Multiple sequence alignment - TraesCS3A01G157000

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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 TraesCS3A01G157000 chr3A 100.000 5743 0 0 1 5743 153599678 153593936 0.000000e+00 10606
1 TraesCS3A01G157000 chr3B 91.596 5105 223 65 734 5736 194647160 194642160 0.000000e+00 6861
2 TraesCS3A01G157000 chr3B 88.158 380 5 17 2 365 194648213 194647858 3.200000e-112 416
3 TraesCS3A01G157000 chr3B 78.448 348 56 14 401 737 194647862 194647523 5.830000e-50 209
4 TraesCS3A01G157000 chr3D 93.119 4534 173 55 695 5141 136268011 136263530 0.000000e+00 6516
5 TraesCS3A01G157000 chr3D 83.717 651 62 24 3 649 136268770 136268160 4.990000e-160 575
6 TraesCS3A01G157000 chr3D 83.710 442 40 12 5210 5650 136261722 136261312 6.980000e-104 388
7 TraesCS3A01G157000 chr1D 87.433 748 52 27 196 925 293195257 293195980 0.000000e+00 822


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 TraesCS3A01G157000 chr3A 153593936 153599678 5742 True 10606.000000 10606 100.000000 1 5743 1 chr3A.!!$R1 5742
1 TraesCS3A01G157000 chr3B 194642160 194648213 6053 True 2495.333333 6861 86.067333 2 5736 3 chr3B.!!$R1 5734
2 TraesCS3A01G157000 chr3D 136261312 136268770 7458 True 2493.000000 6516 86.848667 3 5650 3 chr3D.!!$R1 5647
3 TraesCS3A01G157000 chr1D 293195257 293195980 723 False 822.000000 822 87.433000 196 925 1 chr1D.!!$F1 729

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
829 1339 0.252927 CCCCACCCCTCTTCTTCTCT 60.253 60.000 0.00 0.00 0.00 3.10 F
2098 2704 0.035317 CAACTACCTCAGCTGCACCA 59.965 55.000 9.47 0.00 0.00 4.17 F
2204 2810 0.176449 TGTCACATCTCGCCATGAGG 59.824 55.000 0.00 0.00 45.32 3.86 F
2226 2832 0.251354 TCCATGCAGAAGGAGAGTGC 59.749 55.000 1.49 0.00 37.73 4.40 F
2248 2854 0.381089 CTCCTCGTAAGGTGCCTACG 59.619 60.000 11.34 11.34 43.82 3.51 F
2250 2856 1.226888 CTCGTAAGGTGCCTACGGC 60.227 63.158 15.03 0.00 44.33 5.68 F
4161 4812 1.209261 TCTGCAATTCTATGGGTCGCA 59.791 47.619 0.00 0.00 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 2810 0.179051 CTCTCCTTCTGCATGGAGCC 60.179 60.000 19.63 0.00 46.90 4.70 R
3599 4242 1.643832 GCGATTGATCTCGTTGCCC 59.356 57.895 6.28 0.00 40.73 5.36 R
3859 4509 3.521524 GTGACAAACACTGAACGATCC 57.478 47.619 0.00 0.00 45.13 3.36 R
4123 4774 3.625938 CAGAAAGCAAGCAGAAACTGAC 58.374 45.455 2.81 0.00 32.44 3.51 R
4151 4802 4.709250 TGCTACAAAATATGCGACCCATA 58.291 39.130 0.00 0.00 40.52 2.74 R
4355 5006 3.183775 GCAAAGATTTGTGAAAGCTGCAG 59.816 43.478 10.11 10.11 37.18 4.41 R
5345 7754 1.004044 CCATCACCTCTGGCTTCAAGT 59.996 52.381 0.00 0.00 0.00 3.16 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
64 74 9.364653 AGACACTAATCCCGTAATTAGTTATCT 57.635 33.333 13.92 15.18 45.70 1.98
184 207 2.358957 TCATGCCACGTACGTACTAGT 58.641 47.619 22.34 11.79 0.00 2.57
186 209 3.309682 TCATGCCACGTACGTACTAGTAC 59.690 47.826 22.34 21.06 42.48 2.73
187 210 2.006888 TGCCACGTACGTACTAGTACC 58.993 52.381 22.34 11.55 42.84 3.34
321 347 3.488553 GGGCAATCTGTAACGGCAATAAC 60.489 47.826 0.00 0.00 0.00 1.89
344 370 2.266372 GCATGGCATTGGCAGCAA 59.734 55.556 18.37 0.00 42.43 3.91
372 398 4.322080 TGGTTCTCTAACTCACACAGTG 57.678 45.455 0.00 0.00 34.56 3.66
408 436 3.372060 GTTTCAAAAGAAGAACCCTGCG 58.628 45.455 0.00 0.00 0.00 5.18
