Multiple sequence alignment - TraesCS2B01G083400

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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 TraesCS2B01G083400 chr2B 100.000 2117 0 0 1 2117 46592107 46589991 0.000000e+00 3910.0
1 TraesCS2B01G083400 chr2B 100.000 275 0 0 2350 2624 46589758 46589484 2.330000e-140 508.0
2 TraesCS2B01G083400 chr6D 93.817 1116 60 6 10 1118 16187583 16186470 0.000000e+00 1670.0
3 TraesCS2B01G083400 chr6D 90.070 715 43 8 1130 1816 16185301 16184587 0.000000e+00 902.0
4 TraesCS2B01G083400 chr6D 90.625 64 3 1 1841 1901 16184585 16184522 6.020000e-12 82.4
5 TraesCS2B01G083400 chr6A 91.911 1125 83 5 1 1118 16453556 16452433 0.000000e+00 1567.0
6 TraesCS2B01G083400 chr6A 92.742 620 35 6 1128 1737 16449064 16448445 0.000000e+00 887.0
7 TraesCS2B01G083400 chr6A 89.855 276 20 5 1828 2095 16448119 16448394 5.380000e-92 348.0
8 TraesCS2B01G083400 chr6B 91.853 1031 67 9 91 1118 27938043 27937027 0.000000e+00 1423.0
9 TraesCS2B01G083400 chr6B 87.957 739 46 16 1128 1828 28016370 28017103 0.000000e+00 832.0
10 TraesCS2B01G083400 chr6B 87.736 742 49 16 1128 1828 27923095 27922355 0.000000e+00 828.0
11 TraesCS2B01G083400 chr6B 91.756 558 41 4 565 1118 28013496 28014052 0.000000e+00 771.0
12 TraesCS2B01G083400 chr6B 88.426 216 16 5 1 207 28013280 28013495 4.340000e-63 252.0
13 TraesCS2B01G083400 chr6B 85.366 164 12 4 1828 1989 28017138 28017291 2.700000e-35 159.0
14 TraesCS2B01G083400 chr7A 86.948 498 63 2 1128 1624 644735392 644735888 2.280000e-155 558.0
15 TraesCS2B01G083400 chr7A 82.867 607 94 7 1128 1729 644785475 644786076 1.070000e-148 536.0
16 TraesCS2B01G083400 chr7A 84.557 531 75 4 1128 1655 644722298 644722824 1.080000e-143 520.0


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 TraesCS2B01G083400 chr2B 46589484 46592107 2623 True 2209.0 3910 100.00000 1 2624 2 chr2B.!!$R1 2623
1 TraesCS2B01G083400 chr6D 16184522 16187583 3061 True 884.8 1670 91.50400 10 1901 3 chr6D.!!$R1 1891
2 TraesCS2B01G083400 chr6A 16448445 16453556 5111 True 1227.0 1567 92.32650 1 1737 2 chr6A.!!$R1 1736
3 TraesCS2B01G083400 chr6B 27937027 27938043 1016 True 1423.0 1423 91.85300 91 1118 1 chr6B.!!$R2 1027
4 TraesCS2B01G083400 chr6B 27922355 27923095 740 True 828.0 828 87.73600 1128 1828 1 chr6B.!!$R1 700
5 TraesCS2B01G083400 chr6B 28013280 28017291 4011 False 503.5 832 88.37625 1 1989 4 chr6B.!!$F1 1988
6 TraesCS2B01G083400 chr7A 644785475 644786076 601 False 536.0 536 82.86700 1128 1729 1 chr7A.!!$F3 601
7 TraesCS2B01G083400 chr7A 644722298 644722824 526 False 520.0 520 84.55700 1128 1655 1 chr7A.!!$F1 527

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
607 618 0.036875 GTAGAGGCTGTTGGTGGCTT 59.963 55.0 0.0 0.0 40.49 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 6441 0.108804 CACGGTAACATGACTCGGCT 60.109 55.0 0.0 0.0 0.0 5.52 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
32 36 1.154093 CGGCAGCTGTTCATGCTTG 60.154 57.895 16.64 0.00 42.19 4.01
35 39 1.961378 CAGCTGTTCATGCTTGCCA 59.039 52.632 5.25 0.00 38.92 4.92
38 42 1.246056 GCTGTTCATGCTTGCCAGGA 61.246 55.000 15.81 0.00 31.40 3.86
