Multiple sequence alignment - TraesCS3B01G435900

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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 TraesCS3B01G435900 chr3B 100.000 3796 0 0 1 3796 674422393 674426188 0.000000e+00 7011.0
1 TraesCS3B01G435900 chr3D 91.951 1466 46 8 1897 3323 512261227 512262659 0.000000e+00 1988.0
2 TraesCS3B01G435900 chr3D 93.368 965 52 8 847 1805 512260269 512261227 0.000000e+00 1417.0
3 TraesCS3B01G435900 chr3D 89.161 858 59 8 1 842 512259375 512260214 0.000000e+00 1038.0
4 TraesCS3B01G435900 chr3D 92.126 254 14 3 3544 3796 512263532 512263780 1.680000e-93 353.0
5 TraesCS3B01G435900 chr3D 97.500 120 3 0 3104 3223 24157951 24158070 4.970000e-49 206.0
6 TraesCS3B01G435900 chr3D 97.500 120 3 0 3104 3223 24158465 24158584 4.970000e-49 206.0
7 TraesCS3B01G435900 chr3D 96.226 106 3 1 1798 1903 348135364 348135260 5.040000e-39 172.0
8 TraesCS3B01G435900 chr3A 96.105 1104 32 3 1897 2998 648022603 648023697 0.000000e+00 1790.0
9 TraesCS3B01G435900 chr3A 92.278 790 40 8 616 1402 648021161 648021932 0.000000e+00 1101.0
10 TraesCS3B01G435900 chr3A 89.457 626 47 13 1 612 648020499 648021119 0.000000e+00 773.0
11 TraesCS3B01G435900 chr3A 94.404 411 17 4 1399 1803 648022194 648022604 8.950000e-176 627.0
12 TraesCS3B01G435900 chr3A 89.157 415 19 5 3402 3796 648026621 648027029 9.470000e-136 494.0
13 TraesCS3B01G435900 chr3A 93.833 227 14 0 2999 3225 648023669 648023895 3.630000e-90 342.0
14 TraesCS3B01G435900 chr3A 96.429 56 2 0 3246 3301 648023948 648024003 4.040000e-15 93.5
15 TraesCS3B01G435900 chr4A 82.480 371 44 10 2601 2966 596925016 596924662 4.760000e-79 305.0
16 TraesCS3B01G435900 chr4A 90.909 121 7 4 1800 1920 703218561 703218677 3.920000e-35 159.0
17 TraesCS3B01G435900 chrUn 96.748 123 4 0 3104 3226 298933091 298932969 4.970000e-49 206.0
18 TraesCS3B01G435900 chr7D 96.748 123 4 0 3104 3226 231589295 231589173 4.970000e-49 206.0
19 TraesCS3B01G435900 chr7D 95.283 106 4 1 1795 1899 561963323 561963428 2.350000e-37 167.0
20 TraesCS3B01G435900 chr5D 96.748 123 4 0 3104 3226 6242467 6242345 4.970000e-49 206.0
21 TraesCS3B01G435900 chr5D 97.500 120 3 0 3104 3223 256076463 256076582 4.970000e-49 206.0
22 TraesCS3B01G435900 chr1D 96.748 123 4 0 3104 3226 25804143 25804021 4.970000e-49 206.0
23 TraesCS3B01G435900 chr1D 97.980 99 2 0 1801 1899 208035188 208035286 5.040000e-39 172.0
24 TraesCS3B01G435900 chr7B 98.039 102 2 0 1800 1901 747370730 747370629 1.080000e-40 178.0
25 TraesCS3B01G435900 chr4B 98.990 99 1 0 1801 1899 51475848 51475946 1.080000e-40 178.0
26 TraesCS3B01G435900 chr6B 96.154 104 4 0 1795 1898 517835967 517836070 1.810000e-38 171.0
27 TraesCS3B01G435900 chr2D 95.327 107 5 0 1792 1898 30406638 30406744 1.810000e-38 171.0
28 TraesCS3B01G435900 chr2A 94.444 108 6 0 1798 1905 92494526 92494419 2.350000e-37 167.0


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 TraesCS3B01G435900 chr3B 674422393 674426188 3795 False 7011.000000 7011 100.000000 1 3796 1 chr3B.!!$F1 3795
1 TraesCS3B01G435900 chr3D 512259375 512263780 4405 False 1199.000000 1988 91.651500 1 3796 4 chr3D.!!$F2 3795
2 TraesCS3B01G435900 chr3D 24157951 24158584 633 False 206.000000 206 97.500000 3104 3223 2 chr3D.!!$F1 119
3 TraesCS3B01G435900 chr3A 648020499 648027029 6530 False 745.785714 1790 93.094714 1 3796 7 chr3A.!!$F1 3795

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
877 1000 0.032017 TAGGGAGAACAGAGAGCCCC 60.032 60.0 0.0 0.0 39.68 5.80 F
1219 1348 1.318576 AGCCACCTGCACAAAAGTAC 58.681 50.0 0.0 0.0 44.83 2.73 F
1706 2110 0.736053 ATCCTGACTCGAAGACGCTC 59.264 55.0 0.0 0.0 39.58 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 2093 0.098025 GAGAGCGTCTTCGAGTCAGG 59.902 60.0 0.00 0.00 39.71 3.86 R
2536 2948 0.460109 CATCGAACACGGCATCTCCA 60.460 55.0 0.00 0.00 34.01 3.86 R
