Multiple sequence alignment - TraesCS2B01G388500

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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 TraesCS2B01G388500 chr2B 100.000 3038 0 0 1 3038 551536195 551533158 0.000000e+00 5611.0
1 TraesCS2B01G388500 chr2B 83.869 1525 136 54 849 2304 551567556 551566073 0.000000e+00 1352.0
2 TraesCS2B01G388500 chr2B 81.155 329 53 8 2668 2991 275998767 275998443 3.890000e-64 255.0
3 TraesCS2B01G388500 chr2B 87.379 103 13 0 2293 2395 135771070 135770968 5.320000e-23 119.0
4 TraesCS2B01G388500 chr2B 87.879 99 12 0 2297 2395 222587043 222587141 1.910000e-22 117.0
5 TraesCS2B01G388500 chr2A 92.461 1101 52 11 1183 2262 613703829 613702739 0.000000e+00 1544.0
6 TraesCS2B01G388500 chr2A 92.575 835 35 10 1 809 613720033 613719200 0.000000e+00 1173.0
7 TraesCS2B01G388500 chr2A 88.904 748 53 11 1575 2304 613878068 613877333 0.000000e+00 894.0
8 TraesCS2B01G388500 chr2A 98.731 394 3 1 794 1185 613714257 613713864 0.000000e+00 699.0
9 TraesCS2B01G388500 chr2A 87.239 431 44 7 939 1359 613878534 613878105 5.890000e-132 481.0
10 TraesCS2B01G388500 chr2A 78.755 273 42 9 2398 2663 504491337 504491600 5.210000e-38 169.0
11 TraesCS2B01G388500 chr2D 96.631 742 21 2 642 1381 472231947 472231208 0.000000e+00 1229.0
12 TraesCS2B01G388500 chr2D 94.310 703 31 5 1380 2081 472231126 472230432 0.000000e+00 1068.0
13 TraesCS2B01G388500 chr2D 94.162 668 26 3 1 657 472233189 472232524 0.000000e+00 1005.0
14 TraesCS2B01G388500 chr2D 89.116 588 52 8 1575 2156 472445271 472444690 0.000000e+00 721.0
15 TraesCS2B01G388500 chr2D 87.879 429 42 6 940 1359 472445737 472445310 2.100000e-136 496.0
16 TraesCS2B01G388500 chr2D 85.580 319 43 3 2667 2985 423842228 423841913 6.280000e-87 331.0
17 TraesCS2B01G388500 chr2D 82.353 272 40 8 2401 2666 423842531 423842262 2.360000e-56 230.0
18 TraesCS2B01G388500 chr2D 78.916 332 56 10 2676 2996 235149749 235150077 2.370000e-51 213.0
19 TraesCS2B01G388500 chr2D 77.455 275 45 12 2398 2665 233220361 233220625 6.790000e-32 148.0
20 TraesCS2B01G388500 chr2D 95.890 73 3 0 2167 2239 472444124 472444052 5.320000e-23 119.0
21 TraesCS2B01G388500 chr1B 81.051 628 83 22 2398 2996 466982747 466983367 4.590000e-128 468.0
22 TraesCS2B01G388500 chr1B 88.776 98 11 0 2297 2394 377103638 377103541 1.480000e-23 121.0
23 TraesCS2B01G388500 chr1D 86.866 335 40 3 2662 2996 346692397 346692727 3.700000e-99 372.0
24 TraesCS2B01G388500 chr1D 82.738 336 50 6 2668 2996 168408249 168407915 2.960000e-75 292.0
25 TraesCS2B01G388500 chr1D 95.833 48 2 0 2991 3038 54266066 54266019 9.030000e-11 78.7
26 TraesCS2B01G388500 chr5B 76.238 505 98 17 2401 2898 516222339 516221850 6.500000e-62 248.0
27 TraesCS2B01G388500 chr5B 81.132 265 46 2 2389 2650 450336884 450337147 3.070000e-50 209.0
28 TraesCS2B01G388500 chr5B 100.000 45 0 0 2994 3038 475047912 475047956 1.940000e-12 84.2
29 TraesCS2B01G388500 chr3D 81.818 275 42 5 2398 2666 303113440 303113712 1.100000e-54 224.0
30 TraesCS2B01G388500 chr6D 80.812 271 46 4 2401 2665 168061022 168060752 1.100000e-49 207.0
31 TraesCS2B01G388500 chr6D 80.426 235 37 6 2672 2903 168060712 168060484 1.450000e-38 171.0
32 TraesCS2B01G388500 chr6D 97.917 48 0 1 2991 3038 379182756 379182710 6.980000e-12 82.4
