Multiple sequence alignment - TraesCS2D01G406200

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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 TraesCS2D01G406200 chr2D 100.000 3500 0 0 1 3500 521532439 521535938 0.000000e+00 6464
1 TraesCS2D01G406200 chr2A 91.949 1888 83 31 506 2388 666027037 666025214 0.000000e+00 2580
2 TraesCS2D01G406200 chr2A 96.843 887 23 3 2619 3500 777817420 777818306 0.000000e+00 1478
3 TraesCS2D01G406200 chr2A 83.908 435 41 16 1 428 666027455 666027043 4.240000e-104 388
4 TraesCS2D01G406200 chr2A 96.970 231 5 2 2389 2617 777817146 777817376 1.520000e-103 387
5 TraesCS2D01G406200 chr2B 91.025 1181 52 17 478 1640 614330617 614329473 0.000000e+00 1544
6 TraesCS2D01G406200 chr2B 90.855 1181 54 16 478 1640 614433989 614432845 0.000000e+00 1533
7 TraesCS2D01G406200 chr2B 96.272 751 28 0 1636 2386 614314512 614313762 0.000000e+00 1232
8 TraesCS2D01G406200 chr2B 95.739 751 32 0 1636 2386 614419583 614418833 0.000000e+00 1210
9 TraesCS2D01G406200 chr2B 89.252 214 11 5 1 206 614330996 614330787 1.250000e-64 257
10 TraesCS2D01G406200 chr2B 89.252 214 11 5 1 206 614434403 614434194 1.250000e-64 257
11 TraesCS2D01G406200 chrUn 90.885 1141 63 20 2386 3500 82683795 82682670 0.000000e+00 1493
12 TraesCS2D01G406200 chrUn 90.608 1086 61 20 2386 3445 390432673 390433743 0.000000e+00 1402
13 TraesCS2D01G406200 chrUn 90.608 1086 61 20 2386 3445 390434318 390435388 0.000000e+00 1402
14 TraesCS2D01G406200 chr7A 90.806 1142 63 21 2386 3500 95223372 95224498 0.000000e+00 1489
15 TraesCS2D01G406200 chr7A 90.674 1083 61 19 2443 3500 95230639 95231706 0.000000e+00 1404
16 TraesCS2D01G406200 chr7A 88.102 1059 124 2 1328 2385 198511298 198512355 0.000000e+00 1256
17 TraesCS2D01G406200 chr7B 86.496 1370 166 12 1016 2374 329516550 329515189 0.000000e+00 1487
18 TraesCS2D01G406200 chr7B 92.122 622 20 10 2390 2991 645246757 645246145 0.000000e+00 850
19 TraesCS2D01G406200 chr7B 95.192 520 17 4 2986 3500 645205081 645204565 0.000000e+00 815
20 TraesCS2D01G406200 chr7B 76.141 1052 213 26 1344 2385 557491304 557490281 5.180000e-143 518
21 TraesCS2D01G406200 chr7D 86.291 1386 164 13 1016 2383 186428460 186427083 0.000000e+00 1483
22 TraesCS2D01G406200 chr7D 76.660 964 185 28 1344 2296 523127854 523126920 6.750000e-137 497
23 TraesCS2D01G406200 chr7D 87.079 178 22 1 259 436 478362095 478362271 2.130000e-47 200
24 TraesCS2D01G406200 chr4A 93.576 934 34 17 2379 3289 35792358 35793288 0.000000e+00 1369
25 TraesCS2D01G406200 chr5D 92.889 900 36 20 2386 3276 417829911 417830791 0.000000e+00 1282
26 TraesCS2D01G406200 chr5D 94.650 243 9 2 3262 3500 417830806 417831048 1.190000e-99 374
27 TraesCS2D01G406200 chr6A 83.454 1384 190 30 1029 2385 496577643 496579014 0.000000e+00 1251
28 TraesCS2D01G406200 chr6B 82.893 1362 196 23 1029 2364 534235376 534236726 0.000000e+00 1190
29 TraesCS2D01G406200 chr6D 82.480 1387 204 25 1029 2388 346834309 346832935 0.000000e+00 1179
30 TraesCS2D01G406200 chr1A 92.602 784 38 8 2722 3500 568379031 568379799 0.000000e+00 1109


