Multiple sequence alignment - TraesCS2A01G543700

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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 TraesCS2A01G543700 chr2A 100.000 3822 0 0 1 3822 753438453 753442274 0.000000e+00 7059.0
1 TraesCS2A01G543700 chr2A 88.644 317 26 5 1234 1543 753475314 753475627 1.000000e-100 377.0
2 TraesCS2A01G543700 chr2A 83.516 91 13 2 3706 3795 68243252 68243163 2.450000e-12 84.2
3 TraesCS2A01G543700 chr2A 89.655 58 5 1 2023 2080 431044662 431044718 5.300000e-09 73.1
4 TraesCS2A01G543700 chr2A 100.000 28 0 0 1440 1467 753475318 753475291 7.000000e-03 52.8
5 TraesCS2A01G543700 chr2D 95.276 1630 53 14 2082 3698 621751479 621753097 0.000000e+00 2562.0
6 TraesCS2A01G543700 chr2D 94.922 1280 46 7 808 2080 621750175 621751442 0.000000e+00 1986.0
7 TraesCS2A01G543700 chr2D 93.967 663 19 6 161 822 621748162 621748804 0.000000e+00 983.0
8 TraesCS2A01G543700 chr2D 88.693 283 22 8 488 761 621674169 621674450 1.700000e-88 337.0
9 TraesCS2A01G543700 chr2B 97.490 956 21 3 716 1670 763498002 763498955 0.000000e+00 1629.0
10 TraesCS2A01G543700 chr2B 94.747 1009 29 7 2082 3079 763502975 763503970 0.000000e+00 1548.0
11 TraesCS2A01G543700 chr2B 96.359 714 25 1 2 714 763495579 763496292 0.000000e+00 1173.0
12 TraesCS2A01G543700 chr2B 97.625 421 8 2 1661 2080 763502519 763502938 0.000000e+00 721.0
13 TraesCS2A01G543700 chr2B 96.104 77 2 1 3706 3781 222528549 222528625 1.440000e-24 124.0
14 TraesCS2A01G543700 chr6D 83.078 981 113 34 923 1878 1561743 1560791 0.000000e+00 843.0
15 TraesCS2A01G543700 chr6D 81.591 842 104 23 2107 2909 1560739 1559910 0.000000e+00 649.0
16 TraesCS2A01G543700 chr6A 82.044 1008 117 42 883 1878 1090499 1091454 0.000000e+00 800.0
17 TraesCS2A01G543700 chr3B 82.310 961 112 37 925 1879 160824652 160823744 0.000000e+00 780.0
18 TraesCS2A01G543700 chr3B 86.957 276 36 0 2199 2474 160823651 160823376 1.030000e-80 311.0
19 TraesCS2A01G543700 chr3B 92.903 155 11 0 2527 2681 160823144 160822990 3.840000e-55 226.0
20 TraesCS2A01G543700 chr3A 81.828 941 134 25 941 1880 120692109 120693013 0.000000e+00 756.0
21 TraesCS2A01G543700 chr3A 88.000 225 27 0 2526 2750 120693712 120693936 2.260000e-67 267.0
22 TraesCS2A01G543700 chr3D 86.648 352 42 3 925 1275 109739838 109739491 5.990000e-103 385.0
23 TraesCS2A01G543700 chr3D 89.177 231 25 0 2524 2754 109738791 109738561 4.830000e-74 289.0
24 TraesCS2A01G543700 chr5B 92.308 65 4 1 3701 3765 15842884 15842947 1.460000e-14 91.6
25 TraesCS2A01G543700 chr4A 89.062 64 7 0 3706 3769 377590687 377590624 3.170000e-11 80.5
26 TraesCS2A01G543700 chr4A 100.000 29 0 0 2047 2075 704327728 704327756 2.000000e-03 54.7
27 TraesCS2A01G543700 chr1A 88.235 68 7 1 3702 3769 505077900 505077966 3.170000e-11 80.5
28 TraesCS2A01G543700 chr1D 85.507 69 7 3 2008 2075 312962673 312962739 6.850000e-08 69.4
