Multiple sequence alignment - TraesCS3A01G527200

Loading Multiple Alignment...

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 TraesCS3A01G527200 chr3A 100.000 2336 0 0 1 2336 741626248 741623913 0.000000e+00 4314.0
1 TraesCS3A01G527200 chr3D 81.127 2289 148 132 164 2257 608513010 608510811 0.000000e+00 1572.0
2 TraesCS3A01G527200 chr3D 86.905 84 5 5 46 129 608513097 608513020 3.200000e-14 89.8
3 TraesCS3A01G527200 chr3B 82.232 1756 121 78 417 2066 818927353 818925683 0.000000e+00 1338.0
4 TraesCS3A01G527200 chr3B 92.778 180 4 4 2114 2289 818925431 818925257 3.850000e-63 252.0
5 TraesCS3A01G527200 chr3B 93.151 73 4 1 170 241 818932817 818932745 3.170000e-19 106.0
6 TraesCS3A01G527200 chr3B 97.959 49 1 0 81 129 818932868 818932820 4.140000e-13 86.1
7 TraesCS3A01G527200 chr5D 100.000 30 0 0 1009 1038 99418743 99418714 3.240000e-04 56.5
8 TraesCS3A01G527200 chr5A 100.000 30 0 0 1009 1038 103569118 103569147 3.240000e-04 56.5


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 TraesCS3A01G527200 chr3A 741623913 741626248 2335 True 4314.0 4314 100.000 1 2336 1 chr3A.!!$R1 2335
1 TraesCS3A01G527200 chr3D 608510811 608513097 2286 True 830.9 1572 84.016 46 2257 2 chr3D.!!$R1 2211
2 TraesCS3A01G527200 chr3B 818925257 818927353 2096 True 795.0 1338 87.505 417 2289 2 chr3B.!!$R1 1872

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
32 33 0.108138 AGTTACTGACAGCGGCATCC 60.108 55.0 1.25 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2206 0.315706 GATTCAATCTCTGCGTGCGC 60.316 55.0 9.85 9.85 42.35 6.09 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 4.927773 GTAAAAACGCGAGAGTTACTGAC 58.072 43.478 15.93 0.00 33.41 3.51
23 24 2.787601 AAACGCGAGAGTTACTGACA 57.212 45.000 15.93 0.00 33.41 3.58
24 25 2.333389 AACGCGAGAGTTACTGACAG 57.667 50.000 15.93 0.00 31.74 3.51
25 26 0.109689 ACGCGAGAGTTACTGACAGC 60.110 55.000 15.93 0.00 0.00 4.40
26 27 1.128724 CGCGAGAGTTACTGACAGCG 61.129 60.000 0.00 0.00 40.37 5.18
27 28 0.798771 GCGAGAGTTACTGACAGCGG 60.799 60.000 1.25 0.00 0.00 5.52
28 29 0.798771 CGAGAGTTACTGACAGCGGC 60.799 60.000 1.25 0.00 0.00 6.53
29 30 0.243907 GAGAGTTACTGACAGCGGCA 59.756 55.000 1.25 0.00 0.00 5.69
30 31 0.898320 AGAGTTACTGACAGCGGCAT 59.102 50.000 1.25 0.00 0.00 4.40
31 32 1.134965 AGAGTTACTGACAGCGGCATC 60.135 52.381 1.25 0.00 0.00 3.91
32 33 0.108138 AGTTACTGACAGCGGCATCC 60.108 55.000 1.25 0.00 0.00 3.51
33 34 0.391130 GTTACTGACAGCGGCATCCA 60.391 55.000 1.25 0.00 0.00 3.41
34 35 0.391130 TTACTGACAGCGGCATCCAC 60.391 55.000 1.25 0.00 0.00 4.02
35 36 1.257750 TACTGACAGCGGCATCCACT 61.258 55.000 1.25 0.00 0.00 4.00
36 37 2.046988 TGACAGCGGCATCCACTG 60.047 61.111 1.45 0.00 37.45 3.66
37 38 2.821366 GACAGCGGCATCCACTGG 60.821 66.667 1.45 0.00 35.70 4.00
55 56 1.678970 GCCACCGCCAGGAGAAAAT 60.679 57.895 0.00 0.00 41.02 1.82
57 58 0.527565 CCACCGCCAGGAGAAAATTG 59.472 55.000 0.00 0.00 41.02 2.32
58 59 1.533625 CACCGCCAGGAGAAAATTGA 58.466 50.000 0.00 0.00 41.02 2.57
60 61 2.295909 CACCGCCAGGAGAAAATTGAAA 59.704 45.455 0.00 0.00 41.02 2.69
61 62 3.056607 CACCGCCAGGAGAAAATTGAAAT 60.057 43.478 0.00 0.00 41.02 2.17
62 63 4.157656 CACCGCCAGGAGAAAATTGAAATA 59.842 41.667 0.00 0.00 41.02 1.40
79 80 7.727331 TTGAAATATTCAAAAGGTTGGCTTG 57.273 32.000 3.18 0.00 45.94 4.01
120 121 1.677300 TGCAACGGCTAACATGGGG 60.677 57.895 0.00 0.00 41.91 4.96
