Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401978.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5075.0, 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: 7518
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.28
Warning! 1557 characters in sequence are not A, C, G, or T
Found at i:925 original size:171 final size:170
Alignment explanation
Indices: 394--949 Score: 596
Period size: 169 Copynumber: 3.3 Consensus size: 170
384 AATAAAAATT
* * *
394 AGTAATAAGGCTTTTGAAAGAATGAGTGAGTAAAAATGGACATTTCTTGTCAATGAATGCTTTTT
1 AGTAATAAGGCTTTTGAAAGAATGAGTGAGTATAAATGGACATTTCTTGCCAATGAATGCCTTTT
* * * *
459 TCTTTACATTTTCTGAGGTA-ATATTCAATTATAGTCCGTTTTAATCAAAAATGTAAAAAAATTC
66 TCTTCACATTTTCTGAGGTAGATATTCAATTATAGTCTGTTTTAACCAAAAA-GGAAAAAAATTC
*
523 AACTTAAAATCAATAATGAGATTATAACACCATTTAAAGAG
130 AACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGAG
* * * ** * * **
564 AGTAATAAGGCTTTTGACAGAATGGGTGACTATAAATAAACTTTTCTTGCAAATGAATATCTTTT
1 AGTAATAAGGCTTTTGAAAGAATGAGTGAGTATAAATGGACATTTCTTGCCAATGAATGCCTTTT
* * * * * *
629 TCTTCATA-TTTCTCGAGGTCGACATTCAATTATAGTCTG-TTTAACCAAAAATGTAAAAAATAC
66 TCTTCACATTTTCT-GAGGTAGATATTCAATTATAGTCTGTTTTAACCAAAAAGGAAAAAAATTC
* * *
692 AACTTAAAATCAATTATGAGATTATAAAACCATTTACAGCG
130 AACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGAG
* * * * * *
733 AGCAGTAAGGCTTTGGAAAGAATGAGTAAGTTTAAATGGACATTTCATGCCAATGAATGCCTTTT
1 AGTAATAAGGCTTTTGAAAGAATGAGTGAGTATAAATGGACATTTCTTGCCAATGAATGCCTTTT
* * ********* *
798 TCTTCACATTTTCTGAGGTAGGTACTCAATTATAGTCTGTTTTAACCAANNNNNNNNNNACATTC
66 TCTTCACATTTTCTGAGGTAGATATTCAATTATAGTCTGTTTTAACCAA-AAAGGAAAAAAATTC
* * * *
863 AACTTAAAATCAATAATGAGTTTACAAAACCACTTAAAGTG
130 AACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGAG
* * * *
904 AGTAGTAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTC
1 AGTAATAAGGCTTTTGAAAGAATGAGTGAGTATAAATGGACATTTC
950 NNNNNNNNNN
Statistics
Matches: 311, Mismatches: 70, Indels: 9
0.80 0.18 0.02
Matches are distributed among these distances:
169 128 0.41
170 89 0.29
171 94 0.30
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.33
Consensus pattern (170 bp):
AGTAATAAGGCTTTTGAAAGAATGAGTGAGTATAAATGGACATTTCTTGCCAATGAATGCCTTTT
TCTTCACATTTTCTGAGGTAGATATTCAATTATAGTCTGTTTTAACCAAAAAGGAAAAAAATTCA
ACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGAG
Found at i:2030 original size:171 final size:169
Alignment explanation
Indices: 1441--2208 Score: 650
Period size: 168 Copynumber: 4.5 Consensus size: 169
1431 NNNNNNNNNN
* * ** * *
1441 GGACTTTTCTTGT-CAATGAATATCTTTTTCTTCATGTTTCTTGAGGTAGACATTAAATTATAGT
1 GGACTTTTCTT-TCCAATGAAT-GCATTTTCTTCACATTTCTTGAGGTAGACATTCAATTATAAT
* * * ** * * * * *
1505 CTGTTTTAACTAAAAATATAAATAAATACAATTTAAAATCAA--TTATGATTACAAAACCATTTA
64 CTGTTTTAACCAAAAATGTAAA-AAATTCAACCTAAAATCAACGATAAGATTATAATACTATTTA
* *
1568 AAGCGAGTAATAA-GCTTTTGAAGGAATGGGTGACAATAAAT
128 AAGCGAGTAATAAGGCTTTTGAAGGAATGGGTAACTATAAAT
* * * * * *
1609 GGACTTTTCTTTCCAATAAATGCCTTTCTCTTTATATTTTTTGATGTAGACATTCAATTATAATC
1 GGACTTTTCTTTCCAATGAATGCATTT-TCTTCACATTTCTTGAGGTAGACATTCAATTATAATC
* * ***
