Multiple sequence alignment - TraesCS5B01G338300

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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 TraesCS5B01G338300 chr5B 100.000 9279 0 0 1 9279 522397570 522406848 0.000000e+00 17136.0
1 TraesCS5B01G338300 chr5B 96.198 2946 104 2 3393 6335 522657249 522660189 0.000000e+00 4813.0
2 TraesCS5B01G338300 chr5B 89.629 2854 169 60 610 3365 524417004 524419828 0.000000e+00 3513.0
3 TraesCS5B01G338300 chr5B 94.098 2135 121 2 3393 5527 524419993 524422122 0.000000e+00 3240.0
4 TraesCS5B01G338300 chr5B 94.394 1873 99 3 5639 7508 524446394 524448263 0.000000e+00 2872.0
5 TraesCS5B01G338300 chr5B 93.485 1934 113 7 6379 8312 522660187 522662107 0.000000e+00 2861.0
6 TraesCS5B01G338300 chr5B 91.030 1505 78 25 1660 3139 522655272 522656744 0.000000e+00 1978.0
7 TraesCS5B01G338300 chr5B 92.369 1258 61 16 7662 8919 522864512 522863290 0.000000e+00 1759.0
8 TraesCS5B01G338300 chr5B 92.988 656 27 11 515 1168 522654330 522654968 0.000000e+00 939.0
9 TraesCS5B01G338300 chr5B 88.864 449 37 9 78 515 522653849 522654295 2.950000e-149 540.0
10 TraesCS5B01G338300 chr5B 93.004 243 16 1 3130 3371 522874681 522874439 4.120000e-93 353.0
11 TraesCS5B01G338300 chr5B 87.109 256 21 9 1416 1669 522655009 522655254 7.100000e-71 279.0
12 TraesCS5B01G338300 chr5B 97.403 154 4 0 21 174 524416830 524416983 7.150000e-66 263.0
13 TraesCS5B01G338300 chr5B 90.404 198 12 4 80 275 522890783 522890591 4.300000e-63 254.0
14 TraesCS5B01G338300 chr5B 90.404 198 12 4 80 275 522892798 522892606 4.300000e-63 254.0
15 TraesCS5B01G338300 chr5B 89.899 198 13 4 80 275 522891861 522891669 2.000000e-61 248.0
16 TraesCS5B01G338300 chr5B 89.340 197 15 3 80 275 522877539 522877348 9.310000e-60 243.0
17 TraesCS5B01G338300 chr5B 89.394 198 14 4 80 275 522878827 522878635 9.310000e-60 243.0
18 TraesCS5B01G338300 chr5B 88.889 198 15 4 80 275 522880125 522879933 4.330000e-58 237.0
19 TraesCS5B01G338300 chr5B 88.889 198 15 4 80 275 522890129 522889937 4.330000e-58 237.0
20 TraesCS5B01G338300 chr5B 98.425 127 2 0 5522 5648 524444872 524444998 3.370000e-54 224.0
21 TraesCS5B01G338300 chr5B 77.907 172 20 11 8579 8740 524449327 524449490 3.570000e-14 91.6
22 TraesCS5B01G338300 chr5A 94.888 5164 234 11 3402 8561 546778091 546772954 0.000000e+00 8046.0
23 TraesCS5B01G338300 chr5A 93.762 4328 248 10 4025 8339 547011097 547006779 0.000000e+00 6477.0
24 TraesCS5B01G338300 chr5A 92.595 1526 84 17 1868 3370 547013174 547011655 0.000000e+00 2165.0
25 TraesCS5B01G338300 chr5A 92.653 1293 64 14 1868 3132 546779947 546778658 0.000000e+00 1832.0
26 TraesCS5B01G338300 chr5A 93.268 713 43 4 8569 9279 546772899 546772190 0.000000e+00 1046.0
27 TraesCS5B01G338300 chr5A 94.891 137 6 1 1666 1801 546780528 546780392 7.300000e-51 213.0
28 TraesCS5B01G338300 chr5D 93.881 5181 278 19 1613 6769 513299205 513304370 0.000000e+00 7775.0
29 TraesCS5B01G338300 chr5D 95.104 4269 175 15 1613 5857 431772547 431776805 0.000000e+00 6695.0
30 TraesCS5B01G338300 chr5D 94.539 3351 178 2 3393 6740 433642371 433645719 0.000000e+00 5169.0
31 TraesCS5B01G338300 chr5D 94.126 3371 187 4 3402 6769 513390042 513386680 0.000000e+00 5118.0
32 TraesCS5B01G338300 chr5D 93.763 3319 202 3 3402 6716 431835000 431831683 0.000000e+00 4977.0
33 TraesCS5B01G338300 chr5D 90.821 2571 190 25 6711 9278 513304369 513306896 0.000000e+00 3398.0
34 TraesCS5B01G338300 chr5D 92.358 2316 174 1 4457 6769 433690222 433687907 0.000000e+00 3293.0
35 TraesCS5B01G338300 chr5D 93.483 1780 88 14 1613 3371 513391985 513390213 0.000000e+00 2619.0
36 TraesCS5B01G338300 chr5D 92.921 1780 93 15 1613 3371 433640442 433642209 0.000000e+00 2558.0
