Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397607.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2661.1, 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: 4863
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.34
Warning! 192 characters in sequence are not A, C, G, or T
Found at i:293 original size:172 final size:172
Alignment explanation
Indices: 2--728 Score: 817
Period size: 172 Copynumber: 4.2 Consensus size: 172
1 T
* * * *
2 TCATGTTTCTTGATGTAGACATTCAATTATAATATGTTTTAACT-AAAAA-AGTATAAAAAATAA
1 TCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAA-TGAAAAATA-TAAAAAAAATTA
* * * **
65 AACTTAAAATCAATTTAGAGAGCATAAAACTATTTAAAATGCGTAATAAGGCTTTTGGAGTAATG
64 AACTTAAAATCAATTTTGAGAGCATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGTAATG
* ** *
130 GGAGACTATAAATGGACTTTCCTTGCTGATAAATGCTTTTTTCC
129 GGAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTCC
* * *
174 TCATATTTCTTGAGGTAGACAGTT-AATTATAATCTGTTTTAATGAAAAATATTAAAAAAATTGA
1 TCATGTTTCTTGAGGTAGACA-TTCAATTATAATCTGTTTTAATGAAAAATATAAAAAAAATTAA
* *
238 ACTTAAAATCAATTTTTAGAGCATAAAA-TCATTTAAAGTGAGTAATAAGGCTTTTGAAGTAATG
65 ACTTAAAATCAATTTTGAGAGCATAAAACT-ATTTAAAGTGAGTAATAAGGCTTTTAAAGTAATG
* * *
302 GGAGACTATAAATGAACTTTTGTTGCCGATAAATGTTTTTTTCC
129 GGAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTCC
* * * * * *
346 TCACGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAATGTGAAAAAAAATTGA
1 TCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAATGAAAAATAT-AAAAAAAATTAA
* ** * * *
411 ACTTAAAATCAATTATGAGATTATAAAACCA-TTAAAGTGAGTAATAAGGCTTTTAAAG-GATGA
65 ACTTAAAATCAATTTTGAGAGCATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGTAATGG
* * * *
474 GCGACTACAAATGCACTTTTCTTGCCAATAAATGTTTTTTTCT
130 GAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTCC
* * * * * *
517 TCATGTTTCTTGAAGTAGACATTCAATCATAGTTTGTTTTAA-GTAAAATGTAAAAAAAATTAAA
1 TCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAATGAAAAATATAAAAAAAATTAAA
* * ** * * *
581 CATAAAATCAATTTTAAGATAATAAAACTATTTAAAGTCGA-TAATAAGGCTGTTAAAGGAATCG
66 CTTAAAATCAATTTTGAGAGCATAAAACTATTTAAAGT-GAGTAATAAGGCTTTTAAAGTAATGG
* * *
645 GTGACTATAAATGGACTTTGT-TTGCCAAT-AATGTGTTTTTCT
130 GAGACTATAAATGGACTTT-TCTTGCCAATAAATGTTTTTTTCC
* **
687 TCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAA
1 TCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAA
729 CTAAANNNNN
Statistics
Matches: 478, Mismatches: 66, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
169 37 0.08
170 77 0.16
171 109 0.23
172 216 0.45
173 39 0.08
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (172 bp):
TCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAATGAAAAATATAAAAAAAATTAAA
CTTAAAATCAATTTTGAGAGCATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGTAATGGG
AGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTCC
Found at i:557 original size:171 final size:172
Alignment explanation
Indices: 1--4371 Score: 937
Period size: 171 Copynumber: 25.3 Consensus size: 172
* * * * *
1 TTCATGTTTCTTGATGTAGACATTCAATTATAATATGTTTTAA-CTAAAAAAGTATAAAAAATAA
1 TTCATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAATC-AAAAATGTAAAAAAAATTA
* * * * **
65 AACTTAAAATCAATTTAGAGAGCATAAAACTATTTAAAATGCGTAATAAGGCTTTTGGAGTAATG
