Multiple sequence alignment - TraesCS1D01G209600

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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 TraesCS1D01G209600 chr1D 100.000 3806 0 0 1 3806 295535045 295538850 0.000000e+00 7029.0
1 TraesCS1D01G209600 chr1D 94.915 59 3 0 3368 3426 295538354 295538412 4.050000e-15 93.5
2 TraesCS1D01G209600 chr1D 94.915 59 3 0 3310 3368 295538412 295538470 4.050000e-15 93.5
3 TraesCS1D01G209600 chr1A 93.454 2551 133 18 835 3369 368797451 368799983 0.000000e+00 3755.0
4 TraesCS1D01G209600 chr1A 85.872 453 40 10 3368 3803 368799924 368800369 9.630000e-126 460.0
5 TraesCS1D01G209600 chr1B 91.819 2567 125 35 833 3369 397051913 397054424 0.000000e+00 3498.0
6 TraesCS1D01G209600 chr1B 94.894 803 40 1 1 802 397050280 397051082 0.000000e+00 1254.0
7 TraesCS1D01G209600 chr1B 83.563 870 73 32 1306 2143 48108606 48109437 0.000000e+00 750.0
8 TraesCS1D01G209600 chr1B 88.565 446 31 7 3368 3801 397054365 397054802 1.210000e-144 523.0
9 TraesCS1D01G209600 chr1B 81.159 138 25 1 47 183 363212330 363212467 4.020000e-20 110.0
10 TraesCS1D01G209600 chr1B 78.986 138 28 1 47 183 487297353 487297216 4.050000e-15 93.5
11 TraesCS1D01G209600 chr1B 79.365 126 22 3 55 178 19299858 19299735 6.770000e-13 86.1
12 TraesCS1D01G209600 chrUn 87.034 725 61 17 1306 2005 82063789 82064505 0.000000e+00 787.0
13 TraesCS1D01G209600 chrUn 87.034 725 61 17 1306 2005 377313350 377314066 0.000000e+00 787.0
14 TraesCS1D01G209600 chr7A 87.034 725 61 17 1306 2005 14509146 14508430 0.000000e+00 787.0
15 TraesCS1D01G209600 chr7A 86.483 725 60 19 1306 2005 64563738 64563027 0.000000e+00 761.0
16 TraesCS1D01G209600 chr7A 79.114 158 32 1 42 198 541326962 541326805 1.450000e-19 108.0
17 TraesCS1D01G209600 chr6B 83.986 868 80 27 1306 2143 244812858 244813696 0.000000e+00 778.0
18 TraesCS1D01G209600 chr5D 86.685 721 67 14 1306 2005 41588002 41587290 0.000000e+00 773.0
19 TraesCS1D01G209600 chr2A 86.207 725 67 17 1306 2005 19604517 19603801 0.000000e+00 754.0
20 TraesCS1D01G209600 chr7B 82.896 877 74 33 1306 2143 720575561 720574722 0.000000e+00 719.0
21 TraesCS1D01G209600 chr3B 76.990 804 147 30 28 802 433536700 433535906 3.510000e-115 425.0
22 TraesCS1D01G209600 chr3A 76.214 803 159 24 28 802 452943270 452942472 2.760000e-106 396.0
23 TraesCS1D01G209600 chr3A 77.460 315 63 6 1 308 504815386 504815699 8.400000e-42 182.0
24 TraesCS1D01G209600 chr3D 75.188 798 140 35 55 802 334158553 334157764 1.320000e-84 324.0
25 TraesCS1D01G209600 chr3D 82.639 144 25 0 55 198 239891943 239891800 1.110000e-25 128.0
26 TraesCS1D01G209600 chr6D 79.365 126 25 1 59 183 231719991 231720116 1.880000e-13 87.9
27 TraesCS1D01G209600 chr4A 78.014 141 24 5 47 183 511871063 511871200 8.760000e-12 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 TraesCS1D01G209600 chr1D 295535045 295538850 3805 False 2405.333333 7029 96.610000 1 3806 3 chr1D.!!$F1 3805
1 TraesCS1D01G209600 chr1A 368797451 368800369 2918 False 2107.500000 3755 89.663000 835 3803 2 chr1A.!!$F1 2968
2 TraesCS1D01G209600 chr1B 397050280 397054802 4522 False 1758.333333 3498 91.759333 1 3801 3 chr1B.!!$F3 3800
3 TraesCS1D01G209600 chr1B 48108606 48109437 831 False 750.000000 750 83.563000 1306 2143 1 chr1B.!!$F1 837
4 TraesCS1D01G209600 chrUn 82063789 82064505 716 False 787.000000 787 87.034000 1306 2005 1 chrUn.!!$F1 699
5 TraesCS1D01G209600 chrUn 377313350 377314066 716 False 787.000000 787 87.034000 1306 2005 1 chrUn.!!$F2 699
