Multiple sequence alignment - TraesCS2B01G474700

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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 TraesCS2B01G474700 chr2B 100.000 1505 0 0 814 2318 671901275 671902779 0.000000e+00 2780.0
1 TraesCS2B01G474700 chr2B 100.000 415 0 0 1 415 671900462 671900876 0.000000e+00 767.0
2 TraesCS2B01G474700 chr2B 90.909 99 9 0 2217 2315 671911566 671911664 1.440000e-27 134.0
3 TraesCS2B01G474700 chr2B 96.364 55 2 0 2176 2230 671910943 671910997 8.820000e-15 91.6
4 TraesCS2B01G474700 chr2B 96.875 32 1 0 2128 2159 671910910 671910941 1.000000e-03 54.7
5 TraesCS2B01G474700 chr2A 86.325 1543 108 50 814 2318 702937082 702938559 0.000000e+00 1585.0
6 TraesCS2B01G474700 chr2A 87.383 428 40 6 1 415 702936366 702936792 1.610000e-131 479.0
7 TraesCS2B01G474700 chr2A 83.636 220 14 12 1001 1218 702940274 702940473 1.090000e-43 187.0
8 TraesCS2B01G474700 chr2A 89.256 121 13 0 1075 1195 703382096 703382216 3.990000e-33 152.0
9 TraesCS2B01G474700 chr2D 88.269 1381 75 53 820 2160 562231885 562233218 0.000000e+00 1572.0
10 TraesCS2B01G474700 chr2D 97.744 133 3 0 283 415 562231459 562231591 1.790000e-56 230.0
11 TraesCS2B01G474700 chr2D 88.095 126 15 0 1069 1194 562895846 562895971 1.430000e-32 150.0


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 TraesCS2B01G474700 chr2B 671900462 671902779 2317 False 1773.500000 2780 100.000000 1 2318 2 chr2B.!!$F1 2317
1 TraesCS2B01G474700 chr2A 702936366 702940473 4107 False 750.333333 1585 85.781333 1 2318 3 chr2A.!!$F2 2317
2 TraesCS2B01G474700 chr2D 562231459 562233218 1759 False 901.000000 1572 93.006500 283 2160 2 chr2D.!!$F2 1877

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
201 204 0.309302 CTAGGAGACATGCCTCGTCG 59.691 60.0 7.54 0.0 38.46 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 1445 0.110486 AACACTGGCCGTCCAAGAAT 59.89 50.0 0.0 0.0 42.91 2.4 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
23 24 2.639286 CCAACGTGGCAAGTCAGC 59.361 61.111 6.52 0.00 0.00 4.26
27 28 0.679505 AACGTGGCAAGTCAGCTCTA 59.320 50.000 6.52 0.00 34.17 2.43
28 29 0.679505 ACGTGGCAAGTCAGCTCTAA 59.320 50.000 0.00 0.00 34.17 2.10
32 33 1.276421 TGGCAAGTCAGCTCTAACCTC 59.724 52.381 0.00 0.00 34.17 3.85
73 74 0.870393 CATGATGCCTACCATGACGC 59.130 55.000 0.00 0.00 41.88 5.19
75 76 1.337384 TGATGCCTACCATGACGCCT 61.337 55.000 0.00 0.00 33.29 5.52
99 100 1.433064 CCGGCCGTCATGAAAATGG 59.567 57.895 26.12 0.00 0.00 3.16
101 102 1.312371 CGGCCGTCATGAAAATGGGT 61.312 55.000 19.50 0.00 0.00 4.51