70 80 2.039480 AGAGAGCATGCAGAAGGTTTGA 59.961 45.455 21.98 0.00 0.00 2.69
137 147 1.028868 GTGGAGCTGGTGATCTTGGC 61.029 60.000 0.00 0.00 0.00 4.52
183 193 1.001641 GCAGCAGGGGATGTTCTGT 60.002 57.895 0.00 0.00 33.81 3.41
213 223 1.545651 GCCCAAGACTTTGCACCTACT 60.546 52.381 0.00 0.00 32.79 2.57
225 235 5.894298 TTGCACCTACTGATATGATCCTT 57.106 39.130 0.00 0.00 0.00 3.36
267 277 0.940126 AATTCCACGAGCGATGCATC 59.060 50.000 17.10 17.10 0.00 3.91
355 365 0.838122 CCCTGACCCTGACAAGACCT 60.838 60.000 0.00 0.00 0.00 3.85
396 406 1.537202 GTCAAGGCACAGACAATGGTC 59.463 52.381 0.00 0.00 44.66 4.02
572 583 0.820871 GGAGCTGGAGAGTCAACGAT 59.179 55.000 0.00 0.00 0.00 3.73
607 618 0.036875 GTAGAGGCTGTTGGTGGCTT 59.963 55.000 0.00 0.00 40.49 4.35
770 781 4.065088 GCAGTACTGATTTGTGTTCCAGA 58.935 43.478 27.08 0.00 0.00 3.86
864 875 6.325596 AGTTTGTTCTGAAAACTCTTTGCTC 58.674 36.000 2.43 0.00 42.75 4.26
869 882 3.117888 TCTGAAAACTCTTTGCTCCACCT 60.118 43.478 0.00 0.00 0.00 4.00
895 908 5.814705 CCAAATACTTGTTTTGAAACCTGCA 59.185 36.000 4.32 0.00 38.11 4.41
924 937 0.890683 CCCCTTGTGCCAATTCAGTC 59.109 55.000 0.00 0.00 0.00 3.51
1024 1039 1.331756 GGCTGAAATGCTGTCATACCG 59.668 52.381 0.00 0.00 31.46 4.02
1118 1136 8.631480 AAAATAGCATCATATCTCTGCATCAA 57.369 30.769 0.00 0.00 38.37 2.57
1119 1137 7.851387 AATAGCATCATATCTCTGCATCAAG 57.149 36.000 0.00 0.00 38.37 3.02
1120 1138 5.230323 AGCATCATATCTCTGCATCAAGT 57.770 39.130 0.00 0.00 38.37 3.16
1121 1139 5.622180 AGCATCATATCTCTGCATCAAGTT 58.378 37.500 0.00 0.00 38.37 2.66
1122 1140 5.701750 AGCATCATATCTCTGCATCAAGTTC 59.298 40.000 0.00 0.00 38.37 3.01
1125 1143 7.148606 GCATCATATCTCTGCATCAAGTTCTAC 60.149 40.741 0.00 0.00 35.96 2.59
1191 5554 4.204028 ACGGCCAACAAGCAGGGT 62.204 61.111 2.24 0.00 31.65 4.34
1217 5580 4.988486 GACCGCCGTCAACGTCGT 62.988 66.667 5.26 0.00 39.19 4.34
1305 5668 2.529136 CCTCCTCACACCCACCCA 60.529 66.667 0.00 0.00 0.00 4.51
1366 5729 3.744719 TCGGCTTCGTCACCTCGG 61.745 66.667 0.00 0.00 35.06 4.63
1378 5741 1.609794 ACCTCGGACCCTGAGAACC 60.610 63.158 4.47 0.00 35.43 3.62
1464 5827 9.130661 CATTACCAGTTCAATAATGGGAATACA 57.869 33.333 1.76 0.00 44.27 2.29
1524 5887 1.139058 GGAGTGATCACGGTAGCCAAT 59.861 52.381 19.85 0.00 36.20 3.16
1535 5898 0.596082 GTAGCCAATGCGGTGTTTGT 59.404 50.000 0.00 0.00 44.33 2.83
1536 5899 0.595588 TAGCCAATGCGGTGTTTGTG 59.404 50.000 0.00 0.00 44.33 3.33
1625 5988 4.072131 TGGATCCAAGCACAGTTCTAAAC 58.928 43.478 13.46 0.00 0.00 2.01
1656 6024 2.935042 TCCACGTGTGTTTGTTTGTTG 58.065 42.857 15.65 0.00 0.00 3.33
1659 6027 3.363426 CCACGTGTGTTTGTTTGTTGAAG 59.637 43.478 15.65 0.00 0.00 3.02
1665 6042 7.148373 ACGTGTGTTTGTTTGTTGAAGTAGTAT 60.148 33.333 0.00 0.00 0.00 2.12
1783 6189 6.013812 ACACACCCCTATTTGTTTATTGCAAT 60.014 34.615 17.56 17.56 0.00 3.56
1826 6268 8.620116 ATTTGTCATTATTTTCTTGGGTTTGG 57.380 30.769 0.00 0.00 0.00 3.28
1831 6273 9.016438 GTCATTATTTTCTTGGGTTTGGTAGTA 57.984 33.333 0.00 0.00 0.00 1.82
1852 6294 6.525629 AGTAAATATCTACTGCCGCTGATTT 58.474 36.000 4.02 2.41 30.76 2.17
1857 6299 1.394917 CTACTGCCGCTGATTTGTGTC 59.605 52.381 4.02 0.00 0.00 3.67
1903 6348 2.955660 TGGGACACAAATCCAAGTGAAC 59.044 45.455 0.00 0.00 40.96 3.18
