCTTTATTACTCACTTTAAATAGTTTTATTACCTCAAAATTGATTTTATCTT-TTTTTTTA
62 AAAAGCCTTATTACCCACTTTAAATAGTTTTATTACCTCAAAATTAATTTTATCTTATTTTTTTA
18102 CATTTTTGGTTAAAACAGACTATAANNNNNNNNNNACACTT
127 CATTTTTGGTTAAAACAGACTATAA----------ACACTT
* * *
18143 AGAAACGTGAAGAAAAAGGCATTTATT-AATAAGAAAAGTCCATTTATAGTCATCCATTCCTTAA
1 AGAAACATGAA-AAAAAAGCATTCATTGAA-AAGAAAAGTCCATTTATAGTCA-CCATTCCTTAA
* * * *
18207 AAAGCCTTATTACCCATTTTAAATAGTTTTATTATCTCAAAATTAATTTTTTGTTCAATTTTTTT
63 AAAGCCTTATTACCCACTTTAAATAGTTTTATTACCTCAAAATTAATTTTATCTT--ATTTTTTT
18272 ACATTTTTGGTTAA
126 ACATTTTTGGTTAA
18286 GAGAAACTAT
Statistics
Matches: 257, Mismatches: 33, Indels: 42
0.77 0.10 0.13
Matches are distributed among these distances:
163 3 0.01
164 1 0.00
165 1 0.00
167 36 0.14
168 91 0.35
169 5 0.02
170 1 0.00
171 60 0.23
172 47 0.18
173 12 0.05
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.39
Consensus pattern (157 bp):
AGAAACATGAAAAAAAAGCATTCATTGAAAAGAAAAGTCCATTTATAGTCACCATTCCTTAAAAA
GCCTTATTACCCACTTTAAATAGTTTTATTACCTCAAAATTAATTTTATCTTATTTTTTTACATT
TTTGGTTAAAACAGACTATAAACACTT
Found at i:18387 original size:172 final size:171
Alignment explanation
Indices: 17267--18391 Score: 702
Period size: 172 Copynumber: 6.6 Consensus size: 171
17257 NNNNACAGAT
* * * * * *
17267 TATAATTGAATGTCTACCT-TATGAAACATGAAGAGAAAGGCATTCATT-AGCAAGAAAAGTCCA
1 TATAATTGAATGTCTAACTCGA-GAAACGTGAAGAAAAAAGCATTCATTGA-CAAAAAAAGTCCA
* * *
17330 TTTATAGTCTCTCATTCCATCAAAAGCCCTATTACTCACTTTAAAT-GATTTTA-TATTCTCAAA
64 TTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACCCACTTTAAATAG-TTTTATTA-TCTCAAA
* ** * * * *
17393 ATTGATTTTAAATTTAATTGTTTTTACATATTTT-ATTAAAACAGAT
127 ATTGATTTGATGTTCAATT-TTTTTACAT-TTTTGGTTAAAACAAAC
** * * * * * *
17439 TATAATTGAATGTCTGCCTC-ATGAAACATGAAGAGAAAGGCATTCATTGGTC-AGAAAAGTCTA
1 TATAATTGAATGTCTAACTCGA-GAAACGTGAAGAAAAAAGCATTCATT-GACAAAAAAAGTCCA
* * * ***********************
17502 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTNNNNNNNNNNNNNNNNNNNNNNN
64 TTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACCCACTTTAAATAGTTTTATTATCTCAAAAT
* * * * * * *
17567 NGATTTTAAGTTCAATTGTTTTTACTTTTTTGATTAAAACAGAT
129 TGATTTGATGTTCAATT-TTTTTACATTTTTGGTTAAAACAAAC
** * * * * **
17611 TATAATTGAATGTCTATGTAGAGAAACGTGAAGAAAAAGGTATTCATTGAC-AAGAAAGTCTGTT
1 TATAATTGAATGTCTAACTCGAGAAACGTGAAGAAAAAAGCATTCATTGACAAAAAAAGTCCATT
* * * **********
17675 TATAGTCTCTCATTCCTTCAAAAGTCTTATTACTCACTTTAAATTGTTTTNNNNNNNNNNAATTG
66 TATAGTCTCTCATTCCTTCAAAAGCCTTATTACCCACTTTAAATAGTTTTATTATCTCAAAATTG
* * * *
17740 ATTTGATGTTCAATTTTTTTTACATTATTGGCTAAACCATAC
131 ATTTGATGTTCAA-TTTTTTTACATTTTTGGTTAAAACAAAC
* * * ** * *
17782 TATAATTGAATGTCT-ACATCAAGAAACGTGAAGAAAAAAGTATTTATTGGTAAGAAAAGTTCAT
1 TATAATTGAATGTCTAAC-TCGAGAAACGTGAAGAAAAAAGCATTCATTGACAAAAAAAGTCCAT