158 160 8.401709 GGGTTCATTTTGTGCTTAATTTTGAAA 58.598 29.630 0.00 0.00 0.00 2.69
165 167 4.450419 TGTGCTTAATTTTGAAAATGGGCG 59.550 37.500 3.62 0.00 0.00 6.13
172 175 6.631971 AATTTTGAAAATGGGCGAATTTGT 57.368 29.167 3.62 0.00 30.21 2.83
201 204 0.309302 CTAGGAGACATGCCTCGTCG 59.691 60.000 7.54 0.00 38.46 5.12
202 205 1.101635 TAGGAGACATGCCTCGTCGG 61.102 60.000 7.54 0.00 38.46 4.79
234 243 1.308998 AAAACACCGTGCTTCTCAGG 58.691 50.000 0.00 0.00 0.00 3.86
263 276 4.546829 AAAACTACCGTGCAAGATCCTA 57.453 40.909 0.00 0.00 0.00 2.94
266 279 1.409064 CTACCGTGCAAGATCCTAGCA 59.591 52.381 0.00 0.69 35.63 3.49
269 282 1.134699 CCGTGCAAGATCCTAGCAGAA 60.135 52.381 0.00 0.00 39.21 3.02
934 949 2.888863 CACACCCTCGCTCTCTCC 59.111 66.667 0.00 0.00 0.00 3.71
945 965 3.426615 TCGCTCTCTCCTTCTTCTTCTT 58.573 45.455 0.00 0.00 0.00 2.52
946 966 3.442273 TCGCTCTCTCCTTCTTCTTCTTC 59.558 47.826 0.00 0.00 0.00 2.87
947 967 3.443681 CGCTCTCTCCTTCTTCTTCTTCT 59.556 47.826 0.00 0.00 0.00 2.85
948 968 4.082245 CGCTCTCTCCTTCTTCTTCTTCTT 60.082 45.833 0.00 0.00 0.00 2.52
949 969 5.410924 GCTCTCTCCTTCTTCTTCTTCTTC 58.589 45.833 0.00 0.00 0.00 2.87
950 970 5.185828 GCTCTCTCCTTCTTCTTCTTCTTCT 59.814 44.000 0.00 0.00 0.00 2.85
1188 1216 1.363744 GCTACGAGCAGATGCACTTT 58.636 50.000 7.68 0.00 45.16 2.66
1398 1445 2.123251 GAGGAGGAGGATGCGGGA 60.123 66.667 0.00 0.00 0.00 5.14
1418 1466 0.106918 TTCTTGGACGGCCAGTGTTT 60.107 50.000 11.51 0.00 46.91 2.83
1452 1500 0.034059 GATGCCGATCGGTCCATCTT 59.966 55.000 31.35 17.69 34.26 2.40
1465 1513 3.128242 GGTCCATCTTTTGATCTGCACAG 59.872 47.826 0.00 0.00 36.97 3.66
1466 1514 3.128242 GTCCATCTTTTGATCTGCACAGG 59.872 47.826 0.00 0.00 36.97 4.00
1467 1515 2.426024 CCATCTTTTGATCTGCACAGGG 59.574 50.000 0.00 0.00 36.97 4.45
1468 1516 1.538047 TCTTTTGATCTGCACAGGGC 58.462 50.000 0.00 0.00 45.13 5.19
1495 1543 4.148825 GAGCAGGATCACCGCGGT 62.149 66.667 28.70 28.70 41.83 5.68
1499 1547 1.519455 CAGGATCACCGCGGTCTTC 60.519 63.158 31.80 26.28 41.83 2.87
1509 1557 1.078143 GCGGTCTTCTGATTGGCCT 60.078 57.895 3.32 0.00 0.00 5.19
1511 1559 0.250234 CGGTCTTCTGATTGGCCTCA 59.750 55.000 3.32 0.00 0.00 3.86
1548 1602 1.570979 TGGGTATGAGAGGAGAGAGCA 59.429 52.381 0.00 0.00 0.00 4.26
1627 1681 8.853077 ATTTCTCCAAATTTTGAAGGAAATCC 57.147 30.769 10.72 0.00 32.90 3.01
1652 1706 9.121517 CCGATCATGTTTATTATTCATTTGAGC 57.878 33.333 0.00 0.00 0.00 4.26
1656 1710 8.892723 TCATGTTTATTATTCATTTGAGCGAGT 58.107 29.630 0.00 0.00 0.00 4.18
