Multiple sequence alignment - TraesCS3B01G300500

Loading Multiple Alignment...

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 TraesCS3B01G300500 chr3B 100.000 2525 0 0 1 2525 482126624 482124100 0.000000e+00 4663
1 TraesCS3B01G300500 chr3B 89.747 1502 113 21 1062 2525 105737414 105738912 0.000000e+00 1882
2 TraesCS3B01G300500 chr3B 88.866 1437 112 23 875 2273 669395588 669394162 0.000000e+00 1724
3 TraesCS3B01G300500 chr3B 87.350 917 85 19 1 889 55947695 55946782 0.000000e+00 1022
4 TraesCS3B01G300500 chr7D 90.247 2594 177 33 1 2525 29347290 29349876 0.000000e+00 3319
5 TraesCS3B01G300500 chr7D 89.377 2005 149 32 1 1945 255732877 255734877 0.000000e+00 2464
6 TraesCS3B01G300500 chr7D 88.563 2011 155 39 1 1945 379138702 379136701 0.000000e+00 2370
7 TraesCS3B01G300500 chr7D 91.419 1550 95 19 1013 2525 485589813 485588265 0.000000e+00 2091
8 TraesCS3B01G300500 chr7D 89.832 1013 66 14 1425 2402 281452728 281451718 0.000000e+00 1266
9 TraesCS3B01G300500 chr5D 90.119 2601 173 33 1 2525 361378457 361381049 0.000000e+00 3302
10 TraesCS3B01G300500 chr5D 89.891 1929 131 23 661 2525 125554850 125552922 0.000000e+00 2423
11 TraesCS3B01G300500 chr5D 88.271 1995 140 46 1 1945 217939355 217937405 0.000000e+00 2302
12 TraesCS3B01G300500 chr5D 88.150 1924 152 36 1 1862 129952247 129950338 0.000000e+00 2220
13 TraesCS3B01G300500 chr5D 87.102 2039 168 41 1 1985 417146892 417144895 0.000000e+00 2220
14 TraesCS3B01G300500 chr5D 91.020 902 54 13 1644 2525 530656191 530655297 0.000000e+00 1192
15 TraesCS3B01G300500 chr5D 93.078 549 28 4 1983 2525 305544407 305544951 0.000000e+00 795
16 TraesCS3B01G300500 chr7A 88.488 2606 205 41 1 2525 255832615 255835206 0.000000e+00 3062
17 TraesCS3B01G300500 chr2A 88.522 2605 198 42 1 2524 363692479 363689895 0.000000e+00 3061
18 TraesCS3B01G300500 chr1A 88.750 2569 196 48 1 2525 494617758 494615239 0.000000e+00 3057
19 TraesCS3B01G300500 chr5A 88.156 2592 197 48 1 2525 437513290 437510742 0.000000e+00 2985
20 TraesCS3B01G300500 chr5A 89.461 816 73 11 1 805 321703000 321703813 0.000000e+00 1018
21 TraesCS3B01G300500 chr7B 87.264 2489 193 55 1 2402 222287594 222290045 0.000000e+00 2726
22 TraesCS3B01G300500 chr6D 87.520 2444 190 55 10 2402 139949093 139951472 0.000000e+00 2717
23 TraesCS3B01G300500 chr6D 87.606 2001 149 43 1 1937 465236211 465238176 0.000000e+00 2230
24 TraesCS3B01G300500 chr6D 88.295 1871 156 32 130 1945 359515705 359517567 0.000000e+00 2183
25 TraesCS3B01G300500 chr6D 91.265 1637 89 24 930 2525 56950693 56949070 0.000000e+00 2182
26 TraesCS3B01G300500 chr6D 87.391 1951 151 39 1 1862 37478846 37480790 0.000000e+00 2152
27 TraesCS3B01G300500 chr6D 86.755 1963 154 39 1 1862 48970007 48971964 0.000000e+00 2087
28 TraesCS3B01G300500 chr6D 86.667 1725 128 44 221 1862 316189783 316188078 0.000000e+00 1818
29 TraesCS3B01G300500 chr6D 87.390 1594 122 27 346 1862 143363484 143365075 0.000000e+00 1757
30 TraesCS3B01G300500 chr6D 85.449 1725 135 31 221 1862 344613391 344611700 0.000000e+00 1688
31 TraesCS3B01G300500 chr6D 88.811 1421 92 23 932 2312 112660715 112659322 0.000000e+00 1681
32 TraesCS3B01G300500 chr6D 89.307 1010 78 21 880 1862 11450502 11449496 0.000000e+00 1240
33 TraesCS3B01G300500 chr6D 91.231 650 38 10 1894 2525 9801969 9801321 0.000000e+00 867
34 TraesCS3B01G300500 chr6D 91.091 651 34 13 1894 2525 11449495 11448850 0.000000e+00 859
