Multiple sequence alignment - TraesCS1D01G138300

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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 TraesCS1D01G138300 chr1D 100.000 2777 0 0 1 2777 189706444 189709220 0.000000e+00 5129.0
1 TraesCS1D01G138300 chr1D 97.826 46 1 0 2 47 298574959 298575004 2.290000e-11 80.5
2 TraesCS1D01G138300 chr1D 90.909 55 3 2 1 55 50065004 50064952 3.840000e-09 73.1
3 TraesCS1D01G138300 chr1B 90.747 1459 61 27 406 1837 263571015 263572426 0.000000e+00 1879.0
4 TraesCS1D01G138300 chr1B 90.727 399 28 3 2332 2730 263573877 263574266 8.810000e-145 523.0
5 TraesCS1D01G138300 chr1B 87.975 316 14 7 1 312 263565599 263565894 4.400000e-93 351.0
6 TraesCS1D01G138300 chr1B 92.778 180 10 3 1833 2009 263572474 263572653 9.870000e-65 257.0
7 TraesCS1D01G138300 chr7A 89.695 1310 84 29 547 1837 726422145 726423422 0.000000e+00 1624.0
8 TraesCS1D01G138300 chr7A 91.156 147 9 3 1826 1968 726423636 726423782 2.180000e-46 196.0
9 TraesCS1D01G138300 chr7A 92.857 112 4 3 1953 2060 726423797 726423908 2.860000e-35 159.0
10 TraesCS1D01G138300 chr7A 96.000 50 2 0 1 50 43179994 43180043 6.370000e-12 82.4
11 TraesCS1D01G138300 chr7A 97.872 47 0 1 1 47 99344711 99344666 2.290000e-11 80.5
12 TraesCS1D01G138300 chr7D 85.026 1516 122 46 374 1837 630388884 630390346 0.000000e+00 1445.0
13 TraesCS1D01G138300 chr7D 91.833 502 29 2 1336 1837 630473601 630474090 0.000000e+00 689.0
14 TraesCS1D01G138300 chr7D 90.830 229 14 5 1833 2060 630474153 630474375 1.620000e-77 300.0
15 TraesCS1D01G138300 chr7D 86.364 264 32 4 99 359 630386198 630386460 4.530000e-73 285.0
16 TraesCS1D01G138300 chr7D 95.833 48 2 0 1 48 9830612 9830659 8.250000e-11 78.7
17 TraesCS1D01G138300 chr7D 97.826 46 0 1 1 46 49806855 49806899 8.250000e-11 78.7
18 TraesCS1D01G138300 chr1A 89.715 632 42 4 1208 1837 221816239 221816849 0.000000e+00 785.0
19 TraesCS1D01G138300 chr1A 88.907 622 34 18 43 657 221756090 221756683 0.000000e+00 734.0
20 TraesCS1D01G138300 chr1A 88.612 281 12 11 654 933 221787504 221787765 9.590000e-85 324.0
21 TraesCS1D01G138300 chr1A 92.857 70 5 0 2134 2203 221818684 221818753 4.890000e-18 102.0
22 TraesCS1D01G138300 chr2B 97.826 46 1 0 1 46 673065921 673065876 2.290000e-11 80.5
23 TraesCS1D01G138300 chr2B 100.000 28 0 0 2405 2432 34259434 34259407 5.000000e-03 52.8
24 TraesCS1D01G138300 chr3D 97.826 46 0 1 1 46 607805666 607805710 8.250000e-11 78.7
25 TraesCS1D01G138300 chr5B 92.157 51 3 1 7 57 531293184 531293135 1.380000e-08 71.3


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 TraesCS1D01G138300 chr1D 189706444 189709220 2776 False 5129.000000 5129 100.000000 1 2777 1 chr1D.!!$F1 2776
1 TraesCS1D01G138300 chr1B 263571015 263574266 3251 False 886.333333 1879 91.417333 406 2730 3 chr1B.!!$F2 2324
2 TraesCS1D01G138300 chr7A 726422145 726423908 1763 False 659.666667 1624 91.236000 547 2060 3 chr7A.!!$F2 1513
3 TraesCS1D01G138300 chr7D 630386198 630390346 4148 False 865.000000 1445 85.695000 99 1837 2 chr7D.!!$F3 1738
4 TraesCS1D01G138300 chr7D 630473601 630474375 774 False 494.500000 689 91.331500 1336 2060 2 chr7D.!!$F4 724
5 TraesCS1D01G138300 chr1A 221756090 221756683 593 False 734.000000 734 88.907000 43 657 1 chr1A.!!$F1 614
6 TraesCS1D01G138300 chr1A 221816239 221818753 2514 False 443.500000 785 91.286000 1208 2203 2 chr1A.!!$F3 995

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
884 3334 0.181114 AGACCTGCACACAAGCAAGA 59.819 50.0 0.0 0.0 45.13 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2747 7920 0.109919 CCTTGGCGTCGGTAAAAAGC 60.11 55.0 0.0 0.0 0.0 3.51 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
