Multiple sequence alignment - TraesCS2D01G124500

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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 TraesCS2D01G124500 chr2D 100.000 2582 0 0 1 2582 72967047 72964466 0.000000e+00 4769.0
1 TraesCS2D01G124500 chr2D 92.321 599 37 1 1020 1609 72954963 72954365 0.000000e+00 843.0
2 TraesCS2D01G124500 chr2D 85.938 64 7 2 2498 2560 457663873 457663935 1.660000e-07 67.6
3 TraesCS2D01G124500 chr2B 92.266 931 57 5 1 927 110141573 110140654 0.000000e+00 1306.0
4 TraesCS2D01G124500 chr2B 93.285 685 36 2 935 1609 110140584 110139900 0.000000e+00 1002.0
5 TraesCS2D01G124500 chr2B 89.655 406 41 1 82 487 247031780 247032184 1.370000e-142 516.0
6 TraesCS2D01G124500 chr2B 80.429 373 54 12 2143 2500 110139127 110138759 1.520000e-67 267.0
7 TraesCS2D01G124500 chr2B 81.683 202 35 2 1939 2138 165094795 165094594 1.590000e-37 167.0
8 TraesCS2D01G124500 chr2A 93.605 860 43 5 8 865 71448672 71447823 0.000000e+00 1273.0
9 TraesCS2D01G124500 chr2A 93.578 654 30 4 930 1574 71447719 71447069 0.000000e+00 965.0
10 TraesCS2D01G124500 chr2A 81.591 440 53 16 2076 2500 71446885 71446459 3.180000e-89 339.0
11 TraesCS2D01G124500 chr2A 97.500 40 1 0 877 916 71447826 71447787 4.610000e-08 69.4
12 TraesCS2D01G124500 chr6B 90.274 401 37 2 88 487 186691372 186690973 8.190000e-145 523.0
13 TraesCS2D01G124500 chr4B 89.163 406 44 0 82 487 514592322 514592727 8.240000e-140 507.0
14 TraesCS2D01G124500 chr3B 89.189 407 42 2 82 488 659538264 659538668 8.240000e-140 507.0
15 TraesCS2D01G124500 chr3B 97.727 44 1 0 531 574 59958455 59958498 2.760000e-10 76.8
16 TraesCS2D01G124500 chr3A 88.675 415 47 0 82 496 435362648 435363062 8.240000e-140 507.0
17 TraesCS2D01G124500 chr3A 82.243 214 36 2 1926 2138 32186150 32185938 1.580000e-42 183.0
18 TraesCS2D01G124500 chr3A 88.889 45 5 0 2498 2542 674433261 674433217 3.590000e-04 56.5
19 TraesCS2D01G124500 chr6D 88.971 408 44 1 88 495 380719183 380718777 1.070000e-138 503.0
20 TraesCS2D01G124500 chr6D 86.111 72 10 0 2068 2139 381358717 381358788 7.660000e-11 78.7
21 TraesCS2D01G124500 chr6D 94.595 37 2 0 2500 2536 453797579 453797615 9.980000e-05 58.4
22 TraesCS2D01G124500 chr6D 92.308 39 3 0 2498 2536 13486248 13486210 3.590000e-04 56.5
23 TraesCS2D01G124500 chr7B 89.109 404 43 1 88 491 221308651 221308249 3.840000e-138 501.0
24 TraesCS2D01G124500 chrUn 86.190 420 42 3 1202 1609 262807920 262808335 8.480000e-120 440.0
25 TraesCS2D01G124500 chrUn 84.086 421 48 6 1202 1609 262807197 262807611 3.120000e-104 388.0
26 TraesCS2D01G124500 chr5A 82.917 480 74 6 1111 1582 8918102 8917623 2.370000e-115 425.0
27 TraesCS2D01G124500 chr5D 80.161 373 55 13 1838 2198 495037128 495036763 7.090000e-66 261.0
28 TraesCS2D01G124500 chr5D 100.000 39 0 0 536 574 278284111 278284073 3.560000e-09 73.1
29 TraesCS2D01G124500 chr5D 89.091 55 5 1 2501 2555 488892913 488892860 1.660000e-07 67.6
30 TraesCS2D01G124500 chr6A 79.263 217 39 6 1926 2137 16456052 16456267 2.070000e-31 147.0
31 TraesCS2D01G124500 chr6A 82.353 102 13 4 2067 2168 480304318 480304222 1.650000e-12 84.2
32 TraesCS2D01G124500 chr6A 88.889 63 6 1 518 579 343413504 343413442 2.760000e-10 76.8
33 TraesCS2D01G124500 chr6A 97.778 45 0 1 536 580 581558155 581558198 2.760000e-10 76.8
34 TraesCS2D01G124500 chr4D 77.436 195 42 2 1926 2119 294935760 294935567 5.840000e-22 115.0
35 TraesCS2D01G124500 chr1D 84.946 93 14 0 2025 2117 493785629 493785537 7.610000e-16 95.3
36 TraesCS2D01G124500 chr7A 86.076 79 9 2 2068 2144 649139551 649139629 1.650000e-12 84.2
