Multiple sequence alignment - TraesCS6A01G189700

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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 TraesCS6A01G189700 chr6A 100.000 6299 0 0 1 6299 245768326 245762028 0.000000e+00 11633.0
1 TraesCS6A01G189700 chr6A 91.812 745 59 2 1 744 585802880 585803623 0.000000e+00 1037.0
2 TraesCS6A01G189700 chr6D 95.363 4313 99 20 2060 6299 197316128 197311844 0.000000e+00 6763.0
3 TraesCS6A01G189700 chr6D 97.939 1116 17 3 879 1991 197317632 197316520 0.000000e+00 1929.0
4 TraesCS6A01G189700 chr6D 98.131 107 2 0 775 881 197317773 197317667 3.000000e-43 187.0
5 TraesCS6A01G189700 chr6D 93.548 93 6 0 6083 6175 197311964 197311872 8.520000e-29 139.0
6 TraesCS6A01G189700 chr6B 97.681 2156 46 2 2055 4208 302597725 302595572 0.000000e+00 3701.0
7 TraesCS6A01G189700 chr6B 93.869 1990 81 18 4332 6299 302594696 302592726 0.000000e+00 2961.0
8 TraesCS6A01G189700 chr6B 97.059 1088 21 5 879 1963 302598966 302597887 0.000000e+00 1821.0
9 TraesCS6A01G189700 chr6B 84.058 759 87 22 1 750 173810085 173810818 0.000000e+00 701.0
10 TraesCS6A01G189700 chr6B 84.058 759 87 21 1 750 701616742 701616009 0.000000e+00 701.0
11 TraesCS6A01G189700 chr6B 89.980 499 37 5 246 744 92400655 92400170 3.200000e-177 632.0
12 TraesCS6A01G189700 chr6B 89.178 499 41 6 246 744 92293491 92293006 1.500000e-170 610.0
13 TraesCS6A01G189700 chr6B 88.166 507 39 13 246 748 101640041 101639552 9.100000e-163 584.0
14 TraesCS6A01G189700 chr6B 92.857 112 0 1 778 881 302599112 302599001 8.460000e-34 156.0
15 TraesCS6A01G189700 chr6B 94.624 93 5 0 6083 6175 302592846 302592754 1.830000e-30 145.0
16 TraesCS6A01G189700 chr1D 95.086 753 28 4 1 744 495005683 495006435 0.000000e+00 1177.0
17 TraesCS6A01G189700 chr1D 94.504 746 38 3 1 744 18774595 18775339 0.000000e+00 1147.0
18 TraesCS6A01G189700 chr1D 96.491 171 6 0 574 744 18773973 18773803 3.720000e-72 283.0
19 TraesCS6A01G189700 chr1D 92.308 182 13 1 567 748 495001712 495001532 2.250000e-64 257.0
20 TraesCS6A01G189700 chr7D 94.814 752 29 3 1 744 413536369 413535620 0.000000e+00 1164.0
21 TraesCS6A01G189700 chr7D 92.228 193 13 2 553 744 413540230 413540421 8.050000e-69 272.0
22 TraesCS6A01G189700 chr7D 85.308 211 24 5 3780 3984 398325759 398325968 1.780000e-50 211.0
23 TraesCS6A01G189700 chr3D 94.110 747 41 3 1 745 213205132 213205877 0.000000e+00 1133.0
24 TraesCS6A01G189700 chr3D 91.779 742 51 3 3 744 508195712 508194981 0.000000e+00 1024.0
25 TraesCS6A01G189700 chr3D 84.656 756 88 21 1 750 437677902 437678635 0.000000e+00 728.0
26 TraesCS6A01G189700 chr3D 97.765 179 4 0 567 745 213204517 213204339 6.130000e-80 309.0
27 TraesCS6A01G189700 chr3D 93.258 178 12 0 567 744 519385854 519385677 4.840000e-66 263.0
28 TraesCS6A01G189700 chr3D 90.123 81 5 1 1 78 454425083 454425163 1.120000e-17 102.0
29 TraesCS6A01G189700 chr2D 94.024 753 31 4 1 744 55627488 55628235 0.000000e+00 1129.0
30 TraesCS6A01G189700 chr2D 84.834 211 25 5 3780 3984 201760641 201760850 8.280000e-49 206.0
31 TraesCS6A01G189700 chr2D 78.095 210 34 6 3737 3934 538673712 538673921 8.580000e-24 122.0
32 TraesCS6A01G189700 chr7B 89.382 744 63 8 1 744 329022856 329022129 0.000000e+00 922.0
33 TraesCS6A01G189700 chr7B 87.121 264 32 2 5863 6125 304668872 304669134 1.330000e-76 298.0
