Multiple sequence alignment - TraesCS4D01G353100

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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 TraesCS4D01G353100 chr4D 100.000 4137 0 0 1 4137 503921978 503917842 0.000000e+00 7640.0
1 TraesCS4D01G353100 chr4D 93.553 698 41 3 980 1674 504043283 504043979 0.000000e+00 1037.0
2 TraesCS4D01G353100 chr4D 83.411 1079 177 2 2058 3135 504044738 504045815 0.000000e+00 1000.0
3 TraesCS4D01G353100 chr4D 92.308 78 4 2 1711 1786 341215005 341214928 4.370000e-20 110.0
4 TraesCS4D01G353100 chr4D 100.000 29 0 0 3730 3758 469423044 469423072 2.000000e-03 54.7
5 TraesCS4D01G353100 chr4D 100.000 29 0 0 3730 3758 469423898 469423926 2.000000e-03 54.7
6 TraesCS4D01G353100 chr5A 92.556 2297 136 19 1864 4137 688613535 688611251 0.000000e+00 3262.0
7 TraesCS4D01G353100 chr5A 93.305 478 14 2 127 599 688615058 688614594 0.000000e+00 689.0
8 TraesCS4D01G353100 chr5A 90.047 211 13 2 630 840 688614596 688614394 2.450000e-67 267.0
9 TraesCS4D01G353100 chr5A 94.074 135 7 1 1 134 688615265 688615131 1.950000e-48 204.0
10 TraesCS4D01G353100 chr5A 91.791 134 10 1 856 989 688614409 688614277 7.060000e-43 185.0
11 TraesCS4D01G353100 chr4B 91.417 2202 157 18 1956 4137 649836310 649834121 0.000000e+00 2990.0
12 TraesCS4D01G353100 chr4B 88.184 1845 176 27 1865 3690 650109323 650107502 0.000000e+00 2161.0
13 TraesCS4D01G353100 chr4B 87.751 1845 182 28 1865 3690 650038344 650036525 0.000000e+00 2115.0
14 TraesCS4D01G353100 chr4B 91.770 1288 90 7 1865 3142 650170878 650169597 0.000000e+00 1777.0
15 TraesCS4D01G353100 chr4B 92.841 866 36 5 856 1695 650110255 650109390 0.000000e+00 1232.0
16 TraesCS4D01G353100 chr4B 92.725 866 37 5 856 1695 650039276 650038411 0.000000e+00 1227.0
17 TraesCS4D01G353100 chr4B 92.917 833 33 5 889 1695 650171777 650170945 0.000000e+00 1188.0
18 TraesCS4D01G353100 chr4B 94.906 746 34 3 981 1723 649837073 649836329 0.000000e+00 1164.0
19 TraesCS4D01G353100 chr4B 83.036 1179 194 5 2046 3220 665409609 665408433 0.000000e+00 1064.0
20 TraesCS4D01G353100 chr4B 93.958 662 37 1 1015 1676 667572892 667572234 0.000000e+00 998.0
21 TraesCS4D01G353100 chr4B 94.094 508 18 6 104 599 649839668 649839161 0.000000e+00 761.0
22 TraesCS4D01G353100 chr4B 92.574 404 19 6 1 393 650040221 650039818 1.670000e-158 569.0
23 TraesCS4D01G353100 chr4B 92.327 404 20 5 1 393 650172859 650172456 7.760000e-157 564.0
24 TraesCS4D01G353100 chr4B 92.269 401 20 6 4 393 649842180 649841780 3.610000e-155 558.0
25 TraesCS4D01G353100 chr4B 92.079 404 21 5 1 393 650111199 650110796 3.610000e-155 558.0
26 TraesCS4D01G353100 chr4B 89.573 211 10 3 630 840 650039459 650039261 1.480000e-64 257.0
27 TraesCS4D01G353100 chr4B 89.573 211 10 3 630 840 650110438 650110240 1.480000e-64 257.0
28 TraesCS4D01G353100 chr4B 88.053 226 11 5 621 840 649839176 649838961 1.910000e-63 254.0
29 TraesCS4D01G353100 chr4B 96.992 133 2 2 376 508 649841764 649841634 5.380000e-54 222.0
30 TraesCS4D01G353100 chr4B 96.992 133 2 2 376 508 650039803 650039673 5.380000e-54 222.0
31 TraesCS4D01G353100 chr4B 96.992 133 2 2 376 508 650110782 650110652 5.380000e-54 222.0
32 TraesCS4D01G353100 chr4B 96.992 133 2 2 376 508 650172441 650172311 5.380000e-54 222.0
33 TraesCS4D01G353100 chr4B 93.617 94 6 0 506 599 650039550 650039457 1.550000e-29 141.0
34 TraesCS4D01G353100 chr4B 93.617 94 6 0 506 599 650110529 650110436 1.550000e-29 141.0
35 TraesCS4D01G353100 chr4B 86.364 88 12 0 1785 1872 498407060 498406973 3.400000e-16 97.1
36 TraesCS4D01G353100 chr4B 82.716 81 1 3 918 985 649838930 649838850 4.470000e-05 60.2
37 TraesCS4D01G353100 chr4B 96.970 33 1 0 1864 1896 649836341 649836309 5.780000e-04 56.5
