Multiple sequence alignment - TraesCS7D01G408400

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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 TraesCS7D01G408400 chr7D 100.000 3843 0 0 1 3843 526238910 526242752 0.000000e+00 7097.0
1 TraesCS7D01G408400 chr7B 89.184 2857 154 72 995 3774 562743921 562746699 0.000000e+00 3421.0
2 TraesCS7D01G408400 chr7B 92.748 524 38 0 1 524 570061075 570060552 0.000000e+00 758.0
3 TraesCS7D01G408400 chr7B 81.515 779 110 14 1 777 104970755 104971501 9.130000e-171 610.0
4 TraesCS7D01G408400 chr7A 90.351 1710 94 25 2108 3769 606561520 606563206 0.000000e+00 2178.0
5 TraesCS7D01G408400 chr7A 85.323 1022 71 38 896 1852 606559623 606560630 0.000000e+00 983.0
6 TraesCS7D01G408400 chr7A 92.754 138 9 1 1917 2053 606560642 606560779 8.420000e-47 198.0
7 TraesCS7D01G408400 chr2D 94.458 794 27 2 1 777 562914429 562915222 0.000000e+00 1206.0
8 TraesCS7D01G408400 chr5D 94.466 777 41 1 1 777 355733739 355732965 0.000000e+00 1195.0
9 TraesCS7D01G408400 chr5D 87.463 1021 65 26 1873 2852 388345351 388344353 0.000000e+00 1118.0
10 TraesCS7D01G408400 chr5D 83.417 199 25 4 2903 3101 388344061 388343871 1.100000e-40 178.0
11 TraesCS7D01G408400 chr5D 86.538 52 7 0 2844 2895 388344141 388344090 1.490000e-04 58.4
12 TraesCS7D01G408400 chr6D 87.677 779 76 14 1 777 384299899 384299139 0.000000e+00 889.0
13 TraesCS7D01G408400 chr3A 90.432 648 50 7 1 648 708898465 708897830 0.000000e+00 843.0
14 TraesCS7D01G408400 chr3A 87.156 109 5 1 669 777 708897832 708897733 8.720000e-22 115.0
15 TraesCS7D01G408400 chr4A 84.556 777 102 11 1 777 577197573 577198331 0.000000e+00 754.0


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 TraesCS7D01G408400 chr7D 526238910 526242752 3842 False 7097.000000 7097 100.000 1 3843 1 chr7D.!!$F1 3842
1 TraesCS7D01G408400 chr7B 562743921 562746699 2778 False 3421.000000 3421 89.184 995 3774 1 chr7B.!!$F2 2779
2 TraesCS7D01G408400 chr7B 570060552 570061075 523 True 758.000000 758 92.748 1 524 1 chr7B.!!$R1 523
3 TraesCS7D01G408400 chr7B 104970755 104971501 746 False 610.000000 610 81.515 1 777 1 chr7B.!!$F1 776
4 TraesCS7D01G408400 chr7A 606559623 606563206 3583 False 1119.666667 2178 89.476 896 3769 3 chr7A.!!$F1 2873
5 TraesCS7D01G408400 chr2D 562914429 562915222 793 False 1206.000000 1206 94.458 1 777 1 chr2D.!!$F1 776
6 TraesCS7D01G408400 chr5D 355732965 355733739 774 True 1195.000000 1195 94.466 1 777 1 chr5D.!!$R1 776
7 TraesCS7D01G408400 chr5D 388343871 388345351 1480 True 451.466667 1118 85.806 1873 3101 3 chr5D.!!$R2 1228
8 TraesCS7D01G408400 chr6D 384299139 384299899 760 True 889.000000 889 87.677 1 777 1 chr6D.!!$R1 776
9 TraesCS7D01G408400 chr3A 708897733 708898465 732 True 479.000000 843 88.794 1 777 2 chr3A.!!$R1 776
10 TraesCS7D01G408400 chr4A 577197573 577198331 758 False 754.000000 754 84.556 1 777 1 chr4A.!!$F1 776

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
960 1028 0.037512 GCTGAGCAGAGCAGAGACAA 60.038 55.0 0.0 0.0 38.95 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2895 3986 1.059942 GCACTACCATTTTGCAACGC 58.94 50.0 0.0 0.0 36.22 4.84 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
144 145 2.182181 CATGGCCGATGCGTCATGT 61.182 57.895 6.75 0.00 38.85 3.21
151 152 1.355005 CGATGCGTCATGTAACACCA 58.645 50.000 6.75 0.00 0.00 4.17
284 295 2.142761 ACACTCCTGACAGCAGCCA 61.143 57.895 0.00 0.00 40.91 4.75
412 440 3.231736 AGGAAGCACCACCGACGT 61.232 61.111 0.00 0.00 42.04 4.34
777 828 1.396653 GTGGCTCGCTAGTTAGGGTA 58.603 55.000 3.56 0.00 37.50 3.69
