Multiple sequence alignment - TraesCS2A01G560000

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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 TraesCS2A01G560000 chr2A 100.000 3750 0 0 1 3750 762589249 762592998 0.000000e+00 6926.0
1 TraesCS2A01G560000 chr2A 99.310 869 5 1 2882 3750 718829053 718828186 0.000000e+00 1570.0
2 TraesCS2A01G560000 chr2A 84.420 1380 133 33 391 1749 762567361 762568679 0.000000e+00 1282.0
3 TraesCS2A01G560000 chr2A 86.041 874 116 4 1944 2815 762568759 762569628 0.000000e+00 933.0
4 TraesCS2A01G560000 chr2A 77.341 534 74 24 1257 1767 762618773 762619282 4.770000e-69 272.0
5 TraesCS2A01G560000 chr2A 83.796 216 17 12 471 682 762602574 762602775 4.940000e-44 189.0
6 TraesCS2A01G560000 chr2A 94.828 116 6 0 1944 2059 762555323 762555438 8.270000e-42 182.0
7 TraesCS2A01G560000 chr2A 80.377 265 26 12 1488 1730 762554986 762555246 1.070000e-40 178.0
8 TraesCS2A01G560000 chr2A 88.506 87 9 1 1773 1859 40430421 40430336 1.840000e-18 104.0
9 TraesCS2A01G560000 chr2A 89.091 55 6 0 630 684 762601592 762601646 6.720000e-08 69.4
10 TraesCS2A01G560000 chr7B 99.194 869 7 0 2882 3750 254460030 254460898 0.000000e+00 1567.0
11 TraesCS2A01G560000 chr7B 99.194 869 7 0 2882 3750 614405259 614406127 0.000000e+00 1567.0
12 TraesCS2A01G560000 chr7B 99.194 869 6 1 2882 3750 399865477 399864610 0.000000e+00 1565.0
13 TraesCS2A01G560000 chr2B 99.194 869 7 0 2882 3750 137449111 137448243 0.000000e+00 1567.0
14 TraesCS2A01G560000 chr2B 93.977 963 41 7 812 1774 794806132 794805187 0.000000e+00 1441.0
15 TraesCS2A01G560000 chr2B 86.940 804 32 20 1 785 794806878 794806129 0.000000e+00 835.0
16 TraesCS2A01G560000 chr2B 94.061 522 21 2 1857 2368 794805179 794804658 0.000000e+00 784.0
17 TraesCS2A01G560000 chr2B 81.946 781 123 10 1940 2706 794816928 794816152 0.000000e+00 645.0
18 TraesCS2A01G560000 chr2B 83.139 599 96 3 2160 2756 794865773 794865178 3.290000e-150 542.0
19 TraesCS2A01G560000 chr2B 80.471 722 87 31 1061 1770 794817650 794816971 1.550000e-138 503.0
20 TraesCS2A01G560000 chr2B 77.530 494 77 17 1270 1752 794785997 794786467 2.220000e-67 267.0
21 TraesCS2A01G560000 chr2B 81.944 144 15 3 634 773 794817922 794817786 1.100000e-20 111.0
22 TraesCS2A01G560000 chr6B 99.194 869 6 1 2882 3750 415788834 415787967 0.000000e+00 1565.0
23 TraesCS2A01G560000 chr6B 99.079 869 7 1 2882 3750 470818847 470817980 0.000000e+00 1559.0
24 TraesCS2A01G560000 chr4A 99.079 869 8 0 2882 3750 518797756 518796888 0.000000e+00 1561.0
25 TraesCS2A01G560000 chr4A 74.126 286 55 14 1428 1699 500636742 500636462 2.380000e-17 100.0
26 TraesCS2A01G560000 chr1B 98.855 873 10 0 2878 3750 453802443 453803315 0.000000e+00 1557.0
27 TraesCS2A01G560000 chrUn 93.892 966 42 7 809 1774 308959111 308960059 0.000000e+00 1441.0
28 TraesCS2A01G560000 chrUn 89.317 908 52 3 1979 2886 22333698 22334560 0.000000e+00 1098.0
29 TraesCS2A01G560000 chrUn 86.940 804 32 20 1 785 308958368 308959117 0.000000e+00 835.0
30 TraesCS2A01G560000 chrUn 94.423 520 26 3 2370 2886 347398605 347399124 0.000000e+00 797.0
31 TraesCS2A01G560000 chrUn 94.423 520 26 3 2370 2886 424658053 424657534 0.000000e+00 797.0
32 TraesCS2A01G560000 chrUn 94.220 519 20 2 1857 2365 308960067 308960585 0.000000e+00 784.0
33 TraesCS2A01G560000 chrUn 82.679 560 49 25 380 916 22332794 22333328 1.590000e-123 453.0
