Multiple sequence alignment - TraesCS5A01G156200

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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 TraesCS5A01G156200 chr5A 100.000 5962 0 0 1 5962 334753923 334747962 0.000000e+00 11010.0
1 TraesCS5A01G156200 chr5B 93.205 4106 199 49 1 4063 284372701 284368633 0.000000e+00 5963.0
2 TraesCS5A01G156200 chr5B 92.196 756 34 14 4378 5120 284367523 284366780 0.000000e+00 1046.0
3 TraesCS5A01G156200 chr5B 98.556 277 4 0 4116 4392 284367978 284367702 1.930000e-134 490.0
4 TraesCS5A01G156200 chr5B 96.774 62 2 0 4059 4120 284368519 284368458 2.940000e-18 104.0
5 TraesCS5A01G156200 chr5D 92.396 3906 205 41 1580 5461 251962321 251958484 0.000000e+00 5483.0
6 TraesCS5A01G156200 chr5D 90.964 830 39 16 749 1550 251963140 251962319 0.000000e+00 1085.0
7 TraesCS5A01G156200 chr5D 89.237 734 65 9 1 727 251965113 251964387 0.000000e+00 905.0
8 TraesCS5A01G156200 chr5D 93.308 523 28 4 5445 5962 251958472 251957952 0.000000e+00 765.0
9 TraesCS5A01G156200 chr1A 90.077 1169 80 18 3968 5112 566592052 566593208 0.000000e+00 1483.0
10 TraesCS5A01G156200 chr2D 98.077 52 1 0 3808 3859 72212562 72212511 2.290000e-14 91.6
11 TraesCS5A01G156200 chr7B 98.000 50 1 0 3810 3859 65752894 65752943 2.960000e-13 87.9
12 TraesCS5A01G156200 chrUn 91.803 61 3 2 3801 3859 461112264 461112324 3.830000e-12 84.2
13 TraesCS5A01G156200 chr7D 94.444 54 3 0 3806 3859 49381995 49381942 3.830000e-12 84.2
14 TraesCS5A01G156200 chr4A 96.078 51 2 0 3809 3859 628492807 628492757 3.830000e-12 84.2
15 TraesCS5A01G156200 chr4A 94.444 54 2 1 3806 3859 489039936 489039884 1.380000e-11 82.4
16 TraesCS5A01G156200 chr6D 90.476 63 3 3 3795 3856 148484629 148484689 4.950000e-11 80.5
17 TraesCS5A01G156200 chr3D 90.323 62 5 1 3799 3859 411724324 411724385 4.950000e-11 80.5


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 TraesCS5A01G156200 chr5A 334747962 334753923 5961 True 11010.00 11010 100.00000 1 5962 1 chr5A.!!$R1 5961
1 TraesCS5A01G156200 chr5B 284366780 284372701 5921 True 1900.75 5963 95.18275 1 5120 4 chr5B.!!$R1 5119
2 TraesCS5A01G156200 chr5D 251957952 251965113 7161 True 2059.50 5483 91.47625 1 5962 4 chr5D.!!$R1 5961
3 TraesCS5A01G156200 chr1A 566592052 566593208 1156 False 1483.00 1483 90.07700 3968 5112 1 chr1A.!!$F1 1144

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
355 356 0.032217 CTTGCTCCTCCTCCTCCTCT 60.032 60.000 0.00 0.00 0.00 3.69 F
762 1995 0.035739 TTTAGGGTGCCGGTCAACTC 59.964 55.000 12.63 5.05 31.53 3.01 F
804 2038 0.036306 AGGTACGGCTGGGTCAAAAG 59.964 55.000 0.00 0.00 0.00 2.27 F
821 2055 0.179084 AAGTGTGTGACCGACCACTG 60.179 55.000 8.26 0.00 36.66 3.66 F
1405 2676 0.606604 GTGCTTCCGGGACTCAAGTA 59.393 55.000 0.00 0.00 33.31 2.24 F
1782 3057 1.319541 TGACTGATCCTAGCTACGCC 58.680 55.000 0.00 0.00 0.00 5.68 F
2730 4010 2.159352 TCACACATTGTATGCATGCTGC 60.159 45.455 20.33 9.35 45.29 5.25 F
2739 4019 2.293677 ATGCATGCTGCTGTTTGATG 57.706 45.000 20.33 0.00 45.31 3.07 F
4177 6078 1.952296 GGGACTATGAAAGCCAGCATG 59.048 52.381 0.00 0.00 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 3093 0.788391 CAGAGTTAACGCCGGTGTTC 59.212 55.000 35.16 22.25 33.32 3.18 R
2602 3881 4.996122 TGCATGAAATCCAACCAATGAAAC 59.004 37.500 0.00 0.00 0.00 2.78 R
2774 4054 2.309613 AGCAGCACCAAAGTTTCATGA 58.690 42.857 0.00 0.00 0.00 3.07 R
2797 4077 4.460382 ACTTATCAAATCAACACCTGCAGG 59.540 41.667 31.60 31.60 42.17 4.85 R