3600 6633 0.459489 TGCAATTTTATGGGCGCTCC 59.541 50.0 3.94 6.36 0.00 4.70 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
30 31 1.816863 ATCGACAAGTCCGGCACAGT 61.817 55.000 0.00 0.00 0.00 3.55
58 59 2.569354 GGATCGGATCCTCTGCGCT 61.569 63.158 26.29 0.00 46.19 5.92
77 78 2.967397 CTTACGTCACCGGCTCCA 59.033 61.111 0.00 0.00 38.78 3.86
303 304 2.677325 GCTTTCCCTCCTAAACGTCTCC 60.677 54.545 0.00 0.00 0.00 3.71
305 306 1.848652 TCCCTCCTAAACGTCTCCAG 58.151 55.000 0.00 0.00 0.00 3.86
306 307 0.175989 CCCTCCTAAACGTCTCCAGC 59.824 60.000 0.00 0.00 0.00 4.85
307 308 0.895530 CCTCCTAAACGTCTCCAGCA 59.104 55.000 0.00 0.00 0.00 4.41
420 444 2.043450 CGAGCTCCTGTCCCTCCT 60.043 66.667 8.47 0.00 0.00 3.69
452 477 2.767445 TACGTATGTGCGCGCCTCT 61.767 57.895 30.77 15.12 34.88 3.69
453 478 2.930012 TACGTATGTGCGCGCCTCTG 62.930 60.000 30.77 15.72 34.88 3.35
454 479 2.202743 GTATGTGCGCGCCTCTGA 60.203 61.111 30.77 6.23 0.00 3.27
455 480 2.104928 TATGTGCGCGCCTCTGAG 59.895 61.111 30.77 0.00 0.00 3.35
458 483 4.498520 GTGCGCGCCTCTGAGCTA 62.499 66.667 30.77 2.53 35.53 3.32
459 484 4.198890 TGCGCGCCTCTGAGCTAG 62.199 66.667 30.77 0.00 35.53 3.42
468 493 2.171448 GCCTCTGAGCTAGGGATTTTGA 59.829 50.000 3.19 0.00 34.46 2.69
549 579 1.435515 GAGCTCACTGTAGGCCGAG 59.564 63.158 9.40 0.00 0.00 4.63
611 645 1.519751 CGAGATCCCCGTGCTCCTAG 61.520 65.000 0.00 0.00 0.00 3.02
734 807 1.547372 CCTGACCTGCCTCCAATTTTG 59.453 52.381 0.00 0.00 0.00 2.44
748 821 3.318839 CCAATTTTGTCAGTTCTCTGCCA 59.681 43.478 0.00 0.00 41.10 4.92
829 902 1.882912 TGCTCGTCTGCATTTCTGTT 58.117 45.000 0.00 0.00 38.12 3.16
852 975 3.005554 CCAGAATTCTAGCTGTGTGGTG 58.994 50.000 7.86 0.00 0.00 4.17
870 993 1.618837 GTGCAGTGTAGGGAGAACAGA 59.381 52.381 0.00 0.00 0.00 3.41
871 994 1.895798 TGCAGTGTAGGGAGAACAGAG 59.104 52.381 0.00 0.00 0.00 3.35
877 1000 0.032017 TAGGGAGAACAGAGAGCCCC 60.032 60.000 0.00 0.00 39.68 5.80
925 1048 3.008813 ACAGTCAGGAGAGCAAATGATGT 59.991 43.478 0.00 0.00 0.00 3.06
1011 1135 1.512734 GCAGAAAATGGACGCAGCG 60.513 57.895 14.82 14.82 0.00 5.18
1043 1167 2.124236 AGGCCGTCGTCCTCCTAG 60.124 66.667 0.00 0.00 0.00 3.02
1105 1234 6.755141 GCTAATACTGAGTTGGACACGATTAA 59.245 38.462 0.00 0.00 0.00 1.40
1219 1348 1.318576 AGCCACCTGCACAAAAGTAC 58.681 50.000 0.00 0.00 44.83 2.73
1288 1417 5.694995 TCTCTCAAAATTTCTTCACCTGGT 58.305 37.500 0.00 0.00 0.00 4.00
1325 1457 7.182817 ACTACATTACCAAGCACATTCTCTA 57.817 36.000 0.00 0.00 0.00 2.43
1326 1458 7.620880 ACTACATTACCAAGCACATTCTCTAA 58.379 34.615 0.00 0.00 0.00 2.10
1342 1474 5.441718 TCTCTAATCTTTCAGGCCACAAT 57.558 39.130 5.01 0.00 0.00 2.71
1344 1476 6.957631 TCTCTAATCTTTCAGGCCACAATTA 58.042 36.000 5.01 0.00 0.00 1.40
1357 1489 5.833131 AGGCCACAATTAGAAGAGACAAAAA 59.167 36.000 5.01 0.00 0.00 1.94
1464 1864 3.107642 AGTGGTTGTTTACTCAGGACG 57.892 47.619 0.00 0.00 0.00 4.79
1504 1904 1.569479 GGGCTGACTGTCTGTTTCGC 61.569 60.000 14.85 4.81 0.00 4.70
1663 2067 8.294341 TGCTATAACACTATTTGTATTCGCTC 57.706 34.615 0.00 0.00 37.51 5.03
1689 2093 1.945394 ATGAGCAATCGGCACAGAATC 59.055 47.619 0.00 0.00 46.27 2.52
1691 2095 2.785868 GCAATCGGCACAGAATCCT 58.214 52.632 0.00 0.00 43.97 3.24
1706 2110 0.736053 ATCCTGACTCGAAGACGCTC 59.264 55.000 0.00 0.00 39.58 5.03
1805 2209 7.387948 TCAACCTTGCTCTGTTAGAAAATACTC 59.612 37.037 0.00 0.00 0.00 2.59
1806 2210 6.174049 ACCTTGCTCTGTTAGAAAATACTCC 58.826 40.000 0.00 0.00 0.00 3.85
1807 2211 5.586643 CCTTGCTCTGTTAGAAAATACTCCC 59.413 44.000 0.00 0.00 0.00 4.30
1808 2212 6.374417 TTGCTCTGTTAGAAAATACTCCCT 57.626 37.500 0.00 0.00 0.00 4.20
1809 2213 5.978814 TGCTCTGTTAGAAAATACTCCCTC 58.021 41.667 0.00 0.00 0.00 4.30
1810 2214 5.104900 TGCTCTGTTAGAAAATACTCCCTCC 60.105 44.000 0.00 0.00 0.00 4.30
1811 2215 5.593010 CTCTGTTAGAAAATACTCCCTCCG 58.407 45.833 0.00 0.00 0.00 4.63
1812 2216 5.021458 TCTGTTAGAAAATACTCCCTCCGT 58.979 41.667 0.00 0.00 0.00 4.69
1813 2217 5.126707 TCTGTTAGAAAATACTCCCTCCGTC 59.873 44.000 0.00 0.00 0.00 4.79
