Multiple sequence alignment - TraesCS3D01G167300

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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 TraesCS3D01G167300 chr3D 100.000 2873 0 0 1 2873 141649613 141652485 0.000000e+00 5306.0
1 TraesCS3D01G167300 chr3D 77.558 303 68 0 1556 1858 10804765 10805067 1.760000e-42 183.0
2 TraesCS3D01G167300 chr3A 91.599 2107 107 21 3 2086 160015578 160017637 0.000000e+00 2846.0
3 TraesCS3D01G167300 chr3A 85.999 1757 161 53 346 2068 159994768 159996473 0.000000e+00 1803.0
4 TraesCS3D01G167300 chr3A 97.059 34 0 1 2088 2120 745554106 745554073 4.000000e-04 56.5
5 TraesCS3D01G167300 chr4D 89.885 1740 121 33 346 2053 375115654 375117370 0.000000e+00 2187.0
6 TraesCS3D01G167300 chr4D 80.997 742 113 18 1148 1881 414328434 414327713 5.370000e-157 564.0
7 TraesCS3D01G167300 chr4D 80.645 713 116 13 1148 1858 414336986 414336294 1.520000e-147 532.0
8 TraesCS3D01G167300 chr4D 80.505 713 117 13 1148 1858 414365361 414364669 7.050000e-146 527.0
9 TraesCS3D01G167300 chr4D 84.868 152 16 5 1001 1150 414365607 414365461 2.310000e-31 147.0
10 TraesCS3D01G167300 chr4D 84.211 152 17 5 1001 1150 414337232 414337086 1.070000e-29 141.0
11 TraesCS3D01G167300 chr4D 85.606 132 12 5 1021 1150 414359382 414359256 6.460000e-27 132.0
12 TraesCS3D01G167300 chr3B 89.328 1771 132 24 346 2086 203612414 203614157 0.000000e+00 2170.0
13 TraesCS3D01G167300 chr7B 89.715 632 58 5 2248 2873 733776171 733775541 0.000000e+00 800.0
14 TraesCS3D01G167300 chr7B 95.833 48 2 0 2166 2213 528017284 528017237 8.530000e-11 78.7
15 TraesCS3D01G167300 chr7B 94.000 50 3 0 2164 2213 618452054 618452005 3.070000e-10 76.8
16 TraesCS3D01G167300 chr4A 81.030 738 114 18 1148 1881 49200043 49200758 5.370000e-157 564.0
17 TraesCS3D01G167300 chr4B 79.190 716 123 13 1148 1858 510562431 510561737 9.320000e-130 473.0
18 TraesCS3D01G167300 chr4B 85.526 152 15 5 1001 1150 510482214 510482068 4.960000e-33 152.0
19 TraesCS3D01G167300 chr7A 94.118 85 3 2 2078 2162 210625404 210625322 8.360000e-26 128.0
20 TraesCS3D01G167300 chr7A 97.727 44 1 0 2170 2213 52420847 52420804 3.070000e-10 76.8
21 TraesCS3D01G167300 chr1A 93.976 83 3 2 2088 2169 425234366 425234447 1.080000e-24 124.0
22 TraesCS3D01G167300 chr1A 91.566 83 5 2 2088 2169 406601757 406601676 2.340000e-21 113.0
23 TraesCS3D01G167300 chr1A 91.566 83 5 2 2088 2169 421644936 421644855 2.340000e-21 113.0
24 TraesCS3D01G167300 chr6B 90.698 86 6 2 2087 2171 3275216 3275132 2.340000e-21 113.0
25 TraesCS3D01G167300 chr6B 100.000 31 0 0 2088 2118 3242754 3242724 1.110000e-04 58.4
26 TraesCS3D01G167300 chrUn 87.671 73 6 3 2141 2212 82710093 82710023 6.600000e-12 82.4
27 TraesCS3D01G167300 chr5D 94.340 53 3 0 2160 2212 459143455 459143507 6.600000e-12 82.4
28 TraesCS3D01G167300 chr5D 86.885 61 5 2 3 62 234061836 234061894 6.640000e-07 65.8
29 TraesCS3D01G167300 chr2D 97.872 47 1 0 2167 2213 398306051 398306097 6.600000e-12 82.4
30 TraesCS3D01G167300 chr1D 97.872 47 1 0 2166 2212 307417050 307417004 6.600000e-12 82.4
31 TraesCS3D01G167300 chr1D 84.615 78 11 1 3 79 463861893 463861816 3.070000e-10 76.8
32 TraesCS3D01G167300 chr2B 97.826 46 1 0 2168 2213 101019339 101019384 2.370000e-11 80.5
33 TraesCS3D01G167300 chr2A 90.741 54 3 2 2170 2223 734530359 734530410 1.430000e-08 71.3


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 TraesCS3D01G167300 chr3D 141649613 141652485 2872 False 5306.0 5306 100.0000 1 2873 1 chr3D.!!$F2 2872
1 TraesCS3D01G167300 chr3A 160015578 160017637 2059 False 2846.0 2846 91.5990 3 2086 1 chr3A.!!$F2 2083
2 TraesCS3D01G167300 chr3A 159994768 159996473 1705 False 1803.0 1803 85.9990 346 2068 1 chr3A.!!$F1 1722
3 TraesCS3D01G167300 chr4D 375115654 375117370 1716 False 2187.0 2187 89.8850 346 2053 1 chr4D.!!$F1 1707
4 TraesCS3D01G167300 chr4D 414327713 414328434 721 True 564.0 564 80.9970 1148 1881 1 chr4D.!!$R1 733
5 TraesCS3D01G167300 chr4D 414364669 414365607 938 True 337.0 527 82.6865 1001 1858 2 chr4D.!!$R4 857
6 TraesCS3D01G167300 chr4D 414336294 414337232 938 True 336.5 532 82.4280 1001 1858 2 chr4D.!!$R3 857
7 TraesCS3D01G167300 chr3B 203612414 203614157 1743 False 2170.0 2170 89.3280 346 2086 1 chr3B.!!$F1 1740
8 TraesCS3D01G167300 chr7B 733775541 733776171 630 True 800.0 800 89.7150 2248 2873 1 chr7B.!!$R3 625