3013 4294 4.098416 GGCGTCTCAAAATGTTATGCTTC 58.902 43.478 0.00 0.00 0.00 3.86 R
3523 4806 5.045140 AGGTGCCTACTGCCTAAGATAAAAA 60.045 40.000 0.00 0.00 40.16 1.94 R
4177 6078 1.251251 AAACTTGCACAGATGGCCTC 58.749 50.000 3.32 0.00 0.00 4.70 R
4451 6548 3.721868 TCCTTCCGGGAGCGATTT 58.278 55.556 3.32 0.00 39.58 2.17 R
5140 7251 1.068741 CGCCACATTACCTCCTACTCC 59.931 57.143 0.00 0.00 0.00 3.85 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
21 22 3.135225 CTCATCGTCGGAGATGTAGACT 58.865 50.000 16.56 0.00 45.96 3.24
34 35 2.730382 TGTAGACTACTTCCATGCCGA 58.270 47.619 13.67 0.00 0.00 5.54
40 41 0.973632 TACTTCCATGCCGACACTGT 59.026 50.000 0.00 0.00 0.00 3.55
50 51 3.203442 GACACTGTCGGCCGGATA 58.797 61.111 27.83 11.08 0.00 2.59
173 174 1.743772 CGGTTGGCCTTCATCTTCGAT 60.744 52.381 3.32 0.00 0.00 3.59
178 179 1.221414 GCCTTCATCTTCGATTCCGG 58.779 55.000 0.00 0.00 36.24 5.14
188 189 1.146041 CGATTCCGGCTGGATGGAA 59.854 57.895 16.96 0.00 45.91 3.53
250 251 2.602568 ACCCCGTACTCCGCTTGT 60.603 61.111 0.00 0.00 34.38 3.16
252 253 2.654877 CCCGTACTCCGCTTGTGT 59.345 61.111 0.00 0.00 34.38 3.72
308 309 1.627297 ATCCGCCTCAACTTCCTCCC 61.627 60.000 0.00 0.00 0.00 4.30
309 310 2.294078 CCGCCTCAACTTCCTCCCT 61.294 63.158 0.00 0.00 0.00 4.20
310 311 1.219393 CGCCTCAACTTCCTCCCTC 59.781 63.158 0.00 0.00 0.00 4.30
331 332 3.423154 CCTCCACGTGCGCTTTCC 61.423 66.667 10.91 0.00 0.00 3.13
332 333 3.777925 CTCCACGTGCGCTTTCCG 61.778 66.667 10.91 8.39 40.75 4.30
333 334 4.287781 TCCACGTGCGCTTTCCGA 62.288 61.111 10.91 0.00 40.02 4.55
334 335 4.072088 CCACGTGCGCTTTCCGAC 62.072 66.667 10.91 0.00 40.02 4.79
335 336 4.409588 CACGTGCGCTTTCCGACG 62.410 66.667 9.73 11.87 42.17 5.12
342 343 2.476499 GCTTTCCGACGCTTGCTC 59.524 61.111 0.00 0.00 0.00 4.26
345 346 1.355066 CTTTCCGACGCTTGCTCCTC 61.355 60.000 0.00 0.00 0.00 3.71
355 356 0.032217 CTTGCTCCTCCTCCTCCTCT 60.032 60.000 0.00 0.00 0.00 3.69
372 373 2.500910 CCTCTTCATGCTCCAGAGAGTT 59.499 50.000 10.81 0.00 42.59 3.01
407 408 1.216178 GCAATCCAAGCGGCATGTT 59.784 52.632 1.45 0.00 0.00 2.71
410 411 2.229690 AATCCAAGCGGCATGTTGGC 62.230 55.000 13.09 2.83 42.67 4.52
420 421 1.188863 GCATGTTGGCCCTGAATCTT 58.811 50.000 0.00 0.00 0.00 2.40
460 461 2.606213 TCCGGGGTGAGCATGACA 60.606 61.111 0.00 0.00 0.00 3.58
464 465 0.752658 CGGGGTGAGCATGACATAGA 59.247 55.000 0.00 0.00 0.00 1.98
472 473 5.476614 GTGAGCATGACATAGATGATGCTA 58.523 41.667 15.07 5.55 43.85 3.49
563 569 6.742363 GCAAAGGGGAGAAAAATGAAAGTGAT 60.742 38.462 0.00 0.00 0.00 3.06
608 614 6.141560 GGCTTATTAGCTGAATTTGCTTCT 57.858 37.500 11.25 3.91 46.90 2.85
609 615 6.567959 GGCTTATTAGCTGAATTTGCTTCTT 58.432 36.000 11.25 2.12 46.90 2.52
616 622 3.731089 CTGAATTTGCTTCTTTTGGGCA 58.269 40.909 0.00 0.00 34.75 5.36
619 625 0.829333 TTTGCTTCTTTTGGGCAGCA 59.171 45.000 0.00 0.00 40.53 4.41
647 653 1.335496 GCGTCCTCCTCACTAGATCAC 59.665 57.143 0.00 0.00 0.00 3.06
660 666 0.904649 AGATCACTGGGCAACGATGA 59.095 50.000 0.00 0.00 37.60 2.92
665 671 0.108585 ACTGGGCAACGATGAGTGTT 59.891 50.000 0.00 0.00 37.60 3.32
676 682 0.836400 ATGAGTGTTCGGTGGGTCCT 60.836 55.000 0.00 0.00 0.00 3.85
687 694 2.188817 GGTGGGTCCTCACATTAGTCT 58.811 52.381 11.26 0.00 39.27 3.24
701 708 2.139323 TAGTCTGATGTGGTAGGCGT 57.861 50.000 0.00 0.00 0.00 5.68
705 712 1.346395 TCTGATGTGGTAGGCGTGTTT 59.654 47.619 0.00 0.00 0.00 2.83
706 713 2.563620 TCTGATGTGGTAGGCGTGTTTA 59.436 45.455 0.00 0.00 0.00 2.01
