Multiple sequence alignment - TraesCS5A01G282500

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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 TraesCS5A01G282500 chr5A 100.000 2531 0 0 1 2531 491300909 491303439 0.000000e+00 4674.0
1 TraesCS5A01G282500 chr5D 90.191 1417 80 19 200 1600 388109011 388110384 0.000000e+00 1792.0
2 TraesCS5A01G282500 chr5D 85.340 648 50 26 1873 2497 388111466 388112091 1.650000e-176 628.0
3 TraesCS5A01G282500 chr5D 91.667 60 4 1 1763 1821 377830429 377830370 5.800000e-12 82.4
4 TraesCS5A01G282500 chr5D 88.889 63 6 1 1726 1787 388110455 388110517 2.700000e-10 76.8
5 TraesCS5A01G282500 chr5B 91.045 938 41 16 870 1787 466844140 466845054 0.000000e+00 1227.0
6 TraesCS5A01G282500 chr5B 90.034 883 55 10 1 877 466843084 466843939 0.000000e+00 1112.0
7 TraesCS5A01G282500 chr5B 90.816 196 15 3 2009 2204 466934072 466934264 2.500000e-65 259.0
8 TraesCS5A01G282500 chr1A 83.914 603 65 14 935 1531 300576953 300577529 4.760000e-152 547.0
9 TraesCS5A01G282500 chr1A 81.077 687 79 22 888 1549 300672527 300673187 3.760000e-138 501.0
10 TraesCS5A01G282500 chr1D 81.168 685 82 25 888 1549 246970767 246970107 8.080000e-140 507.0
11 TraesCS5A01G282500 chr1D 81.607 560 82 12 992 1545 246679967 246679423 6.420000e-121 444.0
12 TraesCS5A01G282500 chr1D 78.151 476 89 12 7 475 311755315 311755782 3.190000e-74 289.0
13 TraesCS5A01G282500 chr1D 89.062 64 5 2 1760 1821 43341509 43341572 7.510000e-11 78.7
14 TraesCS5A01G282500 chr1B 80.491 692 84 30 888 1549 331083924 331084594 1.360000e-132 483.0
15 TraesCS5A01G282500 chr1B 81.410 624 71 22 930 1531 330991408 330992008 3.810000e-128 468.0
16 TraesCS5A01G282500 chr1B 81.528 563 77 16 992 1545 331363495 331364039 2.990000e-119 438.0
17 TraesCS5A01G282500 chr1B 75.067 373 74 12 115 474 520780508 520780874 3.370000e-34 156.0
18 TraesCS5A01G282500 chr1B 94.737 57 2 1 1766 1821 104343766 104343822 1.250000e-13 87.9
19 TraesCS5A01G282500 chr7D 79.332 479 84 11 6 477 509561186 509561656 3.140000e-84 322.0
20 TraesCS5A01G282500 chr7D 77.802 455 81 14 8 450 72935829 72936275 1.930000e-66 263.0
21 TraesCS5A01G282500 chr7D 77.404 416 72 18 10 414 635668954 635669358 7.040000e-56 228.0
22 TraesCS5A01G282500 chr7D 78.495 372 62 15 50 414 636338879 636338519 7.040000e-56 228.0
23 TraesCS5A01G282500 chr7D 91.803 61 4 1 1764 1823 436663764 436663704 1.610000e-12 84.2
24 TraesCS5A01G282500 chr4D 80.269 446 72 12 9 447 58273870 58274306 3.140000e-84 322.0
25 TraesCS5A01G282500 chr7A 77.009 448 86 13 8 447 694020258 694020696 9.050000e-60 241.0
26 TraesCS5A01G282500 chr3D 77.918 317 61 9 138 450 457017247 457017558 3.320000e-44 189.0
27 TraesCS5A01G282500 chr3D 90.164 61 5 1 1762 1821 16614434 16614494 7.510000e-11 78.7
28 TraesCS5A01G282500 chr6D 76.510 298 58 12 183 475 12329567 12329277 4.360000e-33 152.0
29 TraesCS5A01G282500 chr6B 93.103 58 3 1 1765 1821 58059103 58059160 1.610000e-12 84.2
30 TraesCS5A01G282500 chr4A 92.982 57 3 1 1766 1821 621123216 621123160 5.800000e-12 82.4
31 TraesCS5A01G282500 chr3B 88.235 68 7 1 1755 1821 664071838 664071905 2.090000e-11 80.5
32 TraesCS5A01G282500 chr2B 91.525 59 4 1 1764 1821 76099745 76099687 2.090000e-11 80.5


