Multiple sequence alignment - TraesCS1B01G365200

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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 TraesCS1B01G365200 chr1B 100.000 1814 0 0 1 1814 596038728 596040541 0.000000e+00 3350.0
1 TraesCS1B01G365200 chr1B 100.000 300 0 0 2121 2420 596040848 596041147 2.720000e-154 555.0
2 TraesCS1B01G365200 chr1D 93.041 1049 48 8 673 1708 439306296 439307332 0.000000e+00 1509.0
3 TraesCS1B01G365200 chr1D 91.774 620 22 16 10 608 439305660 439306271 0.000000e+00 835.0
4 TraesCS1B01G365200 chr1A 92.709 1015 46 10 729 1727 535446185 535447187 0.000000e+00 1439.0
5 TraesCS1B01G365200 chr1A 94.186 344 11 3 10 347 535445452 535445792 1.280000e-142 516.0
6 TraesCS1B01G365200 chr3B 77.647 170 23 9 170 339 511071406 511071560 3.310000e-14 89.8
7 TraesCS1B01G365200 chr3A 98.000 50 1 0 290 339 512308376 512308425 1.190000e-13 87.9
8 TraesCS1B01G365200 chr3D 97.917 48 1 0 292 339 392054756 392054803 1.540000e-12 84.2


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 TraesCS1B01G365200 chr1B 596038728 596041147 2419 False 1952.5 3350 100.0000 1 2420 2 chr1B.!!$F1 2419
1 TraesCS1B01G365200 chr1D 439305660 439307332 1672 False 1172.0 1509 92.4075 10 1708 2 chr1D.!!$F1 1698
2 TraesCS1B01G365200 chr1A 535445452 535447187 1735 False 977.5 1439 93.4475 10 1727 2 chr1A.!!$F1 1717

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
609 743 0.386476 TCCACGCACGTTCTTACTGT 59.614 50.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 2345 0.029834 TAATTCGTCGAGCGCCTACC 59.97 55.0 2.29 0.0 41.07 3.18 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
126 133 2.232941 GGTGGAAAGACGGTACTGATCA 59.767 50.000 9.17 0.00 0.00 2.92
172 179 3.957535 GGCGGCGGCAAGATCATG 61.958 66.667 29.41 0.00 42.47 3.07
395 498 7.945033 AACACGTGCATAAATTTCTCAAAAT 57.055 28.000 17.22 0.00 36.64 1.82
468 589 5.535333 TGTTGCTAGTACTACCAGTTTGTC 58.465 41.667 0.00 0.00 0.00 3.18
488 609 9.309516 GTTTGTCAGTATCGGTTAATGAGATTA 57.690 33.333 0.00 0.00 35.70 1.75
500 621 7.574967 CGGTTAATGAGATTAGCACCAAGTTTT 60.575 37.037 0.00 0.00 29.84 2.43
511 641 4.709886 AGCACCAAGTTTTGAACCTACTTT 59.290 37.500 0.00 0.00 30.08 2.66
529 659 4.359706 ACTTTTCTTGCCGTGTGAAAATC 58.640 39.130 0.00 0.00 38.47 2.17
587 721 4.530161 AGAGTTCCACACTAAAGCTCATCT 59.470 41.667 0.00 0.00 35.01 2.90
592 726 3.431486 CCACACTAAAGCTCATCTCCTCC 60.431 52.174 0.00 0.00 0.00 4.30
608 742 1.060713 CTCCACGCACGTTCTTACTG 58.939 55.000 0.00 0.00 0.00 2.74
609 743 0.386476 TCCACGCACGTTCTTACTGT 59.614 50.000 0.00 0.00 0.00 3.55
610 744 1.608109 TCCACGCACGTTCTTACTGTA 59.392 47.619 0.00 0.00 0.00 2.74
611 745 1.717645 CCACGCACGTTCTTACTGTAC 59.282 52.381 0.00 0.00 0.00 2.90
612 746 2.606308 CCACGCACGTTCTTACTGTACT 60.606 50.000 0.00 0.00 0.00 2.73
613 747 3.365264 CCACGCACGTTCTTACTGTACTA 60.365 47.826 0.00 0.00 0.00 1.82
614 748 4.409570 CACGCACGTTCTTACTGTACTAT 58.590 43.478 0.00 0.00 0.00 2.12
619 753 6.356452 CGCACGTTCTTACTGTACTATACATC 59.644 42.308 0.00 0.00 38.15 3.06
621 755 7.680350 GCACGTTCTTACTGTACTATACATCCA 60.680 40.741 0.00 0.00 38.15 3.41
638 772 4.402155 ACATCCAAATCCGCACAACAATAT 59.598 37.500 0.00 0.00 0.00 1.28
639 773 5.592282 ACATCCAAATCCGCACAACAATATA 59.408 36.000 0.00 0.00 0.00 0.86
643 777 5.006844 CCAAATCCGCACAACAATATACGTA 59.993 40.000 0.00 0.00 0.00 3.57
645 779 3.446799 TCCGCACAACAATATACGTACC 58.553 45.455 0.00 0.00 0.00 3.34
885 1025 1.265365 GAAGTCTGCTTGCTCACCAAC 59.735 52.381 0.00 0.00 34.61 3.77
902 1042 2.044806 AACACACGCCAGCTTCTCCT 62.045 55.000 0.00 0.00 0.00 3.69
1011 1163 1.355718 GGGAGGCCATGGATCAGGAA 61.356 60.000 18.40 0.00 0.00 3.36
1182 1334 4.436998 CGGTCACGCTCCTGGACC 62.437 72.222 0.00 0.00 46.01 4.46
1188 1340 4.778415 CGCTCCTGGACCACGTCG 62.778 72.222 0.00 0.00 32.65 5.12
1224 1376 2.088763 CAACGACGACTGCAGCGAT 61.089 57.895 28.70 16.90 0.00 4.58
1287 1439 4.056125 CACGTCCTGGCTGAGCGA 62.056 66.667 0.00 0.00 0.00 4.93
1420 1572 3.722147 ACCGGATTCATCGAGAAATGAG 58.278 45.455 9.46 0.00 40.22 2.90
1425 1577 4.694509 GGATTCATCGAGAAATGAGATGGG 59.305 45.833 5.06 0.00 41.35 4.00
1446 1599 0.250124 TCAACACCGTGGATGTGGAC 60.250 55.000 3.03 0.00 38.05 4.02
1530 1689 1.069204 AGTTTTCAGTGAGCGCAGAGA 59.931 47.619 11.47 0.00 0.00 3.10
1531 1690 1.458827 GTTTTCAGTGAGCGCAGAGAG 59.541 52.381 11.47 0.00 0.00 3.20
1612 1771 8.446489 TTGTTTAATCGAATTTAGCATGTGTG 57.554 30.769 0.00 0.00 0.00 3.82
1615 1774 7.851387 TTAATCGAATTTAGCATGTGTGGTA 57.149 32.000 0.00 0.00 37.28 3.25
1680 1843 2.025510 AGAGCAAAAGGGAGGAGGATTG 60.026 50.000 0.00 0.00 0.00 2.67
1728 1891 2.652795 GCTACTGCTAGCTACGTAAGC 58.347 52.381 17.23 10.21 42.11 3.09
1729 1892 2.605097 GCTACTGCTAGCTACGTAAGCC 60.605 54.545 17.23 3.35 43.63 4.35
1730 1893 5.094357 GCTACTGCTAGCTACGTAAGCCA 62.094 52.174 17.23 5.28 43.63 4.75
