Multiple sequence alignment - TraesCS1D01G218300

Loading Multiple Alignment...

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 TraesCS1D01G218300 chr1D 100.000 5328 0 0 1 5328 305110287 305115614 0.000000e+00 9840.0
1 TraesCS1D01G218300 chr1B 94.229 4176 138 36 833 4918 412258567 412254405 0.000000e+00 6281.0
2 TraesCS1D01G218300 chr1A 95.123 1702 35 10 1889 3565 382229240 382230918 0.000000e+00 2639.0
3 TraesCS1D01G218300 chr1A 96.188 1364 39 6 3556 4918 382232856 382234207 0.000000e+00 2218.0
4 TraesCS1D01G218300 chr1A 93.023 1032 31 13 777 1794 382228233 382229237 0.000000e+00 1469.0
5 TraesCS1D01G218300 chr1A 89.394 132 10 2 5045 5175 382234203 382234331 4.270000e-36 163.0
6 TraesCS1D01G218300 chr3D 84.336 1296 140 35 3375 4664 15296385 15297623 0.000000e+00 1210.0
7 TraesCS1D01G218300 chr3D 84.065 1299 145 22 3371 4664 54336934 54338175 0.000000e+00 1195.0
8 TraesCS1D01G218300 chr3D 97.143 70 2 0 615 684 234308640 234308571 9.370000e-23 119.0
9 TraesCS1D01G218300 chr6A 83.680 1299 150 24 3371 4664 585065575 585066816 0.000000e+00 1168.0
10 TraesCS1D01G218300 chrUn 83.437 1292 143 31 3378 4664 117284153 117285378 0.000000e+00 1134.0
11 TraesCS1D01G218300 chr5B 82.753 1293 151 33 3378 4664 581762235 581763461 0.000000e+00 1086.0
12 TraesCS1D01G218300 chr5B 86.280 379 40 6 4286 4664 702396306 702396672 8.310000e-108 401.0
13 TraesCS1D01G218300 chr3B 82.276 1292 140 39 3378 4664 51866355 51867562 0.000000e+00 1035.0
14 TraesCS1D01G218300 chr3B 92.368 380 28 1 1 380 349306650 349306272 1.690000e-149 540.0
15 TraesCS1D01G218300 chr3B 90.000 70 6 1 615 684 349305907 349305839 7.350000e-14 89.8
16 TraesCS1D01G218300 chr7A 87.688 398 30 5 1 380 128042755 128042359 3.790000e-121 446.0
17 TraesCS1D01G218300 chr7A 87.143 70 9 0 615 684 44300808 44300877 4.420000e-11 80.5
18 TraesCS1D01G218300 chr5A 87.728 383 33 1 1 369 599654623 599655005 8.190000e-118 435.0
19 TraesCS1D01G218300 chr5A 86.935 398 31 5 1 380 622447170 622446776 1.370000e-115 427.0
20 TraesCS1D01G218300 chr5A 86.224 196 22 3 372 565 622441018 622440826 1.940000e-49 207.0
21 TraesCS1D01G218300 chr5A 91.429 70 6 0 615 684 599655519 599655588 4.390000e-16 97.1
22 TraesCS1D01G218300 chr5A 86.747 83 11 0 615 697 622436310 622436228 5.680000e-15 93.5
23 TraesCS1D01G218300 chr5A 92.593 54 4 0 615 668 11082649 11082702 1.590000e-10 78.7
24 TraesCS1D01G218300 chr5A 86.111 72 10 0 626 697 623020988 623020917 1.590000e-10 78.7
25 TraesCS1D01G218300 chr2A 84.906 212 30 2 1263 1473 115753429 115753639 4.180000e-51 213.0
26 TraesCS1D01G218300 chr2D 84.434 212 31 2 1263 1473 114532607 114532817 1.940000e-49 207.0
27 TraesCS1D01G218300 chr4A 82.468 154 22 4 5175 5327 461225809 461225958 4.330000e-26 130.0


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 TraesCS1D01G218300 chr1D 305110287 305115614 5327 False 9840.00 9840 100.0000 1 5328 1 chr1D.!!$F1 5327
1 TraesCS1D01G218300 chr1B 412254405 412258567 4162 True 6281.00 6281 94.2290 833 4918 1 chr1B.!!$R1 4085
2 TraesCS1D01G218300 chr1A 382228233 382234331 6098 False 1622.25 2639 93.4320 777 5175 4 chr1A.!!$F1 4398
3 TraesCS1D01G218300 chr3D 15296385 15297623 1238 False 1210.00 1210 84.3360 3375 4664 1 chr3D.!!$F1 1289
4 TraesCS1D01G218300 chr3D 54336934 54338175 1241 False 1195.00 1195 84.0650 3371 4664 1 chr3D.!!$F2 1293
5 TraesCS1D01G218300 chr6A 585065575 585066816 1241 False 1168.00 1168 83.6800 3371 4664 1 chr6A.!!$F1 1293
6 TraesCS1D01G218300 chrUn 117284153 117285378 1225 False 1134.00 1134 83.4370 3378 4664 1 chrUn.!!$F1 1286
