Multiple sequence alignment - TraesCS6B01G303100

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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 TraesCS6B01G303100 chr6B 100.000 3092 0 0 1 3092 542584219 542587310 0.000000e+00 5710.0
1 TraesCS6B01G303100 chr6D 96.286 1804 28 8 649 2424 361379349 361381141 0.000000e+00 2924.0
2 TraesCS6B01G303100 chr6D 94.707 529 17 3 1 525 361378829 361379350 0.000000e+00 811.0
3 TraesCS6B01G303100 chr6D 89.696 427 11 9 2655 3058 361409879 361410295 5.910000e-142 514.0
4 TraesCS6B01G303100 chr6D 96.610 177 6 0 2485 2661 361381137 361381313 8.390000e-76 294.0
5 TraesCS6B01G303100 chr6A 94.911 1749 45 9 649 2366 502365828 502367563 0.000000e+00 2697.0
6 TraesCS6B01G303100 chr6A 92.039 515 18 6 12 525 502365337 502365829 0.000000e+00 702.0
7 TraesCS6B01G303100 chr6A 95.652 437 18 1 2375 2810 502367921 502368357 0.000000e+00 701.0
8 TraesCS6B01G303100 chr6A 95.816 239 10 0 2820 3058 502368552 502368790 1.340000e-103 387.0
9 TraesCS6B01G303100 chr4D 78.715 498 100 5 1577 2071 101436892 101437386 8.270000e-86 327.0
10 TraesCS6B01G303100 chr4B 77.912 498 104 5 1577 2071 145371784 145372278 3.870000e-79 305.0
11 TraesCS6B01G303100 chr4B 97.037 135 4 0 523 657 167941116 167941250 8.630000e-56 228.0
12 TraesCS6B01G303100 chr4B 81.373 102 14 3 265 362 53486685 53486585 9.190000e-11 78.7
13 TraesCS6B01G303100 chr4A 76.861 497 111 4 1586 2080 473946044 473945550 8.440000e-71 278.0
14 TraesCS6B01G303100 chr2B 100.000 127 0 0 524 650 104819465 104819591 5.150000e-58 235.0
15 TraesCS6B01G303100 chr2B 95.139 144 5 2 513 655 97944745 97944887 3.100000e-55 226.0
16 TraesCS6B01G303100 chr2D 95.833 144 4 2 513 655 62390412 62390554 6.670000e-57 231.0
17 TraesCS6B01G303100 chr5B 97.037 135 3 1 524 658 640272741 640272874 3.100000e-55 226.0
18 TraesCS6B01G303100 chr7B 97.692 130 3 0 524 653 295083294 295083165 1.120000e-54 224.0
19 TraesCS6B01G303100 chr3B 96.324 136 5 0 516 651 27494257 27494392 1.120000e-54 224.0
20 TraesCS6B01G303100 chr2A 95.105 143 5 2 513 654 63323082 63323223 1.120000e-54 224.0
21 TraesCS6B01G303100 chr5D 95.070 142 6 1 521 661 447459587 447459728 4.010000e-54 222.0


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 TraesCS6B01G303100 chr6B 542584219 542587310 3091 False 5710.00 5710 100.000000 1 3092 1 chr6B.!!$F1 3091
1 TraesCS6B01G303100 chr6D 361378829 361381313 2484 False 1343.00 2924 95.867667 1 2661 3 chr6D.!!$F2 2660
2 TraesCS6B01G303100 chr6A 502365337 502368790 3453 False 1121.75 2697 94.604500 12 3058 4 chr6A.!!$F1 3046

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
462 467 0.034089 AACTGGTAATGCTCCTGCCC 60.034 55.0 0.0 0.0 38.71 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2406 2792 0.407139 ATTCACAGCTTCTGGGCCTT 59.593 50.0 4.53 0.0 34.42 4.35 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
25 26 1.672356 GTTGCGAGCACATCCCTGT 60.672 57.895 0.00 0.00 35.44 4.00
224 226 2.028420 TCCTCGATTGATGTTGGCTG 57.972 50.000 0.00 0.00 0.00 4.85
233 235 1.468127 TGATGTTGGCTGTTATGTGCG 59.532 47.619 0.00 0.00 0.00 5.34
256 258 2.266554 GTTGCTAGTCTGCTAGTGCTG 58.733 52.381 3.95 0.00 44.93 4.41
