Multiple sequence alignment - TraesCS5A01G481800

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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 TraesCS5A01G481800 chr5A 100.000 4874 0 0 1 4874 653950100 653945227 0.000000e+00 9001
1 TraesCS5A01G481800 chr5A 79.390 2819 521 42 1059 3853 653856539 653853757 0.000000e+00 1932
2 TraesCS5A01G481800 chr5A 78.723 2867 515 65 994 3808 653921045 653918222 0.000000e+00 1827
3 TraesCS5A01G481800 chr5A 78.922 612 110 11 1 599 74763084 74763689 9.830000e-107 398
4 TraesCS5A01G481800 chr5A 79.665 418 73 9 3655 4070 653945665 653945258 1.720000e-74 291
5 TraesCS5A01G481800 chr5A 79.665 418 73 9 4436 4843 653946446 653946031 1.720000e-74 291
6 TraesCS5A01G481800 chr5A 80.130 307 37 16 4585 4874 653904224 653903925 1.780000e-49 207
7 TraesCS5A01G481800 chr5D 93.002 3801 242 12 646 4433 526829127 526825338 0.000000e+00 5524
8 TraesCS5A01G481800 chr5D 79.936 2816 503 42 1058 3853 526696128 526693355 0.000000e+00 2013
9 TraesCS5A01G481800 chr5D 90.769 325 30 0 1503 1827 526822449 526822125 7.490000e-118 435
10 TraesCS5A01G481800 chr5D 84.457 341 47 4 1000 1340 526822852 526822518 1.010000e-86 331
11 TraesCS5A01G481800 chr5D 79.572 421 73 10 4436 4843 526826119 526825699 6.170000e-74 289
12 TraesCS5A01G481800 chr5B 94.498 3235 166 7 1208 4433 662600330 662597099 0.000000e+00 4977
13 TraesCS5A01G481800 chr5B 79.495 2814 520 39 1058 3853 662462436 662459662 0.000000e+00 1947
14 TraesCS5A01G481800 chr5B 78.995 2666 493 40 1058 3674 662596526 662593879 0.000000e+00 1759
15 TraesCS5A01G481800 chr6D 73.556 1800 426 39 2080 3865 2505139 2503376 4.110000e-180 641
16 TraesCS5A01G481800 chr4D 79.732 597 107 12 6 596 478775265 478775853 2.100000e-113 420
17 TraesCS5A01G481800 chr1D 80.970 536 91 7 4 535 92094378 92093850 9.760000e-112 414
18 TraesCS5A01G481800 chr3D 79.043 606 113 5 4 598 135049652 135049050 2.110000e-108 403
19 TraesCS5A01G481800 chr3D 80.620 516 84 10 4 506 580981184 580981696 7.650000e-103 385
20 TraesCS5A01G481800 chr2B 80.321 498 84 7 5 489 413058056 413058552 9.970000e-97 364
21 TraesCS5A01G481800 chr2B 77.011 609 122 11 4 598 618742557 618741953 2.810000e-87 333
22 TraesCS5A01G481800 chr7B 78.782 542 100 9 1 530 541195837 541196375 2.790000e-92 350
23 TraesCS5A01G481800 chr2A 79.600 500 87 6 4 493 701491675 701492169 1.300000e-90 344


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 TraesCS5A01G481800 chr5A 653945227 653950100 4873 True 9001.00 9001 100.0000 1 4874 1 chr5A.!!$R4 4873
1 TraesCS5A01G481800 chr5A 653853757 653856539 2782 True 1932.00 1932 79.3900 1059 3853 1 chr5A.!!$R1 2794
2 TraesCS5A01G481800 chr5A 653918222 653921045 2823 True 1827.00 1827 78.7230 994 3808 1 chr5A.!!$R3 2814
3 TraesCS5A01G481800 chr5A 74763084 74763689 605 False 398.00 398 78.9220 1 599 1 chr5A.!!$F1 598
4 TraesCS5A01G481800 chr5A 653945258 653946446 1188 True 291.00 291 79.6650 3655 4843 2 chr5A.!!$R5 1188