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 TraesCS5A01G282500 chr5A 491300909 491303439 2530 False 4674.000000 4674 100.0000 1 2531 1 chr5A.!!$F1 2530
1 TraesCS5A01G282500 chr5D 388109011 388112091 3080 False 832.266667 1792 88.1400 200 2497 3 chr5D.!!$F1 2297
2 TraesCS5A01G282500 chr5B 466843084 466845054 1970 False 1169.500000 1227 90.5395 1 1787 2 chr5B.!!$F2 1786
3 TraesCS5A01G282500 chr1A 300576953 300577529 576 False 547.000000 547 83.9140 935 1531 1 chr1A.!!$F1 596
4 TraesCS5A01G282500 chr1A 300672527 300673187 660 False 501.000000 501 81.0770 888 1549 1 chr1A.!!$F2 661
5 TraesCS5A01G282500 chr1D 246970107 246970767 660 True 507.000000 507 81.1680 888 1549 1 chr1D.!!$R2 661
6 TraesCS5A01G282500 chr1D 246679423 246679967 544 True 444.000000 444 81.6070 992 1545 1 chr1D.!!$R1 553
7 TraesCS5A01G282500 chr1B 331083924 331084594 670 False 483.000000 483 80.4910 888 1549 1 chr1B.!!$F3 661
8 TraesCS5A01G282500 chr1B 330991408 330992008 600 False 468.000000 468 81.4100 930 1531 1 chr1B.!!$F2 601
9 TraesCS5A01G282500 chr1B 331363495 331364039 544 False 438.000000 438 81.5280 992 1545 1 chr1B.!!$F4 553


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
297 302 0.246635 CTTCCCGGGATTCGCGATAT 59.753 55.0 27.48 6.56 42.31 1.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2131 3354 0.109458 TGAAGCGTCGTCGTTGCTAT 60.109 50.0 12.9 5.53 38.17 2.97 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
52 53 0.948623 TCGGACGGATGCAACACTTG 60.949 55.000 0.00 0.00 0.00 3.16
63 67 4.250116 TGCAACACTTGTTTGAGTTTGT 57.750 36.364 0.00 0.00 35.83 2.83
76 80 3.038280 TGAGTTTGTCTTCTGGTCTCCA 58.962 45.455 0.00 0.00 0.00 3.86
91 96 3.516615 GTCTCCAATCCTCTTGAGTTCG 58.483 50.000 0.00 0.00 0.00 3.95
115 120 3.181490 CCAATTGGACATAGTCGACTCGA 60.181 47.826 23.89 5.80 37.39 4.04
135 140 3.523806 GGAGCTCCGGCATAGATTC 57.476 57.895 19.06 0.00 41.70 2.52
164 169 2.568509 CTCCTTGGGACGGTAAGGTTAA 59.431 50.000 7.79 0.00 43.14 2.01
169 174 2.710471 TGGGACGGTAAGGTTAAGGTTT 59.290 45.455 0.00 0.00 0.00 3.27
194 199 0.589729 CGTGTGGCGATATTTGCTGC 60.590 55.000 0.00 0.00 44.77 5.25
237 242 1.604693 GGGTTCAATGACGACGAGTGT 60.605 52.381 0.00 0.00 0.00 3.55
243 248 1.244697 ATGACGACGAGTGTGGCTCT 61.245 55.000 0.00 0.00 41.98 4.09
286 291 2.434359 GCACGAAGACTTCCCGGG 60.434 66.667 16.85 16.85 0.00 5.73
287 292 2.939261 GCACGAAGACTTCCCGGGA 61.939 63.158 22.63 22.63 0.00 5.14
288 293 1.898154 CACGAAGACTTCCCGGGAT 59.102 57.895 27.48 11.07 0.00 3.85
291 296 0.527817 CGAAGACTTCCCGGGATTCG 60.528 60.000 31.62 31.62 38.88 3.34
292 297 0.810426 GAAGACTTCCCGGGATTCGC 60.810 60.000 27.48 16.59 37.59 4.70
293 298 2.573609 AAGACTTCCCGGGATTCGCG 62.574 60.000 27.48 15.46 39.48 5.87
294 299 3.072468 ACTTCCCGGGATTCGCGA 61.072 61.111 27.48 3.71 42.31 5.87
295 300 2.365095 GACTTCCCGGGATTCGCGAT 62.365 60.000 27.48 4.56 42.31 4.58
297 302 0.246635 CTTCCCGGGATTCGCGATAT 59.753 55.000 27.48 6.56 42.31 1.63
298 303 1.475280 CTTCCCGGGATTCGCGATATA 59.525 52.381 27.48 3.61 42.31 0.86
299 304 1.548081 TCCCGGGATTCGCGATATAA 58.452 50.000 22.63 0.00 42.31 0.98
300 305 2.104967 TCCCGGGATTCGCGATATAAT 58.895 47.619 22.63 0.00 42.31 1.28
301 306 2.498481 TCCCGGGATTCGCGATATAATT 59.502 45.455 22.63 0.00 42.31 1.40
302 307 3.055675 TCCCGGGATTCGCGATATAATTT 60.056 43.478 22.63 0.00 42.31 1.82
331 336 1.518774 GATAGGGGAACGGCGACAA 59.481 57.895 16.62 0.00 0.00 3.18
