Multiple sequence alignment - TraesCS2D01G279000

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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 TraesCS2D01G279000 chr2D 100.000 5194 0 0 1 5194 350598673 350603866 0.000000e+00 9592.0
1 TraesCS2D01G279000 chr2B 96.854 4101 87 19 773 4861 416503111 416507181 0.000000e+00 6820.0
2 TraesCS2D01G279000 chr2B 94.872 156 7 1 4938 5092 416507185 416507340 5.200000e-60 243.0
3 TraesCS2D01G279000 chr2A 94.063 2594 90 25 815 3374 467691514 467694077 0.000000e+00 3879.0
4 TraesCS2D01G279000 chr2A 95.750 1247 37 14 3919 5158 467695062 467696299 0.000000e+00 1995.0
5 TraesCS2D01G279000 chr2A 96.500 600 19 2 3326 3924 467694073 467694671 0.000000e+00 990.0
6 TraesCS2D01G279000 chr2A 86.744 430 52 3 350 776 61823974 61823547 1.690000e-129 473.0
7 TraesCS2D01G279000 chr2A 88.142 253 26 2 4943 5192 768985080 768985331 1.090000e-76 298.0
8 TraesCS2D01G279000 chr7A 86.903 901 94 18 3416 4312 33511841 33512721 0.000000e+00 989.0
9 TraesCS2D01G279000 chr7A 85.541 823 98 14 3512 4330 130083290 130082485 0.000000e+00 841.0
10 TraesCS2D01G279000 chr7A 84.479 844 100 19 3512 4330 316026823 316027660 0.000000e+00 804.0
11 TraesCS2D01G279000 chr5A 85.888 822 94 15 3512 4328 353160944 353160140 0.000000e+00 856.0
12 TraesCS2D01G279000 chr7D 85.528 843 92 20 3511 4330 279735912 279735077 0.000000e+00 854.0
13 TraesCS2D01G279000 chr7D 73.536 461 109 13 321 775 167576002 167576455 4.160000e-36 163.0
14 TraesCS2D01G279000 chr5B 84.275 903 98 28 3416 4312 123206138 123207002 0.000000e+00 841.0
15 TraesCS2D01G279000 chr5B 83.942 903 100 26 3416 4312 123406473 123407336 0.000000e+00 822.0
16 TraesCS2D01G279000 chr3A 86.269 772 103 3 5 775 647157259 647158028 0.000000e+00 835.0
17 TraesCS2D01G279000 chr1D 86.305 774 93 7 5 775 13006850 13006087 0.000000e+00 830.0
18 TraesCS2D01G279000 chr4A 84.267 839 101 22 3512 4330 740771287 740772114 0.000000e+00 789.0
19 TraesCS2D01G279000 chr6A 85.592 583 82 1 193 775 613386401 613386981 1.240000e-170 610.0
20 TraesCS2D01G279000 chr3D 90.157 254 20 3 4943 5192 475296918 475296666 5.020000e-85 326.0
21 TraesCS2D01G279000 chr4D 83.908 87 11 2 2874 2957 9998416 9998502 4.310000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G279000 chr2D 350598673 350603866 5193 False 9592.0 9592 100.000000 1 5194 1 chr2D.!!$F1 5193
1 TraesCS2D01G279000 chr2B 416503111 416507340 4229 False 3531.5 6820 95.863000 773 5092 2 chr2B.!!$F1 4319
2 TraesCS2D01G279000 chr2A 467691514 467696299 4785 False 2288.0 3879 95.437667 815 5158 3 chr2A.!!$F2 4343
3 TraesCS2D01G279000 chr7A 33511841 33512721 880 False 989.0 989 86.903000 3416 4312 1 chr7A.!!$F1 896
4 TraesCS2D01G279000 chr7A 130082485 130083290 805 True 841.0 841 85.541000 3512 4330 1 chr7A.!!$R1 818
5 TraesCS2D01G279000 chr7A 316026823 316027660 837 False 804.0 804 84.479000 3512 4330 1 chr7A.!!$F2 818
6 TraesCS2D01G279000 chr5A 353160140 353160944 804 True 856.0 856 85.888000 3512 4328 1 chr5A.!!$R1 816
7 TraesCS2D01G279000 chr7D 279735077 279735912 835 True 854.0 854 85.528000 3511 4330 1 chr7D.!!$R1 819
