Multiple sequence alignment - TraesCS4B01G211100

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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 TraesCS4B01G211100 chr4B 100.000 2843 0 0 1 2843 449518018 449520860 0.000000e+00 5251.0
1 TraesCS4B01G211100 chr4B 95.978 1641 42 10 687 2308 535286169 535287804 0.000000e+00 2643.0
2 TraesCS4B01G211100 chr4B 97.605 835 20 0 1 835 535285563 535286397 0.000000e+00 1432.0
3 TraesCS4B01G211100 chr4B 89.426 331 31 4 604 930 428198144 428197814 5.670000e-112 414.0
4 TraesCS4B01G211100 chr4B 98.077 52 1 0 2525 2576 449524576 449524525 1.080000e-14 91.6
5 TraesCS4B01G211100 chr5D 94.023 2309 90 19 1 2278 420018607 420020898 0.000000e+00 3456.0
6 TraesCS4B01G211100 chr5D 86.334 1661 154 37 669 2308 538687030 538688638 0.000000e+00 1742.0
7 TraesCS4B01G211100 chr5D 87.471 854 75 20 2 828 538686421 538687269 0.000000e+00 955.0
8 TraesCS4B01G211100 chr6A 92.203 2347 123 17 1 2312 571574021 571576342 0.000000e+00 3265.0
9 TraesCS4B01G211100 chr6A 88.148 405 27 6 1924 2308 554477586 554477989 2.000000e-126 462.0
10 TraesCS4B01G211100 chr2B 95.934 1648 45 7 687 2314 358758067 358759712 0.000000e+00 2652.0
11 TraesCS4B01G211100 chr2B 90.835 611 51 2 1 606 579976888 579977498 0.000000e+00 813.0
12 TraesCS4B01G211100 chr2B 96.837 411 13 0 430 840 358757890 358758300 0.000000e+00 688.0
13 TraesCS4B01G211100 chr3B 96.335 1255 26 2 1078 2313 604141017 604139764 0.000000e+00 2045.0
14 TraesCS4B01G211100 chr3B 93.032 775 20 9 1569 2311 576053728 576052956 0.000000e+00 1101.0
15 TraesCS4B01G211100 chr7A 92.993 1370 58 19 975 2311 297775891 297774527 0.000000e+00 1964.0
16 TraesCS4B01G211100 chr7A 95.925 957 38 1 1 957 297785568 297784613 0.000000e+00 1550.0
17 TraesCS4B01G211100 chr7A 86.923 1300 106 35 2 1267 62735477 62736746 0.000000e+00 1400.0
18 TraesCS4B01G211100 chr4A 85.260 1730 174 47 604 2308 629935464 629937137 0.000000e+00 1707.0
19 TraesCS4B01G211100 chr4A 85.311 177 15 5 2310 2480 100954727 100954556 3.770000e-39 172.0
20 TraesCS4B01G211100 chr3D 85.455 1650 171 35 687 2312 339817079 339818683 0.000000e+00 1653.0
21 TraesCS4B01G211100 chr3D 88.720 789 76 9 2 781 339816471 339817255 0.000000e+00 952.0
22 TraesCS4B01G211100 chr3D 83.276 293 25 8 2571 2842 599330543 599330832 6.080000e-62 248.0
23 TraesCS4B01G211100 chr3D 81.911 293 29 5 2571 2842 406139706 406139995 2.850000e-55 226.0
24 TraesCS4B01G211100 chr1A 87.962 1271 132 13 669 1923 80283925 80282660 0.000000e+00 1480.0
25 TraesCS4B01G211100 chr1B 92.893 999 38 9 1341 2308 400360017 400361013 0.000000e+00 1421.0
26 TraesCS4B01G211100 chr1D 86.870 853 81 20 2 828 80673960 80674807 0.000000e+00 926.0
27 TraesCS4B01G211100 chr1D 91.525 295 3 5 2571 2843 474363144 474363438 1.240000e-103 387.0
28 TraesCS4B01G211100 chr1D 98.077 52 1 0 2525 2576 474361499 474361550 1.080000e-14 91.6
29 TraesCS4B01G211100 chr7B 97.436 273 7 0 2571 2843 700195545 700195273 1.540000e-127 466.0
30 TraesCS4B01G211100 chr7B 96.364 55 2 0 2522 2576 700191674 700191728 1.080000e-14 91.6
31 TraesCS4B01G211100 chr4D 92.177 294 2 3 2571 2843 81319557 81319850 2.050000e-106 396.0
32 TraesCS4B01G211100 chr4D 81.739 230 23 10 2301 2524 364049966 364050182 1.050000e-39 174.0
33 TraesCS4B01G211100 chr4D 98.113 53 1 0 2524 2576 81317970 81318022 3.020000e-15 93.5
34 TraesCS4B01G211100 chr5A 85.921 277 17 3 2588 2843 650780222 650779947 2.790000e-70 276.0
35 TraesCS4B01G211100 chr5A 90.385 52 5 0 2525 2576 650776056 650776107 5.080000e-08 69.4
