Multiple sequence alignment - TraesCS3D01G300900

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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 TraesCS3D01G300900 chr3D 100.000 5177 0 0 1 5177 415583516 415578340 0.000000e+00 9561.0
1 TraesCS3D01G300900 chr3B 88.192 2727 204 67 286 2937 541583357 541580674 0.000000e+00 3144.0
2 TraesCS3D01G300900 chr3B 84.926 1360 118 49 3839 5177 541579047 541577754 0.000000e+00 1295.0
3 TraesCS3D01G300900 chr3B 95.218 711 25 8 2904 3611 541580669 541579965 0.000000e+00 1116.0
4 TraesCS3D01G300900 chr3B 89.316 234 17 6 3607 3840 541579381 541579156 2.360000e-73 287.0
5 TraesCS3D01G300900 chr3B 97.059 34 1 0 3679 3712 602297929 602297962 2.010000e-04 58.4
6 TraesCS3D01G300900 chr3B 97.059 34 1 0 3679 3712 602298003 602298036 2.010000e-04 58.4
7 TraesCS3D01G300900 chr3B 97.059 34 1 0 3679 3712 602298407 602298440 2.010000e-04 58.4
8 TraesCS3D01G300900 chr3A 92.613 1787 85 21 1 1765 534986689 534988450 0.000000e+00 2525.0
9 TraesCS3D01G300900 chr3A 90.620 1322 98 16 1867 3176 534988822 534990129 0.000000e+00 1731.0
10 TraesCS3D01G300900 chr3A 92.936 637 25 7 3833 4450 534991429 534992064 0.000000e+00 909.0
11 TraesCS3D01G300900 chr3A 94.956 456 19 2 3156 3611 534990282 534990733 0.000000e+00 712.0
12 TraesCS3D01G300900 chr3A 85.340 648 47 14 4562 5175 534992558 534993191 1.220000e-175 627.0
13 TraesCS3D01G300900 chr3A 90.795 239 9 2 3607 3833 534991084 534991321 1.810000e-79 307.0
14 TraesCS3D01G300900 chr3A 100.000 28 0 0 56 83 627255059 627255086 9.000000e-03 52.8
15 TraesCS3D01G300900 chr4D 95.556 45 2 0 3666 3710 509822412 509822456 7.190000e-09 73.1
16 TraesCS3D01G300900 chr7B 97.500 40 1 0 3666 3705 300086333 300086294 9.300000e-08 69.4
17 TraesCS3D01G300900 chr2D 93.182 44 3 0 3665 3708 247094498 247094541 1.200000e-06 65.8
18 TraesCS3D01G300900 chr2A 93.182 44 3 0 3665 3708 297249515 297249558 1.200000e-06 65.8


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 TraesCS3D01G300900 chr3D 415578340 415583516 5176 True 9561.000000 9561 100.000 1 5177 1 chr3D.!!$R1 5176
1 TraesCS3D01G300900 chr3B 541577754 541583357 5603 True 1460.500000 3144 89.413 286 5177 4 chr3B.!!$R1 4891
2 TraesCS3D01G300900 chr3A 534986689 534993191 6502 False 1135.166667 2525 91.210 1 5175 6 chr3A.!!$F2 5174

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
215 217 0.937304 GACGAGAGCTTGCACAAACA 59.063 50.000 0.00 0.0 0.00 2.83 F
891 952 1.064758 ACTGGCAGGCGATTCCAAATA 60.065 47.619 20.34 0.0 37.29 1.40 F
1821 1906 0.250510 TGGTGTGTGTGTGTGTGTGT 60.251 50.000 0.00 0.0 0.00 3.72 F
1863 2227 0.874390 TTGATCAAGACTGCAACGGC 59.126 50.000 3.38 0.0 41.68 5.68 F
2171 2543 0.894141 ATTTTATGCAGGTTGGCGCA 59.106 45.000 10.83 0.0 43.45 6.09 F
3883 5180 0.679505 AACTTCTACCTGTGCTCGCA 59.320 50.000 0.00 0.0 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1721 0.106769 TTCCAGCTTGCAGTTCACCA 60.107 50.000 0.0 0.0 0.00 4.17 R
1971 2339 0.545171 CTGCCACAGATCCCTGATGT 59.455 55.000 0.0 0.0 43.02 3.06 R
3332 3922 1.490574 AGAATGGAGAGGGAGAACGG 58.509 55.000 0.0 0.0 0.00 4.44 R
3803 4992 1.571919 ACTGCTGACTGAAACGTCAC 58.428 50.000 0.0 0.0 38.89 3.67 R
3924 5221 2.017049 ACACCTGACTGCAACAAAGAC 58.983 47.619 0.0 0.0 0.00 3.01 R
4785 6531 0.886490 GACTTGTGGTGGAGGTGCAG 60.886 60.000 0.0 0.0 0.00 4.41 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
