Multiple sequence alignment - TraesCS3A01G297500

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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 TraesCS3A01G297500 chr3A 100.000 3594 0 0 1 3594 532326709 532323116 0.000000e+00 6637
1 TraesCS3A01G297500 chr3A 100.000 3072 0 0 3937 7008 532322773 532319702 0.000000e+00 5674
2 TraesCS3A01G297500 chr3A 87.959 490 33 10 1 471 12459091 12459573 7.940000e-154 555
3 TraesCS3A01G297500 chr3A 89.474 266 27 1 502 767 12459572 12459836 1.130000e-87 335
4 TraesCS3A01G297500 chr3D 94.844 2851 109 18 768 3594 418776554 418779390 0.000000e+00 4416
5 TraesCS3A01G297500 chr3D 96.077 2014 47 14 4354 6356 418780670 418782662 0.000000e+00 3253
6 TraesCS3A01G297500 chr3D 96.954 591 18 0 6418 7008 418782660 418783250 0.000000e+00 992
7 TraesCS3A01G297500 chr3D 95.540 426 10 5 3937 4362 418779437 418779853 0.000000e+00 673
8 TraesCS3A01G297500 chr3B 93.080 2818 146 24 768 3565 545195471 545198259 0.000000e+00 4078
9 TraesCS3A01G297500 chr3B 91.011 2236 111 27 4810 7008 545200370 545202552 0.000000e+00 2933
10 TraesCS3A01G297500 chr3B 95.000 340 10 2 4483 4815 545198732 545199071 1.730000e-145 527
11 TraesCS3A01G297500 chr3B 89.474 399 34 6 3957 4349 545198278 545198674 1.360000e-136 497
12 TraesCS3A01G297500 chr3B 86.768 461 37 9 1 445 508524524 508524976 6.320000e-135 492
13 TraesCS3A01G297500 chr7A 96.610 767 25 1 1 766 645909639 645910405 0.000000e+00 1271
14 TraesCS3A01G297500 chr7A 89.682 785 58 7 1 768 15682949 15682171 0.000000e+00 979
15 TraesCS3A01G297500 chr7A 82.212 416 58 8 367 768 476297667 476297254 1.870000e-90 344
16 TraesCS3A01G297500 chr7A 85.759 316 40 3 455 766 211806469 211806783 5.240000e-86 329
17 TraesCS3A01G297500 chr7A 84.543 317 46 1 455 768 609635107 609635423 1.900000e-80 311
18 TraesCS3A01G297500 chr6B 83.145 795 101 18 1 766 227722742 227721952 0.000000e+00 695
19 TraesCS3A01G297500 chr1D 82.346 793 94 26 3 766 329503499 329502724 0.000000e+00 647
20 TraesCS3A01G297500 chr1A 81.078 798 102 29 1 765 581587258 581586477 6.050000e-165 592
21 TraesCS3A01G297500 chr1A 82.097 391 56 6 390 767 70692840 70692451 8.770000e-84 322
22 TraesCS3A01G297500 chr5D 86.188 543 47 11 1 517 335860510 335859970 4.750000e-156 562
23 TraesCS3A01G297500 chr2D 90.544 349 29 4 1 346 534341048 534341395 6.410000e-125 459
24 TraesCS3A01G297500 chr6A 88.761 347 28 7 1 343 326812559 326812898 1.410000e-111 414
25 TraesCS3A01G297500 chr7D 82.915 398 57 5 380 766 558927384 558926987 1.450000e-91 348
26 TraesCS3A01G297500 chr2A 82.609 391 53 7 390 767 71663686 71664074 1.460000e-86 331


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 TraesCS3A01G297500 chr3A 532319702 532326709 7007 True 6155.50 6637 100.00000 1 7008 2 chr3A.!!$R1 7007
1 TraesCS3A01G297500 chr3A 12459091 12459836 745 False 445.00 555 88.71650 1 767 2 chr3A.!!$F1 766
2 TraesCS3A01G297500 chr3D 418776554 418783250 6696 False 2333.50 4416 95.85375 768 7008 4 chr3D.!!$F1 6240