778 829 1.753073 GTGGCTCGCTAGTTAGGGTAA 59.247 52.381 3.56 0.00 37.50 2.85
779 830 2.167075 GTGGCTCGCTAGTTAGGGTAAA 59.833 50.000 3.56 0.00 37.50 2.01
780 831 2.833338 TGGCTCGCTAGTTAGGGTAAAA 59.167 45.455 3.56 0.00 37.50 1.52
781 832 3.261390 TGGCTCGCTAGTTAGGGTAAAAA 59.739 43.478 3.56 0.00 37.50 1.94
811 862 2.133281 TCACCCCATGATGCTTCTTG 57.867 50.000 8.13 8.13 29.99 3.02
812 863 1.355381 TCACCCCATGATGCTTCTTGT 59.645 47.619 12.61 0.00 29.99 3.16
813 864 2.575735 TCACCCCATGATGCTTCTTGTA 59.424 45.455 12.61 0.00 29.99 2.41
814 865 3.202818 TCACCCCATGATGCTTCTTGTAT 59.797 43.478 12.61 0.00 29.99 2.29
815 866 3.567164 CACCCCATGATGCTTCTTGTATC 59.433 47.826 12.61 0.00 38.12 2.24
816 867 3.152341 CCCCATGATGCTTCTTGTATCC 58.848 50.000 12.61 0.00 37.04 2.59
817 868 3.152341 CCCATGATGCTTCTTGTATCCC 58.848 50.000 12.61 0.00 37.04 3.85
818 869 3.435457 CCCATGATGCTTCTTGTATCCCA 60.435 47.826 12.61 0.00 37.04 4.37
819 870 3.567164 CCATGATGCTTCTTGTATCCCAC 59.433 47.826 12.61 0.00 37.04 4.61
820 871 3.998913 TGATGCTTCTTGTATCCCACA 57.001 42.857 0.88 0.00 37.04 4.17
821 872 4.508551 TGATGCTTCTTGTATCCCACAT 57.491 40.909 0.88 0.00 37.04 3.21
822 873 5.628797 TGATGCTTCTTGTATCCCACATA 57.371 39.130 0.88 0.00 37.04 2.29
823 874 5.368145 TGATGCTTCTTGTATCCCACATAC 58.632 41.667 0.88 0.00 37.04 2.39
824 875 5.130975 TGATGCTTCTTGTATCCCACATACT 59.869 40.000 0.88 0.00 37.04 2.12
825 876 4.769688 TGCTTCTTGTATCCCACATACTG 58.230 43.478 0.00 0.00 36.90 2.74
826 877 4.225042 TGCTTCTTGTATCCCACATACTGT 59.775 41.667 0.00 0.00 36.90 3.55
840 891 6.549912 CACATACTGTGGTATTGGATGATG 57.450 41.667 0.00 0.00 44.27 3.07
841 892 6.290605 CACATACTGTGGTATTGGATGATGA 58.709 40.000 0.00 0.00 44.27 2.92
842 893 6.767423 CACATACTGTGGTATTGGATGATGAA 59.233 38.462 0.00 0.00 44.27 2.57
843 894 7.446319 CACATACTGTGGTATTGGATGATGAAT 59.554 37.037 0.00 0.00 44.27 2.57
844 895 8.659527 ACATACTGTGGTATTGGATGATGAATA 58.340 33.333 0.00 0.00 36.60 1.75
845 896 9.506018 CATACTGTGGTATTGGATGATGAATAA 57.494 33.333 0.00 0.00 36.60 1.40
847 898 8.455903 ACTGTGGTATTGGATGATGAATAAAG 57.544 34.615 0.00 0.00 0.00 1.85
848 899 8.055181 ACTGTGGTATTGGATGATGAATAAAGT 58.945 33.333 0.00 0.00 0.00 2.66
849 900 8.821686 TGTGGTATTGGATGATGAATAAAGTT 57.178 30.769 0.00 0.00 0.00 2.66
850 901 9.913310 TGTGGTATTGGATGATGAATAAAGTTA 57.087 29.630 0.00 0.00 0.00 2.24
894 945 3.836151 AAAAAGGCAACGGCGAGT 58.164 50.000 16.62 0.00 46.39 4.18
895 946 1.358759 AAAAAGGCAACGGCGAGTG 59.641 52.632 16.62 12.67 46.39 3.51
896 947 2.677573 AAAAAGGCAACGGCGAGTGC 62.678 55.000 24.82 24.82 46.39 4.40
921 972 3.716006 CGCGCCTTGACCACACAG 61.716 66.667 0.00 0.00 0.00 3.66
924 975 1.367471 CGCCTTGACCACACAGAGA 59.633 57.895 0.00 0.00 0.00 3.10
953 1004 2.168666 CTGAGTGGCTGAGCAGAGCA 62.169 60.000 6.82 0.00 41.08 4.26
959 1027 1.590665 GCTGAGCAGAGCAGAGACA 59.409 57.895 0.00 0.00 38.95 3.41
960 1028 0.037512 GCTGAGCAGAGCAGAGACAA 60.038 55.000 0.00 0.00 38.95 3.18
967 1035 3.672295 GAGCAGAGACAAGGCCGGG 62.672 68.421 2.18 0.00 0.00 5.73
1140 1211 2.259204 GTACGTGCGCACCCACTA 59.741 61.111 33.23 15.17 33.60 2.74
1148 1236 2.033602 GCACCCACTACCACCACC 59.966 66.667 0.00 0.00 0.00 4.61
1152 1240 0.838987 ACCCACTACCACCACCGATT 60.839 55.000 0.00 0.00 0.00 3.34
1156 1244 0.321298 ACTACCACCACCGATTGCAC 60.321 55.000 0.00 0.00 0.00 4.57
1178 1273 1.350193 GCACGTCACATCACAGGTAG 58.650 55.000 0.00 0.00 0.00 3.18
1179 1274 1.336887 GCACGTCACATCACAGGTAGT 60.337 52.381 0.00 0.00 0.00 2.73