300 302 2.035193 TGCGGCTCTAAATCTAGCTCTG 59.965 50.000 0.00 0.00 38.80 3.35
462 467 0.034089 AACTGGTAATGCTCCTGCCC 60.034 55.000 0.00 0.00 38.71 5.36
463 468 1.152881 CTGGTAATGCTCCTGCCCC 60.153 63.158 0.00 0.00 38.71 5.80
464 469 1.925285 CTGGTAATGCTCCTGCCCCA 61.925 60.000 0.00 0.00 38.71 4.96
465 470 1.288508 TGGTAATGCTCCTGCCCCAT 61.289 55.000 0.00 0.00 38.71 4.00
466 471 0.825010 GGTAATGCTCCTGCCCCATG 60.825 60.000 0.00 0.00 38.71 3.66
467 472 0.825010 GTAATGCTCCTGCCCCATGG 60.825 60.000 4.14 4.14 38.71 3.66
529 534 9.262358 CTGCTCTGTTATTATTAACTTACTCCC 57.738 37.037 8.54 0.00 38.81 4.30
530 535 8.989131 TGCTCTGTTATTATTAACTTACTCCCT 58.011 33.333 8.54 0.00 38.81 4.20
531 536 9.478768 GCTCTGTTATTATTAACTTACTCCCTC 57.521 37.037 8.54 0.00 38.81 4.30
532 537 9.984190 CTCTGTTATTATTAACTTACTCCCTCC 57.016 37.037 8.54 0.00 38.81 4.30
533 538 8.636213 TCTGTTATTATTAACTTACTCCCTCCG 58.364 37.037 8.54 0.00 38.81 4.63
534 539 8.310122 TGTTATTATTAACTTACTCCCTCCGT 57.690 34.615 8.54 0.00 38.81 4.69
535 540 8.416329 TGTTATTATTAACTTACTCCCTCCGTC 58.584 37.037 8.54 0.00 38.81 4.79
536 541 5.859205 TTATTAACTTACTCCCTCCGTCC 57.141 43.478 0.00 0.00 0.00 4.79
537 542 2.149973 TAACTTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
538 543 0.115745 AACTTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
539 544 0.115745 ACTTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
540 545 1.272807 CTTACTCCCTCCGTCCCAAA 58.727 55.000 0.00 0.00 0.00 3.28
541 546 1.626825 CTTACTCCCTCCGTCCCAAAA 59.373 52.381 0.00 0.00 0.00 2.44
542 547 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
543 548 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
544 549 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
545 550 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
546 551 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
547 552 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
548 553 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
549 554 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
550 555 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
551 556 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
552 557 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
553 558 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
554 559 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
555 560 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
556 561 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
557 562 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
558 563 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
559 564 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
560 565 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
561 566 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
569 574 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
570 575 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
572 577 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
573 578 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
580 585 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