33 TraesCS2B01G388500 chr5D 75.269 465 81 18 2418 2876 102398847 102398411 1.110000e-44 191.0
34 TraesCS2B01G388500 chr7A 77.670 309 64 5 2674 2980 293987543 293987238 1.860000e-42 183.0
35 TraesCS2B01G388500 chr7A 88.235 102 12 0 2294 2395 185591913 185592014 4.110000e-24 122.0
36 TraesCS2B01G388500 chr7A 81.818 110 13 3 702 804 352678243 352678134 5.400000e-13 86.1
37 TraesCS2B01G388500 chr7A 97.826 46 1 0 2993 3038 465435575 465435530 2.510000e-11 80.5
38 TraesCS2B01G388500 chr7A 87.692 65 3 4 2978 3038 41398397 41398334 1.510000e-08 71.3
39 TraesCS2B01G388500 chr7B 77.019 322 64 9 2672 2985 241942584 241942265 3.110000e-40 176.0
40 TraesCS2B01G388500 chr7B 87.879 99 12 0 2297 2395 658058610 658058708 1.910000e-22 117.0
41 TraesCS2B01G388500 chr7B 97.826 46 1 0 2993 3038 744702450 744702495 2.510000e-11 80.5
42 TraesCS2B01G388500 chr4D 78.832 274 41 10 2398 2664 222961243 222960980 5.210000e-38 169.0
43 TraesCS2B01G388500 chr7D 77.941 272 43 11 2399 2663 343151676 343151415 1.460000e-33 154.0
44 TraesCS2B01G388500 chr1A 84.507 142 22 0 2844 2985 217448371 217448230 1.140000e-29 141.0
45 TraesCS2B01G388500 chr1A 86.239 109 14 1 2288 2395 545755490 545755382 1.910000e-22 117.0
46 TraesCS2B01G388500 chr6A 88.119 101 12 0 2295 2395 474329068 474328968 1.480000e-23 121.0
47 TraesCS2B01G388500 chr5A 89.474 95 10 0 2297 2391 556732420 556732514 1.480000e-23 121.0
48 TraesCS2B01G388500 chr3B 87.879 99 12 0 2297 2395 333447924 333447826 1.910000e-22 117.0
49 TraesCS2B01G388500 chr6B 100.000 47 0 0 2992 3038 558283861 558283815 1.500000e-13 87.9
50 TraesCS2B01G388500 chr3A 100.000 45 0 0 2994 3038 569281701 569281657 1.940000e-12 84.2
51 TraesCS2B01G388500 chr4A 94.231 52 1 2 2988 3038 510155446 510155396 9.030000e-11 78.7


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 TraesCS2B01G388500 chr2B 551533158 551536195 3037 True 5611.000000 5611 100.000000 1 3038 1 chr2B.!!$R3 3037
1 TraesCS2B01G388500 chr2B 551566073 551567556 1483 True 1352.000000 1352 83.869000 849 2304 1 chr2B.!!$R4 1455
2 TraesCS2B01G388500 chr2A 613702739 613703829 1090 True 1544.000000 1544 92.461000 1183 2262 1 chr2A.!!$R1 1079
3 TraesCS2B01G388500 chr2A 613719200 613720033 833 True 1173.000000 1173 92.575000 1 809 1 chr2A.!!$R3 808
4 TraesCS2B01G388500 chr2A 613877333 613878534 1201 True 687.500000 894 88.071500 939 2304 2 chr2A.!!$R4 1365
5 TraesCS2B01G388500 chr2D 472230432 472233189 2757 True 1100.666667 1229 95.034333 1 2081 3 chr2D.!!$R2 2080
6 TraesCS2B01G388500 chr2D 472444052 472445737 1685 True 445.333333 721 90.961667 940 2239 3 chr2D.!!$R3 1299
7 TraesCS2B01G388500 chr2D 423841913 423842531 618 True 280.500000 331 83.966500 2401 2985 2 chr2D.!!$R1 584
8 TraesCS2B01G388500 chr1B 466982747 466983367 620 False 468.000000 468 81.051000 2398 2996 1 chr1B.!!$F1 598

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
825 1444 3.691342 CGGGTCGGCCTCAACTCA 61.691 66.667 5.77 0.00 34.45 3.41 F
1856 2625 0.250513 ACGAGGATCCTTGCCAAGAC 59.749 55.000 26.64 5.87 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 2633 0.168788 AAACAGTTGATGCGCATCGG 59.831 50.0 37.23 28.84 40.63 4.18 R
