Multiple sequence alignment - TraesCS4D01G237400

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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 TraesCS4D01G237400 chr4D 100.000 2427 0 0 1 2427 399626583 399629009 0.000000e+00 4482
1 TraesCS4D01G237400 chr4B 90.901 2308 100 35 1 2254 493628645 493630896 0.000000e+00 2998
2 TraesCS4D01G237400 chr4B 89.773 88 4 1 2345 2427 493644136 493644223 9.180000e-20 108
3 TraesCS4D01G237400 chr4A 89.630 1755 69 28 426 2103 57434036 57435754 0.000000e+00 2128
4 TraesCS4D01G237400 chr4A 93.284 402 14 6 1 397 57433651 57434044 4.500000e-162 580


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 TraesCS4D01G237400 chr4D 399626583 399629009 2426 False 4482 4482 100.000 1 2427 1 chr4D.!!$F1 2426
1 TraesCS4D01G237400 chr4B 493628645 493630896 2251 False 2998 2998 90.901 1 2254 1 chr4B.!!$F1 2253
2 TraesCS4D01G237400 chr4A 57433651 57435754 2103 False 1354 2128 91.457 1 2103 2 chr4A.!!$F1 2102

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
987 1055 0.031716 CCCTGATCCCAGAGAGACCA 60.032 60.0 0.0 0.0 43.02 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2322 0.099791 ACCCGTTGCAAAACTGAACG 59.9 50.0 0.0 0.0 41.62 3.95 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
70 72 2.681848 ACGTACCTAGTGAATCCTGTCG 59.318 50.000 0.00 0.00 0.00 4.35
82 87 7.560368 AGTGAATCCTGTCGAGAATTTTAGAT 58.440 34.615 0.00 0.00 0.00 1.98
200 207 1.740043 GAATACGTGTCGCCGTCAGC 61.740 60.000 0.00 0.00 42.00 4.26
326 333 4.715523 GGTAGCTTGGGCACGCCA 62.716 66.667 10.83 0.00 41.70 5.69
328 335 3.947459 TAGCTTGGGCACGCCACA 61.947 61.111 10.83 2.74 41.70 4.17
360 367 2.970324 GCTCGTTTGGCGTCCACA 60.970 61.111 0.00 0.00 42.13 4.17
400 408 1.137086 AGACGTCGATCCTTCCCATTG 59.863 52.381 10.46 0.00 0.00 2.82
410 418 2.716424 TCCTTCCCATTGGAGAAACTGT 59.284 45.455 3.62 0.00 43.07 3.55
414 422 1.812571 CCCATTGGAGAAACTGTTCCG 59.187 52.381 3.62 0.00 36.22 4.30
417 425 1.133363 TTGGAGAAACTGTTCCGGGA 58.867 50.000 0.00 0.00 36.22 5.14
418 426 1.358152 TGGAGAAACTGTTCCGGGAT 58.642 50.000 0.00 0.00 36.22 3.85
419 427 1.003118 TGGAGAAACTGTTCCGGGATG 59.997 52.381 0.00 0.00 36.22 3.51
420 428 1.087501 GAGAAACTGTTCCGGGATGC 58.912 55.000 0.00 0.00 33.92 3.91
499 507 2.717809 GCGACGTTCAACCGAGAGC 61.718 63.158 0.00 0.00 0.00 4.09
648 666 1.812571 CATGAACTACCACCCAAGCAC 59.187 52.381 0.00 0.00 0.00 4.40
653 671 1.350019 ACTACCACCCAAGCACCTTAC 59.650 52.381 0.00 0.00 0.00 2.34
658 676 2.247358 CACCCAAGCACCTTACCAAAT 58.753 47.619 0.00 0.00 0.00 2.32
669 687 5.185056 GCACCTTACCAAATCCAAGTACATT 59.815 40.000 0.00 0.00 0.00 2.71
670 688 6.376018 GCACCTTACCAAATCCAAGTACATTA 59.624 38.462 0.00 0.00 0.00 1.90
671 689 7.627726 GCACCTTACCAAATCCAAGTACATTAC 60.628 40.741 0.00 0.00 0.00 1.89
672 690 7.392113 CACCTTACCAAATCCAAGTACATTACA 59.608 37.037 0.00 0.00 0.00 2.41
673 691 8.113462 ACCTTACCAAATCCAAGTACATTACAT 58.887 33.333 0.00 0.00 0.00 2.29
674 692 8.966868 CCTTACCAAATCCAAGTACATTACATT 58.033 33.333 0.00 0.00 0.00 2.71
708 747 5.641789 TTTCTCCATGTGGATGATGATCT 57.358 39.130 1.54 0.00 44.46 2.75
