Multiple sequence alignment - TraesCS7D01G316300

Loading Multiple Alignment...

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 TraesCS7D01G316300 chr7D 100.000 4714 0 0 1 4714 402509459 402514172 0.000000e+00 8706.0
1 TraesCS7D01G316300 chr7D 91.182 1599 103 16 2277 3848 402346034 402347621 0.000000e+00 2137.0
2 TraesCS7D01G316300 chr7D 100.000 1046 0 0 4952 5997 402514410 402515455 0.000000e+00 1932.0
3 TraesCS7D01G316300 chr7B 95.285 3054 118 12 1671 4712 412075202 412078241 0.000000e+00 4819.0
4 TraesCS7D01G316300 chr7B 92.122 1079 46 15 4952 5997 412078304 412079376 0.000000e+00 1485.0
5 TraesCS7D01G316300 chr7B 90.381 946 69 14 2410 3343 411874585 411875520 0.000000e+00 1223.0
6 TraesCS7D01G316300 chr7B 90.604 745 27 9 601 1305 412074001 412074742 0.000000e+00 948.0
7 TraesCS7D01G316300 chr7B 91.439 549 45 2 3439 3986 411875527 411876074 0.000000e+00 752.0
8 TraesCS7D01G316300 chr7B 91.408 547 17 6 19 559 412073481 412074003 0.000000e+00 723.0
9 TraesCS7D01G316300 chr7B 92.665 409 26 3 3982 4390 411879285 411879689 2.410000e-163 586.0
10 TraesCS7D01G316300 chr7B 96.040 202 7 1 1400 1600 412074727 412074928 1.610000e-85 327.0
11 TraesCS7D01G316300 chr7B 82.653 196 14 7 353 545 411789399 411789577 8.050000e-34 156.0
12 TraesCS7D01G316300 chr7A 92.060 2393 146 22 2108 4477 460441069 460443440 0.000000e+00 3326.0
13 TraesCS7D01G316300 chr7A 87.961 2874 271 36 1868 4704 460726189 460729024 0.000000e+00 3321.0
14 TraesCS7D01G316300 chr7A 85.174 1005 70 34 358 1305 460724727 460725709 0.000000e+00 957.0
15 TraesCS7D01G316300 chr7A 86.957 851 70 21 5184 5997 460730209 460731055 0.000000e+00 918.0
16 TraesCS7D01G316300 chr7A 86.752 785 66 23 5239 5997 460444945 460445717 0.000000e+00 839.0
17 TraesCS7D01G316300 chr7A 86.645 629 46 15 1435 2062 460332803 460333394 0.000000e+00 662.0
18 TraesCS7D01G316300 chr7A 89.549 488 41 7 1400 1883 460725694 460726175 1.430000e-170 610.0
19 TraesCS7D01G316300 chr7A 83.418 591 70 16 5169 5733 460705144 460705732 1.920000e-144 523.0
20 TraesCS7D01G316300 chr7A 92.050 239 17 2 4952 5189 460443897 460444134 9.630000e-88 335.0
21 TraesCS7D01G316300 chr7A 87.288 236 16 6 4955 5189 460729284 460729506 2.140000e-64 257.0
22 TraesCS7D01G316300 chr7A 90.000 190 17 2 5808 5997 460705731 460705918 1.670000e-60 244.0
23 TraesCS7D01G316300 chr7A 95.588 136 6 0 1 136 460724019 460724154 1.010000e-52 219.0
24 TraesCS7D01G316300 chr7A 90.000 160 16 0 3784 3943 460704160 460704319 2.190000e-49 207.0
25 TraesCS7D01G316300 chr7A 91.304 92 8 0 5098 5189 460704353 460704444 6.310000e-25 126.0
26 TraesCS7D01G316300 chr7A 87.736 106 7 3 422 526 460317898 460317998 1.060000e-22 119.0
27 TraesCS7D01G316300 chr7A 94.915 59 3 0 5189 5247 460444874 460444932 6.400000e-15 93.5
28 TraesCS7D01G316300 chr7A 95.000 40 2 0 703 742 460318181 460318220 5.020000e-06 63.9
29 TraesCS7D01G316300 chr7A 100.000 30 0 0 1194 1223 460332645 460332674 8.400000e-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 TraesCS7D01G316300 chr7D 402509459 402515455 5996 False 5319.000000 8706 100.000000 1 5997 2 chr7D.!!$F2 5996
1 TraesCS7D01G316300 chr7D 402346034 402347621 1587 False 2137.000000 2137 91.182000 2277 3848 1 chr7D.!!$F1 1571
2 TraesCS7D01G316300 chr7B 412073481 412079376 5895 False 1660.400000 4819 93.091800 19 5997 5 chr7B.!!$F3 5978