1682 1737 4.734398 TGTTTTGAACCAGCAGATGTTT 57.266 36.364 0.00 0.00 0.00 2.83
1685 1740 6.815089 TGTTTTGAACCAGCAGATGTTTATT 58.185 32.000 0.00 0.00 0.00 1.40
1716 1775 5.448654 ACAATTGATAATTCCTAGCCAGCA 58.551 37.500 13.59 0.00 0.00 4.41
1720 1779 6.849085 TTGATAATTCCTAGCCAGCAAAAA 57.151 33.333 0.00 0.00 0.00 1.94
1728 1787 5.018809 TCCTAGCCAGCAAAAATTTCTCAT 58.981 37.500 0.00 0.00 0.00 2.90
1731 1790 6.753744 CCTAGCCAGCAAAAATTTCTCATAAC 59.246 38.462 0.00 0.00 0.00 1.89
1734 1793 5.060940 GCCAGCAAAAATTTCTCATAACGAC 59.939 40.000 0.00 0.00 0.00 4.34
1743 1806 8.880768 AAATTTCTCATAACGACGAAAGATTG 57.119 30.769 0.00 0.00 29.91 2.67
1751 1814 1.693083 GACGAAAGATTGGCCGTCCG 61.693 60.000 0.00 1.02 43.71 4.79
1752 1815 1.447140 CGAAAGATTGGCCGTCCGA 60.447 57.895 0.00 0.00 34.14 4.55
1753 1816 0.810031 CGAAAGATTGGCCGTCCGAT 60.810 55.000 0.00 0.00 39.22 4.18
1754 1817 1.379527 GAAAGATTGGCCGTCCGATT 58.620 50.000 0.00 0.00 36.59 3.34
1758 1821 1.971357 AGATTGGCCGTCCGATTAGAT 59.029 47.619 0.00 0.00 36.59 1.98
1800 1864 2.233922 ACTTGCCAGTATTACAGCTCGT 59.766 45.455 9.42 0.00 0.00 4.18
1801 1865 2.293677 TGCCAGTATTACAGCTCGTG 57.706 50.000 9.42 0.00 0.00 4.35
1802 1866 0.931005 GCCAGTATTACAGCTCGTGC 59.069 55.000 0.07 0.07 40.05 5.34
1803 1867 1.739035 GCCAGTATTACAGCTCGTGCA 60.739 52.381 12.58 0.00 42.74 4.57
1804 1868 1.927174 CCAGTATTACAGCTCGTGCAC 59.073 52.381 12.58 6.82 42.74 4.57
1805 1869 1.583856 CAGTATTACAGCTCGTGCACG 59.416 52.381 32.76 32.76 42.74 5.34
1806 1870 1.201647 AGTATTACAGCTCGTGCACGT 59.798 47.619 35.74 20.59 42.74 4.49
1807 1871 2.421073 AGTATTACAGCTCGTGCACGTA 59.579 45.455 35.74 22.18 42.74 3.57
1808 1872 2.357327 ATTACAGCTCGTGCACGTAA 57.643 45.000 35.74 26.03 40.77 3.18
1809 1873 1.693467 TTACAGCTCGTGCACGTAAG 58.307 50.000 35.74 27.60 42.74 2.34
1810 1874 0.876399 TACAGCTCGTGCACGTAAGA 59.124 50.000 35.74 18.00 42.74 2.10
1811 1875 0.031585 ACAGCTCGTGCACGTAAGAA 59.968 50.000 35.74 17.62 42.74 2.52
1812 1876 0.435008 CAGCTCGTGCACGTAAGAAC 59.565 55.000 35.74 19.97 42.74 3.01
1813 1877 0.031585 AGCTCGTGCACGTAAGAACA 59.968 50.000 35.74 16.14 42.74 3.18
1814 1878 1.068474 GCTCGTGCACGTAAGAACAT 58.932 50.000 35.74 0.00 43.62 2.71
1815 1879 1.059264 GCTCGTGCACGTAAGAACATC 59.941 52.381 35.74 12.04 43.62 3.06
1816 1880 2.596452 CTCGTGCACGTAAGAACATCT 58.404 47.619 35.74 0.00 43.62 2.90
1817 1881 3.754955 CTCGTGCACGTAAGAACATCTA 58.245 45.455 35.74 13.40 43.62 1.98
1818 1882 4.163458 TCGTGCACGTAAGAACATCTAA 57.837 40.909 35.74 11.63 43.62 2.10
