Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397716.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1015.0, 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: 24331
ACGTcount: A:0.25, C:0.08, G:0.09, T:0.24
Warning! 8452 characters in sequence are not A, C, G, or T
Found at i:397 original size:171 final size:170
Alignment explanation
Indices: 1--1362 Score: 1249
Period size: 171 Copynumber: 8.1 Consensus size: 170
* * * *
1 AAAATATAATAAAATTCAAC-TAGAAATCAATTATAAAATTATAAAATC-ATTTAAAGCGAGTAA
1 AAAATGTAAAAAAATTCAACTTA-AAATCAATTATGAGATTATAAAA-CAATTTAAAGCGAGTAA
* *
64 TAAGCCTTTTGACGGAAT-GGATGACTATAAATGGACTTTTCTTGCCAATGAATG----TT-TTT
64 TAAGACTTTTGAAGGAATAGGA-GACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTT
** * * *
123 ---TTTCTCAAGCAAGACATTTATTTATA-ACTGTTTTAACTA
128 ACATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACTA
* * * * * * * *
162 ATAATGTAAAACAAAAATTGAACCTAAAATCCATTTTGAGATTATAAAACCACTTGAAGCGAGTA
1 AAAATGT--AA-AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTA
** * * * *
227 ATAAGGTTTTTGAAGAAATATGAGACTATAAATGAACTTTTCTTGCCAATAAATGCTTGTTTCTT
63 ATAAGACTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTT-TTTCTT
* ** *
292 CACATTTCTTGAGGTAGACATTTAATTATAGTCTGTTTTAA-TGA
127 TACATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACT-A
*
336 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAGGCGAGTAATA
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATA
* *
401 AGACATTT----G-A-A-G-G---A-AAATGGACTTTTCTTAG-TAATGAATGTCTTTTTCTTTA
66 AGACTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTT-GCCAATGAATG-CTTTTTCTTTA
* * * * *
453 CGTTTCTCAAGTTAGACATTCAACTATAATATGTTTTAACTA
129 CATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACTA
* * ** * * *
495 ATAATGTAAAAAAATTAAACCAAAAATCAATTTTGAGATTATAAAACTATTAAAAGCGAGTAATA
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATA
* * * * *
560 AGGCTTTTGAAGAAATAGGAGACCATAAATGGACTTTTCTTGCCAATGACTACTTTTTTCTTTAC
66 AGACTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGC-TTTTTCTTTAC
* * * *
625 ATTTCTCAATGTAAACATTCAATTATACTCTATTTTAACTA
130 ATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACTA
* ** * * * * * *
666 AAAATCT-AAAAAATTCAACTGGAAATCAGTTATAAGTTTATGAAACCATTTAAAGCGAGTAGTA
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATA
* ** * * *
730 AGA-TCTTTGAAGAAATAAAAAACTATAAATGGACTTTTTTTACCAATGAATGCTTTTTACTTTA
66 AGACT-TTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTT-CTTTA
** * *
794 TGTTTCTCGAGGTA-AGCATTCAATTATAGTCTATTTTAACTA
129 CATTTCTCAAGGTAGA-CATTCAATTATAGTCTGTTTTAACTA
* *
836 AAAATGTAAACAAAATTCAACTAAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
1 AAAATGTAAA-AAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
* ** * * * * * * * *
901 AAGGCTTTAAAAGGGATGGGTGACTATAAATGGA-TATTTTTTGCTAGTGAATGCCTTATTCTTC
65 AAGACTTTTGAAGGAATAGGAGACTATAAATGGACT-TTTCTTGCCAATGAATG-CTTTTTCTTT
** * * * *
965 ATGTTTTTGAAGGTAGACATTCAATCATAGTCTGTTTTAACCA
128 ACATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACTA
* * * *
1008 TAAATGTTAAAAAATTCAACTTAAAATCAATTATGAGGTTATAAAACAATTTAAAGTGAGTAATA
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATA
* * * *
1073 AGACTTTTGAAGGAATAAGAGAATATAAATGAACTTTTCTTGCCAATCAATGCTTGTTTCTTTAC
66 AGACTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTT-TTTCTTTAC
* * * *
1138 ATTTCTCGAGGTAGACAATGAATTATAGTCTGTTTTAACAA
130 ATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACTA
* * * * *
1179 AAAATGTAAAAAAATTCAACTTGAAATCAATTATAAGATTATAAAACCATTTAACGCGTGTAATA
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATA
* * * *
1244 AGACTTTTGAAGGAATA-GATAACTATAAATGGACTTTTCTTGTCAATGAATGTATTTTTCTTCA
66 AGACTTTTGAAGGAATAGGA-GACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTTCTTTA
* * * * *
1308 C-TGTTCTTAAGGTAGACATTCAATTAAAGTCTCTTTTCACCA
129 CAT-TTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACTA
*
1350 AAAATGCAAAAAA
1 AAAATGTAAAAAA
1363 NNNNNNNNNN
Statistics
Matches: 970, Mismatches: 183, Indels: 86
0.78 0.15 0.07
Matches are distributed among these distances:
159 123 0.13
160 6 0.01
161 5 0.01
163 4 0.00
164 87 0.09
165 6 0.01
166 2 0.00
167 1 0.00
169 9 0.01
170 144 0.15
171 404 0.42
172 134 0.14
173 29 0.03
174 16 0.02
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATA
AGACTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTTACA
TTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACTA
Found at i:10187 original size:171 final size:172
Alignment explanation
Indices: 9948--10310 Score: 378
Period size: 171 Copynumber: 2.1 Consensus size: 172
9938 NNNNNNNNNN
* * * * ** * *
9948 GGTTTTATAATATCAAAATTGATTTTAGGTTCAATTTTTTTTACATTATTGGGTAAAAGTATTAT
