Multiple sequence alignment - TraesCS3D01G165600

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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 TraesCS3D01G165600 chr3D 100.000 4656 0 0 1 4656 137489062 137484407 0.000000e+00 8599.0
1 TraesCS3D01G165600 chr3D 97.706 218 5 0 2 219 586301372 586301589 4.400000e-100 375.0
2 TraesCS3D01G165600 chr3D 94.776 134 7 0 2202 2335 606951437 606951304 4.720000e-50 209.0
3 TraesCS3D01G165600 chr3A 97.555 1554 35 3 2329 3879 155430262 155428709 0.000000e+00 2656.0
4 TraesCS3D01G165600 chr3A 92.102 785 28 9 3893 4656 155428584 155427813 0.000000e+00 1075.0
5 TraesCS3D01G165600 chr3A 95.682 579 14 2 1466 2044 155431186 155430619 0.000000e+00 920.0
6 TraesCS3D01G165600 chr3A 93.895 475 27 1 223 695 678037090 678037564 0.000000e+00 715.0
7 TraesCS3D01G165600 chr3A 93.319 479 31 1 223 700 716060913 716060435 0.000000e+00 706.0
8 TraesCS3D01G165600 chr3A 96.709 395 6 4 692 1079 155432352 155431958 0.000000e+00 651.0
9 TraesCS3D01G165600 chr3A 91.123 383 10 13 1100 1471 155431639 155431270 9.000000e-137 497.0
10 TraesCS3D01G165600 chr3A 98.425 127 2 0 2082 2208 155430389 155430263 1.690000e-54 224.0
11 TraesCS3D01G165600 chr3B 95.978 1467 54 4 2328 3789 200874417 200872951 0.000000e+00 2377.0
12 TraesCS3D01G165600 chr3B 94.214 795 20 13 689 1471 200875980 200875200 0.000000e+00 1190.0
13 TraesCS3D01G165600 chr3B 87.854 741 50 25 1467 2207 200875113 200874413 0.000000e+00 833.0
14 TraesCS3D01G165600 chr3B 88.351 558 37 13 4122 4654 200864576 200864022 0.000000e+00 645.0
15 TraesCS3D01G165600 chr3B 90.751 173 15 1 3884 4055 200872854 200872682 3.620000e-56 230.0
16 TraesCS3D01G165600 chr5D 95.702 698 28 2 2 697 138810328 138809631 0.000000e+00 1122.0
17 TraesCS3D01G165600 chr5D 91.391 151 10 3 2183 2331 361648091 361647942 2.200000e-48 204.0
18 TraesCS3D01G165600 chr2A 95.821 694 26 3 2 695 770918976 770919666 0.000000e+00 1118.0
19 TraesCS3D01G165600 chr2A 93.714 700 29 9 2 697 13139498 13140186 0.000000e+00 1035.0
20 TraesCS3D01G165600 chr2A 93.763 481 29 1 223 702 535841889 535842369 0.000000e+00 721.0
21 TraesCS3D01G165600 chr4D 94.109 696 26 3 2 695 494070754 494071436 0.000000e+00 1044.0
22 TraesCS3D01G165600 chr4D 90.260 154 9 5 2181 2331 117643925 117644075 3.680000e-46 196.0
23 TraesCS3D01G165600 chr7A 93.544 697 31 5 2 697 19300286 19299603 0.000000e+00 1026.0
24 TraesCS3D01G165600 chr7A 90.515 485 27 10 1003 1471 312941659 312942140 1.420000e-174 623.0
25 TraesCS3D01G165600 chr7A 90.021 471 32 3 1011 1466 527945438 527944968 3.100000e-166 595.0
26 TraesCS3D01G165600 chr7A 92.500 360 13 6 1466 1824 527944890 527944544 1.930000e-138 503.0
27 TraesCS3D01G165600 chr7A 91.086 359 18 4 1467 1824 312942212 312942557 1.520000e-129 473.0
28 TraesCS3D01G165600 chr7A 96.154 130 5 0 2203 2332 442265753 442265882 3.650000e-51 213.0
29 TraesCS3D01G165600 chr7A 93.846 65 4 0 1258 1322 486142587 486142651 1.070000e-16 99.0
30 TraesCS3D01G165600 chr7A 87.879 66 7 1 4559 4623 591499528 591499593 5.000000e-10 76.8
31 TraesCS3D01G165600 chr1D 92.219 694 35 7 2 693 6406853 6407529 0.000000e+00 965.0
32 TraesCS3D01G165600 chr1D 87.940 398 48 0 2516 2913 165203043 165203440 1.960000e-128 470.0
33 TraesCS3D01G165600 chr1D 94.853 136 6 1 2199 2334 63832662 63832796 1.310000e-50 211.0
34 TraesCS3D01G165600 chr2D 94.492 472 22 4 223 693 381560347 381559879 0.000000e+00 725.0