1819 1883 3.916172 TCGTGCACGTAAGAACATCTAAC 59.084 43.478 35.74 0.00 43.62 2.34
1820 1884 3.241239 CGTGCACGTAAGAACATCTAACG 60.241 47.826 30.50 0.00 43.62 3.18
1821 1885 3.671928 GTGCACGTAAGAACATCTAACGT 59.328 43.478 0.00 0.00 46.72 3.99
1822 1886 3.916172 TGCACGTAAGAACATCTAACGTC 59.084 43.478 0.00 0.00 44.23 4.34
1823 1887 3.916172 GCACGTAAGAACATCTAACGTCA 59.084 43.478 0.00 0.00 44.23 4.35
1824 1888 4.561606 GCACGTAAGAACATCTAACGTCAT 59.438 41.667 0.00 0.00 44.23 3.06
1825 1889 5.740569 GCACGTAAGAACATCTAACGTCATA 59.259 40.000 0.00 0.00 44.23 2.15
1826 1890 6.252015 GCACGTAAGAACATCTAACGTCATAA 59.748 38.462 0.00 0.00 44.23 1.90
1827 1891 7.043590 GCACGTAAGAACATCTAACGTCATAAT 60.044 37.037 0.00 0.00 44.23 1.28
1828 1892 8.469902 CACGTAAGAACATCTAACGTCATAATC 58.530 37.037 0.00 0.00 44.23 1.75
1857 1921 9.113838 CCACAAAACAGCTAATGTATCTATTCT 57.886 33.333 0.00 0.00 43.00 2.40
1898 1963 0.536006 GGGAGCTAGCGCATCCAATT 60.536 55.000 20.45 0.00 39.10 2.32
1912 1977 5.398176 CATCCAATTTGATGCATTTTCCG 57.602 39.130 0.00 0.00 36.07 4.30
1953 2019 5.220835 CGCCATGATTATGTTCTGTTAAGCA 60.221 40.000 0.00 0.00 32.21 3.91
1977 2043 8.557869 CAAAATGCTATTTGCTGTCTAATCTC 57.442 34.615 2.59 0.00 43.37 2.75
1978 2044 8.404000 CAAAATGCTATTTGCTGTCTAATCTCT 58.596 33.333 2.59 0.00 43.37 3.10
1979 2045 7.493743 AATGCTATTTGCTGTCTAATCTCTG 57.506 36.000 0.00 0.00 43.37 3.35
1980 2046 6.225981 TGCTATTTGCTGTCTAATCTCTGA 57.774 37.500 0.00 0.00 43.37 3.27
1985 2051 7.789273 ATTTGCTGTCTAATCTCTGATGAAG 57.211 36.000 0.00 0.00 0.00 3.02
1992 2058 9.681692 CTGTCTAATCTCTGATGAAGAATACTG 57.318 37.037 0.00 0.00 33.37 2.74
1997 2063 6.857437 TCTCTGATGAAGAATACTGAACCA 57.143 37.500 0.00 0.00 33.37 3.67
1999 2065 5.423015 TCTGATGAAGAATACTGAACCAGC 58.577 41.667 0.00 0.00 30.42 4.85
2001 2067 5.181009 TGATGAAGAATACTGAACCAGCTG 58.819 41.667 6.78 6.78 34.37 4.24
2105 2172 4.749598 ACAAGCAAAACCCGATTTTCATTC 59.250 37.500 0.00 0.00 38.50 2.67
2106 2173 4.599047 AGCAAAACCCGATTTTCATTCA 57.401 36.364 0.00 0.00 38.50 2.57
2130 2197 3.187637 CGAATCGAGTAAACAAAAGGCCA 59.812 43.478 5.01 0.00 0.00 5.36
2132 2199 4.766404 ATCGAGTAAACAAAAGGCCAAG 57.234 40.909 5.01 0.00 0.00 3.61
2134 2201 2.621526 CGAGTAAACAAAAGGCCAAGGT 59.378 45.455 5.01 0.00 0.00 3.50
2139 2206 2.586648 ACAAAAGGCCAAGGTAGAGG 57.413 50.000 5.01 0.00 0.00 3.69
2147 2214 3.333680 AGGCCAAGGTAGAGGAAATCAAA 59.666 43.478 5.01 0.00 0.00 2.69
2150 2217 4.949856 GCCAAGGTAGAGGAAATCAAATCA 59.050 41.667 0.00 0.00 0.00 2.57
2152 2219 6.097412 GCCAAGGTAGAGGAAATCAAATCAAT 59.903 38.462 0.00 0.00 0.00 2.57