1674 TGTTTTAACAAAAAATGTAAAAACAATTGAACCTAAAATCAATTTTAAGATTATAATACTATTTA
65 TGTTTTAACCAAAAATGT-AAAA-AATTCAACCTAAAATCAACGATAAGATTATAATACTATTTA
* * *
1739 AAGCGAGTAATAAGGCTTTTAAATGAATAGG-AGACTATAAAT
128 AAGCGAGTAATAAGGCTTTTGAAGGAATGGGTA-ACTATAAAT
* * ** *
1781 GGACTTTTCTTACCCATGAAT-TTTTTTTTTCACATTTCTTGAGGTAGACATTCAATTATAATCT
1 GGACTTTTCTTTCCAATGAATGCATTTTCTTCACATTTCTTGAGGTAGACATTCAATTATAATCT
* ** * **********
1845 GTTTTAATCAAAAATGTAAAAAATTCAA-CTGAAAATTGACGATGAGATTATNNNNNNNNNNAAA
66 GTTTTAACCAAAAATGTAAAAAATTCAACCT-AAAATCAACGATAAGATTATAATACTATTTAAA
1909 GCGAGTAATAAGGCTTTTGAAGGAATGGGTAACTATAAAT
130 GCGAGTAATAAGGCTTTTGAAGGAATGGGTAACTATAAAT
* * *
1949 GGACCTTTCTTTGCCAATGAATGCATTTTGCTTCACATTTCTTGAGGTAGGCACTCAATTATAAT
1 GGACTTTTCTTT-CCAATGAATGCATTTT-CTTCACATTTCTTGAGGTAGACATTCAATTATAAT
* * ** * * ** * * *
2014 TTGTTTTAACCAAAAATATAAAAAAATTTTACTTAAAATTAATTATGAGCTTATAAAACTATTTA
64 CTGTTTTAACCAAAAATGT-AAAAAATTCAACCTAAAATCAACGATAAGATTATAATACTATTTA
* * * *
2079 AAGCGACTAATAAGGCTTTTGAAGGAATCGGTGATTATAAAT
128 AAGCGAGTAATAAGGCTTTTGAAGGAATGGGTAACTATAAAT
* * * * * *** * * *
2121 AGACTTTTCTTGCCAATAAATATCTTTTTCTTCTTGTTTCTCGAGCTAGACATTCAATTATAATA
1 GGACTTTTCTTTCCAATGAAT-GCATTTTCTTCACATTTCTTGAGGTAGACATTCAATTATAATC
*
2186 TGTTTTAACTAAAAATGTAAAAA
65 TGTTTTAACCAAAAATGTAAAAA
2209 NNNNNNNNNN
Statistics
Matches: 480, Mismatches: 104, Indels: 30
0.78 0.17 0.05
Matches are distributed among these distances:
167 7 0.01
168 134 0.28
169 30 0.06
170 57 0.12
171 133 0.28
172 118 0.25
173 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (169 bp):
GGACTTTTCTTTCCAATGAATGCATTTTCTTCACATTTCTTGAGGTAGACATTCAATTATAATCT
GTTTTAACCAAAAATGTAAAAAATTCAACCTAAAATCAACGATAAGATTATAATACTATTTAAAG
CGAGTAATAAGGCTTTTGAAGGAATGGGTAACTATAAAT
Found at i:2077 original size:340 final size:331
Alignment explanation
Indices: 1566--2208 Score: 774
Period size: 340 Copynumber: 1.9 Consensus size: 331
1556 CAAAACCATT
* *
1566 TAAAGCGAGTAATAAGCTTTTGAAGGAATGGGTGACAATAAATGGACTTTTCTTTCCAATAAATG
1 TAAAGCGAGTAATAAGCTTTTGAAGGAATGGGTAACAATAAATGGACCTTTCTTTCCAATAAATG
* * * * * * *
1631 CCTTTCTCTTTATATTTTTTGATGTAGACATTCAATTATAATCTGTTTTAACAAAAAATGTAAAA
66 CATTTCTCTTCACATTTCTTGAGGTAGACACTCAATTATAATCTGTTTTAACAAAAAATATAAAA
* * *
1696 ACAATTGAACCTAAAATCAATTTTAAGATTATAATACTATTTAAAGCGAGTAATAAGGCTTTTAA
131 ACAATTGAACCTAAAATCAATTATAAGATTATAAAACTATTTAAAGCGACTAATAAGGCTTTTAA
* * * * * *
1761 ATGAATAGGAGACTATAAATGGACTTTTCTTACCCATGAAT-T-TTTTTTTTCACATTTCTTGAG
196 AGGAATAGGAGACTATAAATAGACTTTTCTTACCAATAAATATCTTTTTCTTCACATTTCTCGAG
* *
1824 GTAGACATTCAATTATAATCTGTTTTAA-TCAAAAATGTAAAAAATTCAACTGAAAATTGACGAT
261 CTAGACATTCAATTATAATATGTTTTAACT-AAAAATGTAAAAAATTCAACTGAAAATTGACGAT
1888 GAGATTA
325 GAGATTA
*
1895 TNNNNNNNNNNAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTAACTATAAATGGACCTTTCTT
1 T----------AAAGCGAGTAATAA-GCTTTTGAAGGAATGGGTAACAATAAATGGACCTTTCTT
* * *
1960 TGCCAATGAATGCATTT-TGCTTCACATTTCTTGAGGTAGGCACTCAATTATAATTTGTTTTAAC
55 T-CCAATAAATGCATTTCT-CTTCACATTTCTTGAGGTAGACACTCAATTATAATCTGTTTTAAC
* ** * * * *
2024 CAAAAATATAAAAA-AATTTTACTTAAAATTAATTATGAGCTTATAAAACTATTTAAAGCGACTA
