Multiple sequence alignment - TraesCS4D01G228100

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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 TraesCS4D01G228100 chr4D 100.000 3915 0 0 1 3915 387440566 387444480 0.000000e+00 7230.0
1 TraesCS4D01G228100 chr4B 88.660 4021 208 98 1 3915 475810026 475813904 0.000000e+00 4671.0
2 TraesCS4D01G228100 chr4B 86.029 136 14 5 496 627 1803562 1803428 1.470000e-29 141.0
3 TraesCS4D01G228100 chr4B 91.429 70 2 1 252 321 1803631 1803566 4.170000e-15 93.5
4 TraesCS4D01G228100 chr4A 90.327 1985 98 43 1463 3414 68689663 68691586 0.000000e+00 2516.0
5 TraesCS4D01G228100 chr4A 86.778 1437 83 38 1 1393 68688177 68689550 0.000000e+00 1502.0
6 TraesCS4D01G228100 chr4A 90.049 412 25 6 3510 3915 68697289 68697690 1.610000e-143 520.0
7 TraesCS4D01G228100 chr4A 92.857 70 1 1 252 321 654173301 654173236 8.950000e-17 99.0
8 TraesCS4D01G228100 chr6B 86.500 400 28 9 249 627 33444286 33444680 2.180000e-112 416.0
9 TraesCS4D01G228100 chr6B 82.812 384 35 18 252 627 97522429 97522069 8.170000e-82 315.0
10 TraesCS4D01G228100 chr6B 84.211 95 15 0 1293 1387 502484242 502484148 4.170000e-15 93.5
11 TraesCS4D01G228100 chr7B 84.750 400 35 9 249 627 618473290 618473684 1.030000e-100 377.0
12 TraesCS4D01G228100 chr7B 87.500 128 12 4 503 627 33345048 33345174 1.130000e-30 145.0
13 TraesCS4D01G228100 chr7B 86.029 136 14 5 496 627 63521013 63520879 1.470000e-29 141.0
14 TraesCS4D01G228100 chr7B 91.781 73 2 1 249 321 33344968 33345036 8.950000e-17 99.0
15 TraesCS4D01G228100 chr7B 76.978 139 20 6 3608 3739 147754233 147754366 7.020000e-08 69.4
16 TraesCS4D01G228100 chr3B 86.029 136 14 5 496 627 527366646 527366512 1.470000e-29 141.0
17 TraesCS4D01G228100 chr2D 81.006 179 30 4 1210 1386 523028588 523028764 5.270000e-29 139.0
18 TraesCS4D01G228100 chr2A 81.006 179 30 4 1210 1386 668242841 668243017 5.270000e-29 139.0
19 TraesCS4D01G228100 chr2B 85.401 137 13 6 496 627 587674846 587674712 6.820000e-28 135.0
20 TraesCS4D01G228100 chr2B 80.000 180 30 5 1210 1386 616934689 616934865 1.140000e-25 128.0
21 TraesCS4D01G228100 chr2B 91.429 70 2 1 252 321 587674915 587674850 4.170000e-15 93.5
22 TraesCS4D01G228100 chr1A 75.735 272 43 12 3468 3735 45693736 45693988 8.890000e-22 115.0
23 TraesCS4D01G228100 chr7A 87.097 93 7 1 3654 3746 706023462 706023549 2.490000e-17 100.0
24 TraesCS4D01G228100 chr6A 85.263 95 14 0 1293 1387 457686099 457686193 8.950000e-17 99.0
25 TraesCS4D01G228100 chr6D 83.908 87 14 0 1301 1387 320228345 320228431 2.510000e-12 84.2


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 TraesCS4D01G228100 chr4D 387440566 387444480 3914 False 7230 7230 100.0000 1 3915 1 chr4D.!!$F1 3914
1 TraesCS4D01G228100 chr4B 475810026 475813904 3878 False 4671 4671 88.6600 1 3915 1 chr4B.!!$F1 3914
2 TraesCS4D01G228100 chr4A 68688177 68691586 3409 False 2009 2516 88.5525 1 3414 2 chr4A.!!$F2 3413

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
878 964 1.000233 CCATACAAGGGGCAGGCAA 60.000 57.895 0.0 0.0 0.00 4.52 F
1900 2062 0.034574 ATCTGCCCACGCACCAAATA 60.035 50.000 0.0 0.0 41.12 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2249 2416 0.107214 CTGATTAAAGAGCCCGCCCA 60.107 55.0 0.0 0.0 0.0 5.36 R
3212 3404 0.035439 AAACGAAGTCGGGGCATCAT 60.035 50.0 5.6 0.0 45.0 2.45 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
82 83 4.789784 CGAGGAAAAACGGAAAAAGCATA 58.210 39.130 0.00 0.00 0.00 3.14
124 125 1.214589 GTCGCCACCGCTTTCTCTA 59.785 57.895 0.00 0.00 0.00 2.43
190 213 2.028748 CCTTGGAAGCAAAGAATGGGTG 60.029 50.000 0.00 0.00 0.00 4.61
