Multiple sequence alignment - TraesCS1B01G416900

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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 TraesCS1B01G416900 chr1B 100.000 2549 0 0 1 2549 641550466 641547918 0.000000e+00 4708.0
1 TraesCS1B01G416900 chr7D 93.839 1964 101 11 599 2549 94497479 94495523 0.000000e+00 2939.0
2 TraesCS1B01G416900 chr7D 94.000 50 0 2 548 597 223819439 223819485 3.520000e-09 73.1
3 TraesCS1B01G416900 chr4A 93.374 1962 117 10 600 2549 724524710 724522750 0.000000e+00 2891.0
4 TraesCS1B01G416900 chr4A 96.875 32 1 0 563 594 3377286 3377317 1.000000e-03 54.7
5 TraesCS1B01G416900 chr4D 93.371 1961 111 15 601 2549 459886443 459884490 0.000000e+00 2883.0
6 TraesCS1B01G416900 chr2D 93.282 1965 96 11 598 2549 16065483 16067424 0.000000e+00 2865.0
7 TraesCS1B01G416900 chr3B 93.072 1963 120 10 601 2549 599079411 599077451 0.000000e+00 2857.0
8 TraesCS1B01G416900 chr3B 89.766 342 30 4 1 341 243244633 243244296 1.400000e-117 433.0
9 TraesCS1B01G416900 chr7A 92.903 1860 115 12 597 2446 118579715 118581567 0.000000e+00 2687.0
10 TraesCS1B01G416900 chr1D 93.849 1707 93 11 601 2295 25464319 25466025 0.000000e+00 2560.0
11 TraesCS1B01G416900 chr1D 89.507 629 16 11 1 600 464835521 464834914 0.000000e+00 750.0
12 TraesCS1B01G416900 chr6B 93.750 1712 88 13 854 2549 59433392 59431684 0.000000e+00 2551.0
13 TraesCS1B01G416900 chr6B 91.304 46 1 2 549 594 506720198 506720240 2.740000e-05 60.2
14 TraesCS1B01G416900 chr3D 93.267 1708 104 9 599 2295 546485993 546487700 0.000000e+00 2507.0
15 TraesCS1B01G416900 chr3D 89.766 342 30 4 1 341 168191092 168190755 1.400000e-117 433.0
16 TraesCS1B01G416900 chr3D 100.000 30 0 0 563 592 4322386 4322357 3.540000e-04 56.5
17 TraesCS1B01G416900 chr1A 96.594 411 12 2 1 409 557117432 557117022 0.000000e+00 680.0
18 TraesCS1B01G416900 chr1A 94.851 369 18 1 1 369 557192675 557193042 2.200000e-160 575.0
19 TraesCS1B01G416900 chr1A 90.476 42 3 1 550 591 373763451 373763491 1.000000e-03 54.7
20 TraesCS1B01G416900 chr3A 92.616 474 28 5 2080 2549 115066007 115066477 0.000000e+00 675.0
21 TraesCS1B01G416900 chr3A 90.058 342 29 3 1 341 199696679 199697016 3.010000e-119 438.0
22 TraesCS1B01G416900 chr2B 89.171 434 42 3 600 1029 13181550 13181982 1.040000e-148 536.0
23 TraesCS1B01G416900 chr5D 80.822 219 23 10 138 356 240085124 240084925 1.220000e-33 154.0
24 TraesCS1B01G416900 chr5B 81.281 203 22 8 138 340 263521737 263521923 1.580000e-32 150.0
25 TraesCS1B01G416900 chr5A 88.889 108 11 1 138 245 313879985 313880091 5.720000e-27 132.0
26 TraesCS1B01G416900 chr5A 94.286 35 2 0 563 597 635404808 635404774 1.000000e-03 54.7
27 TraesCS1B01G416900 chr6D 89.796 49 2 2 549 597 317479789 317479744 2.740000e-05 60.2
28 TraesCS1B01G416900 chr4B 89.130 46 2 3 550 594 2216958 2217001 1.000000e-03 54.7


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 TraesCS1B01G416900 chr1B 641547918 641550466 2548 True 4708 4708 100.000 1 2549 1 chr1B.!!$R1 2548
1 TraesCS1B01G416900 chr7D 94495523 94497479 1956 True 2939 2939 93.839 599 2549 1 chr7D.!!$R1 1950
2 TraesCS1B01G416900 chr4A 724522750 724524710 1960 True 2891 2891 93.374 600 2549 1 chr4A.!!$R1 1949
3 TraesCS1B01G416900 chr4D 459884490 459886443 1953 True 2883 2883 93.371 601 2549 1 chr4D.!!$R1 1948
4 TraesCS1B01G416900 chr2D 16065483 16067424 1941 False 2865 2865 93.282 598 2549 1 chr2D.!!$F1 1951