38 TraesCS4D01G353100 chrUn 92.003 1288 87 7 1865 3142 350361961 350360680 0.000000e+00 1794.0
39 TraesCS4D01G353100 chrUn 92.917 833 33 5 889 1695 350362860 350362028 0.000000e+00 1188.0
40 TraesCS4D01G353100 chrUn 82.594 1172 196 7 2046 3213 108499120 108500287 0.000000e+00 1027.0
41 TraesCS4D01G353100 chrUn 93.282 655 41 1 1022 1676 30086962 30087613 0.000000e+00 963.0
42 TraesCS4D01G353100 chrUn 89.796 686 61 6 993 1672 108497669 108498351 0.000000e+00 870.0
43 TraesCS4D01G353100 chr6B 80.337 178 14 8 1716 1872 52019707 52019884 9.400000e-22 115.0
44 TraesCS4D01G353100 chr6B 89.873 79 7 1 1779 1857 581913924 581914001 2.630000e-17 100.0
45 TraesCS4D01G353100 chr2D 94.595 74 3 1 1714 1786 316911095 316911168 3.380000e-21 113.0
46 TraesCS4D01G353100 chr2D 95.714 70 2 1 1714 1782 260149815 260149884 1.220000e-20 111.0
47 TraesCS4D01G353100 chr2D 93.056 72 5 0 1786 1857 37051407 37051336 5.660000e-19 106.0
48 TraesCS4D01G353100 chr2D 100.000 30 0 0 3732 3761 604073813 604073784 5.780000e-04 56.5
49 TraesCS4D01G353100 chr1B 92.308 78 5 1 1714 1790 31121842 31121765 4.370000e-20 110.0
50 TraesCS4D01G353100 chr1B 94.444 72 3 1 1716 1786 629315579 629315650 4.370000e-20 110.0
51 TraesCS4D01G353100 chr1B 86.735 98 8 5 1691 1786 437392145 437392051 2.030000e-18 104.0
52 TraesCS4D01G353100 chr7A 91.026 78 7 0 1785 1862 202837666 202837589 5.660000e-19 106.0
53 TraesCS4D01G353100 chr7A 86.000 50 5 2 3730 3779 670505793 670505746 7.000000e-03 52.8
54 TraesCS4D01G353100 chr2B 92.000 75 6 0 1779 1853 489549055 489549129 5.660000e-19 106.0
55 TraesCS4D01G353100 chr2B 90.789 76 7 0 1782 1857 448285101 448285176 7.320000e-18 102.0
56 TraesCS4D01G353100 chr2B 97.222 36 1 0 3721 3756 249922946 249922981 1.240000e-05 62.1
57 TraesCS4D01G353100 chr2B 92.308 39 3 0 3718 3756 671103581 671103543 5.780000e-04 56.5
58 TraesCS4D01G353100 chr5D 90.123 81 6 2 1714 1793 210151051 210150972 2.030000e-18 104.0
59 TraesCS4D01G353100 chr5D 90.123 81 6 2 1714 1793 241497894 241497973 2.030000e-18 104.0
60 TraesCS4D01G353100 chr1A 91.781 73 6 0 1785 1857 412222107 412222035 7.320000e-18 102.0
61 TraesCS4D01G353100 chr1D 87.952 83 10 0 1779 1861 456819392 456819474 9.460000e-17 99.0
62 TraesCS4D01G353100 chr6D 87.500 80 10 0 1782 1861 89735467 89735388 4.400000e-15 93.5
63 TraesCS4D01G353100 chr3D 96.875 32 1 0 3730 3761 461659428 461659459 2.000000e-03 54.7
64 TraesCS4D01G353100 chr3D 100.000 28 0 0 3719 3746 538141759 538141786 7.000000e-03 52.8
65 TraesCS4D01G353100 chr3B 96.875 32 1 0 3730 3761 227826782 227826813 2.000000e-03 54.7
66 TraesCS4D01G353100 chr4A 100.000 28 0 0 3734 3761 725792625 725792598 7.000000e-03 52.8


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 TraesCS4D01G353100 chr4D 503917842 503921978 4136 True 7640.000000 7640 100.000000 1 4137 1 chr4D.!!$R2 4136
1 TraesCS4D01G353100 chr4D 504043283 504045815 2532 False 1018.500000 1037 88.482000 980 3135 2 chr4D.!!$F2 2155
2 TraesCS4D01G353100 chr5A 688611251 688615265 4014 True 921.400000 3262 92.354600 1 4137 5 chr5A.!!$R1 4136
3 TraesCS4D01G353100 chr4B 665408433 665409609 1176 True 1064.000000 1064 83.036000 2046 3220 1 chr4B.!!$R2 1174
4 TraesCS4D01G353100 chr4B 667572234 667572892 658 True 998.000000 998 93.958000 1015 1676 1 chr4B.!!$R3 661
5 TraesCS4D01G353100 chr4B 650169597 650172859 3262 True 937.750000 1777 93.501500 1 3142 4 chr4B.!!$R7 3141
6 TraesCS4D01G353100 chr4B 650107502 650111199 3697 True 761.833333 2161 92.214333 1 3690 6 chr4B.!!$R6 3689
7 TraesCS4D01G353100 chr4B 649834121 649842180 8059 True 758.212500 2990 92.177125 4 4137 8 chr4B.!!$R4 4133