3 TraesCS7D01G316300 chr7B 411874585 411879689 5104 False 853.666667 1223 91.495000 2410 4390 3 chr7B.!!$F2 1980
4 TraesCS7D01G316300 chr7A 460441069 460445717 4648 False 1148.375000 3326 91.444250 2108 5997 4 chr7A.!!$F3 3889
5 TraesCS7D01G316300 chr7A 460724019 460731055 7036 False 1047.000000 3321 88.752833 1 5997 6 chr7A.!!$F5 5996
6 TraesCS7D01G316300 chr7A 460332645 460333394 749 False 359.250000 662 93.322500 1194 2062 2 chr7A.!!$F2 868
7 TraesCS7D01G316300 chr7A 460704160 460705918 1758 False 275.000000 523 88.680500 3784 5997 4 chr7A.!!$F4 2213

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
332 335 0.459585 GCGCGTCAGACCTCCATTAA 60.460 55.000 8.43 0.00 0.00 1.40 F
1294 1785 0.035056 GAACTGGGTGTCCCTCATGG 60.035 60.000 6.38 0.00 45.70 3.66 F
1322 1813 0.109272 CGTCCGACATACTGCAGTGT 60.109 55.000 29.57 20.69 0.00 3.55 F
1348 1839 0.323725 AGGTCATTGACATGTGGGCC 60.324 55.000 18.09 0.00 33.68 5.80 F
1385 1876 0.462581 ACATGTGCGCCCATCTGTAG 60.463 55.000 1.11 0.00 0.00 2.74 F
2084 2821 0.537371 ACCAAGAAAGGCCCAACTCG 60.537 55.000 0.00 0.00 0.00 4.18 F
2421 3171 3.118408 TCATATGGCCTACAGTTTCGCTT 60.118 43.478 3.32 0.00 0.00 4.68 F
3203 3974 3.545703 AGAACATTTATCTCTTGGCGGG 58.454 45.455 0.00 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 1875 0.106369 CATGACATGTGGGCCATCCT 60.106 55.000 10.70 0.00 36.20 3.24 R
2473 3223 0.250209 CCCCTCGATGGAGCATTCAG 60.250 60.000 8.50 0.00 39.06 3.02 R
3260 4031 5.108517 TCAACAGAAATTCCAAAACTGCAC 58.891 37.500 0.00 0.00 32.67 4.57 R
3327 4099 1.253100 CACGTGGGCTTATTTTGGGT 58.747 50.000 7.95 0.00 0.00 4.51 R
3419 4192 7.788026 TCATCCCTACACGTAATAATGAGTTT 58.212 34.615 0.00 0.00 0.00 2.66 R
3569 4344 4.323553 TTTTGGGAAATTTACACGGGTG 57.676 40.909 0.00 0.00 0.00 4.61 R
4399 8392 5.163963 GCAAATAAGTTATGTGCAAACTGGC 60.164 40.000 26.55 2.51 46.39 4.85 R
5006 9012 1.834263 ACTCTTCATGGCTACCCAGAC 59.166 52.381 0.00 0.00 46.24 3.51 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
197 200 2.009774 CCATCATCTCCGTGTTTGACC 58.990 52.381 0.00 0.00 0.00 4.02
198 201 2.615240 CCATCATCTCCGTGTTTGACCA 60.615 50.000 0.00 0.00 0.00 4.02
199 202 3.273434 CATCATCTCCGTGTTTGACCAT 58.727 45.455 0.00 0.00 0.00 3.55
200 203 3.417069 TCATCTCCGTGTTTGACCATT 57.583 42.857 0.00 0.00 0.00 3.16
201 204 4.545208 TCATCTCCGTGTTTGACCATTA 57.455 40.909 0.00 0.00 0.00 1.90
202 205 4.250464 TCATCTCCGTGTTTGACCATTAC 58.750 43.478 0.00 0.00 0.00 1.89
203 206 3.048337 TCTCCGTGTTTGACCATTACC 57.952 47.619 0.00 0.00 0.00 2.85
204 207 2.635915 TCTCCGTGTTTGACCATTACCT 59.364 45.455 0.00 0.00 0.00 3.08
205 208 3.833650 TCTCCGTGTTTGACCATTACCTA 59.166 43.478 0.00 0.00 0.00 3.08
206 209 4.081862 TCTCCGTGTTTGACCATTACCTAG 60.082 45.833 0.00 0.00 0.00 3.02
207 210 2.676342 CCGTGTTTGACCATTACCTAGC 59.324 50.000 0.00 0.00 0.00 3.42
228 231 3.797039 CGCAAGATTCTCCTAACCATGA 58.203 45.455 0.00 0.00 43.02 3.07
242 245 6.672218 TCCTAACCATGACAAGAGGAGAATTA 59.328 38.462 0.00 0.00 0.00 1.40
245 248 6.566079 ACCATGACAAGAGGAGAATTATGA 57.434 37.500 0.00 0.00 0.00 2.15
310 313 1.445066 CAGACGAGTGCGAGCATGT 60.445 57.895 0.00 0.63 41.64 3.21
332 335 0.459585 GCGCGTCAGACCTCCATTAA 60.460 55.000 8.43 0.00 0.00 1.40
333 336 1.806623 GCGCGTCAGACCTCCATTAAT 60.807 52.381 8.43 0.00 0.00 1.40
334 337 2.545113 GCGCGTCAGACCTCCATTAATA 60.545 50.000 8.43 0.00 0.00 0.98
335 338 3.861131 GCGCGTCAGACCTCCATTAATAT 60.861 47.826 8.43 0.00 0.00 1.28