5 TraesCS5A01G481800 chr5D 526693355 526696128 2773 True 2013.00 2013 79.9360 1058 3853 1 chr5D.!!$R1 2795
6 TraesCS5A01G481800 chr5D 526822125 526829127 7002 True 1644.75 5524 86.9500 646 4843 4 chr5D.!!$R2 4197
7 TraesCS5A01G481800 chr5B 662593879 662600330 6451 True 3368.00 4977 86.7465 1058 4433 2 chr5B.!!$R2 3375
8 TraesCS5A01G481800 chr5B 662459662 662462436 2774 True 1947.00 1947 79.4950 1058 3853 1 chr5B.!!$R1 2795
9 TraesCS5A01G481800 chr6D 2503376 2505139 1763 True 641.00 641 73.5560 2080 3865 1 chr6D.!!$R1 1785
10 TraesCS5A01G481800 chr4D 478775265 478775853 588 False 420.00 420 79.7320 6 596 1 chr4D.!!$F1 590
11 TraesCS5A01G481800 chr1D 92093850 92094378 528 True 414.00 414 80.9700 4 535 1 chr1D.!!$R1 531
12 TraesCS5A01G481800 chr3D 135049050 135049652 602 True 403.00 403 79.0430 4 598 1 chr3D.!!$R1 594
13 TraesCS5A01G481800 chr3D 580981184 580981696 512 False 385.00 385 80.6200 4 506 1 chr3D.!!$F1 502
14 TraesCS5A01G481800 chr2B 618741953 618742557 604 True 333.00 333 77.0110 4 598 1 chr2B.!!$R1 594
15 TraesCS5A01G481800 chr7B 541195837 541196375 538 False 350.00 350 78.7820 1 530 1 chr7B.!!$F1 529

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
607 626 0.107654 GATGCCCTAAGGTCGCTTGT 60.108 55.000 0.00 0.0 34.57 3.16 F
1844 4628 0.037590 AGCTGCGGGATTTGTGGTTA 59.962 50.000 0.00 0.0 0.00 2.85 F
1988 4772 1.077716 ACAACCTCATTAGCGGGGC 60.078 57.895 0.00 0.0 0.00 5.80 F
3273 6060 0.930310 CAGGAATCGCGTACATGGTG 59.070 55.000 5.77 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 4698 0.107703 TGAAGGTCGATGGCACCATC 60.108 55.000 18.05 18.05 46.71 3.51 R
2659 5443 0.982704 ACTTGCATCTCTGGTGCTCT 59.017 50.000 4.42 0.00 42.92 4.09 R
3317 6104 1.334869 CTACAAGCATGCCGATTTCCC 59.665 52.381 15.66 0.00 0.00 3.97 R
4846 7695 1.841663 TTCGAGCGCCAACTGCTTTC 61.842 55.000 2.29 0.00 44.18 2.62 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
20 21 0.454196 GTTGGTGTTGTGGTGTGGAC 59.546 55.000 0.00 0.00 0.00 4.02
109 111 2.112815 CGCCGGAATGGGTTTCTCC 61.113 63.158 5.05 0.00 38.63 3.71
182 184 3.704566 GGATGCCGTAGATATATGTCCCA 59.295 47.826 0.00 0.00 0.00 4.37
211 213 1.893137 AGTCACGTGTCTCCAGCATTA 59.107 47.619 16.51 0.00 0.00 1.90
270 272 4.636435 CGGTCGGTGGGCCACTTT 62.636 66.667 33.87 0.00 34.40 2.66
315 317 2.185310 ATTCGCCCTGAGCCGTCTTT 62.185 55.000 0.00 0.00 38.78 2.52
324 326 5.123227 CCCTGAGCCGTCTTTAATATTGAA 58.877 41.667 0.00 0.00 0.00 2.69
418 434 4.324991 GGGCGGTCAGAAACGGGT 62.325 66.667 0.00 0.00 0.00 5.28
427 443 3.414269 GTCAGAAACGGGTTTGGGATTA 58.586 45.455 0.82 0.00 32.11 1.75
435 451 1.493446 GGGTTTGGGATTAGTCCGGAT 59.507 52.381 7.81 0.00 46.09 4.18
471 490 6.478129 TCCCCTACGTTTGTCTTTGATTTAT 58.522 36.000 0.00 0.00 0.00 1.40
473 492 8.102047 TCCCCTACGTTTGTCTTTGATTTATAA 58.898 33.333 0.00 0.00 0.00 0.98
484 503 9.161629 TGTCTTTGATTTATAAGAGAAATCGCA 57.838 29.630 3.02 0.00 43.35 5.10
525 544 1.405872 ATACAGGTCGCCGTTGGATA 58.594 50.000 0.00 0.00 0.00 2.59
548 567 1.522355 CCGCGATCCAGACAATGCT 60.522 57.895 8.23 0.00 0.00 3.79