35 TraesCS3D01G165600 chr2D 78.931 318 65 2 3075 3391 76761822 76761506 1.010000e-51 215.0
36 TraesCS3D01G165600 chr2D 94.667 75 4 0 4455 4529 394532735 394532661 2.940000e-22 117.0
37 TraesCS3D01G165600 chr1A 94.093 474 28 0 223 696 181550625 181550152 0.000000e+00 721.0
38 TraesCS3D01G165600 chr1A 81.319 182 17 8 4455 4619 21676401 21676220 1.050000e-26 132.0
39 TraesCS3D01G165600 chr6A 93.920 477 25 2 223 695 581968265 581968741 0.000000e+00 717.0
40 TraesCS3D01G165600 chr6A 93.478 138 8 1 2195 2332 121886212 121886348 2.200000e-48 204.0
41 TraesCS3D01G165600 chr1B 87.437 398 50 0 2516 2913 246769232 246768835 4.250000e-125 459.0
42 TraesCS3D01G165600 chr1B 96.847 222 6 1 2 222 682999 683220 2.050000e-98 370.0
43 TraesCS3D01G165600 chr1B 85.220 318 47 0 3075 3392 246768725 246768408 1.250000e-85 327.0
44 TraesCS3D01G165600 chr1B 94.161 137 8 0 2195 2331 585330997 585330861 4.720000e-50 209.0
45 TraesCS3D01G165600 chr2B 97.706 218 5 0 2 219 106924559 106924776 4.400000e-100 375.0
46 TraesCS3D01G165600 chr2B 78.997 319 65 2 3075 3392 118060918 118060601 2.820000e-52 217.0
47 TraesCS3D01G165600 chr7B 97.706 218 4 1 2 219 178398911 178398695 1.580000e-99 374.0
48 TraesCS3D01G165600 chr7B 96.241 133 4 1 2200 2331 46022956 46022824 2.820000e-52 217.0
49 TraesCS3D01G165600 chr7B 95.385 65 3 0 1258 1322 453152880 453152816 2.290000e-18 104.0
50 TraesCS3D01G165600 chr4A 91.724 145 10 2 2191 2334 346062695 346062552 2.840000e-47 200.0
51 TraesCS3D01G165600 chr7D 95.385 65 3 0 1258 1322 436740207 436740143 2.290000e-18 104.0
52 TraesCS3D01G165600 chr4B 87.324 71 7 1 4455 4525 652977740 652977808 3.860000e-11 80.5
53 TraesCS3D01G165600 chr5A 94.872 39 2 0 4568 4606 702765090 702765128 1.400000e-05 62.1


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 TraesCS3D01G165600 chr3D 137484407 137489062 4655 True 8599.000000 8599 100.00000 1 4656 1 chr3D.!!$R1 4655
1 TraesCS3D01G165600 chr3A 155427813 155432352 4539 True 1003.833333 2656 95.26600 692 4656 6 chr3A.!!$R2 3964
2 TraesCS3D01G165600 chr3B 200872682 200875980 3298 True 1157.500000 2377 92.19925 689 4055 4 chr3B.!!$R2 3366
3 TraesCS3D01G165600 chr3B 200864022 200864576 554 True 645.000000 645 88.35100 4122 4654 1 chr3B.!!$R1 532
4 TraesCS3D01G165600 chr5D 138809631 138810328 697 True 1122.000000 1122 95.70200 2 697 1 chr5D.!!$R1 695
5 TraesCS3D01G165600 chr2A 770918976 770919666 690 False 1118.000000 1118 95.82100 2 695 1 chr2A.!!$F3 693
6 TraesCS3D01G165600 chr2A 13139498 13140186 688 False 1035.000000 1035 93.71400 2 697 1 chr2A.!!$F1 695
7 TraesCS3D01G165600 chr4D 494070754 494071436 682 False 1044.000000 1044 94.10900 2 695 1 chr4D.!!$F2 693
8 TraesCS3D01G165600 chr7A 19299603 19300286 683 True 1026.000000 1026 93.54400 2 697 1 chr7A.!!$R1 695
9 TraesCS3D01G165600 chr7A 527944544 527945438 894 True 549.000000 595 91.26050 1011 1824 2 chr7A.!!$R2 813
10 TraesCS3D01G165600 chr7A 312941659 312942557 898 False 548.000000 623 90.80050 1003 1824 2 chr7A.!!$F4 821
11 TraesCS3D01G165600 chr1D 6406853 6407529 676 False 965.000000 965 92.21900 2 693 1 chr1D.!!$F1 691
12 TraesCS3D01G165600 chr1B 246768408 246769232 824 True 393.000000 459 86.32850 2516 3392 2 chr1B.!!$R2 876

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
571 581 0.036294 GTAGTCTTCCCAGTGTGCCC 60.036 60.0 0.0 0.0 0.0 5.36 F
2218 2852 0.456628 GCAAGTACTCTCTCCGTCCC 59.543 60.0 0.0 0.0 0.0 4.46 F
