Multiple sequence alignment - TraesCS1B01G276900

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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 TraesCS1B01G276900 chr1B 100.000 2398 0 0 1 2398 484375375 484377772 0.000000e+00 4429.0
1 TraesCS1B01G276900 chr1B 83.657 618 58 27 980 1581 484360514 484361104 2.100000e-150 542.0
2 TraesCS1B01G276900 chr1B 91.083 157 14 0 1889 2045 615414310 615414466 1.870000e-51 213.0
3 TraesCS1B01G276900 chr1B 86.538 156 19 1 606 761 484352692 484352845 1.140000e-38 171.0
4 TraesCS1B01G276900 chr1A 88.791 1597 116 33 44 1630 461371868 461373411 0.000000e+00 1899.0
5 TraesCS1B01G276900 chr1A 81.325 996 124 36 772 1735 461351132 461352097 0.000000e+00 752.0
6 TraesCS1B01G276900 chr1A 92.437 238 12 4 1655 1888 461375076 461375311 3.820000e-88 335.0
7 TraesCS1B01G276900 chr1A 93.671 158 10 0 1888 2045 13488846 13489003 1.110000e-58 237.0
8 TraesCS1B01G276900 chr1A 80.408 245 37 10 2050 2291 461375316 461375552 2.450000e-40 176.0
9 TraesCS1B01G276900 chr1A 97.115 104 2 1 2296 2398 461377778 461377881 8.810000e-40 174.0
10 TraesCS1B01G276900 chr1A 84.483 58 8 1 2100 2156 53435453 53435396 3.330000e-04 56.5
11 TraesCS1B01G276900 chr1D 87.712 765 45 12 379 1126 361913894 361914626 0.000000e+00 846.0
12 TraesCS1B01G276900 chr1D 81.750 937 105 38 784 1688 361844719 361845621 0.000000e+00 723.0
13 TraesCS1B01G276900 chr1D 86.409 699 40 21 1179 1829 361914725 361915416 0.000000e+00 713.0
14 TraesCS1B01G276900 chr1D 87.927 381 36 9 1 376 361913359 361913734 7.870000e-120 440.0
15 TraesCS1B01G276900 chr1D 94.904 157 8 0 1889 2045 223433668 223433824 1.840000e-61 246.0
16 TraesCS1B01G276900 chr1D 81.395 215 23 9 2046 2258 361915636 361915835 2.470000e-35 159.0
17 TraesCS1B01G276900 chr1D 95.385 65 1 2 2296 2358 361916020 361916084 4.220000e-18 102.0
18 TraesCS1B01G276900 chr1D 89.286 56 2 4 2343 2398 361916103 361916154 1.540000e-07 67.6
19 TraesCS1B01G276900 chr1D 100.000 32 0 0 1159 1190 361914662 361914631 2.570000e-05 60.2
20 TraesCS1B01G276900 chr3B 98.718 156 2 0 1890 2045 779140043 779140198 6.530000e-71 278.0
21 TraesCS1B01G276900 chr3B 85.455 110 14 2 2164 2272 107136289 107136181 1.950000e-21 113.0
22 TraesCS1B01G276900 chr3B 83.333 114 16 2 2161 2272 405578907 405578795 4.220000e-18 102.0
23 TraesCS1B01G276900 chr4B 91.304 161 12 2 1888 2048 498369586 498369428 4.010000e-53 219.0
24 TraesCS1B01G276900 chr7A 91.139 158 14 0 1888 2045 249266121 249265964 5.190000e-52 215.0
25 TraesCS1B01G276900 chr7A 83.333 114 16 2 2162 2273 83737267 83737379 4.220000e-18 102.0
26 TraesCS1B01G276900 chr5B 90.625 160 15 0 1889 2048 29625171 29625012 1.870000e-51 213.0
27 TraesCS1B01G276900 chr5B 81.890 127 17 5 2149 2272 605161521 605161398 4.220000e-18 102.0
28 TraesCS1B01G276900 chr2D 90.385 156 13 2 1891 2045 505645768 505645922 1.120000e-48 204.0
29 TraesCS1B01G276900 chr7D 88.820 161 18 0 1884 2044 255892713 255892553 5.230000e-47 198.0
30 TraesCS1B01G276900 chrUn 85.321 109 16 0 2164 2272 70557268 70557376 1.950000e-21 113.0
31 TraesCS1B01G276900 chr7B 84.348 115 18 0 2158 2272 480523366 480523480 1.950000e-21 113.0
32 TraesCS1B01G276900 chr7B 79.429 175 25 5 2098 2272 596983417 596983580 1.950000e-21 113.0
33 TraesCS1B01G276900 chr6D 83.333 114 16 3 2162 2273 454231986 454231874 4.220000e-18 102.0
34 TraesCS1B01G276900 chr6D 96.970 33 1 0 2094 2126 28151116 28151148 3.330000e-04 56.5
35 TraesCS1B01G276900 chr6A 82.203 118 21 0 2153 2270 417446343 417446226 4.220000e-18 102.0