34 TraesCS6A01G189700 chr7B 82.558 258 26 5 3744 3983 505937581 505937837 6.400000e-50 209.0
35 TraesCS6A01G189700 chr4A 84.453 759 83 22 1 750 617013533 617014265 0.000000e+00 715.0
36 TraesCS6A01G189700 chr4A 86.466 266 34 2 5861 6125 315623836 315623572 2.220000e-74 291.0
37 TraesCS6A01G189700 chr4A 97.222 36 1 0 6179 6214 272511688 272511653 1.900000e-05 62.1
38 TraesCS6A01G189700 chr2A 84.211 760 85 23 1 750 761504083 761503349 0.000000e+00 706.0
39 TraesCS6A01G189700 chr2A 86.973 261 32 2 5866 6125 331704039 331703780 6.180000e-75 292.0
40 TraesCS6A01G189700 chr4B 83.926 759 88 22 1 750 399952054 399951321 0.000000e+00 695.0
41 TraesCS6A01G189700 chr4B 86.466 266 32 4 5863 6126 336609590 336609853 7.990000e-74 289.0
42 TraesCS6A01G189700 chr3A 87.170 265 30 4 5863 6125 329202114 329202376 1.330000e-76 298.0
43 TraesCS6A01G189700 chr3A 85.238 210 27 2 3778 3983 246937130 246937339 4.950000e-51 213.0
44 TraesCS6A01G189700 chr7A 86.742 264 33 2 5863 6125 341746793 341747055 6.180000e-75 292.0
45 TraesCS6A01G189700 chr1A 86.973 261 32 2 5866 6125 342236090 342235831 6.180000e-75 292.0
46 TraesCS6A01G189700 chr4D 85.308 211 24 5 3780 3984 180103103 180102894 1.780000e-50 211.0
47 TraesCS6A01G189700 chr2B 84.651 215 26 4 3780 3988 326287701 326287914 2.300000e-49 207.0
48 TraesCS6A01G189700 chr5D 84.834 211 25 5 3780 3984 245393056 245393265 8.280000e-49 206.0
49 TraesCS6A01G189700 chr3B 79.545 264 29 13 3744 3983 137597594 137597856 1.400000e-36 165.0
50 TraesCS6A01G189700 chr5A 78.261 276 34 15 3738 3989 294560885 294561158 3.040000e-33 154.0
51 TraesCS6A01G189700 chrUn 76.806 263 39 10 3744 3984 294213634 294213896 1.840000e-25 128.0
52 TraesCS6A01G189700 chrUn 76.806 263 39 10 3744 3984 294240123 294240385 1.840000e-25 128.0
53 TraesCS6A01G189700 chrUn 76.806 263 39 10 3744 3984 320030083 320029821 1.840000e-25 128.0
54 TraesCS6A01G189700 chrUn 78.140 215 28 11 3737 3934 22157557 22157769 1.110000e-22 119.0
55 TraesCS6A01G189700 chr1B 86.585 82 11 0 663 744 685130282 685130201 2.420000e-14 91.6


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 TraesCS6A01G189700 chr6A 245762028 245768326 6298 True 11633.0 11633 100.000 1 6299 1 chr6A.!!$R1 6298
1 TraesCS6A01G189700 chr6A 585802880 585803623 743 False 1037.0 1037 91.812 1 744 1 chr6A.!!$F1 743
2 TraesCS6A01G189700 chr6D 197311844 197316128 4284 True 6763.0 6763 95.363 2060 6299 1 chr6D.!!$R1 4239
3 TraesCS6A01G189700 chr6D 197316520 197317773 1253 True 1058.0 1929 98.035 775 1991 2 chr6D.!!$R3 1216
4 TraesCS6A01G189700 chr6B 302592726 302599112 6386 True 1756.8 3701 95.218 778 6299 5 chr6B.!!$R5 5521
5 TraesCS6A01G189700 chr6B 173810085 173810818 733 False 701.0 701 84.058 1 750 1 chr6B.!!$F1 749
6 TraesCS6A01G189700 chr6B 701616009 701616742 733 True 701.0 701 84.058 1 750 1 chr6B.!!$R4 749
7 TraesCS6A01G189700 chr1D 495005683 495006435 752 False 1177.0 1177 95.086 1 744 1 chr1D.!!$F2 743
8 TraesCS6A01G189700 chr1D 18774595 18775339 744 False 1147.0 1147 94.504 1 744 1 chr1D.!!$F1 743
9 TraesCS6A01G189700 chr7D 413535620 413536369 749 True 1164.0 1164 94.814 1 744 1 chr7D.!!$R1 743
10 TraesCS6A01G189700 chr3D 213205132 213205877 745 False 1133.0 1133 94.110 1 745 1 chr3D.!!$F1 744