5 TraesCS1B01G416900 chr3B 599077451 599079411 1960 True 2857 2857 93.072 601 2549 1 chr3B.!!$R2 1948
6 TraesCS1B01G416900 chr7A 118579715 118581567 1852 False 2687 2687 92.903 597 2446 1 chr7A.!!$F1 1849
7 TraesCS1B01G416900 chr1D 25464319 25466025 1706 False 2560 2560 93.849 601 2295 1 chr1D.!!$F1 1694
8 TraesCS1B01G416900 chr1D 464834914 464835521 607 True 750 750 89.507 1 600 1 chr1D.!!$R1 599
9 TraesCS1B01G416900 chr6B 59431684 59433392 1708 True 2551 2551 93.750 854 2549 1 chr6B.!!$R1 1695
10 TraesCS1B01G416900 chr3D 546485993 546487700 1707 False 2507 2507 93.267 599 2295 1 chr3D.!!$F1 1696

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
509 510 0.033504 CTCACCACCAGTAGCAACGT 59.966 55.0 0.0 0.0 0.0 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 2431 0.099613 ACGCGTGTGCAAACATTCAA 59.9 45.0 12.93 0.0 42.97 2.69 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
325 326 3.428797 CAGCCCATGATGCCGAAG 58.571 61.111 0.00 0.00 0.00 3.79
326 327 2.517875 AGCCCATGATGCCGAAGC 60.518 61.111 0.00 0.00 40.48 3.86
327 328 3.957535 GCCCATGATGCCGAAGCG 61.958 66.667 0.00 0.00 44.31 4.68
328 329 3.957535 CCCATGATGCCGAAGCGC 61.958 66.667 0.00 0.00 44.31 5.92
329 330 3.204119 CCATGATGCCGAAGCGCA 61.204 61.111 11.47 0.00 44.31 6.09
330 331 2.023741 CATGATGCCGAAGCGCAC 59.976 61.111 11.47 1.68 42.70 5.34
331 332 3.204827 ATGATGCCGAAGCGCACC 61.205 61.111 11.47 0.00 42.70 5.01
417 418 4.218686 GGGTGCTGGTTGGGTGGT 62.219 66.667 0.00 0.00 0.00 4.16
418 419 2.836187 GGGTGCTGGTTGGGTGGTA 61.836 63.158 0.00 0.00 0.00 3.25
419 420 1.303317 GGTGCTGGTTGGGTGGTAG 60.303 63.158 0.00 0.00 0.00 3.18
420 421 1.303317 GTGCTGGTTGGGTGGTAGG 60.303 63.158 0.00 0.00 0.00 3.18
421 422 2.355115 GCTGGTTGGGTGGTAGGG 59.645 66.667 0.00 0.00 0.00 3.53
422 423 2.355115 CTGGTTGGGTGGTAGGGC 59.645 66.667 0.00 0.00 0.00 5.19
423 424 3.622060 CTGGTTGGGTGGTAGGGCG 62.622 68.421 0.00 0.00 0.00 6.13
425 426 4.029809 GTTGGGTGGTAGGGCGCT 62.030 66.667 7.64 8.86 0.00 5.92
426 427 4.028490 TTGGGTGGTAGGGCGCTG 62.028 66.667 14.51 0.00 0.00 5.18
430 431 4.778143 GTGGTAGGGCGCTGGGTG 62.778 72.222 14.51 0.00 0.00 4.61
439 440 4.954970 CGCTGGGTGGGCTTGTGT 62.955 66.667 0.00 0.00 0.00 3.72
440 441 2.985847 GCTGGGTGGGCTTGTGTC 60.986 66.667 0.00 0.00 0.00 3.67
441 442 2.282462 CTGGGTGGGCTTGTGTCC 60.282 66.667 0.00 0.00 38.74 4.02
442 443 4.263572 TGGGTGGGCTTGTGTCCG 62.264 66.667 0.00 0.00 41.88 4.79
444 445 4.265056 GGTGGGCTTGTGTCCGGT 62.265 66.667 0.00 0.00 41.88 5.28
445 446 2.978010 GTGGGCTTGTGTCCGGTG 60.978 66.667 0.00 0.00 41.88 4.94
446 447 3.484806 TGGGCTTGTGTCCGGTGT 61.485 61.111 0.00 0.00 41.88 4.16
447 448 2.978010 GGGCTTGTGTCCGGTGTG 60.978 66.667 0.00 0.00 0.00 3.82
448 449 2.203153 GGCTTGTGTCCGGTGTGT 60.203 61.111 0.00 0.00 0.00 3.72
449 450 2.542907 GGCTTGTGTCCGGTGTGTG 61.543 63.158 0.00 0.00 0.00 3.82
450 451 1.817941 GCTTGTGTCCGGTGTGTGT 60.818 57.895 0.00 0.00 0.00 3.72
451 452 2.013807 CTTGTGTCCGGTGTGTGTG 58.986 57.895 0.00 0.00 0.00 3.82
452 453 0.742990 CTTGTGTCCGGTGTGTGTGT 60.743 55.000 0.00 0.00 0.00 3.72
453 454 1.021920 TTGTGTCCGGTGTGTGTGTG 61.022 55.000 0.00 0.00 0.00 3.82
454 455 1.448893 GTGTCCGGTGTGTGTGTGT 60.449 57.895 0.00 0.00 0.00 3.72
455 456 1.448717 TGTCCGGTGTGTGTGTGTG 60.449 57.895 0.00 0.00 0.00 3.82
456 457 2.177580 GTCCGGTGTGTGTGTGTGG 61.178 63.158 0.00 0.00 0.00 4.17