1814 2218 4.161001 TGTTAGAAAATACTCCCTCCGTCC 59.839 45.833 0.00 0.00 0.00 4.79
1815 2219 2.117051 AGAAAATACTCCCTCCGTCCC 58.883 52.381 0.00 0.00 0.00 4.46
1816 2220 1.835531 GAAAATACTCCCTCCGTCCCA 59.164 52.381 0.00 0.00 0.00 4.37
1817 2221 1.961133 AAATACTCCCTCCGTCCCAA 58.039 50.000 0.00 0.00 0.00 4.12
1818 2222 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
1819 2223 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
1820 2224 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
1821 2225 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1822 2226 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
1823 2227 2.026542 ACTCCCTCCGTCCCAAAATAAC 60.027 50.000 0.00 0.00 0.00 1.89
1824 2228 2.238898 CTCCCTCCGTCCCAAAATAACT 59.761 50.000 0.00 0.00 0.00 2.24
1825 2229 2.026636 TCCCTCCGTCCCAAAATAACTG 60.027 50.000 0.00 0.00 0.00 3.16
1826 2230 2.290705 CCCTCCGTCCCAAAATAACTGT 60.291 50.000 0.00 0.00 0.00 3.55
1827 2231 3.007635 CCTCCGTCCCAAAATAACTGTC 58.992 50.000 0.00 0.00 0.00 3.51
1828 2232 3.307480 CCTCCGTCCCAAAATAACTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
1829 2233 4.324267 CTCCGTCCCAAAATAACTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
1830 2234 5.484715 CTCCGTCCCAAAATAACTGTCTTA 58.515 41.667 0.00 0.00 0.00 2.10
1831 2235 5.867330 TCCGTCCCAAAATAACTGTCTTAA 58.133 37.500 0.00 0.00 0.00 1.85
1832 2236 5.935789 TCCGTCCCAAAATAACTGTCTTAAG 59.064 40.000 0.00 0.00 0.00 1.85
1833 2237 5.391629 CCGTCCCAAAATAACTGTCTTAAGC 60.392 44.000 0.00 0.00 0.00 3.09
1834 2238 5.411669 CGTCCCAAAATAACTGTCTTAAGCT 59.588 40.000 0.00 0.00 0.00 3.74
1835 2239 6.072673 CGTCCCAAAATAACTGTCTTAAGCTT 60.073 38.462 3.48 3.48 0.00 3.74
1836 2240 7.118680 CGTCCCAAAATAACTGTCTTAAGCTTA 59.881 37.037 0.86 0.86 0.00 3.09
1837 2241 8.451748 GTCCCAAAATAACTGTCTTAAGCTTAG 58.548 37.037 6.24 0.00 0.00 2.18
1838 2242 8.161425 TCCCAAAATAACTGTCTTAAGCTTAGT 58.839 33.333 6.24 0.00 0.00 2.24
1839 2243 9.444600 CCCAAAATAACTGTCTTAAGCTTAGTA 57.555 33.333 6.24 0.00 0.00 1.82
1846 2250 8.959705 AACTGTCTTAAGCTTAGTACAACTTT 57.040 30.769 18.24 11.70 0.00 2.66
1847 2251 8.366671 ACTGTCTTAAGCTTAGTACAACTTTG 57.633 34.615 18.24 11.67 0.00 2.77
1848 2252 7.985752 ACTGTCTTAAGCTTAGTACAACTTTGT 59.014 33.333 18.24 12.12 44.86 2.83
1849 2253 9.472361 CTGTCTTAAGCTTAGTACAACTTTGTA 57.528 33.333 18.24 0.00 42.35 2.41
1873 2277 7.148355 ACTAGAGCTAGTACAAAGTTGAGAC 57.852 40.000 8.35 0.00 43.98 3.36
1874 2278 6.715718 ACTAGAGCTAGTACAAAGTTGAGACA 59.284 38.462 8.35 0.00 43.98 3.41
1875 2279 5.774630 AGAGCTAGTACAAAGTTGAGACAC 58.225 41.667 0.00 0.00 0.00 3.67
1876 2280 5.536916 AGAGCTAGTACAAAGTTGAGACACT 59.463 40.000 0.00 0.00 0.00 3.55
1877 2281 6.041069 AGAGCTAGTACAAAGTTGAGACACTT 59.959 38.462 0.00 0.00 38.74 3.16
1878 2282 7.230913 AGAGCTAGTACAAAGTTGAGACACTTA 59.769 37.037 0.00 0.00 35.87 2.24
1879 2283 7.897864 AGCTAGTACAAAGTTGAGACACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
1880 2284 8.368668 AGCTAGTACAAAGTTGAGACACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
1881 2285 8.989980 GCTAGTACAAAGTTGAGACACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
1884 2288 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
1885 2289 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
1886 2290 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
1887 2291 7.287696 ACAAAGTTGAGACACTTATTTTGGGAT 59.712 33.333 0.00 0.00 35.87 3.85
1888 2292 6.824305 AGTTGAGACACTTATTTTGGGATG 57.176 37.500 0.00 0.00 0.00 3.51
1889 2293 5.711976 AGTTGAGACACTTATTTTGGGATGG 59.288 40.000 0.00 0.00 0.00 3.51
1890 2294 5.512942 TGAGACACTTATTTTGGGATGGA 57.487 39.130 0.00 0.00 0.00 3.41
1891 2295 5.500234 TGAGACACTTATTTTGGGATGGAG 58.500 41.667 0.00 0.00 0.00 3.86
1892 2296 4.860022 AGACACTTATTTTGGGATGGAGG 58.140 43.478 0.00 0.00 0.00 4.30
1893 2297 3.954258 GACACTTATTTTGGGATGGAGGG 59.046 47.826 0.00 0.00 0.00 4.30
