Multiple sequence alignment - TraesCS7D01G405600

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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 TraesCS7D01G405600 chr7D 100.000 2621 0 0 1 2621 523049918 523052538 0.000000e+00 4841.0
1 TraesCS7D01G405600 chr7A 91.698 1048 48 19 756 1769 603313000 603314042 0.000000e+00 1417.0
2 TraesCS7D01G405600 chr7A 91.586 309 23 3 434 741 603312631 603312937 8.670000e-115 424.0
3 TraesCS7D01G405600 chr7A 88.953 344 17 12 1764 2107 603314317 603314639 3.140000e-109 405.0
4 TraesCS7D01G405600 chr7A 87.288 236 27 3 1 236 603312416 603312648 1.550000e-67 267.0
5 TraesCS7D01G405600 chr7A 91.713 181 10 5 2282 2459 603325474 603325652 2.010000e-61 246.0
6 TraesCS7D01G405600 chr7B 90.383 1019 85 12 6 1013 557151581 557152597 0.000000e+00 1327.0
7 TraesCS7D01G405600 chr7B 87.564 981 49 16 1015 1949 557170314 557171267 0.000000e+00 1068.0
8 TraesCS7D01G405600 chr7B 93.506 77 3 2 1939 2013 557172518 557172594 2.130000e-21 113.0
9 TraesCS7D01G405600 chr3B 87.805 82 7 2 2108 2186 122824969 122825050 2.780000e-15 93.5
10 TraesCS7D01G405600 chr5A 87.719 57 7 0 2113 2169 671166502 671166558 1.680000e-07 67.6


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 TraesCS7D01G405600 chr7D 523049918 523052538 2620 False 4841.00 4841 100.00000 1 2621 1 chr7D.!!$F1 2620
1 TraesCS7D01G405600 chr7A 603312416 603314639 2223 False 628.25 1417 89.88125 1 2107 4 chr7A.!!$F2 2106
2 TraesCS7D01G405600 chr7B 557151581 557152597 1016 False 1327.00 1327 90.38300 6 1013 1 chr7B.!!$F1 1007
3 TraesCS7D01G405600 chr7B 557170314 557172594 2280 False 590.50 1068 90.53500 1015 2013 2 chr7B.!!$F2 998

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
640 652 1.13428 CCCCTAACTGCCACTCAGATG 60.134 57.143 0.0 0.0 45.72 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 2274 0.036732 AGCCAGGCGAACAATCTTCA 59.963 50.0 5.55 0.0 0.0 3.02 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
53 54 8.164070 ACTTTGTTATGGAGTATTTCAGGAACT 58.836 33.333 0.00 0.00 43.88 3.01
62 63 6.183309 AGTATTTCAGGAACTTCATTTCGC 57.817 37.500 0.00 0.00 34.60 4.70
85 86 5.580297 GCTTGAGAGATAGTGGAGTTTCTTG 59.420 44.000 0.00 0.00 0.00 3.02
105 106 7.326968 TCTTGTTTCAACATGTACATCAACA 57.673 32.000 5.07 7.52 38.95 3.33
292 294 7.778470 TTAACTTTTGGAAAATGCACGAAAT 57.222 28.000 0.00 0.00 0.00 2.17
297 299 6.761731 TTTGGAAAATGCACGAAATACTTG 57.238 33.333 0.00 0.00 0.00 3.16
304 306 9.123709 GAAAATGCACGAAATACTTGAATTACA 57.876 29.630 0.00 0.00 27.84 2.41
507 517 5.464389 GCACATGAATGGCTGGAATATTTTC 59.536 40.000 0.00 0.00 0.00 2.29
519 529 8.994170 GGCTGGAATATTTTCTAGACATACTTC 58.006 37.037 12.38 0.00 45.38 3.01
583 594 7.284034 CAGCAGTATATCTTTTCAGGATTTGGT 59.716 37.037 0.00 0.00 0.00 3.67
638 650 1.553690 GCCCCTAACTGCCACTCAGA 61.554 60.000 0.00 0.00 45.72 3.27
639 651 1.207791 CCCCTAACTGCCACTCAGAT 58.792 55.000 0.00 0.00 45.72 2.90
640 652 1.134280 CCCCTAACTGCCACTCAGATG 60.134 57.143 0.00 0.00 45.72 2.90
641 653 1.556911 CCCTAACTGCCACTCAGATGT 59.443 52.381 0.00 0.00 45.72 3.06
765 825 1.505425 ACGGTTAACAAAGTCGAGCC 58.495 50.000 8.10 0.00 0.00 4.70
848 908 1.613925 CGGAGTCAGTGAAAGTCAGGA 59.386 52.381 0.00 0.00 0.00 3.86
1008 1077 0.036732 AGCATTCCCTCACGCAAGAA 59.963 50.000 0.00 0.00 43.62 2.52
1026 1098 3.274288 AGAAAGCGGCTTCCTAATCTTG 58.726 45.455 16.70 0.00 0.00 3.02
1031 1103 2.555199 CGGCTTCCTAATCTTGTGAGG 58.445 52.381 0.00 0.00 0.00 3.86
1036 1108 3.895232 TCCTAATCTTGTGAGGCTGAC 57.105 47.619 0.00 0.00 0.00 3.51
1462 1543 1.909302 CCCCTGGTCACTAGTGTTGAT 59.091 52.381 21.99 0.00 0.00 2.57
1519 1600 1.216710 GCGTGAGAACAGCCTAGCT 59.783 57.895 0.00 0.00 40.77 3.32
1554 1641 2.365582 TCCAAGTCGATCGATCTGACA 58.634 47.619 32.18 19.58 34.84 3.58
1636 1728 3.619929 ACGTCCCTGTTAATTAATCGTGC 59.380 43.478 0.31 0.00 0.00 5.34
1721 1818 1.807139 ATCTGTATGTGTTGCACGCA 58.193 45.000 5.26 5.26 43.36 5.24
1722 1819 1.587547 TCTGTATGTGTTGCACGCAA 58.412 45.000 0.00 0.00 42.39 4.85
1724 1821 2.043411 CTGTATGTGTTGCACGCAAAC 58.957 47.619 5.94 7.85 42.39 2.93
1729 1854 2.341257 TGTGTTGCACGCAAACAAATT 58.659 38.095 5.94 0.00 35.42 1.82
1731 1856 2.602660 GTGTTGCACGCAAACAAATTCT 59.397 40.909 5.94 0.00 37.70 2.40
1743 1868 7.276658 ACGCAAACAAATTCTGTGTTTTTGATA 59.723 29.630 4.37 0.00 44.73 2.15
1856 2265 1.261619 GATTCGGCATTTCGGCTACAG 59.738 52.381 0.00 0.00 38.27 2.74
1857 2266 1.366111 TTCGGCATTTCGGCTACAGC 61.366 55.000 0.00 0.00 38.27 4.40
1858 2267 2.709475 GGCATTTCGGCTACAGCG 59.291 61.111 0.00 0.00 43.26 5.18
1860 2269 1.366111 GGCATTTCGGCTACAGCGAA 61.366 55.000 0.00 0.00 43.26 4.70
1861 2270 0.247695 GCATTTCGGCTACAGCGAAC 60.248 55.000 7.63 0.00 43.26 3.95
1864 2273 3.636313 TTCGGCTACAGCGAACGGG 62.636 63.158 0.00 0.00 43.26 5.28
1865 2274 4.430765 CGGCTACAGCGAACGGGT 62.431 66.667 0.00 0.00 43.26 5.28
1873 2282 2.840974 AGCGAACGGGTGAAGATTG 58.159 52.632 0.00 0.00 0.00 2.67
1874 2283 0.034896 AGCGAACGGGTGAAGATTGT 59.965 50.000 0.00 0.00 0.00 2.71
1875 2284 0.872388 GCGAACGGGTGAAGATTGTT 59.128 50.000 0.00 0.00 0.00 2.83
