Multiple sequence alignment - TraesCS2B01G223100

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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 TraesCS2B01G223100 chr2B 100.000 2930 0 0 1 2930 212932529 212929600 0.000000e+00 5411.0
1 TraesCS2B01G223100 chr2B 85.417 720 94 10 1964 2675 13205961 13205245 0.000000e+00 737.0
2 TraesCS2B01G223100 chr2D 93.759 705 32 7 1180 1876 155506914 155506214 0.000000e+00 1048.0
3 TraesCS2B01G223100 chr2D 86.087 345 15 11 1 344 155509427 155509115 1.010000e-89 340.0
4 TraesCS2B01G223100 chr2D 85.227 352 20 14 607 950 155507678 155507351 1.680000e-87 333.0
5 TraesCS2B01G223100 chr2D 86.139 202 15 8 342 537 155508088 155507894 3.830000e-49 206.0
6 TraesCS2B01G223100 chr2A 90.921 771 36 13 1115 1876 144657939 144658684 0.000000e+00 1005.0
7 TraesCS2B01G223100 chr2A 87.234 423 20 14 1 418 144656534 144656927 4.450000e-123 451.0
8 TraesCS2B01G223100 chr2A 83.982 437 24 21 529 962 144657180 144657573 7.670000e-101 377.0
9 TraesCS2B01G223100 chr2A 97.059 34 0 1 1898 1930 144658675 144658708 4.080000e-04 56.5
10 TraesCS2B01G223100 chr1D 88.346 798 79 13 1959 2745 10132680 10133474 0.000000e+00 946.0
11 TraesCS2B01G223100 chr4D 87.728 823 83 15 1933 2745 77118609 77117795 0.000000e+00 944.0
12 TraesCS2B01G223100 chr5A 87.321 836 79 17 1930 2745 91967221 91968049 0.000000e+00 931.0
13 TraesCS2B01G223100 chr3D 86.585 820 91 17 1935 2743 27272171 27272982 0.000000e+00 887.0
14 TraesCS2B01G223100 chr3D 86.457 827 78 20 1935 2745 15282527 15281719 0.000000e+00 876.0
15 TraesCS2B01G223100 chr7B 87.936 746 75 14 1935 2673 688047225 688046488 0.000000e+00 865.0
16 TraesCS2B01G223100 chr7B 88.350 721 72 12 1964 2676 586932679 586933395 0.000000e+00 856.0
17 TraesCS2B01G223100 chr7A 85.337 832 92 24 1933 2746 21898857 21898038 0.000000e+00 833.0
18 TraesCS2B01G223100 chr6B 87.938 713 70 13 1964 2667 63152178 63151473 0.000000e+00 826.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G223100 chr2B 212929600 212932529 2929 True 5411.000 5411 100.000 1 2930 1 chr2B.!!$R2 2929
1 TraesCS2B01G223100 chr2B 13205245 13205961 716 True 737.000 737 85.417 1964 2675 1 chr2B.!!$R1 711
2 TraesCS2B01G223100 chr2D 155506214 155509427 3213 True 481.750 1048 87.803 1 1876 4 chr2D.!!$R1 1875
3 TraesCS2B01G223100 chr2A 144656534 144658708 2174 False 472.375 1005 89.799 1 1930 4 chr2A.!!$F1 1929
4 TraesCS2B01G223100 chr1D 10132680 10133474 794 False 946.000 946 88.346 1959 2745 1 chr1D.!!$F1 786
5 TraesCS2B01G223100 chr4D 77117795 77118609 814 True 944.000 944 87.728 1933 2745 1 chr4D.!!$R1 812
6 TraesCS2B01G223100 chr5A 91967221 91968049 828 False 931.000 931 87.321 1930 2745 1 chr5A.!!$F1 815
7 TraesCS2B01G223100 chr3D 27272171 27272982 811 False 887.000 887 86.585 1935 2743 1 chr3D.!!$F1 808
8 TraesCS2B01G223100 chr3D 15281719 15282527 808 True 876.000 876 86.457 1935 2745 1 chr3D.!!$R1 810
9 TraesCS2B01G223100 chr7B 688046488 688047225 737 True 865.000 865 87.936 1935 2673 1 chr7B.!!$R1 738
10 TraesCS2B01G223100 chr7B 586932679 586933395 716 False 856.000 856 88.350 1964 2676 1 chr7B.!!$F1 712
11 TraesCS2B01G223100 chr7A 21898038 21898857 819 True 833.000 833 85.337 1933 2746 1 chr7A.!!$R1 813
12 TraesCS2B01G223100 chr6B 63151473 63152178 705 True 826.000 826 87.938 1964 2667 1 chr6B.!!$R1 703

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
661 1896 0.256464 ATCCTTCTCCGTCTCCGTCT 59.744 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 3656 1.002315 ACATCATGGCAACTTTTGGGC 59.998 47.619 0.0 0.0 37.61 5.36 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
36 37 0.330604 AGCCATGAGCCTGTTGTCAT 59.669 50.000 0.00 0.00 45.47 3.06
37 38 0.454600 GCCATGAGCCTGTTGTCATG 59.545 55.000 0.00 5.51 46.53 3.07
38 39 0.454600 CCATGAGCCTGTTGTCATGC 59.545 55.000 6.77 0.00 45.90 4.06
39 40 1.460504 CATGAGCCTGTTGTCATGCT 58.539 50.000 0.00 0.00 45.44 3.79
40 41 2.635714 CATGAGCCTGTTGTCATGCTA 58.364 47.619 0.00 0.00 43.48 3.49
41 42 3.211865 CATGAGCCTGTTGTCATGCTAT 58.788 45.455 0.00 0.00 43.48 2.97
42 43 4.383173 CATGAGCCTGTTGTCATGCTATA 58.617 43.478 0.00 0.00 43.48 1.31
43 44 4.063998 TGAGCCTGTTGTCATGCTATAG 57.936 45.455 0.00 0.00 43.48 1.31
44 45 3.452264 TGAGCCTGTTGTCATGCTATAGT 59.548 43.478 0.84 0.00 43.48 2.12
136 137 3.717400 TTTTTGTGTGTGTGTGTGTGT 57.283 38.095 0.00 0.00 0.00 3.72
137 138 2.695613 TTTGTGTGTGTGTGTGTGTG 57.304 45.000 0.00 0.00 0.00 3.82
138 139 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
139 140 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
140 141 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
141 142 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
195 205 5.859521 TCTGTCTACTCGTAGTTTCTGTC 57.140 43.478 4.19 0.00 34.84 3.51
196 206 4.388165 TCTGTCTACTCGTAGTTTCTGTCG 59.612 45.833 4.19 0.00 34.84 4.35
215 226 5.353938 TGTCGTGTTAACTTCTGTTAGCTT 58.646 37.500 7.22 0.00 39.54 3.74
236 247 1.135689 CGCCAGGAAAATGTAGTGTGC 60.136 52.381 0.00 0.00 0.00 4.57
428 1472 8.472007 ACCAAAACAATTGTAGTATCCTTTCA 57.528 30.769 12.39 0.00 0.00 2.69
429 1473 8.919145 ACCAAAACAATTGTAGTATCCTTTCAA 58.081 29.630 12.39 0.00 0.00 2.69