1904 6349 2.296190 GGGACACAAATCCAAGTGAACC 59.704 50.000 0.00 0.00 40.96 3.62
1905 6350 2.955660 GGACACAAATCCAAGTGAACCA 59.044 45.455 0.00 0.00 38.77 3.67
1906 6351 3.573967 GGACACAAATCCAAGTGAACCAT 59.426 43.478 0.00 0.00 38.77 3.55
1907 6352 4.549458 GACACAAATCCAAGTGAACCATG 58.451 43.478 0.00 0.00 39.03 3.66
1908 6353 3.243839 ACACAAATCCAAGTGAACCATGC 60.244 43.478 0.00 0.00 39.03 4.06
1909 6354 2.030007 ACAAATCCAAGTGAACCATGCG 60.030 45.455 0.00 0.00 0.00 4.73
1910 6355 1.176527 AATCCAAGTGAACCATGCGG 58.823 50.000 0.00 0.00 38.77 5.69
1930 6375 2.289694 GGTGGAGCTTCTTGTTAGAGCA 60.290 50.000 0.00 0.00 31.22 4.26
1989 6436 1.340889 TGCTTTGAGTTTGGGTCATGC 59.659 47.619 0.00 0.00 0.00 4.06
1990 6437 1.340889 GCTTTGAGTTTGGGTCATGCA 59.659 47.619 0.00 0.00 0.00 3.96
1991 6438 2.028748 GCTTTGAGTTTGGGTCATGCAT 60.029 45.455 0.00 0.00 0.00 3.96
1992 6439 3.193267 GCTTTGAGTTTGGGTCATGCATA 59.807 43.478 0.00 0.00 0.00 3.14
1993 6440 4.142093 GCTTTGAGTTTGGGTCATGCATAT 60.142 41.667 0.00 0.00 0.00 1.78
1994 6441 5.067674 GCTTTGAGTTTGGGTCATGCATATA 59.932 40.000 0.00 0.00 0.00 0.86
1995 6442 6.698008 TTTGAGTTTGGGTCATGCATATAG 57.302 37.500 0.00 0.00 0.00 1.31
1996 6443 4.136796 TGAGTTTGGGTCATGCATATAGC 58.863 43.478 0.00 0.00 45.96 2.97
1997 6444 3.490348 AGTTTGGGTCATGCATATAGCC 58.510 45.455 18.16 18.16 44.83 3.93
1998 6445 2.183478 TTGGGTCATGCATATAGCCG 57.817 50.000 19.15 0.00 44.83 5.52
1999 6446 1.347062 TGGGTCATGCATATAGCCGA 58.653 50.000 19.15 9.72 44.83 5.54
2000 6447 1.276138 TGGGTCATGCATATAGCCGAG 59.724 52.381 19.15 0.00 44.83 4.63
2001 6448 1.276421 GGGTCATGCATATAGCCGAGT 59.724 52.381 12.24 0.00 44.83 4.18
2002 6449 2.611518 GGTCATGCATATAGCCGAGTC 58.388 52.381 0.00 0.00 44.83 3.36
2003 6450 2.029020 GGTCATGCATATAGCCGAGTCA 60.029 50.000 0.00 0.00 44.83 3.41
2004 6451 3.368843 GGTCATGCATATAGCCGAGTCAT 60.369 47.826 0.00 0.00 44.83 3.06
2005 6452 3.615937 GTCATGCATATAGCCGAGTCATG 59.384 47.826 0.00 0.00 44.83 3.07
2006 6453 3.259123 TCATGCATATAGCCGAGTCATGT 59.741 43.478 0.00 0.00 44.83 3.21
2007 6454 3.751479 TGCATATAGCCGAGTCATGTT 57.249 42.857 0.00 0.00 44.83 2.71
2008 6455 4.864704 TGCATATAGCCGAGTCATGTTA 57.135 40.909 0.00 0.00 44.83 2.41
2009 6456 4.556233 TGCATATAGCCGAGTCATGTTAC 58.444 43.478 0.00 0.00 44.83 2.50
2010 6457 3.927142 GCATATAGCCGAGTCATGTTACC 59.073 47.826 0.00 0.00 37.23 2.85
2011 6458 2.795175 ATAGCCGAGTCATGTTACCG 57.205 50.000 0.00 0.00 0.00 4.02
2012 6459 1.466856 TAGCCGAGTCATGTTACCGT 58.533 50.000 0.00 0.00 0.00 4.83
2013 6460 0.108804 AGCCGAGTCATGTTACCGTG 60.109 55.000 0.00 0.00 0.00 4.94
2014 6461 0.389426 GCCGAGTCATGTTACCGTGT 60.389 55.000 0.00 0.00 0.00 4.49
2015 6462 1.346365 CCGAGTCATGTTACCGTGTG 58.654 55.000 0.00 0.00 0.00 3.82
2016 6463 0.713883 CGAGTCATGTTACCGTGTGC 59.286 55.000 0.00 0.00 0.00 4.57
2017 6464 1.790755 GAGTCATGTTACCGTGTGCA 58.209 50.000 0.00 0.00 0.00 4.57
2018 6465 1.459592 GAGTCATGTTACCGTGTGCAC 59.540 52.381 10.75 10.75 0.00 4.57
2031 6478 3.933155 GTGTGCACGGATAGAGAATTG 57.067 47.619 13.13 0.00 0.00 2.32
2032 6479 3.521560 GTGTGCACGGATAGAGAATTGA 58.478 45.455 13.13 0.00 0.00 2.57