8 TraesCS2D01G279000 chr5B 123206138 123207002 864 False 841.0 841 84.275000 3416 4312 1 chr5B.!!$F1 896
9 TraesCS2D01G279000 chr5B 123406473 123407336 863 False 822.0 822 83.942000 3416 4312 1 chr5B.!!$F2 896
10 TraesCS2D01G279000 chr3A 647157259 647158028 769 False 835.0 835 86.269000 5 775 1 chr3A.!!$F1 770
11 TraesCS2D01G279000 chr1D 13006087 13006850 763 True 830.0 830 86.305000 5 775 1 chr1D.!!$R1 770
12 TraesCS2D01G279000 chr4A 740771287 740772114 827 False 789.0 789 84.267000 3512 4330 1 chr4A.!!$F1 818
13 TraesCS2D01G279000 chr6A 613386401 613386981 580 False 610.0 610 85.592000 193 775 1 chr6A.!!$F1 582

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
315 317 0.118346 TTGTAGAGGAAGGGGCTGGA 59.882 55.000 0.00 0.0 0.00 3.86 F
317 319 0.325765 GTAGAGGAAGGGGCTGGAGT 60.326 60.000 0.00 0.0 0.00 3.85 F
335 337 1.070758 AGTCTCGGCGGCAATAATCAT 59.929 47.619 10.53 0.0 0.00 2.45 F
624 627 1.192793 GCTCTGCGAACTAAGTAGCG 58.807 55.000 0.00 0.0 0.00 4.26 F
2283 2299 1.228429 CTGGCCAAAAGGGTTCCGA 60.228 57.895 7.01 0.0 39.65 4.55 F
3041 3060 0.670162 ATGTGTGCCTGAACTTGTGC 59.330 50.000 0.00 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2241 2257 1.172175 CCCTTGCTGAGAGCTTTTCC 58.828 55.000 0.00 0.0 42.97 3.13 R
2581 2597 3.614092 TCAGTTCCAGCCATTGATCTTC 58.386 45.455 0.00 0.0 0.00 2.87 R
2693 2709 7.256286 AGTGTTAATGATACTCTGTACGGAAC 58.744 38.462 5.76 0.0 0.00 3.62 R
2850 2867 6.978343 TGCACAACATGTTATCCTAGTAAC 57.022 37.500 11.53 1.0 35.60 2.50 R
3826 3919 1.888512 GTGAGAAGCCAAGAAATGCCA 59.111 47.619 0.00 0.0 0.00 4.92 R
5166 5694 0.464036 TGGAGCGAAACATCGGCTAT 59.536 50.000 0.07 0.0 0.00 2.97 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
25 26 2.649312 TCAGGATTGGTGGTCTTGGAAT 59.351 45.455 0.00 0.00 0.00 3.01
27 28 3.947834 CAGGATTGGTGGTCTTGGAATAC 59.052 47.826 0.00 0.00 0.00 1.89
31 32 4.447138 TTGGTGGTCTTGGAATACTTGT 57.553 40.909 0.00 0.00 0.00 3.16
34 35 5.205056 TGGTGGTCTTGGAATACTTGTTTT 58.795 37.500 0.00 0.00 0.00 2.43
36 37 6.834451 TGGTGGTCTTGGAATACTTGTTTTTA 59.166 34.615 0.00 0.00 0.00 1.52
38 39 6.861572 GTGGTCTTGGAATACTTGTTTTTAGC 59.138 38.462 0.00 0.00 0.00 3.09
50 51 4.553330 TGTTTTTAGCGGAGGAGAGATT 57.447 40.909 0.00 0.00 0.00 2.40
55 56 1.327303 AGCGGAGGAGAGATTGCTAG 58.673 55.000 0.00 0.00 0.00 3.42
56 57 1.133637 AGCGGAGGAGAGATTGCTAGA 60.134 52.381 0.00 0.00 0.00 2.43
69 70 4.762251 AGATTGCTAGACTTGAAACCCAAC 59.238 41.667 0.00 0.00 0.00 3.77
75 76 1.954382 GACTTGAAACCCAACCTGGAC 59.046 52.381 0.00 0.00 40.96 4.02
78 79 2.286365 TGAAACCCAACCTGGACATC 57.714 50.000 0.00 0.00 40.96 3.06
81 82 2.292828 AACCCAACCTGGACATCAAG 57.707 50.000 0.00 0.00 40.96 3.02
84 85 1.619654 CCAACCTGGACATCAAGCAA 58.380 50.000 0.00 0.00 40.96 3.91
88 89 2.450476 ACCTGGACATCAAGCAAATCC 58.550 47.619 0.00 0.00 0.00 3.01
111 112 2.026822 AGCAGTTGGGAGTTGGTATCTG 60.027 50.000 0.00 0.00 0.00 2.90
122 123 2.238646 GTTGGTATCTGTGGTGGATCCA 59.761 50.000 11.44 11.44 45.01 3.41
138 139 3.617263 GGATCCAACGACAACATACTCAC 59.383 47.826 6.95 0.00 0.00 3.51
141 142 2.661675 CCAACGACAACATACTCACGAG 59.338 50.000 0.00 0.00 0.00 4.18