430 1474 9.757227 CCAAAACAATTGTAGTATCCTTTCAAA 57.243 29.630 12.39 0.00 0.00 2.69
478 1522 6.096423 TCAGTAGTACGTTCTTGCATTATCCT 59.904 38.462 0.00 0.00 0.00 3.24
483 1527 3.877508 ACGTTCTTGCATTATCCTAAGCC 59.122 43.478 0.00 0.00 0.00 4.35
507 1555 9.151471 GCCAATGCTAACTCGAGATAATAAATA 57.849 33.333 21.68 0.00 33.53 1.40
660 1895 1.104630 AATCCTTCTCCGTCTCCGTC 58.895 55.000 0.00 0.00 0.00 4.79
661 1896 0.256464 ATCCTTCTCCGTCTCCGTCT 59.744 55.000 0.00 0.00 0.00 4.18
662 1897 0.392729 TCCTTCTCCGTCTCCGTCTC 60.393 60.000 0.00 0.00 0.00 3.36
663 1898 1.378124 CCTTCTCCGTCTCCGTCTCC 61.378 65.000 0.00 0.00 0.00 3.71
664 1899 1.707239 CTTCTCCGTCTCCGTCTCCG 61.707 65.000 0.00 0.00 0.00 4.63
665 1900 2.436292 CTCCGTCTCCGTCTCCGT 60.436 66.667 0.00 0.00 0.00 4.69
666 1901 2.435586 TCCGTCTCCGTCTCCGTC 60.436 66.667 0.00 0.00 0.00 4.79
667 1902 3.862402 CCGTCTCCGTCTCCGTCG 61.862 72.222 0.00 0.00 0.00 5.12
669 1904 4.176851 GTCTCCGTCTCCGTCGGC 62.177 72.222 6.34 0.00 46.49 5.54
675 1910 2.816360 CGTCTCCGTCGGCGATACA 61.816 63.158 12.93 0.00 41.33 2.29
690 1925 3.494626 GCGATACATGAACCATTCACGAT 59.505 43.478 0.00 0.00 43.48 3.73
769 2004 1.035932 CCGGACCATACACCGTCTCT 61.036 60.000 0.00 0.00 46.53 3.10
773 2008 2.032620 GACCATACACCGTCTCTGGAT 58.967 52.381 0.00 0.00 0.00 3.41
794 2029 4.130281 GCGCACGCGTTCTGTACC 62.130 66.667 10.22 0.00 42.09 3.34
796 2031 3.475774 GCACGCGTTCTGTACCCG 61.476 66.667 10.22 0.00 34.29 5.28
798 2033 2.049802 ACGCGTTCTGTACCCGTG 60.050 61.111 5.58 0.00 39.62 4.94
799 2034 3.475774 CGCGTTCTGTACCCGTGC 61.476 66.667 0.00 0.00 0.00 5.34
801 2036 2.807895 CGTTCTGTACCCGTGCGG 60.808 66.667 3.25 3.25 37.81 5.69
830 2073 1.202359 GCGACACAAACCACAACCATT 60.202 47.619 0.00 0.00 0.00 3.16
831 2074 2.726633 CGACACAAACCACAACCATTC 58.273 47.619 0.00 0.00 0.00 2.67
832 2075 2.098280 CGACACAAACCACAACCATTCA 59.902 45.455 0.00 0.00 0.00 2.57
833 2076 3.428180 CGACACAAACCACAACCATTCAA 60.428 43.478 0.00 0.00 0.00 2.69
834 2077 4.499183 GACACAAACCACAACCATTCAAA 58.501 39.130 0.00 0.00 0.00 2.69
835 2078 4.899502 ACACAAACCACAACCATTCAAAA 58.100 34.783 0.00 0.00 0.00 2.44
836 2079 5.308825 ACACAAACCACAACCATTCAAAAA 58.691 33.333 0.00 0.00 0.00 1.94
954 2197 1.562575 GGCACGTACTCACAAACCCG 61.563 60.000 0.00 0.00 0.00 5.28
957 2200 2.030958 CGTACTCACAAACCCGCCC 61.031 63.158 0.00 0.00 0.00 6.13
959 2202 3.242897 TACTCACAAACCCGCCCCG 62.243 63.158 0.00 0.00 0.00 5.73
1002 2245 3.691342 CTGACGCCCTCCCAACGA 61.691 66.667 0.00 0.00 0.00 3.85
1006 2249 1.644786 GACGCCCTCCCAACGAAATG 61.645 60.000 0.00 0.00 0.00 2.32
1007 2250 1.376683 CGCCCTCCCAACGAAATGA 60.377 57.895 0.00 0.00 0.00 2.57
1008 2251 1.644786 CGCCCTCCCAACGAAATGAC 61.645 60.000 0.00 0.00 0.00 3.06
1009 2252 1.313091 GCCCTCCCAACGAAATGACC 61.313 60.000 0.00 0.00 0.00 4.02
1010 2253 0.328258 CCCTCCCAACGAAATGACCT 59.672 55.000 0.00 0.00 0.00 3.85
1011 2254 1.679032 CCCTCCCAACGAAATGACCTC 60.679 57.143 0.00 0.00 0.00 3.85
1012 2255 1.679032 CCTCCCAACGAAATGACCTCC 60.679 57.143 0.00 0.00 0.00 4.30
1013 2256 0.326927 TCCCAACGAAATGACCTCCC 59.673 55.000 0.00 0.00 0.00 4.30
1014 2257 1.024579 CCCAACGAAATGACCTCCCG 61.025 60.000 0.00 0.00 0.00 5.14
1015 2258 1.024579 CCAACGAAATGACCTCCCGG 61.025 60.000 0.00 0.00 0.00 5.73
1016 2259 0.036765 CAACGAAATGACCTCCCGGA 60.037 55.000 0.73 0.00 0.00 5.14
1017 2260 0.249398 AACGAAATGACCTCCCGGAG 59.751 55.000 0.73 7.56 0.00 4.63
1018 2261 0.613853 ACGAAATGACCTCCCGGAGA 60.614 55.000 16.69 0.00 0.00 3.71
1019 2262 0.179108 CGAAATGACCTCCCGGAGAC 60.179 60.000 16.69 9.91 0.00 3.36
1020 2263 0.902531 GAAATGACCTCCCGGAGACA 59.097 55.000 16.69 14.97 0.00 3.41
1021 2264 1.486726 GAAATGACCTCCCGGAGACAT 59.513 52.381 16.69 16.42 32.00 3.06
1022 2265 1.584724 AATGACCTCCCGGAGACATT 58.415 50.000 22.60 22.60 34.57 2.71
1023 2266 1.584724 ATGACCTCCCGGAGACATTT 58.415 50.000 16.69 0.00 0.00 2.32
1024 2267 2.241281 TGACCTCCCGGAGACATTTA 57.759 50.000 16.69 0.00 0.00 1.40
1025 2268 2.759355 TGACCTCCCGGAGACATTTAT 58.241 47.619 16.69 0.00 0.00 1.40
1026 2269 3.918566 TGACCTCCCGGAGACATTTATA 58.081 45.455 16.69 0.00 0.00 0.98
1027 2270 4.291792 TGACCTCCCGGAGACATTTATAA 58.708 43.478 16.69 0.00 0.00 0.98
1028 2271 4.717778 TGACCTCCCGGAGACATTTATAAA 59.282 41.667 16.69 0.00 0.00 1.40
1029 2272 5.032327 ACCTCCCGGAGACATTTATAAAC 57.968 43.478 16.69 0.00 0.00 2.01
1030 2273 4.720273 ACCTCCCGGAGACATTTATAAACT 59.280 41.667 16.69 0.00 0.00 2.66
1031 2274 5.163332 ACCTCCCGGAGACATTTATAAACTC 60.163 44.000 16.69 3.18 0.00 3.01
1032 2275 5.286267 TCCCGGAGACATTTATAAACTCC 57.714 43.478 17.55 17.55 42.30 3.85
1033 2276 4.102054 TCCCGGAGACATTTATAAACTCCC 59.898 45.833 19.94 11.65 42.63 4.30
1034 2277 4.386711 CCGGAGACATTTATAAACTCCCC 58.613 47.826 19.94 9.94 42.63 4.81
1035 2278 4.386711 CGGAGACATTTATAAACTCCCCC 58.613 47.826 19.94 12.13 42.63 5.40
1061 2304 3.636231 CTCCCTTCCACGCCACCA 61.636 66.667 0.00 0.00 0.00 4.17
1062 2305 3.901797 CTCCCTTCCACGCCACCAC 62.902 68.421 0.00 0.00 0.00 4.16
1063 2306 3.953775 CCCTTCCACGCCACCACT 61.954 66.667 0.00 0.00 0.00 4.00
1064 2307 2.113139 CCTTCCACGCCACCACTT 59.887 61.111 0.00 0.00 0.00 3.16
1065 2308 1.966451 CCTTCCACGCCACCACTTC 60.966 63.158 0.00 0.00 0.00 3.01
