Multiple sequence alignment - TraesCS5A01G509900

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 TraesCS5A01G509900 chr5A 100.000 2501 0 0 1 2501 673714019 673716519 0.000000e+00 4619.0
1 TraesCS5A01G509900 chr4B 85.625 1753 153 45 1 1697 633635766 633637475 0.000000e+00 1749.0
2 TraesCS5A01G509900 chr4B 90.000 40 4 0 1207 1246 28199153 28199192 4.000000e-03 52.8
3 TraesCS5A01G509900 chr4D 82.614 1622 141 63 43 1598 494124775 494126321 0.000000e+00 1303.0
4 TraesCS5A01G509900 chr4D 90.182 713 66 4 1790 2501 494126637 494127346 0.000000e+00 926.0
5 TraesCS5A01G509900 chr4D 93.151 73 5 0 1713 1785 494126598 494126670 9.460000e-20 108.0
6 TraesCS5A01G509900 chr4D 98.000 50 0 1 1 49 494124705 494124754 4.430000e-13 86.1
7 TraesCS5A01G509900 chr6A 100.000 29 0 0 446 474 597835968 597835996 1.000000e-03 54.7


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 TraesCS5A01G509900 chr5A 673714019 673716519 2500 False 4619.000 4619 100.00000 1 2501 1 chr5A.!!$F1 2500
1 TraesCS5A01G509900 chr4B 633635766 633637475 1709 False 1749.000 1749 85.62500 1 1697 1 chr4B.!!$F2 1696
2 TraesCS5A01G509900 chr4D 494124705 494127346 2641 False 605.775 1303 90.98675 1 2501 4 chr4D.!!$F1 2500

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
474 531 0.109723 CTAGGAGGAGGAGGAGGACG 59.89 65.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2410 2749 0.106015 ATTGGGGCCCACTCATAAGC 60.106 55.0 28.84 2.47 30.78 3.09 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
71 100 2.373938 GCAGTTACTAGTGCCTGCG 58.626 57.895 24.07 5.23 43.54 5.18
72 101 1.084370 GCAGTTACTAGTGCCTGCGG 61.084 60.000 24.07 6.39 43.54 5.69
73 102 0.530744 CAGTTACTAGTGCCTGCGGA 59.469 55.000 5.39 0.00 0.00 5.54
74 103 0.818296 AGTTACTAGTGCCTGCGGAG 59.182 55.000 5.39 0.00 0.00 4.63
75 104 0.815734 GTTACTAGTGCCTGCGGAGA 59.184 55.000 5.10 0.00 0.00 3.71
76 105 1.103803 TTACTAGTGCCTGCGGAGAG 58.896 55.000 5.10 0.00 0.00 3.20
111 141 1.603739 GGAAGGCTGGGCGAAAAGT 60.604 57.895 0.00 0.00 0.00 2.66
113 143 2.477972 GAAGGCTGGGCGAAAAGTGC 62.478 60.000 0.00 0.00 0.00 4.40
115 145 2.727544 GCTGGGCGAAAAGTGCAA 59.272 55.556 0.00 0.00 0.00 4.08
120 150 0.951558 GGGCGAAAAGTGCAAGAAGA 59.048 50.000 0.00 0.00 0.00 2.87
189 228 1.153628 CGAAACGGCCGGAGAAGAT 60.154 57.895 31.76 2.42 0.00 2.40
271 314 1.328986 GAAGATTTACGCCTGCTGCTC 59.671 52.381 0.00 0.00 38.05 4.26
310 356 1.446907 CAGCAGACCATGTGAACTCC 58.553 55.000 0.00 0.00 0.00 3.85
349 401 1.852633 ACTGGTGATGACGATGGAGA 58.147 50.000 0.00 0.00 0.00 3.71
352 404 4.155709 ACTGGTGATGACGATGGAGATAT 58.844 43.478 0.00 0.00 0.00 1.63
412 469 1.269998 CCGAGGTTAGATTAGGAGCGG 59.730 57.143 0.00 0.00 0.00 5.52
420 477 2.029307 GATTAGGAGCGGGCGGTTCT 62.029 60.000 8.67 0.00 35.39 3.01
441 498 1.604147 GGCACGAAATTCCTTGGGGG 61.604 60.000 0.00 0.00 0.00 5.40
447 504 0.840288 AAATTCCTTGGGGGTTGGGC 60.840 55.000 0.00 0.00 36.25 5.36
462 519 0.178921 TGGGCTGGCTATCTAGGAGG 60.179 60.000 0.00 0.00 0.00 4.30
474 531 0.109723 CTAGGAGGAGGAGGAGGACG 59.890 65.000 0.00 0.00 0.00 4.79
476 533 2.835895 GAGGAGGAGGAGGACGGC 60.836 72.222 0.00 0.00 0.00 5.68
479 539 2.726351 GGAGGAGGAGGACGGCTTG 61.726 68.421 0.00 0.00 0.00 4.01
504 564 1.500474 TCCATGGAGATGTGGAGGTC 58.500 55.000 11.44 0.00 39.51 3.85
525 585 2.283821 TTGTGCTGGGAATGGGGC 60.284 61.111 0.00 0.00 0.00 5.80
578 652 1.069090 TTGTGCGCTCCTCGTTCTT 59.931 52.632 9.73 0.00 41.07 2.52
584 658 0.734253 CGCTCCTCGTTCTTCACCAG 60.734 60.000 0.00 0.00 0.00 4.00
585 659 1.016653 GCTCCTCGTTCTTCACCAGC 61.017 60.000 0.00 0.00 0.00 4.85
586 660 0.390472 CTCCTCGTTCTTCACCAGCC 60.390 60.000 0.00 0.00 0.00 4.85
587 661 1.376037 CCTCGTTCTTCACCAGCCC 60.376 63.158 0.00 0.00 0.00 5.19
588 662 1.371183 CTCGTTCTTCACCAGCCCA 59.629 57.895 0.00 0.00 0.00 5.36
589 663 0.951040 CTCGTTCTTCACCAGCCCAC 60.951 60.000 0.00 0.00 0.00 4.61
590 664 1.966451 CGTTCTTCACCAGCCCACC 60.966 63.158 0.00 0.00 0.00 4.61
591 665 1.150536 GTTCTTCACCAGCCCACCA 59.849 57.895 0.00 0.00 0.00 4.17
