Multiple sequence alignment - TraesCS7A01G174200

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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 TraesCS7A01G174200 chr7A 100.000 2831 0 0 1 2831 128152932 128155762 0.000000e+00 5228.0
1 TraesCS7A01G174200 chr7A 95.116 778 29 4 947 1723 127907456 127906687 0.000000e+00 1218.0
2 TraesCS7A01G174200 chr7A 78.783 575 78 29 1071 1637 24928081 24928619 2.090000e-91 346.0
3 TraesCS7A01G174200 chr4A 92.824 864 55 7 38 898 446953893 446953034 0.000000e+00 1245.0
4 TraesCS7A01G174200 chr1A 93.445 839 48 7 1990 2825 479581068 479581902 0.000000e+00 1238.0
5 TraesCS7A01G174200 chr1A 86.434 774 54 19 1989 2760 550711837 550711113 0.000000e+00 800.0
6 TraesCS7A01G174200 chr1A 88.732 142 9 4 812 948 536617354 536617493 1.740000e-37 167.0
7 TraesCS7A01G174200 chr1A 85.294 102 13 2 1824 1924 590863524 590863624 1.390000e-18 104.0
8 TraesCS7A01G174200 chr1A 82.203 118 14 6 1824 1940 70915595 70915706 8.350000e-16 95.3
9 TraesCS7A01G174200 chr3A 93.246 844 49 3 1992 2831 582981336 582980497 0.000000e+00 1236.0
10 TraesCS7A01G174200 chr3A 87.908 736 54 17 1989 2718 590678327 590679033 0.000000e+00 833.0
11 TraesCS7A01G174200 chr3A 82.738 168 24 4 1820 1985 724148213 724148049 8.170000e-31 145.0
12 TraesCS7A01G174200 chr1D 91.510 907 61 6 6 898 362919467 362920371 0.000000e+00 1234.0
13 TraesCS7A01G174200 chr1D 90.753 876 53 18 30 898 335078317 335079171 0.000000e+00 1144.0
14 TraesCS7A01G174200 chr1D 85.859 99 11 3 1824 1921 390433320 390433416 4.990000e-18 102.0
15 TraesCS7A01G174200 chr6D 91.798 890 56 3 9 898 148078268 148077396 0.000000e+00 1223.0
16 TraesCS7A01G174200 chr6D 89.570 930 65 20 22 947 354544981 354544080 0.000000e+00 1151.0
17 TraesCS7A01G174200 chr6A 93.074 823 35 7 2010 2831 52906910 52906109 0.000000e+00 1184.0
18 TraesCS7A01G174200 chr6A 89.712 904 59 14 22 898 106477726 106476830 0.000000e+00 1123.0
19 TraesCS7A01G174200 chr6A 90.206 776 52 15 1989 2760 393954960 393954205 0.000000e+00 990.0
20 TraesCS7A01G174200 chr6A 84.884 172 23 3 1812 1982 677912 678081 1.350000e-38 171.0
21 TraesCS7A01G174200 chr6A 81.295 139 13 9 1823 1959 502959742 502959615 1.790000e-17 100.0
22 TraesCS7A01G174200 chr2A 92.575 835 36 5 1992 2825 654711905 654712714 0.000000e+00 1175.0
23 TraesCS7A01G174200 chr2A 91.726 846 64 4 59 898 775207544 775208389 0.000000e+00 1170.0
24 TraesCS7A01G174200 chr2A 91.138 835 56 8 78 898 734648621 734647791 0.000000e+00 1116.0
25 TraesCS7A01G174200 chr2A 85.697 846 91 26 1990 2820 654694579 654693749 0.000000e+00 865.0
26 TraesCS7A01G174200 chr2A 85.047 107 14 2 1814 1918 76371839 76371733 1.070000e-19 108.0
27 TraesCS7A01G174200 chr7D 89.005 955 72 20 22 949 487869260 487870208 0.000000e+00 1151.0
28 TraesCS7A01G174200 chr7D 89.326 890 53 14 953 1823 127420907 127421773 0.000000e+00 1079.0
29 TraesCS7A01G174200 chr7D 76.072 886 148 43 48 898 426174425 426175281 1.220000e-108 403.0
30 TraesCS7A01G174200 chr7D 83.591 323 50 1 1071 1390 24427822 24428144 1.650000e-77 300.0
31 TraesCS7A01G174200 chr7D 87.097 155 20 0 1483 1637 24428203 24428357 2.900000e-40 176.0
32 TraesCS7A01G174200 chr7D 82.738 168 23 5 1824 1987 521971575 521971410 8.170000e-31 145.0
33 TraesCS7A01G174200 chr3D 88.808 956 67 20 9 947 18748263 18749195 0.000000e+00 1136.0
34 TraesCS7A01G174200 chr7B 92.060 806 44 9 1028 1823 88880498 88879703 0.000000e+00 1116.0
35 TraesCS7A01G174200 chr7B 90.654 856 55 12 983 1823 89208643 89209488 0.000000e+00 1114.0
36 TraesCS7A01G174200 chr5A 86.420 810 82 21 1992 2785 580518750 580517953 0.000000e+00 861.0
37 TraesCS7A01G174200 chr5A 86.029 136 16 2 814 947 35643009 35642875 2.940000e-30 143.0