34 TraesCS2A01G560000 chrUn 79.592 490 66 19 1257 1735 24004066 24003600 1.680000e-83 320.0
35 TraesCS2A01G560000 chrUn 88.506 87 8 2 1773 1857 197752395 197752481 1.840000e-18 104.0
36 TraesCS2A01G560000 chrUn 93.617 47 3 0 1438 1484 22333650 22333696 1.870000e-08 71.3
37 TraesCS2A01G560000 chrUn 94.444 36 2 0 1060 1095 24004748 24004713 5.230000e-04 56.5
38 TraesCS2A01G560000 chr2D 83.357 1394 97 50 383 1749 637446285 637445000 0.000000e+00 1164.0
39 TraesCS2A01G560000 chr2D 89.251 828 50 7 2059 2886 381190730 381191518 0.000000e+00 1000.0
40 TraesCS2A01G560000 chr2D 86.803 879 109 5 1936 2811 637444914 637444040 0.000000e+00 974.0
41 TraesCS2A01G560000 chr2D 93.455 550 25 3 1228 1777 381190011 381190549 0.000000e+00 806.0
42 TraesCS2A01G560000 chr2D 79.061 831 140 24 1940 2756 637441827 637441017 1.180000e-149 540.0
43 TraesCS2A01G560000 chr2D 79.775 534 80 11 1257 1780 637442584 637442069 2.750000e-96 363.0
44 TraesCS2A01G560000 chr2D 83.459 399 29 14 490 872 381189408 381189785 1.670000e-88 337.0
45 TraesCS2A01G560000 chr2D 76.495 719 98 40 1061 1748 637505548 637504870 3.610000e-85 326.0
46 TraesCS2A01G560000 chr2D 94.975 199 10 0 987 1185 381189816 381190014 2.810000e-81 313.0
47 TraesCS2A01G560000 chr2D 91.892 185 5 6 1856 2030 381190550 381190734 2.240000e-62 250.0
48 TraesCS2A01G560000 chr2D 85.714 168 14 8 518 682 637443428 637443268 6.440000e-38 169.0
49 TraesCS2A01G560000 chr2D 83.333 126 19 2 1257 1381 637435619 637435495 8.510000e-22 115.0
50 TraesCS2A01G560000 chr3D 86.000 100 12 2 1772 1869 320635163 320635262 5.120000e-19 106.0
51 TraesCS2A01G560000 chr4D 88.506 87 8 2 1773 1857 213708328 213708414 1.840000e-18 104.0
52 TraesCS2A01G560000 chr4D 73.171 287 56 15 1428 1699 87955240 87954960 2.400000e-12 84.2
53 TraesCS2A01G560000 chr5D 88.372 86 8 2 1773 1856 49691488 49691403 6.630000e-18 102.0
54 TraesCS2A01G560000 chr5A 88.372 86 8 2 1773 1856 38998225 38998140 6.630000e-18 102.0
55 TraesCS2A01G560000 chr5A 88.372 86 8 2 1773 1856 39115285 39115200 6.630000e-18 102.0
56 TraesCS2A01G560000 chr1A 86.957 92 10 2 1773 1862 500986409 500986318 6.630000e-18 102.0
57 TraesCS2A01G560000 chr4B 86.957 92 9 3 1773 1863 538964047 538963958 2.380000e-17 100.0
58 TraesCS2A01G560000 chr4B 73.356 289 52 18 1428 1699 124503660 124503380 2.400000e-12 84.2
59 TraesCS2A01G560000 chr7A 82.979 94 11 5 1787 1878 674094027 674093937 3.100000e-11 80.5
60 TraesCS2A01G560000 chr6D 80.000 90 13 5 1793 1881 420536194 420536109 1.120000e-05 62.1


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 TraesCS2A01G560000 chr2A 762589249 762592998 3749 False 6926.000000 6926 100.000000 1 3750 1 chr2A.!!$F1 3749
1 TraesCS2A01G560000 chr2A 718828186 718829053 867 True 1570.000000 1570 99.310000 2882 3750 1 chr2A.!!$R2 868
2 TraesCS2A01G560000 chr2A 762567361 762569628 2267 False 1107.500000 1282 85.230500 391 2815 2 chr2A.!!$F4 2424
3 TraesCS2A01G560000 chr2A 762618773 762619282 509 False 272.000000 272 77.341000 1257 1767 1 chr2A.!!$F2 510
4 TraesCS2A01G560000 chr7B 254460030 254460898 868 False 1567.000000 1567 99.194000 2882 3750 1 chr7B.!!$F1 868
5 TraesCS2A01G560000 chr7B 614405259 614406127 868 False 1567.000000 1567 99.194000 2882 3750 1 chr7B.!!$F2 868
6 TraesCS2A01G560000 chr7B 399864610 399865477 867 True 1565.000000 1565 99.194000 2882 3750 1 chr7B.!!$R1 868
7 TraesCS2A01G560000 chr2B 137448243 137449111 868 True 1567.000000 1567 99.194000 2882 3750 1 chr2B.!!$R1 868
