Multiple sequence alignment - TraesCS7A01G194300

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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 TraesCS7A01G194300 chr7A 100.000 3045 0 0 1 3045 152539401 152542445 0.000000e+00 5624.0
1 TraesCS7A01G194300 chr7A 92.735 234 14 2 2140 2373 112133364 112133594 4.860000e-88 335.0
2 TraesCS7A01G194300 chr7A 88.841 233 22 2 2143 2371 720855633 720855865 1.790000e-72 283.0
3 TraesCS7A01G194300 chr7A 97.561 82 2 0 2293 2374 4784990 4785071 1.140000e-29 141.0
4 TraesCS7A01G194300 chr7A 78.616 159 34 0 1387 1545 620412451 620412293 4.150000e-19 106.0
5 TraesCS7A01G194300 chr7A 89.130 46 4 1 475 519 562894862 562894817 4.240000e-04 56.5
6 TraesCS7A01G194300 chr7B 94.364 1650 55 16 530 2145 114178076 114179721 0.000000e+00 2497.0
7 TraesCS7A01G194300 chr7B 83.276 1166 133 39 967 2093 113770486 113771628 0.000000e+00 1016.0
8 TraesCS7A01G194300 chr7B 87.879 528 33 16 2377 2881 114179709 114180228 2.610000e-165 592.0
9 TraesCS7A01G194300 chr7B 94.286 315 9 2 1 313 114177582 114177889 9.880000e-130 473.0
10 TraesCS7A01G194300 chr7B 92.070 227 14 4 2145 2370 548203805 548203582 1.760000e-82 316.0
11 TraesCS7A01G194300 chr7B 90.756 238 19 2 2139 2373 709324184 709324421 6.340000e-82 315.0
12 TraesCS7A01G194300 chr7B 85.427 199 21 3 1849 2040 113772649 113772846 1.850000e-47 200.0
13 TraesCS7A01G194300 chr7B 77.987 159 35 0 1387 1545 581395682 581395524 1.930000e-17 100.0
14 TraesCS7A01G194300 chr7D 93.457 1452 56 21 719 2145 152120195 152121632 0.000000e+00 2119.0
15 TraesCS7A01G194300 chr7D 82.277 1168 143 42 967 2093 151940671 151939527 0.000000e+00 952.0
16 TraesCS7A01G194300 chr7D 82.889 637 75 18 967 1579 151856654 151856028 2.670000e-150 542.0
17 TraesCS7A01G194300 chr7D 88.069 461 44 8 1641 2093 152098292 152097835 1.240000e-148 536.0
18 TraesCS7A01G194300 chr7D 82.290 655 77 25 967 1593 152099022 152098379 5.780000e-147 531.0
19 TraesCS7A01G194300 chr7D 85.714 462 53 10 1641 2093 151855929 151855472 2.750000e-130 475.0
20 TraesCS7A01G194300 chr7D 88.256 281 19 6 450 729 152118884 152119151 1.050000e-84 324.0
21 TraesCS7A01G194300 chr7D 91.549 213 17 1 2834 3045 152126764 152126976 2.970000e-75 292.0
22 TraesCS7A01G194300 chr7D 92.118 203 8 2 1 203 152118034 152118228 2.310000e-71 279.0
23 TraesCS7A01G194300 chr7D 83.846 260 23 9 201 445 152118651 152118906 2.360000e-56 230.0
24 TraesCS7A01G194300 chr7D 80.866 277 20 15 2448 2692 152125719 152125994 1.440000e-43 187.0
25 TraesCS7A01G194300 chr7D 91.912 136 5 3 2700 2833 152126208 152126339 5.180000e-43 185.0
26 TraesCS7A01G194300 chr7D 78.616 159 34 0 1387 1545 538895309 538895151 4.150000e-19 106.0
27 TraesCS7A01G194300 chr2B 91.915 235 13 4 2143 2372 779349863 779349630 1.050000e-84 324.0
28 TraesCS7A01G194300 chr2B 98.726 157 1 1 2137 2292 798371946 798371790 8.310000e-71 278.0
29 TraesCS7A01G194300 chr4B 90.749 227 19 2 2143 2369 401082555 401082331 4.930000e-78 302.0
30 TraesCS7A01G194300 chr1D 87.013 231 25 4 2143 2369 464400282 464400053 3.900000e-64 255.0
31 TraesCS7A01G194300 chr5D 85.281 231 30 4 2143 2372 544282472 544282245 5.080000e-58 235.0
32 TraesCS7A01G194300 chr1B 92.105 38 3 0 481 518 129884813 129884776 2.000000e-03 54.7


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 TraesCS7A01G194300 chr7A 152539401 152542445 3044 False 5624.000000 5624 100.000000 1 3045 1 chr7A.!!$F3 3044
1 TraesCS7A01G194300 chr7B 114177582 114180228 2646 False 1187.333333 2497 92.176333 1 2881 3 chr7B.!!$F3 2880
2 TraesCS7A01G194300 chr7B 113770486 113772846 2360 False 608.000000 1016 84.351500 967 2093 2 chr7B.!!$F2 1126
3 TraesCS7A01G194300 chr7D 151939527 151940671 1144 True 952.000000 952 82.277000 967 2093 1 chr7D.!!$R1 1126
4 TraesCS7A01G194300 chr7D 152118034 152121632 3598 False 738.000000 2119 89.419250 1 2145 4 chr7D.!!$F1 2144
5 TraesCS7A01G194300 chr7D 152097835 152099022 1187 True 533.500000 536 85.179500 967 2093 2 chr7D.!!$R4 1126
6 TraesCS7A01G194300 chr7D 151855472 151856654 1182 True 508.500000 542 84.301500 967 2093 2 chr7D.!!$R3 1126
7 TraesCS7A01G194300 chr7D 152125719 152126976 1257 False 221.333333 292 88.109000 2448 3045 3 chr7D.!!$F2 597

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
31 32 0.036010 AGTGGGAAGCGAATCTGGTG 60.036 55.0 0.0 0.0 0.00 4.17 F
32 33 0.036388 GTGGGAAGCGAATCTGGTGA 60.036 55.0 0.0 0.0 0.00 4.02 F
861 2379 0.391130 ATGGATGCGTAAGTGCGTGT 60.391 50.0 0.0 0.0 41.68 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1081 2635 0.599204 CACGAGGGCACGTAGTTGTT 60.599 55.000 8.45 0.00 41.61 2.83 R
1626 3305 3.433274 CCTGCGAATATATTGCACGTGAT 59.567 43.478 22.23 7.42 34.42 3.06 R
2229 3937 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.000 4.96 0.00 31.08 2.90 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.036010 AGTGGGAAGCGAATCTGGTG 60.036 55.000 0.00 0.00 0.00 4.17
32 33 0.036388 GTGGGAAGCGAATCTGGTGA 60.036 55.000 0.00 0.00 0.00 4.02
33 34 0.690192 TGGGAAGCGAATCTGGTGAA 59.310 50.000 0.00 0.00 0.00 3.18
34 35 1.087501 GGGAAGCGAATCTGGTGAAC 58.912 55.000 0.00 0.00 0.00 3.18
