Multiple sequence alignment - TraesCS3D01G350300

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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 TraesCS3D01G350300 chr3D 100.000 2273 0 0 1 2273 461590060 461587788 0.000000e+00 4198.0
1 TraesCS3D01G350300 chr3D 86.438 612 57 20 521 1131 461313722 461313136 0.000000e+00 647.0
2 TraesCS3D01G350300 chr3D 85.000 620 62 12 500 1119 461373071 461372483 3.230000e-168 601.0
3 TraesCS3D01G350300 chr3D 86.180 521 46 17 441 958 461426878 461426381 7.140000e-150 540.0
4 TraesCS3D01G350300 chr3D 82.710 214 28 7 1313 1518 461587791 461588003 4.990000e-42 182.0
5 TraesCS3D01G350300 chr3D 82.710 214 28 7 2058 2270 461588543 461588748 4.990000e-42 182.0
6 TraesCS3D01G350300 chr3D 76.818 220 16 14 194 402 461314008 461313813 8.650000e-15 91.6
7 TraesCS3D01G350300 chr3D 97.297 37 1 0 211 247 461427080 461427044 1.880000e-06 63.9
8 TraesCS3D01G350300 chr3A 91.071 1232 72 19 1 1223 603896371 603895169 0.000000e+00 1631.0
9 TraesCS3D01G350300 chr3A 84.367 774 85 16 461 1226 603847386 603846641 0.000000e+00 726.0
10 TraesCS3D01G350300 chr3A 87.362 633 61 6 500 1131 603814119 603813505 0.000000e+00 708.0
11 TraesCS3D01G350300 chr3A 100.000 30 0 0 373 402 603847455 603847426 3.150000e-04 56.5
12 TraesCS3D01G350300 chr3B 91.189 1169 87 9 64 1225 612360774 612359615 0.000000e+00 1574.0
13 TraesCS3D01G350300 chr3B 87.480 615 63 7 521 1131 612104332 612103728 0.000000e+00 697.0
14 TraesCS3D01G350300 chr3B 83.405 699 82 20 442 1127 612296129 612295452 3.210000e-173 617.0
15 TraesCS3D01G350300 chr3B 91.111 90 5 2 60 149 612296918 612296832 3.970000e-23 119.0
16 TraesCS3D01G350300 chr3B 76.389 216 21 17 196 402 612104617 612104423 3.110000e-14 89.8
17 TraesCS3D01G350300 chr1D 87.784 352 37 4 1567 1916 366689569 366689916 7.560000e-110 407.0
18 TraesCS3D01G350300 chr1D 89.189 259 26 2 1311 1569 366688825 366689081 2.820000e-84 322.0
19 TraesCS3D01G350300 chr1D 89.806 206 20 1 1314 1518 366690209 366690004 1.730000e-66 263.0
20 TraesCS3D01G350300 chr1D 82.927 205 27 6 2058 2262 366689030 366688834 6.450000e-41 178.0
21 TraesCS3D01G350300 chr1D 82.119 151 23 4 2121 2269 80967968 80967820 2.370000e-25 126.0
22 TraesCS3D01G350300 chr1D 84.483 116 18 0 2147 2262 424523396 424523281 5.130000e-22 115.0
23 TraesCS3D01G350300 chr6D 86.932 352 41 3 1567 1916 37899912 37900260 7.610000e-105 390.0
24 TraesCS3D01G350300 chr7A 87.209 344 38 4 1567 1908 565369316 565368977 9.850000e-104 387.0
25 TraesCS3D01G350300 chr7A 88.281 256 29 1 1314 1569 565370207 565369953 2.840000e-79 305.0
26 TraesCS3D01G350300 chr7D 86.533 349 40 5 1567 1911 225199158 225198813 5.930000e-101 377.0
27 TraesCS3D01G350300 chr7D 87.069 116 15 0 1321 1436 26481436 26481321 5.090000e-27 132.0
28 TraesCS3D01G350300 chr2B 86.120 317 39 3 1567 1881 774370314 774370627 1.010000e-88 337.0
29 TraesCS3D01G350300 chr2B 82.818 291 41 7 1972 2262 774375672 774375953 3.750000e-63 252.0
30 TraesCS3D01G350300 chr2B 87.923 207 24 1 1312 1518 774375962 774375757 2.260000e-60 243.0
31 TraesCS3D01G350300 chr1B 84.393 346 46 6 1916 2261 636663880 636663543 1.300000e-87 333.0
32 TraesCS3D01G350300 chr1B 86.939 245 29 1 1325 1569 636664818 636664577 2.880000e-69 272.0
33 TraesCS3D01G350300 chr1B 87.245 196 25 0 1323 1518 636663543 636663738 8.170000e-55 224.0
34 TraesCS3D01G350300 chr1B 81.429 210 30 6 2055 2263 636664621 636664822 1.810000e-36 163.0
35 TraesCS3D01G350300 chr7B 87.302 252 29 1 1318 1569 693311702 693311950 3.700000e-73 285.0
36 TraesCS3D01G350300 chr7B 82.857 210 27 7 2055 2263 693311906 693311705 1.790000e-41 180.0
37 TraesCS3D01G350300 chr1A 78.947 114 22 1 2159 2270 573058561 573058448 2.420000e-10 76.8


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 TraesCS3D01G350300 chr3D 461587788 461590060 2272 True 4198.00 4198 100.0000 1 2273 1 chr3D.!!$R2 2272
1 TraesCS3D01G350300 chr3D 461372483 461373071 588 True 601.00 601 85.0000 500 1119 1 chr3D.!!$R1 619
2 TraesCS3D01G350300 chr3D 461313136 461314008 872 True 369.30 647 81.6280 194 1131 2 chr3D.!!$R3 937
3 TraesCS3D01G350300 chr3D 461426381 461427080 699 True 301.95 540 91.7385 211 958 2 chr3D.!!$R4 747
4 TraesCS3D01G350300 chr3A 603895169 603896371 1202 True 1631.00 1631 91.0710 1 1223 1 chr3A.!!$R2 1222
