Multiple sequence alignment - TraesCS2A01G461800

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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 TraesCS2A01G461800 chr2A 100.000 5633 0 0 1 5633 707635009 707629377 0.000000e+00 10403.0
1 TraesCS2A01G461800 chr2A 90.369 1682 134 13 781 2452 707737892 707736229 0.000000e+00 2183.0
2 TraesCS2A01G461800 chr2A 96.500 400 10 2 1 398 25304865 25305262 0.000000e+00 658.0
3 TraesCS2A01G461800 chr2A 96.709 395 11 1 1 395 25255599 25255991 0.000000e+00 656.0
4 TraesCS2A01G461800 chr2A 94.236 399 13 4 1 398 25272565 25272954 8.080000e-168 601.0
5 TraesCS2A01G461800 chr2A 94.236 399 13 3 1 398 25322066 25322455 8.080000e-168 601.0
6 TraesCS2A01G461800 chr2A 93.567 342 21 1 4998 5339 428817012 428816672 5.030000e-140 508.0
7 TraesCS2A01G461800 chr2D 95.320 4487 187 15 461 4940 568130361 568125891 0.000000e+00 7101.0
8 TraesCS2A01G461800 chr2D 89.791 1675 134 13 781 2452 568194063 568192423 0.000000e+00 2111.0
9 TraesCS2A01G461800 chr2D 95.349 344 15 1 4994 5337 346097450 346097792 3.840000e-151 545.0
10 TraesCS2A01G461800 chr2D 94.752 343 16 2 4997 5339 448651906 448652246 2.990000e-147 532.0
11 TraesCS2A01G461800 chr2D 94.169 343 19 1 4997 5339 156823497 156823156 6.470000e-144 521.0
12 TraesCS2A01G461800 chr2D 96.981 265 7 1 5370 5633 156821813 156821549 1.440000e-120 444.0
13 TraesCS2A01G461800 chr2D 95.636 275 9 3 5361 5633 448653274 448653547 6.700000e-119 438.0
14 TraesCS2A01G461800 chr2D 96.604 265 8 1 5370 5633 587276964 587277228 6.700000e-119 438.0
15 TraesCS2A01G461800 chr2D 96.610 59 2 0 4938 4996 568125825 568125767 1.290000e-16 99.0
16 TraesCS2A01G461800 chr2B 94.999 4459 192 20 461 4911 680668713 680664278 0.000000e+00 6970.0
17 TraesCS2A01G461800 chr2B 88.737 1678 162 9 781 2452 680755076 680753420 0.000000e+00 2026.0
18 TraesCS2A01G461800 chr2B 85.356 239 34 1 227 464 798188314 798188552 4.360000e-61 246.0
19 TraesCS2A01G461800 chr6D 94.872 351 16 2 4990 5339 328353437 328353088 1.070000e-151 547.0
20 TraesCS2A01G461800 chr5D 95.195 333 13 3 4997 5328 464134492 464134822 1.800000e-144 523.0
21 TraesCS2A01G461800 chr5D 96.604 265 8 1 5370 5633 433996062 433996326 6.700000e-119 438.0
22 TraesCS2A01G461800 chr5D 95.290 276 9 4 5361 5633 458265770 458266044 8.670000e-118 435.0
23 TraesCS2A01G461800 chr5D 89.243 251 24 2 219 466 79167908 79167658 1.520000e-80 311.0
24 TraesCS2A01G461800 chr4D 93.948 347 19 2 4994 5339 333462715 333462370 1.800000e-144 523.0
25 TraesCS2A01G461800 chr1A 94.169 343 19 1 4997 5339 554093567 554093226 6.470000e-144 521.0
26 TraesCS2A01G461800 chr1A 96.981 265 7 1 5370 5633 566579068 566578804 1.440000e-120 444.0
27 TraesCS2A01G461800 chr1A 96.604 265 8 1 5370 5633 145200769 145200505 6.700000e-119 438.0
28 TraesCS2A01G461800 chr1A 90.076 131 11 1 16 146 535708393 535708265 9.710000e-38 169.0
29 TraesCS2A01G461800 chr7D 93.642 346 19 3 4994 5339 192142313 192142655 1.080000e-141 514.0
30 TraesCS2A01G461800 chr7D 96.981 265 7 1 5370 5633 192143909 192144173 1.440000e-120 444.0
31 TraesCS2A01G461800 chr7D 89.697 165 15 1 300 464 5999096 5998934 5.720000e-50 209.0
32 TraesCS2A01G461800 chr7D 97.143 35 1 0 1213 1247 473096006 473095972 6.090000e-05 60.2
33 TraesCS2A01G461800 chr4A 96.604 265 8 1 5370 5633 5930773 5931037 6.700000e-119 438.0
34 TraesCS2A01G461800 chr4A 93.407 91 6 0 375 465 722278386 722278296 9.840000e-28 135.0
35 TraesCS2A01G461800 chr7A 85.634 355 38 9 1 345 662170359 662170710 1.490000e-95 361.0
