Multiple sequence alignment - TraesCS2A01G179800

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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 TraesCS2A01G179800 chr2A 100.000 3098 0 0 2259 5356 138191067 138187970 0.000000e+00 5722.0
1 TraesCS2A01G179800 chr2A 100.000 2022 0 0 1 2022 138193325 138191304 0.000000e+00 3735.0
2 TraesCS2A01G179800 chr2D 95.271 2474 95 11 2535 4993 131473071 131470605 0.000000e+00 3901.0
3 TraesCS2A01G179800 chr2D 92.441 1151 47 9 867 1993 131474774 131473640 0.000000e+00 1607.0
4 TraesCS2A01G179800 chr2D 88.337 523 48 3 18 530 131479960 131479441 2.740000e-172 616.0
5 TraesCS2A01G179800 chr2D 90.028 361 22 9 5003 5356 131470553 131470200 6.320000e-124 455.0
6 TraesCS2A01G179800 chr2D 96.133 181 6 1 2259 2438 131473358 131473178 1.460000e-75 294.0
7 TraesCS2A01G179800 chr2D 91.667 156 10 2 574 728 131475516 131475363 4.200000e-51 213.0
8 TraesCS2A01G179800 chr2D 89.744 117 12 0 3887 4003 489409540 489409424 3.340000e-32 150.0
9 TraesCS2A01G179800 chr2D 96.610 59 2 0 2477 2535 131473163 131473105 1.230000e-16 99.0
10 TraesCS2A01G179800 chr2D 100.000 30 0 0 727 756 131475142 131475113 7.490000e-04 56.5
11 TraesCS2A01G179800 chr2B 94.667 2269 98 5 2538 4802 185814285 185812036 0.000000e+00 3498.0
12 TraesCS2A01G179800 chr2B 95.722 561 18 2 1435 1995 185815562 185815008 0.000000e+00 898.0
13 TraesCS2A01G179800 chr2B 92.534 442 17 7 953 1393 185815995 185815569 2.120000e-173 619.0
14 TraesCS2A01G179800 chr2B 87.368 285 12 9 2259 2535 185814590 185814322 6.740000e-79 305.0
15 TraesCS2A01G179800 chr2B 88.426 216 16 3 5002 5208 185811782 185811567 8.900000e-63 252.0
16 TraesCS2A01G179800 chr2B 91.975 162 11 2 4789 4950 185812017 185811858 5.400000e-55 226.0
17 TraesCS2A01G179800 chr2B 89.744 117 12 0 3887 4003 572791175 572791059 3.340000e-32 150.0
18 TraesCS2A01G179800 chr3A 75.697 753 120 25 23 728 20296734 20297470 8.660000e-83 318.0
19 TraesCS2A01G179800 chr7D 75.157 636 94 20 134 728 13078550 13079162 1.930000e-59 241.0
20 TraesCS2A01G179800 chr1A 78.571 280 47 8 458 728 517521606 517521331 7.130000e-39 172.0
21 TraesCS2A01G179800 chr5D 90.244 123 12 0 3881 4003 412263451 412263329 1.540000e-35 161.0
22 TraesCS2A01G179800 chr7A 88.462 130 14 1 3874 4003 498590253 498590381 7.180000e-34 156.0
23 TraesCS2A01G179800 chr6B 86.567 134 18 0 3870 4003 314590349 314590482 1.200000e-31 148.0
24 TraesCS2A01G179800 chr6B 100.000 31 0 0 727 757 571742759 571742789 2.080000e-04 58.4
25 TraesCS2A01G179800 chr6A 85.821 134 19 0 3870 4003 352665660 352665793 5.590000e-30 143.0
26 TraesCS2A01G179800 chr5B 85.401 137 19 1 3874 4010 323708753 323708888 2.010000e-29 141.0
27 TraesCS2A01G179800 chr4B 90.361 83 8 0 4911 4993 209048597 209048679 5.670000e-20 110.0


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 TraesCS2A01G179800 chr2A 138187970 138193325 5355 True 4728.500000 5722 100.000000 1 5356 2 chr2A.!!$R1 5355
1 TraesCS2A01G179800 chr2D 131470200 131479960 9760 True 905.187500 3901 93.810875 18 5356 8 chr2D.!!$R2 5338
2 TraesCS2A01G179800 chr2B 185811567 185815995 4428 True 966.333333 3498 91.782000 953 5208 6 chr2B.!!$R2 4255
3 TraesCS2A01G179800 chr3A 20296734 20297470 736 False 318.000000 318 75.697000 23 728 1 chr3A.!!$F1 705
