Multiple sequence alignment - TraesCS3A01G517700

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 TraesCS3A01G517700 chr3A 100.000 9755 0 0 1 9755 734791898 734782144 0.000000e+00 18015.0
1 TraesCS3A01G517700 chr3A 93.677 1977 98 11 3566 5536 182639374 182637419 0.000000e+00 2933.0
2 TraesCS3A01G517700 chr3A 89.301 701 51 14 5803 6498 182637067 182636386 0.000000e+00 857.0
3 TraesCS3A01G517700 chr3A 96.899 129 4 0 3395 3523 182639503 182639375 5.930000e-52 217.0
4 TraesCS3A01G517700 chr3A 81.905 105 13 5 8958 9060 16680722 16680622 6.280000e-12 84.2
5 TraesCS3A01G517700 chr3A 100.000 43 0 0 6500 6542 182636356 182636314 8.120000e-11 80.5
6 TraesCS3A01G517700 chr3D 96.258 7403 195 27 4 7352 604675041 604667667 0.000000e+00 12061.0
7 TraesCS3A01G517700 chr3D 94.789 2418 69 19 7366 9755 604667591 604665203 0.000000e+00 3714.0
8 TraesCS3A01G517700 chr3D 80.180 111 16 5 8952 9060 10269530 10269636 2.920000e-10 78.7
9 TraesCS3A01G517700 chr3B 94.894 5719 206 35 208 5877 812345803 812340122 0.000000e+00 8865.0
10 TraesCS3A01G517700 chr3B 94.343 3270 95 36 5943 9181 812340121 812336911 0.000000e+00 4931.0
11 TraesCS3A01G517700 chr3B 87.845 181 19 3 2253 2433 610299841 610300018 9.930000e-50 209.0
12 TraesCS3A01G517700 chr3B 95.413 109 5 0 5534 5642 505264679 505264571 3.620000e-39 174.0
13 TraesCS3A01G517700 chr3B 95.370 108 5 0 5534 5641 41018580 41018473 1.300000e-38 172.0
14 TraesCS3A01G517700 chr3B 80.180 111 16 5 8952 9060 26682284 26682390 2.920000e-10 78.7
15 TraesCS3A01G517700 chr3B 80.000 105 15 5 8958 9060 15030697 15030597 1.360000e-08 73.1
16 TraesCS3A01G517700 chr6A 77.987 477 85 15 9112 9578 63207360 63207826 2.070000e-71 281.0
17 TraesCS3A01G517700 chr6A 96.330 109 4 0 5534 5642 502244335 502244227 7.780000e-41 180.0
18 TraesCS3A01G517700 chr6A 94.017 117 5 2 5528 5642 222554890 222555006 1.010000e-39 176.0
19 TraesCS3A01G517700 chr6A 91.379 116 10 0 5688 5803 536253932 536253817 1.010000e-34 159.0
20 TraesCS3A01G517700 chr6B 80.449 312 49 7 9112 9416 119242673 119242979 2.740000e-55 228.0
21 TraesCS3A01G517700 chr5B 95.327 107 5 0 5535 5641 364132666 364132772 4.680000e-38 171.0
22 TraesCS3A01G517700 chr5B 88.596 114 13 0 5690 5803 9504756 9504643 1.320000e-28 139.0
23 TraesCS3A01G517700 chr2D 95.327 107 5 0 5535 5641 625519656 625519550 4.680000e-38 171.0
24 TraesCS3A01G517700 chr6D 91.057 123 11 0 5681 5803 389973706 389973584 6.060000e-37 167.0
25 TraesCS3A01G517700 chr4A 91.304 115 10 0 5527 5641 374717053 374717167 3.650000e-34 158.0
26 TraesCS3A01G517700 chr4A 92.453 106 8 0 5688 5793 580297819 580297714 1.700000e-32 152.0
27 TraesCS3A01G517700 chr4B 90.678 118 9 2 5688 5803 33632018 33632135 1.310000e-33 156.0
28 TraesCS3A01G517700 chr1A 89.744 117 12 0 5687 5803 458567870 458567986 6.100000e-32 150.0
29 TraesCS3A01G517700 chr5D 88.596 114 11 2 5690 5803 9495434 9495323 4.750000e-28 137.0
30 TraesCS3A01G517700 chr7B 100.000 28 0 0 5659 5686 744034803 744034776 1.800000e-02 52.8


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 TraesCS3A01G517700 chr3A 734782144 734791898 9754 True 18015.000 18015 100.00000 1 9755 1 chr3A.!!$R2 9754
1 TraesCS3A01G517700 chr3A 182636314 182639503 3189 True 1021.875 2933 94.96925 3395 6542 4 chr3A.!!$R3 3147
2 TraesCS3A01G517700 chr3D 604665203 604675041 9838 True 7887.500 12061 95.52350 4 9755 2 chr3D.!!$R1 9751
3 TraesCS3A01G517700 chr3B 812336911 812345803 8892 True 6898.000 8865 94.61850 208 9181 2 chr3B.!!$R4 8973

