Multiple sequence alignment - TraesCS1A01G162700

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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 TraesCS1A01G162700 chr1A 100.000 2517 0 0 1 2517 292076106 292078622 0 4649
1 TraesCS1A01G162700 chr1B 88.743 1750 145 28 1 1716 325819533 325817802 0 2093
2 TraesCS1A01G162700 chr1B 96.360 467 7 4 2057 2517 325817606 325817144 0 760
3 TraesCS1A01G162700 chr1D 88.283 734 32 15 1808 2517 225710122 225709419 0 830
4 TraesCS1A01G162700 chr1D 90.256 626 51 9 1 623 225712220 225711602 0 809
5 TraesCS1A01G162700 chr1D 86.780 764 49 17 354 1082 225711595 225710849 0 804
6 TraesCS1A01G162700 chr1D 89.676 649 40 14 1069 1698 225710832 225710192 0 802


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 TraesCS1A01G162700 chr1A 292076106 292078622 2516 False 4649.00 4649 100.00000 1 2517 1 chr1A.!!$F1 2516
1 TraesCS1A01G162700 chr1B 325817144 325819533 2389 True 1426.50 2093 92.55150 1 2517 2 chr1B.!!$R1 2516
2 TraesCS1A01G162700 chr1D 225709419 225712220 2801 True 811.25 830 88.74875 1 2517 4 chr1D.!!$R1 2516

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
132 134 0.320374 TACGAGACACCTTGCTTGGG 59.680 55.0 0.0 0.0 0.0 4.12 F
962 1277 0.392706 ATCCACGAGACACACAAGCA 59.607 50.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1234 1582 0.392863 TCCATGCTGATGTTGTCCCG 60.393 55.0 0.0 0.0 0.0 5.14 R
1787 2224 0.690192 TCAGGGGAATTCGTTGCTCA 59.310 50.0 0.0 0.0 0.0 4.26 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
31 32 9.684448 AAGGTTAAGTAAACTTACGTAAGACTC 57.316 33.333 35.60 22.42 41.15 3.36
132 134 0.320374 TACGAGACACCTTGCTTGGG 59.680 55.000 0.00 0.00 0.00 4.12
178 180 7.227711 TGCAACTAACTAACTTTGTAGATTGCA 59.772 33.333 12.66 12.66 0.00 4.08
246 248 6.267699 TGAATGTGAAGAGAGTTAGGACTTGA 59.732 38.462 0.00 0.00 35.88 3.02
290 292 5.768164 GGGTTTTGGAGACTGAACTTTGATA 59.232 40.000 0.00 0.00 0.00 2.15
296 298 9.739276 TTTGGAGACTGAACTTTGATAACATAT 57.261 29.630 0.00 0.00 0.00 1.78
333 335 0.482887 AAGACCCAAGACCCCCTTTG 59.517 55.000 0.00 0.00 31.42 2.77
338 340 2.205342 CCCAAGACCCCCTTTGATAGA 58.795 52.381 0.00 0.00 31.42 1.98
341 343 4.326132 CCCAAGACCCCCTTTGATAGAATT 60.326 45.833 0.00 0.00 31.42 2.17
386 388 2.494471 TCATGCCAAAGCTTGATCCTTG 59.506 45.455 0.00 0.00 45.37 3.61
387 389 1.999648 TGCCAAAGCTTGATCCTTGT 58.000 45.000 0.00 0.00 40.80 3.16
401 403 1.479323 TCCTTGTATTTCGAGGGGTCG 59.521 52.381 1.87 0.00 45.51 4.79
415 417 2.582498 GTCGCGAACCATCCTCCG 60.582 66.667 12.06 0.00 0.00 4.63
440 442 7.333423 CGAACTCAACATCTTTTGGGACTATAA 59.667 37.037 0.00 0.00 30.82 0.98
453 455 6.620877 TGGGACTATAACTGATCAACACTT 57.379 37.500 0.00 0.00 0.00 3.16
510 512 4.831710 TGTCATGATTCATCAAAACCCACA 59.168 37.500 0.00 0.00 40.69 4.17
535 817 2.766828 GGGTCCTAGATGCACTTACAGT 59.233 50.000 0.00 0.00 0.00 3.55
547 829 5.914033 TGCACTTACAGTTTGACTACTTCT 58.086 37.500 0.00 0.00 0.00 2.85
571 856 2.376032 GCCGCGATTGCTTATCTTTTC 58.624 47.619 8.23 0.00 39.65 2.29
577 879 4.333926 GCGATTGCTTATCTTTTCTCCACT 59.666 41.667 0.00 0.00 38.39 4.00
610 912 9.695526 TGCAAATAAATAATGATATGGTTGAGC 57.304 29.630 0.00 0.00 0.00 4.26
611 913 9.143631 GCAAATAAATAATGATATGGTTGAGCC 57.856 33.333 0.00 0.00 37.90 4.70
614 916 6.655078 AAATAATGATATGGTTGAGCCCAC 57.345 37.500 0.00 0.00 37.31 4.61
615 917 3.668141 AATGATATGGTTGAGCCCACA 57.332 42.857 0.00 0.00 37.31 4.17
619 922 5.122707 TGATATGGTTGAGCCCACATAAA 57.877 39.130 0.00 0.00 37.31 1.40
627 930 3.088532 TGAGCCCACATAAACATCCAAC 58.911 45.455 0.00 0.00 0.00 3.77
628 931 2.091541 AGCCCACATAAACATCCAACG 58.908 47.619 0.00 0.00 0.00 4.10
658 961 3.188048 GCCGAAATTCATCTAGCATCCAG 59.812 47.826 0.00 0.00 0.00 3.86
696 1007 0.745486 CTGTTCAGGCATGCGGATGA 60.745 55.000 22.14 12.82 0.00 2.92
707 1018 1.332195 TGCGGATGATCAGGGACTAG 58.668 55.000 0.09 0.00 36.02 2.57
883 1194 1.840635 GCCAGACCCTCTAGAACCATT 59.159 52.381 0.00 0.00 0.00 3.16
901 1212 8.724310 AGAACCATTAAGCACTATAAATACCCT 58.276 33.333 0.00 0.00 0.00 4.34
904 1215 8.101419 ACCATTAAGCACTATAAATACCCTAGC 58.899 37.037 0.00 0.00 0.00 3.42
951 1266 0.606401 AGCAACCAACCATCCACGAG 60.606 55.000 0.00 0.00 0.00 4.18
957 1272 1.148310 CAACCATCCACGAGACACAC 58.852 55.000 0.00 0.00 0.00 3.82
958 1273 0.756294 AACCATCCACGAGACACACA 59.244 50.000 0.00 0.00 0.00 3.72
959 1274 0.756294 ACCATCCACGAGACACACAA 59.244 50.000 0.00 0.00 0.00 3.33