35 36 1.610624 GGGAAGCGAATCTGGTGAACA 60.611 52.381 0.00 0.00 0.00 3.18
36 37 1.464997 GGAAGCGAATCTGGTGAACAC 59.535 52.381 0.00 0.00 0.00 3.32
37 38 2.417719 GAAGCGAATCTGGTGAACACT 58.582 47.619 4.96 0.00 0.00 3.55
127 128 6.072728 TCCATTGTTTCCAGTAATGAAAGACG 60.073 38.462 0.00 0.00 34.55 4.18
198 199 5.689383 TTATGAGTGACAAAAAGAGGCAC 57.311 39.130 0.00 0.00 0.00 5.01
209 634 5.105392 ACAAAAAGAGGCACAGAACAATGAA 60.105 36.000 0.00 0.00 0.00 2.57
212 637 5.382618 AAGAGGCACAGAACAATGAAATC 57.617 39.130 0.00 0.00 0.00 2.17
374 829 4.607955 TCGCTCGATCACCTAAAGTAATG 58.392 43.478 0.00 0.00 0.00 1.90
421 881 5.244785 TGTAAGCGGACTGATTAGTACTG 57.755 43.478 5.39 0.00 37.25 2.74
442 902 4.973168 TGCCTCTGTCTCAAAATAAGTGT 58.027 39.130 0.00 0.00 0.00 3.55
443 903 5.376625 TGCCTCTGTCTCAAAATAAGTGTT 58.623 37.500 0.00 0.00 0.00 3.32
447 907 7.579726 CCTCTGTCTCAAAATAAGTGTTTCAG 58.420 38.462 0.00 0.00 0.00 3.02
448 908 7.227512 CCTCTGTCTCAAAATAAGTGTTTCAGT 59.772 37.037 0.00 0.00 0.00 3.41
449 909 8.142994 TCTGTCTCAAAATAAGTGTTTCAGTC 57.857 34.615 0.00 0.00 0.00 3.51
450 910 7.987458 TCTGTCTCAAAATAAGTGTTTCAGTCT 59.013 33.333 0.00 0.00 0.00 3.24
451 911 7.919690 TGTCTCAAAATAAGTGTTTCAGTCTG 58.080 34.615 0.00 0.00 0.00 3.51
452 912 7.552687 TGTCTCAAAATAAGTGTTTCAGTCTGT 59.447 33.333 0.00 0.00 0.00 3.41
453 913 7.852945 GTCTCAAAATAAGTGTTTCAGTCTGTG 59.147 37.037 0.00 0.00 0.00 3.66
454 914 7.552687 TCTCAAAATAAGTGTTTCAGTCTGTGT 59.447 33.333 0.00 0.00 0.00 3.72
455 915 7.471721 TCAAAATAAGTGTTTCAGTCTGTGTG 58.528 34.615 0.00 0.00 0.00 3.82
459 919 1.940613 GTGTTTCAGTCTGTGTGTCCC 59.059 52.381 0.00 0.00 0.00 4.46
467 927 5.441500 TCAGTCTGTGTGTCCCAAAATAAA 58.558 37.500 0.00 0.00 0.00 1.40
471 931 6.016276 AGTCTGTGTGTCCCAAAATAAATGTC 60.016 38.462 0.00 0.00 0.00 3.06
480 940 9.802039 TGTCCCAAAATAAATGTCTTAAGTACT 57.198 29.630 1.63 0.00 0.00 2.73
510 970 7.275920 AGTTGAGACACTTATTTTCAGACAGT 58.724 34.615 0.00 0.00 0.00 3.55
511 971 7.770897 AGTTGAGACACTTATTTTCAGACAGTT 59.229 33.333 0.00 0.00 0.00 3.16
523 983 4.761235 TCAGACAGTTGGAGTACTAACG 57.239 45.455 0.00 0.00 41.31 3.18
582 1042 5.427036 TCGTTGGGAGTGTTTTTATGTTC 57.573 39.130 0.00 0.00 0.00 3.18
592 1052 7.873505 GGAGTGTTTTTATGTTCTCTCTACACT 59.126 37.037 0.00 0.00 44.35 3.55
677 1137 4.407621 TGCCCTAATCAAAGACCGAGAATA 59.592 41.667 0.00 0.00 0.00 1.75
737 2250 3.868077 CAGTGCTACTAAGAACCATGAGC 59.132 47.826 0.00 0.00 30.48 4.26
741 2254 3.118592 GCTACTAAGAACCATGAGCCTGT 60.119 47.826 0.00 0.00 0.00 4.00
765 2279 7.095102 TGTCTAGTGTTTGTGAATGTGATCATG 60.095 37.037 0.00 0.00 34.19 3.07
861 2379 0.391130 ATGGATGCGTAAGTGCGTGT 60.391 50.000 0.00 0.00 41.68 4.49
905 2446 0.503117 GCCGAATCGATCTAACGTGC 59.497 55.000 3.36 5.44 34.70 5.34
906 2447 1.835121 CCGAATCGATCTAACGTGCA 58.165 50.000 3.36 0.00 34.70 4.57
935 2476 2.217038 ACGCAGTCCACACCTCCAT 61.217 57.895 0.00 0.00 29.74 3.41
1378 2948 0.947244 GGAAGCACCTTATGATGGCG 59.053 55.000 0.00 0.00 35.41 5.69
1626 3305 6.487668 TCAACTTGCATTGAAATCTGAAGAGA 59.512 34.615 0.18 0.00 35.65 3.10
2048 3731 2.101415 TGCAGCTACACTACATAGCCTG 59.899 50.000 0.00 1.10 45.20 4.85
2049 3732 2.546795 GCAGCTACACTACATAGCCTGG 60.547 54.545 0.49 0.00 45.20 4.45
2051 3734 3.889538 CAGCTACACTACATAGCCTGGTA 59.110 47.826 0.00 0.00 45.20 3.25
2059 3742 4.828387 ACTACATAGCCTGGTACTAGCTTC 59.172 45.833 0.00 0.00 38.30 3.86
2067 3754 3.635373 CCTGGTACTAGCTTCGTTGGATA 59.365 47.826 0.00 0.00 0.00 2.59
2111 3819 4.584325 TGGTTATGCATGATTAAAGGAGGC 59.416 41.667 10.16 0.00 0.00 4.70
2130 3838 3.492102 GCCCTCAGCCAATATGTTAGA 57.508 47.619 0.00 0.00 34.35 2.10
2131 3839 3.820557 GCCCTCAGCCAATATGTTAGAA 58.179 45.455 0.00 0.00 34.35 2.10
2133 3841 4.457257 GCCCTCAGCCAATATGTTAGAATC 59.543 45.833 0.00 0.00 34.35 2.52
2134 3842 4.692625 CCCTCAGCCAATATGTTAGAATCG 59.307 45.833 0.00 0.00 0.00 3.34
2135 3843 5.511373 CCCTCAGCCAATATGTTAGAATCGA 60.511 44.000 0.00 0.00 0.00 3.59
2136 3844 5.991606 CCTCAGCCAATATGTTAGAATCGAA 59.008 40.000 0.00 0.00 0.00 3.71
2137 3845 6.652481 CCTCAGCCAATATGTTAGAATCGAAT 59.348 38.462 0.00 0.00 0.00 3.34
2138 3846 7.819415 CCTCAGCCAATATGTTAGAATCGAATA 59.181 37.037 0.00 0.00 0.00 1.75
2139 3847 9.208022 CTCAGCCAATATGTTAGAATCGAATAA 57.792 33.333 0.00 0.00 0.00 1.40
2140 3848 9.725019 TCAGCCAATATGTTAGAATCGAATAAT 57.275 29.630 0.00 0.00 0.00 1.28
2168 3876 3.917988 TGAGCATCAGTACAGACACAAG 58.082 45.455 0.00 0.00 42.56 3.16
2169 3877 2.670414 GAGCATCAGTACAGACACAAGC 59.330 50.000 0.00 0.00 33.17 4.01
2170 3878 1.391485 GCATCAGTACAGACACAAGCG 59.609 52.381 0.00 0.00 0.00 4.68
2171 3879 1.391485 CATCAGTACAGACACAAGCGC 59.609 52.381 0.00 0.00 0.00 5.92
2172 3880 0.673985 TCAGTACAGACACAAGCGCT 59.326 50.000 2.64 2.64 0.00 5.92
2173 3881 1.063806 CAGTACAGACACAAGCGCTC 58.936 55.000 12.06 0.00 0.00 5.03
2174 3882 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
2175 3883 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
2176 3884 2.492088 AGTACAGACACAAGCGCTCATA 59.508 45.455 12.06 0.00 0.00 2.15
2177 3885 2.680312 ACAGACACAAGCGCTCATAT 57.320 45.000 12.06 0.00 0.00 1.78
2178 3886 3.801114 ACAGACACAAGCGCTCATATA 57.199 42.857 12.06 0.00 0.00 0.86