1066 2309 2.280524 TTCCACGCCACCACTTCG 60.281 61.111 0.00 0.00 0.00 3.79
1067 2310 4.980805 TCCACGCCACCACTTCGC 62.981 66.667 0.00 0.00 0.00 4.70
1086 2329 4.856607 CGCCCGACTTCTCGCCTC 62.857 72.222 0.00 0.00 38.70 4.70
1087 2330 3.760035 GCCCGACTTCTCGCCTCA 61.760 66.667 0.00 0.00 38.70 3.86
1088 2331 2.182030 CCCGACTTCTCGCCTCAC 59.818 66.667 0.00 0.00 38.70 3.51
1089 2332 2.182030 CCGACTTCTCGCCTCACC 59.818 66.667 0.00 0.00 38.70 4.02
1090 2333 2.344203 CCGACTTCTCGCCTCACCT 61.344 63.158 0.00 0.00 38.70 4.00
1091 2334 1.137825 CGACTTCTCGCCTCACCTC 59.862 63.158 0.00 0.00 31.91 3.85
1092 2335 1.309499 CGACTTCTCGCCTCACCTCT 61.309 60.000 0.00 0.00 31.91 3.69
1093 2336 0.454196 GACTTCTCGCCTCACCTCTC 59.546 60.000 0.00 0.00 0.00 3.20
1094 2337 0.968393 ACTTCTCGCCTCACCTCTCC 60.968 60.000 0.00 0.00 0.00 3.71
1095 2338 1.671901 CTTCTCGCCTCACCTCTCCC 61.672 65.000 0.00 0.00 0.00 4.30
1096 2339 3.151022 CTCGCCTCACCTCTCCCC 61.151 72.222 0.00 0.00 0.00 4.81
1097 2340 3.670629 CTCGCCTCACCTCTCCCCT 62.671 68.421 0.00 0.00 0.00 4.79
1098 2341 3.151022 CGCCTCACCTCTCCCCTC 61.151 72.222 0.00 0.00 0.00 4.30
1099 2342 2.766229 GCCTCACCTCTCCCCTCC 60.766 72.222 0.00 0.00 0.00 4.30
1100 2343 2.041405 CCTCACCTCTCCCCTCCC 60.041 72.222 0.00 0.00 0.00 4.30
1101 2344 2.041405 CTCACCTCTCCCCTCCCC 60.041 72.222 0.00 0.00 0.00 4.81
1102 2345 2.540910 TCACCTCTCCCCTCCCCT 60.541 66.667 0.00 0.00 0.00 4.79
1103 2346 2.041405 CACCTCTCCCCTCCCCTC 60.041 72.222 0.00 0.00 0.00 4.30
1104 2347 3.369388 ACCTCTCCCCTCCCCTCC 61.369 72.222 0.00 0.00 0.00 4.30
1105 2348 4.179599 CCTCTCCCCTCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1106 2349 4.179599 CTCTCCCCTCCCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
1130 2599 3.889134 CTCCACGCAAGCCAGAGCA 62.889 63.158 0.00 0.00 43.56 4.26
1216 2685 2.590645 CAGCAGCAGCAGAGGGAT 59.409 61.111 3.17 0.00 45.49 3.85
1217 2686 1.077644 CAGCAGCAGCAGAGGGATT 60.078 57.895 3.17 0.00 45.49 3.01
1219 2688 2.119655 GCAGCAGCAGAGGGATTGG 61.120 63.158 0.00 0.00 41.58 3.16
1220 2689 1.605992 CAGCAGCAGAGGGATTGGA 59.394 57.895 0.00 0.00 0.00 3.53
1221 2690 0.034767 CAGCAGCAGAGGGATTGGAA 60.035 55.000 0.00 0.00 0.00 3.53
1222 2691 0.924823 AGCAGCAGAGGGATTGGAAT 59.075 50.000 0.00 0.00 0.00 3.01
1693 3171 6.090493 GTCCGTTCCATTCTTTGTAGTAACTC 59.910 42.308 0.00 0.00 0.00 3.01
1730 3208 1.398958 TTGGCTTGGTTGGTTGGCTC 61.399 55.000 0.00 0.00 0.00 4.70
1785 3263 8.582433 TTGGTTTCTTTTTCGATTATTTGGTC 57.418 30.769 0.00 0.00 0.00 4.02
1786 3264 7.149307 TGGTTTCTTTTTCGATTATTTGGTCC 58.851 34.615 0.00 0.00 0.00 4.46
1797 3277 6.021596 CGATTATTTGGTCCGAAGTTGAAAG 58.978 40.000 0.00 0.00 0.00 2.62
1829 3309 6.992063 ACAGAGTAGAAATTATGCCAGTTG 57.008 37.500 0.00 0.00 0.00 3.16
1847 3327 3.131046 AGTTGGTGCAGAAAGGAAACAAG 59.869 43.478 0.00 0.00 0.00 3.16
1851 3331 3.490933 GGTGCAGAAAGGAAACAAGGTTC 60.491 47.826 0.00 0.00 0.00 3.62
1863 3343 6.771267 AGGAAACAAGGTTCTAAACGAAGAAT 59.229 34.615 0.00 0.00 37.78 2.40
1864 3344 7.935210 AGGAAACAAGGTTCTAAACGAAGAATA 59.065 33.333 0.00 0.00 37.78 1.75
1865 3345 8.013947 GGAAACAAGGTTCTAAACGAAGAATAC 58.986 37.037 0.00 0.00 37.78 1.89
1866 3346 8.672823 AAACAAGGTTCTAAACGAAGAATACT 57.327 30.769 0.00 0.00 37.78 2.12
1867 3347 8.672823 AACAAGGTTCTAAACGAAGAATACTT 57.327 30.769 0.00 2.36 37.78 2.24
1868 3348 8.307921 ACAAGGTTCTAAACGAAGAATACTTC 57.692 34.615 0.00 0.00 46.21 3.01
1881 3361 5.930837 AGAATACTTCTTCTCCTCCTGTG 57.069 43.478 0.00 0.00 36.36 3.66
1882 3362 5.584913 AGAATACTTCTTCTCCTCCTGTGA 58.415 41.667 0.00 0.00 36.36 3.58
1883 3363 6.019748 AGAATACTTCTTCTCCTCCTGTGAA 58.980 40.000 0.00 0.00 36.36 3.18
1884 3364 6.498651 AGAATACTTCTTCTCCTCCTGTGAAA 59.501 38.462 0.00 0.00 36.36 2.69
1885 3365 6.688073 ATACTTCTTCTCCTCCTGTGAAAA 57.312 37.500 0.00 0.00 0.00 2.29
1886 3366 5.373812 ACTTCTTCTCCTCCTGTGAAAAA 57.626 39.130 0.00 0.00 0.00 1.94
1887 3367 5.372373 ACTTCTTCTCCTCCTGTGAAAAAG 58.628 41.667 0.00 0.00 33.03 2.27
1888 3368 5.131142 ACTTCTTCTCCTCCTGTGAAAAAGA 59.869 40.000 0.00 0.00 31.84 2.52
1889 3369 5.630415 TCTTCTCCTCCTGTGAAAAAGAA 57.370 39.130 0.00 0.00 0.00 2.52
1890 3370 6.001449 TCTTCTCCTCCTGTGAAAAAGAAA 57.999 37.500 0.00 0.00 0.00 2.52
1891 3371 6.423182 TCTTCTCCTCCTGTGAAAAAGAAAA 58.577 36.000 0.00 0.00 0.00 2.29
1892 3372 6.889722 TCTTCTCCTCCTGTGAAAAAGAAAAA 59.110 34.615 0.00 0.00 0.00 1.94
1925 3405 5.540337 TCTCCTGTCCTTGTCATGGTATATC 59.460 44.000 4.76 0.00 0.00 1.63
1926 3406 5.215845 TCCTGTCCTTGTCATGGTATATCA 58.784 41.667 4.76 0.00 0.00 2.15
1930 3410 7.012704 CCTGTCCTTGTCATGGTATATCAAAAG 59.987 40.741 4.76 0.00 0.00 2.27
1931 3411 6.828273 TGTCCTTGTCATGGTATATCAAAAGG 59.172 38.462 11.28 11.28 34.30 3.11
1958 3438 2.902608 ACTAACTCCCAGACCATGTGA 58.097 47.619 0.00 0.00 0.00 3.58
1984 3464 1.667830 CACATCGCCCACACGTCTT 60.668 57.895 0.00 0.00 0.00 3.01
1985 3465 1.070786 ACATCGCCCACACGTCTTT 59.929 52.632 0.00 0.00 0.00 2.52
1988 3468 1.327460 CATCGCCCACACGTCTTTATG 59.673 52.381 0.00 0.00 0.00 1.90
1990 3470 1.206132 TCGCCCACACGTCTTTATGAT 59.794 47.619 0.00 0.00 0.00 2.45
2010 3490 2.020720 TCACTCATTTTGCCACGTGTT 58.979 42.857 15.65 0.00 0.00 3.32