3 TraesCS3A01G297500 chr3B 545195471 545202552 7081 False 2008.75 4078 92.14125 768 7008 4 chr3B.!!$F2 6240
4 TraesCS3A01G297500 chr7A 645909639 645910405 766 False 1271.00 1271 96.61000 1 766 1 chr7A.!!$F3 765
5 TraesCS3A01G297500 chr7A 15682171 15682949 778 True 979.00 979 89.68200 1 768 1 chr7A.!!$R1 767
6 TraesCS3A01G297500 chr6B 227721952 227722742 790 True 695.00 695 83.14500 1 766 1 chr6B.!!$R1 765
7 TraesCS3A01G297500 chr1D 329502724 329503499 775 True 647.00 647 82.34600 3 766 1 chr1D.!!$R1 763
8 TraesCS3A01G297500 chr1A 581586477 581587258 781 True 592.00 592 81.07800 1 765 1 chr1A.!!$R2 764
9 TraesCS3A01G297500 chr5D 335859970 335860510 540 True 562.00 562 86.18800 1 517 1 chr5D.!!$R1 516

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
861 944 0.324830 AGCTCTACCCACTCCCAGTC 60.325 60.000 0.00 0.0 0.0 3.51 F
1441 1528 0.458669 CGCCACCGTACTCCAGTTAT 59.541 55.000 0.00 0.0 0.0 1.89 F
2194 2283 0.035630 ATGCCTCTGTGTCCTTCTGC 60.036 55.000 0.00 0.0 0.0 4.26 F
2768 2871 2.267045 GGACCCTTCCATTGCACAC 58.733 57.895 0.00 0.0 42.3 3.82 F
3580 3711 1.527380 GTTCGGGGCCAAGTCAACA 60.527 57.895 4.39 0.0 0.0 3.33 F
4960 7237 0.391130 TGCACCACTGATTCGGCTAC 60.391 55.000 0.00 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 2259 0.036952 AGGACACAGAGGCATCGTTG 60.037 55.000 0.0 0.0 0.0 4.10 R
3247 3378 2.170166 TCCCATGATGTGTCCTTTTGC 58.830 47.619 0.0 0.0 0.0 3.68 R
3565 3696 1.826054 TTGTGTTGACTTGGCCCCG 60.826 57.895 0.0 0.0 0.0 5.73 R
3942 4073 3.689649 GCAACCCCTCAGTGTAGTAAATG 59.310 47.826 0.0 0.0 0.0 2.32 R
5479 7757 1.208535 CACTTATTCGGTGCCCCAGTA 59.791 52.381 0.0 0.0 0.0 2.74 R
6534 8891 0.742505 ACGCCTTGGAATGCATCATG 59.257 50.000 0.0 0.0 0.0 3.07 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
434 471 8.738106 TGCTTTATGAACATGAACAATATGTCA 58.262 29.630 0.00 0.00 37.77 3.58
435 472 9.571810 GCTTTATGAACATGAACAATATGTCAA 57.428 29.630 0.00 0.00 37.77 3.18
446 493 8.039603 TGAACAATATGTCAATCAAGTGGTAC 57.960 34.615 0.00 0.00 0.00 3.34
480 559 1.003233 GGTCTTCTGTTCGAACCCCAT 59.997 52.381 24.78 0.00 0.00 4.00
686 768 3.375699 ACGGAGGGACAAGTTAGATGAT 58.624 45.455 0.00 0.00 0.00 2.45
689 771 4.141937 CGGAGGGACAAGTTAGATGATCAA 60.142 45.833 0.00 0.00 0.00 2.57
694 776 6.434340 AGGGACAAGTTAGATGATCAAAAACC 59.566 38.462 0.00 0.00 0.00 3.27
696 778 6.208599 GGACAAGTTAGATGATCAAAAACCCA 59.791 38.462 0.00 0.00 0.00 4.51
734 816 2.634982 ATTAAACTGACCGTCGCGTA 57.365 45.000 5.77 0.00 0.00 4.42
749 831 3.784994 GTCGCGTACTAGTTTCATGACTC 59.215 47.826 5.77 0.00 0.00 3.36
782 864 3.599348 ACCTCTACCCCTTTCTTCTTGT 58.401 45.455 0.00 0.00 0.00 3.16
812 895 3.303526 CCTGAACGAAAAACCTTGGTACG 60.304 47.826 0.00 0.00 0.00 3.67
813 896 2.613133 TGAACGAAAAACCTTGGTACGG 59.387 45.455 0.00 0.00 0.00 4.02
861 944 0.324830 AGCTCTACCCACTCCCAGTC 60.325 60.000 0.00 0.00 0.00 3.51
868 951 2.227036 CCACTCCCAGTCCCAGCTT 61.227 63.158 0.00 0.00 0.00 3.74
897 980 7.439655 CAGCACCTAAAATCCAGATAACTCTAC 59.560 40.741 0.00 0.00 0.00 2.59
917 1000 4.856607 CCCTCGCCGCTTCTCGAC 62.857 72.222 0.00 0.00 41.67 4.20
