Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402947.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_608.0, 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: 29998
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.23
Warning! 11315 characters in sequence are not A, C, G, or T
Found at i:1140 original size:171 final size:172
Alignment explanation
Indices: 1--1388 Score: 806
Period size: 171 Copynumber: 8.1 Consensus size: 172
* * * * * *
1 AAAAAATTTAACTTAAAATTAATTATGAGTTTATAAAACCATTTAAAGCGAGTAGTAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTT
* * * ********
66 AAAGGAATGGGTGACCT-TAAATGGACTTTTCTTCTCAATGAATAGCTTTTTTTGCNNNNNNNNN
66 AAAGGAATGGGTGA-CTATAAATGGACTTTTTTTCTCAATGAATAGTTTTTTTTTC-ACGTTTCT
* * * * * *
130 NAGGT--AGACATTCAATTATAGTCTGTTTTAACCAAAATTTTAA
129 CAAGTACAGGCATTCAATTATAGTCTGTTTTAACTAAAAATGT-A
* *
173 AAAAAATT-AACTTAAAATCAATTTTG-GCATTATAAAACAATTTAAAGCGAGTAATAAGGCTTT
1 AAAAAATTCAACTTAAAATCAATTATGAG-ATTATAAAACAATTTAAAGTGAGTAATAAGGCTTT
********** * * *
236 NNNNNNNNNNGGTGACTATAAATGGACATTTCTTGC-CAATGAAT-GCTTTTTTTTT-ATGTTTC
65 TAAAGGAATGGGTGACTATAAATGGAC-TTTTTTTCTCAATGAATAG-TTTTTTTTTCACGTTTC
* * * * * * *
298 TCGAGGT--AGACATTCGATTACAGTCTGTTTTAGCCAAAAATATA
128 TC-AAGTACAGGCATTCAATTATAGTCTGTTTTAACTAAAAATGTA
********** * *
342 AAAAAATTCAACTTAAAANNNNNNNNNNGATTATAAAACAATTTAAAGTGAGTAATAAGCCTATT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTT
* * * ** * * *
407 GAAGGAATGAGTGACTAGAAATGGACTTTTCGTGTCAACGAAT-GTGTTTTTCTTCACGTTTCTC
66 AAAGGAATGGGTGACTATAAATGGACTTTTTTTCTCAATGAATAGT-TTTTTTTTCACGTTTCT-
** ********** *
471 CAAGTA-A-AAATTCAATTATAGTCTGNNNNNNNNNNAAATATA
129 CAAGTACAGGCATTCAATTATAGTCTGTTTTAACTAAAAATGTA
* *** *
513 AAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACAATTTAAAACAAATAATAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTT
* ** * *
578 TAAGGAATGGGTGACTATAAATGGACTTTACTTCTCAATGAATAG-CTTTTTTGCACGTTTCTCA
66 AAAGGAATGGGTGACTATAAATGGACTTTTTTTCTCAATGAATAGTTTTTTTTTCACGTTTCTCA
* * * *
642 AG-AGAGGTATTCAATTATAGTCTGTTTTAACAAAAAATAT-
131 AGTACAGGCATTCAATTATAGTCTGTTTTAACTAAAAATGTA
* * * *
682 AAAAAATTAAAATTAAAATCAATTATGAGATTATAAAATAATTTAAAGTGTGTAATAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTT
********** * * * * **
747 NNNNNNNNNNGTGACTATAAATGGACTTTTTTTCTCAATGAATGGTTTTGTTTACATGTTT-TTT
66 AAAGGAATGGGTGACTATAAATGGACTTTTTTTCTCAATGAATAGTTTTTTTTTCACGTTTCTCA
* *
811 AGGACATGCATTCAATTATAG-CTTGTTTTAACTAAAAAT-TCAA
131 AGTACAGGCATTCAATTATAGTC-TGTTTTAACTAAAAATGT--A
* *
854 AAAAAATT-AACTTAAAATCAATTTTGAGATTATAAAACAATTTAAAGCT-AGTGATAAGGCTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAG-TGAGTAATAAGGCTTT
* ********** * * *
917 TAAAGGAATGTGTGACTNNNNNNNNNNTTTTCTTGC-CAATGAAT-GATTTTTTTTTTATGTTTC
65 TAAAGGAATGGGTGACTATAAATGGACTTTT-TTTCTCAATGAATAG-TTTTTTTTTCACGTTTC
* * * * *
980 TCAATGTA-A-ACATTCGATTATAGTCTGTTTTAGCTAAAGATGTG
128 TCAA-GTACAGGCATTCAATTATAGTCTGTTTTAACTAAAAATGTA
* * * *
1024 AAAAAATTCAACTTAAAATCAATTATGAGATTTTAAAACATTTTAAAGTGAGCAATAAGGATTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTT
* *
1089 AAAGGAATGGGTGAATATAAATGGACTTTTTTTCTCAACGAATAGTTTTTTTTTTCACGTTTCTC
