Multiple sequence alignment - TraesCS5B01G511400

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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 TraesCS5B01G511400 chr5B 100.000 3559 0 0 1 3559 676550462 676546904 0.000000e+00 6573
1 TraesCS5B01G511400 chr5B 84.086 1904 190 51 980 2804 676538061 676536192 0.000000e+00 1733
2 TraesCS5B01G511400 chr5B 78.449 993 162 38 1643 2605 676461955 676462925 5.080000e-168 601
3 TraesCS5B01G511400 chr5B 86.099 223 28 3 79 301 535145117 535145336 1.650000e-58 237
4 TraesCS5B01G511400 chr5B 92.188 128 7 2 553 680 344711937 344712061 1.020000e-40 178
5 TraesCS5B01G511400 chr5B 94.737 114 5 1 562 674 519183431 519183544 3.650000e-40 176
6 TraesCS5B01G511400 chr5D 90.512 2909 206 36 676 3559 536280488 536277625 0.000000e+00 3779
7 TraesCS5B01G511400 chr5D 88.243 2909 258 45 685 3559 536024882 536027740 0.000000e+00 3400
8 TraesCS5B01G511400 chr5D 81.457 2389 271 98 815 3121 536255064 536252766 0.000000e+00 1799
9 TraesCS5B01G511400 chr5D 84.872 509 40 19 1 508 536284172 536283700 2.490000e-131 479
10 TraesCS5B01G511400 chr5D 79.661 590 53 36 1 565 37121318 37120771 2.610000e-96 363
11 TraesCS5B01G511400 chr5D 82.812 320 28 11 988 1284 535996604 535996919 9.800000e-66 261
12 TraesCS5B01G511400 chr5D 77.233 347 43 22 923 1233 536003524 536003870 1.700000e-38 171
13 TraesCS5B01G511400 chr5D 75.802 343 45 25 923 1233 536095581 536095917 4.790000e-29 139
14 TraesCS5B01G511400 chr4A 89.318 2771 203 44 819 3556 635303490 635300780 0.000000e+00 3391
15 TraesCS5B01G511400 chr4A 91.273 1971 115 34 856 2805 635744901 635742967 0.000000e+00 2634
16 TraesCS5B01G511400 chr4A 83.266 1990 210 58 813 2726 635275868 635273926 0.000000e+00 1716
17 TraesCS5B01G511400 chr4A 86.659 892 68 27 2197 3053 635300335 635299460 0.000000e+00 941
18 TraesCS5B01G511400 chr4A 80.569 808 117 26 1828 2607 635863384 635862589 1.420000e-163 586
19 TraesCS5B01G511400 chr4A 81.327 407 42 23 906 1284 633378252 633378652 2.080000e-77 300
20 TraesCS5B01G511400 chr4A 78.601 486 56 19 56 531 503707989 503707542 9.730000e-71 278
21 TraesCS5B01G511400 chr4A 76.723 537 100 17 1625 2145 633378956 633379483 3.500000e-70 276
22 TraesCS5B01G511400 chr4A 79.950 399 49 15 909 1287 635864686 635864299 7.580000e-67 265
23 TraesCS5B01G511400 chr4A 79.236 419 47 15 56 473 311019630 311019251 4.560000e-64 255
24 TraesCS5B01G511400 chr4A 77.211 294 38 15 968 1233 633720101 633720393 1.030000e-30 145
25 TraesCS5B01G511400 chr3D 79.701 468 51 15 56 513 577565592 577565159 7.470000e-77 298
26 TraesCS5B01G511400 chr3D 78.706 479 52 20 64 531 367463422 367462983 1.260000e-69 274
27 TraesCS5B01G511400 chr3D 79.279 333 55 9 3229 3553 303562005 303562331 1.660000e-53 220
28 TraesCS5B01G511400 chr5A 78.102 548 58 27 1 520 561176544 561177057 1.250000e-74 291
29 TraesCS5B01G511400 chr1D 84.466 309 32 7 3 299 402839110 402838806 1.250000e-74 291
30 TraesCS5B01G511400 chr2D 81.587 315 42 7 3255 3553 645666333 645666019 2.740000e-61 246
31 TraesCS5B01G511400 chr2D 82.182 275 38 6 3216 3484 258812210 258812479 3.570000e-55 226
32 TraesCS5B01G511400 chr2A 81.818 308 43 8 3259 3555 49759993 49759688 2.740000e-61 246
33 TraesCS5B01G511400 chr2A 85.149 202 17 5 369 557 764192141 764191940 1.010000e-45 195
34 TraesCS5B01G511400 chr2A 93.966 116 7 0 561 676 16546932 16547047 3.650000e-40 176