** * * * * *
17846 TTATAGTCAGTCATTGCTTCAAAAGTCTTATTTACCCATTTTAAACAGATTTATTATCTCAAAAT
65 TTATAGTCTCTCATTCCTTCAAAAGCCTTA-TTACCCACTTTAAATAGTTTTATTATCTCAAAAT
* *
17911 TGATTTGATGTTCAATTGTTTTTACATTTTTGGTTAACACAAGC
129 TGATTTGATGTTCAATT-TTTTTACATTTTTGGTTAAAACAAAC
* * * * *
17955 TTTAATTAAATGTCT-ACTTGGAAAAACATGAA-AAAAAAGCATTCATTGA-AAAGAAAAGTCCA
1 TATAATTGAATGTCTAAC-TCGAGAAACGTGAAGAAAAAAGCATTCATTGACAAA-AAAAGTCCA
* * * * *
18017 TTTATAGT-TCCACATTCTTTCAAAAGCTTTATTACTCACTTTAAATAGTTTTATTACCTCAAAA
64 TTTATAGTCT-CTCATTCCTTCAAAAGCCTTATTACCCACTTTAAATAGTTTTATTATCTCAAAA
* * *
18081 TTGATTTTATCTT---TTTTTTTACATTTTTGGTTAAAACAGAC
128 TTGATTTGATGTTCAATTTTTTTACATTTTTGGTTAAAACAAAC
********** * * * * * *
18122 TATAANNNNNNNNNNACACT-TAGAAACGTGAAGAAAAAGGCATTTATTAATAAGAAAAGTCCAT
1 TATAATTGAATGTCTA-ACTCGAGAAACGTGAAGAAAAAAGCATTCATTGACAAAAAAAGTCCAT
* *
18186 TTATAGTCATC-CATTCCTTAAAAAGCCTTATTACCCATTTTAAATAGTTTTATTATCTCAAAAT
65 TTATAGTC-TCTCATTCCTTCAAAAGCCTTATTACCCACTTTAAATAGTTTTATTATCTCAAAAT
* ** * *
18250 TAATTTTTTGTTCAATTTTTTTACATTTTTGGTTAAGAGAAAC
129 TGATTTGATGTTCAATTTTTTTACATTTTTGGTTAAAACAAAC
* * * *
18293 TATAATTGTATGTCTAACTCGAGAAATGTGAAGAAAAATGCATTAATTGACAAAAAAAGGTCCAT
1 TATAATTGAATGTCTAACTCGAGAAACGTGAAGAAAAAAGCATTCATTGACAAAAAAA-GTCCAT
*
18358 TTATAGTCTCTCATTCTTTCAAAAGCCTTATTAC
65 TTATAGTCTCTCATTCCTTCAAAAGCCTTATTAC
18392 TCGCTTNNNN
Statistics
Matches: 743, Mismatches: 184, Indels: 52
0.76 0.19 0.05
Matches are distributed among these distances:
167 36 0.05
168 90 0.12
169 5 0.01
170 4 0.01
171 241 0.32
172 286 0.38
173 81 0.11
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.37
Consensus pattern (171 bp):
TATAATTGAATGTCTAACTCGAGAAACGTGAAGAAAAAAGCATTCATTGACAAAAAAAGTCCATT
TATAGTCTCTCATTCCTTCAAAAGCCTTATTACCCACTTTAAATAGTTTTATTATCTCAAAATTG
ATTTGATGTTCAATTTTTTTACATTTTTGGTTAAAACAAAC
Found at i:18930 original size:170 final size:169
Alignment explanation
Indices: 18710--19131 Score: 472
Period size: 170 Copynumber: 2.5 Consensus size: 169
18700 CATCGGCAAG
* *
18710 AAAAGTCTATTTATAGTCACTCATTTCTTAAAAAACCTTATTACTCGCTTTAAATGATTTTATAA
1 AAAAGTCTATTTATAGTCACTCATTACTTAAAAAGCCTTATTACTCGCTTTAAATG-TTTTATAA
**********
18775 TCGT-ATAATTGATTTTAAGTTAAATNNNNNNNNNNTTTCATTAAAAAAGACTATAATTCAATGT
65 TC-TCATAATTGATTTTAAGTTAAATTTTTTATGTTTTTCATTAAAAAAGACTATAATTCAATGT
* * * *
18839 CTATCTCGA-GAAACGTGTAGAAAAACTCATTTATTTGAAAA
129 CTACCT-GAGGAAACATATAGAAAAACCCATTTATTTGAAAA
* * * * *
18880 AAAAGTCTATTTATAATCTCTCATTCCTTCAAAAGCCTTATT-CATCGCTTTCAATGGTTTTATA
1 AAAAGTCTATTTATAGTCACTCATTACTTAAAAAGCCTTATTAC-TCGCTTTAAAT-GTTTTATA
* * * * *
18944 ATCTGATAATTGATTTTAAGTTGAATTTTTTATGTTTTTCATTAAAACATACTATAATTGAATGT
64 ATCTCATAATTGATTTTAAGTTAAATTTTTTATGTTTTTCATTAAAAAAGACTATAATTCAATGT
* * *
19009 CTACCTTAGGAAACATATAGGAAAACCCATTTATTTGAAAG