147 148 2.631062 ACAACATACTCACGAGGGAACA 59.369 45.455 0.00 0.00 0.00 3.18
177 178 2.606587 GGTGAGGTGGCCCATGTCT 61.607 63.158 0.00 0.00 0.00 3.41
185 186 0.982852 TGGCCCATGTCTGTCCTAGG 60.983 60.000 0.82 0.82 0.00 3.02
186 187 0.983378 GGCCCATGTCTGTCCTAGGT 60.983 60.000 9.08 0.00 0.00 3.08
195 196 7.335627 CCATGTCTGTCCTAGGTATTACAAAA 58.664 38.462 9.08 0.00 0.00 2.44
219 220 4.589216 TTTCCATCAAGCAAACTCAAGG 57.411 40.909 0.00 0.00 0.00 3.61
224 225 4.021719 CCATCAAGCAAACTCAAGGAACAT 60.022 41.667 0.00 0.00 0.00 2.71
229 230 3.882888 AGCAAACTCAAGGAACATCGAAA 59.117 39.130 0.00 0.00 0.00 3.46
236 237 2.656560 AGGAACATCGAAACGAGAGG 57.343 50.000 0.00 0.00 39.91 3.69
243 244 2.178912 TCGAAACGAGAGGGCAAAAT 57.821 45.000 0.00 0.00 0.00 1.82
247 248 1.256812 AACGAGAGGGCAAAATTGGG 58.743 50.000 0.00 0.00 0.00 4.12
249 250 1.256812 CGAGAGGGCAAAATTGGGTT 58.743 50.000 0.00 0.00 0.00 4.11
270 271 5.364778 GTTAAGCCCAATCCAAAGTTTGTT 58.635 37.500 14.36 0.47 0.00 2.83
273 274 5.213891 AGCCCAATCCAAAGTTTGTTAAG 57.786 39.130 14.36 0.00 0.00 1.85
274 275 4.653801 AGCCCAATCCAAAGTTTGTTAAGT 59.346 37.500 14.36 0.00 0.00 2.24
298 300 9.252962 AGTTAAATGTTGATGCTTCTTTCTTTG 57.747 29.630 0.88 0.00 0.00 2.77
303 305 7.194607 TGTTGATGCTTCTTTCTTTGTAGAG 57.805 36.000 0.88 0.00 0.00 2.43
310 312 4.910458 TCTTTCTTTGTAGAGGAAGGGG 57.090 45.455 0.00 0.00 0.00 4.79
315 317 0.118346 TTGTAGAGGAAGGGGCTGGA 59.882 55.000 0.00 0.00 0.00 3.86
317 319 0.325765 GTAGAGGAAGGGGCTGGAGT 60.326 60.000 0.00 0.00 0.00 3.85
328 330 4.069232 CTGGAGTCTCGGCGGCAA 62.069 66.667 10.53 0.00 0.00 4.52
335 337 1.070758 AGTCTCGGCGGCAATAATCAT 59.929 47.619 10.53 0.00 0.00 2.45
336 338 2.299013 AGTCTCGGCGGCAATAATCATA 59.701 45.455 10.53 0.00 0.00 2.15
378 381 6.992664 TTGGCAGCCCAATGTAAATATATT 57.007 33.333 9.64 0.00 46.01 1.28
381 384 5.480073 GGCAGCCCAATGTAAATATATTCCA 59.520 40.000 0.00 0.00 0.00 3.53
402 405 1.237533 ATGCGCTTGATGTTGTCACA 58.762 45.000 9.73 0.00 36.32 3.58
426 429 1.244019 AAGCGTTGGCAATGAGGGAC 61.244 55.000 23.09 4.84 43.41 4.46
428 431 1.671054 CGTTGGCAATGAGGGACGT 60.671 57.895 14.26 0.00 0.00 4.34
453 456 6.547141 TCCTCATATTTGCTAATTCACTTGGG 59.453 38.462 0.00 0.00 0.00 4.12
498 501 9.201127 GAATCAGATTCATCTATTGTGATCGAA 57.799 33.333 17.07 0.00 39.09 3.71
501 504 9.631452 TCAGATTCATCTATTGTGATCGAATAC 57.369 33.333 0.00 0.00 34.85 1.89
539 542 2.158623 TCTGGAGGAATGTTGCAACAGT 60.159 45.455 33.44 32.09 43.04 3.55
543 546 4.832266 TGGAGGAATGTTGCAACAGTAATT 59.168 37.500 33.44 23.86 43.04 1.40
550 553 4.424626 TGTTGCAACAGTAATTTTCGCAA 58.575 34.783 27.96 0.00 35.68 4.85
576 579 2.345641 CGTGGACGTGTCTTCATTGATC 59.654 50.000 0.00 0.00 34.11 2.92
587 590 4.571176 GTCTTCATTGATCGGGAAGGTTAC 59.429 45.833 16.20 7.65 38.78 2.50
588 591 3.173668 TCATTGATCGGGAAGGTTACG 57.826 47.619 0.00 0.00 0.00 3.18
591 594 2.660189 TGATCGGGAAGGTTACGTTC 57.340 50.000 9.04 9.04 0.00 3.95
597 600 2.809696 CGGGAAGGTTACGTTCAAACAT 59.190 45.455 17.66 0.00 30.94 2.71
609 612 3.546020 CGTTCAAACATTGTGTTCGCTCT 60.546 43.478 0.00 0.00 40.14 4.09
