Multiple sequence alignment - TraesCS3A01G036700

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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 TraesCS3A01G036700 chr3A 100.000 1848 0 0 936 2783 20029326 20027479 0.000000e+00 3413.0
1 TraesCS3A01G036700 chr3A 97.025 773 8 7 2026 2783 625234489 625233717 0.000000e+00 1286.0
2 TraesCS3A01G036700 chr3A 100.000 424 0 0 1 424 20030261 20029838 0.000000e+00 784.0
3 TraesCS3A01G036700 chr3A 84.429 578 66 15 2024 2587 22392299 22392866 5.240000e-152 547.0
4 TraesCS3A01G036700 chr1B 97.809 776 2 7 2023 2783 441997599 441996824 0.000000e+00 1325.0
5 TraesCS3A01G036700 chr2B 97.801 773 3 6 2025 2783 31594430 31593658 0.000000e+00 1321.0
6 TraesCS3A01G036700 chr7A 97.671 773 4 6 2025 2783 691153831 691154603 0.000000e+00 1315.0
7 TraesCS3A01G036700 chr7A 97.552 776 4 7 2023 2783 660472561 660471786 0.000000e+00 1314.0
8 TraesCS3A01G036700 chr7A 97.662 770 4 7 2028 2783 681575362 681576131 0.000000e+00 1310.0
9 TraesCS3A01G036700 chr7A 97.028 774 8 7 2025 2783 721562749 721563522 0.000000e+00 1288.0
10 TraesCS3A01G036700 chr7A 92.105 38 3 0 1904 1941 655739565 655739528 1.000000e-03 54.7
11 TraesCS3A01G036700 chr6B 97.662 770 4 7 2028 2783 586525969 586525200 0.000000e+00 1310.0
12 TraesCS3A01G036700 chr4B 96.766 773 10 7 2025 2783 30854627 30855398 0.000000e+00 1275.0
13 TraesCS3A01G036700 chr2A 96.757 771 11 6 2027 2783 117170859 117171629 0.000000e+00 1273.0
14 TraesCS3A01G036700 chr3B 96.124 774 7 11 2025 2783 762628846 762629611 0.000000e+00 1242.0
15 TraesCS3A01G036700 chr3B 90.411 876 44 14 936 1806 23956094 23956934 0.000000e+00 1116.0
16 TraesCS3A01G036700 chr3B 87.728 383 33 7 7 380 23955628 23956005 4.260000e-118 435.0
17 TraesCS3A01G036700 chr3D 91.799 695 40 4 1145 1835 16514901 16515582 0.000000e+00 952.0
18 TraesCS3A01G036700 chr3D 92.529 174 10 1 936 1109 16514737 16514907 2.140000e-61 246.0
19 TraesCS3A01G036700 chr3D 94.828 58 1 2 367 424 16514642 16514697 3.820000e-14 89.8
20 TraesCS3A01G036700 chr3D 92.105 38 1 2 1969 2005 544448166 544448130 5.000000e-03 52.8
21 TraesCS3A01G036700 chr6D 91.224 433 35 3 1377 1808 137129265 137128835 1.110000e-163 586.0
22 TraesCS3A01G036700 chr6D 86.006 343 37 4 1061 1396 137128488 137128826 9.480000e-95 357.0
23 TraesCS3A01G036700 chr6D 85.423 343 39 4 1061 1396 137126808 137127146 2.050000e-91 346.0
24 TraesCS3A01G036700 chr6D 85.423 343 39 4 1061 1396 137127648 137127986 2.050000e-91 346.0
25 TraesCS3A01G036700 chr7B 90.930 430 36 3 1377 1805 63391596 63392023 2.400000e-160 575.0
26 TraesCS3A01G036700 chr7B 98.148 54 1 0 2024 2077 697083849 697083902 8.210000e-16 95.3
27 TraesCS3A01G036700 chr7D 92.069 290 21 2 1377 1666 482120745 482120458 9.280000e-110 407.0
28 TraesCS3A01G036700 chr5B 85.417 144 5 9 2010 2137 11547367 11547510 4.830000e-28 135.0
29 TraesCS3A01G036700 chr2D 89.831 59 6 0 1906 1964 624124270 624124212 2.970000e-10 76.8
30 TraesCS3A01G036700 chr1A 89.474 57 6 0 1904 1960 572390327 572390271 3.840000e-09 73.1
31 TraesCS3A01G036700 chr1A 87.500 48 6 0 1904 1951 506265442 506265395 3.870000e-04 56.5
32 TraesCS3A01G036700 chr1D 84.211 57 9 0 1904 1960 476593560 476593504 3.870000e-04 56.5


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 TraesCS3A01G036700 chr3A 20027479 20030261 2782 True 2098.500000 3413 100.000000 1 2783 2 chr3A.!!$R2 2782