38 TraesCS7A01G174200 chr3B 80.114 875 109 35 51 898 777021998 777021162 2.430000e-165 592.0
39 TraesCS7A01G174200 chr3B 80.709 254 40 6 2575 2826 147711479 147711233 3.720000e-44 189.0
40 TraesCS7A01G174200 chr1B 84.672 137 17 3 812 947 536119134 536119267 1.770000e-27 134.0
41 TraesCS7A01G174200 chr6B 76.527 311 31 20 673 947 674563351 674563047 6.360000e-27 132.0
42 TraesCS7A01G174200 chr5B 82.258 124 15 6 1818 1940 590702929 590703046 1.790000e-17 100.0
43 TraesCS7A01G174200 chr5B 95.000 60 3 0 890 949 665716889 665716948 8.350000e-16 95.3
44 TraesCS7A01G174200 chr2B 80.315 127 24 1 2695 2821 24538882 24539007 8.350000e-16 95.3
45 TraesCS7A01G174200 chrUn 91.803 61 5 0 890 950 20485371 20485311 5.020000e-13 86.1


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 TraesCS7A01G174200 chr7A 128152932 128155762 2830 False 5228 5228 100.000 1 2831 1 chr7A.!!$F2 2830
1 TraesCS7A01G174200 chr7A 127906687 127907456 769 True 1218 1218 95.116 947 1723 1 chr7A.!!$R1 776
2 TraesCS7A01G174200 chr7A 24928081 24928619 538 False 346 346 78.783 1071 1637 1 chr7A.!!$F1 566
3 TraesCS7A01G174200 chr4A 446953034 446953893 859 True 1245 1245 92.824 38 898 1 chr4A.!!$R1 860
4 TraesCS7A01G174200 chr1A 479581068 479581902 834 False 1238 1238 93.445 1990 2825 1 chr1A.!!$F2 835
5 TraesCS7A01G174200 chr1A 550711113 550711837 724 True 800 800 86.434 1989 2760 1 chr1A.!!$R1 771
6 TraesCS7A01G174200 chr3A 582980497 582981336 839 True 1236 1236 93.246 1992 2831 1 chr3A.!!$R1 839
7 TraesCS7A01G174200 chr3A 590678327 590679033 706 False 833 833 87.908 1989 2718 1 chr3A.!!$F1 729
8 TraesCS7A01G174200 chr1D 362919467 362920371 904 False 1234 1234 91.510 6 898 1 chr1D.!!$F2 892
9 TraesCS7A01G174200 chr1D 335078317 335079171 854 False 1144 1144 90.753 30 898 1 chr1D.!!$F1 868
10 TraesCS7A01G174200 chr6D 148077396 148078268 872 True 1223 1223 91.798 9 898 1 chr6D.!!$R1 889
11 TraesCS7A01G174200 chr6D 354544080 354544981 901 True 1151 1151 89.570 22 947 1 chr6D.!!$R2 925
12 TraesCS7A01G174200 chr6A 52906109 52906910 801 True 1184 1184 93.074 2010 2831 1 chr6A.!!$R1 821
13 TraesCS7A01G174200 chr6A 106476830 106477726 896 True 1123 1123 89.712 22 898 1 chr6A.!!$R2 876
14 TraesCS7A01G174200 chr6A 393954205 393954960 755 True 990 990 90.206 1989 2760 1 chr6A.!!$R3 771
15 TraesCS7A01G174200 chr2A 654711905 654712714 809 False 1175 1175 92.575 1992 2825 1 chr2A.!!$F1 833
16 TraesCS7A01G174200 chr2A 775207544 775208389 845 False 1170 1170 91.726 59 898 1 chr2A.!!$F2 839
17 TraesCS7A01G174200 chr2A 734647791 734648621 830 True 1116 1116 91.138 78 898 1 chr2A.!!$R3 820
18 TraesCS7A01G174200 chr2A 654693749 654694579 830 True 865 865 85.697 1990 2820 1 chr2A.!!$R2 830
19 TraesCS7A01G174200 chr7D 487869260 487870208 948 False 1151 1151 89.005 22 949 1 chr7D.!!$F3 927
20 TraesCS7A01G174200 chr7D 127420907 127421773 866 False 1079 1079 89.326 953 1823 1 chr7D.!!$F1 870
21 TraesCS7A01G174200 chr7D 426174425 426175281 856 False 403 403 76.072 48 898 1 chr7D.!!$F2 850
22 TraesCS7A01G174200 chr7D 24427822 24428357 535 False 238 300 85.344 1071 1637 2 chr7D.!!$F4 566
23 TraesCS7A01G174200 chr3D 18748263 18749195 932 False 1136 1136 88.808 9 947 1 chr3D.!!$F1 938
24 TraesCS7A01G174200 chr7B 88879703 88880498 795 True 1116 1116 92.060 1028 1823 1 chr7B.!!$R1 795
25 TraesCS7A01G174200 chr7B 89208643 89209488 845 False 1114 1114 90.654 983 1823 1 chr7B.!!$F1 840
26 TraesCS7A01G174200 chr5A 580517953 580518750 797 True 861 861 86.420 1992 2785 1 chr5A.!!$R2 793
27 TraesCS7A01G174200 chr3B 777021162 777021998 836 True 592 592 80.114 51 898 1 chr3B.!!$R2 847