118 AAAAAATATAAAAACAATTGAACCTAAAATCAATTATAAGATTATAAAACTATTTAAAGCGACTA
* * * * *
2088 ATAAGGCTTTTGAAGGAATCGGTGATTATAAATAGACTTTTCTTGCCAATAAATATCTTTTTCTT
183 ATAAGGCTTTTAAAGGAATAGGAGACTATAAATAGACTTTTCTTACCAATAAATATCTTTTTCTT
***
2153 CTTGTTTCTCGAGCTAGACATTCAATTATAATATGTTTTAACTAAAAATGTAAAAA
248 CACATTTCTCGAGCTAGACATTCAATTATAATATGTTTTAACTAAAAATGTAAAAA
2209 NNNNNNNNNN
Statistics
Matches: 259, Mismatches: 39, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
329 1 0.00
339 14 0.05
340 124 0.48
341 64 0.25
342 55 0.21
343 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (331 bp):
TAAAGCGAGTAATAAGCTTTTGAAGGAATGGGTAACAATAAATGGACCTTTCTTTCCAATAAATG
CATTTCTCTTCACATTTCTTGAGGTAGACACTCAATTATAATCTGTTTTAACAAAAAATATAAAA
ACAATTGAACCTAAAATCAATTATAAGATTATAAAACTATTTAAAGCGACTAATAAGGCTTTTAA
AGGAATAGGAGACTATAAATAGACTTTTCTTACCAATAAATATCTTTTTCTTCACATTTCTCGAG
CTAGACATTCAATTATAATATGTTTTAACTAAAAATGTAAAAAATTCAACTGAAAATTGACGATG
AGATTA
Found at i:2948 original size:171 final size:171
Alignment explanation
Indices: 2305--3998 Score: 1035
Period size: 172 Copynumber: 9.9 Consensus size: 171
2295 NNNNNNNNNN
* * * * *
2305 CATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGCGAGACTATAAATGGAC-TTCTCTTTCGAA
1 CATTTAAAGCGAGTAATAAGG-ATTTGAAAGAATGAGTGACTATAAATGGACATT-TCTTGCTAA
* * * ** * **
2369 T-AA-AT-ATTTTTTTCAA-TATGTTTCCTAAGACA-ACCATTCAATTATAGTATGTTTTAATGA
64 TGAATGTCTTTTTTTTCAAGT-T-TTT--TGAGGTAGA-CATTCAATTATAGTCTGTTTTAACCA
* *
2429 AAAATGT--AAAAAATTCAACTTCAAATCAATTATGAGATTCTAAAAC
124 AAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* * * ********** * *
2475 AATTTAAAGTGAGTAATAAGGATTTTGAAGGAATGAGTGACTATAANNNNNNNNNNCTTACCAAT
1 CATTTAAAGCGAGTAATAAGGA-TTTGAAAGAATGAGTGACTATAAATGGACATTTCTTGCTAAT
* ** * * ** * * * * * *
2540 GAATGCCTTTTCCTTCATGTTTCTCAAGCTAAACATACAATTATAATATGCTTTAACC---AA--
65 GAATGTCTTTTTTTTCAAGTTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG
2600 -AAAAAAAA-TCAACTTAAAATCAATTATGAGATTA-AAAATC
130 TAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-C
* * ** * *
2640 CATTTAAAGCGAGTACTAAGAGTTTTGAAAGAATGAGAAACTATAAATGGACTTTTCTTGCCAAT
1 CATTTAAAGCGAGTAATAAG-GATTTGAAAGAATGAGTGACTATAAATGGACATTTCTTGCTAAT
*********** * * ** ** * * *
2705 GANNNNNNNNNNCTTCATGTTTCTCAAGGTAGACATTCAACAATAGTCCGTTTTAACCAAAAGTA
65 GAATGTCTTTTTTTTCAAGTTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG
* * *
2770 TAAAAAAAATTC-ACTGAAAATCAGTTTTTG-GATTATAAAAC
130 TAAAAAAAATTCAACTTAAAATCA-ATTATGAGATTATAAAAC
* * *
2811 CATTTAAAGCGAGTAATAAGGTATTTGAAAGAATGGGTTATTATAAATGGACATTTCTTGCTAAT
1 CATTTAAAGCGAGTAATAAGG-ATTTGAAAGAATGAGTGACTATAAATGGACATTTCTTGCTAAT
* * *
2876 G-ATGTCTTTTTTTTCAAGTTTTTTGAGGTACATATTCAATTATAGTCTGTTTTAACTAAAAA-G
65 GAATGTCTTTTTTTTCAAGTTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG
* *
2939 ATAAAAAAAATACAACTTAAATTCAATTATGAGATTATAAAAC
130 -TAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
********** * * *
2982 CATTNNNNNNNNNNAATAAGGCTTTTGAAAGAATGAGTGAATATAAATGGACATTTCTTGCCAAT
1 CATTTAAAGCGAGTAATAAGG-ATTTGAAAGAATGAGTGACTATAAATGGACATTTCTTGCTAAT
* * * * * * * * *
3047 GAATGCCTTTTTATTCACGTTCTCTGAGGCAGGCATTCAATTATAGTCTATTTTACCCAAAAATG