6 TraesCS1D01G209600 chr7A 14508430 14509146 716 True 787.000000 787 87.034000 1306 2005 1 chr7A.!!$R1 699
7 TraesCS1D01G209600 chr7A 64563027 64563738 711 True 761.000000 761 86.483000 1306 2005 1 chr7A.!!$R2 699
8 TraesCS1D01G209600 chr6B 244812858 244813696 838 False 778.000000 778 83.986000 1306 2143 1 chr6B.!!$F1 837
9 TraesCS1D01G209600 chr5D 41587290 41588002 712 True 773.000000 773 86.685000 1306 2005 1 chr5D.!!$R1 699
10 TraesCS1D01G209600 chr2A 19603801 19604517 716 True 754.000000 754 86.207000 1306 2005 1 chr2A.!!$R1 699
11 TraesCS1D01G209600 chr7B 720574722 720575561 839 True 719.000000 719 82.896000 1306 2143 1 chr7B.!!$R1 837
12 TraesCS1D01G209600 chr3B 433535906 433536700 794 True 425.000000 425 76.990000 28 802 1 chr3B.!!$R1 774
13 TraesCS1D01G209600 chr3A 452942472 452943270 798 True 396.000000 396 76.214000 28 802 1 chr3A.!!$R1 774
14 TraesCS1D01G209600 chr3D 334157764 334158553 789 True 324.000000 324 75.188000 55 802 1 chr3D.!!$R2 747

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
452 495 0.321653 AGGAGGAAATGACACGGTGC 60.322 55.0 8.3 1.81 0.0 5.01 F
1237 2091 0.830444 TCCACGTCTGCACCTACCTT 60.830 55.0 0.0 0.00 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2257 3188 0.537143 ACACAGGAATTGCTTCGCCA 60.537 50.0 0.0 0.0 31.75 5.69 R
3231 4178 0.313987 GACGAGGCCCCAAAACAAAG 59.686 55.0 0.0 0.0 0.00 2.77 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
43 47 3.350833 GGAGCAGAGATGAACCATGTTT 58.649 45.455 0.00 0.00 0.00 2.83
204 209 5.808042 TGTCTTCTTAGCTGCATCAAATC 57.192 39.130 1.02 0.00 0.00 2.17
259 267 7.795047 TCTTCAAGAGACTTTGCCATCATATA 58.205 34.615 0.00 0.00 0.00 0.86
452 495 0.321653 AGGAGGAAATGACACGGTGC 60.322 55.000 8.30 1.81 0.00 5.01
591 636 9.221775 GACAACTATTTGTACAACTGAAAACTG 57.778 33.333 8.07 1.74 46.43 3.16
598 643 3.775661 ACAACTGAAAACTGAAACCGG 57.224 42.857 0.00 0.00 0.00 5.28
609 654 2.030007 ACTGAAACCGGCATTTGATGTG 60.030 45.455 0.00 0.00 0.00 3.21
646 691 4.399004 TGCAAATGCCAAACTAAACAGT 57.601 36.364 2.46 0.00 41.18 3.55
664 709 5.791336 ACAGTAGTTCAGACAGTGATGAA 57.209 39.130 10.25 10.25 34.17 2.57
740 785 5.105473 ACATTAGCCGTTTTCACTAGCTCTA 60.105 40.000 0.00 0.00 33.50 2.43
745 790 6.403878 AGCCGTTTTCACTAGCTCTATAAAA 58.596 36.000 0.00 0.00 0.00 1.52
792 846 5.310720 ACTCAAGAAGTTCACCACAAAAC 57.689 39.130 5.50 0.00 33.03 2.43
802 856 7.027778 AGTTCACCACAAAACTTCTTCATAC 57.972 36.000 0.00 0.00 31.81 2.39
804 858 5.120399 TCACCACAAAACTTCTTCATACGT 58.880 37.500 0.00 0.00 0.00 3.57
807 861 7.117236 TCACCACAAAACTTCTTCATACGTATC 59.883 37.037 4.74 0.00 0.00 2.24
808 862 6.370718 ACCACAAAACTTCTTCATACGTATCC 59.629 38.462 4.74 0.00 0.00 2.59
809 863 6.594159 CCACAAAACTTCTTCATACGTATCCT 59.406 38.462 4.74 0.00 0.00 3.24
810 864 7.413000 CCACAAAACTTCTTCATACGTATCCTG 60.413 40.741 4.74 0.00 0.00 3.86
811 865 6.092259 ACAAAACTTCTTCATACGTATCCTGC 59.908 38.462 4.74 0.00 0.00 4.85
813 867 5.537300 ACTTCTTCATACGTATCCTGCAT 57.463 39.130 4.74 0.00 0.00 3.96
814 868 5.918608 ACTTCTTCATACGTATCCTGCATT 58.081 37.500 4.74 0.00 0.00 3.56
815 869 5.755375 ACTTCTTCATACGTATCCTGCATTG 59.245 40.000 4.74 0.00 0.00 2.82
816 870 4.058124 TCTTCATACGTATCCTGCATTGC 58.942 43.478 4.74 0.46 0.00 3.56
818 872 3.802866 TCATACGTATCCTGCATTGCAA 58.197 40.909 13.18 0.00 38.41 4.08
821 875 3.932545 ACGTATCCTGCATTGCAAAAA 57.067 38.095 13.18 1.37 38.41 1.94
822 876 3.574614 ACGTATCCTGCATTGCAAAAAC 58.425 40.909 13.18 7.71 38.41 2.43
824 878 3.609373 CGTATCCTGCATTGCAAAAACTG 59.391 43.478 13.18 0.00 38.41 3.16
