Multiple sequence alignment - TraesCS5D01G495500

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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 TraesCS5D01G495500 chr5D 100.000 7726 0 0 1 7726 526842723 526850448 0.000000e+00 14268.0
1 TraesCS5D01G495500 chr5D 79.887 532 92 12 4175 4697 521672993 521673518 7.320000e-100 375.0
2 TraesCS5D01G495500 chr5D 93.407 91 6 0 138 228 431293733 431293823 1.350000e-27 135.0
3 TraesCS5D01G495500 chr5A 94.703 7401 301 42 367 7726 653955829 653963179 0.000000e+00 11411.0
4 TraesCS5D01G495500 chr5A 93.165 278 18 1 8 284 653955502 653955779 2.600000e-109 407.0
5 TraesCS5D01G495500 chr5A 76.433 157 30 5 7106 7258 79878581 79878734 2.310000e-10 78.7
6 TraesCS5D01G495500 chr5A 76.433 157 30 5 7106 7258 224428346 224428193 2.310000e-10 78.7
7 TraesCS5D01G495500 chr5B 95.038 5038 177 34 321 5330 662602866 662607858 0.000000e+00 7851.0
8 TraesCS5D01G495500 chr5B 93.527 2410 132 14 5326 7726 662625618 662628012 0.000000e+00 3565.0
9 TraesCS5D01G495500 chr5B 76.083 2354 432 84 474 2766 662664640 662666923 0.000000e+00 1107.0
10 TraesCS5D01G495500 chr5B 82.811 861 107 25 4833 5664 662673249 662674097 0.000000e+00 732.0
11 TraesCS5D01G495500 chr5B 82.646 703 99 15 3004 3697 662672294 662672982 1.110000e-167 601.0
12 TraesCS5D01G495500 chr5B 97.799 318 3 4 8 324 662602591 662602905 5.270000e-151 545.0
13 TraesCS5D01G495500 chr5B 82.985 335 50 6 471 802 662757527 662757857 5.860000e-76 296.0
14 TraesCS5D01G495500 chr5B 86.415 265 33 3 6467 6730 662674120 662674382 3.530000e-73 287.0
15 TraesCS5D01G495500 chr5B 92.308 104 7 1 4694 4797 662673148 662673250 6.250000e-31 147.0
16 TraesCS5D01G495500 chr5B 76.923 130 29 1 4884 5012 662674655 662674784 1.080000e-08 73.1
17 TraesCS5D01G495500 chr6B 80.729 851 115 38 3799 4615 5042885 5042050 1.100000e-172 617.0
18 TraesCS5D01G495500 chr4A 81.283 748 119 15 3961 4694 735741390 735742130 3.110000e-163 586.0
19 TraesCS5D01G495500 chr4A 80.692 751 118 21 3960 4694 736821863 736822602 6.770000e-155 558.0
20 TraesCS5D01G495500 chr4A 80.699 715 120 15 3960 4663 736426381 736425674 2.450000e-149 540.0
21 TraesCS5D01G495500 chr3D 87.283 519 53 11 3960 4467 604887034 604887550 1.450000e-161 580.0
22 TraesCS5D01G495500 chr3D 82.955 176 24 5 3995 4167 581422810 581422638 3.730000e-33 154.0
23 TraesCS5D01G495500 chr3D 93.548 93 6 0 144 236 602250729 602250821 1.050000e-28 139.0
24 TraesCS5D01G495500 chr2B 80.609 722 112 21 3960 4663 631608423 631607712 4.100000e-147 532.0
25 TraesCS5D01G495500 chr7D 91.176 102 7 1 128 229 510397744 510397843 3.760000e-28 137.0
26 TraesCS5D01G495500 chr2D 95.294 85 4 0 144 228 14895360 14895276 1.350000e-27 135.0
27 TraesCS5D01G495500 chr2D 73.793 290 64 11 7112 7394 121177846 121177562 3.810000e-18 104.0
28 TraesCS5D01G495500 chr1D 92.553 94 7 0 135 228 252473239 252473146 1.350000e-27 135.0