570 589 2.741211 GAACGGTTGCGGGAGGTC 60.741 66.667 0.00 0.00 0.00 3.85
576 595 2.036098 TTGCGGGAGGTCTACGGA 59.964 61.111 0.00 0.00 0.00 4.69
580 599 1.152819 CGGGAGGTCTACGGATCCA 60.153 63.158 13.41 0.00 33.24 3.41
601 620 3.914426 TCTTGAAGATGCCCTAAGGTC 57.086 47.619 0.00 0.00 34.57 3.85
605 624 0.912486 AAGATGCCCTAAGGTCGCTT 59.088 50.000 0.00 0.00 34.57 4.68
606 625 0.179000 AGATGCCCTAAGGTCGCTTG 59.821 55.000 0.00 0.00 34.57 4.01
607 626 0.107654 GATGCCCTAAGGTCGCTTGT 60.108 55.000 0.00 0.00 34.57 3.16
609 628 1.295423 GCCCTAAGGTCGCTTGTGA 59.705 57.895 0.00 0.00 34.57 3.58
610 629 0.741221 GCCCTAAGGTCGCTTGTGAG 60.741 60.000 0.00 0.00 34.57 3.51
611 630 0.741221 CCCTAAGGTCGCTTGTGAGC 60.741 60.000 5.37 5.37 45.65 4.26
615 634 1.963338 AGGTCGCTTGTGAGCTTGC 60.963 57.895 9.70 0.00 46.96 4.01
616 635 1.963338 GGTCGCTTGTGAGCTTGCT 60.963 57.895 6.18 0.00 46.96 3.91
617 636 0.670546 GGTCGCTTGTGAGCTTGCTA 60.671 55.000 6.18 0.00 46.96 3.49
618 637 0.718343 GTCGCTTGTGAGCTTGCTAG 59.282 55.000 0.00 0.00 46.96 3.42
619 638 0.390340 TCGCTTGTGAGCTTGCTAGG 60.390 55.000 0.00 0.00 46.96 3.02
620 639 0.671781 CGCTTGTGAGCTTGCTAGGT 60.672 55.000 0.00 0.00 46.96 3.08
622 641 1.198637 GCTTGTGAGCTTGCTAGGTTG 59.801 52.381 0.48 0.00 45.65 3.77
623 642 1.808945 CTTGTGAGCTTGCTAGGTTGG 59.191 52.381 0.48 0.00 30.79 3.77
625 644 0.322008 GTGAGCTTGCTAGGTTGGCT 60.322 55.000 0.48 0.00 35.86 4.75
626 645 0.401738 TGAGCTTGCTAGGTTGGCTT 59.598 50.000 0.48 0.00 33.13 4.35
627 646 0.807496 GAGCTTGCTAGGTTGGCTTG 59.193 55.000 0.48 0.00 33.13 4.01
628 647 0.401738 AGCTTGCTAGGTTGGCTTGA 59.598 50.000 0.00 0.00 0.00 3.02
629 648 1.005215 AGCTTGCTAGGTTGGCTTGAT 59.995 47.619 0.00 0.00 0.00 2.57
630 649 2.239654 AGCTTGCTAGGTTGGCTTGATA 59.760 45.455 0.00 0.00 0.00 2.15
631 650 3.117738 AGCTTGCTAGGTTGGCTTGATAT 60.118 43.478 0.00 0.00 0.00 1.63
632 651 3.633986 GCTTGCTAGGTTGGCTTGATATT 59.366 43.478 0.00 0.00 0.00 1.28
633 652 4.098501 GCTTGCTAGGTTGGCTTGATATTT 59.901 41.667 0.00 0.00 0.00 1.40
634 653 5.394553 GCTTGCTAGGTTGGCTTGATATTTT 60.395 40.000 0.00 0.00 0.00 1.82
635 654 6.183360 GCTTGCTAGGTTGGCTTGATATTTTA 60.183 38.462 0.00 0.00 0.00 1.52
636 655 7.470563 GCTTGCTAGGTTGGCTTGATATTTTAT 60.471 37.037 0.00 0.00 0.00 1.40
639 658 5.535753 AGGTTGGCTTGATATTTTATGGC 57.464 39.130 0.00 0.00 0.00 4.40
640 659 5.211201 AGGTTGGCTTGATATTTTATGGCT 58.789 37.500 0.00 0.00 0.00 4.75
641 660 5.662657 AGGTTGGCTTGATATTTTATGGCTT 59.337 36.000 0.00 0.00 0.00 4.35
642 661 6.838612 AGGTTGGCTTGATATTTTATGGCTTA 59.161 34.615 0.00 0.00 0.00 3.09
644 663 7.599998 GGTTGGCTTGATATTTTATGGCTTATG 59.400 37.037 0.00 0.00 0.00 1.90
651 670 6.595326 TGATATTTTATGGCTTATGCTCCTCG 59.405 38.462 0.13 0.00 39.59 4.63
660 679 4.172505 GCTTATGCTCCTCGTAGATGATG 58.827 47.826 0.00 0.00 33.32 3.07
664 683 4.837896 TGCTCCTCGTAGATGATGTAAG 57.162 45.455 0.00 0.00 33.89 2.34
727 751 1.676678 GGACCTGAGCTGCCGACATA 61.677 60.000 0.00 0.00 0.00 2.29
729 753 1.227380 CCTGAGCTGCCGACATACC 60.227 63.158 0.00 0.00 0.00 2.73