36 TraesCS2A01G461800 chr7A 79.393 461 69 18 8 464 5011998 5012436 9.170000e-78 302.0
37 TraesCS2A01G461800 chr7A 91.133 203 18 0 262 464 19697221 19697423 5.560000e-70 276.0
38 TraesCS2A01G461800 chr7A 84.322 236 24 9 161 386 662170737 662170969 9.500000e-53 219.0
39 TraesCS2A01G461800 chr7A 90.141 142 12 2 1 141 19697062 19697202 3.470000e-42 183.0
40 TraesCS2A01G461800 chr3D 84.821 224 33 1 234 456 575414735 575414958 2.040000e-54 224.0
41 TraesCS2A01G461800 chr6A 86.082 194 18 1 272 465 614198461 614198277 3.440000e-47 200.0
42 TraesCS2A01G461800 chr3B 82.941 170 13 2 297 466 799388892 799388739 7.610000e-29 139.0
43 TraesCS2A01G461800 chr7B 93.182 44 1 2 1213 1254 497027101 497027058 4.710000e-06 63.9


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 TraesCS2A01G461800 chr2A 707629377 707635009 5632 True 10403.0 10403 100.0000 1 5633 1 chr2A.!!$R2 5632
1 TraesCS2A01G461800 chr2A 707736229 707737892 1663 True 2183.0 2183 90.3690 781 2452 1 chr2A.!!$R3 1671
2 TraesCS2A01G461800 chr2D 568125767 568130361 4594 True 3600.0 7101 95.9650 461 4996 2 chr2D.!!$R3 4535
3 TraesCS2A01G461800 chr2D 568192423 568194063 1640 True 2111.0 2111 89.7910 781 2452 1 chr2D.!!$R1 1671
4 TraesCS2A01G461800 chr2D 448651906 448653547 1641 False 485.0 532 95.1940 4997 5633 2 chr2D.!!$F3 636
5 TraesCS2A01G461800 chr2D 156821549 156823497 1948 True 482.5 521 95.5750 4997 5633 2 chr2D.!!$R2 636
6 TraesCS2A01G461800 chr2B 680664278 680668713 4435 True 6970.0 6970 94.9990 461 4911 1 chr2B.!!$R1 4450
7 TraesCS2A01G461800 chr2B 680753420 680755076 1656 True 2026.0 2026 88.7370 781 2452 1 chr2B.!!$R2 1671
8 TraesCS2A01G461800 chr7D 192142313 192144173 1860 False 479.0 514 95.3115 4994 5633 2 chr7D.!!$F1 639
9 TraesCS2A01G461800 chr7A 662170359 662170969 610 False 290.0 361 84.9780 1 386 2 chr7A.!!$F3 385

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
106 107 0.109319 CCTTGTGGCGCAATGGTTAC 60.109 55.0 14.66 0.00 36.36 2.50 F
457 684 0.178938 TATTCCGCCCGGTACCCATA 60.179 55.0 6.25 0.00 36.47 2.74 F
465 692 0.472471 CCGGTACCCATAACCATGCT 59.528 55.0 6.25 0.00 36.78 3.79 F
912 1142 0.597637 GACGCCATGGTCCGATGTAG 60.598 60.0 17.30 0.06 0.00 2.74 F
914 1144 0.671796 CGCCATGGTCCGATGTAGTA 59.328 55.0 14.67 0.00 0.00 1.82 F
2717 2960 0.176680 CTCACCATCCTCGACCTTGG 59.823 60.0 2.09 2.09 35.31 3.61 F
4207 4450 0.615331 CATGGCACCAGGTACAGTCT 59.385 55.0 0.00 0.00 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1836 1.301244 GTCCAGATCGCCGATGCAT 60.301 57.895 3.34 0.0 37.32 3.96 R
2334 2577 1.217882 CAACTGAAAGGAACGCGAGT 58.782 50.000 15.93 0.0 44.43 4.18 R
2357 2600 2.125912 CTCCGGTCAGCGAGTTGG 60.126 66.667 0.00 0.0 0.00 3.77 R
2616 2859 0.670854 GCACCTGAAGGGAAGACGAC 60.671 60.000 0.56 0.0 40.27 4.34 R
2917 3160 2.573462 ACAGGTTGAGGTACATCTGCAT 59.427 45.455 9.22 0.0 35.28 3.96 R
4338 4582 0.837691 ACAGCTCCATCACCAGGACA 60.838 55.000 0.00 0.0 0.00 4.02 R
5090 5404 0.037232 CGAAAAGTCCCTCTTCGGCT 60.037 55.000 0.00 0.0 38.57 5.52 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
72 73 2.503869 AGATTAGGCCTGGACTCCAT 57.496 50.000 17.99 0.00 30.82 3.41
78 79 3.584733 AGGCCTGGACTCCATTTTATC 57.415 47.619 3.11 0.00 30.82 1.75
80 81 2.421529 GGCCTGGACTCCATTTTATCGT 60.422 50.000 0.00 0.00 30.82 3.73
106 107 0.109319 CCTTGTGGCGCAATGGTTAC 60.109 55.000 14.66 0.00 36.36 2.50
139 140 1.609208 TTCTCTTGCCTTGAGGTTGC 58.391 50.000 0.00 0.00 37.57 4.17
146 147 1.299648 CCTTGAGGTTGCCGGATCA 59.700 57.895 5.05 0.00 0.00 2.92