8 TraesCS4D01G353100 chr4B 650036525 650040221 3696 True 755.166667 2115 92.205333 1 3690 6 chr4B.!!$R5 3689
9 TraesCS4D01G353100 chrUn 350360680 350362860 2180 True 1491.000000 1794 92.460000 889 3142 2 chrUn.!!$R1 2253
10 TraesCS4D01G353100 chrUn 30086962 30087613 651 False 963.000000 963 93.282000 1022 1676 1 chrUn.!!$F1 654
11 TraesCS4D01G353100 chrUn 108497669 108500287 2618 False 948.500000 1027 86.195000 993 3213 2 chrUn.!!$F2 2220

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
605 3110 0.039256 ACACCACATGCATTTCACGC 60.039 50.0 0.00 0.00 0.00 5.34 F
606 3111 0.039346 CACCACATGCATTTCACGCA 60.039 50.0 0.00 0.00 44.94 5.24 F
1758 6888 0.102300 AGCGCTCATATACACGTGCA 59.898 50.0 17.22 2.06 35.49 4.57 F
1770 6900 0.107703 CACGTGCATACATCACCCCT 60.108 55.0 0.82 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 6881 0.107703 AGGGGTGATGTATGCACGTG 60.108 55.0 12.28 12.28 37.13 4.49 R
1801 6931 0.120377 TATTCCCAGTCCACCAGGGT 59.880 55.0 0.00 0.00 43.31 4.34 R
2966 8434 0.037590 TTAATGCCGAGCACCTGGTT 59.962 50.0 0.00 0.00 43.04 3.67 R
3442 8911 2.818130 ATTGCGTGCAAGAAAACCAT 57.182 40.0 13.25 0.00 39.47 3.55 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
18 19 2.202703 CGACGATTGGGGACGACC 60.203 66.667 0.00 0.00 39.11 4.79
32 33 2.029623 GACGACCACCCAAGCTAGATA 58.970 52.381 0.00 0.00 0.00 1.98
36 37 3.491104 CGACCACCCAAGCTAGATAAGTC 60.491 52.174 0.00 0.00 0.00 3.01
63 64 2.238942 ACATGCGAGTTGACTTGTGA 57.761 45.000 0.00 0.00 0.00 3.58
167 249 7.068716 GGAGAATTAATAATGTCTTGGCCACTT 59.931 37.037 3.88 0.00 0.00 3.16
180 262 4.866508 TGGCCACTTCTATTATACTCGG 57.133 45.455 0.00 0.00 0.00 4.63
225 307 7.391275 TGCATTCAAAATCTCATAGTCTTCACA 59.609 33.333 0.00 0.00 0.00 3.58
543 3048 3.517602 CATCAAGATGGTGCATTTGTGG 58.482 45.455 2.09 0.00 35.24 4.17
551 3056 1.460359 GGTGCATTTGTGGCGAATTTG 59.540 47.619 0.00 0.00 0.00 2.32
599 3104 3.636300 ACACAACTAACACCACATGCATT 59.364 39.130 0.00 0.00 0.00 3.56
600 3105 4.099266 ACACAACTAACACCACATGCATTT 59.901 37.500 0.00 0.00 0.00 2.32
601 3106 4.681025 CACAACTAACACCACATGCATTTC 59.319 41.667 0.00 0.00 0.00 2.17
602 3107 4.340666 ACAACTAACACCACATGCATTTCA 59.659 37.500 0.00 0.00 0.00 2.69
603 3108 4.503741 ACTAACACCACATGCATTTCAC 57.496 40.909 0.00 0.00 0.00 3.18
604 3109 2.420628 AACACCACATGCATTTCACG 57.579 45.000 0.00 0.00 0.00 4.35
605 3110 0.039256 ACACCACATGCATTTCACGC 60.039 50.000 0.00 0.00 0.00 5.34
606 3111 0.039346 CACCACATGCATTTCACGCA 60.039 50.000 0.00 0.00 44.94 5.24
607 3112 0.672889 ACCACATGCATTTCACGCAA 59.327 45.000 0.00 0.00 43.84 4.85
608 3113 1.336148 ACCACATGCATTTCACGCAAG 60.336 47.619 0.00 0.00 43.84 4.01
609 3114 1.068402 CCACATGCATTTCACGCAAGA 60.068 47.619 0.00 0.00 43.84 3.02
610 3115 2.607526 CCACATGCATTTCACGCAAGAA 60.608 45.455 0.00 0.00 43.84 2.52
611 3116 3.051327 CACATGCATTTCACGCAAGAAA 58.949 40.909 0.00 3.39 43.84 2.52
612 3117 3.490155 CACATGCATTTCACGCAAGAAAA 59.510 39.130 0.00 0.00 43.84 2.29
613 3118 4.025896 CACATGCATTTCACGCAAGAAAAA 60.026 37.500 0.00 0.00 43.84 1.94
661 3166 7.134815 GCATGAAATACAAGACGAAGCATAAT 58.865 34.615 0.00 0.00 0.00 1.28
662 3167 7.645340 GCATGAAATACAAGACGAAGCATAATT 59.355 33.333 0.00 0.00 0.00 1.40
828 3339 6.806739 CCATCTAATCATATGCTGCATTTGTG 59.193 38.462 25.25 19.01 0.00 3.33
829 3340 7.308951 CCATCTAATCATATGCTGCATTTGTGA 60.309 37.037 25.25 22.41 0.00 3.58
830 3341 7.754851 TCTAATCATATGCTGCATTTGTGAT 57.245 32.000 25.25 23.29 0.00 3.06
831 3342 7.813645 TCTAATCATATGCTGCATTTGTGATC 58.186 34.615 25.25 0.00 0.00 2.92
832 3343 6.399639 AATCATATGCTGCATTTGTGATCA 57.600 33.333 25.25 11.71 0.00 2.92
833 3344 5.838531 TCATATGCTGCATTTGTGATCAA 57.161 34.783 25.25 8.73 0.00 2.57