1 GGTTTTATAATCTCATAATTAATTTTAAGTTCAATTTTTTGGACATTATTGGGTAAAAATACTAT
** * ** * * *
10013 AATTGAATGTCTAGCT-AGAGTAA-TGTGAAGAAAAAAACATTTA-TAAGC-AAGAAAAGTTCAT
66 AATTGAACCTCTACCTCA-AG-AACCATAAAGAAAAAAACATTCACT-AGCAAAAAAAAGTTCAT
* * *
10074 TTATTGTCAACC-ATTCCTTTGAAAGCCATATTACTCGCTTTAAAT
128 TTATAGT-AACCAATCCCTTTAAAAGCCATATTACTCGCTTTAAAT
* * * *
10119 GGTTTTATAATCTCGTAATTAATTTTAAGTTTAATTTTTTGGA-ATTTTTGGTTAAAACATACTA
1 GGTTTTATAATCTCATAATTAATTTTAAGTTCAATTTTTTGGACATTATTGGGTAAAA-ATACTA
* * ***
10183 TAATTGAACCTTTACCTCAAGAACCATAAAGAATAAGGGATTCACTAGCAAAAAAAAGTTCATTT
65 TAATTGAACCTCTACCTCAAGAACCATAAAGAAAAAAACATTCACTAGCAAAAAAAAGTTCATTT
*
10248 ATAGTAACCAATCCCTTTAAAAGCCTTATTACTCGCTTTAAAT
130 ATAGTAACCAATCCCTTTAAAAGCCATATTACTCGCTTTAAAT
10291 GGTTTTATAATCTCATAATT
1 GGTTTTATAATCTCATAATT
10311 GNNNNNNNNN
Statistics
Matches: 156, Mismatches: 30, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
170 14 0.09
171 73 0.47
172 69 0.44
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (172 bp):
GGTTTTATAATCTCATAATTAATTTTAAGTTCAATTTTTTGGACATTATTGGGTAAAAATACTAT
AATTGAACCTCTACCTCAAGAACCATAAAGAAAAAAACATTCACTAGCAAAAAAAAGTTCATTTA
TAGTAACCAATCCCTTTAAAAGCCATATTACTCGCTTTAAAT
Found at i:11302 original size:171 final size:170
Alignment explanation
Indices: 10772--11986 Score: 1039
Period size: 171 Copynumber: 7.1 Consensus size: 170
10762 NNNNNNNNNN
* * * * * *
10772 CAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTAAAGGGATTGGTGACTATA
1 CAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATAGGAGACTATA
* * * * * * * * * ** **
10837 AATGAACTTTTTTTTGCTAGTGAATCCCTTATTCTTTATGTTTCTTGAGGTAGAGGTTCAATTAT
66 AATGGAC-TTTTCTTACCAATGAAT-GCTTTTTCTTCATATTTCTCAAGGTAGACATTCAATTAT
* *********** *
10902 AGTCTGTTTTAACCANNNNNNNNNNNAAATTAAACTTAAAAT
129 AGTCTATTTTAACCAAAAATCTAAAAAAATTCAACTTAAAAT
** ** * * *
10944 CAATTACAAGATTATAAAACCATTTAAAGTGAGTAATATGGCTTTCGAAGGAAT-GGTTA-ACAA
1 CAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATAGG--AGACTA
* ** * * * * * * *
11007 TAAAATGGACTTTTCTTGCTTATGAATGTTTTTTTCTTCACATTACTCTAGCTAGACAATCAGTT
64 T-AAATGGACTTTTCTTACCAATGAATG-CTTTTTCTTCATATTTCTCAAGGTAGACATTCAATT
* * * * * * *
11072 ATA--ATACTTTTAACCAATAATGTAAAAATATTGAACCTAAAGT
127 ATAGTCTA-TTTTAACCAAAAATCTAAAAAAATTCAACTTAAAAT
* * * **
11115 CAATTTTGAGATTATAAAACTATTTACAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATA
1 CAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATAGGAGACTATA
** * * * * *
11180 AACAGACTTGTCTTTCCAATAAATGCTTGTTTCTTTATATTTCTCAAGGTAGACATTGAATTATA
66 AATGGACTTTTCTTACCAATGAATGCTT-TTTCTTCATATTTCTCAAGGTAGACATTCAATTATA
* ** * * *
11245 GTTTATTTTAATGAAAATTATAAAAAAATTCAACTTGAAAT
130 GTCTATTTTAACCAAAAATCTAAAAAAATTCAACTTAAAAT
* * ** * * *
11286 CAATTATAAGATTATAAAACAAGATAAAGCAAGTAATAAGGCATTTGAAGGAATGGGTGACTATA
1 CAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATAGGAGACTATA
* * *
11351 AATGGACTTTTCTTACCAATGAATGCCTTTTT-TTCACT-TTTCTCAAGATAAACGTTCAATTAT
66 AATGGACTTTTCTTACCAATGAATG-CTTTTTCTTCA-TATTTCTCAAGGTAGACATTCAATTAT
* * *
11414 AGTCTATTTTAACCAATAATGTAAAAAAATTAAAAC-TAAAAT
129 AGTCTATTTTAACCAAAAATCTAAAAAAATT-CAACTTAAAAT
* * ** * *
11456 CAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAAAATAAGAGACCATA
1 CAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATAGGAGACTATA
* * * * *
11521 AATGGACTTTTCTTGCCAATGAATGCTTTTTCTTTACATTTCTCAAGGTAAACA-TCAAATATAG
66 AATGGACTTTTCTTACCAATGAATGCTTTTTCTTCATATTTCTCAAGGTAGACATTCAATTATAG
* ** * *
11585 TCTGTTTTAATAAAAAATCTAGAAAAATTTAACTTAAAAT
131 TCTATTTTAACCAAAAATCTAAAAAAATTCAACTTAAAAT
* * * *
11625 CAATTATGAGATTATAAAACCATTTAAAGCAAATAATAAGGTTTTTGAAGGAATGGGTGACTATA
1 CAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATAGGAGACTATA
* * * * * * ** *
11690 AATGGATTTTTTTTGCCAGTGAATGCCTTTCTCTTCATGTTTCTTGAGGTAGACGTTCAATTATA
66 AATGGACTTTTCTTACCAATGAATG-CTTTTTCTTCATATTTCTCAAGGTAGACATTCAATTATA
* *
11755 CTTTATTTTAACCAAAAATCTAAAAAAATTCAACTTAAAAT
130 GTCTATTTTAACCAAAAATCTAAAAAAATTCAACTTAAAAT
** * * *
11796 CAATTACAAGATTATAAAATCATTTAAAGCAAGTAATAAGGCTTTTGAAGGTATAAGAGACTATA
1 CAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATAGGAGACTATA
* *
11861 AATGGACTTTTCTTACCAATGAATGCTTGTTTCTTCACATTTTTCAAGGTAGACATTCAATTATT
66 AATGGACTTTTCTTACCAATGAATGCTT-TTTCTTCATATTTCTCAAGGTAGACATTCAATTA-T
* * * * *
11926 A-TCTGTTTTAGCCAATAATATAATAAAAATT-GACTTAAAAT
129 AGTCTATTTTAACCAAAAATCTAA-AAAAATTCAACTTAAAAT
11967 CAATTACT-AGATTATAAAAC
1 CAATTA-TGAGATTATAAAAC
11987 NNNNNNNNNN
Statistics
Matches: 829, Mismatches: 192, Indels: 45
0.78 0.18 0.04
Matches are distributed among these distances:
168 3 0.00
169 123 0.15
170 220 0.27
171 370 0.45
172 106 0.13
