Multiple sequence alignment - TraesCS6A01G341400

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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 TraesCS6A01G341400 chr6A 100.000 3512 0 0 1 3512 574241071 574244582 0.000000e+00 6486.0
1 TraesCS6A01G341400 chr6A 85.938 384 27 8 2464 2837 574263277 574263643 5.500000e-103 385.0
2 TraesCS6A01G341400 chr6B 91.763 3375 230 22 1 3350 646239412 646242763 0.000000e+00 4649.0
3 TraesCS6A01G341400 chr6B 85.831 367 32 5 2474 2837 646254180 646254529 4.280000e-99 372.0
4 TraesCS6A01G341400 chr6B 91.228 57 4 1 2866 2922 567852990 567852935 3.760000e-10 76.8
5 TraesCS6A01G341400 chr6D 92.302 2858 146 33 1 2837 429009204 429012008 0.000000e+00 3991.0
6 TraesCS6A01G341400 chr6D 89.138 580 44 9 2831 3392 429012046 429012624 0.000000e+00 704.0
7 TraesCS6A01G341400 chr6D 83.137 510 76 8 2949 3452 429020939 429021444 1.150000e-124 457.0
8 TraesCS6A01G341400 chr6D 87.123 365 27 4 2474 2837 429020498 429020843 2.540000e-106 396.0
9 TraesCS6A01G341400 chr6D 97.959 49 1 0 2875 2923 429020839 429020887 6.250000e-13 86.1
10 TraesCS6A01G341400 chr6D 100.000 30 0 0 2844 2873 8565595 8565624 4.900000e-04 56.5
11 TraesCS6A01G341400 chr6D 100.000 30 0 0 2844 2873 105820724 105820695 4.900000e-04 56.5
12 TraesCS6A01G341400 chr3B 81.596 1717 274 25 759 2457 734437290 734435598 0.000000e+00 1382.0
13 TraesCS6A01G341400 chr3B 81.429 140 9 8 2878 3002 405783497 405783634 8.020000e-17 99.0
14 TraesCS6A01G341400 chr3A 82.290 1581 257 13 883 2457 689502205 689500642 0.000000e+00 1347.0
15 TraesCS6A01G341400 chr3A 81.429 140 9 11 2878 3002 416307146 416307009 8.020000e-17 99.0
16 TraesCS6A01G341400 chr3D 81.053 1710 285 25 760 2456 553233635 553231952 0.000000e+00 1327.0
17 TraesCS6A01G341400 chr3D 82.734 139 10 7 2878 3002 313816935 313816797 1.030000e-20 111.0
18 TraesCS6A01G341400 chr3D 91.803 61 5 0 2942 3002 447584204 447584144 6.250000e-13 86.1
19 TraesCS6A01G341400 chr3D 97.826 46 1 0 2878 2923 73853237 73853192 2.910000e-11 80.5
20 TraesCS6A01G341400 chr3D 100.000 28 0 0 1235 1262 6467695 6467668 6.000000e-03 52.8
21 TraesCS6A01G341400 chr7B 71.711 1064 262 31 1332 2377 130747054 130746012 9.670000e-66 261.0
22 TraesCS6A01G341400 chr7B 87.143 70 6 3 2934 3002 736726874 736726807 3.760000e-10 76.8
23 TraesCS6A01G341400 chr7A 71.711 1064 262 33 1332 2377 167904412 167903370 9.670000e-66 261.0
24 TraesCS6A01G341400 chr5D 94.737 57 3 0 2946 3002 363325706 363325650 4.830000e-14 89.8
25 TraesCS6A01G341400 chr5D 92.727 55 4 0 2949 3003 345970037 345969983 2.910000e-11 80.5
26 TraesCS6A01G341400 chr5D 100.000 30 0 0 2844 2873 70415953 70415924 4.900000e-04 56.5
27 TraesCS6A01G341400 chr4B 89.231 65 7 0 2938 3002 617690946 617690882 8.080000e-12 82.4
28 TraesCS6A01G341400 chr4B 100.000 30 0 0 2844 2873 462218902 462218931 4.900000e-04 56.5
29 TraesCS6A01G341400 chr5A 92.727 55 4 0 2943 2997 558960263 558960317 2.910000e-11 80.5
30 TraesCS6A01G341400 chr2D 86.957 69 6 3 2875 2940 617101060 617101128 1.350000e-09 75.0
31 TraesCS6A01G341400 chr2A 86.957 69 6 3 2875 2940 747272174 747272242 1.350000e-09 75.0
32 TraesCS6A01G341400 chr2A 100.000 31 0 0 2845 2875 31756243 31756213 1.360000e-04 58.4