66 AAAGGAATGGGTGACTATAAATGGACTTTTTTTCTCAATGAATAG-TTTTTTTTTCACGTTTCTC
* * * *
1154 AAGGT--AGGCATTCAATTACAGTCT-TTTTAACCATAGATGTA
130 AA-GTACAGGCATTCAATTATAGTCTGTTTTAACTAAAAATGTA
* * * ********** *
1195 AAAAAATTTAACTTAAAATAAATTTTNNNNNNNNNNAACAATTTAAAGCGAGTAATAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTT
* * * * * * ** *
1260 AACGGATTGGATGACTATAAATAGACTTTTCTTGCT-AATAAATA-CCTTTTTTTCATGTTTCTC
66 AAAGGAATGGGTGACTATAAATGGACTTTT-TTTCTCAATGAATAGTTTTTTTTTCACGTTTCTC
** * * *
1323 AAGATA-A-ATATTCAATTATTGTCTGTTTTAACAAAAAATATA
130 AAG-TACAGGCATTCAATTATAGTCTGTTTTAACTAAAAATGTA
*
1365 AAAAAATTTAACTTAAAATCAATT
1 AAAAAATTCAACTTAAAATCAATT
1389 NNNNNNNNNN
Statistics
Matches: 923, Mismatches: 256, Indels: 76
0.74 0.20 0.06
Matches are distributed among these distances:
168 2 0.00
169 143 0.15
170 237 0.26
171 466 0.50
172 73 0.08
173 2 0.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.35
Consensus pattern (172 bp):
AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTT
AAAGGAATGGGTGACTATAAATGGACTTTTTTTCTCAATGAATAGTTTTTTTTTCACGTTTCTCA
AGTACAGGCATTCAATTATAGTCTGTTTTAACTAAAAATGTA
Found at i:2077 original size:20 final size:20
Alignment explanation
Indices: 2052--2089 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2042 GAATGGGTGA
2052 CAATAAA-AGAATTTTTTTCT
1 CAATAAATAG-ATTTTTTTCT
2072 CAATAAATAGATTTTTTT
1 CAATAAATAGATTTTTTT
2090 ACACGTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (20 bp):
CAATAAATAGATTTTTTTCT
Found at i:3613 original size:170 final size:161
Alignment explanation
Indices: 3420--3748 Score: 295
Period size: 171 Copynumber: 2.0 Consensus size: 161
3410 TAAAGGAATG
* * * *
3420 GGTGACTATAAATAGATTTTTCTTCTTAATAAAT-GCCTTTTTTT-CATGTTTCTCAAGGTAAAC
1 GGTGACCATAAATAGACTTTTCTTCTCAATAAATAG-CTTTTTTTACATGTTTCTCAAGGCAAAC
* * * * * * * *
3483 ATTTAATTGTCA-TCAGTTATAACTAAAAATGTAAAACAATTTAACTTAAAATTAATTATGAGTT
65 AATCAATTAT-AGTCACTTATAACTAAAAATCTAAAACAATATAACTTAAAATCAATTATGAGAT
* * *
3547 TATGAAACCATTTAAAACGAGTAATAAGGCTTT
129 TATAAAACAATTTAAAACAAGTAATAAGGCTTT
* * * *
3580 NNNNNNNNNNGGTGACCATAAATGGACTTTTCTTGTCAATGAATAGTTTTTTTTACATGTTTCTC
1 ----------GGTGACCATAAATAGACTTTTCTTCTCAATAAATAGCTTTTTTTACATGTTTCTC
* * * *
3645 AAGGCAAGCAATCAATTATAGTCTCTTTTAACTAAAAATCTAAAATAATATAACTTAAAATCAAT
56 AAGGCAAACAATCAATTATAGTCACTTATAACTAAAAATCTAAAACAATATAACTTAAAATCAAT
* * *
3710 TTTGAGATTATAAAATAATTTAAAGCAAGTAATAAGGCT
121 TATGAGATTATAAAACAATTTAAAACAAGTAATAAGGCT
3749 NNNNNNNNNN
Statistics
Matches: 130, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
170 36 0.28
171 94 0.72
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.37
Consensus pattern (161 bp):
GGTGACCATAAATAGACTTTTCTTCTCAATAAATAGCTTTTTTTACATGTTTCTCAAGGCAAACA
ATCAATTATAGTCACTTATAACTAAAAATCTAAAACAATATAACTTAAAATCAATTATGAGATTA
TAAAACAATTTAAAACAAGTAATAAGGCTTT
Found at i:5195 original size:171 final size:168
Alignment explanation
Indices: 4613--5381 Score: 527
Period size: 171 Copynumber: 4.5 Consensus size: 168
4603 NNNNNNNNNN
* ** * * *
4613 TTATGAGATTATAAAATAATTTAAAGCGAAAAATAAGGCTATTGAAGGAAT-ATGTGACAAAAAA
1 TTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-GTGACTATAAA
* * * * **
4677 TGGACTTTTCTTGC-CAACGAATGCGTTTTTCTTTAC--GTTTCTCCA-AGTAAAAATTCAATTA
