Multiple sequence alignment - TraesCS5B01G163400

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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 TraesCS5B01G163400 chr5B 100.000 5761 0 0 1 5761 302059768 302065528 0.000000e+00 10639.0
1 TraesCS5B01G163400 chr5A 94.152 4429 149 45 701 5078 354960878 354965247 0.000000e+00 6643.0
2 TraesCS5B01G163400 chr5A 91.647 431 19 10 5290 5706 354969409 354969836 1.080000e-161 580.0
3 TraesCS5B01G163400 chr5A 92.417 211 15 1 5088 5297 354967418 354967628 3.370000e-77 300.0
4 TraesCS5B01G163400 chr5A 100.000 57 0 0 5705 5761 354969875 354969931 7.890000e-19 106.0
5 TraesCS5B01G163400 chr5D 93.884 3679 128 38 701 4331 267614239 267617868 0.000000e+00 5457.0
6 TraesCS5B01G163400 chr5D 90.529 1362 84 13 4352 5694 267617932 267619267 0.000000e+00 1759.0
7 TraesCS5B01G163400 chr7D 90.506 632 51 7 2 631 560252057 560252681 0.000000e+00 826.0
8 TraesCS5B01G163400 chr7D 80.377 265 37 8 3889 4153 134441333 134441582 2.740000e-43 187.0
9 TraesCS5B01G163400 chr7D 79.348 276 36 16 3886 4157 628227649 628227391 2.130000e-39 174.0
10 TraesCS5B01G163400 chr7D 78.832 274 39 14 3886 4155 628228372 628228114 3.570000e-37 167.0
11 TraesCS5B01G163400 chr3A 89.555 651 62 5 1 649 749477440 749476794 0.000000e+00 821.0
12 TraesCS5B01G163400 chr3A 84.337 83 9 2 599 677 44790439 44790521 1.720000e-10 78.7
13 TraesCS5B01G163400 chr6D 90.205 633 54 7 1 631 433920737 433921363 0.000000e+00 819.0
14 TraesCS5B01G163400 chr7B 90.145 619 55 5 1 617 34184220 34184834 0.000000e+00 800.0
15 TraesCS5B01G163400 chr7B 88.346 635 67 6 1 634 622514995 622515623 0.000000e+00 756.0
16 TraesCS5B01G163400 chr7B 79.348 276 36 16 3886 4157 730778666 730778924 2.130000e-39 174.0
17 TraesCS5B01G163400 chr7B 79.348 276 36 16 3886 4157 730805446 730805704 2.130000e-39 174.0
18 TraesCS5B01G163400 chr6A 88.226 637 64 9 3 634 93794449 93793819 0.000000e+00 750.0
19 TraesCS5B01G163400 chr6B 87.850 642 66 6 1 634 22837944 22838581 0.000000e+00 743.0
20 TraesCS5B01G163400 chr2A 87.424 660 64 13 1 649 617664515 617665166 0.000000e+00 741.0
21 TraesCS5B01G163400 chr2B 87.676 641 68 7 1 634 769489670 769490306 0.000000e+00 736.0
22 TraesCS5B01G163400 chr3D 82.437 279 34 6 3886 4162 178651811 178652076 4.490000e-56 230.0
23 TraesCS5B01G163400 chr3B 82.079 279 35 6 3886 4162 257098941 257099206 2.090000e-54 224.0
24 TraesCS5B01G163400 chr1B 83.471 242 22 7 3886 4125 174110170 174109945 5.850000e-50 209.0
25 TraesCS5B01G163400 chr1A 78.723 235 29 15 3889 4113 557424058 557424281 2.800000e-28 137.0
26 TraesCS5B01G163400 chr4A 82.550 149 18 5 5421 5569 577472722 577472582 2.180000e-24 124.0
27 TraesCS5B01G163400 chr4A 97.143 35 0 1 5540 5573 590244692 590244658 2.240000e-04 58.4
28 TraesCS5B01G163400 chr4D 75.269 279 50 9 3885 4160 402546679 402546417 1.310000e-21 115.0


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 TraesCS5B01G163400 chr5B 302059768 302065528 5760 False 10639.00 10639 100.0000 1 5761 1 chr5B.!!$F1 5760
1 TraesCS5B01G163400 chr5A 354960878 354969931 9053 False 1907.25 6643 94.5540 701 5761 4 chr5A.!!$F1 5060
2 TraesCS5B01G163400 chr5D 267614239 267619267 5028 False 3608.00 5457 92.2065 701 5694 2 chr5D.!!$F1 4993