712 719 1.972795 TGGTAGGCGTGTTTAGGTCTT 59.027 47.619 0.00 0.00 0.00 3.01
724 732 5.401674 GTGTTTAGGTCTTCCTATATTCGCG 59.598 44.000 0.00 0.00 44.68 5.87
730 738 2.225019 TCTTCCTATATTCGCGTCGGAC 59.775 50.000 5.77 0.00 0.00 4.79
735 743 2.051879 ATATTCGCGTCGGACATGAG 57.948 50.000 5.77 0.00 0.00 2.90
736 744 0.594028 TATTCGCGTCGGACATGAGC 60.594 55.000 5.77 2.40 0.00 4.26
737 745 2.284798 ATTCGCGTCGGACATGAGCT 62.285 55.000 5.77 0.00 0.00 4.09
739 747 2.181777 GCGTCGGACATGAGCTGA 59.818 61.111 9.10 0.00 0.00 4.26
744 1977 3.384668 CGTCGGACATGAGCTGAATATT 58.615 45.455 9.10 0.00 0.00 1.28
745 1978 3.804325 CGTCGGACATGAGCTGAATATTT 59.196 43.478 9.10 0.00 0.00 1.40
747 1980 5.117745 CGTCGGACATGAGCTGAATATTTAG 59.882 44.000 9.10 2.91 0.00 1.85
759 1992 3.054287 TGAATATTTAGGGTGCCGGTCAA 60.054 43.478 1.90 0.00 0.00 3.18
761 1994 0.696501 ATTTAGGGTGCCGGTCAACT 59.303 50.000 12.63 10.37 31.53 3.16
762 1995 0.035739 TTTAGGGTGCCGGTCAACTC 59.964 55.000 12.63 5.05 31.53 3.01
764 1997 0.907704 TAGGGTGCCGGTCAACTCAT 60.908 55.000 12.63 3.85 31.53 2.90
766 1999 0.743345 GGGTGCCGGTCAACTCATAC 60.743 60.000 12.63 0.00 31.53 2.39
769 2003 0.389296 TGCCGGTCAACTCATACGTG 60.389 55.000 1.90 0.00 0.00 4.49
775 2009 3.436496 GGTCAACTCATACGTGTAGAGC 58.564 50.000 0.00 0.00 32.71 4.09
781 2015 3.497640 ACTCATACGTGTAGAGCCGATAC 59.502 47.826 0.00 0.00 32.71 2.24
784 2018 0.935898 ACGTGTAGAGCCGATACGAG 59.064 55.000 10.22 0.00 38.08 4.18
787 2021 1.532007 GTGTAGAGCCGATACGAGAGG 59.468 57.143 0.00 0.00 0.00 3.69
804 2038 0.036306 AGGTACGGCTGGGTCAAAAG 59.964 55.000 0.00 0.00 0.00 2.27
816 2050 2.732001 GTCAAAAGTGTGTGACCGAC 57.268 50.000 0.00 0.00 38.57 4.79
821 2055 0.179084 AAGTGTGTGACCGACCACTG 60.179 55.000 8.26 0.00 36.66 3.66
829 2082 3.513912 TGTGACCGACCACTGATCTAAAT 59.486 43.478 8.26 0.00 37.89 1.40
831 2084 5.186215 TGTGACCGACCACTGATCTAAATTA 59.814 40.000 8.26 0.00 37.89 1.40
832 2085 6.103997 GTGACCGACCACTGATCTAAATTAA 58.896 40.000 0.00 0.00 34.38 1.40
838 2091 9.503427 CCGACCACTGATCTAAATTAATTTTTC 57.497 33.333 18.14 12.96 0.00 2.29
849 2102 9.962809 TCTAAATTAATTTTTCTAGGGGTCGAA 57.037 29.630 18.14 0.00 0.00 3.71
852 2105 8.589701 AATTAATTTTTCTAGGGGTCGAATGT 57.410 30.769 0.00 0.00 0.00 2.71
853 2106 9.689501 AATTAATTTTTCTAGGGGTCGAATGTA 57.310 29.630 0.00 0.00 0.00 2.29
882 2135 4.568072 ACTTGGCATACTATTGTGTCCA 57.432 40.909 0.00 0.00 0.00 4.02
1011 2270 6.495872 TCCTCACTTTTACTAGTAGAGCCAAA 59.504 38.462 3.59 0.09 0.00 3.28
1052 2311 5.762218 CCTCTCATATCAAAACCCTAAGCAG 59.238 44.000 0.00 0.00 0.00 4.24
1375 2646 2.045926 GGCTCCGTGTGGAATGCT 60.046 61.111 0.00 0.00 45.87 3.79
1405 2676 0.606604 GTGCTTCCGGGACTCAAGTA 59.393 55.000 0.00 0.00 33.31 2.24
1514 2788 7.917505 CCCTTCAGTATGCTTATGAAATCAAAC 59.082 37.037 0.00 0.00 32.87 2.93
1617 2891 4.514401 ACGTCCCAGTGATTTATCTTTCC 58.486 43.478 0.00 0.00 0.00 3.13
1656 2930 7.823745 TTCTAAATTCCATTCCTAGCCAATC 57.176 36.000 0.00 0.00 0.00 2.67
1705 2980 7.306457 GCTCTCAAATTTTCTGCAACTTCTTTC 60.306 37.037 0.00 0.00 0.00 2.62
1782 3057 1.319541 TGACTGATCCTAGCTACGCC 58.680 55.000 0.00 0.00 0.00 5.68
1965 3240 4.644685 GCTTCCTTGGTGGCTTAATCATAA 59.355 41.667 0.00 0.00 35.26 1.90
2361 3636 7.330946 GGAAAATTGTTGGTATGTTAAGCTTCC 59.669 37.037 0.00 0.00 0.00 3.46
2602 3881 9.979270 CTTTAAACAGTTATGAAGCTGATAGTG 57.021 33.333 0.00 0.00 36.62 2.74
2639 3918 7.092716 GGATTTCATGCATTCTGTACTTGTTT 58.907 34.615 0.00 0.00 0.00 2.83