919 1002 4.856607 CTCGCCGCTTCTCGACCC 62.857 72.222 0.00 0.00 41.67 4.46
941 1024 1.140652 CCCTCCTCCAGCTTCTTCATC 59.859 57.143 0.00 0.00 0.00 2.92
942 1025 1.836166 CCTCCTCCAGCTTCTTCATCA 59.164 52.381 0.00 0.00 0.00 3.07
943 1026 2.438763 CCTCCTCCAGCTTCTTCATCAT 59.561 50.000 0.00 0.00 0.00 2.45
953 1036 3.798548 GCTTCTTCATCATCCTCCTCGAC 60.799 52.174 0.00 0.00 0.00 4.20
1037 1120 1.216990 CCTTGGCTCTTCCCAGGTAT 58.783 55.000 0.00 0.00 41.67 2.73
1223 1309 4.258543 CTCGGTAATTACCTGCCTTTGAA 58.741 43.478 27.89 7.16 44.25 2.69
1251 1337 3.896648 ATTGTCGAAAATTGACTGCGT 57.103 38.095 0.00 0.00 37.26 5.24
1387 1474 1.078759 CGATCAGGTGCGTCAAGGAC 61.079 60.000 0.00 0.00 40.80 3.85
1405 1492 5.012328 AGGACGAGTCTATCCATTTTGAC 57.988 43.478 11.70 0.00 37.47 3.18
1426 1513 2.882132 TCGAAGATCGAAGCGCCA 59.118 55.556 2.29 0.00 46.90 5.69
1441 1528 0.458669 CGCCACCGTACTCCAGTTAT 59.541 55.000 0.00 0.00 0.00 1.89
1453 1540 3.576982 ACTCCAGTTATTTCGACTCCACA 59.423 43.478 0.00 0.00 0.00 4.17
1471 1558 1.683707 ATCTGGTCAGCTCGAGCCA 60.684 57.895 32.94 21.87 41.69 4.75
1480 1567 3.753434 CTCGAGCCAGCGTCAGGT 61.753 66.667 0.00 0.00 0.00 4.00
1933 2020 1.815003 GAGGCAGAAATGTGGTCAAGG 59.185 52.381 0.00 0.00 0.00 3.61
1981 2068 2.161609 CACGGTTAGTTCTCAATTGCCC 59.838 50.000 0.00 0.00 0.00 5.36
2030 2117 6.068670 AGTTTTTATTGTGGCTGTCTACCTT 58.931 36.000 0.00 0.00 0.00 3.50
2046 2133 2.114616 ACCTTTTGTCAACATGGCCAA 58.885 42.857 10.96 0.00 0.00 4.52
2105 2194 1.260561 CTACCGCACCGCAATTATGTC 59.739 52.381 0.00 0.00 0.00 3.06
2107 2196 1.011242 CGCACCGCAATTATGTCGG 60.011 57.895 9.16 9.16 45.57 4.79
2160 2249 1.002087 GGTAGCACAGGCACTAGTTGT 59.998 52.381 0.00 0.00 44.61 3.32
2194 2283 0.035630 ATGCCTCTGTGTCCTTCTGC 60.036 55.000 0.00 0.00 0.00 4.26
2311 2414 4.537015 GTGTAGACAATGACAAAGCCAAC 58.463 43.478 0.00 0.00 0.00 3.77
2387 2490 4.174704 TCCCTTATAACTCCGCTACTGA 57.825 45.455 0.00 0.00 0.00 3.41
2575 2678 6.257411 TCCACATTGTAATGCTTGTTTTGTTG 59.743 34.615 4.58 0.00 40.04 3.33
2715 2818 7.176690 AGGAAAGGTTGACTAAATACCACAATG 59.823 37.037 0.00 0.00 34.32 2.82
2758 2861 2.424956 CTGCAGCTTTATTGGACCCTTC 59.575 50.000 0.00 0.00 0.00 3.46
2768 2871 2.267045 GGACCCTTCCATTGCACAC 58.733 57.895 0.00 0.00 42.30 3.82
2791 2894 2.480224 CAGTTGTGCACACCTTTCTG 57.520 50.000 21.56 17.51 0.00 3.02
2858 2965 8.477256 ACCATTAGCATTGTATAGCACATTTTT 58.523 29.630 0.00 0.00 36.90 1.94
2913 3020 6.647895 ACATCTTCCATTTTCAATCTGTTTGC 59.352 34.615 0.00 0.00 35.16 3.68
2922 3029 2.292845 TCAATCTGTTTGCGTTGCATCA 59.707 40.909 0.00 0.00 38.76 3.07
2994 3101 3.505680 TGCGTCACTGGCATAATTTTTCT 59.494 39.130 0.00 0.00 35.04 2.52
3440 3571 8.660373 GTGAAGACCAGATTAAACAGAGTATTG 58.340 37.037 0.00 0.00 0.00 1.90
3441 3572 8.375506 TGAAGACCAGATTAAACAGAGTATTGT 58.624 33.333 0.00 0.00 0.00 2.71
3442 3573 9.220767 GAAGACCAGATTAAACAGAGTATTGTT 57.779 33.333 0.00 0.00 42.82 2.83
3565 3696 8.499403 AATAATCTTGCAAAGTCTAGAGGTTC 57.501 34.615 0.00 0.00 46.34 3.62