36 TraesCS4B01G211100 chr6D 82.935 293 26 5 2571 2842 55874871 55875160 2.830000e-60 243.0
37 TraesCS4B01G211100 chr6D 82.230 287 27 5 2577 2842 55877971 55877688 2.850000e-55 226.0
38 TraesCS4B01G211100 chr7D 82.253 293 28 5 2571 2842 549947764 549948053 6.130000e-57 231.0
39 TraesCS4B01G211100 chr3A 82.824 262 33 9 2588 2841 23149689 23149946 1.020000e-54 224.0


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 TraesCS4B01G211100 chr4B 449518018 449520860 2842 False 5251.00 5251 100.0000 1 2843 1 chr4B.!!$F1 2842
1 TraesCS4B01G211100 chr4B 535285563 535287804 2241 False 2037.50 2643 96.7915 1 2308 2 chr4B.!!$F2 2307
2 TraesCS4B01G211100 chr5D 420018607 420020898 2291 False 3456.00 3456 94.0230 1 2278 1 chr5D.!!$F1 2277
3 TraesCS4B01G211100 chr5D 538686421 538688638 2217 False 1348.50 1742 86.9025 2 2308 2 chr5D.!!$F2 2306
4 TraesCS4B01G211100 chr6A 571574021 571576342 2321 False 3265.00 3265 92.2030 1 2312 1 chr6A.!!$F2 2311
5 TraesCS4B01G211100 chr2B 358757890 358759712 1822 False 1670.00 2652 96.3855 430 2314 2 chr2B.!!$F2 1884
6 TraesCS4B01G211100 chr2B 579976888 579977498 610 False 813.00 813 90.8350 1 606 1 chr2B.!!$F1 605
7 TraesCS4B01G211100 chr3B 604139764 604141017 1253 True 2045.00 2045 96.3350 1078 2313 1 chr3B.!!$R2 1235
8 TraesCS4B01G211100 chr3B 576052956 576053728 772 True 1101.00 1101 93.0320 1569 2311 1 chr3B.!!$R1 742
9 TraesCS4B01G211100 chr7A 297774527 297775891 1364 True 1964.00 1964 92.9930 975 2311 1 chr7A.!!$R1 1336
10 TraesCS4B01G211100 chr7A 297784613 297785568 955 True 1550.00 1550 95.9250 1 957 1 chr7A.!!$R2 956
11 TraesCS4B01G211100 chr7A 62735477 62736746 1269 False 1400.00 1400 86.9230 2 1267 1 chr7A.!!$F1 1265
12 TraesCS4B01G211100 chr4A 629935464 629937137 1673 False 1707.00 1707 85.2600 604 2308 1 chr4A.!!$F1 1704
13 TraesCS4B01G211100 chr3D 339816471 339818683 2212 False 1302.50 1653 87.0875 2 2312 2 chr3D.!!$F3 2310
14 TraesCS4B01G211100 chr1A 80282660 80283925 1265 True 1480.00 1480 87.9620 669 1923 1 chr1A.!!$R1 1254
15 TraesCS4B01G211100 chr1B 400360017 400361013 996 False 1421.00 1421 92.8930 1341 2308 1 chr1B.!!$F1 967
16 TraesCS4B01G211100 chr1D 80673960 80674807 847 False 926.00 926 86.8700 2 828 1 chr1D.!!$F1 826
17 TraesCS4B01G211100 chr1D 474361499 474363438 1939 False 239.30 387 94.8010 2525 2843 2 chr1D.!!$F2 318
18 TraesCS4B01G211100 chr4D 81317970 81319850 1880 False 244.75 396 95.1450 2524 2843 2 chr4D.!!$F2 319

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
200 206 0.471022 GGGTTCTTGCCCCCTTTTCA 60.471 55.0 0.0 0.0 42.89 2.69 F
1075 1286 0.108585 GTCAAGTGGCTTCAGGGACA 59.891 55.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 1843 0.038251 AGACTTCACAAGCGCATCGA 60.038 50.0 11.47 0.00 0.00 3.59 R
2503 2765 0.034574 TGGTTCCTACGCGGGTAGTA 60.035 55.0 30.57 18.11 43.82 1.82 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
200 206 0.471022 GGGTTCTTGCCCCCTTTTCA 60.471 55.000 0.00 0.00 42.89 2.69
644 650 8.518151 TTGTGATGTTTATGCAACTACATTTG 57.482 30.769 10.90 0.00 36.21 2.32
685 753 8.220755 TGGGCAGATTGTATCATTTACTAAAC 57.779 34.615 0.00 0.00 0.00 2.01
716 785 7.760794 ACCATGTATTTGTGATGTTTATGCAAG 59.239 33.333 0.00 0.00 0.00 4.01
745 814 8.667463 CATTTGAATTTATTTGATGGTTGGACC 58.333 33.333 0.00 0.00 39.22 4.46
750 819 5.828299 TTATTTGATGGTTGGACCGATTC 57.172 39.130 0.00 0.00 42.58 2.52
754 823 4.771114 TGATGGTTGGACCGATTCTATT 57.229 40.909 0.00 0.00 42.58 1.73
1075 1286 0.108585 GTCAAGTGGCTTCAGGGACA 59.891 55.000 0.00 0.00 0.00 4.02
1089 1300 3.070590 TCAGGGACATGCATCATAGACAG 59.929 47.826 0.00 0.00 0.00 3.51