29 TraesCS2A01G543700 chr6B 87.931 58 6 1 3702 3759 523950295 523950239 2.460000e-07 67.6
30 TraesCS2A01G543700 chr7B 100.000 28 0 0 3702 3729 679844226 679844199 7.000000e-03 52.8


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 TraesCS2A01G543700 chr2A 753438453 753442274 3821 False 7059.000000 7059 100.000000 1 3822 1 chr2A.!!$F2 3821
1 TraesCS2A01G543700 chr2D 621748162 621753097 4935 False 1843.666667 2562 94.721667 161 3698 3 chr2D.!!$F2 3537
2 TraesCS2A01G543700 chr2B 763495579 763503970 8391 False 1267.750000 1629 96.555250 2 3079 4 chr2B.!!$F2 3077
3 TraesCS2A01G543700 chr6D 1559910 1561743 1833 True 746.000000 843 82.334500 923 2909 2 chr6D.!!$R1 1986
4 TraesCS2A01G543700 chr6A 1090499 1091454 955 False 800.000000 800 82.044000 883 1878 1 chr6A.!!$F1 995
5 TraesCS2A01G543700 chr3B 160822990 160824652 1662 True 439.000000 780 87.390000 925 2681 3 chr3B.!!$R1 1756
6 TraesCS2A01G543700 chr3A 120692109 120693936 1827 False 511.500000 756 84.914000 941 2750 2 chr3A.!!$F1 1809
7 TraesCS2A01G543700 chr3D 109738561 109739838 1277 True 337.000000 385 87.912500 925 2754 2 chr3D.!!$R1 1829

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
912 4009 2.146342 CCCGAGTGCACATGGATATTC 58.854 52.381 24.31 8.41 0.0 1.75 F
1562 4684 1.251251 CCCTTTCAACAGCTCCTTGG 58.749 55.000 1.62 0.00 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 8716 1.541588 CTTCTGGCCCGGAAGAAAAAG 59.458 52.381 25.42 0.0 46.45 2.27 R
3135 10230 1.132689 AGGTGGAGAACTGAAGGGAGT 60.133 52.381 0.00 0.0 0.00 3.85 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
105 106 2.750350 CCACGGAGGAACAAGCCT 59.250 61.111 0.00 0.00 41.22 4.58
122 123 5.045869 ACAAGCCTACATAACAAGCCTCTAA 60.046 40.000 0.00 0.00 0.00 2.10
128 130 9.720769 GCCTACATAACAAGCCTCTAATTTATA 57.279 33.333 0.00 0.00 0.00 0.98
556 558 7.928167 TCATATAGTTTCATAGACTGCAACAGG 59.072 37.037 0.00 0.00 33.94 4.00
573 575 5.920840 GCAACAGGAAGAAATAAAGGTCAAC 59.079 40.000 0.00 0.00 0.00 3.18
851 3946 6.398918 AGATACTTACAGACAAAGCACGAAT 58.601 36.000 0.00 0.00 0.00 3.34
907 4004 4.408821 GGCCCGAGTGCACATGGA 62.409 66.667 24.31 0.00 0.00 3.41
912 4009 2.146342 CCCGAGTGCACATGGATATTC 58.854 52.381 24.31 8.41 0.00 1.75
1194 4294 2.173356 TCCGATCATCCCTTTCAGCAAT 59.827 45.455 0.00 0.00 0.00 3.56
1316 4416 7.361031 CGTCCTTTATCTCGAATTAGCTAGCTA 60.361 40.741 20.67 20.67 0.00 3.32
1562 4684 1.251251 CCCTTTCAACAGCTCCTTGG 58.749 55.000 1.62 0.00 0.00 3.61
1566 4688 3.741476 CAACAGCTCCTTGGGCGC 61.741 66.667 0.00 0.00 34.52 6.53
1666 8363 4.868734 CCAAGTCCACTCGGTTATAAGTTC 59.131 45.833 0.00 0.00 0.00 3.01
2003 8716 8.794406 CACGTGACAAATATTAATTACCAAAGC 58.206 33.333 10.90 0.00 0.00 3.51
2042 8755 3.436577 AGAGAGTACTTTCTCCGACCA 57.563 47.619 10.07 0.00 43.74 4.02
2075 8788 5.087323 GTCCCTCCAATGGATGTATCTAGA 58.913 45.833 0.87 0.00 33.65 2.43
2080 8793 6.174720 TCCAATGGATGTATCTAGAACCAC 57.825 41.667 0.00 0.00 0.00 4.16