2033 6480 3.307242 GTGTGCACGGATAGAGAATTGAC 59.693 47.826 13.13 0.00 0.00 3.18
2034 6481 2.866762 GTGCACGGATAGAGAATTGACC 59.133 50.000 0.00 0.00 0.00 4.02
2035 6482 2.499693 TGCACGGATAGAGAATTGACCA 59.500 45.455 0.00 0.00 0.00 4.02
2036 6483 3.134623 TGCACGGATAGAGAATTGACCAT 59.865 43.478 0.00 0.00 0.00 3.55
2037 6484 3.496130 GCACGGATAGAGAATTGACCATG 59.504 47.826 0.00 0.00 0.00 3.66
2038 6485 4.697514 CACGGATAGAGAATTGACCATGT 58.302 43.478 0.00 0.00 0.00 3.21
2039 6486 4.509230 CACGGATAGAGAATTGACCATGTG 59.491 45.833 0.00 0.00 0.00 3.21
2040 6487 4.162320 ACGGATAGAGAATTGACCATGTGT 59.838 41.667 0.00 0.00 0.00 3.72
2041 6488 4.509230 CGGATAGAGAATTGACCATGTGTG 59.491 45.833 0.00 0.00 0.00 3.82
2042 6489 5.431765 GGATAGAGAATTGACCATGTGTGT 58.568 41.667 0.00 0.00 0.00 3.72
2043 6490 6.582636 GGATAGAGAATTGACCATGTGTGTA 58.417 40.000 0.00 0.00 0.00 2.90
2044 6491 6.480320 GGATAGAGAATTGACCATGTGTGTAC 59.520 42.308 0.00 0.00 0.00 2.90
2045 6492 5.227569 AGAGAATTGACCATGTGTGTACA 57.772 39.130 0.00 0.00 41.89 2.90
2055 6502 2.252976 TGTGTGTACATGCAAGCTGA 57.747 45.000 0.00 0.00 0.00 4.26
2056 6503 2.570135 TGTGTGTACATGCAAGCTGAA 58.430 42.857 0.00 0.00 0.00 3.02
2057 6504 2.948315 TGTGTGTACATGCAAGCTGAAA 59.052 40.909 0.00 0.00 0.00 2.69
2058 6505 3.003585 TGTGTGTACATGCAAGCTGAAAG 59.996 43.478 0.00 0.00 0.00 2.62
2059 6506 3.003689 GTGTGTACATGCAAGCTGAAAGT 59.996 43.478 0.00 0.00 35.30 2.66
2060 6507 3.003585 TGTGTACATGCAAGCTGAAAGTG 59.996 43.478 0.00 0.00 35.30 3.16
2061 6508 3.250762 GTGTACATGCAAGCTGAAAGTGA 59.749 43.478 0.00 0.00 35.30 3.41
2062 6509 3.499537 TGTACATGCAAGCTGAAAGTGAG 59.500 43.478 0.00 0.00 35.30 3.51
2063 6510 2.579873 ACATGCAAGCTGAAAGTGAGT 58.420 42.857 0.00 0.00 35.30 3.41
2064 6511 2.551459 ACATGCAAGCTGAAAGTGAGTC 59.449 45.455 0.00 0.00 35.30 3.36
2065 6512 2.627515 TGCAAGCTGAAAGTGAGTCT 57.372 45.000 0.00 0.00 35.30 3.24
2066 6513 2.487934 TGCAAGCTGAAAGTGAGTCTC 58.512 47.619 0.00 0.00 35.30 3.36
2067 6514 2.158914 TGCAAGCTGAAAGTGAGTCTCA 60.159 45.455 0.00 0.00 35.30 3.27
2068 6515 3.072944 GCAAGCTGAAAGTGAGTCTCAT 58.927 45.455 5.68 0.00 35.30 2.90
2069 6516 3.501445 GCAAGCTGAAAGTGAGTCTCATT 59.499 43.478 5.68 0.00 35.30 2.57
2070 6517 4.692625 GCAAGCTGAAAGTGAGTCTCATTA 59.307 41.667 5.68 0.00 35.30 1.90
2071 6518 5.163874 GCAAGCTGAAAGTGAGTCTCATTAG 60.164 44.000 5.68 0.00 35.30 1.73
2072 6519 4.502962 AGCTGAAAGTGAGTCTCATTAGC 58.497 43.478 5.68 8.07 35.30 3.09
2073 6520 4.020751 AGCTGAAAGTGAGTCTCATTAGCA 60.021 41.667 16.62 9.44 35.30 3.49
2074 6521 4.692625 GCTGAAAGTGAGTCTCATTAGCAA 59.307 41.667 5.68 0.00 35.30 3.91
2075 6522 5.353678 GCTGAAAGTGAGTCTCATTAGCAAT 59.646 40.000 5.68 0.00 35.30 3.56
2076 6523 6.536582 GCTGAAAGTGAGTCTCATTAGCAATA 59.463 38.462 5.68 0.00 35.30 1.90
2077 6524 7.065085 GCTGAAAGTGAGTCTCATTAGCAATAA 59.935 37.037 5.68 0.00 35.30 1.40
2078 6525 8.484641 TGAAAGTGAGTCTCATTAGCAATAAG 57.515 34.615 5.68 0.00 0.00 1.73
2079 6526 8.097038 TGAAAGTGAGTCTCATTAGCAATAAGT 58.903 33.333 5.68 0.00 0.00 2.24
2080 6527 7.840342 AAGTGAGTCTCATTAGCAATAAGTG 57.160 36.000 5.68 0.00 0.00 3.16
2081 6528 6.940739 AGTGAGTCTCATTAGCAATAAGTGT 58.059 36.000 5.68 0.00 0.00 3.55
