Multiple sequence alignment - TraesCS2B01G261800

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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 TraesCS2B01G261800 chr2B 100.000 2454 0 0 1 2454 338729474 338727021 0.000000e+00 4532.0
1 TraesCS2B01G261800 chr2B 93.750 176 11 0 2168 2343 93762503 93762328 5.200000e-67 265.0
2 TraesCS2B01G261800 chr2B 91.257 183 14 2 2165 2346 60142625 60142444 5.240000e-62 248.0
3 TraesCS2B01G261800 chr2B 88.235 102 9 3 1 100 131585497 131585397 4.290000e-23 119.0
4 TraesCS2B01G261800 chr7A 96.851 1715 47 5 98 1805 435733518 435731804 0.000000e+00 2861.0
5 TraesCS2B01G261800 chr7A 96.109 1722 48 10 95 1802 563493481 563495197 0.000000e+00 2791.0
6 TraesCS2B01G261800 chr7A 95.978 920 34 2 887 1805 87693049 87692132 0.000000e+00 1491.0
7 TraesCS2B01G261800 chr7A 95.098 816 27 7 95 898 87693886 87693072 0.000000e+00 1273.0
8 TraesCS2B01G261800 chr7A 88.185 821 65 20 96 898 139135857 139135051 0.000000e+00 950.0
9 TraesCS2B01G261800 chr7A 89.031 547 48 7 886 1431 139135029 139134494 0.000000e+00 667.0
10 TraesCS2B01G261800 chr7A 95.924 368 13 2 1804 2170 87691326 87690960 1.620000e-166 595.0
11 TraesCS2B01G261800 chr7A 95.676 370 16 0 1801 2170 563496033 563496402 1.620000e-166 595.0
12 TraesCS2B01G261800 chr7A 96.143 363 12 1 1809 2169 435730990 435730628 2.100000e-165 592.0
13 TraesCS2B01G261800 chr7A 97.619 126 2 1 2329 2454 563496400 563496524 5.310000e-52 215.0
14 TraesCS2B01G261800 chr7A 98.611 72 0 1 2332 2403 435730626 435730556 2.560000e-25 126.0
15 TraesCS2B01G261800 chr7A 93.220 59 4 0 2396 2454 435730372 435730314 1.210000e-13 87.9
16 TraesCS2B01G261800 chr5A 96.611 1623 47 5 191 1805 690643132 690641510 0.000000e+00 2686.0
17 TraesCS2B01G261800 chr5A 96.881 545 14 2 191 732 698853177 698853721 0.000000e+00 909.0
18 TraesCS2B01G261800 chr5A 97.581 124 3 0 2047 2170 690640509 690640386 1.910000e-51 213.0
19 TraesCS2B01G261800 chr5A 96.032 126 4 1 2329 2454 690640388 690640264 1.150000e-48 204.0
20 TraesCS2B01G261800 chr5A 97.674 43 1 0 1 43 690644122 690644080 9.410000e-10 75.0
21 TraesCS2B01G261800 chr5A 97.674 43 1 0 1 43 698852186 698852228 9.410000e-10 75.0
22 TraesCS2B01G261800 chr3B 97.676 1463 27 5 1 1457 395707834 395706373 0.000000e+00 2507.0
23 TraesCS2B01G261800 chr3B 98.365 367 6 0 1804 2170 395705250 395704884 0.000000e+00 645.0
24 TraesCS2B01G261800 chr3B 98.089 314 6 0 1492 1805 395706372 395706059 4.610000e-152 547.0
25 TraesCS2B01G261800 chr3B 96.825 126 3 1 2329 2454 395704886 395704762 2.470000e-50 209.0
26 TraesCS2B01G261800 chr1D 96.627 919 28 2 887 1805 34022525 34021610 0.000000e+00 1522.0
27 TraesCS2B01G261800 chr1D 96.446 816 16 7 95 898 34023362 34022548 0.000000e+00 1334.0