65 TAGACTTTT-TTTCTCAATGAATG-G-TTTT-TTTACATGTTT-TCCATGGTAAGCATTCAATTA
* * **********
4738 TAGTTTGTTTTAGCCAAAAATATAAAAAAATTCANNNNNNNNNNAA
125 TAGTCTGTTTTA-ACAAAAATAT-AAAAAATTCAACTTAAAATAAA
* * * *
4784 TTATGAGATTATAAAATAATTTAAAGCAAGTAATAAGTCTTTTTAAGGAATG-GTGACTATAAAT
1 TTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAT
* * * * * *
4848 AGACTTTTCTTCTCAATGAATAGCTTTTTTGCATG-TTTCTCAAGGTAAGCATTGAATTATAGTC
66 AGACTTTTTTTCTCAATGAATGGTTTTTTTACATGTTTTC-CATGGTAAGCATTCAATTATAGTC
* *
4912 TATTTTAACAAAACATATAAAAAATTCAACTTAAAATCAA
130 TGTTTTAACAAAA-ATATAAAAAATTCAACTTAAAATAAA
** * * **********
4952 TTATGAGATTATAAAACAATTTAAAATGTGTAATAAGACTTTTGAAGGAATGAGNNNNNNNNNNT
1 TTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAT
* * * *
5017 GGACTTTTTTTCTCAATGAATGGTTTTGTTTACATGTTTTCCATGGCAGGCATTCAATTATAGCC
66 AGACTTTTTTTCTCAATGAATGGTTTT-TTTACATGTTTTCCATGGTAAGCATTCAATTATAGTC
* *
5082 TGTTTTAACTAAAAATTTAAAAACATTTAACTTAAAATAAA
130 TGTTTTAAC-AAAAATATAAAAA-ATTCAACTTAAAATAAA
* * * * * * *
5123 TTTTGAGATTATAAAACAATTTAAAGTGAGTGATAAGGCTTTTAAAGGATTGAGTGACTGTATAT
1 TTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAT
* * * ** ** **
5188 CGACTTTTCTTGC-CAATGAATGATTTTTTTTTTCACAT-TACT-CATGGTAAAAATTTGATTAT
66 AGACTTTT-TTTCTCAATGAATG---GTTTTTTT-ACATGTTTTCCATGGTAAGCATTCAATTAT
* * *
5250 AGTCTGTTTTAGCCAAAGATGTAAAAAAATTCAACTTAAAATAAA
126 AGTCTGTTTTA-ACAAAAATAT-AAAAAATTCAACTTAAAATAAA
* * * * *
5295 TTATGAGATTTTAAAACATTTTAAAGCGAGTAATAAAGATTTTGAAGGAATCAGTGACTATAAAT
1 TTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAT
*
5360 -GAACTTTTCTTGC-CAATGAATG
66 AG-ACTTTT-TTTCTCAATGAATG
5382 TATTTTTCTT
Statistics
Matches: 470, Mismatches: 108, Indels: 39
0.76 0.18 0.06
Matches are distributed among these distances:
167 6 0.01
168 69 0.15
169 55 0.12
170 66 0.14
171 133 0.28
172 122 0.26
173 11 0.02
174 8 0.02
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.36
Consensus pattern (168 bp):
TTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAT
AGACTTTTTTTCTCAATGAATGGTTTTTTTACATGTTTTCCATGGTAAGCATTCAATTATAGTCT
GTTTTAACAAAAATATAAAAAATTCAACTTAAAATAAA
Found at i:5312 original size:172 final size:173
Alignment explanation
Indices: 5073--5388 Score: 438
Period size: 172 Copynumber: 1.8 Consensus size: 173
5063 CAGGCATTCA
* * * * *
5073 ATTATAGCCTGTTTTAACTAAAAATTTAAAAACATTTAACTTAAAATAAATTTTGAGATTATAAA
1 ATTATAGCCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAA
* * * * * * * *
5138 ACAATTTAAAGTGAGTGATAAGGCTTTTAAAGGATTGAGTGACTGTATATCG-ACTTTTCTTGCC
66 ACAATTTAAAGCGAGTAATAAAGATTTTAAAGGAATCAGTGACTATAAAT-GAACTTTTCTTGCC
5202 AATGAATG-ATTTTTTTTTTCACATTACTCATGGTAAAAATTTG
130 AATGAATGTATTTTTTTTTTCACATTACTCATGGTAAAAATTTG
* * * *
5245 ATTATAGTCTGTTTTAGCCAAAGATGTAAAAAAATTCAACTTAAAATAAATTATGAGATTTTAAA
1 ATTATAGCCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAA
* *
5310 ACATTTTAAAGCGAGTAATAAAGATTTTGAAGGAATCAGTGACTATAAATGAACTTTTCTTGCCA
66 ACAATTTAAAGCGAGTAATAAAGATTTTAAAGGAATCAGTGACTATAAATGAACTTTTCTTGCCA
5375 ATGAATGTATTTTT
131 ATGAATGTATTTTT
5389 CTTCACGTTT
Statistics
Matches: 123, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
171 1 0.01
172 116 0.94
