Multiple sequence alignment - TraesCS5B01G085400

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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 TraesCS5B01G085400 chr5B 100.000 3991 0 0 1 3991 108195177 108191187 0.000000e+00 7371.0
1 TraesCS5B01G085400 chr5B 100.000 2206 0 0 4233 6438 108190945 108188740 0.000000e+00 4074.0
2 TraesCS5B01G085400 chr5B 96.296 1593 50 8 1323 2912 108124375 108122789 0.000000e+00 2606.0
3 TraesCS5B01G085400 chr5B 95.613 1550 61 5 1595 3141 108165823 108164278 0.000000e+00 2479.0
4 TraesCS5B01G085400 chr5B 97.079 445 10 2 1135 1576 108167839 108167395 0.000000e+00 747.0
5 TraesCS5B01G085400 chr5B 93.521 463 24 4 849 1310 108129334 108128877 0.000000e+00 684.0
6 TraesCS5B01G085400 chr5B 94.466 253 6 3 848 1099 108168077 108167832 3.640000e-102 383.0
7 TraesCS5B01G085400 chr5B 96.535 202 4 1 2943 3141 108122786 108122585 1.340000e-86 331.0
8 TraesCS5B01G085400 chr5B 100.000 72 0 0 6167 6238 108188941 108188870 4.050000e-27 134.0
9 TraesCS5B01G085400 chr5B 100.000 72 0 0 6237 6308 108189011 108188940 4.050000e-27 134.0
10 TraesCS5B01G085400 chr5B 94.186 86 3 2 5735 5818 108189369 108189284 5.240000e-26 130.0
11 TraesCS5B01G085400 chr5B 94.186 86 3 2 5809 5894 108189443 108189360 5.240000e-26 130.0
12 TraesCS5B01G085400 chr6D 98.323 2624 30 10 1378 3991 132655053 132657672 0.000000e+00 4590.0
13 TraesCS5B01G085400 chr6D 96.792 1590 39 7 1558 3141 132683375 132684958 0.000000e+00 2643.0
14 TraesCS5B01G085400 chr6D 96.192 1602 37 15 4233 5818 132657956 132659549 0.000000e+00 2599.0
15 TraesCS5B01G085400 chr6D 96.795 1248 31 6 849 2093 132630993 132632234 0.000000e+00 2074.0
16 TraesCS5B01G085400 chr6D 97.143 1050 27 1 2095 3141 132632326 132633375 0.000000e+00 1770.0
17 TraesCS5B01G085400 chr6D 98.462 455 5 2 925 1379 132653904 132654356 0.000000e+00 800.0
18 TraesCS5B01G085400 chr6D 88.281 256 12 4 849 1104 132683142 132683379 2.270000e-74 291.0
19 TraesCS5B01G085400 chr6D 93.296 179 7 2 6065 6238 132659841 132660019 6.400000e-65 259.0
20 TraesCS5B01G085400 chr6D 97.561 123 3 0 6237 6359 132659948 132660070 1.820000e-50 211.0
21 TraesCS5B01G085400 chr6D 95.495 111 2 1 744 854 132653016 132653123 2.390000e-39 174.0
22 TraesCS5B01G085400 chr6D 97.000 100 3 0 5908 6007 132659606 132659705 1.110000e-37 169.0
23 TraesCS5B01G085400 chr6D 96.939 98 3 0 5809 5906 132659464 132659561 1.440000e-36 165.0
24 TraesCS5B01G085400 chr6D 92.982 57 0 1 849 905 132652019 132652071 5.350000e-11 80.5
25 TraesCS5B01G085400 chr6D 100.000 32 0 0 874 905 132652172 132652203 6.970000e-05 60.2
26 TraesCS5B01G085400 chr6A 97.861 2618 44 7 1378 3991 166802301 166804910 0.000000e+00 4514.0
27 TraesCS5B01G085400 chr6A 97.694 1561 31 3 4233 5791 166805234 166806791 0.000000e+00 2678.0
28 TraesCS5B01G085400 chr6A 98.520 473 7 0 905 1377 166801136 166801608 0.000000e+00 835.0
29 TraesCS5B01G085400 chr6A 97.000 100 3 0 5908 6007 166807012 166807111 1.110000e-37 169.0
30 TraesCS5B01G085400 chr6A 92.793 111 4 1 744 854 166800344 166800450 2.400000e-34 158.0
