Multiple sequence alignment - TraesCS2D01G581800

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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 TraesCS2D01G581800 chr2D 100.000 2576 0 0 1 2576 643051628 643054203 0.000000e+00 4758
1 TraesCS2D01G581800 chr2D 96.973 2015 32 3 591 2576 648110770 648108756 0.000000e+00 3356
2 TraesCS2D01G581800 chr2D 94.896 431 22 0 2146 2576 39755603 39756033 0.000000e+00 675
3 TraesCS2D01G581800 chr2D 99.492 197 1 0 593 789 643058659 643058463 2.440000e-95 359
4 TraesCS2D01G581800 chr2D 98.039 204 3 1 590 792 648104298 648104501 1.130000e-93 353
5 TraesCS2D01G581800 chr5D 96.299 1378 16 10 593 1937 367799727 367801102 0.000000e+00 2230
6 TraesCS2D01G581800 chr5D 95.823 790 19 10 1794 2576 367800998 367801780 0.000000e+00 1264
7 TraesCS2D01G581800 chr7D 95.052 1354 41 5 593 1937 214764742 214766078 0.000000e+00 2106
8 TraesCS2D01G581800 chr7D 93.028 1090 49 9 588 1652 465836230 465835143 0.000000e+00 1567
9 TraesCS2D01G581800 chr7D 98.287 642 10 1 1935 2576 214766227 214766867 0.000000e+00 1123
10 TraesCS2D01G581800 chr7D 97.050 644 16 3 1935 2576 465834757 465834115 0.000000e+00 1081
11 TraesCS2D01G581800 chr7D 96.939 294 9 0 1644 1937 465835185 465834892 6.400000e-136 494
12 TraesCS2D01G581800 chr7D 98.467 261 3 1 590 849 219288438 219288698 2.340000e-125 459
13 TraesCS2D01G581800 chr3D 93.600 1375 50 8 585 1937 460901756 460900398 0.000000e+00 2017
14 TraesCS2D01G581800 chr3D 97.045 643 17 2 1935 2576 460900249 460899608 0.000000e+00 1081
15 TraesCS2D01G581800 chr2A 88.735 1376 77 17 593 1937 84206501 84207829 0.000000e+00 1611
16 TraesCS2D01G581800 chr2A 92.674 1092 45 7 859 1936 766619140 766618070 0.000000e+00 1541
17 TraesCS2D01G581800 chr2A 97.488 637 14 2 1940 2576 766617929 766617295 0.000000e+00 1086
18 TraesCS2D01G581800 chr2A 95.107 327 14 2 1935 2260 84207964 84208289 4.920000e-142 514
19 TraesCS2D01G581800 chr2B 90.886 1174 73 9 796 1937 1903829 1905000 0.000000e+00 1544
20 TraesCS2D01G581800 chr2B 95.014 361 16 2 1935 2294 1905119 1905478 1.340000e-157 566
21 TraesCS2D01G581800 chr4A 88.071 1073 72 13 886 1937 485007460 485008497 0.000000e+00 1221
22 TraesCS2D01G581800 chr4A 95.956 643 24 2 1935 2576 485008632 485009273 0.000000e+00 1042
23 TraesCS2D01G581800 chr7B 83.933 1307 100 41 593 1834 455230276 455231537 0.000000e+00 1149
24 TraesCS2D01G581800 chr1A 85.436 1078 105 27 592 1641 330088632 330089685 0.000000e+00 1074
25 TraesCS2D01G581800 chr1A 93.750 432 27 0 2145 2576 481626124 481625693 0.000000e+00 649
26 TraesCS2D01G581800 chr6D 98.981 589 6 0 4 592 29466158 29465570 0.000000e+00 1055
27 TraesCS2D01G581800 chr6D 94.851 505 14 3 590 1082 113904167 113904671 0.000000e+00 778
28 TraesCS2D01G581800 chr1B 82.283 841 88 27 942 1755 647247200 647248006 0.000000e+00 671
29 TraesCS2D01G581800 chr5B 82.672 756 91 23 919 1652 538553623 538554360 3.620000e-178 634
30 TraesCS2D01G581800 chr3A 85.166 573 63 13 593 1156 487474701 487474142 3.720000e-158 568


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 TraesCS2D01G581800 chr2D 643051628 643054203 2575 False 4758.000000 4758 100.000000 1 2576 1 chr2D.!!$F2 2575
