Multiple sequence alignment - TraesCS6B01G307700

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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 TraesCS6B01G307700 chr6B 100.000 3479 0 0 1 3479 551791858 551795336 0.000000e+00 6425.0
1 TraesCS6B01G307700 chr6B 90.909 176 16 0 577 752 233030266 233030091 1.610000e-58 237.0
2 TraesCS6B01G307700 chr4D 94.542 1191 61 2 969 2156 57475346 57476535 0.000000e+00 1836.0
3 TraesCS6B01G307700 chr4D 89.295 766 48 17 2713 3461 57477076 57477824 0.000000e+00 929.0
4 TraesCS6B01G307700 chr4D 94.813 482 22 2 2153 2633 57476562 57477041 0.000000e+00 749.0
5 TraesCS6B01G307700 chr4D 85.738 596 31 18 2 591 57474494 57475041 6.470000e-162 580.0
6 TraesCS6B01G307700 chr4D 89.407 236 11 6 749 972 57475038 57475271 5.680000e-73 285.0
7 TraesCS6B01G307700 chr4D 94.118 34 2 0 2664 2697 57477039 57477072 6.000000e-03 52.8
8 TraesCS6B01G307700 chr4A 93.929 1186 68 2 972 2154 539299332 539298148 0.000000e+00 1788.0
9 TraesCS6B01G307700 chr4A 95.316 491 18 3 2156 2645 539298116 539297630 0.000000e+00 774.0
10 TraesCS6B01G307700 chr4A 91.211 512 36 7 2663 3171 539297642 539297137 0.000000e+00 688.0
11 TraesCS6B01G307700 chr4A 87.667 600 45 14 2 591 539300202 539299622 0.000000e+00 671.0
12 TraesCS6B01G307700 chr4A 91.284 218 13 1 755 972 539299621 539299410 3.400000e-75 292.0
13 TraesCS6B01G307700 chr4A 87.352 253 10 13 3245 3479 539297136 539296888 1.590000e-68 270.0
14 TraesCS6B01G307700 chr4A 91.813 171 14 0 581 751 87406082 87406252 4.490000e-59 239.0
15 TraesCS6B01G307700 chr4B 94.902 1020 51 1 969 1988 86061905 86062923 0.000000e+00 1594.0
16 TraesCS6B01G307700 chr4B 92.308 832 50 9 2660 3479 86063071 86063900 0.000000e+00 1170.0
17 TraesCS6B01G307700 chr4B 90.878 581 30 10 2 580 86061042 86061601 0.000000e+00 758.0
18 TraesCS6B01G307700 chr4B 95.376 173 4 3 2475 2645 86062917 86063087 4.420000e-69 272.0
19 TraesCS6B01G307700 chr4B 88.789 223 11 3 755 972 86061617 86061830 9.580000e-66 261.0
20 TraesCS6B01G307700 chr5A 95.152 165 8 0 587 751 82305599 82305763 9.580000e-66 261.0
21 TraesCS6B01G307700 chr5A 92.771 166 12 0 586 751 269823460 269823295 1.250000e-59 241.0
22 TraesCS6B01G307700 chr2B 93.902 164 10 0 588 751 214378248 214378085 7.460000e-62 248.0
23 TraesCS6B01G307700 chr5B 93.373 166 11 0 589 754 145828344 145828179 2.680000e-61 246.0
24 TraesCS6B01G307700 chr1D 91.908 173 13 1 588 760 175953969 175954140 1.250000e-59 241.0
25 TraesCS6B01G307700 chr6D 92.073 164 13 0 589 752 90890444 90890281 7.510000e-57 231.0
26 TraesCS6B01G307700 chr3D 88.889 189 17 4 565 751 547631262 547631448 2.700000e-56 230.0


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 TraesCS6B01G307700 chr6B 551791858 551795336 3478 False 6425.000000 6425 100.000000 1 3479 1 chr6B.!!$F1 3478
1 TraesCS6B01G307700 chr4D 57474494 57477824 3330 False 738.633333 1836 91.318833 2 3461 6 chr4D.!!$F1 3459
2 TraesCS6B01G307700 chr4A 539296888 539300202 3314 True 747.166667 1788 91.126500 2 3479 6 chr4A.!!$R1 3477