2840 4220 0.871722 GCCGCAGTTCATTACACACA 59.128 50.0 0.00 0.00 0.00 3.72 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
35 36 4.092968 GGGTAAACTACGCTGTTCAGATTG 59.907 45.833 3.84 0.00 38.45 2.67
86 98 9.525826 AGAAGTGATTTTTCTAATTCATCACCT 57.474 29.630 6.92 0.00 43.19 4.00
366 388 8.569641 CCTAGAGCGTAGTTTAGTATGAGAAAT 58.430 37.037 0.00 0.00 0.00 2.17
399 421 4.286910 CAATGTTGTGTAAAGGGTGAACG 58.713 43.478 0.00 0.00 0.00 3.95
460 482 6.744537 CAGCATCATTCTTTTGTAACTAGCAC 59.255 38.462 0.00 0.00 0.00 4.40
478 500 8.276252 ACTAGCACAGTTTAGTTTGAGAAAAA 57.724 30.769 0.00 0.00 31.59 1.94
825 1444 3.691342 CGGGTCGGCCTCAACTCA 61.691 66.667 5.77 0.00 34.45 3.41
1104 1738 1.549203 ACTATGGGGCAAAGCTTGTG 58.451 50.000 0.00 1.84 0.00 3.33
1229 1870 8.915036 ACAGATCGATAAGACCAATTACTAGTT 58.085 33.333 0.00 0.00 0.00 2.24
1230 1871 9.751542 CAGATCGATAAGACCAATTACTAGTTT 57.248 33.333 0.00 0.00 0.00 2.66
1290 1938 9.344772 TGTTTCTGTTATAGCTTTCTTTACCAA 57.655 29.630 0.00 0.00 0.00 3.67
1365 2013 8.429641 TGTCTTCCAGAATATTATTACAGTCCC 58.570 37.037 0.00 0.00 0.00 4.46
1624 2386 6.183360 GCACAGGTTCAGAAACTAGTTCTTTT 60.183 38.462 8.95 0.00 44.64 2.27
1625 2387 7.628580 GCACAGGTTCAGAAACTAGTTCTTTTT 60.629 37.037 8.95 0.00 44.64 1.94
1626 2388 8.889717 CACAGGTTCAGAAACTAGTTCTTTTTA 58.110 33.333 8.95 0.00 44.64 1.52
1627 2389 9.110502 ACAGGTTCAGAAACTAGTTCTTTTTAG 57.889 33.333 8.95 0.00 44.64 1.85
1706 2475 3.571571 TCGACGACATTGACAACCTTAG 58.428 45.455 0.00 0.00 0.00 2.18
1856 2625 0.250513 ACGAGGATCCTTGCCAAGAC 59.749 55.000 26.64 5.87 0.00 3.01
1864 2633 0.955919 CCTTGCCAAGACGTTCCCTC 60.956 60.000 5.89 0.00 0.00 4.30
1905 2674 1.308998 CGCCTGGTTTTGTCAAGAGT 58.691 50.000 0.00 0.00 0.00 3.24
1926 2695 2.027325 CATGTCGATGCACATGGGG 58.973 57.895 0.00 0.00 46.84 4.96
2124 2899 5.820423 AGTTGTCAATAAACAGTGTGCAGTA 59.180 36.000 0.00 0.00 0.00 2.74
2139 2914 2.038426 TGCAGTATAACCTGTGCTGTGT 59.962 45.455 0.00 0.00 36.84 3.72
2156 2933 3.081061 TGTGTACTCAAATGGACATGCC 58.919 45.455 0.00 0.00 37.10 4.40
2157 2934 3.244875 TGTGTACTCAAATGGACATGCCT 60.245 43.478 7.54 0.00 37.63 4.75
2158 2935 3.127548 GTGTACTCAAATGGACATGCCTG 59.872 47.826 7.54 0.00 37.63 4.85
2159 2936 2.592102 ACTCAAATGGACATGCCTGT 57.408 45.000 0.00 0.00 38.67 4.00
2160 2937 2.165167 ACTCAAATGGACATGCCTGTG 58.835 47.619 0.00 0.00 35.14 3.66
2162 2939 2.161855 TCAAATGGACATGCCTGTGTC 58.838 47.619 0.00 2.38 46.04 3.67
2278 3621 1.510480 GGCAGGCAATAGGATGACGC 61.510 60.000 0.00 0.00 31.91 5.19
2297 3640 1.303888 ATGGGTGTTGCTGGCTGAG 60.304 57.895 0.00 0.00 0.00 3.35
2300 3643 3.368571 GTGTTGCTGGCTGAGGGC 61.369 66.667 0.00 0.00 40.90 5.19
2301 3644 3.888460 TGTTGCTGGCTGAGGGCA 61.888 61.111 0.00 0.00 45.89 5.36
2302 3645 2.362120 GTTGCTGGCTGAGGGCAT 60.362 61.111 0.00 0.00 46.81 4.40
2303 3646 2.361992 TTGCTGGCTGAGGGCATG 60.362 61.111 0.00 0.00 46.81 4.06
2304 3647 3.214190 TTGCTGGCTGAGGGCATGT 62.214 57.895 0.00 0.00 46.81 3.21
2305 3648 1.851065 TTGCTGGCTGAGGGCATGTA 61.851 55.000 0.00 0.00 46.81 2.29
2306 3649 1.821332 GCTGGCTGAGGGCATGTAC 60.821 63.158 0.00 0.00 46.81 2.90
2307 3650 1.603842 CTGGCTGAGGGCATGTACA 59.396 57.895 0.00 0.00 46.81 2.90
2308 3651 0.035152 CTGGCTGAGGGCATGTACAA 60.035 55.000 0.00 0.00 46.81 2.41