5 TraesCS3D01G350300 chr3A 603813505 603814119 614 True 708.00 708 87.3620 500 1131 1 chr3A.!!$R1 631
6 TraesCS3D01G350300 chr3A 603846641 603847455 814 True 391.25 726 92.1835 373 1226 2 chr3A.!!$R3 853
7 TraesCS3D01G350300 chr3B 612359615 612360774 1159 True 1574.00 1574 91.1890 64 1225 1 chr3B.!!$R1 1161
8 TraesCS3D01G350300 chr3B 612103728 612104617 889 True 393.40 697 81.9345 196 1131 2 chr3B.!!$R2 935
9 TraesCS3D01G350300 chr3B 612295452 612296918 1466 True 368.00 617 87.2580 60 1127 2 chr3B.!!$R3 1067
10 TraesCS3D01G350300 chr1D 366688825 366689916 1091 False 364.50 407 88.4865 1311 1916 2 chr1D.!!$F1 605
11 TraesCS3D01G350300 chr1D 366688834 366690209 1375 True 220.50 263 86.3665 1314 2262 2 chr1D.!!$R3 948
12 TraesCS3D01G350300 chr7A 565368977 565370207 1230 True 346.00 387 87.7450 1314 1908 2 chr7A.!!$R1 594
13 TraesCS3D01G350300 chr1B 636663543 636664818 1275 True 302.50 333 85.6660 1325 2261 2 chr1B.!!$R1 936

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
263 747 0.171903 CCACCCGTACGTACTCCAAG 59.828 60.0 22.55 7.3 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 2033 0.03582 GACCATACTCAAACCGCCCA 60.036 55.0 0.0 0.0 0.0 5.36 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
117 118 7.065923 CACACATGTTGACTAGACTAGCTACTA 59.934 40.741 9.52 0.00 0.00 1.82
119 120 7.281324 CACATGTTGACTAGACTAGCTACTACT 59.719 40.741 9.52 0.00 0.00 2.57
120 121 7.496591 ACATGTTGACTAGACTAGCTACTACTC 59.503 40.741 9.52 0.00 0.00 2.59
172 181 1.594862 AGATCGTGTACGTACCGTAGC 59.405 52.381 25.34 18.19 43.06 3.58
173 182 1.327460 GATCGTGTACGTACCGTAGCA 59.673 52.381 25.34 13.69 43.06 3.49
174 183 0.442310 TCGTGTACGTACCGTAGCAC 59.558 55.000 25.34 15.49 43.06 4.40
175 184 0.443869 CGTGTACGTACCGTAGCACT 59.556 55.000 22.43 0.00 43.06 4.40
187 671 1.810755 CGTAGCACTACTCTCACACCA 59.189 52.381 6.28 0.00 34.04 4.17
247 731 0.456312 CGTCCACGTCTAGAAGCCAC 60.456 60.000 5.51 0.00 34.11 5.01
263 747 0.171903 CCACCCGTACGTACTCCAAG 59.828 60.000 22.55 7.30 0.00 3.61
272 756 5.218139 CGTACGTACTCCAAGAAAGACTTT 58.782 41.667 22.55 0.00 36.61 2.66
274 758 3.808174 ACGTACTCCAAGAAAGACTTTGC 59.192 43.478 4.85 0.00 36.61 3.68
280 764 1.000171 CAAGAAAGACTTTGCTGGGCC 60.000 52.381 4.85 0.00 36.61 5.80
439 941 4.726876 GCCGAAAGTGATTTTACACGATCC 60.727 45.833 0.00 0.00 44.35 3.36
486 1013 3.483869 GGGGACTAGCCTGCCAGG 61.484 72.222 6.32 6.32 38.80 4.45
493 1020 1.814772 CTAGCCTGCCAGGGATCGAG 61.815 65.000 13.78 0.00 35.37 4.04
494 1021 2.589610 TAGCCTGCCAGGGATCGAGT 62.590 60.000 13.78 0.00 35.37 4.18
495 1022 2.134287 GCCTGCCAGGGATCGAGTA 61.134 63.158 13.78 0.00 35.37 2.59
496 1023 1.476007 GCCTGCCAGGGATCGAGTAT 61.476 60.000 13.78 0.00 35.37 2.12
497 1024 1.051812 CCTGCCAGGGATCGAGTATT 58.948 55.000 1.63 0.00 0.00 1.89
498 1025 1.270518 CCTGCCAGGGATCGAGTATTG 60.271 57.143 1.63 0.00 0.00 1.90
516 1061 0.673956 TGGTCCAGACTCGAGAGACG 60.674 60.000 21.68 4.19 44.09 4.18
597 1142 2.895865 CGCCTGCTCATGCTCCTG 60.896 66.667 0.00 0.00 40.48 3.86
628 1185 1.002990 CAGCATCAGCACCACCAGA 60.003 57.895 0.00 0.00 45.49 3.86
763 1332 4.033776 GCCCTAGGCTGCACCACA 62.034 66.667 2.05 0.00 46.69 4.17
1050 1630 0.116342 TCTGCCTGGACCTGAACCTA 59.884 55.000 0.00 0.00 0.00 3.08
1070 1650 2.815647 GCCTTCGGAGAACTGCGG 60.816 66.667 14.78 0.00 45.90 5.69
1211 1797 4.207955 GGGAAGGAATGTTGGGATAAGTC 58.792 47.826 0.00 0.00 0.00 3.01
1226 1812 1.037493 AAGTCGGGAAAAAGGCAACC 58.963 50.000 0.00 0.00 37.17 3.77
1227 1813 0.185175 AGTCGGGAAAAAGGCAACCT 59.815 50.000 0.00 0.00 33.87 3.50
1229 1815 2.158579 AGTCGGGAAAAAGGCAACCTTA 60.159 45.455 0.00 0.00 43.92 2.69
1230 1816 2.823747 GTCGGGAAAAAGGCAACCTTAT 59.176 45.455 0.00 0.00 43.92 1.73
1231 1817 2.823154 TCGGGAAAAAGGCAACCTTATG 59.177 45.455 0.00 0.00 43.92 1.90
1232 1818 2.094234 CGGGAAAAAGGCAACCTTATGG 60.094 50.000 0.00 0.00 43.92 2.74
1233 1819 2.354704 GGGAAAAAGGCAACCTTATGGC 60.355 50.000 0.00 0.00 43.92 4.40
1234 1820 2.301583 GGAAAAAGGCAACCTTATGGCA 59.698 45.455 0.00 0.00 43.92 4.92
1235 1821 3.588955 GAAAAAGGCAACCTTATGGCAG 58.411 45.455 0.00 0.00 43.92 4.85
1236 1822 2.603075 AAAGGCAACCTTATGGCAGA 57.397 45.000 0.00 0.00 43.92 4.26
1237 1823 3.105959 AAAGGCAACCTTATGGCAGAT 57.894 42.857 0.00 0.00 43.92 2.90