11 TraesCS6A01G189700 chr3D 508194981 508195712 731 True 1024.0 1024 91.779 3 744 1 chr3D.!!$R2 741
12 TraesCS6A01G189700 chr3D 437677902 437678635 733 False 728.0 728 84.656 1 750 1 chr3D.!!$F2 749
13 TraesCS6A01G189700 chr2D 55627488 55628235 747 False 1129.0 1129 94.024 1 744 1 chr2D.!!$F1 743
14 TraesCS6A01G189700 chr7B 329022129 329022856 727 True 922.0 922 89.382 1 744 1 chr7B.!!$R1 743
15 TraesCS6A01G189700 chr4A 617013533 617014265 732 False 715.0 715 84.453 1 750 1 chr4A.!!$F1 749
16 TraesCS6A01G189700 chr2A 761503349 761504083 734 True 706.0 706 84.211 1 750 1 chr2A.!!$R2 749
17 TraesCS6A01G189700 chr4B 399951321 399952054 733 True 695.0 695 83.926 1 750 1 chr4B.!!$R1 749

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
431 439 1.003839 CGTGGTCAAGCTAGGGCAA 60.004 57.895 0.0 0.0 41.70 4.52 F
521 539 2.255406 AGCCTCAGAGCAATCCGATAT 58.745 47.619 0.0 0.0 34.23 1.63 F
725 748 3.194861 CGAAGCCCGATATTGAAAGTGA 58.805 45.455 0.0 0.0 41.76 3.41 F
1996 2068 0.901827 TTTAGCATCACCTCGGCTCA 59.098 50.000 0.0 0.0 39.01 4.26 F
2001 2073 1.001293 GCATCACCTCGGCTCATATCA 59.999 52.381 0.0 0.0 0.00 2.15 F
2665 2807 1.338200 ACTGCTACCTTTCTCTTGCCG 60.338 52.381 0.0 0.0 0.00 5.69 F
3573 3716 1.612395 GCCTCTCCCTCTCCAGTGTG 61.612 65.000 0.0 0.0 0.00 3.82 F
4660 5593 1.071314 ACCCCAGACATCCCAAACCA 61.071 55.000 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1768 0.664224 GAACGCGGGTCCAAAAAGAA 59.336 50.000 12.47 0.0 0.00 2.52 R
1701 1770 1.082366 CGAACGCGGGTCCAAAAAG 60.082 57.895 12.47 0.0 0.00 2.27 R
2030 2102 2.301870 GGTTGGTGTCCTATGTGACAGA 59.698 50.000 0.00 0.0 45.40 3.41 R
3573 3716 1.202545 GGAGGGTGAAGAGATAACGCC 60.203 57.143 0.00 0.0 0.00 5.68 R
3923 4073 8.957466 GCTTTGTCCTAAGTCCAACTTTATAAT 58.043 33.333 0.00 0.0 39.51 1.28 R
4082 4232 3.551846 TCCGTATCTGATGAGTGCTACA 58.448 45.455 0.00 0.0 0.00 2.74 R
5235 6168 0.875059 CCCTCCTGCGAAGTTCAAAC 59.125 55.000 3.32 0.0 0.00 2.93 R
6121 7088 1.202818 ACCCTCTCACAAGGCAAGTTC 60.203 52.381 0.00 0.0 34.88 3.01 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
166 170 2.656069 GGGAGGGCGAGTTGTGCTA 61.656 63.158 0.00 0.00 0.00 3.49
172 176 4.072913 CGAGTTGTGCTATCGCGT 57.927 55.556 5.77 0.00 39.65 6.01
174 178 1.742900 CGAGTTGTGCTATCGCGTGG 61.743 60.000 5.77 0.00 39.65 4.94
430 438 2.662596 CGTGGTCAAGCTAGGGCA 59.337 61.111 0.00 0.00 41.70 5.36
431 439 1.003839 CGTGGTCAAGCTAGGGCAA 60.004 57.895 0.00 0.00 41.70 4.52
521 539 2.255406 AGCCTCAGAGCAATCCGATAT 58.745 47.619 0.00 0.00 34.23 1.63
531 549 4.085733 AGCAATCCGATATAGAGCAGACT 58.914 43.478 0.00 0.00 0.00 3.24
536 554 6.751514 ATCCGATATAGAGCAGACTACAAG 57.248 41.667 0.00 0.00 0.00 3.16
565 583 6.928348 TGGATAAGGTAGAAAGACACAAGA 57.072 37.500 0.00 0.00 0.00 3.02
569 587 8.697292 GGATAAGGTAGAAAGACACAAGAGTAT 58.303 37.037 0.00 0.00 0.00 2.12
659 682 6.095440 GCATGGTAATCAAAGTGTACAGGAAT 59.905 38.462 0.00 0.00 0.00 3.01
725 748 3.194861 CGAAGCCCGATATTGAAAGTGA 58.805 45.455 0.00 0.00 41.76 3.41
746 769 4.635765 TGACAAATAGCCGATTTTCTCAGG 59.364 41.667 0.00 0.00 35.45 3.86
747 770 4.589908 ACAAATAGCCGATTTTCTCAGGT 58.410 39.130 0.00 0.00 35.45 4.00
749 772 6.177610 ACAAATAGCCGATTTTCTCAGGTAA 58.822 36.000 0.00 0.00 35.45 2.85
