Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399713.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2959.0, 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: 6029
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.32
Warning! 844 characters in sequence are not A, C, G, or T
Found at i:624 original size:171 final size:171
Alignment explanation
Indices: 447--759 Score: 384
Period size: 171 Copynumber: 1.8 Consensus size: 171
437 NNNNNNNNNN
*** ** *
447 TGACTATAAATGGACTTTTCTTACCACTGGA-TATCTTTCTT-TTCATG-TTTCTTGAGGTAGAC
1 TGACTATAAATGGACTTTTCTTACCA-AAAATTATCTTT-TTCTTCATGTTTTC-TGAGACAAAC
* * *
509 ATTCAATTATT-TTGTATTTTAACCAAAAATGTAAAAACATTTG-ACTTAAAATCAATTATAAGA
63 ATTCAATTATTATT-TATTTAAACAAAAAATGTAAAAA-AATTGAACTTAAAATCAATTATAAGA
572 TTATAAAAACATTTAAAGCGAGTGAAATGCCTTTTGTAAGCGTAGG
126 TTATAAAAACATTTAAAGCGAGTGAAATGCCTTTTGTAAGCGTAGG
* * *
618 TGACTATAAATGGATTTTTCTTGCCAAAAATTATCTTTTTCTTCCTGTTTTCTGAGACAAACATT
1 TGACTATAAATGGACTTTTCTTACCAAAAATTATCTTTTTCTTCATGTTTTCTGAGACAAACATT
* * * * * *
683 CAATTATTATTTGTTTAAATAAAAAATTTAAAAAAATTGAACTTAAAATCCATTATGAGTTTATA
66 CAATTATTATTTATTTAAACAAAAAATGTAAAAAAATTGAACTTAAAATCAATTATAAGATTATA
748 AAAACATTTAAA
131 AAAACATTTAAA
760 CCTAGTAAAA
Statistics
Matches: 119, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
170 7 0.06
171 106 0.89
172 6 0.05
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.39
Consensus pattern (171 bp):
TGACTATAAATGGACTTTTCTTACCAAAAATTATCTTTTTCTTCATGTTTTCTGAGACAAACATT
CAATTATTATTTATTTAAACAAAAAATGTAAAAAAATTGAACTTAAAATCAATTATAAGATTATA
AAAACATTTAAAGCGAGTGAAATGCCTTTTGTAAGCGTAGG
Found at i:930 original size:171 final size:161
Alignment explanation
Indices: 617--917 Score: 291
Period size: 171 Copynumber: 1.8 Consensus size: 161
607 GTAAGCGTAG
** * *
617 GTGACTATAAATGGATTTTTCTTGCCAAAAATTATCTTTTTCTTCCTGTTTTCTGAGACAAACAT
1 GTGACTATAAATGGACGTTTCTTGCCAAAAATTATCTTTTTCTTACTGTTTTCTAAGACAAACAT
* * * * * * *
682 TCAATTATTATTTGTTTAAATAAAAAATTTAAAAAAATTGAACTTAAAATCCATTATGAGTTTAT
66 TCAATTATAATCTGTTTAAATAAAAAATGTAAAAAAATTCAACTTAAAATCAAATATGAGATTAT
747 AAAAACATTTAAACCTAGTAAAAAGGCTTTT
131 AAAAACATTTAAACCTAGTAAAAAGGCTTTT
* *
778 NNNNNNNNNNGTGACTATAAATGGACGTTTCTTGCCAATGAA-TATCTTTTTATTTAC-GTTTTC
1 ----------GTGACTATAAATGGACGTTTCTTGCCAA-AAATTATCTTTTT-CTTACTGTTTTC
** * * * * * *
841 TAAGGTAGACTTTTAATTATAATCTGTTTTAATGAAAAATGTAAAAAACTTCAACTTAAAATCAA
54 TAAGACAAACATTCAATTATAATCTGTTTAAATAAAAAATGTAAAAAAATTCAACTTAAAATCAA
