Multiple sequence alignment - TraesCS3A01G039400

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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 TraesCS3A01G039400 chr3A 100.000 5460 0 0 1 5460 20930615 20936074 0.000000e+00 10083.0
1 TraesCS3A01G039400 chr3A 83.219 1460 189 41 3196 4610 20896881 20898329 0.000000e+00 1288.0
2 TraesCS3A01G039400 chr3A 82.114 1476 205 37 3179 4613 20835713 20837170 0.000000e+00 1208.0
3 TraesCS3A01G039400 chr3A 82.234 940 129 18 1008 1922 20834474 20835400 0.000000e+00 776.0
4 TraesCS3A01G039400 chr3A 81.420 845 138 13 1029 1862 20895650 20896486 0.000000e+00 673.0
5 TraesCS3A01G039400 chr3B 94.723 1838 80 7 2823 4655 22473695 22471870 0.000000e+00 2841.0
6 TraesCS3A01G039400 chr3B 93.857 1107 63 4 830 1932 22474793 22473688 0.000000e+00 1663.0
7 TraesCS3A01G039400 chr3B 93.253 993 53 8 827 1818 22523369 22524348 0.000000e+00 1450.0
8 TraesCS3A01G039400 chr3B 82.645 1452 208 33 3196 4610 22511862 22513306 0.000000e+00 1245.0
9 TraesCS3A01G039400 chr3B 89.325 815 71 13 4649 5460 22462554 22461753 0.000000e+00 1009.0
10 TraesCS3A01G039400 chr3B 81.048 1240 184 45 3536 4752 22344971 22343760 0.000000e+00 941.0
11 TraesCS3A01G039400 chr3B 83.924 846 116 17 1029 1867 22349009 22348177 0.000000e+00 791.0
12 TraesCS3A01G039400 chr3B 92.572 552 28 9 283 830 22475422 22474880 0.000000e+00 780.0
13 TraesCS3A01G039400 chr3B 93.435 457 21 5 297 753 22522906 22523353 0.000000e+00 669.0
14 TraesCS3A01G039400 chr3B 91.197 284 11 3 1 270 22522551 22522834 1.860000e-99 374.0
15 TraesCS3A01G039400 chr3B 94.444 162 9 0 69 230 22475792 22475631 3.270000e-62 250.0
16 TraesCS3A01G039400 chr3D 95.090 1772 68 14 2826 4589 15349250 15347490 0.000000e+00 2772.0
17 TraesCS3A01G039400 chr3D 91.074 1714 100 17 259 1934 15361663 15359965 0.000000e+00 2268.0
18 TraesCS3A01G039400 chr3D 82.967 1456 201 35 3196 4613 15372571 15371125 0.000000e+00 1271.0
19 TraesCS3A01G039400 chr3D 95.479 752 29 4 2077 2824 583586258 583585508 0.000000e+00 1195.0
20 TraesCS3A01G039400 chr3D 82.064 1444 202 41 3202 4613 15395936 15394518 0.000000e+00 1179.0
21 TraesCS3A01G039400 chr3D 90.659 835 50 8 4624 5456 15347491 15346683 0.000000e+00 1085.0
22 TraesCS3A01G039400 chr3D 80.936 876 141 14 1006 1862 15373851 15372983 0.000000e+00 669.0
23 TraesCS3A01G039400 chr3D 93.229 192 10 1 27 218 15362060 15361872 4.160000e-71 279.0
24 TraesCS3A01G039400 chr3D 92.568 148 10 1 1927 2074 129846075 129846221 1.540000e-50 211.0
25 TraesCS3A01G039400 chr2A 95.745 752 30 1 2074 2823 3396286 3395535 0.000000e+00 1210.0
26 TraesCS3A01G039400 chr2A 92.908 141 10 0 1934 2074 3396511 3396371 7.170000e-49 206.0
27 TraesCS3A01G039400 chr2A 90.132 152 14 1 1924 2074 105598630 105598479 4.310000e-46 196.0
28 TraesCS3A01G039400 chr7A 95.503 756 29 3 2074 2824 14668116 14667361 0.000000e+00 1203.0
29 TraesCS3A01G039400 chr7A 94.357 762 41 1 2074 2833 703405279 703404518 0.000000e+00 1168.0
