Multiple sequence alignment - TraesCS3D01G545700

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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 TraesCS3D01G545700 chr3D 100.000 3128 0 0 972 4099 615455465 615458592 0.000000e+00 5777
1 TraesCS3D01G545700 chr3D 100.000 691 0 0 1 691 615454494 615455184 0.000000e+00 1277
2 TraesCS3D01G545700 chr3A 89.564 2041 163 24 2097 4099 748340007 748342035 0.000000e+00 2543
3 TraesCS3D01G545700 chr3A 88.763 970 93 10 2274 3242 749876814 749875860 0.000000e+00 1173
4 TraesCS3D01G545700 chr3A 88.209 670 44 13 1 661 749878111 749877468 0.000000e+00 767
5 TraesCS3D01G545700 chr3A 89.016 610 60 3 997 1604 749877417 749876813 0.000000e+00 749
6 TraesCS3D01G545700 chr3A 87.910 488 52 7 976 1458 748339471 748339956 5.950000e-158 568
7 TraesCS3D01G545700 chr3A 81.818 385 50 13 1 378 748336615 748336986 5.150000e-79 305
8 TraesCS3D01G545700 chr3A 75.472 318 58 15 3238 3540 750289336 750289648 1.990000e-28 137
9 TraesCS3D01G545700 chr3B 88.689 2060 165 23 2097 4098 28607389 28605340 0.000000e+00 2451
10 TraesCS3D01G545700 chr3B 91.554 592 39 7 9 598 825847770 825848352 0.000000e+00 806
11 TraesCS3D01G545700 chr3B 89.701 602 60 1 997 1596 825849363 825849964 0.000000e+00 767
12 TraesCS3D01G545700 chr3B 88.593 526 54 5 2270 2794 825849966 825850486 5.780000e-178 634
13 TraesCS3D01G545700 chr3B 86.139 505 63 7 974 1473 28607927 28607425 4.660000e-149 538
14 TraesCS3D01G545700 chr3B 88.675 415 40 3 2828 3242 825850484 825850891 2.200000e-137 499
15 TraesCS3D01G545700 chr3B 84.530 362 48 5 20 378 788579658 788579302 6.520000e-93 351
16 TraesCS3D01G545700 chr3B 84.877 324 31 9 3243 3548 804547968 804547645 1.110000e-80 311
17 TraesCS3D01G545700 chr3B 86.038 265 30 4 59 323 28623638 28623381 1.120000e-70 278
18 TraesCS3D01G545700 chr3B 83.636 275 36 4 3738 4010 804547231 804546964 2.450000e-62 250
19 TraesCS3D01G545700 chr3B 76.129 310 54 14 3236 3531 730699667 730699364 1.190000e-30 145
20 TraesCS3D01G545700 chr3B 93.151 73 4 1 587 658 825849241 825849313 5.600000e-19 106
21 TraesCS3D01G545700 chrUn 88.727 1375 120 16 1873 3242 37114992 37113648 0.000000e+00 1648
22 TraesCS3D01G545700 chrUn 88.727 1375 120 16 1873 3242 247032284 247033628 0.000000e+00 1648
23 TraesCS3D01G545700 chrUn 88.727 1375 120 16 1873 3242 300943721 300942377 0.000000e+00 1648
24 TraesCS3D01G545700 chrUn 90.741 702 61 3 977 1675 37115888 37115188 0.000000e+00 933
25 TraesCS3D01G545700 chrUn 91.266 687 56 3 977 1660 247031388 247032073 0.000000e+00 933
26 TraesCS3D01G545700 chrUn 90.741 702 61 3 977 1675 300944617 300943917 0.000000e+00 933
27 TraesCS3D01G545700 chrUn 89.641 473 35 6 1 472 247030719 247031178 1.270000e-164 590
28 TraesCS3D01G545700 chrUn 93.889 180 8 2 494 673 247031169 247031345 6.750000e-68 268
29 TraesCS3D01G545700 chrUn 80.982 326 39 10 3243 3555 44702522 44702837 1.900000e-58 237
30 TraesCS3D01G545700 chrUn 87.817 197 15 6 3517 3704 339246732 339246928 5.330000e-54 222
31 TraesCS3D01G545700 chrUn 88.144 194 14 6 3520 3704 345351643 345351450 5.330000e-54 222
32 TraesCS3D01G545700 chrUn 88.144 194 14 6 3520 3704 345354048 345353855 5.330000e-54 222
33 TraesCS3D01G545700 chrUn 87.817 197 15 6 3517 3704 401407487 401407683 5.330000e-54 222
34 TraesCS3D01G545700 chrUn 91.912 136 7 4 3252 3387 451870149 451870280 1.950000e-43 187
35 TraesCS3D01G545700 chr5B 86.957 230 22 4 3242 3464 410726493 410726265 6.800000e-63 252
36 TraesCS3D01G545700 chr5B 75.796 314 55 15 3242 3540 542325561 542325868 5.520000e-29 139
