Multiple sequence alignment - TraesCS3D01G500100

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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 TraesCS3D01G500100 chr3D 100.000 2456 0 0 1 2456 589573841 589571386 0.000000e+00 4536.0
1 TraesCS3D01G500100 chr3D 82.636 1123 119 37 643 1717 589418078 589416984 0.000000e+00 924.0
2 TraesCS3D01G500100 chr3D 85.428 748 83 16 991 1724 589432795 589432060 0.000000e+00 754.0
3 TraesCS3D01G500100 chr3D 90.000 500 44 1 991 1490 589493178 589492685 2.060000e-180 641.0
4 TraesCS3D01G500100 chr3D 88.605 509 49 4 991 1496 589505987 589505485 5.810000e-171 610.0
5 TraesCS3D01G500100 chr3D 87.949 390 34 9 548 931 589506397 589506015 4.820000e-122 448.0
6 TraesCS3D01G500100 chr3D 87.952 249 24 4 688 931 589426843 589426596 3.090000e-74 289.0
7 TraesCS3D01G500100 chr3D 81.088 386 36 19 549 931 589493549 589493198 8.650000e-70 274.0
8 TraesCS3D01G500100 chr3D 87.736 212 21 4 725 931 589433034 589432823 2.440000e-60 243.0
9 TraesCS3D01G500100 chr3D 86.224 196 19 4 1532 1723 589474903 589474712 3.200000e-49 206.0
10 TraesCS3D01G500100 chr3D 88.820 161 14 1 1563 1723 589504622 589504778 6.930000e-46 195.0
11 TraesCS3D01G500100 chr3D 91.736 121 10 0 1722 1842 250916112 250915992 4.200000e-38 169.0
12 TraesCS3D01G500100 chr3D 93.458 107 7 0 1733 1839 597748720 597748826 2.530000e-35 159.0
13 TraesCS3D01G500100 chr3D 94.444 36 1 1 2354 2388 216048866 216048831 1.000000e-03 54.7
14 TraesCS3D01G500100 chr3A 87.821 1404 116 18 991 2355 719354079 719352692 0.000000e+00 1594.0
15 TraesCS3D01G500100 chr3A 87.521 1218 63 26 552 1724 719361204 719360031 0.000000e+00 1325.0
16 TraesCS3D01G500100 chr3A 85.616 730 80 16 769 1490 719337537 719336825 0.000000e+00 743.0
17 TraesCS3D01G500100 chr3A 85.429 700 62 25 769 1456 719350280 719349609 0.000000e+00 691.0
18 TraesCS3D01G500100 chr3A 85.577 416 39 12 1960 2355 719360033 719359619 1.360000e-112 416.0
19 TraesCS3D01G500100 chr3A 85.385 390 23 16 548 931 719354460 719354099 8.290000e-100 374.0
20 TraesCS3D01G500100 chr3A 93.578 109 7 0 1722 1830 333327767 333327875 1.950000e-36 163.0
21 TraesCS3D01G500100 chr3A 97.260 73 2 0 2384 2456 358040423 358040351 9.220000e-25 124.0
22 TraesCS3D01G500100 chr3A 97.059 34 0 1 2355 2387 449248650 449248683 3.410000e-04 56.5
23 TraesCS3D01G500100 chr3B 87.295 1220 103 27 549 1724 788074016 788072805 0.000000e+00 1347.0
24 TraesCS3D01G500100 chr3B 83.283 1322 123 42 447 1724 787989717 787990984 0.000000e+00 1127.0
25 TraesCS3D01G500100 chr3B 86.192 956 92 22 991 1916 788058597 788057652 0.000000e+00 998.0
26 TraesCS3D01G500100 chr3B 84.197 772 73 24 991 1722 787472546 787473308 0.000000e+00 704.0
27 TraesCS3D01G500100 chr3B 79.215 688 111 18 3 672 787986077 787986750 1.340000e-122 449.0
28 TraesCS3D01G500100 chr3B 88.556 367 23 8 2008 2355 788057623 788057257 6.280000e-116 427.0
29 TraesCS3D01G500100 chr3B 84.404 436 48 8 1307 1724 787991337 787991770 6.320000e-111 411.0
30 TraesCS3D01G500100 chr3B 85.641 390 22 10 549 933 787472168 787472528 1.780000e-101 379.0
31 TraesCS3D01G500100 chr3B 81.034 290 52 3 1 290 445115886 445116172 6.830000e-56 228.0
32 TraesCS3D01G500100 chr3B 92.857 112 8 0 1731 1842 312149470 312149359 1.950000e-36 163.0
33 TraesCS3D01G500100 chr3B 82.353 170 20 6 1556 1722 788055125 788054963 3.290000e-29 139.0
34 TraesCS3D01G500100 chr6B 83.280 311 49 2 3 313 192356631 192356938 1.440000e-72 283.0
35 TraesCS3D01G500100 chr7D 84.173 278 42 2 36 313 568186615 568186340 4.030000e-68 268.0
36 TraesCS3D01G500100 chr7D 83.590 195 28 4 108 301 585377348 585377157 1.940000e-41 180.0