1349 1561 6.842282 GCTAATCATTTTGCATAATGTTTGCG 59.158 34.615 24.52 18.78 43.10 4.85
1352 1564 5.417811 TCATTTTGCATAATGTTTGCGGAT 58.582 33.333 23.57 0.00 43.10 4.18
1410 1622 1.962144 GCACTATCATGCCATGGCC 59.038 57.895 33.44 16.23 39.86 5.36
1631 1843 3.312736 AGATGGGTTCAAACTTGTGGT 57.687 42.857 0.00 0.00 0.00 4.16
1871 2088 7.625469 TGATATGGTTGTATGGTTGTCAAGTA 58.375 34.615 0.00 0.00 0.00 2.24
2023 2283 7.225784 TGTATGGCTGTCAAATGTGTTTAAT 57.774 32.000 0.00 0.00 0.00 1.40
2183 2445 0.110486 ACTCCGTGCTTCCAACCAAT 59.890 50.000 0.00 0.00 0.00 3.16
2308 2570 0.041238 TTCCCCAACCAAACACACCA 59.959 50.000 0.00 0.00 0.00 4.17
2314 2576 3.243704 CCCAACCAAACACACCATAACAG 60.244 47.826 0.00 0.00 0.00 3.16
2315 2577 3.383185 CCAACCAAACACACCATAACAGT 59.617 43.478 0.00 0.00 0.00 3.55
2316 2578 4.358851 CAACCAAACACACCATAACAGTG 58.641 43.478 0.00 0.00 41.15 3.66
2317 2579 3.892284 ACCAAACACACCATAACAGTGA 58.108 40.909 0.00 0.00 38.63 3.41
2318 2580 3.630312 ACCAAACACACCATAACAGTGAC 59.370 43.478 0.00 0.00 38.63 3.67
2319 2581 3.303725 CCAAACACACCATAACAGTGACG 60.304 47.826 0.00 0.00 38.63 4.35
2320 2582 1.508632 ACACACCATAACAGTGACGC 58.491 50.000 0.00 0.00 38.63 5.19
2321 2583 0.796312 CACACCATAACAGTGACGCC 59.204 55.000 0.00 0.00 38.63 5.68
2322 2584 0.394938 ACACCATAACAGTGACGCCA 59.605 50.000 0.00 0.00 38.63 5.69
2323 2585 1.078709 CACCATAACAGTGACGCCAG 58.921 55.000 0.00 0.00 37.42 4.85
2324 2586 0.673644 ACCATAACAGTGACGCCAGC 60.674 55.000 0.00 0.00 0.00 4.85
2325 2587 0.391661 CCATAACAGTGACGCCAGCT 60.392 55.000 0.00 0.00 0.00 4.24
2326 2588 1.134818 CCATAACAGTGACGCCAGCTA 60.135 52.381 0.00 0.00 0.00 3.32
2327 2589 1.927174 CATAACAGTGACGCCAGCTAC 59.073 52.381 0.00 0.00 0.00 3.58
2328 2590 0.109458 TAACAGTGACGCCAGCTACG 60.109 55.000 6.76 6.76 0.00 3.51
2329 2591 1.802337 AACAGTGACGCCAGCTACGA 61.802 55.000 14.58 0.00 0.00 3.43
2330 2592 1.515088 CAGTGACGCCAGCTACGAG 60.515 63.158 14.58 0.00 0.00 4.18
2331 2593 1.972223 AGTGACGCCAGCTACGAGT 60.972 57.895 14.58 2.26 0.00 4.18
2332 2594 1.514443 GTGACGCCAGCTACGAGTC 60.514 63.158 14.58 11.64 0.00 3.36
2333 2595 2.102553 GACGCCAGCTACGAGTCC 59.897 66.667 14.58 0.00 0.00 3.85
2334 2596 2.675423 ACGCCAGCTACGAGTCCA 60.675 61.111 14.58 0.00 0.00 4.02
2335 2597 2.005960 GACGCCAGCTACGAGTCCAT 62.006 60.000 14.58 0.00 0.00 3.41
2336 2598 1.299468 CGCCAGCTACGAGTCCATC 60.299 63.158 2.25 0.00 0.00 3.51
2337 2599 1.816537 GCCAGCTACGAGTCCATCA 59.183 57.895 0.00 0.00 0.00 3.07
2338 2600 0.175760 GCCAGCTACGAGTCCATCAA 59.824 55.000 0.00 0.00 0.00 2.57
2339 2601 1.927895 CCAGCTACGAGTCCATCAAC 58.072 55.000 0.00 0.00 0.00 3.18
2340 2602 1.550065 CAGCTACGAGTCCATCAACG 58.450 55.000 0.00 0.00 0.00 4.10
2341 2603 0.179134 AGCTACGAGTCCATCAACGC 60.179 55.000 0.00 0.00 0.00 4.84
2342 2604 1.146358 GCTACGAGTCCATCAACGCC 61.146 60.000 0.00 0.00 0.00 5.68
2343 2605 0.172578 CTACGAGTCCATCAACGCCA 59.827 55.000 0.00 0.00 0.00 5.69
2344 2606 0.604073 TACGAGTCCATCAACGCCAA 59.396 50.000 0.00 0.00 0.00 4.52
2345 2607 0.670546 ACGAGTCCATCAACGCCAAG 60.671 55.000 0.00 0.00 0.00 3.61
2346 2608 1.796796 GAGTCCATCAACGCCAAGC 59.203 57.895 0.00 0.00 0.00 4.01
2347 2609 0.955428 GAGTCCATCAACGCCAAGCA 60.955 55.000 0.00 0.00 0.00 3.91
2348 2610 1.210155 GTCCATCAACGCCAAGCAC 59.790 57.895 0.00 0.00 0.00 4.40
2349 2611 2.176546 CCATCAACGCCAAGCACG 59.823 61.111 0.00 0.00 0.00 5.34
2350 2612 2.502510 CATCAACGCCAAGCACGC 60.503 61.111 0.00 0.00 0.00 5.34
2360 2622 4.962122 AAGCACGCGCGCACAAAG 62.962 61.111 32.58 16.92 45.49 2.77
2363 2625 4.292208 CACGCGCGCACAAAGTCA 62.292 61.111 32.58 0.00 0.00 3.41