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
130 131 0.042131 TCCATTGGTCCCCTCTACGT 59.958 55.000 1.86 0.00 0.00 3.57 F
1498 1522 1.039233 GTGGATAGGTCGTCGGGGAA 61.039 60.000 0.00 0.00 0.00 3.97 F
1928 1956 0.254747 TGCGCTTAGGCCCAACTATT 59.745 50.000 9.73 0.00 34.44 1.73 F
2023 2051 1.095130 TGGACCAGTTCCCCTAGGTA 58.905 55.000 8.29 0.00 45.17 3.08 F
2534 2565 1.311859 ACAGTGAAGTACGTGGACGA 58.688 50.000 6.12 0.00 43.02 4.20 F
3526 3581 1.530323 TTAGAAACGCCTGGCCTTTC 58.470 50.000 25.94 25.94 35.13 2.62 F
3699 3754 1.570501 AGGGGGCAAATTCAGCTCATA 59.429 47.619 5.24 0.00 32.95 2.15 F
3785 3840 3.346315 TGGTAGTATTCGTCGTCAAGGA 58.654 45.455 0.00 0.00 0.00 3.36 F
5797 5863 4.501071 CATGCTTGCTAAAGGAAATTGCT 58.499 39.130 0.00 0.00 37.29 3.91 F
6012 6270 3.238441 GTTGATCTGTCGTGAGAGTGTC 58.762 50.000 0.00 0.00 43.49 3.67 F
7313 7636 0.035152 TGAGGTGGGTGATGTGATGC 60.035 55.000 0.00 0.00 0.00 3.91 F
7374 7759 0.469705 AATGTTTGGCCTGGCACTCA 60.470 50.000 22.05 13.46 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1514 1538 1.144936 GTTCTGAGCCCCGATCCTG 59.855 63.158 0.00 0.00 0.00 3.86 R
3325 3380 1.411394 CTTGCGATTTGTGGTGCTTG 58.589 50.000 0.00 0.00 0.00 4.01 R
3526 3581 2.270986 GCTGCACCCCTTGGAAGTG 61.271 63.158 0.00 5.72 34.81 3.16 R
3785 3840 2.327325 TAGTGCCTCTTCCACTCCTT 57.673 50.000 0.00 0.00 42.22 3.36 R
4249 4309 6.147656 TGCATGGCAAATAGATAACTACGATG 59.852 38.462 0.00 0.00 34.76 3.84 R
4687 4750 3.628008 TCTTGCACGATAAGAGTAGGGA 58.372 45.455 0.00 0.00 31.04 4.20 R
5694 5759 1.593006 CCATCCTCGCGACAACATAAC 59.407 52.381 3.71 0.00 0.00 1.89 R
5835 6092 4.881850 TCTCTTGTCAGTTCCCAAGAAAAC 59.118 41.667 0.00 0.00 44.59 2.43 R
7313 7636 1.880819 GAAGGTGCCAGGCCAACATG 61.881 60.000 9.64 0.00 0.00 3.21 R
7599 7986 2.551912 CCGGGCAAGTGTTCGCTTT 61.552 57.895 0.00 0.00 0.00 3.51 R
8172 8560 0.394192 CTGTGACTCTGCCAAGGACA 59.606 55.000 0.00 0.00 0.00 4.02 R
9366 9779 1.055849 TGCTTTGGGAGTAGTCTGCA 58.944 50.000 0.00 0.00 33.59 4.41 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
86 87 0.785979 GACGTTTACCGATGCGTGTT 59.214 50.000 0.00 0.00 40.70 3.32
115 116 0.830648 TTTTCGATCCCGCTCTCCAT 59.169 50.000 0.00 0.00 35.37 3.41
130 131 0.042131 TCCATTGGTCCCCTCTACGT 59.958 55.000 1.86 0.00 0.00 3.57
176 177 3.185188 CGAAATGTGAGTGACCAGTTCTG 59.815 47.826 0.00 0.00 34.48 3.02
287 292 2.380084 TGTGTAGTGATTTCCCTCGC 57.620 50.000 0.00 0.00 0.00 5.03
309 314 3.349022 CCCCTTTGTGTTATTCGCCTTA 58.651 45.455 0.00 0.00 0.00 2.69
331 336 8.150945 CCTTAAATCCTCGATCCTCTTGAATAA 58.849 37.037 0.00 0.00 0.00 1.40
421 426 7.117236 CAGTAACTCCAACGAATTTAAGTAGCA 59.883 37.037 0.00 0.00 0.00 3.49
426 431 7.604927 ACTCCAACGAATTTAAGTAGCAACATA 59.395 33.333 0.00 0.00 0.00 2.29
493 500 5.517322 AGAGAGCGTGGTTATTAAGTAGG 57.483 43.478 0.00 0.00 0.00 3.18
889 913 2.445845 TCGATCCCCAATCCGGCT 60.446 61.111 0.00 0.00 0.00 5.52
994 1018 3.827898 GAGGGGGCTGACGACGAG 61.828 72.222 0.00 0.00 0.00 4.18
1001 1025 4.538283 CTGACGACGAGGCGCGAT 62.538 66.667 19.52 0.94 44.57 4.58
1002 1026 4.829518 TGACGACGAGGCGCGATG 62.830 66.667 19.52 11.37 44.57 3.84
1003 1027 4.831307 GACGACGAGGCGCGATGT 62.831 66.667 19.52 14.72 44.57 3.06
1004 1028 4.831307 ACGACGAGGCGCGATGTC 62.831 66.667 19.52 10.35 44.57 3.06
1322 1346 2.279136 CGTTGCTCCTCGTATCTTTTCG 59.721 50.000 0.00 0.00 0.00 3.46
1336 1360 2.098443 TCTTTTCGCCGTGCTTTTCTTT 59.902 40.909 0.00 0.00 0.00 2.52