581 586 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
582 587 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
583 588 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
584 589 7.113124 GTCTAAATACGGATGTATCAAGTCACG 59.887 40.741 0.00 0.00 40.42 4.35
585 590 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
586 591 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
587 592 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
588 593 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
589 594 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
590 595 5.575606 ACGGATGTATCAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
591 596 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
592 597 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
593 598 7.434307 CGGATGTATCAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
594 599 9.095065 GGATGTATCAAGTCACGTTTTAGTATT 57.905 33.333 0.00 0.00 0.00 1.89
597 602 9.577110 TGTATCAAGTCACGTTTTAGTATTAGG 57.423 33.333 0.00 0.00 0.00 2.69
598 603 9.578439 GTATCAAGTCACGTTTTAGTATTAGGT 57.422 33.333 0.00 0.00 0.00 3.08
600 605 8.970691 TCAAGTCACGTTTTAGTATTAGGTAC 57.029 34.615 0.00 0.00 0.00 3.34
601 606 8.575589 TCAAGTCACGTTTTAGTATTAGGTACA 58.424 33.333 0.00 0.00 35.67 2.90
602 607 9.362539 CAAGTCACGTTTTAGTATTAGGTACAT 57.637 33.333 0.00 0.00 35.67 2.29
603 608 9.578439 AAGTCACGTTTTAGTATTAGGTACATC 57.422 33.333 0.00 0.00 35.67 3.06
604 609 8.193438 AGTCACGTTTTAGTATTAGGTACATCC 58.807 37.037 0.00 0.00 35.67 3.51
605 610 7.166473 GTCACGTTTTAGTATTAGGTACATCCG 59.834 40.741 0.00 0.00 41.99 4.18
606 611 6.974622 CACGTTTTAGTATTAGGTACATCCGT 59.025 38.462 0.00 0.00 41.99 4.69
607 612 8.128582 CACGTTTTAGTATTAGGTACATCCGTA 58.871 37.037 0.00 0.00 41.99 4.02
608 613 8.850156 ACGTTTTAGTATTAGGTACATCCGTAT 58.150 33.333 0.00 0.00 41.99 3.06
609 614 9.334693 CGTTTTAGTATTAGGTACATCCGTATC 57.665 37.037 0.00 0.00 41.99 2.24
615 620 8.600668 AGTATTAGGTACATCCGTATCTAGACA 58.399 37.037 0.00 0.00 41.33 3.41
616 621 9.224267 GTATTAGGTACATCCGTATCTAGACAA 57.776 37.037 0.00 0.00 41.33 3.18
617 622 8.701908 ATTAGGTACATCCGTATCTAGACAAA 57.298 34.615 0.00 0.00 41.33 2.83
618 623 8.701908 TTAGGTACATCCGTATCTAGACAAAT 57.298 34.615 0.00 0.00 41.33 2.32
619 624 7.598759 AGGTACATCCGTATCTAGACAAATT 57.401 36.000 0.00 0.00 37.29 1.82
620 625 8.019656 AGGTACATCCGTATCTAGACAAATTT 57.980 34.615 0.00 0.00 37.29 1.82
621 626 9.139734 AGGTACATCCGTATCTAGACAAATTTA 57.860 33.333 0.00 0.00 37.29 1.40
622 627 9.754382 GGTACATCCGTATCTAGACAAATTTAA 57.246 33.333 0.00 0.00 0.00 1.52
625 630 9.530633 ACATCCGTATCTAGACAAATTTAAGAC 57.469 33.333 0.00 0.00 0.00 3.01
626 631 9.529325 CATCCGTATCTAGACAAATTTAAGACA 57.471 33.333 0.00 0.00 0.00 3.41
641 646 8.996024 AATTTAAGACAATAATTTTGGGACGG 57.004 30.769 0.00 0.00 0.00 4.79
642 647 7.762588 TTTAAGACAATAATTTTGGGACGGA 57.237 32.000 0.00 0.00 0.00 4.69
643 648 5.897377 AAGACAATAATTTTGGGACGGAG 57.103 39.130 0.00 0.00 0.00 4.63
644 649 4.270008 AGACAATAATTTTGGGACGGAGG 58.730 43.478 0.00 0.00 0.00 4.30
645 650 3.361786 ACAATAATTTTGGGACGGAGGG 58.638 45.455 0.00 0.00 0.00 4.30