35 TraesCS3B01G300500 chr6D 88.655 714 42 18 1235 1945 126949175 126948498 0.000000e+00 833
36 TraesCS3B01G300500 chr6D 90.031 652 40 13 1891 2525 143365073 143365716 0.000000e+00 821
37 TraesCS3B01G300500 chr6D 86.767 665 45 16 1891 2522 302809785 302810439 0.000000e+00 701
38 TraesCS3B01G300500 chr6D 86.727 663 43 19 1894 2525 344611699 344611051 0.000000e+00 695
39 TraesCS3B01G300500 chr6D 90.180 499 30 9 1896 2375 37480793 37481291 1.270000e-177 632
40 TraesCS3B01G300500 chr6D 95.149 268 12 1 2259 2525 214765846 214765579 3.000000e-114 422
41 TraesCS3B01G300500 chr6D 93.727 271 13 1 2259 2525 126948234 126947964 1.090000e-108 403
42 TraesCS3B01G300500 chr6D 90.164 305 16 5 1983 2273 359517574 359517878 3.940000e-103 385
43 TraesCS3B01G300500 chr6D 86.592 358 25 6 1528 1862 302809430 302809787 8.530000e-100 374
44 TraesCS3B01G300500 chr6D 92.827 237 17 0 2289 2525 316187809 316187573 6.690000e-91 344
45 TraesCS3B01G300500 chr4D 89.029 2215 167 34 1 2153 450002088 450004288 0.000000e+00 2675
46 TraesCS3B01G300500 chr4D 84.762 2041 188 49 1 1985 346544975 346546948 0.000000e+00 1932
47 TraesCS3B01G300500 chr4D 89.269 1519 115 20 927 2402 394549107 394550620 0.000000e+00 1858
48 TraesCS3B01G300500 chr4D 90.504 1032 74 17 930 1945 348275274 348274251 0.000000e+00 1341
49 TraesCS3B01G300500 chr4D 91.121 642 37 5 1891 2514 53369531 53370170 0.000000e+00 852
50 TraesCS3B01G300500 chr4D 91.154 260 13 4 1603 1862 53369284 53369533 6.690000e-91 344
51 TraesCS3B01G300500 chr3D 86.856 2427 209 50 1 2340 481657804 481655401 0.000000e+00 2614
52 TraesCS3B01G300500 chr3D 88.744 1999 131 36 1 1937 272546588 272548554 0.000000e+00 2359
53 TraesCS3B01G300500 chr3D 88.358 2010 155 40 1 1945 43176216 43174221 0.000000e+00 2342
54 TraesCS3B01G300500 chr3D 86.772 2026 181 45 1 1985 355772866 355770887 0.000000e+00 2176
55 TraesCS3B01G300500 chr3D 89.159 1771 115 29 571 2273 327716853 327718614 0.000000e+00 2135
56 TraesCS3B01G300500 chr3D 90.268 1603 89 26 951 2525 377156330 377154767 0.000000e+00 2034
57 TraesCS3B01G300500 chr3D 88.127 977 81 20 1 952 558509703 558508737 0.000000e+00 1129
58 TraesCS3B01G300500 chr3D 91.217 649 35 9 1896 2525 22660612 22659967 0.000000e+00 863
59 TraesCS3B01G300500 chr3D 90.755 649 40 10 1896 2525 533590016 533589369 0.000000e+00 848
60 TraesCS3B01G300500 chr2D 89.161 2002 152 32 1 1945 49681740 49683733 0.000000e+00 2435
61 TraesCS3B01G300500 chr2D 88.706 2001 151 39 1 1945 49728540 49730521 0.000000e+00 2374
62 TraesCS3B01G300500 chr2D 87.318 1995 143 49 1 1945 528535417 528533483 0.000000e+00 2182
63 TraesCS3B01G300500 chr2D 90.716 1271 79 15 1040 2272 593863324 593862055 0.000000e+00 1657
64 TraesCS3B01G300500 chr2D 89.224 1225 73 21 1343 2525 504125769 504124562 0.000000e+00 1476
65 TraesCS3B01G300500 chr2D 88.458 979 76 21 1 952 504136701 504135733 0.000000e+00 1147
66 TraesCS3B01G300500 chr2D 90.979 654 39 9 1891 2525 511281148 511281800 0.000000e+00 863
67 TraesCS3B01G300500 chr4A 88.865 1886 139 29 668 2509 683684038 683682180 0.000000e+00 2254
68 TraesCS3B01G300500 chr1D 88.544 1903 139 53 1 1862 50645659 50647523 0.000000e+00 2233
69 TraesCS3B01G300500 chr1D 87.836 1932 158 37 1 1862 250769897 250771821 0.000000e+00 2194
70 TraesCS3B01G300500 chr1D 86.916 1949 164 36 1 1862 386741435 386743379 0.000000e+00 2102
71 TraesCS3B01G300500 chr1D 88.698 1221 95 19 1 1185 331825992 331827205 0.000000e+00 1450