18 19 3.884467 ACCACAGTCCCTCTAACCA 57.116 52.632 0.00 0.00 0.00 3.67
19 20 2.344093 ACCACAGTCCCTCTAACCAT 57.656 50.000 0.00 0.00 0.00 3.55
20 21 2.188817 ACCACAGTCCCTCTAACCATC 58.811 52.381 0.00 0.00 0.00 3.51
21 22 1.486726 CCACAGTCCCTCTAACCATCC 59.513 57.143 0.00 0.00 0.00 3.51
22 23 2.187958 CACAGTCCCTCTAACCATCCA 58.812 52.381 0.00 0.00 0.00 3.41
23 24 2.571653 CACAGTCCCTCTAACCATCCAA 59.428 50.000 0.00 0.00 0.00 3.53
24 25 2.572104 ACAGTCCCTCTAACCATCCAAC 59.428 50.000 0.00 0.00 0.00 3.77
25 26 2.092914 CAGTCCCTCTAACCATCCAACC 60.093 54.545 0.00 0.00 0.00 3.77
26 27 1.913419 GTCCCTCTAACCATCCAACCA 59.087 52.381 0.00 0.00 0.00 3.67
27 28 1.913419 TCCCTCTAACCATCCAACCAC 59.087 52.381 0.00 0.00 0.00 4.16
28 29 1.633432 CCCTCTAACCATCCAACCACA 59.367 52.381 0.00 0.00 0.00 4.17
29 30 2.356125 CCCTCTAACCATCCAACCACAG 60.356 54.545 0.00 0.00 0.00 3.66
30 31 2.356125 CCTCTAACCATCCAACCACAGG 60.356 54.545 0.00 0.00 0.00 4.00
31 32 2.305927 CTCTAACCATCCAACCACAGGT 59.694 50.000 0.00 0.00 37.65 4.00
86 88 5.650266 TGTAAACCTTATGTGTATGCTTGGG 59.350 40.000 0.00 0.00 0.00 4.12
90 92 5.190677 ACCTTATGTGTATGCTTGGGTAAC 58.809 41.667 0.00 0.00 0.00 2.50
109 111 2.126502 GTTTCCCACGCAATGCCG 60.127 61.111 0.00 0.00 0.00 5.69
133 135 4.957971 AGCATGACGAAAATTGTAGAACG 58.042 39.130 0.00 0.00 0.00 3.95
143 145 6.347402 CGAAAATTGTAGAACGTGACAAGGAT 60.347 38.462 14.07 5.23 38.86 3.24
151 153 1.351017 ACGTGACAAGGATGGACCAAT 59.649 47.619 0.00 0.00 42.04 3.16
168 170 3.327464 ACCAATAACTTGCAAAATGGGCT 59.673 39.130 15.66 1.97 0.00 5.19
172 174 6.037391 CCAATAACTTGCAAAATGGGCTATTG 59.963 38.462 0.00 6.25 0.00 1.90
271 276 6.677781 TTCGGAAAAATACAGATGCCTTAG 57.322 37.500 0.00 0.00 0.00 2.18
305 310 2.450476 ACATTCTTGGGCAAGGTCATC 58.550 47.619 0.00 0.00 38.88 2.92
389 2804 2.380064 TGGGTCAGGCTCAACAAATT 57.620 45.000 0.00 0.00 0.00 1.82
390 2805 2.238521 TGGGTCAGGCTCAACAAATTC 58.761 47.619 0.00 0.00 0.00 2.17
394 2809 3.346426 AGGCTCAACAAATTCGCCT 57.654 47.368 0.00 0.00 45.70 5.52
397 2812 3.782889 GGCTCAACAAATTCGCCTTAT 57.217 42.857 0.00 0.00 37.76 1.73
399 2814 3.859386 GGCTCAACAAATTCGCCTTATTG 59.141 43.478 0.00 0.00 37.76 1.90
450 2866 3.930634 GCCAAGAATTAGGCCATCATC 57.069 47.619 5.01 0.00 45.18 2.92
505 2921 6.534079 GCGAGAGTAAGCTTTGTATTTTCCTA 59.466 38.462 3.20 0.00 0.00 2.94
508 2924 8.966069 AGAGTAAGCTTTGTATTTTCCTATCC 57.034 34.615 3.20 0.00 0.00 2.59
524 2943 3.260100 CCAGGTGTTGGGCCTCCT 61.260 66.667 4.53 4.69 43.75 3.69
525 2944 2.352805 CAGGTGTTGGGCCTCCTC 59.647 66.667 4.53 0.00 33.31 3.71
526 2945 2.121963 AGGTGTTGGGCCTCCTCA 60.122 61.111 4.53 0.00 0.00 3.86
527 2946 1.774217 AGGTGTTGGGCCTCCTCAA 60.774 57.895 4.53 0.00 0.00 3.02
528 2947 1.152830 GGTGTTGGGCCTCCTCAAA 59.847 57.895 4.53 0.00 0.00 2.69
529 2948 0.469144 GGTGTTGGGCCTCCTCAAAA 60.469 55.000 4.53 0.00 0.00 2.44
530 2949 1.632589 GTGTTGGGCCTCCTCAAAAT 58.367 50.000 4.53 0.00 0.00 1.82
533 2952 3.769300 GTGTTGGGCCTCCTCAAAATAAT 59.231 43.478 4.53 0.00 0.00 1.28
540 2959 7.358263 TGGGCCTCCTCAAAATAATTAATGTA 58.642 34.615 4.53 0.00 0.00 2.29
633 3082 1.282157 GAAGGGGGCTATATCCGCAAT 59.718 52.381 11.34 0.00 40.48 3.56
712 3161 2.356844 CCCCCTAAGCTTACCTTTCCAC 60.357 54.545 0.86 0.00 34.95 4.02
726 3175 3.135348 CCTTTCCACTCATATGGCTCAGA 59.865 47.826 2.13 0.00 39.85 3.27
730 3179 2.812591 CCACTCATATGGCTCAGATTGC 59.187 50.000 2.13 0.00 31.52 3.56
742 3191 3.181516 GCTCAGATTGCAACTTACCGAAG 60.182 47.826 0.00 0.00 38.76 3.79
