Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402390.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_547.0, 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: 14778
ACGTcount: A:0.24, C:0.09, G:0.10, T:0.23
Warning! 5122 characters in sequence are not A, C, G, or T
Found at i:3327 original size:169 final size:169
Alignment explanation
Indices: 3039--3667 Score: 706
Period size: 172 Copynumber: 3.7 Consensus size: 169
3029 NNNNNNNNNN
* *
3039 GTGATTATAAATGGGCTTTTCTTCCCAATGAATGGGTTTTTCTTCATGTTTCTTGAGGTAAACAT
1 GTGACTATAAATGGGCTTTTCTTCCCAATGAATGGGTTTTTCTTCATGTTTCTCGAGGTAAACAT
* *
3104 TCAATTGTAATCTGTTTTAACCAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAGATTAT
66 TCAATTATAATCTGTTTTAACCAAAAATGTAAAACAATTCAA-TTTAAATCAATTATGAGATTAT
* *
3169 AAAACTATTTAAAGAGAGTAATAAGG-GTTGAAGGCCTGG
130 AAAACTATTTAAAGAGAGTAATAAGGCTTTGAAGGCTTGG
* * * * ** *
3208 GTGACTATAAATAGGTTTTTCTTCCCAATGAATTGGTTTTTCTTCATGTTTCTCAAGCCAAGCAT
1 GTGACTATAAATGGGCTTTTCTTCCCAATGAATGGGTTTTTCTTCATGTTTCTCGAGGTAAACAT
** * * * * * *
3273 TCAATTCCAATTTGTTTTAGCCAACAATGTAATAA-AATTCAATTTAGCATCAATTTTGCA-TTT
66 TCAATTATAATCTGTTTTAACCAAAAATGTAA-AACAATTCAATTTA-AATCAATTATG-AGATT
* * *
3336 ATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAAGCTTAG
128 ATAAAACTATTTAAAGAGAGTAATAAGGC-TTTGAAGGCTTGG
* * * *
3379 GTGACTCATAAATGAGATTTTCTTGCCAATGAATGGGTTTTTCTACATGTTTCTCGAGGTAAACA
1 GTGACT-ATAAATGGGCTTTTCTTCCCAATGAATGGGTTTTTCTTCATGTTTCTCGAGGTAAACA
* * * * * *
3444 TTCAAGTATAATCTGTGTTAACCAAAAATGTAAAATAAATCAACTTCAAATCAATTATAAGATTA
65 TTCAATTATAATCTGTTTTAACCAAAAATGTAAAACAATTCAA-TTTAAATCAATTATGAGATTA
*
3509 TAAAACTATGTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGG
129 TAAAACTATTTAAAGAGAGTAATAAGGC-TTTGAAGGCTTGG
* * * * * ** * *
3551 GCGACTATAAATGGGCTTTTCTTGCCAATAAATGGATTTCTCTTCATGTTTCTTAAGGCAAAAAT
1 GTGACTATAAATGGGCTTTTCTTCCCAATGAATGGGTTTTTCTTCATGTTTCTCGAGGTAAACAT
* * * * * *
3616 TCAAGTATAATCTGTGTTAACCAAAAATATAAAATAAATCAACTTCAAATCA
66 TCAATTATAATCTGTTTTAACCAAAAATGTAAAACAATTCAA-TTTAAATCA
3668 NNNNNNNNNN
Statistics
Matches: 389, Mismatches: 62, Indels: 16
0.83 0.13 0.03
Matches are distributed among these distances:
168 3 0.01
169 128 0.33
170 3 0.01
171 118 0.30
172 134 0.34
173 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (169 bp):
GTGACTATAAATGGGCTTTTCTTCCCAATGAATGGGTTTTTCTTCATGTTTCTCGAGGTAAACAT
TCAATTATAATCTGTTTTAACCAAAAATGTAAAACAATTCAATTTAAATCAATTATGAGATTATA
AAACTATTTAAAGAGAGTAATAAGGCTTTGAAGGCTTGG
Found at i:4249 original size:21 final size:21
Alignment explanation
Indices: 4216--4274 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
4206 TTGGGTGACT