825 879 2.529780 TCCTGCATTGCAAAAACTGG 57.470 45.000 13.18 9.23 38.41 4.00
827 881 1.202675 CCTGCATTGCAAAAACTGGGT 60.203 47.619 13.18 0.00 38.41 4.51
828 882 1.868498 CTGCATTGCAAAAACTGGGTG 59.132 47.619 13.18 0.00 38.41 4.61
829 883 1.209019 TGCATTGCAAAAACTGGGTGT 59.791 42.857 9.33 0.00 34.76 4.16
830 884 2.432146 TGCATTGCAAAAACTGGGTGTA 59.568 40.909 9.33 0.00 34.76 2.90
831 885 3.070734 TGCATTGCAAAAACTGGGTGTAT 59.929 39.130 9.33 0.00 34.76 2.29
843 1697 1.834896 TGGGTGTATTGCAGGATACGT 59.165 47.619 0.00 0.00 46.39 3.57
883 1737 4.318903 CGTAATTACGTTTTCAGGTGCACA 60.319 41.667 26.15 0.00 44.13 4.57
887 1741 3.896648 ACGTTTTCAGGTGCACATTAG 57.103 42.857 20.43 0.01 0.00 1.73
933 1787 2.359967 CCCAGAGGACGAGGGGAAC 61.360 68.421 0.00 0.00 43.57 3.62
940 1794 3.621892 GACGAGGGGAACGACACGG 62.622 68.421 0.00 0.00 34.70 4.94
1221 2075 1.609501 CCCCTTCCTCACTCGTCCA 60.610 63.158 0.00 0.00 0.00 4.02
1237 2091 0.830444 TCCACGTCTGCACCTACCTT 60.830 55.000 0.00 0.00 0.00 3.50
1370 2224 3.191539 GAAGCTGCTCTTCGCCGG 61.192 66.667 1.00 0.00 41.48 6.13
1433 2289 4.344968 CCCACTTCAAATTCCCCCAATATC 59.655 45.833 0.00 0.00 0.00 1.63
1442 2298 3.073411 TCCCCCAATATCCATCTCACA 57.927 47.619 0.00 0.00 0.00 3.58
1574 2443 1.405526 CCATAGTGTTACTGGCGCTGT 60.406 52.381 7.64 9.68 0.00 4.40
1607 2476 1.068885 CATAGCCGAGTTCTCGCTAGG 60.069 57.143 15.54 16.11 34.87 3.02
1724 2611 3.607422 TGTCGCTCACAAAACATCAAG 57.393 42.857 0.00 0.00 29.30 3.02
1916 2824 6.035650 GCTTGACGAATACAGTAGTGCAAATA 59.964 38.462 0.00 0.00 0.00 1.40
1984 2899 5.531634 ACCGTCGAATAGTTTTCAACAGTA 58.468 37.500 0.00 0.00 0.00 2.74
2087 3013 5.006153 TGTGGGAATTCACTGTATACGAG 57.994 43.478 9.56 0.03 38.40 4.18
2313 3244 6.571150 GCTCAATAGTTGGATAATGGGAATGC 60.571 42.308 0.00 0.00 0.00 3.56
2617 3549 1.079825 TCACCTAGTAAAGCCCCTCCA 59.920 52.381 0.00 0.00 0.00 3.86
2662 3594 0.815734 CCACGTCTCGGAGGTTGTAT 59.184 55.000 4.96 0.00 0.00 2.29
2689 3621 8.237811 ACAATCCTTGAAACACTACTTTGATT 57.762 30.769 0.00 0.00 0.00 2.57
2727 3662 2.298610 TGTCGGATAGTAGACTGGCTG 58.701 52.381 0.00 0.00 38.16 4.85
2757 3693 4.526970 TGCTATCTTTCTTTAGGGCAAGG 58.473 43.478 0.00 0.00 0.00 3.61
2909 3847 1.138069 TGGCTGTTTTGACTCGTCTCA 59.862 47.619 0.00 0.00 0.00 3.27
2910 3848 2.210116 GGCTGTTTTGACTCGTCTCAA 58.790 47.619 0.00 0.00 0.00 3.02
2927 3865 6.039270 TCGTCTCAAACTTGTGGAAATGAAAT 59.961 34.615 0.00 0.00 0.00 2.17
2934 3872 9.384682 CAAACTTGTGGAAATGAAATTAATTGC 57.615 29.630 0.39 0.00 33.67 3.56
2936 3874 8.314143 ACTTGTGGAAATGAAATTAATTGCAG 57.686 30.769 14.23 0.73 33.67 4.41
2989 3927 7.664082 ACATGCTATGATGCTAAGTTCATAC 57.336 36.000 0.00 0.00 34.52 2.39
2990 3928 7.448420 ACATGCTATGATGCTAAGTTCATACT 58.552 34.615 0.00 0.00 34.52 2.12
2991 3929 7.387122 ACATGCTATGATGCTAAGTTCATACTG 59.613 37.037 0.00 0.00 34.52 2.74
2992 3930 6.226052 TGCTATGATGCTAAGTTCATACTGG 58.774 40.000 0.00 0.00 34.52 4.00
2997 3935 8.839310 ATGATGCTAAGTTCATACTGGAATAC 57.161 34.615 0.00 0.00 34.01 1.89
2998 3936 7.791029 TGATGCTAAGTTCATACTGGAATACA 58.209 34.615 0.00 0.00 34.01 2.29
3000 3938 9.929180 GATGCTAAGTTCATACTGGAATACATA 57.071 33.333 0.00 0.00 34.01 2.29
3045 3983 3.594603 TTTAGTGTGCCTCTGCTACTC 57.405 47.619 0.00 0.00 37.05 2.59
3081 4019 1.296056 GCAAAGGCCAAATGCTGCTG 61.296 55.000 17.25 0.00 40.92 4.41
3110 4054 7.058525 TGAAGACGTAGAGAATAGAACCCATA 58.941 38.462 0.00 0.00 0.00 2.74
3134 4078 0.321996 GGGAGGAACTGAGTGGTCAC 59.678 60.000 0.00 0.00 41.55 3.67
