Multiple sequence alignment - TraesCS5B01G427300

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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 TraesCS5B01G427300 chr5B 100.000 4882 0 0 1 4882 603466421 603471302 0.000000e+00 9016.0
1 TraesCS5B01G427300 chr5B 94.357 886 45 4 1866 2751 603458696 603459576 0.000000e+00 1354.0
2 TraesCS5B01G427300 chr5B 86.562 893 113 4 1866 2757 254872115 254871229 0.000000e+00 977.0
3 TraesCS5B01G427300 chr5B 92.829 502 34 2 1365 1865 151669790 151669290 0.000000e+00 726.0
4 TraesCS5B01G427300 chr5B 83.871 744 90 18 1132 1865 317445419 317444696 0.000000e+00 682.0
5 TraesCS5B01G427300 chr3B 90.107 1870 138 13 1 1865 213878991 213877164 0.000000e+00 2385.0
6 TraesCS5B01G427300 chr3B 86.480 895 109 9 1866 2757 443657741 443656856 0.000000e+00 972.0
7 TraesCS5B01G427300 chr3B 86.369 895 110 9 1866 2757 275869164 275868279 0.000000e+00 966.0
8 TraesCS5B01G427300 chr3B 89.016 701 68 7 1 701 429990164 429989473 0.000000e+00 859.0
9 TraesCS5B01G427300 chr3B 80.449 890 169 4 3992 4880 807168373 807167488 0.000000e+00 675.0
10 TraesCS5B01G427300 chr3B 76.515 1056 216 29 2752 3792 807169671 807168633 9.240000e-152 547.0
11 TraesCS5B01G427300 chr3B 77.492 311 49 16 629 933 604599494 604599199 3.020000e-37 167.0
12 TraesCS5B01G427300 chr1A 85.033 2138 301 17 2753 4880 348721906 348724034 0.000000e+00 2158.0
13 TraesCS5B01G427300 chr1A 75.374 601 141 7 4089 4685 554925533 554924936 2.880000e-72 283.0
14 TraesCS5B01G427300 chr1A 75.208 601 142 7 4089 4685 93549193 93548596 1.340000e-70 278.0
15 TraesCS5B01G427300 chr1A 94.118 34 2 0 4588 4621 415309099 415309132 9.000000e-03 52.8
16 TraesCS5B01G427300 chr2A 84.939 2138 288 24 2753 4880 530571994 530574107 0.000000e+00 2134.0
17 TraesCS5B01G427300 chr2A 84.697 2078 306 9 2808 4880 174021317 174019247 0.000000e+00 2065.0
18 TraesCS5B01G427300 chr7A 81.538 2145 369 24 2752 4880 642933381 642931248 0.000000e+00 1742.0
19 TraesCS5B01G427300 chr7A 74.830 735 166 17 3024 3748 610689183 610689908 1.020000e-81 315.0
20 TraesCS5B01G427300 chr6B 81.119 2145 376 26 2753 4880 57129078 57131210 0.000000e+00 1690.0
21 TraesCS5B01G427300 chr6B 92.659 504 34 3 1365 1865 194453191 194452688 0.000000e+00 723.0
22 TraesCS5B01G427300 chr6B 79.692 325 64 2 4089 4412 116913181 116912858 2.940000e-57 233.0
23 TraesCS5B01G427300 chr6B 84.810 79 10 2 664 741 663420665 663420742 1.460000e-10 78.7
24 TraesCS5B01G427300 chr6B 87.500 56 7 0 3149 3204 2739041 2738986 1.130000e-06 65.8
25 TraesCS5B01G427300 chr2B 81.110 2144 378 24 2753 4880 516283220 516281088 0.000000e+00 1690.0
26 TraesCS5B01G427300 chr2B 89.599 1048 101 6 1 1045 379353130 379352088 0.000000e+00 1325.0
27 TraesCS5B01G427300 chr2B 92.986 499 33 2 1369 1865 379349627 379349129 0.000000e+00 726.0
28 TraesCS5B01G427300 chr2B 84.917 663 90 7 1211 1865 381902287 381901627 0.000000e+00 662.0
29 TraesCS5B01G427300 chr2B 90.303 330 29 3 1045 1372 379351945 379351617 3.490000e-116 429.0
30 TraesCS5B01G427300 chr2B 80.882 272 35 13 670 928 552577519 552577786 1.070000e-46 198.0
31 TraesCS5B01G427300 chr2B 88.034 117 12 2 816 932 51239732 51239618 2.370000e-28 137.0
32 TraesCS5B01G427300 chr7B 89.089 1054 109 5 1 1050 633479182 633478131 0.000000e+00 1304.0
33 TraesCS5B01G427300 chr7B 92.601 892 63 3 1866 2757 297684810 297683922 0.000000e+00 1279.0
34 TraesCS5B01G427300 chr7B 92.083 821 63 1 1045 1865 633477995 633477177 0.000000e+00 1155.0