906 ATATGAGATTAT
119 ATATGAGATTAT
918 GAAGCCATTT
Statistics
Matches: 107, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
171 102 0.95
172 5 0.05
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.39
Consensus pattern (161 bp):
GTGACTATAAATGGACGTTTCTTGCCAAAAATTATCTTTTTCTTACTGTTTTCTAAGACAAACAT
TCAATTATAATCTGTTTAAATAAAAAATGTAAAAAAATTCAACTTAAAATCAAATATGAGATTAT
AAAAACATTTAAACCTAGTAAAAAGGCTTTT
Found at i:2174 original size:171 final size:169
Alignment explanation
Indices: 1977--3636 Score: 519
Period size: 171 Copynumber: 9.7 Consensus size: 169
1967 ATAAAATCAT
* * * *
1977 TTAAAGCGAGTAATAAGGCTTTCAAAGACATGAGTGACTATAAATGAGCTTTTCTTGGCAATGAA
1 TTAAAGCGAGTAATAAAGCTTTCAAAGACATG-GTGACTATAAATGAACTTTTCTTGTCAATGGA
* ** * *
2042 TACCTTTTTCTTCACATTTCTCGAGGTAAACATTCAATTATAATCTATTTTTAAAAAAAACAG-A
65 TATCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCT-GTTTTAAAAAAAA-AGTA
*
2106 AATAAATTCAACTTAAAATCAAATATGAGATTACAAAGCCAA
128 AACAAATTCAACTTAAAATCAAATATGAGATTACAAAGCCAA
* * **********
2148 TTAAAGCAAGTAATAAAGCTTTCAAAGGCATGGGTGACTATAAATGANNNNNNNNNNTCAATGGA
1 TTAAAGCGAGTAATAAAGCTTTCAAAGACAT-GGTGACTATAAATGAACTTTTCTTGTCAATGGA
* ** *
2213 TATCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTGCAATCTGTTTTAAAAAAAATGTAAA
65 TATCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAAAAAAAAAGTAAA
* * *********
2278 CAAATTCAACTTGAAATCAATTATGAGATTATNNNNNNNN
130 CAAATTCAACTTAAAATCAAATATGAGATTACAAAGCCAA
** * * *
2318 NNAAAGCGAGTAATAAAGCTTTCGAAGTCATGGCTGATTATAAATGAACTTTTCTTGTCAATGGA
1 TTAAAGCGAGTAATAAAGCTTTCAAAGACATGG-TGACTATAAATGAACTTTTCTTGTCAATGGA
* *****************
2383 TATCTTTTTCTTCATGTTTTTCGAGGTAGACATTCAATTATAATCTGNNNNNNNNNNNNNNNNNN
65 TATCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTG-TTTTAAAAAAAAAGTAA
********** * * *
2448 NNNNNNNNNNCTTAAAATCAATTATGAGATTATAGAA-CCAT
129 ACAAATTCAACTTAAAATCAAATATGAGATTACA-AAGCCAA
** ** * *
2489 TTAAAGCGAGTAATAAAGCTTTTGAAGGTATGAGTGAATATAAATCG-ACTTTTCTTGCCAATGG
1 TTAAAGCGAGTAATAAAGCTTTCAAAGACATG-GTGACTATAAAT-GAACTTTTCTTGTCAATGG
* * * ********* *
2553 ATATCTTTTTCCTCAAGTTTCTCAAGGTAGACATTCANNNNNNNNNNGTTTTAACTTAAAATGTA
64 ATATCTTTTTCTTCATGTTTCTCGAGGTAGACATTCA--ATTATAATCTGTT---TT-AAA---A
* * ** * ** *
2618 CAAAAATGTACAA-AAATTCAAGTCAAAATCATTTACGAGATT-CTAAAAACAT
120 -AAAAA-GTA-AACAAATTCAACTTAAAATCAAATATGAGATTAC-AAAGCCAA
* * * * ** * *
2670 TTTAGGC-ATGTAATAAGGGTTTTGAAGACATGGGTGACTATAAATGGACTTTTCTTGTCAATGA