31 TraesCS5B01G085400 chr6A 89.109 101 8 3 6276 6374 166807376 166807475 8.770000e-24 122.0
32 TraesCS5B01G085400 chr6A 98.413 63 0 1 6377 6438 166807444 166807506 6.820000e-20 110.0
33 TraesCS5B01G085400 chr6A 83.333 126 4 5 6066 6186 166807263 166807376 4.110000e-17 100.0
34 TraesCS5B01G085400 chr6A 96.491 57 2 0 5809 5865 166806735 166806791 1.910000e-15 95.3
35 TraesCS5B01G085400 chr3D 94.773 727 32 3 22 745 556074994 556074271 0.000000e+00 1127.0
36 TraesCS5B01G085400 chr3B 89.273 839 57 19 1367 2184 275007202 275006376 0.000000e+00 1020.0
37 TraesCS5B01G085400 chr5D 91.342 693 37 6 1 690 441014812 441015484 0.000000e+00 926.0
38 TraesCS5B01G085400 chrUn 94.819 579 22 5 169 744 110789389 110788816 0.000000e+00 896.0
39 TraesCS5B01G085400 chr1A 89.231 390 11 6 1 390 574808235 574808593 5.880000e-125 459.0
40 TraesCS5B01G085400 chr2A 93.659 205 7 3 540 741 360867743 360867944 1.050000e-77 302.0


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 TraesCS5B01G085400 chr5B 108188740 108195177 6437 True 1995.50 7371 98.062000 1 6438 6 chr5B.!!$R4 6437
1 TraesCS5B01G085400 chr5B 108122585 108124375 1790 True 1468.50 2606 96.415500 1323 3141 2 chr5B.!!$R2 1818
2 TraesCS5B01G085400 chr5B 108164278 108168077 3799 True 1203.00 2479 95.719333 848 3141 3 chr5B.!!$R3 2293
3 TraesCS5B01G085400 chr6D 132630993 132633375 2382 False 1922.00 2074 96.969000 849 3141 2 chr6D.!!$F1 2292
4 TraesCS5B01G085400 chr6D 132683142 132684958 1816 False 1467.00 2643 92.536500 849 3141 2 chr6D.!!$F3 2292
5 TraesCS5B01G085400 chr6D 132652019 132660070 8051 False 910.77 4590 96.625000 744 6359 10 chr6D.!!$F2 5615
6 TraesCS5B01G085400 chr6A 166800344 166807506 7162 False 975.70 4514 94.579333 744 6438 9 chr6A.!!$F1 5694
7 TraesCS5B01G085400 chr3D 556074271 556074994 723 True 1127.00 1127 94.773000 22 745 1 chr3D.!!$R1 723
8 TraesCS5B01G085400 chr3B 275006376 275007202 826 True 1020.00 1020 89.273000 1367 2184 1 chr3B.!!$R1 817
9 TraesCS5B01G085400 chr5D 441014812 441015484 672 False 926.00 926 91.342000 1 690 1 chr5D.!!$F1 689
10 TraesCS5B01G085400 chrUn 110788816 110789389 573 True 896.00 896 94.819000 169 744 1 chrUn.!!$R1 575

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
704 708 1.086696 GCGATGTGCCACACTGTATT 58.913 50.000 0.00 0.0 37.76 1.89 F
823 1078 1.730547 CGCTTTTCTGCCCTTTGCG 60.731 57.895 0.00 0.0 45.60 4.85 F
2210 5565 0.386731 CAAAGGGCAAGCGTAAACGG 60.387 55.000 4.49 0.0 40.23 4.44 F
3227 6590 3.012959 ACCACTTCCAGGGATCTCTTCTA 59.987 47.826 0.00 0.0 0.00 2.10 F
4843 8313 4.006319 GCAAGATGAGTGGAAAGCTACTT 58.994 43.478 0.00 0.0 35.81 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 5006 3.073798 TCCTGTGATAACCAAAGAGGCAA 59.926 43.478 0.0 0.0 43.14 4.52 R
2565 5924 3.795688 TCTTGCTCTTCATCCTTTGGT 57.204 42.857 0.0 0.0 0.00 3.67 R
3326 6689 5.648178 TTACAGTCTTGGAGCGTAATGTA 57.352 39.130 0.0 0.0 0.00 2.29 R
5085 8559 0.618680 AGCAGTAGATCAGCCCACCA 60.619 55.000 0.0 0.0 0.00 4.17 R
6290 10050 0.035458 AAGCAAAGAGTCTGGTCGGG 59.965 55.000 0.0 0.0 0.00 5.14 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
