Multiple sequence alignment - TraesCS2A01G205300

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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 TraesCS2A01G205300 chr2A 100.000 2854 0 0 1 2854 183209195 183206342 0.000000e+00 5271.0
1 TraesCS2A01G205300 chr2B 92.327 1981 82 29 1 1932 230595732 230593773 0.000000e+00 2752.0
2 TraesCS2A01G205300 chr2D 92.845 1146 47 16 805 1937 167427922 167429045 0.000000e+00 1629.0
3 TraesCS2A01G205300 chr2D 93.293 820 37 7 1 804 167427065 167427882 0.000000e+00 1194.0
4 TraesCS2A01G205300 chr5D 87.042 710 76 10 1044 1744 528230692 528229990 0.000000e+00 787.0
5 TraesCS2A01G205300 chr5D 76.923 806 170 14 2006 2808 527926578 527927370 7.260000e-121 444.0
6 TraesCS2A01G205300 chr5D 80.952 84 13 2 858 938 528230910 528230827 2.370000e-06 63.9
7 TraesCS2A01G205300 chr5A 86.695 714 80 11 1043 1749 656210784 656210079 0.000000e+00 778.0
8 TraesCS2A01G205300 chr5A 80.952 84 13 2 858 938 656211028 656210945 2.370000e-06 63.9
9 TraesCS2A01G205300 chr5B 87.463 678 73 6 1074 1744 664998778 664998106 0.000000e+00 771.0
10 TraesCS2A01G205300 chr5B 80.952 84 13 2 858 938 664999031 664998948 2.370000e-06 63.9
11 TraesCS2A01G205300 chrUn 76.923 806 170 14 2006 2808 290614515 290615307 7.260000e-121 444.0
12 TraesCS2A01G205300 chr4A 73.158 190 45 5 2515 2701 645399676 645399490 2.370000e-06 63.9


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 TraesCS2A01G205300 chr2A 183206342 183209195 2853 True 5271.00 5271 100.0000 1 2854 1 chr2A.!!$R1 2853
1 TraesCS2A01G205300 chr2B 230593773 230595732 1959 True 2752.00 2752 92.3270 1 1932 1 chr2B.!!$R1 1931
2 TraesCS2A01G205300 chr2D 167427065 167429045 1980 False 1411.50 1629 93.0690 1 1937 2 chr2D.!!$F1 1936
3 TraesCS2A01G205300 chr5D 527926578 527927370 792 False 444.00 444 76.9230 2006 2808 1 chr5D.!!$F1 802
4 TraesCS2A01G205300 chr5D 528229990 528230910 920 True 425.45 787 83.9970 858 1744 2 chr5D.!!$R1 886
5 TraesCS2A01G205300 chr5A 656210079 656211028 949 True 420.95 778 83.8235 858 1749 2 chr5A.!!$R1 891
6 TraesCS2A01G205300 chr5B 664998106 664999031 925 True 417.45 771 84.2075 858 1744 2 chr5B.!!$R1 886
7 TraesCS2A01G205300 chrUn 290614515 290615307 792 False 444.00 444 76.9230 2006 2808 1 chrUn.!!$F1 802

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
455 470 0.179189 GCGCACTTGATTGCAGGTAC 60.179 55.0 0.3 0.0 43.15 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2363 2541 0.533491 GCTGGCCTTCATCATGCAAA 59.467 50.0 3.32 0.0 0.0 3.68 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
70 72 3.230134 TGGCTTGGTTGCTCTTAACAAT 58.770 40.909 0.00 0.00 32.22 2.71
110 112 8.503458 ACAATGAGGTCAGAAATAATTCAGAG 57.497 34.615 0.00 0.00 38.06 3.35
116 118 5.295540 GGTCAGAAATAATTCAGAGCCTGAC 59.704 44.000 0.00 0.00 41.20 3.51
122 124 7.768120 AGAAATAATTCAGAGCCTGACTACAAG 59.232 37.037 4.59 0.00 40.46 3.16
164 166 3.807538 GGCTGTGAGCATGTGCCG 61.808 66.667 0.57 0.00 44.75 5.69
285 290 6.811253 TCCGTATATGCAAAAAGTTTCACT 57.189 33.333 0.00 0.00 0.00 3.41
331 341 1.060622 GTAGTCGGTGACTCTCGCG 59.939 63.158 0.00 0.00 42.40 5.87
452 467 2.202388 CGCGCACTTGATTGCAGG 60.202 61.111 8.75 0.00 43.15 4.85
455 470 0.179189 GCGCACTTGATTGCAGGTAC 60.179 55.000 0.30 0.00 43.15 3.34
535 550 2.159627 GCAGATAGACAACAACAACCGG 59.840 50.000 0.00 0.00 0.00 5.28
556 571 1.000896 AGCAGCGGCCCATAACTTT 60.001 52.632 4.82 0.00 42.56 2.66
557 572 0.611896 AGCAGCGGCCCATAACTTTT 60.612 50.000 4.82 0.00 42.56 2.27
558 573 1.099689 GCAGCGGCCCATAACTTTTA 58.900 50.000 0.00 0.00 0.00 1.52
559 574 1.065551 GCAGCGGCCCATAACTTTTAG 59.934 52.381 0.00 0.00 0.00 1.85
560 575 1.065551 CAGCGGCCCATAACTTTTAGC 59.934 52.381 0.00 0.00 0.00 3.09
561 576 0.384309 GCGGCCCATAACTTTTAGCC 59.616 55.000 0.00 0.00 37.03 3.93
562 577 1.757682 CGGCCCATAACTTTTAGCCA 58.242 50.000 0.00 0.00 40.49 4.75
563 578 2.306847 CGGCCCATAACTTTTAGCCAT 58.693 47.619 0.00 0.00 40.49 4.40
596 614 1.923204 CAGTGTCATTCTAGAGCACGC 59.077 52.381 0.00 0.00 35.46 5.34
607 625 4.845387 TCTAGAGCACGCGATTTTACTAG 58.155 43.478 15.93 16.35 0.00 2.57
611 630 3.442100 AGCACGCGATTTTACTAGTACC 58.558 45.455 15.93 0.00 0.00 3.34
667 686 2.360801 TCAGCTAAAATATTTGGCGGGC 59.639 45.455 18.56 11.80 0.00 6.13
686 705 0.463204 CATCGGTGAGATCTGCCACT 59.537 55.000 0.00 0.00 37.52 4.00
832 895 3.244665 ACTCACTTCATGATCACCAAGCA 60.245 43.478 13.22 2.85 36.48 3.91
853 916 5.105473 AGCAGCATCAAACAGCAGAATAAAT 60.105 36.000 0.00 0.00 0.00 1.40
987 1060 0.538287 GTTGCTTTCTGGCCTCCACT 60.538 55.000 3.32 0.00 0.00 4.00
994 1067 1.997311 CTGGCCTCCACTCCCATCA 60.997 63.158 3.32 0.00 0.00 3.07
1025 1174 1.923356 AAGCCATTAACACCCACTGG 58.077 50.000 0.00 0.00 37.80 4.00
1034 1183 1.926108 ACACCCACTGGAGAGAGTAC 58.074 55.000 0.00 0.00 34.81 2.73
1118 1281 1.604278 GAACAAGGAGAAGCACCACAC 59.396 52.381 0.00 0.00 0.00 3.82
1120 1283 0.532862 CAAGGAGAAGCACCACACGT 60.533 55.000 0.00 0.00 0.00 4.49