3 TraesCS6B01G307700 chr4B 86061042 86063900 2858 False 811.000000 1594 92.450600 2 3479 5 chr4B.!!$F1 3477

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
842 906 0.548926 TCCAACAGATGCCCCCTACA 60.549 55.0 0.0 0.0 0.0 2.74 F
1829 1974 0.524392 CACGAGCTTGCTAGGAGTCG 60.524 60.0 0.0 10.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 2197 0.108329 CCACTAGAACCGCGGTCAAT 60.108 55.0 34.29 22.21 0.00 2.57 R
2886 3065 0.106669 TCCTCACCGATCACCGATCT 60.107 55.0 2.74 0.00 41.76 2.75 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
72 73 2.102252 GCTCCAGAAGATGAAGACGGAT 59.898 50.000 0.00 0.00 0.00 4.18
85 86 1.003580 AGACGGATGCAACCAATGAGT 59.996 47.619 14.03 1.88 0.00 3.41
260 270 4.663334 TCCAGAGTCTCTAGCAACACTAA 58.337 43.478 0.94 0.00 0.00 2.24
307 322 6.051717 TGAGAAGTCCAGAGAAGAGTTTTTG 58.948 40.000 0.00 0.00 0.00 2.44
316 331 4.346418 AGAGAAGAGTTTTTGGCTGAGAGA 59.654 41.667 0.00 0.00 0.00 3.10
317 332 5.012975 AGAGAAGAGTTTTTGGCTGAGAGAT 59.987 40.000 0.00 0.00 0.00 2.75
318 333 5.629125 AGAAGAGTTTTTGGCTGAGAGATT 58.371 37.500 0.00 0.00 0.00 2.40
319 334 6.773638 AGAAGAGTTTTTGGCTGAGAGATTA 58.226 36.000 0.00 0.00 0.00 1.75
320 335 7.227156 AGAAGAGTTTTTGGCTGAGAGATTAA 58.773 34.615 0.00 0.00 0.00 1.40
321 336 7.887495 AGAAGAGTTTTTGGCTGAGAGATTAAT 59.113 33.333 0.00 0.00 0.00 1.40
322 337 7.388460 AGAGTTTTTGGCTGAGAGATTAATG 57.612 36.000 0.00 0.00 0.00 1.90
323 338 6.944862 AGAGTTTTTGGCTGAGAGATTAATGT 59.055 34.615 0.00 0.00 0.00 2.71
324 339 6.917533 AGTTTTTGGCTGAGAGATTAATGTG 58.082 36.000 0.00 0.00 0.00 3.21
325 340 6.491403 AGTTTTTGGCTGAGAGATTAATGTGT 59.509 34.615 0.00 0.00 0.00 3.72
326 341 6.500684 TTTTGGCTGAGAGATTAATGTGTC 57.499 37.500 3.03 3.03 0.00 3.67
327 342 5.426689 TTGGCTGAGAGATTAATGTGTCT 57.573 39.130 10.55 2.04 0.00 3.41
328 343 6.544928 TTGGCTGAGAGATTAATGTGTCTA 57.455 37.500 10.55 0.00 0.00 2.59
329 344 6.544928 TGGCTGAGAGATTAATGTGTCTAA 57.455 37.500 10.55 0.00 0.00 2.10
330 345 6.946340 TGGCTGAGAGATTAATGTGTCTAAA 58.054 36.000 10.55 0.00 0.00 1.85
331 346 7.568349 TGGCTGAGAGATTAATGTGTCTAAAT 58.432 34.615 10.55 0.00 0.00 1.40
332 347 7.496920 TGGCTGAGAGATTAATGTGTCTAAATG 59.503 37.037 10.55 0.00 0.00 2.32
333 348 7.041508 GGCTGAGAGATTAATGTGTCTAAATGG 60.042 40.741 10.55 0.00 0.00 3.16
334 349 7.519649 GCTGAGAGATTAATGTGTCTAAATGGC 60.520 40.741 10.55 3.33 0.00 4.40
335 350 7.568349 TGAGAGATTAATGTGTCTAAATGGCT 58.432 34.615 10.55 0.00 0.00 4.75
336 351 7.712639 TGAGAGATTAATGTGTCTAAATGGCTC 59.287 37.037 10.55 0.00 0.00 4.70
337 352 6.995091 AGAGATTAATGTGTCTAAATGGCTCC 59.005 38.462 0.00 0.00 0.00 4.70
338 353 5.760253 AGATTAATGTGTCTAAATGGCTCCG 59.240 40.000 0.00 0.00 0.00 4.63
339 354 1.668419 ATGTGTCTAAATGGCTCCGC 58.332 50.000 0.00 0.00 0.00 5.54
340 355 0.739462 TGTGTCTAAATGGCTCCGCG 60.739 55.000 0.00 0.00 0.00 6.46
346 386 2.364324 TCTAAATGGCTCCGCGATACTT 59.636 45.455 8.23 0.00 0.00 2.24
394 434 6.381481 TTGCATAGCACATCCTTTATCTTG 57.619 37.500 0.00 0.00 38.71 3.02
495 539 5.608676 TGGCACAAATTTGCATACAATTG 57.391 34.783 18.12 3.24 44.94 2.32
496 540 5.061853 TGGCACAAATTTGCATACAATTGT 58.938 33.333 18.12 16.68 44.94 2.71