164 165 3.679389 TGCAGAGAATTTGAGGAGGAAC 58.321 45.455 0.00 0.00 0.00 3.62
173 174 6.599638 AGAATTTGAGGAGGAACGGAATAAAG 59.400 38.462 0.00 0.00 0.00 1.85
233 234 1.972588 AGCCTCCTCCACCTAATGTT 58.027 50.000 0.00 0.00 0.00 2.71
372 373 7.013942 AGCATATTTCTGAAGCTATTCATGCAA 59.986 33.333 10.47 0.00 44.32 4.08
443 444 8.865978 GGATGTAACCGATTAATTTTTGAAACC 58.134 33.333 0.00 0.00 0.00 3.27
468 469 5.065704 TGCTTTTGTACTGAAACAAGCAA 57.934 34.783 1.99 0.00 40.29 3.91
561 562 7.686438 ACATACTTTGATGATGCAAGTGTTA 57.314 32.000 0.00 0.00 0.00 2.41
702 706 4.277239 GCGATGTGCCACACTGTA 57.723 55.556 0.00 0.00 37.76 2.74
703 707 2.767536 GCGATGTGCCACACTGTAT 58.232 52.632 0.00 0.00 37.76 2.29
704 708 1.086696 GCGATGTGCCACACTGTATT 58.913 50.000 0.00 0.00 37.76 1.89
705 709 2.276201 GCGATGTGCCACACTGTATTA 58.724 47.619 0.00 0.00 37.76 0.98
707 711 3.303329 GCGATGTGCCACACTGTATTATG 60.303 47.826 0.00 0.00 37.76 1.90
708 712 3.871006 CGATGTGCCACACTGTATTATGT 59.129 43.478 0.00 0.00 35.11 2.29
709 713 5.047188 CGATGTGCCACACTGTATTATGTA 58.953 41.667 0.00 0.00 35.11 2.29
710 714 5.522097 CGATGTGCCACACTGTATTATGTAA 59.478 40.000 0.00 0.00 35.11 2.41
711 715 6.202762 CGATGTGCCACACTGTATTATGTAAT 59.797 38.462 0.00 0.00 35.11 1.89
713 717 9.219603 GATGTGCCACACTGTATTATGTAATAT 57.780 33.333 0.00 0.00 35.11 1.28
823 1078 1.730547 CGCTTTTCTGCCCTTTGCG 60.731 57.895 0.00 0.00 45.60 4.85
868 1547 2.202797 CAGATGGCCTGTCGACCG 60.203 66.667 14.12 6.54 38.10 4.79
869 1548 2.362503 AGATGGCCTGTCGACCGA 60.363 61.111 14.12 0.00 0.00 4.69
1537 3237 3.932710 TGGCTCAAGTAATTGCTAAGACG 59.067 43.478 9.22 0.00 0.00 4.18
1977 5241 8.306313 TCATGGAGTATTAGTGTATGTGACTT 57.694 34.615 0.00 0.00 0.00 3.01
1978 5242 9.416284 TCATGGAGTATTAGTGTATGTGACTTA 57.584 33.333 0.00 0.00 0.00 2.24
2043 5307 8.364142 TGTACTCCTGGGTTCAATTTTATTTTG 58.636 33.333 0.00 0.00 0.00 2.44
2210 5565 0.386731 CAAAGGGCAAGCGTAAACGG 60.387 55.000 4.49 0.00 40.23 4.44
2495 5854 8.571336 GCATGTATTATTTGTCAAGGATAGCTT 58.429 33.333 0.00 0.00 0.00 3.74
2565 5924 7.725251 AGGAAAAACATGCTTCATCAAAGTTA 58.275 30.769 0.00 0.00 37.31 2.24
2581 5940 5.473504 TCAAAGTTACCAAAGGATGAAGAGC 59.526 40.000 0.00 0.00 0.00 4.09
2604 5963 5.688766 GCAAGATGGCTTAAGGGATCTAGTT 60.689 44.000 4.29 0.00 31.81 2.24
3227 6590 3.012959 ACCACTTCCAGGGATCTCTTCTA 59.987 47.826 0.00 0.00 0.00 2.10
3326 6689 5.501156 GTTGGGAAGTCCTCAGTTATCAAT 58.499 41.667 0.00 0.00 36.20 2.57
3351 6714 5.938125 ACATTACGCTCCAAGACTGTAATTT 59.062 36.000 0.00 0.00 34.46 1.82
3606 6971 6.256539 GCCCTTTTTGTCTTCTCTTTTTGAAG 59.743 38.462 0.00 0.00 41.46 3.02
4515 7985 4.142534 CGTGGGAGTAACGTCTAAAGATGA 60.143 45.833 6.21 0.00 36.31 2.92
4516 7986 5.450137 CGTGGGAGTAACGTCTAAAGATGAT 60.450 44.000 6.21 0.00 36.31 2.45
4659 8129 5.068636 AGCTCTTGGCATATCTGGTTATTG 58.931 41.667 0.00 0.00 44.79 1.90
4742 8212 7.554835 CACTATAATAACTAAAACCCACAGCCA 59.445 37.037 0.00 0.00 0.00 4.75
4743 8213 8.110908 ACTATAATAACTAAAACCCACAGCCAA 58.889 33.333 0.00 0.00 0.00 4.52
4843 8313 4.006319 GCAAGATGAGTGGAAAGCTACTT 58.994 43.478 0.00 0.00 35.81 2.24
4957 8429 6.203915 TGCAATTTCGTAACACTTGTATGTCT 59.796 34.615 0.00 0.00 30.55 3.41