3172 3877 0.322456 CCTTCCTGCGTTTCATGGGA 60.322 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 2947 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28 R
3410 4115 0.603569 CAGAGAACTGGTACGCAGGT 59.396 55.000 13.68 8.52 40.14 4.00 R
4073 4943 1.135333 CCTAACCCTCGCTCTCAAGTC 59.865 57.143 0.00 0.00 0.00 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
275 282 4.664150 TGTGAAAAACTGGTGGAATTCC 57.336 40.909 18.17 18.17 0.00 3.01
280 287 2.951229 AACTGGTGGAATTCCGAACT 57.049 45.000 19.57 0.00 39.43 3.01
459 469 6.576551 TTTGAACAATTTTAGAAACGTGCC 57.423 33.333 0.00 0.00 0.00 5.01
525 535 1.379527 GCCCAAATTCTAGTCCGTGG 58.620 55.000 0.00 0.00 0.00 4.94
571 581 0.036294 GTAGTCTTCCCAGTGTGCCC 60.036 60.000 0.00 0.00 0.00 5.36
641 665 4.165779 CAATTTCCGGGATTCAAAGTTCG 58.834 43.478 0.00 0.00 0.00 3.95
1363 1703 3.650907 TTGATTCTGGCGCGGCGTA 62.651 57.895 28.22 15.57 0.00 4.42
1721 2163 4.080807 TGGGCAATCTCAAACCTCGTTATA 60.081 41.667 0.00 0.00 0.00 0.98
1722 2164 4.272748 GGGCAATCTCAAACCTCGTTATAC 59.727 45.833 0.00 0.00 0.00 1.47
1723 2165 5.116882 GGCAATCTCAAACCTCGTTATACT 58.883 41.667 0.00 0.00 0.00 2.12
1729 2171 7.766219 TCTCAAACCTCGTTATACTATTTGC 57.234 36.000 0.00 0.00 0.00 3.68
1906 2348 6.560253 ATTTAATGTCGGATCAGTATTGCC 57.440 37.500 0.00 0.00 0.00 4.52
1958 2400 8.998814 TGGAGGTAGAAATTCCTACATTAATCA 58.001 33.333 4.11 0.00 39.48 2.57
2047 2489 2.879002 ATATGCGGAGTCACAGTCAG 57.121 50.000 0.00 0.00 0.00 3.51
2075 2517 8.894731 TGTAAACACACACACACACTATATTTT 58.105 29.630 0.00 0.00 0.00 1.82
2115 2749 6.014584 TGAGTTGGTAGCAAATCTAACTCTGA 60.015 38.462 28.63 9.37 45.59 3.27
2151 2785 9.620660 TCAACATATGTATTGTAGTATGTAGCG 57.379 33.333 9.21 0.00 36.92 4.26
2206 2840 9.547753 TTGATATCTTGATCCTTAAGCAAGTAC 57.452 33.333 16.24 9.75 39.85 2.73
2207 2841 8.928448 TGATATCTTGATCCTTAAGCAAGTACT 58.072 33.333 16.24 0.00 39.85 2.73
2208 2842 9.418045 GATATCTTGATCCTTAAGCAAGTACTC 57.582 37.037 16.24 10.16 39.85 2.59
2209 2843 6.859112 TCTTGATCCTTAAGCAAGTACTCT 57.141 37.500 16.24 0.00 39.85 3.24
2210 2844 6.868622 TCTTGATCCTTAAGCAAGTACTCTC 58.131 40.000 16.24 0.00 39.85 3.20
2211 2845 6.665680 TCTTGATCCTTAAGCAAGTACTCTCT 59.334 38.462 16.24 0.00 39.85 3.10
2212 2846 6.458232 TGATCCTTAAGCAAGTACTCTCTC 57.542 41.667 0.00 0.00 0.00 3.20
2213 2847 5.361285 TGATCCTTAAGCAAGTACTCTCTCC 59.639 44.000 0.00 0.00 0.00 3.71
2214 2848 3.695060 TCCTTAAGCAAGTACTCTCTCCG 59.305 47.826 0.00 0.00 0.00 4.63
2215 2849 3.444388 CCTTAAGCAAGTACTCTCTCCGT 59.556 47.826 0.00 0.00 0.00 4.69
2216 2850 4.439016 CCTTAAGCAAGTACTCTCTCCGTC 60.439 50.000 0.00 0.00 0.00 4.79
2217 2851 1.465794 AGCAAGTACTCTCTCCGTCC 58.534 55.000 0.00 0.00 0.00 4.79
2218 2852 0.456628 GCAAGTACTCTCTCCGTCCC 59.543 60.000 0.00 0.00 0.00 4.46
2219 2853 1.835494 CAAGTACTCTCTCCGTCCCA 58.165 55.000 0.00 0.00 0.00 4.37
2220 2854 2.168496 CAAGTACTCTCTCCGTCCCAA 58.832 52.381 0.00 0.00 0.00 4.12
2221 2855 2.561419 CAAGTACTCTCTCCGTCCCAAA 59.439 50.000 0.00 0.00 0.00 3.28
2222 2856 2.885616 AGTACTCTCTCCGTCCCAAAA 58.114 47.619 0.00 0.00 0.00 2.44
2223 2857 3.442076 AGTACTCTCTCCGTCCCAAAAT 58.558 45.455 0.00 0.00 0.00 1.82
2224 2858 3.838903 AGTACTCTCTCCGTCCCAAAATT 59.161 43.478 0.00 0.00 0.00 1.82
2225 2859 3.336138 ACTCTCTCCGTCCCAAAATTC 57.664 47.619 0.00 0.00 0.00 2.17
2226 2860 2.907042 ACTCTCTCCGTCCCAAAATTCT 59.093 45.455 0.00 0.00 0.00 2.40
2227 2861 3.328050 ACTCTCTCCGTCCCAAAATTCTT 59.672 43.478 0.00 0.00 0.00 2.52