7 TraesCS1D01G218300 chr5B 581762235 581763461 1226 False 1086.00 1086 82.7530 3378 4664 1 chr5B.!!$F1 1286
8 TraesCS1D01G218300 chr3B 51866355 51867562 1207 False 1035.00 1035 82.2760 3378 4664 1 chr3B.!!$F1 1286
9 TraesCS1D01G218300 chr3B 349305839 349306650 811 True 314.90 540 91.1840 1 684 2 chr3B.!!$R1 683
10 TraesCS1D01G218300 chr5A 599654623 599655588 965 False 266.05 435 89.5785 1 684 2 chr5A.!!$F2 683

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
648 948 0.029700 GTGTACGTTTTGTGGGGTGC 59.970 55.000 0.00 0.0 0.0 5.01 F
1563 1879 1.003112 ATTCGCGCCCCAGTTAACA 60.003 52.632 8.61 0.0 0.0 2.41 F
2488 2855 1.075050 AGAGTCACCGAGTGGAACCTA 59.925 52.381 4.52 0.0 37.8 3.08 F
3805 6145 1.228063 GGTCAGCGATCCCATGCAT 60.228 57.895 0.00 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2488 2855 0.761187 TGCTGTGCCTCAGAAAGTCT 59.239 50.0 9.68 0.0 46.27 3.24 R
3187 3579 1.698506 TGGGTGCTTTGGTTACCTTG 58.301 50.0 2.07 0.0 34.87 3.61 R
3915 6255 0.876399 ACAAACGGCGTGAAATACCC 59.124 50.0 15.70 0.0 0.00 3.69 R
5244 7600 0.040058 TGCCATCTGGTTCCAGCATT 59.960 50.0 13.44 0.0 37.57 3.56 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
29 30 3.717707 TCACCTCAGACGAACTTCAAAG 58.282 45.455 0.00 0.00 0.00 2.77
30 31 3.383505 TCACCTCAGACGAACTTCAAAGA 59.616 43.478 0.00 0.00 0.00 2.52
74 75 0.247736 CAAGCTCCTGCGACCTACTT 59.752 55.000 0.00 0.00 45.42 2.24
193 208 2.610479 GCGAGAAGGTGATGAACAGACA 60.610 50.000 0.00 0.00 0.00 3.41
194 209 3.854666 CGAGAAGGTGATGAACAGACAT 58.145 45.455 0.00 0.00 0.00 3.06
265 281 2.359169 GGTGCCGTCCAGATCAGGA 61.359 63.158 2.05 2.05 34.64 3.86
271 287 1.893786 GTCCAGATCAGGAGCGTGT 59.106 57.895 7.17 0.00 38.64 4.49
281 297 2.408022 GAGCGTGTACGGCGAGAT 59.592 61.111 16.62 0.00 40.23 2.75
284 300 2.488355 CGTGTACGGCGAGATGGT 59.512 61.111 16.62 0.00 35.37 3.55
286 302 1.214589 GTGTACGGCGAGATGGTGT 59.785 57.895 16.62 0.00 0.00 4.16
346 362 1.076632 CGGCTCTACCTCCTCTGGT 60.077 63.158 0.00 0.00 43.66 4.00
353 369 1.845627 TACCTCCTCTGGTCGTCCGT 61.846 60.000 0.00 0.00 41.22 4.69
369 385 1.375396 CGTTGCGTGGGGAAGATGA 60.375 57.895 0.00 0.00 0.00 2.92
370 386 0.744414 CGTTGCGTGGGGAAGATGAT 60.744 55.000 0.00 0.00 0.00 2.45
422 536 4.217159 GGTAGGCGGCGTGGGTAG 62.217 72.222 9.37 0.00 0.00 3.18
423 537 3.455469 GTAGGCGGCGTGGGTAGT 61.455 66.667 9.37 0.00 0.00 2.73
451 565 2.287849 GGAGTTCTTTTGAGCAAGGCAC 60.288 50.000 0.00 0.00 31.68 5.01
453 567 0.667993 TTCTTTTGAGCAAGGCACCG 59.332 50.000 0.00 0.00 0.00 4.94
515 630 2.125269 ACGCGTGATTGTAGGGGC 60.125 61.111 12.93 0.00 0.00 5.80
523 638 3.385749 ATTGTAGGGGCTGCGGACG 62.386 63.158 0.00 0.00 0.00 4.79
549 664 1.287425 CGTCCTATTTTCCTCGGTGC 58.713 55.000 0.00 0.00 0.00 5.01
567 682 1.227527 CAGCACGGTCAGTCAACCA 60.228 57.895 0.00 0.00 39.43 3.67
582 709 5.338559 CAGTCAACCAAAATTACTAAACGCG 59.661 40.000 3.53 3.53 0.00 6.01
607 734 7.148407 CGCACCAGAAAACAGATTAGATTAAGT 60.148 37.037 0.00 0.00 0.00 2.24
645 945 0.532417 TCCGTGTACGTTTTGTGGGG 60.532 55.000 0.00 0.00 37.74 4.96
646 946 0.814812 CCGTGTACGTTTTGTGGGGT 60.815 55.000 0.00 0.00 37.74 4.95
647 947 0.305313 CGTGTACGTTTTGTGGGGTG 59.695 55.000 0.00 0.00 34.11 4.61
648 948 0.029700 GTGTACGTTTTGTGGGGTGC 59.970 55.000 0.00 0.00 0.00 5.01
649 949 1.280444 GTACGTTTTGTGGGGTGCG 59.720 57.895 0.00 0.00 0.00 5.34
762 1062 7.762588 AACTTGTACTAGCTCTAAAGTGAGA 57.237 36.000 4.10 0.00 36.23 3.27
763 1063 7.762588 ACTTGTACTAGCTCTAAAGTGAGAA 57.237 36.000 4.10 0.00 36.23 2.87
764 1064 8.179509 ACTTGTACTAGCTCTAAAGTGAGAAA 57.820 34.615 4.10 0.00 36.23 2.52
765 1065 8.301002 ACTTGTACTAGCTCTAAAGTGAGAAAG 58.699 37.037 4.10 0.00 36.23 2.62