2179 3887 3.448686 ACAGACACAAGCGCTCATATAC 58.551 45.455 12.06 1.00 0.00 1.47
2180 3888 3.119137 ACAGACACAAGCGCTCATATACA 60.119 43.478 12.06 0.00 0.00 2.29
2181 3889 3.243877 CAGACACAAGCGCTCATATACAC 59.756 47.826 12.06 0.00 0.00 2.90
2182 3890 2.193447 ACACAAGCGCTCATATACACG 58.807 47.619 12.06 0.00 0.00 4.49
2186 3894 3.916439 CGCTCATATACACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
2187 3895 2.434688 CGCTCATATACACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
2188 3896 1.613270 CGCTCATATACACGCGCATA 58.387 50.000 5.73 1.53 39.11 3.14
2189 3897 1.317611 CGCTCATATACACGCGCATAC 59.682 52.381 5.73 0.00 39.11 2.39
2190 3898 2.324860 GCTCATATACACGCGCATACA 58.675 47.619 5.73 0.00 0.00 2.29
2191 3899 2.090658 GCTCATATACACGCGCATACAC 59.909 50.000 5.73 0.00 0.00 2.90
2192 3900 3.565516 CTCATATACACGCGCATACACT 58.434 45.455 5.73 0.00 0.00 3.55
2193 3901 3.561503 TCATATACACGCGCATACACTC 58.438 45.455 5.73 0.00 0.00 3.51
2194 3902 3.003897 TCATATACACGCGCATACACTCA 59.996 43.478 5.73 0.00 0.00 3.41
2195 3903 1.556564 ATACACGCGCATACACTCAC 58.443 50.000 5.73 0.00 0.00 3.51
2196 3904 0.457166 TACACGCGCATACACTCACC 60.457 55.000 5.73 0.00 0.00 4.02
2197 3905 2.125673 ACGCGCATACACTCACCC 60.126 61.111 5.73 0.00 0.00 4.61
2198 3906 3.254654 CGCGCATACACTCACCCG 61.255 66.667 8.75 0.00 0.00 5.28
2199 3907 2.125673 GCGCATACACTCACCCGT 60.126 61.111 0.30 0.00 0.00 5.28
2200 3908 1.140161 GCGCATACACTCACCCGTA 59.860 57.895 0.30 0.00 0.00 4.02
2201 3909 0.249322 GCGCATACACTCACCCGTAT 60.249 55.000 0.30 0.00 0.00 3.06
2202 3910 1.487482 CGCATACACTCACCCGTATG 58.513 55.000 0.00 0.00 45.07 2.39
2203 3911 1.066454 CGCATACACTCACCCGTATGA 59.934 52.381 12.46 0.00 45.09 2.15
2204 3912 2.480587 CGCATACACTCACCCGTATGAA 60.481 50.000 12.46 0.00 45.09 2.57
2205 3913 2.864343 GCATACACTCACCCGTATGAAC 59.136 50.000 12.46 0.00 45.09 3.18
2206 3914 3.113322 CATACACTCACCCGTATGAACG 58.887 50.000 3.96 0.00 45.09 3.95
2214 3922 4.997419 CGTATGAACGCACACACG 57.003 55.556 0.00 0.00 43.12 4.49
2215 3923 1.225368 CGTATGAACGCACACACGC 60.225 57.895 0.86 0.00 43.12 5.34
2216 3924 1.856688 GTATGAACGCACACACGCA 59.143 52.632 0.00 0.00 36.19 5.24
2217 3925 0.450482 GTATGAACGCACACACGCAC 60.450 55.000 0.00 0.00 36.19 5.34
2218 3926 0.876342 TATGAACGCACACACGCACA 60.876 50.000 0.00 0.00 36.19 4.57
2219 3927 2.350760 GAACGCACACACGCACAC 60.351 61.111 0.00 0.00 36.19 3.82
2220 3928 3.783588 GAACGCACACACGCACACC 62.784 63.158 0.00 0.00 36.19 4.16
2223 3931 2.280524 GCACACACGCACACCCTA 60.281 61.111 0.00 0.00 0.00 3.53
2224 3932 2.604174 GCACACACGCACACCCTAC 61.604 63.158 0.00 0.00 0.00 3.18
2225 3933 1.959226 CACACACGCACACCCTACC 60.959 63.158 0.00 0.00 0.00 3.18
2226 3934 2.358247 CACACGCACACCCTACCC 60.358 66.667 0.00 0.00 0.00 3.69
2227 3935 3.633116 ACACGCACACCCTACCCC 61.633 66.667 0.00 0.00 0.00 4.95
2228 3936 3.319198 CACGCACACCCTACCCCT 61.319 66.667 0.00 0.00 0.00 4.79
2229 3937 1.985662 CACGCACACCCTACCCCTA 60.986 63.158 0.00 0.00 0.00 3.53
2230 3938 1.002533 ACGCACACCCTACCCCTAT 59.997 57.895 0.00 0.00 0.00 2.57
2231 3939 1.335132 ACGCACACCCTACCCCTATG 61.335 60.000 0.00 0.00 0.00 2.23
2232 3940 1.046472 CGCACACCCTACCCCTATGA 61.046 60.000 0.00 0.00 0.00 2.15
2233 3941 0.759346 GCACACCCTACCCCTATGAG 59.241 60.000 0.00 0.00 0.00 2.90
2234 3942 0.759346 CACACCCTACCCCTATGAGC 59.241 60.000 0.00 0.00 0.00 4.26
2235 3943 0.341961 ACACCCTACCCCTATGAGCA 59.658 55.000 0.00 0.00 0.00 4.26
2236 3944 0.759346 CACCCTACCCCTATGAGCAC 59.241 60.000 0.00 0.00 0.00 4.40
2237 3945 0.400093 ACCCTACCCCTATGAGCACC 60.400 60.000 0.00 0.00 0.00 5.01
2238 3946 0.104934 CCCTACCCCTATGAGCACCT 60.105 60.000 0.00 0.00 0.00 4.00
2239 3947 1.343069 CCTACCCCTATGAGCACCTC 58.657 60.000 0.00 0.00 0.00 3.85
2240 3948 1.343069 CTACCCCTATGAGCACCTCC 58.657 60.000 0.00 0.00 0.00 4.30
2241 3949 0.469331 TACCCCTATGAGCACCTCCG 60.469 60.000 0.00 0.00 0.00 4.63
2242 3950 1.457643 CCCCTATGAGCACCTCCGA 60.458 63.158 0.00 0.00 0.00 4.55
2243 3951 1.467678 CCCCTATGAGCACCTCCGAG 61.468 65.000 0.00 0.00 0.00 4.63
2244 3952 0.468214 CCCTATGAGCACCTCCGAGA 60.468 60.000 0.00 0.00 0.00 4.04
2245 3953 0.958091 CCTATGAGCACCTCCGAGAG 59.042 60.000 0.00 0.00 0.00 3.20
2246 3954 1.477740 CCTATGAGCACCTCCGAGAGA 60.478 57.143 0.00 0.00 0.00 3.10
2247 3955 1.606668 CTATGAGCACCTCCGAGAGAC 59.393 57.143 0.00 0.00 0.00 3.36
2248 3956 0.033601 ATGAGCACCTCCGAGAGACT 60.034 55.000 0.00 0.00 0.00 3.24
2249 3957 0.962855 TGAGCACCTCCGAGAGACTG 60.963 60.000 0.00 0.22 0.00 3.51
2250 3958 0.678366 GAGCACCTCCGAGAGACTGA 60.678 60.000 0.00 0.00 0.00 3.41
2251 3959 0.679640 AGCACCTCCGAGAGACTGAG 60.680 60.000 0.00 0.00 0.00 3.35
2252 3960 1.806568 CACCTCCGAGAGACTGAGC 59.193 63.158 0.00 0.00 0.00 4.26
2253 3961 1.379309 ACCTCCGAGAGACTGAGCC 60.379 63.158 0.00 0.00 0.00 4.70
2254 3962 2.477176 CCTCCGAGAGACTGAGCCG 61.477 68.421 0.00 0.00 0.00 5.52
2255 3963 2.438614 TCCGAGAGACTGAGCCGG 60.439 66.667 0.00 0.00 41.36 6.13
2256 3964 4.200283 CCGAGAGACTGAGCCGGC 62.200 72.222 21.89 21.89 33.47 6.13
2257 3965 3.443925 CGAGAGACTGAGCCGGCA 61.444 66.667 31.54 7.98 0.00 5.69