9 TraesCS3D01G167300 chr4A 49200043 49200758 715 False 564.0 564 81.0300 1148 1881 1 chr4A.!!$F1 733
10 TraesCS3D01G167300 chr4B 510561737 510562431 694 True 473.0 473 79.1900 1148 1858 1 chr4B.!!$R2 710

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
973 1029 0.096976 CAGATAAGTTTGTGGCGGCG 59.903 55.0 0.51 0.51 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2827 3015 0.034089 GCAGGGCTGGGAGTACAAAT 60.034 55.0 0.0 0.0 0.0 2.32 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
106 107 5.772521 ACTGATAACAATTGCAGGTGTTTC 58.227 37.500 18.69 15.66 38.80 2.78
109 110 7.230510 ACTGATAACAATTGCAGGTGTTTCTTA 59.769 33.333 18.69 5.21 38.80 2.10
110 111 7.592938 TGATAACAATTGCAGGTGTTTCTTAG 58.407 34.615 18.69 0.00 38.80 2.18
131 132 5.379732 AGAAAACAAACCTGAAACGTTCA 57.620 34.783 0.00 0.52 38.17 3.18
133 134 6.394809 AGAAAACAAACCTGAAACGTTCATT 58.605 32.000 0.00 0.00 39.30 2.57
195 196 4.162690 CCCCTAGCTGACGTGGCC 62.163 72.222 0.00 0.00 0.00 5.36
212 213 3.074538 GTGGCCCTGATATTAGGTCCATT 59.925 47.826 18.29 0.00 46.62 3.16
213 214 3.330701 TGGCCCTGATATTAGGTCCATTC 59.669 47.826 12.04 0.00 40.76 2.67
266 274 6.997655 ACCATAATCGAATTATCAGCTCTGA 58.002 36.000 1.67 1.67 44.59 3.27
296 304 1.821216 AACTTAACGGACCCTGCATG 58.179 50.000 0.00 0.00 0.00 4.06
337 345 2.572104 TCTTTAGGTCTTCCTTGAGGGC 59.428 50.000 0.00 0.00 42.12 5.19
379 387 1.199615 TCATTACCTGACGATGGGCA 58.800 50.000 0.00 0.00 0.00 5.36
459 468 2.563471 ACGAGACATCCTTTCGTAGC 57.437 50.000 0.00 0.00 44.79 3.58
575 593 3.609214 AATCGCAAAACGCCGCCTG 62.609 57.895 0.00 0.00 43.23 4.85
656 678 4.494199 GCAAAGATCGATAAGAACCAACCG 60.494 45.833 0.00 0.00 0.00 4.44
657 679 4.730949 AAGATCGATAAGAACCAACCGA 57.269 40.909 0.00 0.00 0.00 4.69
667 689 9.797556 CGATAAGAACCAACCGATGATATAATA 57.202 33.333 0.00 0.00 0.00 0.98
890 925 7.874528 CACAAGATCATAACACATCTAGCCATA 59.125 37.037 0.00 0.00 0.00 2.74
905 942 1.688735 GCCATAAGAAGCAAATCCCCC 59.311 52.381 0.00 0.00 0.00 5.40
935 983 3.067106 CGATAGGCAAAGAACACACAGT 58.933 45.455 0.00 0.00 0.00 3.55
937 992 4.024048 CGATAGGCAAAGAACACACAGTTT 60.024 41.667 0.00 0.00 41.51 2.66
951 1007 1.280421 ACAGTTTCCAGATCAGCTCCC 59.720 52.381 0.00 0.00 0.00 4.30
966 1022 4.777896 TCAGCTCCCTACAGATAAGTTTGT 59.222 41.667 0.00 0.00 0.00 2.83
967 1023 4.872691 CAGCTCCCTACAGATAAGTTTGTG 59.127 45.833 0.00 0.00 0.00 3.33
973 1029 0.096976 CAGATAAGTTTGTGGCGGCG 59.903 55.000 0.51 0.51 0.00 6.46
1038 1100 1.432270 GAGCTATTGCGGTGGTGCTC 61.432 60.000 0.00 0.00 45.42 4.26
1476 1642 3.052109 TCCCTGTCATGTACCAGAGGTAT 60.052 47.826 10.13 0.00 40.54 2.73
1482 1652 1.842052 TGTACCAGAGGTATGCACGA 58.158 50.000 0.00 0.00 40.54 4.35
1683 1859 1.487976 TCCATGGATGTCAAGAGCTCC 59.512 52.381 11.44 0.00 0.00 4.70
1770 1946 2.227194 ACCGGAAAAATGCTCTCGTTT 58.773 42.857 9.46 0.00 33.08 3.60
1794 1970 1.003839 GACTGACACGGATGGGCAA 60.004 57.895 0.00 0.00 0.00 4.52
2112 2294 9.280174 TGAGTTCTTTTACAGTACCCTTAAATG 57.720 33.333 0.00 0.00 0.00 2.32
2113 2295 9.498176 GAGTTCTTTTACAGTACCCTTAAATGA 57.502 33.333 0.00 0.00 0.00 2.57
2114 2296 9.856162 AGTTCTTTTACAGTACCCTTAAATGAA 57.144 29.630 11.69 11.69 31.55 2.57
2122 2304 7.459234 ACAGTACCCTTAAATGAATATAGGCC 58.541 38.462 0.00 0.00 0.00 5.19
2123 2305 6.884836 CAGTACCCTTAAATGAATATAGGCCC 59.115 42.308 0.00 0.00 0.00 5.80
2124 2306 6.798050 AGTACCCTTAAATGAATATAGGCCCT 59.202 38.462 0.00 0.00 0.00 5.19
2125 2307 6.140968 ACCCTTAAATGAATATAGGCCCTC 57.859 41.667 0.00 0.00 0.00 4.30
2126 2308 5.015284 ACCCTTAAATGAATATAGGCCCTCC 59.985 44.000 0.00 0.00 0.00 4.30
2127 2309 5.015178 CCCTTAAATGAATATAGGCCCTCCA 59.985 44.000 0.00 0.00 33.74 3.86
2128 2310 6.297830 CCCTTAAATGAATATAGGCCCTCCAT 60.298 42.308 0.00 0.00 33.74 3.41
2129 2311 7.184862 CCTTAAATGAATATAGGCCCTCCATT 58.815 38.462 0.00 0.00 33.74 3.16
2130 2312 7.675619 CCTTAAATGAATATAGGCCCTCCATTT 59.324 37.037 0.00 9.81 36.86 2.32
2131 2313 6.923199 AAATGAATATAGGCCCTCCATTTG 57.077 37.500 0.00 0.00 33.26 2.32
2132 2314 5.865977 ATGAATATAGGCCCTCCATTTGA 57.134 39.130 0.00 0.00 33.74 2.69
2133 2315 5.865977 TGAATATAGGCCCTCCATTTGAT 57.134 39.130 0.00 0.00 33.74 2.57
2134 2316 6.968400 TGAATATAGGCCCTCCATTTGATA 57.032 37.500 0.00 0.00 33.74 2.15
2135 2317 7.529534 TGAATATAGGCCCTCCATTTGATAT 57.470 36.000 0.00 0.00 33.74 1.63