29 TraesCS5D01G495500 chr1D 90.196 102 9 1 128 229 187985484 187985384 1.750000e-26 132.0
30 TraesCS5D01G495500 chr2A 88.182 110 12 1 137 245 682630523 682630414 6.290000e-26 130.0
31 TraesCS5D01G495500 chr2A 72.054 297 66 15 7106 7393 79560145 79559857 1.080000e-08 73.1


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 TraesCS5D01G495500 chr5D 526842723 526850448 7725 False 14268.00 14268 100.0000 1 7726 1 chr5D.!!$F3 7725
1 TraesCS5D01G495500 chr5D 521672993 521673518 525 False 375.00 375 79.8870 4175 4697 1 chr5D.!!$F2 522
2 TraesCS5D01G495500 chr5A 653955502 653963179 7677 False 5909.00 11411 93.9340 8 7726 2 chr5A.!!$F2 7718
3 TraesCS5D01G495500 chr5B 662602591 662607858 5267 False 4198.00 7851 96.4185 8 5330 2 chr5B.!!$F4 5322
4 TraesCS5D01G495500 chr5B 662625618 662628012 2394 False 3565.00 3565 93.5270 5326 7726 1 chr5B.!!$F1 2400
5 TraesCS5D01G495500 chr5B 662664640 662666923 2283 False 1107.00 1107 76.0830 474 2766 1 chr5B.!!$F2 2292
6 TraesCS5D01G495500 chr5B 662672294 662674784 2490 False 368.02 732 84.2206 3004 6730 5 chr5B.!!$F5 3726
7 TraesCS5D01G495500 chr6B 5042050 5042885 835 True 617.00 617 80.7290 3799 4615 1 chr6B.!!$R1 816
8 TraesCS5D01G495500 chr4A 735741390 735742130 740 False 586.00 586 81.2830 3961 4694 1 chr4A.!!$F1 733
9 TraesCS5D01G495500 chr4A 736821863 736822602 739 False 558.00 558 80.6920 3960 4694 1 chr4A.!!$F2 734
10 TraesCS5D01G495500 chr4A 736425674 736426381 707 True 540.00 540 80.6990 3960 4663 1 chr4A.!!$R1 703
11 TraesCS5D01G495500 chr3D 604887034 604887550 516 False 580.00 580 87.2830 3960 4467 1 chr3D.!!$F2 507
12 TraesCS5D01G495500 chr2B 631607712 631608423 711 True 532.00 532 80.6090 3960 4663 1 chr2B.!!$R1 703

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
746 785 2.787473 TGTCATGGGCCTTTACTCAG 57.213 50.000 4.53 0.00 0.00 3.35 F
1537 1593 0.122435 TATTGGGGAGGGTTGGAGGT 59.878 55.000 0.00 0.00 0.00 3.85 F
2295 2393 0.825840 TTTGGTGCTTCGGGGGAAAG 60.826 55.000 0.00 0.00 0.00 2.62 F
2902 3006 1.376424 CAGCATGGAGAGCAACGGT 60.376 57.895 0.00 0.00 0.00 4.83 F
3165 3276 2.226674 TGCTCACTCAAGTACTGTCGAG 59.773 50.000 13.13 13.13 0.00 4.04 F
4562 4867 2.358615 GCACTGATGCCACCGTCA 60.359 61.111 0.00 0.00 46.97 4.35 F
5938 6287 0.332972 ATGGCTCCCCTTGGTTTCTC 59.667 55.000 0.00 0.00 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1696 0.320771 TCTTCCTTCGCTCAACCTGC 60.321 55.000 0.00 0.00 0.00 4.85 R
3295 3406 1.980772 GCATCTTGCAGCCCCACTT 60.981 57.895 0.00 0.00 44.26 3.16 R
3548 3664 3.918977 TGCAGCCACCACGTACGT 61.919 61.111 16.72 16.72 0.00 3.57 R
4562 4867 0.402861 TCCTCCTTCCCACCCTTGTT 60.403 55.000 0.00 0.00 0.00 2.83 R
4716 5025 0.682209 AGGATGGGTGCATGCACTTC 60.682 55.000 40.86 32.78 45.52 3.01 R
6348 6697 0.617820 TCTCCTGGTGTTAGAGGGGC 60.618 60.000 0.00 0.00 28.73 5.80 R
