Multiple sequence alignment - TraesCS7B01G198900

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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 TraesCS7B01G198900 chr7B 100.000 2885 0 0 1 2885 355907506 355904622 0.000000e+00 5328
1 TraesCS7B01G198900 chr7B 91.840 723 42 4 1 707 299400854 299400133 0.000000e+00 992
2 TraesCS7B01G198900 chr7B 90.456 482 24 8 253 715 353973206 353973684 1.470000e-172 616
3 TraesCS7B01G198900 chr7B 88.347 472 32 6 262 715 490109907 490109441 1.950000e-151 545
4 TraesCS7B01G198900 chr7B 86.500 200 19 4 2553 2752 256087735 256087926 2.250000e-51 213
5 TraesCS7B01G198900 chr7B 91.589 107 8 1 615 721 355691820 355691715 2.320000e-31 147
6 TraesCS7B01G198900 chr7A 98.186 1599 26 2 732 2329 397126104 397124508 0.000000e+00 2789
7 TraesCS7B01G198900 chr7A 96.677 331 11 0 2528 2858 397124499 397124169 4.200000e-153 551
8 TraesCS7B01G198900 chr7A 95.858 169 7 0 2324 2492 320981341 320981173 1.020000e-69 274
9 TraesCS7B01G198900 chr7D 98.438 1408 20 2 731 2137 350094197 350095603 0.000000e+00 2477
10 TraesCS7B01G198900 chr7D 94.324 370 8 2 2489 2858 350095896 350096252 3.250000e-154 555
11 TraesCS7B01G198900 chr7D 94.737 76 2 1 2256 2329 350095824 350095899 1.820000e-22 117
12 TraesCS7B01G198900 chr5A 92.562 726 35 4 1 708 131736238 131736962 0.000000e+00 1024
13 TraesCS7B01G198900 chr5A 91.814 733 40 4 1 717 257281012 257280284 0.000000e+00 1003
14 TraesCS7B01G198900 chr5A 96.407 167 6 0 2327 2493 640948092 640948258 2.830000e-70 276
15 TraesCS7B01G198900 chr5A 95.833 168 7 0 2328 2495 206731016 206730849 3.660000e-69 272
16 TraesCS7B01G198900 chr5B 92.233 721 38 4 1 707 158674092 158674808 0.000000e+00 1005
17 TraesCS7B01G198900 chr5B 95.322 171 8 0 2323 2493 427931371 427931201 3.660000e-69 272
18 TraesCS7B01G198900 chr4A 92.138 725 35 4 1 707 481485017 481484297 0.000000e+00 1003
19 TraesCS7B01G198900 chr4A 90.000 110 7 4 615 721 371041092 371040984 3.880000e-29 139
20 TraesCS7B01G198900 chr2A 91.690 722 41 5 1 707 189504280 189504997 0.000000e+00 983
21 TraesCS7B01G198900 chr2A 95.858 169 7 0 2327 2495 746756989 746757157 1.020000e-69 274
22 TraesCS7B01G198900 chr6B 91.869 701 38 5 21 707 207719807 207719112 0.000000e+00 961
23 TraesCS7B01G198900 chr6B 90.807 446 23 5 290 717 494378762 494378317 5.360000e-162 580
24 TraesCS7B01G198900 chr6B 76.286 700 146 19 1054 1743 665716560 665715871 3.540000e-94 355
25 TraesCS7B01G198900 chr6A 90.857 700 44 3 1 684 380415960 380416655 0.000000e+00 920
26 TraesCS7B01G198900 chr6A 75.857 700 149 18 1054 1743 588605062 588604373 3.560000e-89 339
27 TraesCS7B01G198900 chr3B 89.807 726 53 5 1 708 363586750 363586028 0.000000e+00 911
28 TraesCS7B01G198900 chr4B 89.549 488 30 7 253 720 253905612 253906098 1.480000e-167 599
29 TraesCS7B01G198900 chr4B 88.215 297 20 2 434 716 72632983 72632688 9.900000e-90 340
30 TraesCS7B01G198900 chr4B 87.879 297 21 2 434 716 72591891 72591596 4.610000e-88 335
31 TraesCS7B01G198900 chr4B 85.083 181 19 4 2568 2748 311414060 311414232 8.210000e-41 178