2136 2318 8.637108 TGAATATAGGCCCTCCATTTGATATA 57.363 34.615 0.00 0.00 33.74 0.86
2137 2319 9.067963 TGAATATAGGCCCTCCATTTGATATAA 57.932 33.333 0.00 0.00 33.74 0.98
2140 2322 7.777889 ATAGGCCCTCCATTTGATATAATCT 57.222 36.000 0.00 0.00 33.74 2.40
2141 2323 5.824421 AGGCCCTCCATTTGATATAATCTG 58.176 41.667 0.00 0.00 33.74 2.90
2142 2324 5.553162 AGGCCCTCCATTTGATATAATCTGA 59.447 40.000 0.00 0.00 33.74 3.27
2143 2325 6.219146 AGGCCCTCCATTTGATATAATCTGAT 59.781 38.462 0.00 0.00 33.74 2.90
2144 2326 6.320672 GGCCCTCCATTTGATATAATCTGATG 59.679 42.308 0.00 0.00 0.00 3.07
2145 2327 6.320672 GCCCTCCATTTGATATAATCTGATGG 59.679 42.308 12.20 12.20 40.55 3.51
2146 2328 7.636579 CCCTCCATTTGATATAATCTGATGGA 58.363 38.462 16.67 16.67 43.02 3.41
2147 2329 7.555554 CCCTCCATTTGATATAATCTGATGGAC 59.444 40.741 14.99 0.00 41.76 4.02
2148 2330 8.105197 CCTCCATTTGATATAATCTGATGGACA 58.895 37.037 14.99 0.00 41.76 4.02
2149 2331 9.163899 CTCCATTTGATATAATCTGATGGACAG 57.836 37.037 14.99 0.00 41.76 3.51
2150 2332 8.105197 TCCATTTGATATAATCTGATGGACAGG 58.895 37.037 14.99 0.00 45.76 4.00
2151 2333 8.105197 CCATTTGATATAATCTGATGGACAGGA 58.895 37.037 12.72 0.00 45.76 3.86
2152 2334 9.682465 CATTTGATATAATCTGATGGACAGGAT 57.318 33.333 0.00 0.00 45.76 3.24
2154 2336 9.511272 TTTGATATAATCTGATGGACAGGATTG 57.489 33.333 0.00 0.00 45.76 2.67
2155 2337 7.627311 TGATATAATCTGATGGACAGGATTGG 58.373 38.462 0.00 0.00 45.76 3.16
2156 2338 5.919348 ATAATCTGATGGACAGGATTGGT 57.081 39.130 0.00 0.00 45.76 3.67
2157 2339 4.598036 AATCTGATGGACAGGATTGGTT 57.402 40.909 0.00 0.00 45.76 3.67
2158 2340 3.354948 TCTGATGGACAGGATTGGTTG 57.645 47.619 0.00 0.00 45.76 3.77
2159 2341 2.025981 TCTGATGGACAGGATTGGTTGG 60.026 50.000 0.00 0.00 45.76 3.77
2160 2342 1.710244 TGATGGACAGGATTGGTTGGT 59.290 47.619 0.00 0.00 0.00 3.67
2161 2343 2.916269 TGATGGACAGGATTGGTTGGTA 59.084 45.455 0.00 0.00 0.00 3.25
2162 2344 2.871096 TGGACAGGATTGGTTGGTAC 57.129 50.000 0.00 0.00 0.00 3.34
2163 2345 2.344592 TGGACAGGATTGGTTGGTACT 58.655 47.619 0.00 0.00 0.00 2.73
2164 2346 2.304761 TGGACAGGATTGGTTGGTACTC 59.695 50.000 0.00 0.00 0.00 2.59
2165 2347 2.355818 GGACAGGATTGGTTGGTACTCC 60.356 54.545 0.00 0.00 0.00 3.85
2166 2348 2.304761 GACAGGATTGGTTGGTACTCCA 59.695 50.000 0.00 0.00 42.66 3.86
2179 2361 3.709653 TGGTACTCCAACATACTCCATCC 59.290 47.826 0.00 0.00 41.25 3.51
2180 2362 3.243771 GGTACTCCAACATACTCCATCCG 60.244 52.174 0.00 0.00 0.00 4.18
2181 2363 2.467880 ACTCCAACATACTCCATCCGT 58.532 47.619 0.00 0.00 0.00 4.69
2182 2364 2.838202 ACTCCAACATACTCCATCCGTT 59.162 45.455 0.00 0.00 0.00 4.44
2183 2365 3.263425 ACTCCAACATACTCCATCCGTTT 59.737 43.478 0.00 0.00 0.00 3.60
2184 2366 3.869065 TCCAACATACTCCATCCGTTTC 58.131 45.455 0.00 0.00 0.00 2.78
2185 2367 3.262151 TCCAACATACTCCATCCGTTTCA 59.738 43.478 0.00 0.00 0.00 2.69
2186 2368 4.006989 CCAACATACTCCATCCGTTTCAA 58.993 43.478 0.00 0.00 0.00 2.69
2187 2369 4.457603 CCAACATACTCCATCCGTTTCAAA 59.542 41.667 0.00 0.00 0.00 2.69
2188 2370 5.048364 CCAACATACTCCATCCGTTTCAAAA 60.048 40.000 0.00 0.00 0.00 2.44
2189 2371 6.350110 CCAACATACTCCATCCGTTTCAAAAT 60.350 38.462 0.00 0.00 0.00 1.82
2190 2372 7.148154 CCAACATACTCCATCCGTTTCAAAATA 60.148 37.037 0.00 0.00 0.00 1.40
2191 2373 7.553881 ACATACTCCATCCGTTTCAAAATAG 57.446 36.000 0.00 0.00 0.00 1.73
2192 2374 7.335627 ACATACTCCATCCGTTTCAAAATAGA 58.664 34.615 0.00 0.00 0.00 1.98
2193 2375 7.993183 ACATACTCCATCCGTTTCAAAATAGAT 59.007 33.333 0.00 0.00 0.00 1.98
2194 2376 6.683974 ACTCCATCCGTTTCAAAATAGATG 57.316 37.500 9.20 9.20 33.56 2.90
2195 2377 6.414732 ACTCCATCCGTTTCAAAATAGATGA 58.585 36.000 14.42 0.00 34.68 2.92
2196 2378 6.316390 ACTCCATCCGTTTCAAAATAGATGAC 59.684 38.462 14.42 0.00 34.68 3.06
2197 2379 5.588648 TCCATCCGTTTCAAAATAGATGACC 59.411 40.000 14.42 0.00 34.68 4.02
2198 2380 5.221048 CCATCCGTTTCAAAATAGATGACCC 60.221 44.000 14.42 0.00 34.68 4.46
2199 2381 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
2200 2382 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
2201 2383 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
2202 2384 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
2203 2385 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
2204 2386 7.145323 CGTTTCAAAATAGATGACCCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
