Multiple sequence alignment - TraesCS5D01G234600

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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 TraesCS5D01G234600 chr5D 100.000 3465 0 0 1 3465 342173499 342176963 0.000000e+00 6399.0
1 TraesCS5D01G234600 chr5D 84.058 483 38 18 2350 2815 557973622 557974082 2.470000e-116 429.0
2 TraesCS5D01G234600 chr5B 89.768 3528 214 78 1 3465 401665988 401669431 0.000000e+00 4379.0
3 TraesCS5D01G234600 chr5A 89.324 3550 189 97 1 3460 443287799 443291248 0.000000e+00 4281.0
4 TraesCS5D01G234600 chr5A 83.613 476 43 19 2350 2810 666110267 666110722 6.920000e-112 414.0
5 TraesCS5D01G234600 chr5A 78.283 198 27 11 1855 2046 459775655 459775468 2.830000e-21 113.0
6 TraesCS5D01G234600 chr7A 84.222 469 42 16 2355 2810 108870670 108870221 8.890000e-116 427.0
7 TraesCS5D01G234600 chr1D 83.864 471 38 16 2355 2810 451053048 451052601 6.920000e-112 414.0
8 TraesCS5D01G234600 chr1D 81.752 274 48 2 1801 2073 74928505 74928233 9.670000e-56 228.0
9 TraesCS5D01G234600 chr1D 78.873 284 57 1 1775 2058 44970449 44970169 4.570000e-44 189.0
10 TraesCS5D01G234600 chr1D 75.410 183 35 7 1856 2034 479540793 479540969 2.870000e-11 80.5
11 TraesCS5D01G234600 chr4D 79.891 184 33 4 1856 2037 61852297 61852478 7.800000e-27 132.0
12 TraesCS5D01G234600 chr4D 76.374 182 31 11 1263 1440 61851789 61851962 1.710000e-13 87.9
13 TraesCS5D01G234600 chr4A 79.891 184 33 4 1856 2037 535035687 535035868 7.800000e-27 132.0
14 TraesCS5D01G234600 chr4A 76.374 182 31 11 1263 1440 535035176 535035349 1.710000e-13 87.9
15 TraesCS5D01G234600 chr4A 97.143 35 1 0 1405 1439 576576321 576576287 3.730000e-05 60.2
16 TraesCS5D01G234600 chr4B 79.888 179 28 7 1863 2037 90892347 90892173 1.310000e-24 124.0
17 TraesCS5D01G234600 chr4B 88.571 70 6 2 1296 1364 90892824 90892756 2.220000e-12 84.2
18 TraesCS5D01G234600 chr4B 97.222 36 1 0 1405 1440 39289512 39289547 1.040000e-05 62.1
19 TraesCS5D01G234600 chrUn 97.222 36 1 0 1405 1440 61039929 61039894 1.040000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G234600 chr5D 342173499 342176963 3464 False 6399 6399 100.000 1 3465 1 chr5D.!!$F1 3464
1 TraesCS5D01G234600 chr5B 401665988 401669431 3443 False 4379 4379 89.768 1 3465 1 chr5B.!!$F1 3464
2 TraesCS5D01G234600 chr5A 443287799 443291248 3449 False 4281 4281 89.324 1 3460 1 chr5A.!!$F1 3459

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
298 303 0.106918 GCGGTGATAATTGACCCCCA 60.107 55.0 0.0 0.0 0.00 4.96 F
865 905 0.240945 CCTGCAACCGATTCAACACC 59.759 55.0 0.0 0.0 0.00 4.16 F
2312 2373 0.802607 GTAAGCTGAACGGAGCCTCG 60.803 60.0 0.0 0.0 40.08 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 1774 0.100682 GGCGCAGAAGAGATGTACGA 59.899 55.0 10.83 0.0 0.00 3.43 R
2335 2396 0.040942 TTCTCTGCCTCTGCTCTCCT 59.959 55.0 0.00 0.0 38.71 3.69 R
3396 3523 0.469705 GCCATATTGTCATGCCCCCA 60.470 55.0 0.00 0.0 0.00 4.96 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
55 56 3.658757 TGGCTAAGCAAAATTGACACC 57.341 42.857 0.00 0.00 0.00 4.16
56 57 2.961741 TGGCTAAGCAAAATTGACACCA 59.038 40.909 0.00 0.00 0.00 4.17
163 167 6.400568 AGATGCTTAAAATGGGTTTCATGTG 58.599 36.000 0.00 0.00 35.99 3.21
165 169 5.295950 TGCTTAAAATGGGTTTCATGTGTG 58.704 37.500 0.00 0.00 35.99 3.82
190 194 0.371301 CATGATCACCGAGTGTTGCG 59.629 55.000 0.00 0.00 34.79 4.85
