Multiple sequence alignment - TraesCS1A01G408200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G408200 chr1A 100.000 2714 0 0 1 2714 570253924 570256637 0.000000e+00 5012.0
1 TraesCS1A01G408200 chr1D 89.298 2093 126 42 584 2619 474725300 474727351 0.000000e+00 2534.0
2 TraesCS1A01G408200 chr1B 89.979 1397 74 21 610 1965 659974530 659975901 0.000000e+00 1744.0
3 TraesCS1A01G408200 chr1B 86.290 496 36 21 2097 2570 659975942 659976427 6.700000e-141 510.0
4 TraesCS1A01G408200 chr1B 81.517 633 72 19 1 626 659971876 659972470 1.890000e-131 479.0
5 TraesCS1A01G408200 chr1B 95.745 47 2 0 2031 2077 659975896 659975942 2.900000e-10 76.8
6 TraesCS1A01G408200 chr1B 83.117 77 5 2 2641 2714 659978360 659978431 2.260000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G408200 chr1A 570253924 570256637 2713 False 5012.00 5012 100.0000 1 2714 1 chr1A.!!$F1 2713
1 TraesCS1A01G408200 chr1D 474725300 474727351 2051 False 2534.00 2534 89.2980 584 2619 1 chr1D.!!$F1 2035
2 TraesCS1A01G408200 chr1B 659971876 659978431 6555 False 574.74 1744 87.3296 1 2714 5 chr1B.!!$F1 2713

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
325 331 0.098728 CCGCCGCAACCTTTCTTATG 59.901 55.0 0.0 0.0 0.0 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 4224 0.107268 TCATGGGAGATGATGTGCCG 59.893 55.0 0.0 0.0 0.0 5.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.486095 CGTGCAAAAGCATAAGAGAAAAC 57.514 39.130 0.00 0.00 0.00 2.43
24 25 5.630680 CGTGCAAAAGCATAAGAGAAAACAT 59.369 36.000 0.00 0.00 0.00 2.71
26 27 7.325821 CGTGCAAAAGCATAAGAGAAAACATAA 59.674 33.333 0.00 0.00 0.00 1.90
28 29 9.709495 TGCAAAAGCATAAGAGAAAACATAATT 57.291 25.926 0.00 0.00 0.00 1.40
52 53 8.592105 TTTTCTTCACAAAATAAATCTGCAGG 57.408 30.769 15.13 0.00 0.00 4.85
67 68 4.122046 TCTGCAGGAACATGATTCATACG 58.878 43.478 15.13 0.00 0.00 3.06
72 73 6.936335 TGCAGGAACATGATTCATACGATATT 59.064 34.615 0.00 0.00 0.00 1.28
73 74 7.445096 TGCAGGAACATGATTCATACGATATTT 59.555 33.333 0.00 0.00 0.00 1.40
75 76 7.747799 CAGGAACATGATTCATACGATATTTGC 59.252 37.037 0.00 0.00 0.00 3.68
90 91 1.254284 TTTGCTTATTGGGGCCCACG 61.254 55.000 28.84 15.20 30.78 4.94
132 133 4.993029 TTTTTGGGTGTAAGGTCAACTG 57.007 40.909 0.00 0.00 0.00 3.16
133 134 3.655615 TTTGGGTGTAAGGTCAACTGT 57.344 42.857 0.00 0.00 0.00 3.55
134 135 3.655615 TTGGGTGTAAGGTCAACTGTT 57.344 42.857 0.00 0.00 0.00 3.16
135 136 3.655615 TGGGTGTAAGGTCAACTGTTT 57.344 42.857 0.00 0.00 0.00 2.83
136 137 3.283751 TGGGTGTAAGGTCAACTGTTTG 58.716 45.455 0.00 0.00 0.00 2.93
137 138 3.054287 TGGGTGTAAGGTCAACTGTTTGA 60.054 43.478 0.00 0.00 39.55 2.69
167 168 1.048601 TTGAACTCAAGGGCTCTCGT 58.951 50.000 0.00 0.00 0.00 4.18
171 172 0.461961 ACTCAAGGGCTCTCGTATGC 59.538 55.000 0.00 0.00 0.00 3.14
184 185 3.391626 TCTCGTATGCTCTTCCTCCTCTA 59.608 47.826 0.00 0.00 0.00 2.43
202 203 2.516048 TAGCTCTCCTTCCACCCGCT 62.516 60.000 0.00 0.00 0.00 5.52
225 226 4.389576 CAGCGCCGACCAAACTGC 62.390 66.667 2.29 0.00 0.00 4.40
226 227 4.626081 AGCGCCGACCAAACTGCT 62.626 61.111 2.29 0.00 0.00 4.24
227 228 3.660111 GCGCCGACCAAACTGCTT 61.660 61.111 0.00 0.00 0.00 3.91
237 238 2.422231 AAACTGCTTGTTGCCGCCA 61.422 52.632 0.00 0.00 42.00 5.69
238 239 1.747325 AAACTGCTTGTTGCCGCCAT 61.747 50.000 0.00 0.00 42.00 4.40
239 240 1.747325 AACTGCTTGTTGCCGCCATT 61.747 50.000 0.00 0.00 42.00 3.16
240 241 0.893270 ACTGCTTGTTGCCGCCATTA 60.893 50.000 0.00 0.00 42.00 1.90
242 243 1.153842 GCTTGTTGCCGCCATTACC 60.154 57.895 0.00 0.00 35.15 2.85
245 251 1.579084 TTGTTGCCGCCATTACCGTC 61.579 55.000 0.00 0.00 0.00 4.79
265 271 3.838795 GCGGTGCTCTAACACGCG 61.839 66.667 3.53 3.53 41.65 6.01
271 277 3.188786 CTCTAACACGCGCCTGGC 61.189 66.667 9.11 9.11 38.69 4.85
272 278 4.752879 TCTAACACGCGCCTGGCC 62.753 66.667 14.12 0.00 38.94 5.36
290 296 4.048470 GCCCCCTTCCCGCTCTTT 62.048 66.667 0.00 0.00 0.00 2.52
292 298 1.378646 CCCCCTTCCCGCTCTTTTC 60.379 63.158 0.00 0.00 0.00 2.29
293 299 1.378646 CCCCTTCCCGCTCTTTTCC 60.379 63.158 0.00 0.00 0.00 3.13
294 300 1.745489 CCCTTCCCGCTCTTTTCCG 60.745 63.158 0.00 0.00 0.00 4.30
295 301 2.399356 CCTTCCCGCTCTTTTCCGC 61.399 63.158 0.00 0.00 0.00 5.54
325 331 0.098728 CCGCCGCAACCTTTCTTATG 59.901 55.000 0.00 0.00 0.00 1.90
332 338 2.094545 GCAACCTTTCTTATGTGCCCTG 60.095 50.000 0.00 0.00 0.00 4.45
335 341 2.290960 ACCTTTCTTATGTGCCCTGACC 60.291 50.000 0.00 0.00 0.00 4.02