750 773 6.828785 ACAAATAGCCGATTTTCTCAGGTAAT 59.171 34.615 0.00 0.00 35.45 1.89
751 774 7.990886 ACAAATAGCCGATTTTCTCAGGTAATA 59.009 33.333 0.00 0.00 35.45 0.98
752 775 9.003658 CAAATAGCCGATTTTCTCAGGTAATAT 57.996 33.333 0.00 0.00 35.45 1.28
753 776 8.779354 AATAGCCGATTTTCTCAGGTAATATC 57.221 34.615 0.00 0.00 0.00 1.63
754 777 6.426646 AGCCGATTTTCTCAGGTAATATCT 57.573 37.500 0.00 0.00 0.00 1.98
755 778 7.540474 AGCCGATTTTCTCAGGTAATATCTA 57.460 36.000 0.00 0.00 0.00 1.98
756 779 7.607250 AGCCGATTTTCTCAGGTAATATCTAG 58.393 38.462 0.00 0.00 0.00 2.43
757 780 6.814146 GCCGATTTTCTCAGGTAATATCTAGG 59.186 42.308 0.00 0.00 0.00 3.02
758 781 7.525692 GCCGATTTTCTCAGGTAATATCTAGGT 60.526 40.741 0.00 0.00 0.00 3.08
759 782 9.021807 CCGATTTTCTCAGGTAATATCTAGGTA 57.978 37.037 0.00 0.00 0.00 3.08
767 790 9.961264 CTCAGGTAATATCTAGGTAGTACATCA 57.039 37.037 19.32 1.27 29.29 3.07
1811 1882 7.724061 AGCCATAAATCTTTTGGTACCGATTAT 59.276 33.333 7.57 3.45 32.90 1.28
1991 2063 2.868583 CCTGTCATTTAGCATCACCTCG 59.131 50.000 0.00 0.00 0.00 4.63
1992 2064 2.868583 CTGTCATTTAGCATCACCTCGG 59.131 50.000 0.00 0.00 0.00 4.63
1993 2065 1.599542 GTCATTTAGCATCACCTCGGC 59.400 52.381 0.00 0.00 0.00 5.54
1994 2066 1.486310 TCATTTAGCATCACCTCGGCT 59.514 47.619 0.00 0.00 41.51 5.52
1995 2067 1.869767 CATTTAGCATCACCTCGGCTC 59.130 52.381 0.00 0.00 39.01 4.70
1996 2068 0.901827 TTTAGCATCACCTCGGCTCA 59.098 50.000 0.00 0.00 39.01 4.26
1997 2069 1.123077 TTAGCATCACCTCGGCTCAT 58.877 50.000 0.00 0.00 39.01 2.90
1998 2070 1.995376 TAGCATCACCTCGGCTCATA 58.005 50.000 0.00 0.00 39.01 2.15
1999 2071 1.346062 AGCATCACCTCGGCTCATAT 58.654 50.000 0.00 0.00 30.74 1.78
2000 2072 1.274728 AGCATCACCTCGGCTCATATC 59.725 52.381 0.00 0.00 30.74 1.63
2001 2073 1.001293 GCATCACCTCGGCTCATATCA 59.999 52.381 0.00 0.00 0.00 2.15
2002 2074 2.354503 GCATCACCTCGGCTCATATCAT 60.355 50.000 0.00 0.00 0.00 2.45
2003 2075 3.867600 GCATCACCTCGGCTCATATCATT 60.868 47.826 0.00 0.00 0.00 2.57
2004 2076 4.321718 CATCACCTCGGCTCATATCATTT 58.678 43.478 0.00 0.00 0.00 2.32
2005 2077 4.422073 TCACCTCGGCTCATATCATTTT 57.578 40.909 0.00 0.00 0.00 1.82
2006 2078 4.380531 TCACCTCGGCTCATATCATTTTC 58.619 43.478 0.00 0.00 0.00 2.29
2007 2079 4.101585 TCACCTCGGCTCATATCATTTTCT 59.898 41.667 0.00 0.00 0.00 2.52
2008 2080 4.212847 CACCTCGGCTCATATCATTTTCTG 59.787 45.833 0.00 0.00 0.00 3.02
2009 2081 3.750130 CCTCGGCTCATATCATTTTCTGG 59.250 47.826 0.00 0.00 0.00 3.86
2010 2082 3.743521 TCGGCTCATATCATTTTCTGGG 58.256 45.455 0.00 0.00 0.00 4.45
2011 2083 3.136443 TCGGCTCATATCATTTTCTGGGT 59.864 43.478 0.00 0.00 0.00 4.51
2012 2084 4.346709 TCGGCTCATATCATTTTCTGGGTA 59.653 41.667 0.00 0.00 0.00 3.69
2013 2085 5.013079 TCGGCTCATATCATTTTCTGGGTAT 59.987 40.000 0.00 0.00 0.00 2.73
2014 2086 5.707298 CGGCTCATATCATTTTCTGGGTATT 59.293 40.000 0.00 0.00 0.00 1.89
2015 2087 6.128172 CGGCTCATATCATTTTCTGGGTATTC 60.128 42.308 0.00 0.00 0.00 1.75
2016 2088 6.151817 GGCTCATATCATTTTCTGGGTATTCC 59.848 42.308 0.00 0.00 0.00 3.01
2038 2110 4.662278 CCCCCTCTTTTATTTCTGTCACA 58.338 43.478 0.00 0.00 0.00 3.58
2039 2111 5.264395 CCCCCTCTTTTATTTCTGTCACAT 58.736 41.667 0.00 0.00 0.00 3.21
2040 2112 6.423182 CCCCCTCTTTTATTTCTGTCACATA 58.577 40.000 0.00 0.00 0.00 2.29