35 TraesCS5B01G511400 chr3A 77.822 505 38 34 1 473 586867518 586867056 9.870000e-61 244
36 TraesCS5B01G511400 chr6A 80.968 310 53 5 3252 3555 374426155 374426464 1.280000e-59 241
37 TraesCS5B01G511400 chr6A 86.127 173 15 1 369 532 1669759 1669587 1.020000e-40 178
38 TraesCS5B01G511400 chr7D 79.772 351 53 8 3215 3548 601911232 601910883 4.590000e-59 239
39 TraesCS5B01G511400 chr1B 84.426 244 32 5 56 299 540736336 540736099 5.940000e-58 235
40 TraesCS5B01G511400 chr1B 95.370 108 5 0 568 675 604145108 604145215 4.720000e-39 172
41 TraesCS5B01G511400 chr7A 75.639 587 74 43 1 565 667427164 667426625 9.940000e-56 228
42 TraesCS5B01G511400 chr7B 79.279 333 56 8 3213 3538 21199786 21199460 1.660000e-53 220
43 TraesCS5B01G511400 chr7B 95.614 114 4 1 565 677 548384357 548384244 7.850000e-42 182
44 TraesCS5B01G511400 chr3B 88.953 172 16 3 369 539 448762536 448762367 3.600000e-50 209
45 TraesCS5B01G511400 chr3B 83.889 180 16 5 369 539 415042107 415041932 3.680000e-35 159
46 TraesCS5B01G511400 chr6B 96.364 110 4 0 568 677 214085049 214085158 7.850000e-42 182
47 TraesCS5B01G511400 chr2B 94.783 115 4 2 568 680 66708875 66708761 1.020000e-40 178
48 TraesCS5B01G511400 chr2B 92.562 121 8 1 567 686 25114370 25114490 4.720000e-39 172
49 TraesCS5B01G511400 chrUn 94.017 117 5 2 560 674 77508696 77508812 3.650000e-40 176


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 TraesCS5B01G511400 chr5B 676546904 676550462 3558 True 6573.0 6573 100.0000 1 3559 1 chr5B.!!$R2 3558
1 TraesCS5B01G511400 chr5B 676536192 676538061 1869 True 1733.0 1733 84.0860 980 2804 1 chr5B.!!$R1 1824
2 TraesCS5B01G511400 chr5B 676461955 676462925 970 False 601.0 601 78.4490 1643 2605 1 chr5B.!!$F4 962
3 TraesCS5B01G511400 chr5D 536024882 536027740 2858 False 3400.0 3400 88.2430 685 3559 1 chr5D.!!$F3 2874
4 TraesCS5B01G511400 chr5D 536277625 536284172 6547 True 2129.0 3779 87.6920 1 3559 2 chr5D.!!$R3 3558
5 TraesCS5B01G511400 chr5D 536252766 536255064 2298 True 1799.0 1799 81.4570 815 3121 1 chr5D.!!$R2 2306
6 TraesCS5B01G511400 chr5D 37120771 37121318 547 True 363.0 363 79.6610 1 565 1 chr5D.!!$R1 564
7 TraesCS5B01G511400 chr4A 635742967 635744901 1934 True 2634.0 2634 91.2730 856 2805 1 chr4A.!!$R4 1949
8 TraesCS5B01G511400 chr4A 635299460 635303490 4030 True 2166.0 3391 87.9885 819 3556 2 chr4A.!!$R5 2737
9 TraesCS5B01G511400 chr4A 635273926 635275868 1942 True 1716.0 1716 83.2660 813 2726 1 chr4A.!!$R3 1913
10 TraesCS5B01G511400 chr4A 635862589 635864686 2097 True 425.5 586 80.2595 909 2607 2 chr4A.!!$R6 1698
11 TraesCS5B01G511400 chr4A 633378252 633379483 1231 False 288.0 300 79.0250 906 2145 2 chr4A.!!$F2 1239
12 TraesCS5B01G511400 chr5A 561176544 561177057 513 False 291.0 291 78.1020 1 520 1 chr5A.!!$F1 519
13 TraesCS5B01G511400 chr7A 667426625 667427164 539 True 228.0 228 75.6390 1 565 1 chr7A.!!$R1 564

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
676 3667 0.911769 TCCGAACGGAGGGAGTAGTA 59.088 55.0 12.04 0.0 39.76 1.82 F
1589 4863 0.321034 TCAGCAACAGCAGTAGCAGG 60.321 55.0 0.00 0.0 45.49 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2557 6345 0.182775 ACTTGAGTGACCGGGCTTTT 59.817 50.0 9.82 0.0 0.00 2.27 R
2813 6610 0.527565 GGAGCGTGTGCAATGGAATT 59.472 50.0 0.00 0.0 46.23 2.17 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
62 77 6.907206 ACACCAATTTTGAAATGTCTGTTG 57.093 33.333 0.00 0.00 0.00 3.33