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
148 176 0.531532 GGTACTCCGTCGAGATCCGA 60.532 60.0 0.0 2.65 46.35 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2131 0.02577 AAAACGCACGACAACGACAG 59.974 50.0 0.0 0.0 42.66 3.51 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
148 176 0.531532 GGTACTCCGTCGAGATCCGA 60.532 60.000 0.00 2.65 46.35 4.55
259 287 1.206371 CCCCGGTCGTAGATGAACTTT 59.794 52.381 0.00 0.00 40.67 2.66
570 611 4.519540 TCTTCATGTCAGACGATGAACA 57.480 40.909 17.56 10.01 40.43 3.18
594 635 3.582647 TGGTTGGACATATGGCTCGATAT 59.417 43.478 8.85 0.00 0.00 1.63
626 670 1.886542 CCGACGAGGATGATGATGGTA 59.113 52.381 0.00 0.00 45.00 3.25
742 798 7.148457 CGAACTATCTATCTAGTTGCACCGATA 60.148 40.741 1.47 0.00 41.00 2.92
760 818 7.654520 GCACCGATATAAAGTACCTTTGTATCA 59.345 37.037 22.27 0.00 45.83 2.15
913 1091 1.867698 GCCGCAAAGCAGTTTTTAGCA 60.868 47.619 0.00 0.00 0.00 3.49
965 1143 4.825422 CTCTTACCATCTTGACTTCTGCA 58.175 43.478 0.00 0.00 0.00 4.41
986 1164 2.819608 ACATGCACCATACAAAGTCCAC 59.180 45.455 0.00 0.00 0.00 4.02
992 1170 3.003275 CACCATACAAAGTCCACACACAC 59.997 47.826 0.00 0.00 0.00 3.82
996 1174 3.281727 ACAAAGTCCACACACACATCT 57.718 42.857 0.00 0.00 0.00 2.90
1030 1212 1.074566 AGGAGGGGAGAGCAAGTTTTG 59.925 52.381 0.00 0.00 0.00 2.44
1034 1216 4.567747 GGAGGGGAGAGCAAGTTTTGATTA 60.568 45.833 0.00 0.00 0.00 1.75
1046 1228 4.526970 AGTTTTGATTATCCATGGCGACT 58.473 39.130 6.96 0.00 0.00 4.18
1048 1230 5.527582 AGTTTTGATTATCCATGGCGACTAC 59.472 40.000 6.96 0.00 0.00 2.73
1098 1280 0.824109 CCCGAAGCACTACATCCTGA 59.176 55.000 0.00 0.00 0.00 3.86
1242 1431 4.394729 GGTGTTGATCCTAAACTTCACCA 58.605 43.478 0.00 0.00 42.20 4.17
1247 1436 5.715439 TGATCCTAAACTTCACCATGGAT 57.285 39.130 21.47 0.00 35.78 3.41
1315 1504 4.690719 CCGGCTGCGGGTGTACAA 62.691 66.667 17.26 0.00 0.00 2.41
1690 1887 5.828328 TGTCGATATGTGAATCTCTGTAGGT 59.172 40.000 0.00 0.00 0.00 3.08
1705 1902 4.225942 TCTGTAGGTCTGCAGATCCATTTT 59.774 41.667 23.46 7.14 45.16 1.82
1725 1932 7.436673 CCATTTTGTTTCGACAGTCCAAATTTA 59.563 33.333 0.00 0.00 0.00 1.40
1735 1942 6.347725 CGACAGTCCAAATTTAAGTTCTCCAG 60.348 42.308 0.00 0.00 0.00 3.86
1796 2003 4.141274 TGTTCTTCTGGTTTCCTTCCATCA 60.141 41.667 0.00 0.00 34.26 3.07
1807 2014 6.830838 GGTTTCCTTCCATCAACAGAATAGAT 59.169 38.462 0.00 0.00 0.00 1.98
1830 2037 9.154847 AGATTGCATTAAAGAAAATAGGTTTGC 57.845 29.630 0.00 0.00 0.00 3.68
1831 2038 9.154847 GATTGCATTAAAGAAAATAGGTTTGCT 57.845 29.630 0.00 0.00 34.53 3.91
1841 2048 9.860898 AAGAAAATAGGTTTGCTATTTCACATC 57.139 29.630 0.00 0.00 36.37 3.06
1842 2049 9.247861 AGAAAATAGGTTTGCTATTTCACATCT 57.752 29.630 0.00 0.00 36.37 2.90
1845 2052 9.905713 AAATAGGTTTGCTATTTCACATCTAGA 57.094 29.630 0.00 0.00 33.26 2.43
1847 2054 7.798596 AGGTTTGCTATTTCACATCTAGATG 57.201 36.000 27.63 27.63 44.15 2.90
1892 2099 9.132923 TCTAAGTTCATAACCATTAGATCTCGT 57.867 33.333 0.00 0.00 28.84 4.18
1893 2100 9.400638 CTAAGTTCATAACCATTAGATCTCGTC 57.599 37.037 0.00 0.00 0.00 4.20
1894 2101 6.750148 AGTTCATAACCATTAGATCTCGTCC 58.250 40.000 0.00 0.00 0.00 4.79
1895 2102 6.551601 AGTTCATAACCATTAGATCTCGTCCT 59.448 38.462 0.00 0.00 0.00 3.85
1896 2103 7.724506 AGTTCATAACCATTAGATCTCGTCCTA 59.275 37.037 0.00 0.00 0.00 2.94
1897 2104 8.524487 GTTCATAACCATTAGATCTCGTCCTAT 58.476 37.037 0.00 0.00 0.00 2.57
1898 2105 8.282455 TCATAACCATTAGATCTCGTCCTATC 57.718 38.462 0.00 0.00 0.00 2.08
1899 2106 8.110271 TCATAACCATTAGATCTCGTCCTATCT 58.890 37.037 0.00 0.00 36.45 1.98
1900 2107 8.744652 CATAACCATTAGATCTCGTCCTATCTT 58.255 37.037 0.00 0.00 34.36 2.40
1901 2108 6.827586 ACCATTAGATCTCGTCCTATCTTC 57.172 41.667 0.00 0.00 34.36 2.87
