Multiple sequence alignment - TraesCS5D01G131700

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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 TraesCS5D01G131700 chr5D 100.000 5237 0 0 1 5237 209309581 209314817 0.000000e+00 9672.0
1 TraesCS5D01G131700 chr5B 94.815 3356 119 26 1228 4558 222368722 222372047 0.000000e+00 5182.0
2 TraesCS5D01G131700 chr5B 90.588 680 22 10 4584 5233 222372878 222373545 0.000000e+00 863.0
3 TraesCS5D01G131700 chr5B 93.564 404 24 1 1 404 222367174 222367575 7.500000e-168 601.0
4 TraesCS5D01G131700 chr5B 96.512 258 9 0 950 1207 222368278 222368535 1.350000e-115 427.0
5 TraesCS5D01G131700 chr5B 93.814 97 6 0 3688 3784 425880113 425880209 4.230000e-31 147.0
6 TraesCS5D01G131700 chr5B 92.233 103 6 2 3682 3784 352127360 352127260 1.520000e-30 145.0
7 TraesCS5D01G131700 chr5A 96.692 2479 60 8 1228 3696 270179097 270181563 0.000000e+00 4104.0
8 TraesCS5D01G131700 chr5A 95.185 623 29 1 3875 4496 270181562 270182184 0.000000e+00 983.0
9 TraesCS5D01G131700 chr5A 90.976 543 29 6 4611 5141 270182567 270183101 0.000000e+00 713.0
10 TraesCS5D01G131700 chr5A 95.297 404 17 1 1 404 270177561 270177962 1.590000e-179 640.0
11 TraesCS5D01G131700 chr5A 95.349 258 12 0 950 1207 270178653 270178910 1.360000e-110 411.0
12 TraesCS5D01G131700 chr5A 83.777 413 33 18 393 794 270177986 270178375 1.390000e-95 361.0
13 TraesCS5D01G131700 chr3B 90.364 2169 143 35 1232 3360 580038299 580036157 0.000000e+00 2787.0
14 TraesCS5D01G131700 chr3B 81.511 622 79 20 3883 4470 580035792 580035173 3.670000e-131 479.0
15 TraesCS5D01G131700 chr3B 85.757 337 38 7 872 1207 580038713 580038386 1.080000e-91 348.0
16 TraesCS5D01G131700 chr3B 83.735 332 27 12 3370 3696 580036113 580035804 6.640000e-74 289.0
17 TraesCS5D01G131700 chr3B 94.949 99 3 2 3785 3882 588476650 588476747 2.530000e-33 154.0
18 TraesCS5D01G131700 chr3B 92.929 99 5 2 3687 3784 256253815 256253718 5.470000e-30 143.0
19 TraesCS5D01G131700 chr3A 89.243 2073 166 27 1333 3363 583707292 583705235 0.000000e+00 2540.0
20 TraesCS5D01G131700 chr3A 87.414 437 53 2 3930 4365 583704856 583704421 7.830000e-138 501.0
21 TraesCS5D01G131700 chr3A 77.593 723 82 46 487 1171 583707986 583707306 1.070000e-96 364.0
22 TraesCS5D01G131700 chr3A 88.562 306 24 10 3374 3677 583705189 583704893 1.390000e-95 361.0
23 TraesCS5D01G131700 chr3D 92.997 1171 69 9 1231 2397 442504032 442502871 0.000000e+00 1696.0
24 TraesCS5D01G131700 chr3D 89.024 656 49 9 2713 3360 442502501 442501861 0.000000e+00 791.0
25 TraesCS5D01G131700 chr3D 75.892 1261 139 83 1 1207 442505267 442504118 4.710000e-135 492.0
26 TraesCS5D01G131700 chr3D 86.977 430 46 5 3883 4305 442500422 442499996 4.750000e-130 475.0
27 TraesCS5D01G131700 chr3D 88.272 324 25 7 3377 3696 442500748 442500434 4.950000e-100 375.0
28 TraesCS5D01G131700 chr3D 94.949 99 3 2 3785 3882 448433614 448433711 2.530000e-33 154.0
29 TraesCS5D01G131700 chr3D 95.604 91 4 0 3694 3784 138076337 138076247 4.230000e-31 147.0
30 TraesCS5D01G131700 chr3D 100.000 40 0 0 3028 3067 467570101 467570140 2.020000e-09 75.0
31 TraesCS5D01G131700 chr2D 97.872 94 1 1 3785 3878 52051386 52051478 1.510000e-35 161.0
32 TraesCS5D01G131700 chr2D 96.875 96 1 2 3785 3879 445894890 445894984 5.430000e-35 159.0
33 TraesCS5D01G131700 chr2D 94.000 100 5 1 3685 3784 445894875 445894973 3.270000e-32 150.0
34 TraesCS5D01G131700 chr6D 94.949 99 3 2 3785 3882 200398720 200398817 2.530000e-33 154.0