*
4216 ATAAATAGGTTTTTCTTGCCA
1 ATAAATGGGTTTTTCTTGCCA
** *
4237 ATGTATGGGTTTTTCTTGGCA
1 ATAAATGGGTTTTTCTTGCCA
*
4258 ATAAATTGGTTTTTCTT
1 ATAAATGGGTTTTTCTT
4275 CAAGTTTACC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.10, G:0.19, T:0.49
Consensus pattern (21 bp):
ATAAATGGGTTTTTCTTGCCA
Found at i:5512 original size:171 final size:164
Alignment explanation
Indices: 5156--6399 Score: 549
Period size: 171 Copynumber: 7.3 Consensus size: 164
5146 NNNNNNNNNN
* * * **
5156 CTATAAATGGGCTTTTCTTGCTAGTGAATGGGTTTTTCTTCATGTTTCCCAAGGTAAACATTTGA
1 CTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCCCAAGGAAAACATTCAA
* * * *
5221 TTATAATCTATTTTAACTAAAAATGTAAAAAAAATTCAAGTTAAAATCAATTATGAGATTATAAA
66 TTATAATCTGTTTTAACAAAAAATGGAAAAAAAA-TCAACTTAAAATCAATTATGAGATTATAAA
* ***
5286 ACGATTTAAAGAGAGTAATAANNNNNNNNNNGGCTTGGGTGA
130 ACCATTTAAAGAGAGTAATAA-------GGCGGCTTGGGTGA
* * * *
5328 CTATAAATGGGCTTCTCTTGCCAATGAATGGCTTTCTCTTCATGTTTCCCAAGGAAAAGATTCAA
1 CTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCCCAAGGAAAACATTCAA
* *
5393 TTGTAATCTGTTTTAACCAAAAATGGAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAA
66 TTATAATCTGTTTTAACAAAAAATGGAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAA
* ******
5458 CCATTGAAAGAGAGTAATAAGGCNNNNNNNNNNNNNGGTGA
131 CCATTTAAAGAGAGTAATAAGGC-------GGCTTGGGTGA
* * * * *
5499 CTATAAGTGGGCTTTTCTTGTCAATGAATGGGTTTTTCTTCATGTTTCTCAAGGCAAATATTCAA
1 CTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCCCAAGGAAAACATTCAA
* * * * * * *
5564 TTATAATCTGTTTAAACAAAAAATGTG-AAACAATTAAACTTAAAATCAATTTTAAGGTTATAAA
66 TTATAATCTGTTTTAACAAAAAATG-GAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAA
* ***** ** *
5628 ACCATTTAAAGAAAGTGNNNNNNNNNNTGAAGGCTTAGGTGA
130 ACCATTTAAAGAGAGT-------AATAAGGCGGCTTGGGTGA
** ** * * * ** *
5670 CTATAAATGGAATTTT-TGTTTCAATGAATGTGTTTTTCTTCATTTTTCCAAAGTCAAATATTCA
1 CTATAAATGGGCTTTTCT-TGCCAATGAATGGGTTTTTCTTCATGTTTCCCAAGGAAAACATTCA
** *** * *
5734 ATTATAATCTGTTTTGGCCAAAAATACAAAAAAAAAAACCCAACTTAAAATCAACTATGAGATTA
65 ATTATAATCTGTTTT-AACAAAAA-A-TGGAAAAAAAA-TCAACTTAAAATCAATTATGAGATTA
* * ***
5799 TAAATCCATTTAAAGAGTGTAATAAGNNNNNNNNNNGCTTGGGTGA
126 TAAAACCATTTAAAGAGAGTAATAAG-------GCGGCTTGGGTGA
* * * * *
5845 CTATAAATGGGCTTTTCTTTCTAGTGACA-GGGTTTTTCTTCATGTTTCCCAAGGCAAACATTCG
1 CTATAAATGGGCTTTTCTTGCCAATGA-ATGGGTTTTTCTTCATGTTTCCCAAGGAAAACATTCA
* * * * * **********
5909 ATTATAATCTATTTGAACCAAAAATGTAAAAAAATTCAANNNNNNNNNNATTATGAGATTATAAA
65 ATTATAATCTGTTTTAACAAAAAATGGAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAA
* ** * **
5974 ATCATTTAAAGAGAGTAATAA-G-GTTTTTGAAGA
130 ACCATTTAAAGAGAGTAATAAGGCGGCTTGGGTGA
