Multiple sequence alignment - TraesCS4A01G454700

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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 TraesCS4A01G454700 chr4A 100.000 2955 0 0 1 2955 718834241 718837195 0.000000e+00 5457
1 TraesCS4A01G454700 chr4A 90.862 2320 166 16 651 2955 718619831 718617543 0.000000e+00 3068
2 TraesCS4A01G454700 chr4A 95.851 241 10 0 97 337 718745346 718745106 9.930000e-105 390
3 TraesCS4A01G454700 chr4A 84.718 373 53 3 976 1346 718866154 718866524 1.290000e-98 370
4 TraesCS4A01G454700 chr7A 89.678 1492 129 12 680 2166 14931580 14933051 0.000000e+00 1879
5 TraesCS4A01G454700 chr7A 95.388 412 19 0 1 412 14930392 14930803 0.000000e+00 656
6 TraesCS4A01G454700 chr7D 91.159 656 54 2 1540 2192 16148811 16149465 0.000000e+00 887
7 TraesCS4A01G454700 chr7D 87.143 770 92 6 2191 2955 16150951 16151718 0.000000e+00 867
8 TraesCS4A01G454700 chr7D 82.026 612 103 7 2180 2786 3103482 3104091 5.650000e-142 514
9 TraesCS4A01G454700 chr7D 82.026 612 103 7 2180 2786 3160286 3159677 5.650000e-142 514
10 TraesCS4A01G454700 chr7D 83.005 559 75 8 806 1363 26503901 26504440 3.420000e-134 488
11 TraesCS4A01G454700 chr3D 86.719 768 97 5 2191 2955 584704464 584703699 0.000000e+00 848
12 TraesCS4A01G454700 chr3D 91.552 509 39 2 1543 2048 584711631 584711124 0.000000e+00 699
13 TraesCS4A01G454700 chr3D 81.032 717 108 15 654 1363 584713438 584712743 2.000000e-151 545
14 TraesCS4A01G454700 chr3D 80.223 627 111 10 2169 2787 908848 909469 2.680000e-125 459
15 TraesCS4A01G454700 chr3D 87.838 148 17 1 2045 2192 584711045 584710899 3.920000e-39 172
16 TraesCS4A01G454700 chr1B 82.995 641 97 10 2154 2786 573580465 573579829 1.190000e-158 569
17 TraesCS4A01G454700 chr3A 79.575 612 117 8 2181 2787 8608665 8608057 5.850000e-117 431
18 TraesCS4A01G454700 chr5A 78.696 629 121 11 2166 2786 573832726 573833349 9.860000e-110 407


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 TraesCS4A01G454700 chr4A 718834241 718837195 2954 False 5457.0 5457 100.000000 1 2955 1 chr4A.!!$F1 2954
1 TraesCS4A01G454700 chr4A 718617543 718619831 2288 True 3068.0 3068 90.862000 651 2955 1 chr4A.!!$R1 2304
2 TraesCS4A01G454700 chr7A 14930392 14933051 2659 False 1267.5 1879 92.533000 1 2166 2 chr7A.!!$F1 2165
3 TraesCS4A01G454700 chr7D 16148811 16151718 2907 False 877.0 887 89.151000 1540 2955 2 chr7D.!!$F3 1415
4 TraesCS4A01G454700 chr7D 3103482 3104091 609 False 514.0 514 82.026000 2180 2786 1 chr7D.!!$F1 606
5 TraesCS4A01G454700 chr7D 3159677 3160286 609 True 514.0 514 82.026000 2180 2786 1 chr7D.!!$R1 606
6 TraesCS4A01G454700 chr7D 26503901 26504440 539 False 488.0 488 83.005000 806 1363 1 chr7D.!!$F2 557
7 TraesCS4A01G454700 chr3D 584703699 584704464 765 True 848.0 848 86.719000 2191 2955 1 chr3D.!!$R1 764
8 TraesCS4A01G454700 chr3D 584710899 584713438 2539 True 472.0 699 86.807333 654 2192 3 chr3D.!!$R2 1538
9 TraesCS4A01G454700 chr3D 908848 909469 621 False 459.0 459 80.223000 2169 2787 1 chr3D.!!$F1 618
10 TraesCS4A01G454700 chr1B 573579829 573580465 636 True 569.0 569 82.995000 2154 2786 1 chr1B.!!$R1 632
11 TraesCS4A01G454700 chr3A 8608057 8608665 608 True 431.0 431 79.575000 2181 2787 1 chr3A.!!$R1 606
12 TraesCS4A01G454700 chr5A 573832726 573833349 623 False 407.0 407 78.696000 2166 2786 1 chr5A.!!$F1 620

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
193 194 1.062587 CTCTTTATGGCGGCAAACTCG 59.937 52.381 18.31 3.96 0.0 4.18 F
1189 1806 0.888285 GCACAAGAAGCTGCCTGTCT 60.888 55.000 0.00 0.00 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1251 1868 0.041090 AGGCACCATTTTCGGGGAAT 59.959 50.0 0.00 0.0 0.00 3.01 R
