Multiple sequence alignment - TraesCS6D01G302700

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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 TraesCS6D01G302700 chr6D 100.000 2294 0 0 1 2294 411725043 411727336 0.000000e+00 4237.0
1 TraesCS6D01G302700 chr6D 86.116 569 37 18 770 1306 411766923 411767481 1.980000e-160 575.0
2 TraesCS6D01G302700 chr6D 80.357 112 11 5 645 751 411766769 411766874 8.790000e-10 75.0
3 TraesCS6D01G302700 chr6B 85.804 1747 129 61 122 1801 619403836 619405530 0.000000e+00 1742.0
4 TraesCS6D01G302700 chr6B 91.091 449 30 5 909 1353 619483919 619484361 1.170000e-167 599.0
5 TraesCS6D01G302700 chr6B 90.347 259 23 2 2028 2284 89525553 89525295 2.820000e-89 339.0
6 TraesCS6D01G302700 chr6B 88.000 275 30 2 2020 2291 89527485 89527211 2.840000e-84 322.0
7 TraesCS6D01G302700 chr6B 90.840 131 3 1 3 124 619403666 619403796 1.410000e-37 167.0
8 TraesCS6D01G302700 chr6B 87.059 85 8 3 777 860 619483737 619483819 2.430000e-15 93.5
9 TraesCS6D01G302700 chr6A 88.131 1466 103 32 116 1556 556668750 556670169 0.000000e+00 1677.0
10 TraesCS6D01G302700 chr6A 85.248 644 40 23 753 1353 556676587 556677218 1.510000e-171 612.0
11 TraesCS6D01G302700 chr6A 87.868 272 19 8 462 729 556656959 556657220 7.960000e-80 307.0
12 TraesCS6D01G302700 chr6A 82.857 350 45 15 1475 1815 7968504 7968161 1.330000e-77 300.0
13 TraesCS6D01G302700 chr6A 82.571 350 45 16 1475 1815 7866653 7866311 6.200000e-76 294.0
14 TraesCS6D01G302700 chr6A 82.521 349 47 14 1475 1815 7901401 7901059 6.200000e-76 294.0
15 TraesCS6D01G302700 chr6A 82.235 349 48 14 1475 1815 7832693 7832351 2.880000e-74 289.0
16 TraesCS6D01G302700 chr6A 83.019 318 41 13 1506 1815 7933484 7933172 2.240000e-70 276.0
17 TraesCS6D01G302700 chr6A 91.919 99 6 2 751 848 556658335 556658432 1.110000e-28 137.0
18 TraesCS6D01G302700 chr6A 80.531 113 15 5 1377 1489 99974498 99974393 1.890000e-11 80.5
19 TraesCS6D01G302700 chr6A 76.730 159 15 13 611 754 556676422 556676573 4.090000e-08 69.4
20 TraesCS6D01G302700 chr2A 93.818 275 15 2 2019 2292 102111835 102111562 1.640000e-111 412.0
21 TraesCS6D01G302700 chr5A 93.116 276 17 2 2020 2294 613093084 613093358 9.870000e-109 403.0
22 TraesCS6D01G302700 chr5A 92.058 277 20 2 2019 2294 658511013 658511288 2.760000e-104 388.0
23 TraesCS6D01G302700 chr5A 85.855 304 29 12 1521 1815 597336491 597336789 6.150000e-81 311.0
24 TraesCS6D01G302700 chr5A 80.062 321 47 13 1489 1797 643030732 643031047 2.970000e-54 222.0
25 TraesCS6D01G302700 chr7A 89.493 276 22 5 2020 2292 625060550 625060821 2.180000e-90 342.0
26 TraesCS6D01G302700 chr7A 85.866 283 31 7 1536 1810 144123195 144122914 2.230000e-75 292.0
27 TraesCS6D01G302700 chr5B 89.925 268 24 2 2020 2284 465816509 465816776 2.180000e-90 342.0
28 TraesCS6D01G302700 chr1B 95.370 216 9 1 2019 2233 21487071 21487286 2.180000e-90 342.0
29 TraesCS6D01G302700 chr3A 85.075 268 34 3 981 1248 541225951 541226212 3.760000e-68 268.0
30 TraesCS6D01G302700 chr2B 82.514 183 17 10 1811 1983 310463089 310462912 1.840000e-31 147.0
31 TraesCS6D01G302700 chr2B 84.314 102 12 2 1377 1478 235058659 235058756 1.880000e-16 97.1
32 TraesCS6D01G302700 chr4B 88.785 107 12 0 2019 2125 643925474 643925368 5.140000e-27 132.0


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 TraesCS6D01G302700 chr6D 411725043 411727336 2293 False 4237.00 4237 100.0000 1 2294 1 chr6D.!!$F1 2293
1 TraesCS6D01G302700 chr6D 411766769 411767481 712 False 325.00 575 83.2365 645 1306 2 chr6D.!!$F2 661
2 TraesCS6D01G302700 chr6B 619403666 619405530 1864 False 954.50 1742 88.3220 3 1801 2 chr6B.!!$F1 1798
3 TraesCS6D01G302700 chr6B 619483737 619484361 624 False 346.25 599 89.0750 777 1353 2 chr6B.!!$F2 576
4 TraesCS6D01G302700 chr6B 89525295 89527485 2190 True 330.50 339 89.1735 2020 2291 2 chr6B.!!$R1 271
5 TraesCS6D01G302700 chr6A 556668750 556670169 1419 False 1677.00 1677 88.1310 116 1556 1 chr6A.!!$F1 1440
6 TraesCS6D01G302700 chr6A 556676422 556677218 796 False 340.70 612 80.9890 611 1353 2 chr6A.!!$F3 742
7 TraesCS6D01G302700 chr6A 556656959 556658432 1473 False 222.00 307 89.8935 462 848 2 chr6A.!!$F2 386

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
447 513 0.030773 TGTAGATCGATGTGGCTCGC 59.969 55.0 0.54 0.0 38.52 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 3161 0.029967 GTAGGTAGGGCGCGACTTAC 59.97 60.0 24.84 24.84 0.0 2.34 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
23 24 1.456705 TTGGTTGGCCAGTTGGGTC 60.457 57.895 5.11 0.00 46.91 4.46
61 71 1.026718 CCACGGCAAGATCTGGGAAC 61.027 60.000 0.00 0.00 0.00 3.62