1126 1289 0.039798 GAAGCACCACACGTACGAGA 60.040 55.000 24.41 0.00 0.00 4.04
1754 1923 2.146342 CGGCACATGATAGAATGGACC 58.854 52.381 0.00 0.00 31.46 4.46
1755 1924 2.146342 GGCACATGATAGAATGGACCG 58.854 52.381 0.00 0.00 31.46 4.79
1756 1925 1.532868 GCACATGATAGAATGGACCGC 59.467 52.381 0.00 0.00 31.46 5.68
1803 1977 1.823610 AGTGGAAGGAACTACGTAGCC 59.176 52.381 22.40 15.85 38.49 3.93
1816 1990 0.739561 CGTAGCCGGCTAGTTCTTCT 59.260 55.000 36.09 10.62 0.00 2.85
1830 2004 6.128227 GCTAGTTCTTCTCTTCGTGTCTCTAA 60.128 42.308 0.00 0.00 0.00 2.10
1832 2006 6.440436 AGTTCTTCTCTTCGTGTCTCTAAAC 58.560 40.000 0.00 0.00 0.00 2.01
1835 2009 6.982852 TCTTCTCTTCGTGTCTCTAAACAAT 58.017 36.000 0.00 0.00 0.00 2.71
1838 2012 7.639162 TCTCTTCGTGTCTCTAAACAATTTC 57.361 36.000 0.00 0.00 0.00 2.17
1920 2095 9.391006 GTAATGGGAGAATAAACTGTGTTGATA 57.609 33.333 0.00 0.00 0.00 2.15
1932 2107 7.686438 AACTGTGTTGATATATGTGCTTCAA 57.314 32.000 0.00 0.00 0.00 2.69
1933 2108 7.870509 ACTGTGTTGATATATGTGCTTCAAT 57.129 32.000 0.00 0.00 31.39 2.57
1934 2109 8.284945 ACTGTGTTGATATATGTGCTTCAATT 57.715 30.769 0.00 0.00 31.39 2.32
1935 2110 8.742777 ACTGTGTTGATATATGTGCTTCAATTT 58.257 29.630 0.00 0.00 31.39 1.82
1993 2168 8.798859 TTTTTGGAAATGAAAAGGTGAATGAA 57.201 26.923 0.00 0.00 0.00 2.57
1994 2169 8.798859 TTTTGGAAATGAAAAGGTGAATGAAA 57.201 26.923 0.00 0.00 0.00 2.69
1995 2170 8.798859 TTTGGAAATGAAAAGGTGAATGAAAA 57.201 26.923 0.00 0.00 0.00 2.29
1996 2171 8.436046 TTGGAAATGAAAAGGTGAATGAAAAG 57.564 30.769 0.00 0.00 0.00 2.27
1997 2172 6.991531 TGGAAATGAAAAGGTGAATGAAAAGG 59.008 34.615 0.00 0.00 0.00 3.11
1998 2173 6.992123 GGAAATGAAAAGGTGAATGAAAAGGT 59.008 34.615 0.00 0.00 0.00 3.50
1999 2174 8.147704 GGAAATGAAAAGGTGAATGAAAAGGTA 58.852 33.333 0.00 0.00 0.00 3.08
2000 2175 9.196552 GAAATGAAAAGGTGAATGAAAAGGTAG 57.803 33.333 0.00 0.00 0.00 3.18
2001 2176 8.477419 AATGAAAAGGTGAATGAAAAGGTAGA 57.523 30.769 0.00 0.00 0.00 2.59
2002 2177 7.889873 TGAAAAGGTGAATGAAAAGGTAGAA 57.110 32.000 0.00 0.00 0.00 2.10
2003 2178 8.477419 TGAAAAGGTGAATGAAAAGGTAGAAT 57.523 30.769 0.00 0.00 0.00 2.40
2004 2179 9.581289 TGAAAAGGTGAATGAAAAGGTAGAATA 57.419 29.630 0.00 0.00 0.00 1.75
2062 2237 5.121380 AGGTCAAATACATGAGGCTCATT 57.879 39.130 26.87 19.19 34.28 2.57
2065 2240 7.118723 AGGTCAAATACATGAGGCTCATTTTA 58.881 34.615 26.87 19.95 34.28 1.52
2066 2241 7.067494 AGGTCAAATACATGAGGCTCATTTTAC 59.933 37.037 26.87 18.80 34.28 2.01
2067 2242 7.196331 GTCAAATACATGAGGCTCATTTTACC 58.804 38.462 26.87 13.92 34.28 2.85
2070 2245 4.255510 ACATGAGGCTCATTTTACCCAT 57.744 40.909 26.87 1.04 34.28 4.00
2080 2255 0.250381 TTTTACCCATCGTGGTGCGT 60.250 50.000 4.64 0.00 39.53 5.24
2091 2266 2.897350 GGTGCGTAGGCCATGAGC 60.897 66.667 5.01 5.44 38.85 4.26
2100 2275 1.071128 GGCCATGAGCAGCCTAGAG 59.929 63.158 0.00 0.00 46.14 2.43
2107 2285 3.601443 TGAGCAGCCTAGAGAAGAAAC 57.399 47.619 0.00 0.00 0.00 2.78
2110 2288 3.932089 GAGCAGCCTAGAGAAGAAACAAG 59.068 47.826 0.00 0.00 0.00 3.16
2113 2291 4.322349 GCAGCCTAGAGAAGAAACAAGAGA 60.322 45.833 0.00 0.00 0.00 3.10
2114 2292 5.167845 CAGCCTAGAGAAGAAACAAGAGAC 58.832 45.833 0.00 0.00 0.00 3.36
2116 2294 4.321378 GCCTAGAGAAGAAACAAGAGACGT 60.321 45.833 0.00 0.00 0.00 4.34
2123 2301 3.983741 AGAAACAAGAGACGTGAAGGAG 58.016 45.455 0.00 0.00 0.00 3.69
2124 2302 3.637229 AGAAACAAGAGACGTGAAGGAGA 59.363 43.478 0.00 0.00 0.00 3.71
2127 2305 3.223435 ACAAGAGACGTGAAGGAGAGAA 58.777 45.455 0.00 0.00 0.00 2.87
2129 2307 4.233789 CAAGAGACGTGAAGGAGAGAAAG 58.766 47.826 0.00 0.00 0.00 2.62
2132 2310 3.754323 GAGACGTGAAGGAGAGAAAGAGA 59.246 47.826 0.00 0.00 0.00 3.10
2133 2311 3.756434 AGACGTGAAGGAGAGAAAGAGAG 59.244 47.826 0.00 0.00 0.00 3.20
2135 2313 4.340617 ACGTGAAGGAGAGAAAGAGAGAT 58.659 43.478 0.00 0.00 0.00 2.75
2137 2315 4.397730 CGTGAAGGAGAGAAAGAGAGATGA 59.602 45.833 0.00 0.00 0.00 2.92
2138 2316 5.650543 GTGAAGGAGAGAAAGAGAGATGAC 58.349 45.833 0.00 0.00 0.00 3.06
2140 2318 4.329638 AGGAGAGAAAGAGAGATGACCA 57.670 45.455 0.00 0.00 0.00 4.02
2141 2319 4.882559 AGGAGAGAAAGAGAGATGACCAT 58.117 43.478 0.00 0.00 0.00 3.55
2144 2322 3.773667 AGAGAAAGAGAGATGACCATGCA 59.226 43.478 0.00 0.00 0.00 3.96
2145 2323 4.121317 GAGAAAGAGAGATGACCATGCAG 58.879 47.826 0.00 0.00 0.00 4.41
2146 2324 3.773667 AGAAAGAGAGATGACCATGCAGA 59.226 43.478 0.00 0.00 0.00 4.26
2147 2325 4.224594 AGAAAGAGAGATGACCATGCAGAA 59.775 41.667 0.00 0.00 0.00 3.02
2149 2327 3.106054 AGAGAGATGACCATGCAGAACT 58.894 45.455 0.00 0.00 0.00 3.01
2151 2329 4.341806 AGAGAGATGACCATGCAGAACTAG 59.658 45.833 0.00 0.00 0.00 2.57
2152 2330 3.387374 AGAGATGACCATGCAGAACTAGG 59.613 47.826 0.00 0.00 0.00 3.02
2153 2331 2.158842 AGATGACCATGCAGAACTAGGC 60.159 50.000 0.00 0.00 0.00 3.93
2154 2332 0.983467 TGACCATGCAGAACTAGGCA 59.017 50.000 0.00 0.00 45.23 4.75
2155 2333 1.350684 TGACCATGCAGAACTAGGCAA 59.649 47.619 0.00 0.00 44.20 4.52