8 TraesCS2A01G560000 chr2B 794804658 794806878 2220 True 1020.000000 1441 91.659333 1 2368 3 chr2B.!!$R3 2367
9 TraesCS2A01G560000 chr2B 794865178 794865773 595 True 542.000000 542 83.139000 2160 2756 1 chr2B.!!$R2 596
10 TraesCS2A01G560000 chr2B 794816152 794817922 1770 True 419.666667 645 81.453667 634 2706 3 chr2B.!!$R4 2072
11 TraesCS2A01G560000 chr6B 415787967 415788834 867 True 1565.000000 1565 99.194000 2882 3750 1 chr6B.!!$R1 868
12 TraesCS2A01G560000 chr6B 470817980 470818847 867 True 1559.000000 1559 99.079000 2882 3750 1 chr6B.!!$R2 868
13 TraesCS2A01G560000 chr4A 518796888 518797756 868 True 1561.000000 1561 99.079000 2882 3750 1 chr4A.!!$R2 868
14 TraesCS2A01G560000 chr1B 453802443 453803315 872 False 1557.000000 1557 98.855000 2878 3750 1 chr1B.!!$F1 872
15 TraesCS2A01G560000 chrUn 308958368 308960585 2217 False 1020.000000 1441 91.684000 1 2365 3 chrUn.!!$F4 2364
16 TraesCS2A01G560000 chrUn 347398605 347399124 519 False 797.000000 797 94.423000 2370 2886 1 chrUn.!!$F2 516
17 TraesCS2A01G560000 chrUn 424657534 424658053 519 True 797.000000 797 94.423000 2370 2886 1 chrUn.!!$R1 516
18 TraesCS2A01G560000 chrUn 22332794 22334560 1766 False 540.766667 1098 88.537667 380 2886 3 chrUn.!!$F3 2506
19 TraesCS2A01G560000 chr2D 637441017 637446285 5268 True 642.000000 1164 82.942000 383 2811 5 chr2D.!!$R3 2428
20 TraesCS2A01G560000 chr2D 381189408 381191518 2110 False 541.200000 1000 90.606400 490 2886 5 chr2D.!!$F1 2396
21 TraesCS2A01G560000 chr2D 637504870 637505548 678 True 326.000000 326 76.495000 1061 1748 1 chr2D.!!$R2 687

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
275 277 0.469892 AAACCAGAGCAAACAGGGGG 60.470 55.0 0.00 0.00 0.00 5.40 F
1392 1487 0.244721 CTCAGTCGTGACCATGCTGA 59.755 55.0 12.35 12.35 35.29 4.26 F
2608 2772 0.110486 ATGAGGCGTGGTCAAACCTT 59.890 50.0 0.00 0.00 39.58 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1499 1.073722 CCAAGGGTCAGCTTGCTGA 59.926 57.895 19.87 19.87 0.00 4.26 R
2684 2848 0.034767 ACTGCATACACAGCCTGCAT 60.035 50.000 0.00 0.00 44.25 3.96 R
3649 6427 7.841915 TGTTGATGTTATTAATTCGAGCTCA 57.158 32.000 15.40 0.00 0.00 4.26 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
28 29 8.942338 AAGAAAGCACGAATATATTGTACTGA 57.058 30.769 1.78 0.00 0.00 3.41
59 60 4.023792 CAGTTGTTCATGTTAGCTGCTTCA 60.024 41.667 7.79 8.58 0.00 3.02
97 98 5.363101 TCTCTGCTATTGGTGATTAGCTTG 58.637 41.667 0.00 0.00 36.58 4.01
172 174 9.309516 ACATTATCTGAATTTTGATTGATGCAC 57.690 29.630 0.00 0.00 0.00 4.57
173 175 9.529325 CATTATCTGAATTTTGATTGATGCACT 57.471 29.630 0.00 0.00 0.00 4.40
174 176 8.920509 TTATCTGAATTTTGATTGATGCACTG 57.079 30.769 0.00 0.00 0.00 3.66
175 177 5.716094 TCTGAATTTTGATTGATGCACTGG 58.284 37.500 0.00 0.00 0.00 4.00
176 178 5.244402 TCTGAATTTTGATTGATGCACTGGT 59.756 36.000 0.00 0.00 0.00 4.00
177 179 6.433716 TCTGAATTTTGATTGATGCACTGGTA 59.566 34.615 0.00 0.00 0.00 3.25
178 180 6.623486 TGAATTTTGATTGATGCACTGGTAG 58.377 36.000 0.00 0.00 0.00 3.18
179 181 6.209192 TGAATTTTGATTGATGCACTGGTAGT 59.791 34.615 0.00 0.00 0.00 2.73
180 182 6.594788 ATTTTGATTGATGCACTGGTAGTT 57.405 33.333 0.00 0.00 0.00 2.24
181 183 5.627499 TTTGATTGATGCACTGGTAGTTC 57.373 39.130 0.00 0.00 0.00 3.01
182 184 4.284829 TGATTGATGCACTGGTAGTTCA 57.715 40.909 0.00 0.00 0.00 3.18
183 185 4.256110 TGATTGATGCACTGGTAGTTCAG 58.744 43.478 0.00 0.00 40.40 3.02