2258 3966 2.780094 CGAGAGACTGAGCCGGCAT 61.780 63.158 31.54 14.28 0.00 4.40
2259 3967 1.448119 CGAGAGACTGAGCCGGCATA 61.448 60.000 31.54 16.21 0.00 3.14
2260 3968 0.965439 GAGAGACTGAGCCGGCATAT 59.035 55.000 31.54 8.11 0.00 1.78
2261 3969 0.965439 AGAGACTGAGCCGGCATATC 59.035 55.000 31.54 18.63 0.00 1.63
2262 3970 0.676184 GAGACTGAGCCGGCATATCA 59.324 55.000 31.54 22.44 0.00 2.15
2263 3971 1.274728 GAGACTGAGCCGGCATATCAT 59.725 52.381 31.54 13.17 0.00 2.45
2264 3972 1.274728 AGACTGAGCCGGCATATCATC 59.725 52.381 31.54 19.98 0.00 2.92
2265 3973 1.274728 GACTGAGCCGGCATATCATCT 59.725 52.381 31.54 11.40 0.00 2.90
2266 3974 1.696336 ACTGAGCCGGCATATCATCTT 59.304 47.619 31.54 3.33 0.00 2.40
2267 3975 2.074576 CTGAGCCGGCATATCATCTTG 58.925 52.381 31.54 7.95 0.00 3.02
2268 3976 1.693606 TGAGCCGGCATATCATCTTGA 59.306 47.619 31.54 0.00 0.00 3.02
2269 3977 2.289257 TGAGCCGGCATATCATCTTGAG 60.289 50.000 31.54 0.00 0.00 3.02
2270 3978 1.973515 AGCCGGCATATCATCTTGAGA 59.026 47.619 31.54 0.00 0.00 3.27
2271 3979 2.570752 AGCCGGCATATCATCTTGAGAT 59.429 45.455 31.54 0.00 34.56 2.75
2272 3980 3.008813 AGCCGGCATATCATCTTGAGATT 59.991 43.478 31.54 0.00 31.21 2.40
2273 3981 3.755378 GCCGGCATATCATCTTGAGATTT 59.245 43.478 24.80 0.00 31.21 2.17
2274 3982 4.937620 GCCGGCATATCATCTTGAGATTTA 59.062 41.667 24.80 0.00 31.21 1.40
2275 3983 5.163814 GCCGGCATATCATCTTGAGATTTAC 60.164 44.000 24.80 0.00 31.21 2.01
2276 3984 5.062683 CCGGCATATCATCTTGAGATTTACG 59.937 44.000 0.00 0.00 31.21 3.18
2277 3985 5.863935 CGGCATATCATCTTGAGATTTACGA 59.136 40.000 0.00 0.00 31.21 3.43
2278 3986 6.366061 CGGCATATCATCTTGAGATTTACGAA 59.634 38.462 0.00 0.00 31.21 3.85
2279 3987 7.411264 CGGCATATCATCTTGAGATTTACGAAG 60.411 40.741 0.00 0.00 31.21 3.79
2280 3988 7.386299 GGCATATCATCTTGAGATTTACGAAGT 59.614 37.037 0.00 0.00 37.29 3.01
2281 3989 8.431593 GCATATCATCTTGAGATTTACGAAGTC 58.568 37.037 0.00 0.00 35.39 3.01
2282 3990 9.468532 CATATCATCTTGAGATTTACGAAGTCA 57.531 33.333 0.00 0.00 35.39 3.41
2283 3991 7.763172 ATCATCTTGAGATTTACGAAGTCAC 57.237 36.000 0.00 0.00 35.39 3.67
2284 3992 6.100004 TCATCTTGAGATTTACGAAGTCACC 58.900 40.000 0.00 0.00 35.39 4.02
2285 3993 4.482386 TCTTGAGATTTACGAAGTCACCG 58.518 43.478 0.00 0.00 43.93 4.94
2286 3994 3.928727 TGAGATTTACGAAGTCACCGT 57.071 42.857 0.00 0.00 43.93 4.83
2287 3995 5.181811 TCTTGAGATTTACGAAGTCACCGTA 59.818 40.000 0.00 0.00 43.93 4.02
2288 3996 4.978186 TGAGATTTACGAAGTCACCGTAG 58.022 43.478 0.00 0.00 43.93 3.51
2301 4009 4.778415 CGTAGGCGTGCGAGCAGT 62.778 66.667 11.59 0.00 39.27 4.40
2302 4010 2.488355 GTAGGCGTGCGAGCAGTA 59.512 61.111 0.00 0.00 39.27 2.74
2303 4011 1.586564 GTAGGCGTGCGAGCAGTAG 60.587 63.158 0.00 0.00 39.27 2.57
2304 4012 2.771639 TAGGCGTGCGAGCAGTAGG 61.772 63.158 0.00 0.00 39.27 3.18
2305 4013 4.129737 GGCGTGCGAGCAGTAGGA 62.130 66.667 0.00 0.00 39.27 2.94
2306 4014 2.105128 GCGTGCGAGCAGTAGGAT 59.895 61.111 0.00 0.00 37.05 3.24
2307 4015 1.519455 GCGTGCGAGCAGTAGGATT 60.519 57.895 0.00 0.00 37.05 3.01
2308 4016 1.084370 GCGTGCGAGCAGTAGGATTT 61.084 55.000 0.00 0.00 37.05 2.17
2309 4017 0.647410 CGTGCGAGCAGTAGGATTTG 59.353 55.000 0.00 0.00 0.00 2.32
2310 4018 1.735700 CGTGCGAGCAGTAGGATTTGA 60.736 52.381 0.00 0.00 0.00 2.69
2311 4019 2.346803 GTGCGAGCAGTAGGATTTGAA 58.653 47.619 0.00 0.00 0.00 2.69
2312 4020 2.094417 GTGCGAGCAGTAGGATTTGAAC 59.906 50.000 0.00 0.00 0.00 3.18
2313 4021 1.666189 GCGAGCAGTAGGATTTGAACC 59.334 52.381 0.00 0.00 0.00 3.62
2314 4022 2.280628 CGAGCAGTAGGATTTGAACCC 58.719 52.381 0.00 0.00 0.00 4.11
2315 4023 2.093447 CGAGCAGTAGGATTTGAACCCT 60.093 50.000 0.00 0.00 36.60 4.34
2316 4024 3.274288 GAGCAGTAGGATTTGAACCCTG 58.726 50.000 0.00 0.00 34.11 4.45
2317 4025 2.025887 AGCAGTAGGATTTGAACCCTGG 60.026 50.000 0.00 0.00 34.11 4.45
2318 4026 2.290960 GCAGTAGGATTTGAACCCTGGT 60.291 50.000 0.00 0.00 34.11 4.00
2319 4027 3.347216 CAGTAGGATTTGAACCCTGGTG 58.653 50.000 0.00 0.00 34.11 4.17
2320 4028 2.308866 AGTAGGATTTGAACCCTGGTGG 59.691 50.000 0.00 0.00 41.37 4.61
2330 4038 4.179896 CCTGGTGGGTTGGGGATA 57.820 61.111 0.00 0.00 0.00 2.59
2331 4039 1.613061 CCTGGTGGGTTGGGGATAC 59.387 63.158 0.00 0.00 0.00 2.24
2346 4054 3.538634 GGATACCACTGTCCACCTAAC 57.461 52.381 0.00 0.00 34.57 2.34
2347 4055 2.169978 GGATACCACTGTCCACCTAACC 59.830 54.545 0.00 0.00 34.57 2.85
2348 4056 2.402182 TACCACTGTCCACCTAACCA 57.598 50.000 0.00 0.00 0.00 3.67
2349 4057 1.513858 ACCACTGTCCACCTAACCAA 58.486 50.000 0.00 0.00 0.00 3.67
2350 4058 1.142262 ACCACTGTCCACCTAACCAAC 59.858 52.381 0.00 0.00 0.00 3.77
2351 4059 1.420138 CCACTGTCCACCTAACCAACT 59.580 52.381 0.00 0.00 0.00 3.16
2352 4060 2.550208 CCACTGTCCACCTAACCAACTC 60.550 54.545 0.00 0.00 0.00 3.01
2353 4061 2.104111 CACTGTCCACCTAACCAACTCA 59.896 50.000 0.00 0.00 0.00 3.41
2354 4062 2.775384 ACTGTCCACCTAACCAACTCAA 59.225 45.455 0.00 0.00 0.00 3.02
2355 4063 3.139077 CTGTCCACCTAACCAACTCAAC 58.861 50.000 0.00 0.00 0.00 3.18
2356 4064 2.158726 TGTCCACCTAACCAACTCAACC 60.159 50.000 0.00 0.00 0.00 3.77
2357 4065 2.128535 TCCACCTAACCAACTCAACCA 58.871 47.619 0.00 0.00 0.00 3.67
2358 4066 2.158726 TCCACCTAACCAACTCAACCAC 60.159 50.000 0.00 0.00 0.00 4.16