2364 2626 4.293626 ACGCGCGCACAAAGTCAC 62.294 61.111 32.58 0.00 0.00 3.67
2365 2627 4.000557 CGCGCGCACAAAGTCACT 62.001 61.111 32.61 0.00 0.00 3.41
2366 2628 2.653967 CGCGCGCACAAAGTCACTA 61.654 57.895 32.61 0.00 0.00 2.74
2367 2629 1.154654 GCGCGCACAAAGTCACTAC 60.155 57.895 29.10 0.00 0.00 2.73
2368 2630 1.827315 GCGCGCACAAAGTCACTACA 61.827 55.000 29.10 0.00 0.00 2.74
2369 2631 0.790207 CGCGCACAAAGTCACTACAT 59.210 50.000 8.75 0.00 0.00 2.29
2370 2632 1.989864 CGCGCACAAAGTCACTACATA 59.010 47.619 8.75 0.00 0.00 2.29
2371 2633 2.603110 CGCGCACAAAGTCACTACATAT 59.397 45.455 8.75 0.00 0.00 1.78
2372 2634 3.301835 CGCGCACAAAGTCACTACATATC 60.302 47.826 8.75 0.00 0.00 1.63
2373 2635 3.865745 GCGCACAAAGTCACTACATATCT 59.134 43.478 0.30 0.00 0.00 1.98
2374 2636 4.330074 GCGCACAAAGTCACTACATATCTT 59.670 41.667 0.30 0.00 0.00 2.40
2375 2637 5.163854 GCGCACAAAGTCACTACATATCTTT 60.164 40.000 0.30 0.00 0.00 2.52
2376 2638 6.620733 GCGCACAAAGTCACTACATATCTTTT 60.621 38.462 0.30 0.00 0.00 2.27
2377 2639 7.298122 CGCACAAAGTCACTACATATCTTTTT 58.702 34.615 0.00 0.00 0.00 1.94
2408 2670 7.290110 TGAGTATCACTGTTGATAGGTATGG 57.710 40.000 0.00 0.00 43.96 2.74
2409 2671 6.839134 TGAGTATCACTGTTGATAGGTATGGT 59.161 38.462 0.00 0.00 43.96 3.55
2410 2672 8.002459 TGAGTATCACTGTTGATAGGTATGGTA 58.998 37.037 0.00 0.00 43.96 3.25
2411 2673 8.777578 AGTATCACTGTTGATAGGTATGGTAA 57.222 34.615 0.00 0.00 43.96 2.85
2412 2674 9.381038 AGTATCACTGTTGATAGGTATGGTAAT 57.619 33.333 0.00 0.00 43.96 1.89
2413 2675 9.424319 GTATCACTGTTGATAGGTATGGTAATG 57.576 37.037 0.00 0.00 43.96 1.90
2414 2676 6.826668 TCACTGTTGATAGGTATGGTAATGG 58.173 40.000 0.00 0.00 0.00 3.16
2415 2677 6.385759 TCACTGTTGATAGGTATGGTAATGGT 59.614 38.462 0.00 0.00 0.00 3.55
2416 2678 7.565768 TCACTGTTGATAGGTATGGTAATGGTA 59.434 37.037 0.00 0.00 0.00 3.25
2417 2679 8.375506 CACTGTTGATAGGTATGGTAATGGTAT 58.624 37.037 0.00 0.00 0.00 2.73
2418 2680 8.594550 ACTGTTGATAGGTATGGTAATGGTATC 58.405 37.037 0.00 0.00 0.00 2.24
2419 2681 7.913789 TGTTGATAGGTATGGTAATGGTATCC 58.086 38.462 0.00 0.00 0.00 2.59
2420 2682 7.037873 TGTTGATAGGTATGGTAATGGTATCCC 60.038 40.741 0.00 0.00 0.00 3.85
2421 2683 6.822374 TGATAGGTATGGTAATGGTATCCCT 58.178 40.000 0.00 0.00 0.00 4.20
2422 2684 7.260891 TGATAGGTATGGTAATGGTATCCCTT 58.739 38.462 0.00 0.00 0.00 3.95
2423 2685 7.742213 TGATAGGTATGGTAATGGTATCCCTTT 59.258 37.037 0.00 0.00 33.08 3.11
2424 2686 6.858792 AGGTATGGTAATGGTATCCCTTTT 57.141 37.500 0.00 0.00 31.10 2.27
2425 2687 7.233855 AGGTATGGTAATGGTATCCCTTTTT 57.766 36.000 0.00 0.00 31.10 1.94
2449 2711 9.853555 TTTTTAACTTTGATGATACGATTGCAT 57.146 25.926 0.00 0.00 0.00 3.96
2450 2712 8.839947 TTTAACTTTGATGATACGATTGCATG 57.160 30.769 0.00 0.00 0.00 4.06
2451 2713 4.852138 ACTTTGATGATACGATTGCATGC 58.148 39.130 11.82 11.82 0.00 4.06
2452 2714 4.336153 ACTTTGATGATACGATTGCATGCA 59.664 37.500 18.46 18.46 0.00 3.96
2453 2715 4.897025 TTGATGATACGATTGCATGCAA 57.103 36.364 33.57 33.57 40.47 4.08
2454 2716 4.213596 TGATGATACGATTGCATGCAAC 57.786 40.909 34.10 24.48 38.88 4.17
2455 2717 3.626670 TGATGATACGATTGCATGCAACA 59.373 39.130 34.10 25.13 38.88 3.33
2456 2718 3.678915 TGATACGATTGCATGCAACAG 57.321 42.857 34.10 29.38 38.88 3.16
2457 2719 3.269178 TGATACGATTGCATGCAACAGA 58.731 40.909 34.10 19.77 38.88 3.41
2458 2720 3.688673 TGATACGATTGCATGCAACAGAA 59.311 39.130 34.10 20.23 38.88 3.02
2459 2721 4.155644 TGATACGATTGCATGCAACAGAAA 59.844 37.500 34.10 21.73 38.88 2.52
2460 2722 2.937591 ACGATTGCATGCAACAGAAAG 58.062 42.857 34.10 21.72 38.88 2.62