130 182 8.132362 GCATCGACCAATGGTTAAAAATGTATA 58.868 33.333 6.30 0.00 35.25 1.47
169 222 6.034591 CGTACAGTACAGGGAAGATTAACTG 58.965 44.000 11.37 0.00 38.97 3.16
170 223 5.422214 ACAGTACAGGGAAGATTAACTGG 57.578 43.478 0.00 0.00 37.71 4.00
240 302 3.574074 ATCTGCCGCTTGCCAAGGT 62.574 57.895 6.57 0.00 40.16 3.50
294 356 3.479127 TTAACCAACCGCGCCCTGT 62.479 57.895 0.00 0.00 0.00 4.00
370 432 1.000506 ACTGCTTAATCACGTCCGTGT 59.999 47.619 18.23 4.18 45.55 4.49
379 443 1.340568 TCACGTCCGTGTGTTGGAATA 59.659 47.619 18.23 0.00 45.55 1.75
402 467 2.957402 AACCACTGCTTCCAGAATCA 57.043 45.000 0.00 0.00 41.77 2.57
413 479 2.972625 TCCAGAATCAATGGTGACGAC 58.027 47.619 0.00 0.00 39.01 4.34
440 506 4.748892 CTTGGACAAGTGTAGATCGATGT 58.251 43.478 0.54 0.00 33.87 3.06
443 509 2.860735 GACAAGTGTAGATCGATGTGGC 59.139 50.000 0.54 0.00 0.00 5.01
445 511 3.119291 CAAGTGTAGATCGATGTGGCTC 58.881 50.000 0.54 0.00 0.00 4.70
446 512 1.335182 AGTGTAGATCGATGTGGCTCG 59.665 52.381 0.54 0.00 39.99 5.03
447 513 0.030773 TGTAGATCGATGTGGCTCGC 59.969 55.000 0.54 0.00 38.52 5.03
448 514 0.312416 GTAGATCGATGTGGCTCGCT 59.688 55.000 0.54 0.00 38.52 4.93
488 558 0.798776 GGCCAGAGAATCACAACACG 59.201 55.000 0.00 0.00 37.82 4.49
620 707 1.600636 CCCTGGCACACGACACATT 60.601 57.895 0.00 0.00 0.00 2.71
677 768 2.716828 GACACGACGACGCCACATG 61.717 63.158 7.30 0.02 43.96 3.21
819 2039 3.434319 GCGTACACGACCGAGGGA 61.434 66.667 5.84 0.00 43.02 4.20
874 2119 6.422223 CAACACGCAAAGCTCTATATAAAGG 58.578 40.000 0.00 0.00 0.00 3.11
927 2172 4.984785 CGAATCATCCATCGATACACAAGT 59.015 41.667 0.00 0.00 41.43 3.16
928 2173 5.117745 CGAATCATCCATCGATACACAAGTC 59.882 44.000 0.00 0.00 41.43 3.01
929 2174 5.535753 ATCATCCATCGATACACAAGTCA 57.464 39.130 0.00 0.00 0.00 3.41
930 2175 5.535753 TCATCCATCGATACACAAGTCAT 57.464 39.130 0.00 0.00 0.00 3.06
931 2176 5.532557 TCATCCATCGATACACAAGTCATC 58.467 41.667 0.00 0.00 0.00 2.92
932 2177 4.322080 TCCATCGATACACAAGTCATCC 57.678 45.455 0.00 0.00 0.00 3.51
933 2178 3.052745 CCATCGATACACAAGTCATCCG 58.947 50.000 0.00 0.00 0.00 4.18
934 2179 3.490933 CCATCGATACACAAGTCATCCGT 60.491 47.826 0.00 0.00 0.00 4.69
953 2241 3.566261 CGCATCTCGTTTGCCAGT 58.434 55.556 0.00 0.00 36.75 4.00
956 2244 1.160137 GCATCTCGTTTGCCAGTCTT 58.840 50.000 0.00 0.00 33.95 3.01
959 2247 3.814945 CATCTCGTTTGCCAGTCTTTTC 58.185 45.455 0.00 0.00 0.00 2.29
970 2258 4.083324 TGCCAGTCTTTTCGATTGATTGAC 60.083 41.667 0.00 0.00 31.49 3.18
976 2264 4.570772 TCTTTTCGATTGATTGACCGATCC 59.429 41.667 0.00 0.00 0.00 3.36
980 2268 3.321968 TCGATTGATTGACCGATCCATCT 59.678 43.478 8.69 0.00 30.15 2.90
1311 2606 0.877743 GAGCAGCTTGGAGTTTGGAC 59.122 55.000 0.00 0.00 0.00 4.02
1319 2614 1.228154 GGAGTTTGGACCGGTTGCT 60.228 57.895 9.42 2.52 0.00 3.91
1320 2615 0.822121 GGAGTTTGGACCGGTTGCTT 60.822 55.000 9.42 0.00 0.00 3.91
1321 2616 1.543871 GGAGTTTGGACCGGTTGCTTA 60.544 52.381 9.42 0.00 0.00 3.09
1322 2617 2.223745 GAGTTTGGACCGGTTGCTTAA 58.776 47.619 9.42 0.00 0.00 1.85
1436 2731 6.983906 TCATGTGAGCTAGATTTAGATGGA 57.016 37.500 0.00 0.00 0.00 3.41
1492 2787 7.454380 TGGGAGGATGAACAAGTATTTGAAAAT 59.546 33.333 4.81 0.00 37.73 1.82
1820 3147 9.805966 AAAATCAAAAGAAAACAAAAACTCGAC 57.194 25.926 0.00 0.00 0.00 4.20
1821 3148 8.757164 AATCAAAAGAAAACAAAAACTCGACT 57.243 26.923 0.00 0.00 0.00 4.18
1822 3149 7.790861 TCAAAAGAAAACAAAAACTCGACTC 57.209 32.000 0.00 0.00 0.00 3.36
1823 3150 6.804783 TCAAAAGAAAACAAAAACTCGACTCC 59.195 34.615 0.00 0.00 0.00 3.85
1824 3151 6.510879 AAAGAAAACAAAAACTCGACTCCT 57.489 33.333 0.00 0.00 0.00 3.69
1825 3152 6.510879 AAGAAAACAAAAACTCGACTCCTT 57.489 33.333 0.00 0.00 0.00 3.36
1826 3153 6.120378 AGAAAACAAAAACTCGACTCCTTC 57.880 37.500 0.00 0.00 0.00 3.46
1827 3154 4.895224 AAACAAAAACTCGACTCCTTCC 57.105 40.909 0.00 0.00 0.00 3.46
1828 3155 2.847441 ACAAAAACTCGACTCCTTCCC 58.153 47.619 0.00 0.00 0.00 3.97
1829 3156 2.438392 ACAAAAACTCGACTCCTTCCCT 59.562 45.455 0.00 0.00 0.00 4.20
1830 3157 3.118000 ACAAAAACTCGACTCCTTCCCTT 60.118 43.478 0.00 0.00 0.00 3.95
1831 3158 3.404224 AAAACTCGACTCCTTCCCTTC 57.596 47.619 0.00 0.00 0.00 3.46
1832 3159 2.312424 AACTCGACTCCTTCCCTTCT 57.688 50.000 0.00 0.00 0.00 2.85
1833 3160 3.453059 AACTCGACTCCTTCCCTTCTA 57.547 47.619 0.00 0.00 0.00 2.10
1834 3161 3.007473 ACTCGACTCCTTCCCTTCTAG 57.993 52.381 0.00 0.00 0.00 2.43
1835 3162 2.309458 ACTCGACTCCTTCCCTTCTAGT 59.691 50.000 0.00 0.00 0.00 2.57
1836 3163 3.522750 ACTCGACTCCTTCCCTTCTAGTA 59.477 47.826 0.00 0.00 0.00 1.82
1837 3164 4.018597 ACTCGACTCCTTCCCTTCTAGTAA 60.019 45.833 0.00 0.00 0.00 2.24
1838 3165 4.525024 TCGACTCCTTCCCTTCTAGTAAG 58.475 47.826 0.00 0.00 0.00 2.34