3580 3711 1.527380 GTTCGGGGCCAAGTCAACA 60.527 57.895 4.39 0.00 0.00 3.33
4233 4370 4.434520 GGTTGATCTAGGAAAAGGACTCG 58.565 47.826 0.00 0.00 0.00 4.18
4299 4436 1.542472 CATTCACATGCCACTTCTGCA 59.458 47.619 0.00 0.00 43.97 4.41
4374 5336 4.779696 TGCTCTGCATAATGTGTAATCCA 58.220 39.130 0.00 0.00 31.71 3.41
4377 5339 6.997476 TGCTCTGCATAATGTGTAATCCAATA 59.003 34.615 0.00 0.00 31.71 1.90
4390 5352 5.430417 TGTAATCCAATAAGGGAAGCTACCA 59.570 40.000 9.77 0.00 41.12 3.25
4401 5363 5.278061 AGGGAAGCTACCATGTTACTCTTA 58.722 41.667 9.77 0.00 0.00 2.10
4447 5410 9.332502 TCTGACTTGTTTAAACTTATGCAACTA 57.667 29.630 18.72 0.00 0.00 2.24
4525 5488 1.677820 GGTGGTGATCCTGTTTACCCG 60.678 57.143 0.00 0.00 32.20 5.28
4658 5621 6.010219 AGTCCCACATAAAGCATTTTACACT 58.990 36.000 0.00 0.00 40.09 3.55
4659 5622 6.071952 AGTCCCACATAAAGCATTTTACACTG 60.072 38.462 0.00 0.00 40.09 3.66
4695 5660 8.957466 AGGTTTACTAGATTCATGGTTTTTAGC 58.043 33.333 0.00 0.00 0.00 3.09
4870 7146 4.516321 CAGCATGGGATAATGATCACGAAA 59.484 41.667 0.00 0.00 38.45 3.46
4960 7237 0.391130 TGCACCACTGATTCGGCTAC 60.391 55.000 0.00 0.00 0.00 3.58
4965 7242 2.829720 ACCACTGATTCGGCTACAACTA 59.170 45.455 0.00 0.00 0.00 2.24
4985 7262 9.632638 ACAACTAATTGCATATCATAGGTCTTT 57.367 29.630 0.00 0.00 39.66 2.52
5112 7390 3.975035 GTCCATTCGAAGTGCTTGTTTTC 59.025 43.478 3.35 0.00 0.00 2.29
5365 7643 5.734720 ACTGGTTGGAACATAGATACTGTG 58.265 41.667 0.00 0.00 39.30 3.66
5393 7671 8.113462 AGTTGTAGTTGTAATATTGGATGGGTT 58.887 33.333 0.00 0.00 0.00 4.11
5512 7790 3.983988 CGAATAAGTGGGATGAGATGTCG 59.016 47.826 0.00 0.00 0.00 4.35
5718 8021 2.717580 TGGCACGTAGTAACACTGAG 57.282 50.000 0.00 0.00 41.61 3.35
6055 8366 1.160137 GCATGACACAAGGTGAGTCC 58.840 55.000 0.00 0.00 37.20 3.85
6183 8495 5.048921 GGTTGAGTTTCTAGGTTTAGTTGCC 60.049 44.000 0.00 0.00 0.00 4.52
6218 8530 3.558505 CTTCGTTGGAAATGCAAGACAG 58.441 45.455 0.00 0.00 31.35 3.51
6231 8545 3.206150 GCAAGACAGGTGACTTTTCAGA 58.794 45.455 0.00 0.00 40.21 3.27
6232 8546 3.249559 GCAAGACAGGTGACTTTTCAGAG 59.750 47.826 0.00 0.00 40.21 3.35
6353 8667 8.831715 ACAATGATATTATTCGTGCATACTCA 57.168 30.769 0.00 0.00 0.00 3.41
6354 8668 9.440773 ACAATGATATTATTCGTGCATACTCAT 57.559 29.630 0.00 0.00 0.00 2.90
6357 8671 8.479313 TGATATTATTCGTGCATACTCATTCC 57.521 34.615 0.00 0.00 0.00 3.01
6358 8672 8.093927 TGATATTATTCGTGCATACTCATTCCA 58.906 33.333 0.00 0.00 0.00 3.53
6359 8673 9.102757 GATATTATTCGTGCATACTCATTCCAT 57.897 33.333 0.00 0.00 0.00 3.41
6360 8674 6.544038 TTATTCGTGCATACTCATTCCATG 57.456 37.500 0.00 0.00 0.00 3.66
6361 8675 3.541996 TCGTGCATACTCATTCCATGT 57.458 42.857 0.00 0.00 0.00 3.21
6362 8676 4.664150 TCGTGCATACTCATTCCATGTA 57.336 40.909 0.00 0.00 0.00 2.29
6363 8677 4.368315 TCGTGCATACTCATTCCATGTAC 58.632 43.478 0.00 0.00 33.54 2.90
6364 8678 4.099419 TCGTGCATACTCATTCCATGTACT 59.901 41.667 0.00 0.00 34.37 2.73
6365 8679 4.811024 CGTGCATACTCATTCCATGTACTT 59.189 41.667 0.00 0.00 34.37 2.24
6366 8680 5.294306 CGTGCATACTCATTCCATGTACTTT 59.706 40.000 0.00 0.00 34.37 2.66