65 AACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAATG
* ** *
130 GGAGACTATAAATGGACTTTCCTTGCTGATAAATGCTTTTTTC
130 GGAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * * * * * *
173 CTCATATTTCTTGAGGTAGACAGTT-AATTATAATCTGTTTTAATGAAAAATATTAAAAAAATTG
1 TTCATGTTTCTTGAAGTAGACA-TTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAAATTA
* * *
237 AACTTAAAATCAATTTTTAGAGCATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGTAATG
65 AACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAATG
* * *
302 GGAGACTATAAATGAACTTTTGTTGCCGATAAATGTTTTTTTC
130 GGAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * *
345 CTCACGTTTCTT-AAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAATGTGAAAAAAAATT
1 TTCATGTTTCTTGAA-GTAGACATTCAATTATAATCTGTTTTAATCAAAAATGT-AAAAAAAATT
* * ** *
409 GAACTTAAAATCAATTATGAGATTATAAAACCA-TTAAAGTGAGTAATAAGGCTTTTAAAG-GAT
64 AAACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAAT
* * * *
472 GAGCGACTACAAATGCACTTTTCTTGCCAATAAATGTTTTTTTC
129 GGGAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * *
516 TTCATGTTTCTTGAAGTAGACATTCAATCATAGTTTGTTTTAAGT--AAAATGTAAAAAAAATTA
1 TTCATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAA-TCAAAAATGTAAAAAAAATTA
* * ** * * *
579 AACATAAAATCAATTTTAAGATAATAAAACTATTTAAAGTCGA-TAATAAGGCTGTTAAAGGAAT
65 AACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGT-GAGTAATAAGGCTTTTAAAGTAAT
* * *
643 CGGTGACTATAAATGGACTTTGT-TTGCCAAT-AATGTGTTTTTC
129 GGGAGACTATAAATGGACTTT-TCTTGCCAATAAATGTTTTTTTC
* *
686 TTCACGTTTC-TCAAGGTAGACATTCAATTATAATCTGTTTTAA-CTAAANNNNNNNNNNNNNNN
1 TTCATGTTTCTTGAA-GTAGACATTCAATTATAATCTGTTTTAATC-AAA---------------
************** * * * * * ** * *
749 NNNNNNNNNNNNNNNT-GAGTTAGACATTCAATTAT-AG-TCTATTTTAACTAAAAATGTAAAGA
49 -AATGTAAAAAAAATTAAACTTA-A-AATCAATTTTGAGAGC-A---TAA--AACCATTTAAAGT
* * ** * **** * * *
811 AATTGAACATAAAATCAATTTT-GAGATAANNNNNNNNNNTAAAGCGAGTAATAAGG-CTTTTGA
105 GA--GTA-AT-AAGGC--TTTTAAAG-TAA-------TGGGAGA-CTA-TAA-ATGGACTTTT--
** * *
874 AGGAATGAACAACTATAAATGAACTGTTTTTTT
151 ---CTTG--C--CAATAAATG---T-TTTTTTC
* ** * * * **
907 TAATAAATGATTTTTTCTACACATTTCCCAATGCAAGCATTGAATCATTGTCTGTTTTAAT-AGA
1 T--T-CATG----TTTCTTGA-A-GT----A-G--A-CATTCAATTATAATCTGTTTTAATCA-A
* * * * ** ********** **
971 AAATAT-AAAAAAATTCAACTGAAAATCAATTATGAGATTATAANNNNNNNNNNAGCAAGTAATA
48 AAATGTAAAAAAAATTAAACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATA
* * * * * *
1035 AGGCTTTTGAAGAAATAGGG-GACTATAAATAGAGTTTTCTTGCCAATTAATGCTTTTTTC
113 AGGCTTTTAAAGTAAT-GGGAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * * * * * * * *
1095 TTAACGTTTCTTGAGGTAGGCATTCAATTATAGTCCGTTTTAATCAAAAAT-TTATAAAAATTGA
1 TTCATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAAATTAA
*********** * * ** *
1159 ACTTAAAATCAATTANNNNNNNNNNAAACTATTTATAGCAAGTAATAAGGCTTTTGAAA-AAATG
66 ACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTT-AAAGTAATG
* * * * **
1223 GGAGACTATATATAGACTTTTCTTGTCAATGAATGCATTTTTC
130 GGAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * ** * ****
1266 TTCAAGTTTCTTGACGTAGACATTCAATTATTGTCTGTTTTAAACAAAAATGT-AAAAAAANNNN
1 TTCATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAAATTAA
****** * * ** * * * * *
1330 NNNNNNAATCAATTATAAGATTATAAAACTATTTAAAGCGCGAAATAAGGCTTTTGAAG-AGATG