3162 4106 4.440387 GGTCGACTCCTGGTTTATTCTCTC 60.440 50.000 16.46 0.00 0.00 3.20
3218 4165 3.549070 CACTTGCTCTTGTTTTTCTGCAC 59.451 43.478 0.00 0.00 0.00 4.57
3219 4166 2.473530 TGCTCTTGTTTTTCTGCACG 57.526 45.000 0.00 0.00 0.00 5.34
3223 4170 3.242936 GCTCTTGTTTTTCTGCACGGTTA 60.243 43.478 0.00 0.00 0.00 2.85
3231 4178 3.955771 TTCTGCACGGTTAAGTTTCAC 57.044 42.857 0.00 0.00 0.00 3.18
3236 4183 3.440872 TGCACGGTTAAGTTTCACTTTGT 59.559 39.130 0.00 0.00 39.51 2.83
3260 4207 0.869028 GGGCCTCGTCGACGTAATTC 60.869 60.000 34.40 20.91 40.80 2.17
3271 4218 4.616802 GTCGACGTAATTCCGAACAAGTTA 59.383 41.667 0.00 0.00 33.91 2.24
3306 4253 6.635166 TGATTTTGTGCATCAATTTCGATG 57.365 33.333 0.00 2.18 44.69 3.84
3330 4277 1.949257 GGCCTTCCGAACTTGTGTG 59.051 57.895 0.00 0.00 0.00 3.82
3347 4294 1.235724 GTGGTTTTCAGTTCGAGGGG 58.764 55.000 0.00 0.00 0.00 4.79
3356 4303 0.832135 AGTTCGAGGGGCAAGAGTCA 60.832 55.000 0.00 0.00 0.00 3.41
3369 4316 5.241662 GGCAAGAGTCAAGTAAGAGAACAT 58.758 41.667 0.00 0.00 0.00 2.71
3370 4317 5.121454 GGCAAGAGTCAAGTAAGAGAACATG 59.879 44.000 0.00 0.00 0.00 3.21
3371 4318 5.121454 GCAAGAGTCAAGTAAGAGAACATGG 59.879 44.000 0.00 0.00 0.00 3.66
3372 4319 4.826556 AGAGTCAAGTAAGAGAACATGGC 58.173 43.478 0.00 0.00 0.00 4.40
3373 4320 3.935828 GAGTCAAGTAAGAGAACATGGCC 59.064 47.826 0.00 0.00 0.00 5.36
3374 4321 3.584848 AGTCAAGTAAGAGAACATGGCCT 59.415 43.478 3.32 0.00 0.00 5.19
3375 4322 4.042187 AGTCAAGTAAGAGAACATGGCCTT 59.958 41.667 3.32 0.00 0.00 4.35
3376 4323 4.393371 GTCAAGTAAGAGAACATGGCCTTC 59.607 45.833 3.32 0.00 0.00 3.46
3377 4324 3.636153 AGTAAGAGAACATGGCCTTCC 57.364 47.619 3.32 0.00 0.00 3.46
3378 4325 2.093447 AGTAAGAGAACATGGCCTTCCG 60.093 50.000 3.32 0.00 34.14 4.30
3379 4326 0.984230 AAGAGAACATGGCCTTCCGA 59.016 50.000 3.32 0.00 34.14 4.55
3380 4327 0.539051 AGAGAACATGGCCTTCCGAG 59.461 55.000 3.32 0.00 34.14 4.63
3381 4328 0.250513 GAGAACATGGCCTTCCGAGT 59.749 55.000 3.32 0.00 34.14 4.18
3382 4329 0.693049 AGAACATGGCCTTCCGAGTT 59.307 50.000 3.32 0.00 35.52 3.01
3383 4330 1.073923 AGAACATGGCCTTCCGAGTTT 59.926 47.619 3.32 0.00 33.78 2.66
3384 4331 1.200020 GAACATGGCCTTCCGAGTTTG 59.800 52.381 3.32 0.00 33.78 2.93
3385 4332 0.110486 ACATGGCCTTCCGAGTTTGT 59.890 50.000 3.32 0.00 34.14 2.83
3386 4333 0.523072 CATGGCCTTCCGAGTTTGTG 59.477 55.000 3.32 0.00 34.14 3.33
3387 4334 0.110486 ATGGCCTTCCGAGTTTGTGT 59.890 50.000 3.32 0.00 34.14 3.72
3388 4335 0.817634 TGGCCTTCCGAGTTTGTGTG 60.818 55.000 3.32 0.00 34.14 3.82
3389 4336 1.515521 GGCCTTCCGAGTTTGTGTGG 61.516 60.000 0.00 0.00 0.00 4.17
3390 4337 0.818040 GCCTTCCGAGTTTGTGTGGT 60.818 55.000 0.00 0.00 0.00 4.16
3391 4338 1.675552 CCTTCCGAGTTTGTGTGGTT 58.324 50.000 0.00 0.00 0.00 3.67
3392 4339 2.021457 CCTTCCGAGTTTGTGTGGTTT 58.979 47.619 0.00 0.00 0.00 3.27
3393 4340 2.425668 CCTTCCGAGTTTGTGTGGTTTT 59.574 45.455 0.00 0.00 0.00 2.43
3394 4341 3.488553 CCTTCCGAGTTTGTGTGGTTTTC 60.489 47.826 0.00 0.00 0.00 2.29
3395 4342 2.712709 TCCGAGTTTGTGTGGTTTTCA 58.287 42.857 0.00 0.00 0.00 2.69
3396 4343 2.680841 TCCGAGTTTGTGTGGTTTTCAG 59.319 45.455 0.00 0.00 0.00 3.02
3397 4344 2.422127 CCGAGTTTGTGTGGTTTTCAGT 59.578 45.455 0.00 0.00 0.00 3.41
3398 4345 3.119637 CCGAGTTTGTGTGGTTTTCAGTT 60.120 43.478 0.00 0.00 0.00 3.16
3399 4346 4.095610 CGAGTTTGTGTGGTTTTCAGTTC 58.904 43.478 0.00 0.00 0.00 3.01
3400 4347 4.091453 AGTTTGTGTGGTTTTCAGTTCG 57.909 40.909 0.00 0.00 0.00 3.95
3401 4348 3.754323 AGTTTGTGTGGTTTTCAGTTCGA 59.246 39.130 0.00 0.00 0.00 3.71