646 651 3.010808 ACAATAATTTTGGGACGGAGGGA 59.989 43.478 0.00 0.00 0.00 4.20
647 652 3.577805 ATAATTTTGGGACGGAGGGAG 57.422 47.619 0.00 0.00 0.00 4.30
653 658 3.339713 TTGGGACGGAGGGAGTATTAT 57.660 47.619 0.00 0.00 0.00 1.28
790 798 5.048921 ACTTCTCAGCTTTTCACACATCATG 60.049 40.000 0.00 0.00 0.00 3.07
816 824 1.303643 CTTGCTCCCAACCCCTCAC 60.304 63.158 0.00 0.00 0.00 3.51
868 876 7.992008 TGTTCTCTTGTTTTTCCTAAATTCGT 58.008 30.769 0.00 0.00 0.00 3.85
928 936 3.316308 CCAAGCCCAATGCATAGAGTTAC 59.684 47.826 0.00 0.00 44.83 2.50
929 937 4.202441 CAAGCCCAATGCATAGAGTTACT 58.798 43.478 0.00 0.00 44.83 2.24
930 938 4.078639 AGCCCAATGCATAGAGTTACTC 57.921 45.455 3.85 3.85 44.83 2.59
971 979 6.264292 GTCTATGTTCCTCTCTTATGCTCAGA 59.736 42.308 0.00 0.00 0.00 3.27
991 999 4.406972 CAGATCCACACTATCCCTTCTTGA 59.593 45.833 0.00 0.00 0.00 3.02
1263 1295 0.677414 TCATGAGCAGCAATGCCGAA 60.677 50.000 0.00 0.00 34.90 4.30
1417 1449 1.151668 CAGTCTTGAGGCGAAACCAG 58.848 55.000 0.00 0.00 43.14 4.00
1551 1583 1.372582 TCATGGAGCATCTCGCAAAC 58.627 50.000 0.00 0.00 46.13 2.93
1691 1723 2.102084 CGATGAAGGAGAAGAGGATGCA 59.898 50.000 0.00 0.00 0.00 3.96
1858 1890 4.651867 CCATGGACAGGCTGAAGG 57.348 61.111 23.66 10.90 0.00 3.46
1867 1899 2.744202 GACAGGCTGAAGGTTATGTGTG 59.256 50.000 23.66 0.00 0.00 3.82
2001 2033 7.098477 CCTCTTCAGATAAGATGGATGATGTC 58.902 42.308 0.00 0.00 0.00 3.06
2091 2126 1.694150 AGAAGCAGGCCTCGCATATAA 59.306 47.619 23.46 0.00 0.00 0.98
2325 2361 1.937899 ACAACCGTGCTGTTAACTGTC 59.062 47.619 13.27 7.05 0.00 3.51
2373 2409 7.603784 GTCACATCATATACAATCTGGTGCATA 59.396 37.037 0.00 0.00 0.00 3.14
2472 2858 7.931578 TTCGGAAACTTATATGATTGGTTGT 57.068 32.000 0.00 0.00 0.00 3.32
2474 2860 9.621629 TTCGGAAACTTATATGATTGGTTGTAT 57.378 29.630 0.00 0.00 0.00 2.29
2577 2963 2.175202 ACTACTGAACTGAGCCTGGAG 58.825 52.381 0.00 0.00 0.00 3.86
2671 3057 3.446161 GCCAAACCAGGTTTTACTATCCC 59.554 47.826 15.51 0.00 33.10 3.85
2681 3067 5.367060 AGGTTTTACTATCCCAGATCAGGAC 59.633 44.000 5.57 0.00 35.85 3.85
2685 3071 8.652290 GTTTTACTATCCCAGATCAGGACTAAT 58.348 37.037 5.57 0.00 35.85 1.73
2745 3131 7.233389 ACTGATGTAGTCTGTGTTAATCTGT 57.767 36.000 0.00 0.00 37.58 3.41
2795 3181 7.616150 AGAGTAAGTAAGAATGGTAGAAGCTCA 59.384 37.037 0.00 0.00 0.00 4.26
2810 3196 4.335874 AGAAGCTCAGCATTAAGCATCTTG 59.664 41.667 0.00 0.00 42.19 3.02
2811 3197 5.860714 AGAAGCTCAGCATTAAGCATCTTGA 60.861 40.000 0.00 0.00 42.19 3.02
2812 3198 7.300991 AGAAGCTCAGCATTAAGCATCTTGAA 61.301 38.462 0.00 0.00 42.19 2.69
2813 3199 9.014816 AGAAGCTCAGCATTAAGCATCTTGAAG 62.015 40.741 0.00 0.00 42.19 3.02
2915 3486 6.790285 AGCAATGCCAAGAAAATAGTTTTG 57.210 33.333 0.00 0.00 31.94 2.44
2937 3508 4.202284 TGAGGTTAACTTTACGGAACAGCT 60.202 41.667 5.42 0.00 0.00 4.24
2943 3514 5.413969 AACTTTACGGAACAGCTTAACAC 57.586 39.130 0.00 0.00 0.00 3.32
3041 3612 0.924090 CGGTAGATCGTGAAAGCAGC 59.076 55.000 0.00 0.00 0.00 5.25
3042 3613 0.924090 GGTAGATCGTGAAAGCAGCG 59.076 55.000 0.00 0.00 0.00 5.18
3043 3614 0.924090 GTAGATCGTGAAAGCAGCGG 59.076 55.000 0.00 0.00 0.00 5.52
3061 3632 3.896317 GGCTCACCCGATCTATGAC 57.104 57.895 0.00 0.00 0.00 3.06