72 TraesCS3B01G300500 chr1D 91.077 650 39 6 1894 2525 385734679 385734031 0.000000e+00 861
73 TraesCS3B01G300500 chr1D 91.163 645 39 9 1899 2525 386743385 386744029 0.000000e+00 859
74 TraesCS3B01G300500 chr1D 89.291 691 39 13 1603 2273 409934362 409933687 0.000000e+00 833
75 TraesCS3B01G300500 chr1D 89.724 652 40 11 1891 2525 250771819 250772460 0.000000e+00 808
76 TraesCS3B01G300500 chr1D 89.538 650 41 17 1896 2525 380262699 380262057 0.000000e+00 798
77 TraesCS3B01G300500 chr1D 84.521 730 67 26 1266 1985 331827201 331827894 0.000000e+00 680
78 TraesCS3B01G300500 chr3A 90.903 1462 91 19 1101 2525 638081691 638080235 0.000000e+00 1925
79 TraesCS3B01G300500 chr4B 88.280 1570 133 23 877 2402 136098125 136099687 0.000000e+00 1832
80 TraesCS3B01G300500 chr4B 88.921 686 47 14 1610 2273 370155288 370155966 0.000000e+00 819
81 TraesCS3B01G300500 chr4B 89.433 653 49 11 1891 2525 192630135 192630785 0.000000e+00 806
82 TraesCS3B01G300500 chr2B 88.728 1517 117 24 930 2402 604524682 604523176 0.000000e+00 1805


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 TraesCS3B01G300500 chr3B 482124100 482126624 2524 True 4663.0 4663 100.0000 1 2525 1 chr3B.!!$R2 2524
1 TraesCS3B01G300500 chr3B 105737414 105738912 1498 False 1882.0 1882 89.7470 1062 2525 1 chr3B.!!$F1 1463
2 TraesCS3B01G300500 chr3B 669394162 669395588 1426 True 1724.0 1724 88.8660 875 2273 1 chr3B.!!$R3 1398
3 TraesCS3B01G300500 chr3B 55946782 55947695 913 True 1022.0 1022 87.3500 1 889 1 chr3B.!!$R1 888
4 TraesCS3B01G300500 chr7D 29347290 29349876 2586 False 3319.0 3319 90.2470 1 2525 1 chr7D.!!$F1 2524
5 TraesCS3B01G300500 chr7D 255732877 255734877 2000 False 2464.0 2464 89.3770 1 1945 1 chr7D.!!$F2 1944
6 TraesCS3B01G300500 chr7D 379136701 379138702 2001 True 2370.0 2370 88.5630 1 1945 1 chr7D.!!$R2 1944
7 TraesCS3B01G300500 chr7D 485588265 485589813 1548 True 2091.0 2091 91.4190 1013 2525 1 chr7D.!!$R3 1512
8 TraesCS3B01G300500 chr7D 281451718 281452728 1010 True 1266.0 1266 89.8320 1425 2402 1 chr7D.!!$R1 977
9 TraesCS3B01G300500 chr5D 361378457 361381049 2592 False 3302.0 3302 90.1190 1 2525 1 chr5D.!!$F2 2524
10 TraesCS3B01G300500 chr5D 125552922 125554850 1928 True 2423.0 2423 89.8910 661 2525 1 chr5D.!!$R1 1864
11 TraesCS3B01G300500 chr5D 217937405 217939355 1950 True 2302.0 2302 88.2710 1 1945 1 chr5D.!!$R3 1944
12 TraesCS3B01G300500 chr5D 129950338 129952247 1909 True 2220.0 2220 88.1500 1 1862 1 chr5D.!!$R2 1861
13 TraesCS3B01G300500 chr5D 417144895 417146892 1997 True 2220.0 2220 87.1020 1 1985 1 chr5D.!!$R4 1984
14 TraesCS3B01G300500 chr5D 530655297 530656191 894 True 1192.0 1192 91.0200 1644 2525 1 chr5D.!!$R5 881
15 TraesCS3B01G300500 chr5D 305544407 305544951 544 False 795.0 795 93.0780 1983 2525 1 chr5D.!!$F1 542
16 TraesCS3B01G300500 chr7A 255832615 255835206 2591 False 3062.0 3062 88.4880 1 2525 1 chr7A.!!$F1 2524
17 TraesCS3B01G300500 chr2A 363689895 363692479 2584 True 3061.0 3061 88.5220 1 2524 1 chr2A.!!$R1 2523
18 TraesCS3B01G300500 chr1A 494615239 494617758 2519 True 3057.0 3057 88.7500 1 2525 1 chr1A.!!$R1 2524
19 TraesCS3B01G300500 chr5A 437510742 437513290 2548 True 2985.0 2985 88.1560 1 2525 1 chr5A.!!$R1 2524
20 TraesCS3B01G300500 chr5A 321703000 321703813 813 False 1018.0 1018 89.4610 1 805 1 chr5A.!!$F1 804
21 TraesCS3B01G300500 chr7B 222287594 222290045 2451 False 2726.0 2726 87.2640 1 2402 1 chr7B.!!$F1 2401