35 TraesCS5D01G131700 chr6D 92.000 100 8 0 3685 3784 464266291 464266192 1.970000e-29 141.0
36 TraesCS5D01G131700 chr6A 94.118 102 4 2 3785 3886 98239113 98239212 2.530000e-33 154.0
37 TraesCS5D01G131700 chr1D 93.269 104 5 2 3785 3888 12312562 12312461 9.080000e-33 152.0
38 TraesCS5D01G131700 chr1A 94.059 101 4 2 3785 3885 474641767 474641669 9.080000e-33 152.0
39 TraesCS5D01G131700 chr7A 92.857 98 7 0 3687 3784 628008582 628008485 5.470000e-30 143.0
40 TraesCS5D01G131700 chr2A 92.929 99 6 1 3686 3784 68155928 68155831 5.470000e-30 143.0
41 TraesCS5D01G131700 chr4A 84.946 93 12 2 1 92 501966659 501966750 5.580000e-15 93.5
42 TraesCS5D01G131700 chr4D 83.696 92 13 2 1 91 89427074 89427164 9.340000e-13 86.1
43 TraesCS5D01G131700 chr4B 82.796 93 14 2 1 92 126327683 126327774 1.210000e-11 82.4


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 TraesCS5D01G131700 chr5D 209309581 209314817 5236 False 9672.00 9672 100.000000 1 5237 1 chr5D.!!$F1 5236
1 TraesCS5D01G131700 chr5B 222367174 222373545 6371 False 1768.25 5182 93.869750 1 5233 4 chr5B.!!$F2 5232
2 TraesCS5D01G131700 chr5A 270177561 270183101 5540 False 1202.00 4104 92.879333 1 5141 6 chr5A.!!$F1 5140
3 TraesCS5D01G131700 chr3B 580035173 580038713 3540 True 975.75 2787 85.341750 872 4470 4 chr3B.!!$R2 3598
4 TraesCS5D01G131700 chr3A 583704421 583707986 3565 True 941.50 2540 85.703000 487 4365 4 chr3A.!!$R1 3878
5 TraesCS5D01G131700 chr3D 442499996 442505267 5271 True 765.80 1696 86.632400 1 4305 5 chr3D.!!$R2 4304

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
439 500 0.325272 GAGATCCCCGCTTATTCCCC 59.675 60.000 0.00 0.0 0.00 4.81 F
658 739 0.462047 CGCACCGGCTCCTCTTATTT 60.462 55.000 0.00 0.0 38.10 1.40 F
663 744 1.139853 CCGGCTCCTCTTATTTCAGCT 59.860 52.381 0.00 0.0 0.00 4.24 F
721 816 1.446907 CCAGATCTCGCAAGCAAACT 58.553 50.000 0.00 0.0 37.18 2.66 F
2014 2536 2.228822 AGGAAAAGGTTAACTGCATGCG 59.771 45.455 14.09 10.5 0.00 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2224 2750 1.072331 AGCGAACCTGACAAGTCCATT 59.928 47.619 0.00 0.0 0.00 3.16 R
2600 3207 0.955428 TCATTGCCACAGACGCCTTC 60.955 55.000 0.00 0.0 0.00 3.46 R
3190 3887 8.662255 TGGTAGAACCTGAAAAGGAGTAATTTA 58.338 33.333 0.00 0.0 39.58 1.40 R
3234 3931 2.544721 TCTTCTGGATCTGGTTCTGCT 58.455 47.619 0.00 0.0 0.00 4.24 R
4321 6140 0.110486 ATGCAGAACCGGGAAACACT 59.890 50.000 6.32 0.0 0.00 3.55 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
126 138 4.770362 TCCCGCCACCTCCGATGA 62.770 66.667 0.00 0.00 0.00 2.92
321 340 4.976116 CCCTTTTTAACAGCAGTCGAAAAG 59.024 41.667 16.44 16.44 38.24 2.27
404 424 3.573558 TGCCGAACGCATTTCTCC 58.426 55.556 0.00 0.00 44.64 3.71
405 425 2.038269 TGCCGAACGCATTTCTCCC 61.038 57.895 0.00 0.00 44.64 4.30
406 426 2.038269 GCCGAACGCATTTCTCCCA 61.038 57.895 0.00 0.00 37.47 4.37
407 427 1.982073 GCCGAACGCATTTCTCCCAG 61.982 60.000 0.00 0.00 37.47 4.45
408 428 1.425428 CGAACGCATTTCTCCCAGC 59.575 57.895 0.00 0.00 31.20 4.85
409 429 1.803289 GAACGCATTTCTCCCAGCC 59.197 57.895 0.00 0.00 0.00 4.85
439 500 0.325272 GAGATCCCCGCTTATTCCCC 59.675 60.000 0.00 0.00 0.00 4.81
442 503 4.949098 CCCCGCTTATTCCCCGGC 62.949 72.222 0.00 0.00 40.65 6.13
446 507 3.868985 GCTTATTCCCCGGCCGGA 61.869 66.667 45.44 27.01 37.50 5.14
447 508 2.912714 CTTATTCCCCGGCCGGAA 59.087 61.111 45.44 31.97 45.87 4.30
448 509 1.525306 CTTATTCCCCGGCCGGAAC 60.525 63.158 45.44 0.00 44.63 3.62