592 666 0.251341 GTTCTTCACCAGCCCACCAT 60.251 55.000 0.00 0.00 0.00 3.55
638 712 4.864334 GGCATGGGCGGAGTGGAG 62.864 72.222 0.00 0.00 42.47 3.86
639 713 4.864334 GCATGGGCGGAGTGGAGG 62.864 72.222 0.00 0.00 0.00 4.30
640 714 4.181010 CATGGGCGGAGTGGAGGG 62.181 72.222 0.00 0.00 0.00 4.30
641 715 4.414956 ATGGGCGGAGTGGAGGGA 62.415 66.667 0.00 0.00 0.00 4.20
646 720 4.075793 CGGAGTGGAGGGAGGGGA 62.076 72.222 0.00 0.00 0.00 4.81
647 721 2.041405 GGAGTGGAGGGAGGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
648 722 2.041405 GAGTGGAGGGAGGGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
672 746 2.750350 GACAGGACCACCACAGGG 59.250 66.667 0.00 0.00 38.94 4.45
746 861 1.303317 GGGCCCACGTCTGATGTTT 60.303 57.895 19.95 0.00 0.00 2.83
748 863 0.605319 GGCCCACGTCTGATGTTTGA 60.605 55.000 0.00 0.00 0.00 2.69
749 864 1.453155 GCCCACGTCTGATGTTTGAT 58.547 50.000 0.00 0.00 0.00 2.57
751 866 1.739466 CCCACGTCTGATGTTTGATGG 59.261 52.381 0.00 0.00 0.00 3.51
758 873 6.642131 CACGTCTGATGTTTGATGGAATTTTT 59.358 34.615 0.00 0.00 0.00 1.94
801 916 3.460103 TCACCTTCTCGTGGTTTTACAC 58.540 45.455 0.00 0.00 35.28 2.90
884 1001 2.816689 CGAGAAACGGGCATACATACA 58.183 47.619 0.00 0.00 38.46 2.29
904 1029 2.279921 CACATCTCACATGTTACTCGCG 59.720 50.000 0.00 0.00 0.00 5.87
906 1031 0.457853 TCTCACATGTTACTCGCGGC 60.458 55.000 6.13 0.00 0.00 6.53
936 1061 6.210584 GGATCCCTCTTTCTTATCTAGTCCAG 59.789 46.154 0.00 0.00 0.00 3.86
988 1113 2.764547 GGAGGACGGAGAAGGGGG 60.765 72.222 0.00 0.00 0.00 5.40
1020 1145 2.842462 ATCATCACGGCGGCCCTA 60.842 61.111 14.55 0.00 0.00 3.53
1076 1201 1.745115 CGAAGATGGCCCGCTTCAA 60.745 57.895 25.43 0.00 40.31 2.69
1095 1220 0.250513 AAGAGATCTGCGGGTGGTTC 59.749 55.000 0.00 0.00 0.00 3.62
1138 1269 2.967076 CGGCGATTGGGATCACGG 60.967 66.667 0.00 0.00 32.13 4.94
1151 1282 4.351938 CACGGTCTTGGCGACGGA 62.352 66.667 0.00 0.00 43.45 4.69
1186 1317 0.536915 GATGCTTGGAGATGGGGCTC 60.537 60.000 0.00 0.00 0.00 4.70
1195 1326 0.870313 AGATGGGGCTCCTCCTATCA 59.130 55.000 3.07 0.00 44.29 2.15
1203 1334 2.831526 GGCTCCTCCTATCAAGATCCTC 59.168 54.545 0.00 0.00 0.00 3.71
1284 1415 4.083749 GCATATAGATCTCGTGTGTCGTCT 60.084 45.833 0.00 0.00 40.80 4.18
1315 1446 2.282180 CGGAGTTTGTGGTGGGGG 60.282 66.667 0.00 0.00 0.00 5.40
1407 1538 2.456840 CCAAGGAGGGGGAGAGGT 59.543 66.667 0.00 0.00 0.00 3.85
1431 1562 2.589492 CCCGATTCAGATGTCGCGC 61.589 63.158 0.00 0.00 36.57 6.86
1517 1648 2.675772 GGAGTCACTCCGGACGGT 60.676 66.667 8.49 0.00 41.08 4.83
1522 1653 2.677524 CACTCCGGACGGTACCCA 60.678 66.667 10.90 0.00 36.47 4.51
1526 1657 0.680921 CTCCGGACGGTACCCACTTA 60.681 60.000 10.90 0.00 36.47 2.24
1539 1670 0.532862 CCACTTATGGGTGCTAGCCG 60.533 60.000 13.29 0.00 43.04 5.52
1543 1674 0.689745 TTATGGGTGCTAGCCGGAGT 60.690 55.000 13.29 0.00 38.98 3.85
1544 1675 0.186630 TATGGGTGCTAGCCGGAGTA 59.813 55.000 13.29 0.00 38.98 2.59
1549 1680 1.000052 GGTGCTAGCCGGAGTAGATTC 60.000 57.143 13.29 0.00 0.00 2.52
1568 1699 1.495878 CCGATGAGGAATCTTCTGCG 58.504 55.000 0.00 0.00 45.00 5.18
1574 1705 0.674895 AGGAATCTTCTGCGGTGTGC 60.675 55.000 0.00 0.00 46.70 4.57
1598 1729 6.007703 CGGTATGTATAATCAAACCCCCAAT 58.992 40.000 0.00 0.00 0.00 3.16
1599 1730 6.492087 CGGTATGTATAATCAAACCCCCAATT 59.508 38.462 0.00 0.00 0.00 2.32
1600 1731 7.308951 CGGTATGTATAATCAAACCCCCAATTC 60.309 40.741 0.00 0.00 0.00 2.17
1602 1733 7.986553 ATGTATAATCAAACCCCCAATTCAA 57.013 32.000 0.00 0.00 0.00 2.69
1603 1734 7.416964 TGTATAATCAAACCCCCAATTCAAG 57.583 36.000 0.00 0.00 0.00 3.02
1605 1736 6.950860 ATAATCAAACCCCCAATTCAAGTT 57.049 33.333 0.00 0.00 0.00 2.66
1608 1739 4.230455 TCAAACCCCCAATTCAAGTTCAT 58.770 39.130 0.00 0.00 0.00 2.57
1609 1740 4.040217 TCAAACCCCCAATTCAAGTTCATG 59.960 41.667 0.00 0.00 0.00 3.07
1616 1747 5.105228 CCCCAATTCAAGTTCATGTTGCTAT 60.105 40.000 0.00 0.00 0.00 2.97
1622 1753 7.936496 TTCAAGTTCATGTTGCTATGGATAA 57.064 32.000 0.00 0.00 0.00 1.75
1629 1760 9.831737 GTTCATGTTGCTATGGATAAATGTATC 57.168 33.333 0.00 0.00 36.18 2.24