2359 4067 2.422235 CCACCTAACCAACTCAACCACA 60.422 50.000 0.00 0.00 0.00 4.17
2360 4068 2.878406 CACCTAACCAACTCAACCACAG 59.122 50.000 0.00 0.00 0.00 3.66
2361 4069 2.158667 ACCTAACCAACTCAACCACAGG 60.159 50.000 0.00 0.00 0.00 4.00
2362 4070 2.158667 CCTAACCAACTCAACCACAGGT 60.159 50.000 0.00 0.00 37.65 4.00
2371 4079 3.725754 AACCACAGGTTGATTCGCT 57.274 47.368 0.00 0.00 45.07 4.93
2372 4080 2.851263 AACCACAGGTTGATTCGCTA 57.149 45.000 0.00 0.00 45.07 4.26
2373 4081 2.386661 ACCACAGGTTGATTCGCTAG 57.613 50.000 0.00 0.00 27.29 3.42
2374 4082 1.899814 ACCACAGGTTGATTCGCTAGA 59.100 47.619 0.00 0.00 27.29 2.43
2375 4083 2.301870 ACCACAGGTTGATTCGCTAGAA 59.698 45.455 0.00 0.00 34.55 2.10
2427 4139 9.760077 GTGGGATCGTCTCTTTTAATTCTTATA 57.240 33.333 0.00 0.00 0.00 0.98
2507 4225 1.082954 ATGGGTGGTGGACTAGCCT 59.917 57.895 11.99 0.00 44.12 4.58
2508 4226 0.550147 ATGGGTGGTGGACTAGCCTT 60.550 55.000 11.99 3.82 44.12 4.35
2560 4752 8.286800 CCAATTGATTTCAACACTTCTACGTAA 58.713 33.333 7.12 0.00 38.86 3.18
2563 4755 7.633361 TGATTTCAACACTTCTACGTAAGAC 57.367 36.000 5.10 0.00 43.62 3.01
2566 4758 3.890756 TCAACACTTCTACGTAAGACCCA 59.109 43.478 5.10 0.00 43.62 4.51
2567 4759 3.930634 ACACTTCTACGTAAGACCCAC 57.069 47.619 5.10 0.00 43.62 4.61
2669 4897 1.440893 CTCGCAGTGATCCCTCCTG 59.559 63.158 0.00 0.00 0.00 3.86
2673 4901 0.908198 GCAGTGATCCCTCCTGTTCT 59.092 55.000 0.00 0.00 0.00 3.01
2825 5482 5.423886 ACCATTGTCCAAACATTTCGTTTT 58.576 33.333 0.00 0.00 45.79 2.43
2872 5953 9.603921 ACAAGAAAAATGACAAATCAGAATGTT 57.396 25.926 0.00 0.00 38.57 2.71
2933 6014 4.019919 CACAGTTGGATTTGCCTATTCG 57.980 45.455 0.00 0.00 37.63 3.34
2943 6024 3.546002 TTGCCTATTCGTTTTTCACCG 57.454 42.857 0.00 0.00 0.00 4.94
2972 6053 5.572896 GTGAATAAAAGCCGGTCTTGAATTG 59.427 40.000 1.90 0.00 34.67 2.32
2973 6054 2.438868 AAAAGCCGGTCTTGAATTGC 57.561 45.000 1.90 0.00 34.67 3.56
3037 6119 9.959749 AAAAATCAAGAACTTTTAGATTACGCA 57.040 25.926 0.00 0.00 0.00 5.24
3040 6122 7.303634 TCAAGAACTTTTAGATTACGCATCC 57.696 36.000 0.00 0.00 31.20 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.289002 CAGATTCGCTTCCCACTTATGC 59.711 50.000 0.00 0.00 0.00 3.14
31 32 2.508526 AGAATTGCCTGGTCAGTGTTC 58.491 47.619 0.00 1.44 0.00 3.18
32 33 2.664402 AGAATTGCCTGGTCAGTGTT 57.336 45.000 0.00 0.00 0.00 3.32
33 34 3.560025 CCTTAGAATTGCCTGGTCAGTGT 60.560 47.826 0.00 0.00 0.00 3.55
34 35 3.012518 CCTTAGAATTGCCTGGTCAGTG 58.987 50.000 0.00 0.00 0.00 3.66
35 36 2.619074 GCCTTAGAATTGCCTGGTCAGT 60.619 50.000 0.00 0.00 0.00 3.41
36 37 2.019984 GCCTTAGAATTGCCTGGTCAG 58.980 52.381 0.00 0.00 0.00 3.51
37 38 1.340991 GGCCTTAGAATTGCCTGGTCA 60.341 52.381 0.00 0.00 42.01 4.02
99 100 6.573664 TTCATTACTGGAAACAATGGACAG 57.426 37.500 0.00 0.00 42.06 3.51
127 128 1.444895 CGGTGCTCAATTGGCTTGC 60.445 57.895 16.52 11.58 34.66 4.01
198 199 7.088272 TGCATGAAAGAGATTTCATTGTTCTG 58.912 34.615 12.31 4.92 46.24 3.02
209 634 2.163815 GCTGTGCTGCATGAAAGAGATT 59.836 45.455 5.27 0.00 0.00 2.40
212 637 1.166129 AGCTGTGCTGCATGAAAGAG 58.834 50.000 5.27 0.00 37.57 2.85
328 780 5.988310 TCTGTCCTAGTTTCGGTTTATGA 57.012 39.130 0.00 0.00 0.00 2.15
345 797 1.066303 AGGTGATCGAGCGATTCTGTC 59.934 52.381 6.84 0.00 34.60 3.51
346 798 1.107114 AGGTGATCGAGCGATTCTGT 58.893 50.000 6.84 0.00 34.60 3.41
397 852 6.514541 GCAGTACTAATCAGTCCGCTTACATA 60.515 42.308 0.00 0.00 36.14 2.29
406 861 3.702045 ACAGAGGCAGTACTAATCAGTCC 59.298 47.826 0.00 0.00 36.14 3.85
411 866 5.584253 TTGAGACAGAGGCAGTACTAATC 57.416 43.478 0.00 0.00 0.00 1.75
421 881 5.948992 AACACTTATTTTGAGACAGAGGC 57.051 39.130 0.00 0.00 0.00 4.70
442 902 3.358111 TTTGGGACACACAGACTGAAA 57.642 42.857 10.08 0.00 39.29 2.69
443 903 3.358111 TTTTGGGACACACAGACTGAA 57.642 42.857 10.08 0.00 39.29 3.02
447 907 6.016276 AGACATTTATTTTGGGACACACAGAC 60.016 38.462 0.00 0.00 39.29 3.51
448 908 6.068010 AGACATTTATTTTGGGACACACAGA 58.932 36.000 0.00 0.00 39.29 3.41
449 909 6.331369 AGACATTTATTTTGGGACACACAG 57.669 37.500 0.00 0.00 39.29 3.66
450 910 6.723298 AAGACATTTATTTTGGGACACACA 57.277 33.333 0.00 0.00 39.29 3.72
451 911 8.357402 ACTTAAGACATTTATTTTGGGACACAC 58.643 33.333 10.09 0.00 39.29 3.82
452 912 8.472007 ACTTAAGACATTTATTTTGGGACACA 57.528 30.769 10.09 0.00 39.29 3.72
453 913 9.836076 GTACTTAAGACATTTATTTTGGGACAC 57.164 33.333 10.09 0.00 39.29 3.67
454 914 9.802039 AGTACTTAAGACATTTATTTTGGGACA 57.198 29.630 10.09 0.00 0.00 4.02
467 927 9.694137 GTCTCAACTTTGTAGTACTTAAGACAT 57.306 33.333 10.09 0.00 33.17 3.06
471 931 9.530633 AAGTGTCTCAACTTTGTAGTACTTAAG 57.469 33.333 0.00 0.00 37.05 1.85
480 940 9.607988 TCTGAAAATAAGTGTCTCAACTTTGTA 57.392 29.630 0.00 0.00 40.77 2.41
481 941 8.398665 GTCTGAAAATAAGTGTCTCAACTTTGT 58.601 33.333 0.00 0.00 40.77 2.83
482 942 8.397906 TGTCTGAAAATAAGTGTCTCAACTTTG 58.602 33.333 0.00 0.00 40.77 2.77
503 963 4.761235 TCGTTAGTACTCCAACTGTCTG 57.239 45.455 0.00 0.00 0.00 3.51
677 1137 2.293677 TTGCTGATTCAGACGCGTAT 57.706 45.000 13.97 5.94 32.44 3.06
714 1174 3.861840 TCATGGTTCTTAGTAGCACTGC 58.138 45.455 0.00 0.00 0.00 4.40
737 2250 5.056480 TCACATTCACAAACACTAGACAGG 58.944 41.667 0.00 0.00 0.00 4.00