1 TraesCS3A01G036700 chr3A 625233717 625234489 772 True 1286.000000 1286 97.025000 2026 2783 1 chr3A.!!$R1 757
2 TraesCS3A01G036700 chr3A 22392299 22392866 567 False 547.000000 547 84.429000 2024 2587 1 chr3A.!!$F1 563
3 TraesCS3A01G036700 chr1B 441996824 441997599 775 True 1325.000000 1325 97.809000 2023 2783 1 chr1B.!!$R1 760
4 TraesCS3A01G036700 chr2B 31593658 31594430 772 True 1321.000000 1321 97.801000 2025 2783 1 chr2B.!!$R1 758
5 TraesCS3A01G036700 chr7A 691153831 691154603 772 False 1315.000000 1315 97.671000 2025 2783 1 chr7A.!!$F2 758
6 TraesCS3A01G036700 chr7A 660471786 660472561 775 True 1314.000000 1314 97.552000 2023 2783 1 chr7A.!!$R2 760
7 TraesCS3A01G036700 chr7A 681575362 681576131 769 False 1310.000000 1310 97.662000 2028 2783 1 chr7A.!!$F1 755
8 TraesCS3A01G036700 chr7A 721562749 721563522 773 False 1288.000000 1288 97.028000 2025 2783 1 chr7A.!!$F3 758
9 TraesCS3A01G036700 chr6B 586525200 586525969 769 True 1310.000000 1310 97.662000 2028 2783 1 chr6B.!!$R1 755
10 TraesCS3A01G036700 chr4B 30854627 30855398 771 False 1275.000000 1275 96.766000 2025 2783 1 chr4B.!!$F1 758
11 TraesCS3A01G036700 chr2A 117170859 117171629 770 False 1273.000000 1273 96.757000 2027 2783 1 chr2A.!!$F1 756
12 TraesCS3A01G036700 chr3B 762628846 762629611 765 False 1242.000000 1242 96.124000 2025 2783 1 chr3B.!!$F1 758
13 TraesCS3A01G036700 chr3B 23955628 23956934 1306 False 775.500000 1116 89.069500 7 1806 2 chr3B.!!$F2 1799
14 TraesCS3A01G036700 chr3D 16514642 16515582 940 False 429.266667 952 93.052000 367 1835 3 chr3D.!!$F1 1468
15 TraesCS3A01G036700 chr6D 137126808 137128826 2018 False 349.666667 357 85.617333 1061 1396 3 chr6D.!!$F1 335

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
46 48 0.529378 GCTCCTTGTGGGCATTTCTG 59.471 55.000 0.0 0.0 34.39 3.02 F
1071 1123 1.226717 GGACGACGACATCAGCCTC 60.227 63.158 0.0 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 2251 0.179119 GTAGTATCGGTTGCGCAGGT 60.179 55.0 11.31 0.0 0.0 4.00 R
1905 2808 1.261480 AGCATCGACTGAGACTTGGT 58.739 50.0 0.00 0.0 0.0 3.67 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
46 48 0.529378 GCTCCTTGTGGGCATTTCTG 59.471 55.000 0.00 0.00 34.39 3.02
55 57 6.486320 CCTTGTGGGCATTTCTGTTTATTTTT 59.514 34.615 0.00 0.00 0.00 1.94
56 58 7.659390 CCTTGTGGGCATTTCTGTTTATTTTTA 59.341 33.333 0.00 0.00 0.00 1.52
118 120 3.408634 TGGATTTCGAAAACCCACTCTC 58.591 45.455 28.16 13.44 30.46 3.20
119 121 2.747989 GGATTTCGAAAACCCACTCTCC 59.252 50.000 22.87 14.79 0.00 3.71
166 168 7.559897 TGAACCAGGTTTCTCTCTACAAATTTT 59.440 33.333 6.21 0.00 0.00 1.82
172 174 6.863645 GGTTTCTCTCTACAAATTTTTGAGGC 59.136 38.462 9.88 0.00 40.55 4.70
191 193 2.352715 GGCGTGCCTGCTATTTCTTTTT 60.353 45.455 2.98 0.00 34.52 1.94
193 195 4.440112 GGCGTGCCTGCTATTTCTTTTTAT 60.440 41.667 2.98 0.00 34.52 1.40
195 197 5.909610 GCGTGCCTGCTATTTCTTTTTATAG 59.090 40.000 0.00 0.00 0.00 1.31
206 208 6.921486 TTTCTTTTTATAGTGGTTTCCCCC 57.079 37.500 0.00 0.00 0.00 5.40
214 216 7.768324 TTATAGTGGTTTCCCCCTGTATTTA 57.232 36.000 0.00 0.00 0.00 1.40
215 217 6.858792 ATAGTGGTTTCCCCCTGTATTTAT 57.141 37.500 0.00 0.00 0.00 1.40
216 218 5.546035 AGTGGTTTCCCCCTGTATTTATT 57.454 39.130 0.00 0.00 0.00 1.40