3 TraesCS5B01G163400 chr7D 560252057 560252681 624 False 826.00 826 90.5060 2 631 1 chr7D.!!$F2 629
4 TraesCS5B01G163400 chr3A 749476794 749477440 646 True 821.00 821 89.5550 1 649 1 chr3A.!!$R1 648
5 TraesCS5B01G163400 chr6D 433920737 433921363 626 False 819.00 819 90.2050 1 631 1 chr6D.!!$F1 630
6 TraesCS5B01G163400 chr7B 34184220 34184834 614 False 800.00 800 90.1450 1 617 1 chr7B.!!$F1 616
7 TraesCS5B01G163400 chr7B 622514995 622515623 628 False 756.00 756 88.3460 1 634 1 chr7B.!!$F2 633
8 TraesCS5B01G163400 chr6A 93793819 93794449 630 True 750.00 750 88.2260 3 634 1 chr6A.!!$R1 631
9 TraesCS5B01G163400 chr6B 22837944 22838581 637 False 743.00 743 87.8500 1 634 1 chr6B.!!$F1 633
10 TraesCS5B01G163400 chr2A 617664515 617665166 651 False 741.00 741 87.4240 1 649 1 chr2A.!!$F1 648
11 TraesCS5B01G163400 chr2B 769489670 769490306 636 False 736.00 736 87.6760 1 634 1 chr2B.!!$F1 633

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
564 581 0.168568 CAAATTTGGGCCGCAAATGC 59.831 50.000 24.22 0.0 33.13 3.56 F
1343 1368 0.109781 CTGGTTTGAATTCGGCGTGG 60.110 55.000 6.85 0.0 0.00 4.94 F
1429 1454 0.252057 TCCTCACCAACGGAGATCCA 60.252 55.000 0.00 0.0 34.24 3.41 F
1881 1925 2.689983 CCAAATATCGCCCTTCAAAGCT 59.310 45.455 0.00 0.0 0.00 3.74 F
2324 2379 2.756760 GCCCGCATCCAAATCATGATAT 59.243 45.455 9.04 0.0 0.00 1.63 F
4223 4300 0.110238 CCTGCCATGTGTTCGAAACG 60.110 55.000 0.00 0.0 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 1864 1.066573 AGGATGCTCAAGAGGTTGACG 60.067 52.381 0.0 0.0 37.79 4.35 R
2780 2838 2.425143 ATGAGCCATTTCGGTCATGT 57.575 45.000 2.7 0.0 35.48 3.21 R
3095 3158 2.883267 CTACCAGCAGCAGAAGGGGC 62.883 65.000 0.0 0.0 0.00 5.80 R
3739 3805 4.213270 TCAGTTCATAAAGTTTCTGCGTGG 59.787 41.667 0.0 0.0 0.00 4.94 R
4299 4376 0.108804 ACAGGTCTACGATGTTGCGG 60.109 55.000 0.0 0.0 35.12 5.69 R
5247 7553 2.117941 GACGCTGCCCACACAAGTTC 62.118 60.000 0.0 0.0 0.00 3.01 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
149 153 2.203728 TACTCCCAGTGCCACCGT 60.204 61.111 0.00 0.00 0.00 4.83
312 329 1.153449 CTAGGGTTTGCGATCGCCA 60.153 57.895 35.12 23.91 41.09 5.69
334 351 0.962855 GAGGAAGCAAAGGGAGTGGC 60.963 60.000 0.00 0.00 0.00 5.01
362 379 2.100197 CAGATGTGGACGGGAGAAGTA 58.900 52.381 0.00 0.00 0.00 2.24
379 396 3.369410 TAGATGAGGCCGACCCCGT 62.369 63.158 0.00 0.00 36.11 5.28
511 528 4.415332 GCGGACGGCGAGAAGACA 62.415 66.667 16.62 0.00 0.00 3.41
514 531 2.254651 GACGGCGAGAAGACACGT 59.745 61.111 16.62 0.00 40.85 4.49
541 558 4.185413 GCTTCGCGTCCATTCTGA 57.815 55.556 5.77 0.00 0.00 3.27
544 561 1.428448 CTTCGCGTCCATTCTGAACA 58.572 50.000 5.77 0.00 0.00 3.18
564 581 0.168568 CAAATTTGGGCCGCAAATGC 59.831 50.000 24.22 0.00 33.13 3.56
597 614 1.081556 CGACGCGGACATCATTTGGA 61.082 55.000 12.47 0.00 0.00 3.53
635 652 1.215117 CCGCCATTTTTGTCCGCAT 59.785 52.632 0.00 0.00 0.00 4.73
637 654 0.171007 CGCCATTTTTGTCCGCATCT 59.829 50.000 0.00 0.00 0.00 2.90
645 662 5.913137 TTTTTGTCCGCATCTATCCAAAT 57.087 34.783 0.00 0.00 0.00 2.32
649 666 4.522114 TGTCCGCATCTATCCAAATGAAA 58.478 39.130 0.00 0.00 0.00 2.69
650 667 5.132502 TGTCCGCATCTATCCAAATGAAAT 58.867 37.500 0.00 0.00 0.00 2.17
651 668 5.008911 TGTCCGCATCTATCCAAATGAAATG 59.991 40.000 0.00 0.00 0.00 2.32
652 669 4.520111 TCCGCATCTATCCAAATGAAATGG 59.480 41.667 0.00 0.00 39.41 3.16