746 3195 5.049680 TCAGATTGCAACTTACCGAAGAAAC 60.050 40.000 0.00 0.00 36.45 2.78
815 3265 6.418226 CGAACGAAAAGAGAAGAAGAAGAAGA 59.582 38.462 0.00 0.00 0.00 2.87
819 3269 7.982354 ACGAAAAGAGAAGAAGAAGAAGAAGAA 59.018 33.333 0.00 0.00 0.00 2.52
820 3270 8.487176 CGAAAAGAGAAGAAGAAGAAGAAGAAG 58.513 37.037 0.00 0.00 0.00 2.85
821 3271 9.541143 GAAAAGAGAAGAAGAAGAAGAAGAAGA 57.459 33.333 0.00 0.00 0.00 2.87
822 3272 9.898152 AAAAGAGAAGAAGAAGAAGAAGAAGAA 57.102 29.630 0.00 0.00 0.00 2.52
823 3273 9.546428 AAAGAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
824 3274 8.477419 AGAGAAGAAGAAGAAGAAGAAGAAGA 57.523 34.615 0.00 0.00 0.00 2.87
825 3275 8.923270 AGAGAAGAAGAAGAAGAAGAAGAAGAA 58.077 33.333 0.00 0.00 0.00 2.52
826 3276 9.196552 GAGAAGAAGAAGAAGAAGAAGAAGAAG 57.803 37.037 0.00 0.00 0.00 2.85
827 3277 7.657354 AGAAGAAGAAGAAGAAGAAGAAGAAGC 59.343 37.037 0.00 0.00 0.00 3.86
828 3278 6.825610 AGAAGAAGAAGAAGAAGAAGAAGCA 58.174 36.000 0.00 0.00 0.00 3.91
829 3279 6.930722 AGAAGAAGAAGAAGAAGAAGAAGCAG 59.069 38.462 0.00 0.00 0.00 4.24
830 3280 6.418057 AGAAGAAGAAGAAGAAGAAGCAGA 57.582 37.500 0.00 0.00 0.00 4.26
831 3281 6.825610 AGAAGAAGAAGAAGAAGAAGCAGAA 58.174 36.000 0.00 0.00 0.00 3.02
832 3282 6.930722 AGAAGAAGAAGAAGAAGAAGCAGAAG 59.069 38.462 0.00 0.00 0.00 2.85
833 3283 6.418057 AGAAGAAGAAGAAGAAGCAGAAGA 57.582 37.500 0.00 0.00 0.00 2.87
834 3284 6.458210 AGAAGAAGAAGAAGAAGCAGAAGAG 58.542 40.000 0.00 0.00 0.00 2.85
835 3285 6.267471 AGAAGAAGAAGAAGAAGCAGAAGAGA 59.733 38.462 0.00 0.00 0.00 3.10
884 3334 0.181114 AGACCTGCACACAAGCAAGA 59.819 50.000 0.00 0.00 45.13 3.02
886 3336 1.280746 CCTGCACACAAGCAAGACG 59.719 57.895 0.00 0.00 45.13 4.18
887 3337 1.159713 CCTGCACACAAGCAAGACGA 61.160 55.000 0.00 0.00 45.13 4.20
888 3338 0.657312 CTGCACACAAGCAAGACGAA 59.343 50.000 0.00 0.00 45.13 3.85
889 3339 1.265095 CTGCACACAAGCAAGACGAAT 59.735 47.619 0.00 0.00 45.13 3.34
890 3340 1.264020 TGCACACAAGCAAGACGAATC 59.736 47.619 0.00 0.00 42.46 2.52
891 3341 1.264020 GCACACAAGCAAGACGAATCA 59.736 47.619 0.00 0.00 0.00 2.57
892 3342 2.908634 CACACAAGCAAGACGAATCAC 58.091 47.619 0.00 0.00 0.00 3.06
893 3343 1.873591 ACACAAGCAAGACGAATCACC 59.126 47.619 0.00 0.00 0.00 4.02
894 3344 2.146342 CACAAGCAAGACGAATCACCT 58.854 47.619 0.00 0.00 0.00 4.00
895 3345 3.244078 ACACAAGCAAGACGAATCACCTA 60.244 43.478 0.00 0.00 0.00 3.08
896 3346 3.369147 CACAAGCAAGACGAATCACCTAG 59.631 47.826 0.00 0.00 0.00 3.02
897 3347 3.006967 ACAAGCAAGACGAATCACCTAGT 59.993 43.478 0.00 0.00 0.00 2.57
898 3348 4.219944 ACAAGCAAGACGAATCACCTAGTA 59.780 41.667 0.00 0.00 0.00 1.82
899 3349 4.640789 AGCAAGACGAATCACCTAGTAG 57.359 45.455 0.00 0.00 0.00 2.57
900 3350 3.381908 AGCAAGACGAATCACCTAGTAGG 59.618 47.826 15.09 15.09 42.49 3.18
925 3401 4.653868 AGAGTAGACTATATGACCCACGG 58.346 47.826 0.00 0.00 0.00 4.94
972 3450 1.281867 CAAGGCAAGGTGAGGTATCCA 59.718 52.381 0.00 0.00 0.00 3.41
988 3466 5.073428 GGTATCCATTCCTTTCCTTCATCC 58.927 45.833 0.00 0.00 0.00 3.51
997 3475 0.623194 TTCCTTCATCCCCATCGCAA 59.377 50.000 0.00 0.00 0.00 4.85
1034 3512 2.732597 CGTCTCACGTCCTCCTCAAATC 60.733 54.545 0.00 0.00 36.74 2.17
1035 3513 2.231478 GTCTCACGTCCTCCTCAAATCA 59.769 50.000 0.00 0.00 0.00 2.57
1036 3514 2.897326 TCTCACGTCCTCCTCAAATCAA 59.103 45.455 0.00 0.00 0.00 2.57
1038 3516 4.020218 TCTCACGTCCTCCTCAAATCAAAT 60.020 41.667 0.00 0.00 0.00 2.32
1206 3700 3.692406 GAAGTCGACCCCCGCAGT 61.692 66.667 13.01 0.00 38.37 4.40
1259 3753 3.014623 TCATCGTCAACGTCTCAGGTAT 58.985 45.455 2.09 0.00 40.80 2.73