30 TraesCS3A01G039400 chr7A 86.813 273 34 1 3174 3446 63778404 63778674 2.470000e-78 303.0
31 TraesCS3A01G039400 chr7A 91.892 148 12 0 1927 2074 92364733 92364880 1.990000e-49 207.0
32 TraesCS3A01G039400 chr7A 91.667 144 12 0 1931 2074 505022509 505022366 3.340000e-47 200.0
33 TraesCS3A01G039400 chr7A 85.039 127 17 2 2887 3012 13972320 13972195 1.600000e-25 128.0
34 TraesCS3A01G039400 chr7A 77.049 183 40 2 1531 1712 20513111 20512930 2.690000e-18 104.0
35 TraesCS3A01G039400 chr7A 84.314 102 16 0 1528 1629 63782524 63782625 3.480000e-17 100.0
36 TraesCS3A01G039400 chr1A 95.138 761 33 3 2074 2831 482776006 482776765 0.000000e+00 1197.0
37 TraesCS3A01G039400 chr1A 95.000 760 33 4 2074 2830 6636891 6637648 0.000000e+00 1188.0
38 TraesCS3A01G039400 chr1A 88.889 144 16 0 1931 2074 561767308 561767451 1.560000e-40 178.0
39 TraesCS3A01G039400 chr5D 94.960 754 35 2 2074 2824 128585931 128586684 0.000000e+00 1179.0
40 TraesCS3A01G039400 chr5D 82.531 1059 162 18 3596 4643 558346793 558345747 0.000000e+00 909.0
41 TraesCS3A01G039400 chr5D 78.880 786 133 14 1006 1761 558348799 558348017 8.160000e-138 501.0
42 TraesCS3A01G039400 chr5D 87.943 282 32 1 3175 3456 558347246 558346967 1.130000e-86 331.0
43 TraesCS3A01G039400 chr5D 92.199 141 10 1 1935 2074 3785392 3785252 1.200000e-46 198.0
44 TraesCS3A01G039400 chr5D 90.604 149 14 0 1926 2074 390979208 390979356 1.200000e-46 198.0
45 TraesCS3A01G039400 chr5D 89.130 138 15 0 1935 2072 382082675 382082538 7.270000e-39 172.0
46 TraesCS3A01G039400 chr5D 87.143 140 18 0 1935 2074 564120796 564120935 5.660000e-35 159.0
47 TraesCS3A01G039400 chr4A 94.814 752 37 1 2074 2823 617674016 617674767 0.000000e+00 1171.0
48 TraesCS3A01G039400 chr4A 79.385 781 132 11 1009 1761 611271614 611270835 1.740000e-144 523.0
49 TraesCS3A01G039400 chr4A 91.781 146 12 0 1930 2075 71082667 71082522 2.580000e-48 204.0
50 TraesCS3A01G039400 chr4A 92.199 141 11 0 1934 2074 93969786 93969646 3.340000e-47 200.0
51 TraesCS3A01G039400 chr2B 94.357 762 40 2 2074 2833 256325128 256325888 0.000000e+00 1166.0
52 TraesCS3A01G039400 chr5B 79.371 795 122 21 1006 1761 704301329 704302120 6.270000e-144 521.0
53 TraesCS3A01G039400 chr7D 93.750 144 9 0 1931 2074 567651582 567651725 3.310000e-52 217.0
54 TraesCS3A01G039400 chr7D 91.608 143 11 1 1932 2074 65774497 65774356 4.310000e-46 196.0
55 TraesCS3A01G039400 chr7D 87.302 126 16 0 2887 3012 59414917 59415042 1.590000e-30 145.0
56 TraesCS3A01G039400 chr7D 86.022 93 13 0 1538 1630 59467524 59467616 3.480000e-17 100.0
57 TraesCS3A01G039400 chr6A 91.781 146 12 0 1928 2073 58035958 58035813 2.580000e-48 204.0
58 TraesCS3A01G039400 chr6A 90.278 144 14 0 1932 2075 6392972 6393115 7.220000e-44 189.0
59 TraesCS3A01G039400 chr6A 77.926 299 60 4 1399 1697 528351587 528351879 1.210000e-41 182.0
60 TraesCS3A01G039400 chr2D 92.857 140 10 0 1935 2074 399440381 399440242 2.580000e-48 204.0