337 343 0.251916 TTCTTATGTGCCCTGACCGG 59.748 55.000 0.00 0.00 0.00 5.28
353 359 1.674057 CGGCCTTCTTCTCTGGTGT 59.326 57.895 0.00 0.00 0.00 4.16
364 370 4.415150 CTGGTGTCGGCAGCCCAT 62.415 66.667 17.70 0.00 42.04 4.00
379 385 4.530857 CATCCCGCACCCCGAGTC 62.531 72.222 0.00 0.00 40.02 3.36
393 399 4.159108 AGTCCCCCTCGGCCCTAG 62.159 72.222 0.00 0.00 0.00 3.02
407 413 1.227002 CCTAGGTCGCTTTCGGCTC 60.227 63.158 0.00 0.00 40.74 4.70
414 420 2.481009 GCTTTCGGCTCGGCTTTC 59.519 61.111 0.00 0.00 38.06 2.62
416 422 1.376037 CTTTCGGCTCGGCTTTCCT 60.376 57.895 0.00 0.00 0.00 3.36
418 424 2.107041 TTTCGGCTCGGCTTTCCTGA 62.107 55.000 0.00 0.00 0.00 3.86
422 428 2.095252 GCTCGGCTTTCCTGACGAC 61.095 63.158 0.00 0.00 43.13 4.34
423 429 1.446272 CTCGGCTTTCCTGACGACC 60.446 63.158 0.00 0.00 43.13 4.79
424 430 2.809601 CGGCTTTCCTGACGACCG 60.810 66.667 0.00 0.00 41.74 4.79
428 434 4.287781 TTTCCTGACGACCGCGCA 62.288 61.111 8.75 0.00 42.48 6.09
432 438 3.470567 CTGACGACCGCGCACTTC 61.471 66.667 8.75 1.96 42.48 3.01
433 439 4.273257 TGACGACCGCGCACTTCA 62.273 61.111 8.75 4.77 42.48 3.02
438 444 1.153628 GACCGCGCACTTCACCTAT 60.154 57.895 8.75 0.00 0.00 2.57
450 456 5.352846 GCACTTCACCTATCTTTCTTCTTCC 59.647 44.000 0.00 0.00 0.00 3.46
453 459 5.941555 TCACCTATCTTTCTTCTTCCTCC 57.058 43.478 0.00 0.00 0.00 4.30
454 460 5.594777 TCACCTATCTTTCTTCTTCCTCCT 58.405 41.667 0.00 0.00 0.00 3.69
455 461 5.659079 TCACCTATCTTTCTTCTTCCTCCTC 59.341 44.000 0.00 0.00 0.00 3.71
456 462 4.966168 ACCTATCTTTCTTCTTCCTCCTCC 59.034 45.833 0.00 0.00 0.00 4.30
457 463 5.215845 CCTATCTTTCTTCTTCCTCCTCCT 58.784 45.833 0.00 0.00 0.00 3.69
458 464 5.304357 CCTATCTTTCTTCTTCCTCCTCCTC 59.696 48.000 0.00 0.00 0.00 3.71
459 465 3.445987 TCTTTCTTCTTCCTCCTCCTCC 58.554 50.000 0.00 0.00 0.00 4.30
460 466 3.177228 CTTTCTTCTTCCTCCTCCTCCA 58.823 50.000 0.00 0.00 0.00 3.86
463 469 2.383683 TCTTCTTCCTCCTCCTCCAGAA 59.616 50.000 0.00 0.00 0.00 3.02
464 470 3.177228 CTTCTTCCTCCTCCTCCAGAAA 58.823 50.000 0.00 0.00 0.00 2.52
466 472 3.808189 TCTTCCTCCTCCTCCAGAAATT 58.192 45.455 0.00 0.00 0.00 1.82
467 473 3.521126 TCTTCCTCCTCCTCCAGAAATTG 59.479 47.826 0.00 0.00 0.00 2.32
478 484 3.855689 CCAGAAATTGGCTTACACCAG 57.144 47.619 0.00 0.00 41.82 4.00
493 499 7.422399 GCTTACACCAGTTTATTTTTCAGACA 58.578 34.615 0.00 0.00 0.00 3.41
495 501 9.233232 CTTACACCAGTTTATTTTTCAGACAAC 57.767 33.333 0.00 0.00 0.00 3.32
547 554 3.953612 ACCGATGTTTGATAGGGTACGTA 59.046 43.478 0.00 0.00 0.00 3.57
554 561 9.538508 GATGTTTGATAGGGTACGTACTTTTAT 57.461 33.333 24.07 17.72 0.00 1.40
560 567 9.941325 TGATAGGGTACGTACTTTTATGAAAAA 57.059 29.630 24.07 0.00 33.58 1.94
614 622 0.610687 CAGGGGCTCTCGAGAAAAGT 59.389 55.000 17.36 0.00 0.00 2.66
623 2706 5.333721 GGCTCTCGAGAAAAGTTCAAAAGAG 60.334 44.000 17.36 0.34 35.49 2.85
628 2711 6.346096 TCGAGAAAAGTTCAAAAGAGGAGAA 58.654 36.000 0.00 0.00 0.00 2.87
633 2716 5.521906 AAGTTCAAAAGAGGAGAAAAGCC 57.478 39.130 0.00 0.00 0.00 4.35
735 2827 0.953471 TGCATTCTCCCGTTCCGTTG 60.953 55.000 0.00 0.00 0.00 4.10
736 2828 0.672401 GCATTCTCCCGTTCCGTTGA 60.672 55.000 0.00 0.00 0.00 3.18
848 2941 4.250431 GCAACAACGGCAGTGCGT 62.250 61.111 9.45 7.90 0.00 5.24
886 2979 2.835431 CACGGAGAGGGCCTCGAT 60.835 66.667 27.11 11.75 42.89 3.59
963 3056 1.892391 CCTTTTATCCCCGCCGCTC 60.892 63.158 0.00 0.00 0.00 5.03
1035 3128 4.778143 GGCCCGGCTGTCGACATT 62.778 66.667 20.40 0.00 42.43 2.71
1036 3129 3.499737 GCCCGGCTGTCGACATTG 61.500 66.667 20.40 9.72 42.43 2.82
1037 3130 2.047274 CCCGGCTGTCGACATTGT 60.047 61.111 20.40 0.00 42.43 2.71
1082 3187 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1083 3188 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1084 3189 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1098 3203 3.400054 GAGGGGGAGGGGTTCACG 61.400 72.222 0.00 0.00 0.00 4.35
1314 3425 0.375803 GAGGAGAAGACGACGAGCTC 59.624 60.000 2.73 2.73 0.00 4.09
1671 3788 1.990614 GGACCTCCTCGGGCTCTTT 60.991 63.158 0.00 0.00 42.26 2.52
1712 3829 1.908483 GGAGCTACCACCCCTTCTG 59.092 63.158 0.00 0.00 38.79 3.02
1719 3840 0.697854 ACCACCCCTTCTGACCAACT 60.698 55.000 0.00 0.00 0.00 3.16
1720 3841 0.250901 CCACCCCTTCTGACCAACTG 60.251 60.000 0.00 0.00 0.00 3.16
1752 3873 1.535636 CGTCAGCGTGCATCGATCTC 61.536 60.000 11.94 0.00 42.86 2.75