6367 8681 6.183360 CGTGCATACTCATTCCATGTACTTTT 60.183 38.462 0.00 0.00 34.37 2.27
6368 8682 7.011016 CGTGCATACTCATTCCATGTACTTTTA 59.989 37.037 0.00 0.00 34.37 1.52
6369 8683 8.122952 GTGCATACTCATTCCATGTACTTTTAC 58.877 37.037 0.00 0.00 33.92 2.01
6370 8684 7.826744 TGCATACTCATTCCATGTACTTTTACA 59.173 33.333 0.00 0.00 42.53 2.41
6382 8696 6.177310 TGTACTTTTACATGTACTGGTGGT 57.823 37.500 4.68 2.32 39.57 4.16
6383 8697 6.225318 TGTACTTTTACATGTACTGGTGGTC 58.775 40.000 4.68 2.02 39.57 4.02
6384 8698 5.298989 ACTTTTACATGTACTGGTGGTCA 57.701 39.130 4.68 0.00 0.00 4.02
6385 8699 5.686753 ACTTTTACATGTACTGGTGGTCAA 58.313 37.500 4.68 0.00 0.00 3.18
6386 8700 6.303839 ACTTTTACATGTACTGGTGGTCAAT 58.696 36.000 4.68 0.00 0.00 2.57
6387 8701 6.206634 ACTTTTACATGTACTGGTGGTCAATG 59.793 38.462 4.68 0.00 0.00 2.82
6388 8702 3.788227 ACATGTACTGGTGGTCAATGT 57.212 42.857 0.00 0.00 32.62 2.71
6389 8703 4.098914 ACATGTACTGGTGGTCAATGTT 57.901 40.909 0.00 0.00 33.23 2.71
6390 8704 4.072131 ACATGTACTGGTGGTCAATGTTC 58.928 43.478 0.00 0.00 33.23 3.18
6391 8705 4.202461 ACATGTACTGGTGGTCAATGTTCT 60.202 41.667 0.00 0.00 33.23 3.01
6392 8706 5.012664 ACATGTACTGGTGGTCAATGTTCTA 59.987 40.000 0.00 0.00 33.23 2.10
6393 8707 5.554437 TGTACTGGTGGTCAATGTTCTAA 57.446 39.130 0.00 0.00 0.00 2.10
6394 8708 5.931294 TGTACTGGTGGTCAATGTTCTAAA 58.069 37.500 0.00 0.00 0.00 1.85
6395 8709 6.358178 TGTACTGGTGGTCAATGTTCTAAAA 58.642 36.000 0.00 0.00 0.00 1.52
6396 8710 5.767816 ACTGGTGGTCAATGTTCTAAAAC 57.232 39.130 0.00 0.00 35.85 2.43
6397 8711 4.274950 ACTGGTGGTCAATGTTCTAAAACG 59.725 41.667 0.00 0.00 38.28 3.60
6398 8712 4.200874 TGGTGGTCAATGTTCTAAAACGT 58.799 39.130 0.00 0.00 38.28 3.99
6399 8713 4.641094 TGGTGGTCAATGTTCTAAAACGTT 59.359 37.500 0.00 0.00 43.75 3.99
6406 8720 5.493133 AATGTTCTAAAACGTTGACTGCA 57.507 34.783 0.00 0.00 41.86 4.41
6407 8721 4.948608 TGTTCTAAAACGTTGACTGCAA 57.051 36.364 0.00 0.00 38.28 4.08
6408 8722 4.904116 TGTTCTAAAACGTTGACTGCAAG 58.096 39.130 0.00 0.00 38.28 4.01
6409 8723 3.602390 TCTAAAACGTTGACTGCAAGC 57.398 42.857 0.00 0.00 37.60 4.01
6410 8724 2.939756 TCTAAAACGTTGACTGCAAGCA 59.060 40.909 0.00 0.00 37.60 3.91
6411 8725 2.869233 AAAACGTTGACTGCAAGCAT 57.131 40.000 0.00 0.00 37.60 3.79
6412 8726 3.980646 AAAACGTTGACTGCAAGCATA 57.019 38.095 0.00 0.00 37.60 3.14
6413 8727 3.980646 AAACGTTGACTGCAAGCATAA 57.019 38.095 0.00 0.00 37.60 1.90
6414 8728 4.503741 AAACGTTGACTGCAAGCATAAT 57.496 36.364 0.00 0.00 37.60 1.28
6415 8729 4.503741 AACGTTGACTGCAAGCATAATT 57.496 36.364 0.00 0.00 37.60 1.40
6416 8730 5.621197 AACGTTGACTGCAAGCATAATTA 57.379 34.783 0.00 0.00 37.60 1.40
6534 8891 2.362397 GCAAATAGCTTTAGGCCTTCCC 59.638 50.000 12.58 0.00 43.05 3.97
6573 8930 4.377841 GCGTGAAGCTGCATCCTTAATATC 60.378 45.833 0.00 0.00 44.04 1.63
6875 9232 6.404954 GCCAACCGTGTAAAACCATTATGTAT 60.405 38.462 0.00 0.00 0.00 2.29
6907 9264 3.545633 GCTCGCTTGTAACTGTTTTGAG 58.454 45.455 0.00 0.00 0.00 3.02
6921 9278 2.823747 GTTTTGAGGTATGGACCCCAAC 59.176 50.000 0.00 0.00 42.67 3.77
