Multiple sequence alignment - TraesCS7D01G096400

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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 TraesCS7D01G096400 chr7D 100.000 2528 0 0 1 2528 58619833 58622360 0.000000e+00 4669
1 TraesCS7D01G096400 chr7D 90.266 1839 147 23 512 2345 118903585 118901774 0.000000e+00 2375
2 TraesCS7D01G096400 chr5B 92.549 2362 132 11 1 2348 382534442 382536773 0.000000e+00 3347
3 TraesCS7D01G096400 chr7A 92.578 2358 118 19 1 2343 674510603 674508288 0.000000e+00 3332
4 TraesCS7D01G096400 chr5A 92.412 2359 125 17 1 2345 676352811 676355129 0.000000e+00 3315
5 TraesCS7D01G096400 chr5A 91.026 390 21 3 1960 2348 493201787 493202163 4.820000e-142 514
6 TraesCS7D01G096400 chr4A 92.844 2250 126 12 1 2233 690355906 690358137 0.000000e+00 3230
7 TraesCS7D01G096400 chr4A 94.488 127 7 0 2402 2528 675152923 675153049 1.980000e-46 196
8 TraesCS7D01G096400 chr4A 94.488 127 7 0 2402 2528 675175472 675175598 1.980000e-46 196
9 TraesCS7D01G096400 chr4A 91.453 117 10 0 2412 2528 675137616 675137732 7.240000e-36 161
10 TraesCS7D01G096400 chr6B 91.455 2364 151 24 1 2353 118025296 118027619 0.000000e+00 3199
11 TraesCS7D01G096400 chr6B 93.170 1303 74 9 766 2061 708220742 708222036 0.000000e+00 1899
12 TraesCS7D01G096400 chr2D 92.737 1969 101 17 393 2353 518249537 518251471 0.000000e+00 2806
13 TraesCS7D01G096400 chr2D 91.071 392 29 3 1 386 518215302 518215693 2.230000e-145 525
14 TraesCS7D01G096400 chr3B 93.584 1621 78 11 733 2349 283638630 283640228 0.000000e+00 2394
15 TraesCS7D01G096400 chr3B 77.453 581 100 24 1 561 795969763 795970332 4.060000e-83 318
16 TraesCS7D01G096400 chrUn 92.732 399 23 5 1960 2354 50976277 50975881 2.820000e-159 571
17 TraesCS7D01G096400 chrUn 92.732 399 23 5 1960 2354 466482933 466482537 2.820000e-159 571
18 TraesCS7D01G096400 chr3A 92.405 395 25 5 1960 2353 561400911 561401301 2.200000e-155 558
19 TraesCS7D01G096400 chr3A 93.827 324 15 5 2031 2353 561393924 561394243 1.360000e-132 483
20 TraesCS7D01G096400 chr1B 94.326 282 10 1 1 276 638556702 638556421 6.460000e-116 427


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 TraesCS7D01G096400 chr7D 58619833 58622360 2527 False 4669 4669 100.000 1 2528 1 chr7D.!!$F1 2527
1 TraesCS7D01G096400 chr7D 118901774 118903585 1811 True 2375 2375 90.266 512 2345 1 chr7D.!!$R1 1833
2 TraesCS7D01G096400 chr5B 382534442 382536773 2331 False 3347 3347 92.549 1 2348 1 chr5B.!!$F1 2347
3 TraesCS7D01G096400 chr7A 674508288 674510603 2315 True 3332 3332 92.578 1 2343 1 chr7A.!!$R1 2342
4 TraesCS7D01G096400 chr5A 676352811 676355129 2318 False 3315 3315 92.412 1 2345 1 chr5A.!!$F2 2344
5 TraesCS7D01G096400 chr4A 690355906 690358137 2231 False 3230 3230 92.844 1 2233 1 chr4A.!!$F4 2232
6 TraesCS7D01G096400 chr6B 118025296 118027619 2323 False 3199 3199 91.455 1 2353 1 chr6B.!!$F1 2352
7 TraesCS7D01G096400 chr6B 708220742 708222036 1294 False 1899 1899 93.170 766 2061 1 chr6B.!!$F2 1295
8 TraesCS7D01G096400 chr2D 518249537 518251471 1934 False 2806 2806 92.737 393 2353 1 chr2D.!!$F2 1960
9 TraesCS7D01G096400 chr3B 283638630 283640228 1598 False 2394 2394 93.584 733 2349 1 chr3B.!!$F1 1616
10 TraesCS7D01G096400 chr3B 795969763 795970332 569 False 318 318 77.453 1 561 1 chr3B.!!$F2 560

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