33 TraesCS6A01G341400 chrUn 92.683 41 1 2 2832 2872 85641925 85641963 1.360000e-04 58.4
34 TraesCS6A01G341400 chr4D 100.000 30 0 0 2844 2873 489181753 489181782 4.900000e-04 56.5
35 TraesCS6A01G341400 chr4D 100.000 30 0 0 2844 2873 489181792 489181821 4.900000e-04 56.5


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 TraesCS6A01G341400 chr6A 574241071 574244582 3511 False 6486.000000 6486 100.000000 1 3512 1 chr6A.!!$F1 3511
1 TraesCS6A01G341400 chr6B 646239412 646242763 3351 False 4649.000000 4649 91.763000 1 3350 1 chr6B.!!$F1 3349
2 TraesCS6A01G341400 chr6D 429009204 429012624 3420 False 2347.500000 3991 90.720000 1 3392 2 chr6D.!!$F2 3391
3 TraesCS6A01G341400 chr6D 429020498 429021444 946 False 313.033333 457 89.406333 2474 3452 3 chr6D.!!$F3 978
4 TraesCS6A01G341400 chr3B 734435598 734437290 1692 True 1382.000000 1382 81.596000 759 2457 1 chr3B.!!$R1 1698
5 TraesCS6A01G341400 chr3A 689500642 689502205 1563 True 1347.000000 1347 82.290000 883 2457 1 chr3A.!!$R2 1574
6 TraesCS6A01G341400 chr3D 553231952 553233635 1683 True 1327.000000 1327 81.053000 760 2456 1 chr3D.!!$R5 1696
7 TraesCS6A01G341400 chr7B 130746012 130747054 1042 True 261.000000 261 71.711000 1332 2377 1 chr7B.!!$R1 1045
8 TraesCS6A01G341400 chr7A 167903370 167904412 1042 True 261.000000 261 71.711000 1332 2377 1 chr7A.!!$R1 1045

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
419 426 0.036483 TTAGCACGAATGAGCAGCCA 60.036 50.000 0.00 0.00 33.73 4.75 F
420 427 0.460811 TAGCACGAATGAGCAGCCAG 60.461 55.000 0.00 0.00 33.73 4.85 F
1080 1121 1.119684 TCCTATCCATGGTGACCGTG 58.880 55.000 16.86 16.86 40.02 4.94 F
1734 1778 1.133598 CGAGCGTTGGTGGTATCTACA 59.866 52.381 0.00 0.00 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 1832 0.247185 CCATGCGGAACAGGCAAAAT 59.753 50.0 0.00 0.0 44.66 1.82 R
1920 1964 0.985490 GCCCCTTGTCATCCTCCTCT 60.985 60.0 0.00 0.0 0.00 3.69 R
2462 2509 0.322456 ACCTGGCATGCGTGTATTGT 60.322 50.0 12.44 0.0 0.00 2.71 R
2991 3118 0.335361 TCTGTCACCTACTCCCTCCC 59.665 60.0 0.00 0.0 0.00 4.30 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
66 67 3.775316 TCCTGTAGGGAACATTCTCTTCC 59.225 47.826 0.00 0.00 41.91 3.46
80 81 7.609056 ACATTCTCTTCCAGAAATGAAATTGG 58.391 34.615 12.01 0.00 44.66 3.16
83 84 5.009436 TCTTCCAGAAATGAAATTGGGGA 57.991 39.130 0.00 0.00 36.10 4.81
85 86 5.245977 TCTTCCAGAAATGAAATTGGGGAAC 59.754 40.000 0.00 0.00 36.37 3.62
157 158 5.833131 ACCATACTACTGCCCCATTAATTTG 59.167 40.000 0.00 0.00 0.00 2.32
170 171 1.555967 TAATTTGGGCAAGGCAGGTC 58.444 50.000 0.00 0.00 0.00 3.85
185 186 0.974010 AGGTCGGGAATTCGCAGGTA 60.974 55.000 20.97 2.14 0.00 3.08
187 188 0.529992 GTCGGGAATTCGCAGGTAGG 60.530 60.000 20.97 5.12 0.00 3.18
218 219 9.554395 TGTGATATAGTTCAGACAAAGAAACAA 57.446 29.630 0.00 0.00 0.00 2.83
290 295 5.094812 CACGTGGATTGGTTGATAACAATG 58.905 41.667 7.95 0.00 37.43 2.82
339 344 1.820519 GTATATGGGATCGCGGTACCA 59.179 52.381 28.95 28.95 37.41 3.25
366 373 3.495100 CCAGCCACATTCTATCCCTACAC 60.495 52.174 0.00 0.00 0.00 2.90
376 383 2.948801 ATCCCTACACCCTCTCCCGC 62.949 65.000 0.00 0.00 0.00 6.13
393 400 2.425773 CGCACGCACTTCAACAGC 60.426 61.111 0.00 0.00 0.00 4.40
395 402 1.283793 GCACGCACTTCAACAGCAT 59.716 52.632 0.00 0.00 0.00 3.79
396 403 1.000233 GCACGCACTTCAACAGCATG 61.000 55.000 0.00 0.00 46.00 4.06