4958 8430 7.075741 GCAATTTCGTAACACTTGTATGTCTT 58.924 34.615 0.00 0.00 30.55 3.01
5020 8494 6.127703 GGAGTTGAACATACAGCTACTGACTA 60.128 42.308 0.78 0.00 35.18 2.59
5131 8605 6.391227 TTCTCAACCTCTGTTTTTGATTCC 57.609 37.500 0.00 0.00 30.42 3.01
5614 9088 5.707242 TCTAATGGATTAGGTAGAGCGTG 57.293 43.478 6.57 0.00 40.06 5.34
5779 9253 3.245518 TGTTGACATACGTGGATCTGG 57.754 47.619 0.00 0.00 0.00 3.86
5792 9408 2.046729 TGGATCTGGGTTACCCTTACCT 59.953 50.000 22.29 1.68 45.70 3.08
5793 9409 3.120898 GGATCTGGGTTACCCTTACCTT 58.879 50.000 22.29 0.40 45.70 3.50
5794 9410 4.265400 TGGATCTGGGTTACCCTTACCTTA 60.265 45.833 22.29 0.00 45.70 2.69
5795 9411 4.912133 GGATCTGGGTTACCCTTACCTTAT 59.088 45.833 22.29 4.44 45.70 1.73
5796 9412 5.221864 GGATCTGGGTTACCCTTACCTTATG 60.222 48.000 22.29 1.13 45.70 1.90
5797 9413 4.962839 TCTGGGTTACCCTTACCTTATGA 58.037 43.478 22.29 3.34 45.70 2.15
5798 9414 5.544682 TCTGGGTTACCCTTACCTTATGAT 58.455 41.667 22.29 0.00 45.70 2.45
5799 9415 6.695624 TCTGGGTTACCCTTACCTTATGATA 58.304 40.000 22.29 0.00 45.70 2.15
5800 9416 6.556116 TCTGGGTTACCCTTACCTTATGATAC 59.444 42.308 22.29 0.00 45.70 2.24
5801 9417 6.455241 TGGGTTACCCTTACCTTATGATACT 58.545 40.000 22.29 0.00 45.70 2.12
5802 9418 7.603795 TGGGTTACCCTTACCTTATGATACTA 58.396 38.462 22.29 0.00 45.70 1.82
5803 9419 8.243752 TGGGTTACCCTTACCTTATGATACTAT 58.756 37.037 22.29 0.00 45.70 2.12
5804 9420 9.774071 GGGTTACCCTTACCTTATGATACTATA 57.226 37.037 14.22 0.00 41.34 1.31
5835 9451 9.883142 TTCTAATTTTTGTTTTCCACTTGATGT 57.117 25.926 0.00 0.00 0.00 3.06
5836 9452 9.883142 TCTAATTTTTGTTTTCCACTTGATGTT 57.117 25.926 0.00 0.00 0.00 2.71
5837 9453 9.919348 CTAATTTTTGTTTTCCACTTGATGTTG 57.081 29.630 0.00 0.00 0.00 3.33
5838 9454 8.558973 AATTTTTGTTTTCCACTTGATGTTGA 57.441 26.923 0.00 0.00 0.00 3.18
5839 9455 6.959671 TTTTGTTTTCCACTTGATGTTGAC 57.040 33.333 0.00 0.00 0.00 3.18
5840 9456 5.651387 TTGTTTTCCACTTGATGTTGACA 57.349 34.783 0.00 0.00 0.00 3.58
5841 9457 5.850557 TGTTTTCCACTTGATGTTGACAT 57.149 34.783 0.00 0.00 39.70 3.06
5842 9458 6.951062 TGTTTTCCACTTGATGTTGACATA 57.049 33.333 0.00 0.00 36.57 2.29
5843 9459 6.969366 TGTTTTCCACTTGATGTTGACATAG 58.031 36.000 0.00 0.00 36.57 2.23
5844 9460 6.016360 TGTTTTCCACTTGATGTTGACATAGG 60.016 38.462 0.00 0.00 36.57 2.57
5845 9461 4.908601 TCCACTTGATGTTGACATAGGT 57.091 40.909 0.00 0.00 36.57 3.08
5846 9462 4.578871 TCCACTTGATGTTGACATAGGTG 58.421 43.478 0.00 6.61 36.57 4.00
5847 9463 3.691118 CCACTTGATGTTGACATAGGTGG 59.309 47.826 18.80 18.80 40.37 4.61
5848 9464 4.565444 CCACTTGATGTTGACATAGGTGGA 60.565 45.833 23.31 1.32 44.07 4.02
5849 9465 5.188434 CACTTGATGTTGACATAGGTGGAT 58.812 41.667 0.00 0.00 36.57 3.41
5850 9466 5.295292 CACTTGATGTTGACATAGGTGGATC 59.705 44.000 0.00 0.00 36.57 3.36
5851 9467 5.190528 ACTTGATGTTGACATAGGTGGATCT 59.809 40.000 0.00 0.00 36.57 2.75
5852 9468 5.027293 TGATGTTGACATAGGTGGATCTG 57.973 43.478 0.00 0.00 36.57 2.90
5853 9469 3.266510 TGTTGACATAGGTGGATCTGC 57.733 47.619 0.00 0.00 0.00 4.26
5854 9470 2.205074 GTTGACATAGGTGGATCTGCG 58.795 52.381 0.00 0.00 0.00 5.18