1630 1761 9.571816 TTCATGTTGCTATGGATAAATGTATCA 57.428 29.630 5.26 0.00 38.33 2.15
1656 1994 3.838244 CCATCGAGGGATTTAGGTCAA 57.162 47.619 11.55 0.00 0.00 3.18
1662 2000 3.481453 GAGGGATTTAGGTCAAGATGGC 58.519 50.000 0.00 0.00 0.00 4.40
1676 2014 5.238214 GTCAAGATGGCTCATTTGATACTCC 59.762 44.000 11.71 0.00 32.76 3.85
1681 2019 4.264253 TGGCTCATTTGATACTCCTGTTG 58.736 43.478 0.00 0.00 0.00 3.33
1684 2022 5.163713 GGCTCATTTGATACTCCTGTTGTTC 60.164 44.000 0.00 0.00 0.00 3.18
1687 2025 5.408299 TCATTTGATACTCCTGTTGTTCGTG 59.592 40.000 0.00 0.00 0.00 4.35
1707 2045 4.551388 GTGATAGACGAATGTGGAGATCC 58.449 47.826 0.00 0.00 0.00 3.36
1708 2046 4.038042 GTGATAGACGAATGTGGAGATCCA 59.962 45.833 0.00 0.00 45.30 3.41
1756 2094 2.591915 CCCGAGCTAGGGTTTGAGA 58.408 57.895 23.11 0.00 46.38 3.27
1757 2095 0.461961 CCCGAGCTAGGGTTTGAGAG 59.538 60.000 23.11 0.00 46.38 3.20
1758 2096 1.475403 CCGAGCTAGGGTTTGAGAGA 58.525 55.000 4.68 0.00 0.00 3.10
1759 2097 1.407258 CCGAGCTAGGGTTTGAGAGAG 59.593 57.143 4.68 0.00 0.00 3.20
1760 2098 2.370349 CGAGCTAGGGTTTGAGAGAGA 58.630 52.381 0.00 0.00 0.00 3.10
1761 2099 2.357637 CGAGCTAGGGTTTGAGAGAGAG 59.642 54.545 0.00 0.00 0.00 3.20
1762 2100 2.693074 GAGCTAGGGTTTGAGAGAGAGG 59.307 54.545 0.00 0.00 0.00 3.69
1763 2101 1.760029 GCTAGGGTTTGAGAGAGAGGG 59.240 57.143 0.00 0.00 0.00 4.30
1764 2102 2.393646 CTAGGGTTTGAGAGAGAGGGG 58.606 57.143 0.00 0.00 0.00 4.79
1765 2103 0.252927 AGGGTTTGAGAGAGAGGGGG 60.253 60.000 0.00 0.00 0.00 5.40
1766 2104 0.252742 GGGTTTGAGAGAGAGGGGGA 60.253 60.000 0.00 0.00 0.00 4.81
1767 2105 1.199615 GGTTTGAGAGAGAGGGGGAG 58.800 60.000 0.00 0.00 0.00 4.30
1768 2106 1.273324 GGTTTGAGAGAGAGGGGGAGA 60.273 57.143 0.00 0.00 0.00 3.71
1769 2107 2.107366 GTTTGAGAGAGAGGGGGAGAG 58.893 57.143 0.00 0.00 0.00 3.20
1770 2108 1.687492 TTGAGAGAGAGGGGGAGAGA 58.313 55.000 0.00 0.00 0.00 3.10
1771 2109 1.221635 TGAGAGAGAGGGGGAGAGAG 58.778 60.000 0.00 0.00 0.00 3.20
1772 2110 1.274708 TGAGAGAGAGGGGGAGAGAGA 60.275 57.143 0.00 0.00 0.00 3.10
1773 2111 1.421646 GAGAGAGAGGGGGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
1774 2112 0.478507 GAGAGAGGGGGAGAGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
1775 2113 0.998945 AGAGAGGGGGAGAGAGAGGG 60.999 65.000 0.00 0.00 0.00 4.30
1776 2114 0.996762 GAGAGGGGGAGAGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
1777 2115 0.998945 AGAGGGGGAGAGAGAGGGAG 60.999 65.000 0.00 0.00 0.00 4.30
1778 2116 0.996762 GAGGGGGAGAGAGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
1779 2117 0.998945 AGGGGGAGAGAGAGGGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
1780 2118 0.996762 GGGGGAGAGAGAGGGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
1781 2119 0.478507 GGGGAGAGAGAGGGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
1782 2120 1.518367 GGGAGAGAGAGGGAGAGAGA 58.482 60.000 0.00 0.00 0.00 3.10
1783 2121 1.421646 GGGAGAGAGAGGGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
1784 2122 2.408565 GGAGAGAGAGGGAGAGAGAGA 58.591 57.143 0.00 0.00 0.00 3.10
1800 2138 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1806 2144 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
1819 2157 2.774234 AGAGAGAGTGGGAGAGAGAGAG 59.226 54.545 0.00 0.00 0.00 3.20
1820 2158 2.771943 GAGAGAGTGGGAGAGAGAGAGA 59.228 54.545 0.00 0.00 0.00 3.10
1821 2159 2.774234 AGAGAGTGGGAGAGAGAGAGAG 59.226 54.545 0.00 0.00 0.00 3.20
1822 2160 1.846439 AGAGTGGGAGAGAGAGAGAGG 59.154 57.143 0.00 0.00 0.00 3.69
1823 2161 0.258774 AGTGGGAGAGAGAGAGAGGC 59.741 60.000 0.00 0.00 0.00 4.70
1824 2162 1.101049 GTGGGAGAGAGAGAGAGGCG 61.101 65.000 0.00 0.00 0.00 5.52
1825 2163 1.528309 GGGAGAGAGAGAGAGGCGG 60.528 68.421 0.00 0.00 0.00 6.13
1826 2164 1.226262 GGAGAGAGAGAGAGGCGGT 59.774 63.158 0.00 0.00 0.00 5.68
1827 2165 0.470766 GGAGAGAGAGAGAGGCGGTA 59.529 60.000 0.00 0.00 0.00 4.02
1828 2166 1.542547 GGAGAGAGAGAGAGGCGGTAG 60.543 61.905 0.00 0.00 0.00 3.18
1849 2187 0.324285 GGAGGATATGGCTGGAGCTG 59.676 60.000 0.00 0.00 41.70 4.24
1864 2202 4.101077 CTGAGGGGAGAGGGGGCT 62.101 72.222 0.00 0.00 0.00 5.19
