Multiple sequence alignment - TraesCS3D01G255000

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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 TraesCS3D01G255000 chr3D 100.000 2690 0 0 1 2690 356821286 356823975 0.000000e+00 4968.0
1 TraesCS3D01G255000 chr3B 89.336 2063 103 32 1 2038 457964513 457966483 0.000000e+00 2483.0
2 TraesCS3D01G255000 chr3B 90.909 66 5 1 2625 2689 457966933 457966998 1.330000e-13 87.9
3 TraesCS3D01G255000 chr3A 93.183 1379 53 15 673 2038 475716121 475717471 0.000000e+00 1988.0
4 TraesCS3D01G255000 chr3A 84.713 628 67 16 15 639 475714435 475715036 3.830000e-168 601.0
5 TraesCS3D01G255000 chr3A 92.308 65 5 0 2625 2689 475718418 475718482 2.850000e-15 93.5
6 TraesCS3D01G255000 chr3A 100.000 28 0 0 2301 2328 121332110 121332083 5.000000e-03 52.8
7 TraesCS3D01G255000 chr2B 88.732 71 5 2 2233 2300 489480980 489480910 1.720000e-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 TraesCS3D01G255000 chr3D 356821286 356823975 2689 False 4968.000000 4968 100.0000 1 2690 1 chr3D.!!$F1 2689
1 TraesCS3D01G255000 chr3B 457964513 457966998 2485 False 1285.450000 2483 90.1225 1 2689 2 chr3B.!!$F1 2688
2 TraesCS3D01G255000 chr3A 475714435 475718482 4047 False 894.166667 1988 90.0680 15 2689 3 chr3A.!!$F1 2674

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
866 1922 0.671781 CCTTTCACTCGCAGTCCAGG 60.672 60.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2543 4146 0.033601 ACTCCGCTCTGAGACATCCT 60.034 55.0 9.28 0.0 36.22 3.24 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
340 341 8.522178 AATGTTCAAACGTTTTAAACTGTTCA 57.478 26.923 25.03 13.46 34.64 3.18
341 342 7.323046 TGTTCAAACGTTTTAAACTGTTCAC 57.677 32.000 25.03 9.00 31.34 3.18
447 448 9.586435 AGAAAGTGAGAAAACATAAAACAAAGG 57.414 29.630 0.00 0.00 0.00 3.11
622 624 1.130777 AAACTGCTTGTTGGGCCAAT 58.869 45.000 23.95 0.47 39.13 3.16
762 1818 2.905075 TCACCTGACTGTCACACAAAG 58.095 47.619 6.36 0.00 0.00 2.77
787 1843 9.575783 AGAGAAGAAACTCGAGTCAATATTAAC 57.424 33.333 20.33 9.08 41.25 2.01
789 1845 8.242053 AGAAGAAACTCGAGTCAATATTAACGA 58.758 33.333 20.33 0.00 0.00 3.85
796 1852 5.065090 TCGAGTCAATATTAACGACGGAAGA 59.935 40.000 0.00 0.00 34.80 2.87
847 1903 1.329599 CCCGCAGAAATTTACGGCTAC 59.670 52.381 17.13 0.00 44.29 3.58
852 1908 4.659088 GCAGAAATTTACGGCTACCTTTC 58.341 43.478 0.00 0.00 0.00 2.62
866 1922 0.671781 CCTTTCACTCGCAGTCCAGG 60.672 60.000 0.00 0.00 0.00 4.45
884 1940 2.352032 GCCCGTGCTCTCTACCACT 61.352 63.158 0.00 0.00 33.53 4.00
975 2033 1.553704 CTCTTTAGCCCACGTACCCTT 59.446 52.381 0.00 0.00 0.00 3.95
980 2038 3.027675 GCCCACGTACCCTTCTCCC 62.028 68.421 0.00 0.00 0.00 4.30
990 2048 0.985490 CCCTTCTCCCCTCCTTCCAG 60.985 65.000 0.00 0.00 0.00 3.86
1074 2132 4.889856 TCCATCGATGCCCGTGCG 62.890 66.667 20.25 4.60 41.78 5.34
1106 2164 4.148825 CCTCCCCTTCGGCGACAG 62.149 72.222 10.16 10.53 0.00 3.51
1177 2241 7.273598 GCATATGTCAAGAGGTACATACATACG 59.726 40.741 4.29 0.00 40.40 3.06
1181 2245 4.340097 TCAAGAGGTACATACATACGGTGG 59.660 45.833 0.00 0.00 0.00 4.61
1226 2290 3.270027 TGCAGATCAAACATCCTTACGG 58.730 45.455 0.00 0.00 0.00 4.02
1728 2793 1.600916 GCCAGCTTCCGGTTCTGTT 60.601 57.895 0.00 0.00 0.00 3.16
1729 2794 1.578206 GCCAGCTTCCGGTTCTGTTC 61.578 60.000 0.00 0.00 0.00 3.18
1730 2795 0.035458 CCAGCTTCCGGTTCTGTTCT 59.965 55.000 0.00 0.00 0.00 3.01
1731 2796 1.151668 CAGCTTCCGGTTCTGTTCTG 58.848 55.000 0.00 0.00 0.00 3.02
1732 2797 0.759346 AGCTTCCGGTTCTGTTCTGT 59.241 50.000 0.00 0.00 0.00 3.41
1777 2845 5.105635 ACCATTCAGATTTTGGCATGTAGTG 60.106 40.000 0.00 0.00 33.66 2.74
1780 2848 7.362834 CCATTCAGATTTTGGCATGTAGTGTTA 60.363 37.037 0.00 0.00 0.00 2.41
1815 2883 7.857389 CCGCATTACGTGTATTTTAGTCTAGTA 59.143 37.037 0.00 0.00 41.42 1.82
1857 2925 3.275143 TGGGTATTGCGTTTCATAGGTG 58.725 45.455 0.00 0.00 0.00 4.00
1863 2931 1.621317 TGCGTTTCATAGGTGACCTGA 59.379 47.619 15.83 1.18 34.61 3.86
1897 2966 0.320073 TGTCTTTAGTTGACGCCGGG 60.320 55.000 2.18 0.00 37.26 5.73
1898 2967 0.037975 GTCTTTAGTTGACGCCGGGA 60.038 55.000 2.18 0.00 0.00 5.14
1899 2968 0.245539 TCTTTAGTTGACGCCGGGAG 59.754 55.000 2.18 0.00 0.00 4.30
1921 2990 5.176592 AGGAAACTCGCAGGTTTATTCTAC 58.823 41.667 4.37 0.00 39.20 2.59
1929 2998 4.733887 CGCAGGTTTATTCTACTCTGTACG 59.266 45.833 0.00 0.00 0.00 3.67
1950 3019 6.795098 ACGCAGAACAAGTTATATTTGTCA 57.205 33.333 4.24 0.00 37.77 3.58
2038 3108 3.617284 TGCATTAGTCTCTGACTCGGTA 58.383 45.455 3.30 0.00 42.40 4.02
2040 3110 4.096532 TGCATTAGTCTCTGACTCGGTAAG 59.903 45.833 3.30 0.00 42.40 2.34
2041 3111 4.602995 CATTAGTCTCTGACTCGGTAAGC 58.397 47.826 3.30 0.00 42.40 3.09
2042 3112 1.465794 AGTCTCTGACTCGGTAAGCC 58.534 55.000 0.00 0.00 38.71 4.35
2044 3114 1.544691 GTCTCTGACTCGGTAAGCCAA 59.455 52.381 0.00 0.00 34.09 4.52
2045 3115 1.819288 TCTCTGACTCGGTAAGCCAAG 59.181 52.381 0.00 0.00 34.09 3.61
2046 3116 0.246635 TCTGACTCGGTAAGCCAAGC 59.753 55.000 0.00 0.00 34.09 4.01
2047 3117 0.247736 CTGACTCGGTAAGCCAAGCT 59.752 55.000 0.00 0.00 42.56 3.74
2048 3118 0.246635 TGACTCGGTAAGCCAAGCTC 59.753 55.000 0.00 0.00 38.25 4.09
2049 3119 0.246635 GACTCGGTAAGCCAAGCTCA 59.753 55.000 0.00 0.00 38.25 4.26
2050 3120 0.037232 ACTCGGTAAGCCAAGCTCAC 60.037 55.000 0.00 0.00 38.25 3.51
2051 3121 0.247736 CTCGGTAAGCCAAGCTCACT 59.752 55.000 0.00 0.00 38.25 3.41