197 201 0.655733 ACCGAGTGTTGCGAAAACTG 59.344 50.000 0.00 0.00 0.00 3.16
198 202 0.934496 CCGAGTGTTGCGAAAACTGA 59.066 50.000 0.00 0.00 0.00 3.41
223 227 9.618410 GAATTATGTTATTGCAATTTGTTACGC 57.382 29.630 18.75 0.00 0.00 4.42
224 228 5.678910 ATGTTATTGCAATTTGTTACGCG 57.321 34.783 18.75 3.53 0.00 6.01
268 273 1.174783 ACACGTATCCGCTTGAGACT 58.825 50.000 0.00 0.00 37.70 3.24
280 285 2.675348 GCTTGAGACTGACATAAGTGGC 59.325 50.000 0.00 0.00 0.00 5.01
293 298 4.574828 ACATAAGTGGCGGTGATAATTGAC 59.425 41.667 0.00 0.00 0.00 3.18
294 299 2.038387 AGTGGCGGTGATAATTGACC 57.962 50.000 0.00 0.00 0.00 4.02
295 300 1.021968 GTGGCGGTGATAATTGACCC 58.978 55.000 0.00 0.00 0.00 4.46
297 302 0.822121 GGCGGTGATAATTGACCCCC 60.822 60.000 0.00 0.00 0.00 5.40
298 303 0.106918 GCGGTGATAATTGACCCCCA 60.107 55.000 0.00 0.00 0.00 4.96
299 304 1.478654 GCGGTGATAATTGACCCCCAT 60.479 52.381 0.00 0.00 0.00 4.00
313 318 1.573376 CCCCCATGGTTCTATCCCAAA 59.427 52.381 11.73 0.00 35.14 3.28
316 321 3.897505 CCCCATGGTTCTATCCCAAAATC 59.102 47.826 11.73 0.00 35.14 2.17
321 326 3.882888 TGGTTCTATCCCAAAATCGATGC 59.117 43.478 0.00 0.00 0.00 3.91
332 337 3.302365 AAATCGATGCCTGTGTTTTGG 57.698 42.857 0.00 0.00 0.00 3.28
347 352 7.281999 CCTGTGTTTTGGGATTTACAATTGTTT 59.718 33.333 17.78 2.10 0.00 2.83
349 354 7.066284 TGTGTTTTGGGATTTACAATTGTTTGG 59.934 33.333 17.78 0.00 37.15 3.28
352 357 9.110502 GTTTTGGGATTTACAATTGTTTGGTAA 57.889 29.630 17.78 1.09 37.15 2.85
353 358 8.894768 TTTGGGATTTACAATTGTTTGGTAAG 57.105 30.769 17.78 0.00 37.15 2.34
367 372 9.723601 ATTGTTTGGTAAGAATGCATTATTTGT 57.276 25.926 23.14 3.37 0.00 2.83
368 373 8.531622 TGTTTGGTAAGAATGCATTATTTGTG 57.468 30.769 23.14 0.00 0.00 3.33
369 374 8.147058 TGTTTGGTAAGAATGCATTATTTGTGT 58.853 29.630 23.14 2.63 0.00 3.72
370 375 8.987890 GTTTGGTAAGAATGCATTATTTGTGTT 58.012 29.630 23.14 3.18 0.00 3.32
396 401 7.979115 TTATGGTTTTAACATTCGCTATTGC 57.021 32.000 0.00 0.00 0.00 3.56
398 403 5.636837 TGGTTTTAACATTCGCTATTGCTC 58.363 37.500 0.00 0.00 36.97 4.26
407 412 5.121768 ACATTCGCTATTGCTCGTAACTTTT 59.878 36.000 0.00 0.00 36.97 2.27
409 414 3.369756 TCGCTATTGCTCGTAACTTTTGG 59.630 43.478 0.00 0.00 36.97 3.28
411 416 4.403453 GCTATTGCTCGTAACTTTTGGTG 58.597 43.478 0.00 0.00 36.03 4.17
447 452 8.373048 ACACGTTTTCTTACTTGATCACATAA 57.627 30.769 0.00 0.00 0.00 1.90
464 472 7.977789 TCACATAAGTAGCAACTTCAAATCA 57.022 32.000 0.00 0.00 42.42 2.57
468 476 8.299570 ACATAAGTAGCAACTTCAAATCAAAGG 58.700 33.333 0.00 0.00 42.42 3.11
470 478 6.715347 AGTAGCAACTTCAAATCAAAGGTT 57.285 33.333 0.00 0.00 29.00 3.50
471 479 6.739112 AGTAGCAACTTCAAATCAAAGGTTC 58.261 36.000 0.00 0.00 29.00 3.62
472 480 5.596836 AGCAACTTCAAATCAAAGGTTCA 57.403 34.783 0.00 0.00 0.00 3.18
473 481 5.594926 AGCAACTTCAAATCAAAGGTTCAG 58.405 37.500 0.00 0.00 0.00 3.02
503 512 3.823873 ACCGCATTGTGTTTTCCAGATTA 59.176 39.130 0.00 0.00 0.00 1.75
510 519 5.181690 TGTGTTTTCCAGATTAGTTGTGC 57.818 39.130 0.00 0.00 0.00 4.57
522 531 5.824624 AGATTAGTTGTGCCCAGTGATAATG 59.175 40.000 0.00 0.00 0.00 1.90
523 532 3.439857 AGTTGTGCCCAGTGATAATGT 57.560 42.857 0.00 0.00 0.00 2.71
525 534 1.462616 TGTGCCCAGTGATAATGTGC 58.537 50.000 0.00 0.00 0.00 4.57
526 535 1.004628 TGTGCCCAGTGATAATGTGCT 59.995 47.619 0.00 0.00 0.00 4.40
527 536 2.094675 GTGCCCAGTGATAATGTGCTT 58.905 47.619 0.00 0.00 0.00 3.91