2205 2387 8.293867 CGTTTCAAAATAGATGACCCAACTTTA 58.706 33.333 0.00 0.00 0.00 1.85
2213 2395 9.760077 AATAGATGACCCAACTTTATACTAACG 57.240 33.333 0.00 0.00 0.00 3.18
2214 2396 6.579865 AGATGACCCAACTTTATACTAACGG 58.420 40.000 0.00 0.00 0.00 4.44
2215 2397 5.999205 TGACCCAACTTTATACTAACGGA 57.001 39.130 0.00 0.00 0.00 4.69
2216 2398 5.969423 TGACCCAACTTTATACTAACGGAG 58.031 41.667 0.00 0.00 0.00 4.63
2217 2399 5.105228 TGACCCAACTTTATACTAACGGAGG 60.105 44.000 0.00 0.00 0.00 4.30
2218 2400 5.025453 ACCCAACTTTATACTAACGGAGGA 58.975 41.667 0.00 0.00 0.00 3.71
2219 2401 5.484998 ACCCAACTTTATACTAACGGAGGAA 59.515 40.000 0.00 0.00 0.00 3.36
2220 2402 6.047231 CCCAACTTTATACTAACGGAGGAAG 58.953 44.000 0.00 0.00 0.00 3.46
2221 2403 6.351626 CCCAACTTTATACTAACGGAGGAAGT 60.352 42.308 0.00 0.00 0.00 3.01
2222 2404 7.147846 CCCAACTTTATACTAACGGAGGAAGTA 60.148 40.741 0.00 0.00 0.00 2.24
2223 2405 7.919621 CCAACTTTATACTAACGGAGGAAGTAG 59.080 40.741 0.00 0.00 0.00 2.57
2224 2406 8.680903 CAACTTTATACTAACGGAGGAAGTAGA 58.319 37.037 0.00 0.00 0.00 2.59
2225 2407 8.993404 ACTTTATACTAACGGAGGAAGTAGAT 57.007 34.615 0.00 0.00 0.00 1.98
2226 2408 8.848182 ACTTTATACTAACGGAGGAAGTAGATG 58.152 37.037 0.00 0.00 0.00 2.90
2227 2409 8.757982 TTTATACTAACGGAGGAAGTAGATGT 57.242 34.615 0.00 0.00 0.00 3.06
2228 2410 8.757982 TTATACTAACGGAGGAAGTAGATGTT 57.242 34.615 0.00 0.00 0.00 2.71
2229 2411 5.997384 ACTAACGGAGGAAGTAGATGTTT 57.003 39.130 0.00 0.00 0.00 2.83
2230 2412 8.757982 ATACTAACGGAGGAAGTAGATGTTTA 57.242 34.615 0.00 0.00 0.00 2.01
2231 2413 7.098074 ACTAACGGAGGAAGTAGATGTTTAG 57.902 40.000 0.00 0.00 0.00 1.85
2232 2414 5.340439 AACGGAGGAAGTAGATGTTTAGG 57.660 43.478 0.00 0.00 0.00 2.69
2233 2415 4.607239 ACGGAGGAAGTAGATGTTTAGGA 58.393 43.478 0.00 0.00 0.00 2.94
2234 2416 4.645588 ACGGAGGAAGTAGATGTTTAGGAG 59.354 45.833 0.00 0.00 0.00 3.69
2235 2417 4.645588 CGGAGGAAGTAGATGTTTAGGAGT 59.354 45.833 0.00 0.00 0.00 3.85
2236 2418 5.826737 CGGAGGAAGTAGATGTTTAGGAGTA 59.173 44.000 0.00 0.00 0.00 2.59
2237 2419 6.238703 CGGAGGAAGTAGATGTTTAGGAGTAC 60.239 46.154 0.00 0.00 0.00 2.73
2238 2420 6.040729 GGAGGAAGTAGATGTTTAGGAGTACC 59.959 46.154 0.00 0.00 0.00 3.34
2239 2421 6.500336 AGGAAGTAGATGTTTAGGAGTACCA 58.500 40.000 0.00 0.00 38.94 3.25
2240 2422 6.380560 AGGAAGTAGATGTTTAGGAGTACCAC 59.619 42.308 0.00 0.00 38.94 4.16
2241 2423 6.406737 GGAAGTAGATGTTTAGGAGTACCACC 60.407 46.154 0.00 0.00 38.94 4.61
2242 2424 4.643784 AGTAGATGTTTAGGAGTACCACCG 59.356 45.833 0.00 0.00 38.94 4.94
2243 2425 2.167900 AGATGTTTAGGAGTACCACCGC 59.832 50.000 0.00 0.00 38.94 5.68
2244 2426 0.609662 TGTTTAGGAGTACCACCGCC 59.390 55.000 0.00 0.00 38.94 6.13
2245 2427 0.609662 GTTTAGGAGTACCACCGCCA 59.390 55.000 0.00 0.00 38.94 5.69
2246 2428 1.002315 GTTTAGGAGTACCACCGCCAA 59.998 52.381 0.00 0.00 38.94 4.52
2325 2507 0.410663 TGGAAACTACTCCCTCCGGA 59.589 55.000 2.93 2.93 34.22 5.14
2327 2509 1.553706 GAAACTACTCCCTCCGGACA 58.446 55.000 0.00 0.00 33.32 4.02
2334 2516 2.046892 CCCTCCGGACAGCAGTTG 60.047 66.667 0.00 0.00 0.00 3.16
2347 2529 2.713927 GCAGTTGCGGTAATTACGAG 57.286 50.000 9.46 7.33 0.00 4.18
2356 2538 4.565166 TGCGGTAATTACGAGATTTGACTG 59.435 41.667 9.46 0.00 0.00 3.51
2357 2539 4.550255 GCGGTAATTACGAGATTTGACTGC 60.550 45.833 9.46 0.00 0.00 4.40
2390 2573 4.699522 GCCGGCAAGGGACTCGTT 62.700 66.667 24.80 0.00 38.49 3.85
2392 2575 1.153628 CCGGCAAGGGACTCGTTAG 60.154 63.158 0.00 0.00 38.49 2.34
2412 2595 3.820557 AGCCAATAAACTACGGATGCAT 58.179 40.909 0.00 0.00 0.00 3.96
2432 2615 1.134401 TCATCCGAAAGTCATGGCTCC 60.134 52.381 0.00 0.00 0.00 4.70
2443 2626 3.197766 AGTCATGGCTCCTTCGTGATTAA 59.802 43.478 0.00 0.00 33.42 1.40
2450 2633 4.494199 GGCTCCTTCGTGATTAAATCAACG 60.494 45.833 0.00 0.00 41.69 4.10
2451 2634 4.578601 CTCCTTCGTGATTAAATCAACGC 58.421 43.478 0.00 0.00 41.69 4.84
2457 2640 4.867608 TCGTGATTAAATCAACGCATGAGA 59.132 37.500 2.50 0.00 42.53 3.27
2459 2642 5.005682 CGTGATTAAATCAACGCATGAGAGA 59.994 40.000 2.50 0.97 42.53 3.10
2465 2648 1.081094 CAACGCATGAGAGATGCACA 58.919 50.000 2.50 0.00 44.75 4.57
2471 2654 3.609879 CGCATGAGAGATGCACACAAAAA 60.610 43.478 0.00 0.00 44.75 1.94
2498 2681 5.518847 ACGAAACGTGATGTCGATAATCAAT 59.481 36.000 13.48 4.87 39.18 2.57
2555 2738 7.643579 CCAAAGAACTTTTAGAAAGGAGACTG 58.356 38.462 5.52 0.00 42.68 3.51