1401 1425 1.152312 AGGGACAGGGTGAAGTCGT 60.152 57.895 0.00 0.00 35.63 4.34
1442 1466 2.221055 GCTGGACAAGTACAAGAACGTG 59.779 50.000 0.00 0.00 35.34 4.49
1498 1522 1.039233 GTGGATAGGTCGTCGGGGAA 61.039 60.000 0.00 0.00 0.00 3.97
1514 1538 1.515304 GAACGTCGGCAGCTCTCTC 60.515 63.158 0.00 0.00 0.00 3.20
1659 1683 2.349886 GCTACTTCACCGATGCTTTCAG 59.650 50.000 0.00 0.00 0.00 3.02
1671 1695 2.585330 TGCTTTCAGTCAGCAATTCCA 58.415 42.857 0.00 0.00 44.42 3.53
1698 1722 1.093972 TGTATGCCATTGCTTCCACG 58.906 50.000 0.00 0.00 38.71 4.94
1723 1751 6.988580 GGTTGTAGTTAGTTTGAGTTGGTACT 59.011 38.462 0.00 0.00 37.31 2.73
1734 1762 4.076394 TGAGTTGGTACTTTGGGTTATGC 58.924 43.478 0.00 0.00 33.84 3.14
1757 1785 5.345202 GCGTTATGACATATTAGAGGTTCCG 59.655 44.000 0.00 0.00 0.00 4.30
1766 1794 7.668492 ACATATTAGAGGTTCCGTTATTCCTC 58.332 38.462 0.00 0.00 44.61 3.71
1811 1839 2.233605 CTGGTGGTTGGCATGGCATG 62.234 60.000 23.96 22.99 0.00 4.06
1860 1888 4.074970 GACAACAGGTCATGGAAGTGATT 58.925 43.478 0.00 0.00 46.19 2.57
1927 1955 0.474184 ATGCGCTTAGGCCCAACTAT 59.526 50.000 9.73 0.00 34.44 2.12
1928 1956 0.254747 TGCGCTTAGGCCCAACTATT 59.745 50.000 9.73 0.00 34.44 1.73
1932 1960 2.421529 CGCTTAGGCCCAACTATTCCTT 60.422 50.000 0.00 0.00 34.44 3.36
1934 1962 3.371595 GCTTAGGCCCAACTATTCCTTCA 60.372 47.826 0.00 0.00 0.00 3.02
1940 1968 4.385310 GGCCCAACTATTCCTTCAGTGTAT 60.385 45.833 0.00 0.00 0.00 2.29
1947 1975 8.883731 CAACTATTCCTTCAGTGTATCGAATTT 58.116 33.333 0.00 0.00 0.00 1.82
2003 2031 6.512177 CCGTTAGGTCGATTAATCTTTGAG 57.488 41.667 13.45 0.00 0.00 3.02
2004 2032 6.040878 CCGTTAGGTCGATTAATCTTTGAGT 58.959 40.000 13.45 0.00 0.00 3.41
2006 2034 6.019801 CGTTAGGTCGATTAATCTTTGAGTGG 60.020 42.308 13.45 0.00 0.00 4.00
2007 2035 5.677319 AGGTCGATTAATCTTTGAGTGGA 57.323 39.130 13.45 0.00 0.00 4.02
2009 2037 4.571176 GGTCGATTAATCTTTGAGTGGACC 59.429 45.833 13.45 14.30 34.17 4.46
2010 2038 5.175859 GTCGATTAATCTTTGAGTGGACCA 58.824 41.667 13.45 0.00 0.00 4.02
2011 2039 5.292101 GTCGATTAATCTTTGAGTGGACCAG 59.708 44.000 13.45 0.00 0.00 4.00
2013 2041 5.643777 CGATTAATCTTTGAGTGGACCAGTT 59.356 40.000 13.45 0.00 0.00 3.16
2014 2042 6.183360 CGATTAATCTTTGAGTGGACCAGTTC 60.183 42.308 13.45 1.03 0.00 3.01
2015 2043 2.930826 TCTTTGAGTGGACCAGTTCC 57.069 50.000 2.58 0.00 46.13 3.62
2016 2044 1.420138 TCTTTGAGTGGACCAGTTCCC 59.580 52.381 2.58 0.00 45.17 3.97
2023 2051 1.095130 TGGACCAGTTCCCCTAGGTA 58.905 55.000 8.29 0.00 45.17 3.08
2046 2074 4.694509 AGAGATGTGTCAAGATTGAGCAAC 59.305 41.667 0.00 0.00 37.98 4.17
2047 2075 4.392047 AGATGTGTCAAGATTGAGCAACA 58.608 39.130 0.00 2.40 37.98 3.33
2052 2080 5.588246 TGTGTCAAGATTGAGCAACACTTTA 59.412 36.000 13.24 0.00 37.98 1.85
2068 2096 7.764443 GCAACACTTTAATACCATGTCTCTCTA 59.236 37.037 0.00 0.00 0.00 2.43
2091 2119 3.568538 CGAATTCCCTTTTGTTGCTCAG 58.431 45.455 0.00 0.00 0.00 3.35
2221 2251 3.507622 GTCTTCAAAGGCTACCATTTGCT 59.492 43.478 0.00 0.00 36.55 3.91
2345 2376 2.495084 GAGAAGGACAAAAGCTCCGTT 58.505 47.619 0.00 0.00 32.45 4.44
2534 2565 1.311859 ACAGTGAAGTACGTGGACGA 58.688 50.000 6.12 0.00 43.02 4.20
2750 2781 2.632996 TCAGGGGCACTTATCTTATCCG 59.367 50.000 0.00 0.00 0.00 4.18
3068 3106 7.707464 TGTAGTTCATGTAGTTTCGAACTTTCA 59.293 33.333 8.74 6.74 44.23 2.69
3276 3331 1.732917 CTACGCTCAGCTGGAGGAG 59.267 63.158 15.13 8.74 44.22 3.69
3526 3581 1.530323 TTAGAAACGCCTGGCCTTTC 58.470 50.000 25.94 25.94 35.13 2.62
3699 3754 1.570501 AGGGGGCAAATTCAGCTCATA 59.429 47.619 5.24 0.00 32.95 2.15