457 458 2.188207 CCGGTGTGTGTGTGTGGA 59.812 61.111 0.00 0.00 0.00 4.02
458 459 1.887242 CCGGTGTGTGTGTGTGGAG 60.887 63.158 0.00 0.00 0.00 3.86
459 460 1.153449 CGGTGTGTGTGTGTGGAGT 60.153 57.895 0.00 0.00 0.00 3.85
460 461 0.103390 CGGTGTGTGTGTGTGGAGTA 59.897 55.000 0.00 0.00 0.00 2.59
461 462 1.865865 GGTGTGTGTGTGTGGAGTAG 58.134 55.000 0.00 0.00 0.00 2.57
462 463 1.540363 GGTGTGTGTGTGTGGAGTAGG 60.540 57.143 0.00 0.00 0.00 3.18
463 464 1.411246 GTGTGTGTGTGTGGAGTAGGA 59.589 52.381 0.00 0.00 0.00 2.94
464 465 1.686587 TGTGTGTGTGTGGAGTAGGAG 59.313 52.381 0.00 0.00 0.00 3.69
465 466 0.679505 TGTGTGTGTGGAGTAGGAGC 59.320 55.000 0.00 0.00 0.00 4.70
466 467 0.969894 GTGTGTGTGGAGTAGGAGCT 59.030 55.000 0.00 0.00 0.00 4.09
467 468 2.168496 GTGTGTGTGGAGTAGGAGCTA 58.832 52.381 0.00 0.00 0.00 3.32
468 469 2.164624 GTGTGTGTGGAGTAGGAGCTAG 59.835 54.545 0.00 0.00 0.00 3.42
469 470 1.135333 GTGTGTGGAGTAGGAGCTAGC 59.865 57.143 6.62 6.62 0.00 3.42
470 471 0.382515 GTGTGGAGTAGGAGCTAGCG 59.617 60.000 9.55 0.00 0.00 4.26
471 472 1.360911 GTGGAGTAGGAGCTAGCGC 59.639 63.158 10.35 10.35 0.00 5.92
472 473 2.187493 TGGAGTAGGAGCTAGCGCG 61.187 63.158 12.54 0.00 42.32 6.86
473 474 1.892862 GGAGTAGGAGCTAGCGCGA 60.893 63.158 12.10 0.00 42.32 5.87
474 475 1.572447 GAGTAGGAGCTAGCGCGAG 59.428 63.158 12.10 13.72 42.32 5.03
475 476 1.153127 AGTAGGAGCTAGCGCGAGT 60.153 57.895 18.99 5.89 42.32 4.18
476 477 1.009449 GTAGGAGCTAGCGCGAGTG 60.009 63.158 18.99 0.00 42.32 3.51
477 478 2.187493 TAGGAGCTAGCGCGAGTGG 61.187 63.158 18.99 0.00 42.32 4.00
478 479 4.577246 GGAGCTAGCGCGAGTGGG 62.577 72.222 18.99 0.00 42.32 4.61
487 488 4.577246 GCGAGTGGGCTAGCCGAG 62.577 72.222 27.24 16.26 37.38 4.63
488 489 3.141488 CGAGTGGGCTAGCCGAGT 61.141 66.667 24.61 24.61 36.85 4.18
489 490 2.496817 GAGTGGGCTAGCCGAGTG 59.503 66.667 28.68 0.00 36.85 3.51
490 491 3.724914 GAGTGGGCTAGCCGAGTGC 62.725 68.421 28.68 14.81 41.71 4.40
499 500 4.314440 GCCGAGTGCTCACCACCA 62.314 66.667 0.00 0.00 45.83 4.17
500 501 2.047844 CCGAGTGCTCACCACCAG 60.048 66.667 0.00 0.00 45.83 4.00
501 502 2.737180 CGAGTGCTCACCACCAGT 59.263 61.111 0.00 0.00 45.83 4.00
502 503 1.532604 CCGAGTGCTCACCACCAGTA 61.533 60.000 0.00 0.00 45.83 2.74
503 504 0.109086 CGAGTGCTCACCACCAGTAG 60.109 60.000 0.00 0.00 45.83 2.57
504 505 0.390472 GAGTGCTCACCACCAGTAGC 60.390 60.000 0.00 0.00 45.83 3.58
505 506 1.121407 AGTGCTCACCACCAGTAGCA 61.121 55.000 0.00 0.00 45.83 3.49
506 507 0.250295 GTGCTCACCACCAGTAGCAA 60.250 55.000 0.00 0.00 45.81 3.91
507 508 0.250295 TGCTCACCACCAGTAGCAAC 60.250 55.000 0.00 0.00 41.74 4.17
508 509 1.291877 GCTCACCACCAGTAGCAACG 61.292 60.000 0.00 0.00 35.05 4.10
509 510 0.033504 CTCACCACCAGTAGCAACGT 59.966 55.000 0.00 0.00 0.00 3.99
510 511 0.249699 TCACCACCAGTAGCAACGTG 60.250 55.000 0.00 0.00 0.00 4.49
511 512 1.597027 ACCACCAGTAGCAACGTGC 60.597 57.895 0.00 0.00 45.46 5.34
520 521 3.253955 GCAACGTGCGACCTGAAT 58.746 55.556 0.00 0.00 31.71 2.57
521 522 1.132640 GCAACGTGCGACCTGAATC 59.867 57.895 0.00 0.00 31.71 2.52
522 523 1.787847 CAACGTGCGACCTGAATCC 59.212 57.895 0.00 0.00 0.00 3.01
523 524 0.948623 CAACGTGCGACCTGAATCCA 60.949 55.000 0.00 0.00 0.00 3.41
524 525 0.670546 AACGTGCGACCTGAATCCAG 60.671 55.000 0.00 0.00 40.09 3.86
525 526 1.215382 CGTGCGACCTGAATCCAGA 59.785 57.895 0.00 0.00 43.02 3.86
526 527 1.078759 CGTGCGACCTGAATCCAGAC 61.079 60.000 0.00 0.00 43.02 3.51