37 TraesCS3D01G545700 chr2B 81.962 316 39 8 3674 3987 671087084 671086785 6.800000e-63 252


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 TraesCS3D01G545700 chr3D 615454494 615458592 4098 False 3527.000000 5777 100.000000 1 4099 2 chr3D.!!$F1 4098
1 TraesCS3D01G545700 chr3A 748336615 748342035 5420 False 1138.666667 2543 86.430667 1 4099 3 chr3A.!!$F2 4098
2 TraesCS3D01G545700 chr3A 749875860 749878111 2251 True 896.333333 1173 88.662667 1 3242 3 chr3A.!!$R1 3241
3 TraesCS3D01G545700 chr3B 28605340 28607927 2587 True 1494.500000 2451 87.414000 974 4098 2 chr3B.!!$R4 3124
4 TraesCS3D01G545700 chr3B 825847770 825850891 3121 False 562.400000 806 90.334800 9 3242 5 chr3B.!!$F1 3233
5 TraesCS3D01G545700 chr3B 804546964 804547968 1004 True 280.500000 311 84.256500 3243 4010 2 chr3B.!!$R5 767
6 TraesCS3D01G545700 chrUn 37113648 37115888 2240 True 1290.500000 1648 89.734000 977 3242 2 chrUn.!!$R1 2265
7 TraesCS3D01G545700 chrUn 300942377 300944617 2240 True 1290.500000 1648 89.734000 977 3242 2 chrUn.!!$R2 2265
8 TraesCS3D01G545700 chrUn 247030719 247033628 2909 False 859.750000 1648 90.880750 1 3242 4 chrUn.!!$F5 3241
9 TraesCS3D01G545700 chrUn 345351450 345354048 2598 True 222.000000 222 88.144000 3520 3704 2 chrUn.!!$R3 184

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
658 3762 0.029300 GTTGCAACGCACAGACACAT 59.971 50.0 14.90 0.00 38.71 3.21 F
1781 4918 0.323629 AGATGGTACCCCACGTGTTG 59.676 55.0 15.65 7.42 45.65 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 5162 0.110509 GTGTGTGCGCTGACTCAATG 60.111 55.0 9.73 0.0 0.0 2.82 R
3548 6746 0.249699 TTCGACACGTGGCTTGATGT 60.250 50.0 21.24 0.0 0.0 3.06 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
153 161 6.094719 TGCATGTTGAATGAAAGATGTTAGC 58.905 36.000 0.00 0.00 34.25 3.09
225 233 2.177977 CTTTCTGATCCGTCGAACGAG 58.822 52.381 8.63 0.00 46.05 4.18
226 234 1.162698 TTCTGATCCGTCGAACGAGT 58.837 50.000 8.63 0.00 46.05 4.18
227 235 2.014335 TCTGATCCGTCGAACGAGTA 57.986 50.000 8.63 0.00 46.05 2.59
228 236 2.349590 TCTGATCCGTCGAACGAGTAA 58.650 47.619 8.63 0.00 46.05 2.24
229 237 2.941064 TCTGATCCGTCGAACGAGTAAT 59.059 45.455 8.63 0.00 46.05 1.89
350 358 3.442273 ACACACGGCCGATTTGATATTTT 59.558 39.130 35.90 0.00 0.00 1.82
401 2437 7.214467 TGCATTATTTCTTTCTTCCGAACTT 57.786 32.000 0.00 0.00 0.00 2.66
409 2445 6.359480 TCTTTCTTCCGAACTTCTGAAAAC 57.641 37.500 0.00 0.00 0.00 2.43
412 2449 1.942677 TCCGAACTTCTGAAAACGCA 58.057 45.000 0.00 0.00 0.00 5.24
462 2499 0.890996 CAGGTGAAGCCAGGGAACAC 60.891 60.000 0.00 0.00 40.61 3.32
610 3714 1.298859 CCACGGCTGGTAAGTTCTGC 61.299 60.000 0.00 0.00 32.03 4.26
622 3726 5.650703 TGGTAAGTTCTGCCTTTAAATAGCC 59.349 40.000 7.64 0.00 0.00 3.93
652 3756 1.202568 CTCGAGTTGCAACGCACAG 59.797 57.895 28.85 20.48 38.71 3.66
658 3762 0.029300 GTTGCAACGCACAGACACAT 59.971 50.000 14.90 0.00 38.71 3.21
662 3766 1.398451 GCAACGCACAGACACATACAC 60.398 52.381 0.00 0.00 0.00 2.90
667 3797 1.800586 GCACAGACACATACACCACAG 59.199 52.381 0.00 0.00 0.00 3.66
688 3819 3.198635 AGACACAGAGAGAGAGAGAGAGG 59.801 52.174 0.00 0.00 0.00 3.69
994 4125 2.640332 GGGGAGAGAGAGAGTTTTTGGT 59.360 50.000 0.00 0.00 0.00 3.67
1033 4164 0.888619 GATCAGACACCGGACTGTGA 59.111 55.000 9.46 6.97 39.57 3.58
1125 4256 3.019003 GCACGGCTTCCCAGAGCTA 62.019 63.158 0.00 0.00 42.32 3.32
1224 4355 2.832661 GGCACAACTGCACCACCA 60.833 61.111 0.00 0.00 46.28 4.17
1376 4512 1.586422 AGACACATGAGCACACACAC 58.414 50.000 0.00 0.00 0.00 3.82
1396 4532 1.380515 CAACACACCCCCACCACAA 60.381 57.895 0.00 0.00 0.00 3.33
1407 4543 4.954970 ACCACAAGCAGGCCGGTG 62.955 66.667 1.90 6.19 0.00 4.94