152 153 2.301346 GAGGTTGCCGGATCAAATCAT 58.699 47.619 5.05 0.00 0.00 2.45
155 156 2.426738 GGTTGCCGGATCAAATCATTCA 59.573 45.455 5.05 0.00 0.00 2.57
157 158 2.300433 TGCCGGATCAAATCATTCAGG 58.700 47.619 5.05 0.00 0.00 3.86
158 159 1.000938 GCCGGATCAAATCATTCAGGC 60.001 52.381 5.05 0.00 42.10 4.85
159 160 2.300433 CCGGATCAAATCATTCAGGCA 58.700 47.619 0.00 0.00 0.00 4.75
167 168 7.929785 GGATCAAATCATTCAGGCAACATTTAT 59.070 33.333 0.00 0.00 41.41 1.40
235 453 2.025155 TGCATCCTAGAGACTCGAACC 58.975 52.381 0.00 0.00 0.00 3.62
251 469 3.402681 CCCGAGACCACAGGGCAT 61.403 66.667 0.00 0.00 38.51 4.40
253 479 1.410850 CCCGAGACCACAGGGCATAT 61.411 60.000 0.00 0.00 38.51 1.78
255 481 1.691976 CCGAGACCACAGGGCATATAA 59.308 52.381 0.00 0.00 37.90 0.98
259 485 5.512404 CCGAGACCACAGGGCATATAATTAA 60.512 44.000 0.00 0.00 37.90 1.40
260 486 5.995282 CGAGACCACAGGGCATATAATTAAA 59.005 40.000 0.00 0.00 37.90 1.52
264 490 5.219633 CCACAGGGCATATAATTAAAACGC 58.780 41.667 0.00 0.00 0.00 4.84
270 496 3.666797 GCATATAATTAAAACGCCCGTGC 59.333 43.478 0.00 0.00 0.00 5.34
275 501 1.590932 TTAAAACGCCCGTGCTTACA 58.409 45.000 0.00 0.00 34.43 2.41
287 513 0.393448 TGCTTACAAGTACGCCACCA 59.607 50.000 6.29 0.00 30.30 4.17
289 515 1.874739 GCTTACAAGTACGCCACCACA 60.875 52.381 0.00 0.00 0.00 4.17
290 516 2.066262 CTTACAAGTACGCCACCACAG 58.934 52.381 0.00 0.00 0.00 3.66
292 518 2.032071 AAGTACGCCACCACAGCC 59.968 61.111 0.00 0.00 0.00 4.85
317 543 3.246619 CTGTTCGTTCTGAGTTCCTAGC 58.753 50.000 0.00 0.00 0.00 3.42
318 544 2.251893 GTTCGTTCTGAGTTCCTAGCG 58.748 52.381 0.00 0.00 0.00 4.26
329 555 7.278135 TCTGAGTTCCTAGCGTATCTAACTTA 58.722 38.462 0.00 0.00 0.00 2.24
331 557 7.701445 TGAGTTCCTAGCGTATCTAACTTAAC 58.299 38.462 0.00 0.00 0.00 2.01
332 558 7.555554 TGAGTTCCTAGCGTATCTAACTTAACT 59.444 37.037 0.00 0.00 0.00 2.24
333 559 8.291191 AGTTCCTAGCGTATCTAACTTAACTT 57.709 34.615 0.00 0.00 0.00 2.66
386 613 7.980742 AAATTCAAACTTTTTCACTCGGTAC 57.019 32.000 0.00 0.00 0.00 3.34
387 614 6.687081 ATTCAAACTTTTTCACTCGGTACA 57.313 33.333 0.00 0.00 0.00 2.90
388 615 6.497785 TTCAAACTTTTTCACTCGGTACAA 57.502 33.333 0.00 0.00 0.00 2.41
389 616 6.497785 TCAAACTTTTTCACTCGGTACAAA 57.502 33.333 0.00 0.00 0.00 2.83
390 617 6.548171 TCAAACTTTTTCACTCGGTACAAAG 58.452 36.000 0.00 0.00 0.00 2.77
391 618 5.494632 AACTTTTTCACTCGGTACAAAGG 57.505 39.130 0.00 0.00 0.00 3.11
392 619 4.520179 ACTTTTTCACTCGGTACAAAGGT 58.480 39.130 0.00 0.00 0.00 3.50
393 620 4.945543 ACTTTTTCACTCGGTACAAAGGTT 59.054 37.500 0.00 0.00 0.00 3.50
394 621 5.416639 ACTTTTTCACTCGGTACAAAGGTTT 59.583 36.000 0.00 0.00 0.00 3.27
395 622 5.488645 TTTTCACTCGGTACAAAGGTTTC 57.511 39.130 0.00 0.00 0.00 2.78
396 623 4.411256 TTCACTCGGTACAAAGGTTTCT 57.589 40.909 0.00 0.00 0.00 2.52
397 624 3.986277 TCACTCGGTACAAAGGTTTCTC 58.014 45.455 0.00 0.00 0.00 2.87
398 625 2.729882 CACTCGGTACAAAGGTTTCTCG 59.270 50.000 0.00 0.00 0.00 4.04
399 626 2.363359 ACTCGGTACAAAGGTTTCTCGT 59.637 45.455 0.00 0.00 0.00 4.18
400 627 2.729882 CTCGGTACAAAGGTTTCTCGTG 59.270 50.000 0.00 0.00 0.00 4.35
401 628 1.796459 CGGTACAAAGGTTTCTCGTGG 59.204 52.381 0.00 0.00 0.00 4.94
402 629 2.148768 GGTACAAAGGTTTCTCGTGGG 58.851 52.381 0.00 0.00 0.00 4.61
403 630 2.148768 GTACAAAGGTTTCTCGTGGGG 58.851 52.381 0.00 0.00 0.00 4.96
404 631 0.549469 ACAAAGGTTTCTCGTGGGGT 59.451 50.000 0.00 0.00 0.00 4.95
405 632 0.951558 CAAAGGTTTCTCGTGGGGTG 59.048 55.000 0.00 0.00 0.00 4.61
406 633 0.179001 AAAGGTTTCTCGTGGGGTGG 60.179 55.000 0.00 0.00 0.00 4.61