173 6 0.05
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (173 bp):
ATTATAGCCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAA
ACAATTTAAAGCGAGTAATAAAGATTTTAAAGGAATCAGTGACTATAAATGAACTTTTCTTGCCA
ATGAATGTATTTTTTTTTTCACATTACTCATGGTAAAAATTTG
Found at i:7048 original size:171 final size:168
Alignment explanation
Indices: 6832--7154 Score: 375
Period size: 169 Copynumber: 1.9 Consensus size: 168
6822 NNNNNNNNNN
* * *
6832 AGATTATAAAATAATTTAAAGCGAGTAATAAGGCTACTGAAGGAATATGTGACAAAAAATAAACT
1 AGATTATAAAACAATTTAAAGCAAGTAATAAGGCTACTGAAGGAAT-GGTGACAAAAAATAAACT
**
6897 TTTCTTGC-CAACGAAT-GCGTTTTTCTTTACGTTTCTCCAA-GTAAAAACTCAATTATAGTCTG
65 TTTCTT-CTCAACGAATAGC-TTTTT-TGCACGTTT-TCCAAGGTAAAAACTCAATTATAGTCTG
*
6959 TTTTAGCAAAAAATATAAAAAAATTCAACTTGAAATTAATTATG
126 TTTTAACAAAAAATAT-AAAAAATTCAACTTGAAATTAATTATG
** * * * **
7003 AGATTATAAAACAATTTAAAGCAAGTAAT-AGGTCTTTTTAAGGAATGGTGACTATAAATGGACT
1 AGATTATAAAACAATTTAAAGCAAGTAATAAGG-CTACTGAAGGAATGGTGACAAAAAATAAACT
* * ** * *
7067 TTTCTTCTCAATGAATAGCTTTTTTGCACGTTTTTCAAGGTAAGCATTGAATTATAGTCTGTTTT
65 TTTCTTCTCAACGAATAGCTTTTTTGCACGTTTTCCAAGGTAAAAACTCAATTATAGTCTGTTTT
*
7132 AATAAAAAATATAAAAAATTCAA
130 AACAAAAAATATAAAAAATTCAA
7155 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 20, Indels: 11
0.81 0.13 0.07
Matches are distributed among these distances:
168 15 0.12
169 40 0.31
170 34 0.27
171 39 0.30
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (168 bp):
AGATTATAAAACAATTTAAAGCAAGTAATAAGGCTACTGAAGGAATGGTGACAAAAAATAAACTT
TTCTTCTCAACGAATAGCTTTTTTGCACGTTTTCCAAGGTAAAAACTCAATTATAGTCTGTTTTA
ACAAAAAATATAAAAAATTCAACTTGAAATTAATTATG
Found at i:7185 original size:168 final size:160
Alignment explanation
Indices: 6996--7318 Score: 366
Period size: 170 Copynumber: 2.0 Consensus size: 160
6986 ACTTGAAATT
* * *
6996 AATTATGAGATTATAAAACAATTTAAAGCAAGTAATAGGTCTTTTTAAGGAAT-GGTGACTATAA
1 AATTATGAGATTATAAAACAATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAA
* * *
7060 ATGGACTTTTCTTCTCAATGAATAGCTTT-TTTGCACGTTTTTCAAGGTAAGCATTGAATTATAG
66 ATGGACTTTTCTTCTCAATGAATAGCTTTGTTTACACGTTTTTCAAGGCAAGCATTCAATTATAG
7124 TC-TGTTTTAA-TAAAAAATATAAAAAATTCA
131 -CATGTTTTAACT-AAAAATATAAAAAATTCA
***
7154 ANNNNNNNNNNATTATGAGATTATAAAACAATTTAAAGTGTGTAATAAGACTTTTGAAGGAATGG
1 A----------ATTATGAGATTATAAAACAATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGG
* * * * * *
7219 GTGACTATAAATGGACTTTTTTTCTCAATTAATGGTTTTGTTTACACGTTTTTCATGGCAGGCAT
56 GTGACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTGTTTACACGTTTTTCAAGGCAAGCAT
*
7284 TCAATTATAGCATGTTTTAACTAAAAATTTAAAAA
121 TCAATTATAGCATGTTTTAACTAAAAATATAAAAA
7319 CATTTAACTT
Statistics
Matches: 135, Mismatches: 16, Indels: 16
0.81 0.10 0.10
Matches are distributed among these distances:
158 1 0.01
168 46 0.34
169 37 0.27
170 50 0.37
171 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.37
Consensus pattern (160 bp):
AATTATGAGATTATAAAACAATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAA
ATGGACTTTTCTTCTCAATGAATAGCTTTGTTTACACGTTTTTCAAGGCAAGCATTCAATTATAG
CATGTTTTAACTAAAAATATAAAAAATTCA
Found at i:7547 original size:21 final size:21
Alignment explanation
