Multiple sequence alignment - TraesCS1B01G191100

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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 TraesCS1B01G191100 chr1B 100.000 4383 0 0 1 4383 342084876 342089258 0.000000e+00 8094.0
1 TraesCS1B01G191100 chr1D 93.716 2610 80 18 902 3474 236500834 236503396 0.000000e+00 3834.0
2 TraesCS1B01G191100 chr1D 87.687 869 84 14 15 867 219711324 219710463 0.000000e+00 990.0
3 TraesCS1B01G191100 chr1D 86.364 858 100 9 15 859 209473515 209472662 0.000000e+00 920.0
4 TraesCS1B01G191100 chr1D 93.964 497 9 3 3472 3966 236503526 236504003 0.000000e+00 732.0
5 TraesCS1B01G191100 chr1D 94.524 420 22 1 3964 4383 236523320 236523738 0.000000e+00 647.0
6 TraesCS1B01G191100 chr1A 93.742 2317 92 29 902 3186 308953159 308950864 0.000000e+00 3426.0
7 TraesCS1B01G191100 chr1A 87.964 889 44 15 3472 4330 308950032 308949177 0.000000e+00 990.0
8 TraesCS1B01G191100 chr1A 86.957 851 88 12 27 857 445887630 445886783 0.000000e+00 935.0
9 TraesCS1B01G191100 chr1A 94.000 200 8 3 3275 3474 308950441 308950246 2.560000e-77 300.0
10 TraesCS1B01G191100 chr1A 92.453 106 5 2 3172 3277 308950848 308950746 9.820000e-32 148.0
11 TraesCS1B01G191100 chr3B 92.874 856 56 3 1 856 650020565 650021415 0.000000e+00 1238.0
12 TraesCS1B01G191100 chr3B 89.080 870 89 5 1 865 456033425 456032557 0.000000e+00 1075.0
13 TraesCS1B01G191100 chr2D 87.719 855 81 16 15 857 460367315 460366473 0.000000e+00 976.0
14 TraesCS1B01G191100 chr5B 86.395 860 95 15 15 859 203569816 203570668 0.000000e+00 920.0
15 TraesCS1B01G191100 chr5B 87.583 604 62 5 91 684 668608112 668607512 0.000000e+00 688.0
16 TraesCS1B01G191100 chr4B 85.947 861 97 12 15 859 577147748 577146896 0.000000e+00 898.0
17 TraesCS1B01G191100 chr4B 84.936 863 110 10 15 860 166648863 166648004 0.000000e+00 856.0
18 TraesCS1B01G191100 chr2A 85.631 856 83 17 15 857 610171186 610172014 0.000000e+00 863.0
19 TraesCS1B01G191100 chr5D 88.511 618 50 11 15 614 540844953 540844339 0.000000e+00 728.0
20 TraesCS1B01G191100 chr2B 91.770 486 40 0 4 489 43619444 43618959 0.000000e+00 676.0
21 TraesCS1B01G191100 chr3A 84.488 361 49 6 500 857 707170172 707170528 2.510000e-92 350.0
22 TraesCS1B01G191100 chr6B 93.878 49 3 0 856 904 330983295 330983343 1.690000e-09 75.0
23 TraesCS1B01G191100 chr7D 100.000 28 0 0 1362 1389 198714925 198714952 8.000000e-03 52.8
24 TraesCS1B01G191100 chr7A 100.000 28 0 0 1362 1389 208127109 208127136 8.000000e-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 TraesCS1B01G191100 chr1B 342084876 342089258 4382 False 8094 8094 100.00000 1 4383 1 chr1B.!!$F1 4382
1 TraesCS1B01G191100 chr1D 236500834 236504003 3169 False 2283 3834 93.84000 902 3966 2 chr1D.!!$F2 3064
2 TraesCS1B01G191100 chr1D 219710463 219711324 861 True 990 990 87.68700 15 867 1 chr1D.!!$R2 852
3 TraesCS1B01G191100 chr1D 209472662 209473515 853 True 920 920 86.36400 15 859 1 chr1D.!!$R1 844
4 TraesCS1B01G191100 chr1A 308949177 308953159 3982 True 1216 3426 92.03975 902 4330 4 chr1A.!!$R2 3428
5 TraesCS1B01G191100 chr1A 445886783 445887630 847 True 935 935 86.95700 27 857 1 chr1A.!!$R1 830
6 TraesCS1B01G191100 chr3B 650020565 650021415 850 False 1238 1238 92.87400 1 856 1 chr3B.!!$F1 855
7 TraesCS1B01G191100 chr3B 456032557 456033425 868 True 1075 1075 89.08000 1 865 1 chr3B.!!$R1 864
8 TraesCS1B01G191100 chr2D 460366473 460367315 842 True 976 976 87.71900 15 857 1 chr2D.!!$R1 842