28 TraesCS2B01G261800 chr1D 97.548 367 9 0 1804 2170 34020804 34020438 1.600000e-176 628.0
29 TraesCS2B01G261800 chr1D 96.117 206 8 0 1804 2009 123674808 123674603 1.090000e-88 337.0
30 TraesCS2B01G261800 chr1D 96.825 126 3 1 2329 2454 34020440 34020316 2.470000e-50 209.0
31 TraesCS2B01G261800 chr5D 87.531 818 74 17 96 895 448013432 448014239 0.000000e+00 920.0
32 TraesCS2B01G261800 chr5D 88.368 533 50 8 900 1431 448014285 448014806 4.450000e-177 630.0
33 TraesCS2B01G261800 chr5D 92.045 264 20 1 1540 1802 448014875 448015138 1.070000e-98 370.0
34 TraesCS2B01G261800 chr4D 86.358 821 72 20 96 898 170624554 170623756 0.000000e+00 859.0
35 TraesCS2B01G261800 chr4D 85.303 694 64 17 101 787 170691534 170690872 0.000000e+00 682.0
36 TraesCS2B01G261800 chr4D 92.509 267 19 1 1540 1805 170688985 170688719 4.950000e-102 381.0
37 TraesCS2B01G261800 chr4D 92.135 267 20 1 1540 1805 170623130 170622864 2.300000e-100 375.0
38 TraesCS2B01G261800 chr4D 96.651 209 7 0 1801 2009 294695936 294696144 5.020000e-92 348.0
39 TraesCS2B01G261800 chr4D 93.000 100 3 3 1414 1510 414999564 414999662 2.540000e-30 143.0
40 TraesCS2B01G261800 chr1A 87.729 546 55 9 887 1431 291624935 291624401 5.760000e-176 627.0
41 TraesCS2B01G261800 chr1A 91.760 267 21 1 1540 1805 291624332 291624066 1.070000e-98 370.0
42 TraesCS2B01G261800 chr1A 93.064 173 12 0 2161 2333 492657301 492657473 1.130000e-63 254.0
43 TraesCS2B01G261800 chr1B 85.163 492 51 11 95 574 394048717 394048236 3.670000e-133 484.0
44 TraesCS2B01G261800 chr1B 88.930 271 23 6 635 898 394048237 394047967 6.540000e-86 327.0
45 TraesCS2B01G261800 chr4B 83.469 490 61 11 95 574 177114177 177113698 2.900000e-119 438.0
46 TraesCS2B01G261800 chr4B 92.929 99 4 2 1414 1510 511163711 511163808 9.150000e-30 141.0
47 TraesCS2B01G261800 chr2D 97.087 206 6 0 1804 2009 5788962 5788757 5.020000e-92 348.0
48 TraesCS2B01G261800 chr5B 94.737 209 8 1 1801 2009 102917362 102917567 3.040000e-84 322.0
49 TraesCS2B01G261800 chr5B 95.181 166 8 0 2167 2332 145828180 145828345 1.870000e-66 263.0
50 TraesCS2B01G261800 chr5B 93.103 174 11 1 2169 2342 338489197 338489025 1.130000e-63 254.0
51 TraesCS2B01G261800 chr5B 92.157 102 5 2 1414 1513 166379180 166379080 9.150000e-30 141.0
52 TraesCS2B01G261800 chr6B 96.341 164 6 0 2169 2332 468734655 468734818 1.120000e-68 270.0
53 TraesCS2B01G261800 chr6B 95.122 164 8 0 2169 2332 229680784 229680947 2.420000e-65 259.0
54 TraesCS2B01G261800 chr3A 96.341 164 6 0 2169 2332 731100715 731100878 1.120000e-68 270.0
55 TraesCS2B01G261800 chr3A 92.929 99 4 2 1414 1510 470095776 470095679 9.150000e-30 141.0
56 TraesCS2B01G261800 chr6D 95.122 164 8 0 2169 2332 81746768 81746931 2.420000e-65 259.0


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 TraesCS2B01G261800 chr2B 338727021 338729474 2453 True 4532.000000 4532 100.000000 1 2454 1 chr2B.!!$R4 2453