61 TraesCS3A01G039400 chr1D 92.857 140 10 0 1935 2074 108827249 108827388 2.580000e-48 204.0
62 TraesCS3A01G039400 chr1D 82.069 145 21 4 1932 2074 62223509 62223650 9.610000e-23 119.0
63 TraesCS3A01G039400 chr1D 82.069 145 21 4 1932 2074 62233394 62233535 9.610000e-23 119.0
64 TraesCS3A01G039400 chr6D 91.781 146 11 1 1927 2072 38240673 38240529 9.270000e-48 202.0
65 TraesCS3A01G039400 chr6D 90.411 146 14 0 1929 2074 7446935 7447080 5.580000e-45 193.0
66 TraesCS3A01G039400 chr6D 85.106 141 20 1 1930 2069 160965721 160965861 5.700000e-30 143.0
67 TraesCS3A01G039400 chr6D 81.119 143 24 2 1933 2074 205839994 205840134 1.610000e-20 111.0
68 TraesCS3A01G039400 chr6D 82.400 125 20 2 1935 2058 418627967 418628090 2.080000e-19 108.0
69 TraesCS3A01G039400 chr6D 79.861 144 25 3 1933 2074 30533675 30533816 9.680000e-18 102.0
70 TraesCS3A01G039400 chr6D 84.848 99 15 0 1934 2032 22135894 22135796 3.480000e-17 100.0
71 TraesCS3A01G039400 chr4B 92.254 142 11 0 1933 2074 515563238 515563097 9.270000e-48 202.0
72 TraesCS3A01G039400 chr4D 90.541 148 14 0 1927 2074 19346458 19346605 4.310000e-46 196.0
73 TraesCS3A01G039400 chr4D 91.549 142 9 3 1935 2074 396744612 396744472 5.580000e-45 193.0
74 TraesCS3A01G039400 chr4D 85.034 147 20 2 1929 2075 18970053 18970197 1.230000e-31 148.0
75 TraesCS3A01G039400 chrUn 83.200 125 21 0 1934 2058 48201135 48201011 1.240000e-21 115.0
76 TraesCS3A01G039400 chrUn 83.200 125 21 0 1934 2058 384027368 384027492 1.240000e-21 115.0
77 TraesCS3A01G039400 chrUn 78.030 132 27 2 1928 2058 97100341 97100211 1.260000e-11 82.4
78 TraesCS3A01G039400 chrUn 86.441 59 7 1 1935 1993 104277290 104277233 4.570000e-06 63.9


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 TraesCS3A01G039400 chr3A 20930615 20936074 5459 False 10083.000000 10083 100.000000 1 5460 1 chr3A.!!$F1 5459
1 TraesCS3A01G039400 chr3A 20834474 20837170 2696 False 992.000000 1208 82.174000 1008 4613 2 chr3A.!!$F2 3605
2 TraesCS3A01G039400 chr3A 20895650 20898329 2679 False 980.500000 1288 82.319500 1029 4610 2 chr3A.!!$F3 3581
3 TraesCS3A01G039400 chr3B 22471870 22475792 3922 True 1383.500000 2841 93.899000 69 4655 4 chr3B.!!$R3 4586
4 TraesCS3A01G039400 chr3B 22511862 22513306 1444 False 1245.000000 1245 82.645000 3196 4610 1 chr3B.!!$F1 1414
5 TraesCS3A01G039400 chr3B 22461753 22462554 801 True 1009.000000 1009 89.325000 4649 5460 1 chr3B.!!$R1 811
6 TraesCS3A01G039400 chr3B 22343760 22349009 5249 True 866.000000 941 82.486000 1029 4752 2 chr3B.!!$R2 3723
7 TraesCS3A01G039400 chr3B 22522551 22524348 1797 False 831.000000 1450 92.628333 1 1818 3 chr3B.!!$F2 1817
8 TraesCS3A01G039400 chr3D 15346683 15349250 2567 True 1928.500000 2772 92.874500 2826 5456 2 chr3D.!!$R3 2630
9 TraesCS3A01G039400 chr3D 15359965 15362060 2095 True 1273.500000 2268 92.151500 27 1934 2 chr3D.!!$R4 1907
10 TraesCS3A01G039400 chr3D 583585508 583586258 750 True 1195.000000 1195 95.479000 2077 2824 1 chr3D.!!$R2 747