2240 5411 0.179111 TTGTCCACGGATCTCGATGC 60.179 55.0 10.05 0.0 42.43 3.91 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
27 28 1.523711 ATGCCGCGTCCAGGTTATG 60.524 57.895 4.92 0.00 0.00 1.90
36 37 3.678806 GCGTCCAGGTTATGAATCAGTCA 60.679 47.826 0.00 0.00 41.67 3.41
52 53 5.027293 TCAGTCAAGATATGGATGTGTGG 57.973 43.478 0.00 0.00 0.00 4.17
107 108 5.465724 GGAAAGACGTCATGTACTCAACTTT 59.534 40.000 19.50 4.53 0.00 2.66
120 121 8.925161 TGTACTCAACTTTCCATTTTCTTTTG 57.075 30.769 0.00 0.00 0.00 2.44
136 137 3.054139 TCTTTTGACCAGCTGATAGGCAT 60.054 43.478 17.39 0.00 34.17 4.40
143 144 3.181461 ACCAGCTGATAGGCATGTCTAAC 60.181 47.826 17.39 9.51 34.17 2.34
146 147 3.576118 AGCTGATAGGCATGTCTAACGAT 59.424 43.478 11.80 1.57 34.17 3.73
167 168 5.397828 CGATGAGATAGTGTTTCGAGACATG 59.602 44.000 12.37 0.00 0.00 3.21
177 178 1.822506 TCGAGACATGTCGGACTCTT 58.177 50.000 19.85 0.35 40.49 2.85
193 194 1.062587 CTCTTTATGGCGGCAAACTCG 59.937 52.381 18.31 3.96 0.00 4.18
198 199 1.852067 ATGGCGGCAAACTCGTCAAC 61.852 55.000 18.31 0.00 45.38 3.18
199 200 2.539338 GGCGGCAAACTCGTCAACA 61.539 57.895 3.07 0.00 31.94 3.33
276 277 2.009774 CGCTTGTTGAATACTCAGGGG 58.990 52.381 0.00 0.00 31.69 4.79
298 299 2.368875 AGACCGTCCAAGACTTTGATGT 59.631 45.455 7.51 2.13 36.36 3.06
365 366 9.606631 CTTCTAGTTGGCTTATTTCTCACTATT 57.393 33.333 0.00 0.00 0.00 1.73
412 413 6.968131 TCTTCGATCAAATCCACTAGTTTG 57.032 37.500 0.00 0.00 36.82 2.93
413 414 6.697395 TCTTCGATCAAATCCACTAGTTTGA 58.303 36.000 9.54 9.54 45.27 2.69
414 415 7.158697 TCTTCGATCAAATCCACTAGTTTGAA 58.841 34.615 10.85 1.74 44.62 2.69
415 416 7.659799 TCTTCGATCAAATCCACTAGTTTGAAA 59.340 33.333 10.85 2.49 44.62 2.69
416 417 7.921786 TCGATCAAATCCACTAGTTTGAAAT 57.078 32.000 10.85 0.00 44.62 2.17
418 419 6.470235 CGATCAAATCCACTAGTTTGAAATGC 59.530 38.462 10.85 2.76 44.62 3.56
420 421 7.288810 TCAAATCCACTAGTTTGAAATGCTT 57.711 32.000 5.44 0.00 40.31 3.91
422 423 9.023962 TCAAATCCACTAGTTTGAAATGCTTAT 57.976 29.630 5.44 0.00 40.31 1.73
423 424 9.079833 CAAATCCACTAGTTTGAAATGCTTATG 57.920 33.333 0.00 0.00 37.48 1.90
424 425 8.579850 AATCCACTAGTTTGAAATGCTTATGA 57.420 30.769 0.00 0.00 0.00 2.15
425 426 7.615582 TCCACTAGTTTGAAATGCTTATGAG 57.384 36.000 0.00 0.00 0.00 2.90
426 427 7.168219 TCCACTAGTTTGAAATGCTTATGAGT 58.832 34.615 0.00 0.00 0.00 3.41
433 434 9.013229 AGTTTGAAATGCTTATGAGTTATGACA 57.987 29.630 0.00 0.00 0.00 3.58
434 435 9.624697 GTTTGAAATGCTTATGAGTTATGACAA 57.375 29.630 0.00 0.00 0.00 3.18
435 436 9.624697 TTTGAAATGCTTATGAGTTATGACAAC 57.375 29.630 0.00 0.00 0.00 3.32
436 437 8.334263 TGAAATGCTTATGAGTTATGACAACA 57.666 30.769 0.00 0.00 0.00 3.33
437 438 8.959548 TGAAATGCTTATGAGTTATGACAACAT 58.040 29.630 5.86 5.86 40.16 2.71
438 439 9.229784 GAAATGCTTATGAGTTATGACAACATG 57.770 33.333 9.39 0.00 37.87 3.21
439 440 7.870509 ATGCTTATGAGTTATGACAACATGT 57.129 32.000 0.00 0.00 37.87 3.21
440 441 7.075674 TGCTTATGAGTTATGACAACATGTG 57.924 36.000 0.00 0.00 37.87 3.21
441 442 6.093909 TGCTTATGAGTTATGACAACATGTGG 59.906 38.462 0.00 0.00 37.87 4.17
442 443 6.094048 GCTTATGAGTTATGACAACATGTGGT 59.906 38.462 5.28 5.28 37.87 4.16
443 444 5.885230 ATGAGTTATGACAACATGTGGTG 57.115 39.130 11.58 2.87 37.87 4.17
444 445 4.967036 TGAGTTATGACAACATGTGGTGA 58.033 39.130 11.58 1.75 37.87 4.02
445 446 4.754618 TGAGTTATGACAACATGTGGTGAC 59.245 41.667 11.58 1.62 37.87 3.67
446 447 4.713553 AGTTATGACAACATGTGGTGACA 58.286 39.130 11.58 7.87 41.15 3.58
447 448 5.316167 AGTTATGACAACATGTGGTGACAT 58.684 37.500 11.58 14.52 46.49 3.06
448 449 5.412594 AGTTATGACAACATGTGGTGACATC 59.587 40.000 11.58 6.66 42.67 3.06
449 450 3.205784 TGACAACATGTGGTGACATCA 57.794 42.857 11.58 0.00 46.14 3.07