7091 7480 0.172803 CCGAGGTTCTTAGTCCACCG 59.827 60.000 0.00 0.00 35.54 4.94 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
150 152 9.753674 TTTATTTCAATGAATCAACTACTCCCT 57.246 29.630 0.00 0.00 0.00 4.20
152 154 6.627087 TTCAATGAATCAACTACTCCCTCT 57.373 37.500 0.00 0.00 0.00 3.69
315 348 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
316 349 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
317 350 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
318 351 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
319 352 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
320 353 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
322 355 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
323 356 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
324 357 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
326 359 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
327 360 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
328 361 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
329 362 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
330 363 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
331 364 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
332 365 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
333 366 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
334 367 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
335 368 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
336 369 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
337 370 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
338 371 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
339 372 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
340 373 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
341 374 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
342 375 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
343 376 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
344 377 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
345 378 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
346 379 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
347 380 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
348 381 4.207599 GTTGTTGTTGTTGTTGTTGTTGC 58.792 39.130 0.00 0.00 0.00 4.17
349 382 3.457234 TGTTGTTGTTGTTGTTGTTGCA 58.543 36.364 0.00 0.00 0.00 4.08
350 383 4.060900 TGTTGTTGTTGTTGTTGTTGCAT 58.939 34.783 0.00 0.00 0.00 3.96
351 384 5.230182 TGTTGTTGTTGTTGTTGTTGCATA 58.770 33.333 0.00 0.00 0.00 3.14
352 385 5.871524 TGTTGTTGTTGTTGTTGTTGCATAT 59.128 32.000 0.00 0.00 0.00 1.78
353 386 6.369890 TGTTGTTGTTGTTGTTGTTGCATATT 59.630 30.769 0.00 0.00 0.00 1.28
354 387 6.974932 TGTTGTTGTTGTTGTTGCATATTT 57.025 29.167 0.00 0.00 0.00 1.40
355 388 7.369803 TGTTGTTGTTGTTGTTGCATATTTT 57.630 28.000 0.00 0.00 0.00 1.82
