Multiple sequence alignment - TraesCS5B01G287500

Loading Multiple Alignment...

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 TraesCS5B01G287500 chr5B 100.000 3070 0 0 1 3070 473627108 473624039 0.000000e+00 5670.0
1 TraesCS5B01G287500 chr5B 95.752 871 34 1 1399 2269 473454935 473454068 0.000000e+00 1400.0
2 TraesCS5B01G287500 chr5B 83.596 634 66 25 1050 1670 473292147 473291539 7.430000e-156 560.0
3 TraesCS5B01G287500 chr5B 82.043 646 75 28 1042 1664 473448838 473448211 2.110000e-141 512.0
4 TraesCS5B01G287500 chr5B 80.822 657 84 25 1035 1670 473468206 473467571 7.700000e-131 477.0
5 TraesCS5B01G287500 chr5B 87.740 416 34 8 2633 3044 473602888 473602486 1.290000e-128 470.0
6 TraesCS5B01G287500 chr5B 86.701 391 43 9 1015 1400 473455426 473455040 2.830000e-115 425.0
7 TraesCS5B01G287500 chr5B 86.410 390 34 9 2661 3044 473521097 473520721 2.850000e-110 409.0
8 TraesCS5B01G287500 chr5B 97.727 44 1 0 730 773 473626336 473626293 3.280000e-10 76.8
9 TraesCS5B01G287500 chr5B 97.727 44 1 0 773 816 473626379 473626336 3.280000e-10 76.8
10 TraesCS5B01G287500 chr5D 92.857 2310 121 14 1 2285 393754184 393751894 0.000000e+00 3312.0
11 TraesCS5B01G287500 chr5D 83.053 655 82 22 1026 1670 393570169 393569534 4.440000e-158 568.0
12 TraesCS5B01G287500 chr5D 85.638 564 46 17 2516 3070 393740974 393740437 7.430000e-156 560.0
13 TraesCS5B01G287500 chr5D 84.180 512 46 10 2536 3044 393620767 393620288 6.000000e-127 464.0
14 TraesCS5B01G287500 chr5D 86.118 389 43 8 1276 1664 393608496 393608119 2.850000e-110 409.0
15 TraesCS5B01G287500 chr5D 97.727 44 1 0 773 816 393753441 393753398 3.280000e-10 76.8
16 TraesCS5B01G287500 chr5D 95.455 44 2 0 730 773 393753398 393753355 1.530000e-08 71.3
17 TraesCS5B01G287500 chr5D 81.944 72 8 4 8 74 274699943 274699872 4.280000e-04 56.5
18 TraesCS5B01G287500 chr5A 90.370 1433 83 30 1 1400 495842226 495840816 0.000000e+00 1831.0
19 TraesCS5B01G287500 chr5A 89.867 750 57 13 1399 2144 495840695 495839961 0.000000e+00 946.0
20 TraesCS5B01G287500 chr5A 86.268 568 40 15 2516 3070 495730655 495730113 1.590000e-162 582.0
21 TraesCS5B01G287500 chr5A 85.387 568 44 16 2516 3070 495589956 495589415 1.240000e-153 553.0
22 TraesCS5B01G287500 chr5A 82.893 643 77 25 1026 1660 495340105 495339488 5.790000e-152 547.0
23 TraesCS5B01G287500 chr5A 83.412 633 57 16 2425 3044 495398545 495397948 7.490000e-151 544.0
24 TraesCS5B01G287500 chr5A 84.859 568 49 13 2516 3070 495821449 495820906 3.480000e-149 538.0
25 TraesCS5B01G287500 chr5A 81.330 466 41 14 1852 2285 495602132 495601681 1.360000e-88 337.0
26 TraesCS5B01G287500 chr5A 79.266 463 55 21 1852 2285 495735548 495735098 5.010000e-73 285.0
27 TraesCS5B01G287500 chr5A 95.455 44 2 0 730 773 495841440 495841397 1.530000e-08 71.3
28 TraesCS5B01G287500 chr5A 97.222 36 1 0 781 816 495841475 495841440 9.190000e-06 62.1
29 TraesCS5B01G287500 chr2D 83.333 72 7 3 8 74 563308244 563308173 9.190000e-06 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 TraesCS5B01G287500 chr5B 473624039 473627108 3069 True 1941.200000 5670 98.484667 1 3070 3 chr5B.!!$R7 3069
1 TraesCS5B01G287500 chr5B 473454068 473455426 1358 True 912.500000 1400 91.226500 1015 2269 2 chr5B.!!$R6 1254
2 TraesCS5B01G287500 chr5B 473291539 473292147 608 True 560.000000 560 83.596000 1050 1670 1 chr5B.!!$R1 620
3 TraesCS5B01G287500 chr5B 473448211 473448838 627 True 512.000000 512 82.043000 1042 1664 1 chr5B.!!$R2 622
