Multiple sequence alignment - TraesCS3A01G029500

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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 TraesCS3A01G029500 chr3A 100.000 3085 0 0 1 3085 15602670 15605754 0.000000e+00 5698.0
1 TraesCS3A01G029500 chr3A 81.268 1025 149 27 998 1991 15695303 15694291 0.000000e+00 789.0
2 TraesCS3A01G029500 chr3A 80.948 1034 145 33 998 1991 17258528 17257507 0.000000e+00 771.0
3 TraesCS3A01G029500 chr3A 79.474 1179 161 58 969 2094 15780862 15779712 0.000000e+00 761.0
4 TraesCS3A01G029500 chrUn 85.619 2246 145 73 972 3085 35795027 35797226 0.000000e+00 2194.0
5 TraesCS3A01G029500 chrUn 86.738 1493 80 49 923 2350 35203147 35204586 0.000000e+00 1552.0
6 TraesCS3A01G029500 chrUn 80.260 1155 170 38 969 2082 35452401 35451264 0.000000e+00 817.0
7 TraesCS3A01G029500 chrUn 81.749 789 89 17 3 751 35793659 35794432 2.630000e-170 608.0
8 TraesCS3A01G029500 chrUn 91.232 422 29 6 1679 2100 305025109 305025522 4.460000e-158 568.0
9 TraesCS3A01G029500 chrUn 87.293 362 31 8 2732 3085 35204629 35204983 1.720000e-107 399.0
10 TraesCS3A01G029500 chrUn 85.279 394 19 18 2005 2384 35209521 35209889 1.350000e-98 370.0
11 TraesCS3A01G029500 chrUn 82.294 401 31 14 440 809 35202287 35202678 8.310000e-81 311.0
12 TraesCS3A01G029500 chrUn 82.294 401 31 14 440 809 236915035 236914644 8.310000e-81 311.0
13 TraesCS3A01G029500 chrUn 90.000 210 8 6 923 1119 236914175 236913966 3.050000e-65 259.0
14 TraesCS3A01G029500 chrUn 87.719 228 14 5 2162 2384 305025543 305025761 1.420000e-63 254.0
15 TraesCS3A01G029500 chr3D 89.555 1551 74 40 923 2422 5681466 5679953 0.000000e+00 1886.0
16 TraesCS3A01G029500 chr3D 83.672 1133 125 28 969 2071 9948486 9947384 0.000000e+00 1013.0
17 TraesCS3A01G029500 chr3D 82.772 801 94 12 3 771 5682719 5681931 0.000000e+00 675.0
18 TraesCS3A01G029500 chr3D 82.048 830 91 26 3 797 9949390 9948584 0.000000e+00 654.0
19 TraesCS3A01G029500 chr3D 82.143 756 111 17 1342 2094 5609495 5610229 7.260000e-176 627.0
20 TraesCS3A01G029500 chr3D 87.192 406 30 10 2542 2927 5679754 5679351 2.820000e-120 442.0
21 TraesCS3A01G029500 chr3D 94.330 194 7 4 2229 2421 9880761 9880571 8.370000e-76 294.0
22 TraesCS3A01G029500 chr3D 92.268 194 11 3 2229 2421 9947254 9947064 3.920000e-69 272.0
23 TraesCS3A01G029500 chr3D 93.567 171 6 4 2919 3085 5678923 5678754 1.840000e-62 250.0
24 TraesCS3A01G029500 chr3D 82.310 277 31 11 998 1259 5609120 5609393 1.110000e-54 224.0
25 TraesCS3A01G029500 chr3D 84.795 171 22 4 2909 3078 9880397 9880230 5.290000e-38 169.0
26 TraesCS3A01G029500 chr3D 78.723 141 11 9 2420 2545 5679913 5679777 3.300000e-10 76.8
27 TraesCS3A01G029500 chr3D 100.000 37 0 0 2509 2545 9880451 9880415 5.520000e-08 69.4
28 TraesCS3A01G029500 chr3B 88.266 1534 75 47 929 2384 12181821 12180315 0.000000e+00 1738.0
29 TraesCS3A01G029500 chr3B 90.064 1087 69 17 1319 2393 27994405 27995464 0.000000e+00 1373.0