737 761 2.202878 CCGACATACCCGCAGTGG 60.203 66.667 0.00 0.00 37.55 4.00
761 785 3.118482 TGACTGCTCTGATCTGAATTCCC 60.118 47.826 2.27 0.00 0.00 3.97
765 789 3.181447 TGCTCTGATCTGAATTCCCCATC 60.181 47.826 2.27 2.57 0.00 3.51
778 802 1.351017 TCCCCATCGCTTTTGACTTCT 59.649 47.619 0.00 0.00 0.00 2.85
779 803 1.470098 CCCCATCGCTTTTGACTTCTG 59.530 52.381 0.00 0.00 0.00 3.02
794 818 4.142469 TGACTTCTGCGACTATGATTCGAA 60.142 41.667 0.00 0.00 38.85 3.71
842 866 2.096980 GCGCTAAAATTAGGTGGTGGTC 59.903 50.000 0.00 0.00 0.00 4.02
875 902 3.399330 ACTTCCTTACACGAACCACATG 58.601 45.455 0.00 0.00 0.00 3.21
897 924 1.394917 GGTGCATTTCGCTGTCACTAG 59.605 52.381 0.00 0.00 43.06 2.57
898 925 1.078709 TGCATTTCGCTGTCACTAGC 58.921 50.000 0.00 0.00 43.06 3.42
899 926 1.338105 TGCATTTCGCTGTCACTAGCT 60.338 47.619 0.00 0.00 41.51 3.32
906 933 1.668101 GCTGTCACTAGCTACGCCCT 61.668 60.000 0.00 0.00 40.52 5.19
969 996 1.746615 CCATCGCCACTCCACAAGG 60.747 63.158 0.00 0.00 0.00 3.61
976 1003 0.670546 CCACTCCACAAGGCACTACG 60.671 60.000 0.00 0.00 38.49 3.51
1215 3975 2.791927 TCGTGGCGAGACGATGAG 59.208 61.111 5.35 0.00 43.26 2.90
1254 4014 1.956170 CGAGTGCAGCAACCGAACT 60.956 57.895 11.14 0.00 0.00 3.01
1261 4021 2.904866 GCAACCGAACTGGCCACA 60.905 61.111 0.00 0.00 43.94 4.17
1356 4134 2.360483 CACTCTACGACATCTGAGGCAT 59.640 50.000 0.00 0.00 0.00 4.40
1441 4219 0.754957 CCTGACGCATCTCCTCCTCT 60.755 60.000 0.00 0.00 0.00 3.69
1512 4290 2.237143 CAACCTGCTCATCCTTGACCTA 59.763 50.000 0.00 0.00 0.00 3.08
1522 4306 6.687393 GCTCATCCTTGACCTATCAAATCAGA 60.687 42.308 0.00 0.00 44.28 3.27
1545 4329 0.319297 ACAGTTGTTACTCGCCCGAC 60.319 55.000 0.00 0.00 30.26 4.79
1797 4581 3.274288 CAACTACTTGGCTTGGGATCTC 58.726 50.000 0.00 0.00 0.00 2.75
1812 4596 2.627699 GGATCTCCCTGCTCTTAGAGTG 59.372 54.545 11.18 4.50 31.39 3.51
1817 4601 2.234908 TCCCTGCTCTTAGAGTGCTTTC 59.765 50.000 11.18 0.00 35.86 2.62
1836 4620 3.769739 TCAATGTATAGCTGCGGGATT 57.230 42.857 0.00 0.00 0.00 3.01
1839 4623 3.492102 ATGTATAGCTGCGGGATTTGT 57.508 42.857 0.00 0.00 0.00 2.83
1844 4628 0.037590 AGCTGCGGGATTTGTGGTTA 59.962 50.000 0.00 0.00 0.00 2.85
1880 4664 2.277084 CGGAAACTTTACCTCCATCCG 58.723 52.381 0.00 0.00 41.81 4.18
1888 4672 3.769739 TTACCTCCATCCGATCATTGG 57.230 47.619 0.00 0.00 0.00 3.16
1914 4698 3.670625 TGACAATAACAACTTCTCCGGG 58.329 45.455 0.00 0.00 0.00 5.73
1945 4729 3.728845 TCGACCTTCAAGAAACTCAAGG 58.271 45.455 0.00 0.00 41.20 3.61
1988 4772 1.077716 ACAACCTCATTAGCGGGGC 60.078 57.895 0.00 0.00 0.00 5.80
2004 4788 3.866651 CGGGGCCATAGAAGATCTATTG 58.133 50.000 4.39 0.00 37.58 1.90
2005 4789 3.261897 CGGGGCCATAGAAGATCTATTGT 59.738 47.826 4.39 0.00 37.58 2.71
2006 4790 4.263068 CGGGGCCATAGAAGATCTATTGTT 60.263 45.833 4.39 0.00 37.58 2.83
2057 4841 1.102154 TTGCACTTGGACCACAACAG 58.898 50.000 0.00 0.00 34.76 3.16
2058 4842 1.360192 GCACTTGGACCACAACAGC 59.640 57.895 0.00 0.00 34.76 4.40
2104 4888 2.847327 AGAGCACTTTAGCAGCTTGA 57.153 45.000 0.00 0.00 39.02 3.02
