Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402940.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_600.0, 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: 22576
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.27
Warning! 6311 characters in sequence are not A, C, G, or T
Found at i:3040 original size:172 final size:161
Alignment explanation
Indices: 2857--3179 Score: 319
Period size: 171 Copynumber: 1.9 Consensus size: 161
2847 NNNNNNNNNN
* * * * **
2857 TTTATATTTTTTATTAAAATAGACTATAATTGCATCCTTGCCTTGGGAAA-CATGCAGAAAAAAC
1 TTTACATTTTTTATTAAAATAGACTAAAATTGAATCCTTACCTT-AAAAACCATGCAGAAAAAAC
* *
2921 CATTCATTTG-GAAAAAAAAATCCATTTATAGTCTCTTATTCCTTT-AAAAGCCTTATTACTCAC
65 CATTCA-TTGAG-AAAAAAAATCCATTTATAGTCTCTCATT-CTTTAAAAAGCCTTATTAATCAC
*
2984 TTTAAAGGGTTTTATAATCTCATNNNNNNNNNNAAGTTGAATTGT
127 TTTAAAGGATTTTATAATCTCAT----------AAGTTGAATTGT
* * *
3029 TTTACATTTTTTATTAAAATAGACTAAAATTGAATGCTTACCTTAAAAACCATGTAGAAAAAGCC
1 TTTACATTTTTTATTAAAATAGACTAAAATTGAATCCTTACCTTAAAAACCATGCAGAAAAAACC
* * * * * * *
3094 ATTCATTGAGAAGAAAAGTTCATTTATGGTCTCTCATTCTTTAAAAATCCTTGTTAATTACTTTA
66 ATTCATTGAGAAAAAAAATCCATTTATAGTCTCTCATTCTTTAAAAAGCCTTATTAATCACTTTA
*
3159 AATGATTTTATAATCTCATAA
131 AAGGATTTTATAATCTCATAA
3180 CTAAATNNNN
Statistics
Matches: 128, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
161 2 0.02
170 4 0.03
171 64 0.50
172 58 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.38
Consensus pattern (161 bp):
TTTACATTTTTTATTAAAATAGACTAAAATTGAATCCTTACCTTAAAAACCATGCAGAAAAAACC
ATTCATTGAGAAAAAAAATCCATTTATAGTCTCTCATTCTTTAAAAAGCCTTATTAATCACTTTA
AAGGATTTTATAATCTCATAAGTTGAATTGT
Found at i:5721 original size:171 final size:170
Alignment explanation
Indices: 5407--5957 Score: 513
Period size: 171 Copynumber: 3.2 Consensus size: 170
5397 NNNNNNNNNN
* * * * * * *
5407 TTTAAATGGTTTTATAATCTCATAATTGATTTTAGGTTGAAGTTTTTTATAT-TTTTAGTTAAAA
1 TTTAAATTGTTTTATAATGTCATAATTGATTTTAAGTCGAATTTTTTTACATATTTCA-TTAAAA
* * ** * ** * ** * * *
5471 CAGACTATAATTGAATGCCTGTCTTATTACACATGTAGAAAAAGCCATTCATTAGG-AAGAAAAG
65 CAAACTATAATTGAATGTCTACCTCAAAAAACATAAAGAAAAA-ACATTCACT-GGCAAGAAAAA
* * * * *
5535 TCTATTTACAGTCACCCATTCCTTCAAAAGCCCTACTATTTGC
128 TCCATTTATAGTCACCCATTCCTTCAAAAGCCTTACTACTCGC
* * * * **
5578 TTTAAATTATTTTATAGTGTCATAATTGATTTGAAGTTGAATTTTTTTACATATTTGGTTAAAAC
1 TTTAAATTGTTTTATAATGTCATAATTGATTTTAAGTCGAATTTTTTTACATATTTCATTAAAAC
* *
5643 AGACTATAATT-AA-GCATCTACCTCAAAAAACACT-AAGAAACACAA-ATTGACTGGCAA-AAG
66 AAACTATAATTGAATG--TCTACCTCAAAAAACA-TAAAGAAA-A-AACATTCACTGGCAAGAA-
* * * *
5703 AAATCGATTTATAGTCACCCATTCCTTTAAAAACCTTAGTACTCGC
125 AAATCCATTTATAGTCACCCATTCCTTCAAAAGCCTTACTACTCGC
* * * *
5749 TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTCGAATTTTTTTAGATTTTTCATTAAAAC
1 TTTAAATTGTTTTATAATGTCATAATTGATTTTAAGTCGAATTTTTTTACATATTTCATTAAAAC
* * *
5814 AAACTATAATTGAATGTTTACCTCAAAAAACATAAAGAAAAAAGCATTCATTGGCAAGAAAAGTC
66 AAACTATAATTGAATGTCTACCTCAAAAAACATAAAGAAAAAA-CATTCACTGGCAAGAAAAATC
* ** * *
5879 CATTTATAGTCTCTTATTCTTTCAAAAGCCTTATTACTCGC
130 CATTTATAGTCACCCATTCCTTCAAAAGCCTTACTACTCGC
*
5920 TTTAAATTGTTTTATAATGTCATAACTGATTTTAAGTC
1 TTTAAATTGTTTTATAATGTCATAATTGATTTTAAGTC
5958 TACCTCAAGA
Statistics
Matches: 310, Mismatches: 56, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
169 3 0.01
170 8 0.03
171 288 0.93
172 9 0.03
173 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (170 bp):
TTTAAATTGTTTTATAATGTCATAATTGATTTTAAGTCGAATTTTTTTACATATTTCATTAAAAC
AAACTATAATTGAATGTCTACCTCAAAAAACATAAAGAAAAAACATTCACTGGCAAGAAAAATCC
ATTTATAGTCACCCATTCCTTCAAAAGCCTTACTACTCGC
Found at i:7193 original size:341 final size:341
Alignment explanation
Indices: 6542--7538 Score: 830
Period size: 341 Copynumber: 2.9 Consensus size: 341
6532 NNNNNNNNNN
* *
6542 TGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTGAATGTTTTTACAGTTTTTTGTTA
1 TGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTAAATGTTTTTACAGTTTTTTATTA
* * * *
6607 AAATAGAAAATAATTAAATGTCTACCTCATGAAATGTGAAGAAAAGACATTCATTGGCAAGAAAG
66 AAACAGAAAATAATTAAATGTCGACCTCAAGAAATGTGAAGAAAAGACATTCATTGGCAAGAAAA
* * * * * *
6672 GTCCATTTATAGTTACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTC
131 GTCCATTTATAGTTACCCATTCCATCAAAAGCCTTATCACTCACTTGAAATGGTTTTATAAACTA
* **
6737 ATAATTGATTTTAAGTTGAATTTTTTACAATTTTCATTAAAACAGACTATAATTGAATGCCTTCC
196 ATAATTGATTTTAAGTTGAATTTTTTACAATTTTCATTAAAAAAGACTATAATTGAATGCCGACC
* * *
6802 TCAGAAAACATATAGAGAAACCCATTCATTTGGAAGAAAAGTCAATTTATAGTCA-TCCATTTCT
261 TCAGAAAACATATAGAAAAACCCATTCATTAGGAAGAAAAGTCAATTTATAGTCACT-CATTCCT
*
6866 TCAAAAGCCTTATTACT
325 TCAAAACCCTTATTACT
* * * * *
6883 TGCTTAAAATGATTTTATAATCGCATAATTGATTTTAAGTTAAAT-TGTTTTATA-TTTTTTATT
1 TGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTAAATGT-TTTTACAGTTTTTTATT
* * ** *
6946 AAAACA-AATTATCATTGCATGTCGACCTCAAGAAACATGT-AA-AAAAGGCATTCATTTGG-AA
65 AAAACAGAA-AATAATTAAATGTCGACCTCAAG-AA-ATGTGAAGAAAAGACATTCA-TTGGCAA
* * *
7007 GAAAAGTCCATTTATAGTCT-CGCATTCCATCAAAAGTCTTATCACTCACTTGAGAA-GGTTTTC
126 GAAAAGTCCATTTATAGT-TACCCATTCCATCAAAAGCCTTATCACTCACTTGA-AATGGTTTTA
* * ** *
7070 TAAACTAATAACTT-ATTTTAATTTGAATTTTTTTACATTTTTGGTTAAAAAAGATTATAATTGA
189 TAAACTAATAA-TTGATTTTAAGTTGAA-TTTTTTACAATTTTCATTAAAAAAGACTATAATTGA
* * * ** * *
7134 ATGTCGACCTC--AAGACAGATGAAGAAAAAGGCATTCATTAGTAAGAAAAGTCCATTTATAGTC
252 ATGCCGACCTCAGAAAACATAT--AGAAAAACCCATTCATTAGGAAGAAAAGTCAATTTATAGTC
* *
7197 ACTCATTCCTTCAAACCCCTTATTTCT
315 ACTCATTCCTTCAAAACCCTTATTACT
** * * *
7224 CACTTTAAATGGTTTTATAATCTCAAAATTAATTTTTAA-TTGAATTATTTTTACA--TTTTTAG
1 TGCTTTAAATGGTTTTATAATCTCATAATTAA-TTTTAAGTT-AAATGTTTTTACAGTTTTTTA-
* *** * * * ** * * * ** *
7286 TTAAAAAAGGCTATAATTGAGTGTCTACCAT-GGGAAACGTGAAGCGAAAGGCAACCATTGGCAC
63 TTAAAACAGAAAATAATTAAATGTCGACC-TCAAGAAATGTGAAG-AAAAGACATTCATTGGCAA
* * * ** ** * * * ** * *
7350 GAAATGTCTATTTATAGTCACTTAAGCCTTCGAAAGCCTTATTACT-TGTTGTAAATAGTTTTAA
126 GAAAAGTCCATTTATAGTTACCCATTCCATCAAAAGCCTTATCACTCACTTG-AAATGGTTTTAT
* * * *
7414 AAACTAATAATTGATTTTAAGTTGAATATTTTTACATTTTTGATTCAAATAGACTATAATTGAAT
190 AAACTAATAATTGATTTTAAGTTGAAT-TTTTTACAATTTTCATTAAAAAAGACTATAATTGAAT
* * * ** *
7479 GTCTACCT-TGAGAAACATGAATA-AAAAA-GTATTCATT-GGCAAGAAAAGTCTATTTATAGT
254 GCCGACCTCAGA-AAACAT--ATAGAAAAACCCATTCATTAGG-AAGAAAAGTCAATTTATAGT
7539 NNNNNNNNNN
Statistics
Matches: 527, Mismatches: 96, Indels: 64
0.77 0.14 0.09
Matches are distributed among these distances:
339 9 0.02
340 118 0.22
341 191 0.36
342 55 0.10
343 141 0.27
344 6 0.01
345 5 0.01
347 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (341 bp):
TGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTAAATGTTTTTACAGTTTTTTATTA