450 451 2.877786 TGACAACATGTGGTGACATCAC 59.122 45.455 11.58 12.12 46.14 3.06
451 452 3.141398 GACAACATGTGGTGACATCACT 58.859 45.455 19.30 2.99 46.14 3.41
452 453 2.880268 ACAACATGTGGTGACATCACTG 59.120 45.455 19.30 15.94 46.14 3.66
453 454 1.527034 ACATGTGGTGACATCACTGC 58.473 50.000 19.30 5.86 46.14 4.40
454 455 1.072806 ACATGTGGTGACATCACTGCT 59.927 47.619 19.30 2.27 46.14 4.24
455 456 2.156917 CATGTGGTGACATCACTGCTT 58.843 47.619 19.30 0.05 46.14 3.91
456 457 3.244526 ACATGTGGTGACATCACTGCTTA 60.245 43.478 19.30 0.00 46.14 3.09
457 458 3.701205 TGTGGTGACATCACTGCTTAT 57.299 42.857 19.30 0.00 46.14 1.73
458 459 4.817318 TGTGGTGACATCACTGCTTATA 57.183 40.909 19.30 0.00 46.14 0.98
459 460 5.357742 TGTGGTGACATCACTGCTTATAT 57.642 39.130 19.30 0.00 46.14 0.86
460 461 6.478512 TGTGGTGACATCACTGCTTATATA 57.521 37.500 19.30 0.00 46.14 0.86
461 462 7.066307 TGTGGTGACATCACTGCTTATATAT 57.934 36.000 19.30 0.00 46.14 0.86
462 463 8.189119 TGTGGTGACATCACTGCTTATATATA 57.811 34.615 19.30 0.00 46.14 0.86
463 464 8.815912 TGTGGTGACATCACTGCTTATATATAT 58.184 33.333 19.30 0.00 46.14 0.86
464 465 9.091784 GTGGTGACATCACTGCTTATATATATG 57.908 37.037 11.75 0.00 46.14 1.78
465 466 9.034800 TGGTGACATCACTGCTTATATATATGA 57.965 33.333 11.63 3.29 45.73 2.15
466 467 9.307121 GGTGACATCACTGCTTATATATATGAC 57.693 37.037 11.63 2.78 45.73 3.06
467 468 9.014533 GTGACATCACTGCTTATATATATGACG 57.985 37.037 5.44 0.00 43.25 4.35
468 469 8.190784 TGACATCACTGCTTATATATATGACGG 58.809 37.037 5.44 7.97 0.00 4.79
469 470 6.980978 ACATCACTGCTTATATATATGACGGC 59.019 38.462 5.44 5.15 0.00 5.68
470 471 6.524101 TCACTGCTTATATATATGACGGCA 57.476 37.500 0.00 0.00 0.00 5.69
471 472 7.112452 TCACTGCTTATATATATGACGGCAT 57.888 36.000 9.70 9.70 38.54 4.40
472 473 6.980397 TCACTGCTTATATATATGACGGCATG 59.020 38.462 15.86 0.00 35.94 4.06
473 474 5.755375 ACTGCTTATATATATGACGGCATGC 59.245 40.000 15.86 9.90 35.94 4.06
474 475 5.669477 TGCTTATATATATGACGGCATGCA 58.331 37.500 21.36 9.46 35.94 3.96
475 476 6.290605 TGCTTATATATATGACGGCATGCAT 58.709 36.000 21.36 9.34 35.94 3.96
476 477 6.767423 TGCTTATATATATGACGGCATGCATT 59.233 34.615 21.36 4.77 35.94 3.56
477 478 7.930865 TGCTTATATATATGACGGCATGCATTA 59.069 33.333 21.36 3.90 35.94 1.90
482 483 2.346766 TGACGGCATGCATTATTCCT 57.653 45.000 21.36 0.00 0.00 3.36
483 484 2.653726 TGACGGCATGCATTATTCCTT 58.346 42.857 21.36 0.00 0.00 3.36
485 486 3.446873 TGACGGCATGCATTATTCCTTTT 59.553 39.130 21.36 0.00 0.00 2.27
514 515 3.058432 GCAGTGGCACATCATAGCTTATG 60.058 47.826 21.41 5.58 44.52 1.90
522 523 6.237313 CACATCATAGCTTATGTGGACATG 57.763 41.667 20.54 11.39 45.94 3.21
523 524 5.993441 CACATCATAGCTTATGTGGACATGA 59.007 40.000 20.54 9.62 45.94 3.07
524 525 6.653740 CACATCATAGCTTATGTGGACATGAT 59.346 38.462 20.54 11.14 45.94 2.45
525 526 7.820872 CACATCATAGCTTATGTGGACATGATA 59.179 37.037 20.54 0.00 45.94 2.15
526 527 8.039538 ACATCATAGCTTATGTGGACATGATAG 58.960 37.037 0.00 4.30 37.15 2.08
527 528 7.544804 TCATAGCTTATGTGGACATGATAGT 57.455 36.000 0.00 0.00 37.15 2.12
528 529 7.381323 TCATAGCTTATGTGGACATGATAGTG 58.619 38.462 0.00 0.00 37.15 2.74
529 530 5.876651 AGCTTATGTGGACATGATAGTGA 57.123 39.130 0.00 0.00 37.15 3.41
530 531 5.605534 AGCTTATGTGGACATGATAGTGAC 58.394 41.667 0.00 0.00 37.15 3.67
531 532 5.365025 AGCTTATGTGGACATGATAGTGACT 59.635 40.000 0.00 0.00 37.15 3.41
532 533 5.464722 GCTTATGTGGACATGATAGTGACTG 59.535 44.000 0.00 0.00 37.15 3.51
533 534 6.683861 GCTTATGTGGACATGATAGTGACTGA 60.684 42.308 0.00 0.00 37.15 3.41
534 535 4.725790 TGTGGACATGATAGTGACTGAG 57.274 45.455 0.00 0.00 0.00 3.35