2052 3122 0.037326 TCGGTAAGCCAAGCTCACTG 60.037 55.000 0.00 0.00 38.25 3.66
2056 3173 2.072298 GTAAGCCAAGCTCACTGAGTG 58.928 52.381 6.18 6.18 38.25 3.51
2064 3181 1.896694 CTCACTGAGTGCTCCCTCC 59.103 63.158 7.93 0.00 32.98 4.30
2067 3184 1.534235 ACTGAGTGCTCCCTCCGTT 60.534 57.895 0.00 0.00 0.00 4.44
2068 3185 1.122019 ACTGAGTGCTCCCTCCGTTT 61.122 55.000 0.00 0.00 0.00 3.60
2071 3188 0.250513 GAGTGCTCCCTCCGTTTCAT 59.749 55.000 0.00 0.00 0.00 2.57
2072 3189 0.250513 AGTGCTCCCTCCGTTTCATC 59.749 55.000 0.00 0.00 0.00 2.92
2076 3193 2.168521 TGCTCCCTCCGTTTCATCTTAG 59.831 50.000 0.00 0.00 0.00 2.18
2079 3196 4.184629 CTCCCTCCGTTTCATCTTAGTTG 58.815 47.826 0.00 0.00 0.00 3.16
2084 3201 2.993899 CCGTTTCATCTTAGTTGTCGCT 59.006 45.455 0.00 0.00 0.00 4.93
2085 3202 4.082625 TCCGTTTCATCTTAGTTGTCGCTA 60.083 41.667 0.00 0.00 0.00 4.26
2086 3203 4.031426 CCGTTTCATCTTAGTTGTCGCTAC 59.969 45.833 0.00 0.00 0.00 3.58
2087 3204 4.857588 CGTTTCATCTTAGTTGTCGCTACT 59.142 41.667 0.00 0.00 0.00 2.57
2088 3205 5.003590 CGTTTCATCTTAGTTGTCGCTACTC 59.996 44.000 0.00 0.00 0.00 2.59
2089 3206 4.274421 TCATCTTAGTTGTCGCTACTCG 57.726 45.455 0.00 0.00 40.15 4.18
2090 3207 2.539346 TCTTAGTTGTCGCTACTCGC 57.461 50.000 0.00 0.00 38.27 5.03
2091 3208 2.082231 TCTTAGTTGTCGCTACTCGCT 58.918 47.619 0.00 0.00 38.27 4.93
2092 3209 2.095532 TCTTAGTTGTCGCTACTCGCTC 59.904 50.000 0.00 0.00 38.27 5.03
2093 3210 1.445871 TAGTTGTCGCTACTCGCTCA 58.554 50.000 0.00 0.00 38.27 4.26
2095 3212 1.000607 AGTTGTCGCTACTCGCTCAAA 60.001 47.619 0.00 0.00 38.27 2.69
2096 3213 1.124477 GTTGTCGCTACTCGCTCAAAC 59.876 52.381 0.00 0.00 38.27 2.93
2098 3215 0.985549 GTCGCTACTCGCTCAAACAG 59.014 55.000 0.00 0.00 38.27 3.16
2099 3216 0.879090 TCGCTACTCGCTCAAACAGA 59.121 50.000 0.00 0.00 38.27 3.41
2100 3217 1.472878 TCGCTACTCGCTCAAACAGAT 59.527 47.619 0.00 0.00 38.27 2.90
2102 3219 2.611518 GCTACTCGCTCAAACAGATGT 58.388 47.619 0.00 0.00 35.14 3.06
2103 3220 3.730963 CGCTACTCGCTCAAACAGATGTA 60.731 47.826 0.00 0.00 36.13 2.29
2104 3221 4.363999 GCTACTCGCTCAAACAGATGTAT 58.636 43.478 0.00 0.00 35.14 2.29
2106 3223 5.292101 GCTACTCGCTCAAACAGATGTATTT 59.708 40.000 0.00 0.00 35.14 1.40
2107 3224 5.536554 ACTCGCTCAAACAGATGTATTTG 57.463 39.130 0.00 0.00 37.19 2.32
2108 3225 4.393062 ACTCGCTCAAACAGATGTATTTGG 59.607 41.667 0.00 0.00 36.62 3.28
2109 3226 3.126858 TCGCTCAAACAGATGTATTTGGC 59.873 43.478 0.00 0.00 36.62 4.52
2111 3228 4.439153 CGCTCAAACAGATGTATTTGGCAT 60.439 41.667 7.48 0.00 36.62 4.40
2114 3231 7.035004 GCTCAAACAGATGTATTTGGCATAAA 58.965 34.615 0.00 0.00 36.62 1.40
2120 3237 9.985730 AACAGATGTATTTGGCATAAATAATGG 57.014 29.630 6.88 1.05 35.99 3.16
2121 3238 9.146586 ACAGATGTATTTGGCATAAATAATGGT 57.853 29.630 6.88 1.50 35.99 3.55
2122 3239 9.414295 CAGATGTATTTGGCATAAATAATGGTG 57.586 33.333 6.88 1.82 35.99 4.17
2123 3240 9.365906 AGATGTATTTGGCATAAATAATGGTGA 57.634 29.630 6.88 0.00 35.99 4.02
2130 3247 8.862325 TTGGCATAAATAATGGTGATACTAGG 57.138 34.615 0.00 0.00 35.99 3.02
2131 3248 7.402054 TGGCATAAATAATGGTGATACTAGGG 58.598 38.462 0.00 0.00 35.99 3.53
2132 3249 7.238723 TGGCATAAATAATGGTGATACTAGGGA 59.761 37.037 0.00 0.00 35.99 4.20
2133 3250 8.107095 GGCATAAATAATGGTGATACTAGGGAA 58.893 37.037 0.00 0.00 35.99 3.97
2134 3251 9.515226 GCATAAATAATGGTGATACTAGGGAAA 57.485 33.333 0.00 0.00 35.99 3.13
2137 3254 8.848474 AAATAATGGTGATACTAGGGAAATCG 57.152 34.615 0.00 0.00 0.00 3.34
2138 3255 4.891992 ATGGTGATACTAGGGAAATCGG 57.108 45.455 0.00 0.00 0.00 4.18
2139 3256 3.918566 TGGTGATACTAGGGAAATCGGA 58.081 45.455 0.00 0.00 0.00 4.55
2140 3257 4.291792 TGGTGATACTAGGGAAATCGGAA 58.708 43.478 0.00 0.00 0.00 4.30
2141 3258 4.905456 TGGTGATACTAGGGAAATCGGAAT 59.095 41.667 0.00 0.00 0.00 3.01
2142 3259 5.221641 TGGTGATACTAGGGAAATCGGAATG 60.222 44.000 0.00 0.00 0.00 2.67
2143 3260 4.691216 GTGATACTAGGGAAATCGGAATGC 59.309 45.833 0.00 0.00 0.00 3.56
2144 3261 2.640316 ACTAGGGAAATCGGAATGCC 57.360 50.000 0.00 0.00 0.00 4.40
2145 3262 1.143073 ACTAGGGAAATCGGAATGCCC 59.857 52.381 0.13 0.13 39.12 5.36
2146 3263 0.476771 TAGGGAAATCGGAATGCCCC 59.523 55.000 5.41 3.08 39.68 5.80
2147 3264 1.076339 GGGAAATCGGAATGCCCCA 60.076 57.895 0.00 0.00 34.10 4.96
2148 3265 0.469892 GGGAAATCGGAATGCCCCAT 60.470 55.000 0.00 0.00 34.10 4.00
2149 3266 0.675633 GGAAATCGGAATGCCCCATG 59.324 55.000 0.00 0.00 0.00 3.66
2150 3267 0.675633 GAAATCGGAATGCCCCATGG 59.324 55.000 4.14 4.14 0.00 3.66
2163 3280 2.965671 CCCATGGGAGCAGATGTATT 57.034 50.000 28.27 0.00 37.50 1.89
2164 3281 3.234234 CCCATGGGAGCAGATGTATTT 57.766 47.619 28.27 0.00 37.50 1.40
2165 3282 2.889045 CCCATGGGAGCAGATGTATTTG 59.111 50.000 28.27 0.00 37.50 2.32
2166 3283 3.435457 CCCATGGGAGCAGATGTATTTGA 60.435 47.826 28.27 0.00 37.50 2.69
2167 3284 3.567164 CCATGGGAGCAGATGTATTTGAC 59.433 47.826 2.85 0.00 0.00 3.18
2168 3285 3.998913 TGGGAGCAGATGTATTTGACA 57.001 42.857 0.00 0.00 43.97 3.58
2170 3287 9.806305 CCCATGGGAGCAGATGTATTTGACATA 62.806 44.444 28.27 0.00 42.80 2.29
2189 3306 8.757164 TGACATAAATAATGGTGATACTAGCG 57.243 34.615 0.00 0.00 40.16 4.26
2190 3307 8.581578 TGACATAAATAATGGTGATACTAGCGA 58.418 33.333 0.00 0.00 40.16 4.93
2191 3308 9.419297 GACATAAATAATGGTGATACTAGCGAA 57.581 33.333 0.00 0.00 40.16 4.70
2192 3309 9.772973 ACATAAATAATGGTGATACTAGCGAAA 57.227 29.630 0.00 0.00 40.16 3.46