1839 3166 4.018597 TCGACTCCTTCCCTTCTAGTAAGT 60.019 45.833 0.00 0.00 0.00 2.24
1840 3167 4.336153 CGACTCCTTCCCTTCTAGTAAGTC 59.664 50.000 0.00 0.00 0.00 3.01
1841 3168 4.271661 ACTCCTTCCCTTCTAGTAAGTCG 58.728 47.826 0.00 0.00 0.00 4.18
1842 3169 3.022406 TCCTTCCCTTCTAGTAAGTCGC 58.978 50.000 0.00 0.00 0.00 5.19
1843 3170 2.223525 CCTTCCCTTCTAGTAAGTCGCG 60.224 54.545 0.00 0.00 0.00 5.87
1844 3171 0.737219 TCCCTTCTAGTAAGTCGCGC 59.263 55.000 0.00 0.00 0.00 6.86
1845 3172 0.248949 CCCTTCTAGTAAGTCGCGCC 60.249 60.000 0.00 0.00 0.00 6.53
1846 3173 0.248949 CCTTCTAGTAAGTCGCGCCC 60.249 60.000 0.00 0.00 0.00 6.13
1847 3174 0.739561 CTTCTAGTAAGTCGCGCCCT 59.260 55.000 0.00 0.00 0.00 5.19
1848 3175 1.945394 CTTCTAGTAAGTCGCGCCCTA 59.055 52.381 0.00 0.00 0.00 3.53
1849 3176 1.303309 TCTAGTAAGTCGCGCCCTAC 58.697 55.000 0.00 0.00 0.00 3.18
1850 3177 0.310232 CTAGTAAGTCGCGCCCTACC 59.690 60.000 0.00 0.00 0.00 3.18
1851 3178 0.107017 TAGTAAGTCGCGCCCTACCT 60.107 55.000 0.00 2.03 0.00 3.08
1852 3179 0.107017 AGTAAGTCGCGCCCTACCTA 60.107 55.000 0.00 0.00 0.00 3.08
1853 3180 0.029967 GTAAGTCGCGCCCTACCTAC 59.970 60.000 0.00 0.00 0.00 3.18
1854 3181 0.107017 TAAGTCGCGCCCTACCTACT 60.107 55.000 0.00 0.00 0.00 2.57
1855 3182 1.664321 AAGTCGCGCCCTACCTACTG 61.664 60.000 0.00 0.00 0.00 2.74
1856 3183 2.044650 TCGCGCCCTACCTACTGT 60.045 61.111 0.00 0.00 0.00 3.55
1857 3184 1.097547 GTCGCGCCCTACCTACTGTA 61.098 60.000 0.00 0.00 0.00 2.74
1858 3185 1.097547 TCGCGCCCTACCTACTGTAC 61.098 60.000 0.00 0.00 0.00 2.90
1859 3186 1.378882 CGCGCCCTACCTACTGTACA 61.379 60.000 0.00 0.00 0.00 2.90
1860 3187 0.101939 GCGCCCTACCTACTGTACAC 59.898 60.000 0.00 0.00 0.00 2.90
1861 3188 1.466856 CGCCCTACCTACTGTACACA 58.533 55.000 0.00 0.00 0.00 3.72
1862 3189 2.029623 CGCCCTACCTACTGTACACAT 58.970 52.381 0.00 0.00 0.00 3.21
1863 3190 2.223735 CGCCCTACCTACTGTACACATG 60.224 54.545 0.00 0.00 0.00 3.21
1864 3191 2.764572 GCCCTACCTACTGTACACATGT 59.235 50.000 0.00 0.00 0.00 3.21
1865 3192 3.197116 GCCCTACCTACTGTACACATGTT 59.803 47.826 0.00 0.00 0.00 2.71
1866 3193 4.755411 CCCTACCTACTGTACACATGTTG 58.245 47.826 0.00 0.00 0.00 3.33
1867 3194 4.464951 CCCTACCTACTGTACACATGTTGA 59.535 45.833 0.00 0.00 0.00 3.18
1868 3195 5.128827 CCCTACCTACTGTACACATGTTGAT 59.871 44.000 0.00 0.00 0.00 2.57
1869 3196 6.042777 CCTACCTACTGTACACATGTTGATG 58.957 44.000 0.00 0.00 35.49 3.07
1870 3197 4.832248 ACCTACTGTACACATGTTGATGG 58.168 43.478 0.00 0.00 33.39 3.51
1871 3198 4.286032 ACCTACTGTACACATGTTGATGGT 59.714 41.667 0.00 0.00 33.39 3.55
1872 3199 4.631377 CCTACTGTACACATGTTGATGGTG 59.369 45.833 0.00 0.00 33.39 4.17
1873 3200 3.411446 ACTGTACACATGTTGATGGTGG 58.589 45.455 0.00 0.00 33.39 4.61
1874 3201 2.158559 TGTACACATGTTGATGGTGGC 58.841 47.619 0.00 0.00 33.39 5.01
1875 3202 2.158559 GTACACATGTTGATGGTGGCA 58.841 47.619 0.00 0.00 33.39 4.92
1876 3203 0.961019 ACACATGTTGATGGTGGCAC 59.039 50.000 9.70 9.70 33.39 5.01
1877 3204 0.960286 CACATGTTGATGGTGGCACA 59.040 50.000 20.82 6.09 33.39 4.57
1878 3205 1.068125 CACATGTTGATGGTGGCACAG 60.068 52.381 20.82 0.00 33.39 3.66
1879 3206 1.250328 CATGTTGATGGTGGCACAGT 58.750 50.000 20.82 6.85 41.80 3.55
1880 3207 1.068125 CATGTTGATGGTGGCACAGTG 60.068 52.381 20.82 0.00 41.80 3.66
1881 3208 0.106769 TGTTGATGGTGGCACAGTGT 60.107 50.000 20.82 1.23 41.80 3.55
1882 3209 1.032014 GTTGATGGTGGCACAGTGTT 58.968 50.000 20.82 0.00 41.80 3.32
1883 3210 1.408702 GTTGATGGTGGCACAGTGTTT 59.591 47.619 20.82 0.00 41.80 2.83
1884 3211 2.621055 GTTGATGGTGGCACAGTGTTTA 59.379 45.455 20.82 0.00 41.80 2.01
1885 3212 3.153369 TGATGGTGGCACAGTGTTTAT 57.847 42.857 20.82 1.64 41.80 1.40
1886 3213 3.081061 TGATGGTGGCACAGTGTTTATC 58.919 45.455 20.82 10.71 41.80 1.75
1887 3214 2.647683 TGGTGGCACAGTGTTTATCA 57.352 45.000 20.82 1.40 41.80 2.15
1888 3215 2.503331 TGGTGGCACAGTGTTTATCAG 58.497 47.619 20.82 0.00 41.80 2.90
1889 3216 2.158682 TGGTGGCACAGTGTTTATCAGT 60.159 45.455 20.82 0.00 41.80 3.41
1890 3217 3.071747 TGGTGGCACAGTGTTTATCAGTA 59.928 43.478 20.82 0.00 41.80 2.74
1891 3218 3.435671 GGTGGCACAGTGTTTATCAGTAC 59.564 47.826 20.82 0.00 41.80 2.73
1892 3219 4.062293 GTGGCACAGTGTTTATCAGTACA 58.938 43.478 13.86 0.00 41.80 2.90
1893 3220 4.695455 GTGGCACAGTGTTTATCAGTACAT 59.305 41.667 13.86 0.00 41.80 2.29
1894 3221 4.935205 TGGCACAGTGTTTATCAGTACATC 59.065 41.667 1.61 0.00 0.00 3.06
1895 3222 4.032900 GGCACAGTGTTTATCAGTACATCG 59.967 45.833 1.61 0.00 0.00 3.84
1896 3223 4.862574 GCACAGTGTTTATCAGTACATCGA 59.137 41.667 1.61 0.00 0.00 3.59
1897 3224 5.220228 GCACAGTGTTTATCAGTACATCGAC 60.220 44.000 1.61 0.00 0.00 4.20