37 TraesCS3D01G500100 chr7A 82.812 256 41 2 31 286 699309984 699310236 2.460000e-55 226.0
38 TraesCS3D01G500100 chr7A 92.683 41 1 2 2355 2393 78898298 78898258 9.490000e-05 58.4
39 TraesCS3D01G500100 chr2D 94.643 112 6 0 1731 1842 24923759 24923648 9.030000e-40 174.0
40 TraesCS3D01G500100 chr2D 97.260 73 2 0 2384 2456 72972884 72972956 9.220000e-25 124.0
41 TraesCS3D01G500100 chr7B 91.129 124 11 0 1719 1842 301607407 301607284 4.200000e-38 169.0
42 TraesCS3D01G500100 chr4A 91.129 124 11 0 1841 1964 591452672 591452549 4.200000e-38 169.0
43 TraesCS3D01G500100 chr4A 91.129 124 11 0 1841 1964 592264760 592264883 4.200000e-38 169.0
44 TraesCS3D01G500100 chr4A 91.129 124 11 0 1841 1964 592602178 592602301 4.200000e-38 169.0
45 TraesCS3D01G500100 chr4A 91.129 124 11 0 1841 1964 592891298 592891421 4.200000e-38 169.0
46 TraesCS3D01G500100 chr4A 91.129 124 11 0 1841 1964 593162768 593162891 4.200000e-38 169.0
47 TraesCS3D01G500100 chr4A 97.260 73 2 0 2384 2456 183611261 183611333 9.220000e-25 124.0
48 TraesCS3D01G500100 chr4A 92.308 39 0 3 2355 2390 438201628 438201666 4.000000e-03 52.8
49 TraesCS3D01G500100 chr1D 90.909 121 11 0 1841 1961 206049296 206049176 1.950000e-36 163.0
50 TraesCS3D01G500100 chr1D 97.260 73 2 0 2384 2456 174035137 174035065 9.220000e-25 124.0
51 TraesCS3D01G500100 chr6D 92.661 109 8 0 1731 1839 15375610 15375718 9.090000e-35 158.0
52 TraesCS3D01G500100 chr6D 92.593 81 4 2 2377 2456 229200769 229200690 5.550000e-22 115.0
53 TraesCS3D01G500100 chr6D 100.000 28 0 0 2355 2382 113939020 113939047 4.000000e-03 52.8
54 TraesCS3D01G500100 chr2B 90.083 121 10 2 1841 1960 463344653 463344534 3.270000e-34 156.0
55 TraesCS3D01G500100 chr2A 85.484 124 15 2 167 289 750627740 750627861 2.560000e-25 126.0
56 TraesCS3D01G500100 chr4D 97.260 73 2 0 2384 2456 72965217 72965289 9.220000e-25 124.0
57 TraesCS3D01G500100 chr4D 97.297 74 1 1 2384 2456 216421090 216421017 9.220000e-25 124.0
58 TraesCS3D01G500100 chr4D 97.260 73 2 0 2384 2456 408523423 408523495 9.220000e-25 124.0
59 TraesCS3D01G500100 chr4D 97.260 73 2 0 2384 2456 408524939 408525011 9.220000e-25 124.0
60 TraesCS3D01G500100 chr4D 94.286 35 1 1 2355 2388 446769898 446769864 4.000000e-03 52.8
61 TraesCS3D01G500100 chr1A 97.260 73 2 0 2384 2456 505394265 505394193 9.220000e-25 124.0
62 TraesCS3D01G500100 chr1A 94.286 35 1 1 2355 2388 60686616 60686582 4.000000e-03 52.8
63 TraesCS3D01G500100 chr1B 92.683 41 1 2 2355 2393 538379833 538379873 9.490000e-05 58.4
64 TraesCS3D01G500100 chr1B 90.244 41 2 2 2355 2393 362013474 362013434 4.000000e-03 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 TraesCS3D01G500100 chr3D 589571386 589573841 2455 True 4536.000000 4536 100.000000 1 2456 1 chr3D.!!$R6 2455
1 TraesCS3D01G500100 chr3D 589416984 589418078 1094 True 924.000000 924 82.636000 643 1717 1 chr3D.!!$R3 1074
2 TraesCS3D01G500100 chr3D 589505485 589506397 912 True 529.000000 610 88.277000 548 1496 2 chr3D.!!$R9 948
3 TraesCS3D01G500100 chr3D 589432060 589433034 974 True 498.500000 754 86.582000 725 1724 2 chr3D.!!$R7 999
4 TraesCS3D01G500100 chr3D 589492685 589493549 864 True 457.500000 641 85.544000 549 1490 2 chr3D.!!$R8 941
5 TraesCS3D01G500100 chr3A 719349609 719354460 4851 True 886.333333 1594 86.211667 548 2355 3 chr3A.!!$R3 1807
6 TraesCS3D01G500100 chr3A 719359619 719361204 1585 True 870.500000 1325 86.549000 552 2355 2 chr3A.!!$R4 1803
7 TraesCS3D01G500100 chr3A 719336825 719337537 712 True 743.000000 743 85.616000 769 1490 1 chr3A.!!$R2 721
8 TraesCS3D01G500100 chr3B 788072805 788074016 1211 True 1347.000000 1347 87.295000 549 1724 1 chr3B.!!$R2 1175