37 TraesCS2D01G124500 chr7A 96.970 33 1 0 2498 2530 58378278 58378310 3.590000e-04 56.5
38 TraesCS2D01G124500 chr1A 85.526 76 9 2 501 574 117882547 117882622 7.660000e-11 78.7
39 TraesCS2D01G124500 chr4A 88.710 62 7 0 518 579 402275612 402275673 2.760000e-10 76.8
40 TraesCS2D01G124500 chr4A 92.000 50 2 1 535 584 571048098 571048051 4.610000e-08 69.4
41 TraesCS2D01G124500 chr7D 87.931 58 5 2 2502 2559 181005681 181005626 1.660000e-07 67.6
42 TraesCS2D01G124500 chr5B 88.462 52 2 4 2503 2554 51059800 51059753 2.770000e-05 60.2
43 TraesCS2D01G124500 chr3D 92.308 39 3 0 2498 2536 612050645 612050607 3.590000e-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 TraesCS2D01G124500 chr2D 72964466 72967047 2581 True 4769.000000 4769 100.0000 1 2582 1 chr2D.!!$R2 2581
1 TraesCS2D01G124500 chr2D 72954365 72954963 598 True 843.000000 843 92.3210 1020 1609 1 chr2D.!!$R1 589
2 TraesCS2D01G124500 chr2B 110138759 110141573 2814 True 858.333333 1306 88.6600 1 2500 3 chr2B.!!$R2 2499
3 TraesCS2D01G124500 chr2A 71446459 71448672 2213 True 661.600000 1273 91.5685 8 2500 4 chr2A.!!$R1 2492
4 TraesCS2D01G124500 chrUn 262807197 262808335 1138 False 414.000000 440 85.1380 1202 1609 2 chrUn.!!$F1 407

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
204 205 0.601558 AGTACTTGCACCGACGACAT 59.398 50.0 0.0 0.0 0.00 3.06 F
1047 1119 0.733223 GCACCCTCTTCGTCTTCGTC 60.733 60.0 0.0 0.0 38.33 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 1629 0.108329 AGGCGTGGACGTGGATAAAG 60.108 55.0 0.0 0.0 42.22 1.85 R
1849 2185 0.249489 ATGCTACGGGAGTTCGATGC 60.249 55.0 0.0 0.0 43.33 3.91 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
90 91 2.730934 ACATACTCGGGCTACTCTCA 57.269 50.000 0.00 0.00 0.00 3.27
114 115 2.354003 GGCTTTGGTCATTGGTCATTGG 60.354 50.000 0.00 0.00 0.00 3.16
166 167 1.892329 GCTTGGCCCTCCTTTGATTCA 60.892 52.381 0.00 0.00 0.00 2.57
201 202 0.885879 ATGAGTACTTGCACCGACGA 59.114 50.000 0.00 0.00 0.00 4.20
204 205 0.601558 AGTACTTGCACCGACGACAT 59.398 50.000 0.00 0.00 0.00 3.06
238 239 0.846015 CCAAGGCATCCCTCACCATA 59.154 55.000 0.00 0.00 41.90 2.74
243 244 1.490490 GGCATCCCTCACCATACTCAA 59.510 52.381 0.00 0.00 0.00 3.02
264 265 3.808728 AGTCATGGACAATATGGAACGG 58.191 45.455 0.00 0.00 34.60 4.44
366 367 2.182614 ATCGTCGCCGGTGCAAAAAG 62.183 55.000 11.05 0.00 37.32 2.27
389 390 3.379057 GCTAGGGGCTTTAATTTTGCGTA 59.621 43.478 0.00 0.00 38.06 4.42
534 535 2.105821 TCCAGTGTGTTTGAGGGGTAAG 59.894 50.000 0.00 0.00 0.00 2.34
672 677 7.092264 CCATACCCTATCAATTGACATCCCTAT 60.092 40.741 11.07 0.00 0.00 2.57
730 735 2.423185 GCATATGTAGTGGCAAGCACAA 59.577 45.455 4.29 0.00 0.00 3.33
813 819 5.006386 AGAAGTGCCAAAATCTCAGTTAGG 58.994 41.667 0.00 0.00 0.00 2.69
874 880 5.971202 AGCACATTCGTCAAAAGTAAAACTG 59.029 36.000 0.00 0.00 0.00 3.16
885 891 8.752254 GTCAAAAGTAAAACTGCCAAATTACTC 58.248 33.333 0.00 0.00 37.55 2.59
922 979 6.817765 ATGGTCAAATCAAACACGTCTTAT 57.182 33.333 0.00 0.00 0.00 1.73
931 988 2.933495 ACACGTCTTATAGCGAGCAA 57.067 45.000 0.00 0.00 0.00 3.91
932 989 2.527100 ACACGTCTTATAGCGAGCAAC 58.473 47.619 0.00 0.00 0.00 4.17
933 990 2.094906 ACACGTCTTATAGCGAGCAACA 60.095 45.455 0.00 0.00 0.00 3.33
993 1065 2.485426 AGCACACCTCAACAATTCATCG 59.515 45.455 0.00 0.00 0.00 3.84
1047 1119 0.733223 GCACCCTCTTCGTCTTCGTC 60.733 60.000 0.00 0.00 38.33 4.20
1053 1125 3.426426 CCCTCTTCGTCTTCGTCTACTTG 60.426 52.174 0.00 0.00 38.33 3.16
1362 1443 3.645884 GTTGCTCTTGTGCATGAATGTT 58.354 40.909 0.00 0.00 42.96 2.71
1500 1581 1.681327 GGGGTACGTGCTCTGGAGA 60.681 63.158 2.79 0.00 0.00 3.71