2156 2334 2.012673 GACCATGCAGAACTAGGCAAG 58.987 52.381 0.00 0.00 44.20 4.01
2161 2339 2.977914 TGCAGAACTAGGCAAGCTAAG 58.022 47.619 0.00 0.00 37.03 2.18
2165 2343 4.759782 CAGAACTAGGCAAGCTAAGCTAA 58.240 43.478 10.47 0.00 38.25 3.09
2169 2347 2.409399 GGCAAGCTAAGCTAAGCCC 58.591 57.895 1.85 0.67 46.88 5.19
2171 2349 1.020437 GCAAGCTAAGCTAAGCCCAG 58.980 55.000 3.96 0.00 43.86 4.45
2173 2351 2.941415 GCAAGCTAAGCTAAGCCCAGAA 60.941 50.000 3.96 0.00 43.86 3.02
2181 2359 1.889170 GCTAAGCCCAGAAAGTTTGCT 59.111 47.619 0.00 0.00 0.00 3.91
2184 2362 1.911057 AGCCCAGAAAGTTTGCTACC 58.089 50.000 0.00 0.00 0.00 3.18
2195 2373 6.547510 AGAAAGTTTGCTACCAAGACAAGATT 59.452 34.615 0.00 0.00 31.52 2.40
2197 2375 4.022849 AGTTTGCTACCAAGACAAGATTGC 60.023 41.667 0.00 0.00 31.52 3.56
2200 2378 2.159462 GCTACCAAGACAAGATTGCTGC 60.159 50.000 0.00 0.00 0.00 5.25
2204 2382 3.243636 ACCAAGACAAGATTGCTGCTTTG 60.244 43.478 0.00 3.50 0.00 2.77
2205 2383 2.719426 AGACAAGATTGCTGCTTTGC 57.281 45.000 0.00 0.00 0.00 3.68
2207 2385 0.319405 ACAAGATTGCTGCTTTGCCC 59.681 50.000 0.00 0.00 0.00 5.36
2208 2386 0.606604 CAAGATTGCTGCTTTGCCCT 59.393 50.000 0.00 0.00 0.00 5.19
2210 2388 0.039326 AGATTGCTGCTTTGCCCTCT 59.961 50.000 0.00 0.00 0.00 3.69
2236 2414 2.594303 TGCTCGGTGGCACCAAAG 60.594 61.111 34.11 28.84 38.47 2.77
2252 2430 3.821033 ACCAAAGTGATAACAACTCTGCC 59.179 43.478 0.00 0.00 0.00 4.85
2254 2432 3.402628 AAGTGATAACAACTCTGCCGT 57.597 42.857 0.00 0.00 0.00 5.68
2255 2433 2.688507 AGTGATAACAACTCTGCCGTG 58.311 47.619 0.00 0.00 0.00 4.94
2256 2434 2.037251 AGTGATAACAACTCTGCCGTGT 59.963 45.455 0.00 0.00 0.00 4.49
2257 2435 3.257375 AGTGATAACAACTCTGCCGTGTA 59.743 43.478 0.00 0.00 0.00 2.90
2258 2436 4.081642 AGTGATAACAACTCTGCCGTGTAT 60.082 41.667 0.00 0.00 0.00 2.29
2259 2437 4.630069 GTGATAACAACTCTGCCGTGTATT 59.370 41.667 0.00 0.00 0.00 1.89
2270 2448 2.950975 TGCCGTGTATTCGTACATCCTA 59.049 45.455 0.00 0.00 32.03 2.94
2297 2475 1.153647 CGGTGACCAGCGCTTATGA 60.154 57.895 7.50 0.00 45.38 2.15
2303 2481 2.677836 TGACCAGCGCTTATGATTGAAC 59.322 45.455 7.50 0.00 0.00 3.18
2306 2484 2.419673 CCAGCGCTTATGATTGAACACA 59.580 45.455 7.50 0.00 0.00 3.72
2311 2489 3.120338 CGCTTATGATTGAACACACGGTT 60.120 43.478 0.00 0.00 44.10 4.44
2315 2493 6.687105 GCTTATGATTGAACACACGGTTATTC 59.313 38.462 0.00 0.00 40.63 1.75
2321 2499 0.672401 ACACACGGTTATTCCTGGCG 60.672 55.000 0.00 0.00 0.00 5.69
2335 2513 1.845809 CTGGCGTGCCAAAGAGTGAC 61.846 60.000 15.46 0.00 46.63 3.67
2336 2514 1.598130 GGCGTGCCAAAGAGTGACT 60.598 57.895 5.89 0.00 35.81 3.41
2338 2516 0.790814 GCGTGCCAAAGAGTGACTAC 59.209 55.000 0.00 0.00 0.00 2.73
2357 2535 6.005583 ACTACACAAGCAACAATCAGAATG 57.994 37.500 0.00 0.00 37.54 2.67
2359 2537 5.266733 ACACAAGCAACAATCAGAATGTT 57.733 34.783 0.00 0.00 41.50 2.71
2362 2540 5.749588 CACAAGCAACAATCAGAATGTTCAA 59.250 36.000 0.43 0.00 38.90 2.69
2363 2541 6.422701 CACAAGCAACAATCAGAATGTTCAAT 59.577 34.615 0.43 0.00 38.90 2.57
2367 2545 6.073440 AGCAACAATCAGAATGTTCAATTTGC 60.073 34.615 0.43 2.16 38.90 3.68
2368 2546 6.292973 GCAACAATCAGAATGTTCAATTTGCA 60.293 34.615 0.43 0.00 38.90 4.08
2369 2547 7.572353 GCAACAATCAGAATGTTCAATTTGCAT 60.572 33.333 0.43 0.00 38.90 3.96
2374 2552 6.926313 TCAGAATGTTCAATTTGCATGATGA 58.074 32.000 0.00 0.00 37.40 2.92
2376 2554 7.544217 TCAGAATGTTCAATTTGCATGATGAAG 59.456 33.333 0.00 0.00 37.40 3.02
2383 2561 0.612453 TTGCATGATGAAGGCCAGCA 60.612 50.000 5.01 1.90 46.12 4.41
2393 2571 1.064654 GAAGGCCAGCATAAAAGAGCG 59.935 52.381 5.01 0.00 35.48 5.03
2401 2579 2.225491 AGCATAAAAGAGCGCGTTGAAA 59.775 40.909 8.43 0.00 35.48 2.69
2402 2580 2.589841 GCATAAAAGAGCGCGTTGAAAG 59.410 45.455 8.43 0.00 0.00 2.62
2405 2583 2.670401 AAAGAGCGCGTTGAAAGAAG 57.330 45.000 8.43 0.00 0.00 2.85
2408 2586 1.140816 GAGCGCGTTGAAAGAAGTCT 58.859 50.000 8.43 0.00 0.00 3.24
2409 2587 0.861837 AGCGCGTTGAAAGAAGTCTG 59.138 50.000 8.43 0.00 0.00 3.51
2418 2596 6.470160 CGTTGAAAGAAGTCTGATAAATCCG 58.530 40.000 0.00 0.00 0.00 4.18
2419 2597 6.090898 CGTTGAAAGAAGTCTGATAAATCCGT 59.909 38.462 0.00 0.00 0.00 4.69
2423 2601 5.677319 AGAAGTCTGATAAATCCGTGGAA 57.323 39.130 0.00 0.00 0.00 3.53
2426 2604 6.540189 AGAAGTCTGATAAATCCGTGGAATTG 59.460 38.462 0.00 0.00 0.00 2.32
2431 2609 7.280205 GTCTGATAAATCCGTGGAATTGTAAGT 59.720 37.037 0.00 0.00 0.00 2.24
2435 2613 3.965379 TCCGTGGAATTGTAAGTAGCA 57.035 42.857 0.00 0.00 0.00 3.49
2462 2640 3.604582 CAGTTCAAATCTCTCCCAGACC 58.395 50.000 0.00 0.00 32.26 3.85
2467 2645 0.324738 AATCTCTCCCAGACCGCAGA 60.325 55.000 0.00 0.00 32.26 4.26
2468 2646 0.324738 ATCTCTCCCAGACCGCAGAA 60.325 55.000 0.00 0.00 32.26 3.02
2473 2651 3.114616 CCAGACCGCAGAAGCACG 61.115 66.667 0.00 0.00 42.27 5.34
2482 2660 2.036571 CAGAAGCACGGCTGCATCA 61.037 57.895 13.67 0.00 46.97 3.07
2487 2665 1.007502 GCACGGCTGCATCACAAAA 60.008 52.632 0.50 0.00 43.62 2.44
2489 2667 0.664166 CACGGCTGCATCACAAAACC 60.664 55.000 0.50 0.00 0.00 3.27