1408 4544 4.641645 CCACAAGCAGGCCGGTGA 62.642 66.667 1.90 0.00 33.16 4.02
1451 4587 6.535150 TGCTAACACTGATTAAGATCGGAAAG 59.465 38.462 2.44 0.00 40.48 2.62
1459 4595 9.667107 ACTGATTAAGATCGGAAAGAAATTACA 57.333 29.630 2.44 0.00 40.48 2.41
1464 4600 9.607988 TTAAGATCGGAAAGAAATTACAGCATA 57.392 29.630 0.00 0.00 0.00 3.14
1466 4602 9.778741 AAGATCGGAAAGAAATTACAGCATATA 57.221 29.630 0.00 0.00 0.00 0.86
1467 4603 9.429359 AGATCGGAAAGAAATTACAGCATATAG 57.571 33.333 0.00 0.00 0.00 1.31
1486 4622 8.655092 GCATATAGTAGAATGAGATTGTTCAGC 58.345 37.037 0.55 0.00 0.00 4.26
1488 4624 5.330455 AGTAGAATGAGATTGTTCAGCGA 57.670 39.130 0.00 0.00 0.00 4.93
1513 4649 7.265599 TGGAGGGAGTAAGAACATATTTTGA 57.734 36.000 0.00 0.00 0.00 2.69
1516 4652 8.841300 GGAGGGAGTAAGAACATATTTTGATTC 58.159 37.037 0.00 0.00 0.00 2.52
1557 4693 5.327616 TGCATTCTATGTGAAATTGTGGG 57.672 39.130 0.00 0.00 38.29 4.61
1646 4783 8.414003 TGAATAGTTATGACAAGCGAAGTCTAT 58.586 33.333 7.54 3.47 36.94 1.98
1651 4788 8.870879 AGTTATGACAAGCGAAGTCTATAAAAC 58.129 33.333 7.54 5.38 36.94 2.43
1652 4789 8.870879 GTTATGACAAGCGAAGTCTATAAAACT 58.129 33.333 7.54 0.00 36.94 2.66
1660 4797 5.618561 CGAAGTCTATAAAACTGTTGCACC 58.381 41.667 0.00 0.00 0.00 5.01
1661 4798 5.178623 CGAAGTCTATAAAACTGTTGCACCA 59.821 40.000 0.00 0.00 0.00 4.17
1666 4803 4.935352 ATAAAACTGTTGCACCACACAT 57.065 36.364 0.00 0.00 0.00 3.21
1668 4805 3.708563 AAACTGTTGCACCACACATAC 57.291 42.857 0.00 0.00 0.00 2.39
1670 4807 1.202592 ACTGTTGCACCACACATACGA 60.203 47.619 0.00 0.00 0.00 3.43
1675 4812 3.388345 TGCACCACACATACGACTTAA 57.612 42.857 0.00 0.00 0.00 1.85
1676 4813 3.932822 TGCACCACACATACGACTTAAT 58.067 40.909 0.00 0.00 0.00 1.40
1678 4815 4.865925 TGCACCACACATACGACTTAATAC 59.134 41.667 0.00 0.00 0.00 1.89
1679 4816 5.107133 GCACCACACATACGACTTAATACT 58.893 41.667 0.00 0.00 0.00 2.12
1680 4817 6.127675 TGCACCACACATACGACTTAATACTA 60.128 38.462 0.00 0.00 0.00 1.82
1682 4819 7.276218 GCACCACACATACGACTTAATACTAAA 59.724 37.037 0.00 0.00 0.00 1.85
1683 4820 8.804743 CACCACACATACGACTTAATACTAAAG 58.195 37.037 0.00 0.00 0.00 1.85
1685 4822 9.017669 CCACACATACGACTTAATACTAAAGTC 57.982 37.037 6.01 6.01 46.09 3.01
1686 4823 9.017669 CACACATACGACTTAATACTAAAGTCC 57.982 37.037 9.67 0.00 46.60 3.85
1687 4824 8.193438 ACACATACGACTTAATACTAAAGTCCC 58.807 37.037 9.67 0.00 46.60 4.46
1688 4825 8.411683 CACATACGACTTAATACTAAAGTCCCT 58.588 37.037 9.67 0.08 46.60 4.20
1689 4826 9.632638 ACATACGACTTAATACTAAAGTCCCTA 57.367 33.333 9.67 1.95 46.60 3.53
1690 4827 9.890352 CATACGACTTAATACTAAAGTCCCTAC 57.110 37.037 9.67 0.00 46.60 3.18
1691 4828 7.020914 ACGACTTAATACTAAAGTCCCTACG 57.979 40.000 9.67 0.00 46.60 3.51
1692 4829 6.038714 ACGACTTAATACTAAAGTCCCTACGG 59.961 42.308 9.67 0.00 46.60 4.02
1693 4830 6.260936 CGACTTAATACTAAAGTCCCTACGGA 59.739 42.308 9.67 0.00 46.60 4.69
1694 4831 7.201732 CGACTTAATACTAAAGTCCCTACGGAA 60.202 40.741 9.67 0.00 46.60 4.30
1695 4832 8.366359 ACTTAATACTAAAGTCCCTACGGAAA 57.634 34.615 0.00 0.00 40.92 3.13
1697 4834 9.657419 CTTAATACTAAAGTCCCTACGGAAAAA 57.343 33.333 0.00 0.00 40.92 1.94
1724 4861 8.739972 AGACTTACAAAACAAATGACCATATCC 58.260 33.333 0.00 0.00 0.00 2.59
1726 4863 9.034800 ACTTACAAAACAAATGACCATATCCAT 57.965 29.630 0.00 0.00 0.00 3.41
1768 4905 9.747898 TCATTGTGGTTTTTATAACTAGATGGT 57.252 29.630 0.00 0.00 0.00 3.55
1771 4908 9.452287 TTGTGGTTTTTATAACTAGATGGTACC 57.548 33.333 4.43 4.43 0.00 3.34
1772 4909 8.048514 TGTGGTTTTTATAACTAGATGGTACCC 58.951 37.037 10.07 0.00 0.00 3.69
1773 4910 7.500227 GTGGTTTTTATAACTAGATGGTACCCC 59.500 40.741 10.07 0.88 0.00 4.95
1775 4912 7.500227 GGTTTTTATAACTAGATGGTACCCCAC 59.500 40.741 10.07 0.48 45.65 4.61