1902 2109 6.307776 ACCATTAGATCTCGTCCTATCTTCA 58.692 40.000 0.00 0.00 34.36 3.02
1903 2110 6.778069 ACCATTAGATCTCGTCCTATCTTCAA 59.222 38.462 0.00 0.00 34.36 2.69
1904 2111 7.040062 ACCATTAGATCTCGTCCTATCTTCAAG 60.040 40.741 0.00 0.00 34.36 3.02
1905 2112 7.175816 CCATTAGATCTCGTCCTATCTTCAAGA 59.824 40.741 0.00 0.00 34.36 3.02
1906 2113 8.739039 CATTAGATCTCGTCCTATCTTCAAGAT 58.261 37.037 4.98 4.98 38.70 2.40
1907 2114 8.698973 TTAGATCTCGTCCTATCTTCAAGATT 57.301 34.615 4.90 0.00 36.20 2.40
1908 2115 7.214467 AGATCTCGTCCTATCTTCAAGATTC 57.786 40.000 4.90 0.00 36.20 2.52
1909 2116 6.775142 AGATCTCGTCCTATCTTCAAGATTCA 59.225 38.462 4.90 0.00 36.20 2.57
1910 2117 6.137794 TCTCGTCCTATCTTCAAGATTCAC 57.862 41.667 4.90 0.00 36.20 3.18
1911 2118 4.921547 TCGTCCTATCTTCAAGATTCACG 58.078 43.478 4.90 11.37 36.20 4.35
1912 2119 3.487574 CGTCCTATCTTCAAGATTCACGC 59.512 47.826 4.90 0.00 36.20 5.34
1913 2120 4.688021 GTCCTATCTTCAAGATTCACGCT 58.312 43.478 4.90 0.00 36.20 5.07
1914 2121 5.505819 CGTCCTATCTTCAAGATTCACGCTA 60.506 44.000 4.90 0.00 36.20 4.26
1915 2122 5.918011 GTCCTATCTTCAAGATTCACGCTAG 59.082 44.000 4.90 0.00 36.20 3.42
1916 2123 5.594725 TCCTATCTTCAAGATTCACGCTAGT 59.405 40.000 4.90 0.00 36.20 2.57
1917 2124 6.096987 TCCTATCTTCAAGATTCACGCTAGTT 59.903 38.462 4.90 0.00 36.20 2.24
1918 2125 7.284716 TCCTATCTTCAAGATTCACGCTAGTTA 59.715 37.037 4.90 0.00 36.20 2.24
1919 2126 8.085296 CCTATCTTCAAGATTCACGCTAGTTAT 58.915 37.037 4.90 0.00 36.20 1.89
1920 2127 9.469807 CTATCTTCAAGATTCACGCTAGTTATT 57.530 33.333 4.90 0.00 36.20 1.40
1921 2128 8.723942 ATCTTCAAGATTCACGCTAGTTATTT 57.276 30.769 0.00 0.00 28.69 1.40
1922 2129 8.547967 TCTTCAAGATTCACGCTAGTTATTTT 57.452 30.769 0.00 0.00 0.00 1.82
1923 2130 8.999431 TCTTCAAGATTCACGCTAGTTATTTTT 58.001 29.630 0.00 0.00 0.00 1.94
1924 2131 9.267096 CTTCAAGATTCACGCTAGTTATTTTTC 57.733 33.333 0.00 0.00 0.00 2.29
1925 2132 8.547967 TCAAGATTCACGCTAGTTATTTTTCT 57.452 30.769 0.00 0.00 0.00 2.52
1926 2133 8.443160 TCAAGATTCACGCTAGTTATTTTTCTG 58.557 33.333 0.00 0.00 0.00 3.02
1927 2134 7.907214 AGATTCACGCTAGTTATTTTTCTGT 57.093 32.000 0.00 0.00 0.00 3.41
1928 2135 7.965045 AGATTCACGCTAGTTATTTTTCTGTC 58.035 34.615 0.00 0.00 0.00 3.51
1929 2136 5.756950 TCACGCTAGTTATTTTTCTGTCG 57.243 39.130 0.00 0.00 0.00 4.35
1930 2137 5.224888 TCACGCTAGTTATTTTTCTGTCGT 58.775 37.500 0.00 0.00 0.00 4.34
1931 2138 5.693104 TCACGCTAGTTATTTTTCTGTCGTT 59.307 36.000 0.00 0.00 0.00 3.85
1932 2139 5.783654 CACGCTAGTTATTTTTCTGTCGTTG 59.216 40.000 0.00 0.00 0.00 4.10
1933 2140 5.464389 ACGCTAGTTATTTTTCTGTCGTTGT 59.536 36.000 0.00 0.00 0.00 3.32
1934 2141 6.007677 CGCTAGTTATTTTTCTGTCGTTGTC 58.992 40.000 0.00 0.00 0.00 3.18
1935 2142 6.007677 GCTAGTTATTTTTCTGTCGTTGTCG 58.992 40.000 0.00 0.00 38.55 4.35
1936 2143 5.978934 AGTTATTTTTCTGTCGTTGTCGT 57.021 34.783 0.00 0.00 38.33 4.34
1937 2144 5.734311 AGTTATTTTTCTGTCGTTGTCGTG 58.266 37.500 0.00 0.00 38.33 4.35
1938 2145 2.445453 TTTTTCTGTCGTTGTCGTGC 57.555 45.000 0.00 0.00 38.33 5.34
1939 2146 0.299300 TTTTCTGTCGTTGTCGTGCG 59.701 50.000 0.00 0.00 38.33 5.34
1940 2147 0.802994 TTTCTGTCGTTGTCGTGCGT 60.803 50.000 0.00 0.00 38.33 5.24
1941 2148 0.802994 TTCTGTCGTTGTCGTGCGTT 60.803 50.000 0.00 0.00 38.33 4.84
1942 2149 0.802994 TCTGTCGTTGTCGTGCGTTT 60.803 50.000 0.00 0.00 38.33 3.60
1943 2150 0.025770 CTGTCGTTGTCGTGCGTTTT 59.974 50.000 0.00 0.00 38.33 2.43
1944 2151 0.443088 TGTCGTTGTCGTGCGTTTTT 59.557 45.000 0.00 0.00 38.33 1.94
1945 2152 0.828959 GTCGTTGTCGTGCGTTTTTG 59.171 50.000 0.00 0.00 38.33 2.44
1946 2153 0.858135 TCGTTGTCGTGCGTTTTTGC 60.858 50.000 0.00 0.00 38.33 3.68
1947 2154 0.859788 CGTTGTCGTGCGTTTTTGCT 60.860 50.000 0.00 0.00 35.36 3.91