2082 6529 6.815641 AGTGAGTCTCATTAGCAATAAGTGTG 59.184 38.462 5.68 0.00 0.00 3.82
2083 6530 6.591834 GTGAGTCTCATTAGCAATAAGTGTGT 59.408 38.462 5.68 0.00 0.00 3.72
2084 6531 6.591448 TGAGTCTCATTAGCAATAAGTGTGTG 59.409 38.462 0.00 0.00 0.00 3.82
2085 6532 5.352569 AGTCTCATTAGCAATAAGTGTGTGC 59.647 40.000 0.00 0.00 38.59 4.57
2086 6533 5.122239 GTCTCATTAGCAATAAGTGTGTGCA 59.878 40.000 0.00 0.00 40.83 4.57
2087 6534 5.352293 TCTCATTAGCAATAAGTGTGTGCAG 59.648 40.000 0.00 0.00 40.83 4.41
2088 6535 5.244755 TCATTAGCAATAAGTGTGTGCAGA 58.755 37.500 0.00 0.00 40.83 4.26
2089 6536 5.882000 TCATTAGCAATAAGTGTGTGCAGAT 59.118 36.000 0.00 0.00 40.83 2.90
2090 6537 6.375174 TCATTAGCAATAAGTGTGTGCAGATT 59.625 34.615 0.00 0.00 40.83 2.40
2091 6538 7.552330 TCATTAGCAATAAGTGTGTGCAGATTA 59.448 33.333 0.00 0.00 40.83 1.75
2092 6539 5.808042 AGCAATAAGTGTGTGCAGATTAG 57.192 39.130 0.00 0.00 40.83 1.73
2093 6540 4.637534 AGCAATAAGTGTGTGCAGATTAGG 59.362 41.667 0.00 0.00 40.83 2.69
2094 6541 4.201950 GCAATAAGTGTGTGCAGATTAGGG 60.202 45.833 0.00 0.00 38.19 3.53
2095 6542 5.185454 CAATAAGTGTGTGCAGATTAGGGA 58.815 41.667 0.00 0.00 0.00 4.20
2096 6543 3.788227 AAGTGTGTGCAGATTAGGGAA 57.212 42.857 0.00 0.00 0.00 3.97
2097 6544 3.340814 AGTGTGTGCAGATTAGGGAAG 57.659 47.619 0.00 0.00 0.00 3.46
2098 6545 1.740025 GTGTGTGCAGATTAGGGAAGC 59.260 52.381 0.00 0.00 0.00 3.86
2099 6546 1.630369 TGTGTGCAGATTAGGGAAGCT 59.370 47.619 0.00 0.00 0.00 3.74
2106 6553 3.942829 CAGATTAGGGAAGCTGTGAACA 58.057 45.455 0.00 0.00 42.87 3.18
2107 6554 4.521146 CAGATTAGGGAAGCTGTGAACAT 58.479 43.478 0.00 0.00 42.87 2.71
2108 6555 4.334759 CAGATTAGGGAAGCTGTGAACATG 59.665 45.833 0.00 0.00 42.87 3.21
2109 6556 2.787473 TAGGGAAGCTGTGAACATGG 57.213 50.000 0.00 0.00 0.00 3.66
2110 6557 0.610232 AGGGAAGCTGTGAACATGGC 60.610 55.000 0.00 0.00 0.00 4.40
2111 6558 0.895100 GGGAAGCTGTGAACATGGCA 60.895 55.000 0.00 0.00 0.00 4.92
2112 6559 0.961019 GGAAGCTGTGAACATGGCAA 59.039 50.000 0.00 0.00 0.00 4.52
2113 6560 1.068055 GGAAGCTGTGAACATGGCAAG 60.068 52.381 0.00 0.00 0.00 4.01
2114 6561 1.610522 GAAGCTGTGAACATGGCAAGT 59.389 47.619 0.00 0.00 0.00 3.16
2115 6562 1.696063 AGCTGTGAACATGGCAAGTT 58.304 45.000 7.97 7.97 0.00 2.66
2116 6563 2.034124 AGCTGTGAACATGGCAAGTTT 58.966 42.857 9.70 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 39 2.091389 TGCTCTCTAGATGAAGCCTCCT 60.091 50.000 15.43 0.00 0.00 3.69
38 42 2.037511 GCATGCTCTCTAGATGAAGCCT 59.962 50.000 11.37 6.65 0.00 4.58
45 55 3.307506 ACCTTCTGCATGCTCTCTAGAT 58.692 45.455 20.33 0.00 0.00 1.98
52 62 2.490903 ACATCAAACCTTCTGCATGCTC 59.509 45.455 20.33 0.00 0.00 4.26
70 80 2.009681 GGGACCTTCAACCCAAACAT 57.990 50.000 0.00 0.00 44.96 2.71
106 116 0.707616 AGCTCCACCTCTGGTAGAGT 59.292 55.000 12.32 0.00 42.08 3.24
183 193 2.033911 TCTTGGGCGCAGATGCAA 59.966 55.556 10.83 0.00 42.21 4.08
213 223 2.038952 CGGAAGGGCAAGGATCATATCA 59.961 50.000 0.00 0.00 0.00 2.15
267 277 1.174712 GGCCACGAATCCATGGGATG 61.175 60.000 13.02 2.19 42.27 3.51
355 365 2.224314 CGTCATAGCGATCTGAGCTGTA 59.776 50.000 0.00 0.00 45.60 2.74
402 412 2.764128 TCCACTCCAGGCGGATCC 60.764 66.667 0.00 0.00 41.79 3.36