30 TraesCS3A01G029500 chr3B 81.016 1496 182 47 969 2421 14223579 14222143 0.000000e+00 1096.0
31 TraesCS3A01G029500 chr3B 80.375 1172 162 44 969 2093 12401301 12400151 0.000000e+00 828.0
32 TraesCS3A01G029500 chr3B 80.488 1148 168 40 969 2082 28082525 28081400 0.000000e+00 828.0
33 TraesCS3A01G029500 chr3B 81.205 830 106 18 3 797 13995182 13994368 9.390000e-175 623.0
34 TraesCS3A01G029500 chr3B 81.205 830 104 20 3 797 14066810 14065998 3.380000e-174 621.0
35 TraesCS3A01G029500 chr3B 86.176 557 53 14 2542 3085 12180106 12179561 5.730000e-162 580.0
36 TraesCS3A01G029500 chr3B 80.288 832 109 24 3 797 14224504 14223691 7.420000e-161 577.0
37 TraesCS3A01G029500 chr3B 83.333 582 52 15 2508 3078 27995561 27996108 2.140000e-136 496.0
38 TraesCS3A01G029500 chr3B 89.014 355 22 7 923 1260 27993947 27994301 1.020000e-114 424.0
39 TraesCS3A01G029500 chr3B 83.721 387 33 14 440 812 12184178 12183808 3.810000e-89 339.0
40 TraesCS3A01G029500 chr3B 78.147 572 73 24 266 797 14106549 14105990 1.790000e-82 316.0
41 TraesCS3A01G029500 chr3B 89.691 194 16 3 2229 2421 14104649 14104459 8.550000e-61 244.0
42 TraesCS3A01G029500 chr3B 84.713 157 20 3 2909 3065 14110959 14110807 1.480000e-33 154.0
43 TraesCS3A01G029500 chr3B 82.609 138 9 3 2419 2545 12180262 12180129 1.170000e-19 108.0
44 TraesCS3A01G029500 chr2A 80.663 181 30 4 2909 3085 19661729 19661550 5.370000e-28 135.0
45 TraesCS3A01G029500 chr1A 95.238 84 4 0 764 847 527736766 527736683 1.930000e-27 134.0
46 TraesCS3A01G029500 chr2D 95.455 44 1 1 2370 2413 106237711 106237753 5.520000e-08 69.4


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 TraesCS3A01G029500 chr3A 15602670 15605754 3084 False 5698.000000 5698 100.000000 1 3085 1 chr3A.!!$F1 3084
1 TraesCS3A01G029500 chr3A 15694291 15695303 1012 True 789.000000 789 81.268000 998 1991 1 chr3A.!!$R1 993
2 TraesCS3A01G029500 chr3A 17257507 17258528 1021 True 771.000000 771 80.948000 998 1991 1 chr3A.!!$R3 993
3 TraesCS3A01G029500 chr3A 15779712 15780862 1150 True 761.000000 761 79.474000 969 2094 1 chr3A.!!$R2 1125
4 TraesCS3A01G029500 chrUn 35793659 35797226 3567 False 1401.000000 2194 83.684000 3 3085 2 chrUn.!!$F3 3082
5 TraesCS3A01G029500 chrUn 35451264 35452401 1137 True 817.000000 817 80.260000 969 2082 1 chrUn.!!$R1 1113
6 TraesCS3A01G029500 chrUn 35202287 35204983 2696 False 754.000000 1552 85.441667 440 3085 3 chrUn.!!$F2 2645
7 TraesCS3A01G029500 chrUn 305025109 305025761 652 False 411.000000 568 89.475500 1679 2384 2 chrUn.!!$F4 705
8 TraesCS3A01G029500 chrUn 236913966 236915035 1069 True 285.000000 311 86.147000 440 1119 2 chrUn.!!$R2 679
9 TraesCS3A01G029500 chr3D 5678754 5682719 3965 True 665.960000 1886 86.361800 3 3085 5 chr3D.!!$R1 3082
10 TraesCS3A01G029500 chr3D 9947064 9949390 2326 True 646.333333 1013 85.996000 3 2421 3 chr3D.!!$R3 2418