34 36 7.539034 AAAAACCAACTATAGGCATGTCTTT 57.461 32.000 4.49 0.00 0.00 2.52
162 164 2.545810 CCCCAAAAATGGCCCTAAAGA 58.454 47.619 0.00 0.00 0.00 2.52
205 207 1.134670 GCCCAAATACAGACGAGAGCT 60.135 52.381 0.00 0.00 0.00 4.09
215 217 0.937304 GACGAGAGCTTGCACAAACA 59.063 50.000 0.00 0.00 0.00 2.83
749 799 4.570505 CCTTCCCAAAATCAGGAATCAGGA 60.571 45.833 0.00 0.00 41.26 3.86
786 841 2.180769 GGCCCGGAAATTTGTCGC 59.819 61.111 0.73 0.00 0.00 5.19
818 874 1.477558 GGCCCACCATCTTGGATACAG 60.478 57.143 0.00 0.00 40.96 2.74
822 881 7.921258 GGCCCACCATCTTGGATACAGAATT 62.921 48.000 0.00 0.00 40.96 2.17
891 952 1.064758 ACTGGCAGGCGATTCCAAATA 60.065 47.619 20.34 0.00 37.29 1.40
900 961 1.460267 CGATTCCAAATATCGACGCGC 60.460 52.381 5.73 0.00 45.79 6.86
1040 1105 2.041976 CCATAGCGTCCATCTCGGT 58.958 57.895 0.00 0.00 41.68 4.69
1233 1298 1.681076 GTTAGTCCCCTTTGCCGGA 59.319 57.895 5.05 0.00 0.00 5.14
1440 1515 2.811431 TGTCTGTTTATGCCCGTCAAAG 59.189 45.455 0.00 0.00 0.00 2.77
1474 1549 1.946081 TGTTTGCGCTCAATCTGTTCA 59.054 42.857 9.73 0.00 31.33 3.18
1476 1551 3.004629 TGTTTGCGCTCAATCTGTTCATT 59.995 39.130 9.73 0.00 31.33 2.57
1488 1563 7.823665 TCAATCTGTTCATTGAAATTCCTCAG 58.176 34.615 0.00 3.69 39.37 3.35
1524 1599 1.945387 CTGCTGCGTGAGATAATGGT 58.055 50.000 0.00 0.00 0.00 3.55
1540 1615 2.799126 TGGTAAAGCCATGTCCGAAT 57.201 45.000 0.00 0.00 43.61 3.34
1546 1621 4.643795 CCATGTCCGAATGTGGCT 57.356 55.556 0.00 0.00 0.00 4.75
1571 1646 2.089980 AGCTGTCTTTAGCCATTGCAG 58.910 47.619 0.00 0.00 44.76 4.41
1583 1658 5.664294 AGCCATTGCAGTGAATAATTCAA 57.336 34.783 11.31 0.00 40.00 2.69
1584 1659 5.413499 AGCCATTGCAGTGAATAATTCAAC 58.587 37.500 11.31 0.00 40.00 3.18
1622 1697 6.052360 GTGGCTTATGTTTTTCCTTCCAAAA 58.948 36.000 0.00 0.00 0.00 2.44
1646 1721 1.538047 ATTGACGCCAAACTCATGCT 58.462 45.000 0.00 0.00 35.67 3.79
1708 1783 4.438148 GAGCTGAAAGAGGAGACATAACC 58.562 47.826 0.00 0.00 34.07 2.85
1715 1790 1.409427 GAGGAGACATAACCGGAGTGG 59.591 57.143 9.46 0.00 46.41 4.00
1733 1816 1.079336 GTTAGGGTCGTGAGGTGGC 60.079 63.158 0.00 0.00 0.00 5.01
1752 1835 3.537874 CCGCCTCGGGAGTTAGGG 61.538 72.222 0.00 0.00 44.15 3.53
1765 1848 3.447950 GAGTTAGGGGTTAGAACTGGGA 58.552 50.000 0.00 0.00 0.00 4.37
1766 1849 4.038633 GAGTTAGGGGTTAGAACTGGGAT 58.961 47.826 0.00 0.00 0.00 3.85
1791 1876 1.317613 TAGGTTGTGTGCTTGCAAGG 58.682 50.000 27.10 9.80 0.00 3.61
1821 1906 0.250510 TGGTGTGTGTGTGTGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
1822 1907 0.878416 GGTGTGTGTGTGTGTGTGTT 59.122 50.000 0.00 0.00 0.00 3.32
1823 1908 2.077627 GGTGTGTGTGTGTGTGTGTTA 58.922 47.619 0.00 0.00 0.00 2.41
1824 1909 2.095213 GGTGTGTGTGTGTGTGTGTTAG 59.905 50.000 0.00 0.00 0.00 2.34
1825 1910 2.095213 GTGTGTGTGTGTGTGTGTTAGG 59.905 50.000 0.00 0.00 0.00 2.69
1826 1911 1.668751 GTGTGTGTGTGTGTGTTAGGG 59.331 52.381 0.00 0.00 0.00 3.53
1827 1912 1.305201 GTGTGTGTGTGTGTTAGGGG 58.695 55.000 0.00 0.00 0.00 4.79
1828 1913 0.913205 TGTGTGTGTGTGTTAGGGGT 59.087 50.000 0.00 0.00 0.00 4.95
1852 2216 1.409381 GGGAGGGAAGGCTTGATCAAG 60.409 57.143 27.82 27.82 41.24 3.02
1854 2218 2.637947 GAGGGAAGGCTTGATCAAGAC 58.362 52.381 34.43 32.59 46.75 3.01
1860 2224 2.626088 GGCTTGATCAAGACTGCAAC 57.374 50.000 34.43 16.87 43.09 4.17
1861 2225 1.135859 GGCTTGATCAAGACTGCAACG 60.136 52.381 34.43 10.04 43.09 4.10