2556 2739 6.869315 AAGAACTTTTAGAAAGGAGACTGC 57.131 37.500 5.52 0.00 42.68 4.40
2573 2757 1.952296 CTGCTCCTTTATGCATGTCCC 59.048 52.381 10.16 0.00 38.59 4.46
2577 2761 1.134220 TCCTTTATGCATGTCCCGTCC 60.134 52.381 10.16 0.00 0.00 4.79
2593 2777 1.002403 TCCAAGGGCTGGGATACGA 59.998 57.895 0.00 0.00 46.44 3.43
2594 2778 0.399949 TCCAAGGGCTGGGATACGAT 60.400 55.000 0.00 0.00 46.44 3.73
2650 2835 3.328382 TTTCATGGGTGTCGAAGTAGG 57.672 47.619 0.00 0.00 0.00 3.18
2651 2836 2.225382 TCATGGGTGTCGAAGTAGGA 57.775 50.000 0.00 0.00 0.00 2.94
2658 2843 2.329379 GTGTCGAAGTAGGAGCACAAG 58.671 52.381 0.00 0.00 0.00 3.16
2698 2883 1.670087 CCACGGCTATGCGAGATAAGG 60.670 57.143 0.00 0.00 0.00 2.69
2704 2889 2.414824 GCTATGCGAGATAAGGGAGACG 60.415 54.545 0.00 0.00 0.00 4.18
2733 2918 1.312815 GCTTGATCGGGAAATCAGGG 58.687 55.000 0.00 0.00 37.01 4.45
2736 2921 1.590591 TGATCGGGAAATCAGGGGAA 58.409 50.000 0.00 0.00 32.03 3.97
2768 2953 5.240403 GGCCCAGAGAATACATCAAAAGATC 59.760 44.000 0.00 0.00 0.00 2.75
2769 2954 5.049818 GCCCAGAGAATACATCAAAAGATCG 60.050 44.000 0.00 0.00 0.00 3.69
2771 2956 5.049818 CCAGAGAATACATCAAAAGATCGCC 60.050 44.000 0.00 0.00 0.00 5.54
2812 3000 4.223953 AGACTGAAGTACCCTCTCAAACA 58.776 43.478 0.00 0.00 0.00 2.83
2818 3006 1.534163 GTACCCTCTCAAACAAACGGC 59.466 52.381 0.00 0.00 0.00 5.68
2827 3015 3.745799 TCAAACAAACGGCCAGATCTAA 58.254 40.909 2.24 0.00 0.00 2.10
2841 3029 5.059833 CCAGATCTAATTTGTACTCCCAGC 58.940 45.833 0.00 0.00 0.00 4.85
2850 3038 0.764752 GTACTCCCAGCCCTGCCTAT 60.765 60.000 0.00 0.00 0.00 2.57
2858 3046 1.002888 CAGCCCTGCCTATGGAGTATG 59.997 57.143 0.00 0.00 0.00 2.39
2866 3054 3.142217 TGCCTATGGAGTATGAGGGTACT 59.858 47.826 0.00 0.00 37.61 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 7.816640 TCTAAGAAACACCTGCAATTGTTATC 58.183 34.615 11.88 11.24 34.82 1.75
96 97 5.518847 GGTTTGTTTTCTAAGAAACACCTGC 59.481 40.000 11.21 0.00 46.04 4.85
98 99 6.661805 TCAGGTTTGTTTTCTAAGAAACACCT 59.338 34.615 11.21 9.72 46.04 4.00
106 107 7.024768 TGAACGTTTCAGGTTTGTTTTCTAAG 58.975 34.615 0.46 0.00 34.08 2.18
109 110 5.379732 TGAACGTTTCAGGTTTGTTTTCT 57.620 34.783 0.46 0.00 34.08 2.52
110 111 6.454981 CCAATGAACGTTTCAGGTTTGTTTTC 60.455 38.462 0.46 0.00 43.98 2.29
122 123 1.068541 GCACCCTCCAATGAACGTTTC 60.069 52.381 0.46 0.00 0.00 2.78
131 132 1.002134 CGTGAAGGCACCCTCCAAT 60.002 57.895 0.00 0.00 42.09 3.16
133 134 2.525629 TCGTGAAGGCACCCTCCA 60.526 61.111 0.00 0.00 42.09 3.86
193 194 4.917906 AGAATGGACCTAATATCAGGGC 57.082 45.455 0.00 0.00 43.83 5.19
235 236 8.236586 GCTGATAATTCGATTATGGTTGCAATA 58.763 33.333 0.59 0.00 35.68 1.90
266 274 4.935808 GGTCCGTTAAGTTTCATCTGTCAT 59.064 41.667 0.00 0.00 0.00 3.06
267 275 4.312443 GGTCCGTTAAGTTTCATCTGTCA 58.688 43.478 0.00 0.00 0.00 3.58
296 304 4.514401 AGAGTTGAATCCATCCGGTTTAC 58.486 43.478 0.00 0.00 0.00 2.01
337 345 9.903682 ATGATTAGTTCAAGAAACATTGAGTTG 57.096 29.630 0.00 0.00 40.16 3.16
379 387 0.963856 TACTCCACAGCATCGACGGT 60.964 55.000 0.00 0.00 0.00 4.83
389 398 0.671781 GCACTGCACCTACTCCACAG 60.672 60.000 0.00 0.00 0.00 3.66
459 468 2.281208 TTCACGTTCGCCCCTTGG 60.281 61.111 0.00 0.00 0.00 3.61
469 478 2.857483 TGGGATGTTCATGTTCACGTT 58.143 42.857 0.00 0.00 0.00 3.99
473 482 3.524095 ACCTTGGGATGTTCATGTTCA 57.476 42.857 0.00 0.00 0.00 3.18
890 925 2.999185 TCAAGGGGGATTTGCTTCTT 57.001 45.000 0.00 0.00 0.00 2.52
905 942 3.002791 TCTTTGCCTATCGTGCTTCAAG 58.997 45.455 0.00 0.00 0.00 3.02
935 983 2.768527 CTGTAGGGAGCTGATCTGGAAA 59.231 50.000 0.00 0.00 0.00 3.13
937 992 1.570979 TCTGTAGGGAGCTGATCTGGA 59.429 52.381 0.00 0.00 0.00 3.86
951 1007 2.351726 GCCGCCACAAACTTATCTGTAG 59.648 50.000 0.00 0.00 0.00 2.74
973 1029 3.883830 ATCTATCGATGGATGCAGGAC 57.116 47.619 21.94 0.00 34.00 3.85
1038 1100 1.007271 ACAGCAGACGAACGTGAGG 60.007 57.895 4.19 0.00 0.00 3.86
1683 1859 2.097304 TGGCATCCAATCGTTTGAATCG 59.903 45.455 7.79 0.00 34.60 3.34
1770 1946 1.548719 CCATCCGTGTCAGTCAACCTA 59.451 52.381 0.00 0.00 0.00 3.08
1954 2135 5.508200 TTGAACACCAGGACACAAATAAC 57.492 39.130 0.00 0.00 0.00 1.89
2011 2192 9.754382 ACATGCCTTTATTAATGAATTGATGTC 57.246 29.630 0.00 0.00 0.00 3.06
2086 2268 9.280174 CATTTAAGGGTACTGTAAAAGAACTCA 57.720 33.333 0.00 0.00 0.00 3.41
2087 2269 9.498176 TCATTTAAGGGTACTGTAAAAGAACTC 57.502 33.333 0.00 0.00 0.00 3.01