32 TraesCS7B01G198900 chr1A 89.047 493 29 8 253 721 283713957 283713466 3.200000e-164 588
33 TraesCS7B01G198900 chr6D 76.320 701 144 19 1054 1743 440664273 440663584 3.540000e-94 355
34 TraesCS7B01G198900 chr3A 88.776 294 18 4 439 718 361574786 361574494 2.130000e-91 346
35 TraesCS7B01G198900 chr4D 89.399 283 16 3 439 707 366061861 366062143 7.650000e-91 344
36 TraesCS7B01G198900 chr4D 95.402 174 6 2 2324 2497 6588426 6588597 2.830000e-70 276
37 TraesCS7B01G198900 chr4D 93.122 189 10 2 2304 2492 424575712 424575897 1.020000e-69 274
38 TraesCS7B01G198900 chr4D 94.857 175 7 2 2319 2493 404108571 404108743 3.660000e-69 272
39 TraesCS7B01G198900 chr2B 93.407 182 10 2 2327 2507 620632286 620632106 4.740000e-68 268
40 TraesCS7B01G198900 chr2B 85.083 181 19 5 2568 2748 409254361 409254533 8.210000e-41 178


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 TraesCS7B01G198900 chr7B 355904622 355907506 2884 True 5328.000000 5328 100.0000 1 2885 1 chr7B.!!$R3 2884
1 TraesCS7B01G198900 chr7B 299400133 299400854 721 True 992.000000 992 91.8400 1 707 1 chr7B.!!$R1 706
2 TraesCS7B01G198900 chr7A 397124169 397126104 1935 True 1670.000000 2789 97.4315 732 2858 2 chr7A.!!$R2 2126
3 TraesCS7B01G198900 chr7D 350094197 350096252 2055 False 1049.666667 2477 95.8330 731 2858 3 chr7D.!!$F1 2127
4 TraesCS7B01G198900 chr5A 131736238 131736962 724 False 1024.000000 1024 92.5620 1 708 1 chr5A.!!$F1 707
5 TraesCS7B01G198900 chr5A 257280284 257281012 728 True 1003.000000 1003 91.8140 1 717 1 chr5A.!!$R2 716
6 TraesCS7B01G198900 chr5B 158674092 158674808 716 False 1005.000000 1005 92.2330 1 707 1 chr5B.!!$F1 706
7 TraesCS7B01G198900 chr4A 481484297 481485017 720 True 1003.000000 1003 92.1380 1 707 1 chr4A.!!$R2 706
8 TraesCS7B01G198900 chr2A 189504280 189504997 717 False 983.000000 983 91.6900 1 707 1 chr2A.!!$F1 706
9 TraesCS7B01G198900 chr6B 207719112 207719807 695 True 961.000000 961 91.8690 21 707 1 chr6B.!!$R1 686
10 TraesCS7B01G198900 chr6B 665715871 665716560 689 True 355.000000 355 76.2860 1054 1743 1 chr6B.!!$R3 689
11 TraesCS7B01G198900 chr6A 380415960 380416655 695 False 920.000000 920 90.8570 1 684 1 chr6A.!!$F1 683
12 TraesCS7B01G198900 chr6A 588604373 588605062 689 True 339.000000 339 75.8570 1054 1743 1 chr6A.!!$R1 689
13 TraesCS7B01G198900 chr3B 363586028 363586750 722 True 911.000000 911 89.8070 1 708 1 chr3B.!!$R1 707
14 TraesCS7B01G198900 chr6D 440663584 440664273 689 True 355.000000 355 76.3200 1054 1743 1 chr6D.!!$R1 689

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
688 710 0.674581 CAGGTCTCTGCGCCATTTGA 60.675 55.0 4.18 0.0 33.86 2.69 F
690 712 0.955428 GGTCTCTGCGCCATTTGACA 60.955 55.0 4.18 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 1552 0.965363 GGTACCCGAAGTCGTACCCA 60.965 60.000 0.0 0.0 45.92 4.51 R
2047 2072 1.270893 GCTCAAAGGGAAAGACCGAGT 60.271 52.381 0.0 0.0 40.11 4.18 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
50 52 3.154710 TCACAGTGATGTCTACGACCTT 58.845 45.455 0.00 0.00 0.00 3.50
101 103 6.367374 TGTTTGGTTTTCTTCCCTTTTCTT 57.633 33.333 0.00 0.00 0.00 2.52