834 3345 6.399639 TCATATGCTGCATTTGTGATCAAT 57.600 33.333 25.25 7.70 33.32 2.57
835 3346 6.443792 TCATATGCTGCATTTGTGATCAATC 58.556 36.000 25.25 0.00 33.32 2.67
836 3347 3.513680 TGCTGCATTTGTGATCAATCC 57.486 42.857 0.00 0.00 33.32 3.01
837 3348 3.093814 TGCTGCATTTGTGATCAATCCT 58.906 40.909 0.00 0.00 33.32 3.24
838 3349 3.512329 TGCTGCATTTGTGATCAATCCTT 59.488 39.130 0.00 0.00 33.32 3.36
839 3350 4.020928 TGCTGCATTTGTGATCAATCCTTT 60.021 37.500 0.00 0.00 33.32 3.11
840 3351 4.933400 GCTGCATTTGTGATCAATCCTTTT 59.067 37.500 0.00 0.00 33.32 2.27
841 3352 5.410439 GCTGCATTTGTGATCAATCCTTTTT 59.590 36.000 0.00 0.00 33.32 1.94
952 3468 0.179121 CATACCGTGCCGTGAGCTAA 60.179 55.000 0.00 0.00 44.23 3.09
989 5305 3.002451 GCTAGCATCTCAAGACATTGCAG 59.998 47.826 10.63 4.16 36.30 4.41
1044 5363 0.178891 TTCTCCTCCTGGTGCTCCTT 60.179 55.000 6.34 0.00 34.23 3.36
1206 5531 1.357334 CGAGAAGGAGCTAGTCGCC 59.643 63.158 0.00 0.00 40.39 5.54
1620 5945 3.451556 CTGCGCCGACCATCCTGAT 62.452 63.158 4.18 0.00 0.00 2.90
1647 5972 3.003763 GCCAAGGTCTCCCTCGGT 61.004 66.667 0.00 0.00 41.56 4.69
1684 6022 0.108615 CCAGGTACGTGGCTCAAGAG 60.109 60.000 20.88 0.00 0.00 2.85
1688 6026 1.204941 GGTACGTGGCTCAAGAGATGT 59.795 52.381 0.00 0.00 0.00 3.06
1714 6844 9.305925 TCTTTGCATGCATATATATACTCTTCG 57.694 33.333 23.37 0.09 0.00 3.79
1741 6871 1.217882 AACACAGTACAGACGCAAGC 58.782 50.000 0.00 0.00 45.62 4.01
1742 6872 0.939577 ACACAGTACAGACGCAAGCG 60.940 55.000 13.50 13.50 46.03 4.68
1743 6873 2.022129 ACAGTACAGACGCAAGCGC 61.022 57.895 15.09 0.00 44.19 5.92
1745 6875 1.444553 AGTACAGACGCAAGCGCTC 60.445 57.895 12.06 11.06 44.19 5.03
1748 6878 0.454196 TACAGACGCAAGCGCTCATA 59.546 50.000 12.06 5.16 44.19 2.15
1749 6879 0.179100 ACAGACGCAAGCGCTCATAT 60.179 50.000 12.06 0.00 44.19 1.78
1751 6881 1.453524 CAGACGCAAGCGCTCATATAC 59.546 52.381 12.06 1.00 44.19 1.47
1754 6884 0.159554 CGCAAGCGCTCATATACACG 59.840 55.000 12.06 2.00 35.30 4.49
1755 6885 1.209128 GCAAGCGCTCATATACACGT 58.791 50.000 12.06 0.00 34.30 4.49
1756 6886 1.071239 GCAAGCGCTCATATACACGTG 60.071 52.381 12.06 15.48 34.30 4.49
1757 6887 1.071239 CAAGCGCTCATATACACGTGC 60.071 52.381 17.22 0.00 0.00 5.34
1758 6888 0.102300 AGCGCTCATATACACGTGCA 59.898 50.000 17.22 2.06 35.49 4.57
1759 6889 1.139989 GCGCTCATATACACGTGCAT 58.860 50.000 17.22 11.52 33.41 3.96
1760 6890 2.030274 AGCGCTCATATACACGTGCATA 60.030 45.455 17.22 13.68 35.49 3.14
1761 6891 2.090658 GCGCTCATATACACGTGCATAC 59.909 50.000 17.22 0.00 33.41 2.39
1764 6894 4.030641 CGCTCATATACACGTGCATACATC 59.969 45.833 17.22 2.75 0.00 3.06
1765 6895 4.923281 GCTCATATACACGTGCATACATCA 59.077 41.667 17.22 0.00 0.00 3.07
1766 6896 5.164051 GCTCATATACACGTGCATACATCAC 60.164 44.000 17.22 0.00 0.00 3.06
1767 6897 5.227152 TCATATACACGTGCATACATCACC 58.773 41.667 17.22 0.00 0.00 4.02
1769 6899 0.392461 ACACGTGCATACATCACCCC 60.392 55.000 17.22 0.00 0.00 4.95
1770 6900 0.107703 CACGTGCATACATCACCCCT 60.108 55.000 0.82 0.00 0.00 4.79
1773 6903 3.006430 CACGTGCATACATCACCCCTATA 59.994 47.826 0.82 0.00 0.00 1.31
1775 6905 4.101898 ACGTGCATACATCACCCCTATAAA 59.898 41.667 0.00 0.00 0.00 1.40
1777 6907 4.451096 GTGCATACATCACCCCTATAAACG 59.549 45.833 0.00 0.00 0.00 3.60
1780 6910 5.636543 GCATACATCACCCCTATAAACGTAC 59.363 44.000 0.00 0.00 0.00 3.67
1782 6912 5.881923 ACATCACCCCTATAAACGTACAT 57.118 39.130 0.00 0.00 0.00 2.29
1783 6913 6.982160 ACATCACCCCTATAAACGTACATA 57.018 37.500 0.00 0.00 0.00 2.29
1784 6914 6.752168 ACATCACCCCTATAAACGTACATAC 58.248 40.000 0.00 0.00 0.00 2.39
1797 6927 3.992260 GTACATACGAGCATCAGGACT 57.008 47.619 0.00 0.00 33.17 3.85
1798 6928 4.308899 GTACATACGAGCATCAGGACTT 57.691 45.455 0.00 0.00 33.17 3.01
