Multiple sequence alignment - TraesCS1A01G042700

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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 TraesCS1A01G042700 chr1A 100.000 2899 0 0 1 2899 23338618 23341516 0.000000e+00 5354.0
1 TraesCS1A01G042700 chr1A 91.667 48 4 0 2140 2187 26197732 26197685 1.860000e-07 67.6
2 TraesCS1A01G042700 chr1A 94.286 35 2 0 2141 2175 515835902 515835868 1.000000e-03 54.7
3 TraesCS1A01G042700 chr1D 88.632 2208 139 42 88 2226 22438431 22436267 0.000000e+00 2584.0
4 TraesCS1A01G042700 chr1D 90.017 581 26 10 2335 2898 22436007 22435442 0.000000e+00 723.0
5 TraesCS1A01G042700 chr1B 88.350 2103 113 58 212 2226 37798401 37800459 0.000000e+00 2405.0
6 TraesCS1A01G042700 chr1B 88.889 576 35 14 2291 2854 37800618 37801176 0.000000e+00 682.0
7 TraesCS1A01G042700 chr4D 81.951 205 29 8 1244 1444 315597321 315597521 1.790000e-37 167.0
8 TraesCS1A01G042700 chr4D 94.286 35 2 0 2141 2175 402522788 402522754 1.000000e-03 54.7
9 TraesCS1A01G042700 chr4B 81.463 205 30 8 1244 1444 393406268 393406468 8.310000e-36 161.0
10 TraesCS1A01G042700 chr4B 89.286 56 4 2 2141 2195 646120132 646120186 5.180000e-08 69.4
11 TraesCS1A01G042700 chr4A 81.463 205 30 8 1244 1444 159294855 159294655 8.310000e-36 161.0
12 TraesCS1A01G042700 chr2A 81.959 194 29 6 1254 1444 51008487 51008297 2.990000e-35 159.0
13 TraesCS1A01G042700 chr2A 89.583 48 5 0 1408 1455 572486407 572486360 8.670000e-06 62.1
14 TraesCS1A01G042700 chr2D 81.443 194 30 6 1254 1444 48133251 48133441 1.390000e-33 154.0
15 TraesCS1A01G042700 chr2D 81.928 83 14 1 95 176 336734694 336734776 5.180000e-08 69.4
16 TraesCS1A01G042700 chr2D 83.333 72 10 2 1376 1446 417626501 417626571 6.710000e-07 65.8
17 TraesCS1A01G042700 chr2B 81.443 194 30 6 1254 1444 75847568 75847758 1.390000e-33 154.0
18 TraesCS1A01G042700 chr2B 81.944 72 11 2 1376 1446 489850334 489850404 3.120000e-05 60.2
19 TraesCS1A01G042700 chr2B 86.792 53 6 1 1408 1460 771043860 771043911 1.120000e-04 58.4
20 TraesCS1A01G042700 chr3B 79.412 204 42 0 1244 1447 829542126 829541923 8.370000e-31 145.0
21 TraesCS1A01G042700 chr7B 76.442 208 43 6 1254 1458 241107821 241108025 1.100000e-19 108.0
22 TraesCS1A01G042700 chr6D 91.228 57 5 0 1399 1455 292737726 292737670 8.610000e-11 78.7
23 TraesCS1A01G042700 chr6D 82.857 70 9 3 95 163 78348830 78348897 3.120000e-05 60.2
24 TraesCS1A01G042700 chr6D 87.755 49 6 0 95 143 363319419 363319371 1.120000e-04 58.4
25 TraesCS1A01G042700 chr6B 91.228 57 5 0 1399 1455 457216753 457216697 8.610000e-11 78.7
26 TraesCS1A01G042700 chr6B 91.071 56 5 0 2140 2195 120135643 120135698 3.100000e-10 76.8
27 TraesCS1A01G042700 chr7A 83.750 80 13 0 95 174 507170532 507170611 3.100000e-10 76.8
28 TraesCS1A01G042700 chr5D 86.364 66 8 1 2131 2195 299356897 299356832 1.440000e-08 71.3
29 TraesCS1A01G042700 chr5D 85.965 57 8 0 92 148 243313269 243313325 8.670000e-06 62.1
30 TraesCS1A01G042700 chr5A 87.719 57 7 0 2139 2195 285305166 285305222 1.860000e-07 67.6
31 TraesCS1A01G042700 chr5A 88.889 54 6 0 95 148 307710943 307710890 1.860000e-07 67.6
32 TraesCS1A01G042700 chr5B 81.176 85 10 5 95 175 254946220 254946138 2.410000e-06 63.9
33 TraesCS1A01G042700 chr3D 81.690 71 12 1 95 164 587051470 587051400 1.120000e-04 58.4


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 TraesCS1A01G042700 chr1A 23338618 23341516 2898 False 5354.0 5354 100.0000 1 2899 1 chr1A.!!$F1 2898