1 TraesCS2B01G261800 chr7A 563493481 563496524 3043 False 1200.333333 2791 96.468000 95 2454 3 chr7A.!!$F1 2359
2 TraesCS2B01G261800 chr7A 87690960 87693886 2926 True 1119.666667 1491 95.666667 95 2170 3 chr7A.!!$R1 2075
3 TraesCS2B01G261800 chr7A 435730314 435733518 3204 True 916.725000 2861 96.206250 98 2454 4 chr7A.!!$R3 2356
4 TraesCS2B01G261800 chr7A 139134494 139135857 1363 True 808.500000 950 88.608000 96 1431 2 chr7A.!!$R2 1335
5 TraesCS2B01G261800 chr5A 690640264 690644122 3858 True 794.500000 2686 96.974500 1 2454 4 chr5A.!!$R1 2453
6 TraesCS2B01G261800 chr5A 698852186 698853721 1535 False 492.000000 909 97.277500 1 732 2 chr5A.!!$F1 731
7 TraesCS2B01G261800 chr3B 395704762 395707834 3072 True 977.000000 2507 97.738750 1 2454 4 chr3B.!!$R1 2453
8 TraesCS2B01G261800 chr1D 34020316 34023362 3046 True 923.250000 1522 96.861500 95 2454 4 chr1D.!!$R2 2359
9 TraesCS2B01G261800 chr5D 448013432 448015138 1706 False 640.000000 920 89.314667 96 1802 3 chr5D.!!$F1 1706
10 TraesCS2B01G261800 chr4D 170622864 170624554 1690 True 617.000000 859 89.246500 96 1805 2 chr4D.!!$R1 1709
11 TraesCS2B01G261800 chr4D 170688719 170691534 2815 True 531.500000 682 88.906000 101 1805 2 chr4D.!!$R2 1704
12 TraesCS2B01G261800 chr1A 291624066 291624935 869 True 498.500000 627 89.744500 887 1805 2 chr1A.!!$R1 918
13 TraesCS2B01G261800 chr1B 394047967 394048717 750 True 405.500000 484 87.046500 95 898 2 chr1B.!!$R1 803

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
575 1401 2.46521 GCAATGTTTCTGCCGATCTC 57.535 50.0 0.0 0.0 33.51 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 5105 0.036765 TTGCTCCGTATGTGGTCCAC 60.037 55.0 15.64 15.64 34.56 4.02 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
51 52 4.376340 AACTGAAGTTTTCTGCACCTTG 57.624 40.909 0.00 0.00 33.93 3.61
575 1401 2.465210 GCAATGTTTCTGCCGATCTC 57.535 50.000 0.00 0.00 33.51 2.75
758 1586 4.755123 GTGGTGAAGAAAACTAGCAAGCTA 59.245 41.667 1.37 1.37 0.00 3.32
1136 3157 4.228210 TCATCTCATTAGTTGGCTTCCCTT 59.772 41.667 0.00 0.00 0.00 3.95
1687 3732 2.683362 GGAAGTGTTAGCCTGCCATTAC 59.317 50.000 0.00 0.00 0.00 1.89
1930 4818 8.980610 CAAACATCATCATTTCAAAAGTAGCAA 58.019 29.630 0.00 0.00 0.00 3.91
2156 5047 7.581213 AACAACAAAAGTATTGGATGAGACA 57.419 32.000 0.00 0.00 0.00 3.41
2167 5058 1.404391 GGATGAGACAAGGCAAGCATG 59.596 52.381 0.00 0.00 0.00 4.06
2168 5059 2.089980 GATGAGACAAGGCAAGCATGT 58.910 47.619 0.00 2.91 0.00 3.21
2169 5060 2.857186 TGAGACAAGGCAAGCATGTA 57.143 45.000 0.00 0.00 0.00 2.29
2170 5061 2.426522 TGAGACAAGGCAAGCATGTAC 58.573 47.619 0.00 0.00 0.00 2.90
2171 5062 2.038952 TGAGACAAGGCAAGCATGTACT 59.961 45.455 0.00 3.50 0.00 2.73