497 541 5.530171 TGGCACAAATTTGCATACAATTGTT 59.470 32.000 17.78 1.87 44.94 2.83
498 542 6.707608 TGGCACAAATTTGCATACAATTGTTA 59.292 30.769 17.78 3.36 44.94 2.41
564 617 5.916318 TCAAATGTCTCAAGCAAACCAAAT 58.084 33.333 0.00 0.00 0.00 2.32
602 655 2.845363 TTTTGTACTCCCTCCGTTCC 57.155 50.000 0.00 0.00 0.00 3.62
603 656 2.019807 TTTGTACTCCCTCCGTTCCT 57.980 50.000 0.00 0.00 0.00 3.36
604 657 2.905415 TTGTACTCCCTCCGTTCCTA 57.095 50.000 0.00 0.00 0.00 2.94
605 658 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
606 659 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
607 660 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
608 661 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
609 662 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
610 663 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
611 664 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
612 665 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
613 666 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
614 667 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
615 668 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
616 669 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
617 670 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
618 671 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
619 672 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
681 734 9.798994 AGATGCATTTCAAGTTTAGATTCATTC 57.201 29.630 0.00 0.00 0.00 2.67
682 735 9.577110 GATGCATTTCAAGTTTAGATTCATTCA 57.423 29.630 0.00 0.00 0.00 2.57
684 737 9.932207 TGCATTTCAAGTTTAGATTCATTCATT 57.068 25.926 0.00 0.00 0.00 2.57
689 742 9.985730 TTCAAGTTTAGATTCATTCATTTTGCT 57.014 25.926 0.00 0.00 0.00 3.91
690 743 9.630098 TCAAGTTTAGATTCATTCATTTTGCTC 57.370 29.630 0.00 0.00 0.00 4.26
691 744 8.866956 CAAGTTTAGATTCATTCATTTTGCTCC 58.133 33.333 0.00 0.00 0.00 4.70
692 745 7.253422 AGTTTAGATTCATTCATTTTGCTCCG 58.747 34.615 0.00 0.00 0.00 4.63
693 746 6.757897 TTAGATTCATTCATTTTGCTCCGT 57.242 33.333 0.00 0.00 0.00 4.69
694 747 7.857734 TTAGATTCATTCATTTTGCTCCGTA 57.142 32.000 0.00 0.00 0.00 4.02
695 748 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
696 749 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
697 750 4.291540 TCATTCATTTTGCTCCGTATGC 57.708 40.909 0.00 0.00 0.00 3.14
698 751 3.693578 TCATTCATTTTGCTCCGTATGCA 59.306 39.130 0.00 0.00 38.80 3.96
699 752 4.338964 TCATTCATTTTGCTCCGTATGCAT 59.661 37.500 3.79 3.79 40.34 3.96
700 753 4.717233 TTCATTTTGCTCCGTATGCATT 57.283 36.364 3.54 0.00 40.34 3.56
701 754 4.291540 TCATTTTGCTCCGTATGCATTC 57.708 40.909 3.54 0.00 40.34 2.67
702 755 3.066621 TCATTTTGCTCCGTATGCATTCC 59.933 43.478 3.54 0.00 40.34 3.01
703 756 2.121291 TTTGCTCCGTATGCATTCCA 57.879 45.000 3.54 0.00 40.34 3.53
704 757 2.346766 TTGCTCCGTATGCATTCCAT 57.653 45.000 3.54 0.00 40.34 3.41
705 758 1.882912 TGCTCCGTATGCATTCCATC 58.117 50.000 3.54 0.00 35.31 3.51
706 759 1.417517 TGCTCCGTATGCATTCCATCT 59.582 47.619 3.54 0.00 35.31 2.90
707 760 2.632512 TGCTCCGTATGCATTCCATCTA 59.367 45.455 3.54 0.00 35.31 1.98