624 627 1.192793 GCTCTGCGAACTAAGTAGCG 58.807 55.000 0.00 0.00 0.00 4.26
687 690 2.038952 CACTTGGACTGATGAACCTCCA 59.961 50.000 0.00 0.00 0.00 3.86
688 691 2.711009 ACTTGGACTGATGAACCTCCAA 59.289 45.455 0.00 0.00 39.90 3.53
689 692 3.331889 ACTTGGACTGATGAACCTCCAAT 59.668 43.478 0.00 0.00 41.05 3.16
694 697 4.082125 GACTGATGAACCTCCAATTTGGT 58.918 43.478 14.98 0.00 39.03 3.67
696 699 4.281688 ACTGATGAACCTCCAATTTGGTTG 59.718 41.667 14.98 9.77 45.48 3.77
708 711 4.813027 CAATTTGGTTGGTCTCCAAGATG 58.187 43.478 1.16 0.00 44.82 2.90
800 803 9.838339 ACTTTGTATTATATTCCCAAGTCTCAG 57.162 33.333 0.00 0.00 0.00 3.35
1184 1196 2.099652 TTGACACGGCTCCCTCTGTG 62.100 60.000 1.56 1.56 46.13 3.66
1373 1385 4.260743 CGTGATGTGTGTTGTTTGTCTGAT 60.261 41.667 0.00 0.00 0.00 2.90
1374 1386 5.581605 GTGATGTGTGTTGTTTGTCTGATT 58.418 37.500 0.00 0.00 0.00 2.57
1385 1397 7.652909 TGTTGTTTGTCTGATTGATGGAAATTC 59.347 33.333 0.00 0.00 0.00 2.17
1492 1504 2.472695 ATTGCAGCGTAGGTTTCTGA 57.527 45.000 0.00 0.00 33.74 3.27
1500 1512 5.360591 CAGCGTAGGTTTCTGAATAATCCT 58.639 41.667 0.00 0.77 33.74 3.24
1501 1513 5.817816 CAGCGTAGGTTTCTGAATAATCCTT 59.182 40.000 8.44 0.00 33.74 3.36
1505 1517 7.484959 GCGTAGGTTTCTGAATAATCCTTTTTG 59.515 37.037 8.44 1.64 32.17 2.44
1973 1988 4.501571 GGGATCTATAGTTCTTGCGAGCAA 60.502 45.833 10.28 10.28 0.00 3.91
2043 2058 6.578691 GCGTATTGATTTCTTGACGTATACC 58.421 40.000 0.00 0.00 33.05 2.73
2183 2198 6.717084 CCTTTTATTTTGGCCCCATTTAACAA 59.283 34.615 0.00 0.00 0.00 2.83
2241 2257 3.818961 TTTGCGATTCAAGCTTCAGAG 57.181 42.857 0.00 0.00 35.84 3.35
2283 2299 1.228429 CTGGCCAAAAGGGTTCCGA 60.228 57.895 7.01 0.00 39.65 4.55
2406 2422 2.988493 CAAGGCGTGAAAATGTTGATGG 59.012 45.455 0.00 0.00 0.00 3.51
2581 2597 3.355378 TGGTGGTTGATGAATAGCTTGG 58.645 45.455 0.00 0.00 0.00 3.61
2693 2709 5.702865 TGCTTAGCTTGCTATGTTTTTCTG 58.297 37.500 5.60 0.00 0.00 3.02
2746 2763 9.950496 GATCCTGGTGATATATTTGTCTACATT 57.050 33.333 0.00 0.00 32.41 2.71
2850 2867 5.066593 AGAACAGCTTTCTTCCTACAAAGG 58.933 41.667 5.61 0.00 45.21 3.11
3041 3060 0.670162 ATGTGTGCCTGAACTTGTGC 59.330 50.000 0.00 0.00 0.00 4.57
3042 3061 1.009675 GTGTGCCTGAACTTGTGCG 60.010 57.895 0.00 0.00 0.00 5.34
3239 3258 3.190439 ACCTCTGCCCTAGTTAACCAAT 58.810 45.455 0.88 0.00 0.00 3.16
3382 3465 5.406780 CACGTCTCTAGTTTGCTTCAATTCT 59.593 40.000 0.00 0.00 0.00 2.40
3383 3466 5.406780 ACGTCTCTAGTTTGCTTCAATTCTG 59.593 40.000 0.00 0.00 0.00 3.02
3384 3467 5.163913 CGTCTCTAGTTTGCTTCAATTCTGG 60.164 44.000 0.00 0.00 0.00 3.86
3490 3576 3.769300 AGTAAGCTTGCTTATTTTGGGGG 59.231 43.478 11.70 0.00 0.00 5.40
3510 3596 5.476945 GGGGGATGTGTGATATACCATTTTC 59.523 44.000 0.00 0.00 29.47 2.29
3567 3654 8.110860 TGATCTAACATCTTTTCTTTTGGGAC 57.889 34.615 0.00 0.00 0.00 4.46
3755 3845 2.668457 CCTACGTCACATGACTGAAAGC 59.332 50.000 10.18 0.00 42.66 3.51
3826 3919 7.040823 TGCCGGATCTTTAATTTTGCAAAAATT 60.041 29.630 27.10 21.36 34.55 1.82
4351 4871 7.539712 TGTAAGATTATTAGACTGCTGTTGC 57.460 36.000 0.00 0.00 40.20 4.17
4482 5004 4.846779 TTTCATTGGAAACTGGCACTAC 57.153 40.909 0.00 0.00 38.07 2.73