527 528 0.247736 GTGCGACCTGAATCCAGACT 59.752 55.000 0.00 0.00 43.02 3.24
528 529 0.976641 TGCGACCTGAATCCAGACTT 59.023 50.000 0.00 0.00 43.02 3.01
529 530 1.338105 TGCGACCTGAATCCAGACTTG 60.338 52.381 0.00 0.00 43.02 3.16
530 531 1.363744 CGACCTGAATCCAGACTTGC 58.636 55.000 0.00 0.00 43.02 4.01
531 532 1.338105 CGACCTGAATCCAGACTTGCA 60.338 52.381 0.00 0.00 43.02 4.08
532 533 2.354259 GACCTGAATCCAGACTTGCAG 58.646 52.381 0.00 0.00 43.02 4.41
533 534 1.980765 ACCTGAATCCAGACTTGCAGA 59.019 47.619 0.00 0.00 43.02 4.26
534 535 2.027377 ACCTGAATCCAGACTTGCAGAG 60.027 50.000 0.00 0.00 43.02 3.35
535 536 2.027377 CCTGAATCCAGACTTGCAGAGT 60.027 50.000 0.00 1.82 43.02 3.24
536 537 3.196469 CCTGAATCCAGACTTGCAGAGTA 59.804 47.826 0.00 0.00 43.02 2.59
537 538 4.180057 CTGAATCCAGACTTGCAGAGTAC 58.820 47.826 2.17 0.00 43.02 2.73
538 539 3.055819 TGAATCCAGACTTGCAGAGTACC 60.056 47.826 2.17 0.00 39.19 3.34
539 540 0.888619 TCCAGACTTGCAGAGTACCG 59.111 55.000 2.17 0.00 39.19 4.02
540 541 0.888619 CCAGACTTGCAGAGTACCGA 59.111 55.000 2.17 0.00 39.19 4.69
541 542 1.402984 CCAGACTTGCAGAGTACCGAC 60.403 57.143 2.17 0.00 39.19 4.79
542 543 0.889306 AGACTTGCAGAGTACCGACC 59.111 55.000 2.17 0.00 39.19 4.79
543 544 0.601558 GACTTGCAGAGTACCGACCA 59.398 55.000 2.17 0.00 39.19 4.02
544 545 0.317479 ACTTGCAGAGTACCGACCAC 59.683 55.000 0.44 0.00 36.65 4.16
545 546 0.317160 CTTGCAGAGTACCGACCACA 59.683 55.000 0.00 0.00 0.00 4.17
546 547 0.973632 TTGCAGAGTACCGACCACAT 59.026 50.000 0.00 0.00 0.00 3.21
547 548 0.973632 TGCAGAGTACCGACCACATT 59.026 50.000 0.00 0.00 0.00 2.71
548 549 1.346395 TGCAGAGTACCGACCACATTT 59.654 47.619 0.00 0.00 0.00 2.32
549 550 2.224426 TGCAGAGTACCGACCACATTTT 60.224 45.455 0.00 0.00 0.00 1.82
550 551 2.812011 GCAGAGTACCGACCACATTTTT 59.188 45.455 0.00 0.00 0.00 1.94
586 587 6.892658 TTGTTTAGATTGCTTACCACATGT 57.107 33.333 0.00 0.00 0.00 3.21
587 588 6.252967 TGTTTAGATTGCTTACCACATGTG 57.747 37.500 19.31 19.31 0.00 3.21
588 589 5.767665 TGTTTAGATTGCTTACCACATGTGT 59.232 36.000 23.79 14.29 0.00 3.72
589 590 6.072728 TGTTTAGATTGCTTACCACATGTGTC 60.073 38.462 23.79 12.17 0.00 3.67
590 591 4.019792 AGATTGCTTACCACATGTGTCA 57.980 40.909 23.79 8.71 0.00 3.58
591 592 3.753272 AGATTGCTTACCACATGTGTCAC 59.247 43.478 23.79 9.40 0.00 3.67
592 593 2.629336 TGCTTACCACATGTGTCACA 57.371 45.000 23.79 8.40 0.00 3.58
593 594 3.138884 TGCTTACCACATGTGTCACAT 57.861 42.857 23.79 12.87 39.91 3.21
594 595 4.278975 TGCTTACCACATGTGTCACATA 57.721 40.909 23.79 0.00 36.53 2.29
595 596 4.252878 TGCTTACCACATGTGTCACATAG 58.747 43.478 23.79 14.16 36.53 2.23
596 597 4.253685 GCTTACCACATGTGTCACATAGT 58.746 43.478 23.79 16.61 36.53 2.12
627 628 9.010029 GGTTAATTATCCTTTTGTTCTCAGTGA 57.990 33.333 5.46 0.00 0.00 3.41
654 655 3.558931 TCTGCTCAGTTTTGTCCTCAA 57.441 42.857 0.00 0.00 0.00 3.02
665 666 2.634982 TGTCCTCAAATGCGAATTGC 57.365 45.000 0.00 0.00 46.70 3.56
716 717 0.314302 ACTCGTTCCGTGAACTCTGG 59.686 55.000 12.80 1.15 40.05 3.86
717 718 0.314302 CTCGTTCCGTGAACTCTGGT 59.686 55.000 12.80 0.00 40.05 4.00
795 796 6.368791 CAGAGACGACCAATTTTATTCAGACA 59.631 38.462 0.00 0.00 0.00 3.41
928 942 1.153862 CTGACCACAGCGAGAGAGC 60.154 63.158 0.00 0.00 37.33 4.09
929 943 2.183046 GACCACAGCGAGAGAGCC 59.817 66.667 0.00 0.00 38.01 4.70
930 944 3.691744 GACCACAGCGAGAGAGCCG 62.692 68.421 0.00 0.00 38.01 5.52
983 1004 2.956964 GGCGGCGTTGAGATCTCG 60.957 66.667 17.76 8.04 0.00 4.04