2118 4902 1.845809 GCTTGACCACACTTCGGCTG 61.846 60.000 0.00 0.00 0.00 4.85
2186 4970 9.403583 AGAACTCACAAATTTAAAGGAGTTACA 57.596 29.630 18.14 0.00 43.40 2.41
2256 5040 3.764434 TGAACCTGACTAGCCTAGAAGTG 59.236 47.826 5.58 0.76 0.00 3.16
2283 5067 5.299531 GTGGCTCTCCAATAATTCCTTAACC 59.700 44.000 0.00 0.00 45.53 2.85
2284 5068 4.515567 GGCTCTCCAATAATTCCTTAACCG 59.484 45.833 0.00 0.00 0.00 4.44
2515 5299 2.115910 TTGGCAGGCTTCCCACAG 59.884 61.111 0.00 0.00 0.00 3.66
2544 5328 3.763360 TGTTTGGTGGATTGGAAGCTATG 59.237 43.478 0.00 0.00 0.00 2.23
2671 5455 5.069648 CCAACAGATATTAGAGCACCAGAGA 59.930 44.000 0.00 0.00 0.00 3.10
2679 5463 1.085091 GAGCACCAGAGATGCAAGTG 58.915 55.000 0.00 0.00 45.92 3.16
2821 5605 3.003275 TCACGCACCAGAAACTTCAAATC 59.997 43.478 0.00 0.00 0.00 2.17
2828 5612 6.534793 GCACCAGAAACTTCAAATCTTTTCAA 59.465 34.615 0.00 0.00 31.57 2.69
2858 5642 3.832276 TGCATAACAACAATCTTTCGGC 58.168 40.909 0.00 0.00 0.00 5.54
2892 5676 5.909477 TCGTTTCTTCAGAGGTGTAAAGAA 58.091 37.500 0.00 0.00 36.29 2.52
3028 5812 2.618053 GTATCCCTGTTGAACTCACCG 58.382 52.381 0.00 0.00 0.00 4.94
3088 5872 2.845659 ACATCTCAGGGGACATACCAA 58.154 47.619 0.00 0.00 41.20 3.67
3167 5951 5.371115 TTCCAAATTGTCCACTTTCGATC 57.629 39.130 0.00 0.00 0.00 3.69
3209 5996 3.369175 TCATCGATCCCTCTGATATGGG 58.631 50.000 0.00 0.00 44.66 4.00
3273 6060 0.930310 CAGGAATCGCGTACATGGTG 59.070 55.000 5.77 0.00 0.00 4.17
3317 6104 5.053145 CAGATTAACAGGGAAGATTCCTCG 58.947 45.833 11.28 5.60 46.72 4.63
3414 6201 1.639722 TTGGTGAGCTACAGGCAGTA 58.360 50.000 0.00 0.00 44.79 2.74
3513 6304 8.303876 ACCCATTTGAACTTGTCATATAACAAC 58.696 33.333 0.00 0.00 35.70 3.32
4843 7692 9.383519 TGAGCAAACTCCAGTAAGAATAAATAG 57.616 33.333 0.00 0.00 42.74 1.73
4844 7693 9.601217 GAGCAAACTCCAGTAAGAATAAATAGA 57.399 33.333 0.00 0.00 36.90 1.98
4845 7694 9.384764 AGCAAACTCCAGTAAGAATAAATAGAC 57.615 33.333 0.00 0.00 0.00 2.59
4846 7695 8.328864 GCAAACTCCAGTAAGAATAAATAGACG 58.671 37.037 0.00 0.00 0.00 4.18
4847 7696 9.582431 CAAACTCCAGTAAGAATAAATAGACGA 57.418 33.333 0.00 0.00 0.00 4.20
4851 7700 8.644318 TCCAGTAAGAATAAATAGACGAAAGC 57.356 34.615 0.00 0.00 0.00 3.51
4852 7701 8.255206 TCCAGTAAGAATAAATAGACGAAAGCA 58.745 33.333 0.00 0.00 0.00 3.91
4854 7703 9.088512 CAGTAAGAATAAATAGACGAAAGCAGT 57.911 33.333 0.00 0.00 0.00 4.40
4855 7704 9.654663 AGTAAGAATAAATAGACGAAAGCAGTT 57.345 29.630 0.00 0.00 0.00 3.16
4856 7705 9.690434 GTAAGAATAAATAGACGAAAGCAGTTG 57.310 33.333 0.00 0.00 0.00 3.16
4857 7706 7.308782 AGAATAAATAGACGAAAGCAGTTGG 57.691 36.000 0.00 0.00 0.00 3.77
4858 7707 3.831715 AAATAGACGAAAGCAGTTGGC 57.168 42.857 0.00 0.00 45.30 4.52
4867 7716 4.090057 GCAGTTGGCGCTCGAACC 62.090 66.667 7.64 0.00 0.00 3.62
4868 7717 2.357517 CAGTTGGCGCTCGAACCT 60.358 61.111 7.64 0.00 0.00 3.50
4869 7718 2.357517 AGTTGGCGCTCGAACCTG 60.358 61.111 7.64 0.00 0.00 4.00
4870 7719 4.090057 GTTGGCGCTCGAACCTGC 62.090 66.667 7.64 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 90 4.360405 AAACCCATTCCGGCGCCT 62.360 61.111 26.68 1.35 0.00 5.52