660 677 2.951642 TCCAAATGAAATGGATCGCTCC 59.048 45.455 0.00 0.00 41.98 4.70
669 686 2.787473 TGGATCGCTCCATTGAACTT 57.213 45.000 3.28 0.00 46.95 2.66
670 687 2.358957 TGGATCGCTCCATTGAACTTG 58.641 47.619 3.28 0.00 46.95 3.16
671 688 1.064654 GGATCGCTCCATTGAACTTGC 59.935 52.381 0.00 0.00 41.64 4.01
672 689 2.012673 GATCGCTCCATTGAACTTGCT 58.987 47.619 0.00 0.00 0.00 3.91
673 690 1.442769 TCGCTCCATTGAACTTGCTC 58.557 50.000 0.00 0.00 0.00 4.26
674 691 1.002430 TCGCTCCATTGAACTTGCTCT 59.998 47.619 0.00 0.00 0.00 4.09
675 692 1.808945 CGCTCCATTGAACTTGCTCTT 59.191 47.619 0.00 0.00 0.00 2.85
676 693 3.002791 CGCTCCATTGAACTTGCTCTTA 58.997 45.455 0.00 0.00 0.00 2.10
677 694 3.624861 CGCTCCATTGAACTTGCTCTTAT 59.375 43.478 0.00 0.00 0.00 1.73
678 695 4.095483 CGCTCCATTGAACTTGCTCTTATT 59.905 41.667 0.00 0.00 0.00 1.40
679 696 5.576895 GCTCCATTGAACTTGCTCTTATTC 58.423 41.667 0.00 0.00 0.00 1.75
680 697 5.449725 GCTCCATTGAACTTGCTCTTATTCC 60.450 44.000 0.00 0.00 0.00 3.01
681 698 4.635765 TCCATTGAACTTGCTCTTATTCCG 59.364 41.667 0.00 0.00 0.00 4.30
682 699 4.201950 CCATTGAACTTGCTCTTATTCCGG 60.202 45.833 0.00 0.00 0.00 5.14
683 700 2.356135 TGAACTTGCTCTTATTCCGGC 58.644 47.619 0.00 0.00 0.00 6.13
684 701 2.290008 TGAACTTGCTCTTATTCCGGCA 60.290 45.455 0.00 0.00 0.00 5.69
685 702 2.717639 ACTTGCTCTTATTCCGGCAT 57.282 45.000 0.00 0.00 34.59 4.40
686 703 2.292267 ACTTGCTCTTATTCCGGCATG 58.708 47.619 0.00 0.00 36.41 4.06
687 704 2.092968 ACTTGCTCTTATTCCGGCATGA 60.093 45.455 0.00 0.00 35.06 3.07
688 705 2.708216 TGCTCTTATTCCGGCATGAA 57.292 45.000 0.00 0.00 0.00 2.57
689 706 3.213206 TGCTCTTATTCCGGCATGAAT 57.787 42.857 0.00 5.43 38.47 2.57
690 707 3.141398 TGCTCTTATTCCGGCATGAATC 58.859 45.455 0.00 0.00 36.41 2.52
691 708 3.141398 GCTCTTATTCCGGCATGAATCA 58.859 45.455 0.00 0.00 36.41 2.57
692 709 3.565482 GCTCTTATTCCGGCATGAATCAA 59.435 43.478 0.00 0.00 36.41 2.57
693 710 4.036734 GCTCTTATTCCGGCATGAATCAAA 59.963 41.667 0.00 0.00 36.41 2.69
694 711 5.450412 GCTCTTATTCCGGCATGAATCAAAA 60.450 40.000 0.00 0.00 36.41 2.44
695 712 6.713762 TCTTATTCCGGCATGAATCAAAAT 57.286 33.333 0.00 0.00 36.41 1.82
696 713 7.111247 TCTTATTCCGGCATGAATCAAAATT 57.889 32.000 0.00 0.00 36.41 1.82
697 714 6.979817 TCTTATTCCGGCATGAATCAAAATTG 59.020 34.615 0.00 0.00 36.41 2.32
698 715 4.797800 TTCCGGCATGAATCAAAATTGA 57.202 36.364 0.00 0.00 42.14 2.57
699 716 4.374843 TCCGGCATGAATCAAAATTGAG 57.625 40.909 0.00 0.00 41.08 3.02
707 724 9.321562 GGCATGAATCAAAATTGAGATTTACAT 57.678 29.630 0.00 5.01 41.08 2.29
729 746 1.456892 TGTATCCGGGATCTGCCGT 60.457 57.895 13.97 0.00 37.63 5.68
776 793 2.612212 ACGGATTAAAATAGTGGCAGCG 59.388 45.455 0.00 0.00 0.00 5.18
831 848 2.515398 CAACACCACCAGCCCAGA 59.485 61.111 0.00 0.00 0.00 3.86
849 866 0.733729 GACCAGATCTACGACGTGCT 59.266 55.000 11.56 0.00 0.00 4.40
850 867 1.938577 GACCAGATCTACGACGTGCTA 59.061 52.381 11.56 0.00 0.00 3.49
851 868 1.669779 ACCAGATCTACGACGTGCTAC 59.330 52.381 11.56 0.00 0.00 3.58
852 869 1.002684 CCAGATCTACGACGTGCTACC 60.003 57.143 11.56 0.00 0.00 3.18
853 870 0.935898 AGATCTACGACGTGCTACCG 59.064 55.000 11.56 0.00 0.00 4.02
854 871 0.656786 GATCTACGACGTGCTACCGC 60.657 60.000 11.56 0.00 0.00 5.68
1023 1048 3.393970 TGCTCCTTCTCCGGGCTG 61.394 66.667 0.00 0.00 0.00 4.85