398 405 0.870393 ACGCACTTCAACAGCATGAG 59.130 50.000 0.00 0.00 39.69 2.90
399 406 0.870393 CGCACTTCAACAGCATGAGT 59.130 50.000 0.00 0.00 39.69 3.41
400 407 1.265095 CGCACTTCAACAGCATGAGTT 59.735 47.619 0.00 0.00 39.69 3.01
401 408 2.287188 CGCACTTCAACAGCATGAGTTT 60.287 45.455 0.00 0.00 39.69 2.66
402 409 3.058983 CGCACTTCAACAGCATGAGTTTA 60.059 43.478 0.00 0.00 39.69 2.01
405 412 4.023792 CACTTCAACAGCATGAGTTTAGCA 60.024 41.667 0.00 0.00 39.69 3.49
408 415 2.455674 ACAGCATGAGTTTAGCACGA 57.544 45.000 0.00 0.00 39.69 4.35
410 417 3.338249 ACAGCATGAGTTTAGCACGAAT 58.662 40.909 0.00 0.00 39.69 3.34
412 419 3.371898 CAGCATGAGTTTAGCACGAATGA 59.628 43.478 0.00 0.00 39.69 2.57
413 420 3.620374 AGCATGAGTTTAGCACGAATGAG 59.380 43.478 0.00 0.00 0.00 2.90
414 421 3.786818 GCATGAGTTTAGCACGAATGAGC 60.787 47.826 0.00 0.00 0.00 4.26
415 422 3.038788 TGAGTTTAGCACGAATGAGCA 57.961 42.857 0.00 0.00 33.73 4.26
416 423 2.995939 TGAGTTTAGCACGAATGAGCAG 59.004 45.455 0.00 0.00 33.73 4.24
417 424 1.734465 AGTTTAGCACGAATGAGCAGC 59.266 47.619 0.00 0.00 33.73 5.25
418 425 1.086696 TTTAGCACGAATGAGCAGCC 58.913 50.000 0.00 0.00 33.73 4.85
419 426 0.036483 TTAGCACGAATGAGCAGCCA 60.036 50.000 0.00 0.00 33.73 4.75
420 427 0.460811 TAGCACGAATGAGCAGCCAG 60.461 55.000 0.00 0.00 33.73 4.85
421 428 2.789917 CACGAATGAGCAGCCAGC 59.210 61.111 0.00 0.00 46.19 4.85
443 450 5.895534 AGCCCAAATATGTGAACAAGATCAT 59.104 36.000 0.00 0.00 0.00 2.45
460 467 6.952935 AGATCATCGTGAACAACTTTCTAC 57.047 37.500 0.00 0.00 0.00 2.59
461 468 5.869888 AGATCATCGTGAACAACTTTCTACC 59.130 40.000 0.00 0.00 0.00 3.18
462 469 4.951254 TCATCGTGAACAACTTTCTACCA 58.049 39.130 0.00 0.00 0.00 3.25
535 542 1.302511 TTCTTCAGTGAAGGGCGCC 60.303 57.895 28.33 21.18 39.82 6.53
547 554 4.501285 GGCGCCTAAACCCCCTCC 62.501 72.222 22.15 0.00 0.00 4.30
548 555 3.723922 GCGCCTAAACCCCCTCCA 61.724 66.667 0.00 0.00 0.00 3.86
549 556 2.590092 CGCCTAAACCCCCTCCAG 59.410 66.667 0.00 0.00 0.00 3.86
567 574 2.484062 GCTGGATGCCCGTCAATGG 61.484 63.158 0.00 0.00 35.15 3.16
588 595 5.132502 TGGTGACAAAAGAACATCACTGAT 58.867 37.500 3.49 0.00 41.03 2.90
598 605 3.804786 ACATCACTGATGAGCTCTCAG 57.195 47.619 27.54 27.54 42.09 3.35
620 627 3.634397 ACCCATCAGTGGTGATACAAG 57.366 47.619 4.51 0.00 41.85 3.16
645 652 2.986728 AGAACTAAAAGAAGCCCAGGGA 59.013 45.455 10.89 0.00 0.00 4.20
652 659 3.927481 GAAGCCCAGGGACACCAGC 62.927 68.421 10.89 0.00 40.13 4.85
654 661 4.416738 GCCCAGGGACACCAGCTC 62.417 72.222 10.89 0.00 40.13 4.09
657 664 4.087892 CAGGGACACCAGCTCGGG 62.088 72.222 7.06 0.00 40.22 5.14
691 713 3.511477 TGGTCCTTCTAGCAAGAGTTCT 58.489 45.455 0.00 0.00 31.96 3.01
708 730 8.686418 CAAGAGTTCTCGTTATCAGAAATATCG 58.314 37.037 0.00 0.00 31.60 2.92
723 745 8.090831 TCAGAAATATCGAATATCAGTCAAGGG 58.909 37.037 0.00 0.00 0.00 3.95
724 746 7.332926 CAGAAATATCGAATATCAGTCAAGGGG 59.667 40.741 0.00 0.00 0.00 4.79
799 821 3.517296 TGTCTGTTTGGGCTATTTGGA 57.483 42.857 0.00 0.00 0.00 3.53
868 905 3.620427 TGCTACACCGTGTTAATGGAT 57.380 42.857 9.98 0.00 36.21 3.41
1080 1121 1.119684 TCCTATCCATGGTGACCGTG 58.880 55.000 16.86 16.86 40.02 4.94
1124 1168 4.096003 GGTAGCAAGGCTCGGGCA 62.096 66.667 10.74 0.00 40.44 5.36
1300 1344 1.141665 GTCCCATTTGCCGCATTCC 59.858 57.895 0.00 0.00 0.00 3.01