960 1275 1.270305 ACCATCCACGAGACACACAAG 60.270 52.381 0.00 0.00 0.00 3.16
961 1276 0.792640 CATCCACGAGACACACAAGC 59.207 55.000 0.00 0.00 0.00 4.01
962 1277 0.392706 ATCCACGAGACACACAAGCA 59.607 50.000 0.00 0.00 0.00 3.91
1042 1357 3.939837 CTGACTGCGGTGGCGATGT 62.940 63.158 0.80 0.00 44.10 3.06
1059 1374 2.041115 GTTCCTTCTCCTTGCCGCC 61.041 63.158 0.00 0.00 0.00 6.13
1337 1686 0.318445 GCTGCTGCTTCACTTGGTTG 60.318 55.000 8.53 0.00 36.03 3.77
1342 1695 2.564771 CTGCTTCACTTGGTTGACAGA 58.435 47.619 0.00 0.00 0.00 3.41
1344 1697 1.604278 GCTTCACTTGGTTGACAGACC 59.396 52.381 1.21 1.21 40.23 3.85
1357 1714 2.170397 TGACAGACCACACATGAACTGT 59.830 45.455 0.00 0.00 41.31 3.55
1390 1749 0.473886 ACCCCACCAGAGTGCTAGTT 60.474 55.000 0.00 0.00 43.09 2.24
1411 1770 7.736447 AGTTCATTCAAACCTAAGAGAACTG 57.264 36.000 0.00 0.00 41.80 3.16
1412 1771 6.712547 AGTTCATTCAAACCTAAGAGAACTGG 59.287 38.462 0.00 0.00 41.80 4.00
1414 1773 6.467677 TCATTCAAACCTAAGAGAACTGGAG 58.532 40.000 0.00 0.00 0.00 3.86
1415 1774 5.888982 TTCAAACCTAAGAGAACTGGAGT 57.111 39.130 0.00 0.00 0.00 3.85
1416 1775 6.989155 TTCAAACCTAAGAGAACTGGAGTA 57.011 37.500 0.00 0.00 0.00 2.59
1417 1776 6.342338 TCAAACCTAAGAGAACTGGAGTAC 57.658 41.667 0.00 0.00 0.00 2.73
1418 1777 5.836898 TCAAACCTAAGAGAACTGGAGTACA 59.163 40.000 0.00 0.00 0.00 2.90
1419 1778 6.497259 TCAAACCTAAGAGAACTGGAGTACAT 59.503 38.462 0.00 0.00 0.00 2.29
1420 1779 5.923733 ACCTAAGAGAACTGGAGTACATG 57.076 43.478 0.00 0.00 0.00 3.21
1427 1794 6.123651 AGAGAACTGGAGTACATGTACTAGG 58.876 44.000 33.05 25.97 45.63 3.02
1461 1832 6.360148 CCGTTCGAGCTCATTATTCTAAGTAC 59.640 42.308 15.40 0.00 0.00 2.73
1462 1833 6.085198 CGTTCGAGCTCATTATTCTAAGTACG 59.915 42.308 15.40 5.25 0.00 3.67
1463 1834 6.615264 TCGAGCTCATTATTCTAAGTACGT 57.385 37.500 15.40 0.00 0.00 3.57
1464 1835 7.719778 TCGAGCTCATTATTCTAAGTACGTA 57.280 36.000 15.40 0.00 0.00 3.57
1478 1850 8.511465 TCTAAGTACGTAACAATTGAACTGAC 57.489 34.615 13.59 9.73 0.00 3.51
1482 1854 7.428020 AGTACGTAACAATTGAACTGACTGTA 58.572 34.615 13.59 4.79 0.00 2.74
1494 1866 8.472007 TTGAACTGACTGTATTTTGGGTTTAT 57.528 30.769 0.00 0.00 0.00 1.40
1496 1868 8.356657 TGAACTGACTGTATTTTGGGTTTATTG 58.643 33.333 0.00 0.00 0.00 1.90
1509 1881 5.996644 TGGGTTTATTGTTACAGGATCGAT 58.003 37.500 0.00 0.00 0.00 3.59
1525 1897 2.964740 TCGATGGTCTGAAGCAAGAAG 58.035 47.619 0.00 0.00 36.29 2.85
1597 1969 4.448210 TGCTGGAATAAATAAGACGTCCC 58.552 43.478 13.01 3.22 0.00 4.46
1657 2029 6.594788 AATGTATTGCCATTCAGTTGAAGT 57.405 33.333 0.74 0.00 37.48 3.01
1658 2030 6.594788 ATGTATTGCCATTCAGTTGAAGTT 57.405 33.333 0.74 0.00 37.48 2.66
1662 2034 8.584157 TGTATTGCCATTCAGTTGAAGTTATTT 58.416 29.630 0.74 0.00 37.48 1.40
1697 2134 4.273005 ACTTTGACTACGTTGCAACTTG 57.727 40.909 26.09 17.37 0.00 3.16
1709 2146 1.312815 GCAACTTGCAGGACTCTTGT 58.687 50.000 8.97 0.00 44.26 3.16
1710 2147 2.494059 GCAACTTGCAGGACTCTTGTA 58.506 47.619 8.97 0.00 44.26 2.41
1712 2149 3.503748 GCAACTTGCAGGACTCTTGTATT 59.496 43.478 8.97 0.00 44.26 1.89
1713 2150 4.022849 GCAACTTGCAGGACTCTTGTATTT 60.023 41.667 8.97 0.00 44.26 1.40
1714 2151 5.693814 CAACTTGCAGGACTCTTGTATTTC 58.306 41.667 1.40 0.00 0.00 2.17
1715 2152 4.327680 ACTTGCAGGACTCTTGTATTTCC 58.672 43.478 1.40 0.00 0.00 3.13
1716 2153 3.350219 TGCAGGACTCTTGTATTTCCC 57.650 47.619 0.00 0.00 0.00 3.97
1717 2154 2.642311 TGCAGGACTCTTGTATTTCCCA 59.358 45.455 0.00 0.00 0.00 4.37
1718 2155 3.274288 GCAGGACTCTTGTATTTCCCAG 58.726 50.000 0.00 0.00 0.00 4.45
1719 2156 3.878778 CAGGACTCTTGTATTTCCCAGG 58.121 50.000 0.00 0.00 0.00 4.45
1720 2157 3.264450 CAGGACTCTTGTATTTCCCAGGT 59.736 47.826 0.00 0.00 0.00 4.00
1721 2158 3.916989 AGGACTCTTGTATTTCCCAGGTT 59.083 43.478 0.00 0.00 0.00 3.50
1722 2159 4.010349 GGACTCTTGTATTTCCCAGGTTG 58.990 47.826 0.00 0.00 0.00 3.77
1723 2160 4.263331 GGACTCTTGTATTTCCCAGGTTGA 60.263 45.833 0.00 0.00 0.00 3.18
1724 2161 5.501156 GACTCTTGTATTTCCCAGGTTGAT 58.499 41.667 0.00 0.00 0.00 2.57
1725 2162 5.501156 ACTCTTGTATTTCCCAGGTTGATC 58.499 41.667 0.00 0.00 0.00 2.92
1726 2163 5.251700 ACTCTTGTATTTCCCAGGTTGATCT 59.748 40.000 0.00 0.00 0.00 2.75
1727 2164 6.443849 ACTCTTGTATTTCCCAGGTTGATCTA 59.556 38.462 0.00 0.00 0.00 1.98
1728 2165 7.127955 ACTCTTGTATTTCCCAGGTTGATCTAT 59.872 37.037 0.00 0.00 0.00 1.98