2084 8832 5.339008 TGGATGTATCTAGAACCACACAC 57.661 43.478 0.00 0.00 0.00 3.82
2881 9962 1.957877 GAAGCTCTATCCTACGGCTGT 59.042 52.381 2.42 2.42 33.30 4.40
2933 10020 7.074653 ACTCCTTCAATAACTCCACACTTAA 57.925 36.000 0.00 0.00 0.00 1.85
2934 10021 7.690256 ACTCCTTCAATAACTCCACACTTAAT 58.310 34.615 0.00 0.00 0.00 1.40
2936 10023 7.458397 TCCTTCAATAACTCCACACTTAATGT 58.542 34.615 0.00 0.00 44.81 2.71
2937 10024 8.598916 TCCTTCAATAACTCCACACTTAATGTA 58.401 33.333 0.00 0.00 40.64 2.29
2938 10025 8.665685 CCTTCAATAACTCCACACTTAATGTAC 58.334 37.037 0.00 0.00 40.64 2.90
2939 10026 9.436957 CTTCAATAACTCCACACTTAATGTACT 57.563 33.333 0.00 0.00 40.64 2.73
3004 10099 5.528870 GGCGGTATAAATTAAAGCAGCATT 58.471 37.500 0.00 0.00 0.00 3.56
3073 10168 2.486592 GCGTGTGGTGGCTATTTTTACT 59.513 45.455 0.00 0.00 0.00 2.24
3134 10229 5.423886 AGCTTTCTTTAAATCGCTCTAGCT 58.576 37.500 0.00 0.00 39.32 3.32
3135 10230 6.574350 AGCTTTCTTTAAATCGCTCTAGCTA 58.426 36.000 0.00 0.00 39.32 3.32
3138 10233 7.306341 GCTTTCTTTAAATCGCTCTAGCTACTC 60.306 40.741 0.00 0.00 39.32 2.59
3140 10235 4.850347 TTAAATCGCTCTAGCTACTCCC 57.150 45.455 0.00 0.00 39.32 4.30
3141 10236 2.668144 AATCGCTCTAGCTACTCCCT 57.332 50.000 0.00 0.00 39.32 4.20
3142 10237 2.668144 ATCGCTCTAGCTACTCCCTT 57.332 50.000 0.00 0.00 39.32 3.95
3143 10238 1.970092 TCGCTCTAGCTACTCCCTTC 58.030 55.000 0.00 0.00 39.32 3.46
3144 10239 1.212195 TCGCTCTAGCTACTCCCTTCA 59.788 52.381 0.00 0.00 39.32 3.02
3145 10240 1.606668 CGCTCTAGCTACTCCCTTCAG 59.393 57.143 0.00 0.00 39.32 3.02
3146 10241 2.661718 GCTCTAGCTACTCCCTTCAGT 58.338 52.381 0.00 0.00 38.21 3.41
3155 10250 1.132689 ACTCCCTTCAGTTCTCCACCT 60.133 52.381 0.00 0.00 0.00 4.00
3178 10273 5.766590 TCAGAGTCCTACCAATCAGTATCA 58.233 41.667 0.00 0.00 0.00 2.15
3192 10287 7.201794 CCAATCAGTATCAGTGCATTGATTCTT 60.202 37.037 27.09 12.34 38.65 2.52
3237 10336 2.977808 ACTTCTCCATCCCATCGGTAT 58.022 47.619 0.00 0.00 0.00 2.73
3262 10361 5.045869 CAGAACCTTGGAGATAACTAACCCA 60.046 44.000 0.00 0.00 0.00 4.51
3263 10362 5.731678 AGAACCTTGGAGATAACTAACCCAT 59.268 40.000 0.00 0.00 0.00 4.00
3264 10363 5.373812 ACCTTGGAGATAACTAACCCATG 57.626 43.478 0.00 0.00 0.00 3.66
3266 10365 5.672194 ACCTTGGAGATAACTAACCCATGAT 59.328 40.000 0.00 0.00 0.00 2.45
3267 10366 6.849697 ACCTTGGAGATAACTAACCCATGATA 59.150 38.462 0.00 0.00 0.00 2.15
3304 10404 3.208383 CGGCCGCATGCATTGGTA 61.208 61.111 14.67 0.00 43.89 3.25
3339 10439 0.037232 AAGGGAAAAGCTCGAGACGG 60.037 55.000 18.75 0.00 0.00 4.79
3380 10480 2.678934 ACCGGCCAGCTTAGTCGA 60.679 61.111 9.02 0.00 0.00 4.20
3413 10513 2.725312 GGGCCAGCGATGTCAGAGA 61.725 63.158 4.39 0.00 0.00 3.10
3431 10531 8.262933 TGTCAGAGATTAAGATGATTGATGTGT 58.737 33.333 0.00 0.00 0.00 3.72
3434 10534 7.713942 CAGAGATTAAGATGATTGATGTGTCCA 59.286 37.037 0.00 0.00 0.00 4.02
3516 10616 5.610557 TGGGGATTTTCTTTTCTTTTGGGAT 59.389 36.000 0.00 0.00 0.00 3.85