3713 3768 3.498777 CAGCTCATATGGCATCAGACTTG 59.501 47.826 1.65 0.00 0.00 3.16
3785 3840 3.346315 TGGTAGTATTCGTCGTCAAGGA 58.654 45.455 0.00 0.00 0.00 3.36
4717 4780 4.631377 TCTTATCGTGCAAGATGTTTCCAG 59.369 41.667 23.20 10.21 32.39 3.86
4792 4855 8.599624 AGATCTGAATTTGATACCCATGTTTT 57.400 30.769 0.00 0.00 0.00 2.43
5569 5634 5.483811 TCCATATTAGTTGTCGCTCAAACA 58.516 37.500 0.00 0.00 37.81 2.83
5583 5648 4.987285 CGCTCAAACAGATGTATCTAGCAT 59.013 41.667 11.84 0.00 34.68 3.79
5595 5660 7.815068 AGATGTATCTAGCATTGAAATACGTCC 59.185 37.037 0.00 0.00 38.63 4.79
5797 5863 4.501071 CATGCTTGCTAAAGGAAATTGCT 58.499 39.130 0.00 0.00 37.29 3.91
6012 6270 3.238441 GTTGATCTGTCGTGAGAGTGTC 58.762 50.000 0.00 0.00 43.49 3.67
6038 6296 4.096231 CCCTCATTTTGCATCGTATGTTCA 59.904 41.667 0.00 0.00 0.00 3.18
6128 6386 6.363357 GTCACCTCATTGTTTTCAGTAATTGC 59.637 38.462 0.00 0.00 0.00 3.56
6145 6403 8.128582 CAGTAATTGCGTGTTATTCCATATGTT 58.871 33.333 1.24 0.00 0.00 2.71
6147 6405 9.938670 GTAATTGCGTGTTATTCCATATGTTTA 57.061 29.630 1.24 0.00 0.00 2.01
6279 6538 5.600484 AGACTCTTTGATCAGGTGGGTATAG 59.400 44.000 0.00 0.00 0.00 1.31
6307 6566 8.610896 CAGCATTCAATTTTGGTTAAACTCAAA 58.389 29.630 0.00 0.00 0.00 2.69
6308 6567 8.611757 AGCATTCAATTTTGGTTAAACTCAAAC 58.388 29.630 0.00 0.00 33.29 2.93
6362 6621 7.652909 GTCATCATTTCATCCTCTCTAGAGTTG 59.347 40.741 19.21 12.85 40.48 3.16
6396 6655 8.436200 GTTACTGTGAAAACTTAGAGCATACTG 58.564 37.037 0.00 0.00 0.00 2.74
6498 6813 5.015515 TGGTGGAATTGCTTGATATGTTGA 58.984 37.500 0.00 0.00 0.00 3.18
6883 7200 7.698130 CAGTTTGGCATATTTCTTAGTACTTGC 59.302 37.037 0.00 1.58 0.00 4.01
7108 7427 6.201997 GCGGTGTCTAATTCCAAAATTTTGTT 59.798 34.615 25.25 16.98 36.49 2.83
7185 7504 7.539034 AAAAATTGCTGGTACCTGAATACTT 57.461 32.000 21.97 11.70 0.00 2.24
7194 7513 8.827677 GCTGGTACCTGAATACTTTATTAGTTG 58.172 37.037 21.97 0.00 38.33 3.16
7195 7514 9.886132 CTGGTACCTGAATACTTTATTAGTTGT 57.114 33.333 14.36 0.00 38.33 3.32
7220 7539 8.953313 GTATTACCACCTACTTTTTGTTAGCAT 58.047 33.333 0.00 0.00 0.00 3.79
7223 7542 7.826918 ACCACCTACTTTTTGTTAGCATTAA 57.173 32.000 0.00 0.00 0.00 1.40
7224 7543 8.240267 ACCACCTACTTTTTGTTAGCATTAAA 57.760 30.769 0.00 0.00 0.00 1.52
7313 7636 0.035152 TGAGGTGGGTGATGTGATGC 60.035 55.000 0.00 0.00 0.00 3.91
7374 7759 0.469705 AATGTTTGGCCTGGCACTCA 60.470 50.000 22.05 13.46 0.00 3.41
7447 7832 5.344128 CAGTGTTGCATGTTTCTTTCTATGC 59.656 40.000 0.00 0.00 44.56 3.14
7629 8016 1.118356 TTGCCCGGTGCCAGAAATTT 61.118 50.000 11.72 0.00 40.16 1.82
7947 8334 7.599998 ACTTAACTTTGGCATGATGATTTTGTC 59.400 33.333 0.00 0.00 0.00 3.18
7951 8338 4.976224 TGGCATGATGATTTTGTCAGAG 57.024 40.909 0.00 0.00 40.92 3.35
7954 8341 5.298527 TGGCATGATGATTTTGTCAGAGATC 59.701 40.000 0.00 0.00 40.92 2.75
8172 8560 3.562973 CGCAGCTATCAACATCTGGAAAT 59.437 43.478 0.00 0.00 0.00 2.17
8832 9224 9.574458 TTTCGAGTTTTGAATATTGTTCACAAA 57.426 25.926 0.00 0.00 39.55 2.83
8939 9331 5.960113 TGTACAAAAAGAAACACTGCATGT 58.040 33.333 0.00 0.00 46.42 3.21
9221 9634 4.137116 ACACTACAAAAGAGTGACTGCA 57.863 40.909 9.64 0.00 46.01 4.41
9225 9638 5.065218 CACTACAAAAGAGTGACTGCAGTTT 59.935 40.000 22.65 7.95 46.01 2.66
9234 9647 3.936453 AGTGACTGCAGTTTGAAAACGTA 59.064 39.130 22.65 0.00 43.51 3.57
9235 9648 4.393680 AGTGACTGCAGTTTGAAAACGTAA 59.606 37.500 22.65 0.00 43.51 3.18
9236 9649 5.090083 GTGACTGCAGTTTGAAAACGTAAA 58.910 37.500 22.65 0.00 43.51 2.01