791 831 2.850404 GCGCGTCGTCATCACAAA 59.150 55.556 8.43 0.00 0.00 2.83
803 843 7.408395 CGTCGTCATCACAAAATATACTCGATC 60.408 40.741 0.00 0.00 0.00 3.69
804 844 7.591795 GTCGTCATCACAAAATATACTCGATCT 59.408 37.037 0.00 0.00 0.00 2.75
895 963 4.752879 CCCGCCACGGTGTCGATT 62.753 66.667 13.67 0.00 46.80 3.34
896 964 3.487202 CCGCCACGGTGTCGATTG 61.487 66.667 13.67 0.00 42.73 2.67
940 1008 0.250858 CCATGGGCGGATGCTTATGA 60.251 55.000 2.85 0.00 42.25 2.15
964 1032 4.340666 TCGTATACCGCCACCTAATTAACA 59.659 41.667 0.00 0.00 36.19 2.41
987 1055 0.031716 CCCTGATCCCAGAGAGACCA 60.032 60.000 0.00 0.00 43.02 4.02
988 1056 1.623557 CCCTGATCCCAGAGAGACCAA 60.624 57.143 0.00 0.00 43.02 3.67
989 1057 1.761784 CCTGATCCCAGAGAGACCAAG 59.238 57.143 0.00 0.00 43.02 3.61
990 1058 2.625352 CCTGATCCCAGAGAGACCAAGA 60.625 54.545 0.00 0.00 43.02 3.02
991 1059 2.694628 CTGATCCCAGAGAGACCAAGAG 59.305 54.545 0.00 0.00 43.02 2.85
992 1060 2.313041 TGATCCCAGAGAGACCAAGAGA 59.687 50.000 0.00 0.00 0.00 3.10
993 1061 3.245766 TGATCCCAGAGAGACCAAGAGAA 60.246 47.826 0.00 0.00 0.00 2.87
994 1062 3.481559 TCCCAGAGAGACCAAGAGAAT 57.518 47.619 0.00 0.00 0.00 2.40
1171 1239 7.537649 ACGTGTATATACTTCATAATGCAGACG 59.462 37.037 13.89 11.79 0.00 4.18
1224 1294 0.645868 GTCACTTCATAACGCTCGGC 59.354 55.000 0.00 0.00 0.00 5.54
1317 1387 3.387962 TGGAAATGGAGCAGGTAGATCT 58.612 45.455 0.00 0.00 31.91 2.75
1560 1638 1.153997 GAGCTCGTCGGTCTGTTCC 60.154 63.158 0.00 0.00 37.18 3.62
1567 1645 2.805353 CGGTCTGTTCCGCAGTCG 60.805 66.667 0.00 0.00 45.23 4.18
1582 1660 0.455815 AGTCGCATGCATCGTCTGTA 59.544 50.000 19.57 0.00 0.00 2.74
1624 1702 3.444034 GCCTCCTTGTATTTTCCCTGTTC 59.556 47.826 0.00 0.00 0.00 3.18
1751 1857 8.655970 TGTTATACTGTTCTTCGTGATTGATTG 58.344 33.333 0.00 0.00 0.00 2.67
1809 1917 0.600255 CCCGACGTCATAAGATGCCC 60.600 60.000 17.16 0.00 33.96 5.36
1811 1919 1.270305 CCGACGTCATAAGATGCCCAT 60.270 52.381 17.16 0.00 33.96 4.00
1826 1934 2.093341 TGCCCATACGGAAAGGAACTAC 60.093 50.000 0.00 0.00 38.49 2.73
1920 2028 3.427528 GCATTGACTTTGCACTTGTCATG 59.572 43.478 13.91 13.94 39.92 3.07
1946 2058 7.201741 GGTTCCTTTTGCTCCATCTATTACTTC 60.202 40.741 0.00 0.00 0.00 3.01
2134 2277 7.959175 TGCCTCCGTTCTTTATAACTGTATAT 58.041 34.615 0.00 0.00 0.00 0.86
2135 2278 9.081204 TGCCTCCGTTCTTTATAACTGTATATA 57.919 33.333 0.00 0.00 0.00 0.86
2136 2279 9.918630 GCCTCCGTTCTTTATAACTGTATATAA 57.081 33.333 0.00 0.00 0.00 0.98
2157 2300 5.640158 AATTAACGGATACCTTGGATCCA 57.360 39.130 11.44 11.44 42.75 3.41
2178 2321 5.131475 TCCAAGTAAACTCCTGTAGGTTGTT 59.869 40.000 0.00 2.65 35.32 2.83
2179 2322 5.469084 CCAAGTAAACTCCTGTAGGTTGTTC 59.531 44.000 10.58 3.20 35.32 3.18
2182 2325 3.832615 AACTCCTGTAGGTTGTTCGTT 57.167 42.857 0.00 0.00 36.34 3.85
2197 2340 0.378962 TCGTTCAGTTTTGCAACGGG 59.621 50.000 0.00 0.00 42.50 5.28
2202 2345 1.140804 AGTTTTGCAACGGGTGTGC 59.859 52.632 0.00 0.00 38.03 4.57
2206 2349 0.752009 TTTGCAACGGGTGTGCCTAA 60.752 50.000 0.00 0.00 34.45 2.69
2215 2358 3.008704 ACGGGTGTGCCTAAATCTTAGTT 59.991 43.478 0.00 0.00 34.45 2.24