1948 2155 0.837605 GTTGTCGTGCGTTTTTGCTC 59.162 50.000 0.00 0.00 35.36 4.26
1954 2161 2.795389 GCGTTTTTGCTCGCGTCC 60.795 61.111 5.77 0.00 42.79 4.79
1955 2162 2.935955 CGTTTTTGCTCGCGTCCT 59.064 55.556 5.77 0.00 0.00 3.85
1956 2163 1.154654 CGTTTTTGCTCGCGTCCTC 60.155 57.895 5.77 0.00 0.00 3.71
1957 2164 1.154654 GTTTTTGCTCGCGTCCTCG 60.155 57.895 5.77 0.00 40.37 4.63
1958 2165 1.593209 TTTTTGCTCGCGTCCTCGT 60.593 52.632 5.77 0.00 39.49 4.18
1959 2166 1.554042 TTTTTGCTCGCGTCCTCGTC 61.554 55.000 5.77 0.00 39.49 4.20
1960 2167 4.753877 TTGCTCGCGTCCTCGTCG 62.754 66.667 5.77 0.00 39.49 5.12
1962 2169 4.755614 GCTCGCGTCCTCGTCGTT 62.756 66.667 5.77 0.00 39.49 3.85
1963 2170 2.573689 CTCGCGTCCTCGTCGTTC 60.574 66.667 5.77 0.00 39.49 3.95
1964 2171 4.434938 TCGCGTCCTCGTCGTTCG 62.435 66.667 5.77 0.00 39.49 3.95
1965 2172 4.731503 CGCGTCCTCGTCGTTCGT 62.732 66.667 0.00 0.00 40.80 3.85
1966 2173 2.868787 GCGTCCTCGTCGTTCGTC 60.869 66.667 0.00 0.00 40.80 4.20
1967 2174 2.858868 CGTCCTCGTCGTTCGTCT 59.141 61.111 0.00 0.00 40.80 4.18
1968 2175 1.509370 CGTCCTCGTCGTTCGTCTG 60.509 63.158 0.00 0.00 40.80 3.51
1969 2176 1.573436 GTCCTCGTCGTTCGTCTGT 59.427 57.895 0.00 0.00 40.80 3.41
1970 2177 0.725118 GTCCTCGTCGTTCGTCTGTG 60.725 60.000 0.00 0.00 40.80 3.66
1971 2178 2.081212 CCTCGTCGTTCGTCTGTGC 61.081 63.158 0.00 0.00 40.80 4.57
1972 2179 2.418333 CTCGTCGTTCGTCTGTGCG 61.418 63.158 0.00 0.00 40.80 5.34
1973 2180 4.104633 CGTCGTTCGTCTGTGCGC 62.105 66.667 0.00 0.00 34.52 6.09
1974 2181 4.104633 GTCGTTCGTCTGTGCGCG 62.105 66.667 0.00 0.00 0.00 6.86
2015 2222 0.531974 CCTATTCGGCGCCTTAAGCA 60.532 55.000 26.68 9.66 44.04 3.91
2050 2260 1.683943 TCTACTAACGGGCGCATACT 58.316 50.000 10.83 0.00 0.00 2.12
2187 2401 2.674380 CCACCAGGGCAGTTCAGC 60.674 66.667 0.00 0.00 0.00 4.26
2196 2410 2.959357 GCAGTTCAGCTGGCGTGAC 61.959 63.158 15.13 5.53 45.14 3.67
2378 2594 9.717942 AATCGGATGAACCATTTAAAAATTTGA 57.282 25.926 0.00 0.00 38.90 2.69
2379 2595 9.889128 ATCGGATGAACCATTTAAAAATTTGAT 57.111 25.926 0.00 0.00 38.90 2.57
2380 2596 9.149225 TCGGATGAACCATTTAAAAATTTGATG 57.851 29.630 0.00 0.00 38.90 3.07
2381 2597 9.149225 CGGATGAACCATTTAAAAATTTGATGA 57.851 29.630 0.00 0.00 38.90 2.92
2383 2599 9.977762 GATGAACCATTTAAAAATTTGATGAGC 57.022 29.630 0.00 0.00 0.00 4.26
2384 2600 9.729281 ATGAACCATTTAAAAATTTGATGAGCT 57.271 25.926 0.00 0.00 0.00 4.09
2385 2601 9.558396 TGAACCATTTAAAAATTTGATGAGCTT 57.442 25.926 0.00 0.00 0.00 3.74
2405 2641 8.177663 TGAGCTTTTATCAAATTCGATGAACTC 58.822 33.333 0.00 0.00 0.00 3.01
2548 2827 7.504924 ACTTTTGTCAAATCCGATGAACTTA 57.495 32.000 0.00 0.00 0.00 2.24
2804 3168 8.708075 TTTGAATTCGTTGAACTATTTTCGAG 57.292 30.769 0.04 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.423154 GCCGAGGTTGTGAAGCGG 61.423 66.667 0.00 0.00 44.47 5.52
1 2 3.777925 CGCCGAGGTTGTGAAGCG 61.778 66.667 0.00 0.00 37.39 4.68
2 3 4.090057 GCGCCGAGGTTGTGAAGC 62.090 66.667 0.00 0.00 0.00 3.86
3 4 1.901650 GAAGCGCCGAGGTTGTGAAG 61.902 60.000 2.29 0.00 41.18 3.02
4 5 1.959226 GAAGCGCCGAGGTTGTGAA 60.959 57.895 2.29 0.00 41.18 3.18
76 94 4.699522 GAAGAACCCTGGCGGCGT 62.700 66.667 9.37 0.00 33.26 5.68
218 246 4.980805 GTCCAAGCACCACGCCGA 62.981 66.667 0.00 0.00 44.04 5.54
570 611 2.172505 TCGAGCCATATGTCCAACCAAT 59.827 45.455 1.24 0.00 0.00 3.16
626 670 4.679373 ACTCCAAGTCGCTATCATCATT 57.321 40.909 0.00 0.00 0.00 2.57
666 710 7.201679 GGTGCAACTAGATAGAAACTACTACGA 60.202 40.741 0.00 0.00 36.74 3.43
711 767 7.916450 GTGCAACTAGATAGATAGTTCGAAAGT 59.084 37.037 0.00 0.00 42.68 2.66
849 977 2.098298 CTAAAATGCAGCGCGCGT 59.902 55.556 32.35 15.53 46.97 6.01
850 978 3.307262 GCTAAAATGCAGCGCGCG 61.307 61.111 28.44 28.44 46.97 6.86