267 269 7.039784 CCAAGAAAAGAACATCAAATACAGGGA 60.040 37.037 0.00 0.00 0.00 4.20
281 283 3.669939 ACAGGGAAATTACATGGAGGG 57.330 47.619 0.00 0.00 0.00 4.30
321 329 2.159986 GCATGTTGCAACGTGTTTATGC 60.160 45.455 38.54 31.81 45.44 3.14
976 1028 3.738481 CCCCTCCCCAAATCGCCA 61.738 66.667 0.00 0.00 0.00 5.69
1056 1108 2.435586 TCCGTCTCGTCCGAGGAC 60.436 66.667 15.96 12.07 42.20 3.85
1071 1123 1.226717 GGACGACGACATCAGCCTC 60.227 63.158 0.00 0.00 0.00 4.70
1092 1144 2.995574 CCGTCACCTTCCCCGTCT 60.996 66.667 0.00 0.00 0.00 4.18
1098 1150 2.682494 CCTTCCCCGTCTCCCGAA 60.682 66.667 0.00 0.00 39.56 4.30
1173 2068 2.732094 AAGAAACCGCGACGACCG 60.732 61.111 8.23 0.00 42.21 4.79
1365 2264 4.243008 TCCAACCTGCGCAACCGA 62.243 61.111 13.05 0.00 36.29 4.69
1764 2666 4.335647 AAGGTGGCCAGGACGCTG 62.336 66.667 5.11 0.00 0.00 5.18
1870 2773 7.807977 ATAATTCTTTGCTGGTAGTACATGG 57.192 36.000 2.06 0.00 0.00 3.66
1871 2774 4.634012 TTCTTTGCTGGTAGTACATGGT 57.366 40.909 2.06 0.00 0.00 3.55
1872 2775 4.634012 TCTTTGCTGGTAGTACATGGTT 57.366 40.909 2.06 0.00 0.00 3.67
1873 2776 5.748670 TCTTTGCTGGTAGTACATGGTTA 57.251 39.130 2.06 0.00 0.00 2.85
1874 2777 6.308015 TCTTTGCTGGTAGTACATGGTTAT 57.692 37.500 2.06 0.00 0.00 1.89
1875 2778 6.717289 TCTTTGCTGGTAGTACATGGTTATT 58.283 36.000 2.06 0.00 0.00 1.40
1876 2779 7.853299 TCTTTGCTGGTAGTACATGGTTATTA 58.147 34.615 2.06 0.00 0.00 0.98
1877 2780 7.767198 TCTTTGCTGGTAGTACATGGTTATTAC 59.233 37.037 2.06 0.00 0.00 1.89
1878 2781 6.801718 TGCTGGTAGTACATGGTTATTACT 57.198 37.500 2.06 0.00 0.00 2.24
1879 2782 6.578944 TGCTGGTAGTACATGGTTATTACTG 58.421 40.000 2.06 0.00 0.00 2.74
1880 2783 6.381707 TGCTGGTAGTACATGGTTATTACTGA 59.618 38.462 2.06 0.00 0.00 3.41
1881 2784 7.070696 TGCTGGTAGTACATGGTTATTACTGAT 59.929 37.037 2.06 0.00 0.00 2.90
1882 2785 7.931948 GCTGGTAGTACATGGTTATTACTGATT 59.068 37.037 2.06 0.00 0.00 2.57
1883 2786 9.832445 CTGGTAGTACATGGTTATTACTGATTT 57.168 33.333 2.06 0.00 0.00 2.17
1884 2787 9.826574 TGGTAGTACATGGTTATTACTGATTTC 57.173 33.333 2.06 0.00 0.00 2.17
1885 2788 8.975439 GGTAGTACATGGTTATTACTGATTTCG 58.025 37.037 2.06 0.00 0.00 3.46
1886 2789 7.478520 AGTACATGGTTATTACTGATTTCGC 57.521 36.000 0.00 0.00 0.00 4.70
1887 2790 7.045416 AGTACATGGTTATTACTGATTTCGCA 58.955 34.615 0.00 0.00 0.00 5.10
1888 2791 6.751514 ACATGGTTATTACTGATTTCGCAA 57.248 33.333 0.00 0.00 0.00 4.85
1889 2792 7.151999 ACATGGTTATTACTGATTTCGCAAA 57.848 32.000 0.00 0.00 0.00 3.68
1890 2793 7.027161 ACATGGTTATTACTGATTTCGCAAAC 58.973 34.615 0.00 0.00 0.00 2.93
1891 2794 5.623335 TGGTTATTACTGATTTCGCAAACG 58.377 37.500 0.00 0.00 42.01 3.60
1892 2795 5.025826 GGTTATTACTGATTTCGCAAACGG 58.974 41.667 0.00 0.00 40.63 4.44
1893 2796 3.757745 ATTACTGATTTCGCAAACGGG 57.242 42.857 0.00 0.00 40.63 5.28
1894 2797 2.459060 TACTGATTTCGCAAACGGGA 57.541 45.000 0.00 0.00 40.63 5.14
1895 2798 1.821216 ACTGATTTCGCAAACGGGAT 58.179 45.000 0.00 0.00 40.63 3.85
1896 2799 2.159382 ACTGATTTCGCAAACGGGATT 58.841 42.857 0.00 0.00 40.63 3.01
1897 2800 2.095263 ACTGATTTCGCAAACGGGATTG 60.095 45.455 0.00 0.00 40.63 2.67
1907 2810 4.351131 CAAACGGGATTGCTAAGTAACC 57.649 45.455 0.00 0.00 0.00 2.85
1908 2811 3.706600 AACGGGATTGCTAAGTAACCA 57.293 42.857 0.00 0.00 0.00 3.67
1909 2812 3.706600 ACGGGATTGCTAAGTAACCAA 57.293 42.857 0.00 0.00 0.00 3.67