9 TraesCS1B01G191100 chr5B 203569816 203570668 852 False 920 920 86.39500 15 859 1 chr5B.!!$F1 844
10 TraesCS1B01G191100 chr5B 668607512 668608112 600 True 688 688 87.58300 91 684 1 chr5B.!!$R1 593
11 TraesCS1B01G191100 chr4B 577146896 577147748 852 True 898 898 85.94700 15 859 1 chr4B.!!$R2 844
12 TraesCS1B01G191100 chr4B 166648004 166648863 859 True 856 856 84.93600 15 860 1 chr4B.!!$R1 845
13 TraesCS1B01G191100 chr2A 610171186 610172014 828 False 863 863 85.63100 15 857 1 chr2A.!!$F1 842
14 TraesCS1B01G191100 chr5D 540844339 540844953 614 True 728 728 88.51100 15 614 1 chr5D.!!$R1 599

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
985 1016 0.175073 GGCAGTACCTTTCGTCGGAT 59.825 55.000 0.00 0.0 34.51 4.18 F
1008 1039 0.321564 AACTCGTAAGCATGGCAGCA 60.322 50.000 10.71 0.0 36.85 4.41 F
1351 1382 0.830444 TGGTCTACAAGGTGGCGTCT 60.830 55.000 0.00 0.0 0.00 4.18 F
3095 3166 1.338200 GCTGCTACAGTGCTGTTACCT 60.338 52.381 10.28 0.0 41.83 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2832 2902 0.976641 TTGTACTCCCAGTCCTGCAG 59.023 55.000 6.78 6.78 0.00 4.41 R
2901 2971 8.631676 GTAGTGCTAACATTACCTTCTTCTAC 57.368 38.462 0.00 0.00 33.96 2.59 R
3195 3296 6.603940 AGGAGGCATCATACTCTTCTAATC 57.396 41.667 0.00 0.00 34.22 1.75 R
4324 4978 0.103755 TTGCCATGCGTGCTGAAAAA 59.896 45.000 0.00 0.00 0.00 1.94 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
228 241 2.120909 CCATCCACACCCAATCCGC 61.121 63.158 0.00 0.00 0.00 5.54
230 243 3.697439 ATCCACACCCAATCCGCCG 62.697 63.158 0.00 0.00 0.00 6.46
241 254 1.396996 CAATCCGCCGGAAAGTACAAG 59.603 52.381 11.19 0.00 34.34 3.16
317 330 4.649674 ACCGGAGCTAAATTCTACAGATCA 59.350 41.667 9.46 0.00 0.00 2.92
425 438 4.658786 AGGCCCCTCCCGAACAGT 62.659 66.667 0.00 0.00 34.51 3.55
538 559 4.779733 GGGTGCGGGAGGAGAGGA 62.780 72.222 0.00 0.00 0.00 3.71
614 635 1.063717 AGGTGGCTGGGATTTATGGTG 60.064 52.381 0.00 0.00 0.00 4.17
620 641 2.754186 GCTGGGATTTATGGTGATGCCT 60.754 50.000 0.00 0.00 35.09 4.75
676 707 3.602075 TAGGCTCGACCAGGTGGCT 62.602 63.158 0.00 2.81 43.14 4.75
679 710 2.743718 CTCGACCAGGTGGCTGTT 59.256 61.111 0.00 0.00 39.32 3.16
783 814 1.733360 GCGCAAGTATTTGGACCGTAA 59.267 47.619 0.30 0.00 41.68 3.18
807 838 7.687941 ATTCAGGTATTTTGAAGTAGTGGTG 57.312 36.000 0.00 0.00 37.91 4.17
841 872 2.615493 CCGGCTCAAGTTATGTGACCTT 60.615 50.000 0.00 0.00 0.00 3.50
861 892 9.354673 TGACCTTGAGTGAATTTTTCTCTTAAT 57.645 29.630 0.00 0.00 33.98 1.40
885 916 9.887862 AATAATATCATCCATCCCAAGTCTTTT 57.112 29.630 0.00 0.00 0.00 2.27
886 917 7.830099 AATATCATCCATCCCAAGTCTTTTC 57.170 36.000 0.00 0.00 0.00 2.29
887 918 3.968265 TCATCCATCCCAAGTCTTTTCC 58.032 45.455 0.00 0.00 0.00 3.13
888 919 3.333381 TCATCCATCCCAAGTCTTTTCCA 59.667 43.478 0.00 0.00 0.00 3.53
889 920 3.154827 TCCATCCCAAGTCTTTTCCAC 57.845 47.619 0.00 0.00 0.00 4.02
890 921 1.812571 CCATCCCAAGTCTTTTCCACG 59.187 52.381 0.00 0.00 0.00 4.94
891 922 1.200020 CATCCCAAGTCTTTTCCACGC 59.800 52.381 0.00 0.00 0.00 5.34
892 923 0.181587 TCCCAAGTCTTTTCCACGCA 59.818 50.000 0.00 0.00 0.00 5.24
893 924 1.202879 TCCCAAGTCTTTTCCACGCAT 60.203 47.619 0.00 0.00 0.00 4.73
894 925 1.200020 CCCAAGTCTTTTCCACGCATC 59.800 52.381 0.00 0.00 0.00 3.91
895 926 1.200020 CCAAGTCTTTTCCACGCATCC 59.800 52.381 0.00 0.00 0.00 3.51
896 927 1.200020 CAAGTCTTTTCCACGCATCCC 59.800 52.381 0.00 0.00 0.00 3.85
897 928 0.693049 AGTCTTTTCCACGCATCCCT 59.307 50.000 0.00 0.00 0.00 4.20
898 929 0.804989 GTCTTTTCCACGCATCCCTG 59.195 55.000 0.00 0.00 0.00 4.45