1729 2166 7.509546 TCTTGTATTTCCCAGGTTGATCTATC 58.490 38.462 0.00 0.00 0.00 2.08
1730 2167 6.823286 TGTATTTCCCAGGTTGATCTATCA 57.177 37.500 0.00 0.00 34.44 2.15
1731 2168 7.392766 TGTATTTCCCAGGTTGATCTATCAT 57.607 36.000 0.00 0.00 36.56 2.45
1732 2169 7.226441 TGTATTTCCCAGGTTGATCTATCATG 58.774 38.462 0.00 0.00 36.56 3.07
1733 2170 5.715439 TTTCCCAGGTTGATCTATCATGT 57.285 39.130 0.00 0.00 36.56 3.21
1734 2171 5.715439 TTCCCAGGTTGATCTATCATGTT 57.285 39.130 0.00 0.00 36.56 2.71
1735 2172 6.823286 TTCCCAGGTTGATCTATCATGTTA 57.177 37.500 0.00 0.00 36.56 2.41
1736 2173 7.392766 TTCCCAGGTTGATCTATCATGTTAT 57.607 36.000 0.00 0.00 36.56 1.89
1737 2174 6.772605 TCCCAGGTTGATCTATCATGTTATG 58.227 40.000 0.00 0.00 36.56 1.90
1738 2175 6.329986 TCCCAGGTTGATCTATCATGTTATGT 59.670 38.462 0.00 0.00 36.56 2.29
1739 2176 7.000472 CCCAGGTTGATCTATCATGTTATGTT 59.000 38.462 0.00 0.00 36.56 2.71
1740 2177 8.156820 CCCAGGTTGATCTATCATGTTATGTTA 58.843 37.037 0.00 0.00 36.56 2.41
1741 2178 8.993121 CCAGGTTGATCTATCATGTTATGTTAC 58.007 37.037 0.00 0.00 36.56 2.50
1742 2179 9.770097 CAGGTTGATCTATCATGTTATGTTACT 57.230 33.333 0.00 0.00 36.56 2.24
1743 2180 9.988815 AGGTTGATCTATCATGTTATGTTACTC 57.011 33.333 0.00 0.00 36.56 2.59
1744 2181 9.764363 GGTTGATCTATCATGTTATGTTACTCA 57.236 33.333 0.00 0.00 36.56 3.41
1752 2189 7.801716 TCATGTTATGTTACTCAATTAGGGC 57.198 36.000 0.00 0.00 0.00 5.19
1753 2190 7.342581 TCATGTTATGTTACTCAATTAGGGCA 58.657 34.615 0.00 0.00 0.00 5.36
1754 2191 7.831690 TCATGTTATGTTACTCAATTAGGGCAA 59.168 33.333 0.00 0.00 0.00 4.52
1755 2192 8.632679 CATGTTATGTTACTCAATTAGGGCAAT 58.367 33.333 0.00 0.00 0.00 3.56
1756 2193 8.588290 TGTTATGTTACTCAATTAGGGCAATT 57.412 30.769 0.00 0.00 37.32 2.32
1757 2194 8.682710 TGTTATGTTACTCAATTAGGGCAATTC 58.317 33.333 0.00 0.00 34.49 2.17
1758 2195 6.715347 ATGTTACTCAATTAGGGCAATTCC 57.285 37.500 0.00 0.00 34.49 3.01
1759 2196 4.638421 TGTTACTCAATTAGGGCAATTCCG 59.362 41.667 0.00 0.00 34.49 4.30
1760 2197 3.644966 ACTCAATTAGGGCAATTCCGA 57.355 42.857 0.00 0.00 34.49 4.55
1761 2198 3.963129 ACTCAATTAGGGCAATTCCGAA 58.037 40.909 0.00 0.00 34.49 4.30
1762 2199 4.340617 ACTCAATTAGGGCAATTCCGAAA 58.659 39.130 0.00 0.00 34.49 3.46
1763 2200 4.956075 ACTCAATTAGGGCAATTCCGAAAT 59.044 37.500 0.00 0.00 34.49 2.17
1764 2201 5.163519 ACTCAATTAGGGCAATTCCGAAATG 60.164 40.000 0.00 0.00 34.49 2.32
1765 2202 4.952957 TCAATTAGGGCAATTCCGAAATGA 59.047 37.500 0.08 0.00 34.49 2.57
1766 2203 5.420421 TCAATTAGGGCAATTCCGAAATGAA 59.580 36.000 0.08 0.00 34.49 2.57
1767 2204 6.098124 TCAATTAGGGCAATTCCGAAATGAAT 59.902 34.615 0.08 0.00 34.49 2.57
1768 2205 3.806625 AGGGCAATTCCGAAATGAATG 57.193 42.857 0.08 0.00 35.21 2.67
1769 2206 3.364549 AGGGCAATTCCGAAATGAATGA 58.635 40.909 0.08 0.00 35.21 2.57
1770 2207 3.131046 AGGGCAATTCCGAAATGAATGAC 59.869 43.478 0.08 0.00 35.21 3.06
1771 2208 3.119173 GGGCAATTCCGAAATGAATGACA 60.119 43.478 0.08 0.00 35.21 3.58
1772 2209 4.107622 GGCAATTCCGAAATGAATGACAG 58.892 43.478 0.08 0.00 35.21 3.51
1773 2210 3.549070 GCAATTCCGAAATGAATGACAGC 59.451 43.478 0.08 0.00 35.21 4.40
1774 2211 4.735985 CAATTCCGAAATGAATGACAGCA 58.264 39.130 0.00 0.00 35.21 4.41
1775 2212 5.345702 CAATTCCGAAATGAATGACAGCAT 58.654 37.500 0.00 0.00 35.21 3.79
1776 2213 5.587388 ATTCCGAAATGAATGACAGCATT 57.413 34.783 0.00 0.00 47.00 3.56
1777 2214 4.359971 TCCGAAATGAATGACAGCATTG 57.640 40.909 6.99 0.00 44.47 2.82
1778 2215 2.855963 CCGAAATGAATGACAGCATTGC 59.144 45.455 0.00 0.00 44.47 3.56
1779 2216 3.503891 CGAAATGAATGACAGCATTGCA 58.496 40.909 11.91 0.00 44.47 4.08
1780 2217 3.921630 CGAAATGAATGACAGCATTGCAA 59.078 39.130 11.91 0.00 44.47 4.08
1781 2218 4.565166 CGAAATGAATGACAGCATTGCAAT 59.435 37.500 11.91 5.99 44.47 3.56
1782 2219 5.744819 CGAAATGAATGACAGCATTGCAATA 59.255 36.000 12.53 0.00 44.47 1.90
1783 2220 6.253942 CGAAATGAATGACAGCATTGCAATAA 59.746 34.615 12.53 0.00 44.47 1.40
1784 2221 7.514591 CGAAATGAATGACAGCATTGCAATAAG 60.515 37.037 12.53 7.46 44.47 1.73
1785 2222 5.648178 TGAATGACAGCATTGCAATAAGT 57.352 34.783 12.53 10.72 44.47 2.24
1786 2223 6.756299 TGAATGACAGCATTGCAATAAGTA 57.244 33.333 12.53 0.00 44.47 2.24
1787 2224 7.337480 TGAATGACAGCATTGCAATAAGTAT 57.663 32.000 12.53 0.00 44.47 2.12
1788 2225 7.197703 TGAATGACAGCATTGCAATAAGTATG 58.802 34.615 12.53 8.95 44.47 2.39
1789 2226 6.947644 ATGACAGCATTGCAATAAGTATGA 57.052 33.333 12.53 0.12 0.00 2.15