Indices: 7523--7562 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
7513 ATTTTAAAAC
7523 ATTTTAAAGTGAGT-AATAAGG
1 ATTTTAAAG-GAGTCAATAAGG
*
7544 ATTTTGAAGGAGTCAATAA
1 ATTTTAAAGGAGTCAATAA
7563 CTATAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.33
Consensus pattern (21 bp):
ATTTTAAAGGAGTCAATAAGG
Found at i:11318 original size:171 final size:160
Alignment explanation
Indices: 11141--11687 Score: 348
Period size: 170 Copynumber: 3.2 Consensus size: 160
11131 NNNNNNNTCG
* * * * *
11141 CTTTAAATTATTTTATAATCTCAAAATTGATTTTAAGTTAAATTGTTTTGAAATTTTAGTTACAA
1 CTTTAAATTATTTTATAATCTCAAAATTGATTTTAATTTAAATT-TTTTTACATTTTGGTTAAAA
* *
11206 CAGACTATAATTAAATGCCT-GCGTTGAGAAACATGCAAAAAAA-GCTATNNNNNNNNNNGAAAA
65 CAGACTATAATTGAATGCCTAGC-TTGAGAAACATG-AAAAAAAGGC-AT---------AGAAAA
*
11269 GTCCATTTATGGTCACCCAATCCTTCAAAAGCCTTATTACTCA
118 GTCCATTTATAGTCACCCAATCCTTCAAAAGCCTTATTACTCA
* * * * * *
11312 CTTTAAA-TAGTTTTATAAACTTATAATTAATTTTGATTTGAATTTTTTTACATTATTGGTTAAA
1 CTTTAAATTA-TTTTATAATCTCAAAATTGATTTTAATTTAAATTTTTTTACATT-TTGGTTAAA
* * ** * *
11376 ACAAACAATAATTGAATGTTTATCTTGAGAAACATGAAAAAAAGGCANNNNNNNNNNAGAAAAGT
64 ACAGACTATAATTGAATGCCTAGCTTGAGAAACATGAAAAAAAGGCA---------TAGAAAAGT
* * * * * * * *
11441 CTATTTATAGTCATCCATTTCTTTAAAATCTTTATTACTCG
120 CCATTTATAGTCACCCAATCCTTCAAAAGCCTTATTACTCA
*
11482 CTTTAAATTATTTTATAATCTCAAAATTGATTTTAATTTATATTTTTTTACATTTATGGTTAAAA
1 CTTTAAATTATTTTATAATCTCAAAATTGATTTTAATTTAAATTTTTTTACATTT-TGGTTAAAA
* * * * * *
11547 CAGACTATAATTGAATGTCTACCTTCAGAAATGTAT-AAAAAAAGTCATTCATTAAAAAAAAAGT
65 CAGACTATAATTGAATGCCTAGCTTGAGAAA--CATGAAAAAAAG----GCA-T---AGAAAAGT
* * *
11611 CCATTTATAGTCA-CCAATTCCTTGACAAGCCATATTACTCA
120 CCATTTATAGTCACCCAA-TCCTTCAAAAGCCTTATTACTCA
* * * * *
11652 TTTTTAATTGTTTTATAATATCATAATTGATTTTAA
1 CTTTAAATTATTTTATAATCTCAAAATTGATTTTAA
11688 GCTGAATTTT
Statistics
Matches: 292, Mismatches: 59, Indels: 51
0.73 0.15 0.13
Matches are distributed among these distances:
169 4 0.01
170 202 0.69
171 81 0.28
172 3 0.01
175 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.38
Consensus pattern (160 bp):
CTTTAAATTATTTTATAATCTCAAAATTGATTTTAATTTAAATTTTTTTACATTTTGGTTAAAAC
AGACTATAATTGAATGCCTAGCTTGAGAAACATGAAAAAAAGGCATAGAAAAGTCCATTTATAGT
CACCCAATCCTTCAAAAGCCTTATTACTCA
Found at i:12954 original size:171 final size:171
Alignment explanation
Indices: 12576--12995 Score: 467
Period size: 171 Copynumber: 2.5 Consensus size: 171
12566 NNNNNNNNNN
* * * * *
12576 TAGCTTTTTTTGCATGTTTCTCAAAGCAAGCATTCAATTATAGTCTATTTTAACCAAAATTTAAA
1 TAGCTTTTTTTACATGTTTCTCAAGGCAGGCATTCAATTATAGTATATTTTAACCAAAATCTAAA
* * * * *
12641 AAATATTTAACTTAAAATTAATTTTGGGATTATAAAATAATTTAAAGAGAGTAATAAGGCTTTTA
66 AAATATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGAGAGTAATAAGGCTTTTA
* *
12706 AAGGAATGGGTGACTATAAATAGATTTTTTTTGCCAATGAA
131 AAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAA
* * * ** ** * * *
12747 T-GATTTTTTTTTCACGTTTCTTGAGTAAGACATTCAATTATTA-TATGTTTTAACTAGAAATGC
1 TAG-CTTTTTTTACATGTTTCTCAAGGCAGGCATTCAATTA-TAGTATATTTTAACCA-AAAT-C
*
12810 T-AAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCT
62 TAAAAAATATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGAGAGTAATAAGGCT
*