361 366 3.123620 GGCTCGTTCTGGCAGCAG 61.124 66.667 10.34 3.44 34.62 4.24
363 368 2.675056 GCTCGTTCTGGCAGCAGTG 61.675 63.158 10.34 5.61 33.06 3.66
374 379 1.724582 GCAGCAGTGGTGGTCGTTTT 61.725 55.000 22.98 0.00 29.64 2.43
376 381 1.101049 AGCAGTGGTGGTCGTTTTGG 61.101 55.000 0.00 0.00 0.00 3.28
455 460 9.967346 TCGATAAACTTTGATAATAGACCTGAG 57.033 33.333 0.00 0.00 0.00 3.35
466 471 7.769044 TGATAATAGACCTGAGTTACTTTTGCC 59.231 37.037 0.00 0.00 0.00 4.52
559 566 3.642377 TGATGCCCAAACCCATTCATATG 59.358 43.478 0.00 0.00 0.00 1.78
590 597 2.677836 GCCGATCAATCAGCTTTGTGTA 59.322 45.455 0.00 0.00 0.00 2.90
591 598 3.485877 GCCGATCAATCAGCTTTGTGTAC 60.486 47.826 0.00 0.00 0.00 2.90
592 599 3.935203 CCGATCAATCAGCTTTGTGTACT 59.065 43.478 0.00 0.00 0.00 2.73
721 728 3.001406 AGGTACACTCGGGGCCAC 61.001 66.667 4.39 0.00 0.00 5.01
782 789 4.701651 TCTTACTCGTCAAATTCCCTCGTA 59.298 41.667 0.00 0.00 0.00 3.43
783 790 3.227810 ACTCGTCAAATTCCCTCGTAC 57.772 47.619 0.00 0.00 0.00 3.67
784 791 2.824341 ACTCGTCAAATTCCCTCGTACT 59.176 45.455 0.00 0.00 0.00 2.73
914 1139 6.380190 CCTATATAAACTCGTCACCAGTAGC 58.620 44.000 0.00 0.00 0.00 3.58
988 1228 2.186384 CAGGCAGGAGGAGCTTCG 59.814 66.667 0.00 0.00 0.00 3.79
1654 1942 2.490328 ATGCACGTTTGAAGTGTTGG 57.510 45.000 0.00 0.00 41.36 3.77
1678 1966 1.532090 CGTTGCTAATCTCTCGAGCGT 60.532 52.381 7.81 0.00 39.14 5.07
1682 1970 3.203716 TGCTAATCTCTCGAGCGTTAGA 58.796 45.455 23.55 16.01 39.14 2.10
1692 1980 8.242085 TCTCTCGAGCGTTAGATACTTAATAG 57.758 38.462 7.81 0.00 0.00 1.73
1693 1981 7.871973 TCTCTCGAGCGTTAGATACTTAATAGT 59.128 37.037 7.81 0.00 38.44 2.12
1694 1982 9.138062 CTCTCGAGCGTTAGATACTTAATAGTA 57.862 37.037 7.81 0.00 40.96 1.82
1701 1989 9.817365 GCGTTAGATACTTAATAGTATGTCGAA 57.183 33.333 2.74 0.00 45.43 3.71
1714 2002 8.713737 ATAGTATGTCGAATACGTATAGCAGA 57.286 34.615 8.83 3.56 40.69 4.26
1715 2003 7.430992 AGTATGTCGAATACGTATAGCAGAA 57.569 36.000 8.83 0.00 40.69 3.02
1716 2004 8.041829 AGTATGTCGAATACGTATAGCAGAAT 57.958 34.615 8.83 2.20 40.69 2.40
1717 2005 9.159364 AGTATGTCGAATACGTATAGCAGAATA 57.841 33.333 8.83 1.30 40.69 1.75
1718 2006 9.764870 GTATGTCGAATACGTATAGCAGAATAA 57.235 33.333 8.83 0.00 40.69 1.40
1720 2008 9.856488 ATGTCGAATACGTATAGCAGAATAAAT 57.144 29.630 8.83 0.00 40.69 1.40
1721 2009 9.687210 TGTCGAATACGTATAGCAGAATAAATT 57.313 29.630 8.83 0.00 40.69 1.82
1722 2010 9.939047 GTCGAATACGTATAGCAGAATAAATTG 57.061 33.333 8.83 0.00 40.69 2.32
1723 2011 9.135843 TCGAATACGTATAGCAGAATAAATTGG 57.864 33.333 8.83 0.00 40.69 3.16
1724 2012 8.380644 CGAATACGTATAGCAGAATAAATTGGG 58.619 37.037 8.83 0.00 34.56 4.12
1754 2042 6.824958 ATTTACCTGTATGGATGGTAGTGT 57.175 37.500 0.00 0.00 37.59 3.55
1766 2054 4.821805 GGATGGTAGTGTGGGTTTATCATG 59.178 45.833 0.00 0.00 0.00 3.07
1767 2055 4.919774 TGGTAGTGTGGGTTTATCATGT 57.080 40.909 0.00 0.00 0.00 3.21
1768 2056 6.408776 GGATGGTAGTGTGGGTTTATCATGTA 60.409 42.308 0.00 0.00 0.00 2.29
1769 2057 5.736813 TGGTAGTGTGGGTTTATCATGTAC 58.263 41.667 0.00 0.00 0.00 2.90
1770 2058 5.486063 TGGTAGTGTGGGTTTATCATGTACT 59.514 40.000 0.00 0.00 0.00 2.73
1771 2059 6.047231 GGTAGTGTGGGTTTATCATGTACTC 58.953 44.000 0.00 0.00 0.00 2.59
1772 2060 5.099042 AGTGTGGGTTTATCATGTACTCC 57.901 43.478 0.00 0.00 0.00 3.85