766 1066 7.762588 TGTACTAGCTCTAAAGTGAGAAAGT 57.237 36.000 0.00 0.00 36.23 2.66
767 1067 8.179509 TGTACTAGCTCTAAAGTGAGAAAGTT 57.820 34.615 0.00 0.00 36.23 2.66
768 1068 9.293404 TGTACTAGCTCTAAAGTGAGAAAGTTA 57.707 33.333 0.00 0.00 36.23 2.24
769 1069 9.558648 GTACTAGCTCTAAAGTGAGAAAGTTAC 57.441 37.037 0.00 0.00 36.23 2.50
770 1070 8.179509 ACTAGCTCTAAAGTGAGAAAGTTACA 57.820 34.615 0.00 0.00 36.23 2.41
771 1071 8.808092 ACTAGCTCTAAAGTGAGAAAGTTACAT 58.192 33.333 0.00 0.00 36.23 2.29
979 1287 1.123928 CCTCTAGATCAGCCCCGTTT 58.876 55.000 0.00 0.00 0.00 3.60
993 1301 2.019951 CGTTTCCCGTCCAGTCACG 61.020 63.158 0.00 0.00 39.61 4.35
1475 1784 1.229131 ATGCCCATCATCAAGGTCCT 58.771 50.000 0.00 0.00 0.00 3.85
1499 1808 3.819337 CTCCCACTTTCATCCATGCATAG 59.181 47.826 0.00 0.00 0.00 2.23
1500 1809 2.295349 CCCACTTTCATCCATGCATAGC 59.705 50.000 0.00 0.00 0.00 2.97
1501 1810 2.953648 CCACTTTCATCCATGCATAGCA 59.046 45.455 0.00 0.00 44.86 3.49
1525 1840 5.291905 ACCCCTTAATTTGACGATCCTAG 57.708 43.478 0.00 0.00 0.00 3.02
1530 1845 5.237344 CCTTAATTTGACGATCCTAGGCAAG 59.763 44.000 2.96 0.00 37.96 4.01
1557 1873 3.508840 GTTGGATTCGCGCCCCAG 61.509 66.667 0.00 0.00 0.00 4.45
1563 1879 1.003112 ATTCGCGCCCCAGTTAACA 60.003 52.632 8.61 0.00 0.00 2.41
1736 2052 9.862371 GTAATCTCAGTAGAATCACAGAAAAGA 57.138 33.333 0.00 0.00 34.73 2.52
1750 2066 5.578727 CACAGAAAAGATGACTACTGGCTAC 59.421 44.000 0.00 0.00 0.00 3.58
1785 2101 8.906867 ACAAGTGGTCATATTTATGGATTCTTG 58.093 33.333 15.69 15.69 36.76 3.02
1810 2126 5.615289 ACTGTCATAGGCTGTTATGAATCC 58.385 41.667 0.00 0.00 40.64 3.01
1871 2203 3.062774 GTCTTGCCGAGAACTTAGATTGC 59.937 47.826 0.00 0.00 35.79 3.56
1882 2214 5.237344 AGAACTTAGATTGCTGTGTTGTGTC 59.763 40.000 0.00 0.00 0.00 3.67
2003 2335 3.441222 TGCATTCGATTCATCTGCAAACT 59.559 39.130 0.89 0.00 39.68 2.66
2008 2344 6.887376 TTCGATTCATCTGCAAACTAGTAC 57.113 37.500 0.00 0.00 0.00 2.73
2009 2345 5.961272 TCGATTCATCTGCAAACTAGTACA 58.039 37.500 0.00 0.00 0.00 2.90
2134 2501 5.809001 TCTTGTTATGCTGAGGAGAAATGT 58.191 37.500 0.00 0.00 0.00 2.71
2488 2855 1.075050 AGAGTCACCGAGTGGAACCTA 59.925 52.381 4.52 0.00 37.80 3.08
2518 2885 2.267006 CACAGCACGCAGGGAGAT 59.733 61.111 0.00 0.00 0.00 2.75
2562 2929 4.727507 TCTCATCAAGTGACTAGCCTTC 57.272 45.455 0.00 0.00 32.22 3.46
2583 2950 3.960102 TCATGCAAAACTCTTTTCACCCT 59.040 39.130 0.00 0.00 0.00 4.34
2605 2972 5.181811 CCTGCCGCAAATATCATCTGAATTA 59.818 40.000 0.00 0.00 0.00 1.40
2718 3108 3.763360 TGTGGATAATTTGCAAGTCCAGG 59.237 43.478 19.05 0.00 39.47 4.45
3187 3579 1.750193 TTTCCAATCCTGTCGGCATC 58.250 50.000 0.00 0.00 0.00 3.91
3237 3629 2.646930 CTTGCCTGCATATGGTCTTCA 58.353 47.619 4.56 0.00 0.00 3.02
3256 3648 6.700960 GTCTTCAGTGACATCTCTTCATATGG 59.299 42.308 2.13 0.00 36.97 2.74
3389 3782 4.008330 CCATCAATGCTTCACAAGTCTCT 58.992 43.478 0.00 0.00 0.00 3.10
3393 3786 6.974932 TCAATGCTTCACAAGTCTCTTATC 57.025 37.500 0.00 0.00 0.00 1.75
3566 5906 7.227992 GTCACAATCTTATGACTGTCTTAGC 57.772 40.000 9.51 0.00 41.69 3.09
3805 6145 1.228063 GGTCAGCGATCCCATGCAT 60.228 57.895 0.00 0.00 0.00 3.96
3826 6166 1.965930 GAACACCATCAGCGCACCA 60.966 57.895 11.47 0.00 0.00 4.17
3829 6169 2.042259 CACCATCAGCGCACCATGT 61.042 57.895 11.47 0.00 0.00 3.21
3915 6255 6.475727 CGACATAGAACAACCTACTTATGGTG 59.524 42.308 0.00 0.00 37.93 4.17
4180 6527 2.174639 TGGATCCAACACAGTGACCTTT 59.825 45.455 13.46 0.00 0.00 3.11
4189 6536 2.733552 CACAGTGACCTTTGACGATCTG 59.266 50.000 0.00 0.00 0.00 2.90
4192 6539 1.996191 GTGACCTTTGACGATCTGAGC 59.004 52.381 0.00 0.00 0.00 4.26
4371 6718 3.531538 CCCGCAAAACTATCTTCAGCTA 58.468 45.455 0.00 0.00 0.00 3.32