1876 2285 1.136057 GCGAACGGGTGAAGATTGTTC 60.136 52.381 0.00 0.00 36.47 3.18
1877 2286 2.875080 GAACGGGTGAAGATTGTTCG 57.125 50.000 0.00 0.00 30.87 3.95
1878 2287 0.872388 AACGGGTGAAGATTGTTCGC 59.128 50.000 0.00 0.00 0.00 4.70
1879 2288 0.953960 ACGGGTGAAGATTGTTCGCC 60.954 55.000 15.83 15.83 45.72 5.54
1880 2289 0.673644 CGGGTGAAGATTGTTCGCCT 60.674 55.000 21.40 0.00 45.73 5.52
1881 2290 0.804989 GGGTGAAGATTGTTCGCCTG 59.195 55.000 21.40 0.00 45.73 4.85
1882 2291 0.804989 GGTGAAGATTGTTCGCCTGG 59.195 55.000 16.63 0.00 43.73 4.45
1883 2292 0.169009 GTGAAGATTGTTCGCCTGGC 59.831 55.000 9.11 9.11 0.00 4.85
1919 2328 7.317842 TCTATTTTCGTGTCCTACAGTCTAG 57.682 40.000 0.00 0.00 0.00 2.43
2044 3716 0.378962 TGTTCTTCGTTGTTTGGCCG 59.621 50.000 0.00 0.00 0.00 6.13
2046 3718 0.464013 TTCTTCGTTGTTTGGCCGGA 60.464 50.000 5.05 0.00 0.00 5.14
2116 3788 8.760103 CAAATAATTGGATTGACATTGTGTCA 57.240 30.769 8.59 8.59 42.73 3.58
2140 3812 9.747898 TCAAATATTGACTACTAATTGGTTGGT 57.252 29.630 0.00 0.00 34.08 3.67
2146 3818 9.747898 ATTGACTACTAATTGGTTGGTTATCAA 57.252 29.630 0.00 4.94 36.66 2.57
2147 3819 8.786826 TGACTACTAATTGGTTGGTTATCAAG 57.213 34.615 0.00 0.00 35.80 3.02
2148 3820 8.380099 TGACTACTAATTGGTTGGTTATCAAGT 58.620 33.333 0.00 0.00 35.80 3.16
2149 3821 9.227777 GACTACTAATTGGTTGGTTATCAAGTT 57.772 33.333 0.00 0.00 35.80 2.66
2150 3822 9.010029 ACTACTAATTGGTTGGTTATCAAGTTG 57.990 33.333 0.00 0.00 35.80 3.16
2151 3823 7.833285 ACTAATTGGTTGGTTATCAAGTTGT 57.167 32.000 2.11 0.00 35.80 3.32
2152 3824 8.245195 ACTAATTGGTTGGTTATCAAGTTGTT 57.755 30.769 2.11 0.00 35.80 2.83
2153 3825 8.700973 ACTAATTGGTTGGTTATCAAGTTGTTT 58.299 29.630 2.11 0.00 35.80 2.83
2154 3826 9.541143 CTAATTGGTTGGTTATCAAGTTGTTTT 57.459 29.630 2.11 0.00 35.80 2.43
2155 3827 7.784633 ATTGGTTGGTTATCAAGTTGTTTTG 57.215 32.000 2.11 0.00 35.80 2.44
2156 3828 6.287589 TGGTTGGTTATCAAGTTGTTTTGT 57.712 33.333 2.11 0.00 35.80 2.83
2157 3829 6.334202 TGGTTGGTTATCAAGTTGTTTTGTC 58.666 36.000 2.11 0.00 35.80 3.18
2158 3830 6.153680 TGGTTGGTTATCAAGTTGTTTTGTCT 59.846 34.615 2.11 0.00 35.80 3.41
2159 3831 7.339721 TGGTTGGTTATCAAGTTGTTTTGTCTA 59.660 33.333 2.11 0.00 35.80 2.59
2160 3832 8.357402 GGTTGGTTATCAAGTTGTTTTGTCTAT 58.643 33.333 2.11 0.00 35.80 1.98
2161 3833 9.394477 GTTGGTTATCAAGTTGTTTTGTCTATC 57.606 33.333 2.11 0.00 35.80 2.08
2162 3834 8.918202 TGGTTATCAAGTTGTTTTGTCTATCT 57.082 30.769 2.11 0.00 0.00 1.98
2163 3835 8.999431 TGGTTATCAAGTTGTTTTGTCTATCTC 58.001 33.333 2.11 0.00 0.00 2.75
2164 3836 8.999431 GGTTATCAAGTTGTTTTGTCTATCTCA 58.001 33.333 2.11 0.00 0.00 3.27
2203 3875 6.317789 TGACAATGCCAATATTTAGCTAGC 57.682 37.500 6.62 6.62 0.00 3.42
2204 3876 5.241506 TGACAATGCCAATATTTAGCTAGCC 59.758 40.000 12.13 0.00 0.00 3.93
2205 3877 5.139727 ACAATGCCAATATTTAGCTAGCCA 58.860 37.500 12.13 0.00 0.00 4.75
2206 3878 5.598005 ACAATGCCAATATTTAGCTAGCCAA 59.402 36.000 12.13 0.00 0.00 4.52
2207 3879 6.098124 ACAATGCCAATATTTAGCTAGCCAAA 59.902 34.615 12.13 11.38 0.00 3.28
2208 3880 6.923199 ATGCCAATATTTAGCTAGCCAAAT 57.077 33.333 21.96 21.96 0.00 2.32
2209 3881 8.306038 CAATGCCAATATTTAGCTAGCCAAATA 58.694 33.333 24.30 24.30 32.68 1.40
2210 3882 8.599624 ATGCCAATATTTAGCTAGCCAAATAT 57.400 30.769 25.98 25.98 38.40 1.28
2211 3883 8.421249 TGCCAATATTTAGCTAGCCAAATATT 57.579 30.769 31.34 31.34 43.26 1.28
2219 3891 8.553459 TTTAGCTAGCCAAATATTGATAGCTC 57.447 34.615 21.91 5.02 45.04 4.09
2220 3892 6.119240 AGCTAGCCAAATATTGATAGCTCA 57.881 37.500 15.93 0.00 45.04 4.26
2221 3893 6.719301 AGCTAGCCAAATATTGATAGCTCAT 58.281 36.000 15.93 0.62 45.04 2.90
2222 3894 6.598457 AGCTAGCCAAATATTGATAGCTCATG 59.402 38.462 15.93 0.00 45.04 3.07
2223 3895 5.640189 AGCCAAATATTGATAGCTCATGC 57.360 39.130 0.00 0.00 40.05 4.06
2239 3911 2.811317 GCTCGAAGTGCTCCACCG 60.811 66.667 0.00 0.00 44.39 4.94
2240 3912 2.651361 CTCGAAGTGCTCCACCGT 59.349 61.111 0.00 0.00 34.49 4.83
2241 3913 1.734477 CTCGAAGTGCTCCACCGTG 60.734 63.158 0.00 0.00 34.49 4.94
2242 3914 3.414700 CGAAGTGCTCCACCGTGC 61.415 66.667 0.00 0.00 34.49 5.34
2243 3915 3.414700 GAAGTGCTCCACCGTGCG 61.415 66.667 0.00 0.00 34.49 5.34
2244 3916 3.858868 GAAGTGCTCCACCGTGCGA 62.859 63.158 0.00 0.00 34.49 5.10
2245 3917 3.865929 AAGTGCTCCACCGTGCGAG 62.866 63.158 10.88 10.88 34.49 5.03
2249 3921 4.457496 CTCCACCGTGCGAGGCAT 62.457 66.667 8.42 0.00 41.91 4.40
2250 3922 3.958147 CTCCACCGTGCGAGGCATT 62.958 63.158 8.42 0.00 41.91 3.56
2251 3923 3.803082 CCACCGTGCGAGGCATTG 61.803 66.667 0.00 0.00 41.91 2.82
2252 3924 2.741985 CACCGTGCGAGGCATTGA 60.742 61.111 0.00 0.00 41.91 2.57
2253 3925 2.434884 ACCGTGCGAGGCATTGAG 60.435 61.111 0.00 0.00 41.91 3.02
2254 3926 2.434884 CCGTGCGAGGCATTGAGT 60.435 61.111 0.00 0.00 41.91 3.41
2255 3927 2.743752 CCGTGCGAGGCATTGAGTG 61.744 63.158 0.00 0.00 41.91 3.51
2256 3928 2.029288 CGTGCGAGGCATTGAGTGT 61.029 57.895 0.00 0.00 41.91 3.55
2257 3929 1.790387 GTGCGAGGCATTGAGTGTC 59.210 57.895 0.00 0.00 41.91 3.67
2258 3930 1.375908 TGCGAGGCATTGAGTGTCC 60.376 57.895 0.00 0.00 31.71 4.02