111 126 5.803020 AATGCTTAAAAACCGTTTGCAAA 57.197 30.435 8.05 8.05 32.66 3.68
185 219 7.857734 AAATGTTCCCAAATTCGAAAAACTT 57.142 28.000 0.00 0.00 0.00 2.66
277 311 5.984926 GTGAATTTTGAAGAATGAACTGCCA 59.015 36.000 0.00 0.00 0.00 4.92
278 312 6.479660 GTGAATTTTGAAGAATGAACTGCCAA 59.520 34.615 0.00 0.00 0.00 4.52
349 385 9.709495 TGGAATTCAGAAATACCAAGATTTTTG 57.291 29.630 7.93 0.00 34.04 2.44
350 386 9.927668 GGAATTCAGAAATACCAAGATTTTTGA 57.072 29.630 7.93 0.00 37.85 2.69
354 390 9.528018 TTCAGAAATACCAAGATTTTTGACAAC 57.472 29.630 2.59 0.00 38.77 3.32
355 391 8.141268 TCAGAAATACCAAGATTTTTGACAACC 58.859 33.333 0.00 0.00 35.89 3.77
356 392 7.925483 CAGAAATACCAAGATTTTTGACAACCA 59.075 33.333 0.00 0.00 34.43 3.67
357 393 8.482128 AGAAATACCAAGATTTTTGACAACCAA 58.518 29.630 0.00 0.00 0.00 3.67
358 394 8.661352 AAATACCAAGATTTTTGACAACCAAG 57.339 30.769 0.00 0.00 35.94 3.61
359 395 5.930837 ACCAAGATTTTTGACAACCAAGA 57.069 34.783 0.00 0.00 35.94 3.02
360 396 6.484364 ACCAAGATTTTTGACAACCAAGAT 57.516 33.333 0.00 0.00 35.94 2.40
361 397 7.595819 ACCAAGATTTTTGACAACCAAGATA 57.404 32.000 0.00 0.00 35.94 1.98
362 398 8.193953 ACCAAGATTTTTGACAACCAAGATAT 57.806 30.769 0.00 0.00 35.94 1.63
363 399 8.650490 ACCAAGATTTTTGACAACCAAGATATT 58.350 29.630 0.00 0.00 35.94 1.28
364 400 8.928733 CCAAGATTTTTGACAACCAAGATATTG 58.071 33.333 0.00 0.00 35.94 1.90
489 535 6.589139 TGCATTTGTTTCAAAATCATGCGATA 59.411 30.769 11.26 0.00 0.00 2.92
505 551 7.144661 TCATGCGATAAGTTGTGAACAAAATT 58.855 30.769 0.00 0.00 37.63 1.82
532 2315 7.614974 TGGTCATTGTCATTGGAGATTTTGATA 59.385 33.333 0.00 0.00 0.00 2.15
566 2765 3.561143 TGCAACACACAGGTCCTTTTAT 58.439 40.909 0.00 0.00 0.00 1.40
573 2772 4.941873 CACACAGGTCCTTTTATTACTCCC 59.058 45.833 0.00 0.00 0.00 4.30
576 2775 4.473922 ACAGGTCCTTTTATTACTCCCTCC 59.526 45.833 0.00 0.00 0.00 4.30
579 2778 4.080695 GGTCCTTTTATTACTCCCTCCGTT 60.081 45.833 0.00 0.00 0.00 4.44
580 2779 5.114780 GTCCTTTTATTACTCCCTCCGTTC 58.885 45.833 0.00 0.00 0.00 3.95
581 2780 4.778958 TCCTTTTATTACTCCCTCCGTTCA 59.221 41.667 0.00 0.00 0.00 3.18
582 2781 5.248934 TCCTTTTATTACTCCCTCCGTTCAA 59.751 40.000 0.00 0.00 0.00 2.69
584 2783 6.431852 CCTTTTATTACTCCCTCCGTTCAAAA 59.568 38.462 0.00 0.00 0.00 2.44
590 2789 4.981812 ACTCCCTCCGTTCAAAATTACTT 58.018 39.130 0.00 0.00 0.00 2.24
591 2790 4.760204 ACTCCCTCCGTTCAAAATTACTTG 59.240 41.667 0.00 0.00 0.00 3.16
592 2791 4.721132 TCCCTCCGTTCAAAATTACTTGT 58.279 39.130 0.00 0.00 0.00 3.16
594 2793 4.378046 CCCTCCGTTCAAAATTACTTGTCG 60.378 45.833 0.00 0.00 0.00 4.35
597 2796 6.400727 CCTCCGTTCAAAATTACTTGTCGTAG 60.401 42.308 8.26 0.00 0.00 3.51
598 2797 6.215121 TCCGTTCAAAATTACTTGTCGTAGA 58.785 36.000 0.00 0.00 0.00 2.59
600 2799 7.224362 TCCGTTCAAAATTACTTGTCGTAGAAA 59.776 33.333 0.00 0.00 39.69 2.52
601 2800 8.013378 CCGTTCAAAATTACTTGTCGTAGAAAT 58.987 33.333 0.00 0.00 39.69 2.17
647 2846 9.967346 TTAGTTCTAGATACATCCATTTTCGAG 57.033 33.333 0.00 0.00 0.00 4.04
649 2848 8.138712 AGTTCTAGATACATCCATTTTCGAGAC 58.861 37.037 0.00 0.00 0.00 3.36
656 3647 8.964476 ATACATCCATTTTCGAGACAAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
658 3649 7.752695 ACATCCATTTTCGAGACAAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
659 3650 6.737254 TCCATTTTCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
660 3651 5.350365 TCCATTTTCGAGACAAGTAATTCCG 59.650 40.000 0.00 0.00 0.00 4.30
668 3659 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