195 218 1.229177 GCAAAGAATGGGTGGGGGT 60.229 57.895 0.00 0.00 0.00 4.95
196 219 1.543944 GCAAAGAATGGGTGGGGGTG 61.544 60.000 0.00 0.00 0.00 4.61
228 254 2.509336 GCACGGGTCATGACGAGG 60.509 66.667 19.33 12.83 0.00 4.63
229 255 3.001902 GCACGGGTCATGACGAGGA 62.002 63.158 19.33 0.00 0.00 3.71
230 256 1.139734 CACGGGTCATGACGAGGAG 59.860 63.158 19.33 10.63 0.00 3.69
231 257 2.105128 CGGGTCATGACGAGGAGC 59.895 66.667 19.33 4.46 0.00 4.70
302 328 3.687102 TACGCCGGTGACCAGTGG 61.687 66.667 24.59 7.91 0.00 4.00
320 346 1.523154 GGGTGCGAATCTTGGTGCAA 61.523 55.000 0.00 0.00 39.34 4.08
489 527 7.113684 GGATAGAAACTGATGATTAACGACGAG 59.886 40.741 0.00 0.00 0.00 4.18
492 530 3.439293 ACTGATGATTAACGACGAGCAG 58.561 45.455 0.00 0.00 0.00 4.24
493 531 2.193447 TGATGATTAACGACGAGCAGC 58.807 47.619 0.00 0.00 0.00 5.25
494 532 2.193447 GATGATTAACGACGAGCAGCA 58.807 47.619 0.00 0.00 0.00 4.41
495 533 2.073117 TGATTAACGACGAGCAGCAA 57.927 45.000 0.00 0.00 0.00 3.91
496 534 2.616960 TGATTAACGACGAGCAGCAAT 58.383 42.857 0.00 0.00 0.00 3.56
497 535 2.603110 TGATTAACGACGAGCAGCAATC 59.397 45.455 0.00 1.99 0.00 2.67
499 537 3.497297 TTAACGACGAGCAGCAATCTA 57.503 42.857 0.00 0.00 0.00 1.98
500 538 2.586258 AACGACGAGCAGCAATCTAT 57.414 45.000 0.00 0.00 0.00 1.98
501 539 2.126914 ACGACGAGCAGCAATCTATC 57.873 50.000 0.00 0.00 0.00 2.08
502 540 1.678627 ACGACGAGCAGCAATCTATCT 59.321 47.619 0.00 0.00 0.00 1.98
547 595 6.102321 AGGGATATCCATTCACTTGTTCAGAT 59.898 38.462 23.27 0.00 38.24 2.90
548 596 7.293299 AGGGATATCCATTCACTTGTTCAGATA 59.707 37.037 23.27 0.00 38.24 1.98
549 597 8.105829 GGGATATCCATTCACTTGTTCAGATAT 58.894 37.037 23.27 0.00 37.91 1.63
550 598 9.160496 GGATATCCATTCACTTGTTCAGATATC 57.840 37.037 17.34 0.00 39.83 1.63
584 632 6.215845 AGTGCAAAGTAACAACAATTCCATC 58.784 36.000 0.00 0.00 0.00 3.51
585 633 5.982516 GTGCAAAGTAACAACAATTCCATCA 59.017 36.000 0.00 0.00 0.00 3.07
586 634 6.478344 GTGCAAAGTAACAACAATTCCATCAA 59.522 34.615 0.00 0.00 0.00 2.57
597 645 7.069331 ACAACAATTCCATCAACTGTAAAAGGA 59.931 33.333 0.00 0.00 0.00 3.36
599 647 6.777580 ACAATTCCATCAACTGTAAAAGGAGT 59.222 34.615 0.00 0.00 0.00 3.85
602 650 4.518970 TCCATCAACTGTAAAAGGAGTTGC 59.481 41.667 0.00 0.00 45.80 4.17
609 657 6.819397 ACTGTAAAAGGAGTTGCTAATTCC 57.181 37.500 0.00 0.00 37.54 3.01
613 661 6.879458 TGTAAAAGGAGTTGCTAATTCCTCTC 59.121 38.462 11.45 0.00 45.80 3.20
724 796 1.209621 GTACCCCCAGTTGCATCCTA 58.790 55.000 0.00 0.00 0.00 2.94
878 964 1.000233 CCATACAAGGGGCAGGCAA 60.000 57.895 0.00 0.00 0.00 4.52
879 965 1.039233 CCATACAAGGGGCAGGCAAG 61.039 60.000 0.00 0.00 0.00 4.01
880 966 1.039233 CATACAAGGGGCAGGCAAGG 61.039 60.000 0.00 0.00 0.00 3.61
881 967 2.861271 ATACAAGGGGCAGGCAAGGC 62.861 60.000 0.00 0.00 0.00 4.35
1047 1141 1.133809 TCCAGGCCTTTACCACTGCT 61.134 55.000 0.00 0.00 0.00 4.24
1102 1197 8.474577 GCAATTGACGATGTTTATGATGATTTC 58.525 33.333 10.34 0.00 0.00 2.17
1110 1205 0.948623 TATGATGATTTCGCGGCGGG 60.949 55.000 23.46 18.68 0.00 6.13
1411 1506 4.402056 TTCACTCCTTTCTCGTTCACTT 57.598 40.909 0.00 0.00 0.00 3.16
1412 1507 5.524971 TTCACTCCTTTCTCGTTCACTTA 57.475 39.130 0.00 0.00 0.00 2.24
1413 1508 4.868067 TCACTCCTTTCTCGTTCACTTAC 58.132 43.478 0.00 0.00 0.00 2.34
1603 1751 2.548057 TCTAAGTTTTTGCCTGTCAGCG 59.452 45.455 0.00 0.00 34.65 5.18
1619 1767 0.607489 AGCGCAACTGCTCTTTGGAT 60.607 50.000 11.47 0.00 42.95 3.41
1819 1975 4.380841 AATCGCAATCAAGCAATCACAT 57.619 36.364 0.00 0.00 0.00 3.21
1838 1994 5.816777 TCACATATTGCATCGTCATTGAGAA 59.183 36.000 0.00 0.00 0.00 2.87