1773 2061 4.534500 AGTGTGGGTTTATCATGTACTCCA 59.466 41.667 0.00 0.00 0.00 3.86
1774 2062 4.634443 GTGTGGGTTTATCATGTACTCCAC 59.366 45.833 14.11 14.11 42.49 4.02
1775 2063 4.196971 GTGGGTTTATCATGTACTCCACC 58.803 47.826 0.00 4.57 37.89 4.61
1776 2064 3.201266 TGGGTTTATCATGTACTCCACCC 59.799 47.826 11.38 11.38 42.73 4.61
1777 2065 3.463944 GGTTTATCATGTACTCCACCCG 58.536 50.000 0.00 0.00 0.00 5.28
1778 2066 3.118519 GGTTTATCATGTACTCCACCCGT 60.119 47.826 0.00 0.00 0.00 5.28
1779 2067 4.117685 GTTTATCATGTACTCCACCCGTC 58.882 47.826 0.00 0.00 0.00 4.79
1780 2068 2.160721 ATCATGTACTCCACCCGTCT 57.839 50.000 0.00 0.00 0.00 4.18
1781 2069 1.471119 TCATGTACTCCACCCGTCTC 58.529 55.000 0.00 0.00 0.00 3.36
1782 2070 1.182667 CATGTACTCCACCCGTCTCA 58.817 55.000 0.00 0.00 0.00 3.27
1783 2071 1.548719 CATGTACTCCACCCGTCTCAA 59.451 52.381 0.00 0.00 0.00 3.02
1784 2072 1.707106 TGTACTCCACCCGTCTCAAA 58.293 50.000 0.00 0.00 0.00 2.69
1785 2073 2.040939 TGTACTCCACCCGTCTCAAAA 58.959 47.619 0.00 0.00 0.00 2.44
1786 2074 2.635915 TGTACTCCACCCGTCTCAAAAT 59.364 45.455 0.00 0.00 0.00 1.82
1787 2075 2.951229 ACTCCACCCGTCTCAAAATT 57.049 45.000 0.00 0.00 0.00 1.82
1788 2076 2.779506 ACTCCACCCGTCTCAAAATTC 58.220 47.619 0.00 0.00 0.00 2.17
1789 2077 2.372172 ACTCCACCCGTCTCAAAATTCT 59.628 45.455 0.00 0.00 0.00 2.40
1790 2078 2.744202 CTCCACCCGTCTCAAAATTCTG 59.256 50.000 0.00 0.00 0.00 3.02
1791 2079 2.105821 TCCACCCGTCTCAAAATTCTGT 59.894 45.455 0.00 0.00 0.00 3.41
1792 2080 2.884639 CCACCCGTCTCAAAATTCTGTT 59.115 45.455 0.00 0.00 0.00 3.16
1793 2081 3.317993 CCACCCGTCTCAAAATTCTGTTT 59.682 43.478 0.00 0.00 0.00 2.83
1794 2082 4.202111 CCACCCGTCTCAAAATTCTGTTTT 60.202 41.667 0.00 0.00 0.00 2.43
1795 2083 5.009210 CCACCCGTCTCAAAATTCTGTTTTA 59.991 40.000 0.00 0.00 0.00 1.52
1796 2084 6.460399 CCACCCGTCTCAAAATTCTGTTTTAA 60.460 38.462 0.00 0.00 0.00 1.52
1797 2085 6.975772 CACCCGTCTCAAAATTCTGTTTTAAA 59.024 34.615 0.00 0.00 0.00 1.52
1798 2086 7.651704 CACCCGTCTCAAAATTCTGTTTTAAAT 59.348 33.333 0.00 0.00 0.00 1.40
1799 2087 8.201464 ACCCGTCTCAAAATTCTGTTTTAAATT 58.799 29.630 0.00 0.00 0.00 1.82
1800 2088 9.040939 CCCGTCTCAAAATTCTGTTTTAAATTT 57.959 29.630 0.00 0.00 36.81 1.82
1801 2089 9.848172 CCGTCTCAAAATTCTGTTTTAAATTTG 57.152 29.630 0.00 0.00 35.74 2.32
1823 2111 8.601845 TTTGTCTAAATACGGATGTATCATGG 57.398 34.615 0.00 0.00 40.42 3.66
1824 2112 7.533289 TGTCTAAATACGGATGTATCATGGA 57.467 36.000 0.00 0.00 40.42 3.41
1825 2113 7.602753 TGTCTAAATACGGATGTATCATGGAG 58.397 38.462 0.00 0.00 40.42 3.86
1826 2114 7.036220 GTCTAAATACGGATGTATCATGGAGG 58.964 42.308 0.00 0.00 40.42 4.30
1827 2115 6.951778 TCTAAATACGGATGTATCATGGAGGA 59.048 38.462 0.00 0.00 40.42 3.71
1828 2116 6.433847 AAATACGGATGTATCATGGAGGAA 57.566 37.500 0.00 0.00 40.42 3.36
1851 2139 5.243207 AGTATTCGTCTCCGTTCCAAAATT 58.757 37.500 0.00 0.00 35.01 1.82
1855 2143 5.789710 TCGTCTCCGTTCCAAAATTAATC 57.210 39.130 0.00 0.00 35.01 1.75
1861 2149 7.865889 GTCTCCGTTCCAAAATTAATCAAAGTT 59.134 33.333 0.00 0.00 0.00 2.66
1971 3189 3.323751 AAAATGCCTCATGTTTGCTCC 57.676 42.857 0.00 0.00 0.00 4.70
1976 3194 0.967380 CCTCATGTTTGCTCCACCCC 60.967 60.000 0.00 0.00 0.00 4.95
1978 3196 1.303236 CATGTTTGCTCCACCCCGA 60.303 57.895 0.00 0.00 0.00 5.14
1988 3206 1.182385 TCCACCCCGACAAAATTGCC 61.182 55.000 0.00 0.00 0.00 4.52