535 536 4.344104 TGTGGACATGATAGTGACTGAGA 58.656 43.478 0.00 0.00 0.00 3.27
536 537 4.400567 TGTGGACATGATAGTGACTGAGAG 59.599 45.833 0.00 0.00 0.00 3.20
537 538 4.642437 GTGGACATGATAGTGACTGAGAGA 59.358 45.833 0.00 0.00 0.00 3.10
538 539 4.886489 TGGACATGATAGTGACTGAGAGAG 59.114 45.833 0.00 0.00 0.00 3.20
539 540 4.261572 GGACATGATAGTGACTGAGAGAGC 60.262 50.000 0.00 0.00 0.00 4.09
540 541 3.636300 ACATGATAGTGACTGAGAGAGCC 59.364 47.826 0.00 0.00 0.00 4.70
541 542 3.372440 TGATAGTGACTGAGAGAGCCA 57.628 47.619 0.00 0.00 0.00 4.75
542 543 3.286353 TGATAGTGACTGAGAGAGCCAG 58.714 50.000 0.00 0.00 37.64 4.85
543 544 3.054065 TGATAGTGACTGAGAGAGCCAGA 60.054 47.826 0.00 0.00 35.69 3.86
544 545 1.838112 AGTGACTGAGAGAGCCAGAG 58.162 55.000 0.00 0.00 35.69 3.35
545 546 1.354031 AGTGACTGAGAGAGCCAGAGA 59.646 52.381 0.00 0.00 35.69 3.10
546 547 2.166829 GTGACTGAGAGAGCCAGAGAA 58.833 52.381 0.00 0.00 35.69 2.87
547 548 2.094752 GTGACTGAGAGAGCCAGAGAAC 60.095 54.545 0.00 0.00 35.69 3.01
548 549 2.166829 GACTGAGAGAGCCAGAGAACA 58.833 52.381 0.00 0.00 35.69 3.18
549 550 2.760092 GACTGAGAGAGCCAGAGAACAT 59.240 50.000 0.00 0.00 35.69 2.71
550 551 2.496871 ACTGAGAGAGCCAGAGAACATG 59.503 50.000 0.00 0.00 35.69 3.21
551 552 2.496871 CTGAGAGAGCCAGAGAACATGT 59.503 50.000 0.00 0.00 33.65 3.21
552 553 2.902486 TGAGAGAGCCAGAGAACATGTT 59.098 45.455 11.78 11.78 0.00 2.71
553 554 4.089361 TGAGAGAGCCAGAGAACATGTTA 58.911 43.478 11.95 0.00 0.00 2.41
554 555 4.081972 TGAGAGAGCCAGAGAACATGTTAC 60.082 45.833 11.95 8.98 0.00 2.50
555 556 3.834813 AGAGAGCCAGAGAACATGTTACA 59.165 43.478 11.95 0.00 0.00 2.41
556 557 4.081752 AGAGAGCCAGAGAACATGTTACAG 60.082 45.833 11.95 5.94 0.00 2.74
557 558 3.834813 AGAGCCAGAGAACATGTTACAGA 59.165 43.478 11.95 0.00 0.00 3.41
558 559 4.469227 AGAGCCAGAGAACATGTTACAGAT 59.531 41.667 11.95 3.78 0.00 2.90
559 560 5.658634 AGAGCCAGAGAACATGTTACAGATA 59.341 40.000 11.95 0.00 0.00 1.98
560 561 6.155221 AGAGCCAGAGAACATGTTACAGATAA 59.845 38.462 11.95 0.00 0.00 1.75
561 562 6.711277 AGCCAGAGAACATGTTACAGATAAA 58.289 36.000 11.95 0.00 0.00 1.40
562 563 7.168219 AGCCAGAGAACATGTTACAGATAAAA 58.832 34.615 11.95 0.00 0.00 1.52
597 598 5.948992 AAAAAGGCATGTAGAGTCAGTTC 57.051 39.130 0.00 0.00 0.00 3.01
598 599 4.899352 AAAGGCATGTAGAGTCAGTTCT 57.101 40.909 0.00 0.00 0.00 3.01
599 600 3.883830 AGGCATGTAGAGTCAGTTCTG 57.116 47.619 0.00 0.00 0.00 3.02
600 601 2.093764 AGGCATGTAGAGTCAGTTCTGC 60.094 50.000 0.00 0.00 0.00 4.26
602 603 3.594134 GCATGTAGAGTCAGTTCTGCTT 58.406 45.455 0.00 0.00 31.91 3.91
604 605 4.142945 GCATGTAGAGTCAGTTCTGCTTTG 60.143 45.833 0.00 0.00 31.91 2.77
606 607 3.388024 TGTAGAGTCAGTTCTGCTTTGGT 59.612 43.478 0.00 0.00 31.91 3.67
607 608 4.587262 TGTAGAGTCAGTTCTGCTTTGGTA 59.413 41.667 0.00 0.00 31.91 3.25
608 609 3.996480 AGAGTCAGTTCTGCTTTGGTAC 58.004 45.455 0.00 0.00 0.00 3.34
609 610 3.388024 AGAGTCAGTTCTGCTTTGGTACA 59.612 43.478 0.00 0.00 0.00 2.90
610 611 9.251286 TGTAGAGTCAGTTCTGCTTTGGTACAA 62.251 40.741 0.00 0.00 35.59 2.41
624 625 3.876341 TGGTACAAATCGGTTCATACCC 58.124 45.455 15.13 0.00 36.74 3.69
625 626 3.208594 GGTACAAATCGGTTCATACCCC 58.791 50.000 9.08 0.00 41.75 4.95
626 627 3.370739 GGTACAAATCGGTTCATACCCCA 60.371 47.826 9.08 0.00 41.75 4.96
627 628 3.662759 ACAAATCGGTTCATACCCCAT 57.337 42.857 0.00 0.00 41.75 4.00
628 629 3.287222 ACAAATCGGTTCATACCCCATG 58.713 45.455 0.00 0.00 41.75 3.66
629 630 2.622942 CAAATCGGTTCATACCCCATGG 59.377 50.000 4.14 4.14 41.75 3.66
781 1387 3.214328 AGTAAAGAGGCCACACACTTTG 58.786 45.455 5.01 0.00 34.93 2.77
973 1587 5.817616 ACGACACTTTAATCAACACGTAG 57.182 39.130 0.00 0.00 0.00 3.51
974 1588 4.149396 ACGACACTTTAATCAACACGTAGC 59.851 41.667 0.00 0.00 0.00 3.58