4 TraesCS2A01G179800 chr7D 13078550 13079162 612 False 241.000000 241 75.157000 134 728 1 chr7D.!!$F1 594

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
732 4792 0.444651 CGCCGCATTCGACCTTTAAA 59.555 50.000 0.00 0.0 38.10 1.52 F
1288 5709 2.159085 AGACAAATCGCCAGCTACTACC 60.159 50.000 0.00 0.0 0.00 3.18 F
1553 5977 0.253160 TGAGCTAGTTGGGACCCCAT 60.253 55.000 8.45 0.0 46.64 4.00 F
1718 6142 1.227823 TGGTGCCGTTGTTGAGGAG 60.228 57.895 0.00 0.0 0.00 3.69 F
2624 7279 1.446907 CTGATCCTGCACCACTTGTC 58.553 55.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 5977 0.034337 GGCGAGTGACTGTTAACCCA 59.966 55.000 2.48 0.0 0.00 4.51 R
3028 7683 3.299503 AGAGATTGGTGCCAAAAACAGT 58.700 40.909 7.81 0.0 39.55 3.55 R
3029 7684 3.318839 TGAGAGATTGGTGCCAAAAACAG 59.681 43.478 7.81 0.0 39.55 3.16 R
3041 7696 6.754702 AAGAATGTGTGAATGAGAGATTGG 57.245 37.500 0.00 0.0 0.00 3.16 R
4608 9267 0.469892 TCAGTGACAGAGGTGCCTGA 60.470 55.000 0.00 0.0 37.59 3.86 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
60 61 9.442033 AGACGTAAAAATAACTAACTTTTGCAC 57.558 29.630 0.00 0.00 0.00 4.57
67 68 3.202829 ACTAACTTTTGCACCTCCGAA 57.797 42.857 0.00 0.00 0.00 4.30
96 97 6.881065 CCAAAACTCTTCTCCAACAGATGATA 59.119 38.462 0.00 0.00 35.33 2.15
130 133 4.664688 AAAAATCACATCTCCACCTCCT 57.335 40.909 0.00 0.00 0.00 3.69
131 134 5.779241 AAAAATCACATCTCCACCTCCTA 57.221 39.130 0.00 0.00 0.00 2.94
152 155 8.474710 TCCTAGAGATGTAAACTATAACACCC 57.525 38.462 0.00 0.00 0.00 4.61
214 217 2.010582 AAACGCAACCACACGCCAAT 62.011 50.000 0.00 0.00 0.00 3.16
270 284 3.760035 CGCTACCAGCCGACCACT 61.760 66.667 0.00 0.00 38.18 4.00
309 323 4.404098 GACGACCCCGCCATTGGT 62.404 66.667 4.26 0.00 39.95 3.67
310 324 4.404098 ACGACCCCGCCATTGGTC 62.404 66.667 4.26 0.00 46.15 4.02
312 326 2.438434 GACCCCGCCATTGGTCTG 60.438 66.667 4.26 0.00 46.13 3.51
356 399 1.817099 GCTGAGGAGCCACCGATTG 60.817 63.158 0.00 0.00 44.74 2.67
400 443 3.055719 CCGCGACACTTGCCCATT 61.056 61.111 8.23 0.00 0.00 3.16
433 487 2.361610 CGCCCCAGTGCCAAATCT 60.362 61.111 0.00 0.00 0.00 2.40
497 551 2.731571 CCGCCCTCCTCCAAATCGA 61.732 63.158 0.00 0.00 0.00 3.59
506 560 2.027561 TCCTCCAAATCGACCGAATTGT 60.028 45.455 16.04 0.00 34.27 2.71
520 589 0.669318 AATTGTCGCTTCTTCGCCGA 60.669 50.000 0.00 0.00 0.00 5.54
521 590 0.669318 ATTGTCGCTTCTTCGCCGAA 60.669 50.000 0.00 0.00 32.31 4.30
550 619 0.465097 CATGATTTGAGCTCGCCCCT 60.465 55.000 9.64 0.00 0.00 4.79
553 622 0.531753 GATTTGAGCTCGCCCCTCTC 60.532 60.000 9.64 0.00 0.00 3.20
554 623 0.980231 ATTTGAGCTCGCCCCTCTCT 60.980 55.000 9.64 0.00 0.00 3.10
555 624 1.608717 TTTGAGCTCGCCCCTCTCTC 61.609 60.000 9.64 0.00 0.00 3.20
679 4629 2.338620 CCAATCCGCCGCTCGATA 59.661 61.111 0.00 0.00 41.67 2.92
687 4637 2.494445 CCGCTCGATACACAGCCA 59.506 61.111 0.00 0.00 31.37 4.75
689 4639 1.153842 CGCTCGATACACAGCCACA 60.154 57.895 0.00 0.00 31.37 4.17
708 4658 3.443045 CGCCCGCCATTCAAGCTT 61.443 61.111 0.00 0.00 0.00 3.74
729 4679 3.124921 CCGCCGCATTCGACCTTT 61.125 61.111 0.00 0.00 38.10 3.11
730 4680 1.812093 CCGCCGCATTCGACCTTTA 60.812 57.895 0.00 0.00 38.10 1.85
732 4792 0.444651 CGCCGCATTCGACCTTTAAA 59.555 50.000 0.00 0.00 38.10 1.52
741 4801 5.807011 GCATTCGACCTTTAAATTTGCATCT 59.193 36.000 0.00 0.00 0.00 2.90