1862 2226 1.135859 GCTTGATCAAGACTGCAACGG 60.136 52.381 34.43 9.34 40.79 4.44
1863 2227 0.874390 TTGATCAAGACTGCAACGGC 59.126 50.000 3.38 0.00 41.68 5.68
1864 2228 1.291184 TGATCAAGACTGCAACGGCG 61.291 55.000 4.80 4.80 45.35 6.46
1877 2241 4.688419 CGGCGGCTGTGCAACTTG 62.688 66.667 7.61 0.00 38.04 3.16
1907 2273 5.367937 ACTGCATTCTAGGTGGACTATGAAT 59.632 40.000 0.00 0.00 33.59 2.57
1917 2283 7.437713 AGGTGGACTATGAATAGTTGATCAA 57.562 36.000 3.38 3.38 43.27 2.57
1958 2326 8.608844 ACTATAATAGCGCTTTAGCTTTTCAT 57.391 30.769 18.68 0.00 46.80 2.57
1983 2351 1.284198 AGCAGCAAACATCAGGGATCT 59.716 47.619 0.00 0.00 0.00 2.75
1984 2352 1.404391 GCAGCAAACATCAGGGATCTG 59.596 52.381 0.00 0.00 42.21 2.90
1987 2355 1.747355 GCAAACATCAGGGATCTGTGG 59.253 52.381 0.00 0.00 41.59 4.17
1992 2360 1.064906 CATCAGGGATCTGTGGCAGTT 60.065 52.381 0.00 0.00 41.59 3.16
2000 2368 1.953559 TCTGTGGCAGTTCTGTTGAC 58.046 50.000 0.00 0.00 32.61 3.18
2012 2380 6.017934 GCAGTTCTGTTGACTGTATTGAAAGA 60.018 38.462 6.18 0.00 34.27 2.52
2013 2381 7.467267 GCAGTTCTGTTGACTGTATTGAAAGAA 60.467 37.037 6.18 0.00 34.27 2.52
2014 2382 8.066595 CAGTTCTGTTGACTGTATTGAAAGAAG 58.933 37.037 0.00 0.00 0.00 2.85
2015 2383 7.770897 AGTTCTGTTGACTGTATTGAAAGAAGT 59.229 33.333 0.00 0.00 0.00 3.01
2018 2386 8.397906 TCTGTTGACTGTATTGAAAGAAGTTTG 58.602 33.333 0.00 0.00 0.00 2.93
2019 2387 8.050778 TGTTGACTGTATTGAAAGAAGTTTGT 57.949 30.769 0.00 0.00 0.00 2.83
2020 2388 8.519526 TGTTGACTGTATTGAAAGAAGTTTGTT 58.480 29.630 0.00 0.00 0.00 2.83
2021 2389 8.798153 GTTGACTGTATTGAAAGAAGTTTGTTG 58.202 33.333 0.00 0.00 0.00 3.33
2107 2479 7.117236 AGCAACTCATGTAGCATTTTTCATTTG 59.883 33.333 0.00 0.00 0.00 2.32
2116 2488 8.602328 TGTAGCATTTTTCATTTGTCACTTTTG 58.398 29.630 0.00 0.00 0.00 2.44
2119 2491 9.160496 AGCATTTTTCATTTGTCACTTTTGTTA 57.840 25.926 0.00 0.00 0.00 2.41
2171 2543 0.894141 ATTTTATGCAGGTTGGCGCA 59.106 45.000 10.83 0.00 43.45 6.09
2205 2577 3.244700 CCAAGAGGGCATTATCCTAGGTG 60.245 52.174 9.08 0.09 34.21 4.00
2219 2591 3.182887 CTAGGTGAGGATGGAGCCTAT 57.817 52.381 0.00 0.00 38.73 2.57
2277 2649 4.507710 TCTTTAACTGATGGCTGCAGTAG 58.492 43.478 16.64 8.76 45.27 2.57
2283 2655 3.181471 ACTGATGGCTGCAGTAGTGATAC 60.181 47.826 16.64 0.00 44.27 2.24
2284 2656 2.765699 TGATGGCTGCAGTAGTGATACA 59.234 45.455 16.64 2.91 0.00 2.29
2292 2664 5.812642 GCTGCAGTAGTGATACACAAAGTAT 59.187 40.000 16.64 0.00 45.98 2.12
2295 2667 9.534565 CTGCAGTAGTGATACACAAAGTATAAT 57.465 33.333 5.25 0.00 43.39 1.28
2336 2708 3.944015 AGTGCCATAGCTTGTCATCTTTC 59.056 43.478 0.00 0.00 40.80 2.62
2375 2747 5.313280 TGTTTTCACCAACAGGTATAGGT 57.687 39.130 0.00 0.00 33.30 3.08
2402 2774 1.004745 GGATTCCCAAGAGGCTGTTCA 59.995 52.381 0.00 0.00 34.51 3.18
2458 2830 7.259088 TCTCTGAAGCTTTAATTAGAAGGGT 57.741 36.000 0.00 0.00 0.00 4.34
2471 2843 3.790089 AGAAGGGTTGTAAGTTGAGGG 57.210 47.619 0.00 0.00 0.00 4.30
2525 2900 8.834465 AGCTCTATTGATGCTAGTGTAAAATTG 58.166 33.333 0.00 0.00 35.05 2.32
2552 2930 8.641541 AGTTTCTCATGTGGTGTTCATTTTATT 58.358 29.630 0.00 0.00 0.00 1.40
2721 3099 3.518634 TGTTGCTTTCTGTTTTGGGAC 57.481 42.857 0.00 0.00 0.00 4.46
2742 3120 6.293955 GGGACATAACGCATATAAGCACATTT 60.294 38.462 0.34 0.00 0.00 2.32
2858 3238 1.633945 AGAAAACCCGCCAGATAACCT 59.366 47.619 0.00 0.00 0.00 3.50
2915 3295 9.106070 CTCTTGTTACCTTAGTTTTGTGTAAGT 57.894 33.333 0.00 0.00 0.00 2.24