1898 3225 5.003496 CACAGTGTTTATCAGTACATCGACG 59.997 44.000 0.00 0.00 0.00 5.12
1899 3226 5.106436 ACAGTGTTTATCAGTACATCGACGA 60.106 40.000 0.00 0.00 0.00 4.20
1900 3227 5.798434 CAGTGTTTATCAGTACATCGACGAA 59.202 40.000 0.00 0.00 0.00 3.85
1901 3228 6.307077 CAGTGTTTATCAGTACATCGACGAAA 59.693 38.462 0.00 0.00 0.00 3.46
1902 3229 6.307318 AGTGTTTATCAGTACATCGACGAAAC 59.693 38.462 0.00 0.71 0.00 2.78
1903 3230 6.088483 GTGTTTATCAGTACATCGACGAAACA 59.912 38.462 0.00 0.79 0.00 2.83
1904 3231 6.307077 TGTTTATCAGTACATCGACGAAACAG 59.693 38.462 0.00 0.00 0.00 3.16
1905 3232 3.211803 TCAGTACATCGACGAAACAGG 57.788 47.619 0.00 0.00 0.00 4.00
1906 3233 2.094906 TCAGTACATCGACGAAACAGGG 60.095 50.000 0.00 0.00 0.00 4.45
1907 3234 2.094906 CAGTACATCGACGAAACAGGGA 60.095 50.000 0.00 0.00 0.00 4.20
1908 3235 2.163815 AGTACATCGACGAAACAGGGAG 59.836 50.000 0.00 0.00 0.00 4.30
1909 3236 0.246635 ACATCGACGAAACAGGGAGG 59.753 55.000 0.00 0.00 0.00 4.30
1910 3237 0.530744 CATCGACGAAACAGGGAGGA 59.469 55.000 0.00 0.00 0.00 3.71
1911 3238 1.137086 CATCGACGAAACAGGGAGGAT 59.863 52.381 0.00 0.00 0.00 3.24
1912 3239 0.815734 TCGACGAAACAGGGAGGATC 59.184 55.000 0.00 0.00 0.00 3.36
1913 3240 0.525668 CGACGAAACAGGGAGGATCG 60.526 60.000 0.00 0.00 39.30 3.69
1925 3252 4.933064 GGATCGCGCCCTCACGAG 62.933 72.222 0.00 0.00 42.31 4.18
1934 3261 3.382111 CCTCACGAGGGCTCTGTT 58.618 61.111 5.08 0.00 44.87 3.16
1935 3262 1.674057 CCTCACGAGGGCTCTGTTT 59.326 57.895 5.08 0.00 44.87 2.83
1936 3263 0.035458 CCTCACGAGGGCTCTGTTTT 59.965 55.000 5.08 0.00 44.87 2.43
1937 3264 1.543429 CCTCACGAGGGCTCTGTTTTT 60.543 52.381 5.08 0.00 44.87 1.94
1962 3289 9.710979 TTTACTCTATTTTTCCGAAAATATGCG 57.289 29.630 7.12 0.54 43.26 4.73
1963 3290 6.199393 ACTCTATTTTTCCGAAAATATGCGC 58.801 36.000 7.12 0.00 43.26 6.09
1964 3291 6.038271 ACTCTATTTTTCCGAAAATATGCGCT 59.962 34.615 9.73 0.00 43.26 5.92
1965 3292 7.225931 ACTCTATTTTTCCGAAAATATGCGCTA 59.774 33.333 9.73 0.00 43.26 4.26
1966 3293 7.921787 TCTATTTTTCCGAAAATATGCGCTAA 58.078 30.769 9.73 0.00 43.26 3.09
1967 3294 8.067784 TCTATTTTTCCGAAAATATGCGCTAAG 58.932 33.333 9.73 0.00 43.26 2.18
1968 3295 4.545823 TTTCCGAAAATATGCGCTAAGG 57.454 40.909 9.73 0.87 0.00 2.69
1969 3296 2.489971 TCCGAAAATATGCGCTAAGGG 58.510 47.619 9.73 0.00 0.00 3.95
1970 3297 1.535462 CCGAAAATATGCGCTAAGGGG 59.465 52.381 9.73 0.00 0.00 4.79
1995 3322 1.871080 CCATTACGGGCTGATCAGAC 58.129 55.000 27.04 24.21 35.10 3.51
1996 3323 1.491670 CATTACGGGCTGATCAGACG 58.508 55.000 27.04 27.49 37.31 4.18
1997 3324 1.112113 ATTACGGGCTGATCAGACGT 58.888 50.000 33.17 33.17 42.81 4.34
1998 3325 0.454600 TTACGGGCTGATCAGACGTC 59.545 55.000 34.06 18.58 41.38 4.34
1999 3326 0.393944 TACGGGCTGATCAGACGTCT 60.394 55.000 34.06 21.18 41.38 4.18
2000 3327 1.226802 CGGGCTGATCAGACGTCTG 60.227 63.158 34.76 34.76 45.08 3.51
2001 3328 1.142748 GGGCTGATCAGACGTCTGG 59.857 63.158 37.82 25.45 43.91 3.86
2002 3329 1.323271 GGGCTGATCAGACGTCTGGA 61.323 60.000 37.82 26.65 43.91 3.86
2003 3330 0.102120 GGCTGATCAGACGTCTGGAG 59.898 60.000 37.82 30.16 43.91 3.86
2004 3331 0.102120 GCTGATCAGACGTCTGGAGG 59.898 60.000 37.82 26.42 43.91 4.30
2005 3332 1.468985 CTGATCAGACGTCTGGAGGT 58.531 55.000 37.82 24.07 43.91 3.85
2006 3333 1.821753 CTGATCAGACGTCTGGAGGTT 59.178 52.381 37.82 21.13 43.91 3.50
2007 3334 3.017442 CTGATCAGACGTCTGGAGGTTA 58.983 50.000 37.82 22.38 43.91 2.85
2008 3335 3.017442 TGATCAGACGTCTGGAGGTTAG 58.983 50.000 37.82 16.06 43.91 2.34
2009 3336 2.581216 TCAGACGTCTGGAGGTTAGT 57.419 50.000 37.82 3.17 43.91 2.24
2010 3337 2.160205 TCAGACGTCTGGAGGTTAGTG 58.840 52.381 37.82 15.45 43.91 2.74
2011 3338 1.887198 CAGACGTCTGGAGGTTAGTGT 59.113 52.381 33.36 0.00 40.20 3.55
2012 3339 2.296471 CAGACGTCTGGAGGTTAGTGTT 59.704 50.000 33.36 0.00 40.20 3.32
2013 3340 2.963782 AGACGTCTGGAGGTTAGTGTTT 59.036 45.455 19.30 0.00 0.00 2.83
2014 3341 3.005578 AGACGTCTGGAGGTTAGTGTTTC 59.994 47.826 19.30 0.00 0.00 2.78
2015 3342 2.036862 ACGTCTGGAGGTTAGTGTTTCC 59.963 50.000 0.00 0.00 0.00 3.13
2016 3343 2.612221 CGTCTGGAGGTTAGTGTTTCCC 60.612 54.545 0.00 0.00 0.00 3.97
2017 3344 1.621814 TCTGGAGGTTAGTGTTTCCCG 59.378 52.381 0.00 0.00 0.00 5.14
2018 3345 1.621814 CTGGAGGTTAGTGTTTCCCGA 59.378 52.381 0.00 0.00 0.00 5.14
2037 3364 9.509956 TTTCCCGAATCTAACATTCTTAAGAAA 57.490 29.630 21.26 4.81 37.61 2.52
2085 5336 2.990514 CAACATGCACATTGTCCACATG 59.009 45.455 16.65 16.65 42.92 3.21
2091 5342 2.029649 GCACATTGTCCACATGAGCTTT 60.030 45.455 0.00 0.00 0.00 3.51
2118 5369 0.242017 GTCAGCATTCACCTTGCCAC 59.758 55.000 0.00 0.00 41.06 5.01
2120 5371 0.892755 CAGCATTCACCTTGCCACAT 59.107 50.000 0.00 0.00 41.06 3.21