743 4803 7.148590 GCATTCGACCTTTAAATTTGCATCTTT 60.149 33.333 0.00 0.00 0.00 2.52
745 4805 9.921637 ATTCGACCTTTAAATTTGCATCTTTTA 57.078 25.926 0.00 0.00 0.00 1.52
761 4821 5.329035 TCTTTTATTGGAGATGCAAAGGC 57.671 39.130 0.00 0.00 41.68 4.35
849 4944 7.980032 TGGAGATGCTCTTAGATACTAGTACT 58.020 38.462 4.31 0.00 0.00 2.73
850 4945 9.102453 TGGAGATGCTCTTAGATACTAGTACTA 57.898 37.037 4.31 1.89 0.00 1.82
1007 5426 3.933722 CTCGGCGGCCATGGAGAT 61.934 66.667 18.40 0.00 0.00 2.75
1008 5427 3.873026 CTCGGCGGCCATGGAGATC 62.873 68.421 18.40 0.00 0.00 2.75
1010 5429 4.996434 GGCGGCCATGGAGATCGG 62.996 72.222 18.40 2.93 0.00 4.18
1067 5486 3.844090 GCAGACGGCCTCTCCTCC 61.844 72.222 0.00 0.00 36.11 4.30
1084 5503 2.663196 CGTTTCCCGCTTCCTCCT 59.337 61.111 0.00 0.00 0.00 3.69
1275 5696 6.358118 TGCATATACGACCAAAGACAAATC 57.642 37.500 0.00 0.00 0.00 2.17
1288 5709 2.159085 AGACAAATCGCCAGCTACTACC 60.159 50.000 0.00 0.00 0.00 3.18
1365 5786 4.770795 AGCCTGTATTTGTGTCCTATGAC 58.229 43.478 0.00 0.00 42.12 3.06
1366 5787 4.471386 AGCCTGTATTTGTGTCCTATGACT 59.529 41.667 0.00 0.00 42.28 3.41
1367 5788 5.661312 AGCCTGTATTTGTGTCCTATGACTA 59.339 40.000 0.00 0.00 42.28 2.59
1368 5789 6.327626 AGCCTGTATTTGTGTCCTATGACTAT 59.672 38.462 0.00 0.00 42.28 2.12
1369 5790 6.425114 GCCTGTATTTGTGTCCTATGACTATG 59.575 42.308 0.00 0.00 42.28 2.23
1370 5791 7.686859 GCCTGTATTTGTGTCCTATGACTATGA 60.687 40.741 0.00 0.00 42.28 2.15
1384 5805 3.713248 TGACTATGAGGAATCACTGGCAT 59.287 43.478 0.00 0.00 0.00 4.40
1446 5867 7.335422 ACTCAAGTGTCATCTCCAATTAATGTC 59.665 37.037 0.00 0.00 0.00 3.06
1449 5870 7.798596 AGTGTCATCTCCAATTAATGTCATC 57.201 36.000 0.00 0.00 0.00 2.92
1510 5934 5.416952 CCCTTTCTTCACAATTGTGCTCTAT 59.583 40.000 29.84 0.00 45.25 1.98
1553 5977 0.253160 TGAGCTAGTTGGGACCCCAT 60.253 55.000 8.45 0.00 46.64 4.00
1583 6007 1.262151 GTCACTCGCCGTGCTTAAAAA 59.738 47.619 0.47 0.00 43.46 1.94
1634 6058 4.462483 GGACAACATGGGAAAAGAATAGCA 59.538 41.667 0.00 0.00 0.00 3.49
1718 6142 1.227823 TGGTGCCGTTGTTGAGGAG 60.228 57.895 0.00 0.00 0.00 3.69
1869 6293 7.924947 GGGTACTTAACATACAACATAGGACTC 59.075 40.741 0.00 0.00 0.00 3.36
1870 6294 7.646922 GGTACTTAACATACAACATAGGACTCG 59.353 40.741 0.00 0.00 0.00 4.18
1871 6295 7.400599 ACTTAACATACAACATAGGACTCGA 57.599 36.000 0.00 0.00 0.00 4.04
1887 6311 6.354938 AGGACTCGACTGTAGATATGTACAA 58.645 40.000 13.22 0.00 32.49 2.41
1995 6419 6.964934 ACTTCGTGTTGACATTCTGTTTTTAC 59.035 34.615 0.00 0.00 0.00 2.01
1996 6420 5.812652 TCGTGTTGACATTCTGTTTTTACC 58.187 37.500 0.00 0.00 0.00 2.85
1998 6422 5.907391 CGTGTTGACATTCTGTTTTTACCTC 59.093 40.000 0.00 0.00 0.00 3.85
2000 6424 6.912591 GTGTTGACATTCTGTTTTTACCTCAG 59.087 38.462 0.00 0.00 0.00 3.35
2001 6425 6.826231 TGTTGACATTCTGTTTTTACCTCAGA 59.174 34.615 0.00 0.00 36.59 3.27
2003 6427 7.873719 TGACATTCTGTTTTTACCTCAGAAA 57.126 32.000 10.14 0.00 46.41 2.52
2004 6428 7.930217 TGACATTCTGTTTTTACCTCAGAAAG 58.070 34.615 10.14 8.73 46.41 2.62
2005 6429 7.556275 TGACATTCTGTTTTTACCTCAGAAAGT 59.444 33.333 12.46 12.46 46.41 2.66
2006 6430 8.293699 ACATTCTGTTTTTACCTCAGAAAGTT 57.706 30.769 10.14 0.00 46.41 2.66
2007 6431 9.403583 ACATTCTGTTTTTACCTCAGAAAGTTA 57.596 29.630 10.14 0.00 46.41 2.24