3062 3633 1.040646 GGCTCACCCGATCTATGACA 58.959 55.000 0.00 0.00 0.00 3.58
3063 3634 1.412710 GGCTCACCCGATCTATGACAA 59.587 52.381 0.00 0.00 0.00 3.18
3064 3635 2.474816 GCTCACCCGATCTATGACAAC 58.525 52.381 0.00 0.00 0.00 3.32
3065 3636 2.159099 GCTCACCCGATCTATGACAACA 60.159 50.000 0.00 0.00 0.00 3.33
3066 3637 3.493350 GCTCACCCGATCTATGACAACAT 60.493 47.826 0.00 0.00 40.16 2.71
3067 3638 4.262036 GCTCACCCGATCTATGACAACATA 60.262 45.833 0.00 0.00 37.87 2.29
3068 3639 5.567623 GCTCACCCGATCTATGACAACATAT 60.568 44.000 0.00 0.00 38.17 1.78
3069 3640 5.783111 TCACCCGATCTATGACAACATATG 58.217 41.667 0.00 0.00 38.17 1.78
3070 3641 4.931601 CACCCGATCTATGACAACATATGG 59.068 45.833 7.80 0.00 38.17 2.74
3071 3642 4.020218 ACCCGATCTATGACAACATATGGG 60.020 45.833 7.80 1.27 39.78 4.00
3072 3643 4.020218 CCCGATCTATGACAACATATGGGT 60.020 45.833 7.80 4.80 38.17 4.51
3073 3644 5.171476 CCGATCTATGACAACATATGGGTC 58.829 45.833 17.94 17.94 38.17 4.46
3074 3645 5.279456 CCGATCTATGACAACATATGGGTCA 60.279 44.000 25.26 25.26 44.73 4.02
3075 3646 5.635280 CGATCTATGACAACATATGGGTCAC 59.365 44.000 25.45 15.75 43.58 3.67
3076 3647 5.290493 TCTATGACAACATATGGGTCACC 57.710 43.478 25.45 7.13 43.58 4.02
3077 3648 4.968719 TCTATGACAACATATGGGTCACCT 59.031 41.667 25.45 17.17 43.58 4.00
3078 3649 4.591321 ATGACAACATATGGGTCACCTT 57.409 40.909 25.45 13.46 43.58 3.50
3079 3650 3.950397 TGACAACATATGGGTCACCTTC 58.050 45.455 21.58 3.73 36.69 3.46
3080 3651 3.587061 TGACAACATATGGGTCACCTTCT 59.413 43.478 21.58 0.00 36.69 2.85
3081 3652 4.042809 TGACAACATATGGGTCACCTTCTT 59.957 41.667 21.58 0.00 36.69 2.52
3082 3653 5.249622 TGACAACATATGGGTCACCTTCTTA 59.750 40.000 21.58 4.17 36.69 2.10
3083 3654 6.069673 TGACAACATATGGGTCACCTTCTTAT 60.070 38.462 21.58 0.00 36.69 1.73
3084 3655 6.122277 ACAACATATGGGTCACCTTCTTATG 58.878 40.000 7.80 0.00 37.76 1.90
3085 3656 6.069673 ACAACATATGGGTCACCTTCTTATGA 60.070 38.462 7.80 0.00 37.76 2.15
3086 3657 6.179906 ACATATGGGTCACCTTCTTATGAG 57.820 41.667 7.80 0.00 37.76 2.90
3087 3658 3.567478 ATGGGTCACCTTCTTATGAGC 57.433 47.619 0.00 0.00 41.56 4.26
3088 3659 2.265367 TGGGTCACCTTCTTATGAGCA 58.735 47.619 0.00 0.00 43.57 4.26
3089 3660 2.846206 TGGGTCACCTTCTTATGAGCAT 59.154 45.455 0.00 0.00 43.57 3.79
3090 3661 3.266772 TGGGTCACCTTCTTATGAGCATT 59.733 43.478 0.00 0.00 43.57 3.56
3091 3662 4.473196 TGGGTCACCTTCTTATGAGCATTA 59.527 41.667 0.00 0.00 43.57 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
224 226 2.073816 ACTAGCAACACCGCACATAAC 58.926 47.619 0.00 0.00 0.00 1.89
256 258 6.389906 CAAGTTCCTCCAATTGTGTTAATCC 58.610 40.000 4.43 0.00 0.00 3.01
439 444 2.351726 GCAGGAGCATTACCAGTTTACG 59.648 50.000 0.00 0.00 41.58 3.18
523 528 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
524 529 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
525 530 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
526 531 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
527 532 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
528 533 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
529 534 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