1790 2227 6.367686 TGACAGCATTGCAATAAGTATGAG 57.632 37.500 12.53 0.00 0.00 2.90
1791 2228 5.179045 ACAGCATTGCAATAAGTATGAGC 57.821 39.130 12.53 8.76 0.00 4.26
1792 2229 4.641541 ACAGCATTGCAATAAGTATGAGCA 59.358 37.500 12.53 0.00 0.00 4.26
1794 2231 5.457799 CAGCATTGCAATAAGTATGAGCAAC 59.542 40.000 12.53 3.85 46.43 4.17
1795 2232 4.438797 GCATTGCAATAAGTATGAGCAACG 59.561 41.667 12.53 6.89 46.43 4.10
1796 2233 5.730289 GCATTGCAATAAGTATGAGCAACGA 60.730 40.000 12.53 0.00 46.43 3.85
1797 2234 5.871465 TTGCAATAAGTATGAGCAACGAA 57.129 34.783 0.00 0.00 39.95 3.85
1798 2235 6.435430 TTGCAATAAGTATGAGCAACGAAT 57.565 33.333 0.00 0.00 39.95 3.34
1799 2236 6.435430 TGCAATAAGTATGAGCAACGAATT 57.565 33.333 0.00 0.00 31.42 2.17
1800 2237 6.486248 TGCAATAAGTATGAGCAACGAATTC 58.514 36.000 0.00 0.00 31.42 2.17
1801 2238 5.909610 GCAATAAGTATGAGCAACGAATTCC 59.090 40.000 0.00 0.00 0.00 3.01
1802 2239 6.430451 CAATAAGTATGAGCAACGAATTCCC 58.570 40.000 0.00 0.00 0.00 3.97
1803 2240 2.919228 AGTATGAGCAACGAATTCCCC 58.081 47.619 0.00 0.00 0.00 4.81
1804 2241 2.505819 AGTATGAGCAACGAATTCCCCT 59.494 45.455 0.00 0.00 0.00 4.79
1805 2242 1.755179 ATGAGCAACGAATTCCCCTG 58.245 50.000 0.00 0.00 0.00 4.45
1806 2243 0.690192 TGAGCAACGAATTCCCCTGA 59.310 50.000 0.00 0.00 0.00 3.86
1860 2298 4.531854 TGGATGACTGAACTGAAACCAAA 58.468 39.130 0.00 0.00 0.00 3.28
1865 2303 4.083003 TGACTGAACTGAAACCAAACACAC 60.083 41.667 0.00 0.00 0.00 3.82
1866 2304 3.192633 ACTGAACTGAAACCAAACACACC 59.807 43.478 0.00 0.00 0.00 4.16
1871 2309 1.895798 TGAAACCAAACACACCTGCAA 59.104 42.857 0.00 0.00 0.00 4.08
1878 2316 3.495377 CCAAACACACCTGCAAATTCATG 59.505 43.478 0.00 0.00 0.00 3.07
1918 2356 4.972440 GCTTGTGCAAAACAAACAAACAAA 59.028 33.333 0.00 0.00 44.97 2.83
1919 2357 5.108443 GCTTGTGCAAAACAAACAAACAAAC 60.108 36.000 0.00 0.00 44.97 2.93
1920 2358 5.484173 TGTGCAAAACAAACAAACAAACA 57.516 30.435 0.00 0.00 35.24 2.83
1921 2359 5.879237 TGTGCAAAACAAACAAACAAACAA 58.121 29.167 0.00 0.00 35.24 2.83
1923 2361 6.251376 TGTGCAAAACAAACAAACAAACAAAC 59.749 30.769 0.00 0.00 35.24 2.93
1924 2362 6.251376 GTGCAAAACAAACAAACAAACAAACA 59.749 30.769 0.00 0.00 0.00 2.83
1927 2365 8.323854 GCAAAACAAACAAACAAACAAACAATT 58.676 25.926 0.00 0.00 0.00 2.32
1932 2370 9.439537 ACAAACAAACAAACAAACAATTTACAC 57.560 25.926 0.00 0.00 0.00 2.90
1935 2373 7.284351 ACAAACAAACAAACAATTTACACGTG 58.716 30.769 15.48 15.48 0.00 4.49
1936 2374 7.169308 ACAAACAAACAAACAATTTACACGTGA 59.831 29.630 25.01 0.00 0.00 4.35
1946 2384 6.851609 ACAATTTACACGTGAATATGCATGT 58.148 32.000 25.01 10.03 38.49 3.21
1948 2386 8.122330 ACAATTTACACGTGAATATGCATGTAG 58.878 33.333 25.01 6.17 36.31 2.74
1959 2397 6.825213 TGAATATGCATGTAGGAATAGATGCC 59.175 38.462 10.16 1.07 43.53 4.40
1964 2402 4.808665 GCATGTAGGAATAGATGCCCACAT 60.809 45.833 6.20 0.00 39.82 3.21
1981 2419 3.257393 CACATCCTACTTGACTGCAGTC 58.743 50.000 35.04 35.04 44.97 3.51
2005 2443 7.804129 GTCAAACTAAACCGCATACAAACATAA 59.196 33.333 0.00 0.00 0.00 1.90
2006 2444 7.804129 TCAAACTAAACCGCATACAAACATAAC 59.196 33.333 0.00 0.00 0.00 1.89
2007 2445 6.804770 ACTAAACCGCATACAAACATAACA 57.195 33.333 0.00 0.00 0.00 2.41
2008 2446 7.385778 ACTAAACCGCATACAAACATAACAT 57.614 32.000 0.00 0.00 0.00 2.71
2009 2447 8.495361 ACTAAACCGCATACAAACATAACATA 57.505 30.769 0.00 0.00 0.00 2.29
2010 2448 8.392612 ACTAAACCGCATACAAACATAACATAC 58.607 33.333 0.00 0.00 0.00 2.39
2011 2449 6.745159 AACCGCATACAAACATAACATACA 57.255 33.333 0.00 0.00 0.00 2.29
2030 2468 6.697455 ACATACATACATACGCAGAAGACAAG 59.303 38.462 0.00 0.00 0.00 3.16
2037 2475 1.159285 CGCAGAAGACAAGATGGCAA 58.841 50.000 0.00 0.00 0.00 4.52
2038 2476 1.536766 CGCAGAAGACAAGATGGCAAA 59.463 47.619 0.00 0.00 0.00 3.68
2041 2479 3.254166 GCAGAAGACAAGATGGCAAAAGA 59.746 43.478 0.00 0.00 0.00 2.52
2042 2480 4.261741 GCAGAAGACAAGATGGCAAAAGAA 60.262 41.667 0.00 0.00 0.00 2.52
2043 2481 5.737063 GCAGAAGACAAGATGGCAAAAGAAA 60.737 40.000 0.00 0.00 0.00 2.52
2044 2482 6.275335 CAGAAGACAAGATGGCAAAAGAAAA 58.725 36.000 0.00 0.00 0.00 2.29
2045 2483 6.757947 CAGAAGACAAGATGGCAAAAGAAAAA 59.242 34.615 0.00 0.00 0.00 1.94
2046 2484 6.982724 AGAAGACAAGATGGCAAAAGAAAAAG 59.017 34.615 0.00 0.00 0.00 2.27
2047 2485 6.469782 AGACAAGATGGCAAAAGAAAAAGA 57.530 33.333 0.00 0.00 0.00 2.52
2048 2486 6.877236 AGACAAGATGGCAAAAGAAAAAGAA 58.123 32.000 0.00 0.00 0.00 2.52