2010 6434 8.974060 TCTGTTTTTACCTCAGAAAGTTATGT 57.026 30.769 0.00 0.00 35.65 2.29
2011 6435 9.403583 TCTGTTTTTACCTCAGAAAGTTATGTT 57.596 29.630 0.00 0.00 35.65 2.71
2012 6436 9.450807 CTGTTTTTACCTCAGAAAGTTATGTTG 57.549 33.333 0.00 0.00 0.00 3.33
2013 6437 8.410141 TGTTTTTACCTCAGAAAGTTATGTTGG 58.590 33.333 0.00 0.00 0.00 3.77
2014 6438 7.519032 TTTTACCTCAGAAAGTTATGTTGGG 57.481 36.000 0.00 0.00 0.00 4.12
2015 6439 4.034285 ACCTCAGAAAGTTATGTTGGGG 57.966 45.455 0.00 0.00 0.00 4.96
2016 6440 3.245264 ACCTCAGAAAGTTATGTTGGGGG 60.245 47.826 0.00 0.00 0.00 5.40
2311 6889 9.646522 AAATTATGTGTATCCTGCTTATTCCTT 57.353 29.630 0.00 0.00 0.00 3.36
2461 7048 5.128171 ACTGGTCTGTTCCGCTGTATATTTA 59.872 40.000 0.00 0.00 0.00 1.40
2624 7279 1.446907 CTGATCCTGCACCACTTGTC 58.553 55.000 0.00 0.00 0.00 3.18
2672 7327 7.615039 ATTGGAGTCATCAATCAGACTAGAT 57.385 36.000 0.00 0.00 44.61 1.98
2718 7373 7.688372 AGTTCGCTTTCTATTGTTATGTGATG 58.312 34.615 0.00 0.00 0.00 3.07
2744 7399 6.547880 TCTTTTTGTTGCCACAGTTTCCTATA 59.452 34.615 0.00 0.00 33.22 1.31
2811 7466 5.942236 TCTCATTTAAGCTTGTCATTCTGCT 59.058 36.000 9.86 0.00 37.37 4.24
2871 7526 3.012518 CAATTGCTCTTCGGACCAGAAT 58.987 45.455 0.00 0.00 0.00 2.40
2878 7533 5.815740 TGCTCTTCGGACCAGAATTTATAAC 59.184 40.000 0.00 0.00 0.00 1.89
2907 7562 3.565482 TCACATTTCACTGTTTCCTGCTC 59.435 43.478 0.00 0.00 0.00 4.26
3014 7669 1.913403 GAAGCATTTCACCAAATCGCG 59.087 47.619 0.00 0.00 34.15 5.87
3041 7696 4.149221 GCGGTAATTTACTGTTTTTGGCAC 59.851 41.667 15.13 0.00 37.38 5.01
3043 7698 5.602628 GGTAATTTACTGTTTTTGGCACCA 58.397 37.500 6.52 0.00 0.00 4.17
3088 7744 2.095461 GGGGTCTTGCTTCTTGAATCC 58.905 52.381 0.00 0.00 0.00 3.01
3089 7745 2.555227 GGGGTCTTGCTTCTTGAATCCA 60.555 50.000 0.00 0.00 0.00 3.41
3130 7786 3.874392 ATGGGCTGATGCAGTTAAAAC 57.126 42.857 0.00 0.00 41.91 2.43
3141 7797 7.417612 TGATGCAGTTAAAACTTCTCTTGTTC 58.582 34.615 0.00 0.00 37.08 3.18
3355 8011 4.263727 ACAGGCATATGGTGTGAAGGTAAA 60.264 41.667 4.56 0.00 0.00 2.01
3542 8198 1.915141 ACAGGATCCAGTTTGCTTGG 58.085 50.000 15.82 0.00 0.00 3.61
3690 8346 4.184629 CACTTAGAATTGGAGTCCGGAAG 58.815 47.826 5.23 0.00 0.00 3.46
3997 8653 9.667107 CTAATCTAAGTCAACTAATTTGGGACA 57.333 33.333 13.34 0.00 35.69 4.02
4034 8690 7.097192 TGATAAGCTAGAACTGTTGACGAAAT 58.903 34.615 0.00 0.00 0.00 2.17
4059 8715 1.656587 ACCCAGTCCTCTGCAATACA 58.343 50.000 0.00 0.00 40.09 2.29
4373 9029 8.461249 AGCACTAATTCTCTAATGATTTGCAT 57.539 30.769 0.00 0.00 39.43 3.96
4394 9050 3.146066 TGCCACCTTGTAAGTCATTCAC 58.854 45.455 0.00 0.00 0.00 3.18
4397 9053 4.564821 GCCACCTTGTAAGTCATTCACCTA 60.565 45.833 0.00 0.00 0.00 3.08
4452 9108 2.107366 CTGTTTTGGGGAACACCTTGT 58.893 47.619 0.00 0.00 40.03 3.16
4547 9203 3.551551 GCATGGTGTTTGTACTTCGTTC 58.448 45.455 0.00 0.00 0.00 3.95
4557 9213 6.148150 TGTTTGTACTTCGTTCACATAATCCC 59.852 38.462 0.00 0.00 0.00 3.85
4608 9267 1.418334 AACTGTGTCCTCTGTGCTCT 58.582 50.000 0.00 0.00 0.00 4.09
4613 9272 1.217779 GTCCTCTGTGCTCTCAGGC 59.782 63.158 0.00 0.00 36.25 4.85
4640 9299 5.724328 TCTGTCACTGAATACTTCATGGAC 58.276 41.667 11.23 11.23 40.30 4.02
4649 9308 0.667487 ACTTCATGGACGCTCACACG 60.667 55.000 0.00 0.00 39.50 4.49
4660 9319 3.596066 CTCACACGGCCTGGACTGG 62.596 68.421 0.00 0.00 0.00 4.00
