Multiple sequence alignment - TraesCS2B01G591000

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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 TraesCS2B01G591000 chr2B 100.000 2765 0 0 1 2765 776709656 776706892 0.000000e+00 5107
1 TraesCS2B01G591000 chr2D 90.944 2087 114 28 1 2063 633711889 633709854 0.000000e+00 2737
2 TraesCS2B01G591000 chr2D 88.177 406 39 6 2367 2765 633709006 633708603 2.490000e-130 475
3 TraesCS2B01G591000 chr2D 91.304 184 16 0 2181 2364 468000204 468000387 4.570000e-63 252
4 TraesCS2B01G591000 chr2A 90.619 1535 74 34 523 2013 779889731 779891239 0.000000e+00 1973
5 TraesCS2B01G591000 chr2A 89.806 412 33 5 2362 2765 779891691 779892101 1.130000e-143 520
6 TraesCS2B01G591000 chr2A 86.393 463 31 10 1 458 779888981 779889416 6.930000e-131 477
7 TraesCS2B01G591000 chr2A 91.892 185 15 0 2181 2365 593912618 593912802 2.730000e-65 259
8 TraesCS2B01G591000 chr7B 93.678 174 11 0 2189 2362 254091246 254091073 7.600000e-66 261
9 TraesCS2B01G591000 chr5D 92.265 181 14 0 2184 2364 501349998 501349818 9.830000e-65 257
10 TraesCS2B01G591000 chr6D 92.179 179 11 1 2184 2362 440419767 440419592 1.640000e-62 250
11 TraesCS2B01G591000 chr6A 89.944 179 18 0 2186 2364 470142342 470142520 5.960000e-57 231
12 TraesCS2B01G591000 chr6A 89.071 183 18 2 2186 2367 31012745 31012564 2.770000e-55 226
13 TraesCS2B01G591000 chr4A 89.655 174 18 0 2189 2362 185434224 185434051 3.580000e-54 222
14 TraesCS2B01G591000 chr5A 89.205 176 19 0 2186 2361 680718925 680718750 1.290000e-53 220


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 TraesCS2B01G591000 chr2B 776706892 776709656 2764 True 5107 5107 100.000000 1 2765 1 chr2B.!!$R1 2764
1 TraesCS2B01G591000 chr2D 633708603 633711889 3286 True 1606 2737 89.560500 1 2765 2 chr2D.!!$R1 2764
2 TraesCS2B01G591000 chr2A 779888981 779892101 3120 False 990 1973 88.939333 1 2765 3 chr2A.!!$F2 2764

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
272 278 0.037697 CACGCTTACTACCACCTGCA 60.038 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 3200 0.179108 GAACTGATTCTCGACCCCCG 60.179 60.0 0.0 0.0 40.25 5.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 6.073003 GCTTATATATTTCATCTATGCCGCCC 60.073 42.308 0.00 0.00 0.00 6.13
70 71 6.490566 ACACGGGATTATTACTTGAAACAC 57.509 37.500 0.00 0.00 0.00 3.32
71 72 5.998981 ACACGGGATTATTACTTGAAACACA 59.001 36.000 0.00 0.00 0.00 3.72
72 73 6.072893 ACACGGGATTATTACTTGAAACACAC 60.073 38.462 0.00 0.00 0.00 3.82
73 74 5.998981 ACGGGATTATTACTTGAAACACACA 59.001 36.000 0.00 0.00 0.00 3.72
74 75 6.072893 ACGGGATTATTACTTGAAACACACAC 60.073 38.462 0.00 0.00 0.00 3.82
75 76 6.072948 CGGGATTATTACTTGAAACACACACA 60.073 38.462 0.00 0.00 0.00 3.72
76 77 7.081976 GGGATTATTACTTGAAACACACACAC 58.918 38.462 0.00 0.00 0.00 3.82
77 78 7.255312 GGGATTATTACTTGAAACACACACACA 60.255 37.037 0.00 0.00 0.00 3.72
78 79 8.132362 GGATTATTACTTGAAACACACACACAA 58.868 33.333 0.00 0.00 0.00 3.33
79 80 9.509855 GATTATTACTTGAAACACACACACAAA 57.490 29.630 0.00 0.00 0.00 2.83
80 81 9.862371 ATTATTACTTGAAACACACACACAAAA 57.138 25.926 0.00 0.00 0.00 2.44
81 82 9.692749 TTATTACTTGAAACACACACACAAAAA 57.307 25.926 0.00 0.00 0.00 1.94
119 120 3.241900 CGATGTGCGAATGTGAAAGAGAG 60.242 47.826 0.00 0.00 44.57 3.20
163 164 1.008875 TCACGTCACGCATGAAGCTC 61.009 55.000 0.00 0.00 42.61 4.09
165 166 2.456119 CGTCACGCATGAAGCTCCC 61.456 63.158 0.00 0.00 42.61 4.30
170 171 1.821332 CGCATGAAGCTCCCCCTTC 60.821 63.158 0.00 0.00 42.61 3.46
174 175 2.614013 GAAGCTCCCCCTTCCCCA 60.614 66.667 0.00 0.00 36.15 4.96
222 223 1.748493 GCCGGCCTGATTAATGTTCAA 59.252 47.619 18.11 0.00 0.00 2.69
223 224 2.479560 GCCGGCCTGATTAATGTTCAAC 60.480 50.000 18.11 0.00 0.00 3.18
261 262 3.426191 TCAACGTAATCACACACGCTTAC 59.574 43.478 0.00 0.00 41.80 2.34
264 265 4.161333 ACGTAATCACACACGCTTACTAC 58.839 43.478 0.00 0.00 41.80 2.73
272 278 0.037697 CACGCTTACTACCACCTGCA 60.038 55.000 0.00 0.00 0.00 4.41
303 309 1.306141 TGAGAGGCATCTTCCGGGT 60.306 57.895 0.76 0.00 35.30 5.28
361 368 6.170506 TGCCGGATACACATTAATCTATTCC 58.829 40.000 5.05 0.00 0.00 3.01
362 369 5.585047 GCCGGATACACATTAATCTATTCCC 59.415 44.000 5.05 0.00 0.00 3.97
363 370 5.810587 CCGGATACACATTAATCTATTCCCG 59.189 44.000 0.00 0.00 0.00 5.14
386 393 2.357517 CACCTGACCCACGACAGC 60.358 66.667 0.00 0.00 33.40 4.40
474 628 0.999406 CATGTCCTTACTCGGTTGCG 59.001 55.000 0.00 0.00 0.00 4.85
493 647 1.393539 CGACCATTCAACACGATGGAC 59.606 52.381 9.20 2.54 37.60 4.02
543 800 3.011818 TGAGCACATGACTAAATGCCTG 58.988 45.455 0.00 0.00 38.92 4.85
554 811 0.749454 AAATGCCTGGCTCGATGGAC 60.749 55.000 21.03 0.00 0.00 4.02
555 812 1.913951 AATGCCTGGCTCGATGGACA 61.914 55.000 21.03 0.00 0.00 4.02
556 813 2.512515 GCCTGGCTCGATGGACAC 60.513 66.667 12.43 0.00 0.00 3.67
590 848 2.389059 TCGCGTACGACTAGCTAGTAG 58.611 52.381 26.11 26.42 45.12 2.57
707 983 3.615849 GAGACAGCCACTGTTTCAAAG 57.384 47.619 12.02 0.00 45.44 2.77