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 TraesCS2D01G406200 chr2D 521532439 521535938 3499 False 6464.0 6464 100.0000 1 3500 1 chr2D.!!$F1 3499
1 TraesCS2D01G406200 chr2A 666025214 666027455 2241 True 1484.0 2580 87.9285 1 2388 2 chr2A.!!$R1 2387
2 TraesCS2D01G406200 chr2A 777817146 777818306 1160 False 932.5 1478 96.9065 2389 3500 2 chr2A.!!$F1 1111
3 TraesCS2D01G406200 chr2B 614313762 614314512 750 True 1232.0 1232 96.2720 1636 2386 1 chr2B.!!$R1 750
4 TraesCS2D01G406200 chr2B 614418833 614419583 750 True 1210.0 1210 95.7390 1636 2386 1 chr2B.!!$R2 750
5 TraesCS2D01G406200 chr2B 614329473 614330996 1523 True 900.5 1544 90.1385 1 1640 2 chr2B.!!$R3 1639
6 TraesCS2D01G406200 chr2B 614432845 614434403 1558 True 895.0 1533 90.0535 1 1640 2 chr2B.!!$R4 1639
7 TraesCS2D01G406200 chrUn 82682670 82683795 1125 True 1493.0 1493 90.8850 2386 3500 1 chrUn.!!$R1 1114
8 TraesCS2D01G406200 chrUn 390432673 390435388 2715 False 1402.0 1402 90.6080 2386 3445 2 chrUn.!!$F1 1059
9 TraesCS2D01G406200 chr7A 95223372 95224498 1126 False 1489.0 1489 90.8060 2386 3500 1 chr7A.!!$F1 1114
10 TraesCS2D01G406200 chr7A 95230639 95231706 1067 False 1404.0 1404 90.6740 2443 3500 1 chr7A.!!$F2 1057
11 TraesCS2D01G406200 chr7A 198511298 198512355 1057 False 1256.0 1256 88.1020 1328 2385 1 chr7A.!!$F3 1057
12 TraesCS2D01G406200 chr7B 329515189 329516550 1361 True 1487.0 1487 86.4960 1016 2374 1 chr7B.!!$R1 1358
13 TraesCS2D01G406200 chr7B 645246145 645246757 612 True 850.0 850 92.1220 2390 2991 1 chr7B.!!$R4 601
14 TraesCS2D01G406200 chr7B 645204565 645205081 516 True 815.0 815 95.1920 2986 3500 1 chr7B.!!$R3 514
15 TraesCS2D01G406200 chr7B 557490281 557491304 1023 True 518.0 518 76.1410 1344 2385 1 chr7B.!!$R2 1041
16 TraesCS2D01G406200 chr7D 186427083 186428460 1377 True 1483.0 1483 86.2910 1016 2383 1 chr7D.!!$R1 1367
17 TraesCS2D01G406200 chr7D 523126920 523127854 934 True 497.0 497 76.6600 1344 2296 1 chr7D.!!$R2 952
18 TraesCS2D01G406200 chr4A 35792358 35793288 930 False 1369.0 1369 93.5760 2379 3289 1 chr4A.!!$F1 910
19 TraesCS2D01G406200 chr5D 417829911 417831048 1137 False 828.0 1282 93.7695 2386 3500 2 chr5D.!!$F1 1114
20 TraesCS2D01G406200 chr6A 496577643 496579014 1371 False 1251.0 1251 83.4540 1029 2385 1 chr6A.!!$F1 1356
21 TraesCS2D01G406200 chr6B 534235376 534236726 1350 False 1190.0 1190 82.8930 1029 2364 1 chr6B.!!$F1 1335
22 TraesCS2D01G406200 chr6D 346832935 346834309 1374 True 1179.0 1179 82.4800 1029 2388 1 chr6D.!!$R1 1359
23 TraesCS2D01G406200 chr1A 568379031 568379799 768 False 1109.0 1109 92.6020 2722 3500 1 chr1A.!!$F1 778


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
443 612 0.038526 ACTCGGACAACAGTAAGGCG 60.039 55.0 0.0 0.0 0.0 5.52 F
444 613 0.242825 CTCGGACAACAGTAAGGCGA 59.757 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2333 2561 2.278857 CTTCGGCGATGTCCCTCG 60.279 66.667 11.76 0.0 41.54 4.63 R
2499 2728 5.748402 ACACACCACAGAATATCACATGAT 58.252 37.500 0.00 0.0 38.51 2.45 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