66 ACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTA-ATG
* * * * * *
1394 AGAGATTATAAATGGAGTTTTTTTGCCAATGAATGCTTTTTTC
130 GGAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * * * * ** *
1437 TTAATGTTTCTCGAGGTAGATACTT-AATTA-AAGTCTGTTTTAACCAAAAAT-TTGAGAAAATT
1 TTCATGTTTCTTGAAGTAGACA-TTCAATTATAA-TCTGTTTTAATCAAAAATGTAAAAAAAATT
* * ** **********
1499 GAACTTAAAATCAATTATGAGATTATAAAACCNNNNNNNNNNAGTAATAAGGCTTTTGAAAG-AA
64 AAACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTT-AAAGTAA
* * * *
1563 TGGGAGAATATAAATGGACGTTTCTTGCCAATGAATGCTTTTTTC
128 TGGGAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * * * * * *
1608 TTCATATTTCTCGAGGTAAACATTCAACTATAGTCTGTTTTAAGT-AAAAATGTATAAAAAATTA
1 TTCATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAA-TCAAAAATGTAAAAAAAATTA
* ** * * * * * * *
1672 AA-TATAAAATCAATTTTGACATAATAAAATCGTTTAAAGTGGGTAATAGGGCTTTTGATGAAAT
65 AACT-TAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAAT
* * ** **
1736 GGGTA-ATTATAAGTGGACTTTTCTT-CTCAACGAATAACTTTTTT-
129 GGG-AGACTATAAATGGACTTTTCTTGC-CAATAAAT-GTTTTTTTC
* * * * * * * * * *
1780 TACACGTTTC-TCAAGGCA-AGCATTCAATCACAATTTGTTTTAATAAAAAATAT-AAGAAAATT
1 TTCATGTTTCTTGAA-GTAGA-CATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAAATT
* * * ** ** * * *
1842 TAACTTAAAATCAATTATGAGA-CTATAAAACTATTTAAAGCAAAAAATAAGTCTTTTGAAGGAA
64 AAACTTAAAATCAATTTTGAGAGC-ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAA
* * * * *
1906 TGAGAGACTATAAACGGATTTTTCTT-CTCAATGAATGGATTTTTT-
128 TGGGAGACTATAAATGGACTTTTCTTGC-CAATAAAT-GTTTTTTTC
* * * * * * * ***
1951 TACATGTTTCCT-AAGGTAGGCATTGACTTATAGTCTATTTTAA-CTAAAAATGT-AAAAAANNN
1 TTCATGTTTCTTGAA-GTAGACATTCAATTATAATCTGTTTTAATC-AAAAATGTAAAAAAAATT
******* * ** *** ** * * *
2013 NNNNNNNAAATCAATTATGAGATTATAAAATTTTTTAAAACGAGTAATAAGGGTTTTGAAGGAAT
64 AAACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAAT
* * * * *
2078 AGGTGACTATAAACAGG-CTTTTCTTACCGATAAATGTGTTTTTT-
129 GGGAGACTATAAA-TGGACTTTTCTTGCCAATAAATGT-TTTTTTC
** * * * * * * *
2122 TTCACATTTC-TCAAGATAAACATTCAATTATAGTCTGTTTTAACCACAAATAT-AAAAAAATTG
1 TTCATGTTTCTTGAAG-TAGACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAAATTA
* * ** * * * * * *
2185 AACATAAAATTAATTTTGAGATAAGAAAACTATTTAAAGCGAGTAATAAGACTTTTGAAGGAATG
65 AACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAATG
* *** * * * **
2250 GGTGACTATAAACAAACTTTT-TTTCTTAATGAATGGCTTTTTC
130 GGAGACTATAAATGGACTTTTCTTGC-CAATAAATGTTTTTTTC
* ** ** ** * * *
2293 TACACATTT-TCCAAGGTA-ACCATTCAATCGTAATCTGTTTTAATAAAAAATAT-CAAAAAATT
1 TTCATGTTTCTTGAA-GTAGA-CATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAAATT
* * * ** * * * *
2355 TAACTAAAAATCAATTATGCA-ATTATAAAACCATTTAAAGCGAGTAATATGGCTTTTGAAGGAA
64 AAACTTAAAATCAATTTTG-AGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAA
* * * * *
2419 T-GGACGACTATAAATAGACTTTTCTTACCAATGAATGCTTTTTTA
128 TGGGA-GACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * * *
2464 TTCATGTTTC-TCAAGGTAGACATTGAATTATAATATGTTTTAA-CTAAAAATATAAAAAAAAAT
1 TTCATGTTTCTTGAA-GTAGACATTCAATTATAATCTGTTTTAATC-AAAAATGT-AAAAAAAAT
* * ** * * * * * * *
2527 TGAACATAAAATCAATTAAGCCG-GTA-ATAAAGCTTTTGAA--GA--AAT--GGGTATCTACAA
63 TAAACTTAAAATCAATTTTG-AGAGCATA-AAACCATTTAAAGTGAGTAATAAGGCT-TTTA-AA