2195 3312 7.582435 AATAATGGTGATACTAGCGAAATCG 57.418 36.000 0.00 0.00 43.27 3.34
2196 3313 3.364889 TGGTGATACTAGCGAAATCGG 57.635 47.619 4.84 0.00 40.23 4.18
2197 3314 2.953648 TGGTGATACTAGCGAAATCGGA 59.046 45.455 4.84 0.00 40.23 4.55
2198 3315 3.382227 TGGTGATACTAGCGAAATCGGAA 59.618 43.478 4.84 0.00 40.23 4.30
2199 3316 4.038763 TGGTGATACTAGCGAAATCGGAAT 59.961 41.667 4.84 0.00 40.23 3.01
2200 3317 4.386049 GGTGATACTAGCGAAATCGGAATG 59.614 45.833 4.84 0.00 40.23 2.67
2201 3318 3.987868 TGATACTAGCGAAATCGGAATGC 59.012 43.478 4.84 0.00 40.23 3.56
2202 3319 1.583054 ACTAGCGAAATCGGAATGCC 58.417 50.000 4.84 0.00 40.23 4.40
2203 3320 0.868406 CTAGCGAAATCGGAATGCCC 59.132 55.000 4.84 0.00 40.23 5.36
2204 3321 0.468226 TAGCGAAATCGGAATGCCCT 59.532 50.000 4.84 0.00 40.23 5.19
2205 3322 0.815615 AGCGAAATCGGAATGCCCTC 60.816 55.000 4.84 0.00 40.23 4.30
2206 3323 0.815615 GCGAAATCGGAATGCCCTCT 60.816 55.000 4.84 0.00 40.23 3.69
2207 3324 0.940126 CGAAATCGGAATGCCCTCTG 59.060 55.000 0.00 0.00 35.37 3.35
2208 3325 1.473257 CGAAATCGGAATGCCCTCTGA 60.473 52.381 0.00 0.00 35.20 3.27
2209 3326 2.643551 GAAATCGGAATGCCCTCTGAA 58.356 47.619 0.00 0.00 34.41 3.02
2210 3327 2.806945 AATCGGAATGCCCTCTGAAA 57.193 45.000 0.00 0.00 34.41 2.69
2211 3328 3.303351 AATCGGAATGCCCTCTGAAAT 57.697 42.857 0.00 0.00 34.41 2.17
2212 3329 2.042686 TCGGAATGCCCTCTGAAATG 57.957 50.000 0.00 0.00 0.00 2.32
2213 3330 1.027357 CGGAATGCCCTCTGAAATGG 58.973 55.000 0.00 0.00 0.00 3.16
2214 3331 1.408683 CGGAATGCCCTCTGAAATGGA 60.409 52.381 0.00 0.00 0.00 3.41
2215 3332 2.738743 GGAATGCCCTCTGAAATGGAA 58.261 47.619 0.00 0.00 0.00 3.53
2216 3333 2.692041 GGAATGCCCTCTGAAATGGAAG 59.308 50.000 0.00 0.00 0.00 3.46
2217 3334 2.449137 ATGCCCTCTGAAATGGAAGG 57.551 50.000 0.00 0.00 0.00 3.46
2218 3335 0.332632 TGCCCTCTGAAATGGAAGGG 59.667 55.000 1.79 1.79 39.47 3.95
2219 3336 0.625849 GCCCTCTGAAATGGAAGGGA 59.374 55.000 10.46 0.00 38.82 4.20
2220 3337 1.683319 GCCCTCTGAAATGGAAGGGAC 60.683 57.143 10.46 0.00 38.82 4.46
2221 3338 1.635487 CCCTCTGAAATGGAAGGGACA 59.365 52.381 0.00 0.00 38.82 4.02
2222 3339 2.243221 CCCTCTGAAATGGAAGGGACAT 59.757 50.000 0.00 0.00 38.82 3.06
2223 3340 3.549794 CCTCTGAAATGGAAGGGACATC 58.450 50.000 0.00 0.00 0.00 3.06
2224 3341 3.201290 CTCTGAAATGGAAGGGACATCG 58.799 50.000 0.00 0.00 0.00 3.84
2225 3342 2.571653 TCTGAAATGGAAGGGACATCGT 59.428 45.455 0.00 0.00 0.00 3.73
2226 3343 2.939103 CTGAAATGGAAGGGACATCGTC 59.061 50.000 0.00 0.00 0.00 4.20
2227 3344 2.304470 TGAAATGGAAGGGACATCGTCA 59.696 45.455 0.00 0.00 33.68 4.35
2228 3345 3.244735 TGAAATGGAAGGGACATCGTCAA 60.245 43.478 0.00 0.00 33.68 3.18
2229 3346 3.652057 AATGGAAGGGACATCGTCAAT 57.348 42.857 0.00 0.00 33.68 2.57
2230 3347 2.691409 TGGAAGGGACATCGTCAATC 57.309 50.000 0.00 0.00 33.68 2.67
2231 3348 1.905894 TGGAAGGGACATCGTCAATCA 59.094 47.619 0.00 0.00 33.68 2.57
2232 3349 2.304470 TGGAAGGGACATCGTCAATCAA 59.696 45.455 0.00 0.00 33.68 2.57
2233 3350 3.244735 TGGAAGGGACATCGTCAATCAAA 60.245 43.478 0.00 0.00 33.68 2.69
2234 3351 3.756434 GGAAGGGACATCGTCAATCAAAA 59.244 43.478 0.00 0.00 33.68 2.44
2235 3352 4.217550 GGAAGGGACATCGTCAATCAAAAA 59.782 41.667 0.00 0.00 33.68 1.94
2236 3353 5.105756 GGAAGGGACATCGTCAATCAAAAAT 60.106 40.000 0.00 0.00 33.68 1.82
2237 3354 5.567138 AGGGACATCGTCAATCAAAAATC 57.433 39.130 0.00 0.00 33.68 2.17
2238 3355 5.009631 AGGGACATCGTCAATCAAAAATCA 58.990 37.500 0.00 0.00 33.68 2.57
2239 3356 5.476599 AGGGACATCGTCAATCAAAAATCAA 59.523 36.000 0.00 0.00 33.68 2.57
2240 3357 5.801947 GGGACATCGTCAATCAAAAATCAAG 59.198 40.000 0.00 0.00 33.68 3.02
2241 3358 5.287035 GGACATCGTCAATCAAAAATCAAGC 59.713 40.000 0.00 0.00 33.68 4.01
2242 3359 5.771469 ACATCGTCAATCAAAAATCAAGCA 58.229 33.333 0.00 0.00 0.00 3.91
2243 3360 6.392354 ACATCGTCAATCAAAAATCAAGCAT 58.608 32.000 0.00 0.00 0.00 3.79
2244 3361 6.869913 ACATCGTCAATCAAAAATCAAGCATT 59.130 30.769 0.00 0.00 0.00 3.56
2245 3362 6.932901 TCGTCAATCAAAAATCAAGCATTC 57.067 33.333 0.00 0.00 0.00 2.67
2246 3363 6.680810 TCGTCAATCAAAAATCAAGCATTCT 58.319 32.000 0.00 0.00 0.00 2.40
2247 3364 7.147312 TCGTCAATCAAAAATCAAGCATTCTT 58.853 30.769 0.00 0.00 0.00 2.52
2248 3365 8.296000 TCGTCAATCAAAAATCAAGCATTCTTA 58.704 29.630 0.00 0.00 0.00 2.10
2249 3366 9.079833 CGTCAATCAAAAATCAAGCATTCTTAT 57.920 29.630 0.00 0.00 0.00 1.73
2255 3372 9.590451 TCAAAAATCAAGCATTCTTATTCATCC 57.410 29.630 0.00 0.00 0.00 3.51
2256 3373 9.373603 CAAAAATCAAGCATTCTTATTCATCCA 57.626 29.630 0.00 0.00 0.00 3.41
2288 3405 9.866655 TTTTACTAATTAGTATCGTAGGAGGGA 57.133 33.333 22.80 4.12 38.48 4.20
2289 3406 9.512588 TTTACTAATTAGTATCGTAGGAGGGAG 57.487 37.037 22.80 0.00 38.48 4.30
2290 3407 7.089106 ACTAATTAGTATCGTAGGAGGGAGT 57.911 40.000 16.60 0.00 34.13 3.85
2291 3408 7.525165 ACTAATTAGTATCGTAGGAGGGAGTT 58.475 38.462 16.60 0.00 34.13 3.01
2292 3409 8.664079 ACTAATTAGTATCGTAGGAGGGAGTTA 58.336 37.037 16.60 0.00 34.13 2.24
2293 3410 9.683870 CTAATTAGTATCGTAGGAGGGAGTTAT 57.316 37.037 4.18 0.00 0.00 1.89
2294 3411 8.953223 AATTAGTATCGTAGGAGGGAGTTATT 57.047 34.615 0.00 0.00 0.00 1.40
2295 3412 8.953223 ATTAGTATCGTAGGAGGGAGTTATTT 57.047 34.615 0.00 0.00 0.00 1.40
2297 3414 9.866655 TTAGTATCGTAGGAGGGAGTTATTTAA 57.133 33.333 0.00 0.00 0.00 1.52
2298 3415 8.175925 AGTATCGTAGGAGGGAGTTATTTAAC 57.824 38.462 0.00 0.00 36.46 2.01