2461 2723 2.294233 ACGATTGCATGCAACAGAAAGT 59.706 40.909 34.10 22.30 38.88 2.66
2462 2724 3.243501 ACGATTGCATGCAACAGAAAGTT 60.244 39.130 34.10 16.63 42.42 2.66
2463 2725 4.023279 ACGATTGCATGCAACAGAAAGTTA 60.023 37.500 34.10 9.66 38.74 2.24
2464 2726 4.321745 CGATTGCATGCAACAGAAAGTTAC 59.678 41.667 34.10 13.77 38.74 2.50
2465 2727 4.916983 TTGCATGCAACAGAAAGTTACT 57.083 36.364 28.80 0.00 38.74 2.24
2466 2728 6.573664 ATTGCATGCAACAGAAAGTTACTA 57.426 33.333 34.10 8.39 38.74 1.82
2467 2729 5.356882 TGCATGCAACAGAAAGTTACTAC 57.643 39.130 20.30 0.00 38.74 2.73
2468 2730 4.215399 TGCATGCAACAGAAAGTTACTACC 59.785 41.667 20.30 0.00 38.74 3.18
2469 2731 4.669197 GCATGCAACAGAAAGTTACTACCG 60.669 45.833 14.21 0.00 38.74 4.02
2470 2732 2.803956 TGCAACAGAAAGTTACTACCGC 59.196 45.455 0.00 0.00 38.74 5.68
2471 2733 3.064931 GCAACAGAAAGTTACTACCGCT 58.935 45.455 0.00 0.00 38.74 5.52
2472 2734 3.120649 GCAACAGAAAGTTACTACCGCTG 60.121 47.826 0.00 0.00 38.74 5.18
2473 2735 3.314541 ACAGAAAGTTACTACCGCTGG 57.685 47.619 0.00 0.00 0.00 4.85
2474 2736 2.028385 ACAGAAAGTTACTACCGCTGGG 60.028 50.000 0.00 0.00 40.11 4.45
2475 2737 6.021966 AACAGAAAGTTACTACCGCTGGGT 62.022 45.833 0.00 0.00 44.12 4.51
2476 2738 6.738041 AACAGAAAGTTACTACCGCTGGGTA 61.738 44.000 0.00 0.00 41.46 3.69
2477 2739 7.983338 AACAGAAAGTTACTACCGCTGGGTAT 61.983 42.308 0.00 0.00 42.54 2.73
2478 2740 8.720674 AACAGAAAGTTACTACCGCTGGGTATA 61.721 40.741 0.00 0.00 42.54 1.47
2486 2748 1.583054 CCGCTGGGTATAACTTCAGC 58.417 55.000 8.52 8.52 46.32 4.26
2490 2752 3.266510 CTGGGTATAACTTCAGCAGCA 57.733 47.619 0.00 0.00 0.00 4.41
2491 2753 2.939103 CTGGGTATAACTTCAGCAGCAC 59.061 50.000 0.00 0.00 0.00 4.40
2492 2754 2.571653 TGGGTATAACTTCAGCAGCACT 59.428 45.455 0.00 0.00 0.00 4.40
2508 2770 5.401033 CAGCACTGCATTGAAGATACTAC 57.599 43.478 8.44 0.00 0.00 2.73
2509 2771 4.272018 CAGCACTGCATTGAAGATACTACC 59.728 45.833 8.44 0.00 0.00 3.18
2510 2772 3.561725 GCACTGCATTGAAGATACTACCC 59.438 47.826 8.44 0.00 0.00 3.69
2511 2773 3.804325 CACTGCATTGAAGATACTACCCG 59.196 47.826 0.00 0.00 0.00 5.28
2512 2774 2.802816 CTGCATTGAAGATACTACCCGC 59.197 50.000 0.00 0.00 0.00 6.13
2513 2775 1.792949 GCATTGAAGATACTACCCGCG 59.207 52.381 0.00 0.00 0.00 6.46
2514 2776 2.802057 GCATTGAAGATACTACCCGCGT 60.802 50.000 4.92 0.00 0.00 6.01
2515 2777 3.551454 GCATTGAAGATACTACCCGCGTA 60.551 47.826 4.92 0.00 0.00 4.42
2516 2778 3.976793 TTGAAGATACTACCCGCGTAG 57.023 47.619 4.92 5.70 46.41 3.51
2517 2779 2.224606 TGAAGATACTACCCGCGTAGG 58.775 52.381 11.73 1.79 45.45 3.18
2518 2780 2.158769 TGAAGATACTACCCGCGTAGGA 60.159 50.000 11.73 3.28 45.45 2.94
2519 2781 2.645838 AGATACTACCCGCGTAGGAA 57.354 50.000 11.73 0.25 45.45 3.36
2520 2782 2.225467 AGATACTACCCGCGTAGGAAC 58.775 52.381 11.73 2.08 45.45 3.62
2521 2783 1.268079 GATACTACCCGCGTAGGAACC 59.732 57.143 11.73 0.00 45.45 3.62
2522 2784 0.034574 TACTACCCGCGTAGGAACCA 60.035 55.000 11.73 0.00 45.45 3.67
2533 2795 2.352814 CGTAGGAACCAGGAGTGAAGTG 60.353 54.545 0.00 0.00 0.00 3.16
2603 4464 1.625818 GAAACCTCTTCCTCTGCCTCA 59.374 52.381 0.00 0.00 0.00 3.86
2668 4529 1.761784 CTGATCTTCTGGGAGGTCTGG 59.238 57.143 0.00 0.00 0.00 3.86
2705 4566 1.802960 CTGTGAGCTTGTAGTTGCTGG 59.197 52.381 0.00 0.00 39.91 4.85
2710 4592 2.222027 AGCTTGTAGTTGCTGGTTGAC 58.778 47.619 0.00 0.00 38.21 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 147 4.872691 CCAGCATCAACTAGGTAGAACTTG 59.127 45.833 0.00 0.00 0.00 3.16
644 650 4.099881 TCTGCCCAGCCATCAAATAAATTC 59.900 41.667 0.00 0.00 0.00 2.17
685 753 9.859427 ATAAACATCACAAATACATGGTTCAAG 57.141 29.630 0.00 0.00 30.09 3.02