1994 3212 1.184970 CCGACAAAATTGCCCCACCT 61.185 55.000 0.00 0.00 0.00 4.00
2001 3219 4.597075 ACAAAATTGCCCCACCTTTATTCT 59.403 37.500 0.00 0.00 0.00 2.40
2036 3254 7.961326 AATACCTACATTTCTCTTGCCAATT 57.039 32.000 0.00 0.00 0.00 2.32
2043 3261 7.008021 ACATTTCTCTTGCCAATTGGTAAAT 57.992 32.000 25.47 14.67 39.29 1.40
2090 3313 3.790089 AGTGAAAGGGTTCTAGGGTTG 57.210 47.619 0.00 0.00 34.60 3.77
2092 3315 3.720002 AGTGAAAGGGTTCTAGGGTTGAA 59.280 43.478 0.00 0.00 34.60 2.69
2131 3354 2.159156 ACATGGCGATGTTAGCTCGTAA 60.159 45.455 8.73 0.00 40.05 3.18
2132 3355 2.882927 TGGCGATGTTAGCTCGTAAT 57.117 45.000 0.00 0.00 38.37 1.89
2133 3356 3.994204 TGGCGATGTTAGCTCGTAATA 57.006 42.857 0.00 0.00 38.37 0.98
2134 3357 3.897325 TGGCGATGTTAGCTCGTAATAG 58.103 45.455 0.00 0.00 38.37 1.73
2135 3358 2.662156 GGCGATGTTAGCTCGTAATAGC 59.338 50.000 0.00 0.00 43.11 2.97
2188 3413 1.678360 CAATCGCACAAGCTCACAAC 58.322 50.000 0.00 0.00 39.10 3.32
2190 3415 0.599991 ATCGCACAAGCTCACAACGA 60.600 50.000 0.00 0.00 39.10 3.85
2195 3420 1.603802 CACAAGCTCACAACGATGGTT 59.396 47.619 0.00 0.00 36.63 3.67
2232 3458 0.603065 GCAAGAAATTTGAGCGGGGT 59.397 50.000 0.00 0.00 0.00 4.95
2233 3459 1.669795 GCAAGAAATTTGAGCGGGGTG 60.670 52.381 0.00 0.00 0.00 4.61
2245 3471 2.763215 GGGGTGGCAAGGATGTGA 59.237 61.111 0.00 0.00 0.00 3.58
2251 3477 0.622136 TGGCAAGGATGTGAGATGCT 59.378 50.000 0.00 0.00 37.20 3.79
2262 3488 1.266867 TGAGATGCTGCCTGGTGCTA 61.267 55.000 13.23 3.15 42.00 3.49
2269 3495 1.123077 CTGCCTGGTGCTATAGGACA 58.877 55.000 23.76 10.60 42.00 4.02
2270 3496 1.486310 CTGCCTGGTGCTATAGGACAA 59.514 52.381 23.76 13.57 42.00 3.18
2286 3512 1.985895 GACAAAGGGAGGGAGGAGAAA 59.014 52.381 0.00 0.00 0.00 2.52
2295 3521 3.264450 GGAGGGAGGAGAAAACAAGATCA 59.736 47.826 0.00 0.00 0.00 2.92
2311 3537 2.828520 AGATCACACGACCTCTGTTGAT 59.171 45.455 0.00 0.00 0.00 2.57
2312 3538 3.259374 AGATCACACGACCTCTGTTGATT 59.741 43.478 0.00 0.00 0.00 2.57
2313 3539 3.469008 TCACACGACCTCTGTTGATTT 57.531 42.857 0.00 0.00 0.00 2.17
2314 3540 3.804036 TCACACGACCTCTGTTGATTTT 58.196 40.909 0.00 0.00 0.00 1.82
2447 3683 9.885934 GAGAGAAAGAAAGAACTTATGGTTTTC 57.114 33.333 0.00 0.00 38.41 2.29
2462 3698 6.605471 ATGGTTTTCTATTTTGAGGGGAAC 57.395 37.500 0.00 0.00 0.00 3.62
2463 3699 5.711698 TGGTTTTCTATTTTGAGGGGAACT 58.288 37.500 0.00 0.00 0.00 3.01
2465 3701 6.041523 TGGTTTTCTATTTTGAGGGGAACTTG 59.958 38.462 0.00 0.00 0.00 3.16
2466 3702 6.041637 GGTTTTCTATTTTGAGGGGAACTTGT 59.958 38.462 0.00 0.00 0.00 3.16
2467 3703 7.418597 GGTTTTCTATTTTGAGGGGAACTTGTT 60.419 37.037 0.00 0.00 0.00 2.83
2469 3705 7.669089 TTCTATTTTGAGGGGAACTTGTTTT 57.331 32.000 0.00 0.00 0.00 2.43
2523 3759 9.676861 AAAAGGTTTATTTAGGCTATACTCGTT 57.323 29.630 0.00 0.00 0.00 3.85
2525 3761 9.978044 AAGGTTTATTTAGGCTATACTCGTTAG 57.022 33.333 0.00 0.00 0.00 2.34
2526 3762 8.583296 AGGTTTATTTAGGCTATACTCGTTAGG 58.417 37.037 0.00 0.00 0.00 2.69
2527 3763 7.816513 GGTTTATTTAGGCTATACTCGTTAGGG 59.183 40.741 0.00 0.00 0.00 3.53
2528 3764 8.363390 GTTTATTTAGGCTATACTCGTTAGGGT 58.637 37.037 0.00 0.00 34.06 4.34
2529 3765 6.990908 ATTTAGGCTATACTCGTTAGGGTT 57.009 37.500 0.00 0.00 30.72 4.11
2530 3766 6.796785 TTTAGGCTATACTCGTTAGGGTTT 57.203 37.500 0.00 0.00 30.72 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.200716 CACCGCACTTACGAGGACTAA 59.799 52.381 0.00 0.00 34.06 2.24