4668 9327 0.988678 GGCCTGGACTGGGATTAGGT 60.989 60.000 0.00 0.00 0.00 3.08
4708 9367 4.377022 CCCGAAGTTACATTCTGTTGAACG 60.377 45.833 0.00 0.00 34.71 3.95
4746 9405 1.571460 CAGTTTGCAGTGCCGAGAC 59.429 57.895 13.72 5.94 0.00 3.36
4763 9422 3.366476 CGAGACCAAGAGACGACTTCAAT 60.366 47.826 0.00 0.00 0.00 2.57
4821 9512 4.818546 CCCTGATACACTAGAAAGGCATTG 59.181 45.833 0.00 0.00 0.00 2.82
4837 9528 3.577667 GCATTGTGCTGAGCATTTGTAA 58.422 40.909 11.58 2.03 41.91 2.41
4868 9559 0.796312 AGCGAATGCAACCGTGTTAG 59.204 50.000 11.76 0.00 46.23 2.34
4918 9611 5.250235 TCGTAAGAGGATGTGATCTGAAC 57.750 43.478 0.00 0.00 45.01 3.18
4940 9633 5.079643 ACATGGTGCAGAAAGACCTAAATT 58.920 37.500 0.00 0.00 32.98 1.82
4944 9637 5.596361 TGGTGCAGAAAGACCTAAATTGAAA 59.404 36.000 0.00 0.00 32.98 2.69
4946 9639 6.587608 GGTGCAGAAAGACCTAAATTGAAATG 59.412 38.462 0.00 0.00 0.00 2.32
4977 9682 3.904717 TGCCTCTGGAACTTTTTGGTTA 58.095 40.909 0.00 0.00 0.00 2.85
5100 9859 1.645034 CATGATTCGTCGCCTCTTGT 58.355 50.000 0.00 0.00 0.00 3.16
5101 9860 1.325640 CATGATTCGTCGCCTCTTGTG 59.674 52.381 0.00 0.00 0.00 3.33
5102 9861 1.014044 TGATTCGTCGCCTCTTGTGC 61.014 55.000 0.00 0.00 0.00 4.57
5103 9862 0.737715 GATTCGTCGCCTCTTGTGCT 60.738 55.000 0.00 0.00 0.00 4.40
5104 9863 1.016130 ATTCGTCGCCTCTTGTGCTG 61.016 55.000 0.00 0.00 0.00 4.41
5105 9864 3.782244 CGTCGCCTCTTGTGCTGC 61.782 66.667 0.00 0.00 0.00 5.25
5106 9865 2.358003 GTCGCCTCTTGTGCTGCT 60.358 61.111 0.00 0.00 0.00 4.24
5107 9866 2.357881 TCGCCTCTTGTGCTGCTG 60.358 61.111 0.00 0.00 0.00 4.41
5108 9867 2.667536 CGCCTCTTGTGCTGCTGT 60.668 61.111 0.00 0.00 0.00 4.40
5109 9868 2.675056 CGCCTCTTGTGCTGCTGTC 61.675 63.158 0.00 0.00 0.00 3.51
5110 9869 1.598962 GCCTCTTGTGCTGCTGTCA 60.599 57.895 0.00 0.00 0.00 3.58
5111 9870 0.959372 GCCTCTTGTGCTGCTGTCAT 60.959 55.000 0.00 0.00 0.00 3.06
5112 9871 1.531423 CCTCTTGTGCTGCTGTCATT 58.469 50.000 0.00 0.00 0.00 2.57
5113 9872 1.884579 CCTCTTGTGCTGCTGTCATTT 59.115 47.619 0.00 0.00 0.00 2.32
5114 9873 3.076621 CCTCTTGTGCTGCTGTCATTTA 58.923 45.455 0.00 0.00 0.00 1.40
5119 9880 5.939883 TCTTGTGCTGCTGTCATTTAGTAAT 59.060 36.000 0.00 0.00 0.00 1.89
5123 9884 4.701651 TGCTGCTGTCATTTAGTAATTGCT 59.298 37.500 0.56 0.56 0.00 3.91
5153 9914 7.856398 TCGAGCTTAATTCTGAGACTAATTACG 59.144 37.037 0.00 0.00 29.58 3.18
5161 9922 8.649973 ATTCTGAGACTAATTACGTCAATTCC 57.350 34.615 13.84 0.00 37.93 3.01
5168 9929 4.336532 AATTACGTCAATTCCGAGCAAC 57.663 40.909 0.00 0.00 30.73 4.17
5184 9945 4.235360 GAGCAACTTCGAGCTTACACTAA 58.765 43.478 0.00 0.00 42.04 2.24
5193 9954 3.002791 GAGCTTACACTAACATGCTGCA 58.997 45.455 4.13 4.13 0.00 4.41
5196 9957 3.374988 GCTTACACTAACATGCTGCATGA 59.625 43.478 40.25 22.99 43.81 3.07
5210 9971 1.693083 GCATGACGCGTAGGTGAACC 61.693 60.000 13.97 0.00 0.00 3.62
5241 10002 8.179888 AGGATGATAATCCCAGGCTTATAAAT 57.820 34.615 5.34 0.00 41.65 1.40
5326 10087 8.725148 AGTATTTGGGTCGTAGAATACTATACG 58.275 37.037 5.96 0.00 41.19 3.06
5331 10092 5.470098 GGGTCGTAGAATACTATACGGTGAA 59.530 44.000 0.00 0.00 43.73 3.18
5335 10096 6.017934 TCGTAGAATACTATACGGTGAACACC 60.018 42.308 13.32 13.32 43.73 4.16
5337 10098 7.521099 CGTAGAATACTATACGGTGAACACCAT 60.521 40.741 21.41 10.91 45.19 3.55