2172 5063 2.675348 GAGACAAGGCAAGCATGTACTC 59.325 50.000 0.00 7.74 0.00 2.59
2173 5064 1.740025 GACAAGGCAAGCATGTACTCC 59.260 52.381 0.00 0.00 0.00 3.85
2174 5065 1.098050 CAAGGCAAGCATGTACTCCC 58.902 55.000 0.00 0.00 0.00 4.30
2175 5066 0.995024 AAGGCAAGCATGTACTCCCT 59.005 50.000 0.00 0.00 0.00 4.20
2176 5067 0.543749 AGGCAAGCATGTACTCCCTC 59.456 55.000 0.00 0.00 0.00 4.30
2177 5068 0.464554 GGCAAGCATGTACTCCCTCC 60.465 60.000 0.00 0.00 0.00 4.30
2178 5069 0.811616 GCAAGCATGTACTCCCTCCG 60.812 60.000 0.00 0.00 0.00 4.63
2179 5070 0.537188 CAAGCATGTACTCCCTCCGT 59.463 55.000 0.00 0.00 0.00 4.69
2180 5071 1.066143 CAAGCATGTACTCCCTCCGTT 60.066 52.381 0.00 0.00 0.00 4.44
2181 5072 0.824759 AGCATGTACTCCCTCCGTTC 59.175 55.000 0.00 0.00 0.00 3.95
2182 5073 0.179081 GCATGTACTCCCTCCGTTCC 60.179 60.000 0.00 0.00 0.00 3.62
2183 5074 1.486211 CATGTACTCCCTCCGTTCCT 58.514 55.000 0.00 0.00 0.00 3.36
2184 5075 2.662866 CATGTACTCCCTCCGTTCCTA 58.337 52.381 0.00 0.00 0.00 2.94
2185 5076 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
2186 5077 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
2187 5078 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
2188 5079 3.449737 TGTACTCCCTCCGTTCCTAAATG 59.550 47.826 0.00 0.00 0.00 2.32
2189 5080 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
2190 5081 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
2191 5082 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
2192 5083 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
2193 5084 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
2194 5085 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
2195 5086 4.081309 CCCTCCGTTCCTAAATGTAAGTCA 60.081 45.833 0.00 0.00 0.00 3.41
2196 5087 5.396436 CCCTCCGTTCCTAAATGTAAGTCAT 60.396 44.000 0.00 0.00 38.57 3.06
2198 5089 6.037172 CCTCCGTTCCTAAATGTAAGTCATTG 59.963 42.308 0.00 0.00 44.85 2.82
2199 5090 6.469410 TCCGTTCCTAAATGTAAGTCATTGT 58.531 36.000 0.00 0.00 44.85 2.71
2200 5091 7.613585 TCCGTTCCTAAATGTAAGTCATTGTA 58.386 34.615 0.00 0.00 44.85 2.41
2201 5092 8.095792 TCCGTTCCTAAATGTAAGTCATTGTAA 58.904 33.333 0.00 0.00 44.85 2.41
2202 5093 8.723311 CCGTTCCTAAATGTAAGTCATTGTAAA 58.277 33.333 0.00 0.00 44.85 2.01
2203 5094 9.755064 CGTTCCTAAATGTAAGTCATTGTAAAG 57.245 33.333 0.00 0.00 44.85 1.85
2211 5102 9.520515 AATGTAAGTCATTGTAAAGATTCCACT 57.479 29.630 0.00 0.00 44.06 4.00
2213 5104 9.653287 TGTAAGTCATTGTAAAGATTCCACTAG 57.347 33.333 0.00 0.00 0.00 2.57
2214 5105 9.099454 GTAAGTCATTGTAAAGATTCCACTAGG 57.901 37.037 0.00 0.00 0.00 3.02
2215 5106 7.259088 AGTCATTGTAAAGATTCCACTAGGT 57.741 36.000 0.00 0.00 35.89 3.08
2216 5107 7.106239 AGTCATTGTAAAGATTCCACTAGGTG 58.894 38.462 0.00 0.00 35.89 4.00
2227 5118 2.579207 CACTAGGTGGACCACATACG 57.421 55.000 25.75 17.52 38.89 3.06
