Multiple sequence alignment - TraesCS6A01G331400

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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 TraesCS6A01G331400 chr6A 100.000 3088 0 0 1 3088 563538402 563541489 0.000000e+00 5703.0
1 TraesCS6A01G331400 chr6A 86.329 790 89 16 33 813 505032877 505033656 0.000000e+00 843.0
2 TraesCS6A01G331400 chr6B 95.507 1291 47 4 910 2198 633858554 633859835 0.000000e+00 2052.0
3 TraesCS6A01G331400 chr6B 86.039 308 32 5 2688 2993 633860461 633860759 1.380000e-83 320.0
4 TraesCS6A01G331400 chr6D 93.450 1374 60 19 904 2259 420693719 420695080 0.000000e+00 2012.0
5 TraesCS6A01G331400 chr6D 96.557 668 18 3 2420 3086 420695079 420695742 0.000000e+00 1101.0
6 TraesCS6A01G331400 chr6D 85.830 494 40 13 921 1413 406620333 406619869 5.950000e-137 497.0
7 TraesCS6A01G331400 chr6D 78.307 189 33 6 2686 2871 430039851 430039668 7.000000e-22 115.0
8 TraesCS6A01G331400 chr3A 97.877 895 17 2 21 913 82794 81900 0.000000e+00 1546.0
9 TraesCS6A01G331400 chr3A 98.214 168 3 0 2257 2424 682364470 682364637 8.370000e-76 294.0
10 TraesCS6A01G331400 chr3A 97.674 172 3 1 2253 2424 692357206 692357376 8.370000e-76 294.0
11 TraesCS6A01G331400 chr2A 97.436 897 19 3 21 913 16317963 16318859 0.000000e+00 1526.0
12 TraesCS6A01G331400 chr2A 98.214 168 3 0 2256 2423 746687209 746687376 8.370000e-76 294.0
13 TraesCS6A01G331400 chr2A 82.895 76 11 2 1200 1274 15756689 15756763 1.990000e-07 67.6
14 TraesCS6A01G331400 chr5A 97.216 898 21 4 19 914 546992972 546993867 0.000000e+00 1517.0
15 TraesCS6A01G331400 chr5A 82.130 1108 156 27 1006 2090 677485993 677484905 0.000000e+00 911.0
16 TraesCS6A01G331400 chr5A 97.701 174 3 1 2251 2424 371027838 371028010 6.470000e-77 298.0
17 TraesCS6A01G331400 chr5A 98.225 169 3 0 2253 2421 394156741 394156909 2.330000e-76 296.0
18 TraesCS6A01G331400 chr5A 96.571 175 6 0 2250 2424 689934854 689934680 1.080000e-74 291.0
19 TraesCS6A01G331400 chr5D 91.304 874 66 9 48 913 44400547 44399676 0.000000e+00 1184.0
20 TraesCS6A01G331400 chr5D 89.186 897 70 16 21 913 381808248 381809121 0.000000e+00 1094.0
21 TraesCS6A01G331400 chr2D 90.537 856 70 9 51 900 609465611 609464761 0.000000e+00 1122.0
22 TraesCS6A01G331400 chr2D 80.682 88 15 2 1195 1281 13724000 13723914 1.990000e-07 67.6
23 TraesCS6A01G331400 chr4D 81.876 1109 163 27 1006 2090 497224396 497223302 0.000000e+00 900.0
24 TraesCS6A01G331400 chr4D 81.810 1105 165 23 1006 2090 497241121 497240033 0.000000e+00 894.0
25 TraesCS6A01G331400 chr4B 85.786 795 103 10 21 811 7868211 7867423 0.000000e+00 833.0
26 TraesCS6A01G331400 chr4B 79.455 1100 164 40 1006 2090 638148324 638147272 0.000000e+00 723.0
27 TraesCS6A01G331400 chr4B 79.511 654 101 19 1456 2088 638175607 638174966 4.730000e-118 435.0
28 TraesCS6A01G331400 chr4B 89.490 314 32 1 1006 1319 638181317 638181005 2.230000e-106 396.0
29 TraesCS6A01G331400 chr3D 85.414 809 101 12 9 813 3289055 3289850 0.000000e+00 824.0