1181 1276 3.428999 GCACGTCACATCACAGGTAGTAT 60.429 47.826 0.00 0.00 0.00 2.12
1182 1277 4.105486 CACGTCACATCACAGGTAGTATG 58.895 47.826 0.00 0.00 0.00 2.39
1185 1280 5.593095 ACGTCACATCACAGGTAGTATGTAT 59.407 40.000 0.00 0.00 31.55 2.29
1187 1282 6.238648 CGTCACATCACAGGTAGTATGTATCA 60.239 42.308 0.00 0.00 31.55 2.15
1188 1283 7.522236 CGTCACATCACAGGTAGTATGTATCAT 60.522 40.741 0.00 0.00 31.55 2.45
1189 1284 8.144478 GTCACATCACAGGTAGTATGTATCATT 58.856 37.037 0.00 0.00 31.55 2.57
1190 1285 8.143835 TCACATCACAGGTAGTATGTATCATTG 58.856 37.037 0.00 0.00 31.55 2.82
1213 1308 1.966354 TGATGATGGAGGTGATCGAGG 59.034 52.381 0.00 0.00 0.00 4.63
1400 1499 6.073112 CGCCTCTACTGGTAATTACTCTACTC 60.073 46.154 15.05 0.00 0.00 2.59
1418 1517 3.411517 ATTAGCCGCCCTGCCTGT 61.412 61.111 0.00 0.00 0.00 4.00
1419 1518 2.983879 ATTAGCCGCCCTGCCTGTT 61.984 57.895 0.00 0.00 0.00 3.16
1420 1519 1.632018 ATTAGCCGCCCTGCCTGTTA 61.632 55.000 0.00 0.00 0.00 2.41
1520 1640 2.721167 CGAGGACGGGCCATGAGAA 61.721 63.158 4.39 0.00 40.02 2.87
1521 1641 1.832912 GAGGACGGGCCATGAGAAT 59.167 57.895 4.39 0.00 40.02 2.40
1522 1642 0.533755 GAGGACGGGCCATGAGAATG 60.534 60.000 4.39 0.00 40.02 2.67
1544 1666 1.021390 ATGAACGAAGCTCTTGCCCG 61.021 55.000 0.00 0.00 40.80 6.13
1604 1726 1.879380 CATTTCTCACAAGGAACCGCA 59.121 47.619 0.00 0.00 0.00 5.69
1607 1729 1.300620 CTCACAAGGAACCGCACGA 60.301 57.895 0.00 0.00 0.00 4.35
1680 1802 2.074579 CATAGTAGGGAGGGAGGGAGA 58.925 57.143 0.00 0.00 0.00 3.71
1737 1859 5.127031 TGCTTATAGCTGTACATGACACAGA 59.873 40.000 26.02 13.13 45.10 3.41
1749 1871 1.155042 GACACAGAAGGCAGAGCAAG 58.845 55.000 0.00 0.00 0.00 4.01
1750 1872 0.888285 ACACAGAAGGCAGAGCAAGC 60.888 55.000 0.00 0.00 0.00 4.01
1751 1873 0.887836 CACAGAAGGCAGAGCAAGCA 60.888 55.000 0.00 0.00 0.00 3.91
1752 1874 0.179009 ACAGAAGGCAGAGCAAGCAA 60.179 50.000 0.00 0.00 0.00 3.91
1772 1894 4.031652 GCAATACATTTTTGGCATCGTCAC 59.968 41.667 0.00 0.00 0.00 3.67
1793 1915 3.195610 ACGACCATGAGCAACAGAGATAA 59.804 43.478 0.00 0.00 0.00 1.75
1795 1917 4.033358 CGACCATGAGCAACAGAGATAAAC 59.967 45.833 0.00 0.00 0.00 2.01
1796 1918 4.910195 ACCATGAGCAACAGAGATAAACA 58.090 39.130 0.00 0.00 0.00 2.83
1797 1919 4.697352 ACCATGAGCAACAGAGATAAACAC 59.303 41.667 0.00 0.00 0.00 3.32
1867 1996 4.811969 TGCAGCATCTTTCAATGGATTT 57.188 36.364 0.00 0.00 0.00 2.17
1868 1997 5.155278 TGCAGCATCTTTCAATGGATTTT 57.845 34.783 0.00 0.00 0.00 1.82
1869 1998 6.283544 TGCAGCATCTTTCAATGGATTTTA 57.716 33.333 0.00 0.00 0.00 1.52
1909 2038 2.079925 CTGTCTGTTTCTAGCCAAGCC 58.920 52.381 0.00 0.00 0.00 4.35
1926 2055 1.308069 GCCGTTGCACACTGATCCAT 61.308 55.000 0.00 0.00 37.47 3.41
2002 2132 1.742761 TGCTGAAGCTGCTATGTTCC 58.257 50.000 0.90 0.00 42.66 3.62
2036 2166 7.175119 ACAATCTAGGTTTCCTTTCTTGCTTAC 59.825 37.037 0.00 0.00 34.61 2.34
2100 2861 4.617995 GCTGCAGGCACACAATACATTTTA 60.618 41.667 17.12 0.00 41.35 1.52
2108 2869 6.972328 GGCACACAATACATTTTACCACATAG 59.028 38.462 0.00 0.00 0.00 2.23
2182 3006 8.575565 TTTATTTGCTAGCTAGTTAGACATCG 57.424 34.615 21.62 0.00 0.00 3.84
2239 3064 2.567615 ACAAGAGGTCGAGGCAAACTAT 59.432 45.455 0.00 0.00 0.00 2.12
2276 3101 4.183865 TGACGTGCTCAAGATTTATCTGG 58.816 43.478 0.00 0.00 37.19 3.86
2335 3187 0.603065 CCGCGGATGATCACTGGATA 59.397 55.000 24.07 0.00 32.67 2.59
2372 3234 2.031012 CTGGTCGAGCACTTGCCA 59.969 61.111 14.39 0.25 43.38 4.92
2415 3277 3.495100 CGACAATATAGGGCTTCCTTGCT 60.495 47.826 0.00 0.00 41.96 3.91
2459 3321 7.063426 CGACTGTTACAACACACAGATATTCAT 59.937 37.037 6.32 0.00 42.74 2.57