129 CTACCTGAGGAAACATATAGAAAAACCCATTTATTTGAAAA
* * * *
19050 AAAAGTCTATTTATAGTCACCCATTACTTAAAAAGCCTTATGACTCACTTTAAATGGTTTATAAT
1 AAAAGTCTATTTATAGTCACTCATTACTTAAAAAGCCTTATTACTCGCTTTAAATGTTTTATAAT
*
19115 CTCAAAATTGATTTTAA
66 CTCATAATTGATTTTAA
19132 NNNNNNNNNN
Statistics
Matches: 209, Mismatches: 38, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
169 27 0.13
170 180 0.86
171 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.39
Consensus pattern (169 bp):
AAAAGTCTATTTATAGTCACTCATTACTTAAAAAGCCTTATTACTCGCTTTAAATGTTTTATAAT
CTCATAATTGATTTTAAGTTAAATTTTTTATGTTTTTCATTAAAAAAGACTATAATTCAATGTCT
ACCTGAGGAAACATATAGAAAAACCCATTTATTTGAAAA
Found at i:19160 original size:170 final size:170
Alignment explanation
Indices: 18707--19236 Score: 428
Period size: 170 Copynumber: 3.1 Consensus size: 170
18697 ATTCATCGGC
* * * * *
18707 AAGAAAAGTCTATTTATAGTCACTCATTTCTTAAAAAACCTTATTAC-TCGCTTTAAATGATTTT
1 AAGAAAAGTCTATTTATAGTCACCCATTACTTAAAAAGCCTTA-TACATCACTTTAAATGGTTTT
* * ********** * * *
18771 ATAATCGT-ATAATTGATTTTAAGTTAAATNNNNNNNNNNTTTCATTAAAAAAGACTATAATTCA
65 ATAATC-TCAAAATTGATTTTAAGTTGAATTTTTTATGTTTTTAATTAAAACAGACTATAATTGA
* * * * * *
18835 ATGTCTATC-TCGAGAAACGTGTAGAAAAACTCATTTATTTGA
129 ATGTCTACCTTAG-GAAACATATAGGAAAACCCATTTATTTGA
* * * * * * * * *
18877 AAAAAAAGTCTATTTATAATCTCTCATTCCTTCAAAAGCCTTATTCATCGCTTTCAATGGTTTTA
1 AAGAAAAGTCTATTTATAGTCACCCATTACTTAAAAAGCCTTATACATCACTTTAAATGGTTTTA
* * * *
18942 TAATCTGATAATTGATTTTAAGTTGAATTTTTTATGTTTTTCATTAAAACATACTATAATTGAAT
66 TAATCTCAAAATTGATTTTAAGTTGAATTTTTTATGTTTTTAATTAAAACAGACTATAATTGAAT
19007 GTCTACCTTAGGAAACATATAGGAAAACCCATTTATTTGA
131 GTCTACCTTAGGAAACATATAGGAAAACCCATTTATTTGA
19047 AAGAAAAGTCTATTTATAGTCACCCATTACTTAAAAAGCCTTATGAC-TCACTTTAAATGG-TTT
1 AAGAAAAGTCTATTTATAGTCACCCATTACTTAAAAAGCCTTAT-ACATCACTTTAAATGGTTTT
********* *
19110 ATAATCTCAAAATTGATTTTAANNNNNNNNNNTTTACT-TTTTTAATTAAAACAGATTATAATTG
65 ATAATCTCAAAATTGATTTTAA-GTTGAATTTTTTA-TGTTTTTAATTAAAACAGACTATAATTG
* * * ** * * *
19174 AATGTCTACGTCAAGAAACATGA-A-GAAAAAGCATTCATTGGT
128 AATGTCTACCTTAGGAAACAT-ATAGGAAAACCCATTTATTTGA
19216 AAGAAAAGTCTATTTATAGTC
1 AAGAAAAGTCTATTTATAGTC
19237 TCNNNNNNNN
Statistics
Matches: 293, Mismatches: 60, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
169 60 0.20
170 228 0.78
171 5 0.02
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.37
Consensus pattern (170 bp):
AAGAAAAGTCTATTTATAGTCACCCATTACTTAAAAAGCCTTATACATCACTTTAAATGGTTTTA
TAATCTCAAAATTGATTTTAAGTTGAATTTTTTATGTTTTTAATTAAAACAGACTATAATTGAAT
GTCTACCTTAGGAAACATATAGGAAAACCCATTTATTTGA
Found at i:27665 original size:170 final size:169
Alignment explanation
Indices: 27054--27946 Score: 588
Period size: 170 Copynumber: 5.2 Consensus size: 169
27044 NNNNNNNNTG
* * * * *
27054 TAAAAAAGTCAACTTAAAATCAATTATGAAATTATAAAACCTTTTAAAGTGATTAATAAGCCTTT