238 240 9.996554 TTTAGTTTAGTTCATCATTCAGAGACA 57.003 29.630 0.00 0.00 0.00 3.41
474 480 9.515020 GTGTTTGAATCACATAAAAAGAGTTCA 57.485 29.630 1.73 0.00 36.05 3.18
575 597 5.003160 GCAGACCACAATATACATGGCATA 58.997 41.667 0.00 0.00 36.96 3.14
605 627 7.681939 AGTAAAGGAAACTATTTTCATCGCA 57.318 32.000 7.73 0.00 42.72 5.10
625 647 4.556501 CGCAAACATGGCTTTAGTTGAAGA 60.557 41.667 0.00 0.00 0.00 2.87
652 674 9.709495 TTCTTGCAGCATGAAACTATTTTTATT 57.291 25.926 18.86 0.00 39.69 1.40
688 710 0.674581 CAGGTCTCTGCGCCATTTGA 60.675 55.000 4.18 0.00 33.86 2.69
690 712 0.955428 GGTCTCTGCGCCATTTGACA 60.955 55.000 4.18 0.00 0.00 3.58
708 730 3.384146 TGACACAACGGGTCAACTAGTAA 59.616 43.478 0.00 0.00 41.96 2.24
709 731 3.985925 GACACAACGGGTCAACTAGTAAG 59.014 47.826 0.00 0.00 35.36 2.34
710 732 3.638160 ACACAACGGGTCAACTAGTAAGA 59.362 43.478 0.00 0.00 0.00 2.10
713 735 5.524646 CACAACGGGTCAACTAGTAAGAAAA 59.475 40.000 0.00 0.00 0.00 2.29
729 751 3.821995 AAAAACTCACGCGGTGCT 58.178 50.000 12.47 0.00 32.98 4.40
734 756 1.246056 AACTCACGCGGTGCTAGGTA 61.246 55.000 12.47 0.00 32.98 3.08
748 770 2.161030 CTAGGTATGACTACGCCTCCC 58.839 57.143 0.00 0.00 32.90 4.30
884 906 4.287326 CCTCCCCTTCCTCATCTTATTACC 59.713 50.000 0.00 0.00 0.00 2.85
1011 1033 4.899239 GCTCCGATGTCTGCCCCG 62.899 72.222 0.00 0.00 0.00 5.73
1123 1145 2.921797 TTCGCCGTGATCCGTGACA 61.922 57.895 0.00 0.00 33.66 3.58
2047 2072 9.929180 GCTATATCATGGTAGTTCTGTTGAATA 57.071 33.333 0.00 0.00 34.40 1.75
2138 2164 7.264221 ACTGAAAATTGAACTGTTGTGCATTA 58.736 30.769 0.00 0.00 30.60 1.90
2217 2243 3.195396 GCCATATTGCCTTTCTGTGGAAA 59.805 43.478 0.00 0.00 38.90 3.13
2223 2249 4.789012 TGCCTTTCTGTGGAAATCAATC 57.211 40.909 0.00 0.00 40.19 2.67
2333 2463 8.977267 TTCAGTCTAGACTATTAAGTACTCCC 57.023 38.462 24.75 0.00 40.20 4.30
2334 2464 8.334522 TCAGTCTAGACTATTAAGTACTCCCT 57.665 38.462 24.75 0.00 40.20 4.20
2335 2465 8.431222 TCAGTCTAGACTATTAAGTACTCCCTC 58.569 40.741 24.75 0.00 40.20 4.30
2336 2466 8.434392 CAGTCTAGACTATTAAGTACTCCCTCT 58.566 40.741 24.75 0.00 40.20 3.69
2337 2467 8.434392 AGTCTAGACTATTAAGTACTCCCTCTG 58.566 40.741 24.04 0.00 40.43 3.35
2338 2468 8.431222 GTCTAGACTATTAAGTACTCCCTCTGA 58.569 40.741 15.91 0.00 35.56 3.27
2339 2469 9.173231 TCTAGACTATTAAGTACTCCCTCTGAT 57.827 37.037 0.00 0.00 35.56 2.90
2342 2472 8.951541 AGACTATTAAGTACTCCCTCTGATACT 58.048 37.037 0.00 0.00 35.56 2.12
2354 2484 9.440761 ACTCCCTCTGATACTAAATATTTGTCT 57.559 33.333 11.05 0.63 0.00 3.41
2374 2504 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2375 2505 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2376 2506 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2377 2507 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2378 2508 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2379 2509 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2380 2510 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2381 2511 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2382 2512 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2384 2514 