2228 5119 1.136305 CACTAGGTGGACCACATACGG 59.864 57.143 25.75 14.34 38.89 4.02
2229 5120 1.006281 ACTAGGTGGACCACATACGGA 59.994 52.381 25.75 3.07 38.89 4.69
2230 5121 1.681793 CTAGGTGGACCACATACGGAG 59.318 57.143 25.75 9.53 38.89 4.63
2231 5122 1.153429 GGTGGACCACATACGGAGC 60.153 63.158 25.75 2.24 35.86 4.70
2232 5123 1.594833 GTGGACCACATACGGAGCA 59.405 57.895 20.14 0.00 34.08 4.26
2233 5124 0.036765 GTGGACCACATACGGAGCAA 60.037 55.000 20.14 0.00 34.08 3.91
2234 5125 0.687920 TGGACCACATACGGAGCAAA 59.312 50.000 0.00 0.00 0.00 3.68
2235 5126 1.072489 TGGACCACATACGGAGCAAAA 59.928 47.619 0.00 0.00 0.00 2.44
2236 5127 2.290641 TGGACCACATACGGAGCAAAAT 60.291 45.455 0.00 0.00 0.00 1.82
2237 5128 2.097466 GGACCACATACGGAGCAAAATG 59.903 50.000 0.00 0.00 0.00 2.32
2238 5129 3.006940 GACCACATACGGAGCAAAATGA 58.993 45.455 0.00 0.00 0.00 2.57
2239 5130 3.417101 ACCACATACGGAGCAAAATGAA 58.583 40.909 0.00 0.00 0.00 2.57
2240 5131 4.016444 ACCACATACGGAGCAAAATGAAT 58.984 39.130 0.00 0.00 0.00 2.57
2241 5132 4.142403 ACCACATACGGAGCAAAATGAATG 60.142 41.667 0.00 0.00 0.00 2.67
2242 5133 4.096231 CCACATACGGAGCAAAATGAATGA 59.904 41.667 0.00 0.00 0.00 2.57
2243 5134 5.392919 CCACATACGGAGCAAAATGAATGAA 60.393 40.000 0.00 0.00 0.00 2.57
2244 5135 6.267817 CACATACGGAGCAAAATGAATGAAT 58.732 36.000 0.00 0.00 0.00 2.57
2245 5136 6.415867 CACATACGGAGCAAAATGAATGAATC 59.584 38.462 0.00 0.00 0.00 2.52
2246 5137 4.376340 ACGGAGCAAAATGAATGAATCC 57.624 40.909 0.00 0.00 0.00 3.01
2247 5138 3.763360 ACGGAGCAAAATGAATGAATCCA 59.237 39.130 0.00 0.00 0.00 3.41
2248 5139 4.403432 ACGGAGCAAAATGAATGAATCCAT 59.597 37.500 0.00 0.00 33.66 3.41
2249 5140 5.593909 ACGGAGCAAAATGAATGAATCCATA 59.406 36.000 0.00 0.00 31.59 2.74
2250 5141 5.916883 CGGAGCAAAATGAATGAATCCATAC 59.083 40.000 0.00 0.00 31.59 2.39
2251 5142 6.238842 CGGAGCAAAATGAATGAATCCATACT 60.239 38.462 0.00 0.00 31.59 2.12
2252 5143 7.495055 GGAGCAAAATGAATGAATCCATACTT 58.505 34.615 0.00 0.00 31.59 2.24
2253 5144 8.632679 GGAGCAAAATGAATGAATCCATACTTA 58.367 33.333 0.00 0.00 31.59 2.24
2282 5173 9.800572 ATGCATCTATATACATCCGTATCTAGT 57.199 33.333 0.00 0.00 39.17 2.57
2283 5174 9.628500 TGCATCTATATACATCCGTATCTAGTT 57.372 33.333 0.00 0.00 39.17 2.24
2291 5182 6.576662 ACATCCGTATCTAGTTCATAGTGG 57.423 41.667 0.00 0.00 32.85 4.00
2292 5183 6.304624 ACATCCGTATCTAGTTCATAGTGGA 58.695 40.000 0.00 0.00 32.85 4.02
2293 5184 6.776116 ACATCCGTATCTAGTTCATAGTGGAA 59.224 38.462 0.00 0.00 32.85 3.53
2294 5185 7.451877 ACATCCGTATCTAGTTCATAGTGGAAT 59.548 37.037 0.00 0.00 32.85 3.01
2295 5186 7.450124 TCCGTATCTAGTTCATAGTGGAATC 57.550 40.000 0.00 0.00 32.85 2.52
2296 5187 7.232188 TCCGTATCTAGTTCATAGTGGAATCT 58.768 38.462 0.00 0.00 32.85 2.40
2297 5188 7.390996 TCCGTATCTAGTTCATAGTGGAATCTC 59.609 40.741 0.00 0.00 32.85 2.75