418 446 1.782028 GAACCCTGCGGTGACACAAC 61.782 60.000 8.08 0.00 43.71 3.32
419 447 2.978010 CCCTGCGGTGACACAACC 60.978 66.667 8.08 0.00 36.82 3.77
450 478 5.995282 TGAACTAATCCACGTGACATTTTCT 59.005 36.000 19.30 2.80 0.00 2.52
451 479 6.147164 TGAACTAATCCACGTGACATTTTCTC 59.853 38.462 19.30 11.13 0.00 2.87
452 480 5.794894 ACTAATCCACGTGACATTTTCTCT 58.205 37.500 19.30 0.00 0.00 3.10
468 496 9.160496 ACATTTTCTCTTGTGCAATTTTTGTAA 57.840 25.926 0.00 0.00 0.00 2.41
575 605 3.385755 TCCACGCCCTCTAATTAACTACC 59.614 47.826 0.00 0.00 0.00 3.18
581 611 4.685302 GCCCTCTAATTAACTACCACCACC 60.685 50.000 0.00 0.00 0.00 4.61
585 615 6.436738 TCTAATTAACTACCACCACCACAA 57.563 37.500 0.00 0.00 0.00 3.33
617 647 3.343941 TCCAGGTTACATTTTCTCCGG 57.656 47.619 0.00 0.00 0.00 5.14
624 654 1.234615 ACATTTTCTCCGGTGGCACG 61.235 55.000 12.17 7.01 0.00 5.34
644 674 5.213675 CACGCCACGGAATAAACTTAAAAA 58.786 37.500 0.00 0.00 0.00 1.94
645 675 5.859648 CACGCCACGGAATAAACTTAAAAAT 59.140 36.000 0.00 0.00 0.00 1.82
647 677 5.513849 CGCCACGGAATAAACTTAAAAATCC 59.486 40.000 0.00 0.00 0.00 3.01
648 678 6.624204 CGCCACGGAATAAACTTAAAAATCCT 60.624 38.462 0.00 0.00 0.00 3.24
649 679 7.414319 CGCCACGGAATAAACTTAAAAATCCTA 60.414 37.037 0.00 0.00 0.00 2.94
651 681 9.169592 CCACGGAATAAACTTAAAAATCCTAGA 57.830 33.333 0.00 0.00 0.00 2.43
673 807 6.719365 AGAATTATTATTCGTGAGCACAAGC 58.281 36.000 1.20 0.00 43.99 4.01
685 827 1.310933 GCACAAGCCCATCTCAGGTG 61.311 60.000 0.00 0.00 33.58 4.00
688 830 1.001641 AAGCCCATCTCAGGTGCAC 60.002 57.895 8.80 8.80 0.00 4.57
691 833 0.462759 GCCCATCTCAGGTGCACTAC 60.463 60.000 17.98 0.06 0.00 2.73
738 1246 6.199393 CGATTAGTTAATTGGCAGCCTAAAC 58.801 40.000 14.15 7.64 0.00 2.01
829 1339 0.252927 CCCCACCCCTCTTCTTCTCT 60.253 60.000 0.00 0.00 0.00 3.10
911 1436 4.851214 GCTCGCCTCTCCCCTCCT 62.851 72.222 0.00 0.00 0.00 3.69
916 1441 4.465446 CCTCTCCCCTCCTCCGCA 62.465 72.222 0.00 0.00 0.00 5.69
939 1473 0.748005 CTGCCCTACAAATCCCACCG 60.748 60.000 0.00 0.00 0.00 4.94
1331 1909 1.332686 GATCGTGGGCCGGTTTAATTC 59.667 52.381 1.90 0.00 37.11 2.17
1332 1910 0.036448 TCGTGGGCCGGTTTAATTCA 59.964 50.000 1.90 0.00 37.11 2.57
1355 1933 6.654161 TCAAATTTTGAATGGCTATTGGTTGG 59.346 34.615 9.36 0.00 36.59 3.77
1357 1935 5.404466 TTTTGAATGGCTATTGGTTGGAG 57.596 39.130 0.00 0.00 0.00 3.86
1358 1936 4.314522 TTGAATGGCTATTGGTTGGAGA 57.685 40.909 0.00 0.00 0.00 3.71
1402 1987 0.888285 GCTCCTGCTGTTGCTTCTGT 60.888 55.000 0.00 0.00 40.48 3.41
1451 2041 0.107017 ATTGCCCTGTTCCTCGGATG 60.107 55.000 0.00 0.00 0.00 3.51
1458 2048 2.084546 CTGTTCCTCGGATGGGAAAAC 58.915 52.381 0.71 0.00 43.39 2.43
1501 2091 1.617947 GGTGTCCATCCTTCGAGGCT 61.618 60.000 0.00 0.00 34.61 4.58
1559 2154 0.040958 CGCTGCGATTTATTGCCTCC 60.041 55.000 18.66 0.00 36.33 4.30
1601 2199 5.739161 GTGTTTTGTGCTCTTGAAACTACAG 59.261 40.000 11.36 0.00 34.12 2.74
1631 2229 2.397549 GTTGTCTTTGGCTTGTGATGC 58.602 47.619 0.00 0.00 0.00 3.91
1734 2337 4.063689 CTCTGCGATTGCTAATCTTCCAT 58.936 43.478 6.47 0.00 43.34 3.41
1738 2341 5.581605 TGCGATTGCTAATCTTCCATTTTC 58.418 37.500 6.47 0.00 43.34 2.29
1764 2367 5.759273 CCAAATTTTGATGCCTCTTTTGTGA 59.241 36.000 10.72 0.00 0.00 3.58
1766 2369 5.796424 ATTTTGATGCCTCTTTTGTGAGT 57.204 34.783 0.00 0.00 32.50 3.41
1780 2383 1.312815 GTGAGTGTTTCTGGCTGCTT 58.687 50.000 0.00 0.00 0.00 3.91