787 809 0.035152 CTAGCTTGGTGATGGTGCCA 60.035 55.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2479 2531 0.109412 GGCATGTTGCTGACTGCTTC 60.109 55.0 5.87 0.06 44.28 3.86 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
30 31 0.104356 TACCTGGTTGGGAGGGTTCA 60.104 55.000 3.84 0.00 41.11 3.18
91 98 5.640732 GCGAAGATGAATTTGTTGTACCAT 58.359 37.500 0.00 0.00 0.00 3.55
114 121 7.365117 CCATAGGGTATGACTCTTTCTCTTTGT 60.365 40.741 0.00 0.00 38.45 2.83
192 202 6.051717 AGTACTATCTTGTTTATGCTGGCTG 58.948 40.000 0.00 0.00 0.00 4.85
227 237 6.183361 ACCTGGATTTCTATCTCCATTCAGAC 60.183 42.308 0.00 0.00 40.66 3.51
303 313 8.621532 AATGAAAGAGAGTTGTATAACTTGCA 57.378 30.769 6.31 0.00 46.79 4.08
312 322 3.949132 TGTATAACTTGCACCATGCTCA 58.051 40.909 2.02 0.00 45.31 4.26
333 343 5.748402 TCATGCTAGAAATGTTGTGGAGAT 58.252 37.500 0.00 0.00 0.00 2.75
389 407 6.340537 TCTTACGTTCTTGTTCTTTGACAC 57.659 37.500 0.00 0.00 0.00 3.67
399 417 3.054728 TGTTCTTTGACACAGAGGACCAA 60.055 43.478 0.00 0.00 0.00 3.67
562 581 2.045561 TTTGTTGCTTCCGGAAGTCA 57.954 45.000 37.67 31.89 40.45 3.41
564 583 2.045561 TGTTGCTTCCGGAAGTCAAA 57.954 45.000 34.90 27.58 40.45 2.69
627 646 6.166279 TGCTACTTTCATTAGAAGTGTCCAG 58.834 40.000 0.09 0.00 34.71 3.86
680 699 4.023792 GCAATTTGCGGATGAGATGTATGA 60.024 41.667 5.49 0.00 31.71 2.15
736 755 5.489249 TCGAGTAGATAAGTAGCGATGGAT 58.511 41.667 0.00 0.00 0.00 3.41
787 809 0.035152 CTAGCTTGGTGATGGTGCCA 60.035 55.000 0.00 0.00 0.00 4.92
791 813 1.002315 GCTTGGTGATGGTGCCATTTT 59.998 47.619 5.08 0.00 36.70 1.82
863 886 3.568538 ACATGCTTCATCTTTTGTTCGC 58.431 40.909 0.00 0.00 0.00 4.70
1008 1037 1.077828 TGGACTCCTGAGATGGACACT 59.922 52.381 0.22 0.00 31.94 3.55
1036 1065 1.626321 TGGCCGTCCTTGTTGAGAATA 59.374 47.619 0.00 0.00 0.00 1.75
1037 1066 2.280628 GGCCGTCCTTGTTGAGAATAG 58.719 52.381 0.00 0.00 0.00 1.73
1252 1281 3.247006 ACATGGTGTCGGTTGATAGTC 57.753 47.619 0.00 0.00 0.00 2.59
1294 1323 4.453751 TGTGGAGGTACTTAACACCAAAC 58.546 43.478 9.01 1.33 41.55 2.93
1333 1366 8.937634 ATTTTTGCAACTTCAATATCATCTCC 57.062 30.769 0.00 0.00 0.00 3.71
1334 1367 7.465353 TTTTGCAACTTCAATATCATCTCCA 57.535 32.000 0.00 0.00 0.00 3.86
1335 1368 7.465353 TTTGCAACTTCAATATCATCTCCAA 57.535 32.000 0.00 0.00 0.00 3.53
1336 1369 7.465353 TTGCAACTTCAATATCATCTCCAAA 57.535 32.000 0.00 0.00 0.00 3.28
1337 1370 7.649533 TGCAACTTCAATATCATCTCCAAAT 57.350 32.000 0.00 0.00 0.00 2.32
1368 1401 4.577283 TGTTTTGTGTAGGCTAACAAGGAC 59.423 41.667 16.28 17.31 37.57 3.85
1369 1402 4.425180 TTTGTGTAGGCTAACAAGGACA 57.575 40.909 16.28 2.16 37.57 4.02
1397 1430 3.388350 GCCTATAGGAACAAGGTAGTGCT 59.612 47.826 23.61 0.00 37.39 4.40
1524 1558 0.839853 AGAAGCTCCTGAGGTGCCTT 60.840 55.000 20.81 14.22 42.42 4.35
1762 1797 3.537874 ATGGCGCTACCCGAGGAC 61.538 66.667 7.64 0.00 40.02 3.85
1821 1857 8.786826 TTGTTACTATCCTGTTTAGTTGATGG 57.213 34.615 0.00 0.00 32.35 3.51
1855 1891 4.407818 TGTACTTTGTTGTTTGCGAACTG 58.592 39.130 17.65 4.26 36.70 3.16
1858 1894 3.190535 ACTTTGTTGTTTGCGAACTGTCT 59.809 39.130 17.65 0.00 36.70 3.41
1860 1896 5.065988 ACTTTGTTGTTTGCGAACTGTCTAT 59.934 36.000 17.65 0.00 36.70 1.98
2180 2232 6.872585 AACATCCAATTCCATGGTTTGTAT 57.127 33.333 21.02 12.92 41.46 2.29
2233 2285 7.315066 ACCCTGTGATTCCAACAATAAATTT 57.685 32.000 0.00 0.00 0.00 1.82
2273 2325 3.217626 AGAATTCGAATTGGAGCCCATC 58.782 45.455 27.27 10.04 31.53 3.51
2365 2417 1.994779 GCGCAAGGTTCATTTTCATGG 59.005 47.619 0.30 0.00 38.28 3.66
2366 2418 1.994779 CGCAAGGTTCATTTTCATGGC 59.005 47.619 0.00 0.00 0.00 4.40