36 TraesCS1B01G276900 chr6A 94.118 34 2 0 2101 2134 162958605 162958572 4.000000e-03 52.8
37 TraesCS1B01G276900 chr5A 84.746 59 8 1 2097 2155 412105601 412105658 9.260000e-05 58.4
38 TraesCS1B01G276900 chr4A 92.308 39 3 0 2100 2138 27575251 27575289 3.330000e-04 56.5


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 TraesCS1B01G276900 chr1B 484375375 484377772 2397 False 4429.000000 4429 100.00000 1 2398 1 chr1B.!!$F3 2397
1 TraesCS1B01G276900 chr1B 484360514 484361104 590 False 542.000000 542 83.65700 980 1581 1 chr1B.!!$F2 601
2 TraesCS1B01G276900 chr1A 461351132 461352097 965 False 752.000000 752 81.32500 772 1735 1 chr1A.!!$F2 963
3 TraesCS1B01G276900 chr1A 461371868 461377881 6013 False 646.000000 1899 89.68775 44 2398 4 chr1A.!!$F3 2354
4 TraesCS1B01G276900 chr1D 361844719 361845621 902 False 723.000000 723 81.75000 784 1688 1 chr1D.!!$F2 904
5 TraesCS1B01G276900 chr1D 361913359 361916154 2795 False 387.933333 846 88.01900 1 2398 6 chr1D.!!$F3 2397

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
734 918 1.20002 CAAGTCCAAGCCGCCTTTAAG 59.8 52.381 0.0 0.0 0.0 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 4118 0.038166 TGGCAGTGGGTTCATCCTTC 59.962 55.0 0.0 0.0 36.25 3.46 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
27 29 9.260002 CAAATATTTGCACCCTATTCATTTACC 57.740 33.333 14.96 0.00 0.00 2.85
32 34 2.286833 CACCCTATTCATTTACCACGCG 59.713 50.000 3.53 3.53 0.00 6.01
77 79 8.664798 TCAAAATATAAGTCATGAAACCACGAG 58.335 33.333 0.00 0.00 0.00 4.18
189 192 1.937899 ACGTTCTTGTTTGACTTCCGG 59.062 47.619 0.00 0.00 0.00 5.14
191 194 1.673920 GTTCTTGTTTGACTTCCGGCA 59.326 47.619 0.00 0.00 0.00 5.69
197 200 3.745799 TGTTTGACTTCCGGCATAAGAA 58.254 40.909 8.29 0.00 0.00 2.52
247 252 6.126332 TGCAGTGATATTAAAATAGTGGGGGA 60.126 38.462 0.00 0.00 0.00 4.81
251 256 9.951866 AGTGATATTAAAATAGTGGGGGAAAAT 57.048 29.630 0.00 0.00 0.00 1.82
292 297 6.380846 TGAAGAATAAGCATTTATGTGCCCTT 59.619 34.615 0.00 0.00 46.19 3.95
343 349 9.295214 CTCAAGGCGACATAAATATATACTCAG 57.705 37.037 0.00 0.00 0.00 3.35
377 387 2.210116 CCAGGGCACATAATGTCGTAC 58.790 52.381 0.00 0.00 31.63 3.67
380 547 4.502431 CCAGGGCACATAATGTCGTACATA 60.502 45.833 0.00 0.00 37.97 2.29
469 649 1.388065 TTTGGCAACTTCCACACCGG 61.388 55.000 0.00 0.00 35.50 5.28
471 651 2.904866 GCAACTTCCACACCGGCA 60.905 61.111 0.00 0.00 33.14 5.69
497 677 1.283736 CATACGGGTTCGCAGTAACC 58.716 55.000 4.42 4.42 46.90 2.85
579 763 3.108144 GTGCACACACAACATGAAGAAC 58.892 45.455 13.17 0.00 46.61 3.01
580 764 2.751806 TGCACACACAACATGAAGAACA 59.248 40.909 0.00 0.00 0.00 3.18
581 765 3.192212 TGCACACACAACATGAAGAACAA 59.808 39.130 0.00 0.00 0.00 2.83
582 766 4.142204 TGCACACACAACATGAAGAACAAT 60.142 37.500 0.00 0.00 0.00 2.71
583 767 4.442073 GCACACACAACATGAAGAACAATC 59.558 41.667 0.00 0.00 0.00 2.67
584 768 5.580661 CACACACAACATGAAGAACAATCA 58.419 37.500 0.00 0.00 0.00 2.57
585 769 6.035217 CACACACAACATGAAGAACAATCAA 58.965 36.000 0.00 0.00 0.00 2.57
586 770 6.530887 CACACACAACATGAAGAACAATCAAA 59.469 34.615 0.00 0.00 0.00 2.69
587 771 7.063191 CACACACAACATGAAGAACAATCAAAA 59.937 33.333 0.00 0.00 0.00 2.44
588 772 7.601886 ACACACAACATGAAGAACAATCAAAAA 59.398 29.630 0.00 0.00 0.00 1.94
632 816 1.929230 TCGGCGCGAATAGAAATTGA 58.071 45.000 12.10 0.00 31.06 2.57
734 918 1.200020 CAAGTCCAAGCCGCCTTTAAG 59.800 52.381 0.00 0.00 0.00 1.85
741 925 3.317150 CAAGCCGCCTTTAAGGAAAAAG 58.683 45.455 16.18 0.00 37.67 2.27
880 1079 5.180492 CAGCAAATTGGCATGTTTCAAGAAT 59.820 36.000 7.75 0.00 35.83 2.40
906 1105 6.814146 GGACACCTATATATAGAGTTGCTTGC 59.186 42.308 19.51 6.25 32.05 4.01