2025 3505 4.450757 CCACGTGTTAACAGATGACATCAA 59.549 41.667 17.57 0.22 0.00 2.57
2028 3508 5.525745 ACGTGTTAACAGATGACATCAACAA 59.474 36.000 17.57 3.43 0.00 2.83
2035 3515 6.981762 ACAGATGACATCAACAAGAATCTC 57.018 37.500 17.57 0.00 0.00 2.75
2040 3520 7.881751 AGATGACATCAACAAGAATCTCTTTGA 59.118 33.333 17.57 8.40 33.78 2.69
2071 3551 9.285770 CGGCTTAAAAATGTTTTATCTCCTAAC 57.714 33.333 0.00 0.00 0.00 2.34
2132 3614 5.046529 CCATCTCGACGAGATCTTCAAAAT 58.953 41.667 32.23 11.20 45.03 1.82
2135 3617 7.222805 CCATCTCGACGAGATCTTCAAAATTAA 59.777 37.037 32.23 6.49 45.03 1.40
2259 3776 9.760660 GTTTGTAGAGCATGACAATTTTAGTAG 57.239 33.333 0.00 0.00 35.57 2.57
2388 3908 6.094881 TGGCAAGTCTAATTTCTTAATTCCCG 59.905 38.462 0.00 0.00 35.61 5.14
2462 3986 9.630098 GAAACATATCATGACAATTTCAGTGTT 57.370 29.630 0.00 0.00 37.77 3.32
2595 4128 5.982890 ATGGTGAAAACGGATCTTCAATT 57.017 34.783 0.00 0.00 33.52 2.32
2694 4228 6.203915 TGACGTGAAGCAGTTTGTGTTTATAT 59.796 34.615 0.00 0.00 28.05 0.86
2717 4251 1.074775 TGTGGGCGGATTTTGCTCT 59.925 52.632 0.00 0.00 32.72 4.09
2739 4273 3.612681 ACACGTGTGGGCGCTAGT 61.613 61.111 22.71 0.00 34.88 2.57
2746 4280 0.464735 TGTGGGCGCTAGTGTTGTTT 60.465 50.000 7.64 0.00 0.00 2.83
2747 4281 0.666374 GTGGGCGCTAGTGTTGTTTT 59.334 50.000 7.64 0.00 0.00 2.43
2748 4282 1.874872 GTGGGCGCTAGTGTTGTTTTA 59.125 47.619 7.64 0.00 0.00 1.52
2749 4283 2.486592 GTGGGCGCTAGTGTTGTTTTAT 59.513 45.455 7.64 0.00 0.00 1.40
2750 4284 2.745281 TGGGCGCTAGTGTTGTTTTATC 59.255 45.455 7.64 0.00 0.00 1.75
2751 4285 2.745281 GGGCGCTAGTGTTGTTTTATCA 59.255 45.455 7.64 0.00 0.00 2.15
2752 4286 3.189702 GGGCGCTAGTGTTGTTTTATCAA 59.810 43.478 7.64 0.00 0.00 2.57
2753 4287 4.320641 GGGCGCTAGTGTTGTTTTATCAAA 60.321 41.667 7.64 0.00 0.00 2.69
2754 4288 5.216648 GGCGCTAGTGTTGTTTTATCAAAA 58.783 37.500 7.64 0.00 0.00 2.44
2755 4289 5.688176 GGCGCTAGTGTTGTTTTATCAAAAA 59.312 36.000 7.64 0.00 32.15 1.94
2792 4326 7.751047 TTTTTAGCTGTCGTGCTACTAATAG 57.249 36.000 0.00 0.00 44.15 1.73
2793 4327 3.992260 AGCTGTCGTGCTACTAATAGG 57.008 47.619 0.00 0.00 42.10 2.57
2794 4328 3.552875 AGCTGTCGTGCTACTAATAGGA 58.447 45.455 0.00 0.00 42.10 2.94
2795 4329 3.566322 AGCTGTCGTGCTACTAATAGGAG 59.434 47.826 0.00 0.00 42.10 3.69
2796 4330 3.564644 GCTGTCGTGCTACTAATAGGAGA 59.435 47.826 3.16 0.00 27.85 3.71
2797 4331 4.319911 GCTGTCGTGCTACTAATAGGAGAG 60.320 50.000 3.16 0.00 27.85 3.20
2798 4332 5.032327 TGTCGTGCTACTAATAGGAGAGA 57.968 43.478 3.16 0.00 27.85 3.10
2799 4333 5.434408 TGTCGTGCTACTAATAGGAGAGAA 58.566 41.667 3.16 0.00 27.85 2.87
2800 4334 5.296283 TGTCGTGCTACTAATAGGAGAGAAC 59.704 44.000 3.16 0.00 27.85 3.01
2801 4335 5.528320 GTCGTGCTACTAATAGGAGAGAACT 59.472 44.000 3.16 0.00 27.85 3.01
2802 4336 6.038492 GTCGTGCTACTAATAGGAGAGAACTT 59.962 42.308 3.16 0.00 27.85 2.66
2803 4337 6.038382 TCGTGCTACTAATAGGAGAGAACTTG 59.962 42.308 3.16 0.00 27.85 3.16
2804 4338 6.508777 GTGCTACTAATAGGAGAGAACTTGG 58.491 44.000 3.16 0.00 27.85 3.61
2805 4339 6.097129 GTGCTACTAATAGGAGAGAACTTGGT 59.903 42.308 3.16 0.00 27.85 3.67
2806 4340 6.668283 TGCTACTAATAGGAGAGAACTTGGTT 59.332 38.462 3.16 0.00 0.00 3.67
2807 4341 7.180408 TGCTACTAATAGGAGAGAACTTGGTTT 59.820 37.037 3.16 0.00 0.00 3.27
2808 4342 8.041919 GCTACTAATAGGAGAGAACTTGGTTTT 58.958 37.037 3.16 0.00 0.00 2.43
2809 4343 9.945904 CTACTAATAGGAGAGAACTTGGTTTTT 57.054 33.333 0.00 0.00 0.00 1.94
2839 4373 8.807581 GCAGTAATTGTTTATTAGGTGAAATGC 58.192 33.333 0.00 0.00 29.44 3.56
2840 4374 9.853555 CAGTAATTGTTTATTAGGTGAAATGCA 57.146 29.630 0.00 0.00 29.44 3.96
2841 4375 9.855021 AGTAATTGTTTATTAGGTGAAATGCAC 57.145 29.630 0.00 0.00 46.98 4.57
2842 4376 9.855021 GTAATTGTTTATTAGGTGAAATGCACT 57.145 29.630 0.00 0.00 46.86 4.40
2855 4389 9.206870 AGGTGAAATGCACTTAATAAACAATTG 57.793 29.630 3.24 3.24 46.86 2.32
2856 4390 8.442384 GGTGAAATGCACTTAATAAACAATTGG 58.558 33.333 10.83 0.00 46.86 3.16
2857 4391 8.987890 GTGAAATGCACTTAATAAACAATTGGT 58.012 29.630 10.83 0.00 44.27 3.67
2858 4392 9.202273 TGAAATGCACTTAATAAACAATTGGTC 57.798 29.630 10.83 0.00 0.00 4.02
2859 4393 8.546597 AAATGCACTTAATAAACAATTGGTCC 57.453 30.769 10.83 0.00 0.00 4.46
2860 4394 6.656632 TGCACTTAATAAACAATTGGTCCA 57.343 33.333 10.83 0.00 0.00 4.02
2861 4395 7.055667 TGCACTTAATAAACAATTGGTCCAA 57.944 32.000 6.80 6.80 0.00 3.53
2862 4396 7.675062 TGCACTTAATAAACAATTGGTCCAAT 58.325 30.769 11.59 11.59 35.39 3.16
2863 4397 8.153550 TGCACTTAATAAACAATTGGTCCAATT 58.846 29.630 22.00 22.00 43.71 2.32
2876 4410 8.429237 AATTGGTCCAATTGTTTATTAGGTGA 57.571 30.769 25.92 0.00 41.70 4.02
2877 4411 7.841282 TTGGTCCAATTGTTTATTAGGTGAA 57.159 32.000 0.00 0.00 0.00 3.18
2878 4412 7.841282 TGGTCCAATTGTTTATTAGGTGAAA 57.159 32.000 4.43 0.00 0.00 2.69
2879 4413 8.429237 TGGTCCAATTGTTTATTAGGTGAAAT 57.571 30.769 4.43 0.00 0.00 2.17
2880 4414 8.310382 TGGTCCAATTGTTTATTAGGTGAAATG 58.690 33.333 4.43 0.00 0.00 2.32
2881 4415 7.763985 GGTCCAATTGTTTATTAGGTGAAATGG 59.236 37.037 4.43 0.00 0.00 3.16
2882 4416 8.527810 GTCCAATTGTTTATTAGGTGAAATGGA 58.472 33.333 4.43 0.00 0.00 3.41
2883 4417 8.527810 TCCAATTGTTTATTAGGTGAAATGGAC 58.472 33.333 4.43 0.00 0.00 4.02