35 TraesCS5B01G427300 chr7B 77.724 1661 337 29 2752 4401 713133784 713135422 0.000000e+00 987.0
36 TraesCS5B01G427300 chr7B 91.165 532 44 3 1336 1865 451710434 451709904 0.000000e+00 719.0
37 TraesCS5B01G427300 chr7B 82.332 832 122 14 1045 1869 24819463 24818650 0.000000e+00 699.0
38 TraesCS5B01G427300 chr7B 78.293 410 79 8 4089 4493 207900096 207899692 6.270000e-64 255.0
39 TraesCS5B01G427300 chr6A 76.844 2142 474 20 2752 4882 106974347 106976477 0.000000e+00 1188.0
40 TraesCS5B01G427300 chr6A 74.793 603 141 10 4089 4685 116804308 116804905 1.350000e-65 261.0
41 TraesCS5B01G427300 chr2D 90.940 883 71 6 1868 2750 244595726 244594853 0.000000e+00 1179.0
42 TraesCS5B01G427300 chr2D 89.798 892 83 5 1866 2757 244600022 244599139 0.000000e+00 1136.0
43 TraesCS5B01G427300 chr2D 74.801 627 153 5 3036 3659 58995450 58994826 1.340000e-70 278.0
44 TraesCS5B01G427300 chr2D 78.250 400 81 6 4089 4485 546422254 546421858 8.110000e-63 252.0
45 TraesCS5B01G427300 chr1D 76.730 2153 464 33 2752 4882 470128498 470130635 0.000000e+00 1166.0
46 TraesCS5B01G427300 chr1D 88.034 702 74 8 1 701 464197501 464198193 0.000000e+00 822.0
47 TraesCS5B01G427300 chr1D 73.418 711 173 15 4079 4782 432371859 432371158 8.110000e-63 252.0
48 TraesCS5B01G427300 chr3D 89.910 892 82 5 1866 2757 19195203 19194320 0.000000e+00 1142.0
49 TraesCS5B01G427300 chr3D 87.892 702 81 3 1 701 466150382 466151080 0.000000e+00 822.0
50 TraesCS5B01G427300 chr3D 87.037 702 81 7 1 701 339805050 339805742 0.000000e+00 784.0
51 TraesCS5B01G427300 chr3D 88.281 128 13 1 806 933 430842996 430842871 8.460000e-33 152.0
52 TraesCS5B01G427300 chr7D 86.659 892 107 10 1866 2753 583558161 583557278 0.000000e+00 977.0
53 TraesCS5B01G427300 chr7D 74.798 619 139 15 4079 4689 242751625 242752234 3.750000e-66 263.0
54 TraesCS5B01G427300 chr4D 87.607 702 80 4 1 701 351769913 351769218 0.000000e+00 808.0
55 TraesCS5B01G427300 chr4D 87.037 702 80 9 1 701 264275961 264275270 0.000000e+00 782.0
56 TraesCS5B01G427300 chr4D 86.610 702 82 6 1 701 249444788 249444098 0.000000e+00 765.0
57 TraesCS5B01G427300 chr1B 83.353 829 111 16 1045 1865 268980891 268980082 0.000000e+00 741.0
58 TraesCS5B01G427300 chr1B 75.126 595 141 7 4095 4685 602165693 602165102 6.230000e-69 272.0
59 TraesCS5B01G427300 chr1B 80.186 323 61 3 4079 4400 160649648 160649968 6.320000e-59 239.0
60 TraesCS5B01G427300 chr1B 78.102 274 48 11 487 750 687681662 687681391 3.910000e-36 163.0
61 TraesCS5B01G427300 chr1B 88.136 118 12 2 816 933 147973260 147973375 6.590000e-29 139.0
62 TraesCS5B01G427300 chr4B 76.894 1333 291 15 3557 4882 599830613 599831935 0.000000e+00 739.0
63 TraesCS5B01G427300 chr4B 75.345 507 112 11 4119 4619 338442544 338443043 1.060000e-56 231.0
64 TraesCS5B01G427300 chr5D 82.063 669 103 13 1211 1870 54723077 54722417 5.520000e-154 555.0
65 TraesCS5B01G427300 chr5D 80.310 645 112 12 1230 1865 185253681 185253043 1.590000e-129 473.0
66 TraesCS5B01G427300 chr5D 73.773 713 168 17 4079 4782 449646382 449645680 3.750000e-66 263.0
67 TraesCS5B01G427300 chr5D 73.020 808 192 24 4089 4882 253579402 253578607 1.350000e-65 261.0
68 TraesCS5B01G427300 chr5D 77.750 400 83 6 4089 4485 553917641 553917245 1.760000e-59 241.0
69 TraesCS5B01G427300 chr5D 85.294 136 14 5 800 933 436549977 436550108 8.520000e-28 135.0
70 TraesCS5B01G427300 chrUn 85.263 380 56 0 4276 4655 480950984 480950605 4.580000e-105 392.0