708 761 3.070878 TGCTCCGTATGCATTCCATCTAA 59.929 43.478 3.54 0.00 35.31 2.10
709 762 4.256920 GCTCCGTATGCATTCCATCTAAT 58.743 43.478 3.54 0.00 35.34 1.73
710 763 4.093998 GCTCCGTATGCATTCCATCTAATG 59.906 45.833 3.54 0.00 39.41 1.90
728 781 9.829507 CATCTAATGGAATCTCTACAAAGACTT 57.170 33.333 0.00 0.00 0.00 3.01
733 786 9.965902 AATGGAATCTCTACAAAGACTTACATT 57.034 29.630 0.00 0.00 30.67 2.71
734 787 9.965902 ATGGAATCTCTACAAAGACTTACATTT 57.034 29.630 0.00 0.00 0.00 2.32
740 793 9.924650 TCTCTACAAAGACTTACATTTAGGAAC 57.075 33.333 0.00 0.00 0.00 3.62
741 794 9.152595 CTCTACAAAGACTTACATTTAGGAACC 57.847 37.037 0.00 0.00 0.00 3.62
742 795 8.098912 TCTACAAAGACTTACATTTAGGAACCC 58.901 37.037 0.00 0.00 0.00 4.11
743 796 6.607019 ACAAAGACTTACATTTAGGAACCCA 58.393 36.000 0.00 0.00 0.00 4.51
744 797 6.715264 ACAAAGACTTACATTTAGGAACCCAG 59.285 38.462 0.00 0.00 0.00 4.45
745 798 5.437191 AGACTTACATTTAGGAACCCAGG 57.563 43.478 0.00 0.00 0.00 4.45
746 799 4.227527 AGACTTACATTTAGGAACCCAGGG 59.772 45.833 2.85 2.85 0.00 4.45
747 800 4.180723 ACTTACATTTAGGAACCCAGGGA 58.819 43.478 14.54 0.00 0.00 4.20
748 801 4.227527 ACTTACATTTAGGAACCCAGGGAG 59.772 45.833 14.54 0.00 0.00 4.30
749 802 2.644151 ACATTTAGGAACCCAGGGAGT 58.356 47.619 14.54 0.00 0.00 3.85
750 803 3.810623 ACATTTAGGAACCCAGGGAGTA 58.189 45.455 14.54 0.00 0.00 2.59
751 804 3.522343 ACATTTAGGAACCCAGGGAGTAC 59.478 47.826 14.54 0.00 0.00 2.73
760 813 3.323775 ACCCAGGGAGTACAAAAGAAGA 58.676 45.455 14.54 0.00 0.00 2.87
842 906 0.548926 TCCAACAGATGCCCCCTACA 60.549 55.000 0.00 0.00 0.00 2.74
845 909 1.004745 CAACAGATGCCCCCTACAACT 59.995 52.381 0.00 0.00 0.00 3.16
930 994 3.894947 GCGTCTCCTCCTCCTCGC 61.895 72.222 0.00 0.00 37.17 5.03
1094 1239 2.725008 GACGCGCTCCAGCTCTAT 59.275 61.111 5.73 0.00 39.32 1.98
1095 1240 1.516365 GGACGCGCTCCAGCTCTATA 61.516 60.000 18.80 0.00 39.21 1.31
1143 1288 1.673808 CGGACTGCTACACCTACCCC 61.674 65.000 0.00 0.00 0.00 4.95
1488 1633 1.000396 GCAGGGGCAGGAATGTCTT 60.000 57.895 0.00 0.00 40.72 3.01
1689 1834 2.799176 GCAGAATGGTGATGGGGTC 58.201 57.895 0.00 0.00 35.86 4.46
1741 1886 1.133915 GTGAGAAGGTGGGGTTTGACA 60.134 52.381 0.00 0.00 0.00 3.58
1772 1917 0.864455 GTCAGTGTGCTGTCAGCTTC 59.136 55.000 24.76 17.44 42.97 3.86
1774 1919 1.301244 AGTGTGCTGTCAGCTTCCG 60.301 57.895 24.76 0.00 42.97 4.30
1780 1925 4.600576 TGTCAGCTTCCGCACGCA 62.601 61.111 0.00 0.00 39.10 5.24
1818 1963 1.598130 GAAGTGGGTGCACGAGCTT 60.598 57.895 11.45 13.70 42.74 3.74
1829 1974 0.524392 CACGAGCTTGCTAGGAGTCG 60.524 60.000 0.00 10.00 0.00 4.18
1844 1989 3.680786 TCGTGGGCTCGACACTGG 61.681 66.667 3.52 0.00 36.71 4.00
1872 2017 1.234821 TCGGCAATGTTCTTGTGGAC 58.765 50.000 0.00 0.00 0.00 4.02
1887 2032 2.250188 GTGGACATGTACGCAAAATGC 58.750 47.619 16.94 0.00 40.69 3.56
1901 2046 2.642139 AAATGCGGTGAGATTGCTTG 57.358 45.000 0.00 0.00 0.00 4.01
1929 2074 0.818040 AGGCTTTCGAAGGTTTGCGT 60.818 50.000 9.20 4.31 0.00 5.24
2032 2177 2.501316 TCTGCGATGAAAGATCAAGGGA 59.499 45.455 0.00 0.00 39.49 4.20
2052 2197 5.193728 AGGGATAAAGCCTAATTCCTTCACA 59.806 40.000 0.00 0.00 24.96 3.58