1 TTAAAGCGA-GTAATAAAGCTTTCAAAGACAT-GGTGACTATAAATGAACTTTTCTTGTCAATGG
************ * * ** * * * * * *
2734 ATGGNNNNNNNNNNAGGTTTCCCTTGGTAAACATTTAGTTATTATTTGTTTTAATTAAAAATA-T
64 ATATCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAA--AAAAAAAGT
* * * * * *
2798 AAA-AATATTCACCTTGAAATCAATTATGAGATTATAAAACCAT
127 AAACAA-ATTCAACTTAAAATCAAATATGAGATTACAAAGCCAA
********** * ** *
2841 TTAAAGCGAGTAANNNNNNNNNNAAAGGCATGGGTGACTATAAATGGGCTTTTCTTGTCAATGAA
1 TTAAAGCGAGTAATAAAGCTTTCAAAGACAT-GGTGACTATAAATGAACTTTTCTTGTCAATGGA
* * ** * * * * *
2906 TACTTTTTTTTTTCACATTTCTCAAGGTAAAAATTCAATTATAATCAGTTTTAACAAAAAAATAT
65 TA-TCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAA-AAAAAAA-GT
* * *
2971 AAACAAATTCAACCTAAAATTAAATATGAGATTACAAAGCCAT
127 AAACAAATTCAACTTAAAATCAAATATGAGATTACAAAGCCAA
* * ********** * *
3014 TTAAAGCAAGTAATAAGGCNNNNNNNNNNATGGGTGACTATAAATGGACTTTTCTTGCCAATGGA
1 TTAAAGCGAGTAATAAAGCTTTCAAAGACAT-GGTGACTATAAATGAACTTTTCTTGTCAATGGA
* * * * * * *
3079 T-TTTTTTTCTTCAAGTTTTTTGAGGTAGACATTCAATTACAATCTCTTTT-AAAAAAATGTAAA
65 TATCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAAAAAAAAAGT-AA
* *********** * ** *
3142 AAAAATTCAACTTAAAATCAGNNNNNNNNNNATAAAATCAT
129 ACAAATTCAACTTAAAATCAAATATGAGATTACAAAGCCAA
* * ** * *
3183 TTAAAGCGAGTAATAAGGCTTTCGAAGTTATGGTTGATTATAAATGAACTTTTCTTGACAATGGA
1 TTAAAGCGAGTAATAAAGCTTTCAAAGACATGG-TGACTATAAATGAACTTTTCTTGTCAATGGA
* * * *
3248 TATCTTTTTCTTCATGTTTCTCAAGGTAAACAGTCAATTATAATATGTTTTAATAAAAAATA-TA
65 TATCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAA-AAAAAA-AGTA
* ********** * * * *
3312 AAAAAATTCAACTTNNNNNNNNNNATGAGATTATAAAACTAT
128 AACAAATTCAACTTAAAATCAAATATGAGATTACAAAGCCAA
* * * * **
3354 TTAAAGCGAGTAAT-AAGCCATTCGAAAG-CATGGGTAACTATAAATGGACTTTTTTTACCAATG
1 TTAAAGCGAGTAATAAAG-CTTTC-AAAGACAT-GGTGACTATAAATGAACTTTTCTTGTCAATG
* * * * * * *
3417 GATATCTTTTTCTTTACGTTTCTCAAGTTAGACATTCAATTATTATTTATTTTAACTAAAAATAA
63 GATATCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAA--AAAAA-AA
* * * * * *
3482 --AAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAACC-T
125 GTAAACAAATTCAACTTAAAATCAAATATGAGATTA-CAAAGCCAA
** * * * * *
3525 TTAAAATGAGTAAT-AAGACTTTCGAAGGCATGAGTAACTATAGATGAACTTTTCTTTTCAATGG
1 TTAAAGCGAGTAATAAAG-CTTTCAAAGACATG-GTGACTATAAATGAACTTTTCTTGTCAATGG
* * *
3589 ATATCTTTTTCTTCCTGTTTCTTGAGGTAGACATTTAATTATAATCTG
64 ATATCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTG
3637 NNNNNNNNNN
Statistics
Matches: 1065, Mismatches: 377, Indels: 94
0.69 0.25 0.06
Matches are distributed among these distances:
168 3 0.00
169 84 0.08
170 182 0.17
171 544 0.51
172 57 0.05
173 90 0.08
174 3 0.00
175 2 0.00
176 2 0.00
177 1 0.00
179 3 0.00
180 4 0.00
181 89 0.08
182 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.33
Consensus pattern (169 bp):
TTAAAGCGAGTAATAAAGCTTTCAAAGACATGGTGACTATAAATGAACTTTTCTTGTCAATGGAT
ATCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAAAAAAAAAGTAAAC
AAATTCAACTTAAAATCAAATATGAGATTACAAAGCCAA
Found at i:2632 original size:9 final size:10
Alignment explanation
Indices: 2610--2634 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2600 GTTTTAACTT
2610 AAAATGTACA
1 AAAATGTACA
2620 AAAATGTACA
1 AAAATGTACA
2630 AAAAT
1 AAAAT
2635 TCAAGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (10 bp):
AAAATGTACA
Found at i:4101 original size:171 final size:171
Alignment explanation
Indices: 3663--4681 Score: 459
Period size: 171 Copynumber: 6.0 Consensus size: 171
3653 NNNNAATTCA
* * * * * * *
3663 ACTTAAAATTAATTATAAAATTATAAAAACATTTAAAGC-GAGTAATAAGGCC-TTTGAAGGCAT
1 ACTTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAG-GTAA-AAAGCCTTTTGAAAGCGT
* * * * * *
3726 GAGTGATTATAAATGGACTTTTCTTACCAATGAATATCTTTCTCTTAACGTTTCTTGAGGCAGAC
64 GGGTGACTACAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTAACATTTCTTGAGGCAGAC
* *
3791 ATTCAATTATTATTTATTTTAACCAAAAATATAAAAAAATTAG
129 ATTCAATTACTATTTATTTTAACAAAAAATATAAAAAAATTAG
* *
3834 ACTTAAAATCAATTATTAGATTATAAAAATATTTAAAGCAGGTAAAAAGCCTTTTGAAGGCGTGG
1 ACTTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAGGTAAAAAGCCTTTTGAAAGCGTGG
* ********** * * *
3899 GTGACTATAANNNNNNNNNNCTTGCCAATGAATATCTTTTTCTTCATATTTTTTGAGGCAGACAT
66 GTGACTACAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTAACATTTCTTGAGGCAGACAT
*
3964 TCAATTACTATTTATTTTAACAAAAAATATAAGAAAATT-G
131 TCAATTACTATTTATTTTAACAAAAAATATAAAAAAATTAG
* * ********** * *
4004 AACTTGAAATCCATTATGAGATTANNNNNNNNNNTAAAGCTA-GTAAAAAGGCTTTTGAAAGTGT
1 -ACTTAAAATCAATTATGAGATTATAAAAATATTTAAAGC-AGGTAAAAAGCCTTTTGAAAGCGT
* * *** * *
4068 GGGTGACTACAAATGGACTTTTCTTGTCAATGAATATCTTTTTCTTTACATTTCCCAATGTAGAC
64 GGGTGACTACAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTAACATTTCTTGAGGCAGAC
* * * **********
4133 ATTCAATTA-TAATCTGTTTTAATAANNNNNNNNNNAAAATTCA-
129 ATTCAATTACT-ATTTATTTTAACAAAAAATATAAAAAAATT-AG
* * * * * * *