37 TraesCS5B01G338300 chr5D 92.631 1737 89 11 1660 3371 431836893 431835171 0.000000e+00 2462.0
38 TraesCS5B01G338300 chr5D 92.293 1622 115 3 6711 8332 433687908 433686297 0.000000e+00 2294.0
39 TraesCS5B01G338300 chr5D 90.852 1749 87 18 1661 3371 433692641 433690928 0.000000e+00 2276.0
40 TraesCS5B01G338300 chr5D 92.293 1583 117 3 6711 8293 513386681 513385104 0.000000e+00 2242.0
41 TraesCS5B01G338300 chr5D 92.366 1572 113 2 6712 8276 433645748 433647319 0.000000e+00 2231.0
42 TraesCS5B01G338300 chr5D 92.003 1588 123 2 6711 8298 431831631 431830048 0.000000e+00 2226.0
43 TraesCS5B01G338300 chr5D 95.184 976 28 7 712 1669 431837885 431836911 0.000000e+00 1524.0
44 TraesCS5B01G338300 chr5D 92.091 923 49 16 514 1425 433693734 433692825 0.000000e+00 1279.0
45 TraesCS5B01G338300 chr5D 88.889 1071 59 34 514 1543 513393033 513391982 0.000000e+00 1264.0
46 TraesCS5B01G338300 chr5D 88.980 971 52 21 514 1449 513298077 513299027 0.000000e+00 1149.0
47 TraesCS5B01G338300 chr5D 94.126 715 25 11 514 1221 431771499 431772203 0.000000e+00 1072.0
48 TraesCS5B01G338300 chr5D 97.032 539 16 0 3403 3941 433690757 433690219 0.000000e+00 907.0
49 TraesCS5B01G338300 chr5D 89.079 760 38 21 712 1435 433639362 433640112 0.000000e+00 902.0
50 TraesCS5B01G338300 chr5D 78.923 427 53 24 8572 8975 513384759 513384347 1.200000e-63 255.0
51 TraesCS5B01G338300 chr5D 78.973 409 49 24 8579 8965 431829699 431829306 2.590000e-60 244.0
52 TraesCS5B01G338300 chr5D 87.425 167 8 9 1512 1669 433692823 433692661 7.400000e-41 180.0
53 TraesCS5B01G338300 chr5D 79.902 204 18 14 514 715 431838205 431838023 2.720000e-25 128.0
54 TraesCS5B01G338300 chr5D 84.545 110 12 3 8579 8686 513352834 513352728 4.580000e-18 104.0
55 TraesCS5B01G338300 chr5D 82.727 110 14 3 8579 8686 431815982 431815876 9.920000e-15 93.5
56 TraesCS5B01G338300 chr5D 82.727 110 14 3 8579 8686 433647827 433647933 9.920000e-15 93.5
57 TraesCS5B01G338300 chr5D 88.525 61 3 3 656 715 433639167 433639224 4.650000e-08 71.3
58 TraesCS5B01G338300 chr2B 88.770 187 20 1 981 1167 697986241 697986426 2.610000e-55 228.0


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 TraesCS5B01G338300 chr5B 522397570 522406848 9278 False 17136.000000 17136 100.000000 1 9279 1 chr5B.!!$F1 9278
1 TraesCS5B01G338300 chr5B 524416830 524422122 5292 False 2338.666667 3513 93.710000 21 5527 3 chr5B.!!$F3 5506
2 TraesCS5B01G338300 chr5B 522653849 522662107 8258 False 1901.666667 4813 91.612333 78 8312 6 chr5B.!!$F2 8234
3 TraesCS5B01G338300 chr5B 522863290 522864512 1222 True 1759.000000 1759 92.369000 7662 8919 1 chr5B.!!$R1 1257
4 TraesCS5B01G338300 chr5B 524444872 524449490 4618 False 1062.533333 2872 90.242000 5522 8740 3 chr5B.!!$F4 3218
5 TraesCS5B01G338300 chr5B 522874439 522880125 5686 True 269.000000 353 90.156750 80 3371 4 chr5B.!!$R2 3291
6 TraesCS5B01G338300 chr5B 522889937 522892798 2861 True 248.250000 254 89.899000 80 275 4 chr5B.!!$R3 195
7 TraesCS5B01G338300 chr5A 547006779 547013174 6395 True 4321.000000 6477 93.178500 1868 8339 2 chr5A.!!$R2 6471
8 TraesCS5B01G338300 chr5A 546772190 546780528 8338 True 2784.250000 8046 93.925000 1666 9279 4 chr5A.!!$R1 7613
9 TraesCS5B01G338300 chr5D 513298077 513306896 8819 False 4107.333333 7775 91.227333 514 9278 3 chr5D.!!$F3 8764
10 TraesCS5B01G338300 chr5D 431771499 431776805 5306 False 3883.500000 6695 94.615000 514 5857 2 chr5D.!!$F1 5343
11 TraesCS5B01G338300 chr5D 513384347 513393033 8686 True 2299.600000 5118 89.542800 514 8975 5 chr5D.!!$R5 8461
12 TraesCS5B01G338300 chr5D 431829306 431838205 8899 True 1926.833333 4977 88.742667 514 8965 6 chr5D.!!$R3 8451
13 TraesCS5B01G338300 chr5D 433639167 433647933 8766 False 1837.466667 5169 90.026167 656 8686 6 chr5D.!!$F2 8030