356 389 7.810658 TGTTGTTGTTGTTGTTGCATATTTTT 58.189 26.923 0.00 0.00 0.00 1.94
378 411 7.644986 TTTTGTTTCCTAGTTGTTGTTGTTG 57.355 32.000 0.00 0.00 0.00 3.33
379 412 5.968528 TGTTTCCTAGTTGTTGTTGTTGT 57.031 34.783 0.00 0.00 0.00 3.32
380 413 6.334102 TGTTTCCTAGTTGTTGTTGTTGTT 57.666 33.333 0.00 0.00 0.00 2.83
381 414 6.153067 TGTTTCCTAGTTGTTGTTGTTGTTG 58.847 36.000 0.00 0.00 0.00 3.33
382 415 5.968528 TTCCTAGTTGTTGTTGTTGTTGT 57.031 34.783 0.00 0.00 0.00 3.32
454 487 6.567050 AGCACTATTTATTTCGTCGTTCCTA 58.433 36.000 0.00 0.00 0.00 2.94
745 784 3.737559 AATGTCATGGGCCTTTACTCA 57.262 42.857 4.53 0.00 0.00 3.41
746 785 2.787473 TGTCATGGGCCTTTACTCAG 57.213 50.000 4.53 0.00 0.00 3.35
804 844 3.041946 CAGCCCACCTAAATCCTAGTCT 58.958 50.000 0.00 0.00 0.00 3.24
1168 1219 1.415659 CCAAGCATTTTGGGGACACAA 59.584 47.619 0.00 0.00 42.67 3.33
1475 1531 6.040842 GGATGGCCAAGTTGTATGTCATTATT 59.959 38.462 10.96 0.00 0.00 1.40
1537 1593 0.122435 TATTGGGGAGGGTTGGAGGT 59.878 55.000 0.00 0.00 0.00 3.85
1634 1694 3.330720 AAGGGTGAAGGAGGGGCG 61.331 66.667 0.00 0.00 0.00 6.13
1764 1824 1.007734 GACACGAGCACCTCACGAA 60.008 57.895 0.00 0.00 33.00 3.85
2083 2176 2.107953 GGCATCGAGGAGGAGTGC 59.892 66.667 0.00 0.00 35.17 4.40
2295 2393 0.825840 TTTGGTGCTTCGGGGGAAAG 60.826 55.000 0.00 0.00 0.00 2.62
2622 2725 3.528491 AGTTACCACTAGCCTCTCCTACT 59.472 47.826 0.00 0.00 0.00 2.57
2667 2771 7.009179 AGCCGATATTTATCTCTTCATTCCA 57.991 36.000 0.00 0.00 0.00 3.53
2902 3006 1.376424 CAGCATGGAGAGCAACGGT 60.376 57.895 0.00 0.00 0.00 4.83
3105 3214 3.305267 CCGTCAGAAAATGGCAATCAACA 60.305 43.478 0.00 0.00 30.75 3.33
3165 3276 2.226674 TGCTCACTCAAGTACTGTCGAG 59.773 50.000 13.13 13.13 0.00 4.04
3282 3393 4.649692 TGGTTTGTTTATTAGGTACGGCA 58.350 39.130 0.00 0.00 0.00 5.69
3283 3394 5.254901 TGGTTTGTTTATTAGGTACGGCAT 58.745 37.500 0.00 0.00 0.00 4.40
3384 3495 4.097892 TGTGAGCGATGAGAAGCTAATACA 59.902 41.667 0.00 0.00 44.69 2.29
3385 3496 5.043903 GTGAGCGATGAGAAGCTAATACAA 58.956 41.667 0.00 0.00 44.69 2.41
3386 3497 5.694006 GTGAGCGATGAGAAGCTAATACAAT 59.306 40.000 0.00 0.00 44.69 2.71
3387 3498 6.863645 GTGAGCGATGAGAAGCTAATACAATA 59.136 38.462 0.00 0.00 44.69 1.90
3388 3499 7.382488 GTGAGCGATGAGAAGCTAATACAATAA 59.618 37.037 0.00 0.00 44.69 1.40
3548 3664 4.352595 TCCATGAGTTTCTAAACAAGGGGA 59.647 41.667 8.21 6.65 41.30 4.81
3784 3980 4.332819 GCCATGTAGGTCATCAGTACAAAC 59.667 45.833 0.00 0.00 40.61 2.93
3889 4085 3.071479 TCAAAATCAACCTGCGGTAGAC 58.929 45.455 0.62 0.00 33.12 2.59
3958 4158 5.486735 TCTTTAGTTAATCAACCCGTGGA 57.513 39.130 0.00 0.00 35.05 4.02
4349 4640 7.931407 ACCTTAATCAATAGTGCATGATTCGTA 59.069 33.333 14.84 4.15 43.33 3.43
4562 4867 2.358615 GCACTGATGCCACCGTCA 60.359 61.111 0.00 0.00 46.97 4.35
4596 4901 3.110705 AGGAGGATAAGCGGCATCATAT 58.889 45.455 1.45 0.00 0.00 1.78