975 1589 4.384846 CGACACTTTAATCAACACGTAGCT 59.615 41.667 0.00 0.00 0.00 3.32
976 1590 5.570206 CGACACTTTAATCAACACGTAGCTA 59.430 40.000 0.00 0.00 0.00 3.32
1189 1806 0.888285 GCACAAGAAGCTGCCTGTCT 60.888 55.000 0.00 0.00 0.00 3.41
1205 1822 2.745884 CTTCATCCACGGCGGCAA 60.746 61.111 13.24 0.00 33.14 4.52
1251 1868 2.393768 GGAGTACCTCGACGACGCA 61.394 63.158 1.48 0.00 39.58 5.24
1266 1883 0.610785 ACGCATTCCCCGAAAATGGT 60.611 50.000 6.53 1.87 35.19 3.55
1348 1965 8.059543 CCTACGTGGATAACAAGGTATGTTTCA 61.060 40.741 0.00 0.00 43.64 2.69
1432 2049 3.123050 GTTTTGAGTTGGACATGTTGGC 58.877 45.455 0.00 0.00 0.00 4.52
1487 2106 7.223582 ACATTCGCTCTGAGTTGTATTATCTTG 59.776 37.037 6.53 0.00 0.00 3.02
1678 3266 0.332972 AATGCTCCAAGGAAGGGGAC 59.667 55.000 0.00 0.00 0.00 4.46
1899 3487 3.515901 GACAAGGTGGAGGAGTACATCTT 59.484 47.826 0.00 0.00 38.51 2.40
1901 3489 4.712337 ACAAGGTGGAGGAGTACATCTTAG 59.288 45.833 0.00 0.00 35.97 2.18
2012 3600 2.552315 TCGCCTTCAAATTCAGTTGGTC 59.448 45.455 0.00 0.00 0.00 4.02
2137 3812 8.783093 GCTGTTTTGGGAATAAATTAAAGCTTT 58.217 29.630 17.30 17.30 0.00 3.51
2360 5532 0.171231 TCGATGACAGCCGAGAAGTG 59.829 55.000 0.00 0.00 0.00 3.16
2413 5595 2.833533 GCCGCAAGCATCGCCATTA 61.834 57.895 0.00 0.00 42.97 1.90
2516 5699 1.344114 GAGGAGCTGGCAGGAATCTAG 59.656 57.143 17.64 0.00 0.00 2.43
2544 5727 1.887198 CTCTGTCTAATACGCCCCGAT 59.113 52.381 0.00 0.00 0.00 4.18
2599 5782 2.945984 CGCAAAGAAGAAGCGCCA 59.054 55.556 2.29 0.00 45.14 5.69
2613 5796 2.911143 GCCACCATCCATCCGAGT 59.089 61.111 0.00 0.00 0.00 4.18
2651 5834 6.444171 AGAAGCAAAACCCTACCTATCTAAGT 59.556 38.462 0.00 0.00 0.00 2.24
2657 5840 3.979347 ACCCTACCTATCTAAGTCGAGGA 59.021 47.826 0.00 0.00 33.04 3.71
2662 5845 4.607239 ACCTATCTAAGTCGAGGAACCAA 58.393 43.478 0.00 0.00 33.04 3.67
2740 5923 1.787057 GACTCGTCGGCGGAGATCAT 61.787 60.000 18.00 2.85 38.89 2.45
2854 6037 7.541783 ACGTTACTAGTACGAAATGCAATGTTA 59.458 33.333 22.87 0.00 41.33 2.41
2859 6042 6.604735 AGTACGAAATGCAATGTTATCCTC 57.395 37.500 0.00 0.00 0.00 3.71
2864 6047 5.967674 CGAAATGCAATGTTATCCTCTTGAC 59.032 40.000 0.00 0.00 0.00 3.18
2936 6120 9.672086 TTTGTCACGGCAATAAATATAAATAGC 57.328 29.630 0.00 0.00 0.00 2.97
2938 6122 9.008965 TGTCACGGCAATAAATATAAATAGCAT 57.991 29.630 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.204301 CCACACATCCATATCTTGACTGATTC 59.796 42.308 0.00 0.00 0.00 2.52
36 37 5.128205 CACATCACCACACATCCATATCTT 58.872 41.667 0.00 0.00 0.00 2.40
52 53 2.099756 GGGCTAATGCTTTCCACATCAC 59.900 50.000 0.00 0.00 39.59 3.06
107 108 4.214310 TCAGCTGGTCAAAAGAAAATGGA 58.786 39.130 15.13 0.00 0.00 3.41
120 121 1.415659 AGACATGCCTATCAGCTGGTC 59.584 52.381 15.13 10.43 37.02 4.02
136 137 6.093082 TCGAAACACTATCTCATCGTTAGACA 59.907 38.462 0.00 0.00 0.00 3.41
143 144 4.909894 TGTCTCGAAACACTATCTCATCG 58.090 43.478 0.00 0.00 0.00 3.84
146 147 5.641709 GACATGTCTCGAAACACTATCTCA 58.358 41.667 18.83 0.00 30.55 3.27
167 168 1.152383 GCCGCCATAAAGAGTCCGAC 61.152 60.000 0.00 0.00 0.00 4.79
177 178 0.320858 TGACGAGTTTGCCGCCATAA 60.321 50.000 0.00 0.00 0.00 1.90
193 194 8.128582 TGTGAAACATAATCTCAACTTGTTGAC 58.871 33.333 11.62 0.58 45.67 3.18
276 277 2.814280 TCAAAGTCTTGGACGGTCTC 57.186 50.000 8.23 0.00 37.67 3.36
365 366 5.579564 AACTAGTGGTTTTTGCCGTTTAA 57.420 34.783 0.00 0.00 33.90 1.52
378 379 6.371825 GGATTTGATCGAAGAAAACTAGTGGT 59.628 38.462 0.00 0.00 43.58 4.16
412 413 9.229784 CATGTTGTCATAACTCATAAGCATTTC 57.770 33.333 0.00 0.00 32.47 2.17
413 414 8.742777 ACATGTTGTCATAACTCATAAGCATTT 58.257 29.630 0.00 0.00 32.47 2.32
414 415 8.186163 CACATGTTGTCATAACTCATAAGCATT 58.814 33.333 0.00 0.00 32.47 3.56