2299 3416 5.859205 TCGTAGGAGGGAGTTATTTAACC 57.141 43.478 0.00 0.00 36.88 2.85
2300 3417 5.271598 TCGTAGGAGGGAGTTATTTAACCA 58.728 41.667 0.00 0.00 36.88 3.67
2301 3418 5.127682 TCGTAGGAGGGAGTTATTTAACCAC 59.872 44.000 0.00 0.00 36.88 4.16
2302 3419 5.128335 CGTAGGAGGGAGTTATTTAACCACT 59.872 44.000 0.00 0.00 36.88 4.00
2322 3439 9.745880 AACCACTAAAATACGTCTAGATACATG 57.254 33.333 0.00 0.00 0.00 3.21
2323 3440 9.128404 ACCACTAAAATACGTCTAGATACATGA 57.872 33.333 0.00 0.00 0.00 3.07
2332 3449 5.986135 ACGTCTAGATACATGAATTTCAGCC 59.014 40.000 0.00 0.00 0.00 4.85
2337 3454 6.199937 AGATACATGAATTTCAGCCACAAC 57.800 37.500 0.00 0.00 0.00 3.32
2338 3455 3.287312 ACATGAATTTCAGCCACAACG 57.713 42.857 0.00 0.00 0.00 4.10
2340 3457 3.058016 ACATGAATTTCAGCCACAACGAG 60.058 43.478 0.00 0.00 0.00 4.18
2341 3458 2.844946 TGAATTTCAGCCACAACGAGA 58.155 42.857 0.00 0.00 0.00 4.04
2342 3459 3.210227 TGAATTTCAGCCACAACGAGAA 58.790 40.909 0.00 0.00 0.00 2.87
2343 3460 3.003275 TGAATTTCAGCCACAACGAGAAC 59.997 43.478 0.00 0.00 0.00 3.01
2344 3461 0.934496 TTTCAGCCACAACGAGAACG 59.066 50.000 0.00 0.00 45.75 3.95
2345 3462 0.103390 TTCAGCCACAACGAGAACGA 59.897 50.000 0.00 0.00 42.66 3.85
2346 3463 0.103390 TCAGCCACAACGAGAACGAA 59.897 50.000 0.00 0.00 42.66 3.85
2347 3464 0.508641 CAGCCACAACGAGAACGAAG 59.491 55.000 0.00 0.00 42.66 3.79
2348 3465 0.600255 AGCCACAACGAGAACGAAGG 60.600 55.000 0.00 0.00 42.66 3.46
2350 3467 0.032952 CCACAACGAGAACGAAGGGA 59.967 55.000 0.00 0.00 42.66 4.20
2351 3468 1.419374 CACAACGAGAACGAAGGGAG 58.581 55.000 0.00 0.00 42.66 4.30
2352 3469 1.038280 ACAACGAGAACGAAGGGAGT 58.962 50.000 0.00 0.00 42.66 3.85
2353 3470 2.030540 CACAACGAGAACGAAGGGAGTA 60.031 50.000 0.00 0.00 42.66 2.59
2354 3471 2.030451 ACAACGAGAACGAAGGGAGTAC 60.030 50.000 0.00 0.00 42.66 2.73
2356 3473 2.083002 ACGAGAACGAAGGGAGTACTC 58.917 52.381 14.87 14.87 42.66 2.59
2357 3474 1.401199 CGAGAACGAAGGGAGTACTCC 59.599 57.143 30.72 30.72 44.66 3.85
2378 3914 4.320456 CACTGGTCTGGCACGCCT 62.320 66.667 9.92 0.00 36.94 5.52
2389 3925 3.059982 CACGCCTGGGAGAAGACA 58.940 61.111 0.00 0.00 0.00 3.41
2390 3926 1.079543 CACGCCTGGGAGAAGACAG 60.080 63.158 0.00 0.00 34.54 3.51
2398 3934 0.616111 GGGAGAAGACAGAGAGCCCA 60.616 60.000 0.00 0.00 34.25 5.36
2405 3941 1.289231 AGACAGAGAGCCCAGGTCATA 59.711 52.381 0.00 0.00 31.89 2.15
2422 3962 2.025037 TCATACCATCTTGCCCTTGCTT 60.025 45.455 0.00 0.00 38.71 3.91
2441 3981 8.084073 CCTTGCTTTCTTGTGAAGAATTTCATA 58.916 33.333 0.00 0.00 46.15 2.15
2442 3982 9.635520 CTTGCTTTCTTGTGAAGAATTTCATAT 57.364 29.630 0.00 0.00 46.15 1.78
2469 4026 3.108289 CAGAGCTGTCGCCACACG 61.108 66.667 0.00 0.00 45.62 4.49
2484 4086 0.963856 ACACGACACGCCTATCTCCA 60.964 55.000 0.00 0.00 0.00 3.86
2498 4100 0.832135 TCTCCAGGAGACGGCTTTGT 60.832 55.000 15.98 0.00 33.35 2.83
2519 4122 1.210478 AGAATTACAGGTGCGAGCCAT 59.790 47.619 0.00 0.00 0.00 4.40
2534 4137 1.310216 GCCATCACAGCACAGCATCA 61.310 55.000 0.00 0.00 0.00 3.07
2540 4143 3.429141 AGCACAGCATCAGCACGC 61.429 61.111 0.00 0.00 45.49 5.34
2543 4146 1.638388 GCACAGCATCAGCACGCTTA 61.638 55.000 0.00 0.00 45.49 3.09
2545 4148 0.742281 ACAGCATCAGCACGCTTAGG 60.742 55.000 0.00 0.00 45.49 2.69
2546 4149 0.460811 CAGCATCAGCACGCTTAGGA 60.461 55.000 0.00 0.00 45.49 2.94
2547 4150 0.467384 AGCATCAGCACGCTTAGGAT 59.533 50.000 0.00 0.00 45.49 3.24
2548 4151 0.585357 GCATCAGCACGCTTAGGATG 59.415 55.000 11.53 11.53 41.58 3.51
2549 4152 1.945387 CATCAGCACGCTTAGGATGT 58.055 50.000 8.82 0.00 32.68 3.06
2550 4153 1.863454 CATCAGCACGCTTAGGATGTC 59.137 52.381 8.82 0.00 32.68 3.06
2551 4154 1.186200 TCAGCACGCTTAGGATGTCT 58.814 50.000 0.00 0.00 0.00 3.41
2552 4155 1.135139 TCAGCACGCTTAGGATGTCTC 59.865 52.381 0.00 0.00 0.00 3.36
2554 4157 1.135915 AGCACGCTTAGGATGTCTCAG 59.864 52.381 0.00 0.00 0.00 3.35
2557 4160 1.407258 ACGCTTAGGATGTCTCAGAGC 59.593 52.381 0.00 0.00 0.00 4.09
2558 4161 1.599171 CGCTTAGGATGTCTCAGAGCG 60.599 57.143 0.00 0.00 40.42 5.03
2559 4162 1.269517 GCTTAGGATGTCTCAGAGCGG 60.270 57.143 0.00 0.00 0.00 5.52
2561 4164 1.974265 TAGGATGTCTCAGAGCGGAG 58.026 55.000 0.00 0.00 36.21 4.63
2562 4165 0.033601 AGGATGTCTCAGAGCGGAGT 60.034 55.000 0.00 0.00 36.30 3.85
2563 4166 0.102120 GGATGTCTCAGAGCGGAGTG 59.898 60.000 0.00 0.00 36.30 3.51
2564 4167 0.527385 GATGTCTCAGAGCGGAGTGC 60.527 60.000 0.00 0.00 46.98 4.40
2573 4176 3.096791 GCGGAGTGCTCAAGATGC 58.903 61.111 1.41 0.00 41.73 3.91
2575 4178 1.300971 GCGGAGTGCTCAAGATGCAA 61.301 55.000 0.00 0.00 42.41 4.08
2577 4180 1.818642 GGAGTGCTCAAGATGCAAGT 58.181 50.000 0.00 0.00 42.41 3.16
2603 4289 1.493950 GCGATCATGCCAAGGTCTCG 61.494 60.000 0.00 0.00 0.00 4.04
2611 4297 1.153628 CCAAGGTCTCGTTAGCCGG 60.154 63.158 0.00 0.00 37.11 6.13
2612 4298 1.153628 CAAGGTCTCGTTAGCCGGG 60.154 63.158 2.18 0.00 38.86 5.73
2613 4299 2.356780 AAGGTCTCGTTAGCCGGGG 61.357 63.158 2.18 0.00 37.74 5.73
2614 4300 4.525949 GGTCTCGTTAGCCGGGGC 62.526 72.222 2.18 0.18 42.34 5.80
2661 4347 2.281070 AGCTCCACACAACAGCCG 60.281 61.111 0.00 0.00 33.28 5.52
2680 4367 1.592543 CGCCAGCTGTTTTTGGTTTTC 59.407 47.619 13.81 0.00 36.81 2.29
2689 4376 5.064707 GCTGTTTTTGGTTTTCTTTTCTCCC 59.935 40.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 9.913451 CATGAACATTAAAAACGTGTCAAAAAT 57.087 25.926 0.00 0.00 0.00 1.82