4 TraesCS5B01G287500 chr5B 473467571 473468206 635 True 477.000000 477 80.822000 1035 1670 1 chr5B.!!$R3 635
5 TraesCS5B01G287500 chr5D 393751894 393754184 2290 True 1153.366667 3312 95.346333 1 2285 3 chr5D.!!$R6 2284
6 TraesCS5B01G287500 chr5D 393569534 393570169 635 True 568.000000 568 83.053000 1026 1670 1 chr5D.!!$R2 644
7 TraesCS5B01G287500 chr5D 393740437 393740974 537 True 560.000000 560 85.638000 2516 3070 1 chr5D.!!$R5 554
8 TraesCS5B01G287500 chr5A 495839961 495842226 2265 True 727.600000 1831 93.228500 1 2144 4 chr5A.!!$R8 2143
9 TraesCS5B01G287500 chr5A 495730113 495730655 542 True 582.000000 582 86.268000 2516 3070 1 chr5A.!!$R5 554
10 TraesCS5B01G287500 chr5A 495589415 495589956 541 True 553.000000 553 85.387000 2516 3070 1 chr5A.!!$R3 554
11 TraesCS5B01G287500 chr5A 495339488 495340105 617 True 547.000000 547 82.893000 1026 1660 1 chr5A.!!$R1 634
12 TraesCS5B01G287500 chr5A 495397948 495398545 597 True 544.000000 544 83.412000 2425 3044 1 chr5A.!!$R2 619
13 TraesCS5B01G287500 chr5A 495820906 495821449 543 True 538.000000 538 84.859000 2516 3070 1 chr5A.!!$R7 554

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
874 903 0.032515 TCCCTGCGTCTGATCCCTAA 60.033 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2301 2533 0.178998 AATGCATGCCAGCTCTAGGG 60.179 55.0 16.68 0.0 34.99 3.53 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
264 269 5.961843 TGTTGTTTTGTTATTTTTGCATGCG 59.038 32.000 14.09 0.00 0.00 4.73
303 309 9.790389 ACAAATAAACGTTAGTGATTTTCAACA 57.210 25.926 0.00 0.00 29.44 3.33
328 338 4.708726 AAAGACATTAGTGGAAGCATGC 57.291 40.909 10.51 10.51 0.00 4.06
354 364 6.925718 CCCCTATATATGCTGTATCACAATCG 59.074 42.308 0.00 0.00 0.00 3.34
418 428 0.676151 GAGCAGCAGAAGGACAAGGG 60.676 60.000 0.00 0.00 0.00 3.95
464 480 1.887707 GCGACGACCCCATTGATCC 60.888 63.158 0.00 0.00 0.00 3.36
479 495 3.174507 ATCCGCTGATGGATGCGCT 62.175 57.895 9.73 0.00 47.00 5.92
491 507 1.423721 GATGCGCTGCAGATCAACGA 61.424 55.000 20.43 1.88 43.65 3.85
495 511 1.427020 GCTGCAGATCAACGAAGGC 59.573 57.895 20.43 0.00 0.00 4.35
511 527 4.009015 GCCCTTGAGCCTGGAAAG 57.991 61.111 0.00 0.00 0.00 2.62
554 570 4.337555 CAGGACCAAGGCTAATGATTGAAG 59.662 45.833 0.00 0.00 0.00 3.02
555 571 4.228210 AGGACCAAGGCTAATGATTGAAGA 59.772 41.667 0.00 0.00 0.00 2.87
559 575 3.550437 AGGCTAATGATTGAAGAGCGT 57.450 42.857 0.00 0.00 33.85 5.07
573 589 6.268825 TGAAGAGCGTATTAGAGAAGTTGT 57.731 37.500 0.00 0.00 0.00 3.32
779 808 1.917872 TAGGATTTGGTTGGGTGTGC 58.082 50.000 0.00 0.00 0.00 4.57
862 891 1.081242 GTTGCACATGTTCCCTGCG 60.081 57.895 0.00 0.00 33.35 5.18
874 903 0.032515 TCCCTGCGTCTGATCCCTAA 60.033 55.000 0.00 0.00 0.00 2.69
875 904 1.051812 CCCTGCGTCTGATCCCTAAT 58.948 55.000 0.00 0.00 0.00 1.73
916 945 1.687123 GGTGCACTAGACCATACCGAT 59.313 52.381 17.98 0.00 33.25 4.18
917 946 2.288273 GGTGCACTAGACCATACCGATC 60.288 54.545 17.98 0.00 33.25 3.69
918 947 1.607148 TGCACTAGACCATACCGATCG 59.393 52.381 8.51 8.51 0.00 3.69
919 948 1.878088 GCACTAGACCATACCGATCGA 59.122 52.381 18.66 0.00 0.00 3.59
999 1029 2.784356 CCAGCTCTCCAGAGGCTCG 61.784 68.421 9.22 4.13 42.29 5.03
1001 1031 1.108727 CAGCTCTCCAGAGGCTCGAT 61.109 60.000 9.22 0.00 42.29 3.59
1022 1056 3.690460 TGGAAGAAAAGAAGAGGATGCC 58.310 45.455 0.00 0.00 0.00 4.40
1076 1110 3.545481 CGCACTGTCGTCGATGGC 61.545 66.667 1.22 1.22 0.00 4.40