750 1026 3.788766 AAGTCAATCACGCGCGCC 61.789 61.111 32.58 8.75 0.00 6.53
790 1083 0.798771 CGAGACCGGAAGAAAGCTCG 60.799 60.000 9.46 10.53 39.12 5.03
824 1118 2.730094 CCAAGCAGCACCAACCAC 59.270 61.111 0.00 0.00 0.00 4.16
825 1119 2.126596 CCAAGCAGCACCAACCACA 61.127 57.895 0.00 0.00 0.00 4.17
826 1120 1.066257 CAAGCAGCACCAACCACAC 59.934 57.895 0.00 0.00 0.00 3.82
827 1121 1.379710 AAGCAGCACCAACCACACA 60.380 52.632 0.00 0.00 0.00 3.72
852 1150 0.603707 ACTTGACACCAGCCATCACG 60.604 55.000 0.00 0.00 0.00 4.35
874 1172 3.992943 ATAAACTTGGACCCGATCACA 57.007 42.857 0.00 0.00 0.00 3.58
875 1173 2.879103 AAACTTGGACCCGATCACAT 57.121 45.000 0.00 0.00 0.00 3.21
902 1200 3.065575 CCACTACATCGGTGGCTTC 57.934 57.895 0.00 0.00 45.97 3.86
918 1216 5.281727 GTGGCTTCGAACATTTTCTTTCTT 58.718 37.500 0.00 0.00 0.00 2.52
919 1217 5.173854 GTGGCTTCGAACATTTTCTTTCTTG 59.826 40.000 0.00 0.00 0.00 3.02
976 1282 5.873211 GCTGTAAGAAGCAAGAAAACAAC 57.127 39.130 0.00 0.00 43.01 3.32
977 1283 5.582550 GCTGTAAGAAGCAAGAAAACAACT 58.417 37.500 0.00 0.00 43.01 3.16
978 1284 6.725246 GCTGTAAGAAGCAAGAAAACAACTA 58.275 36.000 0.00 0.00 43.01 2.24
1662 1974 0.037326 TCAAGCTGTGGACGATGACC 60.037 55.000 0.00 0.00 0.00 4.02
1733 2045 3.499737 CCGCATCCGCTCCAACAC 61.500 66.667 0.00 0.00 35.30 3.32
1757 2069 2.079925 CACCTTCAAGCTCAAGCCTAC 58.920 52.381 0.00 0.00 43.38 3.18
1759 2071 3.055819 CACCTTCAAGCTCAAGCCTACTA 60.056 47.826 0.00 0.00 43.38 1.82
1760 2072 3.196685 ACCTTCAAGCTCAAGCCTACTAG 59.803 47.826 0.00 0.00 43.38 2.57
1761 2073 3.431486 CCTTCAAGCTCAAGCCTACTAGG 60.431 52.174 0.00 0.00 43.38 3.02
1768 2080 3.189702 GCTCAAGCCTACTAGGTAGATCG 59.810 52.174 3.95 0.00 38.29 3.69
1818 2130 5.694458 GGATTGTGCATATATACGTGTGTCA 59.306 40.000 0.00 0.00 0.00 3.58
1823 2135 6.861055 TGTGCATATATACGTGTGTCATGTAG 59.139 38.462 0.00 0.00 38.90 2.74
1831 2143 4.529897 ACGTGTGTCATGTAGGTAGGATA 58.470 43.478 0.00 0.00 31.23 2.59
1832 2144 4.951715 ACGTGTGTCATGTAGGTAGGATAA 59.048 41.667 0.00 0.00 31.23 1.75
1833 2145 5.597182 ACGTGTGTCATGTAGGTAGGATAAT 59.403 40.000 0.00 0.00 31.23 1.28
1868 2180 2.899900 TCCCCATTCCTGTCGATCTATG 59.100 50.000 0.00 0.00 0.00 2.23
1958 2274 8.289618 GGCTCGCATATTCATTATTTTTAGTGA 58.710 33.333 0.00 0.00 0.00 3.41
1984 2300 7.368833 AGTAAATAAGATCCGAGGTGTATTCG 58.631 38.462 0.00 0.00 37.78 3.34
1990 2307 0.368907 CCGAGGTGTATTCGTTTGCG 59.631 55.000 0.00 0.00 36.37 4.85
2008 2325 3.738982 TGCGATGAGTTTCTTTGGAGAA 58.261 40.909 0.00 0.00 40.07 2.87
2040 2357 5.295950 AGAGAAGATATTGGCTCATGAACG 58.704 41.667 0.00 0.00 0.00 3.95
2046 2363 0.955428 TTGGCTCATGAACGCAGTCC 60.955 55.000 8.97 0.00 45.00 3.85
2047 2364 1.375908 GGCTCATGAACGCAGTCCA 60.376 57.895 8.97 0.00 45.00 4.02
2048 2365 0.745845 GGCTCATGAACGCAGTCCAT 60.746 55.000 8.97 0.00 45.00 3.41
2049 2366 1.473257 GGCTCATGAACGCAGTCCATA 60.473 52.381 8.97 0.00 45.00 2.74
2052 2370 2.212652 TCATGAACGCAGTCCATATGC 58.787 47.619 0.00 0.00 45.00 3.14
2085 3200 2.109181 GGGGCGTCATGAGTAGGC 59.891 66.667 0.00 3.06 0.00 3.93
2093 3211 2.838225 ATGAGTAGGCGGGGGTCG 60.838 66.667 0.00 0.00 42.76 4.79
2123 3241 8.391075 TCAGTTCCAAAGTTCTTTTATACTGG 57.609 34.615 18.87 9.66 34.60 4.00
2124 3242 7.996644 TCAGTTCCAAAGTTCTTTTATACTGGT 59.003 33.333 18.87 0.00 34.60 4.00
2125 3243 8.290325 CAGTTCCAAAGTTCTTTTATACTGGTC 58.710 37.037 15.16 6.01 32.56 4.02
2126 3244 7.996644 AGTTCCAAAGTTCTTTTATACTGGTCA 59.003 33.333 0.00 0.00 0.00 4.02
2127 3245 8.793592 GTTCCAAAGTTCTTTTATACTGGTCAT 58.206 33.333 0.00 0.00 0.00 3.06
2134 3252 9.838339 AGTTCTTTTATACTGGTCATAATGGAG 57.162 33.333 0.00 0.00 0.00 3.86
2135 3253 9.832445 GTTCTTTTATACTGGTCATAATGGAGA 57.168 33.333 0.00 0.00 0.00 3.71
2137 3255 8.150945 TCTTTTATACTGGTCATAATGGAGAGC 58.849 37.037 0.00 0.00 0.00 4.09
2138 3256 6.994421 TTATACTGGTCATAATGGAGAGCA 57.006 37.500 0.00 0.00 39.66 4.26
2139 3257 3.550437 ACTGGTCATAATGGAGAGCAC 57.450 47.619 0.00 0.00 37.34 4.40
2140 3258 2.840038 ACTGGTCATAATGGAGAGCACA 59.160 45.455 0.00 0.00 37.34 4.57
2141 3259 3.457380 ACTGGTCATAATGGAGAGCACAT 59.543 43.478 0.00 0.00 37.34 3.21
2142 3260 3.812262 TGGTCATAATGGAGAGCACATG 58.188 45.455 0.00 0.00 37.34 3.21
2143 3261 3.455543 TGGTCATAATGGAGAGCACATGA 59.544 43.478 0.00 0.00 37.34 3.07
2144 3262 3.812053 GGTCATAATGGAGAGCACATGAC 59.188 47.826 0.00 0.00 40.84 3.06
2145 3263 4.445453 GTCATAATGGAGAGCACATGACA 58.555 43.478 0.00 0.00 41.09 3.58
2146 3264 4.272018 GTCATAATGGAGAGCACATGACAC 59.728 45.833 0.00 0.00 41.09 3.67
2147 3265 4.162888 TCATAATGGAGAGCACATGACACT 59.837 41.667 0.00 0.00 0.00 3.55
2148 3266 2.398252 ATGGAGAGCACATGACACTG 57.602 50.000 0.00 0.00 0.00 3.66
2149 3267 0.322648 TGGAGAGCACATGACACTGG 59.677 55.000 0.00 0.00 0.00 4.00
2150 3268 0.322975 GGAGAGCACATGACACTGGT 59.677 55.000 0.00 0.00 0.00 4.00
2151 3269 1.550524 GGAGAGCACATGACACTGGTA 59.449 52.381 0.00 0.00 0.00 3.25
2152 3270 2.417924 GGAGAGCACATGACACTGGTAG 60.418 54.545 0.00 0.00 0.00 3.18