1075 1286 3.555527 AGCACACTGTCTATGATGCAT 57.444 42.857 0.00 0.00 35.51 3.96
1089 1300 3.664025 GCTCGTTCAAAACAATAGCACAC 59.336 43.478 0.00 0.00 33.78 3.82
1349 1561 0.743097 GGCATCAGCTTTGTGGATCC 59.257 55.000 4.20 4.20 41.70 3.36
1352 1564 1.304381 GGGGCATCAGCTTTGTGGA 60.304 57.895 0.00 0.00 41.70 4.02
1410 1622 2.224018 CCCAATTGTCCCATAAATGGCG 60.224 50.000 4.43 0.00 46.70 5.69
1437 1649 0.106868 CAGATCTGCCATTCAGCCCA 60.107 55.000 10.38 0.00 42.56 5.36
1631 1843 0.038251 AGACTTCACAAGCGCATCGA 60.038 50.000 11.47 0.00 0.00 3.59
1846 2062 6.480763 ACTTGACAACCATACAACCATATCA 58.519 36.000 0.00 0.00 0.00 2.15
1871 2088 4.592942 AGCATACATGTCAGGTTCACATT 58.407 39.130 0.00 0.00 31.83 2.71
2308 2570 1.469251 CGTAGCTGGCGTCACTGTTAT 60.469 52.381 0.00 0.00 0.00 1.89
2314 2576 1.514443 GACTCGTAGCTGGCGTCAC 60.514 63.158 11.31 0.00 0.00 3.67
2315 2577 2.697761 GGACTCGTAGCTGGCGTCA 61.698 63.158 11.31 0.00 0.00 4.35
2316 2578 2.005960 ATGGACTCGTAGCTGGCGTC 62.006 60.000 11.31 6.76 0.00 5.19
2317 2579 2.005960 GATGGACTCGTAGCTGGCGT 62.006 60.000 11.31 0.00 0.00 5.68
2318 2580 1.299468 GATGGACTCGTAGCTGGCG 60.299 63.158 0.00 0.51 0.00 5.69
2319 2581 0.175760 TTGATGGACTCGTAGCTGGC 59.824 55.000 0.00 0.00 0.00 4.85
2320 2582 1.799181 CGTTGATGGACTCGTAGCTGG 60.799 57.143 0.00 0.00 0.00 4.85
2321 2583 1.550065 CGTTGATGGACTCGTAGCTG 58.450 55.000 0.00 0.00 0.00 4.24
2322 2584 0.179134 GCGTTGATGGACTCGTAGCT 60.179 55.000 0.00 0.00 0.00 3.32
2323 2585 1.146358 GGCGTTGATGGACTCGTAGC 61.146 60.000 0.00 0.00 0.00 3.58
2324 2586 0.172578 TGGCGTTGATGGACTCGTAG 59.827 55.000 0.00 0.00 0.00 3.51
2325 2587 0.604073 TTGGCGTTGATGGACTCGTA 59.396 50.000 0.00 0.00 0.00 3.43
2326 2588 0.670546 CTTGGCGTTGATGGACTCGT 60.671 55.000 0.00 0.00 0.00 4.18
2327 2589 1.970917 GCTTGGCGTTGATGGACTCG 61.971 60.000 0.00 0.00 0.00 4.18
2328 2590 0.955428 TGCTTGGCGTTGATGGACTC 60.955 55.000 0.00 0.00 0.00 3.36
2329 2591 1.073025 TGCTTGGCGTTGATGGACT 59.927 52.632 0.00 0.00 0.00 3.85
2330 2592 1.210155 GTGCTTGGCGTTGATGGAC 59.790 57.895 0.00 0.00 0.00 4.02
2331 2593 2.324330 CGTGCTTGGCGTTGATGGA 61.324 57.895 0.00 0.00 0.00 3.41
2332 2594 2.176546 CGTGCTTGGCGTTGATGG 59.823 61.111 0.00 0.00 0.00 3.51
2333 2595 2.502510 GCGTGCTTGGCGTTGATG 60.503 61.111 0.00 0.00 0.00 3.07
2343 2605 4.962122 CTTTGTGCGCGCGTGCTT 62.962 61.111 40.02 0.00 39.65 3.91
2346 2608 4.292208 TGACTTTGTGCGCGCGTG 62.292 61.111 32.35 16.86 0.00 5.34
2347 2609 4.293626 GTGACTTTGTGCGCGCGT 62.294 61.111 32.35 17.92 0.00 6.01
2348 2610 2.653967 TAGTGACTTTGTGCGCGCG 61.654 57.895 28.44 28.44 0.00 6.86
2349 2611 1.154654 GTAGTGACTTTGTGCGCGC 60.155 57.895 27.26 27.26 0.00 6.86
2350 2612 0.790207 ATGTAGTGACTTTGTGCGCG 59.210 50.000 0.00 0.00 0.00 6.86
2351 2613 3.865745 AGATATGTAGTGACTTTGTGCGC 59.134 43.478 0.00 0.00 0.00 6.09
2352 2614 6.408858 AAAGATATGTAGTGACTTTGTGCG 57.591 37.500 0.00 0.00 31.11 5.34
2375 2637 7.873719 TCAACAGTGATACTCAAAGGAAAAA 57.126 32.000 0.00 0.00 0.00 1.94
2376 2638 9.219603 CTATCAACAGTGATACTCAAAGGAAAA 57.780 33.333 0.00 0.00 42.94 2.29
2377 2639 7.824289 CCTATCAACAGTGATACTCAAAGGAAA 59.176 37.037 0.00 0.00 42.94 3.13
2378 2640 7.038302 ACCTATCAACAGTGATACTCAAAGGAA 60.038 37.037 0.00 0.00 42.94 3.36
2379 2641 6.440647 ACCTATCAACAGTGATACTCAAAGGA 59.559 38.462 0.00 0.00 42.94 3.36
2380 2642 6.644347 ACCTATCAACAGTGATACTCAAAGG 58.356 40.000 0.00 0.00 42.94 3.11
2381 2643 9.254133 CATACCTATCAACAGTGATACTCAAAG 57.746 37.037 0.00 0.00 42.94 2.77
2382 2644 8.204160 CCATACCTATCAACAGTGATACTCAAA 58.796 37.037 0.00 0.00 42.94 2.69