20 21 1.980232 ACCAGGGCATGCATGTGTG 60.980 57.895 26.79 19.83 0.00 3.82
40 41 7.925993 TGTGTGGTCTCTGTTATTAACTTTTG 58.074 34.615 7.99 0.00 0.00 2.44
144 148 8.498358 TCGATATGATATTTAGTTTGCTTGCTG 58.502 33.333 0.00 0.00 0.00 4.41
146 150 5.581126 TGATATTTAGTTTGCTTGCTGGG 57.419 39.130 0.00 0.00 0.00 4.45
147 151 5.016173 TGATATTTAGTTTGCTTGCTGGGT 58.984 37.500 0.00 0.00 0.00 4.51
175 186 0.179040 ATGTGGACGGTGTTCGGTTT 60.179 50.000 0.00 0.00 44.45 3.27
176 187 1.090625 TGTGGACGGTGTTCGGTTTG 61.091 55.000 0.00 0.00 44.45 2.93
201 212 1.019805 GCCCTTCTGCTTCGGTACAC 61.020 60.000 0.00 0.00 0.00 2.90
206 217 2.527123 TGCTTCGGTACACCCCCA 60.527 61.111 0.00 0.00 0.00 4.96
207 218 2.119484 CTGCTTCGGTACACCCCCAA 62.119 60.000 0.00 0.00 0.00 4.12
209 220 2.063774 CTTCGGTACACCCCCAACT 58.936 57.895 0.00 0.00 0.00 3.16
210 221 0.321298 CTTCGGTACACCCCCAACTG 60.321 60.000 0.00 0.00 0.00 3.16
211 222 0.763604 TTCGGTACACCCCCAACTGA 60.764 55.000 0.00 0.00 0.00 3.41
212 223 0.763604 TCGGTACACCCCCAACTGAA 60.764 55.000 0.00 0.00 0.00 3.02
215 226 2.027007 CGGTACACCCCCAACTGAATAA 60.027 50.000 0.00 0.00 0.00 1.40
216 227 3.559597 CGGTACACCCCCAACTGAATAAA 60.560 47.826 0.00 0.00 0.00 1.40
218 229 4.401202 GGTACACCCCCAACTGAATAAATG 59.599 45.833 0.00 0.00 0.00 2.32
219 230 3.440127 ACACCCCCAACTGAATAAATGG 58.560 45.455 0.00 0.00 0.00 3.16
220 231 2.168313 CACCCCCAACTGAATAAATGGC 59.832 50.000 0.00 0.00 0.00 4.40
221 232 2.044353 ACCCCCAACTGAATAAATGGCT 59.956 45.455 0.00 0.00 0.00 4.75
222 233 2.431782 CCCCCAACTGAATAAATGGCTG 59.568 50.000 0.00 0.00 0.00 4.85
223 234 3.364549 CCCCAACTGAATAAATGGCTGA 58.635 45.455 0.00 0.00 0.00 4.26
224 235 3.382546 CCCCAACTGAATAAATGGCTGAG 59.617 47.826 0.00 0.00 0.00 3.35
233 396 9.860898 ACTGAATAAATGGCTGAGATTTAAAAC 57.139 29.630 0.00 0.00 30.90 2.43
273 442 1.670811 CTTTATACGGGCTGCAACTGG 59.329 52.381 0.50 0.00 0.00 4.00
292 461 3.230976 TGGAGCTGTACTGAGAAACTCA 58.769 45.455 3.61 0.00 38.25 3.41
293 462 3.641436 TGGAGCTGTACTGAGAAACTCAA 59.359 43.478 3.61 0.00 40.18 3.02
294 463 4.100963 TGGAGCTGTACTGAGAAACTCAAA 59.899 41.667 3.61 0.00 40.18 2.69
295 464 4.688413 GGAGCTGTACTGAGAAACTCAAAG 59.312 45.833 3.61 0.00 40.18 2.77
296 465 4.636249 AGCTGTACTGAGAAACTCAAAGG 58.364 43.478 3.61 0.00 40.18 3.11
297 466 4.345257 AGCTGTACTGAGAAACTCAAAGGA 59.655 41.667 3.61 0.00 40.18 3.36
323 492 3.791973 TTTATTGCGGCTGGTAATTGG 57.208 42.857 0.00 0.00 32.83 3.16
343 512 4.151121 TGGAAGATTGATTGGAGTGCAAA 58.849 39.130 0.00 0.00 0.00 3.68
392 561 0.874390 GATTTGGACTGTCGCTTGCA 59.126 50.000 1.07 0.00 0.00 4.08
429 598 4.568152 AACAAGATTTTGGTGAACTCGG 57.432 40.909 0.57 0.00 38.66 4.63
430 599 3.815809 ACAAGATTTTGGTGAACTCGGA 58.184 40.909 0.57 0.00 38.66 4.55
431 600 3.564225 ACAAGATTTTGGTGAACTCGGAC 59.436 43.478 0.57 0.00 38.66 4.79
432 601 3.485463 AGATTTTGGTGAACTCGGACA 57.515 42.857 0.00 0.00 0.00 4.02
433 602 3.815809 AGATTTTGGTGAACTCGGACAA 58.184 40.909 0.00 0.00 0.00 3.18
434 603 3.564225 AGATTTTGGTGAACTCGGACAAC 59.436 43.478 0.00 0.00 0.00 3.32
435 604 2.404923 TTTGGTGAACTCGGACAACA 57.595 45.000 0.00 0.00 31.63 3.33