1 TraesCS2D01G581800 chr2D 648108756 648110770 2014 True 3356.000000 3356 96.973000 591 2576 1 chr2D.!!$R2 1985
2 TraesCS2D01G581800 chr5D 367799727 367801780 2053 False 1747.000000 2230 96.061000 593 2576 2 chr5D.!!$F1 1983
3 TraesCS2D01G581800 chr7D 214764742 214766867 2125 False 1614.500000 2106 96.669500 593 2576 2 chr7D.!!$F2 1983
4 TraesCS2D01G581800 chr7D 465834115 465836230 2115 True 1047.333333 1567 95.672333 588 2576 3 chr7D.!!$R1 1988
5 TraesCS2D01G581800 chr3D 460899608 460901756 2148 True 1549.000000 2017 95.322500 585 2576 2 chr3D.!!$R1 1991
6 TraesCS2D01G581800 chr2A 766617295 766619140 1845 True 1313.500000 1541 95.081000 859 2576 2 chr2A.!!$R1 1717
7 TraesCS2D01G581800 chr2A 84206501 84208289 1788 False 1062.500000 1611 91.921000 593 2260 2 chr2A.!!$F1 1667
8 TraesCS2D01G581800 chr2B 1903829 1905478 1649 False 1055.000000 1544 92.950000 796 2294 2 chr2B.!!$F1 1498
9 TraesCS2D01G581800 chr4A 485007460 485009273 1813 False 1131.500000 1221 92.013500 886 2576 2 chr4A.!!$F1 1690
10 TraesCS2D01G581800 chr7B 455230276 455231537 1261 False 1149.000000 1149 83.933000 593 1834 1 chr7B.!!$F1 1241
11 TraesCS2D01G581800 chr1A 330088632 330089685 1053 False 1074.000000 1074 85.436000 592 1641 1 chr1A.!!$F1 1049
12 TraesCS2D01G581800 chr6D 29465570 29466158 588 True 1055.000000 1055 98.981000 4 592 1 chr6D.!!$R1 588
13 TraesCS2D01G581800 chr6D 113904167 113904671 504 False 778.000000 778 94.851000 590 1082 1 chr6D.!!$F1 492
14 TraesCS2D01G581800 chr1B 647247200 647248006 806 False 671.000000 671 82.283000 942 1755 1 chr1B.!!$F1 813
15 TraesCS2D01G581800 chr5B 538553623 538554360 737 False 634.000000 634 82.672000 919 1652 1 chr5B.!!$F1 733
16 TraesCS2D01G581800 chr3A 487474142 487474701 559 True 568.000000 568 85.166000 593 1156 1 chr3A.!!$R1 563

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
523 524 0.026803 GCAGTTGATCGTCGCCAATC 59.973 55.0 3.82 0.0 0.0 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 2618 0.336392 TGCTGAGGCTAGGAAGGAGA 59.664 55.0 0.0 0.0 39.59 3.71 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
416 417 3.126453 AGAGGTTTATGGGGAGCAAGAT 58.874 45.455 0.00 0.00 0.00 2.40
417 418 3.137360 AGAGGTTTATGGGGAGCAAGATC 59.863 47.826 0.00 0.00 0.00 2.75
418 419 2.158755 AGGTTTATGGGGAGCAAGATCG 60.159 50.000 0.00 0.00 0.00 3.69
419 420 2.158813 GGTTTATGGGGAGCAAGATCGA 60.159 50.000 0.00 0.00 0.00 3.59
420 421 2.872858 GTTTATGGGGAGCAAGATCGAC 59.127 50.000 0.00 0.00 0.00 4.20
421 422 0.673985 TATGGGGAGCAAGATCGACG 59.326 55.000 0.00 0.00 0.00 5.12
422 423 1.330655 ATGGGGAGCAAGATCGACGT 61.331 55.000 0.00 0.00 0.00 4.34
423 424 1.519455 GGGGAGCAAGATCGACGTG 60.519 63.158 0.00 0.00 0.00 4.49
424 425 1.511305 GGGAGCAAGATCGACGTGA 59.489 57.895 0.00 0.00 0.00 4.35
425 426 0.103208 GGGAGCAAGATCGACGTGAT 59.897 55.000 0.00 0.00 41.06 3.06
426 427 1.203928 GGAGCAAGATCGACGTGATG 58.796 55.000 0.00 0.00 37.47 3.07
427 428 1.203928 GAGCAAGATCGACGTGATGG 58.796 55.000 0.00 0.00 37.47 3.51
428 429 0.179100 AGCAAGATCGACGTGATGGG 60.179 55.000 0.00 0.00 37.47 4.00
429 430 1.154205 GCAAGATCGACGTGATGGGG 61.154 60.000 0.00 0.00 37.47 4.96