407 634 2.671963 GGTTTCTCGTGGGGTGGC 60.672 66.667 0.00 0.00 0.00 5.01
408 635 3.047877 GTTTCTCGTGGGGTGGCG 61.048 66.667 0.00 0.00 0.00 5.69
409 636 3.235481 TTTCTCGTGGGGTGGCGA 61.235 61.111 0.00 0.00 35.70 5.54
410 637 2.589157 TTTCTCGTGGGGTGGCGAT 61.589 57.895 0.00 0.00 36.50 4.58
411 638 1.259142 TTTCTCGTGGGGTGGCGATA 61.259 55.000 0.00 0.00 36.50 2.92
412 639 1.259142 TTCTCGTGGGGTGGCGATAA 61.259 55.000 0.00 0.00 36.50 1.75
413 640 1.219664 CTCGTGGGGTGGCGATAAA 59.780 57.895 0.00 0.00 36.50 1.40
414 641 1.078988 TCGTGGGGTGGCGATAAAC 60.079 57.895 0.00 0.00 31.76 2.01
415 642 1.376166 CGTGGGGTGGCGATAAACA 60.376 57.895 0.00 0.00 0.00 2.83
416 643 1.641123 CGTGGGGTGGCGATAAACAC 61.641 60.000 0.00 0.00 36.89 3.32
417 644 1.376166 TGGGGTGGCGATAAACACG 60.376 57.895 0.00 0.00 38.46 4.49
418 645 2.110352 GGGGTGGCGATAAACACGG 61.110 63.158 0.00 0.00 38.46 4.94
419 646 1.376295 GGGTGGCGATAAACACGGT 60.376 57.895 0.00 0.00 38.46 4.83
420 647 0.956902 GGGTGGCGATAAACACGGTT 60.957 55.000 0.00 0.00 38.46 4.44
421 648 1.675415 GGGTGGCGATAAACACGGTTA 60.675 52.381 0.00 0.00 38.46 2.85
422 649 1.394572 GGTGGCGATAAACACGGTTAC 59.605 52.381 0.00 0.00 38.46 2.50
423 650 1.394572 GTGGCGATAAACACGGTTACC 59.605 52.381 0.00 0.00 0.00 2.85
439 666 3.474000 CCGGGCGGTATCCCAATA 58.526 61.111 0.00 0.00 46.92 1.90
440 667 1.988015 CCGGGCGGTATCCCAATAT 59.012 57.895 0.00 0.00 46.92 1.28
441 668 0.326927 CCGGGCGGTATCCCAATATT 59.673 55.000 0.00 0.00 46.92 1.28
442 669 1.677820 CCGGGCGGTATCCCAATATTC 60.678 57.143 0.00 0.00 46.92 1.75
443 670 1.677820 CGGGCGGTATCCCAATATTCC 60.678 57.143 0.00 0.00 46.92 3.01
444 671 1.677820 GGGCGGTATCCCAATATTCCG 60.678 57.143 6.64 6.64 45.82 4.30
446 673 1.734163 CGGTATCCCAATATTCCGCC 58.266 55.000 0.00 0.00 0.00 6.13
447 674 1.677820 CGGTATCCCAATATTCCGCCC 60.678 57.143 0.00 0.00 0.00 6.13
448 675 1.677820 GGTATCCCAATATTCCGCCCG 60.678 57.143 0.00 0.00 0.00 6.13
449 676 0.616371 TATCCCAATATTCCGCCCGG 59.384 55.000 0.00 0.00 0.00 5.73
450 677 1.423794 ATCCCAATATTCCGCCCGGT 61.424 55.000 6.61 0.00 36.47 5.28
451 678 0.763604 TCCCAATATTCCGCCCGGTA 60.764 55.000 6.61 0.00 36.47 4.02
452 679 0.604511 CCCAATATTCCGCCCGGTAC 60.605 60.000 6.61 0.00 36.47 3.34
453 680 0.604511 CCAATATTCCGCCCGGTACC 60.605 60.000 0.16 0.16 36.47 3.34
454 681 0.604511 CAATATTCCGCCCGGTACCC 60.605 60.000 6.25 0.00 36.47 3.69
455 682 1.055551 AATATTCCGCCCGGTACCCA 61.056 55.000 6.25 0.00 36.47 4.51
456 683 0.838987 ATATTCCGCCCGGTACCCAT 60.839 55.000 6.25 0.00 36.47 4.00
457 684 0.178938 TATTCCGCCCGGTACCCATA 60.179 55.000 6.25 0.00 36.47 2.74
458 685 1.055551 ATTCCGCCCGGTACCCATAA 61.056 55.000 6.25 0.00 36.47 1.90
459 686 1.970352 TTCCGCCCGGTACCCATAAC 61.970 60.000 6.25 0.00 36.47 1.89
460 687 2.109593 CGCCCGGTACCCATAACC 59.890 66.667 6.25 0.00 0.00 2.85
461 688 2.733669 CGCCCGGTACCCATAACCA 61.734 63.158 6.25 0.00 36.78 3.67
462 689 1.841302 GCCCGGTACCCATAACCAT 59.159 57.895 6.25 0.00 36.78 3.55
463 690 0.536460 GCCCGGTACCCATAACCATG 60.536 60.000 6.25 0.00 36.78 3.66
464 691 0.536460 CCCGGTACCCATAACCATGC 60.536 60.000 6.25 0.00 36.78 4.06
465 692 0.472471 CCGGTACCCATAACCATGCT 59.528 55.000 6.25 0.00 36.78 3.79
466 693 1.695242 CCGGTACCCATAACCATGCTA 59.305 52.381 6.25 0.00 36.78 3.49
598 826 7.852971 ATACACTCTCTACAACAGACTAGAC 57.147 40.000 0.00 0.00 0.00 2.59
682 910 2.730094 GTGGGTGCACTGCAAAGG 59.270 61.111 17.98 0.00 41.47 3.11
724 952 6.436843 AACCATCGTCCATTTTCTGTTATC 57.563 37.500 0.00 0.00 0.00 1.75