671 3662 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
672 3663 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
673 3664 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
676 3667 0.911769 TCCGAACGGAGGGAGTAGTA 59.088 55.000 12.04 0.00 39.76 1.82
677 3668 1.281867 TCCGAACGGAGGGAGTAGTAA 59.718 52.381 12.04 0.00 39.76 2.24
678 3669 2.094675 CCGAACGGAGGGAGTAGTAAA 58.905 52.381 7.53 0.00 37.50 2.01
679 3670 2.692041 CCGAACGGAGGGAGTAGTAAAT 59.308 50.000 7.53 0.00 37.50 1.40
680 3671 3.131755 CCGAACGGAGGGAGTAGTAAATT 59.868 47.826 7.53 0.00 37.50 1.82
681 3672 4.339247 CCGAACGGAGGGAGTAGTAAATTA 59.661 45.833 7.53 0.00 37.50 1.40
682 3673 5.277047 CGAACGGAGGGAGTAGTAAATTAC 58.723 45.833 0.00 0.00 0.00 1.89
683 3674 5.163622 CGAACGGAGGGAGTAGTAAATTACA 60.164 44.000 5.89 0.00 0.00 2.41
712 3802 3.959535 ATCATTCGTTTTGCCATGGTT 57.040 38.095 14.67 0.00 0.00 3.67
725 3815 2.479560 GCCATGGTTAAATCCAGAACGC 60.480 50.000 14.67 0.00 41.05 4.84
730 3820 1.664151 GTTAAATCCAGAACGCTCGGG 59.336 52.381 0.00 0.00 38.21 5.14
733 3823 3.379445 TCCAGAACGCTCGGGACC 61.379 66.667 3.39 0.00 40.58 4.46
741 3831 4.301027 GCTCGGGACCTATGGGCG 62.301 72.222 0.00 0.00 35.63 6.13
742 3832 2.838225 CTCGGGACCTATGGGCGT 60.838 66.667 0.00 0.00 35.63 5.68
746 3836 2.108362 GGACCTATGGGCGTTCCG 59.892 66.667 0.00 0.00 38.76 4.30
747 3837 2.428925 GGACCTATGGGCGTTCCGA 61.429 63.158 0.00 0.00 38.76 4.55
786 3876 3.367498 GCATAAAATTTGGGCCGTACACA 60.367 43.478 0.00 0.00 0.00 3.72
880 3972 2.028930 ACACTAAAGCCTTCGTCCTCTG 60.029 50.000 0.00 0.00 0.00 3.35
915 4007 1.266989 CGTATCGACATCCTGCTGCTA 59.733 52.381 0.00 0.00 0.00 3.49
947 4051 1.628846 TCTCAAACCCTACCTTGCTCC 59.371 52.381 0.00 0.00 0.00 4.70
1046 4160 3.127533 GCTTGACTCCGCCGCATT 61.128 61.111 0.00 0.00 0.00 3.56
1299 4506 0.652592 CCGCAGCTTGCTGTATGTAC 59.347 55.000 21.55 5.28 42.25 2.90
1310 4517 3.978687 GCTGTATGTACTGCGGATTACT 58.021 45.455 0.00 0.00 40.42 2.24
1322 4529 0.736325 GGATTACTGCGACGCTGTGT 60.736 55.000 33.85 24.46 40.67 3.72
1323 4530 1.468565 GGATTACTGCGACGCTGTGTA 60.469 52.381 33.85 24.04 40.67 2.90
1324 4531 1.846782 GATTACTGCGACGCTGTGTAG 59.153 52.381 33.85 19.94 40.67 2.74
1442 4688 2.571757 CGGCGTCAAGGTCTAGCA 59.428 61.111 0.00 0.00 0.00 3.49
1461 4709 0.964358 AGTAGGGCGCGTCAGTTAGT 60.964 55.000 14.93 1.55 0.00 2.24
1463 4721 0.604578 TAGGGCGCGTCAGTTAGTTT 59.395 50.000 14.93 0.00 0.00 2.66
1471 4729 1.719780 CGTCAGTTAGTTTCCTCGCAC 59.280 52.381 0.00 0.00 0.00 5.34
1520 4780 4.225497 GCTAATCGGCCTGCAACT 57.775 55.556 0.00 0.00 0.00 3.16
1540 4800 0.723981 GCAAGTTCATCTGTCGAGCC 59.276 55.000 0.00 0.00 0.00 4.70
1542 4802 1.066573 CAAGTTCATCTGTCGAGCCCT 60.067 52.381 0.00 0.00 0.00 5.19
1544 4804 1.751924 AGTTCATCTGTCGAGCCCTAC 59.248 52.381 0.00 0.00 0.00 3.18
1545 4805 1.751924 GTTCATCTGTCGAGCCCTACT 59.248 52.381 0.00 0.00 0.00 2.57
1546 4806 2.145397 TCATCTGTCGAGCCCTACTT 57.855 50.000 0.00 0.00 0.00 2.24
1547 4807 3.292492 TCATCTGTCGAGCCCTACTTA 57.708 47.619 0.00 0.00 0.00 2.24
1552 4821 1.034292 GTCGAGCCCTACTTACCCGT 61.034 60.000 0.00 0.00 0.00 5.28
1560 4834 3.598747 TACTTACCCGTCCGCCCCA 62.599 63.158 0.00 0.00 0.00 4.96
1577 4851 2.288395 CCCCACATTTCAGTTCAGCAAC 60.288 50.000 0.00 0.00 0.00 4.17
1589 4863 0.321034 TCAGCAACAGCAGTAGCAGG 60.321 55.000 0.00 0.00 45.49 4.85
1641 4922 6.372103 TGACGTGTATTTTCCGAATTACCATT 59.628 34.615 0.00 0.00 0.00 3.16