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2385 2515 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2386 2516 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2387 2517 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2388 2518 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2389 2519 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2390 2520 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2391 2521 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2392 2522 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2393 2523 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2394 2524 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2395 2525 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2396 2526 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2397 2527 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2398 2528 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2399 2529 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2400 2530 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2401 2531 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2402 2532 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2403 2533 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2404 2534 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2405 2535 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2406 2536 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2407 2537 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2408 2538 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2444 2574 9.901172 TGTCTATATACATCCGTATGTGATAGT 57.099 33.333 17.08 3.55 45.99 2.12
2451 2581 7.482654 ACATCCGTATGTGATAGTTCATTTG 57.517 36.000 0.00 0.00 44.79 2.32
2452 2582 7.272244 ACATCCGTATGTGATAGTTCATTTGA 58.728 34.615 0.00 0.00 44.79 2.69
2453 2583 7.768582 ACATCCGTATGTGATAGTTCATTTGAA 59.231 33.333 0.00 0.00 44.79 2.69
2454 2584 8.611757 CATCCGTATGTGATAGTTCATTTGAAA 58.388 33.333 0.00 0.00 35.58 2.69
2455 2585 8.731275 TCCGTATGTGATAGTTCATTTGAAAT 57.269 30.769 0.00 0.00 35.58 2.17
2456 2586 8.826710 TCCGTATGTGATAGTTCATTTGAAATC 58.173 33.333 0.00 0.00 35.58 2.17
2457 2587 8.830580 CCGTATGTGATAGTTCATTTGAAATCT 58.169 33.333 0.00 0.00 35.58 2.40
2458 2588 9.855361 CGTATGTGATAGTTCATTTGAAATCTC 57.145 33.333 0.00 0.00 35.58 2.75
2486 2616 8.857694 AAAAGACAAATATTTAGGAACGGAGA 57.142 30.769 0.00 0.00 0.00 3.71
2487 2617 8.494016 AAAGACAAATATTTAGGAACGGAGAG 57.506 34.615 0.00 0.00 0.00 3.20
2560 2690 0.326264 CACAGCCCTAGCACCTCTTT 59.674 55.000 0.00 0.00 43.56 2.52
2566 2696 2.553247 GCCCTAGCACCTCTTTTCAACT 60.553 50.000 0.00 0.00 39.53 3.16
2648 2778 6.535508 GGGACTTGACAGTAATGTAGAATGTC 59.464 42.308 0.00 3.68 40.49 3.06
2722 2852 3.920412 CCAGTTTCTTGCTTTATTTCGCC 59.080 43.478 0.00 0.00 0.00 5.54
2732 2862 4.026407 GCTTTATTTCGCCAACGTATCAC 58.974 43.478 0.00 0.00 41.18 3.06
2733 2863 4.436317 GCTTTATTTCGCCAACGTATCACA 60.436 41.667 0.00 0.00 41.18 3.58
2734 2864 5.608676 TTTATTTCGCCAACGTATCACAA 57.391 34.783 0.00 0.00 41.18 3.33