1311 1355 3.869272 GCATTCCTGGAGTGCGCG 61.869 66.667 25.41 0.00 35.76 6.86
1449 1493 6.476053 GGAAGAAGTACTTAACATTAGAGGCG 59.524 42.308 8.42 0.00 39.13 5.52
1515 1559 5.966503 CGAATTGTTTTCCAAGACAAACGTA 59.033 36.000 12.77 0.00 39.03 3.57
1734 1778 1.133598 CGAGCGTTGGTGGTATCTACA 59.866 52.381 0.00 0.00 0.00 2.74
1788 1832 1.522355 GCGAGCTATGCTTCTGCCA 60.522 57.895 3.25 0.00 39.88 4.92
1866 1910 2.278206 CGACTCCGGCTCATGTCG 60.278 66.667 15.06 15.06 44.41 4.35
2283 2330 9.255029 TCAACTTGGTATGAGCTAGCATATATA 57.745 33.333 18.83 6.80 37.65 0.86
2377 2424 1.965930 GCGGTGTGGAAGTGCATCA 60.966 57.895 0.00 0.00 0.00 3.07
2389 2436 1.151221 TGCATCATTCCATCCCCCG 59.849 57.895 0.00 0.00 0.00 5.73
2394 2441 1.523711 CATTCCATCCCCCGACACG 60.524 63.158 0.00 0.00 0.00 4.49
2400 2447 2.742116 ATCCCCCGACACGAATGGG 61.742 63.158 0.00 0.00 42.92 4.00
2434 2481 1.332195 CATCCTCCGCTATCCAGTGA 58.668 55.000 0.00 0.00 33.92 3.41
2447 2494 2.907892 TCCAGTGAAGATCAAGTCCCT 58.092 47.619 0.00 0.00 0.00 4.20
2457 2504 5.053978 AGATCAAGTCCCTCAAAACAAGT 57.946 39.130 0.00 0.00 0.00 3.16
2461 2508 4.080243 TCAAGTCCCTCAAAACAAGTACCA 60.080 41.667 0.00 0.00 0.00 3.25
2462 2509 4.513406 AGTCCCTCAAAACAAGTACCAA 57.487 40.909 0.00 0.00 0.00 3.67
2472 2519 4.477302 AACAAGTACCAACAATACACGC 57.523 40.909 0.00 0.00 0.00 5.34
2476 2523 2.418628 AGTACCAACAATACACGCATGC 59.581 45.455 7.91 7.91 0.00 4.06
2487 2534 1.303561 ACGCATGCCAGGTCACAAT 60.304 52.632 13.15 0.00 0.00 2.71
2499 2546 5.449177 GCCAGGTCACAATAATAAGCAGTTC 60.449 44.000 0.00 0.00 0.00 3.01
2501 2548 6.150976 CCAGGTCACAATAATAAGCAGTTCAA 59.849 38.462 0.00 0.00 0.00 2.69
2750 2804 7.136772 CACTAATGTGGTTGCTGATATGATTG 58.863 38.462 0.00 0.00 40.33 2.67
2759 2813 4.201657 TGCTGATATGATTGTTGGTCTGG 58.798 43.478 0.00 0.00 0.00 3.86
2842 2940 6.338937 AGGAGGCTTAAAAAGTACTACATCG 58.661 40.000 0.00 0.00 0.00 3.84
2945 3059 3.781846 CACGTTTTAGTGTGTTTGTTCCG 59.218 43.478 0.00 0.00 37.35 4.30
3021 3148 2.114616 AGGTGACAGAGGGATGATCAC 58.885 52.381 0.00 0.00 39.16 3.06
3060 3190 6.322712 AGGCCACATTCAAACTACACTAAAAA 59.677 34.615 5.01 0.00 0.00 1.94
3176 3307 1.004918 GGCTGCTACGAACACCTGT 60.005 57.895 0.00 0.00 0.00 4.00
3340 3471 3.953775 CGTCCTTGCTGGGGGTGT 61.954 66.667 0.00 0.00 36.20 4.16
3342 3473 2.449518 TCCTTGCTGGGGGTGTCA 60.450 61.111 0.00 0.00 36.20 3.58
3416 3547 3.878519 CGTCGACTCGGGCTCCTC 61.879 72.222 14.70 0.00 0.00 3.71
3419 3550 2.835431 CGACTCGGGCTCCTCCAT 60.835 66.667 0.00 0.00 36.21 3.41
3420 3551 2.818132 GACTCGGGCTCCTCCATG 59.182 66.667 0.00 0.00 36.21 3.66
3432 3563 1.680522 CCTCCATGGAGAGTGGGACG 61.681 65.000 38.37 18.03 44.53 4.79
3438 3569 1.296715 GGAGAGTGGGACGTTGCAT 59.703 57.895 0.00 0.00 0.00 3.96
3452 3583 3.726517 GCATGCGGCGTGTTGACT 61.727 61.111 22.12 0.00 0.00 3.41
3453 3584 2.387445 GCATGCGGCGTGTTGACTA 61.387 57.895 22.12 0.00 0.00 2.59
3454 3585 1.419922 CATGCGGCGTGTTGACTAC 59.580 57.895 13.98 0.00 0.00 2.73
3455 3586 1.740296 ATGCGGCGTGTTGACTACC 60.740 57.895 9.37 0.00 0.00 3.18
3456 3587 2.356553 GCGGCGTGTTGACTACCA 60.357 61.111 9.37 0.00 0.00 3.25
3457 3588 2.380410 GCGGCGTGTTGACTACCAG 61.380 63.158 9.37 0.00 0.00 4.00
3458 3589 2.380410 CGGCGTGTTGACTACCAGC 61.380 63.158 0.00 0.00 0.00 4.85