1781 2384 1.678101 GTGAGTGTTTCTGGCTGCTTT 59.322 47.619 0.00 0.00 0.00 3.51
1810 2413 1.726248 CAATTTTGCGCCTTTACCAGC 59.274 47.619 4.18 0.00 0.00 4.85
1842 2445 3.561310 TCTGTTGCGGATCATATTTCAGC 59.439 43.478 0.00 1.90 35.27 4.26
1904 2507 8.019094 GCGTTTATGGTTAAAATCTTACACTGT 58.981 33.333 0.00 0.00 0.00 3.55
1905 2508 9.325150 CGTTTATGGTTAAAATCTTACACTGTG 57.675 33.333 6.19 6.19 0.00 3.66
1932 2535 7.625828 AGAACAGTTTAGCACAAAGTTACTT 57.374 32.000 0.00 0.00 0.00 2.24
1974 2579 8.080417 TCACTAGTATTATCCACGCTTGTTATC 58.920 37.037 0.00 0.00 0.00 1.75
2048 2654 8.221965 AGAGATTTGAAATCGGTTATTTACCC 57.778 34.615 11.83 0.00 44.70 3.69
2081 2687 6.647334 TTGTAATGCAGAGGTTGAATTCAA 57.353 33.333 16.91 16.91 36.42 2.69
2098 2704 0.035317 CAACTACCTCAGCTGCACCA 59.965 55.000 9.47 0.00 0.00 4.17
2111 2717 1.004044 CTGCACCAGTGAAGAAGGGAT 59.996 52.381 0.00 0.00 38.57 3.85
2149 2755 2.255252 GCAAGCGCAAATCGTGGT 59.745 55.556 11.47 0.00 41.07 4.16
2153 2759 1.503818 AAGCGCAAATCGTGGTTCGT 61.504 50.000 11.47 0.00 41.93 3.85
2169 2775 1.710013 TCGTCTGTGAAATCGGCTTC 58.290 50.000 0.00 0.00 0.00 3.86
2204 2810 0.176449 TGTCACATCTCGCCATGAGG 59.824 55.000 0.00 0.00 45.32 3.86
2226 2832 0.251354 TCCATGCAGAAGGAGAGTGC 59.749 55.000 1.49 0.00 37.73 4.40
2248 2854 0.381089 CTCCTCGTAAGGTGCCTACG 59.619 60.000 11.34 11.34 43.82 3.51
2250 2856 1.226888 CTCGTAAGGTGCCTACGGC 60.227 63.158 15.03 0.00 44.33 5.68
2414 3020 3.196469 TGACTCCTCATTGCTCGATTCTT 59.804 43.478 0.00 0.00 0.00 2.52
2416 3022 3.937706 ACTCCTCATTGCTCGATTCTTTG 59.062 43.478 0.00 0.00 0.00 2.77
2719 3344 2.622942 TGAGGTGCGCATTCTTTTCTTT 59.377 40.909 15.91 0.00 0.00 2.52
2753 3378 3.084039 CAGCCTGCTCCTTCAAATGTTA 58.916 45.455 0.00 0.00 0.00 2.41
2858 3483 4.953940 TTCTTAATGTTGCTTGCCCTTT 57.046 36.364 0.00 0.00 0.00 3.11
2863 3488 1.484038 TGTTGCTTGCCCTTTTCAGT 58.516 45.000 0.00 0.00 0.00 3.41
2928 3570 8.630054 TTGTCAATTACCAGTAGTAGCAAATT 57.370 30.769 0.00 0.00 30.92 1.82
2944 3586 5.172460 GCAAATTCCAAATGCTTGTTGTT 57.828 34.783 0.00 0.00 37.12 2.83
2970 3612 6.319658 AGTTGCCGAAAACATCAATCATAGAT 59.680 34.615 3.51 0.00 32.21 1.98
3024 3667 4.638865 ACATAAACGATTAAACCAGCCTCC 59.361 41.667 0.00 0.00 0.00 4.30
3025 3668 2.871096 AACGATTAAACCAGCCTCCA 57.129 45.000 0.00 0.00 0.00 3.86
3063 3706 9.502091 AACTAAAGCTATTGTCAGTACATTTCA 57.498 29.630 0.00 0.00 34.97 2.69
3066 3709 7.840342 AAGCTATTGTCAGTACATTTCAGAG 57.160 36.000 0.00 0.00 34.97 3.35
3070 3713 3.664107 TGTCAGTACATTTCAGAGCACC 58.336 45.455 0.00 0.00 0.00 5.01
3087 3730 7.992608 TCAGAGCACCATACATTAATGTGTTAT 59.007 33.333 27.62 12.96 41.89 1.89
3173 3816 6.940430 TGATAGAGGAATTCATGCAGGATA 57.060 37.500 0.03 0.00 0.00 2.59
3193 3836 5.832060 GGATAGAGTAGCCCTGTTGTAGTAA 59.168 44.000 0.00 0.00 0.00 2.24
3196 3839 4.705991 AGAGTAGCCCTGTTGTAGTAAGAC 59.294 45.833 0.00 0.00 0.00 3.01
3203 3846 4.202430 CCCTGTTGTAGTAAGACACCCTTT 60.202 45.833 0.00 0.00 36.34 3.11
3514 4157 9.624697 GTCACTCTTTTTCATTGTATTAATGCA 57.375 29.630 1.68 1.68 0.00 3.96
3599 4242 6.753279 TCAACTATATTGACCGTTACCTTTCG 59.247 38.462 0.00 0.00 0.00 3.46
3682 4325 5.161358 TGCGTAAGATATTAAGATCCAGCG 58.839 41.667 6.47 9.24 43.02 5.18
3691 4334 5.998454 ATTAAGATCCAGCGACTTCATTG 57.002 39.130 0.00 0.00 0.00 2.82
3693 4336 3.340814 AGATCCAGCGACTTCATTGTT 57.659 42.857 0.00 0.00 0.00 2.83