530 535 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
531 536 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
532 537 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
533 538 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
534 539 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
535 540 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
543 548 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
544 549 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
546 551 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
547 552 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
554 559 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
555 560 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
556 561 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
557 562 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
558 563 7.113124 CGTGACTTGATACATCCGTATTTAGAC 59.887 40.741 0.00 0.00 38.48 2.59
559 564 7.136772 CGTGACTTGATACATCCGTATTTAGA 58.863 38.462 0.00 0.00 38.48 2.10
560 565 6.916387 ACGTGACTTGATACATCCGTATTTAG 59.084 38.462 0.00 0.00 38.48 1.85
561 566 6.798482 ACGTGACTTGATACATCCGTATTTA 58.202 36.000 0.00 0.00 38.48 1.40
562 567 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
563 568 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
564 569 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
565 570 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
566 571 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
567 572 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
568 573 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
571 576 9.577110 CCTAATACTAAAACGTGACTTGATACA 57.423 33.333 0.00 0.00 0.00 2.29
572 577 9.578439 ACCTAATACTAAAACGTGACTTGATAC 57.422 33.333 0.00 0.00 0.00 2.24
574 579 9.578439 GTACCTAATACTAAAACGTGACTTGAT 57.422 33.333 0.00 0.00 0.00 2.57
575 580 8.575589 TGTACCTAATACTAAAACGTGACTTGA 58.424 33.333 0.00 0.00 34.56 3.02
576 581 8.746922 TGTACCTAATACTAAAACGTGACTTG 57.253 34.615 0.00 0.00 34.56 3.16
577 582 9.578439 GATGTACCTAATACTAAAACGTGACTT 57.422 33.333 0.00 0.00 34.56 3.01
578 583 8.193438 GGATGTACCTAATACTAAAACGTGACT 58.807 37.037 0.00 0.00 34.56 3.41
579 584 7.166473 CGGATGTACCTAATACTAAAACGTGAC 59.834 40.741 0.00 0.00 34.56 3.67
580 585 7.148086 ACGGATGTACCTAATACTAAAACGTGA 60.148 37.037 0.00 0.00 34.56 4.35
581 586 6.974622 ACGGATGTACCTAATACTAAAACGTG 59.025 38.462 0.00 0.00 34.56 4.49
582 587 7.100458 ACGGATGTACCTAATACTAAAACGT 57.900 36.000 0.00 0.00 34.56 3.99
583 588 9.334693 GATACGGATGTACCTAATACTAAAACG 57.665 37.037 0.00 0.00 34.56 3.60
589 594 8.600668 TGTCTAGATACGGATGTACCTAATACT 58.399 37.037 0.00 0.00 34.56 2.12
590 595 8.783833 TGTCTAGATACGGATGTACCTAATAC 57.216 38.462 0.00 0.00 36.31 1.89
591 596 9.797642 TTTGTCTAGATACGGATGTACCTAATA 57.202 33.333 0.00 0.00 36.31 0.98
592 597 8.701908 TTTGTCTAGATACGGATGTACCTAAT 57.298 34.615 0.00 0.00 36.31 1.73
593 598 8.701908 ATTTGTCTAGATACGGATGTACCTAA 57.298 34.615 0.00 0.00 36.31 2.69
594 599 8.701908 AATTTGTCTAGATACGGATGTACCTA 57.298 34.615 0.00 0.00 36.31 3.08
595 600 7.598759 AATTTGTCTAGATACGGATGTACCT 57.401 36.000 0.00 0.00 36.31 3.08