12873 TTTGAAA-GAATGGGTGACTATAAATGGACTTTTCTT-CTCAATGAA
127 TTT-AAAGGAATGGGTGACTATAAATAGACTTTTCTTGC-CAATGAA
* * * **
12918 TAGCTTTTTTTACATGTTTCTCAAGGCAGGCATTCAATTGTAGTCTATTTTAACAAAACAAGTAA
1 TAGCTTTTTTTACATGTTTCTCAAGGCAGGCATTCAATTATAGTATATTTTAACCAAA-ATCTAA
12983 AAAA-ATTCAACTT
65 AAAATATTCAACTT
12996 TTTTTTTTTG
Statistics
Matches: 202, Mismatches: 37, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
170 7 0.03
171 179 0.89
172 15 0.07
173 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (171 bp):
TAGCTTTTTTTACATGTTTCTCAAGGCAGGCATTCAATTATAGTATATTTTAACCAAAATCTAAA
AAATATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGAGAGTAATAAGGCTTTTA
AAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAA
Found at i:13641 original size:171 final size:167
Alignment explanation
Indices: 13063--13651 Score: 577
Period size: 171 Copynumber: 3.5 Consensus size: 167
13053 GCAGGCACTC
* * *
13063 AATTATAGTCTATTTTAATCTTA-AATA-TAAAAAAATTTAACTTAAAATCTATT-TTAGGATTA
1 AATTATAGTCTGTTTTAA-C-TAGAA-AGTAAAAAAATTTAACTTAAAATCAATTATGA-GATTA
* * * *
13125 TAAAACAATTTAAAGCGAGTAATAAGCCTTTTAAAGGAATGGGTGACTATAAAT-AGATTTTTCT
62 TAAAACAATTTAAAG-AAGTAATAAGGCTTTTAAAGGAATGGGTGACCATAAATGA-ACTTTTCT
13189 T-CCTAATAAATGCCTTTCTTTTCATGTTTCTCAAGGTAAACATTT
125 TGCC-AATAAATGCCTTT-TTTTCATGTTTCTCAAGGT-AACATTT
* ** * * * * * * * *
13234 AATTGTCA-TCAATTATAACTAAAAATGTAAAAATATATACCTTAAAATTAATTATGAGTTTATG
1 AATTAT-AGTCTGTTTTAACTAGAAA-GTAAAAAAATTTAACTTAAAATCAATTATGAGATTATA
* * *
13298 AAACCATTTAAAACGAA-TAATAAGGGTTTTAAAGGAATGGGTGACCATAAATGGACTTTTCTTG
64 AAACAATTT-AAA-GAAGTAATAAGGCTTTTAAAGGAATGGGTGACCATAAATGAACTTTTCTTG
* * * *
13362 TCAATAAATAG--TTTTTTTACATGTTTCTCAAGGCAAGCAATC
127 CCAATAAAT-GCCTTTTTTT-CATGTTTCTCAAGGTAA-CATTT
* * * * * *
13404 AATTATAGTCTGTTTTAACTAGAAATTCAAAAAACTCTAACTTAAGATCAATTTTGGGATTATAA
1 AATTATAGTCTGTTTTAACTAGAAAGT-AAAAAAATTTAACTTAAAATCAATTATGAGATTATAA
* *
13469 AATAATTTAAAGTAAGTAATAAGGCTTTTAAAGAAATGGGTGACCATAAATGAACTTTTCTTGCC
65 AACAATTTAAAG-AAGTAATAAGGCTTTTAAAGGAATGGGTGACCATAAATGAACTTTTCTTGCC
* *
13534 AATGAATGCCTTTTTCTTCATGTTTC-CTGAGGTAGACATTT
129 AATAAATGCCTTTTT-TTCATGTTTCTC-AAGGTA-ACATTT
*
13575 AATTATTGTCTGTTTTAACTAGAAAGGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAA
1 AATTATAGTCTGTTTTAACTAGAAA-GTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAA
*
13640 AATAATTTAAAG
65 AACAATTTAAAG
13652 CGANNNNNNN
Statistics
Matches: 340, Mismatches: 56, Indels: 44
0.77 0.13 0.10
Matches are distributed among these distances:
168 1 0.00
169 17 0.05
170 126 0.37
171 182 0.54
172 13 0.04
173 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (167 bp):
AATTATAGTCTGTTTTAACTAGAAAGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAA
ACAATTTAAAGAAGTAATAAGGCTTTTAAAGGAATGGGTGACCATAAATGAACTTTTCTTGCCAA
TAAATGCCTTTTTTTCATGTTTCTCAAGGTAACATTT
Found at i:18475 original size:171 final size:156
Alignment explanation
Indices: 18225--18546 Score: 324
Period size: 171 Copynumber: 2.0 Consensus size: 156
18215 TGCCAAGAAA
* *
18225 AGTCCATTTATAGTCACCAATTCCTTTAAAAGCCTTATTACTCGCTTAAAATTGTTCTATAATAT
1 AGTCCATTTATAGTCACCAATTCCTTCAAAAGCCTTATTACTCACTTAAAATTGTTCTATAATAT
*