1841 1997 4.627611 ATTGCATCGTCATTGAGAAAGG 57.372 40.909 0.00 0.00 0.00 3.11
1845 2001 3.529533 CATCGTCATTGAGAAAGGAGCT 58.470 45.455 0.00 0.00 0.00 4.09
1850 2006 3.932089 GTCATTGAGAAAGGAGCTCAGAC 59.068 47.826 17.19 3.76 42.74 3.51
1852 2008 5.019470 TCATTGAGAAAGGAGCTCAGACTA 58.981 41.667 17.19 0.00 42.74 2.59
1856 2012 6.365970 TGAGAAAGGAGCTCAGACTAAAAT 57.634 37.500 17.19 0.00 37.46 1.82
1864 2026 7.856415 AGGAGCTCAGACTAAAATTAAGATGT 58.144 34.615 17.19 0.00 0.00 3.06
1880 2042 0.842635 ATGTGGGGCATCTTCTCTCC 59.157 55.000 0.00 0.00 30.67 3.71
1883 2045 1.135094 TGGGGCATCTTCTCTCCATC 58.865 55.000 0.00 0.00 0.00 3.51
1887 2049 1.542987 GGCATCTTCTCTCCATCTGCC 60.543 57.143 0.00 0.00 40.68 4.85
1891 2053 0.179089 CTTCTCTCCATCTGCCCACG 60.179 60.000 0.00 0.00 0.00 4.94
1893 2055 3.002583 TCTCCATCTGCCCACGCA 61.003 61.111 0.00 0.00 44.78 5.24
1894 2056 2.821366 CTCCATCTGCCCACGCAC 60.821 66.667 0.00 0.00 41.12 5.34
1895 2057 4.408821 TCCATCTGCCCACGCACC 62.409 66.667 0.00 0.00 41.12 5.01
1897 2059 2.672651 CATCTGCCCACGCACCAA 60.673 61.111 0.00 0.00 41.12 3.67
1898 2060 2.115052 ATCTGCCCACGCACCAAA 59.885 55.556 0.00 0.00 41.12 3.28
1899 2061 1.304381 ATCTGCCCACGCACCAAAT 60.304 52.632 0.00 0.00 41.12 2.32
1900 2062 0.034574 ATCTGCCCACGCACCAAATA 60.035 50.000 0.00 0.00 41.12 1.40
1901 2063 0.034574 TCTGCCCACGCACCAAATAT 60.035 50.000 0.00 0.00 41.12 1.28
1904 2066 1.746220 TGCCCACGCACCAAATATAAC 59.254 47.619 0.00 0.00 41.12 1.89
1905 2067 2.021457 GCCCACGCACCAAATATAACT 58.979 47.619 0.00 0.00 34.03 2.24
1906 2068 3.207778 GCCCACGCACCAAATATAACTA 58.792 45.455 0.00 0.00 34.03 2.24
1907 2069 3.250040 GCCCACGCACCAAATATAACTAG 59.750 47.826 0.00 0.00 34.03 2.57
1909 2071 3.813166 CCACGCACCAAATATAACTAGGG 59.187 47.826 0.00 0.00 0.00 3.53
1911 2073 2.478894 CGCACCAAATATAACTAGGGCG 59.521 50.000 0.00 0.00 34.54 6.13
1912 2074 2.225727 GCACCAAATATAACTAGGGCGC 59.774 50.000 0.00 0.00 0.00 6.53
1913 2075 2.812011 CACCAAATATAACTAGGGCGCC 59.188 50.000 21.18 21.18 0.00 6.53
1914 2076 2.709397 ACCAAATATAACTAGGGCGCCT 59.291 45.455 28.56 15.07 37.71 5.52
1915 2077 3.074412 CCAAATATAACTAGGGCGCCTG 58.926 50.000 28.56 18.82 34.61 4.85
1916 2078 3.244422 CCAAATATAACTAGGGCGCCTGA 60.244 47.826 28.56 13.74 34.61 3.86
1917 2079 3.963428 AATATAACTAGGGCGCCTGAG 57.037 47.619 28.56 24.57 34.61 3.35
1918 2080 2.670019 TATAACTAGGGCGCCTGAGA 57.330 50.000 28.56 9.07 34.61 3.27
1924 2086 4.166888 GGGCGCCTGAGAGCATCA 62.167 66.667 28.56 0.00 41.17 3.07
1973 2135 1.300963 GACTCTGCAATCAGCCCCA 59.699 57.895 0.00 0.00 44.83 4.96
1986 2148 1.056700 AGCCCCACATCCTTATCGCT 61.057 55.000 0.00 0.00 0.00 4.93
1987 2149 0.685097 GCCCCACATCCTTATCGCTA 59.315 55.000 0.00 0.00 0.00 4.26
1988 2150 1.071699 GCCCCACATCCTTATCGCTAA 59.928 52.381 0.00 0.00 0.00 3.09
1989 2151 2.872038 GCCCCACATCCTTATCGCTAAG 60.872 54.545 0.00 0.00 35.15 2.18
1994 2156 5.453339 CCCACATCCTTATCGCTAAGAAAGA 60.453 44.000 7.59 0.00 37.16 2.52
2007 2169 4.695928 GCTAAGAAAGAAGGAACACCGAAT 59.304 41.667 0.00 0.00 0.00 3.34
2062 2226 2.313427 TTGTCTGGCCCATACCCCC 61.313 63.158 0.00 0.00 0.00 5.40
2145 2312 2.043953 GGGCCACCATCACCCTTC 60.044 66.667 4.39 0.00 40.75 3.46
2146 2313 2.616458 GGGCCACCATCACCCTTCT 61.616 63.158 4.39 0.00 40.75 2.85
2147 2314 1.077429 GGCCACCATCACCCTTCTC 60.077 63.158 0.00 0.00 0.00 2.87
2176 2343 1.113788 TGCTTTGCTTTGTCCTTGCT 58.886 45.000 0.00 0.00 0.00 3.91
2179 2346 0.104671 TTTGCTTTGTCCTTGCTGCC 59.895 50.000 0.00 0.00 0.00 4.85
2249 2416 1.633945 CTTAACCCCCACAGCTAAGGT 59.366 52.381 3.22 0.00 0.00 3.50