9237 9650 5.741982 GTGACTGCAGTTTGAAAACGTAAAT 59.258 36.000 22.65 0.00 43.51 1.40
9238 9651 6.908284 GTGACTGCAGTTTGAAAACGTAAATA 59.092 34.615 22.65 0.00 43.51 1.40
9239 9652 7.589954 GTGACTGCAGTTTGAAAACGTAAATAT 59.410 33.333 22.65 0.00 43.51 1.28
9240 9653 7.589587 TGACTGCAGTTTGAAAACGTAAATATG 59.410 33.333 22.65 0.00 43.51 1.78
9241 9654 7.644490 ACTGCAGTTTGAAAACGTAAATATGA 58.356 30.769 15.25 0.00 43.51 2.15
9242 9655 7.589954 ACTGCAGTTTGAAAACGTAAATATGAC 59.410 33.333 15.25 0.00 43.51 3.06
9243 9656 7.418408 TGCAGTTTGAAAACGTAAATATGACA 58.582 30.769 0.00 0.00 43.51 3.58
9244 9657 8.079203 TGCAGTTTGAAAACGTAAATATGACAT 58.921 29.630 0.00 0.00 43.51 3.06
9245 9658 8.911662 GCAGTTTGAAAACGTAAATATGACATT 58.088 29.630 0.00 0.00 43.51 2.71
9298 9711 8.587608 TCCAATGACTTGCTTTCTTAATCAATT 58.412 29.630 0.00 0.00 0.00 2.32
9317 9730 7.672983 TCAATTAATCACAAGAGAGTTGTCC 57.327 36.000 0.00 0.00 0.00 4.02
9325 9738 6.223852 TCACAAGAGAGTTGTCCAGTTAATC 58.776 40.000 0.00 0.00 0.00 1.75
9326 9739 5.991606 CACAAGAGAGTTGTCCAGTTAATCA 59.008 40.000 0.00 0.00 0.00 2.57
9341 9754 6.185399 CAGTTAATCAACGAAAAGATAGGCG 58.815 40.000 0.00 0.00 39.78 5.52
9366 9779 3.953712 TCATTACAGACACGACCACAT 57.046 42.857 0.00 0.00 0.00 3.21
9368 9781 1.790755 TTACAGACACGACCACATGC 58.209 50.000 0.00 0.00 0.00 4.06
9397 9810 0.388907 CCAAAGCATGAAACCCTGCG 60.389 55.000 0.00 0.00 43.17 5.18
9494 9907 1.568504 ATGAACCCTAGCGAGAACCA 58.431 50.000 0.00 0.00 0.00 3.67
9507 9920 3.550842 GCGAGAACCATTTGAGCAAAACT 60.551 43.478 0.00 0.00 33.56 2.66
9512 9925 2.035832 ACCATTTGAGCAAAACTTCGGG 59.964 45.455 0.00 0.00 33.56 5.14
9515 9928 0.667993 TTGAGCAAAACTTCGGGCAG 59.332 50.000 0.00 0.00 0.00 4.85
9528 9941 1.079612 GGGCAGCAGCAAAATCACC 60.080 57.895 2.65 0.00 44.61 4.02
9532 9945 0.592637 CAGCAGCAAAATCACCGTGA 59.407 50.000 3.10 3.10 0.00 4.35
9541 9954 5.038033 GCAAAATCACCGTGACAACTAAAA 58.962 37.500 2.57 0.00 0.00 1.52
9549 9962 4.641094 ACCGTGACAACTAAAACCATGAAA 59.359 37.500 0.00 0.00 0.00 2.69
9561 9974 9.023962 ACTAAAACCATGAAAATATGCAGAGAA 57.976 29.630 0.00 0.00 0.00 2.87
9615 10028 9.740710 AATAAAGCTGACTAGACAACCTTAATT 57.259 29.630 0.00 0.00 0.00 1.40
9638 10054 2.880890 GCATGTAACCAGCATAGGGAAG 59.119 50.000 0.00 0.00 0.00 3.46
9640 10056 3.906720 TGTAACCAGCATAGGGAAGAC 57.093 47.619 0.00 0.00 0.00 3.01
9641 10057 3.178046 TGTAACCAGCATAGGGAAGACA 58.822 45.455 0.00 0.00 0.00 3.41
9642 10058 3.585289 TGTAACCAGCATAGGGAAGACAA 59.415 43.478 0.00 0.00 0.00 3.18
9646 10063 0.460284 AGCATAGGGAAGACAACGCG 60.460 55.000 3.53 3.53 0.00 6.01
9656 10073 4.555709 ACAACGCGCCCTTCACCA 62.556 61.111 5.73 0.00 0.00 4.17
9674 10091 2.166664 ACCATAGAGAAGAGGCGTGAAC 59.833 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.680172 GCACATAATAACCATTGCCTTGCA 60.680 41.667 0.00 0.00 36.47 4.08
1 2 3.803778 GCACATAATAACCATTGCCTTGC 59.196 43.478 0.00 0.00 0.00 4.01
2 3 5.008619 TGCACATAATAACCATTGCCTTG 57.991 39.130 0.00 0.00 0.00 3.61
21 22 4.885907 GGAGGATGAAGAGAAATCAATGCA 59.114 41.667 0.00 0.00 0.00 3.96
86 87 3.181491 GCGGGATCGAAAATGGAAAATGA 60.181 43.478 0.00 0.00 39.00 2.57
130 131 6.073980 CGCAACTTAACTTTGCTAGAGTTACA 60.074 38.462 12.87 0.00 45.99 2.41
228 229 2.361104 GGAATGGGTCCAAGCGCA 60.361 61.111 11.47 0.00 46.97 6.09
287 292 0.815095 GGCGAATAACACAAAGGGGG 59.185 55.000 0.00 0.00 0.00 5.40
309 314 9.495572 GTAATTATTCAAGAGGATCGAGGATTT 57.504 33.333 0.00 0.00 42.67 2.17
331 336 5.712917 ACATAAAAATGTCGTGTGGGGTAAT 59.287 36.000 0.00 0.00 0.00 1.89