4696 5220 3.935203 TCTCAGAAAATTAAGCAGCCTCG 59.065 43.478 0.00 0.00 0.00 4.63
4711 5237 0.389166 CCTCGGCTCACAGTCTTGTC 60.389 60.000 0.00 0.00 34.62 3.18
4861 5388 1.852157 TGCTTCATCCCAGGGTGGT 60.852 57.895 5.01 0.00 35.17 4.16
4863 5390 1.221840 CTTCATCCCAGGGTGGTCG 59.778 63.158 5.01 0.00 35.17 4.79
4864 5391 1.537889 TTCATCCCAGGGTGGTCGT 60.538 57.895 5.01 0.00 35.17 4.34
4870 5397 1.301716 CCAGGGTGGTCGTTGTCTG 60.302 63.158 0.00 0.00 31.35 3.51
5100 5628 3.879892 GAGTGGGATGCCTCATTAGTTTC 59.120 47.826 4.35 0.00 0.00 2.78
5106 5634 4.394920 GGATGCCTCATTAGTTTCACGAAA 59.605 41.667 0.00 0.00 0.00 3.46
5144 5672 7.832473 TCTATAGATCCTACCATACCAGTCT 57.168 40.000 0.00 0.00 0.00 3.24
5158 5686 6.316390 CCATACCAGTCTGGATAAAAACAGTC 59.684 42.308 26.18 0.00 40.96 3.51
5159 5687 5.568620 ACCAGTCTGGATAAAAACAGTCT 57.431 39.130 26.18 0.00 40.96 3.24
5160 5688 5.308825 ACCAGTCTGGATAAAAACAGTCTG 58.691 41.667 26.18 10.50 44.70 3.51
5161 5689 4.154918 CCAGTCTGGATAAAAACAGTCTGC 59.845 45.833 14.26 0.00 44.17 4.26
5162 5690 3.997021 AGTCTGGATAAAAACAGTCTGCG 59.003 43.478 0.00 0.00 33.10 5.18
5163 5691 3.746492 GTCTGGATAAAAACAGTCTGCGT 59.254 43.478 0.00 0.00 36.17 5.24
5164 5692 4.927425 GTCTGGATAAAAACAGTCTGCGTA 59.073 41.667 0.00 0.00 36.17 4.42
5165 5693 5.062308 GTCTGGATAAAAACAGTCTGCGTAG 59.938 44.000 0.00 0.00 36.17 3.51
5166 5694 5.047590 TCTGGATAAAAACAGTCTGCGTAGA 60.048 40.000 0.00 0.00 36.17 2.59
5167 5695 5.730550 TGGATAAAAACAGTCTGCGTAGAT 58.269 37.500 6.47 0.00 34.94 1.98
5168 5696 6.869695 TGGATAAAAACAGTCTGCGTAGATA 58.130 36.000 6.47 0.00 34.94 1.98
5169 5697 6.978659 TGGATAAAAACAGTCTGCGTAGATAG 59.021 38.462 6.47 5.08 34.94 2.08
5170 5698 6.074249 GGATAAAAACAGTCTGCGTAGATAGC 60.074 42.308 6.47 0.00 34.94 2.97
5171 5699 2.873133 AACAGTCTGCGTAGATAGCC 57.127 50.000 6.47 0.00 34.94 3.93
5172 5700 0.663688 ACAGTCTGCGTAGATAGCCG 59.336 55.000 6.47 0.00 34.94 5.52
5173 5701 0.945099 CAGTCTGCGTAGATAGCCGA 59.055 55.000 6.47 0.00 34.94 5.54
5174 5702 1.537638 CAGTCTGCGTAGATAGCCGAT 59.462 52.381 6.47 0.00 34.94 4.18
5175 5703 1.537638 AGTCTGCGTAGATAGCCGATG 59.462 52.381 6.47 0.00 34.94 3.84
5176 5704 1.267261 GTCTGCGTAGATAGCCGATGT 59.733 52.381 6.47 0.00 34.94 3.06
5177 5705 1.954382 TCTGCGTAGATAGCCGATGTT 59.046 47.619 0.00 0.00 0.00 2.71
5178 5706 2.361119 TCTGCGTAGATAGCCGATGTTT 59.639 45.455 0.00 0.00 0.00 2.83
5179 5707 2.726760 CTGCGTAGATAGCCGATGTTTC 59.273 50.000 0.00 0.00 0.00 2.78
5180 5708 1.714460 GCGTAGATAGCCGATGTTTCG 59.286 52.381 0.00 0.00 45.08 3.46
5181 5709 1.714460 CGTAGATAGCCGATGTTTCGC 59.286 52.381 0.00 0.00 44.12 4.70
5182 5710 2.604855 CGTAGATAGCCGATGTTTCGCT 60.605 50.000 0.00 0.00 44.12 4.93
5183 5711 2.141535 AGATAGCCGATGTTTCGCTC 57.858 50.000 0.00 0.00 44.12 5.03
5184 5712 1.140816 GATAGCCGATGTTTCGCTCC 58.859 55.000 0.00 0.00 44.12 4.70
5185 5713 0.464036 ATAGCCGATGTTTCGCTCCA 59.536 50.000 0.00 0.00 44.12 3.86
5186 5714 0.464036 TAGCCGATGTTTCGCTCCAT 59.536 50.000 0.00 0.00 44.12 3.41
5187 5715 0.464036 AGCCGATGTTTCGCTCCATA 59.536 50.000 0.00 0.00 44.12 2.74
5188 5716 1.070758 AGCCGATGTTTCGCTCCATAT 59.929 47.619 0.00 0.00 44.12 1.78