1910 2813 3.606687 ACGGGATTGCTAAGTAACCAAG 58.393 45.455 0.00 0.00 0.00 3.61
1911 2814 3.008704 ACGGGATTGCTAAGTAACCAAGT 59.991 43.478 0.00 0.00 0.00 3.16
1912 2815 3.621715 CGGGATTGCTAAGTAACCAAGTC 59.378 47.826 0.00 0.00 0.00 3.01
1913 2816 4.623171 CGGGATTGCTAAGTAACCAAGTCT 60.623 45.833 0.00 0.00 0.00 3.24
1914 2817 4.876679 GGGATTGCTAAGTAACCAAGTCTC 59.123 45.833 0.00 0.00 0.00 3.36
1915 2818 5.488341 GGATTGCTAAGTAACCAAGTCTCA 58.512 41.667 0.00 0.00 0.00 3.27
1916 2819 5.582665 GGATTGCTAAGTAACCAAGTCTCAG 59.417 44.000 0.00 0.00 0.00 3.35
1917 2820 5.546621 TTGCTAAGTAACCAAGTCTCAGT 57.453 39.130 0.00 0.00 0.00 3.41
1918 2821 5.135508 TGCTAAGTAACCAAGTCTCAGTC 57.864 43.478 0.00 0.00 0.00 3.51
1919 2822 4.167268 GCTAAGTAACCAAGTCTCAGTCG 58.833 47.826 0.00 0.00 0.00 4.18
1920 2823 4.082895 GCTAAGTAACCAAGTCTCAGTCGA 60.083 45.833 0.00 0.00 0.00 4.20
1921 2824 5.393243 GCTAAGTAACCAAGTCTCAGTCGAT 60.393 44.000 0.00 0.00 0.00 3.59
1922 2825 4.442375 AGTAACCAAGTCTCAGTCGATG 57.558 45.455 0.00 0.00 0.00 3.84
1923 2826 2.086054 AACCAAGTCTCAGTCGATGC 57.914 50.000 0.00 0.00 0.00 3.91
1924 2827 1.261480 ACCAAGTCTCAGTCGATGCT 58.739 50.000 0.00 0.00 0.00 3.79
1925 2828 2.447443 ACCAAGTCTCAGTCGATGCTA 58.553 47.619 0.00 0.00 0.00 3.49
1926 2829 3.027412 ACCAAGTCTCAGTCGATGCTAT 58.973 45.455 0.00 0.00 0.00 2.97
1927 2830 4.207955 ACCAAGTCTCAGTCGATGCTATA 58.792 43.478 0.00 0.00 0.00 1.31
1928 2831 4.830046 ACCAAGTCTCAGTCGATGCTATAT 59.170 41.667 0.00 0.00 0.00 0.86
1929 2832 5.303078 ACCAAGTCTCAGTCGATGCTATATT 59.697 40.000 0.00 0.00 0.00 1.28
1930 2833 6.183360 ACCAAGTCTCAGTCGATGCTATATTT 60.183 38.462 0.00 0.00 0.00 1.40
1931 2834 6.145209 CCAAGTCTCAGTCGATGCTATATTTG 59.855 42.308 0.00 0.00 0.00 2.32
1932 2835 6.398234 AGTCTCAGTCGATGCTATATTTGT 57.602 37.500 0.00 0.00 0.00 2.83
1933 2836 6.442952 AGTCTCAGTCGATGCTATATTTGTC 58.557 40.000 0.00 0.00 0.00 3.18
1934 2837 5.340932 GTCTCAGTCGATGCTATATTTGTCG 59.659 44.000 0.00 0.00 0.00 4.35
1935 2838 4.546570 TCAGTCGATGCTATATTTGTCGG 58.453 43.478 0.00 0.00 33.46 4.79
1936 2839 4.277423 TCAGTCGATGCTATATTTGTCGGA 59.723 41.667 0.00 0.00 33.46 4.55
1937 2840 5.048013 TCAGTCGATGCTATATTTGTCGGAT 60.048 40.000 0.00 0.00 33.46 4.18
1938 2841 5.287274 CAGTCGATGCTATATTTGTCGGATC 59.713 44.000 0.00 0.00 33.46 3.36
1939 2842 5.184096 AGTCGATGCTATATTTGTCGGATCT 59.816 40.000 0.00 0.00 33.46 2.75
1940 2843 5.864474 GTCGATGCTATATTTGTCGGATCTT 59.136 40.000 0.00 0.00 33.46 2.40
1941 2844 5.863935 TCGATGCTATATTTGTCGGATCTTG 59.136 40.000 0.00 0.00 33.46 3.02
1942 2845 5.445142 CGATGCTATATTTGTCGGATCTTGC 60.445 44.000 0.00 0.00 0.00 4.01
1943 2846 4.702831 TGCTATATTTGTCGGATCTTGCA 58.297 39.130 0.00 0.00 0.00 4.08
1944 2847 5.308014 TGCTATATTTGTCGGATCTTGCAT 58.692 37.500 0.00 0.00 0.00 3.96
1945 2848 5.764686 TGCTATATTTGTCGGATCTTGCATT 59.235 36.000 0.00 0.00 0.00 3.56
1946 2849 6.934083 TGCTATATTTGTCGGATCTTGCATTA 59.066 34.615 0.00 0.00 0.00 1.90
1947 2850 7.443879 TGCTATATTTGTCGGATCTTGCATTAA 59.556 33.333 0.00 0.00 0.00 1.40
1948 2851 7.959651 GCTATATTTGTCGGATCTTGCATTAAG 59.040 37.037 0.00 0.00 37.76 1.85
1985 2888 8.962884 AAATTGCCTTTTTCTTTCTTACATGT 57.037 26.923 2.69 2.69 0.00 3.21
1986 2889 8.962884 AATTGCCTTTTTCTTTCTTACATGTT 57.037 26.923 2.30 0.00 0.00 2.71
1998 2901 9.731819 TCTTTCTTACATGTTATATCACTCGAC 57.268 33.333 2.30 0.00 0.00 4.20