2309 3652 0.625316 TGGCTGAGGGCATGTACAAT 59.375 50.000 0.00 0.00 43.20 2.71
2310 3653 1.027357 GGCTGAGGGCATGTACAATG 58.973 55.000 0.00 0.12 44.01 2.82
2311 3654 1.408683 GGCTGAGGGCATGTACAATGA 60.409 52.381 0.00 0.00 44.01 2.57
2312 3655 2.579873 GCTGAGGGCATGTACAATGAT 58.420 47.619 0.00 0.00 41.35 2.45
2313 3656 2.551459 GCTGAGGGCATGTACAATGATC 59.449 50.000 0.00 0.00 41.35 2.92
2314 3657 3.812262 CTGAGGGCATGTACAATGATCA 58.188 45.455 0.00 0.00 0.00 2.92
2315 3658 3.544684 TGAGGGCATGTACAATGATCAC 58.455 45.455 0.00 0.00 0.00 3.06
2316 3659 3.054508 TGAGGGCATGTACAATGATCACA 60.055 43.478 0.00 0.00 0.00 3.58
2317 3660 4.139786 GAGGGCATGTACAATGATCACAT 58.860 43.478 0.00 0.00 38.50 3.21
2318 3661 5.163216 TGAGGGCATGTACAATGATCACATA 60.163 40.000 0.00 0.00 35.50 2.29
2319 3662 5.884322 AGGGCATGTACAATGATCACATAT 58.116 37.500 0.00 0.00 35.50 1.78
2320 3663 5.708697 AGGGCATGTACAATGATCACATATG 59.291 40.000 0.00 0.00 35.50 1.78
2321 3664 5.106038 GGGCATGTACAATGATCACATATGG 60.106 44.000 7.80 0.00 35.50 2.74
2322 3665 5.706833 GGCATGTACAATGATCACATATGGA 59.293 40.000 7.80 2.05 35.50 3.41
2323 3666 6.376299 GGCATGTACAATGATCACATATGGAT 59.624 38.462 7.80 7.00 35.50 3.41
2324 3667 7.553760 GGCATGTACAATGATCACATATGGATA 59.446 37.037 7.80 0.00 35.50 2.59
2325 3668 9.117183 GCATGTACAATGATCACATATGGATAT 57.883 33.333 7.80 0.00 35.50 1.63
2334 3677 8.255111 TGATCACATATGGATATAGATGTCCC 57.745 38.462 7.80 0.00 37.28 4.46
2335 3678 7.845800 TGATCACATATGGATATAGATGTCCCA 59.154 37.037 7.80 0.00 37.28 4.37
2336 3679 8.809789 ATCACATATGGATATAGATGTCCCAT 57.190 34.615 7.80 0.00 37.28 4.00
2337 3680 8.026396 TCACATATGGATATAGATGTCCCATG 57.974 38.462 7.80 11.97 37.28 3.66
2338 3681 7.845800 TCACATATGGATATAGATGTCCCATGA 59.154 37.037 16.96 6.84 37.28 3.07
2339 3682 7.930325 CACATATGGATATAGATGTCCCATGAC 59.070 40.741 16.96 0.00 42.12 3.06
2354 3697 7.873739 GTCCCATGACAAAAAGTAATTTGAG 57.126 36.000 6.76 0.00 41.73 3.02
2355 3698 6.868339 GTCCCATGACAAAAAGTAATTTGAGG 59.132 38.462 6.76 3.59 41.73 3.86
2356 3699 5.639082 CCCATGACAAAAAGTAATTTGAGGC 59.361 40.000 6.76 0.00 41.73 4.70
2357 3700 6.222389 CCATGACAAAAAGTAATTTGAGGCA 58.778 36.000 6.76 0.00 41.73 4.75
2358 3701 6.875195 CCATGACAAAAAGTAATTTGAGGCAT 59.125 34.615 6.76 3.81 41.73 4.40
2359 3702 7.063780 CCATGACAAAAAGTAATTTGAGGCATC 59.936 37.037 6.09 0.00 41.73 3.91
2360 3703 7.288810 TGACAAAAAGTAATTTGAGGCATCT 57.711 32.000 0.00 0.00 41.73 2.90
2361 3704 8.402798 TGACAAAAAGTAATTTGAGGCATCTA 57.597 30.769 0.00 0.00 41.73 1.98
2362 3705 9.023962 TGACAAAAAGTAATTTGAGGCATCTAT 57.976 29.630 0.00 0.00 41.73 1.98
2388 3731 0.316841 TTTTTCCCCACGATGCAAGC 59.683 50.000 0.00 0.00 0.00 4.01
2389 3732 0.539438 TTTTCCCCACGATGCAAGCT 60.539 50.000 0.00 0.00 0.00 3.74
2390 3733 0.326595 TTTCCCCACGATGCAAGCTA 59.673 50.000 0.00 0.00 0.00 3.32
2391 3734 0.326595 TTCCCCACGATGCAAGCTAA 59.673 50.000 0.00 0.00 0.00 3.09
2392 3735 0.392461 TCCCCACGATGCAAGCTAAC 60.392 55.000 0.00 0.00 0.00 2.34
2393 3736 0.676466 CCCCACGATGCAAGCTAACA 60.676 55.000 0.00 0.00 0.00 2.41
2394 3737 0.447801 CCCACGATGCAAGCTAACAC 59.552 55.000 0.00 0.00 0.00 3.32
2395 3738 1.155889 CCACGATGCAAGCTAACACA 58.844 50.000 0.00 0.00 0.00 3.72