1753 3874 0.248825 GTCAGCGTGCATCGATCTCT 60.249 55.000 11.94 0.00 42.86 3.10
1818 3946 5.434408 TCTTTCAGATTGTGATCCCTGATG 58.566 41.667 0.00 0.00 35.82 3.07
1876 4004 6.053650 TCGTACATATACAGTGACAGTAGCT 58.946 40.000 0.00 0.00 0.00 3.32
1878 4006 5.521906 ACATATACAGTGACAGTAGCTGG 57.478 43.478 0.00 0.00 35.51 4.85
1880 4008 6.127101 ACATATACAGTGACAGTAGCTGGTA 58.873 40.000 0.00 2.85 35.51 3.25
1881 4009 4.985538 ATACAGTGACAGTAGCTGGTAC 57.014 45.455 8.91 8.91 35.51 3.34
1913 4041 7.830697 TCAGATCAAATCCAACATTGTGAGTAT 59.169 33.333 0.00 0.00 0.00 2.12
1959 4181 3.044986 CAAATTGAGTTGCGGTGACAAG 58.955 45.455 0.00 0.00 0.00 3.16
1964 4186 2.948979 TGAGTTGCGGTGACAAGAAATT 59.051 40.909 0.00 0.00 0.00 1.82
1965 4187 3.003275 TGAGTTGCGGTGACAAGAAATTC 59.997 43.478 0.00 0.00 0.00 2.17
1966 4188 3.214328 AGTTGCGGTGACAAGAAATTCT 58.786 40.909 0.00 0.00 0.00 2.40
1967 4189 3.632145 AGTTGCGGTGACAAGAAATTCTT 59.368 39.130 1.80 1.80 37.14 2.52
1968 4190 4.097892 AGTTGCGGTGACAAGAAATTCTTT 59.902 37.500 5.36 0.00 33.78 2.52
1969 4191 3.963665 TGCGGTGACAAGAAATTCTTTG 58.036 40.909 5.36 4.81 33.78 2.77
1970 4192 2.726241 GCGGTGACAAGAAATTCTTTGC 59.274 45.455 5.36 1.90 33.78 3.68
1971 4193 3.795150 GCGGTGACAAGAAATTCTTTGCA 60.795 43.478 5.36 4.51 33.78 4.08
1972 4194 3.976942 CGGTGACAAGAAATTCTTTGCAG 59.023 43.478 5.36 0.00 33.78 4.41
1973 4195 4.498009 CGGTGACAAGAAATTCTTTGCAGT 60.498 41.667 5.36 0.82 33.78 4.40
1974 4196 5.351458 GGTGACAAGAAATTCTTTGCAGTT 58.649 37.500 5.36 0.00 33.78 3.16
1975 4197 6.503524 GGTGACAAGAAATTCTTTGCAGTTA 58.496 36.000 5.36 0.00 33.78 2.24
1976 4198 6.978080 GGTGACAAGAAATTCTTTGCAGTTAA 59.022 34.615 5.36 0.00 33.78 2.01
1977 4199 7.168135 GGTGACAAGAAATTCTTTGCAGTTAAG 59.832 37.037 5.36 0.00 33.78 1.85
1978 4200 6.697019 TGACAAGAAATTCTTTGCAGTTAAGC 59.303 34.615 5.36 0.00 33.78 3.09
1979 4201 6.572519 ACAAGAAATTCTTTGCAGTTAAGCA 58.427 32.000 5.36 0.00 43.99 3.91
1987 4209 2.766970 TGCAGTTAAGCAAACGTTCC 57.233 45.000 0.00 0.00 42.46 3.62
1988 4210 1.335496 TGCAGTTAAGCAAACGTTCCC 59.665 47.619 0.00 0.00 42.46 3.97
1989 4211 1.335496 GCAGTTAAGCAAACGTTCCCA 59.665 47.619 0.00 0.00 43.29 4.37
1990 4212 2.223618 GCAGTTAAGCAAACGTTCCCAA 60.224 45.455 0.00 0.00 43.29 4.12
1991 4213 3.628017 CAGTTAAGCAAACGTTCCCAAG 58.372 45.455 0.00 0.00 43.29 3.61
1992 4214 3.314080 CAGTTAAGCAAACGTTCCCAAGA 59.686 43.478 0.00 0.00 43.29 3.02
1993 4215 3.949113 AGTTAAGCAAACGTTCCCAAGAA 59.051 39.130 0.00 0.00 43.29 2.52
1994 4216 4.399934 AGTTAAGCAAACGTTCCCAAGAAA 59.600 37.500 0.00 0.00 43.29 2.52
1995 4217 5.068591 AGTTAAGCAAACGTTCCCAAGAAAT 59.931 36.000 0.00 0.00 43.29 2.17
1996 4218 4.400529 AAGCAAACGTTCCCAAGAAATT 57.599 36.364 0.00 0.00 32.58 1.82
1997 4219 3.716601 AGCAAACGTTCCCAAGAAATTG 58.283 40.909 0.00 0.00 32.58 2.32
1998 4220 3.132111 AGCAAACGTTCCCAAGAAATTGT 59.868 39.130 0.00 0.00 32.58 2.71
1999 4221 3.868661 GCAAACGTTCCCAAGAAATTGTT 59.131 39.130 0.00 0.00 32.58 2.83
2000 4222 4.026062 GCAAACGTTCCCAAGAAATTGTTC 60.026 41.667 0.00 0.00 32.58 3.18
2001 4223 4.993029 AACGTTCCCAAGAAATTGTTCA 57.007 36.364 0.00 0.00 36.09 3.18
2002 4224 4.301637 ACGTTCCCAAGAAATTGTTCAC 57.698 40.909 0.00 0.00 36.09 3.18
2003 4225 3.242936 ACGTTCCCAAGAAATTGTTCACG 60.243 43.478 0.00 0.00 36.09 4.35
2004 4226 3.638484 GTTCCCAAGAAATTGTTCACGG 58.362 45.455 0.00 0.00 36.09 4.94
2005 4227 1.611491 TCCCAAGAAATTGTTCACGGC 59.389 47.619 0.00 0.00 36.09 5.68
2006 4228 1.339610 CCCAAGAAATTGTTCACGGCA 59.660 47.619 0.00 0.00 36.09 5.69
2007 4229 2.393764 CCAAGAAATTGTTCACGGCAC 58.606 47.619 0.00 0.00 36.09 5.01
2008 4230 2.223688 CCAAGAAATTGTTCACGGCACA 60.224 45.455 0.00 0.00 36.09 4.57
2009 4231 3.552684 CCAAGAAATTGTTCACGGCACAT 60.553 43.478 0.00 0.00 36.09 3.21
2010 4232 3.559238 AGAAATTGTTCACGGCACATC 57.441 42.857 0.00 0.00 36.09 3.06
2011 4233 2.884012 AGAAATTGTTCACGGCACATCA 59.116 40.909 0.00 0.00 36.09 3.07
2012 4234 3.507233 AGAAATTGTTCACGGCACATCAT 59.493 39.130 0.00 0.00 36.09 2.45
2013 4235 3.492421 AATTGTTCACGGCACATCATC 57.508 42.857 0.00 0.00 0.00 2.92
2014 4236 2.183478 TTGTTCACGGCACATCATCT 57.817 45.000 0.00 0.00 0.00 2.90
2015 4237 1.725641 TGTTCACGGCACATCATCTC 58.274 50.000 0.00 0.00 0.00 2.75
2016 4238 1.009829 GTTCACGGCACATCATCTCC 58.990 55.000 0.00 0.00 0.00 3.71
2017 4239 0.107703 TTCACGGCACATCATCTCCC 60.108 55.000 0.00 0.00 0.00 4.30
