Multiple sequence alignment - TraesCS1D01G250000

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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 TraesCS1D01G250000 chr1D 100.000 2709 0 0 1 2709 342449554 342446846 0.000000e+00 5003
1 TraesCS1D01G250000 chr1D 82.514 732 91 16 242 955 238064487 238065199 2.310000e-170 608
2 TraesCS1D01G250000 chr1D 85.818 550 41 15 2176 2709 342437696 342437168 1.420000e-152 549
3 TraesCS1D01G250000 chr1D 86.986 146 18 1 262 407 342449253 342449109 2.160000e-36 163
4 TraesCS1D01G250000 chr1D 86.986 146 18 1 302 446 342449293 342449148 2.160000e-36 163
5 TraesCS1D01G250000 chr1D 84.545 110 17 0 265 374 238064550 238064659 2.850000e-20 110
6 TraesCS1D01G250000 chr1A 95.227 838 27 3 951 1775 442126077 442125240 0.000000e+00 1314
7 TraesCS1D01G250000 chr1A 78.795 415 50 12 559 955 301771793 301772187 7.490000e-61 244
8 TraesCS1D01G250000 chr1B 95.791 784 28 3 995 1775 458634205 458633424 0.000000e+00 1260
9 TraesCS1D01G250000 chr1B 80.090 442 62 16 1926 2360 458633421 458632999 3.390000e-79 305
10 TraesCS1D01G250000 chr3B 93.813 792 47 2 1 792 599092997 599092208 0.000000e+00 1190
11 TraesCS1D01G250000 chr3B 94.286 175 7 3 790 962 599092024 599091851 5.750000e-67 265
12 TraesCS1D01G250000 chr3B 86.806 144 19 0 262 405 599092696 599092553 7.760000e-36 161
13 TraesCS1D01G250000 chr3A 90.738 583 48 2 1 578 735746903 735747484 0.000000e+00 773
14 TraesCS1D01G250000 chr5D 88.393 336 33 3 2375 2704 82689307 82689642 1.510000e-107 399
15 TraesCS1D01G250000 chr5D 83.824 340 45 6 2375 2707 177486097 177485761 5.630000e-82 315
16 TraesCS1D01G250000 chr5D 91.034 145 12 1 1771 1915 558913431 558913574 7.650000e-46 195
17 TraesCS1D01G250000 chr5D 88.889 162 11 3 1774 1929 441117083 441116923 2.750000e-45 193
18 TraesCS1D01G250000 chr5D 79.623 265 49 3 2449 2709 557112161 557112424 4.610000e-43 185
19 TraesCS1D01G250000 chr6B 85.924 341 42 2 2375 2709 480268627 480268287 2.560000e-95 359
20 TraesCS1D01G250000 chr6B 80.826 339 58 5 2375 2707 396504479 396504816 2.680000e-65 259
21 TraesCS1D01G250000 chr6B 93.056 144 7 1 1774 1914 192737978 192737835 9.830000e-50 207
22 TraesCS1D01G250000 chr7B 85.044 341 43 3 2375 2709 146770881 146771219 9.290000e-90 340
23 TraesCS1D01G250000 chr2A 82.991 341 51 3 2375 2709 472578732 472578393 4.380000e-78 302
24 TraesCS1D01G250000 chr2B 82.456 342 52 5 2375 2709 275366776 275366436 2.640000e-75 292
25 TraesCS1D01G250000 chr2B 82.405 341 54 3 2375 2709 621164923 621165263 2.640000e-75 292
26 TraesCS1D01G250000 chr2B 97.368 76 2 0 1 76 740568157 740568232 2.190000e-26 130
27 TraesCS1D01G250000 chr5B 82.334 317 50 3 2375 2686 198766266 198765951 1.240000e-68 270
28 TraesCS1D01G250000 chr4B 81.287 342 54 7 2375 2709 569989286 569988948 4.450000e-68 268
29 TraesCS1D01G250000 chr4B 78.824 340 65 4 2376 2709 638350364 638350702 3.510000e-54 222
30 TraesCS1D01G250000 chr6D 80.994 342 57 7 2375 2709 328439198 328439538 5.750000e-67 265
31 TraesCS1D01G250000 chr3D 80.994 342 58 5 2375 2709 465060319 465059978 5.750000e-67 265
32 TraesCS1D01G250000 chr3D 91.275 149 9 3 1774 1918 452677777 452677629 1.640000e-47 200
33 TraesCS1D01G250000 chr3D 90.196 153 7 3 1774 1918 138759621 138759469 2.750000e-45 193
34 TraesCS1D01G250000 chr6A 80.117 342 55 6 2375 2709 302666257 302665922 2.690000e-60 243
35 TraesCS1D01G250000 chr4A 80.000 335 57 8 2383 2709 394076727 394076395 3.490000e-59 239