1 TAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-CTTTTAAAGCGACTAATAAGACTTT
* * * * *
27119 TGAAGGAATGAGAGACTATAAATAGA--TTT-TTCTTATTAAAATACCTTTCTCTT-CACATTTC
65 TGAAGGAATGAGAGACTATAAATAGACTTTTCTTCTAAATAAATTA-CTTT-TTTTACACGTTTC
* * * ***
27180 AT-G-GG-ATAGACATTCAATTATAATCTTTTTTAACAAAAAATA
128 -TCGAGGCA-AG-CATTTAATTATAGTCTGTTTTATTGAAAAATA
* ** * **********
27222 TTAAAAACATTGAACTTAAAATTGATTTTGAGATTATAAAACTATTTAAAGCGNNNNNNNNNNCT
1 -TAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAACT-TTTAAAGCGACTAATAAGACT
* * * * * * * *
27287 TTTAAAGGAATAAGAGACTATAAATGGACTTTTCTT-AACAATGAA-TGCTTTGTACTT-CATGT
63 TTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTCTA-AATAAATTACTTT-T-TTTACACGT
* * * * ***
27349 TTCTCAAAGCAAACATTCAATTATAGTCTGTTTTAACCAAAAATGTAA
125 TTCTCGAGGCAAGCATTTAATTATAGTCTGTTTTATTGAAAAA--T-A
* * * * **********
27397 AAAAAAATTCAAGTTAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGANNNNNNNNNNTTT
1 TAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACT-TTTAAAGCGACTAATAAGACTTT
* * * *
27462 TGAAGGAATGGGTGACTATAAATAGACTTTTCTTGC-AAATGAATTTA-TTTTTTTTCACGTTTC
65 TGAAGGAATGAGAGACTATAAATAGACTTTTCTT-CTAAAT-AAATTACTTTTTTTACACGTTTC
* * * * *
27525 TTGAGGTAAACATTTAATTATAGTCTGTTTTTTTGAAAAATT
128 TCGAGGCAAGCATTTAATTATAGTCTGTTTTATTGAAAAATA
* * ********* * *
27567 TAAAAAATTTAACTGAAAATCAATTATGAGATTATAAAANNNNNNNNNNCGAGTAATAAGCCTTT
1 TAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-CTTTTAAAGCGACTAATAAGACTTT
* * *
27632 TGAAGGAATAAGAGACTATAAAT-GAAATTTTCTTCTAAATAAATTACTTTTTTTACACATTTCT
65 TGAAGGAATGAGAGACTATAAATAG-ACTTTTCTTCTAAATAAATTACTTTTTTTACACGTTTCT
* * * * *** *
27696 CAAGGCAAGCATTCAATTACAATCTGTTTTAACAAAAAATG
129 CGAGGCAAGCATTTAATTATAGTCTGTTTTATTGAAAAATA
* * * * *
27737 TAAAAAAGTGAACTTAAAATCAATTATGAGAATATTAAAACTTTTAAAGTGACTAATGAGACTTT
1 TAAAAAATTCAACTTAAAATCAATTATGAGATTA-TAAAACTTTTAAAGCGACTAATAAGACTTT
* * * * *
27802 TGAAGGAATGAGATACTATAAATAGACTTTTCTTCTAAATAAATGAGTTTTTTTGCATGTTTCTC
65 TGAAGGAATGAGAGACTATAAATAGACTTTTCTTCTAAATAAATTACTTTTTTTACACGTTTCTC
27867 GAGGCAAGCATTTAATTATAGTCTGTTTTATTGAAAAATA
130 GAGGCAAGCATTTAATTATAGTCTGTTTTATTGAAAAATA
27907 TAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
1 TAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
27947 CATTNNNNNN
Statistics
Matches: 558, Mismatches: 142, Indels: 48
0.75 0.19 0.06
Matches are distributed among these distances:
169 21 0.04
170 337 0.60
171 13 0.02
172 42 0.08
173 131 0.23
174 12 0.02
175 2 0.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.35
Consensus pattern (169 bp):
TAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTTTTAAAGCGACTAATAAGACTTTT
GAAGGAATGAGAGACTATAAATAGACTTTTCTTCTAAATAAATTACTTTTTTTACACGTTTCTCG
AGGCAAGCATTTAATTATAGTCTGTTTTATTGAAAAATA
Done.