173 7 0.01
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (170 bp):
CAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATAGGAGACTATA
AATGGACTTTTCTTACCAATGAATGCTTTTTCTTCATATTTCTCAAGGTAGACATTCAATTATAG
TCTATTTTAACCAAAAATCTAAAAAAATTCAACTTAAAAT
Found at i:11762 original size:510 final size:512
Alignment explanation
Indices: 10928--11986 Score: 1232
Period size: 510 Copynumber: 2.1 Consensus size: 512
10918 NNNNNNNNNN
* * *
10928 AAATTAAACTTAAAATCAATTACAAGATTATAAAACCATTTAAAGTGAGTAATATGGCTTTCGAA
1 AAATTAAACTTAAAATCAATTA-TAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAA
** * ** * *
10993 GGAATGGTTAACAATAAAATGGACTTTTCTTGCTTATGAATGTTTTTTTCTTCACATTACTCTAG
65 AAAATAG-TAACAATAAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACATTACTCAAG
* ** * * * * *
11058 CTAGACAATCAGTTATAATACTTTTAACCAATAATGTAAAAATATTGAACCTAAAGTCAATTTTG
129 CTAAACAATCAAATATAATACTTTTAACAAAAAATCTAAAAATATTGAACCTAAAATCAATTATG
* * ** *
11123 AGATTATAAAACTATTTACAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAACAGACT
194 AGATTATAAAACCATTTAAAGCAAATAATAAGGCTTTTGAAGGAATAGGAGACTATAAACAGACT
* * * *
11188 TGTCTTTCCAATAAATGCTTGTTTCTTTATATTTCTCAAGGTAGACATTGAATTATAGTTTATTT
259 TGTCTTTCCAATAAATGCTTGTCTCTTCATATTTCTCAAGGTAGACATTCAATTATACTTTATTT
** * * *
11253 TAATGAAAATTATAAAAAAATTCAACTTGAAATCAATTATAAGATTATAAAA-CAAGATAAAGCA
324 TAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTACAAGATTATAAAATC-AGATAAAGCA
** *
11317 AGTAATAAGGCATTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTT-T
388 AGTAATAAGGCATTTGAAGGAATAAGAGACTATAAATGGACTTTTCTTACCAATGAATG-CTTGT
* *
11381 TT-TTCAC-TTTTCTCAAGATAAACGTTCAATTA-TAGTCTATTTTAACCAATAATGTAA-AA
452 TTCTTCACATTTT-TCAAGATAAACATTCAATTATTA-TCTATTTTAACCAATAATATAATAA
* *
11440 AAATTAAAAC-TAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGA
1 AAATT-AAACTTAAAATCAATTAT-AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGA
* * *
11504 AAAAATAAG-AGACCAT-AAATGGACTTTTCTTGCCAATGAATG-CTTTTTCTTTACATTTCTCA
64 AAAAAT-AGTA-ACAATAAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACATTACTCA
* * * * *
11566 AGGTAAAC-ATCAAATATAGT-CTGTTTTAATAAAAAATCTAGAAAA-ATTTAACTTAAAATCAA
127 AGCTAAACAATCAAATATAATAC--TTTTAACAAAAAATCTA-AAAATATTGAACCTAAAATCAA
* * * *
11628 TTATGAGATTATAAAACCATTTAAAGCAAATAATAAGGTTTTTGAAGGAATGGGTGACTATAAAT
189 TTATGAGATTATAAAACCATTTAAAGCAAATAATAAGGCTTTTGAAGGAATAGGAGACTATAAAC
* * * * * * ** *
11693 GGA-TTTTTTTTGCCAGTGAATGCCTT-TCTCTTCATGTTTCTTGAGGTAGACGTTCAATTATAC
254 AGACTTGTCTTT-CCAATAAATG-CTTGTCTCTTCATATTTCTCAAGGTAGACATTCAATTATAC
* **
11756 TTTATTTTAACCAAAAATCTAAAAAAATTCAACTTAAAATCAATTACAAGATTATAAAATCATTT
317 TTTATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTACAAGATTATAAAATCAGAT
* *
11821 AAAGCAAGTAATAAGGCTTTTGAAGGTATAAGAGACTATAAATGGACTTTTCTTACCAATGAATG
382 AAAGCAAGTAATAAGGCATTTGAAGGAATAAGAGACTATAAATGGACTTTTCTTACCAATGAATG
* * * *
11886 CTTGTTTCTTCACATTTTTCAAGGTAGACATTCAATTATTATCTGTTTTAGCCAATAATATAATA
447 CTTGTTTCTTCACATTTTTCAAGATAAACATTCAATTATTATCTATTTTAACCAATAATATAATA
11951 A
512 A
*
11952 AAATT-GACTTAAAATCAATTACTAGATTATAAAAC
1 AAATTAAACTTAAAATCAATTA-TAGATTATAAAAC
11987 NNNNNNNNNN
Statistics
Matches: 459, Mismatches: 71, Indels: 35
0.81 0.13 0.06
Matches are distributed among these distances:
508 1 0.00
509 18 0.04
510 263 0.57
511 97 0.21
512 75 0.16
513 5 0.01
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (512 bp):
AAATTAAACTTAAAATCAATTATAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAA
AAATAGTAACAATAAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACATTACTCAAGCT
AAACAATCAAATATAATACTTTTAACAAAAAATCTAAAAATATTGAACCTAAAATCAATTATGAG
ATTATAAAACCATTTAAAGCAAATAATAAGGCTTTTGAAGGAATAGGAGACTATAAACAGACTTG
TCTTTCCAATAAATGCTTGTCTCTTCATATTTCTCAAGGTAGACATTCAATTATACTTTATTTTA
ACCAAAAATATAAAAAAATTCAACTTAAAATCAATTACAAGATTATAAAATCAGATAAAGCAAGT
AATAAGGCATTTGAAGGAATAAGAGACTATAAATGGACTTTTCTTACCAATGAATGCTTGTTTCT
TCACATTTTTCAAGATAAACATTCAATTATTATCTATTTTAACCAATAATATAATAA
Found at i:13725 original size:170 final size:170
Alignment explanation
Indices: 13342--14520 Score: 1280
Period size: 170 Copynumber: 6.9 Consensus size: 170
13332 NNNNNNCTTG
** *
13342 AGGTAGAGGTTCAATTATAGTCTGTTTTAACCAAAA-ATGCTAAAAAATT-ATACTTAAAATCAA
1 AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAATAT--AAAAAAATTGA-ACTTAAAATCAA
* * * * *
13405 TTACGAGATTATAAAACCATTTAAAGCGAGTAATATGGCTTTCGAAAGAAT-GGTTGACAATAAA
63 TTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGG-TGACTATAAA
** ** ** * *
13469 TGGACTTTTCTTGCTTATGAATGTTTTTTTCTTCACATTACTCT
127 TGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCA
* * *
13513 AGCTAGACATTCAATTATAATAC--TTTTAACCAATAATATAAAAAAATTGAACATAAAATCAAT