4559 6908 0.242017 GATGCAGTTTGTGTGAGGGC 59.758 55.000 0.00 0.00 0.00 5.19
4630 6984 6.382859 TGCTGAGACTGGACATAAGGTTTATA 59.617 38.462 0.00 0.00 0.00 0.98
4688 7043 0.935898 TATCTTCTCTCGCGGTCGTC 59.064 55.000 6.13 0.00 36.96 4.20
4719 7074 2.305927 TCGCCCAATTCTTCTTCCTCTT 59.694 45.455 0.00 0.00 0.00 2.85
4722 7077 4.021981 CGCCCAATTCTTCTTCCTCTTTTT 60.022 41.667 0.00 0.00 0.00 1.94
4749 7105 1.075536 GGGATCTCCTCCTCCTCTCTC 59.924 61.905 0.00 0.00 44.28 3.20
4750 7106 1.271379 GGATCTCCTCCTCCTCTCTCG 60.271 61.905 0.00 0.00 41.29 4.04
4752 7108 0.986019 TCTCCTCCTCCTCTCTCGCT 60.986 60.000 0.00 0.00 0.00 4.93
4753 7109 0.819259 CTCCTCCTCCTCTCTCGCTG 60.819 65.000 0.00 0.00 0.00 5.18
4755 7111 1.101049 CCTCCTCCTCTCTCGCTGTC 61.101 65.000 0.00 0.00 0.00 3.51
4756 7112 0.107214 CTCCTCCTCTCTCGCTGTCT 60.107 60.000 0.00 0.00 0.00 3.41
4760 7116 1.670811 CTCCTCTCTCGCTGTCTTCTC 59.329 57.143 0.00 0.00 0.00 2.87
4923 7279 4.819761 GACGGCTGCTGCATCCGA 62.820 66.667 40.80 4.11 44.57 4.55
4924 7280 4.827087 ACGGCTGCTGCATCCGAG 62.827 66.667 40.80 20.63 44.57 4.63
4928 7284 4.478371 CTGCTGCATCCGAGGGCA 62.478 66.667 1.31 0.00 38.52 5.36
4932 7288 3.785859 TGCATCCGAGGGCAGACC 61.786 66.667 0.00 0.00 34.58 3.85
4933 7289 4.899239 GCATCCGAGGGCAGACCG 62.899 72.222 0.00 0.00 46.96 4.79
4934 7290 3.461773 CATCCGAGGGCAGACCGT 61.462 66.667 0.00 0.00 46.96 4.83
4935 7291 3.461773 ATCCGAGGGCAGACCGTG 61.462 66.667 0.00 0.00 46.96 4.94
4938 7294 4.742201 CGAGGGCAGACCGTGGTG 62.742 72.222 0.00 0.00 46.96 4.17
4944 7300 3.625897 CAGACCGTGGTGCTGGGA 61.626 66.667 0.00 0.00 0.00 4.37
4945 7301 3.314331 AGACCGTGGTGCTGGGAG 61.314 66.667 0.00 0.00 0.00 4.30
4956 7312 4.555610 CTGGGAGCAGAATCCAGC 57.444 61.111 0.00 0.00 41.12 4.85
4957 7313 1.523258 CTGGGAGCAGAATCCAGCG 60.523 63.158 0.00 0.00 41.12 5.18
4958 7314 1.964608 CTGGGAGCAGAATCCAGCGA 61.965 60.000 0.00 0.00 41.12 4.93
4959 7315 1.340399 TGGGAGCAGAATCCAGCGAT 61.340 55.000 0.00 0.00 41.52 4.58
4960 7316 0.883814 GGGAGCAGAATCCAGCGATG 60.884 60.000 0.00 0.00 41.52 3.84
4961 7317 0.179062 GGAGCAGAATCCAGCGATGT 60.179 55.000 0.00 0.00 39.34 3.06
4962 7318 1.661341 GAGCAGAATCCAGCGATGTT 58.339 50.000 0.00 0.00 35.48 2.71
4963 7319 1.329906 GAGCAGAATCCAGCGATGTTG 59.670 52.381 0.00 0.00 35.48 3.33
4964 7320 0.379669 GCAGAATCCAGCGATGTTGG 59.620 55.000 0.00 0.00 35.19 3.77
4965 7321 2.013563 GCAGAATCCAGCGATGTTGGA 61.014 52.381 4.83 4.83 46.22 3.53
4966 7322 2.358957 CAGAATCCAGCGATGTTGGAA 58.641 47.619 6.47 0.00 45.38 3.53
4967 7323 2.096496 CAGAATCCAGCGATGTTGGAAC 59.904 50.000 6.47 4.71 45.38 3.62
4968 7324 1.401905 GAATCCAGCGATGTTGGAACC 59.598 52.381 6.47 0.00 45.38 3.62
4969 7325 0.744414 ATCCAGCGATGTTGGAACCG 60.744 55.000 6.47 0.00 45.38 4.44
4970 7326 2.398554 CCAGCGATGTTGGAACCGG 61.399 63.158 0.00 0.00 35.94 5.28
4971 7327 2.746277 AGCGATGTTGGAACCGGC 60.746 61.111 0.00 0.00 0.00 6.13
4972 7328 3.053291 GCGATGTTGGAACCGGCA 61.053 61.111 0.00 0.00 0.00 5.69
4973 7329 2.622011 GCGATGTTGGAACCGGCAA 61.622 57.895 0.00 0.00 0.00 4.52
4974 7330 1.501741 CGATGTTGGAACCGGCAAG 59.498 57.895 0.00 0.00 0.00 4.01
4975 7331 0.953471 CGATGTTGGAACCGGCAAGA 60.953 55.000 0.00 0.00 0.00 3.02
4976 7332 1.243902 GATGTTGGAACCGGCAAGAA 58.756 50.000 0.00 0.00 0.00 2.52
4977 7333 1.818674 GATGTTGGAACCGGCAAGAAT 59.181 47.619 0.00 0.00 0.00 2.40
4978 7334 1.698506 TGTTGGAACCGGCAAGAATT 58.301 45.000 0.00 0.00 0.00 2.17
4979 7335 2.035632 TGTTGGAACCGGCAAGAATTT 58.964 42.857 0.00 0.00 0.00 1.82
4980 7336 2.432510 TGTTGGAACCGGCAAGAATTTT 59.567 40.909 0.00 0.00 0.00 1.82