2250 2417 0.988832 TAACCCCCACAGCTAAGGTG 59.011 55.000 3.22 0.00 37.06 4.00
2290 2461 6.461577 AGATCAGATCTGGAGACCTGTATA 57.538 41.667 22.42 0.00 38.44 1.47
2371 2544 1.749286 GCACCGCCCATACCAATAACT 60.749 52.381 0.00 0.00 0.00 2.24
2450 2628 3.988976 TCAATCAGTTCCTCCTCCTTG 57.011 47.619 0.00 0.00 0.00 3.61
2451 2629 3.251484 TCAATCAGTTCCTCCTCCTTGT 58.749 45.455 0.00 0.00 0.00 3.16
2452 2630 4.425772 TCAATCAGTTCCTCCTCCTTGTA 58.574 43.478 0.00 0.00 0.00 2.41
2453 2631 4.223032 TCAATCAGTTCCTCCTCCTTGTAC 59.777 45.833 0.00 0.00 0.00 2.90
2650 2833 5.227908 CCTCACACGAGTACATACAAAGTT 58.772 41.667 0.00 0.00 37.59 2.66
2678 2864 6.782986 TCATAATTCAGTGGGATTAGGATGG 58.217 40.000 9.13 0.00 0.00 3.51
2700 2886 3.103213 ACAGGCAGTGGGTTGGGT 61.103 61.111 0.00 0.00 0.00 4.51
2701 2887 2.282462 CAGGCAGTGGGTTGGGTC 60.282 66.667 0.00 0.00 0.00 4.46
2702 2888 3.953775 AGGCAGTGGGTTGGGTCG 61.954 66.667 0.00 0.00 0.00 4.79
2724 2910 4.025730 CGGTTACTCGATTGGTTGATGATG 60.026 45.833 0.00 0.00 0.00 3.07
2725 2911 5.116180 GGTTACTCGATTGGTTGATGATGA 58.884 41.667 0.00 0.00 0.00 2.92
2726 2912 5.760253 GGTTACTCGATTGGTTGATGATGAT 59.240 40.000 0.00 0.00 0.00 2.45
2727 2913 6.293081 GGTTACTCGATTGGTTGATGATGATG 60.293 42.308 0.00 0.00 0.00 3.07
2728 2914 5.027293 ACTCGATTGGTTGATGATGATGA 57.973 39.130 0.00 0.00 0.00 2.92
2757 2943 6.753279 TGATTTGTTGCTCTGTTTTTCTCTTG 59.247 34.615 0.00 0.00 0.00 3.02
2788 2974 2.719979 GCGGCGTCGAGGATAAGA 59.280 61.111 16.53 0.00 39.00 2.10
3015 3202 4.764771 TGATTGGGGCTGGCTGGC 62.765 66.667 9.53 9.53 40.96 4.85
3049 3240 2.804167 CCAGCAGTCTCGCTCGAT 59.196 61.111 0.00 0.00 41.38 3.59
3137 3329 1.746787 ACGTGCGTGTGATGTATAGGA 59.253 47.619 0.00 0.00 0.00 2.94
3212 3404 3.438216 TGGAAATTCCACTGATGCTGA 57.562 42.857 11.23 0.00 42.67 4.26
3213 3405 3.972133 TGGAAATTCCACTGATGCTGAT 58.028 40.909 11.23 0.00 42.67 2.90
3270 3467 4.579340 CCGCTCTTCAAGATGGTACTACTA 59.421 45.833 0.00 0.00 0.00 1.82
3271 3468 5.505985 CCGCTCTTCAAGATGGTACTACTAC 60.506 48.000 0.00 0.00 0.00 2.73
3272 3469 5.297278 CGCTCTTCAAGATGGTACTACTACT 59.703 44.000 0.00 0.00 0.00 2.57
3326 3526 2.223947 GGTGAAATTGTTCCAGGCGTTT 60.224 45.455 0.00 0.00 32.28 3.60
3327 3527 3.049912 GTGAAATTGTTCCAGGCGTTTC 58.950 45.455 0.00 0.00 32.28 2.78
3329 3529 3.383185 TGAAATTGTTCCAGGCGTTTCTT 59.617 39.130 0.00 0.00 32.28 2.52
3330 3530 3.643159 AATTGTTCCAGGCGTTTCTTC 57.357 42.857 0.00 0.00 0.00 2.87
3331 3531 2.045561 TTGTTCCAGGCGTTTCTTCA 57.954 45.000 0.00 0.00 0.00 3.02
3347 3547 0.320374 TTCACCTCTGTTACGCCCAG 59.680 55.000 0.00 0.00 0.00 4.45
3349 3549 2.125106 CCTCTGTTACGCCCAGCC 60.125 66.667 0.00 0.00 0.00 4.85
3352 3552 2.257409 CTCTGTTACGCCCAGCCCAT 62.257 60.000 0.00 0.00 0.00 4.00
3415 3615 6.435292 TTTTGTAAGGAACTAGAAGGAGCT 57.565 37.500 0.00 0.00 38.49 4.09
3420 3620 0.808060 GAACTAGAAGGAGCTGCGCC 60.808 60.000 15.06 15.06 0.00 6.53
3426 3626 2.514505 GAAGGAGCTGCGCCGTTTTC 62.515 60.000 16.78 11.37 0.00 2.29
3429 3629 4.947147 AGCTGCGCCGTTTTCCCA 62.947 61.111 4.18 0.00 0.00 4.37
3441 3641 1.804396 TTTTCCCATGGCAGCGTGTG 61.804 55.000 6.09 0.00 0.00 3.82
3448 3648 0.743688 ATGGCAGCGTGTGTTTTTCA 59.256 45.000 0.00 0.00 0.00 2.69
3454 3654 0.934436 GCGTGTGTTTTTCATGCGCT 60.934 50.000 9.73 0.00 43.19 5.92
3455 3655 1.476074 CGTGTGTTTTTCATGCGCTT 58.524 45.000 9.73 0.00 0.00 4.68
3456 3656 1.851666 CGTGTGTTTTTCATGCGCTTT 59.148 42.857 9.73 0.00 0.00 3.51
3457 3657 2.346558 CGTGTGTTTTTCATGCGCTTTG 60.347 45.455 9.73 6.78 0.00 2.77
3458 3658 1.592081 TGTGTTTTTCATGCGCTTTGC 59.408 42.857 9.73 0.00 46.70 3.68