1658 4939 4.739793 ACCATTTCATTCAGGTGGAGAAA 58.260 39.130 0.00 0.00 34.13 2.52
1886 5624 1.072505 GTGGAGGTGCCGGAAGAAA 59.927 57.895 5.05 0.00 40.66 2.52
1888 5626 1.377333 GGAGGTGCCGGAAGAAAGG 60.377 63.158 5.05 0.00 0.00 3.11
2109 5859 3.009473 AGAACCTATTCTGCCTGCTGAAA 59.991 43.478 14.14 5.05 43.86 2.69
2306 6073 0.698238 TCCACTGCCTGCTAAACCAT 59.302 50.000 0.00 0.00 0.00 3.55
2346 6128 7.593644 ACAGTCCGAAATGCAACTTAATTTTAC 59.406 33.333 0.00 0.00 0.00 2.01
2526 6314 2.747855 CGGCACCAAGAGGAAGGC 60.748 66.667 0.00 0.00 38.69 4.35
2557 6345 0.413832 AGAGGTGGAGGAAGCCTGTA 59.586 55.000 0.00 0.00 31.76 2.74
2599 6387 2.739932 GCTGATGATGTCGTAGTGCCTT 60.740 50.000 0.00 0.00 0.00 4.35
2608 6396 0.248539 CGTAGTGCCTTAGTCTCGGC 60.249 60.000 6.21 6.21 46.46 5.54
2612 6400 2.577593 GCCTTAGTCTCGGCGGTT 59.422 61.111 7.21 0.00 36.45 4.44
2650 6440 2.425312 GCTCAGCTTAGTCTGCTCAGTA 59.575 50.000 0.00 0.00 38.92 2.74
2747 6543 0.174845 TGGCCGTTAGATCGAACTGG 59.825 55.000 15.46 17.06 0.00 4.00
2750 6546 2.395654 GCCGTTAGATCGAACTGGATC 58.604 52.381 23.25 10.36 42.52 3.36
2786 6583 4.418392 GTGTCGTCTAATCGTAATGGTGT 58.582 43.478 0.00 0.00 0.00 4.16
2805 6602 0.961019 TGATGCAGCCACTGTTTTCC 59.039 50.000 0.00 0.00 33.43 3.13
2813 6610 0.250553 CCACTGTTTTCCTGCGGGTA 60.251 55.000 12.43 0.00 0.00 3.69
2825 6622 0.814457 TGCGGGTAATTCCATTGCAC 59.186 50.000 0.00 0.00 36.15 4.57
2870 6679 0.946528 TATGCGTGCCTGAATGATGC 59.053 50.000 0.00 0.00 0.00 3.91
2875 6684 0.376152 GTGCCTGAATGATGCGACAG 59.624 55.000 0.00 0.00 0.00 3.51
2883 6692 5.525012 CCTGAATGATGCGACAGAAATCTAA 59.475 40.000 0.00 0.00 32.90 2.10
2962 6771 4.506255 CTGGCCCCGGATGGAACC 62.506 72.222 0.73 0.00 37.49 3.62
2991 6800 9.675464 AAGAATGCAATTAATTTGTCAATGGAT 57.325 25.926 0.00 0.00 36.07 3.41
2993 6802 7.795482 ATGCAATTAATTTGTCAATGGATGG 57.205 32.000 0.00 0.00 37.65 3.51
2998 6807 8.415553 CAATTAATTTGTCAATGGATGGAGCTA 58.584 33.333 0.00 0.00 0.00 3.32
2999 6808 5.841957 AATTTGTCAATGGATGGAGCTAC 57.158 39.130 0.00 0.00 0.00 3.58
3000 6809 3.281727 TTGTCAATGGATGGAGCTACC 57.718 47.619 0.00 0.00 39.54 3.18
3001 6810 2.481441 TGTCAATGGATGGAGCTACCT 58.519 47.619 0.00 0.00 39.86 3.08
3002 6811 2.846206 TGTCAATGGATGGAGCTACCTT 59.154 45.455 0.00 0.00 39.86 3.50
3006 6815 4.660303 TCAATGGATGGAGCTACCTTGTAT 59.340 41.667 0.00 0.00 39.86 2.29
3007 6816 5.843969 TCAATGGATGGAGCTACCTTGTATA 59.156 40.000 0.00 0.00 39.86 1.47
3184 6998 6.217294 GGAAATAGATACTTCCTTCGTCTGG 58.783 44.000 0.00 0.00 38.48 3.86
3190 7004 7.045126 AGATACTTCCTTCGTCTGGAATTAG 57.955 40.000 6.91 0.52 42.03 1.73
3196 7010 5.235516 TCCTTCGTCTGGAATTAGTTGTTC 58.764 41.667 0.00 0.00 33.26 3.18
3239 7057 8.396272 CTTTCTTTTCATGGGAGAAAGTTCTA 57.604 34.615 23.56 6.08 45.61 2.10
3240 7058 7.986085 TTCTTTTCATGGGAGAAAGTTCTAG 57.014 36.000 0.00 0.00 38.60 2.43
3282 7100 5.189928 TGGCAGTACAAAGAACAAAAGAGA 58.810 37.500 0.00 0.00 0.00 3.10
3306 7124 5.941555 AACAAAAATTACAACCAGGTCCA 57.058 34.783 0.00 0.00 0.00 4.02
3308 7126 7.604657 AACAAAAATTACAACCAGGTCCATA 57.395 32.000 0.00 0.00 0.00 2.74
3398 7216 0.035739 GGAGCCGGACAAACCTTGTA 59.964 55.000 5.05 0.00 45.52 2.41
3409 7232 0.834687 AACCTTGTAGGCCAGTCGGA 60.835 55.000 5.01 0.00 39.63 4.55
3412 7235 1.065418 CCTTGTAGGCCAGTCGGAAAT 60.065 52.381 5.01 0.00 0.00 2.17
3417 7240 1.755179 AGGCCAGTCGGAAATTCATG 58.245 50.000 5.01 0.00 0.00 3.07
3461 7284 0.178981 ACACCAGAGCAGCAACCATT 60.179 50.000 0.00 0.00 0.00 3.16