9 TraesCS3D01G500100 chr3B 787986077 787991770 5693 False 662.333333 1127 82.300667 3 1724 3 chr3B.!!$F3 1721
10 TraesCS3D01G500100 chr3B 787472168 787473308 1140 False 541.500000 704 84.919000 549 1722 2 chr3B.!!$F2 1173
11 TraesCS3D01G500100 chr3B 788054963 788058597 3634 True 521.333333 998 85.700333 991 2355 3 chr3B.!!$R3 1364

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
174 176 0.107165 GGGGAAGACAAAGGGATCCG 60.107 60.0 5.45 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 5509 0.470456 ATATGCTTCGGTCCGGGGTA 60.47 55.0 12.29 4.58 0.0 3.69 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.458163 TAGGCTCCACGGAAGCGG 61.458 66.667 0.00 0.00 33.64 5.52
23 24 3.068691 CCACGGAAGCGGAGGAGA 61.069 66.667 0.00 0.00 34.48 3.71
27 28 3.471806 GGAAGCGGAGGAGACCCC 61.472 72.222 0.00 0.00 0.00 4.95
28 29 2.683933 GAAGCGGAGGAGACCCCA 60.684 66.667 0.00 0.00 37.41 4.96
29 30 2.685380 AAGCGGAGGAGACCCCAG 60.685 66.667 0.00 0.00 37.41 4.45
30 31 3.547787 AAGCGGAGGAGACCCCAGT 62.548 63.158 0.00 0.00 37.41 4.00
33 35 2.711922 CGGAGGAGACCCCAGTTCG 61.712 68.421 0.00 0.00 37.41 3.95
35 37 3.003763 AGGAGACCCCAGTTCGCC 61.004 66.667 0.00 0.00 37.41 5.54
38 40 1.985116 GAGACCCCAGTTCGCCTCT 60.985 63.158 0.00 0.00 0.00 3.69
56 58 0.676151 CTGGCTGAAGCACCCTCTTC 60.676 60.000 4.43 0.00 44.36 2.87
61 63 2.032681 AAGCACCCTCTTCGCCAC 59.967 61.111 0.00 0.00 0.00 5.01
65 67 1.079543 CACCCTCTTCGCCACTCTG 60.080 63.158 0.00 0.00 0.00 3.35
66 68 1.534235 ACCCTCTTCGCCACTCTGT 60.534 57.895 0.00 0.00 0.00 3.41
71 73 1.270826 CTCTTCGCCACTCTGTTGAGA 59.729 52.381 0.00 0.00 42.73 3.27
90 92 3.079131 GGCACAGCCGAACATATGA 57.921 52.632 10.38 0.00 39.62 2.15
97 99 5.559035 GCACAGCCGAACATATGAAAGATAC 60.559 44.000 10.38 0.00 0.00 2.24
98 100 4.745125 ACAGCCGAACATATGAAAGATACG 59.255 41.667 10.38 4.26 0.00 3.06
126 128 3.583806 GAATATGCATCTGGGACTCTCG 58.416 50.000 0.19 0.00 0.00 4.04
128 130 2.037620 ATGCATCTGGGACTCTCGGC 62.038 60.000 0.00 0.00 0.00 5.54
130 132 1.900351 CATCTGGGACTCTCGGCAA 59.100 57.895 0.00 0.00 0.00 4.52
132 134 0.755686 ATCTGGGACTCTCGGCAATC 59.244 55.000 0.00 0.00 0.00 2.67
133 135 1.144936 CTGGGACTCTCGGCAATCC 59.855 63.158 0.00 0.00 0.00 3.01
168 170 0.972471 GGCCATGGGGAAGACAAAGG 60.972 60.000 15.13 0.00 35.59 3.11
172 174 2.659428 CATGGGGAAGACAAAGGGATC 58.341 52.381 0.00 0.00 0.00 3.36
174 176 0.107165 GGGGAAGACAAAGGGATCCG 60.107 60.000 5.45 0.00 0.00 4.18
208 210 4.569966 CCGTAGGCTAGTGTAGTATATCCG 59.430 50.000 0.00 0.00 46.14 4.18
217 219 4.523173 AGTGTAGTATATCCGTGTCATGGG 59.477 45.833 11.31 0.00 0.00 4.00
218 220 3.257375 TGTAGTATATCCGTGTCATGGGC 59.743 47.826 11.31 0.00 0.00 5.36
222 224 1.324005 TATCCGTGTCATGGGCGTGA 61.324 55.000 11.31 0.00 0.00 4.35
235 237 3.470567 CGTGAAGCTCCGCGTGAC 61.471 66.667 4.92 0.00 35.55 3.67
257 259 5.649557 ACCGTACGTGCACATAGTTTTATA 58.350 37.500 18.64 0.00 0.00 0.98
259 261 6.418819 ACCGTACGTGCACATAGTTTTATATC 59.581 38.462 18.64 0.00 0.00 1.63
361 379 1.782569 CAACATTTGCGAGCAGTGTTG 59.217 47.619 27.27 27.27 42.22 3.33
367 385 3.044059 GCGAGCAGTGTTGGATGGC 62.044 63.158 0.00 0.00 0.00 4.40
368 386 2.743752 CGAGCAGTGTTGGATGGCG 61.744 63.158 0.00 0.00 0.00 5.69
387 405 2.750888 GCCGTCCGCATTCTTGTCC 61.751 63.158 0.00 0.00 37.47 4.02
389 407 0.744414 CCGTCCGCATTCTTGTCCAT 60.744 55.000 0.00 0.00 0.00 3.41
398 416 2.859165 TTCTTGTCCATGACTGGTCC 57.141 50.000 0.00 0.00 43.61 4.46
401 419 0.692476 TTGTCCATGACTGGTCCCTG 59.308 55.000 0.00 0.00 43.61 4.45
404 422 0.984230 TCCATGACTGGTCCCTGTTC 59.016 55.000 0.00 0.00 43.61 3.18
405 423 0.692476 CCATGACTGGTCCCTGTTCA 59.308 55.000 0.00 0.00 37.79 3.18
406 424 1.611673 CCATGACTGGTCCCTGTTCAC 60.612 57.143 0.00 0.00 37.79 3.18