5189 5717 1.461127 GCCGATGTTTCGCTCCATATC 59.539 52.381 0.00 0.00 44.12 1.63
5190 5718 2.069273 CCGATGTTTCGCTCCATATCC 58.931 52.381 0.00 0.00 44.12 2.59
5191 5719 2.289072 CCGATGTTTCGCTCCATATCCT 60.289 50.000 0.00 0.00 44.12 3.24
5192 5720 3.056821 CCGATGTTTCGCTCCATATCCTA 60.057 47.826 0.00 0.00 44.12 2.94
5193 5721 4.382040 CCGATGTTTCGCTCCATATCCTAT 60.382 45.833 0.00 0.00 44.12 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.525487 TCTCTCCTCCGCTAAAAACAAGTA 59.475 41.667 0.00 0.00 0.00 2.24
27 28 3.926616 TCTCTCCTCCGCTAAAAACAAG 58.073 45.455 0.00 0.00 0.00 3.16
31 32 3.055094 AGCAATCTCTCCTCCGCTAAAAA 60.055 43.478 0.00 0.00 0.00 1.94
34 35 1.781786 AGCAATCTCTCCTCCGCTAA 58.218 50.000 0.00 0.00 0.00 3.09
36 37 1.133637 TCTAGCAATCTCTCCTCCGCT 60.134 52.381 0.00 0.00 0.00 5.52
38 39 2.582052 AGTCTAGCAATCTCTCCTCCG 58.418 52.381 0.00 0.00 0.00 4.63
50 51 2.441750 AGGTTGGGTTTCAAGTCTAGCA 59.558 45.455 0.00 0.00 35.80 3.49
55 56 1.954382 GTCCAGGTTGGGTTTCAAGTC 59.046 52.381 0.00 0.00 38.32 3.01
56 57 1.286553 TGTCCAGGTTGGGTTTCAAGT 59.713 47.619 0.00 0.00 38.32 3.16
69 70 2.731572 AGGATTTGCTTGATGTCCAGG 58.268 47.619 0.00 0.00 0.00 4.45
75 76 4.439700 CCAACTGCTAGGATTTGCTTGATG 60.440 45.833 8.58 0.00 0.00 3.07
78 79 2.165030 CCCAACTGCTAGGATTTGCTTG 59.835 50.000 8.58 0.00 0.00 4.01
81 82 2.019984 CTCCCAACTGCTAGGATTTGC 58.980 52.381 8.58 0.00 0.00 3.68
84 85 2.025887 CCAACTCCCAACTGCTAGGATT 60.026 50.000 0.00 0.00 0.00 3.01
88 89 3.452627 AGATACCAACTCCCAACTGCTAG 59.547 47.826 0.00 0.00 0.00 3.42
122 123 2.352421 CCCTCGTGAGTATGTTGTCGTT 60.352 50.000 0.00 0.00 0.00 3.85
138 139 2.032071 GGTGGTGGTGTTCCCTCG 59.968 66.667 0.00 0.00 0.00 4.63
158 159 3.976701 GACATGGGCCACCTCACCG 62.977 68.421 9.28 0.00 37.76 4.94
159 160 2.044946 GACATGGGCCACCTCACC 60.045 66.667 9.28 0.00 37.76 4.02
195 196 5.993441 CCTTGAGTTTGCTTGATGGAAATTT 59.007 36.000 0.00 0.00 38.23 1.82
201 202 3.318839 TGTTCCTTGAGTTTGCTTGATGG 59.681 43.478 0.00 0.00 0.00 3.51
204 205 3.250762 CGATGTTCCTTGAGTTTGCTTGA 59.749 43.478 0.00 0.00 0.00 3.02
219 220 1.000145 GCCCTCTCGTTTCGATGTTC 59.000 55.000 0.00 0.00 34.61 3.18
224 225 2.178912 ATTTTGCCCTCTCGTTTCGA 57.821 45.000 0.00 0.00 0.00 3.71
229 230 0.112412 ACCCAATTTTGCCCTCTCGT 59.888 50.000 0.00 0.00 0.00 4.18
247 248 4.956085 ACAAACTTTGGATTGGGCTTAAC 58.044 39.130 6.47 0.00 34.12 2.01
249 250 6.325286 ACTTAACAAACTTTGGATTGGGCTTA 59.675 34.615 6.47 0.00 34.12 3.09
273 274 9.034544 ACAAAGAAAGAAGCATCAACATTTAAC 57.965 29.630 0.00 0.00 0.00 2.01
294 296 1.065126 CCAGCCCCTTCCTCTACAAAG 60.065 57.143 0.00 0.00 0.00 2.77
298 300 0.325765 ACTCCAGCCCCTTCCTCTAC 60.326 60.000 0.00 0.00 0.00 2.59
303 305 2.726351 CGAGACTCCAGCCCCTTCC 61.726 68.421 0.00 0.00 0.00 3.46
315 317 0.464036 TGATTATTGCCGCCGAGACT 59.536 50.000 0.00 0.00 0.00 3.24
317 319 2.560981 TCTATGATTATTGCCGCCGAGA 59.439 45.455 0.00 0.00 0.00 4.04
369 372 8.575589 ACATCAAGCGCATTTGGAATATATTTA 58.424 29.630 11.47 0.00 0.00 1.40
378 381 1.612950 ACAACATCAAGCGCATTTGGA 59.387 42.857 11.47 0.00 0.00 3.53
381 384 2.034432 TGTGACAACATCAAGCGCATTT 59.966 40.909 11.47 0.00 39.72 2.32