1799 6929 3.170791 ACATACGAGCATCAGGACTTG 57.829 47.619 0.00 0.00 33.17 3.16
1800 6930 2.760650 ACATACGAGCATCAGGACTTGA 59.239 45.455 0.00 0.00 40.85 3.02
1801 6931 3.195610 ACATACGAGCATCAGGACTTGAA 59.804 43.478 0.00 0.00 39.77 2.69
1802 6932 2.086054 ACGAGCATCAGGACTTGAAC 57.914 50.000 0.00 0.00 39.77 3.18
1803 6933 1.338200 ACGAGCATCAGGACTTGAACC 60.338 52.381 0.00 0.00 39.77 3.62
1804 6934 1.743996 GAGCATCAGGACTTGAACCC 58.256 55.000 0.00 0.00 39.77 4.11
1805 6935 1.280421 GAGCATCAGGACTTGAACCCT 59.720 52.381 0.00 0.00 39.77 4.34
1809 6939 3.329300 CAGGACTTGAACCCTGGTG 57.671 57.895 0.00 0.00 44.68 4.17
1810 6940 0.250901 CAGGACTTGAACCCTGGTGG 60.251 60.000 0.00 0.00 44.68 4.61
1811 6941 0.401395 AGGACTTGAACCCTGGTGGA 60.401 55.000 0.00 0.00 38.00 4.02
1813 6943 0.765510 GACTTGAACCCTGGTGGACT 59.234 55.000 0.00 0.00 38.00 3.85
1815 6945 0.250901 CTTGAACCCTGGTGGACTGG 60.251 60.000 0.00 0.00 38.00 4.00
1822 6952 0.546598 CCTGGTGGACTGGGAATACC 59.453 60.000 0.00 0.00 35.88 2.73
1823 6953 2.183839 CCTGGTGGACTGGGAATACCA 61.184 57.143 0.00 0.00 41.04 3.25
1824 6954 3.499850 CCTGGTGGACTGGGAATACCAT 61.500 54.545 0.00 0.00 41.98 3.55
1825 6955 4.209229 CCTGGTGGACTGGGAATACCATA 61.209 52.174 0.00 0.00 41.98 2.74
1826 6956 6.029018 CCTGGTGGACTGGGAATACCATAG 62.029 54.167 0.00 0.00 41.98 2.23
1839 6969 7.741554 GGAATACCATAGTCCCTCTAATCAT 57.258 40.000 0.00 0.00 36.97 2.45
1840 6970 7.787028 GGAATACCATAGTCCCTCTAATCATC 58.213 42.308 0.00 0.00 36.97 2.92
1841 6971 7.147637 GGAATACCATAGTCCCTCTAATCATCC 60.148 44.444 0.00 0.00 36.97 3.51
1842 6972 5.093236 ACCATAGTCCCTCTAATCATCCA 57.907 43.478 0.00 0.00 31.94 3.41
1843 6973 5.476983 ACCATAGTCCCTCTAATCATCCAA 58.523 41.667 0.00 0.00 31.94 3.53
1844 6974 5.308237 ACCATAGTCCCTCTAATCATCCAAC 59.692 44.000 0.00 0.00 31.94 3.77
1845 6975 5.545723 CCATAGTCCCTCTAATCATCCAACT 59.454 44.000 0.00 0.00 31.94 3.16
1846 6976 6.726299 CCATAGTCCCTCTAATCATCCAACTA 59.274 42.308 0.00 0.00 31.94 2.24
1847 6977 7.310113 CCATAGTCCCTCTAATCATCCAACTAC 60.310 44.444 0.00 0.00 31.94 2.73
1848 6978 5.529289 AGTCCCTCTAATCATCCAACTACA 58.471 41.667 0.00 0.00 0.00 2.74
1849 6979 5.600484 AGTCCCTCTAATCATCCAACTACAG 59.400 44.000 0.00 0.00 0.00 2.74
1850 6980 4.901849 TCCCTCTAATCATCCAACTACAGG 59.098 45.833 0.00 0.00 0.00 4.00
1851 6981 4.656112 CCCTCTAATCATCCAACTACAGGT 59.344 45.833 0.00 0.00 0.00 4.00
1852 6982 5.131142 CCCTCTAATCATCCAACTACAGGTT 59.869 44.000 0.00 0.00 38.93 3.50
1862 6992 1.687563 ACTACAGGTTGGTTTGCACC 58.312 50.000 0.00 0.00 44.56 5.01
1896 7026 1.401761 GTTGCCCACATATGCCATGA 58.598 50.000 1.58 0.00 0.00 3.07
1906 7041 4.763279 CACATATGCCATGACATGTGGTAT 59.237 41.667 19.89 6.36 42.83 2.73
2288 7756 3.249189 TGGCCTTCCGCTCCAGTT 61.249 61.111 3.32 0.00 37.74 3.16
2311 7779 2.419198 GCCGATCTCATCAGCGGT 59.581 61.111 0.00 0.00 45.22 5.68
2596 8064 0.605860 TCGCGCTCTCTAGGGTATCC 60.606 60.000 5.56 0.00 37.95 2.59
2618 8086 2.204237 CATTCATCGCCGACATGAAGA 58.796 47.619 8.83 0.00 42.23 2.87
3142 8610 2.749621 GTTCCAACCCATCTGATGTGTC 59.250 50.000 15.95 0.00 0.00 3.67
3176 8644 7.087007 TGCGTTGAAATTATTTCTGTTGCATA 58.913 30.769 17.16 1.67 40.32 3.14
3270 8738 5.552870 AGTGTCCTATGTGAAGTTGTTCT 57.447 39.130 0.00 0.00 33.38 3.01
3312 8780 5.761234 TGGTTGGTTTGATACACTAGTGTTC 59.239 40.000 32.15 25.66 41.83 3.18
3319 8787 8.443937 GGTTTGATACACTAGTGTTCTTCATTC 58.556 37.037 32.15 22.42 41.83 2.67
3321 8789 7.239763 TGATACACTAGTGTTCTTCATTCCA 57.760 36.000 32.15 11.73 41.83 3.53
3491 8960 4.279671 TCGGCCAATCAATTGTTTTGTAGT 59.720 37.500 2.24 0.00 36.06 2.73
3581 9053 6.978024 TGTAAACAATTTGTACGCACAATC 57.022 33.333 1.23 0.00 44.01 2.67
3587 9059 5.812642 ACAATTTGTACGCACAATCCAAAAA 59.187 32.000 1.23 0.00 44.01 1.94