2696 3975 7.786464 AGGGATTTTCCTCTGCATTGTTATTAT 59.214 33.333 0.00 0.00 36.57 1.28
2722 4002 8.773645 TGTTAGAGTTTCTTCACACATTGTATG 58.226 33.333 0.00 0.00 0.00 2.39
2730 4010 2.159352 TCACACATTGTATGCATGCTGC 60.159 45.455 20.33 9.35 45.29 5.25
2739 4019 2.293677 ATGCATGCTGCTGTTTGATG 57.706 45.000 20.33 0.00 45.31 3.07
2772 4052 8.970691 ACTACTATTGATGATTTTTGTTGCAC 57.029 30.769 0.00 0.00 0.00 4.57
2774 4054 9.577110 CTACTATTGATGATTTTTGTTGCACAT 57.423 29.630 0.00 0.00 0.00 3.21
2790 4070 2.733026 GCACATCATGAAACTTTGGTGC 59.267 45.455 0.00 7.79 42.73 5.01
2797 4077 3.163630 TGAAACTTTGGTGCTGCTTTC 57.836 42.857 0.00 1.38 0.00 2.62
2923 4203 8.087982 TGAAACTTTTCATGTCAGTATCACTC 57.912 34.615 0.07 0.00 41.88 3.51
3013 4294 5.382303 GTCGTTGTGTATGATTTTGGAGTG 58.618 41.667 0.00 0.00 0.00 3.51
3455 4738 5.774690 TCGTGGGTCTCCTAGTTAACTTAAA 59.225 40.000 14.49 0.00 0.00 1.52
3523 4806 5.975988 TTACCTCATCTTTGGGCTTAGAT 57.024 39.130 0.00 0.00 0.00 1.98
3556 4839 4.138487 GCAGTAGGCACCTTACTACATT 57.862 45.455 0.00 0.00 41.49 2.71
3561 4844 4.207891 AGGCACCTTACTACATTGACTG 57.792 45.455 0.00 0.00 0.00 3.51
3586 4870 8.755028 TGTAAGACATTAAAGCTAGTACATGGA 58.245 33.333 0.00 0.00 0.00 3.41
3587 4871 9.032420 GTAAGACATTAAAGCTAGTACATGGAC 57.968 37.037 0.00 0.00 0.00 4.02
3588 4872 7.425224 AGACATTAAAGCTAGTACATGGACT 57.575 36.000 16.54 16.54 0.00 3.85
3589 4873 7.268586 AGACATTAAAGCTAGTACATGGACTG 58.731 38.462 21.47 11.51 0.00 3.51
3590 4874 6.947464 ACATTAAAGCTAGTACATGGACTGT 58.053 36.000 21.47 4.40 42.13 3.55
3591 4875 6.818644 ACATTAAAGCTAGTACATGGACTGTG 59.181 38.462 21.47 13.87 38.92 3.66
3635 4922 9.905713 AATGCTGAAAGACTAAGTTTATATGGA 57.094 29.630 0.00 0.00 34.07 3.41
3686 4973 5.471456 AGCAATCTTATTGGGCTTAGATTCG 59.529 40.000 2.11 0.00 35.70 3.34
3782 5069 2.945668 ACTTGTGCCTTCTCTGTTTCAC 59.054 45.455 0.00 0.00 0.00 3.18
3850 5137 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
4177 6078 1.952296 GGGACTATGAAAGCCAGCATG 59.048 52.381 0.00 0.00 0.00 4.06
4265 6166 9.153721 CGTAGGTTAGTTTGGTTATTCATTACA 57.846 33.333 0.00 0.00 0.00 2.41
4451 6548 3.646162 CCATAACTATGCTGTGGACCCTA 59.354 47.826 0.00 0.00 32.40 3.53
4622 6719 0.376152 CTTCTTGGCTACTGCATGCG 59.624 55.000 14.09 10.50 41.91 4.73
4976 7078 5.470098 CCTTTGAGCTGTTGTATTGTACTGT 59.530 40.000 0.00 0.00 0.00 3.55
5040 7151 4.887071 TCTCCTTTGCTTTGCAGTAGAAAA 59.113 37.500 2.38 3.56 40.61 2.29
5104 7215 6.201806 GCTCCTGAGTTGACAATACATACATC 59.798 42.308 0.00 0.00 0.00 3.06
5140 7251 6.391227 AAGCCCTTAAACCGATGAAATATG 57.609 37.500 0.00 0.00 0.00 1.78
5141 7252 4.827284 AGCCCTTAAACCGATGAAATATGG 59.173 41.667 0.00 0.00 0.00 2.74
5142 7253 4.825085 GCCCTTAAACCGATGAAATATGGA 59.175 41.667 0.00 0.00 0.00 3.41
5143 7254 5.048713 GCCCTTAAACCGATGAAATATGGAG 60.049 44.000 0.00 0.00 0.00 3.86
5144 7255 6.062095 CCCTTAAACCGATGAAATATGGAGT 58.938 40.000 0.00 0.00 0.00 3.85
5198 7309 8.299570 TGATTTTACAGATTCAAGGAAAGAAGC 58.700 33.333 0.00 0.00 0.00 3.86
5227 7338 2.672996 GAAGGGCAGCAGGCGAAA 60.673 61.111 0.00 0.00 46.16 3.46
5244 7355 4.212214 GGCGAAATGAGCTTATAGGTCTTG 59.788 45.833 7.33 0.00 42.83 3.02
5281 7394 5.220854 CGGAGGTGCACTATTGGATTTTTAG 60.221 44.000 17.98 0.00 0.00 1.85
5344 7457 3.997021 CTCTACTGACTTGCGGAACAAAT 59.003 43.478 0.00 0.00 37.96 2.32
5355 7468 2.476185 GCGGAACAAATCATCCAACTCG 60.476 50.000 0.00 0.00 35.34 4.18
5360 7473 5.106157 GGAACAAATCATCCAACTCGTTGAT 60.106 40.000 11.15 1.16 42.93 2.57