402 405 1.741706 CTCATTGCCAACGCTTCAGAT 59.258 47.619 0.00 0.00 35.36 2.90
405 408 1.243342 CCCTCATTGCCAACGCTTCA 61.243 55.000 0.00 0.00 35.36 3.02
411 414 1.305930 GGACGTCCCTCATTGCCAAC 61.306 60.000 24.75 0.00 0.00 3.77
426 429 6.851222 AGTGAATTAGCAAATATGAGGACG 57.149 37.500 0.00 0.00 0.00 4.79
428 431 6.547141 CCCAAGTGAATTAGCAAATATGAGGA 59.453 38.462 0.00 0.00 0.00 3.71
513 516 2.079925 GCAACATTCCTCCAGAGTGTC 58.920 52.381 0.00 0.00 44.06 3.67
517 520 2.486982 CTGTTGCAACATTCCTCCAGAG 59.513 50.000 31.17 12.64 38.41 3.35
519 522 2.233271 ACTGTTGCAACATTCCTCCAG 58.767 47.619 31.17 19.12 38.41 3.86
526 529 5.046529 TGCGAAAATTACTGTTGCAACATT 58.953 33.333 31.17 27.12 38.41 2.71
530 533 6.417327 CATTTTGCGAAAATTACTGTTGCAA 58.583 32.000 2.54 0.00 38.97 4.08
550 553 0.865769 GAAGACACGTCCACGCATTT 59.134 50.000 0.00 0.00 44.43 2.32
561 564 2.293677 TCCCGATCAATGAAGACACG 57.706 50.000 0.00 0.00 0.00 4.49
576 579 2.211806 TGTTTGAACGTAACCTTCCCG 58.788 47.619 0.00 0.00 0.00 5.14
587 590 2.713976 GAGCGAACACAATGTTTGAACG 59.286 45.455 12.22 4.97 42.88 3.95
588 591 3.725740 CAGAGCGAACACAATGTTTGAAC 59.274 43.478 12.22 5.70 42.88 3.18
591 594 2.046313 GCAGAGCGAACACAATGTTTG 58.954 47.619 4.80 4.80 41.28 2.93
624 627 5.368256 AAGCATAATTAGCTAGCACATGC 57.632 39.130 18.83 20.53 42.53 4.06
659 662 5.298276 GGTTCATCAGTCCAAGTGTTACAAA 59.702 40.000 0.00 0.00 0.00 2.83
687 690 4.482990 ACATCTTGGAGACCAACCAAATT 58.517 39.130 0.00 0.00 45.05 1.82
688 691 4.118168 ACATCTTGGAGACCAACCAAAT 57.882 40.909 0.00 0.00 45.05 2.32
689 692 3.593442 ACATCTTGGAGACCAACCAAA 57.407 42.857 0.00 0.00 45.05 3.28
732 735 9.236006 CCATCATGGCTAGCTTTATATTAAACT 57.764 33.333 15.72 0.00 0.00 2.66
788 791 0.693049 GGGCTTTCTGAGACTTGGGA 59.307 55.000 0.00 0.00 32.23 4.37
800 803 2.115343 ATTGGAGAACGAGGGCTTTC 57.885 50.000 0.00 0.00 0.00 2.62
1219 1231 1.212688 TCCACCATCCCTAAGCACATG 59.787 52.381 0.00 0.00 0.00 3.21
1373 1385 4.984295 TCTGACACCAGAATTTCCATCAA 58.016 39.130 0.00 0.00 45.74 2.57
1374 1386 4.639078 TCTGACACCAGAATTTCCATCA 57.361 40.909 0.00 0.00 45.74 3.07
1385 1397 5.448768 GCTGAATCATTGAATCTGACACCAG 60.449 44.000 11.52 0.00 41.74 4.00
1449 1461 7.779754 TTCCCATGTTATGCTGCATAATAAT 57.220 32.000 30.96 24.61 38.37 1.28
1450 1462 7.779754 ATTCCCATGTTATGCTGCATAATAA 57.220 32.000 30.96 23.73 38.37 1.40
1451 1463 7.604549 CAATTCCCATGTTATGCTGCATAATA 58.395 34.615 30.96 28.76 38.37 0.98
1492 1504 7.042119 CGCTTGACCAAAACAAAAAGGATTATT 60.042 33.333 0.00 0.00 0.00 1.40
1500 1512 2.966050 AGCGCTTGACCAAAACAAAAA 58.034 38.095 2.64 0.00 0.00 1.94
1501 1513 2.663826 AGCGCTTGACCAAAACAAAA 57.336 40.000 2.64 0.00 0.00 2.44
1505 1517 2.216203 GCAAGCGCTTGACCAAAAC 58.784 52.632 45.25 26.01 42.93 2.43
1530 1542 8.421249 TGAAATCACAAATCCTCAGGTAAAAT 57.579 30.769 0.00 0.00 0.00 1.82
1636 1648 3.135712 ACACTGTGTCCAAGGTTACATCA 59.864 43.478 7.80 0.00 0.00 3.07
1973 1988 4.079253 GTGGGGAAACATGAACAGTACAT 58.921 43.478 0.00 0.00 0.00 2.29
2043 2058 3.067106 AGTTTGTCGTTGCCTACAGATG 58.933 45.455 0.00 0.00 0.00 2.90
2183 2198 6.326064 ACTGATCCTTAAGTGCAGACAGATAT 59.674 38.462 17.93 0.00 0.00 1.63