98 100 4.796495 GCCGGCGGAGAAACCCAT 62.796 66.667 33.44 0.00 34.64 4.00
182 184 0.038526 GACACGTGACTGGACGGAAT 60.039 55.000 25.01 0.00 43.84 3.01
256 258 0.322997 CCATTAAAGTGGCCCACCGA 60.323 55.000 11.06 0.00 39.70 4.69
315 317 2.526304 AGAGCGCGCCTTCAATATTA 57.474 45.000 30.33 0.00 0.00 0.98
353 356 4.007644 CCGCCAGACACCAGCTGA 62.008 66.667 17.39 0.00 35.39 4.26
418 434 3.570912 GGAATCCGGACTAATCCCAAA 57.429 47.619 6.12 0.00 42.83 3.28
435 451 1.539372 TAGGGGAGGTTTGCGGGAA 60.539 57.895 0.00 0.00 0.00 3.97
471 490 2.223971 GGTCCGGATGCGATTTCTCTTA 60.224 50.000 7.81 0.00 0.00 2.10
473 492 0.105039 GGTCCGGATGCGATTTCTCT 59.895 55.000 7.81 0.00 0.00 3.10
548 567 0.174845 CTCCCGCAACCGTTCAGATA 59.825 55.000 0.00 0.00 0.00 1.98
580 599 3.181461 CGACCTTAGGGCATCTTCAAGAT 60.181 47.826 4.44 0.00 33.70 2.40
605 624 0.606401 GCCAACCTAGCAAGCTCACA 60.606 55.000 0.00 0.00 0.00 3.58
606 625 0.322008 AGCCAACCTAGCAAGCTCAC 60.322 55.000 0.00 0.00 0.00 3.51
607 626 0.401738 AAGCCAACCTAGCAAGCTCA 59.598 50.000 0.00 0.00 32.19 4.26
609 628 0.401738 TCAAGCCAACCTAGCAAGCT 59.598 50.000 0.00 0.00 34.64 3.74
610 629 1.467920 ATCAAGCCAACCTAGCAAGC 58.532 50.000 0.00 0.00 0.00 4.01
611 630 5.841957 AAATATCAAGCCAACCTAGCAAG 57.158 39.130 0.00 0.00 0.00 4.01
612 631 7.201902 CCATAAAATATCAAGCCAACCTAGCAA 60.202 37.037 0.00 0.00 0.00 3.91
615 634 6.491403 AGCCATAAAATATCAAGCCAACCTAG 59.509 38.462 0.00 0.00 0.00 3.02
616 635 6.372931 AGCCATAAAATATCAAGCCAACCTA 58.627 36.000 0.00 0.00 0.00 3.08
617 636 5.211201 AGCCATAAAATATCAAGCCAACCT 58.789 37.500 0.00 0.00 0.00 3.50
618 637 5.535753 AGCCATAAAATATCAAGCCAACC 57.464 39.130 0.00 0.00 0.00 3.77
619 638 7.116805 GCATAAGCCATAAAATATCAAGCCAAC 59.883 37.037 0.00 0.00 33.58 3.77
620 639 7.015487 AGCATAAGCCATAAAATATCAAGCCAA 59.985 33.333 0.00 0.00 43.56 4.52
622 641 6.928520 AGCATAAGCCATAAAATATCAAGCC 58.071 36.000 0.00 0.00 43.56 4.35
623 642 7.031975 GGAGCATAAGCCATAAAATATCAAGC 58.968 38.462 0.00 0.00 43.56 4.01
625 644 7.119699 CGAGGAGCATAAGCCATAAAATATCAA 59.880 37.037 0.00 0.00 43.56 2.57
626 645 6.595326 CGAGGAGCATAAGCCATAAAATATCA 59.405 38.462 0.00 0.00 43.56 2.15
627 646 6.595716 ACGAGGAGCATAAGCCATAAAATATC 59.404 38.462 0.00 0.00 43.56 1.63
628 647 6.476378 ACGAGGAGCATAAGCCATAAAATAT 58.524 36.000 0.00 0.00 43.56 1.28
629 648 5.865085 ACGAGGAGCATAAGCCATAAAATA 58.135 37.500 0.00 0.00 43.56 1.40
630 649 4.718961 ACGAGGAGCATAAGCCATAAAAT 58.281 39.130 0.00 0.00 43.56 1.82
631 650 4.150897 ACGAGGAGCATAAGCCATAAAA 57.849 40.909 0.00 0.00 43.56 1.52
632 651 3.838244 ACGAGGAGCATAAGCCATAAA 57.162 42.857 0.00 0.00 43.56 1.40
633 652 4.149598 TCTACGAGGAGCATAAGCCATAA 58.850 43.478 0.00 0.00 43.56 1.90
634 653 3.763057 TCTACGAGGAGCATAAGCCATA 58.237 45.455 0.00 0.00 43.56 2.74
635 654 2.598565 TCTACGAGGAGCATAAGCCAT 58.401 47.619 0.00 0.00 43.56 4.40
636 655 2.067365 TCTACGAGGAGCATAAGCCA 57.933 50.000 0.00 0.00 43.56 4.75