2494 2672 2.754552 GGCTGCATCACAAAACCAGATA 59.245 45.455 0.50 0.00 0.00 1.98
2507 2685 3.037851 ACCAGATAGCTGATGGACTCA 57.962 47.619 10.19 0.00 45.17 3.41
2510 2688 4.411540 ACCAGATAGCTGATGGACTCAATT 59.588 41.667 10.19 0.00 45.17 2.32
2519 2697 0.609957 TGGACTCAATTGCTGGGCAG 60.610 55.000 0.00 0.00 40.61 4.85
2528 2706 2.336945 TTGCTGGGCAGATATCACAG 57.663 50.000 5.32 8.60 40.61 3.66
2529 2707 1.206878 TGCTGGGCAGATATCACAGT 58.793 50.000 5.32 0.00 33.32 3.55
2530 2708 1.134310 TGCTGGGCAGATATCACAGTG 60.134 52.381 5.32 0.00 33.32 3.66
2531 2709 1.139654 GCTGGGCAGATATCACAGTGA 59.860 52.381 5.50 5.50 0.00 3.41
2536 2714 2.806818 GGCAGATATCACAGTGAGCATG 59.193 50.000 9.64 6.46 0.00 4.06
2537 2715 3.464907 GCAGATATCACAGTGAGCATGT 58.535 45.455 9.64 0.87 0.00 3.21
2539 2717 3.247886 CAGATATCACAGTGAGCATGTGC 59.752 47.826 9.64 0.00 46.11 4.57
2542 2720 0.107268 TCACAGTGAGCATGTGCAGT 59.893 50.000 7.83 0.00 46.11 4.40
2549 2727 4.507021 CAGTGAGCATGTGCAGTAATAGAG 59.493 45.833 7.83 0.00 45.16 2.43
2558 2736 3.195825 GTGCAGTAATAGAGGACCACTGT 59.804 47.826 1.07 0.00 39.03 3.55
2576 2754 6.433093 ACCACTGTTTCTTTACCATATTGTCC 59.567 38.462 0.00 0.00 0.00 4.02
2579 2757 5.806818 TGTTTCTTTACCATATTGTCCCGA 58.193 37.500 0.00 0.00 0.00 5.14
2582 2760 5.018539 TCTTTACCATATTGTCCCGAGTG 57.981 43.478 0.00 0.00 0.00 3.51
2588 2766 3.369471 CCATATTGTCCCGAGTGTTCAGT 60.369 47.826 0.00 0.00 0.00 3.41
2589 2767 2.457366 ATTGTCCCGAGTGTTCAGTC 57.543 50.000 0.00 0.00 0.00 3.51
2591 2769 0.820482 TGTCCCGAGTGTTCAGTCGA 60.820 55.000 25.22 8.89 38.50 4.20
2618 2796 4.039609 CAGAAAGCCAACCAAAGGAAGATT 59.960 41.667 0.00 0.00 0.00 2.40
2624 2802 4.082733 GCCAACCAAAGGAAGATTCTGTAC 60.083 45.833 0.00 0.00 0.00 2.90
2627 2805 6.265422 CCAACCAAAGGAAGATTCTGTACTTT 59.735 38.462 0.00 5.26 0.00 2.66
2629 2807 8.507249 CAACCAAAGGAAGATTCTGTACTTTAG 58.493 37.037 9.02 6.23 0.00 1.85
2633 2811 5.600749 AGGAAGATTCTGTACTTTAGGGGA 58.399 41.667 0.00 0.00 0.00 4.81
2636 2814 6.768381 GGAAGATTCTGTACTTTAGGGGAATG 59.232 42.308 0.00 0.00 0.00 2.67
2642 2820 3.521937 TGTACTTTAGGGGAATGACAGGG 59.478 47.826 0.00 0.00 0.00 4.45
2658 2836 4.280019 GGTCCCAAACCCACCGCT 62.280 66.667 0.00 0.00 42.85 5.52
2663 2841 1.606313 CCAAACCCACCGCTGGAAT 60.606 57.895 0.00 0.00 40.55 3.01
2664 2842 0.322997 CCAAACCCACCGCTGGAATA 60.323 55.000 0.00 0.00 40.55 1.75
2665 2843 0.808755 CAAACCCACCGCTGGAATAC 59.191 55.000 0.00 0.00 40.55 1.89
2666 2844 0.402504 AAACCCACCGCTGGAATACA 59.597 50.000 0.00 0.00 40.55 2.29
2670 2848 0.744414 CCACCGCTGGAATACACTGG 60.744 60.000 0.00 0.00 40.55 4.00
2672 2850 0.249398 ACCGCTGGAATACACTGGTC 59.751 55.000 1.50 0.00 0.00 4.02
2675 2853 1.337728 CGCTGGAATACACTGGTCACA 60.338 52.381 0.00 0.00 0.00 3.58
2678 2856 2.303022 CTGGAATACACTGGTCACACCT 59.697 50.000 0.00 0.00 39.58 4.00
2681 2859 3.589988 GAATACACTGGTCACACCTCTG 58.410 50.000 0.00 0.00 39.58 3.35
2684 2862 1.837439 ACACTGGTCACACCTCTGAAA 59.163 47.619 0.00 0.00 39.58 2.69
2685 2863 2.158900 ACACTGGTCACACCTCTGAAAG 60.159 50.000 0.00 0.00 39.58 2.62
2690 2868 3.964688 TGGTCACACCTCTGAAAGTAAGA 59.035 43.478 0.00 0.00 39.58 2.10
2693 2871 5.453480 GGTCACACCTCTGAAAGTAAGAAGT 60.453 44.000 0.00 0.00 34.73 3.01
2696 2874 5.237344 CACACCTCTGAAAGTAAGAAGTTGG 59.763 44.000 0.00 0.00 33.76 3.77
2702 2880 8.560374 CCTCTGAAAGTAAGAAGTTGGTAAAAG 58.440 37.037 0.00 0.00 33.76 2.27
2703 2881 9.110502 CTCTGAAAGTAAGAAGTTGGTAAAAGT 57.889 33.333 0.00 0.00 33.76 2.66
2709 2887 6.762661 AGTAAGAAGTTGGTAAAAGTACGCAA 59.237 34.615 0.00 0.00 0.00 4.85
2712 2890 7.916914 AGAAGTTGGTAAAAGTACGCAATAT 57.083 32.000 0.00 0.00 0.00 1.28
2720 2898 7.388224 TGGTAAAAGTACGCAATATTCACTTCA 59.612 33.333 0.00 0.00 0.00 3.02
2753 2931 3.929610 GAGAAGAGAAACGATGTTCCTGG 59.070 47.826 0.00 0.00 0.00 4.45
2758 2936 1.244019 AAACGATGTTCCTGGCTGGC 61.244 55.000 5.39 0.00 35.26 4.85
2762 2940 1.001641 ATGTTCCTGGCTGGCAGAC 60.002 57.895 30.23 18.07 35.26 3.51
2765 2943 2.293318 TTCCTGGCTGGCAGACGAT 61.293 57.895 30.23 0.00 35.26 3.73
2768 2946 3.002583 TGGCTGGCAGACGATGGA 61.003 61.111 20.86 0.00 0.00 3.41
2770 2948 1.048160 TGGCTGGCAGACGATGGATA 61.048 55.000 20.86 0.00 0.00 2.59
2777 2955 2.484889 GCAGACGATGGATAAACTCCC 58.515 52.381 0.00 0.00 44.23 4.30
2779 2957 3.681594 GCAGACGATGGATAAACTCCCAA 60.682 47.826 0.00 0.00 44.23 4.12
2785 2963 5.714806 ACGATGGATAAACTCCCAACAAAAT 59.285 36.000 0.00 0.00 44.23 1.82
2786 2964 6.210584 ACGATGGATAAACTCCCAACAAAATT 59.789 34.615 0.00 0.00 44.23 1.82
2788 2966 6.739331 TGGATAAACTCCCAACAAAATTGT 57.261 33.333 0.00 0.00 44.23 2.71
2789 2967 6.754193 TGGATAAACTCCCAACAAAATTGTC 58.246 36.000 0.00 0.00 44.23 3.18
2792 2970 3.733443 ACTCCCAACAAAATTGTCTGC 57.267 42.857 0.00 0.00 41.31 4.26
2811 2989 1.747709 CAGAAGATGCAACTCCCAGG 58.252 55.000 0.00 0.00 0.00 4.45
2812 2990 1.004044 CAGAAGATGCAACTCCCAGGT 59.996 52.381 0.00 0.00 0.00 4.00