5855 9471 1.485124 TGACATAGGTGGATCTGCGT 58.515 50.000 0.00 0.00 0.00 5.24
5856 9472 1.831106 TGACATAGGTGGATCTGCGTT 59.169 47.619 0.00 0.00 0.00 4.84
5857 9473 3.028130 TGACATAGGTGGATCTGCGTTA 58.972 45.455 0.00 0.00 0.00 3.18
5858 9474 3.181479 TGACATAGGTGGATCTGCGTTAC 60.181 47.826 0.00 0.00 0.00 2.50
5859 9475 2.102588 ACATAGGTGGATCTGCGTTACC 59.897 50.000 0.00 0.00 0.00 2.85
5860 9476 1.117150 TAGGTGGATCTGCGTTACCC 58.883 55.000 0.00 0.00 31.80 3.69
5861 9477 0.617820 AGGTGGATCTGCGTTACCCT 60.618 55.000 0.00 0.00 31.80 4.34
5862 9478 0.252197 GGTGGATCTGCGTTACCCTT 59.748 55.000 0.00 0.00 0.00 3.95
5863 9479 1.483415 GGTGGATCTGCGTTACCCTTA 59.517 52.381 0.00 0.00 0.00 2.69
5864 9480 2.547826 GTGGATCTGCGTTACCCTTAC 58.452 52.381 0.00 0.00 0.00 2.34
5865 9481 1.483415 TGGATCTGCGTTACCCTTACC 59.517 52.381 0.00 0.00 0.00 2.85
5906 9522 9.252962 CATATTACAAATTTGGCTGGAGAAATC 57.747 33.333 21.74 0.00 0.00 2.17
5953 9612 9.757227 CTATCTACTATCCCTATAAAAGCATGC 57.243 37.037 10.51 10.51 0.00 4.06
6016 9729 7.216494 TCATCAATCTAATTGTTGGATCGCTA 58.784 34.615 9.62 0.00 39.34 4.26
6027 9740 3.711541 GATCGCTAACCCCGCACGT 62.712 63.158 0.00 0.00 0.00 4.49
6089 9844 2.111878 CATCCTCCGCCATGGACC 59.888 66.667 18.40 0.00 43.74 4.46
6234 9994 3.003763 GCCCCCGACCAGACTCTT 61.004 66.667 0.00 0.00 0.00 2.85
6235 9995 2.593956 GCCCCCGACCAGACTCTTT 61.594 63.158 0.00 0.00 0.00 2.52
6236 9996 1.296715 CCCCCGACCAGACTCTTTG 59.703 63.158 0.00 0.00 0.00 2.77
6237 9997 1.376037 CCCCGACCAGACTCTTTGC 60.376 63.158 0.00 0.00 0.00 3.68
6238 9998 1.371183 CCCGACCAGACTCTTTGCA 59.629 57.895 0.00 0.00 0.00 4.08
6239 9999 0.951040 CCCGACCAGACTCTTTGCAC 60.951 60.000 0.00 0.00 0.00 4.57
6240 10000 0.034059 CCGACCAGACTCTTTGCACT 59.966 55.000 0.00 0.00 0.00 4.40
6241 10001 1.272490 CCGACCAGACTCTTTGCACTA 59.728 52.381 0.00 0.00 0.00 2.74
6242 10002 2.600731 CGACCAGACTCTTTGCACTAG 58.399 52.381 0.00 0.00 0.00 2.57
6243 10003 2.342179 GACCAGACTCTTTGCACTAGC 58.658 52.381 0.00 0.00 42.57 3.42
6244 10004 1.002544 ACCAGACTCTTTGCACTAGCC 59.997 52.381 0.00 0.00 41.13 3.93
6245 10005 1.354040 CAGACTCTTTGCACTAGCCG 58.646 55.000 0.00 0.00 41.13 5.52
6246 10006 0.390472 AGACTCTTTGCACTAGCCGC 60.390 55.000 0.00 0.00 41.13 6.53
6247 10007 1.362406 GACTCTTTGCACTAGCCGCC 61.362 60.000 2.52 0.00 41.13 6.13
6248 10008 2.434185 TCTTTGCACTAGCCGCCG 60.434 61.111 2.52 0.00 41.13 6.46
6249 10009 3.499737 CTTTGCACTAGCCGCCGG 61.500 66.667 0.00 0.00 41.13 6.13
6287 10047 4.742201 CCCCACGCACGAGACCTG 62.742 72.222 0.00 0.00 0.00 4.00
6302 10062 3.775654 CTGCCCCCGACCAGACTC 61.776 72.222 0.00 0.00 0.00 3.36
6303 10063 4.316823 TGCCCCCGACCAGACTCT 62.317 66.667 0.00 0.00 0.00 3.24
6304 10064 3.003763 GCCCCCGACCAGACTCTT 61.004 66.667 0.00 0.00 0.00 2.85
6312 10072 2.613977 CCGACCAGACTCTTTGCTTGAT 60.614 50.000 0.00 0.00 0.00 2.57
6368 10128 3.550656 GTGTGCACACGTAGGAGC 58.449 61.111 32.41 9.15 37.10 4.70
6369 10129 1.006102 GTGTGCACACGTAGGAGCT 60.006 57.895 32.41 0.00 37.10 4.09
6370 10130 1.006220 TGTGCACACGTAGGAGCTG 60.006 57.895 17.42 0.00 0.00 4.24