404 414 2.765807 CCTCCACTCCAGGCGGAT 60.766 66.667 0.00 0.00 41.79 4.18
416 426 3.324930 CAGCCTCTGCCACCTCCA 61.325 66.667 0.00 0.00 38.69 3.86
572 583 3.082548 CTCTACGTCCTCCTTGTCAGAA 58.917 50.000 0.00 0.00 0.00 3.02
607 618 3.825160 GAGTGCAGCCACCCACGAA 62.825 63.158 0.00 0.00 43.09 3.85
770 781 1.617536 TGCCTCAGGATCCCAGCTT 60.618 57.895 8.55 0.00 0.00 3.74
864 875 6.642707 TCAAAACAAGTATTTGGTAGGTGG 57.357 37.500 2.81 0.00 38.66 4.61
869 882 6.981559 GCAGGTTTCAAAACAAGTATTTGGTA 59.018 34.615 7.82 0.00 40.63 3.25
941 954 7.106439 TGAGAAGAGACCAGATATCAAACTC 57.894 40.000 5.32 8.03 0.00 3.01
1111 1129 3.179048 CGACGATGTAGAACTTGATGCA 58.821 45.455 0.00 0.00 0.00 3.96
1217 5580 0.459585 GTTAAGACCGCCGATCTGCA 60.460 55.000 9.90 0.00 0.00 4.41
1305 5668 0.965866 TCAAGATCTCGGTGGAGCGT 60.966 55.000 0.00 0.00 40.26 5.07
1366 5729 0.680061 AAGTGTCGGTTCTCAGGGTC 59.320 55.000 0.00 0.00 0.00 4.46
1378 5741 2.135933 GAGAACCTTGGTGAAGTGTCG 58.864 52.381 0.00 0.00 0.00 4.35
1524 5887 1.885388 CTCCGACACAAACACCGCA 60.885 57.895 0.00 0.00 0.00 5.69
1535 5898 2.685017 AGATGGCAGGCTCCGACA 60.685 61.111 0.00 0.00 0.00 4.35
1536 5899 2.107953 GAGATGGCAGGCTCCGAC 59.892 66.667 8.51 0.00 0.00 4.79
1817 6223 7.771826 GCAGTAGATATTTACTACCAAACCCAA 59.228 37.037 5.66 0.00 40.45 4.12
1819 6225 6.709397 GGCAGTAGATATTTACTACCAAACCC 59.291 42.308 14.96 2.27 40.45 4.11
1820 6226 6.423001 CGGCAGTAGATATTTACTACCAAACC 59.577 42.308 18.32 8.24 37.05 3.27
1826 6268 6.010294 TCAGCGGCAGTAGATATTTACTAC 57.990 41.667 5.66 0.84 40.04 2.73
1831 6273 5.008019 CACAAATCAGCGGCAGTAGATATTT 59.992 40.000 1.45 0.00 0.00 1.40
1836 6278 1.001974 ACACAAATCAGCGGCAGTAGA 59.998 47.619 1.45 0.00 0.00 2.59
1857 6299 1.909700 ACATGTGGGCAGTGTAAAGG 58.090 50.000 0.00 0.00 0.00 3.11
1904 6349 0.957395 ACAAGAAGCTCCACCGCATG 60.957 55.000 0.00 0.00 0.00 4.06
1905 6350 0.250901 AACAAGAAGCTCCACCGCAT 60.251 50.000 0.00 0.00 0.00 4.73
1906 6351 0.394938 TAACAAGAAGCTCCACCGCA 59.605 50.000 0.00 0.00 0.00 5.69
1907 6352 1.079503 CTAACAAGAAGCTCCACCGC 58.920 55.000 0.00 0.00 0.00 5.68
1908 6353 2.611518 CTCTAACAAGAAGCTCCACCG 58.388 52.381 0.00 0.00 0.00 4.94
1909 6354 2.289694 TGCTCTAACAAGAAGCTCCACC 60.290 50.000 0.00 0.00 0.00 4.61
1910 6355 3.045601 TGCTCTAACAAGAAGCTCCAC 57.954 47.619 0.00 0.00 0.00 4.02
1911 6356 3.769739 TTGCTCTAACAAGAAGCTCCA 57.230 42.857 0.00 0.00 0.00 3.86
1912 6357 3.189495 GGTTTGCTCTAACAAGAAGCTCC 59.811 47.826 0.00 0.00 0.00 4.70
1930 6375 5.711506 TGATGAACATCATACAGCAAGGTTT 59.288 36.000 12.61 0.00 42.42 3.27
1945 6390 6.923199 AGGAAAACCAAAGATGATGAACAT 57.077 33.333 0.00 0.00 42.47 2.71
1989 6436 4.166523 CGGTAACATGACTCGGCTATATG 58.833 47.826 0.00 0.00 0.00 1.78
1990 6437 3.825014 ACGGTAACATGACTCGGCTATAT 59.175 43.478 0.00 0.00 0.00 0.86
1991 6438 3.004002 CACGGTAACATGACTCGGCTATA 59.996 47.826 0.00 0.00 0.00 1.31
1992 6439 2.029623 ACGGTAACATGACTCGGCTAT 58.970 47.619 0.00 0.00 0.00 2.97
1993 6440 1.133598 CACGGTAACATGACTCGGCTA 59.866 52.381 0.00 0.00 0.00 3.93
1994 6441 0.108804 CACGGTAACATGACTCGGCT 60.109 55.000 0.00 0.00 0.00 5.52
1995 6442 0.389426 ACACGGTAACATGACTCGGC 60.389 55.000 0.00 0.00 0.00 5.54