2396 3739 1.739466 CCACGATGCAAGCTAACACAT 59.261 47.619 0.00 0.00 0.00 3.21
2399 3742 2.009051 CGATGCAAGCTAACACATGGA 58.991 47.619 0.00 0.00 0.00 3.41
2456 3799 2.328099 GCGCACCCTCCACTTCAAG 61.328 63.158 0.30 0.00 0.00 3.02
2459 3802 1.809684 GCACCCTCCACTTCAAGTAC 58.190 55.000 0.00 0.00 0.00 2.73
2462 3805 2.233922 CACCCTCCACTTCAAGTACGAT 59.766 50.000 0.00 0.00 0.00 3.73
2469 3812 3.325870 CACTTCAAGTACGATGGAGCAA 58.674 45.455 9.25 0.00 0.00 3.91
2506 3849 2.620234 TCTTCGGGGAAGATGGCAT 58.380 52.632 0.00 0.00 42.78 4.40
2507 3850 1.801242 TCTTCGGGGAAGATGGCATA 58.199 50.000 0.00 0.00 42.78 3.14
2522 3865 0.673644 GCATACGCCTGGAGTGTTGT 60.674 55.000 13.68 0.00 40.51 3.32
2537 3880 3.240134 TTGTCCAGAGGGCGACAGC 62.240 63.158 0.00 0.00 39.99 4.40
2603 3949 2.664851 CTCGGCGGTGAACTTGCA 60.665 61.111 7.21 0.00 0.00 4.08
2635 3981 2.433838 CGACACCTCCAGCAGCAG 60.434 66.667 0.00 0.00 0.00 4.24
2684 4064 2.273179 CGGGTCAAGGAGGACGACA 61.273 63.158 0.00 0.00 38.70 4.35
2689 4069 1.738099 CAAGGAGGACGACAAGCCG 60.738 63.158 0.00 0.00 0.00 5.52
2693 4073 4.681978 AGGACGACAAGCCGCCAC 62.682 66.667 0.00 0.00 0.00 5.01
2742 4122 3.062466 CTCCGACTGAGCGTGGGA 61.062 66.667 0.00 0.00 46.72 4.37
2784 4164 2.935481 CTGTGGCCCTTGGGAGGA 60.935 66.667 10.36 0.00 46.74 3.71
2840 4220 2.610859 ATGAAGAGCCCCACGGGT 60.611 61.111 0.41 0.00 46.51 5.28
2883 4263 5.205565 GCTTGCGCCTTTATATTAGTGTTC 58.794 41.667 4.18 0.00 0.00 3.18
2938 4318 3.133365 AAAGGTTCCAGGCTGGCGT 62.133 57.895 29.02 14.24 37.47 5.68
2944 4324 0.546122 TTCCAGGCTGGCGTGATTAT 59.454 50.000 29.02 0.00 37.47 1.28
2945 4325 1.419381 TCCAGGCTGGCGTGATTATA 58.581 50.000 29.02 5.06 37.47 0.98
2948 4328 2.408050 CAGGCTGGCGTGATTATAGTC 58.592 52.381 6.61 0.00 34.13 2.59
2977 4357 4.032452 TGCGCTCATGGCCCTTGA 62.032 61.111 9.73 2.29 37.74 3.02
2997 4377 2.890474 GGTTCGCGCATCGTGGAT 60.890 61.111 8.75 0.00 37.97 3.41
2998 4378 2.321060 GTTCGCGCATCGTGGATG 59.679 61.111 8.75 1.29 42.37 3.51
2999 4379 2.164663 GTTCGCGCATCGTGGATGA 61.165 57.895 8.75 0.00 42.09 2.92
3000 4380 1.446966 TTCGCGCATCGTGGATGAA 60.447 52.632 8.75 0.00 42.09 2.57
3001 4381 1.420641 TTCGCGCATCGTGGATGAAG 61.421 55.000 8.75 3.97 42.09 3.02
3002 4382 2.874694 CGCGCATCGTGGATGAAGG 61.875 63.158 8.75 0.00 42.09 3.46
3003 4383 1.521457 GCGCATCGTGGATGAAGGA 60.521 57.895 0.30 0.00 42.09 3.36
3004 4384 1.089481 GCGCATCGTGGATGAAGGAA 61.089 55.000 0.30 0.00 42.09 3.36
3005 4385 1.368641 CGCATCGTGGATGAAGGAAA 58.631 50.000 9.66 0.00 42.09 3.13
3006 4386 1.942657 CGCATCGTGGATGAAGGAAAT 59.057 47.619 9.66 0.00 42.09 2.17
3007 4387 3.130633 CGCATCGTGGATGAAGGAAATA 58.869 45.455 9.66 0.00 42.09 1.40
3008 4388 3.748048 CGCATCGTGGATGAAGGAAATAT 59.252 43.478 9.66 0.00 42.09 1.28
3009 4389 4.377738 CGCATCGTGGATGAAGGAAATATG 60.378 45.833 9.66 0.00 42.09 1.78
3010 4390 4.614535 GCATCGTGGATGAAGGAAATATGC 60.615 45.833 9.66 0.00 42.09 3.14
3011 4391 3.476552 TCGTGGATGAAGGAAATATGCC 58.523 45.455 0.00 0.00 0.00 4.40
3012 4392 2.554032 CGTGGATGAAGGAAATATGCCC 59.446 50.000 0.00 0.00 0.00 5.36
3013 4393 3.748668 CGTGGATGAAGGAAATATGCCCT 60.749 47.826 0.00 0.00 0.00 5.19
3014 4394 4.504864 CGTGGATGAAGGAAATATGCCCTA 60.505 45.833 0.00 0.00 31.36 3.53
3015 4395 5.006386 GTGGATGAAGGAAATATGCCCTAG 58.994 45.833 0.00 0.00 31.36 3.02