1885 2223 1.887198 GACAGGAACGAGGAAGAGACA 59.113 52.381 0.00 0.00 0.00 3.41
1888 2226 3.056465 ACAGGAACGAGGAAGAGACAATC 60.056 47.826 0.00 0.00 0.00 2.67
1904 2242 8.312669 AGAGACAATCTTAGCTACCAATAACT 57.687 34.615 0.00 0.00 32.99 2.24
1910 2248 6.235231 TCTTAGCTACCAATAACTGAAGGG 57.765 41.667 0.00 0.00 0.00 3.95
1913 2251 4.368067 AGCTACCAATAACTGAAGGGGTA 58.632 43.478 0.00 0.00 0.00 3.69
1935 2273 2.047179 GGTGGAGGTCGTGGAAGC 60.047 66.667 0.00 0.00 0.00 3.86
1944 2282 2.368875 AGGTCGTGGAAGCTATAATGGG 59.631 50.000 0.00 0.00 0.00 4.00
1979 2317 6.725834 AGGAACAACTTGATGGAAAATGGTAT 59.274 34.615 0.00 0.00 0.00 2.73
1980 2318 7.235399 AGGAACAACTTGATGGAAAATGGTATT 59.765 33.333 0.00 0.00 0.00 1.89
1987 2325 8.472413 ACTTGATGGAAAATGGTATTGATCTTG 58.528 33.333 0.00 0.00 0.00 3.02
1988 2326 8.592529 TTGATGGAAAATGGTATTGATCTTGA 57.407 30.769 0.00 0.00 0.00 3.02
1993 2331 6.239402 GGAAAATGGTATTGATCTTGATGGGG 60.239 42.308 0.00 0.00 0.00 4.96
2024 2362 3.118408 GGGAAGGTTTTGAATTATGGGGC 60.118 47.826 0.00 0.00 0.00 5.80
2038 2377 0.038166 TGGGGCAAGTGGAGTGATTC 59.962 55.000 0.00 0.00 0.00 2.52
2090 2429 1.134098 CACACAAGGTCCACTTCTGGT 60.134 52.381 0.00 0.00 37.29 4.00
2148 2487 5.365895 ACAGGTTAGATCCATAACACTACCC 59.634 44.000 7.06 0.00 37.38 3.69
2178 2517 4.526262 TGTCACCAATTGGGAATTTACCTG 59.474 41.667 27.89 13.62 41.15 4.00
2192 2531 5.653255 ATTTACCTGTGCAGATCCCTAAT 57.347 39.130 0.02 0.00 0.00 1.73
2213 2552 2.064434 TGGGAATGCAACAACTGTGA 57.936 45.000 0.00 0.00 0.00 3.58
2237 2576 4.666412 TCCCCAAATTACTCATGTTGGA 57.334 40.909 11.12 0.00 42.66 3.53
2251 2590 2.907892 TGTTGGAGAGAAGGATCCAGT 58.092 47.619 15.82 0.04 46.01 4.00
2275 2614 2.039084 AGGGATCTCTTCACAACACCAC 59.961 50.000 0.00 0.00 0.00 4.16
2294 2633 0.250467 CCATCTTATGGGAGTGGCGG 60.250 60.000 0.00 0.00 46.86 6.13
2299 2638 0.396435 TTATGGGAGTGGCGGCTATG 59.604 55.000 11.43 0.00 0.00 2.23
2325 2664 2.316108 CTTTGTGCCTTACTTTGGGGT 58.684 47.619 0.00 0.00 0.00 4.95
2341 2680 3.696045 TGGGGTTGGAGTTAACATGATG 58.304 45.455 8.61 0.00 32.22 3.07
2348 2687 7.339466 GGGTTGGAGTTAACATGATGACTAATT 59.661 37.037 8.61 0.00 32.22 1.40
2364 2703 6.936279 TGACTAATTAAGGTGTGAGAGAAGG 58.064 40.000 0.00 0.00 0.00 3.46
2367 2706 4.559862 ATTAAGGTGTGAGAGAAGGGTG 57.440 45.455 0.00 0.00 0.00 4.61
2369 2708 1.051812 AGGTGTGAGAGAAGGGTGTG 58.948 55.000 0.00 0.00 0.00 3.82
2382 2721 0.623723 GGGTGTGGTGATGGTGGTAT 59.376 55.000 0.00 0.00 0.00 2.73
2432 2771 1.607225 TATGAGTGGGCCCCAATTCT 58.393 50.000 22.27 9.80 34.18 2.40
2434 2773 0.039618 TGAGTGGGCCCCAATTCTTC 59.960 55.000 22.27 6.80 34.18 2.87
2440 2779 1.467920 GGCCCCAATTCTTCAGTCAG 58.532 55.000 0.00 0.00 0.00 3.51
2447 2786 5.163163 CCCCAATTCTTCAGTCAGATGGATA 60.163 44.000 0.00 0.00 27.82 2.59
2449 2788 5.996513 CCAATTCTTCAGTCAGATGGATAGG 59.003 44.000 0.00 0.00 27.82 2.57
2452 2791 4.871822 TCTTCAGTCAGATGGATAGGTCA 58.128 43.478 0.00 0.00 0.00 4.02
2474 2813 7.557719 GGTCAAGGAAGATGAGAAATAATGGAA 59.442 37.037 0.00 0.00 0.00 3.53
2494 2833 1.461268 TGAAGGAGGTGCTGGTGGA 60.461 57.895 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 100 1.528309 CTCCTCTCTCCGGCTCTCC 60.528 68.421 0.00 0.00 0.00 3.71
72 101 1.528309 CCTCCTCTCTCCGGCTCTC 60.528 68.421 0.00 0.00 0.00 3.20
73 102 2.600731 CCTCCTCTCTCCGGCTCT 59.399 66.667 0.00 0.00 0.00 4.09
74 103 2.520741 CCCTCCTCTCTCCGGCTC 60.521 72.222 0.00 0.00 0.00 4.70
75 104 4.150454 CCCCTCCTCTCTCCGGCT 62.150 72.222 0.00 0.00 0.00 5.52
94 124 1.581447 CACTTTTCGCCCAGCCTTC 59.419 57.895 0.00 0.00 0.00 3.46
111 141 3.671433 GCTCGCAATCAAATCTTCTTGCA 60.671 43.478 6.88 0.00 43.14 4.08
113 143 4.341099 GAGCTCGCAATCAAATCTTCTTG 58.659 43.478 0.00 0.00 0.00 3.02
115 145 2.606725 CGAGCTCGCAATCAAATCTTCT 59.393 45.455 25.07 0.00 0.00 2.85
120 150 2.200067 CTCTCGAGCTCGCAATCAAAT 58.800 47.619 30.97 0.00 39.60 2.32
271 314 0.605589 GTCTGACTCTGACTGTGGGG 59.394 60.000 8.45 0.00 31.22 4.96
275 321 0.965439 GCTGGTCTGACTCTGACTGT 59.035 55.000 13.89 0.00 33.75 3.55