2018 4240 1.221566 CACGGCACATCATCTCCCA 59.778 57.895 0.00 0.00 0.00 4.37
2019 4241 0.179037 CACGGCACATCATCTCCCAT 60.179 55.000 0.00 0.00 0.00 4.00
2020 4242 0.179037 ACGGCACATCATCTCCCATG 60.179 55.000 0.00 0.00 0.00 3.66
2021 4243 0.107268 CGGCACATCATCTCCCATGA 59.893 55.000 0.00 0.00 0.00 3.07
2022 4244 1.271217 CGGCACATCATCTCCCATGAT 60.271 52.381 0.00 0.00 39.16 2.45
2023 4245 2.812983 CGGCACATCATCTCCCATGATT 60.813 50.000 0.00 0.00 36.69 2.57
2024 4246 3.228453 GGCACATCATCTCCCATGATTT 58.772 45.455 0.00 0.00 36.69 2.17
2025 4247 3.005472 GGCACATCATCTCCCATGATTTG 59.995 47.826 0.00 6.42 38.53 2.32
2026 4248 3.635373 GCACATCATCTCCCATGATTTGT 59.365 43.478 10.78 0.52 38.07 2.83
2027 4249 4.499188 GCACATCATCTCCCATGATTTGTG 60.499 45.833 11.49 11.49 38.07 3.33
2028 4250 4.643334 CACATCATCTCCCATGATTTGTGT 59.357 41.667 0.00 0.00 36.69 3.72
2029 4251 4.885907 ACATCATCTCCCATGATTTGTGTC 59.114 41.667 0.00 0.00 36.69 3.67
2030 4252 4.849813 TCATCTCCCATGATTTGTGTCT 57.150 40.909 0.00 0.00 0.00 3.41
2031 4253 5.955961 TCATCTCCCATGATTTGTGTCTA 57.044 39.130 0.00 0.00 0.00 2.59
2032 4254 6.312141 TCATCTCCCATGATTTGTGTCTAA 57.688 37.500 0.00 0.00 0.00 2.10
2033 4255 6.720309 TCATCTCCCATGATTTGTGTCTAAA 58.280 36.000 0.00 0.00 0.00 1.85
2034 4256 7.348815 TCATCTCCCATGATTTGTGTCTAAAT 58.651 34.615 0.00 0.00 33.19 1.40
2037 4259 8.506168 TCTCCCATGATTTGTGTCTAAATTAC 57.494 34.615 0.00 0.00 30.78 1.89
2084 4306 6.709846 AGGAGTAGTACGTATTAGGTAAGCAG 59.290 42.308 0.00 0.00 0.00 4.24
2136 4358 1.593006 GCTGTCCATGAACGAATACGG 59.407 52.381 0.00 0.00 44.46 4.02
2146 4375 1.138036 CGAATACGGTCGTGAGGCA 59.862 57.895 6.25 0.00 37.54 4.75
2160 4404 3.706373 GGCAGGAGGTTCAGGCGA 61.706 66.667 0.00 0.00 0.00 5.54
2161 4405 2.125350 GCAGGAGGTTCAGGCGAG 60.125 66.667 0.00 0.00 0.00 5.03
2178 4422 3.313257 GCGCGTCGATCGACCTTC 61.313 66.667 35.48 24.74 41.76 3.46
2182 4426 1.011019 CGTCGATCGACCTTCTCGG 60.011 63.158 35.48 19.76 43.16 4.63
2201 4445 2.645730 GTGCTCACCTACTCAGACTG 57.354 55.000 0.00 0.00 0.00 3.51
2204 4448 0.453793 CTCACCTACTCAGACTGGCG 59.546 60.000 1.81 0.00 0.00 5.69
2205 4449 1.153745 CACCTACTCAGACTGGCGC 60.154 63.158 0.00 0.00 0.00 6.53
2207 4451 0.034380 ACCTACTCAGACTGGCGCTA 60.034 55.000 7.64 0.00 0.00 4.26
2209 4453 1.268352 CCTACTCAGACTGGCGCTATC 59.732 57.143 7.64 2.30 0.00 2.08
2210 4454 0.945099 TACTCAGACTGGCGCTATCG 59.055 55.000 7.64 0.00 39.07 2.92
2211 4455 0.748367 ACTCAGACTGGCGCTATCGA 60.748 55.000 7.64 0.00 38.10 3.59
2212 4456 0.595588 CTCAGACTGGCGCTATCGAT 59.404 55.000 7.64 2.16 38.10 3.59
2213 4457 0.312102 TCAGACTGGCGCTATCGATG 59.688 55.000 8.54 0.00 38.10 3.84
2214 4458 1.006805 AGACTGGCGCTATCGATGC 60.007 57.895 8.54 8.86 38.10 3.91
2215 4459 1.006805 GACTGGCGCTATCGATGCT 60.007 57.895 8.54 0.00 38.10 3.79
2300 4548 0.316278 CTCGTAGCTGGTCACGATCG 60.316 60.000 14.88 14.88 45.28 3.69
2308 4556 2.161486 GGTCACGATCGTGCTCAGC 61.161 63.158 37.14 27.04 45.04 4.26
2371 4619 7.145323 CACAAATGGAAACCGGATAATTATCC 58.855 38.462 28.11 28.11 46.97 2.59
2490 4744 2.996621 GTCGTTCATCACAGAGGGAAAG 59.003 50.000 0.00 0.00 0.00 2.62
2492 4746 3.071023 TCGTTCATCACAGAGGGAAAGTT 59.929 43.478 0.00 0.00 0.00 2.66
2496 4750 3.648067 TCATCACAGAGGGAAAGTTGTCT 59.352 43.478 0.00 0.00 0.00 3.41
2504 4758 6.656693 ACAGAGGGAAAGTTGTCTCAATTATG 59.343 38.462 0.00 0.00 0.00 1.90
2526 4780 4.202326 TGCGGAGTTCTCTATAAAATCCCC 60.202 45.833 0.00 0.00 37.54 4.81
2602 4905 1.072173 TGTGTCTCCAATCACAGTGGG 59.928 52.381 0.00 0.00 39.23 4.61
2608 4911 2.038952 CTCCAATCACAGTGGGAAGTCA 59.961 50.000 0.00 0.00 36.73 3.41
2619 4922 6.094048 CACAGTGGGAAGTCATTTTGGTATAG 59.906 42.308 0.00 0.00 0.00 1.31
2621 4924 6.316390 CAGTGGGAAGTCATTTTGGTATAGTC 59.684 42.308 0.00 0.00 0.00 2.59
2622 4925 6.215636 AGTGGGAAGTCATTTTGGTATAGTCT 59.784 38.462 0.00 0.00 0.00 3.24
2624 4927 6.884295 TGGGAAGTCATTTTGGTATAGTCTTG 59.116 38.462 0.00 0.00 0.00 3.02
2626 4929 7.065923 GGGAAGTCATTTTGGTATAGTCTTGTC 59.934 40.741 0.00 0.00 0.00 3.18
2627 4930 7.065923 GGAAGTCATTTTGGTATAGTCTTGTCC 59.934 40.741 0.00 0.00 0.00 4.02
2628 4931 7.016153 AGTCATTTTGGTATAGTCTTGTCCA 57.984 36.000 0.00 0.00 0.00 4.02
2629 4932 6.879458 AGTCATTTTGGTATAGTCTTGTCCAC 59.121 38.462 0.00 0.00 0.00 4.02
2630 4933 6.653320 GTCATTTTGGTATAGTCTTGTCCACA 59.347 38.462 0.00 0.00 0.00 4.17