1 TraesCS1A01G042700 chr1D 22435442 22438431 2989 True 1653.5 2584 89.3245 88 2898 2 chr1D.!!$R1 2810
2 TraesCS1A01G042700 chr1B 37798401 37801176 2775 False 1543.5 2405 88.6195 212 2854 2 chr1B.!!$F1 2642

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
935 996 0.034477 CAGGGTAATTGGCCGGAGTT 60.034 55.0 5.05 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2695 3131 0.040204 AAAGAGGCCTCCACAATGGG 59.96 55.0 29.54 0.0 38.32 4.0 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
29 30 8.143835 AGCATATGAAATTTGGTATAACTTGGC 58.856 33.333 6.97 0.00 34.29 4.52
30 31 7.925483 GCATATGAAATTTGGTATAACTTGGCA 59.075 33.333 6.97 0.00 0.00 4.92
31 32 9.814899 CATATGAAATTTGGTATAACTTGGCAA 57.185 29.630 0.00 0.00 0.00 4.52
34 35 8.964476 TGAAATTTGGTATAACTTGGCAAAAA 57.036 26.923 0.00 0.00 0.00 1.94
91 92 8.810652 TTTGTTATAAAAGTTGTCAAGATGGC 57.189 30.769 0.00 0.00 0.00 4.40
92 93 6.607689 TGTTATAAAAGTTGTCAAGATGGCG 58.392 36.000 0.00 0.00 0.00 5.69
93 94 4.701956 ATAAAAGTTGTCAAGATGGCGG 57.298 40.909 0.00 0.00 0.00 6.13
94 95 2.270352 AAAGTTGTCAAGATGGCGGA 57.730 45.000 0.00 0.00 0.00 5.54
95 96 1.523758 AAGTTGTCAAGATGGCGGAC 58.476 50.000 0.00 0.00 0.00 4.79
96 97 0.396435 AGTTGTCAAGATGGCGGACA 59.604 50.000 0.00 0.00 39.60 4.02
116 117 5.689961 GGACACAAATATGCAAACGAAACTT 59.310 36.000 0.00 0.00 0.00 2.66
120 121 9.255304 ACACAAATATGCAAACGAAACTTAATT 57.745 25.926 0.00 0.00 0.00 1.40
153 154 9.496873 TCCGTTTCAAAAGATAGAGTAAATCAA 57.503 29.630 0.00 0.00 0.00 2.57
222 230 5.762825 ACTATACAAAAGCATGCATGAGG 57.237 39.130 30.64 14.97 0.00 3.86
225 234 2.522185 ACAAAAGCATGCATGAGGTCT 58.478 42.857 30.64 14.46 0.00 3.85
268 277 2.159379 GCGAATCTCCAACCAAATGGAC 60.159 50.000 6.42 0.00 44.52 4.02
291 300 3.372514 GGCAAGAATCTCTTTTCTCGACC 59.627 47.826 0.00 0.00 33.78 4.79
295 304 6.313905 GCAAGAATCTCTTTTCTCGACCATTA 59.686 38.462 0.00 0.00 33.78 1.90
305 314 7.822334 TCTTTTCTCGACCATTAATTAGCTCAA 59.178 33.333 0.00 0.00 0.00 3.02
319 328 6.918892 ATTAGCTCAACAAAACCAAAAACC 57.081 33.333 0.00 0.00 0.00 3.27
339 348 2.677836 CCACACCAACTACCGAATCATG 59.322 50.000 0.00 0.00 0.00 3.07
386 395 1.469251 GCCGTGAGCATTCTCGTAAGA 60.469 52.381 0.00 0.00 43.83 2.10
390 417 7.307847 GCCGTGAGCATTCTCGTAAGAAAAA 62.308 44.000 0.00 0.00 44.49 1.94
434 461 3.322541 TGACACGATGGTAGACCTGAAAA 59.677 43.478 0.00 0.00 36.82 2.29
438 465 5.421056 ACACGATGGTAGACCTGAAAATAGA 59.579 40.000 0.00 0.00 36.82 1.98
439 466 5.749109 CACGATGGTAGACCTGAAAATAGAC 59.251 44.000 0.00 0.00 36.82 2.59
445 472 6.127054 TGGTAGACCTGAAAATAGACTCCATG 60.127 42.308 0.00 0.00 36.82 3.66
540 571 0.592637 CACGCAAGGCAATGAACAGA 59.407 50.000 0.00 0.00 46.39 3.41
671 716 0.955428 TCGTCCTTGCAATCAGTGGC 60.955 55.000 0.00 0.00 0.00 5.01
761 818 1.153745 GCTAGGTGCCACTCACTCG 60.154 63.158 0.00 0.00 44.98 4.18
769 826 1.979155 CCACTCACTCGCTCCCTCA 60.979 63.158 0.00 0.00 0.00 3.86
776 833 3.083349 TCGCTCCCTCACCATGGG 61.083 66.667 18.09 5.22 45.90 4.00
777 834 4.864334 CGCTCCCTCACCATGGGC 62.864 72.222 18.09 6.76 44.23 5.36
779 836 3.016971 CTCCCTCACCATGGGCCA 61.017 66.667 18.09 9.61 44.23 5.36
780 837 2.287117 TCCCTCACCATGGGCCAT 60.287 61.111 14.78 14.78 44.23 4.40
788 845 2.196502 CATGGGCCATGGCTAGCA 59.803 61.111 34.26 10.71 38.11 3.49
789 846 1.901948 CATGGGCCATGGCTAGCAG 60.902 63.158 34.26 17.74 38.11 4.24
790 847 2.389449 ATGGGCCATGGCTAGCAGT 61.389 57.895 34.70 13.33 41.60 4.40
791 848 1.061905 ATGGGCCATGGCTAGCAGTA 61.062 55.000 34.70 14.25 41.60 2.74
792 849 1.072159 GGGCCATGGCTAGCAGTAG 59.928 63.158 34.70 3.29 41.60 2.57