1253 1278 0.891373 CCGTCACACATCTCAGGTCT 59.109 55.000 0.00 0.00 0.00 3.85
1276 1301 3.187432 GCACCTTGTTTAGCTCTCTTCAC 59.813 47.826 0.00 0.00 0.00 3.18
1335 1360 1.340889 ACGCATGCACTGGTTTGAATT 59.659 42.857 19.57 0.00 0.00 2.17
1343 1368 0.109781 CTGGTTTGAATTCGGCGTGG 60.110 55.000 6.85 0.00 0.00 4.94
1345 1370 1.211709 GTTTGAATTCGGCGTGGGG 59.788 57.895 6.85 0.00 0.00 4.96
1346 1371 2.631580 TTTGAATTCGGCGTGGGGC 61.632 57.895 6.85 0.00 42.51 5.80
1428 1453 2.591915 TCCTCACCAACGGAGATCC 58.408 57.895 0.00 0.00 34.24 3.36
1429 1454 0.252057 TCCTCACCAACGGAGATCCA 60.252 55.000 0.00 0.00 34.24 3.41
1468 1493 8.352137 TCATTTCATTAAAATCCTGCTTCAGA 57.648 30.769 0.00 0.00 35.32 3.27
1474 1499 9.631257 TCATTAAAATCCTGCTTCAGATTATGA 57.369 29.630 0.00 0.00 32.44 2.15
1551 1576 3.500448 TGCTTCCCACATTGTCAACTA 57.500 42.857 0.00 0.00 0.00 2.24
1576 1601 6.705782 GTGTATACACATTTTGTCCTCATCG 58.294 40.000 27.37 0.00 45.75 3.84
1623 1648 4.100963 TGCGGTGATAGATCTACCAAATGT 59.899 41.667 4.10 0.00 34.10 2.71
1625 1650 5.527582 GCGGTGATAGATCTACCAAATGTTT 59.472 40.000 4.10 0.00 34.10 2.83
1820 1864 5.598416 AAATTTGGCTTAGGTCCAATAGC 57.402 39.130 0.00 0.00 42.57 2.97
1881 1925 2.689983 CCAAATATCGCCCTTCAAAGCT 59.310 45.455 0.00 0.00 0.00 3.74
1882 1926 3.882888 CCAAATATCGCCCTTCAAAGCTA 59.117 43.478 0.00 0.00 0.00 3.32
1947 2002 9.075678 TGACTAGTATATTCTACTAAAGGGTGC 57.924 37.037 0.00 0.00 30.55 5.01
1982 2037 5.065090 TCACGGCATTTCAGTGATAAGATTG 59.935 40.000 0.00 0.00 43.30 2.67
1984 2039 4.614946 GGCATTTCAGTGATAAGATTGCC 58.385 43.478 10.95 10.95 36.73 4.52
1995 2050 6.939163 AGTGATAAGATTGCCTGATGAATACC 59.061 38.462 0.00 0.00 0.00 2.73
2004 2059 9.453572 GATTGCCTGATGAATACCAATCTATTA 57.546 33.333 0.00 0.00 36.97 0.98
2118 2173 8.728337 TTTCTTGTAATCATCTCATTCTCCTG 57.272 34.615 0.00 0.00 0.00 3.86
2123 2178 7.448420 TGTAATCATCTCATTCTCCTGGATTC 58.552 38.462 0.00 0.00 0.00 2.52
2137 2192 3.688673 CCTGGATTCTCTTTTCAGCTGAC 59.311 47.826 18.03 0.76 0.00 3.51
2172 2227 8.902806 TGCTTTGAAGAAAGTTCTTATTCAGAA 58.097 29.630 6.29 0.00 46.84 3.02
2284 2339 5.957842 TTATTGCAGTCAAGGTAAGTTGG 57.042 39.130 0.00 0.00 35.37 3.77
2324 2379 2.756760 GCCCGCATCCAAATCATGATAT 59.243 45.455 9.04 0.00 0.00 1.63
2358 2413 3.325293 TTCATCTTCCAGCTCAGTGAC 57.675 47.619 0.00 0.00 0.00 3.67
2367 2422 5.738619 TCCAGCTCAGTGACATTTACTTA 57.261 39.130 0.00 0.00 0.00 2.24
2400 2455 6.557291 TTTGGTAACTTATGTTGGGTAACG 57.443 37.500 4.33 0.00 37.22 3.18
2441 2498 7.772757 GGTTGACTATCTTCTGATGGAGATTTT 59.227 37.037 0.00 0.00 35.49 1.82
2455 2512 5.481105 TGGAGATTTTGCAGCTTTAATTGG 58.519 37.500 0.00 0.00 0.00 3.16
2456 2513 5.011943 TGGAGATTTTGCAGCTTTAATTGGT 59.988 36.000 0.00 0.00 0.00 3.67
2457 2514 6.210385 TGGAGATTTTGCAGCTTTAATTGGTA 59.790 34.615 0.00 0.00 0.00 3.25
2859 2921 8.142551 TCACTTTAGAGTTTAGACCAGAAGTTC 58.857 37.037 0.00 0.00 32.54 3.01
3035 3098 5.483937 ACTGTACCATCACTAAGGTTGATCA 59.516 40.000 0.00 0.00 39.31 2.92
3039 3102 4.194640 CCATCACTAAGGTTGATCAGTGG 58.805 47.826 9.78 0.00 39.09 4.00
3040 3103 4.080919 CCATCACTAAGGTTGATCAGTGGA 60.081 45.833 9.78 0.12 39.09 4.02
3041 3104 5.397221 CCATCACTAAGGTTGATCAGTGGAT 60.397 44.000 9.78 2.00 39.09 3.41
3496 3562 7.230510 TGTTCATATTTCTGTAGTTTGGCAACT 59.769 33.333 0.00 3.44 45.73 3.16