413 431 1.364901 GTCCCTGTTCACGGACGAA 59.635 57.895 0.00 0.00 39.29 3.85
414 432 0.942884 GTCCCTGTTCACGGACGAAC 60.943 60.000 0.00 7.46 44.56 3.95
415 433 2.019951 CCCTGTTCACGGACGAACG 61.020 63.158 0.00 0.00 46.77 3.95
436 454 3.170585 GACGAAACTCGCGGGTCG 61.171 66.667 14.43 16.31 45.12 4.79
484 502 5.078949 ACATGACATGAATTGGAAGGAACA 58.921 37.500 22.19 0.00 0.00 3.18
486 504 4.468713 TGACATGAATTGGAAGGAACACA 58.531 39.130 0.00 0.00 0.00 3.72
487 505 4.278170 TGACATGAATTGGAAGGAACACAC 59.722 41.667 0.00 0.00 0.00 3.82
493 511 2.248431 GAAGGAACACACGCACGC 59.752 61.111 0.00 0.00 0.00 5.34
496 514 4.643385 GGAACACACGCACGCACG 62.643 66.667 0.00 0.00 39.50 5.34
537 555 0.605589 ACAGTTTCCCGGCTAAGCAC 60.606 55.000 0.00 0.00 0.00 4.40
541 559 0.887387 TTTCCCGGCTAAGCACACAC 60.887 55.000 0.00 0.00 0.00 3.82
546 564 3.711842 GCTAAGCACACACGCGCA 61.712 61.111 5.73 0.00 36.85 6.09
578 3792 0.165944 CGTCGCCGAAGCAGATTTTT 59.834 50.000 0.00 0.00 39.83 1.94
629 3848 0.757188 AGAACCATCTCGATCGGCCT 60.757 55.000 16.41 0.00 0.00 5.19
656 3876 1.833787 AAAGTCACGTACGCCCCCAT 61.834 55.000 16.72 0.00 0.00 4.00
657 3877 2.202837 GTCACGTACGCCCCCATC 60.203 66.667 16.72 0.00 0.00 3.51
809 4039 3.095163 CCTCCCTCCCTGCATGCT 61.095 66.667 20.33 0.00 0.00 3.79
893 4127 1.206072 CAGCAGCAACGCAGAACTC 59.794 57.895 0.00 0.00 0.00 3.01
944 4186 2.160417 GCAGGATCGACCAAAGACAAAG 59.840 50.000 6.78 0.00 42.04 2.77
971 4213 4.081406 TCTAGTTCACCGGTTAGTTAGCA 58.919 43.478 2.97 0.00 0.00 3.49
1282 4541 4.821589 CGCTGAGGGAGGCGTTCC 62.822 72.222 0.00 0.00 45.34 3.62
1480 5520 2.442643 TAGCCTTACCCCGGACCG 60.443 66.667 6.99 6.99 0.00 4.79
1610 5756 1.763968 TGGTCTCGATCGATTGTCCT 58.236 50.000 19.78 0.00 0.00 3.85
1628 5774 3.055094 GTCCTTGCTCTTGGACTTGGATA 60.055 47.826 5.05 0.00 46.65 2.59
1680 8706 5.443170 CGAAATGAATGGAAAACGTGAATGC 60.443 40.000 0.00 0.00 0.00 3.56
1692 8718 1.838112 GTGAATGCATGTGAAGGGGA 58.162 50.000 0.00 0.00 0.00 4.81
1728 8754 2.312390 GGCTCCAAACCCTTTACAACA 58.688 47.619 0.00 0.00 0.00 3.33
1745 8771 4.938080 ACAACACGTTTGGCAATATTTGA 58.062 34.783 0.00 0.00 0.00 2.69
1746 8772 4.981674 ACAACACGTTTGGCAATATTTGAG 59.018 37.500 0.00 0.00 0.00 3.02
1756 8782 6.024563 TGGCAATATTTGAGAAGGGGAATA 57.975 37.500 0.00 0.00 0.00 1.75
1772 8798 6.144625 AGGGGAATAAGAGTTTAGAGTAGGG 58.855 44.000 0.00 0.00 0.00 3.53
1783 8809 7.894364 AGAGTTTAGAGTAGGGAGTTGTATTGA 59.106 37.037 0.00 0.00 0.00 2.57
1790 8816 8.282982 AGAGTAGGGAGTTGTATTGAGATTAGA 58.717 37.037 0.00 0.00 0.00 2.10
1792 8818 7.839705 AGTAGGGAGTTGTATTGAGATTAGACA 59.160 37.037 0.00 0.00 0.00 3.41
1795 8821 6.708054 GGGAGTTGTATTGAGATTAGACATGG 59.292 42.308 0.00 0.00 0.00 3.66
1800 8826 7.616528 TGTATTGAGATTAGACATGGGATGA 57.383 36.000 0.00 0.00 0.00 2.92
1804 8830 5.211201 TGAGATTAGACATGGGATGAGTCA 58.789 41.667 0.00 0.00 34.80 3.41
1805 8831 5.842874 TGAGATTAGACATGGGATGAGTCAT 59.157 40.000 4.98 4.98 34.80 3.06
1819 8845 6.015095 GGGATGAGTCATTTTATTCCCAATCC 60.015 42.308 18.55 7.08 35.13 3.01
1821 8847 7.040132 GGATGAGTCATTTTATTCCCAATCCTC 60.040 40.741 7.16 0.00 0.00 3.71
1870 8896 7.499232 CCCGTGACTATTTCCTTATGAATTCTT 59.501 37.037 7.05 2.84 31.67 2.52
1919 8945 8.897872 TTTAAAGTCTCGTACCTCTTCAATTT 57.102 30.769 0.00 0.00 0.00 1.82
1920 8946 8.530269 TTAAAGTCTCGTACCTCTTCAATTTC 57.470 34.615 0.00 0.00 0.00 2.17
1921 8947 5.074584 AGTCTCGTACCTCTTCAATTTCC 57.925 43.478 0.00 0.00 0.00 3.13
1927 8953 5.045869 TCGTACCTCTTCAATTTCCATTCCT 60.046 40.000 0.00 0.00 0.00 3.36
1931 8957 5.222213 ACCTCTTCAATTTCCATTCCTCAGT 60.222 40.000 0.00 0.00 0.00 3.41
1982 9008 0.391263 GCCTTGTTCGGTAGTCAGGG 60.391 60.000 0.00 0.00 0.00 4.45