2813 2991 1.004044 AGAAGATGCAACTCCCAGGTG 59.996 52.381 0.00 0.00 35.59 4.00
2814 2992 0.038744 AAGATGCAACTCCCAGGTGG 59.961 55.000 0.00 0.00 32.34 4.61
2815 2993 2.036256 ATGCAACTCCCAGGTGGC 59.964 61.111 0.00 0.00 32.34 5.01
2816 2994 3.590466 ATGCAACTCCCAGGTGGCC 62.590 63.158 0.00 0.00 35.42 5.36
2824 3002 4.335647 CCAGGTGGCCGCTTGAGT 62.336 66.667 28.45 0.00 0.00 3.41
2825 3003 2.743928 CAGGTGGCCGCTTGAGTC 60.744 66.667 23.17 0.68 0.00 3.36
2826 3004 3.241530 AGGTGGCCGCTTGAGTCA 61.242 61.111 17.49 0.00 0.00 3.41
2827 3005 2.743928 GGTGGCCGCTTGAGTCAG 60.744 66.667 17.49 0.00 0.00 3.51
2828 3006 2.343758 GTGGCCGCTTGAGTCAGA 59.656 61.111 9.68 0.00 0.00 3.27
2829 3007 1.078848 GTGGCCGCTTGAGTCAGAT 60.079 57.895 9.68 0.00 0.00 2.90
2830 3008 0.674895 GTGGCCGCTTGAGTCAGATT 60.675 55.000 9.68 0.00 0.00 2.40
2831 3009 0.036732 TGGCCGCTTGAGTCAGATTT 59.963 50.000 0.00 0.00 0.00 2.17
2832 3010 0.449388 GGCCGCTTGAGTCAGATTTG 59.551 55.000 0.00 0.00 0.00 2.32
2833 3011 0.449388 GCCGCTTGAGTCAGATTTGG 59.551 55.000 0.00 0.00 0.00 3.28
2834 3012 1.089920 CCGCTTGAGTCAGATTTGGG 58.910 55.000 0.00 0.00 0.00 4.12
2835 3013 1.611673 CCGCTTGAGTCAGATTTGGGT 60.612 52.381 0.00 0.00 0.00 4.51
2836 3014 1.466167 CGCTTGAGTCAGATTTGGGTG 59.534 52.381 0.00 0.00 0.00 4.61
2837 3015 1.200948 GCTTGAGTCAGATTTGGGTGC 59.799 52.381 0.00 0.00 0.00 5.01
2838 3016 2.507484 CTTGAGTCAGATTTGGGTGCA 58.493 47.619 0.00 0.00 0.00 4.57
2839 3017 2.655090 TGAGTCAGATTTGGGTGCAA 57.345 45.000 0.00 0.00 0.00 4.08
2840 3018 2.942804 TGAGTCAGATTTGGGTGCAAA 58.057 42.857 0.00 0.00 0.00 3.68
2841 3019 3.499338 TGAGTCAGATTTGGGTGCAAAT 58.501 40.909 0.00 0.00 37.47 2.32
2842 3020 3.256383 TGAGTCAGATTTGGGTGCAAATG 59.744 43.478 0.00 0.00 35.18 2.32
2843 3021 3.499338 AGTCAGATTTGGGTGCAAATGA 58.501 40.909 0.00 0.00 35.18 2.57
2844 3022 3.896888 AGTCAGATTTGGGTGCAAATGAA 59.103 39.130 0.00 0.00 35.18 2.57
2845 3023 4.529377 AGTCAGATTTGGGTGCAAATGAAT 59.471 37.500 0.00 0.00 35.18 2.57
2846 3024 5.716228 AGTCAGATTTGGGTGCAAATGAATA 59.284 36.000 0.00 0.00 35.18 1.75
2847 3025 6.381994 AGTCAGATTTGGGTGCAAATGAATAT 59.618 34.615 0.00 0.00 35.18 1.28
2848 3026 6.698766 GTCAGATTTGGGTGCAAATGAATATC 59.301 38.462 0.00 0.00 35.18 1.63
2849 3027 5.987347 CAGATTTGGGTGCAAATGAATATCC 59.013 40.000 0.00 0.00 35.18 2.59
2850 3028 5.662208 AGATTTGGGTGCAAATGAATATCCA 59.338 36.000 0.00 0.00 35.18 3.41
2851 3029 5.752036 TTTGGGTGCAAATGAATATCCAA 57.248 34.783 0.00 0.00 0.00 3.53
2852 3030 5.752036 TTGGGTGCAAATGAATATCCAAA 57.248 34.783 0.00 0.00 31.12 3.28
2853 3031 5.752036 TGGGTGCAAATGAATATCCAAAA 57.248 34.783 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 93 5.190528 TCAGGCTCTGAATTATTTCTGACCT 59.809 40.000 14.93 14.93 37.57 3.85
110 112 1.301677 GGCTGTGCTTGTAGTCAGGC 61.302 60.000 0.00 0.00 45.09 4.85
116 118 0.254178 ATCCCAGGCTGTGCTTGTAG 59.746 55.000 14.43 0.00 33.72 2.74
122 124 1.153086 ATCGAATCCCAGGCTGTGC 60.153 57.895 14.43 0.00 0.00 4.57
164 166 2.420372 CCCTTTTCCTTTAGCTTCGCTC 59.580 50.000 0.00 0.00 40.44 5.03
285 290 9.772973 ACTGAGTACGCAAATATATGGATTTAA 57.227 29.630 0.00 0.00 0.00 1.52
331 341 5.353123 TCATATTTAACCTGAGCGTTTCCAC 59.647 40.000 0.00 0.00 0.00 4.02
452 467 4.901814 GCATCATATGGAATCATGCGTAC 58.098 43.478 9.72 0.00 34.96 3.67
516 531 2.874457 GCCCGGTTGTTGTTGTCTATCT 60.874 50.000 0.00 0.00 0.00 1.98
571 586 5.392057 CGTGCTCTAGAATGACACTGTTAGA 60.392 44.000 11.06 0.00 0.00 2.10
667 686 0.463204 AGTGGCAGATCTCACCGATG 59.537 55.000 10.18 0.00 34.67 3.84
686 705 6.879276 AGCGCAACTCATACTAGACTAATA 57.121 37.500 11.47 0.00 0.00 0.98
767 791 0.102481 ATGTGTACCACCGCTCGATC 59.898 55.000 0.00 0.00 32.73 3.69
770 794 1.809619 CCATGTGTACCACCGCTCG 60.810 63.158 0.00 0.00 32.73 5.03
773 797 3.131478 GGCCATGTGTACCACCGC 61.131 66.667 0.00 0.00 32.73 5.68
791 815 2.124122 GTCCCAATTTGCGTTTGACAC 58.876 47.619 0.00 0.00 0.00 3.67
832 895 6.519679 TCATTTATTCTGCTGTTTGATGCT 57.480 33.333 0.00 0.00 0.00 3.79
853 916 1.460743 CGTGCGCTTTGAGATTCTTCA 59.539 47.619 9.73 0.00 0.00 3.02
942 1013 4.575885 TCAACCGAAGAATTTTCCTCGAT 58.424 39.130 11.78 0.00 42.18 3.59
944 1015 3.994392 TCTCAACCGAAGAATTTTCCTCG 59.006 43.478 4.68 4.68 40.00 4.63
987 1060 5.044476 TGGCTTTAAAAGTAGGATGATGGGA 60.044 40.000 0.00 0.00 0.00 4.37
994 1067 7.123697 GGGTGTTAATGGCTTTAAAAGTAGGAT 59.876 37.037 7.10 0.00 31.69 3.24
1025 1174 1.280444 GCGCGCTAGGTACTCTCTC 59.720 63.158 26.67 0.00 41.75 3.20
1118 1281 1.136147 CGGAGGTGGTTCTCGTACG 59.864 63.158 9.53 9.53 34.74 3.67
1756 1925 2.954868 GACGTGCGGCCGTATGAG 60.955 66.667 37.21 24.46 41.98 2.90
1765 1935 0.795735 CTTACAGTACGGACGTGCGG 60.796 60.000 32.46 17.35 35.88 5.69
1803 1977 2.095161 ACACGAAGAGAAGAACTAGCCG 60.095 50.000 0.00 0.00 0.00 5.52
1816 1990 6.984474 ACAGAAATTGTTTAGAGACACGAAGA 59.016 34.615 0.00 0.00 36.31 2.87
1874 2049 9.613957 CCATTACACGTGACATACAAAAATTAA 57.386 29.630 25.01 5.72 0.00 1.40