1731 1894 6.510678 GCTACTGCTAGCTACGTAAGCCAA 62.511 50.000 17.23 3.44 43.63 4.52
1732 1895 7.731666 GCTACTGCTAGCTACGTAAGCCAAT 62.732 48.000 17.23 3.84 43.63 3.16
1739 1902 3.936661 GCTACGTAAGCCAATTGTAAGC 58.063 45.455 4.43 0.65 46.25 3.09
1740 1903 3.543460 GCTACGTAAGCCAATTGTAAGCG 60.543 47.826 4.43 5.11 46.25 4.68
1741 1904 1.735571 ACGTAAGCCAATTGTAAGCGG 59.264 47.619 4.43 0.00 45.62 5.52
1742 1905 1.063469 CGTAAGCCAATTGTAAGCGGG 59.937 52.381 4.43 0.00 0.00 6.13
1743 1906 2.089201 GTAAGCCAATTGTAAGCGGGT 58.911 47.619 4.43 0.00 0.00 5.28
1744 1907 0.887933 AAGCCAATTGTAAGCGGGTG 59.112 50.000 4.43 0.00 0.00 4.61
1745 1908 0.251165 AGCCAATTGTAAGCGGGTGT 60.251 50.000 4.43 0.00 0.00 4.16
1746 1909 0.170339 GCCAATTGTAAGCGGGTGTC 59.830 55.000 4.43 0.00 0.00 3.67
1747 1910 1.821216 CCAATTGTAAGCGGGTGTCT 58.179 50.000 4.43 0.00 0.00 3.41
1748 1911 2.937873 GCCAATTGTAAGCGGGTGTCTA 60.938 50.000 4.43 0.00 0.00 2.59
1749 1912 2.936498 CCAATTGTAAGCGGGTGTCTAG 59.064 50.000 4.43 0.00 0.00 2.43
1750 1913 3.596214 CAATTGTAAGCGGGTGTCTAGT 58.404 45.455 0.00 0.00 0.00 2.57
1751 1914 3.521947 ATTGTAAGCGGGTGTCTAGTC 57.478 47.619 0.00 0.00 0.00 2.59
1752 1915 0.806868 TGTAAGCGGGTGTCTAGTCG 59.193 55.000 0.00 0.00 0.00 4.18
1753 1916 0.807496 GTAAGCGGGTGTCTAGTCGT 59.193 55.000 0.00 0.00 0.00 4.34
1754 1917 1.200948 GTAAGCGGGTGTCTAGTCGTT 59.799 52.381 0.00 0.00 0.00 3.85
1755 1918 0.038526 AAGCGGGTGTCTAGTCGTTG 60.039 55.000 0.00 0.00 0.00 4.10
1756 1919 2.092882 GCGGGTGTCTAGTCGTTGC 61.093 63.158 0.00 0.00 0.00 4.17
1757 1920 1.585006 CGGGTGTCTAGTCGTTGCT 59.415 57.895 0.00 0.00 0.00 3.91
1758 1921 0.806868 CGGGTGTCTAGTCGTTGCTA 59.193 55.000 0.00 0.00 0.00 3.49
1759 1922 1.200716 CGGGTGTCTAGTCGTTGCTAA 59.799 52.381 0.00 0.00 0.00 3.09
1760 1923 2.352030 CGGGTGTCTAGTCGTTGCTAAA 60.352 50.000 0.00 0.00 0.00 1.85
1761 1924 3.675228 CGGGTGTCTAGTCGTTGCTAAAT 60.675 47.826 0.00 0.00 0.00 1.40
1762 1925 4.439153 CGGGTGTCTAGTCGTTGCTAAATA 60.439 45.833 0.00 0.00 0.00 1.40
1763 1926 5.598769 GGGTGTCTAGTCGTTGCTAAATAT 58.401 41.667 0.00 0.00 0.00 1.28
1764 1927 6.513884 CGGGTGTCTAGTCGTTGCTAAATATA 60.514 42.308 0.00 0.00 0.00 0.86
1765 1928 6.862090 GGGTGTCTAGTCGTTGCTAAATATAG 59.138 42.308 0.00 0.00 0.00 1.31
1766 1929 7.424001 GGTGTCTAGTCGTTGCTAAATATAGT 58.576 38.462 0.00 0.00 0.00 2.12
1767 1930 7.378995 GGTGTCTAGTCGTTGCTAAATATAGTG 59.621 40.741 0.00 0.00 0.00 2.74
1768 1931 8.127327 GTGTCTAGTCGTTGCTAAATATAGTGA 58.873 37.037 0.00 0.00 0.00 3.41
1769 1932 8.343366 TGTCTAGTCGTTGCTAAATATAGTGAG 58.657 37.037 0.00 0.00 0.00 3.51
1770 1933 8.557864 GTCTAGTCGTTGCTAAATATAGTGAGA 58.442 37.037 0.00 0.00 0.00 3.27
1771 1934 9.117183 TCTAGTCGTTGCTAAATATAGTGAGAA 57.883 33.333 0.00 0.00 0.00 2.87
1772 1935 9.388346 CTAGTCGTTGCTAAATATAGTGAGAAG 57.612 37.037 0.00 0.00 0.00 2.85
1773 1936 7.203910 AGTCGTTGCTAAATATAGTGAGAAGG 58.796 38.462 0.00 0.00 0.00 3.46
1774 1937 6.979238 GTCGTTGCTAAATATAGTGAGAAGGT 59.021 38.462 0.00 0.00 0.00 3.50
1775 1938 8.133627 GTCGTTGCTAAATATAGTGAGAAGGTA 58.866 37.037 0.00 0.00 0.00 3.08
1776 1939 8.133627 TCGTTGCTAAATATAGTGAGAAGGTAC 58.866 37.037 0.00 0.00 0.00 3.34
1780 1943 9.863650 TGCTAAATATAGTGAGAAGGTACTACT 57.136 33.333 0.00 0.00 38.49 2.57
2143 2306 6.575162 TGAAAATTAAGGAAGAAGGTGAGC 57.425 37.500 0.00 0.00 0.00 4.26
2144 2307 6.068010 TGAAAATTAAGGAAGAAGGTGAGCA 58.932 36.000 0.00 0.00 0.00 4.26
2145 2308 6.721208 TGAAAATTAAGGAAGAAGGTGAGCAT 59.279 34.615 0.00 0.00 0.00 3.79
2146 2309 7.233348 TGAAAATTAAGGAAGAAGGTGAGCATT 59.767 33.333 0.00 0.00 0.00 3.56
2147 2310 6.765915 AATTAAGGAAGAAGGTGAGCATTC 57.234 37.500 0.00 0.00 35.82 2.67
2148 2311 2.393271 AGGAAGAAGGTGAGCATTCG 57.607 50.000 0.00 0.00 40.03 3.34
2149 2312 0.729690 GGAAGAAGGTGAGCATTCGC 59.270 55.000 0.00 0.00 40.03 4.70
2154 2317 2.434185 GGTGAGCATTCGCCGTGA 60.434 61.111 0.00 0.00 43.62 4.35
2155 2318 2.456119 GGTGAGCATTCGCCGTGAG 61.456 63.158 0.00 0.00 43.62 3.51
2168 2331 3.217242 CGTGAGGAGTCTTGTTGGG 57.783 57.895 0.00 0.00 0.00 4.12
2169 2332 0.320771 CGTGAGGAGTCTTGTTGGGG 60.321 60.000 0.00 0.00 0.00 4.96
2170 2333 0.606673 GTGAGGAGTCTTGTTGGGGC 60.607 60.000 0.00 0.00 0.00 5.80
2171 2334 1.002011 GAGGAGTCTTGTTGGGGCC 60.002 63.158 0.00 0.00 0.00 5.80
2172 2335 2.035783 GGAGTCTTGTTGGGGCCC 59.964 66.667 18.17 18.17 0.00 5.80
2173 2336 2.359975 GAGTCTTGTTGGGGCCCG 60.360 66.667 19.83 2.50 0.00 6.13
2174 2337 3.920093 GAGTCTTGTTGGGGCCCGG 62.920 68.421 19.83 5.53 0.00 5.73
2185 2348 4.162009 GGCCCGGGGACTAGGGTA 62.162 72.222 25.28 0.00 45.20 3.69
2186 2349 2.523657 GCCCGGGGACTAGGGTAG 60.524 72.222 25.28 0.00 45.20 3.18
2187 2350 2.200650 CCCGGGGACTAGGGTAGG 59.799 72.222 14.71 0.00 40.32 3.18
2188 2351 2.523657 CCGGGGACTAGGGTAGGC 60.524 72.222 0.00 0.00 0.00 3.93
2189 2352 2.910994 CGGGGACTAGGGTAGGCG 60.911 72.222 0.00 0.00 33.43 5.52