1776 4913 6.409524 TTTATAACTAGATGGTACCCCACG 57.590 41.667 10.07 0.00 45.65 4.94
1777 4914 2.242882 AACTAGATGGTACCCCACGT 57.757 50.000 10.07 0.00 45.65 4.49
1778 4915 1.481871 ACTAGATGGTACCCCACGTG 58.518 55.000 10.07 9.08 45.65 4.49
1779 4916 1.272872 ACTAGATGGTACCCCACGTGT 60.273 52.381 15.65 0.00 45.65 4.49
1780 4917 1.829222 CTAGATGGTACCCCACGTGTT 59.171 52.381 15.65 0.52 45.65 3.32
1781 4918 0.323629 AGATGGTACCCCACGTGTTG 59.676 55.000 15.65 7.42 45.65 3.33
1782 4919 1.302993 ATGGTACCCCACGTGTTGC 60.303 57.895 15.65 1.73 45.65 4.17
1785 4922 2.281208 TACCCCACGTGTTGCTGC 60.281 61.111 15.65 0.00 0.00 5.25
1794 4931 2.676121 TGTTGCTGCGGGGGATTG 60.676 61.111 0.00 0.00 0.00 2.67
1796 4933 2.361104 TTGCTGCGGGGGATTGTC 60.361 61.111 0.00 0.00 0.00 3.18
1798 4935 2.825836 GCTGCGGGGGATTGTCTG 60.826 66.667 0.00 0.00 0.00 3.51
1800 4937 3.626996 CTGCGGGGGATTGTCTGCA 62.627 63.158 0.00 0.00 42.26 4.41
1801 4938 2.361104 GCGGGGGATTGTCTGCAA 60.361 61.111 0.00 0.00 39.16 4.08
1802 4939 1.754234 GCGGGGGATTGTCTGCAAT 60.754 57.895 0.00 0.00 46.99 3.56
1803 4940 0.465460 GCGGGGGATTGTCTGCAATA 60.465 55.000 0.00 0.00 44.61 1.90
1804 4941 1.819305 GCGGGGGATTGTCTGCAATAT 60.819 52.381 0.00 0.00 44.61 1.28
1807 4953 4.335416 CGGGGGATTGTCTGCAATATATT 58.665 43.478 0.00 0.00 44.61 1.28
1809 4955 5.106157 CGGGGGATTGTCTGCAATATATTTC 60.106 44.000 0.00 0.00 44.61 2.17
1811 4957 6.438425 GGGGGATTGTCTGCAATATATTTCAT 59.562 38.462 0.00 0.00 44.61 2.57
1812 4958 7.038799 GGGGGATTGTCTGCAATATATTTCATT 60.039 37.037 0.00 0.00 44.61 2.57
1814 4960 8.579006 GGGATTGTCTGCAATATATTTCATTGA 58.421 33.333 0.00 0.00 44.61 2.57
1888 5044 6.377327 AAAATACATCATCCCGTGCTTAAG 57.623 37.500 0.00 0.00 0.00 1.85
1897 5053 6.177610 TCATCCCGTGCTTAAGTAAAAGATT 58.822 36.000 4.02 0.00 0.00 2.40
1916 5072 3.428413 TTCCTTTTGTACCTGGCTACC 57.572 47.619 0.00 0.00 0.00 3.18
1922 5078 2.779755 TGTACCTGGCTACCATGTTG 57.220 50.000 0.00 0.00 34.41 3.33
1965 5121 8.967664 AAATTGTAATAATGCAAATGCCTGAT 57.032 26.923 2.46 0.00 41.18 2.90
1987 5143 1.670791 GGGACACGTGAAGGAAACAA 58.329 50.000 25.01 0.00 0.00 2.83
2020 5176 0.599991 ACGAACATTGAGTCAGCGCA 60.600 50.000 11.47 0.00 0.00 6.09
2093 5249 4.272504 GCAGTGTTTCAGCAACTGTACTAA 59.727 41.667 4.18 0.00 36.21 2.24
2105 5261 5.004916 GCAACTGTACTAATCTTCTCGCTTC 59.995 44.000 0.00 0.00 0.00 3.86
2128 5284 5.649395 TCTCCAAGTGAATTCATAAGCCTTG 59.351 40.000 20.71 20.71 0.00 3.61
2167 5325 8.409371 GGGCAAAAACCAAAATTTTCTTGATTA 58.591 29.630 0.00 0.00 31.35 1.75
2218 5376 7.829725 TGTGCAATATAATTCATAAGCCATCC 58.170 34.615 0.00 0.00 0.00 3.51
2230 5388 0.855598 AGCCATCCCCTGCATACATT 59.144 50.000 0.00 0.00 0.00 2.71
2237 5395 5.279106 CCATCCCCTGCATACATTAATGTTG 60.279 44.000 25.31 21.19 41.97 3.33
2246 5404 8.054152 TGCATACATTAATGTTGTGACTGATT 57.946 30.769 25.31 0.00 41.97 2.57
2265 5423 6.378280 ACTGATTTGATTTTGACCTCATACCC 59.622 38.462 0.00 0.00 0.00 3.69
2271 5429 0.742505 TTGACCTCATACCCTACGCG 59.257 55.000 3.53 3.53 0.00 6.01
2340 5500 0.462581 CATCGCATGGTACCTGTGCT 60.463 55.000 28.25 15.73 36.74 4.40
2397 5557 4.403137 GCGTTGCCTTCATGCGCA 62.403 61.111 14.96 14.96 42.39 6.09
2450 5610 6.323996 TCGTGAATCCCATAGAGTACTTCAAT 59.676 38.462 0.00 0.00 0.00 2.57
2480 5640 1.350019 GGCCCCAACTACTACAAGTGT 59.650 52.381 0.00 0.00 0.00 3.55
2501 5661 1.304713 CTTCCAGGCAAGCCACCAT 60.305 57.895 14.40 0.00 38.92 3.55
2518 5678 0.374758 CATCACGCATTTGTCCGGAG 59.625 55.000 3.06 0.00 0.00 4.63
2520 5680 2.746277 ACGCATTTGTCCGGAGCC 60.746 61.111 3.06 0.00 0.00 4.70
2521 5681 3.508840 CGCATTTGTCCGGAGCCC 61.509 66.667 3.06 0.00 0.00 5.19