11 TraesCS3A01G039400 chr3D 15394518 15395936 1418 True 1179.000000 1179 82.064000 3202 4613 1 chr3D.!!$R1 1411
12 TraesCS3A01G039400 chr3D 15371125 15373851 2726 True 970.000000 1271 81.951500 1006 4613 2 chr3D.!!$R5 3607
13 TraesCS3A01G039400 chr2A 3395535 3396511 976 True 708.000000 1210 94.326500 1934 2823 2 chr2A.!!$R2 889
14 TraesCS3A01G039400 chr7A 14667361 14668116 755 True 1203.000000 1203 95.503000 2074 2824 1 chr7A.!!$R2 750
15 TraesCS3A01G039400 chr7A 703404518 703405279 761 True 1168.000000 1168 94.357000 2074 2833 1 chr7A.!!$R5 759
16 TraesCS3A01G039400 chr7A 63778404 63782625 4221 False 201.500000 303 85.563500 1528 3446 2 chr7A.!!$F2 1918
17 TraesCS3A01G039400 chr1A 482776006 482776765 759 False 1197.000000 1197 95.138000 2074 2831 1 chr1A.!!$F2 757
18 TraesCS3A01G039400 chr1A 6636891 6637648 757 False 1188.000000 1188 95.000000 2074 2830 1 chr1A.!!$F1 756
19 TraesCS3A01G039400 chr5D 128585931 128586684 753 False 1179.000000 1179 94.960000 2074 2824 1 chr5D.!!$F1 750
20 TraesCS3A01G039400 chr5D 558345747 558348799 3052 True 580.333333 909 83.118000 1006 4643 3 chr5D.!!$R3 3637
21 TraesCS3A01G039400 chr4A 617674016 617674767 751 False 1171.000000 1171 94.814000 2074 2823 1 chr4A.!!$F1 749
22 TraesCS3A01G039400 chr4A 611270835 611271614 779 True 523.000000 523 79.385000 1009 1761 1 chr4A.!!$R3 752
23 TraesCS3A01G039400 chr2B 256325128 256325888 760 False 1166.000000 1166 94.357000 2074 2833 1 chr2B.!!$F1 759
24 TraesCS3A01G039400 chr5B 704301329 704302120 791 False 521.000000 521 79.371000 1006 1761 1 chr5B.!!$F1 755

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
998 1479 0.668535 TGCACTCGTGATAGATCGGG 59.331 55.000 0.39 0.0 0.00 5.14 F
1134 1630 0.319211 TACACTTCGCCACCAAGACG 60.319 55.000 0.00 0.0 0.00 4.18 F
1956 2607 0.658897 AAAACACTAACGCCCACACG 59.341 50.000 0.00 0.0 39.50 4.49 F
1978 2629 0.322322 TGGCCGTTATCCAACTCGTT 59.678 50.000 0.00 0.0 32.09 3.85 F
2300 3039 1.227292 TTGCGAGTACGTGGCAACA 60.227 52.632 14.45 0.0 41.34 3.33 F
2768 3511 1.561076 TGCCTCTTGCTCATACCACAT 59.439 47.619 0.00 0.0 42.00 3.21 F
3278 6580 1.806542 CACATTCAGGACAGGGTTTCG 59.193 52.381 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2619 0.390124 AGGCGTGTAAACGAGTTGGA 59.610 50.000 10.31 0.0 34.64 3.53 R
1977 2628 0.457166 CGACGATCCAGGCGTGTAAA 60.457 55.000 5.57 0.0 42.77 2.01 R
2768 3511 1.962321 ATATGCGCCCACACACCGTA 61.962 55.000 4.18 0.0 0.00 4.02 R
3161 6445 2.045926 CTTCCCCACCTTCGCTGG 60.046 66.667 0.00 0.0 0.00 4.85 R
4139 7588 0.532115 GCCTGTTTCGCAATCCCATT 59.468 50.000 0.00 0.0 0.00 3.16 R
4141 7590 0.611618 ATGCCTGTTTCGCAATCCCA 60.612 50.000 0.00 0.0 40.22 4.37 R
4998 9670 0.036765 GCCACACGACCATGTTCCTA 60.037 55.000 0.00 0.0 0.00 2.94 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
143 154 2.750237 GCCGCCCACTAACCTTGG 60.750 66.667 0.00 0.00 0.00 3.61
208 219 4.986054 ACACAAGGAAATGTACCCTACA 57.014 40.909 0.00 0.00 43.80 2.74