2383 2645 7.344612 ACCATACCTATCAACAGTGATACTCAA 59.655 37.037 0.00 0.00 42.94 3.02
2384 2646 6.839134 ACCATACCTATCAACAGTGATACTCA 59.161 38.462 0.00 0.00 42.94 3.41
2385 2647 7.291411 ACCATACCTATCAACAGTGATACTC 57.709 40.000 0.00 0.00 42.94 2.59
2386 2648 8.777578 TTACCATACCTATCAACAGTGATACT 57.222 34.615 0.00 0.00 42.94 2.12
2387 2649 9.424319 CATTACCATACCTATCAACAGTGATAC 57.576 37.037 0.00 0.00 42.94 2.24
2388 2650 8.593679 CCATTACCATACCTATCAACAGTGATA 58.406 37.037 0.00 0.00 42.94 2.15
2389 2651 7.072454 ACCATTACCATACCTATCAACAGTGAT 59.928 37.037 0.00 0.00 46.52 3.06
2390 2652 6.385759 ACCATTACCATACCTATCAACAGTGA 59.614 38.462 0.00 0.00 38.41 3.41
2391 2653 6.591935 ACCATTACCATACCTATCAACAGTG 58.408 40.000 0.00 0.00 0.00 3.66
2392 2654 6.824958 ACCATTACCATACCTATCAACAGT 57.175 37.500 0.00 0.00 0.00 3.55
2393 2655 8.041323 GGATACCATTACCATACCTATCAACAG 58.959 40.741 0.00 0.00 0.00 3.16
2394 2656 7.913789 GGATACCATTACCATACCTATCAACA 58.086 38.462 0.00 0.00 0.00 3.33
2423 2685 9.853555 ATGCAATCGTATCATCAAAGTTAAAAA 57.146 25.926 0.00 0.00 0.00 1.94
2424 2686 9.288124 CATGCAATCGTATCATCAAAGTTAAAA 57.712 29.630 0.00 0.00 0.00 1.52
2425 2687 7.431960 GCATGCAATCGTATCATCAAAGTTAAA 59.568 33.333 14.21 0.00 0.00 1.52
2426 2688 6.912051 GCATGCAATCGTATCATCAAAGTTAA 59.088 34.615 14.21 0.00 0.00 2.01
2427 2689 6.038050 TGCATGCAATCGTATCATCAAAGTTA 59.962 34.615 20.30 0.00 0.00 2.24
2428 2690 5.163632 TGCATGCAATCGTATCATCAAAGTT 60.164 36.000 20.30 0.00 0.00 2.66
2429 2691 4.336153 TGCATGCAATCGTATCATCAAAGT 59.664 37.500 20.30 0.00 0.00 2.66
2430 2692 4.851010 TGCATGCAATCGTATCATCAAAG 58.149 39.130 20.30 0.00 0.00 2.77
2431 2693 4.897025 TGCATGCAATCGTATCATCAAA 57.103 36.364 20.30 0.00 0.00 2.69
2432 2694 4.096081 TGTTGCATGCAATCGTATCATCAA 59.904 37.500 33.94 6.06 38.28 2.57
2433 2695 3.626670 TGTTGCATGCAATCGTATCATCA 59.373 39.130 33.94 20.89 38.28 3.07
2434 2696 4.024641 TCTGTTGCATGCAATCGTATCATC 60.025 41.667 33.94 18.65 38.28 2.92
2435 2697 3.878699 TCTGTTGCATGCAATCGTATCAT 59.121 39.130 33.94 0.00 38.28 2.45
2436 2698 3.269178 TCTGTTGCATGCAATCGTATCA 58.731 40.909 33.94 23.81 38.28 2.15
2437 2699 3.950087 TCTGTTGCATGCAATCGTATC 57.050 42.857 33.94 20.71 38.28 2.24
2438 2700 4.156556 ACTTTCTGTTGCATGCAATCGTAT 59.843 37.500 33.94 15.00 38.28 3.06
2439 2701 3.501828 ACTTTCTGTTGCATGCAATCGTA 59.498 39.130 33.94 18.92 38.28 3.43
2440 2702 2.294233 ACTTTCTGTTGCATGCAATCGT 59.706 40.909 33.94 20.49 38.28 3.73
2441 2703 2.937591 ACTTTCTGTTGCATGCAATCG 58.062 42.857 33.94 25.92 38.28 3.34
2442 2704 5.464168 AGTAACTTTCTGTTGCATGCAATC 58.536 37.500 33.94 25.69 42.52 2.67
2443 2705 5.458041 AGTAACTTTCTGTTGCATGCAAT 57.542 34.783 33.94 18.67 42.52 3.56
2444 2706 4.916983 AGTAACTTTCTGTTGCATGCAA 57.083 36.364 28.80 28.80 42.52 4.08
2445 2707 4.215399 GGTAGTAACTTTCTGTTGCATGCA 59.785 41.667 18.46 18.46 42.52 3.96
2446 2708 4.669197 CGGTAGTAACTTTCTGTTGCATGC 60.669 45.833 11.82 11.82 42.52 4.06
2447 2709 4.669197 GCGGTAGTAACTTTCTGTTGCATG 60.669 45.833 0.00 0.00 42.52 4.06
2448 2710 3.435671 GCGGTAGTAACTTTCTGTTGCAT 59.564 43.478 0.00 0.00 42.52 3.96
2449 2711 2.803956 GCGGTAGTAACTTTCTGTTGCA 59.196 45.455 0.00 0.00 42.52 4.08
2450 2712 3.064931 AGCGGTAGTAACTTTCTGTTGC 58.935 45.455 0.00 0.00 40.79 4.17
2451 2713 3.432252 CCAGCGGTAGTAACTTTCTGTTG 59.568 47.826 0.00 0.00 39.55 3.33
2452 2714 3.556423 CCCAGCGGTAGTAACTTTCTGTT 60.556 47.826 0.00 0.00 42.31 3.16
2453 2715 2.028385 CCCAGCGGTAGTAACTTTCTGT 60.028 50.000 0.00 0.00 0.00 3.41
2454 2716 2.028385 ACCCAGCGGTAGTAACTTTCTG 60.028 50.000 0.00 0.00 42.18 3.02