741 2254 7.160726 TCATGATCACATTCACAAACACTAGA 58.839 34.615 0.00 0.00 34.15 2.43
765 2279 2.306847 TCCAGTTTGGGTCTTTGCTTC 58.693 47.619 0.00 0.00 38.32 3.86
905 2446 1.409412 GACTGCGTGTCTAGTGTGTG 58.591 55.000 2.87 0.00 42.21 3.82
906 2447 0.314302 GGACTGCGTGTCTAGTGTGT 59.686 55.000 9.09 0.00 44.74 3.72
935 2476 7.996066 TCTTGCTTTATACTTGGCCATGTAATA 59.004 33.333 29.18 19.19 0.00 0.98
1081 2635 0.599204 CACGAGGGCACGTAGTTGTT 60.599 55.000 8.45 0.00 41.61 2.83
1626 3305 3.433274 CCTGCGAATATATTGCACGTGAT 59.567 43.478 22.23 7.42 34.42 3.06
2041 3724 2.946785 ACGAAGCTAGTACCAGGCTAT 58.053 47.619 5.47 0.00 35.06 2.97
2048 3731 5.511234 TCTTATCCAACGAAGCTAGTACC 57.489 43.478 0.00 0.00 0.00 3.34
2049 3732 5.852229 CGATCTTATCCAACGAAGCTAGTAC 59.148 44.000 0.00 0.00 0.00 2.73
2051 3734 4.579340 TCGATCTTATCCAACGAAGCTAGT 59.421 41.667 0.00 0.00 0.00 2.57
2059 3742 7.932120 AACTAGAAATCGATCTTATCCAACG 57.068 36.000 0.00 0.00 0.00 4.10
2111 3819 4.692625 CGATTCTAACATATTGGCTGAGGG 59.307 45.833 0.00 0.00 0.00 4.30
2143 3851 5.122519 TGTGTCTGTACTGATGCTCAAAAA 58.877 37.500 5.69 0.00 0.00 1.94
2144 3852 4.702831 TGTGTCTGTACTGATGCTCAAAA 58.297 39.130 5.69 0.00 0.00 2.44
2145 3853 4.335400 TGTGTCTGTACTGATGCTCAAA 57.665 40.909 5.69 0.00 0.00 2.69
2146 3854 4.309933 CTTGTGTCTGTACTGATGCTCAA 58.690 43.478 5.69 6.69 0.00 3.02
2147 3855 3.862264 GCTTGTGTCTGTACTGATGCTCA 60.862 47.826 5.69 0.00 0.00 4.26
2148 3856 2.670414 GCTTGTGTCTGTACTGATGCTC 59.330 50.000 5.69 0.00 0.00 4.26
2149 3857 2.693069 GCTTGTGTCTGTACTGATGCT 58.307 47.619 5.69 0.00 0.00 3.79
2150 3858 1.391485 CGCTTGTGTCTGTACTGATGC 59.609 52.381 5.69 3.20 0.00 3.91
2151 3859 1.391485 GCGCTTGTGTCTGTACTGATG 59.609 52.381 0.00 0.00 0.00 3.07
2152 3860 1.273606 AGCGCTTGTGTCTGTACTGAT 59.726 47.619 2.64 0.00 0.00 2.90
2153 3861 0.673985 AGCGCTTGTGTCTGTACTGA 59.326 50.000 2.64 0.00 0.00 3.41
2154 3862 1.063806 GAGCGCTTGTGTCTGTACTG 58.936 55.000 13.26 0.00 0.00 2.74
2155 3863 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
2156 3864 1.714794 ATGAGCGCTTGTGTCTGTAC 58.285 50.000 13.26 0.00 0.00 2.90
2157 3865 3.801114 ATATGAGCGCTTGTGTCTGTA 57.199 42.857 13.26 0.00 0.00 2.74
2158 3866 2.680312 ATATGAGCGCTTGTGTCTGT 57.320 45.000 13.26 0.00 0.00 3.41
2159 3867 3.243877 GTGTATATGAGCGCTTGTGTCTG 59.756 47.826 13.26 0.00 0.00 3.51
2160 3868 3.448686 GTGTATATGAGCGCTTGTGTCT 58.551 45.455 13.26 0.00 0.00 3.41
2161 3869 2.216488 CGTGTATATGAGCGCTTGTGTC 59.784 50.000 13.26 0.00 0.00 3.67
2162 3870 2.193447 CGTGTATATGAGCGCTTGTGT 58.807 47.619 13.26 4.27 0.00 3.72
2163 3871 1.071239 GCGTGTATATGAGCGCTTGTG 60.071 52.381 13.26 0.00 45.48 3.33
2164 3872 1.209128 GCGTGTATATGAGCGCTTGT 58.791 50.000 13.26 5.98 45.48 3.16
2165 3873 0.159554 CGCGTGTATATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
2166 3874 2.506544 CGCGTGTATATGAGCGCTT 58.493 52.632 13.26 0.00 46.56 4.68
2167 3875 4.228451 CGCGTGTATATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
2170 3878 2.090658 GTGTATGCGCGTGTATATGAGC 59.909 50.000 13.61 0.41 38.85 4.26
2171 3879 3.565516 AGTGTATGCGCGTGTATATGAG 58.434 45.455 13.61 0.00 0.00 2.90
2172 3880 3.003897 TGAGTGTATGCGCGTGTATATGA 59.996 43.478 13.61 0.00 0.00 2.15
2173 3881 3.119628 GTGAGTGTATGCGCGTGTATATG 59.880 47.826 13.61 0.00 0.00 1.78
2174 3882 3.305964 GTGAGTGTATGCGCGTGTATAT 58.694 45.455 13.61 0.00 0.00 0.86
2175 3883 2.542205 GGTGAGTGTATGCGCGTGTATA 60.542 50.000 13.61 2.40 0.00 1.47
2176 3884 1.556564 GTGAGTGTATGCGCGTGTAT 58.443 50.000 13.61 4.63 0.00 2.29
2177 3885 0.457166 GGTGAGTGTATGCGCGTGTA 60.457 55.000 13.61 0.00 0.00 2.90
2178 3886 1.736645 GGTGAGTGTATGCGCGTGT 60.737 57.895 13.61 0.00 0.00 4.49
2179 3887 2.452813 GGGTGAGTGTATGCGCGTG 61.453 63.158 13.61 0.00 0.00 5.34
2180 3888 2.125673 GGGTGAGTGTATGCGCGT 60.126 61.111 8.43 7.55 0.00 6.01
2181 3889 2.601628 TACGGGTGAGTGTATGCGCG 62.602 60.000 0.00 0.00 41.82 6.86
2182 3890 0.249322 ATACGGGTGAGTGTATGCGC 60.249 55.000 0.00 0.00 30.39 6.09
2183 3891 1.066454 TCATACGGGTGAGTGTATGCG 59.934 52.381 7.34 0.00 44.76 4.73
2184 3892 2.864343 GTTCATACGGGTGAGTGTATGC 59.136 50.000 7.34 0.00 44.76 3.14
2185 3893 3.113322 CGTTCATACGGGTGAGTGTATG 58.887 50.000 6.12 6.12 45.89 2.39
2186 3894 3.431922 CGTTCATACGGGTGAGTGTAT 57.568 47.619 0.00 0.00 43.94 2.29
2187 3895 2.925578 CGTTCATACGGGTGAGTGTA 57.074 50.000 0.00 0.00 43.94 2.90
2188 3896 3.806591 CGTTCATACGGGTGAGTGT 57.193 52.632 0.00 0.00 43.94 3.55
2198 3906 0.450482 GTGCGTGTGTGCGTTCATAC 60.450 55.000 0.00 0.00 37.81 2.39
2199 3907 0.876342 TGTGCGTGTGTGCGTTCATA 60.876 50.000 0.00 0.00 37.81 2.15
2200 3908 2.176926 TGTGCGTGTGTGCGTTCAT 61.177 52.632 0.00 0.00 37.81 2.57
2201 3909 2.815647 TGTGCGTGTGTGCGTTCA 60.816 55.556 0.00 0.00 37.81 3.18
2202 3910 2.350760 GTGTGCGTGTGTGCGTTC 60.351 61.111 0.00 0.00 37.81 3.95
2203 3911 3.871574 GGTGTGCGTGTGTGCGTT 61.872 61.111 0.00 0.00 37.81 4.84
2206 3914 2.280524 TAGGGTGTGCGTGTGTGC 60.281 61.111 0.00 0.00 0.00 4.57
2207 3915 1.959226 GGTAGGGTGTGCGTGTGTG 60.959 63.158 0.00 0.00 0.00 3.82
2208 3916 2.424302 GGTAGGGTGTGCGTGTGT 59.576 61.111 0.00 0.00 0.00 3.72