36 TraesCS1D01G250000 chr7D 79.592 343 59 9 2375 2709 203632606 203632945 4.510000e-58 235
37 TraesCS1D01G250000 chr7D 90.385 156 12 3 1764 1918 16321403 16321556 4.570000e-48 202
38 TraesCS1D01G250000 chr4D 91.781 146 11 1 1774 1918 146299787 146299932 4.570000e-48 202
39 TraesCS1D01G250000 chr4D 90.667 150 9 3 1773 1918 350769144 350768996 7.650000e-46 195
40 TraesCS1D01G250000 chr4D 86.188 181 16 4 1758 1931 458556149 458556327 1.280000e-43 187
41 TraesCS1D01G250000 chr4D 75.953 341 74 5 2376 2709 315202636 315202975 4.640000e-38 169


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 TraesCS1D01G250000 chr1D 342446846 342449554 2708 True 1776.333333 5003 91.3240 1 2709 3 chr1D.!!$R2 2708
1 TraesCS1D01G250000 chr1D 342437168 342437696 528 True 549.000000 549 85.8180 2176 2709 1 chr1D.!!$R1 533
2 TraesCS1D01G250000 chr1D 238064487 238065199 712 False 359.000000 608 83.5295 242 955 2 chr1D.!!$F1 713
3 TraesCS1D01G250000 chr1A 442125240 442126077 837 True 1314.000000 1314 95.2270 951 1775 1 chr1A.!!$R1 824
4 TraesCS1D01G250000 chr1B 458632999 458634205 1206 True 782.500000 1260 87.9405 995 2360 2 chr1B.!!$R1 1365
5 TraesCS1D01G250000 chr3B 599091851 599092997 1146 True 538.666667 1190 91.6350 1 962 3 chr3B.!!$R1 961
6 TraesCS1D01G250000 chr3A 735746903 735747484 581 False 773.000000 773 90.7380 1 578 1 chr3A.!!$F1 577

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
966 1176 1.102222 TCCGAAAACCAAACCCCACG 61.102 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2512 2784 0.172803 CTCCCGAGGTAAAGACGGTG 59.827 60.0 0.0 0.0 44.34 4.94 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
179 185 4.020617 CCCAAGAGCGCCCTGTCA 62.021 66.667 2.29 0.00 0.00 3.58
510 516 2.800541 CGATGCCCTAGCTCCTGCA 61.801 63.158 6.45 6.45 42.74 4.41
609 616 3.395669 CGTCCTCGGCGAATTTCC 58.604 61.111 12.13 0.00 0.00 3.13
654 661 1.532238 GGGCGGCTTAGAAGGGATT 59.468 57.895 9.56 0.00 0.00 3.01
966 1176 1.102222 TCCGAAAACCAAACCCCACG 61.102 55.000 0.00 0.00 0.00 4.94
967 1177 1.102222 CCGAAAACCAAACCCCACGA 61.102 55.000 0.00 0.00 0.00 4.35
1141 1352 1.541310 CCACCTCTTCCGCTACCACA 61.541 60.000 0.00 0.00 0.00 4.17
1550 1773 1.171308 CGGACGGTTCAGTCTCCTAA 58.829 55.000 3.53 0.00 40.76 2.69
1616 1839 7.817478 CCCGAATTCTGCTTGTGTATATATGTA 59.183 37.037 3.52 0.00 0.00 2.29
1633 1856 8.896320 ATATATGTACGTGCCTGTGAATTTAA 57.104 30.769 0.00 0.00 0.00 1.52
1717 1940 4.921470 TCGTCGAATTGAAATGGAAGAC 57.079 40.909 0.00 0.00 0.00 3.01
1719 1942 3.483574 CGTCGAATTGAAATGGAAGACCG 60.484 47.826 0.00 0.00 39.42 4.79
1782 2005 5.188327 GCTTAATGCAAATTACTCCCTCC 57.812 43.478 0.00 0.00 42.31 4.30
1783 2006 4.261197 GCTTAATGCAAATTACTCCCTCCG 60.261 45.833 0.00 0.00 42.31 4.63
1784 2007 3.366052 AATGCAAATTACTCCCTCCGT 57.634 42.857 0.00 0.00 0.00 4.69
1785 2008 2.871096 TGCAAATTACTCCCTCCGTT 57.129 45.000 0.00 0.00 0.00 4.44
1786 2009 2.706890 TGCAAATTACTCCCTCCGTTC 58.293 47.619 0.00 0.00 0.00 3.95
1787 2010 2.014857 GCAAATTACTCCCTCCGTTCC 58.985 52.381 0.00 0.00 0.00 3.62
1788 2011 2.355818 GCAAATTACTCCCTCCGTTCCT 60.356 50.000 0.00 0.00 0.00 3.36
1789 2012 3.118519 GCAAATTACTCCCTCCGTTCCTA 60.119 47.826 0.00 0.00 0.00 2.94
1790 2013 4.624604 GCAAATTACTCCCTCCGTTCCTAA 60.625 45.833 0.00 0.00 0.00 2.69
1791 2014 5.493809 CAAATTACTCCCTCCGTTCCTAAA 58.506 41.667 0.00 0.00 0.00 1.85
1792 2015 5.970501 AATTACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