6371 10131 2.048222 TGCACACGTAGGAGCTGC 60.048 61.111 0.00 0.00 0.00 5.25
6372 10132 2.815647 GCACACGTAGGAGCTGCC 60.816 66.667 0.00 0.00 0.00 4.85
6373 10133 2.507102 CACACGTAGGAGCTGCCG 60.507 66.667 0.00 1.36 43.43 5.69
6374 10134 2.989824 ACACGTAGGAGCTGCCGT 60.990 61.111 0.00 2.11 43.43 5.68
6375 10135 2.202623 CACGTAGGAGCTGCCGTC 60.203 66.667 6.56 0.00 43.43 4.79
6376 10136 3.812019 ACGTAGGAGCTGCCGTCG 61.812 66.667 0.00 7.17 43.43 5.12
6378 10138 3.827898 GTAGGAGCTGCCGTCGCT 61.828 66.667 0.00 0.00 43.43 4.93
6379 10139 3.826754 TAGGAGCTGCCGTCGCTG 61.827 66.667 0.00 0.00 43.43 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
183 184 2.235402 CCGAGCAGGGAAGTTTAGGTAA 59.765 50.000 0.00 0.00 35.97 2.85
233 234 5.985530 CGCACCATCAGTATTTATCTTCAGA 59.014 40.000 0.00 0.00 0.00 3.27
372 373 2.569404 CCTGGAGGAGTGCTAGACTTTT 59.431 50.000 0.00 0.00 33.83 2.27
443 444 4.379793 GCTTGTTTCAGTACAAAAGCATCG 59.620 41.667 0.00 0.00 37.55 3.84
468 469 6.398918 AGTTGTCGTAAGCTTCACTCATTAT 58.601 36.000 0.00 0.00 37.18 1.28
561 562 3.417101 TGCAGGAACGATTACACCATTT 58.583 40.909 0.00 0.00 0.00 2.32
741 745 0.108019 AAGTCTCCGGCCGAACTTTT 59.892 50.000 30.73 12.55 0.00 2.27
742 746 0.602905 CAAGTCTCCGGCCGAACTTT 60.603 55.000 30.73 11.38 0.00 2.66
868 1547 3.846430 GACGGGGATGGGTCGGTC 61.846 72.222 0.00 0.00 0.00 4.79
1475 3174 7.333174 AGACTCTAATCAGCAAAAGAGCTTTAC 59.667 37.037 0.00 0.00 43.70 2.01
1537 3237 5.523916 CCACCAAGTTCACTATATGTACTGC 59.476 44.000 0.00 0.00 37.92 4.40
1743 5006 3.073798 TCCTGTGATAACCAAAGAGGCAA 59.926 43.478 0.00 0.00 43.14 4.52
2043 5307 4.401519 GGAAGGTTCCAAGCTATTTAACCC 59.598 45.833 13.60 3.57 46.76 4.11
2210 5565 5.904362 AATCAAGACTGGATAGTTTTGGC 57.096 39.130 9.80 0.00 44.71 4.52
2565 5924 3.795688 TCTTGCTCTTCATCCTTTGGT 57.204 42.857 0.00 0.00 0.00 3.67
2581 5940 5.559148 ACTAGATCCCTTAAGCCATCTTG 57.441 43.478 15.76 15.63 33.85 3.02
2604 5963 7.147391 TGTCCCTTCTCAAACATATTATGCCTA 60.147 37.037 3.52 0.00 0.00 3.93
2950 6310 8.200792 AGGTAAACAATCAACATTTGCACTAAA 58.799 29.630 0.00 0.00 0.00 1.85
3326 6689 5.648178 TTACAGTCTTGGAGCGTAATGTA 57.352 39.130 0.00 0.00 0.00 2.29
3606 6971 7.823149 AAGAAAATGCTTGAATATCTGCAAC 57.177 32.000 0.00 0.00 38.96 4.17
4235 7602 9.529325 GAAAGGAACACAGCTAAAAATAAAAGT 57.471 29.630 0.00 0.00 0.00 2.66
4236 7603 9.750125 AGAAAGGAACACAGCTAAAAATAAAAG 57.250 29.630 0.00 0.00 0.00 2.27
4237 7604 9.528018 CAGAAAGGAACACAGCTAAAAATAAAA 57.472 29.630 0.00 0.00 0.00 1.52
4238 7605 8.908903 TCAGAAAGGAACACAGCTAAAAATAAA 58.091 29.630 0.00 0.00 0.00 1.40
4239 7606 8.458573 TCAGAAAGGAACACAGCTAAAAATAA 57.541 30.769 0.00 0.00 0.00 1.40
4240 7607 7.308589 GCTCAGAAAGGAACACAGCTAAAAATA 60.309 37.037 0.00 0.00 0.00 1.40
4241 7608 6.515696 GCTCAGAAAGGAACACAGCTAAAAAT 60.516 38.462 0.00 0.00 0.00 1.82
4242 7609 5.221048 GCTCAGAAAGGAACACAGCTAAAAA 60.221 40.000 0.00 0.00 0.00 1.94
4659 8129 5.163540 ACGTTCATTATGGACCAGAGTACTC 60.164 44.000 15.41 15.41 0.00 2.59
4742 8212 9.965902 AAGTATAAAAGATGTGTCATCTCCTTT 57.034 29.630 11.81 11.64 0.00 3.11
4843 8313 9.899661 AATATCACAAGTTTATGCTGTACCTTA 57.100 29.630 0.00 0.00 0.00 2.69