237 238 7.376601 GTCATGAACATTTTTCCAAAATTGCAC 59.623 33.333 0.00 3.35 34.37 4.57
313 314 9.800299 GAACAGTTTAAAACGTTTGAACATTTT 57.200 25.926 27.88 20.79 37.88 1.82
321 322 8.973619 TTTTTGTGAACAGTTTAAAACGTTTG 57.026 26.923 15.46 3.92 36.23 2.93
435 436 7.680062 TGTTTTCGCTTTTCCTTTGTTTTATG 58.320 30.769 0.00 0.00 0.00 1.90
447 448 5.771602 TTGTTTTCCTGTTTTCGCTTTTC 57.228 34.783 0.00 0.00 0.00 2.29
452 453 3.305897 CCTGTTTGTTTTCCTGTTTTCGC 59.694 43.478 0.00 0.00 0.00 4.70
526 528 3.622166 TTTAGAAACCTCCATCCGGTC 57.378 47.619 0.00 0.00 32.46 4.79
550 552 6.503944 AGATTTGTAACCTTCCTAGGAGAGA 58.496 40.000 12.26 0.00 45.05 3.10
762 1818 8.525071 CGTTAATATTGACTCGAGTTTCTTCTC 58.475 37.037 21.08 5.33 0.00 2.87
787 1843 1.725164 GGTTGTAGCTTTCTTCCGTCG 59.275 52.381 0.00 0.00 0.00 5.12
789 1845 2.922740 TGGTTGTAGCTTTCTTCCGT 57.077 45.000 0.00 0.00 0.00 4.69
796 1852 1.995376 CCACCCTTGGTTGTAGCTTT 58.005 50.000 0.00 0.00 38.23 3.51
847 1903 0.671781 CCTGGACTGCGAGTGAAAGG 60.672 60.000 0.00 0.00 0.00 3.11
852 1908 4.767255 GGGCCTGGACTGCGAGTG 62.767 72.222 0.84 0.00 0.00 3.51
866 1922 2.184579 GTGGTAGAGAGCACGGGC 59.815 66.667 0.00 0.00 43.67 6.13
884 1940 6.579666 TGAGAAGAAAGCGGTTAACTAGTA 57.420 37.500 0.00 0.00 0.00 1.82
975 2033 1.613630 GTGCTGGAAGGAGGGGAGA 60.614 63.158 0.00 0.00 31.73 3.71
980 2038 2.352805 GTGGGTGCTGGAAGGAGG 59.647 66.667 0.00 0.00 31.73 4.30
990 2048 1.735571 CGTAGTAACATTGGTGGGTGC 59.264 52.381 0.00 0.00 0.00 5.01
1053 2111 2.664185 CGGGCATCGATGGAGCTG 60.664 66.667 26.00 2.01 42.43 4.24
1074 2132 2.261729 GGGAGGAAGATAGGGTGGATC 58.738 57.143 0.00 0.00 0.00 3.36
1177 2241 2.351726 GCACGTTGTAGATTCATCCACC 59.648 50.000 0.00 0.00 0.00 4.61
1181 2245 2.534939 GCACGCACGTTGTAGATTCATC 60.535 50.000 0.00 0.00 0.00 2.92
1244 2308 2.051435 GCACGCACGCACAAATGA 60.051 55.556 0.00 0.00 0.00 2.57
1368 2432 4.923942 AGCCGCATCTCCGCCATG 62.924 66.667 0.00 0.00 0.00 3.66
1637 2701 4.299547 AGTTGCTGACGAGGCGCA 62.300 61.111 10.83 0.00 0.00 6.09
1693 2757 4.457496 CCTGCATCGTCCACCGCT 62.457 66.667 0.00 0.00 36.19 5.52
1697 2761 2.821366 CTGGCCTGCATCGTCCAC 60.821 66.667 3.32 0.00 0.00 4.02
1728 2793 0.464036 AGAAACGTCAGGTGCACAGA 59.536 50.000 20.43 13.17 0.00 3.41
1729 2794 1.003545 CAAGAAACGTCAGGTGCACAG 60.004 52.381 20.43 10.79 0.00 3.66
1730 2795 1.013596 CAAGAAACGTCAGGTGCACA 58.986 50.000 20.43 0.00 0.00 4.57
1731 2796 0.307760 CCAAGAAACGTCAGGTGCAC 59.692 55.000 8.80 8.80 0.00 4.57
1732 2797 0.179234 TCCAAGAAACGTCAGGTGCA 59.821 50.000 0.00 0.00 0.00 4.57
1777 2845 7.958112 ACACGTAATGCGGAAAATAATTAAC 57.042 32.000 0.00 0.00 46.52 2.01
1780 2848 9.575783 AAAATACACGTAATGCGGAAAATAATT 57.424 25.926 0.00 0.00 46.52 1.40
1815 2883 5.011125 CCCATCCTAGACGACAAATCTACAT 59.989 44.000 0.00 0.00 0.00 2.29
1828 2896 3.470645 AACGCAATACCCATCCTAGAC 57.529 47.619 0.00 0.00 0.00 2.59
1897 2966 4.254492 AGAATAAACCTGCGAGTTTCCTC 58.746 43.478 7.14 6.05 40.38 3.71
1898 2967 4.287766 AGAATAAACCTGCGAGTTTCCT 57.712 40.909 7.14 2.38 40.38 3.36
1899 2968 5.176592 AGTAGAATAAACCTGCGAGTTTCC 58.823 41.667 7.14 0.43 40.38 3.13
1900 2969 6.035112 CAGAGTAGAATAAACCTGCGAGTTTC 59.965 42.308 7.14 0.00 40.38 2.78
1901 2970 5.869888 CAGAGTAGAATAAACCTGCGAGTTT 59.130 40.000 8.70 8.70 42.47 2.66
1902 2971 5.047235 ACAGAGTAGAATAAACCTGCGAGTT 60.047 40.000 0.00 0.00 0.00 3.01
1903 2972 4.463186 ACAGAGTAGAATAAACCTGCGAGT 59.537 41.667 0.00 0.00 0.00 4.18
1904 2973 5.000012 ACAGAGTAGAATAAACCTGCGAG 58.000 43.478 0.00 0.00 0.00 5.03
1905 2974 5.448225 CGTACAGAGTAGAATAAACCTGCGA 60.448 44.000 0.00 0.00 0.00 5.10
1906 2975 4.733887 CGTACAGAGTAGAATAAACCTGCG 59.266 45.833 0.00 0.00 0.00 5.18
1907 2976 4.503370 GCGTACAGAGTAGAATAAACCTGC 59.497 45.833 0.00 0.00 0.00 4.85
1908 2977 5.647589 TGCGTACAGAGTAGAATAAACCTG 58.352 41.667 0.00 0.00 0.00 4.00
1909 2978 5.909621 TGCGTACAGAGTAGAATAAACCT 57.090 39.130 0.00 0.00 0.00 3.50
1929 2998 9.282247 CATTCTGACAAATATAACTTGTTCTGC 57.718 33.333 5.35 0.00 37.14 4.26
2021 3091 3.015327 GGCTTACCGAGTCAGAGACTAA 58.985 50.000 0.00 0.00 43.53 2.24
2038 3108 0.888285 GCACTCAGTGAGCTTGGCTT 60.888 55.000 20.31 0.00 39.88 4.35
2040 3110 1.297456 GAGCACTCAGTGAGCTTGGC 61.297 60.000 20.31 17.22 42.50 4.52
2041 3111 0.673022 GGAGCACTCAGTGAGCTTGG 60.673 60.000 20.31 8.49 42.50 3.61
2042 3112 0.673022 GGGAGCACTCAGTGAGCTTG 60.673 60.000 20.31 12.73 42.50 4.01
2044 3114 1.229145 AGGGAGCACTCAGTGAGCT 60.229 57.895 20.31 13.28 45.03 4.09
2045 3115 1.217779 GAGGGAGCACTCAGTGAGC 59.782 63.158 20.31 8.19 37.44 4.26
2046 3116 1.896694 GGAGGGAGCACTCAGTGAG 59.103 63.158 18.83 18.83 39.27 3.51
2047 3117 1.979155 CGGAGGGAGCACTCAGTGA 60.979 63.158 9.70 0.00 39.27 3.41
2048 3118 1.821061 AACGGAGGGAGCACTCAGTG 61.821 60.000 6.30 0.00 43.48 3.66
2049 3119 1.122019 AAACGGAGGGAGCACTCAGT 61.122 55.000 1.74 0.61 45.63 3.41
2050 3120 0.390472 GAAACGGAGGGAGCACTCAG 60.390 60.000 1.74 0.00 39.27 3.35
2051 3121 1.118965 TGAAACGGAGGGAGCACTCA 61.119 55.000 1.74 0.00 39.27 3.41
2052 3122 0.250513 ATGAAACGGAGGGAGCACTC 59.749 55.000 0.00 0.00 36.76 3.51
2056 3173 2.168728 ACTAAGATGAAACGGAGGGAGC 59.831 50.000 0.00 0.00 0.00 4.70
2064 3181 4.857588 AGTAGCGACAACTAAGATGAAACG 59.142 41.667 0.00 0.00 0.00 3.60
2067 3184 4.659088 CGAGTAGCGACAACTAAGATGAA 58.341 43.478 0.00 0.00 44.57 2.57