22 TraesCS3B01G300500 chr6D 139949093 139951472 2379 False 2717.0 2717 87.5200 10 2402 1 chr6D.!!$F2 2392
23 TraesCS3B01G300500 chr6D 465236211 465238176 1965 False 2230.0 2230 87.6060 1 1937 1 chr6D.!!$F3 1936
24 TraesCS3B01G300500 chr6D 56949070 56950693 1623 True 2182.0 2182 91.2650 930 2525 1 chr6D.!!$R2 1595
25 TraesCS3B01G300500 chr6D 48970007 48971964 1957 False 2087.0 2087 86.7550 1 1862 1 chr6D.!!$F1 1861
26 TraesCS3B01G300500 chr6D 112659322 112660715 1393 True 1681.0 1681 88.8110 932 2312 1 chr6D.!!$R3 1380
27 TraesCS3B01G300500 chr6D 37478846 37481291 2445 False 1392.0 2152 88.7855 1 2375 2 chr6D.!!$F4 2374
28 TraesCS3B01G300500 chr6D 143363484 143365716 2232 False 1289.0 1757 88.7105 346 2525 2 chr6D.!!$F5 2179
29 TraesCS3B01G300500 chr6D 359515705 359517878 2173 False 1284.0 2183 89.2295 130 2273 2 chr6D.!!$F7 2143
30 TraesCS3B01G300500 chr6D 344611051 344613391 2340 True 1191.5 1688 86.0880 221 2525 2 chr6D.!!$R8 2304
31 TraesCS3B01G300500 chr6D 316187573 316189783 2210 True 1081.0 1818 89.7470 221 2525 2 chr6D.!!$R7 2304
32 TraesCS3B01G300500 chr6D 11448850 11450502 1652 True 1049.5 1240 90.1990 880 2525 2 chr6D.!!$R5 1645
33 TraesCS3B01G300500 chr6D 9801321 9801969 648 True 867.0 867 91.2310 1894 2525 1 chr6D.!!$R1 631
34 TraesCS3B01G300500 chr6D 126947964 126949175 1211 True 618.0 833 91.1910 1235 2525 2 chr6D.!!$R6 1290
35 TraesCS3B01G300500 chr6D 302809430 302810439 1009 False 537.5 701 86.6795 1528 2522 2 chr6D.!!$F6 994
36 TraesCS3B01G300500 chr4D 450002088 450004288 2200 False 2675.0 2675 89.0290 1 2153 1 chr4D.!!$F3 2152
37 TraesCS3B01G300500 chr4D 346544975 346546948 1973 False 1932.0 1932 84.7620 1 1985 1 chr4D.!!$F1 1984
38 TraesCS3B01G300500 chr4D 394549107 394550620 1513 False 1858.0 1858 89.2690 927 2402 1 chr4D.!!$F2 1475
39 TraesCS3B01G300500 chr4D 348274251 348275274 1023 True 1341.0 1341 90.5040 930 1945 1 chr4D.!!$R1 1015
40 TraesCS3B01G300500 chr4D 53369284 53370170 886 False 598.0 852 91.1375 1603 2514 2 chr4D.!!$F4 911
41 TraesCS3B01G300500 chr3D 481655401 481657804 2403 True 2614.0 2614 86.8560 1 2340 1 chr3D.!!$R5 2339
42 TraesCS3B01G300500 chr3D 272546588 272548554 1966 False 2359.0 2359 88.7440 1 1937 1 chr3D.!!$F1 1936
43 TraesCS3B01G300500 chr3D 43174221 43176216 1995 True 2342.0 2342 88.3580 1 1945 1 chr3D.!!$R2 1944
44 TraesCS3B01G300500 chr3D 355770887 355772866 1979 True 2176.0 2176 86.7720 1 1985 1 chr3D.!!$R3 1984
45 TraesCS3B01G300500 chr3D 327716853 327718614 1761 False 2135.0 2135 89.1590 571 2273 1 chr3D.!!$F2 1702
46 TraesCS3B01G300500 chr3D 377154767 377156330 1563 True 2034.0 2034 90.2680 951 2525 1 chr3D.!!$R4 1574
47 TraesCS3B01G300500 chr3D 558508737 558509703 966 True 1129.0 1129 88.1270 1 952 1 chr3D.!!$R7 951
48 TraesCS3B01G300500 chr3D 22659967 22660612 645 True 863.0 863 91.2170 1896 2525 1 chr3D.!!$R1 629
49 TraesCS3B01G300500 chr3D 533589369 533590016 647 True 848.0 848 90.7550 1896 2525 1 chr3D.!!$R6 629
50 TraesCS3B01G300500 chr2D 49681740 49683733 1993 False 2435.0 2435 89.1610 1 1945 1 chr2D.!!$F1 1944
51 TraesCS3B01G300500 chr2D 49728540 49730521 1981 False 2374.0 2374 88.7060 1 1945 1 chr2D.!!$F2 1944
52 TraesCS3B01G300500 chr2D 528533483 528535417 1934 True 2182.0 2182 87.3180 1 1945 1 chr2D.!!$R3 1944
53 TraesCS3B01G300500 chr2D 593862055 593863324 1269 True 1657.0 1657 90.7160 1040 2272 1 chr2D.!!$R4 1232
54 TraesCS3B01G300500 chr2D 504124562 504125769 1207 True 1476.0 1476 89.2240 1343 2525 1 chr2D.!!$R1 1182