5135 5467 8.893727 GCTATTGATTTCCTAGTTTCTTGCTTA 58.106 33.333 0.00 0.00 0.00 3.09
5155 5487 8.732746 TGCTTACACTTTTAGGGATAAATCTC 57.267 34.615 0.00 0.00 0.00 2.75
5318 5663 2.933260 GCTGCTAACTTTGAGGCTAGTC 59.067 50.000 0.00 0.00 0.00 2.59
5453 5798 2.625737 ACGCTGATCTGAATGTGAAGG 58.374 47.619 3.42 0.00 0.00 3.46
5578 5924 4.841246 AGAGCCTATCCTAATACAAGGTGG 59.159 45.833 0.00 0.00 37.91 4.61
5594 5943 5.420739 ACAAGGTGGTGTTGTTGTAGATTTT 59.579 36.000 0.00 0.00 34.37 1.82
5753 6102 7.366847 TGTTAATTTCCAAATTGTTCCTCCA 57.633 32.000 7.42 0.00 38.90 3.86
5811 6160 6.174720 AGAACAAGGTTCTGTCACTCAATA 57.825 37.500 10.59 0.00 0.00 1.90
5812 6161 5.992217 AGAACAAGGTTCTGTCACTCAATAC 59.008 40.000 10.59 0.00 0.00 1.89
5894 6243 0.847373 TTGTTGTGGGCACTAGGGAA 59.153 50.000 0.00 0.00 0.00 3.97
5938 6287 0.332972 ATGGCTCCCCTTGGTTTCTC 59.667 55.000 0.00 0.00 0.00 2.87
6058 6407 3.535561 GAATCCTCATTTCCGAAGCTCA 58.464 45.455 0.00 0.00 0.00 4.26
6067 6416 1.078709 TCCGAAGCTCATTTTGCTCG 58.921 50.000 0.00 0.00 40.22 5.03
6118 6467 6.486993 CAGGTACCTTTAGATTGGGCTAATTC 59.513 42.308 13.15 0.00 31.00 2.17
6160 6509 5.966742 ACTCTAGAAAAATTTGACTGGGC 57.033 39.130 0.00 0.00 0.00 5.36
6229 6578 6.539103 GGCCTTGAAAGTTAGTAGTTCCTATG 59.461 42.308 0.00 0.00 0.00 2.23
6284 6633 1.684248 GCTCCCACTTCCAAGATGCAT 60.684 52.381 0.00 0.00 0.00 3.96
6298 6647 4.630644 AGATGCATCTACCTAATGTGGG 57.369 45.455 27.73 0.00 34.85 4.61
6348 6697 4.261994 CCACCCATCAAAACAAACCTACTG 60.262 45.833 0.00 0.00 0.00 2.74
6430 6779 6.768381 GTGAAAGGAAAAAGGAAGAAGAGAGA 59.232 38.462 0.00 0.00 0.00 3.10
6573 6923 9.897744 ACCAACATATGATTGCTATTAAAATCG 57.102 29.630 10.38 0.00 35.89 3.34
6692 7043 2.344592 ACCATGAAGGGTGAACCACTA 58.655 47.619 1.16 0.00 43.89 2.74
7076 7465 3.419793 CCAAGGCTTGGTGAAGACA 57.580 52.632 33.43 0.00 45.93 3.41
7091 7480 0.804989 AGACATAGCCAAAACGCAGC 59.195 50.000 0.00 0.00 0.00 5.25
7118 7507 4.828387 GGACTAAGAACCTCGGTCTGATAT 59.172 45.833 0.00 0.00 0.00 1.63
7264 7654 3.176411 CCCATATGGACTCATGGCTCTA 58.824 50.000 24.00 0.00 40.41 2.43
7274 7664 0.461548 CATGGCTCTAGCGGTCTTGA 59.538 55.000 0.00 0.00 43.26 3.02
7367 7757 2.103094 CCGGCAGGATTCTGATGTTCTA 59.897 50.000 4.75 0.00 43.49 2.10
7413 7803 6.632434 TCGCAAGATTATGCAATGTATTTTCG 59.368 34.615 0.00 0.00 46.76 3.46
7424 7814 3.202829 TGTATTTTCGCATACCCTCCC 57.797 47.619 0.00 0.00 0.00 4.30
7449 7839 5.986135 CCAAAATACCTCTCTCAAGTATCGG 59.014 44.000 0.00 0.00 0.00 4.18
7505 7895 1.427020 GCTCATGCGCTTCTTGGAC 59.573 57.895 9.73 0.00 0.00 4.02
7650 8040 6.118170 TCCAAGCTAGGATGATTTTCTTGAG 58.882 40.000 0.00 0.00 33.34 3.02
7661 8051 8.033626 GGATGATTTTCTTGAGCTTTCTTGATT 58.966 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.199071 TGACGATATACCTGGGTTGCTTT 59.801 43.478 0.00 0.00 0.00 3.51
214 216 1.031029 GCGAAGTACTCCCTCCGTCT 61.031 60.000 0.00 0.00 0.00 4.18