2041 2113 6.543831 CCCCCTCTTTTATTTCTGTCACATAG 59.456 42.308 0.00 0.00 0.00 2.23
2042 2114 6.543831 CCCCTCTTTTATTTCTGTCACATAGG 59.456 42.308 0.00 0.00 0.00 2.57
2043 2115 7.338710 CCCTCTTTTATTTCTGTCACATAGGA 58.661 38.462 0.00 0.00 0.00 2.94
2044 2116 7.281100 CCCTCTTTTATTTCTGTCACATAGGAC 59.719 40.741 0.00 0.00 38.29 3.85
2045 2117 7.824289 CCTCTTTTATTTCTGTCACATAGGACA 59.176 37.037 0.00 0.00 45.06 4.02
2046 2118 8.547967 TCTTTTATTTCTGTCACATAGGACAC 57.452 34.615 0.00 0.00 42.56 3.67
2047 2119 7.606456 TCTTTTATTTCTGTCACATAGGACACC 59.394 37.037 0.00 0.00 42.56 4.16
2048 2120 4.908601 ATTTCTGTCACATAGGACACCA 57.091 40.909 0.00 0.00 42.56 4.17
2049 2121 4.698201 TTTCTGTCACATAGGACACCAA 57.302 40.909 0.00 0.00 42.56 3.67
2050 2122 3.678056 TCTGTCACATAGGACACCAAC 57.322 47.619 0.00 0.00 42.56 3.77
2051 2123 2.301870 TCTGTCACATAGGACACCAACC 59.698 50.000 0.00 0.00 42.56 3.77
2052 2124 2.303022 CTGTCACATAGGACACCAACCT 59.697 50.000 0.00 0.00 42.56 3.50
2053 2125 3.512496 TGTCACATAGGACACCAACCTA 58.488 45.455 0.00 0.00 42.56 3.08
2468 2610 4.502105 TGAATTGCTGCTACATTAGGGA 57.498 40.909 0.00 0.00 0.00 4.20
2478 2620 7.013274 TGCTGCTACATTAGGGATAAATCAAAC 59.987 37.037 0.00 0.00 0.00 2.93
2621 2763 7.974504 TCTCCCAATTTATCCTATGAGGTAAC 58.025 38.462 0.00 0.00 36.53 2.50
2665 2807 1.338200 ACTGCTACCTTTCTCTTGCCG 60.338 52.381 0.00 0.00 0.00 5.69
3061 3204 5.237127 TGTGTAAGCAGAGATTGTTGTCAAG 59.763 40.000 0.00 0.00 36.97 3.02
3490 3633 4.009675 TGAGAGCTGAAACACAAAACACT 58.990 39.130 0.00 0.00 0.00 3.55
3573 3716 1.612395 GCCTCTCCCTCTCCAGTGTG 61.612 65.000 0.00 0.00 0.00 3.82
3923 4073 7.789273 TGTTTTCTATAAACTCGGTCAAACA 57.211 32.000 0.00 0.00 31.04 2.83
4010 4160 3.454375 AGTTGGCCTATACGATTCAACG 58.546 45.455 3.32 0.00 39.30 4.10
4082 4232 1.115467 GACGATCACTGGGACTGGAT 58.885 55.000 0.00 0.00 0.00 3.41
4132 4282 7.856894 GGTATGCACGTTTCTGTTAGTTTTTAA 59.143 33.333 0.00 0.00 0.00 1.52
4329 4508 7.197071 ACGACAAACATAGCTAACAAATTGA 57.803 32.000 0.00 0.00 0.00 2.57
4337 5268 7.298122 ACATAGCTAACAAATTGAACGACTTG 58.702 34.615 0.00 0.00 0.00 3.16
4660 5593 1.071314 ACCCCAGACATCCCAAACCA 61.071 55.000 0.00 0.00 0.00 3.67
5054 5987 8.037758 AGAAGTAACTATTGATGAAGTGGACTG 58.962 37.037 0.00 0.00 0.00 3.51
5171 6104 3.770666 AGTTCAACACGGATACATCTCG 58.229 45.455 0.00 0.00 0.00 4.04
5235 6168 3.664025 TTCTGCTGATGGCGACCGG 62.664 63.158 0.00 0.00 45.43 5.28
5391 6337 3.041946 ACCTTGGATGTAGGATCAGGTC 58.958 50.000 0.00 0.00 36.58 3.85
5450 6396 1.211212 TGTAGAGACTGCTACGGGCTA 59.789 52.381 4.43 0.00 42.84 3.93
5466 6412 4.200874 CGGGCTAATTTATGTGGGTAACA 58.799 43.478 0.00 0.00 44.79 2.41
5549 6499 5.047566 TGAATTGGTTGGATGGACGATAT 57.952 39.130 0.00 0.00 0.00 1.63
5569 6519 8.735315 ACGATATATGGTTTTGTGTCATTTTGA 58.265 29.630 0.00 0.00 0.00 2.69
5602 6552 5.128171 TGACATTAGTTTCGGCCTGTAGTAT 59.872 40.000 0.00 0.00 0.00 2.12
5625 6575 1.505898 CGTAACGCGTTGTAACATGC 58.494 50.000 33.40 8.83 35.54 4.06
5631 6581 1.724654 CGCGTTGTAACATGCCTTGAC 60.725 52.381 0.00 0.00 0.00 3.18
5665 6615 4.280929 TCAGAGGAAATGAACACGAGAGAA 59.719 41.667 0.00 0.00 0.00 2.87
5666 6616 4.387256 CAGAGGAAATGAACACGAGAGAAC 59.613 45.833 0.00 0.00 0.00 3.01
5667 6617 4.282195 AGAGGAAATGAACACGAGAGAACT 59.718 41.667 0.00 0.00 0.00 3.01