71 TraesCS5B01G427300 chrUn 95.431 197 8 1 765 960 23441617 23441813 3.670000e-81 313.0
72 TraesCS5B01G427300 chrUn 79.545 396 74 6 3860 4253 479166262 479165872 4.810000e-70 276.0
73 TraesCS5B01G427300 chrUn 73.558 711 172 15 4079 4782 96581102 96580401 1.740000e-64 257.0
74 TraesCS5B01G427300 chr3A 72.458 708 186 9 3024 3726 710798884 710799587 8.230000e-53 219.0
75 TraesCS5B01G427300 chr6D 73.096 617 156 9 4095 4706 240121005 240120394 1.380000e-50 211.0


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 TraesCS5B01G427300 chr5B 603466421 603471302 4881 False 9016.000000 9016 100.000000 1 4882 1 chr5B.!!$F2 4881
1 TraesCS5B01G427300 chr5B 603458696 603459576 880 False 1354.000000 1354 94.357000 1866 2751 1 chr5B.!!$F1 885
2 TraesCS5B01G427300 chr5B 254871229 254872115 886 True 977.000000 977 86.562000 1866 2757 1 chr5B.!!$R2 891
3 TraesCS5B01G427300 chr5B 151669290 151669790 500 True 726.000000 726 92.829000 1365 1865 1 chr5B.!!$R1 500
4 TraesCS5B01G427300 chr5B 317444696 317445419 723 True 682.000000 682 83.871000 1132 1865 1 chr5B.!!$R3 733
5 TraesCS5B01G427300 chr3B 213877164 213878991 1827 True 2385.000000 2385 90.107000 1 1865 1 chr3B.!!$R1 1864
6 TraesCS5B01G427300 chr3B 443656856 443657741 885 True 972.000000 972 86.480000 1866 2757 1 chr3B.!!$R4 891
7 TraesCS5B01G427300 chr3B 275868279 275869164 885 True 966.000000 966 86.369000 1866 2757 1 chr3B.!!$R2 891
8 TraesCS5B01G427300 chr3B 429989473 429990164 691 True 859.000000 859 89.016000 1 701 1 chr3B.!!$R3 700
9 TraesCS5B01G427300 chr3B 807167488 807169671 2183 True 611.000000 675 78.482000 2752 4880 2 chr3B.!!$R6 2128
10 TraesCS5B01G427300 chr1A 348721906 348724034 2128 False 2158.000000 2158 85.033000 2753 4880 1 chr1A.!!$F1 2127
11 TraesCS5B01G427300 chr1A 554924936 554925533 597 True 283.000000 283 75.374000 4089 4685 1 chr1A.!!$R2 596
12 TraesCS5B01G427300 chr1A 93548596 93549193 597 True 278.000000 278 75.208000 4089 4685 1 chr1A.!!$R1 596
13 TraesCS5B01G427300 chr2A 530571994 530574107 2113 False 2134.000000 2134 84.939000 2753 4880 1 chr2A.!!$F1 2127
14 TraesCS5B01G427300 chr2A 174019247 174021317 2070 True 2065.000000 2065 84.697000 2808 4880 1 chr2A.!!$R1 2072
15 TraesCS5B01G427300 chr7A 642931248 642933381 2133 True 1742.000000 1742 81.538000 2752 4880 1 chr7A.!!$R1 2128
16 TraesCS5B01G427300 chr7A 610689183 610689908 725 False 315.000000 315 74.830000 3024 3748 1 chr7A.!!$F1 724
17 TraesCS5B01G427300 chr6B 57129078 57131210 2132 False 1690.000000 1690 81.119000 2753 4880 1 chr6B.!!$F1 2127
18 TraesCS5B01G427300 chr6B 194452688 194453191 503 True 723.000000 723 92.659000 1365 1865 1 chr6B.!!$R3 500
19 TraesCS5B01G427300 chr2B 516281088 516283220 2132 True 1690.000000 1690 81.110000 2753 4880 1 chr2B.!!$R3 2127
20 TraesCS5B01G427300 chr2B 379349129 379353130 4001 True 826.666667 1325 90.962667 1 1865 3 chr2B.!!$R4 1864
21 TraesCS5B01G427300 chr2B 381901627 381902287 660 True 662.000000 662 84.917000 1211 1865 1 chr2B.!!$R2 654
22 TraesCS5B01G427300 chr7B 297683922 297684810 888 True 1279.000000 1279 92.601000 1866 2757 1 chr7B.!!$R3 891
23 TraesCS5B01G427300 chr7B 633477177 633479182 2005 True 1229.500000 1304 90.586000 1 1865 2 chr7B.!!$R5 1864
24 TraesCS5B01G427300 chr7B 713133784 713135422 1638 False 987.000000 987 77.724000 2752 4401 1 chr7B.!!$F1 1649
25 TraesCS5B01G427300 chr7B 451709904 451710434 530 True 719.000000 719 91.165000 1336 1865 1 chr7B.!!$R4 529