3459 3590 1.004918 GGCGTGTTGACTACCAGCT 60.005 57.895 4.51 0.00 0.00 4.24
3460 3591 0.602905 GGCGTGTTGACTACCAGCTT 60.603 55.000 0.00 0.00 0.00 3.74
3461 3592 0.790814 GCGTGTTGACTACCAGCTTC 59.209 55.000 0.00 0.00 0.00 3.86
3462 3593 1.872237 GCGTGTTGACTACCAGCTTCA 60.872 52.381 0.00 0.00 0.00 3.02
3463 3594 1.792949 CGTGTTGACTACCAGCTTCAC 59.207 52.381 0.00 0.00 0.00 3.18
3464 3595 2.801699 CGTGTTGACTACCAGCTTCACA 60.802 50.000 0.00 0.00 0.00 3.58
3465 3596 2.544267 GTGTTGACTACCAGCTTCACAC 59.456 50.000 0.00 0.00 0.00 3.82
3466 3597 1.792949 GTTGACTACCAGCTTCACACG 59.207 52.381 0.00 0.00 0.00 4.49
3467 3598 1.037493 TGACTACCAGCTTCACACGT 58.963 50.000 0.00 0.00 0.00 4.49
3468 3599 1.411246 TGACTACCAGCTTCACACGTT 59.589 47.619 0.00 0.00 0.00 3.99
3469 3600 1.792949 GACTACCAGCTTCACACGTTG 59.207 52.381 0.00 0.00 0.00 4.10
3470 3601 1.138266 ACTACCAGCTTCACACGTTGT 59.862 47.619 0.00 0.00 0.00 3.32
3471 3602 2.363038 ACTACCAGCTTCACACGTTGTA 59.637 45.455 0.00 0.00 0.00 2.41
3472 3603 1.865865 ACCAGCTTCACACGTTGTAG 58.134 50.000 0.00 0.00 0.00 2.74
3473 3604 1.411246 ACCAGCTTCACACGTTGTAGA 59.589 47.619 7.98 0.13 0.00 2.59
3474 3605 1.792949 CCAGCTTCACACGTTGTAGAC 59.207 52.381 7.98 2.08 0.00 2.59
3475 3606 2.469826 CAGCTTCACACGTTGTAGACA 58.530 47.619 7.98 0.00 0.00 3.41
3476 3607 2.218759 CAGCTTCACACGTTGTAGACAC 59.781 50.000 7.98 0.00 0.00 3.67
3477 3608 1.189446 GCTTCACACGTTGTAGACACG 59.811 52.381 7.98 0.00 0.00 4.49
3478 3609 1.784856 CTTCACACGTTGTAGACACGG 59.215 52.381 0.00 0.00 0.00 4.94
3479 3610 1.023502 TCACACGTTGTAGACACGGA 58.976 50.000 0.00 0.00 0.00 4.69
3480 3611 1.610038 TCACACGTTGTAGACACGGAT 59.390 47.619 0.00 0.00 0.00 4.18
3481 3612 1.719246 CACACGTTGTAGACACGGATG 59.281 52.381 0.00 4.13 0.00 3.51
3482 3613 1.338973 ACACGTTGTAGACACGGATGT 59.661 47.619 0.00 0.00 43.71 3.06
3483 3614 2.223876 ACACGTTGTAGACACGGATGTT 60.224 45.455 0.00 0.00 39.95 2.71
3484 3615 2.407361 CACGTTGTAGACACGGATGTTC 59.593 50.000 0.00 0.00 39.95 3.18
3485 3616 2.295349 ACGTTGTAGACACGGATGTTCT 59.705 45.455 8.68 0.00 39.95 3.01
3486 3617 3.243636 ACGTTGTAGACACGGATGTTCTT 60.244 43.478 8.68 0.00 39.95 2.52
3487 3618 3.364023 CGTTGTAGACACGGATGTTCTTC 59.636 47.826 0.00 0.00 39.95 2.87
3488 3619 4.304110 GTTGTAGACACGGATGTTCTTCA 58.696 43.478 0.00 0.00 39.95 3.02
3489 3620 4.801330 TGTAGACACGGATGTTCTTCAT 57.199 40.909 0.00 0.00 39.95 2.57
3496 3627 2.383170 GATGTTCTTCATCGCGGCA 58.617 52.632 6.13 0.00 42.57 5.69
3497 3628 0.940126 GATGTTCTTCATCGCGGCAT 59.060 50.000 6.13 0.00 42.57 4.40
3498 3629 0.659427 ATGTTCTTCATCGCGGCATG 59.341 50.000 6.13 3.42 29.76 4.06
3499 3630 1.297893 GTTCTTCATCGCGGCATGC 60.298 57.895 9.90 9.90 41.47 4.06
3500 3631 2.472059 TTCTTCATCGCGGCATGCC 61.472 57.895 27.67 27.67 42.08 4.40
3501 3632 3.957535 CTTCATCGCGGCATGCCC 61.958 66.667 30.79 21.30 42.08 5.36
3510 3641 4.256180 GGCATGCCCCCGTCCTAG 62.256 72.222 27.24 0.00 0.00 3.02
3511 3642 4.937431 GCATGCCCCCGTCCTAGC 62.937 72.222 6.36 0.00 0.00 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 4.206477 GGGTTCCCCAATTTCATTTCTG 57.794 45.455 0.00 0.00 44.65 3.02
80 81 4.338012 TCTTTCGAAATTAAGGGGTTCCC 58.662 43.478 11.70 0.00 45.90 3.97
131 132 2.190398 ATGGGGCAGTAGTATGGTGA 57.810 50.000 0.00 0.00 0.00 4.02