AAACAGAAAATAATTAAATGTCGACCTCAAGAAATGTGAAGAAAAGACATTCATTGGCAAGAAAA
GTCCATTTATAGTTACCCATTCCATCAAAAGCCTTATCACTCACTTGAAATGGTTTTATAAACTA
ATAATTGATTTTAAGTTGAATTTTTTACAATTTTCATTAAAAAAGACTATAATTGAATGCCGACC
TCAGAAAACATATAGAAAAACCCATTCATTAGGAAGAAAAGTCAATTTATAGTCACTCATTCCTT
CAAAACCCTTATTACT
Found at i:7195 original size:171 final size:170
Alignment explanation
Indices: 6544--7538 Score: 845
Period size: 171 Copynumber: 5.8 Consensus size: 170
6534 NNNNNNNNTG
* * *
6544 CTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTGAATGTTTTTACAGTTTTTTGTTAAA
1 CTTTAAATGGTTTTATAATCTAATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTTGTTAAA
* ** * * * ** * *
6609 ATAGAAAATAATTAAATGTCTACCTCATGAAATGTGAAG-AAAAGACATTCA-TTGGCAAGAAAG
65 AAAGACTATAATTGAATGTCGACCTCAAGAAACATGAAGAAAAAGGCATTCATTTGG-AAGAAAA
*
6672 GTCCATTTATAGT-TACCCATTCCTTCAAAAGCCTTATTACTCG
129 GTCCATTTATAGTCT--CCATTCCTTCAAAAGCCTTATTACTCA
* * **
6715 CTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTACAATTTTCATTAAAA
1 CTTTAAATGGTTTTATAATCTAATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAA
* * ** * **
6779 CAGACTATAATTGAATGCCTTCCTC-AGAAAACAT-ATAGAGAAACCCATTCATTTGGAAGAAAA
66 AAGACTATAATTGAATGTCGACCTCAAG-AAACATGA-AGAAAAAGGCATTCATTTGGAAGAAAA
* * **
6842 GTCAATTTATAGTCATCCATTTCTTCAAAAGCCTTATTACTTG
129 GTCCATTTATAGTC-TCCATTCCTTCAAAAGCCTTATTACTCA
* * ** * * * *
6885 CTTAAAATGATTTTATAATCGCATAATTGATTTTAAGTTAAATTGTTTTATATTTTTTATTAAAA
1 CTTTAAATGGTTTTATAATCTAATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAA
* * * *
6950 CAA-ATTATCATTGCATGTCGACCTCAAGAAACATGTA-AAAAAGGCATTCATTTGGAAGAAAAG
66 -AAGACTATAATTGAATGTCGACCTCAAGAAACATGAAGAAAAAGGCATTCATTTGGAAGAAAAG
* * *
7013 TCCATTTATAGTCTCGCATTCCATCAAAAGTCTTATCACTCA
130 TCCATTTATAGTCTC-CATTCCTTCAAAAGCCTTATTACTCA
* * * * *
7055 CTTGAGAA-GGTTTTCTAAACTAATAACTT-ATTTTAATTTGAATTTTTTTACATTTTTGGTTAA
1 CTTTA-AATGGTTTTATAATCTAATAA-TTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAA
* * * * *
7118 AAAAGATTATAATTGAATGTCGACCTCAAGACAGATGAAGAAAAAGGCATTCATTAGTAAGAAAA
64 AAAAGACTATAATTGAATGTCGACCTCAAGAAACATGAAGAAAAAGGCATTCATTTGGAAGAAAA
* ** *
7183 GTCCATTTATAGTCACTCATTCCTTCAAACCCCTTATTTCTCA
129 GTCCATTTATAGTCTC-CATTCCTTCAAAAGCCTTATTACTCA
* *
7226 CTTTAAATGGTTTTATAATCTCAA-AATTAATTTTTAA-TTGAATTATTTTTACATTTTTAGTTA
1 CTTTAAATGGTTTTATAATCT-AATAATTGA-TTTTAAGTTGAATT-TTTTTACATTTTTTGTTA
* * * ** * ** ** *
7289 AAAAAGGCTATAATTGAGTGTCTACCAT-GGGAAACGTGAAGCGAAAGGCAACCA-TTGGCACGA
63 AAAAAGACTATAATTGAATGTCGACC-TCAAGAAACATGAAGAAAAAGGCATTCATTTGG-AAGA
* * * * ** * *
7352 AATGTCTATTTATAGTCACTTAAGCCTTCGAAAGCCTTATTACT-T
126 AAAGTCCATTTATAGTCTC-CATTCCTTCAAAAGCCTTATTACTCA
* * * * * *
7397 GTTGTAAATAGTTTTAAAAACTAATAATTGATTTTAAGTTGAATATTTTTACA-TTTTTGATTCA
1 CTT-TAAATGGTTTTATAATCTAATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTG-TTAA
* * ** * * *
7461 AATAGACTATAATTGAATGTCTACCTTGAGAAACATGAATAAAAAAGTATTCA-TTGGCAAGAAA
64 AAAAGACTATAATTGAATGTCGACCTCAAGAAACATGAAGAAAAAGGCATTCATTTGG-AAGAAA
*
7525 AGTCTATTTATAGT
128 AGTCCATTTATAGT
7539 NNNNNNNNNN
Statistics
Matches: 671, Mismatches: 126, Indels: 54
0.79 0.15 0.06
Matches are distributed among these distances:
168 2 0.00
169 39 0.06
170 239 0.36
171 258 0.38
172 132 0.20
173 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (170 bp):
CTTTAAATGGTTTTATAATCTAATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAA
AAGACTATAATTGAATGTCGACCTCAAGAAACATGAAGAAAAAGGCATTCATTTGGAAGAAAAGT
CCATTTATAGTCTCCATTCCTTCAAAAGCCTTATTACTCA
Found at i:8214 original size:170 final size:168
Alignment explanation
Indices: 7677--8359 Score: 551
Period size: 170 Copynumber: 4.0 Consensus size: 168
7667 NNNNNNNNNN
* * ** *
7677 TTATAATCTCATAATTGATTTTATGTTCAATTGTTTTTACATTTTTGGTT-AAA-AAATTATAAA
1 TTATAATCTCATAATTGATTTTAAGTTGAA-TGTTTTTACATTTTTCATTAAAACAAACTAT-AA
* * * * * *
7740 TGAATATCTACCTTGAGAAACGTGATGAAAAAGGCATTTATT-GGCAAGAAAAGTCC-TTCTATA
64 TTAA-ATCTACCTAGAGAAACATGAAGAAAAAGCCATTTATTAAG-AAGAAAAGTCCATT-TATA
* *
7803 GTTATCCATTCCTTCAAAAGCCTTATCACTC-ACTTTAAATAGTT
126 GTCA-CCATTCCTTCAAAAGCCTTATTACTCGA-TTTAAATAGTT
* * * * *
7847 TTATAATCTCATAATTGATTTTAATTTGAATTTTTTTACAATTTTCATCAAAACAAACTAGAATT
1 TTATAATCTCATAATTGATTTTAAGTTGAATGTTTTTACATTTTTCATTAAAACAAACTATAATT
* * * * * *
7912 GAA--TGCCTCAG-GAAATATGTAGAAAAAGCCATTTATTGAGAAAAAAAGTCCATTTATAGTTC
66 AAATCTACCT-AGAGAAACATGAAGAAAAAGCCATTTATTAAGAAGAAAAGTCCATTTATAG-TC
* * *
7974 -CTCATTCCTTCAAAAGCCTTAGTACTTGATTTAAATATTT
129 AC-CATTCCTTCAAAAGCCTTATTACTCGATTTAAATAGTT
********** * * *
8014 TTATAATCTCATANNNNNNNNNNAGTTGAATGTTTTTACATTTTTGATTGAAACAAATTATAATT
1 TTATAATCTCATAATTGATTTTAAGTTGAATGTTTTTACATTTTTCATTAAAACAAACTATAATT
* * *** * * *
8079 AAAGTCTACCTTGTGAAACATGAAGAAAAATTTATTCATT-AGCAAGAAAGGTTCATTTATAGTC
66 AAA-TCTACCTAGAGAAACATGAAGAAAAAGCCATTTATTAAG-AAGAAAAGTCCATTTATAGTC
* * *
8143 ACCAATTCCTTCAAAAGTCTTATTACCCGTTTTAAAT-GATT
129 ACC-ATTCCTTCAAAAGCCTTATTACTCGATTTAAATAG-TT
* *
8184 TTATAATCTCATAATTGATTTTAAGTTGAATGTATTTATATTTTTCATTAAAACAAACTATAATT
1 TTATAATCTCATAATTGATTTTAAGTTGAATGTTTTTACATTTTTCATTAAAACAAACTATAATT
* * * * *
8249 GAATGTCTACCTAGACAAACATGTAGAAAAATCCATTTATTAAGAAGAAAAGTCCTTTTATAGTC
66 -AA-ATCTACCTAGAGAAACATGAAGAAAAAGCCATTTATTAAGAAGAAAAGTCCATTTATAGTC
* * * * * * *
8314 TCTTATTCCTTGAAAAGCCTTATTACTTGCTTTTAATGGTT
129 AC-CATTCCTTCAAAAGCCTTATTACTCGATTTAAATAGTT
8355 TTATA
1 TTATA
8360 NNNNNNNNNN
Statistics
Matches: 396, Mismatches: 96, Indels: 41
0.74 0.18 0.08
Matches are distributed among these distances:
166 1 0.00
167 121 0.31
168 6 0.02
169 21 0.05
170 155 0.39
171 89 0.22
172 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (168 bp):
TTATAATCTCATAATTGATTTTAAGTTGAATGTTTTTACATTTTTCATTAAAACAAACTATAATT
AAATCTACCTAGAGAAACATGAAGAAAAAGCCATTTATTAAGAAGAAAAGTCCATTTATAGTCAC
CATTCCTTCAAAAGCCTTATTACTCGATTTAAATAGTT
Found at i:8998 original size:20 final size:21
Alignment explanation
Indices: 8973--9012 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
8963 TTGGGAAACA
8973 TGTAAAAAAACTT-ATTTATT
1 TGTAAAAAAACTTCATTTATT
*
8993 TGTAAAAAAAGTTCATTTAT
1 TGTAAAAAAACTTCATTTAT
9013 AGTCTCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (21 bp):
TGTAAAAAAACTTCATTTATT
Found at i:10492 original size:171 final size:171
Alignment explanation
Indices: 9746--12324 Score: 1809
Period size: 171 Copynumber: 15.1 Consensus size: 171
9736 NNNNNNNNNN
* * * * *
9746 ACCATTTAAAGTGGGTAATAAGGCTTTTGAAGGAATTG-GTGACTATAAATAGACCTTTCTTGCT
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-TGAGTGACTATAAATAGACTTTTCTTTCC
* * * * *
9810 AATGAATAAAT-TTTTCTTCATGTTTCACAAGGTAAACATT-AATTATAATCTGTTTCAACCAAA
65 AATGAAT-ACTCTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAA
* ********** *