449 510 2.260088 CTTATTCCCCGGCCGGAACA 62.260 60.000 45.44 27.29 44.63 3.18
450 511 1.849975 TTATTCCCCGGCCGGAACAA 61.850 55.000 45.44 31.28 44.63 2.83
466 540 0.674895 ACAACGCATCCAAGCTCCTC 60.675 55.000 0.00 0.00 0.00 3.71
541 615 2.298661 CGACCAAGGTTAGCCCCCT 61.299 63.158 0.00 0.00 34.57 4.79
543 617 0.914902 GACCAAGGTTAGCCCCCTCT 60.915 60.000 0.00 0.00 34.57 3.69
545 619 1.636769 CCAAGGTTAGCCCCCTCTCC 61.637 65.000 0.00 0.00 34.57 3.71
546 620 0.621862 CAAGGTTAGCCCCCTCTCCT 60.622 60.000 0.00 0.00 34.57 3.69
589 663 2.115427 TGCTTATCCGTCTTCATCCCA 58.885 47.619 0.00 0.00 0.00 4.37
596 670 1.341209 CCGTCTTCATCCCATCATCGA 59.659 52.381 0.00 0.00 0.00 3.59
602 676 2.587247 ATCCCATCATCGAGCCCCG 61.587 63.158 0.00 0.00 40.25 5.73
639 720 3.499737 CCAGATCCACCAACGCGC 61.500 66.667 5.73 0.00 0.00 6.86
655 736 4.143333 GCGCACCGGCTCCTCTTA 62.143 66.667 0.30 0.00 38.10 2.10
658 739 0.462047 CGCACCGGCTCCTCTTATTT 60.462 55.000 0.00 0.00 38.10 1.40
659 740 1.300481 GCACCGGCTCCTCTTATTTC 58.700 55.000 0.00 0.00 36.96 2.17
660 741 1.406887 GCACCGGCTCCTCTTATTTCA 60.407 52.381 0.00 0.00 36.96 2.69
661 742 2.555199 CACCGGCTCCTCTTATTTCAG 58.445 52.381 0.00 0.00 0.00 3.02
663 744 1.139853 CCGGCTCCTCTTATTTCAGCT 59.860 52.381 0.00 0.00 0.00 4.24
664 745 2.365617 CCGGCTCCTCTTATTTCAGCTA 59.634 50.000 0.00 0.00 0.00 3.32
703 798 1.537643 CAGCCTCCTCCTATCCCCC 60.538 68.421 0.00 0.00 0.00 5.40
710 805 1.719378 TCCTCCTATCCCCCAGATCTC 59.281 57.143 0.00 0.00 36.33 2.75
721 816 1.446907 CCAGATCTCGCAAGCAAACT 58.553 50.000 0.00 0.00 37.18 2.66
728 824 4.514781 TCTCGCAAGCAAACTTCTACTA 57.485 40.909 0.00 0.00 32.29 1.82
729 825 4.878439 TCTCGCAAGCAAACTTCTACTAA 58.122 39.130 0.00 0.00 32.29 2.24
730 826 5.479306 TCTCGCAAGCAAACTTCTACTAAT 58.521 37.500 0.00 0.00 32.29 1.73
732 828 6.426937 TCTCGCAAGCAAACTTCTACTAATTT 59.573 34.615 0.00 0.00 32.29 1.82
733 829 7.601130 TCTCGCAAGCAAACTTCTACTAATTTA 59.399 33.333 0.00 0.00 32.29 1.40
739 835 9.639601 AAGCAAACTTCTACTAATTTATTTGGC 57.360 29.630 0.00 0.00 0.00 4.52
763 859 7.599998 GGCTGGCAATAAACATTAGATATTTGG 59.400 37.037 0.00 0.00 0.00 3.28
784 923 4.815308 TGGCACCTTTTCATGTTCAAAATG 59.185 37.500 0.00 0.00 0.00 2.32
839 1178 5.818678 TCCCCAATTACGCTAGTGATTAT 57.181 39.130 10.99 0.00 34.82 1.28
859 1200 8.567104 TGATTATGCATGGTGTCAATATTGTAC 58.433 33.333 14.97 14.15 0.00 2.90
860 1201 4.873768 TGCATGGTGTCAATATTGTACG 57.126 40.909 14.97 5.38 0.00 3.67
911 1253 8.877864 TGGACAATATGAGTTTGATTTAAGGT 57.122 30.769 0.00 0.00 0.00 3.50
920 1262 8.974060 TGAGTTTGATTTAAGGTTCACTAGTT 57.026 30.769 0.00 0.00 0.00 2.24
929 1271 2.612212 AGGTTCACTAGTTTGCGTTGTG 59.388 45.455 0.00 0.00 0.00 3.33
932 1274 4.212636 GGTTCACTAGTTTGCGTTGTGTAT 59.787 41.667 0.00 0.00 0.00 2.29
936 1278 6.912082 TCACTAGTTTGCGTTGTGTATACTA 58.088 36.000 4.17 0.00 0.00 1.82
938 1280 8.030692 TCACTAGTTTGCGTTGTGTATACTATT 58.969 33.333 4.17 0.00 29.40 1.73
979 1321 6.761242 TCGGTTATATGATACATGGCTTATGC 59.239 38.462 0.00 0.00 40.59 3.14
1095 1446 8.206126 TGGAAAGCCACATCTATTATCTATCA 57.794 34.615 0.00 0.00 39.92 2.15
1246 1768 3.743521 TGGACTTTCTGTTGAGGATGTG 58.256 45.455 0.00 0.00 0.00 3.21
1247 1769 3.390967 TGGACTTTCTGTTGAGGATGTGA 59.609 43.478 0.00 0.00 0.00 3.58
1283 1805 6.659242 ACCTTACCTTCTAATGAACACAATGG 59.341 38.462 0.00 0.00 0.00 3.16
1301 1823 6.703607 CACAATGGGCATAAGTTTGTACAAAA 59.296 34.615 22.14 8.09 31.33 2.44