1999 2902 9.737427 CTTTCTTACATGTTATATCACTCGACT 57.263 33.333 2.30 0.00 0.00 4.18
2005 2908 8.221965 ACATGTTATATCACTCGACTTAGACA 57.778 34.615 0.00 0.00 0.00 3.41
2006 2909 8.129840 ACATGTTATATCACTCGACTTAGACAC 58.870 37.037 0.00 0.00 0.00 3.67
2007 2910 7.619964 TGTTATATCACTCGACTTAGACACA 57.380 36.000 0.00 0.00 0.00 3.72
2008 2911 7.470079 TGTTATATCACTCGACTTAGACACAC 58.530 38.462 0.00 0.00 0.00 3.82
2009 2912 3.851976 ATCACTCGACTTAGACACACC 57.148 47.619 0.00 0.00 0.00 4.16
2010 2913 1.884579 TCACTCGACTTAGACACACCC 59.115 52.381 0.00 0.00 0.00 4.61
2011 2914 1.611977 CACTCGACTTAGACACACCCA 59.388 52.381 0.00 0.00 0.00 4.51
2012 2915 2.231478 CACTCGACTTAGACACACCCAT 59.769 50.000 0.00 0.00 0.00 4.00
2013 2916 2.492484 ACTCGACTTAGACACACCCATC 59.508 50.000 0.00 0.00 0.00 3.51
2014 2917 2.492088 CTCGACTTAGACACACCCATCA 59.508 50.000 0.00 0.00 0.00 3.07
2015 2918 2.230508 TCGACTTAGACACACCCATCAC 59.769 50.000 0.00 0.00 0.00 3.06
2016 2919 2.231478 CGACTTAGACACACCCATCACT 59.769 50.000 0.00 0.00 0.00 3.41
2017 2920 3.306088 CGACTTAGACACACCCATCACTT 60.306 47.826 0.00 0.00 0.00 3.16
2018 2921 3.997021 GACTTAGACACACCCATCACTTG 59.003 47.826 0.00 0.00 0.00 3.16
2019 2922 3.646162 ACTTAGACACACCCATCACTTGA 59.354 43.478 0.00 0.00 0.00 3.02
2020 2923 2.550830 AGACACACCCATCACTTGAC 57.449 50.000 0.00 0.00 0.00 3.18
2021 2924 2.050144 AGACACACCCATCACTTGACT 58.950 47.619 0.00 0.00 0.00 3.41
2077 2981 4.156922 TCCATTAATTTCGCAATCAACGGT 59.843 37.500 0.00 0.00 0.00 4.83
2079 2983 6.038825 TCCATTAATTTCGCAATCAACGGTAT 59.961 34.615 0.00 0.00 0.00 2.73
2080 2984 6.359617 CCATTAATTTCGCAATCAACGGTATC 59.640 38.462 0.00 0.00 0.00 2.24
2081 2985 3.963383 ATTTCGCAATCAACGGTATCC 57.037 42.857 0.00 0.00 0.00 2.59
2082 2986 2.388310 TTCGCAATCAACGGTATCCA 57.612 45.000 0.00 0.00 0.00 3.41
2083 2987 1.647346 TCGCAATCAACGGTATCCAC 58.353 50.000 0.00 0.00 0.00 4.02
2084 2988 1.066787 TCGCAATCAACGGTATCCACA 60.067 47.619 0.00 0.00 0.00 4.17
2400 3322 1.227853 AAGCAAAAGGACCGAGCGT 60.228 52.632 0.00 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.565652 GGAGCCACCAGAAGTTCTCATAAA 60.566 45.833 1.26 0.00 38.79 1.40
13 14 0.980423 AGGAGCCACCAGAAGTTCTC 59.020 55.000 1.26 0.00 42.04 2.87
90 92 2.607038 GGTTTTCGAAATCCAGGTGCAC 60.607 50.000 26.12 8.80 0.00 4.57
118 120 1.404717 CGTTCCAGGAGAGTGACATGG 60.405 57.143 0.00 0.00 0.00 3.66
119 121 1.273606 ACGTTCCAGGAGAGTGACATG 59.726 52.381 0.00 0.00 0.00 3.21
166 168 0.322456 AAATAGCAGGCACGCCTCAA 60.322 50.000 7.85 0.00 46.28 3.02
172 174 6.907212 CACTATAAAAAGAAATAGCAGGCACG 59.093 38.462 0.00 0.00 0.00 5.34
206 208 5.728255 CGCGGAGAAGTCAAATAAATACAG 58.272 41.667 0.00 0.00 0.00 2.74
214 216 0.320771 ACTGCGCGGAGAAGTCAAAT 60.321 50.000 34.91 5.89 0.00 2.32
215 217 0.531974 AACTGCGCGGAGAAGTCAAA 60.532 50.000 34.91 0.00 0.00 2.69
216 218 0.531974 AAACTGCGCGGAGAAGTCAA 60.532 50.000 34.91 0.00 0.00 3.18
267 269 7.418942 GGCATTACAATTCCCTCCATGTAATTT 60.419 37.037 7.15 0.00 43.02 1.82
281 283 3.779759 TGCAAATCGGGCATTACAATTC 58.220 40.909 0.00 0.00 36.11 2.17
303 305 1.747956 CGCATAAACACGTTGCAACA 58.252 45.000 28.01 8.91 36.15 3.33
321 329 7.041848 TGGATATTCTCACATTTTATCACAGCG 60.042 37.037 0.00 0.00 0.00 5.18
373 382 1.912731 TGTAGCTCAACTGGGCCATTA 59.087 47.619 6.72 0.00 0.00 1.90