2367 2419 2.609984 CGCAAGGTTCATTTTCATGGCA 60.610 45.455 0.00 0.00 0.00 4.92
2368 2420 2.997986 GCAAGGTTCATTTTCATGGCAG 59.002 45.455 0.00 0.00 0.00 4.85
2369 2421 3.306225 GCAAGGTTCATTTTCATGGCAGA 60.306 43.478 0.00 0.00 0.00 4.26
2370 2422 4.800249 GCAAGGTTCATTTTCATGGCAGAA 60.800 41.667 0.00 0.00 0.00 3.02
2371 2423 4.796038 AGGTTCATTTTCATGGCAGAAG 57.204 40.909 0.00 0.00 0.00 2.85
2372 2424 4.154942 AGGTTCATTTTCATGGCAGAAGT 58.845 39.130 0.00 0.00 0.00 3.01
2373 2425 5.324409 AGGTTCATTTTCATGGCAGAAGTA 58.676 37.500 0.00 0.00 0.00 2.24
2374 2426 5.774690 AGGTTCATTTTCATGGCAGAAGTAA 59.225 36.000 0.00 0.00 0.00 2.24
2375 2427 6.267471 AGGTTCATTTTCATGGCAGAAGTAAA 59.733 34.615 0.00 0.00 0.00 2.01
2376 2428 6.366061 GGTTCATTTTCATGGCAGAAGTAAAC 59.634 38.462 0.00 1.90 0.00 2.01
2377 2429 6.899393 TCATTTTCATGGCAGAAGTAAACT 57.101 33.333 0.00 0.00 0.00 2.66
2378 2430 7.994425 TCATTTTCATGGCAGAAGTAAACTA 57.006 32.000 0.00 0.00 0.00 2.24
2379 2431 8.402798 TCATTTTCATGGCAGAAGTAAACTAA 57.597 30.769 0.00 0.00 0.00 2.24
2380 2432 9.023962 TCATTTTCATGGCAGAAGTAAACTAAT 57.976 29.630 0.00 0.00 0.00 1.73
2381 2433 9.643693 CATTTTCATGGCAGAAGTAAACTAATT 57.356 29.630 0.00 0.00 0.00 1.40
2385 2437 7.985476 TCATGGCAGAAGTAAACTAATTTAGC 58.015 34.615 3.28 0.00 30.79 3.09
2386 2438 7.829211 TCATGGCAGAAGTAAACTAATTTAGCT 59.171 33.333 3.28 0.00 30.79 3.32
2387 2439 9.109393 CATGGCAGAAGTAAACTAATTTAGCTA 57.891 33.333 3.28 0.00 30.79 3.32
2388 2440 8.718102 TGGCAGAAGTAAACTAATTTAGCTAG 57.282 34.615 3.28 0.00 30.79 3.42
2389 2441 8.319146 TGGCAGAAGTAAACTAATTTAGCTAGT 58.681 33.333 3.28 0.00 30.79 2.57
2390 2442 8.604890 GGCAGAAGTAAACTAATTTAGCTAGTG 58.395 37.037 3.28 0.00 30.79 2.74
2391 2443 9.152595 GCAGAAGTAAACTAATTTAGCTAGTGT 57.847 33.333 3.28 0.00 30.79 3.55
2399 2451 9.659830 AAACTAATTTAGCTAGTGTCAAAAACG 57.340 29.630 3.28 0.00 29.96 3.60
2400 2452 7.295930 ACTAATTTAGCTAGTGTCAAAAACGC 58.704 34.615 3.28 0.00 38.74 4.84
2402 2454 4.985044 TTAGCTAGTGTCAAAAACGCTC 57.015 40.909 0.00 0.00 45.69 5.03
2403 2455 2.833794 AGCTAGTGTCAAAAACGCTCA 58.166 42.857 0.00 0.00 45.69 4.26
2404 2456 3.403038 AGCTAGTGTCAAAAACGCTCAT 58.597 40.909 0.00 0.00 45.69 2.90
2405 2457 3.433615 AGCTAGTGTCAAAAACGCTCATC 59.566 43.478 0.00 0.00 45.69 2.92
2406 2458 3.186409 GCTAGTGTCAAAAACGCTCATCA 59.814 43.478 0.00 0.00 45.69 3.07
2407 2459 3.885484 AGTGTCAAAAACGCTCATCAG 57.115 42.857 0.00 0.00 45.69 2.90
2408 2460 3.466836 AGTGTCAAAAACGCTCATCAGA 58.533 40.909 0.00 0.00 45.69 3.27
2409 2461 4.067896 AGTGTCAAAAACGCTCATCAGAT 58.932 39.130 0.00 0.00 45.69 2.90
2410 2462 4.516698 AGTGTCAAAAACGCTCATCAGATT 59.483 37.500 0.00 0.00 45.69 2.40
2411 2463 5.700832 AGTGTCAAAAACGCTCATCAGATTA 59.299 36.000 0.00 0.00 45.69 1.75
2412 2464 6.017933 GTGTCAAAAACGCTCATCAGATTAG 58.982 40.000 0.00 0.00 35.42 1.73
2413 2465 5.700832 TGTCAAAAACGCTCATCAGATTAGT 59.299 36.000 0.00 0.00 0.00 2.24
2414 2466 6.871492 TGTCAAAAACGCTCATCAGATTAGTA 59.129 34.615 0.00 0.00 0.00 1.82
2415 2467 7.148639 TGTCAAAAACGCTCATCAGATTAGTAC 60.149 37.037 0.00 0.00 0.00 2.73
2416 2468 5.950965 AAAACGCTCATCAGATTAGTACG 57.049 39.130 0.00 0.00 0.00 3.67
2417 2469 4.895224 AACGCTCATCAGATTAGTACGA 57.105 40.909 0.00 0.00 0.00 3.43
2418 2470 5.440234 AACGCTCATCAGATTAGTACGAT 57.560 39.130 0.00 0.00 0.00 3.73
2419 2471 4.788690 ACGCTCATCAGATTAGTACGATG 58.211 43.478 0.00 0.00 37.25 3.84