1260 3754 4.193865 TCATCGTCAACGTCTCAGGTATA 58.806 43.478 2.09 0.00 40.80 1.47
1323 3833 2.290641 ACTCGTTCCAAACATGTTCTGC 59.709 45.455 12.39 0.51 0.00 4.26
1590 4115 2.411504 GCGAGAAGAGGAGGACGCT 61.412 63.158 0.00 0.00 42.19 5.07
1594 4119 3.708220 GAAGAGGAGGACGCTGGCG 62.708 68.421 13.56 13.56 46.03 5.69
1735 4260 3.329688 CTCTGGCTCGTCGCGTTCT 62.330 63.158 5.77 0.00 40.44 3.01
1786 4311 2.440409 AGAACGAATGAGGCAAGCAAT 58.560 42.857 0.00 0.00 0.00 3.56
1861 4613 0.958382 CAGGATTTGGAACGCGGGAA 60.958 55.000 12.47 0.00 0.00 3.97
1863 4615 0.815095 GGATTTGGAACGCGGGAATT 59.185 50.000 12.47 0.00 0.00 2.17
1894 4646 4.574013 CCAAGTCTCAAGATATCAAGCACC 59.426 45.833 5.32 0.00 0.00 5.01
2004 6013 9.261180 AGTTCAATGTAACCACAGAATATATCG 57.739 33.333 0.00 0.00 38.30 2.92
2142 7268 4.425180 TGTGGTCTTGCTTACCTGTTTA 57.575 40.909 4.67 0.00 37.91 2.01
2155 7281 2.031157 ACCTGTTTACGCTTTCATGTGC 60.031 45.455 0.00 0.00 0.00 4.57
2197 7323 1.478105 TGTCTGATGGATCCAGTCACG 59.522 52.381 21.33 15.27 33.57 4.35
2206 7332 2.093447 GGATCCAGTCACGACTTTCCAT 60.093 50.000 6.95 0.00 40.20 3.41
2233 7359 4.037446 GCAAACCATTGTTGTAGGTCAAGA 59.963 41.667 0.00 0.00 38.85 3.02
2241 7367 5.640189 TGTTGTAGGTCAAGAGTAGCTAC 57.360 43.478 16.43 16.43 44.43 3.58
2248 7374 8.851541 GTAGGTCAAGAGTAGCTACAGTATAT 57.148 38.462 25.28 3.59 43.90 0.86
2280 7406 2.890311 TGCCAAAGTATCTGGGTTGTTG 59.110 45.455 0.00 0.00 34.25 3.33
2293 7419 1.883926 GGTTGTTGTCCATACACCACC 59.116 52.381 0.00 0.00 34.61 4.61
2295 7421 3.219281 GTTGTTGTCCATACACCACCTT 58.781 45.455 0.00 0.00 34.61 3.50
2296 7422 3.134574 TGTTGTCCATACACCACCTTC 57.865 47.619 0.00 0.00 34.61 3.46
2303 7429 8.875604 TTGTCCATACACCACCTTCAAAGGAG 62.876 46.154 15.63 7.48 41.30 3.69
2330 7456 6.037610 GGTTCCAAGTGATGAATGCTAGTTAG 59.962 42.308 0.00 0.00 0.00 2.34
2336 7462 6.467677 AGTGATGAATGCTAGTTAGTGTTGT 58.532 36.000 0.00 0.00 0.00 3.32
2337 7463 7.611770 AGTGATGAATGCTAGTTAGTGTTGTA 58.388 34.615 0.00 0.00 0.00 2.41
2338 7464 7.545965 AGTGATGAATGCTAGTTAGTGTTGTAC 59.454 37.037 0.00 0.00 0.00 2.90
2373 7546 3.066621 TCCACTTATTTGGATGCGCAATC 59.933 43.478 17.11 12.73 41.00 2.67
2384 7557 2.658373 TGCGCAATCATGAAGCATTT 57.342 40.000 8.16 0.00 37.00 2.32
2422 7595 9.971922 AAATTTTCAGAATAGAAAGTTCACCTG 57.028 29.630 0.00 0.00 36.72 4.00
2440 7613 5.073144 TCACCTGGAGTAATGAAAAGGACTT 59.927 40.000 0.00 0.00 0.00 3.01
2479 7652 3.644966 AGACAAAGTCTTCCACAACCA 57.355 42.857 0.00 0.00 40.28 3.67
2504 7677 0.466372 GGGATAGCTTGTTCCCCAGC 60.466 60.000 15.08 0.00 45.08 4.85
2505 7678 0.466372 GGATAGCTTGTTCCCCAGCC 60.466 60.000 0.00 0.00 0.00 4.85
2518 7691 1.449353 CCAGCCTCCTCCTACATGC 59.551 63.158 0.00 0.00 0.00 4.06
2520 7693 1.709578 CAGCCTCCTCCTACATGCTA 58.290 55.000 0.00 0.00 0.00 3.49
2527 7700 1.625818 CCTCCTACATGCTACATCCCC 59.374 57.143 0.00 0.00 0.00 4.81
2537 7710 1.279271 GCTACATCCCCTGTTGTGTCT 59.721 52.381 0.00 0.00 39.39 3.41
2546 7719 3.589988 CCCTGTTGTGTCTGATCACTAC 58.410 50.000 13.44 13.44 41.65 2.73
2549 7722 2.969262 TGTTGTGTCTGATCACTACCCA 59.031 45.455 15.78 0.00 41.01 4.51
2550 7723 3.244078 TGTTGTGTCTGATCACTACCCAC 60.244 47.826 15.78 0.00 41.01 4.61
2597 7770 3.625938 GCTGAGACAAAGCAAAGTTCAG 58.374 45.455 0.00 0.00 40.52 3.02
2600 7773 5.506982 GCTGAGACAAAGCAAAGTTCAGATT 60.507 40.000 3.02 0.00 40.52 2.40
2601 7774 6.064846 TGAGACAAAGCAAAGTTCAGATTC 57.935 37.500 0.00 0.00 0.00 2.52
2602 7775 5.100751 AGACAAAGCAAAGTTCAGATTCG 57.899 39.130 0.00 0.00 0.00 3.34
2618 7791 1.110518 TTCGAGGGGTTTTGGCCAAC 61.111 55.000 20.35 8.63 0.00 3.77