5362 7475 5.003160 ACAAATCATCCAACTCGTTGATGA 58.997 37.500 18.24 18.24 42.93 2.92
5366 7479 6.764308 ATCATCCAACTCGTTGATGAAAAT 57.236 33.333 19.09 8.55 42.93 1.82
5383 7496 7.748683 TGATGAAAATTTTAACTTCGATGTCCG 59.251 33.333 2.75 0.00 40.25 4.79
5384 7497 7.192148 TGAAAATTTTAACTTCGATGTCCGA 57.808 32.000 2.75 0.00 46.94 4.55
5400 7514 3.134623 TGTCCGATGACATTGAGGCTAAT 59.865 43.478 4.07 0.00 46.40 1.73
5405 7519 6.998074 TCCGATGACATTGAGGCTAATTAATT 59.002 34.615 5.89 5.89 0.00 1.40
5424 7538 3.634397 TTCGCCTGGAATGAGATTTCT 57.366 42.857 0.00 0.00 0.00 2.52
5426 7540 2.237143 TCGCCTGGAATGAGATTTCTGT 59.763 45.455 0.00 0.00 0.00 3.41
5433 7547 7.255070 GCCTGGAATGAGATTTCTGTATTCTTC 60.255 40.741 0.00 0.00 31.82 2.87
5441 7555 6.166279 AGATTTCTGTATTCTTCACTCGCAA 58.834 36.000 0.00 0.00 0.00 4.85
5454 7568 5.607119 TCACTCGCAAAAGAAATAGGTTC 57.393 39.130 0.00 0.00 36.38 3.62
5504 7649 8.566260 TCAATCTTAGCTCTTAATAGTACGGTC 58.434 37.037 0.00 0.00 0.00 4.79
5595 7740 4.019174 ACGGGCATTCTGAATTCTTCAAT 58.981 39.130 7.05 0.00 39.58 2.57
5600 7745 6.652062 GGGCATTCTGAATTCTTCAATTGTTT 59.348 34.615 7.05 0.00 39.58 2.83
5622 7767 5.867903 TCACATAATTTTTAGGGGCCATG 57.132 39.130 4.39 0.00 0.00 3.66
5668 7813 6.202954 CCTCAGGGATTTTCATTCGTGTATAC 59.797 42.308 0.00 0.00 33.58 1.47
5683 7828 4.926832 CGTGTATACTCACAAACACATGGA 59.073 41.667 4.17 0.00 41.79 3.41
5761 7906 7.784633 ACAAAACCCACAAAATGAACAATAG 57.215 32.000 0.00 0.00 0.00 1.73
5770 7915 7.980662 CCACAAAATGAACAATAGCATATTCCA 59.019 33.333 0.00 0.00 0.00 3.53
5778 7923 8.506437 TGAACAATAGCATATTCCATTCGATTC 58.494 33.333 0.00 0.00 0.00 2.52
5876 8023 6.743575 AACATCTACTGCACCAAATTAGTC 57.256 37.500 0.00 0.00 0.00 2.59
5885 8032 7.341805 ACTGCACCAAATTAGTCTCATTAGAT 58.658 34.615 0.00 0.00 33.30 1.98
5947 8094 9.434559 GATGTTGCGGATATTAGTAAAACTTTC 57.565 33.333 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.973632 ACAGTGTCGGCATGGAAGTA 59.026 50.000 0.00 0.00 0.00 2.24
34 35 2.423898 CCTATCCGGCCGACAGTGT 61.424 63.158 30.73 7.92 0.00 3.55
50 51 1.153086 GCCAACGATCATGAGGCCT 60.153 57.895 3.86 3.86 39.42 5.19
139 140 3.469863 AACCGTTGCTTCCTCCGCA 62.470 57.895 0.00 0.00 35.22 5.69
153 154 0.391130 TCGAAGATGAAGGCCAACCG 60.391 55.000 5.01 0.00 42.76 4.44
155 156 2.356069 GGAATCGAAGATGAAGGCCAAC 59.644 50.000 5.01 0.00 45.12 3.77
178 179 2.236766 CCATCCTCAATTCCATCCAGC 58.763 52.381 0.00 0.00 0.00 4.85
188 189 2.501492 GCAGCAAGCCATCCTCAAT 58.499 52.632 0.00 0.00 37.23 2.57
250 251 1.164411 GATTCGGCATTGGTGACACA 58.836 50.000 8.08 0.00 42.67 3.72
252 253 1.452110 CAGATTCGGCATTGGTGACA 58.548 50.000 0.00 0.00 39.83 3.58
283 284 1.841302 AAGTTGAGGCGGATCCAGCA 61.841 55.000 23.67 9.20 37.29 4.41
329 330 3.760035 GGAGGAGCAAGCGTCGGA 61.760 66.667 0.00 0.00 0.00 4.55
331 332 2.202676 GAGGAGGAGCAAGCGTCG 60.203 66.667 0.00 0.00 0.00 5.12
332 333 2.185608 GGAGGAGGAGCAAGCGTC 59.814 66.667 0.00 0.00 0.00 5.19
333 334 2.284258 AGGAGGAGGAGCAAGCGT 60.284 61.111 0.00 0.00 0.00 5.07
334 335 2.498726 GAGGAGGAGGAGCAAGCG 59.501 66.667 0.00 0.00 0.00 4.68
335 336 1.685355 GAGGAGGAGGAGGAGCAAGC 61.685 65.000 0.00 0.00 0.00 4.01
336 337 0.032217 AGAGGAGGAGGAGGAGCAAG 60.032 60.000 0.00 0.00 0.00 4.01
337 338 0.415429 AAGAGGAGGAGGAGGAGCAA 59.585 55.000 0.00 0.00 0.00 3.91
338 339 0.032615 GAAGAGGAGGAGGAGGAGCA 60.033 60.000 0.00 0.00 0.00 4.26
339 340 0.032615 TGAAGAGGAGGAGGAGGAGC 60.033 60.000 0.00 0.00 0.00 4.70
342 343 0.758123 GCATGAAGAGGAGGAGGAGG 59.242 60.000 0.00 0.00 0.00 4.30