1890 2065 5.642063 CACAGTTTATTCTCCCATTACACGT 59.358 40.000 0.00 0.00 0.00 4.49
1898 2073 9.559732 CATATATCAACACAGTTTATTCTCCCA 57.440 33.333 0.00 0.00 0.00 4.37
1968 2143 8.798859 TTCATTCACCTTTTCATTTCCAAAAA 57.201 26.923 0.00 0.00 0.00 1.94
1969 2144 8.798859 TTTCATTCACCTTTTCATTTCCAAAA 57.201 26.923 0.00 0.00 0.00 2.44
1970 2145 8.798859 TTTTCATTCACCTTTTCATTTCCAAA 57.201 26.923 0.00 0.00 0.00 3.28
1971 2146 7.498570 CCTTTTCATTCACCTTTTCATTTCCAA 59.501 33.333 0.00 0.00 0.00 3.53
1972 2147 6.991531 CCTTTTCATTCACCTTTTCATTTCCA 59.008 34.615 0.00 0.00 0.00 3.53
1973 2148 6.992123 ACCTTTTCATTCACCTTTTCATTTCC 59.008 34.615 0.00 0.00 0.00 3.13
1974 2149 9.196552 CTACCTTTTCATTCACCTTTTCATTTC 57.803 33.333 0.00 0.00 0.00 2.17
1975 2150 8.923270 TCTACCTTTTCATTCACCTTTTCATTT 58.077 29.630 0.00 0.00 0.00 2.32
1976 2151 8.477419 TCTACCTTTTCATTCACCTTTTCATT 57.523 30.769 0.00 0.00 0.00 2.57
1977 2152 8.477419 TTCTACCTTTTCATTCACCTTTTCAT 57.523 30.769 0.00 0.00 0.00 2.57
1978 2153 7.889873 TTCTACCTTTTCATTCACCTTTTCA 57.110 32.000 0.00 0.00 0.00 2.69
2045 2220 6.194235 TGGGTAAAATGAGCCTCATGTATTT 58.806 36.000 8.21 7.91 37.15 1.40
2046 2221 5.765510 TGGGTAAAATGAGCCTCATGTATT 58.234 37.500 8.21 6.89 37.15 1.89
2091 2266 5.167845 GTCTCTTGTTTCTTCTCTAGGCTG 58.832 45.833 0.00 0.00 0.00 4.85
2100 2275 4.369182 TCCTTCACGTCTCTTGTTTCTTC 58.631 43.478 0.00 0.00 0.00 2.87
2107 2285 3.924918 TTCTCTCCTTCACGTCTCTTG 57.075 47.619 0.00 0.00 0.00 3.02
2110 2288 3.754323 TCTCTTTCTCTCCTTCACGTCTC 59.246 47.826 0.00 0.00 0.00 3.36
2113 2291 3.757270 TCTCTCTTTCTCTCCTTCACGT 58.243 45.455 0.00 0.00 0.00 4.49
2114 2292 4.397730 TCATCTCTCTTTCTCTCCTTCACG 59.602 45.833 0.00 0.00 0.00 4.35
2116 2294 4.709397 GGTCATCTCTCTTTCTCTCCTTCA 59.291 45.833 0.00 0.00 0.00 3.02
2123 2301 4.121317 CTGCATGGTCATCTCTCTTTCTC 58.879 47.826 0.00 0.00 0.00 2.87
2124 2302 3.773667 TCTGCATGGTCATCTCTCTTTCT 59.226 43.478 0.00 0.00 0.00 2.52
2127 2305 3.518705 AGTTCTGCATGGTCATCTCTCTT 59.481 43.478 0.00 0.00 0.00 2.85
2129 2307 3.540314 AGTTCTGCATGGTCATCTCTC 57.460 47.619 0.00 0.00 0.00 3.20
2132 2310 2.158842 GCCTAGTTCTGCATGGTCATCT 60.159 50.000 0.00 0.00 0.00 2.90
2133 2311 2.216898 GCCTAGTTCTGCATGGTCATC 58.783 52.381 0.00 0.00 0.00 2.92
2135 2313 0.983467 TGCCTAGTTCTGCATGGTCA 59.017 50.000 0.00 0.00 31.31 4.02
2137 2315 1.952367 GCTTGCCTAGTTCTGCATGGT 60.952 52.381 0.00 0.00 37.33 3.55
2138 2316 0.737219 GCTTGCCTAGTTCTGCATGG 59.263 55.000 0.00 0.00 37.33 3.66
2140 2318 3.539604 CTTAGCTTGCCTAGTTCTGCAT 58.460 45.455 0.00 0.00 37.33 3.96
2141 2319 2.936993 GCTTAGCTTGCCTAGTTCTGCA 60.937 50.000 0.00 0.00 35.27 4.41
2144 2322 4.682050 GCTTAGCTTAGCTTGCCTAGTTCT 60.682 45.833 17.24 0.00 40.44 3.01
2145 2323 3.558006 GCTTAGCTTAGCTTGCCTAGTTC 59.442 47.826 17.24 0.00 40.44 3.01
2146 2324 3.536570 GCTTAGCTTAGCTTGCCTAGTT 58.463 45.455 17.24 0.00 40.44 2.24
2147 2325 2.158885 GGCTTAGCTTAGCTTGCCTAGT 60.159 50.000 29.70 4.08 45.93 2.57
2149 2327 2.622064 GGCTTAGCTTAGCTTGCCTA 57.378 50.000 29.70 6.61 45.93 3.93
2152 2330 1.020437 CTGGGCTTAGCTTAGCTTGC 58.980 55.000 22.83 16.73 40.44 4.01
2153 2331 2.698855 TCTGGGCTTAGCTTAGCTTG 57.301 50.000 22.83 13.45 40.44 4.01
2154 2332 3.009584 ACTTTCTGGGCTTAGCTTAGCTT 59.990 43.478 22.83 0.00 40.44 3.74
2155 2333 2.573915 ACTTTCTGGGCTTAGCTTAGCT 59.426 45.455 22.83 12.67 43.41 3.32
2156 2334 2.992593 ACTTTCTGGGCTTAGCTTAGC 58.007 47.619 16.30 16.30 40.48 3.09
2161 2339 1.889170 AGCAAACTTTCTGGGCTTAGC 59.111 47.619 0.00 0.00 0.00 3.09
2165 2343 1.144913 TGGTAGCAAACTTTCTGGGCT 59.855 47.619 0.00 0.00 38.55 5.19
2169 2347 5.296780 TCTTGTCTTGGTAGCAAACTTTCTG 59.703 40.000 8.94 0.00 0.00 3.02
2171 2349 5.751243 TCTTGTCTTGGTAGCAAACTTTC 57.249 39.130 8.94 0.00 0.00 2.62
2173 2351 5.507985 GCAATCTTGTCTTGGTAGCAAACTT 60.508 40.000 8.94 0.00 0.00 2.66
2181 2359 3.423539 AGCAGCAATCTTGTCTTGGTA 57.576 42.857 0.00 0.00 33.32 3.25
2184 2362 2.729882 GCAAAGCAGCAATCTTGTCTTG 59.270 45.455 0.00 0.00 0.00 3.02
2195 2373 2.282674 CCAGAGGGCAAAGCAGCA 60.283 61.111 0.00 0.00 35.83 4.41
2219 2397 2.594303 CTTTGGTGCCACCGAGCA 60.594 61.111 9.78 0.00 42.58 4.26
2222 2400 0.687920 TATCACTTTGGTGCCACCGA 59.312 50.000 9.78 4.10 42.58 4.69
2230 2408 3.821033 GGCAGAGTTGTTATCACTTTGGT 59.179 43.478 0.00 0.00 0.00 3.67
2234 2412 3.067106 CACGGCAGAGTTGTTATCACTT 58.933 45.455 0.00 0.00 0.00 3.16
2236 2414 2.413837 ACACGGCAGAGTTGTTATCAC 58.586 47.619 0.00 0.00 0.00 3.06
2245 2423 1.814394 TGTACGAATACACGGCAGAGT 59.186 47.619 0.00 0.00 36.34 3.24
2246 2424 2.554806 TGTACGAATACACGGCAGAG 57.445 50.000 0.00 0.00 36.34 3.35
2248 2426 2.124903 GGATGTACGAATACACGGCAG 58.875 52.381 0.00 0.00 44.11 4.85
2249 2427 1.752498 AGGATGTACGAATACACGGCA 59.248 47.619 0.00 0.00 44.11 5.69
2270 2448 1.400737 GCTGGTCACCGTCCTATACT 58.599 55.000 0.00 0.00 0.00 2.12
2277 2455 1.153628 ATAAGCGCTGGTCACCGTC 60.154 57.895 12.58 0.00 0.00 4.79