2053 2198 6.071320 GGGATAAAGCCTAATTCCTTCACAT 58.929 40.000 0.00 0.00 0.00 3.21
2055 2200 7.428826 GGATAAAGCCTAATTCCTTCACATTG 58.571 38.462 0.00 0.00 0.00 2.82
2166 2341 3.394635 AACACTTGGACGTGCCGGT 62.395 57.895 4.04 0.00 40.66 5.28
2211 2386 0.617935 TCAGGGGAATGTCGATGCAA 59.382 50.000 0.00 0.00 0.00 4.08
2241 2416 2.750237 ATTTGGGGCGCGTTCCTC 60.750 61.111 8.43 0.75 0.00 3.71
2382 2557 1.424493 GAATGCTGGAAGACGCGGAG 61.424 60.000 12.47 0.00 34.07 4.63
2494 2669 2.503356 AGGTAGCAAGCTAGATGCAAGT 59.497 45.455 19.28 5.43 46.22 3.16
2495 2670 3.054802 AGGTAGCAAGCTAGATGCAAGTT 60.055 43.478 19.28 5.15 46.22 2.66
2541 2716 8.798859 AATCAGCTATTTACACATGTTCTCTT 57.201 30.769 0.00 0.00 0.00 2.85
2719 2895 5.167121 CGCCCAATTAAAATGTGATGAACA 58.833 37.500 0.00 0.00 44.79 3.18
2741 2917 6.334989 ACAGTTGCATTATTGGAATGTGATG 58.665 36.000 9.59 0.00 35.50 3.07
2765 2941 6.127225 TGTTACATTAGAGCTGCAGAAGAGAT 60.127 38.462 20.43 2.01 0.00 2.75
2794 2970 9.995003 AAAACAATGCTCCAGAAAATAATGTAA 57.005 25.926 0.00 0.00 0.00 2.41
2886 3065 2.652530 GCACGGGTACTGGACGAA 59.347 61.111 0.00 0.00 40.47 3.85
3040 3219 0.596083 GAGATGCATCGACGGTCCAG 60.596 60.000 20.67 0.00 0.00 3.86
3043 3222 1.269723 GATGCATCGACGGTCCAGATA 59.730 52.381 11.68 0.00 0.00 1.98
3045 3224 1.686587 TGCATCGACGGTCCAGATAAT 59.313 47.619 1.91 0.00 0.00 1.28
3057 3237 5.220605 CGGTCCAGATAATTTTTCTTCGGAC 60.221 44.000 13.47 13.47 39.72 4.79
3070 3250 1.597663 CTTCGGACAAACAAGAACGCT 59.402 47.619 0.00 0.00 0.00 5.07
3071 3251 1.658994 TCGGACAAACAAGAACGCTT 58.341 45.000 0.00 0.00 33.74 4.68
3115 3295 9.696917 AAGTATACTTTTTCCTTTTTCATGCTG 57.303 29.630 12.50 0.00 30.82 4.41
3129 3314 1.064906 CATGCTGGTGGGATGAGTTCT 60.065 52.381 0.00 0.00 44.95 3.01
3172 3360 5.153513 GTTGCAAACTGAAAATGATAGCGA 58.846 37.500 0.00 0.00 45.32 4.93
3261 3451 7.473027 ACGAAGAACGAGAAAGTTTCAAATA 57.527 32.000 17.65 0.00 45.77 1.40
3455 3673 6.912591 AGTGTGCATTCGTTTTTCTCTAAAAG 59.087 34.615 0.00 0.00 36.44 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.003068 CCATCAATGAGCGATTCAACCTC 59.997 47.826 0.00 0.00 39.77 3.85
85 86 0.874175 CTGTTCACGCACGACTCCAA 60.874 55.000 0.00 0.00 0.00 3.53
188 189 2.030274 GTCGGGGGACAATTTGAAAGTG 60.030 50.000 3.59 3.59 0.00 3.16
260 270 9.281371 CTCATGGAAGTAATGATCATGTTACAT 57.719 33.333 17.39 15.59 37.20 2.29
307 322 7.041508 CCATTTAGACACATTAATCTCTCAGCC 60.042 40.741 0.00 0.00 0.00 4.85
334 349 4.360563 ACATTTAGTCAAGTATCGCGGAG 58.639 43.478 6.13 0.00 0.00 4.63
335 350 4.380841 ACATTTAGTCAAGTATCGCGGA 57.619 40.909 6.13 0.00 0.00 5.54
336 351 4.782195 GCAACATTTAGTCAAGTATCGCGG 60.782 45.833 6.13 0.00 0.00 6.46
337 352 4.201676 TGCAACATTTAGTCAAGTATCGCG 60.202 41.667 0.00 0.00 0.00 5.87
338 353 5.216566 TGCAACATTTAGTCAAGTATCGC 57.783 39.130 0.00 0.00 0.00 4.58
339 354 6.246332 CGTTTGCAACATTTAGTCAAGTATCG 59.754 38.462 0.00 0.00 0.00 2.92
340 355 7.075741 ACGTTTGCAACATTTAGTCAAGTATC 58.924 34.615 0.00 0.00 0.00 2.24
378 418 6.485984 ACATGAGATCAAGATAAAGGATGTGC 59.514 38.462 0.00 0.00 0.00 4.57
410 451 6.109359 ACTGGCAAGTTACAGAGATTATGAC 58.891 40.000 12.27 0.00 38.09 3.06