2121 5372 1.274167 CAGCATTCACCTTGCCACATT 59.726 47.619 0.00 0.00 41.06 2.71
2124 5375 2.736400 GCATTCACCTTGCCACATTAGC 60.736 50.000 0.00 0.00 33.95 3.09
2127 5378 1.073763 TCACCTTGCCACATTAGCAGT 59.926 47.619 0.00 0.00 42.17 4.40
2129 5380 1.073763 ACCTTGCCACATTAGCAGTGA 59.926 47.619 0.00 0.00 42.17 3.41
2192 5444 2.003301 GCAAAAACAGCGGTGGAAAAA 58.997 42.857 20.20 0.00 0.00 1.94
2195 5447 3.436700 AAAACAGCGGTGGAAAAAGAG 57.563 42.857 20.20 0.00 0.00 2.85
2199 5451 0.668535 AGCGGTGGAAAAAGAGCAAC 59.331 50.000 0.00 0.00 0.00 4.17
2227 5479 3.990469 CAGTAGTTGTTGCGTGAGATTCT 59.010 43.478 0.00 0.00 0.00 2.40
2235 5487 1.273327 TGCGTGAGATTCTCTTCTGCA 59.727 47.619 14.54 14.41 0.00 4.41
2239 5491 4.676546 CGTGAGATTCTCTTCTGCATACA 58.323 43.478 14.54 0.00 0.00 2.29
2241 5493 5.414360 GTGAGATTCTCTTCTGCATACACA 58.586 41.667 14.54 0.00 0.00 3.72
2246 5498 2.164422 TCTCTTCTGCATACACAGGACG 59.836 50.000 0.00 0.00 38.26 4.79
2276 5529 1.960417 TCCATTTCATTATCGCGGCA 58.040 45.000 6.13 0.00 0.00 5.69
2279 5532 2.805671 CCATTTCATTATCGCGGCACTA 59.194 45.455 6.13 0.00 0.00 2.74
2284 5537 5.493133 TTCATTATCGCGGCACTAATTTT 57.507 34.783 6.13 0.00 0.00 1.82
2285 5538 6.606234 TTCATTATCGCGGCACTAATTTTA 57.394 33.333 6.13 0.00 0.00 1.52
2286 5539 6.795098 TCATTATCGCGGCACTAATTTTAT 57.205 33.333 6.13 0.00 0.00 1.40
2287 5540 7.197071 TCATTATCGCGGCACTAATTTTATT 57.803 32.000 6.13 0.00 0.00 1.40
2288 5541 7.295201 TCATTATCGCGGCACTAATTTTATTC 58.705 34.615 6.13 0.00 0.00 1.75
2289 5542 6.854496 TTATCGCGGCACTAATTTTATTCT 57.146 33.333 6.13 0.00 0.00 2.40
2290 5543 5.751243 ATCGCGGCACTAATTTTATTCTT 57.249 34.783 6.13 0.00 0.00 2.52
2291 5544 5.554822 TCGCGGCACTAATTTTATTCTTT 57.445 34.783 6.13 0.00 0.00 2.52
2292 5545 5.945155 TCGCGGCACTAATTTTATTCTTTT 58.055 33.333 6.13 0.00 0.00 2.27
2293 5546 7.074507 TCGCGGCACTAATTTTATTCTTTTA 57.925 32.000 6.13 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 182 5.243426 ACTGTACGTGCTTGAAACAAAAT 57.757 34.783 4.97 0.00 0.00 1.82
144 197 5.713861 AGTTAATCTTCCCTGTACTGTACGT 59.286 40.000 12.87 0.00 0.00 3.57
169 222 1.521681 GACCGACATGTGGCTAGCC 60.522 63.158 27.71 27.71 0.00 3.93
170 223 0.391130 TTGACCGACATGTGGCTAGC 60.391 55.000 1.15 6.04 0.00 3.42
294 356 0.460459 TGATTGATTAACCGCGGCGA 60.460 50.000 28.58 10.97 0.00 5.54
296 358 1.131504 TGTTGATTGATTAACCGCGGC 59.868 47.619 28.58 9.24 0.00 6.53
298 360 3.296943 CGTTTGTTGATTGATTAACCGCG 59.703 43.478 0.00 0.00 0.00 6.46
300 362 5.209240 ACACGTTTGTTGATTGATTAACCG 58.791 37.500 0.00 0.00 28.43 4.44
370 432 3.153919 GCAGTGGTTTCCTATTCCAACA 58.846 45.455 0.00 0.00 32.82 3.33
402 467 1.541147 CCAAGCAATGTCGTCACCATT 59.459 47.619 0.00 0.00 32.88 3.16
413 479 4.201753 CGATCTACACTTGTCCAAGCAATG 60.202 45.833 6.94 1.44 41.99 2.82
440 506 5.955488 GATAATGACTTATCTAGCGAGCCA 58.045 41.667 0.00 0.00 40.01 4.75
488 558 1.258445 ATGGGTGAGAGGGTGACGTC 61.258 60.000 9.11 9.11 45.47 4.34
530 605 3.004315 CGGCTTGGTTGATTAAACAGTGT 59.996 43.478 0.00 0.00 40.86 3.55
532 607 3.219281 ACGGCTTGGTTGATTAAACAGT 58.781 40.909 0.00 0.00 40.86 3.55
533 608 3.365969 GGACGGCTTGGTTGATTAAACAG 60.366 47.826 0.00 0.00 40.86 3.16
534 609 2.554893 GGACGGCTTGGTTGATTAAACA 59.445 45.455 0.00 0.00 40.86 2.83
535 610 2.554893 TGGACGGCTTGGTTGATTAAAC 59.445 45.455 0.00 0.00 38.12 2.01
536 611 2.865079 TGGACGGCTTGGTTGATTAAA 58.135 42.857 0.00 0.00 0.00 1.52
542 617 0.248866 GTGTTTGGACGGCTTGGTTG 60.249 55.000 0.00 0.00 0.00 3.77
620 707 0.984230 ATCGGCTTGACTTGGGAGAA 59.016 50.000 0.00 0.00 0.00 2.87
677 768 1.762957 TGGGTCGGGATCTTGATCTTC 59.237 52.381 10.03 3.44 0.00 2.87
851 2071 5.527582 CCCTTTATATAGAGCTTTGCGTGTT 59.472 40.000 0.00 0.00 0.00 3.32
908 2153 5.509670 GGATGACTTGTGTATCGATGGATGA 60.510 44.000 8.54 0.00 34.00 2.92
953 2241 4.570772 GGATCGGTCAATCAATCGAAAAGA 59.429 41.667 0.00 0.00 35.25 2.52
956 2244 3.867857 TGGATCGGTCAATCAATCGAAA 58.132 40.909 0.00 0.00 35.25 3.46
959 2247 3.657634 AGATGGATCGGTCAATCAATCG 58.342 45.455 15.50 0.00 39.93 3.34
970 2258 2.256764 CGGCGAGAGATGGATCGG 59.743 66.667 0.00 0.00 39.31 4.18
997 2285 2.037620 ATGAGCGCCTCCTCCATCAC 62.038 60.000 2.29 0.00 0.00 3.06
1032 2320 4.643387 ACCTTGGCCAGCACGTCC 62.643 66.667 5.11 0.00 0.00 4.79
1311 2606 4.201685 CGTCAGAACTAATTAAGCAACCGG 60.202 45.833 0.00 0.00 0.00 5.28
1796 3123 8.757164 AGTCGAGTTTTTGTTTTCTTTTGATT 57.243 26.923 0.00 0.00 0.00 2.57
1797 3124 7.488150 GGAGTCGAGTTTTTGTTTTCTTTTGAT 59.512 33.333 0.00 0.00 0.00 2.57
1798 3125 6.804783 GGAGTCGAGTTTTTGTTTTCTTTTGA 59.195 34.615 0.00 0.00 0.00 2.69
1799 3126 6.806739 AGGAGTCGAGTTTTTGTTTTCTTTTG 59.193 34.615 0.00 0.00 0.00 2.44