1894 2298 3.596046 ACACTTATTTTGGGATGGAGGGA 59.404 43.478 0.00 0.00 0.00 4.20
1895 2299 4.210331 CACTTATTTTGGGATGGAGGGAG 58.790 47.826 0.00 0.00 0.00 4.30
1896 2300 3.858638 ACTTATTTTGGGATGGAGGGAGT 59.141 43.478 0.00 0.00 0.00 3.85
1906 2310 3.764972 GGATGGAGGGAGTAGTATACAGC 59.235 52.174 5.50 0.00 46.26 4.40
2126 2532 4.381612 GGTTCTACGGTGATGAAGATGACA 60.382 45.833 0.00 0.00 0.00 3.58
2170 2582 8.899427 ATGATAATGTTGTTCGAGAAGATGAT 57.101 30.769 0.00 0.00 0.00 2.45
2259 2671 2.861462 GAGCTCAATCTGCTCGTAGT 57.139 50.000 9.40 0.00 45.73 2.73
2303 2715 1.066858 ACCTTGATACTGTCAGGCACG 60.067 52.381 4.53 0.00 38.29 5.34
2411 2823 2.234661 CTGCTCAGAACACCATCCACTA 59.765 50.000 0.00 0.00 0.00 2.74
2481 2893 2.306805 ACAACCTGAATGATCTGCCAGA 59.693 45.455 0.00 0.00 0.00 3.86
2536 2948 2.165998 GGCAAGGTCAAGATGAAGCTT 58.834 47.619 0.00 0.00 33.72 3.74
2560 2972 1.004927 GATGCCGTGTTCGATGTTAGC 60.005 52.381 0.00 0.00 39.71 3.09
2570 2982 3.266510 TCGATGTTAGCTCATGCCTTT 57.733 42.857 0.00 0.00 40.80 3.11
2587 2999 3.002759 GCCTTTGGCGATATGTTCTCTTC 59.997 47.826 0.00 0.00 39.62 2.87
2589 3001 4.034510 CCTTTGGCGATATGTTCTCTTCAC 59.965 45.833 0.00 0.00 0.00 3.18
2641 3053 5.754890 TGTTTACTGTTTAGGTTCTTCCGTC 59.245 40.000 0.00 0.00 41.99 4.79
2821 3233 0.999406 CACGCGAACCGATCAATTCT 59.001 50.000 15.93 0.00 41.02 2.40
2822 3234 2.190161 CACGCGAACCGATCAATTCTA 58.810 47.619 15.93 0.00 41.02 2.10
2823 3235 2.216488 CACGCGAACCGATCAATTCTAG 59.784 50.000 15.93 0.00 41.02 2.43
2984 3396 2.837532 TGCAGCTGATGAGTGTTGTA 57.162 45.000 20.43 0.00 0.00 2.41
2985 3397 3.339253 TGCAGCTGATGAGTGTTGTAT 57.661 42.857 20.43 0.00 0.00 2.29
2986 3398 3.264947 TGCAGCTGATGAGTGTTGTATC 58.735 45.455 20.43 0.00 0.00 2.24
2987 3399 3.055602 TGCAGCTGATGAGTGTTGTATCT 60.056 43.478 20.43 0.00 0.00 1.98
2988 3400 3.937706 GCAGCTGATGAGTGTTGTATCTT 59.062 43.478 20.43 0.00 0.00 2.40
2989 3401 4.201792 GCAGCTGATGAGTGTTGTATCTTG 60.202 45.833 20.43 0.00 0.00 3.02
2990 3402 5.173664 CAGCTGATGAGTGTTGTATCTTGA 58.826 41.667 8.42 0.00 0.00 3.02
2991 3403 5.291371 CAGCTGATGAGTGTTGTATCTTGAG 59.709 44.000 8.42 0.00 0.00 3.02
2992 3404 5.046735 AGCTGATGAGTGTTGTATCTTGAGT 60.047 40.000 0.00 0.00 0.00 3.41
2993 3405 6.153510 AGCTGATGAGTGTTGTATCTTGAGTA 59.846 38.462 0.00 0.00 0.00 2.59
2994 3406 6.254589 GCTGATGAGTGTTGTATCTTGAGTAC 59.745 42.308 0.00 0.00 0.00 2.73
2995 3407 6.631016 TGATGAGTGTTGTATCTTGAGTACC 58.369 40.000 0.00 0.00 0.00 3.34
2996 3408 5.401531 TGAGTGTTGTATCTTGAGTACCC 57.598 43.478 0.00 0.00 0.00 3.69
2997 3409 5.084519 TGAGTGTTGTATCTTGAGTACCCT 58.915 41.667 0.00 0.00 0.00 4.34
2998 3410 5.047306 TGAGTGTTGTATCTTGAGTACCCTG 60.047 44.000 0.00 0.00 0.00 4.45
2999 3411 3.933332 GTGTTGTATCTTGAGTACCCTGC 59.067 47.826 0.00 0.00 0.00 4.85
3000 3412 3.838317 TGTTGTATCTTGAGTACCCTGCT 59.162 43.478 0.00 0.00 0.00 4.24
3001 3413 4.184629 GTTGTATCTTGAGTACCCTGCTG 58.815 47.826 0.00 0.00 0.00 4.41
3002 3414 3.708451 TGTATCTTGAGTACCCTGCTGA 58.292 45.455 0.00 0.00 0.00 4.26
3003 3415 4.290093 TGTATCTTGAGTACCCTGCTGAT 58.710 43.478 0.00 0.00 0.00 2.90
3004 3416 3.834489 ATCTTGAGTACCCTGCTGATG 57.166 47.619 0.00 0.00 0.00 3.07
3005 3417 2.820178 TCTTGAGTACCCTGCTGATGA 58.180 47.619 0.00 0.00 0.00 2.92
3006 3418 2.762887 TCTTGAGTACCCTGCTGATGAG 59.237 50.000 0.00 0.00 0.00 2.90
3007 3419 2.238084 TGAGTACCCTGCTGATGAGT 57.762 50.000 0.00 0.00 0.00 3.41
3008 3420 1.827344 TGAGTACCCTGCTGATGAGTG 59.173 52.381 0.00 0.00 0.00 3.51
3009 3421 1.827969 GAGTACCCTGCTGATGAGTGT 59.172 52.381 0.00 0.00 0.00 3.55
3010 3422 2.234908 GAGTACCCTGCTGATGAGTGTT 59.765 50.000 0.00 0.00 0.00 3.32
3011 3423 2.027745 AGTACCCTGCTGATGAGTGTTG 60.028 50.000 0.00 0.00 0.00 3.33
3012 3424 0.767375 ACCCTGCTGATGAGTGTTGT 59.233 50.000 0.00 0.00 0.00 3.32
3030 3442 5.995897 GTGTTGTATCTTGAGTACCCTTGTT 59.004 40.000 0.00 0.00 0.00 2.83
3051 3463 2.821437 TCTTACTAGCAGGCAGAAGGT 58.179 47.619 0.00 0.00 0.00 3.50