415 416 7.201758 CCACATGTTGTCATAACTCATAAGCAT 60.202 37.037 0.00 0.00 32.47 3.79
416 417 6.093909 CCACATGTTGTCATAACTCATAAGCA 59.906 38.462 0.00 0.00 32.47 3.91
418 419 7.334171 TCACCACATGTTGTCATAACTCATAAG 59.666 37.037 0.00 0.00 32.47 1.73
420 421 6.593770 GTCACCACATGTTGTCATAACTCATA 59.406 38.462 0.00 0.00 32.47 2.15
422 423 4.754618 GTCACCACATGTTGTCATAACTCA 59.245 41.667 0.00 0.00 32.47 3.41
423 424 4.754618 TGTCACCACATGTTGTCATAACTC 59.245 41.667 0.00 0.00 32.47 3.01
424 425 4.713553 TGTCACCACATGTTGTCATAACT 58.286 39.130 0.00 0.00 32.47 2.24
425 426 5.181056 TGATGTCACCACATGTTGTCATAAC 59.819 40.000 9.34 3.51 43.79 1.89
426 427 5.181056 GTGATGTCACCACATGTTGTCATAA 59.819 40.000 9.34 1.82 43.79 1.90
429 430 2.877786 GTGATGTCACCACATGTTGTCA 59.122 45.455 0.00 0.00 43.79 3.58
430 431 3.542712 GTGATGTCACCACATGTTGTC 57.457 47.619 0.00 0.00 43.79 3.18
441 442 9.014533 CGTCATATATATAAGCAGTGATGTCAC 57.985 37.037 5.01 5.01 46.77 3.67
442 443 8.190784 CCGTCATATATATAAGCAGTGATGTCA 58.809 37.037 0.00 0.00 0.00 3.58
443 444 7.168302 GCCGTCATATATATAAGCAGTGATGTC 59.832 40.741 0.00 0.00 0.00 3.06
444 445 6.980978 GCCGTCATATATATAAGCAGTGATGT 59.019 38.462 0.00 0.00 0.00 3.06
445 446 6.980397 TGCCGTCATATATATAAGCAGTGATG 59.020 38.462 0.00 1.76 0.00 3.07
446 447 7.112452 TGCCGTCATATATATAAGCAGTGAT 57.888 36.000 0.00 0.00 0.00 3.06
447 448 6.524101 TGCCGTCATATATATAAGCAGTGA 57.476 37.500 0.00 0.00 0.00 3.41
448 449 6.292542 GCATGCCGTCATATATATAAGCAGTG 60.293 42.308 6.36 10.60 31.70 3.66
449 450 5.755375 GCATGCCGTCATATATATAAGCAGT 59.245 40.000 6.36 2.23 31.70 4.40
450 451 5.754890 TGCATGCCGTCATATATATAAGCAG 59.245 40.000 16.68 7.07 31.70 4.24
451 452 5.669477 TGCATGCCGTCATATATATAAGCA 58.331 37.500 16.68 9.32 0.00 3.91
452 453 6.791887 ATGCATGCCGTCATATATATAAGC 57.208 37.500 16.68 0.00 0.00 3.09
455 456 9.435688 GGAATAATGCATGCCGTCATATATATA 57.564 33.333 16.68 0.00 0.00 0.86
456 457 8.159447 AGGAATAATGCATGCCGTCATATATAT 58.841 33.333 16.68 0.00 37.43 0.86
457 458 7.508687 AGGAATAATGCATGCCGTCATATATA 58.491 34.615 16.68 0.00 37.43 0.86
458 459 6.359804 AGGAATAATGCATGCCGTCATATAT 58.640 36.000 16.68 0.00 37.43 0.86
459 460 5.744171 AGGAATAATGCATGCCGTCATATA 58.256 37.500 16.68 0.00 37.43 0.86
460 461 4.592942 AGGAATAATGCATGCCGTCATAT 58.407 39.130 16.68 3.79 37.43 1.78
461 462 4.019792 AGGAATAATGCATGCCGTCATA 57.980 40.909 16.68 1.39 37.43 2.15
462 463 2.867624 AGGAATAATGCATGCCGTCAT 58.132 42.857 16.68 0.00 37.43 3.06
463 464 2.346766 AGGAATAATGCATGCCGTCA 57.653 45.000 16.68 0.00 37.43 4.35
464 465 3.715628 AAAGGAATAATGCATGCCGTC 57.284 42.857 16.68 5.00 37.43 4.79
465 466 4.470334 AAAAAGGAATAATGCATGCCGT 57.530 36.364 16.68 5.24 37.43 5.68
490 491 6.774921 CATAAGCTATGATGTGCCACTGCAT 61.775 44.000 0.00 2.46 43.41 3.96
491 492 5.515884 CATAAGCTATGATGTGCCACTGCA 61.516 45.833 0.00 0.00 41.07 4.41
494 495 4.132336 CACATAAGCTATGATGTGCCACT 58.868 43.478 18.16 0.00 44.59 4.00
495 496 4.478843 CACATAAGCTATGATGTGCCAC 57.521 45.455 18.16 0.00 44.59 5.01
500 501 6.178607 TCATGTCCACATAAGCTATGATGT 57.821 37.500 9.32 6.59 39.45 3.06
501 502 8.039538 ACTATCATGTCCACATAAGCTATGATG 58.960 37.037 11.37 7.19 39.45 3.07
502 503 8.039538 CACTATCATGTCCACATAAGCTATGAT 58.960 37.037 7.70 7.70 39.45 2.45
504 505 7.330454 GTCACTATCATGTCCACATAAGCTATG 59.670 40.741 0.00 0.00 41.88 2.23
505 506 7.234371 AGTCACTATCATGTCCACATAAGCTAT 59.766 37.037 0.00 0.00 34.26 2.97
507 508 5.365025 AGTCACTATCATGTCCACATAAGCT 59.635 40.000 0.00 0.00 34.26 3.74
514 515 4.642437 TCTCTCAGTCACTATCATGTCCAC 59.358 45.833 0.00 0.00 0.00 4.02
516 517 4.261572 GCTCTCTCAGTCACTATCATGTCC 60.262 50.000 0.00 0.00 0.00 4.02