2884 4418 7.763985 CCAATTGTTTATTAGGTGAAATGGACC 59.236 37.037 4.43 0.00 0.00 4.46
2885 4419 8.310382 CAATTGTTTATTAGGTGAAATGGACCA 58.690 33.333 0.00 0.00 35.76 4.02
2886 4420 7.841282 TTGTTTATTAGGTGAAATGGACCAA 57.159 32.000 0.00 0.00 35.76 3.67
2887 4421 8.429237 TTGTTTATTAGGTGAAATGGACCAAT 57.571 30.769 0.00 0.00 35.76 3.16
2888 4422 8.429237 TGTTTATTAGGTGAAATGGACCAATT 57.571 30.769 0.00 0.00 35.76 2.32
2889 4423 8.310382 TGTTTATTAGGTGAAATGGACCAATTG 58.690 33.333 0.00 0.00 35.76 2.32
2890 4424 8.311109 GTTTATTAGGTGAAATGGACCAATTGT 58.689 33.333 0.00 0.00 35.76 2.71
2891 4425 6.933514 ATTAGGTGAAATGGACCAATTGTT 57.066 33.333 0.00 0.00 35.76 2.83
2892 4426 4.605640 AGGTGAAATGGACCAATTGTTG 57.394 40.909 0.00 0.00 35.76 3.33
2901 4435 3.863681 CCAATTGTTGGTGGTGACG 57.136 52.632 4.43 0.00 45.93 4.35
2902 4436 0.313672 CCAATTGTTGGTGGTGACGG 59.686 55.000 4.43 0.00 45.93 4.79
2903 4437 1.313772 CAATTGTTGGTGGTGACGGA 58.686 50.000 0.00 0.00 0.00 4.69
2904 4438 1.266718 CAATTGTTGGTGGTGACGGAG 59.733 52.381 0.00 0.00 0.00 4.63
2905 4439 0.762418 ATTGTTGGTGGTGACGGAGA 59.238 50.000 0.00 0.00 0.00 3.71
2906 4440 0.179067 TTGTTGGTGGTGACGGAGAC 60.179 55.000 0.00 0.00 0.00 3.36
2907 4441 1.046472 TGTTGGTGGTGACGGAGACT 61.046 55.000 0.00 0.00 0.00 3.24
2908 4442 0.963962 GTTGGTGGTGACGGAGACTA 59.036 55.000 0.00 0.00 0.00 2.59
2909 4443 1.549170 GTTGGTGGTGACGGAGACTAT 59.451 52.381 0.00 0.00 0.00 2.12
2910 4444 1.933021 TGGTGGTGACGGAGACTATT 58.067 50.000 0.00 0.00 0.00 1.73
2911 4445 1.548719 TGGTGGTGACGGAGACTATTG 59.451 52.381 0.00 0.00 0.00 1.90
2912 4446 1.549170 GGTGGTGACGGAGACTATTGT 59.451 52.381 0.00 0.00 0.00 2.71
2913 4447 2.028385 GGTGGTGACGGAGACTATTGTT 60.028 50.000 0.00 0.00 0.00 2.83
2914 4448 3.251571 GTGGTGACGGAGACTATTGTTC 58.748 50.000 0.00 0.00 0.00 3.18
2915 4449 2.894765 TGGTGACGGAGACTATTGTTCA 59.105 45.455 0.00 0.00 0.00 3.18
2916 4450 3.513912 TGGTGACGGAGACTATTGTTCAT 59.486 43.478 0.00 0.00 0.00 2.57
2917 4451 4.113354 GGTGACGGAGACTATTGTTCATC 58.887 47.826 0.00 0.00 0.00 2.92
2918 4452 4.381612 GGTGACGGAGACTATTGTTCATCA 60.382 45.833 0.00 0.00 0.00 3.07
2919 4453 5.352284 GTGACGGAGACTATTGTTCATCAT 58.648 41.667 0.00 0.00 0.00 2.45
2920 4454 5.233050 GTGACGGAGACTATTGTTCATCATG 59.767 44.000 0.00 0.00 0.00 3.07
2921 4455 5.105351 TGACGGAGACTATTGTTCATCATGT 60.105 40.000 0.00 0.00 0.00 3.21
2922 4456 5.734720 ACGGAGACTATTGTTCATCATGTT 58.265 37.500 0.00 0.00 0.00 2.71
2923 4457 6.173339 ACGGAGACTATTGTTCATCATGTTT 58.827 36.000 0.00 0.00 0.00 2.83
2924 4458 6.655003 ACGGAGACTATTGTTCATCATGTTTT 59.345 34.615 0.00 0.00 0.00 2.43
2925 4459 7.174946 ACGGAGACTATTGTTCATCATGTTTTT 59.825 33.333 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 6.014499 GGAAATACCCTCTAGCAACTATAGCA 60.014 42.308 0.00 0.00 0.00 3.49
37 38 6.014499 TGGAAATACCCTCTAGCAACTATAGC 60.014 42.308 0.00 0.00 38.00 2.97
38 39 7.379750 GTGGAAATACCCTCTAGCAACTATAG 58.620 42.308 0.00 0.00 38.00 1.31
39 40 6.269307 GGTGGAAATACCCTCTAGCAACTATA 59.731 42.308 0.00 0.00 38.00 1.31
40 41 5.071923 GGTGGAAATACCCTCTAGCAACTAT 59.928 44.000 0.00 0.00 38.00 2.12
41 42 4.407945 GGTGGAAATACCCTCTAGCAACTA 59.592 45.833 0.00 0.00 38.00 2.24
42 43 3.200165 GGTGGAAATACCCTCTAGCAACT 59.800 47.826 0.00 0.00 38.00 3.16
43 44 3.054655 TGGTGGAAATACCCTCTAGCAAC 60.055 47.826 0.00 0.00 40.09 4.17
44 45 3.186283 TGGTGGAAATACCCTCTAGCAA 58.814 45.455 0.00 0.00 40.09 3.91
118 119 1.950216 ACACACACACACACACACAAA 59.050 42.857 0.00 0.00 0.00 2.83
119 120 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
120 121 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
121 122 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
122 123 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
123 124 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
124 125 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
125 126 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
126 127 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
127 128 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
128 129 0.605050 AGCACACACACACACACACA 60.605 50.000 0.00 0.00 0.00 3.72
129 130 0.521291 AAGCACACACACACACACAC 59.479 50.000 0.00 0.00 0.00 3.82
130 131 0.520847 CAAGCACACACACACACACA 59.479 50.000 0.00 0.00 0.00 3.72
131 132 0.521291 ACAAGCACACACACACACAC 59.479 50.000 0.00 0.00 0.00 3.82
132 133 1.198867 GAACAAGCACACACACACACA 59.801 47.619 0.00 0.00 0.00 3.72
133 134 1.198867 TGAACAAGCACACACACACAC 59.801 47.619 0.00 0.00 0.00 3.82
134 135 1.468127 CTGAACAAGCACACACACACA 59.532 47.619 0.00 0.00 0.00 3.72
135 136 1.737236 TCTGAACAAGCACACACACAC 59.263 47.619 0.00 0.00 0.00 3.82
136 137 2.106477 TCTGAACAAGCACACACACA 57.894 45.000 0.00 0.00 0.00 3.72
137 138 3.365832 CAATCTGAACAAGCACACACAC 58.634 45.455 0.00 0.00 0.00 3.82
138 139 2.358582 CCAATCTGAACAAGCACACACA 59.641 45.455 0.00 0.00 0.00 3.72
139 140 2.358898 ACCAATCTGAACAAGCACACAC 59.641 45.455 0.00 0.00 0.00 3.82
140 141 2.653726 ACCAATCTGAACAAGCACACA 58.346 42.857 0.00 0.00 0.00 3.72
141 142 3.181487 ACAACCAATCTGAACAAGCACAC 60.181 43.478 0.00 0.00 0.00 3.82
195 205 4.931214 CGAAGCTAACAGAAGTTAACACG 58.069 43.478 8.61 0.00 39.58 4.49