3052 3464 3.977312 TCTTACTAGCAGGCAGAAGGTA 58.023 45.455 0.00 0.00 0.00 3.08
3053 3465 4.547671 TCTTACTAGCAGGCAGAAGGTAT 58.452 43.478 0.00 0.00 0.00 2.73
3179 3591 8.641541 AGCTCCAATAATTTCTTTGTTCTCAAA 58.358 29.630 0.00 0.00 40.64 2.69
3208 3620 9.921637 CTCCTATTTAGAGGAATTAGCTACTTG 57.078 37.037 0.37 0.00 45.20 3.16
3337 4252 8.506168 AAAAATATACTACAGCTGCAAAGCTA 57.494 30.769 15.27 5.34 44.30 3.32
3338 4253 8.506168 AAAATATACTACAGCTGCAAAGCTAA 57.494 30.769 15.27 0.00 44.30 3.09
3340 4255 2.427506 ACTACAGCTGCAAAGCTAACC 58.572 47.619 15.27 0.00 44.30 2.85
3341 4256 2.039084 ACTACAGCTGCAAAGCTAACCT 59.961 45.455 15.27 0.00 44.30 3.50
3342 4257 1.986882 ACAGCTGCAAAGCTAACCTT 58.013 45.000 15.27 0.00 44.30 3.50
3343 4258 1.610522 ACAGCTGCAAAGCTAACCTTG 59.389 47.619 15.27 0.00 44.30 3.61
3344 4259 0.600057 AGCTGCAAAGCTAACCTTGC 59.400 50.000 12.87 12.87 44.28 4.01
3347 4262 2.164219 GCTGCAAAGCTAACCTTGCATA 59.836 45.455 20.63 3.01 37.14 3.14
3348 4263 3.762779 CTGCAAAGCTAACCTTGCATAC 58.237 45.455 20.63 0.00 37.14 2.39
3370 6319 0.735978 TACGACAGCGGCAACATCAG 60.736 55.000 1.45 0.00 43.17 2.90
3372 6321 2.033141 ACAGCGGCAACATCAGCT 59.967 55.556 1.45 0.00 41.07 4.24
3400 6349 4.219507 TCCTCTCACAAGCAAACACAAAAA 59.780 37.500 0.00 0.00 0.00 1.94
3405 6418 3.993081 CACAAGCAAACACAAAAAGGTCA 59.007 39.130 0.00 0.00 0.00 4.02
3441 6454 0.108186 TGTCAGATCACGATGGGCAC 60.108 55.000 0.00 0.00 0.00 5.01
3475 6488 1.172812 AGAACCAAAACGGCCAGAGC 61.173 55.000 2.24 0.00 39.03 4.09
3509 6526 3.066190 CCCGTCGGTGCAGGAGTA 61.066 66.667 11.06 0.00 0.00 2.59
3527 6544 0.535335 TAGCTAGAACCCCAACAGCG 59.465 55.000 0.00 0.00 37.32 5.18
3542 6559 1.749638 AGCGACGGACTGAGGTAGG 60.750 63.158 0.00 0.00 0.00 3.18
3565 6598 1.411977 CCAGATCGGAGAGAGCATTGT 59.588 52.381 0.00 0.00 43.63 2.71
3600 6633 3.854669 AATGCCGAGCGGAGGAGG 61.855 66.667 13.94 0.00 37.50 4.30
3623 6656 1.665169 GCGCCCATAAAATTGCAAAGG 59.335 47.619 1.71 0.00 0.00 3.11
3629 6662 5.106594 GCCCATAAAATTGCAAAGGAAGTTG 60.107 40.000 1.71 0.00 0.00 3.16
3670 6703 4.338118 TGGAATTTCAACCAGACAAGTCAC 59.662 41.667 2.72 0.00 0.00 3.67
3671 6704 4.338118 GGAATTTCAACCAGACAAGTCACA 59.662 41.667 2.72 0.00 0.00 3.58
3688 6721 3.128589 GTCACAGACAGCCTGAACAAAAA 59.871 43.478 0.00 0.00 45.78 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 1.442857 CGCAGAGAGGACACGTGTC 60.443 63.158 35.26 35.26 44.04 3.67
145 146 2.266055 CTCCAGGGAAGACGGTGC 59.734 66.667 0.00 0.00 0.00 5.01
147 148 3.382832 CGCTCCAGGGAAGACGGT 61.383 66.667 0.00 0.00 0.00 4.83
148 149 3.068691 TCGCTCCAGGGAAGACGG 61.069 66.667 5.56 0.00 33.89 4.79
155 156 3.827898 GAGACGGTCGCTCCAGGG 61.828 72.222 4.53 0.00 35.57 4.45
250 251 1.879737 TTTACAGTAGGCAGCGCGGA 61.880 55.000 13.03 0.00 0.00 5.54
313 326 1.406898 CTTCTCGATACTGCAGCTGGA 59.593 52.381 17.12 12.70 0.00 3.86
420 444 0.034574 TACGTACCTACTGCCGGGAA 60.035 55.000 2.18 0.00 0.00 3.97
452 477 2.774234 CCTCCTCAAAATCCCTAGCTCA 59.226 50.000 0.00 0.00 0.00 4.26
453 478 3.041946 TCCTCCTCAAAATCCCTAGCTC 58.958 50.000 0.00 0.00 0.00 4.09
454 479 3.136641 TCCTCCTCAAAATCCCTAGCT 57.863 47.619 0.00 0.00 0.00 3.32
455 480 4.445557 AATCCTCCTCAAAATCCCTAGC 57.554 45.455 0.00 0.00 0.00 3.42
456 481 5.942826 GCATAATCCTCCTCAAAATCCCTAG 59.057 44.000 0.00 0.00 0.00 3.02
457 482 5.612688 AGCATAATCCTCCTCAAAATCCCTA 59.387 40.000 0.00 0.00 0.00 3.53
458 483 4.418190 AGCATAATCCTCCTCAAAATCCCT 59.582 41.667 0.00 0.00 0.00 4.20
459 484 4.734266 AGCATAATCCTCCTCAAAATCCC 58.266 43.478 0.00 0.00 0.00 3.85
468 493 2.618794 CTCCCAGAGCATAATCCTCCT 58.381 52.381 0.00 0.00 0.00 3.69
506 536 2.438434 AGGCGGCCAAGAAATCGG 60.438 61.111 23.09 0.00 0.00 4.18
529 559 2.701780 CGGCCTACAGTGAGCTCGT 61.702 63.158 9.64 3.49 0.00 4.18
549 579 1.421646 CACCCCATGGATTCCTCCTAC 59.578 57.143 15.22 0.00 42.59 3.18
611 645 3.006217 AGCAAAGCAAGAACCAGAAATCC 59.994 43.478 0.00 0.00 0.00 3.01