528 537 2.098117 GTGCCCAGTGATAATGTGCTTC 59.902 50.000 0.00 0.00 0.00 3.86
529 538 1.678101 GCCCAGTGATAATGTGCTTCC 59.322 52.381 0.00 0.00 0.00 3.46
530 539 2.684927 GCCCAGTGATAATGTGCTTCCT 60.685 50.000 0.00 0.00 0.00 3.36
531 540 3.209410 CCCAGTGATAATGTGCTTCCTC 58.791 50.000 0.00 0.00 0.00 3.71
532 541 3.370846 CCCAGTGATAATGTGCTTCCTCA 60.371 47.826 0.00 0.00 0.00 3.86
533 542 3.624861 CCAGTGATAATGTGCTTCCTCAC 59.375 47.826 0.00 0.00 37.48 3.51
534 543 3.308053 CAGTGATAATGTGCTTCCTCACG 59.692 47.826 0.00 0.00 39.73 4.35
535 544 3.055819 AGTGATAATGTGCTTCCTCACGT 60.056 43.478 0.00 0.00 39.73 4.49
536 545 3.684788 GTGATAATGTGCTTCCTCACGTT 59.315 43.478 6.59 6.59 45.21 3.99
537 546 4.868171 GTGATAATGTGCTTCCTCACGTTA 59.132 41.667 9.96 9.96 46.32 3.18
540 549 4.685169 AATGTGCTTCCTCACGTTATTG 57.315 40.909 0.06 0.00 42.49 1.90
544 553 2.419673 TGCTTCCTCACGTTATTGCATG 59.580 45.455 0.00 0.00 0.00 4.06
548 557 2.027653 TCCTCACGTTATTGCATGGTGA 60.028 45.455 0.00 0.00 36.33 4.02
556 565 6.196910 CACGTTATTGCATGGTGATATTTGTG 59.803 38.462 0.00 0.00 0.00 3.33
557 566 5.686841 CGTTATTGCATGGTGATATTTGTGG 59.313 40.000 0.00 0.00 0.00 4.17
558 567 6.572519 GTTATTGCATGGTGATATTTGTGGT 58.427 36.000 0.00 0.00 0.00 4.16
559 568 5.680594 ATTGCATGGTGATATTTGTGGTT 57.319 34.783 0.00 0.00 0.00 3.67
560 569 4.453177 TGCATGGTGATATTTGTGGTTG 57.547 40.909 0.00 0.00 0.00 3.77
561 570 3.195182 TGCATGGTGATATTTGTGGTTGG 59.805 43.478 0.00 0.00 0.00 3.77
562 571 3.195396 GCATGGTGATATTTGTGGTTGGT 59.805 43.478 0.00 0.00 0.00 3.67
563 572 4.746729 CATGGTGATATTTGTGGTTGGTG 58.253 43.478 0.00 0.00 0.00 4.17
564 573 4.105754 TGGTGATATTTGTGGTTGGTGA 57.894 40.909 0.00 0.00 0.00 4.02
565 574 4.474394 TGGTGATATTTGTGGTTGGTGAA 58.526 39.130 0.00 0.00 0.00 3.18
566 575 4.895889 TGGTGATATTTGTGGTTGGTGAAA 59.104 37.500 0.00 0.00 0.00 2.69
569 578 6.589907 GGTGATATTTGTGGTTGGTGAAAATC 59.410 38.462 0.00 0.00 0.00 2.17
570 579 6.307800 GTGATATTTGTGGTTGGTGAAAATCG 59.692 38.462 0.00 0.00 0.00 3.34
576 614 5.341617 TGTGGTTGGTGAAAATCGTTAAAC 58.658 37.500 0.00 0.00 0.00 2.01
581 619 2.975193 GGTGAAAATCGTTAAACGTGGC 59.025 45.455 0.00 0.00 43.14 5.01
584 622 3.560481 TGAAAATCGTTAAACGTGGCTGA 59.440 39.130 0.00 0.00 43.14 4.26
608 646 5.047802 ACAGTGCATGCTTACTGCTAATTTT 60.048 36.000 28.68 11.89 46.27 1.82
609 647 5.514204 CAGTGCATGCTTACTGCTAATTTTC 59.486 40.000 21.15 0.00 43.37 2.29
618 656 9.456147 TGCTTACTGCTAATTTTCACCTAATTA 57.544 29.630 0.00 0.00 43.37 1.40
651 689 4.242475 CATGCATTGACAGCTCAAATTGT 58.758 39.130 0.00 0.00 39.90 2.71
653 691 3.068448 TGCATTGACAGCTCAAATTGTGT 59.932 39.130 0.00 0.00 39.90 3.72
657 695 2.287644 TGACAGCTCAAATTGTGTGACG 59.712 45.455 0.00 0.00 0.00 4.35
663 701 4.754618 AGCTCAAATTGTGTGACGAATGTA 59.245 37.500 0.00 0.00 0.00 2.29
710 748 2.625695 ATCCGTGTGATGATGATGCA 57.374 45.000 0.00 0.00 30.54 3.96
711 749 2.399916 TCCGTGTGATGATGATGCAA 57.600 45.000 0.00 0.00 0.00 4.08
712 750 2.709213 TCCGTGTGATGATGATGCAAA 58.291 42.857 0.00 0.00 0.00 3.68
713 751 3.281158 TCCGTGTGATGATGATGCAAAT 58.719 40.909 0.00 0.00 0.00 2.32
714 752 3.695556 TCCGTGTGATGATGATGCAAATT 59.304 39.130 0.00 0.00 0.00 1.82
715 753 3.794564 CCGTGTGATGATGATGCAAATTG 59.205 43.478 0.00 0.00 0.00 2.32
716 754 4.439016 CCGTGTGATGATGATGCAAATTGA 60.439 41.667 0.00 0.00 0.00 2.57