2952 3367 3.811497 CAAGCAATATAGCTGCACTGCTA 59.189 43.478 9.82 9.82 45.89 3.49
3029 3444 4.633126 CCACTTCACTATGTTGTCATCCAG 59.367 45.833 0.00 0.00 35.70 3.86
3249 3839 8.846211 TGTTCAAATCTAACCCTCTTTTACTTG 58.154 33.333 0.00 0.00 0.00 3.16
3257 3847 3.222603 CCCTCTTTTACTTGTTGGCAGT 58.777 45.455 0.00 0.00 0.00 4.40
3332 3922 2.164422 GGCTGGACAGGTTTGCTATTTC 59.836 50.000 1.01 0.00 0.00 2.17
3341 3931 2.422479 GGTTTGCTATTTCCGTTCTCCC 59.578 50.000 0.00 0.00 0.00 4.30
3412 4002 4.785511 ACTGCAGAAGTTATACGTCACT 57.214 40.909 23.35 0.00 34.57 3.41
3484 4074 9.874205 ACCTAATGTAAATGAACATGGATTTTG 57.126 29.630 0.00 0.00 39.98 2.44
3485 4075 9.874205 CCTAATGTAAATGAACATGGATTTTGT 57.126 29.630 0.00 0.00 39.98 2.83
3515 4105 4.517453 TGGAGTTAGAATTTCACCCAAACG 59.483 41.667 0.00 0.00 0.00 3.60
3549 4139 6.347696 TGCATTCAAACCTCACATTTTCTTT 58.652 32.000 0.00 0.00 0.00 2.52
3561 4151 9.796120 CCTCACATTTTCTTTGTTACAAGTTTA 57.204 29.630 0.00 0.00 0.00 2.01
3613 4203 5.279255 TGTGCACCTAAGTTTGTACTACA 57.721 39.130 15.69 0.00 33.17 2.74
3615 4205 6.995364 TGTGCACCTAAGTTTGTACTACATA 58.005 36.000 15.69 0.00 33.17 2.29
3616 4206 7.443477 TGTGCACCTAAGTTTGTACTACATAA 58.557 34.615 15.69 0.00 33.17 1.90
3617 4207 8.098286 TGTGCACCTAAGTTTGTACTACATAAT 58.902 33.333 15.69 0.00 33.17 1.28
3713 4902 1.134946 CTGGGCTGCCCTTTTTAATCG 59.865 52.381 35.80 10.81 45.70 3.34
3803 4992 8.729756 TCTACATTTGACAATGATTTACTGGTG 58.270 33.333 1.97 0.00 42.35 4.17
3833 5022 5.213891 TCAGTCAGCAGTTCTCATGTTAA 57.786 39.130 0.00 0.00 0.00 2.01
3834 5023 4.991056 TCAGTCAGCAGTTCTCATGTTAAC 59.009 41.667 0.00 0.00 0.00 2.01
3881 5178 3.851976 AGTAACTTCTACCTGTGCTCG 57.148 47.619 0.00 0.00 0.00 5.03
3883 5180 0.679505 AACTTCTACCTGTGCTCGCA 59.320 50.000 0.00 0.00 0.00 5.10
3893 5190 2.096496 CCTGTGCTCGCATAAAAGGAAG 59.904 50.000 0.00 0.00 0.00 3.46
3902 5199 8.097038 TGCTCGCATAAAAGGAAGATAATCTAT 58.903 33.333 0.00 0.00 0.00 1.98
3924 5221 3.411446 TCAGTTCTAACCATTGTGCTGG 58.589 45.455 0.00 0.00 42.35 4.85
4049 5346 3.056107 GCTGGTGTGAAGGTACTGACATA 60.056 47.826 0.00 0.00 40.86 2.29
4058 5355 7.928167 TGTGAAGGTACTGACATATGATCATTC 59.072 37.037 14.65 6.22 40.86 2.67
4086 5383 1.668793 GCACTGTTTTGGCATGGGC 60.669 57.895 0.00 0.00 40.13 5.36
4335 5650 5.916661 TTACTAGATCGAGAAAAGCACCT 57.083 39.130 10.07 0.00 0.00 4.00
4353 5668 3.935203 CACCTGTAACTAGTTGCATCCTG 59.065 47.826 24.06 15.72 34.80 3.86
4407 5722 3.821033 ACCATTCTTCTGTAAACTGTGGC 59.179 43.478 0.00 0.00 0.00 5.01
4443 5759 3.345414 ACTCTCACTACGGTCGATTCTT 58.655 45.455 0.00 0.00 0.00 2.52
4467 6128 6.859017 TGCTGTAGTAAATCGTGATAAGTCA 58.141 36.000 0.00 0.00 0.00 3.41
4517 6179 4.777463 CCCCCTAATGAAATAAGTGACGT 58.223 43.478 0.00 0.00 0.00 4.34
4527 6191 3.851976 ATAAGTGACGTGAGGAGACAC 57.148 47.619 0.00 0.00 37.42 3.67
4547 6211 5.938322 ACACACTTTTGTACACAAAGTCAG 58.062 37.500 22.38 19.95 45.34 3.51
4557 6221 3.836949 ACACAAAGTCAGTTTTGCAGTG 58.163 40.909 0.00 0.00 40.80 3.66
4572 6276 4.314440 GTGACACCCGCAGCTCCA 62.314 66.667 0.00 0.00 0.00 3.86
4580 6284 3.385384 CGCAGCTCCACCTCCAGA 61.385 66.667 0.00 0.00 0.00 3.86
4596 6300 0.459237 CAGAGCGCTCCATCTTCGTT 60.459 55.000 32.94 9.10 0.00 3.85
4606 6310 1.005340 CATCTTCGTTGCAGCTCCTC 58.995 55.000 0.00 0.00 0.00 3.71
4637 6341 1.045350 TCCATCTTCTCCTCAGCCCG 61.045 60.000 0.00 0.00 0.00 6.13
4638 6342 1.333636 CCATCTTCTCCTCAGCCCGT 61.334 60.000 0.00 0.00 0.00 5.28