121 122 1.677633 GCAACGGCTAACATGGGGT 60.678 57.895 0.00 0.00 36.96 4.95
122 123 1.933115 GCAACGGCTAACATGGGGTG 61.933 60.000 0.00 0.00 36.96 4.61
123 124 0.322098 CAACGGCTAACATGGGGTGA 60.322 55.000 0.00 0.00 0.00 4.02
124 125 0.623723 AACGGCTAACATGGGGTGAT 59.376 50.000 0.00 0.00 0.00 3.06
125 126 0.623723 ACGGCTAACATGGGGTGATT 59.376 50.000 0.00 0.00 0.00 2.57
135 136 3.193267 ACATGGGGTGATTTGATTTGACG 59.807 43.478 0.00 0.00 0.00 4.35
142 143 0.525761 ATTTGATTTGACGGTGGCGG 59.474 50.000 0.00 0.00 0.00 6.13
206 207 1.277739 GCGATCATGTGGCGTGATG 59.722 57.895 8.38 3.50 39.81 3.07
235 236 1.713597 TGCACAGTGATCGCAGTAAG 58.286 50.000 9.33 0.00 0.00 2.34
238 239 2.672478 GCACAGTGATCGCAGTAAGTCT 60.672 50.000 9.33 0.00 0.00 3.24
240 241 2.094494 ACAGTGATCGCAGTAAGTCTGG 60.094 50.000 9.33 0.00 43.78 3.86
241 242 1.134965 AGTGATCGCAGTAAGTCTGGC 60.135 52.381 9.33 0.00 43.78 4.85
244 245 2.907897 ATCGCAGTAAGTCTGGCGCC 62.908 60.000 22.73 22.73 43.78 6.53
245 246 2.047274 GCAGTAAGTCTGGCGCCA 60.047 61.111 30.59 30.59 43.78 5.69
246 247 2.391389 GCAGTAAGTCTGGCGCCAC 61.391 63.158 29.03 18.06 43.78 5.01
247 248 1.293498 CAGTAAGTCTGGCGCCACT 59.707 57.895 29.03 20.40 40.23 4.00
248 249 0.737715 CAGTAAGTCTGGCGCCACTC 60.738 60.000 29.03 20.98 40.23 3.51
249 250 1.448013 GTAAGTCTGGCGCCACTCC 60.448 63.158 29.03 16.18 0.00 3.85
250 251 1.609501 TAAGTCTGGCGCCACTCCT 60.610 57.895 29.03 18.36 0.00 3.69
251 252 0.323999 TAAGTCTGGCGCCACTCCTA 60.324 55.000 29.03 12.43 0.00 2.94
253 254 3.075005 TCTGGCGCCACTCCTACC 61.075 66.667 29.03 0.00 0.00 3.18
256 286 4.468689 GGCGCCACTCCTACCACC 62.469 72.222 24.80 0.00 0.00 4.61
259 289 1.677552 CGCCACTCCTACCACCTTT 59.322 57.895 0.00 0.00 0.00 3.11
261 291 1.276989 CGCCACTCCTACCACCTTTAA 59.723 52.381 0.00 0.00 0.00 1.52
262 292 2.289819 CGCCACTCCTACCACCTTTAAA 60.290 50.000 0.00 0.00 0.00 1.52
265 295 4.770531 GCCACTCCTACCACCTTTAAATTT 59.229 41.667 0.00 0.00 0.00 1.82
267 297 6.434965 GCCACTCCTACCACCTTTAAATTTTA 59.565 38.462 0.00 0.00 0.00 1.52
282 312 9.987901 CTTTAAATTTTATTTGTACTGCGTGTG 57.012 29.630 0.00 0.00 0.00 3.82
286 316 5.849357 TTTATTTGTACTGCGTGTGGTAG 57.151 39.130 0.00 0.00 0.00 3.18
287 317 2.894763 TTTGTACTGCGTGTGGTAGT 57.105 45.000 0.00 0.00 44.34 2.73
288 318 4.524316 ATTTGTACTGCGTGTGGTAGTA 57.476 40.909 0.00 0.00 42.06 1.82
290 320 2.507484 TGTACTGCGTGTGGTAGTAGT 58.493 47.619 0.00 0.00 43.28 2.73
291 321 3.673902 TGTACTGCGTGTGGTAGTAGTA 58.326 45.455 0.00 0.00 43.28 1.82
292 322 3.686241 TGTACTGCGTGTGGTAGTAGTAG 59.314 47.826 0.00 0.00 43.28 2.57
295 325 1.814394 TGCGTGTGGTAGTAGTAGTGG 59.186 52.381 0.00 0.00 0.00 4.00
296 326 1.815003 GCGTGTGGTAGTAGTAGTGGT 59.185 52.381 0.00 0.00 0.00 4.16
297 327 3.009723 GCGTGTGGTAGTAGTAGTGGTA 58.990 50.000 0.00 0.00 0.00 3.25
319 351 4.387598 AGTACGCTACCACTATACTCCAG 58.612 47.826 0.00 0.00 0.00 3.86
323 355 2.959707 GCTACCACTATACTCCAGCAGT 59.040 50.000 0.00 0.00 39.41 4.40
349 381 4.962122 GCGTGGTTGTGCGTGCAG 62.962 66.667 0.00 0.00 0.00 4.41
350 382 3.572539 CGTGGTTGTGCGTGCAGT 61.573 61.111 0.00 0.00 0.00 4.40
356 388 0.316196 GTTGTGCGTGCAGTGAAGTC 60.316 55.000 0.00 0.00 0.00 3.01
357 389 1.761244 TTGTGCGTGCAGTGAAGTCG 61.761 55.000 0.00 0.00 0.00 4.18
358 390 2.661537 TGCGTGCAGTGAAGTCGG 60.662 61.111 0.00 0.00 0.00 4.79
359 391 3.414700 GCGTGCAGTGAAGTCGGG 61.415 66.667 0.00 0.00 0.00 5.14