1 AGGTAGACATTCAATTATAGT-CTGTTTTAACCAA-AATATAAAAAAATTGAACTTAAAATCAAT
* * * * *
13576 TTTGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAACG
64 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATG
* * *
13641 GACTTGTCTTTCCAATAAATGCCTATTTT-TT-ATGTTTCTCA
129 GACTTTTCTTGCCAATGAATGCCT-TTTTCTTCATGTTTCTCA
* * * * **
13682 AGGTAGACATTGAATTATAGTTTGTTTTAATCAAAACTATAAAAAAATTCAACTTAAAGGCAATT
1 AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAA-TATAAAAAAATTGAACTTAAAATCAATT
* * * * *
13747 ATGAGATTATAAAACAAGTTAAAGCAAGTAATAAGGCATTTGAAGGAATAAGTGACTATAAATGG
65 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGG
* * * *
13812 ACTTTTATTACTAATCAATGCC-TTTTCTTCACT-TTTCTCA
130 ACTTTTCTTGCCAATGAATGCCTTTTTCTTCA-TGTTTCTCA
** * *
13852 AGGTAGACATTCAATTATAGTCCATTTTAACCAATAATGTAAAAAAATTGAACCTAAAATCAATT
1 AGGTAGACATTCAATTATAGTCTGTTTTAACCAA-AATATAAAAAAATTGAACTTAAAATCAATT
* * * ** * * *
13917 TTGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTAAAAAAATAGGAGACCATAAATAG
65 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGG
**
13982 ACTTTTCTTGCCAATGAATG-CTTTTTCTTCACATTTCTCA
130 ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCA
* * ** * *
14022 AGGTAAACA-TCAAATATAGTCTGTTTTAATAAAAAATGTAAAAAAATTTAACTTAAAATCAATT
1 AGGTAGACATTCAATTATAGTCTGTTTTAA-CCAAAATATAAAAAAATTGAACTTAAAATCAATT
* * * *
14086 ATGAAATTATAAAACCATTTAAAGCAAGTAGTAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
65 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGG
* *
14151 ACTTTTTTTGCCACTGAATGCCTTTTTCTTCATGTTTCT-A
130 ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCA
* * * * * * *
14191 GAGGTAGACGTTCAATTATACTCTATTTTACCCTAAAATCTAAAAATATTCAACTTAAAATCAAT
1 -AGGTAGACATTCAATTATAGTCTGTTTTAACC-AAAATATAAAAAAATTGAACTTAAAATCAAT
* *
14256 TATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATG
64 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATG
*
14321 GACTTTTCTTGCCAATGAATG-TTTGTTTCTTCA-GATTTCTCA
129 GACTTTTCTTGCCAATGAATGCCTT-TTTCTTCATG-TTTCTCA
*
14363 AGGTAGACATTTAATTATTA-TCTGTTTTAACCAATAATATAATAAAAATTG-ACTTAAAATCAA
1 AGGTAGACATTCAATTA-TAGTCTGTTTTAACCAA-AATATAA-AAAAATTGAACTTAAAATCAA
* * *
14426 TTACT-AGATTATAAAACAATTTAATA-CGAGTAATAAGCCTTTTAAAGGAATAGGTGACTATAA
63 TTA-TGAGATTATAAAACCATTTAA-AGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
* *
14489 ATGGACTTTTCTT-CTAAATGAATGACTTTTTC
126 ATGGACTTTTCTTGC-CAATGAATGCCTTTTTC
14521 AATTATAGTA
Statistics
Matches: 844, Mismatches: 134, Indels: 60
0.81 0.13 0.06
Matches are distributed among these distances:
168 4 0.00
169 146 0.17
170 390 0.46
171 288 0.34
172 16 0.02
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAATATAAAAAAATTGAACTTAAAATCAATTA
TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGA
CTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCA
Found at i:14981 original size:79 final size:79
Alignment explanation
Indices: 14841--14989 Score: 192
Period size: 79 Copynumber: 1.9 Consensus size: 79
14831 ATGAATACTC
* ** * * *
14841 TTTTCTTCACGTTTCTCAAGGTAGATGTTCAATTATAGTCTGTTTTAACCAAAAAAGT-AAAACA
1 TTTTCTTCACGTTTCTCAAGGTAAACATTCAATTATAGTCAGTATTAACCAAAAAACTAAAAAC-
14905 ATTCAAGGAATGCTT
65 ATTCAAGGAATGCTT
* * * *
14920 TTTTCTTTATGTTTCTTAAGGTAAACATTCAATTATAGTCAGTATTAACCAAAAATCTAAAAACA
1 TTTTCTTCACGTTTCTCAAGGTAAACATTCAATTATAGTCAGTATTAACCAAAAAACTAAAAACA
14985 TTCAA
66 TTCAA
14990 CTTAAAATCA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
79 54 0.92
80 5 0.08
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (79 bp):
TTTTCTTCACGTTTCTCAAGGTAAACATTCAATTATAGTCAGTATTAACCAAAAAACTAAAAACA
TTCAAGGAATGCTT
Found at i:15275 original size:171 final size:171
Alignment explanation
Indices: 14912--16758 Score: 1843
Period size: 171 Copynumber: 10.8 Consensus size: 171
14902 ACAATTCAAG
* * * * * * *
14912 GAATGCTTTTTTCTTTATGTTTCTTAAGGTAAACATTCAATTATAGTCAGTATTAACCAAAAATC
1 GAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG
* * * * * **
14977 TAAAAACATTCAACTTAAAATCAATTACGATATTATAAAATCATTTAAAGCAAGTAATAAAACTT
66 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT
* *
15042 TTG-AGAAATGGGTGACTATAAATGGACTTTTCTTGTCAAT
131 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT
* * * * * *
15082 TAATGCCTTTTTCTTTATGTTTCTCGAGGTAGTCATTCAATCATAGTCTGTTTTAACAAAAAATG
1 GAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG
* ** ********** * *
15147 TAAAACAAATTCAACTTAAACTCAATTATGAGATTATAAAATAATTTNNNNNNNNNNATATGGTT
66 TAAAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
* * * *
15212 TTTGAAGAAATGGGTGACTATAAATGCACTTTTTTTGCCAGT
130 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT
* *
15254 GAATGCCTTTTT-TTCATGTTTCTCAAGGTAGAGATTCAACTATAGTCTGTTTTAACCAAAAATG