65 GAATGTCTTTTTTTTCAAGTTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG
* *
3112 T--AAAAAATTCAACTTAAACTCAATTATGAGATTAAAAAAC
130 TAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* ******** * *
3152 CATTTAAAGCAAGTAATAAGGATTTNNNNNNNNNNGA-TGACTATAAATAGAC-TTTTTTGGCTA
1 CATTTAAAGCGAGTAATAAGGATTT--GAAAGAATGAGTGACTATAAATGGACATTTCTT-GCTA
* * * * * *
3215 ATAAATG-CTTTTTTCTTTACA-TTTCTCGAGGTAGACATTCAACTATAGTTTGTTTTAACCAAA
63 ATGAATGTCTTTTTT-TTCA-AGTTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAA
* * * * * *
3278 AAAG-CAAAAACATTCAACTAAAAAATAAATAATGAGATTATAAAAC
126 AATGTAAAAAAAATTCAACT-TAAAATCAATTATGAGATTATAAAAC
* * * ** * *
3324 AATTTAAAGCGAGTAATAAGGCTTTTGAAACAATGAGAAACTATAAATGAACCTTTCTTGCTAAT
1 CATTTAAAGCGAGTAATAAGG-ATTTGAAAGAATGAGTGACTATAAATGGACATTTCTTGCTAAT
* * ** * * *
3389 GAATGTCTTTTTCTTCATA-TTTCTTGAGGTAGACATTCAACAATAGTCTATTTTAACCGAAGAT
65 GAATGTCTTTTTTTTCA-AGTTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT
* * * **********
3453 GCAAAATAAATTCAACTTAAAATCAGTTATGANNNNNNNNNNC
129 GTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* * * * *
3496 CATTTAAAGCGAGTAATAAGGCATTTGAAAGAATGGGTTACTATAAATGGTCTTTTCTTTCTAAT
1 CATTTAAAGCGAGTAATAAGG-ATTTGAAAGAATGAGTGACTATAAATGGACATTTCTTGCTAAT
* * * * * ** *
3561 GAATATCTTTCTCTTT-AGGTTTTTTGAGGTACACATTCATTTATAGTCTACTTTAACTAAAAAT
65 GAATGTCTTT-TTTTTCAAGTTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT
* *
3625 GTTAAAAAAATGCAACTTAAAATCAATTATGAGATTATAAAAC
129 GTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* * * ** * * *
3668 TATTTATAGCGCGTAATAAGGATTTTGAAAGAAAT-AGTGGGTATAAATGGATATTTTTTTGCCA
1 CATTTAAAGCGAGTAATAAGGA-TTTGAAAG-AATGAGTGACTATAAATGGACA-TTTCTTGCTA
* * * * * * * * * *
3732 ATGAATGCCTTTTTCTAT-ATGTTTTCTAAGGCAAACATTCAATTACAGTCAGTTTTAACTAAAA
63 ATGAATGTCTTTTT-TTTCAAGTTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAA
* * *
3796 ATGT--AAAAAATTCAACTTAAAATCAATTATGACATTAAAAAAT
127 ATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* * * * * * *
3839 CATTTAAAGGGAGTAACAAGGATTTTGAAGGAGTGTGTGACTATAAATAGACTTTTCTTGCTAAT
1 CATTTAAAGCGAGTAATAAGGA-TTTGAAAGAATGAGTGACTATAAATGGACATTTCTTGCTAAT
* * * * * * **
3904 AAATGTCTTTTTCTTCACGATTCTTGAAGTAGACATTCACCTATAGTCTGTTTTAACCAAAAATG
65 GAATGTCTTTTTTTTCAAGTTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG
*
3969 T-AAAAAAATTCAACTTAAAATCAATAATGA
130 TAAAAAAAATTCAACTTAAAATCAATTATGA
3999 NNNNNNNNNN
Statistics
Matches: 1144, Mismatches: 332, Indels: 95
0.73 0.21 0.06
Matches are distributed among these distances:
164 4 0.00
165 109 0.10
166 7 0.01
167 2 0.00
168 1 0.00
169 15 0.01
170 291 0.25
171 269 0.24
172 345 0.30
173 100 0.09
174 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (171 bp):
CATTTAAAGCGAGTAATAAGGATTTGAAAGAATGAGTGACTATAAATGGACATTTCTTGCTAATG
AATGTCTTTTTTTTCAAGTTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
AAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
Found at i:3271 original size:342 final size:339
Alignment explanation
Indices: 2306--3998 Score: 1129
Period size: 342 Copynumber: 5.0 Consensus size: 339