345 346 0.758123 GGAGCATGAAGAGGAGGAGG 59.242 60.000 0.00 0.00 0.00 4.30
355 356 1.205655 CCGAACTCTCTGGAGCATGAA 59.794 52.381 0.00 0.00 42.98 2.57
372 373 3.385384 CAGCTGACCTGCCTCCGA 61.385 66.667 8.42 0.00 34.21 4.55
403 404 2.579860 AGAGAAGATTCAGGGCCAACAT 59.420 45.455 6.18 0.00 0.00 2.71
407 408 2.023015 TCCTAGAGAAGATTCAGGGCCA 60.023 50.000 6.18 0.00 0.00 5.36
410 411 3.321682 CAGCTCCTAGAGAAGATTCAGGG 59.678 52.174 0.00 0.00 0.00 4.45
420 421 1.323271 CCGGTTGCAGCTCCTAGAGA 61.323 60.000 0.00 0.00 0.00 3.10
441 442 2.284625 TCATGCTCACCCCGGAGT 60.285 61.111 0.73 0.00 37.24 3.85
448 449 3.436015 GCATCATCTATGTCATGCTCACC 59.564 47.826 8.58 0.00 38.89 4.02
460 461 4.763793 GGCCAACAACATAGCATCATCTAT 59.236 41.667 0.00 0.00 0.00 1.98
464 465 2.034124 GGGCCAACAACATAGCATCAT 58.966 47.619 4.39 0.00 0.00 2.45
472 473 3.391098 GCCATGGGCCAACAACAT 58.609 55.556 11.89 0.00 44.06 2.71
540 541 7.379059 AATCACTTTCATTTTTCTCCCCTTT 57.621 32.000 0.00 0.00 0.00 3.11
541 542 7.179160 CCTAATCACTTTCATTTTTCTCCCCTT 59.821 37.037 0.00 0.00 0.00 3.95
563 569 2.617021 GGTTGGCGACTTCCAATCCTAA 60.617 50.000 4.59 0.00 46.64 2.69
596 602 3.731089 CTGCCCAAAAGAAGCAAATTCA 58.269 40.909 0.00 0.00 40.67 2.57
606 612 1.537814 CCAGCATGCTGCCCAAAAGA 61.538 55.000 37.11 0.00 46.52 2.52
608 614 1.533513 TCCAGCATGCTGCCCAAAA 60.534 52.632 37.11 17.06 46.52 2.44
609 615 1.980232 CTCCAGCATGCTGCCCAAA 60.980 57.895 37.11 19.67 46.52 3.28
616 622 3.382803 GAGGACGCTCCAGCATGCT 62.383 63.158 16.30 16.30 37.69 3.79
619 625 2.364842 AGGAGGACGCTCCAGCAT 60.365 61.111 11.15 0.00 45.66 3.79
647 653 0.798776 GAACACTCATCGTTGCCCAG 59.201 55.000 0.00 0.00 0.00 4.45
660 666 1.458777 TGAGGACCCACCGAACACT 60.459 57.895 0.00 0.00 44.74 3.55
665 671 1.191535 CTAATGTGAGGACCCACCGA 58.808 55.000 9.73 0.00 44.74 4.69
687 694 2.354303 CCTAAACACGCCTACCACATCA 60.354 50.000 0.00 0.00 0.00 3.07
696 703 1.349067 AGGAAGACCTAAACACGCCT 58.651 50.000 0.00 0.00 45.83 5.52
712 719 1.596603 TGTCCGACGCGAATATAGGA 58.403 50.000 15.93 8.97 0.00 2.94
724 732 5.406780 CCTAAATATTCAGCTCATGTCCGAC 59.593 44.000 0.00 0.00 0.00 4.79
730 738 4.217118 GGCACCCTAAATATTCAGCTCATG 59.783 45.833 0.00 0.00 0.00 3.07
735 743 1.880027 CCGGCACCCTAAATATTCAGC 59.120 52.381 0.00 0.00 0.00 4.26
736 744 3.139077 GACCGGCACCCTAAATATTCAG 58.861 50.000 0.00 0.00 0.00 3.02
737 745 2.506231 TGACCGGCACCCTAAATATTCA 59.494 45.455 0.00 0.00 0.00 2.57
739 747 3.053917 AGTTGACCGGCACCCTAAATATT 60.054 43.478 0.00 0.00 0.00 1.28
744 1977 1.122632 TGAGTTGACCGGCACCCTAA 61.123 55.000 0.00 0.00 0.00 2.69
745 1978 0.907704 ATGAGTTGACCGGCACCCTA 60.908 55.000 0.00 0.00 0.00 3.53
747 1980 0.743345 GTATGAGTTGACCGGCACCC 60.743 60.000 0.00 0.00 0.00 4.61
759 1992 2.034104 TCGGCTCTACACGTATGAGT 57.966 50.000 11.48 0.00 0.00 3.41
761 1994 2.477754 CGTATCGGCTCTACACGTATGA 59.522 50.000 0.00 0.00 0.00 2.15
762 1995 2.477754 TCGTATCGGCTCTACACGTATG 59.522 50.000 0.00 0.00 34.39 2.39
764 1997 2.130395 CTCGTATCGGCTCTACACGTA 58.870 52.381 0.00 0.00 34.39 3.57
766 1999 1.192757 CTCTCGTATCGGCTCTACACG 59.807 57.143 0.00 0.00 0.00 4.49
769 2003 1.881591 ACCTCTCGTATCGGCTCTAC 58.118 55.000 0.00 0.00 0.00 2.59
775 2009 0.883814 AGCCGTACCTCTCGTATCGG 60.884 60.000 0.00 0.00 41.06 4.18
781 2015 2.754658 ACCCAGCCGTACCTCTCG 60.755 66.667 0.00 0.00 0.00 4.04
784 2018 0.035739 TTTTGACCCAGCCGTACCTC 59.964 55.000 0.00 0.00 0.00 3.85