3517 3583 7.420800 CAACTAGTATGAGAAATCATTTGGGC 58.579 38.462 0.00 0.00 0.00 5.36
3739 3805 7.389053 CCCTTTATGCTATGATGTAAGTTCTCC 59.611 40.741 0.00 0.00 0.00 3.71
3742 3808 5.023533 TGCTATGATGTAAGTTCTCCCAC 57.976 43.478 0.00 0.00 0.00 4.61
3837 3903 6.084925 CCTATGCCTAAAACTACTCGTATCG 58.915 44.000 0.00 0.00 0.00 2.92
3977 4043 6.946340 TGACCAACTCTATAGAAAGATGCAA 58.054 36.000 3.57 0.00 0.00 4.08
3979 4045 7.712639 TGACCAACTCTATAGAAAGATGCAATC 59.287 37.037 3.57 0.00 46.04 2.67
3992 4058 4.728917 GATGCAATCAGATCTACAGCAC 57.271 45.455 11.84 5.14 44.70 4.40
3993 4059 2.910199 TGCAATCAGATCTACAGCACC 58.090 47.619 0.00 0.00 0.00 5.01
3994 4060 2.236893 TGCAATCAGATCTACAGCACCA 59.763 45.455 0.00 0.00 0.00 4.17
3995 4061 3.273434 GCAATCAGATCTACAGCACCAA 58.727 45.455 0.00 0.00 0.00 3.67
3996 4062 3.691118 GCAATCAGATCTACAGCACCAAA 59.309 43.478 0.00 0.00 0.00 3.28
3997 4063 4.156556 GCAATCAGATCTACAGCACCAAAA 59.843 41.667 0.00 0.00 0.00 2.44
3998 4064 5.163581 GCAATCAGATCTACAGCACCAAAAT 60.164 40.000 0.00 0.00 0.00 1.82
3999 4065 6.038603 GCAATCAGATCTACAGCACCAAAATA 59.961 38.462 0.00 0.00 0.00 1.40
4133 4210 2.038164 ACTTAGGACAAACCCGGAACTC 59.962 50.000 0.73 0.00 40.05 3.01
4143 4220 5.167845 CAAACCCGGAACTCCAATTATTTG 58.832 41.667 0.73 0.00 35.14 2.32
4196 4273 9.767228 TCTTTGTTAAATACTGCTGTAGTTACA 57.233 29.630 19.16 16.87 38.43 2.41
4217 4294 4.641989 ACATAGAAATCCTGCCATGTGTTC 59.358 41.667 0.00 0.00 0.00 3.18
4223 4300 0.110238 CCTGCCATGTGTTCGAAACG 60.110 55.000 0.00 0.00 0.00 3.60
4260 4337 8.474025 TGTATTTTGTCAAAATTCTCCACAACT 58.526 29.630 24.67 3.77 41.16 3.16
4289 4366 9.515226 AAGTAGCCTATTTTGACACAATTCTTA 57.485 29.630 0.00 0.00 0.00 2.10
4341 4436 6.128007 TGTTCTATGCTAGTAAAAAGGCTTGC 60.128 38.462 0.00 0.00 0.00 4.01
4377 4499 4.806892 ACCATCCATGCAGAATCCATTAA 58.193 39.130 0.00 0.00 0.00 1.40
4712 4851 3.879295 CTGCAGTTCGTCCCAATATTGAT 59.121 43.478 17.23 0.00 0.00 2.57
4763 4902 2.435741 GAAGCACTCGACTTGACGG 58.564 57.895 0.00 0.00 0.00 4.79
4851 4992 7.092079 TGCTTGATTCATTAAAAGTGACATGG 58.908 34.615 0.00 0.00 0.00 3.66
4857 4998 6.573664 TCATTAAAAGTGACATGGTCCTTG 57.426 37.500 3.21 3.21 0.00 3.61
4920 5061 2.352960 GCAGGCTTCACCGATTTAAGAG 59.647 50.000 0.00 0.00 46.52 2.85
4976 5117 5.596836 TTTTTGTGCCAAAGTGAGATTCT 57.403 34.783 0.00 0.00 0.00 2.40
5078 5222 5.588240 TCTGTTGAGCAACCTACATATACG 58.412 41.667 10.54 0.00 40.46 3.06
5079 5223 5.126545 TCTGTTGAGCAACCTACATATACGT 59.873 40.000 10.54 0.00 40.46 3.57
5080 5224 6.319405 TCTGTTGAGCAACCTACATATACGTA 59.681 38.462 10.54 0.00 40.46 3.57
5081 5225 6.267817 TGTTGAGCAACCTACATATACGTAC 58.732 40.000 10.54 0.00 40.46 3.67
5082 5226 6.095860 TGTTGAGCAACCTACATATACGTACT 59.904 38.462 10.54 0.00 40.46 2.73
5084 5228 7.991084 TGAGCAACCTACATATACGTACTAT 57.009 36.000 0.00 0.00 0.00 2.12
5085 5229 7.813645 TGAGCAACCTACATATACGTACTATG 58.186 38.462 16.69 16.69 33.65 2.23
5086 5230 7.446319 TGAGCAACCTACATATACGTACTATGT 59.554 37.037 22.58 22.58 41.46 2.29
5147 7452 6.913673 GCAAGAATTTTGAACACAATTGCATT 59.086 30.769 5.05 0.00 35.96 3.56
5288 7594 2.453983 AATGGAAAATGCGTGGTTGG 57.546 45.000 0.00 0.00 0.00 3.77
5343 9437 4.330074 CGTCGAAAAGTGCAAATAGAGGAT 59.670 41.667 0.00 0.00 0.00 3.24
5345 9439 5.122396 GTCGAAAAGTGCAAATAGAGGATGT 59.878 40.000 0.00 0.00 0.00 3.06