315 348 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
316 349 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
317 350 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
318 351 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
319 352 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
320 353 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
322 355 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
323 356 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
324 357 5.727791 GCAACAACAACAACAACAACAACAA 60.728 36.000 0.00 0.00 0.00 2.83
326 359 4.207599 GCAACAACAACAACAACAACAAC 58.792 39.130 0.00 0.00 0.00 3.32
327 360 3.871006 TGCAACAACAACAACAACAACAA 59.129 34.783 0.00 0.00 0.00 2.83
328 361 3.457234 TGCAACAACAACAACAACAACA 58.543 36.364 0.00 0.00 0.00 3.33
329 362 4.660352 ATGCAACAACAACAACAACAAC 57.340 36.364 0.00 0.00 0.00 3.32
330 363 6.974932 AATATGCAACAACAACAACAACAA 57.025 29.167 0.00 0.00 0.00 2.83
331 364 6.974932 AAATATGCAACAACAACAACAACA 57.025 29.167 0.00 0.00 0.00 3.33
353 386 7.711339 ACAACAACAACAACTAGGAAACAAAAA 59.289 29.630 0.00 0.00 0.00 1.94
354 387 7.210873 ACAACAACAACAACTAGGAAACAAAA 58.789 30.769 0.00 0.00 0.00 2.44
355 388 6.750148 ACAACAACAACAACTAGGAAACAAA 58.250 32.000 0.00 0.00 0.00 2.83
356 389 6.334102 ACAACAACAACAACTAGGAAACAA 57.666 33.333 0.00 0.00 0.00 2.83
357 390 5.968528 ACAACAACAACAACTAGGAAACA 57.031 34.783 0.00 0.00 0.00 2.83
358 391 6.153756 ACAACAACAACAACAACTAGGAAAC 58.846 36.000 0.00 0.00 0.00 2.78
359 392 6.016192 TGACAACAACAACAACAACTAGGAAA 60.016 34.615 0.00 0.00 0.00 3.13
360 393 5.473846 TGACAACAACAACAACAACTAGGAA 59.526 36.000 0.00 0.00 0.00 3.36
361 394 5.004448 TGACAACAACAACAACAACTAGGA 58.996 37.500 0.00 0.00 0.00 2.94
362 395 5.092781 GTGACAACAACAACAACAACTAGG 58.907 41.667 0.00 0.00 0.00 3.02
363 396 4.786068 CGTGACAACAACAACAACAACTAG 59.214 41.667 0.00 0.00 0.00 2.57
364 397 4.213694 ACGTGACAACAACAACAACAACTA 59.786 37.500 0.00 0.00 0.00 2.24
365 398 3.003897 ACGTGACAACAACAACAACAACT 59.996 39.130 0.00 0.00 0.00 3.16
366 399 3.301706 ACGTGACAACAACAACAACAAC 58.698 40.909 0.00 0.00 0.00 3.32
367 400 3.627732 ACGTGACAACAACAACAACAA 57.372 38.095 0.00 0.00 0.00 2.83
368 401 3.300857 CAACGTGACAACAACAACAACA 58.699 40.909 0.00 0.00 0.00 3.33
369 402 2.089887 GCAACGTGACAACAACAACAAC 59.910 45.455 0.00 0.00 0.00 3.32
370 403 2.320367 GCAACGTGACAACAACAACAA 58.680 42.857 0.00 0.00 0.00 2.83
371 404 1.401670 GGCAACGTGACAACAACAACA 60.402 47.619 0.00 0.00 0.00 3.33
372 405 1.135517 AGGCAACGTGACAACAACAAC 60.136 47.619 0.00 0.00 46.39 3.32
373 406 1.169577 AGGCAACGTGACAACAACAA 58.830 45.000 0.00 0.00 46.39 2.83
374 407 1.131504 GAAGGCAACGTGACAACAACA 59.868 47.619 0.00 0.00 46.39 3.33
375 408 1.822581 GAAGGCAACGTGACAACAAC 58.177 50.000 0.00 0.00 46.39 3.32
376 409 0.375454 CGAAGGCAACGTGACAACAA 59.625 50.000 0.00 0.00 46.39 2.83