159 160 1.657751 GAATTCCCGACCTGCCTTGC 61.658 60.000 0.00 0.00 0.00 4.01
170 171 0.177141 TTCCTACCTGCGAATTCCCG 59.823 55.000 0.00 0.00 0.00 5.14
185 186 9.739276 TTTGTCTGAACTATATCACATTTTCCT 57.261 29.630 0.00 0.00 0.00 3.36
218 219 6.919662 CACTTCAACAAACTAAGCATGTCATT 59.080 34.615 0.00 0.00 0.00 2.57
270 275 8.034215 TGATTTCATTGTTATCAACCAATCCAC 58.966 33.333 9.53 0.00 36.33 4.02
290 295 5.289595 GGGAAGTTCAAACCAACTGATTTC 58.710 41.667 5.01 0.00 36.69 2.17
351 358 3.835395 GGAGAGGGTGTAGGGATAGAATG 59.165 52.174 0.00 0.00 0.00 2.67
376 383 2.425773 GCTGTTGAAGTGCGTGCG 60.426 61.111 0.00 0.00 0.00 5.34
383 390 4.023707 GTGCTAAACTCATGCTGTTGAAGT 60.024 41.667 5.01 0.00 0.00 3.01
385 392 3.058983 CGTGCTAAACTCATGCTGTTGAA 60.059 43.478 5.01 0.00 0.00 2.69
386 393 2.480037 CGTGCTAAACTCATGCTGTTGA 59.520 45.455 5.01 0.00 0.00 3.18
387 394 2.480037 TCGTGCTAAACTCATGCTGTTG 59.520 45.455 5.01 0.00 0.00 3.33
393 400 3.371898 TGCTCATTCGTGCTAAACTCATG 59.628 43.478 0.00 0.00 32.76 3.07
395 402 2.995939 CTGCTCATTCGTGCTAAACTCA 59.004 45.455 0.00 0.00 32.76 3.41
396 403 2.222908 GCTGCTCATTCGTGCTAAACTC 60.223 50.000 0.00 0.00 32.76 3.01
398 405 1.202076 GGCTGCTCATTCGTGCTAAAC 60.202 52.381 0.00 0.00 32.76 2.01
399 406 1.086696 GGCTGCTCATTCGTGCTAAA 58.913 50.000 0.00 0.00 32.76 1.85
400 407 0.036483 TGGCTGCTCATTCGTGCTAA 60.036 50.000 0.00 0.00 32.76 3.09
401 408 0.460811 CTGGCTGCTCATTCGTGCTA 60.461 55.000 0.00 0.00 32.76 3.49
402 409 1.744368 CTGGCTGCTCATTCGTGCT 60.744 57.895 0.00 0.00 32.76 4.40
405 412 2.437359 GGCTGGCTGCTCATTCGT 60.437 61.111 16.14 0.00 42.39 3.85
412 419 0.032813 ACATATTTGGGCTGGCTGCT 60.033 50.000 16.14 0.00 42.39 4.24
413 420 0.103572 CACATATTTGGGCTGGCTGC 59.896 55.000 7.96 7.96 41.94 5.25
414 421 1.766494 TCACATATTTGGGCTGGCTG 58.234 50.000 0.00 0.00 0.00 4.85
415 422 2.102578 GTTCACATATTTGGGCTGGCT 58.897 47.619 0.00 0.00 0.00 4.75
416 423 1.824230 TGTTCACATATTTGGGCTGGC 59.176 47.619 0.00 0.00 0.00 4.85
417 424 3.763360 TCTTGTTCACATATTTGGGCTGG 59.237 43.478 0.00 0.00 0.00 4.85
418 425 5.125900 TGATCTTGTTCACATATTTGGGCTG 59.874 40.000 0.00 0.00 0.00 4.85
419 426 5.263599 TGATCTTGTTCACATATTTGGGCT 58.736 37.500 0.00 0.00 0.00 5.19
420 427 5.581126 TGATCTTGTTCACATATTTGGGC 57.419 39.130 0.00 0.00 0.00 5.36
421 428 6.038603 ACGATGATCTTGTTCACATATTTGGG 59.961 38.462 0.00 0.00 0.00 4.12
422 429 6.908820 CACGATGATCTTGTTCACATATTTGG 59.091 38.462 0.00 0.00 0.00 3.28
443 450 4.513692 CCATTGGTAGAAAGTTGTTCACGA 59.486 41.667 0.00 0.00 0.00 4.35
460 467 3.181487 GCTATTGGCACAGTTACCATTGG 60.181 47.826 0.00 0.00 42.39 3.16
461 468 3.181487 GGCTATTGGCACAGTTACCATTG 60.181 47.826 0.00 0.00 42.39 2.82
462 469 3.023832 GGCTATTGGCACAGTTACCATT 58.976 45.455 0.00 0.00 42.39 3.16
535 542 0.914417 TCCAGCTGGAGGGGGTTTAG 60.914 60.000 32.00 1.23 39.78 1.85
547 554 1.452651 ATTGACGGGCATCCAGCTG 60.453 57.895 6.78 6.78 44.79 4.24
548 555 1.452651 CATTGACGGGCATCCAGCT 60.453 57.895 0.00 0.00 44.79 4.24
549 556 2.484062 CCATTGACGGGCATCCAGC 61.484 63.158 0.00 0.00 44.65 4.85
567 574 6.304356 TCATCAGTGATGTTCTTTTGTCAC 57.696 37.500 28.03 0.00 40.55 3.67
576 583 4.114073 CTGAGAGCTCATCAGTGATGTTC 58.886 47.826 28.03 22.65 40.55 3.18
578 585 2.159071 GCTGAGAGCTCATCAGTGATGT 60.159 50.000 28.03 12.93 44.92 3.06