* * * * * * * * ** *
6007 C-CTGAGT-GACTTTTCTTGTCAATGAATGGGTTTTTATTCATGTTTCTCGAGCCAAACATTCAG
1 CTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCCCAAGGAAAACATTCAA
* ** * *** ** * * * * **
6070 TTATAATATACTTTAACTAAAAATATTAAACCATTCAGCTTAAAATAAATTATGGGATTGCAAAA
66 TTATAATCTGTTTTAACAAAAAATGGAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAA
* *
6135 CCATTTAAAGTGAGTAATAAGGCTTTTGAAAGCTTGAGTGA
131 CCATTTAAAGAGAGTAATAAGGC----G---GCTTGGGTGA
********** * *
6176 CTATAAATGGGNNNNNNNNNNCAATGAATGTGTTTTTCTTCATGTTTCCAAAGGAAAACATTCAA
1 CTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCCCAAGGAAAACATTCAA
* * ** * * ********** *
6241 TAATAATTTGTTTTAACAAAAAATATAAAACAATTCANNNNNNNNNNAATTATAAGATTATAAAA
66 TTATAATCTGTTTTAACAAAAAATGGAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAA
* * * *
6306 CCATTGAAAGAGACTAATAAGGGTTTTGAAGGCTTAGGTGA
131 CCATTTAAAGAGAGTAATAA--G----G-CGGCTTGGGTGA
* * * *
6347 CTATAAATGAGCTTTTCTTGCCAATGAATAGGTTTTCCTTCATGTTTCTCAAG
1 CTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCCCAAG
6400 NNNNNNNNNN
Statistics
Matches: 780, Mismatches: 243, Indels: 99
0.70 0.22 0.09
Matches are distributed among these distances:
159 1 0.00
160 104 0.13
161 4 0.01
162 6 0.01
166 1 0.00
168 1 0.00
169 5 0.01
170 4 0.01
171 428 0.55
172 100 0.13
173 3 0.00
174 11 0.01
175 108 0.14
176 2 0.00
177 1 0.00
178 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.33
Consensus pattern (164 bp):
CTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCCCAAGGAAAACATTCAA
TTATAATCTGTTTTAACAAAAAATGGAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAA
CCATTTAAAGAGAGTAATAAGGCGGCTTGGGTGA
Found at i:7507 original size:169 final size:171
Alignment explanation
Indices: 6666--7834 Score: 667
Period size: 171 Copynumber: 6.9 Consensus size: 171
6656 NNNNNNNNNN
** * * * * * *
6666 ATAAGGCTTTTGAAGGTTTGAGTGACTATAAATGGGCTTTTCTTGCCAATGAATTGG-TTTTTAT
1 ATAAGGCTTTCAAAGGCTTGGGTGACTATAAATGGGCCTTTCTTGCCAATGAA-TGGATCTCTCT
** ** * * ** * * * *
6730 TCAAATTTCT-CAAGCCAAATATTCAATTACAGTCTGTTTTAGCTAACAATGTAATGAAATTCAA
65 TCATGTTTCTGC-AGAAAAACATTTAATTGTAATCTGTTTTAACTAAAAATGTAATAAAATTCAA
* * * ****
6794 TTTAGAATCAATT-TTACAGTTATAAAACCATTTAAAGAGNNNN
129 TTTAAAATCAATTATGAGA-TTATAAAACCATTTAAAGAGAGTA
****** * * ** *
6837 NNNNNNCTTTTAAAGGCTTGGGTGACTATCAATGCACTTTTCTTGCCAATGAATGGA--TCTCTT
1 ATAAGGCTTTCAAAGGCTTGGGTGACTATAAATGGGCCTTTCTTGCCAATGAATGGATCTCTCTT
* * * * * * * *
6900 CATGTTTC-CCAGGAAAATATTCAATCGTAATATGTTTTAACAAAAAATGTAA-AACAATTCAAC
66 CATGTTTCTGCAGAAAAACATTTAATTGTAATCTGTTTTAACTAAAAATGTAATAA-AATTCAAT
********** *
6963 TTAANNNNNNNNNNGAGATTAT-AAACTATTTAAAGAGAGTA