2190 2353 3.232483 GGGGACTAGGGTAGGCGC 61.232 72.222 0.00 0.00 45.35 6.53
2191 2354 2.123382 GGGACTAGGGTAGGCGCT 60.123 66.667 7.64 0.00 42.97 5.92
2192 2355 2.201708 GGGACTAGGGTAGGCGCTC 61.202 68.421 7.64 0.00 42.97 5.03
2193 2356 2.553727 GGACTAGGGTAGGCGCTCG 61.554 68.421 7.64 0.00 38.85 5.03
2194 2357 1.525535 GACTAGGGTAGGCGCTCGA 60.526 63.158 7.64 0.00 38.85 4.04
2195 2358 1.784036 GACTAGGGTAGGCGCTCGAC 61.784 65.000 7.64 3.86 38.85 4.20
2209 2372 1.187487 GCTCGACGAATTAGTTAGCGC 59.813 52.381 0.00 0.00 0.00 5.92
2210 2373 2.717530 CTCGACGAATTAGTTAGCGCT 58.282 47.619 17.26 17.26 0.00 5.92
2211 2374 3.847467 GCTCGACGAATTAGTTAGCGCTA 60.847 47.826 14.45 14.45 0.00 4.26
2212 2375 3.611517 TCGACGAATTAGTTAGCGCTAC 58.388 45.455 18.63 12.48 0.00 3.58
2213 2376 3.063861 TCGACGAATTAGTTAGCGCTACA 59.936 43.478 18.63 5.91 0.00 2.74
2214 2377 3.417969 CGACGAATTAGTTAGCGCTACAG 59.582 47.826 18.63 5.01 0.00 2.74
2215 2378 3.703420 ACGAATTAGTTAGCGCTACAGG 58.297 45.455 18.63 3.46 0.00 4.00
2216 2379 3.129988 ACGAATTAGTTAGCGCTACAGGT 59.870 43.478 18.63 4.44 0.00 4.00
2217 2380 4.336433 ACGAATTAGTTAGCGCTACAGGTA 59.664 41.667 18.63 0.00 0.00 3.08
2218 2381 5.009410 ACGAATTAGTTAGCGCTACAGGTAT 59.991 40.000 18.63 4.59 0.00 2.73
2219 2382 5.342525 CGAATTAGTTAGCGCTACAGGTATG 59.657 44.000 18.63 0.13 0.00 2.39
2220 2383 4.579454 TTAGTTAGCGCTACAGGTATGG 57.421 45.455 18.63 0.00 0.00 2.74
2221 2384 2.385803 AGTTAGCGCTACAGGTATGGT 58.614 47.619 18.63 0.00 0.00 3.55
2222 2385 2.361438 AGTTAGCGCTACAGGTATGGTC 59.639 50.000 18.63 0.00 0.00 4.02
2223 2386 0.949397 TAGCGCTACAGGTATGGTCG 59.051 55.000 14.45 0.00 0.00 4.79
2224 2387 0.750546 AGCGCTACAGGTATGGTCGA 60.751 55.000 8.99 0.00 0.00 4.20
2225 2388 0.314302 GCGCTACAGGTATGGTCGAT 59.686 55.000 0.00 0.00 0.00 3.59
2226 2389 1.538512 GCGCTACAGGTATGGTCGATA 59.461 52.381 0.00 0.00 0.00 2.92
2227 2390 2.163815 GCGCTACAGGTATGGTCGATAT 59.836 50.000 0.00 0.00 0.00 1.63
2228 2391 3.759418 CGCTACAGGTATGGTCGATATG 58.241 50.000 0.00 0.00 0.00 1.78
2229 2392 3.190744 CGCTACAGGTATGGTCGATATGT 59.809 47.826 0.00 0.00 0.00 2.29
2230 2393 4.393990 CGCTACAGGTATGGTCGATATGTA 59.606 45.833 0.00 0.00 0.00 2.29
2231 2394 5.638783 GCTACAGGTATGGTCGATATGTAC 58.361 45.833 0.00 0.00 0.00 2.90
2232 2395 5.392811 GCTACAGGTATGGTCGATATGTACC 60.393 48.000 9.79 9.79 36.02 3.34
2233 2396 4.737578 ACAGGTATGGTCGATATGTACCT 58.262 43.478 12.97 12.97 44.40 3.08
2234 2397 5.145564 ACAGGTATGGTCGATATGTACCTT 58.854 41.667 15.01 1.93 41.69 3.50
2235 2398 5.243283 ACAGGTATGGTCGATATGTACCTTC 59.757 44.000 15.01 0.00 41.69 3.46
2236 2399 5.243060 CAGGTATGGTCGATATGTACCTTCA 59.757 44.000 15.01 0.00 41.69 3.02
2237 2400 6.017192 AGGTATGGTCGATATGTACCTTCAT 58.983 40.000 12.97 0.00 41.69 2.57
2238 2401 6.153000 AGGTATGGTCGATATGTACCTTCATC 59.847 42.308 12.97 0.00 41.69 2.92
2239 2402 4.499037 TGGTCGATATGTACCTTCATCG 57.501 45.455 0.00 8.40 41.17 3.84
2240 2403 3.254903 TGGTCGATATGTACCTTCATCGG 59.745 47.826 12.55 0.00 40.43 4.18
2241 2404 3.504906 GGTCGATATGTACCTTCATCGGA 59.495 47.826 12.55 0.00 40.43 4.55
2242 2405 4.158025 GGTCGATATGTACCTTCATCGGAT 59.842 45.833 12.55 0.00 40.43 4.18
2243 2406 5.356190 GGTCGATATGTACCTTCATCGGATA 59.644 44.000 12.55 0.00 40.43 2.59
2244 2407 6.127814 GGTCGATATGTACCTTCATCGGATAA 60.128 42.308 12.55 0.00 40.43 1.75
2245 2408 7.310664 GTCGATATGTACCTTCATCGGATAAA 58.689 38.462 12.55 0.00 40.43 1.40
2246 2409 7.974501 GTCGATATGTACCTTCATCGGATAAAT 59.025 37.037 12.55 0.00 40.43 1.40
2247 2410 8.188799 TCGATATGTACCTTCATCGGATAAATC 58.811 37.037 12.55 0.00 40.43 2.17
2248 2411 7.973944 CGATATGTACCTTCATCGGATAAATCA 59.026 37.037 0.00 0.00 37.28 2.57
2249 2412 9.823647 GATATGTACCTTCATCGGATAAATCAT 57.176 33.333 0.00 0.00 0.00 2.45
2252 2415 7.383687 TGTACCTTCATCGGATAAATCATACC 58.616 38.462 0.00 0.00 0.00 2.73
2253 2416 5.479306 ACCTTCATCGGATAAATCATACCG 58.521 41.667 0.00 0.00 45.61 4.02
2254 2417 5.011738 ACCTTCATCGGATAAATCATACCGT 59.988 40.000 0.00 0.00 44.72 4.83
2255 2418 5.348724 CCTTCATCGGATAAATCATACCGTG 59.651 44.000 0.00 0.00 44.72 4.94
2256 2419 4.242475 TCATCGGATAAATCATACCGTGC 58.758 43.478 0.00 0.00 44.72 5.34
2257 2420 3.737032 TCGGATAAATCATACCGTGCA 57.263 42.857 0.00 0.00 44.72 4.57
2258 2421 4.265904 TCGGATAAATCATACCGTGCAT 57.734 40.909 0.00 0.00 44.72 3.96
2259 2422 3.993736 TCGGATAAATCATACCGTGCATG 59.006 43.478 0.00 0.00 44.72 4.06
2260 2423 3.125146 CGGATAAATCATACCGTGCATGG 59.875 47.826 23.83 23.83 40.42 3.66
2261 2424 3.119849 GGATAAATCATACCGTGCATGGC 60.120 47.826 25.30 4.13 0.00 4.40
2262 2425 1.761449 AAATCATACCGTGCATGGCA 58.239 45.000 25.30 13.33 35.60 4.92
2284 2447 3.888934 CGTGGCACATGGATTTATAAGC 58.111 45.455 19.09 0.00 44.52 3.09
2285 2448 3.304659 CGTGGCACATGGATTTATAAGCC 60.305 47.826 19.09 0.00 44.52 4.35
2286 2449 2.884012 TGGCACATGGATTTATAAGCCG 59.116 45.455 0.00 0.00 43.59 5.52