438 791 2.004017 TGTGTGTTCGAGTGTCAAACC 58.996 47.619 0.00 0.00 0.00 3.27
512 865 2.070861 CGTACCTCGCAAGCAGTTC 58.929 57.895 0.00 0.00 37.18 3.01
576 929 0.787183 GCTATCGCGAATGGAAGAGC 59.213 55.000 15.24 2.96 0.00 4.09
582 935 3.266636 TCGCGAATGGAAGAGCATTAAA 58.733 40.909 6.20 0.00 0.00 1.52
645 1004 5.107133 AGCTAAGCTATCGCGACTTTTTAA 58.893 37.500 12.93 0.00 42.32 1.52
746 1138 1.789751 CATGTACGTGGTGCTGCTG 59.210 57.895 7.22 0.00 0.00 4.41
872 1275 4.963276 TCAAATTGTACTGTATGCCTGC 57.037 40.909 0.00 0.00 0.00 4.85
941 1355 7.458397 TCATTACCAAGTCACTTACCAAGATT 58.542 34.615 0.00 0.00 0.00 2.40
1065 1501 3.776656 CGTAAGTTTCCTCGCCCG 58.223 61.111 0.00 0.00 0.00 6.13
1098 1534 1.523095 GCGTCATCTCTTGTTATCCGC 59.477 52.381 0.00 0.00 0.00 5.54
1107 1543 1.330521 CTTGTTATCCGCCCGATGTTG 59.669 52.381 0.00 0.00 31.92 3.33
1124 1560 0.968405 TTGCAAGATTTCCAGCCCAC 59.032 50.000 0.00 0.00 0.00 4.61
1132 1568 1.337118 TTTCCAGCCCACCACATTTC 58.663 50.000 0.00 0.00 0.00 2.17
1140 1576 1.075374 CCCACCACATTTCCCTTGAGA 59.925 52.381 0.00 0.00 0.00 3.27
1180 1616 3.851969 CGTCTGCACGTTCGCATATATAT 59.148 43.478 0.55 0.00 42.06 0.86
1181 1617 5.025826 CGTCTGCACGTTCGCATATATATA 58.974 41.667 0.55 0.00 42.06 0.86
1287 1778 1.056660 TCCTTGAGAACTGGGTGTCC 58.943 55.000 0.00 0.00 0.00 4.02
1289 1780 1.059913 CTTGAGAACTGGGTGTCCCT 58.940 55.000 6.38 0.00 45.70 4.20
1290 1781 1.002544 CTTGAGAACTGGGTGTCCCTC 59.997 57.143 6.38 0.00 45.70 4.30
1291 1782 0.105194 TGAGAACTGGGTGTCCCTCA 60.105 55.000 6.38 0.00 45.70 3.86
1292 1783 1.280457 GAGAACTGGGTGTCCCTCAT 58.720 55.000 6.38 0.00 45.70 2.90
1293 1784 0.987294 AGAACTGGGTGTCCCTCATG 59.013 55.000 6.38 0.00 45.70 3.07
1294 1785 0.035056 GAACTGGGTGTCCCTCATGG 60.035 60.000 6.38 0.00 45.70 3.66
1295 1786 0.475632 AACTGGGTGTCCCTCATGGA 60.476 55.000 6.38 0.00 45.70 3.41
1304 1795 2.294449 TCCCTCATGGACCTAGATCG 57.706 55.000 0.00 0.00 38.61 3.69
1305 1796 1.499438 TCCCTCATGGACCTAGATCGT 59.501 52.381 0.00 0.00 38.61 3.73
1306 1797 1.889829 CCCTCATGGACCTAGATCGTC 59.110 57.143 0.00 0.00 35.39 4.20
1311 1802 3.091318 GGACCTAGATCGTCCGACA 57.909 57.895 2.93 0.00 40.46 4.35
1312 1803 1.606903 GGACCTAGATCGTCCGACAT 58.393 55.000 2.93 0.00 40.46 3.06
1313 1804 2.775890 GGACCTAGATCGTCCGACATA 58.224 52.381 2.93 0.00 40.46 2.29
1314 1805 2.483491 GGACCTAGATCGTCCGACATAC 59.517 54.545 2.93 0.00 40.46 2.39
1315 1806 3.401182 GACCTAGATCGTCCGACATACT 58.599 50.000 0.00 0.00 0.00 2.12
1316 1807 3.139850 ACCTAGATCGTCCGACATACTG 58.860 50.000 0.00 0.00 0.00 2.74
1317 1808 2.095668 CCTAGATCGTCCGACATACTGC 60.096 54.545 0.00 0.00 0.00 4.40
1318 1809 1.389555 AGATCGTCCGACATACTGCA 58.610 50.000 0.00 0.00 0.00 4.41
1319 1810 1.335182 AGATCGTCCGACATACTGCAG 59.665 52.381 13.48 13.48 0.00 4.41
1320 1811 1.065701 GATCGTCCGACATACTGCAGT 59.934 52.381 25.12 25.12 0.00 4.40
1321 1812 0.170339 TCGTCCGACATACTGCAGTG 59.830 55.000 29.57 16.03 0.00 3.66
1322 1813 0.109272 CGTCCGACATACTGCAGTGT 60.109 55.000 29.57 20.69 0.00 3.55
1323 1814 1.350193 GTCCGACATACTGCAGTGTG 58.650 55.000 34.00 34.00 41.98 3.82
1324 1815 0.389817 TCCGACATACTGCAGTGTGC 60.390 55.000 35.11 26.93 45.29 4.57
1334 1825 3.305709 GCAGTGTGCAGTTAGGTCA 57.694 52.632 0.00 0.00 44.26 4.02
1335 1826 1.813513 GCAGTGTGCAGTTAGGTCAT 58.186 50.000 0.00 0.00 44.26 3.06
1336 1827 2.154462 GCAGTGTGCAGTTAGGTCATT 58.846 47.619 0.00 0.00 44.26 2.57