130 TTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTA
** * * * *
7004 ATAAGGCTTTTGAAGGCTTGGGTGATTATAAATGGGCTTTTCTTGCCAATGAATGGGT-TATTCT
1 ATAAGGCTTTCAAAGGCTTGGGTGACTATAAATGGGCCTTTCTTGCCAATGAATGGATCT-CTCT
* ** * * * * * *
7068 TTATGTTTCT-CGAGGTAAACATTAAATTATAATCAGTTTTAACCAAAAATGTACA-AACCATTT
65 TCATGTTTCTGC-AGAAAAACATTTAATTGTAATCTGTTTTAACTAAAAATGTA-ATAA-AATTC
** * * *
7131 AGCTTAAAATCAATTATG-GTATTACAAAACCATTTGAAGGGAGTA
127 AATTTAAAATCAATTATGAG-ATTATAAAACCATTTAAAGAGAGTA
* * * * *
7176 ATAA--CATCTTCAAAGGCTTGGGTGATTATAAATGGGCTTTTCTTGCCAACGAATTGG-TTTTT
1 ATAAGGC-T-TTCAAAGGCTTGGGTGACTATAAATGGGCCTTTCTTGCCAATGAA-TGGATCTCT
* * * ** * * * ** * *
7238 CTTCAAGTTTCCGAAGCTAAACGTTCAATTATTGTCTGTTTTAGCTAATAATGTAATAAAATTCA
63 CTTCATGTTTCTGCAGAAAAACATTTAATTGTAATCTGTTTTAACTAAAAATGTAATAAAATTCA
* *
7303 ATTTAGAATTAATTTTATG-G-TTATAAAACCATTTAAAGAGAGTA
128 ATTTAAAATCAA--TTATGAGATTATAAAACCATTTAAAGAGAGTA
* ********** **
7347 GTAAGGCTTNNNNNNNNNNGGGTGACTATAAATGGGCCTTTCTTGCCAATGAATGGATCTCTCGC
1 ATAAGGCTTTCAAAGGCTTGGGTGACTATAAATGGGCCTTTCTTGCCAATGAATGGATCTCTCTT
* * *
7412 CATGTTTCTGCAG-AAAACATTTAATTGTAACCCGTTTTAACTAAAAATGTAA-AAAATTCAGTT
66 CATGTTTCTGCAGAAAAACATTTAATTGTAATCTGTTTTAACTAAAAATGTAATAAAATTCAATT
7475 TAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTA
131 TAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTA
*********** * * * * *
7516 ATAAGGCTTTCANNNNNNNNNNNGACTATAAATGGGCTTTTCTTACCAATGAAT-TAGTTTTTCT
1 ATAAGGCTTTCAAAGGCTTGGGTGACTATAAATGGGCCTTTCTTGCCAATGAATGGA-TCTCTCT
** * * * * * * * *
7580 TCATGTTTCT-CAAGCTAAACGTTCAATTGCAGTCTATTTTAGCTAACAATGTAATAAAATTCCA
65 TCATGTTTCTGC-AGAAAAACATTTAATTGTAATCTGTTTTAACTAAAAATGTAATAAAATTCAA
* * *
7644 TTTAGAATCAATT-TTACGGTTATAAAACCATTTAAAGAGAGTA
129 TTTAAAATCAATTATGA-GATTATAAAACCATTTAAAGAGAGTA
* * *
7687 ATAAGGCTTTCGAAGGCTTGGGTGGCTATAAATGGGTCTTTCTTGCCAATGAATGGATCTCTCTT
1 ATAAGGCTTTCAAAGGCTTGGGTGACTATAAATGGGCCTTTCTTGCCAATGAATGGATCTCTCTT
* * * * * *
7752 CATGTTTCTG-GGAAAAACATTTAATTCTAATCTGTTTTAACCAAAAAT-AAAAAAAATTCAACT
66 CATGTTTCTGCAGAAAAACATTTAATTGTAATCTGTTTTAACTAAAAATGTAATAAAATTCAATT
7815 TAAAATCAATTATGAGATTA
131 TAAAATCAATTATGAGATTA
7835 NNNNNNNNNN
Statistics
Matches: 755, Mismatches: 211, Indels: 66
0.73 0.20 0.06
Matches are distributed among these distances:
167 65 0.09
168 50 0.07
169 150 0.20
170 129 0.17
171 240 0.32
172 110 0.15
173 11 0.01
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.34
Consensus pattern (171 bp):
ATAAGGCTTTCAAAGGCTTGGGTGACTATAAATGGGCCTTTCTTGCCAATGAATGGATCTCTCTT
CATGTTTCTGCAGAAAAACATTTAATTGTAATCTGTTTTAACTAAAAATGTAATAAAATTCAATT
TAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTA
Found at i:7578 original size:340 final size:329
Alignment explanation
Indices: 6981--7834 Score: 845
Period size: 340 Copynumber: 2.5 Consensus size: 329
6971 NNNNNNGAGA
* * * *
6981 TTAT-AAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGATTATAAATGGGCTTTT
1 TTATAAAACCATTTAAAGAGAGTAATAAGGCTTTCGAAGGCTTGGGTGACTATAAATGGGCCTTT
* * *** ** * * * *
7045 CTTGCCAATGAATGGGT-TATTCTTTATGTTTCTCGAGGTAAACATTAAATTATAATCAGTTTTA
66 CTTGCCAATGAATGGATCT-CTCGCCATGTTTCT-GAGAAAAACATTTAATTCTAACCCGTTTTA
* ** * * * *
7109 ACCAAAAATGTACAAACCATTTAGCTTAAAATCAATTATG-GTATTACAAAACCATTTGAAGGGA
129 ACCAAAAA--TAAAAAAAATTCAACTTAAAATCAATTATGAG-ATTATAAAACCATTT-AA-AGA
* *** * * *
7173 GTAATAACATCTTCAAAGGCTTGGGTGATTATAAATGGGCTTTTCTTGCCAACGAATTGGTTTTT
189 G-AGT-A-A---T--AAGGCTT-TCAGACTATAAATGGGCTTTTCTTACCAACGAATTAGTTTTT
** * *
7238 CTTCAAGTTTC-CGAAGCTAAACGTTCAATTATTGTCTGTTTTAGCTAATAATGTAATAAAATTC
245 CTTCAAGTTTCTC-AAGCTAAACGTTCAATTACAGTCTATTTTAGCTAACAATGTAATAAAATTC
* *
7302 AATTTAGAATTAATTTTATGG
309 AATTTAGAATCAATTTTACGG
* **********
7323 TTATAAAACCATTTAAAGAGAGTAGTAAGGCTTNNNNNNNNNNGGGTGACTATAAATGGGCCTTT
1 TTATAAAACCATTTAAAGAGAGTAATAAGGCTTTCGAAGGCTTGGGTGACTATAAATGGGCCTTT
*
7388 CTTGCCAATGAATGGATCTCTCGCCATGTTTCTGCAG-AAAACATTTAATTGTAACCCGTTTTAA
66 CTTGCCAATGAATGGATCTCTCGCCATGTTTCTG-AGAAAAACATTTAATTCTAACCCGTTTTAA
* ** **
7452 CTAAAAATGTAAAAAATTCAGTTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAA
130 CCAAAAATAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAA
*
7517 TAAGGCTTTCANNNNNNNNNNNGACTATAAATGGGCTTTTCTTACCAATGAATTAGTTTTTCTTC
195 TAAGGCTTTCA-----------GACTATAAATGGGCTTTTCTTACCAACGAATTAGTTTTTCTTC
* * *
7582 ATGTTTCTCAAGCTAAACGTTCAATTGCAGTCTATTTTAGCTAACAATGTAATAAAATTCCATTT
249 AAGTTTCTCAAGCTAAACGTTCAATTACAGTCTATTTTAGCTAACAATGTAATAAAATTCAATTT
7647 AGAATCAATTTTACGG
314 AGAATCAATTTTACGG
* *
7663 TTATAAAACCATTTAAAGAGAGTAATAAGGCTTTCGAAGGCTTGGGTGGCTATAAATGGGTCTTT
1 TTATAAAACCATTTAAAGAGAGTAATAAGGCTTTCGAAGGCTTGGGTGACTATAAATGGGCCTTT
** * * *
7728 CTTGCCAATGAATGGATCTCTCTTCATGTTTCTGGGAAAAACATTTAATTCTAATCTGTTTTAAC
66 CTTGCCAATGAATGGATCTCTCGCCATGTTTCTGAGAAAAACATTTAATTCTAACCCGTTTTAAC
7793 CAAAAATAAAAAAAATTCAACTTAAAATCAATTATGAGATTA
131 CAAAAATAAAAAAAATTCAACTTAAAATCAATTATGAGATTA
7835 NNNNNNNNNN
Statistics
Matches: 421, Mismatches: 74, Indels: 36
0.79 0.14 0.07
Matches are distributed among these distances:
330 7 0.02
332 1 0.00
335 1 0.00
336 1 0.00
337 2 0.00
338 3 0.01
339 3 0.01
340 293 0.70
341 2 0.00
342 33 0.08
343 74 0.18
344 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.35
Consensus pattern (329 bp):