2631 4934 6.653320 TCATTTTGGTATAGTCTTGTCCACAC 59.347 38.462 0.00 0.00 0.00 3.82
2632 4935 5.554437 TTTGGTATAGTCTTGTCCACACA 57.446 39.130 0.00 0.00 0.00 3.72
2633 4936 4.530710 TGGTATAGTCTTGTCCACACAC 57.469 45.455 0.00 0.00 29.76 3.82
2635 4938 4.243270 GGTATAGTCTTGTCCACACACAC 58.757 47.826 0.00 0.00 29.76 3.82
2636 4939 4.262292 GGTATAGTCTTGTCCACACACACA 60.262 45.833 0.00 0.00 29.76 3.72
2637 4940 2.779755 AGTCTTGTCCACACACACAA 57.220 45.000 0.00 0.00 29.76 3.33
2639 4942 3.417101 AGTCTTGTCCACACACACAAAA 58.583 40.909 0.00 0.00 32.16 2.44
2664 6780 5.064441 ACGTAGTTATGTACTTCCCACAC 57.936 43.478 0.00 0.00 37.78 3.82
2665 6781 4.523943 ACGTAGTTATGTACTTCCCACACA 59.476 41.667 0.00 0.00 37.78 3.72
2666 6782 4.860907 CGTAGTTATGTACTTCCCACACAC 59.139 45.833 0.00 0.00 38.33 3.82
2667 6783 4.967084 AGTTATGTACTTCCCACACACA 57.033 40.909 0.00 0.00 31.29 3.72
2668 6784 4.638304 AGTTATGTACTTCCCACACACAC 58.362 43.478 0.00 0.00 31.29 3.82
2669 6785 4.101898 AGTTATGTACTTCCCACACACACA 59.898 41.667 0.00 0.00 31.29 3.72
2670 6786 3.569194 ATGTACTTCCCACACACACAA 57.431 42.857 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.211485 CCTGCAGATTTATTTTGTGAAGAAAAT 57.789 29.630 17.39 3.94 38.69 1.82
28 29 7.950512 TCCTGCAGATTTATTTTGTGAAGAAA 58.049 30.769 17.39 0.00 0.00 2.52
30 31 7.014134 TGTTCCTGCAGATTTATTTTGTGAAGA 59.986 33.333 17.39 0.93 0.00 2.87
31 32 7.147312 TGTTCCTGCAGATTTATTTTGTGAAG 58.853 34.615 17.39 0.00 0.00 3.02
67 68 3.006859 GTGGGCCCCAATAAGCAAATATC 59.993 47.826 22.27 0.00 34.18 1.63
72 73 1.680651 CGTGGGCCCCAATAAGCAA 60.681 57.895 22.27 0.00 34.18 3.91
73 74 2.044451 CGTGGGCCCCAATAAGCA 60.044 61.111 22.27 0.00 34.18 3.91
75 76 0.179029 CTACCGTGGGCCCCAATAAG 60.179 60.000 22.27 7.80 34.18 1.73
126 127 6.775142 TCAAATCTAATGGGTCAAACAGTTGA 59.225 34.615 0.00 0.00 41.57 3.18
127 128 6.980593 TCAAATCTAATGGGTCAAACAGTTG 58.019 36.000 0.00 0.00 35.95 3.16
128 129 7.287696 AGTTCAAATCTAATGGGTCAAACAGTT 59.712 33.333 0.00 0.00 0.00 3.16
129 130 6.777580 AGTTCAAATCTAATGGGTCAAACAGT 59.222 34.615 0.00 0.00 0.00 3.55
130 131 7.040478 TGAGTTCAAATCTAATGGGTCAAACAG 60.040 37.037 0.00 0.00 0.00 3.16
131 132 6.775142 TGAGTTCAAATCTAATGGGTCAAACA 59.225 34.615 0.00 0.00 0.00 2.83
132 133 7.214467 TGAGTTCAAATCTAATGGGTCAAAC 57.786 36.000 0.00 0.00 0.00 2.93
133 134 7.039784 CCTTGAGTTCAAATCTAATGGGTCAAA 60.040 37.037 0.00 0.00 35.15 2.69
134 135 6.434028 CCTTGAGTTCAAATCTAATGGGTCAA 59.566 38.462 0.00 0.00 35.15 3.18
135 136 5.945784 CCTTGAGTTCAAATCTAATGGGTCA 59.054 40.000 0.00 0.00 35.15 4.02
136 137 5.358160 CCCTTGAGTTCAAATCTAATGGGTC 59.642 44.000 5.41 0.00 35.15 4.46
137 138 5.264395 CCCTTGAGTTCAAATCTAATGGGT 58.736 41.667 5.41 0.00 35.15 4.51
167 168 3.397618 AGAGCTAGAGGAGGAAGAGCATA 59.602 47.826 0.00 0.00 35.55 3.14
171 172 2.443255 AGGAGAGCTAGAGGAGGAAGAG 59.557 54.545 0.00 0.00 0.00 2.85
184 185 3.394836 GCGGGTGGAAGGAGAGCT 61.395 66.667 0.00 0.00 0.00 4.09
202 203 2.739849 TTTGGTCGGCGCTGGATCAA 62.740 55.000 17.88 18.61 32.93 2.57
225 226 1.136565 CGGTAATGGCGGCAACAAG 59.863 57.895 18.31 4.96 0.00 3.16
226 227 1.579084 GACGGTAATGGCGGCAACAA 61.579 55.000 18.31 0.67 0.00 2.83
227 228 2.032834 ACGGTAATGGCGGCAACA 59.967 55.556 18.31 3.28 0.00 3.33
242 243 4.124351 TTAGAGCACCGCCGGACG 62.124 66.667 11.71 8.73 43.15 4.79
245 251 2.813908 GTGTTAGAGCACCGCCGG 60.814 66.667 0.00 0.00 33.53 6.13
283 289 4.445545 GCACGGCGGAAAAGAGCG 62.446 66.667 13.24 0.00 0.00 5.03
284 290 3.050275 AGCACGGCGGAAAAGAGC 61.050 61.111 13.24 3.34 0.00 4.09
286 292 3.353836 GCAGCACGGCGGAAAAGA 61.354 61.111 13.24 0.00 0.00 2.52
287 293 3.357079 AGCAGCACGGCGGAAAAG 61.357 61.111 13.24 0.00 39.27 2.27
311 317 2.094545 CAGGGCACATAAGAAAGGTTGC 60.095 50.000 0.00 0.00 0.00 4.17
332 338 1.219393 CCAGAGAAGAAGGCCGGTC 59.781 63.158 0.00 0.00 0.00 4.79
335 341 0.390472 GACACCAGAGAAGAAGGCCG 60.390 60.000 0.00 0.00 0.00 6.13
337 343 0.390472 CCGACACCAGAGAAGAAGGC 60.390 60.000 0.00 0.00 0.00 4.35
400 406 2.047274 CAGGAAAGCCGAGCCGAA 60.047 61.111 0.00 0.00 39.96 4.30
401 407 2.994995 TCAGGAAAGCCGAGCCGA 60.995 61.111 0.00 0.00 39.96 5.54
407 413 2.809601 CGGTCGTCAGGAAAGCCG 60.810 66.667 0.00 0.00 39.96 5.52
411 417 4.287781 TGCGCGGTCGTCAGGAAA 62.288 61.111 8.83 0.00 38.14 3.13
416 422 4.273257 TGAAGTGCGCGGTCGTCA 62.273 61.111 8.83 7.23 38.14 4.35
422 428 0.460284 AAGATAGGTGAAGTGCGCGG 60.460 55.000 8.83 0.00 0.00 6.46