1337 1828 2.095567 GCAGTGTGCAGTTAGGTCATTG 60.096 50.000 0.00 0.00 44.26 2.82
1338 1829 3.402110 CAGTGTGCAGTTAGGTCATTGA 58.598 45.455 0.00 0.00 0.00 2.57
1339 1830 3.187227 CAGTGTGCAGTTAGGTCATTGAC 59.813 47.826 8.34 8.34 0.00 3.18
1340 1831 3.138304 GTGTGCAGTTAGGTCATTGACA 58.862 45.455 18.09 0.00 33.68 3.58
1341 1832 3.753272 GTGTGCAGTTAGGTCATTGACAT 59.247 43.478 18.09 13.79 33.68 3.06
1342 1833 3.752747 TGTGCAGTTAGGTCATTGACATG 59.247 43.478 18.09 9.25 33.68 3.21
1343 1834 3.753272 GTGCAGTTAGGTCATTGACATGT 59.247 43.478 18.09 0.00 33.68 3.21
1344 1835 3.752747 TGCAGTTAGGTCATTGACATGTG 59.247 43.478 18.09 11.27 33.68 3.21
1345 1836 3.127548 GCAGTTAGGTCATTGACATGTGG 59.872 47.826 18.09 4.87 33.68 4.17
1346 1837 3.691118 CAGTTAGGTCATTGACATGTGGG 59.309 47.826 18.09 0.76 33.68 4.61
1347 1838 2.418368 TAGGTCATTGACATGTGGGC 57.582 50.000 18.09 0.00 33.68 5.36
1348 1839 0.323725 AGGTCATTGACATGTGGGCC 60.324 55.000 18.09 0.00 33.68 5.80
1349 1840 1.322538 GGTCATTGACATGTGGGCCC 61.323 60.000 17.59 17.59 33.68 5.80
1350 1841 1.378382 TCATTGACATGTGGGCCCG 60.378 57.895 19.37 4.81 0.00 6.13
1351 1842 1.678635 CATTGACATGTGGGCCCGT 60.679 57.895 19.37 8.84 0.00 5.28
1352 1843 1.378514 ATTGACATGTGGGCCCGTC 60.379 57.895 19.37 18.54 0.00 4.79
1353 1844 1.852157 ATTGACATGTGGGCCCGTCT 61.852 55.000 23.17 6.54 0.00 4.18
1354 1845 2.436646 GACATGTGGGCCCGTCTG 60.437 66.667 19.37 16.19 0.00 3.51
1355 1846 3.249189 ACATGTGGGCCCGTCTGT 61.249 61.111 19.37 16.89 0.00 3.41
1356 1847 2.436646 CATGTGGGCCCGTCTGTC 60.437 66.667 19.37 3.64 0.00 3.51
1357 1848 4.082523 ATGTGGGCCCGTCTGTCG 62.083 66.667 19.37 0.00 39.52 4.35
1366 1857 3.770040 CGTCTGTCGGATGGCCCA 61.770 66.667 0.00 0.00 35.71 5.36
1367 1858 2.125106 GTCTGTCGGATGGCCCAC 60.125 66.667 0.00 0.00 34.14 4.61
1368 1859 2.606213 TCTGTCGGATGGCCCACA 60.606 61.111 0.00 0.00 34.14 4.17
1369 1860 1.995066 TCTGTCGGATGGCCCACAT 60.995 57.895 0.00 0.00 44.18 3.21
1370 1861 1.820906 CTGTCGGATGGCCCACATG 60.821 63.158 0.00 0.00 40.72 3.21
1371 1862 2.272146 GTCGGATGGCCCACATGT 59.728 61.111 0.00 0.00 40.72 3.21
1372 1863 2.114670 GTCGGATGGCCCACATGTG 61.115 63.158 19.31 19.31 40.72 3.21
1373 1864 3.520862 CGGATGGCCCACATGTGC 61.521 66.667 20.81 10.04 40.72 4.57
1374 1865 3.520862 GGATGGCCCACATGTGCG 61.521 66.667 20.81 13.46 40.72 5.34
1375 1866 4.197498 GATGGCCCACATGTGCGC 62.197 66.667 24.22 24.22 40.72 6.09
1380 1871 3.520862 CCCACATGTGCGCCCATC 61.521 66.667 20.81 0.00 0.00 3.51
1381 1872 2.438975 CCACATGTGCGCCCATCT 60.439 61.111 20.81 0.00 0.00 2.90
1382 1873 2.767445 CCACATGTGCGCCCATCTG 61.767 63.158 20.81 1.20 0.00 2.90
1383 1874 2.042259 CACATGTGCGCCCATCTGT 61.042 57.895 13.94 0.00 0.00 3.41
1384 1875 0.744057 CACATGTGCGCCCATCTGTA 60.744 55.000 13.94 0.00 0.00 2.74
1385 1876 0.462581 ACATGTGCGCCCATCTGTAG 60.463 55.000 1.11 0.00 0.00 2.74
1386 1877 1.146930 ATGTGCGCCCATCTGTAGG 59.853 57.895 4.18 0.00 0.00 3.18
1387 1878 1.337384 ATGTGCGCCCATCTGTAGGA 61.337 55.000 4.18 0.00 0.00 2.94
1388 1879 1.337384 TGTGCGCCCATCTGTAGGAT 61.337 55.000 4.18 0.00 34.51 3.24
1395 1886 3.713902 CATCTGTAGGATGGCCCAC 57.286 57.895 0.00 0.00 45.85 4.61
1396 1887 0.839277 CATCTGTAGGATGGCCCACA 59.161 55.000 0.00 0.00 45.85 4.17
1397 1888 1.422781 CATCTGTAGGATGGCCCACAT 59.577 52.381 0.00 0.00 45.85 3.21
1398 1889 0.839277 TCTGTAGGATGGCCCACATG 59.161 55.000 0.00 0.00 40.72 3.21