18290 CAAAATTAATTTTAAGTTAAATGTTTTTAGATTTTTTATTAAAACAGACTATAATTGAAT-GTCT
66 CAAAATTAATTTTAAGTT-AATGTTTTTAGATTTTTTATTAAAACAGACTATAATTGAATACT-T
*
18354 GCCTTGAAAAACATGTAAAAAAAACCAT
129 GCCTTGAAAAACATGCAAAAAAAACCAT
* * *
18382 NNNNNNNNNNNNNNAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTAGTCACTTTAAA
1 --------------AGTCCATTTATAGTCACCAATTCCTTCAAAAGCCTTATTACTCACTTAAAA
* * * * * * * *
18447 TTGCTT-TATAATCTCATAATTGATTTTAAGTTGATTTTTTTATATTTTTTGTTTAAACAGACTA
52 TTG-TTCTATAATATCAAAATTAATTTTAAGTTAATGTTTTTAGATTTTTTATTAAAACAGACTA
* *
18511 TAATTGAATACTTGCCTTGAGAAACGTGCAAAAAAA
116 TAATTGAATACTTGCCTTGAAAAACATGCAAAAAAA
18547 GCTATTCATT
Statistics
Matches: 132, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
170 57 0.43
171 73 0.55
172 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.38
Consensus pattern (156 bp):
AGTCCATTTATAGTCACCAATTCCTTCAAAAGCCTTATTACTCACTTAAAATTGTTCTATAATAT
CAAAATTAATTTTAAGTTAATGTTTTTAGATTTTTTATTAAAACAGACTATAATTGAATACTTGC
CTTGAAAAACATGCAAAAAAAACCAT
Found at i:18576 original size:170 final size:170
Alignment explanation
Indices: 17730--18637 Score: 803
Period size: 170 Copynumber: 5.3 Consensus size: 170
17720 NNNNNNNNNN
* * * * * *
17730 CCCATTTCTTCAAAATCTTTATTACTTGCTTTAAATTGTTTTATAATCTTATAATTGATTTTAAA
1 CCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAG
* * * *
17795 TTGTATTTTTTTACATCTTTTGTTAAAACAGAC-AGCAATTGAATGTTTACCTTGAGAAACATG-
66 TTG-ATTTTTTTACATTTTTTGTTAAAACAGACTA-TAATTGAATGGTTGCCTTGAGAAACATGT
*
17858 AAAAAAAAGGC-ATTCATTGACAAGAAAAGGT-CATTTATTGTCA
129 AAAAAAAA--CTATTCATTGACAAGAAAA-GTCCATTTATAGTCA
* * * *
17901 CCCATTCCTTTAAAAGCCTTATTACTCGTTTTAAATTGTTTTATAAT-TCCAAAATT-TTTTTAA
1 CCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCT-CATAATTGATTTTAA
* * * * * * *
17964 GTTGAATTTTGTTACATTTCTTGTCAAAA-AAACTATAATTGAATGGTTGCCTTAAAAAATATGT
65 GTTG-ATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATGGTTGCCTTGAGAAACATGT
* * *
18028 AAACAAAACTATTCATTGAGAAGAAAAGTTCATTTATAGTCA
129 AAAAAAAACTATTCATTGACAAGAAAAGTCCATTTATAGTCA
* * **********
18070 -CCATTCCTTTAAAAGGCTTATTACTCGCTTTAAATTGTTTTATAATNNNNNNNNNNATTTTAAG
1 CCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAG
* * * ** * *
18134 TTAAATTTTTTTACATTTTTGGTTAAAACAGACAATAATCAAATGTTTACCTTGAG-AA-ATGTG
66 TT-GATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATGGTTGCCTTGAGAAACATGT-
* *
18197 AAAAAACAAATCATTCATTGCCAAGAAAAGTCCATTTATAGTCA
129 AAAAAA-AACT-ATTCATTGACAAGAAAAGTCCATTTATAGTCA
* * * * * * *
18241 CCAATTCCTTTAAAAGCCTTATTACTCGCTTAAAATTGTTCTATAATATCAAAATTAATTTTAAG
1 CCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAG
* * * * *
18306 TTAAATGTTTTTAGATTTTTTATTAAAACAGACTATAATTGAAT-GTCTGCCTTGAAAAACATGT
66 TT-GATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATGGT-TGCCTTGAGAAACATGT
* **************
18370 AAAAAAAACCATNNNNNNNNNNNNNNAGTCCATTTATAGTCA
129 AAAAAAAACTATTCATTGACAAGAAAAGTCCATTTATAGTCA
* * *
18412 CCCATTCCTTCAAAAGCCTTATTAGTCACTTTAAATTGCTTTATAATCTCATAATTGATTTTAAG
1 CCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAG
* * ** * *
18477 TTGATTTTTTTATATTTTTTGTTTAAACAGACTATAATTGAATACTTGCCTTGAGAAACGTGCAA
66 TTGATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATGGTTGCCTTGAGAAACATGTAA