1793 2016 7.277396 CAAATTACTCCCTCCGTTCCTAAATA 58.723 38.462 0.00 0.00 0.00 1.40
1794 2017 7.628501 AATTACTCCCTCCGTTCCTAAATAT 57.371 36.000 0.00 0.00 0.00 1.28
1795 2018 7.628501 ATTACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
1796 2019 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
1797 2020 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
1798 2021 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
1799 2022 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
1800 2023 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
1801 2024 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
1802 2025 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
1803 2026 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
1804 2027 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
1805 2028 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
1806 2029 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
1807 2030 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
1859 2082 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
1860 2083 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
1861 2084 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
1862 2085 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
1863 2086 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
1864 2087 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
1865 2088 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
1866 2089 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
1867 2090 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
1868 2091 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
1869 2092 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
1870 2093 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
1871 2094 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
1872 2095 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
1873 2096 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
1874 2097 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
1875 2098 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
1876 2099 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
1877 2100 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
1878 2101 4.460034 TGCTCCGTATGTAGTCACTTGTTA 59.540 41.667 0.00 0.00 0.00 2.41
1879 2102 5.047872 TGCTCCGTATGTAGTCACTTGTTAA 60.048 40.000 0.00 0.00 0.00 2.01
1880 2103 5.865552 GCTCCGTATGTAGTCACTTGTTAAA 59.134 40.000 0.00 0.00 0.00 1.52
1881 2104 6.366877 GCTCCGTATGTAGTCACTTGTTAAAA 59.633 38.462 0.00 0.00 0.00 1.52
1882 2105 7.064253 GCTCCGTATGTAGTCACTTGTTAAAAT 59.936 37.037 0.00 0.00 0.00 1.82
1883 2106 8.246908 TCCGTATGTAGTCACTTGTTAAAATG 57.753 34.615 0.00 0.00 0.00 2.32
1884 2107 7.874016 TCCGTATGTAGTCACTTGTTAAAATGT 59.126 33.333 0.00 0.00 0.00 2.71
1885 2108 8.166706 CCGTATGTAGTCACTTGTTAAAATGTC 58.833 37.037 0.00 0.00 0.00 3.06
1886 2109 8.922676 CGTATGTAGTCACTTGTTAAAATGTCT 58.077 33.333 0.00 0.00 0.00 3.41
1893 2116 9.832445 AGTCACTTGTTAAAATGTCTAGAAAGA 57.168 29.630 0.00 0.00 0.00 2.52
1913 2136 9.454859 AGAAAGACAAATATTTAGGAACAGAGG 57.545 33.333 0.00 0.00 0.00 3.69
1914 2137 8.581253 AAAGACAAATATTTAGGAACAGAGGG 57.419 34.615 0.00 0.00 0.00 4.30
1915 2138 7.510675 AGACAAATATTTAGGAACAGAGGGA 57.489 36.000 0.00 0.00 0.00 4.20
1916 2139 7.569240 AGACAAATATTTAGGAACAGAGGGAG 58.431 38.462 0.00 0.00 0.00 4.30