1285 1376 0.452585 GCTTAGCTCTTCGAGTCCGT 59.547 55.000 0.00 0.00 37.05 4.69
1818 2043 3.858868 GACGGGAGCTTCGTGTGCA 62.859 63.158 18.39 0.00 41.22 4.57
1992 2223 2.028125 TAGTAGCACCATGAGCCGGC 62.028 60.000 21.89 21.89 0.00 6.13
2057 2289 0.107410 TGCCGGCCTTTGACGATAAT 60.107 50.000 26.77 0.00 0.00 1.28
2122 2354 7.993821 ATGTAATGAGTTCATGTTAGACTCG 57.006 36.000 12.81 0.00 36.56 4.18
2125 2357 7.915923 TGTAATGAGTTCATGTTAGACTCGATC 59.084 37.037 12.81 0.00 36.56 3.69
2232 2464 3.481453 AGAAGCTCTTCAAGTTTGGGTC 58.519 45.455 11.69 0.00 41.84 4.46
2292 2524 8.002984 ACATCTCTAAGTTAGACTAGCTTTCC 57.997 38.462 15.67 0.00 31.49 3.13
2293 2525 7.837187 ACATCTCTAAGTTAGACTAGCTTTCCT 59.163 37.037 15.67 0.00 31.49 3.36
2294 2526 8.691797 CATCTCTAAGTTAGACTAGCTTTCCTT 58.308 37.037 15.67 0.00 31.49 3.36
2295 2527 8.283699 TCTCTAAGTTAGACTAGCTTTCCTTC 57.716 38.462 15.67 0.00 31.49 3.46
2296 2528 7.889073 TCTCTAAGTTAGACTAGCTTTCCTTCA 59.111 37.037 15.67 0.00 31.49 3.02
2297 2529 8.596781 TCTAAGTTAGACTAGCTTTCCTTCAT 57.403 34.615 15.67 0.00 31.49 2.57
2298 2530 8.470805 TCTAAGTTAGACTAGCTTTCCTTCATG 58.529 37.037 15.67 0.00 31.49 3.07
2299 2531 6.859112 AGTTAGACTAGCTTTCCTTCATGA 57.141 37.500 0.00 0.00 0.00 3.07
2300 2532 7.430760 AGTTAGACTAGCTTTCCTTCATGAT 57.569 36.000 0.00 0.00 0.00 2.45
2301 2533 7.496747 AGTTAGACTAGCTTTCCTTCATGATC 58.503 38.462 0.00 0.00 0.00 2.92
2302 2534 5.289083 AGACTAGCTTTCCTTCATGATCC 57.711 43.478 0.00 0.00 0.00 3.36
2303 2535 4.102367 AGACTAGCTTTCCTTCATGATCCC 59.898 45.833 0.00 0.00 0.00 3.85
2304 2536 4.043596 ACTAGCTTTCCTTCATGATCCCT 58.956 43.478 0.00 0.00 0.00 4.20
2305 2537 5.219739 ACTAGCTTTCCTTCATGATCCCTA 58.780 41.667 0.00 0.00 0.00 3.53
2306 2538 4.703379 AGCTTTCCTTCATGATCCCTAG 57.297 45.455 0.00 0.00 0.00 3.02
2307 2539 4.302067 AGCTTTCCTTCATGATCCCTAGA 58.698 43.478 0.00 0.00 0.00 2.43
2308 2540 4.347583 AGCTTTCCTTCATGATCCCTAGAG 59.652 45.833 0.00 0.00 0.00 2.43
2309 2541 4.640364 CTTTCCTTCATGATCCCTAGAGC 58.360 47.826 0.00 0.00 0.00 4.09
2310 2542 3.627041 TCCTTCATGATCCCTAGAGCT 57.373 47.619 0.00 0.00 0.00 4.09
2311 2543 3.237746 TCCTTCATGATCCCTAGAGCTG 58.762 50.000 0.00 0.00 0.00 4.24
2312 2544 2.302445 CCTTCATGATCCCTAGAGCTGG 59.698 54.545 0.00 0.00 0.00 4.85
2313 2545 1.346062 TCATGATCCCTAGAGCTGGC 58.654 55.000 0.00 0.00 0.00 4.85
2314 2546 1.054231 CATGATCCCTAGAGCTGGCA 58.946 55.000 0.00 0.00 0.00 4.92
2315 2547 1.629353 CATGATCCCTAGAGCTGGCAT 59.371 52.381 0.00 0.00 0.00 4.40
2316 2548 1.054231 TGATCCCTAGAGCTGGCATG 58.946 55.000 0.00 0.00 0.00 4.06
2317 2549 0.321475 GATCCCTAGAGCTGGCATGC 60.321 60.000 9.90 9.90 0.00 4.06
2318 2550 1.058428 ATCCCTAGAGCTGGCATGCA 61.058 55.000 21.36 4.79 34.99 3.96
2319 2551 1.058428 TCCCTAGAGCTGGCATGCAT 61.058 55.000 21.36 1.34 34.99 3.96
2320 2552 0.178998 CCCTAGAGCTGGCATGCATT 60.179 55.000 21.36 0.62 34.99 3.56
2321 2553 1.688772 CCTAGAGCTGGCATGCATTT 58.311 50.000 21.36 1.02 34.99 2.32
2322 2554 1.337071 CCTAGAGCTGGCATGCATTTG 59.663 52.381 21.36 7.05 34.99 2.32
2323 2555 2.022195 CTAGAGCTGGCATGCATTTGT 58.978 47.619 21.36 2.90 34.99 2.83
2324 2556 1.263356 AGAGCTGGCATGCATTTGTT 58.737 45.000 21.36 3.79 34.99 2.83
2325 2557 1.067142 AGAGCTGGCATGCATTTGTTG 60.067 47.619 21.36 1.97 34.99 3.33
2326 2558 0.970640 AGCTGGCATGCATTTGTTGA 59.029 45.000 21.36 0.00 34.99 3.18
2327 2559 1.553248 AGCTGGCATGCATTTGTTGAT 59.447 42.857 21.36 0.00 34.99 2.57