436 605 1.948104 TTGGTGAACTCGGACAACAG 58.052 50.000 0.00 0.00 35.15 3.16
437 606 0.828022 TGGTGAACTCGGACAACAGT 59.172 50.000 0.00 0.00 0.00 3.55
438 607 2.033372 TGGTGAACTCGGACAACAGTA 58.967 47.619 0.00 0.00 0.00 2.74
439 608 2.431419 TGGTGAACTCGGACAACAGTAA 59.569 45.455 0.00 0.00 0.00 2.24
440 609 3.057734 GGTGAACTCGGACAACAGTAAG 58.942 50.000 0.00 0.00 0.00 2.34
441 610 3.057734 GTGAACTCGGACAACAGTAAGG 58.942 50.000 0.00 0.00 0.00 2.69
442 611 2.067013 GAACTCGGACAACAGTAAGGC 58.933 52.381 0.00 0.00 0.00 4.35
443 612 0.038526 ACTCGGACAACAGTAAGGCG 60.039 55.000 0.00 0.00 0.00 5.52
444 613 0.242825 CTCGGACAACAGTAAGGCGA 59.757 55.000 0.00 0.00 0.00 5.54
445 614 0.892755 TCGGACAACAGTAAGGCGAT 59.107 50.000 0.00 0.00 0.00 4.58
446 615 1.135199 TCGGACAACAGTAAGGCGATC 60.135 52.381 0.00 0.00 0.00 3.69
447 616 1.403647 CGGACAACAGTAAGGCGATCA 60.404 52.381 0.00 0.00 0.00 2.92
448 617 2.695359 GGACAACAGTAAGGCGATCAA 58.305 47.619 0.00 0.00 0.00 2.57
449 618 2.415512 GGACAACAGTAAGGCGATCAAC 59.584 50.000 0.00 0.00 0.00 3.18
450 619 3.064207 GACAACAGTAAGGCGATCAACA 58.936 45.455 0.00 0.00 0.00 3.33
451 620 2.806244 ACAACAGTAAGGCGATCAACAC 59.194 45.455 0.00 0.00 0.00 3.32
452 621 2.805671 CAACAGTAAGGCGATCAACACA 59.194 45.455 0.00 0.00 0.00 3.72
453 622 3.120321 ACAGTAAGGCGATCAACACAA 57.880 42.857 0.00 0.00 0.00 3.33
454 623 3.674997 ACAGTAAGGCGATCAACACAAT 58.325 40.909 0.00 0.00 0.00 2.71
455 624 3.436704 ACAGTAAGGCGATCAACACAATG 59.563 43.478 0.00 0.00 0.00 2.82
456 625 3.436704 CAGTAAGGCGATCAACACAATGT 59.563 43.478 0.00 0.00 0.00 2.71
457 626 4.629634 CAGTAAGGCGATCAACACAATGTA 59.370 41.667 0.00 0.00 0.00 2.29
458 627 5.294306 CAGTAAGGCGATCAACACAATGTAT 59.706 40.000 0.00 0.00 0.00 2.29
459 628 4.621068 AAGGCGATCAACACAATGTATG 57.379 40.909 0.00 0.00 0.00 2.39
460 629 3.609853 AGGCGATCAACACAATGTATGT 58.390 40.909 0.00 0.00 45.34 2.29
461 630 4.009675 AGGCGATCAACACAATGTATGTT 58.990 39.130 0.00 0.00 41.46 2.71
468 637 4.771590 AACACAATGTATGTTGGAGCTG 57.228 40.909 0.00 0.00 41.46 4.24
469 638 3.754965 ACACAATGTATGTTGGAGCTGT 58.245 40.909 0.00 0.00 41.46 4.40
470 639 4.144297 ACACAATGTATGTTGGAGCTGTT 58.856 39.130 0.00 0.00 41.46 3.16
471 640 4.584325 ACACAATGTATGTTGGAGCTGTTT 59.416 37.500 0.00 0.00 41.46 2.83
472 641 5.156355 CACAATGTATGTTGGAGCTGTTTC 58.844 41.667 0.00 0.00 41.46 2.78
473 642 5.048504 CACAATGTATGTTGGAGCTGTTTCT 60.049 40.000 0.00 0.00 41.46 2.52
474 643 5.536161 ACAATGTATGTTGGAGCTGTTTCTT 59.464 36.000 0.00 0.00 40.06 2.52
475 644 5.886960 ATGTATGTTGGAGCTGTTTCTTC 57.113 39.130 0.00 0.00 0.00 2.87
476 645 4.713553 TGTATGTTGGAGCTGTTTCTTCA 58.286 39.130 0.00 0.00 0.00 3.02
603 776 3.625764 ACTCAGCAAAGTTAGCAAAACGA 59.374 39.130 0.00 0.00 0.00 3.85
664 852 7.061905 CCGTCAATTGATCAGTATATTCCGTAC 59.938 40.741 12.12 0.00 0.00 3.67
666 854 8.916654 GTCAATTGATCAGTATATTCCGTACAG 58.083 37.037 12.12 0.00 0.00 2.74
667 855 8.638873 TCAATTGATCAGTATATTCCGTACAGT 58.361 33.333 3.38 0.00 0.00 3.55
668 856 9.908152 CAATTGATCAGTATATTCCGTACAGTA 57.092 33.333 0.00 0.00 0.00 2.74