11 TraesCS3A01G029500 chr3D 5609120 5610229 1109 False 425.500000 627 82.226500 998 2094 2 chr3D.!!$F1 1096
12 TraesCS3A01G029500 chr3B 14222143 14224504 2361 True 836.500000 1096 80.652000 3 2421 2 chr3B.!!$R8 2418
13 TraesCS3A01G029500 chr3B 12400151 12401301 1150 True 828.000000 828 80.375000 969 2093 1 chr3B.!!$R1 1124
14 TraesCS3A01G029500 chr3B 28081400 28082525 1125 True 828.000000 828 80.488000 969 2082 1 chr3B.!!$R5 1113
15 TraesCS3A01G029500 chr3B 27993947 27996108 2161 False 764.333333 1373 87.470333 923 3078 3 chr3B.!!$F1 2155
16 TraesCS3A01G029500 chr3B 12179561 12184178 4617 True 691.250000 1738 85.193000 440 3085 4 chr3B.!!$R6 2645
17 TraesCS3A01G029500 chr3B 13994368 13995182 814 True 623.000000 623 81.205000 3 797 1 chr3B.!!$R2 794
18 TraesCS3A01G029500 chr3B 14065998 14066810 812 True 621.000000 621 81.205000 3 797 1 chr3B.!!$R3 794
19 TraesCS3A01G029500 chr3B 14104459 14106549 2090 True 280.000000 316 83.919000 266 2421 2 chr3B.!!$R7 2155

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
540 569 0.523966 CCACGTGTTTGTTGGTGTGT 59.476 50.0 15.65 0.0 0.0 3.72 F
931 2994 1.048601 TGGAACAGTGTGGACCTCTC 58.951 55.0 0.00 0.0 0.0 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 4290 0.459899 AGCTTGTCGATGCGGATGTA 59.540 50.0 0.0 0.0 0.00 2.29 R
2102 4380 1.580845 AACTGCCTTGAGTGCATCGC 61.581 55.0 0.0 0.0 38.22 4.58 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
78 80 3.159472 TGTTCAAGCCTTTCTCATGCAT 58.841 40.909 0.00 0.00 0.00 3.96
101 103 3.552890 CGATGCGAGGATGATCTTGGTTA 60.553 47.826 0.00 0.00 0.00 2.85
136 140 6.334102 GGTTATCCACCTGTGTCTCTATAG 57.666 45.833 0.00 0.00 43.29 1.31
143 147 3.300388 CCTGTGTCTCTATAGCCTCCAA 58.700 50.000 0.00 0.00 0.00 3.53
153 157 2.447408 TAGCCTCCAACTACGGATGA 57.553 50.000 0.00 0.00 33.56 2.92
170 174 4.576873 CGGATGACTGCTTAGAAGTCTCTA 59.423 45.833 19.98 1.83 43.69 2.43
173 177 6.320164 GGATGACTGCTTAGAAGTCTCTAGAA 59.680 42.308 19.98 0.39 43.69 2.10
218 227 2.880268 CCGATGGATTGCTCATTGCTTA 59.120 45.455 0.00 0.00 43.37 3.09
226 235 5.221382 GGATTGCTCATTGCTTATTGATGGT 60.221 40.000 0.00 0.00 43.37 3.55
241 250 4.149511 TGATGGTATCTGCCGAATCAAA 57.850 40.909 0.00 0.00 0.00 2.69
260 269 5.974108 TCAAAGGGTTATTTCTCCTACTCG 58.026 41.667 0.00 0.00 0.00 4.18
261 270 4.403585 AAGGGTTATTTCTCCTACTCGC 57.596 45.455 0.00 0.00 0.00 5.03
296 305 4.927978 ATCAACATTTTTGTTGTCGGGA 57.072 36.364 16.02 0.47 46.55 5.14
316 325 3.519913 GGAGTCTCCAAAATCCAGTACCT 59.480 47.826 14.46 0.00 36.28 3.08
334 344 3.265489 ACCTTATTCCAGGGGTCTTTCA 58.735 45.455 0.00 0.00 38.42 2.69
350 361 3.582647 TCTTTCAGAGGCTTGTGGTCATA 59.417 43.478 0.00 0.00 0.00 2.15
380 391 3.721868 GCTGGTGGCAGGTAGGTA 58.278 61.111 0.00 0.00 41.35 3.08
381 392 1.522569 GCTGGTGGCAGGTAGGTAG 59.477 63.158 0.00 0.00 41.35 3.18
390 402 1.339151 GCAGGTAGGTAGCCCATATGC 60.339 57.143 0.00 0.00 0.00 3.14
392 404 1.132527 AGGTAGGTAGCCCATATGCCA 60.133 52.381 0.00 0.00 0.00 4.92