2155 2222 8.910944 CAAGGTAGAGGAAATCAAATCAATCAT 58.089 33.333 0.00 0.00 0.00 2.45
2158 2225 9.342308 GGTAGAGGAAATCAAATCAATCATGTA 57.658 33.333 0.00 0.00 0.00 2.29
2160 2227 8.230472 AGAGGAAATCAAATCAATCATGTACC 57.770 34.615 0.00 0.00 0.00 3.34
2162 2229 8.543293 AGGAAATCAAATCAATCATGTACCAT 57.457 30.769 0.00 0.00 0.00 3.55
2163 2230 9.645128 AGGAAATCAAATCAATCATGTACCATA 57.355 29.630 0.00 0.00 0.00 2.74
2188 2280 2.767644 AGTAAACAAAGGGCCAAGGT 57.232 45.000 6.18 0.00 0.00 3.50
2221 2313 9.985730 AAATCAAATCAAACATGATACACACTT 57.014 25.926 0.00 0.00 33.60 3.16
2258 2351 7.068593 GTGGAGGAAATCAAATCAACCATGATA 59.931 37.037 0.00 0.00 45.60 2.15
2266 2359 2.818751 TCAACCATGATACCCCAACC 57.181 50.000 0.00 0.00 0.00 3.77
2288 2381 1.153369 CAATCCTCCGGCGTCACAT 60.153 57.895 6.01 0.00 0.00 3.21
2293 2386 2.126228 TCCGGCGTCACATTCGTC 60.126 61.111 6.01 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.679505 TAGAGCTGACTTGCCACGTT 59.320 50.000 0.00 0.00 0.00 3.99
23 24 1.133976 CAAGGGGCCATGAGGTTAGAG 60.134 57.143 4.39 0.00 37.19 2.43
27 28 0.259938 GATCAAGGGGCCATGAGGTT 59.740 55.000 15.28 0.99 37.19 3.50
28 29 0.920763 TGATCAAGGGGCCATGAGGT 60.921 55.000 15.28 0.00 37.19 3.85
32 33 4.593033 CCTGATCAAGGGGCCATG 57.407 61.111 4.39 3.67 43.15 3.66
51 52 2.531522 TCATGGTAGGCATCATGACG 57.468 50.000 0.00 0.00 43.09 4.35
122 123 9.791801 AAGCACAAAATGAACCCTATTTAAATT 57.208 25.926 5.91 0.00 0.00 1.82
131 133 7.278875 TCAAAATTAAGCACAAAATGAACCCT 58.721 30.769 0.00 0.00 0.00 4.34
136 138 9.947669 CCATTTTCAAAATTAAGCACAAAATGA 57.052 25.926 13.28 0.00 40.07 2.57
146 148 8.288913 ACAAATTCGCCCATTTTCAAAATTAAG 58.711 29.630 0.00 0.00 0.00 1.85
158 160 4.878397 TGAAAAACAACAAATTCGCCCATT 59.122 33.333 0.00 0.00 0.00 3.16
165 167 8.188139 TGTCTCCTAGTGAAAAACAACAAATTC 58.812 33.333 0.00 0.00 0.00 2.17
172 175 4.518970 GGCATGTCTCCTAGTGAAAAACAA 59.481 41.667 0.00 0.00 0.00 2.83
218 227 0.468226 TTTCCTGAGAAGCACGGTGT 59.532 50.000 10.24 0.00 32.35 4.16
241 254 3.751518 AGGATCTTGCACGGTAGTTTTT 58.248 40.909 0.00 0.00 0.00 1.94
246 259 1.409064 TGCTAGGATCTTGCACGGTAG 59.591 52.381 0.34 0.00 37.31 3.18
247 260 1.409064 CTGCTAGGATCTTGCACGGTA 59.591 52.381 0.34 0.00 37.31 4.02
260 273 1.414550 GACTAGGGGCTTTCTGCTAGG 59.585 57.143 0.00 0.00 42.39 3.02
263 276 1.275421 GGGACTAGGGGCTTTCTGCT 61.275 60.000 0.00 0.00 42.39 4.24
266 279 1.024536 TAGGGGACTAGGGGCTTTCT 58.975 55.000 0.00 0.00 43.67 2.52
269 282 1.317321 GGTAGGGGACTAGGGGCTT 59.683 63.158 0.00 0.00 45.49 4.35