55 TraesCS3B01G300500 chr2D 504135733 504136701 968 True 1147.0 1147 88.4580 1 952 1 chr2D.!!$R2 951
56 TraesCS3B01G300500 chr2D 511281148 511281800 652 False 863.0 863 90.9790 1891 2525 1 chr2D.!!$F3 634
57 TraesCS3B01G300500 chr4A 683682180 683684038 1858 True 2254.0 2254 88.8650 668 2509 1 chr4A.!!$R1 1841
58 TraesCS3B01G300500 chr1D 50645659 50647523 1864 False 2233.0 2233 88.5440 1 1862 1 chr1D.!!$F1 1861
59 TraesCS3B01G300500 chr1D 250769897 250772460 2563 False 1501.0 2194 88.7800 1 2525 2 chr1D.!!$F2 2524
60 TraesCS3B01G300500 chr1D 386741435 386744029 2594 False 1480.5 2102 89.0395 1 2525 2 chr1D.!!$F4 2524
61 TraesCS3B01G300500 chr1D 331825992 331827894 1902 False 1065.0 1450 86.6095 1 1985 2 chr1D.!!$F3 1984
62 TraesCS3B01G300500 chr1D 385734031 385734679 648 True 861.0 861 91.0770 1894 2525 1 chr1D.!!$R2 631
63 TraesCS3B01G300500 chr1D 409933687 409934362 675 True 833.0 833 89.2910 1603 2273 1 chr1D.!!$R3 670
64 TraesCS3B01G300500 chr1D 380262057 380262699 642 True 798.0 798 89.5380 1896 2525 1 chr1D.!!$R1 629
65 TraesCS3B01G300500 chr3A 638080235 638081691 1456 True 1925.0 1925 90.9030 1101 2525 1 chr3A.!!$R1 1424
66 TraesCS3B01G300500 chr4B 136098125 136099687 1562 False 1832.0 1832 88.2800 877 2402 1 chr4B.!!$F1 1525
67 TraesCS3B01G300500 chr4B 370155288 370155966 678 False 819.0 819 88.9210 1610 2273 1 chr4B.!!$F3 663
68 TraesCS3B01G300500 chr4B 192630135 192630785 650 False 806.0 806 89.4330 1891 2525 1 chr4B.!!$F2 634
69 TraesCS3B01G300500 chr2B 604523176 604524682 1506 True 1805.0 1805 88.7280 930 2402 1 chr2B.!!$R1 1472

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
888 1108 0.178961 GGTTGTGCCTCCCCTTTCTT 60.179 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2213 3046 3.445008 TCTCTAGATGGATATGGTGGCC 58.555 50.0 0.0 0.0 0.0 5.36 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
32 34 5.748402 AGTCATGAGAATGTGCTCCAAATA 58.252 37.500 0.00 0.00 33.95 1.40
63 65 4.793201 AGCTAGGATAAACAACCCCATTC 58.207 43.478 0.00 0.00 0.00 2.67
64 66 4.478686 AGCTAGGATAAACAACCCCATTCT 59.521 41.667 0.00 0.00 0.00 2.40
366 456 4.152402 CCTTGGTCTCTATGAAACGTTGTG 59.848 45.833 0.00 0.00 0.00 3.33
378 468 3.036026 CGTTGTGCGTGATAGCTCT 57.964 52.632 0.00 0.00 38.13 4.09
388 479 4.112634 GCGTGATAGCTCTTATGTGTGAA 58.887 43.478 0.00 0.00 0.00 3.18
588 720 3.917329 TCTCCTCGTTAGTGTGTCTTG 57.083 47.619 0.00 0.00 0.00 3.02
692 839 3.117284 ACCAGCTCAAAACCCCTCTAAAA 60.117 43.478 0.00 0.00 0.00 1.52
820 979 1.728490 GGCTTCGCACCATTGGATCC 61.728 60.000 10.37 4.20 0.00 3.36
885 1105 0.759060 GTTGGTTGTGCCTCCCCTTT 60.759 55.000 0.00 0.00 38.35 3.11
886 1106 0.469144 TTGGTTGTGCCTCCCCTTTC 60.469 55.000 0.00 0.00 38.35 2.62
887 1107 1.360393 TGGTTGTGCCTCCCCTTTCT 61.360 55.000 0.00 0.00 38.35 2.52
888 1108 0.178961 GGTTGTGCCTCCCCTTTCTT 60.179 55.000 0.00 0.00 0.00 2.52
889 1109 1.248486 GTTGTGCCTCCCCTTTCTTC 58.752 55.000 0.00 0.00 0.00 2.87
890 1110 1.149101 TTGTGCCTCCCCTTTCTTCT 58.851 50.000 0.00 0.00 0.00 2.85
891 1111 0.401738 TGTGCCTCCCCTTTCTTCTG 59.598 55.000 0.00 0.00 0.00 3.02
892 1112 0.402121 GTGCCTCCCCTTTCTTCTGT 59.598 55.000 0.00 0.00 0.00 3.41
893 1113 1.149101 TGCCTCCCCTTTCTTCTGTT 58.851 50.000 0.00 0.00 0.00 3.16
894 1114 1.202927 TGCCTCCCCTTTCTTCTGTTG 60.203 52.381 0.00 0.00 0.00 3.33
895 1115 1.539157 CCTCCCCTTTCTTCTGTTGC 58.461 55.000 0.00 0.00 0.00 4.17
896 1116 1.074566 CCTCCCCTTTCTTCTGTTGCT 59.925 52.381 0.00 0.00 0.00 3.91