1 GAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG
* ********** ** * *
15318 CAANNNNNNNNNNCTTAAAATCAATTACAAGATTGTAAAACCATTTAAAGCGAGTAATATGGCTT
66 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT
* * * * *
15383 TTGAAAGAATGGATGACCATAAATGGAGTTTTCCTGCCAAT
131 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT
* * * * * *
15424 GAATGTC-TTTTCTTCATGTTTCT-AGAGCTAGACATTCGATTATAATCTGTTTTAACTAATAAT
1 GAATGCCTTTTTCTTCATGTTTCTCA-AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT
* * *
15487 GTAAAAACAATTGAACCTAAAATCAATTTTGAGATTATAAAACCATTTAAAG-GTAGTAATAAGG
65 GTAAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG-AGTAATAAGG
* ** *
15551 CTTTTGAAGGAATGGGAGACTATAAATAAACTTTTCTTGCTAAT
128 CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT
*
15595 GAATG-CTTGTTAT-TTCATGTTTCTCAAGGTAGACATTCAATTATAGTTTGTTTTAACCAAAAA
1 GAATGCCTT-TT-TCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAA
* * * * *
15658 TGTAAAAAAATTCAACTTAAAACCAATTATGAGGTTATAAAACAATTTAAAACAAGTAATAAGGC
64 TGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGC
* **** * *
15723 TTTTAAAGGAATAAAAGACTGTAAATGGACTTTTCTT-CATAAT
129 TTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGC-CAAT
** * ** * *
15766 GAATG-CTTATTTCTTCACATTTGTTGAGGTAGACATTCAATTATAGTATTTTTTAACCAAAAAT
1 GAATGCCTT-TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT
*
15830 GTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAACGCT
65 GTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
* ** * * * *
15895 TTTGAAGGGATTTGTGACTATAAATGAACTTTTTTTGCTAGT
130 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT
* * * * * * *
15937 GAATACCTTATTCTTCATGTTTCTCAAGGTAAACGTTCAGTTATAGTCTCTTTTAACTAAAAATA
1 GAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT-
* ** * *
16002 CT-AAAAAATTCAACTTAAAATCAATTGCGAGATTATAAAACCATTCAAAGCGAGTAATATGGCT
65 GTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
* * * *
16066 TTTGAAGGAATGAGTGACTATAAATAGATTTTTCTTGCTAAT
130 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT
* ** * ** * * * * * *
16108 GAATGTCTTTTTCTTCACATTACTCAAACTAGACATTCAATTATAATATTTTTTGAGCAATAATG
1 GAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG
* * * * * *
16173 TAAAAAAAAATGAACCTAAAATCAATTTTGAGGTTATAAAACTATTTAAAGCG-GCTAATAAGGC
66 T-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG-TAATAAGGC
* * * * * *
16237 TTTTGAAAGAATAGGAGACTATAAACGGACTTGTCTTTCCAAT
129 TTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT
* * *
16280 GAATG-CTTGTTTCTTCATGTTTCTCGAGGTAGACATTTAATTATAGTATGTTTTAACCAAAAAT
1 GAATGCCTT-TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT
* * *
16344 GTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATACGGCT
65 GTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
* * *
16409 TTTGAAGGAATGGCTGACTATTAATAGACTTTTCTTGCCAAT
130 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT
* *
16451 GAATGCCTTTTTCTTCACT-TTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCCAGAAT
1 GAATGCCTTTTTCTTCA-TGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT
* * * * *
16515 GCAAAAAAAATT-AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGAAATATGAC
65 G-TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGC
** * * *
16579 TTTTGAAAAAATAGGTGACTATAAATGAACCTTTCTTGCCAAT
129 TTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT
* * * * * * * *
16622 GAATGTCTTTTTTTTTTATGTTTCTCAAGTTAGACATTCAATTGTAATATGTTTTAACCAATAAT
1 GAATG-CCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT
** * *
16687 GTAAAAAAAATT-ATACCAAAAATCAATTTTGAGATTATAAAACCATTTAAAGAGAGTAATAAGG
65 GT-AAAAAAATTCA-ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG
16751 CTTTTGAA
128 CTTTTGAA
16759 NNNNNNNNNN
Statistics
Matches: 1363, Mismatches: 286, Indels: 53
0.80 0.17 0.03
Matches are distributed among these distances:
169 5 0.00
170 182 0.13
171 815 0.60
172 307 0.23
173 54 0.04
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.35
Consensus pattern (171 bp):
GAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG
TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT
TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT
Found at i:16370 original size:514 final size:508
Alignment explanation
Indices: 14920--16758 Score: 1727
Period size: 514 Copynumber: 3.6 Consensus size: 508
14910 AGGAATGCTT
* * * * * * *
14920 TTTTCTTTATGTTTCTTAAGGTAAACATTCAATTATAGTCAGTATTAACCAAAAATCTAAAAACA
1 TTTTCTTCATGTTTCTCAAGGTAGACATTCAGTTATAGTCTGTTTTAACTAAAAATCTAAAAA-A
* * * * *** *
14985 TTCAACTTAAAATCAATTACGATATTATAAAATCATTTAAAGCAAGTAATAAAACTTTTG-AGAA
65 TT-AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG-GAGTAATATGGCTTTTGAAGGA