951 1150 5.056480 CAGCATAAACCATCATTCTACGGA 58.944 41.667 0.00 0.00 0.00 4.69
952 1151 5.527214 CAGCATAAACCATCATTCTACGGAA 59.473 40.000 0.00 0.00 35.78 4.30
967 1168 2.537143 ACGGAATAGACAGGACAAGGT 58.463 47.619 0.00 0.00 0.00 3.50
996 1200 3.766676 TGCTAGAGAAGTGTAGAAGCG 57.233 47.619 0.00 0.00 0.00 4.68
1100 1306 3.236816 CGTGCTGATTGCCTTTTTGTAG 58.763 45.455 0.00 0.00 42.00 2.74
1129 1382 5.967088 TGGAGATCTTAGCTTACAAGTGAC 58.033 41.667 0.00 0.00 0.00 3.67
1131 1384 5.808030 GGAGATCTTAGCTTACAAGTGACAC 59.192 44.000 0.00 0.00 0.00 3.67
1142 1395 6.347725 GCTTACAAGTGACACTTAACTGATGG 60.348 42.308 20.17 8.29 36.03 3.51
1148 1401 4.697352 GTGACACTTAACTGATGGCAATCT 59.303 41.667 2.00 0.00 31.78 2.40
1159 1412 6.711277 ACTGATGGCAATCTAGTTAACAAGA 58.289 36.000 8.61 0.00 33.61 3.02
1160 1413 7.341805 ACTGATGGCAATCTAGTTAACAAGAT 58.658 34.615 8.61 0.00 33.87 2.40
1162 1415 6.543465 TGATGGCAATCTAGTTAACAAGATGG 59.457 38.462 8.61 0.00 32.79 3.51
1164 1417 5.880332 TGGCAATCTAGTTAACAAGATGGTC 59.120 40.000 8.61 0.00 32.79 4.02
1165 1418 6.116126 GGCAATCTAGTTAACAAGATGGTCT 58.884 40.000 8.61 0.00 32.79 3.85
1166 1419 6.599638 GGCAATCTAGTTAACAAGATGGTCTT 59.400 38.462 8.61 0.00 37.14 3.01
1193 1463 9.221775 GTAAGGTGATTAACTAATTTGATTGCG 57.778 33.333 0.00 0.00 0.00 4.85
1197 1467 8.178964 GGTGATTAACTAATTTGATTGCGTGTA 58.821 33.333 0.00 0.00 0.00 2.90
1199 1469 9.715123 TGATTAACTAATTTGATTGCGTGTATG 57.285 29.630 0.00 0.00 0.00 2.39
1414 1692 2.004733 CTGATCGCACATGCTCAGAAA 58.995 47.619 14.77 0.00 42.49 2.52
1415 1693 2.612672 CTGATCGCACATGCTCAGAAAT 59.387 45.455 14.77 0.00 42.49 2.17
1432 1710 3.438781 AGAAATTAAGATGTTGCGCCGAA 59.561 39.130 4.18 0.00 0.00 4.30
1433 1711 3.840890 AATTAAGATGTTGCGCCGAAA 57.159 38.095 4.18 0.00 0.00 3.46
1434 1712 3.840890 ATTAAGATGTTGCGCCGAAAA 57.159 38.095 4.18 0.00 0.00 2.29
1435 1713 3.840890 TTAAGATGTTGCGCCGAAAAT 57.159 38.095 4.18 0.00 0.00 1.82
1475 1757 1.148310 CAGAGCCGTTGTGGTTGTAG 58.852 55.000 0.00 0.00 41.21 2.74
1476 1758 0.756903 AGAGCCGTTGTGGTTGTAGT 59.243 50.000 0.00 0.00 41.21 2.73
1477 1759 1.965643 AGAGCCGTTGTGGTTGTAGTA 59.034 47.619 0.00 0.00 41.21 1.82
1583 1893 1.075542 TGTTGCTCCGTGAATAAGCG 58.924 50.000 0.00 0.00 38.90 4.68
1604 1929 4.021822 CGCTTGTATCAGTTTATGCGTTG 58.978 43.478 0.00 0.00 37.80 4.10
1623 1948 5.666185 GCGTTGCTGCTCAATCAAATAAAAC 60.666 40.000 0.00 0.00 36.99 2.43
1742 3708 1.229400 AGTCGGGCTAACAAGGGGA 60.229 57.895 0.00 0.00 0.00 4.81
1750 3716 3.132824 GGGCTAACAAGGGGATCATTTTG 59.867 47.826 0.00 0.00 0.00 2.44
1757 3724 6.840780 ACAAGGGGATCATTTTGTCTAAAG 57.159 37.500 0.00 0.00 0.00 1.85
1819 3786 3.309600 AGCGGGTACTCCAGTATACTT 57.690 47.619 1.56 0.00 34.36 2.24
1851 3984 6.043127 TGAATAGTTAGCCAGCCAATCATCTA 59.957 38.462 0.00 0.00 0.00 1.98
1857 3990 2.615912 GCCAGCCAATCATCTAGTGAAC 59.384 50.000 0.00 0.00 40.97 3.18
1860 3993 5.614308 CCAGCCAATCATCTAGTGAACATA 58.386 41.667 0.00 0.00 40.97 2.29
1887 4022 3.903876 GCATCATGCACGTTACCAG 57.096 52.632 4.20 0.00 44.26 4.00
1888 4023 0.248215 GCATCATGCACGTTACCAGC 60.248 55.000 4.20 0.00 44.26 4.85
1889 4024 1.085893 CATCATGCACGTTACCAGCA 58.914 50.000 0.00 0.00 43.14 4.41
1890 4025 1.063027 CATCATGCACGTTACCAGCAG 59.937 52.381 3.81 0.00 42.14 4.24
1891 4026 0.673333 TCATGCACGTTACCAGCAGG 60.673 55.000 3.38 3.38 42.14 4.85
1892 4027 1.377202 ATGCACGTTACCAGCAGGG 60.377 57.895 0.00 0.00 42.14 4.45
1893 4028 1.836999 ATGCACGTTACCAGCAGGGA 61.837 55.000 0.00 0.00 42.14 4.20
1894 4029 2.033194 GCACGTTACCAGCAGGGAC 61.033 63.158 0.00 0.00 41.15 4.46