421 426 2.290071 CCCGAAACTGACCACCTATGTT 60.290 50.000 0.00 0.00 0.00 2.71
426 431 0.471211 TCTCCCGAAACTGACCACCT 60.471 55.000 0.00 0.00 0.00 4.00
493 500 4.344865 ACGTGCCCACCCATGTCC 62.345 66.667 0.00 0.00 29.23 4.02
662 686 8.357290 TGGTCAATCATCATTTCATTTCTCTT 57.643 30.769 0.00 0.00 0.00 2.85
996 1020 4.271816 CCTCCTCCCGACATCGCG 62.272 72.222 0.00 0.00 38.18 5.87
997 1021 2.833582 TCCTCCTCCCGACATCGC 60.834 66.667 0.00 0.00 38.18 4.58
998 1022 2.196925 CCTCCTCCTCCCGACATCG 61.197 68.421 0.00 0.00 39.44 3.84
999 1023 0.825840 CTCCTCCTCCTCCCGACATC 60.826 65.000 0.00 0.00 0.00 3.06
1000 1024 1.231641 CTCCTCCTCCTCCCGACAT 59.768 63.158 0.00 0.00 0.00 3.06
1001 1025 2.684104 CTCCTCCTCCTCCCGACA 59.316 66.667 0.00 0.00 0.00 4.35
1002 1026 2.123640 CCTCCTCCTCCTCCCGAC 60.124 72.222 0.00 0.00 0.00 4.79
1003 1027 2.286962 TCCTCCTCCTCCTCCCGA 60.287 66.667 0.00 0.00 0.00 5.14
1004 1028 2.197324 CTCCTCCTCCTCCTCCCG 59.803 72.222 0.00 0.00 0.00 5.14
1005 1029 2.612251 CCTCCTCCTCCTCCTCCC 59.388 72.222 0.00 0.00 0.00 4.30
1006 1030 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
1007 1031 1.152546 GAGCCTCCTCCTCCTCCTC 60.153 68.421 0.00 0.00 31.68 3.71
1008 1032 3.024217 GAGCCTCCTCCTCCTCCT 58.976 66.667 0.00 0.00 31.68 3.69
1322 1346 2.074920 CGCGAAAGAAAAGCACGGC 61.075 57.895 0.00 0.00 0.00 5.68
1336 1360 3.792047 GAGCAGCAATGCACGCGA 61.792 61.111 15.93 0.00 35.04 5.87
1401 1425 1.280133 CTTCTGGATGGACTCCTGCAA 59.720 52.381 0.00 0.00 45.21 4.08
1498 1522 2.673341 TGAGAGAGCTGCCGACGT 60.673 61.111 0.00 0.00 0.00 4.34
1506 1530 1.152567 CCCCGATCCTGAGAGAGCT 60.153 63.158 0.00 0.00 0.00 4.09
1514 1538 1.144936 GTTCTGAGCCCCGATCCTG 59.855 63.158 0.00 0.00 0.00 3.86
1659 1683 2.919229 CAAGCGAAATGGAATTGCTGAC 59.081 45.455 0.00 0.00 36.10 3.51
1667 1691 2.441410 TGGCATACAAGCGAAATGGAA 58.559 42.857 0.00 0.00 34.64 3.53
1671 1695 2.428171 AGCAATGGCATACAAGCGAAAT 59.572 40.909 0.00 0.00 44.61 2.17
1698 1722 6.988580 AGTACCAACTCAAACTAACTACAACC 59.011 38.462 0.00 0.00 0.00 3.77
1723 1751 7.575414 AATATGTCATAACGCATAACCCAAA 57.425 32.000 0.00 0.00 32.23 3.28
1734 1762 6.444633 ACGGAACCTCTAATATGTCATAACG 58.555 40.000 0.00 0.00 0.00 3.18
1927 1955 7.064609 GTCATGAAATTCGATACACTGAAGGAA 59.935 37.037 0.00 0.00 0.00 3.36
1928 1956 6.535150 GTCATGAAATTCGATACACTGAAGGA 59.465 38.462 0.00 0.00 0.00 3.36
1932 1960 6.630071 TCAGTCATGAAATTCGATACACTGA 58.370 36.000 0.00 0.00 30.61 3.41
1947 1975 8.175925 TCCACAATGTTTTAATTCAGTCATGA 57.824 30.769 0.00 0.00 0.00 3.07
1985 2013 5.420409 GTCCACTCAAAGATTAATCGACCT 58.580 41.667 9.78 0.00 0.00 3.85
2006 2034 2.244252 TCTCTACCTAGGGGAACTGGTC 59.756 54.545 14.81 0.00 34.11 4.02
2007 2035 2.295143 TCTCTACCTAGGGGAACTGGT 58.705 52.381 14.81 0.00 35.61 4.00
2009 2037 3.639094 CACATCTCTACCTAGGGGAACTG 59.361 52.174 14.81 12.21 36.25 3.16
2010 2038 3.272551 ACACATCTCTACCTAGGGGAACT 59.727 47.826 14.81 0.00 36.25 3.01
2011 2039 3.637694 GACACATCTCTACCTAGGGGAAC 59.362 52.174 14.81 0.00 36.25 3.62
2013 2041 2.856864 TGACACATCTCTACCTAGGGGA 59.143 50.000 14.81 9.97 36.25 4.81
2014 2042 3.314307 TGACACATCTCTACCTAGGGG 57.686 52.381 14.81 5.68 38.88 4.79
2015 2043 4.537751 TCTTGACACATCTCTACCTAGGG 58.462 47.826 14.81 0.00 0.00 3.53
2016 2044 6.322456 TCAATCTTGACACATCTCTACCTAGG 59.678 42.308 7.41 7.41 31.01 3.02
2023 2051 4.548451 TGCTCAATCTTGACACATCTCT 57.452 40.909 0.00 0.00 32.90 3.10