897 1117 2.489802 CCTCCCCTTTCTTCTGTTGCTT 60.490 50.000 0.00 0.00 0.00 3.91
898 1118 3.244911 CCTCCCCTTTCTTCTGTTGCTTA 60.245 47.826 0.00 0.00 0.00 3.09
899 1119 4.568592 CCTCCCCTTTCTTCTGTTGCTTAT 60.569 45.833 0.00 0.00 0.00 1.73
900 1120 4.998051 TCCCCTTTCTTCTGTTGCTTATT 58.002 39.130 0.00 0.00 0.00 1.40
901 1121 5.010282 TCCCCTTTCTTCTGTTGCTTATTC 58.990 41.667 0.00 0.00 0.00 1.75
902 1122 5.012893 CCCCTTTCTTCTGTTGCTTATTCT 58.987 41.667 0.00 0.00 0.00 2.40
903 1123 5.105997 CCCCTTTCTTCTGTTGCTTATTCTG 60.106 44.000 0.00 0.00 0.00 3.02
904 1124 5.397326 CCTTTCTTCTGTTGCTTATTCTGC 58.603 41.667 0.00 0.00 0.00 4.26
905 1125 4.668576 TTCTTCTGTTGCTTATTCTGCG 57.331 40.909 0.00 0.00 0.00 5.18
906 1126 3.002791 TCTTCTGTTGCTTATTCTGCGG 58.997 45.455 0.00 0.00 0.00 5.69
907 1127 2.472695 TCTGTTGCTTATTCTGCGGT 57.527 45.000 0.00 0.00 0.00 5.68
908 1128 2.076100 TCTGTTGCTTATTCTGCGGTG 58.924 47.619 0.00 0.00 0.00 4.94
909 1129 2.076100 CTGTTGCTTATTCTGCGGTGA 58.924 47.619 0.00 0.00 0.00 4.02
910 1130 1.804151 TGTTGCTTATTCTGCGGTGAC 59.196 47.619 0.00 0.00 0.00 3.67
922 1142 2.574399 GGTGACGAGAGGAGCCAC 59.426 66.667 0.00 0.00 0.00 5.01
923 1143 1.979693 GGTGACGAGAGGAGCCACT 60.980 63.158 0.00 0.00 0.00 4.00
924 1144 1.509004 GTGACGAGAGGAGCCACTC 59.491 63.158 4.14 4.14 37.77 3.51
935 1156 1.229464 AGCCACTCCTCCTCTGCTT 60.229 57.895 0.00 0.00 0.00 3.91
939 1160 1.206849 CCACTCCTCCTCTGCTTCTTC 59.793 57.143 0.00 0.00 0.00 2.87
944 1165 3.096092 TCCTCCTCTGCTTCTTCTTCTC 58.904 50.000 0.00 0.00 0.00 2.87
985 1370 1.821753 CCTCTGCTTCTTCTTCTCCGA 59.178 52.381 0.00 0.00 0.00 4.55
986 1371 2.430332 CCTCTGCTTCTTCTTCTCCGAT 59.570 50.000 0.00 0.00 0.00 4.18
1333 1781 2.738743 AGCGGATTCAATTCAATGGGT 58.261 42.857 0.00 0.00 0.00 4.51
1407 1855 0.886490 GTGCTCCTGTGACAGTTGGG 60.886 60.000 12.15 0.00 0.00 4.12
1408 1856 1.053835 TGCTCCTGTGACAGTTGGGA 61.054 55.000 12.15 1.33 0.00 4.37
1409 1857 0.108585 GCTCCTGTGACAGTTGGGAA 59.891 55.000 12.15 0.00 0.00 3.97
1410 1858 1.271597 GCTCCTGTGACAGTTGGGAAT 60.272 52.381 12.15 0.00 0.00 3.01
1411 1859 2.430465 CTCCTGTGACAGTTGGGAATG 58.570 52.381 12.15 0.00 0.00 2.67
1412 1860 0.883833 CCTGTGACAGTTGGGAATGC 59.116 55.000 12.15 0.00 0.00 3.56
1413 1861 1.608055 CTGTGACAGTTGGGAATGCA 58.392 50.000 4.01 0.00 0.00 3.96
1457 1914 7.872113 AGAAGATGAACAAGAACTTGAAGTT 57.128 32.000 19.35 10.82 42.93 2.66
1599 2058 1.667724 GTGGTGTCATGTGCTCTATGC 59.332 52.381 0.00 0.00 43.25 3.14
1601 2060 2.208431 GGTGTCATGTGCTCTATGCTC 58.792 52.381 0.00 0.00 43.37 4.26
1608 2067 1.277273 TGTGCTCTATGCTCTGTGCTT 59.723 47.619 3.20 0.00 43.37 3.91
1641 2103 5.577945 GTGTTGCTTAATTTGTGGATCATGG 59.422 40.000 0.00 0.00 0.00 3.66
1650 2198 2.693210 TGTGGATCATGGGCTCTATGA 58.307 47.619 0.00 4.24 38.76 2.15
1671 2220 6.389830 TGATCTGTGTTGCTTAATTTGTGT 57.610 33.333 0.00 0.00 0.00 3.72
1739 2429 7.118101 TGTTAGTTTCGTCAGTTTTGTACACTT 59.882 33.333 0.00 0.00 0.00 3.16
1740 2430 6.490566 AGTTTCGTCAGTTTTGTACACTTT 57.509 33.333 0.00 0.00 0.00 2.66
1741 2431 6.905578 AGTTTCGTCAGTTTTGTACACTTTT 58.094 32.000 0.00 0.00 0.00 2.27
1742 2432 8.031848 AGTTTCGTCAGTTTTGTACACTTTTA 57.968 30.769 0.00 0.00 0.00 1.52
1743 2433 8.173130 AGTTTCGTCAGTTTTGTACACTTTTAG 58.827 33.333 0.00 0.00 0.00 1.85
1744 2434 7.599630 TTCGTCAGTTTTGTACACTTTTAGT 57.400 32.000 0.00 0.00 0.00 2.24
1745 2435 7.599630 TCGTCAGTTTTGTACACTTTTAGTT 57.400 32.000 0.00 0.00 0.00 2.24