3793 9271 3.868077 AGCTGTATCTGAAAATGTCTCGC 59.132 43.478 0.00 0.00 0.00 5.03
3814 9292 4.029625 CGCGTGTAATTAAAATGCTCAACG 60.030 41.667 0.00 0.00 0.00 4.10
3929 9410 2.226262 AAAATGTTCGATGTGCGTCG 57.774 45.000 7.42 7.42 42.74 5.12
3953 9434 6.308524 CGAACACATGTTTAACGTGTATAGGA 59.691 38.462 20.64 0.00 45.79 2.94
4085 9570 7.889589 ACTGAAAAGAAAAACACAGAAAAGG 57.110 32.000 0.00 0.00 0.00 3.11
4103 9588 8.413229 CAGAAAAGGGAAAAGAACAACTTATGA 58.587 33.333 0.00 0.00 37.93 2.15
4110 9595 7.438160 GGGAAAAGAACAACTTATGAAACCTTG 59.562 37.037 0.00 0.00 37.93 3.61
4122 9607 3.223435 TGAAACCTTGCCAAAACCGATA 58.777 40.909 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.802948 ACGACTTATCTAGCTTGGGTG 57.197 47.619 0.00 0.00 0.00 4.61
32 33 1.726791 CTCGCATGTTGCTAACGACTT 59.273 47.619 0.00 0.00 42.25 3.01
36 37 1.459209 TCAACTCGCATGTTGCTAACG 59.541 47.619 12.33 0.00 44.83 3.18
63 64 1.478105 CCACATATGGGCATGACAGCT 60.478 52.381 7.80 0.00 43.04 4.24
167 249 0.169672 GCGCGGCCGAGTATAATAGA 59.830 55.000 33.48 0.00 36.29 1.98
188 270 1.500108 TTGAATGCAAAAGCAAGCCG 58.500 45.000 0.00 0.00 0.00 5.52
225 307 1.831106 TGCAGATGGGACGTCATACTT 59.169 47.619 18.91 5.13 0.00 2.24
551 3056 2.202743 TATGCAGAGGTCGCGTGC 60.203 61.111 5.77 9.09 37.73 5.34
614 3119 4.630111 CATGCATGTGGTGTTAGGTTTTT 58.370 39.130 18.91 0.00 0.00 1.94
615 3120 3.554752 GCATGCATGTGGTGTTAGGTTTT 60.555 43.478 26.79 0.00 0.00 2.43
616 3121 2.029110 GCATGCATGTGGTGTTAGGTTT 60.029 45.455 26.79 0.00 0.00 3.27
617 3122 1.545582 GCATGCATGTGGTGTTAGGTT 59.454 47.619 26.79 0.00 0.00 3.50
618 3123 1.176527 GCATGCATGTGGTGTTAGGT 58.823 50.000 26.79 0.00 0.00 3.08
619 3124 1.175654 TGCATGCATGTGGTGTTAGG 58.824 50.000 26.79 0.00 0.00 2.69
620 3125 2.804647 CATGCATGCATGTGGTGTTAG 58.195 47.619 40.30 20.25 46.20 2.34
621 3126 2.943449 CATGCATGCATGTGGTGTTA 57.057 45.000 40.30 10.77 46.20 2.41
622 3127 3.824621 CATGCATGCATGTGGTGTT 57.175 47.368 40.30 15.64 46.20 3.32
630 3135 4.336153 TCGTCTTGTATTTCATGCATGCAT 59.664 37.500 27.46 27.46 37.08 3.96
631 3136 3.688673 TCGTCTTGTATTTCATGCATGCA 59.311 39.130 25.04 25.04 0.00 3.96
641 3146 9.503427 GCTTTAATTATGCTTCGTCTTGTATTT 57.497 29.630 4.36 0.00 0.00 1.40
650 3155 6.449635 TTGATGGCTTTAATTATGCTTCGT 57.550 33.333 9.75 0.00 0.00 3.85
661 3166 9.575783 GTTTTTACCGAATATTGATGGCTTTAA 57.424 29.630 0.00 0.00 0.00 1.52
662 3167 8.740906 TGTTTTTACCGAATATTGATGGCTTTA 58.259 29.630 0.00 0.00 0.00 1.85
663 3168 7.607250 TGTTTTTACCGAATATTGATGGCTTT 58.393 30.769 0.00 0.00 0.00 3.51
664 3169 7.164230 TGTTTTTACCGAATATTGATGGCTT 57.836 32.000 0.00 0.00 0.00 4.35
844 3355 1.403814 TGATCACAACCCCGCAAAAA 58.596 45.000 0.00 0.00 0.00 1.94
845 3356 1.403814 TTGATCACAACCCCGCAAAA 58.596 45.000 0.00 0.00 0.00 2.44
846 3357 1.543802 GATTGATCACAACCCCGCAAA 59.456 47.619 0.00 0.00 38.90 3.68
847 3358 1.173043 GATTGATCACAACCCCGCAA 58.827 50.000 0.00 0.00 38.90 4.85
848 3359 0.679640 GGATTGATCACAACCCCGCA 60.680 55.000 0.00 0.00 38.90 5.69
849 3360 0.679640 TGGATTGATCACAACCCCGC 60.680 55.000 0.00 0.00 38.87 6.13
850 3361 2.057137 ATGGATTGATCACAACCCCG 57.943 50.000 0.00 0.00 38.87 5.73
851 3362 3.364549 TCAATGGATTGATCACAACCCC 58.635 45.455 0.00 0.00 38.87 4.95
879 3390 0.719465 CGGAACACGTAACCATCTGC 59.281 55.000 0.00 0.00 37.93 4.26
989 5305 1.153005 CCCTCCATTGCTCAGCTCC 60.153 63.158 0.00 0.00 0.00 4.70
1359 5684 0.988832 TTTCCACCGTCATAAGCCCT 59.011 50.000 0.00 0.00 0.00 5.19
1647 5972 2.029964 GAAACGACGCCCAGGACA 59.970 61.111 0.00 0.00 0.00 4.02
1688 6026 9.305925 CGAAGAGTATATATATGCATGCAAAGA 57.694 33.333 26.68 13.63 0.00 2.52
1722 6852 1.217882 GCTTGCGTCTGTACTGTGTT 58.782 50.000 0.00 0.00 0.00 3.32