4891 8361 3.823873 TGAACAGGCGACAAATATTTGGT 59.176 39.130 27.43 15.53 42.34 3.67
4902 8372 2.370281 TTCATCTCTGAACAGGCGAC 57.630 50.000 1.93 0.00 36.46 5.19
4995 8469 4.865365 GTCAGTAGCTGTATGTTCAACTCC 59.135 45.833 0.00 0.00 32.61 3.85
5085 8559 0.618680 AGCAGTAGATCAGCCCACCA 60.619 55.000 0.00 0.00 0.00 4.17
5434 8908 1.745653 GCAGGATTGCTACCCTTTCAC 59.254 52.381 0.00 0.00 46.95 3.18
5614 9088 5.163513 CAAGTTTTGATGTAGATGCCAACC 58.836 41.667 0.00 0.00 0.00 3.77
5809 9425 9.883142 ACATCAAGTGGAAAACAAAAATTAGAA 57.117 25.926 0.00 0.00 0.00 2.10
5810 9426 9.883142 AACATCAAGTGGAAAACAAAAATTAGA 57.117 25.926 0.00 0.00 0.00 2.10
5811 9427 9.919348 CAACATCAAGTGGAAAACAAAAATTAG 57.081 29.630 0.00 0.00 0.00 1.73
5812 9428 9.658799 TCAACATCAAGTGGAAAACAAAAATTA 57.341 25.926 0.00 0.00 0.00 1.40
5813 9429 8.450180 GTCAACATCAAGTGGAAAACAAAAATT 58.550 29.630 0.00 0.00 30.15 1.82
5814 9430 7.605691 TGTCAACATCAAGTGGAAAACAAAAAT 59.394 29.630 0.00 0.00 30.15 1.82
5815 9431 6.931281 TGTCAACATCAAGTGGAAAACAAAAA 59.069 30.769 0.00 0.00 30.15 1.94
5816 9432 6.459066 TGTCAACATCAAGTGGAAAACAAAA 58.541 32.000 0.00 0.00 30.15 2.44
5817 9433 6.030548 TGTCAACATCAAGTGGAAAACAAA 57.969 33.333 0.00 0.00 30.15 2.83
5818 9434 5.651387 TGTCAACATCAAGTGGAAAACAA 57.349 34.783 0.00 0.00 30.15 2.83
5819 9435 5.850557 ATGTCAACATCAAGTGGAAAACA 57.149 34.783 0.00 0.00 30.15 2.83
5820 9436 6.016276 ACCTATGTCAACATCAAGTGGAAAAC 60.016 38.462 0.00 0.00 37.76 2.43
5821 9437 6.016360 CACCTATGTCAACATCAAGTGGAAAA 60.016 38.462 0.00 0.00 37.76 2.29
5822 9438 5.473162 CACCTATGTCAACATCAAGTGGAAA 59.527 40.000 0.00 0.00 37.76 3.13
5823 9439 5.003160 CACCTATGTCAACATCAAGTGGAA 58.997 41.667 0.00 0.00 37.76 3.53
5824 9440 4.565444 CCACCTATGTCAACATCAAGTGGA 60.565 45.833 22.41 0.00 44.79 4.02
5825 9441 3.691118 CCACCTATGTCAACATCAAGTGG 59.309 47.826 17.56 17.56 40.85 4.00
5826 9442 4.578871 TCCACCTATGTCAACATCAAGTG 58.421 43.478 0.00 6.12 37.76 3.16
5827 9443 4.908601 TCCACCTATGTCAACATCAAGT 57.091 40.909 0.00 0.00 37.76 3.16
5828 9444 5.526479 CAGATCCACCTATGTCAACATCAAG 59.474 44.000 0.00 0.00 37.76 3.02
5829 9445 5.430886 CAGATCCACCTATGTCAACATCAA 58.569 41.667 0.00 0.00 37.76 2.57
5830 9446 4.684214 GCAGATCCACCTATGTCAACATCA 60.684 45.833 0.00 0.00 37.76 3.07
5831 9447 3.812053 GCAGATCCACCTATGTCAACATC 59.188 47.826 0.00 0.00 37.76 3.06
5832 9448 3.742327 CGCAGATCCACCTATGTCAACAT 60.742 47.826 0.70 0.70 40.22 2.71
5833 9449 2.418609 CGCAGATCCACCTATGTCAACA 60.419 50.000 0.00 0.00 0.00 3.33
5834 9450 2.205074 CGCAGATCCACCTATGTCAAC 58.795 52.381 0.00 0.00 0.00 3.18
5835 9451 1.831106 ACGCAGATCCACCTATGTCAA 59.169 47.619 0.00 0.00 0.00 3.18
5836 9452 1.485124 ACGCAGATCCACCTATGTCA 58.515 50.000 0.00 0.00 0.00 3.58
5837 9453 2.604046 AACGCAGATCCACCTATGTC 57.396 50.000 0.00 0.00 0.00 3.06
5838 9454 2.102588 GGTAACGCAGATCCACCTATGT 59.897 50.000 0.00 0.00 0.00 2.29
5839 9455 2.548067 GGGTAACGCAGATCCACCTATG 60.548 54.545 0.00 0.00 37.60 2.23
5840 9456 1.692519 GGGTAACGCAGATCCACCTAT 59.307 52.381 0.00 0.00 37.60 2.57
5841 9457 1.117150 GGGTAACGCAGATCCACCTA 58.883 55.000 0.00 0.00 37.60 3.08