986 1007 1.352156 GCGGCGTTGAGATCTCGTTT 61.352 55.000 17.76 0.00 0.00 3.60
1009 1030 1.227089 CCGAGCTCCATGTCTTCCG 60.227 63.158 8.47 0.00 0.00 4.30
1047 1068 3.063704 CAGATGCAAAGCCGGGCA 61.064 61.111 23.09 4.17 45.23 5.36
1086 1107 4.357947 GTCTGTCTGCGGTGCCGA 62.358 66.667 15.45 0.00 42.83 5.54
1114 1135 0.902531 TGATCGGAGGGTTTCTCACC 59.097 55.000 0.00 0.00 46.46 4.02
1454 1534 4.495690 AGGTTAGGAAGCTTGAAGATCC 57.504 45.455 2.10 8.82 35.27 3.36
1524 1604 5.087391 TGGTAATCGCACTGGTTGTAATA 57.913 39.130 0.00 0.00 0.00 0.98
1739 1827 1.001746 CTCTGCTCTGCCTTTCTGTCA 59.998 52.381 0.00 0.00 0.00 3.58
1851 1949 3.305064 GGGTTCGCTTGCATGTTTTTCTA 60.305 43.478 1.14 0.00 0.00 2.10
1856 1954 6.689178 TCGCTTGCATGTTTTTCTATTTTC 57.311 33.333 1.14 0.00 0.00 2.29
2181 2288 3.311110 GGTGCGTCTGGGGACTCA 61.311 66.667 0.00 0.00 40.10 3.41
2251 2358 2.482839 GCTAGGACAGATGGCAAGACTC 60.483 54.545 0.00 0.00 0.00 3.36
2391 2503 0.187361 TTGGAGGGTTGGAAGGTTGG 59.813 55.000 0.00 0.00 0.00 3.77
2416 2528 1.801771 GTATGTTTGCACTGCCACGTA 59.198 47.619 0.00 0.00 0.00 3.57
2432 2544 4.453136 GCCACGTAATTTTGGTTAGAGTGA 59.547 41.667 0.00 0.00 35.09 3.41
2508 2620 9.979578 AAATTTGCATGTTAGTTCATGACTTAA 57.020 25.926 10.28 0.00 45.41 1.85
2533 2646 2.286365 TGAATGAAACGGAGGGCTTT 57.714 45.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 4.624364 CACCAGCCTCCACGTGCA 62.624 66.667 10.91 0.00 0.00 4.57
400 401 2.764637 CTACCACCCAACCAGCACCC 62.765 65.000 0.00 0.00 0.00 4.61
401 402 1.303317 CTACCACCCAACCAGCACC 60.303 63.158 0.00 0.00 0.00 5.01
402 403 1.303317 CCTACCACCCAACCAGCAC 60.303 63.158 0.00 0.00 0.00 4.40
403 404 2.534396 CCCTACCACCCAACCAGCA 61.534 63.158 0.00 0.00 0.00 4.41
404 405 2.355115 CCCTACCACCCAACCAGC 59.645 66.667 0.00 0.00 0.00 4.85
405 406 2.355115 GCCCTACCACCCAACCAG 59.645 66.667 0.00 0.00 0.00 4.00
406 407 3.642503 CGCCCTACCACCCAACCA 61.643 66.667 0.00 0.00 0.00 3.67
408 409 4.029809 AGCGCCCTACCACCCAAC 62.030 66.667 2.29 0.00 0.00 3.77
409 410 4.028490 CAGCGCCCTACCACCCAA 62.028 66.667 2.29 0.00 0.00 4.12
413 414 4.778143 CACCCAGCGCCCTACCAC 62.778 72.222 2.29 0.00 0.00 4.16
422 423 4.954970 ACACAAGCCCACCCAGCG 62.955 66.667 0.00 0.00 34.64 5.18
423 424 2.985847 GACACAAGCCCACCCAGC 60.986 66.667 0.00 0.00 0.00 4.85
424 425 2.282462 GGACACAAGCCCACCCAG 60.282 66.667 0.00 0.00 0.00 4.45
425 426 4.263572 CGGACACAAGCCCACCCA 62.264 66.667 0.00 0.00 0.00 4.51
427 428 4.265056 ACCGGACACAAGCCCACC 62.265 66.667 9.46 0.00 0.00 4.61
428 429 2.978010 CACCGGACACAAGCCCAC 60.978 66.667 9.46 0.00 0.00 4.61
429 430 3.484806 ACACCGGACACAAGCCCA 61.485 61.111 9.46 0.00 0.00 5.36
430 431 2.978010 CACACCGGACACAAGCCC 60.978 66.667 9.46 0.00 0.00 5.19
431 432 2.203153 ACACACCGGACACAAGCC 60.203 61.111 9.46 0.00 0.00 4.35
432 433 1.817941 ACACACACCGGACACAAGC 60.818 57.895 9.46 0.00 0.00 4.01
433 434 0.742990 ACACACACACCGGACACAAG 60.743 55.000 9.46 0.00 0.00 3.16
434 435 1.021920 CACACACACACCGGACACAA 61.022 55.000 9.46 0.00 0.00 3.33
435 436 1.448717 CACACACACACCGGACACA 60.449 57.895 9.46 0.00 0.00 3.72
436 437 1.448893 ACACACACACACCGGACAC 60.449 57.895 9.46 0.00 0.00 3.67
437 438 1.448717 CACACACACACACCGGACA 60.449 57.895 9.46 0.00 0.00 4.02
438 439 2.177580 CCACACACACACACCGGAC 61.178 63.158 9.46 0.00 0.00 4.79
439 440 2.188207 CCACACACACACACCGGA 59.812 61.111 9.46 0.00 0.00 5.14