2287 2450 2.884639 GGCACATGGATTTATAAGCCGT 59.115 45.455 0.00 0.00 40.70 5.68
2288 2451 4.069304 GGCACATGGATTTATAAGCCGTA 58.931 43.478 0.00 0.00 40.70 4.02
2289 2452 4.083484 GGCACATGGATTTATAAGCCGTAC 60.083 45.833 0.00 0.00 40.70 3.67
2290 2453 4.513692 GCACATGGATTTATAAGCCGTACA 59.486 41.667 0.00 0.00 40.70 2.90
2291 2454 5.008217 GCACATGGATTTATAAGCCGTACAA 59.992 40.000 0.00 0.00 40.70 2.41
2292 2455 6.293955 GCACATGGATTTATAAGCCGTACAAT 60.294 38.462 0.00 0.00 40.70 2.71
2293 2456 7.648142 CACATGGATTTATAAGCCGTACAATT 58.352 34.615 0.00 0.00 40.70 2.32
2294 2457 8.134895 CACATGGATTTATAAGCCGTACAATTT 58.865 33.333 0.00 0.00 40.70 1.82
2295 2458 8.691797 ACATGGATTTATAAGCCGTACAATTTT 58.308 29.630 0.00 0.00 40.70 1.82
2296 2459 8.967218 CATGGATTTATAAGCCGTACAATTTTG 58.033 33.333 0.00 0.00 40.70 2.44
2297 2460 8.282455 TGGATTTATAAGCCGTACAATTTTGA 57.718 30.769 0.00 0.00 40.70 2.69
2298 2461 8.402472 TGGATTTATAAGCCGTACAATTTTGAG 58.598 33.333 0.00 0.00 40.70 3.02
2299 2462 8.617809 GGATTTATAAGCCGTACAATTTTGAGA 58.382 33.333 0.00 0.00 0.00 3.27
2300 2463 9.997482 GATTTATAAGCCGTACAATTTTGAGAA 57.003 29.630 0.00 0.00 0.00 2.87
2303 2466 9.834628 TTATAAGCCGTACAATTTTGAGAAAAG 57.165 29.630 0.00 0.00 33.22 2.27
2304 2467 5.767816 AGCCGTACAATTTTGAGAAAAGT 57.232 34.783 0.00 0.00 33.22 2.66
2305 2468 6.870971 AGCCGTACAATTTTGAGAAAAGTA 57.129 33.333 0.00 0.00 33.22 2.24
2306 2469 7.266922 AGCCGTACAATTTTGAGAAAAGTAA 57.733 32.000 0.00 0.00 33.22 2.24
2307 2470 7.708998 AGCCGTACAATTTTGAGAAAAGTAAA 58.291 30.769 0.00 0.00 33.22 2.01
2308 2471 7.860872 AGCCGTACAATTTTGAGAAAAGTAAAG 59.139 33.333 0.00 0.00 33.22 1.85
2309 2472 7.858879 GCCGTACAATTTTGAGAAAAGTAAAGA 59.141 33.333 0.00 0.00 33.22 2.52
2310 2473 9.382244 CCGTACAATTTTGAGAAAAGTAAAGAG 57.618 33.333 0.00 0.00 33.22 2.85
2341 2504 7.939784 AGAGAATTTATTACTTGGTGAACCC 57.060 36.000 0.00 0.00 34.29 4.11
2342 2505 7.699878 AGAGAATTTATTACTTGGTGAACCCT 58.300 34.615 0.00 0.00 34.29 4.34
2343 2506 8.832735 AGAGAATTTATTACTTGGTGAACCCTA 58.167 33.333 0.00 0.00 34.29 3.53
2344 2507 9.628500 GAGAATTTATTACTTGGTGAACCCTAT 57.372 33.333 0.00 0.00 34.29 2.57
2350 2513 9.895138 TTATTACTTGGTGAACCCTATAGAAAC 57.105 33.333 0.00 0.00 34.29 2.78
2351 2514 7.563724 TTACTTGGTGAACCCTATAGAAACT 57.436 36.000 0.00 0.00 34.29 2.66
2352 2515 8.669055 TTACTTGGTGAACCCTATAGAAACTA 57.331 34.615 0.00 0.00 34.29 2.24
2353 2516 7.184067 ACTTGGTGAACCCTATAGAAACTAG 57.816 40.000 0.00 0.00 34.29 2.57
2354 2517 6.958192 ACTTGGTGAACCCTATAGAAACTAGA 59.042 38.462 0.00 0.00 34.29 2.43
2355 2518 7.456902 ACTTGGTGAACCCTATAGAAACTAGAA 59.543 37.037 0.00 0.00 34.29 2.10
2356 2519 7.419711 TGGTGAACCCTATAGAAACTAGAAG 57.580 40.000 0.00 0.00 34.29 2.85
2357 2520 7.186972 TGGTGAACCCTATAGAAACTAGAAGA 58.813 38.462 0.00 0.00 34.29 2.87
2358 2521 7.123847 TGGTGAACCCTATAGAAACTAGAAGAC 59.876 40.741 0.00 0.00 34.29 3.01
2359 2522 7.342541 GGTGAACCCTATAGAAACTAGAAGACT 59.657 40.741 0.00 0.00 0.00 3.24
2360 2523 8.751242 GTGAACCCTATAGAAACTAGAAGACTT 58.249 37.037 0.00 0.00 0.00 3.01
2361 2524 8.968969 TGAACCCTATAGAAACTAGAAGACTTC 58.031 37.037 7.14 7.14 0.00 3.01
2362 2525 8.896722 AACCCTATAGAAACTAGAAGACTTCA 57.103 34.615 17.34 3.02 0.00 3.02
2363 2526 8.896722 ACCCTATAGAAACTAGAAGACTTCAA 57.103 34.615 17.34 0.00 0.00 2.69
2364 2527 9.322769 ACCCTATAGAAACTAGAAGACTTCAAA 57.677 33.333 17.34 4.26 0.00 2.69
2369 2532 9.832445 ATAGAAACTAGAAGACTTCAAAACACA 57.168 29.630 17.34 0.00 0.00 3.72
2370 2533 8.561738 AGAAACTAGAAGACTTCAAAACACAA 57.438 30.769 17.34 0.00 0.00 3.33
2371 2534 9.010029 AGAAACTAGAAGACTTCAAAACACAAA 57.990 29.630 17.34 0.00 0.00 2.83
2372 2535 9.620660 GAAACTAGAAGACTTCAAAACACAAAA 57.379 29.630 17.34 0.00 0.00 2.44
2374 2537 9.573133 AACTAGAAGACTTCAAAACACAAAATG 57.427 29.630 17.34 0.00 0.00 2.32
2375 2538 8.739972 ACTAGAAGACTTCAAAACACAAAATGT 58.260 29.630 17.34 0.00 46.42 2.71
2381 2544 9.868277 AGACTTCAAAACACAAAATGTAATTCA 57.132 25.926 0.00 0.00 42.31 2.57
2409 2572 8.763984 ATAGTACTGCTAGTATACCAACAAGT 57.236 34.615 5.39 0.70 32.65 3.16
2410 2573 9.857656 ATAGTACTGCTAGTATACCAACAAGTA 57.142 33.333 5.39 0.00 32.65 2.24
2411 2574 8.585471 AGTACTGCTAGTATACCAACAAGTAA 57.415 34.615 0.00 0.00 32.65 2.24
2412 2575 8.465201 AGTACTGCTAGTATACCAACAAGTAAC 58.535 37.037 0.00 0.00 32.65 2.50
2413 2576 7.477945 ACTGCTAGTATACCAACAAGTAACT 57.522 36.000 0.00 0.00 0.00 2.24
2414 2577 7.904205 ACTGCTAGTATACCAACAAGTAACTT 58.096 34.615 0.00 0.00 0.00 2.66
2415 2578 8.033626 ACTGCTAGTATACCAACAAGTAACTTC 58.966 37.037 0.00 0.00 0.00 3.01
2416 2579 8.130671 TGCTAGTATACCAACAAGTAACTTCT 57.869 34.615 0.00 0.00 0.00 2.85
2417 2580 8.591072 TGCTAGTATACCAACAAGTAACTTCTT 58.409 33.333 0.00 0.00 0.00 2.52
2418 2581 9.433153 GCTAGTATACCAACAAGTAACTTCTTT 57.567 33.333 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 147 4.162690 GCCGCCGTCCTTCTCCAT 62.163 66.667 0.00 0.00 0.00 3.41