1308 1830 9.483916 GGGCATAAGTTTGTACAAAATAACTTT 57.516 29.630 22.14 8.66 40.30 2.66
1336 1858 6.653740 GCTACTATTTCTGGGTTGTACAAACT 59.346 38.462 22.41 4.90 0.00 2.66
1352 1874 6.690957 TGTACAAACTTTTTGAGCGAATTCAG 59.309 34.615 6.22 0.00 0.00 3.02
1424 1946 5.443283 TCTGGAGTACGATATGTTACTGGT 58.557 41.667 0.00 0.00 0.00 4.00
1805 2327 3.118038 TGGTTCCTAATGCAGTGGATACC 60.118 47.826 18.38 18.38 34.58 2.73
2013 2535 3.942130 AGGAAAAGGTTAACTGCATGC 57.058 42.857 11.82 11.82 0.00 4.06
2014 2536 2.228822 AGGAAAAGGTTAACTGCATGCG 59.771 45.455 14.09 10.50 0.00 4.73
2222 2748 9.627123 TGGATTATGTTCCCTCAGTTAATAAAG 57.373 33.333 0.00 0.00 34.67 1.85
2224 2750 9.120538 GATTATGTTCCCTCAGTTAATAAAGCA 57.879 33.333 0.00 0.00 0.00 3.91
2230 2756 5.885912 TCCCTCAGTTAATAAAGCAATGGAC 59.114 40.000 0.00 0.00 0.00 4.02
2471 3073 5.751243 TGTGCCTTTTTCTGTTCTTACTC 57.249 39.130 0.00 0.00 0.00 2.59
2600 3207 8.970691 AACTGTCCATTGAATTCTAAAAATCG 57.029 30.769 7.05 0.00 0.00 3.34
2718 3393 2.350772 CGCTTTGGATCTTTGTGGTCAC 60.351 50.000 0.00 0.00 0.00 3.67
2888 3566 4.983671 AGAAAAGAGCTTTTGGTTTCGT 57.016 36.364 12.50 0.00 42.26 3.85
2889 3567 5.324784 AGAAAAGAGCTTTTGGTTTCGTT 57.675 34.783 12.50 0.00 42.26 3.85
2893 3571 7.815549 AGAAAAGAGCTTTTGGTTTCGTTTTTA 59.184 29.630 12.50 0.00 42.26 1.52
2905 3593 8.631676 TGGTTTCGTTTTTATTTTCACTTACC 57.368 30.769 0.00 0.00 0.00 2.85
3190 3887 5.419788 TCAGCTATTTGGACAATTTGCAGAT 59.580 36.000 12.98 0.00 0.00 2.90
3234 3931 9.286170 GTTCTACCAGATGACATGATAGTACTA 57.714 37.037 4.77 4.77 0.00 1.82
3336 4033 0.035439 ATCGCCGGGTGAGTTTCAAT 60.035 50.000 16.40 0.00 0.00 2.57
3348 4045 5.183904 GGTGAGTTTCAATTCTATGCACCTT 59.816 40.000 0.00 0.00 39.96 3.50
3360 4057 0.250727 TGCACCTTGCTGACCTTACC 60.251 55.000 0.00 0.00 45.31 2.85
3363 4060 1.296715 CCTTGCTGACCTTACCGCT 59.703 57.895 0.00 0.00 0.00 5.52
3365 4062 0.247736 CTTGCTGACCTTACCGCTCT 59.752 55.000 0.00 0.00 0.00 4.09
3557 5352 3.181465 CCGGTGAGTATAAGGCAGAACAT 60.181 47.826 0.00 0.00 0.00 2.71
3589 5384 9.766277 GTAAATTCATCTTCTGTCACTCATTTC 57.234 33.333 0.00 0.00 0.00 2.17
3590 5385 7.991084 AATTCATCTTCTGTCACTCATTTCA 57.009 32.000 0.00 0.00 0.00 2.69
3591 5386 7.612668 ATTCATCTTCTGTCACTCATTTCAG 57.387 36.000 0.00 0.00 0.00 3.02
3592 5387 6.350629 TCATCTTCTGTCACTCATTTCAGA 57.649 37.500 0.00 0.00 35.54 3.27
3787 5587 5.082251 ACACTTATTTTAGGACGGACTCC 57.918 43.478 0.00 0.00 39.81 3.85
3868 5668 6.540438 TGAGACACTTATTTTAGGACGGAT 57.460 37.500 0.00 0.00 0.00 4.18
3894 5699 9.877222 TGGGAGTATAATGATTAGTTCTACTGA 57.123 33.333 2.01 0.00 0.00 3.41
4034 5844 7.247728 TGTTTTGCCTCGTTATGATCATAAAC 58.752 34.615 25.95 19.23 35.30 2.01
4279 6091 0.387929 TGGATCGTATTGGAGGTCGC 59.612 55.000 0.00 0.00 0.00 5.19
4321 6140 4.999950 GCTCTCACTCTGGAATTTCTTTCA 59.000 41.667 0.00 0.00 35.94 2.69
4373 6192 2.554032 AGAACAAGTCTTTGGCGAATGG 59.446 45.455 0.00 0.00 38.66 3.16
4391 6231 7.414540 GGCGAATGGGATAACTATGAAATCATC 60.415 40.741 0.00 0.00 37.76 2.92
4438 6278 5.591643 ACAGTCGTGTTGCATAAAGTTAG 57.408 39.130 0.00 0.00 30.30 2.34
4498 6338 4.326826 TGATGTGTCTCTTGTTCCAATCC 58.673 43.478 0.00 0.00 0.00 3.01
4500 6340 4.437682 TGTGTCTCTTGTTCCAATCCTT 57.562 40.909 0.00 0.00 0.00 3.36
4555 6395 4.580995 ACCACTAGAGATATGACGGTCTTG 59.419 45.833 9.88 0.00 0.00 3.02
4559 6399 2.101582 AGAGATATGACGGTCTTGGTGC 59.898 50.000 9.88 0.00 0.00 5.01
4561 6401 3.296854 AGATATGACGGTCTTGGTGCTA 58.703 45.455 9.88 0.00 0.00 3.49