1896 4031 2.654877 CGTTACCAGCAGGGACGT 59.345 61.111 15.11 0.00 41.05 4.34
1897 4032 1.885157 CGTTACCAGCAGGGACGTA 59.115 57.895 15.11 0.00 41.05 3.57
1898 4033 0.179145 CGTTACCAGCAGGGACGTAG 60.179 60.000 15.11 0.00 41.05 3.51
1899 4034 0.459759 GTTACCAGCAGGGACGTAGC 60.460 60.000 0.00 0.00 41.15 3.58
1900 4035 0.613853 TTACCAGCAGGGACGTAGCT 60.614 55.000 0.00 0.00 41.15 3.32
1903 4038 3.775654 AGCAGGGACGTAGCTGCC 61.776 66.667 0.00 0.00 41.03 4.85
1904 4039 3.775654 GCAGGGACGTAGCTGCCT 61.776 66.667 0.00 0.00 35.60 4.75
1905 4040 2.496817 CAGGGACGTAGCTGCCTC 59.503 66.667 0.00 0.00 28.59 4.70
1906 4041 2.037367 AGGGACGTAGCTGCCTCA 59.963 61.111 0.00 0.00 0.00 3.86
1907 4042 1.381872 AGGGACGTAGCTGCCTCAT 60.382 57.895 0.00 0.00 0.00 2.90
1908 4043 0.106167 AGGGACGTAGCTGCCTCATA 60.106 55.000 0.00 0.00 0.00 2.15
1909 4044 0.315568 GGGACGTAGCTGCCTCATAG 59.684 60.000 0.00 0.00 0.00 2.23
1910 4045 0.315568 GGACGTAGCTGCCTCATAGG 59.684 60.000 0.00 0.00 38.80 2.57
1920 4055 3.733709 CCTCATAGGCATTGGGGTC 57.266 57.895 0.00 0.00 29.49 4.46
1921 4056 0.846015 CCTCATAGGCATTGGGGTCA 59.154 55.000 0.00 0.00 29.49 4.02
1922 4057 1.215173 CCTCATAGGCATTGGGGTCAA 59.785 52.381 0.00 0.00 37.28 3.18
1923 4058 2.158415 CCTCATAGGCATTGGGGTCAAT 60.158 50.000 0.00 0.00 43.79 2.57
1924 4059 3.569491 CTCATAGGCATTGGGGTCAATT 58.431 45.455 0.00 0.00 41.29 2.32
1925 4060 3.298619 TCATAGGCATTGGGGTCAATTG 58.701 45.455 0.00 0.00 41.29 2.32
1926 4061 3.053019 TCATAGGCATTGGGGTCAATTGA 60.053 43.478 3.38 3.38 41.29 2.57
1927 4062 1.560505 AGGCATTGGGGTCAATTGAC 58.439 50.000 27.16 27.16 41.29 3.18
1940 4075 5.665916 GTCAATTGACCCCAATGAAATCT 57.334 39.130 25.26 0.00 41.84 2.40
1941 4076 6.773976 GTCAATTGACCCCAATGAAATCTA 57.226 37.500 25.26 0.00 41.84 1.98
1942 4077 7.169158 GTCAATTGACCCCAATGAAATCTAA 57.831 36.000 25.26 0.00 41.84 2.10
1943 4078 7.610865 GTCAATTGACCCCAATGAAATCTAAA 58.389 34.615 25.26 0.00 41.84 1.85
1944 4079 8.093927 GTCAATTGACCCCAATGAAATCTAAAA 58.906 33.333 25.26 0.00 41.84 1.52
1945 4080 8.824783 TCAATTGACCCCAATGAAATCTAAAAT 58.175 29.630 3.38 0.00 41.84 1.82
1946 4081 9.452287 CAATTGACCCCAATGAAATCTAAAATT 57.548 29.630 0.00 0.00 41.84 1.82
1947 4082 9.671279 AATTGACCCCAATGAAATCTAAAATTC 57.329 29.630 0.00 0.00 41.84 2.17
1948 4083 7.181569 TGACCCCAATGAAATCTAAAATTCC 57.818 36.000 0.00 0.00 0.00 3.01
1949 4084 6.959366 TGACCCCAATGAAATCTAAAATTCCT 59.041 34.615 0.00 0.00 0.00 3.36
1950 4085 7.457535 TGACCCCAATGAAATCTAAAATTCCTT 59.542 33.333 0.00 0.00 0.00 3.36
1951 4086 7.851228 ACCCCAATGAAATCTAAAATTCCTTC 58.149 34.615 0.00 0.00 0.00 3.46
1952 4087 7.457535 ACCCCAATGAAATCTAAAATTCCTTCA 59.542 33.333 0.00 0.00 0.00 3.02
1953 4088 7.765819 CCCCAATGAAATCTAAAATTCCTTCAC 59.234 37.037 0.00 0.00 0.00 3.18
1954 4089 8.534496 CCCAATGAAATCTAAAATTCCTTCACT 58.466 33.333 0.00 0.00 0.00 3.41
1972 4107 9.750783 TCCTTCACTAATTTAGTACTAGTCACT 57.249 33.333 8.71 4.52 37.23 3.41
1994 4129 9.832445 TCACTAACATTTATAGAAGGATGAACC 57.168 33.333 0.00 0.00 39.35 3.62
1995 4130 9.057089 CACTAACATTTATAGAAGGATGAACCC 57.943 37.037 0.00 0.00 40.05 4.11
1996 4131 8.778059 ACTAACATTTATAGAAGGATGAACCCA 58.222 33.333 0.00 0.00 40.05 4.51
1997 4132 7.881775 AACATTTATAGAAGGATGAACCCAC 57.118 36.000 0.00 0.00 40.05 4.61
1998 4133 7.213178 ACATTTATAGAAGGATGAACCCACT 57.787 36.000 0.00 0.00 40.05 4.00
1999 4134 7.056635 ACATTTATAGAAGGATGAACCCACTG 58.943 38.462 0.00 0.00 40.05 3.66
2000 4135 3.567478 ATAGAAGGATGAACCCACTGC 57.433 47.619 0.00 0.00 40.05 4.40
2001 4136 0.329596 AGAAGGATGAACCCACTGCC 59.670 55.000 0.00 0.00 40.05 4.85