* ****** *
2584 ATATACTTTTCTTCTCA-ACGAATGG-C-TTT-TT--C-A-ACATG---TTTTC
124 GTA-A-TGGGAGACT-ATA--AATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * * * ** *
2627 --CAAG------GCAG--G-TATTCAATCATAGCCTGTTTTAATAAAAAATGTAAAAAAAAATTA
1 TTCATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAATCAAAAATGT-AAAAAAAATTA
* ************** * *
2681 AACTTAAAATCAATTATGAGATTNNNNNNNNNNNNAAAGTGAGTAATAAGGCTTTTGAAGGAATG
65 AACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAATG
* * * ** *
2746 GGAGACTATAAATGGACTTCTCTTTCCAATGAATGCCTTTTCC
130 GGAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * * * ***
2789 TTCATGTTTCTTGATGTACACATTCAATTATAATTTGTTTTAA-CAAAAAAAGTAAAAAAANNNN
1 TTCATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAATC-AAAAATGTAAAAAAA-ATT
****** * * * *
2853 NNNNNNAAAATCAATTTTGAGAGTATAAAACCATTTAAAGTTAGTAATGAGGCTTTTAAAGGAAT
64 AAACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAAT
* * * *
2918 -GGAGGACTATAAATAGAATTTTCTTG-CAGATGAATACTTTTTTTC
129 GGGA-GACTATAAATGGACTTTTCTTGCCA-ATAAAT-GTTTTTTTC
* * * * * *
2963 -TCACGTTTCTTGAGGTAGACATTTAATTATAGTCTATTTTAA-CTAAAAATGT-AAAAAAATTC
1 TTCATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAATC-AAAAATGTAAAAAAAATTA
* * ********** * ** * * *
3025 TACTTAAAATCAATTATGNNNNNNNNNNACTATTTAAAGAAAGTAGTAAGGCTTTTGAAGGAAT-
65 AACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAATG
* * * * *
3089 AGATGACTGTAAATGGACTTTTCTTGCCACTGAATGTATTTTTC
130 GGA-GACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * * ** * *
3133 TTCATATTTCTCGAGGTAGACATTCAATTATTGTCTGTTTTAA-CTACAAATGT-AAAAAAATTC
1 TTCATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAATC-AAAAATGTAAAAAAAATTA
* *** * * * *
3196 AACTTAAAATCAATTATGAGATTGTAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATG
65 AACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAATG
* * * *
3261 AGAGACTATAAATGGACTTTTCTTGCTAATGAATGTATTTTTC
130 GGAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * * * **
3304 TTCATGTTTC-TCAATGTAGACATGCAATTATAATCTGTTTTAA-CTAAAAAAGTATAAAAAANN
1 TTCATGTTTCTTGAA-GTAGACATTCAATTATAATCTGTTTTAATC-AAAAATGTAAAAAAAATT
******** * * *
3367 NNNNNNNNAATCAATTTTGAGAGCATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGTAAA
64 AAACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAAT
* * * * *
3432 GAGAGACTATAAATAGACTTTTCTTACCGATAAATGCTTTTTTC
129 GGGAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * ********** * *
3476 CTCATGTTTCTTGAGGTAGACATTCAATNNNNNNNNNNTTTAATAAAAAATAT-AAAAAAATT-A
1 TTCATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAAATTAA
* * ** * * *
3539 ACTTAAAATCAATTATGAGA-CTATAAAACCATTTAAAGTGAGAAATAAATCTGTTGAAGGAATG
66 ACTTAAAATCAATTTTGAGAGC-ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAATG
* * **
3603 AGAGACTATAAATGGACTTTTCTT-CTCAATGAATGGATTTTTC
130 GGAGACTATAAATGGACTTTTCTTGC-CAATAAATGTTTTTTTC
* * * * * * * * *
3646 TACATGTTTCCTGAGGTAGGCATTGACTTATAGTCTATTTTGA-CAAAAAATGTAAAAAAAATT-
1 TTCATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAATC-AAAAATGTAAAAAAAATTA
* * ** ********* * * * *
3709 AATTTAAAATCAATTATGAGATTATAANNNNNNNNNNAA-CGAGTAATAAGGCTTTTGACGAAAT
65 AACTTAAAATCAATTTTGAGAGCATAA-AACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAAT
* * * *
3773 AGGTGACTATAAATGGACTTTTCTTACCAATAAATGTGTTTTTC
129 GGGAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* ** * * * * *
3817 TTCAAGTATT-TCAAAGAAGACATTCAATTACAATCT-ATTTAA-CTAAAAA-GTAAAAAGATTT
1 TTCATGT-TTCTTGAAGTAGACATTCAATTATAATCTGTTTTAATC-AAAAATGTAAAAAAAATT
* ** * * *
3878 GAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAG---T--GAC-TTTAAAGGAA-
64 AAACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAAT
** * * * *
3936 AAGATGACTATAAATGAACTTTTCTTACCAATAAATTCTTTTTTTT
129 GGGA-GACTATAAATGGACTTTTCTTGCCAATAAA-TGTTTTTTTC
* * * * * *
3982 TTCACGTTTCTTG-AGTTACACATTCAATTATAGTCTGTTTTAACCAAAAATAT-AAGAAAATTA
1 TTCATGTTTCTTGAAG-TAGACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAAATTA
* ** *********** *
4045 AA-TATAAAATTAATTTTGAGATAATAAAACCATTTAAAGCT-AGTAANNNNNNNNNNGAAGGAA
65 AACT-TAAAATCAATTTTGAGAGCATAAAACCATTTAAAG-TGAGTAATAAGGCTTTTAAAGTAA
* * * * * **
4108 TGAGTGACTATAAACGGACTTTTCTT-CTTAATGAATGGCTTTTTC
128 TGGGAGACTATAAATGGACTTTTCTTGC-CAATAAATGTTTTTTTC
* ** ** * * * *
4153 TAT-ATATTT-TCCAAGGTA-AGCATTTTATCATAGTCTGTTTTAATCAAAAA--TATAAAAATT
1 T-TCATGTTTCTTGAA-GTAGA-CATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAAAT
* * ** * * * * *
4213 TAAACTTAAAATCAATTATAAGATTATAAAATCATTTAAAGTGAGTAATATGACTTTTGAAGGAA
63 TAAACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAA
* * * * * *
4278 T-AGACGATTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTA
128 TGGGA-GACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
* * * * * *
4323 TTTATATTTC-TCAGGGTAGACATTGAATTATAATCTGTTTTAACCAAAA
1 TTCATGTTTCTTGA-AGTAGACATTCAATTATAATCTGTTTTAATCAAAA
4372 NNNNNNNNNN
Statistics
Matches: 3074, Mismatches: 885, Indels: 482
0.69 0.20 0.11
Matches are distributed among these distances:
151 1 0.00
152 59 0.02
153 3 0.00
154 8 0.00
155 4 0.00
156 7 0.00
157 3 0.00
158 4 0.00
159 3 0.00
161 3 0.00
162 4 0.00
163 6 0.00
164 43 0.01
165 33 0.01
166 56 0.02
167 7 0.00
168 3 0.00
169 65 0.02
170 391 0.13
171 1412 0.46
172 538 0.18
173 224 0.07
174 6 0.00
175 1 0.00
179 1 0.00
181 6 0.00
185 3 0.00
186 5 0.00
187 5 0.00
188 15 0.00
190 3 0.00
191 1 0.00
192 16 0.01
194 2 0.00
195 2 0.00
196 5 0.00
197 2 0.00
198 5 0.00
200 2 0.00
201 7 0.00
202 2 0.00
203 1 0.00
205 1 0.00
206 3 0.00
207 7 0.00
208 3 0.00
210 6 0.00
211 2 0.00
212 5 0.00
213 2 0.00
214 3 0.00
216 7 0.00
217 4 0.00
218 3 0.00
220 10 0.00
221 11 0.00
222 4 0.00
223 1 0.00
224 2 0.00
228 4 0.00
229 2 0.00
230 2 0.00
234 1 0.00
235 1 0.00
237 2 0.00
238 21 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.34
Consensus pattern (172 bp):
TTCATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAAATTAA
ACTTAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGTAATGG
GAGACTATAAATGGACTTTTCTTGCCAATAAATGTTTTTTTC
Found at i:3497 original size:172 final size:171
Alignment explanation
Indices: 2716--4371 Score: 946
Period size: 171 Copynumber: 9.7 Consensus size: 171
2706 NNNNNNNNNN
* * * *
2716 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTCTCTTTCCAATGAATG
1 AAAGTGAGTAATAAGGCTTTTGAAGGAAAGAGAGACTATAAATGGACTTTTCTTGCCAATGAATG
* * * * *
2781 C-CTTTTCCTTCATGTTTCTTGATGTACACATTCAATTATAATTTGTTTTAACAAAAAAAGTAAA
66 CTTTTTTCC-TCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTAAA
******** * *
2845 AAAANNNNNNNNNNAAAATCAATTTTGAGAGTATAAAACCATTT
130 AAAA--TTCAACTTAAAATCAATTATGAGAGTATAAAACTATTT
* * * * * *
2889 AAAGTTAGTAATGAGGCTTTTAAAGGAATG-GAGGACTATAAATAGAATTTTCTTG-CAGATGAA
1 AAAGTGAGTAATAAGGCTTTTGAAGGAAAGAGA-GACTATAAATGGACTTTTCTTGCCA-ATGAA
* * * * * * *
2952 TACTTTTTTTCTCACGTTTCTTGAGGTAGACATTTAATTATAGTCTATTTTAACTAAAAATGTAA
64 TGCTTTTTTCCTCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTAA
* **********
3017 AAAAATTCTACTTAAAATCAATTATGNNNNNNNNNNACTATTT
129 AAAAATTCAACTTAAAATCAATTATGAGAGTATAAAACTATTT
** * * * *
3060 AAAGAAAGTAGTAAGGCTTTTGAAGGAATAGA-TGACTGTAAATGGACTTTTCTTGCCACTGAAT
1 AAAGTGAGTAATAAGGCTTTTGAAGGAA-AGAGAGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * ** * *
3124 G-TATTTTTCTTCATATTTCTCGAGGTAGACATTCAATTATTGTCTGTTTTAACTACAAATGTAA
65 GCT-TTTTTCCTCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTAA
* *
3188 AAAAATTCAACTTAAAATCAATTATGAGATTGTAAAACTATTT
129 AAAAATTCAACTTAAAATCAATTATGAGAGTATAAAACTATTT
* *
3231 AAAGCGAGTAATAAGGCTTTTGAA-GAAATGAGAGACTATAAATGGACTTTTCTTGCTAATGAAT
1 AAAGTGAGTAATAAGGCTTTTGAAGGAAA-GAGAGACTATAAATGGACTTTTCTTGCCAATGAAT
* ** * *
3295 G-TATTTTTCTTCATGTTTCTCAATGTAGACATGCAATTATAATCTGTTTTAACTAAAAAAGTAT
65 GCT-TTTTTCCTCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTA-
********** * *
3359 AAAAAANNNNNNNNNNAATCAATTTTGAGAGCATAAAACTATTT
128 AAAAAATTCAACTTAAAATCAATTATGAGAGTATAAAACTATTT
* * * * *
3403 AAAGTGAGTAATAAGGCTTTTGAAGTAAAGAGAGACTATAAATAGACTTTTCTTACCGATAAATG
1 AAAGTGAGTAATAAGGCTTTTGAAGGAAAGAGAGACTATAAATGGACTTTTCTTGCCAATGAATG
********** *
3468 CTTTTTTCCTCATGTTTCTTGAGGTAGACATTCAATNNNNNNNNNNTTTAA-TAAAAAATATAAA
66 CTTTTTTCCTCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAA-GTAAA
* *
3532 AAAATT-AACTTAAAATCAATTATGAGACTATAAAACCATTT
130 AAAATTCAACTTAAAATCAATTATGAGAGTATAAAACTATTT
* ** * *
3573 AAAGTGAGAAATAAATCTGTTGAAGGAATGAGAGACTATAAATGGACTTTTCTT-CTCAATGAAT
1 AAAGTGAGTAATAAGGCTTTTGAAGGAAAGAGAGACTATAAATGGACTTTTCTTGC-CAATGAAT
** * * * * * * *
3637 GGATTTTT-CTACATGTTTCCTGAGGTAGGCATTGACTTATAGTCTATTTTGAC-AAAAAATGTA
65 GCTTTTTTCCT-CATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAA-GT-
* * ********
3700 AAAAAAATT-AATTTAAAATCAATTATGAGATTATAANNNNNNNNN
127 AAAAAAATTCAACTTAAAATCAATTATGAGAGTATAA-AACTATTT
* * * * * * *
3745 NAA-CGAGTAATAAGGCTTTTG-ACGAAATAGGTGACTATAAATGGACTTTTCTTACCAATAAAT
1 AAAGTGAGTAATAAGGCTTTTGAAGGAAAGA-GAGACTATAAATGGACTTTTCTTGCCAATGAAT
* * ** * * * *
3808 G-TGTTTTTCTTCAAGTATT-TCAAAGAAGACATTCAATTACAATCT-ATTTAACT-AAAAAGTA
65 GCT-TTTTTCCTCATGT-TTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTA
* * * * *
3869 AAAAGATTTGAACTTAAAATCAATTTTGAGATTATAAAACCATTT
128 AAAA-AATTCAACTTAAAATCAATTATGAGAGTATAAAACTATTT
* * * * * *
3914 AAAGCGAG---T--GAC-TTTAAAGGAAA-AGATGACTATAAATGAACTTTTCTTACCAATAAAT
1 AAAGTGAGTAATAAGGCTTTTGAAGGAAAGAGA-GACTATAAATGGACTTTTCTTGCCAATGAAT
* ** * * * * *
3972 TCTTTTTTTTTTCACGTTTCTTGAGTTACACATTCAATTATAGTCTGTTTTAACCAAAAATA-TA
65 GC-TTTTTTCCTCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAA-AGTA
* * * * *
4036 AGAAAATT-AAATATAAAATTAATTTTGAGA-TAATAAAACCATTT
128 AAAAAATTCAACT-TAAAATCAATTATGAGAGT-ATAAAACTATTT
********** * * * *
4080 AAAGCT-AGTAANNNNNNNNNNGAAGGAATGAGTGACTATAAACGGACTTTTCTT-CTTAATGAA