1610 1715 1.944676 CGGTCGCCTTAGACGCATC 60.945 63.158 0.00 0.00 41.81 3.91
1611 1716 1.944676 GGTCGCCTTAGACGCATCG 60.945 63.158 0.00 0.00 41.81 3.84
1613 1718 2.582226 CGCCTTAGACGCATCGCA 60.582 61.111 0.00 0.00 0.00 5.10
1615 1720 0.663269 CGCCTTAGACGCATCGCATA 60.663 55.000 0.00 0.00 0.00 3.14
1616 1721 1.714794 GCCTTAGACGCATCGCATAT 58.285 50.000 0.00 0.00 0.00 1.78
1617 1722 1.391485 GCCTTAGACGCATCGCATATG 59.609 52.381 0.00 0.00 0.00 1.78
1618 1723 1.391485 CCTTAGACGCATCGCATATGC 59.609 52.381 18.08 18.08 41.35 3.14
1619 1724 2.061028 CTTAGACGCATCGCATATGCA 58.939 47.619 26.52 14.35 44.75 3.96
1622 1727 0.095935 GACGCATCGCATATGCATCC 59.904 55.000 26.52 10.82 44.75 3.51
1624 1729 1.066929 ACGCATCGCATATGCATCCTA 60.067 47.619 26.52 7.25 44.75 2.94
1626 1731 2.610833 CGCATCGCATATGCATCCTATT 59.389 45.455 26.52 0.87 44.75 1.73
1627 1732 3.064408 CGCATCGCATATGCATCCTATTT 59.936 43.478 26.52 0.00 44.75 1.40
1630 1735 6.140786 GCATCGCATATGCATCCTATTTATG 58.859 40.000 26.52 14.54 44.00 1.90
1631 1736 6.665465 CATCGCATATGCATCCTATTTATGG 58.335 40.000 26.52 6.30 42.21 2.74
1638 1743 9.309516 CATATGCATCCTATTTATGGCATTTTC 57.690 33.333 4.78 0.00 0.00 2.29
1640 1745 5.301551 TGCATCCTATTTATGGCATTTTCGT 59.698 36.000 4.78 0.00 0.00 3.85
1642 1747 6.701400 GCATCCTATTTATGGCATTTTCGTTT 59.299 34.615 4.78 0.00 0.00 3.60
1644 1749 9.097257 CATCCTATTTATGGCATTTTCGTTTTT 57.903 29.630 4.78 0.00 0.00 1.94
1674 1955 6.788458 GGTTGTTTTCGTTTTCTTTTTCACAC 59.212 34.615 0.00 0.00 0.00 3.82
1745 2053 3.194116 GTGGACGGAATACTACCACTGAA 59.806 47.826 0.00 0.00 44.91 3.02
1747 2055 4.179298 GGACGGAATACTACCACTGAAAC 58.821 47.826 0.00 0.00 0.00 2.78
1749 2057 5.476614 GACGGAATACTACCACTGAAACTT 58.523 41.667 0.00 0.00 0.00 2.66
1750 2058 5.476614 ACGGAATACTACCACTGAAACTTC 58.523 41.667 0.00 0.00 0.00 3.01
1752 2060 6.106673 CGGAATACTACCACTGAAACTTCAT 58.893 40.000 0.00 0.00 36.46 2.57
1753 2061 7.093640 ACGGAATACTACCACTGAAACTTCATA 60.094 37.037 0.00 0.00 36.46 2.15
1754 2062 7.926555 CGGAATACTACCACTGAAACTTCATAT 59.073 37.037 0.00 0.00 36.46 1.78
1779 2115 6.825284 TTCAGTAAAATTTGTGTGCATGTG 57.175 33.333 0.00 0.00 0.00 3.21
1780 2116 4.744137 TCAGTAAAATTTGTGTGCATGTGC 59.256 37.500 0.00 0.00 42.50 4.57
1792 2128 2.363276 ATGTGCATGCAGGGGGTG 60.363 61.111 23.41 0.00 0.00 4.61
1793 2129 3.968837 ATGTGCATGCAGGGGGTGG 62.969 63.158 23.41 0.00 0.00 4.61
1817 2153 3.657350 CGGTGGTGGGTGGGGATT 61.657 66.667 0.00 0.00 0.00 3.01
1819 2155 1.304962 GGTGGTGGGTGGGGATTTC 60.305 63.158 0.00 0.00 0.00 2.17
1820 2156 1.774300 GTGGTGGGTGGGGATTTCT 59.226 57.895 0.00 0.00 0.00 2.52
1822 2158 1.077716 GGTGGGTGGGGATTTCTCG 60.078 63.158 0.00 0.00 0.00 4.04
1823 2159 1.683441 GTGGGTGGGGATTTCTCGT 59.317 57.895 0.00 0.00 0.00 4.18
1824 2160 0.676782 GTGGGTGGGGATTTCTCGTG 60.677 60.000 0.00 0.00 0.00 4.35
1825 2161 1.131303 TGGGTGGGGATTTCTCGTGT 61.131 55.000 0.00 0.00 0.00 4.49
1827 2163 1.406477 GGGTGGGGATTTCTCGTGTAC 60.406 57.143 0.00 0.00 0.00 2.90
1828 2164 1.406477 GGTGGGGATTTCTCGTGTACC 60.406 57.143 0.00 0.00 0.00 3.34
1829 2165 0.533491 TGGGGATTTCTCGTGTACCG 59.467 55.000 0.00 0.00 38.13 4.02
1830 2166 0.179092 GGGGATTTCTCGTGTACCGG 60.179 60.000 0.00 0.00 37.11 5.28
1831 2167 0.533951 GGGATTTCTCGTGTACCGGT 59.466 55.000 13.98 13.98 37.11 5.28
1832 2168 1.636988 GGATTTCTCGTGTACCGGTG 58.363 55.000 19.93 0.00 37.11 4.94
1833 2169 0.997196 GATTTCTCGTGTACCGGTGC 59.003 55.000 19.93 18.21 37.11 5.01
1834 2170 0.606604 ATTTCTCGTGTACCGGTGCT 59.393 50.000 23.67 0.00 37.11 4.40