310 356 1.642037 TTAGTCGTCGTCCTCGCAGG 61.642 60.000 0.00 0.00 36.46 4.85
368 420 2.956964 CGATCCGGTCTGCTTCGC 60.957 66.667 0.00 0.00 0.00 4.70
420 477 0.897863 CCCAAGGAATTTCGTGCCCA 60.898 55.000 0.00 0.00 0.00 5.36
441 498 1.346068 CTCCTAGATAGCCAGCCCAAC 59.654 57.143 0.00 0.00 0.00 3.77
447 504 2.291540 CCTCCTCCTCCTAGATAGCCAG 60.292 59.091 0.00 0.00 0.00 4.85
462 519 0.683504 TACAAGCCGTCCTCCTCCTC 60.684 60.000 0.00 0.00 0.00 3.71
474 531 4.646492 ACATCTCCATGGAATTTACAAGCC 59.354 41.667 17.00 0.00 33.82 4.35
476 533 5.887598 TCCACATCTCCATGGAATTTACAAG 59.112 40.000 17.00 1.11 42.14 3.16
479 539 4.823989 CCTCCACATCTCCATGGAATTTAC 59.176 45.833 17.00 0.00 44.42 2.01
504 564 1.601419 CCCATTCCCAGCACAAGCAG 61.601 60.000 0.00 0.00 45.49 4.24
525 585 2.222027 GGAGTGCGGAATAAATCCCAG 58.778 52.381 0.00 0.00 46.39 4.45
578 652 2.927856 ACGATGGTGGGCTGGTGA 60.928 61.111 0.00 0.00 0.00 4.02
589 663 3.118454 GTGCCACGACCACGATGG 61.118 66.667 0.00 0.00 45.02 3.51
590 664 2.048222 AGTGCCACGACCACGATG 60.048 61.111 0.00 0.00 42.66 3.84
591 665 2.048222 CAGTGCCACGACCACGAT 60.048 61.111 0.00 0.00 42.66 3.73
592 666 4.293648 CCAGTGCCACGACCACGA 62.294 66.667 0.00 0.00 42.66 4.35
630 704 2.041405 CTCCCCTCCCTCCACTCC 60.041 72.222 0.00 0.00 0.00 3.85
631 705 2.041405 CCTCCCCTCCCTCCACTC 60.041 72.222 0.00 0.00 0.00 3.51
632 706 3.700350 CCCTCCCCTCCCTCCACT 61.700 72.222 0.00 0.00 0.00 4.00
635 709 4.179599 CTCCCCTCCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
636 710 3.369388 ACTCCCCTCCCCTCCCTC 61.369 72.222 0.00 0.00 0.00 4.30
637 711 3.700350 CACTCCCCTCCCCTCCCT 61.700 72.222 0.00 0.00 0.00 4.20
638 712 4.825679 CCACTCCCCTCCCCTCCC 62.826 77.778 0.00 0.00 0.00 4.30
639 713 3.695825 TCCACTCCCCTCCCCTCC 61.696 72.222 0.00 0.00 0.00 4.30
640 714 2.365768 GTCCACTCCCCTCCCCTC 60.366 72.222 0.00 0.00 0.00 4.30
641 715 3.208592 TGTCCACTCCCCTCCCCT 61.209 66.667 0.00 0.00 0.00 4.79
642 716 2.689034 CTGTCCACTCCCCTCCCC 60.689 72.222 0.00 0.00 0.00 4.81
643 717 2.689034 CCTGTCCACTCCCCTCCC 60.689 72.222 0.00 0.00 0.00 4.30
644 718 1.990614 GTCCTGTCCACTCCCCTCC 60.991 68.421 0.00 0.00 0.00 4.30
645 719 1.990614 GGTCCTGTCCACTCCCCTC 60.991 68.421 0.00 0.00 0.00 4.30
646 720 2.122954 GGTCCTGTCCACTCCCCT 59.877 66.667 0.00 0.00 0.00 4.79
647 721 2.203938 TGGTCCTGTCCACTCCCC 60.204 66.667 0.00 0.00 31.96 4.81
731 845 1.739466 CCATCAAACATCAGACGTGGG 59.261 52.381 0.00 0.00 0.00 4.61
758 873 7.009723 GGTGAAAACGCTATTTTGAGTGAAAAA 59.990 33.333 0.72 0.00 37.10 1.94
759 874 6.474102 GGTGAAAACGCTATTTTGAGTGAAAA 59.526 34.615 0.72 0.00 37.93 2.29
760 875 5.974751 GGTGAAAACGCTATTTTGAGTGAAA 59.025 36.000 0.72 0.00 0.00 2.69
763 878 5.108385 AGGTGAAAACGCTATTTTGAGTG 57.892 39.130 0.72 0.00 0.00 3.51
781 896 3.872560 GTGTAAAACCACGAGAAGGTG 57.127 47.619 0.00 0.00 39.86 4.00
844 961 8.976986 TTCTCGGAAGAATTACAAGTAGTAAC 57.023 34.615 0.00 0.00 39.73 2.50
850 967 5.840940 CGTTTCTCGGAAGAATTACAAGT 57.159 39.130 0.00 0.00 41.12 3.16
865 982 3.527533 TGTGTATGTATGCCCGTTTCTC 58.472 45.455 0.00 0.00 0.00 2.87
875 992 8.877808 AGTAACATGTGAGATGTGTATGTATG 57.122 34.615 0.00 0.00 32.18 2.39
879 996 5.051441 GCGAGTAACATGTGAGATGTGTATG 60.051 44.000 0.00 0.00 31.80 2.39
884 1001 2.530177 CGCGAGTAACATGTGAGATGT 58.470 47.619 0.00 0.00 0.00 3.06
911 1036 6.078664 TGGACTAGATAAGAAAGAGGGATCC 58.921 44.000 1.92 1.92 0.00 3.36
912 1037 6.210584 CCTGGACTAGATAAGAAAGAGGGATC 59.789 46.154 0.00 0.00 0.00 3.36
913 1038 6.081356 CCTGGACTAGATAAGAAAGAGGGAT 58.919 44.000 0.00 0.00 0.00 3.85
915 1040 4.039852 GCCTGGACTAGATAAGAAAGAGGG 59.960 50.000 0.00 0.00 0.00 4.30
918 1043 4.338682 GTCGCCTGGACTAGATAAGAAAGA 59.661 45.833 0.00 0.00 42.62 2.52
919 1044 4.500035 GGTCGCCTGGACTAGATAAGAAAG 60.500 50.000 0.00 0.00 45.35 2.62
920 1045 3.383825 GGTCGCCTGGACTAGATAAGAAA 59.616 47.826 0.00 0.00 45.35 2.52
921 1046 2.957006 GGTCGCCTGGACTAGATAAGAA 59.043 50.000 0.00 0.00 45.35 2.52
926 1051 0.324368 TGTGGTCGCCTGGACTAGAT 60.324 55.000 0.00 0.00 45.35 1.98
954 1079 0.322636 TCCCTCGAGCTTCGTCTCTT 60.323 55.000 6.99 0.00 41.35 2.85