3519 10619 6.430925 GGGATTTTCTTTTCTTTTGGGATTGG 59.569 38.462 0.00 0.00 0.00 3.16
3547 10647 6.640518 AGTAGACAGAGAAACAGAACAAACA 58.359 36.000 0.00 0.00 0.00 2.83
3590 10690 8.225107 GTGTTGTTAACTTTTTCCCAAAGAAAC 58.775 33.333 7.22 6.04 44.20 2.78
3605 10705 6.209361 CCAAAGAAACAAAACCTTAGCTCTC 58.791 40.000 0.00 0.00 0.00 3.20
3607 10707 4.704965 AGAAACAAAACCTTAGCTCTCGT 58.295 39.130 0.00 0.00 0.00 4.18
3616 10716 3.182967 CCTTAGCTCTCGTCATGTCAAC 58.817 50.000 0.00 0.00 0.00 3.18
3617 10717 3.367395 CCTTAGCTCTCGTCATGTCAACA 60.367 47.826 0.00 0.00 0.00 3.33
3654 10754 2.016704 CGGCGATACTGCGATGGAC 61.017 63.158 0.00 0.00 35.06 4.02
3664 10764 2.278206 CGATGGACTGAGGCGTCG 60.278 66.667 1.39 0.00 34.75 5.12
3698 10798 7.782168 TGGTGCCATCAATAGTTCCATTTATTA 59.218 33.333 0.00 0.00 0.00 0.98
3699 10799 8.806146 GGTGCCATCAATAGTTCCATTTATTAT 58.194 33.333 0.00 0.00 0.00 1.28
3711 10811 9.560860 AGTTCCATTTATTATTTTTCTTCCCCT 57.439 29.630 0.00 0.00 0.00 4.79
3714 10814 9.654919 TCCATTTATTATTTTTCTTCCCCTAGG 57.345 33.333 0.06 0.06 0.00 3.02
3715 10815 8.870116 CCATTTATTATTTTTCTTCCCCTAGGG 58.130 37.037 22.25 22.25 46.11 3.53
3716 10816 9.434275 CATTTATTATTTTTCTTCCCCTAGGGT 57.566 33.333 26.66 7.04 44.74 4.34
3718 10818 9.846725 TTTATTATTTTTCTTCCCCTAGGGTTT 57.153 29.630 26.66 2.94 44.74 3.27
3719 10819 7.973048 ATTATTTTTCTTCCCCTAGGGTTTC 57.027 36.000 26.66 0.00 44.74 2.78
3720 10820 3.820195 TTTTCTTCCCCTAGGGTTTCC 57.180 47.619 26.66 0.00 44.74 3.13
3721 10821 1.677490 TTCTTCCCCTAGGGTTTCCC 58.323 55.000 26.66 0.00 44.74 3.97
3730 10830 4.593677 GGGTTTCCCTAGGGTCCA 57.406 61.111 27.58 10.25 41.34 4.02
3731 10831 2.795406 GGGTTTCCCTAGGGTCCAA 58.205 57.895 27.58 15.59 41.34 3.53
3732 10832 0.330604 GGGTTTCCCTAGGGTCCAAC 59.669 60.000 27.58 24.39 41.34 3.77
3733 10833 1.369403 GGTTTCCCTAGGGTCCAACT 58.631 55.000 27.58 0.00 36.47 3.16
3734 10834 1.281287 GGTTTCCCTAGGGTCCAACTC 59.719 57.143 27.58 16.46 36.47 3.01
3735 10835 2.267192 GTTTCCCTAGGGTCCAACTCT 58.733 52.381 27.58 0.00 36.47 3.24
3736 10836 2.643304 GTTTCCCTAGGGTCCAACTCTT 59.357 50.000 27.58 0.00 36.47 2.85
3737 10837 2.249309 TCCCTAGGGTCCAACTCTTC 57.751 55.000 27.58 0.00 36.47 2.87
3738 10838 1.205055 CCCTAGGGTCCAACTCTTCC 58.795 60.000 20.88 0.00 27.79 3.46
3739 10839 1.273896 CCCTAGGGTCCAACTCTTCCT 60.274 57.143 20.88 0.00 27.79 3.36
3740 10840 2.112190 CCTAGGGTCCAACTCTTCCTC 58.888 57.143 0.00 0.00 27.79 3.71
3741 10841 2.112190 CTAGGGTCCAACTCTTCCTCC 58.888 57.143 0.00 0.00 27.79 4.30
3742 10842 0.905337 AGGGTCCAACTCTTCCTCCG 60.905 60.000 0.00 0.00 0.00 4.63
3743 10843 1.597461 GGTCCAACTCTTCCTCCGG 59.403 63.158 0.00 0.00 0.00 5.14
3744 10844 1.079057 GTCCAACTCTTCCTCCGGC 60.079 63.158 0.00 0.00 0.00 6.13
3745 10845 2.125512 CCAACTCTTCCTCCGGCG 60.126 66.667 0.00 0.00 0.00 6.46
3746 10846 2.125512 CAACTCTTCCTCCGGCGG 60.126 66.667 22.51 22.51 0.00 6.13
3747 10847 4.083862 AACTCTTCCTCCGGCGGC 62.084 66.667 23.83 0.00 0.00 6.53