2420 2472 3.605916 CGCTCATCAGATTAGTACGATGC 59.394 47.826 0.00 0.00 36.13 3.91
2421 2473 4.550422 GCTCATCAGATTAGTACGATGCA 58.450 43.478 0.00 0.00 36.13 3.96
2422 2474 4.384247 GCTCATCAGATTAGTACGATGCAC 59.616 45.833 0.00 0.00 36.13 4.57
2423 2475 4.871513 TCATCAGATTAGTACGATGCACC 58.128 43.478 0.00 0.00 36.13 5.01
2424 2476 4.584743 TCATCAGATTAGTACGATGCACCT 59.415 41.667 0.00 0.00 36.13 4.00
2425 2477 4.307443 TCAGATTAGTACGATGCACCTG 57.693 45.455 0.00 0.00 0.00 4.00
2426 2478 2.797156 CAGATTAGTACGATGCACCTGC 59.203 50.000 0.00 0.00 42.50 4.85
2436 2488 2.436646 GCACCTGCATAGCCACGT 60.437 61.111 0.00 0.00 41.59 4.49
2437 2489 2.040544 GCACCTGCATAGCCACGTT 61.041 57.895 0.00 0.00 41.59 3.99
2438 2490 1.982073 GCACCTGCATAGCCACGTTC 61.982 60.000 0.00 0.00 41.59 3.95
2439 2491 0.391661 CACCTGCATAGCCACGTTCT 60.392 55.000 0.00 0.00 0.00 3.01
2440 2492 0.324943 ACCTGCATAGCCACGTTCTT 59.675 50.000 0.00 0.00 0.00 2.52
2441 2493 1.271379 ACCTGCATAGCCACGTTCTTT 60.271 47.619 0.00 0.00 0.00 2.52
2442 2494 1.812571 CCTGCATAGCCACGTTCTTTT 59.187 47.619 0.00 0.00 0.00 2.27
2443 2495 2.414559 CCTGCATAGCCACGTTCTTTTG 60.415 50.000 0.00 0.00 0.00 2.44
2444 2496 2.226330 TGCATAGCCACGTTCTTTTGT 58.774 42.857 0.00 0.00 0.00 2.83
2445 2497 2.621055 TGCATAGCCACGTTCTTTTGTT 59.379 40.909 0.00 0.00 0.00 2.83
2446 2498 3.815962 TGCATAGCCACGTTCTTTTGTTA 59.184 39.130 0.00 0.00 0.00 2.41
2447 2499 4.083537 TGCATAGCCACGTTCTTTTGTTAG 60.084 41.667 0.00 0.00 0.00 2.34
2448 2500 4.403453 CATAGCCACGTTCTTTTGTTAGC 58.597 43.478 0.00 0.00 0.00 3.09
2449 2501 2.294074 AGCCACGTTCTTTTGTTAGCA 58.706 42.857 0.00 0.00 0.00 3.49
2450 2502 2.032924 AGCCACGTTCTTTTGTTAGCAC 59.967 45.455 0.00 0.00 0.00 4.40
2451 2503 2.032924 GCCACGTTCTTTTGTTAGCACT 59.967 45.455 0.00 0.00 0.00 4.40
2452 2504 3.488553 GCCACGTTCTTTTGTTAGCACTT 60.489 43.478 0.00 0.00 0.00 3.16
2453 2505 4.668289 CCACGTTCTTTTGTTAGCACTTT 58.332 39.130 0.00 0.00 0.00 2.66
2454 2506 4.733405 CCACGTTCTTTTGTTAGCACTTTC 59.267 41.667 0.00 0.00 0.00 2.62
2455 2507 5.328691 CACGTTCTTTTGTTAGCACTTTCA 58.671 37.500 0.00 0.00 0.00 2.69
2456 2508 5.797934 CACGTTCTTTTGTTAGCACTTTCAA 59.202 36.000 0.00 0.00 0.00 2.69
2457 2509 6.021468 CACGTTCTTTTGTTAGCACTTTCAAG 60.021 38.462 0.00 0.00 0.00 3.02
2458 2510 6.027749 CGTTCTTTTGTTAGCACTTTCAAGT 58.972 36.000 0.00 0.00 40.60 3.16
2459 2511 6.526674 CGTTCTTTTGTTAGCACTTTCAAGTT 59.473 34.615 0.00 0.00 37.08 2.66
2460 2512 7.061789 CGTTCTTTTGTTAGCACTTTCAAGTTT 59.938 33.333 0.00 0.00 37.08 2.66
2461 2513 8.373256 GTTCTTTTGTTAGCACTTTCAAGTTTC 58.627 33.333 0.00 0.00 37.08 2.78
2462 2514 7.598278 TCTTTTGTTAGCACTTTCAAGTTTCA 58.402 30.769 0.00 0.00 37.08 2.69
2463 2515 8.085296 TCTTTTGTTAGCACTTTCAAGTTTCAA 58.915 29.630 0.00 0.00 37.08 2.69
2464 2516 8.594881 TTTTGTTAGCACTTTCAAGTTTCAAA 57.405 26.923 0.00 0.00 37.08 2.69
2465 2517 8.770438 TTTGTTAGCACTTTCAAGTTTCAAAT 57.230 26.923 0.00 0.00 37.08 2.32
2466 2518 7.985634 TGTTAGCACTTTCAAGTTTCAAATC 57.014 32.000 0.00 0.00 37.08 2.17
2467 2519 6.690957 TGTTAGCACTTTCAAGTTTCAAATCG 59.309 34.615 0.00 0.00 37.08 3.34
2468 2520 4.610945 AGCACTTTCAAGTTTCAAATCGG 58.389 39.130 0.00 0.00 37.08 4.18
2469 2521 3.182372 GCACTTTCAAGTTTCAAATCGGC 59.818 43.478 0.00 0.00 37.08 5.54
2470 2522 3.735746 CACTTTCAAGTTTCAAATCGGCC 59.264 43.478 0.00 0.00 37.08 6.13
2471 2523 2.697431 TTCAAGTTTCAAATCGGCCG 57.303 45.000 22.12 22.12 0.00 6.13
2472 2524 0.878416 TCAAGTTTCAAATCGGCCGG 59.122 50.000 27.83 9.38 0.00 6.13