2522 5682 2.361104 GCATTTGTCCGGAGCCCA 60.361 61.111 3.06 0.00 0.00 5.36
2523 5683 1.754234 GCATTTGTCCGGAGCCCAT 60.754 57.895 3.06 0.00 0.00 4.00
2524 5684 2.008268 GCATTTGTCCGGAGCCCATG 62.008 60.000 3.06 6.43 0.00 3.66
2526 5686 0.107017 ATTTGTCCGGAGCCCATGAG 60.107 55.000 3.06 0.00 0.00 2.90
2528 5688 0.616395 TTGTCCGGAGCCCATGAGTA 60.616 55.000 3.06 0.00 0.00 2.59
2529 5689 1.043116 TGTCCGGAGCCCATGAGTAG 61.043 60.000 3.06 0.00 0.00 2.57
2530 5690 1.043673 GTCCGGAGCCCATGAGTAGT 61.044 60.000 3.06 0.00 0.00 2.73
2531 5691 0.325296 TCCGGAGCCCATGAGTAGTT 60.325 55.000 0.00 0.00 0.00 2.24
2532 5692 0.105039 CCGGAGCCCATGAGTAGTTC 59.895 60.000 0.00 0.00 0.00 3.01
2537 5697 2.950309 GAGCCCATGAGTAGTTCGTCTA 59.050 50.000 0.00 0.00 0.00 2.59
2544 5704 7.434492 CCCATGAGTAGTTCGTCTATGTATTT 58.566 38.462 0.00 0.00 0.00 1.40
2556 5716 5.702670 CGTCTATGTATTTTCAGATGCCCAT 59.297 40.000 0.00 0.00 0.00 4.00
2559 5719 6.938596 TCTATGTATTTTCAGATGCCCATGAG 59.061 38.462 0.00 0.00 0.00 2.90
2572 5737 2.287915 GCCCATGAGTAACTATTGCACG 59.712 50.000 0.00 0.00 0.00 5.34
2609 5774 5.946298 ACGTATATATGTGTATGGTCCACG 58.054 41.667 6.80 0.00 35.56 4.94
2730 5895 0.312416 CGATGAGGAGATGGACGACC 59.688 60.000 0.00 0.00 0.00 4.79
2780 5945 2.202797 CTCACCGAGGCCGACATG 60.203 66.667 0.00 0.00 38.22 3.21
3114 6279 2.311463 TCTGATCCCGAAGTCCAGATC 58.689 52.381 0.00 0.00 36.49 2.75
3120 6285 0.028242 CCGAAGTCCAGATCGACTCG 59.972 60.000 4.03 8.74 42.35 4.18
3139 6305 0.940126 GACTATCCATGTGCTTGCGG 59.060 55.000 0.00 0.00 0.00 5.69
3152 6318 1.859998 GCTTGCGGTTGTCACTGTTTC 60.860 52.381 0.00 0.00 0.00 2.78
3288 6454 1.371558 GTGGGGCGAACTCTGAAGT 59.628 57.895 0.00 0.00 37.32 3.01
3296 6463 6.126997 TGGGGCGAACTCTGAAGTATAATTTA 60.127 38.462 0.00 0.00 33.48 1.40
3403 6577 8.878769 ACAAAGAAAATGTAAACATGTTTGTCC 58.121 29.630 29.72 18.55 34.12 4.02
3548 6746 1.876799 CCCACGCTCAATGTAACACAA 59.123 47.619 0.00 0.00 0.00 3.33
3569 6767 2.267426 CATCAAGCCACGTGTCGAATA 58.733 47.619 15.65 0.00 0.00 1.75
3663 7041 4.098960 CGGGTACTTGGATTGAAGCTACTA 59.901 45.833 0.00 0.00 0.00 1.82
3664 7042 5.394883 CGGGTACTTGGATTGAAGCTACTAA 60.395 44.000 0.00 0.00 0.00 2.24
3668 7046 5.491982 ACTTGGATTGAAGCTACTAACAGG 58.508 41.667 0.00 0.00 0.00 4.00
3669 7047 3.873910 TGGATTGAAGCTACTAACAGGC 58.126 45.455 0.00 0.00 0.00 4.85
3670 7048 3.519510 TGGATTGAAGCTACTAACAGGCT 59.480 43.478 0.00 0.00 37.99 4.58
3717 7164 0.833287 CATCCCGAAGTCCAGATGGT 59.167 55.000 0.00 0.00 33.92 3.55
3725 7172 4.141937 CCGAAGTCCAGATGGTCTCAAATA 60.142 45.833 0.00 0.00 32.46 1.40
3796 7270 9.442047 CACTAAAATTCAGAAACATACCTCTCT 57.558 33.333 0.00 0.00 0.00 3.10
3830 7304 4.511786 GGAGCCTTTTTCTCCTCCTATT 57.488 45.455 2.01 0.00 45.13 1.73
3837 7311 6.039159 GCCTTTTTCTCCTCCTATTCATCTTG 59.961 42.308 0.00 0.00 0.00 3.02
3879 7353 3.127533 CGCTACTGTTGGCTGCCC 61.128 66.667 17.53 1.56 0.00 5.36
4014 7508 1.185618 ACTGGAGCCGCTACTTGTCA 61.186 55.000 3.74 0.00 0.00 3.58
4020 7514 2.094659 CCGCTACTTGTCACGCCTG 61.095 63.158 0.00 0.00 0.00 4.85
4048 8133 1.657594 CAGATGCTAACACTGACGCTG 59.342 52.381 0.00 0.00 34.07 5.18
4050 8135 0.320683 ATGCTAACACTGACGCTGCA 60.321 50.000 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 161 1.832883 TGAACAATTGGTGATCCCCG 58.167 50.000 10.83 0.00 0.00 5.73
227 235 8.302438 GGCAGCTAGCTCATCAAATAATTAATT 58.698 33.333 16.15 5.89 44.79 1.40
228 236 7.668886 AGGCAGCTAGCTCATCAAATAATTAAT 59.331 33.333 16.15 0.00 44.79 1.40
229 237 7.000472 AGGCAGCTAGCTCATCAAATAATTAA 59.000 34.615 16.15 0.00 44.79 1.40
451 2488 0.389948 CACTAGTCGTGTTCCCTGGC 60.390 60.000 0.00 0.00 38.84 4.85