2068 3185 3.487042 GCGAGTAGCGACAACTAAGATGA 60.487 47.826 0.00 0.00 44.57 2.92
2071 3188 2.539346 GCGAGTAGCGACAACTAAGA 57.461 50.000 0.00 0.00 44.57 2.10
2084 3201 5.580691 CCAAATACATCTGTTTGAGCGAGTA 59.419 40.000 0.00 0.00 37.48 2.59
2085 3202 4.393062 CCAAATACATCTGTTTGAGCGAGT 59.607 41.667 0.00 0.00 37.48 4.18
2086 3203 4.728882 GCCAAATACATCTGTTTGAGCGAG 60.729 45.833 0.00 0.00 37.48 5.03
2087 3204 3.126858 GCCAAATACATCTGTTTGAGCGA 59.873 43.478 0.00 0.00 37.48 4.93
2088 3205 3.119884 TGCCAAATACATCTGTTTGAGCG 60.120 43.478 0.00 0.00 37.48 5.03
2089 3206 4.439305 TGCCAAATACATCTGTTTGAGC 57.561 40.909 0.00 0.00 37.48 4.26
2095 3212 9.146586 ACCATTATTTATGCCAAATACATCTGT 57.853 29.630 1.23 0.00 32.60 3.41
2096 3213 9.414295 CACCATTATTTATGCCAAATACATCTG 57.586 33.333 1.23 0.00 32.60 2.90
2104 3221 9.295825 CCTAGTATCACCATTATTTATGCCAAA 57.704 33.333 0.00 0.00 32.60 3.28
2106 3223 7.238723 TCCCTAGTATCACCATTATTTATGCCA 59.761 37.037 0.00 0.00 32.60 4.92
2107 3224 7.630082 TCCCTAGTATCACCATTATTTATGCC 58.370 38.462 0.00 0.00 32.60 4.40
2108 3225 9.515226 TTTCCCTAGTATCACCATTATTTATGC 57.485 33.333 0.00 0.00 32.60 3.14
2111 3228 9.938280 CGATTTCCCTAGTATCACCATTATTTA 57.062 33.333 0.00 0.00 0.00 1.40
2114 3231 6.729100 TCCGATTTCCCTAGTATCACCATTAT 59.271 38.462 0.00 0.00 0.00 1.28
2117 3234 4.489737 TCCGATTTCCCTAGTATCACCAT 58.510 43.478 0.00 0.00 0.00 3.55
2118 3235 3.918566 TCCGATTTCCCTAGTATCACCA 58.081 45.455 0.00 0.00 0.00 4.17
2119 3236 4.950205 TTCCGATTTCCCTAGTATCACC 57.050 45.455 0.00 0.00 0.00 4.02
2120 3237 4.691216 GCATTCCGATTTCCCTAGTATCAC 59.309 45.833 0.00 0.00 0.00 3.06
2121 3238 4.262894 GGCATTCCGATTTCCCTAGTATCA 60.263 45.833 0.00 0.00 0.00 2.15
2122 3239 4.254492 GGCATTCCGATTTCCCTAGTATC 58.746 47.826 0.00 0.00 0.00 2.24
2123 3240 3.009143 GGGCATTCCGATTTCCCTAGTAT 59.991 47.826 0.00 0.00 34.19 2.12
2124 3241 2.370849 GGGCATTCCGATTTCCCTAGTA 59.629 50.000 0.00 0.00 34.19 1.82
2125 3242 1.143073 GGGCATTCCGATTTCCCTAGT 59.857 52.381 0.00 0.00 34.19 2.57
2126 3243 1.545651 GGGGCATTCCGATTTCCCTAG 60.546 57.143 0.00 0.00 37.16 3.02
2127 3244 0.476771 GGGGCATTCCGATTTCCCTA 59.523 55.000 0.00 0.00 37.16 3.53
2128 3245 1.230212 GGGGCATTCCGATTTCCCT 59.770 57.895 0.00 0.00 37.16 4.20
2129 3246 0.469892 ATGGGGCATTCCGATTTCCC 60.470 55.000 0.00 0.00 36.01 3.97
2130 3247 0.675633 CATGGGGCATTCCGATTTCC 59.324 55.000 0.00 0.00 31.10 3.13
2131 3248 0.675633 CCATGGGGCATTCCGATTTC 59.324 55.000 2.85 0.00 31.10 2.17
2132 3249 0.760189 CCCATGGGGCATTCCGATTT 60.760 55.000 24.53 0.00 35.35 2.17
2133 3250 1.152483 CCCATGGGGCATTCCGATT 60.152 57.895 24.53 0.00 35.35 3.34
2134 3251 2.072874 CTCCCATGGGGCATTCCGAT 62.073 60.000 30.93 0.00 43.94 4.18
2135 3252 2.694240 TCCCATGGGGCATTCCGA 60.694 61.111 30.93 5.59 43.94 4.55
2136 3253 2.203394 CTCCCATGGGGCATTCCG 60.203 66.667 30.93 2.14 43.94 4.30
2137 3254 2.522680 GCTCCCATGGGGCATTCC 60.523 66.667 30.93 8.97 43.94 3.01
2138 3255 1.831286 CTGCTCCCATGGGGCATTC 60.831 63.158 33.76 19.26 43.94 2.67
2139 3256 1.661990 ATCTGCTCCCATGGGGCATT 61.662 55.000 33.76 25.02 43.94 3.56
2140 3257 2.089368 ATCTGCTCCCATGGGGCAT 61.089 57.895 33.76 23.30 43.94 4.40
2141 3258 2.697263 ATCTGCTCCCATGGGGCA 60.697 61.111 32.37 32.37 43.94 5.36
2142 3259 1.708993 TACATCTGCTCCCATGGGGC 61.709 60.000 30.93 29.28 43.94 5.80
2143 3260 1.070604 ATACATCTGCTCCCATGGGG 58.929 55.000 30.93 21.33 46.11 4.96
2144 3261 2.889045 CAAATACATCTGCTCCCATGGG 59.111 50.000 26.30 26.30 0.00 4.00
2145 3262 3.567164 GTCAAATACATCTGCTCCCATGG 59.433 47.826 4.14 4.14 0.00 3.66
2146 3263 4.201657 TGTCAAATACATCTGCTCCCATG 58.798 43.478 0.00 0.00 31.43 3.66
2147 3264 4.508551 TGTCAAATACATCTGCTCCCAT 57.491 40.909 0.00 0.00 31.43 4.00
2148 3265 3.998913 TGTCAAATACATCTGCTCCCA 57.001 42.857 0.00 0.00 31.43 4.37
2149 3266 6.942532 TTTATGTCAAATACATCTGCTCCC 57.057 37.500 0.00 0.00 46.15 4.30
2163 3280 9.203421 CGCTAGTATCACCATTATTTATGTCAA 57.797 33.333 0.00 0.00 31.99 3.18
2164 3281 8.581578 TCGCTAGTATCACCATTATTTATGTCA 58.418 33.333 0.00 0.00 31.99 3.58
2165 3282 8.981724 TCGCTAGTATCACCATTATTTATGTC 57.018 34.615 0.00 0.00 31.99 3.06
2166 3283 9.772973 TTTCGCTAGTATCACCATTATTTATGT 57.227 29.630 0.00 0.00 31.99 2.29
2169 3286 9.135843 CGATTTCGCTAGTATCACCATTATTTA 57.864 33.333 0.00 0.00 0.00 1.40
2170 3287 7.117812 CCGATTTCGCTAGTATCACCATTATTT 59.882 37.037 0.00 0.00 38.18 1.40
2171 3288 6.590292 CCGATTTCGCTAGTATCACCATTATT 59.410 38.462 0.00 0.00 38.18 1.40
2172 3289 6.071560 TCCGATTTCGCTAGTATCACCATTAT 60.072 38.462 0.00 0.00 38.18 1.28
2173 3290 5.242171 TCCGATTTCGCTAGTATCACCATTA 59.758 40.000 0.00 0.00 38.18 1.90
2174 3291 4.038763 TCCGATTTCGCTAGTATCACCATT 59.961 41.667 0.00 0.00 38.18 3.16
2175 3292 3.572682 TCCGATTTCGCTAGTATCACCAT 59.427 43.478 0.00 0.00 38.18 3.55
2176 3293 2.953648 TCCGATTTCGCTAGTATCACCA 59.046 45.455 0.00 0.00 38.18 4.17
2177 3294 3.637998 TCCGATTTCGCTAGTATCACC 57.362 47.619 0.00 0.00 38.18 4.02
2178 3295 4.143305 GCATTCCGATTTCGCTAGTATCAC 60.143 45.833 0.00 0.00 38.18 3.06
2179 3296 3.987868 GCATTCCGATTTCGCTAGTATCA 59.012 43.478 0.00 0.00 38.18 2.15
2180 3297 3.368236 GGCATTCCGATTTCGCTAGTATC 59.632 47.826 0.00 0.00 38.18 2.24
2181 3298 3.326747 GGCATTCCGATTTCGCTAGTAT 58.673 45.455 0.00 0.00 38.18 2.12
2182 3299 2.547218 GGGCATTCCGATTTCGCTAGTA 60.547 50.000 0.00 0.00 38.18 1.82