215 226 4.534500 AGGAAATGTACCCTACACATGACA 59.466 41.667 0.00 0.00 42.23 3.58
218 229 3.953712 TGTACCCTACACATGACACAG 57.046 47.619 0.00 0.00 32.89 3.66
287 656 8.194104 TGAAAGCTAGAAATTTAGCAAACACAA 58.806 29.630 13.94 0.00 46.69 3.33
344 721 4.453819 CCGGCATGATAAGAAAGAGAATCC 59.546 45.833 0.00 0.00 33.66 3.01
351 728 7.847711 TGATAAGAAAGAGAATCCCTCCTAG 57.152 40.000 0.00 0.00 42.97 3.02
355 732 9.731001 ATAAGAAAGAGAATCCCTCCTAGTTTA 57.269 33.333 0.00 0.00 42.97 2.01
356 733 8.450780 AAGAAAGAGAATCCCTCCTAGTTTAA 57.549 34.615 0.00 0.00 42.97 1.52
699 1088 6.035368 ACAAATTATGCTGCCATTGTAACA 57.965 33.333 0.00 0.00 32.85 2.41
725 1114 9.334947 ACATTGACAATTATCTAGTGATTCAGG 57.665 33.333 0.00 0.00 34.32 3.86
776 1166 1.615883 AGTCTGAGTGTGCGTTGATCT 59.384 47.619 0.00 0.00 0.00 2.75
798 1188 4.497473 TTCCAAAGTAATGTGCCTTTCG 57.503 40.909 0.00 0.00 0.00 3.46
828 1305 1.512156 ATGGGTGCGTTGGTCGTTTC 61.512 55.000 0.00 0.00 42.13 2.78
949 1426 1.198713 TCTCATCTGGCAGAAGGGAC 58.801 55.000 22.84 0.00 0.00 4.46
998 1479 0.668535 TGCACTCGTGATAGATCGGG 59.331 55.000 0.39 0.00 0.00 5.14
1101 1597 0.605589 CCACTCTCTCCAAGAACGCT 59.394 55.000 0.00 0.00 32.23 5.07
1107 1603 1.004560 CTCCAAGAACGCTGCCTCA 60.005 57.895 0.00 0.00 0.00 3.86
1134 1630 0.319211 TACACTTCGCCACCAAGACG 60.319 55.000 0.00 0.00 0.00 4.18
1353 1858 2.891941 ATACCACGGGAGCGTACGGA 62.892 60.000 18.39 0.00 0.00 4.69
1511 2028 3.576356 CGGCGTCATGGACATGGC 61.576 66.667 11.98 9.48 39.89 4.40
1512 2029 2.124570 GGCGTCATGGACATGGCT 60.125 61.111 14.19 0.00 41.05 4.75
1633 2150 0.692476 CAACTCCACCATGTCCCTGA 59.308 55.000 0.00 0.00 0.00 3.86
1765 2409 1.926511 GACCAAACGCAGGAGCATGG 61.927 60.000 0.00 0.00 41.68 3.66
1867 2518 3.532542 AGGCGAAGAAAAGGTATGCTAC 58.467 45.455 0.00 0.00 0.00 3.58
1881 2532 6.270156 GGTATGCTACCTAATGACCTAGTC 57.730 45.833 5.42 0.00 45.52 2.59
1905 2556 2.606272 ACGTTGTTCCTTCACGTTCTTC 59.394 45.455 0.00 0.00 32.90 2.87
1953 2604 0.939419 ACGAAAACACTAACGCCCAC 59.061 50.000 0.00 0.00 0.00 4.61
1956 2607 0.658897 AAAACACTAACGCCCACACG 59.341 50.000 0.00 0.00 39.50 4.49
1968 2619 3.960237 CACACGTGTGGCCGTTAT 58.040 55.556 35.65 1.93 42.10 1.89
1977 2628 0.390735 GTGGCCGTTATCCAACTCGT 60.391 55.000 0.00 0.00 35.01 4.18
1978 2629 0.322322 TGGCCGTTATCCAACTCGTT 59.678 50.000 0.00 0.00 32.09 3.85
1979 2630 1.270947 TGGCCGTTATCCAACTCGTTT 60.271 47.619 0.00 0.00 32.09 3.60
2013 2664 3.792956 TCGTCGTTCACTGTCTTTTACAC 59.207 43.478 0.00 0.00 33.45 2.90
2025 2676 6.706270 ACTGTCTTTTACACGAATCTTGACAT 59.294 34.615 0.00 0.00 33.45 3.06
2045 2696 5.144100 ACATGAAAAGGTGGATTTGGTGTA 58.856 37.500 0.00 0.00 0.00 2.90
2057 2708 3.435846 TGGTGTACCACGTAGGACA 57.564 52.632 10.46 2.78 42.01 4.02
2139 2875 3.514309 GACACTACTACCTTGTGGATGGT 59.486 47.826 0.00 0.00 40.12 3.55
2144 2880 6.379133 CACTACTACCTTGTGGATGGTAACTA 59.621 42.308 0.00 0.00 38.22 2.24
2182 2918 2.479837 CAACTCGGTACACACACATGT 58.520 47.619 0.00 0.00 40.80 3.21