669 857 9.909644 AATTGATCAGTATATTCCGTACAGTAC 57.090 33.333 0.00 0.00 0.00 2.73
702 890 2.665000 CTCCGGCCTCTTTCAGCA 59.335 61.111 0.00 0.00 0.00 4.41
735 926 3.713826 AAGAAAAAGGATGAGCCGGTA 57.286 42.857 1.90 0.00 43.43 4.02
736 927 3.268023 AGAAAAAGGATGAGCCGGTAG 57.732 47.619 1.90 0.00 43.43 3.18
737 928 2.092914 AGAAAAAGGATGAGCCGGTAGG 60.093 50.000 1.90 0.00 43.43 3.18
738 929 1.286248 AAAAGGATGAGCCGGTAGGT 58.714 50.000 1.90 0.00 43.43 3.08
739 930 0.541863 AAAGGATGAGCCGGTAGGTG 59.458 55.000 1.90 0.00 43.43 4.00
740 931 1.972660 AAGGATGAGCCGGTAGGTGC 61.973 60.000 1.90 0.00 43.43 5.01
741 932 2.731571 GGATGAGCCGGTAGGTGCA 61.732 63.158 1.90 0.00 40.50 4.57
742 933 1.521681 GATGAGCCGGTAGGTGCAC 60.522 63.158 8.80 8.80 40.50 4.57
743 934 3.371097 ATGAGCCGGTAGGTGCACG 62.371 63.158 11.45 0.00 40.50 5.34
747 938 3.454573 CCGGTAGGTGCACGGCTA 61.455 66.667 11.45 4.68 41.23 3.93
748 939 2.792947 CCGGTAGGTGCACGGCTAT 61.793 63.158 11.45 0.00 41.23 2.97
749 940 1.591594 CGGTAGGTGCACGGCTATG 60.592 63.158 11.45 1.48 0.00 2.23
750 941 1.820581 GGTAGGTGCACGGCTATGA 59.179 57.895 11.45 0.00 0.00 2.15
751 942 0.393077 GGTAGGTGCACGGCTATGAT 59.607 55.000 11.45 0.00 0.00 2.45
752 943 1.605712 GGTAGGTGCACGGCTATGATC 60.606 57.143 11.45 0.00 0.00 2.92
753 944 0.679505 TAGGTGCACGGCTATGATCC 59.320 55.000 11.45 0.00 0.00 3.36
754 945 1.146041 GGTGCACGGCTATGATCCA 59.854 57.895 11.45 0.00 0.00 3.41
755 946 1.160329 GGTGCACGGCTATGATCCAC 61.160 60.000 11.45 0.00 0.00 4.02
756 947 0.461870 GTGCACGGCTATGATCCACA 60.462 55.000 0.00 0.00 0.00 4.17
759 950 1.290203 CACGGCTATGATCCACACAC 58.710 55.000 0.00 0.00 0.00 3.82
777 968 3.808656 GCTCGCCCTTCAGCAAGC 61.809 66.667 0.00 0.00 35.56 4.01
785 976 0.956633 CCTTCAGCAAGCAAAGCAGA 59.043 50.000 0.00 0.00 0.00 4.26
786 977 1.068472 CCTTCAGCAAGCAAAGCAGAG 60.068 52.381 0.00 0.00 0.00 3.35
809 1000 1.098050 AGAAACTGGAATGCGATGCC 58.902 50.000 0.00 0.00 0.00 4.40
818 1009 2.786512 AATGCGATGCCCCCACTTGT 62.787 55.000 0.00 0.00 0.00 3.16
820 1011 2.112815 GCGATGCCCCCACTTGTAC 61.113 63.158 0.00 0.00 0.00 2.90
821 1012 1.602237 CGATGCCCCCACTTGTACT 59.398 57.895 0.00 0.00 0.00 2.73
823 1014 1.202533 CGATGCCCCCACTTGTACTAG 60.203 57.143 2.56 2.56 0.00 2.57
824 1015 1.838077 GATGCCCCCACTTGTACTAGT 59.162 52.381 3.98 3.98 0.00 2.57
825 1016 0.981183 TGCCCCCACTTGTACTAGTG 59.019 55.000 24.95 24.95 44.07 2.74
826 1017 0.981943 GCCCCCACTTGTACTAGTGT 59.018 55.000 27.91 5.91 43.17 3.55
827 1018 1.066358 GCCCCCACTTGTACTAGTGTC 60.066 57.143 27.91 14.80 43.17 3.67
828 1019 1.553704 CCCCCACTTGTACTAGTGTCC 59.446 57.143 27.91 0.00 43.17 4.02
830 1021 2.838202 CCCCACTTGTACTAGTGTCCAT 59.162 50.000 27.91 0.00 43.17 3.41
831 1022 3.118738 CCCCACTTGTACTAGTGTCCATC 60.119 52.174 27.91 0.00 43.17 3.51
832 1023 3.769844 CCCACTTGTACTAGTGTCCATCT 59.230 47.826 27.91 0.00 43.17 2.90
833 1024 4.142138 CCCACTTGTACTAGTGTCCATCTC 60.142 50.000 27.91 0.00 43.17 2.75
837 1028 6.929049 CACTTGTACTAGTGTCCATCTCAAAA 59.071 38.462 23.98 0.00 40.48 2.44
874 1065 2.094894 CAGCAACAGCTCACCGATTAAG 59.905 50.000 0.00 0.00 36.19 1.85