430 431 1.144057 AAGATCGACGTGATGGGGC 59.856 57.895 0.00 0.00 37.47 5.80
431 432 1.330655 AAGATCGACGTGATGGGGCT 61.331 55.000 0.00 0.00 37.47 5.19
432 433 1.592669 GATCGACGTGATGGGGCTG 60.593 63.158 0.00 0.00 37.47 4.85
433 434 2.978452 GATCGACGTGATGGGGCTGG 62.978 65.000 0.00 0.00 37.47 4.85
434 435 3.770040 CGACGTGATGGGGCTGGA 61.770 66.667 0.00 0.00 0.00 3.86
435 436 2.125106 GACGTGATGGGGCTGGAC 60.125 66.667 0.00 0.00 0.00 4.02
436 437 2.927856 ACGTGATGGGGCTGGACA 60.928 61.111 0.00 0.00 0.00 4.02
437 438 2.257409 GACGTGATGGGGCTGGACAT 62.257 60.000 0.00 0.00 0.00 3.06
438 439 1.820906 CGTGATGGGGCTGGACATG 60.821 63.158 0.00 0.00 0.00 3.21
439 440 1.454479 GTGATGGGGCTGGACATGG 60.454 63.158 0.00 0.00 0.00 3.66
440 441 1.619057 TGATGGGGCTGGACATGGA 60.619 57.895 0.00 0.00 0.00 3.41
441 442 1.150081 GATGGGGCTGGACATGGAG 59.850 63.158 0.00 0.00 0.00 3.86
442 443 2.972892 GATGGGGCTGGACATGGAGC 62.973 65.000 0.00 1.09 34.23 4.70
443 444 3.415087 GGGGCTGGACATGGAGCT 61.415 66.667 11.90 0.00 35.42 4.09
444 445 2.124403 GGGCTGGACATGGAGCTG 60.124 66.667 11.90 0.00 35.42 4.24
445 446 2.827642 GGCTGGACATGGAGCTGC 60.828 66.667 0.00 0.00 35.42 5.25
446 447 2.271497 GCTGGACATGGAGCTGCT 59.729 61.111 6.82 0.00 32.12 4.24
447 448 1.524002 GCTGGACATGGAGCTGCTA 59.476 57.895 6.82 0.00 32.12 3.49
448 449 0.813210 GCTGGACATGGAGCTGCTAC 60.813 60.000 4.51 4.51 32.12 3.58
449 450 0.179062 CTGGACATGGAGCTGCTACC 60.179 60.000 9.87 10.02 0.00 3.18
450 451 1.227380 GGACATGGAGCTGCTACCG 60.227 63.158 9.87 2.97 0.00 4.02
451 452 1.517832 GACATGGAGCTGCTACCGT 59.482 57.895 9.87 6.58 0.00 4.83
452 453 0.108138 GACATGGAGCTGCTACCGTT 60.108 55.000 9.87 0.00 0.00 4.44
453 454 0.108138 ACATGGAGCTGCTACCGTTC 60.108 55.000 9.87 0.00 0.00 3.95
454 455 1.141881 ATGGAGCTGCTACCGTTCG 59.858 57.895 9.87 0.00 0.00 3.95
455 456 2.202756 GGAGCTGCTACCGTTCGG 60.203 66.667 0.15 9.81 0.00 4.30
456 457 2.202756 GAGCTGCTACCGTTCGGG 60.203 66.667 15.66 0.00 43.62 5.14
457 458 3.718210 GAGCTGCTACCGTTCGGGG 62.718 68.421 15.66 8.78 41.60 5.73
459 460 4.832608 CTGCTACCGTTCGGGGCC 62.833 72.222 20.90 0.00 41.60 5.80
483 484 3.556306 CGGATGTGCCCCGGGTAT 61.556 66.667 21.85 8.17 43.05 2.73
484 485 2.211410 CGGATGTGCCCCGGGTATA 61.211 63.158 21.85 6.83 43.05 1.47
485 486 1.677552 GGATGTGCCCCGGGTATAG 59.322 63.158 21.85 4.65 0.00 1.31
486 487 1.003718 GATGTGCCCCGGGTATAGC 60.004 63.158 21.85 16.48 0.00 2.97
487 488 2.465055 GATGTGCCCCGGGTATAGCC 62.465 65.000 21.85 11.13 0.00 3.93
488 489 2.847715 GTGCCCCGGGTATAGCCT 60.848 66.667 21.85 0.00 37.43 4.58
489 490 2.847234 TGCCCCGGGTATAGCCTG 60.847 66.667 21.85 12.07 43.41 4.85
494 495 4.621269 CGGGTATAGCCTGGGACT 57.379 61.111 18.51 0.00 40.02 3.85
495 496 2.050269 CGGGTATAGCCTGGGACTG 58.950 63.158 18.51 0.00 40.02 3.51
496 497 0.469331 CGGGTATAGCCTGGGACTGA 60.469 60.000 18.51 0.00 40.02 3.41
497 498 1.802553 GGGTATAGCCTGGGACTGAA 58.197 55.000 13.90 0.00 37.43 3.02
498 499 1.694696 GGGTATAGCCTGGGACTGAAG 59.305 57.143 13.90 0.00 37.43 3.02
499 500 1.694696 GGTATAGCCTGGGACTGAAGG 59.305 57.143 0.00 0.00 36.58 3.46
500 501 2.399580 GTATAGCCTGGGACTGAAGGT 58.600 52.381 0.00 0.00 35.86 3.50