596 601 9.754382 TTAAATTTGTCTAGATACGGATGTACC 57.246 33.333 0.00 0.00 32.26 3.34
599 604 9.530633 GTCTTAAATTTGTCTAGATACGGATGT 57.469 33.333 0.00 0.00 0.00 3.06
600 605 9.529325 TGTCTTAAATTTGTCTAGATACGGATG 57.471 33.333 0.00 0.00 0.00 3.51
615 620 9.430623 CCGTCCCAAAATTATTGTCTTAAATTT 57.569 29.630 0.00 0.00 35.01 1.82
616 621 8.808092 TCCGTCCCAAAATTATTGTCTTAAATT 58.192 29.630 0.00 0.00 0.00 1.82
617 622 8.356000 TCCGTCCCAAAATTATTGTCTTAAAT 57.644 30.769 0.00 0.00 0.00 1.40
618 623 7.094118 CCTCCGTCCCAAAATTATTGTCTTAAA 60.094 37.037 0.00 0.00 0.00 1.52
619 624 6.376018 CCTCCGTCCCAAAATTATTGTCTTAA 59.624 38.462 0.00 0.00 0.00 1.85
620 625 5.883673 CCTCCGTCCCAAAATTATTGTCTTA 59.116 40.000 0.00 0.00 0.00 2.10
621 626 4.705023 CCTCCGTCCCAAAATTATTGTCTT 59.295 41.667 0.00 0.00 0.00 3.01
622 627 4.270008 CCTCCGTCCCAAAATTATTGTCT 58.730 43.478 0.00 0.00 0.00 3.41
623 628 3.380320 CCCTCCGTCCCAAAATTATTGTC 59.620 47.826 0.00 0.00 0.00 3.18
624 629 3.010808 TCCCTCCGTCCCAAAATTATTGT 59.989 43.478 0.00 0.00 0.00 2.71
625 630 3.626930 TCCCTCCGTCCCAAAATTATTG 58.373 45.455 0.00 0.00 0.00 1.90
626 631 3.268595 ACTCCCTCCGTCCCAAAATTATT 59.731 43.478 0.00 0.00 0.00 1.40
627 632 2.850568 ACTCCCTCCGTCCCAAAATTAT 59.149 45.455 0.00 0.00 0.00 1.28
628 633 2.271777 ACTCCCTCCGTCCCAAAATTA 58.728 47.619 0.00 0.00 0.00 1.40
629 634 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
630 635 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
631 636 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
632 637 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
633 638 2.852714 TAATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
634 639 3.339713 AATAATACTCCCTCCGTCCCA 57.660 47.619 0.00 0.00 0.00 4.37
635 640 4.701651 AAAATAATACTCCCTCCGTCCC 57.298 45.455 0.00 0.00 0.00 4.46
636 641 5.699915 GCTAAAAATAATACTCCCTCCGTCC 59.300 44.000 0.00 0.00 0.00 4.79
637 642 5.699915 GGCTAAAAATAATACTCCCTCCGTC 59.300 44.000 0.00 0.00 0.00 4.79
638 643 5.131475 TGGCTAAAAATAATACTCCCTCCGT 59.869 40.000 0.00 0.00 0.00 4.69
639 644 5.617252 TGGCTAAAAATAATACTCCCTCCG 58.383 41.667 0.00 0.00 0.00 4.63
640 645 6.016192 GCTTGGCTAAAAATAATACTCCCTCC 60.016 42.308 0.00 0.00 0.00 4.30
641 646 6.773200 AGCTTGGCTAAAAATAATACTCCCTC 59.227 38.462 0.00 0.00 36.99 4.30
642 647 6.673583 AGCTTGGCTAAAAATAATACTCCCT 58.326 36.000 0.00 0.00 36.99 4.20
643 648 6.961360 AGCTTGGCTAAAAATAATACTCCC 57.039 37.500 0.00 0.00 36.99 4.30
644 649 7.501225 TGGTAGCTTGGCTAAAAATAATACTCC 59.499 37.037 0.00 0.00 43.07 3.85
645 650 8.343366 GTGGTAGCTTGGCTAAAAATAATACTC 58.657 37.037 0.00 0.00 43.07 2.59
646 651 8.053355 AGTGGTAGCTTGGCTAAAAATAATACT 58.947 33.333 0.00 0.00 43.07 2.12
647 652 8.221965 AGTGGTAGCTTGGCTAAAAATAATAC 57.778 34.615 0.00 0.00 43.07 1.89
790 798 1.228245 TTGGGAGCAAGCAGACCAC 60.228 57.895 0.00 0.00 0.00 4.16
868 876 9.141400 GTTTACACAAATTAACCAAAGTTGACA 57.859 29.630 5.09 0.00 44.07 3.58
928 936 3.749226 AGACAGCTTTTTCAAGGAGGAG 58.251 45.455 0.00 0.00 0.00 3.69
929 937 3.864789 AGACAGCTTTTTCAAGGAGGA 57.135 42.857 0.00 0.00 0.00 3.71