1835 2171 0.390124 TTTCTCGTGTACCGGTGCTT 59.610 50.000 23.67 0.00 37.11 3.91
1836 2172 0.319211 TTCTCGTGTACCGGTGCTTG 60.319 55.000 23.67 15.28 37.11 4.01
1837 2173 1.006571 CTCGTGTACCGGTGCTTGT 60.007 57.895 23.67 0.00 37.11 3.16
1838 2174 1.282248 CTCGTGTACCGGTGCTTGTG 61.282 60.000 23.67 12.30 37.11 3.33
1839 2175 2.314647 CGTGTACCGGTGCTTGTGG 61.315 63.158 23.67 4.63 0.00 4.17
1840 2176 2.281208 TGTACCGGTGCTTGTGGC 60.281 61.111 23.67 1.39 42.22 5.01
1841 2177 3.419759 GTACCGGTGCTTGTGGCG 61.420 66.667 19.93 0.00 45.43 5.69
1860 2196 2.460330 CACCAGTGCATCGAACTCC 58.540 57.895 0.00 0.00 0.00 3.85
1861 2197 1.021390 CACCAGTGCATCGAACTCCC 61.021 60.000 0.00 0.00 0.00 4.30
1862 2198 1.811266 CCAGTGCATCGAACTCCCG 60.811 63.158 0.00 0.00 0.00 5.14
1863 2199 1.079819 CAGTGCATCGAACTCCCGT 60.080 57.895 0.00 0.00 0.00 5.28
1864 2200 0.172578 CAGTGCATCGAACTCCCGTA 59.827 55.000 0.00 0.00 0.00 4.02
1865 2201 0.456221 AGTGCATCGAACTCCCGTAG 59.544 55.000 0.00 0.00 0.00 3.51
1866 2202 1.141019 TGCATCGAACTCCCGTAGC 59.859 57.895 0.00 0.00 0.00 3.58
1867 2203 1.141019 GCATCGAACTCCCGTAGCA 59.859 57.895 0.00 0.00 33.36 3.49
1868 2204 0.249489 GCATCGAACTCCCGTAGCAT 60.249 55.000 0.00 0.00 33.36 3.79
1869 2205 1.000607 GCATCGAACTCCCGTAGCATA 60.001 52.381 0.00 0.00 33.36 3.14
1870 2206 2.352814 GCATCGAACTCCCGTAGCATAT 60.353 50.000 0.00 0.00 33.36 1.78
1871 2207 3.502920 CATCGAACTCCCGTAGCATATC 58.497 50.000 0.00 0.00 0.00 1.63
1872 2208 2.860009 TCGAACTCCCGTAGCATATCT 58.140 47.619 0.00 0.00 0.00 1.98
1873 2209 3.220110 TCGAACTCCCGTAGCATATCTT 58.780 45.455 0.00 0.00 0.00 2.40
1874 2210 4.392047 TCGAACTCCCGTAGCATATCTTA 58.608 43.478 0.00 0.00 0.00 2.10
1875 2211 4.823442 TCGAACTCCCGTAGCATATCTTAA 59.177 41.667 0.00 0.00 0.00 1.85
1876 2212 5.300034 TCGAACTCCCGTAGCATATCTTAAA 59.700 40.000 0.00 0.00 0.00 1.52
1877 2213 5.981315 CGAACTCCCGTAGCATATCTTAAAA 59.019 40.000 0.00 0.00 0.00 1.52
1878 2214 6.645415 CGAACTCCCGTAGCATATCTTAAAAT 59.355 38.462 0.00 0.00 0.00 1.82
1879 2215 7.359264 CGAACTCCCGTAGCATATCTTAAAATG 60.359 40.741 0.00 0.00 0.00 2.32
1880 2216 6.827727 ACTCCCGTAGCATATCTTAAAATGT 58.172 36.000 0.00 0.00 0.00 2.71
1881 2217 7.280356 ACTCCCGTAGCATATCTTAAAATGTT 58.720 34.615 0.00 0.00 0.00 2.71
1882 2218 7.773690 ACTCCCGTAGCATATCTTAAAATGTTT 59.226 33.333 0.00 0.00 0.00 2.83
1883 2219 7.925993 TCCCGTAGCATATCTTAAAATGTTTG 58.074 34.615 0.00 0.00 0.00 2.93
1884 2220 7.771361 TCCCGTAGCATATCTTAAAATGTTTGA 59.229 33.333 0.00 0.00 0.00 2.69
1885 2221 8.402472 CCCGTAGCATATCTTAAAATGTTTGAA 58.598 33.333 0.00 0.00 0.00 2.69
1886 2222 9.781834 CCGTAGCATATCTTAAAATGTTTGAAA 57.218 29.630 0.00 0.00 0.00 2.69
1910 2246 9.466741 AAAATTTTGAAAAATAACACGTTCACG 57.533 25.926 1.75 0.00 40.31 4.35
1911 2247 5.607858 TTTGAAAAATAACACGTTCACGC 57.392 34.783 0.00 0.00 44.43 5.34
1912 2248 4.274421 TGAAAAATAACACGTTCACGCA 57.726 36.364 0.00 0.00 44.43 5.24
1913 2249 4.659088 TGAAAAATAACACGTTCACGCAA 58.341 34.783 0.00 0.00 44.43 4.85
1914 2250 5.274718 TGAAAAATAACACGTTCACGCAAT 58.725 33.333 0.00 0.00 44.43 3.56
1915 2251 6.427974 TGAAAAATAACACGTTCACGCAATA 58.572 32.000 0.00 0.00 44.43 1.90
1916 2252 7.078851 TGAAAAATAACACGTTCACGCAATAT 58.921 30.769 0.00 0.00 44.43 1.28
1917 2253 7.269511 TGAAAAATAACACGTTCACGCAATATC 59.730 33.333 0.00 0.00 44.43 1.63
1918 2254 5.788055 AATAACACGTTCACGCAATATCA 57.212 34.783 0.00 0.00 44.43 2.15
1919 2255 5.788055 ATAACACGTTCACGCAATATCAA 57.212 34.783 0.00 0.00 44.43 2.57
1920 2256 4.678509 AACACGTTCACGCAATATCAAT 57.321 36.364 0.00 0.00 44.43 2.57