3486 7309 7.704271 TGTCGATGAAGAAAGTCGTAGATTAT 58.296 34.615 0.00 0.00 40.67 1.28
3510 7333 8.936070 ATAAGGAACAAACTTGTAAACAAACC 57.064 30.769 0.00 0.00 41.31 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 74 4.142988 TGAATCGGCGAACAATTCTACAAC 60.143 41.667 15.93 0.00 31.99 3.32
62 77 4.593597 TTGAATCGGCGAACAATTCTAC 57.406 40.909 15.93 0.00 31.99 2.59
159 174 8.275015 AGTTTTTCGAATTTGGGAACATTTTT 57.725 26.923 0.00 0.00 42.32 1.94
185 219 4.338400 ACATACCTTCGATCATTCGTGAGA 59.662 41.667 0.00 0.00 45.65 3.27
213 247 8.506437 CACAAAGACTCAGAAGCATTACAATTA 58.494 33.333 0.00 0.00 0.00 1.40
277 311 7.400339 ACATACTATGATATTCCGATCCACCTT 59.600 37.037 2.90 0.00 0.00 3.50
278 312 6.897966 ACATACTATGATATTCCGATCCACCT 59.102 38.462 2.90 0.00 0.00 4.00
335 371 7.595819 TCTTGGTTGTCAAAAATCTTGGTAT 57.404 32.000 0.00 0.00 34.56 2.73
336 372 7.595819 ATCTTGGTTGTCAAAAATCTTGGTA 57.404 32.000 0.00 0.00 34.56 3.25
338 374 8.928733 CAATATCTTGGTTGTCAAAAATCTTGG 58.071 33.333 0.00 0.00 34.56 3.61
339 375 9.480053 ACAATATCTTGGTTGTCAAAAATCTTG 57.520 29.630 0.00 0.00 33.53 3.02
489 535 7.390162 ACAATGACCAAATTTTGTTCACAACTT 59.610 29.630 11.02 0.57 34.83 2.66
505 551 6.267242 TCAAAATCTCCAATGACAATGACCAA 59.733 34.615 0.00 0.00 0.00 3.67
540 2324 0.730265 GACCTGTGTGTTGCAACGAA 59.270 50.000 23.79 12.18 0.00 3.85
551 2335 4.850386 AGGGAGTAATAAAAGGACCTGTGT 59.150 41.667 0.00 0.00 0.00 3.72
566 2765 6.117975 AGTAATTTTGAACGGAGGGAGTAA 57.882 37.500 0.00 0.00 0.00 2.24
573 2772 5.338614 ACGACAAGTAATTTTGAACGGAG 57.661 39.130 13.67 0.00 36.55 4.63
576 2775 8.928844 ATTTCTACGACAAGTAATTTTGAACG 57.071 30.769 0.00 5.24 37.38 3.95
622 2821 9.350951 TCTCGAAAATGGATGTATCTAGAACTA 57.649 33.333 0.00 0.00 0.00 2.24
623 2822 8.138712 GTCTCGAAAATGGATGTATCTAGAACT 58.861 37.037 0.00 0.00 0.00 3.01
624 2823 7.921214 TGTCTCGAAAATGGATGTATCTAGAAC 59.079 37.037 0.00 0.00 0.00 3.01
625 2824 8.007405 TGTCTCGAAAATGGATGTATCTAGAA 57.993 34.615 0.00 0.00 0.00 2.10
626 2825 7.582667 TGTCTCGAAAATGGATGTATCTAGA 57.417 36.000 0.00 0.00 0.00 2.43
629 2828 6.644347 ACTTGTCTCGAAAATGGATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
630 2829 6.910536 ACTTGTCTCGAAAATGGATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
631 2830 8.964476 ATTACTTGTCTCGAAAATGGATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
632 2831 8.786826 AATTACTTGTCTCGAAAATGGATGTA 57.213 30.769 0.00 0.00 0.00 2.29
633 2832 7.148239 GGAATTACTTGTCTCGAAAATGGATGT 60.148 37.037 0.00 0.00 0.00 3.06
636 2835 5.350365 CGGAATTACTTGTCTCGAAAATGGA 59.650 40.000 0.00 0.00 0.00 3.41
637 2836 5.350365 TCGGAATTACTTGTCTCGAAAATGG 59.650 40.000 0.00 0.00 0.00 3.16
638 2837 6.403333 TCGGAATTACTTGTCTCGAAAATG 57.597 37.500 0.00 0.00 0.00 2.32
639 2838 6.400727 CGTTCGGAATTACTTGTCTCGAAAAT 60.401 38.462 0.00 0.00 37.00 1.82
641 2840 4.383649 CGTTCGGAATTACTTGTCTCGAAA 59.616 41.667 0.00 0.00 37.00 3.46
643 2842 3.495193 CGTTCGGAATTACTTGTCTCGA 58.505 45.455 0.00 0.00 0.00 4.04
644 2843 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
645 2844 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
647 2846 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
649 2848 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
656 3647 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
658 3649 1.755179 TTACTACTCCCTCCGTTCGG 58.245 55.000 4.74 4.74 0.00 4.30