TTATAAAACCATTTAAAGAGAGTAATAAGGCTTTCGAAGGCTTGGGTGACTATAAATGGGCCTTT
CTTGCCAATGAATGGATCTCTCGCCATGTTTCTGAGAAAAACATTTAATTCTAACCCGTTTTAAC
CAAAAATAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAAT
AAGGCTTTCAGACTATAAATGGGCTTTTCTTACCAACGAATTAGTTTTTCTTCAAGTTTCTCAAG
CTAAACGTTCAATTACAGTCTATTTTAGCTAACAATGTAATAAAATTCAATTTAGAATCAATTTT
ACGG
Found at i:8503 original size:172 final size:170
Alignment explanation
Indices: 8204--9081 Score: 1034
Period size: 171 Copynumber: 5.1 Consensus size: 170
8194 NNNNNNNNNN
** *
8204 ACTATAAATGGGCTTTTCTTGCCAATGAATTAGTTTTTCTTCATGTTTCTCAAGCG-AAACATTC
1 ACTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCTCGAG-GTAAACATTC
** * * * *
8268 AATTGCAATTTGTTTTAGCCAAAAATGTAATAAAATTCAA--TCTAATATCAATTTTACGATTAT
65 AATTATAATCTGTTTTAACCAAAAATGTAA-AAAATTCAACTTC-AA-ATCAATTATAAGATTAT
*
8331 AAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGTTTGGGTG
127 AAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTG
* * *
8375 ACTCATAAATGGGATTTTCTTGCCAATGAATGGGTTTTTCCTCATGCTTCTCGAGGTAAACATTC
1 ACT-ATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCTCGAGGTAAACATTC
* * *
8440 AAGTATAATCTGTGTTAACCAAAAATGTAAAATAAATCAACTTCAAATCAATTATAAGATTATAA
65 AATTATAATCTGTTTTAACCAAAAATGTAAAA-AATTCAACTTCAAATCAATTATAAGATTATAA
* * *
8505 AACCATGTAAAGAGAGTAATAAGGCTTTTGAAGTCTTGGGCG
129 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTG
* * *
8547 ACTATAAATGGGCTTTTCTTGCCAATAAATGGATTTTTCTTCATATTTCTCGAGGTAAACATTCA
1 ACTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCTCGAGGTAAACATTCA
* * *
8612 AGTATAATCTGTGTTAA-CAAAAATTGTAAAATAAATCAACTTCAAATCAATTATAAGATTATAA
66 ATTATAATCTGTTTTAACCAAAAA-TGTAAAA-AATTCAACTTCAAATCAATTATAAGATTATAA
*
8676 AACCATTTAAAGA-ATATAATAAGGCTTTTGAAGGCTTGGGTG
129 AACCATTTAAAGAGA-GTAATAAGGCTTTTGAAGGCTTGGGTG
* * * * * * *
8718 ACTATAAATGGGCTTTTTTTGTCAATGAATAGCTTTTTCTTTAGGTTTCAT-GAGGCAAACATTC
1 ACTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTC-TCGAGGTAAACATTC
* * * * * ** *
8782 AATTATAATCAGTTTTAACTAAAAATGTAAAAACCATTTAGCTTAAAATCAATTATGGGATTACA
65 AATTATAATCTGTTTTAACCAAAAATGTAAAAA--ATTCAACTTCAAATCAATTATAAGATTATA
*
8847 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCTTGGGTG
128 AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTG
* * *
8890 ACTATAAATGGGCTTTGCTTGCCAATGAATTGGTTTTTCTTCAGGTTTCTC-AGGCTAAACATTC
1 ACTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCTCGAGG-TAAACATTC
* * *** * * * * * *
8954 AATTACAGTCTGTTTTAGTTAACAATGTAATAAAATTCAA-TTTAGAGTCAATTTTACGGTTATA
65 AATTATAATCTGTTTTAACCAAAAATGTAA-AAAATTCAACTTCA-AATCAATTATAAGATTATA
* *
9018 AAACCATTTGAAGAGAGTAGTAAGGCTTTTGAAGGCTTGGGTG