26 TraesCS5B01G427300 chr7B 24818650 24819463 813 True 699.000000 699 82.332000 1045 1869 1 chr7B.!!$R1 824
27 TraesCS5B01G427300 chr6A 106974347 106976477 2130 False 1188.000000 1188 76.844000 2752 4882 1 chr6A.!!$F1 2130
28 TraesCS5B01G427300 chr6A 116804308 116804905 597 False 261.000000 261 74.793000 4089 4685 1 chr6A.!!$F2 596
29 TraesCS5B01G427300 chr2D 244594853 244600022 5169 True 1157.500000 1179 90.369000 1866 2757 2 chr2D.!!$R3 891
30 TraesCS5B01G427300 chr2D 58994826 58995450 624 True 278.000000 278 74.801000 3036 3659 1 chr2D.!!$R1 623
31 TraesCS5B01G427300 chr1D 470128498 470130635 2137 False 1166.000000 1166 76.730000 2752 4882 1 chr1D.!!$F2 2130
32 TraesCS5B01G427300 chr1D 464197501 464198193 692 False 822.000000 822 88.034000 1 701 1 chr1D.!!$F1 700
33 TraesCS5B01G427300 chr1D 432371158 432371859 701 True 252.000000 252 73.418000 4079 4782 1 chr1D.!!$R1 703
34 TraesCS5B01G427300 chr3D 19194320 19195203 883 True 1142.000000 1142 89.910000 1866 2757 1 chr3D.!!$R1 891
35 TraesCS5B01G427300 chr3D 466150382 466151080 698 False 822.000000 822 87.892000 1 701 1 chr3D.!!$F2 700
36 TraesCS5B01G427300 chr3D 339805050 339805742 692 False 784.000000 784 87.037000 1 701 1 chr3D.!!$F1 700
37 TraesCS5B01G427300 chr7D 583557278 583558161 883 True 977.000000 977 86.659000 1866 2753 1 chr7D.!!$R1 887
38 TraesCS5B01G427300 chr7D 242751625 242752234 609 False 263.000000 263 74.798000 4079 4689 1 chr7D.!!$F1 610
39 TraesCS5B01G427300 chr4D 351769218 351769913 695 True 808.000000 808 87.607000 1 701 1 chr4D.!!$R3 700
40 TraesCS5B01G427300 chr4D 264275270 264275961 691 True 782.000000 782 87.037000 1 701 1 chr4D.!!$R2 700
41 TraesCS5B01G427300 chr4D 249444098 249444788 690 True 765.000000 765 86.610000 1 701 1 chr4D.!!$R1 700
42 TraesCS5B01G427300 chr1B 268980082 268980891 809 True 741.000000 741 83.353000 1045 1865 1 chr1B.!!$R1 820
43 TraesCS5B01G427300 chr1B 602165102 602165693 591 True 272.000000 272 75.126000 4095 4685 1 chr1B.!!$R2 590
44 TraesCS5B01G427300 chr4B 599830613 599831935 1322 False 739.000000 739 76.894000 3557 4882 1 chr4B.!!$F2 1325
45 TraesCS5B01G427300 chr5D 54722417 54723077 660 True 555.000000 555 82.063000 1211 1870 1 chr5D.!!$R1 659
46 TraesCS5B01G427300 chr5D 185253043 185253681 638 True 473.000000 473 80.310000 1230 1865 1 chr5D.!!$R2 635
47 TraesCS5B01G427300 chr5D 449645680 449646382 702 True 263.000000 263 73.773000 4079 4782 1 chr5D.!!$R4 703
48 TraesCS5B01G427300 chr5D 253578607 253579402 795 True 261.000000 261 73.020000 4089 4882 1 chr5D.!!$R3 793
49 TraesCS5B01G427300 chrUn 96580401 96581102 701 True 257.000000 257 73.558000 4079 4782 1 chrUn.!!$R1 703
50 TraesCS5B01G427300 chr3A 710798884 710799587 703 False 219.000000 219 72.458000 3024 3726 1 chr3A.!!$F1 702
51 TraesCS5B01G427300 chr6D 240120394 240121005 611 True 211.000000 211 73.096000 4095 4706 1 chr6D.!!$R1 611

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
168 170 0.701147 CTTCAGAAAGGAAGCCCCCT 59.299 55.000 0.00 0.0 38.01 4.79 F
748 754 1.224315 CATCGGCATGAGGGGTGAA 59.776 57.895 0.00 0.0 30.57 3.18 F
2406 8875 1.341913 TGGGGTGCGCCATATGTAGT 61.342 55.000 19.98 0.0 36.17 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1100 1255 0.112995 AAAGTCAATGGAGCAGGGCA 59.887 50.0 0.00 0.00 0.00 5.36 R
2417 8886 0.107312 AGAGCCATTCGAATGCAGCT 60.107 50.0 30.01 30.01 36.87 4.24 R