2298 5189 7.392113 CCGTATCTAGTTCATAGTGGAATCTCT 59.608 40.741 0.00 0.00 32.85 3.10
2299 5190 9.438228 CGTATCTAGTTCATAGTGGAATCTCTA 57.562 37.037 0.00 0.00 32.85 2.43
2302 5193 9.647918 ATCTAGTTCATAGTGGAATCTCTACAA 57.352 33.333 0.00 0.00 29.47 2.41
2303 5194 9.475620 TCTAGTTCATAGTGGAATCTCTACAAA 57.524 33.333 0.00 0.00 29.47 2.83
2304 5195 9.743057 CTAGTTCATAGTGGAATCTCTACAAAG 57.257 37.037 0.00 0.00 29.47 2.77
2305 5196 8.367660 AGTTCATAGTGGAATCTCTACAAAGA 57.632 34.615 0.00 0.00 29.47 2.52
2306 5197 8.254508 AGTTCATAGTGGAATCTCTACAAAGAC 58.745 37.037 0.00 0.00 29.47 3.01
2307 5198 7.962995 TCATAGTGGAATCTCTACAAAGACT 57.037 36.000 0.00 0.00 29.47 3.24
2308 5199 8.367660 TCATAGTGGAATCTCTACAAAGACTT 57.632 34.615 0.00 0.00 29.47 3.01
2309 5200 9.475620 TCATAGTGGAATCTCTACAAAGACTTA 57.524 33.333 0.00 0.00 29.47 2.24
2325 5216 9.379791 ACAAAGACTTATATTTAGAAACGGAGG 57.620 33.333 0.00 0.00 0.00 4.30
2326 5217 8.827677 CAAAGACTTATATTTAGAAACGGAGGG 58.172 37.037 0.00 0.00 0.00 4.30
2327 5218 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
2410 5301 7.235935 ACTGTGGCTTGTACTACTATTGTAA 57.764 36.000 0.00 0.00 0.00 2.41
2444 5526 6.818644 TGGTTGTCTTGAGCTTAATATGAGAC 59.181 38.462 0.00 0.00 34.24 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
377 1196 7.974501 ACGAAACAAATGTTGTGGTTAATTACA 59.025 29.630 0.00 0.00 44.59 2.41
571 1395 8.099364 TGCATTTCTTTTAGTTCTTTCGAGAT 57.901 30.769 0.00 0.00 0.00 2.75
575 1401 5.343325 GGCTGCATTTCTTTTAGTTCTTTCG 59.657 40.000 0.50 0.00 0.00 3.46
758 1586 5.523916 GTGCACGTATGAATTTCTCCTATGT 59.476 40.000 0.00 0.00 0.00 2.29
1072 3093 0.323633 TCGACAATCCGGTGAGGGTA 60.324 55.000 0.00 0.00 41.52 3.69
1687 3732 2.103263 GTCAGGCCCTATACTCAACTGG 59.897 54.545 0.00 0.00 0.00 4.00
2156 5047 0.995024 AGGGAGTACATGCTTGCCTT 59.005 50.000 0.00 0.00 26.86 4.35
2167 5058 3.450096 ACATTTAGGAACGGAGGGAGTAC 59.550 47.826 0.00 0.00 0.00 2.73
2168 5059 3.716431 ACATTTAGGAACGGAGGGAGTA 58.284 45.455 0.00 0.00 0.00 2.59
2169 5060 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85
2170 5061 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2171 5062 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2172 5063 4.081309 TGACTTACATTTAGGAACGGAGGG 60.081 45.833 0.00 0.00 0.00 4.30
2173 5064 5.080969 TGACTTACATTTAGGAACGGAGG 57.919 43.478 0.00 0.00 0.00 4.30
2174 5065 6.594159 ACAATGACTTACATTTAGGAACGGAG 59.406 38.462 0.00 0.00 45.60 4.63
2175 5066 6.469410 ACAATGACTTACATTTAGGAACGGA 58.531 36.000 0.00 0.00 45.60 4.69
2176 5067 6.737254 ACAATGACTTACATTTAGGAACGG 57.263 37.500 0.00 0.00 45.60 4.44
2177 5068 9.755064 CTTTACAATGACTTACATTTAGGAACG 57.245 33.333 0.00 0.00 45.60 3.95
2187 5078 9.653287 CTAGTGGAATCTTTACAATGACTTACA 57.347 33.333 0.00 0.00 0.00 2.41