2483 3353 5.314923 ACATGGAAATACACATGCTGTTC 57.685 39.130 0.00 0.00 46.35 3.18
2578 3449 1.209504 TCAGGCAGGAAAAGGTATCGG 59.790 52.381 0.00 0.00 0.00 4.18
2767 3638 3.055602 GCATTTTGGGGATCAGAAGCTTT 60.056 43.478 0.00 0.00 0.00 3.51
2879 3970 2.420022 ACCTGCAGTGATAAACAATCGC 59.580 45.455 13.81 0.00 44.12 4.58
2887 3978 6.677920 GCAGTGATAAACAATCGCCAGTTAAT 60.678 38.462 0.00 0.00 44.75 1.40
2895 3986 7.867445 AACAATCGCCAGTTAATTACAAAAG 57.133 32.000 0.00 0.00 0.00 2.27
3109 4221 6.405216 CAAAACAAAGAAAAAGCTGTCATCG 58.595 36.000 0.00 0.00 0.00 3.84
3256 4368 6.152661 TGAATGAATTCCCTCCAATTGTGTAC 59.847 38.462 4.43 0.00 35.97 2.90
3314 4437 7.593825 ACCAGAAGCATCACAAAAGTATAAAC 58.406 34.615 0.00 0.00 0.00 2.01
3321 4444 8.454106 AGCATCACAAAAGTATAAACATCAGTC 58.546 33.333 0.00 0.00 0.00 3.51
3331 4454 1.139989 AACATCAGTCAACGAGCACG 58.860 50.000 0.76 0.76 45.75 5.34
3543 4686 1.468127 CGTACATGCATCAACAAGGCA 59.532 47.619 0.00 0.00 42.43 4.75
3594 4737 1.456678 CGTCGTCGCTGAGATGAACG 61.457 60.000 4.85 7.75 45.61 3.95
3647 4790 6.044682 GCAACCTGCATTCTAAATAAGCATT 58.955 36.000 0.00 0.00 44.26 3.56
3660 4803 9.534565 TCTAAATAAGCATTCATCAGTACTGAC 57.465 33.333 27.41 13.62 43.11 3.51
3664 4807 6.537453 AAGCATTCATCAGTACTGACTACT 57.463 37.500 27.41 15.37 43.11 2.57
3738 4881 7.336931 ACTCTGTCCATGTTTTATGGTATTCAC 59.663 37.037 5.89 0.00 40.06 3.18
3747 4890 8.415950 TGTTTTATGGTATTCACACTTTGGAT 57.584 30.769 0.00 0.00 0.00 3.41
3776 4919 9.875691 AAAATTGTAATTTCTTGGGCTAGAATC 57.124 29.630 0.00 0.00 37.62 2.52
3777 4920 8.829373 AATTGTAATTTCTTGGGCTAGAATCT 57.171 30.769 0.00 0.00 34.33 2.40
3778 4921 9.920946 AATTGTAATTTCTTGGGCTAGAATCTA 57.079 29.630 0.00 0.00 34.33 1.98
3784 4927 7.872061 TTTCTTGGGCTAGAATCTATATCCA 57.128 36.000 0.00 0.00 34.33 3.41
3785 4928 8.454859 TTTCTTGGGCTAGAATCTATATCCAT 57.545 34.615 0.00 0.00 34.33 3.41
3786 4929 7.667575 TCTTGGGCTAGAATCTATATCCATC 57.332 40.000 0.00 0.00 0.00 3.51
3787 4930 7.425834 TCTTGGGCTAGAATCTATATCCATCT 58.574 38.462 0.00 0.00 0.00 2.90
3788 4931 8.569596 TCTTGGGCTAGAATCTATATCCATCTA 58.430 37.037 0.00 0.00 0.00 1.98
3789 4932 9.206690 CTTGGGCTAGAATCTATATCCATCTAA 57.793 37.037 0.00 0.00 0.00 2.10
3790 4933 8.540507 TGGGCTAGAATCTATATCCATCTAAC 57.459 38.462 0.00 0.00 0.00 2.34
3791 4934 8.347591 TGGGCTAGAATCTATATCCATCTAACT 58.652 37.037 0.00 0.00 0.00 2.24
3792 4935 9.869667 GGGCTAGAATCTATATCCATCTAACTA 57.130 37.037 0.00 0.00 0.00 2.24
3806 4949 8.279970 TCCATCTAACTATTTTGGTGATGTTG 57.720 34.615 0.00 0.00 0.00 3.33
3807 4950 7.888021 TCCATCTAACTATTTTGGTGATGTTGT 59.112 33.333 0.00 0.00 0.00 3.32
3808 4951 8.184192 CCATCTAACTATTTTGGTGATGTTGTC 58.816 37.037 0.00 0.00 0.00 3.18
3809 4952 8.950210 CATCTAACTATTTTGGTGATGTTGTCT 58.050 33.333 0.00 0.00 0.00 3.41
3810 4953 8.918202 TCTAACTATTTTGGTGATGTTGTCTT 57.082 30.769 0.00 0.00 0.00 3.01
3811 4954 8.783093 TCTAACTATTTTGGTGATGTTGTCTTG 58.217 33.333 0.00 0.00 0.00 3.02
3812 4955 6.959639 ACTATTTTGGTGATGTTGTCTTGT 57.040 33.333 0.00 0.00 0.00 3.16
3813 4956 7.346751 ACTATTTTGGTGATGTTGTCTTGTT 57.653 32.000 0.00 0.00 0.00 2.83
3814 4957 7.781056 ACTATTTTGGTGATGTTGTCTTGTTT 58.219 30.769 0.00 0.00 0.00 2.83
3815 4958 6.907206 ATTTTGGTGATGTTGTCTTGTTTG 57.093 33.333 0.00 0.00 0.00 2.93
3816 4959 4.383850 TTGGTGATGTTGTCTTGTTTGG 57.616 40.909 0.00 0.00 0.00 3.28
3817 4960 3.360867 TGGTGATGTTGTCTTGTTTGGT 58.639 40.909 0.00 0.00 0.00 3.67
3818 4961 4.527944 TGGTGATGTTGTCTTGTTTGGTA 58.472 39.130 0.00 0.00 0.00 3.25
3819 4962 4.336993 TGGTGATGTTGTCTTGTTTGGTAC 59.663 41.667 0.00 0.00 0.00 3.34