1917 2140 7.182930 AGACAAATATTTAGGAACAGAGGGAGT 59.817 37.037 0.00 0.00 0.00 3.85
1918 2141 7.112779 ACAAATATTTAGGAACAGAGGGAGTG 58.887 38.462 0.00 0.00 0.00 3.51
1919 2142 6.893020 AATATTTAGGAACAGAGGGAGTGT 57.107 37.500 0.00 0.00 0.00 3.55
1920 2143 7.989947 AATATTTAGGAACAGAGGGAGTGTA 57.010 36.000 0.00 0.00 0.00 2.90
1921 2144 8.568617 AATATTTAGGAACAGAGGGAGTGTAT 57.431 34.615 0.00 0.00 0.00 2.29
1922 2145 9.670442 AATATTTAGGAACAGAGGGAGTGTATA 57.330 33.333 0.00 0.00 0.00 1.47
1923 2146 7.989947 ATTTAGGAACAGAGGGAGTGTATAA 57.010 36.000 0.00 0.00 0.00 0.98
1924 2147 7.419711 TTTAGGAACAGAGGGAGTGTATAAG 57.580 40.000 0.00 0.00 0.00 1.73
1932 2155 6.097129 ACAGAGGGAGTGTATAAGTAGAAAGC 59.903 42.308 0.00 0.00 0.00 3.51
1961 2184 4.321156 GGTGCAAGCAATTGATACTTGTGA 60.321 41.667 19.19 8.88 42.20 3.58
1962 2185 5.221880 GTGCAAGCAATTGATACTTGTGAA 58.778 37.500 19.19 8.31 42.20 3.18
1987 2212 5.922960 AATGTTTATGGCTATACCTGGGA 57.077 39.130 0.00 0.00 40.22 4.37
2092 2319 5.745294 GTCACGCGATAAACCAAGAACTATA 59.255 40.000 15.93 0.00 0.00 1.31
2108 2335 3.115390 ACTATAGTGGTGCCATTGGACT 58.885 45.455 6.95 3.38 0.00 3.85
2109 2336 3.523564 ACTATAGTGGTGCCATTGGACTT 59.476 43.478 6.95 0.00 0.00 3.01
2113 2340 0.105760 TGGTGCCATTGGACTTGGTT 60.106 50.000 6.95 0.00 36.57 3.67
2114 2341 1.145945 TGGTGCCATTGGACTTGGTTA 59.854 47.619 6.95 0.00 36.57 2.85
2116 2343 2.630580 GGTGCCATTGGACTTGGTTAAA 59.369 45.455 6.95 0.00 36.57 1.52
2117 2344 3.070302 GGTGCCATTGGACTTGGTTAAAA 59.930 43.478 6.95 0.00 36.57 1.52
2118 2345 4.443598 GGTGCCATTGGACTTGGTTAAAAA 60.444 41.667 6.95 0.00 36.57 1.94
2136 2363 1.616159 AAAATTCAGTGGTGGGACGG 58.384 50.000 0.00 0.00 0.00 4.79
2137 2364 0.768622 AAATTCAGTGGTGGGACGGA 59.231 50.000 0.00 0.00 0.00 4.69
2138 2365 0.324943 AATTCAGTGGTGGGACGGAG 59.675 55.000 0.00 0.00 0.00 4.63
2139 2366 1.553690 ATTCAGTGGTGGGACGGAGG 61.554 60.000 0.00 0.00 0.00 4.30
2140 2367 2.603473 CAGTGGTGGGACGGAGGA 60.603 66.667 0.00 0.00 0.00 3.71
2141 2368 2.203182 AGTGGTGGGACGGAGGAA 59.797 61.111 0.00 0.00 0.00 3.36
2142 2369 1.913762 AGTGGTGGGACGGAGGAAG 60.914 63.158 0.00 0.00 0.00 3.46
2154 2381 5.583854 GGGACGGAGGAAGTAATTTCTAAAC 59.416 44.000 0.00 0.00 36.03 2.01
2164 2391 9.880064 GGAAGTAATTTCTAAACTTGTGACTTC 57.120 33.333 0.00 0.00 38.75 3.01
2167 2394 8.837389 AGTAATTTCTAAACTTGTGACTTCCAC 58.163 33.333 0.00 0.00 45.88 4.02
2191 2418 5.330571 CGACACTACTCGTTAATAACATGCG 60.331 44.000 3.91 0.00 0.00 4.73
2203 2430 1.898330 AACATGCGCCCCCAATTTCC 61.898 55.000 4.18 0.00 0.00 3.13
2206 2433 2.679996 GCGCCCCCAATTTCCAGT 60.680 61.111 0.00 0.00 0.00 4.00
2288 2544 9.309516 GAATTATCTATTTCAGTACGTGGTTGA 57.690 33.333 0.00 0.00 0.00 3.18
2292 2548 6.460781 TCTATTTCAGTACGTGGTTGACAAT 58.539 36.000 0.00 5.26 0.00 2.71
2298 2554 4.450757 CAGTACGTGGTTGACAATGATTGA 59.549 41.667 12.80 0.00 0.00 2.57
2336 2596 6.428465 TCGGTTCAGCTGTCAATTGTTAAATA 59.572 34.615 14.67 0.00 0.00 1.40
2337 2597 6.742718 CGGTTCAGCTGTCAATTGTTAAATAG 59.257 38.462 14.67 0.00 0.00 1.73
2372 2632 1.291588 CTGTCTCCACGAGCAAGCT 59.708 57.895 0.00 0.00 0.00 3.74
2391 2657 1.987855 GACTGGTCGGATGGTCCCA 60.988 63.158 0.00 0.00 31.13 4.37
2394 2660 4.530857 GGTCGGATGGTCCCAGCG 62.531 72.222 0.00 0.00 31.13 5.18
2411 2677 3.905249 GGTCAAAGGTGATCGGGC 58.095 61.111 0.00 0.00 35.80 6.13
2412 2678 1.002624 GGTCAAAGGTGATCGGGCA 60.003 57.895 0.00 0.00 35.80 5.36
2413 2679 0.608035 GGTCAAAGGTGATCGGGCAA 60.608 55.000 0.00 0.00 35.80 4.52