4176 ACTTAAAATTAATTGTAAGATTATAAAAACATTTAAA--ATGAGTAATAAGGCTTTT-AAAGGCA
1 ACTTAAAATCAATTATGAGATTATAAAAATATTTAAAGCA-G-GTAAAAAGCCTTTTGAAA-GCG
** * * ********** * ** * * * *
4238 TGACTGACTATAAAAGGACTTTTCNNNNNNNNNNATATCTTTTTCTTCATGTTTCCTAAGGTAAA
63 TGGGTGACTACAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTAACATTTCTTGAGGCAGA
* * * ** * **
4303 CATTCAA-TATTTATCTGTTTTAATGAAACACGTAAAAAAATTCA-
128 CATTCAATTA-CTATTTATTTTAACAAAAAATATAAAAAAATT-AG
* ********** * * * *
4347 ATTTAAAATCAATTATGAGATTATANNNNNNNNNNAAGC-GAGTAATAAGACTTTTGAAGGCATG
1 ACTTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAG-GTAAAAAGCCTTTTGAAAGCGTG
* * * * * * * *
4411 AGTGACTATAAATGGACTTTTCTAGCCACTGGATATTTTTTTCTT--CATGTT-TTCCAAGGTAG
65 GGTGACTACAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTAACAT-TTCTT--GAGGCAG
* * * **
4473 ACATTCAATTATTATTTATTTTAACTAAAAATGTAAAAAAATTTC
127 ACATTCAATTACTATTTATTTTAACAAAAAATATAAAAAAATTAG
* * * *
4518 ACTTAAAATCAATTATGGGATTATAAAAACATTTAAAGC-GAGTAAAAAGTCTTTTGAAGGCGTG
1 ACTTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAG-GTAAAAAGCCTTTTGAAAGCGTG
* * * * ** **
4582 AGTGACTATAAATGGACTTTTCTTGCAAATAAATATCTTTTTCTTCCCATTTCCCGAGGCAGACA
65 GGTGACTACAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTAACATTTCTTGAGGCAGACA
* * * * *
4647 TTCAATTATTATCTGTTTTAACCAAAAATGTAAAA
130 TTCAATTACTATTTATTTTAACAAAAAATATAAAA
4682 NNNNNNNNNN
Statistics
Matches: 631, Mismatches: 193, Indels: 48
0.72 0.22 0.06
Matches are distributed among these distances:
168 1 0.00
169 2 0.00
170 14 0.02
171 602 0.95
172 9 0.01
173 3 0.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.35
Consensus pattern (171 bp):
ACTTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAGGTAAAAAGCCTTTTGAAAGCGTGG
GTGACTACAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTAACATTTCTTGAGGCAGACAT
TCAATTACTATTTATTTTAACAAAAAATATAAAAAAATTAG
Found at i:4620 original size:342 final size:334
Alignment explanation
Indices: 3355--4674 Score: 815
Period size: 342 Copynumber: 3.9 Consensus size: 334
3345 TAAAACTATT
* * * * * * * *
3355 TAAAGCGAGTAATAAGCCATTCGAAAGCATGGGTAACTATAAATGGACTTTTTTTA-CCAATGGA
1 TAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGAC-TTTTCTAGCCAATGAA
* * *
3419 TATCTTTTTCTTTACG-TTTCTCAAGTTAGACATTCAATTATTATTTATTTTAACTAAAAATAAA
65 TATCTTTTTCTTAACGTTTTC-CAAGGTAGACATTCAATTATTATTTATTTTAACTAAAAATATA
* * * ** * * *
3483 AAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAACCTTTAAAATGAGTAATAAGACTTTC
129 AAAAAATTTCACTTAAAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAAAAAGCCTTTT
* * * * * * ** * * *
3548 GAAGGCATGAGTAACTATAGATGAACTTTTCTTTTC-AATGGATATCTTTTTCTTCCTGTTTCTT
194 GAAGGCGTGAGTGACTATAAAAGGACTTTTC-TTGCAAATAAATATCTTTTTCTTCATATTTCCT
* * * ******************** *
3612 GAGGTAGACATTTAATTATAATCTG-NNNNNNNNNNNNNNNNNNNNAATTCAACTTAAAATTAAT
258 GAGGCAGACATTCAATTATTATCTGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAAT
* *
3676 TATAAAATTATAAAAACA
323 TATGAGATTAT------A
* *
3694 TTTAAAGCGAGTAATAAGGCCTTTGAAGGCATGAGTGATTATAAATGGACTTTTCTTA-CCAATG
1 --TAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTTTC-TAGCCAATG
* ** * *
3758 AATATCTTTCTCTTAACG-TTTCTTGAGGCAGACATTCAATTATTATTTATTTTAACCAAAAATA
63 AATATCTTTTTCTTAACGTTTTC-CAAGGTAGACATTCAATTATTATTTATTTTAACTAAAAATA
** * *
3822 TAAAAAAATTAGACTTAAAATCAATTATTAGATTATAAAAATATTTAAAGC-AGGTAAAAAGCCT
127 TAAAAAAATTTCACTTAAAATCAATTATAAGATTATAAAAACATTTAAAGCGA-GTAAAAAGCCT
* ********** * * *
3886 TTTGAAGGCGTGGGTGACTATAANNNNNNNNNNCTTGCCAATGAATATCTTTTTCTTCATATTTT
191 TTTGAAGGCGTGAGTGACTATAAAAGGACTTTTCTTGCAAATAAATATCTTTTTCTTCATATTTC
* * * * * * * * *
3951 TTGAGGCAGACATTCAATTACTATTTATTTTAACAAAAAATATAAGAAAATTGAACTTGAAATCC
256 CTGAGGCAGACATTCAATTATTATCTGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCA
**
4016 ATTATGAGATTANNNNNNNNNN
321 ATTATGAGATTA--------TA
* * * ** * * * *
4038 TAAAGCTAGTAAAAAGGCTTTTGAAAGTGTGGGTGACTACAAATGGACTTTTCTTGTCAATGAAT
1 TAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTTTCTAGCCAATGAAT
* * * * * * * ********
4103 ATCTTTTTCTTTACATTTCCCAATGTAGACATTCAATTATAATCTGTTTTAA-TAANNNNNNNNN
66 ATCTTTTTCTTAACGTTTTCCAAGGTAGACATTCAATTATTATTTATTTTAACTAA-AAATATAA
* * * ** * *
4167 NAAAA-TTCAACTTAAAATTAATTGTAAGATTATAAAAACATTTAAAATGAGTAATAAGGCTTTT
130 AAAAATTTC-ACTTAAAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAAAAAGCCTTTT
* * * ********** * *
4231 AAAGGCATGACTGACTATAAAAGGACTTTTCNNNNNNNNNNATATCTTTTTCTTCATGTTTCCTA
194 GAAGGCGTGAGTGACTATAAAAGGACTTTTCTTGCAAATAAATATCTTTTTCTTCATATTTCCTG
* * ** * * *
4296 AGGTAAACATTCAA-TATTTATCTGTTTTAATGAAACACGTAAAAAAATTCAATTTAAAATCAAT
259 AGGCAGACATTCAATTA-TTATCTGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAAT
4360 TATGAGATTATA
323 TATGAGATTATA
** *
4372 NNNNNNNNNNAAGCGAGTAATAAGACTTTTGAAGGCATGAGTGACTATAAATGGACTTTTCTAGC
1 --------TAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTTTCTAGC
* * * * *
4437 CACTGGATATTTTTTTCTTCATGTTTTCCAAGGTAGACATTCAATTATTATTTATTTTAACTAAA
58 CAATGAATATCTTTTTCTTAACGTTTTCCAAGGTAGACATTCAATTATTATTTATTTTAACTAAA
* **
4502 AATGTAAAAAAATTTCACTTAAAATCAATTATGGGATTATAAAAACATTTAAAGCGAGTAAAAAG
123 AATATAAAAAAATTTCACTTAAAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAAAAAG
* * **
4567 TCTTTTGAAGGCGTGAGTGACTATAAATGGACTTTTCTTGCAAATAAATATCTTTTTCTTCCCAT
188 CCTTTTGAAGGCGTGAGTGACTATAAAAGGACTTTTCTTGCAAATAAATATCTTTTTCTTCATAT
* *
4632 TTCCCGAGGCAGACATTCAATTATTATCTGTTTTAACCAAAAA
253 TTCCTGAGGCAGACATTCAATTATTATCTGTTTTAACAAAAAA
4675 TGTAAAANNN
Statistics
Matches: 719, Mismatches: 231, Indels: 57
0.71 0.23 0.06
Matches are distributed among these distances:
340 8 0.01
341 225 0.31
342 474 0.66
343 12 0.02
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.35
Consensus pattern (334 bp):
TAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATGGACTTTTCTAGCCAATGAAT
ATCTTTTTCTTAACGTTTTCCAAGGTAGACATTCAATTATTATTTATTTTAACTAAAAATATAAA
AAAATTTCACTTAAAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAAAAAGCCTTTTGA
AGGCGTGAGTGACTATAAAAGGACTTTTCTTGCAAATAAATATCTTTTTCTTCATATTTCCTGAG
GCAGACATTCAATTATTATCTGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTAT
GAGATTATA
Found at i:5608 original size:171 final size:169
Alignment explanation
Indices: 5217--5649 Score: 498
Period size: 171 Copynumber: 2.5 Consensus size: 169
5207 NNNNNNNNNN
* * ** * * * * **
5217 TTAAGTTAAA-TTTTTTATATTTTTTATTAAAATAGATTATAATTGAATGTCTACAT-TGGAAAA
1 TTAAGTCAAATTTTTTTAAATTTTTGGTTAAAATAAATAATAATTGAATGTCTGCCTCAAGAAAA
* *
5280 TGTGAAGAAAAATATATTCATTGGTAAGAAAAGTCCATTTGTAGTCACCCATACCTTCAAAAGCC
66 TG-G-AGAAAAATATATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCC
* *
5345 TTTTTACAGGTTTAAATATTTTTATAATCTTATAATGGATT
129 TTTTTACAGCTTTAAATATTTTTATAATCTAATAATGGATT
* * * * * * *
5386 TCATGTTC-AATTTTCTTACATTTTTGGTTAAAGTTAATAGTAATTGAATGTCTGCCTCAAGAAA
1 TTAAG-TCAAATTTTTTTAAATTTTTGGTTAAAATAAATAATAATTGAATGTCTGCCTCAAGAAA
* * * * * *
5450 CATGGAGAAAAATATATTTATTGGCAAGAAAAGTCTATTTATAGTCACTCATGCCTTTAAAAGGC
65 -ATGGAGAAAAATATATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCC
*
5515 TTTTTACCTA-CTTTAAATATTTTTATAATCTAATAATTGATT
129 TTTTTA-C-AGCTTTAAATATTTTTATAATCTAATAATGGATT
5557 TTAAGTCAAATTTTTTTAAATTTTTGGTTAAAATAAATAATAATTGAATGTCTGCCTCAAG-AAA
1 TTAAGTCAAATTTTTTTAAATTTTTGGTTAAAATAAATAATAATTGAATGTCTGCCTCAAGAAAA
*
5621 TGTGAAGAAAAAGATATTCATTGGCAAGA