988 1113 2.048690 GATCATCTCCGCTCCGCC 60.049 66.667 0.00 0.00 0.00 6.13
989 1114 0.735632 GATGATCATCTCCGCTCCGC 60.736 60.000 25.47 0.00 35.04 5.54
990 1115 0.600057 TGATGATCATCTCCGCTCCG 59.400 55.000 30.65 0.00 38.60 4.63
991 1116 1.668337 CGTGATGATCATCTCCGCTCC 60.668 57.143 30.65 8.30 38.60 4.70
992 1117 1.668337 CCGTGATGATCATCTCCGCTC 60.668 57.143 30.65 9.88 38.60 5.03
1020 1145 0.339859 TGTGCCCTATCCACTCCTCT 59.660 55.000 0.00 0.00 34.38 3.69
1076 1201 0.250513 GAACCACCCGCAGATCTCTT 59.749 55.000 0.00 0.00 0.00 2.85
1095 1220 4.082523 AGCGTGTCCATGTCGGGG 62.083 66.667 0.00 0.00 34.36 5.73
1186 1317 3.577848 CAGTGGAGGATCTTGATAGGAGG 59.422 52.174 0.00 0.00 33.73 4.30
1195 1326 2.053244 CATAGCCCAGTGGAGGATCTT 58.947 52.381 11.95 0.00 33.73 2.40
1203 1334 0.399454 CCTCCATCATAGCCCAGTGG 59.601 60.000 0.63 0.63 0.00 4.00
1240 1371 2.506061 CCCATCTCCTCCTCTGCCG 61.506 68.421 0.00 0.00 0.00 5.69
1284 1415 2.612430 TCCGCTGGATTTGGGGGA 60.612 61.111 0.00 0.00 41.25 4.81
1315 1446 0.392998 ACAAGGATCACCATGACCGC 60.393 55.000 0.00 0.00 38.15 5.68
1355 1486 2.838467 CCTCCCATCCCTGGCATCC 61.838 68.421 0.00 0.00 41.64 3.51
1362 1493 2.150051 GGCGATTCCTCCCATCCCT 61.150 63.158 0.00 0.00 0.00 4.20
1407 1538 1.815003 CATCTGAATCGGGCGCACA 60.815 57.895 11.77 0.00 0.00 4.57
1417 1548 3.264897 GCGGCGCGACATCTGAAT 61.265 61.111 19.09 0.00 0.00 2.57
1473 1604 4.379243 CCAGACCCGCGAGCAAGT 62.379 66.667 8.23 0.00 0.00 3.16
1488 1619 3.075005 GACTCCTACTGCCCGCCA 61.075 66.667 0.00 0.00 0.00 5.69
1522 1653 0.689745 TCCGGCTAGCACCCATAAGT 60.690 55.000 18.24 0.00 0.00 2.24
1526 1657 1.075525 TACTCCGGCTAGCACCCAT 60.076 57.895 18.24 0.96 0.00 4.00
1549 1680 1.495878 CGCAGAAGATTCCTCATCGG 58.504 55.000 0.00 0.00 36.93 4.18
1568 1699 5.277634 GGTTTGATTATACATACCGCACACC 60.278 44.000 0.00 0.00 33.74 4.16
1574 1705 4.975631 TGGGGGTTTGATTATACATACCG 58.024 43.478 0.00 0.00 40.82 4.02
1598 1729 7.936496 TTATCCATAGCAACATGAACTTGAA 57.064 32.000 0.00 0.00 0.00 2.69
1599 1730 7.936496 TTTATCCATAGCAACATGAACTTGA 57.064 32.000 0.00 0.00 0.00 3.02
1600 1731 8.192774 ACATTTATCCATAGCAACATGAACTTG 58.807 33.333 0.00 0.00 0.00 3.16
1602 1733 7.886629 ACATTTATCCATAGCAACATGAACT 57.113 32.000 0.00 0.00 0.00 3.01
1603 1734 9.831737 GATACATTTATCCATAGCAACATGAAC 57.168 33.333 0.00 0.00 0.00 3.18
1605 1736 9.743581 ATGATACATTTATCCATAGCAACATGA 57.256 29.630 0.00 0.00 34.18 3.07
1616 1747 7.037945 TCGATGGGGTAATGATACATTTATCCA 60.038 37.037 2.40 8.03 34.18 3.41
1622 1753 5.165961 CCTCGATGGGGTAATGATACATT 57.834 43.478 0.00 0.00 33.45 2.71
1651 1989 5.128919 AGTATCAAATGAGCCATCTTGACC 58.871 41.667 11.22 7.93 30.41 4.02
1652 1990 5.238214 GGAGTATCAAATGAGCCATCTTGAC 59.762 44.000 11.22 0.00 36.25 3.18
1653 1991 5.131642 AGGAGTATCAAATGAGCCATCTTGA 59.868 40.000 11.31 11.31 36.25 3.02
1654 1992 5.238868 CAGGAGTATCAAATGAGCCATCTTG 59.761 44.000 0.00 0.00 36.25 3.02
1655 1993 5.104193 ACAGGAGTATCAAATGAGCCATCTT 60.104 40.000 0.00 0.00 36.25 2.40
1656 1994 4.411540 ACAGGAGTATCAAATGAGCCATCT 59.588 41.667 0.00 0.00 36.25 2.90
1662 2000 5.639506 ACGAACAACAGGAGTATCAAATGAG 59.360 40.000 0.00 0.00 36.25 2.90
1684 2022 4.849074 GGATCTCCACATTCGTCTATCACG 60.849 50.000 0.00 0.00 42.30 4.35
1687 2025 4.855715 TGGATCTCCACATTCGTCTATC 57.144 45.455 0.00 0.00 42.01 2.08
1700 2038 6.546484 TCTTCCCAATCAATTATGGATCTCC 58.454 40.000 5.83 0.00 39.12 3.71
1701 2039 6.658391 CCTCTTCCCAATCAATTATGGATCTC 59.342 42.308 5.83 0.00 39.12 2.75
1702 2040 6.333702 TCCTCTTCCCAATCAATTATGGATCT 59.666 38.462 5.83 0.00 39.12 2.75
1703 2041 6.546484 TCCTCTTCCCAATCAATTATGGATC 58.454 40.000 5.83 0.00 39.12 3.36
1704 2042 6.535161 TCCTCTTCCCAATCAATTATGGAT 57.465 37.500 5.83 0.00 39.12 3.41
1705 2043 5.992564 TCCTCTTCCCAATCAATTATGGA 57.007 39.130 5.83 0.00 39.12 3.41
1706 2044 5.302823 GGTTCCTCTTCCCAATCAATTATGG 59.697 44.000 0.00 0.00 36.42 2.74
1707 2045 6.131961 AGGTTCCTCTTCCCAATCAATTATG 58.868 40.000 0.00 0.00 0.00 1.90
1708 2046 6.347061 AGGTTCCTCTTCCCAATCAATTAT 57.653 37.500 0.00 0.00 0.00 1.28