639 658 5.384063 ACATCATCTACGAGGAGCATAAG 57.616 43.478 0.00 0.00 0.00 1.73
640 659 6.570571 GCTTACATCATCTACGAGGAGCATAA 60.571 42.308 0.00 0.00 0.00 1.90
641 660 5.106118 GCTTACATCATCTACGAGGAGCATA 60.106 44.000 0.00 0.00 0.00 3.14
642 661 4.321601 GCTTACATCATCTACGAGGAGCAT 60.322 45.833 0.00 0.00 0.00 3.79
644 663 3.570559 GCTTACATCATCTACGAGGAGC 58.429 50.000 0.00 0.00 0.00 4.70
651 670 7.709269 TGAAATAACCGCTTACATCATCTAC 57.291 36.000 0.00 0.00 0.00 2.59
689 708 8.869109 TCAGGTCCATTTCTTTCAAACAAATAT 58.131 29.630 0.00 0.00 0.00 1.28
695 714 4.279420 AGCTCAGGTCCATTTCTTTCAAAC 59.721 41.667 0.00 0.00 0.00 2.93
700 719 2.165998 GCAGCTCAGGTCCATTTCTTT 58.834 47.619 0.00 0.00 0.00 2.52
703 727 1.372087 CGGCAGCTCAGGTCCATTTC 61.372 60.000 0.00 0.00 0.00 2.17
706 730 2.685017 TCGGCAGCTCAGGTCCAT 60.685 61.111 0.00 0.00 0.00 3.41
737 761 3.540314 ATTCAGATCAGAGCAGTCACC 57.460 47.619 0.00 0.00 0.00 4.02
761 785 2.253392 GCAGAAGTCAAAAGCGATGG 57.747 50.000 0.00 0.00 0.00 3.51
778 802 3.186909 CTGGTTTCGAATCATAGTCGCA 58.813 45.455 0.00 0.00 38.39 5.10
779 803 3.187700 ACTGGTTTCGAATCATAGTCGC 58.812 45.455 0.00 0.00 38.39 5.19
785 809 2.742053 CCAACGACTGGTTTCGAATCAT 59.258 45.455 0.00 0.00 41.78 2.45
809 833 3.840890 TTTTAGCGCGTGAAATTCCAT 57.159 38.095 8.43 0.00 0.00 3.41
855 882 3.186409 CACATGTGGTTCGTGTAAGGAAG 59.814 47.826 18.51 0.00 41.92 3.46
884 911 3.990546 CGTAGCTAGTGACAGCGAA 57.009 52.632 0.00 0.00 46.52 4.70
898 925 1.280142 CAGTCGATCGAGGGCGTAG 59.720 63.158 20.09 0.00 38.98 3.51
899 926 2.184830 CCAGTCGATCGAGGGCGTA 61.185 63.158 20.09 0.00 38.98 4.42
906 933 1.981256 TGGATCATCCAGTCGATCGA 58.019 50.000 15.15 15.15 42.67 3.59
969 996 0.580104 GTGTGGTGTGTTCGTAGTGC 59.420 55.000 0.00 0.00 0.00 4.40
976 1003 2.634600 TGGTACTTGTGTGGTGTGTTC 58.365 47.619 0.00 0.00 0.00 3.18
1212 3972 1.683385 CCTATCCATCGACAGCACTCA 59.317 52.381 0.00 0.00 0.00 3.41
1215 3975 0.941463 CGCCTATCCATCGACAGCAC 60.941 60.000 0.00 0.00 0.00 4.40
1254 4014 0.745486 CGAGCTTGATGATGTGGCCA 60.745 55.000 0.00 0.00 0.00 5.36
1280 4040 0.545787 ACCCATGGTGTTAGACCCGA 60.546 55.000 11.73 0.00 45.45 5.14
1441 4219 2.314647 CGCCGAAAAACGAGCCAGA 61.315 57.895 0.00 0.00 45.77 3.86
1512 4290 5.717078 AACAACTGTGCATCTGATTTGAT 57.283 34.783 0.00 0.00 0.00 2.57
1522 4306 1.156736 GGCGAGTAACAACTGTGCAT 58.843 50.000 0.00 0.00 0.00 3.96
1545 4329 4.147449 TGCGAGACCCATGCGAGG 62.147 66.667 0.00 0.00 0.00 4.63
1578 4362 1.279271 ACCTGAGACATGCCAAGGTAC 59.721 52.381 4.85 0.00 0.00 3.34
1797 4581 2.027745 TGAAAGCACTCTAAGAGCAGGG 60.028 50.000 2.35 0.00 34.13 4.45
1812 4596 2.031682 CCCGCAGCTATACATTGAAAGC 60.032 50.000 0.00 0.00 35.16 3.51
1817 4601 3.565482 ACAAATCCCGCAGCTATACATTG 59.435 43.478 0.00 0.00 0.00 2.82
1836 4620 3.202829 GCGGAAGGGATATAACCACAA 57.797 47.619 0.99 0.00 0.00 3.33
1880 4664 6.757897 TGTTATTGTCAAGGACCAATGATC 57.242 37.500 3.60 0.00 0.00 2.92
1888 4672 5.107065 CGGAGAAGTTGTTATTGTCAAGGAC 60.107 44.000 0.00 0.00 0.00 3.85
1914 4698 0.107703 TGAAGGTCGATGGCACCATC 60.108 55.000 18.05 18.05 46.71 3.51