2153 3271 2.232452 GAGAGCACATGACACTGGTAGT 59.768 50.000 0.00 0.00 0.00 2.73
2154 3272 2.232452 AGAGCACATGACACTGGTAGTC 59.768 50.000 0.00 0.00 36.55 2.59
2155 3273 2.232452 GAGCACATGACACTGGTAGTCT 59.768 50.000 0.00 0.00 36.94 3.24
2156 3274 3.431415 AGCACATGACACTGGTAGTCTA 58.569 45.455 0.00 0.00 36.94 2.59
2157 3275 3.832490 AGCACATGACACTGGTAGTCTAA 59.168 43.478 0.00 0.00 36.94 2.10
2158 3276 4.081972 AGCACATGACACTGGTAGTCTAAG 60.082 45.833 0.00 0.00 36.94 2.18
2159 3277 4.322049 GCACATGACACTGGTAGTCTAAGT 60.322 45.833 0.00 0.00 36.94 2.24
2160 3278 5.784177 CACATGACACTGGTAGTCTAAGTT 58.216 41.667 0.00 0.00 36.94 2.66
2161 3279 6.223852 CACATGACACTGGTAGTCTAAGTTT 58.776 40.000 0.00 0.00 36.94 2.66
2162 3280 7.375834 CACATGACACTGGTAGTCTAAGTTTA 58.624 38.462 0.00 0.00 36.94 2.01
2163 3281 7.328737 CACATGACACTGGTAGTCTAAGTTTAC 59.671 40.741 0.00 0.00 36.94 2.01
2164 3282 6.336842 TGACACTGGTAGTCTAAGTTTACC 57.663 41.667 0.00 0.00 37.84 2.85
2165 3283 5.834742 TGACACTGGTAGTCTAAGTTTACCA 59.165 40.000 4.50 4.50 43.30 3.25
2166 3284 6.495872 TGACACTGGTAGTCTAAGTTTACCAT 59.504 38.462 4.93 0.00 44.16 3.55
2167 3285 6.932947 ACACTGGTAGTCTAAGTTTACCATC 58.067 40.000 4.93 0.00 44.16 3.51
2168 3286 6.724905 ACACTGGTAGTCTAAGTTTACCATCT 59.275 38.462 4.93 0.00 44.16 2.90
2169 3287 7.234988 ACACTGGTAGTCTAAGTTTACCATCTT 59.765 37.037 4.93 0.00 44.16 2.40
2170 3288 8.095169 CACTGGTAGTCTAAGTTTACCATCTTT 58.905 37.037 4.93 0.00 44.16 2.52
2171 3289 9.317827 ACTGGTAGTCTAAGTTTACCATCTTTA 57.682 33.333 4.93 0.00 44.16 1.85
2177 3295 9.819267 AGTCTAAGTTTACCATCTTTATAGTGC 57.181 33.333 0.00 0.00 0.00 4.40
2178 3296 9.595823 GTCTAAGTTTACCATCTTTATAGTGCA 57.404 33.333 0.00 0.00 0.00 4.57
2182 3300 8.281212 AGTTTACCATCTTTATAGTGCAAAGG 57.719 34.615 0.00 0.00 34.43 3.11
2183 3301 8.107095 AGTTTACCATCTTTATAGTGCAAAGGA 58.893 33.333 0.00 0.00 34.43 3.36
2184 3302 8.736244 GTTTACCATCTTTATAGTGCAAAGGAA 58.264 33.333 0.00 0.00 34.43 3.36
2185 3303 6.759497 ACCATCTTTATAGTGCAAAGGAAC 57.241 37.500 0.00 0.00 34.43 3.62
2186 3304 6.245408 ACCATCTTTATAGTGCAAAGGAACA 58.755 36.000 0.00 0.00 34.43 3.18
2187 3305 6.891908 ACCATCTTTATAGTGCAAAGGAACAT 59.108 34.615 0.00 0.00 34.43 2.71
2188 3306 8.052748 ACCATCTTTATAGTGCAAAGGAACATA 58.947 33.333 0.00 0.00 34.43 2.29
2189 3307 9.071276 CCATCTTTATAGTGCAAAGGAACATAT 57.929 33.333 0.00 0.00 34.43 1.78
2194 3312 9.860650 TTTATAGTGCAAAGGAACATATATGGT 57.139 29.630 16.96 10.62 0.00 3.55
2195 3313 9.860650 TTATAGTGCAAAGGAACATATATGGTT 57.139 29.630 16.96 8.61 0.00 3.67
2196 3314 6.455360 AGTGCAAAGGAACATATATGGTTG 57.545 37.500 16.96 6.73 0.00 3.77
2197 3315 5.043248 GTGCAAAGGAACATATATGGTTGC 58.957 41.667 16.96 16.05 36.91 4.17
2198 3316 4.708909 TGCAAAGGAACATATATGGTTGCA 59.291 37.500 19.27 19.27 38.82 4.08
2199 3317 5.363292 TGCAAAGGAACATATATGGTTGCAT 59.637 36.000 19.27 7.33 38.82 3.96
2200 3318 6.127111 TGCAAAGGAACATATATGGTTGCATT 60.127 34.615 19.27 11.60 38.82 3.56
2201 3319 6.762661 GCAAAGGAACATATATGGTTGCATTT 59.237 34.615 16.71 7.90 38.82 2.32
2202 3320 7.925483 GCAAAGGAACATATATGGTTGCATTTA 59.075 33.333 16.71 0.00 38.82 1.40
2203 3321 9.985730 CAAAGGAACATATATGGTTGCATTTAT 57.014 29.630 16.96 0.00 38.82 1.40
2207 3325 9.573133 GGAACATATATGGTTGCATTTATTAGC 57.427 33.333 16.96 0.00 36.69 3.09
2214 3332 7.880160 ATGGTTGCATTTATTAGCTTGTAGA 57.120 32.000 0.00 0.00 0.00 2.59
2215 3333 7.083875 TGGTTGCATTTATTAGCTTGTAGAC 57.916 36.000 0.00 0.00 0.00 2.59
2216 3334 6.884295 TGGTTGCATTTATTAGCTTGTAGACT 59.116 34.615 0.00 0.00 0.00 3.24
2217 3335 7.065803 TGGTTGCATTTATTAGCTTGTAGACTC 59.934 37.037 0.00 0.00 0.00 3.36
2218 3336 7.065803 GGTTGCATTTATTAGCTTGTAGACTCA 59.934 37.037 0.00 0.00 0.00 3.41
2219 3337 8.450964 GTTGCATTTATTAGCTTGTAGACTCAA 58.549 33.333 0.00 0.00 0.00 3.02
2220 3338 7.974675 TGCATTTATTAGCTTGTAGACTCAAC 58.025 34.615 0.00 0.00 0.00 3.18
2221 3339 7.824289 TGCATTTATTAGCTTGTAGACTCAACT 59.176 33.333 0.00 0.00 0.00 3.16
2222 3340 8.669243 GCATTTATTAGCTTGTAGACTCAACTT 58.331 33.333 0.00 0.00 0.00 2.66
2243 3361 3.717400 TTTTTGGCAAACGCTATGTGA 57.283 38.095 13.10 0.00 0.00 3.58
2244 3362 3.932545 TTTTGGCAAACGCTATGTGAT 57.067 38.095 13.10 0.00 0.00 3.06
2245 3363 2.917701 TTGGCAAACGCTATGTGATG 57.082 45.000 0.00 0.00 0.00 3.07
2246 3364 1.093972 TGGCAAACGCTATGTGATGG 58.906 50.000 0.00 0.00 0.00 3.51
2247 3365 1.094785 GGCAAACGCTATGTGATGGT 58.905 50.000 0.00 0.00 0.00 3.55
2248 3366 2.285083 GGCAAACGCTATGTGATGGTA 58.715 47.619 0.00 0.00 0.00 3.25
2249 3367 2.680841 GGCAAACGCTATGTGATGGTAA 59.319 45.455 0.00 0.00 0.00 2.85
2250 3368 3.486875 GGCAAACGCTATGTGATGGTAAC 60.487 47.826 0.00 0.00 0.00 2.50
2274 3392 8.788325 ACATAATAAGTTACTCCAAACACCTC 57.212 34.615 0.00 0.00 0.00 3.85
2275 3393 8.603304 ACATAATAAGTTACTCCAAACACCTCT 58.397 33.333 0.00 0.00 0.00 3.69
2276 3394 9.099454 CATAATAAGTTACTCCAAACACCTCTC 57.901 37.037 0.00 0.00 0.00 3.20