3016 4396 4.913355 TGGATGAAGGAAATATGCCCTAGA 59.087 41.667 0.00 0.00 31.36 2.43
3017 4397 5.013495 TGGATGAAGGAAATATGCCCTAGAG 59.987 44.000 0.00 0.00 31.36 2.43
3018 4398 5.249393 GGATGAAGGAAATATGCCCTAGAGA 59.751 44.000 0.00 0.00 31.36 3.10
3019 4399 5.552870 TGAAGGAAATATGCCCTAGAGAC 57.447 43.478 0.00 0.00 31.36 3.36
3020 4400 4.968719 TGAAGGAAATATGCCCTAGAGACA 59.031 41.667 0.00 0.00 31.36 3.41
3021 4401 5.428457 TGAAGGAAATATGCCCTAGAGACAA 59.572 40.000 0.00 0.00 31.36 3.18
3022 4402 6.101734 TGAAGGAAATATGCCCTAGAGACAAT 59.898 38.462 0.00 0.00 31.36 2.71
3023 4403 7.292356 TGAAGGAAATATGCCCTAGAGACAATA 59.708 37.037 0.00 0.00 31.36 1.90
3024 4404 7.633018 AGGAAATATGCCCTAGAGACAATAA 57.367 36.000 0.00 0.00 0.00 1.40
3025 4405 8.224620 AGGAAATATGCCCTAGAGACAATAAT 57.775 34.615 0.00 0.00 0.00 1.28
3026 4406 9.338968 AGGAAATATGCCCTAGAGACAATAATA 57.661 33.333 0.00 0.00 0.00 0.98
3027 4407 9.959721 GGAAATATGCCCTAGAGACAATAATAA 57.040 33.333 0.00 0.00 0.00 1.40
3032 4412 8.682936 ATGCCCTAGAGACAATAATAAAGTTG 57.317 34.615 0.00 0.00 0.00 3.16
3033 4413 7.630082 TGCCCTAGAGACAATAATAAAGTTGT 58.370 34.615 0.00 0.00 40.97 3.32
3034 4414 8.107095 TGCCCTAGAGACAATAATAAAGTTGTT 58.893 33.333 0.00 0.00 38.57 2.83
3035 4415 9.609346 GCCCTAGAGACAATAATAAAGTTGTTA 57.391 33.333 0.00 0.00 38.57 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 6.970484 ACATAAACACCAATGAGAAGTCAAC 58.030 36.000 0.00 0.00 35.88 3.18
366 388 8.892723 CCTTTACACAACATTGCTAAGATATGA 58.107 33.333 0.00 0.00 0.00 2.15
376 398 4.048504 GTTCACCCTTTACACAACATTGC 58.951 43.478 0.00 0.00 0.00 3.56
378 400 3.949113 ACGTTCACCCTTTACACAACATT 59.051 39.130 0.00 0.00 0.00 2.71
399 421 5.882557 TGATTTCTGGAATCCAAGCTTCTAC 59.117 40.000 2.61 0.00 42.90 2.59
543 565 8.402798 TGCAGAATTTTAGGATTGTCAACTTA 57.597 30.769 0.00 0.00 0.00 2.24
645 672 5.939883 TCATTGCTCCTGTATGTAATATGGC 59.060 40.000 0.00 0.00 0.00 4.40
680 1299 1.407258 TGCTTGCACACCCAAACTTAC 59.593 47.619 0.00 0.00 0.00 2.34
691 1310 2.275134 TGAGGAATTCTGCTTGCACA 57.725 45.000 5.23 0.00 0.00 4.57
974 1608 6.643770 GCTTTCAACCTATCCATGCATAAATG 59.356 38.462 0.00 0.00 0.00 2.32
1365 2013 5.063944 CCAATCTCTTATTTGACACTCCGTG 59.936 44.000 0.00 0.00 39.75 4.94
1373 2021 7.775561 ACAGGAATACCCAATCTCTTATTTGAC 59.224 37.037 0.00 0.00 37.41 3.18
1387 2118 7.206789 TCATTTATGAGAACAGGAATACCCA 57.793 36.000 0.00 0.00 32.80 4.51
1427 2158 6.151691 GCTTATTGCATCTGACAAAACAAGA 58.848 36.000 0.00 0.00 42.31 3.02
1458 2189 7.667043 TGAACACGAAGCTAAACTGAAATAT 57.333 32.000 0.00 0.00 0.00 1.28
1542 2302 4.174704 TGAAGGATGAGGATTTGGATGG 57.825 45.455 0.00 0.00 0.00 3.51
1544 2304 5.658198 TGATGAAGGATGAGGATTTGGAT 57.342 39.130 0.00 0.00 0.00 3.41
1595 2357 5.193679 ACTAGTTTCTGAACCTGTGCTTTT 58.806 37.500 0.00 0.00 36.39 2.27
1626 2388 9.231297 TGCTCAAGAAAACAATACTTATTAGCT 57.769 29.630 0.00 0.00 31.11 3.32
1627 2389 9.495754 CTGCTCAAGAAAACAATACTTATTAGC 57.504 33.333 0.00 0.00 0.00 3.09
1706 2475 5.185056 AGAAGCTCCTCTAGTCTCTTTTCAC 59.815 44.000 0.00 0.00 0.00 3.18
1856 2625 4.812476 TGCGCATCGGAGGGAACG 62.812 66.667 5.66 0.00 0.00 3.95
1864 2633 0.168788 AAACAGTTGATGCGCATCGG 59.831 50.000 37.23 28.84 40.63 4.18