1709 2047 5.629133 CGAGGTTCCTCTTCCCAATCAATTA 60.629 44.000 15.60 0.00 0.00 1.40
1710 2048 4.604156 GAGGTTCCTCTTCCCAATCAATT 58.396 43.478 11.20 0.00 0.00 2.32
1711 2049 3.370953 CGAGGTTCCTCTTCCCAATCAAT 60.371 47.826 15.60 0.00 0.00 2.57
1751 2089 1.568597 CTCTCTCCCCCTCTCTCTCAA 59.431 57.143 0.00 0.00 0.00 3.02
1752 2090 1.221635 CTCTCTCCCCCTCTCTCTCA 58.778 60.000 0.00 0.00 0.00 3.27
1753 2091 1.421646 CTCTCTCTCCCCCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
1754 2092 1.522900 CTCTCTCTCCCCCTCTCTCT 58.477 60.000 0.00 0.00 0.00 3.10
1755 2093 0.478507 CCTCTCTCTCCCCCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
1756 2094 0.998945 CCCTCTCTCTCCCCCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
1757 2095 0.996762 TCCCTCTCTCTCCCCCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
1758 2096 0.998945 CTCCCTCTCTCTCCCCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
1759 2097 0.996762 TCTCCCTCTCTCTCCCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
1760 2098 0.998945 CTCTCCCTCTCTCTCCCCCT 60.999 65.000 0.00 0.00 0.00 4.79
1761 2099 0.996762 TCTCTCCCTCTCTCTCCCCC 60.997 65.000 0.00 0.00 0.00 5.40
1762 2100 0.478507 CTCTCTCCCTCTCTCTCCCC 59.521 65.000 0.00 0.00 0.00 4.81
1763 2101 1.421646 CTCTCTCTCCCTCTCTCTCCC 59.578 61.905 0.00 0.00 0.00 4.30
1764 2102 2.370189 CTCTCTCTCTCCCTCTCTCTCC 59.630 59.091 0.00 0.00 0.00 3.71
1765 2103 3.309296 TCTCTCTCTCTCCCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
1766 2104 3.051803 TCTCTCTCTCTCTCCCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
1767 2105 3.309296 TCTCTCTCTCTCTCCCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
1768 2106 3.051803 TCTCTCTCTCTCTCTCCCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
1769 2107 3.309296 TCTCTCTCTCTCTCTCCCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
1770 2108 3.051803 TCTCTCTCTCTCTCTCTCCCTCT 60.052 52.174 0.00 0.00 0.00 3.69
1771 2109 3.309296 TCTCTCTCTCTCTCTCTCCCTC 58.691 54.545 0.00 0.00 0.00 4.30
1772 2110 3.051803 TCTCTCTCTCTCTCTCTCTCCCT 60.052 52.174 0.00 0.00 0.00 4.20
1773 2111 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
1774 2112 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
1775 2113 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1776 2114 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1777 2115 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1778 2116 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1779 2117 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1780 2118 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1781 2119 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1782 2120 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1783 2121 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
1784 2122 4.648762 CACTCTCTCTCTCTCTCTCTCTCT 59.351 50.000 0.00 0.00 0.00 3.10
1800 2138 2.774234 CTCTCTCTCTCTCCCACTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
1806 2144 1.225983 CGCCTCTCTCTCTCTCCCA 59.774 63.158 0.00 0.00 0.00 4.37
1819 2157 2.096248 CATATCCTCCTCTACCGCCTC 58.904 57.143 0.00 0.00 0.00 4.70
1820 2158 1.272760 CCATATCCTCCTCTACCGCCT 60.273 57.143 0.00 0.00 0.00 5.52
1821 2159 1.187087 CCATATCCTCCTCTACCGCC 58.813 60.000 0.00 0.00 0.00 6.13
1822 2160 0.533032 GCCATATCCTCCTCTACCGC 59.467 60.000 0.00 0.00 0.00 5.68
1823 2161 1.821753 CAGCCATATCCTCCTCTACCG 59.178 57.143 0.00 0.00 0.00 4.02
1824 2162 2.183679 CCAGCCATATCCTCCTCTACC 58.816 57.143 0.00 0.00 0.00 3.18
1825 2163 3.096092 CTCCAGCCATATCCTCCTCTAC 58.904 54.545 0.00 0.00 0.00 2.59
1826 2164 2.558575 GCTCCAGCCATATCCTCCTCTA 60.559 54.545 0.00 0.00 34.31 2.43
1827 2165 1.830883 GCTCCAGCCATATCCTCCTCT 60.831 57.143 0.00 0.00 34.31 3.69
1828 2166 0.612744 GCTCCAGCCATATCCTCCTC 59.387 60.000 0.00 0.00 34.31 3.71
1849 2187 4.095400 TCAGCCCCCTCTCCCCTC 62.095 72.222 0.00 0.00 0.00 4.30
1863 2201 2.094957 GTCTCTTCCTCGTTCCTGTCAG 60.095 54.545 0.00 0.00 0.00 3.51