5668 6618 4.310769 AGGAAATGAACACGAGAGAACTG 58.689 43.478 0.00 0.00 0.00 3.16
5669 6619 3.433615 GGAAATGAACACGAGAGAACTGG 59.566 47.826 0.00 0.00 0.00 4.00
5670 6620 4.307432 GAAATGAACACGAGAGAACTGGA 58.693 43.478 0.00 0.00 0.00 3.86
5671 6621 4.543590 AATGAACACGAGAGAACTGGAT 57.456 40.909 0.00 0.00 0.00 3.41
5672 6622 3.303881 TGAACACGAGAGAACTGGATG 57.696 47.619 0.00 0.00 0.00 3.51
5690 6647 4.117685 GGATGTACGGTTTTATCTCGCTT 58.882 43.478 0.00 0.00 0.00 4.68
5811 6778 4.451774 GCAATTGACAAAGCAAATTGCCTA 59.548 37.500 15.04 0.00 46.52 3.93
5838 6805 5.793817 ACTTTTGCAAACAGGAGAAAAACT 58.206 33.333 12.39 0.00 0.00 2.66
5864 6831 5.716703 TGTCTCATCAACCTGTCTGATTAGA 59.283 40.000 0.00 0.00 33.29 2.10
5896 6863 2.554032 GGTGTGTCATTTGAAGTCCTGG 59.446 50.000 0.00 0.00 0.00 4.45
5900 6867 2.076863 GTCATTTGAAGTCCTGGGTCG 58.923 52.381 0.00 0.00 0.00 4.79
5918 6885 3.304794 GGTCGAAGGATATGAGAGTTCCG 60.305 52.174 0.00 0.00 34.61 4.30
5927 6894 2.032681 AGAGTTCCGGTGCAAGCC 59.967 61.111 0.00 0.00 0.00 4.35
5983 6950 4.283467 TGTGTTTGCTCTCTTTCCTAGCTA 59.717 41.667 0.00 0.00 37.16 3.32
6121 7088 6.925610 TTTCAGCATAGGTTAGCTAATGTG 57.074 37.500 9.88 4.55 39.50 3.21
6185 7152 0.600057 CCCTTGAGGTTGCTCTTTGC 59.400 55.000 0.00 0.00 43.25 3.68
6197 7164 5.008911 GGTTGCTCTTTGCCAATTTGATTTT 59.991 36.000 0.00 0.00 42.00 1.82
6224 7191 6.700520 GCATAGGTTAGCTAATGTAAACTCGT 59.299 38.462 9.88 0.00 30.00 4.18
6271 7238 1.228367 CAACAGCAGCCCTTGAGGT 60.228 57.895 0.00 0.00 38.26 3.85
6274 7241 2.856000 AGCAGCCCTTGAGGTGGT 60.856 61.111 0.00 0.00 40.86 4.16
6280 7247 1.843421 CCCTTGAGGTGGTGACCAA 59.157 57.895 5.57 0.00 45.98 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 170 4.552365 CCCATGCCTCCACGCGAT 62.552 66.667 15.93 0.00 0.00 4.58
327 335 1.583477 CTCGTCACTGCAGCTCTCA 59.417 57.895 15.27 0.00 0.00 3.27
453 463 1.153901 CGCCGTACCTCGTTGATGT 60.154 57.895 0.00 0.00 37.94 3.06
521 539 4.142071 CCAATCTGCTTGTAGTCTGCTCTA 60.142 45.833 0.00 0.00 32.61 2.43
531 549 7.432148 TTCTACCTTATCCAATCTGCTTGTA 57.568 36.000 0.00 0.00 32.61 2.41
536 554 6.258947 GTGTCTTTCTACCTTATCCAATCTGC 59.741 42.308 0.00 0.00 0.00 4.26
659 682 3.191791 GGCTTCGTAAAAATGCCACCTAA 59.808 43.478 0.00 0.00 42.79 2.69
698 721 2.750166 TCAATATCGGGCTTCGCAAAAA 59.250 40.909 0.00 0.00 39.05 1.94
725 748 4.589908 ACCTGAGAAAATCGGCTATTTGT 58.410 39.130 0.00 0.00 37.85 2.83
751 774 8.258708 GGAAGTTTGTTGATGTACTACCTAGAT 58.741 37.037 0.00 0.00 0.00 1.98
752 775 7.453752 AGGAAGTTTGTTGATGTACTACCTAGA 59.546 37.037 0.00 0.00 0.00 2.43
753 776 7.612677 AGGAAGTTTGTTGATGTACTACCTAG 58.387 38.462 0.00 0.00 0.00 3.02
754 777 7.549147 AGGAAGTTTGTTGATGTACTACCTA 57.451 36.000 0.00 0.00 0.00 3.08
755 778 6.435292 AGGAAGTTTGTTGATGTACTACCT 57.565 37.500 0.00 0.00 0.00 3.08
763 786 9.490379 GGTAGGTATATAGGAAGTTTGTTGATG 57.510 37.037 0.00 0.00 0.00 3.07
764 787 9.448587 AGGTAGGTATATAGGAAGTTTGTTGAT 57.551 33.333 0.00 0.00 0.00 2.57
765 788 8.849543 AGGTAGGTATATAGGAAGTTTGTTGA 57.150 34.615 0.00 0.00 0.00 3.18
1081 1149 1.300775 CCGCTAGCTGCATCTCCTG 60.301 63.158 13.93 0.00 43.06 3.86
1107 1175 2.771762 GGGAGGGCAGAGGCAGAT 60.772 66.667 0.00 0.00 43.71 2.90
1546 1614 9.764363 TTAAAACATCATATAGAACAGCTCGAT 57.236 29.630 0.00 0.00 0.00 3.59