517 518 4.261572 GGCTCTCTCAGTCACTATCATGTC 60.262 50.000 0.00 0.00 0.00 3.06
518 519 3.636300 GGCTCTCTCAGTCACTATCATGT 59.364 47.826 0.00 0.00 0.00 3.21
519 520 3.635836 TGGCTCTCTCAGTCACTATCATG 59.364 47.826 0.00 0.00 28.92 3.07
520 521 3.890756 CTGGCTCTCTCAGTCACTATCAT 59.109 47.826 0.00 0.00 31.56 2.45
522 523 3.550820 TCTGGCTCTCTCAGTCACTATC 58.449 50.000 0.00 0.00 31.56 2.08
523 524 3.201930 TCTCTGGCTCTCTCAGTCACTAT 59.798 47.826 0.00 0.00 31.56 2.12
524 525 2.573915 TCTCTGGCTCTCTCAGTCACTA 59.426 50.000 0.00 0.00 31.56 2.74
525 526 1.354031 TCTCTGGCTCTCTCAGTCACT 59.646 52.381 0.00 0.00 31.56 3.41
526 527 1.832883 TCTCTGGCTCTCTCAGTCAC 58.167 55.000 0.00 0.00 31.56 3.67
527 528 2.166829 GTTCTCTGGCTCTCTCAGTCA 58.833 52.381 0.00 0.00 34.68 3.41
528 529 2.166829 TGTTCTCTGGCTCTCTCAGTC 58.833 52.381 0.00 0.00 34.15 3.51
529 530 2.300956 TGTTCTCTGGCTCTCTCAGT 57.699 50.000 0.00 0.00 34.15 3.41
530 531 2.496871 ACATGTTCTCTGGCTCTCTCAG 59.503 50.000 0.00 0.00 0.00 3.35
531 532 2.533916 ACATGTTCTCTGGCTCTCTCA 58.466 47.619 0.00 0.00 0.00 3.27
532 533 3.608316 AACATGTTCTCTGGCTCTCTC 57.392 47.619 4.92 0.00 0.00 3.20
533 534 3.834813 TGTAACATGTTCTCTGGCTCTCT 59.165 43.478 15.85 0.00 0.00 3.10
534 535 4.081972 TCTGTAACATGTTCTCTGGCTCTC 60.082 45.833 15.85 0.00 0.00 3.20
535 536 3.834813 TCTGTAACATGTTCTCTGGCTCT 59.165 43.478 15.85 0.00 0.00 4.09
536 537 4.193826 TCTGTAACATGTTCTCTGGCTC 57.806 45.455 15.85 0.00 0.00 4.70
537 538 4.833478 ATCTGTAACATGTTCTCTGGCT 57.167 40.909 15.85 3.41 0.00 4.75
538 539 6.985188 TTTATCTGTAACATGTTCTCTGGC 57.015 37.500 15.85 0.80 0.00 4.85
577 578 4.573900 CAGAACTGACTCTACATGCCTTT 58.426 43.478 0.00 0.00 0.00 3.11
581 582 3.244033 AGCAGAACTGACTCTACATGC 57.756 47.619 5.97 0.00 0.00 4.06
582 583 4.391216 CCAAAGCAGAACTGACTCTACATG 59.609 45.833 5.97 0.00 0.00 3.21
583 584 4.040952 ACCAAAGCAGAACTGACTCTACAT 59.959 41.667 5.97 0.00 0.00 2.29
585 586 3.996480 ACCAAAGCAGAACTGACTCTAC 58.004 45.455 5.97 0.00 0.00 2.59
586 587 4.587262 TGTACCAAAGCAGAACTGACTCTA 59.413 41.667 5.97 0.00 0.00 2.43
587 588 3.388024 TGTACCAAAGCAGAACTGACTCT 59.612 43.478 5.97 0.00 0.00 3.24
588 589 3.728845 TGTACCAAAGCAGAACTGACTC 58.271 45.455 5.97 0.00 0.00 3.36
589 590 3.838244 TGTACCAAAGCAGAACTGACT 57.162 42.857 5.97 0.12 0.00 3.41
592 593 4.466828 CGATTTGTACCAAAGCAGAACTG 58.533 43.478 5.89 0.00 0.00 3.16
593 594 3.502211 CCGATTTGTACCAAAGCAGAACT 59.498 43.478 5.89 0.00 0.00 3.01
594 595 3.252458 ACCGATTTGTACCAAAGCAGAAC 59.748 43.478 5.89 0.00 0.00 3.01
595 596 3.482436 ACCGATTTGTACCAAAGCAGAA 58.518 40.909 5.89 0.00 0.00 3.02
596 597 3.134574 ACCGATTTGTACCAAAGCAGA 57.865 42.857 5.89 0.00 0.00 4.26
597 598 3.252215 TGAACCGATTTGTACCAAAGCAG 59.748 43.478 5.89 0.00 0.00 4.24
598 599 3.215151 TGAACCGATTTGTACCAAAGCA 58.785 40.909 5.89 0.00 0.00 3.91
599 600 3.907894 TGAACCGATTTGTACCAAAGC 57.092 42.857 0.00 0.00 0.00 3.51
600 601 5.875930 GGTATGAACCGATTTGTACCAAAG 58.124 41.667 0.67 0.00 35.62 2.77
622 623 8.698973 TTGTTATAATTATGTGTACCATGGGG 57.301 34.615 18.09 0.00 41.29 4.96
625 626 9.624697 GCCATTGTTATAATTATGTGTACCATG 57.375 33.333 8.28 8.01 34.86 3.66
626 627 9.360901 TGCCATTGTTATAATTATGTGTACCAT 57.639 29.630 8.28 0.00 37.58 3.55
627 628 8.753497 TGCCATTGTTATAATTATGTGTACCA 57.247 30.769 8.28 0.00 0.00 3.25
641 642 9.435688 GTCCTCTTTTTATTTTGCCATTGTTAT 57.564 29.630 0.00 0.00 0.00 1.89
642 643 8.424918 TGTCCTCTTTTTATTTTGCCATTGTTA 58.575 29.630 0.00 0.00 0.00 2.41
643 644 7.226523 GTGTCCTCTTTTTATTTTGCCATTGTT 59.773 33.333 0.00 0.00 0.00 2.83
644 645 6.705825 GTGTCCTCTTTTTATTTTGCCATTGT 59.294 34.615 0.00 0.00 0.00 2.71