30 TraesCS6A01G331400 chr1A 95.604 182 8 0 2244 2425 500357208 500357389 3.010000e-75 292.0
31 TraesCS6A01G331400 chr1A 96.023 176 7 0 2248 2423 494815588 494815413 1.400000e-73 287.0
32 TraesCS6A01G331400 chr3B 95.082 183 8 1 2245 2426 306557573 306557391 1.400000e-73 287.0


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 TraesCS6A01G331400 chr6A 563538402 563541489 3087 False 5703.0 5703 100.0000 1 3088 1 chr6A.!!$F2 3087
1 TraesCS6A01G331400 chr6A 505032877 505033656 779 False 843.0 843 86.3290 33 813 1 chr6A.!!$F1 780
2 TraesCS6A01G331400 chr6B 633858554 633860759 2205 False 1186.0 2052 90.7730 910 2993 2 chr6B.!!$F1 2083
3 TraesCS6A01G331400 chr6D 420693719 420695742 2023 False 1556.5 2012 95.0035 904 3086 2 chr6D.!!$F1 2182
4 TraesCS6A01G331400 chr3A 81900 82794 894 True 1546.0 1546 97.8770 21 913 1 chr3A.!!$R1 892
5 TraesCS6A01G331400 chr2A 16317963 16318859 896 False 1526.0 1526 97.4360 21 913 1 chr2A.!!$F2 892
6 TraesCS6A01G331400 chr5A 546992972 546993867 895 False 1517.0 1517 97.2160 19 914 1 chr5A.!!$F3 895
7 TraesCS6A01G331400 chr5A 677484905 677485993 1088 True 911.0 911 82.1300 1006 2090 1 chr5A.!!$R1 1084
8 TraesCS6A01G331400 chr5D 44399676 44400547 871 True 1184.0 1184 91.3040 48 913 1 chr5D.!!$R1 865
9 TraesCS6A01G331400 chr5D 381808248 381809121 873 False 1094.0 1094 89.1860 21 913 1 chr5D.!!$F1 892
10 TraesCS6A01G331400 chr2D 609464761 609465611 850 True 1122.0 1122 90.5370 51 900 1 chr2D.!!$R2 849
11 TraesCS6A01G331400 chr4D 497223302 497224396 1094 True 900.0 900 81.8760 1006 2090 1 chr4D.!!$R1 1084
12 TraesCS6A01G331400 chr4D 497240033 497241121 1088 True 894.0 894 81.8100 1006 2090 1 chr4D.!!$R2 1084
13 TraesCS6A01G331400 chr4B 7867423 7868211 788 True 833.0 833 85.7860 21 811 1 chr4B.!!$R1 790
14 TraesCS6A01G331400 chr4B 638147272 638148324 1052 True 723.0 723 79.4550 1006 2090 1 chr4B.!!$R2 1084
15 TraesCS6A01G331400 chr4B 638174966 638175607 641 True 435.0 435 79.5110 1456 2088 1 chr4B.!!$R3 632
16 TraesCS6A01G331400 chr3D 3289055 3289850 795 False 824.0 824 85.4140 9 813 1 chr3D.!!$F1 804

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
959 980 0.323816 AGAGGAGATCGAGGTGTGCA 60.324 55.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2487 2792 0.811281 GTGTATCTTGCCTTGGGTGC 59.189 55.0 0.0 0.0 0.0 5.01 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
528 542 5.351948 TGGGTTCGACAATAGAATCATCA 57.648 39.130 0.00 0.00 30.70 3.07
954 975 1.527380 GGCGAGAGGAGATCGAGGT 60.527 63.158 0.00 0.00 42.76 3.85
959 980 0.323816 AGAGGAGATCGAGGTGTGCA 60.324 55.000 0.00 0.00 0.00 4.57
977 998 1.337447 GCATAAATACTCGGCCGGCTA 60.337 52.381 28.56 15.19 0.00 3.93
989 1010 3.686045 CGGCTAGATCGGGGGAGC 61.686 72.222 0.00 0.00 0.00 4.70
1152 1173 1.584495 CGTGGTCGACATGTCCTCA 59.416 57.895 20.03 12.40 39.71 3.86
1467 1488 2.285868 CCCGAGGGGTACAGGGAT 59.714 66.667 0.00 0.00 46.64 3.85
1690 1718 2.651361 CGCTCACCGTCCTCTTGT 59.349 61.111 0.00 0.00 0.00 3.16