2219 2362 5.246307 GGTGTGCCTAAATCTTAGTTGACT 58.754 41.667 0.00 0.00 0.00 3.41
2222 2365 6.426937 GTGTGCCTAAATCTTAGTTGACTGAA 59.573 38.462 0.00 0.00 0.00 3.02
2237 2381 7.054751 AGTTGACTGAAACTTAACTAAGCCTT 58.945 34.615 0.00 0.00 37.05 4.35
2242 2386 6.867293 ACTGAAACTTAACTAAGCCTTAGTCG 59.133 38.462 17.09 11.13 45.33 4.18
2245 2389 4.996344 ACTTAACTAAGCCTTAGTCGAGC 58.004 43.478 17.09 0.00 45.33 5.03
2254 2398 3.819337 AGCCTTAGTCGAGCGACATATAA 59.181 43.478 22.96 12.65 46.76 0.98
2255 2399 3.913163 GCCTTAGTCGAGCGACATATAAC 59.087 47.826 22.96 6.11 46.76 1.89
2256 2400 4.556104 GCCTTAGTCGAGCGACATATAACA 60.556 45.833 22.96 0.57 46.76 2.41
2257 2401 5.700846 CCTTAGTCGAGCGACATATAACAT 58.299 41.667 22.96 4.40 46.76 2.71
2258 2402 6.622245 GCCTTAGTCGAGCGACATATAACATA 60.622 42.308 22.96 3.50 46.76 2.29
2259 2403 7.473366 CCTTAGTCGAGCGACATATAACATAT 58.527 38.462 22.96 3.08 46.76 1.78
2260 2404 8.610035 CCTTAGTCGAGCGACATATAACATATA 58.390 37.037 22.96 2.19 46.76 0.86
2261 2405 9.983804 CTTAGTCGAGCGACATATAACATATAA 57.016 33.333 22.96 9.07 46.76 0.98
2264 2408 9.687210 AGTCGAGCGACATATAACATATAAAAA 57.313 29.630 22.96 0.00 46.76 1.94
2265 2409 9.939047 GTCGAGCGACATATAACATATAAAAAG 57.061 33.333 17.21 0.00 44.02 2.27
2266 2410 9.902196 TCGAGCGACATATAACATATAAAAAGA 57.098 29.630 0.00 0.00 0.00 2.52
2305 2449 8.373212 CATGTTCTTCATGTAAAAATCTCACG 57.627 34.615 0.00 0.00 46.18 4.35
2306 2450 7.722795 TGTTCTTCATGTAAAAATCTCACGA 57.277 32.000 0.00 0.00 0.00 4.35
2307 2451 8.148807 TGTTCTTCATGTAAAAATCTCACGAA 57.851 30.769 0.00 0.00 0.00 3.85
2308 2452 8.783093 TGTTCTTCATGTAAAAATCTCACGAAT 58.217 29.630 0.00 0.00 0.00 3.34
2313 2457 9.554724 TTCATGTAAAAATCTCACGAATAAAGC 57.445 29.630 0.00 0.00 0.00 3.51
2314 2458 8.726068 TCATGTAAAAATCTCACGAATAAAGCA 58.274 29.630 0.00 0.00 0.00 3.91
2315 2459 9.507280 CATGTAAAAATCTCACGAATAAAGCAT 57.493 29.630 0.00 0.00 0.00 3.79
2316 2460 9.722056 ATGTAAAAATCTCACGAATAAAGCATC 57.278 29.630 0.00 0.00 0.00 3.91
2317 2461 7.902917 TGTAAAAATCTCACGAATAAAGCATCG 59.097 33.333 0.00 0.00 44.33 3.84
2318 2462 6.662414 AAAATCTCACGAATAAAGCATCGA 57.338 33.333 1.84 0.00 41.43 3.59
2319 2463 6.851222 AAATCTCACGAATAAAGCATCGAT 57.149 33.333 1.84 0.00 41.43 3.59
2320 2464 6.851222 AATCTCACGAATAAAGCATCGATT 57.149 33.333 0.00 0.00 41.43 3.34
2321 2465 5.641777 TCTCACGAATAAAGCATCGATTG 57.358 39.130 0.00 0.00 41.43 2.67
2322 2466 5.348164 TCTCACGAATAAAGCATCGATTGA 58.652 37.500 0.00 0.00 41.43 2.57
2323 2467 5.460091 TCTCACGAATAAAGCATCGATTGAG 59.540 40.000 0.00 2.55 40.57 3.02
2324 2468 5.348164 TCACGAATAAAGCATCGATTGAGA 58.652 37.500 0.00 0.00 41.43 3.27
2325 2469 5.232202 TCACGAATAAAGCATCGATTGAGAC 59.768 40.000 0.00 0.00 41.43 3.36
2326 2470 5.233050 CACGAATAAAGCATCGATTGAGACT 59.767 40.000 0.00 0.00 41.43 3.24
2327 2471 5.812642 ACGAATAAAGCATCGATTGAGACTT 59.187 36.000 0.00 0.00 41.43 3.01
2328 2472 6.125419 CGAATAAAGCATCGATTGAGACTTG 58.875 40.000 0.00 0.00 41.43 3.16
2329 2473 5.998454 ATAAAGCATCGATTGAGACTTGG 57.002 39.130 0.00 0.00 0.00 3.61
2330 2474 3.340814 AAGCATCGATTGAGACTTGGT 57.659 42.857 0.00 0.00 0.00 3.67