3820 4963 4.336993 GGTGATGTTGTCTTGTTTGGTACA 59.663 41.667 0.00 0.00 34.12 2.90
3821 4964 5.270853 GTGATGTTGTCTTGTTTGGTACAC 58.729 41.667 0.00 0.00 39.29 2.90
3822 4965 5.065988 GTGATGTTGTCTTGTTTGGTACACT 59.934 40.000 0.00 0.00 39.29 3.55
3823 4966 4.955925 TGTTGTCTTGTTTGGTACACTG 57.044 40.909 0.00 0.00 39.29 3.66
3824 4967 4.328536 TGTTGTCTTGTTTGGTACACTGT 58.671 39.130 0.00 0.00 39.29 3.55
3825 4968 4.393680 TGTTGTCTTGTTTGGTACACTGTC 59.606 41.667 0.00 0.00 39.29 3.51
3826 4969 4.209307 TGTCTTGTTTGGTACACTGTCA 57.791 40.909 0.00 0.00 39.29 3.58
3827 4970 3.936453 TGTCTTGTTTGGTACACTGTCAC 59.064 43.478 0.00 0.00 39.29 3.67
3828 4971 4.189231 GTCTTGTTTGGTACACTGTCACT 58.811 43.478 0.00 0.00 39.29 3.41
3829 4972 4.034048 GTCTTGTTTGGTACACTGTCACTG 59.966 45.833 0.00 0.00 39.29 3.66
3830 4973 3.897141 TGTTTGGTACACTGTCACTGA 57.103 42.857 0.00 0.00 39.29 3.41
3831 4974 4.415881 TGTTTGGTACACTGTCACTGAT 57.584 40.909 0.00 0.00 39.29 2.90
3832 4975 4.776349 TGTTTGGTACACTGTCACTGATT 58.224 39.130 0.00 0.00 39.29 2.57
3833 4976 5.919755 TGTTTGGTACACTGTCACTGATTA 58.080 37.500 0.00 0.00 39.29 1.75
3834 4977 6.530120 TGTTTGGTACACTGTCACTGATTAT 58.470 36.000 0.00 0.00 39.29 1.28
3835 4978 6.995686 TGTTTGGTACACTGTCACTGATTATT 59.004 34.615 0.00 0.00 39.29 1.40
3836 4979 8.151596 TGTTTGGTACACTGTCACTGATTATTA 58.848 33.333 0.00 0.00 39.29 0.98
3837 4980 8.995220 GTTTGGTACACTGTCACTGATTATTAA 58.005 33.333 0.00 0.00 39.29 1.40
3838 4981 8.542497 TTGGTACACTGTCACTGATTATTAAC 57.458 34.615 0.00 0.00 39.29 2.01
3839 4982 7.903145 TGGTACACTGTCACTGATTATTAACT 58.097 34.615 0.00 0.00 0.00 2.24
3840 4983 9.027202 TGGTACACTGTCACTGATTATTAACTA 57.973 33.333 0.00 0.00 0.00 2.24
3841 4984 9.298774 GGTACACTGTCACTGATTATTAACTAC 57.701 37.037 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 3.188786 GAGGATGGTGTGCGACGC 61.189 66.667 14.19 14.19 0.00 5.19
84 85 0.881118 GCGGTGTGAACAACATGGAT 59.119 50.000 0.00 0.00 41.97 3.41
144 145 1.594836 GTGCGGGTCGTTGGTGTTA 60.595 57.895 0.00 0.00 0.00 2.41
151 152 4.695231 CTCGTCGTGCGGGTCGTT 62.695 66.667 0.00 0.00 41.72 3.85
268 279 0.539051 GTATGGCTGCTGTCAGGAGT 59.461 55.000 21.00 5.80 40.65 3.85
779 830 7.986889 GCATCATGGGGTGATAAATAACTTTTT 59.013 33.333 0.00 0.00 45.76 1.94
780 831 7.345392 AGCATCATGGGGTGATAAATAACTTTT 59.655 33.333 0.00 0.00 45.76 2.27
781 832 6.840705 AGCATCATGGGGTGATAAATAACTTT 59.159 34.615 0.00 0.00 45.76 2.66
782 833 6.376248 AGCATCATGGGGTGATAAATAACTT 58.624 36.000 0.00 0.00 45.76 2.66
783 834 5.957132 AGCATCATGGGGTGATAAATAACT 58.043 37.500 0.00 0.00 45.76 2.24
784 835 6.491403 AGAAGCATCATGGGGTGATAAATAAC 59.509 38.462 0.00 0.00 45.76 1.89
785 836 6.613699 AGAAGCATCATGGGGTGATAAATAA 58.386 36.000 0.00 0.00 45.76 1.40
786 837 6.204852 AGAAGCATCATGGGGTGATAAATA 57.795 37.500 0.00 0.00 45.76 1.40
787 838 5.070823 AGAAGCATCATGGGGTGATAAAT 57.929 39.130 0.00 0.00 45.76 1.40
788 839 4.524802 AGAAGCATCATGGGGTGATAAA 57.475 40.909 0.00 0.00 45.76 1.40
789 840 4.209538 CAAGAAGCATCATGGGGTGATAA 58.790 43.478 0.00 0.00 45.76 1.75
790 841 3.202818 ACAAGAAGCATCATGGGGTGATA 59.797 43.478 0.00 0.00 45.76 2.15
792 843 1.355381 ACAAGAAGCATCATGGGGTGA 59.645 47.619 0.00 0.00 42.06 4.02
793 844 1.843368 ACAAGAAGCATCATGGGGTG 58.157 50.000 0.00 0.00 0.00 4.61
794 845 3.435601 GGATACAAGAAGCATCATGGGGT 60.436 47.826 0.00 0.00 0.00 4.95
795 846 3.152341 GGATACAAGAAGCATCATGGGG 58.848 50.000 0.00 0.00 0.00 4.96
796 847 3.152341 GGGATACAAGAAGCATCATGGG 58.848 50.000 0.00 0.00 39.74 4.00