2735 2865 5.608676 TTATTTCGCCAACGTATCACAAA 57.391 34.783 0.00 0.00 41.18 2.83
2736 2866 4.695217 ATTTCGCCAACGTATCACAAAT 57.305 36.364 0.00 0.00 41.18 2.32
2737 2867 5.804692 ATTTCGCCAACGTATCACAAATA 57.195 34.783 0.00 0.00 41.18 1.40
2738 2868 4.587211 TTCGCCAACGTATCACAAATAC 57.413 40.909 0.00 0.00 41.18 1.89
2739 2869 2.931325 TCGCCAACGTATCACAAATACC 59.069 45.455 0.00 0.00 41.18 2.73
2740 2870 2.673862 CGCCAACGTATCACAAATACCA 59.326 45.455 0.00 0.00 33.53 3.25
2741 2871 3.311322 CGCCAACGTATCACAAATACCAT 59.689 43.478 0.00 0.00 33.53 3.55
2742 2872 4.201871 CGCCAACGTATCACAAATACCATT 60.202 41.667 0.00 0.00 33.53 3.16
2743 2873 5.646606 GCCAACGTATCACAAATACCATTT 58.353 37.500 0.00 0.00 0.00 2.32
2858 3000 7.502561 TCTTCACAGGTGATAAGATAAGATCGA 59.497 37.037 2.52 0.00 39.64 3.59
2859 3001 7.208225 TCACAGGTGATAAGATAAGATCGAG 57.792 40.000 0.00 0.00 34.14 4.04
2860 3002 6.207614 TCACAGGTGATAAGATAAGATCGAGG 59.792 42.308 0.00 0.00 34.14 4.63
2861 3003 6.015856 CACAGGTGATAAGATAAGATCGAGGT 60.016 42.308 0.00 0.00 0.00 3.85
2862 3004 6.207810 ACAGGTGATAAGATAAGATCGAGGTC 59.792 42.308 0.00 0.00 0.00 3.85
2863 3005 6.432783 CAGGTGATAAGATAAGATCGAGGTCT 59.567 42.308 0.00 0.00 0.00 3.85
2864 3006 7.007723 AGGTGATAAGATAAGATCGAGGTCTT 58.992 38.462 6.52 6.52 41.18 3.01
2865 3007 7.175990 AGGTGATAAGATAAGATCGAGGTCTTC 59.824 40.741 4.58 0.00 39.15 2.87
2866 3008 7.175990 GGTGATAAGATAAGATCGAGGTCTTCT 59.824 40.741 4.58 0.00 39.15 2.85
2867 3009 8.573035 GTGATAAGATAAGATCGAGGTCTTCTT 58.427 37.037 4.58 4.20 39.15 2.52
2868 3010 9.137459 TGATAAGATAAGATCGAGGTCTTCTTT 57.863 33.333 4.58 2.33 39.15 2.52
2869 3011 9.974980 GATAAGATAAGATCGAGGTCTTCTTTT 57.025 33.333 4.58 1.08 39.15 2.27
2870 3012 9.757227 ATAAGATAAGATCGAGGTCTTCTTTTG 57.243 33.333 4.58 0.00 39.15 2.44
2871 3013 6.578023 AGATAAGATCGAGGTCTTCTTTTGG 58.422 40.000 4.58 0.00 39.15 3.28
2872 3014 4.891992 AAGATCGAGGTCTTCTTTTGGA 57.108 40.909 0.00 0.00 33.24 3.53
2873 3015 4.891992 AGATCGAGGTCTTCTTTTGGAA 57.108 40.909 0.00 0.00 0.00 3.53
2874 3016 4.570930 AGATCGAGGTCTTCTTTTGGAAC 58.429 43.478 0.00 0.00 0.00 3.62
2875 3017 2.750948 TCGAGGTCTTCTTTTGGAACG 58.249 47.619 0.00 0.00 0.00 3.95
2876 3018 1.798813 CGAGGTCTTCTTTTGGAACGG 59.201 52.381 0.00 0.00 0.00 4.44
2877 3019 2.547218 CGAGGTCTTCTTTTGGAACGGA 60.547 50.000 0.00 0.00 0.00 4.69
2878 3020 3.067833 GAGGTCTTCTTTTGGAACGGAG 58.932 50.000 0.00 0.00 0.00 4.63
2879 3021 2.152016 GGTCTTCTTTTGGAACGGAGG 58.848 52.381 0.00 0.00 0.00 4.30
2880 3022 2.152016 GTCTTCTTTTGGAACGGAGGG 58.848 52.381 0.00 0.00 0.00 4.30
2881 3023 2.051692 TCTTCTTTTGGAACGGAGGGA 58.948 47.619 0.00 0.00 0.00 4.20
2882 3024 2.038557 TCTTCTTTTGGAACGGAGGGAG 59.961 50.000 0.00 0.00 0.00 4.30
2883 3025 1.430992 TCTTTTGGAACGGAGGGAGT 58.569 50.000 0.00 0.00 0.00 3.85
2884 3026 2.612000 TCTTTTGGAACGGAGGGAGTA 58.388 47.619 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 78 7.669089 AGAAAAGGGAAGAAAACCAAACATA 57.331 32.000 0.00 0.00 0.00 2.29
238 240 7.235399 ACCTGTGAAGGACAAAAATATTCCATT 59.765 33.333 0.00 0.00 32.80 3.16
474 480 8.604035 CGTGTTGCAAGTATGAATAAGAACTAT 58.396 33.333 0.00 0.00 0.00 2.12