6929 9286 0.850883 ATGGACCCCAACACCCTCAT 60.851 55.000 0.00 0.00 36.95 2.90
6939 9296 3.790437 ACCCTCATGGCCTCGCTG 61.790 66.667 3.32 0.00 37.83 5.18
6975 9332 4.038282 GGTTTTCAACGGATTACCAAACCT 59.962 41.667 0.00 0.00 40.74 3.50
6996 9353 1.519408 CGTTTGAACACCCCTACCTG 58.481 55.000 0.00 0.00 0.00 4.00
6998 9355 2.037511 CGTTTGAACACCCCTACCTGTA 59.962 50.000 0.00 0.00 0.00 2.74
7000 9357 2.708037 TGAACACCCCTACCTGTACT 57.292 50.000 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
434 471 3.071479 ACAAATCGCGTACCACTTGATT 58.929 40.909 5.77 0.00 0.00 2.57
435 472 2.695359 ACAAATCGCGTACCACTTGAT 58.305 42.857 5.77 0.00 0.00 2.57
446 493 1.324736 GAAGACCTGCTACAAATCGCG 59.675 52.381 0.00 0.00 0.00 5.87
453 500 2.235891 TCGAACAGAAGACCTGCTACA 58.764 47.619 0.00 0.00 46.81 2.74
480 559 4.582701 ATGAAAAATGCCGAACAGACAA 57.417 36.364 0.00 0.00 0.00 3.18
714 796 2.634982 ACGCGACGGTCAGTTTAATA 57.365 45.000 15.93 0.00 0.00 0.98
717 799 0.874390 AGTACGCGACGGTCAGTTTA 59.126 50.000 15.93 0.00 0.00 2.01
734 816 3.321111 ACACCACGAGTCATGAAACTAGT 59.679 43.478 0.00 0.00 35.78 2.57
749 831 3.181472 GGGGTAGAGGTAAATACACCACG 60.181 52.174 0.00 0.00 43.71 4.94
812 895 2.757099 CATGGTTGGGCTGGCTCC 60.757 66.667 0.00 2.71 0.00 4.70
813 896 2.757099 CCATGGTTGGGCTGGCTC 60.757 66.667 2.57 0.00 39.56 4.70
861 944 1.852157 TTAGGTGCTGGGAAGCTGGG 61.852 60.000 0.00 0.00 35.49 4.45
868 951 2.274542 TCTGGATTTTAGGTGCTGGGA 58.725 47.619 0.00 0.00 0.00 4.37
879 962 5.648330 GGGGGTAGAGTTATCTGGATTTT 57.352 43.478 0.00 0.00 36.96 1.82
919 1002 1.617839 AAGAAGCTGGAGGAGGGGG 60.618 63.158 0.00 0.00 0.00 5.40
1037 1120 3.436704 GCTTGAAATGAGGAACATGACGA 59.563 43.478 0.00 0.00 39.39 4.20
1223 1309 5.010012 AGTCAATTTTCGACAATTTGGAGCT 59.990 36.000 6.80 0.00 35.77 4.09
1251 1337 0.106521 TAGCACAGACAGCAACTGCA 59.893 50.000 4.22 0.00 45.16 4.41
1261 1347 6.402226 CCGAGAACCTAAATTTTAGCACAGAC 60.402 42.308 10.16 0.99 0.00 3.51
1387 1474 3.123804 CGGGTCAAAATGGATAGACTCG 58.876 50.000 0.00 0.00 46.68 4.18
1426 1513 3.760684 AGTCGAAATAACTGGAGTACGGT 59.239 43.478 0.00 0.00 41.57 4.83
1453 1540 1.674764 CTGGCTCGAGCTGACCAGAT 61.675 60.000 34.46 0.00 43.16 2.90
1663 1750 1.468985 CGTCATCTCCACTGGTCTCT 58.531 55.000 0.00 0.00 0.00 3.10
1981 2068 4.273235 TCACAAGCCATCATTATAAGTGCG 59.727 41.667 0.00 0.00 0.00 5.34
2030 2117 6.007076 TCTACTAATTGGCCATGTTGACAAA 58.993 36.000 6.09 0.00 0.00 2.83
2160 2249 3.752796 GCATCGTTGTGCCCTAGTA 57.247 52.632 0.00 0.00 39.18 1.82
2170 2259 0.036952 AGGACACAGAGGCATCGTTG 60.037 55.000 0.00 0.00 0.00 4.10
2194 2283 7.092137 ACAATGATTCACACATACAGAATGG 57.908 36.000 0.00 0.00 43.62 3.16
2311 2414 3.312421 CACTCCTACCCATACGCAAAATG 59.688 47.826 0.00 0.00 0.00 2.32
2387 2490 2.532235 CAAGCAATGCACGCACATTAT 58.468 42.857 8.35 0.00 38.19 1.28
2575 2678 4.438148 TGCCTTTGCAAAGACCTAAAAAC 58.562 39.130 35.25 15.26 46.66 2.43
2676 2779 7.996644 AGTCAACCTTTCCTCTTTGTGTAAATA 59.003 33.333 0.00 0.00 0.00 1.40
2715 2818 6.638468 GCAGCATATACTTATGAGCAAAAACC 59.362 38.462 0.00 0.00 37.94 3.27