3764 10864 3.740397 CGCCGTCGGAGTACACCA 61.740 66.667 17.49 0.00 0.00 4.17
3765 10865 2.652530 GCCGTCGGAGTACACCAA 59.347 61.111 17.49 0.00 0.00 3.67
3766 10866 1.005867 GCCGTCGGAGTACACCAAA 60.006 57.895 17.49 0.00 0.00 3.28
3767 10867 0.600782 GCCGTCGGAGTACACCAAAA 60.601 55.000 17.49 0.00 0.00 2.44
3768 10868 1.942586 GCCGTCGGAGTACACCAAAAT 60.943 52.381 17.49 0.00 0.00 1.82
3769 10869 1.997606 CCGTCGGAGTACACCAAAATC 59.002 52.381 4.91 0.00 0.00 2.17
3770 10870 1.997606 CGTCGGAGTACACCAAAATCC 59.002 52.381 10.13 0.00 0.00 3.01
3771 10871 2.610976 CGTCGGAGTACACCAAAATCCA 60.611 50.000 10.13 0.00 0.00 3.41
3772 10872 2.740447 GTCGGAGTACACCAAAATCCAC 59.260 50.000 10.13 0.00 0.00 4.02
3773 10873 1.730064 CGGAGTACACCAAAATCCACG 59.270 52.381 10.13 0.00 0.00 4.94
3774 10874 2.774687 GGAGTACACCAAAATCCACGT 58.225 47.619 4.24 0.00 0.00 4.49
3775 10875 3.614630 CGGAGTACACCAAAATCCACGTA 60.615 47.826 10.13 0.00 0.00 3.57
3776 10876 4.317488 GGAGTACACCAAAATCCACGTAA 58.683 43.478 4.24 0.00 0.00 3.18
3778 10878 5.217978 AGTACACCAAAATCCACGTAAGA 57.782 39.130 0.00 0.00 43.62 2.10
3779 10879 5.801380 AGTACACCAAAATCCACGTAAGAT 58.199 37.500 0.00 0.00 43.62 2.40
3780 10880 6.938507 AGTACACCAAAATCCACGTAAGATA 58.061 36.000 0.00 0.00 43.62 1.98
3781 10881 7.562135 AGTACACCAAAATCCACGTAAGATAT 58.438 34.615 0.00 0.00 43.62 1.63
3782 10882 8.698210 AGTACACCAAAATCCACGTAAGATATA 58.302 33.333 0.00 0.00 43.62 0.86
3783 10883 9.485206 GTACACCAAAATCCACGTAAGATATAT 57.515 33.333 1.02 0.00 43.62 0.86
3784 10884 8.603242 ACACCAAAATCCACGTAAGATATATC 57.397 34.615 4.42 4.42 43.62 1.63
3785 10885 8.208224 ACACCAAAATCCACGTAAGATATATCA 58.792 33.333 15.08 0.00 43.62 2.15
3786 10886 9.219603 CACCAAAATCCACGTAAGATATATCAT 57.780 33.333 15.08 5.60 43.62 2.45
3787 10887 9.793259 ACCAAAATCCACGTAAGATATATCATT 57.207 29.630 15.08 8.60 43.62 2.57
3794 10894 8.894731 TCCACGTAAGATATATCATTAGAGAGC 58.105 37.037 15.08 0.00 43.62 4.09
3795 10895 8.132362 CCACGTAAGATATATCATTAGAGAGCC 58.868 40.741 15.08 0.00 43.62 4.70
3796 10896 8.678199 CACGTAAGATATATCATTAGAGAGCCA 58.322 37.037 15.08 0.00 43.62 4.75
3797 10897 8.898761 ACGTAAGATATATCATTAGAGAGCCAG 58.101 37.037 15.08 0.00 43.62 4.85
3798 10898 8.349245 CGTAAGATATATCATTAGAGAGCCAGG 58.651 40.741 15.08 0.00 43.02 4.45
3799 10899 7.673641 AAGATATATCATTAGAGAGCCAGGG 57.326 40.000 15.08 0.00 0.00 4.45
3800 10900 6.991064 AGATATATCATTAGAGAGCCAGGGA 58.009 40.000 15.08 0.00 0.00 4.20
3801 10901 7.603795 AGATATATCATTAGAGAGCCAGGGAT 58.396 38.462 15.08 0.00 0.00 3.85
3802 10902 7.729881 AGATATATCATTAGAGAGCCAGGGATC 59.270 40.741 15.08 0.00 0.00 3.36
3803 10903 2.242926 TCATTAGAGAGCCAGGGATCG 58.757 52.381 0.00 0.00 35.44 3.69
3804 10904 0.972883 ATTAGAGAGCCAGGGATCGC 59.027 55.000 0.54 0.54 35.44 4.58
3805 10905 1.456196 TTAGAGAGCCAGGGATCGCG 61.456 60.000 0.00 0.00 35.59 5.87
3806 10906 4.959596 GAGAGCCAGGGATCGCGC 62.960 72.222 0.00 0.00 35.44 6.86