5374 9468 1.377987 GCCCCGCACTCAAATACCA 60.378 57.895 0.00 0.00 0.00 3.25
5648 9756 7.846066 TGGAAATTTCTTTTCTGAGTTTTCCA 58.154 30.769 17.42 9.14 42.83 3.53
5696 9804 8.223769 CCTCGCACTTATACACATGAAATAATC 58.776 37.037 0.00 0.00 0.00 1.75
5697 9805 8.887036 TCGCACTTATACACATGAAATAATCT 57.113 30.769 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.379143 CACGACGACGAGGTGCGA 62.379 66.667 15.32 0.00 44.57 5.10
78 80 0.179113 CCGCACCATTGGTATTTGGC 60.179 55.000 8.31 6.52 36.41 4.52
129 133 1.899437 CGGTGGCACTGGGAGTACAT 61.899 60.000 18.87 0.00 0.00 2.29
293 310 1.153429 GGCGATCGCAAACCCTAGT 60.153 57.895 38.00 0.00 44.11 2.57
306 323 0.605319 TTTGCTTCCTCGTTGGCGAT 60.605 50.000 0.00 0.00 46.80 4.58
312 329 0.765510 ACTCCCTTTGCTTCCTCGTT 59.234 50.000 0.00 0.00 0.00 3.85
362 379 4.779733 ACGGGGTCGGCCTCATCT 62.780 66.667 6.79 0.00 41.39 2.90
532 549 4.502950 GCCCAAATTTGTGTTCAGAATGGA 60.503 41.667 16.73 0.00 36.16 3.41
534 551 3.747529 GGCCCAAATTTGTGTTCAGAATG 59.252 43.478 16.73 0.00 37.54 2.67
535 552 3.554752 CGGCCCAAATTTGTGTTCAGAAT 60.555 43.478 16.73 0.00 0.00 2.40
539 556 0.249657 GCGGCCCAAATTTGTGTTCA 60.250 50.000 16.73 0.00 0.00 3.18
541 558 0.179000 TTGCGGCCCAAATTTGTGTT 59.821 45.000 16.73 0.00 0.00 3.32
590 607 1.795162 GCGCCGACTCAAATCCAAATG 60.795 52.381 0.00 0.00 0.00 2.32
597 614 2.677003 CCAACGCGCCGACTCAAAT 61.677 57.895 5.73 0.00 0.00 2.32
650 667 2.358957 CAAGTTCAATGGAGCGATCCA 58.641 47.619 26.87 26.87 44.85 3.41
651 668 1.064654 GCAAGTTCAATGGAGCGATCC 59.935 52.381 14.17 14.17 0.00 3.36
652 669 2.012673 AGCAAGTTCAATGGAGCGATC 58.987 47.619 0.00 0.00 0.00 3.69
653 670 2.012673 GAGCAAGTTCAATGGAGCGAT 58.987 47.619 0.00 0.00 0.00 4.58
654 671 1.002430 AGAGCAAGTTCAATGGAGCGA 59.998 47.619 0.00 0.00 0.00 4.93
655 672 1.446907 AGAGCAAGTTCAATGGAGCG 58.553 50.000 0.00 0.00 0.00 5.03
656 673 5.449725 GGAATAAGAGCAAGTTCAATGGAGC 60.450 44.000 0.00 0.00 0.00 4.70
657 674 5.220739 CGGAATAAGAGCAAGTTCAATGGAG 60.221 44.000 0.00 0.00 0.00 3.86
658 675 4.635765 CGGAATAAGAGCAAGTTCAATGGA 59.364 41.667 0.00 0.00 0.00 3.41
659 676 4.201950 CCGGAATAAGAGCAAGTTCAATGG 60.202 45.833 0.00 0.00 0.00 3.16
660 677 4.731773 GCCGGAATAAGAGCAAGTTCAATG 60.732 45.833 5.05 0.00 0.00 2.82
661 678 3.378427 GCCGGAATAAGAGCAAGTTCAAT 59.622 43.478 5.05 0.00 0.00 2.57
662 679 2.747446 GCCGGAATAAGAGCAAGTTCAA 59.253 45.455 5.05 0.00 0.00 2.69
663 680 2.290008 TGCCGGAATAAGAGCAAGTTCA 60.290 45.455 5.05 0.00 30.97 3.18
664 681 2.356135 TGCCGGAATAAGAGCAAGTTC 58.644 47.619 5.05 0.00 30.97 3.01
665 682 2.489938 TGCCGGAATAAGAGCAAGTT 57.510 45.000 5.05 0.00 30.97 2.66
666 683 2.092968 TCATGCCGGAATAAGAGCAAGT 60.093 45.455 5.05 0.00 38.99 3.16
667 684 2.564771 TCATGCCGGAATAAGAGCAAG 58.435 47.619 5.05 0.00 38.99 4.01
668 685 2.708216 TCATGCCGGAATAAGAGCAA 57.292 45.000 5.05 0.00 38.99 3.91
669 686 2.708216 TTCATGCCGGAATAAGAGCA 57.292 45.000 5.05 0.00 40.00 4.26
670 687 3.141398 TGATTCATGCCGGAATAAGAGC 58.859 45.455 5.05 0.00 37.61 4.09
671 688 5.756195 TTTGATTCATGCCGGAATAAGAG 57.244 39.130 5.05 0.00 37.61 2.85
672 689 6.713762 ATTTTGATTCATGCCGGAATAAGA 57.286 33.333 5.05 0.00 37.61 2.10
673 690 6.979817 TCAATTTTGATTCATGCCGGAATAAG 59.020 34.615 5.05 0.00 37.61 1.73
674 691 6.871844 TCAATTTTGATTCATGCCGGAATAA 58.128 32.000 5.05 0.00 37.61 1.40