2331 2475 3.340814 AGCATCGATTGAGACTTGGTT 57.659 42.857 0.00 0.00 0.00 3.67
2332 2476 4.471904 AGCATCGATTGAGACTTGGTTA 57.528 40.909 0.00 0.00 0.00 2.85
2333 2477 4.832248 AGCATCGATTGAGACTTGGTTAA 58.168 39.130 0.00 0.00 0.00 2.01
2334 2478 4.872691 AGCATCGATTGAGACTTGGTTAAG 59.127 41.667 0.00 0.00 39.86 1.85
2335 2479 4.494855 GCATCGATTGAGACTTGGTTAAGC 60.495 45.833 0.00 0.00 37.43 3.09
2336 2480 3.596214 TCGATTGAGACTTGGTTAAGCC 58.404 45.455 1.51 0.00 37.43 4.35
2337 2481 3.260884 TCGATTGAGACTTGGTTAAGCCT 59.739 43.478 1.51 0.00 37.43 4.58
2338 2482 3.619038 CGATTGAGACTTGGTTAAGCCTC 59.381 47.826 1.51 2.25 41.97 4.70
2340 2484 3.685139 TGAGACTTGGTTAAGCCTCAG 57.315 47.619 1.51 0.00 44.95 3.35
2341 2485 2.972713 TGAGACTTGGTTAAGCCTCAGT 59.027 45.455 1.51 1.77 44.95 3.41
2342 2486 3.006967 TGAGACTTGGTTAAGCCTCAGTC 59.993 47.826 15.72 15.72 44.95 3.51
2343 2487 2.028930 AGACTTGGTTAAGCCTCAGTCG 60.029 50.000 16.74 0.00 45.34 4.18
2344 2488 1.968493 ACTTGGTTAAGCCTCAGTCGA 59.032 47.619 1.51 0.00 37.43 4.20
2345 2489 2.567615 ACTTGGTTAAGCCTCAGTCGAT 59.432 45.455 1.51 0.00 37.43 3.59
2346 2490 3.008049 ACTTGGTTAAGCCTCAGTCGATT 59.992 43.478 1.51 0.00 37.43 3.34
2347 2491 4.222145 ACTTGGTTAAGCCTCAGTCGATTA 59.778 41.667 1.51 0.00 37.43 1.75
2348 2492 4.811969 TGGTTAAGCCTCAGTCGATTAA 57.188 40.909 1.51 0.00 38.35 1.40
2349 2493 4.755411 TGGTTAAGCCTCAGTCGATTAAG 58.245 43.478 1.51 0.00 38.35 1.85
2350 2494 4.464951 TGGTTAAGCCTCAGTCGATTAAGA 59.535 41.667 1.51 0.00 38.35 2.10
2351 2495 5.128827 TGGTTAAGCCTCAGTCGATTAAGAT 59.871 40.000 1.51 0.00 38.35 2.40
2352 2496 6.049790 GGTTAAGCCTCAGTCGATTAAGATT 58.950 40.000 0.00 0.00 0.00 2.40
2353 2497 6.539103 GGTTAAGCCTCAGTCGATTAAGATTT 59.461 38.462 0.00 0.00 0.00 2.17
2354 2498 7.709613 GGTTAAGCCTCAGTCGATTAAGATTTA 59.290 37.037 0.00 0.00 0.00 1.40
2355 2499 8.756864 GTTAAGCCTCAGTCGATTAAGATTTAG 58.243 37.037 0.00 0.00 0.00 1.85
2356 2500 5.293560 AGCCTCAGTCGATTAAGATTTAGC 58.706 41.667 0.00 0.00 0.00 3.09
2357 2501 5.050490 GCCTCAGTCGATTAAGATTTAGCA 58.950 41.667 0.00 0.00 0.00 3.49
2358 2502 5.523916 GCCTCAGTCGATTAAGATTTAGCAA 59.476 40.000 0.00 0.00 0.00 3.91
2359 2503 6.203723 GCCTCAGTCGATTAAGATTTAGCAAT 59.796 38.462 0.00 0.00 0.00 3.56
2360 2504 7.570324 GCCTCAGTCGATTAAGATTTAGCAATC 60.570 40.741 0.00 0.00 39.45 2.67
2370 2514 5.627499 AGATTTAGCAATCTCGTTTTGCA 57.373 34.783 17.33 0.00 45.26 4.08
2371 2515 6.012658 AGATTTAGCAATCTCGTTTTGCAA 57.987 33.333 17.33 0.00 45.26 4.08
2372 2516 5.858581 AGATTTAGCAATCTCGTTTTGCAAC 59.141 36.000 17.33 0.00 45.26 4.17
2373 2517 6.294176 AGATTTAGCAATCTCGTTTTGCAACT 60.294 34.615 17.33 0.00 45.26 3.16
2374 2518 8.046220 AGATTTAGCAATCTCGTTTTGCAACTC 61.046 37.037 17.33 13.16 45.26 3.01
2375 2519 2.998772 GCAATCTCGTTTTGCAACTCA 58.001 42.857 0.00 0.00 46.78 3.41
2376 2520 3.568538 GCAATCTCGTTTTGCAACTCAT 58.431 40.909 0.00 0.00 46.78 2.90
2377 2521 4.722194 GCAATCTCGTTTTGCAACTCATA 58.278 39.130 0.00 0.00 46.78 2.15
2378 2522 5.153513 GCAATCTCGTTTTGCAACTCATAA 58.846 37.500 0.00 0.00 46.78 1.90
2379 2523 5.629020 GCAATCTCGTTTTGCAACTCATAAA 59.371 36.000 0.00 0.00 46.78 1.40