1825 1876 1.904852 CTTGCAGCGTCGCATCAACT 61.905 55.000 21.09 0.00 42.62 3.16
1826 1877 0.669012 TTGCAGCGTCGCATCAACTA 60.669 50.000 21.09 0.00 42.62 2.24
1827 1878 0.460109 TGCAGCGTCGCATCAACTAT 60.460 50.000 21.09 0.00 36.86 2.12
1829 1880 2.061773 GCAGCGTCGCATCAACTATAT 58.938 47.619 21.09 0.00 0.00 0.86
1830 1881 3.242518 GCAGCGTCGCATCAACTATATA 58.757 45.455 21.09 0.00 0.00 0.86
1831 1882 3.859961 GCAGCGTCGCATCAACTATATAT 59.140 43.478 21.09 0.00 0.00 0.86
1867 1919 7.405469 TCACATGTGTTAATTTGCATTGTTC 57.595 32.000 24.63 0.00 0.00 3.18
1907 1959 1.448013 GAGGTACAAGGCCGTGCTC 60.448 63.158 19.37 13.16 0.00 4.26
2170 2228 3.542712 ACATTTCATGCGTGTCTGTTC 57.457 42.857 5.68 0.00 0.00 3.18
2249 2552 4.563337 AAGTTAAGGCTTTCGTTTGGAC 57.437 40.909 4.45 0.00 0.00 4.02
2257 2560 3.057526 GGCTTTCGTTTGGACAGCTTTAT 60.058 43.478 2.38 0.00 45.70 1.40
2258 2561 4.155280 GGCTTTCGTTTGGACAGCTTTATA 59.845 41.667 2.38 0.00 45.70 0.98
2259 2562 5.086727 GCTTTCGTTTGGACAGCTTTATAC 58.913 41.667 0.00 0.00 43.59 1.47
2260 2563 5.106673 GCTTTCGTTTGGACAGCTTTATACT 60.107 40.000 0.00 0.00 43.59 2.12
2261 2564 6.476243 TTTCGTTTGGACAGCTTTATACTC 57.524 37.500 0.00 0.00 0.00 2.59
2262 2565 4.501071 TCGTTTGGACAGCTTTATACTCC 58.499 43.478 0.00 0.00 0.00 3.85
2263 2566 3.621715 CGTTTGGACAGCTTTATACTCCC 59.378 47.826 0.00 0.00 0.00 4.30
2264 2567 4.623171 CGTTTGGACAGCTTTATACTCCCT 60.623 45.833 0.00 0.00 0.00 4.20
2265 2568 4.755266 TTGGACAGCTTTATACTCCCTC 57.245 45.455 0.00 0.00 0.00 4.30
2266 2569 3.039011 TGGACAGCTTTATACTCCCTCC 58.961 50.000 0.00 0.00 0.00 4.30
2267 2570 2.036089 GGACAGCTTTATACTCCCTCCG 59.964 54.545 0.00 0.00 0.00 4.63
2268 2571 2.694109 GACAGCTTTATACTCCCTCCGT 59.306 50.000 0.00 0.00 0.00 4.69
2269 2572 3.105283 ACAGCTTTATACTCCCTCCGTT 58.895 45.455 0.00 0.00 0.00 4.44
2270 2573 3.132467 ACAGCTTTATACTCCCTCCGTTC 59.868 47.826 0.00 0.00 0.00 3.95
2271 2574 2.699321 AGCTTTATACTCCCTCCGTTCC 59.301 50.000 0.00 0.00 0.00 3.62
2272 2575 2.699321 GCTTTATACTCCCTCCGTTCCT 59.301 50.000 0.00 0.00 0.00 3.36
2273 2576 3.893813 GCTTTATACTCCCTCCGTTCCTA 59.106 47.826 0.00 0.00 0.00 2.94
2274 2577 4.343239 GCTTTATACTCCCTCCGTTCCTAA 59.657 45.833 0.00 0.00 0.00 2.69
2275 2578 5.163374 GCTTTATACTCCCTCCGTTCCTAAA 60.163 44.000 0.00 0.00 0.00 1.85
2276 2579 6.464039 GCTTTATACTCCCTCCGTTCCTAAAT 60.464 42.308 0.00 0.00 0.00 1.40
2277 2580 7.256083 GCTTTATACTCCCTCCGTTCCTAAATA 60.256 40.741 0.00 0.00 0.00 1.40
2278 2581 7.530426 TTATACTCCCTCCGTTCCTAAATAC 57.470 40.000 0.00 0.00 0.00 1.89
2279 2582 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
2280 2583 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
2281 2584 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
2282 2585 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
2283 2586 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
2284 2587 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
2285 2588 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2286 2589 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2287 2590 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