5347 10108 2.066262 GTGAACACCATGTGAGTACGG 58.934 52.381 0.49 0.00 36.96 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 8.791355 AGGTGCAAAAGTTAGTTATTTTTACG 57.209 30.769 0.00 0.00 0.00 3.18
39 40 8.077386 CGGAGGTGCAAAAGTTAGTTATTTTTA 58.923 33.333 0.00 0.00 0.00 1.52
60 61 0.960861 GAGTTTTGGGGCTTCGGAGG 60.961 60.000 0.00 0.00 0.00 4.30
67 68 1.149101 TGGAGAAGAGTTTTGGGGCT 58.851 50.000 0.00 0.00 0.00 5.19
114 115 2.853077 TCTCTAGGAGGTGGAGATGTGA 59.147 50.000 0.00 0.00 37.84 3.58
115 118 3.304911 TCTCTAGGAGGTGGAGATGTG 57.695 52.381 0.00 0.00 37.84 3.21
124 127 9.134055 GTGTTATAGTTTACATCTCTAGGAGGT 57.866 37.037 4.39 4.39 42.00 3.85
130 133 6.835488 ACGGGGTGTTATAGTTTACATCTCTA 59.165 38.462 0.00 0.00 0.00 2.43
131 134 5.659971 ACGGGGTGTTATAGTTTACATCTCT 59.340 40.000 0.00 0.00 0.00 3.10
182 185 2.766970 TGCGTTTTTACAACTCCTGC 57.233 45.000 0.00 0.00 0.00 4.85
189 192 2.516923 CGTGTGGTTGCGTTTTTACAA 58.483 42.857 0.00 0.00 0.00 2.41
214 217 3.632604 TGAAATAAACGACAGTTGGGCAA 59.367 39.130 0.00 0.00 41.05 4.52
256 259 3.702048 GGCAGTGGTCGGCTGGTA 61.702 66.667 0.00 0.00 35.25 3.25
340 383 2.989639 CCAATCGGTGGCTCCTCA 59.010 61.111 3.83 0.00 41.72 3.86
359 402 2.933287 AAGTGCGGTGGGATGGGA 60.933 61.111 0.00 0.00 0.00 4.37
417 471 2.353610 CCAGATTTGGCACTGGGGC 61.354 63.158 13.41 0.00 46.76 5.80
418 472 4.023137 CCAGATTTGGCACTGGGG 57.977 61.111 13.41 0.00 46.76 4.96
466 520 4.129737 GGCGGCGACAGAGTAGCA 62.130 66.667 12.98 0.00 35.94 3.49
506 560 4.088421 GATTCGGCGAAGAAGCGA 57.912 55.556 27.35 2.66 38.18 4.93
520 589 2.480610 AAATCATGCGGCGGCGATT 61.481 52.632 36.87 22.03 44.10 3.34
521 590 2.901840 AAATCATGCGGCGGCGAT 60.902 55.556 36.87 21.64 44.10 4.58
550 619 0.175760 CTTGAATTCGGCGGGAGAGA 59.824 55.000 7.21 0.00 0.00 3.10
553 622 2.472909 GGCTTGAATTCGGCGGGAG 61.473 63.158 7.21 0.00 0.00 4.30
554 623 2.437716 GGCTTGAATTCGGCGGGA 60.438 61.111 7.21 0.00 0.00 5.14
555 624 3.876198 CGGCTTGAATTCGGCGGG 61.876 66.667 17.62 9.00 44.21 6.13
562 631 0.318955 GCAAGTGTGCGGCTTGAATT 60.319 50.000 15.74 0.00 44.29 2.17
597 4547 0.603975 GAGTCTGGCAGCGGAAAAGT 60.604 55.000 10.34 0.00 0.00 2.66
687 4637 4.652131 TTGAATGGCGGGCGGTGT 62.652 61.111 0.00 0.00 0.00 4.16
756 4816 8.962884 AATTTACATCTTCAAAAAGTGCCTTT 57.037 26.923 0.00 0.00 34.94 3.11
757 4817 8.962884 AAATTTACATCTTCAAAAAGTGCCTT 57.037 26.923 0.00 0.00 33.95 4.35
758 4818 8.962884 AAAATTTACATCTTCAAAAAGTGCCT 57.037 26.923 0.00 0.00 33.95 4.75
999 5418 1.658717 GTCGTCGCCGATCTCCATG 60.659 63.158 0.00 0.00 46.30 3.66
1006 5425 4.831307 GCAGTCGTCGTCGCCGAT 62.831 66.667 0.29 0.00 46.30 4.18
1057 5476 2.585153 GGGAAACGGAGGAGAGGC 59.415 66.667 0.00 0.00 0.00 4.70
1069 5488 2.656069 CGGAGGAGGAAGCGGGAAA 61.656 63.158 0.00 0.00 0.00 3.13
1202 5621 2.376518 ACAGAAACAGTGGATGGATGGT 59.623 45.455 0.00 0.00 0.00 3.55
1275 5696 1.355916 GAGTCGGTAGTAGCTGGCG 59.644 63.158 0.00 0.00 0.00 5.69
1365 5786 4.347360 TCATGCCAGTGATTCCTCATAG 57.653 45.455 0.00 0.00 32.98 2.23
1366 5787 4.164796 AGTTCATGCCAGTGATTCCTCATA 59.835 41.667 0.00 0.00 32.98 2.15
1367 5788 3.053842 AGTTCATGCCAGTGATTCCTCAT 60.054 43.478 0.00 0.00 32.98 2.90
1368 5789 2.306805 AGTTCATGCCAGTGATTCCTCA 59.693 45.455 0.00 0.00 0.00 3.86
1369 5790 2.681848 CAGTTCATGCCAGTGATTCCTC 59.318 50.000 0.00 0.00 0.00 3.71