* * * * * *
18542 AAAAAGCTATTCATTTAGAAAAAAAGTGCATTTATGGTCA
131 AAAAAACTATTCATTGACAAGAAAAGTCCATTTATAGTCA
** *
18582 CCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAAACTCATAATT
1 CCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATT
18638 TTGTTACATT
Statistics
Matches: 583, Mismatches: 137, Indels: 35
0.77 0.18 0.05
Matches are distributed among these distances:
168 51 0.09
169 88 0.15
170 184 0.32
171 152 0.26
172 96 0.16
173 8 0.01
174 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.38
Consensus pattern (170 bp):
CCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAG
TTGATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATGGTTGCCTTGAGAAACATGTAA
AAAAAACTATTCATTGACAAGAAAAGTCCATTTATAGTCA
Found at i:18855 original size:97 final size:97
Alignment explanation
Indices: 18677--18856 Score: 270
Period size: 97 Copynumber: 1.9 Consensus size: 97
18667 NNNNNNNNNN
* *
18677 CTACCTCAAGAAAAGTGAAGAAAAAGACATTAATTGGTAAGAAAGTCTATTTATAGTCACCAATT
1 CTACCTAAAGAAAAGTGAAGAAAAAGACATTAATTGGTAAGAAAGTCCATTTATAGTCACCAATT
*
18742 CCTTCAAAAGCCTTATTATTATAATTGAATGT
66 CCTTCAAAAGCATTATTATTATAATTGAATGT
* * * * *
18774 CTACCTAAAGAACAGTGAAGAAAAAGGCATTCATTGGTACGAAAGTCCATTTATAGTCACCCATT
1 CTACCTAAAGAAAAGTGAAGAAAAAGACATTAATTGGTAAGAAAGTCCATTTATAGTCACCAATT
* *
18839 CTTTCAAAAGTATTATTA
66 CCTTCAAAAGCATTATTA
18857 CTCGCTTTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 73 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (97 bp):
CTACCTAAAGAAAAGTGAAGAAAAAGACATTAATTGGTAAGAAAGTCCATTTATAGTCACCAATT
CCTTCAAAAGCATTATTATTATAATTGAATGT
Found at i:28810 original size:170 final size:169
Alignment explanation
Indices: 28514--28906 Score: 396
Period size: 170 Copynumber: 2.3 Consensus size: 169
28504 AAAAAAAGCT
* * * *
28514 ATTCATTGAG-AAGAAAAGTCCATTTATGGTCACCCATTCCTTGAAAAGCCTTATTAGTCGCTTT
1 ATTCATT-AGCAAGAAAAGTCCATTTATAGTCA-CCATTCCTTCAAAAGCCTTATTACTCACTTT
* * * ********** *
28578 AAATAGTTTTATAAACTCATAATTGATTTTGATTTGAATTTTNNNNNNNNNNTGGTTAAAACAAA
64 AAATAGTTTTATAAACGCATAATTGATTTTCAGTTGAATTTTATTATACTTTTGGCTAAAACAAA
* * * **
28643 CAATAATTGAATGTTTACCTTGAGAAACATGAA-AAAGAGGC
129 CAATAATTGAATGTCTACC-TCAGAAACATGAAGAAAAACAC
* * *
28684 ATTCATTAGCAAGAAAAGTCTATTTATAGTAATCCATTCCTTTAAAAGCCTTATTACTCACTTTA
1 ATTCATTAGCAAGAAAAGTCCATTTATAGTCA-CCATTCCTTCAAAAGCCTTATTACTCACTTTA
* * * *
28749 AATTGTTTTATAATCGCATAATTGATTTTCAGTTGAATGTTT-TTATACTTTTTGCTAAAACAGA
65 AATAGTTTTATAAACGCATAATTGATTTTCAGTTGAAT-TTTATTATACTTTTGGCTAAAACAAA
** *
28813 TTATAATTGAATGTCTACCTCAGAAACGTGAAGAAAAACAC
129 CAATAATTGAATGTCTACCTCAGAAACATGAAGAAAAACAC
* *
28854 ATTCATTGGCAAGAAAAATCCATTTATAGTCACTCATTCCTTCAAAAGCCTTA
1 ATTCATTAGCAAGAAAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGCCTTA
28907 NNNNNNNNNN
Statistics
Matches: 182, Mismatches: 37, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
169 14 0.08
170 165 0.91
171 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.35
Consensus pattern (169 bp):
ATTCATTAGCAAGAAAAGTCCATTTATAGTCACCATTCCTTCAAAAGCCTTATTACTCACTTTAA
ATAGTTTTATAAACGCATAATTGATTTTCAGTTGAATTTTATTATACTTTTGGCTAAAACAAACA
ATAATTGAATGTCTACCTCAGAAACATGAAGAAAAACAC
Done.