2288 2591 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
2289 2592 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
2290 2593 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
2291 2594 8.248945 CCGTTCCTAAATACTTGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
2361 2664 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2362 2665 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2363 2666 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2364 2667 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2365 2668 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2366 2669 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2367 2670 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2368 2671 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2369 2672 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2370 2673 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2371 2674 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2372 2675 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2373 2676 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2374 2677 5.109210 TCATTTTGCTCCGTATGTAGTCAG 58.891 41.667 0.00 0.00 0.00 3.51
2375 2678 4.530710 TTTTGCTCCGTATGTAGTCAGT 57.469 40.909 0.00 0.00 0.00 3.41
2376 2679 4.530710 TTTGCTCCGTATGTAGTCAGTT 57.469 40.909 0.00 0.00 0.00 3.16
2377 2680 3.503827 TGCTCCGTATGTAGTCAGTTG 57.496 47.619 0.00 0.00 0.00 3.16
2378 2681 2.823747 TGCTCCGTATGTAGTCAGTTGT 59.176 45.455 0.00 0.00 0.00 3.32
2379 2682 3.257375 TGCTCCGTATGTAGTCAGTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2380 2683 3.612860 GCTCCGTATGTAGTCAGTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2381 2684 4.617530 GCTCCGTATGTAGTCAGTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2382 2685 5.456548 TCCGTATGTAGTCAGTTGTTGAA 57.543 39.130 0.00 0.00 37.61 2.69
2383 2686 5.845103 TCCGTATGTAGTCAGTTGTTGAAA 58.155 37.500 0.00 0.00 37.61 2.69
2384 2687 6.460781 TCCGTATGTAGTCAGTTGTTGAAAT 58.539 36.000 0.00 0.00 37.61 2.17
2385 2688 6.367695 TCCGTATGTAGTCAGTTGTTGAAATG 59.632 38.462 0.00 0.00 37.61 2.32
2386 2689 6.015504 CGTATGTAGTCAGTTGTTGAAATGC 58.984 40.000 0.00 0.00 37.61 3.56
2387 2690 4.829064 TGTAGTCAGTTGTTGAAATGCC 57.171 40.909 0.00 0.00 37.61 4.40
2388 2691 4.460263 TGTAGTCAGTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 37.61 4.75
2389 2692 5.616270 TGTAGTCAGTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 37.61 3.93
2390 2693 5.700832 TGTAGTCAGTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 37.61 3.02
2391 2694 4.973168 AGTCAGTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 37.61 2.43
2392 2695 5.376625 AGTCAGTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 37.61 2.10
2393 2696 5.827797 AGTCAGTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 37.61 2.52
2394 2697 6.016777 AGTCAGTTGTTGAAATGCCTAGAAAG 60.017 38.462 0.00 0.00 37.61 2.62