431 443 2.045340 GGGAACGGTGGGATGTGG 60.045 66.667 0.00 0.00 0.00 4.17
496 508 9.439500 TCCTTTGTACTATTTGGTTACATGTAC 57.561 33.333 4.68 1.11 0.00 2.90
540 569 0.523966 CCACGTGTTTGTTGGTGTGT 59.476 50.000 15.65 0.00 0.00 3.72
544 573 2.246789 CGTGTTTGTTGGTGTGTTGTC 58.753 47.619 0.00 0.00 0.00 3.18
545 574 2.350868 CGTGTTTGTTGGTGTGTTGTCA 60.351 45.455 0.00 0.00 0.00 3.58
546 575 3.241701 GTGTTTGTTGGTGTGTTGTCAG 58.758 45.455 0.00 0.00 0.00 3.51
547 576 2.258755 GTTTGTTGGTGTGTTGTCAGC 58.741 47.619 0.00 0.00 36.52 4.26
548 577 1.832883 TTGTTGGTGTGTTGTCAGCT 58.167 45.000 0.00 0.00 36.85 4.24
549 578 1.093972 TGTTGGTGTGTTGTCAGCTG 58.906 50.000 7.63 7.63 36.85 4.24
577 608 2.945668 GAGTCAAAAGCACTCCACTGTT 59.054 45.455 0.00 0.00 35.19 3.16
595 626 4.082571 ACTGTTAATCAATGAAGCAGGCAC 60.083 41.667 4.31 0.00 0.00 5.01
662 698 7.202016 TCAATGTTTCTAGAACAACATGGAC 57.798 36.000 18.96 7.82 41.74 4.02
670 706 2.821969 AGAACAACATGGACCTGCAATC 59.178 45.455 0.00 0.00 0.00 2.67
771 822 9.298774 GAACACGGCTTATATCTAACCATATAC 57.701 37.037 0.00 0.00 0.00 1.47
773 824 8.467598 ACACGGCTTATATCTAACCATATACTG 58.532 37.037 0.00 0.00 0.00 2.74
816 2812 1.327303 GTGACCCACAATTTGGCTCA 58.673 50.000 0.78 2.31 45.37 4.26
818 2814 3.088532 GTGACCCACAATTTGGCTCATA 58.911 45.455 0.78 0.00 41.28 2.15
830 2826 9.529823 ACAATTTGGCTCATATATCATGAAGAT 57.470 29.630 0.00 0.00 40.86 2.40
834 2830 9.749340 TTTGGCTCATATATCATGAAGATCATT 57.251 29.630 0.00 0.00 34.28 2.57
838 2834 7.282450 GCTCATATATCATGAAGATCATTGGCA 59.718 37.037 0.00 0.00 34.28 4.92
840 2836 9.174166 TCATATATCATGAAGATCATTGGCAAG 57.826 33.333 5.96 0.00 34.28 4.01
841 2837 9.174166 CATATATCATGAAGATCATTGGCAAGA 57.826 33.333 5.96 3.99 34.28 3.02
845 2841 6.598503 TCATGAAGATCATTGGCAAGATACT 58.401 36.000 5.96 0.12 34.28 2.12
846 2842 6.709397 TCATGAAGATCATTGGCAAGATACTC 59.291 38.462 5.96 8.99 34.28 2.59
847 2843 5.371526 TGAAGATCATTGGCAAGATACTCC 58.628 41.667 5.96 0.00 0.00 3.85
852 2848 5.282055 TCATTGGCAAGATACTCCACTAG 57.718 43.478 5.96 0.00 0.00 2.57
884 2907 1.441732 GGTTGTGTGGACCGGTCAAC 61.442 60.000 31.80 31.80 38.00 3.18
907 2934 6.049790 ACGAGGAAGGAAAGCATTTATAGTC 58.950 40.000 0.00 0.00 39.27 2.59
931 2994 1.048601 TGGAACAGTGTGGACCTCTC 58.951 55.000 0.00 0.00 0.00 3.20
933 2996 1.048601 GAACAGTGTGGACCTCTCCA 58.951 55.000 0.00 0.00 45.11 3.86
954 3023 2.858768 ACTTCTCCTCTCTCTCTCCCAT 59.141 50.000 0.00 0.00 0.00 4.00
1138 3266 2.379459 GGAGGAGGGGAAGGAAGCC 61.379 68.421 0.00 0.00 0.00 4.35
1260 3394 2.264794 CCCGTCTTCCAGGTTCCG 59.735 66.667 0.00 0.00 0.00 4.30
1327 3541 4.437930 CCTTCCTCAAGATTCGATTTGTGC 60.438 45.833 0.00 0.00 0.00 4.57
1330 3544 3.064545 CCTCAAGATTCGATTTGTGCTCC 59.935 47.826 0.00 0.00 0.00 4.70
1331 3545 3.937706 CTCAAGATTCGATTTGTGCTCCT 59.062 43.478 0.00 0.00 0.00 3.69
1855 4072 1.149101 AAGATGTGGGTCAACCTGGT 58.851 50.000 0.00 0.00 41.11 4.00