1699 1768 0.664224 GAACGCGGGTCCAAAAAGAA 59.336 50.000 12.47 0.00 0.00 2.52
1700 1769 1.500512 CGAACGCGGGTCCAAAAAGA 61.501 55.000 12.47 0.00 0.00 2.52
1701 1770 1.082366 CGAACGCGGGTCCAAAAAG 60.082 57.895 12.47 0.00 0.00 2.27
1811 1882 6.371548 CCAAAGCAGATAACAAAGTAGCTACA 59.628 38.462 25.28 4.19 0.00 2.74
1991 2063 6.151817 GGAATACCCAGAAAATGATATGAGCC 59.848 42.308 0.00 0.00 34.14 4.70
1992 2064 7.150783 GGAATACCCAGAAAATGATATGAGC 57.849 40.000 0.00 0.00 34.14 4.26
2016 2088 4.662278 TGTGACAGAAATAAAAGAGGGGG 58.338 43.478 0.00 0.00 0.00 5.40
2017 2089 6.543831 CCTATGTGACAGAAATAAAAGAGGGG 59.456 42.308 0.00 0.00 0.00 4.79
2018 2090 7.281100 GTCCTATGTGACAGAAATAAAAGAGGG 59.719 40.741 0.00 0.00 35.29 4.30
2019 2091 7.824289 TGTCCTATGTGACAGAAATAAAAGAGG 59.176 37.037 0.00 0.00 40.22 3.69
2020 2092 8.660373 GTGTCCTATGTGACAGAAATAAAAGAG 58.340 37.037 0.00 0.00 45.40 2.85
2021 2093 7.606456 GGTGTCCTATGTGACAGAAATAAAAGA 59.394 37.037 0.00 0.00 45.40 2.52
2022 2094 7.390440 TGGTGTCCTATGTGACAGAAATAAAAG 59.610 37.037 0.00 0.00 45.40 2.27
2023 2095 7.227873 TGGTGTCCTATGTGACAGAAATAAAA 58.772 34.615 0.00 0.00 45.40 1.52
2024 2096 6.774673 TGGTGTCCTATGTGACAGAAATAAA 58.225 36.000 0.00 0.00 45.40 1.40
2025 2097 6.367374 TGGTGTCCTATGTGACAGAAATAA 57.633 37.500 0.00 0.00 45.40 1.40
2026 2098 6.170506 GTTGGTGTCCTATGTGACAGAAATA 58.829 40.000 0.00 0.00 45.40 1.40
2027 2099 4.908601 TGGTGTCCTATGTGACAGAAAT 57.091 40.909 0.00 0.00 45.40 2.17
2028 2100 4.385825 GTTGGTGTCCTATGTGACAGAAA 58.614 43.478 0.00 0.00 45.40 2.52
2029 2101 3.244422 GGTTGGTGTCCTATGTGACAGAA 60.244 47.826 0.00 0.00 45.40 3.02
2030 2102 2.301870 GGTTGGTGTCCTATGTGACAGA 59.698 50.000 0.00 0.00 45.40 3.41
2031 2103 2.303022 AGGTTGGTGTCCTATGTGACAG 59.697 50.000 0.00 0.00 45.40 3.51
2032 2104 2.334977 AGGTTGGTGTCCTATGTGACA 58.665 47.619 0.00 0.00 42.75 3.58
2033 2105 4.755266 ATAGGTTGGTGTCCTATGTGAC 57.245 45.455 4.02 0.00 43.90 3.67
2034 2106 5.772393 AAATAGGTTGGTGTCCTATGTGA 57.228 39.130 5.43 0.00 44.53 3.58
2035 2107 5.818136 CAAATAGGTTGGTGTCCTATGTG 57.182 43.478 7.48 7.48 44.53 3.21
2047 2119 2.340337 GCAAAGCTGCCAAATAGGTTG 58.660 47.619 0.00 0.00 43.26 3.77
2048 2120 2.749280 GCAAAGCTGCCAAATAGGTT 57.251 45.000 0.00 0.00 43.26 3.50
2468 2610 6.024552 ACATGGACGCAAAGTTTGATTTAT 57.975 33.333 19.82 3.80 0.00 1.40
2478 2620 2.419673 TGATTGCTACATGGACGCAAAG 59.580 45.455 18.12 0.00 45.46 2.77
2530 2672 4.191033 TGAACTAAAATTGCATGCCCAG 57.809 40.909 16.68 5.57 0.00 4.45
2613 2755 2.991190 GCGTGAGAATTTCGTTACCTCA 59.009 45.455 0.00 0.00 0.00 3.86
2621 2763 4.901814 AGAAATCATGCGTGAGAATTTCG 58.098 39.130 20.06 0.00 36.59 3.46
2665 2807 5.060662 TGCGATAACTATATCTGGACTGC 57.939 43.478 0.00 0.00 36.55 4.40
3061 3204 3.049912 CGTGGCTTTAACTTGCTTTTCC 58.950 45.455 0.00 0.00 0.00 3.13
3133 3276 8.127327 CCTTCTGACTTTGCATATTTACAGATG 58.873 37.037 0.00 0.00 34.07 2.90
3490 3633 2.169561 GGTGGCCCTTTTTCTTTTGTCA 59.830 45.455 0.00 0.00 0.00 3.58
3573 3716 1.202545 GGAGGGTGAAGAGATAACGCC 60.203 57.143 0.00 0.00 0.00 5.68
3923 4073 8.957466 GCTTTGTCCTAAGTCCAACTTTATAAT 58.043 33.333 0.00 0.00 39.51 1.28
4010 4160 6.127925 TGTCAATTTACTCACCATCTCAATGC 60.128 38.462 0.00 0.00 0.00 3.56
4082 4232 3.551846 TCCGTATCTGATGAGTGCTACA 58.448 45.455 0.00 0.00 0.00 2.74