2296 NNNNNNNNNC
* * * * *
2306 ATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGCGAGACTATAAATGGAC-TTCTCTTTCGAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGAATATAAATGGACATT-TCTTGCCAAT
* *** * * * * * **
2370 AAATATTTTTTTCAAT-ATGTTTCCTAAGACA-ACCATTCAATTATAGTATGTTTTAATGAAAAA
65 GAATGCCTTTTTC-TTCATGTTT-CTGAGGCAGA-CATTCAATTATAGTCTATTTTAACCAAAAA
* * ** * *
2433 TGTAAAAAATTCAACTTCAAATCAATTATGAGATTCTAAAACAATTTAAAGTGAGTAATAAGGAT
127 TGTAAAAAATTCAACTTAAAATCAATTATGACATTAAAAAACCATTTAAAGCGAGTAATAAGGA-
* * * ********** * * * * * * **
2498 TTTGAAGGAATGAGTGACTATAANNNNNNNNNNCTTACCAATGAATGCCTTTTCCTTCATGTTTC
191 TTTGAAAGAAGGGGTGACTATAAATAGACTTTTCTTGCTAATAAATGCTTTTTTCTTTACATTTC
** * * * * * * *
2563 TCAAGCTAAACATACAATTATAATATGCTTTAACC--AAA---AAAAAAA-TCAACTTAAAATCA
256 TTGAGGTACACATTCAACTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCA
* *
2622 ATTATGAGATTA-AAAATCC
321 ATAATGAGATTATAAAA-CA
* * *
2641 ATTTAAAGCGAGTACTAAGAG-TTTTGAAAGAATGAG-AAACTATAAATGGACTTTTCTTGCCAA
1 ATTTAAAGCGAGTAATAAG-GCTTTTGAAAGAATGAGTGAA-TATAAATGGACATTTCTTGCCAA
********** * * ** **
2704 TGANNNNNNNNNNCTTCATGTTTCTCAAGGTAGACATTCAACAATAGTCCGTTTTAACCAAAAGT
64 TGAATGCCTTTTTCTTCATGTTTCT-GAGGCAGACATTCAATTATAGTCTATTTTAACCAAAA--
** * * * * *
2769 ATAAAAAAAATTC-ACTGAAAATCAGTTTTTG-GATTATAAAACCATTTAAAGCGAGTAATAAGG
126 ATGTAAAAAATTCAACTTAAAATCA-ATTATGACATTAAAAAACCATTTAAAGCGAGTAATAAGG
* * * * * * *
2832 TATTTGAAAGAATGGGTTATTATAAATGGACATTTCTTGCTAAT-GATGTCTTTTTT-TTCA-AG
190 -ATTTGAAAGAAGGGGTGACTATAAATAGACTTTTCTTGCTAATAAATG-CTTTTTTCTTTACA-
* * * * *
2894 TTTTTTGAGGTACATATTCAATTATAGTCTGTTTTAACTAAAAA-GATAAAAAAAATACAACTTA
252 TTTCTTGAGGTACACATTCAACTATAGTCTGTTTTAACCAAAAATG-T-AAAAAAATTCAACTTA
* * *
2958 AATTCAATTATGAGATTATAAAACC
315 AAATCAATAATGAGATTATAAAACA
**********
2983 ATTNNNNNNNNNNAATAAGGCTTTTGAAAGAATGAGTGAATATAAATGGACATTTCTTGCCAATG
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGAATATAAATGGACATTTCTTGCCAATG
* * * *
3048 AATGCCTTTTTATTCACGTTCTCTGAGGCAGGCATTCAATTATAGTCTATTTTACCCAAAAATGT
66 AATGCCTTTTTCTTCATGTT-TCTGAGGCAGACATTCAATTATAGTCTATTTTAACCAAAAATGT
* * *
3113 AAAAAATTCAACTTAAACTCAATTATGAGATTAAAAAACCATTTAAAGCAAGTAATAAGGATTTN
130 AAAAAATTCAACTTAAAATCAATTATGACATTAAAAAACCATTTAAAGCGAGTAATAAGGATTT-
********* * *
3178 NNNNNNNNNGATGACTATAAATAGACTTTT-TTGGCTAATAAATGCTTTTTTCTTTACATTTCTC
194 GAAAGAAGGGGTGACTATAAATAGACTTTTCTT-GCTAATAAATGCTTTTTTCTTTACATTTCTT
* * * * * * *
3242 GAGGTAGACATTCAACTATAGTTTGTTTTAACCAAAAAAGCAAAAACATTCAACTAAAAAATAAA
258 GAGGTACACATTCAACTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACT-TAAAATCAA
3307 TAATGAGATTATAAAACA
322 TAATGAGATTATAAAACA
* * * * *
3325 ATTTAAAGCGAGTAATAAGGCTTTTGAAACAATGAG-AAACTATAAATGAACCTTTCTTGCTAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGAA-TATAAATGGACATTTCTTGCCAAT
* * * ** * *
3389 GAATGTCTTTTTCTTCATATTTCTTGAGGTAGACATTCAACAATAGTCTATTTTAACCGAAGATG
65 GAATGCCTTTTTCTTCATGTTTC-TGAGGCAGACATTCAATTATAGTCTATTTTAACCAAAAATG
* * **********
3454 CAAAATAAATTCAACTTAAAATCAGTTATGANNNNNNNNNNCCATTTAAAGCGAGTAATAAGGCA
129 -TAAA-AAATTCAACTTAAAATCAATTATGACATTAAAAAACCATTTAAAGCGAGTAATAAGG-A