3816 10916 2.797439 GATCGCGCGGATCTCGTC 60.797 66.667 31.69 12.52 46.66 4.20
3817 10917 4.329697 ATCGCGCGGATCTCGTCC 62.330 66.667 31.69 0.00 44.10 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.041644 CCTTTTACGAACCAATCAGAGTGTTTA 60.042 37.037 0.00 0.00 0.00 2.01
17 18 6.707161 ACATACAAAGTAGTTGCCTTTTACGA 59.293 34.615 0.00 0.00 41.31 3.43
122 123 7.944729 ACAGAGGCACAGAACATTTATAAAT 57.055 32.000 4.81 4.81 0.00 1.40
128 130 5.171339 AGATACAGAGGCACAGAACATTT 57.829 39.130 0.00 0.00 0.00 2.32
133 135 5.449553 TCATCTAGATACAGAGGCACAGAA 58.550 41.667 4.54 0.00 0.00 3.02
135 137 5.981088 ATCATCTAGATACAGAGGCACAG 57.019 43.478 4.54 0.00 34.43 3.66
245 247 3.206150 AGATTGAACGCACACAGTCTTT 58.794 40.909 0.00 0.00 30.99 2.52
362 364 8.725148 CCAGTTTATGATTCAACAGCTATATCC 58.275 37.037 0.00 0.00 0.00 2.59
369 371 6.149474 ACTGTACCAGTTTATGATTCAACAGC 59.851 38.462 8.52 0.00 42.59 4.40
499 501 4.672587 TCAACAGCTATAGGCAGTTAGG 57.327 45.455 1.04 0.00 46.40 2.69
549 551 5.705609 TGACCTTTATTTCTTCCTGTTGC 57.294 39.130 0.00 0.00 0.00 4.17
851 3946 2.165234 CCATCGCTCAAGTTCTCTGAGA 59.835 50.000 2.58 2.58 31.79 3.27
1045 4145 3.011517 GCTGGCCAGGAGAGGGAA 61.012 66.667 33.46 0.00 0.00 3.97
1316 4416 6.357367 TCTCTCTAACAAAAACCTGAAAGCT 58.643 36.000 0.00 0.00 0.00 3.74
1566 4688 2.811317 GGAACCAGTCGAGCTGCG 60.811 66.667 0.00 0.00 43.71 5.18
1647 4773 7.763071 ACAAATAGAACTTATAACCGAGTGGAC 59.237 37.037 0.00 0.00 39.21 4.02
2003 8716 1.541588 CTTCTGGCCCGGAAGAAAAAG 59.458 52.381 25.42 0.00 46.45 2.27
2458 9217 5.873164 TCTTTTGGAGCTTACCGAATCTTAC 59.127 40.000 0.00 0.00 33.86 2.34
2881 9962 3.986572 CACGCATGCAAAATGAAAGGTTA 59.013 39.130 19.57 0.00 0.00 2.85
2904 9991 7.122948 AGTGTGGAGTTATTGAAGGAGTAGTAG 59.877 40.741 0.00 0.00 0.00 2.57
2905 9992 6.952358 AGTGTGGAGTTATTGAAGGAGTAGTA 59.048 38.462 0.00 0.00 0.00 1.82
2906 9993 5.780793 AGTGTGGAGTTATTGAAGGAGTAGT 59.219 40.000 0.00 0.00 0.00 2.73
3028 10123 2.852449 AGGAAGGGAAACATCAGCCATA 59.148 45.455 0.00 0.00 0.00 2.74
3134 10229 2.111972 AGGTGGAGAACTGAAGGGAGTA 59.888 50.000 0.00 0.00 0.00 2.59
3135 10230 1.132689 AGGTGGAGAACTGAAGGGAGT 60.133 52.381 0.00 0.00 0.00 3.85
3138 10233 1.277557 CTGAGGTGGAGAACTGAAGGG 59.722 57.143 0.00 0.00 0.00 3.95
3140 10235 2.896685 ACTCTGAGGTGGAGAACTGAAG 59.103 50.000 9.85 0.00 35.10 3.02
3141 10236 2.894126 GACTCTGAGGTGGAGAACTGAA 59.106 50.000 9.85 0.00 35.10 3.02
3142 10237 2.520069 GACTCTGAGGTGGAGAACTGA 58.480 52.381 9.85 0.00 35.10 3.41
3143 10238 1.548269 GGACTCTGAGGTGGAGAACTG 59.452 57.143 9.85 0.00 35.10 3.16
3144 10239 1.431243 AGGACTCTGAGGTGGAGAACT 59.569 52.381 9.85 0.00 35.10 3.01
3145 10240 1.931635 AGGACTCTGAGGTGGAGAAC 58.068 55.000 9.85 0.00 35.10 3.01
3146 10241 2.291670 GGTAGGACTCTGAGGTGGAGAA 60.292 54.545 9.85 0.00 35.10 2.87
3155 10250 5.766590 TGATACTGATTGGTAGGACTCTGA 58.233 41.667 0.00 0.00 0.00 3.27