4981 7337 3.118592 TGTTGGAACCGGCAAGAATTTTT 60.119 39.130 0.00 0.00 0.00 1.94
4982 7338 3.104843 TGGAACCGGCAAGAATTTTTG 57.895 42.857 0.00 4.38 0.00 2.44
4991 7347 1.715519 CAAGAATTTTTGCTGCCGACG 59.284 47.619 0.00 0.00 0.00 5.12
4992 7348 0.387239 AGAATTTTTGCTGCCGACGC 60.387 50.000 0.00 0.00 0.00 5.19
4993 7349 1.664643 GAATTTTTGCTGCCGACGCG 61.665 55.000 3.53 3.53 38.08 6.01
4994 7350 2.123988 AATTTTTGCTGCCGACGCGA 62.124 50.000 15.93 0.00 38.08 5.87
4995 7351 1.922135 ATTTTTGCTGCCGACGCGAT 61.922 50.000 15.93 0.00 38.08 4.58
4996 7352 2.507322 TTTTTGCTGCCGACGCGATC 62.507 55.000 15.93 5.79 38.08 3.69
4997 7353 3.932580 TTTGCTGCCGACGCGATCT 62.933 57.895 15.93 0.00 38.08 2.75
4998 7354 3.932580 TTGCTGCCGACGCGATCTT 62.933 57.895 15.93 0.00 38.08 2.40
4999 7355 3.188786 GCTGCCGACGCGATCTTT 61.189 61.111 15.93 0.00 38.08 2.52
5000 7356 2.740714 GCTGCCGACGCGATCTTTT 61.741 57.895 15.93 0.00 38.08 2.27
5001 7357 1.787847 CTGCCGACGCGATCTTTTT 59.212 52.632 15.93 0.00 38.08 1.94
5022 7378 2.969157 CTAGTGAGCACATGCCGAG 58.031 57.895 0.00 0.00 43.38 4.63
5023 7379 0.457443 CTAGTGAGCACATGCCGAGA 59.543 55.000 0.00 0.00 43.38 4.04
5024 7380 1.068281 CTAGTGAGCACATGCCGAGAT 59.932 52.381 0.00 0.00 43.38 2.75
5025 7381 0.461516 AGTGAGCACATGCCGAGATG 60.462 55.000 0.00 0.00 43.38 2.90
5026 7382 1.816679 TGAGCACATGCCGAGATGC 60.817 57.895 0.00 0.00 43.38 3.91
5027 7383 2.588439 AGCACATGCCGAGATGCT 59.412 55.556 0.00 0.67 43.50 3.79
5028 7384 1.818363 AGCACATGCCGAGATGCTG 60.818 57.895 5.52 0.00 46.42 4.41
5029 7385 2.831366 GCACATGCCGAGATGCTGG 61.831 63.158 0.00 0.00 35.16 4.85
5030 7386 1.153309 CACATGCCGAGATGCTGGA 60.153 57.895 0.00 0.00 0.00 3.86
5031 7387 0.745486 CACATGCCGAGATGCTGGAA 60.745 55.000 0.00 0.00 0.00 3.53
5032 7388 0.745845 ACATGCCGAGATGCTGGAAC 60.746 55.000 0.00 0.00 0.00 3.62
5033 7389 1.153086 ATGCCGAGATGCTGGAACC 60.153 57.895 0.00 0.00 0.00 3.62
5034 7390 2.892425 GCCGAGATGCTGGAACCG 60.892 66.667 0.00 0.00 0.00 4.44
5035 7391 2.202932 CCGAGATGCTGGAACCGG 60.203 66.667 0.00 0.00 0.00 5.28
5036 7392 2.579201 CGAGATGCTGGAACCGGT 59.421 61.111 0.00 0.00 0.00 5.28
5037 7393 1.672854 CCGAGATGCTGGAACCGGTA 61.673 60.000 8.00 0.00 33.02 4.02
5038 7394 0.389391 CGAGATGCTGGAACCGGTAT 59.611 55.000 8.00 0.00 0.00 2.73
5039 7395 1.611977 CGAGATGCTGGAACCGGTATA 59.388 52.381 8.00 0.00 0.00 1.47
5040 7396 2.035449 CGAGATGCTGGAACCGGTATAA 59.965 50.000 8.00 0.00 0.00 0.98
5041 7397 3.491964 CGAGATGCTGGAACCGGTATAAA 60.492 47.826 8.00 0.00 0.00 1.40
5042 7398 4.058817 GAGATGCTGGAACCGGTATAAAG 58.941 47.826 8.00 4.70 0.00 1.85
5043 7399 2.032680 TGCTGGAACCGGTATAAAGC 57.967 50.000 8.00 15.67 0.00 3.51
5044 7400 0.935196 GCTGGAACCGGTATAAAGCG 59.065 55.000 8.00 0.00 46.00 4.68
5117 7473 1.716172 GATGAAAACGGCGAGCTCC 59.284 57.895 16.62 0.47 0.00 4.70
5129 7485 4.021925 AGCTCCGGTGCTCCAACC 62.022 66.667 24.87 0.00 39.34 3.77
5136 7492 3.364277 GGTGCTCCAACCGTAGATC 57.636 57.895 0.00 0.00 0.00 2.75
5137 7493 0.824759 GGTGCTCCAACCGTAGATCT 59.175 55.000 0.00 0.00 0.00 2.75
5184 7540 3.030652 AAAAACTCGCCGGTGCTG 58.969 55.556 11.05 8.23 34.43 4.41
5185 7541 3.194272 AAAAACTCGCCGGTGCTGC 62.194 57.895 11.05 0.00 34.43 5.25
5186 7542 4.927782 AAACTCGCCGGTGCTGCA 62.928 61.111 11.05 0.00 34.43 4.41
5187 7543 4.927782 AACTCGCCGGTGCTGCAA 62.928 61.111 11.05 0.00 34.43 4.08
5195 7551 4.617875 GGTGCTGCAACCGTAGAT 57.382 55.556 6.36 0.00 0.00 1.98
5196 7552 2.854522 GGTGCTGCAACCGTAGATT 58.145 52.632 6.36 0.00 0.00 2.40
5197 7553 1.165270 GGTGCTGCAACCGTAGATTT 58.835 50.000 6.36 0.00 0.00 2.17
5198 7554 1.539827 GGTGCTGCAACCGTAGATTTT 59.460 47.619 6.36 0.00 0.00 1.82