2300 3039 1.227292 TTGCGAGTACGTGGCAACA 60.227 52.632 14.45 0.00 41.34 3.33
2388 3127 4.662278 ACTAGGTAAACACACATGGCAAT 58.338 39.130 0.00 0.00 0.00 3.56
2454 3193 5.334569 GCAACTACGGTTTGATTACACATGT 60.335 40.000 0.00 0.00 32.73 3.21
2586 3326 2.277084 GCAACTAAATCGTCATCCCGT 58.723 47.619 0.00 0.00 0.00 5.28
2768 3511 1.561076 TGCCTCTTGCTCATACCACAT 59.439 47.619 0.00 0.00 42.00 3.21
2786 3529 1.962321 ATACGGTGTGTGGGCGCATA 61.962 55.000 10.83 0.00 37.46 3.14
2884 3694 5.459505 TCTAGTGAATTTAGGGAGAGAGGG 58.540 45.833 0.00 0.00 0.00 4.30
2937 3747 6.817765 TCTCTTTGTTTCACTTTGAACAGT 57.182 33.333 0.00 0.00 35.89 3.55
2955 3765 3.157087 CAGTTATTGGAGGCCACAAGTT 58.843 45.455 16.51 5.54 30.78 2.66
3014 3830 3.770046 TGGTGCTGTCTACAAGGTACTA 58.230 45.455 0.00 0.00 38.49 1.82
3015 3831 3.508793 TGGTGCTGTCTACAAGGTACTAC 59.491 47.826 0.00 0.00 38.49 2.73
3114 4645 9.733556 AAACATGTATGTCTACATTGAACCTAA 57.266 29.630 0.00 0.00 44.42 2.69
3161 6445 8.446599 TTTAAACGGGAGAGGATGATTAATTC 57.553 34.615 0.00 0.00 0.00 2.17
3190 6492 2.574824 GGTGGGGAAGAGCCTAACTTTA 59.425 50.000 0.00 0.00 36.66 1.85
3278 6580 1.806542 CACATTCAGGACAGGGTTTCG 59.193 52.381 0.00 0.00 0.00 3.46
3472 6781 3.569250 AATTATTGTCCGTGGTTGTGC 57.431 42.857 0.00 0.00 0.00 4.57
3626 7008 7.389053 AGAGCTTTACTAGATTGGACAAAACTG 59.611 37.037 0.00 0.00 0.00 3.16
3783 7165 3.066621 CGGGCTAGCAAAAATATTCAGCA 59.933 43.478 18.24 0.00 0.00 4.41
3784 7166 4.439974 CGGGCTAGCAAAAATATTCAGCAA 60.440 41.667 18.24 0.00 0.00 3.91
3836 7218 4.775780 AGAGTGGTTGGCACATAGTAAGTA 59.224 41.667 0.00 0.00 39.30 2.24
4090 7489 5.008911 TGGATATGTAAGCGTATACACACGT 59.991 40.000 3.32 0.00 43.79 4.49
4175 7625 0.391528 GGCATGGCAATTGTGGGAAC 60.392 55.000 15.47 0.00 0.00 3.62
4180 7630 1.543944 GGCAATTGTGGGAACAGGGG 61.544 60.000 7.40 0.00 44.46 4.79
4221 7671 3.213206 TGCATCATTGGTCCCTGATAC 57.787 47.619 4.22 0.77 31.05 2.24
4413 7863 1.079127 CGTCCAATGCTCCCGAGTT 60.079 57.895 0.00 0.00 0.00 3.01
4672 9100 5.119694 TCCCTTTTTGGTGTTGCAAAATAC 58.880 37.500 0.00 0.54 31.46 1.89
4885 9557 0.462581 GTCATGGCATGCGGAGAAGA 60.463 55.000 22.56 0.00 0.00 2.87
4924 9596 1.133407 GAGTAGAGGAGGTTGTCGCTG 59.867 57.143 0.00 0.00 0.00 5.18
4952 9624 1.226688 CTCACGACACCGATCGCAT 60.227 57.895 10.32 0.00 46.22 4.73
4972 9644 1.444933 TGGAAGAAGGGGAAGAAGCA 58.555 50.000 0.00 0.00 0.00 3.91
4991 9663 3.075005 GCTCACCACGGGCTCCTA 61.075 66.667 0.00 0.00 0.00 2.94
4998 9670 1.686110 CACGGGCTCCTAGGGAAGT 60.686 63.158 9.46 0.00 0.00 3.01
5051 9723 3.306088 CGAAGGTTAGGAGTCTTTGCTCA 60.306 47.826 0.00 0.00 37.24 4.26
5093 9766 1.375908 GCAAGTGCTCGATGGGTGA 60.376 57.895 0.00 0.00 38.21 4.02
5098 9771 1.134580 AGTGCTCGATGGGTGAATCTG 60.135 52.381 0.00 0.00 0.00 2.90
5226 9899 7.112779 TCAGAAAAATCTTAAGGGACCAGATC 58.887 38.462 1.85 0.00 0.00 2.75
5231 9904 7.996758 AAATCTTAAGGGACCAGATCTAGAA 57.003 36.000 1.85 0.00 0.00 2.10