725 953 4.881850 ACCATCGTCCATTTTCTGTTATCC 59.118 41.667 0.00 0.00 0.00 2.59
726 954 4.881273 CCATCGTCCATTTTCTGTTATCCA 59.119 41.667 0.00 0.00 0.00 3.41
727 955 5.356751 CCATCGTCCATTTTCTGTTATCCAA 59.643 40.000 0.00 0.00 0.00 3.53
728 956 6.127758 CCATCGTCCATTTTCTGTTATCCAAA 60.128 38.462 0.00 0.00 0.00 3.28
729 957 6.249035 TCGTCCATTTTCTGTTATCCAAAC 57.751 37.500 0.00 0.00 0.00 2.93
911 1141 1.440060 GACGCCATGGTCCGATGTA 59.560 57.895 17.30 0.00 0.00 2.29
912 1142 0.597637 GACGCCATGGTCCGATGTAG 60.598 60.000 17.30 0.06 0.00 2.74
913 1143 1.327690 ACGCCATGGTCCGATGTAGT 61.328 55.000 17.30 0.61 0.00 2.73
914 1144 0.671796 CGCCATGGTCCGATGTAGTA 59.328 55.000 14.67 0.00 0.00 1.82
1593 1836 3.642503 ACCGGCCAAATCCCGTCA 61.643 61.111 0.00 0.00 44.13 4.35
1608 1851 1.858041 GTCATGCATCGGCGATCTG 59.142 57.895 21.25 16.95 45.35 2.90
1653 1896 4.181578 CCTTTATGAACAATCTCGACGGT 58.818 43.478 0.00 0.00 0.00 4.83
1960 2203 2.909965 AGATCCCGAGCTCGCTCC 60.910 66.667 30.49 17.46 39.77 4.70
2148 2391 1.000283 CTGTCGCTCAACCAGAACTCT 60.000 52.381 0.00 0.00 0.00 3.24
2186 2429 1.945354 GAGAACATCGGGTCGCTCCA 61.945 60.000 0.00 0.00 38.11 3.86
2235 2478 4.916314 TCCCTCTCCGGCCCGATC 62.916 72.222 3.71 0.00 0.00 3.69
2260 2503 3.422303 GCATCGCCAACTGCACGA 61.422 61.111 0.00 0.00 41.33 4.35
2334 2577 1.677633 GCTTGGCCGGCTAAAGGAA 60.678 57.895 30.60 11.77 0.00 3.36
2356 2599 1.082104 GCGTTCCTTTCAGTTGGCG 60.082 57.895 0.00 0.00 0.00 5.69
2357 2600 1.082104 CGTTCCTTTCAGTTGGCGC 60.082 57.895 0.00 0.00 0.00 6.53
2492 2735 4.127040 CGAGCTCAGACGGCTGCT 62.127 66.667 15.33 8.45 42.01 4.24
2572 2815 3.417275 ATCGACCTGAAGCTCGGCG 62.417 63.158 0.00 0.00 0.00 6.46
2616 2859 1.769098 CGGCGAGCATCTCCAACATG 61.769 60.000 0.00 0.00 40.96 3.21
2709 2952 2.202987 CGGCAGCTCACCATCCTC 60.203 66.667 3.29 0.00 0.00 3.71
2710 2953 2.202987 GGCAGCTCACCATCCTCG 60.203 66.667 0.00 0.00 0.00 4.63
2715 2958 0.616111 AGCTCACCATCCTCGACCTT 60.616 55.000 0.00 0.00 0.00 3.50
2717 2960 0.176680 CTCACCATCCTCGACCTTGG 59.823 60.000 2.09 2.09 35.31 3.61
2775 3018 3.441290 AACCTCCGGTCGCTCTCG 61.441 66.667 0.00 0.00 33.12 4.04
2776 3019 4.719106 ACCTCCGGTCGCTCTCGT 62.719 66.667 0.00 0.00 36.96 4.18
3146 3389 2.041686 AGCTCGACCTCCTGACGAC 61.042 63.158 0.00 0.00 32.72 4.34
3245 3488 4.754818 GTCGAGCAACGCGTTCGC 62.755 66.667 27.55 27.55 46.77 4.70
3465 3708 3.302347 GAGGACAGGGCTCGTGGTG 62.302 68.421 0.00 0.00 0.00 4.17
3504 3747 2.175322 GCGTTGCTGCTGCTCTTC 59.825 61.111 17.00 3.94 40.48 2.87
3606 3849 3.562779 GACCTTCGTCGTGCCGGAA 62.563 63.158 5.05 0.00 0.00 4.30
3621 3864 1.550524 CCGGAACTGAGGAGATTCACA 59.449 52.381 0.00 0.00 0.00 3.58
3637 3880 2.052690 ACATACGGCGAGCTGGAGT 61.053 57.895 16.62 1.02 0.00 3.85
3803 4046 2.202676 CTTCCTCACGGAGCTCGC 60.203 66.667 7.83 0.00 41.25 5.03
4060 4303 1.371558 GTCAAGCCCTCCAACGTCT 59.628 57.895 0.00 0.00 0.00 4.18
4207 4450 0.615331 CATGGCACCAGGTACAGTCT 59.385 55.000 0.00 0.00 0.00 3.24
4210 4453 1.263356 GGCACCAGGTACAGTCTACA 58.737 55.000 0.00 0.00 0.00 2.74
4211 4454 1.621814 GGCACCAGGTACAGTCTACAA 59.378 52.381 0.00 0.00 0.00 2.41
4212 4455 2.612221 GGCACCAGGTACAGTCTACAAC 60.612 54.545 0.00 0.00 0.00 3.32
4213 4456 2.299297 GCACCAGGTACAGTCTACAACT 59.701 50.000 0.00 0.00 39.44 3.16
4214 4457 3.244112 GCACCAGGTACAGTCTACAACTT 60.244 47.826 0.00 0.00 35.45 2.66
4215 4458 4.557205 CACCAGGTACAGTCTACAACTTC 58.443 47.826 0.00 0.00 35.45 3.01
4216 4459 4.281182 CACCAGGTACAGTCTACAACTTCT 59.719 45.833 0.00 0.00 35.45 2.85