360 392 2.338620 CGTGCAGTGAAGTCGGGA 59.661 61.111 0.00 0.00 0.00 5.14
361 393 1.734477 CGTGCAGTGAAGTCGGGAG 60.734 63.158 0.00 0.00 0.00 4.30
363 395 1.533033 TGCAGTGAAGTCGGGAGGA 60.533 57.895 0.00 0.00 0.00 3.71
365 397 1.251527 GCAGTGAAGTCGGGAGGAGA 61.252 60.000 0.00 0.00 0.00 3.71
366 398 0.528470 CAGTGAAGTCGGGAGGAGAC 59.472 60.000 0.00 0.00 38.81 3.36
367 399 0.112606 AGTGAAGTCGGGAGGAGACA 59.887 55.000 0.00 0.00 40.84 3.41
369 401 0.112606 TGAAGTCGGGAGGAGACAGT 59.887 55.000 0.00 0.00 40.84 3.55
371 403 0.178958 AAGTCGGGAGGAGACAGTGT 60.179 55.000 0.00 0.00 40.84 3.55
454 510 2.865598 ATCTCGAGATGGCAGGGCG 61.866 63.158 26.78 0.00 32.68 6.13
482 538 4.096003 ACGGGCCACAGGATTCCG 62.096 66.667 4.39 0.00 45.42 4.30
488 547 1.815421 CCACAGGATTCCGCTTCCG 60.815 63.158 0.00 0.00 38.36 4.30
541 603 2.094494 ACAGACGGAATGTACTCTGCTG 60.094 50.000 7.30 9.36 34.60 4.41
544 606 1.284657 CGGAATGTACTCTGCTGCTG 58.715 55.000 0.00 0.00 0.00 4.41
549 611 1.153469 GTACTCTGCTGCTGGGAGC 60.153 63.158 13.67 7.14 42.82 4.70
577 639 0.320858 TGCGTTTTCATGGCGGTAGA 60.321 50.000 0.00 0.00 0.00 2.59
633 719 4.033776 TGGTAGCTGGTGCCTGGC 62.034 66.667 12.87 12.87 40.80 4.85
635 721 2.437359 GTAGCTGGTGCCTGGCTG 60.437 66.667 21.03 8.53 40.80 4.85
636 722 3.720601 TAGCTGGTGCCTGGCTGG 61.721 66.667 21.03 5.98 40.80 4.85
639 725 4.421515 CTGGTGCCTGGCTGGGAG 62.422 72.222 21.03 6.70 36.62 4.30
666 752 2.036733 AGTTGTCTTCCATCCGTCGAAA 59.963 45.455 0.00 0.00 0.00 3.46
676 762 1.228033 CCGTCGAAAGGTTGGGGTT 60.228 57.895 0.00 0.00 0.00 4.11
767 875 4.856801 CGGCCCCATTCCCACTCG 62.857 72.222 0.00 0.00 0.00 4.18
792 900 2.039624 TCCCTCACTCCCTGCTCC 59.960 66.667 0.00 0.00 0.00 4.70
830 938 3.376234 CACCATTCATTGATTCACTCGCT 59.624 43.478 0.00 0.00 0.00 4.93
831 939 3.624861 ACCATTCATTGATTCACTCGCTC 59.375 43.478 0.00 0.00 0.00 5.03
832 940 3.302935 CCATTCATTGATTCACTCGCTCG 60.303 47.826 0.00 0.00 0.00 5.03
833 941 1.280982 TCATTGATTCACTCGCTCGC 58.719 50.000 0.00 0.00 0.00 5.03
834 942 0.302890 CATTGATTCACTCGCTCGCC 59.697 55.000 0.00 0.00 0.00 5.54
835 943 0.811616 ATTGATTCACTCGCTCGCCC 60.812 55.000 0.00 0.00 0.00 6.13
836 944 2.956964 GATTCACTCGCTCGCCCG 60.957 66.667 0.00 0.00 0.00 6.13
868 976 4.950050 TCGCTCCATTTCTTCTTCTATCC 58.050 43.478 0.00 0.00 0.00 2.59
908 1029 1.448540 GCACTGTCCACTCCATCCG 60.449 63.158 0.00 0.00 0.00 4.18
924 1047 1.127567 TCCGTCCATCCCCATCCATC 61.128 60.000 0.00 0.00 0.00 3.51
925 1048 1.130054 CCGTCCATCCCCATCCATCT 61.130 60.000 0.00 0.00 0.00 2.90
926 1049 0.322975 CGTCCATCCCCATCCATCTC 59.677 60.000 0.00 0.00 0.00 2.75
927 1050 0.695347 GTCCATCCCCATCCATCTCC 59.305 60.000 0.00 0.00 0.00 3.71
928 1051 0.271619 TCCATCCCCATCCATCTCCA 59.728 55.000 0.00 0.00 0.00 3.86
929 1052 0.403271 CCATCCCCATCCATCTCCAC 59.597 60.000 0.00 0.00 0.00 4.02
930 1053 0.403271 CATCCCCATCCATCTCCACC 59.597 60.000 0.00 0.00 0.00 4.61
931 1054 1.130054 ATCCCCATCCATCTCCACCG 61.130 60.000 0.00 0.00 0.00 4.94
956 1079 1.530323 GACCCACCTGCATTTACGTT 58.470 50.000 0.00 0.00 0.00 3.99
958 1081 1.883926 ACCCACCTGCATTTACGTTTC 59.116 47.619 0.00 0.00 0.00 2.78
1224 1372 0.973496 AGAAGAAGGAGGAGGCCGAC 60.973 60.000 0.00 0.00 0.00 4.79
1381 1529 0.388520 GGCCGCCACATTCTTTCAAC 60.389 55.000 3.91 0.00 0.00 3.18
1400 1548 1.202698 ACCGTTTGCTTCTGCTCTTCT 60.203 47.619 0.00 0.00 40.48 2.85