899 930 0.322456 TCTTTTCCACGCATCCCTGG 60.322 55.000 0.00 0.00 0.00 4.45
900 931 1.937546 CTTTTCCACGCATCCCTGGC 61.938 60.000 0.00 0.00 0.00 4.85
944 975 4.484912 AGAGTAGTTCAAGGTCAAGGAGT 58.515 43.478 0.00 0.00 0.00 3.85
985 1016 0.175073 GGCAGTACCTTTCGTCGGAT 59.825 55.000 0.00 0.00 34.51 4.18
986 1017 1.557651 GCAGTACCTTTCGTCGGATC 58.442 55.000 0.00 0.00 0.00 3.36
987 1018 1.823828 CAGTACCTTTCGTCGGATCG 58.176 55.000 0.00 0.00 0.00 3.69
988 1019 1.131883 CAGTACCTTTCGTCGGATCGT 59.868 52.381 0.00 0.00 0.00 3.73
989 1020 2.352651 CAGTACCTTTCGTCGGATCGTA 59.647 50.000 0.00 0.00 0.00 3.43
990 1021 3.009723 AGTACCTTTCGTCGGATCGTAA 58.990 45.455 0.00 0.00 0.00 3.18
991 1022 2.268730 ACCTTTCGTCGGATCGTAAC 57.731 50.000 0.00 0.00 0.00 2.50
999 1030 2.370515 GTCGGATCGTAACTCGTAAGC 58.629 52.381 0.00 0.00 40.80 3.09
1008 1039 0.321564 AACTCGTAAGCATGGCAGCA 60.322 50.000 10.71 0.00 36.85 4.41
1167 1198 2.893215 TCTCGGGGAAGAGTGAGTTA 57.107 50.000 0.00 0.00 39.21 2.24
1351 1382 0.830444 TGGTCTACAAGGTGGCGTCT 60.830 55.000 0.00 0.00 0.00 4.18
1657 1688 3.228453 ACTCCTTCAGAACTCGGTTGTA 58.772 45.455 0.00 0.00 0.00 2.41
1817 1856 8.548880 TGCTAGGTCTAGTAGTATTCCAAATT 57.451 34.615 6.84 0.00 35.65 1.82
1818 1857 8.639761 TGCTAGGTCTAGTAGTATTCCAAATTC 58.360 37.037 6.84 0.00 35.65 2.17
1819 1858 8.639761 GCTAGGTCTAGTAGTATTCCAAATTCA 58.360 37.037 6.84 0.00 35.65 2.57
1822 1861 9.892130 AGGTCTAGTAGTATTCCAAATTCAAAG 57.108 33.333 0.00 0.00 0.00 2.77
1823 1862 9.110502 GGTCTAGTAGTATTCCAAATTCAAAGG 57.889 37.037 0.00 0.00 0.00 3.11
1824 1863 8.613482 GTCTAGTAGTATTCCAAATTCAAAGGC 58.387 37.037 0.00 0.00 0.00 4.35
1825 1864 8.325787 TCTAGTAGTATTCCAAATTCAAAGGCA 58.674 33.333 0.00 0.00 0.00 4.75
1826 1865 7.396540 AGTAGTATTCCAAATTCAAAGGCAG 57.603 36.000 0.00 0.00 0.00 4.85
1827 1866 6.948309 AGTAGTATTCCAAATTCAAAGGCAGT 59.052 34.615 0.00 0.00 0.00 4.40
1828 1867 8.107095 AGTAGTATTCCAAATTCAAAGGCAGTA 58.893 33.333 0.00 0.00 0.00 2.74
1829 1868 7.961326 AGTATTCCAAATTCAAAGGCAGTAT 57.039 32.000 0.00 0.00 0.00 2.12
1898 1965 8.862325 ACACATTGACCTGAGTTGATATTTTA 57.138 30.769 0.00 0.00 0.00 1.52
1937 2004 2.099592 TGCAGTGACTTTCTTTGGCAAG 59.900 45.455 0.00 0.00 0.00 4.01
2017 2084 7.170965 ACCAGTTGTTCATGAGATATTTGACT 58.829 34.615 0.00 0.00 0.00 3.41
2127 2194 1.467342 GTTGGTATGTTTGGAGCCGAC 59.533 52.381 0.00 0.00 0.00 4.79
2343 2413 8.738645 AAACTGATACTATCAAACAGGGAATC 57.261 34.615 0.42 0.00 39.11 2.52
2344 2414 7.682787 ACTGATACTATCAAACAGGGAATCT 57.317 36.000 0.42 0.00 39.11 2.40
2641 2711 6.527023 GCTATATGTACTACCACATAGCGTTG 59.473 42.308 0.00 0.00 42.93 4.10
2642 2712 4.730949 ATGTACTACCACATAGCGTTGT 57.269 40.909 0.00 0.00 37.37 3.32
2653 2723 5.294306 CCACATAGCGTTGTACATTGATCTT 59.706 40.000 0.00 0.00 0.00 2.40
2832 2902 1.745653 GTCCATTTGAGCTTAGTGCCC 59.254 52.381 0.00 0.00 44.23 5.36
2901 2971 1.453155 CATCAAAGGAACAGGACCCG 58.547 55.000 0.00 0.00 0.00 5.28
2909 2979 1.897802 GGAACAGGACCCGTAGAAGAA 59.102 52.381 0.00 0.00 0.00 2.52
3095 3166 1.338200 GCTGCTACAGTGCTGTTACCT 60.338 52.381 10.28 0.00 41.83 3.08
3096 3167 2.094182 GCTGCTACAGTGCTGTTACCTA 60.094 50.000 10.28 0.00 41.83 3.08
3097 3168 3.775202 CTGCTACAGTGCTGTTACCTAG 58.225 50.000 10.28 2.79 41.83 3.02
3195 3296 9.967346 TTAAGTATCGAATGACTGAATTAGAGG 57.033 33.333 0.00 0.00 0.00 3.69
3217 3318 5.483583 AGGATTAGAAGAGTATGATGCCTCC 59.516 44.000 0.00 0.00 0.00 4.30
3263 3364 5.105392 TGCTGTTGATTTTCCTTTGTCAAGT 60.105 36.000 0.00 0.00 31.84 3.16