501 502 1.207791 ATAGCCTGGGACTGAAGGTG 58.792 55.000 0.00 0.00 35.86 4.00
502 503 0.909610 TAGCCTGGGACTGAAGGTGG 60.910 60.000 0.00 0.00 35.86 4.61
503 504 2.529744 GCCTGGGACTGAAGGTGGT 61.530 63.158 0.00 0.00 35.86 4.16
504 505 1.376466 CCTGGGACTGAAGGTGGTG 59.624 63.158 0.00 0.00 0.00 4.17
505 506 1.302832 CTGGGACTGAAGGTGGTGC 60.303 63.158 0.00 0.00 0.00 5.01
506 507 2.055689 CTGGGACTGAAGGTGGTGCA 62.056 60.000 0.00 0.00 0.00 4.57
507 508 1.302832 GGGACTGAAGGTGGTGCAG 60.303 63.158 0.00 0.00 35.81 4.41
508 509 1.451936 GGACTGAAGGTGGTGCAGT 59.548 57.895 0.00 0.00 44.87 4.40
509 510 0.179018 GGACTGAAGGTGGTGCAGTT 60.179 55.000 0.00 0.00 42.47 3.16
510 511 0.947244 GACTGAAGGTGGTGCAGTTG 59.053 55.000 0.00 0.00 42.47 3.16
511 512 0.546122 ACTGAAGGTGGTGCAGTTGA 59.454 50.000 0.00 0.00 39.69 3.18
512 513 1.143684 ACTGAAGGTGGTGCAGTTGAT 59.856 47.619 0.00 0.00 39.69 2.57
513 514 1.808945 CTGAAGGTGGTGCAGTTGATC 59.191 52.381 0.00 0.00 0.00 2.92
514 515 0.798776 GAAGGTGGTGCAGTTGATCG 59.201 55.000 0.00 0.00 0.00 3.69
515 516 0.108585 AAGGTGGTGCAGTTGATCGT 59.891 50.000 0.00 0.00 0.00 3.73
516 517 0.320771 AGGTGGTGCAGTTGATCGTC 60.321 55.000 0.00 0.00 0.00 4.20
517 518 1.626654 GGTGGTGCAGTTGATCGTCG 61.627 60.000 0.00 0.00 0.00 5.12
518 519 2.027073 TGGTGCAGTTGATCGTCGC 61.027 57.895 0.00 0.00 0.00 5.19
519 520 2.740714 GGTGCAGTTGATCGTCGCC 61.741 63.158 0.00 0.00 0.00 5.54
520 521 2.027073 GTGCAGTTGATCGTCGCCA 61.027 57.895 0.00 0.00 0.00 5.69
521 522 1.301322 TGCAGTTGATCGTCGCCAA 60.301 52.632 0.00 0.00 0.00 4.52
522 523 0.673333 TGCAGTTGATCGTCGCCAAT 60.673 50.000 3.82 0.00 0.00 3.16
523 524 0.026803 GCAGTTGATCGTCGCCAATC 59.973 55.000 3.82 0.00 0.00 2.67
524 525 1.645034 CAGTTGATCGTCGCCAATCT 58.355 50.000 3.82 1.89 0.00 2.40
525 526 2.002586 CAGTTGATCGTCGCCAATCTT 58.997 47.619 3.82 0.00 0.00 2.40
526 527 2.029728 CAGTTGATCGTCGCCAATCTTC 59.970 50.000 3.82 0.00 0.00 2.87
527 528 2.093973 AGTTGATCGTCGCCAATCTTCT 60.094 45.455 3.82 0.00 0.00 2.85
528 529 1.926561 TGATCGTCGCCAATCTTCTG 58.073 50.000 0.00 0.00 0.00 3.02
529 530 0.579156 GATCGTCGCCAATCTTCTGC 59.421 55.000 0.00 0.00 0.00 4.26
530 531 0.108186 ATCGTCGCCAATCTTCTGCA 60.108 50.000 0.00 0.00 0.00 4.41
531 532 0.108186 TCGTCGCCAATCTTCTGCAT 60.108 50.000 0.00 0.00 0.00 3.96
532 533 0.027194 CGTCGCCAATCTTCTGCATG 59.973 55.000 0.00 0.00 0.00 4.06
533 534 0.379669 GTCGCCAATCTTCTGCATGG 59.620 55.000 0.00 0.00 36.00 3.66
537 538 2.865343 CCAATCTTCTGCATGGCTTC 57.135 50.000 0.00 0.00 0.00 3.86
538 539 2.097036 CCAATCTTCTGCATGGCTTCA 58.903 47.619 0.00 0.00 0.00 3.02
539 540 2.159282 CCAATCTTCTGCATGGCTTCAC 60.159 50.000 0.00 0.00 0.00 3.18
540 541 1.376543 ATCTTCTGCATGGCTTCACG 58.623 50.000 0.00 0.00 0.00 4.35
541 542 0.035317 TCTTCTGCATGGCTTCACGT 59.965 50.000 0.00 0.00 0.00 4.49
542 543 0.445436 CTTCTGCATGGCTTCACGTC 59.555 55.000 0.00 0.00 0.00 4.34
543 544 1.291184 TTCTGCATGGCTTCACGTCG 61.291 55.000 0.00 0.00 0.00 5.12
544 545 2.741985 TGCATGGCTTCACGTCGG 60.742 61.111 0.00 0.00 0.00 4.79
545 546 3.499737 GCATGGCTTCACGTCGGG 61.500 66.667 0.00 0.00 0.00 5.14
546 547 2.819595 CATGGCTTCACGTCGGGG 60.820 66.667 0.00 0.00 0.00 5.73
547 548 4.778143 ATGGCTTCACGTCGGGGC 62.778 66.667 0.00 0.00 0.00 5.80