2228 2862 3.674997 TCTCTCCGTCCCAAAATTCTTG 58.325 45.455 0.00 0.00 0.00 3.02
2229 2863 3.072476 TCTCTCCGTCCCAAAATTCTTGT 59.928 43.478 0.00 0.00 0.00 3.16
2230 2864 3.408634 TCTCCGTCCCAAAATTCTTGTC 58.591 45.455 0.00 0.00 0.00 3.18
2231 2865 3.072476 TCTCCGTCCCAAAATTCTTGTCT 59.928 43.478 0.00 0.00 0.00 3.41
2232 2866 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2233 2867 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2234 2868 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2235 2869 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2236 2870 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2237 2871 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2238 2872 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2239 2873 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2240 2874 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2241 2875 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2242 2876 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2250 2884 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
2251 2885 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
2253 2887 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
2254 2888 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
2259 2893 9.477484 AGATTTGTCTAAATACGGATGTATCAC 57.523 33.333 0.00 0.00 40.42 3.06
2260 2894 7.688478 TTTGTCTAAATACGGATGTATCACG 57.312 36.000 0.00 0.00 40.42 4.35
2261 2895 6.381481 TGTCTAAATACGGATGTATCACGT 57.619 37.500 11.24 11.24 40.42 4.49
2262 2896 6.432936 TGTCTAAATACGGATGTATCACGTC 58.567 40.000 10.24 0.00 40.42 4.34
2263 2897 6.038492 TGTCTAAATACGGATGTATCACGTCA 59.962 38.462 10.24 0.00 40.42 4.35
2264 2898 6.359087 GTCTAAATACGGATGTATCACGTCAC 59.641 42.308 10.24 0.00 40.42 3.67
2265 2899 4.642445 AATACGGATGTATCACGTCACA 57.358 40.909 10.24 0.00 40.42 3.58
2266 2900 4.848562 ATACGGATGTATCACGTCACAT 57.151 40.909 6.66 6.66 36.56 3.21
2267 2901 3.520290 ACGGATGTATCACGTCACATT 57.480 42.857 8.03 0.00 35.87 2.71
2268 2902 3.857052 ACGGATGTATCACGTCACATTT 58.143 40.909 8.03 0.00 35.87 2.32
2269 2903 4.250464 ACGGATGTATCACGTCACATTTT 58.750 39.130 8.03 0.00 35.87 1.82
2270 2904 5.412640 ACGGATGTATCACGTCACATTTTA 58.587 37.500 8.03 0.00 35.87 1.52
2271 2905 5.518847 ACGGATGTATCACGTCACATTTTAG 59.481 40.000 8.03 4.30 35.87 1.85
2272 2906 5.746721 CGGATGTATCACGTCACATTTTAGA 59.253 40.000 8.03 0.00 35.87 2.10
2273 2907 6.254804 CGGATGTATCACGTCACATTTTAGAA 59.745 38.462 8.03 0.00 35.87 2.10
2274 2908 7.042725 CGGATGTATCACGTCACATTTTAGAAT 60.043 37.037 8.03 0.00 35.87 2.40
2275 2909 8.612619 GGATGTATCACGTCACATTTTAGAATT 58.387 33.333 8.03 0.00 35.87 2.17
2278 2912 9.863845 TGTATCACGTCACATTTTAGAATTAGA 57.136 29.630 0.00 0.00 0.00 2.10
2282 2916 9.863845 TCACGTCACATTTTAGAATTAGATACA 57.136 29.630 0.00 0.00 0.00 2.29
2318 2952 9.546428 AGACAAATTTAAGACAAGAATTTTGGG 57.454 29.630 0.00 0.00 33.39 4.12
2319 2953 9.541143 GACAAATTTAAGACAAGAATTTTGGGA 57.459 29.630 0.00 0.00 33.39 4.37
2320 2954 9.325198 ACAAATTTAAGACAAGAATTTTGGGAC 57.675 29.630 0.00 0.00 33.39 4.46
2321 2955 8.487176 CAAATTTAAGACAAGAATTTTGGGACG 58.513 33.333 0.00 0.00 32.35 4.79
2322 2956 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
2323 2957 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2324 2958 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2325 2959 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2326 2960 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2461 3100 6.713762 AATTGTGTGGAACTGAAGAATCAA 57.286 33.333 0.00 0.00 38.04 2.57