2183 3300 1.583054 GGCATTCCGATTTCGCTAGT 58.417 50.000 0.00 0.00 38.18 2.57
2184 3301 0.868406 GGGCATTCCGATTTCGCTAG 59.132 55.000 0.00 0.00 38.18 3.42
2185 3302 0.468226 AGGGCATTCCGATTTCGCTA 59.532 50.000 0.00 0.00 41.52 4.26
2186 3303 0.815615 GAGGGCATTCCGATTTCGCT 60.816 55.000 0.00 0.00 41.52 4.93
2187 3304 0.815615 AGAGGGCATTCCGATTTCGC 60.816 55.000 0.00 0.00 41.52 4.70
2188 3305 0.940126 CAGAGGGCATTCCGATTTCG 59.060 55.000 0.00 0.00 41.52 3.46
2189 3306 2.332063 TCAGAGGGCATTCCGATTTC 57.668 50.000 0.00 0.00 41.52 2.17
2190 3307 2.806945 TTCAGAGGGCATTCCGATTT 57.193 45.000 0.00 0.00 41.52 2.17
2191 3308 2.806945 TTTCAGAGGGCATTCCGATT 57.193 45.000 0.00 0.00 41.52 3.34
2192 3309 2.579873 CATTTCAGAGGGCATTCCGAT 58.420 47.619 0.00 0.00 41.52 4.18
2193 3310 1.408683 CCATTTCAGAGGGCATTCCGA 60.409 52.381 0.00 0.00 41.52 4.55
2194 3311 1.027357 CCATTTCAGAGGGCATTCCG 58.973 55.000 0.00 0.00 41.52 4.30
2195 3312 2.442236 TCCATTTCAGAGGGCATTCC 57.558 50.000 0.00 0.00 0.00 3.01
2196 3313 2.692041 CCTTCCATTTCAGAGGGCATTC 59.308 50.000 0.00 0.00 0.00 2.67
2197 3314 2.625087 CCCTTCCATTTCAGAGGGCATT 60.625 50.000 0.00 0.00 42.18 3.56
2198 3315 1.063417 CCCTTCCATTTCAGAGGGCAT 60.063 52.381 0.00 0.00 42.18 4.40
2199 3316 0.332632 CCCTTCCATTTCAGAGGGCA 59.667 55.000 0.00 0.00 42.18 5.36
2200 3317 0.625849 TCCCTTCCATTTCAGAGGGC 59.374 55.000 2.37 0.00 46.88 5.19
2202 3319 3.549794 GATGTCCCTTCCATTTCAGAGG 58.450 50.000 0.00 0.00 0.00 3.69
2203 3320 3.201290 CGATGTCCCTTCCATTTCAGAG 58.799 50.000 0.00 0.00 0.00 3.35
2204 3321 2.571653 ACGATGTCCCTTCCATTTCAGA 59.428 45.455 0.00 0.00 0.00 3.27
2205 3322 2.939103 GACGATGTCCCTTCCATTTCAG 59.061 50.000 0.00 0.00 0.00 3.02
2206 3323 2.304470 TGACGATGTCCCTTCCATTTCA 59.696 45.455 0.00 0.00 0.00 2.69
2207 3324 2.985896 TGACGATGTCCCTTCCATTTC 58.014 47.619 0.00 0.00 0.00 2.17
2208 3325 3.433306 TTGACGATGTCCCTTCCATTT 57.567 42.857 0.00 0.00 0.00 2.32
2209 3326 3.054434 TGATTGACGATGTCCCTTCCATT 60.054 43.478 0.00 0.00 0.00 3.16
2210 3327 2.505407 TGATTGACGATGTCCCTTCCAT 59.495 45.455 0.00 0.00 0.00 3.41
2211 3328 1.905894 TGATTGACGATGTCCCTTCCA 59.094 47.619 0.00 0.00 0.00 3.53
2212 3329 2.691409 TGATTGACGATGTCCCTTCC 57.309 50.000 0.00 0.00 0.00 3.46
2213 3330 5.371115 TTTTTGATTGACGATGTCCCTTC 57.629 39.130 0.00 0.00 0.00 3.46
2214 3331 5.476599 TGATTTTTGATTGACGATGTCCCTT 59.523 36.000 0.00 0.00 0.00 3.95
2215 3332 5.009631 TGATTTTTGATTGACGATGTCCCT 58.990 37.500 0.00 0.00 0.00 4.20
2216 3333 5.309323 TGATTTTTGATTGACGATGTCCC 57.691 39.130 0.00 0.00 0.00 4.46
2217 3334 5.287035 GCTTGATTTTTGATTGACGATGTCC 59.713 40.000 0.00 0.00 0.00 4.02
2218 3335 5.858049 TGCTTGATTTTTGATTGACGATGTC 59.142 36.000 0.00 0.00 0.00 3.06
2219 3336 5.771469 TGCTTGATTTTTGATTGACGATGT 58.229 33.333 0.00 0.00 0.00 3.06
2220 3337 6.880822 ATGCTTGATTTTTGATTGACGATG 57.119 33.333 0.00 0.00 0.00 3.84
2221 3338 7.318141 AGAATGCTTGATTTTTGATTGACGAT 58.682 30.769 0.00 0.00 0.00 3.73
2222 3339 6.680810 AGAATGCTTGATTTTTGATTGACGA 58.319 32.000 0.00 0.00 0.00 4.20
2223 3340 6.939551 AGAATGCTTGATTTTTGATTGACG 57.060 33.333 0.00 0.00 0.00 4.35
2229 3346 9.590451 GGATGAATAAGAATGCTTGATTTTTGA 57.410 29.630 0.00 0.00 35.56 2.69
2230 3347 9.373603 TGGATGAATAAGAATGCTTGATTTTTG 57.626 29.630 0.00 0.00 35.56 2.44
2262 3379 9.866655 TCCCTCCTACGATACTAATTAGTAAAA 57.133 33.333 25.21 8.96 41.64 1.52
2263 3380 9.512588 CTCCCTCCTACGATACTAATTAGTAAA 57.487 37.037 25.21 9.65 41.64 2.01
2264 3381 8.664079 ACTCCCTCCTACGATACTAATTAGTAA 58.336 37.037 25.21 10.98 41.64 2.24
2265 3382 8.212259 ACTCCCTCCTACGATACTAATTAGTA 57.788 38.462 24.01 24.01 42.43 1.82
2266 3383 7.089106 ACTCCCTCCTACGATACTAATTAGT 57.911 40.000 21.35 21.35 40.24 2.24
2267 3384 7.999450 AACTCCCTCCTACGATACTAATTAG 57.001 40.000 11.05 11.05 0.00 1.73
2269 3386 8.953223 AATAACTCCCTCCTACGATACTAATT 57.047 34.615 0.00 0.00 0.00 1.40
2270 3387 8.953223 AAATAACTCCCTCCTACGATACTAAT 57.047 34.615 0.00 0.00 0.00 1.73
2271 3388 9.866655 TTAAATAACTCCCTCCTACGATACTAA 57.133 33.333 0.00 0.00 0.00 2.24
2272 3389 9.289782 GTTAAATAACTCCCTCCTACGATACTA 57.710 37.037 0.00 0.00 33.52 1.82
2273 3390 7.232330 GGTTAAATAACTCCCTCCTACGATACT 59.768 40.741 3.55 0.00 36.47 2.12
2274 3391 7.014615 TGGTTAAATAACTCCCTCCTACGATAC 59.985 40.741 3.55 0.00 36.47 2.24
2275 3392 7.014615 GTGGTTAAATAACTCCCTCCTACGATA 59.985 40.741 3.55 0.00 36.47 2.92
2276 3393 5.901276 TGGTTAAATAACTCCCTCCTACGAT 59.099 40.000 3.55 0.00 36.47 3.73
2277 3394 5.127682 GTGGTTAAATAACTCCCTCCTACGA 59.872 44.000 3.55 0.00 36.47 3.43
2278 3395 5.128335 AGTGGTTAAATAACTCCCTCCTACG 59.872 44.000 3.55 0.00 36.47 3.51
2279 3396 6.556974 AGTGGTTAAATAACTCCCTCCTAC 57.443 41.667 3.55 0.00 36.47 3.18
2280 3397 8.683776 TTTAGTGGTTAAATAACTCCCTCCTA 57.316 34.615 3.55 0.00 36.47 2.94
2281 3398 7.578458 TTTAGTGGTTAAATAACTCCCTCCT 57.422 36.000 3.55 0.00 36.47 3.69
2282 3399 8.818622 ATTTTAGTGGTTAAATAACTCCCTCC 57.181 34.615 3.55 0.00 36.47 4.30
2284 3401 9.387257 CGTATTTTAGTGGTTAAATAACTCCCT 57.613 33.333 3.55 0.93 36.47 4.20
2285 3402 9.166173 ACGTATTTTAGTGGTTAAATAACTCCC 57.834 33.333 3.55 0.00 36.47 4.30
2296 3413 9.745880 CATGTATCTAGACGTATTTTAGTGGTT 57.254 33.333 0.00 0.00 0.00 3.67
2297 3414 9.128404 TCATGTATCTAGACGTATTTTAGTGGT 57.872 33.333 0.00 0.00 0.00 4.16