2380 2524 6.308766 GCAATCTCGTTTTGCAACTCATAAAT 59.691 34.615 0.00 0.00 46.78 1.40
2381 2525 7.461938 GCAATCTCGTTTTGCAACTCATAAATC 60.462 37.037 0.00 0.00 46.78 2.17
2382 2526 5.938322 TCTCGTTTTGCAACTCATAAATCC 58.062 37.500 0.00 0.00 0.00 3.01
2383 2527 5.471797 TCTCGTTTTGCAACTCATAAATCCA 59.528 36.000 0.00 0.00 0.00 3.41
2384 2528 6.150976 TCTCGTTTTGCAACTCATAAATCCAT 59.849 34.615 0.00 0.00 0.00 3.41
2385 2529 6.092092 TCGTTTTGCAACTCATAAATCCATG 58.908 36.000 0.00 0.00 0.00 3.66
2386 2530 5.220265 CGTTTTGCAACTCATAAATCCATGC 60.220 40.000 0.00 0.00 0.00 4.06
2387 2531 4.389890 TTGCAACTCATAAATCCATGCC 57.610 40.909 0.00 0.00 0.00 4.40
2388 2532 2.694628 TGCAACTCATAAATCCATGCCC 59.305 45.455 0.00 0.00 0.00 5.36
2389 2533 2.036346 GCAACTCATAAATCCATGCCCC 59.964 50.000 0.00 0.00 0.00 5.80
2390 2534 2.629617 CAACTCATAAATCCATGCCCCC 59.370 50.000 0.00 0.00 0.00 5.40
2391 2535 2.146998 ACTCATAAATCCATGCCCCCT 58.853 47.619 0.00 0.00 0.00 4.79
2392 2536 2.108952 ACTCATAAATCCATGCCCCCTC 59.891 50.000 0.00 0.00 0.00 4.30
2393 2537 2.108776 CTCATAAATCCATGCCCCCTCA 59.891 50.000 0.00 0.00 0.00 3.86
2394 2538 2.723563 TCATAAATCCATGCCCCCTCAT 59.276 45.455 0.00 0.00 0.00 2.90
2395 2539 3.142597 TCATAAATCCATGCCCCCTCATT 59.857 43.478 0.00 0.00 0.00 2.57
2396 2540 2.574074 AAATCCATGCCCCCTCATTT 57.426 45.000 0.00 0.00 0.00 2.32
2397 2541 3.704545 AAATCCATGCCCCCTCATTTA 57.295 42.857 0.00 0.00 0.00 1.40
2398 2542 3.704545 AATCCATGCCCCCTCATTTAA 57.295 42.857 0.00 0.00 0.00 1.52
2399 2543 3.704545 ATCCATGCCCCCTCATTTAAA 57.295 42.857 0.00 0.00 0.00 1.52
2400 2544 3.481559 TCCATGCCCCCTCATTTAAAA 57.518 42.857 0.00 0.00 0.00 1.52
2401 2545 3.796111 TCCATGCCCCCTCATTTAAAAA 58.204 40.909 0.00 0.00 0.00 1.94
2417 2561 2.772102 AAAAATCCAGGGCCCAACC 58.228 52.632 27.56 0.00 37.93 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
352 359 2.202171 CGAACGCATTGTGGACGC 60.202 61.111 1.77 0.00 0.00 5.19
400 408 1.739067 CATCCCGGAACAGTTTCTCC 58.261 55.000 0.73 0.00 31.71 3.71
648 666 7.931578 TGTAATGTACTTGGATTTGGTAAGG 57.068 36.000 0.00 0.00 0.00 2.69
686 704 7.639534 ATGAAGATCATCATCCACATGGAGAAA 60.640 37.037 7.61 0.00 39.26 2.52
687 705 6.183361 ATGAAGATCATCATCCACATGGAGAA 60.183 38.462 7.61 0.00 39.26 2.87
688 706 5.309806 ATGAAGATCATCATCCACATGGAGA 59.690 40.000 7.61 4.87 39.26 3.71
689 707 5.561679 ATGAAGATCATCATCCACATGGAG 58.438 41.667 7.61 0.00 39.26 3.86
708 747 4.579340 GTCTCTGTCCGTATACTGGATGAA 59.421 45.833 16.10 7.62 37.93 2.57
719 758 0.322648 TCTCACCGTCTCTGTCCGTA 59.677 55.000 0.00 0.00 0.00 4.02
720 759 0.956410 CTCTCACCGTCTCTGTCCGT 60.956 60.000 0.00 0.00 0.00 4.69
721 760 1.797441 CTCTCACCGTCTCTGTCCG 59.203 63.158 0.00 0.00 0.00 4.79
803 843 3.441290 AGGTCTCCGGCGTTCGAG 61.441 66.667 6.01 5.67 42.43 4.04
804 844 3.744719 CAGGTCTCCGGCGTTCGA 61.745 66.667 6.01 0.00 42.43 3.71
894 962 7.461043 ACTTATATATAGGGAACTGATGGCCAA 59.539 37.037 10.96 0.00 43.88 4.52
895 963 6.965866 ACTTATATATAGGGAACTGATGGCCA 59.034 38.462 8.56 8.56 43.88 5.36
896 964 7.419172 GGACTTATATATAGGGAACTGATGGCC 60.419 44.444 0.00 0.00 43.88 5.36