2473 2525 0.732538 CAAGTTTCAAATCGGCCGGC 60.733 55.000 27.83 21.18 0.00 6.13
2474 2526 1.873270 AAGTTTCAAATCGGCCGGCC 61.873 55.000 36.69 36.69 0.00 6.13
2475 2527 3.065567 TTTCAAATCGGCCGGCCC 61.066 61.111 39.24 21.72 0.00 5.80
2488 2540 4.329545 GGCCCGGTGAAGCAGTCA 62.330 66.667 0.00 0.00 0.00 3.41
2489 2541 2.743928 GCCCGGTGAAGCAGTCAG 60.744 66.667 0.00 0.00 36.74 3.51
2498 2550 0.109412 GAAGCAGTCAGCAACATGCC 60.109 55.000 0.00 0.00 46.52 4.40
2499 2551 0.824595 AAGCAGTCAGCAACATGCCA 60.825 50.000 0.00 0.00 46.52 4.92
2500 2552 0.824595 AGCAGTCAGCAACATGCCAA 60.825 50.000 0.00 0.00 46.52 4.52
2501 2553 0.665369 GCAGTCAGCAACATGCCAAC 60.665 55.000 0.00 0.00 46.52 3.77
2502 2554 0.669619 CAGTCAGCAACATGCCAACA 59.330 50.000 0.00 0.00 46.52 3.33
2503 2555 1.271379 CAGTCAGCAACATGCCAACAT 59.729 47.619 0.00 0.00 46.52 2.71
2517 2569 2.445427 CCAACATGGGCACTTATGTCA 58.555 47.619 0.00 0.00 35.74 3.58
2518 2570 2.424601 CCAACATGGGCACTTATGTCAG 59.575 50.000 0.00 0.00 35.74 3.51
2519 2571 1.755179 ACATGGGCACTTATGTCAGC 58.245 50.000 0.00 0.00 32.60 4.26
2520 2572 1.283029 ACATGGGCACTTATGTCAGCT 59.717 47.619 0.00 0.00 32.60 4.24
2521 2573 1.945394 CATGGGCACTTATGTCAGCTC 59.055 52.381 0.00 0.00 29.15 4.09
2522 2574 1.279496 TGGGCACTTATGTCAGCTCT 58.721 50.000 0.00 0.00 29.15 4.09
2523 2575 2.466846 TGGGCACTTATGTCAGCTCTA 58.533 47.619 0.00 0.00 29.15 2.43
2524 2576 2.168521 TGGGCACTTATGTCAGCTCTAC 59.831 50.000 0.00 0.00 29.15 2.59
2525 2577 2.168521 GGGCACTTATGTCAGCTCTACA 59.831 50.000 1.06 1.06 29.15 2.74
2526 2578 3.452474 GGCACTTATGTCAGCTCTACAG 58.548 50.000 4.83 0.00 0.00 2.74
2527 2579 3.452474 GCACTTATGTCAGCTCTACAGG 58.548 50.000 4.83 1.29 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.999071 GCACTCTCGAGTCCGATGCT 61.999 60.000 13.13 0.00 44.62 3.79
91 98 6.497259 ACACAAAGAGAAAGAGTCATACCCTA 59.503 38.462 0.00 0.00 0.00 3.53
134 143 9.199982 TGACAAGTATGTAAGTTAGCTAACAAC 57.800 33.333 32.48 28.01 40.74 3.32
192 202 4.236527 AGAAATCCAGGTCCATTGGTAC 57.763 45.455 1.86 0.00 37.02 3.34
227 237 0.682852 TTCAAGTGGTACCGAGTGGG 59.317 55.000 7.57 0.00 40.75 4.61
312 322 6.543831 GGTTATCTCCACAACATTTCTAGCAT 59.456 38.462 0.00 0.00 0.00 3.79
333 343 5.923733 TTTCTTCAACAAGCCAAAGGTTA 57.076 34.783 0.00 0.00 30.94 2.85
363 373 6.759356 TGTCAAAGAACAAGAACGTAAGATGA 59.241 34.615 0.00 0.00 43.62 2.92
370 380 4.250464 TCTGTGTCAAAGAACAAGAACGT 58.750 39.130 0.00 0.00 0.00 3.99
389 407 3.997021 GACATGTGTTACTTGGTCCTCTG 59.003 47.826 1.15 0.00 0.00 3.35
399 417 6.899393 ACAATCAAATGGACATGTGTTACT 57.101 33.333 1.15 0.00 30.18 2.24
471 490 7.377766 ACACGCATTAATAAGACAAATCTGT 57.622 32.000 0.00 0.00 38.98 3.41
478 497 5.237561 ACACACAACACGCATTAATAAGACA 59.762 36.000 0.00 0.00 0.00 3.41
577 596 2.499289 CTGCAGGTTCAGGAGTCATAGT 59.501 50.000 5.57 0.00 0.00 2.12
627 646 6.484818 AAATTAGACCATGCATTTGTTTGC 57.515 33.333 0.00 0.00 43.07 3.68
645 664 4.081972 TCCGCAAATTGCTGCCTAAAATTA 60.082 37.500 16.42 0.00 42.25 1.40
680 699 0.253044 ATGCGCCACAAGGTACTCAT 59.747 50.000 4.18 0.00 38.49 2.90
736 755 3.259374 GGCACCATCAGCTAGCTATCTAA 59.741 47.826 18.86 1.06 0.00 2.10
791 813 1.180456 CCAGCATGCTCCCACACAAA 61.180 55.000 19.68 0.00 31.97 2.83
800 823 1.725557 CCATCACAGCCAGCATGCTC 61.726 60.000 19.68 7.90 40.32 4.26
970 994 6.406737 GGAGTCCATGTAAGGTAAACTCTACC 60.407 46.154 3.60 0.00 37.86 3.18
