Multiple sequence alignment - TraesCS6B01G342400

Loading Multiple Alignment...

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 TraesCS6B01G342400 chr6B 100.000 2701 0 0 1 2701 602963291 602960591 0.000000e+00 4988.0
1 TraesCS6B01G342400 chr6B 88.991 109 12 0 1014 1122 502997653 502997545 5.270000e-28 135.0
2 TraesCS6B01G342400 chr6B 86.916 107 14 0 1014 1120 502998500 502998394 1.480000e-23 121.0
3 TraesCS6B01G342400 chr6B 85.981 107 15 0 1014 1120 502999136 502999030 6.870000e-22 115.0
4 TraesCS6B01G342400 chr6B 100.000 44 0 0 2989 3032 602960303 602960260 6.970000e-12 82.4
5 TraesCS6B01G342400 chr6A 94.866 935 35 9 1428 2353 548420263 548419333 0.000000e+00 1448.0
6 TraesCS6B01G342400 chr6A 91.516 554 36 7 576 1122 548421229 548420680 0.000000e+00 752.0
7 TraesCS6B01G342400 chr6A 88.993 427 37 7 7 428 548421733 548421312 1.250000e-143 520.0
8 TraesCS6B01G342400 chr6A 90.426 188 11 5 2395 2580 548419328 548419146 1.090000e-59 241.0
9 TraesCS6B01G342400 chr6A 92.793 111 8 0 444 554 548421328 548421218 8.700000e-36 161.0
10 TraesCS6B01G342400 chr6D 91.974 922 46 13 1428 2344 402135902 402135004 0.000000e+00 1267.0
11 TraesCS6B01G342400 chr6D 90.643 855 41 12 576 1411 402136791 402135957 0.000000e+00 1099.0
12 TraesCS6B01G342400 chr6D 89.720 428 30 8 7 426 402137296 402136875 4.450000e-148 534.0
13 TraesCS6B01G342400 chr6D 90.043 231 15 6 2395 2624 402134986 402134763 2.960000e-75 292.0
14 TraesCS6B01G342400 chr6D 90.991 111 9 1 444 554 402136889 402136780 6.770000e-32 148.0
15 TraesCS6B01G342400 chr6D 97.727 44 1 0 2349 2392 95288746 95288703 3.240000e-10 76.8
16 TraesCS6B01G342400 chr6D 95.238 42 2 0 2630 2671 402134713 402134672 1.950000e-07 67.6
17 TraesCS6B01G342400 chr1A 82.723 191 24 6 934 1122 319323618 319323435 8.700000e-36 161.0
18 TraesCS6B01G342400 chr4A 97.872 47 1 0 2350 2396 473693167 473693213 6.970000e-12 82.4
19 TraesCS6B01G342400 chr2D 97.872 47 1 0 2350 2396 29153269 29153223 6.970000e-12 82.4
20 TraesCS6B01G342400 chr2D 94.000 50 3 0 2347 2396 490677424 490677473 3.240000e-10 76.8
21 TraesCS6B01G342400 chr7D 97.778 45 1 0 2352 2396 452998917 452998961 9.010000e-11 78.7
22 TraesCS6B01G342400 chr7D 95.745 47 2 0 2350 2396 168580862 168580908 3.240000e-10 76.8
23 TraesCS6B01G342400 chr7B 97.778 45 1 0 2352 2396 572400400 572400356 9.010000e-11 78.7
24 TraesCS6B01G342400 chr5D 95.745 47 2 0 2350 2396 539788371 539788417 3.240000e-10 76.8
25 TraesCS6B01G342400 chr3B 94.118 51 2 1 2346 2396 51027098 51027147 3.240000e-10 76.8
26 TraesCS6B01G342400 chrUn 80.645 93 15 3 2216 2307 89793432 89793342 5.420000e-08 69.4


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 TraesCS6B01G342400 chr6B 602960260 602963291 3031 True 2535.200000 4988 100.000000 1 3032 2 chr6B.!!$R2 3031
1 TraesCS6B01G342400 chr6A 548419146 548421733 2587 True 624.400000 1448 91.718800 7 2580 5 chr6A.!!$R1 2573
2 TraesCS6B01G342400 chr6D 402134672 402137296 2624 True 567.933333 1267 91.434833 7 2671 6 chr6D.!!$R2 2664

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