797 848 3.567164 GTGGGATACAAGAAGCATCATGG 59.433 47.826 0.00 0.00 39.74 3.66
798 849 4.201657 TGTGGGATACAAGAAGCATCATG 58.798 43.478 0.00 0.00 36.06 3.07
799 850 4.508551 TGTGGGATACAAGAAGCATCAT 57.491 40.909 0.00 0.00 36.06 2.45
800 851 3.998913 TGTGGGATACAAGAAGCATCA 57.001 42.857 0.00 0.00 36.06 3.07
801 852 5.468072 CAGTATGTGGGATACAAGAAGCATC 59.532 44.000 0.00 0.00 43.77 3.91
802 853 5.371526 CAGTATGTGGGATACAAGAAGCAT 58.628 41.667 0.00 0.00 43.77 3.79
803 854 4.769688 CAGTATGTGGGATACAAGAAGCA 58.230 43.478 0.00 0.00 43.77 3.91
819 870 7.991084 ATTCATCATCCAATACCACAGTATG 57.009 36.000 0.00 0.00 39.21 2.39
821 872 9.559732 CTTTATTCATCATCCAATACCACAGTA 57.440 33.333 0.00 0.00 0.00 2.74
822 873 8.055181 ACTTTATTCATCATCCAATACCACAGT 58.945 33.333 0.00 0.00 0.00 3.55
823 874 8.455903 ACTTTATTCATCATCCAATACCACAG 57.544 34.615 0.00 0.00 0.00 3.66
824 875 8.821686 AACTTTATTCATCATCCAATACCACA 57.178 30.769 0.00 0.00 0.00 4.17
877 928 1.358759 CACTCGCCGTTGCCTTTTT 59.641 52.632 0.00 0.00 0.00 1.94
878 929 3.030652 CACTCGCCGTTGCCTTTT 58.969 55.556 0.00 0.00 0.00 2.27
879 930 3.660111 GCACTCGCCGTTGCCTTT 61.660 61.111 2.63 0.00 0.00 3.11
902 953 3.712881 GTGTGGTCAAGGCGCGTC 61.713 66.667 0.21 0.21 0.00 5.19
903 954 4.539083 TGTGTGGTCAAGGCGCGT 62.539 61.111 8.43 0.00 0.00 6.01
904 955 3.716006 CTGTGTGGTCAAGGCGCG 61.716 66.667 0.00 0.00 0.00 6.86
905 956 2.280797 TCTGTGTGGTCAAGGCGC 60.281 61.111 0.00 0.00 0.00 6.53
906 957 0.668706 CTCTCTGTGTGGTCAAGGCG 60.669 60.000 0.00 0.00 0.00 5.52
907 958 0.952984 GCTCTCTGTGTGGTCAAGGC 60.953 60.000 0.00 0.00 0.00 4.35
908 959 0.394192 TGCTCTCTGTGTGGTCAAGG 59.606 55.000 0.00 0.00 0.00 3.61
909 960 1.793258 CTGCTCTCTGTGTGGTCAAG 58.207 55.000 0.00 0.00 0.00 3.02
910 961 0.250038 GCTGCTCTCTGTGTGGTCAA 60.250 55.000 0.00 0.00 0.00 3.18
911 962 1.368950 GCTGCTCTCTGTGTGGTCA 59.631 57.895 0.00 0.00 0.00 4.02
912 963 1.735920 CGCTGCTCTCTGTGTGGTC 60.736 63.158 0.00 0.00 0.00 4.02
946 997 1.744741 GGCCTTGTCTCTGCTCTGC 60.745 63.158 0.00 0.00 0.00 4.26
953 1004 4.021925 GTGCCCGGCCTTGTCTCT 62.022 66.667 7.03 0.00 0.00 3.10
1129 1200 4.323477 TGGTGGTAGTGGGTGCGC 62.323 66.667 0.00 0.00 0.00 6.09
1131 1202 2.033602 GGTGGTGGTAGTGGGTGC 59.966 66.667 0.00 0.00 0.00 5.01
1133 1204 0.838987 AATCGGTGGTGGTAGTGGGT 60.839 55.000 0.00 0.00 0.00 4.51
1135 1206 1.024579 GCAATCGGTGGTGGTAGTGG 61.025 60.000 0.00 0.00 0.00 4.00
1136 1207 0.321210 TGCAATCGGTGGTGGTAGTG 60.321 55.000 0.00 0.00 0.00 2.74
1137 1208 0.321298 GTGCAATCGGTGGTGGTAGT 60.321 55.000 0.00 0.00 0.00 2.73
1138 1209 1.358725 CGTGCAATCGGTGGTGGTAG 61.359 60.000 0.00 0.00 0.00 3.18
1140 1211 2.668212 CGTGCAATCGGTGGTGGT 60.668 61.111 0.00 0.00 0.00 4.16
1156 1244 3.339353 CTGTGATGTGACGTGCGCG 62.339 63.158 19.78 19.78 44.93 6.86
1163 1251 7.039313 TGATACATACTACCTGTGATGTGAC 57.961 40.000 0.00 0.00 34.46 3.67
1164 1252 7.839680 ATGATACATACTACCTGTGATGTGA 57.160 36.000 0.00 0.00 34.46 3.58
1185 1280 3.266513 TCACCTCCATCATCAACCAATGA 59.733 43.478 0.00 0.00 43.67 2.57
1187 1282 4.467769 GATCACCTCCATCATCAACCAAT 58.532 43.478 0.00 0.00 0.00 3.16
1188 1283 3.682436 CGATCACCTCCATCATCAACCAA 60.682 47.826 0.00 0.00 0.00 3.67
1189 1284 2.158914 CGATCACCTCCATCATCAACCA 60.159 50.000 0.00 0.00 0.00 3.67
1190 1285 2.103094 TCGATCACCTCCATCATCAACC 59.897 50.000 0.00 0.00 0.00 3.77
1213 1308 0.672711 GCCTTGTCGTCCCCTACAAC 60.673 60.000 0.00 0.00 32.43 3.32
1420 1519 9.137459 AGCATGTATAGTTAACTCATCAGTACT 57.863 33.333 12.39 5.99 30.14 2.73
1442 1562 2.426024 CAGGCTGCACAGAATTAAGCAT 59.574 45.455 0.00 0.00 36.28 3.79