964 1032 0.693767 CTCTCTGGGATCAGGGGCTT 60.694 60.000 0.00 0.00 41.75 4.35
987 1055 4.565817 AGGAGGCCATCTCTTATTCTCTT 58.434 43.478 5.01 0.00 42.10 2.85
988 1056 4.212070 AGGAGGCCATCTCTTATTCTCT 57.788 45.455 5.01 0.00 42.10 3.10
989 1057 4.592778 AGAAGGAGGCCATCTCTTATTCTC 59.407 45.833 5.01 0.00 42.10 2.87
990 1058 4.565817 AGAAGGAGGCCATCTCTTATTCT 58.434 43.478 5.01 3.27 42.10 2.40
991 1059 4.262851 GGAGAAGGAGGCCATCTCTTATTC 60.263 50.000 20.35 11.98 44.75 1.75
992 1060 3.650461 GGAGAAGGAGGCCATCTCTTATT 59.350 47.826 20.35 5.99 44.75 1.40
993 1061 3.247162 GGAGAAGGAGGCCATCTCTTAT 58.753 50.000 20.35 9.86 44.75 1.73
994 1062 2.023015 TGGAGAAGGAGGCCATCTCTTA 60.023 50.000 20.35 11.64 44.75 2.10
1171 1239 2.461110 CGTACGATTGCCACAGCCC 61.461 63.158 10.44 0.00 38.69 5.19
1176 1244 0.785979 AACGAACGTACGATTGCCAC 59.214 50.000 24.41 0.00 37.03 5.01
1224 1294 4.201753 CCTGCAGATCATTAACACAACGAG 60.202 45.833 17.39 0.00 0.00 4.18
1317 1387 1.752358 GCATCCTCTCATCGCCTCCA 61.752 60.000 0.00 0.00 0.00 3.86
1433 1503 1.207593 CGGTTTCAGGCTTTCAGCG 59.792 57.895 0.00 0.00 43.62 5.18
1452 1530 1.404315 GGAGTCCTTCGTAAGCACCAG 60.404 57.143 0.41 0.00 37.18 4.00
1567 1645 5.155509 TGTAATTTACAGACGATGCATGC 57.844 39.130 11.82 11.82 34.06 4.06
1582 1660 3.057734 GCGGCGACTATAGCTGTAATTT 58.942 45.455 12.98 0.00 42.62 1.82
1624 1702 5.124457 CAGATACATGACCTGAAAACAAGGG 59.876 44.000 0.00 0.00 39.30 3.95
1751 1857 6.284475 TCGTCGTCTTAACTCTATAGCTTC 57.716 41.667 0.00 0.00 0.00 3.86
1809 1917 3.788333 TCGGTAGTTCCTTTCCGTATG 57.212 47.619 0.00 0.00 42.95 2.39
1811 1919 4.202202 TGTTTTCGGTAGTTCCTTTCCGTA 60.202 41.667 0.00 0.00 42.95 4.02
1826 1934 3.686241 TCATCTCTCTGCATTGTTTTCGG 59.314 43.478 0.00 0.00 0.00 4.30
1920 2028 6.122964 AGTAATAGATGGAGCAAAAGGAACC 58.877 40.000 0.00 0.00 0.00 3.62
1946 2058 4.253685 AGGAGTACGACAAACAATGATGG 58.746 43.478 0.00 0.00 0.00 3.51
2092 2215 2.030412 ATGTTGAGCGACCGTGCA 59.970 55.556 0.00 0.00 37.31 4.57
2103 2226 2.270352 AAAGAACGGAGGCATGTTGA 57.730 45.000 0.00 0.00 0.00 3.18
2104 2227 5.354234 AGTTATAAAGAACGGAGGCATGTTG 59.646 40.000 0.00 0.00 34.36 3.33
2134 2277 6.750660 TGGATCCAAGGTATCCGTTAATTA 57.249 37.500 13.46 0.00 45.05 1.40
2135 2278 5.640158 TGGATCCAAGGTATCCGTTAATT 57.360 39.130 13.46 0.00 45.05 1.40
2136 2279 5.621193 CTTGGATCCAAGGTATCCGTTAAT 58.379 41.667 37.26 0.00 46.88 1.40
2137 2280 5.031066 CTTGGATCCAAGGTATCCGTTAA 57.969 43.478 37.26 9.85 46.88 2.01
2138 2281 4.682778 CTTGGATCCAAGGTATCCGTTA 57.317 45.455 37.26 10.04 46.88 3.18
2139 2282 3.560636 CTTGGATCCAAGGTATCCGTT 57.439 47.619 37.26 0.00 46.88 4.44
2151 2294 4.470304 ACCTACAGGAGTTTACTTGGATCC 59.530 45.833 4.20 4.20 38.94 3.36
2156 2299 5.176958 CGAACAACCTACAGGAGTTTACTTG 59.823 44.000 1.29 0.00 37.20 3.16
2157 2300 5.163374 ACGAACAACCTACAGGAGTTTACTT 60.163 40.000 1.29 0.00 37.20 2.24
2178 2321 0.378962 CCCGTTGCAAAACTGAACGA 59.621 50.000 0.00 0.00 44.04 3.85
2179 2322 0.099791 ACCCGTTGCAAAACTGAACG 59.900 50.000 0.00 0.00 41.62 3.95
2182 2325 0.453793 CACACCCGTTGCAAAACTGA 59.546 50.000 0.00 0.00 0.00 3.41