1984 9010 0.249398 CTTGTTCGGTAGTCAGGGGG 59.751 60.000 0.00 0.00 0.00 5.40
2003 9029 2.006415 CCAACCCCCTAGGCCATCA 61.006 63.158 5.01 0.00 40.58 3.07
2066 9092 3.858135 TCCATGTAGGGATTAGACCTCC 58.142 50.000 0.00 0.00 39.54 4.30
2091 9136 6.039717 CAGATCCCAATCATGTTCGGTTAAAT 59.960 38.462 0.00 0.00 34.07 1.40
2138 9183 1.003839 AGTTCGCATTGGGCTTCGA 60.004 52.632 0.00 0.00 41.67 3.71
2220 9265 1.030488 TGTTTCCCCGTGTTTTCGCA 61.030 50.000 0.00 0.00 0.00 5.10
2227 9272 0.309302 CCGTGTTTTCGCATGGTTGA 59.691 50.000 0.00 0.00 39.92 3.18
2228 9273 1.662876 CCGTGTTTTCGCATGGTTGAG 60.663 52.381 0.00 0.00 39.92 3.02
2235 9280 0.608035 TCGCATGGTTGAGGGGTTTC 60.608 55.000 0.00 0.00 0.00 2.78
2345 9390 1.679944 CGTGTGGATTGAGCAGGGAAT 60.680 52.381 0.00 0.00 0.00 3.01
2355 9400 1.743995 GCAGGGAATACCGCGTGTT 60.744 57.895 4.92 0.00 46.96 3.32
2356 9401 1.977594 GCAGGGAATACCGCGTGTTG 61.978 60.000 4.92 0.00 46.96 3.33
2357 9402 0.390603 CAGGGAATACCGCGTGTTGA 60.391 55.000 4.92 0.00 46.96 3.18
2358 9403 0.539986 AGGGAATACCGCGTGTTGAT 59.460 50.000 4.92 0.00 46.96 2.57
2360 9405 1.365699 GGAATACCGCGTGTTGATGT 58.634 50.000 4.92 0.00 0.00 3.06
2361 9406 1.326548 GGAATACCGCGTGTTGATGTC 59.673 52.381 4.92 0.00 0.00 3.06
2364 9409 2.267188 TACCGCGTGTTGATGTCTAC 57.733 50.000 4.92 0.00 0.00 2.59
2366 9411 1.814394 ACCGCGTGTTGATGTCTACTA 59.186 47.619 4.92 0.00 0.00 1.82
2367 9412 2.182825 CCGCGTGTTGATGTCTACTAC 58.817 52.381 4.92 0.00 0.00 2.73
2369 9414 1.582502 GCGTGTTGATGTCTACTACGC 59.417 52.381 18.93 18.93 40.74 4.42
2370 9415 2.858839 CGTGTTGATGTCTACTACGCA 58.141 47.619 0.00 0.00 0.00 5.24
2373 9418 4.326278 CGTGTTGATGTCTACTACGCAAAT 59.674 41.667 0.00 0.00 30.01 2.32
2375 9420 6.599437 GTGTTGATGTCTACTACGCAAATTT 58.401 36.000 0.00 0.00 30.01 1.82
2376 9421 7.411049 CGTGTTGATGTCTACTACGCAAATTTA 60.411 37.037 0.00 0.00 30.01 1.40
2379 9424 9.422196 GTTGATGTCTACTACGCAAATTTATTC 57.578 33.333 0.00 0.00 30.01 1.75
2380 9425 8.942338 TGATGTCTACTACGCAAATTTATTCT 57.058 30.769 0.00 0.00 0.00 2.40
2381 9426 9.378551 TGATGTCTACTACGCAAATTTATTCTT 57.621 29.630 0.00 0.00 0.00 2.52
2391 9436 8.880878 ACGCAAATTTATTCTTTAAACTTGGT 57.119 26.923 0.00 0.00 28.15 3.67
2392 9437 9.320352 ACGCAAATTTATTCTTTAAACTTGGTT 57.680 25.926 0.00 0.00 28.15 3.67
2403 9448 9.863845 TTCTTTAAACTTGGTTTTTAACTCCTG 57.136 29.630 0.99 0.00 37.01 3.86
2410 11451 7.948357 ACTTGGTTTTTAACTCCTGTAATTCC 58.052 34.615 0.00 0.00 0.00 3.01
2417 11458 9.589111 TTTTTAACTCCTGTAATTCCAAAACAC 57.411 29.630 0.00 0.00 0.00 3.32
2418 11459 5.432885 AACTCCTGTAATTCCAAAACACG 57.567 39.130 0.00 0.00 0.00 4.49
2419 11460 3.252458 ACTCCTGTAATTCCAAAACACGC 59.748 43.478 0.00 0.00 0.00 5.34
2421 11462 2.556622 CCTGTAATTCCAAAACACGCCT 59.443 45.455 0.00 0.00 0.00 5.52
2422 11463 3.005367 CCTGTAATTCCAAAACACGCCTT 59.995 43.478 0.00 0.00 0.00 4.35
2428 11469 6.779115 AATTCCAAAACACGCCTTAAAATC 57.221 33.333 0.00 0.00 0.00 2.17
2429 11470 4.920640 TCCAAAACACGCCTTAAAATCA 57.079 36.364 0.00 0.00 0.00 2.57
2435 11476 6.763303 AAACACGCCTTAAAATCATGAAAC 57.237 33.333 0.00 0.00 0.00 2.78
2436 11477 5.705609 ACACGCCTTAAAATCATGAAACT 57.294 34.783 0.00 0.00 0.00 2.66
2438 11479 5.920273 ACACGCCTTAAAATCATGAAACTTG 59.080 36.000 0.00 0.00 0.00 3.16
2439 11480 5.345741 CACGCCTTAAAATCATGAAACTTGG 59.654 40.000 0.00 0.00 0.00 3.61
2440 11481 4.327087 CGCCTTAAAATCATGAAACTTGGC 59.673 41.667 0.00 8.99 0.00 4.52
2441 11482 5.237048 GCCTTAAAATCATGAAACTTGGCA 58.763 37.500 17.94 0.00 35.94 4.92
2442 11483 5.876460 GCCTTAAAATCATGAAACTTGGCAT 59.124 36.000 17.94 0.00 35.94 4.40
2443 11484 6.183360 GCCTTAAAATCATGAAACTTGGCATG 60.183 38.462 17.94 0.00 42.41 4.06