1403 1554 2.413453 CGTTTGCTTCTGCTCTTCTACC 59.587 50.000 0.00 0.00 40.48 3.18
1440 1598 3.923273 ACATTTCCTTCCCCCTTTCTT 57.077 42.857 0.00 0.00 0.00 2.52
1441 1599 3.510459 ACATTTCCTTCCCCCTTTCTTG 58.490 45.455 0.00 0.00 0.00 3.02
1442 1600 2.694616 TTTCCTTCCCCCTTTCTTGG 57.305 50.000 0.00 0.00 0.00 3.61
1443 1601 0.114364 TTCCTTCCCCCTTTCTTGGC 59.886 55.000 0.00 0.00 0.00 4.52
1444 1602 0.776080 TCCTTCCCCCTTTCTTGGCT 60.776 55.000 0.00 0.00 0.00 4.75
1488 1649 9.545105 CATCCATTCTCAGCCTATATAATCTTC 57.455 37.037 0.00 0.00 0.00 2.87
1489 1650 8.907829 TCCATTCTCAGCCTATATAATCTTCT 57.092 34.615 0.00 0.00 0.00 2.85
1490 1651 9.331466 TCCATTCTCAGCCTATATAATCTTCTT 57.669 33.333 0.00 0.00 0.00 2.52
1551 1743 3.909732 TCTTGATGTTTTTCCCCACTGT 58.090 40.909 0.00 0.00 0.00 3.55
1609 1808 1.463674 CACCAGCACCAAGGTAATCC 58.536 55.000 0.00 0.00 36.07 3.01
1611 1810 1.271926 ACCAGCACCAAGGTAATCCAC 60.272 52.381 0.00 0.00 36.07 4.02
1695 1915 4.184079 TCGCTCTGTTTTTCCTAGTACC 57.816 45.455 0.00 0.00 0.00 3.34
1698 1918 3.678548 GCTCTGTTTTTCCTAGTACCACG 59.321 47.826 0.00 0.00 0.00 4.94
1734 1957 4.142534 TGTGCAGCTAGCTTCATTTCAATC 60.143 41.667 20.04 6.19 45.94 2.67
1739 1964 6.534079 GCAGCTAGCTTCATTTCAATCAAATT 59.466 34.615 16.46 0.00 41.15 1.82
1748 1973 8.761575 TTCATTTCAATCAAATTTGTCCTAGC 57.238 30.769 17.47 0.00 31.79 3.42
1749 1974 7.894708 TCATTTCAATCAAATTTGTCCTAGCA 58.105 30.769 17.47 0.00 31.79 3.49
1752 1977 5.076182 TCAATCAAATTTGTCCTAGCACCA 58.924 37.500 17.47 0.00 0.00 4.17
1753 1978 5.183713 TCAATCAAATTTGTCCTAGCACCAG 59.816 40.000 17.47 0.00 0.00 4.00
1769 1995 3.676646 GCACCAGCTGATGTTTTGATTTC 59.323 43.478 17.39 0.00 37.91 2.17
1777 2003 5.611796 TGATGTTTTGATTTCGAGTGAGG 57.388 39.130 0.00 0.00 0.00 3.86
1782 2008 0.537188 TGATTTCGAGTGAGGGAGGC 59.463 55.000 0.00 0.00 0.00 4.70
1783 2009 0.179070 GATTTCGAGTGAGGGAGGCC 60.179 60.000 0.00 0.00 0.00 5.19
1785 2011 3.881019 TTCGAGTGAGGGAGGCCGT 62.881 63.158 0.00 0.00 0.00 5.68
1787 2013 2.266055 GAGTGAGGGAGGCCGTTG 59.734 66.667 0.00 0.00 0.00 4.10
1788 2014 2.203788 AGTGAGGGAGGCCGTTGA 60.204 61.111 0.00 0.00 0.00 3.18
1789 2015 1.827399 GAGTGAGGGAGGCCGTTGAA 61.827 60.000 0.00 0.00 0.00 2.69
1790 2016 1.376037 GTGAGGGAGGCCGTTGAAG 60.376 63.158 0.00 0.00 0.00 3.02
1792 2018 3.249189 AGGGAGGCCGTTGAAGCA 61.249 61.111 0.00 0.00 0.00 3.91
1794 2033 1.901464 GGGAGGCCGTTGAAGCAAA 60.901 57.895 0.00 0.00 0.00 3.68
1802 2041 2.863704 GCCGTTGAAGCAAAGCAAGATT 60.864 45.455 0.00 0.00 0.00 2.40
1803 2042 2.727798 CCGTTGAAGCAAAGCAAGATTG 59.272 45.455 0.00 0.00 0.00 2.67
1816 2055 3.624861 AGCAAGATTGATCCATGTCGTTC 59.375 43.478 0.00 0.00 0.00 3.95
1817 2056 3.242870 GCAAGATTGATCCATGTCGTTCC 60.243 47.826 0.00 0.00 0.00 3.62
1818 2057 3.912496 AGATTGATCCATGTCGTTCCA 57.088 42.857 0.00 0.00 0.00 3.53
1827 2066 3.751175 TCCATGTCGTTCCATTCTTTCAC 59.249 43.478 0.00 0.00 0.00 3.18
1832 2071 4.036262 TGTCGTTCCATTCTTTCACCTTTG 59.964 41.667 0.00 0.00 0.00 2.77
1849 2091 4.022416 ACCTTTGCGTTGATTAATTGCTGA 60.022 37.500 0.00 0.00 0.00 4.26
1860 2102 5.527214 TGATTAATTGCTGATCCTTGTACCG 59.473 40.000 0.00 0.00 0.00 4.02
1870 2113 1.619827 TCCTTGTACCGGTACCAACAG 59.380 52.381 35.71 25.47 35.26 3.16
1887 2134 2.333014 ACAGTTTGTTGTTTGCGGTTG 58.667 42.857 0.00 0.00 0.00 3.77
1927 2190 2.452767 GTCAATTGACCGGACGGAC 58.547 57.895 25.26 12.18 39.07 4.79