2209 3917 2.358247 GGGTAGGGTGTGCGTGTG 60.358 66.667 0.00 0.00 0.00 3.82
2210 3918 2.735151 TAGGGGTAGGGTGTGCGTGT 62.735 60.000 0.00 0.00 0.00 4.49
2211 3919 1.335132 ATAGGGGTAGGGTGTGCGTG 61.335 60.000 0.00 0.00 0.00 5.34
2212 3920 1.002533 ATAGGGGTAGGGTGTGCGT 59.997 57.895 0.00 0.00 0.00 5.24
2213 3921 1.046472 TCATAGGGGTAGGGTGTGCG 61.046 60.000 0.00 0.00 0.00 5.34
2214 3922 0.759346 CTCATAGGGGTAGGGTGTGC 59.241 60.000 0.00 0.00 0.00 4.57
2215 3923 0.759346 GCTCATAGGGGTAGGGTGTG 59.241 60.000 0.00 0.00 0.00 3.82
2216 3924 0.341961 TGCTCATAGGGGTAGGGTGT 59.658 55.000 0.00 0.00 0.00 4.16
2217 3925 0.759346 GTGCTCATAGGGGTAGGGTG 59.241 60.000 0.00 0.00 0.00 4.61
2218 3926 0.400093 GGTGCTCATAGGGGTAGGGT 60.400 60.000 0.00 0.00 0.00 4.34
2219 3927 0.104934 AGGTGCTCATAGGGGTAGGG 60.105 60.000 0.00 0.00 0.00 3.53
2220 3928 1.343069 GAGGTGCTCATAGGGGTAGG 58.657 60.000 0.00 0.00 0.00 3.18
2221 3929 1.343069 GGAGGTGCTCATAGGGGTAG 58.657 60.000 0.00 0.00 31.08 3.18
2222 3930 0.469331 CGGAGGTGCTCATAGGGGTA 60.469 60.000 0.00 0.00 31.08 3.69
2223 3931 1.762460 CGGAGGTGCTCATAGGGGT 60.762 63.158 0.00 0.00 31.08 4.95
2224 3932 1.457643 TCGGAGGTGCTCATAGGGG 60.458 63.158 0.00 0.00 31.08 4.79
2225 3933 0.468214 TCTCGGAGGTGCTCATAGGG 60.468 60.000 4.96 0.00 31.08 3.53
2226 3934 0.958091 CTCTCGGAGGTGCTCATAGG 59.042 60.000 4.96 0.00 31.08 2.57
2227 3935 1.606668 GTCTCTCGGAGGTGCTCATAG 59.393 57.143 4.96 0.00 31.08 2.23
2228 3936 1.213182 AGTCTCTCGGAGGTGCTCATA 59.787 52.381 4.96 0.00 31.08 2.15
2229 3937 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.000 4.96 0.00 31.08 2.90
2230 3938 0.962855 CAGTCTCTCGGAGGTGCTCA 60.963 60.000 4.96 0.00 31.08 4.26
2231 3939 0.678366 TCAGTCTCTCGGAGGTGCTC 60.678 60.000 4.96 0.00 0.00 4.26
2232 3940 0.679640 CTCAGTCTCTCGGAGGTGCT 60.680 60.000 4.96 0.00 35.32 4.40
2233 3941 1.806568 CTCAGTCTCTCGGAGGTGC 59.193 63.158 4.96 0.00 35.32 5.01
2234 3942 1.662438 GGCTCAGTCTCTCGGAGGTG 61.662 65.000 4.96 0.00 38.48 4.00
2235 3943 1.379309 GGCTCAGTCTCTCGGAGGT 60.379 63.158 4.96 0.00 38.48 3.85
2236 3944 2.477176 CGGCTCAGTCTCTCGGAGG 61.477 68.421 4.96 0.00 38.48 4.30
2237 3945 2.477176 CCGGCTCAGTCTCTCGGAG 61.477 68.421 0.00 0.00 42.94 4.63
2238 3946 2.438614 CCGGCTCAGTCTCTCGGA 60.439 66.667 0.00 0.00 42.94 4.55
2239 3947 4.200283 GCCGGCTCAGTCTCTCGG 62.200 72.222 22.15 0.00 43.13 4.63
2240 3948 1.448119 TATGCCGGCTCAGTCTCTCG 61.448 60.000 29.70 0.00 0.00 4.04
2241 3949 0.965439 ATATGCCGGCTCAGTCTCTC 59.035 55.000 29.70 0.00 0.00 3.20
2242 3950 0.965439 GATATGCCGGCTCAGTCTCT 59.035 55.000 29.70 3.16 0.00 3.10
2243 3951 0.676184 TGATATGCCGGCTCAGTCTC 59.324 55.000 29.70 15.31 0.00 3.36
2244 3952 1.274728 GATGATATGCCGGCTCAGTCT 59.725 52.381 29.70 8.26 0.00 3.24
2245 3953 1.274728 AGATGATATGCCGGCTCAGTC 59.725 52.381 29.70 19.55 0.00 3.51
2246 3954 1.346062 AGATGATATGCCGGCTCAGT 58.654 50.000 29.70 13.44 0.00 3.41
2247 3955 2.074576 CAAGATGATATGCCGGCTCAG 58.925 52.381 29.70 7.35 0.00 3.35
2248 3956 1.693606 TCAAGATGATATGCCGGCTCA 59.306 47.619 29.70 23.34 0.00 4.26
2249 3957 2.028658 TCTCAAGATGATATGCCGGCTC 60.029 50.000 29.70 17.89 0.00 4.70
2250 3958 1.973515 TCTCAAGATGATATGCCGGCT 59.026 47.619 29.70 15.76 0.00 5.52
2251 3959 2.462456 TCTCAAGATGATATGCCGGC 57.538 50.000 22.73 22.73 0.00 6.13
2252 3960 5.062683 CGTAAATCTCAAGATGATATGCCGG 59.937 44.000 0.00 0.00 34.49 6.13
2253 3961 5.863935 TCGTAAATCTCAAGATGATATGCCG 59.136 40.000 0.00 0.00 34.49 5.69
2254 3962 7.386299 ACTTCGTAAATCTCAAGATGATATGCC 59.614 37.037 0.00 0.00 34.49 4.40
2255 3963 8.304202 ACTTCGTAAATCTCAAGATGATATGC 57.696 34.615 0.00 0.00 34.49 3.14
2256 3964 9.468532 TGACTTCGTAAATCTCAAGATGATATG 57.531 33.333 0.00 0.00 34.49 1.78
2257 3965 9.469807 GTGACTTCGTAAATCTCAAGATGATAT 57.530 33.333 0.00 0.00 34.49 1.63
2258 3966 7.921214 GGTGACTTCGTAAATCTCAAGATGATA 59.079 37.037 0.00 0.00 34.49 2.15
2259 3967 6.758886 GGTGACTTCGTAAATCTCAAGATGAT 59.241 38.462 0.00 0.00 34.49 2.45
2260 3968 6.100004 GGTGACTTCGTAAATCTCAAGATGA 58.900 40.000 0.00 0.00 34.49 2.92
2261 3969 5.004821 CGGTGACTTCGTAAATCTCAAGATG 59.995 44.000 0.00 0.00 34.49 2.90
2262 3970 5.103000 CGGTGACTTCGTAAATCTCAAGAT 58.897 41.667 0.00 0.00 36.07 2.40
2263 3971 4.022589 ACGGTGACTTCGTAAATCTCAAGA 60.023 41.667 0.00 0.00 39.22 3.02
2264 3972 4.235360 ACGGTGACTTCGTAAATCTCAAG 58.765 43.478 0.00 0.00 39.22 3.02
2265 3973 4.247267 ACGGTGACTTCGTAAATCTCAA 57.753 40.909 0.00 0.00 39.22 3.02
2266 3974 3.928727 ACGGTGACTTCGTAAATCTCA 57.071 42.857 0.00 0.00 39.22 3.27
2267 3975 4.349501 CCTACGGTGACTTCGTAAATCTC 58.650 47.826 0.00 0.00 41.62 2.75
2268 3976 3.428589 GCCTACGGTGACTTCGTAAATCT 60.429 47.826 0.00 0.00 41.62 2.40
2269 3977 2.856557 GCCTACGGTGACTTCGTAAATC 59.143 50.000 0.00 0.00 41.62 2.17
2270 3978 2.733227 CGCCTACGGTGACTTCGTAAAT 60.733 50.000 0.00 0.00 41.62 1.40
2271 3979 1.401409 CGCCTACGGTGACTTCGTAAA 60.401 52.381 0.00 0.00 41.62 2.01
2272 3980 0.168788 CGCCTACGGTGACTTCGTAA 59.831 55.000 0.00 0.00 41.62 3.18
2273 3981 0.955428 ACGCCTACGGTGACTTCGTA 60.955 55.000 0.00 0.00 46.04 3.43
2274 3982 2.263741 ACGCCTACGGTGACTTCGT 61.264 57.895 0.00 0.00 46.04 3.85