2278 2456 1.447838 CATAAGCGCTGGTCACCGT 60.448 57.895 12.58 0.00 0.00 4.83
2282 2460 2.677836 GTTCAATCATAAGCGCTGGTCA 59.322 45.455 12.58 0.00 0.00 4.02
2294 2472 5.123820 CAGGAATAACCGTGTGTTCAATCAT 59.876 40.000 0.00 0.00 44.74 2.45
2297 2475 3.756434 CCAGGAATAACCGTGTGTTCAAT 59.244 43.478 0.00 0.00 44.74 2.57
2303 2481 0.672401 ACGCCAGGAATAACCGTGTG 60.672 55.000 0.00 0.00 44.74 3.82
2306 2484 1.743995 GCACGCCAGGAATAACCGT 60.744 57.895 0.00 0.00 44.74 4.83
2321 2499 2.833794 TGTGTAGTCACTCTTTGGCAC 58.166 47.619 0.00 0.00 44.14 5.01
2335 2513 6.005583 ACATTCTGATTGTTGCTTGTGTAG 57.994 37.500 0.00 0.00 0.00 2.74
2336 2514 6.039159 TGAACATTCTGATTGTTGCTTGTGTA 59.961 34.615 19.26 0.00 37.43 2.90
2338 2516 5.283294 TGAACATTCTGATTGTTGCTTGTG 58.717 37.500 19.26 0.00 37.43 3.33
2341 2519 7.519328 GCAAATTGAACATTCTGATTGTTGCTT 60.519 33.333 19.26 9.15 37.43 3.91
2350 2528 6.926313 TCATCATGCAAATTGAACATTCTGA 58.074 32.000 0.00 0.00 0.00 3.27
2351 2529 7.201522 CCTTCATCATGCAAATTGAACATTCTG 60.202 37.037 0.00 0.00 0.00 3.02
2357 2535 3.619929 GGCCTTCATCATGCAAATTGAAC 59.380 43.478 0.00 0.00 0.00 3.18
2359 2537 2.832733 TGGCCTTCATCATGCAAATTGA 59.167 40.909 3.32 0.00 0.00 2.57
2362 2540 1.138266 GCTGGCCTTCATCATGCAAAT 59.862 47.619 3.32 0.00 0.00 2.32
2363 2541 0.533491 GCTGGCCTTCATCATGCAAA 59.467 50.000 3.32 0.00 0.00 3.68
2367 2545 4.340097 TCTTTTATGCTGGCCTTCATCATG 59.660 41.667 3.32 0.00 34.46 3.07
2368 2546 4.539726 TCTTTTATGCTGGCCTTCATCAT 58.460 39.130 3.32 2.77 36.36 2.45
2369 2547 3.949754 CTCTTTTATGCTGGCCTTCATCA 59.050 43.478 3.32 0.00 0.00 3.07
2374 2552 1.098050 CGCTCTTTTATGCTGGCCTT 58.902 50.000 3.32 0.00 0.00 4.35
2376 2554 1.064783 GCGCTCTTTTATGCTGGCC 59.935 57.895 0.00 0.00 0.00 5.36
2383 2561 4.213482 ACTTCTTTCAACGCGCTCTTTTAT 59.787 37.500 5.73 0.00 0.00 1.40
2386 2564 1.940613 ACTTCTTTCAACGCGCTCTTT 59.059 42.857 5.73 0.00 0.00 2.52
2388 2566 1.140816 GACTTCTTTCAACGCGCTCT 58.859 50.000 5.73 0.00 0.00 4.09
2393 2571 6.251549 GGATTTATCAGACTTCTTTCAACGC 58.748 40.000 0.00 0.00 0.00 4.84
2401 2579 5.677319 TTCCACGGATTTATCAGACTTCT 57.323 39.130 0.00 0.00 0.00 2.85
2402 2580 6.316390 ACAATTCCACGGATTTATCAGACTTC 59.684 38.462 0.00 0.00 0.00 3.01
2405 2583 7.280205 ACTTACAATTCCACGGATTTATCAGAC 59.720 37.037 0.00 0.00 0.00 3.51
2408 2586 7.225931 GCTACTTACAATTCCACGGATTTATCA 59.774 37.037 0.00 0.00 0.00 2.15
2409 2587 7.225931 TGCTACTTACAATTCCACGGATTTATC 59.774 37.037 0.00 0.00 0.00 1.75
2418 2596 5.123820 TGCTTGATGCTACTTACAATTCCAC 59.876 40.000 0.00 0.00 43.37 4.02
2419 2597 5.252547 TGCTTGATGCTACTTACAATTCCA 58.747 37.500 0.00 0.00 43.37 3.53
2423 2601 5.939883 TGAACTGCTTGATGCTACTTACAAT 59.060 36.000 0.00 0.00 43.37 2.71
2426 2604 5.862924 TTGAACTGCTTGATGCTACTTAC 57.137 39.130 0.00 0.00 43.37 2.34
2431 2609 5.494724 AGAGATTTGAACTGCTTGATGCTA 58.505 37.500 0.00 0.00 43.37 3.49
2435 2613 4.263639 TGGGAGAGATTTGAACTGCTTGAT 60.264 41.667 0.00 0.00 0.00 2.57
2444 2622 1.066143 GCGGTCTGGGAGAGATTTGAA 60.066 52.381 0.00 0.00 31.63 2.69
2450 2628 0.967887 CTTCTGCGGTCTGGGAGAGA 60.968 60.000 0.00 0.00 35.72 3.10
2473 2651 0.961019 TCTGGTTTTGTGATGCAGCC 59.039 50.000 0.00 0.00 0.00 4.85
2474 2652 3.733077 GCTATCTGGTTTTGTGATGCAGC 60.733 47.826 0.00 0.00 0.00 5.25
2475 2653 3.693085 AGCTATCTGGTTTTGTGATGCAG 59.307 43.478 0.00 0.00 0.00 4.41
2482 2660 4.018960 AGTCCATCAGCTATCTGGTTTTGT 60.019 41.667 7.92 0.00 40.69 2.83
2487 2665 3.037851 TGAGTCCATCAGCTATCTGGT 57.962 47.619 7.92 0.00 40.69 4.00
2489 2667 4.213694 GCAATTGAGTCCATCAGCTATCTG 59.786 45.833 10.34 0.00 39.68 2.90
2494 2672 2.366533 CAGCAATTGAGTCCATCAGCT 58.633 47.619 10.34 0.00 39.68 4.24
2507 2685 3.220110 CTGTGATATCTGCCCAGCAATT 58.780 45.455 3.98 0.00 38.41 2.32
2510 2688 1.134310 CACTGTGATATCTGCCCAGCA 60.134 52.381 0.32 0.00 36.92 4.41
2519 2697 3.200483 TGCACATGCTCACTGTGATATC 58.800 45.455 11.45 4.63 45.44 1.63
2528 2706 3.806521 CCTCTATTACTGCACATGCTCAC 59.193 47.826 5.31 0.00 42.66 3.51
2529 2707 3.706086 TCCTCTATTACTGCACATGCTCA 59.294 43.478 5.31 0.00 42.66 4.26
2530 2708 4.054671 GTCCTCTATTACTGCACATGCTC 58.945 47.826 5.31 0.00 42.66 4.26
2531 2709 3.181461 GGTCCTCTATTACTGCACATGCT 60.181 47.826 5.31 0.00 42.66 3.79
2536 2714 3.195825 ACAGTGGTCCTCTATTACTGCAC 59.804 47.826 0.00 0.00 41.74 4.57
2537 2715 3.441101 ACAGTGGTCCTCTATTACTGCA 58.559 45.455 0.00 0.00 41.74 4.41
2539 2717 6.287589 AGAAACAGTGGTCCTCTATTACTG 57.712 41.667 0.00 0.00 43.20 2.74
2542 2720 7.236019 TGGTAAAGAAACAGTGGTCCTCTATTA 59.764 37.037 0.00 0.00 0.00 0.98
2549 2727 6.433093 ACAATATGGTAAAGAAACAGTGGTCC 59.567 38.462 0.00 0.00 0.00 4.46
2558 2736 5.878116 CACTCGGGACAATATGGTAAAGAAA 59.122 40.000 0.00 0.00 0.00 2.52
2576 2754 1.080705 GGGTCGACTGAACACTCGG 60.081 63.158 16.46 0.00 31.55 4.63
2579 2757 0.469331 TCTGGGGTCGACTGAACACT 60.469 55.000 16.46 0.00 35.69 3.55
2582 2760 1.797025 CTTTCTGGGGTCGACTGAAC 58.203 55.000 16.46 4.08 0.00 3.18