1008 1037 1.530419 AAGGACGGCCAACAATGCA 60.530 52.632 11.69 0.00 36.29 3.96
1036 1065 0.604578 GCATGGTCACCATTGTTGCT 59.395 50.000 6.58 0.00 42.23 3.91
1037 1066 0.604578 AGCATGGTCACCATTGTTGC 59.395 50.000 6.58 9.58 42.23 4.17
1252 1281 4.091945 CACATATTGAGACCACACTTCGTG 59.908 45.833 0.00 0.00 45.92 4.35
1333 1366 7.437862 AGCCTACACAAAACACACAAATATTTG 59.562 33.333 23.60 23.60 43.62 2.32
1334 1367 7.496747 AGCCTACACAAAACACACAAATATTT 58.503 30.769 0.00 0.00 0.00 1.40
1335 1368 7.049799 AGCCTACACAAAACACACAAATATT 57.950 32.000 0.00 0.00 0.00 1.28
1336 1369 6.648879 AGCCTACACAAAACACACAAATAT 57.351 33.333 0.00 0.00 0.00 1.28
1337 1370 7.067129 TGTTAGCCTACACAAAACACACAAATA 59.933 33.333 0.00 0.00 0.00 1.40
1368 1401 2.665649 TGTTCCTATAGGCACGTGTG 57.334 50.000 18.38 0.00 33.92 3.82
1369 1402 2.093658 CCTTGTTCCTATAGGCACGTGT 60.094 50.000 18.38 0.00 33.92 4.49
1397 1430 6.823286 TGGTATTGATAGACTCCCAATTGA 57.177 37.500 7.12 0.00 33.21 2.57
1504 1538 1.220477 GGCACCTCAGGAGCTTCTC 59.780 63.158 13.38 0.00 39.22 2.87
1524 1558 0.605319 CCCAGTGCGTTGCCTCTTAA 60.605 55.000 0.00 0.00 0.00 1.85
1821 1857 8.773404 AACAACAAAGTACATAGTAGTCCATC 57.227 34.615 0.00 0.00 0.00 3.51
1855 1891 7.759886 TGTCTCTTACACATAGCACAAATAGAC 59.240 37.037 0.00 0.00 31.43 2.59
1860 1896 8.840833 TTTATGTCTCTTACACATAGCACAAA 57.159 30.769 0.00 0.00 42.09 2.83
1923 1959 8.788806 AGAACACAACACGGATAATAATTTTGA 58.211 29.630 0.00 0.00 0.00 2.69
1938 1974 7.532571 AGTTTAAAGTACCAAGAACACAACAC 58.467 34.615 0.00 0.00 0.00 3.32
2190 2242 3.763897 GGGTAGCACTCAATTCCAATTGT 59.236 43.478 11.01 0.00 44.66 2.71
2233 2285 5.781210 TTCTATTGTTTGGTTGTGCATGA 57.219 34.783 0.00 0.00 0.00 3.07
2353 2405 7.288810 AGTTTACTTCTGCCATGAAAATGAA 57.711 32.000 0.00 0.00 0.00 2.57
2354 2406 6.899393 AGTTTACTTCTGCCATGAAAATGA 57.101 33.333 0.00 0.00 0.00 2.57
2355 2407 9.643693 AATTAGTTTACTTCTGCCATGAAAATG 57.356 29.630 0.00 0.00 0.00 2.32
2359 2411 8.458843 GCTAAATTAGTTTACTTCTGCCATGAA 58.541 33.333 1.68 0.00 0.00 2.57
2360 2412 7.829211 AGCTAAATTAGTTTACTTCTGCCATGA 59.171 33.333 1.68 0.00 0.00 3.07
2361 2413 7.989826 AGCTAAATTAGTTTACTTCTGCCATG 58.010 34.615 1.68 0.00 0.00 3.66
2362 2414 9.331282 CTAGCTAAATTAGTTTACTTCTGCCAT 57.669 33.333 1.68 0.00 0.00 4.40
2363 2415 8.319146 ACTAGCTAAATTAGTTTACTTCTGCCA 58.681 33.333 1.68 0.00 0.00 4.92
2364 2416 8.604890 CACTAGCTAAATTAGTTTACTTCTGCC 58.395 37.037 1.68 0.00 0.00 4.85
2365 2417 9.152595 ACACTAGCTAAATTAGTTTACTTCTGC 57.847 33.333 1.68 0.00 0.00 4.26
2373 2425 9.659830 CGTTTTTGACACTAGCTAAATTAGTTT 57.340 29.630 1.68 0.00 0.00 2.66
2374 2426 7.801783 GCGTTTTTGACACTAGCTAAATTAGTT 59.198 33.333 1.68 0.00 0.00 2.24
2375 2427 7.172703 AGCGTTTTTGACACTAGCTAAATTAGT 59.827 33.333 1.68 0.00 0.00 2.24
2376 2428 7.519002 AGCGTTTTTGACACTAGCTAAATTAG 58.481 34.615 0.00 0.00 0.00 1.73
2377 2429 7.171848 TGAGCGTTTTTGACACTAGCTAAATTA 59.828 33.333 0.00 0.00 33.26 1.40
2378 2430 6.017440 TGAGCGTTTTTGACACTAGCTAAATT 60.017 34.615 0.00 0.00 33.26 1.82
2379 2431 5.468746 TGAGCGTTTTTGACACTAGCTAAAT 59.531 36.000 0.00 0.00 33.26 1.40
2380 2432 4.812091 TGAGCGTTTTTGACACTAGCTAAA 59.188 37.500 0.00 0.00 33.26 1.85
2381 2433 4.373527 TGAGCGTTTTTGACACTAGCTAA 58.626 39.130 0.00 0.00 33.26 3.09
2382 2434 3.985008 TGAGCGTTTTTGACACTAGCTA 58.015 40.909 0.00 0.00 33.26 3.32
2383 2435 2.833794 TGAGCGTTTTTGACACTAGCT 58.166 42.857 0.00 0.00 36.06 3.32
2384 2436 3.186409 TGATGAGCGTTTTTGACACTAGC 59.814 43.478 0.00 0.00 0.00 3.42