2277 3395 6.936968 ATAAGTTACTCCAAACACCTCTCT 57.063 37.500 0.00 0.00 0.00 3.10
2278 3396 5.632034 AAGTTACTCCAAACACCTCTCTT 57.368 39.130 0.00 0.00 0.00 2.85
2279 3397 5.632034 AGTTACTCCAAACACCTCTCTTT 57.368 39.130 0.00 0.00 0.00 2.52
2280 3398 6.002653 AGTTACTCCAAACACCTCTCTTTT 57.997 37.500 0.00 0.00 0.00 2.27
2281 3399 6.424032 AGTTACTCCAAACACCTCTCTTTTT 58.576 36.000 0.00 0.00 0.00 1.94
2282 3400 7.571025 AGTTACTCCAAACACCTCTCTTTTTA 58.429 34.615 0.00 0.00 0.00 1.52
2283 3401 8.218488 AGTTACTCCAAACACCTCTCTTTTTAT 58.782 33.333 0.00 0.00 0.00 1.40
2284 3402 8.847196 GTTACTCCAAACACCTCTCTTTTTATT 58.153 33.333 0.00 0.00 0.00 1.40
2286 3404 8.990163 ACTCCAAACACCTCTCTTTTTATTAA 57.010 30.769 0.00 0.00 0.00 1.40
2287 3405 9.588096 ACTCCAAACACCTCTCTTTTTATTAAT 57.412 29.630 0.00 0.00 0.00 1.40
2294 3412 8.678199 ACACCTCTCTTTTTATTAATTAGCTGC 58.322 33.333 0.00 0.00 0.00 5.25
2295 3413 8.131731 CACCTCTCTTTTTATTAATTAGCTGCC 58.868 37.037 0.00 0.00 0.00 4.85
2296 3414 7.834181 ACCTCTCTTTTTATTAATTAGCTGCCA 59.166 33.333 0.00 0.00 0.00 4.92
2297 3415 8.131731 CCTCTCTTTTTATTAATTAGCTGCCAC 58.868 37.037 0.00 0.00 0.00 5.01
2298 3416 8.574251 TCTCTTTTTATTAATTAGCTGCCACA 57.426 30.769 0.00 0.00 0.00 4.17
2299 3417 9.189156 TCTCTTTTTATTAATTAGCTGCCACAT 57.811 29.630 0.00 0.00 0.00 3.21
2303 3421 9.528018 TTTTTATTAATTAGCTGCCACATAAGC 57.472 29.630 0.00 0.00 39.82 3.09
2304 3422 7.815840 TTATTAATTAGCTGCCACATAAGCA 57.184 32.000 0.00 0.00 42.06 3.91
2305 3423 6.713762 ATTAATTAGCTGCCACATAAGCAA 57.286 33.333 0.00 0.00 42.06 3.91
2306 3424 6.522625 TTAATTAGCTGCCACATAAGCAAA 57.477 33.333 0.00 0.00 42.06 3.68
2307 3425 3.848272 TTAGCTGCCACATAAGCAAAC 57.152 42.857 0.00 0.00 42.06 2.93
2308 3426 1.915141 AGCTGCCACATAAGCAAACT 58.085 45.000 0.00 0.00 42.06 2.66
2309 3427 2.242043 AGCTGCCACATAAGCAAACTT 58.758 42.857 0.00 0.00 42.06 2.66
2310 3428 2.029649 AGCTGCCACATAAGCAAACTTG 60.030 45.455 0.00 0.00 42.06 3.16
2311 3429 2.288395 GCTGCCACATAAGCAAACTTGT 60.288 45.455 0.00 0.00 40.35 3.16
2312 3430 3.568538 CTGCCACATAAGCAAACTTGTC 58.431 45.455 0.00 0.00 40.35 3.18
2313 3431 3.221771 TGCCACATAAGCAAACTTGTCT 58.778 40.909 0.00 0.00 37.28 3.41
2314 3432 3.253188 TGCCACATAAGCAAACTTGTCTC 59.747 43.478 0.00 0.00 37.28 3.36
2315 3433 3.667960 GCCACATAAGCAAACTTGTCTCG 60.668 47.826 0.00 0.00 36.57 4.04
2316 3434 3.120199 CCACATAAGCAAACTTGTCTCGG 60.120 47.826 0.00 0.00 36.57 4.63
2317 3435 3.074412 ACATAAGCAAACTTGTCTCGGG 58.926 45.455 0.00 0.00 36.57 5.14
2318 3436 3.244422 ACATAAGCAAACTTGTCTCGGGA 60.244 43.478 0.00 0.00 36.57 5.14
2319 3437 2.568623 AAGCAAACTTGTCTCGGGAT 57.431 45.000 0.00 0.00 33.84 3.85
2320 3438 3.695830 AAGCAAACTTGTCTCGGGATA 57.304 42.857 0.00 0.00 33.84 2.59
2321 3439 3.914426 AGCAAACTTGTCTCGGGATAT 57.086 42.857 0.00 0.00 0.00 1.63
2322 3440 3.535561 AGCAAACTTGTCTCGGGATATG 58.464 45.455 0.00 0.00 0.00 1.78
2323 3441 3.055094 AGCAAACTTGTCTCGGGATATGT 60.055 43.478 0.00 0.00 0.00 2.29
2324 3442 3.689649 GCAAACTTGTCTCGGGATATGTT 59.310 43.478 7.39 7.39 34.32 2.71
2325 3443 4.873827 GCAAACTTGTCTCGGGATATGTTA 59.126 41.667 12.65 0.00 32.71 2.41
2326 3444 5.527582 GCAAACTTGTCTCGGGATATGTTAT 59.472 40.000 12.65 2.85 32.71 1.89
2327 3445 6.511767 GCAAACTTGTCTCGGGATATGTTATG 60.512 42.308 12.65 13.02 32.71 1.90
2328 3446 5.871396 ACTTGTCTCGGGATATGTTATGT 57.129 39.130 0.00 0.00 0.00 2.29
2329 3447 6.235231 ACTTGTCTCGGGATATGTTATGTT 57.765 37.500 0.00 0.00 0.00 2.71
2330 3448 7.356089 ACTTGTCTCGGGATATGTTATGTTA 57.644 36.000 0.00 0.00 0.00 2.41
2331 3449 7.208080 ACTTGTCTCGGGATATGTTATGTTAC 58.792 38.462 0.00 0.00 0.00 2.50
2332 3450 6.971726 TGTCTCGGGATATGTTATGTTACT 57.028 37.500 0.00 0.00 0.00 2.24
2333 3451 7.356089 TGTCTCGGGATATGTTATGTTACTT 57.644 36.000 0.00 0.00 0.00 2.24
2334 3452 8.467963 TGTCTCGGGATATGTTATGTTACTTA 57.532 34.615 0.00 0.00 0.00 2.24
2335 3453 8.355169 TGTCTCGGGATATGTTATGTTACTTAC 58.645 37.037 0.00 0.00 0.00 2.34
2336 3454 8.574737 GTCTCGGGATATGTTATGTTACTTACT 58.425 37.037 0.00 0.00 0.00 2.24
2337 3455 9.797642 TCTCGGGATATGTTATGTTACTTACTA 57.202 33.333 0.00 0.00 0.00 1.82
2359 3477 7.450903 ACTATGTTATTCCCACTATAACCAGC 58.549 38.462 0.00 0.00 37.56 4.85
2360 3478 5.043737 TGTTATTCCCACTATAACCAGCC 57.956 43.478 0.00 0.00 37.56 4.85
2361 3479 4.724798 TGTTATTCCCACTATAACCAGCCT 59.275 41.667 0.00 0.00 37.56 4.58
2362 3480 5.192923 TGTTATTCCCACTATAACCAGCCTT 59.807 40.000 0.00 0.00 37.56 4.35
2363 3481 6.387513 TGTTATTCCCACTATAACCAGCCTTA 59.612 38.462 0.00 0.00 37.56 2.69
2364 3482 7.073215 TGTTATTCCCACTATAACCAGCCTTAT 59.927 37.037 0.00 0.00 37.56 1.73
2365 3483 4.974645 TCCCACTATAACCAGCCTTATG 57.025 45.455 0.00 0.00 0.00 1.90
2382 3500 4.503296 CCTTATGAGTTAAGCCGCACCTAT 60.503 45.833 0.00 0.00 36.71 2.57
2394 3512 2.618709 CCGCACCTATCCAAATTCCTTC 59.381 50.000 0.00 0.00 0.00 3.46
2406 3524 4.020839 CCAAATTCCTTCAACTGCTCCAAT 60.021 41.667 0.00 0.00 0.00 3.16