717 755 4.497966 CGTGTGATGATGATGCAAATTGAC 59.502 41.667 0.00 0.00 0.00 3.18
718 756 5.404096 GTGTGATGATGATGCAAATTGACA 58.596 37.500 0.00 0.00 0.00 3.58
719 757 5.515270 GTGTGATGATGATGCAAATTGACAG 59.485 40.000 0.00 0.00 0.00 3.51
720 758 4.503007 GTGATGATGATGCAAATTGACAGC 59.497 41.667 0.00 0.00 0.00 4.40
721 759 3.139603 TGATGATGCAAATTGACAGCG 57.860 42.857 0.00 0.00 0.00 5.18
722 760 1.850441 GATGATGCAAATTGACAGCGC 59.150 47.619 0.00 0.00 0.00 5.92
723 761 0.597072 TGATGCAAATTGACAGCGCA 59.403 45.000 11.47 0.00 36.95 6.09
730 768 3.181537 GCAAATTGACAGCGCAGAAAATC 60.182 43.478 11.47 0.00 0.00 2.17
760 798 0.460459 AACAAAAACGGCCGGGTTTG 60.460 50.000 35.28 35.28 39.88 2.93
787 825 2.369394 GCCCGTCTTGATTGATCCTTT 58.631 47.619 0.00 0.00 0.00 3.11
865 905 0.240945 CCTGCAACCGATTCAACACC 59.759 55.000 0.00 0.00 0.00 4.16
1376 1425 3.628646 GATGCCGGTGGTGGAGCTT 62.629 63.158 1.90 0.00 0.00 3.74
1777 1835 3.639541 CTCTCAACTCCAGCGCGCT 62.640 63.158 31.32 31.32 0.00 5.92
2240 2301 2.283388 AACGGTACCGCCTCCTCA 60.283 61.111 33.62 0.00 44.19 3.86
2312 2373 0.802607 GTAAGCTGAACGGAGCCTCG 60.803 60.000 0.00 0.00 40.08 4.63
2431 2492 9.066892 TCATTGCATTACTTTTCTTTCTGTAGT 57.933 29.630 0.00 0.00 0.00 2.73
2440 2509 6.990349 ACTTTTCTTTCTGTAGTTTGGATCGA 59.010 34.615 0.00 0.00 0.00 3.59
2442 2511 7.596749 TTTCTTTCTGTAGTTTGGATCGATC 57.403 36.000 17.36 17.36 0.00 3.69
2446 2515 4.421058 TCTGTAGTTTGGATCGATCGTTG 58.579 43.478 18.81 2.49 0.00 4.10
2447 2516 3.517602 TGTAGTTTGGATCGATCGTTGG 58.482 45.455 18.81 0.00 0.00 3.77
2448 2517 2.762535 AGTTTGGATCGATCGTTGGT 57.237 45.000 18.81 1.08 0.00 3.67
2449 2518 3.053831 AGTTTGGATCGATCGTTGGTT 57.946 42.857 18.81 0.67 0.00 3.67
2450 2519 3.000727 AGTTTGGATCGATCGTTGGTTC 58.999 45.455 18.81 4.13 0.00 3.62
2451 2520 2.018542 TTGGATCGATCGTTGGTTCC 57.981 50.000 18.81 14.14 0.00 3.62
2607 2680 3.181458 TGGTCTGTTCTTGTCCCTGTAAC 60.181 47.826 0.00 0.00 0.00 2.50
2609 2682 4.058817 GTCTGTTCTTGTCCCTGTAACTG 58.941 47.826 0.00 0.00 0.00 3.16
2610 2683 3.709653 TCTGTTCTTGTCCCTGTAACTGT 59.290 43.478 0.00 0.00 0.00 3.55
2612 2685 5.364446 TCTGTTCTTGTCCCTGTAACTGTAA 59.636 40.000 0.00 0.00 0.00 2.41
2613 2686 5.607477 TGTTCTTGTCCCTGTAACTGTAAG 58.393 41.667 0.00 0.00 42.29 2.34
2693 2776 5.987953 GCTTGTAGTATCATCTCATGCTCAA 59.012 40.000 0.00 0.00 0.00 3.02
2698 2781 6.862711 AGTATCATCTCATGCTCAATTGTG 57.137 37.500 5.13 4.05 0.00 3.33
2699 2782 4.569761 ATCATCTCATGCTCAATTGTGC 57.430 40.909 22.41 22.41 35.32 4.57
2727 2810 2.281345 CATGATCGGAGGCAGCCC 60.281 66.667 8.22 0.00 0.00 5.19
2810 2898 1.817099 CCTGCGCTTTCCTGCTAGG 60.817 63.158 9.73 0.00 36.46 3.02
2811 2899 1.219124 CTGCGCTTTCCTGCTAGGA 59.781 57.895 9.73 1.25 44.10 2.94
2834 2922 5.741011 AGTAGAATAATGGTCCTTTTGCGA 58.259 37.500 0.00 0.00 0.00 5.10
2883 2974 2.476241 GCAGCGCCATTTTTATAATGCC 59.524 45.455 2.29 0.00 0.00 4.40
2884 2975 3.059166 CAGCGCCATTTTTATAATGCCC 58.941 45.455 2.29 0.00 0.00 5.36
2913 3010 1.890979 GATGCATCCCCACGAGCAG 60.891 63.158 16.23 0.00 40.71 4.24
2933 3036 4.302455 CAGGAGCAGATAGATTAACGTGG 58.698 47.826 0.00 0.00 0.00 4.94
2945 3048 4.828387 AGATTAACGTGGGCCTAAACAAAA 59.172 37.500 4.53 0.00 0.00 2.44
3029 3136 2.028190 CCATCGCCAGCTACTCGG 59.972 66.667 0.00 0.00 0.00 4.63
3038 3145 2.822764 CCAGCTACTCGGTATGGAAAC 58.177 52.381 0.00 0.00 32.55 2.78