588 595 0.906282 TGATGGGTGCTGAGAGCTCA 60.906 55.000 17.77 0.00 42.97 4.26
614 621 7.608376 GGGCTTCTTTTAGTTCTTCTCTTGTAT 59.392 37.037 0.00 0.00 0.00 2.29
619 626 5.513962 CCTGGGCTTCTTTTAGTTCTTCTCT 60.514 44.000 0.00 0.00 0.00 3.10
620 627 4.697828 CCTGGGCTTCTTTTAGTTCTTCTC 59.302 45.833 0.00 0.00 0.00 2.87
652 659 3.958147 ATGTGGTTGCGAGCCCGAG 62.958 63.158 0.00 0.00 38.22 4.63
654 661 3.803082 CATGTGGTTGCGAGCCCG 61.803 66.667 0.00 0.00 39.16 6.13
731 753 2.997986 CGTGTAACATGGTACTTGGGAC 59.002 50.000 21.18 9.92 35.74 4.46
732 754 2.633967 ACGTGTAACATGGTACTTGGGA 59.366 45.455 21.18 0.00 35.74 4.37
733 755 3.048337 ACGTGTAACATGGTACTTGGG 57.952 47.619 21.18 10.20 35.74 4.12
741 763 5.815222 TCCATTCTGATAACGTGTAACATGG 59.185 40.000 0.00 0.00 35.74 3.66
799 821 9.832445 ATAGATCACCGAACTAAACATATTGTT 57.168 29.630 0.00 0.00 43.41 2.83
868 905 8.147058 ACCAACTAATTGTGCAAATGAAATGTA 58.853 29.630 0.00 0.00 33.60 2.29
1124 1168 1.109920 CCGACCCAGGATCTCATCGT 61.110 60.000 0.00 0.00 0.00 3.73
1311 1355 0.457853 TGAGTGTAGACGATTGGCGC 60.458 55.000 0.00 0.00 46.04 6.53
1321 1365 1.068748 GCTCCGTTCGTTGAGTGTAGA 60.069 52.381 0.00 0.00 0.00 2.59
1515 1559 5.133941 AGTATGTCGATAGTGTCAGGACAT 58.866 41.667 5.29 12.61 43.97 3.06
1788 1832 0.247185 CCATGCGGAACAGGCAAAAT 59.753 50.000 0.00 0.00 44.66 1.82
1866 1910 1.783434 GGTAAGCGTACGCACAACC 59.217 57.895 38.58 33.64 44.88 3.77
1920 1964 0.985490 GCCCCTTGTCATCCTCCTCT 60.985 60.000 0.00 0.00 0.00 3.69
2377 2424 1.268992 TTCGTGTCGGGGGATGGAAT 61.269 55.000 0.00 0.00 0.00 3.01
2383 2430 3.395702 CCCATTCGTGTCGGGGGA 61.396 66.667 0.00 0.00 41.49 4.81
2389 2436 2.120909 CCCATGGCCCATTCGTGTC 61.121 63.158 6.09 0.00 0.00 3.67
2420 2467 2.666317 TGATCTTCACTGGATAGCGGA 58.334 47.619 0.00 0.00 0.00 5.54
2434 2481 5.449553 ACTTGTTTTGAGGGACTTGATCTT 58.550 37.500 0.00 0.00 41.55 2.40
2447 2494 6.487960 CGTGTATTGTTGGTACTTGTTTTGA 58.512 36.000 0.00 0.00 0.00 2.69
2457 2504 1.740585 GGCATGCGTGTATTGTTGGTA 59.259 47.619 12.44 0.00 0.00 3.25
2461 2508 0.810648 CCTGGCATGCGTGTATTGTT 59.189 50.000 12.44 0.00 0.00 2.83
2462 2509 0.322456 ACCTGGCATGCGTGTATTGT 60.322 50.000 12.44 0.00 0.00 2.71
2472 2519 4.338964 TGCTTATTATTGTGACCTGGCATG 59.661 41.667 0.00 0.00 0.00 4.06
2476 2523 5.647658 TGAACTGCTTATTATTGTGACCTGG 59.352 40.000 0.00 0.00 0.00 4.45
2487 2534 8.445275 TTCAAGTGTCTTTGAACTGCTTATTA 57.555 30.769 0.00 0.00 40.95 0.98
2499 2546 1.676006 AGCCCGTTTCAAGTGTCTTTG 59.324 47.619 0.00 0.00 0.00 2.77
2501 2548 2.876550 GTTAGCCCGTTTCAAGTGTCTT 59.123 45.455 0.00 0.00 0.00 3.01
2750 2804 8.843262 ACTAGTTTATTAAACAACCAGACCAAC 58.157 33.333 18.83 0.00 43.79 3.77
2785 2839 2.106683 GCGTGTGCCCACCACTATC 61.107 63.158 0.00 0.00 44.92 2.08
2873 2974 0.467290 TTGTGAACCAAGGGAGCACC 60.467 55.000 0.00 0.00 40.67 5.01
2876 2977 5.885912 TCTTATATTTGTGAACCAAGGGAGC 59.114 40.000 0.00 0.00 33.75 4.70
2988 3115 1.196012 GTCACCTACTCCCTCCCTTG 58.804 60.000 0.00 0.00 0.00 3.61
2991 3118 0.335361 TCTGTCACCTACTCCCTCCC 59.665 60.000 0.00 0.00 0.00 4.30
3021 3148 7.397221 TGAATGTGGCCTATCTATCCTATTTG 58.603 38.462 3.32 0.00 0.00 2.32
3060 3190 6.585416 TGATATGTCACTTGTGCATATCTGT 58.415 36.000 30.05 15.77 45.55 3.41
3092 3222 5.246307 TCAGCGATCCGATTCTATAGAAGA 58.754 41.667 19.51 12.24 37.48 2.87