440 441 1.887242 CTCCACACACACACACCGG 60.887 63.158 0.00 0.00 0.00 5.28
441 442 0.103390 TACTCCACACACACACACCG 59.897 55.000 0.00 0.00 0.00 4.94
442 443 1.540363 CCTACTCCACACACACACACC 60.540 57.143 0.00 0.00 0.00 4.16
443 444 1.411246 TCCTACTCCACACACACACAC 59.589 52.381 0.00 0.00 0.00 3.82
444 445 1.686587 CTCCTACTCCACACACACACA 59.313 52.381 0.00 0.00 0.00 3.72
445 446 1.605712 GCTCCTACTCCACACACACAC 60.606 57.143 0.00 0.00 0.00 3.82
446 447 0.679505 GCTCCTACTCCACACACACA 59.320 55.000 0.00 0.00 0.00 3.72
447 448 0.969894 AGCTCCTACTCCACACACAC 59.030 55.000 0.00 0.00 0.00 3.82
448 449 2.447443 CTAGCTCCTACTCCACACACA 58.553 52.381 0.00 0.00 0.00 3.72
449 450 1.135333 GCTAGCTCCTACTCCACACAC 59.865 57.143 7.70 0.00 0.00 3.82
450 451 1.475403 GCTAGCTCCTACTCCACACA 58.525 55.000 7.70 0.00 0.00 3.72
451 452 0.382515 CGCTAGCTCCTACTCCACAC 59.617 60.000 13.93 0.00 0.00 3.82
452 453 1.384989 GCGCTAGCTCCTACTCCACA 61.385 60.000 13.93 0.00 41.01 4.17
453 454 1.360911 GCGCTAGCTCCTACTCCAC 59.639 63.158 13.93 0.00 41.01 4.02
454 455 2.187493 CGCGCTAGCTCCTACTCCA 61.187 63.158 13.93 0.00 42.32 3.86
455 456 1.847890 CTCGCGCTAGCTCCTACTCC 61.848 65.000 13.93 0.00 42.32 3.85
456 457 1.161563 ACTCGCGCTAGCTCCTACTC 61.162 60.000 13.93 0.00 42.32 2.59
457 458 1.153127 ACTCGCGCTAGCTCCTACT 60.153 57.895 13.93 0.00 42.32 2.57
458 459 1.009449 CACTCGCGCTAGCTCCTAC 60.009 63.158 13.93 0.00 42.32 3.18
459 460 2.187493 CCACTCGCGCTAGCTCCTA 61.187 63.158 13.93 0.00 42.32 2.94
460 461 3.522731 CCACTCGCGCTAGCTCCT 61.523 66.667 13.93 0.00 42.32 3.69
461 462 4.577246 CCCACTCGCGCTAGCTCC 62.577 72.222 13.93 2.55 42.32 4.70
464 465 3.832720 CTAGCCCACTCGCGCTAGC 62.833 68.421 9.13 4.06 45.80 3.42
465 466 2.333225 CTAGCCCACTCGCGCTAG 59.667 66.667 7.49 7.49 46.20 3.42
466 467 3.900892 GCTAGCCCACTCGCGCTA 61.901 66.667 5.56 0.00 36.53 4.26
470 471 4.577246 CTCGGCTAGCCCACTCGC 62.577 72.222 28.09 1.17 33.93 5.03
471 472 3.141488 ACTCGGCTAGCCCACTCG 61.141 66.667 28.09 15.65 0.00 4.18
472 473 2.496817 CACTCGGCTAGCCCACTC 59.503 66.667 28.09 2.76 0.00 3.51
473 474 3.775654 GCACTCGGCTAGCCCACT 61.776 66.667 28.09 7.05 40.25 4.00
482 483 4.314440 TGGTGGTGAGCACTCGGC 62.314 66.667 14.88 0.00 45.30 5.54
483 484 1.532604 TACTGGTGGTGAGCACTCGG 61.533 60.000 14.88 11.75 0.00 4.63
484 485 0.109086 CTACTGGTGGTGAGCACTCG 60.109 60.000 14.88 8.31 0.00 4.18
485 486 0.390472 GCTACTGGTGGTGAGCACTC 60.390 60.000 14.88 5.60 34.96 3.51
486 487 1.121407 TGCTACTGGTGGTGAGCACT 61.121 55.000 14.88 0.00 39.93 4.40
487 488 0.250295 TTGCTACTGGTGGTGAGCAC 60.250 55.000 6.17 6.17 44.28 4.40
488 489 0.250295 GTTGCTACTGGTGGTGAGCA 60.250 55.000 0.00 0.00 42.98 4.26
489 490 1.291877 CGTTGCTACTGGTGGTGAGC 61.292 60.000 0.00 0.00 35.43 4.26
490 491 0.033504 ACGTTGCTACTGGTGGTGAG 59.966 55.000 0.00 0.00 0.00 3.51
491 492 0.249699 CACGTTGCTACTGGTGGTGA 60.250 55.000 0.00 0.00 0.00 4.02
492 493 1.841663 GCACGTTGCTACTGGTGGTG 61.842 60.000 8.00 4.32 40.96 4.17
493 494 1.597027 GCACGTTGCTACTGGTGGT 60.597 57.895 8.00 0.00 40.96 4.16
494 495 2.667318 CGCACGTTGCTACTGGTGG 61.667 63.158 8.00 0.00 42.25 4.61
495 496 1.663388 TCGCACGTTGCTACTGGTG 60.663 57.895 8.07 0.00 42.25 4.17
496 497 1.663702 GTCGCACGTTGCTACTGGT 60.664 57.895 8.07 0.00 42.25 4.00
497 498 2.380410 GGTCGCACGTTGCTACTGG 61.380 63.158 12.02 0.00 42.25 4.00
498 499 1.372997 AGGTCGCACGTTGCTACTG 60.373 57.895 12.02 0.00 42.25 2.74