* * * * * * **
3519 TTTGAAAGAATGGGTTACTATAAATGGTCTTTTCTTTCTAATGAATAT-C-TTTCTCTTTAGGTT
191 TTTGAAAGAAGGGGTGACTATAAATAGACTTTTCTTGCTAAT-AA-ATGCTTTTTTCTTTACATT
* ** ** * *
3582 TTTTGAGGTACACATTCATTTATAGTCTACTTTAACTAAAAATGTTAAAAAAATGCAACTTAAAA
254 TCTTGAGGTACACATTCAACTATAGTCTGTTTTAACCAAAAATG-TAAAAAAATTCAACTTAAAA
* *
3647 TCAATTATGAGATTATAAAACT
318 TCAATAATGAGATTATAAAACA
* * * ** * *
3669 ATTTATAGCGCGTAATAAGGATTTTGAAAGAAAT-AGTGGGTATAAATGGATATTTTTTTGCCAA
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAAG-AATGAGTGAATATAAATGGACA-TTTCTTGCCAA
* * * *
3733 TGAATGCCTTTTTCTAT-ATGTTTTCTAAGGCAAACATTCAATTACAGTC-AGTTTTAACTAAAA
64 TGAATGCCTTTTTCT-TCATG-TTTCTGAGGCAGACATTCAATTATAGTCTA-TTTTAACCAAAA
* * *
3796 ATGTAAAAAATTCAACTTAAAATCAATTATGACATTAAAAAATCATTTAAAGGGAGTAACAAGGA
126 ATGTAAAAAATTCAACTTAAAATCAATTATGACATTAAAAAACCATTTAAAGCGAGTAATAAGGA
* * *
3861 TTTTG-AAGGAGTGTGTGACTATAAATAGACTTTTCTTGCTAATAAATG-TCTTTTTCTTCACGA
191 -TTTGAAAGAAG-GGGTGACTATAAATAGACTTTTCTTGCTAATAAATGCT-TTTTTCTTTAC-A
* * *
3924 -TTCTTGAAGTAGACATTCACCTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAA
252 TTTCTTGAGGTACACATTCAACTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAA
3988 ATCAATAATGA
317 ATCAATAATGA
3999 NNNNNNNNNN
Statistics
Matches: 1032, Mismatches: 273, Indels: 99
0.74 0.19 0.07
Matches are distributed among these distances:
334 4 0.00
335 121 0.12
336 73 0.07
337 19 0.02
340 21 0.02
341 94 0.09
342 307 0.30
343 132 0.13
344 175 0.17
345 79 0.08
346 7 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (339 bp):
ATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGAATATAAATGGACATTTCTTGCCAATG
AATGCCTTTTTCTTCATGTTTCTGAGGCAGACATTCAATTATAGTCTATTTTAACCAAAAATGTA
AAAAATTCAACTTAAAATCAATTATGACATTAAAAAACCATTTAAAGCGAGTAATAAGGATTTGA
AAGAAGGGGTGACTATAAATAGACTTTTCTTGCTAATAAATGCTTTTTTCTTTACATTTCTTGAG
GTACACATTCAACTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATAAT
GAGATTATAAAACA
Found at i:4429 original size:170 final size:171
Alignment explanation
Indices: 4064--4484 Score: 510
Period size: 170 Copynumber: 2.5 Consensus size: 171
4054 NNNNAATGGA
* * *
4064 TGACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCATGTCTCTCAAGGTAGACATT
1 TGACTATAAATGCACTTTTCTTACCAATGAATGTCTTTTTCTTCATGTTTCTCAAGGTAGACATT
* *
4129 CAGTTATATTCTGTTTTAACCAAAAATATAAAAAAAATTCAAATTAATATTAATTATGAGATTAT
66 CAATTATAATCTGTTTTAACCAAAAATAT-AAAAAAATTCAAATTAATATTAATTATGAGATTAT
*
4194 AAAACCATTTAAAGCAAGTAATAAGGCTTTTTAAAGAATGAG
130 AAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGAG
* *
4236 TGACTATAAATGCACTTTTCTTACCCATGAATG-CTTTTTTCTTCACGTTTCTCAAGGTAGACAT
1 TGACTATAAATGCACTTTTCTTACCAATGAATGTC-TTTTTCTTCATGTTTCTCAAGGTAGACAT
* * **********
4300 TCAAATATAGTCTGTTTTAACCAAAAATAT-AAAAAATTC-AATATANNNNNNNNNNTGAGATTA
65 TCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAAAT-TAATATTAATTATGAGATTA
* *
4363 TAAAACCATTTAAAGCGATTAATTAA-GCTTTTGAAAGAAT-AGG
129 TAAAACCATTTAAAGCAAGTAA-TAAGGCTTTTGAAAGAATGA-G
** * * * *
4406 TGACTATAAATATACTTTTCTTACGAATGAATATCTTTTTCTTCATGTTTCTCGAGATAGACATT
1 TGACTATAAATGCACTTTTCTTACCAATGAATGTCTTTTTCTTCATGTTTCTCAAGGTAGACATT