2046 2074 6.918569 CGGTAGAGAGACATGGTATTAAAGTG 59.081 42.308 0.00 0.00 0.00 3.16
2047 2075 6.832384 TCGGTAGAGAGACATGGTATTAAAGT 59.168 38.462 0.00 0.00 0.00 2.66
2052 2080 6.239345 GGAATTCGGTAGAGAGACATGGTATT 60.239 42.308 0.00 0.00 0.00 1.89
2068 2096 2.296190 GAGCAACAAAAGGGAATTCGGT 59.704 45.455 0.00 0.00 0.00 4.69
2091 2119 2.882761 GTGGGGACTTTAACTCAACCAC 59.117 50.000 0.00 0.00 40.11 4.16
2183 2211 8.338259 CCTTTGAAGACATAATAAGGATGAACG 58.662 37.037 0.00 0.00 34.18 3.95
2184 2212 8.131731 GCCTTTGAAGACATAATAAGGATGAAC 58.868 37.037 0.00 0.00 34.18 3.18
2221 2251 3.516615 CGGCCAAAGAGTCAAAACAAAA 58.483 40.909 2.24 0.00 0.00 2.44
2345 2376 3.363627 TGATGTGGCATTGGCAATTCTA 58.636 40.909 15.17 0.00 43.71 2.10
2534 2565 8.212259 ACCTAAATGGAATAGCATCACTAGAT 57.788 34.615 0.00 0.00 39.71 1.98
2750 2781 8.564574 TGTCTGTCATACAACAATTAAAAGGAC 58.435 33.333 0.00 0.00 0.00 3.85
3276 3331 3.119352 GGTGCTTCTTCCCATTCATCAAC 60.119 47.826 0.00 0.00 0.00 3.18
3325 3380 1.411394 CTTGCGATTTGTGGTGCTTG 58.589 50.000 0.00 0.00 0.00 4.01
3526 3581 2.270986 GCTGCACCCCTTGGAAGTG 61.271 63.158 0.00 5.72 34.81 3.16
3699 3754 4.334759 CGAGAAAATCAAGTCTGATGCCAT 59.665 41.667 0.00 0.00 41.66 4.40
3785 3840 2.327325 TAGTGCCTCTTCCACTCCTT 57.673 50.000 0.00 0.00 42.22 3.36
4249 4309 6.147656 TGCATGGCAAATAGATAACTACGATG 59.852 38.462 0.00 0.00 34.76 3.84
4289 4349 6.694877 AGAATTCATCAACCATGAGACATG 57.305 37.500 8.44 4.94 42.76 3.21
4687 4750 3.628008 TCTTGCACGATAAGAGTAGGGA 58.372 45.455 0.00 0.00 31.04 4.20
4717 4780 8.794335 AGGAATACAGAAGTTGAGGATTTTAC 57.206 34.615 0.00 0.00 0.00 2.01
5569 5634 7.815068 GGACGTATTTCAATGCTAGATACATCT 59.185 37.037 0.00 0.00 40.86 2.90
5583 5648 5.163488 ACGGATGTATCTGGACGTATTTCAA 60.163 40.000 5.74 0.00 37.50 2.69
5595 5660 2.535984 GTCGCTGAAACGGATGTATCTG 59.464 50.000 0.00 0.00 39.11 2.90
5680 5745 3.719268 ACATAACTTGCCATCCTGACA 57.281 42.857 0.00 0.00 0.00 3.58
5694 5759 1.593006 CCATCCTCGCGACAACATAAC 59.407 52.381 3.71 0.00 0.00 1.89
5835 6092 4.881850 TCTCTTGTCAGTTCCCAAGAAAAC 59.118 41.667 0.00 0.00 44.59 2.43
5898 6155 9.793259 ACTTCCAAAATTTGTCTGATCTAGTTA 57.207 29.630 4.92 0.00 0.00 2.24
6012 6270 1.086696 ACGATGCAAAATGAGGGTCG 58.913 50.000 0.00 0.00 0.00 4.79
6038 6296 3.237268 TGCAGTTGGTTCACCCTAAAT 57.763 42.857 0.00 0.00 34.29 1.40
6145 6403 9.661563 ACGACCATGATTTGAGTTAATAAGTAA 57.338 29.630 0.00 0.00 0.00 2.24
6147 6405 7.065803 CCACGACCATGATTTGAGTTAATAAGT 59.934 37.037 0.00 0.00 0.00 2.24
6279 6538 7.437862 TGAGTTTAACCAAAATTGAATGCTGAC 59.562 33.333 0.00 0.00 0.00 3.51
6362 6621 9.042008 TCTAAGTTTTCACAGTAACTTCATGTC 57.958 33.333 3.62 0.00 42.06 3.06
6498 6813 7.766278 GGTACTATCAATTTGTCACATGAGACT 59.234 37.037 21.53 4.83 39.27 3.24
6642 6957 5.317733 ACCGTTTCAAATTGACTCAAACA 57.682 34.783 0.00 0.00 0.00 2.83
7108 7427 2.832778 TTGCTCCAGGCTCCTGCAA 61.833 57.895 10.37 8.90 42.35 4.08
7194 7513 8.326680 TGCTAACAAAAAGTAGGTGGTAATAC 57.673 34.615 0.00 0.00 0.00 1.89
7195 7514 9.523168 AATGCTAACAAAAAGTAGGTGGTAATA 57.477 29.630 0.00 0.00 0.00 0.98
7313 7636 1.880819 GAAGGTGCCAGGCCAACATG 61.881 60.000 9.64 0.00 0.00 3.21
7599 7986 2.551912 CCGGGCAAGTGTTCGCTTT 61.552 57.895 0.00 0.00 0.00 3.51
7629 8016 2.880890 GCAGCTTTTCTCTGTTTCCTCA 59.119 45.455 0.00 0.00 34.21 3.86
7947 8334 6.709846 GGATACCTCATGAAAAAGGATCTCTG 59.290 42.308 5.76 0.00 36.46 3.35
8172 8560 0.394192 CTGTGACTCTGCCAAGGACA 59.606 55.000 0.00 0.00 0.00 4.02
8388 8776 1.669440 GTCCGTGAACCAGGCACTA 59.331 57.895 0.00 0.00 36.02 2.74