4172 10739 0.037790 GAAGCTCCTTCACTGTCGCT 60.038 55.0 0.00 0.00 39.95 4.93 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
73 75 2.699954 CTTGCGGAACACTTAGGTCAT 58.300 47.619 0.00 0.00 34.85 3.06
78 80 4.081365 TGCGGAACACTTAGGTCATTATGA 60.081 41.667 0.00 0.00 34.85 2.15
117 119 5.718649 ATACATGAACAAGGAACGAATCG 57.281 39.130 0.00 0.00 0.00 3.34
135 137 8.516811 ACGAATCGGTACAAGTATAATCATTC 57.483 34.615 7.80 0.00 0.00 2.67
136 138 8.139350 ACGAATCGGTACAAGTATAATCATTCA 58.861 33.333 7.80 0.00 0.00 2.57
140 142 9.607988 ATCGGTACAAGTATAATCATTCACAAA 57.392 29.630 0.00 0.00 0.00 2.83
168 170 0.701147 CTTCAGAAAGGAAGCCCCCT 59.299 55.000 0.00 0.00 38.01 4.79
317 320 3.319137 TGAGCATGAAAGCGACTTAGT 57.681 42.857 0.00 0.00 40.15 2.24
410 413 4.821589 GAGGTGGCCGAGCGAAGG 62.822 72.222 0.00 0.00 0.00 3.46
731 737 1.302431 CCGATGTCAACACAGGGCA 60.302 57.895 0.00 0.00 35.41 5.36
748 754 1.224315 CATCGGCATGAGGGGTGAA 59.776 57.895 0.00 0.00 30.57 3.18
980 987 3.362986 CGATCATAAAACGCCAGGATTCG 60.363 47.826 0.00 0.00 0.00 3.34
1036 1043 3.381908 GGGCTGATCGAGATATACGGAAT 59.618 47.826 0.00 0.00 0.00 3.01
1098 1253 4.344865 ACCGTGTGGACATGCCCC 62.345 66.667 0.00 0.00 39.21 5.80
1100 1255 4.697756 CGTGTGGACATGCCCCGT 62.698 66.667 0.00 0.00 34.97 5.28
1193 1355 2.093711 TGTTGCTGTGATGCGTATACCT 60.094 45.455 0.00 0.00 35.36 3.08
1274 1436 1.741401 CTCAATGCGTTGCCTCCGA 60.741 57.895 14.04 0.00 35.26 4.55
1322 1488 5.176958 ACGTCTGCGGATAAAATTACATAGC 59.823 40.000 0.00 0.00 43.45 2.97
1334 1500 3.520290 TTACATAGCCCGACAACAGAG 57.480 47.619 0.00 0.00 0.00 3.35
1474 3636 3.125829 TCAATATCCGGCGTATCTCGTAC 59.874 47.826 6.01 0.00 42.13 3.67
1803 3971 3.749679 TATAAGGCCGTGGGGGTCCTT 62.750 57.143 0.00 11.38 46.97 3.36
1905 4073 1.573108 GCTATGGGCTGCCCTAGATA 58.427 55.000 35.80 23.86 45.70 1.98
1936 4104 1.381327 CCTAGGGCCTCGAGGTTCA 60.381 63.158 31.43 14.05 37.57 3.18
1969 4138 5.914085 ACAAGAAGAACAGACGAAGAATG 57.086 39.130 0.00 0.00 0.00 2.67
1970 4139 5.601662 ACAAGAAGAACAGACGAAGAATGA 58.398 37.500 0.00 0.00 0.00 2.57
1996 4165 7.680739 AGAGGAAGAAGAAGAACTAGGGTTAAT 59.319 37.037 0.00 0.00 35.58 1.40
2177 4348 5.540719 TGGTTTTATCCGAACTTCCCAAAAT 59.459 36.000 0.00 0.00 0.00 1.82
2383 8851 3.742327 CGCTACCCATCAGACATCATGTT 60.742 47.826 0.00 0.00 0.00 2.71
2392 8860 2.892852 CAGACATCATGTTTTGTGGGGT 59.107 45.455 0.00 0.00 0.00 4.95
2406 8875 1.341913 TGGGGTGCGCCATATGTAGT 61.342 55.000 19.98 0.00 36.17 2.73
2414 8883 1.667177 CGCCATATGTAGTCTCCTGCG 60.667 57.143 1.24 2.55 0.00 5.18
2417 8886 3.149981 CCATATGTAGTCTCCTGCGAGA 58.850 50.000 1.24 0.00 43.08 4.04
2486 8955 8.293157 TGAGATGAGTTGTATATCAGAATCGAC 58.707 37.037 0.00 0.00 0.00 4.20
2572 9041 6.038356 GCTTAATACGCCAAACTGTACTCTA 58.962 40.000 0.00 0.00 0.00 2.43
2780 9249 4.131596 CTCGTTAGGGTTTGTTTTCCTCA 58.868 43.478 0.00 0.00 32.46 3.86
2838 9311 1.621072 CCTACCTCTCCTGGCTCTTGT 60.621 57.143 0.00 0.00 0.00 3.16
2871 9345 1.904771 CAATCTAGGGTGGCCGTCA 59.095 57.895 0.00 0.00 0.00 4.35
2881 9356 4.530857 GGCCGTCAGGTCATCCGG 62.531 72.222 0.00 0.00 43.06 5.14
2982 9467 2.814336 GTTTCGAGATGGCTTCAACCTT 59.186 45.455 3.03 0.00 0.00 3.50
3080 9565 1.258445 GGAGGACCTGGACGATGTGT 61.258 60.000 0.00 0.00 0.00 3.72
3131 9617 1.377725 CTCGCTGGATTGCCCTTGT 60.378 57.895 0.00 0.00 35.38 3.16
3225 9711 3.486383 CCAAGAGGTAAAGTTCAAGCCA 58.514 45.455 0.00 0.00 0.00 4.75
3331 9817 0.109086 CGACGCTGTCATCCTCAAGT 60.109 55.000 8.91 0.00 32.09 3.16
3354 9840 6.260936 AGTCTTATGATGGATTAGCAAAACCG 59.739 38.462 0.00 0.00 30.24 4.44