52 53 4.273724 GGAGACCAGAAGACAAACTCAAAC 59.726 45.833 0.00 0.00 0.00 2.93
63 67 3.481559 AGAGGATTGGAGACCAGAAGA 57.518 47.619 0.00 0.00 33.81 2.87
76 80 4.559862 ATTGGACGAACTCAAGAGGATT 57.440 40.909 1.73 0.00 0.00 3.01
135 140 1.225704 GTCCCAAGGAGATGGCAGG 59.774 63.158 0.00 0.00 39.26 4.85
164 169 1.300697 GCCACACGACGAGAAACCT 60.301 57.895 0.00 0.00 0.00 3.50
194 199 3.877559 TGAATACATCTGAAGCACCTGG 58.122 45.455 0.00 0.00 0.00 4.45
254 259 2.033448 TGCACGTGCCCCTAAAGG 59.967 61.111 35.72 0.00 41.18 3.11
286 291 4.550255 GCCGGCTAAATTATATCGCGAATC 60.550 45.833 22.15 0.00 0.00 2.52
287 292 3.308866 GCCGGCTAAATTATATCGCGAAT 59.691 43.478 22.15 10.88 0.00 3.34
288 293 2.669434 GCCGGCTAAATTATATCGCGAA 59.331 45.455 22.15 2.68 0.00 4.70
291 296 2.608090 GGAGCCGGCTAAATTATATCGC 59.392 50.000 32.97 12.23 0.00 4.58
292 297 2.858344 CGGAGCCGGCTAAATTATATCG 59.142 50.000 32.97 16.90 35.56 2.92
293 298 4.119442 TCGGAGCCGGCTAAATTATATC 57.881 45.455 32.97 13.92 40.25 1.63
294 299 4.755266 ATCGGAGCCGGCTAAATTATAT 57.245 40.909 32.97 13.18 40.25 0.86
295 300 4.098960 CCTATCGGAGCCGGCTAAATTATA 59.901 45.833 32.97 20.08 40.25 0.98
297 302 2.232941 CCTATCGGAGCCGGCTAAATTA 59.767 50.000 32.97 17.70 40.25 1.40
298 303 1.002087 CCTATCGGAGCCGGCTAAATT 59.998 52.381 32.97 17.50 40.25 1.82
299 304 0.608640 CCTATCGGAGCCGGCTAAAT 59.391 55.000 32.97 23.98 40.25 1.40
300 305 1.469335 CCCTATCGGAGCCGGCTAAA 61.469 60.000 32.97 18.50 40.25 1.85
301 306 1.906824 CCCTATCGGAGCCGGCTAA 60.907 63.158 32.97 18.91 40.25 3.09
302 307 2.282958 CCCTATCGGAGCCGGCTA 60.283 66.667 32.97 15.82 40.25 3.93
360 365 0.034863 ACACCAAAACGACCACCACT 60.035 50.000 0.00 0.00 0.00 4.00
361 366 0.379316 GACACCAAAACGACCACCAC 59.621 55.000 0.00 0.00 0.00 4.16
363 368 1.064952 CAAGACACCAAAACGACCACC 59.935 52.381 0.00 0.00 0.00 4.61
374 379 1.924731 ATCGAGACTCCAAGACACCA 58.075 50.000 0.00 0.00 0.00 4.17
376 381 9.915629 ATAAATTATATCGAGACTCCAAGACAC 57.084 33.333 0.00 0.00 0.00 3.67
559 566 1.064654 GATTGATCGGCAAGTGCTTCC 59.935 52.381 2.85 0.00 40.42 3.46
607 614 1.638133 CTCTTCGCACAGAGATGGTG 58.362 55.000 3.44 0.00 42.81 4.17
608 615 0.108424 GCTCTTCGCACAGAGATGGT 60.108 55.000 12.40 0.00 42.81 3.55
714 721 2.504920 GCCTGATTAAAGTGGCCCC 58.495 57.895 0.00 0.00 39.49 5.80
721 728 2.168521 TCGAGACAGGGCCTGATTAAAG 59.831 50.000 38.99 22.48 35.18 1.85
782 789 5.808366 TGTCCTTTTCAGATGAGTGTAGT 57.192 39.130 0.00 0.00 0.00 2.73
783 790 6.875726 TCAATGTCCTTTTCAGATGAGTGTAG 59.124 38.462 0.00 0.00 0.00 2.74
784 791 6.768483 TCAATGTCCTTTTCAGATGAGTGTA 58.232 36.000 0.00 0.00 0.00 2.90
914 1139 2.264794 GTGGCCGTGGGTACTGAG 59.735 66.667 0.00 0.00 0.00 3.35
1203 1482 4.218686 ATAATGCCCGGGGTGCCC 62.219 66.667 25.28 5.15 41.09 5.36
1569 1851 0.750911 ATACCCTCCAGTCGTCGTCC 60.751 60.000 0.00 0.00 0.00 4.79
1615 1899 4.698276 CATACGCACACAGAAACAACTAC 58.302 43.478 0.00 0.00 0.00 2.73
1654 1942 3.102276 CTCGAGAGATTAGCAACGACAC 58.898 50.000 6.58 0.00 40.84 3.67
1692 1980 9.764870 TTATTCTGCTATACGTATTCGACATAC 57.235 33.333 14.33 0.00 40.62 2.39
1694 1982 9.856488 ATTTATTCTGCTATACGTATTCGACAT 57.144 29.630 14.33 2.73 40.62 3.06
1701 1989 7.913789 TCCCCAATTTATTCTGCTATACGTAT 58.086 34.615 13.54 13.54 0.00 3.06