1800 3127 6.920817 AGGAGTCGAGTTTTTGTTTTCTTTT 58.079 32.000 0.00 0.00 0.00 2.27
1801 3128 6.510879 AGGAGTCGAGTTTTTGTTTTCTTT 57.489 33.333 0.00 0.00 0.00 2.52
1802 3129 6.404403 GGAAGGAGTCGAGTTTTTGTTTTCTT 60.404 38.462 0.00 0.00 0.00 2.52
1803 3130 5.066117 GGAAGGAGTCGAGTTTTTGTTTTCT 59.934 40.000 0.00 0.00 0.00 2.52
1804 3131 5.271625 GGAAGGAGTCGAGTTTTTGTTTTC 58.728 41.667 0.00 0.00 0.00 2.29
1805 3132 4.097437 GGGAAGGAGTCGAGTTTTTGTTTT 59.903 41.667 0.00 0.00 0.00 2.43
1806 3133 3.630769 GGGAAGGAGTCGAGTTTTTGTTT 59.369 43.478 0.00 0.00 0.00 2.83
1807 3134 3.118000 AGGGAAGGAGTCGAGTTTTTGTT 60.118 43.478 0.00 0.00 0.00 2.83
1808 3135 2.438392 AGGGAAGGAGTCGAGTTTTTGT 59.562 45.455 0.00 0.00 0.00 2.83
1809 3136 3.127425 AGGGAAGGAGTCGAGTTTTTG 57.873 47.619 0.00 0.00 0.00 2.44
1810 3137 3.391626 AGAAGGGAAGGAGTCGAGTTTTT 59.608 43.478 0.00 0.00 0.00 1.94
1811 3138 2.973406 AGAAGGGAAGGAGTCGAGTTTT 59.027 45.455 0.00 0.00 0.00 2.43
1812 3139 2.610873 AGAAGGGAAGGAGTCGAGTTT 58.389 47.619 0.00 0.00 0.00 2.66
1813 3140 2.312424 AGAAGGGAAGGAGTCGAGTT 57.688 50.000 0.00 0.00 0.00 3.01
1814 3141 2.309458 ACTAGAAGGGAAGGAGTCGAGT 59.691 50.000 0.00 0.00 0.00 4.18
1815 3142 3.007473 ACTAGAAGGGAAGGAGTCGAG 57.993 52.381 0.00 0.00 0.00 4.04
1816 3143 4.018597 ACTTACTAGAAGGGAAGGAGTCGA 60.019 45.833 0.00 0.00 0.00 4.20
1817 3144 4.271661 ACTTACTAGAAGGGAAGGAGTCG 58.728 47.826 0.00 0.00 0.00 4.18
1818 3145 4.336153 CGACTTACTAGAAGGGAAGGAGTC 59.664 50.000 0.00 0.00 31.79 3.36
1819 3146 4.271661 CGACTTACTAGAAGGGAAGGAGT 58.728 47.826 0.00 0.00 0.00 3.85
1820 3147 3.067040 GCGACTTACTAGAAGGGAAGGAG 59.933 52.174 0.00 0.00 0.00 3.69
1821 3148 3.022406 GCGACTTACTAGAAGGGAAGGA 58.978 50.000 0.00 0.00 0.00 3.36
1822 3149 2.223525 CGCGACTTACTAGAAGGGAAGG 60.224 54.545 0.00 0.00 0.00 3.46
1823 3150 2.795331 GCGCGACTTACTAGAAGGGAAG 60.795 54.545 12.10 0.00 0.00 3.46
1824 3151 1.133790 GCGCGACTTACTAGAAGGGAA 59.866 52.381 12.10 0.00 0.00 3.97
1825 3152 0.737219 GCGCGACTTACTAGAAGGGA 59.263 55.000 12.10 0.00 0.00 4.20
1826 3153 0.248949 GGCGCGACTTACTAGAAGGG 60.249 60.000 12.10 0.00 0.00 3.95
1827 3154 0.248949 GGGCGCGACTTACTAGAAGG 60.249 60.000 13.91 0.00 0.00 3.46
1828 3155 0.739561 AGGGCGCGACTTACTAGAAG 59.260 55.000 13.91 0.00 0.00 2.85
1829 3156 1.672881 GTAGGGCGCGACTTACTAGAA 59.327 52.381 25.46 0.00 0.00 2.10
1830 3157 1.303309 GTAGGGCGCGACTTACTAGA 58.697 55.000 25.46 0.00 0.00 2.43
1831 3158 0.310232 GGTAGGGCGCGACTTACTAG 59.690 60.000 30.12 0.00 0.00 2.57
1832 3159 0.107017 AGGTAGGGCGCGACTTACTA 60.107 55.000 30.12 13.00 0.00 1.82
1833 3160 0.107017 TAGGTAGGGCGCGACTTACT 60.107 55.000 30.12 19.41 0.00 2.24
1834 3161 0.029967 GTAGGTAGGGCGCGACTTAC 59.970 60.000 24.84 24.84 0.00 2.34
1835 3162 0.107017 AGTAGGTAGGGCGCGACTTA 60.107 55.000 13.91 5.48 0.00 2.24
1836 3163 1.379576 AGTAGGTAGGGCGCGACTT 60.380 57.895 13.91 6.97 0.00 3.01
1837 3164 2.119655 CAGTAGGTAGGGCGCGACT 61.120 63.158 13.91 10.80 0.00 4.18
1838 3165 1.097547 TACAGTAGGTAGGGCGCGAC 61.098 60.000 12.10 6.99 0.00 5.19
1839 3166 1.097547 GTACAGTAGGTAGGGCGCGA 61.098 60.000 12.10 0.00 31.13 5.87
1840 3167 1.358046 GTACAGTAGGTAGGGCGCG 59.642 63.158 0.00 0.00 31.13 6.86
1841 3168 0.101939 GTGTACAGTAGGTAGGGCGC 59.898 60.000 0.00 0.00 31.13 6.53
1842 3169 1.466856 TGTGTACAGTAGGTAGGGCG 58.533 55.000 0.00 0.00 31.13 6.13
1843 3170 2.764572 ACATGTGTACAGTAGGTAGGGC 59.235 50.000 0.00 0.00 31.13 5.19
1844 3171 4.464951 TCAACATGTGTACAGTAGGTAGGG 59.535 45.833 0.00 0.00 31.13 3.53
1845 3172 5.654603 TCAACATGTGTACAGTAGGTAGG 57.345 43.478 0.00 0.00 31.13 3.18
1846 3173 6.042777 CCATCAACATGTGTACAGTAGGTAG 58.957 44.000 0.00 0.00 31.13 3.18
1847 3174 5.482526 ACCATCAACATGTGTACAGTAGGTA 59.517 40.000 0.00 0.00 0.00 3.08
1848 3175 4.286032 ACCATCAACATGTGTACAGTAGGT 59.714 41.667 0.00 0.00 0.00 3.08
1849 3176 4.631377 CACCATCAACATGTGTACAGTAGG 59.369 45.833 0.00 0.00 0.00 3.18
1850 3177 4.631377 CCACCATCAACATGTGTACAGTAG 59.369 45.833 0.00 0.00 0.00 2.57
1851 3178 4.574892 CCACCATCAACATGTGTACAGTA 58.425 43.478 0.00 0.00 0.00 2.74
1852 3179 3.411446 CCACCATCAACATGTGTACAGT 58.589 45.455 0.00 0.00 0.00 3.55
1853 3180 2.162208 GCCACCATCAACATGTGTACAG 59.838 50.000 0.00 0.00 0.00 2.74
1854 3181 2.158559 GCCACCATCAACATGTGTACA 58.841 47.619 0.00 0.00 0.00 2.90
1855 3182 2.095263 GTGCCACCATCAACATGTGTAC 60.095 50.000 0.00 0.00 0.00 2.90
1856 3183 2.158559 GTGCCACCATCAACATGTGTA 58.841 47.619 0.00 0.00 0.00 2.90
1857 3184 0.961019 GTGCCACCATCAACATGTGT 59.039 50.000 0.00 0.00 0.00 3.72
1858 3185 0.960286 TGTGCCACCATCAACATGTG 59.040 50.000 0.00 0.00 0.00 3.21