2259 3931 2.456119 GCGAGGCATTGAGTGTCCG 61.456 63.158 0.00 0.00 30.86 4.79
2260 3932 2.456119 CGAGGCATTGAGTGTCCGC 61.456 63.158 0.00 0.00 30.86 5.54
2261 3933 2.045926 AGGCATTGAGTGTCCGCC 60.046 61.111 0.00 0.00 43.31 6.13
2262 3934 2.359850 GGCATTGAGTGTCCGCCA 60.360 61.111 0.00 0.00 42.50 5.69
2263 3935 1.750399 GGCATTGAGTGTCCGCCAT 60.750 57.895 0.00 0.00 42.50 4.40
2264 3936 1.718757 GGCATTGAGTGTCCGCCATC 61.719 60.000 0.00 0.00 42.50 3.51
2265 3937 2.009108 CATTGAGTGTCCGCCATCG 58.991 57.895 0.00 0.00 0.00 3.84
2275 3947 3.869272 CGCCATCGGTCTTGCTGC 61.869 66.667 0.00 0.00 0.00 5.25
2276 3948 3.512516 GCCATCGGTCTTGCTGCC 61.513 66.667 0.00 0.00 0.00 4.85
2281 3953 3.960237 CGGTCTTGCTGCCGTTTA 58.040 55.556 0.00 0.00 42.73 2.01
2282 3954 1.787847 CGGTCTTGCTGCCGTTTAG 59.212 57.895 0.00 0.00 42.73 1.85
2283 3955 0.949105 CGGTCTTGCTGCCGTTTAGT 60.949 55.000 0.00 0.00 42.73 2.24
2284 3956 1.670674 CGGTCTTGCTGCCGTTTAGTA 60.671 52.381 0.00 0.00 42.73 1.82
2285 3957 1.730612 GGTCTTGCTGCCGTTTAGTAC 59.269 52.381 0.00 0.00 0.00 2.73
2286 3958 2.612221 GGTCTTGCTGCCGTTTAGTACT 60.612 50.000 0.00 0.00 0.00 2.73
2287 3959 3.367703 GGTCTTGCTGCCGTTTAGTACTA 60.368 47.826 0.00 0.00 0.00 1.82
2288 3960 4.430908 GTCTTGCTGCCGTTTAGTACTAT 58.569 43.478 2.79 0.00 0.00 2.12
2289 3961 4.503370 GTCTTGCTGCCGTTTAGTACTATC 59.497 45.833 2.79 0.00 0.00 2.08
2290 3962 4.401519 TCTTGCTGCCGTTTAGTACTATCT 59.598 41.667 2.79 0.00 0.00 1.98
2291 3963 4.730949 TGCTGCCGTTTAGTACTATCTT 57.269 40.909 2.79 0.00 0.00 2.40
2292 3964 5.840243 TGCTGCCGTTTAGTACTATCTTA 57.160 39.130 2.79 0.00 0.00 2.10
2293 3965 5.828747 TGCTGCCGTTTAGTACTATCTTAG 58.171 41.667 2.79 0.11 0.00 2.18
2294 3966 4.680567 GCTGCCGTTTAGTACTATCTTAGC 59.319 45.833 2.79 6.12 0.00 3.09
2295 3967 4.852138 TGCCGTTTAGTACTATCTTAGCG 58.148 43.478 2.79 2.68 0.00 4.26
2296 3968 4.225208 GCCGTTTAGTACTATCTTAGCGG 58.775 47.826 18.13 18.13 41.29 5.52
2297 3969 4.023707 GCCGTTTAGTACTATCTTAGCGGA 60.024 45.833 23.66 0.00 41.02 5.54
2298 3970 5.335504 GCCGTTTAGTACTATCTTAGCGGAT 60.336 44.000 23.66 0.00 41.02 4.18
2299 3971 6.313252 CCGTTTAGTACTATCTTAGCGGATC 58.687 44.000 17.77 0.00 41.02 3.36
2300 3972 6.313252 CGTTTAGTACTATCTTAGCGGATCC 58.687 44.000 2.79 0.00 0.00 3.36
2301 3973 6.313252 GTTTAGTACTATCTTAGCGGATCCG 58.687 44.000 30.03 30.03 43.09 4.18
2313 3985 1.096416 CGGATCCGCTAGAGATACCC 58.904 60.000 23.37 0.00 0.00 3.69
2314 3986 1.340211 CGGATCCGCTAGAGATACCCT 60.340 57.143 23.37 0.00 0.00 4.34
2315 3987 2.371306 GGATCCGCTAGAGATACCCTC 58.629 57.143 0.00 0.00 42.28 4.30
2316 3988 2.291024 GGATCCGCTAGAGATACCCTCA 60.291 54.545 0.00 0.00 44.40 3.86
2317 3989 3.422796 GATCCGCTAGAGATACCCTCAA 58.577 50.000 0.00 0.00 44.40 3.02
2318 3990 3.308035 TCCGCTAGAGATACCCTCAAA 57.692 47.619 0.00 0.00 44.40 2.69
2319 3991 2.957006 TCCGCTAGAGATACCCTCAAAC 59.043 50.000 0.00 0.00 44.40 2.93
2320 3992 2.693591 CCGCTAGAGATACCCTCAAACA 59.306 50.000 0.00 0.00 44.40 2.83
2321 3993 3.491104 CCGCTAGAGATACCCTCAAACAC 60.491 52.174 0.00 0.00 44.40 3.32
2322 3994 3.381908 CGCTAGAGATACCCTCAAACACT 59.618 47.826 0.00 0.00 44.40 3.55
2323 3995 4.579340 CGCTAGAGATACCCTCAAACACTA 59.421 45.833 0.00 0.00 44.40 2.74
2324 3996 5.067413 CGCTAGAGATACCCTCAAACACTAA 59.933 44.000 0.00 0.00 44.40 2.24
2325 3997 6.405508 CGCTAGAGATACCCTCAAACACTAAA 60.406 42.308 0.00 0.00 44.40 1.85
2326 3998 6.981559 GCTAGAGATACCCTCAAACACTAAAG 59.018 42.308 0.00 0.00 44.40 1.85
2327 3999 7.147880 GCTAGAGATACCCTCAAACACTAAAGA 60.148 40.741 0.00 0.00 44.40 2.52
2328 4000 6.937392 AGAGATACCCTCAAACACTAAAGAC 58.063 40.000 0.00 0.00 44.40 3.01
2329 4001 6.497259 AGAGATACCCTCAAACACTAAAGACA 59.503 38.462 0.00 0.00 44.40 3.41
2330 4002 6.465084 AGATACCCTCAAACACTAAAGACAC 58.535 40.000 0.00 0.00 0.00 3.67
2331 4003 4.497291 ACCCTCAAACACTAAAGACACA 57.503 40.909 0.00 0.00 0.00 3.72
2332 4004 4.850680 ACCCTCAAACACTAAAGACACAA 58.149 39.130 0.00 0.00 0.00 3.33
2333 4005 5.445964 ACCCTCAAACACTAAAGACACAAT 58.554 37.500 0.00 0.00 0.00 2.71
2334 4006 5.299279 ACCCTCAAACACTAAAGACACAATG 59.701 40.000 0.00 0.00 0.00 2.82
2335 4007 5.299279 CCCTCAAACACTAAAGACACAATGT 59.701 40.000 0.00 0.00 0.00 2.71
2336 4008 6.183360 CCCTCAAACACTAAAGACACAATGTT 60.183 38.462 0.00 0.00 31.82 2.71
2337 4009 7.012894 CCCTCAAACACTAAAGACACAATGTTA 59.987 37.037 0.00 0.00 30.40 2.41
2338 4010 7.855904 CCTCAAACACTAAAGACACAATGTTAC 59.144 37.037 0.00 0.00 30.40 2.50
2339 4011 8.270080 TCAAACACTAAAGACACAATGTTACA 57.730 30.769 0.00 0.00 30.40 2.41
2340 4012 8.898761 TCAAACACTAAAGACACAATGTTACAT 58.101 29.630 0.00 0.00 30.40 2.29
2388 4060 5.490139 AATATGTGGATCAAAACTGCTCG 57.510 39.130 0.00 0.00 0.00 5.03
2389 4061 0.874390 TGTGGATCAAAACTGCTCGC 59.126 50.000 0.00 0.00 0.00 5.03
2390 4062 0.169009 GTGGATCAAAACTGCTCGCC 59.831 55.000 0.00 0.00 0.00 5.54
2391 4063 0.036732 TGGATCAAAACTGCTCGCCT 59.963 50.000 0.00 0.00 0.00 5.52
2392 4064 0.449388 GGATCAAAACTGCTCGCCTG 59.551 55.000 0.00 0.00 0.00 4.85
2393 4065 1.442769 GATCAAAACTGCTCGCCTGA 58.557 50.000 0.00 0.00 0.00 3.86