787 2021 0.872388 CACTTTTGACCCAGCCGTAC 59.128 55.000 0.00 0.00 0.00 3.67
804 2038 0.033504 ATCAGTGGTCGGTCACACAC 59.966 55.000 10.66 0.00 39.99 3.82
831 2084 8.491958 ACTATACATTCGACCCCTAGAAAAATT 58.508 33.333 0.00 0.00 0.00 1.82
832 2085 8.030913 ACTATACATTCGACCCCTAGAAAAAT 57.969 34.615 0.00 0.00 0.00 1.82
838 2091 6.040616 AGTTTGACTATACATTCGACCCCTAG 59.959 42.308 0.00 0.00 0.00 3.02
846 2099 5.794687 TGCCAAGTTTGACTATACATTCG 57.205 39.130 0.00 0.00 0.00 3.34
852 2105 9.325198 CACAATAGTATGCCAAGTTTGACTATA 57.675 33.333 5.09 0.00 31.53 1.31
853 2106 7.829211 ACACAATAGTATGCCAAGTTTGACTAT 59.171 33.333 0.00 0.00 32.78 2.12
875 2128 1.754803 AGAGAAACAGACGTGGACACA 59.245 47.619 0.00 0.00 0.00 3.72
882 2135 1.749634 CCCCGATAGAGAAACAGACGT 59.250 52.381 0.00 0.00 39.76 4.34
1011 2270 0.545548 AGGTTTCTTCCTCCTCCGCT 60.546 55.000 0.00 0.00 31.32 5.52
1405 2676 2.433436 GTATTGAAAACCACCTCGCCT 58.567 47.619 0.00 0.00 0.00 5.52
1617 2891 8.950210 TGGAATTTAGAAATTAGAGCAAGACAG 58.050 33.333 0.28 0.00 38.64 3.51
1656 2930 5.277058 GCATACTGAGACAAATCCTAAAGCG 60.277 44.000 0.00 0.00 0.00 4.68
1705 2980 5.402398 TGAAAGAGTCACATATCTGACACG 58.598 41.667 12.86 0.00 42.74 4.49
1782 3057 3.628017 GGTCATCAAAACAAACTGACCG 58.372 45.455 4.44 0.00 44.47 4.79
1818 3093 0.788391 CAGAGTTAACGCCGGTGTTC 59.212 55.000 35.16 22.25 33.32 3.18
1892 3167 9.265901 ACAAGAGAGTCCAAATAATATTCATCG 57.734 33.333 0.00 0.00 0.00 3.84
2148 3423 7.609146 TGAATTAGAAGCAAGACTCAATGATGT 59.391 33.333 0.00 0.00 0.00 3.06
2311 3586 5.963176 ATTTTTGGCCATTTCCAACAATC 57.037 34.783 6.09 0.00 45.08 2.67
2602 3881 4.996122 TGCATGAAATCCAACCAATGAAAC 59.004 37.500 0.00 0.00 0.00 2.78
2639 3918 7.445096 TCACAAAGCTAATTTCTTCACATCTCA 59.555 33.333 0.00 0.00 0.00 3.27
2696 3975 8.773645 CATACAATGTGTGAAGAAACTCTAACA 58.226 33.333 3.97 0.00 0.00 2.41
2772 4052 2.991190 GCAGCACCAAAGTTTCATGATG 59.009 45.455 0.00 8.77 0.00 3.07
2774 4054 2.309613 AGCAGCACCAAAGTTTCATGA 58.690 42.857 0.00 0.00 0.00 3.07
2797 4077 4.460382 ACTTATCAAATCAACACCTGCAGG 59.540 41.667 31.60 31.60 42.17 4.85
2977 4258 8.092068 TCATACACAACGACCTATATAATTGGG 58.908 37.037 0.00 0.00 0.00 4.12
2978 4259 9.653287 ATCATACACAACGACCTATATAATTGG 57.347 33.333 0.00 0.00 0.00 3.16
3013 4294 4.098416 GGCGTCTCAAAATGTTATGCTTC 58.902 43.478 0.00 0.00 0.00 3.86
3455 4738 6.022163 ACATGAAGCTAACTTAGTACACGT 57.978 37.500 0.00 0.00 35.82 4.49
3523 4806 5.045140 AGGTGCCTACTGCCTAAGATAAAAA 60.045 40.000 0.00 0.00 40.16 1.94
3556 4839 8.799367 TGTACTAGCTTTAATGTCTTACAGTCA 58.201 33.333 0.00 0.00 0.00 3.41
3561 4844 9.032420 GTCCATGTACTAGCTTTAATGTCTTAC 57.968 37.037 0.00 0.00 0.00 2.34
3586 4870 5.680619 TCACAAAACTATGGTCTTCACAGT 58.319 37.500 0.00 0.00 0.00 3.55
3587 4871 6.618287 TTCACAAAACTATGGTCTTCACAG 57.382 37.500 0.00 0.00 0.00 3.66
3588 4872 6.514870 GCATTCACAAAACTATGGTCTTCACA 60.515 38.462 0.00 0.00 0.00 3.58
3589 4873 5.858581 GCATTCACAAAACTATGGTCTTCAC 59.141 40.000 0.00 0.00 0.00 3.18
3590 4874 5.769662 AGCATTCACAAAACTATGGTCTTCA 59.230 36.000 0.00 0.00 0.00 3.02
3591 4875 6.072508 TCAGCATTCACAAAACTATGGTCTTC 60.073 38.462 0.00 0.00 0.00 2.87
3782 5069 3.915437 AATTAACTGTGCAAACCCTCG 57.085 42.857 0.00 0.00 0.00 4.63
4177 6078 1.251251 AAACTTGCACAGATGGCCTC 58.749 50.000 3.32 0.00 0.00 4.70
4265 6166 5.068460 TGCTGCTTAAACACCAGTACAATTT 59.932 36.000 0.00 0.00 0.00 1.82
4400 6494 6.098679 GCATACCAAATCAAATGTTACAGCA 58.901 36.000 0.00 0.00 0.00 4.41
4451 6548 3.721868 TCCTTCCGGGAGCGATTT 58.278 55.556 3.32 0.00 39.58 2.17