4563 6403 1.267121 ATGACGGTCTTGGTGCTACT 58.733 50.000 9.88 0.00 0.00 2.57
4564 6404 1.045407 TGACGGTCTTGGTGCTACTT 58.955 50.000 9.88 0.00 0.00 2.24
4565 6405 2.241160 TGACGGTCTTGGTGCTACTTA 58.759 47.619 9.88 0.00 0.00 2.24
4566 6406 2.230508 TGACGGTCTTGGTGCTACTTAG 59.769 50.000 9.88 0.00 0.00 2.18
4569 6409 2.230508 CGGTCTTGGTGCTACTTAGTGA 59.769 50.000 0.00 0.00 0.00 3.41
4570 6410 3.119101 CGGTCTTGGTGCTACTTAGTGAT 60.119 47.826 0.00 0.00 0.00 3.06
4573 6413 5.360144 GGTCTTGGTGCTACTTAGTGATCTA 59.640 44.000 0.00 0.00 0.00 1.98
4574 6414 6.460399 GGTCTTGGTGCTACTTAGTGATCTAG 60.460 46.154 0.00 0.00 0.00 2.43
4575 6415 6.319152 GTCTTGGTGCTACTTAGTGATCTAGA 59.681 42.308 0.00 0.00 0.00 2.43
4577 6417 4.575236 TGGTGCTACTTAGTGATCTAGACG 59.425 45.833 0.00 0.00 0.00 4.18
4579 6419 4.273969 GTGCTACTTAGTGATCTAGACGCT 59.726 45.833 0.00 4.20 0.00 5.07
4580 6420 4.512198 TGCTACTTAGTGATCTAGACGCTC 59.488 45.833 10.41 0.00 0.00 5.03
4582 6422 5.237779 GCTACTTAGTGATCTAGACGCTCTT 59.762 44.000 10.41 2.41 0.00 2.85
4585 7231 7.429636 ACTTAGTGATCTAGACGCTCTTATC 57.570 40.000 10.41 0.00 0.00 1.75
4598 7244 6.207614 AGACGCTCTTATCTGCAGATTGTATA 59.792 38.462 32.94 13.21 36.05 1.47
4685 7451 0.312102 CGATCAGCGTAGGAGCATCA 59.688 55.000 0.00 0.00 40.15 3.07
4727 7511 1.973281 CCGCAGCCCACAACTGATT 60.973 57.895 0.00 0.00 37.32 2.57
4841 7637 0.812014 TTTGGCTCGCACGAGAACAA 60.812 50.000 23.33 21.15 44.53 2.83
4882 7681 8.983307 ATTTGAGCAATTGATTCTTCTTCTTC 57.017 30.769 10.34 0.00 0.00 2.87
4883 7682 7.756395 TTGAGCAATTGATTCTTCTTCTTCT 57.244 32.000 10.34 0.00 0.00 2.85
4884 7683 7.756395 TGAGCAATTGATTCTTCTTCTTCTT 57.244 32.000 10.34 0.00 0.00 2.52
4921 7720 0.391228 GCCCCCGCTCTTTTCAAAAA 59.609 50.000 0.00 0.00 0.00 1.94
4923 7722 1.270094 CCCCCGCTCTTTTCAAAAACC 60.270 52.381 0.00 0.00 0.00 3.27
4924 7723 1.686587 CCCCGCTCTTTTCAAAAACCT 59.313 47.619 0.00 0.00 0.00 3.50
4959 7758 3.489416 TGAAGTCAGAATTGAACGTGACG 59.511 43.478 2.24 2.24 43.38 4.35
4985 7784 5.622448 CACATGTGAAGTCAGAAATTCAACG 59.378 40.000 21.64 0.00 37.19 4.10
4989 7788 5.198274 GTGAAGTCAGAAATTCAACGTGTC 58.802 41.667 0.00 0.00 37.19 3.67
5008 7807 5.388475 CGTGTCTCTTGTATAACTGCACAAC 60.388 44.000 0.00 0.00 31.61 3.32
5047 7846 3.309682 TGTTGCTTTCAGAGACAACTTCG 59.690 43.478 11.43 0.00 40.22 3.79
5149 7948 9.838339 AGTAGATTTTGCACAATATAACTAGCT 57.162 29.630 1.68 0.00 0.00 3.32
5161 7960 0.608640 AACTAGCTGCCGCTACAAGT 59.391 50.000 5.65 1.91 46.79 3.16
5182 7981 1.270732 GGATGAGCTCATAGCCCAGTG 60.271 57.143 28.78 0.00 43.77 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 128 1.378646 TCAGCTCGTCATCGGAGGT 60.379 57.895 0.00 0.00 37.69 3.85
268 280 3.055719 CCTGGCACGAACCGCAAT 61.056 61.111 0.00 0.00 0.00 3.56
352 372 0.178767 TGACCATTCCGCCAGATCAG 59.821 55.000 0.00 0.00 0.00 2.90
391 411 1.657751 GGGCTGGGAGAAATGCGTTC 61.658 60.000 0.00 0.00 36.38 3.95
405 425 3.854669 CTCGGGCTACCTGGGCTG 61.855 72.222 0.00 0.00 39.17 4.85
406 426 3.396822 ATCTCGGGCTACCTGGGCT 62.397 63.158 0.00 0.00 28.52 5.19
407 427 2.844839 ATCTCGGGCTACCTGGGC 60.845 66.667 0.00 0.00 28.52 5.36
408 428 2.210711 GGATCTCGGGCTACCTGGG 61.211 68.421 0.00 0.00 33.28 4.45
409 429 2.210711 GGGATCTCGGGCTACCTGG 61.211 68.421 0.00 0.00 33.28 4.45
421 482 1.481056 CGGGGAATAAGCGGGGATCT 61.481 60.000 0.00 0.00 0.00 2.75
439 500 4.160635 GATGCGTTGTTCCGGCCG 62.161 66.667 21.04 21.04 0.00 6.13