14 TraesCS5B01G338300 chr5D 433686297 433693734 7437 True 1704.833333 3293 92.008500 514 8332 6 chr5D.!!$R4 7818

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
335 340 0.179084 ACATAAGATCCCGTGGCACG 60.179 55.000 31.78 31.78 42.11 5.34 F
341 346 0.672401 GATCCCGTGGCACGAGAAAA 60.672 55.000 38.91 19.56 46.05 2.29 F
1848 6557 0.323360 TTGGGATTAGGCACTGTGGC 60.323 55.000 25.03 25.03 41.52 5.01 F
1865 6574 0.106521 GGCAGCACAAAACCCACATT 59.893 50.000 0.00 0.00 0.00 2.71 F
2508 8424 0.252696 ACCCTGATGGAGTAGCACCA 60.253 55.000 0.00 0.00 41.83 4.17 F
3892 10301 0.250252 TGAGGAAGAACATGCACGCA 60.250 50.000 0.00 0.00 0.00 5.24 F
4000 10409 1.197430 AGGCAGAGAACAGGGTGGAG 61.197 60.000 0.00 0.00 0.00 3.86 F
4846 11255 1.482182 TCTGATGGGAAGTGGATGTCG 59.518 52.381 0.00 0.00 0.00 4.35 F
5716 13536 0.179018 GGGAGGCATCGGCTTACATT 60.179 55.000 0.00 0.00 38.98 2.71 F
6647 14480 0.771127 TGGTGGCTTAGGCAAAGAGT 59.229 50.000 10.78 0.00 40.46 3.24 F
7414 15310 0.451783 CCGTAACCAATTGCTCTGCC 59.548 55.000 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 6555 0.106521 AATGTGGGTTTTGTGCTGCC 59.893 50.000 0.0 0.00 0.00 4.85 R
1857 6566 2.269940 AGGCTCAGAGTTAATGTGGGT 58.730 47.619 0.0 0.00 0.00 4.51 R
3685 10094 0.824759 AAGGCAGGACGATACAGGTC 59.175 55.000 0.0 0.00 0.00 3.85 R
3847 10256 7.757624 ACTTCAAAGTTCTTCTCACTCGATATC 59.242 37.037 0.0 0.00 35.21 1.63 R
4439 10848 2.981560 CTGGTTTGAGCCGCGCAAT 61.982 57.895 10.5 0.00 0.00 3.56 R
5037 11446 0.766752 AAAAGCAATGGCAGGCCTTT 59.233 45.000 0.0 8.73 44.61 3.11 R
5200 11613 2.622977 GCCCATCAGTCCAACCCATTTA 60.623 50.000 0.0 0.00 0.00 1.40 R
6346 14179 0.107214 TCGATGCCTGGTCAAATCCC 60.107 55.000 0.0 0.00 0.00 3.85 R
7184 15080 0.178831 ACCCATTCTCCACTTCCCCT 60.179 55.000 0.0 0.00 0.00 4.79 R
7835 15731 0.829333 ACATTCAGCAGGCGAGAGAT 59.171 50.000 0.0 0.00 0.00 2.75 R
8812 16950 0.040425 CGAAAAGGCGGACCAACAAG 60.040 55.000 0.0 0.00 39.06 3.16 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
234 237 5.050091 AGCTTCATTACACTCAAACAAGACG 60.050 40.000 0.00 0.00 0.00 4.18
243 246 2.996621 CTCAAACAAGACGGTGATCTCC 59.003 50.000 3.58 3.58 0.00 3.71
262 265 1.148310 CGTGAACCGCAGAATTGAGT 58.852 50.000 0.00 0.00 0.00 3.41
267 270 2.254546 ACCGCAGAATTGAGTGACAA 57.745 45.000 0.00 0.00 42.95 3.18
328 333 5.269459 CGAATAGCAAACATAAGATCCCG 57.731 43.478 0.00 0.00 0.00 5.14
331 336 2.643551 AGCAAACATAAGATCCCGTGG 58.356 47.619 0.00 0.00 0.00 4.94
335 340 0.179084 ACATAAGATCCCGTGGCACG 60.179 55.000 31.78 31.78 42.11 5.34
341 346 0.672401 GATCCCGTGGCACGAGAAAA 60.672 55.000 38.91 19.56 46.05 2.29
344 349 1.890041 CCGTGGCACGAGAAAACCA 60.890 57.895 38.91 0.00 46.05 3.67
352 357 3.308530 GCACGAGAAAACCAAAGGAATG 58.691 45.455 0.00 0.00 0.00 2.67
368 373 3.196254 AGGAATGGTCATTTGAATGGCAC 59.804 43.478 10.16 0.00 42.66 5.01
593 3274 1.191535 GGCACCATTCCTTTTACCCC 58.808 55.000 0.00 0.00 0.00 4.95
894 4682 1.679898 CACTCCTCCACTTCCCACC 59.320 63.158 0.00 0.00 0.00 4.61
933 4721 1.341383 CCAACCATCTTCCTCCCCTTG 60.341 57.143 0.00 0.00 0.00 3.61
1230 5222 8.926715 TTTGTCTACTGTACAATGCTACTATG 57.073 34.615 0.00 0.00 36.75 2.23
1269 5276 4.533919 AGTCTTCAGAGTGTGGATTCTG 57.466 45.455 0.00 0.00 41.67 3.02
1280 5287 1.737236 GTGGATTCTGTTATGCGTGCA 59.263 47.619 0.00 0.00 0.00 4.57
1394 5418 3.841643 CATTTGGTTCATCTTGTGCTCC 58.158 45.455 0.00 0.00 0.00 4.70
1410 5434 3.498777 GTGCTCCTCGCCTATAAAAATCC 59.501 47.826 0.00 0.00 38.05 3.01
1602 5870 3.947612 TCCGTATCTCTGTACCTTCCT 57.052 47.619 0.00 0.00 0.00 3.36
1750 6051 1.301716 TGCTCACCGCAGTTTCCTC 60.302 57.895 0.00 0.00 45.47 3.71
1808 6109 8.879427 TTCAGTTGCATAGTATAGCTAGGATA 57.121 34.615 0.00 0.00 33.63 2.59