1724 6854 1.775344 CGCTTGCGTCTGTACTGTG 59.225 57.895 6.86 0.00 0.00 3.66
1727 6857 1.444553 GAGCGCTTGCGTCTGTACT 60.445 57.895 13.26 3.73 45.69 2.73
1728 6858 1.078759 ATGAGCGCTTGCGTCTGTAC 61.079 55.000 13.26 0.00 45.69 2.90
1731 6861 1.453524 GTATATGAGCGCTTGCGTCTG 59.546 52.381 13.26 0.00 45.69 3.51
1732 6862 1.067060 TGTATATGAGCGCTTGCGTCT 59.933 47.619 13.26 13.17 45.69 4.18
1733 6863 1.190323 GTGTATATGAGCGCTTGCGTC 59.810 52.381 13.26 12.36 45.69 5.19
1734 6864 1.209128 GTGTATATGAGCGCTTGCGT 58.791 50.000 13.26 3.24 45.69 5.24
1736 6866 1.071239 CACGTGTATATGAGCGCTTGC 60.071 52.381 13.26 0.00 39.58 4.01
1740 6870 1.139989 ATGCACGTGTATATGAGCGC 58.860 50.000 18.03 0.00 32.85 5.92
1741 6871 3.305110 TGTATGCACGTGTATATGAGCG 58.695 45.455 25.81 0.00 32.85 5.03
1742 6872 4.923281 TGATGTATGCACGTGTATATGAGC 59.077 41.667 25.81 18.82 0.00 4.26
1743 6873 5.346011 GGTGATGTATGCACGTGTATATGAG 59.654 44.000 25.81 0.00 37.13 2.90
1745 6875 4.388773 GGGTGATGTATGCACGTGTATATG 59.611 45.833 25.81 0.00 37.13 1.78
1748 6878 2.484770 GGGGTGATGTATGCACGTGTAT 60.485 50.000 22.72 22.72 37.13 2.29
1749 6879 1.134640 GGGGTGATGTATGCACGTGTA 60.135 52.381 18.38 14.09 37.13 2.90
1751 6881 0.107703 AGGGGTGATGTATGCACGTG 60.108 55.000 12.28 12.28 37.13 4.49
1754 6884 4.451096 CGTTTATAGGGGTGATGTATGCAC 59.549 45.833 0.00 0.00 35.56 4.57
1755 6885 4.101898 ACGTTTATAGGGGTGATGTATGCA 59.898 41.667 0.00 0.00 0.00 3.96
1756 6886 4.638304 ACGTTTATAGGGGTGATGTATGC 58.362 43.478 0.00 0.00 0.00 3.14
1757 6887 6.751157 TGTACGTTTATAGGGGTGATGTATG 58.249 40.000 0.00 0.00 0.00 2.39
1758 6888 6.982160 TGTACGTTTATAGGGGTGATGTAT 57.018 37.500 0.00 0.00 0.00 2.29
1759 6889 6.982160 ATGTACGTTTATAGGGGTGATGTA 57.018 37.500 0.00 0.00 0.00 2.29
1760 6890 5.881923 ATGTACGTTTATAGGGGTGATGT 57.118 39.130 0.00 0.00 0.00 3.06
1761 6891 5.860182 CGTATGTACGTTTATAGGGGTGATG 59.140 44.000 0.00 0.00 44.13 3.07
1777 6907 3.992260 AGTCCTGATGCTCGTATGTAC 57.008 47.619 0.00 0.00 0.00 2.90
1780 6910 3.443099 TCAAGTCCTGATGCTCGTATG 57.557 47.619 0.00 0.00 0.00 2.39
1782 6912 2.094182 GGTTCAAGTCCTGATGCTCGTA 60.094 50.000 0.00 0.00 32.78 3.43
1783 6913 1.338200 GGTTCAAGTCCTGATGCTCGT 60.338 52.381 0.00 0.00 32.78 4.18
1784 6914 1.363744 GGTTCAAGTCCTGATGCTCG 58.636 55.000 0.00 0.00 32.78 5.03
1785 6915 1.280421 AGGGTTCAAGTCCTGATGCTC 59.720 52.381 0.00 0.00 32.78 4.26
1787 6917 3.965888 AGGGTTCAAGTCCTGATGC 57.034 52.632 0.00 0.00 32.78 3.91
1793 6923 0.250770 GTCCACCAGGGTTCAAGTCC 60.251 60.000 0.00 0.00 38.11 3.85
1794 6924 0.765510 AGTCCACCAGGGTTCAAGTC 59.234 55.000 0.00 0.00 38.11 3.01
1795 6925 0.474184 CAGTCCACCAGGGTTCAAGT 59.526 55.000 0.00 0.00 38.11 3.16
1796 6926 0.250901 CCAGTCCACCAGGGTTCAAG 60.251 60.000 0.00 0.00 38.11 3.02
1797 6927 1.715019 CCCAGTCCACCAGGGTTCAA 61.715 60.000 0.00 0.00 37.81 2.69
1798 6928 2.153401 CCCAGTCCACCAGGGTTCA 61.153 63.158 0.00 0.00 37.81 3.18
1799 6929 1.423794 TTCCCAGTCCACCAGGGTTC 61.424 60.000 0.00 0.00 43.31 3.62
1800 6930 0.776080 ATTCCCAGTCCACCAGGGTT 60.776 55.000 0.00 0.00 43.31 4.11
1801 6931 0.120377 TATTCCCAGTCCACCAGGGT 59.880 55.000 0.00 0.00 43.31 4.34
1802 6932 0.546598 GTATTCCCAGTCCACCAGGG 59.453 60.000 0.00 0.00 44.22 4.45
1803 6933 0.546598 GGTATTCCCAGTCCACCAGG 59.453 60.000 0.00 0.00 0.00 4.45
1804 6934 1.285280 TGGTATTCCCAGTCCACCAG 58.715 55.000 0.00 0.00 38.72 4.00
1805 6935 3.503974 TGGTATTCCCAGTCCACCA 57.496 52.632 0.00 0.00 38.72 4.17
1810 6940 3.579151 GAGGGACTATGGTATTCCCAGTC 59.421 52.174 13.05 10.19 46.99 3.51
1811 6941 3.210074 AGAGGGACTATGGTATTCCCAGT 59.790 47.826 13.05 0.00 46.99 4.00
1813 6943 5.427857 TTAGAGGGACTATGGTATTCCCA 57.572 43.478 13.05 0.00 46.99 4.37