534 545 0.037882 TGCACTCCTCGAAAGCAGAG 60.038 55.0 0.0 0.0 36.44 3.35 F
561 572 0.112606 CTCCCTACTAGATCCCCGCA 59.887 60.0 0.0 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 1922 0.508641 CGGACAGCTTTGAGTTGACG 59.491 55.0 0.0 0.33 30.5 4.35 R
2099 2259 0.667993 AACGCATGGTGAAGTTGGTG 59.332 50.0 0.0 0.00 0.0 4.17 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
26 27 9.941664 CATGACAAATATTTCTATTGACAGGTC 57.058 33.333 0.00 0.02 0.00 3.85
37 38 6.533730 TCTATTGACAGGTCTGTGAACATTT 58.466 36.000 8.49 0.00 45.05 2.32
40 41 7.581213 ATTGACAGGTCTGTGAACATTTTTA 57.419 32.000 8.49 0.00 45.05 1.52
82 85 9.166126 GCGCATATTTTAGGTTTTCTGTAATAC 57.834 33.333 0.30 0.00 0.00 1.89
123 126 0.447801 GCGACCCACTAACAAGCATG 59.552 55.000 0.00 0.00 0.00 4.06
341 348 9.190858 TGTTGCAAGTAAAAATATTCACACATC 57.809 29.630 0.00 0.00 0.00 3.06
345 352 7.489113 GCAAGTAAAAATATTCACACATCTGGG 59.511 37.037 0.00 0.00 0.00 4.45
358 369 6.718912 TCACACATCTGGGAAAAATATGTTCA 59.281 34.615 0.00 0.00 0.00 3.18
359 370 6.808212 CACACATCTGGGAAAAATATGTTCAC 59.192 38.462 0.00 0.00 0.00 3.18
512 523 8.843504 GTGTTCGCACATTAAAAATACATTTG 57.156 30.769 0.00 0.00 46.85 2.32
528 539 0.812014 TTTGCGTGCACTCCTCGAAA 60.812 50.000 16.19 0.00 32.48 3.46
534 545 0.037882 TGCACTCCTCGAAAGCAGAG 60.038 55.000 0.00 0.00 36.44 3.35
556 567 6.987403 AGACAAATTCTCCCTACTAGATCC 57.013 41.667 0.00 0.00 0.00 3.36
557 568 5.841783 AGACAAATTCTCCCTACTAGATCCC 59.158 44.000 0.00 0.00 0.00 3.85
558 569 4.908481 ACAAATTCTCCCTACTAGATCCCC 59.092 45.833 0.00 0.00 0.00 4.81
559 570 2.973983 TTCTCCCTACTAGATCCCCG 57.026 55.000 0.00 0.00 0.00 5.73
560 571 0.404812 TCTCCCTACTAGATCCCCGC 59.595 60.000 0.00 0.00 0.00 6.13
561 572 0.112606 CTCCCTACTAGATCCCCGCA 59.887 60.000 0.00 0.00 0.00 5.69
562 573 0.559205 TCCCTACTAGATCCCCGCAA 59.441 55.000 0.00 0.00 0.00 4.85
563 574 1.062734 TCCCTACTAGATCCCCGCAAA 60.063 52.381 0.00 0.00 0.00 3.68
564 575 1.766496 CCCTACTAGATCCCCGCAAAA 59.234 52.381 0.00 0.00 0.00 2.44
565 576 2.171870 CCCTACTAGATCCCCGCAAAAA 59.828 50.000 0.00 0.00 0.00 1.94
608 619 1.692519 GGTTGTACAGTGAGGACACCT 59.307 52.381 0.00 0.00 46.99 4.00
627 638 5.598830 ACACCTCCGACTAATGAGAATATGT 59.401 40.000 0.00 0.00 0.00 2.29
654 665 2.479730 CGGAGGACACGGTAGATTGAAG 60.480 54.545 0.00 0.00 0.00 3.02
680 691 5.475220 AGACCGATCTATAGTCCAATCACTG 59.525 44.000 0.00 0.00 31.46 3.66
681 692 7.472526 AGACCGATCTATAGTCCAATCACTGG 61.473 46.154 0.00 0.00 39.09 4.00
684 695 6.349445 CCGATCTATAGTCCAATCACTGGTAC 60.349 46.154 0.00 0.00 46.51 3.34
685 696 6.206829 CGATCTATAGTCCAATCACTGGTACA 59.793 42.308 0.00 0.00 46.51 2.90
686 697 7.094162 CGATCTATAGTCCAATCACTGGTACAT 60.094 40.741 0.00 0.00 46.51 2.29
687 698 9.244292 GATCTATAGTCCAATCACTGGTACATA 57.756 37.037 0.00 0.00 46.51 2.29
688 699 8.405418 TCTATAGTCCAATCACTGGTACATAC 57.595 38.462 0.00 0.00 46.51 2.39
689 700 4.755266 AGTCCAATCACTGGTACATACC 57.245 45.455 0.75 0.75 46.51 2.73
690 701 4.362677 AGTCCAATCACTGGTACATACCT 58.637 43.478 9.46 0.00 46.51 3.08
691 702 4.162320 AGTCCAATCACTGGTACATACCTG 59.838 45.833 12.12 12.12 46.51 4.00