3359 9845 2.980568 TGGATTAGCAAAACCGTCGAT 58.019 42.857 0.00 0.00 30.24 3.59
3362 9848 3.059800 GGATTAGCAAAACCGTCGATAGC 60.060 47.826 0.00 0.00 0.00 2.97
3365 9851 0.743345 GCAAAACCGTCGATAGCCCT 60.743 55.000 0.00 0.00 0.00 5.19
3432 9918 1.078426 GTACGCCCATCTTGTGCCT 60.078 57.895 0.00 0.00 0.00 4.75
3538 10024 3.941483 CAGGATCAATGTTACGAAGCCTT 59.059 43.478 0.00 0.00 0.00 4.35
3551 10037 2.485426 CGAAGCCTTTGAAGAATGCAGA 59.515 45.455 0.00 0.00 0.00 4.26
3554 10040 5.163723 CGAAGCCTTTGAAGAATGCAGATTA 60.164 40.000 0.00 0.00 0.00 1.75
3563 10049 7.255491 TGAAGAATGCAGATTACATGATCAC 57.745 36.000 0.00 0.00 0.00 3.06
3660 10148 4.440663 GGGCATCTTTTTAAGGAGCATGAC 60.441 45.833 0.00 0.00 32.71 3.06
3665 10153 2.851263 TTTAAGGAGCATGACACCGT 57.149 45.000 0.00 0.00 33.55 4.83
3699 10187 4.882427 CCATCAGCACTGATCTTCAAGAAT 59.118 41.667 10.19 0.00 46.57 2.40
3754 10243 3.826282 CAGGTGGTGGATGGGACT 58.174 61.111 0.00 0.00 0.00 3.85
3759 10248 0.693049 GTGGTGGATGGGACTGAAGT 59.307 55.000 0.00 0.00 0.00 3.01
3761 10250 0.984230 GGTGGATGGGACTGAAGTGA 59.016 55.000 0.00 0.00 0.00 3.41
3769 10258 1.009389 GGACTGAAGTGAAGGACGCG 61.009 60.000 3.53 3.53 0.00 6.01
3804 10305 4.139234 GGCCGTACCAGGGACGAC 62.139 72.222 27.14 14.98 42.98 4.34
3825 10326 1.595093 CTTTTGGGGACGATGGTGGC 61.595 60.000 0.00 0.00 0.00 5.01
3845 10346 3.452474 GCGATGATAGCAAGAACTCTGT 58.548 45.455 0.00 0.00 34.19 3.41
3869 10436 1.202770 TGCTGATGCAGAGATGGATGG 60.203 52.381 0.00 0.00 45.31 3.51
3933 10500 4.899239 GCGGGATCTGGAGTGGCG 62.899 72.222 0.00 0.00 0.00 5.69
3934 10501 4.899239 CGGGATCTGGAGTGGCGC 62.899 72.222 0.00 0.00 0.00 6.53
3936 10503 2.202987 GGATCTGGAGTGGCGCAG 60.203 66.667 10.83 0.00 0.00 5.18
3949 10516 3.118775 AGTGGCGCAGACTATGTTAATGA 60.119 43.478 10.83 0.00 34.59 2.57
4052 10619 5.032327 TCTCCATCATCCAATGACAAGAG 57.968 43.478 0.00 0.30 43.01 2.85
4081 10648 5.163457 GGGAAGAACAACTCCAATGACAAAA 60.163 40.000 0.00 0.00 0.00 2.44
4093 10660 4.507388 CCAATGACAAAACTTCAAATGCGT 59.493 37.500 0.00 0.00 0.00 5.24
4192 10759 0.319900 GCGACAGTGAAGGAGCTTCA 60.320 55.000 0.00 0.00 46.50 3.02
4255 10823 4.080638 CCTGGAAACTCAGATAGAAGGCTT 60.081 45.833 0.00 0.00 36.93 4.35
4386 10954 4.632153 TGAAGTTTCTGGTTACTCAGAGC 58.368 43.478 0.00 3.15 43.64 4.09
4418 10992 0.605319 TGGTTGTTGATGACCTCGCC 60.605 55.000 0.00 0.00 36.86 5.54
4536 11110 1.128200 CCTCCCGTGGGATGTTATCA 58.872 55.000 8.37 0.00 44.24 2.15
4582 11156 3.276857 GACATGAGCATGATGGAGTTGT 58.723 45.455 16.70 0.00 41.20 3.32
4597 11171 3.883489 GGAGTTGTTAACAGAAGCCAAGT 59.117 43.478 8.56 0.00 0.00 3.16
4621 11195 4.487948 CAAATGGATGCTTTTCGTGATGT 58.512 39.130 0.00 0.00 0.00 3.06
4723 11297 1.301087 CCCGTGTACGCCTTGACAA 60.301 57.895 0.00 0.00 38.18 3.18
4732 11306 3.120321 ACGCCTTGACAAATGTGTAGA 57.880 42.857 0.00 0.00 38.41 2.59
4851 11428 2.672181 GCATGCAAAATGGGCCCCT 61.672 57.895 22.27 6.51 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.887783 TCGTGTGTTTACCCCTACGTTA 59.112 45.455 0.00 0.00 33.68 3.18
73 75 9.606631 TGTATTACGCCATAATATGCATCATAA 57.393 29.630 0.19 0.00 37.91 1.90
78 80 8.397906 GTTCATGTATTACGCCATAATATGCAT 58.602 33.333 3.79 3.79 37.91 3.96
87 89 4.776349 TCCTTGTTCATGTATTACGCCAT 58.224 39.130 0.00 0.00 0.00 4.40
135 137 4.654091 TTCTGAAGCCTTTCCTTTTGTG 57.346 40.909 0.00 0.00 32.09 3.33
136 138 4.100035 CCTTTCTGAAGCCTTTCCTTTTGT 59.900 41.667 0.00 0.00 32.09 2.83