4471 CAATTATAATCTGT
66 CAATTATAATCTGT
4485 NNNNNNNNNN
Statistics
Matches: 213, Mismatches: 31, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
169 4 0.02
170 120 0.56
171 5 0.02
172 84 0.39
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.37
Consensus pattern (171 bp):
TGACTATAAATGCACTTTTCTTACCAATGAATGTCTTTTTCTTCATGTTTCTCAAGGTAGACATT
CAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAAATTAATATTAATTATGAGATTATA
AAACCATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGAG
Found at i:5896 original size:172 final size:167
Alignment explanation
Indices: 5537--6391 Score: 525
Period size: 172 Copynumber: 5.0 Consensus size: 167
5527 NNNNNNNAAG
* * * * *
5537 GAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGTCTTTTTCTTCCCGTTTCTTGAGGT
1 GAATGGGTAACTATAAATGGACTTTTCTTACCAATGAATGTCTTTTTCTT-CAGTTTCTCGAAGT
* * *
5602 AGACATTCAACTATAATCTGTCTTAATCAAAAATAC-AAAAAAATTCAACTTAAAATCAATTATG
65 AGACATTCAACTATAGTCTGTTTTAACCAAAAATACAAAAAAAATTCAACTTAAAATCAATTATG
****** *
5666 AGATNNNNNNNNNNTTTAAAGCGAGTAATAAGGCTTTTGAAA
130 AGAT----AAACTATTTAAAGCGAGTAATAAGGCATTTGAAA
* * * * *
5708 GAATGTGAAACTATAAATGGACTTTTCTTACCAATAAATGCCTTTTTCTTCAGGTTTCTCAAAGT
1 GAATGGGTAACTATAAATGGACTTTTCTTACCAATGAATGTCTTTTTCTTCA-GTTTCTCGAAGT
* *
5773 AGACATTCAACAATAGTCTGTTTTAACCAAAAATACAAAAAAAATTCAACTTAAAATCAGTTANN
65 AGACATTCAACTATAGTCTGTTTTAACCAAAAATACAAAAAAAATTCAACTTAAAATCAATTA--
******
5838 NNNNNNNNAAACTATTTAAAGCGAGTAATAAGGCATTTGAAA
128 --TGAGATAAACTATTTAAAGCGAGTAATAAGGCATTTGAAA
* * * * * **
5880 GAATGGGTTACTATAAATGGACTTTTTTTGCCAATGCATGTCTTTTTCTTCTAGTTTTTCGATTT
1 GAATGGGTAACTATAAATGGACTTTTCTTACCAATGAATGTCTTTTTCTTC-AGTTTCTCGAAGT
* * * * ** **
5945 ACACATTCAATTATAGTATGTTTTAACTAAAAATGTAAAAAAAATAAAACTTAAAATCAATTATG
65 AGACATTCAACTATAGTCTGTTTTAACCAAAAATACAAAAAAAATTCAACTTAAAATCAATTATG
* *
6010 AGATCATAAAACCATTTACAGCGAGTAATAAGGC-TTTCGAAA
130 AG---AT-AAACTATTTAAAGCGAGTAATAAGGCATTT-GAAA
* * * * * * *
6052 -AGATGAGTGAGTGTAAATGGACATTTCTTACCAATG-ACGATATTTTTCTTCACGTTT-TCTGA
1 GA-ATGGGTAACTATAAATGGACTTTTCTTACCAATGAATG-TCTTTTTCTTCA-GTTTCTC-GA
* * ********** ** *
6114 GGTAGACATTCAATTATAGTNNNNNNNNNNCAAAAAT--GTAAAAAATTCAACTTCAAATCAATT
62 AGTAGACATTCAACTATAGTCTGTTTTAACCAAAAATACAAAAAAAATTCAACTTAAAATCAATT
* * * *
6177 ATGAGATTAAAAAATCATTTAAAGTGTGTAATTAGG-ATTTTG-AA
127 ATGAGA-T--AAACT-ATTTAAAGCGAGTAATAAGGCA-TTTGAAA
* * * *
6221 GCAATGGGTGACTATAAATGGACTTTT-TT-CGCTAATGAATATATTTTTC-TCTACGTTTCT-T
1 G-AATGGGTAACTATAAATGGACTTTTCTTAC-C-AATGAATGTCTTTTTCTTC-A-GTTTCTCG
** ** * *
6282 AAGGTAGACATTCAACTATAGTCTGTTTTAAGTAAAAAT-GTAAAAACATTTAA-TTGAAAATCA
61 AA-GTAGACATTCAACTATAGTCTGTTTTAACCAAAAATACAAAAAAAATTCAACTT-AAAATCA
* * *
6345 ATTATGAGATTATAAAACCATTTAAGGCGAGTAATAAGGCTTTTGAA
124 ATTATGAG---AT-AAACTATTTAAAGCGAGTAATAAGGCATTTGAA
6392 NNNNNNNNNN
Statistics
Matches: 524, Mismatches: 124, Indels: 71
0.73 0.17 0.10
Matches are distributed among these distances:
167 1 0.00
168 2 0.00
169 12 0.02
170 108 0.21
171 143 0.27
172 255 0.49
173 2 0.00
174 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (167 bp):