4639 6343 0.179089 CATCTTCTCCTCAGCCCGTG 60.179 60.000 0.00 0.00 0.00 4.94
4671 6375 4.385405 GCCTGAGGCTGTGCTCGT 62.385 66.667 17.96 0.00 46.69 4.18
4687 6415 2.581354 GTGATCCAGCGCCTGAGT 59.419 61.111 2.29 0.00 32.44 3.41
4730 6476 1.110442 CGCTCCTTCTCCAGATCAGT 58.890 55.000 0.00 0.00 0.00 3.41
4752 6498 1.376424 CACCTGCACTTCCAGCGAT 60.376 57.895 0.00 0.00 33.85 4.58
4753 6499 0.957395 CACCTGCACTTCCAGCGATT 60.957 55.000 0.00 0.00 33.85 3.34
4772 6518 3.668386 GGCAGCGCCTACAGTTTT 58.332 55.556 2.29 0.00 46.69 2.43
4773 6519 1.956802 GGCAGCGCCTACAGTTTTT 59.043 52.632 2.29 0.00 46.69 1.94
4814 6560 2.951642 CCACCACAAGTCAGATTGTTGT 59.048 45.455 0.00 0.00 41.41 3.32
4847 6593 0.250209 CGGCAAGAGGAGGATGATGG 60.250 60.000 0.00 0.00 0.00 3.51
4899 6661 2.703007 AGGAGGATGATGTACCTGAAGC 59.297 50.000 0.00 0.00 36.57 3.86
4909 6671 3.357203 TGTACCTGAAGCTCCAGTAGAG 58.643 50.000 0.00 0.00 46.29 2.43
4910 6672 1.859302 ACCTGAAGCTCCAGTAGAGG 58.141 55.000 0.00 0.00 43.46 3.69
4933 6695 5.363939 GAGGATAATCCACAAGAGGAAGTG 58.636 45.833 0.00 0.00 41.92 3.16
4974 6736 1.339438 TGATCCACAAGAGGAAGCAGC 60.339 52.381 0.00 0.00 41.92 5.25
4975 6737 0.694771 ATCCACAAGAGGAAGCAGCA 59.305 50.000 0.00 0.00 41.92 4.41
4976 6738 0.035881 TCCACAAGAGGAAGCAGCAG 59.964 55.000 0.00 0.00 33.93 4.24
5006 6768 5.931294 TGTCCAATGTAACTTTACTCCACA 58.069 37.500 1.04 0.00 34.77 4.17
5036 6798 7.875971 ACTGAAACAGAAACAATATTGAGACC 58.124 34.615 22.16 7.87 35.18 3.85
5103 6865 5.476945 GGATCATGTGTTACTCCAGGTTTTT 59.523 40.000 0.00 0.00 0.00 1.94
5163 6925 6.313164 GCTGTATACTTGGAGTACTTGAAACC 59.687 42.308 4.17 0.00 32.84 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.644374 AAAGACATGCCTATAGTTGGTTTTTA 57.356 30.769 0.00 0.00 0.00 1.52
129 131 2.937959 TTTGGGGGACTTGTGGGTGC 62.938 60.000 0.00 0.00 0.00 5.01
162 164 5.277058 GCGCAAAATCATCTCTATCGACTTT 60.277 40.000 0.30 0.00 0.00 2.66
205 207 3.737663 GCTCCAATTGTCTGTTTGTGCAA 60.738 43.478 4.43 0.00 0.00 4.08
215 217 4.872691 CAGTCTAAATCGCTCCAATTGTCT 59.127 41.667 4.43 0.00 0.00 3.41
273 275 4.388485 GGATTGGTTTGCCTTTTGTTGAT 58.612 39.130 0.00 0.00 35.27 2.57
412 416 9.549078 GTTTGGGGTTCTAAATTTTGTTTATCA 57.451 29.630 0.00 0.00 0.00 2.15
749 799 2.159382 CGGCCCATTAGTGTTTCAAGT 58.841 47.619 0.00 0.00 0.00 3.16
818 874 4.761739 TCGGCCTGGAATTGATGATAATTC 59.238 41.667 0.00 0.00 43.19 2.17
822 881 2.437651 TGTCGGCCTGGAATTGATGATA 59.562 45.455 0.00 0.00 0.00 2.15
868 929 1.153086 GGAATCGCCTGCCAGTCAT 60.153 57.895 0.00 0.00 0.00 3.06
869 930 2.123248 TTGGAATCGCCTGCCAGTCA 62.123 55.000 0.00 0.00 37.63 3.41
873 934 2.229792 GATATTTGGAATCGCCTGCCA 58.770 47.619 0.00 0.00 37.63 4.92
900 961 3.728845 TCCCTCTTCTGTTGACTTTTCG 58.271 45.455 0.00 0.00 0.00 3.46
1233 1298 3.647771 GGGGCGGTGAAAGAGGGT 61.648 66.667 0.00 0.00 0.00 4.34
1440 1515 5.399013 AGCGCAAACACAAATTTAGGATAC 58.601 37.500 11.47 0.00 0.00 2.24
1488 1563 1.801178 GCAGCAGACTACCAGTTTCAC 59.199 52.381 0.00 0.00 0.00 3.18
1524 1599 2.364632 CCACATTCGGACATGGCTTTA 58.635 47.619 0.00 0.00 0.00 1.85
1598 1673 4.864704 TGGAAGGAAAAACATAAGCCAC 57.135 40.909 0.00 0.00 0.00 5.01
1612 1687 3.490078 GCGTCAATTGTGTTTTGGAAGGA 60.490 43.478 5.13 0.00 0.00 3.36
1622 1697 2.020720 TGAGTTTGGCGTCAATTGTGT 58.979 42.857 1.89 0.00 32.28 3.72
1625 1700 1.987770 GCATGAGTTTGGCGTCAATTG 59.012 47.619 1.89 0.00 32.28 2.32