* * * * * * *
15049 ATGGGTGACTATAAATGGACTTTTCTTG-TCAATTAATGCCTTTTTCTTTATGTTTCTCGAGGTA
128 ATGAGTGACTATAAATAGACTTTTCTTGCT-AATGAATGTCTTTTT-TTCATGTTTCTCAAGCTA
* * * * * * * * * * *
15113 GTCATTCAATCATAGTCTGTTTTAACAAAAAATGTAAAACAAATTCAACTTAAACTCAATTATGA
191 GACATTCAATTATAATATTTTTTAACCAATAATGTAAAA-AAAATCAACCTAAAATCAATTTTGA
* * ********* * * * **** * *
15178 GATTATAAAATAATTTNNNNNNNNNNATATGGTTTTTG-AAGAAATGGGTGACTATAAATGCACT
255 GGTTATAAAACAATTT-AAAGCGGTAATAAGGCTTTTGAAAGGAATAAAAGACTATAAACGGACT
* * * ** * * * *
15242 TTTTTTGC-CAGTGAATGCCTT-TTT-TTCATGTTTCTCAAGGTAGAGATTCAACTATAGTCTGT
319 TGTCTT-CACAATGAATG-CTTATTTCTTCACATTTCTCGAGGTAGACATTCAATTATAGTATGT
* ********** ** *
15304 TTTAACCAAAAATGCAANNNNNNNNNNCTTAAAATCAATTACAAGATTGTAAAACCATTTAAAGC
382 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGC
** * * * * * *
15369 GAGTAATATGGCTTTTGAAAGAATGGATGACCATAAATGGAGTTTTCCTGCCAATGAATGTC
447 GAGTAATAACGCTTTTGAAGGAATGGATGACTATAAATGAACTTTTCTTGCCAATGAATGCC
* * * *
15431 TTTTCTTCATGTTTCT-AGAGCTAGACATTC-GATTATAATCTGTTTTAACTAATAATGTAAAAA
1 TTTTCTTCATGTTTCTCA-AGGTAGACATTCAG-TTATAGTCTGTTTTAACTAAAAATCT-AAAA
* * *
15494 CAATTGAACCTAAAATCAATTTTGAGATTATAAAACCATTTAAAGGTAGTAATAAGGCTTTTGAA
63 -AATT-AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGG-AGTAATATGGCTTTTGAA
* * *
15559 GGAATGGGAGACTATAAATAAACTTTTCTTGCTAATGAATG-CTTGTTATTTCATGTTTCTCAAG
125 GGAATGAGTGACTATAAATAGACTTTTCTTGCTAATGAATGTCTT-TT-TTTCATGTTTCTCAAG
* * * * * * *
15623 GTAGACATTCAATTATAGT-TTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAACCAATTA
188 CTAGACATTCAATTATAATATT-TTTTAACCAATAATGTAAAAAAAATCAACCTAAAATCAATTT
* * * *
15687 TGAGGTTATAAAACAATTTAAAACAAGTAATAAGGCTTTT-AAAGGAATAAAAGACTGTAAATGG
252 TGAGGTTATAAAACAATTTAAAGC-GGTAATAAGGCTTTTGAAAGGAATAAAAGACTATAAACGG
* * * * *
15751 ACTTTTCTTCATAATGAATGCTTATTTCTTCACATTTGTTGAGGTAGACATTCAATTATAGTATT
316 ACTTGTCTTCACAATGAATGCTTATTTCTTCACATTTCTCGAGGTAGACATTCAATTATAGTATG
15816 TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
381 TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * * * *
15881 CGAGTAATAACGCTTTTGAAGGGATTTG-TGACTATAAATGAACTTTTTTTGCTAGTGAATACC
446 CGAGTAATAACGCTTTTGAA-GGAATGGATGACTATAAATGAACTTTTCTTGCCAATGAATGCC
* * *
15944 TTATTCTTCATGTTTCTCAAGGTAAACGTTCAGTTATAGTCTCTTTTAACTAAAAATACTAAAAA
1 TT-TTCTTCATGTTTCTCAAGGTAGACATTCAGTTATAGTCTGTTTTAACTAAAAAT-CTAAAAA
** *
16009 ATTCAACTTAAAATCAATTGCGAGATTATAAAACCATTCAAAGCGAGTAATATGGCTTTTGAAGG
64 ATT-AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG-GAGTAATATGGCTTTTGAAGG
* ** * *
16074 AATGAGTGACTATAAATAGATTTTTCTTGCTAATGAATGTCTTTTTCTTCACATTACTCAAACTA
127 AATGAGTGACTATAAATAGACTTTTCTTGCTAATGAATGTCTTTTT-TTCATGTTTCTCAAGCTA
* * *
16139 GACATTCAATTATAATATTTTTTGAGCAATAATGTAAAAAAAAATGAACCTAAAATCAATTTTGA
191 GACATTCAATTATAATATTTTTTAACCAATAATGT-AAAAAAAATCAACCTAAAATCAATTTTGA
* **
16204 GGTTATAAAACTATTTAAAGCGGCTAATAAGGCTTTTGAAA-GAATAGGAGACTATAAACGGACT
255 GGTTATAAAACAATTTAAAGCGG-TAATAAGGCTTTTGAAAGGAATAAAAGACTATAAACGGACT
* ** *
16268 TGTCTTTC-CAATGAATGCTTGTTTCTTCATGTTTCTCGAGGTAGACATTTAATTATAGTATGTT
319 TGTC-TTCACAATGAATGCTTATTTCTTCACATTTCTCGAGGTAGACATTCAATTATAGTATGTT
* *
16332 TTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTG
383 TTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* *
16397 AGTAAT-ACGGCTTTTGAAGGAATGGCTGACTATTAAT-AGACTTTTCTTGCCAATGAATGCC
448 AGTAATAAC-GCTTTTGAAGGAATGGATGACTATAAATGA-ACTTTTCTTGCCAATGAATGCC
* ** * *
16458 TTTTTCTTCACT-TTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCCAGAATGCAAAAA
1 -TTTTCTTCA-TGTTTCTCAAGGTAGACATTCAGTTATAGTCTGTTTTAACTAAAAAT-C-TAAA
* * *
16522 AAATTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGAAATATGACTTTTGAAA
62 AAATTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG-GAGTAATATGGCTTTTGAAG
* * * *
16587 AAAT-AGGTGACTATAAAT-GAACCTTTCTTGCCAATGAATGTCTTTTTTTTTTATGTTTCTCAA
126 GAATGA-GTGACTATAAATAG-ACTTTTCTTGCTAATGAATGTC--TTTTTTTCATGTTTCTCAA
* * * * *
16650 GTTAGACATTCAATTGTAATATGTTTTAACCAATAATGTAAAAAAAATTATACCAAAAATCAATT
187 GCTAGACATTCAATTATAATATTTTTTAACCAATAATGTAAAAAAAATCA-ACCTAAAATCAATT
* * *
16715 TTGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAA
251 TTGAGGTTATAAAACAATTTAAAGCG-GTAATAAGGCTTTTGAA
16759 NNNNNNNNNN
Statistics
Matches: 1105, Mismatches: 183, Indels: 76
0.81 0.13 0.06
Matches are distributed among these distances:
510 1 0.00
511 49 0.04
512 140 0.13
513 359 0.32
514 435 0.39
515 115 0.10
516 6 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.35
Consensus pattern (508 bp):
TTTTCTTCATGTTTCTCAAGGTAGACATTCAGTTATAGTCTGTTTTAACTAAAAATCTAAAAAAT
TAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGGAGTAATATGGCTTTTGAAGGAATG