2328 2560 2.027561 AGCTGGCATGCATTTGTTGATT 60.028 40.909 21.36 0.00 34.99 2.57
2329 2561 2.745281 GCTGGCATGCATTTGTTGATTT 59.255 40.909 21.36 0.00 0.00 2.17
2330 2562 3.189702 GCTGGCATGCATTTGTTGATTTT 59.810 39.130 21.36 0.00 0.00 1.82
2331 2563 4.320641 GCTGGCATGCATTTGTTGATTTTT 60.321 37.500 21.36 0.00 0.00 1.94
2353 2585 7.730364 TTTTTGTTCTTTTGCTTTTGTACCA 57.270 28.000 0.00 0.00 0.00 3.25
2354 2586 7.913674 TTTTGTTCTTTTGCTTTTGTACCAT 57.086 28.000 0.00 0.00 0.00 3.55
2355 2587 7.913674 TTTGTTCTTTTGCTTTTGTACCATT 57.086 28.000 0.00 0.00 0.00 3.16
2356 2588 7.913674 TTGTTCTTTTGCTTTTGTACCATTT 57.086 28.000 0.00 0.00 0.00 2.32
2357 2589 7.913674 TGTTCTTTTGCTTTTGTACCATTTT 57.086 28.000 0.00 0.00 0.00 1.82
2358 2590 9.436957 TTGTTCTTTTGCTTTTGTACCATTTTA 57.563 25.926 0.00 0.00 0.00 1.52
2359 2591 9.436957 TGTTCTTTTGCTTTTGTACCATTTTAA 57.563 25.926 0.00 0.00 0.00 1.52
2360 2592 9.697250 GTTCTTTTGCTTTTGTACCATTTTAAC 57.303 29.630 0.00 0.00 0.00 2.01
2361 2593 9.660180 TTCTTTTGCTTTTGTACCATTTTAACT 57.340 25.926 0.00 0.00 0.00 2.24
2362 2594 9.660180 TCTTTTGCTTTTGTACCATTTTAACTT 57.340 25.926 0.00 0.00 0.00 2.66
2420 2652 8.964476 ACGATTGTTCTATCCAAATGATAAGT 57.036 30.769 0.00 0.00 35.53 2.24
2421 2653 8.830580 ACGATTGTTCTATCCAAATGATAAGTG 58.169 33.333 0.00 0.00 35.53 3.16
2422 2654 8.830580 CGATTGTTCTATCCAAATGATAAGTGT 58.169 33.333 0.00 0.00 35.53 3.55
2424 2656 9.685276 ATTGTTCTATCCAAATGATAAGTGTCA 57.315 29.630 0.00 0.00 35.53 3.58
2425 2657 8.492673 TGTTCTATCCAAATGATAAGTGTCAC 57.507 34.615 0.00 0.00 35.53 3.67
2426 2658 8.100164 TGTTCTATCCAAATGATAAGTGTCACA 58.900 33.333 5.62 0.00 35.53 3.58
2427 2659 9.113838 GTTCTATCCAAATGATAAGTGTCACAT 57.886 33.333 5.62 0.00 35.53 3.21
2428 2660 8.667076 TCTATCCAAATGATAAGTGTCACATG 57.333 34.615 5.62 0.00 35.53 3.21
2447 2679 2.816689 TGGTGTAGTTTGACGTCACAG 58.183 47.619 19.90 0.00 31.89 3.66
2449 2681 2.132762 GTGTAGTTTGACGTCACAGGG 58.867 52.381 19.90 0.00 31.14 4.45
2453 2685 2.830104 AGTTTGACGTCACAGGGTAAC 58.170 47.619 19.90 18.06 0.00 2.50
2470 2702 4.756502 GGTAACCGCTCTATCAGTTCTTT 58.243 43.478 0.00 0.00 0.00 2.52
2471 2703 4.567159 GGTAACCGCTCTATCAGTTCTTTG 59.433 45.833 0.00 0.00 0.00 2.77
2476 2708 4.564769 CCGCTCTATCAGTTCTTTGAAGTC 59.435 45.833 0.00 0.00 0.00 3.01
2480 2712 7.148507 CGCTCTATCAGTTCTTTGAAGTCATTT 60.149 37.037 0.00 0.00 0.00 2.32
2482 2714 9.212641 CTCTATCAGTTCTTTGAAGTCATTTGA 57.787 33.333 0.00 0.00 0.00 2.69
2483 2715 9.730705 TCTATCAGTTCTTTGAAGTCATTTGAT 57.269 29.630 0.00 0.00 0.00 2.57
2491 2723 9.695526 TTCTTTGAAGTCATTTGATATTGTTGG 57.304 29.630 0.00 0.00 0.00 3.77
2492 2724 8.859090 TCTTTGAAGTCATTTGATATTGTTGGT 58.141 29.630 0.00 0.00 0.00 3.67
2493 2725 9.480053 CTTTGAAGTCATTTGATATTGTTGGTT 57.520 29.630 0.00 0.00 0.00 3.67
2497 2734 9.774742 GAAGTCATTTGATATTGTTGGTTACTC 57.225 33.333 0.00 0.00 0.00 2.59
2531 2768 4.262036 GGTCACATGATAGAGCGATTACCA 60.262 45.833 0.00 0.00 0.00 3.25
2532 2769 5.473931 GTCACATGATAGAGCGATTACCAT 58.526 41.667 0.00 0.00 0.00 3.55
2533 2770 5.928839 GTCACATGATAGAGCGATTACCATT 59.071 40.000 0.00 0.00 0.00 3.16
2534 2771 6.090088 GTCACATGATAGAGCGATTACCATTC 59.910 42.308 0.00 0.00 0.00 2.67
2544 2781 3.063452 GCGATTACCATTCATGTGACGTT 59.937 43.478 0.00 0.00 0.00 3.99
2582 2819 4.824537 TCATCCGAACTCCAAAATGAACAA 59.175 37.500 0.00 0.00 0.00 2.83
2589 2826 7.326063 CCGAACTCCAAAATGAACAATTCTTAC 59.674 37.037 0.00 0.00 0.00 2.34