1926 2695 1.374758 CTCCTCAGGCGTCAACACC 60.375 63.158 0.00 0.00 0.00 4.16
1962 2731 1.898154 GGGCAAGAGAGCGACCTTA 59.102 57.895 0.00 0.00 34.64 2.69
2124 2899 4.617253 TTGAGTACACAGCACAGGTTAT 57.383 40.909 0.00 0.00 0.00 1.89
2139 2914 3.244875 ACACAGGCATGTCCATTTGAGTA 60.245 43.478 0.00 0.00 37.65 2.59
2156 2933 3.928992 GGATCATACACACAGTGACACAG 59.071 47.826 7.81 1.82 36.96 3.66
2157 2934 3.323403 TGGATCATACACACAGTGACACA 59.677 43.478 7.81 0.00 36.96 3.72
2158 2935 3.925379 TGGATCATACACACAGTGACAC 58.075 45.455 7.81 0.00 36.96 3.67
2159 2936 4.824479 ATGGATCATACACACAGTGACA 57.176 40.909 7.81 0.00 36.96 3.58
2160 2937 6.203530 CCAATATGGATCATACACACAGTGAC 59.796 42.308 7.81 0.00 40.96 3.67
2162 2939 6.057533 ACCAATATGGATCATACACACAGTG 58.942 40.000 2.85 0.00 40.96 3.66
2278 3621 1.592400 CTCAGCCAGCAACACCCATG 61.592 60.000 0.00 0.00 0.00 3.66
2297 3640 5.106038 CCATATGTGATCATTGTACATGCCC 60.106 44.000 0.00 0.00 36.52 5.36
2308 3651 8.878211 GGGACATCTATATCCATATGTGATCAT 58.122 37.037 0.00 0.00 36.65 2.45
2309 3652 7.845800 TGGGACATCTATATCCATATGTGATCA 59.154 37.037 9.21 0.00 36.65 2.92
2310 3653 8.255111 TGGGACATCTATATCCATATGTGATC 57.745 38.462 9.21 0.00 36.65 2.92
2330 3673 6.868339 CCTCAAATTACTTTTTGTCATGGGAC 59.132 38.462 0.00 0.00 44.57 4.46
2331 3674 6.518200 GCCTCAAATTACTTTTTGTCATGGGA 60.518 38.462 0.00 0.00 37.73 4.37
2332 3675 5.639082 GCCTCAAATTACTTTTTGTCATGGG 59.361 40.000 0.00 0.00 37.73 4.00
2333 3676 6.222389 TGCCTCAAATTACTTTTTGTCATGG 58.778 36.000 0.00 0.00 37.73 3.66
2334 3677 7.816031 AGATGCCTCAAATTACTTTTTGTCATG 59.184 33.333 0.00 0.00 37.73 3.07
2335 3678 7.899973 AGATGCCTCAAATTACTTTTTGTCAT 58.100 30.769 0.00 0.00 37.73 3.06
2336 3679 7.288810 AGATGCCTCAAATTACTTTTTGTCA 57.711 32.000 0.00 0.00 37.73 3.58
2369 3712 0.316841 GCTTGCATCGTGGGGAAAAA 59.683 50.000 0.00 0.00 0.00 1.94
2370 3713 0.539438 AGCTTGCATCGTGGGGAAAA 60.539 50.000 0.00 0.00 0.00 2.29
2371 3714 0.326595 TAGCTTGCATCGTGGGGAAA 59.673 50.000 0.00 0.00 0.00 3.13
2372 3715 0.326595 TTAGCTTGCATCGTGGGGAA 59.673 50.000 0.00 0.00 0.00 3.97
2373 3716 0.392461 GTTAGCTTGCATCGTGGGGA 60.392 55.000 0.00 0.00 0.00 4.81
2374 3717 0.676466 TGTTAGCTTGCATCGTGGGG 60.676 55.000 0.00 0.00 0.00 4.96
2375 3718 0.447801 GTGTTAGCTTGCATCGTGGG 59.552 55.000 0.00 0.00 0.00 4.61
2376 3719 1.155889 TGTGTTAGCTTGCATCGTGG 58.844 50.000 0.00 0.00 0.00 4.94
2377 3720 2.476686 CCATGTGTTAGCTTGCATCGTG 60.477 50.000 0.00 0.00 0.00 4.35
2378 3721 1.739466 CCATGTGTTAGCTTGCATCGT 59.261 47.619 0.00 0.00 0.00 3.73
2379 3722 2.009051 TCCATGTGTTAGCTTGCATCG 58.991 47.619 0.00 0.00 0.00 3.84
2380 3723 3.243301 CCATCCATGTGTTAGCTTGCATC 60.243 47.826 0.00 0.00 0.00 3.91
2381 3724 2.691526 CCATCCATGTGTTAGCTTGCAT 59.308 45.455 0.00 0.00 0.00 3.96
2382 3725 2.093890 CCATCCATGTGTTAGCTTGCA 58.906 47.619 0.00 0.00 0.00 4.08
2383 3726 1.202336 GCCATCCATGTGTTAGCTTGC 60.202 52.381 0.00 0.00 0.00 4.01
2384 3727 2.093890 TGCCATCCATGTGTTAGCTTG 58.906 47.619 0.00 0.00 0.00 4.01
2385 3728 2.025981 TCTGCCATCCATGTGTTAGCTT 60.026 45.455 0.00 0.00 0.00 3.74
2386 3729 1.561076 TCTGCCATCCATGTGTTAGCT 59.439 47.619 0.00 0.00 0.00 3.32
2387 3730 1.672881 GTCTGCCATCCATGTGTTAGC 59.327 52.381 0.00 0.00 0.00 3.09
2388 3731 2.989909 TGTCTGCCATCCATGTGTTAG 58.010 47.619 0.00 0.00 0.00 2.34