2414 2680 0.521735 GTCAAAGGTGATCGGGCAAC 59.478 55.000 0.00 0.00 35.80 4.17
2415 2681 2.814716 GTCAAAGGTGATCGGGCAACC 61.815 57.143 0.00 0.00 45.53 3.77
2434 2700 3.793797 CCCGACCATGGGTTAAATTTC 57.206 47.619 18.09 0.25 44.76 2.17
2442 2711 3.791953 TGGGTTAAATTTCGGGACAGA 57.208 42.857 0.00 0.00 0.00 3.41
2447 2716 4.392138 GGTTAAATTTCGGGACAGACTCTG 59.608 45.833 4.36 4.36 37.52 3.35
2462 2731 2.279517 CTGCGGCGTAGACATCCC 60.280 66.667 20.69 0.00 27.25 3.85
2470 2739 0.866061 CGTAGACATCCCGAAGTGCG 60.866 60.000 0.00 0.00 40.47 5.34
2485 2754 0.611714 GTGCGGGTTTCCTCTCCTTA 59.388 55.000 0.00 0.00 0.00 2.69
2508 2780 6.881067 AGGTATATGTGTGGCATAGATCAT 57.119 37.500 0.00 0.00 42.68 2.45
2509 2781 7.978099 AGGTATATGTGTGGCATAGATCATA 57.022 36.000 0.00 0.00 42.68 2.15
2510 2782 8.558713 AGGTATATGTGTGGCATAGATCATAT 57.441 34.615 0.00 4.44 42.68 1.78
2511 2783 8.996655 AGGTATATGTGTGGCATAGATCATATT 58.003 33.333 9.86 0.00 42.68 1.28
2512 2784 9.265901 GGTATATGTGTGGCATAGATCATATTC 57.734 37.037 9.86 6.39 42.68 1.75
2513 2785 9.822185 GTATATGTGTGGCATAGATCATATTCA 57.178 33.333 9.86 0.00 42.68 2.57
2526 2798 6.750148 AGATCATATTCACCGTCTTTACCTC 58.250 40.000 0.00 0.00 0.00 3.85
2567 2839 0.611618 TCCATTGTTCGGCCTGCAAT 60.612 50.000 0.00 5.83 33.64 3.56
2585 2857 2.510768 ATGTTCCTTATCGTCCTCGC 57.489 50.000 0.00 0.00 36.96 5.03
2590 2862 1.355563 CTTATCGTCCTCGCTGCGA 59.644 57.895 24.43 24.43 39.02 5.10
2615 2887 0.249868 TTTGCCTGTGTCCTCGACTG 60.250 55.000 0.00 0.00 33.15 3.51
2625 2897 2.167693 TGTCCTCGACTGTGAGTTTGTT 59.832 45.455 0.00 0.00 34.04 2.83
2653 2925 3.755112 TTGATCACCCAACAGTTACGA 57.245 42.857 0.00 0.00 0.00 3.43
2670 2942 2.600173 ATTGGTGTGGTTGGCGGG 60.600 61.111 0.00 0.00 0.00 6.13
2674 2946 2.281900 GTGTGGTTGGCGGGCTTA 60.282 61.111 2.38 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.604378 CTCTTCCTCGGGGCATTGT 59.396 57.895 0.00 0.00 0.00 2.71
403 409 4.966787 GTGGCAGTTTGGGGCGGA 62.967 66.667 0.00 0.00 0.00 5.54
443 449 1.433534 GCAGAGGAGAAGTTCAACGG 58.566 55.000 5.50 0.00 0.00 4.44
609 616 1.999024 GCTCCTCTTTTCTCTTGCTCG 59.001 52.381 0.00 0.00 0.00 5.03
687 694 0.467659 GAGCTAACCGCCTCTCCCTA 60.468 60.000 0.00 0.00 40.39 3.53
922 1131 4.037208 TCAATAACTCCCGAACGTCCTATC 59.963 45.833 0.00 0.00 0.00 2.08
1252 1466 4.760047 CCACTGCCGGGTCCGAAG 62.760 72.222 11.39 10.23 42.83 3.79
1507 1730 1.977293 GATCCCCACCTCAGCAGACC 61.977 65.000 0.00 0.00 0.00 3.85
1550 1773 1.760086 CAGGAGAGAGACGGGGCAT 60.760 63.158 0.00 0.00 0.00 4.40
1616 1839 2.159382 CCCTTAAATTCACAGGCACGT 58.841 47.619 0.00 0.00 0.00 4.49
1717 1940 7.549488 AGAAAATAGAAGGTCTTGTTCATACGG 59.451 37.037 0.00 0.00 0.00 4.02
1775 1998 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
1776 1999 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
1777 2000 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
1778 2001 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
1779 2002 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
1780 2003 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
1781 2004 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
1837 2060 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
1838 2061 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
1839 2062 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
1840 2063 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
1841 2064 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