2037 4290 0.326264 GTCCATGGAAGTGCCTCTGT 59.674 55.000 18.20 0.00 37.63 3.41
2099 4377 3.010420 GGTTTGATTAGGTCCAGCACTC 58.990 50.000 0.00 0.00 0.00 3.51
2100 4378 3.010420 GTTTGATTAGGTCCAGCACTCC 58.990 50.000 0.00 0.00 0.00 3.85
2101 4379 2.254152 TGATTAGGTCCAGCACTCCT 57.746 50.000 0.00 0.00 35.60 3.69
2102 4380 1.833630 TGATTAGGTCCAGCACTCCTG 59.166 52.381 0.00 0.00 41.41 3.86
2134 4412 0.517316 GGCAGTTCGTGGTTGCTTAG 59.483 55.000 0.00 0.00 37.93 2.18
2135 4413 1.226746 GCAGTTCGTGGTTGCTTAGT 58.773 50.000 0.00 0.00 35.05 2.24
2136 4414 2.409975 GCAGTTCGTGGTTGCTTAGTA 58.590 47.619 0.00 0.00 35.05 1.82
2143 4421 4.391155 TCGTGGTTGCTTAGTATTTTGGT 58.609 39.130 0.00 0.00 0.00 3.67
2171 4466 6.882678 TCCAGCTTAAACTAAGTATTTGGGTC 59.117 38.462 0.00 0.00 38.07 4.46
2176 4471 8.520351 GCTTAAACTAAGTATTTGGGTCATGTT 58.480 33.333 0.00 0.00 38.07 2.71
2186 4483 9.807921 AGTATTTGGGTCATGTTATAATTAGGG 57.192 33.333 0.00 0.00 0.00 3.53
2423 4786 6.441093 TGTCAAGAAATGTTATCCATGAGC 57.559 37.500 0.00 0.00 32.82 4.26
2449 4812 2.310538 AGGAGGCCTTGTGTCAAAAAG 58.689 47.619 6.77 0.00 0.00 2.27
2450 4813 2.091885 AGGAGGCCTTGTGTCAAAAAGA 60.092 45.455 6.77 0.00 0.00 2.52
2451 4814 2.693074 GGAGGCCTTGTGTCAAAAAGAA 59.307 45.455 6.77 0.00 0.00 2.52
2452 4815 3.132111 GGAGGCCTTGTGTCAAAAAGAAA 59.868 43.478 6.77 0.00 0.00 2.52
2456 4819 6.883744 AGGCCTTGTGTCAAAAAGAAAAATA 58.116 32.000 0.00 0.00 0.00 1.40
2468 4831 9.762933 TCAAAAAGAAAAATATCCCAACTCTTG 57.237 29.630 0.00 0.00 0.00 3.02
2472 4835 8.712228 AAGAAAAATATCCCAACTCTTGTCTT 57.288 30.769 0.00 0.00 0.00 3.01
2569 4989 7.361201 CCATATTTATCCAAACGTCTGCTATGG 60.361 40.741 0.00 0.00 0.00 2.74
2589 5009 4.241681 TGGAAGTTTGTTCAGTTTTGCAC 58.758 39.130 0.00 0.00 0.00 4.57
2590 5010 4.021544 TGGAAGTTTGTTCAGTTTTGCACT 60.022 37.500 0.00 0.00 35.35 4.40
2592 5012 5.391312 AAGTTTGTTCAGTTTTGCACTCT 57.609 34.783 0.00 0.00 30.92 3.24
2623 5048 0.321671 ACTTCTTCTAGCGGCTGCAA 59.678 50.000 21.93 4.25 46.23 4.08
2626 5051 0.528466 TCTTCTAGCGGCTGCAATCG 60.528 55.000 21.93 4.64 46.23 3.34
2632 5057 1.137404 GCGGCTGCAATCGTCAATT 59.863 52.632 14.08 0.00 42.15 2.32
2637 5062 3.174375 GGCTGCAATCGTCAATTCTTTC 58.826 45.455 0.50 0.00 0.00 2.62
2651 5077 4.574599 ATTCTTTCAACTGGAACACTGC 57.425 40.909 0.00 0.00 34.56 4.40
2678 5108 4.732285 TTTTCTCTGATTGCACGACTTC 57.268 40.909 0.00 0.00 0.00 3.01
2683 5113 1.654105 CTGATTGCACGACTTCGGTAC 59.346 52.381 3.30 0.00 44.95 3.34
2712 5142 2.419159 GGAGGCCAAGGATTTGATTTGC 60.419 50.000 5.01 0.00 36.36 3.68
2720 5150 3.985127 AGGATTTGATTTGCCATCCTGA 58.015 40.909 0.00 0.00 43.35 3.86
2725 5155 6.183360 GGATTTGATTTGCCATCCTGAACATA 60.183 38.462 0.00 0.00 33.57 2.29
2726 5156 5.581126 TTGATTTGCCATCCTGAACATAC 57.419 39.130 0.00 0.00 0.00 2.39
2727 5157 4.598022 TGATTTGCCATCCTGAACATACA 58.402 39.130 0.00 0.00 0.00 2.29
2728 5158 4.641541 TGATTTGCCATCCTGAACATACAG 59.358 41.667 0.00 0.00 37.61 2.74