2012 2284 2.202783 GCGGGCCAATGATTGTGC 60.203 61.111 4.39 7.18 0.00 4.57
2021 2293 4.823989 GGCCAATGATTGTGCTAGTCTTAT 59.176 41.667 14.96 0.00 0.00 1.73
2023 2295 6.486657 GGCCAATGATTGTGCTAGTCTTATTA 59.513 38.462 14.96 0.00 0.00 0.98
2025 2297 7.227512 GCCAATGATTGTGCTAGTCTTATTAGT 59.772 37.037 4.27 0.00 0.00 2.24
2026 2298 8.554528 CCAATGATTGTGCTAGTCTTATTAGTG 58.445 37.037 4.27 0.00 0.00 2.74
2028 2300 7.418337 TGATTGTGCTAGTCTTATTAGTGGA 57.582 36.000 0.00 0.00 0.00 4.02
2049 2323 2.278206 CGGTCGTCGATCTGCTGG 60.278 66.667 3.63 0.00 42.43 4.85
2050 2324 2.105128 GGTCGTCGATCTGCTGGG 59.895 66.667 0.00 0.00 0.00 4.45
2068 2350 0.846015 GGTGGTGATGATGATGGGGA 59.154 55.000 0.00 0.00 0.00 4.81
2091 2373 2.783510 AGTACAATTAGGTGGGGGATGG 59.216 50.000 0.00 0.00 0.00 3.51
2092 2374 0.933700 ACAATTAGGTGGGGGATGGG 59.066 55.000 0.00 0.00 0.00 4.00
2094 2376 1.133482 CAATTAGGTGGGGGATGGGAC 60.133 57.143 0.00 0.00 0.00 4.46
2117 2604 3.873805 CGCAAGTGAGTGAGAGTGA 57.126 52.632 0.00 0.00 0.00 3.41
2118 2605 1.695813 CGCAAGTGAGTGAGAGTGAG 58.304 55.000 0.00 0.00 0.00 3.51
2119 2606 1.000827 CGCAAGTGAGTGAGAGTGAGT 60.001 52.381 0.00 0.00 0.00 3.41
2120 2607 2.402305 GCAAGTGAGTGAGAGTGAGTG 58.598 52.381 0.00 0.00 0.00 3.51
2121 2608 2.035193 GCAAGTGAGTGAGAGTGAGTGA 59.965 50.000 0.00 0.00 0.00 3.41
2252 2743 6.910536 AGACCAAATGTTCGCTTAATCTAG 57.089 37.500 0.00 0.00 0.00 2.43
2264 2755 1.051812 TAATCTAGCAGCTGGGCCTC 58.948 55.000 17.12 0.00 0.00 4.70
2267 2758 3.397613 CTAGCAGCTGGGCCTCACC 62.398 68.421 17.12 0.00 37.93 4.02
2278 2769 4.873129 CCTCACCCGTCGCCATCG 62.873 72.222 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.442073 TGTCAGTAACTCTCGCGTTTTTAC 59.558 41.667 5.77 9.89 0.00 2.01
1 2 4.609947 TGTCAGTAACTCTCGCGTTTTTA 58.390 39.130 5.77 0.00 0.00 1.52
2 3 3.450578 TGTCAGTAACTCTCGCGTTTTT 58.549 40.909 5.77 0.00 0.00 1.94
3 4 3.050619 CTGTCAGTAACTCTCGCGTTTT 58.949 45.455 5.77 0.00 0.00 2.43
4 5 2.662700 CTGTCAGTAACTCTCGCGTTT 58.337 47.619 5.77 0.00 0.00 3.60
5 6 1.666311 GCTGTCAGTAACTCTCGCGTT 60.666 52.381 5.77 0.00 0.00 4.84
6 7 0.109689 GCTGTCAGTAACTCTCGCGT 60.110 55.000 5.77 0.00 0.00 6.01
7 8 1.128724 CGCTGTCAGTAACTCTCGCG 61.129 60.000 0.00 0.00 0.00 5.87
8 9 0.798771 CCGCTGTCAGTAACTCTCGC 60.799 60.000 0.93 0.00 0.00 5.03
9 10 0.798771 GCCGCTGTCAGTAACTCTCG 60.799 60.000 0.93 0.00 0.00 4.04
10 11 0.243907 TGCCGCTGTCAGTAACTCTC 59.756 55.000 0.93 0.00 0.00 3.20
11 12 0.898320 ATGCCGCTGTCAGTAACTCT 59.102 50.000 0.93 0.00 0.00 3.24
12 13 1.281899 GATGCCGCTGTCAGTAACTC 58.718 55.000 0.93 0.00 0.00 3.01
13 14 0.108138 GGATGCCGCTGTCAGTAACT 60.108 55.000 0.93 0.00 0.00 2.24
14 15 0.391130 TGGATGCCGCTGTCAGTAAC 60.391 55.000 0.93 0.00 0.00 2.50
15 16 0.391130 GTGGATGCCGCTGTCAGTAA 60.391 55.000 0.93 0.00 0.00 2.24
16 17 1.218047 GTGGATGCCGCTGTCAGTA 59.782 57.895 0.93 0.00 0.00 2.74
17 18 2.046892 GTGGATGCCGCTGTCAGT 60.047 61.111 0.93 0.00 0.00 3.41
18 19 2.267006 AGTGGATGCCGCTGTCAG 59.733 61.111 0.00 0.00 43.37 3.51
37 38 1.250840 AATTTTCTCCTGGCGGTGGC 61.251 55.000 0.00 0.00 38.90 5.01
38 39 0.527565 CAATTTTCTCCTGGCGGTGG 59.472 55.000 0.00 0.00 0.00 4.61
39 40 1.533625 TCAATTTTCTCCTGGCGGTG 58.466 50.000 0.00 0.00 0.00 4.94
40 41 2.286365 TTCAATTTTCTCCTGGCGGT 57.714 45.000 0.00 0.00 0.00 5.68
41 42 3.874392 ATTTCAATTTTCTCCTGGCGG 57.126 42.857 0.00 0.00 0.00 6.13