66 TG-G-AGAAAAATATATTCATTGGCAAGA
5650 NNNNNNNNNN
Statistics
Matches: 219, Mismatches: 36, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
169 8 0.04
170 99 0.45
171 108 0.49
172 4 0.02
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (169 bp):
TTAAGTCAAATTTTTTTAAATTTTTGGTTAAAATAAATAATAATTGAATGTCTGCCTCAAGAAAA
TGGAGAAAAATATATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTT
TTTACAGCTTTAAATATTTTTATAATCTAATAATGGATT
Found at i:5702 original size:171 final size:169
Alignment explanation
Indices: 5227--5799 Score: 492
Period size: 171 Copynumber: 3.4 Consensus size: 169
5217 TTAAGTTAAA
* ** * * * * ** *
5227 TTTTTTATATTTTTTATTAAAATAGATTATAATTGAATGTCTACAT-TGGAAAATGTGAAGAAAA
1 TTTTTTACATTTTTGGTTAAAATAAATAATAATTGAATGTCTGCCTCAAG-AAACGTGAAGAAAA
* * * * * * *
5291 ATATATTCATTGGTAAGAAAAGTCCATTTGTAGTCACCCAT-ACCTTCAAAAGCCTTTTTACAGG
65 AGATATTCATTGGCAAGAAAAGTCTATTTATAATCACCCATGA-CTTCAAAAGCCTTTTTACCGC
* * *
5355 TTTAAATATTTTTATAATCTTATAATGGATTTCATGTTCAAT
129 TTTAAATATTTTTATAATCTAATAATTGATTTCAAG-TCAAT
* * * * * *
5397 TTTCTTACATTTTTGGTTAAAGTTAATAGTAATTGAATGTCTGCCTCAAGAAACATGGAGAAAAA
1 TTTTTTACATTTTTGGTTAAAATAAATAATAATTGAATGTCTGCCTCAAGAAACGTGAAGAAAAA
* * * * * * * *
5462 TATATTTATTGGCAAGAAAAGTCTATTTATAGTCACTCATGCCTTTAAAAGGCTTTTTACCTACT
66 GATATTCATTGGCAAGAAAAGTCTATTTATAATCACCCATGACTTCAAAAGCCTTTTTACC-GCT
*
5527 TTAAATATTTTTATAATCTAATAATTGATTTTAAGTCAAAT
130 TTAAATATTTTTATAATCTAATAATTGATTTCAAGTC-AAT
* *
5568 TTTTTTAAATTTTTGGTTAAAATAAATAATAATTGAATGTCTGCCTCAAGAAATGTGAAGAAAAA
1 TTTTTTACATTTTTGGTTAAAATAAATAATAATTGAATGTCTGCCTCAAGAAACGTGAAGAAAAA
************ * *
5633 GATATTCATTGGCAAGANNNNNNNNNNNNTAATCACCCATGACTTCGAAAGCCTTATTACTCGCT
66 GATATTCATTGGCAAGAAAAGTCTATTTATAATCACCCATGACTTCAAAAGCCTTTTTAC-CGCT
** *
5698 TTAAATGA-TTTTATAATCGCATAATTGATTTCAAGTTGAAT
130 TTAAAT-ATTTTTATAATCTAATAATTGATTTCAAG-TCAAT
* * * *
5739 TTTTTTACATTTTAT--TTAAAACAAAT-TTCAATTGAATGTCTACCTCGAGAAACGTGAAGAA
1 TTTTTTACATTTT-TGGTTAAAATAAATAAT-AATTGAATGTCTGCCTCAAGAAACGTGAAGAA
5800 NNNNNNNNNN
Statistics
Matches: 323, Mismatches: 71, Indels: 18
0.78 0.17 0.04
Matches are distributed among these distances:
169 1 0.00
170 139 0.43
171 179 0.55
172 4 0.01
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (169 bp):
TTTTTTACATTTTTGGTTAAAATAAATAATAATTGAATGTCTGCCTCAAGAAACGTGAAGAAAAA
GATATTCATTGGCAAGAAAAGTCTATTTATAATCACCCATGACTTCAAAAGCCTTTTTACCGCTT
TAAATATTTTTATAATCTAATAATTGATTTCAAGTCAAT
Done.