9873 AATGTAAAAACATTCAACTTNNNNNNNNNNATGAGATTATAAA
129 AATGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
** *** * ** *
9916 AATATTTAAAATAAGTAATAAGGCTTTTGAAGGAATGGGAAACTATAAATGGACTTTTC-TTCTC
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTTC-C
* * * * * * * **
9980 AATAAATGGCT-TTTTCTACATGTTTC-C-CGAT-G-CATTCAATTCTAGTTTGTTTTAATGAAA
65 AATGAAT-ACTCTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAA
* * *
10040 ATTGTAAAAAAATTCAACTTAAAATCAAGTATGAGATTATAAA
129 AATGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
* * * *
10083 ACCATTTAAAGTGAGTGATAAGGCTTTCGAAGGAATG-GATGACTATAGAAT-GACTTTTCTTAC
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAG-TGACTATA-AATAGACTTTTCTTTC
* * * *
10146 CAATGAATAC-CTTTTTCTTCATGTTTCTCAAGGTAGACAATCATTTATAATTTGTTTTAACCAA
64 CAATGAATACTC-TTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAA
* * *
10210 AAATGTAAAAGAAATTGAACATAAAATCAATTATGAGATTATAAA
128 AAATGTAAAA-AAATTCAACTTAAAATCAATTATTAGATTATAAA
* ** * *
10255 ATCATTTAAAGCGAGTAATAATACTTTTGAAGGAATGAGTGACTATAAAGAGACTTTTCTTGCCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTTCCA
* * * *
10320 ATGAATACTCTTTTATTCATGTTGCTCAAGGTAGACATTCAATTATAGTCTATTTGAACCAAAAA
66 ATGAATACTCTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAA
* * * *
10385 TATAAAAATATTCAACTTAAAATCAATTATTAGTTTATTAA
131 TGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
* * ** * * * *
10426 ACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCTTAAGTGACTATAAGTAGACTTTTCGTGCCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTTCCA
** * * ** * * * * * * *
10491 ATGGTTGGCT-TTTGCTTCACATTCCCCATGGTAGACACTCAATTATAGCCTTTTTTTTAATCAA
66 ATGAAT-ACTCTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAG--TCTGTTTTAACCAA
* * *
10555 AACTGTAAAAAAATTTAA-TTAAAAATTAATT-TTGAGATTATAAA
128 AAATGTAAAAAAATTCAACTT-AAAATCAATTATT-AGATTATAAA
* * * * * *
10599 ACCATTTAAAGTGAGAAATAAGGATTTTGAAGGCATGAGTGATTATAAATAGACTTTTCTTTCTA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTTCCA
* * ** *
10664 ATGAATGC-CTTTTTCTTCACT-TGTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAA
66 ATGAATACTC-TTTTCTTCA-TGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAA
* * *
10727 AATGTAAAAAAATTCAAATTAAAATCAGTTATTAGTTTATAAA
129 AATGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
* * * * * *
10770 ACC-TTCTCAAGCGAGTGATAAGACTTTT-AATGGAATGAGAGATTATAAATGGACTTTTC-TTC
1 ACCATT-TAAAGCGAGTAATAAGGCTTTTGAA-GGAATGAGTGACTATAAATAGACTTTTCTTTC
* *
10832 CAAATGAATGACT-TTTT-TTACATGTTTCTCAAGGTCAG-CATTCAATGATAGT-TTTTTTAA-
64 C-AATGAAT-ACTCTTTTCTT-CATGTTTCTCAAGGT-AGACATTCAATTATAGTCTGTTTTAAC
* * *
10892 TAAAAATGTAAAAAAATTTAACTTAAAATC-ATTGA-TACAATTATAAA
125 CAAAAATGTAAAAAAATTCAACTTAAAATCAATT-ATTA-GATTATAAA
* * * * * *
10939 ACCATTCAAAGCAAGTAATAAGGTTTTTGAAGGAATGAGGGACTATAAATAGACTTCTCTTACCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTTCCA
* * * * * *
11004 ATGAATACTTTTTTCTTCATATTTCTCATGGTAGACATTCAATTGTAATCTGTTTAAACCAAAAT
66 ATGAATACTCTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAA-
* * ** *
11069 AT-AAAAAAAATTGAACACAAAATCAATT-TTGAGATAATAAA
130 ATGTAAAAAAATTCAACTTAAAATCAATTATT-AGATTATAAA
* * * * *
11110 ACTATTTAAAGTGAGTAATAAGGCTTTTCAAGGAATGGGTGACTATAAATAGAGTTTTC-TTCGC
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTTC-C
* * * * * * *
11174 AATGAAT-GTGTTTTTTTCATGTTTTTCGAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAA
65 AATGAATACTCTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAAC-CAAA
* * *
11238 AATATAAAAAAATTCAACTTAAAATCAATTATGATATTATAAA
129 AATGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
* * * * * *
11281 ACCATTTCAAGTGAATAATAAGGCTTTTGAAGGAATGGGTGCCTATAAATCGACTTTTC-TTCCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTTCC-
* * * ** ** * * **
11345 AATGAATGGA-T-TTCTCTACATGTTTTTTGAGAAAGGCATTCAATTATAGTCTATTTTAATGAA
65 AATGAAT--ACTCTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAA
* * * *
11408 AAATGT-AAAAAACTCAACTTAAAATCAATAATGAGATTATAAC
128 AAATGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
* * * * * * *
11451 GCCATTTAAAGGGAGTAATAAGGCTTTTGAAGGAATGGGTGATTAT-AATGGACCTTTCTTACCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTTCCA
* * ** * *
11515 ATGAATGC-CTTTTCTTTACATTTCAT-GAGGTAGACATTCAATTATTA-TCTGTTTTAATCAAA
66 ATGAATACTCTTTTCTTCATGTTTC-TCAAGGTAGACATTCAATTA-TAGTCTGTTTTAACCAAA
* * * * *
11577 AATGTAAAAAAATTCAAATTCAAATTAGTTATTAGTTTATAAA
129 AATGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
* *
11620 ACC-TTCTAAAGTGAGTAATAAGGCTTTTGATA-GAATG-GAAGACTATAAATATG-CTTTTC-T
1 ACCATT-TAAAGCGAGTAATAAGGCTTTTGA-AGGAATGAG-TGACTATAAATA-GACTTTTCTT
* * * * * * * *
11680 TCTAAATGAATGCCTCTTTT-TACATGTTTC-CTGAGGTCAG-CATGCAATGATAATTTGTTTTA
62 TC-CAATGAAT-ACTCTTTTCTTCATGTTTCTC-AAGGT-AGACATTCAATTATAGTCTGTTTTA
** **
11742 ATGAAAAATGTAAAACAAATT-AACTTAAAATCAATTATGCGATTATAAA
123 ACCAAAAATGTAAAA-AAATTCAACTTAAAATCAATTATTAGATTATAAA
* * *
11791 ACTATTTTAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATCA-ACTTTTC-TTCC
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAT-AGACTTTTCTTTCC
** * ** * * * **
11854 AAATGAATGGGT-TTCTCAACATGTTT-TCTGAGGAAGGCATTCAATTATAGTCTGTTTTAATGA
65 -AATGAAT-ACTCTTTTCTTCATGTTTCTC-AAGGTAGACATTCAATTATAGTCTGTTTTAACCA
* **********
11917 AACATGT-AAAAAATTCAACTTAAANNNNNNNNNNAGATTATAAA
127 AAAATGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
* * * * * *
11961 ACCATTTAAAGCGAGCAATAAGGCTTTTGAAGGAATGGGCGACTATAAATGGACCTTTCTTGCCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTTCCA
** * * * * *
12026 ATGAATA-TCTTTTCTTCACATTTCAT-GAGATAGACATTTAATTATTA-TCTATTTTAACAAAA
66 ATGAATACTCTTTTCTTCATGTTTC-TCAAGGTAGACATTCAATTA-TAGTCTGTTTTAACCAAA
* **************
12088 AATGTAAAAACATTCAACTTAANNNNNNNNNNNNNNTTATAAA
129 AATGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
* * * * *
12131 ACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAGATGGGCTTTTCTTGT-C
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTT-TCC
** ********** * * *
12195 AATGAATAC-CTTTTTCTTCATGTTTCTTGAGGTANNNNNNNNNNTATAATCTATTTTAACTAAA
65 AATGAATACTC-TTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAA
* * * * *
12259 AATGTTAAAAACTTAAACATAAAATCAATTATGAGATTATAAA
129 AATGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
12302 ACCATTTAAAGCGAGTAATAAGG
1 ACCATTTAAAGCGAGTAATAAGG
12325 NNNNNNNNNN
Statistics
Matches: 1915, Mismatches: 397, Indels: 193
0.76 0.16 0.08
Matches are distributed among these distances:
166 6 0.00
167 114 0.06
168 63 0.03
169 249 0.13
170 428 0.22
171 706 0.37
172 221 0.12
173 128 0.07
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (171 bp):
ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTTCCA
ATGAATACTCTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAA
TGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
Found at i:11009 original size:340 final size:338
Alignment explanation
Indices: 9746--12324 Score: 1820
Period size: 340 Copynumber: 7.6 Consensus size: 338
9736 NNNNNNNNNN
* * * * *
9746 ACCATTTAAAGTGGGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATAGACCTTTCTTGCTA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTT-CCA
* * * * * * * *
9811 ATGAATAAATTTTTCTT-CATGTTTCACAAGGTAAACATT-AATTATAATCTGTTTCAACCAAAA
65 ATGAATGACTTTTT-TTACATGTTTCTCAAGGTAGACATTCAATTATAGTCTTTTTTAATCAAAA
* ********* ** * ***
9874 ATGTAAAAACATTCAACTTNNNNNNNNNNATGAGATTATAAAAATATTTAAAATAAGTAATAAGG
129 ATGTAAAAAAATTCAACTT-AAAATCATTATGAGATTATAAAACCATTCAAAGCGAGTAATAAGG
* * * * *
9939 CTTTTGAAGGAATGGGAAACTATAAATGGACTTTTCTTCTCAATAAATGGCTTTTTC-T-ACATG
193 CTTTTGAAGGAATGGG-GACTATAAATAGACTTTTCTTC-CAATGAATGCCTTTTTCTTCACTTG
*** * * * ** *
10002 T-TTCCCG-ATG-CATTCAATTCTAGTTTGTTTTAATGAAAATTGTAAAAAAATTCAACTTAAAA
256 TCTTGAGGTA-GACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAA
*
10064 TCAAGTATGAGATTATAAA
320 TCAATTATGAGATTATAAA
* * * *
10083 ACCATTTAAAGTGAGTGATAAGGCTTTCGAAGGAATGGATGACTATAGAAT-GACTTTTCTTACC
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATA-AATAGACTTTTCTT-CC
* * * *
10147 AATGAAT-ACCTTTTTCTT-CATGTTTCTCAAGGTAGACAATCATTTATAAT-TTGTTTTAACCA
64 AATGAATGA-CTTTTT-TTACATGTTTCTCAAGGTAGACATTCAATTATAGTCTT-TTTTAATCA
* * * *
10209 AAAATGTAAAAGAAATTGAACATAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAAT
126 AAAATGTAAAA-AAATTCAACTTAAAATC-ATTATGAGATTATAAAACCATTCAAAGCGAGTAAT
** * * * *
10274 AATACTTTTGAAGGAATGAGTGACTATAAAGAGACTTTTCTTGCCAATGAAT-ACTCTTTTATTC
189 AAGGCTTTTGAAGGAATG-GGGACTATAAATAGACTTTTCTT-CCAATGAATGCCT-TTTTCTTC
* ** * * * * *
10338 ATGTTG-CTCAAGGTAGACATTCAATTATAGTCTATTTGAACCAAAAATATAAAAATATTCAACT
251 A-CTTGTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACT
* * *
10402 TAAAATCAATTATTAGTTTATTAA
315 TAAAATCAATTATGAGATTATAAA
* * ** ** * *
10426 ACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCTTAAGTGACTATAAGTAGACTTTTCGTGCCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTC-TTCCA
** * * * * * * *
10491 ATGGTTGGCTTTTGCTTCACA--TTCCCCATGGTAGACACTCAATTATAGCCTTTTTTTTAATCA
65 ATGAATGACTTTT--TTTACATGTTTCTCAAGGTAGACATTCAATTATAG--TCTTTTTTAATCA
* * * * * * *
10554 AAACTGTAAAAAAATTTAA-TTAAAAATTAATTTTGAGATTATAAAACCATTTAAAGTGAGAAAT
126 AAAATGTAAAAAAATTCAACTT-AAAA-TCATTATGAGATTATAAAACCATTCAAAGCGAGTAAT
* * * * *
10618 AAGGATTTTGAAGGCATGAGTGATTATAAATAGACTTTTCTTTCTAATGAATGCCTTTTTCTTCA
189 AAGGCTTTTGAAGGAATG-GGGACTATAAATAGACTTTTC-TTCCAATGAATGCCTTTTTCTTCA
*
10683 CTTGTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAAATTA
252 CTTGTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTA
* * *
10748 AAATCAGTTATTAGTTTATAAA
317 AAATCAATTATGAGATTATAAA
* * * * * * *
10770 ACC-TTCTCAAGCGAGTGATAAGACTTTT-AATGGAATGAGAGATTATAAATGGACTTTTCTTCC
1 ACCATT-TAAAGCGAGTAATAAGGCTTTTGAA-GGAATGGGTGACTATAAATAGACTTTTCTTCC
*
10833 AAATGAATGACTTTTTTTACATGTTTCTCAAGGTCAG-CATTCAATGATAGT-TTTTTTAAT-AA
64 -AATGAATGACTTTTTTTACATGTTTCTCAAGGT-AGACATTCAATTATAGTCTTTTTTAATCAA
* * *
10895 AAATGTAAAAAAATTTAACTTAAAATCATTGAT-ACAATTATAAAACCATTCAAAGCAAGTAATA
127 AAATGTAAAAAAATTCAACTTAAAATCATT-ATGA-GATTATAAAACCATTCAAAGCGAGTAATA
* * * *
10959 AGGTTTTTGAAGGAATGAGGGACTATAAATAGACTTCTCTTACCAATGAATACTTTTTTCTTCA-
190 AGGCTTTTGAAGGAATG-GGGACTATAAATAGACTTTTCTT-CCAATGAATGCCTTTTTCTTCAC
* * * * * * *
11023 TATTTC-TCATGGTAGACATTCAATTGTAATCTGTTTAAACCAAAATAT-AAAAAAAATTGAACA
253 T-TGTCTTGA-GGTAGACATTCAATTATAATCTGTTTTAACCAAAA-ATGTAAAAAAATTCAACT
* * *
11086 CAAAATCAATTTTGAGATAATAAA
315 TAAAATCAATTATGAGATTATAAA
* * * *
11110 ACTATTTAAAGTGAGTAATAAGGCTTTTCAAGGAATGGGTGACTATAAATAGAGTTTTCTTCGCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTC-CA
** * * * *
11175 ATGAATGTGTTTTTTT-CATGTTTTTCGAGGTAAACATTCAATTATAGTCTGTTTTAA-CAAAAA
65 ATGAATGACTTTTTTTACATGTTTCTCAAGGTAGACATTCAATTATAGTCTTTTTTAATC--AAA
* * * *
11238 AATATAAAAAAATTCAACTTAAAATCAATTATGATATTATAAAACCATTTC-AAGTGAATAATAA
128 AATGTAAAAAAATTCAACTTAAAATC-ATTATGAGATTATAAAACCA-TTCAAAGCGAGTAATAA
* * ** * *
11302 GGCTTTTGAAGGAATGGGTGCCTATAAATCGACTTTTCTTCCAAATGAATGGATTTCTCTACA-T
191 GGCTTTTGAAGGAATGGG-GACTATAAATAGACTTTTCTTCC-AATGAATGCCTTTTTCTTCACT
* * ** * * * ** *
11366 GTTTTTTGAGAAAGGCATTCAATTATAGTCTATTTTAATGAAAAATGT-AAAAAACTCAACTTAA
254 -TGTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAA
* *
11430 AATCAATAATGAGATTATAAC
318 AATCAATTATGAGATTATAAA
* * * * *
11451 GCCATTTAAAGGGAGTAATAAGGCTTTTGAAGGAATGGGTGATTAT-AATGGACCTTTCTTACCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTT-CCA
* * *
11515 ATGAATGCCTTTTCTTTACA--TTTCAT-GAGGTAGACATTCAATTATTA-TCTGTTTTAATCAA
65 ATGAATGACTTTT-TTTACATGTTTC-TCAAGGTAGACATTCAATTA-TAGTCTTTTTTAATCAA
* * * * * *
11576 AAATGTAAAAAAATTCAAATTCAAATTAGTTATTAGTTTATAAAACC-TTCTAAAGTGAGTAATA
127 AAATGTAAAAAAATTCAACTTAAAATCA-TTATGAGATTATAAAACCATTC-AAAGCGAGTAATA
* * *
11640 AGGCTTTTGATA-GAATGGAAGACTATAAATATG-CTTTTCTTCTAAATGAATGCCTCTTT-TT-
190 AGGCTTTTGA-AGGAATGG-GGACTATAAATA-GACTTTTCTTC-CAATGAATGCCTTTTTCTTC
* * * * * **
11701 ACATGTTTCCTGAGGTCAG-CATGCAATGATAATTTGTTTTAATGAAAAATGTAAAACAAATT-A
251 AC-T-TGTCTTGAGGT-AGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAA-AAATTCA
*
11764 ACTTAAAATCAATTATGCGATTATAAA
312 ACTTAAAATCAATTATGAGATTATAAA
* *
11791 ACTATTTTAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATCA-ACTTTTCTTCCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-AGACTTTTCTTCC-
** * ** * * * * *
11855 AATGAATGGGTTTCTCAACATGTTT-TCTGAGGAAGGCATTCAATTATAGTCTGTTTTAATGAAA
64 AATGAATGACTTTTTTTACATGTTTCTC-AAGGTAGACATTCAATTATAGTCTTTTTTAATCAAA
* ********* * *
11919 CATGT-AAAAAATTCAACTTAAANNNNNNNNNNAGATTATAAAACCATTTAAAGCGAGCAATAAG
128 AATGTAAAAAAATTCAACTTAAA-ATCATTATGAGATTATAAAACCATTCAAAGCGAGTAATAAG
* * **
11983 GCTTTTGAAGGAATGGGCGACTATAAATGGACCTTTCTTGCCAATGAATATC-TTTTCTTCACAT
192 GCTTTTGAAGGAATGGG-GACTATAAATAGACTTTTCTT-CCAATGAATGCCTTTTTCTTCAC-T
* * * * * * * *
12047 T-TCATGAGATAGACATTTAATTATTATCTATTTTAACAAAAAATGTAAAAACATTCAACTTAAN
254 TGTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAA
*************
12111 NNNNNNNNNNNNNTTATAAA
319 ATCAATTATGAGATTATAAA
* * * * *
12131 ACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAGATGGGCTTTTCTTGTCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTT-CCA
** ********** * *
12196 ATGAAT-ACCTTTTTCTT-CATGTTTCTTGAGGTANNNNNNNNNNTATAATCTATTTTAA-CTAA
65 ATGAATGA-CTTTTT-TTACATGTTTCTCAAGGTAGACATTCAATTATAGTCTTTTTTAATC-AA
* * * * *
12258 AAATGTTAAAAACTTAAACATAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