482 526 9.330063 TCCAAATTTGTAACAATTGTATGCAAA 57.670 25.926 24.16 24.16 38.21 3.68
483 527 8.893219 TCCAAATTTGTAACAATTGTATGCAA 57.107 26.923 12.39 14.11 39.16 4.08
591 644 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
592 645 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
593 646 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
655 708 9.798994 GAATGAATCTAAACTTGAAATGCATCT 57.201 29.630 0.00 0.00 0.00 2.90
656 709 9.577110 TGAATGAATCTAAACTTGAAATGCATC 57.423 29.630 0.00 0.00 0.00 3.91
658 711 9.932207 AATGAATGAATCTAAACTTGAAATGCA 57.068 25.926 0.00 0.00 0.00 3.96
663 716 9.985730 AGCAAAATGAATGAATCTAAACTTGAA 57.014 25.926 0.00 0.00 0.00 2.69
664 717 9.630098 GAGCAAAATGAATGAATCTAAACTTGA 57.370 29.630 0.00 0.00 0.00 3.02
665 718 8.866956 GGAGCAAAATGAATGAATCTAAACTTG 58.133 33.333 0.00 0.00 0.00 3.16
666 719 7.756722 CGGAGCAAAATGAATGAATCTAAACTT 59.243 33.333 0.00 0.00 0.00 2.66
667 720 7.094205 ACGGAGCAAAATGAATGAATCTAAACT 60.094 33.333 0.00 0.00 0.00 2.66
668 721 7.029563 ACGGAGCAAAATGAATGAATCTAAAC 58.970 34.615 0.00 0.00 0.00 2.01
669 722 7.156876 ACGGAGCAAAATGAATGAATCTAAA 57.843 32.000 0.00 0.00 0.00 1.85
670 723 6.757897 ACGGAGCAAAATGAATGAATCTAA 57.242 33.333 0.00 0.00 0.00 2.10
671 724 7.520453 GCATACGGAGCAAAATGAATGAATCTA 60.520 37.037 0.00 0.00 0.00 1.98
672 725 6.732154 CATACGGAGCAAAATGAATGAATCT 58.268 36.000 0.00 0.00 0.00 2.40
673 726 5.400485 GCATACGGAGCAAAATGAATGAATC 59.600 40.000 0.00 0.00 0.00 2.52
674 727 5.163530 TGCATACGGAGCAAAATGAATGAAT 60.164 36.000 0.00 0.00 39.39 2.57
675 728 4.157472 TGCATACGGAGCAAAATGAATGAA 59.843 37.500 0.00 0.00 39.39 2.57
676 729 3.693578 TGCATACGGAGCAAAATGAATGA 59.306 39.130 0.00 0.00 39.39 2.57
677 730 4.031418 TGCATACGGAGCAAAATGAATG 57.969 40.909 0.00 0.00 39.39 2.67
678 731 4.924305 ATGCATACGGAGCAAAATGAAT 57.076 36.364 0.00 0.00 46.27 2.57
679 732 4.439974 GGAATGCATACGGAGCAAAATGAA 60.440 41.667 0.00 0.00 46.27 2.57
680 733 3.066621 GGAATGCATACGGAGCAAAATGA 59.933 43.478 0.00 0.00 46.27 2.57
681 734 3.181488 TGGAATGCATACGGAGCAAAATG 60.181 43.478 0.00 0.00 46.27 2.32
682 735 3.023119 TGGAATGCATACGGAGCAAAAT 58.977 40.909 0.00 0.00 46.27 1.82
683 736 2.441410 TGGAATGCATACGGAGCAAAA 58.559 42.857 0.00 0.00 46.27 2.44
684 737 2.121291 TGGAATGCATACGGAGCAAA 57.879 45.000 0.00 0.00 46.27 3.68
685 738 2.158769 AGATGGAATGCATACGGAGCAA 60.159 45.455 0.00 0.00 46.27 3.91
687 740 2.175878 AGATGGAATGCATACGGAGC 57.824 50.000 0.00 0.00 0.00 4.70
688 741 5.791367 CATTAGATGGAATGCATACGGAG 57.209 43.478 0.00 0.00 30.43 4.63
702 755 9.829507 AAGTCTTTGTAGAGATTCCATTAGATG 57.170 33.333 0.00 0.00 0.00 2.90
707 760 9.965902 AATGTAAGTCTTTGTAGAGATTCCATT 57.034 29.630 0.00 0.00 0.00 3.16
708 761 9.965902 AAATGTAAGTCTTTGTAGAGATTCCAT 57.034 29.630 0.00 0.00 0.00 3.41
714 767 9.924650 GTTCCTAAATGTAAGTCTTTGTAGAGA 57.075 33.333 0.00 0.00 0.00 3.10
715 768 9.152595 GGTTCCTAAATGTAAGTCTTTGTAGAG 57.847 37.037 0.00 0.00 0.00 2.43
716 769 8.098912 GGGTTCCTAAATGTAAGTCTTTGTAGA 58.901 37.037 0.00 0.00 0.00 2.59