1238 1824 3.444029 AAAGGCAACCTTATGGCAGATT 58.556 40.909 0.00 0.00 43.92 2.40
1239 1825 2.877043 GGCAACCTTATGGCAGATTG 57.123 50.000 0.00 0.00 44.66 2.67
1240 1826 1.410153 GGCAACCTTATGGCAGATTGG 59.590 52.381 0.00 0.00 44.66 3.16
1241 1827 2.378038 GCAACCTTATGGCAGATTGGA 58.622 47.619 8.36 0.00 36.63 3.53
1242 1828 2.760092 GCAACCTTATGGCAGATTGGAA 59.240 45.455 8.36 0.00 36.63 3.53
1243 1829 3.181483 GCAACCTTATGGCAGATTGGAAG 60.181 47.826 8.36 2.61 36.63 3.46
1244 1830 4.272489 CAACCTTATGGCAGATTGGAAGA 58.728 43.478 8.36 0.00 36.63 2.87
1245 1831 4.803329 ACCTTATGGCAGATTGGAAGAT 57.197 40.909 8.36 0.00 36.63 2.40
1246 1832 5.134725 ACCTTATGGCAGATTGGAAGATT 57.865 39.130 8.36 0.00 36.63 2.40
1247 1833 5.136105 ACCTTATGGCAGATTGGAAGATTC 58.864 41.667 8.36 0.00 36.63 2.52
1248 1834 5.103771 ACCTTATGGCAGATTGGAAGATTCT 60.104 40.000 8.36 0.00 36.63 2.40
1249 1835 6.101734 ACCTTATGGCAGATTGGAAGATTCTA 59.898 38.462 8.36 0.00 36.63 2.10
1250 1836 7.000472 CCTTATGGCAGATTGGAAGATTCTAA 59.000 38.462 0.00 0.00 32.12 2.10
1251 1837 7.668886 CCTTATGGCAGATTGGAAGATTCTAAT 59.331 37.037 4.08 4.08 40.47 1.73
1252 1838 9.730705 CTTATGGCAGATTGGAAGATTCTAATA 57.269 33.333 4.39 0.00 38.31 0.98
1254 1840 8.804912 ATGGCAGATTGGAAGATTCTAATATC 57.195 34.615 4.39 0.00 38.31 1.63
1255 1841 7.982252 TGGCAGATTGGAAGATTCTAATATCT 58.018 34.615 4.39 0.00 38.31 1.98
1256 1842 8.099537 TGGCAGATTGGAAGATTCTAATATCTC 58.900 37.037 4.39 0.00 38.31 2.75
1257 1843 7.552330 GGCAGATTGGAAGATTCTAATATCTCC 59.448 40.741 4.39 2.57 38.31 3.71
1258 1844 8.099537 GCAGATTGGAAGATTCTAATATCTCCA 58.900 37.037 4.39 0.00 38.31 3.86
1272 1858 9.631257 TCTAATATCTCCATTTCAATTTGCTGA 57.369 29.630 0.00 0.00 0.00 4.26
1275 1861 9.542462 AATATCTCCATTTCAATTTGCTGATTG 57.458 29.630 6.35 6.35 38.16 2.67
1276 1862 6.593268 TCTCCATTTCAATTTGCTGATTGA 57.407 33.333 10.10 10.10 42.58 2.57
1277 1863 7.177832 TCTCCATTTCAATTTGCTGATTGAT 57.822 32.000 13.55 1.28 43.43 2.57
1278 1864 7.039270 TCTCCATTTCAATTTGCTGATTGATG 58.961 34.615 13.55 10.63 43.43 3.07
1279 1865 5.583061 TCCATTTCAATTTGCTGATTGATGC 59.417 36.000 13.55 0.00 43.43 3.91
1280 1866 5.584649 CCATTTCAATTTGCTGATTGATGCT 59.415 36.000 13.55 2.92 43.43 3.79
1281 1867 6.093495 CCATTTCAATTTGCTGATTGATGCTT 59.907 34.615 13.55 0.00 43.43 3.91
1282 1868 7.361713 CCATTTCAATTTGCTGATTGATGCTTT 60.362 33.333 13.55 0.00 43.43 3.51
1283 1869 8.661257 CATTTCAATTTGCTGATTGATGCTTTA 58.339 29.630 13.55 0.00 43.43 1.85
1284 1870 8.604640 TTTCAATTTGCTGATTGATGCTTTAA 57.395 26.923 13.55 4.52 43.43 1.52
1285 1871 8.780846 TTCAATTTGCTGATTGATGCTTTAAT 57.219 26.923 13.55 0.00 43.43 1.40
1286 1872 8.192068 TCAATTTGCTGATTGATGCTTTAATG 57.808 30.769 10.10 0.00 40.20 1.90
1287 1873 7.279090 TCAATTTGCTGATTGATGCTTTAATGG 59.721 33.333 10.10 0.00 40.20 3.16
1288 1874 5.918426 TTGCTGATTGATGCTTTAATGGA 57.082 34.783 0.00 0.00 0.00 3.41
1289 1875 5.918426 TGCTGATTGATGCTTTAATGGAA 57.082 34.783 0.00 0.00 0.00 3.53
1290 1876 5.898174 TGCTGATTGATGCTTTAATGGAAG 58.102 37.500 0.00 0.00 0.00 3.46
1291 1877 5.419788 TGCTGATTGATGCTTTAATGGAAGT 59.580 36.000 0.00 0.00 0.00 3.01
1292 1878 5.747197 GCTGATTGATGCTTTAATGGAAGTG 59.253 40.000 0.00 0.00 0.00 3.16
1293 1879 5.653507 TGATTGATGCTTTAATGGAAGTGC 58.346 37.500 0.00 0.00 0.00 4.40
1294 1880 5.185442 TGATTGATGCTTTAATGGAAGTGCA 59.815 36.000 0.00 0.00 34.38 4.57
1295 1881 5.465532 TTGATGCTTTAATGGAAGTGCAA 57.534 34.783 0.00 0.00 33.85 4.08
1296 1882 5.664294 TGATGCTTTAATGGAAGTGCAAT 57.336 34.783 0.00 0.00 33.85 3.56
1297 1883 5.412640 TGATGCTTTAATGGAAGTGCAATG 58.587 37.500 0.00 0.00 33.85 2.82
1298 1884 4.191033 TGCTTTAATGGAAGTGCAATGG 57.809 40.909 0.00 0.00 0.00 3.16
1299 1885 3.831333 TGCTTTAATGGAAGTGCAATGGA 59.169 39.130 0.00 0.00 0.00 3.41
1300 1886 4.176271 GCTTTAATGGAAGTGCAATGGAC 58.824 43.478 0.00 0.00 0.00 4.02
1301 1887 4.414852 CTTTAATGGAAGTGCAATGGACG 58.585 43.478 0.00 0.00 0.00 4.79
1302 1888 1.909700 AATGGAAGTGCAATGGACGT 58.090 45.000 0.00 0.00 0.00 4.34
1303 1889 1.909700 ATGGAAGTGCAATGGACGTT 58.090 45.000 0.00 0.00 0.00 3.99
1304 1890 0.950836 TGGAAGTGCAATGGACGTTG 59.049 50.000 0.00 0.00 0.00 4.10
1313 1899 3.829886 CAATGGACGTTGCACACTAAT 57.170 42.857 0.00 0.00 0.00 1.73
1314 1900 4.159377 CAATGGACGTTGCACACTAATT 57.841 40.909 0.00 0.00 0.00 1.40