1622 2114 5.221880 TGTGTTGTTCAATCTATTTGCAGC 58.778 37.500 0.00 0.00 35.16 5.25
1722 2417 3.007506 TGTTGCGAGAATCCAAGGTTCTA 59.992 43.478 0.00 0.00 36.13 2.10
1745 2440 1.818674 TGCATCGAAGTCTCTGCTACA 59.181 47.619 7.83 0.00 35.66 2.74
1746 2441 2.428530 TGCATCGAAGTCTCTGCTACAT 59.571 45.455 7.83 0.00 35.66 2.29
1835 2532 9.953565 ACTAGCTATAAAAACACACCAAATCTA 57.046 29.630 0.00 0.00 0.00 1.98
2040 2777 1.203994 GTAGGTTCTGCTAGGCGACAA 59.796 52.381 0.00 0.00 0.00 3.18
2084 2821 0.537371 ACCAAGAAAGGCCCAACTCG 60.537 55.000 0.00 0.00 0.00 4.18
2184 2921 7.933577 TGGCTCTTATATGAAACTTATGTCCAG 59.066 37.037 0.00 0.00 0.00 3.86
2218 2955 4.155099 TGGAGGCAAACATTAACATGTACG 59.845 41.667 0.00 0.00 43.34 3.67
2255 2992 6.151691 CCTACTTGTCAATTTGTGGTTCATG 58.848 40.000 0.00 0.00 0.00 3.07
2408 3158 6.715347 ACAATTTAGTTTCCTCATATGGCC 57.285 37.500 2.13 0.00 0.00 5.36
2421 3171 3.118408 TCATATGGCCTACAGTTTCGCTT 60.118 43.478 3.32 0.00 0.00 4.68
3203 3974 3.545703 AGAACATTTATCTCTTGGCGGG 58.454 45.455 0.00 0.00 0.00 6.13
3265 4036 9.662947 TCCTCTTTATATCATGATAATGTGCAG 57.337 33.333 19.03 10.58 0.00 4.41
3645 4420 6.727824 ATTTACTTTCTCACATGTCTTCCG 57.272 37.500 0.00 0.00 0.00 4.30
3743 4518 4.290985 TGGAGTGGGAAATCCTATCAACAA 59.709 41.667 0.00 0.00 36.50 2.83
3974 4749 4.269363 GTGTTATTATCCGTCCTCAAACCG 59.731 45.833 0.00 0.00 0.00 4.44
4026 8016 4.526970 ACTCCTGAGAACAACACAACAAT 58.473 39.130 0.22 0.00 0.00 2.71
4160 8151 6.830114 AAAAGTAGAACACTCTTGAACTCG 57.170 37.500 0.00 0.00 36.04 4.18
4403 8396 9.466497 AACATATGGTATTTTATATGGAGCCAG 57.534 33.333 7.80 0.00 40.10 4.85
4708 8704 0.958091 CCGTGAAAATCCTGTTGCCA 59.042 50.000 0.00 0.00 0.00 4.92
4712 8708 3.642705 GTGAAAATCCTGTTGCCAAGAC 58.357 45.455 0.00 0.00 0.00 3.01
5006 9012 5.188327 TCTAGGTCAATGAGCTAATGTCG 57.812 43.478 20.69 10.53 41.20 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.404391 TCTCGTGGAATTACTCGGCTC 59.596 52.381 11.94 0.00 0.00 4.70
76 77 0.664761 CATGCATAGGCTTTCACCGG 59.335 55.000 0.00 0.00 41.91 5.28
88 89 6.591001 TGGAGCTTAATCAGTAACATGCATA 58.409 36.000 0.00 0.00 0.00 3.14
171 174 2.179427 ACACGGAGATGATGGAAGACA 58.821 47.619 0.00 0.00 0.00 3.41
197 200 3.743396 GGAGAATCTTGCGCTAGGTAATG 59.257 47.826 18.64 0.00 33.73 1.90
198 201 3.643792 AGGAGAATCTTGCGCTAGGTAAT 59.356 43.478 18.64 3.89 33.73 1.89
199 202 3.031736 AGGAGAATCTTGCGCTAGGTAA 58.968 45.455 18.64 0.00 33.73 2.85
200 203 2.667470 AGGAGAATCTTGCGCTAGGTA 58.333 47.619 18.64 0.58 33.73 3.08
201 204 1.490574 AGGAGAATCTTGCGCTAGGT 58.509 50.000 18.64 9.16 33.73 3.08
202 205 3.385577 GTTAGGAGAATCTTGCGCTAGG 58.614 50.000 18.64 3.83 33.73 3.02
203 206 3.181475 TGGTTAGGAGAATCTTGCGCTAG 60.181 47.826 12.92 12.92 33.73 3.42
204 207 2.764010 TGGTTAGGAGAATCTTGCGCTA 59.236 45.455 9.73 0.00 33.73 4.26
205 208 1.555075 TGGTTAGGAGAATCTTGCGCT 59.445 47.619 9.73 0.00 33.73 5.92
206 209 2.024176 TGGTTAGGAGAATCTTGCGC 57.976 50.000 0.00 0.00 33.73 6.09
207 210 3.557595 GTCATGGTTAGGAGAATCTTGCG 59.442 47.826 0.00 0.00 33.73 4.85
228 231 7.809238 TGATGGATTCATAATTCTCCTCTTGT 58.191 34.615 0.00 0.00 32.98 3.16
242 245 6.699242 ATCACCTAGTCATGATGGATTCAT 57.301 37.500 16.03 0.00 46.27 2.57
245 248 8.153550 GTCTAAATCACCTAGTCATGATGGATT 58.846 37.037 16.03 8.99 35.71 3.01
310 313 4.357947 GGAGGTCTGACGCGCACA 62.358 66.667 5.73 6.17 0.00 4.57
332 335 7.203361 TCTCTCTCTCTCTCTGGGGTATATAT 58.797 42.308 0.00 0.00 0.00 0.86