1718 2006 8.933653 CCATACAGGTAAATTTATTCCCCAATT 58.066 33.333 0.31 0.00 0.00 2.32
1719 2007 8.293216 TCCATACAGGTAAATTTATTCCCCAAT 58.707 33.333 0.31 0.00 39.02 3.16
1720 2008 7.653503 TCCATACAGGTAAATTTATTCCCCAA 58.346 34.615 0.31 0.00 39.02 4.12
1721 2009 7.227355 TCCATACAGGTAAATTTATTCCCCA 57.773 36.000 0.31 0.00 39.02 4.96
1722 2010 7.178451 CCATCCATACAGGTAAATTTATTCCCC 59.822 40.741 0.31 0.00 39.02 4.81
1723 2011 7.728532 ACCATCCATACAGGTAAATTTATTCCC 59.271 37.037 0.31 0.00 39.02 3.97
1724 2012 8.706322 ACCATCCATACAGGTAAATTTATTCC 57.294 34.615 0.31 0.00 39.02 3.01
1754 2042 3.201266 GGGTGGAGTACATGATAAACCCA 59.799 47.826 16.07 6.68 44.52 4.51
1766 2054 2.825861 TTTTGAGACGGGTGGAGTAC 57.174 50.000 0.00 0.00 0.00 2.73
1767 2055 3.581332 AGAATTTTGAGACGGGTGGAGTA 59.419 43.478 0.00 0.00 0.00 2.59
1768 2056 2.372172 AGAATTTTGAGACGGGTGGAGT 59.628 45.455 0.00 0.00 0.00 3.85
1769 2057 2.744202 CAGAATTTTGAGACGGGTGGAG 59.256 50.000 0.00 0.00 0.00 3.86
1770 2058 2.105821 ACAGAATTTTGAGACGGGTGGA 59.894 45.455 2.48 0.00 0.00 4.02
1771 2059 2.504367 ACAGAATTTTGAGACGGGTGG 58.496 47.619 2.48 0.00 0.00 4.61
1772 2060 4.568152 AAACAGAATTTTGAGACGGGTG 57.432 40.909 2.48 0.00 0.00 4.61
1773 2061 6.702716 TTAAAACAGAATTTTGAGACGGGT 57.297 33.333 2.48 0.00 0.00 5.28
1774 2062 8.587952 AATTTAAAACAGAATTTTGAGACGGG 57.412 30.769 2.48 0.00 0.00 5.28
1775 2063 9.848172 CAAATTTAAAACAGAATTTTGAGACGG 57.152 29.630 2.48 0.00 34.25 4.79
1797 2085 9.219603 CCATGATACATCCGTATTTAGACAAAT 57.780 33.333 0.00 0.00 38.48 2.32
1798 2086 8.425703 TCCATGATACATCCGTATTTAGACAAA 58.574 33.333 0.00 0.00 38.48 2.83
1799 2087 7.958088 TCCATGATACATCCGTATTTAGACAA 58.042 34.615 0.00 0.00 38.48 3.18
1800 2088 7.309805 CCTCCATGATACATCCGTATTTAGACA 60.310 40.741 0.00 0.00 38.48 3.41
1801 2089 7.036220 CCTCCATGATACATCCGTATTTAGAC 58.964 42.308 0.00 0.00 38.48 2.59
1802 2090 6.951778 TCCTCCATGATACATCCGTATTTAGA 59.048 38.462 0.00 0.00 38.48 2.10
1803 2091 7.170393 TCCTCCATGATACATCCGTATTTAG 57.830 40.000 0.00 0.00 38.48 1.85
1804 2092 7.234782 ACTTCCTCCATGATACATCCGTATTTA 59.765 37.037 0.00 0.00 38.48 1.40
1805 2093 6.043243 ACTTCCTCCATGATACATCCGTATTT 59.957 38.462 0.00 0.00 38.48 1.40
1806 2094 5.544176 ACTTCCTCCATGATACATCCGTATT 59.456 40.000 0.00 0.00 38.48 1.89
1807 2095 5.087323 ACTTCCTCCATGATACATCCGTAT 58.913 41.667 0.00 0.00 41.16 3.06
1808 2096 4.480115 ACTTCCTCCATGATACATCCGTA 58.520 43.478 0.00 0.00 0.00 4.02
1809 2097 3.309296 ACTTCCTCCATGATACATCCGT 58.691 45.455 0.00 0.00 0.00 4.69
1810 2098 5.667539 ATACTTCCTCCATGATACATCCG 57.332 43.478 0.00 0.00 0.00 4.18
1811 2099 6.102663 CGAATACTTCCTCCATGATACATCC 58.897 44.000 0.00 0.00 0.00 3.51
1812 2100 6.692486 ACGAATACTTCCTCCATGATACATC 58.308 40.000 0.00 0.00 0.00 3.06
1813 2101 6.495181 AGACGAATACTTCCTCCATGATACAT 59.505 38.462 0.00 0.00 0.00 2.29
1814 2102 5.833667 AGACGAATACTTCCTCCATGATACA 59.166 40.000 0.00 0.00 0.00 2.29
1815 2103 6.334102 AGACGAATACTTCCTCCATGATAC 57.666 41.667 0.00 0.00 0.00 2.24
1816 2104 5.477291 GGAGACGAATACTTCCTCCATGATA 59.523 44.000 0.00 0.00 0.00 2.15
1817 2105 4.282195 GGAGACGAATACTTCCTCCATGAT 59.718 45.833 0.00 0.00 0.00 2.45
1818 2106 3.637229 GGAGACGAATACTTCCTCCATGA 59.363 47.826 0.00 0.00 0.00 3.07
1819 2107 3.983741 GGAGACGAATACTTCCTCCATG 58.016 50.000 0.00 0.00 0.00 3.66