2049 2487 6.758416 AGACAAGATGGCAAAAGAAAAAGAAC 59.242 34.615 0.00 0.00 0.00 3.01
2050 2488 6.643388 ACAAGATGGCAAAAGAAAAAGAACT 58.357 32.000 0.00 0.00 0.00 3.01
2051 2489 6.536224 ACAAGATGGCAAAAGAAAAAGAACTG 59.464 34.615 0.00 0.00 0.00 3.16
2052 2490 6.469782 AGATGGCAAAAGAAAAAGAACTGA 57.530 33.333 0.00 0.00 0.00 3.41
2053 2491 6.510536 AGATGGCAAAAGAAAAAGAACTGAG 58.489 36.000 0.00 0.00 0.00 3.35
2054 2492 4.432712 TGGCAAAAGAAAAAGAACTGAGC 58.567 39.130 0.00 0.00 0.00 4.26
2055 2493 4.081752 TGGCAAAAGAAAAAGAACTGAGCA 60.082 37.500 0.00 0.00 0.00 4.26
2133 2575 1.494721 ACAACTCAGTGGTTCATGGGT 59.505 47.619 0.00 0.00 0.00 4.51
2139 2581 0.844661 AGTGGTTCATGGGTGGCCTA 60.845 55.000 3.32 0.00 0.00 3.93
2194 2636 1.519455 CTCGCCCTCCACGAATCAC 60.519 63.158 0.00 0.00 39.39 3.06
2195 2637 2.225791 CTCGCCCTCCACGAATCACA 62.226 60.000 0.00 0.00 39.39 3.58
2196 2638 1.153369 CGCCCTCCACGAATCACAT 60.153 57.895 0.00 0.00 0.00 3.21
2197 2639 0.104120 CGCCCTCCACGAATCACATA 59.896 55.000 0.00 0.00 0.00 2.29
2304 2749 1.731424 CGTCTACACCGTCACCATCAC 60.731 57.143 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.357161 CAATAATCCTACACCTACTAAGAGTCT 57.643 37.037 0.00 0.00 0.00 3.24
31 32 7.289317 TGTCCCAATAATCCTACACCTACTAAG 59.711 40.741 0.00 0.00 0.00 2.18
68 69 3.341823 TCTACTCACGTTCTGTACCTCC 58.658 50.000 0.00 0.00 0.00 4.30
76 77 6.980051 ACAAAAACTTTCTACTCACGTTCT 57.020 33.333 0.00 0.00 0.00 3.01
132 134 0.310854 CTTTGTGCGTTTCAGACCCC 59.689 55.000 0.00 0.00 0.00 4.95
167 169 3.432749 GGAGCCTCTGATGCAATCTACAA 60.433 47.826 7.66 0.00 45.81 2.41
169 171 2.765122 GGAGCCTCTGATGCAATCTAC 58.235 52.381 7.66 0.00 45.81 2.59
178 180 0.399091 TTCCATCCGGAGCCTCTGAT 60.399 55.000 11.34 0.00 44.10 2.90
212 214 5.047731 ACTCTCTTCACATTCATCTGTTCGA 60.048 40.000 0.00 0.00 0.00 3.71
296 298 6.183361 TGGGTCTTGTGAGAAGTATTTCTTGA 60.183 38.462 1.61 0.00 43.63 3.02
333 335 6.754209 CGAGTCATAGGTATGCCAATTCTATC 59.246 42.308 1.54 0.00 37.19 2.08
338 340 4.955811 TCGAGTCATAGGTATGCCAATT 57.044 40.909 1.54 0.00 37.19 2.32
341 343 3.068165 CACTTCGAGTCATAGGTATGCCA 59.932 47.826 1.54 0.00 37.19 4.92
386 388 0.179129 TTCGCGACCCCTCGAAATAC 60.179 55.000 9.15 0.00 43.06 1.89
387 389 0.179129 GTTCGCGACCCCTCGAAATA 60.179 55.000 9.15 0.00 44.76 1.40
401 403 0.806492 GAGTTCGGAGGATGGTTCGC 60.806 60.000 0.00 0.00 0.00 4.70
411 413 3.189287 CCCAAAAGATGTTGAGTTCGGAG 59.811 47.826 0.00 0.00 0.00 4.63
415 417 8.451748 GTTATAGTCCCAAAAGATGTTGAGTTC 58.548 37.037 0.00 0.00 0.00 3.01
440 442 7.338800 ACAATTTCTCAAAGTGTTGATCAGT 57.661 32.000 0.00 0.00 46.25 3.41
478 480 8.620116 TTTGATGAATCATGACAACAAGACTA 57.380 30.769 0.00 0.00 36.56 2.59
510 512 1.898863 AGTGCATCTAGGACCCCATT 58.101 50.000 0.00 0.00 39.79 3.16
535 817 1.403249 GCGGCCGTAGAAGTAGTCAAA 60.403 52.381 28.70 0.00 0.00 2.69
547 829 0.942410 GATAAGCAATCGCGGCCGTA 60.942 55.000 28.70 16.32 45.49 4.02
610 912 1.815613 TGCGTTGGATGTTTATGTGGG 59.184 47.619 0.00 0.00 0.00 4.61
611 913 3.489059 GGATGCGTTGGATGTTTATGTGG 60.489 47.826 0.00 0.00 0.00 4.17
614 916 4.292599 CATGGATGCGTTGGATGTTTATG 58.707 43.478 0.00 0.00 0.00 1.90
615 917 3.243501 GCATGGATGCGTTGGATGTTTAT 60.244 43.478 0.00 0.00 44.67 1.40
619 922 2.109431 GCATGGATGCGTTGGATGT 58.891 52.632 0.00 0.00 44.67 3.06
658 961 3.704061 ACAGAACTTCAGATAGAGAGGCC 59.296 47.826 0.00 0.00 0.00 5.19
696 1007 4.020128 GGTGAGTTTGTTCTAGTCCCTGAT 60.020 45.833 0.00 0.00 0.00 2.90
707 1018 5.163663 TGTGAGAATGTTGGTGAGTTTGTTC 60.164 40.000 0.00 0.00 0.00 3.18
797 1108 1.153588 CCGGCCATGGAAATGCAAC 60.154 57.895 18.40 0.00 0.00 4.17
883 1194 7.311046 CCATGGCTAGGGTATTTATAGTGCTTA 60.311 40.741 0.00 0.00 0.00 3.09
901 1212 1.153188 CGGTGATGTGCCATGGCTA 60.153 57.895 35.53 24.89 42.51 3.93
951 1266 0.028505 CTGTGCTGTGCTTGTGTGTC 59.971 55.000 0.00 0.00 0.00 3.67
957 1272 2.050351 GCTGCTGTGCTGTGCTTG 60.050 61.111 0.00 0.00 0.00 4.01
958 1273 3.657059 CGCTGCTGTGCTGTGCTT 61.657 61.111 0.00 0.00 32.06 3.91
980 1295 0.881796 CTTGCCGGAGTTTTCCCTTC 59.118 55.000 5.05 0.00 40.67 3.46
1042 1357 2.351276 GGCGGCAAGGAGAAGGAA 59.649 61.111 3.07 0.00 0.00 3.36
1234 1582 0.392863 TCCATGCTGATGTTGTCCCG 60.393 55.000 0.00 0.00 0.00 5.14
1337 1686 2.838736 ACAGTTCATGTGTGGTCTGTC 58.161 47.619 0.00 0.00 41.91 3.51
1357 1714 1.003118 GTGGGGTAAGCATGTCAGTCA 59.997 52.381 0.00 0.00 0.00 3.41