2455 2717 2.254508 ACCCAGCGGTAGTAACTTTCT 58.745 47.619 0.00 0.00 42.18 2.52
2456 2718 2.756840 ACCCAGCGGTAGTAACTTTC 57.243 50.000 0.00 0.00 42.18 2.62
2467 2729 1.583054 GCTGAAGTTATACCCAGCGG 58.417 55.000 0.00 0.00 41.86 5.52
2470 2732 2.939103 GTGCTGCTGAAGTTATACCCAG 59.061 50.000 0.00 0.00 0.00 4.45
2471 2733 2.571653 AGTGCTGCTGAAGTTATACCCA 59.428 45.455 0.00 0.00 0.00 4.51
2472 2734 3.268023 AGTGCTGCTGAAGTTATACCC 57.732 47.619 0.00 0.00 0.00 3.69
2486 2748 4.272018 GGTAGTATCTTCAATGCAGTGCTG 59.728 45.833 17.60 7.38 0.00 4.41
2487 2749 4.446371 GGTAGTATCTTCAATGCAGTGCT 58.554 43.478 17.60 2.02 0.00 4.40
2488 2750 3.561725 GGGTAGTATCTTCAATGCAGTGC 59.438 47.826 9.79 8.58 0.00 4.40
2489 2751 3.804325 CGGGTAGTATCTTCAATGCAGTG 59.196 47.826 8.08 8.08 0.00 3.66
2490 2752 3.741388 GCGGGTAGTATCTTCAATGCAGT 60.741 47.826 0.00 0.00 0.00 4.40
2491 2753 2.802816 GCGGGTAGTATCTTCAATGCAG 59.197 50.000 0.00 0.00 0.00 4.41
2492 2754 2.801699 CGCGGGTAGTATCTTCAATGCA 60.802 50.000 0.00 0.00 0.00 3.96
2493 2755 1.792949 CGCGGGTAGTATCTTCAATGC 59.207 52.381 0.00 0.00 0.00 3.56
2494 2756 3.093717 ACGCGGGTAGTATCTTCAATG 57.906 47.619 12.47 0.00 0.00 2.82
2495 2757 3.255149 CCTACGCGGGTAGTATCTTCAAT 59.745 47.826 30.57 0.00 43.82 2.57
2496 2758 2.620115 CCTACGCGGGTAGTATCTTCAA 59.380 50.000 30.57 1.95 43.82 2.69
2497 2759 2.158769 TCCTACGCGGGTAGTATCTTCA 60.159 50.000 30.57 9.01 43.82 3.02
2498 2760 2.498167 TCCTACGCGGGTAGTATCTTC 58.502 52.381 30.57 0.00 43.82 2.87
2499 2761 2.620585 GTTCCTACGCGGGTAGTATCTT 59.379 50.000 30.57 0.00 43.82 2.40
2500 2762 2.225467 GTTCCTACGCGGGTAGTATCT 58.775 52.381 30.57 0.53 43.82 1.98
2501 2763 1.268079 GGTTCCTACGCGGGTAGTATC 59.732 57.143 30.57 21.00 43.82 2.24
2502 2764 1.322442 GGTTCCTACGCGGGTAGTAT 58.678 55.000 30.57 1.98 43.82 2.12
2503 2765 0.034574 TGGTTCCTACGCGGGTAGTA 60.035 55.000 30.57 18.11 43.82 1.82
2504 2766 1.304381 TGGTTCCTACGCGGGTAGT 60.304 57.895 30.57 2.71 43.82 2.73
2505 2767 1.436336 CTGGTTCCTACGCGGGTAG 59.564 63.158 27.69 27.69 44.72 3.18
2506 2768 2.053865 CCTGGTTCCTACGCGGGTA 61.054 63.158 12.47 12.17 0.00 3.69
2507 2769 3.387947 CCTGGTTCCTACGCGGGT 61.388 66.667 12.47 10.91 0.00 5.28
2508 2770 3.072468 TCCTGGTTCCTACGCGGG 61.072 66.667 12.47 2.26 0.00 6.13
2509 2771 2.348888 ACTCCTGGTTCCTACGCGG 61.349 63.158 12.47 0.00 0.00 6.46
2510 2772 1.153823 CACTCCTGGTTCCTACGCG 60.154 63.158 3.53 3.53 0.00 6.01
2511 2773 0.606604 TTCACTCCTGGTTCCTACGC 59.393 55.000 0.00 0.00 0.00 4.42
2512 2774 1.893801 ACTTCACTCCTGGTTCCTACG 59.106 52.381 0.00 0.00 0.00 3.51
2513 2775 2.633481 ACACTTCACTCCTGGTTCCTAC 59.367 50.000 0.00 0.00 0.00 3.18
2514 2776 2.632996 CACACTTCACTCCTGGTTCCTA 59.367 50.000 0.00 0.00 0.00 2.94
2515 2777 1.417890 CACACTTCACTCCTGGTTCCT 59.582 52.381 0.00 0.00 0.00 3.36
2516 2778 1.416401 TCACACTTCACTCCTGGTTCC 59.584 52.381 0.00 0.00 0.00 3.62
2517 2779 2.910688 TCACACTTCACTCCTGGTTC 57.089 50.000 0.00 0.00 0.00 3.62
2518 2780 3.279434 GTTTCACACTTCACTCCTGGTT 58.721 45.455 0.00 0.00 0.00 3.67
2519 2781 2.238646 TGTTTCACACTTCACTCCTGGT 59.761 45.455 0.00 0.00 0.00 4.00
2520 2782 2.874701 CTGTTTCACACTTCACTCCTGG 59.125 50.000 0.00 0.00 0.00 4.45
2521 2783 3.557595 GTCTGTTTCACACTTCACTCCTG 59.442 47.826 0.00 0.00 0.00 3.86
2522 2784 3.432326 GGTCTGTTTCACACTTCACTCCT 60.432 47.826 0.00 0.00 0.00 3.69
2603 4464 3.301274 GGAGGAAGTACATCTACTGGCT 58.699 50.000 0.00 0.00 33.14 4.75
2668 4529 0.676151 CAGCCAGGCTCCTCAAGTTC 60.676 60.000 12.53 0.00 36.40 3.01


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

AutoCloner maintained by Alex Coulton.