1370 5791 2.040813 ACAGTTCATGCCAGTGATTCCT 59.959 45.455 6.57 0.00 0.00 3.36
1384 5805 4.332543 CACAAAGAACAGTGCTACAGTTCA 59.667 41.667 19.02 0.00 44.07 3.18
1406 5827 3.374988 CACTTGAGTGCTGACAGAAAACA 59.625 43.478 6.65 0.00 39.39 2.83
1446 5867 6.932356 ACAGCCTAAAGTATCAACATGATG 57.068 37.500 0.00 0.00 37.70 3.07
1449 5870 9.710900 TGATATACAGCCTAAAGTATCAACATG 57.289 33.333 0.00 0.00 33.34 3.21
1524 5948 6.882678 GGTCCCAACTAGCTCAACTAATAAAA 59.117 38.462 0.00 0.00 0.00 1.52
1553 5977 0.034337 GGCGAGTGACTGTTAACCCA 59.966 55.000 2.48 0.00 0.00 4.51
1634 6058 6.039941 CCTCTCCGAACTCATTCAGTATTACT 59.960 42.308 0.00 0.00 32.30 2.24
1718 6142 1.098050 CATTTGCTAGCTCCACCCAC 58.902 55.000 17.23 0.00 0.00 4.61
1899 6323 7.429340 GCAACAAATAACCATAGAACAATCGAG 59.571 37.037 0.00 0.00 0.00 4.04
1995 6419 3.356290 CCCCCAACATAACTTTCTGAGG 58.644 50.000 0.00 0.00 0.00 3.86
2482 7069 3.626670 GGAAGTCAATGGAAGAGCATGAG 59.373 47.826 0.00 0.00 0.00 2.90
2672 7327 9.507280 CGAACTAAACTAACCGTAATGATAGAA 57.493 33.333 0.00 0.00 0.00 2.10
2878 7533 6.150641 AGGAAACAGTGAAATGTGATCTCATG 59.849 38.462 10.87 2.16 32.52 3.07
2907 7562 6.763135 ACCTGAGCATATACAGTAACATGTTG 59.237 38.462 21.42 7.93 34.56 3.33
3014 7669 6.641989 CCAAAAACAGTAAATTACCGCAAAC 58.358 36.000 0.00 0.00 0.00 2.93
3028 7683 3.299503 AGAGATTGGTGCCAAAAACAGT 58.700 40.909 7.81 0.00 39.55 3.55
3029 7684 3.318839 TGAGAGATTGGTGCCAAAAACAG 59.681 43.478 7.81 0.00 39.55 3.16
3041 7696 6.754702 AAGAATGTGTGAATGAGAGATTGG 57.245 37.500 0.00 0.00 0.00 3.16
3043 7698 8.086522 CCAAAAAGAATGTGTGAATGAGAGATT 58.913 33.333 0.00 0.00 0.00 2.40
3088 7744 8.332996 CCATAGGGATCAATACAAGAATCTTG 57.667 38.462 20.35 20.35 35.59 3.02
3130 7786 8.648557 TGGATAATTATCACGAACAAGAGAAG 57.351 34.615 23.54 0.00 34.40 2.85
3355 8011 8.375506 TGACCAAATCAGACTTCAGTAGTTTAT 58.624 33.333 0.00 0.00 31.94 1.40
3542 8198 9.174166 TCATTCAAGGAAATAAAGTACCTTAGC 57.826 33.333 0.00 0.00 40.21 3.09
3552 8208 8.634335 TGACACATCTCATTCAAGGAAATAAA 57.366 30.769 0.00 0.00 0.00 1.40
3690 8346 7.100458 AGGCAAATATGTAAAACAGATGTCC 57.900 36.000 0.00 0.00 29.41 4.02
3969 8625 9.667107 TCCCAAATTAGTTGACTTAGATTAGTG 57.333 33.333 0.00 0.00 39.87 2.74
3997 8653 7.343316 AGTTCTAGCTTATCATGTACAACCTCT 59.657 37.037 0.00 0.00 0.00 3.69
4034 8690 2.334977 TGCAGAGGACTGGGTAGAAAA 58.665 47.619 0.00 0.00 43.62 2.29
4059 8715 7.433680 CAAAGAAGGCATACTTTGGTAACTTT 58.566 34.615 17.08 0.00 44.95 2.66
4354 9010 6.278363 GTGGCATGCAAATCATTAGAGAATT 58.722 36.000 21.36 0.00 31.79 2.17
4358 9014 3.635373 AGGTGGCATGCAAATCATTAGAG 59.365 43.478 21.36 0.00 31.79 2.43
4361 9017 3.514706 ACAAGGTGGCATGCAAATCATTA 59.485 39.130 21.36 0.00 31.79 1.90
4373 9029 3.146066 GTGAATGACTTACAAGGTGGCA 58.854 45.455 0.00 0.00 0.00 4.92
4394 9050 2.268298 CGTCAAAACGGAGGACATAGG 58.732 52.381 0.00 0.00 45.21 2.57
4452 9108 3.628487 GCAAAACCATACATACCCGCTTA 59.372 43.478 0.00 0.00 0.00 3.09
4547 9203 3.502211 GGGCAGAATTACGGGATTATGTG 59.498 47.826 8.68 0.08 32.33 3.21
4576 9232 5.997385 AGGACACAGTTAAAATGCTAAACG 58.003 37.500 0.00 0.00 0.00 3.60
4608 9267 0.469892 TCAGTGACAGAGGTGCCTGA 60.470 55.000 0.00 0.00 37.59 3.86
4649 9308 0.988678 ACCTAATCCCAGTCCAGGCC 60.989 60.000 0.00 0.00 0.00 5.19
4660 9319 5.019785 ACCATACGAGAACAACCTAATCC 57.980 43.478 0.00 0.00 0.00 3.01