3264 3365 6.096141 TGCTGTTGATTTTCCTTTGTCAAGTA 59.904 34.615 0.00 0.00 31.84 2.24
3265 3366 6.638468 GCTGTTGATTTTCCTTTGTCAAGTAG 59.362 38.462 0.00 0.00 31.84 2.57
3266 3367 7.639113 TGTTGATTTTCCTTTGTCAAGTAGT 57.361 32.000 0.00 0.00 31.84 2.73
3365 3773 3.792709 ACCTCATGGTGGGCAAAAT 57.207 47.368 9.80 0.00 46.51 1.82
3367 3775 1.203162 ACCTCATGGTGGGCAAAATCA 60.203 47.619 9.80 0.00 46.51 2.57
3376 3784 4.202440 TGGTGGGCAAAATCAATGTCATTT 60.202 37.500 0.00 0.00 0.00 2.32
3377 3785 5.012458 TGGTGGGCAAAATCAATGTCATTTA 59.988 36.000 0.00 0.00 0.00 1.40
3382 3790 9.327628 TGGGCAAAATCAATGTCATTTATATTG 57.672 29.630 0.00 1.72 37.87 1.90
3455 3863 7.816945 AACTGACATGAAAAGAAAAACAGTG 57.183 32.000 0.00 0.00 36.45 3.66
3456 3864 7.156876 ACTGACATGAAAAGAAAAACAGTGA 57.843 32.000 0.00 0.00 35.31 3.41
3547 4171 6.252995 ACTTTTTGTTAATCCCAGCCTCATA 58.747 36.000 0.00 0.00 0.00 2.15
3676 4309 2.034104 TTGCTGAGATGAGGCATGAC 57.966 50.000 0.00 0.00 35.84 3.06
3677 4310 0.906775 TGCTGAGATGAGGCATGACA 59.093 50.000 0.00 0.00 0.00 3.58
3678 4311 1.279846 TGCTGAGATGAGGCATGACAA 59.720 47.619 0.00 0.00 0.00 3.18
3679 4312 2.290450 TGCTGAGATGAGGCATGACAAA 60.290 45.455 0.00 0.00 0.00 2.83
3680 4313 2.751259 GCTGAGATGAGGCATGACAAAA 59.249 45.455 0.00 0.00 0.00 2.44
3681 4314 3.427233 GCTGAGATGAGGCATGACAAAAC 60.427 47.826 0.00 0.00 0.00 2.43
3682 4315 4.008330 CTGAGATGAGGCATGACAAAACT 58.992 43.478 0.00 0.00 0.00 2.66
3683 4316 3.754850 TGAGATGAGGCATGACAAAACTG 59.245 43.478 0.00 0.00 0.00 3.16
3684 4317 4.005650 GAGATGAGGCATGACAAAACTGA 58.994 43.478 0.00 0.00 0.00 3.41
3685 4318 3.755378 AGATGAGGCATGACAAAACTGAC 59.245 43.478 0.00 0.00 0.00 3.51
3686 4319 2.929641 TGAGGCATGACAAAACTGACA 58.070 42.857 0.00 0.00 0.00 3.58
3687 4320 2.618241 TGAGGCATGACAAAACTGACAC 59.382 45.455 0.00 0.00 0.00 3.67
3688 4321 2.618241 GAGGCATGACAAAACTGACACA 59.382 45.455 0.00 0.00 0.00 3.72
3689 4322 2.358898 AGGCATGACAAAACTGACACAC 59.641 45.455 0.00 0.00 0.00 3.82
3690 4323 2.098934 GGCATGACAAAACTGACACACA 59.901 45.455 0.00 0.00 0.00 3.72
3691 4324 3.428725 GGCATGACAAAACTGACACACAA 60.429 43.478 0.00 0.00 0.00 3.33
3692 4325 3.792956 GCATGACAAAACTGACACACAAG 59.207 43.478 0.00 0.00 0.00 3.16
3693 4326 4.438608 GCATGACAAAACTGACACACAAGA 60.439 41.667 0.00 0.00 0.00 3.02
3694 4327 4.944962 TGACAAAACTGACACACAAGAG 57.055 40.909 0.00 0.00 0.00 2.85
3758 4391 7.604164 CAGTTTATGATACCTCCAAGCGATAAT 59.396 37.037 0.00 0.00 0.00 1.28
3800 4437 9.846248 AGAACATGAAGACAAACTATAAATTGC 57.154 29.630 0.00 0.00 0.00 3.56
3824 4461 3.956199 AGTTTGGGATGCATGGATTGTAG 59.044 43.478 2.46 0.00 0.00 2.74
3954 4607 2.079925 GATGTCTGAACCAGTGGAAGC 58.920 52.381 18.40 4.92 32.61 3.86
3963 4617 0.178992 CCAGTGGAAGCCAAAGGACA 60.179 55.000 1.68 0.00 34.18 4.02
3986 4640 7.331026 ACAGTAGTAGAATTTAAGCATGAGCA 58.669 34.615 0.00 0.00 45.49 4.26
3994 4648 2.315925 TAAGCATGAGCAGCAGTACC 57.684 50.000 0.00 0.00 45.49 3.34
3999 4653 0.747255 ATGAGCAGCAGTACCGGTAG 59.253 55.000 16.41 5.41 0.00 3.18
4012 4666 1.955080 ACCGGTAGAAGATAAGCCTCG 59.045 52.381 4.49 0.00 0.00 4.63
4017 4671 1.428869 AGAAGATAAGCCTCGCCCAT 58.571 50.000 0.00 0.00 0.00 4.00
4085 4739 1.344438 TGGTGCGTGATCTCTTGACTT 59.656 47.619 0.00 0.00 0.00 3.01
4088 4742 3.799420 GGTGCGTGATCTCTTGACTTATC 59.201 47.826 0.00 0.00 0.00 1.75
4090 4744 5.105752 GTGCGTGATCTCTTGACTTATCTT 58.894 41.667 0.00 0.00 0.00 2.40
4167 4821 2.993899 CACTCTACCTTAAACGCACAGG 59.006 50.000 0.00 0.00 0.00 4.00
4261 4915 6.968131 TCATATTTTTCTGAGGTTCTGACG 57.032 37.500 0.00 0.00 0.00 4.35