794 851 0.034616 GGCCATGGCTAGCAGTAGAG 59.965 60.000 34.70 0.62 41.60 2.43
795 852 0.755686 GCCATGGCTAGCAGTAGAGT 59.244 55.000 29.98 0.00 38.26 3.24
796 853 1.964223 GCCATGGCTAGCAGTAGAGTA 59.036 52.381 29.98 0.00 38.26 2.59
797 854 2.564947 GCCATGGCTAGCAGTAGAGTAT 59.435 50.000 29.98 0.00 38.26 2.12
798 855 3.764434 GCCATGGCTAGCAGTAGAGTATA 59.236 47.826 29.98 0.00 38.26 1.47
799 856 4.381079 GCCATGGCTAGCAGTAGAGTATAC 60.381 50.000 29.98 0.00 38.26 1.47
800 857 5.013547 CCATGGCTAGCAGTAGAGTATACT 58.986 45.833 18.24 4.68 0.00 2.12
849 906 0.736053 CGTCCAGAGTCTAGCTCCAC 59.264 60.000 9.65 0.00 45.21 4.02
854 911 2.114616 CAGAGTCTAGCTCCACCCATT 58.885 52.381 9.65 0.00 45.21 3.16
855 912 3.300388 CAGAGTCTAGCTCCACCCATTA 58.700 50.000 9.65 0.00 45.21 1.90
856 913 3.320541 CAGAGTCTAGCTCCACCCATTAG 59.679 52.174 9.65 0.00 45.21 1.73
857 914 2.036604 GAGTCTAGCTCCACCCATTAGC 59.963 54.545 0.00 0.00 38.27 3.09
858 915 1.762957 GTCTAGCTCCACCCATTAGCA 59.237 52.381 0.00 0.00 38.75 3.49
908 965 1.822371 ACGAGCTTCTCTTTCTCCTCC 59.178 52.381 0.00 0.00 0.00 4.30
910 967 2.099098 CGAGCTTCTCTTTCTCCTCCTC 59.901 54.545 0.00 0.00 0.00 3.71
911 968 2.099098 GAGCTTCTCTTTCTCCTCCTCG 59.901 54.545 0.00 0.00 0.00 4.63
912 969 1.136110 GCTTCTCTTTCTCCTCCTCGG 59.864 57.143 0.00 0.00 0.00 4.63
913 970 1.754226 CTTCTCTTTCTCCTCCTCGGG 59.246 57.143 0.00 0.00 0.00 5.14
935 996 0.034477 CAGGGTAATTGGCCGGAGTT 60.034 55.000 5.05 0.00 0.00 3.01
936 997 0.034477 AGGGTAATTGGCCGGAGTTG 60.034 55.000 5.05 0.00 0.00 3.16
937 998 0.034863 GGGTAATTGGCCGGAGTTGA 60.035 55.000 5.05 0.00 0.00 3.18
938 999 1.614850 GGGTAATTGGCCGGAGTTGAA 60.615 52.381 5.05 0.00 0.00 2.69
960 1021 3.876589 GAAGCCGGCGGTGAAGACA 62.877 63.158 28.82 0.00 0.00 3.41
966 1036 2.432628 GCGGTGAAGACACGAGGG 60.433 66.667 0.00 0.00 46.77 4.30
986 1056 3.474600 GGGGATCATCAGTTCATCACAG 58.525 50.000 0.00 0.00 0.00 3.66
994 1064 5.126061 TCATCAGTTCATCACAGAGATCGAA 59.874 40.000 0.00 0.00 33.72 3.71
996 1066 3.545475 CAGTTCATCACAGAGATCGAACG 59.455 47.826 12.75 0.00 42.74 3.95
1204 1276 6.349300 GCCAGTCACCATTAATCTTCTTCTA 58.651 40.000 0.00 0.00 0.00 2.10
1215 1290 1.291335 TCTTCTTCTACCTCCCCTCCC 59.709 57.143 0.00 0.00 0.00 4.30
1238 1313 1.956170 CGTGTTCTCGGCTGTGCTT 60.956 57.895 0.00 0.00 0.00 3.91
1240 1315 1.664649 TGTTCTCGGCTGTGCTTCG 60.665 57.895 0.00 0.00 0.00 3.79
1304 1379 2.285144 AACTACCTCCACCCGGGG 60.285 66.667 27.92 12.73 37.22 5.73
1499 1574 1.630244 CCAAGAAGAAGGCTGTCGCG 61.630 60.000 0.00 0.00 36.88 5.87
1500 1575 1.374758 AAGAAGAAGGCTGTCGCGG 60.375 57.895 6.13 0.00 36.88 6.46
1501 1576 1.816863 AAGAAGAAGGCTGTCGCGGA 61.817 55.000 6.13 0.00 36.88 5.54
1503 1578 3.302347 AAGAAGGCTGTCGCGGAGG 62.302 63.158 6.13 0.00 36.88 4.30
1661 1751 1.066114 CGTCGGTGAGCGAAGAGAAC 61.066 60.000 14.37 0.00 0.00 3.01
1700 1790 3.071837 TGCTCCGCCGTGGACATA 61.072 61.111 0.00 0.00 43.74 2.29
1709 1799 0.179100 CCGTGGACATAGACCAGCTG 60.179 60.000 6.78 6.78 38.14 4.24
1724 1814 1.086067 AGCTGTGGAATGACATCGCG 61.086 55.000 0.00 0.00 0.00 5.87
1788 1881 4.117372 GAAACGTCGCTGTCGCCG 62.117 66.667 0.00 0.00 35.26 6.46
1859 1952 1.139095 GTGGAGGATCGACGACCAC 59.861 63.158 16.64 16.64 42.83 4.16
1877 1970 5.464030 ACCACGAGTACTACAACAAGATT 57.536 39.130 0.00 0.00 0.00 2.40
1903 1996 1.895798 ACACGCTCTGAATTGAGAGGA 59.104 47.619 21.41 0.00 40.04 3.71
1907 2000 5.111989 CACGCTCTGAATTGAGAGGATTTA 58.888 41.667 21.41 0.00 40.04 1.40