2241 2257 1.172175 CCCTTGCTGAGAGCTTTTCC 58.828 55.000 0.00 0.00 42.97 3.13
2581 2597 3.614092 TCAGTTCCAGCCATTGATCTTC 58.386 45.455 0.00 0.00 0.00 2.87
2693 2709 7.256286 AGTGTTAATGATACTCTGTACGGAAC 58.744 38.462 5.76 0.00 0.00 3.62
2797 2814 9.852091 GAAATGAAATGCTAATGAGAGAGTTTT 57.148 29.630 0.00 0.00 0.00 2.43
2850 2867 6.978343 TGCACAACATGTTATCCTAGTAAC 57.022 37.500 11.53 1.00 35.60 2.50
3106 3125 5.239306 TGACTGTTGCTTTCTTGGAAGTATG 59.761 40.000 0.00 0.00 0.00 2.39
3239 3258 6.388689 AGGTACCTACATTCATCAACCCATTA 59.611 38.462 14.41 0.00 0.00 1.90
3249 3268 7.016153 TGTTCTGAAAGGTACCTACATTCAT 57.984 36.000 22.12 1.43 34.94 2.57
3382 3465 5.307456 TCTTAACCTACATACAACACCACCA 59.693 40.000 0.00 0.00 0.00 4.17
3383 3466 5.640783 GTCTTAACCTACATACAACACCACC 59.359 44.000 0.00 0.00 0.00 4.61
3384 3467 6.461640 AGTCTTAACCTACATACAACACCAC 58.538 40.000 0.00 0.00 0.00 4.16
3567 3654 2.079925 GGACTTTCAGCCTACAAGCAG 58.920 52.381 0.00 0.00 34.23 4.24
3755 3845 2.464459 GCCCAACGCCTTGAGATCG 61.464 63.158 0.00 0.00 0.00 3.69
3826 3919 1.888512 GTGAGAAGCCAAGAAATGCCA 59.111 47.619 0.00 0.00 0.00 4.92
4351 4871 3.314635 GGAAAGCATGCAGACCAGATAAG 59.685 47.826 21.98 0.00 0.00 1.73
4482 5004 9.119418 TGAAGAATCTCAACTCTATGACTCTAG 57.881 37.037 0.00 0.00 0.00 2.43
4643 5166 7.832503 AATTTCAACACCTTGTTTCTTTCTG 57.167 32.000 0.00 0.00 38.77 3.02
4696 5220 2.344950 CATGAGACAAGACTGTGAGCC 58.655 52.381 0.00 0.00 35.30 4.70
4711 5237 2.636403 TGCATCCCTAGATCACCATGAG 59.364 50.000 0.00 0.00 0.00 2.90
4861 5388 2.530497 GGCAACGCACAGACAACGA 61.530 57.895 0.00 0.00 0.00 3.85
4863 5390 2.186826 AGGGCAACGCACAGACAAC 61.187 57.895 0.00 0.00 32.33 3.32
4864 5391 2.186160 CAGGGCAACGCACAGACAA 61.186 57.895 0.00 0.00 32.33 3.18
4870 5397 3.631487 GATTGGCAGGGCAACGCAC 62.631 63.158 10.62 0.20 37.60 5.34
5076 5604 0.758734 TAATGAGGCATCCCACTCGG 59.241 55.000 0.00 0.00 36.53 4.63
5144 5672 5.142061 TCTACGCAGACTGTTTTTATCCA 57.858 39.130 3.99 0.00 0.00 3.41
5158 5686 2.423926 AACATCGGCTATCTACGCAG 57.576 50.000 0.00 0.00 0.00 5.18
5159 5687 2.739292 GAAACATCGGCTATCTACGCA 58.261 47.619 0.00 0.00 0.00 5.24
5160 5688 1.714460 CGAAACATCGGCTATCTACGC 59.286 52.381 0.00 0.00 0.00 4.42
5161 5689 1.714460 GCGAAACATCGGCTATCTACG 59.286 52.381 0.07 0.00 0.00 3.51
5162 5690 2.981140 GAGCGAAACATCGGCTATCTAC 59.019 50.000 0.07 0.00 0.00 2.59
5163 5691 2.030185 GGAGCGAAACATCGGCTATCTA 60.030 50.000 0.07 0.00 0.00 1.98
5164 5692 1.269831 GGAGCGAAACATCGGCTATCT 60.270 52.381 0.07 0.00 0.00 1.98
5165 5693 1.140816 GGAGCGAAACATCGGCTATC 58.859 55.000 0.07 0.00 0.00 2.08
5166 5694 0.464036 TGGAGCGAAACATCGGCTAT 59.536 50.000 0.07 0.00 0.00 2.97
5167 5695 0.464036 ATGGAGCGAAACATCGGCTA 59.536 50.000 0.07 0.00 0.00 3.93
5168 5696 0.464036 TATGGAGCGAAACATCGGCT 59.536 50.000 0.07 0.00 0.00 5.52
5169 5697 1.461127 GATATGGAGCGAAACATCGGC 59.539 52.381 0.07 0.00 0.00 5.54
5170 5698 2.069273 GGATATGGAGCGAAACATCGG 58.931 52.381 0.07 0.00 0.00 4.18
5171 5699 3.032017 AGGATATGGAGCGAAACATCG 57.968 47.619 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.