2506 3145 2.767960 TGGCATGACTCTAATCTCTGCA 59.232 45.455 0.00 0.00 32.73 4.41
2943 3582 4.037923 GCAAGAATGTTTCCTCTTGTCCAA 59.962 41.667 12.09 0.00 46.76 3.53
2975 3614 8.385849 GTGCAATACACCTGGATACAAGATCAT 61.386 40.741 0.00 0.00 44.23 2.45
2997 3636 6.322456 TCATCCCTCATACAGAGTAGTTCTTG 59.678 42.308 0.00 0.00 43.12 3.02
3004 3643 8.678593 TCATACAGAGTAGTTCTTGATACGAT 57.321 34.615 0.00 0.00 32.41 3.73
3066 3705 9.421806 CTCTTTTTGATGCATTTGTTTGGTATA 57.578 29.630 0.00 0.00 0.00 1.47
3115 3820 2.072298 CAGTACTTCTGCCTGCACTTC 58.928 52.381 0.00 0.00 37.36 3.01
3172 3877 0.322456 CCTTCCTGCGTTTCATGGGA 60.322 55.000 0.00 0.00 0.00 4.37
3571 4280 5.347364 CGTTTCATGGTTTTGTCTTTGTTGT 59.653 36.000 0.00 0.00 0.00 3.32
3610 4319 7.104290 GCTAGGATGACCTTGTAAAGTAAACT 58.896 38.462 0.00 0.00 45.36 2.66
3630 4339 5.683876 ACTCTGTATATATGGCATCCCAC 57.316 43.478 1.65 0.00 45.77 4.61
3646 4355 3.106054 TCCCACGGCTTATTACAGGTTA 58.894 45.455 0.00 0.00 0.00 2.85
3805 4543 5.069119 GCCTTCAGAGGGTTTATAATTTGGG 59.931 44.000 0.00 0.00 43.75 4.12
3854 4592 4.516698 CAGTGTGGATTAGTCTTTGCACTT 59.483 41.667 8.08 0.00 34.25 3.16
3861 4599 2.557920 AGTCTTTGCACTTGGAGAGG 57.442 50.000 0.00 0.00 0.00 3.69
3865 4603 0.473755 TTTGCACTTGGAGAGGCTGA 59.526 50.000 0.00 0.00 0.00 4.26
3879 4617 4.093011 AGAGGCTGAGACTGATGTTAAGT 58.907 43.478 0.00 0.00 0.00 2.24
3880 4618 5.265191 AGAGGCTGAGACTGATGTTAAGTA 58.735 41.667 0.00 0.00 0.00 2.24
3882 4620 5.020132 AGGCTGAGACTGATGTTAAGTACT 58.980 41.667 0.00 0.00 0.00 2.73
3973 4823 6.944096 TGCTCCAGGATAATCTTATCTGATG 58.056 40.000 9.23 6.63 39.53 3.07
4004 4854 5.061684 TGACTTGAGTAATGCGTTAATGTCG 59.938 40.000 2.88 0.00 0.00 4.35
4073 4943 0.254178 CAGACCAGAACCTCATGGGG 59.746 60.000 11.11 11.11 41.13 4.96
4074 4944 0.119155 AGACCAGAACCTCATGGGGA 59.881 55.000 21.59 0.00 41.13 4.81
4114 4984 4.038642 AGGAGCTGACGGAGATATCTTTTC 59.961 45.833 6.70 4.66 0.00 2.29
4142 5012 4.463186 ACGTACAAGTTAGAGGCTCTTGAT 59.537 41.667 24.13 5.77 40.35 2.57
4163 5033 9.168451 CTTGATGAAAGTCTAGTACTCTACAGA 57.832 37.037 0.00 0.00 37.50 3.41
4210 5080 6.737254 TCAAATAAAAATGAGACCGGAGAC 57.263 37.500 9.46 0.00 0.00 3.36
4378 5251 7.696992 TTTTCAACTTGTACTGGTCTTTTCT 57.303 32.000 0.00 0.00 0.00 2.52
4556 5451 6.530181 GCCTTAAATATTCTGGTTTTTGTCGG 59.470 38.462 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
525 535 1.749033 CCGGGATTCCAGCTACTCC 59.251 63.158 4.80 0.00 0.00 3.85
565 575 1.488705 CCCTAGACCTGTTGGGCACA 61.489 60.000 0.00 0.00 46.30 4.57
571 581 3.502123 TTTTGGACCCTAGACCTGTTG 57.498 47.619 0.00 0.00 0.00 3.33
641 665 5.468540 AGACAAAAGCTAAATCAAACCCC 57.531 39.130 0.00 0.00 0.00 4.95
684 708 6.015940 CCACTATCTTTGCTTGGAAAAAGTCT 60.016 38.462 0.00 0.00 35.38 3.24
697 721 2.493278 ACCATGTTGCCACTATCTTTGC 59.507 45.455 0.00 0.00 0.00 3.68
799 823 1.033746 ATTATTGCTGCTGCCGTGCT 61.034 50.000 13.47 0.00 38.71 4.40
1363 1703 2.203015 GCACACCCGACACACAGT 60.203 61.111 0.00 0.00 0.00 3.55
1514 1956 9.473007 TCCCAATGAACAAGAACAATGATATAA 57.527 29.630 0.00 0.00 0.00 0.98
1515 1957 9.645128 ATCCCAATGAACAAGAACAATGATATA 57.355 29.630 0.00 0.00 0.00 0.86
1516 1958 7.959658 TCCCAATGAACAAGAACAATGATAT 57.040 32.000 0.00 0.00 0.00 1.63
1517 1959 7.959658 ATCCCAATGAACAAGAACAATGATA 57.040 32.000 0.00 0.00 0.00 2.15