2858 2965 7.581213 AATTAATGTTTCAGAATATGGCGGA 57.419 32.000 0.00 0.00 0.00 5.54
2913 3020 6.196910 CACCACATATTTGTTATGATGCAACG 59.803 38.462 0.00 0.00 40.22 4.10
2994 3101 4.013728 ACAGTACAAGCTTTGGTCAAACA 58.986 39.130 0.00 0.00 34.12 2.83
3247 3378 2.170166 TCCCATGATGTGTCCTTTTGC 58.830 47.619 0.00 0.00 0.00 3.68
3450 3581 6.713276 AGATGAATCAATCAAAATTTGGGCA 58.287 32.000 5.83 0.00 42.54 5.36
3547 3678 2.289444 CCCGAACCTCTAGACTTTGCAA 60.289 50.000 0.00 0.00 0.00 4.08
3565 3696 1.826054 TTGTGTTGACTTGGCCCCG 60.826 57.895 0.00 0.00 0.00 5.73
3942 4073 3.689649 GCAACCCCTCAGTGTAGTAAATG 59.310 47.826 0.00 0.00 0.00 2.32
4032 4164 9.569122 AGCTCAAACTAAGTTATGTAGGAAAAA 57.431 29.630 0.00 0.00 0.00 1.94
4050 4182 5.447573 CAGCTCTTGAAACTTAGCTCAAAC 58.552 41.667 0.00 0.00 43.26 2.93
4233 4370 4.096382 AGTCACATTGTGTTCAACTCCAAC 59.904 41.667 16.06 3.66 36.33 3.77
4374 5336 6.387220 AGAGTAACATGGTAGCTTCCCTTATT 59.613 38.462 6.95 0.00 0.00 1.40
4377 5339 4.104831 AGAGTAACATGGTAGCTTCCCTT 58.895 43.478 6.95 0.00 0.00 3.95
4480 5443 5.286797 CCAAACTGCATATTTGAATGTCACG 59.713 40.000 19.91 2.89 39.01 4.35
4525 5488 5.105146 AGGATCCTGAACATAGTTCACAGTC 60.105 44.000 15.29 6.75 0.00 3.51
4658 5621 3.835978 TCTAGTAAACCTTAGCTGGCACA 59.164 43.478 0.00 0.00 0.00 4.57
4659 5622 4.467198 TCTAGTAAACCTTAGCTGGCAC 57.533 45.455 0.00 0.00 0.00 5.01
4765 5730 7.921787 TGTCACACGATTAACATTTTTAGTGT 58.078 30.769 0.00 0.00 41.52 3.55
4870 7146 2.549754 CAAACGTGCATCCAGTTCTTCT 59.450 45.455 0.00 0.00 0.00 2.85
5112 7390 4.423732 CACCGAGGCATTTTTATGGAAAG 58.576 43.478 0.00 0.00 0.00 2.62
5365 7643 7.417612 CCATCCAATATTACAACTACAACTGC 58.582 38.462 0.00 0.00 0.00 4.40
5393 7671 5.540337 TGTTGGGGTTGCACATAATAAAAGA 59.460 36.000 0.00 0.00 0.00 2.52
5479 7757 1.208535 CACTTATTCGGTGCCCCAGTA 59.791 52.381 0.00 0.00 0.00 2.74
5718 8021 4.630111 TGACCAACAAGAATTTCATTGCC 58.370 39.130 0.00 0.00 0.00 4.52
6124 8436 3.845781 GAGTATGGCTCAGGATTTCCA 57.154 47.619 0.00 0.00 43.58 3.53
6183 8495 3.188460 CCAACGAAGGGAGTATGTTTGTG 59.812 47.826 0.00 0.00 0.00 3.33
6218 8530 3.644884 TCGAGACTCTGAAAAGTCACC 57.355 47.619 6.79 0.00 46.65 4.02
6231 8545 3.248602 GTCAAAACTGTGCATTCGAGACT 59.751 43.478 0.00 0.00 0.00 3.24
6232 8546 3.248602 AGTCAAAACTGTGCATTCGAGAC 59.751 43.478 0.00 0.00 33.32 3.36
6299 8613 5.509622 GTCTTGCGAAATTCATTTCTGCTAC 59.490 40.000 19.96 14.75 42.96 3.58
6333 8647 8.479313 TGGAATGAGTATGCACGAATAATATC 57.521 34.615 0.00 0.00 0.00 1.63
6359 8673 6.177310 ACCACCAGTACATGTAAAAGTACA 57.823 37.500 7.25 0.00 44.29 2.90
6360 8674 6.225318 TGACCACCAGTACATGTAAAAGTAC 58.775 40.000 7.25 0.00 40.60 2.73
6361 8675 6.422344 TGACCACCAGTACATGTAAAAGTA 57.578 37.500 7.25 0.00 0.00 2.24
6362 8676 5.298989 TGACCACCAGTACATGTAAAAGT 57.701 39.130 7.25 2.17 0.00 2.66
6363 8677 6.206634 ACATTGACCACCAGTACATGTAAAAG 59.793 38.462 7.25 1.51 32.04 2.27
6364 8678 6.065374 ACATTGACCACCAGTACATGTAAAA 58.935 36.000 7.25 0.00 32.04 1.52
6365 8679 5.626142 ACATTGACCACCAGTACATGTAAA 58.374 37.500 7.25 0.00 32.04 2.01