1921 2257 4.002267 ACACGTTCACGCAATATCAATG 57.998 40.909 0.00 0.00 44.43 2.82
1922 2258 3.682377 ACACGTTCACGCAATATCAATGA 59.318 39.130 0.00 0.00 44.43 2.57
1923 2259 4.332543 ACACGTTCACGCAATATCAATGAT 59.667 37.500 0.00 0.00 44.43 2.45
1924 2260 5.163764 ACACGTTCACGCAATATCAATGATT 60.164 36.000 0.00 0.00 44.43 2.57
1925 2261 6.036626 ACACGTTCACGCAATATCAATGATTA 59.963 34.615 0.00 0.00 44.43 1.75
1926 2262 6.904543 CACGTTCACGCAATATCAATGATTAA 59.095 34.615 0.00 0.00 44.43 1.40
1927 2263 7.427895 CACGTTCACGCAATATCAATGATTAAA 59.572 33.333 0.00 0.00 44.43 1.52
1928 2264 7.965655 ACGTTCACGCAATATCAATGATTAAAA 59.034 29.630 0.00 0.00 44.43 1.52
1929 2265 8.957028 CGTTCACGCAATATCAATGATTAAAAT 58.043 29.630 0.00 0.00 0.00 1.82
2012 2348 9.998106 ATAGTACATAACATATTTTCGGCTTCT 57.002 29.630 0.00 0.00 0.00 2.85
2021 2357 1.614996 TTTCGGCTTCTGATTTGGCA 58.385 45.000 0.00 0.00 0.00 4.92
2023 2359 1.135315 CGGCTTCTGATTTGGCACG 59.865 57.895 0.00 0.00 0.00 5.34
2032 2368 4.260985 TCTGATTTGGCACGTTATCACAT 58.739 39.130 0.00 0.00 0.00 3.21
2038 2374 3.342719 TGGCACGTTATCACATTGATGT 58.657 40.909 0.00 0.00 42.84 3.06
2039 2375 3.373748 TGGCACGTTATCACATTGATGTC 59.626 43.478 0.00 0.00 39.39 3.06
2042 2378 5.023920 GCACGTTATCACATTGATGTCAAG 58.976 41.667 1.65 0.00 39.39 3.02
2057 2393 7.522901 TGATGTCAAGTTTGTCATTTTTGTG 57.477 32.000 6.16 0.00 37.13 3.33
2060 2396 6.450545 TGTCAAGTTTGTCATTTTTGTGTCA 58.549 32.000 0.00 0.00 0.00 3.58
2062 2398 5.570973 TCAAGTTTGTCATTTTTGTGTCACG 59.429 36.000 0.00 0.00 0.00 4.35
2063 2399 4.420168 AGTTTGTCATTTTTGTGTCACGG 58.580 39.130 0.00 0.00 0.00 4.94
2065 2401 1.678627 TGTCATTTTTGTGTCACGGGG 59.321 47.619 0.00 0.00 0.00 5.73
2069 2405 3.005261 TCATTTTTGTGTCACGGGGAATG 59.995 43.478 11.73 11.73 0.00 2.67
2070 2406 2.060050 TTTTGTGTCACGGGGAATGT 57.940 45.000 0.00 0.00 0.00 2.71
2071 2407 2.060050 TTTGTGTCACGGGGAATGTT 57.940 45.000 0.00 0.00 0.00 2.71
2072 2408 2.060050 TTGTGTCACGGGGAATGTTT 57.940 45.000 0.00 0.00 0.00 2.83
2073 2409 1.600023 TGTGTCACGGGGAATGTTTC 58.400 50.000 0.00 0.00 0.00 2.78
2074 2410 1.134068 TGTGTCACGGGGAATGTTTCA 60.134 47.619 0.00 0.00 0.00 2.69
2079 2415 4.100189 TGTCACGGGGAATGTTTCAAATTT 59.900 37.500 0.00 0.00 0.00 1.82
2085 2421 7.548780 CACGGGGAATGTTTCAAATTTTGATAT 59.451 33.333 12.39 5.67 39.84 1.63
2179 2658 5.755330 ACATTTTAAAATTTGCTACGCCG 57.245 34.783 10.77 0.00 0.00 6.46
2227 2706 3.803778 GGTGGGTTACCGATTACATTACG 59.196 47.826 0.00 0.00 40.26 3.18
2228 2707 4.441356 GGTGGGTTACCGATTACATTACGA 60.441 45.833 0.00 0.00 40.26 3.43
2230 2709 3.737774 GGGTTACCGATTACATTACGAGC 59.262 47.826 0.00 0.00 0.00 5.03
2233 2712 1.677576 ACCGATTACATTACGAGCGGA 59.322 47.619 6.26 0.00 40.39 5.54
2314 2804 2.726821 CCTGCCCACATGTAACATCTT 58.273 47.619 0.00 0.00 0.00 2.40
2315 2805 2.684881 CCTGCCCACATGTAACATCTTC 59.315 50.000 0.00 0.00 0.00 2.87
2473 2969 6.775142 TGAAAAATCTAACCATTGTGGAGACA 59.225 34.615 2.45 0.00 40.96 3.41
2577 3073 8.749841 TTTGTTCACCCAATAATTTTCATACG 57.250 30.769 0.00 0.00 0.00 3.06
2578 3074 7.455641 TGTTCACCCAATAATTTTCATACGT 57.544 32.000 0.00 0.00 0.00 3.57
2579 3075 7.531716 TGTTCACCCAATAATTTTCATACGTC 58.468 34.615 0.00 0.00 0.00 4.34
2580 3076 6.352682 TCACCCAATAATTTTCATACGTCG 57.647 37.500 0.00 0.00 0.00 5.12
2581 3077 4.967575 CACCCAATAATTTTCATACGTCGC 59.032 41.667 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 2.676748 TGACCAATGACCAAAGCCTTT 58.323 42.857 0.00 0.00 0.00 3.11
114 115 4.868314 AGCCCGAGTATGTAGTATTTCC 57.132 45.455 0.00 0.00 0.00 3.13
166 167 7.259088 AGTACTCATCCACCAATCTTTAACT 57.741 36.000 0.00 0.00 0.00 2.24