2002 4137 0.038166 GAAGGATGAACCCACTGCCA 59.962 55.000 0.00 0.00 40.05 4.92
2003 4138 0.706433 AAGGATGAACCCACTGCCAT 59.294 50.000 0.00 0.00 40.05 4.40
2004 4139 1.595311 AGGATGAACCCACTGCCATA 58.405 50.000 0.00 0.00 40.05 2.74
2005 4140 2.138542 AGGATGAACCCACTGCCATAT 58.861 47.619 0.00 0.00 40.05 1.78
2006 4141 3.326521 AGGATGAACCCACTGCCATATA 58.673 45.455 0.00 0.00 40.05 0.86
2007 4142 3.328931 AGGATGAACCCACTGCCATATAG 59.671 47.826 0.00 0.00 40.05 1.31
2008 4143 3.327757 GGATGAACCCACTGCCATATAGA 59.672 47.826 0.00 0.00 0.00 1.98
2009 4144 4.018960 GGATGAACCCACTGCCATATAGAT 60.019 45.833 0.00 0.00 0.00 1.98
2010 4145 4.356405 TGAACCCACTGCCATATAGATG 57.644 45.455 0.00 0.00 0.00 2.90
2011 4146 3.973305 TGAACCCACTGCCATATAGATGA 59.027 43.478 0.00 0.00 34.73 2.92
2012 4147 4.202357 TGAACCCACTGCCATATAGATGAC 60.202 45.833 0.00 0.00 34.73 3.06
2013 4148 2.639839 ACCCACTGCCATATAGATGACC 59.360 50.000 0.00 0.00 34.73 4.02
2014 4149 2.026822 CCCACTGCCATATAGATGACCC 60.027 54.545 0.00 0.00 34.73 4.46
2015 4150 2.026822 CCACTGCCATATAGATGACCCC 60.027 54.545 0.00 0.00 34.73 4.95
2016 4151 2.639347 CACTGCCATATAGATGACCCCA 59.361 50.000 0.00 0.00 34.73 4.96
2017 4152 3.265221 CACTGCCATATAGATGACCCCAT 59.735 47.826 0.00 0.00 34.73 4.00
2112 4255 8.903820 GTTGCAAATATACTACTCCCTTCATTT 58.096 33.333 0.00 0.00 0.00 2.32
2145 4291 9.606631 ACAAGTCTTCATAGAAATTCCACTATC 57.393 33.333 0.00 0.00 30.65 2.08
2151 4297 7.303182 TCATAGAAATTCCACTATCGACCAT 57.697 36.000 0.00 0.00 0.00 3.55
2159 4305 6.570672 TTCCACTATCGACCATATACAGAC 57.429 41.667 0.00 0.00 0.00 3.51
2160 4306 5.877491 TCCACTATCGACCATATACAGACT 58.123 41.667 0.00 0.00 0.00 3.24
2162 4308 7.631007 TCCACTATCGACCATATACAGACTAT 58.369 38.462 0.00 0.00 0.00 2.12
2163 4309 8.765517 TCCACTATCGACCATATACAGACTATA 58.234 37.037 0.00 0.00 0.00 1.31
2164 4310 9.562408 CCACTATCGACCATATACAGACTATAT 57.438 37.037 0.00 0.00 0.00 0.86
2219 4365 7.144722 TGATTCACTCATTTTGCTTCGTATT 57.855 32.000 0.00 0.00 0.00 1.89
2224 4370 7.739295 TCACTCATTTTGCTTCGTATTTAGTC 58.261 34.615 0.00 0.00 0.00 2.59
2230 4376 9.221775 CATTTTGCTTCGTATTTAGTCCATAAC 57.778 33.333 0.00 0.00 0.00 1.89
2293 4572 8.240267 AGTAGGTATGATCTCTCTTTGGTTAC 57.760 38.462 0.00 0.00 0.00 2.50
2294 4573 8.062536 AGTAGGTATGATCTCTCTTTGGTTACT 58.937 37.037 0.00 0.00 0.00 2.24
2365 6896 1.211969 CTCACGGTGTCGATCGGTT 59.788 57.895 16.41 0.00 40.11 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.156922 CGTGGTAAATGAATAGGGTGCAAA 59.843 41.667 0.00 0.00 0.00 3.68
12 13 2.168936 TCGCGTGGTAAATGAATAGGGT 59.831 45.455 5.77 0.00 0.00 4.34
13 14 2.828877 TCGCGTGGTAAATGAATAGGG 58.171 47.619 5.77 0.00 0.00 3.53
20 22 2.344142 GCCAAATTTCGCGTGGTAAATG 59.656 45.455 13.47 0.70 34.71 2.32
27 29 0.777631 CTTGTGCCAAATTTCGCGTG 59.222 50.000 5.77 0.00 0.00 5.34
67 69 8.287503 ACATAAAAATGTAACTCTCGTGGTTTC 58.712 33.333 0.00 0.00 32.14 2.78
69 71 7.739498 ACATAAAAATGTAACTCTCGTGGTT 57.261 32.000 0.00 0.00 32.14 3.67
202 205 3.558418 GCACCATATTTTCACGTACCGAT 59.442 43.478 0.00 0.00 0.00 4.18
241 246 6.183361 CCCAGAGTGTATTATATTTTCCCCCA 60.183 42.308 0.00 0.00 0.00 4.96
270 275 5.069516 CCAAGGGCACATAAATGCTTATTCT 59.930 40.000 0.00 0.00 45.38 2.40
301 306 5.392380 CGCCTTGAGCTGAAATGATAGTTTT 60.392 40.000 0.00 0.00 40.39 2.43
302 307 4.095483 CGCCTTGAGCTGAAATGATAGTTT 59.905 41.667 0.00 0.00 40.39 2.66
322 328 9.751542 AATAGCTGAGTATATATTTATGTCGCC 57.248 33.333 0.00 0.00 0.00 5.54
353 361 1.490490 GACATTATGTGCCCTGGGAGA 59.510 52.381 19.27 0.00 0.00 3.71