499 500 1.372997 CAGGTCGCACGTTGCTACT 60.373 57.895 12.02 4.38 42.25 2.57
500 501 0.942410 TTCAGGTCGCACGTTGCTAC 60.942 55.000 8.07 7.11 42.25 3.58
501 502 0.037697 ATTCAGGTCGCACGTTGCTA 60.038 50.000 8.07 0.00 42.25 3.49
502 503 1.291877 GATTCAGGTCGCACGTTGCT 61.292 55.000 8.07 0.00 42.25 3.91
503 504 1.132640 GATTCAGGTCGCACGTTGC 59.867 57.895 0.00 0.00 40.69 4.17
504 505 0.948623 TGGATTCAGGTCGCACGTTG 60.949 55.000 0.00 0.00 0.00 4.10
505 506 0.670546 CTGGATTCAGGTCGCACGTT 60.671 55.000 0.00 0.00 37.36 3.99
506 507 1.079819 CTGGATTCAGGTCGCACGT 60.080 57.895 0.00 0.00 37.36 4.49
507 508 1.078759 GTCTGGATTCAGGTCGCACG 61.079 60.000 0.00 0.00 41.23 5.34
508 509 0.247736 AGTCTGGATTCAGGTCGCAC 59.752 55.000 0.00 0.00 41.23 5.34
509 510 0.976641 AAGTCTGGATTCAGGTCGCA 59.023 50.000 0.00 0.00 41.23 5.10
510 511 1.363744 CAAGTCTGGATTCAGGTCGC 58.636 55.000 0.00 0.00 41.23 5.19
511 512 1.338105 TGCAAGTCTGGATTCAGGTCG 60.338 52.381 0.00 0.00 41.23 4.79
512 513 2.027745 TCTGCAAGTCTGGATTCAGGTC 60.028 50.000 0.00 0.00 41.23 3.85
513 514 1.980765 TCTGCAAGTCTGGATTCAGGT 59.019 47.619 0.00 0.00 41.23 4.00
514 515 2.027377 ACTCTGCAAGTCTGGATTCAGG 60.027 50.000 0.00 0.00 41.23 3.86
515 516 3.331478 ACTCTGCAAGTCTGGATTCAG 57.669 47.619 0.00 0.00 42.21 3.02
516 517 3.055819 GGTACTCTGCAAGTCTGGATTCA 60.056 47.826 5.04 0.00 39.55 2.57
517 518 3.526534 GGTACTCTGCAAGTCTGGATTC 58.473 50.000 5.04 0.00 39.55 2.52
518 519 2.093973 CGGTACTCTGCAAGTCTGGATT 60.094 50.000 5.04 0.00 39.55 3.01
519 520 1.478510 CGGTACTCTGCAAGTCTGGAT 59.521 52.381 5.04 0.00 39.55 3.41
520 521 0.888619 CGGTACTCTGCAAGTCTGGA 59.111 55.000 5.04 0.00 39.55 3.86
521 522 0.888619 TCGGTACTCTGCAAGTCTGG 59.111 55.000 5.04 0.00 39.55 3.86
522 523 1.402984 GGTCGGTACTCTGCAAGTCTG 60.403 57.143 5.04 4.03 39.55 3.51
523 524 0.889306 GGTCGGTACTCTGCAAGTCT 59.111 55.000 5.04 0.00 39.55 3.24
524 525 0.601558 TGGTCGGTACTCTGCAAGTC 59.398 55.000 5.04 0.00 39.55 3.01
525 526 0.317479 GTGGTCGGTACTCTGCAAGT 59.683 55.000 6.74 6.74 42.33 3.16
526 527 0.317160 TGTGGTCGGTACTCTGCAAG 59.683 55.000 0.00 0.00 0.00 4.01
527 528 0.973632 ATGTGGTCGGTACTCTGCAA 59.026 50.000 0.00 0.00 0.00 4.08
528 529 0.973632 AATGTGGTCGGTACTCTGCA 59.026 50.000 0.00 0.00 0.00 4.41
529 530 2.094762 AAATGTGGTCGGTACTCTGC 57.905 50.000 0.00 0.00 0.00 4.26
560 561 9.019656 ACATGTGGTAAGCAATCTAAACAATAA 57.980 29.630 0.00 0.00 0.00 1.40
561 562 8.458052 CACATGTGGTAAGCAATCTAAACAATA 58.542 33.333 18.51 0.00 0.00 1.90
562 563 7.039784 ACACATGTGGTAAGCAATCTAAACAAT 60.040 33.333 28.64 0.00 34.19 2.71
563 564 6.264292 ACACATGTGGTAAGCAATCTAAACAA 59.736 34.615 28.64 0.00 34.19 2.83
564 565 5.767665 ACACATGTGGTAAGCAATCTAAACA 59.232 36.000 28.64 0.00 34.19 2.83
565 566 6.072728 TGACACATGTGGTAAGCAATCTAAAC 60.073 38.462 28.64 0.70 34.19 2.01
566 567 6.000840 TGACACATGTGGTAAGCAATCTAAA 58.999 36.000 28.64 0.00 34.19 1.85
567 568 5.411361 GTGACACATGTGGTAAGCAATCTAA 59.589 40.000 28.64 0.00 34.19 2.10
568 569 4.935205 GTGACACATGTGGTAAGCAATCTA 59.065 41.667 28.64 4.34 34.19 1.98
569 570 3.753272 GTGACACATGTGGTAAGCAATCT 59.247 43.478 28.64 4.36 34.19 2.40
570 571 3.501828 TGTGACACATGTGGTAAGCAATC 59.498 43.478 28.64 14.99 34.19 2.67
571 572 3.485394 TGTGACACATGTGGTAAGCAAT 58.515 40.909 28.64 5.90 34.19 3.56
572 573 2.924421 TGTGACACATGTGGTAAGCAA 58.076 42.857 28.64 5.83 34.19 3.91
573 574 2.629336 TGTGACACATGTGGTAAGCA 57.371 45.000 28.64 16.41 34.19 3.91