3694 4337 3.679389 AGATCCAGCGACTTCATTGTTT 58.321 40.909 0.00 0.00 0.00 2.83
3695 4338 4.832248 AGATCCAGCGACTTCATTGTTTA 58.168 39.130 0.00 0.00 0.00 2.01
3696 4339 5.431765 AGATCCAGCGACTTCATTGTTTAT 58.568 37.500 0.00 0.00 0.00 1.40
3697 4340 5.882557 AGATCCAGCGACTTCATTGTTTATT 59.117 36.000 0.00 0.00 0.00 1.40
3698 4341 5.957842 TCCAGCGACTTCATTGTTTATTT 57.042 34.783 0.00 0.00 0.00 1.40
3699 4342 7.552687 AGATCCAGCGACTTCATTGTTTATTTA 59.447 33.333 0.00 0.00 0.00 1.40
3746 4396 8.971321 GGCATTTCATTGTTAGCATACTAATTG 58.029 33.333 0.00 0.00 40.43 2.32
3749 4399 8.909708 TTTCATTGTTAGCATACTAATTGTGC 57.090 30.769 0.00 0.00 40.43 4.57
3824 4474 5.011090 TCTGCTACATCACTGACAATACC 57.989 43.478 0.00 0.00 0.00 2.73
3859 4509 7.223582 GGATGAGGTTAGTGATATATTGCATCG 59.776 40.741 0.00 0.00 0.00 3.84
3903 4553 7.550551 CACTTTGTCTCTGCCATTCTCTAATTA 59.449 37.037 0.00 0.00 0.00 1.40
4032 4682 3.426963 GCATTGGCAAATTTCATGGCTTG 60.427 43.478 3.01 0.00 43.24 4.01
4081 4732 9.213799 CTATTTCTTGCTTACCATAGGAGATTC 57.786 37.037 0.00 0.00 0.00 2.52
4123 4774 4.586421 TGTGATGAGGTATAGCTCTCTTGG 59.414 45.833 27.39 0.00 0.00 3.61
4128 4779 4.211920 GAGGTATAGCTCTCTTGGTCAGT 58.788 47.826 21.97 0.00 0.00 3.41
4159 4810 3.242870 GCTTTCTGCAATTCTATGGGTCG 60.243 47.826 0.00 0.00 42.31 4.79
4160 4811 1.953559 TCTGCAATTCTATGGGTCGC 58.046 50.000 0.00 0.00 0.00 5.19
4161 4812 1.209261 TCTGCAATTCTATGGGTCGCA 59.791 47.619 0.00 0.00 0.00 5.10
4162 4813 2.158769 TCTGCAATTCTATGGGTCGCAT 60.159 45.455 7.61 7.61 0.00 4.73
4386 5037 7.148853 GCTTTCACAAATCTTTGCAGTATCAAG 60.149 37.037 2.63 0.00 41.79 3.02
4397 5048 4.074259 TGCAGTATCAAGATGTTGCTTGT 58.926 39.130 16.25 0.00 44.30 3.16
4493 5144 4.343581 TCGGAGCTATGCGATTGC 57.656 55.556 0.00 0.00 44.95 3.56
4952 5612 2.081462 GTGGTATTGTAGTGGTGTGCC 58.919 52.381 0.00 0.00 0.00 5.01
4959 5619 2.729194 TGTAGTGGTGTGCCTTTTGTT 58.271 42.857 0.00 0.00 35.27 2.83
4960 5620 3.093057 TGTAGTGGTGTGCCTTTTGTTT 58.907 40.909 0.00 0.00 35.27 2.83
4961 5621 2.959507 AGTGGTGTGCCTTTTGTTTC 57.040 45.000 0.00 0.00 35.27 2.78
4962 5622 1.480545 AGTGGTGTGCCTTTTGTTTCC 59.519 47.619 0.00 0.00 35.27 3.13
4963 5623 1.480545 GTGGTGTGCCTTTTGTTTCCT 59.519 47.619 0.00 0.00 35.27 3.36
4964 5624 2.093711 GTGGTGTGCCTTTTGTTTCCTT 60.094 45.455 0.00 0.00 35.27 3.36
4965 5625 2.093764 TGGTGTGCCTTTTGTTTCCTTG 60.094 45.455 0.00 0.00 35.27 3.61
4966 5626 1.933181 GTGTGCCTTTTGTTTCCTTGC 59.067 47.619 0.00 0.00 0.00 4.01
4967 5627 1.134551 TGTGCCTTTTGTTTCCTTGCC 60.135 47.619 0.00 0.00 0.00 4.52
4968 5628 1.138859 GTGCCTTTTGTTTCCTTGCCT 59.861 47.619 0.00 0.00 0.00 4.75
4969 5629 1.836802 TGCCTTTTGTTTCCTTGCCTT 59.163 42.857 0.00 0.00 0.00 4.35
4970 5630 2.238395 TGCCTTTTGTTTCCTTGCCTTT 59.762 40.909 0.00 0.00 0.00 3.11
4971 5631 3.278574 GCCTTTTGTTTCCTTGCCTTTT 58.721 40.909 0.00 0.00 0.00 2.27
4972 5632 3.065233 GCCTTTTGTTTCCTTGCCTTTTG 59.935 43.478 0.00 0.00 0.00 2.44
4973 5633 4.260985 CCTTTTGTTTCCTTGCCTTTTGT 58.739 39.130 0.00 0.00 0.00 2.83
5045 5709 3.220110 TGTACCTATAGTCTTGAGCCCG 58.780 50.000 0.00 0.00 0.00 6.13
5133 5801 3.316308 GGCATAATACTTCACTTGGCTGG 59.684 47.826 0.00 0.00 0.00 4.85
5138 5806 1.214589 CTTCACTTGGCTGGCATGC 59.785 57.895 9.90 9.90 0.00 4.06
5141 5809 2.678934 ACTTGGCTGGCATGCTGG 60.679 61.111 18.92 11.58 0.00 4.85