1935 3150 9.445878 TGAGGCATTTTATCAATTATGCAAAAA 57.554 25.926 10.04 0.00 43.89 1.94
1940 3155 8.597662 AACATGAGGCATTTTATCAATTATGC 57.402 30.769 0.00 0.00 41.94 3.14
1957 3175 0.967380 GGGGTGGAGCAAACATGAGG 60.967 60.000 0.00 0.00 0.00 3.86
1971 3189 1.291906 GGGCAATTTTGTCGGGGTG 59.708 57.895 0.00 0.00 32.44 4.61
1976 3194 0.678950 AAGGTGGGGCAATTTTGTCG 59.321 50.000 0.00 0.00 32.44 4.35
1978 3196 4.597075 AGAATAAAGGTGGGGCAATTTTGT 59.403 37.500 0.00 0.00 0.00 2.83
1988 3206 4.510167 ATCCACAGAGAATAAAGGTGGG 57.490 45.455 9.04 0.00 46.93 4.61
2001 3219 9.832445 GAGAAATGTAGGTATTTTATCCACAGA 57.168 33.333 0.00 0.00 30.78 3.41
2014 3232 5.652014 CCAATTGGCAAGAGAAATGTAGGTA 59.348 40.000 12.53 0.00 0.00 3.08
2090 3313 2.860136 GTTGAAAGTGTGCAAGCCTTTC 59.140 45.455 19.47 19.47 42.69 2.62
2092 3315 1.824230 TGTTGAAAGTGTGCAAGCCTT 59.176 42.857 0.00 0.00 0.00 4.35
2126 3349 1.801618 CGTCGTCGTTGCTATTACGA 58.198 50.000 0.00 4.38 44.88 3.43
2131 3354 0.109458 TGAAGCGTCGTCGTTGCTAT 60.109 50.000 12.90 5.53 38.17 2.97
2132 3355 1.000233 GTGAAGCGTCGTCGTTGCTA 61.000 55.000 12.90 0.00 38.17 3.49
2133 3356 2.027024 TGAAGCGTCGTCGTTGCT 59.973 55.556 3.66 7.91 41.60 3.91
2134 3357 2.084763 TTGTGAAGCGTCGTCGTTGC 62.085 55.000 3.66 0.00 39.49 4.17
2135 3358 0.381428 GTTGTGAAGCGTCGTCGTTG 60.381 55.000 3.66 0.00 39.49 4.10
2176 3401 1.603802 CAACCATCGTTGTGAGCTTGT 59.396 47.619 0.00 0.00 43.73 3.16
2188 3413 1.626654 GCGTGTGAGGACAACCATCG 61.627 60.000 0.00 0.00 38.94 3.84
2190 3415 0.603707 CAGCGTGTGAGGACAACCAT 60.604 55.000 0.00 0.00 38.94 3.55
2195 3420 1.668793 CATGCAGCGTGTGAGGACA 60.669 57.895 6.43 0.00 0.00 4.02
2232 3458 0.622136 AGCATCTCACATCCTTGCCA 59.378 50.000 0.00 0.00 33.85 4.92
2233 3459 1.022735 CAGCATCTCACATCCTTGCC 58.977 55.000 0.00 0.00 33.85 4.52
2262 3488 1.657162 TCCTCCCTCCCTTTGTCCTAT 59.343 52.381 0.00 0.00 0.00 2.57
2269 3495 2.428901 TGTTTTCTCCTCCCTCCCTTT 58.571 47.619 0.00 0.00 0.00 3.11
2270 3496 2.133858 TGTTTTCTCCTCCCTCCCTT 57.866 50.000 0.00 0.00 0.00 3.95
2286 3512 2.365617 ACAGAGGTCGTGTGATCTTGTT 59.634 45.455 0.00 0.00 35.06 2.83
2321 3547 0.616964 AACCTCTACGGGTCCCTTCC 60.617 60.000 6.29 0.00 38.87 3.46
2322 3548 1.273759 AAACCTCTACGGGTCCCTTC 58.726 55.000 6.29 0.00 38.87 3.46
2324 3550 1.738474 AAAAACCTCTACGGGTCCCT 58.262 50.000 6.29 0.00 38.87 4.20
2440 3676 5.711698 AGTTCCCCTCAAAATAGAAAACCA 58.288 37.500 0.00 0.00 0.00 3.67
2497 3733 9.676861 AACGAGTATAGCCTAAATAAACCTTTT 57.323 29.630 0.00 0.00 0.00 2.27
2499 3735 9.978044 CTAACGAGTATAGCCTAAATAAACCTT 57.022 33.333 0.00 0.00 0.00 3.50
2500 3736 8.583296 CCTAACGAGTATAGCCTAAATAAACCT 58.417 37.037 0.00 0.00 0.00 3.50
2501 3737 7.816513 CCCTAACGAGTATAGCCTAAATAAACC 59.183 40.741 0.00 0.00 0.00 3.27
2502 3738 8.363390 ACCCTAACGAGTATAGCCTAAATAAAC 58.637 37.037 0.00 0.00 0.00 2.01
2503 3739 8.482852 ACCCTAACGAGTATAGCCTAAATAAA 57.517 34.615 0.00 0.00 0.00 1.40
2504 3740 8.482852 AACCCTAACGAGTATAGCCTAAATAA 57.517 34.615 0.00 0.00 0.00 1.40
2505 3741 8.482852 AAACCCTAACGAGTATAGCCTAAATA 57.517 34.615 0.00 0.00 0.00 1.40
2506 3742 6.990908 AACCCTAACGAGTATAGCCTAAAT 57.009 37.500 0.00 0.00 0.00 1.40
2507 3743 6.796785 AAACCCTAACGAGTATAGCCTAAA 57.203 37.500 0.00 0.00 0.00 1.85



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

AutoCloner maintained by Alex Coulton.