2445 3563 2.091541 TGCCGGCTCTTAATTTTGAGG 58.908 47.619 29.70 0.00 0.00 3.86
2462 3580 0.264657 AGGCCCCCAAACAAGTTCTT 59.735 50.000 0.00 0.00 0.00 2.52
2487 3606 4.617762 GCAAAAAGATCCCTTCAGCTTCAG 60.618 45.833 0.00 0.00 0.00 3.02
2488 3607 3.362870 AAAGATCCCTTCAGCTTCAGG 57.637 47.619 1.27 1.27 0.00 3.86
2489 3608 1.963985 AGATCCCTTCAGCTTCAGGT 58.036 50.000 7.12 0.00 0.00 4.00
2493 3617 0.695347 CCCTTCAGCTTCAGGTTCCT 59.305 55.000 7.12 0.00 0.00 3.36
2545 3669 4.830765 CCGCCTCCGCCGATTTCA 62.831 66.667 0.00 0.00 0.00 2.69
2549 3673 0.455815 GCCTCCGCCGATTTCATTTT 59.544 50.000 0.00 0.00 0.00 1.82
2555 3679 2.163412 CCGCCGATTTCATTTTCCTCAA 59.837 45.455 0.00 0.00 0.00 3.02
2565 3689 5.209818 TCATTTTCCTCAACGACTACTGT 57.790 39.130 0.00 0.00 0.00 3.55
2576 3700 4.742201 CTACTGTGCACGCCGGCT 62.742 66.667 26.68 8.92 34.04 5.52
2643 3768 4.357947 GCTCGTCGGCTGACACCA 62.358 66.667 24.91 7.56 45.80 4.17
2646 3771 1.583495 CTCGTCGGCTGACACCACTA 61.583 60.000 24.91 2.59 45.80 2.74
2680 3805 3.524826 CATATCTCCCTCCTTCCCATGA 58.475 50.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.045942 TCAAGGGCGGCATAGATGAAATATA 60.046 40.000 12.47 0.00 0.00 0.86
14 15 2.158623 TCAAGGGCGGCATAGATGAAAT 60.159 45.455 12.47 0.00 0.00 2.17
15 16 1.211703 TCAAGGGCGGCATAGATGAAA 59.788 47.619 12.47 0.00 0.00 2.69
16 17 0.836606 TCAAGGGCGGCATAGATGAA 59.163 50.000 12.47 0.00 0.00 2.57
17 18 0.394192 CTCAAGGGCGGCATAGATGA 59.606 55.000 12.47 3.56 0.00 2.92
18 19 0.394192 TCTCAAGGGCGGCATAGATG 59.606 55.000 12.47 0.00 0.00 2.90
31 32 5.479306 TCCCGTGTTAAGAAGATTCTCAAG 58.521 41.667 0.00 0.00 36.28 3.02
98 99 3.928992 TCTCTCTTTCACATTCGCACATC 59.071 43.478 0.00 0.00 0.00 3.06
165 166 4.410400 GGTGCGTCTGGGGAAGGG 62.410 72.222 0.00 0.00 0.00 3.95
210 211 6.198216 GTGGTTGTGTGTGTTGAACATTAATC 59.802 38.462 0.00 0.00 41.97 1.75
222 223 1.450669 GACCGGTGGTTGTGTGTGT 60.451 57.895 14.63 0.00 35.25 3.72
223 224 1.027255 TTGACCGGTGGTTGTGTGTG 61.027 55.000 14.63 0.00 35.25 3.82
261 262 2.434884 CAGCCGTGCAGGTGGTAG 60.435 66.667 5.57 0.00 43.70 3.18
303 309 4.491676 GGGACGCTATCGCTGAATAATTA 58.508 43.478 0.00 0.00 39.84 1.40
327 334 0.239347 GTATCCGGCAATGCATCAGC 59.761 55.000 7.79 13.95 42.57 4.26
328 335 1.265095 GTGTATCCGGCAATGCATCAG 59.735 52.381 7.79 0.00 0.00 2.90
361 368 0.602905 GTGGGTCAGGTGAAAGTCGG 60.603 60.000 0.00 0.00 0.00 4.79
362 369 0.944311 CGTGGGTCAGGTGAAAGTCG 60.944 60.000 0.00 0.00 0.00 4.18
363 370 0.391597 TCGTGGGTCAGGTGAAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
386 393 4.147449 TCACGGGATGCCTCAGCG 62.147 66.667 0.28 0.00 44.31 5.18
394 401 0.528466 CTCCATCGTGTCACGGGATG 60.528 60.000 24.33 19.78 42.81 3.51
474 628 2.673368 GAGTCCATCGTGTTGAATGGTC 59.327 50.000 1.62 0.00 35.74 4.02
493 647 0.363512 CACGTTGCACTTCGATCGAG 59.636 55.000 18.54 14.40 0.00 4.04
543 800 1.933853 GTTATGTGTGTCCATCGAGCC 59.066 52.381 0.00 0.00 0.00 4.70
590 848 1.757118 TGCAGGCAGATGTAGGAGTAC 59.243 52.381 0.00 0.00 0.00 2.73
593 851 0.538584 TGTGCAGGCAGATGTAGGAG 59.461 55.000 0.00 0.00 0.00 3.69
594 852 1.134310 CATGTGCAGGCAGATGTAGGA 60.134 52.381 19.76 0.00 41.14 2.94
595 853 1.306148 CATGTGCAGGCAGATGTAGG 58.694 55.000 19.76 0.00 41.14 3.18
618 876 2.297701 TGTGTGAACTTTTCTGGCTCC 58.702 47.619 0.00 0.00 0.00 4.70
619 877 4.370364 TTTGTGTGAACTTTTCTGGCTC 57.630 40.909 0.00 0.00 0.00 4.70
620 878 4.799564 TTTTGTGTGAACTTTTCTGGCT 57.200 36.364 0.00 0.00 0.00 4.75
621 879 6.313658 AGAAATTTTGTGTGAACTTTTCTGGC 59.686 34.615 0.00 0.00 32.41 4.85
707 983 5.357314 GGCCTTCTTACTACCATTTTCTTCC 59.643 44.000 0.00 0.00 0.00 3.46
750 1026 2.119801 ACCTTGACTTGGCTGCTATG 57.880 50.000 0.00 0.00 0.00 2.23
751 1027 2.716217 GAACCTTGACTTGGCTGCTAT 58.284 47.619 0.00 0.00 0.00 2.97
790 1083 5.003804 TGCTTGGGTTTCTTTCTAGATGTC 58.996 41.667 0.00 0.00 0.00 3.06
824 1118 1.401552 CTGGTGTCAAGTTGGTGTGTG 59.598 52.381 2.34 0.00 0.00 3.82
825 1119 1.750193 CTGGTGTCAAGTTGGTGTGT 58.250 50.000 2.34 0.00 0.00 3.72
826 1120 0.381801 GCTGGTGTCAAGTTGGTGTG 59.618 55.000 2.34 0.00 0.00 3.82
827 1121 0.751643 GGCTGGTGTCAAGTTGGTGT 60.752 55.000 2.34 0.00 0.00 4.16
852 1150 4.761975 TGTGATCGGGTCCAAGTTTATAC 58.238 43.478 0.00 0.00 0.00 1.47
874 1172 2.695666 CCGATGTAGTGGGAGTTGAGAT 59.304 50.000 0.00 0.00 0.00 2.75
875 1173 2.100197 CCGATGTAGTGGGAGTTGAGA 58.900 52.381 0.00 0.00 0.00 3.27
902 1200 6.751888 ACTGGTTTCAAGAAAGAAAATGTTCG 59.248 34.615 0.00 0.00 39.05 3.95
919 1217 1.734465 CTCGCAGGATGAACTGGTTTC 59.266 52.381 0.00 0.00 39.69 2.78
969 1267 4.163458 TCACCTGACTGGAGTAGTTGTTTT 59.837 41.667 5.22 0.00 40.53 2.43
972 1270 2.958818 TCACCTGACTGGAGTAGTTGT 58.041 47.619 5.22 0.00 40.53 3.32
975 1281 3.074687 TCTCTTCACCTGACTGGAGTAGT 59.925 47.826 5.22 0.00 44.02 2.73
976 1282 3.691575 TCTCTTCACCTGACTGGAGTAG 58.308 50.000 5.22 0.99 39.71 2.57
977 1283 3.691575 CTCTCTTCACCTGACTGGAGTA 58.308 50.000 5.22 0.00 39.71 2.59
978 1284 2.524306 CTCTCTTCACCTGACTGGAGT 58.476 52.381 5.22 0.00 39.71 3.85