5142 5810 3.458163 CTTGGCTGGCATGCTGGG 61.458 66.667 18.92 9.03 0.00 4.45
5143 5811 3.949885 CTTGGCTGGCATGCTGGGA 62.950 63.158 18.92 0.00 0.00 4.37
5160 5834 3.049288 AGGCCCCTCCCTCCCATA 61.049 66.667 0.00 0.00 34.51 2.74
5168 5842 3.246498 CCCCTCCCTCCCATATATGAGAA 60.246 52.174 14.54 0.00 0.00 2.87
5170 5844 4.411540 CCCTCCCTCCCATATATGAGAATG 59.588 50.000 14.54 0.83 0.00 2.67
5173 5847 4.784838 TCCCTCCCATATATGAGAATGTGG 59.215 45.833 14.54 4.03 37.75 4.17
5174 5848 4.537688 CCCTCCCATATATGAGAATGTGGT 59.462 45.833 14.54 0.00 36.63 4.16
5177 5851 6.114187 TCCCATATATGAGAATGTGGTGTC 57.886 41.667 14.54 0.00 36.63 3.67
5179 5853 5.511373 CCCATATATGAGAATGTGGTGTCGT 60.511 44.000 14.54 0.00 36.63 4.34
5180 5854 5.991606 CCATATATGAGAATGTGGTGTCGTT 59.008 40.000 14.54 0.00 34.39 3.85
5181 5855 6.073602 CCATATATGAGAATGTGGTGTCGTTG 60.074 42.308 14.54 0.00 34.39 4.10
5261 7670 3.881089 TCCTGCATGATGCTGTATTGAAG 59.119 43.478 19.19 4.62 45.31 3.02
5286 7695 7.636259 AAATGACAAAACATTTCATACGGTG 57.364 32.000 0.00 0.00 43.95 4.94
5288 7697 4.277174 TGACAAAACATTTCATACGGTGCT 59.723 37.500 0.00 0.00 0.00 4.40
5345 7754 9.613428 TCTTCAGAGTTGTTTTCAAGATTTCTA 57.387 29.630 0.00 0.00 40.74 2.10
5363 7772 3.445008 TCTACTTGAAGCCAGAGGTGAT 58.555 45.455 0.00 0.00 0.00 3.06
5392 7802 1.141657 GAATAGCAGATGGTGGCTGGA 59.858 52.381 0.00 0.00 41.25 3.86
5416 7826 4.278419 GCTTTTGTGTTAGATGTGGTCCTT 59.722 41.667 0.00 0.00 0.00 3.36
5422 7832 3.901222 TGTTAGATGTGGTCCTTGACTCA 59.099 43.478 0.00 0.00 32.47 3.41
5436 7846 8.360390 GGTCCTTGACTCACAGAAAATTTAATT 58.640 33.333 0.00 0.00 32.47 1.40
5586 7996 5.278071 CGTCTAGTGGCTGAAGACTATAAGG 60.278 48.000 10.45 0.00 37.97 2.69
5633 8043 5.751243 ATGGTAGCATTCCGTTTGTATTC 57.249 39.130 0.40 0.00 0.00 1.75
5680 8090 8.425577 AGATGTATAACAAGTCTGCAACATAC 57.574 34.615 0.00 0.00 0.00 2.39
5685 8095 9.193133 GTATAACAAGTCTGCAACATACGATAT 57.807 33.333 0.00 0.00 0.00 1.63
5691 8101 9.573133 CAAGTCTGCAACATACGATATATATCA 57.427 33.333 20.18 4.66 32.98 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.733960 GCGGGTTTGAACCTCCGC 61.734 66.667 16.67 16.67 46.68 5.54
184 207 0.817654 CTCGATGCACACTCCTGGTA 59.182 55.000 0.00 0.00 0.00 3.25
186 209 1.812922 GCTCGATGCACACTCCTGG 60.813 63.158 0.00 0.00 42.31 4.45
187 210 2.163390 CGCTCGATGCACACTCCTG 61.163 63.158 0.00 0.00 43.06 3.86
338 364 3.558099 GAACCAAGGCCGTTGCTGC 62.558 63.158 0.00 0.00 37.74 5.25
339 365 1.856265 GAGAACCAAGGCCGTTGCTG 61.856 60.000 0.00 0.00 37.74 4.41
340 366 1.600916 GAGAACCAAGGCCGTTGCT 60.601 57.895 0.00 0.00 37.74 3.91
344 370 1.275573 GAGTTAGAGAACCAAGGCCGT 59.724 52.381 0.00 0.00 36.08 5.68
372 398 3.955650 TGAAACCAGGAGTACTAGTGC 57.044 47.619 5.39 3.75 0.00 4.40
408 436 2.597510 GCCCAGGGTTGTGTCACC 60.598 66.667 7.55 0.00 35.88 4.02
418 446 0.918983 TGGATTAGTTCAGCCCAGGG 59.081 55.000 0.00 0.00 0.00 4.45
419 447 1.743772 CGTGGATTAGTTCAGCCCAGG 60.744 57.143 0.00 0.00 0.00 4.45
575 605 4.927978 TTAAACTTCCATTGTGGTGGTG 57.072 40.909 0.00 0.00 39.03 4.17
581 611 5.982890 ACCTGGATTAAACTTCCATTGTG 57.017 39.130 0.00 0.00 42.26 3.33
585 615 8.664669 AAATGTAACCTGGATTAAACTTCCAT 57.335 30.769 0.00 0.00 42.26 3.41
603 633 2.156098 GTGCCACCGGAGAAAATGTAA 58.844 47.619 9.46 0.00 0.00 2.41
624 654 6.627243 AGGATTTTTAAGTTTATTCCGTGGC 58.373 36.000 0.00 0.00 0.00 5.01