333 336 6.576360 TCTCTCTCTCTCTCTGGGGTATATA 58.424 44.000 0.00 0.00 0.00 0.86
334 337 5.420455 TCTCTCTCTCTCTCTGGGGTATAT 58.580 45.833 0.00 0.00 0.00 0.86
335 338 4.833672 TCTCTCTCTCTCTCTGGGGTATA 58.166 47.826 0.00 0.00 0.00 1.47
562 915 3.673746 TTTAATGCTCTTCCATTCGCG 57.326 42.857 0.00 0.00 36.80 5.87
576 929 4.270084 AGACCATACGCGTGACATTTAATG 59.730 41.667 24.59 14.50 0.00 1.90
582 935 1.640428 CAAGACCATACGCGTGACAT 58.360 50.000 24.59 4.19 0.00 3.06
730 1121 1.826340 ATCCAGCAGCACCACGTACA 61.826 55.000 0.00 0.00 0.00 2.90
746 1138 2.819608 TGGCAGCAGTCAAAGTTAATCC 59.180 45.455 0.00 0.00 0.00 3.01
805 1208 4.014406 ACAAAATTTATCGACCTGGGGAC 58.986 43.478 0.00 0.00 0.00 4.46
872 1275 2.020016 GATGCGCGCGTACACAAG 59.980 61.111 32.35 0.04 0.00 3.16
922 1336 5.997746 TCTTGAATCTTGGTAAGTGACTTGG 59.002 40.000 8.33 0.00 0.00 3.61
1057 1493 2.854187 GAAGAAGAACCCGGGCGAGG 62.854 65.000 24.08 0.00 0.00 4.63
1065 1501 2.003301 GATGACGCAGAAGAAGAACCC 58.997 52.381 0.00 0.00 0.00 4.11
1098 1534 1.818060 TGGAAATCTTGCAACATCGGG 59.182 47.619 0.00 0.00 0.00 5.14
1107 1543 0.899717 TGGTGGGCTGGAAATCTTGC 60.900 55.000 0.00 0.00 0.00 4.01
1124 1560 4.529897 TGATCATCTCAAGGGAAATGTGG 58.470 43.478 0.00 0.00 0.00 4.17
1132 1568 3.136763 CACGGATTGATCATCTCAAGGG 58.863 50.000 0.00 0.00 46.71 3.95
1140 1576 1.487482 CGTACGCACGGATTGATCAT 58.513 50.000 0.52 0.00 44.59 2.45
1180 1616 2.355363 AAAGCTCGCACGCACGTA 60.355 55.556 0.00 0.00 0.00 3.57
1181 1617 4.000557 CAAAGCTCGCACGCACGT 62.001 61.111 0.00 0.00 0.00 4.49
1294 1785 3.186817 CAGTATGTCGGACGATCTAGGTC 59.813 52.174 3.34 0.00 0.00 3.85
1295 1786 3.139850 CAGTATGTCGGACGATCTAGGT 58.860 50.000 3.34 0.00 0.00 3.08
1296 1787 2.095668 GCAGTATGTCGGACGATCTAGG 60.096 54.545 3.34 0.00 39.31 3.02
1297 1788 2.548480 TGCAGTATGTCGGACGATCTAG 59.452 50.000 3.34 0.00 39.31 2.43
1298 1789 2.548480 CTGCAGTATGTCGGACGATCTA 59.452 50.000 5.25 0.00 39.31 1.98
1299 1790 1.335182 CTGCAGTATGTCGGACGATCT 59.665 52.381 5.25 0.00 39.31 2.75
1300 1791 1.065701 ACTGCAGTATGTCGGACGATC 59.934 52.381 20.16 0.00 39.31 3.69
1301 1792 1.103803 ACTGCAGTATGTCGGACGAT 58.896 50.000 20.16 1.49 39.31 3.73
1302 1793 0.170339 CACTGCAGTATGTCGGACGA 59.830 55.000 21.20 0.00 39.31 4.20
1303 1794 0.109272 ACACTGCAGTATGTCGGACG 60.109 55.000 21.20 6.25 39.31 4.79
1304 1795 1.350193 CACACTGCAGTATGTCGGAC 58.650 55.000 21.20 0.00 39.31 4.79
1305 1796 0.389817 GCACACTGCAGTATGTCGGA 60.390 55.000 25.10 0.00 44.26 4.55
1306 1797 2.081526 GCACACTGCAGTATGTCGG 58.918 57.895 25.10 12.12 44.26 4.79
1316 1807 1.813513 ATGACCTAACTGCACACTGC 58.186 50.000 0.00 0.00 45.29 4.40
1317 1808 3.187227 GTCAATGACCTAACTGCACACTG 59.813 47.826 1.10 0.00 0.00 3.66
1318 1809 3.181455 TGTCAATGACCTAACTGCACACT 60.181 43.478 11.24 0.00 0.00 3.55
1319 1810 3.138304 TGTCAATGACCTAACTGCACAC 58.862 45.455 11.24 0.00 0.00 3.82
1320 1811 3.483808 TGTCAATGACCTAACTGCACA 57.516 42.857 11.24 0.00 0.00 4.57
1321 1812 3.753272 ACATGTCAATGACCTAACTGCAC 59.247 43.478 11.24 0.00 37.24 4.57
1322 1813 3.752747 CACATGTCAATGACCTAACTGCA 59.247 43.478 11.24 0.00 37.24 4.41
1323 1814 3.127548 CCACATGTCAATGACCTAACTGC 59.872 47.826 11.24 0.00 37.24 4.40
1324 1815 3.691118 CCCACATGTCAATGACCTAACTG 59.309 47.826 11.24 3.65 37.24 3.16
1325 1816 3.873801 GCCCACATGTCAATGACCTAACT 60.874 47.826 11.24 0.00 37.24 2.24
1326 1817 2.423538 GCCCACATGTCAATGACCTAAC 59.576 50.000 11.24 0.00 37.24 2.34