846 863 2.557452 CCCTGCACACCCCTCTTATTTT 60.557 50.000 0.00 0.00 0.00 1.82
847 864 2.493278 CCTGCACACCCCTCTTATTTTG 59.507 50.000 0.00 0.00 0.00 2.44
848 865 1.892474 TGCACACCCCTCTTATTTTGC 59.108 47.619 0.00 0.00 0.00 3.68
873 890 2.751806 CCTCTTCCTGAGCCAAACAATC 59.248 50.000 0.00 0.00 41.35 2.67
874 891 2.751806 CTCTTCCTGAGCCAAACAATCC 59.248 50.000 0.00 0.00 35.84 3.01
875 892 2.108075 TCTTCCTGAGCCAAACAATCCA 59.892 45.455 0.00 0.00 0.00 3.41
877 894 1.144708 TCCTGAGCCAAACAATCCACA 59.855 47.619 0.00 0.00 0.00 4.17
986 1004 1.006922 GCTTCAGGTTGCAACAGCC 60.007 57.895 29.55 13.94 34.90 4.85
1008 1026 4.646492 CCAAATTAGGCTACAATGGCTCTT 59.354 41.667 0.00 0.00 42.90 2.85
1154 1206 5.063880 TGTTTCTCCTTTTTGGTAGAGAGC 58.936 41.667 0.00 0.00 36.76 4.09
1263 1326 5.251932 TCCTTGGTCCTTGTTGTTATATCCA 59.748 40.000 0.00 0.00 0.00 3.41
1271 1334 8.148351 GTCCTTGTTGTTATATCCACTAGCATA 58.852 37.037 0.00 0.00 0.00 3.14
1291 1357 7.357471 AGCATATACCAAAAGGAAAGGAGAAT 58.643 34.615 0.00 0.00 0.00 2.40
1292 1358 7.841222 AGCATATACCAAAAGGAAAGGAGAATT 59.159 33.333 0.00 0.00 0.00 2.17
1293 1359 8.478066 GCATATACCAAAAGGAAAGGAGAATTT 58.522 33.333 0.00 0.00 0.00 1.82
1369 1484 2.359214 CTCTGCTCAAGCTATGGTCGTA 59.641 50.000 3.32 0.00 42.66 3.43
1387 1503 7.437748 TGGTCGTATTTGAATGAATGGTTTTT 58.562 30.769 0.00 0.00 0.00 1.94
1417 1533 5.533533 CTCTCTGAGCATCTTTGTCTTTG 57.466 43.478 0.00 0.00 34.92 2.77
1418 1534 4.965814 TCTCTGAGCATCTTTGTCTTTGT 58.034 39.130 0.00 0.00 34.92 2.83
1419 1535 4.993584 TCTCTGAGCATCTTTGTCTTTGTC 59.006 41.667 0.00 0.00 34.92 3.18
1420 1536 4.965814 TCTGAGCATCTTTGTCTTTGTCT 58.034 39.130 0.00 0.00 34.92 3.41
1421 1537 5.371526 TCTGAGCATCTTTGTCTTTGTCTT 58.628 37.500 0.00 0.00 34.92 3.01
1422 1538 5.237996 TCTGAGCATCTTTGTCTTTGTCTTG 59.762 40.000 0.00 0.00 34.92 3.02
1423 1539 4.883585 TGAGCATCTTTGTCTTTGTCTTGT 59.116 37.500 0.00 0.00 34.92 3.16
1425 1541 6.542005 TGAGCATCTTTGTCTTTGTCTTGTTA 59.458 34.615 0.00 0.00 34.92 2.41
1426 1542 7.066887 TGAGCATCTTTGTCTTTGTCTTGTTAA 59.933 33.333 0.00 0.00 34.92 2.01
1575 1729 1.525077 GTGAACCAACGGCACTCCA 60.525 57.895 0.00 0.00 0.00 3.86
1580 1734 0.398696 ACCAACGGCACTCCATACAA 59.601 50.000 0.00 0.00 0.00 2.41
1625 1779 3.149981 TGCGTCAATAACAATTGGTGGA 58.850 40.909 6.16 0.00 32.65 4.02
1811 1965 4.690719 CCGGCCTGGTACGCACAA 62.691 66.667 0.00 0.00 0.00 3.33
1817 1971 0.041663 CCTGGTACGCACAACAAACG 60.042 55.000 0.00 0.00 0.00 3.60
1819 1973 1.352404 GGTACGCACAACAAACGCA 59.648 52.632 0.00 0.00 0.00 5.24
1856 2013 0.872388 AAATCCTTTCACGTCCGTGC 59.128 50.000 14.64 0.00 45.04 5.34
1859 2016 1.594293 CCTTTCACGTCCGTGCAGT 60.594 57.895 14.64 0.00 45.04 4.40
1879 2036 2.030946 GTGATCCTAATGAACTGCGTGC 59.969 50.000 0.00 0.00 0.00 5.34
1882 2039 0.097674 CCTAATGAACTGCGTGCTGC 59.902 55.000 0.00 0.00 46.70 5.25
1929 2087 2.191375 TCGAGCCCGTACGAGGAT 59.809 61.111 18.76 15.09 37.05 3.24
1953 2111 1.634973 TGGATGATCAAGGTGAAGCCA 59.365 47.619 0.00 0.00 40.61 4.75
2347 2513 3.636300 AGCTTGTGCCAAGATTGTTGTTA 59.364 39.130 16.28 0.00 40.80 2.41