1520 1640 2.935201 GCAAGAGCTTCGTTCATCTCAT 59.065 45.455 0.00 0.00 37.91 2.90
1521 1641 2.341257 GCAAGAGCTTCGTTCATCTCA 58.659 47.619 0.00 0.00 37.91 3.27
1522 1642 1.663135 GGCAAGAGCTTCGTTCATCTC 59.337 52.381 0.00 0.00 41.70 2.75
1572 1694 3.072330 TGTGAGAAATGCAGTCCCAGTAA 59.928 43.478 0.00 0.00 0.00 2.24
1604 1726 0.722848 AATTTACGCCGCGATTTCGT 59.277 45.000 21.79 13.96 42.22 3.85
1607 1729 0.027063 CGGAATTTACGCCGCGATTT 59.973 50.000 21.79 6.86 41.17 2.17
1640 1762 2.697229 TGATCTCTTCACCGCATGATCT 59.303 45.455 0.00 0.00 37.11 2.75
1680 1802 7.607991 AGAAAGTACAGAAATTCCATGACGATT 59.392 33.333 0.00 0.00 0.00 3.34
1737 1859 2.205022 TGTATTGCTTGCTCTGCCTT 57.795 45.000 0.00 0.00 0.00 4.35
1749 1871 4.031652 GTGACGATGCCAAAAATGTATTGC 59.968 41.667 0.00 0.00 0.00 3.56
1750 1872 4.262743 CGTGACGATGCCAAAAATGTATTG 59.737 41.667 0.00 0.00 0.00 1.90
1751 1873 4.155099 TCGTGACGATGCCAAAAATGTATT 59.845 37.500 2.39 0.00 0.00 1.89
1752 1874 3.687212 TCGTGACGATGCCAAAAATGTAT 59.313 39.130 2.39 0.00 0.00 2.29
1772 1894 2.306341 ATCTCTGTTGCTCATGGTCG 57.694 50.000 0.00 0.00 0.00 4.79
1793 1915 5.011329 AGTTGAAGGCATTCATTCATGTGTT 59.989 36.000 15.42 0.00 44.75 3.32
1795 1917 4.862574 CAGTTGAAGGCATTCATTCATGTG 59.137 41.667 15.42 3.02 44.75 3.21
1796 1918 4.768448 TCAGTTGAAGGCATTCATTCATGT 59.232 37.500 15.42 0.00 44.75 3.21
1797 1919 5.319140 TCAGTTGAAGGCATTCATTCATG 57.681 39.130 15.42 11.03 44.75 3.07
1847 1976 6.474751 GTCTAAAATCCATTGAAAGATGCTGC 59.525 38.462 0.00 0.00 0.00 5.25
1867 1996 5.017490 AGGAATCCTCAACTTCTCGTCTAA 58.983 41.667 0.00 0.00 0.00 2.10
1868 1997 4.399618 CAGGAATCCTCAACTTCTCGTCTA 59.600 45.833 0.00 0.00 0.00 2.59
1869 1998 3.194542 CAGGAATCCTCAACTTCTCGTCT 59.805 47.826 0.00 0.00 0.00 4.18
1909 2038 1.536766 ACAATGGATCAGTGTGCAACG 59.463 47.619 0.09 0.00 41.15 4.10
1926 2055 4.021544 AGTTCAGCAGGTTTGTTTCAACAA 60.022 37.500 0.79 0.79 46.35 2.83
2002 2132 5.308825 AGGAAACCTAGATTGTTGACAGTG 58.691 41.667 0.00 0.00 28.47 3.66
2100 2861 5.483685 ACTGACAACATGTACTATGTGGT 57.516 39.130 14.53 14.53 38.78 4.16
2108 2869 5.769367 TGTGAGTCTACTGACAACATGTAC 58.231 41.667 0.00 0.00 45.20 2.90
2182 3006 7.798516 CGCAAAATGTTGTATATGATAGTGGTC 59.201 37.037 0.00 0.00 37.06 4.02
2239 3064 3.270027 CACGTCAGCTGGATTAATTGGA 58.730 45.455 15.13 0.00 0.00 3.53
2335 3187 1.406069 GGTCTCGGATCACAAGTGCAT 60.406 52.381 0.00 0.00 0.00 3.96
2372 3234 1.599542 GCTGTCGAACTGAGCTGTTTT 59.400 47.619 0.00 0.00 0.00 2.43
2415 3277 2.690497 GTCGAATCATCAGGTCAGAGGA 59.310 50.000 0.00 0.00 32.39 3.71
2483 3353 6.506500 AATTTGCATTCTGAGTACTTCTGG 57.493 37.500 0.00 0.00 0.00 3.86
2511 3382 7.502895 TGGTAAGCTAAAATAGTGTCCAACAAA 59.497 33.333 0.00 0.00 0.00 2.83
2578 3449 1.154073 CCCGTTCGACTCTCGGTTC 60.154 63.158 13.62 0.00 42.30 3.62
2879 3970 4.979197 TGCAACGCTTTTGTAATTAACTGG 59.021 37.500 0.00 0.00 0.00 4.00
2887 3978 4.184629 ACCATTTTGCAACGCTTTTGTAA 58.815 34.783 0.00 0.00 0.00 2.41
2895 3986 1.059942 GCACTACCATTTTGCAACGC 58.940 50.000 0.00 0.00 36.22 4.84
3109 4221 5.731599 TTGTTTGTTCATGAATGCAAACC 57.268 34.783 31.40 21.68 45.71 3.27
3271 4386 6.403866 TCTGGTCTAACATTGTTGCAATTT 57.596 33.333 12.30 0.00 0.00 1.82
3291 4406 9.282247 GATGTTTATACTTTTGTGATGCTTCTG 57.718 33.333 0.88 0.00 0.00 3.02
3292 4407 9.013229 TGATGTTTATACTTTTGTGATGCTTCT 57.987 29.630 0.88 0.00 0.00 2.85
3314 4437 1.418373 TTCGTGCTCGTTGACTGATG 58.582 50.000 8.17 0.00 38.33 3.07
3321 4444 2.949714 AACTTGATTCGTGCTCGTTG 57.050 45.000 8.17 0.00 38.33 4.10