1627 1702 1.200716 CAGCATGAGTTTGGCGTCAAT 59.799 47.619 1.89 0.00 39.69 2.57
1646 1721 0.106769 TTCCAGCTTGCAGTTCACCA 60.107 50.000 0.00 0.00 0.00 4.17
1708 1783 1.214589 CACGACCCTAACCACTCCG 59.785 63.158 0.00 0.00 0.00 4.63
1715 1790 1.079336 GCCACCTCACGACCCTAAC 60.079 63.158 0.00 0.00 0.00 2.34
1733 1816 4.570663 CTAACTCCCGAGGCGGCG 62.571 72.222 0.51 0.51 46.86 6.46
1740 1823 2.043526 AGTTCTAACCCCTAACTCCCGA 59.956 50.000 0.00 0.00 0.00 5.14
1746 1829 4.038633 AGATCCCAGTTCTAACCCCTAAC 58.961 47.826 0.00 0.00 0.00 2.34
1749 1832 2.482494 CAGATCCCAGTTCTAACCCCT 58.518 52.381 0.00 0.00 0.00 4.79
1752 1835 3.636153 AAGCAGATCCCAGTTCTAACC 57.364 47.619 0.00 0.00 0.00 2.85
1765 1848 2.816087 CAAGCACACAACCTAAGCAGAT 59.184 45.455 0.00 0.00 0.00 2.90
1766 1849 2.221169 CAAGCACACAACCTAAGCAGA 58.779 47.619 0.00 0.00 0.00 4.26
1794 1879 1.472082 CACACACACACCAACACATGT 59.528 47.619 0.00 0.00 0.00 3.21
1835 1920 2.026449 CAGTCTTGATCAAGCCTTCCCT 60.026 50.000 27.45 13.79 38.28 4.20
1839 1924 2.555757 GTTGCAGTCTTGATCAAGCCTT 59.444 45.455 27.45 13.88 38.28 4.35
1840 1925 2.157738 GTTGCAGTCTTGATCAAGCCT 58.842 47.619 27.45 20.78 38.28 4.58
1857 2221 4.980903 GTTGCACAGCCGCCGTTG 62.981 66.667 0.00 0.00 0.00 4.10
1860 2224 4.688419 CAAGTTGCACAGCCGCCG 62.688 66.667 0.00 0.00 0.00 6.46
1861 2225 4.347453 CCAAGTTGCACAGCCGCC 62.347 66.667 0.00 0.00 0.00 6.13
1862 2226 4.347453 CCCAAGTTGCACAGCCGC 62.347 66.667 0.00 0.00 0.00 6.53
1863 2227 4.347453 GCCCAAGTTGCACAGCCG 62.347 66.667 0.00 0.00 0.00 5.52
1864 2228 3.994853 GGCCCAAGTTGCACAGCC 61.995 66.667 0.00 3.16 0.00 4.85
1865 2229 4.347453 CGGCCCAAGTTGCACAGC 62.347 66.667 0.00 0.00 0.00 4.40
1877 2241 1.227674 CCTAGAATGCAGTCGGCCC 60.228 63.158 8.74 0.00 43.89 5.80
1958 2326 2.557924 CCCTGATGTTTGCTGCTTTGTA 59.442 45.455 0.00 0.00 0.00 2.41
1971 2339 0.545171 CTGCCACAGATCCCTGATGT 59.455 55.000 0.00 0.00 43.02 3.06
1972 2340 0.545171 ACTGCCACAGATCCCTGATG 59.455 55.000 0.78 0.00 43.02 3.07
1983 2351 1.065491 ACAGTCAACAGAACTGCCACA 60.065 47.619 3.30 0.00 46.48 4.17
1984 2352 1.668419 ACAGTCAACAGAACTGCCAC 58.332 50.000 3.30 0.00 46.48 5.01
1987 2355 5.673337 TTCAATACAGTCAACAGAACTGC 57.327 39.130 3.30 0.00 46.48 4.40
1992 2360 8.397906 CAAACTTCTTTCAATACAGTCAACAGA 58.602 33.333 0.00 0.00 0.00 3.41
2000 2368 7.967854 TGTCACAACAAACTTCTTTCAATACAG 59.032 33.333 0.00 0.00 30.70 2.74
2012 2380 9.467258 CTGAATAAATGATGTCACAACAAACTT 57.533 29.630 0.00 0.00 39.30 2.66
2013 2381 8.632679 ACTGAATAAATGATGTCACAACAAACT 58.367 29.630 0.00 0.00 39.30 2.66
2014 2382 8.693504 CACTGAATAAATGATGTCACAACAAAC 58.306 33.333 0.00 0.00 39.30 2.93
2015 2383 8.628280 TCACTGAATAAATGATGTCACAACAAA 58.372 29.630 0.00 0.00 39.30 2.83
2018 2386 9.069078 CATTCACTGAATAAATGATGTCACAAC 57.931 33.333 3.88 0.00 33.22 3.32
2019 2387 8.795513 ACATTCACTGAATAAATGATGTCACAA 58.204 29.630 3.88 0.00 35.03 3.33
2020 2388 8.238631 CACATTCACTGAATAAATGATGTCACA 58.761 33.333 3.88 0.00 35.03 3.58
2021 2389 8.453320 TCACATTCACTGAATAAATGATGTCAC 58.547 33.333 3.88 0.00 35.03 3.67
2073 2441 4.095334 TGCTACATGAGTTGCTATTTGCTG 59.905 41.667 0.00 0.00 45.02 4.41
2079 2447 7.395190 TGAAAAATGCTACATGAGTTGCTAT 57.605 32.000 0.00 0.00 45.02 2.97
2094 2462 9.424659 CTAACAAAAGTGACAAATGAAAAATGC 57.575 29.630 0.00 0.00 0.00 3.56
2119 2491 8.237811 AGGTACAAAAATCAGAATGTTTGACT 57.762 30.769 7.81 1.81 41.01 3.41