2620 7793 1.830847 GAGGGGTTTTGGCCAACGT 60.831 57.895 20.35 8.32 0.00 3.99
2635 7808 4.501071 GCCAACGTTCTCAAGGTATAAGA 58.499 43.478 0.00 0.00 0.00 2.10
2641 7814 4.806247 CGTTCTCAAGGTATAAGAAGGCAG 59.194 45.833 0.00 0.00 30.88 4.85
2643 7816 3.134804 TCTCAAGGTATAAGAAGGCAGCC 59.865 47.826 1.84 1.84 0.00 4.85
2662 7835 6.566491 CAGCCTCTGAAGCTTGGAACAAAC 62.566 50.000 2.10 0.00 38.95 2.93
2675 7848 3.565902 TGGAACAAACATGTTCGTGCATA 59.434 39.130 12.39 0.00 46.55 3.14
2712 7885 6.354102 CGCATTCAAAAATACAAAGTTGTTGC 59.646 34.615 1.35 2.33 42.35 4.17
2730 7903 2.751436 GCATGGCGAAAGGGCTCA 60.751 61.111 0.00 0.00 42.84 4.26
2731 7904 2.342650 GCATGGCGAAAGGGCTCAA 61.343 57.895 0.00 0.00 42.84 3.02
2732 7905 1.876497 GCATGGCGAAAGGGCTCAAA 61.876 55.000 0.00 0.00 42.84 2.69
2733 7906 0.819582 CATGGCGAAAGGGCTCAAAT 59.180 50.000 0.00 0.00 42.84 2.32
2734 7907 1.106285 ATGGCGAAAGGGCTCAAATC 58.894 50.000 0.00 0.00 42.84 2.17
2735 7908 0.965363 TGGCGAAAGGGCTCAAATCC 60.965 55.000 0.00 0.00 42.84 3.01
2736 7909 1.667154 GGCGAAAGGGCTCAAATCCC 61.667 60.000 0.00 0.00 44.25 3.85
2745 7918 2.785868 CTCAAATCCCGGAGCAAGG 58.214 57.895 0.73 0.00 0.00 3.61
2746 7919 0.253044 CTCAAATCCCGGAGCAAGGA 59.747 55.000 0.73 0.00 36.36 3.36
2747 7920 0.253044 TCAAATCCCGGAGCAAGGAG 59.747 55.000 0.73 0.00 35.08 3.69
2748 7921 1.077429 AAATCCCGGAGCAAGGAGC 60.077 57.895 0.73 0.00 46.19 4.70
2759 7932 2.613730 GCAAGGAGCTTTTTACCGAC 57.386 50.000 0.00 0.00 41.15 4.79
2760 7933 1.136057 GCAAGGAGCTTTTTACCGACG 60.136 52.381 0.00 0.00 41.15 5.12
2761 7934 1.136057 CAAGGAGCTTTTTACCGACGC 60.136 52.381 0.00 0.00 0.00 5.19
2762 7935 0.672711 AGGAGCTTTTTACCGACGCC 60.673 55.000 0.00 0.00 0.00 5.68
2763 7936 0.952010 GGAGCTTTTTACCGACGCCA 60.952 55.000 0.00 0.00 0.00 5.69
2764 7937 0.869730 GAGCTTTTTACCGACGCCAA 59.130 50.000 0.00 0.00 0.00 4.52
2765 7938 0.872388 AGCTTTTTACCGACGCCAAG 59.128 50.000 0.00 0.00 0.00 3.61
2766 7939 0.109919 GCTTTTTACCGACGCCAAGG 60.110 55.000 0.00 0.00 0.00 3.61
2767 7940 1.232119 CTTTTTACCGACGCCAAGGT 58.768 50.000 0.00 0.00 44.08 3.50
2768 7941 0.945813 TTTTTACCGACGCCAAGGTG 59.054 50.000 0.00 0.00 41.51 4.00
2769 7942 1.508808 TTTTACCGACGCCAAGGTGC 61.509 55.000 0.00 0.00 41.51 5.01
2770 7943 2.661840 TTTACCGACGCCAAGGTGCA 62.662 55.000 0.00 0.00 41.51 4.57
2771 7944 2.661840 TTACCGACGCCAAGGTGCAA 62.662 55.000 0.00 0.00 41.51 4.08
2772 7945 2.457743 TACCGACGCCAAGGTGCAAT 62.458 55.000 0.00 0.00 41.51 3.56
2773 7946 2.625823 CCGACGCCAAGGTGCAATT 61.626 57.895 0.00 0.00 0.00 2.32
2774 7947 1.285641 CGACGCCAAGGTGCAATTT 59.714 52.632 0.00 0.00 0.00 1.82
2775 7948 0.729140 CGACGCCAAGGTGCAATTTC 60.729 55.000 0.00 0.00 0.00 2.17
2776 7949 0.313672 GACGCCAAGGTGCAATTTCA 59.686 50.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.486726 GGATGGTTAGAGGGACTGTGG 59.513 57.143 0.00 0.00 41.55 4.17
2 3 2.187958 TGGATGGTTAGAGGGACTGTG 58.812 52.381 0.00 0.00 41.55 3.66
3 4 2.572104 GTTGGATGGTTAGAGGGACTGT 59.428 50.000 0.00 0.00 41.55 3.55
4 5 2.092914 GGTTGGATGGTTAGAGGGACTG 60.093 54.545 0.00 0.00 41.55 3.51
6 7 1.913419 TGGTTGGATGGTTAGAGGGAC 59.087 52.381 0.00 0.00 0.00 4.46
7 8 1.913419 GTGGTTGGATGGTTAGAGGGA 59.087 52.381 0.00 0.00 0.00 4.20
8 9 1.633432 TGTGGTTGGATGGTTAGAGGG 59.367 52.381 0.00 0.00 0.00 4.30
9 10 2.356125 CCTGTGGTTGGATGGTTAGAGG 60.356 54.545 0.00 0.00 0.00 3.69
10 11 2.305927 ACCTGTGGTTGGATGGTTAGAG 59.694 50.000 0.00 0.00 27.29 2.43
11 12 2.344592 ACCTGTGGTTGGATGGTTAGA 58.655 47.619 0.00 0.00 27.29 2.10