158 165 3.113745 CACCATGATCTTGCCGCC 58.886 61.111 3.07 0.00 0.00 6.13
159 166 2.410469 GCACCATGATCTTGCCGC 59.590 61.111 3.07 4.29 0.00 6.53
160 167 3.113745 GGCACCATGATCTTGCCG 58.886 61.111 10.58 2.89 46.11 5.69
395 498 4.295051 GTTGAGCGCACAAGGAAATTTAA 58.705 39.130 20.75 0.00 0.00 1.52
468 589 6.366332 GGTGCTAATCTCATTAACCGATACTG 59.634 42.308 0.00 0.00 0.00 2.74
488 609 3.898482 AGTAGGTTCAAAACTTGGTGCT 58.102 40.909 0.00 0.00 0.00 4.40
500 621 2.875933 CACGGCAAGAAAAGTAGGTTCA 59.124 45.455 0.00 0.00 0.00 3.18
511 641 2.293122 CTGGATTTTCACACGGCAAGAA 59.707 45.455 0.00 0.00 0.00 2.52
529 659 1.726791 CTTCGTTTGACCGATGACTGG 59.273 52.381 0.00 0.00 36.62 4.00
587 721 0.038892 GTAAGAACGTGCGTGGAGGA 60.039 55.000 0.00 0.00 0.00 3.71
592 726 2.658285 AGTACAGTAAGAACGTGCGTG 58.342 47.619 0.00 0.00 0.00 5.34
608 742 5.294356 TGTGCGGATTTGGATGTATAGTAC 58.706 41.667 0.00 0.00 0.00 2.73
609 743 5.538849 TGTGCGGATTTGGATGTATAGTA 57.461 39.130 0.00 0.00 0.00 1.82
610 744 4.415881 TGTGCGGATTTGGATGTATAGT 57.584 40.909 0.00 0.00 0.00 2.12
611 745 4.574421 TGTTGTGCGGATTTGGATGTATAG 59.426 41.667 0.00 0.00 0.00 1.31
612 746 4.518249 TGTTGTGCGGATTTGGATGTATA 58.482 39.130 0.00 0.00 0.00 1.47
613 747 3.351740 TGTTGTGCGGATTTGGATGTAT 58.648 40.909 0.00 0.00 0.00 2.29
614 748 2.784347 TGTTGTGCGGATTTGGATGTA 58.216 42.857 0.00 0.00 0.00 2.29
619 753 4.201871 ACGTATATTGTTGTGCGGATTTGG 60.202 41.667 0.00 0.00 0.00 3.28
621 755 5.006941 GGTACGTATATTGTTGTGCGGATTT 59.993 40.000 0.00 0.00 0.00 2.17
626 760 4.843879 TTGGTACGTATATTGTTGTGCG 57.156 40.909 0.00 0.00 0.00 5.34
653 787 3.061403 CGGAGAAAATCGTGTACGTATGC 60.061 47.826 0.00 0.00 40.80 3.14
656 790 3.829886 ACGGAGAAAATCGTGTACGTA 57.170 42.857 4.20 0.00 38.25 3.57
657 791 2.712057 ACGGAGAAAATCGTGTACGT 57.288 45.000 4.20 0.00 38.25 3.57
885 1025 1.294659 GAAGGAGAAGCTGGCGTGTG 61.295 60.000 0.00 0.00 0.00 3.82
902 1042 1.476833 GGTGTGCTGTGGAAGGAAGAA 60.477 52.381 0.00 0.00 0.00 2.52
1011 1163 1.289380 GACGTCGGCTTCTTGGAGT 59.711 57.895 0.00 0.00 0.00 3.85
1042 1194 2.280592 GCGGTGGTCGGAGTTGTT 60.281 61.111 0.00 0.00 39.69 2.83
1085 1237 0.167470 GTCTCCGTCGACGTTGATGA 59.833 55.000 33.49 22.30 37.74 2.92
1088 1240 0.109919 CATGTCTCCGTCGACGTTGA 60.110 55.000 33.49 26.56 36.71 3.18
1170 1322 3.681835 GACGTGGTCCAGGAGCGT 61.682 66.667 18.37 11.61 38.55 5.07
1224 1376 3.109547 GTGCATCGAACGTCGCCA 61.110 61.111 0.00 0.00 40.21 5.69
1233 1385 3.109547 GCGTCGTTGGTGCATCGA 61.110 61.111 0.00 0.00 33.98 3.59
1425 1577 0.591170 CCACATCCACGGTGTTGAAC 59.409 55.000 7.45 0.00 34.46 3.18
1446 1599 4.659111 TCCCAAGCAATGAAGCAATATG 57.341 40.909 0.00 0.00 36.85 1.78
1530 1689 5.559148 ACATCTCTTGTCTTTCTTCACCT 57.441 39.130 0.00 0.00 30.89 4.00
1531 1690 6.459923 ACTACATCTCTTGTCTTTCTTCACC 58.540 40.000 0.00 0.00 39.87 4.02
1587 1746 7.540400 CCACACATGCTAAATTCGATTAAACAA 59.460 33.333 0.00 0.00 0.00 2.83
1612 1771 2.711924 GCAAGCTGCTCGCATACC 59.288 61.111 7.87 0.00 40.96 2.73
1680 1843 2.024176 TCGGCTCCAGTTAGCATTTC 57.976 50.000 0.00 0.00 44.64 2.17
1722 1885 1.063469 CCCGCTTACAATTGGCTTACG 59.937 52.381 10.83 6.76 0.00 3.18
1727 1890 0.170339 GACACCCGCTTACAATTGGC 59.830 55.000 10.83 2.67 0.00 4.52
1728 1891 1.821216 AGACACCCGCTTACAATTGG 58.179 50.000 10.83 0.00 0.00 3.16
1729 1892 3.596214 ACTAGACACCCGCTTACAATTG 58.404 45.455 3.24 3.24 0.00 2.32
1730 1893 3.675228 CGACTAGACACCCGCTTACAATT 60.675 47.826 0.00 0.00 0.00 2.32
1731 1894 2.159282 CGACTAGACACCCGCTTACAAT 60.159 50.000 0.00 0.00 0.00 2.71
1732 1895 1.200716 CGACTAGACACCCGCTTACAA 59.799 52.381 0.00 0.00 0.00 2.41
1733 1896 0.806868 CGACTAGACACCCGCTTACA 59.193 55.000 0.00 0.00 0.00 2.41
1734 1897 0.807496 ACGACTAGACACCCGCTTAC 59.193 55.000 0.00 0.00 0.00 2.34
1735 1898 1.200716 CAACGACTAGACACCCGCTTA 59.799 52.381 0.00 0.00 0.00 3.09
1736 1899 0.038526 CAACGACTAGACACCCGCTT 60.039 55.000 0.00 0.00 0.00 4.68
1737 1900 1.585006 CAACGACTAGACACCCGCT 59.415 57.895 0.00 0.00 0.00 5.52
1738 1901 2.092882 GCAACGACTAGACACCCGC 61.093 63.158 0.00 0.00 0.00 6.13
1739 1902 0.806868 TAGCAACGACTAGACACCCG 59.193 55.000 0.00 0.00 0.00 5.28
1740 1903 3.308438 TTTAGCAACGACTAGACACCC 57.692 47.619 0.00 0.00 0.00 4.61
1741 1904 7.378995 CACTATATTTAGCAACGACTAGACACC 59.621 40.741 0.00 0.00 0.00 4.16
1742 1905 8.127327 TCACTATATTTAGCAACGACTAGACAC 58.873 37.037 0.00 0.00 0.00 3.67
1743 1906 8.217131 TCACTATATTTAGCAACGACTAGACA 57.783 34.615 0.00 0.00 0.00 3.41
1744 1907 8.557864 TCTCACTATATTTAGCAACGACTAGAC 58.442 37.037 0.00 0.00 0.00 2.59
1745 1908 8.672823 TCTCACTATATTTAGCAACGACTAGA 57.327 34.615 0.00 0.00 0.00 2.43
1746 1909 9.388346 CTTCTCACTATATTTAGCAACGACTAG 57.612 37.037 0.00 0.00 0.00 2.57
1747 1910 8.350722 CCTTCTCACTATATTTAGCAACGACTA 58.649 37.037 0.00 0.00 0.00 2.59