2139 2511 8.007405 ACCTGCATAAAATGGATTTTAGGTAC 57.993 34.615 14.61 3.99 43.17 3.34
2215 2587 8.783833 AGTTACATATCATAAAGCAGCATAGG 57.216 34.615 0.00 0.00 0.00 2.57
2219 2591 8.681486 ATCAAGTTACATATCATAAAGCAGCA 57.319 30.769 0.00 0.00 0.00 4.41
2247 2619 6.095377 CAGCCATCAGTTAAAGAATTTGGAC 58.905 40.000 0.00 0.00 39.63 4.02
2254 2626 3.754965 ACTGCAGCCATCAGTTAAAGAA 58.245 40.909 15.27 0.00 41.61 2.52
2255 2627 3.423539 ACTGCAGCCATCAGTTAAAGA 57.576 42.857 15.27 0.00 41.61 2.52
2262 2634 2.616634 ATCACTACTGCAGCCATCAG 57.383 50.000 15.27 6.00 37.56 2.90
2292 2664 6.992123 CACTTGGCCTATCACAACTATCATTA 59.008 38.462 3.32 0.00 0.00 1.90
2295 2667 4.769688 CACTTGGCCTATCACAACTATCA 58.230 43.478 3.32 0.00 0.00 2.15
2299 2671 1.826385 GCACTTGGCCTATCACAACT 58.174 50.000 3.32 0.00 36.11 3.16
2372 2744 4.325344 CCTCTTGGGAATCCATTGTAACCT 60.325 45.833 0.09 0.00 43.63 3.50
2375 2747 3.269381 AGCCTCTTGGGAATCCATTGTAA 59.731 43.478 0.09 0.00 43.63 2.41
2402 2774 2.511218 TGCCCAAGGAAGCTTATCATCT 59.489 45.455 0.00 0.00 0.00 2.90
2437 2809 7.454260 ACAACCCTTCTAATTAAAGCTTCAG 57.546 36.000 0.00 0.00 0.00 3.02
2458 2830 3.153919 GTGAATGGCCCTCAACTTACAA 58.846 45.455 0.00 0.00 0.00 2.41
2499 2874 8.834465 CAATTTTACACTAGCATCAATAGAGCT 58.166 33.333 0.00 0.00 42.14 4.09
2522 2897 5.132502 TGAACACCACATGAGAAACTCAAT 58.867 37.500 0.00 0.00 44.04 2.57
2525 2900 5.695851 AATGAACACCACATGAGAAACTC 57.304 39.130 0.00 0.00 0.00 3.01
2563 2941 3.143807 TCCAGCAAACGTGTCAAAAAG 57.856 42.857 0.00 0.00 0.00 2.27
2564 2942 3.577649 TTCCAGCAAACGTGTCAAAAA 57.422 38.095 0.00 0.00 0.00 1.94
2565 2943 3.791973 ATTCCAGCAAACGTGTCAAAA 57.208 38.095 0.00 0.00 0.00 2.44
2679 3057 8.479280 CAACAACCATTTTACTGAAGAAAATCG 58.521 33.333 0.00 0.00 34.93 3.34
2682 3060 7.327214 AGCAACAACCATTTTACTGAAGAAAA 58.673 30.769 0.00 0.00 0.00 2.29
2721 3099 6.300668 CGACAAATGTGCTTATATGCGTTATG 59.699 38.462 6.16 4.55 35.36 1.90
2836 3216 2.617021 GGTTATCTGGCGGGTTTTCTGA 60.617 50.000 0.00 0.00 0.00 3.27
2847 3227 5.691754 CACAAAACAGAAAAGGTTATCTGGC 59.308 40.000 7.59 0.00 45.80 4.85
2878 3258 9.628500 ACTAAGGTAACAAGAGTTTCTTTCAAT 57.372 29.630 0.00 0.00 39.15 2.57
2920 3300 7.446319 TGCAGCTATATTGCTTGTAAGATCAAT 59.554 33.333 9.05 0.24 41.98 2.57
2952 3367 3.190874 GCGAGCTAGACAATTGCTAACT 58.809 45.455 5.05 8.65 40.27 2.24
3249 3839 3.674753 GCATGAACAACATAACTGCCAAC 59.325 43.478 0.00 0.00 37.46 3.77
3332 3922 1.490574 AGAATGGAGAGGGAGAACGG 58.509 55.000 0.00 0.00 0.00 4.44
3412 4002 4.625324 GCACACTCATTACAGGGGAACATA 60.625 45.833 0.00 0.00 0.00 2.29
3484 4074 7.598869 GGGTGAAATTCTAACTCCAAAATGAAC 59.401 37.037 0.00 0.00 0.00 3.18
3485 4075 7.288852 TGGGTGAAATTCTAACTCCAAAATGAA 59.711 33.333 0.00 0.00 0.00 2.57
3515 4105 5.927689 TGAGGTTTGAATGCATTTCATCAAC 59.072 36.000 14.33 13.34 43.73 3.18
3580 4170 9.507280 CAAACTTAGGTGCACATTTATAGAATG 57.493 33.333 20.43 8.10 0.00 2.67
3648 4825 4.807039 CCGACCACTTACGGCCCG 62.807 72.222 0.00 0.00 42.55 6.13
3682 4871 4.394712 AGCCCAGTGCACGTAGCC 62.395 66.667 19.84 6.87 44.83 3.93
3766 4955 4.211164 TGTCAAATGTAGAGTCTTTGCACG 59.789 41.667 0.00 0.00 31.50 5.34
3803 4992 1.571919 ACTGCTGACTGAAACGTCAC 58.428 50.000 0.00 0.00 38.89 3.67
3833 5022 8.999431 CCACATAAAAATAGTGTGAGTAGTTGT 58.001 33.333 6.32 0.00 44.48 3.32
3834 5023 9.214957 TCCACATAAAAATAGTGTGAGTAGTTG 57.785 33.333 6.32 0.00 44.48 3.16