355 363 0.180171 CGACATTATGTGCCCTGGGA 59.820 55.000 19.27 0.00 0.00 4.37
540 724 0.320771 ACGTCCAATCACCTCAGTGC 60.321 55.000 0.00 0.00 44.16 4.40
595 779 1.000717 CGAAGCGGTGGGTTGATTTTT 60.001 47.619 0.00 0.00 33.17 1.94
596 780 0.596082 CGAAGCGGTGGGTTGATTTT 59.404 50.000 0.00 0.00 33.17 1.82
597 781 1.241315 CCGAAGCGGTGGGTTGATTT 61.241 55.000 0.00 0.00 42.73 2.17
658 842 2.472695 ATGCGCACCTACTTTCTCAA 57.527 45.000 14.90 0.00 0.00 3.02
734 918 4.217767 AGCTTGGACGTATTTCCTTTTTCC 59.782 41.667 0.00 0.00 36.51 3.13
741 925 2.210961 GGCTAGCTTGGACGTATTTCC 58.789 52.381 15.72 0.00 36.03 3.13
782 966 1.268283 ACTCCTGGCTAGCTTGGACC 61.268 60.000 20.03 2.81 0.00 4.46
880 1079 7.525526 GCAAGCAACTCTATATATAGGTGTCCA 60.526 40.741 17.81 0.00 0.00 4.02
917 1116 2.083774 GTTTATGCTGTAGCTGTGCCA 58.916 47.619 5.38 0.00 42.66 4.92
924 1123 6.346919 CGTAGAATGATGGTTTATGCTGTAGC 60.347 42.308 0.00 0.00 42.50 3.58
951 1150 3.196685 GCTCTCACCTTGTCCTGTCTATT 59.803 47.826 0.00 0.00 0.00 1.73
952 1151 2.763448 GCTCTCACCTTGTCCTGTCTAT 59.237 50.000 0.00 0.00 0.00 1.98
967 1168 3.576118 ACACTTCTCTAGCAAAGCTCTCA 59.424 43.478 0.00 0.00 40.44 3.27
996 1200 1.192793 GCGTGCTACTCTTCATCGTC 58.807 55.000 0.00 0.00 0.00 4.20
1100 1306 2.926778 AGCTAAGATCTCCATGCCAC 57.073 50.000 0.00 0.00 0.00 5.01
1129 1382 6.992063 AACTAGATTGCCATCAGTTAAGTG 57.008 37.500 3.73 3.73 33.02 3.16
1131 1384 8.492673 TGTTAACTAGATTGCCATCAGTTAAG 57.507 34.615 21.87 8.20 39.89 1.85
1142 1395 7.467623 CAAGACCATCTTGTTAACTAGATTGC 58.532 38.462 24.20 17.30 46.50 3.56
1159 1412 9.975218 AATTAGTTAATCACCTTACAAGACCAT 57.025 29.630 0.00 0.00 0.00 3.55
1160 1413 9.802039 AAATTAGTTAATCACCTTACAAGACCA 57.198 29.630 0.00 0.00 0.00 4.02
1167 1420 9.221775 CGCAATCAAATTAGTTAATCACCTTAC 57.778 33.333 0.00 0.00 0.00 2.34
1169 1422 7.754924 CACGCAATCAAATTAGTTAATCACCTT 59.245 33.333 0.00 0.00 0.00 3.50
1171 1424 7.027161 ACACGCAATCAAATTAGTTAATCACC 58.973 34.615 0.00 0.00 0.00 4.02
1172 1425 9.716507 ATACACGCAATCAAATTAGTTAATCAC 57.283 29.630 0.00 0.00 0.00 3.06
1193 1463 2.802667 CTCGGCTGCACGCATACAC 61.803 63.158 0.50 0.00 41.67 2.90
1197 1467 3.121030 GAACTCGGCTGCACGCAT 61.121 61.111 0.50 0.00 41.67 4.73
1385 1663 4.112634 GCATGTGCGATCAGTACTTCTTA 58.887 43.478 0.00 0.00 36.37 2.10
1414 1692 3.840890 TTTTCGGCGCAACATCTTAAT 57.159 38.095 10.83 0.00 0.00 1.40
1415 1693 3.840890 ATTTTCGGCGCAACATCTTAA 57.159 38.095 10.83 0.00 0.00 1.85
1432 1710 5.336451 GCTCAACCCATCCGAGTTTTTATTT 60.336 40.000 0.00 0.00 0.00 1.40
1433 1711 4.157840 GCTCAACCCATCCGAGTTTTTATT 59.842 41.667 0.00 0.00 0.00 1.40
1434 1712 3.694566 GCTCAACCCATCCGAGTTTTTAT 59.305 43.478 0.00 0.00 0.00 1.40
1435 1713 3.078837 GCTCAACCCATCCGAGTTTTTA 58.921 45.455 0.00 0.00 0.00 1.52
1514 1796 0.179094 ACGACGAGGACAACAGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
1518 1800 3.489180 AGATAACGACGAGGACAACAG 57.511 47.619 0.00 0.00 0.00 3.16
1519 1801 3.928727 AAGATAACGACGAGGACAACA 57.071 42.857 0.00 0.00 0.00 3.33
1520 1802 4.922103 AGAAAAGATAACGACGAGGACAAC 59.078 41.667 0.00 0.00 0.00 3.32
1521 1803 5.130292 AGAAAAGATAACGACGAGGACAA 57.870 39.130 0.00 0.00 0.00 3.18
1522 1804 4.778534 AGAAAAGATAACGACGAGGACA 57.221 40.909 0.00 0.00 0.00 4.02
1523 1805 5.400703 AGAAGAAAAGATAACGACGAGGAC 58.599 41.667 0.00 0.00 0.00 3.85
1583 1893 3.786048 GCAACGCATAAACTGATACAAGC 59.214 43.478 0.00 0.00 0.00 4.01
1604 1929 7.799784 ACAAATGTTTTATTTGATTGAGCAGC 58.200 30.769 16.60 0.00 40.42 5.25
1650 3588 6.297080 TGCACCATTGGAAATGAACATTAT 57.703 33.333 10.37 0.00 0.00 1.28
1653 3619 4.509616 CATGCACCATTGGAAATGAACAT 58.490 39.130 10.37 0.00 0.00 2.71