140 142 3.884037 TCCTTTCTGAAGCCTTTCCTT 57.116 42.857 0.00 0.00 32.09 3.36
168 170 7.447853 ACACAAATTCAAATACCCCGTTTACTA 59.552 33.333 0.00 0.00 0.00 1.82
317 320 3.570125 TCAATGCCGAACACATTAACCAA 59.430 39.130 0.00 0.00 36.00 3.67
346 349 4.379243 CCGCACCAAGCTCGGACT 62.379 66.667 0.00 0.00 45.53 3.85
444 447 1.669440 GTTCCACCTCGCCACACTA 59.331 57.895 0.00 0.00 0.00 2.74
524 528 5.180117 CGGGGCTTCATCATAACTTCATTAG 59.820 44.000 0.00 0.00 0.00 1.73
731 737 0.331278 TTTTCACCCCTCATGCCGAT 59.669 50.000 0.00 0.00 0.00 4.18
748 754 3.190535 CGACCCTGTGAATTCGGATTTTT 59.809 43.478 0.04 0.00 0.00 1.94
892 899 4.390603 TGTTCTAGTTATTCGCGTTGCATT 59.609 37.500 5.77 0.00 0.00 3.56
894 901 3.318886 TGTTCTAGTTATTCGCGTTGCA 58.681 40.909 5.77 0.00 0.00 4.08
898 905 4.390603 TGCAATTGTTCTAGTTATTCGCGT 59.609 37.500 5.77 0.00 0.00 6.01
998 1005 1.188219 GCCCAGTCTGGAGTCACTCA 61.188 60.000 21.23 0.00 40.96 3.41
1036 1043 2.405805 CCGCGTTGATGATTGGCCA 61.406 57.895 0.00 0.00 0.00 5.36
1098 1253 2.046023 TCAATGGAGCAGGGCACG 60.046 61.111 0.00 0.00 0.00 5.34
1100 1255 0.112995 AAAGTCAATGGAGCAGGGCA 59.887 50.000 0.00 0.00 0.00 5.36
1193 1355 3.517602 GATTCCATGTACACGCACACTA 58.482 45.455 0.00 0.00 0.00 2.74
1274 1436 9.239002 CGTATTCTAGATCGAAACAGAAAGAAT 57.761 33.333 9.22 9.50 34.96 2.40
1322 1488 3.670625 TGGTAAATTCTCTGTTGTCGGG 58.329 45.455 0.00 0.00 0.00 5.14
1415 3577 0.963856 CATTGAGAGCTTGCTGGGCA 60.964 55.000 0.00 0.00 36.47 5.36
1424 3586 2.574006 TGGTGCTTTCATTGAGAGCT 57.426 45.000 24.54 0.00 39.95 4.09
1561 3726 4.922206 ACAATCAAAAGCAGGATGTAGGA 58.078 39.130 0.00 0.00 39.31 2.94
1770 3938 1.884067 GCCTTATACTCATGGGCCAGC 60.884 57.143 13.78 1.21 37.12 4.85
1803 3971 1.408127 CCGATCAGTTACATTGGGCCA 60.408 52.381 0.00 0.00 0.00 5.36
1905 4073 1.152440 CCTAGGGGCGATCAGGTCT 60.152 63.158 0.00 0.00 0.00 3.85
1936 4104 1.898574 CTTCTTGTTGCAGGGCGGT 60.899 57.895 0.00 0.00 0.00 5.68
1969 4138 5.020795 ACCCTAGTTCTTCTTCTTCCTCTC 58.979 45.833 0.00 0.00 0.00 3.20
1970 4139 5.018374 ACCCTAGTTCTTCTTCTTCCTCT 57.982 43.478 0.00 0.00 0.00 3.69
2028 4199 5.490139 ACACACAATCGATCAATTCATCC 57.510 39.130 0.00 0.00 0.00 3.51
2177 4348 2.223618 GCAGCCAGTTTAAACCGAACAA 60.224 45.455 14.72 0.00 0.00 2.83
2332 8799 1.648720 GCTGTCTTGCGCAAGTGAA 59.351 52.632 40.37 27.82 39.38 3.18
2383 8851 1.000270 ATATGGCGCACCCCACAAA 60.000 52.632 10.83 0.00 37.79 2.83
2392 8860 1.341209 CAGGAGACTACATATGGCGCA 59.659 52.381 10.83 0.00 40.21 6.09
2406 8875 1.611474 AATGCAGCTCTCGCAGGAGA 61.611 55.000 3.44 0.00 46.90 3.71
2414 8883 0.307146 GCCATTCGAATGCAGCTCTC 59.693 55.000 28.90 9.89 35.08 3.20
2417 8886 0.107312 AGAGCCATTCGAATGCAGCT 60.107 50.000 30.01 30.01 36.87 4.24
2854 9327 1.338136 CCTGACGGCCACCCTAGATT 61.338 60.000 2.24 0.00 0.00 2.40
2863 9336 3.770040 CGGATGACCTGACGGCCA 61.770 66.667 2.24 0.00 0.00 5.36
2871 9345 2.122813 CTAGCCCCCGGATGACCT 60.123 66.667 0.73 0.00 0.00 3.85
2880 9355 4.271016 CAATCCCGCCTAGCCCCC 62.271 72.222 0.00 0.00 0.00 5.40
2881 9356 4.271016 CCAATCCCGCCTAGCCCC 62.271 72.222 0.00 0.00 0.00 5.80
2895 9372 1.229951 ATCCTCTCCACCCTGCCAA 60.230 57.895 0.00 0.00 0.00 4.52
2904 9381 4.290942 GAGAAACCCTAAGATCCTCTCCA 58.709 47.826 0.00 0.00 0.00 3.86
2982 9467 2.049156 CAGCAGCGTCCGAAGTCA 60.049 61.111 0.00 0.00 0.00 3.41
3080 9565 0.816018 TGCCGCTTCCTCGTCAAAAA 60.816 50.000 0.00 0.00 0.00 1.94
3131 9617 0.766131 TTTGGAGCCGTGAACCCTAA 59.234 50.000 0.00 0.00 0.00 2.69
3225 9711 6.434340 GGATGGTGTAAAGATTTTCTTCCAGT 59.566 38.462 0.00 0.00 35.27 4.00