128 AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTG
*
9061 ACTATAAATGGGCCTTTCTTG
1 ACTATAAATGGGCTTTTCTTG
9082 NNNNNNNNNN
Statistics
Matches: 613, Mismatches: 78, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
170 11 0.02
171 310 0.51
172 284 0.46
173 6 0.01
174 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (170 bp):
ACTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCTCGAGGTAAACATTCA
ATTATAATCTGTTTTAACCAAAAATGTAAAAAATTCAACTTCAAATCAATTATAAGATTATAAAA
CCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTG
Found at i:8833 original size:343 final size:340
Alignment explanation
Indices: 8204--9081 Score: 1072
Period size: 343 Copynumber: 2.6 Consensus size: 340
8194 NNNNNNNNNN
* *
8204 ACTATAAATGGGCTTTTCTTGCCAATGAAT-TAGTTTTTCTTCATGTTTCTCAAGCG-AAACATT
1 ACTATAAATGGGCTTTTCTTGCCAATAAATGGA-TTTTTCTTCATGTTTCTC-AG-GTAAACATT
* * *
8267 CAATTGCAATTTGTTTTAGCCAAAAATGTAATAAAATTCAA-TCTAATATCAATTTTACGATTAT
63 CAATTACAATCTGTTTTAGACAAAAATGTAATAAAATTCAATTC-AA-ATCAATTTTACGATTAT
* *
8331 AAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGTTTGGGTGACTCATAAATGGGATTTTCTT
126 AAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACT-ATAAATGGGCTTTTCTT
* * * * *
8396 GCCAATGAATGGGTTTTTCCTCATGCTTCTCGAGGTAAACATTCAAGTATAATCTGTGTTAACCA
190 GCCAATGAATAGCTTTTTCCTCAGGCTTCTCGAGGCAAACATTCAAGTATAATCAGTGTTAACCA
* *
8461 AAAATGTAAAATAAATCAACTTCAAATCAATTATAAGATTATAAAACCATGTAAAGAGAGTAATA
255 AAAATGTAAAATAAATCAACTTAAAATCAATTATAAGATTACAAAACCATGTAAAGAGAGTAATA
*
8526 AGGCTTTTGAAGTCTTGGGCG
320 AGGCTTTTGAAGGCTTGGGCG
*
8547 ACTATAAATGGGCTTTTCTTGCCAATAAATGGATTTTTCTTCATATTTCTCGAGGTAAACATTCA
1 ACTATAAATGGGCTTTTCTTGCCAATAAATGGATTTTTCTTCATGTTTCTC-AGGTAAACATTCA
* * * * * *
8612 AGTATAATCTGTGTTA-ACAAAAATTGTAA-AATAAATCAACTTCAAATCAATTATAAGATTATA
65 ATTACAATCTGTTTTAGACAAAAA-TGTAATAA-AATTCAA-TTCAAATCAATTTTACGATTATA
* *
8675 AAACCATTTAAAGA-ATATAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTTTTG
127 AAACCATTTAAAGAGA-GTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTG
* * * * * * *
8739 TCAATGAATAGCTTTTTCTTTAGGTTTCAT-GAGGCAAACATTCAATTATAATCAGTTTTAACTA
191 CCAATGAATAGCTTTTTCCTCAGGCTTC-TCGAGGCAAACATTCAAGTATAATCAGTGTTAACCA
* * * ** * *
8803 AAAATGTAAAA-ACCATTTAGCTTAAAATCAATTATGGGATTACAAAACCATTTAAAGTGAGTAA
255 AAAATGTAAAATA--AATCAACTTAAAATCAATTATAAGATTACAAAACCATGTAAAGAGAGTAA
*
8867 TAAGGCTTTTGAAGGCTTGGGTG
318 TAAGGCTTTTGAAGGCTTGGGCG
* * *
8890 ACTATAAATGGGCTTTGCTTGCCAATGAATTGG-TTTTTCTTCAGGTTTCTCAGGCTAAACATTC
1 ACTATAAATGGGCTTTTCTTGCCAAT-AAATGGATTTTTCTTCATGTTTCTCAGG-TAAACATTC
* ** * * * *
8954 AATTACAGTCTGTTTTAGTTAACAATGTAATAAAATTCAATTTAGAGTCAATTTTACGGTTATAA