2394 4066 1.129437 GATCAAAACTGCTCGCCTGAC 59.871 52.381 0.00 0.00 0.00 3.51
2395 4067 0.106708 TCAAAACTGCTCGCCTGACT 59.893 50.000 0.00 0.00 0.00 3.41
2396 4068 0.947244 CAAAACTGCTCGCCTGACTT 59.053 50.000 0.00 0.00 0.00 3.01
2397 4069 1.334869 CAAAACTGCTCGCCTGACTTT 59.665 47.619 0.00 0.00 0.00 2.66
2398 4070 1.680338 AAACTGCTCGCCTGACTTTT 58.320 45.000 0.00 0.00 0.00 2.27
2399 4071 0.947244 AACTGCTCGCCTGACTTTTG 59.053 50.000 0.00 0.00 0.00 2.44
2400 4072 0.886490 ACTGCTCGCCTGACTTTTGG 60.886 55.000 0.00 0.00 0.00 3.28
2401 4073 0.886490 CTGCTCGCCTGACTTTTGGT 60.886 55.000 0.00 0.00 0.00 3.67
2402 4074 0.465460 TGCTCGCCTGACTTTTGGTT 60.465 50.000 0.00 0.00 0.00 3.67
2403 4075 0.238553 GCTCGCCTGACTTTTGGTTC 59.761 55.000 0.00 0.00 0.00 3.62
2404 4076 0.512952 CTCGCCTGACTTTTGGTTCG 59.487 55.000 0.00 0.00 0.00 3.95
2405 4077 1.082104 CGCCTGACTTTTGGTTCGC 60.082 57.895 0.00 0.00 0.00 4.70
2406 4078 1.507141 CGCCTGACTTTTGGTTCGCT 61.507 55.000 0.00 0.00 0.00 4.93
2407 4079 0.668535 GCCTGACTTTTGGTTCGCTT 59.331 50.000 0.00 0.00 0.00 4.68
2408 4080 1.067060 GCCTGACTTTTGGTTCGCTTT 59.933 47.619 0.00 0.00 0.00 3.51
2409 4081 2.858646 GCCTGACTTTTGGTTCGCTTTC 60.859 50.000 0.00 0.00 0.00 2.62
2410 4082 2.618709 CCTGACTTTTGGTTCGCTTTCT 59.381 45.455 0.00 0.00 0.00 2.52
2411 4083 3.304057 CCTGACTTTTGGTTCGCTTTCTC 60.304 47.826 0.00 0.00 0.00 2.87
2412 4084 3.275143 TGACTTTTGGTTCGCTTTCTCA 58.725 40.909 0.00 0.00 0.00 3.27
2413 4085 3.882888 TGACTTTTGGTTCGCTTTCTCAT 59.117 39.130 0.00 0.00 0.00 2.90
2414 4086 4.338118 TGACTTTTGGTTCGCTTTCTCATT 59.662 37.500 0.00 0.00 0.00 2.57
2415 4087 5.163561 TGACTTTTGGTTCGCTTTCTCATTT 60.164 36.000 0.00 0.00 0.00 2.32
2416 4088 5.660460 ACTTTTGGTTCGCTTTCTCATTTT 58.340 33.333 0.00 0.00 0.00 1.82
2417 4089 5.748630 ACTTTTGGTTCGCTTTCTCATTTTC 59.251 36.000 0.00 0.00 0.00 2.29
2418 4090 4.909696 TTGGTTCGCTTTCTCATTTTCA 57.090 36.364 0.00 0.00 0.00 2.69
2419 4091 5.452078 TTGGTTCGCTTTCTCATTTTCAT 57.548 34.783 0.00 0.00 0.00 2.57
2420 4092 5.452078 TGGTTCGCTTTCTCATTTTCATT 57.548 34.783 0.00 0.00 0.00 2.57
2421 4093 5.841810 TGGTTCGCTTTCTCATTTTCATTT 58.158 33.333 0.00 0.00 0.00 2.32
2422 4094 6.279882 TGGTTCGCTTTCTCATTTTCATTTT 58.720 32.000 0.00 0.00 0.00 1.82
2423 4095 6.760770 TGGTTCGCTTTCTCATTTTCATTTTT 59.239 30.769 0.00 0.00 0.00 1.94
2482 4154 9.872757 TTTATGAACACTTAAATTCGTGAACTC 57.127 29.630 8.82 4.44 35.23 3.01
2483 4155 7.730364 ATGAACACTTAAATTCGTGAACTCT 57.270 32.000 8.82 0.00 35.23 3.24
2484 4156 7.548196 TGAACACTTAAATTCGTGAACTCTT 57.452 32.000 8.82 0.00 35.23 2.85
2485 4157 8.651391 TGAACACTTAAATTCGTGAACTCTTA 57.349 30.769 8.82 0.00 35.23 2.10
2486 4158 8.761497 TGAACACTTAAATTCGTGAACTCTTAG 58.239 33.333 8.82 0.00 35.23 2.18
2487 4159 7.118422 ACACTTAAATTCGTGAACTCTTAGC 57.882 36.000 8.82 0.00 35.23 3.09
2488 4160 6.704493 ACACTTAAATTCGTGAACTCTTAGCA 59.296 34.615 8.82 0.00 35.23 3.49
2489 4161 7.225931 ACACTTAAATTCGTGAACTCTTAGCAA 59.774 33.333 8.82 0.00 35.23 3.91
2490 4162 8.067784 CACTTAAATTCGTGAACTCTTAGCAAA 58.932 33.333 0.00 0.00 33.04 3.68
2491 4163 8.784043 ACTTAAATTCGTGAACTCTTAGCAAAT 58.216 29.630 0.00 0.00 0.00 2.32
2492 4164 9.612620 CTTAAATTCGTGAACTCTTAGCAAATT 57.387 29.630 0.00 0.00 0.00 1.82
2493 4165 9.607285 TTAAATTCGTGAACTCTTAGCAAATTC 57.393 29.630 0.00 0.00 0.00 2.17
2494 4166 6.801539 ATTCGTGAACTCTTAGCAAATTCA 57.198 33.333 0.00 0.00 0.00 2.57
2495 4167 5.591643 TCGTGAACTCTTAGCAAATTCAC 57.408 39.130 5.53 5.53 43.62 3.18
2496 4168 5.053811 TCGTGAACTCTTAGCAAATTCACA 58.946 37.500 13.91 1.48 46.09 3.58
2497 4169 5.525745 TCGTGAACTCTTAGCAAATTCACAA 59.474 36.000 13.91 0.00 46.09 3.33
2498 4170 6.037720 TCGTGAACTCTTAGCAAATTCACAAA 59.962 34.615 13.91 1.26 46.09 2.83
2499 4171 6.690957 CGTGAACTCTTAGCAAATTCACAAAA 59.309 34.615 13.91 0.00 46.09 2.44
2500 4172 7.379529 CGTGAACTCTTAGCAAATTCACAAAAT 59.620 33.333 13.91 0.00 46.09 1.82
2501 4173 9.677567 GTGAACTCTTAGCAAATTCACAAAATA 57.322 29.630 9.84 0.00 45.43 1.40
2578 4250 8.758633 TTTTTGATTTAACCAACTTCGTCAAA 57.241 26.923 0.00 0.00 33.88 2.69
2579 4251 7.743520 TTTGATTTAACCAACTTCGTCAAAC 57.256 32.000 0.00 0.00 31.62 2.93
2580 4252 5.823353 TGATTTAACCAACTTCGTCAAACC 58.177 37.500 0.00 0.00 0.00 3.27
2581 4253 5.357314 TGATTTAACCAACTTCGTCAAACCA 59.643 36.000 0.00 0.00 0.00 3.67
2582 4254 4.619437 TTAACCAACTTCGTCAAACCAC 57.381 40.909 0.00 0.00 0.00 4.16
2583 4255 1.385528 ACCAACTTCGTCAAACCACC 58.614 50.000 0.00 0.00 0.00 4.61
2584 4256 1.340211 ACCAACTTCGTCAAACCACCA 60.340 47.619 0.00 0.00 0.00 4.17
2585 4257 1.746220 CCAACTTCGTCAAACCACCAA 59.254 47.619 0.00 0.00 0.00 3.67
2586 4258 2.223479 CCAACTTCGTCAAACCACCAAG 60.223 50.000 0.00 0.00 0.00 3.61
2587 4259 2.680841 CAACTTCGTCAAACCACCAAGA 59.319 45.455 0.00 0.00 0.00 3.02
2588 4260 2.993937 ACTTCGTCAAACCACCAAGAA 58.006 42.857 0.00 0.00 0.00 2.52
2589 4261 3.349022 ACTTCGTCAAACCACCAAGAAA 58.651 40.909 0.00 0.00 0.00 2.52
2590 4262 3.759618 ACTTCGTCAAACCACCAAGAAAA 59.240 39.130 0.00 0.00 0.00 2.29