2395 2698 6.017109 GTCAGTTGTTGAAATGCCTAGAAAGA 60.017 38.462 0.00 0.00 37.61 2.52
2396 2699 6.017109 TCAGTTGTTGAAATGCCTAGAAAGAC 60.017 38.462 0.00 0.00 31.34 3.01
2397 2700 5.827797 AGTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
2398 2701 6.321181 AGTTGTTGAAATGCCTAGAAAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
2399 2702 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
2400 2703 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
2401 2704 6.995686 TGTTGAAATGCCTAGAAAGACAAGTA 59.004 34.615 0.00 0.00 0.00 2.24
2402 2705 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
2403 2706 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
2404 2707 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
2405 2708 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
2407 2710 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
2408 2711 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
2409 2712 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
2410 2713 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
2411 2714 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
2412 2715 8.248945 CCTAGAAAGACAAGTATTTAGGAACGA 58.751 37.037 4.01 0.00 26.70 3.85
2413 2716 9.635520 CTAGAAAGACAAGTATTTAGGAACGAA 57.364 33.333 0.00 0.00 0.00 3.85
2414 2717 8.535690 AGAAAGACAAGTATTTAGGAACGAAG 57.464 34.615 0.00 0.00 0.00 3.79
2415 2718 7.603024 AGAAAGACAAGTATTTAGGAACGAAGG 59.397 37.037 0.00 0.00 0.00 3.46
2416 2719 5.731591 AGACAAGTATTTAGGAACGAAGGG 58.268 41.667 0.00 0.00 0.00 3.95
2417 2720 5.482878 AGACAAGTATTTAGGAACGAAGGGA 59.517 40.000 0.00 0.00 0.00 4.20
2418 2721 5.731591 ACAAGTATTTAGGAACGAAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
2480 2785 2.887783 AGAACACCACACAAACACACAA 59.112 40.909 0.00 0.00 0.00 3.33
2481 2786 3.319405 AGAACACCACACAAACACACAAA 59.681 39.130 0.00 0.00 0.00 2.83
2487 2792 2.403368 CACACAAACACACAAACACACG 59.597 45.455 0.00 0.00 0.00 4.49
2544 2849 2.341846 ACCACAACACCTCAAACGAT 57.658 45.000 0.00 0.00 0.00 3.73
2555 2860 5.763204 ACACCTCAAACGATTCAAAGTACAT 59.237 36.000 0.00 0.00 0.00 2.29
2600 2906 1.282447 AGTAGTCGGAGCTCTTCTGGA 59.718 52.381 14.64 0.98 32.69 3.86
2634 2940 3.500680 GCGAATAGGTGAAGAACAAACCA 59.499 43.478 0.00 0.00 36.37 3.67
2665 2971 6.272324 TCCTAGAAAATGTCTTCAGGAAGGAA 59.728 38.462 9.03 0.00 38.88 3.36
2723 3087 5.984725 TCAATAAGGTAATGACGTCCACAT 58.015 37.500 14.12 3.19 0.00 3.21
2753 3117 0.823356 GTCTGCCTGACCAAAGCCAA 60.823 55.000 0.00 0.00 39.69 4.52
2759 3123 1.688197 CCTGACCAAAGCCAAACATGT 59.312 47.619 0.00 0.00 0.00 3.21
2760 3124 2.102925 CCTGACCAAAGCCAAACATGTT 59.897 45.455 4.92 4.92 0.00 2.71
2920 3284 0.393944 ACGGAGGCTGAGACGATACA 60.394 55.000 0.00 0.00 0.00 2.29
3020 3385 0.740868 TGTGAGCACTATGAAGCCGC 60.741 55.000 1.99 0.00 0.00 6.53
3086 3451 2.461695 ACCATGACCTCCTAGACAGTG 58.538 52.381 0.00 0.00 0.00 3.66