5305 9979 3.127548 CGCCTTGTCAAGCAATAGTCAAT 59.872 43.478 7.09 0.00 36.36 2.57
5325 9999 0.037303 AGACTGGTTGGCATCCACTG 59.963 55.000 13.23 7.63 30.78 3.66
5351 10025 4.395959 AACTAGTCAACAAACTGGTCGA 57.604 40.909 0.00 0.00 39.73 4.20
5392 10293 5.280945 TGCTTTGCATTCTTACAAGTCAAC 58.719 37.500 0.00 0.00 31.71 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
190 201 5.354234 GTCATGTGTAGGGTACATTTCCTTG 59.646 44.000 0.00 0.00 41.34 3.61
208 219 5.124457 GTGCTTTATGATTCCTGTGTCATGT 59.876 40.000 0.00 0.00 36.53 3.21
295 672 4.081087 AGCGAGGATAGAAGCTTGGTTTTA 60.081 41.667 2.10 0.00 36.41 1.52
435 813 6.093357 GCAAAACTGATGAGGAAAAACCAAAA 59.907 34.615 0.00 0.00 42.04 2.44
570 952 7.605410 TTTTGGATCGTAAGGAGTACATTTC 57.395 36.000 0.00 0.00 38.47 2.17
630 1019 3.244526 TGTCATGGCTTCAGTTCAGCTTA 60.245 43.478 0.00 0.00 37.43 3.09
631 1020 2.157738 GTCATGGCTTCAGTTCAGCTT 58.842 47.619 0.00 0.00 37.43 3.74
632 1021 1.072806 TGTCATGGCTTCAGTTCAGCT 59.927 47.619 0.00 0.00 37.43 4.24
633 1022 1.467734 CTGTCATGGCTTCAGTTCAGC 59.532 52.381 0.00 0.00 36.45 4.26
657 1046 6.363167 TTTGTACTCCCTCCGATCTAAAAA 57.637 37.500 0.00 0.00 0.00 1.94
699 1088 9.334947 CCTGAATCACTAGATAATTGTCAATGT 57.665 33.333 4.92 0.00 33.08 2.71
776 1166 4.865776 CGAAAGGCACATTACTTTGGAAA 58.134 39.130 0.00 0.00 37.07 3.13
798 1188 3.055719 CACCCATCACCGTGCACC 61.056 66.667 12.15 0.00 0.00 5.01
828 1305 2.797087 GCTGATTTCGCATGGGTCAATG 60.797 50.000 9.86 0.00 0.00 2.82
859 1336 5.578727 CACTTGGAAAAATGAACACGGAAAA 59.421 36.000 0.00 0.00 0.00 2.29
949 1426 5.180117 AGCTAGCTACAACATGTTTCTTGTG 59.820 40.000 17.69 0.00 32.77 3.33
998 1479 1.524863 GAGCAGGATGATGGCCATGC 61.525 60.000 26.56 21.13 43.09 4.06
1101 1597 0.902984 AGTGTACCGGTGATGAGGCA 60.903 55.000 19.93 1.68 0.00 4.75
1107 1603 1.217244 GGCGAAGTGTACCGGTGAT 59.783 57.895 19.93 0.00 0.00 3.06
1353 1858 2.281484 AATGGCGGCGTGTTGTCT 60.281 55.556 9.37 0.00 0.00 3.41
1443 1960 2.599281 TTCTCCGCGGTCTCCACA 60.599 61.111 27.15 1.93 0.00 4.17
1511 2028 1.134580 TCGGGTAGGTCGTCACTCTAG 60.135 57.143 0.00 0.00 0.00 2.43
1512 2029 0.904649 TCGGGTAGGTCGTCACTCTA 59.095 55.000 0.00 0.00 0.00 2.43
1633 2150 1.380785 CCATCTGCCCACCAATGCT 60.381 57.895 0.00 0.00 0.00 3.79
1765 2409 2.103537 ACTACCGCAATTACCCACAC 57.896 50.000 0.00 0.00 0.00 3.82
1867 2518 4.103357 CAACGTTCGACTAGGTCATTAGG 58.897 47.826 0.00 0.00 32.09 2.69
1881 2532 0.925466 ACGTGAAGGAACAACGTTCG 59.075 50.000 0.00 0.00 43.60 3.95
1956 2607 1.084289 GAGTTGGATAACGGCCACAC 58.916 55.000 2.24 0.00 41.71 3.82
1968 2619 0.390124 AGGCGTGTAAACGAGTTGGA 59.610 50.000 10.31 0.00 34.64 3.53
1977 2628 0.457166 CGACGATCCAGGCGTGTAAA 60.457 55.000 5.57 0.00 42.77 2.01
1978 2629 1.138036 CGACGATCCAGGCGTGTAA 59.862 57.895 5.57 0.00 42.77 2.41
1979 2630 2.795973 CGACGATCCAGGCGTGTA 59.204 61.111 5.57 0.00 42.77 2.90
2013 2664 4.455533 TCCACCTTTTCATGTCAAGATTCG 59.544 41.667 7.86 0.00 0.00 3.34
2025 2676 3.892588 GGTACACCAAATCCACCTTTTCA 59.107 43.478 0.00 0.00 35.64 2.69