644 674 8.367911 TGTGCTCACGAATAATAATTCTAGGAT 58.632 33.333 0.00 0.00 39.56 3.24
645 675 7.722363 TGTGCTCACGAATAATAATTCTAGGA 58.278 34.615 0.00 0.00 39.56 2.94
647 677 8.006590 GCTTGTGCTCACGAATAATAATTCTAG 58.993 37.037 0.00 0.00 36.82 2.43
648 678 7.042051 GGCTTGTGCTCACGAATAATAATTCTA 60.042 37.037 0.00 0.00 38.33 2.10
649 679 6.238484 GGCTTGTGCTCACGAATAATAATTCT 60.238 38.462 0.00 0.00 38.33 2.40
651 681 5.221048 GGGCTTGTGCTCACGAATAATAATT 60.221 40.000 0.00 0.00 40.03 1.40
673 807 0.904649 TGTAGTGCACCTGAGATGGG 59.095 55.000 14.63 0.00 0.00 4.00
685 827 0.593128 CAAACTGCCCTGTGTAGTGC 59.407 55.000 0.00 0.00 39.18 4.40
688 830 4.853924 AAATTCAAACTGCCCTGTGTAG 57.146 40.909 0.00 0.00 0.00 2.74
691 833 4.448732 GCTTAAAATTCAAACTGCCCTGTG 59.551 41.667 0.00 0.00 0.00 3.66
693 835 3.674753 CGCTTAAAATTCAAACTGCCCTG 59.325 43.478 0.00 0.00 0.00 4.45
753 1261 5.476945 TCCTTTCAAAATAGTTTCCTGCCTC 59.523 40.000 0.00 0.00 0.00 4.70
815 1325 1.045911 CGGGGAGAGAAGAAGAGGGG 61.046 65.000 0.00 0.00 0.00 4.79
816 1326 0.324830 ACGGGGAGAGAAGAAGAGGG 60.325 60.000 0.00 0.00 0.00 4.30
844 1354 2.283173 CCTGGGGTTTGGGACTGC 60.283 66.667 0.00 0.00 0.00 4.40
916 1441 1.077716 GGATTTGTAGGGCAGCGGT 60.078 57.895 0.00 0.00 0.00 5.68
939 1473 3.637273 ACAACCACCGAGGCCTCC 61.637 66.667 27.20 9.59 43.14 4.30
944 1478 2.281484 CCACCACAACCACCGAGG 60.281 66.667 0.00 0.00 45.67 4.63
945 1479 2.978010 GCCACCACAACCACCGAG 60.978 66.667 0.00 0.00 0.00 4.63
1122 1680 2.282674 TTCTTGGCCTGCTGCTGG 60.283 61.111 19.96 19.96 40.92 4.85
1248 1806 1.457346 AAAAGGCAATCTCTCAGGCG 58.543 50.000 0.00 0.00 0.00 5.52
1275 1839 4.232221 GCAACCATTTCATCTCACAACAG 58.768 43.478 0.00 0.00 0.00 3.16
1283 1847 2.086869 CAGACGGCAACCATTTCATCT 58.913 47.619 0.00 0.00 0.00 2.90
1331 1909 6.654161 TCCAACCAATAGCCATTCAAAATTTG 59.346 34.615 0.00 0.00 0.00 2.32
1332 1910 6.777782 TCCAACCAATAGCCATTCAAAATTT 58.222 32.000 0.00 0.00 0.00 1.82
1349 1927 2.111999 CTCGTGCCCTTCTCCAACCA 62.112 60.000 0.00 0.00 0.00 3.67
1351 1929 2.035442 GCTCGTGCCCTTCTCCAAC 61.035 63.158 0.00 0.00 0.00 3.77
1353 1931 4.069232 CGCTCGTGCCCTTCTCCA 62.069 66.667 3.52 0.00 35.36 3.86
1355 1933 4.742201 TGCGCTCGTGCCCTTCTC 62.742 66.667 9.73 0.00 35.36 2.87
1402 1987 1.128200 CATCCGTAGAACCCCATGGA 58.872 55.000 15.22 0.00 34.81 3.41
1451 2041 0.108329 TCCGCATCGAGAGTTTTCCC 60.108 55.000 0.00 0.00 0.00 3.97
1458 2048 1.067669 TCCAAATCTCCGCATCGAGAG 59.932 52.381 0.00 0.00 42.06 3.20
1501 2091 9.971744 GAAAAACTACTAAACGTTTGACTTGTA 57.028 29.630 23.46 15.08 33.93 2.41
1540 2130 0.040958 GGAGGCAATAAATCGCAGCG 60.041 55.000 9.06 9.06 0.00 5.18
1541 2131 1.002033 CAGGAGGCAATAAATCGCAGC 60.002 52.381 0.00 0.00 0.00 5.25
1559 2154 0.391661 ACGCTGCTGATTGGGTACAG 60.392 55.000 0.00 0.00 37.22 2.74
1601 2199 2.481276 GCCAAAGACAACCCAGAAACAC 60.481 50.000 0.00 0.00 0.00 3.32
1615 2213 2.297033 GGAAAGCATCACAAGCCAAAGA 59.703 45.455 0.00 0.00 0.00 2.52
1616 2214 2.036217 TGGAAAGCATCACAAGCCAAAG 59.964 45.455 0.00 0.00 0.00 2.77
1648 2246 3.923017 AGGAAAAGTGGAAAATGAGCG 57.077 42.857 0.00 0.00 0.00 5.03
1649 2247 8.498358 CAATTTTAGGAAAAGTGGAAAATGAGC 58.502 33.333 4.62 0.00 41.34 4.26
1734 2337 4.350520 AGAGGCATCAAAATTTGGGGAAAA 59.649 37.500 5.83 0.00 0.00 2.29
1738 2341 3.986996 AAGAGGCATCAAAATTTGGGG 57.013 42.857 5.83 0.00 0.00 4.96