1390 1749 6.043243 ACTCCAGTTCTCTTAGGTTTGAATGA 59.957 38.462 0.00 0.00 0.00 2.57
1411 1770 3.819337 TCGATGCCTAGTACATGTACTCC 59.181 47.826 35.69 25.39 44.58 3.85
1412 1771 5.394802 CATCGATGCCTAGTACATGTACTC 58.605 45.833 35.69 23.96 44.58 2.59
1461 1832 8.891928 CAAAATACAGTCAGTTCAATTGTTACG 58.108 33.333 5.13 3.06 0.00 3.18
1462 1833 9.180678 CCAAAATACAGTCAGTTCAATTGTTAC 57.819 33.333 5.13 5.44 0.00 2.50
1463 1834 8.356657 CCCAAAATACAGTCAGTTCAATTGTTA 58.643 33.333 5.13 0.00 0.00 2.41
1464 1835 7.147742 ACCCAAAATACAGTCAGTTCAATTGTT 60.148 33.333 5.13 0.00 0.00 2.83
1478 1850 8.798402 TCCTGTAACAATAAACCCAAAATACAG 58.202 33.333 0.00 0.00 38.15 2.74
1482 1854 7.394923 TCGATCCTGTAACAATAAACCCAAAAT 59.605 33.333 0.00 0.00 0.00 1.82
1494 1866 3.767131 TCAGACCATCGATCCTGTAACAA 59.233 43.478 14.78 0.00 0.00 2.83
1496 1868 4.363999 CTTCAGACCATCGATCCTGTAAC 58.636 47.826 14.78 0.00 0.00 2.50
1509 1881 1.271054 GCCTCTTCTTGCTTCAGACCA 60.271 52.381 0.00 0.00 0.00 4.02
1597 1969 1.469251 CGTCCACCTATGAGTTGACCG 60.469 57.143 0.00 0.00 30.59 4.79
1665 2037 8.866956 GCAACGTAGTCAAAGTATAATACAACT 58.133 33.333 0.00 0.00 45.00 3.16
1666 2038 8.649841 TGCAACGTAGTCAAAGTATAATACAAC 58.350 33.333 0.00 0.00 45.00 3.32
1668 2040 8.649841 GTTGCAACGTAGTCAAAGTATAATACA 58.350 33.333 14.90 0.00 45.00 2.29
1697 2134 3.274288 CTGGGAAATACAAGAGTCCTGC 58.726 50.000 0.00 0.00 0.00 4.85
1699 2136 3.532102 ACCTGGGAAATACAAGAGTCCT 58.468 45.455 0.00 0.00 0.00 3.85
1700 2137 4.010349 CAACCTGGGAAATACAAGAGTCC 58.990 47.826 0.00 0.00 0.00 3.85
1703 2140 5.749462 AGATCAACCTGGGAAATACAAGAG 58.251 41.667 0.00 0.00 0.00 2.85
1704 2141 5.779241 AGATCAACCTGGGAAATACAAGA 57.221 39.130 0.00 0.00 0.00 3.02
1705 2142 7.282585 TGATAGATCAACCTGGGAAATACAAG 58.717 38.462 0.00 0.00 33.08 3.16
1706 2143 7.206789 TGATAGATCAACCTGGGAAATACAA 57.793 36.000 0.00 0.00 33.08 2.41
1707 2144 6.823286 TGATAGATCAACCTGGGAAATACA 57.177 37.500 0.00 0.00 33.08 2.29
1708 2145 7.227156 ACATGATAGATCAACCTGGGAAATAC 58.773 38.462 0.00 0.00 40.69 1.89
1709 2146 7.392766 ACATGATAGATCAACCTGGGAAATA 57.607 36.000 0.00 0.00 40.69 1.40
1710 2147 6.271585 ACATGATAGATCAACCTGGGAAAT 57.728 37.500 0.00 0.00 40.69 2.17
1712 2149 5.715439 AACATGATAGATCAACCTGGGAA 57.285 39.130 0.00 0.00 40.69 3.97
1713 2150 6.329986 ACATAACATGATAGATCAACCTGGGA 59.670 38.462 0.00 0.00 40.69 4.37
1714 2151 6.537355 ACATAACATGATAGATCAACCTGGG 58.463 40.000 0.00 0.00 40.69 4.45
1715 2152 8.993121 GTAACATAACATGATAGATCAACCTGG 58.007 37.037 0.00 0.00 40.69 4.45
1716 2153 9.770097 AGTAACATAACATGATAGATCAACCTG 57.230 33.333 0.00 0.00 40.69 4.00
1717 2154 9.988815 GAGTAACATAACATGATAGATCAACCT 57.011 33.333 0.00 0.00 40.69 3.50
1718 2155 9.764363 TGAGTAACATAACATGATAGATCAACC 57.236 33.333 0.00 0.00 40.69 3.77
1726 2163 9.502091 GCCCTAATTGAGTAACATAACATGATA 57.498 33.333 0.00 0.00 0.00 2.15
1727 2164 7.998383 TGCCCTAATTGAGTAACATAACATGAT 59.002 33.333 0.00 0.00 0.00 2.45
1728 2165 7.342581 TGCCCTAATTGAGTAACATAACATGA 58.657 34.615 0.00 0.00 0.00 3.07
1729 2166 7.566760 TGCCCTAATTGAGTAACATAACATG 57.433 36.000 0.00 0.00 0.00 3.21
1730 2167 8.766994 ATTGCCCTAATTGAGTAACATAACAT 57.233 30.769 0.00 0.00 0.00 2.71
1731 2168 8.588290 AATTGCCCTAATTGAGTAACATAACA 57.412 30.769 0.00 0.00 37.59 2.41
1732 2169 8.135529 GGAATTGCCCTAATTGAGTAACATAAC 58.864 37.037 0.00 0.00 39.06 1.89
1733 2170 7.012894 CGGAATTGCCCTAATTGAGTAACATAA 59.987 37.037 0.00 0.00 39.06 1.90
1734 2171 6.485313 CGGAATTGCCCTAATTGAGTAACATA 59.515 38.462 0.00 0.00 39.06 2.29
1735 2172 5.299279 CGGAATTGCCCTAATTGAGTAACAT 59.701 40.000 0.00 0.00 39.06 2.71
1736 2173 4.638421 CGGAATTGCCCTAATTGAGTAACA 59.362 41.667 0.00 0.00 39.06 2.41
1737 2174 4.879545 TCGGAATTGCCCTAATTGAGTAAC 59.120 41.667 0.00 0.00 39.06 2.50
1738 2175 5.105567 TCGGAATTGCCCTAATTGAGTAA 57.894 39.130 0.00 0.00 39.06 2.24
1739 2176 4.764050 TCGGAATTGCCCTAATTGAGTA 57.236 40.909 0.00 0.00 39.06 2.59
1740 2177 3.644966 TCGGAATTGCCCTAATTGAGT 57.355 42.857 0.00 0.00 39.06 3.41
1741 2178 4.981806 TTTCGGAATTGCCCTAATTGAG 57.018 40.909 0.00 0.00 39.06 3.02
1742 2179 4.952957 TCATTTCGGAATTGCCCTAATTGA 59.047 37.500 7.56 0.00 39.06 2.57
1743 2180 5.261209 TCATTTCGGAATTGCCCTAATTG 57.739 39.130 7.56 0.00 39.06 2.32
1744 2181 5.930837 TTCATTTCGGAATTGCCCTAATT 57.069 34.783 7.56 0.00 41.59 1.40
1745 2182 5.598005 TCATTCATTTCGGAATTGCCCTAAT 59.402 36.000 7.56 1.28 35.37 1.73