2389 3732 3.650281 ATGTCTGCCATCCATGTGTTA 57.350 42.857 0.00 0.00 0.00 2.41
2390 3733 2.519771 ATGTCTGCCATCCATGTGTT 57.480 45.000 0.00 0.00 0.00 3.32
2391 3734 2.372264 GAATGTCTGCCATCCATGTGT 58.628 47.619 0.00 0.00 31.75 3.72
2392 3735 1.332686 CGAATGTCTGCCATCCATGTG 59.667 52.381 0.00 0.00 31.75 3.21
2393 3736 1.671979 CGAATGTCTGCCATCCATGT 58.328 50.000 0.00 0.00 31.75 3.21
2394 3737 0.309922 GCGAATGTCTGCCATCCATG 59.690 55.000 0.00 0.00 31.75 3.66
2395 3738 2.711711 GCGAATGTCTGCCATCCAT 58.288 52.632 0.00 0.00 31.75 3.41
2396 3739 4.223800 GCGAATGTCTGCCATCCA 57.776 55.556 0.00 0.00 31.75 3.41
2456 3799 1.740043 GCGTCGTTGCTCCATCGTAC 61.740 60.000 0.00 0.00 0.00 3.67
2459 3802 2.507102 AGCGTCGTTGCTCCATCG 60.507 61.111 0.00 0.00 42.95 3.84
2506 3849 1.116536 TGGACAACACTCCAGGCGTA 61.117 55.000 0.00 0.00 35.23 4.42
2507 3850 2.426023 GGACAACACTCCAGGCGT 59.574 61.111 0.00 0.00 0.00 5.68
2522 3865 3.385384 CTGCTGTCGCCCTCTGGA 61.385 66.667 0.00 0.00 34.43 3.86
2630 3976 2.588314 GAGGAGATGCCGCTGCTG 60.588 66.667 0.70 0.00 43.43 4.41
2631 3977 3.859414 GGAGGAGATGCCGCTGCT 61.859 66.667 0.70 0.00 43.43 4.24
2698 4078 1.687612 CTCCTTGACAGGGGCACAT 59.312 57.895 3.41 0.00 41.25 3.21
2699 4079 2.528818 CCTCCTTGACAGGGGCACA 61.529 63.158 3.41 0.00 39.86 4.57
2701 4081 1.920325 CTCCTCCTTGACAGGGGCA 60.920 63.158 3.41 0.00 39.86 5.36
2762 4142 4.748144 CCAAGGGCCACAGCTCCC 62.748 72.222 6.18 0.00 42.22 4.30
2768 4148 3.256960 GTCCTCCCAAGGGCCACA 61.257 66.667 6.18 0.00 41.85 4.17
2840 4220 0.871722 GCCGCAGTTCATTACACACA 59.128 50.000 0.00 0.00 0.00 3.72
2918 4298 2.335712 GCCAGCCTGGAACCTTTCG 61.336 63.158 16.85 0.00 40.96 3.46
2929 4309 2.039418 TGACTATAATCACGCCAGCCT 58.961 47.619 0.00 0.00 0.00 4.58
2938 4318 6.049149 GCACCAAGCTAAGTGACTATAATCA 58.951 40.000 17.77 0.00 41.15 2.57
2944 4324 1.671850 GCGCACCAAGCTAAGTGACTA 60.672 52.381 17.77 0.00 42.61 2.59
2945 4325 0.951040 GCGCACCAAGCTAAGTGACT 60.951 55.000 17.77 0.00 42.61 3.41
2948 4328 0.950555 TGAGCGCACCAAGCTAAGTG 60.951 55.000 11.47 10.88 46.13 3.16
2985 4365 1.089481 TTCCTTCATCCACGATGCGC 61.089 55.000 0.00 0.00 39.63 6.09
2988 4368 4.083110 GGCATATTTCCTTCATCCACGATG 60.083 45.833 0.00 0.00 41.00 3.84
2992 4372 3.837355 AGGGCATATTTCCTTCATCCAC 58.163 45.455 0.00 0.00 0.00 4.02
2996 4376 5.608437 TGTCTCTAGGGCATATTTCCTTCAT 59.392 40.000 0.00 0.00 34.75 2.57
2997 4377 4.968719 TGTCTCTAGGGCATATTTCCTTCA 59.031 41.667 0.00 0.00 34.75 3.02
2998 4378 5.552870 TGTCTCTAGGGCATATTTCCTTC 57.447 43.478 0.00 0.00 34.75 3.46
2999 4379 5.975988 TTGTCTCTAGGGCATATTTCCTT 57.024 39.130 0.00 0.00 34.75 3.36
3000 4380 7.633018 TTATTGTCTCTAGGGCATATTTCCT 57.367 36.000 0.00 0.00 37.18 3.36
3001 4381 9.959721 TTATTATTGTCTCTAGGGCATATTTCC 57.040 33.333 0.00 0.00 0.00 3.13
3006 4386 9.778741 CAACTTTATTATTGTCTCTAGGGCATA 57.221 33.333 0.00 0.00 0.00 3.14
3007 4387 8.275040 ACAACTTTATTATTGTCTCTAGGGCAT 58.725 33.333 0.00 0.00 33.80 4.40
3008 4388 7.630082 ACAACTTTATTATTGTCTCTAGGGCA 58.370 34.615 0.00 0.00 33.80 5.36
3009 4389 8.507524 AACAACTTTATTATTGTCTCTAGGGC 57.492 34.615 0.00 0.00 38.08 5.19


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

AutoCloner maintained by Alex Coulton.