184 186 4.020307 TGATTGATGCACTGGTAGTTCAGA 60.020 41.667 0.00 0.00 38.11 3.27
185 187 4.558226 TTGATGCACTGGTAGTTCAGAT 57.442 40.909 0.00 0.00 38.11 2.90
186 188 4.558226 TGATGCACTGGTAGTTCAGATT 57.442 40.909 0.00 0.00 38.11 2.40
187 189 4.910195 TGATGCACTGGTAGTTCAGATTT 58.090 39.130 0.00 0.00 38.11 2.17
188 190 4.696877 TGATGCACTGGTAGTTCAGATTTG 59.303 41.667 0.00 0.00 38.11 2.32
189 191 2.813754 TGCACTGGTAGTTCAGATTTGC 59.186 45.455 0.00 0.00 38.11 3.68
190 192 2.813754 GCACTGGTAGTTCAGATTTGCA 59.186 45.455 0.00 0.00 35.60 4.08
191 193 3.441572 GCACTGGTAGTTCAGATTTGCAT 59.558 43.478 0.00 0.00 35.60 3.96
192 194 4.437930 GCACTGGTAGTTCAGATTTGCATC 60.438 45.833 0.00 0.00 35.60 3.91
193 195 4.940046 CACTGGTAGTTCAGATTTGCATCT 59.060 41.667 0.00 0.00 40.79 2.90
194 196 6.108687 CACTGGTAGTTCAGATTTGCATCTA 58.891 40.000 0.00 0.00 37.71 1.98
195 197 6.595326 CACTGGTAGTTCAGATTTGCATCTAA 59.405 38.462 0.00 0.00 37.71 2.10
196 198 6.820656 ACTGGTAGTTCAGATTTGCATCTAAG 59.179 38.462 0.00 0.00 37.71 2.18
267 269 4.647424 ATTGAAAACGAAACCAGAGCAA 57.353 36.364 0.00 0.00 0.00 3.91
268 270 4.442375 TTGAAAACGAAACCAGAGCAAA 57.558 36.364 0.00 0.00 0.00 3.68
272 274 1.308998 ACGAAACCAGAGCAAACAGG 58.691 50.000 0.00 0.00 0.00 4.00
273 275 0.593128 CGAAACCAGAGCAAACAGGG 59.407 55.000 0.00 0.00 0.00 4.45
274 276 0.961753 GAAACCAGAGCAAACAGGGG 59.038 55.000 0.00 0.00 0.00 4.79
275 277 0.469892 AAACCAGAGCAAACAGGGGG 60.470 55.000 0.00 0.00 0.00 5.40
342 344 4.500127 GGGCAACACAAAAACTAAACAGT 58.500 39.130 0.00 0.00 39.74 3.55
516 532 5.231991 GCATTGTGTTAATTATGAAAGGGCG 59.768 40.000 0.00 0.00 0.00 6.13
577 599 4.508124 GGTACATGATCTTAGTTTGGCTCG 59.492 45.833 0.00 0.00 0.00 5.03
612 634 9.681062 CATCCTACTATTTCCTTTTGGTAAAGA 57.319 33.333 0.00 0.00 42.78 2.52
614 636 9.681062 TCCTACTATTTCCTTTTGGTAAAGATG 57.319 33.333 0.00 0.00 42.78 2.90
615 637 9.681062 CCTACTATTTCCTTTTGGTAAAGATGA 57.319 33.333 0.00 0.00 42.78 2.92
624 646 9.753674 TCCTTTTGGTAAAGATGATTTGATAGT 57.246 29.630 0.00 0.00 42.78 2.12
729 755 8.520351 GTGTAATTAAGTTCCTTTGCACCTAAT 58.480 33.333 0.00 0.00 31.22 1.73
730 756 9.742144 TGTAATTAAGTTCCTTTGCACCTAATA 57.258 29.630 0.00 0.00 0.00 0.98
735 761 5.067954 AGTTCCTTTGCACCTAATAACGTT 58.932 37.500 5.88 5.88 0.00 3.99
736 762 5.048991 AGTTCCTTTGCACCTAATAACGTTG 60.049 40.000 11.99 0.00 0.00 4.10
737 763 4.391155 TCCTTTGCACCTAATAACGTTGT 58.609 39.130 11.99 0.00 0.00 3.32
738 764 4.214545 TCCTTTGCACCTAATAACGTTGTG 59.785 41.667 11.99 11.06 0.00 3.33
740 766 2.537639 GCACCTAATAACGTTGTGCC 57.462 50.000 23.01 10.35 44.89 5.01
741 767 2.081462 GCACCTAATAACGTTGTGCCT 58.919 47.619 23.01 1.79 44.89 4.75
742 768 3.264104 GCACCTAATAACGTTGTGCCTA 58.736 45.455 23.01 2.81 44.89 3.93
743 769 3.685756 GCACCTAATAACGTTGTGCCTAA 59.314 43.478 23.01 0.00 44.89 2.69
744 770 4.436451 GCACCTAATAACGTTGTGCCTAAC 60.436 45.833 23.01 3.04 44.89 2.34
745 771 4.933400 CACCTAATAACGTTGTGCCTAACT 59.067 41.667 11.99 0.00 0.00 2.24
795 836 9.701098 TGACACCGTCCTATAATAATTCATTAC 57.299 33.333 0.00 0.00 31.88 1.89
810 862 4.927267 TCATTACCCATATCATGTCCCC 57.073 45.455 0.00 0.00 0.00 4.81
925 994 8.609617 TCTTGCCCTATATATATACACAAGCT 57.390 34.615 18.95 0.00 33.69 3.74
935 1009 9.809096 ATATATATACACAAGCTCGAATTCAGG 57.191 33.333 6.22 0.00 0.00 3.86
937 1011 3.340814 ACACAAGCTCGAATTCAGGAT 57.659 42.857 6.22 0.00 0.00 3.24