1996 6443 1.346365 CACACGGTAACATGACTCGG 58.654 55.000 0.00 0.00 0.00 4.63
1997 6444 0.713883 GCACACGGTAACATGACTCG 59.286 55.000 0.00 0.18 0.00 4.18
1998 6445 1.459592 GTGCACACGGTAACATGACTC 59.540 52.381 13.17 0.00 0.00 3.36
1999 6446 1.508632 GTGCACACGGTAACATGACT 58.491 50.000 13.17 0.00 0.00 3.41
2011 6458 3.307242 GTCAATTCTCTATCCGTGCACAC 59.693 47.826 18.64 0.00 0.00 3.82
2012 6459 3.521560 GTCAATTCTCTATCCGTGCACA 58.478 45.455 18.64 0.00 0.00 4.57
2013 6460 2.866762 GGTCAATTCTCTATCCGTGCAC 59.133 50.000 6.82 6.82 0.00 4.57
2014 6461 2.499693 TGGTCAATTCTCTATCCGTGCA 59.500 45.455 0.00 0.00 0.00 4.57
2015 6462 3.179443 TGGTCAATTCTCTATCCGTGC 57.821 47.619 0.00 0.00 0.00 5.34
2016 6463 4.509230 CACATGGTCAATTCTCTATCCGTG 59.491 45.833 0.00 0.00 37.79 4.94
2017 6464 4.162320 ACACATGGTCAATTCTCTATCCGT 59.838 41.667 0.00 0.00 0.00 4.69
2018 6465 4.509230 CACACATGGTCAATTCTCTATCCG 59.491 45.833 0.00 0.00 0.00 4.18
2019 6466 5.431765 ACACACATGGTCAATTCTCTATCC 58.568 41.667 0.00 0.00 0.00 2.59
2020 6467 7.041721 TGTACACACATGGTCAATTCTCTATC 58.958 38.462 0.00 0.00 0.00 2.08
2021 6468 6.946340 TGTACACACATGGTCAATTCTCTAT 58.054 36.000 0.00 0.00 0.00 1.98
2022 6469 6.353404 TGTACACACATGGTCAATTCTCTA 57.647 37.500 0.00 0.00 0.00 2.43
2023 6470 5.227569 TGTACACACATGGTCAATTCTCT 57.772 39.130 0.00 0.00 0.00 3.10
2035 6482 2.781923 TCAGCTTGCATGTACACACAT 58.218 42.857 0.00 0.00 46.58 3.21
2036 6483 2.252976 TCAGCTTGCATGTACACACA 57.747 45.000 0.00 0.00 39.52 3.72
2037 6484 3.003689 ACTTTCAGCTTGCATGTACACAC 59.996 43.478 0.00 0.00 0.00 3.82
2038 6485 3.003585 CACTTTCAGCTTGCATGTACACA 59.996 43.478 0.00 0.00 0.00 3.72
2039 6486 3.250762 TCACTTTCAGCTTGCATGTACAC 59.749 43.478 0.00 0.00 0.00 2.90
2040 6487 3.475575 TCACTTTCAGCTTGCATGTACA 58.524 40.909 0.00 0.00 0.00 2.90
2041 6488 3.499918 ACTCACTTTCAGCTTGCATGTAC 59.500 43.478 1.14 0.00 0.00 2.90
2042 6489 3.743521 ACTCACTTTCAGCTTGCATGTA 58.256 40.909 1.14 0.00 0.00 2.29
2043 6490 2.551459 GACTCACTTTCAGCTTGCATGT 59.449 45.455 1.14 0.00 0.00 3.21
2044 6491 2.812591 AGACTCACTTTCAGCTTGCATG 59.187 45.455 0.00 0.00 0.00 4.06
2045 6492 3.072944 GAGACTCACTTTCAGCTTGCAT 58.927 45.455 0.00 0.00 0.00 3.96
2046 6493 2.158914 TGAGACTCACTTTCAGCTTGCA 60.159 45.455 0.00 0.00 0.00 4.08
2047 6494 2.487934 TGAGACTCACTTTCAGCTTGC 58.512 47.619 0.00 0.00 0.00 4.01
2048 6495 5.163874 GCTAATGAGACTCACTTTCAGCTTG 60.164 44.000 7.47 0.00 0.00 4.01
2049 6496 4.934602 GCTAATGAGACTCACTTTCAGCTT 59.065 41.667 7.47 0.00 0.00 3.74
2050 6497 4.020751 TGCTAATGAGACTCACTTTCAGCT 60.021 41.667 7.47 0.00 0.00 4.24
2051 6498 4.248859 TGCTAATGAGACTCACTTTCAGC 58.751 43.478 7.47 11.91 0.00 4.26
2052 6499 6.981762 ATTGCTAATGAGACTCACTTTCAG 57.018 37.500 7.47 2.19 0.00 3.02
2053 6500 8.097038 ACTTATTGCTAATGAGACTCACTTTCA 58.903 33.333 7.47 1.45 0.00 2.69
2054 6501 8.386606 CACTTATTGCTAATGAGACTCACTTTC 58.613 37.037 7.47 0.00 0.00 2.62
2055 6502 7.880195 ACACTTATTGCTAATGAGACTCACTTT 59.120 33.333 7.47 1.74 0.00 2.66
2056 6503 7.332926 CACACTTATTGCTAATGAGACTCACTT 59.667 37.037 7.47 6.37 0.00 3.16
2057 6504 6.815641 CACACTTATTGCTAATGAGACTCACT 59.184 38.462 7.47 0.00 0.00 3.41