1315 1901 5.289917 CAATGGACGTTGCACACTAATTA 57.710 39.130 0.00 0.00 0.00 1.40
1316 1902 5.879237 CAATGGACGTTGCACACTAATTAT 58.121 37.500 0.00 0.00 0.00 1.28
1317 1903 7.010697 CAATGGACGTTGCACACTAATTATA 57.989 36.000 0.00 0.00 0.00 0.98
1318 1904 7.468441 CAATGGACGTTGCACACTAATTATAA 58.532 34.615 0.00 0.00 0.00 0.98
1361 1947 8.469309 TTCATCCTTGAATTCTCTCAAAAGTT 57.531 30.769 7.05 0.00 36.94 2.66
1381 1967 7.761038 AAGTTTAGAAATCGTCCCTCAATTT 57.239 32.000 0.00 0.00 0.00 1.82
1382 1968 7.761038 AGTTTAGAAATCGTCCCTCAATTTT 57.239 32.000 0.00 0.00 0.00 1.82
1414 2000 9.057089 CAGTAAAACTCAGTCCTTGAACTAATT 57.943 33.333 0.00 0.00 34.81 1.40
1421 2007 6.761312 TCAGTCCTTGAACTAATTAAACCGA 58.239 36.000 0.00 0.00 31.34 4.69
1436 2022 4.707030 AAACCGAATAATTTTCGTCCCC 57.293 40.909 16.21 0.00 40.04 4.81
1447 2033 3.405823 TTTCGTCCCCGATAACACTTT 57.594 42.857 0.00 0.00 43.80 2.66
1464 2050 1.472480 CTTTGGGCGGTTTGAGTATGG 59.528 52.381 0.00 0.00 0.00 2.74
1466 2052 0.035820 TGGGCGGTTTGAGTATGGTC 60.036 55.000 0.00 0.00 0.00 4.02
1471 2057 2.420129 GCGGTTTGAGTATGGTCTGGAT 60.420 50.000 0.00 0.00 0.00 3.41
1489 2075 3.010420 GGATCTGGTTTTGACTAGCACC 58.990 50.000 0.00 0.00 0.00 5.01
1524 2110 1.984297 GTTTGACCGCTACGTCTCTTC 59.016 52.381 0.00 0.00 33.70 2.87
1555 2141 4.148825 GGAGCTGATGGACGCCGT 62.149 66.667 0.00 0.00 0.00 5.68
1569 2155 2.167861 GCCGTTAGCTGCTCCTTCG 61.168 63.158 4.91 7.05 38.99 3.79
1579 2845 3.064987 GCTCCTTCGTGCCGAGCTA 62.065 63.158 1.14 0.00 44.52 3.32
1585 2851 1.248785 TTCGTGCCGAGCTAGAGGTT 61.249 55.000 0.00 0.00 37.14 3.50
1639 2905 2.517402 CTACCTCGAGCTCGGCCT 60.517 66.667 33.98 18.76 40.29 5.19
1641 2907 2.951475 CTACCTCGAGCTCGGCCTCT 62.951 65.000 33.98 15.42 40.29 3.69
1661 3109 1.411246 TGTGTGTGTTACCTCGAGCTT 59.589 47.619 6.99 0.00 0.00 3.74
1694 3219 4.560743 TGCGTGCCACCTTGAGCA 62.561 61.111 0.00 0.00 36.44 4.26
1706 3231 1.466866 CCTTGAGCACGAACGATACGA 60.467 52.381 0.14 0.00 34.70 3.43
1708 3233 0.518195 TGAGCACGAACGATACGACA 59.482 50.000 0.14 0.00 34.70 4.35
1709 3234 1.069091 TGAGCACGAACGATACGACAA 60.069 47.619 0.14 0.00 34.70 3.18
1716 3241 0.457337 AACGATACGACAACGGAGGC 60.457 55.000 0.00 0.00 44.46 4.70
1737 3264 0.602638 GCATGGACTGACACGTGGAA 60.603 55.000 21.57 6.37 0.00 3.53
1743 3270 1.003355 CTGACACGTGGAAGGGCAT 60.003 57.895 21.57 0.00 0.00 4.40
1754 3281 1.432270 GAAGGGCATGCACTAGTCGC 61.432 60.000 25.68 6.90 0.00 5.19
1755 3282 1.903877 AAGGGCATGCACTAGTCGCT 61.904 55.000 25.68 2.59 0.00 4.93
1762 3289 1.179174 TGCACTAGTCGCTGAGTGGT 61.179 55.000 15.28 2.57 42.77 4.16
1872 3516 2.044806 GCATCCCTGGTCGCCATACT 62.045 60.000 0.00 0.00 30.82 2.12
1889 3533 3.686760 TCCTCACGGAGCAGACAG 58.313 61.111 0.00 0.00 33.30 3.51
1890 3534 1.979155 TCCTCACGGAGCAGACAGG 60.979 63.158 0.00 0.00 33.30 4.00
1891 3535 2.125753 CTCACGGAGCAGACAGGC 60.126 66.667 0.00 0.00 0.00 4.85
1892 3536 2.917227 TCACGGAGCAGACAGGCA 60.917 61.111 0.00 0.00 35.83 4.75
1893 3537 2.236223 CTCACGGAGCAGACAGGCAT 62.236 60.000 0.00 0.00 35.83 4.40
1894 3538 2.104859 CACGGAGCAGACAGGCATG 61.105 63.158 0.00 0.00 35.83 4.06
1895 3539 3.200593 CGGAGCAGACAGGCATGC 61.201 66.667 9.90 9.90 42.87 4.06
1899 3543 3.991999 GCAGACAGGCATGCTGAA 58.008 55.556 18.92 0.00 39.38 3.02
1900 3544 1.505353 GCAGACAGGCATGCTGAAC 59.495 57.895 18.92 12.47 39.38 3.18
1901 3545 1.792301 CAGACAGGCATGCTGAACG 59.208 57.895 18.92 4.32 34.46 3.95
1902 3546 1.376424 AGACAGGCATGCTGAACGG 60.376 57.895 18.92 3.89 0.00 4.44
1903 3547 2.360350 ACAGGCATGCTGAACGGG 60.360 61.111 18.92 1.56 0.00 5.28
1904 3548 2.360350 CAGGCATGCTGAACGGGT 60.360 61.111 18.92 0.00 0.00 5.28
1905 3549 1.078497 CAGGCATGCTGAACGGGTA 60.078 57.895 18.92 0.00 0.00 3.69
1906 3550 1.078426 AGGCATGCTGAACGGGTAC 60.078 57.895 18.92 0.00 0.00 3.34
1908 3552 2.461110 GCATGCTGAACGGGTACGG 61.461 63.158 11.37 0.00 46.48 4.02
1909 3553 2.125269 ATGCTGAACGGGTACGGC 60.125 61.111 0.00 0.00 46.48 5.68
1910 3554 4.728102 TGCTGAACGGGTACGGCG 62.728 66.667 4.80 4.80 46.48 6.46
1930 3574 4.496336 GCTGGCCGCCATTCTCCT 62.496 66.667 13.86 0.00 30.82 3.69
1931 3575 2.203126 CTGGCCGCCATTCTCCTC 60.203 66.667 13.86 0.00 30.82 3.71
1932 3576 3.008517 TGGCCGCCATTCTCCTCA 61.009 61.111 8.43 0.00 0.00 3.86
1933 3577 2.335092 CTGGCCGCCATTCTCCTCAT 62.335 60.000 13.86 0.00 30.82 2.90