1841 6550 3.534357 TGTTTTCCTTGGGATTAGGCA 57.466 42.857 0.00 0.00 32.59 4.75
1842 6551 3.161866 TGTTTTCCTTGGGATTAGGCAC 58.838 45.455 0.00 0.00 32.59 5.01
1843 6552 3.181423 TGTTTTCCTTGGGATTAGGCACT 60.181 43.478 0.00 0.00 46.37 4.40
1844 6553 2.806945 TTCCTTGGGATTAGGCACTG 57.193 50.000 0.00 0.00 41.52 3.66
1845 6554 1.668826 TCCTTGGGATTAGGCACTGT 58.331 50.000 0.00 0.00 41.52 3.55
1846 6555 1.281867 TCCTTGGGATTAGGCACTGTG 59.718 52.381 2.76 2.76 41.52 3.66
1847 6556 1.683011 CCTTGGGATTAGGCACTGTGG 60.683 57.143 10.21 0.00 41.52 4.17
1848 6557 0.323360 TTGGGATTAGGCACTGTGGC 60.323 55.000 25.03 25.03 41.52 5.01
1849 6558 1.302949 GGGATTAGGCACTGTGGCA 59.697 57.895 31.92 15.96 46.46 4.92
1850 6559 0.749454 GGGATTAGGCACTGTGGCAG 60.749 60.000 31.92 0.00 46.46 4.85
1851 6560 1.379642 GGATTAGGCACTGTGGCAGC 61.380 60.000 31.92 17.43 46.46 5.25
1852 6561 0.677731 GATTAGGCACTGTGGCAGCA 60.678 55.000 31.92 17.58 46.46 4.41
1853 6562 0.962356 ATTAGGCACTGTGGCAGCAC 60.962 55.000 31.92 4.80 46.46 4.40
1854 6563 2.336484 TTAGGCACTGTGGCAGCACA 62.336 55.000 31.92 11.73 46.46 4.57
1855 6564 2.336484 TAGGCACTGTGGCAGCACAA 62.336 55.000 31.92 10.43 46.46 3.33
1856 6565 2.784356 GGCACTGTGGCAGCACAAA 61.784 57.895 27.01 0.00 43.14 2.83
1857 6566 1.141449 GCACTGTGGCAGCACAAAA 59.859 52.632 10.21 0.00 34.37 2.44
1858 6567 1.147557 GCACTGTGGCAGCACAAAAC 61.148 55.000 10.21 0.00 34.37 2.43
1859 6568 0.528249 CACTGTGGCAGCACAAAACC 60.528 55.000 0.00 0.00 34.37 3.27
1860 6569 1.067916 CTGTGGCAGCACAAAACCC 59.932 57.895 0.00 0.00 34.35 4.11
1861 6570 1.674764 CTGTGGCAGCACAAAACCCA 61.675 55.000 0.00 0.00 34.35 4.51
1862 6571 1.227234 GTGGCAGCACAAAACCCAC 60.227 57.895 0.00 0.00 39.14 4.61
1863 6572 1.683707 TGGCAGCACAAAACCCACA 60.684 52.632 0.00 0.00 0.00 4.17
1864 6573 1.047596 TGGCAGCACAAAACCCACAT 61.048 50.000 0.00 0.00 0.00 3.21
1865 6574 0.106521 GGCAGCACAAAACCCACATT 59.893 50.000 0.00 0.00 0.00 2.71
1866 6575 1.342819 GGCAGCACAAAACCCACATTA 59.657 47.619 0.00 0.00 0.00 1.90
2190 6966 7.047891 AGAAACTATTGCAGATCCGATGTAAA 58.952 34.615 0.00 0.00 0.00 2.01
2232 7008 7.994425 TGAGAACATTTTCAGTTTGCCTATA 57.006 32.000 0.00 0.00 33.72 1.31
2419 8335 6.037940 TCAGATTAATGCACTTGATTCAGCTC 59.962 38.462 0.00 0.00 0.00 4.09
2508 8424 0.252696 ACCCTGATGGAGTAGCACCA 60.253 55.000 0.00 0.00 41.83 4.17
2523 8439 3.087031 AGCACCATCATTGGAGTTTCTG 58.913 45.455 0.00 0.00 46.92 3.02
2664 8580 0.402861 AGGGAAACAGGGACAAGGGA 60.403 55.000 0.00 0.00 0.00 4.20
2692 8608 4.655963 TGGAGAGAAAGGTGAATCTTTGG 58.344 43.478 0.00 0.00 37.13 3.28
2710 8626 5.416952 TCTTTGGAGCTCATGAATCCTTTTC 59.583 40.000 21.43 0.00 34.04 2.29
2779 8695 2.546368 TCAATTTTGTTAGCGCGTCACT 59.454 40.909 8.43 0.00 0.00 3.41
2807 8723 4.260907 GGAACTTTCCCTGTCAAACGTTAC 60.261 45.833 0.00 0.00 41.62 2.50
2808 8724 3.876341 ACTTTCCCTGTCAAACGTTACA 58.124 40.909 0.00 1.96 0.00 2.41
2811 8727 4.822036 TTCCCTGTCAAACGTTACAATG 57.178 40.909 0.00 0.00 0.00 2.82
3316 9580 7.816995 TGGCACATCAACTTTATTACCAATTTC 59.183 33.333 0.00 0.00 0.00 2.17
3673 10082 7.514127 ATCAAACAGATATATGGGTCTACCAGT 59.486 37.037 1.85 0.00 44.14 4.00
3685 10094 1.616865 TCTACCAGTGACCTTCCAACG 59.383 52.381 0.00 0.00 0.00 4.10
3892 10301 0.250252 TGAGGAAGAACATGCACGCA 60.250 50.000 0.00 0.00 0.00 5.24
4000 10409 1.197430 AGGCAGAGAACAGGGTGGAG 61.197 60.000 0.00 0.00 0.00 3.86
4546 10955 4.429108 GAACCTACATTCTCAGCTCTCAC 58.571 47.826 0.00 0.00 0.00 3.51
4596 11005 8.690884 TGTTCTTACATTTCTGGATGTCAAAAA 58.309 29.630 0.00 0.00 40.54 1.94
4814 11223 5.060427 AGCTAGTCAGTGGAGTGATAGAT 57.940 43.478 0.00 0.00 0.00 1.98
4846 11255 1.482182 TCTGATGGGAAGTGGATGTCG 59.518 52.381 0.00 0.00 0.00 4.35