2348 2514 3.735746 GCTTGTGCCAAGATTGTTGTTAC 59.264 43.478 16.28 0.00 0.00 2.50
2349 2515 3.617540 TGTGCCAAGATTGTTGTTACG 57.382 42.857 0.00 0.00 0.00 3.18
2350 2516 2.946329 TGTGCCAAGATTGTTGTTACGT 59.054 40.909 0.00 0.00 0.00 3.57
2352 2518 4.024725 TGTGCCAAGATTGTTGTTACGTAC 60.025 41.667 0.00 0.00 0.00 3.67
2353 2519 4.212636 GTGCCAAGATTGTTGTTACGTACT 59.787 41.667 0.00 0.00 0.00 2.73
2355 2521 4.142966 GCCAAGATTGTTGTTACGTACTCC 60.143 45.833 0.00 0.00 0.00 3.85
2356 2522 4.390909 CCAAGATTGTTGTTACGTACTCCC 59.609 45.833 0.00 0.00 0.00 4.30
2357 2523 5.235516 CAAGATTGTTGTTACGTACTCCCT 58.764 41.667 0.00 0.00 0.00 4.20
2358 2524 5.069501 AGATTGTTGTTACGTACTCCCTC 57.930 43.478 0.00 0.00 0.00 4.30
2359 2525 3.665745 TTGTTGTTACGTACTCCCTCC 57.334 47.619 0.00 0.00 0.00 4.30
2360 2526 1.541147 TGTTGTTACGTACTCCCTCCG 59.459 52.381 0.00 0.00 0.00 4.63
2361 2527 1.541588 GTTGTTACGTACTCCCTCCGT 59.458 52.381 0.00 0.00 38.53 4.69
2362 2528 2.747446 GTTGTTACGTACTCCCTCCGTA 59.253 50.000 0.00 0.00 36.12 4.02
2363 2529 3.066291 TGTTACGTACTCCCTCCGTAA 57.934 47.619 0.00 0.00 42.70 3.18
2364 2530 3.417101 TGTTACGTACTCCCTCCGTAAA 58.583 45.455 0.00 0.00 45.29 2.01
2365 2531 3.440173 TGTTACGTACTCCCTCCGTAAAG 59.560 47.826 0.00 0.00 45.29 1.85
2366 2532 2.496899 ACGTACTCCCTCCGTAAAGA 57.503 50.000 0.00 0.00 32.22 2.52
2367 2533 2.795329 ACGTACTCCCTCCGTAAAGAA 58.205 47.619 0.00 0.00 32.22 2.52
2368 2534 3.157087 ACGTACTCCCTCCGTAAAGAAA 58.843 45.455 0.00 0.00 32.22 2.52
2369 2535 3.766051 ACGTACTCCCTCCGTAAAGAAAT 59.234 43.478 0.00 0.00 32.22 2.17
2370 2536 4.949856 ACGTACTCCCTCCGTAAAGAAATA 59.050 41.667 0.00 0.00 32.22 1.40
2371 2537 5.595952 ACGTACTCCCTCCGTAAAGAAATAT 59.404 40.000 0.00 0.00 32.22 1.28
2372 2538 6.772716 ACGTACTCCCTCCGTAAAGAAATATA 59.227 38.462 0.00 0.00 32.22 0.86
2373 2539 7.285401 ACGTACTCCCTCCGTAAAGAAATATAA 59.715 37.037 0.00 0.00 32.22 0.98
2374 2540 8.137437 CGTACTCCCTCCGTAAAGAAATATAAA 58.863 37.037 0.00 0.00 0.00 1.40
2375 2541 9.822185 GTACTCCCTCCGTAAAGAAATATAAAA 57.178 33.333 0.00 0.00 0.00 1.52
2376 2542 8.959705 ACTCCCTCCGTAAAGAAATATAAAAG 57.040 34.615 0.00 0.00 0.00 2.27
2377 2543 8.546322 ACTCCCTCCGTAAAGAAATATAAAAGT 58.454 33.333 0.00 0.00 0.00 2.66
2378 2544 8.726870 TCCCTCCGTAAAGAAATATAAAAGTG 57.273 34.615 0.00 0.00 0.00 3.16
2379 2545 8.323567 TCCCTCCGTAAAGAAATATAAAAGTGT 58.676 33.333 0.00 0.00 0.00 3.55
2380 2546 8.953313 CCCTCCGTAAAGAAATATAAAAGTGTT 58.047 33.333 0.00 0.00 0.00 3.32
2405 2571 4.773149 AGACCACTAAAGTACCTCCTCTTG 59.227 45.833 0.00 0.00 0.00 3.02
2432 2598 9.080915 CCGTATATCATCTGTCACATCATAAAG 57.919 37.037 0.00 0.00 0.00 1.85
2479 2646 5.674525 TGACAATCATTGGAGATGTCCTAC 58.325 41.667 10.72 0.00 44.30 3.18
2511 2678 8.546597 AAACACAAATTATTTTAGCCATGGAC 57.453 30.769 18.40 7.03 0.00 4.02
2561 2729 8.782137 ATGGGTATATTAGTTTGAGCCAATTT 57.218 30.769 0.00 0.00 40.77 1.82
2562 2730 8.602472 TGGGTATATTAGTTTGAGCCAATTTT 57.398 30.769 0.00 0.00 34.86 1.82
2609 2777 2.203582 GGTGAAAACCCCGGCCTT 60.204 61.111 0.00 0.00 0.00 4.35