1937 2030 6.249260 CGTTTCTCTTGTTGTTCTTGTTCTTG 59.751 38.462 0.00 0.00 0.00 3.02
1938 2031 7.305474 GTTTCTCTTGTTGTTCTTGTTCTTGA 58.695 34.615 0.00 0.00 0.00 3.02
1939 2032 7.630242 TTCTCTTGTTGTTCTTGTTCTTGAT 57.370 32.000 0.00 0.00 0.00 2.57
1940 2033 7.630242 TCTCTTGTTGTTCTTGTTCTTGATT 57.370 32.000 0.00 0.00 0.00 2.57
2043 2147 9.967346 GTTGTGAGATTATATTAGTGACAGCTA 57.033 33.333 0.00 0.00 0.00 3.32
2045 2149 8.300286 TGTGAGATTATATTAGTGACAGCTAGC 58.700 37.037 6.62 6.62 0.00 3.42
2047 2151 9.083422 TGAGATTATATTAGTGACAGCTAGCTT 57.917 33.333 16.46 6.82 0.00 3.74
2052 2156 9.667107 TTATATTAGTGACAGCTAGCTTTTTGT 57.333 29.630 16.46 11.11 0.00 2.83
2103 2211 6.600882 ATTTCTGGAGAATCTGTTGCAAAT 57.399 33.333 0.00 0.00 33.54 2.32
2105 2213 7.523293 TTTCTGGAGAATCTGTTGCAAATTA 57.477 32.000 0.00 0.00 33.54 1.40
2189 2299 5.695818 ACAAATATTGTTCTTCCGTTTCGG 58.304 37.500 1.45 1.45 44.89 4.30
2226 2338 3.916035 TCTCCGGCCTCTGCATATATAT 58.084 45.455 0.00 0.00 40.13 0.86
2227 2339 4.290093 TCTCCGGCCTCTGCATATATATT 58.710 43.478 0.00 0.00 40.13 1.28
2228 2340 4.716784 TCTCCGGCCTCTGCATATATATTT 59.283 41.667 0.00 0.00 40.13 1.40
2229 2341 5.023533 TCCGGCCTCTGCATATATATTTC 57.976 43.478 0.00 0.00 40.13 2.17
2231 2343 5.045942 TCCGGCCTCTGCATATATATTTCAA 60.046 40.000 0.00 0.00 40.13 2.69
2232 2344 5.065218 CCGGCCTCTGCATATATATTTCAAC 59.935 44.000 0.00 0.00 40.13 3.18
2233 2345 5.643348 CGGCCTCTGCATATATATTTCAACA 59.357 40.000 0.00 0.00 40.13 3.33
2234 2346 6.183360 CGGCCTCTGCATATATATTTCAACAG 60.183 42.308 0.00 0.00 40.13 3.16
2235 2347 6.881065 GGCCTCTGCATATATATTTCAACAGA 59.119 38.462 0.00 1.79 40.13 3.41
2236 2348 7.555554 GGCCTCTGCATATATATTTCAACAGAT 59.444 37.037 0.00 0.00 40.13 2.90
2238 2350 9.107177 CCTCTGCATATATATTTCAACAGATCC 57.893 37.037 0.00 0.00 32.89 3.36
2239 2351 9.887629 CTCTGCATATATATTTCAACAGATCCT 57.112 33.333 0.00 0.00 32.89 3.24
2243 2355 9.565213 GCATATATATTTCAACAGATCCTTTGC 57.435 33.333 0.00 0.00 0.00 3.68
2247 2359 7.893124 ATATTTCAACAGATCCTTTGCATCT 57.107 32.000 0.00 0.00 0.00 2.90
2248 2360 8.985315 ATATTTCAACAGATCCTTTGCATCTA 57.015 30.769 0.00 0.00 0.00 1.98
2249 2361 7.893124 ATTTCAACAGATCCTTTGCATCTAT 57.107 32.000 0.00 0.00 0.00 1.98
2250 2362 8.985315 ATTTCAACAGATCCTTTGCATCTATA 57.015 30.769 0.00 0.00 0.00 1.31
2251 2363 7.792374 TTCAACAGATCCTTTGCATCTATAC 57.208 36.000 0.00 0.00 0.00 1.47
2252 2364 5.985530 TCAACAGATCCTTTGCATCTATACG 59.014 40.000 0.00 0.00 0.00 3.06
2254 2366 5.533482 ACAGATCCTTTGCATCTATACGTC 58.467 41.667 0.00 0.00 0.00 4.34
2255 2367 5.303078 ACAGATCCTTTGCATCTATACGTCT 59.697 40.000 0.00 0.00 0.00 4.18
2256 2368 5.632764 CAGATCCTTTGCATCTATACGTCTG 59.367 44.000 0.00 0.00 0.00 3.51
2272 2567 2.159572 CGTCTGCGTTTAAATCCAAGGG 60.160 50.000 0.00 0.00 0.00 3.95
2284 2579 2.963599 TCCAAGGGTGGGTAAGAAAC 57.036 50.000 0.00 0.00 46.01 2.78
2288 2583 3.901222 CCAAGGGTGGGTAAGAAACATTT 59.099 43.478 0.00 0.00 41.77 2.32
2289 2584 4.021456 CCAAGGGTGGGTAAGAAACATTTC 60.021 45.833 0.00 0.00 41.77 2.17
2408 2838 2.669808 TTCGCGCATTTTTGCACGGT 62.670 50.000 8.75 0.00 40.28 4.83
2419 2849 6.970043 GCATTTTTGCACGGTTAGATATTACA 59.030 34.615 0.00 0.00 34.41 2.41
2449 2879 9.400638 CGCAAAGTGAAAAATGGTATAACTTTA 57.599 29.630 0.00 0.00 35.30 1.85
2468 2898 2.780065 AACGGTAGATATACGCGCAA 57.220 45.000 5.73 0.00 0.00 4.85
2622 3058 5.338365 CAACTTGCTAGATCAAAAGATGCC 58.662 41.667 1.04 0.00 0.00 4.40
2676 3112 3.825328 AGCAAGGAAGAAGCAAGAAGAA 58.175 40.909 0.00 0.00 0.00 2.52