462 2499 1.215647 GGGCTGTCCACACTAGTCG 59.784 63.158 0.00 0.00 35.00 4.18
610 3714 2.243736 TGTGGGAGGGGCTATTTAAAGG 59.756 50.000 0.00 0.00 0.00 3.11
622 3726 3.465403 CTCGAGCCTGTGGGAGGG 61.465 72.222 0.00 0.00 43.07 4.30
652 3756 3.059884 CTGTGTCTGTGGTGTATGTGTC 58.940 50.000 0.00 0.00 0.00 3.67
658 3762 3.149981 CTCTCTCTGTGTCTGTGGTGTA 58.850 50.000 0.00 0.00 0.00 2.90
662 3766 2.749076 CTCTCTCTCTCTGTGTCTGTGG 59.251 54.545 0.00 0.00 0.00 4.17
667 3797 3.535561 CCTCTCTCTCTCTCTCTGTGTC 58.464 54.545 0.00 0.00 0.00 3.67
971 4102 2.909662 CAAAAACTCTCTCTCTCCCCCT 59.090 50.000 0.00 0.00 0.00 4.79
972 4103 2.026729 CCAAAAACTCTCTCTCTCCCCC 60.027 54.545 0.00 0.00 0.00 5.40
994 4125 1.065410 ACCACACCCTCCATGGTCAA 61.065 55.000 12.58 0.00 43.40 3.18
1033 4164 2.483876 CATCGATATGCCGTTCACCTT 58.516 47.619 0.00 0.00 0.00 3.50
1125 4256 2.644555 GATGGCGCCACGAGTACCAT 62.645 60.000 35.50 13.21 43.72 3.55
1212 4343 3.025924 CACATCTGGTGGTGCAGTT 57.974 52.632 0.00 0.00 44.04 3.16
1224 4355 0.537188 CGGTGTAAGAGGCCACATCT 59.463 55.000 5.01 0.00 33.19 2.90
1343 4474 7.443272 TGCTCATGTGTCTTATGGATAATTGAG 59.557 37.037 0.00 0.00 33.54 3.02
1346 4477 7.012704 GTGTGCTCATGTGTCTTATGGATAATT 59.987 37.037 0.00 0.00 0.00 1.40
1355 4486 3.130633 GTGTGTGTGCTCATGTGTCTTA 58.869 45.455 0.00 0.00 0.00 2.10
1376 4512 2.124693 GTGGTGGGGGTGTGTTGTG 61.125 63.158 0.00 0.00 0.00 3.33
1407 4543 1.131126 CATCTGATTTGTGGGCGTGTC 59.869 52.381 0.00 0.00 0.00 3.67
1408 4544 1.167851 CATCTGATTTGTGGGCGTGT 58.832 50.000 0.00 0.00 0.00 4.49
1413 4549 4.012374 AGTGTTAGCATCTGATTTGTGGG 58.988 43.478 0.00 0.00 0.00 4.61
1415 4551 5.868043 TCAGTGTTAGCATCTGATTTGTG 57.132 39.130 7.44 0.00 34.00 3.33
1459 4595 9.926158 CTGAACAATCTCATTCTACTATATGCT 57.074 33.333 0.00 0.00 0.00 3.79
1464 4600 7.043961 TCGCTGAACAATCTCATTCTACTAT 57.956 36.000 0.00 0.00 0.00 2.12
1466 4602 5.330455 TCGCTGAACAATCTCATTCTACT 57.670 39.130 0.00 0.00 0.00 2.57
1467 4603 5.050499 CCATCGCTGAACAATCTCATTCTAC 60.050 44.000 0.00 0.00 0.00 2.59
1476 4612 1.134401 TCCCTCCATCGCTGAACAATC 60.134 52.381 0.00 0.00 0.00 2.67
1486 4622 5.730296 ATATGTTCTTACTCCCTCCATCG 57.270 43.478 0.00 0.00 0.00 3.84
1488 4624 7.872138 TCAAAATATGTTCTTACTCCCTCCAT 58.128 34.615 0.00 0.00 0.00 3.41
1575 4711 7.380333 GTGGCCTTTTGTTTAGTAAATGTACAC 59.620 37.037 3.32 0.00 32.12 2.90
1583 4719 3.637694 GGTGGTGGCCTTTTGTTTAGTAA 59.362 43.478 3.32 0.00 0.00 2.24
1586 4722 2.035632 TGGTGGTGGCCTTTTGTTTAG 58.964 47.619 3.32 0.00 0.00 1.85
1587 4723 2.160721 TGGTGGTGGCCTTTTGTTTA 57.839 45.000 3.32 0.00 0.00 2.01
1646 4783 4.260825 CGTATGTGTGGTGCAACAGTTTTA 60.261 41.667 3.59 0.00 39.98 1.52
1651 4788 1.194547 GTCGTATGTGTGGTGCAACAG 59.805 52.381 3.59 0.00 39.98 3.16
1652 4789 1.202592 AGTCGTATGTGTGGTGCAACA 60.203 47.619 0.00 0.00 39.98 3.33
1694 4831 9.665719 ATGGTCATTTGTTTTGTAAGTCTTTTT 57.334 25.926 0.00 0.00 0.00 1.94
1700 4837 8.415950 TGGATATGGTCATTTGTTTTGTAAGT 57.584 30.769 0.00 0.00 0.00 2.24
1767 4904 2.613506 GCAGCAACACGTGGGGTAC 61.614 63.158 21.57 8.25 0.00 3.34
1768 4905 2.281208 GCAGCAACACGTGGGGTA 60.281 61.111 21.57 0.00 0.00 3.69
1776 4913 2.676471 AATCCCCCGCAGCAACAC 60.676 61.111 0.00 0.00 0.00 3.32
1777 4914 2.676121 CAATCCCCCGCAGCAACA 60.676 61.111 0.00 0.00 0.00 3.33
1778 4915 2.676471 ACAATCCCCCGCAGCAAC 60.676 61.111 0.00 0.00 0.00 4.17
1779 4916 2.361104 GACAATCCCCCGCAGCAA 60.361 61.111 0.00 0.00 0.00 3.91
1780 4917 3.329889 AGACAATCCCCCGCAGCA 61.330 61.111 0.00 0.00 0.00 4.41
1781 4918 2.825836 CAGACAATCCCCCGCAGC 60.826 66.667 0.00 0.00 0.00 5.25