2058 6505 6.591834 ACACACTTATTGCTAATGAGACTCAC 59.408 38.462 7.47 0.00 0.00 3.51
2059 6506 6.591448 CACACACTTATTGCTAATGAGACTCA 59.409 38.462 7.80 7.80 0.00 3.41
2060 6507 6.456181 GCACACACTTATTGCTAATGAGACTC 60.456 42.308 0.00 0.00 33.26 3.36
2061 6508 5.352569 GCACACACTTATTGCTAATGAGACT 59.647 40.000 7.37 0.00 33.26 3.24
2062 6509 5.122239 TGCACACACTTATTGCTAATGAGAC 59.878 40.000 7.37 0.00 37.16 3.36
2063 6510 5.244755 TGCACACACTTATTGCTAATGAGA 58.755 37.500 7.37 0.00 37.16 3.27
2064 6511 5.352293 TCTGCACACACTTATTGCTAATGAG 59.648 40.000 0.00 0.00 37.16 2.90
2065 6512 5.244755 TCTGCACACACTTATTGCTAATGA 58.755 37.500 0.00 0.00 37.16 2.57
2066 6513 5.550232 TCTGCACACACTTATTGCTAATG 57.450 39.130 0.00 0.00 37.16 1.90
2067 6514 6.764308 AATCTGCACACACTTATTGCTAAT 57.236 33.333 0.00 0.00 37.16 1.73
2068 6515 6.316140 CCTAATCTGCACACACTTATTGCTAA 59.684 38.462 0.00 0.00 37.16 3.09
2069 6516 5.817296 CCTAATCTGCACACACTTATTGCTA 59.183 40.000 0.00 0.00 37.16 3.49
2070 6517 4.637534 CCTAATCTGCACACACTTATTGCT 59.362 41.667 0.00 0.00 37.16 3.91
2071 6518 4.201950 CCCTAATCTGCACACACTTATTGC 60.202 45.833 0.00 0.00 36.76 3.56
2072 6519 5.185454 TCCCTAATCTGCACACACTTATTG 58.815 41.667 0.00 0.00 0.00 1.90
2073 6520 5.435686 TCCCTAATCTGCACACACTTATT 57.564 39.130 0.00 0.00 0.00 1.40
2074 6521 5.431765 CTTCCCTAATCTGCACACACTTAT 58.568 41.667 0.00 0.00 0.00 1.73
2075 6522 4.832248 CTTCCCTAATCTGCACACACTTA 58.168 43.478 0.00 0.00 0.00 2.24
2076 6523 3.679389 CTTCCCTAATCTGCACACACTT 58.321 45.455 0.00 0.00 0.00 3.16
2077 6524 2.616510 GCTTCCCTAATCTGCACACACT 60.617 50.000 0.00 0.00 0.00 3.55
2078 6525 1.740025 GCTTCCCTAATCTGCACACAC 59.260 52.381 0.00 0.00 0.00 3.82
2079 6526 1.630369 AGCTTCCCTAATCTGCACACA 59.370 47.619 0.00 0.00 0.00 3.72
2080 6527 2.012673 CAGCTTCCCTAATCTGCACAC 58.987 52.381 0.00 0.00 0.00 3.82
2081 6528 1.630369 ACAGCTTCCCTAATCTGCACA 59.370 47.619 0.00 0.00 33.09 4.57
2082 6529 2.012673 CACAGCTTCCCTAATCTGCAC 58.987 52.381 0.00 0.00 33.09 4.57
2083 6530 1.908619 TCACAGCTTCCCTAATCTGCA 59.091 47.619 0.00 0.00 33.09 4.41
2084 6531 2.680339 GTTCACAGCTTCCCTAATCTGC 59.320 50.000 0.00 0.00 33.09 4.26
2085 6532 3.942829 TGTTCACAGCTTCCCTAATCTG 58.057 45.455 0.00 0.00 35.43 2.90
2086 6533 4.521146 CATGTTCACAGCTTCCCTAATCT 58.479 43.478 0.00 0.00 0.00 2.40
2087 6534 3.629398 CCATGTTCACAGCTTCCCTAATC 59.371 47.826 0.00 0.00 0.00 1.75
2088 6535 3.624777 CCATGTTCACAGCTTCCCTAAT 58.375 45.455 0.00 0.00 0.00 1.73
2089 6536 2.879756 GCCATGTTCACAGCTTCCCTAA 60.880 50.000 0.00 0.00 0.00 2.69
2090 6537 1.340017 GCCATGTTCACAGCTTCCCTA 60.340 52.381 0.00 0.00 0.00 3.53
2091 6538 0.610232 GCCATGTTCACAGCTTCCCT 60.610 55.000 0.00 0.00 0.00 4.20
2092 6539 0.895100 TGCCATGTTCACAGCTTCCC 60.895 55.000 0.00 0.00 0.00 3.97
2093 6540 0.961019 TTGCCATGTTCACAGCTTCC 59.039 50.000 0.00 0.00 0.00 3.46
2094 6541 1.610522 ACTTGCCATGTTCACAGCTTC 59.389 47.619 0.00 0.00 0.00 3.86
2095 6542 1.696063 ACTTGCCATGTTCACAGCTT 58.304 45.000 0.00 0.00 0.00 3.74
2096 6543 1.696063 AACTTGCCATGTTCACAGCT 58.304 45.000 0.00 0.00 0.00 4.24
2097 6544 2.514205 AAACTTGCCATGTTCACAGC 57.486 45.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.