1748 1911 7.147880 ACCTTCTCACTATATTTAGCAACGACT 60.148 37.037 0.00 0.00 0.00 4.18
1749 1912 6.979238 ACCTTCTCACTATATTTAGCAACGAC 59.021 38.462 0.00 0.00 0.00 4.34
1750 1913 7.108841 ACCTTCTCACTATATTTAGCAACGA 57.891 36.000 0.00 0.00 0.00 3.85
1751 1914 8.136165 AGTACCTTCTCACTATATTTAGCAACG 58.864 37.037 0.00 0.00 0.00 4.10
1754 1917 9.863650 AGTAGTACCTTCTCACTATATTTAGCA 57.136 33.333 0.00 0.00 30.37 3.49
2120 2283 6.068010 TGCTCACCTTCTTCCTTAATTTTCA 58.932 36.000 0.00 0.00 0.00 2.69
2121 2284 6.575162 TGCTCACCTTCTTCCTTAATTTTC 57.425 37.500 0.00 0.00 0.00 2.29
2122 2285 7.544804 AATGCTCACCTTCTTCCTTAATTTT 57.455 32.000 0.00 0.00 0.00 1.82
2123 2286 6.127897 CGAATGCTCACCTTCTTCCTTAATTT 60.128 38.462 0.00 0.00 0.00 1.82
2124 2287 5.355350 CGAATGCTCACCTTCTTCCTTAATT 59.645 40.000 0.00 0.00 0.00 1.40
2125 2288 4.878397 CGAATGCTCACCTTCTTCCTTAAT 59.122 41.667 0.00 0.00 0.00 1.40
2126 2289 4.253685 CGAATGCTCACCTTCTTCCTTAA 58.746 43.478 0.00 0.00 0.00 1.85
2127 2290 3.861840 CGAATGCTCACCTTCTTCCTTA 58.138 45.455 0.00 0.00 0.00 2.69
2128 2291 2.704572 CGAATGCTCACCTTCTTCCTT 58.295 47.619 0.00 0.00 0.00 3.36
2129 2292 1.677217 GCGAATGCTCACCTTCTTCCT 60.677 52.381 0.00 0.00 38.39 3.36
2130 2293 0.729690 GCGAATGCTCACCTTCTTCC 59.270 55.000 0.00 0.00 38.39 3.46
2131 2294 0.729690 GGCGAATGCTCACCTTCTTC 59.270 55.000 0.00 0.00 42.25 2.87
2132 2295 1.021390 CGGCGAATGCTCACCTTCTT 61.021 55.000 0.00 0.00 42.25 2.52
2133 2296 1.448540 CGGCGAATGCTCACCTTCT 60.449 57.895 0.00 0.00 42.25 2.85
2134 2297 1.741770 ACGGCGAATGCTCACCTTC 60.742 57.895 16.62 0.00 42.25 3.46
2135 2298 2.034879 CACGGCGAATGCTCACCTT 61.035 57.895 16.62 0.00 42.25 3.50
2136 2299 2.434884 CACGGCGAATGCTCACCT 60.435 61.111 16.62 0.00 42.25 4.00
2137 2300 2.434185 TCACGGCGAATGCTCACC 60.434 61.111 16.62 0.00 42.25 4.02
2138 2301 2.456119 CCTCACGGCGAATGCTCAC 61.456 63.158 16.62 0.00 42.25 3.51
2139 2302 2.125552 CCTCACGGCGAATGCTCA 60.126 61.111 16.62 0.00 42.25 4.26
2140 2303 1.880340 CTCCTCACGGCGAATGCTC 60.880 63.158 16.62 0.00 42.25 4.26
2141 2304 2.185350 CTCCTCACGGCGAATGCT 59.815 61.111 16.62 0.00 42.25 3.79
2142 2305 2.125512 ACTCCTCACGGCGAATGC 60.126 61.111 16.62 0.00 41.71 3.56
2143 2306 0.108615 AAGACTCCTCACGGCGAATG 60.109 55.000 16.62 1.50 0.00 2.67
2144 2307 0.108615 CAAGACTCCTCACGGCGAAT 60.109 55.000 16.62 0.00 0.00 3.34
2145 2308 1.289066 CAAGACTCCTCACGGCGAA 59.711 57.895 16.62 0.00 0.00 4.70
2146 2309 1.461091 AACAAGACTCCTCACGGCGA 61.461 55.000 16.62 0.00 0.00 5.54
2147 2310 1.006102 AACAAGACTCCTCACGGCG 60.006 57.895 4.80 4.80 0.00 6.46
2148 2311 0.951040 CCAACAAGACTCCTCACGGC 60.951 60.000 0.00 0.00 0.00 5.68
2149 2312 0.320771 CCCAACAAGACTCCTCACGG 60.321 60.000 0.00 0.00 0.00 4.94
2150 2313 0.320771 CCCCAACAAGACTCCTCACG 60.321 60.000 0.00 0.00 0.00 4.35
2151 2314 0.606673 GCCCCAACAAGACTCCTCAC 60.607 60.000 0.00 0.00 0.00 3.51
2152 2315 1.761174 GCCCCAACAAGACTCCTCA 59.239 57.895 0.00 0.00 0.00 3.86
2153 2316 1.002011 GGCCCCAACAAGACTCCTC 60.002 63.158 0.00 0.00 0.00 3.71
2154 2317 2.539081 GGGCCCCAACAAGACTCCT 61.539 63.158 12.23 0.00 0.00 3.69
2155 2318 2.035783 GGGCCCCAACAAGACTCC 59.964 66.667 12.23 0.00 0.00 3.85
2156 2319 2.359975 CGGGCCCCAACAAGACTC 60.360 66.667 18.66 0.00 0.00 3.36
2157 2320 3.966543 CCGGGCCCCAACAAGACT 61.967 66.667 18.66 0.00 0.00 3.24
2168 2331 4.162009 TACCCTAGTCCCCGGGCC 62.162 72.222 17.73 7.78 44.63 5.80
2169 2332 2.523657 CTACCCTAGTCCCCGGGC 60.524 72.222 17.73 1.34 44.63 6.13
2170 2333 2.200650 CCTACCCTAGTCCCCGGG 59.799 72.222 15.80 15.80 46.26 5.73
2171 2334 2.523657 GCCTACCCTAGTCCCCGG 60.524 72.222 0.00 0.00 0.00 5.73
2172 2335 2.910994 CGCCTACCCTAGTCCCCG 60.911 72.222 0.00 0.00 0.00 5.73
2173 2336 3.232483 GCGCCTACCCTAGTCCCC 61.232 72.222 0.00 0.00 0.00 4.81
2174 2337 2.123382 AGCGCCTACCCTAGTCCC 60.123 66.667 2.29 0.00 0.00 4.46
2175 2338 2.553727 CGAGCGCCTACCCTAGTCC 61.554 68.421 2.29 0.00 0.00 3.85
2176 2339 1.525535 TCGAGCGCCTACCCTAGTC 60.526 63.158 2.29 0.00 0.00 2.59
2177 2340 1.823041 GTCGAGCGCCTACCCTAGT 60.823 63.158 2.29 0.00 0.00 2.57
2178 2341 2.894565 CGTCGAGCGCCTACCCTAG 61.895 68.421 2.29 0.00 0.00 3.02
2179 2342 2.874648 TTCGTCGAGCGCCTACCCTA 62.875 60.000 2.29 0.00 41.07 3.53
2180 2343 4.790962 TCGTCGAGCGCCTACCCT 62.791 66.667 2.29 0.00 41.07 4.34
2181 2344 2.624437 AATTCGTCGAGCGCCTACCC 62.624 60.000 2.29 0.00 41.07 3.69
2182 2345 0.029834 TAATTCGTCGAGCGCCTACC 59.970 55.000 2.29 0.00 41.07 3.18
2183 2346 1.268437 ACTAATTCGTCGAGCGCCTAC 60.268 52.381 2.29 0.00 41.07 3.18
2184 2347 1.019673 ACTAATTCGTCGAGCGCCTA 58.980 50.000 2.29 0.00 41.07 3.93
2185 2348 0.172803 AACTAATTCGTCGAGCGCCT 59.827 50.000 2.29 0.00 41.07 5.52
2186 2349 1.779724 CTAACTAATTCGTCGAGCGCC 59.220 52.381 2.29 0.00 41.07 6.53
2187 2350 1.187487 GCTAACTAATTCGTCGAGCGC 59.813 52.381 0.00 0.00 41.07 5.92