1781 2384 3.791245 AGGCGCAAAATTGAGTGAAAAA 58.209 36.364 10.83 0.00 0.00 1.94
1810 2413 0.236711 CCGCAACAGAAAGAGCAGTG 59.763 55.000 0.00 0.00 0.00 3.66
1842 2445 4.057406 TGCCAGAAAATGAACCAAACTG 57.943 40.909 0.00 0.00 0.00 3.16
1904 2507 5.123227 ACTTTGTGCTAAACTGTTCTAGCA 58.877 37.500 22.07 22.07 46.32 3.49
1905 2508 5.674933 ACTTTGTGCTAAACTGTTCTAGC 57.325 39.130 19.03 19.03 40.82 3.42
1974 2579 9.248291 AGCAAAGTTGAATTACAAATTGTACAG 57.752 29.630 5.19 0.00 44.24 2.74
1996 2602 1.130938 CACGCATGCATCAGTAAGCAA 59.869 47.619 19.57 0.00 44.88 3.91
2048 2654 6.917533 ACCTCTGCATTACAAATTCAGAAAG 58.082 36.000 4.09 2.18 33.93 2.62
2081 2687 0.833834 ACTGGTGCAGCTGAGGTAGT 60.834 55.000 26.72 13.40 34.37 2.73
2098 2704 2.376518 TGGCAAAGATCCCTTCTTCACT 59.623 45.455 0.00 0.00 44.09 3.41
2149 2755 2.066262 GAAGCCGATTTCACAGACGAA 58.934 47.619 0.00 0.00 0.00 3.85
2153 2759 1.808411 GTGGAAGCCGATTTCACAGA 58.192 50.000 2.79 0.00 45.53 3.41
2169 2775 2.360852 CAGGAGCTGGCTTGGTGG 60.361 66.667 0.00 0.00 0.00 4.61
2204 2810 0.179051 CTCTCCTTCTGCATGGAGCC 60.179 60.000 19.63 0.00 46.90 4.70
2226 2832 0.684805 AGGCACCTTACGAGGAGGAG 60.685 60.000 9.77 4.16 46.74 3.69
2320 2926 5.407407 ACATAGTCTCGTCAGTGGAAATT 57.593 39.130 0.00 0.00 0.00 1.82
2414 3020 1.007964 CATTTGCCCGTCGTTGCAA 60.008 52.632 13.48 13.48 45.12 4.08
2416 3022 0.318275 TTTCATTTGCCCGTCGTTGC 60.318 50.000 0.00 0.00 0.00 4.17
2419 3025 0.312729 GGTTTTCATTTGCCCGTCGT 59.687 50.000 0.00 0.00 0.00 4.34
2632 3257 3.118482 ACAGCTGTGGATCCTCATAGTTG 60.118 47.826 20.97 15.27 40.74 3.16
2719 3344 2.039480 AGCAGGCTGAAAGAAGATGTCA 59.961 45.455 20.86 0.00 34.07 3.58
2816 3441 1.949525 ACATGCGCAAACTGAAGAAGT 59.050 42.857 17.11 0.00 42.60 3.01
2858 3483 4.039245 CAGACCTCTAGACCACAAACTGAA 59.961 45.833 0.00 0.00 0.00 3.02
2863 3488 2.557056 CGACAGACCTCTAGACCACAAA 59.443 50.000 0.00 0.00 0.00 2.83
2928 3570 4.367450 GCAACTAACAACAAGCATTTGGA 58.633 39.130 0.00 0.00 38.66 3.53
2944 3586 5.895636 ATGATTGATGTTTTCGGCAACTA 57.104 34.783 0.00 0.00 0.00 2.24
3104 3747 5.235516 ACACTACCTTTTGACATCCTAACG 58.764 41.667 0.00 0.00 0.00 3.18
3173 3816 4.705991 GTCTTACTACAACAGGGCTACTCT 59.294 45.833 0.00 0.00 0.00 3.24
3193 3836 4.529377 TCCATTACGACTTAAAGGGTGTCT 59.471 41.667 0.00 0.00 30.56 3.41
3196 3839 4.828829 ACTCCATTACGACTTAAAGGGTG 58.171 43.478 0.00 0.00 30.56 4.61
3481 4124 4.713792 ATGAAAAAGAGTGACCTCCAGT 57.286 40.909 0.00 0.00 38.58 4.00
3599 4242 1.643832 GCGATTGATCTCGTTGCCC 59.356 57.895 6.28 0.00 40.73 5.36
3699 4342 9.729281 AATGCCAATCAAGAGTAAATGAAAAAT 57.271 25.926 0.00 0.00 0.00 1.82
3746 4396 8.604035 TCATATTTACTGAAAATCGAAGAGCAC 58.396 33.333 0.00 0.00 43.63 4.40
3749 4399 9.534565 TCCTCATATTTACTGAAAATCGAAGAG 57.465 33.333 0.00 0.00 43.63 2.85
3824 4474 6.531503 TCACTAACCTCATCCTTGAAGTAG 57.468 41.667 0.00 0.00 0.00 2.57
3859 4509 3.521524 GTGACAAACACTGAACGATCC 57.478 47.619 0.00 0.00 45.13 3.36
4032 4682 6.459923 AGAGAAAGTGAGATTCAGTTGGTAC 58.540 40.000 0.27 0.00 38.97 3.34
4081 4732 4.988598 ACTTGTGCAGCCCGGACG 62.989 66.667 0.73 0.00 39.19 4.79
4123 4774 3.625938 CAGAAAGCAAGCAGAAACTGAC 58.374 45.455 2.81 0.00 32.44 3.51
4151 4802 4.709250 TGCTACAAAATATGCGACCCATA 58.291 39.130 0.00 0.00 40.52 2.74