423 429 1.324736 GAAAGATAGGTGAAGTGCGCG 59.675 52.381 0.00 0.00 0.00 6.86
424 430 2.622436 AGAAAGATAGGTGAAGTGCGC 58.378 47.619 0.00 0.00 0.00 6.09
428 434 6.070481 GGAGGAAGAAGAAAGATAGGTGAAGT 60.070 42.308 0.00 0.00 0.00 3.01
432 438 5.163353 GGAGGAGGAAGAAGAAAGATAGGTG 60.163 48.000 0.00 0.00 0.00 4.00
433 439 4.966168 GGAGGAGGAAGAAGAAAGATAGGT 59.034 45.833 0.00 0.00 0.00 3.08
438 444 3.181406 TGGAGGAGGAGGAAGAAGAAAGA 60.181 47.826 0.00 0.00 0.00 2.52
459 465 4.853924 AACTGGTGTAAGCCAATTTCTG 57.146 40.909 0.00 0.00 38.18 3.02
460 466 7.539034 AATAAACTGGTGTAAGCCAATTTCT 57.461 32.000 0.00 0.00 37.35 2.52
463 469 8.207545 TGAAAAATAAACTGGTGTAAGCCAATT 58.792 29.630 0.00 0.00 38.18 2.32
464 470 7.731054 TGAAAAATAAACTGGTGTAAGCCAAT 58.269 30.769 0.00 0.00 38.18 3.16
466 472 6.547880 TCTGAAAAATAAACTGGTGTAAGCCA 59.452 34.615 0.00 0.00 36.97 4.75
467 473 6.861572 GTCTGAAAAATAAACTGGTGTAAGCC 59.138 38.462 0.00 0.00 0.00 4.35
469 475 9.233232 GTTGTCTGAAAAATAAACTGGTGTAAG 57.767 33.333 0.00 0.00 0.00 2.34
470 476 8.962679 AGTTGTCTGAAAAATAAACTGGTGTAA 58.037 29.630 0.00 0.00 0.00 2.41
471 477 8.514330 AGTTGTCTGAAAAATAAACTGGTGTA 57.486 30.769 0.00 0.00 0.00 2.90
472 478 7.404671 AGTTGTCTGAAAAATAAACTGGTGT 57.595 32.000 0.00 0.00 0.00 4.16
473 479 9.233232 GTAAGTTGTCTGAAAAATAAACTGGTG 57.767 33.333 0.00 0.00 0.00 4.17
474 480 8.962679 TGTAAGTTGTCTGAAAAATAAACTGGT 58.037 29.630 0.00 0.00 0.00 4.00
522 528 4.276678 CGTACCCTATCAAACATCGGTAGA 59.723 45.833 0.00 0.00 0.00 2.59
523 529 4.037208 ACGTACCCTATCAAACATCGGTAG 59.963 45.833 0.00 0.00 0.00 3.18
527 533 5.179045 AGTACGTACCCTATCAAACATCG 57.821 43.478 21.80 0.00 0.00 3.84
534 540 9.941325 TTTTTCATAAAAGTACGTACCCTATCA 57.059 29.630 21.80 3.68 0.00 2.15
577 584 4.282496 CCCTGTCACTCACTCCTATAGTT 58.718 47.826 0.00 0.00 35.76 2.24
582 589 0.614979 GCCCCTGTCACTCACTCCTA 60.615 60.000 0.00 0.00 0.00 2.94
614 622 2.293399 GCGGCTTTTCTCCTCTTTTGAA 59.707 45.455 0.00 0.00 0.00 2.69
623 2706 0.960364 TCCATGTGCGGCTTTTCTCC 60.960 55.000 0.00 0.00 0.00 3.71
628 2711 0.396139 ATCCATCCATGTGCGGCTTT 60.396 50.000 0.00 0.00 0.00 3.51
633 2716 0.321034 ATCCGATCCATCCATGTGCG 60.321 55.000 0.00 0.00 0.00 5.34
985 3078 2.892425 CATGGCTCCGCTCCGTTC 60.892 66.667 0.00 0.00 0.00 3.95
986 3079 4.473520 CCATGGCTCCGCTCCGTT 62.474 66.667 0.00 0.00 0.00 4.44
1032 3125 3.549471 CGTCTGGATCTTCTCGAACAATG 59.451 47.826 0.00 0.00 0.00 2.82
1035 3128 2.420372 CTCGTCTGGATCTTCTCGAACA 59.580 50.000 0.00 0.00 0.00 3.18
1036 3129 2.223386 CCTCGTCTGGATCTTCTCGAAC 60.223 54.545 0.00 0.00 0.00 3.95
1037 3130 2.017782 CCTCGTCTGGATCTTCTCGAA 58.982 52.381 0.00 0.00 0.00 3.71
1082 3187 3.805151 AACGTGAACCCCTCCCCCT 62.805 63.158 0.00 0.00 0.00 4.79
1083 3188 3.254617 AACGTGAACCCCTCCCCC 61.255 66.667 0.00 0.00 0.00 5.40
1084 3189 2.350134 GAACGTGAACCCCTCCCC 59.650 66.667 0.00 0.00 0.00 4.81
1183 3288 1.406860 GCATCCTCCTCCACCTCCTC 61.407 65.000 0.00 0.00 0.00 3.71
1254 3362 2.745492 GACGACGACGAGGACCCT 60.745 66.667 15.32 0.00 42.66 4.34
1295 3406 0.375803 GAGCTCGTCGTCTTCTCCTC 59.624 60.000 0.00 0.00 0.00 3.71
1298 3409 4.655154 CGAGCTCGTCGTCTTCTC 57.345 61.111 27.79 0.00 44.20 2.87
1328 3439 0.904865 CCACAGGCAGTAGGTCTCCA 60.905 60.000 0.00 0.00 0.00 3.86
1458 3575 1.374758 CTTCTCCTTGCCGTCGCTT 60.375 57.895 0.00 0.00 35.36 4.68
1742 3863 0.796491 GATCGGCGAGAGATCGATGC 60.796 60.000 17.22 0.00 44.50 3.91
1743 3864 3.304586 GATCGGCGAGAGATCGATG 57.695 57.895 17.22 0.00 44.50 3.84
1747 3868 2.262303 ACCCGATCGGCGAGAGATC 61.262 63.158 29.12 6.97 44.57 2.75
1752 3873 4.143333 AACCACCCGATCGGCGAG 62.143 66.667 29.12 19.61 44.57 5.03
1753 3874 4.444838 CAACCACCCGATCGGCGA 62.445 66.667 29.12 13.87 44.57 5.54
1818 3946 2.556534 ATTCTACACGCCGTGTACTC 57.443 50.000 24.95 0.00 45.56 2.59
1876 4004 5.596772 TGGATTTGATCTGATCTACGTACCA 59.403 40.000 17.82 15.07 0.00 3.25
1878 4006 6.978659 TGTTGGATTTGATCTGATCTACGTAC 59.021 38.462 17.82 8.44 0.00 3.67
1880 4008 5.977635 TGTTGGATTTGATCTGATCTACGT 58.022 37.500 17.82 0.00 0.00 3.57
1881 4009 7.011763 ACAATGTTGGATTTGATCTGATCTACG 59.988 37.037 17.82 0.00 0.00 3.51
1913 4041 6.255453 GCAACTGAAGAAATTGCTGTACAAAA 59.745 34.615 0.00 0.00 44.26 2.44
1968 4190 1.335496 GGGAACGTTTGCTTAACTGCA 59.665 47.619 0.46 0.00 41.65 4.41