1934 3578 1.895707 GGCCGCCATTCTCCTCATG 60.896 63.158 3.91 0.00 0.00 3.07
1935 3579 1.895707 GCCGCCATTCTCCTCATGG 60.896 63.158 0.00 0.00 43.81 3.66
1936 3580 1.832219 CCGCCATTCTCCTCATGGA 59.168 57.895 3.01 0.00 43.70 3.41
1956 3600 1.239296 GCAGACAGGCATGCTGAACA 61.239 55.000 18.92 0.00 39.38 3.18
1959 3603 0.607489 GACAGGCATGCTGAACAGGT 60.607 55.000 18.92 5.45 30.99 4.00
1960 3604 0.692476 ACAGGCATGCTGAACAGGTA 59.308 50.000 18.92 0.00 30.99 3.08
1966 3762 2.048503 GCTGAACAGGTACGCGGT 60.049 61.111 12.47 0.00 0.00 5.68
1983 3779 4.063967 TGCTCACGTACAGCCGGG 62.064 66.667 14.43 0.00 35.89 5.73
2000 3796 2.032071 GGTAGTGCGGCTGGTTGT 59.968 61.111 0.00 0.00 0.00 3.32
2001 3797 1.294138 GGTAGTGCGGCTGGTTGTA 59.706 57.895 0.00 0.00 0.00 2.41
2013 3809 1.805945 GGTTGTAGACGAGCTGGCG 60.806 63.158 0.00 0.00 37.29 5.69
2014 3810 1.805945 GTTGTAGACGAGCTGGCGG 60.806 63.158 0.00 0.00 35.12 6.13
2055 3851 0.108992 CTCGCCCGTTTGCTACAGTA 60.109 55.000 0.00 0.00 0.00 2.74
2067 3909 0.526211 CTACAGTAGCGTGGCTGTCA 59.474 55.000 10.24 0.00 43.91 3.58
2100 3942 2.032030 CGTGGCCACTGTTAGTCAAAAG 60.032 50.000 32.28 9.17 0.00 2.27
2101 3943 2.949644 GTGGCCACTGTTAGTCAAAAGT 59.050 45.455 29.12 0.00 0.00 2.66
2102 3944 3.003378 GTGGCCACTGTTAGTCAAAAGTC 59.997 47.826 29.12 0.00 0.00 3.01
2103 3945 3.211045 GGCCACTGTTAGTCAAAAGTCA 58.789 45.455 0.00 0.00 0.00 3.41
2104 3946 3.630312 GGCCACTGTTAGTCAAAAGTCAA 59.370 43.478 0.00 0.00 0.00 3.18
2105 3947 4.097286 GGCCACTGTTAGTCAAAAGTCAAA 59.903 41.667 0.00 0.00 0.00 2.69
2106 3948 5.393678 GGCCACTGTTAGTCAAAAGTCAAAA 60.394 40.000 0.00 0.00 0.00 2.44
2108 3950 6.033966 CCACTGTTAGTCAAAAGTCAAAACC 58.966 40.000 0.00 0.00 0.00 3.27
2109 3951 6.349777 CCACTGTTAGTCAAAAGTCAAAACCA 60.350 38.462 0.00 0.00 0.00 3.67
2110 3952 6.747280 CACTGTTAGTCAAAAGTCAAAACCAG 59.253 38.462 0.00 0.00 0.00 4.00
2111 3953 6.127730 ACTGTTAGTCAAAAGTCAAAACCAGG 60.128 38.462 0.00 0.00 0.00 4.45
2112 3954 5.712917 TGTTAGTCAAAAGTCAAAACCAGGT 59.287 36.000 0.00 0.00 0.00 4.00
2113 3955 4.718940 AGTCAAAAGTCAAAACCAGGTG 57.281 40.909 0.00 0.00 0.00 4.00
2114 3956 4.086457 AGTCAAAAGTCAAAACCAGGTGT 58.914 39.130 0.00 0.00 0.00 4.16
2115 3957 4.082245 AGTCAAAAGTCAAAACCAGGTGTG 60.082 41.667 0.00 0.00 0.00 3.82
2119 3961 3.222173 AGTCAAAACCAGGTGTGCATA 57.778 42.857 0.00 0.00 0.00 3.14
2120 3962 3.149196 AGTCAAAACCAGGTGTGCATAG 58.851 45.455 0.00 0.00 0.00 2.23
2134 3976 1.296727 GCATAGTACTCAAACCGCCC 58.703 55.000 0.00 0.00 0.00 6.13
2139 3981 1.375013 TACTCAAACCGCCCGAAGC 60.375 57.895 0.00 0.00 38.52 3.86
2155 3997 2.613691 GAAGCGTTATCAGGGACGAAA 58.386 47.619 0.00 0.00 41.53 3.46
2157 3999 3.048337 AGCGTTATCAGGGACGAAAAA 57.952 42.857 0.00 0.00 41.53 1.94
2165 4007 2.158871 TCAGGGACGAAAAATATCCGGG 60.159 50.000 0.00 0.00 32.90 5.73
2176 4018 6.910433 CGAAAAATATCCGGGTTGATTAGTTG 59.090 38.462 0.00 0.00 0.00 3.16
2199 4041 4.793201 AGGGACTGAGTTTTGCTAGTTTT 58.207 39.130 0.00 0.00 37.18 2.43
2201 4043 4.578928 GGGACTGAGTTTTGCTAGTTTTGA 59.421 41.667 0.00 0.00 0.00 2.69
2203 4045 6.202226 GGACTGAGTTTTGCTAGTTTTGAAG 58.798 40.000 0.00 0.00 0.00 3.02
2221 4063 5.477607 TGAAGTTGAGGGACGATTTCTAA 57.522 39.130 0.00 0.00 32.19 2.10
2226 4068 5.932883 AGTTGAGGGACGATTTCTAAACTTC 59.067 40.000 0.00 0.00 0.00 3.01
2229 4071 2.934553 GGGACGATTTCTAAACTTCCGG 59.065 50.000 0.00 0.00 0.00 5.14
2230 4072 2.934553 GGACGATTTCTAAACTTCCGGG 59.065 50.000 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.098614 CTGACTCTTCTAGAGCAGCCA 58.901 52.381 3.68 0.00 46.12 4.75
117 118 4.204012 GTCATGTGAGTCTAGCTAGGAGT 58.796 47.826 20.58 10.08 0.00 3.85
119 120 3.118371 TCGTCATGTGAGTCTAGCTAGGA 60.118 47.826 20.58 4.56 0.00 2.94
120 121 3.206964 TCGTCATGTGAGTCTAGCTAGG 58.793 50.000 20.58 2.12 0.00 3.02
172 181 0.729478 CGCGTGGTGTGAGAGTAGTG 60.729 60.000 0.00 0.00 0.00 2.74
173 182 1.579932 CGCGTGGTGTGAGAGTAGT 59.420 57.895 0.00 0.00 0.00 2.73
174 183 1.154016 CCGCGTGGTGTGAGAGTAG 60.154 63.158 6.91 0.00 0.00 2.57
175 184 2.632544 CCCGCGTGGTGTGAGAGTA 61.633 63.158 15.14 0.00 0.00 2.59
247 731 2.489329 TCTTTCTTGGAGTACGTACGGG 59.511 50.000 21.06 9.44 0.00 5.28
263 747 0.540597 AGGGCCCAGCAAAGTCTTTC 60.541 55.000 27.56 0.00 0.00 2.62
272 756 3.009115 GACCACTAGGGCCCAGCA 61.009 66.667 27.56 7.67 42.05 4.41