2385 2437 4.686091 TCTGATGAGCGTTTTTGACACTAG 59.314 41.667 0.00 0.00 0.00 2.57
2386 2438 4.627058 TCTGATGAGCGTTTTTGACACTA 58.373 39.130 0.00 0.00 0.00 2.74
2387 2439 3.466836 TCTGATGAGCGTTTTTGACACT 58.533 40.909 0.00 0.00 0.00 3.55
2388 2440 3.878086 TCTGATGAGCGTTTTTGACAC 57.122 42.857 0.00 0.00 0.00 3.67
2389 2441 5.700832 ACTAATCTGATGAGCGTTTTTGACA 59.299 36.000 1.70 0.00 0.00 3.58
2390 2442 6.170675 ACTAATCTGATGAGCGTTTTTGAC 57.829 37.500 1.70 0.00 0.00 3.18
2391 2443 6.034577 CGTACTAATCTGATGAGCGTTTTTGA 59.965 38.462 1.70 0.00 0.00 2.69
2392 2444 6.034577 TCGTACTAATCTGATGAGCGTTTTTG 59.965 38.462 1.70 0.00 0.00 2.44
2393 2445 6.097356 TCGTACTAATCTGATGAGCGTTTTT 58.903 36.000 1.70 0.00 0.00 1.94
2394 2446 5.647589 TCGTACTAATCTGATGAGCGTTTT 58.352 37.500 1.70 0.00 0.00 2.43
2395 2447 5.244785 TCGTACTAATCTGATGAGCGTTT 57.755 39.130 1.70 0.00 0.00 3.60
2396 2448 4.895224 TCGTACTAATCTGATGAGCGTT 57.105 40.909 1.70 0.00 0.00 4.84
2397 2449 4.788690 CATCGTACTAATCTGATGAGCGT 58.211 43.478 1.70 0.00 40.45 5.07
2398 2450 3.605916 GCATCGTACTAATCTGATGAGCG 59.394 47.826 1.70 0.00 40.45 5.03
2399 2451 4.384247 GTGCATCGTACTAATCTGATGAGC 59.616 45.833 1.70 0.00 40.45 4.26
2400 2452 4.920340 GGTGCATCGTACTAATCTGATGAG 59.080 45.833 9.52 0.16 40.45 2.90
2401 2453 4.584743 AGGTGCATCGTACTAATCTGATGA 59.415 41.667 9.52 0.00 40.45 2.92
2402 2454 4.683320 CAGGTGCATCGTACTAATCTGATG 59.317 45.833 0.00 2.79 40.84 3.07
2403 2455 4.797604 GCAGGTGCATCGTACTAATCTGAT 60.798 45.833 0.00 0.00 41.59 2.90
2404 2456 3.490933 GCAGGTGCATCGTACTAATCTGA 60.491 47.826 0.00 0.00 41.59 3.27
2405 2457 2.797156 GCAGGTGCATCGTACTAATCTG 59.203 50.000 0.00 0.00 41.59 2.90
2406 2458 3.099267 GCAGGTGCATCGTACTAATCT 57.901 47.619 0.00 0.00 41.59 2.40
2419 2471 1.982073 GAACGTGGCTATGCAGGTGC 61.982 60.000 0.00 0.00 42.50 5.01
2420 2472 0.391661 AGAACGTGGCTATGCAGGTG 60.392 55.000 0.00 0.00 0.00 4.00
2421 2473 0.324943 AAGAACGTGGCTATGCAGGT 59.675 50.000 0.00 0.00 0.00 4.00
2422 2474 1.453155 AAAGAACGTGGCTATGCAGG 58.547 50.000 0.00 0.00 0.00 4.85
2423 2475 2.226437 ACAAAAGAACGTGGCTATGCAG 59.774 45.455 0.00 0.00 0.00 4.41
2424 2476 2.226330 ACAAAAGAACGTGGCTATGCA 58.774 42.857 0.00 0.00 0.00 3.96
2425 2477 2.989422 ACAAAAGAACGTGGCTATGC 57.011 45.000 0.00 0.00 0.00 3.14
2426 2478 4.083537 TGCTAACAAAAGAACGTGGCTATG 60.084 41.667 0.00 0.00 0.00 2.23
2427 2479 4.069304 TGCTAACAAAAGAACGTGGCTAT 58.931 39.130 0.00 0.00 0.00 2.97
2428 2480 3.249080 GTGCTAACAAAAGAACGTGGCTA 59.751 43.478 0.00 0.00 0.00 3.93
2429 2481 2.032924 GTGCTAACAAAAGAACGTGGCT 59.967 45.455 0.00 0.00 0.00 4.75
2430 2482 2.032924 AGTGCTAACAAAAGAACGTGGC 59.967 45.455 0.00 0.00 29.48 5.01
2431 2483 3.963383 AGTGCTAACAAAAGAACGTGG 57.037 42.857 0.00 0.00 29.48 4.94
2432 2484 5.328691 TGAAAGTGCTAACAAAAGAACGTG 58.671 37.500 0.00 0.00 29.48 4.49
2433 2485 5.554822 TGAAAGTGCTAACAAAAGAACGT 57.445 34.783 0.00 0.00 29.48 3.99
2434 2486 6.027749 ACTTGAAAGTGCTAACAAAAGAACG 58.972 36.000 0.00 0.00 37.98 3.95
2435 2487 7.812309 AACTTGAAAGTGCTAACAAAAGAAC 57.188 32.000 0.00 0.00 39.66 3.01
2436 2488 8.085296 TGAAACTTGAAAGTGCTAACAAAAGAA 58.915 29.630 0.00 0.00 39.66 2.52
2437 2489 7.598278 TGAAACTTGAAAGTGCTAACAAAAGA 58.402 30.769 0.00 0.00 39.66 2.52
2438 2490 7.810766 TGAAACTTGAAAGTGCTAACAAAAG 57.189 32.000 0.00 0.00 39.66 2.27
2439 2491 8.594881 TTTGAAACTTGAAAGTGCTAACAAAA 57.405 26.923 0.00 0.00 39.66 2.44