3178 10273 3.760684 GGAGGTTGAAGAATCAATGCACT 59.239 43.478 0.00 0.00 46.67 4.40
3237 10336 5.189145 GGGTTAGTTATCTCCAAGGTTCTGA 59.811 44.000 0.00 0.00 0.00 3.27
3262 10361 4.820775 ACAGTGGGTCCTAGTCATATCAT 58.179 43.478 0.00 0.00 0.00 2.45
3263 10362 4.215908 GACAGTGGGTCCTAGTCATATCA 58.784 47.826 0.00 0.00 40.83 2.15
3264 10363 4.038162 GTGACAGTGGGTCCTAGTCATATC 59.962 50.000 1.37 0.00 46.38 1.63
3266 10365 3.362706 GTGACAGTGGGTCCTAGTCATA 58.637 50.000 1.37 0.00 46.38 2.15
3267 10366 2.180276 GTGACAGTGGGTCCTAGTCAT 58.820 52.381 1.37 0.00 46.38 3.06
3303 10403 4.444611 TCCCTTTGAAAATCCTCTCCCTA 58.555 43.478 0.00 0.00 0.00 3.53
3304 10404 3.269034 TCCCTTTGAAAATCCTCTCCCT 58.731 45.455 0.00 0.00 0.00 4.20
3339 10439 1.488261 GCATAGACGCAAGGTACCGC 61.488 60.000 6.18 3.77 46.39 5.68
3370 10470 1.810532 CTTCGCCCTCGACTAAGCT 59.189 57.895 0.00 0.00 45.43 3.74
3394 10494 3.002583 TCTGACATCGCTGGCCCA 61.003 61.111 0.00 0.00 0.00 5.36
3399 10499 5.527033 TCATCTTAATCTCTGACATCGCTG 58.473 41.667 0.00 0.00 0.00 5.18
3413 10513 6.548622 CCCTTGGACACATCAATCATCTTAAT 59.451 38.462 0.00 0.00 0.00 1.40
3431 10531 1.394963 GGAGTCCCTACCCCTTGGA 59.605 63.158 0.00 0.00 34.81 3.53
3434 10534 2.367378 CCGGAGTCCCTACCCCTT 59.633 66.667 2.80 0.00 0.00 3.95
3516 10616 5.362717 TCTGTTTCTCTGTCTACTTGTCCAA 59.637 40.000 0.00 0.00 0.00 3.53
3519 10619 6.273825 TGTTCTGTTTCTCTGTCTACTTGTC 58.726 40.000 0.00 0.00 0.00 3.18
3590 10690 3.997021 ACATGACGAGAGCTAAGGTTTTG 59.003 43.478 0.00 0.00 0.00 2.44
3616 10716 3.190878 GCGTTCCAAGGCCTCATG 58.809 61.111 5.23 0.16 33.94 3.07
3636 10736 2.016704 GTCCATCGCAGTATCGCCG 61.017 63.158 0.00 0.00 0.00 6.46
3654 10754 4.135153 CTGTCCCCGACGCCTCAG 62.135 72.222 0.00 0.00 34.95 3.35
3664 10764 2.044946 GATGGCACCACTGTCCCC 60.045 66.667 0.00 0.00 0.00 4.81
3715 10815 2.267192 AGAGTTGGACCCTAGGGAAAC 58.733 52.381 35.38 29.26 38.96 2.78
3716 10816 2.735259 AGAGTTGGACCCTAGGGAAA 57.265 50.000 35.38 21.02 38.96 3.13
3717 10817 2.547990 GAAGAGTTGGACCCTAGGGAA 58.452 52.381 35.38 15.80 38.96 3.97
3718 10818 1.273666 GGAAGAGTTGGACCCTAGGGA 60.274 57.143 35.38 9.56 38.96 4.20
3719 10819 1.205055 GGAAGAGTTGGACCCTAGGG 58.795 60.000 27.36 27.36 42.03 3.53
3720 10820 2.112190 GAGGAAGAGTTGGACCCTAGG 58.888 57.143 0.06 0.06 0.00 3.02
3721 10821 2.112190 GGAGGAAGAGTTGGACCCTAG 58.888 57.143 0.00 0.00 0.00 3.02
3722 10822 1.618888 CGGAGGAAGAGTTGGACCCTA 60.619 57.143 0.00 0.00 0.00 3.53
3723 10823 0.905337 CGGAGGAAGAGTTGGACCCT 60.905 60.000 0.00 0.00 0.00 4.34
3724 10824 1.597461 CGGAGGAAGAGTTGGACCC 59.403 63.158 0.00 0.00 0.00 4.46
3747 10847 2.752322 TTTGGTGTACTCCGACGGCG 62.752 60.000 9.66 1.94 37.24 6.46
3748 10848 0.600782 TTTTGGTGTACTCCGACGGC 60.601 55.000 9.66 0.00 0.00 5.68
3749 10849 1.997606 GATTTTGGTGTACTCCGACGG 59.002 52.381 7.84 7.84 0.00 4.79
3750 10850 1.997606 GGATTTTGGTGTACTCCGACG 59.002 52.381 9.33 0.00 0.00 5.12