1969 4191 1.335496 TGGGAACGTTTGCTTAACTGC 59.665 47.619 0.46 0.00 34.46 4.40
1970 4192 3.314080 TCTTGGGAACGTTTGCTTAACTG 59.686 43.478 0.46 0.00 34.46 3.16
1971 4193 3.547746 TCTTGGGAACGTTTGCTTAACT 58.452 40.909 0.46 0.00 34.46 2.24
1972 4194 3.974871 TCTTGGGAACGTTTGCTTAAC 57.025 42.857 0.46 0.00 0.00 2.01
1973 4195 4.985538 TTTCTTGGGAACGTTTGCTTAA 57.014 36.364 0.46 0.00 0.00 1.85
1974 4196 5.163499 ACAATTTCTTGGGAACGTTTGCTTA 60.163 36.000 0.46 0.00 36.64 3.09
1975 4197 4.119136 CAATTTCTTGGGAACGTTTGCTT 58.881 39.130 0.46 0.00 0.00 3.91
1976 4198 3.132111 ACAATTTCTTGGGAACGTTTGCT 59.868 39.130 0.46 0.00 36.64 3.91
1977 4199 3.453424 ACAATTTCTTGGGAACGTTTGC 58.547 40.909 0.46 0.00 36.64 3.68
1978 4200 5.005299 GTGAACAATTTCTTGGGAACGTTTG 59.995 40.000 0.46 0.00 36.64 2.93
1979 4201 5.106442 GTGAACAATTTCTTGGGAACGTTT 58.894 37.500 0.46 0.00 36.64 3.60
1980 4202 4.678622 GTGAACAATTTCTTGGGAACGTT 58.321 39.130 0.00 0.00 36.64 3.99
1981 4203 3.242936 CGTGAACAATTTCTTGGGAACGT 60.243 43.478 0.00 0.00 36.64 3.99
1982 4204 3.296628 CGTGAACAATTTCTTGGGAACG 58.703 45.455 0.00 0.00 36.64 3.95
1983 4205 3.638484 CCGTGAACAATTTCTTGGGAAC 58.362 45.455 0.00 0.00 36.64 3.62
1984 4206 2.035321 GCCGTGAACAATTTCTTGGGAA 59.965 45.455 0.00 0.00 36.64 3.97
1985 4207 1.611491 GCCGTGAACAATTTCTTGGGA 59.389 47.619 0.00 0.00 36.64 4.37
1986 4208 1.339610 TGCCGTGAACAATTTCTTGGG 59.660 47.619 0.00 0.00 36.64 4.12
1987 4209 2.223688 TGTGCCGTGAACAATTTCTTGG 60.224 45.455 0.00 0.00 36.64 3.61
1988 4210 3.077229 TGTGCCGTGAACAATTTCTTG 57.923 42.857 0.00 0.00 38.39 3.02
1989 4211 3.317711 TGATGTGCCGTGAACAATTTCTT 59.682 39.130 0.00 0.00 32.36 2.52
1990 4212 2.884012 TGATGTGCCGTGAACAATTTCT 59.116 40.909 0.00 0.00 32.36 2.52
1991 4213 3.281341 TGATGTGCCGTGAACAATTTC 57.719 42.857 0.00 0.00 0.00 2.17
1992 4214 3.507233 AGATGATGTGCCGTGAACAATTT 59.493 39.130 0.00 0.00 0.00 1.82
1993 4215 3.084039 AGATGATGTGCCGTGAACAATT 58.916 40.909 0.00 0.00 0.00 2.32
1994 4216 2.679837 GAGATGATGTGCCGTGAACAAT 59.320 45.455 0.00 0.00 0.00 2.71
1995 4217 2.076100 GAGATGATGTGCCGTGAACAA 58.924 47.619 0.00 0.00 0.00 2.83
1996 4218 1.675714 GGAGATGATGTGCCGTGAACA 60.676 52.381 0.00 0.00 0.00 3.18
1997 4219 1.009829 GGAGATGATGTGCCGTGAAC 58.990 55.000 0.00 0.00 0.00 3.18
1998 4220 0.107703 GGGAGATGATGTGCCGTGAA 60.108 55.000 0.00 0.00 0.00 3.18
1999 4221 1.264045 TGGGAGATGATGTGCCGTGA 61.264 55.000 0.00 0.00 0.00 4.35
2000 4222 0.179037 ATGGGAGATGATGTGCCGTG 60.179 55.000 0.00 0.00 0.00 4.94
2001 4223 0.179037 CATGGGAGATGATGTGCCGT 60.179 55.000 0.00 0.00 0.00 5.68
2002 4224 0.107268 TCATGGGAGATGATGTGCCG 59.893 55.000 0.00 0.00 0.00 5.69
2003 4225 2.581216 ATCATGGGAGATGATGTGCC 57.419 50.000 0.00 0.00 37.37 5.01
2004 4226 3.635373 ACAAATCATGGGAGATGATGTGC 59.365 43.478 12.74 0.00 43.95 4.57
2005 4227 4.643334 ACACAAATCATGGGAGATGATGTG 59.357 41.667 11.64 11.64 45.03 3.21
2006 4228 4.863548 ACACAAATCATGGGAGATGATGT 58.136 39.130 0.00 0.00 38.62 3.06
2007 4229 5.131067 AGACACAAATCATGGGAGATGATG 58.869 41.667 0.00 0.00 38.62 3.07
2008 4230 5.384145 AGACACAAATCATGGGAGATGAT 57.616 39.130 0.00 0.00 40.20 2.45
2009 4231 4.849813 AGACACAAATCATGGGAGATGA 57.150 40.909 0.00 0.00 35.35 2.92
2010 4232 7.578310 ATTTAGACACAAATCATGGGAGATG 57.422 36.000 0.00 0.00 35.35 2.90
2011 4233 9.125026 GTAATTTAGACACAAATCATGGGAGAT 57.875 33.333 0.00 0.00 35.35 2.75
2012 4234 7.279981 CGTAATTTAGACACAAATCATGGGAGA 59.720 37.037 0.00 0.00 35.35 3.71
2013 4235 7.409697 CGTAATTTAGACACAAATCATGGGAG 58.590 38.462 0.00 0.00 35.35 4.30
2014 4236 6.183360 GCGTAATTTAGACACAAATCATGGGA 60.183 38.462 0.00 0.00 35.35 4.37
2015 4237 5.971202 GCGTAATTTAGACACAAATCATGGG 59.029 40.000 0.00 0.00 38.89 4.00
2016 4238 6.550843 TGCGTAATTTAGACACAAATCATGG 58.449 36.000 0.00 0.00 0.00 3.66
2017 4239 7.909641 TCATGCGTAATTTAGACACAAATCATG 59.090 33.333 0.00 0.00 32.76 3.07
2018 4240 7.984391 TCATGCGTAATTTAGACACAAATCAT 58.016 30.769 0.00 0.00 0.00 2.45
2019 4241 7.371126 TCATGCGTAATTTAGACACAAATCA 57.629 32.000 0.00 0.00 0.00 2.57
2020 4242 6.412072 GCTCATGCGTAATTTAGACACAAATC 59.588 38.462 0.00 0.00 0.00 2.17
2021 4243 6.258160 GCTCATGCGTAATTTAGACACAAAT 58.742 36.000 0.00 0.00 0.00 2.32
2022 4244 5.391523 GGCTCATGCGTAATTTAGACACAAA 60.392 40.000 0.00 0.00 40.82 2.83
2023 4245 4.094294 GGCTCATGCGTAATTTAGACACAA 59.906 41.667 0.00 0.00 40.82 3.33