12 13 2.879103 ACCTGTGGTTGGATGGTTAG 57.121 50.000 0.00 0.00 27.29 2.34
32 33 4.382040 TTTTCACTGAAAATTGGCGAACCA 60.382 37.500 12.12 0.00 39.20 3.67
33 34 3.363341 TTCACTGAAAATTGGCGAACC 57.637 42.857 0.00 0.00 0.00 3.62
34 35 5.905480 ATTTTCACTGAAAATTGGCGAAC 57.095 34.783 19.82 0.00 46.07 3.95
86 88 2.920647 GCATTGCGTGGGAAACTGTTAC 60.921 50.000 0.00 0.00 0.00 2.50
90 92 1.080569 GGCATTGCGTGGGAAACTG 60.081 57.895 1.91 0.00 0.00 3.16
109 111 5.324697 GTTCTACAATTTTCGTCATGCTCC 58.675 41.667 0.00 0.00 0.00 4.70
133 135 4.589908 AGTTATTGGTCCATCCTTGTCAC 58.410 43.478 0.00 0.00 37.07 3.67
143 145 4.262808 CCCATTTTGCAAGTTATTGGTCCA 60.263 41.667 0.00 0.00 36.88 4.02
151 153 4.222588 AGCAATAGCCCATTTTGCAAGTTA 59.777 37.500 0.00 0.00 46.28 2.24
271 276 5.163416 CCCAAGAATGTTAATGGATCCAACC 60.163 44.000 20.67 7.42 34.82 3.77
322 327 2.159128 AGTCGACAAGCATGAGATCCAG 60.159 50.000 19.50 0.00 0.00 3.86
389 2804 2.172505 ACCACCATCATCAATAAGGCGA 59.827 45.455 0.00 0.00 0.00 5.54
390 2805 2.291465 CACCACCATCATCAATAAGGCG 59.709 50.000 0.00 0.00 0.00 5.52
394 2809 2.092699 TCGCCACCACCATCATCAATAA 60.093 45.455 0.00 0.00 0.00 1.40
397 2812 0.255604 ATCGCCACCACCATCATCAA 59.744 50.000 0.00 0.00 0.00 2.57
399 2814 0.179048 TGATCGCCACCACCATCATC 60.179 55.000 0.00 0.00 0.00 2.92
450 2866 1.377725 ACTCAAATGCCTGGCCTCG 60.378 57.895 17.53 2.03 0.00 4.63
508 2924 2.067932 TTGAGGAGGCCCAACACCTG 62.068 60.000 0.00 0.00 37.77 4.00
608 3052 3.442076 CGGATATAGCCCCCTTCTACTT 58.558 50.000 0.34 0.00 0.00 2.24
657 3106 5.071653 AGGATAAGAAGATTGAGAAGGGCTC 59.928 44.000 0.00 0.00 44.21 4.70
712 3161 4.135306 AGTTGCAATCTGAGCCATATGAG 58.865 43.478 0.59 0.00 0.00 2.90
726 3175 4.819630 TCTGTTTCTTCGGTAAGTTGCAAT 59.180 37.500 0.59 0.00 34.13 3.56
730 3179 4.378459 GGCATCTGTTTCTTCGGTAAGTTG 60.378 45.833 0.00 0.00 34.13 3.16
746 3195 9.956720 CTTCCATTTTATAACTTAAGGCATCTG 57.043 33.333 7.53 0.00 0.00 2.90
815 3265 4.937015 GCATCTCTTCTGCTTCTTCTTCTT 59.063 41.667 0.00 0.00 36.68 2.52
819 3269 3.977134 TGCATCTCTTCTGCTTCTTCT 57.023 42.857 0.00 0.00 40.34 2.85
820 3270 3.312973 CCATGCATCTCTTCTGCTTCTTC 59.687 47.826 0.00 0.00 40.34 2.87
821 3271 3.280295 CCATGCATCTCTTCTGCTTCTT 58.720 45.455 0.00 0.00 40.34 2.52
822 3272 2.239150 ACCATGCATCTCTTCTGCTTCT 59.761 45.455 0.00 0.00 40.34 2.85
823 3273 2.641305 ACCATGCATCTCTTCTGCTTC 58.359 47.619 0.00 0.00 40.34 3.86
824 3274 2.803030 ACCATGCATCTCTTCTGCTT 57.197 45.000 0.00 0.00 40.34 3.91
825 3275 2.485124 GCTACCATGCATCTCTTCTGCT 60.485 50.000 0.00 0.00 40.34 4.24
826 3276 1.872313 GCTACCATGCATCTCTTCTGC 59.128 52.381 0.00 0.00 40.10 4.26
827 3277 2.871022 GTGCTACCATGCATCTCTTCTG 59.129 50.000 0.00 0.00 45.23 3.02
828 3278 2.770802 AGTGCTACCATGCATCTCTTCT 59.229 45.455 0.00 0.00 45.23 2.85
829 3279 3.191078 AGTGCTACCATGCATCTCTTC 57.809 47.619 0.00 0.00 45.23 2.87
830 3280 3.054875 TGAAGTGCTACCATGCATCTCTT 60.055 43.478 0.00 0.00 45.23 2.85
831 3281 2.502947 TGAAGTGCTACCATGCATCTCT 59.497 45.455 0.00 0.00 45.23 3.10
832 3282 2.871022 CTGAAGTGCTACCATGCATCTC 59.129 50.000 0.00 0.00 45.23 2.75
833 3283 2.421107 CCTGAAGTGCTACCATGCATCT 60.421 50.000 0.00 0.00 45.23 2.90
834 3284 1.945394 CCTGAAGTGCTACCATGCATC 59.055 52.381 0.00 0.00 45.23 3.91
835 3285 1.409241 CCCTGAAGTGCTACCATGCAT 60.409 52.381 0.00 0.00 45.23 3.96
895 3345 8.605065 GGGTCATATAGTCTACTCTTACCTACT 58.395 40.741 0.00 0.00 0.00 2.57
896 3346 8.381636 TGGGTCATATAGTCTACTCTTACCTAC 58.618 40.741 0.00 0.00 0.00 3.18
897 3347 8.381636 GTGGGTCATATAGTCTACTCTTACCTA 58.618 40.741 0.00 0.00 0.00 3.08