551 552 4.452733 CTTCACGTCGGGGCTCCC 62.453 72.222 0.00 0.00 41.09 4.30
562 563 4.329545 GGCTCCCTGACGGCACAA 62.330 66.667 0.00 0.00 0.00 3.33
563 564 3.050275 GCTCCCTGACGGCACAAC 61.050 66.667 0.00 0.00 0.00 3.32
564 565 2.738521 CTCCCTGACGGCACAACG 60.739 66.667 0.00 0.00 40.31 4.10
565 566 3.220999 CTCCCTGACGGCACAACGA 62.221 63.158 0.00 0.00 37.61 3.85
566 567 2.738521 CCCTGACGGCACAACGAG 60.739 66.667 0.00 0.00 37.61 4.18
567 568 2.738521 CCTGACGGCACAACGAGG 60.739 66.667 0.00 0.00 37.61 4.63
568 569 2.738521 CTGACGGCACAACGAGGG 60.739 66.667 0.00 0.00 37.61 4.30
569 570 3.220999 CTGACGGCACAACGAGGGA 62.221 63.158 0.00 0.00 37.61 4.20
570 571 2.432628 GACGGCACAACGAGGGAG 60.433 66.667 0.00 0.00 37.61 4.30
571 572 4.681978 ACGGCACAACGAGGGAGC 62.682 66.667 0.00 0.00 37.61 4.70
572 573 4.680237 CGGCACAACGAGGGAGCA 62.680 66.667 0.00 0.00 35.47 4.26
573 574 2.743928 GGCACAACGAGGGAGCAG 60.744 66.667 0.00 0.00 0.00 4.24
574 575 3.426568 GCACAACGAGGGAGCAGC 61.427 66.667 0.00 0.00 0.00 5.25
575 576 2.345244 CACAACGAGGGAGCAGCT 59.655 61.111 0.00 0.00 0.00 4.24
576 577 1.739562 CACAACGAGGGAGCAGCTC 60.740 63.158 14.69 14.69 0.00 4.09
577 578 2.210013 ACAACGAGGGAGCAGCTCA 61.210 57.895 24.09 0.00 31.08 4.26
578 579 1.004560 CAACGAGGGAGCAGCTCAA 60.005 57.895 24.09 0.00 31.08 3.02
579 580 1.004440 AACGAGGGAGCAGCTCAAC 60.004 57.895 24.09 15.56 31.08 3.18
580 581 1.758440 AACGAGGGAGCAGCTCAACA 61.758 55.000 24.09 0.00 31.08 3.33
581 582 1.220206 CGAGGGAGCAGCTCAACAT 59.780 57.895 24.09 5.09 31.08 2.71
582 583 1.088340 CGAGGGAGCAGCTCAACATG 61.088 60.000 24.09 8.69 31.08 3.21
583 584 0.747283 GAGGGAGCAGCTCAACATGG 60.747 60.000 24.09 0.00 31.08 3.66
584 585 1.203441 AGGGAGCAGCTCAACATGGA 61.203 55.000 24.09 0.00 31.08 3.41
585 586 0.747283 GGGAGCAGCTCAACATGGAG 60.747 60.000 24.09 0.00 37.97 3.86
586 587 0.747283 GGAGCAGCTCAACATGGAGG 60.747 60.000 24.09 0.00 35.41 4.30
587 588 0.251354 GAGCAGCTCAACATGGAGGA 59.749 55.000 18.17 0.00 35.41 3.71
588 589 0.252479 AGCAGCTCAACATGGAGGAG 59.748 55.000 0.00 1.83 35.41 3.69
1428 1553 4.337836 GGCTTTGAAGATGGAAGAAGATCC 59.662 45.833 0.00 0.00 40.10 3.36
1564 1689 3.118112 AGTGCTGCTAGGCATTTCTATGT 60.118 43.478 0.00 0.00 44.34 2.29
2271 2618 7.521669 AGAGCAATACCTATTAGCCTCATTTT 58.478 34.615 0.00 0.00 0.00 1.82
2417 2764 2.489329 GCTTTATTCTCAGCAGCCACAA 59.511 45.455 0.00 0.00 35.95 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.205297 TCCTGATCGACGATCGTGTATATATA 58.795 38.462 28.12 9.52 41.51 0.86
1 2 6.047231 TCCTGATCGACGATCGTGTATATAT 58.953 40.000 28.12 9.19 41.51 0.86
2 3 5.413499 TCCTGATCGACGATCGTGTATATA 58.587 41.667 28.12 10.79 41.51 0.86
416 417 3.770040 CCAGCCCCATCACGTCGA 61.770 66.667 0.00 0.00 0.00 4.20
417 418 3.770040 TCCAGCCCCATCACGTCG 61.770 66.667 0.00 0.00 0.00 5.12
418 419 2.125106 GTCCAGCCCCATCACGTC 60.125 66.667 0.00 0.00 0.00 4.34
419 420 2.300967 ATGTCCAGCCCCATCACGT 61.301 57.895 0.00 0.00 0.00 4.49
420 421 1.820906 CATGTCCAGCCCCATCACG 60.821 63.158 0.00 0.00 0.00 4.35
421 422 1.454479 CCATGTCCAGCCCCATCAC 60.454 63.158 0.00 0.00 0.00 3.06
422 423 1.619057 TCCATGTCCAGCCCCATCA 60.619 57.895 0.00 0.00 0.00 3.07