675 692 6.320926 TCTCAATTTTGATTCATGCCGGAATA 59.679 34.615 5.05 0.00 37.61 1.75
676 693 5.127519 TCTCAATTTTGATTCATGCCGGAAT 59.872 36.000 5.05 0.00 40.10 3.01
677 694 4.462132 TCTCAATTTTGATTCATGCCGGAA 59.538 37.500 5.05 0.00 36.46 4.30
678 695 4.015764 TCTCAATTTTGATTCATGCCGGA 58.984 39.130 5.05 0.00 36.46 5.14
679 696 4.374843 TCTCAATTTTGATTCATGCCGG 57.625 40.909 0.00 0.00 36.46 6.13
680 697 6.897259 AAATCTCAATTTTGATTCATGCCG 57.103 33.333 3.91 0.00 36.46 5.69
681 698 8.706492 TGTAAATCTCAATTTTGATTCATGCC 57.294 30.769 3.91 0.00 36.49 4.40
697 714 5.477291 TCCCGGATACAGAGATGTAAATCTC 59.523 44.000 14.28 14.28 45.58 2.75
698 715 5.394738 TCCCGGATACAGAGATGTAAATCT 58.605 41.667 0.73 0.00 0.00 2.40
699 716 5.723672 TCCCGGATACAGAGATGTAAATC 57.276 43.478 0.73 0.00 0.00 2.17
707 724 1.621992 GCAGATCCCGGATACAGAGA 58.378 55.000 0.73 0.00 0.00 3.10
747 764 5.006358 CCACTATTTTAATCCGTTGAGGTCG 59.994 44.000 0.00 0.00 41.99 4.79
831 848 1.669779 GTAGCACGTCGTAGATCTGGT 59.330 52.381 5.18 0.00 40.67 4.00
1023 1048 2.713894 GGTGTCGTACAGCGCGTTC 61.714 63.158 8.43 4.84 36.84 3.95
1209 1234 1.746991 GCCCTTCTTCTTGGCGAGG 60.747 63.158 0.97 0.00 35.08 4.63
1253 1278 3.181455 TGAAGAGAGCTAAACAAGGTGCA 60.181 43.478 0.00 0.00 35.60 4.57
1428 1453 3.243035 TGAAATGAGAAAGTTGCCGTGTG 60.243 43.478 0.00 0.00 0.00 3.82
1429 1454 2.948979 TGAAATGAGAAAGTTGCCGTGT 59.051 40.909 0.00 0.00 0.00 4.49
1468 1493 8.708378 TGACATAATTGAGGAGACACTCATAAT 58.292 33.333 0.00 0.00 46.07 1.28
1474 1499 4.223700 TGCTGACATAATTGAGGAGACACT 59.776 41.667 0.00 0.00 0.00 3.55
1507 1532 4.563061 TCCAGTAAAGTAGGAGCGAAAAC 58.437 43.478 0.00 0.00 0.00 2.43
1551 1576 6.535150 CGATGAGGACAAAATGTGTATACACT 59.465 38.462 30.69 16.95 46.55 3.55
1576 1601 4.242475 GGTTTGGTCCATTCGGAATTTTC 58.758 43.478 0.00 0.00 45.20 2.29
1623 1648 3.074412 GGCTGTCTCTCCGAATCAAAAA 58.926 45.455 0.00 0.00 0.00 1.94
1625 1650 1.623311 TGGCTGTCTCTCCGAATCAAA 59.377 47.619 0.00 0.00 0.00 2.69
1791 1835 6.201591 TGGACCTAAGCCAAATTTAATGGAT 58.798 36.000 0.00 0.00 40.56 3.41
1820 1864 1.066573 AGGATGCTCAAGAGGTTGACG 60.067 52.381 0.00 0.00 37.79 4.35
1921 1973 9.075678 GCACCCTTTAGTAGAATATACTAGTCA 57.924 37.037 0.00 0.00 32.35 3.41
1945 2000 1.286501 GCCGTGATATTCGTCTTGCA 58.713 50.000 0.00 0.00 0.00 4.08
1946 2001 1.286501 TGCCGTGATATTCGTCTTGC 58.713 50.000 1.79 0.00 0.00 4.01
1947 2002 4.033932 TGAAATGCCGTGATATTCGTCTTG 59.966 41.667 1.79 0.00 0.00 3.02
1977 2032 5.950023 AGATTGGTATTCATCAGGCAATCT 58.050 37.500 0.00 0.00 34.51 2.40
2031 2086 3.928005 ACAACCAGAGCATGATGATCT 57.072 42.857 7.49 7.49 45.00 2.75
2101 2156 6.559539 AGAGAATCCAGGAGAATGAGATGATT 59.440 38.462 0.00 0.00 33.66 2.57
2118 2173 2.675348 CCGTCAGCTGAAAAGAGAATCC 59.325 50.000 20.19 0.35 33.66 3.01
2123 2178 1.270305 TGTCCCGTCAGCTGAAAAGAG 60.270 52.381 20.19 7.64 0.00 2.85
2137 2192 4.396166 ACTTTCTTCAAAGCATATGTCCCG 59.604 41.667 4.29 0.00 42.66 5.14
2284 2339 5.237344 GCGGGCATGATATCTATTTGTATCC 59.763 44.000 3.98 1.37 0.00 2.59
2427 2484 3.361281 AGCTGCAAAATCTCCATCAGA 57.639 42.857 1.02 0.00 34.78 3.27
2441 2498 6.176896 TGTGATACTACCAATTAAAGCTGCA 58.823 36.000 1.02 0.00 0.00 4.41
2680 2737 5.777850 TGTACACAAGACAGCAGTAAGTA 57.222 39.130 0.00 0.00 0.00 2.24
2722 2780 3.873910 CACCCCTATTGTAGTTGTCCAG 58.126 50.000 0.00 0.00 0.00 3.86