2591 4263 4.401202 ACTTCGTCAAACCACCAAGAAAAT 59.599 37.500 0.00 0.00 0.00 1.82
2592 4264 5.591067 ACTTCGTCAAACCACCAAGAAAATA 59.409 36.000 0.00 0.00 0.00 1.40
2593 4265 6.264518 ACTTCGTCAAACCACCAAGAAAATAT 59.735 34.615 0.00 0.00 0.00 1.28
2594 4266 7.446013 ACTTCGTCAAACCACCAAGAAAATATA 59.554 33.333 0.00 0.00 0.00 0.86
2595 4267 7.372451 TCGTCAAACCACCAAGAAAATATAG 57.628 36.000 0.00 0.00 0.00 1.31
2596 4268 6.027749 CGTCAAACCACCAAGAAAATATAGC 58.972 40.000 0.00 0.00 0.00 2.97
2597 4269 6.330278 GTCAAACCACCAAGAAAATATAGCC 58.670 40.000 0.00 0.00 0.00 3.93
2598 4270 5.124776 TCAAACCACCAAGAAAATATAGCCG 59.875 40.000 0.00 0.00 0.00 5.52
2599 4271 3.551846 ACCACCAAGAAAATATAGCCGG 58.448 45.455 0.00 0.00 0.00 6.13
2600 4272 3.053917 ACCACCAAGAAAATATAGCCGGT 60.054 43.478 1.90 0.00 0.00 5.28
2601 4273 3.951680 CCACCAAGAAAATATAGCCGGTT 59.048 43.478 1.90 0.00 0.00 4.44
2602 4274 4.401202 CCACCAAGAAAATATAGCCGGTTT 59.599 41.667 1.90 0.00 0.00 3.27
2603 4275 5.105513 CCACCAAGAAAATATAGCCGGTTTT 60.106 40.000 1.90 0.60 0.00 2.43
2604 4276 6.394809 CACCAAGAAAATATAGCCGGTTTTT 58.605 36.000 1.90 2.23 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 6.092807 AGCGAAATGAAGTTCCTGAAATACTC 59.907 38.462 0.00 0.00 0.00 2.59
41 42 6.429692 TCAAGCGAAATGAAGTTCCTGAAATA 59.570 34.615 0.00 0.00 0.00 1.40
43 44 4.578516 TCAAGCGAAATGAAGTTCCTGAAA 59.421 37.500 0.00 0.00 0.00 2.69
53 54 5.105351 TCCACTATCTCTCAAGCGAAATGAA 60.105 40.000 0.00 0.00 0.00 2.57
62 63 6.696411 ACAAGAAACTCCACTATCTCTCAAG 58.304 40.000 0.00 0.00 0.00 3.02
85 86 5.920273 CCCTTGTTGATGTACATGTTGAAAC 59.080 40.000 14.43 9.88 0.00 2.78
105 106 2.113139 CAAGCCACCGACACCCTT 59.887 61.111 0.00 0.00 0.00 3.95
276 278 5.697473 TCAAGTATTTCGTGCATTTTCCA 57.303 34.783 0.00 0.00 0.00 3.53
277 279 7.581011 AATTCAAGTATTTCGTGCATTTTCC 57.419 32.000 0.00 0.00 0.00 3.13
278 280 9.123709 TGTAATTCAAGTATTTCGTGCATTTTC 57.876 29.630 0.00 0.00 0.00 2.29
285 287 9.882996 ATATGCATGTAATTCAAGTATTTCGTG 57.117 29.630 10.16 0.00 0.00 4.35
626 637 1.001746 CAGTCACATCTGAGTGGCAGT 59.998 52.381 12.17 0.00 46.23 4.40
637 649 3.319137 TCCAACTGCTACAGTCACATC 57.681 47.619 0.00 0.00 44.62 3.06
638 650 3.988976 ATCCAACTGCTACAGTCACAT 57.011 42.857 0.00 0.00 44.62 3.21
639 651 3.402110 CAATCCAACTGCTACAGTCACA 58.598 45.455 0.00 0.00 44.62 3.58
640 652 2.744202 CCAATCCAACTGCTACAGTCAC 59.256 50.000 0.00 0.00 44.62 3.67
641 653 2.290260 CCCAATCCAACTGCTACAGTCA 60.290 50.000 0.00 0.00 44.62 3.41
765 825 2.407090 TGCATATCCGCGAGATCTTTG 58.593 47.619 8.23 8.79 36.33 2.77
848 908 0.107897 TGCCCGTGCACGAAGATATT 60.108 50.000 39.10 0.00 44.23 1.28
1008 1077 2.027192 TCACAAGATTAGGAAGCCGCTT 60.027 45.455 4.98 4.98 0.00 4.68
1018 1090 3.902881 AGGTCAGCCTCACAAGATTAG 57.097 47.619 0.00 0.00 42.67 1.73
1026 1098 2.010582 CTCGCCTAGGTCAGCCTCAC 62.011 65.000 11.31 0.00 45.64 3.51
1031 1103 2.415426 GCTCTCGCCTAGGTCAGC 59.585 66.667 11.31 8.94 0.00 4.26
1051 1123 1.424638 TCCCACCCATAGCTCTAAGC 58.575 55.000 0.00 0.00 42.84 3.09
1090 1162 0.547712 CTCCTCCTCCCTTTCCACCA 60.548 60.000 0.00 0.00 0.00 4.17
1462 1543 8.892723 CATTATTGGAGTAGCTACAAACATTGA 58.107 33.333 25.28 13.20 37.88 2.57
1554 1641 3.857052 TGCATTGCGTTACTAGCTAACT 58.143 40.909 3.84 0.00 33.64 2.24
1636 1728 1.577328 ATCTGGAAAACCAGCACGCG 61.577 55.000 3.53 3.53 37.69 6.01
1698 1795 3.980775 GCGTGCAACACATACAGATTTTT 59.019 39.130 0.00 0.00 35.74 1.94
1702 1799 1.807139 TGCGTGCAACACATACAGAT 58.193 45.000 0.00 0.00 35.74 2.90
1716 1813 4.838665 AAACACAGAATTTGTTTGCGTG 57.161 36.364 6.04 0.00 43.84 5.34
1717 1814 5.406780 TCAAAAACACAGAATTTGTTTGCGT 59.593 32.000 7.35 0.00 44.56 5.24
1719 1816 8.816144 TCTATCAAAAACACAGAATTTGTTTGC 58.184 29.630 7.35 0.00 44.56 3.68
1722 1819 9.533253 CCTTCTATCAAAAACACAGAATTTGTT 57.467 29.630 0.00 0.00 38.16 2.83
1724 1821 7.148918 CGCCTTCTATCAAAAACACAGAATTTG 60.149 37.037 0.00 0.00 35.81 2.32
1729 1854 4.637276 TCGCCTTCTATCAAAAACACAGA 58.363 39.130 0.00 0.00 0.00 3.41
1731 1856 5.335583 CCATTCGCCTTCTATCAAAAACACA 60.336 40.000 0.00 0.00 0.00 3.72
1743 1868 1.195115 TACAGAGCCATTCGCCTTCT 58.805 50.000 0.00 0.00 38.78 2.85
1805 2214 1.283793 CGCCAGCTTCACAACCTTG 59.716 57.895 0.00 0.00 0.00 3.61
1856 2265 0.872388 AACAATCTTCACCCGTTCGC 59.128 50.000 0.00 0.00 0.00 4.70
1857 2266 2.875080 GAACAATCTTCACCCGTTCG 57.125 50.000 0.00 0.00 0.00 3.95
1858 2267 1.136057 GCGAACAATCTTCACCCGTTC 60.136 52.381 0.00 0.00 34.10 3.95
1860 2269 0.953960 GGCGAACAATCTTCACCCGT 60.954 55.000 0.00 0.00 0.00 5.28
1861 2270 0.673644 AGGCGAACAATCTTCACCCG 60.674 55.000 0.00 0.00 0.00 5.28
1864 2273 0.169009 GCCAGGCGAACAATCTTCAC 59.831 55.000 0.00 0.00 0.00 3.18
1865 2274 0.036732 AGCCAGGCGAACAATCTTCA 59.963 50.000 5.55 0.00 0.00 3.02
1866 2275 1.135575 CAAGCCAGGCGAACAATCTTC 60.136 52.381 5.55 0.00 0.00 2.87
1867 2276 0.883833 CAAGCCAGGCGAACAATCTT 59.116 50.000 5.55 0.00 0.00 2.40
1868 2277 1.589716 GCAAGCCAGGCGAACAATCT 61.590 55.000 5.55 0.00 0.00 2.40
1869 2278 1.153958 GCAAGCCAGGCGAACAATC 60.154 57.895 5.55 0.00 0.00 2.67