1056 1108 2.105128 GGGAGGCTGATGTCGTCG 59.895 66.667 0.00 0.00 0.00 5.12
1080 1132 3.534704 TTCGGGAGACGGGGAAGGT 62.535 63.158 0.00 0.00 44.45 3.50
1092 1144 3.228243 TTCGGGAGAGGGTTCGGGA 62.228 63.158 0.00 0.00 41.75 5.14
1098 1150 0.969409 CGTAAGGTTCGGGAGAGGGT 60.969 60.000 0.00 0.00 41.75 4.34
1152 2047 4.084888 CGTCGCGGTTTCTTGGCC 62.085 66.667 6.13 0.00 0.00 5.36
1352 2251 0.179119 GTAGTATCGGTTGCGCAGGT 60.179 55.000 11.31 0.00 0.00 4.00
1634 2536 3.441011 ATCATCCCGAACGCCGTCC 62.441 63.158 0.00 0.00 36.31 4.79
1731 2633 3.997064 CTTGTCCCTCAGCTCGGCG 62.997 68.421 0.00 0.00 0.00 6.46
1745 2647 4.643387 GCGTCCTGGCCACCTTGT 62.643 66.667 0.00 0.00 0.00 3.16
1747 2649 4.335647 CAGCGTCCTGGCCACCTT 62.336 66.667 0.00 0.00 35.38 3.50
1844 2747 9.507329 CCATGTACTACCAGCAAAGAATTATAT 57.493 33.333 0.00 0.00 0.00 0.86
1845 2748 8.491134 ACCATGTACTACCAGCAAAGAATTATA 58.509 33.333 0.00 0.00 0.00 0.98
1846 2749 7.346471 ACCATGTACTACCAGCAAAGAATTAT 58.654 34.615 0.00 0.00 0.00 1.28
1847 2750 6.717289 ACCATGTACTACCAGCAAAGAATTA 58.283 36.000 0.00 0.00 0.00 1.40
1848 2751 5.570320 ACCATGTACTACCAGCAAAGAATT 58.430 37.500 0.00 0.00 0.00 2.17
1849 2752 5.179452 ACCATGTACTACCAGCAAAGAAT 57.821 39.130 0.00 0.00 0.00 2.40
1850 2753 4.634012 ACCATGTACTACCAGCAAAGAA 57.366 40.909 0.00 0.00 0.00 2.52
1851 2754 4.634012 AACCATGTACTACCAGCAAAGA 57.366 40.909 0.00 0.00 0.00 2.52
1852 2755 7.769044 AGTAATAACCATGTACTACCAGCAAAG 59.231 37.037 0.00 0.00 0.00 2.77
1853 2756 7.551262 CAGTAATAACCATGTACTACCAGCAAA 59.449 37.037 0.00 0.00 0.00 3.68
1854 2757 7.045416 CAGTAATAACCATGTACTACCAGCAA 58.955 38.462 0.00 0.00 0.00 3.91
1855 2758 6.381707 TCAGTAATAACCATGTACTACCAGCA 59.618 38.462 0.00 0.00 0.00 4.41
1856 2759 6.812998 TCAGTAATAACCATGTACTACCAGC 58.187 40.000 0.00 0.00 0.00 4.85
1857 2760 9.832445 AAATCAGTAATAACCATGTACTACCAG 57.168 33.333 0.00 0.00 0.00 4.00
1858 2761 9.826574 GAAATCAGTAATAACCATGTACTACCA 57.173 33.333 0.00 0.00 0.00 3.25
1859 2762 8.975439 CGAAATCAGTAATAACCATGTACTACC 58.025 37.037 0.00 0.00 0.00 3.18
1860 2763 8.485591 GCGAAATCAGTAATAACCATGTACTAC 58.514 37.037 0.00 0.00 0.00 2.73
1861 2764 8.198778 TGCGAAATCAGTAATAACCATGTACTA 58.801 33.333 0.00 0.00 0.00 1.82
1862 2765 7.045416 TGCGAAATCAGTAATAACCATGTACT 58.955 34.615 0.00 0.00 0.00 2.73
1863 2766 7.241663 TGCGAAATCAGTAATAACCATGTAC 57.758 36.000 0.00 0.00 0.00 2.90
1864 2767 7.851387 TTGCGAAATCAGTAATAACCATGTA 57.149 32.000 0.00 0.00 0.00 2.29
1865 2768 6.751514 TTGCGAAATCAGTAATAACCATGT 57.248 33.333 0.00 0.00 0.00 3.21
1866 2769 6.194508 CGTTTGCGAAATCAGTAATAACCATG 59.805 38.462 0.00 0.00 41.33 3.66
1867 2770 6.255215 CGTTTGCGAAATCAGTAATAACCAT 58.745 36.000 0.00 0.00 41.33 3.55
1868 2771 5.391097 CCGTTTGCGAAATCAGTAATAACCA 60.391 40.000 0.00 0.00 41.33 3.67
1869 2772 5.025826 CCGTTTGCGAAATCAGTAATAACC 58.974 41.667 0.00 0.00 41.33 2.85
1870 2773 5.025826 CCCGTTTGCGAAATCAGTAATAAC 58.974 41.667 0.00 0.00 41.33 1.89
1871 2774 4.936411 TCCCGTTTGCGAAATCAGTAATAA 59.064 37.500 0.00 0.00 41.33 1.40
1872 2775 4.505808 TCCCGTTTGCGAAATCAGTAATA 58.494 39.130 0.00 0.00 41.33 0.98
1873 2776 3.340034 TCCCGTTTGCGAAATCAGTAAT 58.660 40.909 0.00 0.00 41.33 1.89
1874 2777 2.768698 TCCCGTTTGCGAAATCAGTAA 58.231 42.857 0.00 0.00 41.33 2.24
1875 2778 2.459060 TCCCGTTTGCGAAATCAGTA 57.541 45.000 0.00 0.00 41.33 2.74