1859 3186 1.250328 CTGTGCCACCATCAACATGT 58.750 50.000 0.00 0.00 0.00 3.21
1860 3187 1.068125 CACTGTGCCACCATCAACATG 60.068 52.381 0.00 0.00 0.00 3.21
1861 3188 1.250328 CACTGTGCCACCATCAACAT 58.750 50.000 0.00 0.00 0.00 2.71
1862 3189 0.106769 ACACTGTGCCACCATCAACA 60.107 50.000 7.90 0.00 0.00 3.33
1863 3190 1.032014 AACACTGTGCCACCATCAAC 58.968 50.000 7.90 0.00 0.00 3.18
1864 3191 1.774110 AAACACTGTGCCACCATCAA 58.226 45.000 7.90 0.00 0.00 2.57
1865 3192 2.647683 TAAACACTGTGCCACCATCA 57.352 45.000 7.90 0.00 0.00 3.07
1866 3193 3.081061 TGATAAACACTGTGCCACCATC 58.919 45.455 7.90 4.88 0.00 3.51
1867 3194 3.084039 CTGATAAACACTGTGCCACCAT 58.916 45.455 7.90 0.00 0.00 3.55
1868 3195 2.158682 ACTGATAAACACTGTGCCACCA 60.159 45.455 7.90 0.00 0.00 4.17
1869 3196 2.504367 ACTGATAAACACTGTGCCACC 58.496 47.619 7.90 0.00 0.00 4.61
1870 3197 4.062293 TGTACTGATAAACACTGTGCCAC 58.938 43.478 7.90 0.00 0.00 5.01
1871 3198 4.344359 TGTACTGATAAACACTGTGCCA 57.656 40.909 7.90 0.00 0.00 4.92
1872 3199 4.032900 CGATGTACTGATAAACACTGTGCC 59.967 45.833 7.90 0.00 0.00 5.01
1873 3200 4.862574 TCGATGTACTGATAAACACTGTGC 59.137 41.667 7.90 0.00 0.00 4.57
1874 3201 5.003496 CGTCGATGTACTGATAAACACTGTG 59.997 44.000 6.19 6.19 0.00 3.66
1875 3202 5.093457 CGTCGATGTACTGATAAACACTGT 58.907 41.667 0.00 0.00 0.00 3.55
1876 3203 5.329493 TCGTCGATGTACTGATAAACACTG 58.671 41.667 4.21 0.00 0.00 3.66
1877 3204 5.556355 TCGTCGATGTACTGATAAACACT 57.444 39.130 4.21 0.00 0.00 3.55
1878 3205 6.088483 TGTTTCGTCGATGTACTGATAAACAC 59.912 38.462 12.07 0.00 32.59 3.32
1879 3206 6.151004 TGTTTCGTCGATGTACTGATAAACA 58.849 36.000 12.07 12.07 33.88 2.83
1880 3207 6.237490 CCTGTTTCGTCGATGTACTGATAAAC 60.237 42.308 4.21 6.70 0.00 2.01
1881 3208 5.803461 CCTGTTTCGTCGATGTACTGATAAA 59.197 40.000 4.21 0.00 0.00 1.40
1882 3209 5.337554 CCTGTTTCGTCGATGTACTGATAA 58.662 41.667 4.21 0.00 0.00 1.75
1883 3210 4.201980 CCCTGTTTCGTCGATGTACTGATA 60.202 45.833 4.21 0.00 0.00 2.15
1884 3211 3.428999 CCCTGTTTCGTCGATGTACTGAT 60.429 47.826 4.21 0.00 0.00 2.90
1885 3212 2.094906 CCCTGTTTCGTCGATGTACTGA 60.095 50.000 4.21 0.00 0.00 3.41
1886 3213 2.094906 TCCCTGTTTCGTCGATGTACTG 60.095 50.000 4.21 8.18 0.00 2.74
1887 3214 2.163815 CTCCCTGTTTCGTCGATGTACT 59.836 50.000 4.21 0.00 0.00 2.73
1888 3215 2.527100 CTCCCTGTTTCGTCGATGTAC 58.473 52.381 4.21 5.25 0.00 2.90
1889 3216 1.475280 CCTCCCTGTTTCGTCGATGTA 59.525 52.381 4.21 0.00 0.00 2.29
1890 3217 0.246635 CCTCCCTGTTTCGTCGATGT 59.753 55.000 4.21 0.00 0.00 3.06
1891 3218 0.530744 TCCTCCCTGTTTCGTCGATG 59.469 55.000 0.00 0.00 0.00 3.84
1892 3219 1.409427 GATCCTCCCTGTTTCGTCGAT 59.591 52.381 0.00 0.00 0.00 3.59
1893 3220 0.815734 GATCCTCCCTGTTTCGTCGA 59.184 55.000 0.00 0.00 0.00 4.20
1894 3221 0.525668 CGATCCTCCCTGTTTCGTCG 60.526 60.000 0.00 0.00 0.00 5.12
1895 3222 0.806492 GCGATCCTCCCTGTTTCGTC 60.806 60.000 0.00 0.00 32.65 4.20
1896 3223 1.218316 GCGATCCTCCCTGTTTCGT 59.782 57.895 0.00 0.00 32.65 3.85
1897 3224 1.878522 CGCGATCCTCCCTGTTTCG 60.879 63.158 0.00 0.00 0.00 3.46
1898 3225 2.174319 GCGCGATCCTCCCTGTTTC 61.174 63.158 12.10 0.00 0.00 2.78
1899 3226 2.125106 GCGCGATCCTCCCTGTTT 60.125 61.111 12.10 0.00 0.00 2.83
1900 3227 4.162690 GGCGCGATCCTCCCTGTT 62.163 66.667 12.10 0.00 0.00 3.16
1918 3245 1.884235 AAAAACAGAGCCCTCGTGAG 58.116 50.000 0.00 0.00 34.09 3.51
1936 3263 9.710979 CGCATATTTTCGGAAAAATAGAGTAAA 57.289 29.630 18.78 0.00 45.68 2.01
1937 3264 7.853929 GCGCATATTTTCGGAAAAATAGAGTAA 59.146 33.333 18.78 0.00 45.68 2.24
1938 3265 7.225931 AGCGCATATTTTCGGAAAAATAGAGTA 59.774 33.333 18.78 7.12 45.68 2.59
1939 3266 6.038271 AGCGCATATTTTCGGAAAAATAGAGT 59.962 34.615 18.78 5.19 45.68 3.24
1940 3267 6.430451 AGCGCATATTTTCGGAAAAATAGAG 58.570 36.000 18.78 13.35 45.68 2.43
1941 3268 6.371809 AGCGCATATTTTCGGAAAAATAGA 57.628 33.333 18.78 6.49 45.68 1.98
1942 3269 7.323656 CCTTAGCGCATATTTTCGGAAAAATAG 59.676 37.037 18.78 12.24 45.68 1.73
1943 3270 7.136119 CCTTAGCGCATATTTTCGGAAAAATA 58.864 34.615 18.78 12.09 46.22 1.40
1944 3271 5.977129 CCTTAGCGCATATTTTCGGAAAAAT 59.023 36.000 18.78 11.15 45.02 1.82
1945 3272 5.336744 CCTTAGCGCATATTTTCGGAAAAA 58.663 37.500 18.78 9.55 38.66 1.94
1946 3273 4.201970 CCCTTAGCGCATATTTTCGGAAAA 60.202 41.667 17.39 17.39 34.41 2.29
1947 3274 3.314080 CCCTTAGCGCATATTTTCGGAAA 59.686 43.478 11.47 0.00 0.00 3.13
1948 3275 2.875933 CCCTTAGCGCATATTTTCGGAA 59.124 45.455 11.47 0.00 0.00 4.30
1949 3276 2.489971 CCCTTAGCGCATATTTTCGGA 58.510 47.619 11.47 0.00 0.00 4.55
1950 3277 1.535462 CCCCTTAGCGCATATTTTCGG 59.465 52.381 11.47 0.00 0.00 4.30