5199 7555 2.030274 GGTGCTGCAACCGTAGATTTTT 60.030 45.455 6.36 0.00 0.00 1.94
5222 7578 4.473643 CTGGAACCACCTGCGAAA 57.526 55.556 0.00 0.00 39.86 3.46
5223 7579 2.714259 CTGGAACCACCTGCGAAAA 58.286 52.632 0.00 0.00 39.86 2.29
5224 7580 1.028905 CTGGAACCACCTGCGAAAAA 58.971 50.000 0.00 0.00 39.86 1.94
5239 7595 3.731295 AAAAACTGCAACCACCGTG 57.269 47.368 0.00 0.00 0.00 4.94
5240 7596 0.459411 AAAAACTGCAACCACCGTGC 60.459 50.000 0.00 0.00 42.55 5.34
5242 7598 2.278182 AAACTGCAACCACCGTGCAC 62.278 55.000 6.82 6.82 46.76 4.57
5243 7599 2.901840 CTGCAACCACCGTGCACT 60.902 61.111 16.19 0.00 46.76 4.40
5244 7600 1.596752 CTGCAACCACCGTGCACTA 60.597 57.895 16.19 0.00 46.76 2.74
5245 7601 1.153147 TGCAACCACCGTGCACTAA 60.153 52.632 16.19 0.00 46.76 2.24
5246 7602 0.536233 TGCAACCACCGTGCACTAAT 60.536 50.000 16.19 0.00 46.76 1.73
5247 7603 0.109781 GCAACCACCGTGCACTAATG 60.110 55.000 16.19 9.86 41.80 1.90
5261 7617 2.947652 CACTAATGCTGGAACCAGATGG 59.052 50.000 22.96 12.48 46.30 3.51
5262 7618 1.952296 CTAATGCTGGAACCAGATGGC 59.048 52.381 22.96 9.97 46.30 4.40
5263 7619 0.040058 AATGCTGGAACCAGATGGCA 59.960 50.000 22.96 14.95 46.30 4.92
5264 7620 0.260816 ATGCTGGAACCAGATGGCAT 59.739 50.000 22.96 16.39 46.30 4.40
5265 7621 0.394762 TGCTGGAACCAGATGGCATC 60.395 55.000 22.96 19.78 46.30 3.91
5266 7622 0.394762 GCTGGAACCAGATGGCATCA 60.395 55.000 27.93 6.44 46.30 3.07
5267 7623 1.956636 GCTGGAACCAGATGGCATCAA 60.957 52.381 27.93 4.94 46.30 2.57
5268 7624 2.022195 CTGGAACCAGATGGCATCAAG 58.978 52.381 27.93 20.14 46.30 3.02
5269 7625 1.341285 TGGAACCAGATGGCATCAAGG 60.341 52.381 27.93 27.60 39.32 3.61
5270 7626 1.064463 GGAACCAGATGGCATCAAGGA 60.064 52.381 32.54 0.00 39.32 3.36
5271 7627 2.423947 GGAACCAGATGGCATCAAGGAT 60.424 50.000 32.54 25.38 39.32 3.24
5272 7628 2.653234 ACCAGATGGCATCAAGGATC 57.347 50.000 32.54 9.51 39.32 3.36
5273 7629 1.848388 ACCAGATGGCATCAAGGATCA 59.152 47.619 32.54 0.00 39.32 2.92
5274 7630 2.445905 ACCAGATGGCATCAAGGATCAT 59.554 45.455 32.54 16.05 39.32 2.45
5275 7631 3.117246 ACCAGATGGCATCAAGGATCATT 60.117 43.478 32.54 15.77 39.32 2.57
5276 7632 4.105217 ACCAGATGGCATCAAGGATCATTA 59.895 41.667 32.54 0.00 39.32 1.90
5277 7633 5.222275 ACCAGATGGCATCAAGGATCATTAT 60.222 40.000 32.54 14.67 39.32 1.28
5278 7634 5.125578 CCAGATGGCATCAAGGATCATTATG 59.874 44.000 27.93 12.95 0.00 1.90
5279 7635 4.705507 AGATGGCATCAAGGATCATTATGC 59.294 41.667 27.93 18.18 41.69 3.14
5280 7636 4.108501 TGGCATCAAGGATCATTATGCT 57.891 40.909 22.08 0.00 42.01 3.79
5281 7637 3.824443 TGGCATCAAGGATCATTATGCTG 59.176 43.478 22.08 6.54 42.01 4.41
5282 7638 3.192844 GGCATCAAGGATCATTATGCTGG 59.807 47.826 22.08 1.98 42.01 4.85
5283 7639 3.192844 GCATCAAGGATCATTATGCTGGG 59.807 47.826 18.70 0.00 39.80 4.45
5284 7640 4.659115 CATCAAGGATCATTATGCTGGGA 58.341 43.478 0.00 0.00 33.47 4.37
5285 7641 4.090761 TCAAGGATCATTATGCTGGGAC 57.909 45.455 0.00 0.00 33.47 4.46
5286 7642 3.152341 CAAGGATCATTATGCTGGGACC 58.848 50.000 0.00 0.00 33.47 4.46
5287 7643 1.707427 AGGATCATTATGCTGGGACCC 59.293 52.381 2.45 2.45 31.67 4.46
5288 7644 1.425066 GGATCATTATGCTGGGACCCA 59.575 52.381 14.08 14.08 0.00 4.51
5289 7645 2.508526 GATCATTATGCTGGGACCCAC 58.491 52.381 9.95 7.65 0.00 4.61
5290 7646 1.294041 TCATTATGCTGGGACCCACA 58.706 50.000 9.95 13.45 0.00 4.17
5291 7647 1.638070 TCATTATGCTGGGACCCACAA 59.362 47.619 9.95 0.09 0.00 3.33
5292 7648 2.244510 TCATTATGCTGGGACCCACAAT 59.755 45.455 9.95 8.76 0.00 2.71
5293 7649 2.435372 TTATGCTGGGACCCACAATC 57.565 50.000 9.95 0.00 0.00 2.67
5294 7650 1.294041 TATGCTGGGACCCACAATCA 58.706 50.000 9.95 5.81 0.00 2.57