2624 2792 2.358582 CGGCCTTTGCATCATTGTGATA 59.641 45.455 0.00 0.00 34.28 2.15
2626 2794 3.365832 GCCTTTGCATCATTGTGATACG 58.634 45.455 0.00 0.00 34.28 3.06
2629 2797 4.498513 CCTTTGCATCATTGTGATACGCAT 60.499 41.667 5.98 0.00 36.24 4.73
2630 2798 3.883631 TGCATCATTGTGATACGCATC 57.116 42.857 2.07 0.00 34.28 3.91
2631 2799 3.469739 TGCATCATTGTGATACGCATCT 58.530 40.909 0.00 0.00 34.28 2.90
2632 2800 3.249080 TGCATCATTGTGATACGCATCTG 59.751 43.478 0.00 0.00 34.28 2.90
2633 2801 3.364664 GCATCATTGTGATACGCATCTGG 60.365 47.826 0.00 0.00 34.28 3.86
2634 2802 2.212652 TCATTGTGATACGCATCTGGC 58.787 47.619 0.00 0.00 39.90 4.85
2635 2803 1.265095 CATTGTGATACGCATCTGGCC 59.735 52.381 0.00 0.00 40.31 5.36
2671 2883 5.409826 GCTGATTTTCTCTTTTCTCGAAGGA 59.590 40.000 0.00 0.00 0.00 3.36
2672 2884 6.093357 GCTGATTTTCTCTTTTCTCGAAGGAT 59.907 38.462 0.00 0.00 0.00 3.24
2673 2885 7.361628 GCTGATTTTCTCTTTTCTCGAAGGATT 60.362 37.037 0.00 0.00 0.00 3.01
2674 2886 7.810658 TGATTTTCTCTTTTCTCGAAGGATTG 58.189 34.615 0.00 0.00 0.00 2.67
2675 2887 7.445402 TGATTTTCTCTTTTCTCGAAGGATTGT 59.555 33.333 0.00 0.00 0.00 2.71
2676 2888 8.848474 ATTTTCTCTTTTCTCGAAGGATTGTA 57.152 30.769 0.00 0.00 0.00 2.41
2677 2889 7.891183 TTTCTCTTTTCTCGAAGGATTGTAG 57.109 36.000 0.00 0.00 0.00 2.74
2678 2890 6.835819 TCTCTTTTCTCGAAGGATTGTAGA 57.164 37.500 0.00 0.00 0.00 2.59
2679 2891 7.411486 TCTCTTTTCTCGAAGGATTGTAGAT 57.589 36.000 0.00 0.00 0.00 1.98
2680 2892 7.261325 TCTCTTTTCTCGAAGGATTGTAGATG 58.739 38.462 0.00 0.00 0.00 2.90
2681 2893 5.812642 TCTTTTCTCGAAGGATTGTAGATGC 59.187 40.000 0.00 0.00 0.00 3.91
2682 2894 4.736126 TTCTCGAAGGATTGTAGATGCA 57.264 40.909 0.00 0.00 0.00 3.96
2683 2895 4.736126 TCTCGAAGGATTGTAGATGCAA 57.264 40.909 0.00 0.00 0.00 4.08
2684 2896 5.282055 TCTCGAAGGATTGTAGATGCAAT 57.718 39.130 0.00 0.00 41.28 3.56
2694 2906 3.654020 GATGCAATCGCGCCTCCC 61.654 66.667 0.00 0.00 42.97 4.30
3009 3221 4.764050 AGATGTAGAAGAGAGTCGAGGA 57.236 45.455 0.00 0.00 0.00 3.71
3010 3222 4.448210 AGATGTAGAAGAGAGTCGAGGAC 58.552 47.826 0.00 0.00 0.00 3.85
3011 3223 2.619147 TGTAGAAGAGAGTCGAGGACG 58.381 52.381 0.00 0.00 37.67 4.79
3012 3224 2.028294 TGTAGAAGAGAGTCGAGGACGT 60.028 50.000 0.00 0.00 37.67 4.34
3013 3225 2.188062 AGAAGAGAGTCGAGGACGTT 57.812 50.000 0.00 0.00 37.67 3.99
3014 3226 2.506444 AGAAGAGAGTCGAGGACGTTT 58.494 47.619 0.00 0.00 37.67 3.60
3015 3227 2.885894 AGAAGAGAGTCGAGGACGTTTT 59.114 45.455 0.00 0.00 37.67 2.43
3016 3228 3.318557 AGAAGAGAGTCGAGGACGTTTTT 59.681 43.478 0.00 0.00 37.67 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.941664 GACCTGTCAATAGAAATATTTGTCATG 57.058 33.333 5.17 4.88 0.00 3.07
1 2 9.911788 AGACCTGTCAATAGAAATATTTGTCAT 57.088 29.630 5.17 0.00 0.00 3.06
2 3 9.166173 CAGACCTGTCAATAGAAATATTTGTCA 57.834 33.333 5.17 0.00 0.00 3.58
3 4 9.167311 ACAGACCTGTCAATAGAAATATTTGTC 57.833 33.333 5.17 3.00 40.24 3.18
4 5 8.950210 CACAGACCTGTCAATAGAAATATTTGT 58.050 33.333 5.17 4.02 42.83 2.83
5 6 9.166173 TCACAGACCTGTCAATAGAAATATTTG 57.834 33.333 5.17 0.00 42.83 2.32
26 27 6.370593 ACATAGTGCGTAAAAATGTTCACAG 58.629 36.000 0.00 0.00 0.00 3.66