201 202 0.675633 GGCTTGTCTGTTTGGCATGT 59.324 50.000 0.00 0.00 0.00 3.21
204 205 0.746063 CTTGGCTTGTCTGTTTGGCA 59.254 50.000 0.00 0.00 0.00 4.92
238 239 5.698741 TCCATATTGTCCATGACTTGAGT 57.301 39.130 0.00 0.00 33.15 3.41
243 244 3.433598 CCCGTTCCATATTGTCCATGACT 60.434 47.826 0.00 0.00 33.15 3.41
264 265 2.894307 AAAAACTCTCGCATTACGCC 57.106 45.000 0.00 0.00 43.23 5.68
366 367 2.481276 CGCAAAATTAAAGCCCCTAGCC 60.481 50.000 0.00 0.00 45.47 3.93
389 390 1.447838 CACGGCATGCGGACTACTT 60.448 57.895 29.51 5.15 0.00 2.24
486 487 7.254421 CGGCATTAGCAAAAGTCTTTTCTTTTT 60.254 33.333 7.62 0.00 43.09 1.94
487 488 6.200854 CGGCATTAGCAAAAGTCTTTTCTTTT 59.799 34.615 7.62 0.00 44.95 2.27
488 489 5.691754 CGGCATTAGCAAAAGTCTTTTCTTT 59.308 36.000 7.62 0.14 44.61 2.52
489 490 5.221244 ACGGCATTAGCAAAAGTCTTTTCTT 60.221 36.000 7.62 2.42 44.61 2.52
490 491 4.278419 ACGGCATTAGCAAAAGTCTTTTCT 59.722 37.500 7.62 10.34 44.61 2.52
621 626 4.641094 CGTGAGTACAATCCTCTTCTACCT 59.359 45.833 0.00 0.00 0.00 3.08
672 677 2.126463 CTCGAACTCGCTTCCGCA 60.126 61.111 0.00 0.00 39.60 5.69
743 748 0.861866 CCATGCTCTCGTACACGTCG 60.862 60.000 1.19 0.00 40.80 5.12
813 819 0.250901 TGTGCCTCTTCAAAGCCTCC 60.251 55.000 0.00 0.00 0.00 4.30
874 880 1.398390 CTGCTCCACGAGTAATTTGGC 59.602 52.381 0.00 0.00 31.39 4.52
885 891 1.338674 TGACCATAAACCTGCTCCACG 60.339 52.381 0.00 0.00 0.00 4.94
922 979 1.713597 CACAGATGTGTTGCTCGCTA 58.286 50.000 4.77 0.00 40.96 4.26
933 990 7.132863 CGTATATATATAGCACGCACAGATGT 58.867 38.462 13.59 0.00 0.00 3.06
1226 1307 4.920112 CCACCACGTGCCCGAACA 62.920 66.667 10.91 0.00 37.88 3.18
1236 1317 1.800315 GTCGTCGATCACCACCACG 60.800 63.158 0.00 0.00 0.00 4.94
1521 1602 1.503542 GTCGAGGACGGCGTTCTTA 59.496 57.895 23.72 11.29 40.21 2.10
1546 1627 1.472728 GGCGTGGACGTGGATAAAGAT 60.473 52.381 0.00 0.00 42.22 2.40
1548 1629 0.108329 AGGCGTGGACGTGGATAAAG 60.108 55.000 0.00 0.00 42.22 1.85
1574 1679 3.831883 ATGGCGTCCATCATGCAC 58.168 55.556 5.65 0.00 40.74 4.57
1610 1715 4.336153 TGCCATAAATAGGATGCATATGCG 59.664 41.667 22.21 4.77 45.83 4.73
1611 1716 5.840243 TGCCATAAATAGGATGCATATGC 57.160 39.130 21.09 21.09 42.50 3.14
1613 1718 8.192774 CGAAAATGCCATAAATAGGATGCATAT 58.807 33.333 0.00 0.00 0.00 1.78
1615 1720 6.015180 ACGAAAATGCCATAAATAGGATGCAT 60.015 34.615 0.00 0.00 0.00 3.96
1616 1721 5.301551 ACGAAAATGCCATAAATAGGATGCA 59.698 36.000 0.00 0.00 0.00 3.96
1617 1722 5.772521 ACGAAAATGCCATAAATAGGATGC 58.227 37.500 0.00 0.00 0.00 3.91
1618 1723 8.647143 AAAACGAAAATGCCATAAATAGGATG 57.353 30.769 0.00 0.00 0.00 3.51
1642 1747 4.448060 AGAAAACGAAAACAACCGCAAAAA 59.552 33.333 0.00 0.00 0.00 1.94
1644 1749 3.576648 AGAAAACGAAAACAACCGCAAA 58.423 36.364 0.00 0.00 0.00 3.68
1648 1753 6.004694 GTGAAAAAGAAAACGAAAACAACCG 58.995 36.000 0.00 0.00 0.00 4.44
1650 1755 7.338462 TGTGTGAAAAAGAAAACGAAAACAAC 58.662 30.769 0.00 0.00 0.00 3.32
1753 2061 9.142515 CACATGCACACAAATTTTACTGAATAT 57.857 29.630 0.00 0.00 0.00 1.28
1754 2062 7.116090 GCACATGCACACAAATTTTACTGAATA 59.884 33.333 0.00 0.00 41.59 1.75
1755 2063 6.073657 GCACATGCACACAAATTTTACTGAAT 60.074 34.615 0.00 0.00 41.59 2.57
1757 2065 4.744137 GCACATGCACACAAATTTTACTGA 59.256 37.500 0.00 0.00 41.59 3.41
1758 2066 5.009048 GCACATGCACACAAATTTTACTG 57.991 39.130 0.00 0.00 41.59 2.74
1774 2110 2.363276 ACCCCCTGCATGCACATG 60.363 61.111 18.46 7.43 41.60 3.21
1776 2112 4.682334 CCACCCCCTGCATGCACA 62.682 66.667 18.46 0.00 0.00 4.57
1800 2136 3.218386 AAATCCCCACCCACCACCG 62.218 63.158 0.00 0.00 0.00 4.94