944 1018 4.521146 AGCTCGAATTCAGGATCACAAAT 58.479 39.130 6.22 0.00 0.00 2.32
946 1020 5.065731 AGCTCGAATTCAGGATCACAAATTC 59.934 40.000 6.22 12.43 35.67 2.17
947 1021 5.731686 GCTCGAATTCAGGATCACAAATTCC 60.732 44.000 6.22 0.00 35.62 3.01
982 1057 1.137282 GCTAGGTAGACAAGCCACTCC 59.863 57.143 0.00 0.00 0.00 3.85
983 1058 1.405821 CTAGGTAGACAAGCCACTCCG 59.594 57.143 0.00 0.00 0.00 4.63
984 1059 1.218316 GGTAGACAAGCCACTCCGG 59.782 63.158 0.00 0.00 38.11 5.14
1034 1109 2.213513 TGGTGGATGTCGACTGCCA 61.214 57.895 20.98 20.98 0.00 4.92
1225 1319 3.345714 CGCATTGTCGTAATTTCTGCTC 58.654 45.455 0.00 0.00 0.00 4.26
1241 1336 9.688592 AATTTCTGCTCTTGTATTTTCTTTGAG 57.311 29.630 0.00 0.00 0.00 3.02
1245 1340 7.498900 TCTGCTCTTGTATTTTCTTTGAGAACA 59.501 33.333 0.00 0.00 33.26 3.18
1248 1343 7.041098 GCTCTTGTATTTTCTTTGAGAACAGGA 60.041 37.037 0.00 0.00 33.26 3.86
1389 1484 0.459237 CTCCTCAGTCGTGACCATGC 60.459 60.000 0.00 0.00 0.00 4.06
1390 1485 0.900182 TCCTCAGTCGTGACCATGCT 60.900 55.000 0.00 0.00 0.00 3.79
1391 1486 0.738762 CCTCAGTCGTGACCATGCTG 60.739 60.000 0.00 0.00 0.00 4.41
1392 1487 0.244721 CTCAGTCGTGACCATGCTGA 59.755 55.000 12.35 12.35 35.29 4.26
1393 1488 0.897621 TCAGTCGTGACCATGCTGAT 59.102 50.000 10.24 0.00 32.09 2.90
1394 1489 1.004595 CAGTCGTGACCATGCTGATG 58.995 55.000 0.00 0.00 0.00 3.07
1404 1499 2.673200 ATGCTGATGCTGGTCGGGT 61.673 57.895 0.00 0.00 40.48 5.28
1489 1594 0.747255 CCTACATGGACCTGGACGAG 59.253 60.000 0.00 0.00 38.35 4.18
1629 1768 1.446966 GCGACCCTGTCTTCAGCTC 60.447 63.158 0.00 0.00 40.09 4.09
1778 1920 3.631227 ACTGACTGCTAACGTATACTCCC 59.369 47.826 0.56 0.00 0.00 4.30
1780 1922 3.630769 TGACTGCTAACGTATACTCCCTG 59.369 47.826 0.56 0.00 0.00 4.45
1781 1923 3.629087 ACTGCTAACGTATACTCCCTGT 58.371 45.455 0.56 0.00 0.00 4.00
1782 1924 4.785301 ACTGCTAACGTATACTCCCTGTA 58.215 43.478 0.56 0.00 35.37 2.74
1784 1926 5.472820 ACTGCTAACGTATACTCCCTGTATC 59.527 44.000 0.56 0.00 41.64 2.24
1785 1927 5.628130 TGCTAACGTATACTCCCTGTATCT 58.372 41.667 0.56 0.00 41.64 1.98
1789 1931 7.551974 GCTAACGTATACTCCCTGTATCTCATA 59.448 40.741 0.56 0.00 41.64 2.15
1790 1932 9.445878 CTAACGTATACTCCCTGTATCTCATAA 57.554 37.037 0.56 0.00 41.64 1.90
1791 1933 7.684937 ACGTATACTCCCTGTATCTCATAAC 57.315 40.000 0.56 0.00 41.64 1.89
1792 1934 7.229308 ACGTATACTCCCTGTATCTCATAACA 58.771 38.462 0.56 0.00 41.64 2.41
1793 1935 7.889073 ACGTATACTCCCTGTATCTCATAACAT 59.111 37.037 0.56 0.00 41.64 2.71
1794 1936 9.392259 CGTATACTCCCTGTATCTCATAACATA 57.608 37.037 0.56 0.00 41.64 2.29
1798 1940 8.783660 ACTCCCTGTATCTCATAACATAAGAA 57.216 34.615 0.00 0.00 0.00 2.52
1799 1941 9.386122 ACTCCCTGTATCTCATAACATAAGAAT 57.614 33.333 0.00 0.00 0.00 2.40
1800 1942 9.650539 CTCCCTGTATCTCATAACATAAGAATG 57.349 37.037 0.00 0.00 39.17 2.67
1816 1958 9.120538 ACATAAGAATGTTTTTGACACTACACT 57.879 29.630 0.00 0.00 44.07 3.55
1817 1959 9.385902 CATAAGAATGTTTTTGACACTACACTG 57.614 33.333 0.00 0.00 42.04 3.66
1818 1960 6.377327 AGAATGTTTTTGACACTACACTGG 57.623 37.500 0.00 0.00 42.04 4.00
1819 1961 5.885912 AGAATGTTTTTGACACTACACTGGT 59.114 36.000 0.00 0.00 42.04 4.00
1820 1962 4.955925 TGTTTTTGACACTACACTGGTG 57.044 40.909 0.00 0.00 40.19 4.17
1828 1970 4.957759 ACACTACACTGGTGTCAAAAAC 57.042 40.909 9.77 0.00 43.35 2.43
1829 1971 4.328536 ACACTACACTGGTGTCAAAAACA 58.671 39.130 9.77 0.00 43.35 2.83
1845 1987 9.967451 TGTCAAAAACACTCTTATATTATGGGA 57.033 29.630 0.00 0.00 31.20 4.37