2445 11486 4.895668 AAATCATGAAACTTGGCATGGT 57.104 36.364 0.00 0.00 41.60 3.55
2446 11487 3.880047 ATCATGAAACTTGGCATGGTG 57.120 42.857 0.00 0.00 41.60 4.17
2447 11488 2.596346 TCATGAAACTTGGCATGGTGT 58.404 42.857 5.31 0.00 41.60 4.16
2448 11489 2.557924 TCATGAAACTTGGCATGGTGTC 59.442 45.455 5.31 5.06 41.60 3.67
2450 11491 2.596346 TGAAACTTGGCATGGTGTCAT 58.404 42.857 9.10 0.00 29.04 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.458163 CCGCTTCCGTGGAGCCTA 61.458 66.667 0.00 0.00 43.70 3.93
17 18 2.579738 GCGAACTGGGGTCTCCTC 59.420 66.667 0.00 0.00 36.20 3.71
42 44 2.347490 GGCGAAGAGGGTGCTTCA 59.653 61.111 0.00 0.00 43.44 3.02
44 46 2.032681 GTGGCGAAGAGGGTGCTT 59.967 61.111 0.00 0.00 0.00 3.91
56 58 4.586618 CCTCTCAACAGAGTGGCG 57.413 61.111 1.20 0.00 44.49 5.69
61 63 0.673022 GGCTGTGCCTCTCAACAGAG 60.673 60.000 6.98 0.00 46.69 3.35
74 76 5.332581 CGTATCTTTCATATGTTCGGCTGTG 60.333 44.000 1.90 0.00 0.00 3.66
75 77 4.745125 CGTATCTTTCATATGTTCGGCTGT 59.255 41.667 1.90 0.00 0.00 4.40
78 80 3.432252 CCCGTATCTTTCATATGTTCGGC 59.568 47.826 1.90 0.00 35.09 5.54
81 83 4.995487 GTCCCCCGTATCTTTCATATGTTC 59.005 45.833 1.90 0.00 0.00 3.18
88 90 1.559368 TTCGTCCCCCGTATCTTTCA 58.441 50.000 0.00 0.00 37.94 2.69
90 92 3.556423 GCATATTCGTCCCCCGTATCTTT 60.556 47.826 0.00 0.00 37.94 2.52
97 99 0.321671 AGATGCATATTCGTCCCCCG 59.678 55.000 0.00 0.00 38.13 5.73
98 100 1.611673 CCAGATGCATATTCGTCCCCC 60.612 57.143 0.00 0.00 0.00 5.40
106 108 2.301296 CCGAGAGTCCCAGATGCATATT 59.699 50.000 0.00 0.00 0.00 1.28
109 111 2.037620 GCCGAGAGTCCCAGATGCAT 62.038 60.000 0.00 0.00 0.00 3.96
113 115 0.755686 GATTGCCGAGAGTCCCAGAT 59.244 55.000 0.00 0.00 0.00 2.90
116 118 3.309582 GGATTGCCGAGAGTCCCA 58.690 61.111 0.00 0.00 0.00 4.37
158 160 2.347731 GTGACGGATCCCTTTGTCTTC 58.652 52.381 15.76 7.77 32.64 2.87
185 187 4.569966 CGGATATACTACACTAGCCTACGG 59.430 50.000 0.00 0.00 0.00 4.02
196 198 3.257375 GCCCATGACACGGATATACTACA 59.743 47.826 0.00 0.00 0.00 2.74
202 204 0.249868 CACGCCCATGACACGGATAT 60.250 55.000 0.00 0.00 0.00 1.63
208 210 1.639298 GAGCTTCACGCCCATGACAC 61.639 60.000 0.00 0.00 40.39 3.67
231 233 1.265568 CTATGTGCACGTACGGTCAC 58.734 55.000 25.34 25.34 0.00 3.67
235 237 6.639686 AGATATAAAACTATGTGCACGTACGG 59.360 38.462 21.06 9.00 0.00 4.02
341 359 1.782569 CAACACTGCTCGCAAATGTTG 59.217 47.619 23.07 23.07 41.90 3.33
344 362 0.592637 TCCAACACTGCTCGCAAATG 59.407 50.000 0.00 0.00 0.00 2.32
345 363 1.200716 CATCCAACACTGCTCGCAAAT 59.799 47.619 0.00 0.00 0.00 2.32
347 365 1.236616 CCATCCAACACTGCTCGCAA 61.237 55.000 0.00 0.00 0.00 4.85
350 368 2.743752 CGCCATCCAACACTGCTCG 61.744 63.158 0.00 0.00 0.00 5.03
352 370 2.360350 CCGCCATCCAACACTGCT 60.360 61.111 0.00 0.00 0.00 4.24
368 386 2.746277 ACAAGAATGCGGACGGCC 60.746 61.111 0.00 0.00 42.61 6.13
372 390 1.398390 GTCATGGACAAGAATGCGGAC 59.602 52.381 0.00 0.00 32.09 4.79
373 391 1.278985 AGTCATGGACAAGAATGCGGA 59.721 47.619 0.00 0.00 34.60 5.54
387 405 1.813513 GTGAACAGGGACCAGTCATG 58.186 55.000 0.00 0.83 0.00 3.07
389 407 1.745890 CGTGAACAGGGACCAGTCA 59.254 57.895 0.00 0.00 0.00 3.41
398 416 2.654912 GCGTTCGTCCGTGAACAGG 61.655 63.158 11.41 0.00 46.77 4.00
401 419 3.759828 CCGCGTTCGTCCGTGAAC 61.760 66.667 4.92 3.19 43.76 3.18
432 450 1.632948 GCCACTCTTTAACGGCGACC 61.633 60.000 16.62 0.00 34.26 4.79
436 454 0.947180 TCGTGCCACTCTTTAACGGC 60.947 55.000 0.00 0.00 45.11 5.68
441 459 0.739462 CGCCATCGTGCCACTCTTTA 60.739 55.000 0.00 0.00 0.00 1.85
442 460 2.034879 CGCCATCGTGCCACTCTTT 61.035 57.895 0.00 0.00 0.00 2.52
444 462 3.381983 TCGCCATCGTGCCACTCT 61.382 61.111 0.00 0.00 36.96 3.24
445 463 3.188786 GTCGCCATCGTGCCACTC 61.189 66.667 0.00 0.00 36.96 3.51