4315 4969 6.201425 GTCACTTTGAACATGTCAATGCAAAT 59.799 34.615 0.00 0.00 45.71 2.32
4316 4970 6.201234 TCACTTTGAACATGTCAATGCAAATG 59.799 34.615 0.00 0.00 45.71 2.32
4324 4978 6.460781 ACATGTCAATGCAAATGTTTGAGAT 58.539 32.000 9.53 4.31 39.84 2.75
4330 4984 8.336806 GTCAATGCAAATGTTTGAGATTTTTCA 58.663 29.630 9.53 0.00 40.55 2.69
4331 4985 8.552865 TCAATGCAAATGTTTGAGATTTTTCAG 58.447 29.630 9.53 0.00 40.55 3.02
4332 4986 6.289745 TGCAAATGTTTGAGATTTTTCAGC 57.710 33.333 9.53 0.00 40.55 4.26
4333 4987 5.816258 TGCAAATGTTTGAGATTTTTCAGCA 59.184 32.000 9.53 0.00 40.55 4.41
4334 4988 6.131389 GCAAATGTTTGAGATTTTTCAGCAC 58.869 36.000 9.53 0.00 40.55 4.40
4335 4989 6.349426 CAAATGTTTGAGATTTTTCAGCACG 58.651 36.000 0.00 0.00 40.55 5.34
4336 4990 3.371168 TGTTTGAGATTTTTCAGCACGC 58.629 40.909 0.00 0.00 0.00 5.34
4337 4991 3.181492 TGTTTGAGATTTTTCAGCACGCA 60.181 39.130 0.00 0.00 0.00 5.24
4338 4992 3.921119 TTGAGATTTTTCAGCACGCAT 57.079 38.095 0.00 0.00 0.00 4.73
4339 4993 3.206034 TGAGATTTTTCAGCACGCATG 57.794 42.857 0.00 0.00 0.00 4.06
4340 4994 2.095110 TGAGATTTTTCAGCACGCATGG 60.095 45.455 0.00 0.00 0.00 3.66
4341 4995 0.994263 GATTTTTCAGCACGCATGGC 59.006 50.000 0.00 0.00 0.00 4.40
4342 4996 0.317799 ATTTTTCAGCACGCATGGCA 59.682 45.000 0.00 0.00 0.00 4.92
4343 4997 0.103755 TTTTTCAGCACGCATGGCAA 59.896 45.000 0.00 0.00 0.00 4.52
4344 4998 0.597118 TTTTCAGCACGCATGGCAAC 60.597 50.000 0.00 0.00 0.00 4.17
4345 4999 2.419057 TTTCAGCACGCATGGCAACC 62.419 55.000 0.00 0.00 0.00 3.77
4346 5000 3.672447 CAGCACGCATGGCAACCA 61.672 61.111 0.00 0.00 38.19 3.67
4347 5001 2.677524 AGCACGCATGGCAACCAT 60.678 55.556 0.00 0.00 46.37 3.55
4357 5011 2.079170 TGGCAACCATGGAGAAAACA 57.921 45.000 21.47 6.63 0.00 2.83
4358 5012 2.607499 TGGCAACCATGGAGAAAACAT 58.393 42.857 21.47 0.00 0.00 2.71
4359 5013 2.562298 TGGCAACCATGGAGAAAACATC 59.438 45.455 21.47 0.00 0.00 3.06
4360 5014 2.562298 GGCAACCATGGAGAAAACATCA 59.438 45.455 21.47 0.00 0.00 3.07
4361 5015 3.196254 GGCAACCATGGAGAAAACATCAT 59.804 43.478 21.47 0.00 0.00 2.45
4362 5016 4.402155 GGCAACCATGGAGAAAACATCATA 59.598 41.667 21.47 0.00 0.00 2.15
4363 5017 5.105392 GGCAACCATGGAGAAAACATCATAA 60.105 40.000 21.47 0.00 0.00 1.90
4364 5018 6.397272 GCAACCATGGAGAAAACATCATAAA 58.603 36.000 21.47 0.00 0.00 1.40
4365 5019 6.873076 GCAACCATGGAGAAAACATCATAAAA 59.127 34.615 21.47 0.00 0.00 1.52
4366 5020 7.550196 GCAACCATGGAGAAAACATCATAAAAT 59.450 33.333 21.47 0.00 0.00 1.82
4367 5021 9.439500 CAACCATGGAGAAAACATCATAAAATT 57.561 29.630 21.47 0.00 0.00 1.82
4368 5022 9.657419 AACCATGGAGAAAACATCATAAAATTC 57.343 29.630 21.47 0.00 0.00 2.17
4369 5023 8.814931 ACCATGGAGAAAACATCATAAAATTCA 58.185 29.630 21.47 0.00 0.00 2.57
4370 5024 9.656040 CCATGGAGAAAACATCATAAAATTCAA 57.344 29.630 5.56 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 155 1.138266 AGTGTTGCGTCCTGTGTTAGT 59.862 47.619 0.00 0.00 0.00 2.24
197 210 2.916934 TGTGGATGGTAGGGTTTTAGCT 59.083 45.455 0.00 0.00 0.00 3.32
228 241 2.228103 GGGCTTTTCTTGTACTTTCCGG 59.772 50.000 0.00 0.00 0.00 5.14
230 243 4.929819 TTGGGCTTTTCTTGTACTTTCC 57.070 40.909 0.00 0.00 0.00 3.13
241 254 1.819288 GAGCTAGGGTTTGGGCTTTTC 59.181 52.381 0.00 0.00 35.01 2.29
317 330 2.982130 CCAGTAGCTCCGGTGCTT 59.018 61.111 33.65 16.20 43.74 3.91
473 486 2.430244 GAGCTCGTCGGCGTTGAA 60.430 61.111 10.18 0.00 39.49 2.69
505 522 2.041115 CCCTCTCTGCTCGTCGTCA 61.041 63.158 0.00 0.00 0.00 4.35
565 586 2.283532 ACCAGCTCGCTGTCTCCT 60.284 61.111 16.82 0.00 42.15 3.69