3459 3659 1.860326 GTGTTTTTCATGCGCTTTGCT 59.140 42.857 9.73 0.00 46.63 3.91
3460 3660 1.859703 TGTTTTTCATGCGCTTTGCTG 59.140 42.857 9.73 0.00 46.63 4.41
3461 3661 0.860533 TTTTTCATGCGCTTTGCTGC 59.139 45.000 9.73 0.00 46.63 5.25
3469 3669 3.466879 GCTTTGCTGCGCCAAATC 58.533 55.556 4.18 0.72 34.50 2.17
3472 3680 0.387112 CTTTGCTGCGCCAAATCGAA 60.387 50.000 4.18 0.00 34.50 3.71
3483 3691 5.031578 GCGCCAAATCGAAACAACATAATA 58.968 37.500 0.00 0.00 0.00 0.98
3560 3771 5.539955 AGGACAAAAGCATACACCAATCTTT 59.460 36.000 0.00 0.00 0.00 2.52
3570 3781 7.712639 AGCATACACCAATCTTTGTATACTCAG 59.287 37.037 4.17 0.22 36.90 3.35
3650 3862 6.998074 AGGTAGATCAACTTGAACACATTTCA 59.002 34.615 0.00 0.00 0.00 2.69
3651 3863 7.173907 AGGTAGATCAACTTGAACACATTTCAG 59.826 37.037 0.00 0.00 0.00 3.02
3652 3864 5.766222 AGATCAACTTGAACACATTTCAGC 58.234 37.500 0.00 0.00 0.00 4.26
3670 3883 2.805099 CAGCTGGTGTGAAGAGAAGTTC 59.195 50.000 5.57 0.00 0.00 3.01
3686 3899 9.902684 AAGAGAAGTTCTGACATTCATCATATT 57.097 29.630 10.90 0.00 35.91 1.28
3699 3912 9.363763 ACATTCATCATATTTACTCTAGCATCG 57.636 33.333 0.00 0.00 0.00 3.84
3743 3956 3.118112 AGCTGCAACTCTAGCATACCATT 60.118 43.478 1.02 0.00 41.82 3.16
3747 3960 6.194796 TGCAACTCTAGCATACCATTTTTC 57.805 37.500 0.00 0.00 37.02 2.29
3751 3964 7.814587 GCAACTCTAGCATACCATTTTTCTTTT 59.185 33.333 0.00 0.00 0.00 2.27
3778 3991 4.942761 TTTTTGAAAGATCCAGCAGCTT 57.057 36.364 0.00 0.00 0.00 3.74
3841 4054 9.492973 AAATACAAAAGGTGGATTTTGATCAAG 57.507 29.630 16.40 0.00 46.92 3.02
3890 4103 2.983592 CCGGTGGCCAACAAGGTC 60.984 66.667 23.36 0.00 44.53 3.85
3910 4123 1.835121 GTTTTGTCAGGCAAACGACC 58.165 50.000 0.00 0.00 45.70 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 4.150454 CGGGGGCTCCTCTCCTCT 62.150 72.222 0.52 0.00 0.00 3.69
105 106 2.221906 TAGAGAAAGCGGTGGCGACC 62.222 60.000 8.02 8.02 46.35 4.79
124 125 0.240945 CCATTTGCCGCGAGAAAAGT 59.759 50.000 8.23 0.00 0.00 2.66
228 254 1.731257 GCCTAGCATCTACGCGCTC 60.731 63.158 5.73 0.00 39.70 5.03
229 255 2.336809 GCCTAGCATCTACGCGCT 59.663 61.111 5.73 0.00 42.34 5.92
230 256 3.100191 CGCCTAGCATCTACGCGC 61.100 66.667 5.73 0.00 36.02 6.86
231 257 2.429236 CCGCCTAGCATCTACGCG 60.429 66.667 3.53 3.53 42.37 6.01
302 328 0.109597 CTTGCACCAAGATTCGCACC 60.110 55.000 0.00 0.00 43.42 5.01
303 329 0.874390 TCTTGCACCAAGATTCGCAC 59.126 50.000 3.69 0.00 44.27 5.34
304 330 3.320823 TCTTGCACCAAGATTCGCA 57.679 47.368 3.69 0.00 44.27 5.10
489 527 3.006752 AGTCTGCCTAGATAGATTGCTGC 59.993 47.826 0.00 0.00 34.94 5.25
492 530 4.599047 ACAGTCTGCCTAGATAGATTGC 57.401 45.455 14.34 0.00 34.98 3.56
493 531 8.121305 AGATAACAGTCTGCCTAGATAGATTG 57.879 38.462 13.41 13.41 36.90 2.67
494 532 8.584157 CAAGATAACAGTCTGCCTAGATAGATT 58.416 37.037 0.00 0.00 34.94 2.40
495 533 7.947332 TCAAGATAACAGTCTGCCTAGATAGAT 59.053 37.037 0.00 0.00 34.94 1.98
496 534 7.290813 TCAAGATAACAGTCTGCCTAGATAGA 58.709 38.462 0.00 0.00 34.94 1.98
497 535 7.517614 TCAAGATAACAGTCTGCCTAGATAG 57.482 40.000 0.00 0.00 34.94 2.08
499 537 6.183360 CCTTCAAGATAACAGTCTGCCTAGAT 60.183 42.308 0.00 0.00 34.94 1.98
500 538 5.127845 CCTTCAAGATAACAGTCTGCCTAGA 59.872 44.000 0.00 0.00 0.00 2.43
501 539 5.355596 CCTTCAAGATAACAGTCTGCCTAG 58.644 45.833 0.00 0.00 0.00 3.02
502 540 4.162320 CCCTTCAAGATAACAGTCTGCCTA 59.838 45.833 0.00 0.00 0.00 3.93
550 598 9.803315 TGTTGTTACTTTGCACTAGATAGATAG 57.197 33.333 0.00 0.00 0.00 2.08
575 623 7.219484 ACTCCTTTTACAGTTGATGGAATTG 57.781 36.000 0.00 0.00 29.54 2.32
585 633 7.004691 AGGAATTAGCAACTCCTTTTACAGTT 58.995 34.615 0.00 0.00 36.06 3.16