5037 11446 6.708949 GTGGTTAAGTCCTTGAACTGTGATAA 59.291 38.462 0.00 0.00 0.00 1.75
5082 11495 5.491070 TCACTTTCTGTACCATTCATCCAG 58.509 41.667 0.00 0.00 0.00 3.86
5200 11613 5.499004 TTCTAGTTCCTGCAAATGGTAGT 57.501 39.130 0.00 0.00 0.00 2.73
5306 11719 1.079336 GCCGGGAACTACACACCTC 60.079 63.158 2.18 0.00 0.00 3.85
5455 11868 6.686630 ACTGCAATGGATACGAAATTTGAAA 58.313 32.000 0.00 0.00 42.51 2.69
5590 12005 3.826729 AGTGGGGTAATCTCTTGCAAAAC 59.173 43.478 0.00 0.00 0.00 2.43
5716 13536 0.179018 GGGAGGCATCGGCTTACATT 60.179 55.000 0.00 0.00 38.98 2.71
5887 13713 4.044317 ACTCTAGGTTACAGGTCTCCTTCA 59.956 45.833 0.00 0.00 0.00 3.02
6032 13865 4.570369 GTGTCCAAGTTGGGTTTGAAAATG 59.430 41.667 21.85 0.00 38.32 2.32
6033 13866 4.467795 TGTCCAAGTTGGGTTTGAAAATGA 59.532 37.500 21.85 0.00 38.32 2.57
6141 13974 1.362224 ATCCGGTATGCTAGCCCATT 58.638 50.000 13.29 0.00 0.00 3.16
6169 14002 3.951775 TTCTTGAGGAAGCTCAGAGAC 57.048 47.619 0.00 0.00 34.56 3.36
6211 14044 1.069935 GGGATTCCGTGCTCCTAGC 59.930 63.158 0.00 0.00 42.82 3.42
6230 14063 5.819901 CCTAGCGAATCTTTTCTTCTGGATT 59.180 40.000 0.00 0.00 0.00 3.01
6231 14064 5.557891 AGCGAATCTTTTCTTCTGGATTG 57.442 39.130 0.00 0.00 0.00 2.67
6251 14084 1.134068 GGGAATGGGAGTGCCTTCTAC 60.134 57.143 1.06 0.00 0.00 2.59
6259 14092 2.224548 GGAGTGCCTTCTACAGGTGTTT 60.225 50.000 0.00 0.00 46.07 2.83
6282 14115 5.491070 TGATGGAGTTCCTGTAGTTGATTG 58.509 41.667 0.00 0.00 36.82 2.67
6346 14179 2.751166 AGAAGACAGGGTTGATCACG 57.249 50.000 0.00 0.00 0.00 4.35
6375 14208 1.620819 CCAGGCATCGAAGGCTATAGT 59.379 52.381 16.76 0.00 43.24 2.12
6647 14480 0.771127 TGGTGGCTTAGGCAAAGAGT 59.229 50.000 10.78 0.00 40.46 3.24
6735 14625 4.927049 AGGTTTGTCATCAATGGTCTCAT 58.073 39.130 0.00 0.00 33.32 2.90
6780 14670 2.439338 TGCAGCCACCGTGTTGTT 60.439 55.556 0.00 0.00 0.00 2.83
6970 14860 4.098501 GGCCCTTTCATCGATGAATCTTTT 59.901 41.667 34.66 0.00 45.30 2.27
6988 14878 5.734720 TCTTTTTATGGTTCAGAGATCGCT 58.265 37.500 0.00 0.00 0.00 4.93
7414 15310 0.451783 CCGTAACCAATTGCTCTGCC 59.548 55.000 0.00 0.00 0.00 4.85
7676 15572 3.263170 TGTTCAGGCAGTATCCAAAGCTA 59.737 43.478 0.00 0.00 0.00 3.32
7835 15731 1.073025 AAAGAGCGGCACACCATGA 59.927 52.632 1.45 0.00 34.57 3.07
8320 16355 4.342862 AGTGATGATGCCACTGTATACC 57.657 45.455 0.00 0.00 42.68 2.73
8416 16457 2.357034 GCGTTCCTCCGTGCAGAA 60.357 61.111 0.00 0.00 0.00 3.02
8496 16550 0.106167 ATGCTGCAATGGAGCCTGAT 60.106 50.000 23.47 8.21 35.43 2.90
8506 16560 5.221382 GCAATGGAGCCTGATATTTGTCAAT 60.221 40.000 0.00 0.00 0.00 2.57
8561 16628 0.984230 CAGGGAGAGCTTTGGTGGTA 59.016 55.000 0.00 0.00 0.00 3.25
8565 16632 0.320697 GAGAGCTTTGGTGGTACCGT 59.679 55.000 7.57 0.00 42.58 4.83
8636 16758 5.170803 GCTGTTTTGCTTGTTTTCGTAGTAC 59.829 40.000 0.00 0.00 0.00 2.73
8655 16777 1.625818 ACCTTGTGTGGATCTCTGTCC 59.374 52.381 0.00 0.00 38.81 4.02
8690 16814 7.869016 TCTGTTTAATTAAGTGTCTGAGACG 57.131 36.000 8.23 0.00 34.95 4.18
8740 16872 7.425224 AGTTAGTTATGCTGTCTCTGGTTAT 57.575 36.000 0.00 0.00 0.00 1.89
8768 16905 4.740934 GCATTAGTATCTGGTGTCTGGGAC 60.741 50.000 0.00 0.00 0.00 4.46
8805 16943 7.147983 TGCACAGTTCTTGTTGGTTAAGTTTAT 60.148 33.333 0.00 0.00 38.16 1.40
8812 16950 8.117813 TCTTGTTGGTTAAGTTTATGGGAATC 57.882 34.615 0.00 0.00 0.00 2.52
8814 16952 8.485578 TTGTTGGTTAAGTTTATGGGAATCTT 57.514 30.769 0.00 0.00 0.00 2.40
8815 16953 7.891561 TGTTGGTTAAGTTTATGGGAATCTTG 58.108 34.615 0.00 0.00 0.00 3.02
8816 16954 7.507616 TGTTGGTTAAGTTTATGGGAATCTTGT 59.492 33.333 0.00 0.00 0.00 3.16
8817 16955 8.364894 GTTGGTTAAGTTTATGGGAATCTTGTT 58.635 33.333 0.00 0.00 0.00 2.83
8818 16956 7.891561 TGGTTAAGTTTATGGGAATCTTGTTG 58.108 34.615 0.00 0.00 0.00 3.33