494 500 1.159713 TTGCAGAGCCTCACGTGTTG 61.160 55.000 16.51 9.02 0.00 3.33
605 627 7.530426 AGAATCTTCAACTAAAGCCATGTTT 57.470 32.000 0.00 0.00 0.00 2.83
625 647 9.880157 ATAAAAATAGTTTCATGCTGCAAGAAT 57.120 25.926 19.40 9.53 34.07 2.40
688 710 3.638160 TCTTACTAGTTGACCCGTTGTGT 59.362 43.478 0.00 0.00 0.00 3.72
690 712 4.942761 TTCTTACTAGTTGACCCGTTGT 57.057 40.909 0.00 0.00 0.00 3.32
713 735 0.949105 CCTAGCACCGCGTGAGTTTT 60.949 55.000 4.92 0.00 35.23 2.43
717 739 0.595053 CATACCTAGCACCGCGTGAG 60.595 60.000 4.92 0.00 35.23 3.51
718 740 1.033202 TCATACCTAGCACCGCGTGA 61.033 55.000 4.92 0.00 35.23 4.35
719 741 0.870307 GTCATACCTAGCACCGCGTG 60.870 60.000 4.92 4.73 36.51 5.34
720 742 1.035932 AGTCATACCTAGCACCGCGT 61.036 55.000 4.92 0.00 0.00 6.01
721 743 0.949397 TAGTCATACCTAGCACCGCG 59.051 55.000 0.00 0.00 0.00 6.46
722 744 1.334779 CGTAGTCATACCTAGCACCGC 60.335 57.143 0.00 0.00 0.00 5.68
723 745 1.334779 GCGTAGTCATACCTAGCACCG 60.335 57.143 0.00 0.00 0.00 4.94
724 746 1.000496 GGCGTAGTCATACCTAGCACC 60.000 57.143 0.00 0.00 0.00 5.01
725 747 1.955080 AGGCGTAGTCATACCTAGCAC 59.045 52.381 0.00 0.00 0.00 4.40
726 748 2.228059 GAGGCGTAGTCATACCTAGCA 58.772 52.381 0.00 0.00 30.95 3.49
727 749 1.540707 GGAGGCGTAGTCATACCTAGC 59.459 57.143 0.00 0.00 30.95 3.42
728 750 2.161030 GGGAGGCGTAGTCATACCTAG 58.839 57.143 0.00 0.00 30.95 3.02
729 751 1.202976 GGGGAGGCGTAGTCATACCTA 60.203 57.143 0.00 0.00 30.95 3.08
734 756 0.831307 GAAAGGGGAGGCGTAGTCAT 59.169 55.000 0.00 0.00 0.00 3.06
748 770 2.025793 GGGGAAGAAAGGAGAGGAAAGG 60.026 54.545 0.00 0.00 0.00 3.11
884 906 4.096003 ATCGGCGTGGTGGGGAAG 62.096 66.667 6.85 0.00 0.00 3.46
1330 1352 1.308998 CGAAAGTTGAACTGCCAGGT 58.691 50.000 0.00 0.00 0.00 4.00
1527 1552 0.965363 GGTACCCGAAGTCGTACCCA 60.965 60.000 0.00 0.00 45.92 4.51
2047 2072 1.270893 GCTCAAAGGGAAAGACCGAGT 60.271 52.381 0.00 0.00 40.11 4.18
2147 2173 6.784473 TGACACCTCTATATGAATGACTGGAT 59.216 38.462 0.00 0.00 0.00 3.41
2148 2174 6.136155 TGACACCTCTATATGAATGACTGGA 58.864 40.000 0.00 0.00 0.00 3.86
2217 2243 7.719483 ACACAAACAATGAAGAGTTGATTGAT 58.281 30.769 13.36 0.00 39.96 2.57
2223 2249 7.760131 AATCAACACAAACAATGAAGAGTTG 57.240 32.000 0.00 0.00 35.05 3.16
2328 2458 9.440761 AGACAAATATTTAGTATCAGAGGGAGT 57.559 33.333 0.00 0.00 0.00 3.85
2348 2478 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2349 2479 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2350 2480 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2351 2481 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2352 2482 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2353 2483 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2354 2484 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2355 2485 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2356 2486 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2357 2487 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2358 2488 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2359 2489 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2360 2490 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2361 2491 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2362 2492 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2363 2493 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2364 2494 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2365 2495 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