442 503 1.501741 CTTGGATGCGTTGTTCCGG 59.498 57.895 0.00 0.00 34.58 5.14
445 506 0.169009 GGAGCTTGGATGCGTTGTTC 59.831 55.000 0.00 0.00 38.13 3.18
446 507 0.250901 AGGAGCTTGGATGCGTTGTT 60.251 50.000 0.00 0.00 38.13 2.83
447 508 0.674895 GAGGAGCTTGGATGCGTTGT 60.675 55.000 0.00 0.00 38.13 3.32
448 509 0.392193 AGAGGAGCTTGGATGCGTTG 60.392 55.000 0.00 0.00 38.13 4.10
449 510 0.107945 GAGAGGAGCTTGGATGCGTT 60.108 55.000 0.00 0.00 38.13 4.84
450 511 1.519719 GAGAGGAGCTTGGATGCGT 59.480 57.895 0.00 0.00 38.13 5.24
452 513 1.227497 CGGAGAGGAGCTTGGATGC 60.227 63.158 0.00 0.00 0.00 3.91
453 514 1.227497 GCGGAGAGGAGCTTGGATG 60.227 63.158 0.00 0.00 0.00 3.51
454 515 1.382420 AGCGGAGAGGAGCTTGGAT 60.382 57.895 0.00 0.00 41.52 3.41
494 568 4.397832 GGAAGGTAACCGCCGGCA 62.398 66.667 28.98 2.89 37.17 5.69
505 579 1.000612 GACGGAGGAGGAGGAAGGT 59.999 63.158 0.00 0.00 0.00 3.50
541 615 1.286553 GTGGAAGAGGAGGAGAGGAGA 59.713 57.143 0.00 0.00 0.00 3.71
543 617 0.336737 GGTGGAAGAGGAGGAGAGGA 59.663 60.000 0.00 0.00 0.00 3.71
545 619 1.687996 GGAGGTGGAAGAGGAGGAGAG 60.688 61.905 0.00 0.00 0.00 3.20
546 620 0.336737 GGAGGTGGAAGAGGAGGAGA 59.663 60.000 0.00 0.00 0.00 3.71
589 663 3.157252 AGTGCGGGGCTCGATGAT 61.157 61.111 12.93 0.00 42.43 2.45
596 670 4.479993 GCTCATCAGTGCGGGGCT 62.480 66.667 0.00 0.00 0.00 5.19
602 676 1.423056 GCAACGAGCTCATCAGTGC 59.577 57.895 15.40 10.96 41.15 4.40
639 720 0.462047 AAATAAGAGGAGCCGGTGCG 60.462 55.000 1.90 0.00 44.33 5.34
653 734 4.868171 GGTGATGTGACGTAGCTGAAATAA 59.132 41.667 0.00 0.00 0.00 1.40
655 736 3.262420 GGTGATGTGACGTAGCTGAAAT 58.738 45.455 0.00 0.00 0.00 2.17
658 739 0.170339 CGGTGATGTGACGTAGCTGA 59.830 55.000 0.00 0.00 0.00 4.26
659 740 0.802222 CCGGTGATGTGACGTAGCTG 60.802 60.000 0.00 0.00 0.00 4.24
660 741 1.248785 ACCGGTGATGTGACGTAGCT 61.249 55.000 6.12 0.00 0.00 3.32
661 742 1.076533 CACCGGTGATGTGACGTAGC 61.077 60.000 31.31 0.00 35.74 3.58
663 744 0.524414 CTCACCGGTGATGTGACGTA 59.476 55.000 36.21 12.13 37.80 3.57
664 745 1.289066 CTCACCGGTGATGTGACGT 59.711 57.895 36.21 0.00 37.80 4.34
703 798 2.740981 AGAAGTTTGCTTGCGAGATCTG 59.259 45.455 4.70 0.00 34.61 2.90
710 805 8.895932 AATAAATTAGTAGAAGTTTGCTTGCG 57.104 30.769 0.00 0.00 34.61 4.85
721 816 7.710676 TTGCCAGCCAAATAAATTAGTAGAA 57.289 32.000 0.00 0.00 0.00 2.10
728 824 8.578448 AATGTTTATTGCCAGCCAAATAAATT 57.422 26.923 9.67 2.08 36.92 1.82
729 825 9.328845 CTAATGTTTATTGCCAGCCAAATAAAT 57.671 29.630 9.67 1.00 36.92 1.40
730 826 8.535335 TCTAATGTTTATTGCCAGCCAAATAAA 58.465 29.630 4.61 4.61 36.92 1.40
732 828 7.652524 TCTAATGTTTATTGCCAGCCAAATA 57.347 32.000 0.00 0.00 36.92 1.40
733 829 6.543430 TCTAATGTTTATTGCCAGCCAAAT 57.457 33.333 0.00 0.00 36.92 2.32
739 835 8.143193 TGCCAAATATCTAATGTTTATTGCCAG 58.857 33.333 0.00 0.00 0.00 4.85
763 859 6.790285 ATCATTTTGAACATGAAAAGGTGC 57.210 33.333 0.00 0.00 34.31 5.01
794 933 8.604890 GGGAAAATTGAACACGAAAATGTTTTA 58.395 29.630 0.00 0.00 42.89 1.52
795 934 7.414651 GGGGAAAATTGAACACGAAAATGTTTT 60.415 33.333 0.00 0.00 42.89 2.43
797 936 5.525745 GGGGAAAATTGAACACGAAAATGTT 59.474 36.000 0.00 0.00 45.52 2.71
798 937 5.053811 GGGGAAAATTGAACACGAAAATGT 58.946 37.500 0.00 0.00 0.00 2.71
799 938 5.053145 TGGGGAAAATTGAACACGAAAATG 58.947 37.500 0.00 0.00 0.00 2.32
800 939 5.283457 TGGGGAAAATTGAACACGAAAAT 57.717 34.783 0.00 0.00 0.00 1.82
802 941 4.737855 TTGGGGAAAATTGAACACGAAA 57.262 36.364 0.00 0.00 0.00 3.46