127 AAATGTAAAAAAATTCAACTTAAAATC-ATTATGAGATTATAAAACCATTCAAAGCGAGTAATAA
12323 GG
191 GG
12325 NNNNNNNNNN
Statistics
Matches: 1781, Mismatches: 360, Indels: 198
0.76 0.15 0.08
Matches are distributed among these distances:
336 1 0.00
337 91 0.05
338 35 0.02
339 255 0.14
340 523 0.29
341 261 0.15
342 188 0.11
343 159 0.09
344 237 0.13
345 29 0.02
346 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (338 bp):
ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTCCAA
TGAATGACTTTTTTTACATGTTTCTCAAGGTAGACATTCAATTATAGTCTTTTTTAATCAAAAAT
GTAAAAAAATTCAACTTAAAATCATTATGAGATTATAAAACCATTCAAAGCGAGTAATAAGGCTT
TTGAAGGAATGGGGACTATAAATAGACTTTTCTTCCAATGAATGCCTTTTTCTTCACTTGTCTTG
AGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATT
ATGAGATTATAAA
Found at i:11681 original size:510 final size:510
Alignment explanation
Indices: 9746--12323 Score: 2123
Period size: 511 Copynumber: 5.0 Consensus size: 510
9736 NNNNNNNNNN
* * * * * * * *
9746 ACCATTTAAAGTGGGTAATAAGGCTTTTGAAGGAATTG-GTGACTATAAATAGACCTTTCTTGCT
1 ACCATTTCAAGCGAGTAATAAGACTTTTGAAGGAA-TGAGTGACTATAAATCGACTTTTCTTCCA
* * * * * * * * * **
9810 AATGAATAAATTTTTCTTCATGTTTCACAAGGTAA-ACATT-AATTATAATCTGTTTCAACCAAA
65 AATGAATGACTTTCTCTACATGTTTCTCAAGG-AAGGCATTCAATTATAGTCTATTTTAATGAAA
********** ** **
9873 AATGTAAAAACATTCAACTTNNNNNNNNNNATGAGATTATAAAAATATTTAAAATAAGTAATAAG
129 AATGTAAAAA-ATTCAACTTAAAATCAATAAT-AGATTATAAAACCATTTAAAGCAAGTAATAAG
** * * * * **
9938 GCTTTTGAAGGAATGGGAAACTATAAATGGACTTTTCTT-CTCAATAAATGGCTTTTTCTACATG
192 GCTTTTGAAGGAATGGGTGACTATAAATGGACCTTTCTTAC-CAATGAAT-GCCTTTTCTTCACA
** * * * * *
10002 TTTCCCGA--T-G-CATTCAATT-CTAGTTTGTTTTAATGAAAATTGTAAAAAAATTCAACTTAA
255 TTTCATGAGGTAGACATTCAATTATTA-TCTGTTTTAATCAAAAATGTAAAAAAATTCAAATTAA
* * * * *
10062 AATCAAGTATGAGATTATAAAACCATTTAAAGTGAGTGATAAGGCTTTCGAAGGAATGGATGACT
319 AATTAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACT
* * * * * *
10127 ATAGAAT-GACTTTTCTTACCAATGAATACCTTTTTCTTCATGTTTCTCAAGGTAGACAATCATT
384 ATA-AATAGACTTTTCTT-CCAATGAATGCCTTTTTCTTCATGTTTTTCGAGGTAAACATTCAAT
* * * *
10191 TATAATTTGTTTTAACCAAAAATGTAAAAGAAATTGAACATAAAATCAATTATGAGATTATAAA
447 TATAATCTGTTTTAACCAAAAATGTAAAACAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * **
10255 ATCATTTAAAGCGAGTAATAATACTTTTGAAGGAATGAGTGACTATAAAGAGACTTTTCTTGCC-
1 ACCATTTCAAGCGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATCGACTTTTCTT-CCA
* * * * * * * **
10319 AATGAAT-ACTCTTTTATTCATGTTGCTCAAGGTAGACATTCAATTATAGTCTATTTGAACCAAA
65 AATGAATGACT-TTCTCTACATGTTTCTCAAGGAAGGCATTCAATTATAGTCTATTTTAATGAAA
* * * *
10383 AATATAAAAATATTCAACTTAAAATCAATTATTAGTTTATTAAACCATTTAAAGCAAGTAATAAG
129 AATGTAAAAA-ATTCAACTTAAAATCAA-TAATAGATTATAAAACCATTTAAAGCAAGTAATAAG
* ** ** * * * * * ** *
10448 GCTTTCGAAGGCTTAAGTGACTATAAGTAGACTTTTCGTGCCAATGGTTGGCTTTTGCTTCACAT
192 GCTTTTGAAGGAATGGGTGACTATAAATGGACCTTTCTTACCAATGAATGCCTTTT-CTTCACAT
* * * * * *
10513 TCCCCAT--GGTAGACACTCAATTA-TAGCCTTTTTTTTAATCAAAACTGTAAAAAAATT-TAAT
256 T--TCATGAGGTAGACATTCAATTATTA---TCTGTTTTAATCAAAAATGTAAAAAAATTCAAAT
* * *
10574 TAAAAATTAATTTTGAGATTATAAAACCATTTAAAGTGAGAAATAAGGATTTTGAAGGCAT-GAG
316 T-AAAATTAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGA-
* * * *
10638 TGATTATAAATAGACTTTTCTTTCTAATGAATGCCTTTTTCTTCACT-TGTCTT-GAGGTAGACA
379 TGACTATAAATAGACTTTTC-TTCCAATGAATGCCTTTTTCTTCA-TGT-TTTTCGAGGTAAACA
* * * *
10701 TTCAATTATAATCTGTTTTAACCAAAAATGTAAAA-AAATTCAAATTAAAATCAGTTATTAGTTT
441 TTCAATTATAATCTGTTTTAACCAAAAATGTAAAACAAATTCAACTTAAAATCAATTATGAGATT
10765 ATAAA
506 ATAAA
* * * *
10770 ACC-TTCTCAAGCGAGTGATAAGACTTTT-AATGGAATGAGAGATTATAAATGGACTTTTCTTCC
1 ACCATT-TCAAGCGAGTAATAAGACTTTTGAA-GGAATGAGTGACTATAAATCGACTTTTCTTCC
* * * * *
10833 AAATGAATGACTTTTTTTACATGTTTCTCAAGGTCA-GCATTCAATGATAGT-TTTTTTAAT-AA
64 AAATGAATGACTTTCTCTACATGTTTCTCAAGG-AAGGCATTCAATTATAGTCTATTTTAATGAA
* * * * *
10895 AAATGTAAAAAAATTTAACTTAAAATCATTGATACAATTATAAAACCATTCAAAGCAAGTAATAA
128 AAATGT-AAAAAATTCAACTTAAAATCAATAATA-GATTATAAAACCATTTAAAGCAAGTAATAA
* * * *
10960 GGTTTTTGAAGGAATGAGG-GACTATAAATAGA-CTTCTCTTACCAATGAATACTTTTTTCTTCA
191 GGCTTTTGAAGGAATG-GGTGACTATAAATGGACCTT-TCTTACCAATGAATGC-CTTTTCTTCA
* * * * * * * *
11023 TATTTC-TCATGGTAGACATTCAATTGTAATCTGTTTAAACCAAAATAT-AAAAAAAATTGAACA
253 CATTTCATGA-GGTAGACATTCAATTATTATCTGTTTTAATCAAAA-ATGTAAAAAAATTCAA-A
* * * * * *
11086 -CAAAATCAATTTTGAGATAATAAAACTATTTAAAGTGAGTAATAAGGCTTTTCAAGGAATGGGT
315 TTAAAATTAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGAT
* **
11150 GACTATAAATAGAGTTTTCTTCGCAATGAATGTGTTTTT-TTCATGTTTTTCGAGGTAAACATTC
380 GACTATAAATAGACTTTTCTTC-CAATGAATGCCTTTTTCTTCATGTTTTTCGAGGTAAACATTC
* * * *
11214 AATTATAGTCTGTTTTAACAAAAAAATATAAAA-AAATTCAACTTAAAATCAATTATGATATTAT
444 AATTATAATCTGTTTTAAC-CAAAAATGTAAAACAAATTCAACTTAAAATCAATTATGAGATTAT
11278 AAA
508 AAA
* * * * *
11281 ACCATTTCAAGTGAATAATAAGGCTTTTGAAGGAATGGGTGCCTATAAATCGACTTTTCTTCCAA
1 ACCATTTCAAGCGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATCGACTTTTCTTCCAA
* ** *
11346 ATGAATGGA-TTTCTCTACATGTTTTTTGAGAAAGGCATTCAATTATAGTCTATTTTAATGAAAA
66 ATGAAT-GACTTTCTCTACATGTTTCTCAAGGAAGGCATTCAATTATAGTCTATTTTAATGAAAA
* ** **
11410 ATGTAAAAAACTCAACTTAAAATCAATAATGAGATTATAACGCCATTTAAAGGGAGTAATAAGGC
130 ATGTAAAAAATTCAACTTAAAATCAATAAT-AGATTATAAAACCATTTAAAGCAAGTAATAAGGC
* *
11475 TTTTGAAGGAATGGGTGATTAT-AATGGACCTTTCTTACCAATGAATGCCTTTTCTTTACATTTC
194 TTTTGAAGGAATGGGTGACTATAAATGGACCTTTCTTACCAATGAATGCCTTTTCTTCACATTTC
*
11539 ATGAGGTAGACATTCAATTATTATCTGTTTTAATCAAAAATGTAAAAAAATTCAAATTCAAATTA
259 ATGAGGTAGACATTCAATTATTATCTGTTTTAATCAAAAATGTAAAAAAATTCAAATTAAAATTA
* * *
11604 GTTATT-AGTTTATAAAACC-TTCTAAAGTGAGTAATAAGGCTTTTGATA-GAATGGAAGACTAT
324 ATT-TTGAGATTATAAAACCATT-TAAAGTGAGTAATAAGGCTTTTGA-AGGAATGGATGACTAT
* * * * * *
11666 AAATATG-CTTTTCTTCTAAATGAATGCCTCTTTT-TACATG-TTTCCTGAGGTCAGCATGCAAT
386 AAATA-GACTTTTCTTC-CAATGAATGCCT-TTTTCTTCATGTTTTTC-GAGGTAAACATTCAAT
* * ** *
11728 GATAATTTGTTTTAATGAAAAATGTAAAACAAATT-AACTTAAAATCAATTATGCGATTATAAA
447 TATAATCTGTTTTAACCAAAAATGTAAAACAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * * *
11791 ACTATTTTAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATCAACTTTTCTTCCAA
1 ACCATTTCAAGCGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATCGACTTTTCTTCCAA
** * * * *
11856 ATGAATGGGTTTCTCAACATGTTT-TCTGAGGAAGGCATTCAATTATAGTCTGTTTTAATGAAAC
66 ATGAATGACTTTCTCTACATGTTTCTC-AAGGAAGGCATTCAATTATAGTCTATTTTAATGAAAA
********* * *
11920 ATGTAAAAAATTCAACTTAAANNNNNNNNNNAGATTATAAAACCATTTAAAGCGAGCAATAAGGC
130 ATGTAAAAAATTCAACTTAAA-ATCAATAATAGATTATAAAACCATTTAAAGCAAGTAATAAGGC
* * **
11985 TTTTGAAGGAATGGGCGACTATAAATGGACCTTTCTTGCCAATGAATATCTTTTCTTCACATTTC
194 TTTTGAAGGAATGGGTGACTATAAATGGACCTTTCTTACCAATGAATGCCTTTTCTTCACATTTC