1849 1991 8.996651 AAAACACTCTTATATTATGGGAAGGG 57.003 34.615 0.00 0.00 0.00 3.95
1850 1992 6.704056 ACACTCTTATATTATGGGAAGGGG 57.296 41.667 0.00 0.00 0.00 4.79
1851 1993 5.551977 ACACTCTTATATTATGGGAAGGGGG 59.448 44.000 0.00 0.00 0.00 5.40
1869 2011 4.489306 GGGGGTAGTATCTATCATTGCC 57.511 50.000 0.00 0.00 0.00 4.52
1875 2017 6.210784 GGGTAGTATCTATCATTGCCACACTA 59.789 42.308 0.00 0.00 0.00 2.74
1885 2029 4.808895 TCATTGCCACACTATACATTCGAC 59.191 41.667 0.00 0.00 0.00 4.20
1919 2063 1.133025 CTGACAGGCCGCTTAATTTGG 59.867 52.381 0.00 0.00 0.00 3.28
2124 2276 2.512286 AGGCATGCCGATGACACG 60.512 61.111 30.50 0.00 40.57 4.49
2125 2277 2.511373 GGCATGCCGATGACACGA 60.511 61.111 23.48 0.00 37.57 4.35
2197 2349 4.069232 TGGAAGCTGTCGGAGGCG 62.069 66.667 0.00 0.00 28.88 5.52
2203 2355 2.584608 CTGTCGGAGGCGGGAATT 59.415 61.111 0.00 0.00 32.94 2.17
2221 2373 0.823356 TTCAGTTCCTGCCCAGCAAC 60.823 55.000 0.00 0.00 38.41 4.17
2608 2772 0.110486 ATGAGGCGTGGTCAAACCTT 59.890 50.000 0.00 0.00 39.58 3.50
2684 2848 0.866427 GCTCGTCGTCGGAGATATCA 59.134 55.000 5.32 0.00 40.67 2.15
2708 2872 3.129109 CAGGCTGTGTATGCAGTCATAG 58.871 50.000 6.28 11.37 43.05 2.23
2709 2873 2.103771 AGGCTGTGTATGCAGTCATAGG 59.896 50.000 15.40 4.25 43.05 2.57
2793 2969 5.982465 TGCAAACAATAAAAAGTGGAAGC 57.018 34.783 0.00 0.00 0.00 3.86
2862 3038 2.743636 TTCTCTCCCATCGTGTGTTC 57.256 50.000 0.00 0.00 0.00 3.18
3262 3442 4.457257 GCTCTGAAGATAACCTGCAAAACT 59.543 41.667 0.00 0.00 27.65 2.66
3649 6427 4.021719 CACACATGCTTGGAAGAAGGAATT 60.022 41.667 4.44 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.942338 TCAGTACAATATATTCGTGCTTTCTT 57.058 30.769 12.47 0.00 0.00 2.52
13 14 7.116948 ACTGCTGCGAATCAGTACAATATATTC 59.883 37.037 0.00 0.00 44.66 1.75
28 29 1.881973 ACATGAACAACTGCTGCGAAT 59.118 42.857 0.00 0.00 0.00 3.34
73 74 5.212532 AGCTAATCACCAATAGCAGAGAG 57.787 43.478 7.45 0.00 45.48 3.20
97 98 1.266989 GAGGCTACCTGCAACACAAAC 59.733 52.381 0.00 0.00 45.15 2.93
161 163 4.020307 TCTGAACTACCAGTGCATCAATCA 60.020 41.667 0.00 0.00 32.25 2.57
172 174 6.820656 ACTTAGATGCAAATCTGAACTACCAG 59.179 38.462 0.00 0.00 35.55 4.00
173 175 6.711277 ACTTAGATGCAAATCTGAACTACCA 58.289 36.000 0.00 0.00 32.36 3.25
174 176 7.617041 AACTTAGATGCAAATCTGAACTACC 57.383 36.000 0.00 0.00 32.36 3.18
175 177 9.899226 AAAAACTTAGATGCAAATCTGAACTAC 57.101 29.630 0.00 0.00 32.36 2.73
202 204 4.967084 TTTGTGCCTTCCTGTTACTCTA 57.033 40.909 0.00 0.00 0.00 2.43
233 235 8.718102 TTTCGTTTTCAATAAAAATGGAACCA 57.282 26.923 0.00 0.00 41.99 3.67
273 275 0.396974 TATGCTTGAATGTGGCCCCC 60.397 55.000 0.00 0.00 0.00 5.40
274 276 0.746659 GTATGCTTGAATGTGGCCCC 59.253 55.000 0.00 0.00 0.00 5.80
275 277 0.381801 CGTATGCTTGAATGTGGCCC 59.618 55.000 0.00 0.00 0.00 5.80
276 278 0.248621 GCGTATGCTTGAATGTGGCC 60.249 55.000 0.00 0.00 38.39 5.36
277 279 3.240684 GCGTATGCTTGAATGTGGC 57.759 52.632 0.00 0.00 38.39 5.01
326 328 7.254852 TCCAGCTTAACTGTTTAGTTTTTGTG 58.745 34.615 8.18 0.00 44.57 3.33
508 524 0.036294 AGAGTTGCTACCGCCCTTTC 60.036 55.000 0.00 0.00 34.43 2.62
522 538 0.478072 TTCATGGTGGTGGCAGAGTT 59.522 50.000 0.00 0.00 0.00 3.01
524 540 0.037303 ACTTCATGGTGGTGGCAGAG 59.963 55.000 0.00 0.00 0.00 3.35
525 541 0.478072 AACTTCATGGTGGTGGCAGA 59.522 50.000 0.00 0.00 0.00 4.26
526 542 2.198827 TAACTTCATGGTGGTGGCAG 57.801 50.000 0.00 0.00 0.00 4.85
534 552 7.116075 TGTACCATTATGCTTAACTTCATGGT 58.884 34.615 15.12 15.12 41.15 3.55