6366 8680 5.235850 ACATTGACCACCAGTACATGTAA 57.764 39.130 7.25 0.00 32.04 2.41
6367 8681 4.901197 ACATTGACCACCAGTACATGTA 57.099 40.909 0.08 0.08 32.04 2.29
6368 8682 3.788227 ACATTGACCACCAGTACATGT 57.212 42.857 2.69 2.69 0.00 3.21
6369 8683 4.326826 AGAACATTGACCACCAGTACATG 58.673 43.478 0.00 0.00 0.00 3.21
6370 8684 4.640771 AGAACATTGACCACCAGTACAT 57.359 40.909 0.00 0.00 0.00 2.29
6371 8685 5.554437 TTAGAACATTGACCACCAGTACA 57.446 39.130 0.00 0.00 0.00 2.90
6372 8686 6.565247 CGTTTTAGAACATTGACCACCAGTAC 60.565 42.308 0.00 0.00 35.44 2.73
6373 8687 5.467399 CGTTTTAGAACATTGACCACCAGTA 59.533 40.000 0.00 0.00 35.44 2.74
6374 8688 4.274950 CGTTTTAGAACATTGACCACCAGT 59.725 41.667 0.00 0.00 35.44 4.00
6375 8689 4.274950 ACGTTTTAGAACATTGACCACCAG 59.725 41.667 0.00 0.00 35.44 4.00
6376 8690 4.200874 ACGTTTTAGAACATTGACCACCA 58.799 39.130 0.00 0.00 35.44 4.17
6377 8691 4.823790 ACGTTTTAGAACATTGACCACC 57.176 40.909 0.00 0.00 35.44 4.61
6378 8692 5.812652 TCAACGTTTTAGAACATTGACCAC 58.187 37.500 3.77 0.00 41.44 4.16
6382 8696 5.065346 TGCAGTCAACGTTTTAGAACATTGA 59.935 36.000 3.77 3.77 43.33 2.57
6383 8697 5.270083 TGCAGTCAACGTTTTAGAACATTG 58.730 37.500 0.00 0.00 39.58 2.82
6384 8698 5.493133 TGCAGTCAACGTTTTAGAACATT 57.507 34.783 0.00 0.00 35.44 2.71
6385 8699 5.493133 TTGCAGTCAACGTTTTAGAACAT 57.507 34.783 0.00 0.00 35.44 2.71
6386 8700 4.729458 GCTTGCAGTCAACGTTTTAGAACA 60.729 41.667 0.00 0.00 35.44 3.18
6387 8701 3.724257 GCTTGCAGTCAACGTTTTAGAAC 59.276 43.478 0.00 0.00 0.00 3.01
6388 8702 3.375610 TGCTTGCAGTCAACGTTTTAGAA 59.624 39.130 0.00 0.00 0.00 2.10
6389 8703 2.939756 TGCTTGCAGTCAACGTTTTAGA 59.060 40.909 0.00 0.00 0.00 2.10
6390 8704 3.332761 TGCTTGCAGTCAACGTTTTAG 57.667 42.857 0.00 0.00 0.00 1.85
6391 8705 3.980646 ATGCTTGCAGTCAACGTTTTA 57.019 38.095 0.00 0.00 0.00 1.52
6392 8706 2.869233 ATGCTTGCAGTCAACGTTTT 57.131 40.000 0.00 0.00 0.00 2.43
6393 8707 3.980646 TTATGCTTGCAGTCAACGTTT 57.019 38.095 0.00 0.00 0.00 3.60
6394 8708 4.503741 AATTATGCTTGCAGTCAACGTT 57.496 36.364 0.00 0.00 0.00 3.99
6395 8709 5.621197 TTAATTATGCTTGCAGTCAACGT 57.379 34.783 0.87 0.00 0.00 3.99
6396 8710 8.613613 TTAATTAATTATGCTTGCAGTCAACG 57.386 30.769 8.70 0.00 0.00 4.10
6416 8730 8.686334 CCAGAACTGTAAGGTGCATAATTAATT 58.314 33.333 5.89 5.89 39.30 1.40
6534 8891 0.742505 ACGCCTTGGAATGCATCATG 59.257 50.000 0.00 0.00 0.00 3.07
6573 8930 4.144297 TGACTTTGTTGAATCCCTTGAGG 58.856 43.478 0.00 0.00 0.00 3.86
6739 9096 2.812011 GCAGGTCGAAGTGTTTTATGGT 59.188 45.455 0.00 0.00 0.00 3.55
6825 9182 0.817634 CGCACTTGAACAACCCTGGA 60.818 55.000 0.00 0.00 0.00 3.86
6907 9264 1.212250 AGGGTGTTGGGGTCCATACC 61.212 60.000 10.55 10.55 45.97 2.73
6921 9278 3.790437 AGCGAGGCCATGAGGGTG 61.790 66.667 5.01 0.00 39.65 4.61
6939 9296 1.953686 TGAAAACCAGTACAGGCAAGC 59.046 47.619 3.83 0.00 0.00 4.01
6975 9332 0.535553 GGTAGGGGTGTTCAAACGCA 60.536 55.000 8.54 0.00 41.06 5.24


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

AutoCloner maintained by Alex Coulton.