1870 2279 1.604593 AGCAAGCCAGGCGAACAAT 60.605 52.632 5.55 0.00 36.08 2.71
1871 2280 2.203337 AGCAAGCCAGGCGAACAA 60.203 55.556 5.55 0.00 36.08 2.83
1872 2281 2.979676 CAGCAAGCCAGGCGAACA 60.980 61.111 5.55 0.00 36.08 3.18
1873 2282 3.741476 CCAGCAAGCCAGGCGAAC 61.741 66.667 5.55 0.00 36.08 3.95
1874 2283 3.790416 AACCAGCAAGCCAGGCGAA 62.790 57.895 5.55 0.00 36.08 4.70
1875 2284 4.269523 AACCAGCAAGCCAGGCGA 62.270 61.111 5.55 0.00 36.08 5.54
1876 2285 4.047059 CAACCAGCAAGCCAGGCG 62.047 66.667 5.55 0.00 36.08 5.52
1877 2286 2.426122 GAACAACCAGCAAGCCAGGC 62.426 60.000 1.84 1.84 0.00 4.85
1878 2287 0.825010 AGAACAACCAGCAAGCCAGG 60.825 55.000 0.20 0.20 0.00 4.45
1879 2288 1.896220 TAGAACAACCAGCAAGCCAG 58.104 50.000 0.00 0.00 0.00 4.85
1880 2289 2.584835 ATAGAACAACCAGCAAGCCA 57.415 45.000 0.00 0.00 0.00 4.75
1881 2290 3.942130 AAATAGAACAACCAGCAAGCC 57.058 42.857 0.00 0.00 0.00 4.35
1882 2291 3.914364 CGAAAATAGAACAACCAGCAAGC 59.086 43.478 0.00 0.00 0.00 4.01
1883 2292 4.911610 CACGAAAATAGAACAACCAGCAAG 59.088 41.667 0.00 0.00 0.00 4.01
1919 2328 5.460091 GCTCAGAACAACAGAATTTTTGGAC 59.540 40.000 0.00 0.00 0.00 4.02
2062 3734 1.942657 CCATGCTTGTAGATGAACCCG 59.057 52.381 0.00 0.00 0.00 5.28
2065 3737 4.458989 TCAAACCCATGCTTGTAGATGAAC 59.541 41.667 0.00 0.00 0.00 3.18
2114 3786 9.747898 ACCAACCAATTAGTAGTCAATATTTGA 57.252 29.630 0.00 0.00 37.33 2.69
2120 3792 9.747898 TTGATAACCAACCAATTAGTAGTCAAT 57.252 29.630 0.00 0.00 0.00 2.57
2121 3793 9.226606 CTTGATAACCAACCAATTAGTAGTCAA 57.773 33.333 0.00 0.00 0.00 3.18
2122 3794 8.380099 ACTTGATAACCAACCAATTAGTAGTCA 58.620 33.333 0.00 0.00 0.00 3.41
2123 3795 8.788325 ACTTGATAACCAACCAATTAGTAGTC 57.212 34.615 0.00 0.00 0.00 2.59
2124 3796 9.010029 CAACTTGATAACCAACCAATTAGTAGT 57.990 33.333 0.00 0.00 0.00 2.73
2125 3797 9.010029 ACAACTTGATAACCAACCAATTAGTAG 57.990 33.333 0.00 0.00 0.00 2.57
2126 3798 8.927675 ACAACTTGATAACCAACCAATTAGTA 57.072 30.769 0.00 0.00 0.00 1.82
2127 3799 7.833285 ACAACTTGATAACCAACCAATTAGT 57.167 32.000 0.00 0.00 0.00 2.24
2128 3800 9.541143 AAAACAACTTGATAACCAACCAATTAG 57.459 29.630 0.00 0.00 0.00 1.73
2129 3801 9.319143 CAAAACAACTTGATAACCAACCAATTA 57.681 29.630 0.00 0.00 0.00 1.40
2130 3802 7.826744 ACAAAACAACTTGATAACCAACCAATT 59.173 29.630 0.00 0.00 0.00 2.32
2131 3803 7.334858 ACAAAACAACTTGATAACCAACCAAT 58.665 30.769 0.00 0.00 0.00 3.16
2132 3804 6.702329 ACAAAACAACTTGATAACCAACCAA 58.298 32.000 0.00 0.00 0.00 3.67
2133 3805 6.153680 AGACAAAACAACTTGATAACCAACCA 59.846 34.615 0.00 0.00 0.00 3.67
2134 3806 6.569780 AGACAAAACAACTTGATAACCAACC 58.430 36.000 0.00 0.00 0.00 3.77
2135 3807 9.394477 GATAGACAAAACAACTTGATAACCAAC 57.606 33.333 0.00 0.00 0.00 3.77
2136 3808 9.349713 AGATAGACAAAACAACTTGATAACCAA 57.650 29.630 0.00 0.00 0.00 3.67
2137 3809 8.918202 AGATAGACAAAACAACTTGATAACCA 57.082 30.769 0.00 0.00 0.00 3.67
2138 3810 8.999431 TGAGATAGACAAAACAACTTGATAACC 58.001 33.333 0.00 0.00 0.00 2.85
2177 3849 7.869429 GCTAGCTAAATATTGGCATTGTCAAAT 59.131 33.333 7.91 0.90 39.92 2.32
2178 3850 7.202526 GCTAGCTAAATATTGGCATTGTCAAA 58.797 34.615 7.91 0.00 39.92 2.69
2179 3851 6.239008 GGCTAGCTAAATATTGGCATTGTCAA 60.239 38.462 15.72 6.09 39.92 3.18
2180 3852 5.241506 GGCTAGCTAAATATTGGCATTGTCA 59.758 40.000 15.72 0.00 39.92 3.58
2181 3853 5.241506 TGGCTAGCTAAATATTGGCATTGTC 59.758 40.000 15.72 7.09 39.92 3.18
2182 3854 5.139727 TGGCTAGCTAAATATTGGCATTGT 58.860 37.500 15.72 0.00 39.92 2.71
2183 3855 5.710513 TGGCTAGCTAAATATTGGCATTG 57.289 39.130 15.72 6.42 39.92 2.82
2184 3856 6.729690 TTTGGCTAGCTAAATATTGGCATT 57.270 33.333 20.96 0.00 39.92 3.56
2185 3857 6.923199 ATTTGGCTAGCTAAATATTGGCAT 57.077 33.333 30.78 10.98 39.92 4.40
2193 3865 9.171877 GAGCTATCAATATTTGGCTAGCTAAAT 57.828 33.333 32.93 32.93 44.77 1.40
2194 3866 8.156820 TGAGCTATCAATATTTGGCTAGCTAAA 58.843 33.333 25.87 25.87 44.77 1.85
2195 3867 7.679783 TGAGCTATCAATATTTGGCTAGCTAA 58.320 34.615 15.72 12.74 44.77 3.09
2196 3868 7.244886 TGAGCTATCAATATTTGGCTAGCTA 57.755 36.000 15.72 5.44 44.77 3.32
2197 3869 6.119240 TGAGCTATCAATATTTGGCTAGCT 57.881 37.500 15.72 17.43 46.04 3.32
2198 3870 6.677431 GCATGAGCTATCAATATTTGGCTAGC 60.677 42.308 6.04 6.04 39.39 3.42
2199 3871 6.783162 GCATGAGCTATCAATATTTGGCTAG 58.217 40.000 0.00 0.00 39.39 3.42
2200 3872 6.748333 GCATGAGCTATCAATATTTGGCTA 57.252 37.500 0.00 0.00 39.39 3.93
2201 3873 5.640189 GCATGAGCTATCAATATTTGGCT 57.360 39.130 0.00 0.00 39.39 4.75
2216 3888 1.427592 GGAGCACTTCGAGCATGAGC 61.428 60.000 0.00 0.00 42.56 4.26
2217 3889 0.108472 TGGAGCACTTCGAGCATGAG 60.108 55.000 0.00 0.00 0.00 2.90
2218 3890 0.390340 GTGGAGCACTTCGAGCATGA 60.390 55.000 0.00 0.00 0.00 3.07
2219 3891 1.364626 GGTGGAGCACTTCGAGCATG 61.365 60.000 0.00 0.00 34.40 4.06
2220 3892 1.078848 GGTGGAGCACTTCGAGCAT 60.079 57.895 0.00 0.00 34.40 3.79
2221 3893 2.343758 GGTGGAGCACTTCGAGCA 59.656 61.111 0.00 0.00 34.40 4.26
2222 3894 2.811317 CGGTGGAGCACTTCGAGC 60.811 66.667 0.00 0.00 34.40 5.03
2223 3895 1.734477 CACGGTGGAGCACTTCGAG 60.734 63.158 0.00 0.00 34.40 4.04