898 3348 7.232910 GTGGGTCATATAGTCTACTCTTACCT 58.767 42.308 0.00 0.00 0.00 3.08
899 3349 6.149142 CGTGGGTCATATAGTCTACTCTTACC 59.851 46.154 0.00 0.00 0.00 2.85
900 3350 6.149142 CCGTGGGTCATATAGTCTACTCTTAC 59.851 46.154 0.00 0.00 0.00 2.34
901 3351 6.043590 TCCGTGGGTCATATAGTCTACTCTTA 59.956 42.308 0.00 0.00 0.00 2.10
902 3352 5.071370 CCGTGGGTCATATAGTCTACTCTT 58.929 45.833 0.00 0.00 0.00 2.85
906 3356 8.921353 ATATATCCGTGGGTCATATAGTCTAC 57.079 38.462 0.00 0.00 0.00 2.59
925 3401 8.706936 CCGACAGCATGCTGAAATATATATATC 58.293 37.037 45.50 28.41 46.30 1.63
972 3450 3.435601 CGATGGGGATGAAGGAAAGGAAT 60.436 47.826 0.00 0.00 0.00 3.01
997 3475 7.883217 ACGTGAGACGAAAGATATACCATATT 58.117 34.615 2.62 0.00 46.05 1.28
1099 3589 1.712081 CTTGAATGCGAGCCGAGTG 59.288 57.895 0.00 0.00 0.00 3.51
1180 3674 1.215647 GGTCGACTTCAGCCACGAT 59.784 57.895 16.46 0.00 37.14 3.73
1246 3740 2.416431 GCAACGGTATACCTGAGACGTT 60.416 50.000 19.68 13.64 44.15 3.99
1259 3753 1.335496 GTTGGAAAAGCAGCAACGGTA 59.665 47.619 0.00 0.00 0.00 4.02
1260 3754 0.102300 GTTGGAAAAGCAGCAACGGT 59.898 50.000 0.00 0.00 0.00 4.83
1323 3833 0.041047 CGGCATGCGTGTCAATATGG 60.041 55.000 12.44 0.00 0.00 2.74
1548 4073 1.079750 GTCCTCTTGGCTGTCGTCC 60.080 63.158 0.00 0.00 0.00 4.79
1735 4260 1.962822 CGCTCTGCTTGCTGTTGGA 60.963 57.895 0.00 0.00 0.00 3.53
1786 4311 3.252964 GCTGTGCGTGCATGTGTA 58.747 55.556 7.93 0.00 0.00 2.90
1863 4615 9.519191 TTGATATCTTGAGACTTGGATTTGAAA 57.481 29.630 3.98 0.00 0.00 2.69
2004 6013 5.627780 CGTGCAAGTTTTATGGACCTTAAAC 59.372 40.000 11.17 9.41 35.93 2.01
2063 6925 1.290203 CCGTATGTCCAGACACATGC 58.710 55.000 1.88 0.00 45.05 4.06
2085 6949 5.346281 GGAGATCGTGTGTTTCTCAAACTAG 59.654 44.000 0.00 0.00 41.90 2.57
2125 6989 3.064931 AGCGTAAACAGGTAAGCAAGAC 58.935 45.455 0.00 0.00 31.72 3.01
2126 6990 3.396260 AGCGTAAACAGGTAAGCAAGA 57.604 42.857 0.00 0.00 31.72 3.02
2142 7268 1.265095 CTCAACAGCACATGAAAGCGT 59.735 47.619 0.00 1.03 35.48 5.07
2197 7323 4.525912 ATGGTTTGCTTCATGGAAAGTC 57.474 40.909 0.00 0.00 36.67 3.01
2206 7332 3.957497 ACCTACAACAATGGTTTGCTTCA 59.043 39.130 0.00 0.00 36.22 3.02
2248 7374 7.014518 CCCAGATACTTTGGCATTTCATATTCA 59.985 37.037 0.00 0.00 34.26 2.57
2268 7394 3.561313 GGTGTATGGACAACAACCCAGAT 60.561 47.826 0.00 0.00 43.33 2.90
2280 7406 3.081804 CCTTTGAAGGTGGTGTATGGAC 58.918 50.000 1.49 0.00 41.41 4.02
2293 7419 3.817647 CACTTGGAACCTCTCCTTTGAAG 59.182 47.826 0.00 0.00 45.64 3.02
2295 7421 3.045634 TCACTTGGAACCTCTCCTTTGA 58.954 45.455 0.00 0.00 45.64 2.69
2296 7422 3.492102 TCACTTGGAACCTCTCCTTTG 57.508 47.619 0.00 0.00 45.64 2.77
2303 7429 3.350833 AGCATTCATCACTTGGAACCTC 58.649 45.455 0.00 0.00 0.00 3.85
2336 7462 3.306472 AGTGGAGCAAAAGGTTTGGTA 57.694 42.857 5.48 0.00 0.00 3.25
2337 7463 2.159179 AGTGGAGCAAAAGGTTTGGT 57.841 45.000 5.18 5.18 0.00 3.67
2338 7464 4.871933 ATAAGTGGAGCAAAAGGTTTGG 57.128 40.909 3.12 0.00 0.00 3.28
2373 7546 7.697352 TTAGTGTTGTTTGAAATGCTTCATG 57.303 32.000 0.00 0.00 41.22 3.07
2422 7595 3.939592 CGGGAAGTCCTTTTCATTACTCC 59.060 47.826 0.00 0.00 35.95 3.85
2440 7613 2.105134 TCTAAAGCAACCAAAGTCGGGA 59.895 45.455 0.00 0.00 0.00 5.14
2479 7652 2.659428 GGAACAAGCTATCCCAAGCAT 58.341 47.619 0.00 0.00 45.30 3.79
2501 7674 1.342819 GTAGCATGTAGGAGGAGGCTG 59.657 57.143 0.00 0.00 33.10 4.85
2504 7677 2.564947 GGATGTAGCATGTAGGAGGAGG 59.435 54.545 0.00 0.00 0.00 4.30
2505 7678 2.564947 GGGATGTAGCATGTAGGAGGAG 59.435 54.545 0.00 0.00 0.00 3.69
2518 7691 2.567169 TCAGACACAACAGGGGATGTAG 59.433 50.000 0.00 0.00 43.00 2.74
2520 7693 1.434188 TCAGACACAACAGGGGATGT 58.566 50.000 0.00 0.00 46.97 3.06