2197 2340 5.932303 TCAGTCAACTAAGATTTAGGCACAC 59.068 40.000 1.40 0.00 0.00 3.82
2215 2358 7.732996 ACTAAGGCTTAGTTAAGTTTCAGTCA 58.267 34.615 29.55 0.00 43.70 3.41
2219 2362 6.985117 TCGACTAAGGCTTAGTTAAGTTTCA 58.015 36.000 33.74 14.21 46.01 2.69
2222 2365 5.409211 GCTCGACTAAGGCTTAGTTAAGTT 58.591 41.667 33.74 15.45 46.01 2.66
2234 2378 5.104562 TGTTATATGTCGCTCGACTAAGG 57.895 43.478 20.92 0.00 44.80 2.69
2281 2425 8.322906 TCGTGAGATTTTTACATGAAGAACAT 57.677 30.769 0.00 0.00 35.61 2.71
2282 2426 7.722795 TCGTGAGATTTTTACATGAAGAACA 57.277 32.000 0.00 0.00 33.31 3.18
2287 2431 9.554724 GCTTTATTCGTGAGATTTTTACATGAA 57.445 29.630 0.00 0.00 41.53 2.57
2288 2432 8.726068 TGCTTTATTCGTGAGATTTTTACATGA 58.274 29.630 0.00 0.00 41.60 3.07
2289 2433 8.894409 TGCTTTATTCGTGAGATTTTTACATG 57.106 30.769 0.00 0.00 41.60 3.21
2290 2434 9.722056 GATGCTTTATTCGTGAGATTTTTACAT 57.278 29.630 0.00 0.00 41.60 2.29
2291 2435 7.902917 CGATGCTTTATTCGTGAGATTTTTACA 59.097 33.333 0.00 0.00 41.60 2.41
2292 2436 8.114290 TCGATGCTTTATTCGTGAGATTTTTAC 58.886 33.333 0.00 0.00 41.60 2.01
2293 2437 8.192068 TCGATGCTTTATTCGTGAGATTTTTA 57.808 30.769 0.00 0.00 41.60 1.52
2294 2438 7.072177 TCGATGCTTTATTCGTGAGATTTTT 57.928 32.000 0.00 0.00 41.60 1.94
2295 2439 6.662414 TCGATGCTTTATTCGTGAGATTTT 57.338 33.333 0.00 0.00 41.60 1.82
2296 2440 6.851222 ATCGATGCTTTATTCGTGAGATTT 57.149 33.333 0.00 0.00 41.60 2.17
2297 2441 6.479990 TCAATCGATGCTTTATTCGTGAGATT 59.520 34.615 0.00 0.00 41.60 2.40
2298 2442 5.985530 TCAATCGATGCTTTATTCGTGAGAT 59.014 36.000 0.00 0.00 41.60 2.75
2299 2443 5.348164 TCAATCGATGCTTTATTCGTGAGA 58.652 37.500 0.00 0.00 39.20 3.27
2300 2444 5.460091 TCTCAATCGATGCTTTATTCGTGAG 59.540 40.000 0.00 4.38 33.19 3.51
2301 2445 5.232202 GTCTCAATCGATGCTTTATTCGTGA 59.768 40.000 0.00 0.00 0.00 4.35
2302 2446 5.233050 AGTCTCAATCGATGCTTTATTCGTG 59.767 40.000 0.00 0.00 0.00 4.35
2303 2447 5.352284 AGTCTCAATCGATGCTTTATTCGT 58.648 37.500 0.00 0.00 0.00 3.85
2304 2448 5.896922 AGTCTCAATCGATGCTTTATTCG 57.103 39.130 0.00 0.00 0.00 3.34
2305 2449 6.037610 ACCAAGTCTCAATCGATGCTTTATTC 59.962 38.462 0.00 0.00 0.00 1.75
2306 2450 5.882557 ACCAAGTCTCAATCGATGCTTTATT 59.117 36.000 0.00 0.00 0.00 1.40
2307 2451 5.431765 ACCAAGTCTCAATCGATGCTTTAT 58.568 37.500 0.00 0.00 0.00 1.40
2308 2452 4.832248 ACCAAGTCTCAATCGATGCTTTA 58.168 39.130 0.00 0.00 0.00 1.85
2309 2453 3.679389 ACCAAGTCTCAATCGATGCTTT 58.321 40.909 0.00 0.00 0.00 3.51
2310 2454 3.340814 ACCAAGTCTCAATCGATGCTT 57.659 42.857 0.00 0.00 0.00 3.91
2311 2455 3.340814 AACCAAGTCTCAATCGATGCT 57.659 42.857 0.00 0.00 0.00 3.79
2312 2456 4.494855 GCTTAACCAAGTCTCAATCGATGC 60.495 45.833 0.00 0.00 34.00 3.91
2313 2457 4.034510 GGCTTAACCAAGTCTCAATCGATG 59.965 45.833 0.00 0.00 38.86 3.84
2314 2458 4.080863 AGGCTTAACCAAGTCTCAATCGAT 60.081 41.667 0.00 0.00 43.33 3.59
2315 2459 3.260884 AGGCTTAACCAAGTCTCAATCGA 59.739 43.478 0.00 0.00 43.33 3.59
2316 2460 3.600388 AGGCTTAACCAAGTCTCAATCG 58.400 45.455 0.00 0.00 43.33 3.34
2323 2467 2.029290 TCGACTGAGGCTTAACCAAGTC 60.029 50.000 13.75 13.75 44.89 3.01