593 614 2.174639 CACCATAAATCCCAGCCACCTA 59.825 50.000 0.00 0.00 0.00 3.08
783 814 6.151144 GCACCACTACTTCAAAATACCTGAAT 59.849 38.462 0.00 0.00 32.53 2.57
807 838 1.003718 AGCCGGGTGACACTTTAGC 60.004 57.895 4.72 4.15 0.00 3.09
861 892 7.944554 GGAAAAGACTTGGGATGGATGATATTA 59.055 37.037 0.00 0.00 0.00 0.98
863 894 6.126097 TGGAAAAGACTTGGGATGGATGATAT 60.126 38.462 0.00 0.00 0.00 1.63
864 895 5.193527 TGGAAAAGACTTGGGATGGATGATA 59.806 40.000 0.00 0.00 0.00 2.15
867 898 3.445096 GTGGAAAAGACTTGGGATGGATG 59.555 47.826 0.00 0.00 0.00 3.51
868 899 3.701664 GTGGAAAAGACTTGGGATGGAT 58.298 45.455 0.00 0.00 0.00 3.41
869 900 2.552155 CGTGGAAAAGACTTGGGATGGA 60.552 50.000 0.00 0.00 0.00 3.41
870 901 1.812571 CGTGGAAAAGACTTGGGATGG 59.187 52.381 0.00 0.00 0.00 3.51
871 902 1.200020 GCGTGGAAAAGACTTGGGATG 59.800 52.381 0.00 0.00 0.00 3.51
872 903 1.202879 TGCGTGGAAAAGACTTGGGAT 60.203 47.619 0.00 0.00 0.00 3.85
873 904 0.181587 TGCGTGGAAAAGACTTGGGA 59.818 50.000 0.00 0.00 0.00 4.37
874 905 1.200020 GATGCGTGGAAAAGACTTGGG 59.800 52.381 0.00 0.00 0.00 4.12
875 906 1.200020 GGATGCGTGGAAAAGACTTGG 59.800 52.381 0.00 0.00 0.00 3.61
876 907 1.200020 GGGATGCGTGGAAAAGACTTG 59.800 52.381 0.00 0.00 0.00 3.16
877 908 1.073923 AGGGATGCGTGGAAAAGACTT 59.926 47.619 0.00 0.00 0.00 3.01
878 909 0.693049 AGGGATGCGTGGAAAAGACT 59.307 50.000 0.00 0.00 0.00 3.24
879 910 0.804989 CAGGGATGCGTGGAAAAGAC 59.195 55.000 0.00 0.00 0.00 3.01
880 911 0.322456 CCAGGGATGCGTGGAAAAGA 60.322 55.000 20.15 0.00 35.67 2.52
881 912 1.937546 GCCAGGGATGCGTGGAAAAG 61.938 60.000 27.70 3.15 35.67 2.27
882 913 1.976474 GCCAGGGATGCGTGGAAAA 60.976 57.895 27.70 0.00 35.67 2.29
883 914 2.361104 GCCAGGGATGCGTGGAAA 60.361 61.111 27.70 0.00 35.67 3.13
884 915 2.424842 AAAGCCAGGGATGCGTGGAA 62.425 55.000 27.70 0.00 35.67 3.53
885 916 2.905996 AAAGCCAGGGATGCGTGGA 61.906 57.895 27.70 0.00 35.67 4.02
886 917 2.361610 AAAGCCAGGGATGCGTGG 60.362 61.111 20.45 20.45 36.85 4.94
887 918 1.675310 TCAAAGCCAGGGATGCGTG 60.675 57.895 0.00 0.00 0.00 5.34
888 919 1.675641 GTCAAAGCCAGGGATGCGT 60.676 57.895 0.00 0.00 0.00 5.24
889 920 2.409870 GGTCAAAGCCAGGGATGCG 61.410 63.158 0.00 0.00 0.00 4.73
890 921 1.304381 TGGTCAAAGCCAGGGATGC 60.304 57.895 0.00 0.00 33.97 3.91
897 928 0.535780 CAGTCAGCTGGTCAAAGCCA 60.536 55.000 15.13 0.00 44.68 4.75
898 929 0.536006 ACAGTCAGCTGGTCAAAGCC 60.536 55.000 15.13 0.00 46.62 4.35
899 930 1.801178 GTACAGTCAGCTGGTCAAAGC 59.199 52.381 15.13 0.00 46.62 3.51
900 931 3.062763 CTGTACAGTCAGCTGGTCAAAG 58.937 50.000 15.13 1.06 46.62 2.77
944 975 0.392706 CTGACACAGTACAGGCACCA 59.607 55.000 0.00 0.00 0.00 4.17
985 1016 1.202817 TGCCATGCTTACGAGTTACGA 59.797 47.619 0.00 0.00 45.77 3.43
987 1018 1.327764 GCTGCCATGCTTACGAGTTAC 59.672 52.381 0.00 0.00 0.00 2.50
988 1019 1.066502 TGCTGCCATGCTTACGAGTTA 60.067 47.619 0.00 0.00 0.00 2.24
989 1020 0.321564 TGCTGCCATGCTTACGAGTT 60.322 50.000 0.00 0.00 0.00 3.01
990 1021 0.107508 ATGCTGCCATGCTTACGAGT 60.108 50.000 0.00 0.00 0.00 4.18
991 1022 0.306840 CATGCTGCCATGCTTACGAG 59.693 55.000 0.00 0.00 42.08 4.18
999 1030 2.413351 GCTGAGCATGCTGCCATG 59.587 61.111 28.27 12.25 46.52 3.66
1008 1039 2.909577 GCAGAGAGGGCTGAGCAT 59.090 61.111 6.82 0.00 38.14 3.79
1167 1198 4.389077 CCTCGCTAAAACTCGAAAACAGAT 59.611 41.667 0.00 0.00 34.07 2.90
1388 1419 3.790437 ATCAGCCACCTCCTGCCG 61.790 66.667 0.00 0.00 0.00 5.69
1438 1469 3.083997 GCCGTGATCTCCCCCACT 61.084 66.667 0.00 0.00 0.00 4.00