675 748 0.394352 CCAGACCCCCAAAATCCTCG 60.394 60.000 0.00 0.00 0.00 4.63
852 975 2.165437 CTCTCTGTTCTCCCTACACTGC 59.835 54.545 0.00 0.00 0.00 4.40
877 1000 2.357881 TTCAGTGCTCTGCTGCCG 60.358 61.111 10.95 0.00 41.10 5.69
940 1063 3.492829 GCTCAGTGTAGCCATAGGTTACC 60.493 52.174 7.45 0.00 38.37 2.85
943 1066 2.187958 TGCTCAGTGTAGCCATAGGTT 58.812 47.619 10.72 0.00 42.05 3.50
946 1069 3.812053 GGATTTGCTCAGTGTAGCCATAG 59.188 47.826 10.72 0.00 42.05 2.23
953 1076 4.019792 ACATGTGGATTTGCTCAGTGTA 57.980 40.909 0.00 0.00 0.00 2.90
1029 1153 1.433879 CTTGCTAGGAGGACGACGG 59.566 63.158 0.00 0.00 0.00 4.79
1043 1167 2.239907 AGAATCCTAGAACCCACCTTGC 59.760 50.000 0.00 0.00 0.00 4.01
1141 1270 6.094603 ACTTGAGCTTCTGTGGCTATTTAATG 59.905 38.462 0.00 0.00 40.40 1.90
1198 1327 1.194218 ACTTTTGTGCAGGTGGCTTT 58.806 45.000 0.00 0.00 45.15 3.51
1201 1330 0.313987 GGTACTTTTGTGCAGGTGGC 59.686 55.000 0.00 0.00 45.13 5.01
1219 1348 5.555017 TCAAATCAAGGAGAAGAGAAGTGG 58.445 41.667 0.00 0.00 0.00 4.00
1274 1403 6.779860 ACTGTAACATACCAGGTGAAGAAAT 58.220 36.000 0.76 0.00 0.00 2.17
1278 1407 7.159372 AGTAAACTGTAACATACCAGGTGAAG 58.841 38.462 0.76 0.00 0.00 3.02
1325 1457 6.248433 TCTTCTAATTGTGGCCTGAAAGATT 58.752 36.000 3.32 0.00 34.07 2.40
1326 1458 5.819991 TCTTCTAATTGTGGCCTGAAAGAT 58.180 37.500 3.32 0.00 34.07 2.40
1344 1476 8.906867 TCTTCATCAATTGTTTTTGTCTCTTCT 58.093 29.630 5.13 0.00 0.00 2.85
1357 1489 9.288576 TGTCTTCATTAACTCTTCATCAATTGT 57.711 29.630 5.13 0.00 0.00 2.71
1416 1813 2.044758 ACTATCCGACCCCAATACCAC 58.955 52.381 0.00 0.00 0.00 4.16
1420 1817 9.007494 ACTATATAGTACTATCCGACCCCAATA 57.993 37.037 18.68 7.22 34.13 1.90
1464 1864 3.305608 CCCAGACAGAAAGGAACAATTGC 60.306 47.826 5.05 0.00 0.00 3.56
1642 2046 6.761242 TGCAGAGCGAATACAAATAGTGTTAT 59.239 34.615 0.00 0.00 41.98 1.89
1663 2067 1.093496 TGCCGATTGCTCATCTGCAG 61.093 55.000 7.63 7.63 44.62 4.41
1689 2093 0.098025 GAGAGCGTCTTCGAGTCAGG 59.902 60.000 0.00 0.00 39.71 3.86
1691 2095 1.524848 AAGAGAGCGTCTTCGAGTCA 58.475 50.000 0.00 0.00 42.26 3.41
1706 2110 0.532573 TAACTCCGGCTGCAGAAGAG 59.467 55.000 20.43 20.35 0.00 2.85
1787 2191 5.361427 GGAGGGAGTATTTTCTAACAGAGC 58.639 45.833 0.00 0.00 0.00 4.09
1805 2209 2.290705 ACAGTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
1806 2210 3.007635 GACAGTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
1807 2211 3.939066 AGACAGTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
1808 2212 4.360951 AAGACAGTTATTTTGGGACGGA 57.639 40.909 0.00 0.00 0.00 4.69
1809 2213 5.391629 GCTTAAGACAGTTATTTTGGGACGG 60.392 44.000 6.67 0.00 0.00 4.79
1810 2214 5.411669 AGCTTAAGACAGTTATTTTGGGACG 59.588 40.000 6.67 0.00 0.00 4.79
1811 2215 6.819397 AGCTTAAGACAGTTATTTTGGGAC 57.181 37.500 6.67 0.00 0.00 4.46
1812 2216 8.161425 ACTAAGCTTAAGACAGTTATTTTGGGA 58.839 33.333 6.67 0.00 0.00 4.37
1813 2217 8.336801 ACTAAGCTTAAGACAGTTATTTTGGG 57.663 34.615 6.67 0.00 0.00 4.12
1821 2225 8.827677 CAAAGTTGTACTAAGCTTAAGACAGTT 58.172 33.333 15.83 12.28 0.00 3.16
1822 2226 7.985752 ACAAAGTTGTACTAAGCTTAAGACAGT 59.014 33.333 15.83 10.85 40.16 3.55
1823 2227 8.366671 ACAAAGTTGTACTAAGCTTAAGACAG 57.633 34.615 15.83 6.05 40.16 3.51
1848 2252 7.881751 TGTCTCAACTTTGTACTAGCTCTAGTA 59.118 37.037 11.59 11.59 43.98 1.82
1850 2254 7.024768 GTGTCTCAACTTTGTACTAGCTCTAG 58.975 42.308 0.00 2.55 39.04 2.43
1851 2255 6.715718 AGTGTCTCAACTTTGTACTAGCTCTA 59.284 38.462 0.00 0.00 0.00 2.43
1852 2256 5.536916 AGTGTCTCAACTTTGTACTAGCTCT 59.463 40.000 0.00 0.00 0.00 4.09
1853 2257 5.774630 AGTGTCTCAACTTTGTACTAGCTC 58.225 41.667 0.00 0.00 0.00 4.09
1854 2258 5.793030 AGTGTCTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
1855 2259 8.535690 AATAAGTGTCTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
1858 2262 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
1859 2263 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