2638 2875 3.438668 CCCTCTAATCCTTGCTCTCCCTA 60.439 52.174 0.00 0.00 0.00 3.53
2703 2944 3.531538 ACCGATTCCACATGACACATAC 58.468 45.455 0.00 0.00 0.00 2.39
2742 2985 6.913170 ACAAGTTTTTGGCAGTATAGTGATG 58.087 36.000 11.91 0.00 38.66 3.07
2761 3004 1.019673 GTGGCATATGTGGTGAGCAG 58.980 55.000 4.29 0.00 0.00 4.24
2763 3006 1.450531 GGCATATGTGGTGAGCAGGC 61.451 60.000 4.29 0.00 0.00 4.85
2791 3034 1.349688 ACTAGGACCAACCGATGCAAA 59.650 47.619 0.00 0.00 44.74 3.68
2792 3035 1.737793 CTAGGACCAACCGATGCAAAC 59.262 52.381 0.00 0.00 44.74 2.93
2793 3036 0.110486 AGGACCAACCGATGCAAACT 59.890 50.000 0.00 0.00 44.74 2.66
2794 3037 0.521735 GGACCAACCGATGCAAACTC 59.478 55.000 0.00 0.00 0.00 3.01
2795 3038 1.523758 GACCAACCGATGCAAACTCT 58.476 50.000 0.00 0.00 0.00 3.24
2796 3039 1.464997 GACCAACCGATGCAAACTCTC 59.535 52.381 0.00 0.00 0.00 3.20
2797 3040 1.202758 ACCAACCGATGCAAACTCTCA 60.203 47.619 0.00 0.00 0.00 3.27
2798 3041 1.879380 CCAACCGATGCAAACTCTCAA 59.121 47.619 0.00 0.00 0.00 3.02
2799 3042 2.293122 CCAACCGATGCAAACTCTCAAA 59.707 45.455 0.00 0.00 0.00 2.69
2800 3043 3.243367 CCAACCGATGCAAACTCTCAAAA 60.243 43.478 0.00 0.00 0.00 2.44
2801 3044 3.904136 ACCGATGCAAACTCTCAAAAG 57.096 42.857 0.00 0.00 0.00 2.27
2823 3066 4.016444 GTCAAAACATAGAAGGGGCATGA 58.984 43.478 0.00 0.00 0.00 3.07
2867 3110 1.134965 GGTGAGAAGATGGAGTCCACG 60.135 57.143 15.86 0.00 35.80 4.94
2884 3131 2.430694 CCACGAGTCATTGACCTGGATA 59.569 50.000 13.14 0.00 32.18 2.59
2885 3132 3.070159 CCACGAGTCATTGACCTGGATAT 59.930 47.826 13.14 0.00 32.18 1.63
2886 3133 4.443457 CCACGAGTCATTGACCTGGATATT 60.443 45.833 13.14 0.00 32.18 1.28
2887 3134 4.747108 CACGAGTCATTGACCTGGATATTC 59.253 45.833 13.14 1.33 32.18 1.75
2959 3209 7.435068 AAGTGTCGTAAAATTAAGAGCATGT 57.565 32.000 0.00 0.00 0.00 3.21
2960 3210 7.061752 AGTGTCGTAAAATTAAGAGCATGTC 57.938 36.000 0.00 0.00 0.00 3.06
2961 3211 6.649141 AGTGTCGTAAAATTAAGAGCATGTCA 59.351 34.615 0.00 0.00 0.00 3.58
2962 3212 7.334421 AGTGTCGTAAAATTAAGAGCATGTCAT 59.666 33.333 0.00 0.00 0.00 3.06
3001 3263 2.401592 CGCTCAGTCGACGGAGAG 59.598 66.667 38.66 33.42 39.97 3.20
3053 3315 7.466746 ACTAAAAACATATTCAGCATGGTGT 57.533 32.000 23.35 8.90 36.16 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
264 269 7.155858 ACGTTTATTTGTGTGTTATTTGCAC 57.844 32.000 0.00 0.00 37.37 4.57
328 338 6.560003 TTGTGATACAGCATATATAGGGGG 57.440 41.667 0.00 0.00 0.00 5.40
479 495 1.377202 GGGCCTTCGTTGATCTGCA 60.377 57.895 0.84 0.00 0.00 4.41
495 511 1.760192 CATCTTTCCAGGCTCAAGGG 58.240 55.000 0.00 0.00 0.00 3.95
511 527 5.051816 CCTGAGAAGAGAGAAGATTGCATC 58.948 45.833 0.00 0.00 0.00 3.91
554 570 3.552294 GGCACAACTTCTCTAATACGCTC 59.448 47.826 0.00 0.00 0.00 5.03
555 571 3.522553 GGCACAACTTCTCTAATACGCT 58.477 45.455 0.00 0.00 0.00 5.07
559 575 6.479001 GCTAAATCGGCACAACTTCTCTAATA 59.521 38.462 0.00 0.00 0.00 0.98
573 589 0.107263 TGCATGGAGCTAAATCGGCA 60.107 50.000 0.00 0.00 45.94 5.69
642 671 4.248058 CCGGCCGGGTTTATTTATAGTAG 58.752 47.826 37.42 3.70 0.00 2.57
694 723 4.070552 GCTGGCGGTCGAGGAAGT 62.071 66.667 0.00 0.00 0.00 3.01
862 891 8.016229 CGTGCGTATATATATTAGGGATCAGAC 58.984 40.741 0.00 0.00 0.00 3.51
874 903 5.160699 CGTGGGTACGTGCGTATATATAT 57.839 43.478 7.72 0.00 44.99 0.86
875 904 4.598406 CGTGGGTACGTGCGTATATATA 57.402 45.455 7.72 0.00 44.99 0.86
899 928 1.878088 TCGATCGGTATGGTCTAGTGC 59.122 52.381 16.41 0.00 0.00 4.40