4355 5006 3.183775 GCAAAGATTTGTGAAAGCTGCAG 59.816 43.478 10.11 10.11 37.18 4.41
4386 5037 4.858935 TGTTAGCTCAAACAAGCAACATC 58.141 39.130 0.00 0.00 45.00 3.06
4397 5048 6.014070 TGGGAAGTAGTACATGTTAGCTCAAA 60.014 38.462 2.30 0.00 0.00 2.69
4952 5612 5.878332 AACAAAAGGCAAGGAAACAAAAG 57.122 34.783 0.00 0.00 0.00 2.27
4959 5619 3.772025 TCAAGGAAACAAAAGGCAAGGAA 59.228 39.130 0.00 0.00 0.00 3.36
4960 5620 3.132111 GTCAAGGAAACAAAAGGCAAGGA 59.868 43.478 0.00 0.00 0.00 3.36
4961 5621 3.132824 AGTCAAGGAAACAAAAGGCAAGG 59.867 43.478 0.00 0.00 0.00 3.61
4962 5622 4.391405 AGTCAAGGAAACAAAAGGCAAG 57.609 40.909 0.00 0.00 0.00 4.01
4963 5623 4.020662 ACAAGTCAAGGAAACAAAAGGCAA 60.021 37.500 0.00 0.00 0.00 4.52
4964 5624 3.513515 ACAAGTCAAGGAAACAAAAGGCA 59.486 39.130 0.00 0.00 0.00 4.75
4965 5625 4.112634 GACAAGTCAAGGAAACAAAAGGC 58.887 43.478 0.00 0.00 0.00 4.35
4966 5626 4.402474 AGGACAAGTCAAGGAAACAAAAGG 59.598 41.667 2.29 0.00 0.00 3.11
4967 5627 5.582689 AGGACAAGTCAAGGAAACAAAAG 57.417 39.130 2.29 0.00 0.00 2.27
4968 5628 5.105513 GGAAGGACAAGTCAAGGAAACAAAA 60.106 40.000 2.29 0.00 0.00 2.44
4969 5629 4.401202 GGAAGGACAAGTCAAGGAAACAAA 59.599 41.667 2.29 0.00 0.00 2.83
4970 5630 3.951680 GGAAGGACAAGTCAAGGAAACAA 59.048 43.478 2.29 0.00 0.00 2.83
4971 5631 3.202151 AGGAAGGACAAGTCAAGGAAACA 59.798 43.478 2.29 0.00 0.00 2.83
4972 5632 3.815962 GAGGAAGGACAAGTCAAGGAAAC 59.184 47.826 2.29 0.00 0.00 2.78
4973 5633 3.716872 AGAGGAAGGACAAGTCAAGGAAA 59.283 43.478 2.29 0.00 0.00 3.13
5038 5702 1.228429 CCTGAAAAACCCGGGCTCA 60.228 57.895 24.08 17.12 0.00 4.26
5045 5709 2.625790 TGTACATGCACCTGAAAAACCC 59.374 45.455 0.00 0.00 0.00 4.11
5094 5758 9.801873 GTATTATGCCATTACAAACAAGATGTT 57.198 29.630 0.00 0.00 43.41 2.71
5142 5810 2.423479 ATATGGGAGGGAGGGGCCTC 62.423 65.000 0.84 0.00 42.04 4.70
5143 5811 1.092616 TATATGGGAGGGAGGGGCCT 61.093 60.000 0.84 0.00 36.66 5.19
5147 5821 3.784311 TCTCATATATGGGAGGGAGGG 57.216 52.381 11.44 0.00 30.96 4.30
5160 5834 4.832248 ACAACGACACCACATTCTCATAT 58.168 39.130 0.00 0.00 0.00 1.78
5168 5842 3.069016 TCAGACTAACAACGACACCACAT 59.931 43.478 0.00 0.00 0.00 3.21
5170 5844 3.088194 TCAGACTAACAACGACACCAC 57.912 47.619 0.00 0.00 0.00 4.16
5173 5847 8.906636 TTAAGATATCAGACTAACAACGACAC 57.093 34.615 5.32 0.00 0.00 3.67
5279 7688 3.070159 ACAGAGCAATATCAGCACCGTAT 59.930 43.478 3.33 0.00 0.00 3.06
5286 7695 3.273434 TGGAACACAGAGCAATATCAGC 58.727 45.455 0.00 0.00 0.00 4.26
5288 7697 5.534278 TGTTTTGGAACACAGAGCAATATCA 59.466 36.000 0.00 0.00 40.71 2.15
5345 7754 1.004044 CCATCACCTCTGGCTTCAAGT 59.996 52.381 0.00 0.00 0.00 3.16
5363 7772 2.158856 CCATCTGCTATTCTGCTGTCCA 60.159 50.000 0.00 0.00 34.27 4.02
5392 7802 3.821033 GGACCACATCTAACACAAAAGCT 59.179 43.478 0.00 0.00 0.00 3.74
5436 7846 8.156820 ACATCTCCATGACATATTCGGAAATAA 58.843 33.333 0.00 0.00 33.72 1.40
5439 7849 5.928976 ACATCTCCATGACATATTCGGAAA 58.071 37.500 0.00 0.00 33.72 3.13
5443 7853 6.703165 TGAGAAACATCTCCATGACATATTCG 59.297 38.462 0.00 0.00 35.97 3.34
5586 7996 2.973694 ATGCCAAATGCTGAATGTCC 57.026 45.000 0.00 0.00 42.00 4.02
5680 8090 7.733608 AGCTGCGAAGTTTTTGATATATATCG 58.266 34.615 16.21 5.46 35.48 2.92
5685 8095 5.799936 GCAAAGCTGCGAAGTTTTTGATATA 59.200 36.000 20.20 0.00 39.20 0.86


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

AutoCloner maintained by Alex Coulton.