577 599 3.710209 AATAGTAGGATGATGCTGGCC 57.290 47.619 0.00 0.00 0.00 5.36
585 607 9.681062 CTTTACCAAAAGGAAATAGTAGGATGA 57.319 33.333 0.00 0.00 38.77 2.92
671 693 5.716094 TGCTTAACGTCATTTAGACTAGCA 58.284 37.500 0.00 0.00 45.32 3.49
729 755 5.242393 AGAGTTAGAGTTAGGCACAACGTTA 59.758 40.000 0.00 0.00 33.50 3.18
730 756 4.038883 AGAGTTAGAGTTAGGCACAACGTT 59.961 41.667 0.00 0.00 33.50 3.99
731 757 3.573110 AGAGTTAGAGTTAGGCACAACGT 59.427 43.478 0.00 0.00 33.50 3.99
732 758 4.175787 AGAGTTAGAGTTAGGCACAACG 57.824 45.455 0.00 0.00 33.50 4.10
735 761 4.279145 CCCTAGAGTTAGAGTTAGGCACA 58.721 47.826 0.00 0.00 32.97 4.57
736 762 3.637694 CCCCTAGAGTTAGAGTTAGGCAC 59.362 52.174 0.00 0.00 32.97 5.01
737 763 3.530564 TCCCCTAGAGTTAGAGTTAGGCA 59.469 47.826 0.00 0.00 32.97 4.75
738 764 3.890756 GTCCCCTAGAGTTAGAGTTAGGC 59.109 52.174 0.00 0.00 32.97 3.93
739 765 5.126699 TGTCCCCTAGAGTTAGAGTTAGG 57.873 47.826 0.00 0.00 33.89 2.69
740 766 5.595133 CCTTGTCCCCTAGAGTTAGAGTTAG 59.405 48.000 0.00 0.00 0.00 2.34
741 767 5.516984 CCTTGTCCCCTAGAGTTAGAGTTA 58.483 45.833 0.00 0.00 0.00 2.24
742 768 4.354662 CCTTGTCCCCTAGAGTTAGAGTT 58.645 47.826 0.00 0.00 0.00 3.01
743 769 3.882515 GCCTTGTCCCCTAGAGTTAGAGT 60.883 52.174 0.00 0.00 0.00 3.24
744 770 2.696187 GCCTTGTCCCCTAGAGTTAGAG 59.304 54.545 0.00 0.00 0.00 2.43
745 771 2.043939 TGCCTTGTCCCCTAGAGTTAGA 59.956 50.000 0.00 0.00 0.00 2.10
916 985 3.953712 TCCTGAATTCGAGCTTGTGTA 57.046 42.857 0.00 0.00 0.00 2.90
920 989 3.264947 TGTGATCCTGAATTCGAGCTTG 58.735 45.455 0.04 0.00 0.00 4.01
921 990 3.616956 TGTGATCCTGAATTCGAGCTT 57.383 42.857 0.04 0.00 0.00 3.74
923 992 4.889832 ATTTGTGATCCTGAATTCGAGC 57.110 40.909 0.04 0.00 0.00 5.03
925 994 4.332543 CGGAATTTGTGATCCTGAATTCGA 59.667 41.667 0.04 0.00 38.66 3.71
935 1009 4.270325 GGTAGCTACACGGAATTTGTGATC 59.730 45.833 24.75 0.00 39.73 2.92
937 1011 3.259876 AGGTAGCTACACGGAATTTGTGA 59.740 43.478 24.75 2.73 39.73 3.58
982 1057 3.673484 CCTGCAACCAAGTGGCCG 61.673 66.667 0.00 0.00 39.32 6.13
983 1058 1.607467 ATCCTGCAACCAAGTGGCC 60.607 57.895 0.00 0.00 39.32 5.36
984 1059 1.181098 ACATCCTGCAACCAAGTGGC 61.181 55.000 0.00 0.00 39.32 5.01
985 1060 0.883833 GACATCCTGCAACCAAGTGG 59.116 55.000 0.00 0.00 42.17 4.00
1050 1125 2.614013 ACCACCCATCCCTCCACC 60.614 66.667 0.00 0.00 0.00 4.61
1103 1178 1.817099 CATCTCAGCACCTTCGCCC 60.817 63.158 0.00 0.00 0.00 6.13
1225 1319 9.801873 TTTTCCTGTTCTCAAAGAAAATACAAG 57.198 29.630 0.00 0.00 35.75 3.16
1241 1336 4.627035 GCTGCCATTACATTTTTCCTGTTC 59.373 41.667 0.00 0.00 0.00 3.18
1245 1340 2.417243 GCGCTGCCATTACATTTTTCCT 60.417 45.455 0.00 0.00 0.00 3.36
1248 1343 1.201181 TCGCGCTGCCATTACATTTTT 59.799 42.857 5.56 0.00 0.00 1.94
1389 1484 1.153489 CTGACCCGACCAGCATCAG 60.153 63.158 0.00 0.00 0.00 2.90
1390 1485 2.981302 CTGACCCGACCAGCATCA 59.019 61.111 0.00 0.00 0.00 3.07
1404 1499 1.073722 CCAAGGGTCAGCTTGCTGA 59.926 57.895 19.87 19.87 0.00 4.26
1442 1547 2.125912 CTCGTCCGCCACCTTCTG 60.126 66.667 0.00 0.00 0.00 3.02
1489 1594 3.319198 TTCTCACCCCGCCACTCC 61.319 66.667 0.00 0.00 0.00 3.85
1629 1768 1.490693 GATGTGCTGGATGCCGTACG 61.491 60.000 8.69 8.69 42.00 3.67
1790 1932 9.120538 AGTGTAGTGTCAAAAACATTCTTATGT 57.879 29.630 0.00 0.00 46.85 2.29
1791 1933 9.385902 CAGTGTAGTGTCAAAAACATTCTTATG 57.614 33.333 0.00 0.00 40.80 1.90
1792 1934 8.567948 CCAGTGTAGTGTCAAAAACATTCTTAT 58.432 33.333 0.00 0.00 40.80 1.73