2440 2492 8.770438 ATTTGAAACTTGAAAGTGCTAACAAA 57.230 26.923 0.00 0.00 39.66 2.83
2441 2493 7.219917 CGATTTGAAACTTGAAAGTGCTAACAA 59.780 33.333 0.00 0.00 39.66 2.83
2442 2494 6.690957 CGATTTGAAACTTGAAAGTGCTAACA 59.309 34.615 0.00 0.00 39.66 2.41
2443 2495 6.142320 CCGATTTGAAACTTGAAAGTGCTAAC 59.858 38.462 0.00 0.00 39.66 2.34
2444 2496 6.205784 CCGATTTGAAACTTGAAAGTGCTAA 58.794 36.000 0.00 0.00 39.66 3.09
2445 2497 5.757886 CCGATTTGAAACTTGAAAGTGCTA 58.242 37.500 0.00 0.00 39.66 3.49
2446 2498 4.610945 CCGATTTGAAACTTGAAAGTGCT 58.389 39.130 0.00 0.00 39.66 4.40
2447 2499 3.182372 GCCGATTTGAAACTTGAAAGTGC 59.818 43.478 0.00 0.00 39.66 4.40
2448 2500 3.735746 GGCCGATTTGAAACTTGAAAGTG 59.264 43.478 0.00 0.00 39.66 3.16
2449 2501 3.550030 CGGCCGATTTGAAACTTGAAAGT 60.550 43.478 24.07 0.00 42.04 2.66
2450 2502 2.979813 CGGCCGATTTGAAACTTGAAAG 59.020 45.455 24.07 0.00 0.00 2.62
2451 2503 2.287909 CCGGCCGATTTGAAACTTGAAA 60.288 45.455 30.73 0.00 0.00 2.69
2452 2504 1.268352 CCGGCCGATTTGAAACTTGAA 59.732 47.619 30.73 0.00 0.00 2.69
2453 2505 0.878416 CCGGCCGATTTGAAACTTGA 59.122 50.000 30.73 0.00 0.00 3.02
2454 2506 0.732538 GCCGGCCGATTTGAAACTTG 60.733 55.000 30.73 5.91 0.00 3.16
2455 2507 1.584495 GCCGGCCGATTTGAAACTT 59.416 52.632 30.73 0.00 0.00 2.66
2456 2508 2.340328 GGCCGGCCGATTTGAAACT 61.340 57.895 33.60 0.00 0.00 2.66
2457 2509 2.180769 GGCCGGCCGATTTGAAAC 59.819 61.111 33.60 2.25 0.00 2.78
2458 2510 3.065567 GGGCCGGCCGATTTGAAA 61.066 61.111 38.22 0.00 36.85 2.69
2471 2523 4.329545 TGACTGCTTCACCGGGCC 62.330 66.667 6.32 0.00 0.00 5.80
2472 2524 2.743928 CTGACTGCTTCACCGGGC 60.744 66.667 6.32 0.00 0.00 6.13
2473 2525 2.743928 GCTGACTGCTTCACCGGG 60.744 66.667 6.32 0.00 38.95 5.73
2474 2526 1.597854 TTGCTGACTGCTTCACCGG 60.598 57.895 0.00 0.00 43.37 5.28
2475 2527 1.159713 TGTTGCTGACTGCTTCACCG 61.160 55.000 5.87 0.00 43.37 4.94
2476 2528 1.068748 CATGTTGCTGACTGCTTCACC 60.069 52.381 5.87 0.00 43.37 4.02
2477 2529 1.665161 GCATGTTGCTGACTGCTTCAC 60.665 52.381 5.87 1.28 40.96 3.18
2478 2530 0.594602 GCATGTTGCTGACTGCTTCA 59.405 50.000 5.87 5.40 40.96 3.02
2479 2531 0.109412 GGCATGTTGCTGACTGCTTC 60.109 55.000 5.87 0.06 44.28 3.86
2480 2532 0.824595 TGGCATGTTGCTGACTGCTT 60.825 50.000 5.87 0.00 44.28 3.91
2481 2533 0.824595 TTGGCATGTTGCTGACTGCT 60.825 50.000 5.87 0.00 44.28 4.24
2482 2534 0.665369 GTTGGCATGTTGCTGACTGC 60.665 55.000 0.00 0.00 44.28 4.40
2483 2535 0.669619 TGTTGGCATGTTGCTGACTG 59.330 50.000 0.00 0.00 44.28 3.51
2484 2536 1.271379 CATGTTGGCATGTTGCTGACT 59.729 47.619 0.00 0.00 45.48 3.41
2485 2537 1.705256 CATGTTGGCATGTTGCTGAC 58.295 50.000 0.00 0.08 45.48 3.51
2497 2549 2.424601 CTGACATAAGTGCCCATGTTGG 59.575 50.000 0.00 0.00 35.55 3.77
2498 2550 2.159338 GCTGACATAAGTGCCCATGTTG 60.159 50.000 0.00 0.00 35.55 3.33
2499 2551 2.094675 GCTGACATAAGTGCCCATGTT 58.905 47.619 0.00 0.00 35.55 2.71
2500 2552 1.283029 AGCTGACATAAGTGCCCATGT 59.717 47.619 0.00 0.00 38.08 3.21
2501 2553 1.945394 GAGCTGACATAAGTGCCCATG 59.055 52.381 0.00 0.00 0.00 3.66
2502 2554 1.842562 AGAGCTGACATAAGTGCCCAT 59.157 47.619 0.00 0.00 0.00 4.00
2503 2555 1.279496 AGAGCTGACATAAGTGCCCA 58.721 50.000 0.00 0.00 0.00 5.36
2504 2556 2.168521 TGTAGAGCTGACATAAGTGCCC 59.831 50.000 0.00 0.00 0.00 5.36
2505 2557 3.452474 CTGTAGAGCTGACATAAGTGCC 58.548 50.000 0.00 0.00 0.00 5.01
2506 2558 3.452474 CCTGTAGAGCTGACATAAGTGC 58.548 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.