42 43 6.563422 TGAATATTTCAATTTTCTCCTGGCG 58.437 36.000 0.00 0.00 36.59 5.69
55 56 8.648319 GGCAAGCCAACCTTTTGAATATTTCAA 61.648 37.037 6.14 0.00 40.80 2.69
57 58 5.122239 GGCAAGCCAACCTTTTGAATATTTC 59.878 40.000 6.14 0.00 34.24 2.17
58 59 5.003160 GGCAAGCCAACCTTTTGAATATTT 58.997 37.500 6.14 0.00 34.24 1.40
60 61 3.368323 CGGCAAGCCAACCTTTTGAATAT 60.368 43.478 12.19 0.00 34.24 1.28
61 62 2.029470 CGGCAAGCCAACCTTTTGAATA 60.029 45.455 12.19 0.00 34.24 1.75
62 63 1.270252 CGGCAAGCCAACCTTTTGAAT 60.270 47.619 12.19 0.00 34.24 2.57
120 121 2.595386 GCCACCGTCAAATCAAATCAC 58.405 47.619 0.00 0.00 0.00 3.06
121 122 1.198867 CGCCACCGTCAAATCAAATCA 59.801 47.619 0.00 0.00 0.00 2.57
122 123 1.467374 CCGCCACCGTCAAATCAAATC 60.467 52.381 0.00 0.00 0.00 2.17
123 124 0.525761 CCGCCACCGTCAAATCAAAT 59.474 50.000 0.00 0.00 0.00 2.32
124 125 1.519751 CCCGCCACCGTCAAATCAAA 61.520 55.000 0.00 0.00 0.00 2.69
125 126 1.969064 CCCGCCACCGTCAAATCAA 60.969 57.895 0.00 0.00 0.00 2.57
206 207 2.099141 TCACTGTGCATAACCTCTGC 57.901 50.000 2.12 0.00 40.10 4.26
216 217 1.000843 ACTTACTGCGATCACTGTGCA 59.999 47.619 2.12 0.00 37.07 4.57
235 236 2.184579 GTAGGAGTGGCGCCAGAC 59.815 66.667 33.73 25.63 0.00 3.51
238 239 3.702048 GTGGTAGGAGTGGCGCCA 61.702 66.667 29.03 29.03 0.00 5.69
240 241 2.465055 AAAGGTGGTAGGAGTGGCGC 62.465 60.000 0.00 0.00 0.00 6.53
241 242 0.899720 TAAAGGTGGTAGGAGTGGCG 59.100 55.000 0.00 0.00 0.00 5.69
251 252 9.483916 GCAGTACAAATAAAATTTAAAGGTGGT 57.516 29.630 0.00 0.00 0.00 4.16
253 254 9.187455 ACGCAGTACAAATAAAATTTAAAGGTG 57.813 29.630 0.00 0.00 41.94 4.00
256 286 9.987901 CACACGCAGTACAAATAAAATTTAAAG 57.012 29.630 0.00 0.00 41.61 1.85
259 289 7.649973 ACCACACGCAGTACAAATAAAATTTA 58.350 30.769 0.00 0.00 41.61 1.40
261 291 6.079424 ACCACACGCAGTACAAATAAAATT 57.921 33.333 0.00 0.00 41.61 1.82
262 292 5.699097 ACCACACGCAGTACAAATAAAAT 57.301 34.783 0.00 0.00 41.61 1.82
265 295 4.885413 ACTACCACACGCAGTACAAATAA 58.115 39.130 0.00 0.00 41.61 1.40
267 297 3.396260 ACTACCACACGCAGTACAAAT 57.604 42.857 0.00 0.00 41.61 2.32
282 312 4.698575 AGCGTACTACCACTACTACTACC 58.301 47.826 0.00 0.00 0.00 3.18
295 325 5.300752 TGGAGTATAGTGGTAGCGTACTAC 58.699 45.833 0.00 4.34 46.85 2.73
296 326 5.545588 CTGGAGTATAGTGGTAGCGTACTA 58.454 45.833 0.00 0.00 34.23 1.82
297 327 4.387598 CTGGAGTATAGTGGTAGCGTACT 58.612 47.826 0.00 0.00 0.00 2.73
323 355 4.249020 CAACCACGCACGCAGCAA 62.249 61.111 0.00 0.00 46.13 3.91
347 379 0.528470 GTCTCCTCCCGACTTCACTG 59.472 60.000 0.00 0.00 0.00 3.66
349 381 0.528470 CTGTCTCCTCCCGACTTCAC 59.472 60.000 0.00 0.00 32.70 3.18
350 382 0.112606 ACTGTCTCCTCCCGACTTCA 59.887 55.000 0.00 0.00 32.70 3.02
356 388 0.811915 CACTACACTGTCTCCTCCCG 59.188 60.000 0.00 0.00 0.00 5.14
357 389 1.926108 ACACTACACTGTCTCCTCCC 58.074 55.000 0.00 0.00 0.00 4.30
358 390 3.018149 CCTACACTACACTGTCTCCTCC 58.982 54.545 0.00 0.00 0.00 4.30
359 391 3.688235 ACCTACACTACACTGTCTCCTC 58.312 50.000 0.00 0.00 0.00 3.71
360 392 3.810721 ACCTACACTACACTGTCTCCT 57.189 47.619 0.00 0.00 0.00 3.69
361 393 3.693578 GGTACCTACACTACACTGTCTCC 59.306 52.174 4.06 0.00 0.00 3.71
363 395 4.377762 TGGTACCTACACTACACTGTCT 57.622 45.455 14.36 0.00 0.00 3.41
365 397 4.217510 TGTTGGTACCTACACTACACTGT 58.782 43.478 23.00 0.00 0.00 3.55
366 398 4.521639 TCTGTTGGTACCTACACTACACTG 59.478 45.833 23.00 12.79 0.00 3.66
367 399 4.733165 TCTGTTGGTACCTACACTACACT 58.267 43.478 23.00 0.00 0.00 3.55