509 527 3.056328 GGAAACTGTGGGCGCCTC 61.056 66.667 28.56 19.88 0.00 4.70
514 532 2.757980 TTAGCCGGGAAACTGTGGGC 62.758 60.000 2.18 0.00 44.07 5.36
517 535 0.605319 TGCTTAGCCGGGAAACTGTG 60.605 55.000 2.18 0.00 33.66 3.66
521 539 0.887387 TGTGTGCTTAGCCGGGAAAC 60.887 55.000 2.18 0.00 0.00 2.78
524 542 2.345991 GTGTGTGCTTAGCCGGGA 59.654 61.111 2.18 0.00 0.00 5.14
537 555 2.089433 AAAGTTCGAGTGCGCGTGTG 62.089 55.000 8.43 0.00 37.46 3.82
541 559 1.154654 GGAAAAGTTCGAGTGCGCG 60.155 57.895 0.00 0.00 37.46 6.86
546 564 0.942884 GGCGACGGAAAAGTTCGAGT 60.943 55.000 0.00 0.00 0.00 4.18
629 3848 1.210870 GTACGTGACTTTGGCGTGAA 58.789 50.000 0.00 0.00 39.31 3.18
809 4039 1.811558 GCGCTCCATGGAAGCTTCATA 60.812 52.381 27.02 15.93 0.00 2.15
839 4070 1.317611 GCGCGTGTGCATATATACTCG 59.682 52.381 8.43 5.96 42.97 4.18
888 4119 3.601443 TCCTCTGCTTTGCTAGAGTTC 57.399 47.619 0.00 0.00 38.98 3.01
893 4127 3.894427 TCCTAGATCCTCTGCTTTGCTAG 59.106 47.826 0.00 0.00 0.00 3.42
944 4186 0.243095 AACCGGTGAACTAGACGCTC 59.757 55.000 8.52 0.00 0.00 5.03
989 4231 1.212751 GCAACCATTCTTGCCGGAC 59.787 57.895 5.05 0.00 40.68 4.79
1282 4541 2.613977 GCCCTTCCATCTCATACATCCG 60.614 54.545 0.00 0.00 0.00 4.18
1425 5465 4.805219 TCATGATCTTGAACTCGTCGAAA 58.195 39.130 8.76 0.00 0.00 3.46
1469 5509 0.470456 ATATGCTTCGGTCCGGGGTA 60.470 55.000 12.29 4.58 0.00 3.69
1480 5520 3.406764 CACTGAAGGGGCTATATGCTTC 58.593 50.000 0.00 0.00 42.39 3.86
1499 5612 8.712285 ATCAAATGAATGAATGAATGAACCAC 57.288 30.769 0.00 0.00 32.06 4.16
1501 5614 9.158233 ACAATCAAATGAATGAATGAATGAACC 57.842 29.630 5.52 0.00 34.53 3.62
1540 5657 7.536964 TGTGCGTCATCATTACAAATTTTGTAG 59.463 33.333 18.56 10.78 45.92 2.74
1561 5691 6.588348 TTCACATAGATCAATTACTGTGCG 57.412 37.500 0.00 0.00 35.22 5.34
1610 5756 3.307691 CCACTATCCAAGTCCAAGAGCAA 60.308 47.826 0.00 0.00 35.76 3.91
1621 5767 3.430929 CCTCGAGAAACCCACTATCCAAG 60.431 52.174 15.71 0.00 0.00 3.61
1628 5774 2.637872 TGAATTCCTCGAGAAACCCACT 59.362 45.455 15.71 0.00 38.21 4.00
1680 8706 3.012518 GACAAGTCATCCCCTTCACATG 58.987 50.000 0.00 0.00 0.00 3.21
1728 8754 4.082245 CCCTTCTCAAATATTGCCAAACGT 60.082 41.667 0.00 0.00 0.00 3.99
1745 8771 7.565768 CCTACTCTAAACTCTTATTCCCCTTCT 59.434 40.741 0.00 0.00 0.00 2.85
1746 8772 7.202020 CCCTACTCTAAACTCTTATTCCCCTTC 60.202 44.444 0.00 0.00 0.00 3.46
1756 8782 8.532819 CAATACAACTCCCTACTCTAAACTCTT 58.467 37.037 0.00 0.00 0.00 2.85
1772 8798 7.500992 TCCCATGTCTAATCTCAATACAACTC 58.499 38.462 0.00 0.00 0.00 3.01
1783 8809 6.760440 AATGACTCATCCCATGTCTAATCT 57.240 37.500 0.00 0.00 0.00 2.40
1790 8816 5.835280 GGGAATAAAATGACTCATCCCATGT 59.165 40.000 7.91 0.00 43.65 3.21
1795 8821 6.779539 AGGATTGGGAATAAAATGACTCATCC 59.220 38.462 0.00 0.00 0.00 3.51
1800 8826 6.735556 ACAGAGGATTGGGAATAAAATGACT 58.264 36.000 0.00 0.00 0.00 3.41
1804 8830 6.352137 GCCAAACAGAGGATTGGGAATAAAAT 60.352 38.462 6.67 0.00 44.66 1.82
1805 8831 5.046663 GCCAAACAGAGGATTGGGAATAAAA 60.047 40.000 6.67 0.00 44.66 1.52
1819 8845 0.647410 CTATCGTGCGCCAAACAGAG 59.353 55.000 4.18 0.00 0.00 3.35
1821 8847 1.635844 TACTATCGTGCGCCAAACAG 58.364 50.000 4.18 0.00 0.00 3.16
1839 8865 7.124599 TTCATAAGGAAATAGTCACGGGACTTA 59.875 37.037 28.01 10.75 41.21 2.24
1856 8882 7.705912 TGGAGGGATTAAGAATTCATAAGGA 57.294 36.000 8.44 0.00 0.00 3.36
1870 8896 6.395780 TCTATTGTTTGGTTGGAGGGATTA 57.604 37.500 0.00 0.00 0.00 1.75
1878 8904 9.626045 GAGACTTTAAATCTATTGTTTGGTTGG 57.374 33.333 0.00 0.00 0.00 3.77
1919 8945 5.132144 GGGGTAATTAGAACTGAGGAATGGA 59.868 44.000 0.00 0.00 0.00 3.41
1920 8946 5.377478 GGGGTAATTAGAACTGAGGAATGG 58.623 45.833 0.00 0.00 0.00 3.16