586 634 6.543735 AGGAATTAGCAACTCCTTTTACAGT 58.456 36.000 0.00 0.00 36.06 3.55
597 645 6.798427 TGTGATAGAGAGGAATTAGCAACT 57.202 37.500 0.00 0.00 0.00 3.16
599 647 8.862325 TTTTTGTGATAGAGAGGAATTAGCAA 57.138 30.769 0.00 0.00 0.00 3.91
601 649 8.499403 ACTTTTTGTGATAGAGAGGAATTAGC 57.501 34.615 0.00 0.00 0.00 3.09
609 657 6.712547 ACAGGGAAACTTTTTGTGATAGAGAG 59.287 38.462 0.00 0.00 0.00 3.20
613 661 8.716646 AAAAACAGGGAAACTTTTTGTGATAG 57.283 30.769 0.00 0.00 29.91 2.08
756 835 2.908351 AGCAGCCCAAAATTCCATTCTT 59.092 40.909 0.00 0.00 0.00 2.52
784 863 4.438336 GGGTCGGCTTTATACAAAAGAAGC 60.438 45.833 1.78 0.00 42.76 3.86
1047 1141 1.069090 AGACGCGTCAAGGAAAGCA 59.931 52.632 37.85 0.00 0.00 3.91
1085 1179 3.908382 GCCGCGAAATCATCATAAACATC 59.092 43.478 8.23 0.00 0.00 3.06
1110 1205 3.649986 GTCGCCTGCACACACCAC 61.650 66.667 0.00 0.00 0.00 4.16
1411 1506 8.929827 TGATTTAATCGATTTGACGGTAAGTA 57.070 30.769 17.19 0.00 0.00 2.24
1412 1507 7.837202 TGATTTAATCGATTTGACGGTAAGT 57.163 32.000 17.19 0.00 0.00 2.24
1413 1508 7.798516 CCATGATTTAATCGATTTGACGGTAAG 59.201 37.037 17.19 0.00 0.00 2.34
1603 1751 4.792057 GCATATCATCCAAAGAGCAGTTGC 60.792 45.833 0.00 0.00 42.49 4.17
1619 1767 8.764287 CGTAGTTTATGAATGACTTGCATATCA 58.236 33.333 3.12 3.12 35.78 2.15
1762 1915 7.347222 AGTTGGTAGGACTATGGTCAATTGATA 59.653 37.037 12.12 4.62 43.77 2.15
1819 1975 5.427378 TCCTTTCTCAATGACGATGCAATA 58.573 37.500 0.00 0.00 0.00 1.90
1832 1988 5.808366 TTTAGTCTGAGCTCCTTTCTCAA 57.192 39.130 12.15 0.19 39.77 3.02
1838 1994 8.325046 ACATCTTAATTTTAGTCTGAGCTCCTT 58.675 33.333 12.15 0.00 0.00 3.36
1841 1997 7.011857 CCCACATCTTAATTTTAGTCTGAGCTC 59.988 40.741 6.82 6.82 0.00 4.09
1845 2001 5.885912 GCCCCACATCTTAATTTTAGTCTGA 59.114 40.000 0.00 0.00 0.00 3.27
1864 2026 1.135094 GATGGAGAGAAGATGCCCCA 58.865 55.000 0.00 0.00 0.00 4.96
1874 2036 2.725312 GCGTGGGCAGATGGAGAGA 61.725 63.158 0.00 0.00 39.62 3.10
1887 2049 3.813166 CCCTAGTTATATTTGGTGCGTGG 59.187 47.826 0.00 0.00 0.00 4.94
1891 2053 2.225727 GCGCCCTAGTTATATTTGGTGC 59.774 50.000 0.00 0.00 41.51 5.01
1893 2055 2.709397 AGGCGCCCTAGTTATATTTGGT 59.291 45.455 26.15 0.00 28.47 3.67
1894 2056 3.074412 CAGGCGCCCTAGTTATATTTGG 58.926 50.000 26.15 0.00 29.64 3.28
1895 2057 3.997021 CTCAGGCGCCCTAGTTATATTTG 59.003 47.826 26.15 10.44 29.64 2.32
1897 2059 3.507411 TCTCAGGCGCCCTAGTTATATT 58.493 45.455 26.15 0.00 29.64 1.28
1898 2060 3.093057 CTCTCAGGCGCCCTAGTTATAT 58.907 50.000 26.15 0.00 29.64 0.86
1899 2061 2.515854 CTCTCAGGCGCCCTAGTTATA 58.484 52.381 26.15 3.68 29.64 0.98
1900 2062 1.333177 CTCTCAGGCGCCCTAGTTAT 58.667 55.000 26.15 0.00 29.64 1.89
1901 2063 1.392710 GCTCTCAGGCGCCCTAGTTA 61.393 60.000 26.15 4.82 29.64 2.24
1904 2066 2.433231 GATGCTCTCAGGCGCCCTAG 62.433 65.000 26.15 21.09 34.52 3.02
1905 2067 2.444706 ATGCTCTCAGGCGCCCTA 60.445 61.111 26.15 10.98 34.52 3.53
1906 2068 3.859414 GATGCTCTCAGGCGCCCT 61.859 66.667 26.15 7.86 34.52 5.19
1907 2069 3.687321 TTGATGCTCTCAGGCGCCC 62.687 63.158 26.15 7.06 34.68 6.13
1909 2071 0.742281 TTCTTGATGCTCTCAGGCGC 60.742 55.000 0.00 0.00 34.68 6.53
1911 2073 3.693085 TCAATTTCTTGATGCTCTCAGGC 59.307 43.478 0.00 0.00 36.46 4.85
1912 2074 4.698780 TGTCAATTTCTTGATGCTCTCAGG 59.301 41.667 0.00 0.00 43.08 3.86
1913 2075 5.163744 CCTGTCAATTTCTTGATGCTCTCAG 60.164 44.000 0.00 0.00 43.08 3.35
1914 2076 4.698780 CCTGTCAATTTCTTGATGCTCTCA 59.301 41.667 0.00 0.00 43.08 3.27
1915 2077 4.940046 TCCTGTCAATTTCTTGATGCTCTC 59.060 41.667 0.00 0.00 43.08 3.20
1916 2078 4.914983 TCCTGTCAATTTCTTGATGCTCT 58.085 39.130 0.00 0.00 43.08 4.09