1763 1802 5.774690 AGAACAATTCATTTGCTTCCAGGTA 59.225 36.000 0.00 0.00 39.03 3.08
1817 1856 6.545666 TGACTCTTCAAAAATACTGCCTTTGA 59.454 34.615 0.00 0.00 37.30 2.69
1818 1857 6.738114 TGACTCTTCAAAAATACTGCCTTTG 58.262 36.000 0.00 0.00 0.00 2.77
1819 1858 6.959639 TGACTCTTCAAAAATACTGCCTTT 57.040 33.333 0.00 0.00 0.00 3.11
1822 1861 6.458888 GCCTATGACTCTTCAAAAATACTGCC 60.459 42.308 0.00 0.00 34.61 4.85
1823 1862 6.094048 TGCCTATGACTCTTCAAAAATACTGC 59.906 38.462 0.00 0.00 34.61 4.40
1824 1863 7.335422 ACTGCCTATGACTCTTCAAAAATACTG 59.665 37.037 0.00 0.00 34.61 2.74
1825 1864 7.398024 ACTGCCTATGACTCTTCAAAAATACT 58.602 34.615 0.00 0.00 34.61 2.12
1826 1865 7.617041 ACTGCCTATGACTCTTCAAAAATAC 57.383 36.000 0.00 0.00 34.61 1.89
1827 1866 7.665559 ACAACTGCCTATGACTCTTCAAAAATA 59.334 33.333 0.00 0.00 34.61 1.40
1828 1867 6.491403 ACAACTGCCTATGACTCTTCAAAAAT 59.509 34.615 0.00 0.00 34.61 1.82
1829 1868 5.827797 ACAACTGCCTATGACTCTTCAAAAA 59.172 36.000 0.00 0.00 34.61 1.94
1898 1965 2.846206 TGCAGTTCCCATAGTCCAGAAT 59.154 45.455 0.00 0.00 0.00 2.40
1937 2004 4.393371 CCTTTCTTTGCTAGACACTTAGGC 59.607 45.833 0.00 0.00 30.90 3.93
2045 2112 5.357742 TCCAGAAGTCTATTTGCAGCATA 57.642 39.130 0.00 0.00 0.00 3.14
2062 2129 4.767478 CATCAGAATTGAGAAGCTCCAGA 58.233 43.478 0.00 0.00 36.61 3.86
2127 2194 2.794350 GCTTTGAACAATTGAACCCACG 59.206 45.455 13.59 0.00 0.00 4.94
2343 2413 6.732896 ATAGTCCAGGTAATTAGGTGTGAG 57.267 41.667 0.00 0.00 0.00 3.51
2344 2414 8.792830 AATATAGTCCAGGTAATTAGGTGTGA 57.207 34.615 0.00 0.00 0.00 3.58
2428 2498 9.233232 CAAAAGTTACAGTCCATAAAGAACAAC 57.767 33.333 0.00 0.00 0.00 3.32
2522 2592 2.365617 TCTTGGAGAAGGGATATGCGTC 59.634 50.000 0.00 0.00 0.00 5.19
2576 2646 3.731652 TGATGGCAAAAGGTTGAGTTG 57.268 42.857 0.00 0.00 36.83 3.16
2635 2705 5.063944 GTGATGAAGATCAATGTACAACGCT 59.936 40.000 0.00 0.00 40.39 5.07
2641 2711 6.749118 GCCAAAAGTGATGAAGATCAATGTAC 59.251 38.462 0.00 0.00 40.39 2.90
2642 2712 6.660521 AGCCAAAAGTGATGAAGATCAATGTA 59.339 34.615 0.00 0.00 40.39 2.29
2653 2723 2.034939 CAGCAACAGCCAAAAGTGATGA 59.965 45.455 0.00 0.00 0.00 2.92
2832 2902 0.976641 TTGTACTCCCAGTCCTGCAG 59.023 55.000 6.78 6.78 0.00 4.41
2901 2971 8.631676 GTAGTGCTAACATTACCTTCTTCTAC 57.368 38.462 0.00 0.00 33.96 2.59
3095 3166 8.478775 AATTACACTCCAGATAGCATGTACTA 57.521 34.615 0.00 0.00 0.00 1.82
3096 3167 6.985653 ATTACACTCCAGATAGCATGTACT 57.014 37.500 0.00 0.00 0.00 2.73
3097 3168 7.169982 GTGAATTACACTCCAGATAGCATGTAC 59.830 40.741 0.00 0.00 45.13 2.90
3195 3296 6.603940 AGGAGGCATCATACTCTTCTAATC 57.396 41.667 0.00 0.00 34.22 1.75
3263 3364 9.325198 CAACTAATAACATGGAAGCATGTACTA 57.675 33.333 0.00 0.00 44.19 1.82
3264 3365 7.283127 CCAACTAATAACATGGAAGCATGTACT 59.717 37.037 0.00 0.00 44.19 2.73
3265 3366 7.282224 TCCAACTAATAACATGGAAGCATGTAC 59.718 37.037 0.00 0.00 44.19 2.90
3266 3367 7.342581 TCCAACTAATAACATGGAAGCATGTA 58.657 34.615 0.00 0.00 44.19 2.29
3382 3790 9.788960 ACTTAGAATTTTCTGTGACTTTTGTTC 57.211 29.630 3.07 0.00 38.19 3.18
3455 3863 6.682863 GCACTTGACATGTACGTTATCATTTC 59.317 38.462 0.00 0.52 0.00 2.17
3456 3864 6.403200 GGCACTTGACATGTACGTTATCATTT 60.403 38.462 0.00 0.00 0.00 2.32
3547 4171 3.243336 GAACTCGTTCGTGACATAAGCT 58.757 45.455 1.45 0.00 0.00 3.74
3676 4309 3.763097 TGCTCTTGTGTGTCAGTTTTG 57.237 42.857 0.00 0.00 0.00 2.44
3677 4310 4.782019 TTTGCTCTTGTGTGTCAGTTTT 57.218 36.364 0.00 0.00 0.00 2.43
3678 4311 4.218417 AGTTTTGCTCTTGTGTGTCAGTTT 59.782 37.500 0.00 0.00 0.00 2.66