2683 3119 4.503991 GGAAGAAGCAAGAAGAAGAGACCA 60.504 45.833 0.00 0.00 0.00 4.02
2685 3121 2.849294 AGCAAGAAGAAGAGACCACC 57.151 50.000 0.00 0.00 0.00 4.61
2686 3122 2.050144 AGCAAGAAGAAGAGACCACCA 58.950 47.619 0.00 0.00 0.00 4.17
2687 3123 2.641815 AGCAAGAAGAAGAGACCACCAT 59.358 45.455 0.00 0.00 0.00 3.55
2688 3124 2.746362 GCAAGAAGAAGAGACCACCATG 59.254 50.000 0.00 0.00 0.00 3.66
2689 3125 2.746362 CAAGAAGAAGAGACCACCATGC 59.254 50.000 0.00 0.00 0.00 4.06
2690 3126 1.980765 AGAAGAAGAGACCACCATGCA 59.019 47.619 0.00 0.00 0.00 3.96
2691 3127 2.575279 AGAAGAAGAGACCACCATGCAT 59.425 45.455 0.00 0.00 0.00 3.96
2692 3128 2.706339 AGAAGAGACCACCATGCATC 57.294 50.000 0.00 0.00 0.00 3.91
2693 3129 1.911357 AGAAGAGACCACCATGCATCA 59.089 47.619 0.00 0.00 0.00 3.07
2694 3130 2.508716 AGAAGAGACCACCATGCATCAT 59.491 45.455 0.00 0.00 0.00 2.45
2695 3131 2.634815 AGAGACCACCATGCATCATC 57.365 50.000 0.00 0.00 0.00 2.92
2696 3132 1.142465 AGAGACCACCATGCATCATCC 59.858 52.381 0.00 0.00 0.00 3.51
2697 3133 0.184451 AGACCACCATGCATCATCCC 59.816 55.000 0.00 0.00 0.00 3.85
2698 3134 0.106569 GACCACCATGCATCATCCCA 60.107 55.000 0.00 0.00 0.00 4.37
2708 3144 1.325355 CATCATCCCATTGTGGAGGC 58.675 55.000 0.00 0.00 40.96 4.70
2735 3171 5.452078 TTCCAACTTTTCATCATGTCCAC 57.548 39.130 0.00 0.00 0.00 4.02
2736 3172 3.826157 TCCAACTTTTCATCATGTCCACC 59.174 43.478 0.00 0.00 0.00 4.61
2751 3187 0.745845 CCACCTCTGCCTTTCCATCG 60.746 60.000 0.00 0.00 0.00 3.84
2782 3218 3.317430 GCCTGTTCAAATCCCATCTGATC 59.683 47.826 0.00 0.00 0.00 2.92
2798 3234 6.312426 CCATCTGATCACAGTACTCTTTTCAC 59.688 42.308 0.00 0.00 43.81 3.18
2864 3314 2.568090 CATGGGCGCCAGTGAAAC 59.432 61.111 30.85 9.47 36.75 2.78
2898 3348 5.651387 TCTCCTATTTCTGTCACTCACTG 57.349 43.478 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.925483 TGCCAAGTTATACCAAATTTCATATGC 59.075 33.333 0.00 0.00 0.00 3.14
5 6 9.814899 TTGCCAAGTTATACCAAATTTCATATG 57.185 29.630 0.00 0.00 0.00 1.78
8 9 9.566432 TTTTTGCCAAGTTATACCAAATTTCAT 57.434 25.926 0.00 0.00 0.00 2.57
9 10 8.964476 TTTTTGCCAAGTTATACCAAATTTCA 57.036 26.923 0.00 0.00 0.00 2.69
65 66 9.255304 GCCATCTTGACAACTTTTATAACAAAA 57.745 29.630 0.00 0.00 0.00 2.44
66 67 7.593273 CGCCATCTTGACAACTTTTATAACAAA 59.407 33.333 0.00 0.00 0.00 2.83
67 68 7.081349 CGCCATCTTGACAACTTTTATAACAA 58.919 34.615 0.00 0.00 0.00 2.83
68 69 6.348950 CCGCCATCTTGACAACTTTTATAACA 60.349 38.462 0.00 0.00 0.00 2.41
69 70 6.027749 CCGCCATCTTGACAACTTTTATAAC 58.972 40.000 0.00 0.00 0.00 1.89
70 71 5.941058 TCCGCCATCTTGACAACTTTTATAA 59.059 36.000 0.00 0.00 0.00 0.98
71 72 5.353123 GTCCGCCATCTTGACAACTTTTATA 59.647 40.000 0.00 0.00 0.00 0.98
72 73 4.156008 GTCCGCCATCTTGACAACTTTTAT 59.844 41.667 0.00 0.00 0.00 1.40
73 74 3.500680 GTCCGCCATCTTGACAACTTTTA 59.499 43.478 0.00 0.00 0.00 1.52
74 75 2.293399 GTCCGCCATCTTGACAACTTTT 59.707 45.455 0.00 0.00 0.00 2.27
75 76 1.880027 GTCCGCCATCTTGACAACTTT 59.120 47.619 0.00 0.00 0.00 2.66
76 77 1.202758 TGTCCGCCATCTTGACAACTT 60.203 47.619 0.00 0.00 36.16 2.66
77 78 0.396435 TGTCCGCCATCTTGACAACT 59.604 50.000 0.00 0.00 36.16 3.16
78 79 0.517316 GTGTCCGCCATCTTGACAAC 59.483 55.000 0.00 0.00 40.41 3.32
79 80 0.107643 TGTGTCCGCCATCTTGACAA 59.892 50.000 0.00 0.00 40.41 3.18
80 81 0.107643 TTGTGTCCGCCATCTTGACA 59.892 50.000 0.00 0.00 36.71 3.58
81 82 1.234821 TTTGTGTCCGCCATCTTGAC 58.765 50.000 0.00 0.00 0.00 3.18
82 83 2.198827 ATTTGTGTCCGCCATCTTGA 57.801 45.000 0.00 0.00 0.00 3.02
83 84 3.793129 GCATATTTGTGTCCGCCATCTTG 60.793 47.826 0.00 0.00 0.00 3.02