377 410 0.741574 ACGAAGGCAACGTGACAACA 60.742 50.000 8.04 0.00 42.37 3.33
378 411 1.071041 GTACGAAGGCAACGTGACAAC 60.071 52.381 16.54 5.59 43.73 3.32
379 412 1.210870 GTACGAAGGCAACGTGACAA 58.789 50.000 16.54 0.00 43.73 3.18
380 413 0.598158 GGTACGAAGGCAACGTGACA 60.598 55.000 16.54 0.00 43.73 3.58
381 414 2.147820 GGTACGAAGGCAACGTGAC 58.852 57.895 16.54 11.15 43.73 3.67
382 415 4.659480 GGTACGAAGGCAACGTGA 57.341 55.556 16.54 1.90 43.73 4.35
746 785 1.343142 GGCTAGGCTTAGAGAAGAGGC 59.657 57.143 9.46 0.00 38.61 4.70
804 844 4.591924 GCTAGGATTTAGGTGGGCTAACTA 59.408 45.833 0.00 0.00 0.00 2.24
891 932 2.683362 GCGAAAAATGAGGAGGGTTAGG 59.317 50.000 0.00 0.00 0.00 2.69
1060 1110 4.699522 ACGGCTTTCGGGAGCACC 62.700 66.667 11.96 0.00 44.49 5.01
1061 1111 2.221906 TAGACGGCTTTCGGGAGCAC 62.222 60.000 0.00 4.40 44.49 4.40
1062 1112 1.980232 TAGACGGCTTTCGGGAGCA 60.980 57.895 0.00 0.00 44.49 4.26
1154 1205 1.000731 CGTGCATTGTGTCCCCAAAAT 59.999 47.619 0.00 0.00 0.00 1.82
1475 1531 8.623030 GGGTAAAACGCCTCATAAATTATTACA 58.377 33.333 0.00 0.00 0.00 2.41
1636 1696 0.320771 TCTTCCTTCGCTCAACCTGC 60.321 55.000 0.00 0.00 0.00 4.85
1637 1697 2.072298 CTTCTTCCTTCGCTCAACCTG 58.928 52.381 0.00 0.00 0.00 4.00
1688 1748 4.148825 CCGCCGAACCTCCTCTGG 62.149 72.222 0.00 0.00 0.00 3.86
1764 1824 0.509929 CATGCGACGATGATTGCGAT 59.490 50.000 0.00 0.00 0.00 4.58
2083 2176 1.148310 CTATTACGCTTCATGCCCGG 58.852 55.000 0.00 0.00 38.78 5.73
2295 2393 9.956720 CAATATAATGTCCTGGAACAAAATCTC 57.043 33.333 0.00 0.00 38.70 2.75
2902 3006 2.168326 TCTCGATCTGCAGCAAAACA 57.832 45.000 9.47 0.00 0.00 2.83
3105 3214 5.537295 TCATATTCTTGCAAGCTGCCATAAT 59.463 36.000 21.99 15.44 44.23 1.28
3165 3276 7.416154 TGTAATACCTATTACGCAAGCAATC 57.584 36.000 9.59 0.00 46.84 2.67
3282 3393 6.782000 TGCAGCCCCACTTTTATATAATTCAT 59.218 34.615 0.00 0.00 0.00 2.57
3283 3394 6.132658 TGCAGCCCCACTTTTATATAATTCA 58.867 36.000 0.00 0.00 0.00 2.57
3295 3406 1.980772 GCATCTTGCAGCCCCACTT 60.981 57.895 0.00 0.00 44.26 3.16
3548 3664 3.918977 TGCAGCCACCACGTACGT 61.919 61.111 16.72 16.72 0.00 3.57
3712 3908 7.490079 ACAGCTAATTGCAAATGTGATATGTTG 59.510 33.333 1.71 0.00 45.94 3.33
3856 4052 4.082733 GGTTGATTTTGAAGGAGTACAGGC 60.083 45.833 0.00 0.00 0.00 4.85
4304 4595 8.640063 TTAAGGTTGTCCCCTAAATAGTTTTC 57.360 34.615 0.00 0.00 33.33 2.29
4349 4640 6.260936 CCGGATGTAGCAAGTATGAAAGAAAT 59.739 38.462 0.00 0.00 0.00 2.17
4562 4867 0.402861 TCCTCCTTCCCACCCTTGTT 60.403 55.000 0.00 0.00 0.00 2.83
4596 4901 0.901827 AGGTCCACGTGCATCACATA 59.098 50.000 10.91 0.00 33.40 2.29
4627 4932 6.058183 GTCCCTAGCACAATAATCATGACTT 58.942 40.000 0.00 0.00 0.00 3.01
4716 5025 0.682209 AGGATGGGTGCATGCACTTC 60.682 55.000 40.86 32.78 45.52 3.01
4820 5129 5.545658 TTGTCGAAGATTTCAACTATGCC 57.454 39.130 0.00 0.00 40.67 4.40