2527 7700 3.006859 TGGGTAGTGATCAGACACAACAG 59.993 47.826 9.67 0.00 42.45 3.16
2546 7719 0.679002 CATTGGAGAGCACCAGTGGG 60.679 60.000 15.21 3.56 41.73 4.61
2549 7722 1.001641 GGCATTGGAGAGCACCAGT 60.002 57.895 0.00 0.00 41.19 4.00
2550 7723 1.001764 TGGCATTGGAGAGCACCAG 60.002 57.895 0.00 0.00 41.19 4.00
2579 7752 5.050091 TCGAATCTGAACTTTGCTTTGTCTC 60.050 40.000 0.00 0.00 0.00 3.36
2597 7770 0.610785 TGGCCAAAACCCCTCGAATC 60.611 55.000 0.61 0.00 0.00 2.52
2600 7773 1.529713 GTTGGCCAAAACCCCTCGA 60.530 57.895 22.47 0.00 0.00 4.04
2601 7774 2.914908 CGTTGGCCAAAACCCCTCG 61.915 63.158 22.47 14.02 0.00 4.63
2602 7775 1.396607 AACGTTGGCCAAAACCCCTC 61.397 55.000 22.47 4.67 0.00 4.30
2618 7791 4.755411 TGCCTTCTTATACCTTGAGAACG 58.245 43.478 0.00 0.00 0.00 3.95
2620 7793 4.384208 GGCTGCCTTCTTATACCTTGAGAA 60.384 45.833 12.43 0.00 0.00 2.87
2635 7808 0.608582 CAAGCTTCAGAGGCTGCCTT 60.609 55.000 24.26 10.04 40.19 4.35
2641 7814 1.609208 TTGTTCCAAGCTTCAGAGGC 58.391 50.000 0.00 0.00 0.00 4.70
2643 7816 4.037208 ACATGTTTGTTCCAAGCTTCAGAG 59.963 41.667 0.00 0.00 29.55 3.35
2662 7835 0.587242 GCGCACTATGCACGAACATG 60.587 55.000 0.30 0.00 45.36 3.21
2682 7855 5.752955 ACTTTGTATTTTTGAATGCGCAGTT 59.247 32.000 18.32 10.58 0.00 3.16
2683 7856 5.288804 ACTTTGTATTTTTGAATGCGCAGT 58.711 33.333 18.32 15.17 0.00 4.40
2684 7857 5.827568 ACTTTGTATTTTTGAATGCGCAG 57.172 34.783 18.32 0.00 0.00 5.18
2685 7858 5.521735 ACAACTTTGTATTTTTGAATGCGCA 59.478 32.000 14.96 14.96 40.16 6.09
2686 7859 5.973158 ACAACTTTGTATTTTTGAATGCGC 58.027 33.333 0.00 0.00 40.16 6.09
2687 7860 6.354102 GCAACAACTTTGTATTTTTGAATGCG 59.646 34.615 0.00 0.00 41.31 4.73
2688 7861 6.354102 CGCAACAACTTTGTATTTTTGAATGC 59.646 34.615 0.00 0.00 41.31 3.56
2689 7862 6.354102 GCGCAACAACTTTGTATTTTTGAATG 59.646 34.615 0.30 0.00 41.31 2.67
2730 7903 1.077429 GCTCCTTGCTCCGGGATTT 60.077 57.895 0.00 0.00 38.95 2.17
2731 7904 2.592308 GCTCCTTGCTCCGGGATT 59.408 61.111 0.00 0.00 38.95 3.01
2740 7913 1.136057 CGTCGGTAAAAAGCTCCTTGC 60.136 52.381 0.00 0.00 43.29 4.01
2741 7914 1.136057 GCGTCGGTAAAAAGCTCCTTG 60.136 52.381 0.00 0.00 0.00 3.61
2742 7915 1.154197 GCGTCGGTAAAAAGCTCCTT 58.846 50.000 0.00 0.00 0.00 3.36
2743 7916 0.672711 GGCGTCGGTAAAAAGCTCCT 60.673 55.000 0.00 0.00 0.00 3.69
2744 7917 0.952010 TGGCGTCGGTAAAAAGCTCC 60.952 55.000 0.00 0.00 0.00 4.70
2745 7918 0.869730 TTGGCGTCGGTAAAAAGCTC 59.130 50.000 0.00 0.00 0.00 4.09
2746 7919 0.872388 CTTGGCGTCGGTAAAAAGCT 59.128 50.000 0.00 0.00 0.00 3.74
2747 7920 0.109919 CCTTGGCGTCGGTAAAAAGC 60.110 55.000 0.00 0.00 0.00 3.51
2748 7921 1.069500 CACCTTGGCGTCGGTAAAAAG 60.069 52.381 0.00 0.00 30.91 2.27
2749 7922 0.945813 CACCTTGGCGTCGGTAAAAA 59.054 50.000 0.00 0.00 30.91 1.94
2750 7923 1.508808 GCACCTTGGCGTCGGTAAAA 61.509 55.000 0.00 0.00 30.91 1.52
2751 7924 1.962306 GCACCTTGGCGTCGGTAAA 60.962 57.895 0.00 0.00 30.91 2.01
2752 7925 2.357760 GCACCTTGGCGTCGGTAA 60.358 61.111 0.00 0.00 30.91 2.85
2753 7926 2.457743 ATTGCACCTTGGCGTCGGTA 62.458 55.000 0.00 0.00 36.28 4.02
2754 7927 3.842925 ATTGCACCTTGGCGTCGGT 62.843 57.895 0.00 0.00 36.28 4.69
2755 7928 2.141122 AAATTGCACCTTGGCGTCGG 62.141 55.000 0.00 0.00 36.28 4.79
2756 7929 0.729140 GAAATTGCACCTTGGCGTCG 60.729 55.000 0.00 0.00 36.28 5.12
2757 7930 0.313672 TGAAATTGCACCTTGGCGTC 59.686 50.000 0.00 0.00 36.28 5.19
2758 7931 2.424474 TGAAATTGCACCTTGGCGT 58.576 47.368 0.00 0.00 36.28 5.68


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

AutoCloner maintained by Alex Coulton.