84 85 2.358898 GCATATTTGTGTCCGCCATCTT 59.641 45.455 0.00 0.00 0.00 2.40
85 86 1.949525 GCATATTTGTGTCCGCCATCT 59.050 47.619 0.00 0.00 0.00 2.90
86 87 1.675483 TGCATATTTGTGTCCGCCATC 59.325 47.619 0.00 0.00 0.00 3.51
87 88 1.761449 TGCATATTTGTGTCCGCCAT 58.239 45.000 0.00 0.00 0.00 4.40
88 89 1.539157 TTGCATATTTGTGTCCGCCA 58.461 45.000 0.00 0.00 0.00 5.69
89 90 2.258755 GTTTGCATATTTGTGTCCGCC 58.741 47.619 0.00 0.00 0.00 6.13
90 91 1.910819 CGTTTGCATATTTGTGTCCGC 59.089 47.619 0.00 0.00 0.00 5.54
91 92 3.463533 TCGTTTGCATATTTGTGTCCG 57.536 42.857 0.00 0.00 0.00 4.79
92 93 5.219633 AGTTTCGTTTGCATATTTGTGTCC 58.780 37.500 0.00 0.00 0.00 4.02
93 94 6.747659 AAGTTTCGTTTGCATATTTGTGTC 57.252 33.333 0.00 0.00 0.00 3.67
94 95 8.810652 ATTAAGTTTCGTTTGCATATTTGTGT 57.189 26.923 0.00 0.00 0.00 3.72
120 121 9.720769 ACTCTATCTTTTGAAACGGAAATCTAA 57.279 29.630 0.00 0.00 0.00 2.10
178 179 4.224991 TGCATGAGTCATCCATCTCAAA 57.775 40.909 1.56 0.00 42.67 2.69
179 180 3.918294 TGCATGAGTCATCCATCTCAA 57.082 42.857 1.56 0.00 42.67 3.02
268 277 3.061429 GTCGAGAAAAGAGATTCTTGCCG 59.939 47.826 0.00 0.00 39.70 5.69
295 304 6.881602 TGGTTTTTGGTTTTGTTGAGCTAATT 59.118 30.769 0.00 0.00 0.00 1.40
305 314 3.771577 TGGTGTGGTTTTTGGTTTTGT 57.228 38.095 0.00 0.00 0.00 2.83
319 328 3.125146 CACATGATTCGGTAGTTGGTGTG 59.875 47.826 0.00 0.00 0.00 3.82
339 348 1.201987 ACGCACGAAAACTCAACACAC 60.202 47.619 0.00 0.00 0.00 3.82
386 395 5.446143 TGATACAACCGCACAAGATTTTT 57.554 34.783 0.00 0.00 0.00 1.94
390 417 2.009774 GCTGATACAACCGCACAAGAT 58.990 47.619 0.00 0.00 0.00 2.40
434 461 6.540189 CGATTTTTCTTCACCATGGAGTCTAT 59.460 38.462 21.47 0.00 0.00 1.98
438 465 4.651778 TCGATTTTTCTTCACCATGGAGT 58.348 39.130 21.47 0.00 0.00 3.85
439 466 5.627499 TTCGATTTTTCTTCACCATGGAG 57.373 39.130 21.47 11.61 0.00 3.86
445 472 5.163713 CCTCCTGATTCGATTTTTCTTCACC 60.164 44.000 0.00 0.00 0.00 4.02
520 551 0.311790 CTGTTCATTGCCTTGCGTGT 59.688 50.000 0.00 0.00 0.00 4.49
523 554 2.642139 AATCTGTTCATTGCCTTGCG 57.358 45.000 0.00 0.00 0.00 4.85
540 571 1.188863 GCCATGCCAAGGTCTCAAAT 58.811 50.000 0.00 0.00 0.00 2.32
587 632 2.110967 CCAGCTGCCTGTCAATCGG 61.111 63.158 8.66 0.00 37.38 4.18
610 655 3.380320 TCGTGACACCATAGTCCATACTG 59.620 47.826 0.00 0.00 37.73 2.74
613 658 2.956333 CCTCGTGACACCATAGTCCATA 59.044 50.000 0.00 0.00 37.73 2.74
614 659 1.757118 CCTCGTGACACCATAGTCCAT 59.243 52.381 0.00 0.00 37.73 3.41
615 660 1.182667 CCTCGTGACACCATAGTCCA 58.817 55.000 0.00 0.00 37.73 4.02
616 661 0.179108 GCCTCGTGACACCATAGTCC 60.179 60.000 0.00 0.00 37.73 3.85
617 662 0.530744 TGCCTCGTGACACCATAGTC 59.469 55.000 0.00 0.00 38.99 2.59
618 663 0.246635 GTGCCTCGTGACACCATAGT 59.753 55.000 0.00 0.00 0.00 2.12
619 664 0.802222 CGTGCCTCGTGACACCATAG 60.802 60.000 0.00 0.00 33.09 2.23
671 716 1.544246 TGGATCCGGTACAGATATGCG 59.456 52.381 7.39 0.00 0.00 4.73
776 833 0.755686 ACTCTACTGCTAGCCATGGC 59.244 55.000 30.12 30.12 42.33 4.40
777 834 5.013547 AGTATACTCTACTGCTAGCCATGG 58.986 45.833 13.29 7.63 0.00 3.66
798 855 7.994334 CCGGGTTATATATAGAGCTAAGAGAGT 59.006 40.741 0.00 0.00 0.00 3.24
799 856 7.994334 ACCGGGTTATATATAGAGCTAAGAGAG 59.006 40.741 6.32 0.00 0.00 3.20
800 857 7.774157 CACCGGGTTATATATAGAGCTAAGAGA 59.226 40.741 6.32 0.00 0.00 3.10
849 906 4.197750 GAGATGGATGCTATGCTAATGGG 58.802 47.826 0.00 0.00 0.00 4.00
854 911 1.827344 CCGGAGATGGATGCTATGCTA 59.173 52.381 0.00 0.00 0.00 3.49
855 912 0.612229 CCGGAGATGGATGCTATGCT 59.388 55.000 0.00 0.00 0.00 3.79