2188 2351 1.443540 CGCTAACTAATTCGTCGAGCG 59.556 52.381 18.54 18.54 40.46 5.03
2189 2352 1.187487 GCGCTAACTAATTCGTCGAGC 59.813 52.381 0.00 6.81 0.00 5.03
2190 2353 2.717530 AGCGCTAACTAATTCGTCGAG 58.282 47.619 8.99 0.00 0.00 4.04
2191 2354 2.838386 AGCGCTAACTAATTCGTCGA 57.162 45.000 8.99 0.00 0.00 4.20
2192 2355 3.357021 TGTAGCGCTAACTAATTCGTCG 58.643 45.455 20.73 0.00 0.00 5.12
2193 2356 3.729716 CCTGTAGCGCTAACTAATTCGTC 59.270 47.826 20.73 2.90 0.00 4.20
2194 2357 3.129988 ACCTGTAGCGCTAACTAATTCGT 59.870 43.478 20.73 4.18 0.00 3.85
2195 2358 3.703420 ACCTGTAGCGCTAACTAATTCG 58.297 45.455 20.73 3.55 0.00 3.34
2196 2359 5.634020 CCATACCTGTAGCGCTAACTAATTC 59.366 44.000 20.73 5.29 0.00 2.17
2197 2360 5.070047 ACCATACCTGTAGCGCTAACTAATT 59.930 40.000 20.73 4.29 0.00 1.40
2198 2361 4.587684 ACCATACCTGTAGCGCTAACTAAT 59.412 41.667 20.73 6.71 0.00 1.73
2199 2362 3.956199 ACCATACCTGTAGCGCTAACTAA 59.044 43.478 20.73 4.43 0.00 2.24
2200 2363 3.559069 ACCATACCTGTAGCGCTAACTA 58.441 45.455 20.73 7.89 0.00 2.24
2201 2364 2.361438 GACCATACCTGTAGCGCTAACT 59.639 50.000 20.73 4.21 0.00 2.24
2202 2365 2.740452 GACCATACCTGTAGCGCTAAC 58.260 52.381 20.73 13.83 0.00 2.34
2203 2366 1.335810 CGACCATACCTGTAGCGCTAA 59.664 52.381 20.73 2.95 0.00 3.09
2204 2367 0.949397 CGACCATACCTGTAGCGCTA 59.051 55.000 14.45 14.45 0.00 4.26
2205 2368 0.750546 TCGACCATACCTGTAGCGCT 60.751 55.000 17.26 17.26 0.00 5.92
2206 2369 0.314302 ATCGACCATACCTGTAGCGC 59.686 55.000 0.00 0.00 0.00 5.92
2207 2370 3.190744 ACATATCGACCATACCTGTAGCG 59.809 47.826 0.00 0.00 0.00 4.26
2208 2371 4.785511 ACATATCGACCATACCTGTAGC 57.214 45.455 0.00 0.00 0.00 3.58
2209 2372 5.944599 AGGTACATATCGACCATACCTGTAG 59.055 44.000 15.23 0.00 43.19 2.74
2210 2373 5.884322 AGGTACATATCGACCATACCTGTA 58.116 41.667 15.23 2.47 43.19 2.74
2211 2374 4.737578 AGGTACATATCGACCATACCTGT 58.262 43.478 15.23 3.24 43.19 4.00
2212 2375 5.243060 TGAAGGTACATATCGACCATACCTG 59.757 44.000 16.21 0.00 43.88 4.00
2213 2376 5.391256 TGAAGGTACATATCGACCATACCT 58.609 41.667 11.76 11.76 46.06 3.08
2214 2377 5.717078 TGAAGGTACATATCGACCATACC 57.283 43.478 8.32 8.32 38.27 2.73
2215 2378 6.028368 CGATGAAGGTACATATCGACCATAC 58.972 44.000 6.82 0.00 43.60 2.39
2216 2379 5.124936 CCGATGAAGGTACATATCGACCATA 59.875 44.000 12.84 0.00 43.60 2.74
2217 2380 4.082190 CCGATGAAGGTACATATCGACCAT 60.082 45.833 12.84 0.00 43.60 3.55
2218 2381 3.254903 CCGATGAAGGTACATATCGACCA 59.745 47.826 12.84 0.00 43.60 4.02
2219 2382 3.504906 TCCGATGAAGGTACATATCGACC 59.495 47.826 12.84 0.00 43.60 4.79
2220 2383 4.761235 TCCGATGAAGGTACATATCGAC 57.239 45.455 12.84 0.00 43.60 4.20
2221 2384 7.457024 TTTATCCGATGAAGGTACATATCGA 57.543 36.000 12.84 0.00 43.60 3.59
2222 2385 7.973944 TGATTTATCCGATGAAGGTACATATCG 59.026 37.037 5.85 5.85 41.35 2.92
2223 2386 9.823647 ATGATTTATCCGATGAAGGTACATATC 57.176 33.333 0.00 0.00 0.00 1.63
2226 2389 8.041323 GGTATGATTTATCCGATGAAGGTACAT 58.959 37.037 0.00 0.00 0.00 2.29
2227 2390 7.383687 GGTATGATTTATCCGATGAAGGTACA 58.616 38.462 0.00 0.00 0.00 2.90
2228 2391 6.530534 CGGTATGATTTATCCGATGAAGGTAC 59.469 42.308 0.00 0.00 44.86 3.34
2229 2392 6.209986 ACGGTATGATTTATCCGATGAAGGTA 59.790 38.462 9.37 0.00 44.86 3.08
2230 2393 5.011738 ACGGTATGATTTATCCGATGAAGGT 59.988 40.000 9.37 0.00 44.86 3.50
2231 2394 5.348724 CACGGTATGATTTATCCGATGAAGG 59.651 44.000 9.37 0.00 44.86 3.46
2232 2395 5.163953 GCACGGTATGATTTATCCGATGAAG 60.164 44.000 9.37 0.00 44.86 3.02
2233 2396 4.688879 GCACGGTATGATTTATCCGATGAA 59.311 41.667 9.37 0.00 44.86 2.57
2234 2397 4.242475 GCACGGTATGATTTATCCGATGA 58.758 43.478 9.37 0.00 44.86 2.92
2235 2398 3.993736 TGCACGGTATGATTTATCCGATG 59.006 43.478 9.37 5.37 44.86 3.84
2236 2399 4.265904 TGCACGGTATGATTTATCCGAT 57.734 40.909 9.37 0.00 44.86 4.18
2237 2400 3.737032 TGCACGGTATGATTTATCCGA 57.263 42.857 9.37 0.00 44.86 4.55
2238 2401 3.125146 CCATGCACGGTATGATTTATCCG 59.875 47.826 0.00 0.00 46.98 4.18
2239 2402 3.119849 GCCATGCACGGTATGATTTATCC 60.120 47.826 0.00 0.00 0.00 2.59
2240 2403 3.501828 TGCCATGCACGGTATGATTTATC 59.498 43.478 0.00 0.00 31.71 1.75
2241 2404 3.485394 TGCCATGCACGGTATGATTTAT 58.515 40.909 0.00 0.00 31.71 1.40
2242 2405 2.924421 TGCCATGCACGGTATGATTTA 58.076 42.857 0.00 0.00 31.71 1.40
2243 2406 1.761449 TGCCATGCACGGTATGATTT 58.239 45.000 0.00 0.00 31.71 2.17
2244 2407 3.493028 TGCCATGCACGGTATGATT 57.507 47.368 0.00 0.00 31.71 2.57
2255 2418 3.751246 ATGTGCCACGTGCCATGC 61.751 61.111 10.91 8.91 40.16 4.06
2256 2419 2.179767 CATGTGCCACGTGCCATG 59.820 61.111 19.65 19.65 40.10 3.66
2257 2420 2.842188 ATCCATGTGCCACGTGCCAT 62.842 55.000 10.91 8.81 40.16 4.40
2258 2421 3.565961 ATCCATGTGCCACGTGCCA 62.566 57.895 10.91 1.16 40.16 4.92
2259 2422 1.876497 AAATCCATGTGCCACGTGCC 61.876 55.000 10.91 0.00 40.16 5.01
2260 2423 0.808125 TAAATCCATGTGCCACGTGC 59.192 50.000 10.91 6.53 41.77 5.34