1 AAAG-TGAGTAATAAGGCTTTTGAAGGAAAGAGAGACTATAAATGGACTTTTCTTGC-CAATGAA
* * ** * * *
4143 TGGC-TTTTT-CT-ATATATT-TTCCAAGGTA-AGCATTTTATCATAGTCTGTTTTAA-TCAAAA
64 T-GCTTTTTTCCTCATGT-TTCTT--GAGGTAGA-CATTCAATTATAATCTGTTTTAACTAAAAA
* * * *
4202 A-TATAAAAATTTAAACTTAAAATCAATTATAAGATTATAAAA-TCATTT
124 AGTA-AAAAAATTCAACTTAAAATCAATTATGAGAGTATAAAACT-ATTT
* * * * *
4250 AAAGTGAGTAATATGACTTTTGAAGGAATAGA-CGATTATAAATGGACTTTTCTTACCAATGAAT
1 AAAGTGAGTAATAAGGCTTTTGAAGGAA-AGAGAGACTATAAATGGACTTTTCTTGCCAATGAAT
** * * * * *
4314 GCTTTTTTATTTATATTTC-TCAGGGTAGACATTGAATTATAATCTGTTTTAACCAAAA
65 GCTTTTTTCCTCATGTTTCTTGA-GGTAGACATTCAATTATAATCTGTTTTAACTAAAA
4372 NNNNNNNNNN
Statistics
Matches: 1129, Mismatches: 289, Indels: 132
0.73 0.19 0.09
Matches are distributed among these distances:
163 1 0.00
164 36 0.03
165 40 0.04
166 44 0.04
167 10 0.01
168 6 0.01
169 22 0.02
170 275 0.24
171 413 0.37
172 168 0.15
173 109 0.10
174 5 0.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
AAAGTGAGTAATAAGGCTTTTGAAGGAAAGAGAGACTATAAATGGACTTTTCTTGCCAATGAATG
CTTTTTTCCTCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTAAAA
AAATTCAACTTAAAATCAATTATGAGAGTATAAAACTATTT
Found at i:3754 original size:513 final size:506
Alignment explanation
Indices: 2716--4371 Score: 1295
Period size: 513 Copynumber: 3.2 Consensus size: 506
2706 NNNNNNNNNN
* * * * *
2716 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTCTCTTTCCAATGAATG
1 AAAGCGAGTAATAAGGCTTTTGAAGAAATGAGAGACTATAAATGGACTTTTCTTACCAATGAATG
** * ** * * *
2781 CCTTTTCCTTCATGTTTCTTGATGTACACATTCAATTATAATTTGTTTTAACAAAAAAAGTAAAA
66 TATTTTTCTTCATGTTTCTCAATGTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTAAAA
* * * *
2846 AAANNNNNNNNNNAAAATCAATTTTGAGAGTATAAAACCATTTAAAGTTAGTAATGAGGCTTTTA
131 AAA---------AAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTA
* * * *
2911 AAGGAATGGAGGACTATAAATAGAATTTTCTTGCAGATGAATACTTTTTTTCTCACGTTTCTTGA
187 AAGGAAAGGAGGACTATAAATAGAATTTTCTTACAGATAAATACTTTTTTCCTCACGTTTCTTGA
* * *
2976 GGTAGACATTTAATTATAGTCTATTTTAACTAAAAATGTAAAAAAATTCTACTTAAAATCAATTA
252 GGTAGACATTCAATTATAGTCTATTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTA
********** * * * * * *
3041 TGNNNNNNNNNNACTATTTAAAGAAAGTAGTAAGGCTTTTGAAGGAATAGATGACTGTAAATGGA
317 TGAGACTATAAAACCATTTAAAGAAAGAAATAAAGCTGTTGAAGGAATAGATGACTATAAATGGA
* * * * *
3106 CTTTTCTTGCCACTGAATGTATTTTTCTTCATATTTCTCGAGGTAGACATTCAATTATTGTCTGT
382 CTTTTCTTGCCAATGAATGGATTTTTCTACATATTTCTCGAGGTAGACATTCAATTATAGTCTAT
* * *
3171 TTTAACTACAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTGTAAAACTATTT
447 TTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTT
* *
3231 AAAGCGAGTAATAAGGCTTTTGAAGAAATGAGAGACTATAAATGGACTTTTCTTGCTAATGAATG
1 AAAGCGAGTAATAAGGCTTTTGAAGAAATGAGAGACTATAAATGGACTTTTCTTACCAATGAATG
*
3296 TATTTTTCTTCATGTTTCTCAATGTAGACATGCAATTATAATCTGTTTTAACTAAAAAAGTATAA
66 TATTTTTCTTCATGTTTCTCAATGTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTA-AA
*** * *
3361 AAAANNNNNNNNNNAATCAATTTTGAGAGCATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGA
130 AAAA-------AAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAA
* * * * *
3426 AGTAAA-GAGAGACTATAAATAGACTTTTCTTACCGATAAATGCTTTTTTCCTCATGTTTCTTGA
188 AGGAAAGGAG-GACTATAAATAGAATTTTCTTACAGATAAATACTTTTTTCCTCACGTTTCTTGA