1876 2779 1.821216 ATCCCGTTTGCGAAATCAGT 58.179 45.000 0.00 0.00 41.33 3.41
1877 2780 2.518949 CAATCCCGTTTGCGAAATCAG 58.481 47.619 0.00 0.00 41.33 2.90
1878 2781 1.402194 GCAATCCCGTTTGCGAAATCA 60.402 47.619 0.00 0.00 42.22 2.57
1879 2782 1.268265 GCAATCCCGTTTGCGAAATC 58.732 50.000 0.00 0.00 42.22 2.17
1880 2783 3.416955 GCAATCCCGTTTGCGAAAT 57.583 47.368 0.00 0.00 42.22 2.17
1881 2784 4.955089 GCAATCCCGTTTGCGAAA 57.045 50.000 0.00 0.00 42.22 3.46
1886 2789 3.754323 TGGTTACTTAGCAATCCCGTTTG 59.246 43.478 0.00 0.00 0.00 2.93
1887 2790 4.023726 TGGTTACTTAGCAATCCCGTTT 57.976 40.909 0.00 0.00 0.00 3.60
1888 2791 3.706600 TGGTTACTTAGCAATCCCGTT 57.293 42.857 0.00 0.00 0.00 4.44
1889 2792 3.008704 ACTTGGTTACTTAGCAATCCCGT 59.991 43.478 0.00 0.00 42.86 5.28
1890 2793 3.606687 ACTTGGTTACTTAGCAATCCCG 58.393 45.455 0.00 0.00 42.86 5.14
1891 2794 4.844884 AGACTTGGTTACTTAGCAATCCC 58.155 43.478 0.00 0.00 42.86 3.85
1892 2795 5.488341 TGAGACTTGGTTACTTAGCAATCC 58.512 41.667 0.00 0.00 42.86 3.01
1893 2796 6.166982 ACTGAGACTTGGTTACTTAGCAATC 58.833 40.000 0.00 0.00 42.86 2.67
1894 2797 6.115448 ACTGAGACTTGGTTACTTAGCAAT 57.885 37.500 0.00 0.00 42.86 3.56
1895 2798 5.539048 GACTGAGACTTGGTTACTTAGCAA 58.461 41.667 0.00 0.00 41.68 3.91
1896 2799 4.321008 CGACTGAGACTTGGTTACTTAGCA 60.321 45.833 0.00 0.00 0.00 3.49
1897 2800 4.082895 TCGACTGAGACTTGGTTACTTAGC 60.083 45.833 0.00 0.00 0.00 3.09
1898 2801 5.624344 TCGACTGAGACTTGGTTACTTAG 57.376 43.478 0.00 0.00 0.00 2.18
1899 2802 5.621555 GCATCGACTGAGACTTGGTTACTTA 60.622 44.000 0.00 0.00 0.00 2.24
1900 2803 4.810790 CATCGACTGAGACTTGGTTACTT 58.189 43.478 0.00 0.00 0.00 2.24
1901 2804 3.367498 GCATCGACTGAGACTTGGTTACT 60.367 47.826 0.00 0.00 0.00 2.24
1902 2805 2.924290 GCATCGACTGAGACTTGGTTAC 59.076 50.000 0.00 0.00 0.00 2.50
1903 2806 2.826128 AGCATCGACTGAGACTTGGTTA 59.174 45.455 0.00 0.00 0.00 2.85
1904 2807 1.620819 AGCATCGACTGAGACTTGGTT 59.379 47.619 0.00 0.00 0.00 3.67
1905 2808 1.261480 AGCATCGACTGAGACTTGGT 58.739 50.000 0.00 0.00 0.00 3.67
1906 2809 3.724508 ATAGCATCGACTGAGACTTGG 57.275 47.619 0.00 0.00 0.00 3.61
1907 2810 6.699204 ACAAATATAGCATCGACTGAGACTTG 59.301 38.462 0.00 0.00 0.00 3.16
1908 2811 6.810911 ACAAATATAGCATCGACTGAGACTT 58.189 36.000 0.00 0.00 0.00 3.01
1909 2812 6.398234 ACAAATATAGCATCGACTGAGACT 57.602 37.500 0.00 0.00 0.00 3.24
1910 2813 5.340932 CGACAAATATAGCATCGACTGAGAC 59.659 44.000 0.00 0.00 34.77 3.36
1911 2814 5.452777 CGACAAATATAGCATCGACTGAGA 58.547 41.667 0.00 0.00 34.77 3.27
1912 2815 4.618912 CCGACAAATATAGCATCGACTGAG 59.381 45.833 0.00 0.00 34.77 3.35
1913 2816 4.277423 TCCGACAAATATAGCATCGACTGA 59.723 41.667 0.00 0.00 34.77 3.41
1914 2817 4.546570 TCCGACAAATATAGCATCGACTG 58.453 43.478 0.00 0.00 34.77 3.51
1915 2818 4.848562 TCCGACAAATATAGCATCGACT 57.151 40.909 0.00 0.00 34.77 4.18
1916 2819 5.403246 AGATCCGACAAATATAGCATCGAC 58.597 41.667 0.00 0.00 34.77 4.20
1917 2820 5.644977 AGATCCGACAAATATAGCATCGA 57.355 39.130 0.00 0.00 34.77 3.59
1918 2821 5.445142 GCAAGATCCGACAAATATAGCATCG 60.445 44.000 0.00 0.00 0.00 3.84
1919 2822 5.409520 TGCAAGATCCGACAAATATAGCATC 59.590 40.000 0.00 0.00 0.00 3.91
1920 2823 5.308014 TGCAAGATCCGACAAATATAGCAT 58.692 37.500 0.00 0.00 0.00 3.79
1921 2824 4.702831 TGCAAGATCCGACAAATATAGCA 58.297 39.130 0.00 0.00 0.00 3.49