82 85 8.521059 GTCGCACTTGTTAAAAGAGTTTTAAAG 58.479 33.333 6.23 4.76 44.13 1.85
100 103 1.878953 CTTGTTAGTGGGTCGCACTT 58.121 50.000 25.58 11.48 34.38 3.16
281 286 5.936054 TGTTTGGCACAGAAAACATTTTTG 58.064 33.333 0.00 0.00 40.41 2.44
341 348 8.980143 AAAATACGTGAACATATTTTTCCCAG 57.020 30.769 0.00 0.00 37.60 4.45
431 442 5.799213 ACATGAATATTTTCCCCGCAAAAA 58.201 33.333 0.00 0.00 0.00 1.94
432 443 5.413309 ACATGAATATTTTCCCCGCAAAA 57.587 34.783 0.00 0.00 0.00 2.44
433 444 6.549364 AGATACATGAATATTTTCCCCGCAAA 59.451 34.615 0.00 0.00 0.00 3.68
434 445 6.068010 AGATACATGAATATTTTCCCCGCAA 58.932 36.000 0.00 0.00 0.00 4.85
435 446 5.630121 AGATACATGAATATTTTCCCCGCA 58.370 37.500 0.00 0.00 0.00 5.69
436 447 5.163854 CGAGATACATGAATATTTTCCCCGC 60.164 44.000 0.00 0.00 0.00 6.13
437 448 6.163476 TCGAGATACATGAATATTTTCCCCG 58.837 40.000 0.00 0.00 0.00 5.73
438 449 7.979444 TTCGAGATACATGAATATTTTCCCC 57.021 36.000 0.00 0.00 0.00 4.81
507 518 1.133253 CGAGGAGTGCACGCAAATG 59.867 57.895 22.36 5.04 0.00 2.32
512 523 3.016474 GCTTTCGAGGAGTGCACGC 62.016 63.158 12.67 12.67 0.00 5.34
534 545 5.012251 GGGGATCTAGTAGGGAGAATTTGTC 59.988 48.000 0.00 0.00 0.00 3.18
545 556 3.553828 TTTTTGCGGGGATCTAGTAGG 57.446 47.619 0.00 0.00 0.00 3.18
578 589 4.597004 TCACTGTACAACCCTCTAGTAGG 58.403 47.826 0.00 0.00 46.09 3.18
608 619 5.278315 CGTGGACATATTCTCATTAGTCGGA 60.278 44.000 0.00 0.00 0.00 4.55
610 621 4.383052 GCGTGGACATATTCTCATTAGTCG 59.617 45.833 0.00 0.00 0.00 4.18
654 665 6.655848 AGTGATTGGACTATAGATCGGTCTAC 59.344 42.308 7.76 0.00 39.66 2.59
680 691 3.832615 AAATCGTCCCAGGTATGTACC 57.167 47.619 0.81 0.81 46.82 3.34
681 692 4.761975 TGAAAATCGTCCCAGGTATGTAC 58.238 43.478 0.00 0.00 0.00 2.90
684 695 4.137116 TCTGAAAATCGTCCCAGGTATG 57.863 45.455 0.00 0.00 0.00 2.39
685 696 4.656112 AGATCTGAAAATCGTCCCAGGTAT 59.344 41.667 0.00 0.00 0.00 2.73
686 697 4.030913 AGATCTGAAAATCGTCCCAGGTA 58.969 43.478 0.00 0.00 0.00 3.08
687 698 2.840651 AGATCTGAAAATCGTCCCAGGT 59.159 45.455 0.00 0.00 0.00 4.00
688 699 3.118629 TGAGATCTGAAAATCGTCCCAGG 60.119 47.826 0.00 0.00 0.00 4.45
689 700 4.128925 TGAGATCTGAAAATCGTCCCAG 57.871 45.455 0.00 0.00 0.00 4.45
690 701 4.551702 TTGAGATCTGAAAATCGTCCCA 57.448 40.909 0.00 0.00 0.00 4.37
691 702 6.442513 AATTTGAGATCTGAAAATCGTCCC 57.557 37.500 11.48 0.00 0.00 4.46
727 743 5.652014 AGCTTGGTCCAAATTCGATTGATTA 59.348 36.000 5.64 0.00 31.84 1.75
728 744 4.463891 AGCTTGGTCCAAATTCGATTGATT 59.536 37.500 5.64 0.00 31.84 2.57
873 890 2.135189 TGGGAGGATAGGGAAATGTGG 58.865 52.381 0.00 0.00 0.00 4.17
874 891 2.485479 CGTGGGAGGATAGGGAAATGTG 60.485 54.545 0.00 0.00 0.00 3.21
875 892 1.768870 CGTGGGAGGATAGGGAAATGT 59.231 52.381 0.00 0.00 0.00 2.71
877 894 1.435256 CCGTGGGAGGATAGGGAAAT 58.565 55.000 0.00 0.00 0.00 2.17
986 1004 5.841957 AAGAGCCATTGTAGCCTAATTTG 57.158 39.130 0.00 0.00 0.00 2.32
1008 1026 2.189191 CTGAGCTTGCCCACAGCCTA 62.189 60.000 0.00 0.00 42.71 3.93
1080 1098 7.004691 TGGAGAAGTATCTGGAGATCGAATAA 58.995 38.462 0.00 0.00 35.54 1.40