276 289 2.443390 GCGGCTGGTAGGGGACTA 60.443 66.667 0.00 0.00 43.67 2.59
357 370 0.178990 GGAAAGTGTGCTGGGGAAGT 60.179 55.000 0.00 0.00 0.00 3.01
934 949 5.047660 TCGGGAGAAGAAGAAGAAGAAGAAG 60.048 44.000 0.00 0.00 34.75 2.85
945 965 1.924731 TCTTGCTCGGGAGAAGAAGA 58.075 50.000 0.00 1.25 39.18 2.87
946 966 2.751166 TTCTTGCTCGGGAGAAGAAG 57.249 50.000 14.04 7.32 39.18 2.85
949 969 0.898320 TCCTTCTTGCTCGGGAGAAG 59.102 55.000 6.75 6.75 45.32 2.85
950 970 0.898320 CTCCTTCTTGCTCGGGAGAA 59.102 55.000 0.00 0.00 45.79 2.87
1111 1139 1.736126 CATGAAGATGTCGCTGTTGCT 59.264 47.619 0.00 0.00 36.97 3.91
1344 1391 5.356190 GCAAAAAGGGTACATAGTTCCTACC 59.644 44.000 0.00 0.00 0.00 3.18
1398 1445 0.110486 AACACTGGCCGTCCAAGAAT 59.890 50.000 0.00 0.00 42.91 2.40
1434 1482 0.469917 AAAGATGGACCGATCGGCAT 59.530 50.000 33.62 27.36 39.32 4.40
1444 1492 3.128242 CCTGTGCAGATCAAAAGATGGAC 59.872 47.826 0.02 0.00 34.92 4.02
1447 1495 2.159282 GCCCTGTGCAGATCAAAAGATG 60.159 50.000 0.02 0.00 40.77 2.90
1452 1500 1.675310 CCGCCCTGTGCAGATCAAA 60.675 57.895 0.02 0.00 41.33 2.69
1465 1513 4.802051 TGCTCAGATTGCCCGCCC 62.802 66.667 0.00 0.00 0.00 6.13
1466 1514 3.207669 CTGCTCAGATTGCCCGCC 61.208 66.667 0.00 0.00 0.00 6.13
1467 1515 2.955022 ATCCTGCTCAGATTGCCCGC 62.955 60.000 0.00 0.00 0.00 6.13
1468 1516 0.883814 GATCCTGCTCAGATTGCCCG 60.884 60.000 0.00 0.00 0.00 6.13
1477 1525 4.147449 CCGCGGTGATCCTGCTCA 62.147 66.667 19.50 0.00 33.49 4.26
1495 1543 3.765511 CCAAAATGAGGCCAATCAGAAGA 59.234 43.478 5.01 0.00 31.44 2.87
1499 1547 1.483415 CCCCAAAATGAGGCCAATCAG 59.517 52.381 5.01 0.00 31.44 2.90
1509 1557 2.173569 CCAAACCCAAACCCCAAAATGA 59.826 45.455 0.00 0.00 0.00 2.57
1511 1559 1.496857 CCCAAACCCAAACCCCAAAAT 59.503 47.619 0.00 0.00 0.00 1.82
1626 1680 9.121517 GCTCAAATGAATAATAAACATGATCGG 57.878 33.333 0.00 0.00 0.00 4.18
1627 1681 8.834212 CGCTCAAATGAATAATAAACATGATCG 58.166 33.333 0.00 0.00 0.00 3.69
1651 1705 4.148174 GCTGGTTCAAAACAAAATACTCGC 59.852 41.667 0.00 0.00 0.00 5.03
1652 1706 5.277825 TGCTGGTTCAAAACAAAATACTCG 58.722 37.500 0.00 0.00 0.00 4.18
1656 1710 6.815089 ACATCTGCTGGTTCAAAACAAAATA 58.185 32.000 0.00 0.00 0.00 1.40
1659 1713 4.734398 ACATCTGCTGGTTCAAAACAAA 57.266 36.364 0.00 0.00 0.00 2.83
1685 1740 7.665559 GCTAGGAATTATCAATTGTACCATCCA 59.334 37.037 17.92 8.43 0.00 3.41
1701 1760 7.178274 TGAGAAATTTTTGCTGGCTAGGAATTA 59.822 33.333 4.55 0.00 34.05 1.40
1707 1766 6.470235 CGTTATGAGAAATTTTTGCTGGCTAG 59.530 38.462 0.00 0.00 0.00 3.42