1327 1818 2.620367 GGCCCACATGTCAATGACCTAA 60.620 50.000 11.24 0.00 37.24 2.69
1328 1819 1.064758 GGCCCACATGTCAATGACCTA 60.065 52.381 11.24 0.00 37.24 3.08
1329 1820 0.323725 GGCCCACATGTCAATGACCT 60.324 55.000 11.24 0.00 37.24 3.85
1330 1821 1.322538 GGGCCCACATGTCAATGACC 61.323 60.000 19.95 0.00 37.24 4.02
1331 1822 1.656818 CGGGCCCACATGTCAATGAC 61.657 60.000 24.92 6.41 37.24 3.06
1332 1823 1.378382 CGGGCCCACATGTCAATGA 60.378 57.895 24.92 0.00 37.24 2.57
1333 1824 1.656818 GACGGGCCCACATGTCAATG 61.657 60.000 24.92 3.12 39.89 2.82
1334 1825 1.378514 GACGGGCCCACATGTCAAT 60.379 57.895 24.92 0.00 0.00 2.57
1335 1826 2.033448 GACGGGCCCACATGTCAA 59.967 61.111 24.92 0.00 0.00 3.18
1336 1827 2.927856 AGACGGGCCCACATGTCA 60.928 61.111 24.92 0.00 33.83 3.58
1337 1828 2.436646 CAGACGGGCCCACATGTC 60.437 66.667 24.92 20.51 0.00 3.06
1338 1829 3.249189 ACAGACGGGCCCACATGT 61.249 61.111 24.92 19.34 0.00 3.21
1339 1830 2.436646 GACAGACGGGCCCACATG 60.437 66.667 24.92 18.63 0.00 3.21
1340 1831 4.082523 CGACAGACGGGCCCACAT 62.083 66.667 24.92 6.17 38.46 3.21
1349 1840 3.770040 TGGGCCATCCGACAGACG 61.770 66.667 0.00 0.00 38.76 4.18
1350 1841 2.125106 GTGGGCCATCCGACAGAC 60.125 66.667 10.70 0.00 40.39 3.51
1351 1842 2.606213 TGTGGGCCATCCGACAGA 60.606 61.111 10.70 0.00 44.61 3.41
1354 1845 2.114670 CACATGTGGGCCATCCGAC 61.115 63.158 18.51 0.00 40.98 4.79
1355 1846 2.271821 CACATGTGGGCCATCCGA 59.728 61.111 18.51 0.00 38.76 4.55
1356 1847 3.520862 GCACATGTGGGCCATCCG 61.521 66.667 26.55 3.14 38.87 4.18
1357 1848 3.520862 CGCACATGTGGGCCATCC 61.521 66.667 27.32 8.46 42.67 3.51
1363 1854 3.520862 GATGGGCGCACATGTGGG 61.521 66.667 33.41 32.24 45.07 4.61
1364 1855 2.438975 AGATGGGCGCACATGTGG 60.439 61.111 33.41 17.21 0.00 4.17
1365 1856 0.744057 TACAGATGGGCGCACATGTG 60.744 55.000 39.11 39.11 44.87 3.21
1366 1857 0.462581 CTACAGATGGGCGCACATGT 60.463 55.000 33.41 26.56 0.00 3.21
1367 1858 1.162181 CCTACAGATGGGCGCACATG 61.162 60.000 33.41 21.67 0.00 3.21
1368 1859 1.146930 CCTACAGATGGGCGCACAT 59.853 57.895 28.39 28.39 0.00 3.21
1369 1860 1.337384 ATCCTACAGATGGGCGCACA 61.337 55.000 18.16 18.16 32.41 4.57
1370 1861 1.447643 ATCCTACAGATGGGCGCAC 59.552 57.895 10.83 6.04 32.41 5.34
1371 1862 3.970332 ATCCTACAGATGGGCGCA 58.030 55.556 10.83 5.70 32.41 6.09
1382 1873 0.546122 TGACATGTGGGCCATCCTAC 59.454 55.000 10.70 2.61 43.46 3.18
1383 1874 1.143481 CATGACATGTGGGCCATCCTA 59.857 52.381 10.70 0.00 36.20 2.94
1384 1875 0.106369 CATGACATGTGGGCCATCCT 60.106 55.000 10.70 0.00 36.20 3.24
1385 1876 1.111116 CCATGACATGTGGGCCATCC 61.111 60.000 10.70 0.00 32.98 3.51
1386 1877 1.741327 GCCATGACATGTGGGCCATC 61.741 60.000 10.70 3.15 40.55 3.51
1387 1878 1.759299 GCCATGACATGTGGGCCAT 60.759 57.895 10.70 6.71 40.55 4.40
1388 1879 2.362760 GCCATGACATGTGGGCCA 60.363 61.111 17.78 0.00 40.55 5.36
1391 1882 0.750546 CTGAGGCCATGACATGTGGG 60.751 60.000 14.26 2.93 37.22 4.61
1392 1883 0.253894 TCTGAGGCCATGACATGTGG 59.746 55.000 14.26 0.00 39.80 4.17
1393 1884 2.219458 GATCTGAGGCCATGACATGTG 58.781 52.381 14.26 7.05 0.00 3.21
1394 1885 1.202615 CGATCTGAGGCCATGACATGT 60.203 52.381 14.26 0.00 0.00 3.21
1395 1886 1.069668 TCGATCTGAGGCCATGACATG 59.930 52.381 5.01 8.56 0.00 3.21
1396 1887 1.417288 TCGATCTGAGGCCATGACAT 58.583 50.000 5.01 0.00 0.00 3.06
1397 1888 1.417288 ATCGATCTGAGGCCATGACA 58.583 50.000 5.01 0.00 0.00 3.58