1020 1211 4.778143 GCGGACAGGCCAACGGAT 62.778 66.667 5.01 0.00 35.94 4.18
1094 1285 4.161295 CATGCTCCCCTTCGCCGA 62.161 66.667 0.00 0.00 0.00 5.54
1324 1542 4.069232 CGCTCTCCACCGGAAGCA 62.069 66.667 9.46 0.00 36.43 3.91
1476 1694 2.579684 CTTACCTCTCCGTGCCCAGC 62.580 65.000 0.00 0.00 0.00 4.85
2496 2725 1.561076 TCAGCCATGCAGTGTATTCCT 59.439 47.619 0.00 0.00 0.00 3.36
2499 2728 2.025981 AGCCATGCAGTGTATTCCTTGA 60.026 45.455 0.00 0.00 0.00 3.02
2732 3023 9.946165 GTAGTAGTAACATTCATAAAAATGCCC 57.054 33.333 0.00 0.00 39.72 5.36
2913 3205 9.774742 CAGCTAGTTAAACATAAAGTTCCATTC 57.225 33.333 0.00 0.00 40.26 2.67
2918 3210 9.912634 AGTTAAACATAAAGTTCCATTCACATG 57.087 29.630 0.00 0.00 40.26 3.21
3211 5168 3.958147 TCTATACAACGGGCATCAGAGAA 59.042 43.478 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.679977 GACCACACATGCATGCCCT 60.680 57.895 26.53 4.35 0.00 5.19
127 131 5.799827 AAACCCAGCAAGCAAACTAAATA 57.200 34.783 0.00 0.00 0.00 1.40
156 160 0.179040 AAACCGAACACCGTCCACAT 60.179 50.000 0.00 0.00 36.31 3.21
158 162 1.091197 ACAAACCGAACACCGTCCAC 61.091 55.000 0.00 0.00 36.31 4.02
161 172 0.728542 ACAACAAACCGAACACCGTC 59.271 50.000 0.00 0.00 36.31 4.79
170 181 0.744281 AGAAGGGCAACAACAAACCG 59.256 50.000 0.00 0.00 39.74 4.44
175 186 1.032014 GAAGCAGAAGGGCAACAACA 58.968 50.000 0.00 0.00 39.74 3.33
176 187 0.040067 CGAAGCAGAAGGGCAACAAC 60.040 55.000 0.00 0.00 39.74 3.32
201 212 2.431782 CAGCCATTTATTCAGTTGGGGG 59.568 50.000 0.00 0.00 0.00 5.40
207 218 9.860898 GTTTTAAATCTCAGCCATTTATTCAGT 57.139 29.630 0.00 0.00 0.00 3.41
218 229 9.727627 CTGATTGATTAGTTTTAAATCTCAGCC 57.272 33.333 2.03 0.00 33.03 4.85
246 412 5.477607 TGCAGCCCGTATAAAGTACATAT 57.522 39.130 0.00 0.00 0.00 1.78
260 426 4.711949 AGCTCCAGTTGCAGCCCG 62.712 66.667 0.00 0.00 36.17 6.13
261 427 2.469465 TACAGCTCCAGTTGCAGCCC 62.469 60.000 0.00 0.00 36.17 5.19
273 442 4.688413 CCTTTGAGTTTCTCAGTACAGCTC 59.312 45.833 0.00 0.00 41.75 4.09
322 491 4.488879 GTTTGCACTCCAATCAATCTTCC 58.511 43.478 0.00 0.00 32.49 3.46
323 492 4.161333 CGTTTGCACTCCAATCAATCTTC 58.839 43.478 0.00 0.00 32.49 2.87
343 512 0.250234 TGCTTCAGCCATTAGAGCGT 59.750 50.000 0.00 0.00 41.18 5.07
392 561 0.894141 TGTTGCAACCAGCTGTTTGT 59.106 45.000 26.14 7.05 45.94 2.83
425 594 0.242825 TCGCCTTACTGTTGTCCGAG 59.757 55.000 0.00 0.00 0.00 4.63
427 596 1.278238 GATCGCCTTACTGTTGTCCG 58.722 55.000 0.00 0.00 0.00 4.79
428 597 2.380084 TGATCGCCTTACTGTTGTCC 57.620 50.000 0.00 0.00 0.00 4.02
429 598 3.064207 TGTTGATCGCCTTACTGTTGTC 58.936 45.455 0.00 0.00 0.00 3.18
430 599 2.806244 GTGTTGATCGCCTTACTGTTGT 59.194 45.455 0.00 0.00 0.00 3.32
431 600 2.805671 TGTGTTGATCGCCTTACTGTTG 59.194 45.455 0.00 0.00 0.00 3.33
432 601 3.120321 TGTGTTGATCGCCTTACTGTT 57.880 42.857 0.00 0.00 0.00 3.16
433 602 2.831685 TGTGTTGATCGCCTTACTGT 57.168 45.000 0.00 0.00 0.00 3.55
434 603 3.436704 ACATTGTGTTGATCGCCTTACTG 59.563 43.478 0.00 0.00 0.00 2.74
435 604 3.674997 ACATTGTGTTGATCGCCTTACT 58.325 40.909 0.00 0.00 0.00 2.24
436 605 5.064707 ACATACATTGTGTTGATCGCCTTAC 59.935 40.000 0.00 0.00 37.11 2.34