1842 2065 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
1843 2066 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
1844 2067 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
1845 2068 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
1846 2069 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
1847 2070 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
1848 2071 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
1849 2072 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
1850 2073 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
1851 2074 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
1852 2075 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
1853 2076 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
1854 2077 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
1855 2078 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
1856 2079 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
1857 2080 7.878477 TTTTAACAAGTGACTACATACGGAG 57.122 36.000 0.00 0.00 0.00 4.63
1858 2081 7.874016 ACATTTTAACAAGTGACTACATACGGA 59.126 33.333 0.00 0.00 0.00 4.69
1859 2082 8.025243 ACATTTTAACAAGTGACTACATACGG 57.975 34.615 0.00 0.00 0.00 4.02
1860 2083 8.922676 AGACATTTTAACAAGTGACTACATACG 58.077 33.333 0.00 0.00 0.00 3.06
1867 2090 9.832445 TCTTTCTAGACATTTTAACAAGTGACT 57.168 29.630 0.00 0.00 31.45 3.41
1887 2110 9.454859 CCTCTGTTCCTAAATATTTGTCTTTCT 57.545 33.333 11.05 0.00 0.00 2.52
1888 2111 8.678199 CCCTCTGTTCCTAAATATTTGTCTTTC 58.322 37.037 11.05 0.00 0.00 2.62
1889 2112 8.390921 TCCCTCTGTTCCTAAATATTTGTCTTT 58.609 33.333 11.05 0.00 0.00 2.52
1890 2113 7.928873 TCCCTCTGTTCCTAAATATTTGTCTT 58.071 34.615 11.05 0.00 0.00 3.01
1891 2114 7.182930 ACTCCCTCTGTTCCTAAATATTTGTCT 59.817 37.037 11.05 0.00 0.00 3.41
1892 2115 7.281100 CACTCCCTCTGTTCCTAAATATTTGTC 59.719 40.741 11.05 0.00 0.00 3.18
1893 2116 7.112779 CACTCCCTCTGTTCCTAAATATTTGT 58.887 38.462 11.05 0.00 0.00 2.83
1894 2117 7.112779 ACACTCCCTCTGTTCCTAAATATTTG 58.887 38.462 11.05 1.40 0.00 2.32
1895 2118 7.272144 ACACTCCCTCTGTTCCTAAATATTT 57.728 36.000 5.89 5.89 0.00 1.40
1896 2119 6.893020 ACACTCCCTCTGTTCCTAAATATT 57.107 37.500 0.00 0.00 0.00 1.28
1897 2120 9.670442 TTATACACTCCCTCTGTTCCTAAATAT 57.330 33.333 0.00 0.00 0.00 1.28
1898 2121 9.144298 CTTATACACTCCCTCTGTTCCTAAATA 57.856 37.037 0.00 0.00 0.00 1.40
1899 2122 7.624077 ACTTATACACTCCCTCTGTTCCTAAAT 59.376 37.037 0.00 0.00 0.00 1.40
1900 2123 6.958192 ACTTATACACTCCCTCTGTTCCTAAA 59.042 38.462 0.00 0.00 0.00 1.85
1901 2124 6.500336 ACTTATACACTCCCTCTGTTCCTAA 58.500 40.000 0.00 0.00 0.00 2.69
1902 2125 6.088541 ACTTATACACTCCCTCTGTTCCTA 57.911 41.667 0.00 0.00 0.00 2.94
1903 2126 4.949121 ACTTATACACTCCCTCTGTTCCT 58.051 43.478 0.00 0.00 0.00 3.36
1904 2127 6.127793 TCTACTTATACACTCCCTCTGTTCC 58.872 44.000 0.00 0.00 0.00 3.62
1905 2128 7.642082 TTCTACTTATACACTCCCTCTGTTC 57.358 40.000 0.00 0.00 0.00 3.18
1906 2129 7.363968 GCTTTCTACTTATACACTCCCTCTGTT 60.364 40.741 0.00 0.00 0.00 3.16
1907 2130 6.097129 GCTTTCTACTTATACACTCCCTCTGT 59.903 42.308 0.00 0.00 0.00 3.41
1908 2131 6.096987 TGCTTTCTACTTATACACTCCCTCTG 59.903 42.308 0.00 0.00 0.00 3.35
1909 2132 6.195700 TGCTTTCTACTTATACACTCCCTCT 58.804 40.000 0.00 0.00 0.00 3.69
1910 2133 6.097129 ACTGCTTTCTACTTATACACTCCCTC 59.903 42.308 0.00 0.00 0.00 4.30
1911 2134 5.958987 ACTGCTTTCTACTTATACACTCCCT 59.041 40.000 0.00 0.00 0.00 4.20