3087 3452 1.137872 CCATGACCTCCTAGACAGTGC 59.862 57.143 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.112709 GAACCGGCTCTGCGTGAC 61.113 66.667 0.00 0.00 0.00 3.67
15 16 2.652382 TTTGAACCGGCTCTGCGTGA 62.652 55.000 0.00 0.00 0.00 4.35
16 17 2.175184 CTTTGAACCGGCTCTGCGTG 62.175 60.000 0.00 0.00 0.00 5.34
17 18 1.961277 CTTTGAACCGGCTCTGCGT 60.961 57.895 0.00 0.00 0.00 5.24
582 596 5.241403 ACCATGTGAGTCTGGATAAACAA 57.759 39.130 4.00 0.00 36.35 2.83
587 601 5.698741 ATCAAACCATGTGAGTCTGGATA 57.301 39.130 4.00 0.00 36.35 2.59
936 957 1.527380 ACCTCGATCTCCTCTCGCC 60.527 63.158 0.00 0.00 36.11 5.54
954 975 1.577468 CGGCCGAGTATTTATGCACA 58.423 50.000 24.07 0.00 0.00 4.57
959 980 2.522185 TCTAGCCGGCCGAGTATTTAT 58.478 47.619 30.73 2.07 0.00 1.40
1687 1715 2.338620 CTGCACCTCGTCGGACAA 59.661 61.111 9.10 0.00 36.31 3.18
1844 1895 6.074409 ACGAACAATGCAAATTAACACATGTG 60.074 34.615 24.25 24.25 0.00 3.21
1867 1919 2.728318 CCGTTGCTCATGATCTATCACG 59.272 50.000 0.00 0.49 40.03 4.35
2170 2228 4.298332 CAACCACCAAAGAAGAAAATCCG 58.702 43.478 0.00 0.00 0.00 4.18
2225 2283 5.911280 GTCCAAACGAAAGCCTTAACTTAAC 59.089 40.000 0.00 0.00 0.00 2.01
2228 2286 3.949113 TGTCCAAACGAAAGCCTTAACTT 59.051 39.130 0.00 0.00 0.00 2.66
2229 2287 3.547746 TGTCCAAACGAAAGCCTTAACT 58.452 40.909 0.00 0.00 0.00 2.24
2241 2544 3.621715 GGGAGTATAAAGCTGTCCAAACG 59.378 47.826 0.00 0.00 0.00 3.60
2249 2552 3.492829 GGAACGGAGGGAGTATAAAGCTG 60.493 52.174 0.00 0.00 0.00 4.24
2257 2560 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
2258 2561 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
2259 2562 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2260 2563 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2261 2564 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2262 2565 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2263 2566 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
2264 2567 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
2265 2568 8.248945 TCTAGAAAGACAAGTATTTAGGAACGG 58.751 37.037 0.00 0.00 0.00 4.44
2339 2642 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2340 2643 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2341 2644 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2342 2645 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2343 2646 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2344 2647 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2345 2648 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2346 2649 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2347 2650 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2348 2651 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2349 2652 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2350 2653 5.109210 TGACTACATACGGAGCAAAATGAG 58.891 41.667 0.00 0.00 0.00 2.90
2351 2654 5.079689 TGACTACATACGGAGCAAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