916 945 2.230025 CCAAGAAGTCTCTCTGCTTCGA 59.770 50.000 0.00 0.00 39.87 3.71
917 946 2.230025 TCCAAGAAGTCTCTCTGCTTCG 59.770 50.000 0.00 0.00 39.87 3.79
918 947 3.509575 TCTCCAAGAAGTCTCTCTGCTTC 59.490 47.826 0.00 0.00 39.87 3.86
919 948 3.505386 TCTCCAAGAAGTCTCTCTGCTT 58.495 45.455 0.00 0.00 42.43 3.91
990 1020 2.680312 TTTCTTCCATCGAGCCTCTG 57.320 50.000 0.00 0.00 0.00 3.35
999 1029 4.337836 GGCATCCTCTTCTTTTCTTCCATC 59.662 45.833 0.00 0.00 0.00 3.51
1001 1031 3.562176 GGGCATCCTCTTCTTTTCTTCCA 60.562 47.826 0.00 0.00 0.00 3.53
1022 1056 0.173481 TGGAAAGATCGAGCGAGTGG 59.827 55.000 0.00 0.00 0.00 4.00
1076 1110 4.889856 TCCGCATCATCACCCGCG 62.890 66.667 0.00 0.00 46.96 6.46
1081 1115 0.462581 TCCAGCTTCCGCATCATCAC 60.463 55.000 0.00 0.00 39.10 3.06
1143 1177 2.811317 CGTTCCTGGAGCGTCTGC 60.811 66.667 22.67 0.00 43.24 4.26
1146 1180 2.507324 GAGCGTTCCTGGAGCGTC 60.507 66.667 29.17 21.87 38.46 5.19
1818 2043 4.473444 TCATTTGCTTGGGTCTTCTTTCT 58.527 39.130 0.00 0.00 0.00 2.52
1906 2137 1.649664 CGCATCCTCCTTGTCTTCTG 58.350 55.000 0.00 0.00 0.00 3.02
2015 2247 4.819105 AACCCTTGTCATGAGATTACGA 57.181 40.909 0.00 0.00 0.00 3.43
2057 2289 4.634883 CCGCTACTACTCTAGAACACAAGA 59.365 45.833 0.00 0.00 0.00 3.02
2166 2398 3.236816 GCAAAATGATTGACACGACCAG 58.763 45.455 0.00 0.00 0.00 4.00
2232 2464 6.197364 AGTCTAACTTAGAGATGGTGTTCG 57.803 41.667 0.00 0.00 35.04 3.95
2285 2517 4.302067 TCTAGGGATCATGAAGGAAAGCT 58.698 43.478 0.00 0.00 0.00 3.74
2286 2518 4.640364 CTCTAGGGATCATGAAGGAAAGC 58.360 47.826 0.00 0.00 0.00 3.51
2287 2519 4.347583 AGCTCTAGGGATCATGAAGGAAAG 59.652 45.833 0.00 0.00 0.00 2.62
2288 2520 4.102210 CAGCTCTAGGGATCATGAAGGAAA 59.898 45.833 0.00 0.00 0.00 3.13
2289 2521 3.645212 CAGCTCTAGGGATCATGAAGGAA 59.355 47.826 0.00 0.00 0.00 3.36
2290 2522 3.237746 CAGCTCTAGGGATCATGAAGGA 58.762 50.000 0.00 0.00 0.00 3.36
2291 2523 2.302445 CCAGCTCTAGGGATCATGAAGG 59.698 54.545 0.00 0.00 0.00 3.46
2292 2524 2.289569 GCCAGCTCTAGGGATCATGAAG 60.290 54.545 0.00 0.00 0.00 3.02
2293 2525 1.696336 GCCAGCTCTAGGGATCATGAA 59.304 52.381 0.00 0.00 0.00 2.57
2294 2526 1.346062 GCCAGCTCTAGGGATCATGA 58.654 55.000 0.00 0.00 0.00 3.07
2295 2527 1.054231 TGCCAGCTCTAGGGATCATG 58.946 55.000 0.00 0.00 0.00 3.07
2296 2528 1.629353 CATGCCAGCTCTAGGGATCAT 59.371 52.381 0.00 0.00 34.71 2.45
2297 2529 1.054231 CATGCCAGCTCTAGGGATCA 58.946 55.000 0.00 0.00 34.71 2.92
2298 2530 0.321475 GCATGCCAGCTCTAGGGATC 60.321 60.000 6.36 0.00 34.71 3.36
2299 2531 1.058428 TGCATGCCAGCTCTAGGGAT 61.058 55.000 16.68 0.00 37.73 3.85
2300 2532 1.058428 ATGCATGCCAGCTCTAGGGA 61.058 55.000 16.68 0.00 34.99 4.20
2301 2533 0.178998 AATGCATGCCAGCTCTAGGG 60.179 55.000 16.68 0.00 34.99 3.53
2302 2534 1.337071 CAAATGCATGCCAGCTCTAGG 59.663 52.381 16.68 0.00 34.99 3.02
2303 2535 2.022195 ACAAATGCATGCCAGCTCTAG 58.978 47.619 16.68 0.00 34.99 2.43
2304 2536 2.133281 ACAAATGCATGCCAGCTCTA 57.867 45.000 16.68 0.00 34.99 2.43
2305 2537 1.067142 CAACAAATGCATGCCAGCTCT 60.067 47.619 16.68 0.00 34.99 4.09
2306 2538 1.067425 TCAACAAATGCATGCCAGCTC 60.067 47.619 16.68 0.00 34.99 4.09
2307 2539 0.970640 TCAACAAATGCATGCCAGCT 59.029 45.000 16.68 0.00 34.99 4.24
2308 2540 2.018542 ATCAACAAATGCATGCCAGC 57.981 45.000 16.68 0.00 0.00 4.85
2309 2541 5.365403 AAAAATCAACAAATGCATGCCAG 57.635 34.783 16.68 4.71 0.00 4.85
2329 2561 7.730364 TGGTACAAAAGCAAAAGAACAAAAA 57.270 28.000 0.00 0.00 31.92 1.94