803 942 4.946478 ATTGGGGAAAATTGAACACGAA 57.054 36.364 0.00 0.00 0.00 3.85
804 943 4.946478 AATTGGGGAAAATTGAACACGA 57.054 36.364 0.00 0.00 0.00 4.35
807 946 4.282195 AGCGTAATTGGGGAAAATTGAACA 59.718 37.500 0.00 0.00 32.16 3.18
808 947 4.816392 AGCGTAATTGGGGAAAATTGAAC 58.184 39.130 0.00 0.00 32.16 3.18
809 948 5.712917 ACTAGCGTAATTGGGGAAAATTGAA 59.287 36.000 0.00 0.00 32.16 2.69
810 949 5.124776 CACTAGCGTAATTGGGGAAAATTGA 59.875 40.000 0.00 0.00 32.16 2.57
811 950 5.124776 TCACTAGCGTAATTGGGGAAAATTG 59.875 40.000 0.00 0.00 32.16 2.32
812 951 5.258051 TCACTAGCGTAATTGGGGAAAATT 58.742 37.500 0.00 0.00 34.24 1.82
813 952 4.850680 TCACTAGCGTAATTGGGGAAAAT 58.149 39.130 0.00 0.00 0.00 1.82
818 1157 4.154195 GCATAATCACTAGCGTAATTGGGG 59.846 45.833 0.00 0.00 0.00 4.96
839 1178 4.508662 TCGTACAATATTGACACCATGCA 58.491 39.130 22.16 0.00 0.00 3.96
875 1217 6.450545 ACTCATATTGTCCATATCGACACAG 58.549 40.000 2.32 0.00 42.37 3.66
909 1251 2.353579 ACACAACGCAAACTAGTGAACC 59.646 45.455 0.00 0.00 34.47 3.62
911 1253 6.218019 AGTATACACAACGCAAACTAGTGAA 58.782 36.000 5.50 0.00 34.47 3.18
955 1297 6.763135 AGCATAAGCCATGTATCATATAACCG 59.237 38.462 0.00 0.00 43.56 4.44
979 1321 5.740569 CCATTGCGTGTGAAATCTGAAATAG 59.259 40.000 0.00 0.00 0.00 1.73
1095 1446 1.271597 CCAAGCTTAAGGAGGCACTGT 60.272 52.381 0.00 0.00 41.55 3.55
1172 1524 7.921214 CCAGTAGCTTATCTTACATTCTCGAAA 59.079 37.037 0.00 0.00 0.00 3.46
1225 1730 3.390967 TCACATCCTCAACAGAAAGTCCA 59.609 43.478 0.00 0.00 0.00 4.02
1227 1732 4.142730 GCATCACATCCTCAACAGAAAGTC 60.143 45.833 0.00 0.00 0.00 3.01
1228 1733 3.755378 GCATCACATCCTCAACAGAAAGT 59.245 43.478 0.00 0.00 0.00 2.66
1230 1735 4.025040 AGCATCACATCCTCAACAGAAA 57.975 40.909 0.00 0.00 0.00 2.52
1232 1737 3.708403 AAGCATCACATCCTCAACAGA 57.292 42.857 0.00 0.00 0.00 3.41
1234 1739 2.821378 CCAAAGCATCACATCCTCAACA 59.179 45.455 0.00 0.00 0.00 3.33
1235 1740 3.084039 TCCAAAGCATCACATCCTCAAC 58.916 45.455 0.00 0.00 0.00 3.18
1246 1768 3.636153 AGGTAAGGTCTCCAAAGCATC 57.364 47.619 0.00 0.00 0.00 3.91
1247 1769 3.589288 AGAAGGTAAGGTCTCCAAAGCAT 59.411 43.478 0.00 0.00 0.00 3.79
1308 1830 7.426606 TGTACAACCCAGAAATAGTAGCATA 57.573 36.000 0.00 0.00 0.00 3.14
1336 1858 8.641499 AATAACAAACTGAATTCGCTCAAAAA 57.359 26.923 0.04 0.00 0.00 1.94
1424 1946 4.159506 GGCACATAATAAACCTTCAAGCCA 59.840 41.667 0.00 0.00 37.23 4.75
1805 2327 2.280628 GAGGAGGGAGTAAACATTGCG 58.719 52.381 0.00 0.00 0.00 4.85
2013 2535 4.594136 GAACTTGTTCCACCTTTAACACG 58.406 43.478 2.31 0.00 35.43 4.49
2014 2536 4.095334 ACGAACTTGTTCCACCTTTAACAC 59.905 41.667 7.78 0.00 35.43 3.32
2222 2748 1.197721 CGAACCTGACAAGTCCATTGC 59.802 52.381 0.00 0.00 43.15 3.56
2224 2750 1.072331 AGCGAACCTGACAAGTCCATT 59.928 47.619 0.00 0.00 0.00 3.16
2230 2756 4.749245 ACAATAAAGCGAACCTGACAAG 57.251 40.909 0.00 0.00 0.00 3.16
2600 3207 0.955428 TCATTGCCACAGACGCCTTC 60.955 55.000 0.00 0.00 0.00 3.46
3190 3887 8.662255 TGGTAGAACCTGAAAAGGAGTAATTTA 58.338 33.333 0.00 0.00 39.58 1.40
3234 3931 2.544721 TCTTCTGGATCTGGTTCTGCT 58.455 47.619 0.00 0.00 0.00 4.24
3557 5352 6.650807 GTGACAGAAGATGAATTTACAGTCCA 59.349 38.462 0.00 0.00 0.00 4.02
3589 5384 8.389779 TCTTCAGCTATAACTACTCTGATCTG 57.610 38.462 0.00 0.00 34.26 2.90
3592 5387 9.461312 CCTATCTTCAGCTATAACTACTCTGAT 57.539 37.037 0.00 0.00 34.26 2.90
3703 5503 5.690865 AGTTGAGACACTTATTTTGGGACA 58.309 37.500 0.00 0.00 0.00 4.02