1398 1889 2.560542 AGTATCGATCTGAGGCCATGAC 59.439 50.000 5.01 0.00 0.00 3.06
1601 2093 5.009911 ACAGCTGCAAATAGATTGAACAACA 59.990 36.000 15.27 0.00 41.85 3.33
1604 2096 5.710513 AACAGCTGCAAATAGATTGAACA 57.289 34.783 15.27 0.00 41.85 3.18
1608 2100 7.647907 AAGAAAAACAGCTGCAAATAGATTG 57.352 32.000 15.27 0.00 42.21 2.67
1609 2101 8.553696 CAAAAGAAAAACAGCTGCAAATAGATT 58.446 29.630 15.27 0.00 0.00 2.40
1656 2149 4.727507 TTTGCTCAAAACAGGCTAAACA 57.272 36.364 0.00 0.00 0.00 2.83
1693 2388 2.685388 TGGATTCTCGCAACAACAACAA 59.315 40.909 0.00 0.00 0.00 2.83
1694 2389 2.293170 TGGATTCTCGCAACAACAACA 58.707 42.857 0.00 0.00 0.00 3.33
1722 2417 1.206610 AGCAGAGACTTCGATGCACAT 59.793 47.619 8.95 0.00 41.14 3.21
1786 2482 1.129811 CAAGGGTCCGCGAAATGTAAC 59.870 52.381 8.23 0.00 0.00 2.50
1835 2532 7.538334 GGTTCACAAAAACAAGTTAACTACGTT 59.462 33.333 8.92 12.40 0.00 3.99
1844 2541 4.391523 GCACATGGTTCACAAAAACAAGTT 59.608 37.500 0.00 0.00 0.00 2.66
2004 2730 4.792521 ACCTACTGTTGCTGTAGAGAAG 57.207 45.455 12.62 2.04 37.86 2.85
2084 2821 3.316308 ACAACCTGCTGAATTGTTCTCAC 59.684 43.478 7.18 0.00 32.70 3.51
2184 2921 4.698575 TGTTTGCCTCCAAATTTACAACC 58.301 39.130 0.00 0.00 42.44 3.77
2255 2992 6.454795 TGCAATCCTTGGATTTAGTTCAAAC 58.545 36.000 11.82 0.00 0.00 2.93
2402 3152 4.475051 TTAAGCGAAACTGTAGGCCATA 57.525 40.909 5.01 0.00 0.00 2.74
2473 3223 0.250209 CCCCTCGATGGAGCATTCAG 60.250 60.000 8.50 0.00 39.06 3.02
2603 3354 5.763876 AGCTAAGTCTTTACCAGGACAAT 57.236 39.130 0.00 0.00 35.18 2.71
2640 3392 7.406031 AGACTAATTAGCCGCATATAAGCTA 57.594 36.000 12.54 0.00 38.06 3.32
2822 3579 8.742554 ACGAAAAACTTATGAGCTTATTTTGG 57.257 30.769 0.00 0.00 0.00 3.28
3074 3835 7.968405 ACTTTTAGAATAGCAAATTACGCAAGG 59.032 33.333 2.92 0.00 46.39 3.61
3260 4031 5.108517 TCAACAGAAATTCCAAAACTGCAC 58.891 37.500 0.00 0.00 32.67 4.57
3265 4036 5.812127 ACTTGCTCAACAGAAATTCCAAAAC 59.188 36.000 0.00 0.00 0.00 2.43
3327 4099 1.253100 CACGTGGGCTTATTTTGGGT 58.747 50.000 7.95 0.00 0.00 4.51
3419 4192 7.788026 TCATCCCTACACGTAATAATGAGTTT 58.212 34.615 0.00 0.00 0.00 2.66
3569 4344 4.323553 TTTTGGGAAATTTACACGGGTG 57.676 40.909 0.00 0.00 0.00 4.61
3570 4345 6.667558 TTATTTTGGGAAATTTACACGGGT 57.332 33.333 2.10 0.00 36.82 5.28
3743 4518 6.192970 CCATCCTGGTAGAATTATCCTGTT 57.807 41.667 0.00 0.00 31.35 3.16
3848 4623 9.515020 CTTACACAAGTTTTGCAAGAGAAAATA 57.485 29.630 0.00 0.00 0.00 1.40
3859 4634 8.810652 TGGATTAAATCTTACACAAGTTTTGC 57.189 30.769 4.48 0.00 35.46 3.68
4040 8030 7.257790 TCTCATGTGATCCCTTTCTTAAAGA 57.742 36.000 0.99 0.00 41.02 2.52
4160 8151 6.283161 AGAACTTTAGAAGCAACAACGTAC 57.717 37.500 0.00 0.00 0.00 3.67
4251 8242 5.747675 GCGTAGGTCCTAGAAACATAACTTC 59.252 44.000 0.00 0.00 0.00 3.01
4399 8392 5.163963 GCAAATAAGTTATGTGCAAACTGGC 60.164 40.000 26.55 2.51 46.39 4.85
4639 8635 4.940654 TCCAACGATTGATGCATCTACAAA 59.059 37.500 26.32 13.33 0.00 2.83
5006 9012 1.834263 ACTCTTCATGGCTACCCAGAC 59.166 52.381 0.00 0.00 46.24 3.51
5108 9147 7.154435 ACATAGGAGTATATTATTCACGCGT 57.846 36.000 5.58 5.58 0.00 6.01
5636 10481 5.147162 GTTGCACTTAAGAAACAGAATCCG 58.853 41.667 10.09 0.00 0.00 4.18
5639 10484 8.850156 AGTATTGTTGCACTTAAGAAACAGAAT 58.150 29.630 10.09 10.02 34.28 2.40
5754 10600 6.593382 GCTGGCAATTTTACCAAAATCATGTA 59.407 34.615 0.00 0.00 40.05 2.29


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

AutoCloner maintained by Alex Coulton.