1746 2436 8.031848 TCGTCAGTTTTGTACACTTTTAGTTT 57.968 30.769 0.00 0.00 0.00 2.66
1747 2437 8.170553 TCGTCAGTTTTGTACACTTTTAGTTTC 58.829 33.333 0.00 0.00 0.00 2.78
2061 2849 2.384382 GGCACAACACTTTGATTGACG 58.616 47.619 0.00 0.00 36.48 4.35
2065 2853 2.223479 ACAACACTTTGATTGACGTGCC 60.223 45.455 0.00 0.00 36.48 5.01
2213 3046 1.176527 AAAGTCCGATGGCACCATTG 58.823 50.000 9.64 9.64 36.70 2.82
2283 3159 6.379417 CACCATATCCATCTAGAGAGCATGTA 59.621 42.308 0.00 0.00 0.00 2.29
2342 3304 7.277319 CGATATCTCATGTAGCAAGCATACATT 59.723 37.037 11.70 4.43 40.92 2.71
2380 3346 7.792032 AGTAGCAACCATAGCATACTTCTTAA 58.208 34.615 0.00 0.00 0.00 1.85
2441 3407 8.647226 CCACAAACTATACAAAAATTAGCTTGC 58.353 33.333 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 50 8.664669 ACTTGATTAAGAATGGGGTTGTTTAT 57.335 30.769 3.94 0.00 37.36 1.40
306 373 5.346181 TCCCTTCGGTTTTTGAAAATTGT 57.654 34.783 0.00 0.00 0.00 2.71
307 374 5.007234 GGTTCCCTTCGGTTTTTGAAAATTG 59.993 40.000 0.00 0.00 0.00 2.32
341 431 4.189639 ACGTTTCATAGAGACCAAGGAC 57.810 45.455 0.00 0.00 0.00 3.85
366 456 3.706698 TCACACATAAGAGCTATCACGC 58.293 45.455 0.00 0.00 0.00 5.34
569 700 3.644884 ACAAGACACACTAACGAGGAG 57.355 47.619 0.00 0.00 0.00 3.69
588 720 3.426525 ACCTTCGTCGTTCGTCATTTTAC 59.573 43.478 0.00 0.00 40.80 2.01
641 788 3.243839 GGTTTGCAAGGCTTTGAATGAGA 60.244 43.478 13.48 0.00 36.36 3.27
646 793 0.467804 GGGGTTTGCAAGGCTTTGAA 59.532 50.000 13.48 0.00 36.36 2.69
849 1038 0.317160 AACAAGTCTCACGGATCGCA 59.683 50.000 0.00 0.00 0.00 5.10
885 1105 3.002791 CCGCAGAATAAGCAACAGAAGA 58.997 45.455 0.00 0.00 0.00 2.87
886 1106 2.744202 ACCGCAGAATAAGCAACAGAAG 59.256 45.455 0.00 0.00 0.00 2.85
887 1107 2.483877 CACCGCAGAATAAGCAACAGAA 59.516 45.455 0.00 0.00 0.00 3.02
888 1108 2.076100 CACCGCAGAATAAGCAACAGA 58.924 47.619 0.00 0.00 0.00 3.41
889 1109 2.076100 TCACCGCAGAATAAGCAACAG 58.924 47.619 0.00 0.00 0.00 3.16
890 1110 1.804151 GTCACCGCAGAATAAGCAACA 59.196 47.619 0.00 0.00 0.00 3.33
891 1111 1.201921 CGTCACCGCAGAATAAGCAAC 60.202 52.381 0.00 0.00 0.00 4.17
892 1112 1.075542 CGTCACCGCAGAATAAGCAA 58.924 50.000 0.00 0.00 0.00 3.91
893 1113 0.245266 TCGTCACCGCAGAATAAGCA 59.755 50.000 0.00 0.00 0.00 3.91
894 1114 0.924090 CTCGTCACCGCAGAATAAGC 59.076 55.000 0.00 0.00 0.00 3.09
895 1115 2.455032 CTCTCGTCACCGCAGAATAAG 58.545 52.381 0.00 0.00 0.00 1.73
896 1116 1.134367 CCTCTCGTCACCGCAGAATAA 59.866 52.381 0.00 0.00 0.00 1.40
897 1117 0.738975 CCTCTCGTCACCGCAGAATA 59.261 55.000 0.00 0.00 0.00 1.75
898 1118 0.965866 TCCTCTCGTCACCGCAGAAT 60.966 55.000 0.00 0.00 0.00 2.40
899 1119 1.587043 CTCCTCTCGTCACCGCAGAA 61.587 60.000 0.00 0.00 0.00 3.02
900 1120 2.033602 TCCTCTCGTCACCGCAGA 59.966 61.111 0.00 0.00 0.00 4.26
901 1121 2.487428 CTCCTCTCGTCACCGCAG 59.513 66.667 0.00 0.00 0.00 5.18
902 1122 3.749064 GCTCCTCTCGTCACCGCA 61.749 66.667 0.00 0.00 0.00 5.69
903 1123 4.500116 GGCTCCTCTCGTCACCGC 62.500 72.222 0.00 0.00 0.00 5.68
904 1124 3.062466 TGGCTCCTCTCGTCACCG 61.062 66.667 0.00 0.00 0.00 4.94
905 1125 1.939769 GAGTGGCTCCTCTCGTCACC 61.940 65.000 2.66 0.00 0.00 4.02
906 1126 1.509004 GAGTGGCTCCTCTCGTCAC 59.491 63.158 2.66 0.00 0.00 3.67
907 1127 1.679305 GGAGTGGCTCCTCTCGTCA 60.679 63.158 7.86 0.00 46.41 4.35
908 1128 3.202467 GGAGTGGCTCCTCTCGTC 58.798 66.667 7.86 0.00 46.41 4.20
916 1136 1.264045 AAGCAGAGGAGGAGTGGCTC 61.264 60.000 0.00 0.00 0.00 4.70
917 1137 1.229464 AAGCAGAGGAGGAGTGGCT 60.229 57.895 0.00 0.00 0.00 4.75