1152 1464 4.069232 CGCCGAGGTGCCTTCAGA 62.069 66.667 0.00 0.00 0.00 3.27
1156 1468 4.394712 CTTCCGCCGAGGTGCCTT 62.395 66.667 0.00 0.00 41.99 4.35
1158 1470 4.821589 CTCTTCCGCCGAGGTGCC 62.822 72.222 0.00 0.00 41.99 5.01
1164 1476 4.069232 CTGTGCCTCTTCCGCCGA 62.069 66.667 0.00 0.00 0.00 5.54
1733 2045 0.879765 CTTGAGCTTGAAGGTGCAGG 59.120 55.000 0.00 0.00 0.00 4.85
1757 2069 4.096081 ACGGTTTGAGAACGATCTACCTAG 59.904 45.833 10.36 0.85 35.54 3.02
1759 2071 2.824341 ACGGTTTGAGAACGATCTACCT 59.176 45.455 10.36 0.00 35.54 3.08
1760 2072 3.227810 ACGGTTTGAGAACGATCTACC 57.772 47.619 0.00 0.00 35.54 3.18
1761 2073 4.682860 TCAAACGGTTTGAGAACGATCTAC 59.317 41.667 27.49 0.00 44.21 2.59
1818 2130 6.559429 ACCTCGGTAATTATCCTACCTACAT 58.441 40.000 0.00 0.00 37.29 2.29
1823 2135 5.641783 GAGACCTCGGTAATTATCCTACC 57.358 47.826 0.00 0.00 36.27 3.18
1852 2164 6.820335 TCAATCAACATAGATCGACAGGAAT 58.180 36.000 0.00 0.00 0.00 3.01
1868 2180 2.473816 TGCCGATCGATCTCAATCAAC 58.526 47.619 22.43 4.33 31.76 3.18
1958 2274 7.866393 CGAATACACCTCGGATCTTATTTACTT 59.134 37.037 0.00 0.00 32.62 2.24
1960 2276 7.144000 ACGAATACACCTCGGATCTTATTTAC 58.856 38.462 0.00 0.00 40.64 2.01
1984 2300 4.024048 TCTCCAAAGAAACTCATCGCAAAC 60.024 41.667 0.00 0.00 0.00 2.93
2040 2357 1.094785 AAACCACGCATATGGACTGC 58.905 50.000 4.56 0.00 43.02 4.40
2081 3196 1.831286 GATTCTCGACCCCCGCCTA 60.831 63.158 0.00 0.00 38.37 3.93
2085 3200 0.179108 GAACTGATTCTCGACCCCCG 60.179 60.000 0.00 0.00 40.25 5.73
2119 3237 2.840038 TGTGCTCTCCATTATGACCAGT 59.160 45.455 0.00 0.00 0.00 4.00
2120 3238 3.548745 TGTGCTCTCCATTATGACCAG 57.451 47.619 0.00 0.00 0.00 4.00
2121 3239 3.455543 TCATGTGCTCTCCATTATGACCA 59.544 43.478 0.00 0.00 30.11 4.02
2122 3240 3.812053 GTCATGTGCTCTCCATTATGACC 59.188 47.826 0.00 0.00 40.84 4.02
2123 3241 4.272018 GTGTCATGTGCTCTCCATTATGAC 59.728 45.833 0.00 0.00 43.61 3.06
2124 3242 4.162888 AGTGTCATGTGCTCTCCATTATGA 59.837 41.667 0.00 0.00 31.59 2.15
2125 3243 4.272748 CAGTGTCATGTGCTCTCCATTATG 59.727 45.833 0.00 0.00 0.00 1.90
2126 3244 4.449131 CAGTGTCATGTGCTCTCCATTAT 58.551 43.478 0.00 0.00 0.00 1.28
2127 3245 3.369787 CCAGTGTCATGTGCTCTCCATTA 60.370 47.826 0.00 0.00 0.00 1.90
2128 3246 2.617276 CCAGTGTCATGTGCTCTCCATT 60.617 50.000 0.00 0.00 0.00 3.16
2129 3247 1.065636 CCAGTGTCATGTGCTCTCCAT 60.066 52.381 0.00 0.00 0.00 3.41
2130 3248 0.322648 CCAGTGTCATGTGCTCTCCA 59.677 55.000 0.00 0.00 0.00 3.86
2131 3249 0.322975 ACCAGTGTCATGTGCTCTCC 59.677 55.000 0.00 0.00 0.00 3.71
2132 3250 2.232452 ACTACCAGTGTCATGTGCTCTC 59.768 50.000 0.00 0.00 0.00 3.20
2133 3251 2.232452 GACTACCAGTGTCATGTGCTCT 59.768 50.000 0.00 0.00 34.80 4.09
2134 3252 2.232452 AGACTACCAGTGTCATGTGCTC 59.768 50.000 0.00 0.00 36.94 4.26
2135 3253 2.251818 AGACTACCAGTGTCATGTGCT 58.748 47.619 0.00 0.00 36.94 4.40
2136 3254 2.751166 AGACTACCAGTGTCATGTGC 57.249 50.000 0.00 0.00 36.94 4.57
2137 3255 5.392767 ACTTAGACTACCAGTGTCATGTG 57.607 43.478 0.00 0.00 36.94 3.21
2138 3256 6.420913 AAACTTAGACTACCAGTGTCATGT 57.579 37.500 0.00 0.00 36.94 3.21
2139 3257 6.812160 GGTAAACTTAGACTACCAGTGTCATG 59.188 42.308 8.77 0.00 36.00 3.07
2140 3258 6.495872 TGGTAAACTTAGACTACCAGTGTCAT 59.504 38.462 11.25 0.00 40.09 3.06
2141 3259 5.834742 TGGTAAACTTAGACTACCAGTGTCA 59.165 40.000 11.25 0.00 40.09 3.58
2142 3260 6.336842 TGGTAAACTTAGACTACCAGTGTC 57.663 41.667 11.25 0.00 40.09 3.67
2143 3261 6.724905 AGATGGTAAACTTAGACTACCAGTGT 59.275 38.462 17.24 6.26 46.21 3.55
2144 3262 7.171630 AGATGGTAAACTTAGACTACCAGTG 57.828 40.000 17.24 0.00 46.21 3.66
2145 3263 7.793948 AAGATGGTAAACTTAGACTACCAGT 57.206 36.000 17.24 8.67 46.21 4.00
2151 3269 9.819267 GCACTATAAAGATGGTAAACTTAGACT 57.181 33.333 0.00 0.00 0.00 3.24
2152 3270 9.595823 TGCACTATAAAGATGGTAAACTTAGAC 57.404 33.333 0.00 0.00 0.00 2.59
2156 3274 8.739972 CCTTTGCACTATAAAGATGGTAAACTT 58.260 33.333 0.00 0.00 37.33 2.66
2157 3275 8.107095 TCCTTTGCACTATAAAGATGGTAAACT 58.893 33.333 0.00 0.00 37.33 2.66
2158 3276 8.276252 TCCTTTGCACTATAAAGATGGTAAAC 57.724 34.615 0.00 0.00 37.33 2.01
2159 3277 8.736244 GTTCCTTTGCACTATAAAGATGGTAAA 58.264 33.333 0.00 0.00 37.33 2.01
2160 3278 7.885922 TGTTCCTTTGCACTATAAAGATGGTAA 59.114 33.333 0.00 0.00 37.33 2.85
2161 3279 7.398829 TGTTCCTTTGCACTATAAAGATGGTA 58.601 34.615 0.00 0.00 37.33 3.25
2162 3280 6.245408 TGTTCCTTTGCACTATAAAGATGGT 58.755 36.000 0.00 0.00 37.33 3.55
2163 3281 6.757897 TGTTCCTTTGCACTATAAAGATGG 57.242 37.500 0.00 0.00 37.33 3.51
2168 3286 9.860650 ACCATATATGTTCCTTTGCACTATAAA 57.139 29.630 11.73 0.00 0.00 1.40
2169 3287 9.860650 AACCATATATGTTCCTTTGCACTATAA 57.139 29.630 11.73 0.00 0.00 0.98
2170 3288 9.283768 CAACCATATATGTTCCTTTGCACTATA 57.716 33.333 11.73 0.00 0.00 1.31
2171 3289 7.255590 GCAACCATATATGTTCCTTTGCACTAT 60.256 37.037 18.61 0.00 38.36 2.12
2172 3290 6.039270 GCAACCATATATGTTCCTTTGCACTA 59.961 38.462 18.61 0.00 38.36 2.74