1782 4919 2.825836 GCAGACAATCCCCCGCAG 60.826 66.667 0.00 0.00 0.00 5.18
1785 4922 2.276732 ATATTGCAGACAATCCCCCG 57.723 50.000 0.00 0.00 43.08 5.73
1860 5006 5.885912 AGCACGGGATGATGTATTTTTAGTT 59.114 36.000 0.00 0.00 0.00 2.24
1861 5007 5.437060 AGCACGGGATGATGTATTTTTAGT 58.563 37.500 0.00 0.00 0.00 2.24
1862 5008 6.377327 AAGCACGGGATGATGTATTTTTAG 57.623 37.500 0.00 0.00 0.00 1.85
1863 5009 7.554835 ACTTAAGCACGGGATGATGTATTTTTA 59.445 33.333 1.29 0.00 0.00 1.52
1864 5010 6.377146 ACTTAAGCACGGGATGATGTATTTTT 59.623 34.615 1.29 0.00 0.00 1.94
1865 5011 5.885912 ACTTAAGCACGGGATGATGTATTTT 59.114 36.000 1.29 0.00 0.00 1.82
1866 5012 5.437060 ACTTAAGCACGGGATGATGTATTT 58.563 37.500 1.29 0.00 0.00 1.40
1868 5014 4.689612 ACTTAAGCACGGGATGATGTAT 57.310 40.909 1.29 0.00 0.00 2.29
1869 5015 5.601583 TTACTTAAGCACGGGATGATGTA 57.398 39.130 1.29 0.00 0.00 2.29
1871 5017 5.584649 TCTTTTACTTAAGCACGGGATGATG 59.415 40.000 1.29 0.00 0.00 3.07
1872 5018 5.741011 TCTTTTACTTAAGCACGGGATGAT 58.259 37.500 1.29 0.00 0.00 2.45
1873 5019 5.155278 TCTTTTACTTAAGCACGGGATGA 57.845 39.130 1.29 0.00 0.00 2.92
1874 5020 6.436843 AATCTTTTACTTAAGCACGGGATG 57.563 37.500 1.29 0.00 0.00 3.51
1875 5021 5.589050 GGAATCTTTTACTTAAGCACGGGAT 59.411 40.000 1.29 0.00 0.00 3.85
1876 5022 4.939439 GGAATCTTTTACTTAAGCACGGGA 59.061 41.667 1.29 0.00 0.00 5.14
1877 5023 4.941873 AGGAATCTTTTACTTAAGCACGGG 59.058 41.667 1.29 0.00 0.00 5.28
1897 5053 2.340731 TGGTAGCCAGGTACAAAAGGA 58.659 47.619 9.06 0.00 0.00 3.36
1910 5066 7.328277 TGTTTGATTATACAACATGGTAGCC 57.672 36.000 0.00 0.00 0.00 3.93
1944 5100 6.282167 CCAATCAGGCATTTGCATTATTACA 58.718 36.000 4.74 0.00 44.36 2.41
1965 5121 0.547075 TTTCCTTCACGTGTCCCCAA 59.453 50.000 16.51 0.53 0.00 4.12
2001 5157 0.599991 TGCGCTGACTCAATGTTCGT 60.600 50.000 9.73 0.00 0.00 3.85
2002 5158 0.179240 GTGCGCTGACTCAATGTTCG 60.179 55.000 9.73 0.00 0.00 3.95
2003 5159 0.867746 TGTGCGCTGACTCAATGTTC 59.132 50.000 9.73 0.00 0.00 3.18
2004 5160 0.588252 GTGTGCGCTGACTCAATGTT 59.412 50.000 9.73 0.00 0.00 2.71
2005 5161 0.532640 TGTGTGCGCTGACTCAATGT 60.533 50.000 9.73 0.00 0.00 2.71
2006 5162 0.110509 GTGTGTGCGCTGACTCAATG 60.111 55.000 9.73 0.00 0.00 2.82
2007 5163 0.532640 TGTGTGTGCGCTGACTCAAT 60.533 50.000 9.73 0.00 0.00 2.57
2008 5164 0.532640 ATGTGTGTGCGCTGACTCAA 60.533 50.000 9.73 0.00 0.00 3.02
2009 5165 1.069596 ATGTGTGTGCGCTGACTCA 59.930 52.632 9.73 12.37 0.00 3.41
2010 5166 1.494628 CATGTGTGTGCGCTGACTC 59.505 57.895 9.73 6.72 0.00 3.36
2011 5167 1.962822 CCATGTGTGTGCGCTGACT 60.963 57.895 9.73 0.00 0.00 3.41
2012 5168 1.506309 TTCCATGTGTGTGCGCTGAC 61.506 55.000 9.73 5.61 0.00 3.51
2013 5169 1.227793 TTCCATGTGTGTGCGCTGA 60.228 52.632 9.73 0.00 0.00 4.26
2014 5170 1.208358 CTTCCATGTGTGTGCGCTG 59.792 57.895 9.73 0.00 0.00 5.18
2015 5171 1.968017 CCTTCCATGTGTGTGCGCT 60.968 57.895 9.73 0.00 0.00 5.92
2020 5176 5.441718 AGAATATCACCTTCCATGTGTGT 57.558 39.130 0.00 0.00 35.25 3.72
2079 5235 4.266502 GCGAGAAGATTAGTACAGTTGCTG 59.733 45.833 0.00 0.00 37.52 4.41
2082 5238 6.326375 AGAAGCGAGAAGATTAGTACAGTTG 58.674 40.000 0.00 0.00 0.00 3.16
2093 5249 2.828520 TCACTTGGAGAAGCGAGAAGAT 59.171 45.455 0.00 0.00 31.68 2.40
2105 5261 5.416952 ACAAGGCTTATGAATTCACTTGGAG 59.583 40.000 26.61 15.71 38.43 3.86
2128 5284 2.570442 TTTGCCCAACGAGAAAACAC 57.430 45.000 0.00 0.00 0.00 3.32
2167 5325 9.492730 AACAAATCTCCCCTGATATTAACAAAT 57.507 29.630 0.00 0.00 0.00 2.32
2182 5340 8.196771 TGAATTATATTGCACAACAAATCTCCC 58.803 33.333 0.00 0.00 42.86 4.30
2218 5376 5.357878 AGTCACAACATTAATGTATGCAGGG 59.642 40.000 21.07 10.32 40.80 4.45