2045 2696 2.119832 AGCCCTGTCCTACGTGGT 59.880 61.111 0.00 0.00 37.07 4.16
2182 2918 4.211164 CGTGTAGCAAAGAATCACAGTTGA 59.789 41.667 0.00 0.00 35.73 3.18
2300 3039 4.584325 ACAGTTGCCATGTGTGTTTATCTT 59.416 37.500 0.00 0.00 0.00 2.40
2454 3193 9.952030 TTGTCATGTCTAATTTATGGTAGTTGA 57.048 29.630 0.00 0.00 0.00 3.18
2586 3326 1.477553 CAGCTACGTTAGGTACCCCA 58.522 55.000 8.74 0.00 34.67 4.96
2768 3511 1.962321 ATATGCGCCCACACACCGTA 61.962 55.000 4.18 0.00 0.00 4.02
2786 3529 2.469826 CACACGTGTGGCATATACGAT 58.530 47.619 35.65 0.33 45.42 3.73
2937 3747 6.926630 AAAATAACTTGTGGCCTCCAATAA 57.073 33.333 3.32 0.00 34.18 1.40
3013 3829 5.968676 AACCTCATAGGCCTACAAATGTA 57.031 39.130 16.61 0.00 39.63 2.29
3014 3830 4.862641 AACCTCATAGGCCTACAAATGT 57.137 40.909 16.61 6.30 39.63 2.71
3015 3831 6.119536 TGTAAACCTCATAGGCCTACAAATG 58.880 40.000 16.61 11.01 39.63 2.32
3161 6445 2.045926 CTTCCCCACCTTCGCTGG 60.046 66.667 0.00 0.00 0.00 4.85
3278 6580 5.631096 GCTGGACTTCATTTTTAAACTCAGC 59.369 40.000 0.00 0.00 36.46 4.26
3626 7008 9.162764 TGTGCTACTCCTTCAATTATTTCTAAC 57.837 33.333 0.00 0.00 0.00 2.34
3783 7165 2.948979 TGTCGCCTTCAGTGTCATTTTT 59.051 40.909 0.00 0.00 0.00 1.94
3784 7166 2.290641 GTGTCGCCTTCAGTGTCATTTT 59.709 45.455 0.00 0.00 0.00 1.82
4139 7588 0.532115 GCCTGTTTCGCAATCCCATT 59.468 50.000 0.00 0.00 0.00 3.16
4141 7590 0.611618 ATGCCTGTTTCGCAATCCCA 60.612 50.000 0.00 0.00 40.22 4.37
4150 7600 2.070783 CACAATTGCCATGCCTGTTTC 58.929 47.619 5.05 0.00 0.00 2.78
4175 7625 2.158696 GGAGATCAATCCACTTCCCCTG 60.159 54.545 0.00 0.00 39.34 4.45
4221 7671 4.520492 ACCTCATTAACTTTGCCAAGTGAG 59.480 41.667 3.60 6.45 42.89 3.51
4672 9100 7.609760 TGTGCACATCATTAAAGTAAGGTAG 57.390 36.000 17.42 0.00 0.00 3.18
4788 9460 2.430332 GAGCACTCCATCTACTTCTGCT 59.570 50.000 0.00 0.00 36.22 4.24
4924 9596 1.071567 GTGTCGTGAGCTACTTCGCC 61.072 60.000 0.00 0.00 0.00 5.54
4952 9624 1.780309 TGCTTCTTCCCCTTCTTCCAA 59.220 47.619 0.00 0.00 0.00 3.53
4991 9663 1.831736 CGACCATGTTCCTACTTCCCT 59.168 52.381 0.00 0.00 0.00 4.20
4998 9670 0.036765 GCCACACGACCATGTTCCTA 60.037 55.000 0.00 0.00 0.00 2.94
5025 9697 0.611340 AGACTCCTAACCTTCGCCGT 60.611 55.000 0.00 0.00 0.00 5.68
5065 9737 4.684265 GCACTTGCATGCATCGAG 57.316 55.556 23.37 18.48 45.39 4.04
5093 9766 0.909610 TTGTCCCCGAGCTCCAGATT 60.910 55.000 8.47 0.00 0.00 2.40
5098 9771 1.674651 GGTTTTGTCCCCGAGCTCC 60.675 63.158 8.47 0.00 0.00 4.70
5159 9832 8.630917 TCATGTTTCAAAACCGGATAACTTTAA 58.369 29.630 9.46 0.00 38.11 1.52
5160 9833 8.167605 TCATGTTTCAAAACCGGATAACTTTA 57.832 30.769 9.46 0.00 38.11 1.85
5298 9972 8.531960 GTGGATGCCAACCAGTCTATTGACTA 62.532 46.154 9.54 0.00 42.78 2.59
5305 9979 1.278985 CAGTGGATGCCAACCAGTCTA 59.721 52.381 0.00 0.00 38.80 2.59
5314 9988 2.363306 AGTTTTCACAGTGGATGCCA 57.637 45.000 0.00 0.00 0.00 4.92
5325 9999 6.190954 ACCAGTTTGTTGACTAGTTTTCAC 57.809 37.500 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.