423 424 1.150081 CTCCATGTCCAGCCCCATC 59.850 63.158 0.00 0.00 0.00 3.51
424 425 3.065787 GCTCCATGTCCAGCCCCAT 62.066 63.158 0.00 0.00 0.00 4.00
425 426 3.731728 GCTCCATGTCCAGCCCCA 61.732 66.667 0.00 0.00 0.00 4.96
426 427 3.415087 AGCTCCATGTCCAGCCCC 61.415 66.667 5.21 0.00 36.17 5.80
427 428 2.124403 CAGCTCCATGTCCAGCCC 60.124 66.667 5.21 0.00 36.17 5.19
428 429 1.976132 TAGCAGCTCCATGTCCAGCC 61.976 60.000 0.00 0.00 36.17 4.85
429 430 0.813210 GTAGCAGCTCCATGTCCAGC 60.813 60.000 0.00 0.00 35.73 4.85
430 431 0.179062 GGTAGCAGCTCCATGTCCAG 60.179 60.000 0.00 0.00 0.00 3.86
431 432 1.907739 GGTAGCAGCTCCATGTCCA 59.092 57.895 0.00 0.00 0.00 4.02
432 433 1.227380 CGGTAGCAGCTCCATGTCC 60.227 63.158 0.00 0.00 0.00 4.02
433 434 0.108138 AACGGTAGCAGCTCCATGTC 60.108 55.000 0.00 0.00 0.00 3.06
434 435 0.108138 GAACGGTAGCAGCTCCATGT 60.108 55.000 0.00 0.00 0.00 3.21
435 436 1.148157 CGAACGGTAGCAGCTCCATG 61.148 60.000 0.00 0.00 0.00 3.66
436 437 1.141881 CGAACGGTAGCAGCTCCAT 59.858 57.895 0.00 0.00 0.00 3.41
437 438 2.571757 CGAACGGTAGCAGCTCCA 59.428 61.111 0.00 0.00 0.00 3.86
438 439 2.202756 CCGAACGGTAGCAGCTCC 60.203 66.667 0.00 0.00 0.00 4.70
439 440 2.202756 CCCGAACGGTAGCAGCTC 60.203 66.667 12.23 0.00 0.00 4.09
440 441 3.771160 CCCCGAACGGTAGCAGCT 61.771 66.667 12.23 0.00 0.00 4.24
442 443 4.832608 GGCCCCGAACGGTAGCAG 62.833 72.222 20.83 4.27 35.22 4.24
466 467 2.167398 CTATACCCGGGGCACATCCG 62.167 65.000 27.92 0.12 46.43 4.18
467 468 1.677552 CTATACCCGGGGCACATCC 59.322 63.158 27.92 0.00 0.00 3.51
468 469 1.003718 GCTATACCCGGGGCACATC 60.004 63.158 27.92 5.22 0.00 3.06
469 470 2.526046 GGCTATACCCGGGGCACAT 61.526 63.158 27.92 14.51 0.00 3.21
470 471 3.165685 GGCTATACCCGGGGCACA 61.166 66.667 27.92 7.18 0.00 4.57
471 472 2.847715 AGGCTATACCCGGGGCAC 60.848 66.667 27.92 12.08 40.58 5.01
472 473 2.847234 CAGGCTATACCCGGGGCA 60.847 66.667 27.92 13.20 40.58 5.36
473 474 3.637273 CCAGGCTATACCCGGGGC 61.637 72.222 27.92 18.62 40.58 5.80
475 476 2.203182 TCCCAGGCTATACCCGGG 59.797 66.667 22.25 22.25 40.58 5.73
476 477 1.152312 AGTCCCAGGCTATACCCGG 60.152 63.158 0.00 0.00 40.58 5.73
477 478 0.469331 TCAGTCCCAGGCTATACCCG 60.469 60.000 0.00 0.00 40.58 5.28
478 479 1.694696 CTTCAGTCCCAGGCTATACCC 59.305 57.143 0.00 0.00 40.58 3.69
479 480 1.694696 CCTTCAGTCCCAGGCTATACC 59.305 57.143 0.00 0.00 39.61 2.73
480 481 2.103263 CACCTTCAGTCCCAGGCTATAC 59.897 54.545 0.00 0.00 32.79 1.47
481 482 2.398588 CACCTTCAGTCCCAGGCTATA 58.601 52.381 0.00 0.00 32.79 1.31
482 483 1.207791 CACCTTCAGTCCCAGGCTAT 58.792 55.000 0.00 0.00 32.79 2.97
483 484 0.909610 CCACCTTCAGTCCCAGGCTA 60.910 60.000 0.00 0.00 32.79 3.93
484 485 2.227036 CCACCTTCAGTCCCAGGCT 61.227 63.158 0.00 0.00 32.79 4.58
485 486 2.352805 CCACCTTCAGTCCCAGGC 59.647 66.667 0.00 0.00 32.79 4.85
486 487 1.376466 CACCACCTTCAGTCCCAGG 59.624 63.158 0.00 0.00 36.10 4.45
487 488 1.302832 GCACCACCTTCAGTCCCAG 60.303 63.158 0.00 0.00 0.00 4.45
488 489 2.055689 CTGCACCACCTTCAGTCCCA 62.056 60.000 0.00 0.00 0.00 4.37
489 490 1.302832 CTGCACCACCTTCAGTCCC 60.303 63.158 0.00 0.00 0.00 4.46
490 491 0.179018 AACTGCACCACCTTCAGTCC 60.179 55.000 0.00 0.00 39.86 3.85