4217 4460 4.281182 ACCAGGTACAGTCTACAACTTCTG 59.719 45.833 0.00 0.00 35.45 3.02
4239 4483 8.037382 TCTGATTTCAGTGATGATTTCTGAAC 57.963 34.615 7.42 4.54 44.34 3.18
4244 4488 5.624159 TCAGTGATGATTTCTGAACCTTGT 58.376 37.500 0.00 0.00 35.65 3.16
4300 4544 1.298157 TGCAGAGTTGGCGTACATGC 61.298 55.000 0.00 10.67 35.08 4.06
4338 4582 1.300697 GGACGTGTTCAGCTTCGGT 60.301 57.895 0.00 0.00 0.00 4.69
4342 4586 1.557443 CGTGTTCAGCTTCGGTGTCC 61.557 60.000 0.00 0.00 32.43 4.02
4503 4747 1.742768 GGTGGCCACCGAGATAGAG 59.257 63.158 38.35 0.00 42.29 2.43
4629 4873 1.896694 CAGAGCCTGTGGAGGAGAC 59.103 63.158 0.00 0.00 42.93 3.36
4767 5011 3.380004 TGTTCATTTTGGGTGTCACAGAC 59.620 43.478 5.12 0.00 0.00 3.51
4790 5034 4.192429 AGCAAAGCTGTTTTTGTCAACT 57.808 36.364 0.00 0.00 39.62 3.16
4791 5035 4.568956 AGCAAAGCTGTTTTTGTCAACTT 58.431 34.783 0.00 0.00 39.62 2.66
4792 5036 5.719173 AGCAAAGCTGTTTTTGTCAACTTA 58.281 33.333 0.00 0.00 39.62 2.24
4915 5159 5.301551 TGTTGGAGTGCTTTCACATAATGTT 59.698 36.000 0.00 0.00 45.49 2.71
4977 5291 5.824624 AGCATCAAAAAGTGAAGAACTCTCA 59.175 36.000 0.00 0.00 40.50 3.27
4990 5304 8.462811 GTGAAGAACTCTCAGATATAGTCAACA 58.537 37.037 0.00 0.00 0.00 3.33
5090 5404 1.987855 CCCTGTCGGCCTCCTGTTA 60.988 63.158 0.00 0.00 0.00 2.41
5127 5441 4.329831 GCCTACCATTGGCCGAAA 57.670 55.556 1.54 0.00 44.32 3.46
5130 5444 1.834188 CCTACCATTGGCCGAAAAGT 58.166 50.000 1.54 0.00 0.00 2.66
5131 5445 1.743394 CCTACCATTGGCCGAAAAGTC 59.257 52.381 1.54 0.00 0.00 3.01
5132 5446 1.743394 CTACCATTGGCCGAAAAGTCC 59.257 52.381 1.54 0.00 0.00 3.85
5144 5458 3.821306 AAAGTCCACTTTTCGGCCT 57.179 47.368 0.00 0.00 43.07 5.19
5227 5541 4.020485 ACACCGGCTCTACTGTTTTAGAAT 60.020 41.667 0.00 0.00 0.00 2.40
5234 5548 9.046296 CGGCTCTACTGTTTTAGAATATTCATT 57.954 33.333 17.56 0.44 0.00 2.57
5541 7192 1.403679 CAACTGTTGGCCGAAAAGTCA 59.596 47.619 12.66 0.00 0.00 3.41
5547 7198 5.163499 ACTGTTGGCCGAAAAGTCATTTTTA 60.163 36.000 0.00 0.00 39.06 1.52
5609 7260 2.093341 GGCCGACAGGGTGATACTTTTA 60.093 50.000 0.00 0.00 38.44 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 3.584733 AAATGGAGTCCAGGCCTAATC 57.415 47.619 18.69 0.00 36.75 1.75
72 73 4.822036 CACAAGGTGGTTCACGATAAAA 57.178 40.909 0.00 0.00 34.83 1.52
99 100 1.418637 ACACCCACAAGACGTAACCAT 59.581 47.619 0.00 0.00 0.00 3.55
106 107 2.240493 AGAGAAACACCCACAAGACG 57.760 50.000 0.00 0.00 0.00 4.18
139 140 2.300433 TGCCTGAATGATTTGATCCGG 58.700 47.619 0.00 0.00 0.00 5.14
152 153 7.307870 GCATGTGAAAAATAAATGTTGCCTGAA 60.308 33.333 0.00 0.00 0.00 3.02
155 156 5.996513 TGCATGTGAAAAATAAATGTTGCCT 59.003 32.000 0.00 0.00 0.00 4.75
157 158 7.745015 AGATGCATGTGAAAAATAAATGTTGC 58.255 30.769 2.46 0.00 0.00 4.17
158 159 9.749490 GAAGATGCATGTGAAAAATAAATGTTG 57.251 29.630 2.46 0.00 0.00 3.33
159 160 8.938906 GGAAGATGCATGTGAAAAATAAATGTT 58.061 29.630 2.46 0.00 0.00 2.71
219 437 0.907486 TCGGGTTCGAGTCTCTAGGA 59.093 55.000 0.00 0.00 40.88 2.94
235 453 1.338107 TATATGCCCTGTGGTCTCGG 58.662 55.000 0.00 0.00 0.00 4.63
264 490 1.356527 GGCGTACTTGTAAGCACGGG 61.357 60.000 16.46 0.00 43.98 5.28
266 492 0.437295 GTGGCGTACTTGTAAGCACG 59.563 55.000 17.41 11.88 45.95 5.34
267 493 0.794473 GGTGGCGTACTTGTAAGCAC 59.206 55.000 17.41 13.38 0.00 4.40
270 496 2.066262 CTGTGGTGGCGTACTTGTAAG 58.934 52.381 0.00 0.00 0.00 2.34
275 501 1.189524 TAGGCTGTGGTGGCGTACTT 61.190 55.000 0.00 0.00 37.59 2.24
289 515 1.203523 CTCAGAACGAACAGCTAGGCT 59.796 52.381 0.00 0.00 40.77 4.58