2780 2838 2.425143 ATGAGCCATTTCGGTCATGT 57.575 45.000 2.70 0.00 35.48 3.21
3035 3098 8.281212 AGTAAATCGATTTTGCTAAATCCACT 57.719 30.769 27.10 16.88 44.40 4.00
3095 3158 2.883267 CTACCAGCAGCAGAAGGGGC 62.883 65.000 0.00 0.00 0.00 5.80
3124 3190 6.703607 CACATAACTAACAGGCTAATCCTCAG 59.296 42.308 0.00 0.00 45.52 3.35
3428 3494 8.668510 ATCAATTACACTAGATTGCCTTACAG 57.331 34.615 0.00 0.00 34.15 2.74
3462 3528 9.878599 AACTACAGAAATATGAACAAAAGTTCG 57.121 29.630 4.18 0.00 36.21 3.95
3476 3542 9.378551 CATACTAGTTGCCAAACTACAGAAATA 57.621 33.333 0.00 0.00 45.01 1.40
3496 3562 4.515191 GCGCCCAAATGATTTCTCATACTA 59.485 41.667 0.00 0.00 41.34 1.82
3553 3619 5.426689 AAGAAGTCCAGCACTCATCATAA 57.573 39.130 0.00 0.00 32.30 1.90
3739 3805 4.213270 TCAGTTCATAAAGTTTCTGCGTGG 59.787 41.667 0.00 0.00 0.00 4.94
3742 3808 5.342806 TGTCAGTTCATAAAGTTTCTGCG 57.657 39.130 0.00 0.00 0.00 5.18
3815 3881 6.866010 TCGATACGAGTAGTTTTAGGCATA 57.134 37.500 0.00 0.00 0.00 3.14
3977 4043 6.058183 GGTATTTTGGTGCTGTAGATCTGAT 58.942 40.000 5.18 0.00 0.00 2.90
3979 4045 5.185454 TGGTATTTTGGTGCTGTAGATCTG 58.815 41.667 5.18 0.00 0.00 2.90
3989 4055 8.940768 ATTATGTGTATTTGGTATTTTGGTGC 57.059 30.769 0.00 0.00 0.00 5.01
4143 4220 5.733676 TGTTTAATTACTACCTCCGTTCCC 58.266 41.667 0.00 0.00 0.00 3.97
4196 4273 3.879295 CGAACACATGGCAGGATTTCTAT 59.121 43.478 5.99 0.00 0.00 1.98
4260 4337 5.142061 TGTGTCAAAATAGGCTACTTCGA 57.858 39.130 0.00 0.00 0.00 3.71
4295 4372 1.017177 GTCTACGATGTTGCGGCCAA 61.017 55.000 2.24 0.00 35.12 4.52
4299 4376 0.108804 ACAGGTCTACGATGTTGCGG 60.109 55.000 0.00 0.00 35.12 5.69
4351 4446 2.422519 GGATTCTGCATGGATGGTCAGT 60.423 50.000 0.00 0.00 0.00 3.41
4362 4465 5.648247 AGCCCTAATTAATGGATTCTGCAT 58.352 37.500 5.14 0.00 0.00 3.96
4396 4518 5.299279 GTCTTGATCCAGTTCCAGACAAAAA 59.701 40.000 5.51 0.00 37.97 1.94
4397 4519 4.821805 GTCTTGATCCAGTTCCAGACAAAA 59.178 41.667 5.51 0.00 37.97 2.44
4398 4520 4.141505 TGTCTTGATCCAGTTCCAGACAAA 60.142 41.667 9.16 0.00 42.28 2.83
4399 4521 3.390967 TGTCTTGATCCAGTTCCAGACAA 59.609 43.478 9.16 0.00 42.28 3.18
4712 4851 9.996554 AGTTTATCAACGTGGATGATAATATCA 57.003 29.630 16.00 5.32 44.73 2.15
4763 4902 4.518970 TCTGTTGAAGCAGTTCCATTTACC 59.481 41.667 0.00 0.00 37.70 2.85
4851 4992 6.708054 CCTTCCATACAATGACTATCAAGGAC 59.292 42.308 0.00 0.00 0.00 3.85
4920 5061 0.035630 AGACATCAGGAACAGCCAGC 60.036 55.000 0.00 0.00 40.02 4.85
5247 7553 2.117941 GACGCTGCCCACACAAGTTC 62.118 60.000 0.00 0.00 0.00 3.01
5288 7594 3.896272 ACTATAGCTAGTGGTGCCCTTAC 59.104 47.826 0.00 0.00 36.81 2.34
5550 9658 8.612619 TCACTTCAGATCTGTAAAACTTTGTTC 58.387 33.333 21.92 0.00 0.00 3.18
5557 9665 7.865707 ACATGTTCACTTCAGATCTGTAAAAC 58.134 34.615 21.92 17.98 0.00 2.43
5599 9707 7.745594 CCATGTTTCAAAAACACTCAAAAACAG 59.254 33.333 7.36 0.00 38.20 3.16
5671 9779 8.982685 AGATTATTTCATGTGTATAAGTGCGAG 58.017 33.333 0.00 0.00 0.00 5.03
5699 9807 8.362464 TGTACTTGTATGTCTTCCTCTACAAT 57.638 34.615 0.00 0.00 34.56 2.71
5700 9808 7.770366 TGTACTTGTATGTCTTCCTCTACAA 57.230 36.000 0.00 0.00 34.08 2.41
5702 9810 7.755822 CAGTTGTACTTGTATGTCTTCCTCTAC 59.244 40.741 0.00 0.00 0.00 2.59
5703 9811 7.668469 TCAGTTGTACTTGTATGTCTTCCTCTA 59.332 37.037 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.