3543 4686 5.637387 GGCGTTTTGGATCAATTTGTACAAT 59.363 36.000 9.56 0.00 0.00 2.71
3551 4694 4.675146 CGAGATTGGCGTTTTGGATCAATT 60.675 41.667 0.00 0.00 0.00 2.32
3594 4737 0.038310 AGCTGGCAGAAGTAAACCCC 59.962 55.000 20.86 0.00 0.00 4.95
3637 4780 9.319143 GTAGTCAGTACTGATGAATGCTTATTT 57.681 33.333 27.54 1.59 42.18 1.40
3677 4820 7.649533 TCATGATGCTTTGGACTTGATTTAT 57.350 32.000 0.00 0.00 0.00 1.40
3707 4850 6.777580 ACCATAAAACATGGACAGAGTTCTTT 59.222 34.615 10.19 0.00 41.64 2.52
3747 4890 9.747898 TCTAGCCCAAGAAATTACAATTTTAGA 57.252 29.630 1.69 1.53 38.64 2.10
3780 4923 8.906867 CAACATCACCAAAATAGTTAGATGGAT 58.093 33.333 0.00 0.00 36.59 3.41
3781 4924 7.888021 ACAACATCACCAAAATAGTTAGATGGA 59.112 33.333 0.00 0.00 36.59 3.41
3782 4925 8.055279 ACAACATCACCAAAATAGTTAGATGG 57.945 34.615 0.00 2.72 36.59 3.51
3783 4926 8.950210 AGACAACATCACCAAAATAGTTAGATG 58.050 33.333 0.00 0.00 37.85 2.90
3784 4927 9.520515 AAGACAACATCACCAAAATAGTTAGAT 57.479 29.630 0.00 0.00 0.00 1.98
3785 4928 8.783093 CAAGACAACATCACCAAAATAGTTAGA 58.217 33.333 0.00 0.00 0.00 2.10
3786 4929 8.567948 ACAAGACAACATCACCAAAATAGTTAG 58.432 33.333 0.00 0.00 0.00 2.34
3787 4930 8.458573 ACAAGACAACATCACCAAAATAGTTA 57.541 30.769 0.00 0.00 0.00 2.24
3788 4931 7.346751 ACAAGACAACATCACCAAAATAGTT 57.653 32.000 0.00 0.00 0.00 2.24
3789 4932 6.959639 ACAAGACAACATCACCAAAATAGT 57.040 33.333 0.00 0.00 0.00 2.12
3790 4933 7.169645 CCAAACAAGACAACATCACCAAAATAG 59.830 37.037 0.00 0.00 0.00 1.73
3791 4934 6.983307 CCAAACAAGACAACATCACCAAAATA 59.017 34.615 0.00 0.00 0.00 1.40
3792 4935 5.816777 CCAAACAAGACAACATCACCAAAAT 59.183 36.000 0.00 0.00 0.00 1.82
3793 4936 5.174395 CCAAACAAGACAACATCACCAAAA 58.826 37.500 0.00 0.00 0.00 2.44
3794 4937 4.221703 ACCAAACAAGACAACATCACCAAA 59.778 37.500 0.00 0.00 0.00 3.28
3795 4938 3.766591 ACCAAACAAGACAACATCACCAA 59.233 39.130 0.00 0.00 0.00 3.67
3796 4939 3.360867 ACCAAACAAGACAACATCACCA 58.639 40.909 0.00 0.00 0.00 4.17
3797 4940 4.336993 TGTACCAAACAAGACAACATCACC 59.663 41.667 0.00 0.00 34.29 4.02
3798 4941 5.065988 AGTGTACCAAACAAGACAACATCAC 59.934 40.000 0.00 0.00 40.63 3.06
3799 4942 5.065859 CAGTGTACCAAACAAGACAACATCA 59.934 40.000 0.00 0.00 40.63 3.07
3800 4943 5.065988 ACAGTGTACCAAACAAGACAACATC 59.934 40.000 0.00 0.00 40.63 3.06
3801 4944 4.947388 ACAGTGTACCAAACAAGACAACAT 59.053 37.500 0.00 0.00 40.63 2.71
3802 4945 4.328536 ACAGTGTACCAAACAAGACAACA 58.671 39.130 0.00 0.00 40.63 3.33
3803 4946 4.393680 TGACAGTGTACCAAACAAGACAAC 59.606 41.667 0.00 0.00 40.63 3.32
3804 4947 4.393680 GTGACAGTGTACCAAACAAGACAA 59.606 41.667 0.00 0.00 40.63 3.18
3805 4948 3.936453 GTGACAGTGTACCAAACAAGACA 59.064 43.478 0.00 0.00 40.63 3.41
3806 4949 4.034048 CAGTGACAGTGTACCAAACAAGAC 59.966 45.833 0.00 0.00 40.63 3.01
3807 4950 4.081365 TCAGTGACAGTGTACCAAACAAGA 60.081 41.667 10.07 0.00 40.63 3.02
3808 4951 4.188462 TCAGTGACAGTGTACCAAACAAG 58.812 43.478 10.07 0.00 40.63 3.16
3809 4952 4.209307 TCAGTGACAGTGTACCAAACAA 57.791 40.909 10.07 0.00 40.63 2.83
3810 4953 3.897141 TCAGTGACAGTGTACCAAACA 57.103 42.857 10.07 0.00 35.06 2.83
3811 4954 7.435068 AATAATCAGTGACAGTGTACCAAAC 57.565 36.000 10.07 0.00 0.00 2.93
3812 4955 8.995220 GTTAATAATCAGTGACAGTGTACCAAA 58.005 33.333 10.07 0.00 0.00 3.28
3813 4956 8.372459 AGTTAATAATCAGTGACAGTGTACCAA 58.628 33.333 10.07 0.00 0.00 3.67
3814 4957 7.903145 AGTTAATAATCAGTGACAGTGTACCA 58.097 34.615 10.07 0.00 0.00 3.25
3815 4958 9.298774 GTAGTTAATAATCAGTGACAGTGTACC 57.701 37.037 10.07 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.