1657 3623 2.817665 TCCATGCACCATTGGAAATGA 58.182 42.857 10.37 0.00 0.00 2.57
1660 3626 2.109774 GGATCCATGCACCATTGGAAA 58.890 47.619 10.37 0.00 33.78 3.13
1742 3708 8.150296 CCCCTTGTTTTCTTTAGACAAAATGAT 58.850 33.333 0.00 0.00 33.37 2.45
1750 3716 7.468141 AATGATCCCCTTGTTTTCTTTAGAC 57.532 36.000 0.00 0.00 0.00 2.59
1757 3724 6.751888 CGTGAATTAATGATCCCCTTGTTTTC 59.248 38.462 0.00 0.00 0.00 2.29
1779 3746 0.603569 ACTACCCTCTGACTTGCGTG 59.396 55.000 0.00 0.00 0.00 5.34
1819 3786 5.130311 TGGCTGGCTAACTATTCAGTAATGA 59.870 40.000 2.00 0.00 33.48 2.57
1851 3984 2.781923 TGCACTGCATGTATGTTCACT 58.218 42.857 0.00 0.00 31.71 3.41
1875 4010 2.031919 CCCTGCTGGTAACGTGCA 59.968 61.111 9.00 0.00 44.44 4.57
1880 4015 0.459759 GCTACGTCCCTGCTGGTAAC 60.460 60.000 9.00 5.70 34.77 2.50
1881 4016 0.613853 AGCTACGTCCCTGCTGGTAA 60.614 55.000 9.00 0.00 35.54 2.85
1882 4017 1.000019 AGCTACGTCCCTGCTGGTA 60.000 57.895 9.00 0.00 35.54 3.25
1883 4018 2.283966 AGCTACGTCCCTGCTGGT 60.284 61.111 9.00 0.00 35.54 4.00
1888 4023 1.680522 ATGAGGCAGCTACGTCCCTG 61.681 60.000 10.17 10.17 0.00 4.45
1889 4024 0.106167 TATGAGGCAGCTACGTCCCT 60.106 55.000 4.25 0.00 0.00 4.20
1890 4025 0.315568 CTATGAGGCAGCTACGTCCC 59.684 60.000 4.25 0.00 0.00 4.46
1891 4026 0.315568 CCTATGAGGCAGCTACGTCC 59.684 60.000 4.25 0.00 0.00 4.79
1892 4027 3.875838 CCTATGAGGCAGCTACGTC 57.124 57.895 0.00 0.00 0.00 4.34
1901 4036 5.915228 ATTGACCCCAATGCCTATGAGGC 62.915 52.174 10.68 10.68 46.87 4.70
1902 4037 0.846015 TGACCCCAATGCCTATGAGG 59.154 55.000 0.00 0.00 38.80 3.86
1903 4038 2.734755 TTGACCCCAATGCCTATGAG 57.265 50.000 0.00 0.00 0.00 2.90
1904 4039 3.053019 TCAATTGACCCCAATGCCTATGA 60.053 43.478 3.38 0.00 41.84 2.15
1905 4040 3.068590 GTCAATTGACCCCAATGCCTATG 59.931 47.826 25.26 0.00 41.84 2.23
1906 4041 3.299503 GTCAATTGACCCCAATGCCTAT 58.700 45.455 25.26 0.00 41.84 2.57
1907 4042 2.733956 GTCAATTGACCCCAATGCCTA 58.266 47.619 25.26 0.00 41.84 3.93
1908 4043 1.560505 GTCAATTGACCCCAATGCCT 58.439 50.000 25.26 0.00 41.84 4.75
1918 4053 5.665916 AGATTTCATTGGGGTCAATTGAC 57.334 39.130 27.16 27.16 41.29 3.18
1919 4054 7.789202 TTTAGATTTCATTGGGGTCAATTGA 57.211 32.000 3.38 3.38 41.29 2.57
1920 4055 9.452287 AATTTTAGATTTCATTGGGGTCAATTG 57.548 29.630 0.00 0.00 41.29 2.32
1921 4056 9.671279 GAATTTTAGATTTCATTGGGGTCAATT 57.329 29.630 0.00 0.00 41.29 2.32
1922 4057 8.267183 GGAATTTTAGATTTCATTGGGGTCAAT 58.733 33.333 0.00 0.00 43.79 2.57
1923 4058 7.457535 AGGAATTTTAGATTTCATTGGGGTCAA 59.542 33.333 0.00 0.00 37.28 3.18
1924 4059 6.959366 AGGAATTTTAGATTTCATTGGGGTCA 59.041 34.615 0.00 0.00 0.00 4.02
1925 4060 7.423844 AGGAATTTTAGATTTCATTGGGGTC 57.576 36.000 0.00 0.00 0.00 4.46
1926 4061 7.457535 TGAAGGAATTTTAGATTTCATTGGGGT 59.542 33.333 0.00 0.00 0.00 4.95
1927 4062 7.765819 GTGAAGGAATTTTAGATTTCATTGGGG 59.234 37.037 0.00 0.00 0.00 4.96
1928 4063 8.534496 AGTGAAGGAATTTTAGATTTCATTGGG 58.466 33.333 0.00 0.00 0.00 4.12
1946 4081 9.750783 AGTGACTAGTACTAAATTAGTGAAGGA 57.249 33.333 15.34 0.00 39.81 3.36
1968 4103 9.832445 GGTTCATCCTTCTATAAATGTTAGTGA 57.168 33.333 0.00 0.00 0.00 3.41
1969 4104 9.057089 GGGTTCATCCTTCTATAAATGTTAGTG 57.943 37.037 0.00 0.00 36.25 2.74
1970 4105 8.778059 TGGGTTCATCCTTCTATAAATGTTAGT 58.222 33.333 0.00 0.00 36.25 2.24
1971 4106 9.057089 GTGGGTTCATCCTTCTATAAATGTTAG 57.943 37.037 0.00 0.00 36.25 2.34
1972 4107 8.778059 AGTGGGTTCATCCTTCTATAAATGTTA 58.222 33.333 0.00 0.00 36.25 2.41
1973 4108 7.557719 CAGTGGGTTCATCCTTCTATAAATGTT 59.442 37.037 0.00 0.00 36.25 2.71