8819 16957 7.039363 TGGTTAAGTTTATGGGAATCTTGTTGG 60.039 37.037 0.00 0.00 0.00 3.77
8820 16958 7.039293 GGTTAAGTTTATGGGAATCTTGTTGGT 60.039 37.037 0.00 0.00 0.00 3.67
8863 17001 2.571653 ACTTGCTACCAGGTTGCTGATA 59.428 45.455 24.17 3.80 35.51 2.15
8951 17090 8.460831 AATTATGGCGTTAGTTTTCATTGAAC 57.539 30.769 0.00 0.00 0.00 3.18
8967 17106 3.485463 TGAACAGTTCATTCGGGAAGT 57.515 42.857 12.24 0.00 34.08 3.01
9023 17162 5.070770 AGTAGTTGCAGAGTGAGAAGATG 57.929 43.478 0.00 0.00 0.00 2.90
9055 17194 0.821301 TCACGGCCATTTGCTTGTGA 60.821 50.000 2.24 2.20 45.98 3.58
9079 17218 2.618709 AGTGCCTTCAACTTCGGAAAAG 59.381 45.455 0.00 0.00 0.00 2.27
9219 17358 3.506810 CTTGGCGTCAAGTTTGTTTGAA 58.493 40.909 21.55 0.00 43.92 2.69
9247 17386 0.249615 TGCAGTGTCAGCTGTCTCAC 60.250 55.000 21.85 21.85 38.65 3.51
9267 17406 2.884012 ACGTGCATGAAGAAAACATGGA 59.116 40.909 14.17 0.00 43.39 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.089551 CGATATACAAACATCGGAGACATTCC 59.910 42.308 0.00 0.00 42.51 3.01
14 15 7.038926 CGATATACAAACATCGGAGACATTC 57.961 40.000 0.00 0.00 42.51 2.67
24 25 8.428186 TTTAACTCCACCGATATACAAACATC 57.572 34.615 0.00 0.00 0.00 3.06
59 60 1.951602 GATATGCAAGCATCTGGCACA 59.048 47.619 11.32 0.00 43.74 4.57
63 64 2.074576 CGAGGATATGCAAGCATCTGG 58.925 52.381 11.32 0.69 37.82 3.86
197 199 8.175716 AGTGTAATGAAGCTACTTTTTATTCGC 58.824 33.333 0.00 0.00 0.00 4.70
215 217 4.509970 TCACCGTCTTGTTTGAGTGTAATG 59.490 41.667 0.00 0.00 0.00 1.90
234 237 1.810030 GCGGTTCACGGAGATCACC 60.810 63.158 0.00 0.00 44.51 4.02
282 285 8.178313 TCGCATTTTCGTTGATTTTGTATGATA 58.822 29.630 0.00 0.00 0.00 2.15
291 296 5.398169 TGCTATTCGCATTTTCGTTGATTT 58.602 33.333 0.00 0.00 45.47 2.17
293 298 4.614555 TGCTATTCGCATTTTCGTTGAT 57.385 36.364 0.00 0.00 45.47 2.57
328 333 1.269051 CCTTTGGTTTTCTCGTGCCAC 60.269 52.381 0.00 0.00 0.00 5.01
331 336 3.308530 CATTCCTTTGGTTTTCTCGTGC 58.691 45.455 0.00 0.00 0.00 5.34
344 349 4.286549 TGCCATTCAAATGACCATTCCTTT 59.713 37.500 4.30 0.00 38.70 3.11
352 357 0.243365 TGCGTGCCATTCAAATGACC 59.757 50.000 4.30 0.00 38.70 4.02
368 373 4.321745 GCAATGAGTATGTGTTTTCTTGCG 59.678 41.667 0.00 0.00 0.00 4.85
449 454 6.999272 TCTTACATTTGTTTAAGTAGTGGCCA 59.001 34.615 0.00 0.00 0.00 5.36
450 455 7.443259 TCTTACATTTGTTTAAGTAGTGGCC 57.557 36.000 0.00 0.00 0.00 5.36
451 456 8.512138 ACATCTTACATTTGTTTAAGTAGTGGC 58.488 33.333 0.00 0.00 0.00 5.01
518 614 5.945784 TGCCTTGCATATATAAGGATCCAAC 59.054 40.000 15.82 1.23 44.98 3.77
894 4682 1.003718 GTGGTTTCGGAGGTGGGAG 60.004 63.158 0.00 0.00 0.00 4.30
933 4721 3.967335 CTCGTCGATCGGGCTCCC 61.967 72.222 16.41 0.00 40.32 4.30
1269 5276 3.370978 ACACTAATCTGTGCACGCATAAC 59.629 43.478 13.13 0.00 41.30 1.89
1280 5287 8.877864 TGGAAATAAAATCCACACTAATCTGT 57.122 30.769 0.00 0.00 41.98 3.41
1394 5418 5.817816 AGAACTGTGGATTTTTATAGGCGAG 59.182 40.000 0.00 0.00 0.00 5.03
1602 5870 5.060506 TGTTGCTTCGTATTGGAGAAAGAA 58.939 37.500 0.00 0.00 0.00 2.52
1750 6051 5.293814 CCTACTTGACATCAAATGAGCTCAG 59.706 44.000 22.96 8.88 35.15 3.35
1808 6109 8.879227 TCCCAAGGAAAACATCTTTATCAATTT 58.121 29.630 0.00 0.00 0.00 1.82
1844 6553 1.227234 GTGGGTTTTGTGCTGCCAC 60.227 57.895 0.00 0.00 42.40 5.01
1845 6554 1.047596 ATGTGGGTTTTGTGCTGCCA 61.048 50.000 0.00 0.00 0.00 4.92
1846 6555 0.106521 AATGTGGGTTTTGTGCTGCC 59.893 50.000 0.00 0.00 0.00 4.85
1847 6556 2.799978 GTTAATGTGGGTTTTGTGCTGC 59.200 45.455 0.00 0.00 0.00 5.25
1848 6557 4.037923 AGAGTTAATGTGGGTTTTGTGCTG 59.962 41.667 0.00 0.00 0.00 4.41
1849 6558 4.037923 CAGAGTTAATGTGGGTTTTGTGCT 59.962 41.667 0.00 0.00 0.00 4.40
1850 6559 4.037446 TCAGAGTTAATGTGGGTTTTGTGC 59.963 41.667 0.00 0.00 0.00 4.57
1851 6560 5.762045 CTCAGAGTTAATGTGGGTTTTGTG 58.238 41.667 0.00 0.00 0.00 3.33