2173 3291 5.163519 GCAACCATATATGTTCCTTTGCACT 60.164 40.000 18.61 0.00 38.36 4.40
2174 3292 5.043248 GCAACCATATATGTTCCTTTGCAC 58.957 41.667 18.61 0.00 38.36 4.57
2175 3293 4.708909 TGCAACCATATATGTTCCTTTGCA 59.291 37.500 20.53 20.53 44.23 4.08
2176 3294 5.261209 TGCAACCATATATGTTCCTTTGC 57.739 39.130 11.73 15.44 38.83 3.68
2177 3295 9.985730 ATAAATGCAACCATATATGTTCCTTTG 57.014 29.630 11.73 7.61 0.00 2.77
2181 3299 9.573133 GCTAATAAATGCAACCATATATGTTCC 57.427 33.333 11.73 0.00 0.00 3.62
2188 3306 9.573166 TCTACAAGCTAATAAATGCAACCATAT 57.427 29.630 0.00 0.00 0.00 1.78
2189 3307 8.836413 GTCTACAAGCTAATAAATGCAACCATA 58.164 33.333 0.00 0.00 0.00 2.74
2190 3308 7.557719 AGTCTACAAGCTAATAAATGCAACCAT 59.442 33.333 0.00 0.00 0.00 3.55
2191 3309 6.884295 AGTCTACAAGCTAATAAATGCAACCA 59.116 34.615 0.00 0.00 0.00 3.67
2192 3310 7.065803 TGAGTCTACAAGCTAATAAATGCAACC 59.934 37.037 0.00 0.00 0.00 3.77
2193 3311 7.974675 TGAGTCTACAAGCTAATAAATGCAAC 58.025 34.615 0.00 0.00 0.00 4.17
2194 3312 8.450964 GTTGAGTCTACAAGCTAATAAATGCAA 58.549 33.333 0.00 0.00 0.00 4.08
2195 3313 7.824289 AGTTGAGTCTACAAGCTAATAAATGCA 59.176 33.333 7.47 0.00 0.00 3.96
2196 3314 8.202745 AGTTGAGTCTACAAGCTAATAAATGC 57.797 34.615 7.47 0.00 0.00 3.56
2223 3341 3.717400 TCACATAGCGTTTGCCAAAAA 57.283 38.095 0.00 0.00 44.31 1.94
2224 3342 3.573598 CATCACATAGCGTTTGCCAAAA 58.426 40.909 0.00 0.00 44.31 2.44
2225 3343 2.094803 CCATCACATAGCGTTTGCCAAA 60.095 45.455 0.00 0.00 44.31 3.28
2226 3344 1.472082 CCATCACATAGCGTTTGCCAA 59.528 47.619 0.00 0.00 44.31 4.52
2227 3345 1.093972 CCATCACATAGCGTTTGCCA 58.906 50.000 0.00 0.00 44.31 4.92
2228 3346 1.094785 ACCATCACATAGCGTTTGCC 58.905 50.000 0.00 0.00 44.31 4.52
2229 3347 3.126171 TGTTACCATCACATAGCGTTTGC 59.874 43.478 0.00 0.00 43.24 3.68
2230 3348 4.937696 TGTTACCATCACATAGCGTTTG 57.062 40.909 0.00 0.00 0.00 2.93
2231 3349 7.801716 ATTATGTTACCATCACATAGCGTTT 57.198 32.000 0.00 0.00 38.16 3.60
2232 3350 8.896320 TTATTATGTTACCATCACATAGCGTT 57.104 30.769 0.00 0.00 38.16 4.84
2233 3351 8.148351 ACTTATTATGTTACCATCACATAGCGT 58.852 33.333 0.00 0.00 38.16 5.07
2234 3352 8.534333 ACTTATTATGTTACCATCACATAGCG 57.466 34.615 0.00 0.00 38.16 4.26
2239 3357 9.826574 GGAGTAACTTATTATGTTACCATCACA 57.173 33.333 20.54 0.00 46.31 3.58
2240 3358 9.826574 TGGAGTAACTTATTATGTTACCATCAC 57.173 33.333 20.54 11.90 46.31 3.06
2248 3366 9.227777 GAGGTGTTTGGAGTAACTTATTATGTT 57.772 33.333 1.21 1.21 0.00 2.71
2249 3367 8.603304 AGAGGTGTTTGGAGTAACTTATTATGT 58.397 33.333 0.00 0.00 0.00 2.29
2250 3368 9.099454 GAGAGGTGTTTGGAGTAACTTATTATG 57.901 37.037 0.00 0.00 0.00 1.90
2251 3369 9.047947 AGAGAGGTGTTTGGAGTAACTTATTAT 57.952 33.333 0.00 0.00 0.00 1.28
2252 3370 8.431910 AGAGAGGTGTTTGGAGTAACTTATTA 57.568 34.615 0.00 0.00 0.00 0.98
2253 3371 7.317722 AGAGAGGTGTTTGGAGTAACTTATT 57.682 36.000 0.00 0.00 0.00 1.40
2254 3372 6.936968 AGAGAGGTGTTTGGAGTAACTTAT 57.063 37.500 0.00 0.00 0.00 1.73
2255 3373 6.742559 AAGAGAGGTGTTTGGAGTAACTTA 57.257 37.500 0.00 0.00 0.00 2.24
2256 3374 5.632034 AAGAGAGGTGTTTGGAGTAACTT 57.368 39.130 0.00 0.00 0.00 2.66
2257 3375 5.632034 AAAGAGAGGTGTTTGGAGTAACT 57.368 39.130 0.00 0.00 0.00 2.24
2258 3376 6.694877 AAAAAGAGAGGTGTTTGGAGTAAC 57.305 37.500 0.00 0.00 0.00 2.50
2259 3377 8.990163 AATAAAAAGAGAGGTGTTTGGAGTAA 57.010 30.769 0.00 0.00 0.00 2.24
2261 3379 8.990163 TTAATAAAAAGAGAGGTGTTTGGAGT 57.010 30.769 0.00 0.00 0.00 3.85
2268 3386 8.678199 GCAGCTAATTAATAAAAAGAGAGGTGT 58.322 33.333 0.00 0.00 33.57 4.16
2269 3387 8.131731 GGCAGCTAATTAATAAAAAGAGAGGTG 58.868 37.037 0.00 0.00 34.03 4.00
2270 3388 7.834181 TGGCAGCTAATTAATAAAAAGAGAGGT 59.166 33.333 0.00 0.00 0.00 3.85
2271 3389 8.131731 GTGGCAGCTAATTAATAAAAAGAGAGG 58.868 37.037 0.00 0.00 0.00 3.69
2272 3390 8.677300 TGTGGCAGCTAATTAATAAAAAGAGAG 58.323 33.333 0.00 0.00 0.00 3.20
2273 3391 8.574251 TGTGGCAGCTAATTAATAAAAAGAGA 57.426 30.769 0.00 0.00 0.00 3.10
2277 3395 9.528018 GCTTATGTGGCAGCTAATTAATAAAAA 57.472 29.630 0.00 0.00 32.87 1.94
2278 3396 8.690884 TGCTTATGTGGCAGCTAATTAATAAAA 58.309 29.630 0.00 0.00 36.92 1.52
2279 3397 8.231692 TGCTTATGTGGCAGCTAATTAATAAA 57.768 30.769 0.00 0.00 36.92 1.40
2280 3398 7.815840 TGCTTATGTGGCAGCTAATTAATAA 57.184 32.000 0.00 0.00 36.92 1.40
2281 3399 7.815840 TTGCTTATGTGGCAGCTAATTAATA 57.184 32.000 0.00 0.00 40.90 0.98
2282 3400 6.713762 TTGCTTATGTGGCAGCTAATTAAT 57.286 33.333 0.00 0.00 40.90 1.40
2283 3401 6.152661 AGTTTGCTTATGTGGCAGCTAATTAA 59.847 34.615 0.00 0.00 40.90 1.40
2284 3402 5.652014 AGTTTGCTTATGTGGCAGCTAATTA 59.348 36.000 0.00 0.00 40.90 1.40
2285 3403 4.463891 AGTTTGCTTATGTGGCAGCTAATT 59.536 37.500 0.00 0.00 40.90 1.40
2286 3404 4.019174 AGTTTGCTTATGTGGCAGCTAAT 58.981 39.130 0.00 0.00 40.90 1.73
2287 3405 3.420893 AGTTTGCTTATGTGGCAGCTAA 58.579 40.909 0.00 0.00 40.90 3.09
2288 3406 3.071874 AGTTTGCTTATGTGGCAGCTA 57.928 42.857 0.00 0.00 40.90 3.32
2289 3407 1.915141 AGTTTGCTTATGTGGCAGCT 58.085 45.000 0.00 0.00 40.90 4.24