1746 2183 4.952957 TCATTCATTTCGGAATTGCCCTAA 59.047 37.500 7.56 0.00 35.37 2.69
1747 2184 4.338118 GTCATTCATTTCGGAATTGCCCTA 59.662 41.667 7.56 0.00 35.37 3.53
1748 2185 3.131046 GTCATTCATTTCGGAATTGCCCT 59.869 43.478 7.56 0.00 35.37 5.19
1749 2186 3.119173 TGTCATTCATTTCGGAATTGCCC 60.119 43.478 7.56 0.00 35.37 5.36
1750 2187 4.107622 CTGTCATTCATTTCGGAATTGCC 58.892 43.478 7.56 0.00 35.37 4.52
1751 2188 3.549070 GCTGTCATTCATTTCGGAATTGC 59.451 43.478 7.56 0.00 35.37 3.56
1752 2189 4.735985 TGCTGTCATTCATTTCGGAATTG 58.264 39.130 6.34 6.34 35.37 2.32
1753 2190 5.587388 ATGCTGTCATTCATTTCGGAATT 57.413 34.783 0.00 0.00 35.37 2.17
1754 2191 5.345702 CAATGCTGTCATTCATTTCGGAAT 58.654 37.500 0.00 0.00 40.74 3.01
1755 2192 4.735985 CAATGCTGTCATTCATTTCGGAA 58.264 39.130 0.00 0.00 40.74 4.30
1756 2193 3.427909 GCAATGCTGTCATTCATTTCGGA 60.428 43.478 0.00 0.00 40.74 4.55
1757 2194 2.855963 GCAATGCTGTCATTCATTTCGG 59.144 45.455 0.00 0.00 40.74 4.30
1758 2195 3.503891 TGCAATGCTGTCATTCATTTCG 58.496 40.909 6.82 0.00 40.74 3.46
1759 2196 7.277098 ACTTATTGCAATGCTGTCATTCATTTC 59.723 33.333 22.27 0.00 40.74 2.17
1760 2197 7.101054 ACTTATTGCAATGCTGTCATTCATTT 58.899 30.769 22.27 0.00 40.74 2.32
1761 2198 6.636705 ACTTATTGCAATGCTGTCATTCATT 58.363 32.000 22.27 0.00 40.74 2.57
1762 2199 6.216801 ACTTATTGCAATGCTGTCATTCAT 57.783 33.333 22.27 0.00 40.74 2.57
1763 2200 5.648178 ACTTATTGCAATGCTGTCATTCA 57.352 34.783 22.27 0.00 40.74 2.57
1764 2201 7.420002 TCATACTTATTGCAATGCTGTCATTC 58.580 34.615 22.27 0.00 40.74 2.67
1765 2202 7.337480 TCATACTTATTGCAATGCTGTCATT 57.663 32.000 22.27 0.00 43.31 2.57
1766 2203 6.514541 GCTCATACTTATTGCAATGCTGTCAT 60.515 38.462 22.27 4.94 33.53 3.06
1767 2204 5.220912 GCTCATACTTATTGCAATGCTGTCA 60.221 40.000 22.27 0.00 0.00 3.58
1768 2205 5.210715 GCTCATACTTATTGCAATGCTGTC 58.789 41.667 22.27 2.56 0.00 3.51
1769 2206 4.641541 TGCTCATACTTATTGCAATGCTGT 59.358 37.500 22.27 17.76 0.00 4.40
1770 2207 5.177725 TGCTCATACTTATTGCAATGCTG 57.822 39.130 22.27 13.24 0.00 4.41
1771 2208 5.585390 GTTGCTCATACTTATTGCAATGCT 58.415 37.500 22.27 6.40 43.87 3.79
1772 2209 4.438797 CGTTGCTCATACTTATTGCAATGC 59.561 41.667 22.27 13.84 43.87 3.56
1773 2210 5.809464 TCGTTGCTCATACTTATTGCAATG 58.191 37.500 22.27 8.68 46.08 2.82
1774 2211 6.435430 TTCGTTGCTCATACTTATTGCAAT 57.565 33.333 17.56 17.56 43.87 3.56
1775 2212 5.871465 TTCGTTGCTCATACTTATTGCAA 57.129 34.783 0.00 0.00 40.65 4.08
1776 2213 6.435430 AATTCGTTGCTCATACTTATTGCA 57.565 33.333 0.00 0.00 0.00 4.08
1777 2214 5.909610 GGAATTCGTTGCTCATACTTATTGC 59.090 40.000 0.00 0.00 0.00 3.56
1778 2215 6.430451 GGGAATTCGTTGCTCATACTTATTG 58.570 40.000 0.00 0.00 0.00 1.90
1779 2216 5.531287 GGGGAATTCGTTGCTCATACTTATT 59.469 40.000 0.00 0.00 0.00 1.40
1780 2217 5.063880 GGGGAATTCGTTGCTCATACTTAT 58.936 41.667 0.00 0.00 0.00 1.73
1781 2218 4.163458 AGGGGAATTCGTTGCTCATACTTA 59.837 41.667 0.00 0.00 0.00 2.24
1782 2219 3.054361 AGGGGAATTCGTTGCTCATACTT 60.054 43.478 0.00 0.00 0.00 2.24
1783 2220 2.505819 AGGGGAATTCGTTGCTCATACT 59.494 45.455 0.00 0.00 0.00 2.12
1784 2221 2.614057 CAGGGGAATTCGTTGCTCATAC 59.386 50.000 0.00 0.00 0.00 2.39
1785 2222 2.503765 TCAGGGGAATTCGTTGCTCATA 59.496 45.455 0.00 0.00 0.00 2.15
1786 2223 1.281867 TCAGGGGAATTCGTTGCTCAT 59.718 47.619 0.00 0.00 0.00 2.90
1787 2224 0.690192 TCAGGGGAATTCGTTGCTCA 59.310 50.000 0.00 0.00 0.00 4.26
1788 2225 2.044123 ATCAGGGGAATTCGTTGCTC 57.956 50.000 0.00 0.00 0.00 4.26
1789 2226 3.864789 ATATCAGGGGAATTCGTTGCT 57.135 42.857 0.00 0.00 0.00 3.91
1790 2227 5.940470 AGATAATATCAGGGGAATTCGTTGC 59.060 40.000 2.84 0.00 0.00 4.17
1791 2228 9.672673 ATTAGATAATATCAGGGGAATTCGTTG 57.327 33.333 2.84 0.00 0.00 4.10
1792 2229 9.892130 GATTAGATAATATCAGGGGAATTCGTT 57.108 33.333 2.84 0.00 0.00 3.85
1793 2230 9.273137 AGATTAGATAATATCAGGGGAATTCGT 57.727 33.333 2.84 0.00 0.00 3.85
1798 2235 8.826765 GGTCAAGATTAGATAATATCAGGGGAA 58.173 37.037 2.84 0.00 0.00 3.97
1799 2236 7.961431 TGGTCAAGATTAGATAATATCAGGGGA 59.039 37.037 2.84 0.00 0.00 4.81
1800 2237 8.150827 TGGTCAAGATTAGATAATATCAGGGG 57.849 38.462 2.84 0.00 0.00 4.79
1801 2238 8.820831 ACTGGTCAAGATTAGATAATATCAGGG 58.179 37.037 2.84 0.00 0.00 4.45
1802 2239 9.650539 CACTGGTCAAGATTAGATAATATCAGG 57.349 37.037 2.84 0.00 0.00 3.86
1860 2298 4.669206 TTTCATGAATTTGCAGGTGTGT 57.331 36.364 9.40 0.00 0.00 3.72