2352 2655 4.870426 ACTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2353 2656 5.086104 ACTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2354 2657 4.530710 ACTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2355 2658 4.242475 CAACTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2356 2659 3.257375 ACAACTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2357 2660 2.823747 ACAACTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2358 2661 3.505464 ACAACTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2359 2662 5.055642 TCAACAACTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2360 2663 5.456548 TTCAACAACTGACTACATACGGA 57.543 39.130 0.00 0.00 32.21 4.69
2361 2664 6.534059 CATTTCAACAACTGACTACATACGG 58.466 40.000 0.00 0.00 32.21 4.02
2362 2665 6.015504 GCATTTCAACAACTGACTACATACG 58.984 40.000 0.00 0.00 32.21 3.06
2363 2666 6.149474 AGGCATTTCAACAACTGACTACATAC 59.851 38.462 0.00 0.00 28.71 2.39
2364 2667 6.237901 AGGCATTTCAACAACTGACTACATA 58.762 36.000 0.00 0.00 28.71 2.29
2365 2668 5.072741 AGGCATTTCAACAACTGACTACAT 58.927 37.500 0.00 0.00 28.71 2.29
2366 2669 4.460263 AGGCATTTCAACAACTGACTACA 58.540 39.130 0.00 0.00 28.71 2.74
2367 2670 5.932303 TCTAGGCATTTCAACAACTGACTAC 59.068 40.000 0.00 0.00 32.80 2.73
2368 2671 6.109156 TCTAGGCATTTCAACAACTGACTA 57.891 37.500 0.00 0.00 32.80 2.59
2369 2672 4.973168 TCTAGGCATTTCAACAACTGACT 58.027 39.130 0.00 0.00 34.88 3.41
2370 2673 5.689383 TTCTAGGCATTTCAACAACTGAC 57.311 39.130 0.00 0.00 32.21 3.51
2371 2674 6.017109 GTCTTTCTAGGCATTTCAACAACTGA 60.017 38.462 0.00 0.00 0.00 3.41
2372 2675 6.145535 GTCTTTCTAGGCATTTCAACAACTG 58.854 40.000 0.00 0.00 0.00 3.16
2373 2676 5.827797 TGTCTTTCTAGGCATTTCAACAACT 59.172 36.000 0.00 0.00 29.10 3.16
2374 2677 6.072112 TGTCTTTCTAGGCATTTCAACAAC 57.928 37.500 0.00 0.00 29.10 3.32
2375 2678 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
2376 2679 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
2377 2680 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
2378 2681 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
2379 2682 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
2381 2684 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
2382 2685 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
2383 2686 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
2384 2687 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
2385 2688 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
2386 2689 8.248945 TCGTTCCTAAATACTTGTCTTTCTAGG 58.751 37.037 0.00 0.00 0.00 3.02
2387 2690 9.635520 TTCGTTCCTAAATACTTGTCTTTCTAG 57.364 33.333 0.00 0.00 0.00 2.43
2388 2691 9.635520 CTTCGTTCCTAAATACTTGTCTTTCTA 57.364 33.333 0.00 0.00 0.00 2.10
2389 2692 7.603024 CCTTCGTTCCTAAATACTTGTCTTTCT 59.397 37.037 0.00 0.00 0.00 2.52
2390 2693 7.148457 CCCTTCGTTCCTAAATACTTGTCTTTC 60.148 40.741 0.00 0.00 0.00 2.62
2391 2694 6.653740 CCCTTCGTTCCTAAATACTTGTCTTT 59.346 38.462 0.00 0.00 0.00 2.52
2392 2695 6.013984 TCCCTTCGTTCCTAAATACTTGTCTT 60.014 38.462 0.00 0.00 0.00 3.01