856 913 1.023513 GCCGGAGATGGATGCTATGC 61.024 60.000 5.05 0.00 0.00 3.14
857 914 0.392193 GGCCGGAGATGGATGCTATG 60.392 60.000 5.05 0.00 0.00 2.23
858 915 0.837691 TGGCCGGAGATGGATGCTAT 60.838 55.000 5.05 0.00 0.00 2.97
908 965 2.017113 GCCAATTACCCTGAACCCGAG 61.017 57.143 0.00 0.00 0.00 4.63
910 967 1.035385 GGCCAATTACCCTGAACCCG 61.035 60.000 0.00 0.00 0.00 5.28
911 968 1.035385 CGGCCAATTACCCTGAACCC 61.035 60.000 2.24 0.00 0.00 4.11
912 969 1.035385 CCGGCCAATTACCCTGAACC 61.035 60.000 2.24 0.00 0.00 3.62
913 970 0.034863 TCCGGCCAATTACCCTGAAC 60.035 55.000 2.24 0.00 0.00 3.18
935 996 4.735132 CCGCCGGCTTCGTCTTCA 62.735 66.667 26.68 0.00 0.00 3.02
936 997 4.736896 ACCGCCGGCTTCGTCTTC 62.737 66.667 26.68 0.00 0.00 2.87
953 1014 0.252057 TGATCCCCCTCGTGTCTTCA 60.252 55.000 0.00 0.00 0.00 3.02
960 1021 1.123928 GAACTGATGATCCCCCTCGT 58.876 55.000 0.00 0.00 0.00 4.18
966 1036 4.100653 TCTCTGTGATGAACTGATGATCCC 59.899 45.833 0.00 0.00 36.30 3.85
986 1056 0.460284 ACACATGGCCGTTCGATCTC 60.460 55.000 0.00 0.00 0.00 2.75
994 1064 1.234821 CTGTTGTTACACATGGCCGT 58.765 50.000 0.00 0.00 0.00 5.68
996 1066 0.109781 CGCTGTTGTTACACATGGCC 60.110 55.000 0.00 0.00 0.00 5.36
1501 1576 3.673597 TGGTCGAGGAGGAGGCCT 61.674 66.667 3.86 3.86 42.17 5.19
1503 1578 3.827898 CGTGGTCGAGGAGGAGGC 61.828 72.222 0.00 0.00 39.71 4.70
1526 1610 2.202324 GAGCAGGTCGTCGTCGTC 60.202 66.667 1.33 0.00 38.33 4.20
1602 1689 0.108992 TCGTCGTCCATGCTTGTACC 60.109 55.000 0.00 0.00 0.00 3.34
1603 1690 1.269166 CTCGTCGTCCATGCTTGTAC 58.731 55.000 0.00 0.00 0.00 2.90
1607 1694 2.125512 GCCTCGTCGTCCATGCTT 60.126 61.111 0.00 0.00 0.00 3.91
1648 1738 0.667487 CGCCTTGTTCTCTTCGCTCA 60.667 55.000 0.00 0.00 0.00 4.26
1655 1745 1.674057 CACCTCCGCCTTGTTCTCT 59.326 57.895 0.00 0.00 0.00 3.10
1661 1751 4.641645 TGCACCACCTCCGCCTTG 62.642 66.667 0.00 0.00 0.00 3.61
1700 1790 1.059098 TGTCATTCCACAGCTGGTCT 58.941 50.000 19.93 0.00 38.90 3.85
1709 1799 2.709475 GCCGCGATGTCATTCCAC 59.291 61.111 8.23 0.00 0.00 4.02
1724 1814 3.902086 GGGTAGCTCTCCGACGCC 61.902 72.222 0.00 0.00 0.00 5.68
1764 1854 3.986006 AGCGACGTTTCCGGCTGA 61.986 61.111 0.00 0.00 41.07 4.26
1791 1884 4.873129 CGACGATGGCTCCACGGG 62.873 72.222 12.78 0.00 0.00 5.28
1859 1952 7.328493 TGTTGATCAATCTTGTTGTAGTACTCG 59.672 37.037 12.12 0.00 0.00 4.18
1877 1970 3.663025 TCAATTCAGAGCGTGTTGATCA 58.337 40.909 0.00 0.00 34.70 2.92
1907 2000 7.758495 ACAAGAACAACAAGAGAAACGTAATT 58.242 30.769 0.00 0.00 0.00 1.40
2014 2118 9.175060 CTGTCACTAATATAATCTCACAACTCG 57.825 37.037 0.00 0.00 0.00 4.18
2043 2147 2.965572 ACACATGTGCACAAAAAGCT 57.034 40.000 25.72 2.45 0.00 3.74
2044 2148 4.111916 ACTTACACATGTGCACAAAAAGC 58.888 39.130 25.72 0.00 0.00 3.51
2045 2149 5.339177 TGACTTACACATGTGCACAAAAAG 58.661 37.500 25.72 21.77 0.00 2.27
2047 2151 4.972514 TGACTTACACATGTGCACAAAA 57.027 36.364 25.72 11.93 0.00 2.44
2138 2248 9.035607 TCATCGATTAATTAAGCAGAAGAGAAC 57.964 33.333 13.48 0.00 0.00 3.01
2144 2254 8.716646 TTGTCTCATCGATTAATTAAGCAGAA 57.283 30.769 13.48 0.00 0.00 3.02
2189 2299 4.083961 GCCGGAGAACTAGTTGACTTTTTC 60.084 45.833 14.14 0.00 0.00 2.29
2226 2338 7.011389 CGTATAGATGCAAAGGATCTGTTGAAA 59.989 37.037 10.72 1.83 32.32 2.69
2227 2339 6.479990 CGTATAGATGCAAAGGATCTGTTGAA 59.520 38.462 10.72 3.26 32.32 2.69
2228 2340 5.985530 CGTATAGATGCAAAGGATCTGTTGA 59.014 40.000 10.72 0.00 32.32 3.18
2229 2341 5.755375 ACGTATAGATGCAAAGGATCTGTTG 59.245 40.000 10.72 0.00 32.32 3.33