AGTGACTATAAATAGACTTTTCTTGCTAATGAATGTCTTTTTTTCATGTTTCTCAAGCTAGACAT
TCAATTATAATATTTTTTAACCAATAATGTAAAAAAAATCAACCTAAAATCAATTTTGAGGTTAT
AAAACAATTTAAAGCGGTAATAAGGCTTTTGAAAGGAATAAAAGACTATAAACGGACTTGTCTTC
ACAATGAATGCTTATTTCTTCACATTTCTCGAGGTAGACATTCAATTATAGTATGTTTTAACCAA
AAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
CGCTTTTGAAGGAATGGATGACTATAAATGAACTTTTCTTGCCAATGAATGCC
Found at i:17864 original size:171 final size:171
Alignment explanation
Indices: 17508--17881 Score: 403
Period size: 171 Copynumber: 2.2 Consensus size: 171
17498 AAATTGACTT
* * *
17508 AAAATTAATTACT-AGATTATAAAATAATTTAAAGCAAGTAATAAACTTTTTGAAGGAATGGGTG
1 AAAATCAATTA-TGAGATTATAAAATAATTTAAAGCAAGTAATAAACTTTTTAAAGGAATGAGTG
* ** * * *
17572 ACTATAAATAGACTTTTTTTCTAAATGAATGGCTTTTTCTGCATGTTTCTTGAGGCAGACATTCA
65 AATATAAATAGACTTTCCTTCTAAATGAATGACTTTTTCTGCAAGTTTCTTAAGGCAGACATTCA
* * * **
17637 ATTACAGTGTGTTTTAACTAAAAATATAAAAAAATTTAACNN
130 ATTACAGTCTGTTTTAACCAAAAATATAAAAAAATTCAACCC
******** ** * *
17679 NNNNNNNNTTATGAGATTATAAAATAATTTAAAGTGAGTAGTAAGGC-TTTTAAAGGAATGAGTG
1 AAAATCAATTATGAGATTATAAAATAATTTAAAGCAAGTAATAA-ACTTTTTAAAGGAATGAGTG
* * *
17743 AATATAAATGGGCTTTCCTTCTCAATGAATGACTTTTTCTGCAAGTTTCTTAAGGCAGACATTCA
65 AATATAAATAGACTTTCCTTCTAAATGAATGACTTTTTCTGCAAGTTTCTTAAGGCAGACATTCA
** * * *
17808 ATTGTAGTCTGTTTTAGCCAAATATGTAAAAAAATTCAACCC
130 ATTACAGTCTGTTTTAACCAAAAATATAAAAAAATTCAACCC
17850 AAAATCAATTATGAGATTATAAAAT-ATTTAAA
1 AAAATCAATTATGAGATTATAAAATAATTTAAA
17882 NNNNNNNNNN
Statistics
Matches: 160, Mismatches: 41, Indels: 5
0.78 0.20 0.02
Matches are distributed among these distances:
170 8 0.05
171 151 0.94
172 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.35
Consensus pattern (171 bp):
AAAATCAATTATGAGATTATAAAATAATTTAAAGCAAGTAATAAACTTTTTAAAGGAATGAGTGA
ATATAAATAGACTTTCCTTCTAAATGAATGACTTTTTCTGCAAGTTTCTTAAGGCAGACATTCAA
TTACAGTCTGTTTTAACCAAAAATATAAAAAAATTCAACCC
Found at i:19970 original size:171 final size:170
Alignment explanation
Indices: 19558--20511 Score: 829
Period size: 171 Copynumber: 5.6 Consensus size: 170
19548 NNNNNNNNNN
** * ** *
19558 AAATCAATTATGAGATTATAAAATAATTTAAAGTGAGTAATAAGGCTTTTGAATAAATAGGTGAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGTGAC
* * * * * * * *
19623 TATAAATGAACTTTTCTTACCAATCAATGCTTTTTTCTTTATGTTTCTTAAGGTCAACAATGAAT
66 TATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTTGAGGTAAACATTCAAT
* *
19688 CATAGTCTGTTTTAACCAAAAATGTAAAAAATTCAACTTA
131 TATAGTCTATTTTAACCAAAAATGTAAAAAATTCAACTTA
* ********** * * * *
19728 AAATGAATNNNNNNNNNNTAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAAGAGAG
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGTGAC
* * * * *
19793 TATAAATGGAATTTTTTTGTCAATGAATG-CTTTTTCCTTTATCTTTCTTGAGGTAAACATTTAA
66 TATAAATGGACTTTTCTTGCCAATGAATGCCTTTTT-CTTTATGTTTCTTGAGGTAAACATTCAA
* ** *
19857 TTATAGTCTATTTGAATAAAAAATGTAAAGAAATTCTACTTA
130 TTATAGTCTATTTTAACCAAAAATGTAAA-AAATTCAACTTA
* * * **
19899 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTAAAGGGATGGGTGAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGTGAC
* * * * ** * *
19964 TATAAATGGACTTTTTTTGCTAGTGAATGCCTTATTCTTTATGTTTCTCAAGGTAAAC-GTCAGT
66 TATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTTGAGGTAAACATTCAAT
* *
20028 TATAGTCTCTTTTAACTAAAAATGCTAAAAAATTCAACTTA
131 TATAGTCTATTTTAACCAAAAATG-TAAAAAATTCAACTTA
* ** * * ********** *
20069 AAGTCAATTGCGAGATTATAAAACCATTTAAAGTGAGTAATATGGCNNNNNNNNNNATGAGTGAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGTGAC
** * * ** * *
20134 TATAAATGGACTTTTCTTGTTAATGAATGTCTTTTTCTTCACATTACTTGAGGAAAACATTCAAT
66 TATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTTGAGGTAAACATTCAAT
* * * * * * *
20199 TATAATATTTTTTAAGCAATAATGTAAAAAAATTGAACATA
131 TATAGTCTATTTTAACCAAAAATGT-AAAAAATTCAACTTA
* * * * *
20240 AAATCAATTTTGAGGTTATAAAACCATTTAAAAC-AGTTAATAAGGCTTTTGAAAGAAT-AGAAG
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAG-TAATAAGGCTTTTGAAGGAATAAG-TG
* * * * * * *
20303 ACTATAAACGGACTTGTCTTTCCAATGAATG-CTTGTTTCTTCATGTTTCTCGAGGTAGACATTT
64 ACTATAAATGGACTTTTCTTGCCAATGAATGCCTT-TTTCTTTATGTTTCTTGAGGTAAACATTC
*
20367 AATTATAGTCTATTTTAACCAAAAATGTAAAAAAATTTAACTTA
128 AATTATAGTCTATTTTAACCAAAAATGT-AAAAAATTCAACTTA
* * * * * * *
20411 AAATTAATTATAATATTATAAAACCATTTAAAGTGAGTAATACGGCTTTTGAAGGAATGACTGAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGTGAC
* *
20476 TATAAATAGACTTTTCTTACCAATGAATGCCTTTTT
66 TATAAATGGACTTTTCTTGCCAATGAATGCCTTTTT
20512 TTTCACTNNN
Statistics
Matches: 608, Mismatches: 164, Indels: 23
0.76 0.21 0.03
Matches are distributed among these distances:
169 5 0.01
170 252 0.41
171 340 0.56
172 11 0.02
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.36