274 758 2.683933 ACGACCACTAGGGCCCAG 60.684 66.667 27.56 21.21 41.31 4.45
280 764 2.809601 GCACGCACGACCACTAGG 60.810 66.667 0.00 0.00 42.21 3.02
439 941 1.878522 GGCGGTGTGCTACTCGATG 60.879 63.158 0.00 0.00 45.43 3.84
486 1013 2.959707 AGTCTGGACCAATACTCGATCC 59.040 50.000 0.00 0.00 0.00 3.36
493 1020 3.065648 GTCTCTCGAGTCTGGACCAATAC 59.934 52.174 13.13 0.00 0.00 1.89
494 1021 3.280295 GTCTCTCGAGTCTGGACCAATA 58.720 50.000 13.13 0.00 0.00 1.90
495 1022 2.096248 GTCTCTCGAGTCTGGACCAAT 58.904 52.381 13.13 0.00 0.00 3.16
496 1023 1.535833 GTCTCTCGAGTCTGGACCAA 58.464 55.000 13.13 0.00 0.00 3.67
497 1024 0.673956 CGTCTCTCGAGTCTGGACCA 60.674 60.000 13.13 0.00 42.86 4.02
498 1025 0.674269 ACGTCTCTCGAGTCTGGACC 60.674 60.000 13.13 0.00 42.86 4.46
516 1061 0.809241 CTCTCTTGCTCATGGCCGAC 60.809 60.000 0.00 0.00 40.92 4.79
607 1152 3.807538 GTGGTGCTGATGCTGGCG 61.808 66.667 0.00 0.00 40.48 5.69
608 1153 3.446570 GGTGGTGCTGATGCTGGC 61.447 66.667 0.00 0.00 40.48 4.85
609 1154 2.034532 TGGTGGTGCTGATGCTGG 59.965 61.111 0.00 0.00 40.48 4.85
610 1155 1.002990 TCTGGTGGTGCTGATGCTG 60.003 57.895 0.00 0.00 40.48 4.41
611 1156 1.298993 CTCTGGTGGTGCTGATGCT 59.701 57.895 0.00 0.00 40.48 3.79
612 1157 2.404995 GCTCTGGTGGTGCTGATGC 61.405 63.158 0.00 0.00 40.20 3.91
613 1158 2.104859 CGCTCTGGTGGTGCTGATG 61.105 63.158 0.00 0.00 32.84 3.07
614 1159 2.267006 CGCTCTGGTGGTGCTGAT 59.733 61.111 0.00 0.00 32.84 2.90
615 1160 4.007644 CCGCTCTGGTGGTGCTGA 62.008 66.667 0.00 0.00 38.25 4.26
750 1316 2.429930 GGTGTGTGGTGCAGCCTA 59.570 61.111 14.36 0.00 38.35 3.93
1026 1598 1.692042 CAGGTCCAGGCAGATCCCT 60.692 63.158 0.00 0.00 34.93 4.20
1070 1650 2.877582 CCGCGCTCTTGCATTTGC 60.878 61.111 5.56 0.00 39.64 3.68
1211 1797 2.094234 CCATAAGGTTGCCTTTTTCCCG 60.094 50.000 5.69 0.00 41.69 5.14
1226 1812 8.632906 ATTAGAATCTTCCAATCTGCCATAAG 57.367 34.615 0.00 0.00 0.00 1.73
1228 1814 9.896645 GATATTAGAATCTTCCAATCTGCCATA 57.103 33.333 0.00 0.00 0.00 2.74
1229 1815 8.613034 AGATATTAGAATCTTCCAATCTGCCAT 58.387 33.333 0.00 0.00 32.09 4.40
1230 1816 7.982252 AGATATTAGAATCTTCCAATCTGCCA 58.018 34.615 0.00 0.00 32.09 4.92
1231 1817 7.552330 GGAGATATTAGAATCTTCCAATCTGCC 59.448 40.741 0.00 0.00 36.33 4.85
1232 1818 8.099537 TGGAGATATTAGAATCTTCCAATCTGC 58.900 37.037 0.00 3.79 36.33 4.26
1246 1832 9.631257 TCAGCAAATTGAAATGGAGATATTAGA 57.369 29.630 0.00 0.00 0.00 2.10
1249 1835 9.542462 CAATCAGCAAATTGAAATGGAGATATT 57.458 29.630 0.00 0.00 38.64 1.28
1250 1836 8.920174 TCAATCAGCAAATTGAAATGGAGATAT 58.080 29.630 10.36 0.00 41.47 1.63
1251 1837 8.296211 TCAATCAGCAAATTGAAATGGAGATA 57.704 30.769 10.36 0.00 41.47 1.98
1252 1838 7.177832 TCAATCAGCAAATTGAAATGGAGAT 57.822 32.000 10.36 0.00 41.47 2.75
1253 1839 6.593268 TCAATCAGCAAATTGAAATGGAGA 57.407 33.333 10.36 0.00 41.47 3.71
1254 1840 6.238103 GCATCAATCAGCAAATTGAAATGGAG 60.238 38.462 15.15 5.72 45.91 3.86
1255 1841 5.583061 GCATCAATCAGCAAATTGAAATGGA 59.417 36.000 15.15 0.00 45.91 3.41
1256 1842 5.584649 AGCATCAATCAGCAAATTGAAATGG 59.415 36.000 15.15 8.49 45.91 3.16
1257 1843 6.662414 AGCATCAATCAGCAAATTGAAATG 57.338 33.333 15.15 11.76 45.91 2.32
1258 1844 7.681939 AAAGCATCAATCAGCAAATTGAAAT 57.318 28.000 15.15 4.77 45.91 2.17
1259 1845 8.604640 TTAAAGCATCAATCAGCAAATTGAAA 57.395 26.923 15.15 4.48 45.91 2.69
1260 1846 8.661257 CATTAAAGCATCAATCAGCAAATTGAA 58.339 29.630 15.15 1.43 45.91 2.69
1261 1847 7.279090 CCATTAAAGCATCAATCAGCAAATTGA 59.721 33.333 13.97 13.97 46.60 2.57
1262 1848 7.279090 TCCATTAAAGCATCAATCAGCAAATTG 59.721 33.333 5.05 5.05 37.87 2.32
1263 1849 7.332557 TCCATTAAAGCATCAATCAGCAAATT 58.667 30.769 0.00 0.00 0.00 1.82
1264 1850 6.880484 TCCATTAAAGCATCAATCAGCAAAT 58.120 32.000 0.00 0.00 0.00 2.32
1265 1851 6.283544 TCCATTAAAGCATCAATCAGCAAA 57.716 33.333 0.00 0.00 0.00 3.68
1266 1852 5.918426 TCCATTAAAGCATCAATCAGCAA 57.082 34.783 0.00 0.00 0.00 3.91
1267 1853 5.419788 ACTTCCATTAAAGCATCAATCAGCA 59.580 36.000 0.00 0.00 0.00 4.41
1268 1854 5.747197 CACTTCCATTAAAGCATCAATCAGC 59.253 40.000 0.00 0.00 0.00 4.26
1269 1855 5.747197 GCACTTCCATTAAAGCATCAATCAG 59.253 40.000 0.00 0.00 0.00 2.90
1270 1856 5.185442 TGCACTTCCATTAAAGCATCAATCA 59.815 36.000 0.00 0.00 0.00 2.57
1271 1857 5.653507 TGCACTTCCATTAAAGCATCAATC 58.346 37.500 0.00 0.00 0.00 2.67
1272 1858 5.664294 TGCACTTCCATTAAAGCATCAAT 57.336 34.783 0.00 0.00 0.00 2.57