1852 6561 4.278419 GCTCAGAGTTAATGTGGGTTTTGT 59.722 41.667 0.00 0.00 0.00 2.83
1853 6562 4.321230 GGCTCAGAGTTAATGTGGGTTTTG 60.321 45.833 0.00 0.00 0.00 2.44
1854 6563 3.826729 GGCTCAGAGTTAATGTGGGTTTT 59.173 43.478 0.00 0.00 0.00 2.43
1855 6564 3.074538 AGGCTCAGAGTTAATGTGGGTTT 59.925 43.478 0.00 0.00 0.00 3.27
1856 6565 2.644798 AGGCTCAGAGTTAATGTGGGTT 59.355 45.455 0.00 0.00 0.00 4.11
1857 6566 2.269940 AGGCTCAGAGTTAATGTGGGT 58.730 47.619 0.00 0.00 0.00 4.51
1858 6567 4.696479 ATAGGCTCAGAGTTAATGTGGG 57.304 45.455 0.00 0.00 0.00 4.61
1859 6568 7.275920 AGTTTATAGGCTCAGAGTTAATGTGG 58.724 38.462 0.00 0.00 0.00 4.17
1860 6569 8.607459 CAAGTTTATAGGCTCAGAGTTAATGTG 58.393 37.037 0.00 0.00 0.00 3.21
1861 6570 7.281100 GCAAGTTTATAGGCTCAGAGTTAATGT 59.719 37.037 0.00 0.00 0.00 2.71
1862 6571 7.280876 TGCAAGTTTATAGGCTCAGAGTTAATG 59.719 37.037 0.00 0.00 0.00 1.90
1863 6572 7.338710 TGCAAGTTTATAGGCTCAGAGTTAAT 58.661 34.615 0.00 0.00 0.00 1.40
1864 6573 6.707290 TGCAAGTTTATAGGCTCAGAGTTAA 58.293 36.000 0.00 0.00 0.00 2.01
1865 6574 6.294361 TGCAAGTTTATAGGCTCAGAGTTA 57.706 37.500 0.00 0.00 0.00 2.24
1866 6575 5.165961 TGCAAGTTTATAGGCTCAGAGTT 57.834 39.130 0.00 0.00 0.00 3.01
1914 6649 4.911514 AATGTACTGTGGTGTGAAAACC 57.088 40.909 0.00 0.00 40.94 3.27
1952 6687 2.755103 CCCGCCAAAAATAGAAGAAGCT 59.245 45.455 0.00 0.00 0.00 3.74
1980 6727 7.531857 TTTGGAGAACATAAAGCCAAATACA 57.468 32.000 0.00 0.00 42.01 2.29
2134 6910 9.892130 GTGGAAAAGAAATAAAGGAGATCTCTA 57.108 33.333 21.81 7.60 0.00 2.43
2190 6966 5.165961 TCTCAAGGCTAAAGCTACAATGT 57.834 39.130 1.39 0.00 41.70 2.71
2419 8335 9.961265 AACATGAATGTGATATTGAGCAAATAG 57.039 29.630 0.00 0.00 41.61 1.73
2508 8424 6.484288 TGATGTTACCAGAAACTCCAATGAT 58.516 36.000 0.00 0.00 0.00 2.45
2523 8439 4.393062 CCAGTGATGTCAGTTGATGTTACC 59.607 45.833 0.00 0.00 0.00 2.85
2664 8580 7.205515 AGATTCACCTTTCTCTCCAATGTAT 57.794 36.000 0.00 0.00 0.00 2.29
2692 8608 5.413833 TGAACAGAAAAGGATTCATGAGCTC 59.586 40.000 6.82 6.82 0.00 4.09
2710 8626 4.448732 GCTTAAAATTGGCCAAGTGAACAG 59.551 41.667 24.94 15.67 0.00 3.16
2807 8723 8.047413 TGTCATTTGATATATAGCAGCCATTG 57.953 34.615 0.30 0.00 0.00 2.82
2808 8724 8.818622 ATGTCATTTGATATATAGCAGCCATT 57.181 30.769 0.30 0.00 0.00 3.16
3165 9426 9.593134 GAGACAATAGTGAAATACAGAAGTGAT 57.407 33.333 0.00 0.00 0.00 3.06
3400 9809 7.959175 TGTACATAACCACAGACTAACTCTTT 58.041 34.615 0.00 0.00 0.00 2.52
3673 10082 1.707106 TACAGGTCGTTGGAAGGTCA 58.293 50.000 0.00 0.00 0.00 4.02
3685 10094 0.824759 AAGGCAGGACGATACAGGTC 59.175 55.000 0.00 0.00 0.00 3.85
3847 10256 7.757624 ACTTCAAAGTTCTTCTCACTCGATATC 59.242 37.037 0.00 0.00 35.21 1.63
3892 10301 7.091443 CAGATAAAAAGACCGTGTAAGACTCT 58.909 38.462 0.00 0.00 0.00 3.24
4000 10409 4.027295 CACTCATCGATTTCAGTACGCTTC 60.027 45.833 0.00 0.00 0.00 3.86
4439 10848 2.981560 CTGGTTTGAGCCGCGCAAT 61.982 57.895 10.50 0.00 0.00 3.56
4546 10955 3.740832 TGTTGTATGCACTCTTGTCGAAG 59.259 43.478 0.00 0.00 0.00 3.79
4621 11030 3.853355 AGATTAGACCCCTGAATGCAG 57.147 47.619 0.00 0.00 41.93 4.41
4628 11037 2.237143 TGCTGACAAGATTAGACCCCTG 59.763 50.000 0.00 0.00 0.00 4.45
4814 11223 1.478916 CCCATCAGATGCAATGCACAA 59.521 47.619 11.23 0.00 43.04 3.33
4846 11255 1.340017 TGGTTCCAGCTGATAAGCCAC 60.340 52.381 17.39 0.49 34.90 5.01
5037 11446 0.766752 AAAAGCAATGGCAGGCCTTT 59.233 45.000 0.00 8.73 44.61 3.11
5082 11495 6.817184 TGGTAGCTCTCCATGTAATTCTTAC 58.183 40.000 6.48 0.00 36.67 2.34
5200 11613 2.622977 GCCCATCAGTCCAACCCATTTA 60.623 50.000 0.00 0.00 0.00 1.40
5455 11868 6.010219 AGCTGGTAATTGTACACCTTTTGAT 58.990 36.000 0.00 0.00 35.73 2.57
5590 12005 3.543680 ATATCAACACAGGAAGACCCG 57.456 47.619 0.00 0.00 40.87 5.28