2231 2343 5.303078 AGACGTATAGATGCAAAGGATCTGT 59.697 40.000 10.72 7.07 32.32 3.41
2232 2344 5.632764 CAGACGTATAGATGCAAAGGATCTG 59.367 44.000 10.72 0.00 32.32 2.90
2233 2345 5.777802 CAGACGTATAGATGCAAAGGATCT 58.222 41.667 6.29 6.29 34.47 2.75
2234 2346 4.387256 GCAGACGTATAGATGCAAAGGATC 59.613 45.833 0.00 0.00 36.56 3.36
2235 2347 4.310769 GCAGACGTATAGATGCAAAGGAT 58.689 43.478 0.00 0.00 36.56 3.24
2236 2348 3.717707 GCAGACGTATAGATGCAAAGGA 58.282 45.455 0.00 0.00 36.56 3.36
2238 2350 3.760264 CGCAGACGTATAGATGCAAAG 57.240 47.619 0.00 0.00 36.42 2.77
2252 2364 2.817844 ACCCTTGGATTTAAACGCAGAC 59.182 45.455 0.00 0.00 0.00 3.51
2254 2366 3.216147 CACCCTTGGATTTAAACGCAG 57.784 47.619 0.00 0.00 0.00 5.18
2270 2565 5.738619 AATGAAATGTTTCTTACCCACCC 57.261 39.130 6.99 0.00 38.02 4.61
2272 2567 7.441836 AGGAAAATGAAATGTTTCTTACCCAC 58.558 34.615 6.99 0.00 38.02 4.61
2346 2776 8.966868 GGTTGAATAAATATCAAGTTCTCCCAA 58.033 33.333 0.00 0.00 37.46 4.12
2347 2777 8.336235 AGGTTGAATAAATATCAAGTTCTCCCA 58.664 33.333 0.00 0.00 37.46 4.37
2348 2778 8.753497 AGGTTGAATAAATATCAAGTTCTCCC 57.247 34.615 0.00 0.00 37.46 4.30
2408 2838 6.103330 TCACTTTGCGCTGTGTAATATCTAA 58.897 36.000 21.20 0.00 35.82 2.10
2419 2849 2.159114 ACCATTTTTCACTTTGCGCTGT 60.159 40.909 9.73 1.72 0.00 4.40
2449 2879 2.780065 TTGCGCGTATATCTACCGTT 57.220 45.000 8.43 0.00 0.00 4.44
2547 2978 4.637387 TTGGATTCCCATGCAATTTTGT 57.363 36.364 0.00 0.00 43.12 2.83
2548 2979 5.186942 TCATTGGATTCCCATGCAATTTTG 58.813 37.500 11.13 0.00 46.32 2.44
2622 3058 2.071262 AGCTGGCCTCCTGATCTGG 61.071 63.158 12.30 12.30 0.00 3.86
2676 3112 1.142465 GGATGATGCATGGTGGTCTCT 59.858 52.381 2.46 0.00 0.00 3.10
2683 3119 2.036387 CACAATGGGATGATGCATGGT 58.964 47.619 2.46 0.00 0.00 3.55
2685 3121 2.296190 CTCCACAATGGGATGATGCATG 59.704 50.000 2.46 0.00 38.32 4.06
2686 3122 2.594131 CTCCACAATGGGATGATGCAT 58.406 47.619 0.00 0.00 38.32 3.96
2687 3123 1.410507 CCTCCACAATGGGATGATGCA 60.411 52.381 0.00 0.00 38.32 3.96
2688 3124 1.325355 CCTCCACAATGGGATGATGC 58.675 55.000 0.00 0.00 38.32 3.91
2689 3125 1.325355 GCCTCCACAATGGGATGATG 58.675 55.000 0.00 0.00 38.32 3.07
2690 3126 0.186873 GGCCTCCACAATGGGATGAT 59.813 55.000 0.00 0.00 38.32 2.45
2691 3127 0.920763 AGGCCTCCACAATGGGATGA 60.921 55.000 0.00 0.00 38.32 2.92
2692 3128 0.466922 GAGGCCTCCACAATGGGATG 60.467 60.000 23.19 0.00 38.32 3.51
2693 3129 0.625683 AGAGGCCTCCACAATGGGAT 60.626 55.000 29.54 3.28 38.32 3.85
2694 3130 0.846427 AAGAGGCCTCCACAATGGGA 60.846 55.000 29.54 0.00 38.32 4.37
2695 3131 0.040204 AAAGAGGCCTCCACAATGGG 59.960 55.000 29.54 0.00 38.32 4.00
2696 3132 1.467920 GAAAGAGGCCTCCACAATGG 58.532 55.000 29.54 0.00 39.43 3.16
2697 3133 1.272092 TGGAAAGAGGCCTCCACAATG 60.272 52.381 29.54 0.00 36.79 2.82
2698 3134 1.075601 TGGAAAGAGGCCTCCACAAT 58.924 50.000 29.54 7.47 36.79 2.71
2708 3144 6.336842 ACATGATGAAAAGTTGGAAAGAGG 57.663 37.500 0.00 0.00 0.00 3.69
2735 3171 0.813210 GAGCGATGGAAAGGCAGAGG 60.813 60.000 0.00 0.00 0.00 3.69
2736 3172 0.813210 GGAGCGATGGAAAGGCAGAG 60.813 60.000 0.00 0.00 0.00 3.35
2782 3218 4.369182 ACGAAGGTGAAAAGAGTACTGTG 58.631 43.478 0.00 0.00 0.00 3.66
2798 3234 1.160329 GGATCGGCCATTGACGAAGG 61.160 60.000 2.24 0.00 42.88 3.46
2864 3314 8.503458 ACAGAAATAGGAGATGTGATTTTCAG 57.497 34.615 0.00 0.00 0.00 3.02
2866 3316 8.394121 GTGACAGAAATAGGAGATGTGATTTTC 58.606 37.037 0.00 0.00 0.00 2.29
2874 3324 6.041511 CAGTGAGTGACAGAAATAGGAGATG 58.958 44.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.