1815 6945 7.147637 GGATGATTAGAGGGACTATGGTATTCC 60.148 44.444 0.00 0.00 41.55 3.01
1816 6946 7.400339 TGGATGATTAGAGGGACTATGGTATTC 59.600 40.741 0.00 0.00 41.55 1.75
1817 6947 7.256399 TGGATGATTAGAGGGACTATGGTATT 58.744 38.462 0.00 0.00 41.55 1.89
1818 6948 6.815880 TGGATGATTAGAGGGACTATGGTAT 58.184 40.000 0.00 0.00 41.55 2.73
1819 6949 6.227624 TGGATGATTAGAGGGACTATGGTA 57.772 41.667 0.00 0.00 41.55 3.25
1820 6950 5.093236 TGGATGATTAGAGGGACTATGGT 57.907 43.478 0.00 0.00 41.55 3.55
1821 6951 5.545723 AGTTGGATGATTAGAGGGACTATGG 59.454 44.000 0.00 0.00 41.55 2.74
1822 6952 6.678568 AGTTGGATGATTAGAGGGACTATG 57.321 41.667 0.00 0.00 41.55 2.23
1823 6953 7.306013 TGTAGTTGGATGATTAGAGGGACTAT 58.694 38.462 0.00 0.00 41.55 2.12
1824 6954 6.679542 TGTAGTTGGATGATTAGAGGGACTA 58.320 40.000 0.00 0.00 41.55 2.59
1826 6956 5.221541 CCTGTAGTTGGATGATTAGAGGGAC 60.222 48.000 0.00 0.00 0.00 4.46
1827 6957 4.901849 CCTGTAGTTGGATGATTAGAGGGA 59.098 45.833 0.00 0.00 0.00 4.20
1828 6958 4.656112 ACCTGTAGTTGGATGATTAGAGGG 59.344 45.833 0.00 0.00 32.45 4.30
1829 6959 5.878406 ACCTGTAGTTGGATGATTAGAGG 57.122 43.478 0.00 0.00 33.91 3.69
1842 6972 2.028876 GGTGCAAACCAACCTGTAGTT 58.971 47.619 0.00 0.00 40.16 2.24
1843 6973 1.687563 GGTGCAAACCAACCTGTAGT 58.312 50.000 0.00 0.00 0.00 2.73
1850 6980 0.458260 AACGAAGGGTGCAAACCAAC 59.542 50.000 10.96 3.93 0.00 3.77
1851 6981 1.187087 AAACGAAGGGTGCAAACCAA 58.813 45.000 10.96 0.00 0.00 3.67
1852 6982 1.187087 AAAACGAAGGGTGCAAACCA 58.813 45.000 10.96 0.00 0.00 3.67
1853 6983 3.653539 ATAAAACGAAGGGTGCAAACC 57.346 42.857 0.43 0.43 0.00 3.27
1854 6984 5.158494 CCTAATAAAACGAAGGGTGCAAAC 58.842 41.667 0.00 0.00 0.00 2.93
1855 6985 4.828387 ACCTAATAAAACGAAGGGTGCAAA 59.172 37.500 0.00 0.00 33.16 3.68
1856 6986 4.400120 ACCTAATAAAACGAAGGGTGCAA 58.600 39.130 0.00 0.00 33.16 4.08
1857 6987 4.023726 ACCTAATAAAACGAAGGGTGCA 57.976 40.909 0.00 0.00 33.16 4.57
1858 6988 4.729595 CAACCTAATAAAACGAAGGGTGC 58.270 43.478 0.00 0.00 39.81 5.01
1896 7026 8.314021 CAGATATACACATACCATACCACATGT 58.686 37.037 0.00 0.00 31.91 3.21
1906 7041 4.953940 TGCAGCAGATATACACATACCA 57.046 40.909 0.00 0.00 0.00 3.25
1983 7431 5.621228 GTGCACAAAAGAGAGTAACAATTCG 59.379 40.000 13.17 0.00 0.00 3.34
2299 7767 2.420058 TGACTCTACCGCTGATGAGA 57.580 50.000 8.46 0.00 0.00 3.27
2311 7779 2.744760 AGAAGCTCCTGCATGACTCTA 58.255 47.619 0.00 0.00 42.74 2.43
2596 8064 1.083209 CATGTCGGCGATGAATGCG 60.083 57.895 14.79 0.00 0.00 4.73
2618 8086 0.605589 GGGTTGCTGTTACGGAGCTT 60.606 55.000 0.00 0.00 37.35 3.74
2650 8118 1.029408 CCAAACCGGCATCGATTCCA 61.029 55.000 14.60 0.00 39.00 3.53
2966 8434 0.037590 TTAATGCCGAGCACCTGGTT 59.962 50.000 0.00 0.00 43.04 3.67
3142 8610 3.915437 AATTTCAACGCAACCACCTAG 57.085 42.857 0.00 0.00 0.00 3.02
3176 8644 7.781324 AATGTTCACAAAAGTATCCAAGGAT 57.219 32.000 6.84 6.84 38.54 3.24
3270 8738 3.757270 ACCAACAATCATACCGGTGAAA 58.243 40.909 19.93 0.00 0.00 2.69
3442 8911 2.818130 ATTGCGTGCAAGAAAACCAT 57.182 40.000 13.25 0.00 39.47 3.55
3547 9019 6.225318 ACAAATTGTTTACATTGCATGAGCT 58.775 32.000 0.00 0.00 42.74 4.09
3549 9021 7.656468 CGTACAAATTGTTTACATTGCATGAG 58.344 34.615 3.17 0.00 0.00 2.90
3699 9174 9.814899 TGAACATTTTCTGAATACACATTTTGT 57.185 25.926 0.00 0.00 36.04 2.83
3793 9271 5.849081 ACACGTTGAGCATTTTAATTACACG 59.151 36.000 0.00 0.00 0.00 4.49
4051 9536 9.967245 GTGTTTTTCTTTTCAGTTTTCATTACC 57.033 29.630 0.00 0.00 0.00 2.85
4085 9570 7.042725 GCAAGGTTTCATAAGTTGTTCTTTTCC 60.043 37.037 0.00 0.00 37.56 3.13
4103 9588 3.492337 TCTATCGGTTTTGGCAAGGTTT 58.508 40.909 0.00 0.00 0.00 3.27
4110 9595 3.945285 TGGAATCTTCTATCGGTTTTGGC 59.055 43.478 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.