1951 3278 1.069227 GCCCCTTAGCGCATATTTTCG 60.069 52.381 11.47 0.00 0.00 3.46
1952 3279 2.030805 CAGCCCCTTAGCGCATATTTTC 60.031 50.000 11.47 0.00 38.01 2.29
1953 3280 1.956477 CAGCCCCTTAGCGCATATTTT 59.044 47.619 11.47 0.00 38.01 1.82
1954 3281 1.142870 TCAGCCCCTTAGCGCATATTT 59.857 47.619 11.47 0.00 38.01 1.40
1955 3282 0.764890 TCAGCCCCTTAGCGCATATT 59.235 50.000 11.47 0.00 38.01 1.28
1956 3283 0.035458 GTCAGCCCCTTAGCGCATAT 59.965 55.000 11.47 0.00 38.01 1.78
1957 3284 1.445942 GTCAGCCCCTTAGCGCATA 59.554 57.895 11.47 0.00 38.01 3.14
1958 3285 2.190578 GTCAGCCCCTTAGCGCAT 59.809 61.111 11.47 0.00 38.01 4.73
1959 3286 4.096003 GGTCAGCCCCTTAGCGCA 62.096 66.667 11.47 0.00 38.01 6.09
1976 3303 1.869754 CGTCTGATCAGCCCGTAATGG 60.870 57.143 18.36 0.00 37.55 3.16
1977 3304 1.202417 ACGTCTGATCAGCCCGTAATG 60.202 52.381 27.81 15.02 35.22 1.90
1978 3305 1.067212 GACGTCTGATCAGCCCGTAAT 59.933 52.381 28.50 14.57 36.42 1.89
1979 3306 0.454600 GACGTCTGATCAGCCCGTAA 59.545 55.000 28.50 7.65 36.42 3.18
1980 3307 0.393944 AGACGTCTGATCAGCCCGTA 60.394 55.000 28.50 8.30 36.42 4.02
1981 3308 1.679305 AGACGTCTGATCAGCCCGT 60.679 57.895 28.70 28.70 38.04 5.28
1982 3309 1.226802 CAGACGTCTGATCAGCCCG 60.227 63.158 36.73 24.20 46.59 6.13
1983 3310 1.142748 CCAGACGTCTGATCAGCCC 59.857 63.158 40.21 9.72 46.59 5.19
1984 3311 0.102120 CTCCAGACGTCTGATCAGCC 59.898 60.000 40.21 5.64 46.59 4.85
1985 3312 0.102120 CCTCCAGACGTCTGATCAGC 59.898 60.000 40.21 11.88 46.59 4.26
1986 3313 1.468985 ACCTCCAGACGTCTGATCAG 58.531 55.000 40.21 30.12 46.59 2.90
1987 3314 1.924731 AACCTCCAGACGTCTGATCA 58.075 50.000 40.21 24.33 46.59 2.92
1988 3315 3.018149 ACTAACCTCCAGACGTCTGATC 58.982 50.000 40.21 4.96 46.59 2.92
1989 3316 2.755655 CACTAACCTCCAGACGTCTGAT 59.244 50.000 40.21 23.83 46.59 2.90
1990 3317 2.160205 CACTAACCTCCAGACGTCTGA 58.840 52.381 40.21 26.20 46.59 3.27
1991 3318 1.887198 ACACTAACCTCCAGACGTCTG 59.113 52.381 33.87 33.87 43.40 3.51
1992 3319 2.289592 ACACTAACCTCCAGACGTCT 57.710 50.000 13.58 13.58 0.00 4.18
1993 3320 3.315418 GAAACACTAACCTCCAGACGTC 58.685 50.000 7.70 7.70 0.00 4.34
1994 3321 2.036862 GGAAACACTAACCTCCAGACGT 59.963 50.000 0.00 0.00 0.00 4.34
1995 3322 2.612221 GGGAAACACTAACCTCCAGACG 60.612 54.545 0.00 0.00 0.00 4.18
1996 3323 2.612221 CGGGAAACACTAACCTCCAGAC 60.612 54.545 0.00 0.00 0.00 3.51
1997 3324 1.621814 CGGGAAACACTAACCTCCAGA 59.378 52.381 0.00 0.00 0.00 3.86
1998 3325 1.621814 TCGGGAAACACTAACCTCCAG 59.378 52.381 0.00 0.00 0.00 3.86
1999 3326 1.719529 TCGGGAAACACTAACCTCCA 58.280 50.000 0.00 0.00 0.00 3.86
2000 3327 2.845363 TTCGGGAAACACTAACCTCC 57.155 50.000 0.00 0.00 0.00 4.30
2001 3328 4.203654 AGATTCGGGAAACACTAACCTC 57.796 45.455 0.00 0.00 0.00 3.85
2002 3329 5.012354 TGTTAGATTCGGGAAACACTAACCT 59.988 40.000 20.25 0.00 36.25 3.50
2003 3330 5.240121 TGTTAGATTCGGGAAACACTAACC 58.760 41.667 20.25 0.00 36.25 2.85
2004 3331 6.980051 ATGTTAGATTCGGGAAACACTAAC 57.020 37.500 18.39 18.39 36.81 2.34
2005 3332 7.391620 AGAATGTTAGATTCGGGAAACACTAA 58.608 34.615 0.00 0.00 34.89 2.24
2006 3333 6.942976 AGAATGTTAGATTCGGGAAACACTA 58.057 36.000 0.00 0.00 34.89 2.74
2007 3334 5.805728 AGAATGTTAGATTCGGGAAACACT 58.194 37.500 0.00 0.00 34.89 3.55
2008 3335 6.496338 AAGAATGTTAGATTCGGGAAACAC 57.504 37.500 0.00 0.00 34.89 3.32
2009 3336 8.098286 TCTTAAGAATGTTAGATTCGGGAAACA 58.902 33.333 1.68 0.00 36.37 2.83
2010 3337 8.488651 TCTTAAGAATGTTAGATTCGGGAAAC 57.511 34.615 1.68 0.00 33.51 2.78
2011 3338 9.509956 TTTCTTAAGAATGTTAGATTCGGGAAA 57.490 29.630 18.37 4.41 33.54 3.13
2012 3339 9.681062 ATTTCTTAAGAATGTTAGATTCGGGAA 57.319 29.630 18.37 0.00 33.54 3.97
2013 3340 9.681062 AATTTCTTAAGAATGTTAGATTCGGGA 57.319 29.630 18.37 0.00 33.54 5.14
2014 3341 9.722056 CAATTTCTTAAGAATGTTAGATTCGGG 57.278 33.333 18.37 0.50 33.54 5.14
2015 3342 9.226345 GCAATTTCTTAAGAATGTTAGATTCGG 57.774 33.333 18.37 5.26 33.54 4.30
2016 3343 9.994432 AGCAATTTCTTAAGAATGTTAGATTCG 57.006 29.630 18.37 9.65 33.54 3.34
2037 3364 1.972588 AGGTAGAAGTGGGGAGCAAT 58.027 50.000 0.00 0.00 0.00 3.56
2085 5336 2.019249 TGCTGACATGGCATAAAGCTC 58.981 47.619 21.53 5.85 44.79 4.09
2199 5451 3.005823 GCAACAACTACTGCATGCG 57.994 52.632 14.09 10.50 38.48 4.73
2227 5479 1.893137 ACGTCCTGTGTATGCAGAAGA 59.107 47.619 0.00 0.00 38.70 2.87
2239 5491 2.040178 GGATAATCTCCCACGTCCTGT 58.960 52.381 0.00 0.00 38.19 4.00
2241 5493 2.471815 TGGATAATCTCCCACGTCCT 57.528 50.000 0.00 0.00 44.23 3.85
2246 5498 7.414540 GCGATAATGAAATGGATAATCTCCCAC 60.415 40.741 0.00 0.00 44.23 4.61
2264 5517 7.298122 AGAATAAAATTAGTGCCGCGATAATG 58.702 34.615 8.23 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.