2088 2270 9.856162 TTCATTTAAGGGTACTGTAAAAGAACT 57.144 29.630 0.00 0.00 0.00 3.01
2096 2278 8.599792 GGCCTATATTCATTTAAGGGTACTGTA 58.400 37.037 0.00 0.00 0.00 2.74
2097 2279 7.459234 GGCCTATATTCATTTAAGGGTACTGT 58.541 38.462 0.00 0.00 0.00 3.55
2098 2280 6.884836 GGGCCTATATTCATTTAAGGGTACTG 59.115 42.308 0.84 0.00 0.00 2.74
2099 2281 6.798050 AGGGCCTATATTCATTTAAGGGTACT 59.202 38.462 2.82 0.00 0.00 2.73
2100 2282 7.029053 AGGGCCTATATTCATTTAAGGGTAC 57.971 40.000 2.82 0.00 0.00 3.34
2101 2283 6.216868 GGAGGGCCTATATTCATTTAAGGGTA 59.783 42.308 5.73 0.00 0.00 3.69
2102 2284 5.015284 GGAGGGCCTATATTCATTTAAGGGT 59.985 44.000 5.73 0.00 0.00 4.34
2103 2285 5.015178 TGGAGGGCCTATATTCATTTAAGGG 59.985 44.000 5.73 0.00 34.31 3.95
2104 2286 6.139679 TGGAGGGCCTATATTCATTTAAGG 57.860 41.667 5.73 0.00 34.31 2.69
2105 2287 8.526147 CAAATGGAGGGCCTATATTCATTTAAG 58.474 37.037 20.44 12.08 33.69 1.85
2106 2288 8.231007 TCAAATGGAGGGCCTATATTCATTTAA 58.769 33.333 20.44 11.32 33.69 1.52
2107 2289 7.764617 TCAAATGGAGGGCCTATATTCATTTA 58.235 34.615 20.44 12.34 33.69 1.40
2108 2290 6.623329 TCAAATGGAGGGCCTATATTCATTT 58.377 36.000 5.73 14.34 34.83 2.32
2109 2291 6.218195 TCAAATGGAGGGCCTATATTCATT 57.782 37.500 5.73 9.16 34.31 2.57
2110 2292 5.865977 TCAAATGGAGGGCCTATATTCAT 57.134 39.130 5.73 2.96 34.31 2.57
2111 2293 5.865977 ATCAAATGGAGGGCCTATATTCA 57.134 39.130 5.73 0.32 34.31 2.57
2114 2296 9.471016 AGATTATATCAAATGGAGGGCCTATAT 57.529 33.333 5.73 7.00 34.31 0.86
2115 2297 8.717717 CAGATTATATCAAATGGAGGGCCTATA 58.282 37.037 5.73 0.00 34.31 1.31
2116 2298 7.407033 TCAGATTATATCAAATGGAGGGCCTAT 59.593 37.037 5.73 0.00 34.31 2.57
2117 2299 6.735229 TCAGATTATATCAAATGGAGGGCCTA 59.265 38.462 5.73 0.00 34.31 3.93
2118 2300 5.553162 TCAGATTATATCAAATGGAGGGCCT 59.447 40.000 5.25 5.25 34.31 5.19
2119 2301 5.819991 TCAGATTATATCAAATGGAGGGCC 58.180 41.667 0.00 0.00 0.00 5.80
2120 2302 6.320672 CCATCAGATTATATCAAATGGAGGGC 59.679 42.308 11.77 0.00 41.99 5.19
2121 2303 7.555554 GTCCATCAGATTATATCAAATGGAGGG 59.444 40.741 16.74 0.00 45.33 4.30
2122 2304 8.105197 TGTCCATCAGATTATATCAAATGGAGG 58.895 37.037 16.74 0.00 45.33 4.30
2123 2305 9.163899 CTGTCCATCAGATTATATCAAATGGAG 57.836 37.037 16.74 8.17 45.33 3.86
2124 2306 8.105197 CCTGTCCATCAGATTATATCAAATGGA 58.895 37.037 14.18 14.18 46.27 3.41
2125 2307 8.105197 TCCTGTCCATCAGATTATATCAAATGG 58.895 37.037 11.27 11.27 46.27 3.16
2126 2308 9.682465 ATCCTGTCCATCAGATTATATCAAATG 57.318 33.333 0.00 0.00 46.27 2.32
2128 2310 9.511272 CAATCCTGTCCATCAGATTATATCAAA 57.489 33.333 0.00 0.00 46.27 2.69
2129 2311 8.105197 CCAATCCTGTCCATCAGATTATATCAA 58.895 37.037 0.00 0.00 46.27 2.57
2130 2312 7.238305 ACCAATCCTGTCCATCAGATTATATCA 59.762 37.037 0.00 0.00 46.27 2.15
2131 2313 7.628234 ACCAATCCTGTCCATCAGATTATATC 58.372 38.462 0.00 0.00 46.27 1.63
2132 2314 7.579940 ACCAATCCTGTCCATCAGATTATAT 57.420 36.000 0.00 0.00 46.27 0.86
2133 2315 7.226441 CAACCAATCCTGTCCATCAGATTATA 58.774 38.462 0.00 0.00 46.27 0.98
2134 2316 5.919348 ACCAATCCTGTCCATCAGATTAT 57.081 39.130 0.00 0.00 46.27 1.28
2135 2317 5.439721 CAACCAATCCTGTCCATCAGATTA 58.560 41.667 0.00 0.00 46.27 1.75
2136 2318 4.275810 CAACCAATCCTGTCCATCAGATT 58.724 43.478 0.00 0.00 46.27 2.40
2137 2319 3.372349 CCAACCAATCCTGTCCATCAGAT 60.372 47.826 0.00 0.00 46.27 2.90
2138 2320 2.025981 CCAACCAATCCTGTCCATCAGA 60.026 50.000 0.00 0.00 46.27 3.27
2139 2321 2.291153 ACCAACCAATCCTGTCCATCAG 60.291 50.000 0.00 0.00 43.27 2.90
2140 2322 1.710244 ACCAACCAATCCTGTCCATCA 59.290 47.619 0.00 0.00 0.00 3.07
2141 2323 2.514458 ACCAACCAATCCTGTCCATC 57.486 50.000 0.00 0.00 0.00 3.51
2142 2324 2.919602 AGTACCAACCAATCCTGTCCAT 59.080 45.455 0.00 0.00 0.00 3.41
2143 2325 2.304761 GAGTACCAACCAATCCTGTCCA 59.695 50.000 0.00 0.00 0.00 4.02
2144 2326 2.355818 GGAGTACCAACCAATCCTGTCC 60.356 54.545 0.00 0.00 35.97 4.02
2145 2327 2.304761 TGGAGTACCAACCAATCCTGTC 59.695 50.000 2.23 0.00 43.91 3.51
2146 2328 2.344592 TGGAGTACCAACCAATCCTGT 58.655 47.619 2.23 0.00 43.91 4.00
2157 2339 3.709653 GGATGGAGTATGTTGGAGTACCA 59.290 47.826 0.00 0.00 45.34 3.25
2158 2340 3.243771 CGGATGGAGTATGTTGGAGTACC 60.244 52.174 0.00 0.00 0.00 3.34
2159 2341 3.383825 ACGGATGGAGTATGTTGGAGTAC 59.616 47.826 0.00 0.00 0.00 2.73
2160 2342 3.638860 ACGGATGGAGTATGTTGGAGTA 58.361 45.455 0.00 0.00 0.00 2.59