1974 4109 7.056635 CAGTGGGTTCATCCTTCTATAAATGT 58.943 38.462 0.00 0.00 36.25 2.71
1975 4110 6.016777 GCAGTGGGTTCATCCTTCTATAAATG 60.017 42.308 0.00 0.00 36.25 2.32
1976 4111 6.064717 GCAGTGGGTTCATCCTTCTATAAAT 58.935 40.000 0.00 0.00 36.25 1.40
1977 4112 5.437060 GCAGTGGGTTCATCCTTCTATAAA 58.563 41.667 0.00 0.00 36.25 1.40
1978 4113 4.141482 GGCAGTGGGTTCATCCTTCTATAA 60.141 45.833 0.00 0.00 36.25 0.98
1979 4114 3.391296 GGCAGTGGGTTCATCCTTCTATA 59.609 47.826 0.00 0.00 36.25 1.31
1980 4115 2.173569 GGCAGTGGGTTCATCCTTCTAT 59.826 50.000 0.00 0.00 36.25 1.98
1981 4116 1.559682 GGCAGTGGGTTCATCCTTCTA 59.440 52.381 0.00 0.00 36.25 2.10
1982 4117 0.329596 GGCAGTGGGTTCATCCTTCT 59.670 55.000 0.00 0.00 36.25 2.85
1983 4118 0.038166 TGGCAGTGGGTTCATCCTTC 59.962 55.000 0.00 0.00 36.25 3.46
1984 4119 0.706433 ATGGCAGTGGGTTCATCCTT 59.294 50.000 0.00 0.00 36.25 3.36
1985 4120 1.595311 TATGGCAGTGGGTTCATCCT 58.405 50.000 0.00 0.00 36.25 3.24
1986 4121 2.664402 ATATGGCAGTGGGTTCATCC 57.336 50.000 0.00 0.00 0.00 3.51
1987 4122 4.623932 TCTATATGGCAGTGGGTTCATC 57.376 45.455 0.00 0.00 0.00 2.92
1988 4123 4.598807 TCATCTATATGGCAGTGGGTTCAT 59.401 41.667 0.00 0.00 33.61 2.57
1989 4124 3.973305 TCATCTATATGGCAGTGGGTTCA 59.027 43.478 0.00 0.00 33.61 3.18
1990 4125 4.319177 GTCATCTATATGGCAGTGGGTTC 58.681 47.826 0.00 0.00 37.67 3.62
1991 4126 3.073062 GGTCATCTATATGGCAGTGGGTT 59.927 47.826 0.00 0.00 39.62 4.11
1992 4127 2.639839 GGTCATCTATATGGCAGTGGGT 59.360 50.000 0.00 0.00 39.62 4.51
1993 4128 2.026822 GGGTCATCTATATGGCAGTGGG 60.027 54.545 0.00 0.00 39.62 4.61
1994 4129 2.026822 GGGGTCATCTATATGGCAGTGG 60.027 54.545 0.00 0.00 39.62 4.00
1995 4130 2.639347 TGGGGTCATCTATATGGCAGTG 59.361 50.000 0.00 0.00 39.62 3.66
1996 4131 2.990195 TGGGGTCATCTATATGGCAGT 58.010 47.619 0.00 0.00 39.62 4.40
1997 4132 4.148128 GATGGGGTCATCTATATGGCAG 57.852 50.000 0.00 0.00 44.73 4.85
2025 4160 2.370849 ACCAGGGACGAAGCTAGAAAAA 59.629 45.455 0.00 0.00 0.00 1.94
2026 4161 1.975680 ACCAGGGACGAAGCTAGAAAA 59.024 47.619 0.00 0.00 0.00 2.29
2027 4162 1.640917 ACCAGGGACGAAGCTAGAAA 58.359 50.000 0.00 0.00 0.00 2.52
2028 4163 1.640917 AACCAGGGACGAAGCTAGAA 58.359 50.000 0.00 0.00 0.00 2.10
2029 4164 2.097825 GTAACCAGGGACGAAGCTAGA 58.902 52.381 0.00 0.00 0.00 2.43
2030 4165 1.136500 GGTAACCAGGGACGAAGCTAG 59.864 57.143 0.00 0.00 0.00 3.42
2031 4166 1.188863 GGTAACCAGGGACGAAGCTA 58.811 55.000 0.00 0.00 0.00 3.32
2032 4167 0.834687 TGGTAACCAGGGACGAAGCT 60.835 55.000 0.00 0.00 0.00 3.74
2033 4168 1.675219 TGGTAACCAGGGACGAAGC 59.325 57.895 0.00 0.00 0.00 3.86
2043 4178 0.457035 GACGCGTATCCTGGTAACCA 59.543 55.000 13.97 0.00 0.00 3.67
2044 4179 0.743097 AGACGCGTATCCTGGTAACC 59.257 55.000 13.97 0.00 0.00 2.85
2072 4215 0.391228 TGCAACCGACAAGCTAGACA 59.609 50.000 0.00 0.00 0.00 3.41
2120 4266 8.759641 CGATAGTGGAATTTCTATGAAGACTTG 58.240 37.037 0.00 0.00 0.00 3.16
2134 4280 7.451877 AGTCTGTATATGGTCGATAGTGGAATT 59.548 37.037 0.00 0.00 37.40 2.17
2138 4284 7.867305 ATAGTCTGTATATGGTCGATAGTGG 57.133 40.000 0.00 0.00 37.40 4.00
2191 4337 7.765307 ACGAAGCAAAATGAGTGAATCAATAT 58.235 30.769 0.00 0.00 42.53 1.28
2195 4341 6.741992 ATACGAAGCAAAATGAGTGAATCA 57.258 33.333 0.00 0.00 43.70 2.57
2200 4346 6.961554 GGACTAAATACGAAGCAAAATGAGTG 59.038 38.462 0.00 0.00 0.00 3.51
2204 4350 9.221775 GTTATGGACTAAATACGAAGCAAAATG 57.778 33.333 0.00 0.00 0.00 2.32
2247 4393 9.211485 CCTACTCCTTTCGTTTCTAAATGTAAA 57.789 33.333 0.00 0.00 0.00 2.01
2258 4537 6.608002 AGAGATCATACCTACTCCTTTCGTTT 59.392 38.462 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.