2393 2625 9.869844 CTTATCATTTGGATAGAACAATCGTTC 57.130 33.333 0.00 0.00 43.16 3.95
2394 2626 9.396022 ACTTATCATTTGGATAGAACAATCGTT 57.604 29.630 0.00 0.00 39.57 3.85
2395 2627 8.830580 CACTTATCATTTGGATAGAACAATCGT 58.169 33.333 0.00 0.00 39.57 3.73
2396 2628 8.830580 ACACTTATCATTTGGATAGAACAATCG 58.169 33.333 0.00 0.00 39.57 3.34
2398 2630 9.685276 TGACACTTATCATTTGGATAGAACAAT 57.315 29.630 0.00 0.00 39.57 2.71
2399 2631 8.946085 GTGACACTTATCATTTGGATAGAACAA 58.054 33.333 0.00 0.00 39.57 2.83
2400 2632 8.100164 TGTGACACTTATCATTTGGATAGAACA 58.900 33.333 7.20 0.00 39.57 3.18
2401 2633 8.492673 TGTGACACTTATCATTTGGATAGAAC 57.507 34.615 7.20 0.00 39.57 3.01
2402 2634 9.112725 CATGTGACACTTATCATTTGGATAGAA 57.887 33.333 7.20 0.00 39.57 2.10
2403 2635 7.716560 CCATGTGACACTTATCATTTGGATAGA 59.283 37.037 7.20 0.00 39.57 1.98
2404 2636 7.500227 ACCATGTGACACTTATCATTTGGATAG 59.500 37.037 7.20 0.00 39.57 2.08
2405 2637 7.282901 CACCATGTGACACTTATCATTTGGATA 59.717 37.037 7.20 0.00 37.13 2.59
2406 2638 6.095860 CACCATGTGACACTTATCATTTGGAT 59.904 38.462 7.20 0.00 37.13 3.41
2407 2639 5.415389 CACCATGTGACACTTATCATTTGGA 59.585 40.000 7.20 0.00 37.13 3.53
2408 2640 5.183713 ACACCATGTGACACTTATCATTTGG 59.816 40.000 7.20 0.00 38.50 3.28
2409 2641 6.258230 ACACCATGTGACACTTATCATTTG 57.742 37.500 7.20 0.00 36.96 2.32
2410 2642 7.168219 ACTACACCATGTGACACTTATCATTT 58.832 34.615 7.20 0.00 36.96 2.32
2411 2643 6.711277 ACTACACCATGTGACACTTATCATT 58.289 36.000 7.20 0.00 36.96 2.57
2412 2644 6.299805 ACTACACCATGTGACACTTATCAT 57.700 37.500 7.20 0.00 36.96 2.45
2413 2645 5.738619 ACTACACCATGTGACACTTATCA 57.261 39.130 7.20 0.00 36.96 2.15
2414 2646 6.649141 TCAAACTACACCATGTGACACTTATC 59.351 38.462 7.20 0.00 36.96 1.75
2415 2647 6.426937 GTCAAACTACACCATGTGACACTTAT 59.573 38.462 7.20 0.00 36.96 1.73
2416 2648 5.756347 GTCAAACTACACCATGTGACACTTA 59.244 40.000 7.20 0.00 36.96 2.24
2417 2649 4.574828 GTCAAACTACACCATGTGACACTT 59.425 41.667 7.20 0.00 36.96 3.16
2418 2650 4.127171 GTCAAACTACACCATGTGACACT 58.873 43.478 7.20 0.00 36.96 3.55
2419 2651 3.059868 CGTCAAACTACACCATGTGACAC 60.060 47.826 0.00 0.00 36.10 3.67
2420 2652 3.127589 CGTCAAACTACACCATGTGACA 58.872 45.455 0.49 0.00 36.10 3.58
2421 2653 3.128349 ACGTCAAACTACACCATGTGAC 58.872 45.455 0.49 0.00 36.96 3.67
2422 2654 3.181474 TGACGTCAAACTACACCATGTGA 60.181 43.478 17.62 0.00 36.96 3.58
2423 2655 3.059868 GTGACGTCAAACTACACCATGTG 60.060 47.826 21.95 0.00 39.75 3.21
2424 2656 3.128349 GTGACGTCAAACTACACCATGT 58.872 45.455 21.95 0.00 0.00 3.21
2425 2657 3.127589 TGTGACGTCAAACTACACCATG 58.872 45.455 21.95 0.00 0.00 3.66
2426 2658 3.390135 CTGTGACGTCAAACTACACCAT 58.610 45.455 21.95 0.00 0.00 3.55
2427 2659 2.482316 CCTGTGACGTCAAACTACACCA 60.482 50.000 21.95 10.35 0.00 4.17
2428 2660 2.132762 CCTGTGACGTCAAACTACACC 58.867 52.381 21.95 5.66 0.00 4.16
2447 2679 2.694109 AGAACTGATAGAGCGGTTACCC 59.306 50.000 0.00 0.00 37.49 3.69
2449 2681 5.408356 TCAAAGAACTGATAGAGCGGTTAC 58.592 41.667 0.00 0.00 37.49 2.50
2453 2685 4.499183 ACTTCAAAGAACTGATAGAGCGG 58.501 43.478 0.00 0.00 0.00 5.52
2462 2694 9.903682 ACAATATCAAATGACTTCAAAGAACTG 57.096 29.630 0.00 0.00 0.00 3.16
2470 2702 9.295825 AGTAACCAACAATATCAAATGACTTCA 57.704 29.630 0.00 0.00 0.00 3.02
2471 2703 9.774742 GAGTAACCAACAATATCAAATGACTTC 57.225 33.333 0.00 0.00 0.00 3.01
2476 2708 7.692291 GTGACGAGTAACCAACAATATCAAATG 59.308 37.037 0.00 0.00 0.00 2.32