3402 4349 4.095610 GTTTGTGTGGTTTTCAGTTCGAG 58.904 43.478 0.00 0.00 0.00 4.04
3403 4350 2.285083 TGTGTGGTTTTCAGTTCGAGG 58.715 47.619 0.00 0.00 0.00 4.63
3404 4351 1.602377 GTGTGGTTTTCAGTTCGAGGG 59.398 52.381 0.00 0.00 0.00 4.30
3405 4352 1.235724 GTGGTTTTCAGTTCGAGGGG 58.764 55.000 0.00 0.00 0.00 4.79
3406 4353 0.536460 TGGTTTTCAGTTCGAGGGGC 60.536 55.000 0.00 0.00 0.00 5.80
3407 4354 0.536460 GGTTTTCAGTTCGAGGGGCA 60.536 55.000 0.00 0.00 0.00 5.36
3408 4355 1.314730 GTTTTCAGTTCGAGGGGCAA 58.685 50.000 0.00 0.00 0.00 4.52
3409 4356 1.266989 GTTTTCAGTTCGAGGGGCAAG 59.733 52.381 0.00 0.00 0.00 4.01
3410 4357 0.762418 TTTCAGTTCGAGGGGCAAGA 59.238 50.000 0.00 0.00 0.00 3.02
3411 4358 0.321671 TTCAGTTCGAGGGGCAAGAG 59.678 55.000 0.00 0.00 0.00 2.85
3412 4359 0.832135 TCAGTTCGAGGGGCAAGAGT 60.832 55.000 0.00 0.00 0.00 3.24
3413 4360 0.390472 CAGTTCGAGGGGCAAGAGTC 60.390 60.000 0.00 0.00 0.00 3.36
3414 4361 0.832135 AGTTCGAGGGGCAAGAGTCA 60.832 55.000 0.00 0.00 0.00 3.41
3415 4362 0.034896 GTTCGAGGGGCAAGAGTCAA 59.965 55.000 0.00 0.00 0.00 3.18
3416 4363 0.321671 TTCGAGGGGCAAGAGTCAAG 59.678 55.000 0.00 0.00 0.00 3.02
3417 4364 0.832135 TCGAGGGGCAAGAGTCAAGT 60.832 55.000 0.00 0.00 0.00 3.16
3418 4365 0.895530 CGAGGGGCAAGAGTCAAGTA 59.104 55.000 0.00 0.00 0.00 2.24
3419 4366 1.275291 CGAGGGGCAAGAGTCAAGTAA 59.725 52.381 0.00 0.00 0.00 2.24
3420 4367 2.675317 CGAGGGGCAAGAGTCAAGTAAG 60.675 54.545 0.00 0.00 0.00 2.34
3421 4368 2.567615 GAGGGGCAAGAGTCAAGTAAGA 59.432 50.000 0.00 0.00 0.00 2.10
3422 4369 2.569404 AGGGGCAAGAGTCAAGTAAGAG 59.431 50.000 0.00 0.00 0.00 2.85
3423 4370 2.567615 GGGGCAAGAGTCAAGTAAGAGA 59.432 50.000 0.00 0.00 0.00 3.10
3424 4371 3.008049 GGGGCAAGAGTCAAGTAAGAGAA 59.992 47.826 0.00 0.00 0.00 2.87
3425 4372 3.997681 GGGCAAGAGTCAAGTAAGAGAAC 59.002 47.826 0.00 0.00 0.00 3.01
3426 4373 3.675698 GGCAAGAGTCAAGTAAGAGAACG 59.324 47.826 0.00 0.00 0.00 3.95
3489 4437 6.361433 TGGACAAATTTGACTACCAGAAAGA 58.639 36.000 24.64 3.41 0.00 2.52
3493 4441 7.931275 ACAAATTTGACTACCAGAAAGAGAAC 58.069 34.615 24.64 0.00 0.00 3.01
3659 4624 2.282674 ACCTGGCGACGGTGACTA 60.283 61.111 3.91 0.00 36.20 2.59
3679 4645 4.471386 ACTACATCTTACAGAAGCCCATGT 59.529 41.667 0.00 0.00 34.07 3.21
3680 4646 3.878778 ACATCTTACAGAAGCCCATGTC 58.121 45.455 0.00 0.00 26.95 3.06
3681 4647 3.264193 ACATCTTACAGAAGCCCATGTCA 59.736 43.478 0.00 0.00 26.95 3.58
3789 4755 1.055849 TGGAAACCACTAGCTGCTCA 58.944 50.000 4.91 0.00 0.00 4.26
3803 4769 2.604132 GCTGCTCAGAACTTTCAACAGC 60.604 50.000 0.29 0.00 42.00 4.40
3804 4770 2.615447 CTGCTCAGAACTTTCAACAGCA 59.385 45.455 8.43 8.43 35.47 4.41
3805 4771 2.355756 TGCTCAGAACTTTCAACAGCAC 59.644 45.455 5.75 0.00 33.33 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 47 4.769688 TCTTCAGTCTCAGTTTCAAGCAA 58.230 39.130 0.00 0.00 0.00 3.91
76 80 0.165295 GTTGAAGTCGCCGCCTAAAC 59.835 55.000 0.00 0.00 0.00 2.01
193 198 4.133078 GGGTCCTCTTAGATTTGATGCAG 58.867 47.826 0.00 0.00 0.00 4.41
259 267 7.615365 TGTTTATCTTTCAGATTGCTAACCCAT 59.385 33.333 0.00 0.00 36.20 4.00
287 295 5.590530 TGCAAAACCTGTTATTTGTCTGT 57.409 34.783 0.00 0.00 38.48 3.41
394 437 8.520835 TCTGGACGATGATCTTAATAATTTCG 57.479 34.615 0.00 0.00 0.00 3.46
452 495 0.039798 GGTGAAGCTGCACACACATG 60.040 55.000 26.30 0.00 40.52 3.21
477 520 6.486253 TCTGTTGTTGATCTGTATTTCAGC 57.514 37.500 0.00 0.00 43.32 4.26
481 524 6.882610 TGCTTCTGTTGTTGATCTGTATTT 57.117 33.333 0.00 0.00 0.00 1.40
584 629 3.712187 TCAAATGCCGGTTTCAGTTTTC 58.288 40.909 1.90 0.00 0.00 2.29