1273 1859 5.465532 TTGCACTTCCATTAAAGCATCAA 57.534 34.783 0.00 0.00 30.83 2.57
1274 1860 5.412640 CATTGCACTTCCATTAAAGCATCA 58.587 37.500 0.00 0.00 30.83 3.07
1275 1861 4.807304 CCATTGCACTTCCATTAAAGCATC 59.193 41.667 0.00 0.00 30.83 3.91
1276 1862 4.467082 TCCATTGCACTTCCATTAAAGCAT 59.533 37.500 0.00 0.00 30.83 3.79
1277 1863 3.831333 TCCATTGCACTTCCATTAAAGCA 59.169 39.130 0.00 0.00 0.00 3.91
1278 1864 4.176271 GTCCATTGCACTTCCATTAAAGC 58.824 43.478 0.00 0.00 0.00 3.51
1279 1865 4.082787 ACGTCCATTGCACTTCCATTAAAG 60.083 41.667 0.00 0.00 0.00 1.85
1280 1866 3.823873 ACGTCCATTGCACTTCCATTAAA 59.176 39.130 0.00 0.00 0.00 1.52
1281 1867 3.417101 ACGTCCATTGCACTTCCATTAA 58.583 40.909 0.00 0.00 0.00 1.40
1282 1868 3.066291 ACGTCCATTGCACTTCCATTA 57.934 42.857 0.00 0.00 0.00 1.90
1283 1869 1.909700 ACGTCCATTGCACTTCCATT 58.090 45.000 0.00 0.00 0.00 3.16
1284 1870 1.541147 CAACGTCCATTGCACTTCCAT 59.459 47.619 0.00 0.00 0.00 3.41
1285 1871 0.950836 CAACGTCCATTGCACTTCCA 59.049 50.000 0.00 0.00 0.00 3.53
1286 1872 3.773117 CAACGTCCATTGCACTTCC 57.227 52.632 0.00 0.00 0.00 3.46
1293 1879 3.829886 ATTAGTGTGCAACGTCCATTG 57.170 42.857 0.00 0.00 42.39 2.82
1294 1880 7.618502 TTATAATTAGTGTGCAACGTCCATT 57.381 32.000 0.00 0.00 42.39 3.16
1295 1881 7.801716 ATTATAATTAGTGTGCAACGTCCAT 57.198 32.000 0.00 0.00 42.39 3.41
1296 1882 7.439955 CCTATTATAATTAGTGTGCAACGTCCA 59.560 37.037 2.68 0.00 42.39 4.02
1297 1883 7.095355 CCCTATTATAATTAGTGTGCAACGTCC 60.095 40.741 2.68 0.00 42.39 4.79
1298 1884 7.654520 TCCCTATTATAATTAGTGTGCAACGTC 59.345 37.037 2.68 0.00 42.39 4.34
1299 1885 7.502696 TCCCTATTATAATTAGTGTGCAACGT 58.497 34.615 2.68 0.00 42.39 3.99
1300 1886 7.956420 TCCCTATTATAATTAGTGTGCAACG 57.044 36.000 2.68 0.00 42.39 4.10
1361 1947 7.753309 TTCAAAATTGAGGGACGATTTCTAA 57.247 32.000 0.00 0.00 40.50 2.10
1381 1967 5.751586 AGGACTGAGTTTTACTGGTTTCAA 58.248 37.500 0.00 0.00 0.00 2.69
1382 1968 5.367945 AGGACTGAGTTTTACTGGTTTCA 57.632 39.130 0.00 0.00 0.00 2.69
1414 2000 5.816449 GGGGACGAAAATTATTCGGTTTA 57.184 39.130 19.59 0.00 45.34 2.01
1436 2022 1.161843 AACCGCCCAAAGTGTTATCG 58.838 50.000 0.00 0.00 0.00 2.92
1447 2033 0.035820 GACCATACTCAAACCGCCCA 60.036 55.000 0.00 0.00 0.00 5.36
1464 2050 3.935828 GCTAGTCAAAACCAGATCCAGAC 59.064 47.826 0.00 0.00 0.00 3.51
1466 2052 3.686726 GTGCTAGTCAAAACCAGATCCAG 59.313 47.826 0.00 0.00 0.00 3.86
1471 2057 1.270625 CCGGTGCTAGTCAAAACCAGA 60.271 52.381 0.00 0.00 32.69 3.86
1514 2100 4.379186 CGAAACCTAAGCTGAAGAGACGTA 60.379 45.833 0.00 0.00 0.00 3.57
1524 2110 0.250513 AGCTCCCGAAACCTAAGCTG 59.749 55.000 0.00 0.00 41.54 4.24
1555 2141 1.079127 GGCACGAAGGAGCAGCTAA 60.079 57.895 0.00 0.00 34.39 3.09
1569 2155 0.101579 GAGAACCTCTAGCTCGGCAC 59.898 60.000 0.00 0.00 0.00 5.01
1579 2845 2.284258 AGGCTGCCGAGAACCTCT 60.284 61.111 13.96 0.00 0.00 3.69
1639 2905 1.000607 GCTCGAGGTAACACACACAGA 60.001 52.381 15.58 0.00 41.41 3.41
1641 2907 1.037493 AGCTCGAGGTAACACACACA 58.963 50.000 16.99 0.00 41.41 3.72
1694 3219 0.516877 TCCGTTGTCGTATCGTTCGT 59.483 50.000 0.00 0.00 35.01 3.85
1708 3233 4.778143 GTCCATGCCGCCTCCGTT 62.778 66.667 0.00 0.00 0.00 4.44
1716 3241 2.048222 ACGTGTCAGTCCATGCCG 60.048 61.111 0.00 0.00 0.00 5.69
1737 3264 2.187946 GCGACTAGTGCATGCCCT 59.812 61.111 16.68 12.26 0.00 5.19
1743 3270 1.179174 ACCACTCAGCGACTAGTGCA 61.179 55.000 16.27 0.00 41.45 4.57
1754 3281 4.767255 GGCCTCGGCACCACTCAG 62.767 72.222 10.51 0.00 44.11 3.35
1888 3532 1.078426 GTACCCGTTCAGCATGCCT 60.078 57.895 15.66 0.00 34.76 4.75
1889 3533 2.461110 CGTACCCGTTCAGCATGCC 61.461 63.158 15.66 0.00 34.76 4.40
1890 3534 2.461110 CCGTACCCGTTCAGCATGC 61.461 63.158 10.51 10.51 34.76 4.06
1891 3535 2.461110 GCCGTACCCGTTCAGCATG 61.461 63.158 0.00 0.00 37.54 4.06
1892 3536 2.125269 GCCGTACCCGTTCAGCAT 60.125 61.111 0.00 0.00 0.00 3.79
1893 3537 4.728102 CGCCGTACCCGTTCAGCA 62.728 66.667 0.00 0.00 0.00 4.41
1914 3558 2.203126 GAGGAGAATGGCGGCCAG 60.203 66.667 27.62 0.00 36.75 4.85
1915 3559 2.377810 ATGAGGAGAATGGCGGCCA 61.378 57.895 26.11 26.11 38.19 5.36
1916 3560 1.895707 CATGAGGAGAATGGCGGCC 60.896 63.158 13.32 13.32 0.00 6.13
1917 3561 1.895707 CCATGAGGAGAATGGCGGC 60.896 63.158 0.00 0.00 38.32 6.53
1918 3562 1.832219 TCCATGAGGAGAATGGCGG 59.168 57.895 0.00 0.00 43.70 6.13