2161 2343 2.467880 ACGGATGGAGTATGTTGGAGT 58.532 47.619 0.00 0.00 0.00 3.85
2162 2344 3.543680 AACGGATGGAGTATGTTGGAG 57.456 47.619 0.00 0.00 0.00 3.86
2163 2345 3.262151 TGAAACGGATGGAGTATGTTGGA 59.738 43.478 0.00 0.00 0.00 3.53
2164 2346 3.605634 TGAAACGGATGGAGTATGTTGG 58.394 45.455 0.00 0.00 0.00 3.77
2165 2347 5.621197 TTTGAAACGGATGGAGTATGTTG 57.379 39.130 0.00 0.00 0.00 3.33
2166 2348 6.834168 ATTTTGAAACGGATGGAGTATGTT 57.166 33.333 0.00 0.00 0.00 2.71
2167 2349 7.335627 TCTATTTTGAAACGGATGGAGTATGT 58.664 34.615 0.00 0.00 0.00 2.29
2168 2350 7.786178 TCTATTTTGAAACGGATGGAGTATG 57.214 36.000 0.00 0.00 0.00 2.39
2169 2351 8.210946 TCATCTATTTTGAAACGGATGGAGTAT 58.789 33.333 14.63 0.00 34.20 2.12
2170 2352 7.494625 GTCATCTATTTTGAAACGGATGGAGTA 59.505 37.037 14.63 1.43 34.20 2.59
2171 2353 6.316390 GTCATCTATTTTGAAACGGATGGAGT 59.684 38.462 14.63 0.00 34.20 3.85
2172 2354 6.238484 GGTCATCTATTTTGAAACGGATGGAG 60.238 42.308 14.63 0.00 34.20 3.86
2173 2355 5.588648 GGTCATCTATTTTGAAACGGATGGA 59.411 40.000 14.63 0.00 34.20 3.41
2174 2356 5.221048 GGGTCATCTATTTTGAAACGGATGG 60.221 44.000 14.63 0.00 34.20 3.51
2175 2357 5.356751 TGGGTCATCTATTTTGAAACGGATG 59.643 40.000 11.16 11.16 34.46 3.51
2176 2358 5.505780 TGGGTCATCTATTTTGAAACGGAT 58.494 37.500 0.00 0.00 0.00 4.18
2177 2359 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
2178 2360 5.183140 AGTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
2179 2361 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
2187 2369 9.760077 CGTTAGTATAAAGTTGGGTCATCTATT 57.240 33.333 0.00 0.00 0.00 1.73
2188 2370 8.365647 CCGTTAGTATAAAGTTGGGTCATCTAT 58.634 37.037 0.00 0.00 0.00 1.98
2189 2371 7.560991 TCCGTTAGTATAAAGTTGGGTCATCTA 59.439 37.037 0.00 0.00 0.00 1.98
2190 2372 6.381994 TCCGTTAGTATAAAGTTGGGTCATCT 59.618 38.462 0.00 0.00 0.00 2.90
2191 2373 6.576185 TCCGTTAGTATAAAGTTGGGTCATC 58.424 40.000 0.00 0.00 0.00 2.92
2192 2374 6.407752 CCTCCGTTAGTATAAAGTTGGGTCAT 60.408 42.308 0.00 0.00 0.00 3.06
2193 2375 5.105228 CCTCCGTTAGTATAAAGTTGGGTCA 60.105 44.000 0.00 0.00 0.00 4.02
2194 2376 5.127682 TCCTCCGTTAGTATAAAGTTGGGTC 59.872 44.000 0.00 0.00 0.00 4.46
2195 2377 5.025453 TCCTCCGTTAGTATAAAGTTGGGT 58.975 41.667 0.00 0.00 0.00 4.51
2196 2378 5.603170 TCCTCCGTTAGTATAAAGTTGGG 57.397 43.478 0.00 0.00 0.00 4.12
2197 2379 6.637657 ACTTCCTCCGTTAGTATAAAGTTGG 58.362 40.000 0.00 0.00 0.00 3.77
2198 2380 8.680903 TCTACTTCCTCCGTTAGTATAAAGTTG 58.319 37.037 0.00 0.00 0.00 3.16
2199 2381 8.814038 TCTACTTCCTCCGTTAGTATAAAGTT 57.186 34.615 0.00 0.00 0.00 2.66
2200 2382 8.848182 CATCTACTTCCTCCGTTAGTATAAAGT 58.152 37.037 0.00 0.00 0.00 2.66
2201 2383 8.848182 ACATCTACTTCCTCCGTTAGTATAAAG 58.152 37.037 0.00 0.00 0.00 1.85
2202 2384 8.757982 ACATCTACTTCCTCCGTTAGTATAAA 57.242 34.615 0.00 0.00 0.00 1.40
2203 2385 8.757982 AACATCTACTTCCTCCGTTAGTATAA 57.242 34.615 0.00 0.00 0.00 0.98
2204 2386 8.757982 AAACATCTACTTCCTCCGTTAGTATA 57.242 34.615 0.00 0.00 0.00 1.47
2205 2387 7.657023 AAACATCTACTTCCTCCGTTAGTAT 57.343 36.000 0.00 0.00 0.00 2.12
2206 2388 7.284034 CCTAAACATCTACTTCCTCCGTTAGTA 59.716 40.741 0.00 0.00 0.00 1.82
2207 2389 5.997384 AAACATCTACTTCCTCCGTTAGT 57.003 39.130 0.00 0.00 0.00 2.24
2208 2390 6.320672 TCCTAAACATCTACTTCCTCCGTTAG 59.679 42.308 0.00 0.00 0.00 2.34
2209 2391 6.189859 TCCTAAACATCTACTTCCTCCGTTA 58.810 40.000 0.00 0.00 0.00 3.18
2210 2392 5.021458 TCCTAAACATCTACTTCCTCCGTT 58.979 41.667 0.00 0.00 0.00 4.44
2211 2393 4.607239 TCCTAAACATCTACTTCCTCCGT 58.393 43.478 0.00 0.00 0.00 4.69
2212 2394 4.645588 ACTCCTAAACATCTACTTCCTCCG 59.354 45.833 0.00 0.00 0.00 4.63
2213 2395 6.040729 GGTACTCCTAAACATCTACTTCCTCC 59.959 46.154 0.00 0.00 0.00 4.30
2214 2396 6.606395 TGGTACTCCTAAACATCTACTTCCTC 59.394 42.308 0.00 0.00 34.23 3.71
2215 2397 6.380560 GTGGTACTCCTAAACATCTACTTCCT 59.619 42.308 0.00 0.00 34.23 3.36
2216 2398 6.406737 GGTGGTACTCCTAAACATCTACTTCC 60.407 46.154 0.00 0.00 39.21 3.46
2217 2399 6.571605 GGTGGTACTCCTAAACATCTACTTC 58.428 44.000 0.00 0.00 39.21 3.01
2218 2400 5.126707 CGGTGGTACTCCTAAACATCTACTT 59.873 44.000 0.00 0.00 40.32 2.24
2219 2401 4.643784 CGGTGGTACTCCTAAACATCTACT 59.356 45.833 0.00 0.00 40.32 2.57
2220 2402 4.735873 GCGGTGGTACTCCTAAACATCTAC 60.736 50.000 0.00 0.00 40.32 2.59
2221 2403 3.382546 GCGGTGGTACTCCTAAACATCTA 59.617 47.826 0.00 0.00 40.32 1.98