1263 1326 7.127339 TCTCCTTTCCTTTTGGTATATGCTAGT 59.873 37.037 0.00 0.00 41.38 2.57
1309 1375 8.618240 TTCTGAAAACAGTATCCCTCCTATTA 57.382 34.615 0.00 0.00 0.00 0.98
1575 1729 5.829391 TGACATATGGAAAGCATGCTTGTAT 59.171 36.000 32.54 25.50 36.26 2.29
1580 1734 4.280174 GGATTGACATATGGAAAGCATGCT 59.720 41.667 16.30 16.30 0.00 3.79
1625 1779 3.882326 CCCGAGATGGCCCTGCAT 61.882 66.667 0.00 0.00 35.87 3.96
1672 1826 3.241530 TGGCTCACCTTCGTGCCT 61.242 61.111 0.00 0.00 44.21 4.75
1768 1922 0.508641 CGGACAGCTTTGAGTTGACG 59.491 55.000 0.00 0.33 30.50 4.35
1811 1965 3.118454 CGGAGGCGATGCGTTTGT 61.118 61.111 0.00 0.00 38.06 2.83
1817 1971 3.420214 TAACCGACGGAGGCGATGC 62.420 63.158 23.38 0.00 33.69 3.91
1819 1973 1.033746 TTCTAACCGACGGAGGCGAT 61.034 55.000 23.38 0.00 33.69 4.58
1856 2013 3.308053 CACGCAGTTCATTAGGATCACTG 59.692 47.826 0.00 0.00 41.61 3.66
1859 2016 2.093500 AGCACGCAGTTCATTAGGATCA 60.093 45.455 0.00 0.00 41.61 2.92
1929 2087 1.667595 TCACCTTGATCATCCACCCA 58.332 50.000 0.00 0.00 0.00 4.51
2099 2259 0.667993 AACGCATGGTGAAGTTGGTG 59.332 50.000 0.00 0.00 0.00 4.17
2104 2264 1.873591 GAACTGAACGCATGGTGAAGT 59.126 47.619 0.00 0.00 0.00 3.01
2307 2471 7.549488 GCACAAGCTCTAAGGTAAAATAAGAGA 59.451 37.037 1.97 0.00 36.60 3.10
2310 2474 6.374333 TGGCACAAGCTCTAAGGTAAAATAAG 59.626 38.462 0.00 0.00 41.70 1.73
2313 2477 4.662278 TGGCACAAGCTCTAAGGTAAAAT 58.338 39.130 0.00 0.00 41.70 1.82
2347 2513 2.496899 TCTTTACGGAGGGAGTACGT 57.503 50.000 0.00 0.00 43.88 3.57
2348 2514 3.855689 TTTCTTTACGGAGGGAGTACG 57.144 47.619 0.00 0.00 0.00 3.67
2349 2515 9.822185 TTTTATATTTCTTTACGGAGGGAGTAC 57.178 33.333 0.00 0.00 0.00 2.73
2352 2518 8.827677 CACTTTTATATTTCTTTACGGAGGGAG 58.172 37.037 0.00 0.00 0.00 4.30
2353 2519 8.323567 ACACTTTTATATTTCTTTACGGAGGGA 58.676 33.333 0.00 0.00 0.00 4.20
2371 2537 9.546428 GGTACTTTAGTGGTCTAAACACTTTTA 57.454 33.333 2.54 0.00 46.38 1.52
2372 2538 8.270030 AGGTACTTTAGTGGTCTAAACACTTTT 58.730 33.333 2.54 0.00 40.82 2.27
2373 2539 7.799081 AGGTACTTTAGTGGTCTAAACACTTT 58.201 34.615 2.54 0.00 40.82 2.66
2374 2540 7.370905 AGGTACTTTAGTGGTCTAAACACTT 57.629 36.000 2.54 0.00 40.82 3.16
2375 2541 6.014755 GGAGGTACTTTAGTGGTCTAAACACT 60.015 42.308 2.82 2.82 46.02 3.55
2376 2542 6.014755 AGGAGGTACTTTAGTGGTCTAAACAC 60.015 42.308 0.00 0.00 41.55 3.32
2377 2543 6.080009 AGGAGGTACTTTAGTGGTCTAAACA 58.920 40.000 0.00 0.00 41.55 2.83
2378 2544 6.436847 AGAGGAGGTACTTTAGTGGTCTAAAC 59.563 42.308 0.00 0.00 41.55 2.01
2379 2545 6.559429 AGAGGAGGTACTTTAGTGGTCTAAA 58.441 40.000 0.00 0.00 41.55 1.85
2380 2546 6.150034 AGAGGAGGTACTTTAGTGGTCTAA 57.850 41.667 0.00 0.00 41.55 2.10
2381 2547 5.793034 AGAGGAGGTACTTTAGTGGTCTA 57.207 43.478 0.00 0.00 41.55 2.59
2382 2548 4.678538 AGAGGAGGTACTTTAGTGGTCT 57.321 45.455 0.00 0.00 41.55 3.85
2383 2549 4.621038 GCAAGAGGAGGTACTTTAGTGGTC 60.621 50.000 0.00 0.00 41.55 4.02
2384 2550 3.261137 GCAAGAGGAGGTACTTTAGTGGT 59.739 47.826 0.00 0.00 41.55 4.16
2385 2551 3.369576 GGCAAGAGGAGGTACTTTAGTGG 60.370 52.174 0.00 0.00 41.55 4.00
2386 2552 3.676324 CGGCAAGAGGAGGTACTTTAGTG 60.676 52.174 0.00 0.00 41.55 2.74