918 1138 1.220477 GAAGCAGAGGAGGAGTGGC 59.780 63.158 0.00 0.00 0.00 5.01
919 1139 1.206849 GAAGAAGCAGAGGAGGAGTGG 59.793 57.143 0.00 0.00 0.00 4.00
920 1140 2.178580 AGAAGAAGCAGAGGAGGAGTG 58.821 52.381 0.00 0.00 0.00 3.51
921 1141 2.621556 AGAAGAAGCAGAGGAGGAGT 57.378 50.000 0.00 0.00 0.00 3.85
922 1142 3.099141 AGAAGAAGAAGCAGAGGAGGAG 58.901 50.000 0.00 0.00 0.00 3.69
923 1143 3.096092 GAGAAGAAGAAGCAGAGGAGGA 58.904 50.000 0.00 0.00 0.00 3.71
924 1144 2.168313 GGAGAAGAAGAAGCAGAGGAGG 59.832 54.545 0.00 0.00 0.00 4.30
925 1145 2.830923 TGGAGAAGAAGAAGCAGAGGAG 59.169 50.000 0.00 0.00 0.00 3.69
928 1149 3.257873 TCACTGGAGAAGAAGAAGCAGAG 59.742 47.826 0.00 0.00 0.00 3.35
935 1156 3.078097 CTCTCGTCACTGGAGAAGAAGA 58.922 50.000 0.00 0.00 39.86 2.87
939 1160 1.742831 CTCCTCTCGTCACTGGAGAAG 59.257 57.143 0.00 0.00 46.53 2.85
944 1165 1.979155 TGGCTCCTCTCGTCACTGG 60.979 63.158 0.00 0.00 0.00 4.00
985 1370 5.104193 AGCTTGACATATCTCCCAAAGTCAT 60.104 40.000 0.00 0.00 36.10 3.06
986 1371 4.225942 AGCTTGACATATCTCCCAAAGTCA 59.774 41.667 0.00 0.00 34.54 3.41
1035 1475 1.065418 GGAAGTGGACCATACTGGGTG 60.065 57.143 0.00 0.00 43.37 4.61
1242 1689 6.488683 TCTGAAACGAAAACATGAACCCTAAT 59.511 34.615 0.00 0.00 0.00 1.73
1407 1855 3.864789 TCCCCCTTTAGATCTGCATTC 57.135 47.619 5.18 0.00 0.00 2.67
1408 1856 4.821532 ATTCCCCCTTTAGATCTGCATT 57.178 40.909 5.18 0.00 0.00 3.56
1409 1857 4.821532 AATTCCCCCTTTAGATCTGCAT 57.178 40.909 5.18 0.00 0.00 3.96
1410 1858 5.725551 TTAATTCCCCCTTTAGATCTGCA 57.274 39.130 5.18 0.00 0.00 4.41
1411 1859 6.365520 TCTTTAATTCCCCCTTTAGATCTGC 58.634 40.000 5.18 0.00 0.00 4.26
1412 1860 8.275040 TCTTCTTTAATTCCCCCTTTAGATCTG 58.725 37.037 5.18 0.00 0.00 2.90
1413 1861 8.407313 TCTTCTTTAATTCCCCCTTTAGATCT 57.593 34.615 0.00 0.00 0.00 2.75
1457 1914 5.716094 CCTGCTTGTTCAATTGAATCATCA 58.284 37.500 23.05 13.63 36.33 3.07
1608 2067 4.916983 AATTAAGCAACACAGAGCACAA 57.083 36.364 0.00 0.00 0.00 3.33
1641 2103 3.191078 AGCAACACAGATCATAGAGCC 57.809 47.619 0.00 0.00 0.00 4.70
1650 2198 8.109705 TGATACACAAATTAAGCAACACAGAT 57.890 30.769 0.00 0.00 0.00 2.90
1739 2429 8.706492 TGTCTAACGAAACTGAAGAAACTAAA 57.294 30.769 0.00 0.00 0.00 1.85
1740 2430 8.598075 GTTGTCTAACGAAACTGAAGAAACTAA 58.402 33.333 0.00 0.00 0.00 2.24
1741 2431 7.760794 TGTTGTCTAACGAAACTGAAGAAACTA 59.239 33.333 0.00 0.00 39.71 2.24
1742 2432 6.592607 TGTTGTCTAACGAAACTGAAGAAACT 59.407 34.615 0.00 0.00 39.71 2.66
1743 2433 6.681599 GTGTTGTCTAACGAAACTGAAGAAAC 59.318 38.462 0.00 0.00 39.71 2.78
1744 2434 6.183360 GGTGTTGTCTAACGAAACTGAAGAAA 60.183 38.462 0.00 0.00 39.71 2.52
1745 2435 5.292589 GGTGTTGTCTAACGAAACTGAAGAA 59.707 40.000 0.00 0.00 39.71 2.52
1746 2436 4.807304 GGTGTTGTCTAACGAAACTGAAGA 59.193 41.667 0.00 0.00 39.71 2.87
1747 2437 4.317839 CGGTGTTGTCTAACGAAACTGAAG 60.318 45.833 0.00 0.00 39.71 3.02
1947 2684 5.363101 TCATGCACTATTTTTGTTTGGCAA 58.637 33.333 0.00 0.00 33.33 4.52
2002 2755 4.134563 AGGAAATTGCCACGATATGTACC 58.865 43.478 4.92 0.00 0.00 3.34
2061 2849 7.542824 ACAAAAACATGTTTATAATACCGGCAC 59.457 33.333 23.53 0.00 31.63 5.01
2065 2853 9.627395 TCCAACAAAAACATGTTTATAATACCG 57.373 29.630 23.53 8.20 41.44 4.02
2213 3046 3.445008 TCTCTAGATGGATATGGTGGCC 58.555 50.000 0.00 0.00 0.00 5.36
2283 3159 3.974757 GCCGTAGCCGAGCCGTAT 61.975 66.667 0.00 0.00 35.63 3.06
2342 3304 9.764363 CTATGGTTGCTACTTTCTATGTTATGA 57.236 33.333 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.