2188 5079 9.099454 CCTAGTGGAATCTTTACAATGACTTAC 57.901 37.037 0.00 0.00 34.57 2.34
2189 5080 8.822805 ACCTAGTGGAATCTTTACAATGACTTA 58.177 33.333 0.00 0.00 37.04 2.24
2190 5081 7.607991 CACCTAGTGGAATCTTTACAATGACTT 59.392 37.037 0.00 0.00 37.04 3.01
2191 5082 7.106239 CACCTAGTGGAATCTTTACAATGACT 58.894 38.462 0.00 0.00 37.04 3.41
2192 5083 7.308782 CACCTAGTGGAATCTTTACAATGAC 57.691 40.000 0.00 0.00 37.04 3.06
2208 5099 1.136305 CCGTATGTGGTCCACCTAGTG 59.864 57.143 19.57 9.04 36.82 2.74
2209 5100 1.006281 TCCGTATGTGGTCCACCTAGT 59.994 52.381 19.57 5.65 36.82 2.57
2210 5101 1.681793 CTCCGTATGTGGTCCACCTAG 59.318 57.143 19.57 8.03 36.82 3.02
2211 5102 1.771565 CTCCGTATGTGGTCCACCTA 58.228 55.000 19.57 11.14 36.82 3.08
2212 5103 1.614241 GCTCCGTATGTGGTCCACCT 61.614 60.000 19.57 12.22 36.82 4.00
2213 5104 1.153429 GCTCCGTATGTGGTCCACC 60.153 63.158 19.57 3.13 32.73 4.61
2214 5105 0.036765 TTGCTCCGTATGTGGTCCAC 60.037 55.000 15.64 15.64 34.56 4.02
2215 5106 0.687920 TTTGCTCCGTATGTGGTCCA 59.312 50.000 0.00 0.00 0.00 4.02
2216 5107 1.816074 TTTTGCTCCGTATGTGGTCC 58.184 50.000 0.00 0.00 0.00 4.46
2217 5108 3.006940 TCATTTTGCTCCGTATGTGGTC 58.993 45.455 0.00 0.00 0.00 4.02
2218 5109 3.066291 TCATTTTGCTCCGTATGTGGT 57.934 42.857 0.00 0.00 0.00 4.16
2219 5110 4.096231 TCATTCATTTTGCTCCGTATGTGG 59.904 41.667 0.00 0.00 0.00 4.17
2220 5111 5.233957 TCATTCATTTTGCTCCGTATGTG 57.766 39.130 0.00 0.00 0.00 3.21
2221 5112 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
2222 5113 5.916883 GGATTCATTCATTTTGCTCCGTATG 59.083 40.000 0.00 0.00 0.00 2.39
2223 5114 5.593909 TGGATTCATTCATTTTGCTCCGTAT 59.406 36.000 0.00 0.00 0.00 3.06
2224 5115 4.946772 TGGATTCATTCATTTTGCTCCGTA 59.053 37.500 0.00 0.00 0.00 4.02
2225 5116 3.763360 TGGATTCATTCATTTTGCTCCGT 59.237 39.130 0.00 0.00 0.00 4.69
2226 5117 4.374843 TGGATTCATTCATTTTGCTCCG 57.625 40.909 0.00 0.00 0.00 4.63
2227 5118 7.047460 AGTATGGATTCATTCATTTTGCTCC 57.953 36.000 0.00 0.00 34.96 4.70
2265 5156 9.392259 CCACTATGAACTAGATACGGATGTATA 57.608 37.037 0.00 0.00 41.37 1.47
2266 5157 8.107729 TCCACTATGAACTAGATACGGATGTAT 58.892 37.037 0.00 0.00 43.97 2.29
2267 5158 7.455891 TCCACTATGAACTAGATACGGATGTA 58.544 38.462 0.00 0.00 34.45 2.29
2268 5159 6.304624 TCCACTATGAACTAGATACGGATGT 58.695 40.000 0.00 0.00 0.00 3.06
2269 5160 6.819397 TCCACTATGAACTAGATACGGATG 57.181 41.667 0.00 0.00 0.00 3.51
2270 5161 7.891183 AGATTCCACTATGAACTAGATACGGAT 59.109 37.037 0.00 0.00 0.00 4.18
2271 5162 7.232188 AGATTCCACTATGAACTAGATACGGA 58.768 38.462 0.00 0.00 0.00 4.69
2272 5163 7.392113 AGAGATTCCACTATGAACTAGATACGG 59.608 40.741 0.00 0.00 0.00 4.02
2273 5164 8.330466 AGAGATTCCACTATGAACTAGATACG 57.670 38.462 0.00 0.00 0.00 3.06
2276 5167 9.647918 TTGTAGAGATTCCACTATGAACTAGAT 57.352 33.333 0.00 0.00 0.00 1.98