1921 8947 5.104109 TGGGGGTAATTAGAACTGAGGAATG 60.104 44.000 0.00 0.00 0.00 2.67
1927 8953 3.917629 TGGTTGGGGGTAATTAGAACTGA 59.082 43.478 0.00 0.00 0.00 3.41
1931 8957 4.833938 GTGTTTGGTTGGGGGTAATTAGAA 59.166 41.667 0.00 0.00 0.00 2.10
1984 9010 3.429580 ATGGCCTAGGGGGTTGGC 61.430 66.667 11.72 0.00 45.42 4.52
2032 9058 2.514458 ACATGGATTGGTTGAGGGAC 57.486 50.000 0.00 0.00 0.00 4.46
2060 9086 2.441001 ACATGATTGGGATCTGGAGGTC 59.559 50.000 0.00 0.00 33.28 3.85
2066 9092 2.923121 ACCGAACATGATTGGGATCTG 58.077 47.619 13.49 0.00 33.28 2.90
2091 9136 2.365635 GCTACCTGCCAGGAGGGA 60.366 66.667 19.90 0.00 37.67 4.20
2109 9154 3.044305 GCGAACTCGGCAGCAGTT 61.044 61.111 0.69 0.00 40.23 3.16
2110 9155 3.596066 ATGCGAACTCGGCAGCAGT 62.596 57.895 0.69 0.00 43.20 4.40
2115 9160 2.745884 CCCAATGCGAACTCGGCA 60.746 61.111 0.69 0.36 40.23 5.69
2145 9190 4.586618 CCTGCAGGTGAACTCTCG 57.413 61.111 25.53 0.00 0.00 4.04
2220 9265 0.481128 AACCGAAACCCCTCAACCAT 59.519 50.000 0.00 0.00 0.00 3.55
2227 9272 2.086194 TTCCCCAACCGAAACCCCT 61.086 57.895 0.00 0.00 0.00 4.79
2228 9273 1.904865 GTTCCCCAACCGAAACCCC 60.905 63.158 0.00 0.00 0.00 4.95
2318 9363 0.673644 CTCAATCCACACGGGTCCAC 60.674 60.000 0.00 0.00 38.11 4.02
2345 9390 1.814394 AGTAGACATCAACACGCGGTA 59.186 47.619 12.47 0.00 0.00 4.02
2355 9400 8.942338 AGAATAAATTTGCGTAGTAGACATCA 57.058 30.769 0.00 0.00 0.00 3.07
2366 9411 8.880878 ACCAAGTTTAAAGAATAAATTTGCGT 57.119 26.923 0.00 7.21 34.72 5.24
2383 9428 9.811995 GAATTACAGGAGTTAAAAACCAAGTTT 57.188 29.630 0.00 0.00 37.34 2.66
2384 9429 8.418662 GGAATTACAGGAGTTAAAAACCAAGTT 58.581 33.333 0.00 0.00 0.00 2.66
2386 9431 7.947282 TGGAATTACAGGAGTTAAAAACCAAG 58.053 34.615 0.00 0.00 0.00 3.61
2387 9432 7.899648 TGGAATTACAGGAGTTAAAAACCAA 57.100 32.000 0.00 0.00 0.00 3.67
2388 9433 7.899648 TTGGAATTACAGGAGTTAAAAACCA 57.100 32.000 0.00 0.00 0.00 3.67
2389 9434 9.037737 GTTTTGGAATTACAGGAGTTAAAAACC 57.962 33.333 0.00 0.00 31.09 3.27
2390 9435 9.589111 TGTTTTGGAATTACAGGAGTTAAAAAC 57.411 29.630 4.18 4.18 35.44 2.43
2391 9436 9.589111 GTGTTTTGGAATTACAGGAGTTAAAAA 57.411 29.630 0.00 0.00 0.00 1.94
2392 9437 7.916450 CGTGTTTTGGAATTACAGGAGTTAAAA 59.084 33.333 0.00 0.00 31.29 1.52
2393 9438 7.419204 CGTGTTTTGGAATTACAGGAGTTAAA 58.581 34.615 0.00 0.00 31.29 1.52
2395 9440 5.049267 GCGTGTTTTGGAATTACAGGAGTTA 60.049 40.000 0.00 0.00 31.29 2.24
2396 9441 4.261447 GCGTGTTTTGGAATTACAGGAGTT 60.261 41.667 0.00 0.00 31.29 3.01
2397 9442 3.252458 GCGTGTTTTGGAATTACAGGAGT 59.748 43.478 0.00 0.00 31.29 3.85
2398 9443 3.365969 GGCGTGTTTTGGAATTACAGGAG 60.366 47.826 0.00 0.00 31.29 3.69
2399 9444 2.554893 GGCGTGTTTTGGAATTACAGGA 59.445 45.455 0.00 0.00 31.29 3.86
2400 9445 2.556622 AGGCGTGTTTTGGAATTACAGG 59.443 45.455 0.00 0.00 0.00 4.00
2401 9446 3.915437 AGGCGTGTTTTGGAATTACAG 57.085 42.857 0.00 0.00 0.00 2.74
2402 9447 5.769484 TTAAGGCGTGTTTTGGAATTACA 57.231 34.783 0.00 0.00 0.00 2.41
2403 9448 7.382759 TGATTTTAAGGCGTGTTTTGGAATTAC 59.617 33.333 0.00 0.00 0.00 1.89
2410 11451 6.761731 TTCATGATTTTAAGGCGTGTTTTG 57.238 33.333 0.00 0.00 0.00 2.44
2417 11458 4.327087 GCCAAGTTTCATGATTTTAAGGCG 59.673 41.667 0.00 0.00 0.00 5.52
2418 11459 5.237048 TGCCAAGTTTCATGATTTTAAGGC 58.763 37.500 14.85 14.85 37.75 4.35
2419 11460 6.314400 CCATGCCAAGTTTCATGATTTTAAGG 59.686 38.462 13.66 0.00 41.82 2.69
2421 11462 6.649973 CACCATGCCAAGTTTCATGATTTTAA 59.350 34.615 13.66 0.00 41.82 1.52
2422 11463 6.164876 CACCATGCCAAGTTTCATGATTTTA 58.835 36.000 13.66 0.00 41.82 1.52
2428 11469 2.296752 TGACACCATGCCAAGTTTCATG 59.703 45.455 7.55 7.55 39.67 3.07
2429 11470 2.596346 TGACACCATGCCAAGTTTCAT 58.404 42.857 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.