1860 2264 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
1861 2265 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
1862 2266 7.038154 TCCCAAAATAAGTGTCTCAACTTTG 57.962 36.000 0.00 0.00 40.77 2.77
1863 2267 7.255942 CCATCCCAAAATAAGTGTCTCAACTTT 60.256 37.037 0.00 0.00 40.77 2.66
1864 2268 6.209391 CCATCCCAAAATAAGTGTCTCAACTT 59.791 38.462 0.00 0.00 42.89 2.66
1865 2269 5.711976 CCATCCCAAAATAAGTGTCTCAACT 59.288 40.000 0.00 0.00 0.00 3.16
1866 2270 5.710099 TCCATCCCAAAATAAGTGTCTCAAC 59.290 40.000 0.00 0.00 0.00 3.18
1867 2271 5.886609 TCCATCCCAAAATAAGTGTCTCAA 58.113 37.500 0.00 0.00 0.00 3.02
1868 2272 5.500234 CTCCATCCCAAAATAAGTGTCTCA 58.500 41.667 0.00 0.00 0.00 3.27
1869 2273 4.884164 CCTCCATCCCAAAATAAGTGTCTC 59.116 45.833 0.00 0.00 0.00 3.36
1870 2274 4.325344 CCCTCCATCCCAAAATAAGTGTCT 60.325 45.833 0.00 0.00 0.00 3.41
1871 2275 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
1872 2276 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
1873 2277 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
1874 2278 3.858638 ACTCCCTCCATCCCAAAATAAGT 59.141 43.478 0.00 0.00 0.00 2.24
1875 2279 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
1876 2280 5.043762 ACTACTCCCTCCATCCCAAAATAA 58.956 41.667 0.00 0.00 0.00 1.40
1877 2281 4.641868 ACTACTCCCTCCATCCCAAAATA 58.358 43.478 0.00 0.00 0.00 1.40
1878 2282 3.474920 ACTACTCCCTCCATCCCAAAAT 58.525 45.455 0.00 0.00 0.00 1.82
1879 2283 2.929301 ACTACTCCCTCCATCCCAAAA 58.071 47.619 0.00 0.00 0.00 2.44
1880 2284 2.661176 ACTACTCCCTCCATCCCAAA 57.339 50.000 0.00 0.00 0.00 3.28
1881 2285 4.171243 TGTATACTACTCCCTCCATCCCAA 59.829 45.833 4.17 0.00 0.00 4.12
1882 2286 3.730594 TGTATACTACTCCCTCCATCCCA 59.269 47.826 4.17 0.00 0.00 4.37
1883 2287 4.345854 CTGTATACTACTCCCTCCATCCC 58.654 52.174 4.17 0.00 0.00 3.85
1884 2288 3.764972 GCTGTATACTACTCCCTCCATCC 59.235 52.174 4.17 0.00 0.00 3.51
1885 2289 4.668636 AGCTGTATACTACTCCCTCCATC 58.331 47.826 4.17 0.00 0.00 3.51
1886 2290 4.509482 GGAGCTGTATACTACTCCCTCCAT 60.509 50.000 23.73 0.00 42.44 3.41
1887 2291 3.181431 GGAGCTGTATACTACTCCCTCCA 60.181 52.174 23.73 0.00 42.44 3.86
1888 2292 3.423749 GGAGCTGTATACTACTCCCTCC 58.576 54.545 23.73 15.61 42.44 4.30
1892 2296 4.216708 ACAAGGGAGCTGTATACTACTCC 58.783 47.826 25.12 25.12 46.61 3.85
1893 2297 4.888239 TGACAAGGGAGCTGTATACTACTC 59.112 45.833 14.02 14.02 0.00 2.59
1894 2298 4.868268 TGACAAGGGAGCTGTATACTACT 58.132 43.478 4.17 1.14 0.00 2.57
1895 2299 5.302059 TCATGACAAGGGAGCTGTATACTAC 59.698 44.000 4.17 0.00 0.00 2.73
1896 2300 5.454966 TCATGACAAGGGAGCTGTATACTA 58.545 41.667 4.17 0.00 0.00 1.82
1906 2310 0.907486 TGCCTCTCATGACAAGGGAG 59.093 55.000 17.30 10.59 0.00 4.30
1942 2346 3.214328 CAAGGCAAGTACAGACCAAAGT 58.786 45.455 0.00 0.00 0.00 2.66
2046 2452 5.070001 TCCTAGTGGAATGTTTTGGTCAAG 58.930 41.667 0.00 0.00 39.87 3.02
2126 2532 1.835494 TCATCTTCGTCCTCGTCCTT 58.165 50.000 0.00 0.00 38.33 3.36
2170 2582 5.421056 AGACTCCGGTAACTCAACATCATTA 59.579 40.000 0.00 0.00 0.00 1.90
2259 2671 3.254093 TGGTGTAGGGTTCAGAGAAGA 57.746 47.619 0.00 0.00 0.00 2.87
2368 2780 2.303022 AGGAAGAGATTTCGGCAACTGA 59.697 45.455 0.00 0.00 0.00 3.41
2411 2823 4.043435 GGCCCTTCCATTCCTATGAACTAT 59.957 45.833 0.00 0.00 33.37 2.12
2481 2893 0.552848 CATCTTGCCCATGTACCCCT 59.447 55.000 0.00 0.00 0.00 4.79
2536 2948 0.460109 CATCGAACACGGCATCTCCA 60.460 55.000 0.00 0.00 34.01 3.86
2570 2982 2.425668 TCGTGAAGAGAACATATCGCCA 59.574 45.455 0.00 0.00 0.00 5.69
2587 2999 3.724295 TCGATATCGTGCTAGATCGTG 57.276 47.619 23.61 0.00 41.44 4.35
2589 3001 5.843360 CACATATCGATATCGTGCTAGATCG 59.157 44.000 23.61 10.39 41.93 3.69
2803 3215 2.159282 ACTAGAATTGATCGGTTCGCGT 60.159 45.455 5.77 0.00 0.00 6.01
2821 3233 7.228507 CACACCATATTTGCCAAGCTATTACTA 59.771 37.037 0.00 0.00 0.00 1.82
2822 3234 6.039717 CACACCATATTTGCCAAGCTATTACT 59.960 38.462 0.00 0.00 0.00 2.24