591 636 3.296322 TTCACATCAAATGCCGGTTTC 57.704 42.857 1.90 0.00 0.00 2.78
598 643 3.991773 ACTGCATGTTTCACATCAAATGC 59.008 39.130 0.00 0.00 36.53 3.56
675 720 5.066764 TGCCTTCAAACTTTGTTGTAGTACC 59.933 40.000 0.00 0.00 0.00 3.34
792 846 5.333645 GCAATGCAGGATACGTATGAAGAAG 60.334 44.000 13.97 0.00 46.39 2.85
802 856 3.609373 CAGTTTTTGCAATGCAGGATACG 59.391 43.478 8.31 0.00 40.61 3.06
804 858 3.055963 CCCAGTTTTTGCAATGCAGGATA 60.056 43.478 8.31 0.00 40.61 2.59
807 861 1.202675 ACCCAGTTTTTGCAATGCAGG 60.203 47.619 8.31 6.95 40.61 4.85
808 862 1.868498 CACCCAGTTTTTGCAATGCAG 59.132 47.619 8.31 0.00 40.61 4.41
809 863 1.209019 ACACCCAGTTTTTGCAATGCA 59.791 42.857 2.72 2.72 36.47 3.96
810 864 1.952193 ACACCCAGTTTTTGCAATGC 58.048 45.000 0.00 0.00 0.00 3.56
811 865 4.083908 GCAATACACCCAGTTTTTGCAATG 60.084 41.667 0.00 0.00 42.75 2.82
813 867 3.118629 TGCAATACACCCAGTTTTTGCAA 60.119 39.130 12.68 0.00 46.25 4.08
814 868 2.432146 TGCAATACACCCAGTTTTTGCA 59.568 40.909 11.63 11.63 46.66 4.08
815 869 3.059166 CTGCAATACACCCAGTTTTTGC 58.941 45.455 0.00 0.00 43.15 3.68
816 870 3.320541 TCCTGCAATACACCCAGTTTTTG 59.679 43.478 0.00 0.00 0.00 2.44
818 872 3.237268 TCCTGCAATACACCCAGTTTT 57.763 42.857 0.00 0.00 0.00 2.43
821 875 2.158957 CGTATCCTGCAATACACCCAGT 60.159 50.000 8.80 0.00 32.66 4.00
822 876 2.158957 ACGTATCCTGCAATACACCCAG 60.159 50.000 8.80 0.00 32.66 4.45
824 878 2.614829 ACGTATCCTGCAATACACCC 57.385 50.000 8.80 0.00 32.66 4.61
825 879 5.352016 TGTTTTACGTATCCTGCAATACACC 59.648 40.000 8.80 0.00 32.66 4.16
827 881 6.651643 AGTTGTTTTACGTATCCTGCAATACA 59.348 34.615 8.80 0.00 32.66 2.29
828 882 7.068692 AGTTGTTTTACGTATCCTGCAATAC 57.931 36.000 0.00 0.00 0.00 1.89
829 883 8.036575 AGTAGTTGTTTTACGTATCCTGCAATA 58.963 33.333 0.00 0.00 0.00 1.90
830 884 6.877322 AGTAGTTGTTTTACGTATCCTGCAAT 59.123 34.615 0.00 0.00 0.00 3.56
831 885 6.146510 CAGTAGTTGTTTTACGTATCCTGCAA 59.853 38.462 0.00 0.00 0.00 4.08
843 1697 6.864360 AATTACGTGCCAGTAGTTGTTTTA 57.136 33.333 0.00 0.00 0.00 1.52
883 1737 6.543100 TCGACCACAACAAAAAGTTACCTAAT 59.457 34.615 0.00 0.00 38.74 1.73
887 1741 4.095334 ACTCGACCACAACAAAAAGTTACC 59.905 41.667 0.00 0.00 38.74 2.85
895 1749 2.420722 GGTTTGACTCGACCACAACAAA 59.579 45.455 0.00 0.00 35.95 2.83
896 1750 2.011222 GGTTTGACTCGACCACAACAA 58.989 47.619 0.00 0.00 35.95 2.83
990 1844 4.592192 GCCGCCATCTCGCAGCTA 62.592 66.667 0.00 0.00 0.00 3.32
1221 2075 1.204941 GATGAAGGTAGGTGCAGACGT 59.795 52.381 0.00 0.00 0.00 4.34
1237 2091 2.105649 TGTGTTAGCACCAGTTGGATGA 59.894 45.455 7.29 0.00 44.65 2.92
1433 2289 1.887854 TGTTTGCCACATGTGAGATGG 59.112 47.619 27.46 11.19 36.51 3.51
1463 2319 4.160814 AGCAAAGCAAAGATGGCATTATCA 59.839 37.500 0.00 0.00 0.00 2.15
1538 2399 5.426509 ACACTATGGAGAGAAATGGTGATGA 59.573 40.000 6.21 0.00 37.43 2.92
1574 2443 1.065551 CGGCTATGACATCACTCGTCA 59.934 52.381 0.00 0.00 46.77 4.35
1724 2611 6.818644 TCCTGAATATAGTTTTGAGTCACAGC 59.181 38.462 0.00 0.00 0.00 4.40
1916 2824 6.535963 TCAGTGAGTGACATTCATGATACT 57.464 37.500 3.76 0.00 33.03 2.12
1926 2834 6.701145 ATACGTAGATTCAGTGAGTGACAT 57.299 37.500 0.08 0.00 33.71 3.06
1984 2899 8.630054 TGTACAATGGAAAGCTGTTAAACTAT 57.370 30.769 0.00 0.00 0.00 2.12
2104 3030 5.718724 AAGCTTTTGAGAGAAAGAATGGG 57.281 39.130 0.00 0.00 38.60 4.00
2257 3188 0.537143 ACACAGGAATTGCTTCGCCA 60.537 50.000 0.00 0.00 31.75 5.69
2313 3244 7.775120 ACTATTAGAAACATCCCAGCAATTTG 58.225 34.615 0.00 0.00 0.00 2.32
2617 3549 2.249139 ACCCTCTTCGTGACTTTAGCT 58.751 47.619 0.00 0.00 0.00 3.32