659 3650 4.382345 AATTTACTACTCCCTCCGTTCG 57.618 45.455 0.00 0.00 0.00 3.95
660 3651 6.212888 TGTAATTTACTACTCCCTCCGTTC 57.787 41.667 7.99 0.00 0.00 3.95
693 3783 4.855715 TTAACCATGGCAAAACGAATGA 57.144 36.364 13.04 0.00 0.00 2.57
695 3785 5.175127 GGATTTAACCATGGCAAAACGAAT 58.825 37.500 13.04 2.84 0.00 3.34
699 3789 5.146010 TCTGGATTTAACCATGGCAAAAC 57.854 39.130 13.04 10.98 39.34 2.43
701 3791 4.321601 CGTTCTGGATTTAACCATGGCAAA 60.322 41.667 13.04 13.02 39.34 3.68
712 3802 1.134907 GTCCCGAGCGTTCTGGATTTA 60.135 52.381 15.06 0.00 38.72 1.40
725 3815 2.365095 GAACGCCCATAGGTCCCGAG 62.365 65.000 0.00 0.00 34.57 4.63
754 3844 5.566627 GCCCAAATTTTATGCGCATACCTAT 60.567 40.000 29.01 18.40 0.00 2.57
760 3850 1.805871 CGGCCCAAATTTTATGCGCAT 60.806 47.619 28.23 28.23 0.00 4.73
764 3854 3.183754 GTGTACGGCCCAAATTTTATGC 58.816 45.455 0.00 0.00 0.00 3.14
771 3861 1.459450 GACATGTGTACGGCCCAAAT 58.541 50.000 1.15 0.00 0.00 2.32
786 3876 1.346062 ACAGAGTGAGTGCTGGACAT 58.654 50.000 1.24 0.00 36.47 3.06
915 4007 3.395941 AGGGTTTGAGATTTGTGAGAGGT 59.604 43.478 0.00 0.00 0.00 3.85
947 4051 0.409876 TCGGGATCTGGAGGGATAGG 59.590 60.000 0.00 0.00 0.00 2.57
1097 4280 4.115199 ATTCGTGGGCTGGGGCTC 62.115 66.667 0.00 0.00 39.89 4.70
1210 4393 2.489528 ATTACCTGGGGATCCGAGAA 57.510 50.000 5.45 0.00 35.24 2.87
1299 4506 2.860628 GCGTCGCAGTAATCCGCAG 61.861 63.158 13.44 0.00 43.53 5.18
1304 4511 1.846782 CTACACAGCGTCGCAGTAATC 59.153 52.381 21.09 0.00 0.00 1.75
1308 4515 2.430921 GCTACACAGCGTCGCAGT 60.431 61.111 21.09 15.43 38.22 4.40
1325 4532 0.388391 GCGGAGATGCTAGCTGCTAG 60.388 60.000 28.07 28.07 43.37 3.42
1339 4546 3.597728 GGAGGTAGCGAGGCGGAG 61.598 72.222 0.00 0.00 0.00 4.63
1432 4672 1.677637 GCGCCCTACTGCTAGACCTT 61.678 60.000 0.00 0.00 0.00 3.50
1442 4688 0.964358 ACTAACTGACGCGCCCTACT 60.964 55.000 5.73 0.00 0.00 2.57
1461 4709 3.585862 GTCACAGATTAGTGCGAGGAAA 58.414 45.455 0.00 0.00 39.35 3.13
1463 4721 1.476891 GGTCACAGATTAGTGCGAGGA 59.523 52.381 0.00 0.00 39.35 3.71
1471 4729 0.811616 GCCAGCCGGTCACAGATTAG 60.812 60.000 1.90 0.00 33.28 1.73
1519 4779 1.392853 GCTCGACAGATGAACTTGCAG 59.607 52.381 0.00 0.00 0.00 4.41
1520 4780 1.432514 GCTCGACAGATGAACTTGCA 58.567 50.000 0.00 0.00 0.00 4.08
1523 4783 1.270907 AGGGCTCGACAGATGAACTT 58.729 50.000 0.00 0.00 0.00 2.66
1524 4784 1.751924 GTAGGGCTCGACAGATGAACT 59.248 52.381 0.00 0.00 0.00 3.01
1537 4797 1.755783 CGGACGGGTAAGTAGGGCT 60.756 63.158 0.00 0.00 0.00 5.19
1538 4798 2.810403 CGGACGGGTAAGTAGGGC 59.190 66.667 0.00 0.00 0.00 5.19
1540 4800 2.789715 GGGCGGACGGGTAAGTAGG 61.790 68.421 0.00 0.00 0.00 3.18
1542 4802 2.759560 GGGGCGGACGGGTAAGTA 60.760 66.667 0.00 0.00 0.00 2.24
1544 4804 4.462280 GTGGGGCGGACGGGTAAG 62.462 72.222 0.00 0.00 0.00 2.34
1552 4821 0.608035 GAACTGAAATGTGGGGCGGA 60.608 55.000 0.00 0.00 0.00 5.54
1560 4834 2.689471 TGCTGTTGCTGAACTGAAATGT 59.311 40.909 0.00 0.00 40.48 2.71
1577 4851 0.809241 GCTGCTACCTGCTACTGCTG 60.809 60.000 0.00 0.00 43.37 4.41
1598 4872 3.481467 CGTCAACGAACGAGAAAATAGCC 60.481 47.826 0.14 0.00 45.37 3.93
1602 4876 2.861935 ACACGTCAACGAACGAGAAAAT 59.138 40.909 9.88 0.00 45.37 1.82
1603 4877 2.261345 ACACGTCAACGAACGAGAAAA 58.739 42.857 9.88 0.00 45.37 2.29
1604 4878 1.912001 ACACGTCAACGAACGAGAAA 58.088 45.000 9.88 0.00 45.37 2.52
1607 4881 4.364817 AAAATACACGTCAACGAACGAG 57.635 40.909 9.88 10.08 45.37 4.18
1641 4922 4.982241 AGAGTTTCTCCACCTGAATGAA 57.018 40.909 0.00 0.00 0.00 2.57