2387 2553 2.496470 CGGCAAGAGGAGGTACTTTAGT 59.504 50.000 0.00 0.00 41.55 2.24
2388 2554 2.496470 ACGGCAAGAGGAGGTACTTTAG 59.504 50.000 0.00 0.00 41.55 1.85
2389 2555 2.532843 ACGGCAAGAGGAGGTACTTTA 58.467 47.619 0.00 0.00 41.55 1.85
2390 2556 1.349067 ACGGCAAGAGGAGGTACTTT 58.651 50.000 0.00 0.00 41.55 2.66
2391 2557 2.226962 TACGGCAAGAGGAGGTACTT 57.773 50.000 0.00 0.00 41.55 2.24
2393 2559 3.825014 TGATATACGGCAAGAGGAGGTAC 59.175 47.826 0.00 0.00 0.00 3.34
2405 2571 4.809673 TGATGTGACAGATGATATACGGC 58.190 43.478 0.00 0.00 0.00 5.68
2434 2600 9.308000 TGTCAATTTTGTCACCTAGGATTTAAT 57.692 29.630 17.98 4.46 0.00 1.40
2435 2601 8.698973 TGTCAATTTTGTCACCTAGGATTTAA 57.301 30.769 17.98 2.46 0.00 1.52
2436 2602 8.698973 TTGTCAATTTTGTCACCTAGGATTTA 57.301 30.769 17.98 0.00 0.00 1.40
2583 2751 3.224269 CGGGGTTTTCACCTCCTTTAAA 58.776 45.455 0.00 0.00 41.26 1.52
2593 2761 1.365999 CAAAGGCCGGGGTTTTCAC 59.634 57.895 2.18 0.00 0.00 3.18
2595 2763 1.826340 ATGCAAAGGCCGGGGTTTTC 61.826 55.000 2.18 0.00 40.13 2.29
2599 2767 2.803593 AATGATGCAAAGGCCGGGGT 62.804 55.000 2.18 0.00 40.13 4.95
2609 2777 3.878699 AGATGCGTATCACAATGATGCAA 59.121 39.130 16.11 0.00 38.64 4.08
2629 2797 1.680522 GCTTCTCCATCTCGGCCAGA 61.681 60.000 2.24 5.36 34.78 3.86
2630 2798 1.227497 GCTTCTCCATCTCGGCCAG 60.227 63.158 2.24 0.00 33.14 4.85
2631 2799 1.687146 AGCTTCTCCATCTCGGCCA 60.687 57.895 2.24 0.00 33.14 5.36
2632 2800 1.227497 CAGCTTCTCCATCTCGGCC 60.227 63.158 0.00 0.00 33.14 6.13
2633 2801 0.392336 ATCAGCTTCTCCATCTCGGC 59.608 55.000 0.00 0.00 33.14 5.54
2634 2802 2.906691 AATCAGCTTCTCCATCTCGG 57.093 50.000 0.00 0.00 0.00 4.63
2635 2803 4.440880 AGAAAATCAGCTTCTCCATCTCG 58.559 43.478 0.00 0.00 0.00 4.04
2671 2883 0.588252 GGCGCGATTGCATCTACAAT 59.412 50.000 12.10 0.00 42.88 2.71
2672 2884 0.461870 AGGCGCGATTGCATCTACAA 60.462 50.000 12.10 0.00 42.97 2.41
2673 2885 0.875908 GAGGCGCGATTGCATCTACA 60.876 55.000 12.10 0.00 42.10 2.74
2674 2886 1.560860 GGAGGCGCGATTGCATCTAC 61.561 60.000 12.10 0.00 44.59 2.59
2675 2887 1.300931 GGAGGCGCGATTGCATCTA 60.301 57.895 12.10 0.00 44.59 1.98
2676 2888 2.590007 GGAGGCGCGATTGCATCT 60.590 61.111 12.10 1.03 44.59 2.90
2677 2889 3.654020 GGGAGGCGCGATTGCATC 61.654 66.667 12.10 0.00 44.47 3.91
2988 3200 4.448210 GTCCTCGACTCTCTTCTACATCT 58.552 47.826 0.00 0.00 0.00 2.90
2989 3201 3.246699 CGTCCTCGACTCTCTTCTACATC 59.753 52.174 0.00 0.00 39.71 3.06
2990 3202 3.199677 CGTCCTCGACTCTCTTCTACAT 58.800 50.000 0.00 0.00 39.71 2.29
2991 3203 2.028294 ACGTCCTCGACTCTCTTCTACA 60.028 50.000 0.00 0.00 40.62 2.74
2992 3204 2.620242 ACGTCCTCGACTCTCTTCTAC 58.380 52.381 0.00 0.00 40.62 2.59
2993 3205 3.331478 AACGTCCTCGACTCTCTTCTA 57.669 47.619 0.00 0.00 40.62 2.10
2994 3206 2.188062 AACGTCCTCGACTCTCTTCT 57.812 50.000 0.00 0.00 40.62 2.85
2995 3207 2.993449 AAACGTCCTCGACTCTCTTC 57.007 50.000 0.00 0.00 40.62 2.87
2996 3208 3.729862 AAAAACGTCCTCGACTCTCTT 57.270 42.857 0.00 0.00 40.62 2.85


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

AutoCloner maintained by Alex Coulton.