290 516 1.067495 ACTCAGAACGAACAGCTAGGC 60.067 52.381 0.00 0.00 0.00 3.93
292 518 3.057174 AGGAACTCAGAACGAACAGCTAG 60.057 47.826 0.00 0.00 0.00 3.42
302 528 4.904253 AGATACGCTAGGAACTCAGAAC 57.096 45.455 0.00 0.00 41.75 3.01
305 531 6.380095 AAGTTAGATACGCTAGGAACTCAG 57.620 41.667 0.00 0.00 41.75 3.35
333 559 9.517609 TCGAAATTTTTGAATTTAAACTCCGAA 57.482 25.926 0.00 0.00 32.92 4.30
364 591 6.687081 TGTACCGAGTGAAAAAGTTTGAAT 57.313 33.333 0.00 0.00 0.00 2.57
378 605 2.363359 ACGAGAAACCTTTGTACCGAGT 59.637 45.455 0.00 0.00 0.00 4.18
379 606 2.729882 CACGAGAAACCTTTGTACCGAG 59.270 50.000 0.00 0.00 0.00 4.63
386 613 0.951558 CACCCCACGAGAAACCTTTG 59.048 55.000 0.00 0.00 0.00 2.77
387 614 0.179001 CCACCCCACGAGAAACCTTT 60.179 55.000 0.00 0.00 0.00 3.11
388 615 1.454539 CCACCCCACGAGAAACCTT 59.545 57.895 0.00 0.00 0.00 3.50
389 616 3.157680 CCACCCCACGAGAAACCT 58.842 61.111 0.00 0.00 0.00 3.50
390 617 2.671963 GCCACCCCACGAGAAACC 60.672 66.667 0.00 0.00 0.00 3.27
391 618 2.798148 ATCGCCACCCCACGAGAAAC 62.798 60.000 0.00 0.00 42.31 2.78
392 619 1.259142 TATCGCCACCCCACGAGAAA 61.259 55.000 0.00 0.00 42.31 2.52
393 620 1.259142 TTATCGCCACCCCACGAGAA 61.259 55.000 0.00 0.00 42.31 2.87
394 621 1.259142 TTTATCGCCACCCCACGAGA 61.259 55.000 0.00 0.00 42.31 4.04
395 622 1.087771 GTTTATCGCCACCCCACGAG 61.088 60.000 0.00 0.00 42.31 4.18
396 623 1.078988 GTTTATCGCCACCCCACGA 60.079 57.895 0.00 0.00 43.33 4.35
397 624 1.376166 TGTTTATCGCCACCCCACG 60.376 57.895 0.00 0.00 0.00 4.94
398 625 1.641123 CGTGTTTATCGCCACCCCAC 61.641 60.000 0.00 0.00 0.00 4.61
399 626 1.376166 CGTGTTTATCGCCACCCCA 60.376 57.895 0.00 0.00 0.00 4.96
400 627 2.110352 CCGTGTTTATCGCCACCCC 61.110 63.158 0.00 0.00 0.00 4.95
401 628 0.956902 AACCGTGTTTATCGCCACCC 60.957 55.000 0.00 0.00 0.00 4.61
402 629 1.394572 GTAACCGTGTTTATCGCCACC 59.605 52.381 0.00 0.00 0.00 4.61
403 630 1.394572 GGTAACCGTGTTTATCGCCAC 59.605 52.381 0.00 0.00 0.00 5.01
404 631 1.724429 GGTAACCGTGTTTATCGCCA 58.276 50.000 0.00 0.00 0.00 5.69
405 632 0.646895 CGGTAACCGTGTTTATCGCC 59.353 55.000 0.00 0.00 42.73 5.54
406 633 0.646895 CCGGTAACCGTGTTTATCGC 59.353 55.000 0.00 0.00 46.80 4.58
407 634 1.280066 CCCGGTAACCGTGTTTATCG 58.720 55.000 0.00 0.00 46.80 2.92
408 635 1.009078 GCCCGGTAACCGTGTTTATC 58.991 55.000 0.00 0.00 46.80 1.75
409 636 0.740516 CGCCCGGTAACCGTGTTTAT 60.741 55.000 0.00 0.00 46.80 1.40
410 637 1.373999 CGCCCGGTAACCGTGTTTA 60.374 57.895 0.00 0.00 46.80 2.01
411 638 2.665854 CGCCCGGTAACCGTGTTT 60.666 61.111 0.00 0.00 46.80 2.83
412 639 4.685467 CCGCCCGGTAACCGTGTT 62.685 66.667 0.00 0.00 46.80 3.32
429 656 1.677820 CCGGGCGGAATATTGGGATAC 60.678 57.143 0.00 0.00 37.50 2.24
430 657 0.616371 CCGGGCGGAATATTGGGATA 59.384 55.000 0.00 0.00 37.50 2.59
431 658 1.378762 CCGGGCGGAATATTGGGAT 59.621 57.895 0.00 0.00 37.50 3.85
432 659 0.763604 TACCGGGCGGAATATTGGGA 60.764 55.000 6.32 0.00 38.96 4.37
433 660 0.604511 GTACCGGGCGGAATATTGGG 60.605 60.000 6.32 0.00 38.96 4.12
434 661 0.604511 GGTACCGGGCGGAATATTGG 60.605 60.000 6.32 0.00 38.96 3.16
435 662 0.604511 GGGTACCGGGCGGAATATTG 60.605 60.000 6.32 0.00 40.86 1.90
436 663 1.756665 GGGTACCGGGCGGAATATT 59.243 57.895 6.32 0.00 40.86 1.28
437 664 3.475192 GGGTACCGGGCGGAATAT 58.525 61.111 6.32 0.00 40.86 1.28
449 676 3.502211 GCATGTAGCATGGTTATGGGTAC 59.498 47.826 17.88 4.84 44.79 3.34
450 677 3.750371 GCATGTAGCATGGTTATGGGTA 58.250 45.455 17.88 0.00 44.79 3.69
451 678 2.586425 GCATGTAGCATGGTTATGGGT 58.414 47.619 17.88 0.00 44.79 4.51