5135 5467 6.678857 AGGAGGAGATTTATCCCTAAAAGTGT 59.321 38.462 0.00 0.00 40.53 3.55
5155 5487 8.752005 TGAATGTTGGAGAAAATATTAGGAGG 57.248 34.615 0.00 0.00 0.00 4.30
5206 5538 8.194769 ACACCTTAATTTGTTACCAAAAGTCTG 58.805 33.333 0.00 0.00 43.43 3.51
5305 5650 1.677217 GCACCTGGACTAGCCTCAAAG 60.677 57.143 0.00 0.00 37.63 2.77
5318 5663 4.262164 GCCCAATAGATTTAATGCACCTGG 60.262 45.833 0.00 0.00 0.00 4.45
5665 6014 6.431234 AGCAAGAGATTGGATTTTACGTTCTT 59.569 34.615 0.00 0.00 0.00 2.52
5728 6077 7.796054 TGGAGGAACAATTTGGAAATTAACAA 58.204 30.769 0.78 0.00 36.52 2.83
5753 6102 7.918076 TCTTCTCTTTAGTTTGTGGTATGGAT 58.082 34.615 0.00 0.00 0.00 3.41
5811 6160 2.494059 CTTGTCAGGTTGAATCGGTGT 58.506 47.619 0.00 0.00 0.00 4.16
5812 6161 1.197721 GCTTGTCAGGTTGAATCGGTG 59.802 52.381 0.00 0.00 0.00 4.94
5894 6243 2.503356 CAGCATGGGGTTAGAAGAGTCT 59.497 50.000 0.00 0.00 37.95 3.24
6058 6407 1.923356 ATCAACCCCACGAGCAAAAT 58.077 45.000 0.00 0.00 0.00 1.82
6067 6416 2.772515 ACCTTAGAGCTATCAACCCCAC 59.227 50.000 0.00 0.00 0.00 4.61
6118 6467 5.420104 AGAGTTAAAAAGGCATTGGAGATGG 59.580 40.000 0.00 0.00 0.00 3.51
6160 6509 2.029020 TGAGAGGACATGAACTTCGTGG 60.029 50.000 14.27 0.00 37.70 4.94
6284 6633 6.884472 TCATCTTTTCCCACATTAGGTAGA 57.116 37.500 0.00 0.00 0.00 2.59
6348 6697 0.617820 TCTCCTGGTGTTAGAGGGGC 60.618 60.000 0.00 0.00 28.73 5.80
6404 6753 6.663734 TCTCTTCTTCCTTTTTCCTTTCACT 58.336 36.000 0.00 0.00 0.00 3.41
6524 6874 8.296000 TGGTATGAGTGAAAACACATACATTTG 58.704 33.333 20.42 0.00 42.16 2.32
6590 6940 5.606348 TTGGTTTCACCTTGCAAAAGTAT 57.394 34.783 0.00 0.00 39.58 2.12
6628 6978 6.261826 CCTATTAGGCTTCTTGTTGAGAATGG 59.738 42.308 0.00 0.00 43.23 3.16
6692 7043 5.072741 ACTGATTTAGGTTCATTGTGCAGT 58.927 37.500 0.00 0.00 0.00 4.40
6755 7141 5.718146 TGAGACAGTCATTGAAGAGATCAC 58.282 41.667 2.66 0.00 37.92 3.06
7076 7465 1.674322 ACCGCTGCGTTTTGGCTAT 60.674 52.632 21.59 0.00 0.00 2.97
7091 7480 0.172803 CCGAGGTTCTTAGTCCACCG 59.827 60.000 0.00 0.00 35.54 4.94
7264 7654 0.834687 TGGGGTTACTCAAGACCGCT 60.835 55.000 10.32 0.00 45.93 5.52
7274 7664 6.682537 ACATGGAATTTATCATGGGGTTACT 58.317 36.000 16.35 0.00 43.49 2.24
7367 7757 4.333649 CGATGTATGCAACAGAATCAAGGT 59.666 41.667 0.00 0.00 42.70 3.50
7396 7786 6.264292 AGGGTATGCGAAAATACATTGCATAA 59.736 34.615 9.40 0.00 46.49 1.90
7413 7803 2.594131 GTATTTTGGGGGAGGGTATGC 58.406 52.381 0.00 0.00 0.00 3.14
7424 7814 5.986135 CGATACTTGAGAGAGGTATTTTGGG 59.014 44.000 0.00 0.00 0.00 4.12
7449 7839 2.755103 CCCTAGAGGCACCAAAATGAAC 59.245 50.000 0.00 0.00 0.00 3.18
7623 8013 3.872459 AAATCATCCTAGCTTGGAGGG 57.128 47.619 24.99 17.72 39.78 4.30
7650 8040 5.393896 CCTTGGATGAGGAAATCAAGAAAGC 60.394 44.000 0.00 0.00 42.53 3.51
7661 8051 2.239654 CAAGCCTACCTTGGATGAGGAA 59.760 50.000 9.88 0.00 45.78 3.36


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

AutoCloner maintained by Alex Coulton.