892 1044 1.867698 GCTAAAAACTGCTTTGCGGCA 60.868 47.619 0.00 0.00 38.71 5.69
965 1143 2.819608 GTGGACTTTGTATGGTGCATGT 59.180 45.455 0.00 0.00 36.31 3.21
986 1164 3.862267 GCTAGAAGCTGTAGATGTGTGTG 59.138 47.826 7.43 0.00 38.45 3.82
1030 1212 3.006967 AGTGGTAGTCGCCATGGATAATC 59.993 47.826 18.40 0.00 41.08 1.75
1034 1216 0.465705 CAGTGGTAGTCGCCATGGAT 59.534 55.000 18.40 0.00 41.08 3.41
1046 1228 0.976641 CAGTGAGCTTCCCAGTGGTA 59.023 55.000 8.74 0.00 32.75 3.25
1048 1230 0.617413 ATCAGTGAGCTTCCCAGTGG 59.383 55.000 0.63 0.63 36.05 4.00
1170 1352 1.134901 CGGTCACGGAGAAGACGAG 59.865 63.158 0.00 0.00 37.08 4.18
1242 1431 2.440796 CGGGTTGGCAGCATCCAT 60.441 61.111 3.14 0.00 35.77 3.41
1340 1529 4.293648 TGGACCACCGTCTGCACG 62.294 66.667 0.00 0.00 46.29 5.34
1398 1587 3.123620 GCACGGAAGCTGCTCCAG 61.124 66.667 1.00 0.00 34.91 3.86
1690 1887 4.071423 TCGAAACAAAATGGATCTGCAGA 58.929 39.130 20.79 20.79 0.00 4.26
1705 1902 6.687081 ACTTAAATTTGGACTGTCGAAACA 57.313 33.333 18.17 6.16 27.18 2.83
1725 1932 3.395941 AGAACCATTCACCTGGAGAACTT 59.604 43.478 8.77 1.55 39.73 2.66
1735 1942 1.615392 AGCAAAGCAGAACCATTCACC 59.385 47.619 0.00 0.00 0.00 4.02
1823 2030 7.798596 CATCTAGATGTGAAATAGCAAACCT 57.201 36.000 22.42 0.00 34.23 3.50
1866 2073 9.132923 ACGAGATCTAATGGTTATGAACTTAGA 57.867 33.333 0.00 4.49 34.61 2.10
1867 2074 9.400638 GACGAGATCTAATGGTTATGAACTTAG 57.599 37.037 0.00 0.00 0.00 2.18
1868 2075 8.358148 GGACGAGATCTAATGGTTATGAACTTA 58.642 37.037 0.00 0.00 0.00 2.24
1869 2076 7.070074 AGGACGAGATCTAATGGTTATGAACTT 59.930 37.037 0.00 0.00 0.00 2.66
1870 2077 6.551601 AGGACGAGATCTAATGGTTATGAACT 59.448 38.462 0.00 0.00 0.00 3.01
1871 2078 6.750148 AGGACGAGATCTAATGGTTATGAAC 58.250 40.000 0.00 0.00 0.00 3.18
1872 2079 6.978674 AGGACGAGATCTAATGGTTATGAA 57.021 37.500 0.00 0.00 0.00 2.57
1873 2080 8.110271 AGATAGGACGAGATCTAATGGTTATGA 58.890 37.037 0.00 0.00 30.47 2.15
1874 2081 8.287439 AGATAGGACGAGATCTAATGGTTATG 57.713 38.462 0.00 0.00 30.47 1.90
1875 2082 8.887264 AAGATAGGACGAGATCTAATGGTTAT 57.113 34.615 0.00 0.00 32.03 1.89
1876 2083 7.942894 TGAAGATAGGACGAGATCTAATGGTTA 59.057 37.037 0.00 0.00 32.03 2.85
1877 2084 6.778069 TGAAGATAGGACGAGATCTAATGGTT 59.222 38.462 0.00 0.00 32.03 3.67
1878 2085 6.307776 TGAAGATAGGACGAGATCTAATGGT 58.692 40.000 0.00 0.00 32.03 3.55
1879 2086 6.825944 TGAAGATAGGACGAGATCTAATGG 57.174 41.667 0.00 0.00 32.03 3.16
1880 2087 8.105097 TCTTGAAGATAGGACGAGATCTAATG 57.895 38.462 0.00 0.00 32.03 1.90
1881 2088 8.877864 ATCTTGAAGATAGGACGAGATCTAAT 57.122 34.615 5.78 0.00 32.12 1.73
1882 2089 8.698973 AATCTTGAAGATAGGACGAGATCTAA 57.301 34.615 8.30 0.00 32.89 2.10
1883 2090 7.939588 TGAATCTTGAAGATAGGACGAGATCTA 59.060 37.037 8.30 0.00 32.89 1.98
1884 2091 6.775142 TGAATCTTGAAGATAGGACGAGATCT 59.225 38.462 8.30 0.00 32.89 2.75
1885 2092 6.861055 GTGAATCTTGAAGATAGGACGAGATC 59.139 42.308 8.30 0.00 32.89 2.75
1886 2093 6.514212 CGTGAATCTTGAAGATAGGACGAGAT 60.514 42.308 20.11 0.00 34.94 2.75
1887 2094 5.220873 CGTGAATCTTGAAGATAGGACGAGA 60.221 44.000 20.11 0.00 34.94 4.04
1888 2095 4.973051 CGTGAATCTTGAAGATAGGACGAG 59.027 45.833 20.11 3.76 34.94 4.18
1889 2096 4.733815 GCGTGAATCTTGAAGATAGGACGA 60.734 45.833 25.12 2.32 34.94 4.20
1890 2097 3.487574 GCGTGAATCTTGAAGATAGGACG 59.512 47.826 20.30 20.30 32.89 4.79
1891 2098 4.688021 AGCGTGAATCTTGAAGATAGGAC 58.312 43.478 8.30 4.85 32.89 3.85
1892 2099 5.594725 ACTAGCGTGAATCTTGAAGATAGGA 59.405 40.000 8.30 0.00 32.89 2.94
1893 2100 5.837437 ACTAGCGTGAATCTTGAAGATAGG 58.163 41.667 8.30 0.97 32.89 2.57
1894 2101 9.469807 AATAACTAGCGTGAATCTTGAAGATAG 57.530 33.333 8.30 2.93 32.89 2.08