2480 2712 5.172934 GGTGACGAGTAACCAACAATATCA 58.827 41.667 4.89 0.00 34.05 2.15
2482 2714 5.155278 TGGTGACGAGTAACCAACAATAT 57.845 39.130 9.95 0.00 41.11 1.28
2483 2715 4.603989 TGGTGACGAGTAACCAACAATA 57.396 40.909 9.95 0.00 41.11 1.90
2484 2716 3.478857 TGGTGACGAGTAACCAACAAT 57.521 42.857 9.95 0.00 41.11 2.71
2485 2717 2.983907 TGGTGACGAGTAACCAACAA 57.016 45.000 9.95 0.00 41.11 2.83
2486 2718 2.983907 TTGGTGACGAGTAACCAACA 57.016 45.000 18.72 1.04 46.55 3.33
2489 2721 1.069513 CCAGTTGGTGACGAGTAACCA 59.930 52.381 8.36 8.36 42.34 3.67
2490 2722 1.792006 CCAGTTGGTGACGAGTAACC 58.208 55.000 2.74 2.74 34.50 2.85
2510 2747 5.728637 ATGGTAATCGCTCTATCATGTGA 57.271 39.130 0.00 0.00 0.00 3.58
2531 2768 7.667043 ATGTGTAGTTTAACGTCACATGAAT 57.333 32.000 26.04 13.04 41.53 2.57
2544 2781 7.778083 AGTTCGGATGATACATGTGTAGTTTA 58.222 34.615 9.11 0.00 33.52 2.01
2589 2826 8.189460 AGTATGGACTTAAGTTTTCTAGCGTAG 58.811 37.037 10.02 0.00 28.61 3.51
2591 2828 6.932947 AGTATGGACTTAAGTTTTCTAGCGT 58.067 36.000 10.02 0.00 28.61 5.07
2742 2985 1.019673 CTGCTCACCACATATGCCAC 58.980 55.000 1.58 0.00 0.00 5.01
2761 3004 2.552743 GTTGGTCCTAGTGTTTTGAGCC 59.447 50.000 0.00 0.00 0.00 4.70
2763 3006 2.806244 CGGTTGGTCCTAGTGTTTTGAG 59.194 50.000 0.00 0.00 0.00 3.02
2791 3034 7.229506 CCCTTCTATGTTTTGACTTTTGAGAGT 59.770 37.037 0.00 0.00 0.00 3.24
2792 3035 7.308830 CCCCTTCTATGTTTTGACTTTTGAGAG 60.309 40.741 0.00 0.00 0.00 3.20
2793 3036 6.490040 CCCCTTCTATGTTTTGACTTTTGAGA 59.510 38.462 0.00 0.00 0.00 3.27
2794 3037 6.681777 CCCCTTCTATGTTTTGACTTTTGAG 58.318 40.000 0.00 0.00 0.00 3.02
2795 3038 5.010617 GCCCCTTCTATGTTTTGACTTTTGA 59.989 40.000 0.00 0.00 0.00 2.69
2796 3039 5.221422 TGCCCCTTCTATGTTTTGACTTTTG 60.221 40.000 0.00 0.00 0.00 2.44
2797 3040 4.898861 TGCCCCTTCTATGTTTTGACTTTT 59.101 37.500 0.00 0.00 0.00 2.27
2798 3041 4.479158 TGCCCCTTCTATGTTTTGACTTT 58.521 39.130 0.00 0.00 0.00 2.66
2799 3042 4.112634 TGCCCCTTCTATGTTTTGACTT 57.887 40.909 0.00 0.00 0.00 3.01
2800 3043 3.806949 TGCCCCTTCTATGTTTTGACT 57.193 42.857 0.00 0.00 0.00 3.41
2801 3044 4.016444 TCATGCCCCTTCTATGTTTTGAC 58.984 43.478 0.00 0.00 0.00 3.18
2846 3089 1.134965 GTGGACTCCATCTTCTCACCG 60.135 57.143 0.00 0.00 35.28 4.94
2867 3110 7.012799 GGAAAAGAATATCCAGGTCAATGACTC 59.987 40.741 13.53 3.69 35.71 3.36
2884 3131 6.084060 TCCCTTTGGAAAGATGGAAAAGAAT 58.916 36.000 0.47 0.00 37.86 2.40
2885 3132 5.463154 TCCCTTTGGAAAGATGGAAAAGAA 58.537 37.500 0.47 0.00 37.86 2.52
2886 3133 5.073437 TCCCTTTGGAAAGATGGAAAAGA 57.927 39.130 0.47 0.00 37.86 2.52
2887 3134 5.718607 AGATCCCTTTGGAAAGATGGAAAAG 59.281 40.000 0.47 0.00 45.98 2.27
2933 3183 9.162764 ACATGCTCTTAATTTTACGACACTTAT 57.837 29.630 0.00 0.00 0.00 1.73
2936 3186 6.649141 TGACATGCTCTTAATTTTACGACACT 59.351 34.615 0.00 0.00 0.00 3.55
2956 3206 3.943381 CGCTCCCATAATATGCATGACAT 59.057 43.478 10.16 2.13 43.18 3.06
2957 3207 3.007831 TCGCTCCCATAATATGCATGACA 59.992 43.478 10.16 0.00 0.00 3.58
2958 3208 3.372206 GTCGCTCCCATAATATGCATGAC 59.628 47.826 10.16 0.00 0.00 3.06
2959 3209 3.261643 AGTCGCTCCCATAATATGCATGA 59.738 43.478 10.16 0.00 0.00 3.07
2960 3210 3.603532 AGTCGCTCCCATAATATGCATG 58.396 45.455 10.16 0.00 0.00 4.06
2961 3211 3.988976 AGTCGCTCCCATAATATGCAT 57.011 42.857 3.79 3.79 0.00 3.96
2962 3212 3.368427 GCTAGTCGCTCCCATAATATGCA 60.368 47.826 0.00 0.00 35.14 3.96


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

AutoCloner maintained by Alex Coulton.