1865 2303 8.557864 TGTAAATTGTTTTCATGAATTTGCAGG 58.442 29.630 9.40 0.00 33.04 4.85
1866 2304 9.372541 GTGTAAATTGTTTTCATGAATTTGCAG 57.627 29.630 17.20 0.00 36.59 4.41
1871 2309 7.933033 AGCAGGTGTAAATTGTTTTCATGAATT 59.067 29.630 9.40 1.94 0.00 2.17
1878 2316 5.276820 GCACAAGCAGGTGTAAATTGTTTTC 60.277 40.000 9.16 0.00 40.89 2.29
1913 2351 7.639162 TTCACGTGTAAATTGTTTGTTTGTT 57.361 28.000 16.51 0.00 0.00 2.83
1914 2352 7.820044 ATTCACGTGTAAATTGTTTGTTTGT 57.180 28.000 16.51 0.00 0.00 2.83
1918 2356 7.142021 TGCATATTCACGTGTAAATTGTTTGT 58.858 30.769 16.51 0.00 0.00 2.83
1919 2357 7.559835 TGCATATTCACGTGTAAATTGTTTG 57.440 32.000 16.51 6.52 0.00 2.93
1920 2358 7.812191 ACATGCATATTCACGTGTAAATTGTTT 59.188 29.630 16.51 0.00 34.33 2.83
1921 2359 7.312154 ACATGCATATTCACGTGTAAATTGTT 58.688 30.769 16.51 0.00 34.33 2.83
1923 2361 7.587392 CCTACATGCATATTCACGTGTAAATTG 59.413 37.037 16.51 9.29 37.71 2.32
1924 2362 7.497579 TCCTACATGCATATTCACGTGTAAATT 59.502 33.333 16.51 0.00 37.71 1.82
1927 2365 5.908341 TCCTACATGCATATTCACGTGTAA 58.092 37.500 16.51 9.07 37.71 2.41
1929 2367 4.400529 TCCTACATGCATATTCACGTGT 57.599 40.909 16.51 0.00 39.31 4.49
1932 2370 7.465111 GCATCTATTCCTACATGCATATTCACG 60.465 40.741 0.00 0.00 41.16 4.35
1935 2373 6.261826 GGGCATCTATTCCTACATGCATATTC 59.738 42.308 0.00 0.00 42.94 1.75
1936 2374 6.125029 GGGCATCTATTCCTACATGCATATT 58.875 40.000 0.00 0.00 42.94 1.28
1959 2397 2.027745 ACTGCAGTCAAGTAGGATGTGG 60.028 50.000 15.25 0.00 0.00 4.17
1973 2411 1.602377 GCGGTTTAGTTTGACTGCAGT 59.398 47.619 21.88 21.88 45.28 4.40
1981 2419 7.591795 TGTTATGTTTGTATGCGGTTTAGTTTG 59.408 33.333 0.00 0.00 0.00 2.93
2005 2443 6.144078 TGTCTTCTGCGTATGTATGTATGT 57.856 37.500 0.00 0.00 0.00 2.29
2006 2444 6.918022 TCTTGTCTTCTGCGTATGTATGTATG 59.082 38.462 0.00 0.00 0.00 2.39
2007 2445 7.039313 TCTTGTCTTCTGCGTATGTATGTAT 57.961 36.000 0.00 0.00 0.00 2.29
2008 2446 6.445357 TCTTGTCTTCTGCGTATGTATGTA 57.555 37.500 0.00 0.00 0.00 2.29
2009 2447 5.324784 TCTTGTCTTCTGCGTATGTATGT 57.675 39.130 0.00 0.00 0.00 2.29
2010 2448 5.176406 CCATCTTGTCTTCTGCGTATGTATG 59.824 44.000 0.00 0.00 0.00 2.39
2011 2449 5.292765 CCATCTTGTCTTCTGCGTATGTAT 58.707 41.667 0.00 0.00 0.00 2.29
2019 2457 3.254166 TCTTTTGCCATCTTGTCTTCTGC 59.746 43.478 0.00 0.00 0.00 4.26
2030 2468 5.176406 GCTCAGTTCTTTTTCTTTTGCCATC 59.824 40.000 0.00 0.00 0.00 3.51
2037 2475 7.654923 GGATTGATTGCTCAGTTCTTTTTCTTT 59.345 33.333 0.00 0.00 31.68 2.52
2038 2476 7.150640 GGATTGATTGCTCAGTTCTTTTTCTT 58.849 34.615 0.00 0.00 31.68 2.52
2041 2479 5.279657 GGGGATTGATTGCTCAGTTCTTTTT 60.280 40.000 0.00 0.00 31.68 1.94
2042 2480 4.221482 GGGGATTGATTGCTCAGTTCTTTT 59.779 41.667 0.00 0.00 31.68 2.27
2043 2481 3.766051 GGGGATTGATTGCTCAGTTCTTT 59.234 43.478 0.00 0.00 31.68 2.52
2044 2482 3.245371 TGGGGATTGATTGCTCAGTTCTT 60.245 43.478 0.00 0.00 31.68 2.52
2045 2483 2.309755 TGGGGATTGATTGCTCAGTTCT 59.690 45.455 0.00 0.00 31.68 3.01
2046 2484 2.726821 TGGGGATTGATTGCTCAGTTC 58.273 47.619 0.00 0.00 31.68 3.01
2047 2485 2.905415 TGGGGATTGATTGCTCAGTT 57.095 45.000 0.00 0.00 31.68 3.16
2048 2486 2.905415 TTGGGGATTGATTGCTCAGT 57.095 45.000 0.00 0.00 31.68 3.41
2049 2487 3.563223 AGATTGGGGATTGATTGCTCAG 58.437 45.455 0.00 0.00 31.68 3.35
2050 2488 3.203710 AGAGATTGGGGATTGATTGCTCA 59.796 43.478 0.00 0.00 0.00 4.26
2051 2489 3.819902 GAGAGATTGGGGATTGATTGCTC 59.180 47.826 0.00 0.00 0.00 4.26
2052 2490 3.436180 GGAGAGATTGGGGATTGATTGCT 60.436 47.826 0.00 0.00 0.00 3.91
2053 2491 2.889678 GGAGAGATTGGGGATTGATTGC 59.110 50.000 0.00 0.00 0.00 3.56
2054 2492 3.494332 GGGAGAGATTGGGGATTGATTG 58.506 50.000 0.00 0.00 0.00 2.67
2055 2493 2.448577 GGGGAGAGATTGGGGATTGATT 59.551 50.000 0.00 0.00 0.00 2.57
2133 2575 1.614317 GGCTGCTTCTTTTCTAGGCCA 60.614 52.381 5.01 0.00 38.35 5.36
2139 2581 4.852388 GGGGGCTGCTTCTTTTCT 57.148 55.556 0.00 0.00 0.00 2.52
2194 2636 4.356405 TTGGGCTGGATGAGTATGTATG 57.644 45.455 0.00 0.00 0.00 2.39
2195 2637 5.133221 GTTTTGGGCTGGATGAGTATGTAT 58.867 41.667 0.00 0.00 0.00 2.29
2196 2638 4.018870 TGTTTTGGGCTGGATGAGTATGTA 60.019 41.667 0.00 0.00 0.00 2.29
2197 2639 3.245229 TGTTTTGGGCTGGATGAGTATGT 60.245 43.478 0.00 0.00 0.00 2.29
2304 2749 3.056821 TCCAAGTTCTCGTGAGTGTATGG 60.057 47.826 0.00 3.19 0.00 2.74


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

AutoCloner maintained by Alex Coulton.