1912 2135 6.223351 ACTGCTTTCTACTTATACACTCCC 57.777 41.667 0.00 0.00 0.00 4.30
1913 2136 7.064728 CCAAACTGCTTTCTACTTATACACTCC 59.935 40.741 0.00 0.00 0.00 3.85
1914 2137 7.603024 ACCAAACTGCTTTCTACTTATACACTC 59.397 37.037 0.00 0.00 0.00 3.51
1915 2138 7.387948 CACCAAACTGCTTTCTACTTATACACT 59.612 37.037 0.00 0.00 0.00 3.55
1916 2139 7.519002 CACCAAACTGCTTTCTACTTATACAC 58.481 38.462 0.00 0.00 0.00 2.90
1917 2140 6.148811 GCACCAAACTGCTTTCTACTTATACA 59.851 38.462 0.00 0.00 34.06 2.29
1918 2141 6.148811 TGCACCAAACTGCTTTCTACTTATAC 59.851 38.462 0.00 0.00 38.07 1.47
1919 2142 6.234920 TGCACCAAACTGCTTTCTACTTATA 58.765 36.000 0.00 0.00 38.07 0.98
1920 2143 5.070001 TGCACCAAACTGCTTTCTACTTAT 58.930 37.500 0.00 0.00 38.07 1.73
1921 2144 4.456535 TGCACCAAACTGCTTTCTACTTA 58.543 39.130 0.00 0.00 38.07 2.24
1922 2145 3.287222 TGCACCAAACTGCTTTCTACTT 58.713 40.909 0.00 0.00 38.07 2.24
1923 2146 2.930950 TGCACCAAACTGCTTTCTACT 58.069 42.857 0.00 0.00 38.07 2.57
1924 2147 3.632189 CTTGCACCAAACTGCTTTCTAC 58.368 45.455 0.00 0.00 38.07 2.59
1932 2155 2.823984 TCAATTGCTTGCACCAAACTG 58.176 42.857 0.00 4.83 32.11 3.16
1962 2185 7.129425 TCCCAGGTATAGCCATAAACATTTTT 58.871 34.615 0.00 0.00 40.61 1.94
1967 2190 4.724798 AGTTCCCAGGTATAGCCATAAACA 59.275 41.667 0.00 0.00 40.61 2.83
1968 2191 5.306114 AGTTCCCAGGTATAGCCATAAAC 57.694 43.478 0.00 0.00 40.61 2.01
1981 2206 1.308069 CGACCATGCAAGTTCCCAGG 61.308 60.000 0.00 0.00 0.00 4.45
1987 2212 2.297701 ACAGTTTCGACCATGCAAGTT 58.702 42.857 0.00 0.00 0.00 2.66
2073 2299 6.018994 CACCACTATAGTTCTTGGTTTATCGC 60.019 42.308 9.48 0.00 40.51 4.58
2074 2300 6.018994 GCACCACTATAGTTCTTGGTTTATCG 60.019 42.308 9.48 1.57 40.51 2.92
2092 2319 0.540365 CCAAGTCCAATGGCACCACT 60.540 55.000 0.00 0.00 0.00 4.00
2116 2343 1.960689 CCGTCCCACCACTGAATTTTT 59.039 47.619 0.00 0.00 0.00 1.94
2117 2344 1.144093 TCCGTCCCACCACTGAATTTT 59.856 47.619 0.00 0.00 0.00 1.82
2118 2345 0.768622 TCCGTCCCACCACTGAATTT 59.231 50.000 0.00 0.00 0.00 1.82
2119 2346 0.324943 CTCCGTCCCACCACTGAATT 59.675 55.000 0.00 0.00 0.00 2.17
2120 2347 1.553690 CCTCCGTCCCACCACTGAAT 61.554 60.000 0.00 0.00 0.00 2.57
2124 2351 1.913762 CTTCCTCCGTCCCACCACT 60.914 63.158 0.00 0.00 0.00 4.00
2125 2352 0.901580 TACTTCCTCCGTCCCACCAC 60.902 60.000 0.00 0.00 0.00 4.16
2126 2353 0.178926 TTACTTCCTCCGTCCCACCA 60.179 55.000 0.00 0.00 0.00 4.17
2127 2354 1.201424 ATTACTTCCTCCGTCCCACC 58.799 55.000 0.00 0.00 0.00 4.61
2129 2356 3.178865 AGAAATTACTTCCTCCGTCCCA 58.821 45.455 0.00 0.00 34.21 4.37
2130 2357 3.908643 AGAAATTACTTCCTCCGTCCC 57.091 47.619 0.00 0.00 34.21 4.46
2131 2358 6.404708 AGTTTAGAAATTACTTCCTCCGTCC 58.595 40.000 0.00 0.00 34.21 4.79
2132 2359 7.387122 ACAAGTTTAGAAATTACTTCCTCCGTC 59.613 37.037 0.00 0.00 34.21 4.79
2134 2361 7.386848 TCACAAGTTTAGAAATTACTTCCTCCG 59.613 37.037 0.00 0.00 34.21 4.63
2135 2362 8.504815 GTCACAAGTTTAGAAATTACTTCCTCC 58.495 37.037 0.00 0.00 34.21 4.30
2136 2363 9.274206 AGTCACAAGTTTAGAAATTACTTCCTC 57.726 33.333 0.00 0.00 34.21 3.71
2137 2364 9.628500 AAGTCACAAGTTTAGAAATTACTTCCT 57.372 29.630 0.00 0.00 34.21 3.36
2138 2365 9.880064 GAAGTCACAAGTTTAGAAATTACTTCC 57.120 33.333 0.00 0.00 35.32 3.46
2139 2366 9.880064 GGAAGTCACAAGTTTAGAAATTACTTC 57.120 33.333 0.00 0.00 38.75 3.01
2140 2367 9.403583 TGGAAGTCACAAGTTTAGAAATTACTT 57.596 29.630 0.00 0.00 32.60 2.24
2141 2368 8.837389 GTGGAAGTCACAAGTTTAGAAATTACT 58.163 33.333 0.00 0.00 45.39 2.24