1716 1775 9.893305 AATCTTTCGTCGTTATGAGAAATTTTT 57.107 25.926 0.00 0.00 32.97 1.94
1720 1779 6.456988 GCCAATCTTTCGTCGTTATGAGAAAT 60.457 38.462 0.00 0.00 32.97 2.17
1728 1787 1.337074 ACGGCCAATCTTTCGTCGTTA 60.337 47.619 2.24 0.00 0.00 3.18
1731 1790 1.708027 GACGGCCAATCTTTCGTCG 59.292 57.895 2.24 0.00 41.60 5.12
1734 1793 0.810031 ATCGGACGGCCAATCTTTCG 60.810 55.000 8.76 0.00 0.00 3.46
1743 1806 1.340248 TCTGAATCTAATCGGACGGCC 59.660 52.381 0.00 0.00 29.78 6.13
1751 1814 6.690194 ACAATTGTGCCTCTGAATCTAATC 57.310 37.500 11.07 0.00 0.00 1.75
1752 1815 7.472334 AAACAATTGTGCCTCTGAATCTAAT 57.528 32.000 12.82 0.00 0.00 1.73
1753 1816 6.899393 AAACAATTGTGCCTCTGAATCTAA 57.101 33.333 12.82 0.00 0.00 2.10
1754 1817 6.489700 TGAAAACAATTGTGCCTCTGAATCTA 59.510 34.615 12.82 0.00 0.00 1.98
1758 1821 4.402155 AGTGAAAACAATTGTGCCTCTGAA 59.598 37.500 12.82 0.00 0.00 3.02
1805 1869 8.480853 GCAGATTATGACGTTAGATGTTCTTAC 58.519 37.037 0.00 0.00 0.00 2.34
1806 1870 7.652105 GGCAGATTATGACGTTAGATGTTCTTA 59.348 37.037 0.00 0.00 0.00 2.10
1807 1871 6.480320 GGCAGATTATGACGTTAGATGTTCTT 59.520 38.462 0.00 0.00 0.00 2.52
1808 1872 5.986135 GGCAGATTATGACGTTAGATGTTCT 59.014 40.000 0.00 0.00 0.00 3.01
1809 1873 5.753438 TGGCAGATTATGACGTTAGATGTTC 59.247 40.000 0.00 0.00 41.39 3.18
1810 1874 5.523916 GTGGCAGATTATGACGTTAGATGTT 59.476 40.000 0.00 0.00 41.39 2.71
1811 1875 5.050490 GTGGCAGATTATGACGTTAGATGT 58.950 41.667 0.00 0.00 41.39 3.06
1812 1876 5.049828 TGTGGCAGATTATGACGTTAGATG 58.950 41.667 0.00 0.00 41.39 2.90
1813 1877 5.276461 TGTGGCAGATTATGACGTTAGAT 57.724 39.130 0.00 0.00 41.39 1.98
1814 1878 4.729227 TGTGGCAGATTATGACGTTAGA 57.271 40.909 0.00 0.00 41.39 2.10
1815 1879 5.794687 TTTGTGGCAGATTATGACGTTAG 57.205 39.130 0.00 0.00 41.39 2.34
1816 1880 5.470437 TGTTTTGTGGCAGATTATGACGTTA 59.530 36.000 0.00 0.00 41.39 3.18
1817 1881 4.277174 TGTTTTGTGGCAGATTATGACGTT 59.723 37.500 0.00 0.00 41.39 3.99
1818 1882 3.818210 TGTTTTGTGGCAGATTATGACGT 59.182 39.130 0.00 0.00 41.39 4.34
1819 1883 4.406069 CTGTTTTGTGGCAGATTATGACG 58.594 43.478 0.00 0.00 41.39 4.35
1820 1884 4.082571 AGCTGTTTTGTGGCAGATTATGAC 60.083 41.667 0.00 0.00 37.50 3.06
1821 1885 4.081406 AGCTGTTTTGTGGCAGATTATGA 58.919 39.130 0.00 0.00 34.87 2.15
1822 1886 4.445452 AGCTGTTTTGTGGCAGATTATG 57.555 40.909 0.00 0.00 34.87 1.90
1823 1887 6.153340 ACATTAGCTGTTTTGTGGCAGATTAT 59.847 34.615 0.00 0.00 32.90 1.28
1824 1888 5.476599 ACATTAGCTGTTTTGTGGCAGATTA 59.523 36.000 0.00 0.00 32.90 1.75
1825 1889 4.281688 ACATTAGCTGTTTTGTGGCAGATT 59.718 37.500 0.00 0.00 32.90 2.40