647 648 6.670695 AGTGTCCTCTTTTTATTTTGCCAT 57.329 33.333 0.00 0.00 0.00 4.40
648 649 6.478512 AAGTGTCCTCTTTTTATTTTGCCA 57.521 33.333 0.00 0.00 0.00 4.92
649 650 9.489084 AATTAAGTGTCCTCTTTTTATTTTGCC 57.511 29.630 0.00 0.00 0.00 4.52
678 1194 2.034179 GCCACGCCTTTCTTTAGTTGTT 59.966 45.455 0.00 0.00 0.00 2.83
691 1290 3.673484 GTGTGCATTGCCACGCCT 61.673 61.111 6.12 0.00 39.64 5.52
735 1334 0.961019 GCACAAGGACCAATGAAGCA 59.039 50.000 4.46 0.00 0.00 3.91
781 1387 1.227380 CCACGAGCTAGTCATGGGC 60.227 63.158 0.00 0.00 0.00 5.36
860 1470 1.202114 GCCTTGAAATGTGCAATCGGA 59.798 47.619 0.00 0.00 0.00 4.55
953 1563 5.840940 AGCTACGTGTTGATTAAAGTGTC 57.159 39.130 0.00 0.00 0.00 3.67
973 1587 3.440228 GTCGTTGAAGGATCTCTGTAGC 58.560 50.000 0.00 0.00 0.00 3.58
974 1588 3.374367 TCGTCGTTGAAGGATCTCTGTAG 59.626 47.826 0.00 0.00 0.00 2.74
975 1589 3.340928 TCGTCGTTGAAGGATCTCTGTA 58.659 45.455 0.00 0.00 0.00 2.74
976 1590 2.160205 TCGTCGTTGAAGGATCTCTGT 58.840 47.619 0.00 0.00 0.00 3.41
1158 1775 3.057033 GCTTCTTGTGCACAGAATTGGAT 60.057 43.478 20.59 0.00 0.00 3.41
1165 1782 1.168407 GGCAGCTTCTTGTGCACAGA 61.168 55.000 20.59 16.15 41.75 3.41
1189 1806 2.745884 CTTGCCGCCGTGGATGAA 60.746 61.111 0.88 0.00 42.00 2.57
1205 1822 4.057428 GCGACTCACAGACGGGCT 62.057 66.667 0.00 0.00 34.19 5.19
1251 1868 0.041090 AGGCACCATTTTCGGGGAAT 59.959 50.000 0.00 0.00 0.00 3.01
1266 1883 3.092511 GCAGGGAGGATGGAGGCA 61.093 66.667 0.00 0.00 0.00 4.75
1311 1928 3.081409 ACGTAGGCGGCCCAGAAT 61.081 61.111 17.02 0.00 43.45 2.40
1348 1965 1.568504 TGGGCCAAACTAGACGAGAT 58.431 50.000 2.13 0.00 0.00 2.75
1406 2023 6.148480 CCAACATGTCCAACTCAAAACAAAAA 59.852 34.615 0.00 0.00 0.00 1.94
1871 3459 2.046892 CTCCACCTTGTCTGCCGG 60.047 66.667 0.00 0.00 0.00 6.13
1876 3464 2.696526 TGTACTCCTCCACCTTGTCT 57.303 50.000 0.00 0.00 0.00 3.41
1899 3487 4.020039 TCCACTTTGGATAAAGAACCGCTA 60.020 41.667 6.77 0.00 42.67 4.26
1901 3489 3.078837 TCCACTTTGGATAAAGAACCGC 58.921 45.455 6.77 0.00 42.67 5.68
2087 3762 4.217836 ACTCAGATTGATGACAGTGCAT 57.782 40.909 0.00 0.00 0.00 3.96
2097 3772 5.510179 CCCAAAACAGCAAACTCAGATTGAT 60.510 40.000 0.00 0.00 0.00 2.57
2100 3775 3.960102 TCCCAAAACAGCAAACTCAGATT 59.040 39.130 0.00 0.00 0.00 2.40
2137 3812 6.070897 TGAAAAAGCGATCAAAGAATGACA 57.929 33.333 0.00 0.00 41.93 3.58
2142 3817 5.067153 TGTCCTTGAAAAAGCGATCAAAGAA 59.933 36.000 0.00 0.00 35.31 2.52
2240 5411 0.179111 TTGTCCACGGATCTCGATGC 60.179 55.000 10.05 0.00 42.43 3.91
2326 5498 1.194781 ATCGACAAGGTCCAGCCAGT 61.195 55.000 0.00 0.00 40.61 4.00
2328 5500 1.191489 TCATCGACAAGGTCCAGCCA 61.191 55.000 0.00 0.00 40.61 4.75
2516 5699 2.745102 GTATTAGACAGAGCTTCGGCC 58.255 52.381 0.00 0.00 43.01 6.13
2544 5727 4.705110 TGATCCTCCTCAAGTTTGTTCA 57.295 40.909 0.00 0.00 0.00 3.18
2583 5766 1.081175 GGTGGCGCTTCTTCTTTGC 60.081 57.895 7.64 0.00 0.00 3.68
2599 5782 1.524002 CAGCACTCGGATGGATGGT 59.476 57.895 0.00 0.00 0.00 3.55
2613 5796 1.601759 GCTTCTCACAAGGGCAGCA 60.602 57.895 0.00 0.00 0.00 4.41
2651 5834 2.764572 GAGGGTATTCTTGGTTCCTCGA 59.235 50.000 0.00 0.00 32.67 4.04
2657 5840 0.916809 CGGGGAGGGTATTCTTGGTT 59.083 55.000 0.00 0.00 0.00 3.67
2662 5845 2.070650 GTGGCGGGGAGGGTATTCT 61.071 63.158 0.00 0.00 0.00 2.40
2740 5923 5.805728 GACTTGGGAAAGTCATCTTCCTTA 58.194 41.667 12.54 0.00 46.34 2.69
2765 5948 0.951558 TTGTTTCCCTTCTCGCAAGC 59.048 50.000 0.00 0.00 37.18 4.01
2800 5983 5.305128 TGACGGGGTAAAATCGGATAAGTAT 59.695 40.000 0.00 0.00 0.00 2.12
2905 6089 9.944663 TTATATTTATTGCCGTGACAAAATCTC 57.055 29.630 0.00 0.00 32.27 2.75
2914 6098 8.458052 CCATGCTATTTATATTTATTGCCGTGA 58.542 33.333 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.