717 770 7.881232 TGGGTTCCTAAATGTAAGTCTTTGTAG 59.119 37.037 0.00 0.00 0.00 2.74
718 771 7.747690 TGGGTTCCTAAATGTAAGTCTTTGTA 58.252 34.615 0.00 0.00 0.00 2.41
719 772 6.607019 TGGGTTCCTAAATGTAAGTCTTTGT 58.393 36.000 0.00 0.00 0.00 2.83
720 773 6.151144 CCTGGGTTCCTAAATGTAAGTCTTTG 59.849 42.308 0.00 0.00 0.00 2.77
721 774 6.246163 CCTGGGTTCCTAAATGTAAGTCTTT 58.754 40.000 0.00 0.00 0.00 2.52
722 775 5.281037 CCCTGGGTTCCTAAATGTAAGTCTT 60.281 44.000 3.97 0.00 0.00 3.01
723 776 4.227527 CCCTGGGTTCCTAAATGTAAGTCT 59.772 45.833 3.97 0.00 0.00 3.24
724 777 4.226620 TCCCTGGGTTCCTAAATGTAAGTC 59.773 45.833 13.56 0.00 0.00 3.01
725 778 4.180723 TCCCTGGGTTCCTAAATGTAAGT 58.819 43.478 13.56 0.00 0.00 2.24
726 779 4.227527 ACTCCCTGGGTTCCTAAATGTAAG 59.772 45.833 13.56 0.00 0.00 2.34
727 780 4.180723 ACTCCCTGGGTTCCTAAATGTAA 58.819 43.478 13.56 0.00 0.00 2.41
728 781 3.810623 ACTCCCTGGGTTCCTAAATGTA 58.189 45.455 13.56 0.00 0.00 2.29
729 782 2.644151 ACTCCCTGGGTTCCTAAATGT 58.356 47.619 13.56 0.00 0.00 2.71
730 783 3.521937 TGTACTCCCTGGGTTCCTAAATG 59.478 47.826 13.56 0.00 0.00 2.32
731 784 3.810623 TGTACTCCCTGGGTTCCTAAAT 58.189 45.455 13.56 0.00 0.00 1.40
732 785 3.278987 TGTACTCCCTGGGTTCCTAAA 57.721 47.619 13.56 0.00 0.00 1.85
733 786 3.278987 TTGTACTCCCTGGGTTCCTAA 57.721 47.619 13.56 1.68 0.00 2.69
734 787 3.278987 TTTGTACTCCCTGGGTTCCTA 57.721 47.619 13.56 0.00 0.00 2.94
735 788 2.127651 TTTGTACTCCCTGGGTTCCT 57.872 50.000 13.56 0.00 0.00 3.36
736 789 2.374170 TCTTTTGTACTCCCTGGGTTCC 59.626 50.000 13.56 0.16 0.00 3.62
737 790 3.782656 TCTTTTGTACTCCCTGGGTTC 57.217 47.619 13.56 2.73 0.00 3.62
738 791 3.720002 TCTTCTTTTGTACTCCCTGGGTT 59.280 43.478 13.56 3.64 0.00 4.11
739 792 3.072622 GTCTTCTTTTGTACTCCCTGGGT 59.927 47.826 13.56 0.00 0.00 4.51
740 793 3.676093 GTCTTCTTTTGTACTCCCTGGG 58.324 50.000 6.33 6.33 0.00 4.45
741 794 3.244112 ACGTCTTCTTTTGTACTCCCTGG 60.244 47.826 0.00 0.00 0.00 4.45
742 795 3.991367 ACGTCTTCTTTTGTACTCCCTG 58.009 45.455 0.00 0.00 0.00 4.45
743 796 4.321824 GCTACGTCTTCTTTTGTACTCCCT 60.322 45.833 0.00 0.00 0.00 4.20
744 797 3.925299 GCTACGTCTTCTTTTGTACTCCC 59.075 47.826 0.00 0.00 0.00 4.30
745 798 4.807443 AGCTACGTCTTCTTTTGTACTCC 58.193 43.478 0.00 0.00 0.00 3.85
746 799 7.462988 GCATAAGCTACGTCTTCTTTTGTACTC 60.463 40.741 0.00 0.00 37.91 2.59
747 800 6.310711 GCATAAGCTACGTCTTCTTTTGTACT 59.689 38.462 0.00 0.00 37.91 2.73
748 801 6.467648 GCATAAGCTACGTCTTCTTTTGTAC 58.532 40.000 0.00 0.00 37.91 2.90
749 802 6.642683 GCATAAGCTACGTCTTCTTTTGTA 57.357 37.500 0.00 0.00 37.91 2.41
750 803 5.532025 GCATAAGCTACGTCTTCTTTTGT 57.468 39.130 0.00 0.00 37.91 2.83
842 906 4.699522 GGCGGTTGCGGGAGAGTT 62.700 66.667 0.00 0.00 44.10 3.01
966 1030 1.213013 CGTCGAACACCCTGAGGAG 59.787 63.158 0.00 0.00 36.73 3.69
1260 1405 0.399949 CCCCCTCCTGGCAGTACATA 60.400 60.000 14.43 0.00 0.00 2.29
1426 1571 0.103208 GTGATCTCGTTCGGGAGCAT 59.897 55.000 15.62 0.00 33.98 3.79
1635 1780 2.506962 GTGTTCCGGGACACCACA 59.493 61.111 32.58 8.85 43.16 4.17
1645 1790 1.305219 ATGGCAACCATCGTGTTCCG 61.305 55.000 0.00 0.00 40.74 4.30