2393 2696 5.482878 TCCCTTCGTTCCTAAATACTTGTCT 59.517 40.000 0.00 0.00 0.00 3.41
2394 2697 5.727434 TCCCTTCGTTCCTAAATACTTGTC 58.273 41.667 0.00 0.00 0.00 3.18
2395 2698 5.247792 ACTCCCTTCGTTCCTAAATACTTGT 59.752 40.000 0.00 0.00 0.00 3.16
2396 2699 5.731591 ACTCCCTTCGTTCCTAAATACTTG 58.268 41.667 0.00 0.00 0.00 3.16
2397 2700 6.894103 TCTACTCCCTTCGTTCCTAAATACTT 59.106 38.462 0.00 0.00 0.00 2.24
2398 2701 6.430007 TCTACTCCCTTCGTTCCTAAATACT 58.570 40.000 0.00 0.00 0.00 2.12
2399 2702 6.705863 TCTACTCCCTTCGTTCCTAAATAC 57.294 41.667 0.00 0.00 0.00 1.89
2400 2703 9.425248 TTTATCTACTCCCTTCGTTCCTAAATA 57.575 33.333 0.00 0.00 0.00 1.40
2401 2704 7.909485 TTATCTACTCCCTTCGTTCCTAAAT 57.091 36.000 0.00 0.00 0.00 1.40
2402 2705 7.632245 GCTTTATCTACTCCCTTCGTTCCTAAA 60.632 40.741 0.00 0.00 0.00 1.85
2403 2706 6.183360 GCTTTATCTACTCCCTTCGTTCCTAA 60.183 42.308 0.00 0.00 0.00 2.69
2404 2707 5.301298 GCTTTATCTACTCCCTTCGTTCCTA 59.699 44.000 0.00 0.00 0.00 2.94
2405 2708 4.099727 GCTTTATCTACTCCCTTCGTTCCT 59.900 45.833 0.00 0.00 0.00 3.36
2406 2709 4.370049 GCTTTATCTACTCCCTTCGTTCC 58.630 47.826 0.00 0.00 0.00 3.62
2407 2710 4.043073 CGCTTTATCTACTCCCTTCGTTC 58.957 47.826 0.00 0.00 0.00 3.95
2408 2711 3.698040 TCGCTTTATCTACTCCCTTCGTT 59.302 43.478 0.00 0.00 0.00 3.85
2409 2712 3.066481 GTCGCTTTATCTACTCCCTTCGT 59.934 47.826 0.00 0.00 0.00 3.85
2410 2713 3.066342 TGTCGCTTTATCTACTCCCTTCG 59.934 47.826 0.00 0.00 0.00 3.79
2411 2714 4.361420 GTGTCGCTTTATCTACTCCCTTC 58.639 47.826 0.00 0.00 0.00 3.46
2412 2715 3.132467 GGTGTCGCTTTATCTACTCCCTT 59.868 47.826 0.00 0.00 0.00 3.95
2413 2716 2.694109 GGTGTCGCTTTATCTACTCCCT 59.306 50.000 0.00 0.00 0.00 4.20
2414 2717 2.223994 GGGTGTCGCTTTATCTACTCCC 60.224 54.545 0.00 0.00 38.19 4.30
2415 2718 2.429610 TGGGTGTCGCTTTATCTACTCC 59.570 50.000 0.00 0.00 0.00 3.85
2416 2719 3.795623 TGGGTGTCGCTTTATCTACTC 57.204 47.619 0.00 0.00 0.00 2.59
2417 2720 3.259876 TGTTGGGTGTCGCTTTATCTACT 59.740 43.478 0.00 0.00 0.00 2.57
2418 2721 3.592059 TGTTGGGTGTCGCTTTATCTAC 58.408 45.455 0.00 0.00 0.00 2.59
2480 2785 3.216292 GCCTTGGGTGCGTGTGTT 61.216 61.111 0.00 0.00 0.00 3.32
2481 2786 4.497984 TGCCTTGGGTGCGTGTGT 62.498 61.111 0.00 0.00 0.00 3.72
2487 2792 0.811281 GTGTATCTTGCCTTGGGTGC 59.189 55.000 0.00 0.00 0.00 5.01
2600 2906 1.625616 CTATTCGCGGTGTCTTTCGT 58.374 50.000 6.13 0.00 0.00 3.85
2634 2940 7.038017 TCCTGAAGACATTTTCTAGGAAGTCAT 60.038 37.037 6.06 0.00 34.45 3.06
2665 2971 3.490759 CAGCGCTTCGGCATCGTT 61.491 61.111 7.50 0.00 41.88 3.85
2693 2999 6.338937 ACGTCATTACCTTATTGAAGTCTCC 58.661 40.000 0.00 0.00 29.28 3.71
2996 3360 3.452474 GCTTCATAGTGCTCACAGGTAG 58.548 50.000 2.63 0.00 0.00 3.18
2997 3361 2.168521 GGCTTCATAGTGCTCACAGGTA 59.831 50.000 2.63 0.00 0.00 3.08
2999 3363 1.661341 GGCTTCATAGTGCTCACAGG 58.339 55.000 2.63 0.00 0.00 4.00
3001 3365 0.740868 GCGGCTTCATAGTGCTCACA 60.741 55.000 2.63 0.00 0.00 3.58
3002 3366 1.432270 GGCGGCTTCATAGTGCTCAC 61.432 60.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.