1793 1935 7.554835 ACCAGTGTAGTGTCAAAAACATTCTTA 59.445 33.333 0.00 0.00 40.80 2.10
1794 1936 6.377146 ACCAGTGTAGTGTCAAAAACATTCTT 59.623 34.615 0.00 0.00 40.80 2.52
1795 1937 5.885912 ACCAGTGTAGTGTCAAAAACATTCT 59.114 36.000 0.00 0.00 40.80 2.40
1796 1938 5.971202 CACCAGTGTAGTGTCAAAAACATTC 59.029 40.000 0.00 0.00 40.80 2.67
1797 1939 5.417580 ACACCAGTGTAGTGTCAAAAACATT 59.582 36.000 0.54 0.00 45.13 2.71
1798 1940 4.947388 ACACCAGTGTAGTGTCAAAAACAT 59.053 37.500 0.54 0.00 45.13 2.71
1799 1941 4.328536 ACACCAGTGTAGTGTCAAAAACA 58.671 39.130 0.54 0.00 45.13 2.83
1800 1942 4.957759 ACACCAGTGTAGTGTCAAAAAC 57.042 40.909 0.54 0.00 45.13 2.43
1808 1950 4.955925 TGTTTTTGACACCAGTGTAGTG 57.044 40.909 2.85 0.00 45.05 2.74
1819 1961 9.967451 TCCCATAATATAAGAGTGTTTTTGACA 57.033 29.630 0.00 0.00 35.42 3.58
1823 1965 9.421399 CCCTTCCCATAATATAAGAGTGTTTTT 57.579 33.333 0.00 0.00 0.00 1.94
1824 1966 8.004801 CCCCTTCCCATAATATAAGAGTGTTTT 58.995 37.037 0.00 0.00 0.00 2.43
1825 1967 7.422562 CCCCCTTCCCATAATATAAGAGTGTTT 60.423 40.741 0.00 0.00 0.00 2.83
1826 1968 6.045577 CCCCCTTCCCATAATATAAGAGTGTT 59.954 42.308 0.00 0.00 0.00 3.32
1827 1969 5.551977 CCCCCTTCCCATAATATAAGAGTGT 59.448 44.000 0.00 0.00 0.00 3.55
1828 1970 6.067217 CCCCCTTCCCATAATATAAGAGTG 57.933 45.833 0.00 0.00 0.00 3.51
1848 1990 3.844211 TGGCAATGATAGATACTACCCCC 59.156 47.826 0.00 0.00 0.00 5.40
1849 1991 4.286032 TGTGGCAATGATAGATACTACCCC 59.714 45.833 0.00 0.00 0.00 4.95
1850 1992 5.012148 AGTGTGGCAATGATAGATACTACCC 59.988 44.000 0.00 0.00 0.00 3.69
1851 1993 6.102897 AGTGTGGCAATGATAGATACTACC 57.897 41.667 0.00 0.00 0.00 3.18
1852 1994 9.790389 GTATAGTGTGGCAATGATAGATACTAC 57.210 37.037 0.00 0.00 0.00 2.73
1853 1995 9.528489 TGTATAGTGTGGCAATGATAGATACTA 57.472 33.333 0.00 0.00 0.00 1.82
1854 1996 8.422577 TGTATAGTGTGGCAATGATAGATACT 57.577 34.615 0.00 0.00 0.00 2.12
1869 2011 5.286320 GTGTCTGTGTCGAATGTATAGTGTG 59.714 44.000 0.00 0.00 0.00 3.82
1875 2017 5.854010 ATAGGTGTCTGTGTCGAATGTAT 57.146 39.130 0.00 0.00 0.00 2.29
1885 2029 3.854666 CCTGTCAGAATAGGTGTCTGTG 58.145 50.000 0.00 0.00 42.63 3.66
1919 2063 8.127327 GCATCATCATTTATGTCCATACATAGC 58.873 37.037 0.00 0.00 46.58 2.97
2062 2214 2.957402 TGATCTGACTTGTGCCCTTT 57.043 45.000 0.00 0.00 0.00 3.11
2124 2276 1.264288 CGCTGACCTCCTTTGTTGTTC 59.736 52.381 0.00 0.00 0.00 3.18
2125 2277 1.308998 CGCTGACCTCCTTTGTTGTT 58.691 50.000 0.00 0.00 0.00 2.83
2221 2373 4.103103 TCGTCGAGGCAGCTCGTG 62.103 66.667 11.39 6.65 45.91 4.35
2608 2772 3.195825 GGCTCCTGAAGTACTTGCTCTTA 59.804 47.826 14.14 0.00 0.00 2.10
2684 2848 0.034767 ACTGCATACACAGCCTGCAT 60.035 50.000 0.00 0.00 44.25 3.96
2708 2872 3.056465 CCCTTCTCGTTAGGATCATAGCC 60.056 52.174 0.00 0.00 34.56 3.93
2709 2873 3.615351 GCCCTTCTCGTTAGGATCATAGC 60.615 52.174 0.00 0.00 34.56 2.97
2777 2953 7.769272 TCAAGTTTGCTTCCACTTTTTATTG 57.231 32.000 0.00 0.00 30.48 1.90
2793 2969 4.095410 TGTGCACAACTCTTCAAGTTTG 57.905 40.909 19.28 1.30 46.26 2.93
2829 3005 6.491408 TGGGAGAGAAAGAGGGAGATATAT 57.509 41.667 0.00 0.00 0.00 0.86
2831 3007 4.841813 TGGGAGAGAAAGAGGGAGATAT 57.158 45.455 0.00 0.00 0.00 1.63
2833 3009 3.586429 GATGGGAGAGAAAGAGGGAGAT 58.414 50.000 0.00 0.00 0.00 2.75
3262 3442 9.134734 GTCTTTAACAGAACAACAAACATTCAA 57.865 29.630 0.00 0.00 31.28 2.69
3649 6427 7.841915 TGTTGATGTTATTAATTCGAGCTCA 57.158 32.000 15.40 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.