1518 1960 6.862469 ATCCCAATGAACAAGAACAATGAT 57.138 33.333 0.00 0.00 0.00 2.45
1519 1961 6.669125 AATCCCAATGAACAAGAACAATGA 57.331 33.333 0.00 0.00 0.00 2.57
1520 1962 7.359431 CGAAAATCCCAATGAACAAGAACAATG 60.359 37.037 0.00 0.00 0.00 2.82
1721 2163 3.806949 TGGGACCAGAAAGCAAATAGT 57.193 42.857 0.00 0.00 0.00 2.12
1722 2164 4.530875 AGATGGGACCAGAAAGCAAATAG 58.469 43.478 0.00 0.00 0.00 1.73
1723 2165 4.591321 AGATGGGACCAGAAAGCAAATA 57.409 40.909 0.00 0.00 0.00 1.40
1729 2171 6.660949 ACAGAAAATAAGATGGGACCAGAAAG 59.339 38.462 0.00 0.00 0.00 2.62
1906 2348 9.953697 AAGAGCAGTAATAGATTAGTTTCGTAG 57.046 33.333 0.00 0.00 0.00 3.51
1958 2400 7.263100 TGAAATAAGCAGTTCGATTGCATAT 57.737 32.000 20.33 15.96 43.92 1.78
2016 2458 6.815641 GTGACTCCGCATATATCTGATTGATT 59.184 38.462 0.00 0.00 36.65 2.57
2047 2489 4.413495 AGTGTGTGTGTGTGTTTACAAC 57.587 40.909 0.00 0.00 38.82 3.32
2055 2497 7.042119 TGACTGAAAATATAGTGTGTGTGTGTG 60.042 37.037 0.00 0.00 0.00 3.82
2057 2499 7.420184 TGACTGAAAATATAGTGTGTGTGTG 57.580 36.000 0.00 0.00 0.00 3.82
2059 2501 8.171196 GTGATGACTGAAAATATAGTGTGTGTG 58.829 37.037 0.00 0.00 0.00 3.82
2060 2502 7.334421 GGTGATGACTGAAAATATAGTGTGTGT 59.666 37.037 0.00 0.00 0.00 3.72
2061 2503 7.464577 CGGTGATGACTGAAAATATAGTGTGTG 60.465 40.741 0.00 0.00 0.00 3.82
2062 2504 6.535150 CGGTGATGACTGAAAATATAGTGTGT 59.465 38.462 0.00 0.00 0.00 3.72
2063 2505 6.535150 ACGGTGATGACTGAAAATATAGTGTG 59.465 38.462 0.00 0.00 32.19 3.82
2064 2506 6.535150 CACGGTGATGACTGAAAATATAGTGT 59.465 38.462 0.74 0.00 32.19 3.55
2065 2507 6.535150 ACACGGTGATGACTGAAAATATAGTG 59.465 38.462 16.29 0.00 32.19 2.74
2070 2512 4.888917 TCACACGGTGATGACTGAAAATA 58.111 39.130 16.29 0.00 37.67 1.40
2075 2517 1.328279 ACTCACACGGTGATGACTGA 58.672 50.000 16.29 6.67 41.94 3.41
2151 2785 4.569564 GCATGAAAATCTTCCCTTTGCATC 59.430 41.667 0.00 0.00 30.88 3.91
2202 2836 2.599408 TTTGGGACGGAGAGAGTACT 57.401 50.000 0.00 0.00 0.00 2.73
2203 2837 3.889520 ATTTTGGGACGGAGAGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
2204 2838 4.094476 AGAATTTTGGGACGGAGAGAGTA 58.906 43.478 0.00 0.00 0.00 2.59
2205 2839 2.907042 AGAATTTTGGGACGGAGAGAGT 59.093 45.455 0.00 0.00 0.00 3.24
2206 2840 3.618690 AGAATTTTGGGACGGAGAGAG 57.381 47.619 0.00 0.00 0.00 3.20
2207 2841 3.072476 ACAAGAATTTTGGGACGGAGAGA 59.928 43.478 0.00 0.00 0.00 3.10
2208 2842 3.412386 ACAAGAATTTTGGGACGGAGAG 58.588 45.455 0.00 0.00 0.00 3.20
2209 2843 3.072476 AGACAAGAATTTTGGGACGGAGA 59.928 43.478 0.00 0.00 0.00 3.71
2210 2844 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2211 2845 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2212 2846 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2213 2847 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2214 2848 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2215 2849 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2216 2850 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2224 2858 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
2225 2859 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
2227 2861 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
2228 2862 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
2233 2867 9.477484 GTGATACATCCGTATTTAGACAAATCT 57.523 33.333 0.00 0.00 38.48 2.40
2234 2868 8.425491 CGTGATACATCCGTATTTAGACAAATC 58.575 37.037 0.00 0.00 38.48 2.17