491 492 0.947244 CAACTGCACCACCTTCAGTC 59.053 55.000 0.00 0.00 39.86 3.51
492 493 0.546122 TCAACTGCACCACCTTCAGT 59.454 50.000 0.00 0.00 42.28 3.41
493 494 1.808945 GATCAACTGCACCACCTTCAG 59.191 52.381 0.00 0.00 0.00 3.02
494 495 1.877680 CGATCAACTGCACCACCTTCA 60.878 52.381 0.00 0.00 0.00 3.02
495 496 0.798776 CGATCAACTGCACCACCTTC 59.201 55.000 0.00 0.00 0.00 3.46
496 497 0.108585 ACGATCAACTGCACCACCTT 59.891 50.000 0.00 0.00 0.00 3.50
497 498 0.320771 GACGATCAACTGCACCACCT 60.321 55.000 0.00 0.00 0.00 4.00
498 499 1.626654 CGACGATCAACTGCACCACC 61.627 60.000 0.00 0.00 0.00 4.61
499 500 1.781555 CGACGATCAACTGCACCAC 59.218 57.895 0.00 0.00 0.00 4.16
500 501 2.027073 GCGACGATCAACTGCACCA 61.027 57.895 0.00 0.00 0.00 4.17
501 502 2.740714 GGCGACGATCAACTGCACC 61.741 63.158 0.00 0.00 0.00 5.01
502 503 1.565156 TTGGCGACGATCAACTGCAC 61.565 55.000 0.00 0.00 0.00 4.57
503 504 0.673333 ATTGGCGACGATCAACTGCA 60.673 50.000 0.00 0.00 0.00 4.41
504 505 2.089854 ATTGGCGACGATCAACTGC 58.910 52.632 0.00 0.00 0.00 4.40
511 512 0.108186 TGCAGAAGATTGGCGACGAT 60.108 50.000 0.00 0.00 37.06 3.73
512 513 0.108186 ATGCAGAAGATTGGCGACGA 60.108 50.000 0.00 0.00 0.00 4.20
513 514 0.027194 CATGCAGAAGATTGGCGACG 59.973 55.000 0.00 0.00 0.00 5.12
514 515 0.379669 CCATGCAGAAGATTGGCGAC 59.620 55.000 0.00 0.00 0.00 5.19
515 516 1.378882 GCCATGCAGAAGATTGGCGA 61.379 55.000 10.78 0.00 44.58 5.54
516 517 1.065273 GCCATGCAGAAGATTGGCG 59.935 57.895 10.78 0.00 44.58 5.69
518 519 2.097036 TGAAGCCATGCAGAAGATTGG 58.903 47.619 0.00 0.00 0.00 3.16
519 520 2.477357 CGTGAAGCCATGCAGAAGATTG 60.477 50.000 0.00 0.00 0.00 2.67
520 521 1.741706 CGTGAAGCCATGCAGAAGATT 59.258 47.619 0.00 0.00 0.00 2.40
521 522 1.339438 ACGTGAAGCCATGCAGAAGAT 60.339 47.619 0.00 0.00 32.58 2.40
522 523 0.035317 ACGTGAAGCCATGCAGAAGA 59.965 50.000 0.00 0.00 32.58 2.87
523 524 0.445436 GACGTGAAGCCATGCAGAAG 59.555 55.000 0.00 0.00 32.58 2.85
524 525 1.291184 CGACGTGAAGCCATGCAGAA 61.291 55.000 0.00 0.00 32.58 3.02
525 526 1.737735 CGACGTGAAGCCATGCAGA 60.738 57.895 0.00 0.00 32.58 4.26
526 527 2.743752 CCGACGTGAAGCCATGCAG 61.744 63.158 0.00 0.00 32.58 4.41
527 528 2.741985 CCGACGTGAAGCCATGCA 60.742 61.111 0.00 0.00 32.58 3.96
528 529 3.499737 CCCGACGTGAAGCCATGC 61.500 66.667 0.00 0.00 32.58 4.06
529 530 2.819595 CCCCGACGTGAAGCCATG 60.820 66.667 0.00 0.00 35.46 3.66
530 531 4.778143 GCCCCGACGTGAAGCCAT 62.778 66.667 0.00 0.00 0.00 4.40
534 535 4.452733 GGGAGCCCCGACGTGAAG 62.453 72.222 0.00 0.00 32.13 3.02
545 546 4.329545 TTGTGCCGTCAGGGAGCC 62.330 66.667 0.00 0.00 39.06 4.70
546 547 3.050275 GTTGTGCCGTCAGGGAGC 61.050 66.667 0.00 0.00 39.06 4.70
547 548 2.738521 CGTTGTGCCGTCAGGGAG 60.739 66.667 0.00 0.00 39.06 4.30
548 549 3.220999 CTCGTTGTGCCGTCAGGGA 62.221 63.158 0.00 0.00 38.47 4.20
549 550 2.738521 CTCGTTGTGCCGTCAGGG 60.739 66.667 0.00 0.00 38.20 4.45
550 551 2.738521 CCTCGTTGTGCCGTCAGG 60.739 66.667 0.00 0.00 41.62 3.86
551 552 2.738521 CCCTCGTTGTGCCGTCAG 60.739 66.667 0.00 0.00 0.00 3.51
552 553 3.220999 CTCCCTCGTTGTGCCGTCA 62.221 63.158 0.00 0.00 0.00 4.35
553 554 2.432628 CTCCCTCGTTGTGCCGTC 60.433 66.667 0.00 0.00 0.00 4.79
554 555 4.681978 GCTCCCTCGTTGTGCCGT 62.682 66.667 0.00 0.00 0.00 5.68