3745 5545 4.443394 GTGTCTCAACCGTAGTACAACTTG 59.557 45.833 0.38 0.00 0.00 3.16
3757 5557 5.061808 CGTCCTAAAATAAGTGTCTCAACCG 59.938 44.000 0.00 0.00 0.00 4.44
3787 5587 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
3868 5668 9.877222 TCAGTAGAACTAATCATTATACTCCCA 57.123 33.333 0.00 0.00 33.01 4.37
3894 5699 3.168035 TGGTATTGCCCACACTTTGAT 57.832 42.857 0.00 0.00 36.04 2.57
4034 5844 1.072331 AGAAGGCACCACACAAGGTAG 59.928 52.381 0.00 0.00 40.77 3.18
4101 5912 7.334090 CCCGTTATAATCTCATCAATCTCCAT 58.666 38.462 0.00 0.00 0.00 3.41
4279 6091 5.971763 AGAGCCAGCCTAAAATAGATATCG 58.028 41.667 0.00 0.00 0.00 2.92
4321 6140 0.110486 ATGCAGAACCGGGAAACACT 59.890 50.000 6.32 0.00 0.00 3.55
4373 6192 7.867909 TGTGACGAGATGATTTCATAGTTATCC 59.132 37.037 0.00 0.00 36.57 2.59
4438 6278 3.670625 TGGCATTAAGTACTCACACCAC 58.329 45.455 0.00 0.00 0.00 4.16
4498 6338 2.110901 AGAAGCAGCTGATGTCCAAG 57.889 50.000 20.43 0.00 0.00 3.61
4500 6340 1.612462 CCAAGAAGCAGCTGATGTCCA 60.612 52.381 20.43 0.00 0.00 4.02
4555 6395 4.555116 GCGTCTAGATCACTAAGTAGCACC 60.555 50.000 0.00 0.00 0.00 5.01
4559 6399 6.854496 AAGAGCGTCTAGATCACTAAGTAG 57.146 41.667 0.00 0.00 37.82 2.57
4561 6401 7.172532 CAGATAAGAGCGTCTAGATCACTAAGT 59.827 40.741 0.00 0.00 37.82 2.24
4563 6403 6.072948 GCAGATAAGAGCGTCTAGATCACTAA 60.073 42.308 0.00 0.00 37.82 2.24
4564 6404 5.410132 GCAGATAAGAGCGTCTAGATCACTA 59.590 44.000 0.00 0.00 37.82 2.74
4565 6405 4.215399 GCAGATAAGAGCGTCTAGATCACT 59.785 45.833 0.00 0.00 37.82 3.41
4566 6406 4.023622 TGCAGATAAGAGCGTCTAGATCAC 60.024 45.833 0.00 0.00 37.82 3.06
4569 6409 4.393834 TCTGCAGATAAGAGCGTCTAGAT 58.606 43.478 13.74 0.00 0.00 1.98
4570 6410 3.809905 TCTGCAGATAAGAGCGTCTAGA 58.190 45.455 13.74 0.00 0.00 2.43
4573 6413 3.131933 ACAATCTGCAGATAAGAGCGTCT 59.868 43.478 28.92 7.78 33.73 4.18
4574 6414 3.452474 ACAATCTGCAGATAAGAGCGTC 58.548 45.455 28.92 0.00 33.73 5.19
4575 6415 3.533606 ACAATCTGCAGATAAGAGCGT 57.466 42.857 28.92 15.64 33.73 5.07
4577 6417 9.868277 ATAAGTATACAATCTGCAGATAAGAGC 57.132 33.333 28.92 16.79 33.73 4.09
4585 7231 9.102757 ACTGAACAATAAGTATACAATCTGCAG 57.897 33.333 7.63 7.63 0.00 4.41
4598 7244 5.707298 CCCTGTCAATGACTGAACAATAAGT 59.293 40.000 19.67 0.00 35.22 2.24
4685 7451 3.874543 TGTGCTTATTCACACTTGAACGT 59.125 39.130 0.00 0.00 44.66 3.99
4727 7511 1.004277 GCCCCACATGTTAAGGAGTGA 59.996 52.381 9.29 0.00 33.99 3.41
4841 7637 6.252995 TGCTCAAATAAATACAAACTCCCCT 58.747 36.000 0.00 0.00 0.00 4.79
4884 7683 4.526650 GGGGGCTATCTCAAAACAGAAAAA 59.473 41.667 0.00 0.00 0.00 1.94
4921 7720 5.008331 TGACTTCACAGATACGTCTAAGGT 58.992 41.667 0.00 0.00 32.09 3.50
4923 7722 6.424176 TCTGACTTCACAGATACGTCTAAG 57.576 41.667 0.00 0.00 41.21 2.18
4924 7723 6.812879 TTCTGACTTCACAGATACGTCTAA 57.187 37.500 0.00 0.00 44.67 2.10
4959 7758 6.304356 TGAATTTCTGACTTCACATGTGAC 57.696 37.500 27.88 16.94 39.66 3.67
4985 7784 5.388475 CGTTGTGCAGTTATACAAGAGACAC 60.388 44.000 0.00 0.00 37.46 3.67
4989 7788 3.991069 GCGTTGTGCAGTTATACAAGAG 58.009 45.455 0.00 0.00 45.45 2.85
5008 7807 1.227999 ACACGGTGTTTCTCCATGCG 61.228 55.000 8.21 0.00 0.00 4.73
5090 7889 5.634118 AGAATGTTGGATTGACTTGGAAGA 58.366 37.500 0.00 0.00 0.00 2.87
5147 7946 1.450312 ATCCACTTGTAGCGGCAGC 60.450 57.895 0.00 0.00 45.58 5.25
5148 7947 0.108186 TCATCCACTTGTAGCGGCAG 60.108 55.000 1.45 0.00 0.00 4.85
5149 7948 0.108186 CTCATCCACTTGTAGCGGCA 60.108 55.000 1.45 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.