8832 9224 3.778265 ACTCCACTTGCACCCATTAAAT 58.222 40.909 0.00 0.00 0.00 1.40
8841 9233 8.283291 GCAAATTATATAGTACTCCACTTGCAC 58.717 37.037 0.00 0.00 38.80 4.57
8939 9331 8.630054 AACAGTGCCAAGTTCACTAATAATAA 57.370 30.769 0.00 0.00 42.38 1.40
8940 9332 7.880713 TGAACAGTGCCAAGTTCACTAATAATA 59.119 33.333 9.22 0.00 46.46 0.98
8941 9333 6.714810 TGAACAGTGCCAAGTTCACTAATAAT 59.285 34.615 9.22 0.00 46.46 1.28
8942 9334 6.058833 TGAACAGTGCCAAGTTCACTAATAA 58.941 36.000 9.22 0.00 46.46 1.40
8943 9335 5.616270 TGAACAGTGCCAAGTTCACTAATA 58.384 37.500 9.22 0.00 46.46 0.98
8944 9336 4.460263 TGAACAGTGCCAAGTTCACTAAT 58.540 39.130 9.22 0.00 46.46 1.73
8950 9342 3.141398 TCAGATGAACAGTGCCAAGTTC 58.859 45.455 4.76 4.76 43.31 3.01
9089 9481 5.534654 GCCATTGCAAACCCATATTCTAGTA 59.465 40.000 1.71 0.00 37.47 1.82
9186 9599 8.644216 TCTTTTGTAGTGTTGGACTAAGTGATA 58.356 33.333 0.00 0.00 38.96 2.15
9203 9616 5.294306 TCAAACTGCAGTCACTCTTTTGTAG 59.706 40.000 21.95 0.00 0.00 2.74
9221 9634 9.959749 ACAATGTCATATTTACGTTTTCAAACT 57.040 25.926 0.00 0.00 36.77 2.66
9294 9707 7.173907 ACTGGACAACTCTCTTGTGATTAATTG 59.826 37.037 0.00 0.00 31.96 2.32
9298 9711 5.808366 ACTGGACAACTCTCTTGTGATTA 57.192 39.130 0.00 0.00 31.96 1.75
9301 9714 5.607939 TTAACTGGACAACTCTCTTGTGA 57.392 39.130 0.00 0.00 31.96 3.58
9317 9730 6.035650 TCGCCTATCTTTTCGTTGATTAACTG 59.964 38.462 0.00 0.00 34.60 3.16
9325 9738 5.627172 TGATTTTCGCCTATCTTTTCGTTG 58.373 37.500 0.00 0.00 0.00 4.10
9326 9739 5.873179 TGATTTTCGCCTATCTTTTCGTT 57.127 34.783 0.00 0.00 0.00 3.85
9341 9754 5.178623 TGTGGTCGTGTCTGTAATGATTTTC 59.821 40.000 0.00 0.00 0.00 2.29
9366 9779 1.055849 TGCTTTGGGAGTAGTCTGCA 58.944 50.000 0.00 0.00 33.59 4.41
9368 9781 3.616956 TCATGCTTTGGGAGTAGTCTG 57.383 47.619 0.00 0.00 0.00 3.51
9434 9847 4.870123 ATGTTGATGGCTTGCAGTTTTA 57.130 36.364 0.00 0.00 0.00 1.52
9475 9888 1.568504 TGGTTCTCGCTAGGGTTCAT 58.431 50.000 6.70 0.00 0.00 2.57
9476 9889 1.568504 ATGGTTCTCGCTAGGGTTCA 58.431 50.000 6.70 0.68 0.00 3.18
9494 9907 1.686052 TGCCCGAAGTTTTGCTCAAAT 59.314 42.857 0.00 0.00 0.00 2.32
9507 9920 1.177895 TGATTTTGCTGCTGCCCGAA 61.178 50.000 13.47 5.57 38.71 4.30
9512 9925 1.005294 CACGGTGATTTTGCTGCTGC 61.005 55.000 8.89 8.89 40.20 5.25
9515 9928 0.310543 TGTCACGGTGATTTTGCTGC 59.689 50.000 14.78 0.00 0.00 5.25
9528 9941 8.849490 CATATTTTCATGGTTTTAGTTGTCACG 58.151 33.333 0.00 0.00 0.00 4.35
9532 9945 8.584157 TCTGCATATTTTCATGGTTTTAGTTGT 58.416 29.630 0.00 0.00 0.00 3.32
9541 9954 7.781693 ACCTTATTCTCTGCATATTTTCATGGT 59.218 33.333 0.00 0.00 0.00 3.55
9549 9962 6.169094 CGGATGACCTTATTCTCTGCATATT 58.831 40.000 0.00 0.00 0.00 1.28
9561 9974 4.640201 CCAAATGTTGACGGATGACCTTAT 59.360 41.667 0.00 0.00 0.00 1.73
9615 10028 2.240921 TCCCTATGCTGGTTACATGCAA 59.759 45.455 5.73 0.00 40.24 4.08
9638 10054 3.723348 GGTGAAGGGCGCGTTGTC 61.723 66.667 8.43 0.81 0.00 3.18
9640 10056 1.705337 CTATGGTGAAGGGCGCGTTG 61.705 60.000 8.43 0.00 0.00 4.10
9641 10057 1.449601 CTATGGTGAAGGGCGCGTT 60.450 57.895 8.43 0.00 0.00 4.84
9642 10058 2.186903 CTATGGTGAAGGGCGCGT 59.813 61.111 8.43 0.00 0.00 6.01
9646 10063 2.103941 CCTCTTCTCTATGGTGAAGGGC 59.896 54.545 17.52 0.00 40.33 5.19
9656 10073 2.853731 CGTTCACGCCTCTTCTCTAT 57.146 50.000 0.00 0.00 0.00 1.98
9674 10091 2.285834 GCACATAAAGTCATCCTTCGCG 60.286 50.000 0.00 0.00 31.27 5.87


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

AutoCloner maintained by Alex Coulton.