1927 3571 1.620739 GCCTGTCTGCTCCATGAGGA 61.621 60.000 0.00 0.00 43.21 3.71
1928 3572 1.153208 GCCTGTCTGCTCCATGAGG 60.153 63.158 0.00 0.00 0.00 3.86
1929 3573 0.180642 ATGCCTGTCTGCTCCATGAG 59.819 55.000 0.00 0.00 0.00 2.90
1930 3574 0.107361 CATGCCTGTCTGCTCCATGA 60.107 55.000 0.00 0.00 36.32 3.07
1931 3575 1.725557 GCATGCCTGTCTGCTCCATG 61.726 60.000 6.36 0.00 37.07 3.66
1932 3576 1.453379 GCATGCCTGTCTGCTCCAT 60.453 57.895 6.36 0.00 35.49 3.41
1933 3577 2.045634 GCATGCCTGTCTGCTCCA 60.046 61.111 6.36 0.00 35.49 3.86
1934 3578 2.113433 CAGCATGCCTGTCTGCTCC 61.113 63.158 15.66 0.00 45.30 4.70
1935 3579 0.675837 TTCAGCATGCCTGTCTGCTC 60.676 55.000 15.66 0.00 45.30 4.26
1937 3581 1.239296 TGTTCAGCATGCCTGTCTGC 61.239 55.000 15.66 0.00 42.38 4.26
1938 3582 0.803117 CTGTTCAGCATGCCTGTCTG 59.197 55.000 15.66 5.73 42.38 3.51
1939 3583 0.322277 CCTGTTCAGCATGCCTGTCT 60.322 55.000 15.66 0.00 42.38 3.41
1940 3584 0.607489 ACCTGTTCAGCATGCCTGTC 60.607 55.000 15.66 10.11 42.38 3.51
1941 3585 0.692476 TACCTGTTCAGCATGCCTGT 59.308 50.000 15.66 3.95 42.38 4.00
1942 3586 1.089920 GTACCTGTTCAGCATGCCTG 58.910 55.000 15.66 12.20 43.17 4.85
1943 3587 0.391661 CGTACCTGTTCAGCATGCCT 60.392 55.000 15.66 0.00 34.76 4.75
1956 3600 4.415332 CGTGAGCACCGCGTACCT 62.415 66.667 4.92 0.00 43.27 3.08
1966 3762 4.063967 CCCGGCTGTACGTGAGCA 62.064 66.667 19.46 6.46 38.27 4.26
1983 3779 0.739813 CTACAACCAGCCGCACTACC 60.740 60.000 0.00 0.00 0.00 3.18
1992 3788 0.737715 CCAGCTCGTCTACAACCAGC 60.738 60.000 0.00 0.00 41.91 4.85
1997 3793 2.571757 CCGCCAGCTCGTCTACAA 59.428 61.111 0.00 0.00 0.00 2.41
2026 3822 1.466025 AACGGGCGAGAAGGTGTACA 61.466 55.000 0.00 0.00 0.00 2.90
2055 3851 2.542907 CGGTTTTGACAGCCACGCT 61.543 57.895 0.00 0.00 40.77 5.07
2063 3905 2.902846 CGTGGCCCGGTTTTGACA 60.903 61.111 0.00 0.00 0.00 3.58
2087 3929 6.127730 ACCTGGTTTTGACTTTTGACTAACAG 60.128 38.462 0.00 0.00 0.00 3.16
2090 3932 5.712917 ACACCTGGTTTTGACTTTTGACTAA 59.287 36.000 0.00 0.00 0.00 2.24
2100 3942 2.884639 ACTATGCACACCTGGTTTTGAC 59.115 45.455 9.01 2.33 0.00 3.18
2101 3943 3.222173 ACTATGCACACCTGGTTTTGA 57.778 42.857 9.01 0.00 0.00 2.69
2102 3944 4.072131 AGTACTATGCACACCTGGTTTTG 58.928 43.478 0.00 0.00 0.00 2.44
2103 3945 4.202419 TGAGTACTATGCACACCTGGTTTT 60.202 41.667 0.00 0.00 0.00 2.43
2104 3946 3.326588 TGAGTACTATGCACACCTGGTTT 59.673 43.478 0.00 0.00 0.00 3.27
2105 3947 2.903784 TGAGTACTATGCACACCTGGTT 59.096 45.455 0.00 0.00 0.00 3.67
2106 3948 2.536066 TGAGTACTATGCACACCTGGT 58.464 47.619 0.00 0.00 0.00 4.00
2108 3950 3.684788 GGTTTGAGTACTATGCACACCTG 59.315 47.826 9.90 0.00 31.43 4.00
2109 3951 3.616560 CGGTTTGAGTACTATGCACACCT 60.617 47.826 13.53 0.00 31.82 4.00
2110 3952 2.671396 CGGTTTGAGTACTATGCACACC 59.329 50.000 0.00 1.79 0.00 4.16
2111 3953 2.093783 GCGGTTTGAGTACTATGCACAC 59.906 50.000 0.00 0.00 0.00 3.82
2112 3954 2.343101 GCGGTTTGAGTACTATGCACA 58.657 47.619 0.00 0.00 0.00 4.57
2113 3955 1.664151 GGCGGTTTGAGTACTATGCAC 59.336 52.381 0.00 0.00 0.00 4.57
2114 3956 1.406341 GGGCGGTTTGAGTACTATGCA 60.406 52.381 0.00 0.00 0.00 3.96
2115 3957 1.296727 GGGCGGTTTGAGTACTATGC 58.703 55.000 0.00 0.00 0.00 3.14
2119 3961 0.037605 CTTCGGGCGGTTTGAGTACT 60.038 55.000 0.00 0.00 0.00 2.73
2120 3962 1.632948 GCTTCGGGCGGTTTGAGTAC 61.633 60.000 0.00 0.00 0.00 2.73
2134 3976 0.099968 TCGTCCCTGATAACGCTTCG 59.900 55.000 0.00 0.00 38.72 3.79
2139 3981 5.107607 CGGATATTTTTCGTCCCTGATAACG 60.108 44.000 0.00 0.00 40.17 3.18
2155 3997 6.062095 CCTCAACTAATCAACCCGGATATTT 58.938 40.000 0.73 0.00 0.00 1.40
2157 3999 4.041691 CCCTCAACTAATCAACCCGGATAT 59.958 45.833 0.73 0.00 0.00 1.63
2165 4007 5.153950 ACTCAGTCCCTCAACTAATCAAC 57.846 43.478 0.00 0.00 0.00 3.18
2176 4018 3.686916 ACTAGCAAAACTCAGTCCCTC 57.313 47.619 0.00 0.00 0.00 4.30
2199 4041 5.477607 TTAGAAATCGTCCCTCAACTTCA 57.522 39.130 0.00 0.00 0.00 3.02
2201 4043 5.866207 AGTTTAGAAATCGTCCCTCAACTT 58.134 37.500 0.00 0.00 0.00 2.66
2203 4045 5.121925 GGAAGTTTAGAAATCGTCCCTCAAC 59.878 44.000 0.00 0.00 0.00 3.18
2221 4063 2.642807 TCCTTGAATTCTCCCGGAAGTT 59.357 45.455 0.73 0.00 37.36 2.66
2226 4068 3.281727 TTCATCCTTGAATTCTCCCGG 57.718 47.619 7.05 0.00 36.94 5.73


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

AutoCloner maintained by Alex Coulton.