4132 4282 8.585471 ATGAACTCATGATGATACAAGGTTTT 57.415 30.769 0.00 0.00 34.83 2.43
4295 4474 4.083802 GCTATGTTTGTCGTTCAGAAAGCT 60.084 41.667 0.00 0.00 0.00 3.74
4329 4508 4.995487 GTCTTAAATCACCTCCAAGTCGTT 59.005 41.667 0.00 0.00 0.00 3.85
4337 5268 3.700038 TCCTCGAGTCTTAAATCACCTCC 59.300 47.826 12.31 0.00 0.00 4.30
4435 5368 6.776603 TGCCATCAATTATTACATCCACATCA 59.223 34.615 0.00 0.00 0.00 3.07
4660 5593 4.781934 AGAAATTATAGCCGCTCCTGTTT 58.218 39.130 0.00 0.00 0.00 2.83
5054 5987 4.513318 GCATATCTCCTTTACTGACCTTGC 59.487 45.833 0.00 0.00 0.00 4.01
5171 6104 3.134458 GTGGTATCAATGCTAGGCTCAC 58.866 50.000 0.00 0.00 0.00 3.51
5235 6168 0.875059 CCCTCCTGCGAAGTTCAAAC 59.125 55.000 3.32 0.00 0.00 2.93
5370 6316 3.041946 GACCTGATCCTACATCCAAGGT 58.958 50.000 0.00 0.00 35.48 3.50
5416 6362 6.259608 GCAGTCTCTACAACAATGCTGATATT 59.740 38.462 0.00 0.00 0.00 1.28
5549 6499 9.829507 AAGAAATCAAAATGACACAAAACCATA 57.170 25.926 0.00 0.00 0.00 2.74
5569 6519 5.619981 GCCGAAACTAATGTCAGCAAGAAAT 60.620 40.000 0.00 0.00 0.00 2.17
5625 6575 4.153117 CCTCTGAATTCAAGTTCGTCAAGG 59.847 45.833 9.88 2.27 0.00 3.61
5631 6581 6.486253 TCATTTCCTCTGAATTCAAGTTCG 57.514 37.500 9.88 0.00 0.00 3.95
5665 6615 4.679662 CGAGATAAAACCGTACATCCAGT 58.320 43.478 0.00 0.00 0.00 4.00
5666 6616 3.489785 GCGAGATAAAACCGTACATCCAG 59.510 47.826 0.00 0.00 0.00 3.86
5667 6617 3.131577 AGCGAGATAAAACCGTACATCCA 59.868 43.478 0.00 0.00 0.00 3.41
5668 6618 3.714391 AGCGAGATAAAACCGTACATCC 58.286 45.455 0.00 0.00 0.00 3.51
5669 6619 6.204359 TCTAAGCGAGATAAAACCGTACATC 58.796 40.000 0.00 0.00 0.00 3.06
5670 6620 6.140303 TCTAAGCGAGATAAAACCGTACAT 57.860 37.500 0.00 0.00 0.00 2.29
5671 6621 5.565592 TCTAAGCGAGATAAAACCGTACA 57.434 39.130 0.00 0.00 0.00 2.90
5672 6622 6.204359 TCATCTAAGCGAGATAAAACCGTAC 58.796 40.000 4.11 0.00 43.52 3.67
5690 6647 3.370527 GGTTGTGCCTAAGCCTTCATCTA 60.371 47.826 0.00 0.00 38.69 1.98
5811 6778 6.959639 TTTCTCCTGTTTGCAAAAGTCTAT 57.040 33.333 14.67 0.00 0.00 1.98
5838 6805 6.550938 AATCAGACAGGTTGATGAGACATA 57.449 37.500 0.00 0.00 35.54 2.29
5874 6841 3.213506 CAGGACTTCAAATGACACACCA 58.786 45.455 0.00 0.00 0.00 4.17
5888 6855 2.544844 TATCCTTCGACCCAGGACTT 57.455 50.000 6.48 0.00 43.52 3.01
5896 6863 3.304794 CGGAACTCTCATATCCTTCGACC 60.305 52.174 0.00 0.00 0.00 4.79
5900 6867 3.800604 GCACCGGAACTCTCATATCCTTC 60.801 52.174 9.46 0.00 0.00 3.46
5918 6885 2.970974 GCTCTTGACGGCTTGCACC 61.971 63.158 0.00 0.00 0.00 5.01
5927 6894 4.321745 GTGCAACAATTAATGCTCTTGACG 59.678 41.667 13.79 0.00 42.97 4.35
5983 6950 4.853007 AGGAGCTCAAATTCATGCTAACT 58.147 39.130 17.19 0.00 35.76 2.24
6121 7088 1.202818 ACCCTCTCACAAGGCAAGTTC 60.203 52.381 0.00 0.00 34.88 3.01
6150 7117 5.508994 CCTCAAGGGTTGTTGTTGTAAATCC 60.509 44.000 0.00 0.00 0.00 3.01
6176 7143 8.224393 ATGCTAAAATCAAATTGGCAAAGAGCA 61.224 33.333 3.01 8.66 45.42 4.26
6185 7152 8.416329 AGCTAACCTATGCTAAAATCAAATTGG 58.584 33.333 0.00 0.00 37.81 3.16
6197 7164 8.080417 CGAGTTTACATTAGCTAACCTATGCTA 58.920 37.037 8.70 0.00 40.35 3.49
6271 7238 1.234821 GAAGCACGAATTGGTCACCA 58.765 50.000 0.00 0.00 33.68 4.17
6274 7241 1.606668 GTTGGAAGCACGAATTGGTCA 59.393 47.619 0.00 0.00 33.68 4.02


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

AutoCloner maintained by Alex Coulton.