5295 7651 0.409092 ATGCTGGGACCCACAATCAA 59.591 50.000 9.95 0.00 0.00 2.57
5296 7652 0.187117 TGCTGGGACCCACAATCAAA 59.813 50.000 9.95 0.00 0.00 2.69
5297 7653 1.203162 TGCTGGGACCCACAATCAAAT 60.203 47.619 9.95 0.00 0.00 2.32
5298 7654 1.901833 GCTGGGACCCACAATCAAATT 59.098 47.619 9.95 0.00 0.00 1.82
5299 7655 2.302733 GCTGGGACCCACAATCAAATTT 59.697 45.455 9.95 0.00 0.00 1.82
5300 7656 3.865684 GCTGGGACCCACAATCAAATTTG 60.866 47.826 9.95 12.15 0.00 2.32
5301 7657 2.038295 TGGGACCCACAATCAAATTTGC 59.962 45.455 9.95 0.00 0.00 3.68
5302 7658 2.302733 GGGACCCACAATCAAATTTGCT 59.697 45.455 13.54 0.29 0.00 3.91
5303 7659 3.328505 GGACCCACAATCAAATTTGCTG 58.671 45.455 13.54 14.34 0.00 4.41
5304 7660 3.328505 GACCCACAATCAAATTTGCTGG 58.671 45.455 13.54 13.31 32.36 4.85
5305 7661 2.971330 ACCCACAATCAAATTTGCTGGA 59.029 40.909 13.54 0.00 33.39 3.86
5306 7662 3.390639 ACCCACAATCAAATTTGCTGGAA 59.609 39.130 13.54 0.00 33.39 3.53
5307 7663 3.747529 CCCACAATCAAATTTGCTGGAAC 59.252 43.478 13.54 0.00 33.39 3.62
5308 7664 3.747529 CCACAATCAAATTTGCTGGAACC 59.252 43.478 13.54 0.00 33.39 3.62
5309 7665 4.378774 CACAATCAAATTTGCTGGAACCA 58.621 39.130 13.54 0.00 0.00 3.67
5310 7666 4.449743 CACAATCAAATTTGCTGGAACCAG 59.550 41.667 13.54 15.64 46.15 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.609409 GCAACACCCGATCTTTGTTCTTC 60.609 47.826 0.00 0.00 30.98 2.87
30 31 2.293399 GCAACACCCGATCTTTGTTCTT 59.707 45.455 0.00 0.00 30.98 2.52
74 75 2.033793 GAGCCGACGATCTGGATCA 58.966 57.895 10.62 0.00 40.37 2.92
193 208 1.000283 GATCCAGCCGAGATTCGTCAT 60.000 52.381 0.00 0.00 38.40 3.06
194 209 0.385751 GATCCAGCCGAGATTCGTCA 59.614 55.000 0.00 0.00 38.40 4.35
265 281 2.102357 CATCTCGCCGTACACGCT 59.898 61.111 0.00 0.00 38.18 5.07
271 287 1.985447 GACGACACCATCTCGCCGTA 61.985 60.000 0.00 0.00 34.34 4.02
281 297 4.700365 CGAGCTGCGACGACACCA 62.700 66.667 14.67 0.00 44.57 4.17
305 321 2.099921 CGTCTCCCTCATTCACCTACAG 59.900 54.545 0.00 0.00 0.00 2.74
353 369 1.140852 CCTATCATCTTCCCCACGCAA 59.859 52.381 0.00 0.00 0.00 4.85
369 385 2.064581 GCCACCTGACCCGTCCTAT 61.065 63.158 0.00 0.00 0.00 2.57
370 386 2.682494 GCCACCTGACCCGTCCTA 60.682 66.667 0.00 0.00 0.00 2.94
402 514 2.852563 TACCCACGCCGCCTACCTAA 62.853 60.000 0.00 0.00 0.00 2.69
403 517 3.357444 TACCCACGCCGCCTACCTA 62.357 63.158 0.00 0.00 0.00 3.08
407 521 3.454573 CACTACCCACGCCGCCTA 61.455 66.667 0.00 0.00 0.00 3.93
436 550 1.372128 GCGGTGCCTTGCTCAAAAG 60.372 57.895 0.00 0.00 0.00 2.27
451 565 2.733227 GCAATCTCCTCAATTTGTGCGG 60.733 50.000 0.00 0.00 32.92 5.69
453 567 2.162208 TCGCAATCTCCTCAATTTGTGC 59.838 45.455 0.00 0.00 31.41 4.57
480 594 1.131126 CGTGAGGCATGCGAAAAGAAT 59.869 47.619 12.44 0.00 0.00 2.40
482 596 1.911293 GCGTGAGGCATGCGAAAAGA 61.911 55.000 12.44 0.00 42.87 2.52
523 638 0.651031 GGAAAATAGGACGCGCTCAC 59.349 55.000 5.73 0.00 0.00 3.51
534 649 1.398390 GTGCTGCACCGAGGAAAATAG 59.602 52.381 21.78 0.00 0.00 1.73
549 664 0.813610 TTGGTTGACTGACCGTGCTG 60.814 55.000 0.00 0.00 42.83 4.41
567 682 3.499157 TCTGGTGCGCGTTTAGTAATTTT 59.501 39.130 8.43 0.00 0.00 1.82
582 709 8.045176 ACTTAATCTAATCTGTTTTCTGGTGC 57.955 34.615 0.00 0.00 0.00 5.01
607 734 5.186992 CACGGATCCATTACCACCATATAGA 59.813 44.000 13.41 0.00 0.00 1.98
611 738 3.042682 ACACGGATCCATTACCACCATA 58.957 45.455 13.41 0.00 0.00 2.74
612 739 1.843851 ACACGGATCCATTACCACCAT 59.156 47.619 13.41 0.00 0.00 3.55
627 926 0.814812 ACCCCACAAAACGTACACGG 60.815 55.000 6.72 0.00 44.95 4.94
645 945 7.302524 TCCAACATTATCTTCTTTAAACGCAC 58.697 34.615 0.00 0.00 0.00 5.34
646 946 7.441890 TCCAACATTATCTTCTTTAAACGCA 57.558 32.000 0.00 0.00 0.00 5.24