1658 4939 1.333177 AGCAAGTCTCCACGAAGAGT 58.667 50.000 0.00 0.00 35.28 3.24
1886 5624 2.743718 CACCACCTCTTGTCGCCT 59.256 61.111 0.00 0.00 0.00 5.52
1888 5626 2.031163 AGCACCACCTCTTGTCGC 59.969 61.111 0.00 0.00 0.00 5.19
1891 5629 2.113986 GGCAGCACCACCTCTTGT 59.886 61.111 0.00 0.00 38.86 3.16
2054 5804 4.088762 CATGACGTGCGGCGCTTT 62.089 61.111 33.26 16.77 46.11 3.51
2109 5859 0.980423 GGTGCCTCCTCTTTCAGAGT 59.020 55.000 0.21 0.00 40.72 3.24
2306 6073 1.072331 GGACTGTGCCTCCTCTTTTGA 59.928 52.381 0.00 0.00 0.00 2.69
2346 6128 0.250640 AGCTTGTTCCTGACCTGCAG 60.251 55.000 6.78 6.78 44.49 4.41
2526 6314 0.321653 CCACCTCTTCTTGAACGGGG 60.322 60.000 0.00 0.00 0.00 5.73
2557 6345 0.182775 ACTTGAGTGACCGGGCTTTT 59.817 50.000 9.82 0.00 0.00 2.27
2599 6387 5.126061 AGACTAAATTAAACCGCCGAGACTA 59.874 40.000 0.00 0.00 0.00 2.59
2608 6396 8.922058 TGAGCTAACTAGACTAAATTAAACCG 57.078 34.615 0.00 0.00 0.00 4.44
2650 6440 0.956633 CACTGCAACTCAGCACCAAT 59.043 50.000 0.00 0.00 46.76 3.16
2747 6543 7.807680 AGACGACACCTTTTAAGAAATTGATC 58.192 34.615 0.00 0.00 0.00 2.92
2750 6546 9.543018 GATTAGACGACACCTTTTAAGAAATTG 57.457 33.333 0.00 0.00 0.00 2.32
2786 6583 0.961019 GGAAAACAGTGGCTGCATCA 59.039 50.000 0.50 0.00 34.37 3.07
2805 6602 1.102154 TGCAATGGAATTACCCGCAG 58.898 50.000 0.00 0.00 32.46 5.18
2813 6610 0.527565 GGAGCGTGTGCAATGGAATT 59.472 50.000 0.00 0.00 46.23 2.17
2825 6622 1.656652 CACTGAATTAGGGGAGCGTG 58.343 55.000 0.00 0.00 0.00 5.34
2870 6679 9.586150 GTATGCATGTATTTTAGATTTCTGTCG 57.414 33.333 10.16 0.00 0.00 4.35
2883 6692 6.772233 TGCAGGTAATCTGTATGCATGTATTT 59.228 34.615 10.16 0.00 45.08 1.40
2914 6723 3.170791 TCAACCATTGAGAGATCGAGC 57.829 47.619 0.00 0.00 34.08 5.03
2962 6771 7.579589 TTGACAAATTAATTGCATTCTTCCG 57.420 32.000 0.39 0.00 43.13 4.30
3107 6919 7.442969 AGTGATGCAAACATTGTGAATTCAATT 59.557 29.630 10.35 0.00 36.35 2.32
3159 6973 6.217294 CAGACGAAGGAAGTATCTATTTCCC 58.783 44.000 7.63 0.00 41.47 3.97
3173 6987 4.884668 ACAACTAATTCCAGACGAAGGA 57.115 40.909 0.00 0.00 32.78 3.36
3184 6998 5.934935 TCCGTTTGAGGAACAACTAATTC 57.065 39.130 0.00 0.00 38.18 2.17
3190 7004 1.607148 CCCTTCCGTTTGAGGAACAAC 59.393 52.381 0.00 0.00 44.66 3.32
3196 7010 0.981943 AGTACCCCTTCCGTTTGAGG 59.018 55.000 0.00 0.00 0.00 3.86
3253 7071 9.906660 CTTTTGTTCTTTGTACTGCCATAATTA 57.093 29.630 0.00 0.00 0.00 1.40
3276 7094 9.981114 CCTGGTTGTAATTTTTGTTATCTCTTT 57.019 29.630 0.00 0.00 0.00 2.52
3282 7100 7.604657 TGGACCTGGTTGTAATTTTTGTTAT 57.395 32.000 0.00 0.00 0.00 1.89
3306 7124 0.529378 GTCGTCGTTGGGTGGTCTAT 59.471 55.000 0.00 0.00 0.00 1.98
3308 7126 0.538057 TAGTCGTCGTTGGGTGGTCT 60.538 55.000 0.00 0.00 0.00 3.85
3398 7216 1.281867 TCATGAATTTCCGACTGGCCT 59.718 47.619 3.32 0.00 34.14 5.19
3409 7232 7.664731 CCTATGAGGTCTTAGCATCATGAATTT 59.335 37.037 0.00 0.00 34.38 1.82
3412 7235 5.840693 TCCTATGAGGTCTTAGCATCATGAA 59.159 40.000 0.00 0.00 36.53 2.57
3417 7240 3.898123 TGGTCCTATGAGGTCTTAGCATC 59.102 47.826 0.00 0.00 36.53 3.91
3461 7284 5.562506 ATCTACGACTTTCTTCATCGACA 57.437 39.130 0.00 0.00 39.16 4.35
3486 7309 7.893658 TGGTTTGTTTACAAGTTTGTTCCTTA 58.106 30.769 2.46 0.00 42.35 2.69
3508 7331 0.768622 TGGATCCGGTCTTTGTTGGT 59.231 50.000 7.39 0.00 0.00 3.67
3510 7333 3.367292 CCATTTGGATCCGGTCTTTGTTG 60.367 47.826 7.39 0.00 37.39 3.33


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

AutoCloner maintained by Alex Coulton.