437 606 5.182487 ACATACATTGTGTTGATCGCCTTA 58.818 37.500 0.00 0.00 37.11 2.69
438 607 4.009675 ACATACATTGTGTTGATCGCCTT 58.990 39.130 0.00 0.00 37.11 4.35
439 608 3.609853 ACATACATTGTGTTGATCGCCT 58.390 40.909 0.00 0.00 37.11 5.52
440 609 4.355543 AACATACATTGTGTTGATCGCC 57.644 40.909 0.00 0.00 38.99 5.54
447 616 4.144297 ACAGCTCCAACATACATTGTGTT 58.856 39.130 0.00 0.00 38.99 3.32
448 617 3.754965 ACAGCTCCAACATACATTGTGT 58.245 40.909 0.00 0.00 38.99 3.72
449 618 4.771590 AACAGCTCCAACATACATTGTG 57.228 40.909 0.00 0.00 38.99 3.33
450 619 5.072741 AGAAACAGCTCCAACATACATTGT 58.927 37.500 0.00 0.00 41.53 2.71
451 620 5.633830 AGAAACAGCTCCAACATACATTG 57.366 39.130 0.00 0.00 0.00 2.82
452 621 5.769662 TGAAGAAACAGCTCCAACATACATT 59.230 36.000 0.00 0.00 0.00 2.71
453 622 5.182001 GTGAAGAAACAGCTCCAACATACAT 59.818 40.000 0.00 0.00 0.00 2.29
454 623 4.515191 GTGAAGAAACAGCTCCAACATACA 59.485 41.667 0.00 0.00 0.00 2.29
455 624 4.377431 CGTGAAGAAACAGCTCCAACATAC 60.377 45.833 0.00 0.00 0.00 2.39
456 625 3.745975 CGTGAAGAAACAGCTCCAACATA 59.254 43.478 0.00 0.00 0.00 2.29
457 626 2.549754 CGTGAAGAAACAGCTCCAACAT 59.450 45.455 0.00 0.00 0.00 2.71
458 627 1.939934 CGTGAAGAAACAGCTCCAACA 59.060 47.619 0.00 0.00 0.00 3.33
459 628 1.264288 CCGTGAAGAAACAGCTCCAAC 59.736 52.381 0.00 0.00 0.00 3.77
460 629 1.140052 TCCGTGAAGAAACAGCTCCAA 59.860 47.619 0.00 0.00 0.00 3.53
461 630 0.756294 TCCGTGAAGAAACAGCTCCA 59.244 50.000 0.00 0.00 0.00 3.86
462 631 1.270358 ACTCCGTGAAGAAACAGCTCC 60.270 52.381 0.00 0.00 0.00 4.70
463 632 1.795286 CACTCCGTGAAGAAACAGCTC 59.205 52.381 0.00 0.00 35.23 4.09
464 633 1.871080 CACTCCGTGAAGAAACAGCT 58.129 50.000 0.00 0.00 35.23 4.24
465 634 0.235926 GCACTCCGTGAAGAAACAGC 59.764 55.000 0.00 0.00 35.23 4.40
466 635 1.871080 AGCACTCCGTGAAGAAACAG 58.129 50.000 0.00 0.00 35.23 3.16
467 636 2.158957 AGAAGCACTCCGTGAAGAAACA 60.159 45.455 0.00 0.00 35.23 2.83
468 637 2.484889 AGAAGCACTCCGTGAAGAAAC 58.515 47.619 0.00 0.00 35.23 2.78
469 638 2.910688 AGAAGCACTCCGTGAAGAAA 57.089 45.000 0.00 0.00 35.23 2.52
470 639 3.509967 TGATAGAAGCACTCCGTGAAGAA 59.490 43.478 0.00 0.00 35.23 2.52
471 640 3.089284 TGATAGAAGCACTCCGTGAAGA 58.911 45.455 0.00 0.00 35.23 2.87
472 641 3.510388 TGATAGAAGCACTCCGTGAAG 57.490 47.619 0.00 0.00 35.23 3.02
473 642 3.701542 AGATGATAGAAGCACTCCGTGAA 59.298 43.478 0.00 0.00 35.23 3.18
474 643 3.291584 AGATGATAGAAGCACTCCGTGA 58.708 45.455 0.00 0.00 35.23 4.35
475 644 3.724508 AGATGATAGAAGCACTCCGTG 57.275 47.619 0.00 0.00 36.51 4.94
476 645 4.160439 TCAAAGATGATAGAAGCACTCCGT 59.840 41.667 0.00 0.00 0.00 4.69
486 655 6.324770 TGGTAGCAGTCATCAAAGATGATAGA 59.675 38.462 12.31 0.00 44.53 1.98
616 796 9.297586 GACGGAATTAATAAAATTGGAGAAACC 57.702 33.333 0.00 0.00 39.54 3.27
666 854 6.861593 CGGAGCCCGGCTAAGAATTAGTAC 62.862 54.167 13.29 0.00 43.77 2.73
667 855 4.866858 CGGAGCCCGGCTAAGAATTAGTA 61.867 52.174 13.29 0.00 43.77 1.82
668 856 4.177120 CGGAGCCCGGCTAAGAATTAGT 62.177 54.545 13.29 0.00 43.77 2.24
669 857 1.605712 CGGAGCCCGGCTAAGAATTAG 60.606 57.143 13.29 0.00 44.30 1.73