930 938 5.006386 ACATAGACAGCTTTTTCAAGGAGG 58.994 41.667 0.00 0.00 0.00 4.30
971 979 5.779241 TTTCAAGAAGGGATAGTGTGGAT 57.221 39.130 0.00 0.00 0.00 3.41
991 999 6.015918 TCCTGTCCACAACCATGATTAATTT 58.984 36.000 0.00 0.00 0.00 1.82
1263 1295 1.298859 GCCGAAAGAATGTCCGCACT 61.299 55.000 0.00 0.00 0.00 4.40
1272 1304 2.807676 ACCAATCCAAGCCGAAAGAAT 58.192 42.857 0.00 0.00 0.00 2.40
1495 1527 2.517959 CTCAATTTCAGAGTGCCCCAA 58.482 47.619 0.00 0.00 0.00 4.12
1551 1583 2.257207 TCCTCCTTAGTGTCCAACAGG 58.743 52.381 0.00 0.00 0.00 4.00
1691 1723 4.261741 GCATGTCTTTGATGGTCAAACACT 60.262 41.667 10.61 0.00 41.02 3.55
1858 1890 4.923281 GCCAAGGATGTTTTCACACATAAC 59.077 41.667 0.00 0.00 37.52 1.89
1867 1899 3.823304 AGACTCTTGCCAAGGATGTTTTC 59.177 43.478 4.30 0.00 0.00 2.29
2001 2033 1.668628 GCATAACCTTTGGTTGCCACG 60.669 52.381 11.78 0.00 46.35 4.94
2395 2781 6.716628 CAGCTTCTGGGCCTTGAATAATTATA 59.283 38.462 4.53 0.00 0.00 0.98
2406 2792 0.407139 ATTCACAGCTTCTGGGCCTT 59.593 50.000 4.53 0.00 34.42 4.35
2577 2963 8.733458 ACCGAATAAATTGAGTAAACTTTACCC 58.267 33.333 7.89 0.00 0.00 3.69
2633 3019 2.806945 TGGCCTTTGGAGTAAGATGG 57.193 50.000 3.32 0.00 0.00 3.51
2671 3057 4.700700 TGATGTGCATTAGTCCTGATCTG 58.299 43.478 0.00 0.00 0.00 2.90
2681 3067 5.047802 ACCTTTCCAGTTTGATGTGCATTAG 60.048 40.000 0.00 0.00 0.00 1.73
2685 3071 2.665165 ACCTTTCCAGTTTGATGTGCA 58.335 42.857 0.00 0.00 0.00 4.57
2784 3170 3.535561 TGCTTAATGCTGAGCTTCTACC 58.464 45.455 5.83 0.00 43.37 3.18
2785 3171 5.055812 AGATGCTTAATGCTGAGCTTCTAC 58.944 41.667 5.83 0.00 45.76 2.59
2795 3181 5.408356 CAAAGCTTCAAGATGCTTAATGCT 58.592 37.500 19.41 5.22 46.73 3.79
2843 3414 2.822561 TGATTTTGTTCGGGCTTATGCA 59.177 40.909 2.72 0.00 41.91 3.96
2915 3486 4.313282 AGCTGTTCCGTAAAGTTAACCTC 58.687 43.478 0.88 0.00 0.00 3.85
2937 3508 4.515361 TCTCAAAAGGTTCCGTGTGTTAA 58.485 39.130 0.00 0.00 0.00 2.01
2943 3514 8.673711 TGAATAATAATCTCAAAAGGTTCCGTG 58.326 33.333 0.00 0.00 0.00 4.94
2996 3567 2.361104 TTCCTGTTGCATCCGGGC 60.361 61.111 0.00 0.00 0.00 6.13
3043 3614 1.040646 TGTCATAGATCGGGTGAGCC 58.959 55.000 0.00 0.00 0.00 4.70
3050 3621 5.152623 ACCCATATGTTGTCATAGATCGG 57.847 43.478 1.24 0.00 39.49 4.18
3058 3629 3.587061 AGAAGGTGACCCATATGTTGTCA 59.413 43.478 16.97 16.97 36.71 3.58
3059 3630 4.222124 AGAAGGTGACCCATATGTTGTC 57.778 45.455 13.14 13.14 0.00 3.18
3060 3631 4.657814 AAGAAGGTGACCCATATGTTGT 57.342 40.909 0.00 0.00 0.00 3.32
3061 3632 6.356556 TCATAAGAAGGTGACCCATATGTTG 58.643 40.000 0.00 0.00 0.00 3.33
3062 3633 6.575244 TCATAAGAAGGTGACCCATATGTT 57.425 37.500 0.00 0.00 0.00 2.71
3063 3634 5.455326 GCTCATAAGAAGGTGACCCATATGT 60.455 44.000 0.00 0.00 0.00 2.29
3064 3635 4.999950 GCTCATAAGAAGGTGACCCATATG 59.000 45.833 0.00 2.80 0.00 1.78
3065 3636 4.660303 TGCTCATAAGAAGGTGACCCATAT 59.340 41.667 0.00 0.00 0.00 1.78
3066 3637 4.037222 TGCTCATAAGAAGGTGACCCATA 58.963 43.478 0.00 0.00 0.00 2.74
3067 3638 2.846206 TGCTCATAAGAAGGTGACCCAT 59.154 45.455 0.00 0.00 0.00 4.00
3068 3639 2.265367 TGCTCATAAGAAGGTGACCCA 58.735 47.619 0.00 0.00 0.00 4.51
3069 3640 3.567478 ATGCTCATAAGAAGGTGACCC 57.433 47.619 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.