1689 1834 1.884926 GAAGAGCTTGATCGCCCGG 60.885 63.158 0.00 0.00 0.00 5.73
1702 1847 3.196469 TCACTAAGCATCCTGTGGAAGAG 59.804 47.826 0.00 0.00 34.34 2.85
1741 1886 1.781786 ACACTGACCAGAGTGACAGT 58.218 50.000 7.65 0.00 45.39 3.55
1780 1925 2.203788 TGTCTCAAGGGCTCCCGT 60.204 61.111 0.00 0.00 41.95 5.28
1818 1963 2.037367 AGCCCACGACTCCTAGCA 59.963 61.111 0.00 0.00 0.00 3.49
1829 1974 2.357517 CACCAGTGTCGAGCCCAC 60.358 66.667 0.00 0.00 0.00 4.61
1844 1989 1.369091 AACATTGCCGATCCTCGCAC 61.369 55.000 0.00 0.00 38.82 5.34
1901 2046 4.766088 CGAAAGCCTGCCTTGCGC 62.766 66.667 0.00 0.00 45.02 6.09
1917 2062 1.961277 AGGCTCACGCAAACCTTCG 60.961 57.895 0.00 0.00 38.10 3.79
1929 2074 0.473755 ATGACACAACACCAGGCTCA 59.526 50.000 0.00 0.00 0.00 4.26
2003 2148 3.579709 TCTTTCATCGCAGAGAACAGAC 58.420 45.455 0.00 0.00 43.63 3.51
2032 2177 7.068716 GGTCAATGTGAAGGAATTAGGCTTTAT 59.931 37.037 0.00 0.00 0.00 1.40
2052 2197 0.108329 CCACTAGAACCGCGGTCAAT 60.108 55.000 34.29 22.21 0.00 2.57
2053 2198 1.290955 CCACTAGAACCGCGGTCAA 59.709 57.895 34.29 18.72 0.00 3.18
2055 2200 2.508663 GCCACTAGAACCGCGGTC 60.509 66.667 34.29 23.98 0.00 4.79
2080 2225 2.189594 TCATCAACAAGGCCAGAGTG 57.810 50.000 5.01 0.00 0.00 3.51
2166 2341 6.871492 TGATTTCATACGCTTCAACAAGTCTA 59.129 34.615 0.00 0.00 31.45 2.59
2211 2386 1.331214 CCCAAATGCACTTGTCTGGT 58.669 50.000 7.18 0.00 0.00 4.00
2382 2557 0.395862 TCATGGTCCTCCTCGTCCTC 60.396 60.000 0.00 0.00 34.23 3.71
2662 2838 7.976734 CCATTGTACAGTTAACAAGGTGAAAAA 59.023 33.333 8.61 0.00 40.00 1.94
2663 2839 7.416890 CCCATTGTACAGTTAACAAGGTGAAAA 60.417 37.037 8.61 1.20 40.00 2.29
2664 2840 6.039941 CCCATTGTACAGTTAACAAGGTGAAA 59.960 38.462 8.61 3.33 40.00 2.69
2665 2841 5.533154 CCCATTGTACAGTTAACAAGGTGAA 59.467 40.000 8.61 2.10 40.00 3.18
2666 2842 5.067273 CCCATTGTACAGTTAACAAGGTGA 58.933 41.667 8.61 0.00 40.00 4.02
2667 2843 4.217550 CCCCATTGTACAGTTAACAAGGTG 59.782 45.833 8.61 0.00 40.00 4.00
2719 2895 6.534475 ACATCACATTCCAATAATGCAACT 57.466 33.333 0.00 0.00 0.00 3.16
2741 2917 5.655488 TCTCTTCTGCAGCTCTAATGTAAC 58.345 41.667 9.47 0.00 0.00 2.50
2765 2941 8.991026 CATTATTTTCTGGAGCATTGTTTTCAA 58.009 29.630 0.00 0.00 44.33 2.69
2820 2999 3.006430 TCGGCAGAAGTCTGAACATTACA 59.994 43.478 12.54 0.00 46.59 2.41
2823 3002 2.808543 GTTCGGCAGAAGTCTGAACATT 59.191 45.455 12.54 0.00 46.59 2.71
2886 3065 0.106669 TCCTCACCGATCACCGATCT 60.107 55.000 2.74 0.00 41.76 2.75
3040 3219 9.458374 TTCTTGTTTGTCCGAAGAAAAATTATC 57.542 29.630 0.00 0.00 33.75 1.75
3043 3222 6.252655 CGTTCTTGTTTGTCCGAAGAAAAATT 59.747 34.615 0.00 0.00 37.44 1.82
3045 3224 5.090083 CGTTCTTGTTTGTCCGAAGAAAAA 58.910 37.500 0.00 0.00 37.44 1.94
3070 3250 9.929180 GTATACTTAATCAGTCATCTGCCATAA 57.071 33.333 0.00 0.00 41.10 1.90
3071 3251 9.314133 AGTATACTTAATCAGTCATCTGCCATA 57.686 33.333 0.00 0.00 41.10 2.74
3115 3295 2.158842 CCTCATCAGAACTCATCCCACC 60.159 54.545 0.00 0.00 0.00 4.61
3129 3314 5.551233 CAACTTCTTTGTCCTACCTCATCA 58.449 41.667 0.00 0.00 0.00 3.07
3187 3375 5.668080 TGGTGGGTGGAATATATGTGAAGTA 59.332 40.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.