369 401 6.675413 AATTCTGTTGGTACCTACACTACA 57.325 37.500 23.00 11.31 0.00 2.74
371 403 9.715121 CTAAAAATTCTGTTGGTACCTACACTA 57.285 33.333 23.00 14.64 0.00 2.74
408 441 2.969238 CCGCCGCAGAAGCCTATG 60.969 66.667 0.00 0.00 37.52 2.23
409 442 4.918201 GCCGCCGCAGAAGCCTAT 62.918 66.667 0.00 0.00 37.52 2.57
413 446 3.953444 GAAAAGCCGCCGCAGAAGC 62.953 63.158 0.00 0.00 37.52 3.86
414 447 1.856265 AAGAAAAGCCGCCGCAGAAG 61.856 55.000 0.00 0.00 37.52 2.85
415 448 1.852067 GAAGAAAAGCCGCCGCAGAA 61.852 55.000 0.00 0.00 37.52 3.02
488 547 1.429148 GATCGATCAACGGTGGTGGC 61.429 60.000 20.52 0.00 42.82 5.01
509 568 2.126965 CGTCTGTGACCGACCGAC 60.127 66.667 1.53 0.00 35.90 4.79
551 613 1.339235 CCATGAAAACGCAAGCGCAG 61.339 55.000 15.09 2.01 44.19 5.18
577 639 1.228063 CACTCACTGTGCTTGGCCT 60.228 57.895 3.32 0.00 40.06 5.19
600 678 2.737180 CACCGCACCACTCTCACT 59.263 61.111 0.00 0.00 0.00 3.41
604 682 2.943978 GCTACCACCGCACCACTCT 61.944 63.158 0.00 0.00 0.00 3.24
633 719 0.900647 AGACAACTCGTCCCTCCCAG 60.901 60.000 0.00 0.00 46.69 4.45
635 721 0.246910 GAAGACAACTCGTCCCTCCC 59.753 60.000 0.00 0.00 46.69 4.30
636 722 0.246910 GGAAGACAACTCGTCCCTCC 59.753 60.000 0.00 0.00 46.69 4.30
637 723 0.966920 TGGAAGACAACTCGTCCCTC 59.033 55.000 0.95 0.00 46.69 4.30
638 724 1.550976 GATGGAAGACAACTCGTCCCT 59.449 52.381 0.95 0.00 46.69 4.20
639 725 1.405661 GGATGGAAGACAACTCGTCCC 60.406 57.143 0.95 0.00 46.69 4.46
643 729 1.630148 GACGGATGGAAGACAACTCG 58.370 55.000 0.00 0.00 0.00 4.18
666 752 3.576259 CGACCCCAACCCCAACCT 61.576 66.667 0.00 0.00 0.00 3.50
676 762 0.186386 ACAAATGAAACCCGACCCCA 59.814 50.000 0.00 0.00 0.00 4.96
732 835 2.041405 CCCTGTCTCCTCCCCCTC 60.041 72.222 0.00 0.00 0.00 4.30
733 836 4.423209 GCCCTGTCTCCTCCCCCT 62.423 72.222 0.00 0.00 0.00 4.79
767 875 2.363172 GGAGTGAGGGAGTGGGAGC 61.363 68.421 0.00 0.00 0.00 4.70
868 976 0.809241 GTGGAATGAGCAGAGCGAGG 60.809 60.000 0.00 0.00 0.00 4.63
908 1029 0.695347 GGAGATGGATGGGGATGGAC 59.305 60.000 0.00 0.00 0.00 4.02
942 1065 2.478894 CGACTGAAACGTAAATGCAGGT 59.521 45.455 0.00 0.00 0.00 4.00
1381 1529 1.517242 AGAAGAGCAGAAGCAAACGG 58.483 50.000 0.00 0.00 45.49 4.44
1422 1573 2.827003 GCCAAGAAAGGGGGAAGGAAAT 60.827 50.000 0.00 0.00 0.00 2.17
1423 1574 1.482365 GCCAAGAAAGGGGGAAGGAAA 60.482 52.381 0.00 0.00 0.00 3.13
1426 1584 0.613012 CAGCCAAGAAAGGGGGAAGG 60.613 60.000 0.00 0.00 0.00 3.46
1488 1649 6.650390 AGCAAGAAGAAGAAGAAGAAGCTAAG 59.350 38.462 0.00 0.00 0.00 2.18
1489 1650 6.426328 CAGCAAGAAGAAGAAGAAGAAGCTAA 59.574 38.462 0.00 0.00 0.00 3.09
1490 1651 5.931146 CAGCAAGAAGAAGAAGAAGAAGCTA 59.069 40.000 0.00 0.00 0.00 3.32
1491 1652 4.756135 CAGCAAGAAGAAGAAGAAGAAGCT 59.244 41.667 0.00 0.00 0.00 3.74
1551 1743 4.293662 TGTACTGTACATGCCCAAATCA 57.706 40.909 16.26 0.00 32.89 2.57
1560 1752 6.756185 GCTCATGGCTGATGTACTGTACATG 61.756 48.000 31.80 21.19 42.56 3.21
1609 1808 1.038130 ACGGGACTGCTAGCTAGGTG 61.038 60.000 22.10 4.20 0.00 4.00
1611 1810 0.752009 TGACGGGACTGCTAGCTAGG 60.752 60.000 22.10 9.03 0.00 3.02
1695 1915 4.466828 CTGCACAAATTTAAGTCTCCGTG 58.533 43.478 0.00 0.00 0.00 4.94
1698 1918 4.773323 AGCTGCACAAATTTAAGTCTCC 57.227 40.909 1.02 0.00 0.00 3.71
1734 1957 3.221964 GCTGGTGCTAGGACAAATTTG 57.778 47.619 16.81 16.67 36.03 2.32
1748 1973 3.916172 CGAAATCAAAACATCAGCTGGTG 59.084 43.478 25.51 25.51 0.00 4.17