2261 2424 4.789481 GCTTATAAATCCATGTGCCACGTG 60.789 45.833 9.08 9.08 34.96 4.49
2262 2425 3.315191 GCTTATAAATCCATGTGCCACGT 59.685 43.478 0.00 0.00 0.00 4.49
2263 2426 3.304659 GGCTTATAAATCCATGTGCCACG 60.305 47.826 0.00 0.00 38.99 4.94
2264 2427 3.304659 CGGCTTATAAATCCATGTGCCAC 60.305 47.826 8.35 0.00 39.09 5.01
2265 2428 2.884012 CGGCTTATAAATCCATGTGCCA 59.116 45.455 8.35 0.00 39.09 4.92
2266 2429 2.884639 ACGGCTTATAAATCCATGTGCC 59.115 45.455 0.00 0.00 36.14 5.01
2267 2430 4.513692 TGTACGGCTTATAAATCCATGTGC 59.486 41.667 0.00 0.00 0.00 4.57
2268 2431 6.612247 TTGTACGGCTTATAAATCCATGTG 57.388 37.500 0.00 0.00 0.00 3.21
2269 2432 7.817418 AATTGTACGGCTTATAAATCCATGT 57.183 32.000 0.00 0.00 0.00 3.21
2270 2433 8.967218 CAAAATTGTACGGCTTATAAATCCATG 58.033 33.333 4.80 0.00 0.00 3.66
2271 2434 8.908903 TCAAAATTGTACGGCTTATAAATCCAT 58.091 29.630 4.80 0.00 0.00 3.41
2272 2435 8.282455 TCAAAATTGTACGGCTTATAAATCCA 57.718 30.769 4.80 0.00 0.00 3.41
2273 2436 8.617809 TCTCAAAATTGTACGGCTTATAAATCC 58.382 33.333 0.00 0.00 0.00 3.01
2274 2437 9.997482 TTCTCAAAATTGTACGGCTTATAAATC 57.003 29.630 0.00 0.00 0.00 2.17
2277 2440 9.834628 CTTTTCTCAAAATTGTACGGCTTATAA 57.165 29.630 0.00 0.00 0.00 0.98
2278 2441 9.005777 ACTTTTCTCAAAATTGTACGGCTTATA 57.994 29.630 0.00 0.00 0.00 0.98
2279 2442 7.882179 ACTTTTCTCAAAATTGTACGGCTTAT 58.118 30.769 0.00 0.00 0.00 1.73
2280 2443 7.266922 ACTTTTCTCAAAATTGTACGGCTTA 57.733 32.000 0.00 0.00 0.00 3.09
2281 2444 6.144078 ACTTTTCTCAAAATTGTACGGCTT 57.856 33.333 0.00 0.00 0.00 4.35
2282 2445 5.767816 ACTTTTCTCAAAATTGTACGGCT 57.232 34.783 0.00 0.00 0.00 5.52
2283 2446 7.858879 TCTTTACTTTTCTCAAAATTGTACGGC 59.141 33.333 0.00 0.00 0.00 5.68
2284 2447 9.382244 CTCTTTACTTTTCTCAAAATTGTACGG 57.618 33.333 0.00 0.00 0.00 4.02
2315 2478 9.457436 GGGTTCACCAAGTAATAAATTCTCTAA 57.543 33.333 0.00 0.00 39.85 2.10
2316 2479 8.832735 AGGGTTCACCAAGTAATAAATTCTCTA 58.167 33.333 0.00 0.00 43.89 2.43
2317 2480 7.699878 AGGGTTCACCAAGTAATAAATTCTCT 58.300 34.615 0.00 0.00 43.89 3.10
2318 2481 7.939784 AGGGTTCACCAAGTAATAAATTCTC 57.060 36.000 0.00 0.00 43.89 2.87
2324 2487 9.895138 GTTTCTATAGGGTTCACCAAGTAATAA 57.105 33.333 0.00 0.00 43.89 1.40
2325 2488 9.275572 AGTTTCTATAGGGTTCACCAAGTAATA 57.724 33.333 0.00 0.00 43.89 0.98
2326 2489 8.159229 AGTTTCTATAGGGTTCACCAAGTAAT 57.841 34.615 0.00 0.00 43.89 1.89
2327 2490 7.563724 AGTTTCTATAGGGTTCACCAAGTAA 57.436 36.000 0.00 0.00 43.89 2.24
2328 2491 8.117956 TCTAGTTTCTATAGGGTTCACCAAGTA 58.882 37.037 0.00 0.00 43.89 2.24
2329 2492 6.958192 TCTAGTTTCTATAGGGTTCACCAAGT 59.042 38.462 0.00 0.00 43.89 3.16
2330 2493 7.419711 TCTAGTTTCTATAGGGTTCACCAAG 57.580 40.000 0.00 0.00 43.89 3.61
2331 2494 7.676893 TCTTCTAGTTTCTATAGGGTTCACCAA 59.323 37.037 0.00 0.00 43.89 3.67
2332 2495 7.123847 GTCTTCTAGTTTCTATAGGGTTCACCA 59.876 40.741 0.00 0.00 43.89 4.17
2333 2496 7.342541 AGTCTTCTAGTTTCTATAGGGTTCACC 59.657 40.741 0.00 0.00 40.67 4.02
2334 2497 8.296211 AGTCTTCTAGTTTCTATAGGGTTCAC 57.704 38.462 0.00 0.00 0.00 3.18
2335 2498 8.896722 AAGTCTTCTAGTTTCTATAGGGTTCA 57.103 34.615 0.00 0.00 0.00 3.18
2336 2499 8.968969 TGAAGTCTTCTAGTTTCTATAGGGTTC 58.031 37.037 13.67 0.00 0.00 3.62
2337 2500 8.896722 TGAAGTCTTCTAGTTTCTATAGGGTT 57.103 34.615 13.67 0.00 0.00 4.11
2338 2501 8.896722 TTGAAGTCTTCTAGTTTCTATAGGGT 57.103 34.615 13.67 0.00 0.00 4.34
2343 2506 9.832445 TGTGTTTTGAAGTCTTCTAGTTTCTAT 57.168 29.630 13.67 0.00 0.00 1.98
2344 2507 9.661563 TTGTGTTTTGAAGTCTTCTAGTTTCTA 57.338 29.630 13.67 0.00 0.00 2.10
2345 2508 8.561738 TTGTGTTTTGAAGTCTTCTAGTTTCT 57.438 30.769 13.67 0.00 0.00 2.52
2346 2509 9.620660 TTTTGTGTTTTGAAGTCTTCTAGTTTC 57.379 29.630 13.67 2.30 0.00 2.78
2348 2511 9.573133 CATTTTGTGTTTTGAAGTCTTCTAGTT 57.427 29.630 13.67 0.00 0.00 2.24
2349 2512 8.739972 ACATTTTGTGTTTTGAAGTCTTCTAGT 58.260 29.630 13.67 0.00 38.01 2.57
2355 2518 9.868277 TGAATTACATTTTGTGTTTTGAAGTCT 57.132 25.926 0.00 0.00 42.29 3.24
2383 2546 9.198475 ACTTGTTGGTATACTAGCAGTACTATT 57.802 33.333 5.94 0.00 37.49 1.73
2384 2547 8.763984 ACTTGTTGGTATACTAGCAGTACTAT 57.236 34.615 5.94 0.00 37.49 2.12
2385 2548 9.685276 TTACTTGTTGGTATACTAGCAGTACTA 57.315 33.333 5.94 0.00 37.49 1.82
2386 2549 8.465201 GTTACTTGTTGGTATACTAGCAGTACT 58.535 37.037 5.94 0.00 37.49 2.73
2387 2550 8.465201 AGTTACTTGTTGGTATACTAGCAGTAC 58.535 37.037 5.94 4.20 37.49 2.73
2388 2551 8.585471 AGTTACTTGTTGGTATACTAGCAGTA 57.415 34.615 5.94 8.05 37.49 2.74
2389 2552 7.477945 AGTTACTTGTTGGTATACTAGCAGT 57.522 36.000 5.94 8.83 37.49 4.40
2390 2553 8.251721 AGAAGTTACTTGTTGGTATACTAGCAG 58.748 37.037 0.93 4.13 37.49 4.24
2391 2554 8.130671 AGAAGTTACTTGTTGGTATACTAGCA 57.869 34.615 0.93 1.57 0.00 3.49
2392 2555 8.999220 AAGAAGTTACTTGTTGGTATACTAGC 57.001 34.615 6.70 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.