2142 2369 7.797123 CGTGGAAGTCACAAGTTTAGAAATTAC 59.203 37.037 0.00 0.00 46.36 1.89
2154 2381 2.225068 AGTGTCGTGGAAGTCACAAG 57.775 50.000 0.00 0.00 46.36 3.16
2167 2394 5.330571 CGCATGTTATTAACGAGTAGTGTCG 60.331 44.000 2.30 0.00 45.76 4.35
2191 2418 1.182667 GTGTACTGGAAATTGGGGGC 58.817 55.000 0.00 0.00 0.00 5.80
2203 2430 6.560253 ACTGAGCCAAAATTTAGTGTACTG 57.440 37.500 0.00 0.00 0.00 2.74
2206 2433 8.630054 ACATTACTGAGCCAAAATTTAGTGTA 57.370 30.769 0.00 0.00 0.00 2.90
2265 2521 7.604549 TGTCAACCACGTACTGAAATAGATAA 58.395 34.615 0.00 0.00 0.00 1.75
2268 2524 5.456548 TGTCAACCACGTACTGAAATAGA 57.543 39.130 0.00 0.00 0.00 1.98
2336 2596 6.867293 GGAGACAGTCGTTCTTTATACAAACT 59.133 38.462 0.00 0.00 0.00 2.66
2337 2597 6.643770 TGGAGACAGTCGTTCTTTATACAAAC 59.356 38.462 0.00 0.00 35.01 2.93
2372 2632 1.987855 GGGACCATCCGACCAGTCA 60.988 63.158 0.00 0.00 37.43 3.41
2391 2657 1.079127 CCGATCACCTTTGACCGCT 60.079 57.895 0.00 0.00 37.45 5.52
2394 2660 0.608035 TTGCCCGATCACCTTTGACC 60.608 55.000 0.00 0.00 33.38 4.02
2415 2681 2.098443 CCGAAATTTAACCCATGGTCGG 59.902 50.000 18.30 18.30 33.12 4.79
2416 2682 2.098443 CCCGAAATTTAACCCATGGTCG 59.902 50.000 11.73 10.41 33.12 4.79
2417 2683 3.129813 GTCCCGAAATTTAACCCATGGTC 59.870 47.826 11.73 0.00 33.12 4.02
2418 2684 3.093814 GTCCCGAAATTTAACCCATGGT 58.906 45.455 11.73 0.00 37.65 3.55
2419 2685 3.093057 TGTCCCGAAATTTAACCCATGG 58.907 45.455 4.14 4.14 0.00 3.66
2422 2688 3.073356 AGTCTGTCCCGAAATTTAACCCA 59.927 43.478 0.00 0.00 0.00 4.51
2434 2700 4.803426 GCCGCAGAGTCTGTCCCG 62.803 72.222 21.06 15.37 33.43 5.14
2442 2711 1.433879 GATGTCTACGCCGCAGAGT 59.566 57.895 0.00 0.00 0.00 3.24
2447 2716 3.420214 TTCGGGATGTCTACGCCGC 62.420 63.158 0.00 0.00 0.00 6.53
2462 2731 1.004918 AGAGGAAACCCGCACTTCG 60.005 57.895 0.00 0.00 38.08 3.79
2470 2739 5.845065 ACATATACCTAAGGAGAGGAAACCC 59.155 44.000 0.00 0.00 39.15 4.11
2471 2740 6.326843 ACACATATACCTAAGGAGAGGAAACC 59.673 42.308 0.00 0.00 39.15 3.27
2485 2754 6.881067 ATGATCTATGCCACACATATACCT 57.119 37.500 0.00 0.00 40.48 3.08
2508 2780 2.428171 CCCGAGGTAAAGACGGTGAATA 59.572 50.000 0.00 0.00 44.34 1.75
2509 2781 1.206371 CCCGAGGTAAAGACGGTGAAT 59.794 52.381 0.00 0.00 44.34 2.57
2510 2782 0.604578 CCCGAGGTAAAGACGGTGAA 59.395 55.000 0.00 0.00 44.34 3.18
2511 2783 0.251297 TCCCGAGGTAAAGACGGTGA 60.251 55.000 0.00 0.00 44.34 4.02
2512 2784 0.172803 CTCCCGAGGTAAAGACGGTG 59.827 60.000 0.00 0.00 44.34 4.94
2513 2785 0.969409 CCTCCCGAGGTAAAGACGGT 60.969 60.000 2.31 0.00 44.34 4.83
2526 2798 0.894835 CCAAAAACAATCCCCTCCCG 59.105 55.000 0.00 0.00 0.00 5.14
2561 2833 3.535561 AGGACGATAAGGAACATTGCAG 58.464 45.455 0.00 0.00 0.00 4.41
2567 2839 1.134367 CAGCGAGGACGATAAGGAACA 59.866 52.381 0.00 0.00 42.66 3.18
2585 2857 2.674380 AGGCAAAAGCCCTCGCAG 60.674 61.111 2.33 0.00 37.52 5.18
2590 2862 1.531602 GGACACAGGCAAAAGCCCT 60.532 57.895 2.33 0.00 0.00 5.19
2610 2882 0.307760 GGCCAACAAACTCACAGTCG 59.692 55.000 0.00 0.00 0.00 4.18
2615 2887 2.165437 TCAAACAGGCCAACAAACTCAC 59.835 45.455 5.01 0.00 0.00 3.51
2625 2897 0.187117 TTGGGTGATCAAACAGGCCA 59.813 50.000 5.01 0.00 0.00 5.36
2653 2925 2.600173 CCCGCCAACCACACCAAT 60.600 61.111 0.00 0.00 0.00 3.16
2670 2942 1.883084 CACGGCACCTCGGATAAGC 60.883 63.158 0.00 0.00 0.00 3.09
2674 2946 2.764128 ATCCACGGCACCTCGGAT 60.764 61.111 1.85 1.85 33.31 4.18


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

AutoCloner maintained by Alex Coulton.