463 690 4.488126 TTTTTCTGTCTGTGCATGTAGC 57.512 40.909 0.00 0.00 45.96 3.58
598 826 2.051334 TGTTTGGTCAACACAGAGGG 57.949 50.000 0.00 0.00 40.71 4.30
682 910 1.112113 TTCGGACCAGACTAGATGCC 58.888 55.000 0.00 0.00 0.00 4.40
708 936 6.590234 AGGTTTGGATAACAGAAAATGGAC 57.410 37.500 0.00 0.00 0.00 4.02
724 952 1.094785 CCGACATGGCTTAGGTTTGG 58.905 55.000 0.00 0.00 0.00 3.28
926 1156 2.284150 TCGAATCGAATGAATTGGCGAC 59.716 45.455 1.57 0.00 35.44 5.19
1558 1801 1.880027 GGTGAGGTTGTTGATGTCCAC 59.120 52.381 0.00 0.00 0.00 4.02
1593 1836 1.301244 GTCCAGATCGCCGATGCAT 60.301 57.895 3.34 0.00 37.32 3.96
1736 1979 1.394618 CGAGAAGTTCCCGATCTCCT 58.605 55.000 0.00 0.00 36.99 3.69
2186 2429 1.403679 CGACGAGCTTCTGGAGATTCT 59.596 52.381 0.00 0.00 0.00 2.40
2212 2455 4.475135 GCCGGAGAGGGAGTTGGC 62.475 72.222 5.05 0.00 41.48 4.52
2334 2577 1.217882 CAACTGAAAGGAACGCGAGT 58.782 50.000 15.93 0.00 44.43 4.18
2356 2599 4.373116 TCCGGTCAGCGAGTTGGC 62.373 66.667 0.00 0.00 0.00 4.52
2357 2600 2.125912 CTCCGGTCAGCGAGTTGG 60.126 66.667 0.00 0.00 0.00 3.77
2492 2735 1.965930 AGCGCGTTCCATTGCAGAA 60.966 52.632 8.43 0.00 0.00 3.02
2616 2859 0.670854 GCACCTGAAGGGAAGACGAC 60.671 60.000 0.56 0.00 40.27 4.34
2917 3160 2.573462 ACAGGTTGAGGTACATCTGCAT 59.427 45.455 9.22 0.00 35.28 3.96
3146 3389 0.602905 GTTGTGGGAGACGTTGAGGG 60.603 60.000 0.00 0.00 0.00 4.30
3339 3582 0.034059 CGCTCAGGTTCCTGAACACT 59.966 55.000 20.06 4.25 41.78 3.55
3447 3690 2.997897 ACCACGAGCCCTGTCCTC 60.998 66.667 0.00 0.00 0.00 3.71
3504 3747 4.092120 CAACTAGAATCGTCACGAGTGAG 58.908 47.826 4.13 4.65 40.75 3.51
3606 3849 2.101582 GCCGTATGTGAATCTCCTCAGT 59.898 50.000 0.00 0.00 0.00 3.41
3621 3864 2.835705 CGACTCCAGCTCGCCGTAT 61.836 63.158 0.00 0.00 0.00 3.06
4020 4263 1.750399 GCAGTGCACGATGGGGAAT 60.750 57.895 11.09 0.00 0.00 3.01
4207 4450 8.853077 AATCATCACTGAAATCAGAAGTTGTA 57.147 30.769 16.93 5.77 46.59 2.41
4210 4453 8.512956 CAGAAATCATCACTGAAATCAGAAGTT 58.487 33.333 16.93 2.29 46.59 2.66
4211 4454 7.881751 TCAGAAATCATCACTGAAATCAGAAGT 59.118 33.333 16.93 0.00 46.59 3.01
4212 4455 8.265165 TCAGAAATCATCACTGAAATCAGAAG 57.735 34.615 16.93 8.91 46.59 2.85
4213 4456 8.509690 GTTCAGAAATCATCACTGAAATCAGAA 58.490 33.333 16.93 5.26 46.98 3.02
4214 4457 7.120285 GGTTCAGAAATCATCACTGAAATCAGA 59.880 37.037 16.93 0.00 46.98 3.27
4215 4458 7.120873 AGGTTCAGAAATCATCACTGAAATCAG 59.879 37.037 8.84 8.84 46.98 2.90
4216 4459 6.944290 AGGTTCAGAAATCATCACTGAAATCA 59.056 34.615 0.00 0.00 46.98 2.57
4217 4460 7.388460 AGGTTCAGAAATCATCACTGAAATC 57.612 36.000 0.00 0.00 46.98 2.17
4239 4483 7.678947 ATGTTATCAGAAGTTCAGAACAAGG 57.321 36.000 15.85 2.47 0.00 3.61
4338 4582 0.837691 ACAGCTCCATCACCAGGACA 60.838 55.000 0.00 0.00 0.00 4.02
4342 4586 1.446907 GTGAACAGCTCCATCACCAG 58.553 55.000 10.54 0.00 37.97 4.00
4474 4718 4.424711 GGCCACCTTCATGCCGGA 62.425 66.667 5.05 0.00 35.08 5.14
4629 4873 2.279385 GCTGCAGCTCGGCTCTAG 60.279 66.667 31.33 0.00 43.74 2.43
4767 5011 4.389687 AGTTGACAAAAACAGCTTTGCTTG 59.610 37.500 0.00 0.00 39.46 4.01
4935 5179 3.754965 TGCTTCTGCATGACTTTTACCT 58.245 40.909 0.00 0.00 45.31 3.08
5025 5339 9.550406 CATTAGGGTGTATAGTTTCCGAATTTA 57.450 33.333 0.00 0.00 0.00 1.40
5090 5404 0.037232 CGAAAAGTCCCTCTTCGGCT 60.037 55.000 0.00 0.00 38.57 5.52
5127 5441 1.271217 GGTAGGCCGAAAAGTGGACTT 60.271 52.381 0.00 0.00 44.68 3.01
5144 5458 1.626825 AGTCCTTTTTGGCTAGCGGTA 59.373 47.619 9.00 0.00 35.26 4.02


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

AutoCloner maintained by Alex Coulton.