2277 5168 9.475620 TTTGTAGAGATTCCACTATGAACTAGA 57.524 33.333 0.00 0.00 0.00 2.43
2278 5169 9.743057 CTTTGTAGAGATTCCACTATGAACTAG 57.257 37.037 0.00 0.00 0.00 2.57
2279 5170 9.475620 TCTTTGTAGAGATTCCACTATGAACTA 57.524 33.333 0.00 0.00 0.00 2.24
2280 5171 8.254508 GTCTTTGTAGAGATTCCACTATGAACT 58.745 37.037 0.00 0.00 0.00 3.01
2281 5172 8.254508 AGTCTTTGTAGAGATTCCACTATGAAC 58.745 37.037 0.00 0.00 0.00 3.18
2282 5173 8.367660 AGTCTTTGTAGAGATTCCACTATGAA 57.632 34.615 0.00 0.00 0.00 2.57
2283 5174 7.962995 AGTCTTTGTAGAGATTCCACTATGA 57.037 36.000 0.00 0.00 0.00 2.15
2299 5190 9.379791 CCTCCGTTTCTAAATATAAGTCTTTGT 57.620 33.333 0.00 0.00 0.00 2.83
2300 5191 8.827677 CCCTCCGTTTCTAAATATAAGTCTTTG 58.172 37.037 0.00 0.00 0.00 2.77
2301 5192 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
2302 5193 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
2303 5194 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
2304 5195 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
2305 5196 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
2309 5200 9.338622 CAAAATACTCCCTCCGTTTCTAAATAT 57.661 33.333 0.00 0.00 0.00 1.28
2310 5201 7.281549 GCAAAATACTCCCTCCGTTTCTAAATA 59.718 37.037 0.00 0.00 0.00 1.40
2311 5202 6.095021 GCAAAATACTCCCTCCGTTTCTAAAT 59.905 38.462 0.00 0.00 0.00 1.40
2312 5203 5.413523 GCAAAATACTCCCTCCGTTTCTAAA 59.586 40.000 0.00 0.00 0.00 1.85
2313 5204 4.939439 GCAAAATACTCCCTCCGTTTCTAA 59.061 41.667 0.00 0.00 0.00 2.10
2314 5205 4.224370 AGCAAAATACTCCCTCCGTTTCTA 59.776 41.667 0.00 0.00 0.00 2.10
2315 5206 3.009143 AGCAAAATACTCCCTCCGTTTCT 59.991 43.478 0.00 0.00 0.00 2.52
2316 5207 3.344515 AGCAAAATACTCCCTCCGTTTC 58.655 45.455 0.00 0.00 0.00 2.78
2317 5208 3.434940 AGCAAAATACTCCCTCCGTTT 57.565 42.857 0.00 0.00 0.00 3.60
2318 5209 3.081804 CAAGCAAAATACTCCCTCCGTT 58.918 45.455 0.00 0.00 0.00 4.44
2319 5210 2.711542 CAAGCAAAATACTCCCTCCGT 58.288 47.619 0.00 0.00 0.00 4.69
2320 5211 1.401905 GCAAGCAAAATACTCCCTCCG 59.598 52.381 0.00 0.00 0.00 4.63
2321 5212 2.446435 TGCAAGCAAAATACTCCCTCC 58.554 47.619 0.00 0.00 0.00 4.30
2322 5213 3.181483 CCATGCAAGCAAAATACTCCCTC 60.181 47.826 0.00 0.00 0.00 4.30
2323 5214 2.762327 CCATGCAAGCAAAATACTCCCT 59.238 45.455 0.00 0.00 0.00 4.20
2324 5215 2.497273 ACCATGCAAGCAAAATACTCCC 59.503 45.455 0.00 0.00 0.00 4.30
2325 5216 3.731867 CGACCATGCAAGCAAAATACTCC 60.732 47.826 0.00 0.00 0.00 3.85
2326 5217 3.429085 CGACCATGCAAGCAAAATACTC 58.571 45.455 0.00 0.00 0.00 2.59
2327 5218 2.415893 GCGACCATGCAAGCAAAATACT 60.416 45.455 0.00 0.00 34.15 2.12
2395 5286 7.258441 CAGCTCTGCTTTACAATAGTAGTACA 58.742 38.462 2.52 0.00 36.40 2.90
2410 5301 1.141657 TCAAGACAACCAGCTCTGCTT 59.858 47.619 0.00 0.00 36.40 3.91


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

AutoCloner maintained by Alex Coulton.