64 AATTACAATCTGTTTTAGACAAAAATGTAATAAAATTCAATTCA-AATCAATTTTACGATTATAA
* * *
9019 AACCATTTGAAGAGAGTAGTAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCCTTTCTTG
128 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTG
9082 NNNNNNNNNN
Statistics
Matches: 457, Mismatches: 62, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
341 1 0.00
342 93 0.20
343 346 0.76
344 15 0.03
345 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (340 bp):
ACTATAAATGGGCTTTTCTTGCCAATAAATGGATTTTTCTTCATGTTTCTCAGGTAAACATTCAA
TTACAATCTGTTTTAGACAAAAATGTAATAAAATTCAATTCAAATCAATTTTACGATTATAAAAC
CATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCCAAT
GAATAGCTTTTTCCTCAGGCTTCTCGAGGCAAACATTCAAGTATAATCAGTGTTAACCAAAAATG
TAAAATAAATCAACTTAAAATCAATTATAAGATTACAAAACCATGTAAAGAGAGTAATAAGGCTT
TTGAAGGCTTGGGCG
Found at i:9929 original size:170 final size:170
Alignment explanation
Indices: 9490--9977 Score: 453
Period size: 170 Copynumber: 2.9 Consensus size: 170
9480 TTGAATGTAA
* *
9490 AAAATTCAACTTAAAATCAATTATGAGATTATGAAA-TCATATAAAGAGAGTAATAAGGCTTTTG
1 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACTAAT-TAAAGAGAGTAATAAGGCTTTTG
* * * * * * * *
9554 AAGGCCTGTGTGACTATAAATGGGCTTTTCATGACAATGAATTGGTTTTTCTTCTTGTTTCTCAA
65 AAGGCCTGGGTGACTATAAATGGGATTTTCTTGCCAATGAA-TGGTCTCTCTTCATGTTTCGCAA
* * *
9619 GCCAAACATTCAATTGCAATTTGTTTTAGCCAACAATATAAT
129 GCAAAACATTCAATTGCAATTTGTTTTAACCAAAAATATAAT
* * * * * *
9661 AAAATTCAATTTAAAATCAATTTTGTGGTTATAAAACTAATTAAAGAGACTAATAAGGCATTTGA
1 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACTAATTAAAGAGAGTAATAAGGCTTTTGA
* **********
9726 AGGCTTGGGTGACTATANNNNNNNNNNTCTTGCCAATGAATGGATCTCTCTTCATGTTT-GCAAG
66 AGGCCTGGGTGACTATAAATGGGATTTTCTTGCCAATGAATGG-TCTCTCTTCATGTTTCGCAAG
* *
9790 GAAAACATTCAATTGCAATTTTTTTTAACCAAAAATATAA-
130 CAAAACATTCAATTGCAATTTGTTTTAACCAAAAATATAAT
* **********
9830 AACAATTCAACTTAAAATCGATTATGAGATTATNNNNNNNNNNAAAGAGAGTAATAAGGCTTTTG
1 AA-AATTCAACTTAAAATCAATTATGAGATTATAAAACTAATTAAAGAGAGTAATAAGGCTTTTG
* * *
9895 AAGGCCTGGGTGACTATAAATGGGATTTTCTTGCCAATGAATTAGTTTTTCTTCATGTTTCTG-A
65 AAGGCCTGGGTGACTATAAATGGGATTTTCTTGCCAATGAA-TGGTCTCTCTTCATGTTTC-GCA
* * *
9959 ACCCAAACACTCAATTGCA
128 AGCAAAACATTCAATTGCA
9978 NNNNNNNNNN
Statistics
Matches: 245, Mismatches: 66, Indels: 12
0.76 0.20 0.04
Matches are distributed among these distances:
169 2 0.01
170 130 0.53
171 109 0.44
172 4 0.02
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.33
Consensus pattern (170 bp):
AAAATTCAACTTAAAATCAATTATGAGATTATAAAACTAATTAAAGAGAGTAATAAGGCTTTTGA
AGGCCTGGGTGACTATAAATGGGATTTTCTTGCCAATGAATGGTCTCTCTTCATGTTTCGCAAGC
AAAACATTCAATTGCAATTTGTTTTAACCAAAAATATAAT
Done.