1864 2202 1.887198 GTCTCTTCCTCGTTCCTGTCA 59.113 52.381 0.00 0.00 0.00 3.58
1885 2223 7.283329 CCCTTCAGTTATTGGTAGCTAAGATT 58.717 38.462 0.00 0.00 0.00 2.40
1888 2226 5.104485 ACCCCTTCAGTTATTGGTAGCTAAG 60.104 44.000 0.00 0.00 0.00 2.18
1902 2240 0.991920 CACCACCATACCCCTTCAGT 59.008 55.000 0.00 0.00 0.00 3.41
1904 2242 0.178858 TCCACCACCATACCCCTTCA 60.179 55.000 0.00 0.00 0.00 3.02
1910 2248 1.262640 ACGACCTCCACCACCATACC 61.263 60.000 0.00 0.00 0.00 2.73
1913 2251 2.592993 CCACGACCTCCACCACCAT 61.593 63.158 0.00 0.00 0.00 3.55
1951 2289 6.434028 CCATTTTCCATCAAGTTGTTCCTAGA 59.566 38.462 2.11 0.00 0.00 2.43
1952 2290 6.209391 ACCATTTTCCATCAAGTTGTTCCTAG 59.791 38.462 2.11 0.00 0.00 3.02
1953 2291 6.074648 ACCATTTTCCATCAAGTTGTTCCTA 58.925 36.000 2.11 0.00 0.00 2.94
1954 2292 4.901250 ACCATTTTCCATCAAGTTGTTCCT 59.099 37.500 2.11 0.00 0.00 3.36
1955 2293 5.213891 ACCATTTTCCATCAAGTTGTTCC 57.786 39.130 2.11 0.00 0.00 3.62
1964 2302 8.635328 CATCAAGATCAATACCATTTTCCATCA 58.365 33.333 0.00 0.00 0.00 3.07
1966 2304 7.015877 CCCATCAAGATCAATACCATTTTCCAT 59.984 37.037 0.00 0.00 0.00 3.41
1970 2308 6.442961 TCCCCATCAAGATCAATACCATTTT 58.557 36.000 0.00 0.00 0.00 1.82
1979 2317 1.565759 CCACCTCCCCATCAAGATCAA 59.434 52.381 0.00 0.00 0.00 2.57
1980 2318 1.216064 CCACCTCCCCATCAAGATCA 58.784 55.000 0.00 0.00 0.00 2.92
1987 2325 3.813724 CCCAGCCACCTCCCCATC 61.814 72.222 0.00 0.00 0.00 3.51
1988 2326 3.908712 TTCCCAGCCACCTCCCCAT 62.909 63.158 0.00 0.00 0.00 4.00
1993 2331 0.178961 AAAACCTTCCCAGCCACCTC 60.179 55.000 0.00 0.00 0.00 3.85
2024 2362 2.038952 TGTCCCTGAATCACTCCACTTG 59.961 50.000 0.00 0.00 0.00 3.16
2038 2377 1.630878 AGCCTAGGTTTTCTGTCCCTG 59.369 52.381 11.31 0.00 0.00 4.45
2090 2429 6.183361 CCCACTCTGGATTCTATTCAGATCAA 60.183 42.308 0.00 0.00 40.96 2.57
2124 2463 5.365895 GGGTAGTGTTATGGATCTAACCTGT 59.634 44.000 0.00 0.00 37.30 4.00
2148 2487 1.820519 CCCAATTGGTGACATCCACTG 59.179 52.381 22.91 0.00 45.03 3.66
2153 2492 5.422012 AGGTAAATTCCCAATTGGTGACATC 59.578 40.000 22.91 7.73 42.32 3.06
2192 2531 3.760738 TCACAGTTGTTGCATTCCCATA 58.239 40.909 0.00 0.00 0.00 2.74
2197 2536 3.989817 GGGAAATCACAGTTGTTGCATTC 59.010 43.478 0.00 0.00 0.00 2.67
2202 2541 4.399004 TTTGGGGAAATCACAGTTGTTG 57.601 40.909 0.00 0.00 0.00 3.33
2208 2547 6.153340 ACATGAGTAATTTGGGGAAATCACAG 59.847 38.462 0.00 0.00 0.00 3.66
2213 2552 6.022315 TCCAACATGAGTAATTTGGGGAAAT 58.978 36.000 0.00 0.00 39.27 2.17
2237 2576 2.045047 TCCCTTGACTGGATCCTTCTCT 59.955 50.000 14.23 0.00 0.00 3.10
2251 2590 3.244561 GGTGTTGTGAAGAGATCCCTTGA 60.245 47.826 0.00 0.00 0.00 3.02
2294 2633 1.273327 AGGCACAAAGTTTGGCATAGC 59.727 47.619 19.45 13.59 41.91 2.97
2299 2638 3.452755 AAGTAAGGCACAAAGTTTGGC 57.547 42.857 19.45 17.66 39.80 4.52
2309 2648 0.966179 CCAACCCCAAAGTAAGGCAC 59.034 55.000 0.00 0.00 0.00 5.01
2341 2680 6.070710 ACCCTTCTCTCACACCTTAATTAGTC 60.071 42.308 0.00 0.00 0.00 2.59
2348 2687 2.632996 CACACCCTTCTCTCACACCTTA 59.367 50.000 0.00 0.00 0.00 2.69
2350 2689 1.051812 CACACCCTTCTCTCACACCT 58.948 55.000 0.00 0.00 0.00 4.00
2364 2703 2.091541 CAATACCACCATCACCACACC 58.908 52.381 0.00 0.00 0.00 4.16
2367 2706 2.507407 ACCAATACCACCATCACCAC 57.493 50.000 0.00 0.00 0.00 4.16
2369 2708 5.763204 CACTATTACCAATACCACCATCACC 59.237 44.000 0.00 0.00 0.00 4.02
2406 2745 0.106519 GGGCCCACTCATAAGCACAT 60.107 55.000 19.95 0.00 0.00 3.21
2410 2749 0.106015 ATTGGGGCCCACTCATAAGC 60.106 55.000 28.84 2.47 30.78 3.09
2432 2771 4.406972 CCTTGACCTATCCATCTGACTGAA 59.593 45.833 0.00 0.00 0.00 3.02
2434 2773 3.963374 TCCTTGACCTATCCATCTGACTG 59.037 47.826 0.00 0.00 0.00 3.51
2440 2779 5.541868 TCTCATCTTCCTTGACCTATCCATC 59.458 44.000 0.00 0.00 0.00 3.51
2447 2786 7.059156 CCATTATTTCTCATCTTCCTTGACCT 58.941 38.462 0.00 0.00 0.00 3.85
2449 2788 8.511604 TTCCATTATTTCTCATCTTCCTTGAC 57.488 34.615 0.00 0.00 0.00 3.18
2452 2791 8.331740 TCACTTCCATTATTTCTCATCTTCCTT 58.668 33.333 0.00 0.00 0.00 3.36
2474 2813 1.757306 CACCAGCACCTCCTTCACT 59.243 57.895 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.