2854 5299 3.078837 CGAGTAGATCTTCCCCTAGCTC 58.921 54.545 0.00 0.00 0.00 4.09
2923 5368 3.914426 TGAAGCCATCTCCTTCCTAAC 57.086 47.619 0.00 0.00 38.29 2.34
2979 5859 8.817092 TTGCTAATAATAAAGTGTTAAGCCCT 57.183 30.769 0.00 0.00 0.00 5.19
3037 5928 9.298774 CTAGTAACTTTTACTACACATAGCCAC 57.701 37.037 2.31 0.00 30.75 5.01
3068 5961 7.739022 TCTTTTATATGAATGCGCTTTGTTG 57.261 32.000 13.85 0.00 0.00 3.33
3069 5962 7.534282 TCTTTTATATGAATGCGCTTTGTTGA 58.466 30.769 13.85 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 80 1.000171 CCAAGATCATCCTCGCATCGA 60.000 52.381 0.00 0.00 0.00 3.59
101 103 3.474798 TGGATAACCAGAGAGGACACT 57.525 47.619 0.00 0.00 41.77 3.55
136 140 0.824759 AGTCATCCGTAGTTGGAGGC 59.175 55.000 0.00 0.00 42.45 4.70
143 147 4.017808 ACTTCTAAGCAGTCATCCGTAGT 58.982 43.478 0.00 0.00 0.00 2.73
153 157 7.284489 CACCTATTCTAGAGACTTCTAAGCAGT 59.716 40.741 0.00 0.00 35.55 4.40
170 174 2.441750 ACACCACACAACCACCTATTCT 59.558 45.455 0.00 0.00 0.00 2.40
173 177 1.202879 CCACACCACACAACCACCTAT 60.203 52.381 0.00 0.00 0.00 2.57
218 227 4.356405 TGATTCGGCAGATACCATCAAT 57.644 40.909 0.00 0.00 0.00 2.57
226 235 3.644966 AACCCTTTGATTCGGCAGATA 57.355 42.857 0.00 0.00 0.00 1.98
241 250 3.644335 AGCGAGTAGGAGAAATAACCCT 58.356 45.455 0.00 0.00 0.00 4.34
280 289 3.058224 GGAGACTCCCGACAACAAAAATG 60.058 47.826 10.74 0.00 0.00 2.32
288 297 2.290071 GGATTTTGGAGACTCCCGACAA 60.290 50.000 19.11 3.43 35.03 3.18
289 298 1.278127 GGATTTTGGAGACTCCCGACA 59.722 52.381 19.11 1.33 35.03 4.35
296 305 6.893020 ATAAGGTACTGGATTTTGGAGACT 57.107 37.500 0.00 0.00 40.86 3.24
316 325 3.523564 CCTCTGAAAGACCCCTGGAATAA 59.476 47.826 0.00 0.00 38.67 1.40
334 344 4.012374 CAACAATATGACCACAAGCCTCT 58.988 43.478 0.00 0.00 0.00 3.69
350 361 3.663025 GCCACCAGCAAATAACAACAAT 58.337 40.909 0.00 0.00 42.97 2.71
374 385 4.164221 ACATATGGCATATGGGCTACCTAC 59.836 45.833 37.31 0.00 45.36 3.18
375 386 4.164030 CACATATGGCATATGGGCTACCTA 59.836 45.833 37.31 6.54 45.36 3.08
384 395 4.423732 TCGATCGACACATATGGCATATG 58.576 43.478 34.74 34.74 46.26 1.78
390 402 3.900941 TGTCATCGATCGACACATATGG 58.099 45.455 22.06 3.03 38.45 2.74
392 404 4.540824 CACTGTCATCGATCGACACATAT 58.459 43.478 24.58 16.37 38.45 1.78
431 443 1.128188 ACTTCTCACCCAGGTCACCC 61.128 60.000 0.00 0.00 0.00 4.61
496 508 6.451064 AGCCCATAAAAAGAAAAGGATACG 57.549 37.500 0.00 0.00 46.39 3.06
540 569 1.078918 CTCCATCGCCAGCTGACAA 60.079 57.895 17.39 0.00 0.00 3.18
544 573 0.674581 TTTGACTCCATCGCCAGCTG 60.675 55.000 6.78 6.78 0.00 4.24
545 574 0.036732 TTTTGACTCCATCGCCAGCT 59.963 50.000 0.00 0.00 0.00 4.24
546 575 0.449388 CTTTTGACTCCATCGCCAGC 59.551 55.000 0.00 0.00 0.00 4.85
547 576 0.449388 GCTTTTGACTCCATCGCCAG 59.551 55.000 0.00 0.00 0.00 4.85
548 577 0.250684 TGCTTTTGACTCCATCGCCA 60.251 50.000 0.00 0.00 0.00 5.69
549 578 0.169009 GTGCTTTTGACTCCATCGCC 59.831 55.000 0.00 0.00 0.00 5.54