215 226 2.422597 CACACTACATTTTCCTGGCGA 58.577 47.619 0.00 0.00 0.00 5.54
289 304 0.182537 ACAGCACAAGTTGTAGGGCA 59.817 50.000 16.46 0.00 37.43 5.36
440 1484 7.823149 ACGTACTACTGATACAATTGTTTCC 57.177 36.000 17.78 6.97 0.00 3.13
445 1489 7.062956 TGCAAGAACGTACTACTGATACAATTG 59.937 37.037 3.24 3.24 0.00 2.32
447 1491 6.627243 TGCAAGAACGTACTACTGATACAAT 58.373 36.000 0.00 0.00 0.00 2.71
448 1492 6.016213 TGCAAGAACGTACTACTGATACAA 57.984 37.500 0.00 0.00 0.00 2.41
449 1493 5.632244 TGCAAGAACGTACTACTGATACA 57.368 39.130 0.00 0.00 0.00 2.29
450 1494 8.798748 ATAATGCAAGAACGTACTACTGATAC 57.201 34.615 0.00 0.00 0.00 2.24
452 1496 6.924060 GGATAATGCAAGAACGTACTACTGAT 59.076 38.462 0.00 0.00 0.00 2.90
453 1497 6.096423 AGGATAATGCAAGAACGTACTACTGA 59.904 38.462 0.00 0.00 0.00 3.41
454 1498 6.273825 AGGATAATGCAAGAACGTACTACTG 58.726 40.000 0.00 0.00 0.00 2.74
455 1499 6.466885 AGGATAATGCAAGAACGTACTACT 57.533 37.500 0.00 0.00 0.00 2.57
497 1545 9.974750 GCGCTTCCTATCACTTTATTTATTATC 57.025 33.333 0.00 0.00 0.00 1.75
507 1555 4.040952 AGGATATGCGCTTCCTATCACTTT 59.959 41.667 20.73 0.66 40.62 2.66
593 1827 0.886490 CCCGCTCAGCCATAACCATC 60.886 60.000 0.00 0.00 0.00 3.51
625 1860 3.178865 AGGATTGACCCGGTAAAGAAGA 58.821 45.455 0.00 0.00 40.05 2.87
660 1895 0.030235 TTCATGTATCGCCGACGGAG 59.970 55.000 20.50 16.01 40.63 4.63
661 1896 0.248743 GTTCATGTATCGCCGACGGA 60.249 55.000 20.50 0.00 40.63 4.69
662 1897 1.213094 GGTTCATGTATCGCCGACGG 61.213 60.000 10.29 10.29 40.63 4.79
663 1898 0.526739 TGGTTCATGTATCGCCGACG 60.527 55.000 0.00 0.00 42.01 5.12
664 1899 1.865865 ATGGTTCATGTATCGCCGAC 58.134 50.000 0.00 0.00 0.00 4.79
665 1900 2.159028 TGAATGGTTCATGTATCGCCGA 60.159 45.455 0.00 0.00 34.08 5.54
666 1901 2.032894 GTGAATGGTTCATGTATCGCCG 60.033 50.000 0.00 0.00 42.47 6.46
667 1902 2.032894 CGTGAATGGTTCATGTATCGCC 60.033 50.000 4.20 0.00 42.47 5.54
668 1903 2.863740 TCGTGAATGGTTCATGTATCGC 59.136 45.455 10.65 0.00 44.93 4.58
669 1904 5.010249 CATCGTGAATGGTTCATGTATCG 57.990 43.478 10.65 3.43 44.93 2.92
707 1942 4.808077 TCGTACGATGGAGAATACAGTC 57.192 45.455 15.28 0.00 0.00 3.51
710 1945 5.007430 GTCTCTTCGTACGATGGAGAATACA 59.993 44.000 32.99 19.48 36.20 2.29
712 1947 4.210746 CGTCTCTTCGTACGATGGAGAATA 59.789 45.833 32.99 19.97 41.55 1.75
747 1982 2.510691 CGGTGTATGGTCCGGTGC 60.511 66.667 0.00 0.00 42.61 5.01
801 2036 2.530497 TTTGTGTCGCAGTCGCACC 61.530 57.895 8.75 0.00 39.88 5.01
807 2050 0.450184 GTTGTGGTTTGTGTCGCAGT 59.550 50.000 0.00 0.00 0.00 4.40
808 2051 0.248458 GGTTGTGGTTTGTGTCGCAG 60.248 55.000 0.00 0.00 0.00 5.18
830 2073 5.420421 TCTGGGTCTGTGTTTTGATTTTTGA 59.580 36.000 0.00 0.00 0.00 2.69
831 2074 5.659463 TCTGGGTCTGTGTTTTGATTTTTG 58.341 37.500 0.00 0.00 0.00 2.44
832 2075 5.930837 TCTGGGTCTGTGTTTTGATTTTT 57.069 34.783 0.00 0.00 0.00 1.94
833 2076 5.660460 GTTCTGGGTCTGTGTTTTGATTTT 58.340 37.500 0.00 0.00 0.00 1.82
834 2077 4.202010 CGTTCTGGGTCTGTGTTTTGATTT 60.202 41.667 0.00 0.00 0.00 2.17
835 2078 3.315191 CGTTCTGGGTCTGTGTTTTGATT 59.685 43.478 0.00 0.00 0.00 2.57
836 2079 2.878406 CGTTCTGGGTCTGTGTTTTGAT 59.122 45.455 0.00 0.00 0.00 2.57
984 2227 4.760047 CGTTGGGAGGGCGTCAGG 62.760 72.222 9.66 0.00 0.00 3.86
1009 2252 5.298347 GGAGTTTATAAATGTCTCCGGGAG 58.702 45.833 18.25 18.25 35.94 4.30
1010 2253 4.102054 GGGAGTTTATAAATGTCTCCGGGA 59.898 45.833 19.49 0.00 43.72 5.14
1011 2254 4.386711 GGGAGTTTATAAATGTCTCCGGG 58.613 47.826 19.49 0.00 43.72 5.73
1012 2255 4.386711 GGGGAGTTTATAAATGTCTCCGG 58.613 47.826 19.49 0.00 43.72 5.14
1013 2256 4.386711 GGGGGAGTTTATAAATGTCTCCG 58.613 47.826 19.49 0.00 43.72 4.63
1044 2287 3.636231 TGGTGGCGTGGAAGGGAG 61.636 66.667 0.00 0.00 0.00 4.30
1045 2288 3.948719 GTGGTGGCGTGGAAGGGA 61.949 66.667 0.00 0.00 0.00 4.20
1046 2289 3.491598 AAGTGGTGGCGTGGAAGGG 62.492 63.158 0.00 0.00 0.00 3.95
1047 2290 1.966451 GAAGTGGTGGCGTGGAAGG 60.966 63.158 0.00 0.00 0.00 3.46
1048 2291 2.317609 CGAAGTGGTGGCGTGGAAG 61.318 63.158 0.00 0.00 0.00 3.46
1049 2292 2.280524 CGAAGTGGTGGCGTGGAA 60.281 61.111 0.00 0.00 0.00 3.53
1050 2293 4.980805 GCGAAGTGGTGGCGTGGA 62.981 66.667 0.00 0.00 0.00 4.02
1069 2312 4.856607 GAGGCGAGAAGTCGGGCG 62.857 72.222 0.00 0.00 46.91 6.13
1070 2313 3.760035 TGAGGCGAGAAGTCGGGC 61.760 66.667 0.00 0.00 46.91 6.13
1071 2314 2.182030 GTGAGGCGAGAAGTCGGG 59.818 66.667 0.00 0.00 46.91 5.14
1072 2315 2.182030 GGTGAGGCGAGAAGTCGG 59.818 66.667 0.00 0.00 46.91 4.79
1074 2317 0.454196 GAGAGGTGAGGCGAGAAGTC 59.546 60.000 0.00 0.00 0.00 3.01
1075 2318 0.968393 GGAGAGGTGAGGCGAGAAGT 60.968 60.000 0.00 0.00 0.00 3.01
1076 2319 1.671901 GGGAGAGGTGAGGCGAGAAG 61.672 65.000 0.00 0.00 0.00 2.85
1077 2320 1.682684 GGGAGAGGTGAGGCGAGAA 60.683 63.158 0.00 0.00 0.00 2.87
1078 2321 2.043852 GGGAGAGGTGAGGCGAGA 60.044 66.667 0.00 0.00 0.00 4.04
1079 2322 3.151022 GGGGAGAGGTGAGGCGAG 61.151 72.222 0.00 0.00 0.00 5.03
1080 2323 3.663815 GAGGGGAGAGGTGAGGCGA 62.664 68.421 0.00 0.00 0.00 5.54
1081 2324 3.151022 GAGGGGAGAGGTGAGGCG 61.151 72.222 0.00 0.00 0.00 5.52
1082 2325 2.766229 GGAGGGGAGAGGTGAGGC 60.766 72.222 0.00 0.00 0.00 4.70
1083 2326 2.041405 GGGAGGGGAGAGGTGAGG 60.041 72.222 0.00 0.00 0.00 3.86