1945 4729 8.119226 GTGTGATAATCTGAGCATTTGTAGTTC 58.881 37.037 0.00 0.00 0.00 3.01
1988 4772 9.887629 ATCTATGCAACAATAGATCTTCTATGG 57.112 33.333 0.00 0.00 43.38 2.74
2078 4862 3.061429 GCTGCTAAAGTGCTCTAAACGAG 59.939 47.826 0.00 0.00 42.88 4.18
2082 4866 4.452455 GTCAAGCTGCTAAAGTGCTCTAAA 59.548 41.667 0.90 0.00 35.85 1.85
2104 4888 0.396435 TCATTCAGCCGAAGTGTGGT 59.604 50.000 0.00 0.00 33.74 4.16
2118 4902 7.040409 ACCTCTCCAAATAGTTTGTTGTCATTC 60.040 37.037 2.22 0.00 38.98 2.67
2186 4970 7.272037 CCATGTAGGTTGTTTGAGTTTAACT 57.728 36.000 0.00 0.00 0.00 2.24
2256 5040 4.273318 AGGAATTATTGGAGAGCCACAAC 58.727 43.478 0.00 0.00 45.94 3.32
2515 5299 5.017294 TCCAATCCACCAAACAGAAAAAC 57.983 39.130 0.00 0.00 0.00 2.43
2544 5328 8.317679 AGCTGGTTAGAACTGATATCCAATATC 58.682 37.037 0.00 0.88 41.56 1.63
2650 5434 5.279406 GCATCTCTGGTGCTCTAATATCTGT 60.279 44.000 0.00 0.00 39.45 3.41
2659 5443 0.982704 ACTTGCATCTCTGGTGCTCT 59.017 50.000 4.42 0.00 42.92 4.09
2671 5455 3.571748 AGAGCATGAGCACTTGCAT 57.428 47.368 20.88 8.80 45.55 3.96
2679 5463 5.069501 AGGAATTTTTGAAGAGCATGAGC 57.930 39.130 0.00 0.00 42.56 4.26
2748 5532 7.455008 AGTTGGTTCTCTGATAGGTCTAAGAAA 59.545 37.037 0.00 0.00 31.81 2.52
2828 5612 5.416952 AGATTGTTGTTATGCAAGCTAAGCT 59.583 36.000 11.76 0.00 39.21 3.74
2839 5623 5.295431 TCTGCCGAAAGATTGTTGTTATG 57.705 39.130 0.00 0.00 0.00 1.90
2858 5642 6.402983 CCTCTGAAGAAACGATGGAAATTCTG 60.403 42.308 0.00 0.00 32.72 3.02
2892 5676 7.568349 TGTATGCTAGATCAAGGAATTTCAGT 58.432 34.615 0.00 0.00 0.00 3.41
2910 5694 5.163478 GCTCCCAGAAAATTGATTGTATGCT 60.163 40.000 0.00 0.00 0.00 3.79
3088 5872 3.640029 GCCATGAGATTCCCAAATGACAT 59.360 43.478 0.00 0.00 0.00 3.06
3094 5878 3.836146 CCATAGCCATGAGATTCCCAAA 58.164 45.455 0.00 0.00 33.67 3.28
3167 5951 3.997021 GAGGAACATATATGTGGAAGCCG 59.003 47.826 18.94 0.00 41.61 5.52
3209 5996 2.335316 TGTGACCACCACCAAACTAC 57.665 50.000 0.00 0.00 45.09 2.73
3273 6060 5.984926 TCTGTTGCAGGAAAAATCAATGTTC 59.015 36.000 0.00 0.00 31.51 3.18
3317 6104 1.334869 CTACAAGCATGCCGATTTCCC 59.665 52.381 15.66 0.00 0.00 3.97
3347 6134 7.340232 TGAGATGATTCCAAGACAAATTTAGGG 59.660 37.037 0.00 0.00 0.00 3.53
3414 6201 6.459024 CGTTATGAGAGAGGTCGAAAGATTCT 60.459 42.308 0.00 0.00 45.19 2.40
3513 6304 3.005897 CAGATGGTATAGTTCCCGTCAGG 59.994 52.174 0.00 0.00 38.91 3.86
4843 7692 2.127232 GCGCCAACTGCTTTCGTC 60.127 61.111 0.00 0.00 38.05 4.20
4844 7693 2.591715 AGCGCCAACTGCTTTCGT 60.592 55.556 2.29 0.00 40.48 3.85
4845 7694 2.174349 GAGCGCCAACTGCTTTCG 59.826 61.111 2.29 0.00 44.18 3.46
4846 7695 1.841663 TTCGAGCGCCAACTGCTTTC 61.842 55.000 2.29 0.00 44.18 2.62
4847 7696 1.891919 TTCGAGCGCCAACTGCTTT 60.892 52.632 2.29 0.00 44.18 3.51
4848 7697 2.280797 TTCGAGCGCCAACTGCTT 60.281 55.556 2.29 0.00 44.18 3.91
4851 7700 2.357517 AGGTTCGAGCGCCAACTG 60.358 61.111 2.29 0.00 0.00 3.16
4852 7701 2.357517 CAGGTTCGAGCGCCAACT 60.358 61.111 2.29 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.