2324 2468 1.968493 TCGACTGAGGCTTAACCAAGT 59.032 47.619 0.00 0.00 43.14 3.16
2325 2469 2.743636 TCGACTGAGGCTTAACCAAG 57.256 50.000 0.00 0.00 43.14 3.61
2326 2470 3.695830 AATCGACTGAGGCTTAACCAA 57.304 42.857 0.00 0.00 43.14 3.67
2327 2471 4.464951 TCTTAATCGACTGAGGCTTAACCA 59.535 41.667 0.00 0.00 43.14 3.67
2328 2472 5.007385 TCTTAATCGACTGAGGCTTAACC 57.993 43.478 0.00 0.00 39.61 2.85
2329 2473 7.541122 AAATCTTAATCGACTGAGGCTTAAC 57.459 36.000 0.00 0.00 0.00 2.01
2330 2474 7.438459 GCTAAATCTTAATCGACTGAGGCTTAA 59.562 37.037 0.00 0.00 0.00 1.85
2331 2475 6.924060 GCTAAATCTTAATCGACTGAGGCTTA 59.076 38.462 0.00 0.00 0.00 3.09
2332 2476 5.755861 GCTAAATCTTAATCGACTGAGGCTT 59.244 40.000 0.00 0.00 0.00 4.35
2333 2477 5.163405 TGCTAAATCTTAATCGACTGAGGCT 60.163 40.000 0.00 0.00 0.00 4.58
2334 2478 5.050490 TGCTAAATCTTAATCGACTGAGGC 58.950 41.667 0.00 0.00 0.00 4.70
2335 2479 7.721286 ATTGCTAAATCTTAATCGACTGAGG 57.279 36.000 0.00 0.00 0.00 3.86
2356 2500 7.008628 GGATTTATGAGTTGCAAAACGAGATTG 59.991 37.037 0.00 0.00 0.00 2.67
2357 2501 7.029563 GGATTTATGAGTTGCAAAACGAGATT 58.970 34.615 0.00 0.00 0.00 2.40
2358 2502 6.150976 TGGATTTATGAGTTGCAAAACGAGAT 59.849 34.615 0.00 0.00 0.00 2.75
2359 2503 5.471797 TGGATTTATGAGTTGCAAAACGAGA 59.528 36.000 0.00 0.00 0.00 4.04
2360 2504 5.698832 TGGATTTATGAGTTGCAAAACGAG 58.301 37.500 0.00 0.00 0.00 4.18
2361 2505 5.697473 TGGATTTATGAGTTGCAAAACGA 57.303 34.783 0.00 0.00 0.00 3.85
2362 2506 5.220265 GCATGGATTTATGAGTTGCAAAACG 60.220 40.000 0.00 0.00 0.00 3.60
2363 2507 5.063817 GGCATGGATTTATGAGTTGCAAAAC 59.936 40.000 0.00 0.00 0.00 2.43
2364 2508 5.177326 GGCATGGATTTATGAGTTGCAAAA 58.823 37.500 0.00 0.00 0.00 2.44
2365 2509 4.382901 GGGCATGGATTTATGAGTTGCAAA 60.383 41.667 0.00 0.00 0.00 3.68
2366 2510 3.132646 GGGCATGGATTTATGAGTTGCAA 59.867 43.478 0.00 0.00 0.00 4.08
2367 2511 2.694628 GGGCATGGATTTATGAGTTGCA 59.305 45.455 0.00 0.00 0.00 4.08
2368 2512 2.036346 GGGGCATGGATTTATGAGTTGC 59.964 50.000 0.00 0.00 0.00 4.17
2369 2513 2.629617 GGGGGCATGGATTTATGAGTTG 59.370 50.000 0.00 0.00 0.00 3.16
2370 2514 2.519691 AGGGGGCATGGATTTATGAGTT 59.480 45.455 0.00 0.00 0.00 3.01
2371 2515 2.108952 GAGGGGGCATGGATTTATGAGT 59.891 50.000 0.00 0.00 0.00 3.41
2372 2516 2.108776 TGAGGGGGCATGGATTTATGAG 59.891 50.000 0.00 0.00 0.00 2.90
2373 2517 2.142756 TGAGGGGGCATGGATTTATGA 58.857 47.619 0.00 0.00 0.00 2.15
2374 2518 2.681319 TGAGGGGGCATGGATTTATG 57.319 50.000 0.00 0.00 0.00 1.90
2375 2519 3.929245 AATGAGGGGGCATGGATTTAT 57.071 42.857 0.00 0.00 0.00 1.40
2376 2520 3.704545 AAATGAGGGGGCATGGATTTA 57.295 42.857 0.00 0.00 0.00 1.40
2377 2521 2.574074 AAATGAGGGGGCATGGATTT 57.426 45.000 0.00 0.00 0.00 2.17
2378 2522 3.704545 TTAAATGAGGGGGCATGGATT 57.295 42.857 0.00 0.00 0.00 3.01
2379 2523 3.704545 TTTAAATGAGGGGGCATGGAT 57.295 42.857 0.00 0.00 0.00 3.41
2380 2524 3.481559 TTTTAAATGAGGGGGCATGGA 57.518 42.857 0.00 0.00 0.00 3.41
2399 2543 2.772102 GGTTGGGCCCTGGATTTTT 58.228 52.632 25.70 0.00 0.00 1.94
2400 2544 4.559148 GGTTGGGCCCTGGATTTT 57.441 55.556 25.70 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.