2235 2869 7.924412 ACGTGATACATCCGTATTTAGACAAAT 59.076 33.333 0.00 0.00 38.48 2.32
2236 2870 7.259882 ACGTGATACATCCGTATTTAGACAAA 58.740 34.615 0.00 0.00 38.48 2.83
2237 2871 6.798482 ACGTGATACATCCGTATTTAGACAA 58.202 36.000 0.00 0.00 38.48 3.18
2238 2872 6.038492 TGACGTGATACATCCGTATTTAGACA 59.962 38.462 0.00 0.00 38.48 3.41
2239 2873 6.359087 GTGACGTGATACATCCGTATTTAGAC 59.641 42.308 0.00 0.00 38.48 2.59
2240 2874 6.038492 TGTGACGTGATACATCCGTATTTAGA 59.962 38.462 0.00 0.00 38.48 2.10
2241 2875 6.203647 TGTGACGTGATACATCCGTATTTAG 58.796 40.000 0.00 0.00 38.48 1.85
2242 2876 6.134040 TGTGACGTGATACATCCGTATTTA 57.866 37.500 0.00 0.00 38.48 1.40
2243 2877 5.001237 TGTGACGTGATACATCCGTATTT 57.999 39.130 0.00 0.00 38.48 1.40
2244 2878 4.642445 TGTGACGTGATACATCCGTATT 57.358 40.909 0.00 0.00 38.48 1.89
2245 2879 4.848562 ATGTGACGTGATACATCCGTAT 57.151 40.909 0.00 0.00 41.16 3.06
2246 2880 4.642445 AATGTGACGTGATACATCCGTA 57.358 40.909 0.00 0.00 36.56 4.02
2247 2881 3.520290 AATGTGACGTGATACATCCGT 57.480 42.857 0.00 5.73 36.56 4.69
2248 2882 4.857871 AAAATGTGACGTGATACATCCG 57.142 40.909 0.00 0.00 36.56 4.18
2249 2883 7.534085 TTCTAAAATGTGACGTGATACATCC 57.466 36.000 0.00 0.00 36.56 3.51
2252 2886 9.863845 TCTAATTCTAAAATGTGACGTGATACA 57.136 29.630 0.00 0.00 0.00 2.29
2256 2890 9.863845 TGTATCTAATTCTAAAATGTGACGTGA 57.136 29.630 0.00 0.00 0.00 4.35
2292 2926 9.546428 CCCAAAATTCTTGTCTTAAATTTGTCT 57.454 29.630 0.00 0.00 33.95 3.41
2293 2927 9.541143 TCCCAAAATTCTTGTCTTAAATTTGTC 57.459 29.630 0.00 0.00 33.95 3.18
2294 2928 9.325198 GTCCCAAAATTCTTGTCTTAAATTTGT 57.675 29.630 0.00 0.00 33.95 2.83
2295 2929 8.487176 CGTCCCAAAATTCTTGTCTTAAATTTG 58.513 33.333 0.00 0.00 33.95 2.32
2296 2930 7.655732 CCGTCCCAAAATTCTTGTCTTAAATTT 59.344 33.333 0.00 0.00 34.86 1.82
2297 2931 7.014808 TCCGTCCCAAAATTCTTGTCTTAAATT 59.985 33.333 0.00 0.00 0.00 1.82
2298 2932 6.492087 TCCGTCCCAAAATTCTTGTCTTAAAT 59.508 34.615 0.00 0.00 0.00 1.40
2299 2933 5.828859 TCCGTCCCAAAATTCTTGTCTTAAA 59.171 36.000 0.00 0.00 0.00 1.52
2300 2934 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
2301 2935 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2302 2936 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2303 2937 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2304 2938 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2305 2939 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2306 2940 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2307 2941 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2308 2942 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2309 2943 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2310 2944 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2311 2945 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2312 2946 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2313 2947 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
2314 2948 0.178926 TTGTACTCCCTCCGTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
2315 2949 0.901580 GTTGTACTCCCTCCGTCCCA 60.902 60.000 0.00 0.00 0.00 4.37
2316 2950 1.895966 GTTGTACTCCCTCCGTCCC 59.104 63.158 0.00 0.00 0.00 4.46
2317 2951 1.509923 CGTTGTACTCCCTCCGTCC 59.490 63.158 0.00 0.00 0.00 4.79
2318 2952 1.153881 GCGTTGTACTCCCTCCGTC 60.154 63.158 0.00 0.00 0.00 4.79
2319 2953 1.605738 AGCGTTGTACTCCCTCCGT 60.606 57.895 0.00 0.00 0.00 4.69
2320 2954 1.153823 CAGCGTTGTACTCCCTCCG 60.154 63.158 0.00 0.00 0.00 4.63