1917 2079 5.633830 TTCCTGTCAATTTCTTGATGCTC 57.366 39.130 0.00 0.00 43.08 4.26
1918 2080 6.436532 AGATTTCCTGTCAATTTCTTGATGCT 59.563 34.615 0.00 0.00 43.08 3.79
1924 2086 5.771666 TCTGCAGATTTCCTGTCAATTTCTT 59.228 36.000 13.74 0.00 44.71 2.52
1973 2135 6.098409 TCCTTCTTTCTTAGCGATAAGGATGT 59.902 38.462 19.57 0.00 36.87 3.06
1986 2148 5.865552 CGTATTCGGTGTTCCTTCTTTCTTA 59.134 40.000 0.00 0.00 0.00 2.10
1987 2149 4.689345 CGTATTCGGTGTTCCTTCTTTCTT 59.311 41.667 0.00 0.00 0.00 2.52
1988 2150 4.243270 CGTATTCGGTGTTCCTTCTTTCT 58.757 43.478 0.00 0.00 0.00 2.52
1989 2151 3.181523 GCGTATTCGGTGTTCCTTCTTTC 60.182 47.826 0.00 0.00 37.56 2.62
1994 2156 2.277084 GATGCGTATTCGGTGTTCCTT 58.723 47.619 0.00 0.00 37.56 3.36
2007 2169 6.422400 GGAAAATGGAAAAAGTTTGATGCGTA 59.578 34.615 0.00 0.00 0.00 4.42
2062 2226 0.662619 TTGAGTTTGACAAGGCAGCG 59.337 50.000 0.00 0.00 0.00 5.18
2140 2307 2.512705 AGCAAGCAAGAAAGAGAAGGG 58.487 47.619 0.00 0.00 0.00 3.95
2141 2308 4.296690 CAAAGCAAGCAAGAAAGAGAAGG 58.703 43.478 0.00 0.00 0.00 3.46
2144 2311 2.954318 AGCAAAGCAAGCAAGAAAGAGA 59.046 40.909 0.00 0.00 0.00 3.10
2145 2312 3.366440 AGCAAAGCAAGCAAGAAAGAG 57.634 42.857 0.00 0.00 0.00 2.85
2146 2313 3.806625 AAGCAAAGCAAGCAAGAAAGA 57.193 38.095 0.00 0.00 0.00 2.52
2147 2314 3.619929 ACAAAGCAAAGCAAGCAAGAAAG 59.380 39.130 0.00 0.00 0.00 2.62
2176 2343 1.890876 ACAGTAACAAAGATGCGGCA 58.109 45.000 4.58 4.58 0.00 5.69
2179 2346 3.498397 AGGACAACAGTAACAAAGATGCG 59.502 43.478 0.00 0.00 0.00 4.73
2249 2416 0.107214 CTGATTAAAGAGCCCGCCCA 60.107 55.000 0.00 0.00 0.00 5.36
2250 2417 0.180406 TCTGATTAAAGAGCCCGCCC 59.820 55.000 0.00 0.00 0.00 6.13
2251 2418 2.147150 GATCTGATTAAAGAGCCCGCC 58.853 52.381 0.00 0.00 0.00 6.13
2252 2419 2.805099 CTGATCTGATTAAAGAGCCCGC 59.195 50.000 0.00 0.00 31.42 6.13
2332 2503 1.821332 CTGCTTTCGATGAGGGGCC 60.821 63.158 0.00 0.00 0.00 5.80
2384 2557 4.586001 AGCCAGTGAAATGTTGACTGAAAT 59.414 37.500 8.86 0.00 39.64 2.17
2450 2628 7.010183 TCGTGCTTGCTTTTGATAAGATAGTAC 59.990 37.037 0.00 0.00 0.00 2.73
2451 2629 7.039270 TCGTGCTTGCTTTTGATAAGATAGTA 58.961 34.615 0.00 0.00 0.00 1.82
2452 2630 5.874810 TCGTGCTTGCTTTTGATAAGATAGT 59.125 36.000 0.00 0.00 0.00 2.12
2453 2631 6.349973 TCGTGCTTGCTTTTGATAAGATAG 57.650 37.500 0.00 0.00 0.00 2.08
2505 2688 7.336176 AGGCTTGCTAACCTAACAGTATTTAAC 59.664 37.037 0.00 0.00 33.38 2.01
2510 2693 4.225267 ACAGGCTTGCTAACCTAACAGTAT 59.775 41.667 0.00 0.00 33.38 2.12
2650 2833 7.638444 TCCTAATCCCACTGAATTATGAAACA 58.362 34.615 0.00 0.00 0.00 2.83
2693 2879 0.533951 ATCGAGTAACCGACCCAACC 59.466 55.000 0.00 0.00 41.70 3.77
2700 2886 3.193903 TCATCAACCAATCGAGTAACCGA 59.806 43.478 0.00 0.00 43.16 4.69
2701 2887 3.517602 TCATCAACCAATCGAGTAACCG 58.482 45.455 0.00 0.00 0.00 4.44
2702 2888 5.116180 TCATCATCAACCAATCGAGTAACC 58.884 41.667 0.00 0.00 0.00 2.85
2703 2889 6.479990 TCATCATCATCAACCAATCGAGTAAC 59.520 38.462 0.00 0.00 0.00 2.50
2724 2910 6.132791 ACAGAGCAACAAATCATCATCATC 57.867 37.500 0.00 0.00 0.00 2.92
2725 2911 6.525578 AACAGAGCAACAAATCATCATCAT 57.474 33.333 0.00 0.00 0.00 2.45
2726 2912 5.970317 AACAGAGCAACAAATCATCATCA 57.030 34.783 0.00 0.00 0.00 3.07
2727 2913 7.597743 AGAAAAACAGAGCAACAAATCATCATC 59.402 33.333 0.00 0.00 0.00 2.92
2728 2914 7.439381 AGAAAAACAGAGCAACAAATCATCAT 58.561 30.769 0.00 0.00 0.00 2.45
2788 2974 0.530744 TCGCGTACAGAATCTTGGCT 59.469 50.000 5.77 0.00 0.00 4.75
3015 3202 2.263741 GGCAGAGCACACCAACCAG 61.264 63.158 0.00 0.00 0.00 4.00
3049 3240 0.389817 CAAACCCTCGTCAGATCGCA 60.390 55.000 0.00 0.00 0.00 5.10
3137 3329 0.971959 CTGCCACTCTCTCAGCTCCT 60.972 60.000 0.00 0.00 0.00 3.69