5842 9458 0.617820 AGGGTAACGCAGATCCACCT 60.618 55.000 0.00 0.00 37.60 4.00
5843 9459 0.252197 AAGGGTAACGCAGATCCACC 59.748 55.000 0.00 0.00 37.60 4.61
5844 9460 2.547826 GTAAGGGTAACGCAGATCCAC 58.452 52.381 0.00 0.00 37.60 4.02
5845 9461 1.483415 GGTAAGGGTAACGCAGATCCA 59.517 52.381 0.00 0.00 37.60 3.41
5846 9462 1.761198 AGGTAAGGGTAACGCAGATCC 59.239 52.381 0.00 0.00 37.60 3.36
5847 9463 3.538634 AAGGTAAGGGTAACGCAGATC 57.461 47.619 0.00 0.00 37.60 2.75
5848 9464 4.652421 TCATAAGGTAAGGGTAACGCAGAT 59.348 41.667 0.00 0.00 37.60 2.90
5849 9465 4.025360 TCATAAGGTAAGGGTAACGCAGA 58.975 43.478 0.00 0.00 37.60 4.26
5850 9466 4.395959 TCATAAGGTAAGGGTAACGCAG 57.604 45.455 0.00 0.00 37.60 5.18
5851 9467 5.599656 AGTATCATAAGGTAAGGGTAACGCA 59.400 40.000 0.00 0.00 37.60 5.24
5852 9468 6.094193 AGTATCATAAGGTAAGGGTAACGC 57.906 41.667 0.00 0.00 37.60 4.84
5906 9522 8.295288 AGATAGCAACAAAGAGAAAAATGTCTG 58.705 33.333 0.00 0.00 0.00 3.51
5953 9612 3.688272 CTTAATTGTGGATCTGCGCTTG 58.312 45.455 9.73 1.08 0.00 4.01
6007 9666 3.078196 TGCGGGGTTAGCGATCCA 61.078 61.111 0.00 0.00 37.44 3.41
6008 9667 2.588034 GTGCGGGGTTAGCGATCC 60.588 66.667 0.00 0.00 37.44 3.36
6009 9668 2.960129 CGTGCGGGGTTAGCGATC 60.960 66.667 0.00 0.00 37.44 3.69
6011 9670 4.424566 GACGTGCGGGGTTAGCGA 62.425 66.667 0.00 0.00 37.44 4.93
6122 9877 1.287815 CACGTACCTGAAGACGGCA 59.712 57.895 0.00 0.00 43.32 5.69
6125 9880 0.170561 CTCCCACGTACCTGAAGACG 59.829 60.000 0.00 0.00 44.57 4.18
6127 9882 1.255667 GGCTCCCACGTACCTGAAGA 61.256 60.000 0.00 0.00 0.00 2.87
6270 10030 4.742201 CAGGTCTCGTGCGTGGGG 62.742 72.222 0.00 0.00 0.00 4.96
6285 10045 3.775654 GAGTCTGGTCGGGGGCAG 61.776 72.222 0.00 0.00 0.00 4.85
6286 10046 3.846405 AAGAGTCTGGTCGGGGGCA 62.846 63.158 0.00 0.00 0.00 5.36
6287 10047 2.593956 AAAGAGTCTGGTCGGGGGC 61.594 63.158 0.00 0.00 0.00 5.80
6288 10048 1.296715 CAAAGAGTCTGGTCGGGGG 59.703 63.158 0.00 0.00 0.00 5.40
6289 10049 1.376037 GCAAAGAGTCTGGTCGGGG 60.376 63.158 0.00 0.00 0.00 5.73
6290 10050 0.035458 AAGCAAAGAGTCTGGTCGGG 59.965 55.000 0.00 0.00 0.00 5.14
6291 10051 1.151668 CAAGCAAAGAGTCTGGTCGG 58.848 55.000 0.00 0.00 0.00 4.79
6292 10052 2.154854 TCAAGCAAAGAGTCTGGTCG 57.845 50.000 0.00 0.00 0.00 4.79
6293 10053 2.161211 GCATCAAGCAAAGAGTCTGGTC 59.839 50.000 0.00 0.00 44.79 4.02
6294 10054 2.157738 GCATCAAGCAAAGAGTCTGGT 58.842 47.619 0.00 0.00 44.79 4.00
6295 10055 2.915738 GCATCAAGCAAAGAGTCTGG 57.084 50.000 0.00 0.00 44.79 3.86
6312 10072 1.153842 CGACAGTGTAGCCGATGCA 60.154 57.895 0.00 0.00 41.13 3.96
6359 10119 3.812019 CGACGGCAGCTCCTACGT 61.812 66.667 0.00 0.00 42.88 3.57
6361 10121 3.827898 AGCGACGGCAGCTCCTAC 61.828 66.667 1.61 0.00 41.83 3.18
6362 10122 3.826754 CAGCGACGGCAGCTCCTA 61.827 66.667 4.59 0.00 44.06 2.94
6373 10133 2.432628 CTTCACGTCCCCAGCGAC 60.433 66.667 0.00 0.00 0.00 5.19
6374 10134 4.373116 GCTTCACGTCCCCAGCGA 62.373 66.667 0.00 0.00 0.00 4.93
6375 10135 4.680237 TGCTTCACGTCCCCAGCG 62.680 66.667 0.00 0.00 34.82 5.18
6376 10136 3.050275 GTGCTTCACGTCCCCAGC 61.050 66.667 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.