1084 2327 2.041405 GGGGAGGGGAGAGGTGAG 60.041 72.222 0.00 0.00 0.00 3.51
1085 2328 2.540910 AGGGGAGGGGAGAGGTGA 60.541 66.667 0.00 0.00 0.00 4.02
1086 2329 2.041405 GAGGGGAGGGGAGAGGTG 60.041 72.222 0.00 0.00 0.00 4.00
1087 2330 3.369388 GGAGGGGAGGGGAGAGGT 61.369 72.222 0.00 0.00 0.00 3.85
1088 2331 4.179599 GGGAGGGGAGGGGAGAGG 62.180 77.778 0.00 0.00 0.00 3.69
1089 2332 4.179599 GGGGAGGGGAGGGGAGAG 62.180 77.778 0.00 0.00 0.00 3.20
1109 2352 3.730761 CTGGCTTGCGTGGAGTGC 61.731 66.667 0.00 0.00 0.00 4.40
1110 2353 2.031012 TCTGGCTTGCGTGGAGTG 59.969 61.111 0.00 0.00 0.00 3.51
1111 2354 2.345244 CTCTGGCTTGCGTGGAGT 59.655 61.111 0.00 0.00 0.00 3.85
1112 2355 3.123620 GCTCTGGCTTGCGTGGAG 61.124 66.667 0.00 0.00 35.22 3.86
1113 2356 3.939939 TGCTCTGGCTTGCGTGGA 61.940 61.111 0.00 0.00 39.59 4.02
1145 2614 0.103208 TTTTGTTTGGCGCCGTTGAT 59.897 45.000 23.90 0.00 0.00 2.57
1146 2615 0.802607 GTTTTGTTTGGCGCCGTTGA 60.803 50.000 23.90 0.00 0.00 3.18
1148 2617 1.874466 CGTTTTGTTTGGCGCCGTT 60.874 52.632 23.90 0.00 0.00 4.44
1205 2674 1.590932 CGATTCCAATCCCTCTGCTG 58.409 55.000 0.00 0.00 31.68 4.41
1216 2685 2.710377 CTGAACACCATCCGATTCCAA 58.290 47.619 0.00 0.00 0.00 3.53
1217 2686 1.678728 GCTGAACACCATCCGATTCCA 60.679 52.381 0.00 0.00 0.00 3.53
1219 2688 0.652592 CGCTGAACACCATCCGATTC 59.347 55.000 0.00 0.00 0.00 2.52
1220 2689 0.744414 CCGCTGAACACCATCCGATT 60.744 55.000 0.00 0.00 0.00 3.34
1221 2690 1.153369 CCGCTGAACACCATCCGAT 60.153 57.895 0.00 0.00 0.00 4.18
1222 2691 2.264480 CCGCTGAACACCATCCGA 59.736 61.111 0.00 0.00 0.00 4.55
1693 3171 7.290842 CAAGCCAATATGTACAGCGTTTATAG 58.709 38.462 0.33 0.00 0.00 1.31
1730 3208 1.002366 CCGTCTTGATTTCTCGCTGG 58.998 55.000 0.00 0.00 0.00 4.85
1785 3263 6.866770 TCTGTTATACAGTCTTTCAACTTCGG 59.133 38.462 6.71 0.00 46.03 4.30
1786 3264 7.595502 ACTCTGTTATACAGTCTTTCAACTTCG 59.404 37.037 6.71 0.00 46.03 3.79
1811 3291 4.157656 TGCACCAACTGGCATAATTTCTAC 59.842 41.667 0.00 0.00 39.32 2.59
1812 3292 4.339748 TGCACCAACTGGCATAATTTCTA 58.660 39.130 0.00 0.00 39.32 2.10
1813 3293 3.164268 TGCACCAACTGGCATAATTTCT 58.836 40.909 0.00 0.00 39.32 2.52
1825 3305 2.733956 TGTTTCCTTTCTGCACCAACT 58.266 42.857 0.00 0.00 0.00 3.16
1829 3309 2.031870 ACCTTGTTTCCTTTCTGCACC 58.968 47.619 0.00 0.00 0.00 5.01
1863 3343 6.326583 TCTTTTTCACAGGAGGAGAAGAAGTA 59.673 38.462 0.00 0.00 35.89 2.24
1864 3344 5.131142 TCTTTTTCACAGGAGGAGAAGAAGT 59.869 40.000 0.00 0.00 35.89 3.01
1865 3345 5.615289 TCTTTTTCACAGGAGGAGAAGAAG 58.385 41.667 0.00 0.00 35.81 2.85
1866 3346 5.630415 TCTTTTTCACAGGAGGAGAAGAA 57.370 39.130 0.00 0.00 0.00 2.52
1867 3347 5.630415 TTCTTTTTCACAGGAGGAGAAGA 57.370 39.130 0.00 0.00 0.00 2.87
1868 3348 6.699575 TTTTCTTTTTCACAGGAGGAGAAG 57.300 37.500 0.00 0.00 0.00 2.85
1890 3370 4.445557 AGGACAGGAGAAGAAGCTTTTT 57.554 40.909 0.00 0.00 0.00 1.94
1891 3371 4.140536 CAAGGACAGGAGAAGAAGCTTTT 58.859 43.478 0.00 0.00 0.00 2.27
1892 3372 3.137360 ACAAGGACAGGAGAAGAAGCTTT 59.863 43.478 0.00 0.00 0.00 3.51
1893 3373 2.708325 ACAAGGACAGGAGAAGAAGCTT 59.292 45.455 0.00 0.00 0.00 3.74
1894 3374 2.301583 GACAAGGACAGGAGAAGAAGCT 59.698 50.000 0.00 0.00 0.00 3.74
1895 3375 2.037772 TGACAAGGACAGGAGAAGAAGC 59.962 50.000 0.00 0.00 0.00 3.86
1896 3376 4.252073 CATGACAAGGACAGGAGAAGAAG 58.748 47.826 0.00 0.00 0.00 2.85
1944 3424 1.956869 AGATGTCACATGGTCTGGGA 58.043 50.000 0.00 0.00 33.87 4.37
1949 3429 2.153645 TGTGCAAGATGTCACATGGTC 58.846 47.619 0.00 0.00 38.18 4.02
1984 3464 4.699735 ACGTGGCAAAATGAGTGATCATAA 59.300 37.500 0.00 0.00 0.00 1.90
1985 3465 4.094739 CACGTGGCAAAATGAGTGATCATA 59.905 41.667 7.95 0.00 0.00 2.15
1988 3468 2.226437 ACACGTGGCAAAATGAGTGATC 59.774 45.455 21.57 0.00 34.16 2.92
1990 3470 1.674359 ACACGTGGCAAAATGAGTGA 58.326 45.000 21.57 0.00 34.16 3.41
2010 3490 8.316946 AGAGATTCTTGTTGATGTCATCTGTTA 58.683 33.333 13.90 0.00 0.00 2.41
2025 3505 5.474876 AGCCGAAAATCAAAGAGATTCTTGT 59.525 36.000 0.00 0.00 46.09 3.16
2028 3508 7.687941 TTAAGCCGAAAATCAAAGAGATTCT 57.312 32.000 0.00 0.00 46.09 2.40
2035 3515 9.715123 AAAACATTTTTAAGCCGAAAATCAAAG 57.285 25.926 0.00 0.00 35.21 2.77
2080 3561 9.982651 TTAATGGTGAAACGGATTTTTAATTGA 57.017 25.926 0.00 0.00 38.12 2.57
2094 3576 4.698304 TCGAGATGGGTTTAATGGTGAAAC 59.302 41.667 0.00 0.00 36.29 2.78
2132 3614 6.659668 TCGAAACATATCAACATGGGGTTTAA 59.340 34.615 0.00 0.00 37.72 1.52
2135 3617 4.594970 TCGAAACATATCAACATGGGGTT 58.405 39.130 0.00 0.00 41.47 4.11
2170 3656 1.002315 ACATCATGGCAACTTTTGGGC 59.998 47.619 0.00 0.00 37.61 5.36
2259 3776 7.383102 AGTACTGGAATTGTCATCATCAAAC 57.617 36.000 0.00 0.00 0.00 2.93
2462 3986 3.368220 GCACATGAATTGCCATGGTGTTA 60.368 43.478 14.67 0.00 46.06 2.41
2561 4090 5.121768 CCGTTTTCACCATTAAATCTCTCGT 59.878 40.000 0.00 0.00 0.00 4.18
2566 4095 7.393234 TGAAGATCCGTTTTCACCATTAAATCT 59.607 33.333 0.00 0.00 0.00 2.40
2676 4209 4.217550 ACGCCATATAAACACAAACTGCTT 59.782 37.500 0.00 0.00 0.00 3.91
2677 4210 3.756434 ACGCCATATAAACACAAACTGCT 59.244 39.130 0.00 0.00 0.00 4.24
2683 4216 2.750166 CCCACACGCCATATAAACACAA 59.250 45.455 0.00 0.00 0.00 3.33
2694 4228 4.652131 AAATCCGCCCACACGCCA 62.652 61.111 0.00 0.00 0.00 5.69
2772 4306 4.711399 TCCTATTAGTAGCACGACAGCTA 58.289 43.478 0.00 0.00 44.50 3.32