574 575 4.253685 ACTATGTGACACATGTGGTAAGC 58.746 43.478 28.64 14.25 39.53 3.09
575 576 7.867909 CCTATACTATGTGACACATGTGGTAAG 59.132 40.741 28.64 18.65 39.53 2.34
576 577 7.201965 CCCTATACTATGTGACACATGTGGTAA 60.202 40.741 28.64 11.62 39.53 2.85
577 578 6.266786 CCCTATACTATGTGACACATGTGGTA 59.733 42.308 28.64 23.97 39.53 3.25
578 579 5.070446 CCCTATACTATGTGACACATGTGGT 59.930 44.000 28.64 22.92 39.53 4.16
579 580 5.070446 ACCCTATACTATGTGACACATGTGG 59.930 44.000 28.64 20.26 39.53 4.17
580 581 6.161855 ACCCTATACTATGTGACACATGTG 57.838 41.667 27.66 24.25 39.53 3.21
581 582 6.808321 AACCCTATACTATGTGACACATGT 57.192 37.500 27.66 23.27 39.53 3.21
582 583 9.778741 AATTAACCCTATACTATGTGACACATG 57.221 33.333 27.66 19.61 39.53 3.21
618 619 2.836372 AGCAGATGGACATCACTGAGAA 59.164 45.455 14.16 0.00 40.22 2.87
619 620 2.429971 GAGCAGATGGACATCACTGAGA 59.570 50.000 14.16 0.00 40.22 3.27
627 628 3.755378 GACAAAACTGAGCAGATGGACAT 59.245 43.478 4.21 0.00 0.00 3.06
654 655 2.704725 AACTGAACGCAATTCGCATT 57.295 40.000 0.00 0.00 42.60 3.56
665 666 1.804748 GACTAGGGGCAAAACTGAACG 59.195 52.381 0.00 0.00 0.00 3.95
667 668 1.271163 CGGACTAGGGGCAAAACTGAA 60.271 52.381 0.00 0.00 0.00 3.02
716 717 0.663568 CGTTGACCTGACGGAGACAC 60.664 60.000 0.00 0.00 36.90 3.67
717 718 1.105167 ACGTTGACCTGACGGAGACA 61.105 55.000 1.64 0.00 44.34 3.41
795 796 3.952675 CAAGCCACGCGTGCAACT 61.953 61.111 33.17 24.79 30.89 3.16
813 814 4.154347 GCTCTCTGCTGGGTCCCG 62.154 72.222 2.65 0.00 38.95 5.14
910 916 1.153862 GCTCTCTCGCTGTGGTCAG 60.154 63.158 0.00 0.00 43.87 3.51
981 1002 2.261671 GAGCTCGGAGCCAAACGA 59.738 61.111 25.49 0.00 43.77 3.85
983 1004 1.078143 ATGGAGCTCGGAGCCAAAC 60.078 57.895 25.49 13.85 43.77 2.93
986 1007 2.685017 ACATGGAGCTCGGAGCCA 60.685 61.111 25.49 17.60 43.77 4.75
1047 1068 1.188219 AGACAGGCATCTCCACACGT 61.188 55.000 0.00 0.00 37.29 4.49
1056 1077 1.203523 AGACAGACGAAGACAGGCATC 59.796 52.381 0.00 0.00 0.00 3.91
1086 1107 2.103143 CTCCGATCAACGCTCGCT 59.897 61.111 0.00 0.00 41.07 4.93
1114 1135 0.460284 CGATTCTGGTTCCTCGGTGG 60.460 60.000 0.00 0.00 37.10 4.61
1454 1534 3.181487 GCAAATGGGTATTGGTAGTGCTG 60.181 47.826 0.00 0.00 0.00 4.41
1524 1604 7.185318 TCATGCCTTTCCATACATTTTCAAT 57.815 32.000 0.00 0.00 0.00 2.57
1745 1833 2.224257 TGAATTTGGCCCAAGAGCAAAC 60.224 45.455 0.00 0.00 0.00 2.93
1746 1834 2.037511 CTGAATTTGGCCCAAGAGCAAA 59.962 45.455 0.00 0.00 0.00 3.68
1875 1973 7.435068 AAGTTTCAGCGTTATGATTTACTGT 57.565 32.000 0.00 0.00 0.00 3.55
1889 1987 2.535574 GCTTCCACAAAAAGTTTCAGCG 59.464 45.455 0.00 0.00 0.00 5.18
2032 2133 2.895404 AGCTGAGGCACATTTTTCATGT 59.105 40.909 0.00 0.00 41.70 3.21
2037 2138 1.891150 CCAGAGCTGAGGCACATTTTT 59.109 47.619 0.00 0.00 41.70 1.94
2170 2277 4.761163 TGGGTTTGAGTCCCCAGA 57.239 55.556 1.71 0.00 46.06 3.86
2251 2358 1.879575 TCCTTCCCTACCCATGTCAG 58.120 55.000 0.00 0.00 0.00 3.51
2319 2431 0.099613 ACGCGTGTGCAAACATTCAA 59.900 45.000 12.93 0.00 42.97 2.69
2391 2503 2.287308 TGGCAGTGCAAACATACGTTTC 60.287 45.455 18.61 0.00 43.57 2.78
2416 2528 5.891551 ACCAAGTGTCACTCTAACCAAAATT 59.108 36.000 5.82 0.00 0.00 1.82
2432 2544 4.202430 CCACTCTAACCCTAAACCAAGTGT 60.202 45.833 0.00 0.00 32.88 3.55
2524 2637 2.037367 GGGGGTGAAAAGCCCTCC 59.963 66.667 12.46 2.23 45.39 4.30


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

AutoCloner maintained by Alex Coulton.