1895 2102 9.817809 AAATAACTAGCGTGAATCTTGAAGATA 57.182 29.630 8.30 0.00 32.89 1.98
1896 2103 8.723942 AAATAACTAGCGTGAATCTTGAAGAT 57.276 30.769 0.97 0.97 36.28 2.40
1897 2104 8.547967 AAAATAACTAGCGTGAATCTTGAAGA 57.452 30.769 0.00 0.00 0.00 2.87
1898 2105 9.267096 GAAAAATAACTAGCGTGAATCTTGAAG 57.733 33.333 0.00 0.00 0.00 3.02
1899 2106 8.999431 AGAAAAATAACTAGCGTGAATCTTGAA 58.001 29.630 0.00 0.00 0.00 2.69
1900 2107 8.443160 CAGAAAAATAACTAGCGTGAATCTTGA 58.557 33.333 0.00 0.00 0.00 3.02
1901 2108 8.230486 ACAGAAAAATAACTAGCGTGAATCTTG 58.770 33.333 0.00 0.00 0.00 3.02
1902 2109 8.324163 ACAGAAAAATAACTAGCGTGAATCTT 57.676 30.769 0.00 0.00 0.00 2.40
1903 2110 7.201444 CGACAGAAAAATAACTAGCGTGAATCT 60.201 37.037 0.00 0.00 0.00 2.40
1904 2111 6.895040 CGACAGAAAAATAACTAGCGTGAATC 59.105 38.462 0.00 0.00 0.00 2.52
1905 2112 6.367969 ACGACAGAAAAATAACTAGCGTGAAT 59.632 34.615 0.00 0.00 0.00 2.57
1906 2113 5.693104 ACGACAGAAAAATAACTAGCGTGAA 59.307 36.000 0.00 0.00 0.00 3.18
1907 2114 5.224888 ACGACAGAAAAATAACTAGCGTGA 58.775 37.500 0.00 0.00 0.00 4.35
1908 2115 5.511088 ACGACAGAAAAATAACTAGCGTG 57.489 39.130 0.00 0.00 0.00 5.34
1909 2116 5.464389 ACAACGACAGAAAAATAACTAGCGT 59.536 36.000 0.00 0.00 0.00 5.07
1910 2117 5.912528 ACAACGACAGAAAAATAACTAGCG 58.087 37.500 0.00 0.00 0.00 4.26
1911 2118 6.007677 CGACAACGACAGAAAAATAACTAGC 58.992 40.000 0.00 0.00 42.66 3.42
1912 2119 7.001922 CACGACAACGACAGAAAAATAACTAG 58.998 38.462 0.00 0.00 42.66 2.57
1913 2120 6.562640 GCACGACAACGACAGAAAAATAACTA 60.563 38.462 0.00 0.00 42.66 2.24
1914 2121 5.734311 CACGACAACGACAGAAAAATAACT 58.266 37.500 0.00 0.00 42.66 2.24
1915 2122 4.374828 GCACGACAACGACAGAAAAATAAC 59.625 41.667 0.00 0.00 42.66 1.89
1916 2123 4.520078 GCACGACAACGACAGAAAAATAA 58.480 39.130 0.00 0.00 42.66 1.40
1917 2124 3.362207 CGCACGACAACGACAGAAAAATA 60.362 43.478 0.00 0.00 42.66 1.40
1918 2125 2.598907 CGCACGACAACGACAGAAAAAT 60.599 45.455 0.00 0.00 42.66 1.82
1919 2126 1.267136 CGCACGACAACGACAGAAAAA 60.267 47.619 0.00 0.00 42.66 1.94
1920 2127 0.299300 CGCACGACAACGACAGAAAA 59.701 50.000 0.00 0.00 42.66 2.29
1921 2128 0.802994 ACGCACGACAACGACAGAAA 60.803 50.000 0.00 0.00 42.66 2.52
1922 2129 0.802994 AACGCACGACAACGACAGAA 60.803 50.000 0.00 0.00 42.66 3.02
1923 2130 0.802994 AAACGCACGACAACGACAGA 60.803 50.000 0.00 0.00 42.66 3.41
1924 2131 0.025770 AAAACGCACGACAACGACAG 59.974 50.000 0.00 0.00 42.66 3.51
1925 2132 0.443088 AAAAACGCACGACAACGACA 59.557 45.000 0.00 0.00 42.66 4.35
1926 2133 0.828959 CAAAAACGCACGACAACGAC 59.171 50.000 0.00 0.00 42.66 4.34
1927 2134 0.858135 GCAAAAACGCACGACAACGA 60.858 50.000 0.00 0.00 42.66 3.85
1928 2135 0.859788 AGCAAAAACGCACGACAACG 60.860 50.000 0.00 0.00 45.75 4.10
1929 2136 0.837605 GAGCAAAAACGCACGACAAC 59.162 50.000 0.00 0.00 0.00 3.32
1930 2137 0.587737 CGAGCAAAAACGCACGACAA 60.588 50.000 0.00 0.00 46.94 3.18
1931 2138 1.011684 CGAGCAAAAACGCACGACA 60.012 52.632 0.00 0.00 46.94 4.35
1932 2139 3.796709 CGAGCAAAAACGCACGAC 58.203 55.556 0.00 0.00 46.94 4.34
1938 2145 1.154654 GAGGACGCGAGCAAAAACG 60.155 57.895 15.93 0.00 0.00 3.60
1939 2146 1.154654 CGAGGACGCGAGCAAAAAC 60.155 57.895 15.93 0.00 0.00 2.43
1940 2147 1.554042 GACGAGGACGCGAGCAAAAA 61.554 55.000 15.93 0.00 43.96 1.94
1941 2148 2.019951 GACGAGGACGCGAGCAAAA 61.020 57.895 15.93 0.00 43.96 2.44
1942 2149 2.430244 GACGAGGACGCGAGCAAA 60.430 61.111 15.93 0.00 43.96 3.68
1943 2150 4.753877 CGACGAGGACGCGAGCAA 62.754 66.667 15.93 0.00 43.96 3.91
1945 2152 4.755614 AACGACGAGGACGCGAGC 62.756 66.667 15.93 3.71 43.96 5.03
1946 2153 2.573689 GAACGACGAGGACGCGAG 60.574 66.667 15.93 0.45 43.96 5.03
1947 2154 4.434938 CGAACGACGAGGACGCGA 62.435 66.667 15.93 0.00 45.77 5.87