2366 2496 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2367 2497 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2368 2498 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2369 2499 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2370 2500 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2371 2501 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2372 2502 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2373 2503 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2374 2504 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2375 2505 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2376 2506 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2377 2507 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2378 2508 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2379 2509 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2380 2510 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2381 2511 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2382 2512 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2383 2513 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2384 2514 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2385 2515 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2386 2516 6.148480 ACAGTGTAGATTCACTCATTTTGCTC 59.852 38.462 0.00 0.00 45.37 4.26
2387 2517 6.000219 ACAGTGTAGATTCACTCATTTTGCT 59.000 36.000 0.00 0.00 45.37 3.91
2388 2518 6.246420 ACAGTGTAGATTCACTCATTTTGC 57.754 37.500 0.00 0.00 45.37 3.68
2418 2548 9.901172 ACTATCACATACGGATGTATATAGACA 57.099 33.333 30.73 11.02 44.82 3.41
2425 2555 9.208022 CAAATGAACTATCACATACGGATGTAT 57.792 33.333 14.23 10.02 44.82 2.29
2426 2556 8.417884 TCAAATGAACTATCACATACGGATGTA 58.582 33.333 14.23 2.61 44.82 2.29
2428 2558 7.713764 TCAAATGAACTATCACATACGGATG 57.286 36.000 5.94 5.94 38.69 3.51
2429 2559 8.731275 TTTCAAATGAACTATCACATACGGAT 57.269 30.769 0.00 0.00 38.69 4.18
2430 2560 8.731275 ATTTCAAATGAACTATCACATACGGA 57.269 30.769 0.00 0.00 38.69 4.69
2431 2561 8.830580 AGATTTCAAATGAACTATCACATACGG 58.169 33.333 9.37 0.00 38.69 4.02
2432 2562 9.855361 GAGATTTCAAATGAACTATCACATACG 57.145 33.333 9.37 0.00 38.69 3.06
2460 2590 9.292195 TCTCCGTTCCTAAATATTTGTCTTTTT 57.708 29.630 11.05 0.00 0.00 1.94
2461 2591 8.857694 TCTCCGTTCCTAAATATTTGTCTTTT 57.142 30.769 11.05 0.00 0.00 2.27
2462 2592 8.319146 TCTCTCCGTTCCTAAATATTTGTCTTT 58.681 33.333 11.05 0.00 0.00 2.52
2463 2593 7.848128 TCTCTCCGTTCCTAAATATTTGTCTT 58.152 34.615 11.05 0.00 0.00 3.01
2464 2594 7.124448 ACTCTCTCCGTTCCTAAATATTTGTCT 59.876 37.037 11.05 0.00 0.00 3.41
2465 2595 7.266400 ACTCTCTCCGTTCCTAAATATTTGTC 58.734 38.462 11.05 0.00 0.00 3.18