2024 4246 3.621268 GGCTCATGCGTAATTTAGACACA 59.379 43.478 0.00 0.00 40.82 3.72
2025 4247 3.621268 TGGCTCATGCGTAATTTAGACAC 59.379 43.478 0.00 0.00 40.82 3.67
2026 4248 3.867857 TGGCTCATGCGTAATTTAGACA 58.132 40.909 0.00 0.00 40.82 3.41
2027 4249 4.875544 TTGGCTCATGCGTAATTTAGAC 57.124 40.909 0.00 0.00 40.82 2.59
2028 4250 4.941263 ACTTTGGCTCATGCGTAATTTAGA 59.059 37.500 0.00 0.00 40.82 2.10
2029 4251 5.065218 AGACTTTGGCTCATGCGTAATTTAG 59.935 40.000 0.00 0.00 40.82 1.85
2030 4252 4.941263 AGACTTTGGCTCATGCGTAATTTA 59.059 37.500 0.00 0.00 40.82 1.40
2031 4253 3.758554 AGACTTTGGCTCATGCGTAATTT 59.241 39.130 0.00 0.00 40.82 1.82
2032 4254 3.347216 AGACTTTGGCTCATGCGTAATT 58.653 40.909 0.00 0.00 40.82 1.40
2033 4255 2.991250 AGACTTTGGCTCATGCGTAAT 58.009 42.857 0.00 0.00 40.82 1.89
2034 4256 2.472695 AGACTTTGGCTCATGCGTAA 57.527 45.000 0.00 0.00 40.82 3.18
2037 4259 4.361451 AATTAAGACTTTGGCTCATGCG 57.639 40.909 0.00 0.00 40.82 4.73
2077 4299 2.096594 GCTCGTTGCGCTGCTTAC 59.903 61.111 9.73 0.00 0.00 2.34
2136 4358 1.079750 GAACCTCCTGCCTCACGAC 60.080 63.158 0.00 0.00 0.00 4.34
2141 4363 2.270527 GCCTGAACCTCCTGCCTC 59.729 66.667 0.00 0.00 0.00 4.70
2146 4375 3.764466 CGCTCGCCTGAACCTCCT 61.764 66.667 0.00 0.00 0.00 3.69
2160 4404 3.736482 GAAGGTCGATCGACGCGCT 62.736 63.158 34.69 25.56 45.41 5.92
2161 4405 3.313257 GAAGGTCGATCGACGCGC 61.313 66.667 34.69 23.96 45.41 6.86
2182 4426 1.203523 CCAGTCTGAGTAGGTGAGCAC 59.796 57.143 0.00 0.00 0.00 4.40
2183 4427 1.550327 CCAGTCTGAGTAGGTGAGCA 58.450 55.000 0.00 0.00 0.00 4.26
2196 4440 1.006805 GCATCGATAGCGCCAGTCT 60.007 57.895 2.29 0.00 37.46 3.24
2198 4442 0.598680 GAAGCATCGATAGCGCCAGT 60.599 55.000 2.29 0.00 37.46 4.00
2201 4445 0.601311 AAGGAAGCATCGATAGCGCC 60.601 55.000 2.29 17.92 37.46 6.53
2204 4448 1.609320 GGGGAAGGAAGCATCGATAGC 60.609 57.143 0.00 4.59 0.00 2.97
2205 4449 1.694150 TGGGGAAGGAAGCATCGATAG 59.306 52.381 0.00 0.00 0.00 2.08
2207 4451 0.918983 TTGGGGAAGGAAGCATCGAT 59.081 50.000 0.00 0.00 0.00 3.59
2209 4453 0.811281 GTTTGGGGAAGGAAGCATCG 59.189 55.000 0.00 0.00 0.00 3.84
2210 4454 2.222227 AGTTTGGGGAAGGAAGCATC 57.778 50.000 0.00 0.00 0.00 3.91
2211 4455 2.702270 AAGTTTGGGGAAGGAAGCAT 57.298 45.000 0.00 0.00 0.00 3.79
2212 4456 2.470057 AAAGTTTGGGGAAGGAAGCA 57.530 45.000 0.00 0.00 0.00 3.91
2213 4457 3.497332 AGTAAAGTTTGGGGAAGGAAGC 58.503 45.455 0.00 0.00 0.00 3.86
2214 4458 4.986783 AGAGTAAAGTTTGGGGAAGGAAG 58.013 43.478 0.00 0.00 0.00 3.46
2215 4459 5.382616 GAAGAGTAAAGTTTGGGGAAGGAA 58.617 41.667 0.00 0.00 0.00 3.36
2308 4556 2.267961 GTACGTTCAGGGCCCAGG 59.732 66.667 27.56 16.57 0.00 4.45
2315 4563 1.343506 GCCACTTACGTACGTTCAGG 58.656 55.000 27.92 22.13 0.00 3.86
2335 4583 3.055719 ATTTGTGTGGCTCCGGCG 61.056 61.111 0.00 0.00 39.81 6.46
2371 4619 6.855836 TGCAAAGTTTAATTAGATGGCAGAG 58.144 36.000 0.00 0.00 0.00 3.35
2405 4653 2.608261 GCTACCGTTCTAGCTAGCCATG 60.608 54.545 16.35 9.95 36.88 3.66
2480 4734 6.404074 GCATAATTGAGACAACTTTCCCTCTG 60.404 42.308 0.00 0.00 0.00 3.35
2490 4744 4.631813 AGAACTCCGCATAATTGAGACAAC 59.368 41.667 0.00 0.00 0.00 3.32
2492 4746 4.160439 AGAGAACTCCGCATAATTGAGACA 59.840 41.667 0.00 0.00 0.00 3.41
2496 4750 9.778741 ATTTTATAGAGAACTCCGCATAATTGA 57.221 29.630 0.00 0.00 0.00 2.57
2504 4758 4.202326 TGGGGATTTTATAGAGAACTCCGC 60.202 45.833 0.00 0.00 35.49 5.54
2570 4824 2.948979 TGGAGACACAACGAAGCAATTT 59.051 40.909 0.00 0.00 33.40 1.82
2571 4825 2.571212 TGGAGACACAACGAAGCAATT 58.429 42.857 0.00 0.00 33.40 2.32
2572 4826 2.254546 TGGAGACACAACGAAGCAAT 57.745 45.000 0.00 0.00 33.40 3.56
2579 4882 2.221749 CACTGTGATTGGAGACACAACG 59.778 50.000 0.32 0.00 44.50 4.10
2602 4905 7.606456 TGGACAAGACTATACCAAAATGACTTC 59.394 37.037 0.00 0.00 0.00 3.01
2608 4911 6.430000 GTGTGTGGACAAGACTATACCAAAAT 59.570 38.462 0.00 0.00 32.49 1.82
2619 4922 3.840890 TTTTGTGTGTGTGGACAAGAC 57.159 42.857 0.00 0.00 33.73 3.01
2639 4942 6.424812 GTGTGGGAAGTACATAACTACGTTTT 59.575 38.462 0.00 0.00 37.50 2.43
2644 6760 5.636543 GTGTGTGTGGGAAGTACATAACTAC 59.363 44.000 0.00 0.00 37.50 2.73
2651 6767 3.351794 TTTGTGTGTGTGGGAAGTACA 57.648 42.857 0.00 0.00 0.00 2.90
2677 6793 5.347620 TCGGCCTTGTTGTACATAACTAT 57.652 39.130 0.00 0.00 0.00 2.12
2681 6797 7.337184 TCAATAATTCGGCCTTGTTGTACATAA 59.663 33.333 0.00 0.00 0.00 1.90


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.