3902 5199 3.820467 CCAGCACAATGGTTAGAACTGAA 59.180 43.478 0.00 0.00 35.47 3.02
3924 5221 2.017049 ACACCTGACTGCAACAAAGAC 58.983 47.619 0.00 0.00 0.00 3.01
4049 5346 7.687388 ACAGTGCTTATATGAGGAATGATCAT 58.313 34.615 20.34 1.18 36.70 2.45
4058 5355 4.398988 TGCCAAAACAGTGCTTATATGAGG 59.601 41.667 0.00 0.00 0.00 3.86
4086 5383 7.871463 TGTGAGAGATGATGCATAAGAATGTAG 59.129 37.037 0.00 0.00 35.38 2.74
4282 5596 7.657761 ACTGATTACAATATACAACAGCTAGGC 59.342 37.037 0.00 0.00 0.00 3.93
4320 5635 4.273148 AGTTACAGGTGCTTTTCTCGAT 57.727 40.909 0.00 0.00 0.00 3.59
4322 5637 4.557205 ACTAGTTACAGGTGCTTTTCTCG 58.443 43.478 0.00 0.00 0.00 4.04
4335 5650 3.751175 GCAACAGGATGCAACTAGTTACA 59.249 43.478 10.92 10.92 45.70 2.41
4353 5668 4.225984 TGAGCACATACAAATTTCGCAAC 58.774 39.130 0.00 0.00 0.00 4.17
4407 5722 4.940046 AGTGAGAGTTAAATCATGGTGCAG 59.060 41.667 5.62 0.00 0.00 4.41
4443 5759 6.859017 TGACTTATCACGATTTACTACAGCA 58.141 36.000 0.00 0.00 0.00 4.41
4496 6158 5.424757 TCACGTCACTTATTTCATTAGGGG 58.575 41.667 0.00 0.00 0.00 4.79
4499 6161 7.221067 GTCTCCTCACGTCACTTATTTCATTAG 59.779 40.741 0.00 0.00 0.00 1.73
4503 6165 4.279922 TGTCTCCTCACGTCACTTATTTCA 59.720 41.667 0.00 0.00 0.00 2.69
4517 6179 4.081365 TGTGTACAAAAGTGTGTCTCCTCA 60.081 41.667 0.00 0.00 38.82 3.86
4527 6191 7.619161 GCAAAACTGACTTTGTGTACAAAAGTG 60.619 37.037 26.56 19.62 44.24 3.16
4547 6211 1.299089 GCGGGTGTCACTGCAAAAC 60.299 57.895 13.56 0.00 42.32 2.43
4572 6276 2.364842 ATGGAGCGCTCTGGAGGT 60.365 61.111 34.46 13.05 0.00 3.85
4580 6284 2.103042 GCAACGAAGATGGAGCGCT 61.103 57.895 11.27 11.27 0.00 5.92
4596 6300 3.397439 GCTGGAGGAGGAGCTGCA 61.397 66.667 8.35 0.00 32.12 4.41
4623 6327 2.125350 GCACGGGCTGAGGAGAAG 60.125 66.667 0.00 0.00 36.96 2.85
4637 6341 3.730761 CGCCTGGAGCACAAGCAC 61.731 66.667 0.00 0.00 45.49 4.40
4671 6375 2.580815 CACTCAGGCGCTGGATCA 59.419 61.111 7.64 0.00 31.51 2.92
4720 6466 1.229625 AGGTGCCCACTGATCTGGA 60.230 57.895 2.56 0.00 32.30 3.86
4724 6470 2.042831 GTGCAGGTGCCCACTGATC 61.043 63.158 0.00 0.00 41.18 2.92
4730 6476 3.496309 CTGGAAGTGCAGGTGCCCA 62.496 63.158 0.00 0.00 41.18 5.36
4761 6507 1.069227 CAGGACGCAAAAACTGTAGGC 60.069 52.381 0.00 0.00 0.00 3.93
4784 6530 1.601759 CTTGTGGTGGAGGTGCAGG 60.602 63.158 0.00 0.00 0.00 4.85
4785 6531 0.886490 GACTTGTGGTGGAGGTGCAG 60.886 60.000 0.00 0.00 0.00 4.41
4814 6560 1.539388 CTTGCCGGCAAACTGAATGTA 59.461 47.619 38.96 16.29 35.33 2.29
4847 6593 3.119955 GGACTAAAGTTCAAATCGGGCAC 60.120 47.826 0.00 0.00 0.00 5.01
4909 6671 4.410555 ACTTCCTCTTGTGGATTATCCTCC 59.589 45.833 12.91 3.88 37.46 4.30
4910 6672 5.129485 TCACTTCCTCTTGTGGATTATCCTC 59.871 44.000 12.91 9.51 37.46 3.71
4916 6678 5.246981 TCATTCACTTCCTCTTGTGGATT 57.753 39.130 0.00 0.00 35.83 3.01
4933 6695 5.007034 TCATCCTCCTCTACTCGATCATTC 58.993 45.833 0.00 0.00 0.00 2.67
4974 6736 6.817765 AAGTTACATTGGACATTGTACCTG 57.182 37.500 6.57 0.00 29.93 4.00
4975 6737 8.161425 AGTAAAGTTACATTGGACATTGTACCT 58.839 33.333 6.57 3.45 36.12 3.08
4976 6738 8.331730 AGTAAAGTTACATTGGACATTGTACC 57.668 34.615 6.57 0.00 36.12 3.34
5006 6768 8.196771 TCAATATTGTTTCTGTTTCAGTTTGCT 58.803 29.630 14.97 0.00 32.61 3.91
5019 6781 9.082313 ACTGAATTTGGTCTCAATATTGTTTCT 57.918 29.630 14.97 0.00 32.28 2.52


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

AutoCloner maintained by Alex Coulton.