2224 3896 2.338620 CACGGTGGAGCACTTCGA 59.661 61.111 0.00 0.00 34.40 3.71
2225 3897 3.414700 GCACGGTGGAGCACTTCG 61.415 66.667 10.60 0.00 34.40 3.79
2226 3898 3.414700 CGCACGGTGGAGCACTTC 61.415 66.667 10.60 0.00 34.40 3.01
2227 3899 3.865929 CTCGCACGGTGGAGCACTT 62.866 63.158 10.60 0.00 34.40 3.16
2228 3900 4.363990 CTCGCACGGTGGAGCACT 62.364 66.667 10.60 0.00 34.40 4.40
2232 3904 3.958147 AATGCCTCGCACGGTGGAG 62.958 63.158 10.60 13.60 43.04 3.86
2233 3905 4.015406 AATGCCTCGCACGGTGGA 62.015 61.111 10.60 4.83 43.04 4.02
2234 3906 3.803082 CAATGCCTCGCACGGTGG 61.803 66.667 10.60 0.26 43.04 4.61
2235 3907 2.741985 TCAATGCCTCGCACGGTG 60.742 61.111 3.15 3.15 43.04 4.94
2236 3908 2.434884 CTCAATGCCTCGCACGGT 60.435 61.111 0.00 0.00 43.04 4.83
2237 3909 2.434884 ACTCAATGCCTCGCACGG 60.435 61.111 0.00 0.00 43.04 4.94
2238 3910 1.959899 GACACTCAATGCCTCGCACG 61.960 60.000 0.00 0.00 43.04 5.34
2239 3911 1.639298 GGACACTCAATGCCTCGCAC 61.639 60.000 0.00 0.00 43.04 5.34
2240 3912 1.375908 GGACACTCAATGCCTCGCA 60.376 57.895 0.00 0.00 44.86 5.10
2241 3913 2.456119 CGGACACTCAATGCCTCGC 61.456 63.158 0.00 0.00 0.00 5.03
2242 3914 2.456119 GCGGACACTCAATGCCTCG 61.456 63.158 0.00 0.00 0.00 4.63
2243 3915 2.109126 GGCGGACACTCAATGCCTC 61.109 63.158 0.00 0.00 42.44 4.70
2244 3916 2.045926 GGCGGACACTCAATGCCT 60.046 61.111 0.00 0.00 42.44 4.75
2245 3917 1.718757 GATGGCGGACACTCAATGCC 61.719 60.000 0.00 0.00 45.91 4.40
2246 3918 1.723870 GATGGCGGACACTCAATGC 59.276 57.895 0.00 0.00 0.00 3.56
2247 3919 2.009108 CGATGGCGGACACTCAATG 58.991 57.895 0.00 0.00 0.00 2.82
2248 3920 4.521075 CGATGGCGGACACTCAAT 57.479 55.556 0.00 0.00 0.00 2.57
2258 3930 3.869272 GCAGCAAGACCGATGGCG 61.869 66.667 0.00 0.00 37.24 5.69
2259 3931 3.512516 GGCAGCAAGACCGATGGC 61.513 66.667 0.00 0.00 40.79 4.40
2265 3937 1.730612 GTACTAAACGGCAGCAAGACC 59.269 52.381 0.00 0.00 0.00 3.85
2266 3938 2.685100 AGTACTAAACGGCAGCAAGAC 58.315 47.619 0.00 0.00 0.00 3.01
2267 3939 4.401519 AGATAGTACTAAACGGCAGCAAGA 59.598 41.667 6.70 0.00 0.00 3.02
2268 3940 4.683832 AGATAGTACTAAACGGCAGCAAG 58.316 43.478 6.70 0.00 0.00 4.01
2269 3941 4.730949 AGATAGTACTAAACGGCAGCAA 57.269 40.909 6.70 0.00 0.00 3.91
2270 3942 4.730949 AAGATAGTACTAAACGGCAGCA 57.269 40.909 6.70 0.00 0.00 4.41
2271 3943 4.680567 GCTAAGATAGTACTAAACGGCAGC 59.319 45.833 6.70 7.58 0.00 5.25
2272 3944 4.910456 CGCTAAGATAGTACTAAACGGCAG 59.090 45.833 6.70 1.61 0.00 4.85
2273 3945 4.261322 CCGCTAAGATAGTACTAAACGGCA 60.261 45.833 6.70 0.00 0.00 5.69
2274 3946 4.023707 TCCGCTAAGATAGTACTAAACGGC 60.024 45.833 6.70 7.30 36.91 5.68
2275 3947 5.679734 TCCGCTAAGATAGTACTAAACGG 57.320 43.478 6.70 12.95 38.27 4.44
2276 3948 6.313252 GGATCCGCTAAGATAGTACTAAACG 58.687 44.000 6.70 4.92 0.00 3.60
2277 3949 6.313252 CGGATCCGCTAAGATAGTACTAAAC 58.687 44.000 23.37 4.64 0.00 2.01
2278 3950 6.492007 CGGATCCGCTAAGATAGTACTAAA 57.508 41.667 23.37 0.00 0.00 1.85
2294 3966 1.096416 GGGTATCTCTAGCGGATCCG 58.904 60.000 30.03 30.03 43.09 4.18
2295 3967 2.291024 TGAGGGTATCTCTAGCGGATCC 60.291 54.545 0.00 0.00 42.86 3.36
2296 3968 3.074675 TGAGGGTATCTCTAGCGGATC 57.925 52.381 2.14 0.00 42.86 3.36
2297 3969 3.527507 TTGAGGGTATCTCTAGCGGAT 57.472 47.619 4.06 4.06 42.86 4.18
2298 3970 2.957006 GTTTGAGGGTATCTCTAGCGGA 59.043 50.000 0.00 0.00 42.86 5.54
2299 3971 2.693591 TGTTTGAGGGTATCTCTAGCGG 59.306 50.000 0.00 0.00 42.86 5.52
2300 3972 3.381908 AGTGTTTGAGGGTATCTCTAGCG 59.618 47.826 0.00 0.00 42.86 4.26
2301 3973 6.466885 TTAGTGTTTGAGGGTATCTCTAGC 57.533 41.667 0.00 0.00 42.86 3.42
2302 3974 8.192110 GTCTTTAGTGTTTGAGGGTATCTCTAG 58.808 40.741 0.00 0.00 42.86 2.43
2303 3975 7.672660 TGTCTTTAGTGTTTGAGGGTATCTCTA 59.327 37.037 0.00 0.00 42.86 2.43
2304 3976 6.497259 TGTCTTTAGTGTTTGAGGGTATCTCT 59.503 38.462 0.00 0.00 42.86 3.10
2305 3977 6.590677 GTGTCTTTAGTGTTTGAGGGTATCTC 59.409 42.308 0.00 0.00 42.74 2.75
2306 3978 6.042781 TGTGTCTTTAGTGTTTGAGGGTATCT 59.957 38.462 0.00 0.00 0.00 1.98
2307 3979 6.228258 TGTGTCTTTAGTGTTTGAGGGTATC 58.772 40.000 0.00 0.00 0.00 2.24
2308 3980 6.182507 TGTGTCTTTAGTGTTTGAGGGTAT 57.817 37.500 0.00 0.00 0.00 2.73
2309 3981 5.617528 TGTGTCTTTAGTGTTTGAGGGTA 57.382 39.130 0.00 0.00 0.00 3.69
2310 3982 4.497291 TGTGTCTTTAGTGTTTGAGGGT 57.503 40.909 0.00 0.00 0.00 4.34
2311 3983 5.299279 ACATTGTGTCTTTAGTGTTTGAGGG 59.701 40.000 0.00 0.00 0.00 4.30
2312 3984 6.377327 ACATTGTGTCTTTAGTGTTTGAGG 57.623 37.500 0.00 0.00 0.00 3.86
2313 3985 8.394877 TGTAACATTGTGTCTTTAGTGTTTGAG 58.605 33.333 0.00 0.00 32.64 3.02
2314 3986 8.270080 TGTAACATTGTGTCTTTAGTGTTTGA 57.730 30.769 0.00 0.00 32.64 2.69
2363 4035 6.808212 CGAGCAGTTTTGATCCACATATTTTT 59.192 34.615 0.00 0.00 36.37 1.94
2364 4036 6.324819 CGAGCAGTTTTGATCCACATATTTT 58.675 36.000 0.00 0.00 36.37 1.82
2365 4037 5.677091 GCGAGCAGTTTTGATCCACATATTT 60.677 40.000 0.00 0.00 36.37 1.40
2366 4038 4.201950 GCGAGCAGTTTTGATCCACATATT 60.202 41.667 0.00 0.00 36.37 1.28
2367 4039 3.313526 GCGAGCAGTTTTGATCCACATAT 59.686 43.478 0.00 0.00 36.37 1.78
2368 4040 2.677836 GCGAGCAGTTTTGATCCACATA 59.322 45.455 0.00 0.00 36.37 2.29