2588 2766 1.072505 GTTGGCTTTCTGGGGTCGA 59.927 57.895 0.00 0.00 0.00 4.20
2589 2767 1.971695 GGTTGGCTTTCTGGGGTCG 60.972 63.158 0.00 0.00 0.00 4.79
2591 2769 0.031616 TTTGGTTGGCTTTCTGGGGT 60.032 50.000 0.00 0.00 0.00 4.95
2618 2796 4.469945 CCTGTCATTCCCCTAAAGTACAGA 59.530 45.833 0.00 0.00 36.13 3.41
2624 2802 2.092375 GGACCCTGTCATTCCCCTAAAG 60.092 54.545 0.00 0.00 33.68 1.85
2627 2805 0.327191 GGGACCCTGTCATTCCCCTA 60.327 60.000 2.09 0.00 43.07 3.53
2629 2807 3.007542 GGGACCCTGTCATTCCCC 58.992 66.667 2.09 0.00 43.07 4.81
2633 2811 3.765968 GGTTTGGGACCCTGTCATT 57.234 52.632 13.00 0.00 43.06 2.57
2642 2820 2.983592 CAGCGGTGGGTTTGGGAC 60.984 66.667 6.74 0.00 0.00 4.46
2655 2833 1.337728 TGTGACCAGTGTATTCCAGCG 60.338 52.381 0.00 0.00 0.00 5.18
2658 2836 2.301870 GAGGTGTGACCAGTGTATTCCA 59.698 50.000 0.00 0.00 41.95 3.53
2663 2841 2.375014 TCAGAGGTGTGACCAGTGTA 57.625 50.000 0.00 0.00 41.95 2.90
2664 2842 1.496060 TTCAGAGGTGTGACCAGTGT 58.504 50.000 0.00 0.00 41.95 3.55
2665 2843 2.158900 ACTTTCAGAGGTGTGACCAGTG 60.159 50.000 0.00 0.00 41.95 3.66
2666 2844 2.119495 ACTTTCAGAGGTGTGACCAGT 58.881 47.619 0.00 0.00 41.95 4.00
2670 2848 5.602628 ACTTCTTACTTTCAGAGGTGTGAC 58.397 41.667 0.00 0.00 29.84 3.67
2672 2850 5.237344 CCAACTTCTTACTTTCAGAGGTGTG 59.763 44.000 0.00 0.00 31.34 3.82
2675 2853 5.632034 ACCAACTTCTTACTTTCAGAGGT 57.368 39.130 0.00 0.00 32.20 3.85
2681 2859 7.795734 GCGTACTTTTACCAACTTCTTACTTTC 59.204 37.037 0.00 0.00 0.00 2.62
2684 2862 6.282930 TGCGTACTTTTACCAACTTCTTACT 58.717 36.000 0.00 0.00 0.00 2.24
2685 2863 6.529463 TGCGTACTTTTACCAACTTCTTAC 57.471 37.500 0.00 0.00 0.00 2.34
2690 2868 8.019094 GTGAATATTGCGTACTTTTACCAACTT 58.981 33.333 0.00 0.00 0.00 2.66
2693 2871 7.675962 AGTGAATATTGCGTACTTTTACCAA 57.324 32.000 0.00 0.00 0.00 3.67
2696 2874 9.769093 AATGAAGTGAATATTGCGTACTTTTAC 57.231 29.630 0.00 0.00 32.23 2.01
2726 2904 8.356657 CAGGAACATCGTTTCTCTTCTCTATAT 58.643 37.037 0.00 0.00 0.00 0.86
2729 2907 5.105716 CCAGGAACATCGTTTCTCTTCTCTA 60.106 44.000 0.00 0.00 0.00 2.43
2735 2913 1.625818 AGCCAGGAACATCGTTTCTCT 59.374 47.619 0.00 0.00 0.00 3.10
2740 2918 1.675641 GCCAGCCAGGAACATCGTT 60.676 57.895 0.00 0.00 41.22 3.85
2743 2921 1.028868 GTCTGCCAGCCAGGAACATC 61.029 60.000 0.00 0.00 42.05 3.06
2744 2922 1.001641 GTCTGCCAGCCAGGAACAT 60.002 57.895 0.00 0.00 42.05 2.71
2747 2925 2.293318 ATCGTCTGCCAGCCAGGAA 61.293 57.895 0.00 0.00 42.05 3.36
2750 2928 2.321263 ATCCATCGTCTGCCAGCCAG 62.321 60.000 0.00 0.00 43.17 4.85
2753 2931 1.599542 GTTTATCCATCGTCTGCCAGC 59.400 52.381 0.00 0.00 0.00 4.85
2762 2940 7.790707 ACAATTTTGTTGGGAGTTTATCCATCG 60.791 37.037 0.00 0.00 44.21 3.84
2765 2943 6.553100 AGACAATTTTGTTGGGAGTTTATCCA 59.447 34.615 0.00 0.00 45.62 3.41
2768 2946 6.183360 TGCAGACAATTTTGTTGGGAGTTTAT 60.183 34.615 0.00 0.00 42.43 1.40
2770 2948 4.081198 TGCAGACAATTTTGTTGGGAGTTT 60.081 37.500 0.00 0.00 42.43 2.66
2777 2955 6.448053 CATCTTCTGCAGACAATTTTGTTG 57.552 37.500 18.03 0.71 42.43 3.33
2792 2970 1.004044 ACCTGGGAGTTGCATCTTCTG 59.996 52.381 3.08 2.21 0.00 3.02
2808 2986 2.743928 GACTCAAGCGGCCACCTG 60.744 66.667 2.24 0.00 0.00 4.00
2809 2987 3.241530 TGACTCAAGCGGCCACCT 61.242 61.111 2.24 0.00 0.00 4.00
2810 2988 2.527951 ATCTGACTCAAGCGGCCACC 62.528 60.000 2.24 0.00 0.00 4.61
2811 2989 0.674895 AATCTGACTCAAGCGGCCAC 60.675 55.000 2.24 0.00 0.00 5.01
2812 2990 0.036732 AAATCTGACTCAAGCGGCCA 59.963 50.000 2.24 0.00 0.00 5.36
2813 2991 0.449388 CAAATCTGACTCAAGCGGCC 59.551 55.000 0.00 0.00 0.00 6.13
2814 2992 0.449388 CCAAATCTGACTCAAGCGGC 59.551 55.000 0.00 0.00 0.00 6.53
2815 2993 1.089920 CCCAAATCTGACTCAAGCGG 58.910 55.000 0.00 0.00 0.00 5.52
2816 2994 1.466167 CACCCAAATCTGACTCAAGCG 59.534 52.381 0.00 0.00 0.00 4.68
2817 2995 1.200948 GCACCCAAATCTGACTCAAGC 59.799 52.381 0.00 0.00 0.00 4.01
2818 2996 2.507484 TGCACCCAAATCTGACTCAAG 58.493 47.619 0.00 0.00 0.00 3.02
2819 2997 2.655090 TGCACCCAAATCTGACTCAA 57.345 45.000 0.00 0.00 0.00 3.02
2820 2998 2.655090 TTGCACCCAAATCTGACTCA 57.345 45.000 0.00 0.00 0.00 3.41
2821 2999 3.507233 TCATTTGCACCCAAATCTGACTC 59.493 43.478 0.00 0.00 45.99 3.36
2822 3000 3.499338 TCATTTGCACCCAAATCTGACT 58.501 40.909 0.00 0.00 45.99 3.41
2823 3001 3.940209 TCATTTGCACCCAAATCTGAC 57.060 42.857 0.00 0.00 45.99 3.51
2824 3002 6.183360 GGATATTCATTTGCACCCAAATCTGA 60.183 38.462 0.00 0.00 45.99 3.27
2825 3003 5.987347 GGATATTCATTTGCACCCAAATCTG 59.013 40.000 0.00 0.00 45.99 2.90
2826 3004 5.662208 TGGATATTCATTTGCACCCAAATCT 59.338 36.000 0.00 0.00 45.99 2.40
2827 3005 5.916318 TGGATATTCATTTGCACCCAAATC 58.084 37.500 0.00 0.00 45.99 2.17
2829 3007 5.752036 TTGGATATTCATTTGCACCCAAA 57.248 34.783 0.00 0.00 44.39 3.28
2830 3008 5.752036 TTTGGATATTCATTTGCACCCAA 57.248 34.783 0.00 0.00 0.00 4.12
2831 3009 5.752036 TTTTGGATATTCATTTGCACCCA 57.248 34.783 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.