2230 5388 9.462174 GTCAAAATCAAATCAGTCACAACATTA 57.538 29.630 0.00 0.00 0.00 1.90
2237 5395 6.317789 TGAGGTCAAAATCAAATCAGTCAC 57.682 37.500 0.00 0.00 0.00 3.67
2246 5404 5.424757 CGTAGGGTATGAGGTCAAAATCAA 58.575 41.667 0.00 0.00 0.00 2.57
2265 5423 2.670905 TCATTTCAACCATGACGCGTAG 59.329 45.455 13.97 5.12 34.61 3.51
2271 5429 4.853924 ACACCTTCATTTCAACCATGAC 57.146 40.909 0.00 0.00 34.61 3.06
2340 5500 3.608662 ACGCTCCGGACGGAACAA 61.609 61.111 23.77 0.00 44.66 2.83
2371 5531 0.517316 GAAGGCAACGCTGGTGTTAG 59.483 55.000 0.00 0.00 46.39 2.34
2372 5532 0.179043 TGAAGGCAACGCTGGTGTTA 60.179 50.000 0.00 0.00 46.39 2.41
2384 5544 1.242665 TGATGTTGCGCATGAAGGCA 61.243 50.000 12.75 2.18 38.06 4.75
2501 5661 2.032634 GCTCCGGACAAATGCGTGA 61.033 57.895 0.00 0.00 38.12 4.35
2518 5678 3.068307 ACATAGACGAACTACTCATGGGC 59.932 47.826 0.00 0.00 33.62 5.36
2520 5680 8.873215 AAAATACATAGACGAACTACTCATGG 57.127 34.615 0.00 0.00 33.62 3.66
2521 5681 9.516314 TGAAAATACATAGACGAACTACTCATG 57.484 33.333 0.00 0.00 33.62 3.07
2522 5682 9.737427 CTGAAAATACATAGACGAACTACTCAT 57.263 33.333 0.00 0.00 33.62 2.90
2523 5683 8.953313 TCTGAAAATACATAGACGAACTACTCA 58.047 33.333 0.00 0.00 33.62 3.41
2524 5684 9.953697 ATCTGAAAATACATAGACGAACTACTC 57.046 33.333 0.00 0.00 33.62 2.59
2526 5686 8.480853 GCATCTGAAAATACATAGACGAACTAC 58.519 37.037 0.00 0.00 33.62 2.73
2528 5688 6.480320 GGCATCTGAAAATACATAGACGAACT 59.520 38.462 0.00 0.00 0.00 3.01
2529 5689 6.292919 GGGCATCTGAAAATACATAGACGAAC 60.293 42.308 0.00 0.00 0.00 3.95
2530 5690 5.758296 GGGCATCTGAAAATACATAGACGAA 59.242 40.000 0.00 0.00 0.00 3.85
2531 5691 5.163353 TGGGCATCTGAAAATACATAGACGA 60.163 40.000 0.00 0.00 0.00 4.20
2532 5692 5.056480 TGGGCATCTGAAAATACATAGACG 58.944 41.667 0.00 0.00 0.00 4.18
2537 5697 5.452255 ACTCATGGGCATCTGAAAATACAT 58.548 37.500 0.00 0.00 0.00 2.29
2544 5704 5.894298 ATAGTTACTCATGGGCATCTGAA 57.106 39.130 0.00 0.00 0.00 3.02
2556 5716 7.609760 AATGATTTCGTGCAATAGTTACTCA 57.390 32.000 0.00 0.00 0.00 3.41
2559 5719 9.549509 TTTGTAATGATTTCGTGCAATAGTTAC 57.450 29.630 0.00 0.00 0.00 2.50
2609 5774 0.389948 CGACACCTGGCTCCTGTAAC 60.390 60.000 0.00 0.00 0.00 2.50
2711 5876 0.312416 GGTCGTCCATCTCCTCATCG 59.688 60.000 0.00 0.00 0.00 3.84
2730 5895 1.722011 GGTGATGTCGGGTACTTGTG 58.278 55.000 0.00 0.00 0.00 3.33
2780 5945 4.065789 CAAAGGAGGTGACAAAGTAGTCC 58.934 47.826 0.00 0.00 37.73 3.85
3114 6279 1.335182 AGCACATGGATAGTCGAGTCG 59.665 52.381 6.09 6.09 0.00 4.18
3120 6285 0.940126 CCGCAAGCACATGGATAGTC 59.060 55.000 0.00 0.00 0.00 2.59
3139 6305 3.291585 CGCAAGATGAAACAGTGACAAC 58.708 45.455 0.00 0.00 43.02 3.32
3152 6318 2.693797 AAACAGACAAGCGCAAGATG 57.306 45.000 11.47 5.50 43.02 2.90
3296 6463 5.426504 TCTGTGTTGGTTTTGCATCAAAAT 58.573 33.333 7.81 0.00 43.66 1.82
3548 6746 0.249699 TTCGACACGTGGCTTGATGT 60.250 50.000 21.24 0.00 0.00 3.06
3569 6767 1.086696 CGTGGAAACGGAGAATGCAT 58.913 50.000 0.00 0.00 0.00 3.96
3717 7164 2.028876 TGCGGTCGGAGATATTTGAGA 58.971 47.619 0.00 0.00 40.67 3.27
3725 7172 1.399714 TCTACAATGCGGTCGGAGAT 58.600 50.000 0.00 0.00 40.67 2.75
3796 7270 0.899720 AGGCTCCCAAATACGAACGA 59.100 50.000 0.14 0.00 0.00 3.85
3830 7304 0.461870 CGGCATTCGGACCAAGATGA 60.462 55.000 0.00 0.00 34.75 2.92
4007 7501 2.974698 GCAGCAGGCGTGACAAGT 60.975 61.111 11.29 0.00 0.00 3.16
4020 7514 1.028330 TGTTAGCATCTGCAGGCAGC 61.028 55.000 15.13 15.16 45.16 5.25
4048 8133 0.727122 GTTCACGCAGATGCAGTTGC 60.727 55.000 13.60 13.60 42.21 4.17
4050 8135 0.870393 CAGTTCACGCAGATGCAGTT 59.130 50.000 5.55 0.00 42.21 3.16


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

AutoCloner maintained by Alex Coulton.