2823 3235 6.208644 CACACCATATTTGCCAAGCTATTAC 58.791 40.000 0.00 0.00 0.00 1.89
2984 3396 3.378512 TCATCAGCAGGGTACTCAAGAT 58.621 45.455 0.00 0.00 0.00 2.40
2985 3397 2.762887 CTCATCAGCAGGGTACTCAAGA 59.237 50.000 0.00 0.00 0.00 3.02
2986 3398 2.499289 ACTCATCAGCAGGGTACTCAAG 59.501 50.000 0.00 0.00 0.00 3.02
2987 3399 2.234661 CACTCATCAGCAGGGTACTCAA 59.765 50.000 0.00 0.00 0.00 3.02
2988 3400 1.827344 CACTCATCAGCAGGGTACTCA 59.173 52.381 0.00 0.00 0.00 3.41
2989 3401 1.827969 ACACTCATCAGCAGGGTACTC 59.172 52.381 0.00 0.00 0.00 2.59
2990 3402 1.944177 ACACTCATCAGCAGGGTACT 58.056 50.000 0.00 0.00 0.00 2.73
2991 3403 2.289694 ACAACACTCATCAGCAGGGTAC 60.290 50.000 0.00 0.00 0.00 3.34
2992 3404 1.977854 ACAACACTCATCAGCAGGGTA 59.022 47.619 0.00 0.00 0.00 3.69
2993 3405 0.767375 ACAACACTCATCAGCAGGGT 59.233 50.000 0.00 0.00 0.00 4.34
2994 3406 2.768253 TACAACACTCATCAGCAGGG 57.232 50.000 0.00 0.00 0.00 4.45
2995 3407 4.134379 AGATACAACACTCATCAGCAGG 57.866 45.455 0.00 0.00 0.00 4.85
2996 3408 5.173664 TCAAGATACAACACTCATCAGCAG 58.826 41.667 0.00 0.00 0.00 4.24
2997 3409 5.151297 TCAAGATACAACACTCATCAGCA 57.849 39.130 0.00 0.00 0.00 4.41
2998 3410 5.174395 ACTCAAGATACAACACTCATCAGC 58.826 41.667 0.00 0.00 0.00 4.26
2999 3411 6.754209 GGTACTCAAGATACAACACTCATCAG 59.246 42.308 0.00 0.00 0.00 2.90
3000 3412 6.351033 GGGTACTCAAGATACAACACTCATCA 60.351 42.308 0.00 0.00 0.00 3.07
3001 3413 6.043411 GGGTACTCAAGATACAACACTCATC 58.957 44.000 0.00 0.00 0.00 2.92
3002 3414 5.721960 AGGGTACTCAAGATACAACACTCAT 59.278 40.000 0.00 0.00 0.00 2.90
3003 3415 5.084519 AGGGTACTCAAGATACAACACTCA 58.915 41.667 0.00 0.00 0.00 3.41
3004 3416 5.662674 AGGGTACTCAAGATACAACACTC 57.337 43.478 0.00 0.00 0.00 3.51
3005 3417 5.307196 ACAAGGGTACTCAAGATACAACACT 59.693 40.000 0.00 0.00 0.00 3.55
3006 3418 5.548406 ACAAGGGTACTCAAGATACAACAC 58.452 41.667 0.00 0.00 0.00 3.32
3007 3419 5.818678 ACAAGGGTACTCAAGATACAACA 57.181 39.130 0.00 0.00 0.00 3.33
3008 3420 6.935208 AGAAACAAGGGTACTCAAGATACAAC 59.065 38.462 0.00 0.00 0.00 3.32
3009 3421 7.074653 AGAAACAAGGGTACTCAAGATACAA 57.925 36.000 0.00 0.00 0.00 2.41
3010 3422 6.681729 AGAAACAAGGGTACTCAAGATACA 57.318 37.500 0.00 0.00 0.00 2.29
3011 3423 8.312564 AGTAAGAAACAAGGGTACTCAAGATAC 58.687 37.037 0.00 0.00 0.00 2.24
3012 3424 8.431910 AGTAAGAAACAAGGGTACTCAAGATA 57.568 34.615 0.00 0.00 0.00 1.98
3030 3442 3.173965 ACCTTCTGCCTGCTAGTAAGAA 58.826 45.455 0.00 0.00 0.00 2.52
3179 3591 6.088137 AGCTAATTCCTCTAAATAGGAGGCT 58.912 40.000 5.01 0.00 46.29 4.58
3208 3620 5.169836 AGACAAAACATCAAAGGTCGTTC 57.830 39.130 0.00 0.00 0.00 3.95
3337 4252 3.585862 CTGTCGTACAGTATGCAAGGTT 58.414 45.455 0.00 0.00 41.19 3.50
3338 4253 3.232213 CTGTCGTACAGTATGCAAGGT 57.768 47.619 0.00 0.00 41.19 3.50
3370 6319 1.759445 TGCTTGTGAGAGGAGGATAGC 59.241 52.381 0.00 0.00 0.00 2.97
3372 6321 3.582647 TGTTTGCTTGTGAGAGGAGGATA 59.417 43.478 0.00 0.00 0.00 2.59
3441 6454 1.026718 GTTCTTCTCCATGGTGGCCG 61.027 60.000 12.58 1.91 37.47 6.13
3475 6488 2.179517 GAGACTCGGCCTCACGTG 59.820 66.667 9.94 9.94 34.94 4.49
3509 6526 1.192146 TCGCTGTTGGGGTTCTAGCT 61.192 55.000 0.00 0.00 32.43 3.32
3527 6544 2.424733 GCCCCTACCTCAGTCCGTC 61.425 68.421 0.00 0.00 0.00 4.79
3542 6559 2.866726 GCTCTCTCCGATCTGGCCC 61.867 68.421 0.00 0.00 37.80 5.80
3565 6598 1.571955 TTGATCTAGTGGCAGAGGCA 58.428 50.000 0.00 0.00 43.71 4.75
3600 6633 0.459489 TGCAATTTTATGGGCGCTCC 59.541 50.000 3.94 6.36 0.00 4.70
3623 6656 9.722056 CCATTCTTTACATGCTATAACAACTTC 57.278 33.333 0.00 0.00 0.00 3.01
3670 6703 3.492011 GCAATTTTTGTTCAGGCTGTCTG 59.508 43.478 15.27 2.07 44.68 3.51
3671 6704 3.132646 TGCAATTTTTGTTCAGGCTGTCT 59.867 39.130 15.27 0.00 0.00 3.41
3680 6713 5.516090 TCTAGACCGTTGCAATTTTTGTTC 58.484 37.500 0.59 0.00 0.00 3.18
3688 6721 4.471904 TGAGATTCTAGACCGTTGCAAT 57.528 40.909 0.59 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.