2290 3408 2.288395 ACAAGTTTGCTTATGTGGCAGC 60.288 45.455 0.00 0.00 40.90 5.25
2291 3409 3.254166 AGACAAGTTTGCTTATGTGGCAG 59.746 43.478 0.00 0.00 40.90 4.85
2292 3410 3.221771 AGACAAGTTTGCTTATGTGGCA 58.778 40.909 0.00 0.00 37.97 4.92
2293 3411 3.667960 CGAGACAAGTTTGCTTATGTGGC 60.668 47.826 0.00 0.00 32.87 5.01
2294 3412 3.120199 CCGAGACAAGTTTGCTTATGTGG 60.120 47.826 0.00 0.00 32.87 4.17
2295 3413 3.120199 CCCGAGACAAGTTTGCTTATGTG 60.120 47.826 0.00 0.00 32.87 3.21
2296 3414 3.074412 CCCGAGACAAGTTTGCTTATGT 58.926 45.455 0.00 0.00 32.87 2.29
2297 3415 3.334691 TCCCGAGACAAGTTTGCTTATG 58.665 45.455 0.00 0.00 32.87 1.90
2298 3416 3.695830 TCCCGAGACAAGTTTGCTTAT 57.304 42.857 0.00 0.00 32.87 1.73
2299 3417 3.695830 ATCCCGAGACAAGTTTGCTTA 57.304 42.857 0.00 0.00 32.87 3.09
2300 3418 2.568623 ATCCCGAGACAAGTTTGCTT 57.431 45.000 0.00 0.00 34.82 3.91
2301 3419 3.055094 ACATATCCCGAGACAAGTTTGCT 60.055 43.478 0.00 0.00 0.00 3.91
2302 3420 3.270877 ACATATCCCGAGACAAGTTTGC 58.729 45.455 0.00 0.00 0.00 3.68
2303 3421 6.538742 ACATAACATATCCCGAGACAAGTTTG 59.461 38.462 0.00 0.00 0.00 2.93
2304 3422 6.650120 ACATAACATATCCCGAGACAAGTTT 58.350 36.000 0.00 0.00 0.00 2.66
2305 3423 6.235231 ACATAACATATCCCGAGACAAGTT 57.765 37.500 0.00 0.00 0.00 2.66
2306 3424 5.871396 ACATAACATATCCCGAGACAAGT 57.129 39.130 0.00 0.00 0.00 3.16
2307 3425 7.434492 AGTAACATAACATATCCCGAGACAAG 58.566 38.462 0.00 0.00 0.00 3.16
2308 3426 7.356089 AGTAACATAACATATCCCGAGACAA 57.644 36.000 0.00 0.00 0.00 3.18
2309 3427 6.971726 AGTAACATAACATATCCCGAGACA 57.028 37.500 0.00 0.00 0.00 3.41
2310 3428 8.574737 AGTAAGTAACATAACATATCCCGAGAC 58.425 37.037 0.00 0.00 0.00 3.36
2311 3429 8.701908 AGTAAGTAACATAACATATCCCGAGA 57.298 34.615 0.00 0.00 0.00 4.04
2333 3451 8.591072 GCTGGTTATAGTGGGAATAACATAGTA 58.409 37.037 7.92 0.00 40.19 1.82
2334 3452 7.450903 GCTGGTTATAGTGGGAATAACATAGT 58.549 38.462 7.92 0.00 40.19 2.12
2335 3453 6.879458 GGCTGGTTATAGTGGGAATAACATAG 59.121 42.308 7.92 6.68 40.19 2.23
2336 3454 6.561070 AGGCTGGTTATAGTGGGAATAACATA 59.439 38.462 7.92 0.00 40.19 2.29
2337 3455 5.372661 AGGCTGGTTATAGTGGGAATAACAT 59.627 40.000 7.92 0.00 40.19 2.71
2338 3456 4.724798 AGGCTGGTTATAGTGGGAATAACA 59.275 41.667 7.92 0.00 40.19 2.41
2339 3457 5.306114 AGGCTGGTTATAGTGGGAATAAC 57.694 43.478 0.00 0.00 38.52 1.89
2340 3458 5.987019 AAGGCTGGTTATAGTGGGAATAA 57.013 39.130 0.00 0.00 0.00 1.40
2341 3459 6.790461 TCATAAGGCTGGTTATAGTGGGAATA 59.210 38.462 0.00 0.00 0.00 1.75
2342 3460 5.610982 TCATAAGGCTGGTTATAGTGGGAAT 59.389 40.000 0.00 0.00 0.00 3.01
2343 3461 4.972568 TCATAAGGCTGGTTATAGTGGGAA 59.027 41.667 0.00 0.00 0.00 3.97
2344 3462 4.562767 TCATAAGGCTGGTTATAGTGGGA 58.437 43.478 0.00 0.00 0.00 4.37
2345 3463 4.348168 ACTCATAAGGCTGGTTATAGTGGG 59.652 45.833 0.00 0.00 0.00 4.61
2346 3464 5.552870 ACTCATAAGGCTGGTTATAGTGG 57.447 43.478 0.00 0.00 0.00 4.00
2347 3465 7.171678 GCTTAACTCATAAGGCTGGTTATAGTG 59.828 40.741 0.00 0.00 41.19 2.74
2348 3466 7.217906 GCTTAACTCATAAGGCTGGTTATAGT 58.782 38.462 0.00 0.00 41.19 2.12
2349 3467 7.659652 GCTTAACTCATAAGGCTGGTTATAG 57.340 40.000 0.00 0.00 41.19 1.31
2359 3477 1.940613 GGTGCGGCTTAACTCATAAGG 59.059 52.381 0.00 0.00 41.19 2.69
2360 3478 2.906354 AGGTGCGGCTTAACTCATAAG 58.094 47.619 0.00 0.00 43.32 1.73
2361 3479 4.502604 GGATAGGTGCGGCTTAACTCATAA 60.503 45.833 0.00 0.00 0.00 1.90
2362 3480 3.006537 GGATAGGTGCGGCTTAACTCATA 59.993 47.826 0.00 0.00 0.00 2.15
2363 3481 2.224305 GGATAGGTGCGGCTTAACTCAT 60.224 50.000 0.00 0.00 0.00 2.90
2364 3482 1.138266 GGATAGGTGCGGCTTAACTCA 59.862 52.381 0.00 0.00 0.00 3.41
2365 3483 1.138266 TGGATAGGTGCGGCTTAACTC 59.862 52.381 0.00 0.00 0.00 3.01
2382 3500 3.157087 GGAGCAGTTGAAGGAATTTGGA 58.843 45.455 0.00 0.00 0.00 3.53
2445 3563 1.810031 GCAAAGAACTTGTTTGGGGGC 60.810 52.381 12.07 0.00 37.36 5.80
2462 3580 3.233507 AGCTGAAGGGATCTTTTTGCAA 58.766 40.909 0.00 0.00 32.52 4.08
2487 3606 1.478916 GAGTGAGAGGTAGCAGGAACC 59.521 57.143 0.00 0.00 37.27 3.62
2488 3607 1.133407 CGAGTGAGAGGTAGCAGGAAC 59.867 57.143 0.00 0.00 0.00 3.62
2489 3608 1.004394 TCGAGTGAGAGGTAGCAGGAA 59.996 52.381 0.00 0.00 0.00 3.36
2493 3617 0.036671 TCGTCGAGTGAGAGGTAGCA 60.037 55.000 0.00 0.00 0.00 3.49
2538 3662 5.283060 AGTCGTTGAGGAAAATGAAATCG 57.717 39.130 0.00 0.00 0.00 3.34
2545 3669 3.746492 GCACAGTAGTCGTTGAGGAAAAT 59.254 43.478 0.00 0.00 0.00 1.82
2549 3673 1.000607 GTGCACAGTAGTCGTTGAGGA 60.001 52.381 13.17 0.00 0.00 3.71
2555 3679 2.049433 GGCGTGCACAGTAGTCGT 60.049 61.111 18.64 0.00 0.00 4.34
2594 3718 2.356793 CCGAGAGATCGGCATGGC 60.357 66.667 9.69 9.69 46.76 4.40
2643 3768 1.037493 TATGCGGCGATTCCAGTAGT 58.963 50.000 12.98 0.00 34.01 2.73
2646 3771 0.681733 AGATATGCGGCGATTCCAGT 59.318 50.000 12.98 0.00 34.01 4.00
2680 3805 1.001641 GTCCACAAGCTCCAGGCAT 60.002 57.895 0.00 0.00 44.79 4.40


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

AutoCloner maintained by Alex Coulton.