702 890 7.448469 TCATCCTTTTTCTTTTCCTTCGAATCT 59.552 33.333 0.00 0.00 0.00 2.40
735 926 1.337384 TGGATCATAGCCGTGCACCT 61.337 55.000 12.15 6.03 0.00 4.00
736 927 1.146041 TGGATCATAGCCGTGCACC 59.854 57.895 12.15 0.00 0.00 5.01
737 928 0.461870 TGTGGATCATAGCCGTGCAC 60.462 55.000 6.82 6.82 35.16 4.57
738 929 0.461870 GTGTGGATCATAGCCGTGCA 60.462 55.000 0.00 0.00 0.00 4.57
739 930 0.461870 TGTGTGGATCATAGCCGTGC 60.462 55.000 0.00 0.00 0.00 5.34
740 931 1.290203 GTGTGTGGATCATAGCCGTG 58.710 55.000 0.00 0.00 0.00 4.94
741 932 0.179111 CGTGTGTGGATCATAGCCGT 60.179 55.000 0.00 0.00 0.00 5.68
742 933 1.490693 GCGTGTGTGGATCATAGCCG 61.491 60.000 0.00 0.00 0.00 5.52
743 934 0.179073 AGCGTGTGTGGATCATAGCC 60.179 55.000 0.00 0.00 0.00 3.93
744 935 1.212616 GAGCGTGTGTGGATCATAGC 58.787 55.000 0.00 0.00 0.00 2.97
745 936 1.481240 CGAGCGTGTGTGGATCATAG 58.519 55.000 0.00 0.00 0.00 2.23
746 937 0.527600 GCGAGCGTGTGTGGATCATA 60.528 55.000 0.00 0.00 0.00 2.15
747 938 1.811266 GCGAGCGTGTGTGGATCAT 60.811 57.895 0.00 0.00 0.00 2.45
748 939 2.432456 GCGAGCGTGTGTGGATCA 60.432 61.111 0.00 0.00 0.00 2.92
749 940 3.188786 GGCGAGCGTGTGTGGATC 61.189 66.667 0.00 0.00 0.00 3.36
750 941 4.760047 GGGCGAGCGTGTGTGGAT 62.760 66.667 0.00 0.00 0.00 3.41
752 943 4.988598 AAGGGCGAGCGTGTGTGG 62.989 66.667 0.00 0.00 0.00 4.17
753 944 3.414700 GAAGGGCGAGCGTGTGTG 61.415 66.667 0.00 0.00 0.00 3.82
754 945 3.865929 CTGAAGGGCGAGCGTGTGT 62.866 63.158 0.00 0.00 0.00 3.72
755 946 3.114616 CTGAAGGGCGAGCGTGTG 61.115 66.667 0.00 0.00 0.00 3.82
759 950 3.494336 CTTGCTGAAGGGCGAGCG 61.494 66.667 0.00 0.00 38.09 5.03
777 968 2.225963 CCAGTTTCTGCTCTCTGCTTTG 59.774 50.000 0.00 0.00 43.37 2.77
785 976 1.002430 TCGCATTCCAGTTTCTGCTCT 59.998 47.619 0.00 0.00 32.48 4.09
786 977 1.442769 TCGCATTCCAGTTTCTGCTC 58.557 50.000 0.00 0.00 32.48 4.26
837 1028 1.466851 GCTGTGCCTGCTCCCTTTTT 61.467 55.000 0.00 0.00 0.00 1.94
839 1030 2.282745 GCTGTGCCTGCTCCCTTT 60.283 61.111 0.00 0.00 0.00 3.11
842 1033 3.368571 GTTGCTGTGCCTGCTCCC 61.369 66.667 5.84 0.00 0.00 4.30
843 1034 2.595463 TGTTGCTGTGCCTGCTCC 60.595 61.111 5.84 0.00 0.00 4.70
874 1065 9.502145 TTTGAATTGCATCGATTGATAAAGTAC 57.498 29.630 0.00 0.00 32.18 2.73
1004 1195 0.880278 CATATCCGTTGGCCTGTCCG 60.880 60.000 3.32 0.15 37.80 4.79
2125 2353 4.161295 CTCCGCGATGCCCTCCAA 62.161 66.667 8.23 0.00 0.00 3.53
2156 2384 3.777925 CGAAGAACGGCCAGCACG 61.778 66.667 2.24 0.00 38.46 5.34
2324 2552 2.579684 GATGTCCCTCGTCACCTGCC 62.580 65.000 0.00 0.00 32.71 4.85
2333 2561 2.278857 CTTCGGCGATGTCCCTCG 60.279 66.667 11.76 0.00 41.54 4.63
2496 2725 6.316890 CACACCACAGAATATCACATGATCAA 59.683 38.462 0.00 0.00 36.05 2.57
2499 2728 5.748402 ACACACCACAGAATATCACATGAT 58.252 37.500 0.00 0.00 38.51 2.45
2732 3023 3.577649 TTGTCGACTCTGCTAGAAAGG 57.422 47.619 17.92 0.00 0.00 3.11
3211 5168 1.066787 GCGTTAAGGCTTCCTCTCAGT 60.067 52.381 12.78 0.00 30.89 3.41
3377 5363 4.022849 CGTGATGGATCTAGTAGCACATGA 60.023 45.833 0.00 0.00 0.00 3.07



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

AutoCloner maintained by Alex Coulton.