2774 4308 3.564644 TCTCCTATTAGTAGCACGACAGC 59.435 47.826 0.00 0.00 0.00 4.40
2775 4309 5.057819 TCTCTCCTATTAGTAGCACGACAG 58.942 45.833 0.00 0.00 0.00 3.51
2776 4310 5.032327 TCTCTCCTATTAGTAGCACGACA 57.968 43.478 0.00 0.00 0.00 4.35
2777 4311 5.528320 AGTTCTCTCCTATTAGTAGCACGAC 59.472 44.000 0.00 0.00 0.00 4.34
2778 4312 5.682659 AGTTCTCTCCTATTAGTAGCACGA 58.317 41.667 0.00 0.00 0.00 4.35
2779 4313 6.202937 CAAGTTCTCTCCTATTAGTAGCACG 58.797 44.000 0.00 0.00 0.00 5.34
2780 4314 6.097129 ACCAAGTTCTCTCCTATTAGTAGCAC 59.903 42.308 0.00 0.00 0.00 4.40
2781 4315 6.195700 ACCAAGTTCTCTCCTATTAGTAGCA 58.804 40.000 0.00 0.00 0.00 3.49
2782 4316 6.718522 ACCAAGTTCTCTCCTATTAGTAGC 57.281 41.667 0.00 0.00 0.00 3.58
2783 4317 9.945904 AAAAACCAAGTTCTCTCCTATTAGTAG 57.054 33.333 0.00 0.00 0.00 2.57
2813 4347 8.807581 GCATTTCACCTAATAAACAATTACTGC 58.192 33.333 0.00 0.00 0.00 4.40
2814 4348 9.853555 TGCATTTCACCTAATAAACAATTACTG 57.146 29.630 0.00 0.00 0.00 2.74
2815 4349 9.855021 GTGCATTTCACCTAATAAACAATTACT 57.145 29.630 0.00 0.00 39.79 2.24
2816 4350 9.855021 AGTGCATTTCACCTAATAAACAATTAC 57.145 29.630 0.00 0.00 46.81 1.89
2829 4363 9.206870 CAATTGTTTATTAAGTGCATTTCACCT 57.793 29.630 0.00 0.00 46.81 4.00
2830 4364 8.442384 CCAATTGTTTATTAAGTGCATTTCACC 58.558 33.333 4.43 0.00 46.81 4.02
2831 4365 8.987890 ACCAATTGTTTATTAAGTGCATTTCAC 58.012 29.630 4.43 0.00 45.98 3.18
2832 4366 9.202273 GACCAATTGTTTATTAAGTGCATTTCA 57.798 29.630 4.43 0.00 0.00 2.69
2833 4367 8.655970 GGACCAATTGTTTATTAAGTGCATTTC 58.344 33.333 4.43 0.00 0.00 2.17
2834 4368 8.153550 TGGACCAATTGTTTATTAAGTGCATTT 58.846 29.630 4.43 0.00 30.33 2.32
2835 4369 7.675062 TGGACCAATTGTTTATTAAGTGCATT 58.325 30.769 4.43 0.00 30.33 3.56
2836 4370 7.238486 TGGACCAATTGTTTATTAAGTGCAT 57.762 32.000 4.43 0.00 30.33 3.96
2837 4371 6.656632 TGGACCAATTGTTTATTAAGTGCA 57.343 33.333 4.43 1.25 31.79 4.57
2838 4372 8.546597 AATTGGACCAATTGTTTATTAAGTGC 57.453 30.769 27.95 0.00 41.70 4.40
2851 4385 8.429237 TCACCTAATAAACAATTGGACCAATT 57.571 30.769 24.12 24.12 43.71 2.32
2852 4386 8.429237 TTCACCTAATAAACAATTGGACCAAT 57.571 30.769 14.28 14.28 35.39 3.16
2853 4387 7.841282 TTCACCTAATAAACAATTGGACCAA 57.159 32.000 9.92 9.92 0.00 3.67
2854 4388 7.841282 TTTCACCTAATAAACAATTGGACCA 57.159 32.000 10.83 0.00 0.00 4.02
2855 4389 7.763985 CCATTTCACCTAATAAACAATTGGACC 59.236 37.037 10.83 0.00 0.00 4.46
2856 4390 8.527810 TCCATTTCACCTAATAAACAATTGGAC 58.472 33.333 10.83 0.00 0.00 4.02
2857 4391 8.527810 GTCCATTTCACCTAATAAACAATTGGA 58.472 33.333 10.83 0.00 0.00 3.53
2858 4392 7.763985 GGTCCATTTCACCTAATAAACAATTGG 59.236 37.037 10.83 0.00 0.00 3.16
2859 4393 8.310382 TGGTCCATTTCACCTAATAAACAATTG 58.690 33.333 3.24 3.24 34.66 2.32
2860 4394 8.429237 TGGTCCATTTCACCTAATAAACAATT 57.571 30.769 0.00 0.00 34.66 2.32
2861 4395 8.429237 TTGGTCCATTTCACCTAATAAACAAT 57.571 30.769 0.00 0.00 34.66 2.71
2862 4396 7.841282 TTGGTCCATTTCACCTAATAAACAA 57.159 32.000 0.00 0.00 34.66 2.83
2863 4397 8.310382 CAATTGGTCCATTTCACCTAATAAACA 58.690 33.333 0.00 0.00 34.66 2.83
2864 4398 8.311109 ACAATTGGTCCATTTCACCTAATAAAC 58.689 33.333 10.83 0.00 34.66 2.01
2865 4399 8.429237 ACAATTGGTCCATTTCACCTAATAAA 57.571 30.769 10.83 0.00 34.66 1.40
2866 4400 8.310382 CAACAATTGGTCCATTTCACCTAATAA 58.690 33.333 10.83 0.00 34.66 1.40
2867 4401 7.093552 CCAACAATTGGTCCATTTCACCTAATA 60.094 37.037 10.83 0.00 45.93 0.98
2868 4402 6.295802 CCAACAATTGGTCCATTTCACCTAAT 60.296 38.462 10.83 0.00 45.93 1.73
2869 4403 5.011533 CCAACAATTGGTCCATTTCACCTAA 59.988 40.000 10.83 0.00 45.93 2.69
2870 4404 4.526262 CCAACAATTGGTCCATTTCACCTA 59.474 41.667 10.83 0.00 45.93 3.08
2871 4405 3.324556 CCAACAATTGGTCCATTTCACCT 59.675 43.478 10.83 0.00 45.93 4.00
2872 4406 3.663025 CCAACAATTGGTCCATTTCACC 58.337 45.455 10.83 0.00 45.93 4.02
2884 4418 1.266718 CTCCGTCACCACCAACAATTG 59.733 52.381 3.24 3.24 0.00 2.32
2885 4419 1.142060 TCTCCGTCACCACCAACAATT 59.858 47.619 0.00 0.00 0.00 2.32
2886 4420 0.762418 TCTCCGTCACCACCAACAAT 59.238 50.000 0.00 0.00 0.00 2.71
2887 4421 0.179067 GTCTCCGTCACCACCAACAA 60.179 55.000 0.00 0.00 0.00 2.83
2888 4422 1.046472 AGTCTCCGTCACCACCAACA 61.046 55.000 0.00 0.00 0.00 3.33
2889 4423 0.963962 TAGTCTCCGTCACCACCAAC 59.036 55.000 0.00 0.00 0.00 3.77
2890 4424 1.933021 ATAGTCTCCGTCACCACCAA 58.067 50.000 0.00 0.00 0.00 3.67
2891 4425 1.548719 CAATAGTCTCCGTCACCACCA 59.451 52.381 0.00 0.00 0.00 4.17
2892 4426 1.549170 ACAATAGTCTCCGTCACCACC 59.451 52.381 0.00 0.00 0.00 4.61
2893 4427 3.251571 GAACAATAGTCTCCGTCACCAC 58.748 50.000 0.00 0.00 0.00 4.16
2894 4428 2.894765 TGAACAATAGTCTCCGTCACCA 59.105 45.455 0.00 0.00 0.00 4.17
2895 4429 3.587797 TGAACAATAGTCTCCGTCACC 57.412 47.619 0.00 0.00 0.00 4.02
2896 4430 4.744570 TGATGAACAATAGTCTCCGTCAC 58.255 43.478 0.00 0.00 0.00 3.67
2897 4431 5.105351 ACATGATGAACAATAGTCTCCGTCA 60.105 40.000 0.00 0.00 0.00 4.35
2898 4432 5.352284 ACATGATGAACAATAGTCTCCGTC 58.648 41.667 0.00 0.00 0.00 4.79
2899 4433 5.344743 ACATGATGAACAATAGTCTCCGT 57.655 39.130 0.00 0.00 0.00 4.69
2900 4434 6.668541 AAACATGATGAACAATAGTCTCCG 57.331 37.500 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.