555 556 4.680237 TGCTCCCTCGTTGTGCCG 62.680 66.667 0.00 0.00 0.00 5.69
556 557 2.743928 CTGCTCCCTCGTTGTGCC 60.744 66.667 0.00 0.00 0.00 5.01
557 558 3.426568 GCTGCTCCCTCGTTGTGC 61.427 66.667 0.00 0.00 0.00 4.57
558 559 1.739562 GAGCTGCTCCCTCGTTGTG 60.740 63.158 18.80 0.00 0.00 3.33
559 560 1.758440 TTGAGCTGCTCCCTCGTTGT 61.758 55.000 25.61 0.00 31.98 3.32
560 561 1.004560 TTGAGCTGCTCCCTCGTTG 60.005 57.895 25.61 0.00 31.98 4.10
561 562 1.004440 GTTGAGCTGCTCCCTCGTT 60.004 57.895 25.61 0.00 31.98 3.85
562 563 1.548357 ATGTTGAGCTGCTCCCTCGT 61.548 55.000 25.61 14.17 31.98 4.18
563 564 1.088340 CATGTTGAGCTGCTCCCTCG 61.088 60.000 25.61 7.84 31.98 4.63
564 565 0.747283 CCATGTTGAGCTGCTCCCTC 60.747 60.000 25.61 15.85 0.00 4.30
565 566 1.203441 TCCATGTTGAGCTGCTCCCT 61.203 55.000 25.61 5.94 0.00 4.20
566 567 0.747283 CTCCATGTTGAGCTGCTCCC 60.747 60.000 25.61 16.64 0.00 4.30
567 568 0.747283 CCTCCATGTTGAGCTGCTCC 60.747 60.000 25.61 12.52 0.00 4.70
568 569 0.251354 TCCTCCATGTTGAGCTGCTC 59.749 55.000 22.38 22.38 0.00 4.26
569 570 0.252479 CTCCTCCATGTTGAGCTGCT 59.748 55.000 0.00 0.00 0.00 4.24
570 571 0.251354 TCTCCTCCATGTTGAGCTGC 59.749 55.000 0.00 0.00 0.00 5.25
571 572 3.640498 TCTATCTCCTCCATGTTGAGCTG 59.360 47.826 0.00 0.00 0.00 4.24
572 573 3.896888 CTCTATCTCCTCCATGTTGAGCT 59.103 47.826 0.00 0.00 0.00 4.09
573 574 3.640967 ACTCTATCTCCTCCATGTTGAGC 59.359 47.826 0.00 0.00 0.00 4.26
574 575 6.968263 TTACTCTATCTCCTCCATGTTGAG 57.032 41.667 0.00 0.00 0.00 3.02
575 576 7.733773 TTTTACTCTATCTCCTCCATGTTGA 57.266 36.000 0.00 0.00 0.00 3.18
576 577 7.041508 GCATTTTACTCTATCTCCTCCATGTTG 60.042 40.741 0.00 0.00 0.00 3.33
577 578 6.995091 GCATTTTACTCTATCTCCTCCATGTT 59.005 38.462 0.00 0.00 0.00 2.71
578 579 6.100279 TGCATTTTACTCTATCTCCTCCATGT 59.900 38.462 0.00 0.00 0.00 3.21
579 580 6.426328 GTGCATTTTACTCTATCTCCTCCATG 59.574 42.308 0.00 0.00 0.00 3.66
580 581 6.328672 AGTGCATTTTACTCTATCTCCTCCAT 59.671 38.462 0.00 0.00 0.00 3.41
581 582 5.663106 AGTGCATTTTACTCTATCTCCTCCA 59.337 40.000 0.00 0.00 0.00 3.86
582 583 5.988561 CAGTGCATTTTACTCTATCTCCTCC 59.011 44.000 0.00 0.00 0.00 4.30
583 584 5.988561 CCAGTGCATTTTACTCTATCTCCTC 59.011 44.000 0.00 0.00 0.00 3.71
584 585 5.686124 GCCAGTGCATTTTACTCTATCTCCT 60.686 44.000 0.00 0.00 37.47 3.69
585 586 4.513318 GCCAGTGCATTTTACTCTATCTCC 59.487 45.833 0.00 0.00 37.47 3.71
586 587 4.210120 CGCCAGTGCATTTTACTCTATCTC 59.790 45.833 0.00 0.00 37.32 2.75
587 588 4.122776 CGCCAGTGCATTTTACTCTATCT 58.877 43.478 0.00 0.00 37.32 1.98
588 589 3.248602 CCGCCAGTGCATTTTACTCTATC 59.751 47.826 0.00 0.00 37.32 2.08
1193 1309 1.667724 GACGCCAGAAATCACCATCAG 59.332 52.381 0.00 0.00 0.00 2.90
1564 1689 4.456911 GCATCAACTCCATCACTTCTTCAA 59.543 41.667 0.00 0.00 0.00 2.69
1608 1749 6.070767 CCAGTTCATCTCCTAACAAACTAGGA 60.071 42.308 0.00 0.00 44.32 2.94
2158 2505 5.181811 CAGAGGCACTTCAATGTTTGACATA 59.818 40.000 0.00 0.00 41.55 2.29
2271 2618 0.336392 TGCTGAGGCTAGGAAGGAGA 59.664 55.000 0.00 0.00 39.59 3.71
2417 2764 7.052873 CAGATCATTATGGAGACCAAGAAAGT 58.947 38.462 0.00 0.00 36.95 2.66


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

AutoCloner maintained by Alex Coulton.