577 608 4.018490 ACATGTGCCTGCTTCATTGATTA 58.982 39.130 0.00 0.00 0.00 1.75
608 642 5.635549 AATTGTAAGCGCAAGTTTTGTTC 57.364 34.783 11.47 0.00 42.31 3.18
611 645 6.689178 ACATAATTGTAAGCGCAAGTTTTG 57.311 33.333 11.47 3.70 42.31 2.44
617 651 4.697828 TGAGGAACATAATTGTAAGCGCAA 59.302 37.500 11.47 0.00 34.06 4.85
662 698 1.238439 ACAAGGTTGACGATTGCAGG 58.762 50.000 0.00 0.00 0.00 4.85
725 775 9.825972 CGTGTTCTTAATCAATTTCATTAGTGT 57.174 29.630 0.00 0.00 0.00 3.55
728 778 8.184192 AGCCGTGTTCTTAATCAATTTCATTAG 58.816 33.333 0.00 0.00 0.00 1.73
747 797 8.467598 CAGTATATGGTTAGATATAAGCCGTGT 58.532 37.037 6.82 2.37 0.00 4.49
816 2812 9.922477 ATCTTGCCAATGATCTTCATGATATAT 57.078 29.630 0.00 0.00 37.15 0.86
818 2814 9.175312 GTATCTTGCCAATGATCTTCATGATAT 57.825 33.333 0.00 0.00 37.15 1.63
830 2826 4.101585 CCTAGTGGAGTATCTTGCCAATGA 59.898 45.833 0.00 0.00 32.68 2.57
834 2830 3.116096 ACCTAGTGGAGTATCTTGCCA 57.884 47.619 0.00 0.00 37.04 4.92
838 2834 6.183361 CCTGCATTAACCTAGTGGAGTATCTT 60.183 42.308 0.00 0.00 33.13 2.40
840 2836 5.511545 CCCTGCATTAACCTAGTGGAGTATC 60.512 48.000 0.00 0.00 33.13 2.24
841 2837 4.348168 CCCTGCATTAACCTAGTGGAGTAT 59.652 45.833 0.00 0.00 33.13 2.12
845 2841 1.843851 CCCCTGCATTAACCTAGTGGA 59.156 52.381 0.00 0.00 37.04 4.02
846 2842 1.133792 CCCCCTGCATTAACCTAGTGG 60.134 57.143 0.00 0.00 39.83 4.00
847 2843 1.564348 ACCCCCTGCATTAACCTAGTG 59.436 52.381 0.00 0.00 0.00 2.74
852 2848 0.894835 CACAACCCCCTGCATTAACC 59.105 55.000 0.00 0.00 0.00 2.85
884 2907 6.284459 AGACTATAAATGCTTTCCTTCCTCG 58.716 40.000 0.00 0.00 0.00 4.63
895 2918 7.766278 CACTGTTCCAAGTAGACTATAAATGCT 59.234 37.037 0.00 0.00 0.00 3.79
907 2934 2.368875 AGGTCCACACTGTTCCAAGTAG 59.631 50.000 0.00 0.00 0.00 2.57
931 2994 2.654863 GGAGAGAGAGAGGAGAAGTGG 58.345 57.143 0.00 0.00 0.00 4.00
933 2996 2.283834 TGGGAGAGAGAGAGGAGAAGT 58.716 52.381 0.00 0.00 0.00 3.01
954 3023 5.568620 AAGAAAACCTTTCTAGCAGGAGA 57.431 39.130 13.35 0.00 35.14 3.71
1128 3256 1.153147 GACGATGGGGCTTCCTTCC 60.153 63.158 0.00 0.00 36.61 3.46
1131 3259 4.162690 GCGACGATGGGGCTTCCT 62.163 66.667 0.00 0.00 36.20 3.36
1217 3351 3.507143 AAGGGGAGGGTGCAGAGGT 62.507 63.158 0.00 0.00 0.00 3.85
1260 3394 2.096657 GCCAATCGAGGAAAGAAAGAGC 59.903 50.000 0.00 0.00 0.00 4.09
1327 3541 2.187424 GCAGCAGCAGGAGAGGAG 59.813 66.667 0.00 0.00 41.58 3.69
1656 3870 3.127533 GGCCTTGCCGTACTGCAG 61.128 66.667 13.48 13.48 43.21 4.41
1864 4114 3.984193 ATGTCCTCCTTGCCGCAGC 62.984 63.158 0.00 0.00 40.48 5.25
1946 4196 1.374947 CACCATCAGGAACGTGGGT 59.625 57.895 0.00 0.00 37.33 4.51
2037 4290 0.459899 AGCTTGTCGATGCGGATGTA 59.540 50.000 0.00 0.00 0.00 2.29
2099 4377 2.758089 GCCTTGAGTGCATCGCAGG 61.758 63.158 0.00 0.00 40.08 4.85
2100 4378 1.978712 CTGCCTTGAGTGCATCGCAG 61.979 60.000 0.00 0.00 40.08 5.18
2101 4379 2.032376 TGCCTTGAGTGCATCGCA 59.968 55.556 0.00 0.00 35.60 5.10
2102 4380 1.580845 AACTGCCTTGAGTGCATCGC 61.581 55.000 0.00 0.00 38.22 4.58