2369 4041 1.470098 GCGAGCAGTTTTGATCCACAT 59.530 47.619 0.00 0.00 36.37 3.21
2370 4042 0.874390 GCGAGCAGTTTTGATCCACA 59.126 50.000 0.00 0.00 36.37 4.17
2371 4043 0.169009 GGCGAGCAGTTTTGATCCAC 59.831 55.000 0.00 0.00 36.37 4.02
2372 4044 0.036732 AGGCGAGCAGTTTTGATCCA 59.963 50.000 0.00 0.00 36.37 3.41
2373 4045 0.449388 CAGGCGAGCAGTTTTGATCC 59.551 55.000 0.00 0.00 36.37 3.36
2374 4046 1.129437 GTCAGGCGAGCAGTTTTGATC 59.871 52.381 0.00 0.00 36.39 2.92
2375 4047 1.160137 GTCAGGCGAGCAGTTTTGAT 58.840 50.000 0.00 0.00 0.00 2.57
2376 4048 0.106708 AGTCAGGCGAGCAGTTTTGA 59.893 50.000 0.00 0.00 0.00 2.69
2377 4049 0.947244 AAGTCAGGCGAGCAGTTTTG 59.053 50.000 0.00 0.00 0.00 2.44
2378 4050 1.680338 AAAGTCAGGCGAGCAGTTTT 58.320 45.000 0.00 0.00 0.00 2.43
2379 4051 1.334869 CAAAAGTCAGGCGAGCAGTTT 59.665 47.619 0.00 0.00 0.00 2.66
2380 4052 0.947244 CAAAAGTCAGGCGAGCAGTT 59.053 50.000 0.00 0.00 0.00 3.16
2381 4053 0.886490 CCAAAAGTCAGGCGAGCAGT 60.886 55.000 0.00 0.00 0.00 4.40
2382 4054 0.886490 ACCAAAAGTCAGGCGAGCAG 60.886 55.000 0.00 0.00 0.00 4.24
2383 4055 0.465460 AACCAAAAGTCAGGCGAGCA 60.465 50.000 0.00 0.00 0.00 4.26
2384 4056 0.238553 GAACCAAAAGTCAGGCGAGC 59.761 55.000 0.00 0.00 0.00 5.03
2385 4057 0.512952 CGAACCAAAAGTCAGGCGAG 59.487 55.000 0.00 0.00 0.00 5.03
2386 4058 1.503818 GCGAACCAAAAGTCAGGCGA 61.504 55.000 0.00 0.00 0.00 5.54
2387 4059 1.082104 GCGAACCAAAAGTCAGGCG 60.082 57.895 0.00 0.00 0.00 5.52
2388 4060 0.668535 AAGCGAACCAAAAGTCAGGC 59.331 50.000 0.00 0.00 0.00 4.85
2389 4061 2.618709 AGAAAGCGAACCAAAAGTCAGG 59.381 45.455 0.00 0.00 0.00 3.86
2390 4062 3.312421 TGAGAAAGCGAACCAAAAGTCAG 59.688 43.478 0.00 0.00 0.00 3.51
2391 4063 3.275143 TGAGAAAGCGAACCAAAAGTCA 58.725 40.909 0.00 0.00 0.00 3.41
2392 4064 3.963383 TGAGAAAGCGAACCAAAAGTC 57.037 42.857 0.00 0.00 0.00 3.01
2393 4065 4.918810 AATGAGAAAGCGAACCAAAAGT 57.081 36.364 0.00 0.00 0.00 2.66
2394 4066 5.748152 TGAAAATGAGAAAGCGAACCAAAAG 59.252 36.000 0.00 0.00 0.00 2.27
2395 4067 5.655488 TGAAAATGAGAAAGCGAACCAAAA 58.345 33.333 0.00 0.00 0.00 2.44
2396 4068 5.255710 TGAAAATGAGAAAGCGAACCAAA 57.744 34.783 0.00 0.00 0.00 3.28
2397 4069 4.909696 TGAAAATGAGAAAGCGAACCAA 57.090 36.364 0.00 0.00 0.00 3.67
2398 4070 5.452078 AATGAAAATGAGAAAGCGAACCA 57.548 34.783 0.00 0.00 0.00 3.67
2399 4071 6.769608 AAAATGAAAATGAGAAAGCGAACC 57.230 33.333 0.00 0.00 0.00 3.62
2456 4128 9.872757 GAGTTCACGAATTTAAGTGTTCATAAA 57.127 29.630 0.00 0.00 39.25 1.40
2457 4129 9.268268 AGAGTTCACGAATTTAAGTGTTCATAA 57.732 29.630 0.00 0.00 39.25 1.90
2458 4130 8.827177 AGAGTTCACGAATTTAAGTGTTCATA 57.173 30.769 0.00 0.00 39.25 2.15
2459 4131 7.730364 AGAGTTCACGAATTTAAGTGTTCAT 57.270 32.000 0.00 0.00 39.25 2.57
2460 4132 7.548196 AAGAGTTCACGAATTTAAGTGTTCA 57.452 32.000 0.00 0.00 39.25 3.18
2461 4133 7.740781 GCTAAGAGTTCACGAATTTAAGTGTTC 59.259 37.037 0.00 6.54 39.25 3.18
2462 4134 7.225931 TGCTAAGAGTTCACGAATTTAAGTGTT 59.774 33.333 0.00 0.00 39.25 3.32
2463 4135 6.704493 TGCTAAGAGTTCACGAATTTAAGTGT 59.296 34.615 0.00 0.00 39.25 3.55
2464 4136 7.117241 TGCTAAGAGTTCACGAATTTAAGTG 57.883 36.000 0.00 4.04 39.55 3.16
2465 4137 7.724305 TTGCTAAGAGTTCACGAATTTAAGT 57.276 32.000 0.00 0.00 0.00 2.24
2466 4138 9.612620 AATTTGCTAAGAGTTCACGAATTTAAG 57.387 29.630 0.00 0.00 0.00 1.85
2467 4139 9.607285 GAATTTGCTAAGAGTTCACGAATTTAA 57.393 29.630 0.00 0.00 0.00 1.52
2468 4140 8.779303 TGAATTTGCTAAGAGTTCACGAATTTA 58.221 29.630 0.00 0.00 0.00 1.40
2469 4141 7.591426 GTGAATTTGCTAAGAGTTCACGAATTT 59.409 33.333 9.13 0.00 39.21 1.82
2470 4142 7.078228 GTGAATTTGCTAAGAGTTCACGAATT 58.922 34.615 9.13 0.00 39.21 2.17
2471 4143 6.603095 GTGAATTTGCTAAGAGTTCACGAAT 58.397 36.000 9.13 0.00 39.21 3.34
2472 4144 5.985781 GTGAATTTGCTAAGAGTTCACGAA 58.014 37.500 9.13 0.00 39.21 3.85
2473 4145 5.591643 GTGAATTTGCTAAGAGTTCACGA 57.408 39.130 9.13 0.00 39.21 4.35
2475 4147 7.985634 TTTTGTGAATTTGCTAAGAGTTCAC 57.014 32.000 14.80 14.80 45.34 3.18
2569 4241 4.364415 TTTTCTTGGTGGTTTGACGAAG 57.636 40.909 0.00 0.00 34.07 3.79
2570 4242 4.993029 ATTTTCTTGGTGGTTTGACGAA 57.007 36.364 0.00 0.00 0.00 3.85
2571 4243 6.128117 GCTATATTTTCTTGGTGGTTTGACGA 60.128 38.462 0.00 0.00 0.00 4.20
2572 4244 6.027749 GCTATATTTTCTTGGTGGTTTGACG 58.972 40.000 0.00 0.00 0.00 4.35
2573 4245 6.330278 GGCTATATTTTCTTGGTGGTTTGAC 58.670 40.000 0.00 0.00 0.00 3.18
2574 4246 5.124776 CGGCTATATTTTCTTGGTGGTTTGA 59.875 40.000 0.00 0.00 0.00 2.69
2575 4247 5.339990 CGGCTATATTTTCTTGGTGGTTTG 58.660 41.667 0.00 0.00 0.00 2.93
2576 4248 4.401202 CCGGCTATATTTTCTTGGTGGTTT 59.599 41.667 0.00 0.00 0.00 3.27
2577 4249 3.951680 CCGGCTATATTTTCTTGGTGGTT 59.048 43.478 0.00 0.00 0.00 3.67
2578 4250 3.053917 ACCGGCTATATTTTCTTGGTGGT 60.054 43.478 0.00 0.00 0.00 4.16
2579 4251 3.551846 ACCGGCTATATTTTCTTGGTGG 58.448 45.455 0.00 0.00 0.00 4.61
2580 4252 5.576447 AAACCGGCTATATTTTCTTGGTG 57.424 39.130 0.00 0.00 0.00 4.17
2581 4253 6.599356 AAAAACCGGCTATATTTTCTTGGT 57.401 33.333 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.