4879 6977 4.851639 AGGTTTGGTCAGCTGATAAGAT 57.148 40.909 21.47 5.78 0.00 2.40
4976 7078 7.172532 ACGTCACAAACAGAAATAGAATAAGCA 59.827 33.333 0.00 0.00 0.00 3.91
5040 7151 6.273495 AGTCCTAGGGAATTCTGTTTTCTTCT 59.727 38.462 9.46 0.00 31.38 2.85
5104 7215 6.594547 GGTTTAAGGGCTTAACAGTAAGAGAG 59.405 42.308 0.00 0.00 39.36 3.20
5140 7251 1.068741 CGCCACATTACCTCCTACTCC 59.931 57.143 0.00 0.00 0.00 3.85
5141 7252 1.755380 ACGCCACATTACCTCCTACTC 59.245 52.381 0.00 0.00 0.00 2.59
5142 7253 1.480954 CACGCCACATTACCTCCTACT 59.519 52.381 0.00 0.00 0.00 2.57
5143 7254 1.479323 TCACGCCACATTACCTCCTAC 59.521 52.381 0.00 0.00 0.00 3.18
5144 7255 1.754803 CTCACGCCACATTACCTCCTA 59.245 52.381 0.00 0.00 0.00 2.94
5198 7309 2.424956 GCTGCCCTTCCACTTTTATCAG 59.575 50.000 0.00 0.00 0.00 2.90
5205 7316 2.437897 CCTGCTGCCCTTCCACTT 59.562 61.111 0.00 0.00 0.00 3.16
5227 7338 3.326297 GCCTCCAAGACCTATAAGCTCAT 59.674 47.826 0.00 0.00 0.00 2.90
5244 7355 4.154347 CTCCGACCAGCTGCCTCC 62.154 72.222 8.66 0.00 0.00 4.30
5298 7411 6.151817 AGTGCTCTGAGTTAAAAATCCAATCC 59.848 38.462 6.53 0.00 0.00 3.01
5344 7457 6.573664 AATTTTCATCAACGAGTTGGATGA 57.426 33.333 14.99 16.93 40.78 2.92
5360 7473 7.192148 TCGGACATCGAAGTTAAAATTTTCA 57.808 32.000 6.72 0.00 45.86 2.69
5383 7496 6.798959 GCGAATTAATTAGCCTCAATGTCATC 59.201 38.462 19.21 0.00 33.14 2.92
5384 7497 6.672147 GCGAATTAATTAGCCTCAATGTCAT 58.328 36.000 19.21 0.00 33.14 3.06
5385 7498 6.060028 GCGAATTAATTAGCCTCAATGTCA 57.940 37.500 19.21 0.00 33.14 3.58
5400 7514 6.038603 CAGAAATCTCATTCCAGGCGAATTAA 59.961 38.462 0.00 0.00 39.28 1.40
5405 7519 2.237143 ACAGAAATCTCATTCCAGGCGA 59.763 45.455 0.00 0.00 0.00 5.54
5424 7538 6.612247 TTTCTTTTGCGAGTGAAGAATACA 57.388 33.333 1.07 0.00 38.69 2.29
5426 7540 7.606456 ACCTATTTCTTTTGCGAGTGAAGAATA 59.394 33.333 1.07 0.00 38.69 1.75
5433 7547 4.151689 TCGAACCTATTTCTTTTGCGAGTG 59.848 41.667 0.00 0.00 31.20 3.51
5454 7568 6.050454 AGTCTTCGTGTCTATACTCAATCG 57.950 41.667 0.00 0.00 0.00 3.34
5536 7681 5.410439 AGACGCGGTGTAGAATTTTGTTTAT 59.590 36.000 12.47 0.00 0.00 1.40
5546 7691 4.357142 GAATATGAAGACGCGGTGTAGAA 58.643 43.478 12.47 0.00 0.00 2.10
5548 7693 3.050619 GGAATATGAAGACGCGGTGTAG 58.949 50.000 12.47 0.00 0.00 2.74
5600 7745 5.362430 GTCATGGCCCCTAAAAATTATGTGA 59.638 40.000 0.00 0.00 0.00 3.58
5622 7767 5.001874 AGGATTTGGTTTAACCGAAGAGTC 58.998 41.667 20.04 13.36 44.41 3.36
5659 7804 4.926832 CCATGTGTTTGTGAGTATACACGA 59.073 41.667 5.50 0.00 42.81 4.35
5661 7806 6.985188 ATCCATGTGTTTGTGAGTATACAC 57.015 37.500 5.50 0.00 40.87 2.90
5668 7813 6.573664 TTAAGGAATCCATGTGTTTGTGAG 57.426 37.500 0.61 0.00 0.00 3.51
5716 7861 9.658799 TTTTGTAAATGTTTTGATGTTCTGGAA 57.341 25.926 0.00 0.00 0.00 3.53
5761 7906 7.935338 ATGTTTTGAATCGAATGGAATATGC 57.065 32.000 0.00 0.00 0.00 3.14
5770 7915 7.373493 AGAGCTTCAAATGTTTTGAATCGAAT 58.627 30.769 13.94 0.00 37.72 3.34
5773 7918 6.744537 CCTAGAGCTTCAAATGTTTTGAATCG 59.255 38.462 13.94 6.70 37.72 3.34
5778 7923 7.373493 ACAATCCTAGAGCTTCAAATGTTTTG 58.627 34.615 0.00 0.00 0.00 2.44
5849 7996 9.899661 ACTAATTTGGTGCAGTAGATGTTAATA 57.100 29.630 0.00 0.00 0.00 0.98
5853 8000 6.476378 AGACTAATTTGGTGCAGTAGATGTT 58.524 36.000 0.00 0.00 0.00 2.71
5917 8064 9.730420 GTTTTACTAATATCCGCAACATCAAAT 57.270 29.630 0.00 0.00 0.00 2.32
5918 8065 8.952278 AGTTTTACTAATATCCGCAACATCAAA 58.048 29.630 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.