* * * * * ****
12050 ATGAGATAGACATTTAATTATTATCTATTTTAA-CAAAAAATGTAAAAACATTCAACTTAANNNN
259 ATGAGGTAGACATTCAATTATTATCTGTTTTAATC-AAAAATGTAAAAAAATTCAAATTAAAATT
********** ** * *
12114 NNNNNNNNNNTTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAG
323 AATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAA
* * * * **********
12179 ATGGGCTTTTCTTGTCAATGAATACCTTTTTCTTCATGTTTCTT-GAGGTANNNNNNNNNNTATA
388 ATAGACTTTTCTT-CCAATGAATGCCTTTTTCTTCATGTTT-TTCGAGGTAAACATTCAATTATA
* * * * * *
12243 ATCTATTTTAACTAAAAATGTTAAA-AACTTAAACATAAAATCAATTATGAGATTATAAA
451 ATCTGTTTTAACCAAAAATGTAAAACAAATTCAACTTAAAATCAATTATGAGATTATAAA
*
12302 ACCATTTAAAGCGAGTAATAAG
1 ACCATTTCAAGCGAGTAATAAG
12324 GNNNNNNNNN
Statistics
Matches: 1674, Mismatches: 317, Indels: 154
0.78 0.15 0.07
Matches are distributed among these distances:
508 5 0.00
509 97 0.06
510 509 0.30
511 534 0.32
512 97 0.06
513 115 0.07
514 33 0.02
515 121 0.07
516 158 0.09
517 5 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (510 bp):
ACCATTTCAAGCGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATCGACTTTTCTTCCAA
ATGAATGACTTTCTCTACATGTTTCTCAAGGAAGGCATTCAATTATAGTCTATTTTAATGAAAAA
TGTAAAAAATTCAACTTAAAATCAATAATAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTT
TTGAAGGAATGGGTGACTATAAATGGACCTTTCTTACCAATGAATGCCTTTTCTTCACATTTCAT
GAGGTAGACATTCAATTATTATCTGTTTTAATCAAAAATGTAAAAAAATTCAAATTAAAATTAAT
TTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATA
GACTTTTCTTCCAATGAATGCCTTTTTCTTCATGTTTTTCGAGGTAAACATTCAATTATAATCTG
TTTTAACCAAAAATGTAAAACAAATTCAACTTAAAATCAATTATGAGATTATAAA
Found at i:14649 original size:170 final size:171
Alignment explanation
Indices: 14076--15790 Score: 1303
Period size: 171 Copynumber: 10.0 Consensus size: 171
14066 NNNNNNNNNN
* * * * *
14076 ATAATTGATTTTAAGTTGAA-TTTTTTACATTTTTTACTAAAACAGACTATAATTGAATGCCTTC
1 ATAATTGATTTTAAGTTAAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGTCTAC
* * ** * * ** * *
14140 TT-TAGAAAACATGT-AGAGAAACCCATTCGTTTGGAAGAAAAGTTGATTTATAATCACCTATTC
66 TTAT-GAGAA-ATGTAAGAAAAAAGCATTCATTGGGAAGAAAAGTCCATTTATAGTCACCCATTC
* * * * * *
14203 TTTTAAAAGCCTTATTACGCGCTTGAAATAGTTTTATAATATC
129 CTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTC
* * * * * * *
14246 ATACTTAATTTTATGTTTAATTTTTTTATATTTTTTTATTAAAACATACTATAATTGAATGTCTA
1 ATAATTGATTTTAAGTTAAATTTTTTTACA-TTTTTGATTAAAACAGACTATAATTGAATGTCTA
* * * ** * *
14311 CCT-CGAGAAACACG-AAGAAAAACA-CATTCATTGACAAGAAAACTCTATTTATAGTCACCCAT
65 CTTATGAG-AA-ATGTAAGAAAAA-AGCATTCATTGGGAAGAAAAGTCCATTTATAGTCACCCAT
* ** * *
14373 TCTTTGGAAAGCCTTATTACTCACTTTAAATGGTTTTATTATCTC
127 TCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTC
* * * * * * * * *
14418 AAAATTAATTTTATGTTCAATTTTTTTTACA-TGTTGGTTTAAACATATTATAATTGAATGTCTA
1 ATAATTGATTTTAAGTT-AAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGTCTA
* *
14482 -TTATGAGAAATGTGAAGAAAAAAGTATTCATTGGGAAGAAAAGT-AATTTATAGTC-CCCAATT
65 CTTATGAGAAATGT-AAGAAAAAAGCATTCATTGGGAAGAAAAGTCCATTTATAGTCACCC-ATT
* * * * * * *
14544 CCTTCGAAAGCCTTATTATTCACTTTGAATAGATTTATAATCGC
128 CCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTC
* * * * *
14588 ATAATTGATTTTAAGTTAAATTGTTTTACATTTTTCATTAAAACAAACTATCATTGAATGTCGAC
1 ATAATTGATTTTAAGTTAAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGTCTA-
* * * * * *
14653 CTTAGGA-AACATGTAAG-AAAAGGCATTCATTTGGAAGAAAA-ACCTATTTATAGTCTCTCATT
65 CTTATGAGAA-ATGTAAGAAAAAAGCATTCATTGGGAAGAAAAGTCC-ATTTATAGTCACCCATT
* * * * *
14715 CCATCAAAAGCCTTATCACTCACTTTAGAA-GGTTTTATAAACTA
128 CCTTCAAAAGCCTTATTACTCGCTTTA-AATGGTTTTATAATCTC
* * * * * * *
14759 ATTACTGATTTTAATTTGAATTTTTTTACATTTTTGATTAAAACATA-TAAAAATTAAATGTCTA
1 ATAATTGATTTTAAGTTAAATTTTTTTACATTTTTGATTAAAACAGACT-ATAATTGAATGTCTA
* * * * *
14823 CCTCAT--GAAATGTAA-AGAAAAGACATTCATTGGCAAGAAAGGTCCATTTATAATCACCCATT
65 -CTTATGAGAAATGTAAGAAAAAAG-CATTCATTGGGAAGAAAAGTCCATTTATAGTCACCCATT
14885 CCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTC
128 CCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTC
** * * * * * * *
14929 ATTGTTGATTTTAAGTT-GAGTTTTTTACATTTTTCATTAAAATAGATTATAATTGAATGCCTTC
1 ATAATTGATTTTAAGTTAAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGTC-TA
*** * * ** * * *
14993 CCCCT-AAAACATGTAA-AGAAATTCATTCATTTGGAAGAAAAGTCGATTTACAGTCACCCATTC
65 CTTATGAGAA-ATGTAAGAAAAAAGCATTCATTGGGAAGAAAAGTCCATTTATAGTCACCCATTC
* * * *
15056 CTTCAAAAGCCTTATTACTCACTTGAAATGGTTTTACAATATC
129 CTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTC
* * *
15099 ATAAGTGATTTTAAGTTAAATTTTTTTATATTCTTT-AGTTAAAATAGACTATAATTGAATGTCT
1 ATAATTGATTTTAAGTTAAATTTTTTTACATT-TTTGA-TTAAAACAGACTATAATTGAATGTCT
* * * *
15163 ACCT-TGAGAAACATG-AAGAAAAACA-TATTCATTGGCAAGATAAAGTCTATTTATAGTCACCC
64 ACTTATGAG-AA-ATGTAAGAAAAA-AGCATTCATTGGGAAGA-AAAGTCCATTTATAGTCACCC
** * *
15225 ATTCCTTCAACAAGTAATAATTACTCGCTTTAAATGATTTTATAATCTC
125 ATTCCTTCAA-AAG-CCTTATTACTCGCTTTAAATGGTTTTATAATCTC
* * * * * *
15274 ATAATTGATTTTATGTTCAATATTTTTTACACTTTTGGTTAAAAC-GAATTATAAATGAATGTCT
1 ATAATTGATTTTAAGTTAAAT-TTTTTTACATTTTTGATTAAAACAG-ACTATAATTGAATGTCT
* * * ***** * *
15338 ACCT-TGAGAAACGTAAAGAAAAAGGCATTCATTCATTCGTTTAAA-TCC-TTCTATAGTCATCC
64 ACTTATGAGAAATGT-AAGAAAAAAGCATTCATTGGGAAG--AAAAGTCCATT-TATAGTCACCC
* *
15400 ATTCGTTCAAAAGCCTTATCACTCGCTTTAAATGG-TTTATAATCTC
125 ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTC
* * * * *
15446 ATGATTGATTTTATGTTTAATTTTTTTACAATTTTT-ATTAAAACAAACTAGAATTGAATG-C--
1 ATAATTGATTTTAAGTTAAATTTTTTTAC-ATTTTTGATTAAAACAGACTATAATTGAATGTCTA
* * * * *
15507 CTCAGGACACATGT-AG-AAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTTC-CCCATT
65 CTTATGAGAAATGTAAGAAAAAAG-CATTCATTGGGAAGAAAAGTCCATTTATAG-TCACCCATT
* * **
15569 CCTTCAAAAGTCTTATTACTTGCTTTAAATATTTTTATAATCTC
128 CCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTC
* * * * * * *
15613 ATAATTGATTTTAAGTTGAATGTTTTTACATTTTTGGTTGAAGCAGATTATAATTAAATGTCTAC
1 ATAATTGATTTTAAGTTAAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGTCTA-
* *** * * **
15678 CTTGTGA-AACATG-AAGAAAAATTTATTCATTGGCAAGAAAGGTCCATTTATAGTCACTAATTC
65 CTTATGAGAA-ATGTAAGAAAAAAGCATTCATTGGGAAGAAAAGTCCATTTATAGTCACCCATTC
* *
15741 TTTCAAAAGCCTTATTACCCGCTTTAAATGGTTTTATAATCTC
129 CTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTC
15784 ATAATTG
1 ATAATTG
15791 NNNNNNNNNN
Statistics
Matches: 1230, Mismatches: 250, Indels: 129
0.76 0.16 0.08
Matches are distributed among these distances:
165 3 0.00
166 50 0.04
167 69 0.06
168 2 0.00
169 71 0.06
170 307 0.25
171 310 0.25
172 224 0.18
173 58 0.05
174 11 0.01
175 113 0.09
176 12 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (171 bp):
ATAATTGATTTTAAGTTAAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGTCTAC
TTATGAGAAATGTAAGAAAAAAGCATTCATTGGGAAGAAAAGTCCATTTATAGTCACCCATTCCT
TCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTC
Found at i:14727 original size:341 final size:341
Alignment explanation
Indices: 14076--15790 Score: 1418
Period size: 341 Copynumber: 5.0 Consensus size: 341
14066 NNNNNNNNNN
* * * * * * *
14076 ATAATTGATTTTAAGTTGAA-TTTTTTACATTTTTTACTAAAACAGACTATAATTGAATGCCTTC
1 ATAATTGATTTTATGTTAAATTTTTTTACA-TTTTGATTAAAACATACTATAATTGAATGTCTAC
* * ** * ** * *
14140 T-TTAGAAAACATGT--AGAGAAACCCATTCGTTTGG-AAGAAAAGTTGATTTATAATCACCTAT
65 TCAT-GAGAA-ATGTGAAGA-AAAAACATTC-ATTGGCAAGAAAAGTCCATTTATAGTCACCCAT
* * * * * * * *
14201 TCTTTTAAAAGCCTTATTACGCGCTTGAAATAGTTTTATAATATCATACTTAATTTTATGTTTAA
126 TCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAG-TTAA
* * * * * * *
14266 TTTTTTTATATTTTTTTATTAAAACATACTATAATTGAATGTCTACCTCGAGAAACACG-AAGAA
190 ATTTTTTACA-TTTTTCATTAAAACAAATTATAATTGAATGTCTACCTTGAGAAACATGTAAGAA
** * * **
14330 AAACACATTCA-TTGACAAG-AAAACTCTATTTATAGTCACCCATTCTTTGGAAAGCCTTATTAC
254 AAAGGCATTCATTTG-GAAGAAAAAC-CTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTAC
*
14393 TCACTTTAAATGGTTTTATTATCTC
317 TCACTTTAAATGGTTTTATAATCTC
* * * * * * *
14418 AAAATTAATTTTATGTTCAATTTTTTTTACATGTTGGTTTAAACATATTATAATTGAATGTCTA-
1 ATAATTGATTTTATGTT-AAATTTTTTTACATTTTGATTAAAACATACTATAATTGAATGTCTAC
* * * *
14482 TTATGAGAAATGTGAAGAAAAAAGTATTCATTGGGAAGAAAAGT-AATTTATAGTC-CCCAATTC
65 TCATGAGAAATGTGAAGAAAAAA-CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCC-ATTC
* * * * * *
14545 CTTCGAAAGCCTTATTATTCACTTTGAATAGATTTATAATCGCATAATTGATTTTAAGTTAAATT
128 CTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATT
* * *
14610 GTTTTACATTTTTCATTAAAACAAACTATCATTGAATGTCGACCTT-AGGAAACATGTAAG-AAA
193 -TTTTACATTTTTCATTAAAACAAATTATAATTGAATGTCTACCTTGA-GAAACATGTAAGAAAA
* * * *
14673 AGGCATTCATTTGGAAGAAAAACCTATTTATAGTCTCTCATTCCATCAAAAGCCTTATCACTCAC
256 AGGCATTCATTTGGAAGAAAAACCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCAC
* *
14738 TTTAGAA-GGTTTTATAAACTA
321 TTTA-AATGGTTTTATAATCTC
* * * * *
14759 ATTACTGATTTTAAT-TTGAATTTTTTTACATTTTTGATTAAAACATA-TAAAAATTAAATGTCT
1 ATAATTGATTTT-ATGTTAAATTTTTTTACA-TTTTGATTAAAACATACT-ATAATTGAATGTCT
* * * *
14822 ACCTCAT--GAAATGTAAAGAAAAGACATTCATTGGCAAGAAAGGTCCATTTATAATCACCCATT
63 A-CTCATGAGAAATGTGAAGAAAAAACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATT
* ** * *
14885 CCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATTGTTGATTTTAAGTTGAGT
127 CCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAAT
* * * * * *
14950 TTTTTACATTTTTCATTAAAATAGATTATAATTGAATGCCTTCCCCCT-A-AAACATGTAA-AGA
192 TTTTTACATTTTTCATTAAAACAAATTATAATTGAATGTC-T-ACCTTGAGAAACATGTAAGAAA
** ** * *
15012 AATTCATTCATTTGGAAGAAAAGTCGATTTACAGTCACCCATTCCTTCAAAAGCCTTATTACTCA
255 AAGGCATTCATTTGGAAGAAAAACCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCA
* * *
15077 CTTGAAATGGTTTTACAATATC
320 CTTTAAATGGTTTTATAATCTC
* * * * * *
15099 ATAAGTGATTTTAAGTTAAATTTTTTTATATTCTTTAGTTAAAATAGACTATAATTGAATGTCTA
1 ATAATTGATTTTATGTTAAATTTTTTTACATT-TTGA-TTAAAACATACTATAATTGAATGTCTA
* ** * *
15164 C-CTTGAGAAACATGAAGAAAAACATATTCATTGGCAAGATAAAGTCTATTTATAGTCACCCATT
64 CTCATGAGAAATGTGAAGAAAAA-ACATTCATTGGCAAGA-AAAGTCCATTTATAGTCACCCATT
** * *
15228 CCTTCAACAAGTAATAATTACTCGCTTTAAAT-GATTTTATAATCTCATAATTGATTTTATGTTC
127 CCTTCAA-AAG-CCTTATTACTCGCTTTAAATAG-TTTTATAATCTCATAATTGATTTTAAGTT-
* ** * *
15292 AATATTTTTTACACTTTTGGTTAAAACGAATTATAAATGAATGTCTACCTTGAGAAAC--GTAAA
188 AA-ATTTTTTACATTTTTCATTAAAACAAATTATAATTGAATGTCTACCTTGAGAAACATGT-AA
* *** * * * *
15355 GAAAAAGGCATTCATTCATTCG-TTTAAATCCT-TCTATAGTCATCCATTCGTTCAAAAGCCTTA
251 GAAAAAGGCATTCA-T--TTGGAAGAAAAACCTATTTATAGTCACCCATTCCTTCAAAAGCCTTA
* *
15418 TCACTCGCTTTAAATGG-TTTATAATCTC
313 TTACTCACTTTAAATGGTTTTATAATCTC
* * * * *
15446 ATGATTGATTTTATGTTTAATTTTTTTACAATTTTTATTAAAACAAACTAGAATTGAATG-C--C
1 ATAATTGATTTTATGTTAAATTTTTTTAC-ATTTTGATTAAAACATACTATAATTGAATGTCTAC
* * * *
15508 TCAGGACACATGT--AGAAAAAGCCATTCATTGAG-AAGAAAAGTCCATTTATAGTTC-CCCATT
65 TCATGAGAAATGTGAAGAAAAA-ACATTCATTG-GCAAGAAAAGTCCATTTATAG-TCACCCATT
* * * *
15569 CCTTCAAAAGTCTTATTACTTGCTTTAAATATTTTTATAATCTCATAATTGATTTTAAGTTGAAT
127 CCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAAT
** * * * * *
15634 GTTTTTACATTTTTGGTTGAAGCAGATTATAATTAAATGTCTACCTTGTGAAACATG-AAGAAAA
192 -TTTTTACATTTTTCATTAAAACAAATTATAATTGAATGTCTACCTTGAGAAACATGTAAGAAAA
*** ** ** * *
15698 ATTTATTCA-TTGGCAAGAAAGGTCC-ATTTATAGTCACTAATTCTTTCAAAAGCCTTATTACCC
256 AGGCATTCATTTGG-AAGAAA-AACCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTC
*
15761 GCTTTAAATGGTTTTATAATCTC
319 ACTTTAAATGGTTTTATAATCTC
15784 ATAATTG
1 ATAATTG
15791 NNNNNNNNNN
Statistics
Matches: 1098, Mismatches: 217, Indels: 120
0.77 0.15 0.08
Matches are distributed among these distances:
334 3 0.00
336 2 0.00
337 46 0.04
338 76 0.07
339 51 0.05
340 175 0.16
341 293 0.27
342 148 0.13
343 75 0.07
344 19 0.02
345 49 0.04
346 25 0.02
347 84 0.08
348 45 0.04
349 4 0.00
350 3 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (341 bp):
ATAATTGATTTTATGTTAAATTTTTTTACATTTTGATTAAAACATACTATAATTGAATGTCTACT
CATGAGAAATGTGAAGAAAAAACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTT
CAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTT
TACATTTTTCATTAAAACAAATTATAATTGAATGTCTACCTTGAGAAACATGTAAGAAAAAGGCA
TTCATTTGGAAGAAAAACCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAA
ATGGTTTTATAATCTC
Found at i:16568 original size:171 final size:171
Alignment explanation
Indices: 16197--16742 Score: 514
Period size: 171 Copynumber: 3.2 Consensus size: 171
16187 NNNNNNNATG
* * * * * * * *
16197 AAACCATTTAAAGCGAGTAATTAA-GCTTTTGAAGGAATGAGTGACCATAAATGGACTTTTTTTA
1 AAACCATTTAAAGCGAGTAA-TAAGGCTTATGAAAGAATGGGTGACAATAAGTAGACTTTTCTTG
* * * * *
16261 CTAATGAATAC-TTTTTTTCTCTACG--TGTCATAGGGTAAACATTCAATTATAATTTGTTTTGA
65 CCAATGAATGCATTTTTCT-TC-ACGTTTTTCAT--GGTAAACATTCAATTATAATCTGTTTTGA
* * *
16323 CCAAAAATGTAAAAACAAATTGAAACTGAAATCAATTATAAGATTATA
126 CCAAAAATATAAAAA-AAATTG-AACTAAAATCAATTATGAGATTATA
* *
16371 AAACCATTTAAAGTGAGTAATAAGGCTTATGAAGGAATGGGTGACAATAAGTAGACTTTTCTTGC
1 AAACCATTTAAAGCGAGTAATAAGGCTTATGAAAGAATGGGTGACAATAAGTAGACTTTTCTTGC
* * *
16436 TAAT-AATTGCATTTTTCTTCATGTTTCTTGA-GGTAAACATTCAATTATAATCTGTTTT-ACCA
66 CAATGAA-TGCATTTTTCTTCACGTTT-TTCATGGTAAACATTCAATTATAATCTGTTTTGACC-
*
16498 AAAAATATAAAAAAAATT-AACTTAAAATCAATTATGAGATCATA
128 AAAAATATAAAAAAAATTGAAC-TAAAATCAATTATGAGATTATA
* * * * **********
16542 AAACCTTTTAAAGCGGGTACTAAGGCTTTTGAAAGAATGGGTGACAATAANNNNNNNNNNCTTGC
1 AAACCATTTAAAGCGAGTAATAAGGCTTATGAAAGAATGGGTGACAATAAGTAGACTTTTCTTGC
* * * * *