1922 2825 5.869753 ATGCAAGATCCGACAAATATAGC 57.130 39.130 0.00 0.00 0.00 2.97
1923 2826 9.208022 TCTTAATGCAAGATCCGACAAATATAG 57.792 33.333 0.00 0.00 38.39 1.31
1959 2862 9.394767 ACATGTAAGAAAGAAAAAGGCAATTTT 57.605 25.926 0.00 1.31 43.04 1.82
1960 2863 8.962884 ACATGTAAGAAAGAAAAAGGCAATTT 57.037 26.923 0.00 0.00 0.00 1.82
1961 2864 8.962884 AACATGTAAGAAAGAAAAAGGCAATT 57.037 26.923 0.00 0.00 0.00 2.32
1972 2875 9.731819 GTCGAGTGATATAACATGTAAGAAAGA 57.268 33.333 0.00 0.00 0.00 2.52
1973 2876 9.737427 AGTCGAGTGATATAACATGTAAGAAAG 57.263 33.333 0.00 0.00 0.00 2.62
1979 2882 9.333724 TGTCTAAGTCGAGTGATATAACATGTA 57.666 33.333 0.00 0.00 0.00 2.29
1980 2883 8.129840 GTGTCTAAGTCGAGTGATATAACATGT 58.870 37.037 0.00 0.00 0.00 3.21
1981 2884 8.129211 TGTGTCTAAGTCGAGTGATATAACATG 58.871 37.037 0.00 0.00 0.00 3.21
1982 2885 8.129840 GTGTGTCTAAGTCGAGTGATATAACAT 58.870 37.037 0.00 0.00 0.00 2.71
1983 2886 7.414873 GGTGTGTCTAAGTCGAGTGATATAACA 60.415 40.741 0.00 0.00 0.00 2.41
1984 2887 6.911511 GGTGTGTCTAAGTCGAGTGATATAAC 59.088 42.308 0.00 0.00 0.00 1.89
1985 2888 6.039047 GGGTGTGTCTAAGTCGAGTGATATAA 59.961 42.308 0.00 0.00 0.00 0.98
1986 2889 5.530171 GGGTGTGTCTAAGTCGAGTGATATA 59.470 44.000 0.00 0.00 0.00 0.86
1987 2890 4.338682 GGGTGTGTCTAAGTCGAGTGATAT 59.661 45.833 0.00 0.00 0.00 1.63
1988 2891 3.693085 GGGTGTGTCTAAGTCGAGTGATA 59.307 47.826 0.00 0.00 0.00 2.15
1989 2892 2.492484 GGGTGTGTCTAAGTCGAGTGAT 59.508 50.000 0.00 0.00 0.00 3.06
1990 2893 1.884579 GGGTGTGTCTAAGTCGAGTGA 59.115 52.381 0.00 0.00 0.00 3.41
1991 2894 1.611977 TGGGTGTGTCTAAGTCGAGTG 59.388 52.381 0.00 0.00 0.00 3.51
1992 2895 1.991121 TGGGTGTGTCTAAGTCGAGT 58.009 50.000 0.00 0.00 0.00 4.18
1993 2896 2.492088 TGATGGGTGTGTCTAAGTCGAG 59.508 50.000 0.00 0.00 0.00 4.04
1994 2897 2.230508 GTGATGGGTGTGTCTAAGTCGA 59.769 50.000 0.00 0.00 0.00 4.20
1995 2898 2.231478 AGTGATGGGTGTGTCTAAGTCG 59.769 50.000 0.00 0.00 0.00 4.18
1996 2899 3.963428 AGTGATGGGTGTGTCTAAGTC 57.037 47.619 0.00 0.00 0.00 3.01
1997 2900 3.646162 TCAAGTGATGGGTGTGTCTAAGT 59.354 43.478 0.00 0.00 0.00 2.24
1998 2901 3.997021 GTCAAGTGATGGGTGTGTCTAAG 59.003 47.826 0.00 0.00 0.00 2.18
1999 2902 3.646162 AGTCAAGTGATGGGTGTGTCTAA 59.354 43.478 0.00 0.00 0.00 2.10
2000 2903 3.239449 AGTCAAGTGATGGGTGTGTCTA 58.761 45.455 0.00 0.00 0.00 2.59
2001 2904 2.050144 AGTCAAGTGATGGGTGTGTCT 58.950 47.619 0.00 0.00 0.00 3.41
2002 2905 2.550830 AGTCAAGTGATGGGTGTGTC 57.449 50.000 0.00 0.00 0.00 3.67
2003 2906 3.297134 AAAGTCAAGTGATGGGTGTGT 57.703 42.857 0.00 0.00 0.00 3.72
2004 2907 4.654091 AAAAAGTCAAGTGATGGGTGTG 57.346 40.909 0.00 0.00 0.00 3.82
2077 2981 4.018870 TGGGCACTAAGAACATTGTGGATA 60.019 41.667 0.00 0.00 0.00 2.59
2079 2983 2.107378 TGGGCACTAAGAACATTGTGGA 59.893 45.455 0.00 0.00 0.00 4.02
2080 2984 2.513753 TGGGCACTAAGAACATTGTGG 58.486 47.619 0.00 0.00 0.00 4.17
2081 2985 4.298332 GTTTGGGCACTAAGAACATTGTG 58.702 43.478 0.00 0.00 0.00 3.33
2082 2986 3.320826 GGTTTGGGCACTAAGAACATTGT 59.679 43.478 0.00 0.00 0.00 2.71
2083 2987 3.320541 TGGTTTGGGCACTAAGAACATTG 59.679 43.478 0.00 0.00 0.00 2.82
2084 2988 3.320826 GTGGTTTGGGCACTAAGAACATT 59.679 43.478 0.00 0.00 0.00 2.71
2400 3322 3.076621 CAGATTGGTTAGCAGTGCTCAA 58.923 45.455 23.64 19.74 40.44 3.02


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

AutoCloner maintained by Alex Coulton.