1826 1890 3.828451 ACATTAGCTGTTTTGTGGCAGAT 59.172 39.130 0.00 0.00 32.90 2.90
1827 1891 3.221771 ACATTAGCTGTTTTGTGGCAGA 58.778 40.909 0.00 0.00 32.90 4.26
1828 1892 3.648339 ACATTAGCTGTTTTGTGGCAG 57.352 42.857 0.00 0.00 32.90 4.85
1898 1963 2.162608 CGGTTACCGGAAAATGCATCAA 59.837 45.455 17.00 0.00 44.15 2.57
1974 2040 6.629068 GCTGGTTCAGTATTCTTCATCAGAGA 60.629 42.308 0.00 0.00 33.43 3.10
1975 2041 5.523188 GCTGGTTCAGTATTCTTCATCAGAG 59.477 44.000 0.00 0.00 33.43 3.35
1976 2042 5.188555 AGCTGGTTCAGTATTCTTCATCAGA 59.811 40.000 0.00 0.00 33.43 3.27
1977 2043 5.293814 CAGCTGGTTCAGTATTCTTCATCAG 59.706 44.000 5.57 0.00 33.43 2.90
1978 2044 5.181009 CAGCTGGTTCAGTATTCTTCATCA 58.819 41.667 5.57 0.00 33.43 3.07
1979 2045 4.574013 CCAGCTGGTTCAGTATTCTTCATC 59.426 45.833 25.53 0.00 33.43 2.92
1980 2046 4.521146 CCAGCTGGTTCAGTATTCTTCAT 58.479 43.478 25.53 0.00 33.43 2.57
2001 2067 3.140814 GATTTGCTGGGGCCGACC 61.141 66.667 0.00 0.00 37.74 4.79
2003 2069 1.753848 CATGATTTGCTGGGGCCGA 60.754 57.895 0.00 0.00 37.74 5.54
2004 2070 0.751277 TACATGATTTGCTGGGGCCG 60.751 55.000 0.00 0.00 37.74 6.13
2005 2071 0.746659 GTACATGATTTGCTGGGGCC 59.253 55.000 0.00 0.00 37.74 5.80
2006 2072 1.406539 CAGTACATGATTTGCTGGGGC 59.593 52.381 0.00 0.00 39.26 5.80
2007 2073 3.003394 TCAGTACATGATTTGCTGGGG 57.997 47.619 0.00 0.00 31.12 4.96
2105 2172 4.394795 CCTTTTGTTTACTCGATTCGCTG 58.605 43.478 0.00 0.00 0.00 5.18
2106 2173 3.120304 GCCTTTTGTTTACTCGATTCGCT 60.120 43.478 0.00 0.00 0.00 4.93
2130 2197 8.910944 CATGATTGATTTGATTTCCTCTACCTT 58.089 33.333 0.00 0.00 0.00 3.50
2132 2199 8.230472 ACATGATTGATTTGATTTCCTCTACC 57.770 34.615 0.00 0.00 0.00 3.18
2134 2201 9.342308 GGTACATGATTGATTTGATTTCCTCTA 57.658 33.333 0.00 0.00 0.00 2.43
2158 2225 7.235812 TGGCCCTTTGTTTACTTAATTTATGGT 59.764 33.333 0.00 0.00 0.00 3.55
2159 2226 7.616313 TGGCCCTTTGTTTACTTAATTTATGG 58.384 34.615 0.00 0.00 0.00 2.74
2160 2227 9.150348 CTTGGCCCTTTGTTTACTTAATTTATG 57.850 33.333 0.00 0.00 0.00 1.90
2162 2229 7.290481 ACCTTGGCCCTTTGTTTACTTAATTTA 59.710 33.333 0.00 0.00 0.00 1.40
2163 2230 6.100569 ACCTTGGCCCTTTGTTTACTTAATTT 59.899 34.615 0.00 0.00 0.00 1.82
2221 2313 3.003173 CCTCCACCTTCGGCCTGA 61.003 66.667 0.00 0.00 0.00 3.86
2258 2351 4.376170 GGATTGGCCGGTTGGGGT 62.376 66.667 1.90 0.00 35.78 4.95
2288 2381 2.350899 TAATTGAGGCGTTCGACGAA 57.649 45.000 6.10 6.10 46.05 3.85
2293 2386 5.864986 ACAGTAAAATAATTGAGGCGTTCG 58.135 37.500 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.