16607 CAATGAATGCCTTTTTCTTCACGTTTTTCATAGTAGACATTGAATTATAATCTGTTTTGACCAAT
66 CAATGAATGCATTTTTCTTCACGTTTTTCATGGTAAACATTCAATTATAATCTGTTTTGACCAAA
* *
16672 AATATAAAAGAAGATTGAGCCTAAAATCAATTATGAGATTATA
131 AATATAAAA-AAAATTGA-ACTAAAATCAATTATGAGATTATA
* *
16715 AAACCATTTAAAGCAAGCAATAAGGCTT
1 AAACCATTTAAAGCGAGTAATAAGGCTT
16743 TTTCTGTATG
Statistics
Matches: 308, Mismatches: 50, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
170 6 0.02
171 123 0.40
172 18 0.06
173 90 0.29
174 62 0.20
175 7 0.02
176 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.33
Consensus pattern (171 bp):
AAACCATTTAAAGCGAGTAATAAGGCTTATGAAAGAATGGGTGACAATAAGTAGACTTTTCTTGC
CAATGAATGCATTTTTCTTCACGTTTTTCATGGTAAACATTCAATTATAATCTGTTTTGACCAAA
AATATAAAAAAAATTGAACTAAAATCAATTATGAGATTATA
Found at i:18820 original size:171 final size:170
Alignment explanation
Indices: 18530--19224 Score: 540
Period size: 171 Copynumber: 4.1 Consensus size: 170
18520 NNNNNNNNNN
* * * * * *
18530 TATATATGGACTTTTCTTCTCAATGAATAGCTTTTTCTGCATGTTTCCTGAGGCACACATTCAAT
1 TATAAATGGACTTTTCTTCT-AATGAATACCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAAT
* * * * *
18595 TATTGTGTGTTTTAATGAAAAATATAAAAAAATTCAATTTAAAATCGATTATGAGATTAAAAAAT
65 TATAGTCTGTTTTAATGAAAAATATAAAAAAATTCAAATTAAAATCAATTATGAGATTAAAAAAG
* * * * * *
18660 CATTTAAAGGGAGTAATAAGGCTTTTGCAGGAATGGGTGAC
130 AATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATGAGAGAC
* *
18701 TATAAATGGACTTTTCTTACTAATAAATACCTTTTTCTTCACT-TTTCTTAAGGTAGACATTCAA
1 TATAAATGGACTTTTCTT-CTAATGAATACCTTTTTCTTCA-TGTTTCTTGAGGTAGACATTCAA
* * * *
18765 TTATAATCTGTTTTAATGAATAATATAAAAAAATTGAAATTAAAATCAATTATGAGATTATAAAA
64 TTATAGTCTGTTTTAATGAAAAATATAAAAAAATTCAAATTAAAATCAATTATGAGATTAAAAAA
*
18830 GAATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATGAGAGAT
129 GAATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATGAGAGAC
** * * * * * *
18872 TATAAATATACTTTTCCTGCCAACGAATGCTTTTTTCTTTATGTTTCTTGAGGTAGACATTCAAT
1 TATAAATGGACTTTT-CTTCTAATGAATACCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAAT
*********** * * ** *
18937 TATAGTCTGNNNNNNNNNNNNAA-GTAAAACAATTCAACCTAAAATC-ATATATGAGATTATAAA
65 TATAGTCTG-TTTTAATGAAAAATATAAAAAAATTCAAATTAAAATCAAT-TATGAGATTAAAAA
** * * * *
19000 ACCATTTAAAGCTAGTAATAAGGTTTTTGAAAGAATGAGAGAC
128 AGAATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATGAGAGAC
* * * * * *
19043 TATAAAAGGACTTTT-TCTCAAAATGAATGA--TTTTT-TTACACGTTTCGTGAGGCAAACATTC
1 TATAAATGGACTTTTCT-TC-TAATGAAT-ACCTTTTTCTT-CATGTTTCTTGAGGTAGACATTC
*********** * *
19104 AATTATAGTCTGTTTTAATGAAAAATGNNNNNNNNNNCAACTTAAAATCAATTATGAGATTATAA
62 AATTATAGTCTGTTTTAATGAAAAATATAAAAAAATTCAAATTAAAATCAATTATGAGATTAAAA
** * * *
19169 AACTATTTAAAGGCGGGTAATAAGGCTTTTGAAGGAATGAGTGAC
127 AAGAATTTAAA-GCGAGTAATAAGGCTTTCGAAGGAATGAGAGAC
19214 TATAAATGGAC
1 TATAAATGGAC
19225 CTTTNNNNNN
Statistics
Matches: 412, Mismatches: 99, Indels: 26
0.77 0.18 0.05
Matches are distributed among these distances:
169 5 0.01
170 74 0.18
171 326 0.79
172 7 0.02
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.34
Consensus pattern (170 bp):
TATAAATGGACTTTTCTTCTAATGAATACCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATT
ATAGTCTGTTTTAATGAAAAATATAAAAAAATTCAAATTAAAATCAATTATGAGATTAAAAAAGA
ATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATGAGAGAC
Found at i:21215 original size:170 final size:169
Alignment explanation
Indices: 20355--21387 Score: 545
Period size: 170 Copynumber: 6.0 Consensus size: 169
20345 NNNNNNNNNN
* * ** *
20355 TTTTTCT-TCACGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAATGAATAATGTACAAA
1 TTTTTCTAT-ACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGT--AAA
* * ********* * *
20419 AAATTGAACCTAAAATCAATTATGAGATTANNNNNNNNNNT-AAAGCGAGTAATAATGCTTTTGA
63 AAATTCAACTTAAAATCAATTATGAGATTA-TAAAACCATTCAAAACGAGTAATAAGGCTTTTGA
* * **
20483 AGGAATGGGAGACTATAAATATACTTTTCTTGCCAATGAATG-C
127 AAGAAT-GGTGACTATAAATGGACTTTTCTTGCCAATGAATGTC
* ********** * *
20526 TTTTTTCTTTANNNNNNNNNNGGTAGACATTCAGTTATAGTCTGTTTTCACCAAAAAA-GTAAAA
1 -TTTTTCTATACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTT-AACAAAAAATGTAAAA
* * * * * * **********
20590 CAATTCAACCTAGAATC-ATATATAAGATTATAAAACTATTTAAAGCGAGTAATNNNNNNNNNNA
64 -AATTCAACTTAAAATCAAT-TATGAGATTATAAAACCATTCAAAACGAGTAATAAGGCTTTTGA
* * * *
20654 AGGAATGGATGACTATAAATGGACTTTTGTTCCCAATGAATGGC
127 AAGAATGG-TGACTATAAATGGACTTTTCTTGCCAATGAATGTC
* * * *
20698 TTTTTCTACATGTTTC-CTGAGGCAGACATTCAATTATAGTCTGTTTTAACAAAGAATGTAAAAA
1 TTTTTCTATACGTTTCTC-GAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAA
********** * * *
20762 ATTCAACTTAAAATCAATTATNNNNNNNNNNAACCATTTAAAATGAGTAATAAGGCTTTTGTAAG
65 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTCAAAACGAGTAATAAGGCTTTTGAAAG
* * **
20827 AATTGGTGACTATAAATGGACTTTGCTTGCCAAAGAACATC
130 AA-TGGTGACTATAAATGGACTTTTCTTGCCAATGAATGTC
* * * * * * *
20868 TTTCTCT-TCACATTTCTCGAGGTAGACATTCAATTATAAT-TTTTTTAACCAATAATTTAAAAA
1 TTTTTCTAT-ACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAA
* * * * * * *
20931 ATTTTGAACCTAAAATCAATTATGAGATTATAAAATCATTGATAGCGACTAATAAGGCTTTTGAA
65 A--TTCAACTTAAAATCAATTATGAGATTATAAAACCATTCAAAACGAGTAATAAGGCTTTTGAA
* ** * * *** * *
20996 GGAATGAGCAAATATAAATGGACTTTTGTTATAAATAAATGTG
128 AGAATG-GTGACTATAAATGGACTTTTCTTGCCAATGAATGTC
* ** *
21039 TTTTTCTATACGTTTCTCGAGATAGGTATTCAATTGTAGTCTGTTTTAACAAAAAATGTAAAAAA
1 TTTTTCTATACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAA
* * * *
21104 CTCCACTTAAATTCAATTGTGAGATTATAAAACCATTCAAAACGAGTAATAAGGCTTTTGAAAGA
66 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTCAAAACGAGTAATAAGGCTTTTGAAAGA
* *
21169 ATAGGTGACTATAGATAGACTTTTCTTGCCAATGAATGTC
131 AT-GGTGACTATAAATGGACTTTTCTTGCCAATGAATGTC
* ** * * * * * * *
21209 TTTTTCTTTATTTTTCAT-GAGGTAAATATTTAAATATAGTCTATTTTAACTAAAAATATAAAAA
1 TTTTTCTATACGTTTC-TCGAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGT-AAAA
********** * * * * * *
21273 AGANNNNNNNNNNAATCAATTATGACATTATAAAACTATTTAAAGCGAGTAATAAGGCATTGGAA
64 A-ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTCAAAACGAGTAATAAGGCTTTTGAA
* * * **
21338 GGAATGGGTGACTATAATTGGACTTTTCTTACCAATGAATACC
128 AGAAT-GGTGACTATAAATGGACTTTTCTTGCCAATGAATGTC
21381 TTTTTCT
1 TTTTTCT
21388 TCANNNNNNN
Statistics
Matches: 632, Mismatches: 207, Indels: 44
0.72 0.23 0.05
Matches are distributed among these distances:
169 20 0.03
170 240 0.38
171 222 0.35
172 144 0.23
173 6 0.01
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.34
Consensus pattern (169 bp):
TTTTTCTATACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAA
TTCAACTTAAAATCAATTATGAGATTATAAAACCATTCAAAACGAGTAATAAGGCTTTTGAAAGA
ATGGTGACTATAAATGGACTTTTCTTGCCAATGAATGTC
Done.