3040 3147 2.097825 AGCTACTCGGTATGGAAACGT 58.902 47.619 0.00 0.00 0.00 3.99
3041 3148 3.065786 CAGCTACTCGGTATGGAAACGTA 59.934 47.826 0.00 0.00 0.00 3.57
3042 3149 3.314635 AGCTACTCGGTATGGAAACGTAG 59.685 47.826 0.00 0.00 30.93 3.51
3043 3150 3.549625 GCTACTCGGTATGGAAACGTAGG 60.550 52.174 0.00 0.00 30.93 3.18
3044 3151 1.753073 ACTCGGTATGGAAACGTAGGG 59.247 52.381 0.00 0.00 30.93 3.53
3117 3234 6.366332 ACACATTCTTGTCTCGTGTAATTCTC 59.634 38.462 0.00 0.00 38.95 2.87
3211 3336 2.129397 ACCATCCCCACCATCCCA 59.871 61.111 0.00 0.00 0.00 4.37
3374 3501 2.052104 GCAATTAGGCGGCAACCCT 61.052 57.895 13.08 0.00 40.02 4.34
3394 3521 1.468520 TGCTTAGCGAAAGTGAATGGC 59.531 47.619 0.00 0.00 37.53 4.40
3396 3523 2.098117 GCTTAGCGAAAGTGAATGGCAT 59.902 45.455 0.00 0.00 37.53 4.40
3409 3536 2.364056 GGCATGGGGGCATGACAA 60.364 61.111 0.00 0.00 40.24 3.18
3410 3537 1.763256 GGCATGGGGGCATGACAAT 60.763 57.895 0.00 0.00 40.24 2.71
3425 3552 2.158827 TGACAATATGGCATGCGGTAGT 60.159 45.455 12.44 5.23 24.43 2.73
3427 3554 3.664107 ACAATATGGCATGCGGTAGTAG 58.336 45.455 12.44 1.33 0.00 2.57
3429 3556 2.003937 TATGGCATGCGGTAGTAGGA 57.996 50.000 12.44 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.942376 AGATGTCGCTTGTGTCACAAAA 59.058 40.909 18.68 5.58 37.69 2.44
78 79 6.115446 AGCATAGCACATTTAGAGTTGCTAA 58.885 36.000 6.26 0.00 38.19 3.09
141 145 5.933463 CACACATGAAACCCATTTTAAGCAT 59.067 36.000 0.00 0.00 31.94 3.79
163 167 2.094494 ACTCGGTGATCATGTGAGACAC 60.094 50.000 21.49 11.82 35.84 3.67
165 169 2.094494 ACACTCGGTGATCATGTGAGAC 60.094 50.000 21.49 0.00 36.96 3.36
197 201 9.618410 GCGTAACAAATTGCAATAACATAATTC 57.382 29.630 13.39 0.00 0.00 2.17
198 202 8.317460 CGCGTAACAAATTGCAATAACATAATT 58.683 29.630 13.39 0.00 0.00 1.40
221 225 5.448438 ACATAATATATTTGCCACAACGCG 58.552 37.500 3.53 3.53 0.00 6.01
268 273 3.897141 TTATCACCGCCACTTATGTCA 57.103 42.857 0.00 0.00 0.00 3.58
280 285 2.229792 CATGGGGGTCAATTATCACCG 58.770 52.381 0.00 0.00 32.89 4.94
293 298 1.231018 TTGGGATAGAACCATGGGGG 58.769 55.000 18.09 0.00 44.81 5.40
294 299 3.396685 TTTTGGGATAGAACCATGGGG 57.603 47.619 18.09 0.00 37.93 4.96
295 300 3.569701 CGATTTTGGGATAGAACCATGGG 59.430 47.826 18.09 0.00 37.93 4.00
297 302 5.563475 GCATCGATTTTGGGATAGAACCATG 60.563 44.000 0.00 0.00 37.93 3.66
298 303 4.520492 GCATCGATTTTGGGATAGAACCAT 59.480 41.667 0.00 0.00 37.93 3.55
299 304 3.882888 GCATCGATTTTGGGATAGAACCA 59.117 43.478 0.00 0.00 35.88 3.67
304 309 3.251729 CACAGGCATCGATTTTGGGATAG 59.748 47.826 0.00 0.00 0.00 2.08
313 318 1.545582 CCCAAAACACAGGCATCGATT 59.454 47.619 0.00 0.00 0.00 3.34
316 321 1.176527 ATCCCAAAACACAGGCATCG 58.823 50.000 0.00 0.00 0.00 3.84
321 326 6.287525 ACAATTGTAAATCCCAAAACACAGG 58.712 36.000 9.97 0.00 0.00 4.00
332 337 8.655970 GCATTCTTACCAAACAATTGTAAATCC 58.344 33.333 12.39 0.00 34.60 3.01
370 375 9.672086 GCAATAGCGAATGTTAAAACCATAATA 57.328 29.630 0.00 0.00 0.00 0.98
396 401 4.809426 ACTGTTCTCACCAAAAGTTACGAG 59.191 41.667 0.00 0.00 0.00 4.18
398 403 5.479716 AACTGTTCTCACCAAAAGTTACG 57.520 39.130 0.00 0.00 0.00 3.18
407 412 3.530265 ACGTGTAAACTGTTCTCACCA 57.470 42.857 16.50 0.27 0.00 4.17
409 414 6.103222 AGAAAACGTGTAAACTGTTCTCAC 57.897 37.500 13.99 13.99 0.00 3.51
411 416 7.903062 AGTAAGAAAACGTGTAAACTGTTCTC 58.097 34.615 0.00 0.00 0.00 2.87