2222 2404 2.167900 GCGGTGGTACTCCTAAACATCT 59.832 50.000 0.00 0.00 40.32 2.90
2223 2405 2.547826 GCGGTGGTACTCCTAAACATC 58.452 52.381 0.00 0.00 40.32 3.06
2224 2406 1.208776 GGCGGTGGTACTCCTAAACAT 59.791 52.381 0.00 0.00 40.32 2.71
2225 2407 0.609662 GGCGGTGGTACTCCTAAACA 59.390 55.000 0.00 0.00 40.32 2.83
2226 2408 0.609662 TGGCGGTGGTACTCCTAAAC 59.390 55.000 0.00 0.00 40.32 2.01
2227 2409 1.350071 TTGGCGGTGGTACTCCTAAA 58.650 50.000 0.00 0.00 40.32 1.85
2228 2410 1.350071 TTTGGCGGTGGTACTCCTAA 58.650 50.000 0.00 0.00 40.32 2.69
2229 2411 1.350071 TTTTGGCGGTGGTACTCCTA 58.650 50.000 0.00 0.00 40.32 2.94
2230 2412 0.475044 TTTTTGGCGGTGGTACTCCT 59.525 50.000 0.00 0.00 40.32 3.69
2231 2413 1.541379 ATTTTTGGCGGTGGTACTCC 58.459 50.000 0.00 0.00 38.86 3.85
2232 2414 2.352323 CCAATTTTTGGCGGTGGTACTC 60.352 50.000 0.00 0.00 45.17 2.59
2233 2415 1.616374 CCAATTTTTGGCGGTGGTACT 59.384 47.619 0.00 0.00 45.17 2.73
2234 2416 2.073117 CCAATTTTTGGCGGTGGTAC 57.927 50.000 0.00 0.00 45.17 3.34
2241 2423 4.628266 AAGGTACTCCCCAATTTTTGGCG 61.628 47.826 0.57 0.00 45.04 5.69
2242 2424 2.903784 AAGGTACTCCCCAATTTTTGGC 59.096 45.455 0.57 0.00 45.04 4.52
2243 2425 4.156477 TCAAGGTACTCCCCAATTTTTGG 58.844 43.478 0.00 0.00 45.76 3.28
2244 2426 6.358974 AATCAAGGTACTCCCCAATTTTTG 57.641 37.500 0.00 0.00 38.49 2.44
2245 2427 7.387265 AAAATCAAGGTACTCCCCAATTTTT 57.613 32.000 0.00 0.00 38.49 1.94
2246 2428 8.499288 TTAAAATCAAGGTACTCCCCAATTTT 57.501 30.769 0.00 0.00 38.49 1.82
2297 2479 6.374613 GGAGGGAGTAGTTTCCAACTTAATTG 59.625 42.308 0.00 0.00 42.81 2.32
2322 2504 1.019278 ATTACCGCAACTGCTGTCCG 61.019 55.000 1.78 3.40 39.23 4.79
2325 2507 1.730064 CGTAATTACCGCAACTGCTGT 59.270 47.619 10.01 4.18 41.33 4.40
2327 2509 2.094390 TCTCGTAATTACCGCAACTGCT 60.094 45.455 10.01 0.00 39.32 4.24
2334 2516 4.550255 GCAGTCAAATCTCGTAATTACCGC 60.550 45.833 10.01 0.00 0.00 5.68
2343 2525 1.736126 CTGCATGCAGTCAAATCTCGT 59.264 47.619 34.76 0.00 39.10 4.18
2345 2527 1.531264 CGCTGCATGCAGTCAAATCTC 60.531 52.381 39.95 23.78 45.24 2.75
2347 2529 1.138047 GCGCTGCATGCAGTCAAATC 61.138 55.000 39.95 25.06 45.24 2.17
2379 2562 4.019591 AGTTTATTGGCTAACGAGTCCCTT 60.020 41.667 0.00 0.00 0.00 3.95
2386 2569 4.717233 TCCGTAGTTTATTGGCTAACGA 57.283 40.909 0.00 0.00 0.00 3.85
2390 2573 4.409718 TGCATCCGTAGTTTATTGGCTA 57.590 40.909 0.00 0.00 0.00 3.93
2392 2575 3.563808 TGATGCATCCGTAGTTTATTGGC 59.436 43.478 23.67 0.00 0.00 4.52
2412 2595 1.134401 GGAGCCATGACTTTCGGATGA 60.134 52.381 0.00 0.00 0.00 2.92
2432 2615 5.559227 TCATGCGTTGATTTAATCACGAAG 58.441 37.500 23.28 15.42 39.39 3.79
2450 2633 3.564235 TTTTGTGTGCATCTCTCATGC 57.436 42.857 0.00 0.00 44.76 4.06
2471 2654 5.579384 TTATCGACATCACGTTTCGTTTT 57.421 34.783 0.00 0.00 38.32 2.43
2555 2738 0.947244 CGGGACATGCATAAAGGAGC 59.053 55.000 0.00 0.00 0.00 4.70
2556 2739 2.213499 GACGGGACATGCATAAAGGAG 58.787 52.381 0.00 0.00 0.00 3.69
2563 2746 1.077501 CCTTGGACGGGACATGCAT 60.078 57.895 0.00 0.00 0.00 3.96
2577 2761 0.250467 CCATCGTATCCCAGCCCTTG 60.250 60.000 0.00 0.00 0.00 3.61
2582 2766 1.135257 CGATCTCCATCGTATCCCAGC 60.135 57.143 0.00 0.00 45.90 4.85
2593 2777 3.620785 GGCGAGGCCGATCTCCAT 61.621 66.667 0.00 0.00 39.62 3.41
2619 2804 1.892338 CCATGAAAACATGGCGCCT 59.108 52.632 29.70 10.60 44.64 5.52
2642 2827 0.037326 TGGCTTGTGCTCCTACTTCG 60.037 55.000 0.00 0.00 39.59 3.79
2650 2835 2.045536 CTCCCCTGGCTTGTGCTC 60.046 66.667 0.00 0.00 39.59 4.26
2651 2836 3.655211 CCTCCCCTGGCTTGTGCT 61.655 66.667 0.00 0.00 39.59 4.40
2658 2843 3.803162 GCCTTCTCCTCCCCTGGC 61.803 72.222 0.00 0.00 0.00 4.85
2698 2883 3.774702 GCGCAAACCGTCGTCTCC 61.775 66.667 0.30 0.00 39.71 3.71
2704 2889 1.225745 CGATCAAGCGCAAACCGTC 60.226 57.895 11.47 0.00 39.71 4.79
2733 2918 4.772886 TTCTCTGGGCCTACTAATTTCC 57.227 45.455 4.53 0.00 0.00 3.13
2736 2921 6.558775 TGATGTATTCTCTGGGCCTACTAATT 59.441 38.462 4.53 0.00 0.00 1.40
2795 2983 3.497262 CCGTTTGTTTGAGAGGGTACTTC 59.503 47.826 0.00 0.00 0.00 3.01
2812 3000 5.497474 AGTACAAATTAGATCTGGCCGTTT 58.503 37.500 5.18 0.00 0.00 3.60
2818 3006 5.059833 GCTGGGAGTACAAATTAGATCTGG 58.940 45.833 5.18 0.00 0.00 3.86
2827 3015 0.034089 GCAGGGCTGGGAGTACAAAT 60.034 55.000 0.00 0.00 0.00 2.32
2841 3029 1.905215 CCTCATACTCCATAGGCAGGG 59.095 57.143 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.