2134 4412 6.745116 AGTTTAAGCTGGAACACCAAAATAC 58.255 36.000 13.16 0.00 32.95 1.89
2135 4413 6.969993 AGTTTAAGCTGGAACACCAAAATA 57.030 33.333 13.16 0.00 32.95 1.40
2136 4414 5.869649 AGTTTAAGCTGGAACACCAAAAT 57.130 34.783 13.16 0.00 32.95 1.82
2143 4421 7.175990 CCCAAATACTTAGTTTAAGCTGGAACA 59.824 37.037 13.16 0.03 39.39 3.18
2171 4466 7.448161 TGAACTGCATCCCCTAATTATAACATG 59.552 37.037 0.00 0.00 0.00 3.21
2251 4562 7.973048 AGCATAATATCCTCCGATTTAGGTA 57.027 36.000 0.00 0.00 35.48 3.08
2252 4563 6.875972 AGCATAATATCCTCCGATTTAGGT 57.124 37.500 0.00 0.00 35.48 3.08
2253 4564 6.540189 CCAAGCATAATATCCTCCGATTTAGG 59.460 42.308 0.00 0.00 35.26 2.69
2254 4565 7.065085 CACCAAGCATAATATCCTCCGATTTAG 59.935 40.741 0.00 0.00 0.00 1.85
2423 4786 1.882623 GACACAAGGCCTCCTTTCTTG 59.117 52.381 5.23 0.00 41.69 3.02
2449 4812 8.360390 ACAAAGACAAGAGTTGGGATATTTTTC 58.640 33.333 0.00 0.00 34.12 2.29
2450 4813 8.250143 ACAAAGACAAGAGTTGGGATATTTTT 57.750 30.769 0.00 0.00 34.12 1.94
2451 4814 7.839680 ACAAAGACAAGAGTTGGGATATTTT 57.160 32.000 0.00 0.00 34.12 1.82
2452 4815 8.960591 CATACAAAGACAAGAGTTGGGATATTT 58.039 33.333 0.00 0.00 34.12 1.40
2456 4819 6.126863 TCATACAAAGACAAGAGTTGGGAT 57.873 37.500 0.00 0.00 34.12 3.85
2501 4885 3.138884 TCAGGAATTACTGCACTGCAA 57.861 42.857 13.28 0.00 38.41 4.08
2569 4989 5.287035 CAGAGTGCAAAACTGAACAAACTTC 59.713 40.000 9.49 0.00 40.07 3.01
2589 5009 3.347077 AGAAGTCCCATTGCTTCAGAG 57.653 47.619 6.99 0.00 42.42 3.35
2590 5010 3.328931 AGAAGAAGTCCCATTGCTTCAGA 59.671 43.478 0.00 0.00 42.42 3.27
2592 5012 3.795688 AGAAGAAGTCCCATTGCTTCA 57.204 42.857 0.00 0.00 42.42 3.02
2623 5048 5.530915 TGTTCCAGTTGAAAGAATTGACGAT 59.469 36.000 0.00 0.00 33.94 3.73
2626 5051 5.973565 CAGTGTTCCAGTTGAAAGAATTGAC 59.026 40.000 0.00 0.00 33.94 3.18
2632 5057 3.281727 AGCAGTGTTCCAGTTGAAAGA 57.718 42.857 0.00 0.00 33.94 2.52
2637 5062 4.376340 AAAAGAAGCAGTGTTCCAGTTG 57.624 40.909 0.00 0.00 0.00 3.16
2683 5113 1.675641 CCTTGGCCTCCGGAACTTG 60.676 63.158 5.23 0.00 0.00 3.16
2720 5150 9.471702 AGATCAAAGAAATCAATCCTGTATGTT 57.528 29.630 0.00 0.00 0.00 2.71
2725 5155 7.668886 AGACAAGATCAAAGAAATCAATCCTGT 59.331 33.333 0.00 0.00 0.00 4.00
2726 5156 8.053026 AGACAAGATCAAAGAAATCAATCCTG 57.947 34.615 0.00 0.00 0.00 3.86
2727 5157 8.647256 AAGACAAGATCAAAGAAATCAATCCT 57.353 30.769 0.00 0.00 0.00 3.24
2728 5158 8.517878 TGAAGACAAGATCAAAGAAATCAATCC 58.482 33.333 0.00 0.00 0.00 3.01
2730 5160 9.075678 ACTGAAGACAAGATCAAAGAAATCAAT 57.924 29.630 0.00 0.00 0.00 2.57
2923 5368 3.930848 GTGTACAGACATAAGTTTCCCCG 59.069 47.826 0.00 0.00 38.04 5.73
2979 5859 1.819305 GCAAACTCCAGCCCTCAAAGA 60.819 52.381 0.00 0.00 0.00 2.52
3021 5909 7.620880 AGAAGAATTGTGGCTATGTGTAGTAA 58.379 34.615 0.00 0.00 0.00 2.24
3037 5928 8.792831 AGCGCATTCATATAAAAGAAGAATTG 57.207 30.769 11.47 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.