447 452 6.321181 TGAACCTTTGATTTGAAGTTGCTACT 59.679 34.615 0.00 0.00 35.68 2.57
464 472 1.202891 CGGTTTCTCCCCTGAACCTTT 60.203 52.381 0.00 0.00 0.00 3.11
468 476 0.322546 ATGCGGTTTCTCCCCTGAAC 60.323 55.000 0.00 0.00 0.00 3.18
470 478 0.322456 CAATGCGGTTTCTCCCCTGA 60.322 55.000 0.00 0.00 0.00 3.86
471 479 0.609131 ACAATGCGGTTTCTCCCCTG 60.609 55.000 0.00 0.00 0.00 4.45
472 480 0.609131 CACAATGCGGTTTCTCCCCT 60.609 55.000 0.00 0.00 0.00 4.79
473 481 0.893727 ACACAATGCGGTTTCTCCCC 60.894 55.000 0.00 0.00 0.00 4.81
489 498 4.546570 GGCACAACTAATCTGGAAAACAC 58.453 43.478 0.00 0.00 0.00 3.32
503 512 3.084039 CACATTATCACTGGGCACAACT 58.916 45.455 0.00 0.00 0.00 3.16
510 519 3.209410 GAGGAAGCACATTATCACTGGG 58.791 50.000 0.00 0.00 0.00 4.45
522 531 1.804151 TGCAATAACGTGAGGAAGCAC 59.196 47.619 0.00 0.00 35.46 4.40
523 532 2.177394 TGCAATAACGTGAGGAAGCA 57.823 45.000 0.00 0.00 0.00 3.91
525 534 3.009723 ACCATGCAATAACGTGAGGAAG 58.990 45.455 0.00 0.00 0.00 3.46
526 535 2.746904 CACCATGCAATAACGTGAGGAA 59.253 45.455 0.00 0.00 0.00 3.36
527 536 2.027653 TCACCATGCAATAACGTGAGGA 60.028 45.455 0.00 0.00 0.00 3.71
528 537 2.355197 TCACCATGCAATAACGTGAGG 58.645 47.619 0.00 0.00 0.00 3.86
529 538 5.929697 ATATCACCATGCAATAACGTGAG 57.070 39.130 0.00 0.00 36.93 3.51
530 539 6.094742 ACAAATATCACCATGCAATAACGTGA 59.905 34.615 0.00 0.00 37.81 4.35
531 540 6.196910 CACAAATATCACCATGCAATAACGTG 59.803 38.462 0.00 0.00 0.00 4.49
532 541 6.264832 CACAAATATCACCATGCAATAACGT 58.735 36.000 0.00 0.00 0.00 3.99
533 542 5.686841 CCACAAATATCACCATGCAATAACG 59.313 40.000 0.00 0.00 0.00 3.18
534 543 6.572519 ACCACAAATATCACCATGCAATAAC 58.427 36.000 0.00 0.00 0.00 1.89
535 544 6.788598 ACCACAAATATCACCATGCAATAA 57.211 33.333 0.00 0.00 0.00 1.40
536 545 6.406737 CCAACCACAAATATCACCATGCAATA 60.407 38.462 0.00 0.00 0.00 1.90
537 546 5.421277 CAACCACAAATATCACCATGCAAT 58.579 37.500 0.00 0.00 0.00 3.56
540 549 3.195396 ACCAACCACAAATATCACCATGC 59.805 43.478 0.00 0.00 0.00 4.06
544 553 5.461032 TTTCACCAACCACAAATATCACC 57.539 39.130 0.00 0.00 0.00 4.02
548 557 6.339587 ACGATTTTCACCAACCACAAATAT 57.660 33.333 0.00 0.00 0.00 1.28
556 565 4.438471 CACGTTTAACGATTTTCACCAACC 59.562 41.667 24.57 0.00 46.05 3.77
557 566 4.438471 CCACGTTTAACGATTTTCACCAAC 59.562 41.667 24.57 0.00 46.05 3.77
558 567 4.599047 CCACGTTTAACGATTTTCACCAA 58.401 39.130 24.57 0.00 46.05 3.67
559 568 3.548415 GCCACGTTTAACGATTTTCACCA 60.548 43.478 24.57 0.00 46.05 4.17
560 569 2.975193 GCCACGTTTAACGATTTTCACC 59.025 45.455 24.57 0.10 46.05 4.02
561 570 3.662186 CAGCCACGTTTAACGATTTTCAC 59.338 43.478 24.57 6.00 46.05 3.18
562 571 3.560481 TCAGCCACGTTTAACGATTTTCA 59.440 39.130 24.57 0.95 46.05 2.69
563 572 3.904234 GTCAGCCACGTTTAACGATTTTC 59.096 43.478 24.57 7.95 46.05 2.29
564 573 3.312973 TGTCAGCCACGTTTAACGATTTT 59.687 39.130 24.57 0.00 46.05 1.82
565 574 2.873472 TGTCAGCCACGTTTAACGATTT 59.127 40.909 24.57 0.00 46.05 2.17
566 575 2.478894 CTGTCAGCCACGTTTAACGATT 59.521 45.455 24.57 0.00 46.05 3.34
570 579 1.333791 GCACTGTCAGCCACGTTTAAC 60.334 52.381 0.00 0.00 0.00 2.01
576 614 2.865308 CATGCACTGTCAGCCACG 59.135 61.111 0.00 0.00 0.00 4.94
581 619 1.129998 GCAGTAAGCATGCACTGTCAG 59.870 52.381 28.74 12.32 43.33 3.51
618 656 7.101054 AGCTGTCAATGCATGTTTTCATTATT 58.899 30.769 0.00 0.00 38.64 1.40
621 659 4.890088 AGCTGTCAATGCATGTTTTCATT 58.110 34.783 0.00 0.00 38.64 2.57