5648 13468 4.142609 TGAGTTCCTCCTTGTATGCATC 57.857 45.455 0.19 0.00 0.00 3.91
5716 13536 4.783621 GACATGAGCCGCCTGCCA 62.784 66.667 0.00 0.00 42.71 4.92
6141 13974 5.563592 TGAGCTTCCTCAAGAAATCATCAA 58.436 37.500 0.00 0.00 44.79 2.57
6211 14044 4.943705 TCCCAATCCAGAAGAAAAGATTCG 59.056 41.667 0.00 0.00 40.63 3.34
6230 14063 0.846427 AGAAGGCACTCCCATTCCCA 60.846 55.000 0.00 0.00 38.49 4.37
6231 14064 1.134068 GTAGAAGGCACTCCCATTCCC 60.134 57.143 0.00 0.00 38.49 3.97
6251 14084 2.816087 CAGGAACTCCATCAAACACCTG 59.184 50.000 0.00 0.00 34.60 4.00
6259 14092 5.013079 ACAATCAACTACAGGAACTCCATCA 59.987 40.000 0.00 0.00 34.60 3.07
6282 14115 5.751586 TGATCTTACTCCCATAAAACCCAC 58.248 41.667 0.00 0.00 0.00 4.61
6346 14179 0.107214 TCGATGCCTGGTCAAATCCC 60.107 55.000 0.00 0.00 0.00 3.85
6375 14208 5.471797 TCGACCATCTGCTTGAAAATGTTTA 59.528 36.000 0.00 0.00 0.00 2.01
6647 14480 3.009033 AGCTCAGCCTTGTAACCATGTAA 59.991 43.478 0.00 0.00 0.00 2.41
6780 14670 3.476552 CTCTTAACAGACCCAAGCAACA 58.523 45.455 0.00 0.00 0.00 3.33
6970 14860 4.736126 TGAAGCGATCTCTGAACCATAA 57.264 40.909 0.00 0.00 0.00 1.90
6988 14878 1.820519 GCCAGTGCATCCTTGAATGAA 59.179 47.619 0.00 0.00 37.47 2.57
7184 15080 0.178831 ACCCATTCTCCACTTCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
7185 15081 0.256177 GACCCATTCTCCACTTCCCC 59.744 60.000 0.00 0.00 0.00 4.81
7186 15082 0.991920 TGACCCATTCTCCACTTCCC 59.008 55.000 0.00 0.00 0.00 3.97
7414 15310 2.479049 CCTTGCGATGAATTGCCAGAAG 60.479 50.000 5.40 1.07 36.33 2.85
7676 15572 4.499183 ACAAAAGAATCGCTCTTCTCGAT 58.501 39.130 0.74 0.00 44.00 3.59
7743 15639 4.836825 CAGACCAACACTGATAACCTCAT 58.163 43.478 0.00 0.00 37.54 2.90
7835 15731 0.829333 ACATTCAGCAGGCGAGAGAT 59.171 50.000 0.00 0.00 0.00 2.75
8281 16187 5.223449 TCACTAGGGAAAAATTCAGACGT 57.777 39.130 0.00 0.00 0.00 4.34
8320 16355 9.658799 TTGTCCATAAAGAAGAAGATTAGAGTG 57.341 33.333 0.00 0.00 0.00 3.51
8506 16560 5.136828 TCAACAGCCTGTATCAAGGAAAAA 58.863 37.500 0.00 0.00 40.02 1.94
8561 16628 3.350219 AATTGCCTTGAGATACACGGT 57.650 42.857 0.00 0.00 39.67 4.83
8636 16758 1.905215 AGGACAGAGATCCACACAAGG 59.095 52.381 0.00 0.00 41.73 3.61
8690 16814 5.886960 ATCAGTTCCAACAGCATTAAGAC 57.113 39.130 0.00 0.00 0.00 3.01
8740 16872 6.108687 CAGACACCAGATACTAATGCAAAGA 58.891 40.000 6.45 0.00 0.00 2.52
8805 16943 0.608035 GCGGACCAACAAGATTCCCA 60.608 55.000 0.00 0.00 0.00 4.37
8812 16950 0.040425 CGAAAAGGCGGACCAACAAG 60.040 55.000 0.00 0.00 39.06 3.16
8814 16952 0.464013 TTCGAAAAGGCGGACCAACA 60.464 50.000 0.00 0.00 39.06 3.33
8815 16953 0.040692 GTTCGAAAAGGCGGACCAAC 60.041 55.000 0.00 0.00 39.06 3.77
8816 16954 2.323213 GTTCGAAAAGGCGGACCAA 58.677 52.632 0.00 0.00 39.06 3.67
8817 16955 4.052519 GTTCGAAAAGGCGGACCA 57.947 55.556 0.00 0.00 39.06 4.02
8819 16957 1.302271 AGGGTTCGAAAAGGCGGAC 60.302 57.895 0.00 0.00 39.04 4.79
8820 16958 1.302192 CAGGGTTCGAAAAGGCGGA 60.302 57.895 0.00 0.00 0.00 5.54
8863 17001 2.557805 CACATTCGCAGCGCAGTT 59.442 55.556 10.87 0.00 0.00 3.16
8951 17090 2.350522 CCTGACTTCCCGAATGAACTG 58.649 52.381 0.00 0.00 0.00 3.16
8967 17106 3.245984 TGGATCTTCAGAGGTAACCCTGA 60.246 47.826 0.00 0.00 42.86 3.86
9023 17162 1.002033 GGCCGTGAGCATGATCAATTC 60.002 52.381 16.53 7.11 46.50 2.17
9055 17194 0.886490 CCGAAGTTGAAGGCACTGCT 60.886 55.000 0.00 0.00 40.86 4.24
9066 17205 1.069906 CGTCCTGCTTTTCCGAAGTTG 60.070 52.381 0.00 0.00 0.00 3.16
9079 17218 2.866762 GGAAACTGATACATCGTCCTGC 59.133 50.000 0.00 0.00 0.00 4.85
9176 17315 2.107950 TATTTTCCTGGCCGACACAG 57.892 50.000 0.00 0.00 35.74 3.66
9247 17386 3.495193 CTCCATGTTTTCTTCATGCACG 58.505 45.455 0.00 0.00 40.63 5.34


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

AutoCloner maintained by Alex Coulton.