2298 3415 9.961265 TTCATGTATCTAGACGTATTTTAGTGG 57.039 33.333 0.00 0.00 0.00 4.00
2309 3426 5.985530 TGGCTGAAATTCATGTATCTAGACG 59.014 40.000 0.00 0.00 0.00 4.18
2320 3437 3.411446 TCTCGTTGTGGCTGAAATTCAT 58.589 40.909 0.00 0.00 0.00 2.57
2322 3439 3.555518 GTTCTCGTTGTGGCTGAAATTC 58.444 45.455 0.00 0.00 0.00 2.17
2323 3440 2.032030 CGTTCTCGTTGTGGCTGAAATT 60.032 45.455 0.00 0.00 0.00 1.82
2329 3446 0.600255 CCTTCGTTCTCGTTGTGGCT 60.600 55.000 0.00 0.00 38.33 4.75
2332 3449 1.269621 ACTCCCTTCGTTCTCGTTGTG 60.270 52.381 0.00 0.00 38.33 3.33
2337 3454 1.401199 GGAGTACTCCCTTCGTTCTCG 59.599 57.143 28.87 0.00 43.94 4.04
2350 3467 1.085715 AGACCAGTGGAGGGAGTACT 58.914 55.000 18.40 0.00 0.00 2.73
2351 3468 1.187087 CAGACCAGTGGAGGGAGTAC 58.813 60.000 18.40 0.00 0.00 2.73
2352 3469 0.041238 CCAGACCAGTGGAGGGAGTA 59.959 60.000 18.40 0.00 40.44 2.59
2353 3470 1.229336 CCAGACCAGTGGAGGGAGT 60.229 63.158 18.40 0.00 40.44 3.85
2354 3471 2.664081 GCCAGACCAGTGGAGGGAG 61.664 68.421 18.40 1.26 40.44 4.30
2356 3473 2.930019 TGCCAGACCAGTGGAGGG 60.930 66.667 18.40 14.63 40.44 4.30
2357 3474 2.348998 GTGCCAGACCAGTGGAGG 59.651 66.667 18.40 15.33 40.44 4.30
2358 3475 2.047844 CGTGCCAGACCAGTGGAG 60.048 66.667 18.40 5.07 40.44 3.86
2359 3476 4.314440 GCGTGCCAGACCAGTGGA 62.314 66.667 18.40 0.00 40.44 4.02
2361 3478 4.320456 AGGCGTGCCAGACCAGTG 62.320 66.667 14.29 0.00 38.92 3.66
2362 3479 4.320456 CAGGCGTGCCAGACCAGT 62.320 66.667 14.29 0.00 38.92 4.00
2378 3914 0.616111 GGGCTCTCTGTCTTCTCCCA 60.616 60.000 0.00 0.00 32.68 4.37
2389 3925 0.339859 TGGTATGACCTGGGCTCTCT 59.660 55.000 0.00 0.00 39.58 3.10
2390 3926 1.346068 GATGGTATGACCTGGGCTCTC 59.654 57.143 0.00 0.00 39.58 3.20
2405 3941 1.203100 AGAAAGCAAGGGCAAGATGGT 60.203 47.619 0.00 0.00 44.61 3.55
2469 4026 0.671251 CTCCTGGAGATAGGCGTGTC 59.329 60.000 19.13 0.00 37.76 3.67
2470 4027 0.259065 TCTCCTGGAGATAGGCGTGT 59.741 55.000 22.30 0.00 37.76 4.49
2472 4029 0.820074 CGTCTCCTGGAGATAGGCGT 60.820 60.000 27.96 0.00 40.98 5.68
2473 4030 1.519751 CCGTCTCCTGGAGATAGGCG 61.520 65.000 27.96 24.06 40.98 5.52
2474 4031 2.346597 CCGTCTCCTGGAGATAGGC 58.653 63.158 27.96 14.71 40.98 3.93
2475 4032 0.178975 AGCCGTCTCCTGGAGATAGG 60.179 60.000 30.77 30.77 40.98 2.57
2476 4033 1.698506 AAGCCGTCTCCTGGAGATAG 58.301 55.000 27.96 22.88 40.98 2.08
2484 4086 3.983044 AATTCTACAAAGCCGTCTCCT 57.017 42.857 0.00 0.00 0.00 3.69
2498 4100 1.828595 TGGCTCGCACCTGTAATTCTA 59.171 47.619 0.00 0.00 0.00 2.10
2519 4122 1.071814 TGCTGATGCTGTGCTGTGA 59.928 52.632 0.00 0.00 40.48 3.58
2534 4137 1.135915 CTGAGACATCCTAAGCGTGCT 59.864 52.381 0.00 0.00 0.00 4.40
2540 4143 2.293122 CTCCGCTCTGAGACATCCTAAG 59.707 54.545 9.28 0.00 34.11 2.18
2543 4146 0.033601 ACTCCGCTCTGAGACATCCT 60.034 55.000 9.28 0.00 36.22 3.24
2545 4148 0.527385 GCACTCCGCTCTGAGACATC 60.527 60.000 9.28 0.00 37.77 3.06
2546 4149 1.515020 GCACTCCGCTCTGAGACAT 59.485 57.895 9.28 0.00 37.77 3.06
2547 4150 2.965783 GCACTCCGCTCTGAGACA 59.034 61.111 9.28 0.00 37.77 3.41
2557 4160 0.725686 CTTGCATCTTGAGCACTCCG 59.274 55.000 0.00 0.00 42.54 4.63
2558 4161 1.467734 CACTTGCATCTTGAGCACTCC 59.532 52.381 0.00 0.00 42.54 3.85
2559 4162 2.415857 CTCACTTGCATCTTGAGCACTC 59.584 50.000 6.76 0.00 42.54 3.51
2561 4164 1.467734 CCTCACTTGCATCTTGAGCAC 59.532 52.381 12.21 0.00 42.54 4.40
2562 4165 1.348696 TCCTCACTTGCATCTTGAGCA 59.651 47.619 12.21 0.00 40.85 4.26
2563 4166 2.008329 CTCCTCACTTGCATCTTGAGC 58.992 52.381 12.21 0.00 36.26 4.26
2564 4167 2.630158 CCTCCTCACTTGCATCTTGAG 58.370 52.381 11.14 11.14 37.17 3.02
2565 4168 1.339438 GCCTCCTCACTTGCATCTTGA 60.339 52.381 0.00 0.00 0.00 3.02
2566 4169 1.093159 GCCTCCTCACTTGCATCTTG 58.907 55.000 0.00 0.00 0.00 3.02
2568 4171 1.220206 CGCCTCCTCACTTGCATCT 59.780 57.895 0.00 0.00 0.00 2.90
2569 4172 0.179062 ATCGCCTCCTCACTTGCATC 60.179 55.000 0.00 0.00 0.00 3.91
2570 4173 0.179062 GATCGCCTCCTCACTTGCAT 60.179 55.000 0.00 0.00 0.00 3.96
2571 4174 1.219124 GATCGCCTCCTCACTTGCA 59.781 57.895 0.00 0.00 0.00 4.08
2573 4176 1.579698 CATGATCGCCTCCTCACTTG 58.420 55.000 0.00 0.00 0.00 3.16
2575 4178 1.445095 GCATGATCGCCTCCTCACT 59.555 57.895 0.00 0.00 0.00 3.41
2615 4301 1.834822 CTCCATCCGGACCTCCTCC 60.835 68.421 6.12 0.00 35.91 4.30
2616 4302 1.834822 CCTCCATCCGGACCTCCTC 60.835 68.421 6.12 0.00 35.91 3.71
2617 4303 1.669927 ATCCTCCATCCGGACCTCCT 61.670 60.000 6.12 0.00 35.91 3.69
2618 4304 1.152226 ATCCTCCATCCGGACCTCC 60.152 63.158 6.12 0.00 35.91 4.30
2619 4305 1.528292 CGATCCTCCATCCGGACCTC 61.528 65.000 6.12 0.00 35.91 3.85
2620 4306 1.531840 CGATCCTCCATCCGGACCT 60.532 63.158 6.12 0.00 35.91 3.85
2621 4307 3.052081 CGATCCTCCATCCGGACC 58.948 66.667 6.12 0.00 35.91 4.46
2622 4308 2.340443 GCGATCCTCCATCCGGAC 59.660 66.667 6.12 0.00 35.91 4.79
2623 4309 3.295273 CGCGATCCTCCATCCGGA 61.295 66.667 6.61 6.61 39.79 5.14
2624 4310 3.151958 AACGCGATCCTCCATCCGG 62.152 63.158 15.93 0.00 32.47 5.14
2625 4311 1.951130 CAACGCGATCCTCCATCCG 60.951 63.158 15.93 0.00 33.67 4.18
2626 4312 0.598680 CTCAACGCGATCCTCCATCC 60.599 60.000 15.93 0.00 0.00 3.51
2627 4313 1.218230 GCTCAACGCGATCCTCCATC 61.218 60.000 15.93 0.00 0.00 3.51
2661 4347 2.905075 AGAAAACCAAAAACAGCTGGC 58.095 42.857 19.93 0.00 36.03 4.85


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

AutoCloner maintained by Alex Coulton.