623 661 3.318557 TGAGCTGTCAATGCATGTTTTCA 59.681 39.130 0.00 0.00 0.00 2.69
624 662 3.904571 TGAGCTGTCAATGCATGTTTTC 58.095 40.909 0.00 0.00 0.00 2.29
632 670 3.427528 CACACAATTTGAGCTGTCAATGC 59.572 43.478 2.79 0.00 42.41 3.56
651 689 3.127589 CCACTGTTGTACATTCGTCACA 58.872 45.455 0.00 0.00 0.00 3.58
653 691 3.127589 CACCACTGTTGTACATTCGTCA 58.872 45.455 0.00 0.00 0.00 4.35
657 695 4.084745 CGTGTACACCACTGTTGTACATTC 60.085 45.833 21.66 12.79 46.37 2.67
663 701 1.149361 CGCGTGTACACCACTGTTGT 61.149 55.000 20.11 0.00 42.20 3.32
694 732 4.497966 GTCAATTTGCATCATCATCACACG 59.502 41.667 0.00 0.00 0.00 4.49
695 733 5.404096 TGTCAATTTGCATCATCATCACAC 58.596 37.500 0.00 0.00 0.00 3.82
706 744 0.883153 TCTGCGCTGTCAATTTGCAT 59.117 45.000 9.73 0.00 34.66 3.96
707 745 0.667453 TTCTGCGCTGTCAATTTGCA 59.333 45.000 9.73 0.00 0.00 4.08
708 746 1.769733 TTTCTGCGCTGTCAATTTGC 58.230 45.000 9.73 0.00 0.00 3.68
709 747 3.982701 TGATTTTCTGCGCTGTCAATTTG 59.017 39.130 9.73 0.00 0.00 2.32
710 748 4.241590 TGATTTTCTGCGCTGTCAATTT 57.758 36.364 9.73 0.00 0.00 1.82
711 749 3.921119 TGATTTTCTGCGCTGTCAATT 57.079 38.095 9.73 2.82 0.00 2.32
712 750 3.428452 CCATGATTTTCTGCGCTGTCAAT 60.428 43.478 9.73 10.85 0.00 2.57
713 751 2.095110 CCATGATTTTCTGCGCTGTCAA 60.095 45.455 9.73 6.17 0.00 3.18
714 752 1.469703 CCATGATTTTCTGCGCTGTCA 59.530 47.619 9.73 8.40 0.00 3.58
715 753 1.739466 TCCATGATTTTCTGCGCTGTC 59.261 47.619 9.73 2.04 0.00 3.51
716 754 1.741706 CTCCATGATTTTCTGCGCTGT 59.258 47.619 9.73 0.00 0.00 4.40
717 755 1.065102 CCTCCATGATTTTCTGCGCTG 59.935 52.381 9.73 8.88 0.00 5.18
718 756 1.340405 ACCTCCATGATTTTCTGCGCT 60.340 47.619 9.73 0.00 0.00 5.92
719 757 1.064654 GACCTCCATGATTTTCTGCGC 59.935 52.381 0.00 0.00 0.00 6.09
720 758 2.358957 TGACCTCCATGATTTTCTGCG 58.641 47.619 0.00 0.00 0.00 5.18
721 759 4.022068 TGTTTGACCTCCATGATTTTCTGC 60.022 41.667 0.00 0.00 0.00 4.26
722 760 5.710513 TGTTTGACCTCCATGATTTTCTG 57.289 39.130 0.00 0.00 0.00 3.02
723 761 6.729690 TTTGTTTGACCTCCATGATTTTCT 57.270 33.333 0.00 0.00 0.00 2.52
730 768 3.380142 CCGTTTTTGTTTGACCTCCATG 58.620 45.455 0.00 0.00 0.00 3.66
787 825 2.236146 AGTAAACATGGACCGCTGATCA 59.764 45.455 0.00 0.00 0.00 2.92
999 1048 7.514473 AGGAGATAAGAGTATAAAAAGGGAGGG 59.486 40.741 0.00 0.00 0.00 4.30
1000 1049 8.499288 AGGAGATAAGAGTATAAAAAGGGAGG 57.501 38.462 0.00 0.00 0.00 4.30
1001 1050 8.301002 CGAGGAGATAAGAGTATAAAAAGGGAG 58.699 40.741 0.00 0.00 0.00 4.30
1002 1051 7.255871 GCGAGGAGATAAGAGTATAAAAAGGGA 60.256 40.741 0.00 0.00 0.00 4.20
1152 1201 2.420890 CATGCTCCGCTCTCCCTC 59.579 66.667 0.00 0.00 0.00 4.30
1153 1202 3.160047 CCATGCTCCGCTCTCCCT 61.160 66.667 0.00 0.00 0.00 4.20
1154 1203 3.157252 TCCATGCTCCGCTCTCCC 61.157 66.667 0.00 0.00 0.00 4.30
1155 1204 2.420890 CTCCATGCTCCGCTCTCC 59.579 66.667 0.00 0.00 0.00 3.71
1156 1205 2.420890 CCTCCATGCTCCGCTCTC 59.579 66.667 0.00 0.00 0.00 3.20
1157 1206 3.859414 GCCTCCATGCTCCGCTCT 61.859 66.667 0.00 0.00 0.00 4.09
1719 1774 0.100682 GGCGCAGAAGAGATGTACGA 59.899 55.000 10.83 0.00 0.00 3.43
1868 1926 1.234615 CGGTGAACTTGGTGCGGAAT 61.235 55.000 0.00 0.00 0.00 3.01
1991 2049 1.301677 CCTTGAAGACGCCCTTGCTC 61.302 60.000 0.00 0.00 34.68 4.26
2210 2271 1.127951 GTACCGTTCATGTTGAAGCCG 59.872 52.381 0.00 0.00 37.00 5.52
2294 2355 1.248785 ACGAGGCTCCGTTCAGCTTA 61.249 55.000 9.32 0.00 40.17 3.09