Consensus pattern (170 bp):
AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGTGAC
TATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTTGAGGTAAACATTCAAT
TATAGTCTATTTTAACCAAAAATGTAAAAAATTCAACTTA
Found at i:20186 original size:341 final size:332
Alignment explanation
Indices: 19558--20452 Score: 714
Period size: 341 Copynumber: 2.6 Consensus size: 332
19548 NNNNNNNNNN
** ** **
19558 AAATCAATTATGAGATTATAAAATAATTTAAAGTGAG-TAATAAGGCTTTTGAATA-AATAGGTG
1 AAATCAATTATGAGATTATAAAACCATTTAAA-ACAGTTAATAAGGCTTTTGAA-AGAATAGAAG
* * * * * ** * * * * *
19621 ACTATAAATGAACTTTTCTTACCAATCAATGCTTTTTTCTTTATGTTTCTTAAGGTCAACAATGA
64 ACTATAAACGGACTTGTCTTTCCAATGAATGCTTGATTCTTCATGTTTCTCAAGGTAAACAGTCA
* * * **********
19686 ATCATAGTCTGTTTTAACCAAAAATGT-AAAAAATTCAACTTAAAATGAATNNNNNNNNNNTAAA
129 ATTATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTACAAGATTATAAA
** * * * *
19750 ACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAAGAGAGTATAAATGGAATTTTTTTGTCA
194 ACCATTTAAAGTGAGTAATATGGC--ATG-AG---T----GACTATAAATGGAATTTTCTTGTCA
* * * * * * *
19815 ATGAATGCTTTTTCCTTTATCTTTCTTGAGGTAAACATTTAATTATAGTCTATTTGAATAAAAAA
249 ATGAATGCTTTTTCCTTCATCTTACTTGAGGAAAACATTCAATTATAATATATTTGAAGAAAAAA
* * *
19880 TGTAAAGAAATTCTACTTA
314 TGTAAAAAAATTCAACATA
* * * * **
19899 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAG-TAATAAGGCTTTT-AAAGGGATGGGTG
1 AAATCAATTATGAGATTATAAAACCATTTAAAAC-AGTTAATAAGGCTTTTGAAA-GAATAGAAG
* * * * *
19962 ACTATAAATGGACTT-TTTTTGCTAGTGAATGCCTT-ATTCTTTATGTTTCTCAAGGTAAAC-GT
64 ACTATAAACGGACTTGTCTTT-CCAATGAATG-CTTGATTCTTCATGTTTCTCAAGGTAAACAGT
* * * * * *
20024 CAGTTATAGTCTCTTTTAACTAAAAATGCT-AAAAAATTCAACTTAAAGTCAATTGCGAGATTAT
127 CAATTATAGTCTATTTTAACCAAAAATG-TAAAAAAATTCAACTTAAAATCAATTACAAGATTAT
*
20088 AAAACCATTTAAAGTGAGTAATATGGCNNNNNNNNNNATGAGTGACTATAAATGGACTTTTCTTG
191 AAAACCATTTAAAGTGAGTAATATGGC----------ATGAGTGACTATAAATGGAATTTTCTTG
* * * *
20153 TTAATGAATGTCTTTTT-CTTCA-CATTACTTGAGGAAAACATTCAATTATAATATTTTTTAAGC
246 TCAATGAATG-CTTTTTCCTTCATC-TTACTTGAGGAAAACATTCAATTATAATATATTTGAAGA
* *
20216 AATAATGTAAAAAAATTGAACATA
309 AAAAATGTAAAAAAATTCAACATA
* *
20240 AAATCAATTTTGAGGTTATAAAACCATTTAAAACAGTTAATAAGGCTTTTGAAAGAATAGAAGAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAACAGTTAATAAGGCTTTTGAAAGAATAGAAGAC
* * * * *
20305 TATAAACGGACTTGTCTTTCCAATGAATGCTTGTTTCTTCATGTTTCTCGAGGTAGACATTTAAT
66 TATAAACGGACTTGTCTTTCCAATGAATGCTTGATTCTTCATGTTTCTCAAGGTAAACAGTCAAT
* * * *
20370 TATAGTCTATTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATTAATTATAATATTATAAAAC
131 TATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTACAAGATTATAAAAC
20435 CATTTAAAGTGAGTAATA
196 CATTTAAAGTGAGTAATA
20453 CGGCTTTTGA
Statistics
Matches: 446, Mismatches: 86, Indels: 43
0.78 0.15 0.07
Matches are distributed among these distances:
339 1 0.00
340 35 0.08
341 314 0.70
342 91 0.20
345 1 0.00
348 2 0.00
349 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.36
Consensus pattern (332 bp):
AAATCAATTATGAGATTATAAAACCATTTAAAACAGTTAATAAGGCTTTTGAAAGAATAGAAGAC
TATAAACGGACTTGTCTTTCCAATGAATGCTTGATTCTTCATGTTTCTCAAGGTAAACAGTCAAT
TATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTACAAGATTATAAAAC
CATTTAAAGTGAGTAATATGGCATGAGTGACTATAAATGGAATTTTCTTGTCAATGAATGCTTTT
TCCTTCATCTTACTTGAGGAAAACATTCAATTATAATATATTTGAAGAAAAAATGTAAAAAAATT
CAACATA
Found at i:21200 original size:171 final size:171
Alignment explanation
Indices: 20893--21203 Score: 439
Period size: 171 Copynumber: 1.8 Consensus size: 171
20883 NNNNNNNNCG
*
20893 AGTAATAAGGCTTTTGAAGAAATAGGAGACCATAAATGGACTTTTCTTGCCAGTGAATGCTTTTC
1 AGTAATAAGGCTTTTGAAGAAATAGGAGACCATAAATGGACTTTTCTTACCAGTGAATGCTTTTC
* * * *
20958 TCTTTACATTTCTGAAGGTAAACATTCAATTATACTCTGTTTTAACCAATAATCTAAAACAATTC
66 TCTTCACATTTCTGAAAGTAAACATTCAATTATACTCTGTTTTAACCAAAAATCTAAAAAAATTC
21023 AACTTAAAATTAATTATGAGAGTATAAAATCATTTAAAGTA
131 AACTTAAAATTAATTATGAGAGTATAAAATCATTTAAAGTA
* * *
21064 AGTAATAAGGCTTTTGAAGGAAT-GGATGACTATAAATGGACATTTT-TTACCAGTGATTGCCTT
1 AGTAATAAGGCTTTTGAAGAAATAGGA-GACCATAAATGGAC-TTTTCTTACCAGTGAATG-CTT
* * * * * *
21127 TT-TCTTCACGTTTCTTAAAGTAGACGTTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAA
63 TTCTCTTCACATTTCTGAAAGTAAACATTCAATTATACTCTGTTTTAACCAAAAATCTAAAAAAA
*
21191 TTTAACTTAAAAT
128 TTCAACTTAAAAT
21204 CAANNNNNNN
Statistics
Matches: 122, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
170 3 0.02
171 110 0.90
172 9 0.07
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (171 bp):
AGTAATAAGGCTTTTGAAGAAATAGGAGACCATAAATGGACTTTTCTTACCAGTGAATGCTTTTC
TCTTCACATTTCTGAAAGTAAACATTCAATTATACTCTGTTTTAACCAAAAATCTAAAAAAATTC
AACTTAAAATTAATTATGAGAGTATAAAATCATTTAAAGTA
Done.