4708 9367 2.099921 TGCTTCGCCTCTACTGAAGATC 59.900 50.000 5.45 0.00 41.21 2.75
4746 9405 3.070018 AGCAATTGAAGTCGTCTCTTGG 58.930 45.455 10.34 0.00 0.00 3.61
4763 9422 0.325933 ACATAGCCTCACAGCAGCAA 59.674 50.000 0.00 0.00 34.23 3.91
4837 9528 5.220854 GGTTGCATTCGCTATACTGAACATT 60.221 40.000 0.00 0.00 39.64 2.71
4868 9559 2.368548 ACATTTTCCCTCTGCAAAACCC 59.631 45.455 0.00 0.00 0.00 4.11
4915 9606 2.508526 AGGTCTTTCTGCACCATGTTC 58.491 47.619 0.00 0.00 34.80 3.18
4918 9611 5.183713 TCAATTTAGGTCTTTCTGCACCATG 59.816 40.000 0.00 0.00 34.80 3.66
4940 9633 3.009723 GAGGCATCTTCCGTTCATTTCA 58.990 45.455 0.00 0.00 0.00 2.69
4944 9637 1.134280 CCAGAGGCATCTTCCGTTCAT 60.134 52.381 0.00 0.00 31.64 2.57
4946 9639 0.537188 TCCAGAGGCATCTTCCGTTC 59.463 55.000 0.00 0.00 31.64 3.95
4984 9689 3.335183 TGGATAGAACCAAAATCACCCCA 59.665 43.478 0.00 0.00 36.96 4.96
4994 9699 3.266772 ACCATCAGCTTGGATAGAACCAA 59.733 43.478 11.52 0.00 46.02 3.67
4995 9700 2.846206 ACCATCAGCTTGGATAGAACCA 59.154 45.455 11.52 0.00 39.25 3.67
4997 9702 3.065925 GCAACCATCAGCTTGGATAGAAC 59.934 47.826 11.52 0.00 39.25 3.01
4998 9703 3.282021 GCAACCATCAGCTTGGATAGAA 58.718 45.455 11.52 0.00 39.25 2.10
4999 9704 2.742856 CGCAACCATCAGCTTGGATAGA 60.743 50.000 11.52 0.00 39.25 1.98
5048 9802 1.208293 GGCTCAAGTAAGGTCTCCAGG 59.792 57.143 0.00 0.00 0.00 4.45
5100 9859 4.701651 AGCAATTACTAAATGACAGCAGCA 59.298 37.500 0.00 0.00 0.00 4.41
5101 9860 5.240713 AGCAATTACTAAATGACAGCAGC 57.759 39.130 0.00 0.00 0.00 5.25
5102 9861 9.443283 GAAATAGCAATTACTAAATGACAGCAG 57.557 33.333 0.00 0.00 0.00 4.24
5103 9862 8.122330 CGAAATAGCAATTACTAAATGACAGCA 58.878 33.333 0.00 0.00 0.00 4.41
5104 9863 8.335356 TCGAAATAGCAATTACTAAATGACAGC 58.665 33.333 0.00 0.00 0.00 4.40
5105 9864 9.855361 CTCGAAATAGCAATTACTAAATGACAG 57.145 33.333 0.00 0.00 0.00 3.51
5106 9865 8.335356 GCTCGAAATAGCAATTACTAAATGACA 58.665 33.333 0.00 0.00 42.30 3.58
5107 9866 8.552034 AGCTCGAAATAGCAATTACTAAATGAC 58.448 33.333 0.00 0.00 45.30 3.06
5108 9867 8.662781 AGCTCGAAATAGCAATTACTAAATGA 57.337 30.769 0.00 0.00 45.30 2.57
5114 9873 9.331282 AGAATTAAGCTCGAAATAGCAATTACT 57.669 29.630 0.00 0.00 45.30 2.24
5119 9880 7.010552 GTCTCAGAATTAAGCTCGAAATAGCAA 59.989 37.037 0.00 0.00 45.30 3.91
5153 9914 2.066262 TCGAAGTTGCTCGGAATTGAC 58.934 47.619 0.00 0.00 39.35 3.18
5161 9922 1.387084 GTGTAAGCTCGAAGTTGCTCG 59.613 52.381 0.00 0.00 37.41 5.03
5168 9929 4.032217 CAGCATGTTAGTGTAAGCTCGAAG 59.968 45.833 0.00 0.00 0.00 3.79
5184 9945 1.423721 CTACGCGTCATGCAGCATGT 61.424 55.000 30.38 16.25 46.97 3.21
5193 9954 1.153901 CGGTTCACCTACGCGTCAT 60.154 57.895 18.63 0.00 0.00 3.06
5196 9957 1.310933 ATCTCGGTTCACCTACGCGT 61.311 55.000 19.17 19.17 0.00 6.01
5318 10079 4.705991 TCACATGGTGTTCACCGTATAGTA 59.294 41.667 15.16 0.00 34.79 1.82
5319 10080 3.512329 TCACATGGTGTTCACCGTATAGT 59.488 43.478 15.16 7.82 34.79 2.12
5320 10081 4.112634 CTCACATGGTGTTCACCGTATAG 58.887 47.826 15.16 9.71 34.79 1.31
5326 10087 2.066262 CGTACTCACATGGTGTTCACC 58.934 52.381 14.31 14.31 34.79 4.02
5331 10092 1.819288 CTCTCCGTACTCACATGGTGT 59.181 52.381 0.00 0.00 34.79 4.16
5335 10096 3.850122 TGAACTCTCCGTACTCACATG 57.150 47.619 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.