2335 2396 0.040942 TTCTCTGCCTCTGCTCTCCT 59.959 55.000 0.00 0.00 38.71 3.69
2431 2492 2.289756 TGGAACCAACGATCGATCCAAA 60.290 45.455 24.34 3.80 34.21 3.28
2440 2509 7.094506 GGTTAATTTCTTAGTGGAACCAACGAT 60.095 37.037 0.00 0.00 37.80 3.73
2442 2511 6.376177 GGTTAATTTCTTAGTGGAACCAACG 58.624 40.000 0.00 0.00 37.80 4.10
2446 2515 5.326900 TGGGGTTAATTTCTTAGTGGAACC 58.673 41.667 0.00 0.00 37.80 3.62
2447 2516 6.717997 TCTTGGGGTTAATTTCTTAGTGGAAC 59.282 38.462 0.00 0.00 0.00 3.62
2448 2517 6.854578 TCTTGGGGTTAATTTCTTAGTGGAA 58.145 36.000 0.00 0.00 0.00 3.53
2449 2518 6.457159 TCTTGGGGTTAATTTCTTAGTGGA 57.543 37.500 0.00 0.00 0.00 4.02
2450 2519 7.309805 CCTTTCTTGGGGTTAATTTCTTAGTGG 60.310 40.741 0.00 0.00 0.00 4.00
2451 2520 7.309805 CCCTTTCTTGGGGTTAATTTCTTAGTG 60.310 40.741 0.00 0.00 43.45 2.74
2607 2680 1.009829 GGCGGATGCTCAACTTACAG 58.990 55.000 0.00 0.00 42.25 2.74
2609 2682 1.429148 CGGGCGGATGCTCAACTTAC 61.429 60.000 0.00 0.00 43.95 2.34
2610 2683 1.153449 CGGGCGGATGCTCAACTTA 60.153 57.895 0.00 0.00 43.95 2.24
2612 2685 3.665675 GACGGGCGGATGCTCAACT 62.666 63.158 0.00 0.00 43.95 3.16
2613 2686 3.195698 GACGGGCGGATGCTCAAC 61.196 66.667 0.00 0.00 43.95 3.18
2625 2698 1.002033 CTTCTATTACGGACGGACGGG 60.002 57.143 6.00 0.00 38.39 5.28
2669 2749 5.536260 TGAGCATGAGATGATACTACAAGC 58.464 41.667 0.00 0.00 0.00 4.01
2693 2776 2.488937 TCATGAATTCACAGCGCACAAT 59.511 40.909 11.07 0.00 0.00 2.71
2698 2781 1.333524 CCGATCATGAATTCACAGCGC 60.334 52.381 11.07 0.00 0.00 5.92
2699 2782 2.204237 TCCGATCATGAATTCACAGCG 58.796 47.619 11.07 14.33 0.00 5.18
2810 2898 5.815740 TCGCAAAAGGACCATTATTCTACTC 59.184 40.000 0.00 0.00 0.00 2.59
2811 2899 5.741011 TCGCAAAAGGACCATTATTCTACT 58.259 37.500 0.00 0.00 0.00 2.57
2913 3010 3.654414 CCCACGTTAATCTATCTGCTCC 58.346 50.000 0.00 0.00 0.00 4.70
2933 3036 1.344438 AGCTTGGCTTTTGTTTAGGCC 59.656 47.619 0.00 0.00 44.31 5.19
2945 3048 3.713764 AGGTGATGTCTTATAGCTTGGCT 59.286 43.478 0.00 0.00 43.41 4.75
3029 3136 2.364647 CCTCCTCCCTACGTTTCCATAC 59.635 54.545 0.00 0.00 0.00 2.39
3038 3145 3.512219 ATTCTACTCCTCCTCCCTACG 57.488 52.381 0.00 0.00 0.00 3.51
3040 3147 4.286549 CGACTATTCTACTCCTCCTCCCTA 59.713 50.000 0.00 0.00 0.00 3.53
3041 3148 3.073356 CGACTATTCTACTCCTCCTCCCT 59.927 52.174 0.00 0.00 0.00 4.20
3042 3149 3.181441 ACGACTATTCTACTCCTCCTCCC 60.181 52.174 0.00 0.00 0.00 4.30
3043 3150 4.067192 GACGACTATTCTACTCCTCCTCC 58.933 52.174 0.00 0.00 0.00 4.30
3044 3151 3.742369 CGACGACTATTCTACTCCTCCTC 59.258 52.174 0.00 0.00 0.00 3.71
3117 3234 3.217626 GAAAGGGAGCATACATGGAAGG 58.782 50.000 0.00 0.00 0.00 3.46
3151 3268 2.783288 CGGGTTCGGGAGGAGCTAC 61.783 68.421 0.00 0.00 35.75 3.58
3183 3300 4.759205 GGATGGTGGTGGGGTGCC 62.759 72.222 0.00 0.00 0.00 5.01
3186 3303 4.626745 TGGGGATGGTGGTGGGGT 62.627 66.667 0.00 0.00 0.00 4.95
3374 3501 1.468520 GCCATTCACTTTCGCTAAGCA 59.531 47.619 0.00 0.00 37.37 3.91
3396 3523 0.469705 GCCATATTGTCATGCCCCCA 60.470 55.000 0.00 0.00 0.00 4.96
3406 3533 2.638480 ACTACCGCATGCCATATTGT 57.362 45.000 13.15 0.99 0.00 2.71
3409 3536 2.233922 GTCCTACTACCGCATGCCATAT 59.766 50.000 13.15 0.00 0.00 1.78
3410 3537 1.616865 GTCCTACTACCGCATGCCATA 59.383 52.381 13.15 3.65 0.00 2.74


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

AutoCloner maintained by Alex Coulton.