2275 3983 1.800315 CACGCCTACGGTGACTTCG 60.800 63.158 0.00 0.00 46.04 3.79
2276 3984 2.092882 GCACGCCTACGGTGACTTC 61.093 63.158 0.00 0.00 46.04 3.01
2277 3985 2.048503 GCACGCCTACGGTGACTT 60.049 61.111 0.00 0.00 46.04 3.01
2278 3986 4.415332 CGCACGCCTACGGTGACT 62.415 66.667 0.00 0.00 46.04 3.41
2279 3987 4.409218 TCGCACGCCTACGGTGAC 62.409 66.667 0.00 0.00 46.04 3.67
2280 3988 4.111016 CTCGCACGCCTACGGTGA 62.111 66.667 0.00 0.00 46.04 4.02
2285 3993 1.586564 CTACTGCTCGCACGCCTAC 60.587 63.158 0.00 0.00 0.00 3.18
2286 3994 2.771639 CCTACTGCTCGCACGCCTA 61.772 63.158 0.00 0.00 0.00 3.93
2287 3995 4.135153 CCTACTGCTCGCACGCCT 62.135 66.667 0.00 0.00 0.00 5.52
2288 3996 2.907897 AATCCTACTGCTCGCACGCC 62.908 60.000 0.00 0.00 0.00 5.68
2289 3997 1.084370 AAATCCTACTGCTCGCACGC 61.084 55.000 0.00 0.00 0.00 5.34
2290 3998 0.647410 CAAATCCTACTGCTCGCACG 59.353 55.000 0.00 0.00 0.00 5.34
2291 3999 2.010145 TCAAATCCTACTGCTCGCAC 57.990 50.000 0.00 0.00 0.00 5.34
2292 4000 2.346803 GTTCAAATCCTACTGCTCGCA 58.653 47.619 0.00 0.00 0.00 5.10
2293 4001 1.666189 GGTTCAAATCCTACTGCTCGC 59.334 52.381 0.00 0.00 0.00 5.03
2294 4002 2.093447 AGGGTTCAAATCCTACTGCTCG 60.093 50.000 0.00 0.00 37.89 5.03
2295 4003 3.274288 CAGGGTTCAAATCCTACTGCTC 58.726 50.000 0.00 0.00 37.45 4.26
2296 4004 2.025887 CCAGGGTTCAAATCCTACTGCT 60.026 50.000 0.00 0.00 37.45 4.24
2297 4005 2.290960 ACCAGGGTTCAAATCCTACTGC 60.291 50.000 0.00 0.00 37.45 4.40
2298 4006 3.347216 CACCAGGGTTCAAATCCTACTG 58.653 50.000 0.00 0.00 37.45 2.74
2299 4007 2.308866 CCACCAGGGTTCAAATCCTACT 59.691 50.000 0.00 0.00 37.45 2.57
2300 4008 2.723273 CCACCAGGGTTCAAATCCTAC 58.277 52.381 0.00 0.00 37.45 3.18
2313 4021 1.613061 GTATCCCCAACCCACCAGG 59.387 63.158 0.00 0.00 43.78 4.45
2314 4022 1.211567 TGGTATCCCCAACCCACCAG 61.212 60.000 0.00 0.00 41.50 4.00
2315 4023 1.151565 TGGTATCCCCAACCCACCA 60.152 57.895 0.00 0.00 41.50 4.17
2316 4024 3.844063 TGGTATCCCCAACCCACC 58.156 61.111 0.00 0.00 41.50 4.61
2323 4031 0.912487 GGTGGACAGTGGTATCCCCA 60.912 60.000 0.00 0.00 42.51 4.96
2324 4032 0.620700 AGGTGGACAGTGGTATCCCC 60.621 60.000 0.00 0.00 33.69 4.81
2325 4033 2.169978 GTTAGGTGGACAGTGGTATCCC 59.830 54.545 0.00 0.00 33.69 3.85
2326 4034 2.169978 GGTTAGGTGGACAGTGGTATCC 59.830 54.545 0.00 0.00 35.37 2.59
2327 4035 2.835764 TGGTTAGGTGGACAGTGGTATC 59.164 50.000 0.00 0.00 0.00 2.24
2328 4036 2.910544 TGGTTAGGTGGACAGTGGTAT 58.089 47.619 0.00 0.00 0.00 2.73
2329 4037 2.369532 GTTGGTTAGGTGGACAGTGGTA 59.630 50.000 0.00 0.00 0.00 3.25
2330 4038 1.142262 GTTGGTTAGGTGGACAGTGGT 59.858 52.381 0.00 0.00 0.00 4.16
2331 4039 1.420138 AGTTGGTTAGGTGGACAGTGG 59.580 52.381 0.00 0.00 0.00 4.00
2332 4040 2.104111 TGAGTTGGTTAGGTGGACAGTG 59.896 50.000 0.00 0.00 0.00 3.66
2333 4041 2.404559 TGAGTTGGTTAGGTGGACAGT 58.595 47.619 0.00 0.00 0.00 3.55
2334 4042 3.139077 GTTGAGTTGGTTAGGTGGACAG 58.861 50.000 0.00 0.00 0.00 3.51
2335 4043 2.158726 GGTTGAGTTGGTTAGGTGGACA 60.159 50.000 0.00 0.00 0.00 4.02
2336 4044 2.158726 TGGTTGAGTTGGTTAGGTGGAC 60.159 50.000 0.00 0.00 0.00 4.02
2337 4045 2.128535 TGGTTGAGTTGGTTAGGTGGA 58.871 47.619 0.00 0.00 0.00 4.02
2338 4046 2.227194 GTGGTTGAGTTGGTTAGGTGG 58.773 52.381 0.00 0.00 0.00 4.61
2339 4047 2.878406 CTGTGGTTGAGTTGGTTAGGTG 59.122 50.000 0.00 0.00 0.00 4.00
2340 4048 2.158667 CCTGTGGTTGAGTTGGTTAGGT 60.159 50.000 0.00 0.00 0.00 3.08
2341 4049 2.158667 ACCTGTGGTTGAGTTGGTTAGG 60.159 50.000 0.00 0.00 27.29 2.69
2342 4050 3.208747 ACCTGTGGTTGAGTTGGTTAG 57.791 47.619 0.00 0.00 27.29 2.34
2343 4051 3.655615 AACCTGTGGTTGAGTTGGTTA 57.344 42.857 0.71 0.00 45.07 2.85
2344 4052 2.525105 AACCTGTGGTTGAGTTGGTT 57.475 45.000 0.71 0.00 45.07 3.67
2353 4061 4.565652 ATTCTAGCGAATCAACCTGTGGTT 60.566 41.667 0.00 0.00 38.19 3.67
2354 4062 1.899814 TCTAGCGAATCAACCTGTGGT 59.100 47.619 0.00 0.00 37.65 4.16
2355 4063 2.672961 TCTAGCGAATCAACCTGTGG 57.327 50.000 0.00 0.00 0.00 4.17
2367 4075 6.394809 TGCCAATATTATTCGATTCTAGCGA 58.605 36.000 0.00 0.00 35.76 4.93
2368 4076 6.647212 TGCCAATATTATTCGATTCTAGCG 57.353 37.500 0.00 0.00 0.00 4.26
2369 4077 8.201554 TGATGCCAATATTATTCGATTCTAGC 57.798 34.615 0.00 0.00 0.00 3.42
2500 4218 3.963428 ACAACTCGAATGAAGGCTAGT 57.037 42.857 4.99 0.00 0.00 2.57
2507 4225 3.442273 GGCCCATTAACAACTCGAATGAA 59.558 43.478 4.99 0.00 33.28 2.57
2508 4226 3.013921 GGCCCATTAACAACTCGAATGA 58.986 45.455 4.99 0.00 33.28 2.57
2645 4873 1.086634 GGGATCACTGCGAGCAAGAC 61.087 60.000 0.00 0.00 0.00 3.01
2669 4897 1.936547 GGATGGAAGCATCGTCAGAAC 59.063 52.381 0.00 0.00 32.60 3.01
2673 4901 0.904649 AGTGGATGGAAGCATCGTCA 59.095 50.000 0.00 0.00 32.60 4.35
2912 5993 3.440173 ACGAATAGGCAAATCCAACTGTG 59.560 43.478 0.00 0.00 37.29 3.66
2918 5999 5.465935 GTGAAAAACGAATAGGCAAATCCA 58.534 37.500 0.00 0.00 37.29 3.41
2919 6000 4.862574 GGTGAAAAACGAATAGGCAAATCC 59.137 41.667 0.00 0.00 0.00 3.01
2925 6006 2.475685 GCTCGGTGAAAAACGAATAGGC 60.476 50.000 0.00 0.00 38.79 3.93
2943 6024 2.084546 ACCGGCTTTTATTCACAGCTC 58.915 47.619 0.00 0.00 33.76 4.09
2986 6068 2.742053 ACAACCTTGATACGTGATGCAC 59.258 45.455 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.