2689 3621 8.746052 ATCCGACATATTAAACTTCCATTCAA 57.254 30.769 0.00 0.00 0.00 2.69
2707 3639 2.298610 CAGCCAGTCTACTATCCGACA 58.701 52.381 0.00 0.00 32.68 4.35
2708 3640 2.299521 ACAGCCAGTCTACTATCCGAC 58.700 52.381 0.00 0.00 0.00 4.79
2727 3662 8.722394 GCCCTAAAGAAAGATAGCATACATTAC 58.278 37.037 0.00 0.00 0.00 1.89
2757 3693 3.768922 AGCAGAGCTCCTCGCACC 61.769 66.667 19.15 0.00 42.61 5.01
2909 3847 9.118300 TGCAATTAATTTCATTTCCACAAGTTT 57.882 25.926 0.00 0.00 0.00 2.66
2910 3848 8.674263 TGCAATTAATTTCATTTCCACAAGTT 57.326 26.923 0.00 0.00 0.00 2.66
2927 3865 5.402997 TTCATGCCATGAACTGCAATTAA 57.597 34.783 15.94 0.00 43.84 1.40
3013 3951 8.253113 CAGAGGCACACTAAATTTGGAAAATAT 58.747 33.333 8.72 0.00 0.00 1.28
3014 3952 7.601856 CAGAGGCACACTAAATTTGGAAAATA 58.398 34.615 8.72 0.00 0.00 1.40
3015 3953 6.458210 CAGAGGCACACTAAATTTGGAAAAT 58.542 36.000 8.72 0.00 0.00 1.82
3016 3954 5.738783 GCAGAGGCACACTAAATTTGGAAAA 60.739 40.000 8.72 0.00 40.72 2.29
3017 3955 4.261994 GCAGAGGCACACTAAATTTGGAAA 60.262 41.667 8.72 0.00 40.72 3.13
3018 3956 3.255642 GCAGAGGCACACTAAATTTGGAA 59.744 43.478 8.72 0.00 40.72 3.53
3019 3957 2.819608 GCAGAGGCACACTAAATTTGGA 59.180 45.455 8.72 0.00 40.72 3.53
3020 3958 2.821969 AGCAGAGGCACACTAAATTTGG 59.178 45.455 0.00 0.00 44.61 3.28
3021 3959 4.697352 AGTAGCAGAGGCACACTAAATTTG 59.303 41.667 0.00 0.00 44.61 2.32
3022 3960 4.911390 AGTAGCAGAGGCACACTAAATTT 58.089 39.130 0.00 0.00 44.61 1.82
3023 3961 4.020218 TGAGTAGCAGAGGCACACTAAATT 60.020 41.667 0.00 0.00 44.61 1.82
3029 3967 1.270305 TGTTGAGTAGCAGAGGCACAC 60.270 52.381 0.00 0.00 44.61 3.82
3030 3968 1.047801 TGTTGAGTAGCAGAGGCACA 58.952 50.000 0.00 0.00 44.61 4.57
3045 3983 4.818546 CCTTTGCATCCTCTACCTATGTTG 59.181 45.833 0.00 0.00 0.00 3.33
3081 4019 5.994887 TCTATTCTCTACGTCTTCAGAGC 57.005 43.478 8.00 0.00 38.54 4.09
3110 4054 3.456277 GACCACTCAGTTCCTCCCAATAT 59.544 47.826 0.00 0.00 0.00 1.28
3134 4078 0.961358 AACCAGGAGTCGACCTCTCG 60.961 60.000 13.01 5.42 40.30 4.04
3162 4106 9.301153 GCCATAACTGAAATAAAATAACACAGG 57.699 33.333 0.00 0.00 0.00 4.00
3231 4178 0.313987 GACGAGGCCCCAAAACAAAG 59.686 55.000 0.00 0.00 0.00 2.77
3236 4183 2.031465 GTCGACGAGGCCCCAAAA 59.969 61.111 0.00 0.00 0.00 2.44
3260 4207 6.371548 TCATTCCTCTTTCATAACTTGTTCGG 59.628 38.462 0.00 0.00 0.00 4.30
3271 4218 6.349243 TGCACAAAATCATTCCTCTTTCAT 57.651 33.333 0.00 0.00 0.00 2.57
3319 4266 3.757745 ACTGAAAACCACACAAGTTCG 57.242 42.857 0.00 0.00 0.00 3.95
3323 4270 3.242739 CCTCGAACTGAAAACCACACAAG 60.243 47.826 0.00 0.00 0.00 3.16
3330 4277 0.536460 TGCCCCTCGAACTGAAAACC 60.536 55.000 0.00 0.00 0.00 3.27
3347 4294 5.121454 CCATGTTCTCTTACTTGACTCTTGC 59.879 44.000 0.00 0.00 0.00 4.01
3356 4303 3.619979 CGGAAGGCCATGTTCTCTTACTT 60.620 47.826 5.01 0.00 0.00 2.24
3369 4316 0.817634 CACACAAACTCGGAAGGCCA 60.818 55.000 5.01 0.00 0.00 5.36
3370 4317 1.515521 CCACACAAACTCGGAAGGCC 61.516 60.000 0.00 0.00 0.00 5.19
3371 4318 0.818040 ACCACACAAACTCGGAAGGC 60.818 55.000 0.00 0.00 0.00 4.35
3372 4319 1.675552 AACCACACAAACTCGGAAGG 58.324 50.000 0.00 0.00 0.00 3.46
3373 4320 3.127895 TGAAAACCACACAAACTCGGAAG 59.872 43.478 0.00 0.00 0.00 3.46
3374 4321 3.082548 TGAAAACCACACAAACTCGGAA 58.917 40.909 0.00 0.00 0.00 4.30
3375 4322 2.680841 CTGAAAACCACACAAACTCGGA 59.319 45.455 0.00 0.00 0.00 4.55
3376 4323 2.422127 ACTGAAAACCACACAAACTCGG 59.578 45.455 0.00 0.00 0.00 4.63
3377 4324 3.757745 ACTGAAAACCACACAAACTCG 57.242 42.857 0.00 0.00 0.00 4.18
3378 4325 4.095610 CGAACTGAAAACCACACAAACTC 58.904 43.478 0.00 0.00 0.00 3.01