1948 2155 4.731503 ACGAACGACGAGGACGCG 62.732 66.667 3.53 3.53 45.77 6.01
1949 2156 2.868787 GACGAACGACGAGGACGC 60.869 66.667 0.00 0.00 45.77 5.19
1950 2157 1.509370 CAGACGAACGACGAGGACG 60.509 63.158 0.00 4.12 45.77 4.79
1951 2158 0.725118 CACAGACGAACGACGAGGAC 60.725 60.000 0.00 0.00 45.77 3.85
1952 2159 1.572941 CACAGACGAACGACGAGGA 59.427 57.895 0.00 0.00 45.77 3.71
1953 2160 2.081212 GCACAGACGAACGACGAGG 61.081 63.158 0.00 0.00 45.77 4.63
1954 2161 2.418333 CGCACAGACGAACGACGAG 61.418 63.158 0.00 0.00 45.77 4.18
1955 2162 2.426261 CGCACAGACGAACGACGA 60.426 61.111 0.00 0.00 45.77 4.20
1957 2164 4.104633 CGCGCACAGACGAACGAC 62.105 66.667 8.75 0.00 34.06 4.34
1978 2185 1.376037 GAACCAGCCTCGAGTTGGG 60.376 63.158 27.29 19.83 36.28 4.12
1979 2186 1.376037 GGAACCAGCCTCGAGTTGG 60.376 63.158 24.12 24.12 37.98 3.77
1980 2187 0.895530 TAGGAACCAGCCTCGAGTTG 59.104 55.000 12.31 9.29 39.50 3.16
1981 2188 1.867363 ATAGGAACCAGCCTCGAGTT 58.133 50.000 12.31 0.00 39.50 3.01
1982 2189 1.757699 GAATAGGAACCAGCCTCGAGT 59.242 52.381 12.31 0.00 39.50 4.18
1983 2190 1.269309 CGAATAGGAACCAGCCTCGAG 60.269 57.143 5.13 5.13 39.50 4.04
1984 2191 0.744874 CGAATAGGAACCAGCCTCGA 59.255 55.000 0.00 0.00 39.50 4.04
1985 2192 0.249489 CCGAATAGGAACCAGCCTCG 60.249 60.000 0.00 0.00 45.00 4.63
1986 2193 0.533085 GCCGAATAGGAACCAGCCTC 60.533 60.000 0.00 0.00 45.00 4.70
1987 2194 1.527370 GCCGAATAGGAACCAGCCT 59.473 57.895 0.00 0.00 45.00 4.58
2015 2222 2.631545 AGTAGAAACAACTGTAGCGGGT 59.368 45.455 0.00 0.00 0.00 5.28
2050 2260 1.773635 CCCAATGTGACAAGGGGGA 59.226 57.895 16.22 0.00 37.80 4.81
2091 2305 8.865001 CGGAGTTTTTGATGTTTAGAAAACAAA 58.135 29.630 9.08 0.00 41.83 2.83
2092 2306 7.009723 GCGGAGTTTTTGATGTTTAGAAAACAA 59.990 33.333 9.08 0.00 41.83 2.83
2106 2320 0.033504 AGCTCTCGCGGAGTTTTTGA 59.966 50.000 20.69 2.48 43.62 2.69
2140 2354 2.263540 GCTCGGAACTTGCCCGTA 59.736 61.111 0.00 0.00 46.53 4.02
2196 2410 7.652507 AGAAGAAGAAAGAAAACCTGTACGTAG 59.347 37.037 0.00 0.00 0.00 3.51
2376 2592 8.212317 TCATCGAATTTGATAAAAGCTCATCA 57.788 30.769 7.90 0.00 0.00 3.07
2377 2593 8.951969 GTTCATCGAATTTGATAAAAGCTCATC 58.048 33.333 7.90 0.00 0.00 2.92
2378 2594 8.680903 AGTTCATCGAATTTGATAAAAGCTCAT 58.319 29.630 7.90 0.00 0.00 2.90
2379 2595 8.044060 AGTTCATCGAATTTGATAAAAGCTCA 57.956 30.769 7.90 0.00 0.00 4.26
2380 2596 8.177663 TGAGTTCATCGAATTTGATAAAAGCTC 58.822 33.333 7.90 12.52 0.00 4.09
2381 2597 8.044060 TGAGTTCATCGAATTTGATAAAAGCT 57.956 30.769 7.90 4.80 0.00 3.74
2382 2598 8.847444 ATGAGTTCATCGAATTTGATAAAAGC 57.153 30.769 7.90 0.40 28.78 3.51
2388 2604 9.695526 TTTCAAAATGAGTTCATCGAATTTGAT 57.304 25.926 15.17 2.01 38.28 2.57
2389 2605 9.695526 ATTTCAAAATGAGTTCATCGAATTTGA 57.304 25.926 12.33 12.33 37.47 2.69
2393 2609 8.928733 CCAAATTTCAAAATGAGTTCATCGAAT 58.071 29.630 0.00 0.00 35.10 3.34
2394 2610 7.925483 ACCAAATTTCAAAATGAGTTCATCGAA 59.075 29.630 0.00 0.00 35.10 3.71
2395 2611 7.381948 CACCAAATTTCAAAATGAGTTCATCGA 59.618 33.333 0.00 0.00 35.10 3.59
2476 2754 6.402118 CGCCGAATTAGAAAAAGATTCACTGA 60.402 38.462 0.00 0.00 31.69 3.41
2484 2762 4.320870 AGGTTCGCCGAATTAGAAAAAGA 58.679 39.130 1.55 0.00 43.66 2.52
2485 2763 4.680171 AGGTTCGCCGAATTAGAAAAAG 57.320 40.909 1.55 0.00 43.66 2.27
2530 2808 8.964420 TTGAAAATAAGTTCATCGGATTTGAC 57.036 30.769 0.00 0.00 37.36 3.18
2548 2827 9.717942 TTTAAATGGTTCATCCGATTTGAAAAT 57.282 25.926 0.00 0.00 39.52 1.82
2726 3089 9.489393 TCATCGATTTTCAATAAAAGTTCATCG 57.511 29.630 0.00 0.00 37.97 3.84
2804 3168 7.410485 AGAGTTTGAGAAAAAGTTCATCGAAC 58.590 34.615 0.00 0.00 42.25 3.95


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

AutoCloner maintained by Alex Coulton.