**********
3490 GGTAGACATTCAATNNNNNNNNNNTTTAA-TAAAAAATATAAAAAAATT-AACTTAAAATCAATT
252 GGTAGACATTCAATTATAGTCTATTTTAACT-AAAAATATAAAAAAATTCAACTTAAAATCAATT
** *
3553 ATGAGACTATAAAACCATTTAAAGTGAGAAATAAATCTGTTGAAGGAATGAGA-GACTATAAATG
316 ATGAGACTATAAAACCATTTAAAGAAAGAAATAAAGCTGTTGAAGGAAT-AGATGACTATAAATG
* * * *
3617 GACTTTTCTT-CTCAATGAATGGATTTTTCTACATGTTTC-CTGAGGTAGGCATTGACTTATAGT
380 GACTTTTCTTGC-CAATGAATGGATTTTTCTACATATTTCTC-GAGGTAGACATTCAATTATAGT
* * *******
3680 CTATTTTGACAAAAAATGTAAAAAAAATT-AATTTAAAATCAATTATGAGATTATAANNNNNNNN
443 CTATTTTAACAAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAA-AACTATT
*
3744 N
506 T
* * * *
3745 NAA-CGAGTAATAAGGCTTTTGACGAAAT-AGGTGACTATAAATGGACTTTTCTTACCAATAAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGAAATGA-GAGACTATAAATGGACTTTTCTTACCAATGAAT
* * * * * *
3808 GTGTTTTTCTTCAAGTATT-TCAAAGAAGACATTCAATTACAATCT-ATTTAACT-AAAAAGTAA
65 GTATTTTTCTTCATGT-TTCTCAATGTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTAA
** * *
3870 AAAGATTTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAG---T--GAC-TTT
129 AAA-A----AA---AAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTT
* * * **
3929 AAAGGAAAAGATGACTATAAAT-GAACTTTTCTTACCA-ATAAATTCTTTTTTTTTTCACGTTTC
186 AAAGGAAAGGAGGACTATAAATAGAA-TTTTCTTA-CAGATAAATAC-TTTTTTCCTCACGTTTC
* * * * * * *
3992 TTGAGTTACACATTCAATTATAGTCTGTTTTAACCAAAAATATAAGAAAATT-AAATATAAAATT
248 TTGAGGTAGACATTCAATTATAGTCTATTTTAACTAAAAATATAAAAAAATTCAACT-TAAAATC
* ** * **********
4056 AATTTTGAGA-TAATAAAACCATTTAAAGCTAGTAANNNNNNNNNNGAAGGAAT-GAGTGACTAT
312 AATTATGAGACT-ATAAAACCATTTAAAGAAAGAAATAAAGCTGTTGAAGGAATAGA-TGACTAT
* * * * * **
4119 AAACGGACTTTTCTT-CTTAATGAATGGCTTTTTCTATATATTT-TCCAAGGTA-AGCATTTTAT
375 AAATGGACTTTTCTTGC-CAATGAATGGATTTTTCTACATATTTCT-CGAGGTAGA-CATTCAAT
* * * * * *
4181 CATAGTCTGTTTTAATC-AAAAATAT-AAAAATTTAAACTTAAAATCAATTATAAGATTATAAAA
437 TATAGTCTATTTTAA-CAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
4244 -TCATTT
501 CT-ATTT
* * * * *
4250 AAAGTGAGTAATATGACTTTTGAAGGAAT-AGACGATTATAAATGGACTTTTCTTACCAATGAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGAAATGAGA-GACTATAAATGGACTTTTCTTACCAATGAAT
* * * ** * *
4314 GCT-TTTTTATTTATATTTCTCAGGGTAGACATTGAATTATAATCTGTTTTAACCAAAA
65 G-TATTTTTCTTCATGTTTCTCAATGTAGACATTCAATTATAATCTGTTTTAACTAAAA
4372 NNNNNNNNNN
Statistics
Matches: 913, Mismatches: 189, Indels: 85
0.77 0.16 0.07
Matches are distributed among these distances:
504 2 0.00
505 48 0.05
506 166 0.18
507 123 0.13
508 6 0.01
510 4 0.00
511 41 0.04
512 10 0.01
513 239 0.26
514 155 0.17
515 113 0.12
516 6 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (506 bp):
AAAGCGAGTAATAAGGCTTTTGAAGAAATGAGAGACTATAAATGGACTTTTCTTACCAATGAATG
TATTTTTCTTCATGTTTCTCAATGTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTAAAA
AAAAAAAATCAATTTTGAGAGCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAAAGG
AGGACTATAAATAGAATTTTCTTACAGATAAATACTTTTTTCCTCACGTTTCTTGAGGTAGACAT
TCAATTATAGTCTATTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGACTAT
AAAACCATTTAAAGAAAGAAATAAAGCTGTTGAAGGAATAGATGACTATAAATGGACTTTTCTTG
CCAATGAATGGATTTTTCTACATATTTCTCGAGGTAGACATTCAATTATAGTCTATTTTAACAAA
AAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTT
Done.