3379 4326 3.754323 TCGAACTGAAAACCACACAAACT 59.246 39.130 0.00 0.00 0.00 2.66
3380 4327 4.086199 TCGAACTGAAAACCACACAAAC 57.914 40.909 0.00 0.00 0.00 2.93
3381 4328 3.127895 CCTCGAACTGAAAACCACACAAA 59.872 43.478 0.00 0.00 0.00 2.83
3382 4329 2.680841 CCTCGAACTGAAAACCACACAA 59.319 45.455 0.00 0.00 0.00 3.33
3383 4330 2.285083 CCTCGAACTGAAAACCACACA 58.715 47.619 0.00 0.00 0.00 3.72
3384 4331 1.602377 CCCTCGAACTGAAAACCACAC 59.398 52.381 0.00 0.00 0.00 3.82
3385 4332 1.476110 CCCCTCGAACTGAAAACCACA 60.476 52.381 0.00 0.00 0.00 4.17
3386 4333 1.235724 CCCCTCGAACTGAAAACCAC 58.764 55.000 0.00 0.00 0.00 4.16
3387 4334 0.536460 GCCCCTCGAACTGAAAACCA 60.536 55.000 0.00 0.00 0.00 3.67
3388 4335 0.536460 TGCCCCTCGAACTGAAAACC 60.536 55.000 0.00 0.00 0.00 3.27
3389 4336 1.266989 CTTGCCCCTCGAACTGAAAAC 59.733 52.381 0.00 0.00 0.00 2.43
3390 4337 1.142060 TCTTGCCCCTCGAACTGAAAA 59.858 47.619 0.00 0.00 0.00 2.29
3391 4338 0.762418 TCTTGCCCCTCGAACTGAAA 59.238 50.000 0.00 0.00 0.00 2.69
3392 4339 0.321671 CTCTTGCCCCTCGAACTGAA 59.678 55.000 0.00 0.00 0.00 3.02
3393 4340 0.832135 ACTCTTGCCCCTCGAACTGA 60.832 55.000 0.00 0.00 0.00 3.41
3394 4341 0.390472 GACTCTTGCCCCTCGAACTG 60.390 60.000 0.00 0.00 0.00 3.16
3395 4342 0.832135 TGACTCTTGCCCCTCGAACT 60.832 55.000 0.00 0.00 0.00 3.01
3396 4343 0.034896 TTGACTCTTGCCCCTCGAAC 59.965 55.000 0.00 0.00 0.00 3.95
3397 4344 0.321671 CTTGACTCTTGCCCCTCGAA 59.678 55.000 0.00 0.00 0.00 3.71
3398 4345 0.832135 ACTTGACTCTTGCCCCTCGA 60.832 55.000 0.00 0.00 0.00 4.04
3399 4346 0.895530 TACTTGACTCTTGCCCCTCG 59.104 55.000 0.00 0.00 0.00 4.63
3400 4347 2.567615 TCTTACTTGACTCTTGCCCCTC 59.432 50.000 0.00 0.00 0.00 4.30
3401 4348 2.569404 CTCTTACTTGACTCTTGCCCCT 59.431 50.000 0.00 0.00 0.00 4.79
3402 4349 2.567615 TCTCTTACTTGACTCTTGCCCC 59.432 50.000 0.00 0.00 0.00 5.80
3403 4350 3.963428 TCTCTTACTTGACTCTTGCCC 57.037 47.619 0.00 0.00 0.00 5.36
3404 4351 3.675698 CGTTCTCTTACTTGACTCTTGCC 59.324 47.826 0.00 0.00 0.00 4.52
3405 4352 4.547532 TCGTTCTCTTACTTGACTCTTGC 58.452 43.478 0.00 0.00 0.00 4.01
3406 4353 6.863645 TGATTCGTTCTCTTACTTGACTCTTG 59.136 38.462 0.00 0.00 0.00 3.02
3407 4354 6.982852 TGATTCGTTCTCTTACTTGACTCTT 58.017 36.000 0.00 0.00 0.00 2.85
3408 4355 6.576662 TGATTCGTTCTCTTACTTGACTCT 57.423 37.500 0.00 0.00 0.00 3.24
3409 4356 9.522804 AATATGATTCGTTCTCTTACTTGACTC 57.477 33.333 0.00 0.00 0.00 3.36
3419 4366 8.768955 GCAAACTGATAATATGATTCGTTCTCT 58.231 33.333 0.00 0.00 0.00 3.10
3420 4367 8.768955 AGCAAACTGATAATATGATTCGTTCTC 58.231 33.333 0.00 0.00 0.00 2.87
3421 4368 8.668510 AGCAAACTGATAATATGATTCGTTCT 57.331 30.769 0.00 0.00 0.00 3.01
3422 4369 8.551205 TGAGCAAACTGATAATATGATTCGTTC 58.449 33.333 0.00 0.00 0.00 3.95
3423 4370 8.437360 TGAGCAAACTGATAATATGATTCGTT 57.563 30.769 0.00 0.00 0.00 3.85
3424 4371 8.437360 TTGAGCAAACTGATAATATGATTCGT 57.563 30.769 0.00 0.00 0.00 3.85
3425 4372 9.378597 CTTTGAGCAAACTGATAATATGATTCG 57.621 33.333 0.00 0.00 0.00 3.34
3475 4423 7.540474 AACATAGTTCTCTTTCTGGTAGTCA 57.460 36.000 0.00 0.00 0.00 3.41
3489 4437 8.368668 AGCTCACTGTTTAGTTAACATAGTTCT 58.631 33.333 8.61 0.00 45.31 3.01
3493 4441 6.535508 GGGAGCTCACTGTTTAGTTAACATAG 59.464 42.308 17.19 0.00 45.31 2.23
3659 4624 3.264193 TGACATGGGCTTCTGTAAGATGT 59.736 43.478 0.00 0.00 46.36 3.06
3770 4736 1.002430 CTGAGCAGCTAGTGGTTTCCA 59.998 52.381 0.00 0.00 36.87 3.53
3780 4746 4.060900 CTGTTGAAAGTTCTGAGCAGCTA 58.939 43.478 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.