1801 2137 1.304962 GAAATCCCCACCCACCACC 60.305 63.158 0.00 0.00 0.00 4.61
1802 2138 0.323451 GAGAAATCCCCACCCACCAC 60.323 60.000 0.00 0.00 0.00 4.16
1803 2139 1.847798 CGAGAAATCCCCACCCACCA 61.848 60.000 0.00 0.00 0.00 4.17
1804 2140 1.077716 CGAGAAATCCCCACCCACC 60.078 63.158 0.00 0.00 0.00 4.61
1806 2142 1.131303 ACACGAGAAATCCCCACCCA 61.131 55.000 0.00 0.00 0.00 4.51
1807 2143 0.906775 TACACGAGAAATCCCCACCC 59.093 55.000 0.00 0.00 0.00 4.61
1808 2144 1.406477 GGTACACGAGAAATCCCCACC 60.406 57.143 0.00 0.00 0.00 4.61
1809 2145 2.019948 GGTACACGAGAAATCCCCAC 57.980 55.000 0.00 0.00 0.00 4.61
1822 2158 2.613506 GCCACAAGCACCGGTACAC 61.614 63.158 6.87 0.00 42.97 2.90
1823 2159 2.281208 GCCACAAGCACCGGTACA 60.281 61.111 6.87 0.00 42.97 2.90
1824 2160 3.419759 CGCCACAAGCACCGGTAC 61.420 66.667 6.87 0.00 44.04 3.34
1831 2167 4.873810 ACTGGTGCGCCACAAGCA 62.874 61.111 16.89 0.08 38.88 3.91
1832 2168 4.332637 CACTGGTGCGCCACAAGC 62.333 66.667 16.89 0.00 38.88 4.01
1842 2178 1.021390 GGGAGTTCGATGCACTGGTG 61.021 60.000 0.00 0.00 0.00 4.17
1843 2179 1.296715 GGGAGTTCGATGCACTGGT 59.703 57.895 0.00 0.00 0.00 4.00
1844 2180 1.811266 CGGGAGTTCGATGCACTGG 60.811 63.158 0.00 0.00 0.00 4.00
1845 2181 0.172578 TACGGGAGTTCGATGCACTG 59.827 55.000 0.00 0.00 43.33 3.66
1846 2182 0.456221 CTACGGGAGTTCGATGCACT 59.544 55.000 0.00 0.00 43.33 4.40
1847 2183 1.146358 GCTACGGGAGTTCGATGCAC 61.146 60.000 0.00 0.00 43.33 4.57
1848 2184 1.141019 GCTACGGGAGTTCGATGCA 59.859 57.895 0.00 0.00 43.33 3.96
1849 2185 0.249489 ATGCTACGGGAGTTCGATGC 60.249 55.000 0.00 0.00 43.33 3.91
1850 2186 3.191581 AGATATGCTACGGGAGTTCGATG 59.808 47.826 0.00 0.00 43.33 3.84
1851 2187 3.422796 AGATATGCTACGGGAGTTCGAT 58.577 45.455 0.00 0.00 43.33 3.59
1852 2188 2.860009 AGATATGCTACGGGAGTTCGA 58.140 47.619 0.00 0.00 43.33 3.71
1853 2189 3.644884 AAGATATGCTACGGGAGTTCG 57.355 47.619 0.00 0.00 43.33 3.95
1854 2190 7.441458 ACATTTTAAGATATGCTACGGGAGTTC 59.559 37.037 0.00 0.00 43.33 3.01
1855 2191 7.280356 ACATTTTAAGATATGCTACGGGAGTT 58.720 34.615 0.00 0.00 43.33 3.01
1857 2193 7.730364 AACATTTTAAGATATGCTACGGGAG 57.270 36.000 0.00 0.00 0.00 4.30
1858 2194 7.771361 TCAAACATTTTAAGATATGCTACGGGA 59.229 33.333 0.00 0.00 0.00 5.14
1859 2195 7.925993 TCAAACATTTTAAGATATGCTACGGG 58.074 34.615 0.00 0.00 0.00 5.28
1860 2196 9.781834 TTTCAAACATTTTAAGATATGCTACGG 57.218 29.630 0.00 0.00 0.00 4.02
1884 2220 9.466741 CGTGAACGTGTTATTTTTCAAAATTTT 57.533 25.926 0.00 0.00 36.02 1.82
1885 2221 7.632897 GCGTGAACGTGTTATTTTTCAAAATTT 59.367 29.630 4.59 0.00 39.26 1.82
1886 2222 7.114289 GCGTGAACGTGTTATTTTTCAAAATT 58.886 30.769 4.59 0.00 39.26 1.82
1887 2223 6.253727 TGCGTGAACGTGTTATTTTTCAAAAT 59.746 30.769 4.59 3.13 40.45 1.82
1888 2224 5.571741 TGCGTGAACGTGTTATTTTTCAAAA 59.428 32.000 4.59 0.00 42.22 2.44
1889 2225 5.093457 TGCGTGAACGTGTTATTTTTCAAA 58.907 33.333 4.59 0.00 42.22 2.69
1890 2226 4.659088 TGCGTGAACGTGTTATTTTTCAA 58.341 34.783 4.59 0.00 42.22 2.69
1891 2227 4.274421 TGCGTGAACGTGTTATTTTTCA 57.726 36.364 4.59 0.00 42.22 2.69
1892 2228 5.799542 ATTGCGTGAACGTGTTATTTTTC 57.200 34.783 4.59 0.00 42.22 2.29
1893 2229 7.078851 TGATATTGCGTGAACGTGTTATTTTT 58.921 30.769 4.59 0.00 42.22 1.94
1894 2230 6.604012 TGATATTGCGTGAACGTGTTATTTT 58.396 32.000 4.59 0.00 42.22 1.82
1895 2231 6.171932 TGATATTGCGTGAACGTGTTATTT 57.828 33.333 4.59 0.00 42.22 1.40
1896 2232 5.788055 TGATATTGCGTGAACGTGTTATT 57.212 34.783 4.59 0.00 42.22 1.40
1897 2233 5.788055 TTGATATTGCGTGAACGTGTTAT 57.212 34.783 4.59 0.00 42.22 1.89
1898 2234 5.348997 TCATTGATATTGCGTGAACGTGTTA 59.651 36.000 4.59 0.00 42.22 2.41