3751 10851 2.740447 GTGGATTTTGGTGTACTCCGAC 59.260 50.000 9.33 0.00 0.00 4.79
3752 10852 2.610976 CGTGGATTTTGGTGTACTCCGA 60.611 50.000 9.33 4.64 0.00 4.55
3753 10853 1.730064 CGTGGATTTTGGTGTACTCCG 59.270 52.381 9.33 0.00 0.00 4.63
3754 10854 2.774687 ACGTGGATTTTGGTGTACTCC 58.225 47.619 7.03 7.03 0.00 3.85
3755 10855 5.232463 TCTTACGTGGATTTTGGTGTACTC 58.768 41.667 0.00 0.00 0.00 2.59
3756 10856 5.217978 TCTTACGTGGATTTTGGTGTACT 57.782 39.130 0.00 0.00 0.00 2.73
3757 10857 7.781548 ATATCTTACGTGGATTTTGGTGTAC 57.218 36.000 0.00 0.00 0.00 2.90
3758 10858 9.701098 GATATATCTTACGTGGATTTTGGTGTA 57.299 33.333 5.42 0.00 0.00 2.90
3759 10859 8.208224 TGATATATCTTACGTGGATTTTGGTGT 58.792 33.333 13.79 0.00 0.00 4.16
3760 10860 8.601845 TGATATATCTTACGTGGATTTTGGTG 57.398 34.615 13.79 0.00 0.00 4.17
3761 10861 9.793259 AATGATATATCTTACGTGGATTTTGGT 57.207 29.630 13.79 0.00 0.00 3.67
3768 10868 8.894731 GCTCTCTAATGATATATCTTACGTGGA 58.105 37.037 13.79 0.00 0.00 4.02
3769 10869 8.132362 GGCTCTCTAATGATATATCTTACGTGG 58.868 40.741 13.79 0.00 0.00 4.94
3770 10870 8.678199 TGGCTCTCTAATGATATATCTTACGTG 58.322 37.037 13.79 4.31 0.00 4.49
3771 10871 8.809468 TGGCTCTCTAATGATATATCTTACGT 57.191 34.615 13.79 0.00 0.00 3.57
3772 10872 8.349245 CCTGGCTCTCTAATGATATATCTTACG 58.651 40.741 13.79 3.28 0.00 3.18
3773 10873 8.637986 CCCTGGCTCTCTAATGATATATCTTAC 58.362 40.741 13.79 0.00 0.00 2.34
3774 10874 8.569596 TCCCTGGCTCTCTAATGATATATCTTA 58.430 37.037 13.79 8.72 0.00 2.10
3775 10875 7.425834 TCCCTGGCTCTCTAATGATATATCTT 58.574 38.462 13.79 4.85 0.00 2.40
3776 10876 6.991064 TCCCTGGCTCTCTAATGATATATCT 58.009 40.000 13.79 0.00 0.00 1.98
3777 10877 7.309133 CGATCCCTGGCTCTCTAATGATATATC 60.309 44.444 5.73 5.73 0.00 1.63
3778 10878 6.493115 CGATCCCTGGCTCTCTAATGATATAT 59.507 42.308 0.00 0.00 0.00 0.86
3779 10879 5.830457 CGATCCCTGGCTCTCTAATGATATA 59.170 44.000 0.00 0.00 0.00 0.86
3780 10880 4.648762 CGATCCCTGGCTCTCTAATGATAT 59.351 45.833 0.00 0.00 0.00 1.63
3781 10881 4.019858 CGATCCCTGGCTCTCTAATGATA 58.980 47.826 0.00 0.00 0.00 2.15
3782 10882 2.830923 CGATCCCTGGCTCTCTAATGAT 59.169 50.000 0.00 0.00 0.00 2.45
3783 10883 2.242926 CGATCCCTGGCTCTCTAATGA 58.757 52.381 0.00 0.00 0.00 2.57
3784 10884 1.337635 GCGATCCCTGGCTCTCTAATG 60.338 57.143 0.00 0.00 0.00 1.90
3785 10885 0.972883 GCGATCCCTGGCTCTCTAAT 59.027 55.000 0.00 0.00 0.00 1.73
3786 10886 1.456196 CGCGATCCCTGGCTCTCTAA 61.456 60.000 0.00 0.00 0.00 2.10
3787 10887 1.899054 CGCGATCCCTGGCTCTCTA 60.899 63.158 0.00 0.00 0.00 2.43
3788 10888 3.222855 CGCGATCCCTGGCTCTCT 61.223 66.667 0.00 0.00 0.00 3.10
3789 10889 4.959596 GCGCGATCCCTGGCTCTC 62.960 72.222 12.10 0.00 0.00 3.20
3799 10899 2.797439 GACGAGATCCGCGCGATC 60.797 66.667 34.63 28.51 46.86 3.69
3800 10900 4.329697 GGACGAGATCCGCGCGAT 62.330 66.667 34.63 22.40 42.77 4.58


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

AutoCloner maintained by Alex Coulton.