2321 2955 0.606604 TTCAGCGTTGTACTCCCTCC 59.393 55.000 0.00 0.00 0.00 4.30
2322 2956 2.674796 ATTCAGCGTTGTACTCCCTC 57.325 50.000 0.00 0.00 0.00 4.30
2323 2957 5.304614 ACATATATTCAGCGTTGTACTCCCT 59.695 40.000 0.00 0.00 0.00 4.20
2324 2958 5.539048 ACATATATTCAGCGTTGTACTCCC 58.461 41.667 0.00 0.00 0.00 4.30
2325 2959 7.148787 GCTTACATATATTCAGCGTTGTACTCC 60.149 40.741 0.00 0.00 0.00 3.85
2326 2960 7.381408 TGCTTACATATATTCAGCGTTGTACTC 59.619 37.037 0.00 0.00 32.85 2.59
2461 3100 4.844349 AACCAGCACTACATAGGACATT 57.156 40.909 0.00 0.00 0.00 2.71
2506 3145 4.399004 TTTTGGCACTGTAAATGCAGTT 57.601 36.364 4.23 4.23 46.45 3.16
2932 3571 3.476552 TGCACTAAAGTTGGACAAGAGG 58.523 45.455 0.00 0.00 0.00 3.69
2943 3582 4.634012 TCCAGGTGTATTGCACTAAAGT 57.366 40.909 4.86 0.00 46.86 2.66
2967 3606 5.804944 ACTCTGTATGAGGGATGATCTTG 57.195 43.478 0.00 0.00 46.72 3.02
2975 3614 5.827756 TCAAGAACTACTCTGTATGAGGGA 58.172 41.667 0.00 0.00 46.72 4.20
2997 3636 9.909644 ATACAAGGTTACATTACTCATCGTATC 57.090 33.333 0.00 0.00 0.00 2.24
3066 3705 3.701040 ACAGTGAAACACCTGCTCAAAAT 59.299 39.130 0.00 0.00 41.43 1.82
3115 3820 2.437359 CCAAGCTGGAAGGCCTCG 60.437 66.667 5.23 0.00 40.96 4.63
3172 3877 2.103143 CGCGCCTCATTCTCGTCT 59.897 61.111 0.00 0.00 0.00 4.18
3410 4115 0.603569 CAGAGAACTGGTACGCAGGT 59.396 55.000 13.68 8.52 40.14 4.00
3482 4189 6.036517 GGATAGGCGATATCATGTCAAATGAC 59.963 42.308 6.60 6.60 41.94 3.06
3487 4194 3.119137 CGGGATAGGCGATATCATGTCAA 60.119 47.826 3.12 0.00 41.94 3.18
3571 4280 4.165950 TCATCCTAGCCTCCTAATTTTGCA 59.834 41.667 0.00 0.00 0.00 4.08
3610 4319 3.450817 CCGTGGGATGCCATATATACAGA 59.549 47.826 10.01 0.00 0.00 3.41
3630 4339 4.054780 TGAGCTAACCTGTAATAAGCCG 57.945 45.455 0.00 0.00 33.63 5.52
3805 4543 1.352083 TCATCATACTAGGCCCCAGC 58.648 55.000 0.00 0.00 38.76 4.85
3854 4592 1.272928 ACATCAGTCTCAGCCTCTCCA 60.273 52.381 0.00 0.00 0.00 3.86
3861 4599 5.955488 TGAGTACTTAACATCAGTCTCAGC 58.045 41.667 0.00 0.00 31.00 4.26
3865 4603 7.468141 TGTCATGAGTACTTAACATCAGTCT 57.532 36.000 0.00 0.00 0.00 3.24
3879 4617 5.409520 GTCAAGCTGTCAAATGTCATGAGTA 59.590 40.000 0.00 0.00 0.00 2.59
3880 4618 4.214971 GTCAAGCTGTCAAATGTCATGAGT 59.785 41.667 0.00 0.00 0.00 3.41
3882 4620 3.503363 GGTCAAGCTGTCAAATGTCATGA 59.497 43.478 0.00 0.00 0.00 3.07
3939 4788 1.661463 TCCTGGAGCAGAAGTCCATT 58.339 50.000 0.00 0.00 43.33 3.16
3948 4797 6.602410 TCAGATAAGATTATCCTGGAGCAG 57.398 41.667 1.52 0.00 40.26 4.24
3973 4823 5.109903 ACGCATTACTCAAGTCACTAATCC 58.890 41.667 0.00 0.00 0.00 3.01
4004 4854 1.787847 CGTTGCCCGTCTTGATGAC 59.212 57.895 0.00 0.00 42.06 3.06
4073 4943 1.135333 CCTAACCCTCGCTCTCAAGTC 59.865 57.143 0.00 0.00 0.00 3.01
4074 4944 1.187087 CCTAACCCTCGCTCTCAAGT 58.813 55.000 0.00 0.00 0.00 3.16
4114 4984 2.793933 GCCTCTAACTTGTACGTAGCCG 60.794 54.545 0.00 0.00 40.83 5.52
4142 5012 8.566260 GTGTTTCTGTAGAGTACTAGACTTTCA 58.434 37.037 0.00 0.00 39.06 2.69
4183 5053 8.098286 TCTCCGGTCTCATTTTTATTTGAAGTA 58.902 33.333 0.00 0.00 0.00 2.24
4210 5080 4.634443 CCAGTCCGGTCTTTAAAAGTATGG 59.366 45.833 0.00 0.00 0.00 2.74
4358 5231 9.849166 TTTTAAAGAAAAGACCAGTACAAGTTG 57.151 29.630 0.00 0.00 30.89 3.16
4543 5438 4.048504 GGTTCATTTCCGACAAAAACCAG 58.951 43.478 0.00 0.00 0.00 4.00
4556 5451 3.574614 CACCGGTTCATTGGTTCATTTC 58.425 45.455 2.97 0.00 35.96 2.17


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

AutoCloner maintained by Alex Coulton.