1899 2235 4.153296 TCATTGATATTGCGTGAACGTGTT 59.847 37.500 4.59 0.00 42.22 3.32
1900 2236 3.682377 TCATTGATATTGCGTGAACGTGT 59.318 39.130 4.59 0.00 42.22 4.49
1901 2237 4.257536 TCATTGATATTGCGTGAACGTG 57.742 40.909 4.59 0.00 42.22 4.49
1902 2238 5.484173 AATCATTGATATTGCGTGAACGT 57.516 34.783 4.59 0.00 42.22 3.99
1903 2239 7.890879 TTTAATCATTGATATTGCGTGAACG 57.109 32.000 0.00 0.00 43.27 3.95
1953 2289 9.757227 TCGAATTTATCATTTTTGTTTTCCAGT 57.243 25.926 0.00 0.00 0.00 4.00
1955 2291 9.973450 TCTCGAATTTATCATTTTTGTTTTCCA 57.027 25.926 0.00 0.00 0.00 3.53
2001 2337 1.959985 TGCCAAATCAGAAGCCGAAAA 59.040 42.857 0.00 0.00 0.00 2.29
2002 2338 1.269448 GTGCCAAATCAGAAGCCGAAA 59.731 47.619 0.00 0.00 0.00 3.46
2004 2340 1.298157 CGTGCCAAATCAGAAGCCGA 61.298 55.000 0.00 0.00 0.00 5.54
2005 2341 1.135315 CGTGCCAAATCAGAAGCCG 59.865 57.895 0.00 0.00 0.00 5.52
2010 2346 3.669536 TGTGATAACGTGCCAAATCAGA 58.330 40.909 0.00 0.00 0.00 3.27
2012 2348 4.457257 TCAATGTGATAACGTGCCAAATCA 59.543 37.500 0.00 0.00 0.00 2.57
2021 2357 6.801539 AACTTGACATCAATGTGATAACGT 57.198 33.333 0.00 0.00 41.95 3.99
2023 2359 8.075574 TGACAAACTTGACATCAATGTGATAAC 58.924 33.333 0.00 0.00 41.95 1.89
2032 2368 7.601886 ACACAAAAATGACAAACTTGACATCAA 59.398 29.630 7.65 0.00 41.39 2.57
2038 2374 5.570973 CGTGACACAAAAATGACAAACTTGA 59.429 36.000 6.37 0.00 0.00 3.02
2039 2375 5.220191 CCGTGACACAAAAATGACAAACTTG 60.220 40.000 6.37 0.00 0.00 3.16
2042 2378 3.549873 CCCGTGACACAAAAATGACAAAC 59.450 43.478 6.37 0.00 0.00 2.93
2057 2393 3.934457 ATTTGAAACATTCCCCGTGAC 57.066 42.857 0.00 0.00 0.00 3.67
2060 2396 5.283457 TCAAAATTTGAAACATTCCCCGT 57.717 34.783 5.87 0.00 36.59 5.28
2062 2398 9.447157 TTCATATCAAAATTTGAAACATTCCCC 57.553 29.630 12.75 0.00 43.95 4.81
2191 2670 3.945640 ACCCACCCTTGTAATGATACC 57.054 47.619 0.00 0.00 0.00 2.73
2195 2674 2.027007 CGGTAACCCACCCTTGTAATGA 60.027 50.000 0.00 0.00 45.52 2.57
2216 2695 2.609737 CCCCTCCGCTCGTAATGTAATC 60.610 54.545 0.00 0.00 0.00 1.75
2217 2696 1.343465 CCCCTCCGCTCGTAATGTAAT 59.657 52.381 0.00 0.00 0.00 1.89
2218 2697 0.748450 CCCCTCCGCTCGTAATGTAA 59.252 55.000 0.00 0.00 0.00 2.41
2219 2698 1.111116 CCCCCTCCGCTCGTAATGTA 61.111 60.000 0.00 0.00 0.00 2.29
2220 2699 2.432300 CCCCCTCCGCTCGTAATGT 61.432 63.158 0.00 0.00 0.00 2.71
2221 2700 2.421739 CCCCCTCCGCTCGTAATG 59.578 66.667 0.00 0.00 0.00 1.90
2421 2911 9.699410 TTGAGAGAAAACCAACATCCATATTAT 57.301 29.630 0.00 0.00 0.00 1.28
2429 2925 8.647143 TTTTTCATTGAGAGAAAACCAACATC 57.353 30.769 0.00 0.00 42.68 3.06
2463 2959 3.142951 CGTTATTTGGGTGTCTCCACAA 58.857 45.455 0.00 0.00 43.71 3.33
2464 2960 2.773487 CGTTATTTGGGTGTCTCCACA 58.227 47.619 0.00 0.00 43.71 4.17
2465 2961 1.467342 GCGTTATTTGGGTGTCTCCAC 59.533 52.381 0.00 0.00 41.06 4.02
2551 3047 9.197694 CGTATGAAAATTATTGGGTGAACAAAA 57.802 29.630 0.00 0.00 33.48 2.44
2552 3048 8.361139 ACGTATGAAAATTATTGGGTGAACAAA 58.639 29.630 0.00 0.00 33.48 2.83
2553 3049 7.887381 ACGTATGAAAATTATTGGGTGAACAA 58.113 30.769 0.00 0.00 34.41 2.83
2554 3050 7.455641 ACGTATGAAAATTATTGGGTGAACA 57.544 32.000 0.00 0.00 0.00 3.18
2555 3051 6.685403 CGACGTATGAAAATTATTGGGTGAAC 59.315 38.462 0.00 0.00 0.00 3.18
2556 3052 6.675971 GCGACGTATGAAAATTATTGGGTGAA 60.676 38.462 0.00 0.00 0.00 3.18
2557 3053 5.220700 GCGACGTATGAAAATTATTGGGTGA 60.221 40.000 0.00 0.00 0.00 4.02
2558 3054 4.967575 GCGACGTATGAAAATTATTGGGTG 59.032 41.667 0.00 0.00 0.00 4.61
2559 3055 5.164606 GCGACGTATGAAAATTATTGGGT 57.835 39.130 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.