3212 3404 0.035439 AAACGAAGTCGGGGCATCAT 60.035 50.000 5.60 0.00 45.00 2.45
3213 3405 0.953471 CAAACGAAGTCGGGGCATCA 60.953 55.000 5.60 0.00 45.00 3.07
3270 3467 1.066143 CCCAGAGCAATCAACCGTAGT 60.066 52.381 0.00 0.00 0.00 2.73
3271 3468 1.066143 ACCCAGAGCAATCAACCGTAG 60.066 52.381 0.00 0.00 0.00 3.51
3272 3469 0.981183 ACCCAGAGCAATCAACCGTA 59.019 50.000 0.00 0.00 0.00 4.02
3326 3526 0.606604 GGGCGTAACAGAGGTGAAGA 59.393 55.000 0.00 0.00 0.00 2.87
3327 3527 0.320374 TGGGCGTAACAGAGGTGAAG 59.680 55.000 0.00 0.00 0.00 3.02
3329 3529 1.972198 CTGGGCGTAACAGAGGTGA 59.028 57.895 0.00 0.00 38.20 4.02
3330 3530 1.741770 GCTGGGCGTAACAGAGGTG 60.742 63.158 7.21 0.00 38.20 4.00
3331 3531 2.663196 GCTGGGCGTAACAGAGGT 59.337 61.111 7.21 0.00 38.20 3.85
3347 3547 5.109210 GTCCTTACAAATTTTGCTATGGGC 58.891 41.667 9.04 9.61 42.22 5.36
3349 3549 5.799936 CGTGTCCTTACAAATTTTGCTATGG 59.200 40.000 9.04 11.23 37.36 2.74
3352 3552 5.992829 TCTCGTGTCCTTACAAATTTTGCTA 59.007 36.000 9.04 0.00 37.36 3.49
3357 3557 5.855045 AGTCTCTCGTGTCCTTACAAATTT 58.145 37.500 0.00 0.00 37.36 1.82
3415 3615 3.369400 CCATGGGAAAACGGCGCA 61.369 61.111 10.83 0.00 0.00 6.09
3420 3620 2.179018 CGCTGCCATGGGAAAACG 59.821 61.111 15.13 11.12 0.00 3.60
3426 3626 2.086251 AAAACACACGCTGCCATGGG 62.086 55.000 15.13 0.00 0.00 4.00
3429 3629 0.743688 TGAAAAACACACGCTGCCAT 59.256 45.000 0.00 0.00 0.00 4.40
3434 3634 0.934436 GCGCATGAAAAACACACGCT 60.934 50.000 0.30 0.00 45.95 5.07
3441 3641 1.397567 GCAGCAAAGCGCATGAAAAAC 60.398 47.619 11.47 0.00 46.13 2.43
3458 3658 1.052287 GTTGTTTCGATTTGGCGCAG 58.948 50.000 10.83 0.00 0.00 5.18
3459 3659 0.382158 TGTTGTTTCGATTTGGCGCA 59.618 45.000 10.83 0.00 0.00 6.09
3460 3660 1.696988 ATGTTGTTTCGATTTGGCGC 58.303 45.000 0.00 0.00 0.00 6.53
3461 3661 7.643764 AGAATATTATGTTGTTTCGATTTGGCG 59.356 33.333 0.00 0.00 0.00 5.69
3462 3662 8.856490 AGAATATTATGTTGTTTCGATTTGGC 57.144 30.769 0.00 0.00 0.00 4.52
3512 3722 4.458989 AGGAATGCGCTGTAATTTTTCTCA 59.541 37.500 9.73 0.00 0.00 3.27
3524 3735 1.737838 TTTGTCCTAGGAATGCGCTG 58.262 50.000 14.65 0.00 0.00 5.18
3618 3829 8.136165 GTGTTCAAGTTGATCTACCTATACGAT 58.864 37.037 6.36 0.00 0.00 3.73
3619 3830 7.121611 TGTGTTCAAGTTGATCTACCTATACGA 59.878 37.037 6.36 0.00 0.00 3.43
3621 3832 9.601217 AATGTGTTCAAGTTGATCTACCTATAC 57.399 33.333 6.36 0.00 0.00 1.47
3650 3862 2.703007 AGAACTTCTCTTCACACCAGCT 59.297 45.455 0.00 0.00 0.00 4.24
3651 3863 2.805099 CAGAACTTCTCTTCACACCAGC 59.195 50.000 0.00 0.00 29.07 4.85
3652 3864 4.054671 GTCAGAACTTCTCTTCACACCAG 58.945 47.826 0.00 0.00 29.07 4.00
3670 3883 9.702494 TGCTAGAGTAAATATGATGAATGTCAG 57.298 33.333 0.00 0.00 0.00 3.51
3686 3899 6.697455 CAGTAATTTGCTCGATGCTAGAGTAA 59.303 38.462 0.00 3.93 43.37 2.24
3712 3925 3.799281 AGAGTTGCAGCTACTGAGATC 57.201 47.619 14.67 0.00 32.44 2.75
3751 3964 8.752187 AGCTGCTGGATCTTTCAAAAATAAATA 58.248 29.630 0.00 0.00 0.00 1.40
3752 3965 7.618137 AGCTGCTGGATCTTTCAAAAATAAAT 58.382 30.769 0.00 0.00 0.00 1.40
3756 3969 5.235516 CAAGCTGCTGGATCTTTCAAAAAT 58.764 37.500 1.35 0.00 0.00 1.82
3758 3971 3.553508 GCAAGCTGCTGGATCTTTCAAAA 60.554 43.478 8.57 0.00 40.96 2.44
3778 3991 3.817084 GCTATGATCAATACAAGCCAGCA 59.183 43.478 0.00 0.00 0.00 4.41
3860 4073 0.176910 CCACCGGTGGCAAAGTTTTT 59.823 50.000 39.44 0.00 44.73 1.94
3873 4086 2.983592 GACCTTGTTGGCCACCGG 60.984 66.667 3.88 6.04 40.22 5.28
3879 4092 1.133407 TGACAAAACGACCTTGTTGGC 59.867 47.619 0.00 0.00 37.14 4.52


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

AutoCloner maintained by Alex Coulton.