1749 1974 3.820467 TCGAAATCAAAACATCAGCTGGT 59.180 39.130 15.13 2.68 0.00 4.00
1752 1977 4.756642 TCACTCGAAATCAAAACATCAGCT 59.243 37.500 0.00 0.00 0.00 4.24
1753 1978 5.034554 TCACTCGAAATCAAAACATCAGC 57.965 39.130 0.00 0.00 0.00 4.26
1757 1983 4.651778 TCCCTCACTCGAAATCAAAACAT 58.348 39.130 0.00 0.00 0.00 2.71
1760 1986 3.674997 CCTCCCTCACTCGAAATCAAAA 58.325 45.455 0.00 0.00 0.00 2.44
1769 1995 3.382832 AACGGCCTCCCTCACTCG 61.383 66.667 0.00 0.00 0.00 4.18
1777 2003 1.581447 CTTTGCTTCAACGGCCTCC 59.419 57.895 0.00 0.00 0.00 4.30
1782 2008 2.712057 ATCTTGCTTTGCTTCAACGG 57.288 45.000 0.00 0.00 0.00 4.44
1783 2009 3.631144 TCAATCTTGCTTTGCTTCAACG 58.369 40.909 0.00 0.00 0.00 4.10
1785 2011 4.281435 TGGATCAATCTTGCTTTGCTTCAA 59.719 37.500 0.00 0.00 0.00 2.69
1787 2013 4.445452 TGGATCAATCTTGCTTTGCTTC 57.555 40.909 0.00 0.00 0.00 3.86
1788 2014 4.222145 ACATGGATCAATCTTGCTTTGCTT 59.778 37.500 0.00 0.00 0.00 3.91
1789 2015 3.767673 ACATGGATCAATCTTGCTTTGCT 59.232 39.130 0.00 0.00 0.00 3.91
1790 2016 4.110482 GACATGGATCAATCTTGCTTTGC 58.890 43.478 0.00 0.00 0.00 3.68
1792 2018 4.012374 ACGACATGGATCAATCTTGCTTT 58.988 39.130 0.00 0.00 0.00 3.51
1794 2033 3.272574 ACGACATGGATCAATCTTGCT 57.727 42.857 0.00 0.00 0.00 3.91
1802 2041 3.912496 AGAATGGAACGACATGGATCA 57.088 42.857 0.00 0.00 0.00 2.92
1803 2042 4.635765 TGAAAGAATGGAACGACATGGATC 59.364 41.667 0.00 0.00 0.00 3.36
1816 2055 3.052036 CAACGCAAAGGTGAAAGAATGG 58.948 45.455 0.00 0.00 40.93 3.16
1817 2056 3.963665 TCAACGCAAAGGTGAAAGAATG 58.036 40.909 0.00 0.00 44.92 2.67
1827 2066 4.484236 TCAGCAATTAATCAACGCAAAGG 58.516 39.130 0.00 0.00 0.00 3.11
1832 2071 4.558538 AGGATCAGCAATTAATCAACGC 57.441 40.909 0.00 0.00 0.00 4.84
1849 2091 2.235402 CTGTTGGTACCGGTACAAGGAT 59.765 50.000 38.26 4.54 37.78 3.24
1870 2113 4.493382 GGATTTCAACCGCAAACAACAAAC 60.493 41.667 0.00 0.00 0.00 2.93
1943 2206 0.315706 GATTCAATCTCTGCGTGCGC 60.316 55.000 9.85 9.85 42.35 6.09
1997 2269 1.678101 GACTAGCACAATCATTGGCCC 59.322 52.381 0.00 0.00 34.12 5.80
2012 2284 3.304525 CCGGCGTCCACTAATAAGACTAG 60.305 52.174 6.01 0.00 0.00 2.57
2049 2323 0.846015 TCCCCATCATCATCACCACC 59.154 55.000 0.00 0.00 0.00 4.61
2050 2324 1.770658 TCTCCCCATCATCATCACCAC 59.229 52.381 0.00 0.00 0.00 4.16
2068 2350 3.502051 TCCCCCACCTAATTGTACTCT 57.498 47.619 0.00 0.00 0.00 3.24
2091 2373 2.244651 ACTCACTTGCGTTGCGTCC 61.245 57.895 0.00 0.00 0.00 4.79
2092 2374 1.083401 CACTCACTTGCGTTGCGTC 60.083 57.895 0.00 0.00 0.00 5.19
2094 2376 1.202568 CTCACTCACTTGCGTTGCG 59.797 57.895 0.00 0.00 0.00 4.85
2100 2383 2.035193 TCACTCACTCTCACTCACTTGC 59.965 50.000 0.00 0.00 0.00 4.01
2113 2600 1.265236 CAAGCTCCCTCTCACTCACT 58.735 55.000 0.00 0.00 0.00 3.41
2114 2601 0.972883 ACAAGCTCCCTCTCACTCAC 59.027 55.000 0.00 0.00 0.00 3.51
2115 2602 1.261480 GACAAGCTCCCTCTCACTCA 58.739 55.000 0.00 0.00 0.00 3.41
2116 2603 1.261480 TGACAAGCTCCCTCTCACTC 58.739 55.000 0.00 0.00 0.00 3.51
2117 2604 1.722034 TTGACAAGCTCCCTCTCACT 58.278 50.000 0.00 0.00 0.00 3.41
2118 2605 2.777832 ATTGACAAGCTCCCTCTCAC 57.222 50.000 0.00 0.00 0.00 3.51
2119 2606 3.181440 ACAAATTGACAAGCTCCCTCTCA 60.181 43.478 0.00 0.00 0.00 3.27
2120 2607 3.416156 ACAAATTGACAAGCTCCCTCTC 58.584 45.455 0.00 0.00 0.00 3.20
2121 2608 3.515602 ACAAATTGACAAGCTCCCTCT 57.484 42.857 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.