3331 9817 6.119536 ACGGTTTTGCTAATCCATCATAAGA 58.880 36.000 8.42 0.00 0.00 2.10
3354 9840 4.477413 TCGAGGAGGGCTATCGAC 57.523 61.111 0.00 0.00 40.29 4.20
3359 9845 0.325296 AATGGTGTCGAGGAGGGCTA 60.325 55.000 0.00 0.00 0.00 3.93
3362 9848 0.176680 CTCAATGGTGTCGAGGAGGG 59.823 60.000 0.00 0.00 0.00 4.30
3365 9851 3.321968 CCATATCTCAATGGTGTCGAGGA 59.678 47.826 0.00 0.00 41.38 3.71
3538 10024 7.337436 TGTGATCATGTAATCTGCATTCTTCAA 59.663 33.333 0.00 0.00 0.00 2.69
3551 10037 5.440610 GTTTCCCCTCTGTGATCATGTAAT 58.559 41.667 0.00 0.00 0.00 1.89
3554 10040 2.355108 CGTTTCCCCTCTGTGATCATGT 60.355 50.000 0.00 0.00 0.00 3.21
3563 10049 0.830648 TATCTGGCGTTTCCCCTCTG 59.169 55.000 0.00 0.00 0.00 3.35
3660 10148 2.158827 TGATGGTGGATGGATTACGGTG 60.159 50.000 0.00 0.00 0.00 4.94
3665 10153 2.779430 AGTGCTGATGGTGGATGGATTA 59.221 45.455 0.00 0.00 0.00 1.75
3699 10187 1.144716 GACCCATGATGCTCGCAGA 59.855 57.895 0.00 0.00 0.00 4.26
3748 10237 0.679505 CGTCCTTCACTTCAGTCCCA 59.320 55.000 0.00 0.00 0.00 4.37
3752 10241 1.006102 CCGCGTCCTTCACTTCAGT 60.006 57.895 4.92 0.00 0.00 3.41
3754 10243 0.319555 CTTCCGCGTCCTTCACTTCA 60.320 55.000 4.92 0.00 0.00 3.02
3759 10248 3.702048 CCCCTTCCGCGTCCTTCA 61.702 66.667 4.92 0.00 0.00 3.02
3769 10258 4.759205 ACCATTGCGGCCCCTTCC 62.759 66.667 0.00 0.00 39.03 3.46
3804 10305 1.453155 CACCATCGTCCCCAAAAGAG 58.547 55.000 0.00 0.00 0.00 2.85
3825 10326 5.105063 TCAACAGAGTTCTTGCTATCATCG 58.895 41.667 0.00 0.00 0.00 3.84
3869 10436 5.763698 CCCCTTTTCCTATTTAATCCGACTC 59.236 44.000 0.00 0.00 0.00 3.36
3918 10485 3.746949 CTGCGCCACTCCAGATCCC 62.747 68.421 4.18 0.00 0.00 3.85
3933 10500 6.090088 CGCCTTCTATCATTAACATAGTCTGC 59.910 42.308 4.07 4.59 0.00 4.26
3934 10501 6.587990 CCGCCTTCTATCATTAACATAGTCTG 59.412 42.308 4.07 0.00 0.00 3.51
3936 10503 5.869888 CCCGCCTTCTATCATTAACATAGTC 59.130 44.000 4.07 0.00 0.00 2.59
3949 10516 3.875865 GGTTTGTCCCGCCTTCTAT 57.124 52.632 0.00 0.00 0.00 1.98
4028 10595 6.743490 GCTCTTGTCATTGGATGATGGAGATA 60.743 42.308 15.20 0.00 42.04 1.98
4052 10619 1.239347 GGAGTTGTTCTTCCCACTGC 58.761 55.000 0.00 0.00 0.00 4.40
4081 10648 1.851658 GCCAAACACGCATTTGAAGT 58.148 45.000 12.31 0.00 41.28 3.01
4172 10739 0.037790 GAAGCTCCTTCACTGTCGCT 60.038 55.000 0.00 0.00 39.95 4.93
4192 10759 2.810274 GCATATTGCCTCGTCATGTCAT 59.190 45.455 0.00 0.00 37.42 3.06
4255 10823 7.833786 AGTACTGGATAAATTCTCAACACGTA 58.166 34.615 0.00 0.00 0.00 3.57
4418 10992 7.599245 ACAAAAGTAACTCTAGATTGAACTCCG 59.401 37.037 6.92 0.11 0.00 4.63
4497 11071 3.016736 GGGTACTTGTGCATGCAATACT 58.983 45.455 24.58 8.18 0.00 2.12
4506 11080 1.839747 ACGGGAGGGTACTTGTGCA 60.840 57.895 0.00 0.00 0.00 4.57
4536 11110 9.739276 TCCATGTAACACTTCATTAAAATCTCT 57.261 29.630 0.00 0.00 0.00 3.10
4582 11156 4.501229 CCATTTGCACTTGGCTTCTGTTAA 60.501 41.667 1.32 0.00 45.15 2.01
4597 11171 2.295629 TCACGAAAAGCATCCATTTGCA 59.704 40.909 0.00 0.00 45.23 4.08
4621 11195 2.356665 TAGGCTGCAAGTGTCCAAAA 57.643 45.000 0.50 0.00 35.30 2.44
4656 11230 1.166531 AACGTCCAGCTGTTTCCTGC 61.167 55.000 13.81 0.00 35.90 4.85
4723 11297 5.367937 ACCCAATCTGAGCTATCTACACATT 59.632 40.000 0.00 0.00 0.00 2.71
4732 11306 2.368221 GAGAGCACCCAATCTGAGCTAT 59.632 50.000 0.00 0.00 35.36 2.97
4851 11428 7.067372 CCACATGAGTTCATATTTAAAGCTCCA 59.933 37.037 0.00 0.00 34.26 3.86


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

AutoCloner maintained by Alex Coulton.