3097 3227 4.271291 CGAGATCAGCGATCCGATTCTATA 59.729 45.833 12.81 0.00 39.66 1.31
3099 3229 2.416893 CGAGATCAGCGATCCGATTCTA 59.583 50.000 12.81 0.00 39.66 2.10
3189 3320 1.132554 CAGGCCCTATGGAGATGGCT 61.133 60.000 0.00 0.00 43.50 4.75
3280 3411 4.271016 GGCCCCGGATCCATGGAC 62.271 72.222 18.99 13.04 0.00 4.02
3340 3471 1.913262 ACTGCCTCCGGACATGTGA 60.913 57.895 1.15 0.00 0.00 3.58
3342 3473 1.913262 TCACTGCCTCCGGACATGT 60.913 57.895 0.00 0.00 0.00 3.21
3358 3489 5.163184 TGGTAATAGGTGGTCAAAGTTGTCA 60.163 40.000 0.00 0.00 0.00 3.58
3400 3531 3.519930 GGAGGAGCCCGAGTCGAC 61.520 72.222 15.64 7.70 0.00 4.20
3401 3532 3.360423 ATGGAGGAGCCCGAGTCGA 62.360 63.158 15.64 0.00 34.97 4.20
3403 3534 2.801631 CCATGGAGGAGCCCGAGTC 61.802 68.421 5.56 0.00 41.22 3.36
3416 3547 0.391661 CAACGTCCCACTCTCCATGG 60.392 60.000 4.97 4.97 36.94 3.66
3419 3550 1.480212 ATGCAACGTCCCACTCTCCA 61.480 55.000 0.00 0.00 0.00 3.86
3420 3551 1.021390 CATGCAACGTCCCACTCTCC 61.021 60.000 0.00 0.00 0.00 3.71
3432 3563 3.098958 CAACACGCCGCATGCAAC 61.099 61.111 19.57 7.74 41.33 4.17
3438 3569 2.356553 GGTAGTCAACACGCCGCA 60.357 61.111 0.00 0.00 0.00 5.69
3443 3574 1.792949 GTGAAGCTGGTAGTCAACACG 59.207 52.381 0.00 0.00 0.00 4.49
3452 3583 2.624364 TCTACAACGTGTGAAGCTGGTA 59.376 45.455 0.00 0.00 0.00 3.25
3453 3584 1.411246 TCTACAACGTGTGAAGCTGGT 59.589 47.619 0.00 0.00 0.00 4.00
3454 3585 1.792949 GTCTACAACGTGTGAAGCTGG 59.207 52.381 0.00 0.00 0.00 4.85
3455 3586 2.218759 GTGTCTACAACGTGTGAAGCTG 59.781 50.000 0.00 0.00 0.00 4.24
3456 3587 2.470821 GTGTCTACAACGTGTGAAGCT 58.529 47.619 0.00 0.00 0.00 3.74
3457 3588 1.189446 CGTGTCTACAACGTGTGAAGC 59.811 52.381 0.00 0.00 0.00 3.86
3458 3589 1.784856 CCGTGTCTACAACGTGTGAAG 59.215 52.381 0.00 0.00 0.00 3.02
3459 3590 1.404748 TCCGTGTCTACAACGTGTGAA 59.595 47.619 0.00 0.00 0.00 3.18
3460 3591 1.023502 TCCGTGTCTACAACGTGTGA 58.976 50.000 0.00 0.00 0.00 3.58
3461 3592 1.719246 CATCCGTGTCTACAACGTGTG 59.281 52.381 0.00 0.00 0.00 3.82
3462 3593 1.338973 ACATCCGTGTCTACAACGTGT 59.661 47.619 0.00 0.00 31.41 4.49
3463 3594 2.060326 ACATCCGTGTCTACAACGTG 57.940 50.000 0.00 0.00 31.41 4.49
3464 3595 2.295349 AGAACATCCGTGTCTACAACGT 59.705 45.455 0.00 0.00 37.67 3.99
3465 3596 2.942710 AGAACATCCGTGTCTACAACG 58.057 47.619 0.00 0.00 37.67 4.10
3466 3597 4.304110 TGAAGAACATCCGTGTCTACAAC 58.696 43.478 0.00 0.00 37.67 3.32
3467 3598 4.594123 TGAAGAACATCCGTGTCTACAA 57.406 40.909 0.00 0.00 37.67 2.41
3468 3599 4.744570 GATGAAGAACATCCGTGTCTACA 58.255 43.478 0.00 0.00 46.78 2.74
3479 3610 0.659427 CATGCCGCGATGAAGAACAT 59.341 50.000 8.23 0.00 42.47 2.71
3480 3611 1.980951 GCATGCCGCGATGAAGAACA 61.981 55.000 8.23 0.00 0.00 3.18
3481 3612 1.297893 GCATGCCGCGATGAAGAAC 60.298 57.895 8.23 0.00 0.00 3.01
3482 3613 2.472059 GGCATGCCGCGATGAAGAA 61.472 57.895 23.48 0.00 43.84 2.52
3483 3614 2.896854 GGCATGCCGCGATGAAGA 60.897 61.111 23.48 0.00 43.84 2.87
3484 3615 3.957535 GGGCATGCCGCGATGAAG 61.958 66.667 29.90 0.00 43.84 3.02
3493 3624 4.256180 CTAGGACGGGGGCATGCC 62.256 72.222 29.47 29.47 0.00 4.40
3494 3625 4.937431 GCTAGGACGGGGGCATGC 62.937 72.222 9.90 9.90 0.00 4.06


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

AutoCloner maintained by Alex Coulton.