3679 4312 3.758554 AGTTTTGCTCTTGTGTGTCAGTT 59.241 39.130 0.00 0.00 0.00 3.16
3680 4313 3.127548 CAGTTTTGCTCTTGTGTGTCAGT 59.872 43.478 0.00 0.00 0.00 3.41
3681 4314 3.374988 TCAGTTTTGCTCTTGTGTGTCAG 59.625 43.478 0.00 0.00 0.00 3.51
3682 4315 3.126858 GTCAGTTTTGCTCTTGTGTGTCA 59.873 43.478 0.00 0.00 0.00 3.58
3683 4316 3.126858 TGTCAGTTTTGCTCTTGTGTGTC 59.873 43.478 0.00 0.00 0.00 3.67
3684 4317 3.081061 TGTCAGTTTTGCTCTTGTGTGT 58.919 40.909 0.00 0.00 0.00 3.72
3685 4318 3.119884 TGTGTCAGTTTTGCTCTTGTGTG 60.120 43.478 0.00 0.00 0.00 3.82
3686 4319 3.081061 TGTGTCAGTTTTGCTCTTGTGT 58.919 40.909 0.00 0.00 0.00 3.72
3687 4320 3.119884 TGTGTGTCAGTTTTGCTCTTGTG 60.120 43.478 0.00 0.00 0.00 3.33
3688 4321 3.081061 TGTGTGTCAGTTTTGCTCTTGT 58.919 40.909 0.00 0.00 0.00 3.16
3689 4322 3.763097 TGTGTGTCAGTTTTGCTCTTG 57.237 42.857 0.00 0.00 0.00 3.02
3690 4323 4.009675 TCTTGTGTGTCAGTTTTGCTCTT 58.990 39.130 0.00 0.00 0.00 2.85
3691 4324 3.609853 TCTTGTGTGTCAGTTTTGCTCT 58.390 40.909 0.00 0.00 0.00 4.09
3692 4325 3.790123 GCTCTTGTGTGTCAGTTTTGCTC 60.790 47.826 0.00 0.00 0.00 4.26
3693 4326 2.098117 GCTCTTGTGTGTCAGTTTTGCT 59.902 45.455 0.00 0.00 0.00 3.91
3694 4327 2.159393 TGCTCTTGTGTGTCAGTTTTGC 60.159 45.455 0.00 0.00 0.00 3.68
3800 4437 1.784358 ATCCATGCATCCCAAACTGG 58.216 50.000 0.00 0.00 37.25 4.00
3824 4461 4.180057 TGTTAAATCATGCAAAATCCCGC 58.820 39.130 0.00 0.00 0.00 6.13
3954 4607 7.606456 TGCTTAAATTCTACTACTGTCCTTTGG 59.394 37.037 0.00 0.00 0.00 3.28
3963 4617 6.481644 GCTGCTCATGCTTAAATTCTACTACT 59.518 38.462 0.00 0.00 40.48 2.57
3986 4640 3.318557 GCTTATCTTCTACCGGTACTGCT 59.681 47.826 11.16 0.00 0.00 4.24
3994 4648 1.336056 GGCGAGGCTTATCTTCTACCG 60.336 57.143 0.00 0.00 0.00 4.02
3999 4653 1.876156 CAATGGGCGAGGCTTATCTTC 59.124 52.381 0.00 0.00 0.00 2.87
4012 4666 3.004862 CAAGAAGCATTTTCCAATGGGC 58.995 45.455 0.00 0.00 40.36 5.36
4017 4671 3.253188 CCTCGTCAAGAAGCATTTTCCAA 59.747 43.478 0.00 0.00 0.00 3.53
4066 4720 2.086054 AAGTCAAGAGATCACGCACC 57.914 50.000 0.00 0.00 0.00 5.01
4099 4753 7.307811 GCTTAATTTGTGAAAGTAGAGACGGTT 60.308 37.037 0.00 0.00 0.00 4.44
4144 4798 4.056050 CTGTGCGTTTAAGGTAGAGTGTT 58.944 43.478 0.00 0.00 0.00 3.32
4167 4821 3.764885 ATGCGGAAATAGCTGTGTTTC 57.235 42.857 0.00 4.54 34.01 2.78
4183 4837 4.149922 TGACTTTGACGTCTTCTTTATGCG 59.850 41.667 17.92 0.00 35.00 4.73
4261 4915 1.063031 GTGAAATTTCTTGCGCTGCC 58.937 50.000 18.64 0.00 0.00 4.85
4315 4969 3.181492 TGCGTGCTGAAAAATCTCAAACA 60.181 39.130 0.00 0.00 0.00 2.83
4316 4970 3.371168 TGCGTGCTGAAAAATCTCAAAC 58.629 40.909 0.00 0.00 0.00 2.93
4324 4978 0.103755 TTGCCATGCGTGCTGAAAAA 59.896 45.000 0.00 0.00 0.00 1.94
4330 4984 2.677524 ATGGTTGCCATGCGTGCT 60.678 55.556 0.00 0.00 43.39 4.40
4337 4991 2.607499 TGTTTTCTCCATGGTTGCCAT 58.393 42.857 12.58 0.00 46.37 4.40
4338 4992 2.079170 TGTTTTCTCCATGGTTGCCA 57.921 45.000 12.58 0.00 38.19 4.92
4339 4993 2.562298 TGATGTTTTCTCCATGGTTGCC 59.438 45.455 12.58 0.00 0.00 4.52
4340 4994 3.940209 TGATGTTTTCTCCATGGTTGC 57.060 42.857 12.58 0.00 0.00 4.17
4341 4995 9.439500 AATTTTATGATGTTTTCTCCATGGTTG 57.561 29.630 12.58 6.40 0.00 3.77
4342 4996 9.657419 GAATTTTATGATGTTTTCTCCATGGTT 57.343 29.630 12.58 0.00 0.00 3.67
4343 4997 8.814931 TGAATTTTATGATGTTTTCTCCATGGT 58.185 29.630 12.58 0.00 0.00 3.55
4344 4998 9.656040 TTGAATTTTATGATGTTTTCTCCATGG 57.344 29.630 4.97 4.97 0.00 3.66


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

AutoCloner maintained by Alex Coulton.