2466 2596 7.184067 ACTCTCTCCGTTCCTAAATATTTGT 57.816 36.000 11.05 0.00 0.00 2.83
2467 2597 9.197694 CATACTCTCTCCGTTCCTAAATATTTG 57.802 37.037 11.05 1.40 0.00 2.32
2468 2598 8.925338 ACATACTCTCTCCGTTCCTAAATATTT 58.075 33.333 5.89 5.89 0.00 1.40
2469 2599 8.480133 ACATACTCTCTCCGTTCCTAAATATT 57.520 34.615 0.00 0.00 0.00 1.28
2470 2600 7.177041 GGACATACTCTCTCCGTTCCTAAATAT 59.823 40.741 0.00 0.00 0.00 1.28
2471 2601 6.489361 GGACATACTCTCTCCGTTCCTAAATA 59.511 42.308 0.00 0.00 0.00 1.40
2472 2602 5.302313 GGACATACTCTCTCCGTTCCTAAAT 59.698 44.000 0.00 0.00 0.00 1.40
2473 2603 4.643784 GGACATACTCTCTCCGTTCCTAAA 59.356 45.833 0.00 0.00 0.00 1.85
2474 2604 4.205587 GGACATACTCTCTCCGTTCCTAA 58.794 47.826 0.00 0.00 0.00 2.69
2475 2605 3.201487 TGGACATACTCTCTCCGTTCCTA 59.799 47.826 0.00 0.00 0.00 2.94
2476 2606 2.025226 TGGACATACTCTCTCCGTTCCT 60.025 50.000 0.00 0.00 0.00 3.36
2477 2607 2.376109 TGGACATACTCTCTCCGTTCC 58.624 52.381 0.00 0.00 0.00 3.62
2478 2608 4.174762 GTTTGGACATACTCTCTCCGTTC 58.825 47.826 0.00 0.00 0.00 3.95
2479 2609 3.576982 TGTTTGGACATACTCTCTCCGTT 59.423 43.478 0.00 0.00 0.00 4.44
2480 2610 3.162666 TGTTTGGACATACTCTCTCCGT 58.837 45.455 0.00 0.00 0.00 4.69
2481 2611 3.868757 TGTTTGGACATACTCTCTCCG 57.131 47.619 0.00 0.00 0.00 4.63
2482 2612 5.091261 ACATGTTTGGACATACTCTCTCC 57.909 43.478 0.00 0.00 44.55 3.71
2483 2613 6.876257 AGAAACATGTTTGGACATACTCTCTC 59.124 38.462 27.85 8.61 44.55 3.20
2484 2614 6.652481 CAGAAACATGTTTGGACATACTCTCT 59.348 38.462 27.85 11.36 44.55 3.10
2485 2615 6.621596 GCAGAAACATGTTTGGACATACTCTC 60.622 42.308 27.85 9.24 44.55 3.20
2486 2616 5.182001 GCAGAAACATGTTTGGACATACTCT 59.818 40.000 27.85 12.57 44.55 3.24
2487 2617 5.048782 TGCAGAAACATGTTTGGACATACTC 60.049 40.000 27.85 10.46 44.55 2.59
2560 2690 6.318648 GCAGGACATCCATTACAATAGTTGAA 59.681 38.462 0.00 0.00 38.89 2.69
2566 2696 5.132502 CCTTGCAGGACATCCATTACAATA 58.867 41.667 0.00 0.00 37.67 1.90
2589 2719 4.395231 GGGAGCCAGTCAAATAGTGTTTAC 59.605 45.833 0.00 0.00 0.00 2.01
2648 2778 5.125417 TGCACCTAAAAGGCTGCTAAAATAG 59.875 40.000 16.21 0.00 40.58 1.73
2722 2852 7.526608 ACTGAAATGGTATTTGTGATACGTTG 58.473 34.615 0.00 0.00 0.00 4.10
2740 2870 4.009675 TCAAGCTCCGCATTTACTGAAAT 58.990 39.130 0.00 0.00 35.56 2.17
2741 2871 3.407698 TCAAGCTCCGCATTTACTGAAA 58.592 40.909 0.00 0.00 0.00 2.69
2742 2872 3.052455 TCAAGCTCCGCATTTACTGAA 57.948 42.857 0.00 0.00 0.00 3.02
2743 2873 2.760634 TCAAGCTCCGCATTTACTGA 57.239 45.000 0.00 0.00 0.00 3.41
2858 3000 2.224548 CCTCCGTTCCAAAAGAAGACCT 60.225 50.000 0.00 0.00 34.29 3.85
2859 3001 2.152016 CCTCCGTTCCAAAAGAAGACC 58.848 52.381 0.00 0.00 34.29 3.85
2860 3002 2.152016 CCCTCCGTTCCAAAAGAAGAC 58.848 52.381 0.00 0.00 34.29 3.01
2861 3003 2.038557 CTCCCTCCGTTCCAAAAGAAGA 59.961 50.000 0.00 0.00 34.29 2.87
2862 3004 2.224548 ACTCCCTCCGTTCCAAAAGAAG 60.225 50.000 0.00 0.00 34.29 2.85
2863 3005 1.772453 ACTCCCTCCGTTCCAAAAGAA 59.228 47.619 0.00 0.00 0.00 2.52
2864 3006 1.430992 ACTCCCTCCGTTCCAAAAGA 58.569 50.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.