GAATGGGTAACTATAAATGGACTTTTCTTACCAATGAATGTCTTTTTCTTCAGTTTCTCGAAGTA
GACATTCAACTATAGTCTGTTTTAACCAAAAATACAAAAAAAATTCAACTTAAAATCAATTATGA
GATAAACTATTTAAAGCGAGTAATAAGGCATTTGAAA
Found at i:7402 original size:171 final size:170
Alignment explanation
Indices: 6529--7424 Score: 917
Period size: 171 Copynumber: 5.2 Consensus size: 170
6519 TTTAACTGAC
*
6529 AATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTTC-CGTTTCTCGAGGT
1 AATGGGTGACTATAAATGGACTTTTCTT-CCAATGAATGCCTTTTTC-TTCACGTTTCTCGAGGT
* ****
6593 AGACATTCAACTATAATCTGTTTTAACCAAAAATACAAAAAAATTCAACTTAAAATCAATTNNNN
64 AGACATTCAACTATAGTCTGTTTTAACCAAAAATACAAAAAAATTCAACTTAAAATCAATTATGA
******
6658 NNNNNNAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAG
129 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAG
* ** * * *
6700 AATGTGAAACTATAAATGCACTTTTCTTGCCAATGAATGCCTTTTTCTTCAGGTTTCTCAAGGTA
1 AATGGGTGACTATAAATGGACTTTTCTT-CCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTA
* * * * *
6765 GACATTCAACAATAGTCTGCTTTAAACAAAAATACAAAAAAAAATTCAACTTAAAATCAGTTATA
65 GACATTCAACTATAGTCTGTTTTAACCAAAAATAC--AAAAAAATTCAACTTAAAATCAATTATG
* *
6830 AGATTCTAAAACCATTTAAAGCGAGTAATAAGGCATTTGAAAG
128 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAG
* * * * * **
6873 AATGGGTTAATATAAATGGATTTTTCTTGCCAATGAATGTCTTTTTCTTCTA-GTTTTTCGATTT
1 AATGGGTGACTATAAATGGACTTTTCTT-CCAATGAATGCCTTTTTCTTC-ACGTTTCTCGAGGT
* ** * * *
6937 AGACATTCAATTATAGTCTGTTTTAAATAAAAATATAAAAAAAATACAACTTAAAATTAATTATG
64 AGACATTCAACTATAGTCTGTTTTAACCAAAAATA-CAAAAAAATTCAACTTAAAATCAATTATG
* *
7002 AGATTATAAAACCATTTACAGCGAGTAATAAGGCCTTTGAAAG
128 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAG
* * * * * * * * * * *
7045 GATGAGTAAGTATAAATGAACATGTCTTGCCAATGACTACATTTTTCTTCACGTTT-TCTGTGGT
1 AATGGGTGACTATAAATGGACTTTTCTT-CCAATGAATGCCTTTTTCTTCACGTTTCTC-GAGGT
* ** * *
7109 A-AGCATTCAATTATAGTCTGTTTTAACCAAAAAT-GTAAAAAACTCAACTTCAAATCAATTATG
64 AGA-CATTCAACTATAGTCTGTTTTAACCAAAAATACAAAAAAATTCAACTTAAAATCAATTATG
* * * * * *
7172 AGATTAAAAAACAATTTAAACCGAGTAATTAGGATTTTGAAGG
128 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAG
** * *
7215 AATGGGTGACTATAAATGGACTTTT-TTCACTAATGAATATCTTTTTCTACATGTTTCTCGAGGT
1 AATGGGTGACTATAAATGGACTTTTCTTC-C-AATGAATGCCTTTTTCTTCACGTTTCTCGAGGT
* * * *
7279 AGACATTCAACTATAG-CTTGTTTTAACCAAAAATGCAAAGAAATTTAA-TTGAAAATCAATAAT
64 AGACATTCAACTATAGTC-TGTTTTAACCAAAAATACAAAAAAATTCAACTT-AAAATCAATTAT
* *
7342 GACATTATAAAACCATTTAAGGCGAGTAATAAGGCTTTTGAAAG
127 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAG
* * *
7386 AATGGGTGATTATAAATAGACTTTTCTTATCAATGAATG
1 AATGGGTGACTATAAATGGACTTTTCTT-CCAATGAATG
7425 TCNNNNNNNN
Statistics
Matches: 597, Mismatches: 111, Indels: 34
0.80 0.15 0.05
Matches are distributed among these distances:
168 1 0.00
169 4 0.01
170 134 0.22
171 175 0.29
172 141 0.24
173 141 0.24
174 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (170 bp):
AATGGGTGACTATAAATGGACTTTTCTTCCAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTAG
ACATTCAACTATAGTCTGTTTTAACCAAAAATACAAAAAAATTCAACTTAAAATCAATTATGAGA
TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAG
Done.