647 947 8.798153 CAATCCAACATTATCTTCTTTAAACGC 58.202 33.333 0.00 0.00 0.00 4.84
648 948 9.840427 ACAATCCAACATTATCTTCTTTAAACG 57.160 29.630 0.00 0.00 0.00 3.60
736 1036 9.463902 TCTCACTTTAGAGCTAGTACAAGTTAT 57.536 33.333 0.00 0.00 35.59 1.89
737 1037 8.859236 TCTCACTTTAGAGCTAGTACAAGTTA 57.141 34.615 0.00 0.00 35.59 2.24
738 1038 7.762588 TCTCACTTTAGAGCTAGTACAAGTT 57.237 36.000 0.00 0.00 35.59 2.66
739 1039 7.762588 TTCTCACTTTAGAGCTAGTACAAGT 57.237 36.000 0.00 0.00 35.59 3.16
740 1040 8.301002 ACTTTCTCACTTTAGAGCTAGTACAAG 58.699 37.037 0.00 0.00 35.59 3.16
741 1041 8.179509 ACTTTCTCACTTTAGAGCTAGTACAA 57.820 34.615 0.00 0.00 35.59 2.41
742 1042 7.762588 ACTTTCTCACTTTAGAGCTAGTACA 57.237 36.000 0.00 0.00 35.59 2.90
743 1043 9.558648 GTAACTTTCTCACTTTAGAGCTAGTAC 57.441 37.037 0.00 0.00 35.59 2.73
744 1044 9.293404 TGTAACTTTCTCACTTTAGAGCTAGTA 57.707 33.333 0.00 0.00 35.59 1.82
745 1045 8.179509 TGTAACTTTCTCACTTTAGAGCTAGT 57.820 34.615 0.00 0.00 35.59 2.57
979 1287 3.986006 GTGCGTGACTGGACGGGA 61.986 66.667 0.00 0.00 39.81 5.14
993 1301 3.512516 GGAGCCGCCATTGAGTGC 61.513 66.667 0.00 0.00 36.34 4.40
1051 1359 4.918201 GCGGGCGGAGATGAAGGG 62.918 72.222 0.00 0.00 0.00 3.95
1475 1784 2.575735 TGCATGGATGAAAGTGGGAGTA 59.424 45.455 0.00 0.00 0.00 2.59
1499 1808 4.215613 GGATCGTCAAATTAAGGGGTATGC 59.784 45.833 0.00 0.00 0.00 3.14
1500 1809 5.621193 AGGATCGTCAAATTAAGGGGTATG 58.379 41.667 0.00 0.00 0.00 2.39
1501 1810 5.906772 AGGATCGTCAAATTAAGGGGTAT 57.093 39.130 0.00 0.00 0.00 2.73
1502 1811 5.306160 CCTAGGATCGTCAAATTAAGGGGTA 59.694 44.000 1.05 0.00 0.00 3.69
1504 1813 4.642429 CCTAGGATCGTCAAATTAAGGGG 58.358 47.826 1.05 0.00 0.00 4.79
1505 1814 4.065789 GCCTAGGATCGTCAAATTAAGGG 58.934 47.826 14.75 0.00 0.00 3.95
1530 1845 1.287425 CGAATCCAACGGAAGGCTAC 58.713 55.000 0.00 0.00 34.34 3.58
1557 1873 6.713450 TCAGAAGGACATAAACCCTTGTTAAC 59.287 38.462 0.00 0.00 42.43 2.01
1736 2052 4.651045 TGTCATGATGTAGCCAGTAGTCAT 59.349 41.667 0.00 0.00 0.00 3.06
1771 2087 9.347240 CCTATGACAGTTCAAGAATCCATAAAT 57.653 33.333 0.00 0.00 34.61 1.40
1785 2101 6.203723 GGATTCATAACAGCCTATGACAGTTC 59.796 42.308 1.32 0.00 37.89 3.01
1863 2195 5.696270 CAGTAGACACAACACAGCAATCTAA 59.304 40.000 0.00 0.00 0.00 2.10
1871 2203 4.882671 AAAAGCAGTAGACACAACACAG 57.117 40.909 0.00 0.00 0.00 3.66
2125 2492 8.341892 AGGAGAACATTTAGAAACATTTCTCC 57.658 34.615 20.88 20.88 43.72 3.71
2134 2501 8.742777 CAATCATGGAAGGAGAACATTTAGAAA 58.257 33.333 0.00 0.00 0.00 2.52
2224 2591 4.889409 CCAACCTGAAATACATAGTGCCAT 59.111 41.667 0.00 0.00 0.00 4.40
2488 2855 0.761187 TGCTGTGCCTCAGAAAGTCT 59.239 50.000 9.68 0.00 46.27 3.24
2518 2885 8.079211 AGATCAAGTAGCAATTTAGTCACCTA 57.921 34.615 0.00 0.00 0.00 3.08
2562 2929 4.053295 CAGGGTGAAAAGAGTTTTGCATG 58.947 43.478 0.00 0.00 34.39 4.06
2583 2950 6.631971 TTAATTCAGATGATATTTGCGGCA 57.368 33.333 0.00 0.00 0.00 5.69
2718 3108 7.810766 TCAGTTGTTTGACAAAATCACTTTC 57.189 32.000 1.27 0.00 40.15 2.62
2893 3285 5.083533 ACCTGCTCAGAGAAGAACATAAG 57.916 43.478 7.05 0.00 0.00 1.73
3187 3579 1.698506 TGGGTGCTTTGGTTACCTTG 58.301 50.000 2.07 0.00 34.87 3.61
3237 3629 5.563876 ATGCCATATGAAGAGATGTCACT 57.436 39.130 3.65 0.00 0.00 3.41
3256 3648 7.377766 TCAGGACTTCAGTAAAAACATATGC 57.622 36.000 1.58 0.00 0.00 3.14
3389 3782 6.934645 AGACCACAAAACTGAAAGATCGATAA 59.065 34.615 0.00 0.00 37.43 1.75
3393 3786 4.083802 GGAGACCACAAAACTGAAAGATCG 60.084 45.833 0.00 0.00 37.43 3.69
3826 6166 2.306805 TGATCTTGTCTTGAGCCCACAT 59.693 45.455 0.00 0.00 0.00 3.21
3829 6169 3.614092 GAATGATCTTGTCTTGAGCCCA 58.386 45.455 0.00 0.00 0.00 5.36
3915 6255 0.876399 ACAAACGGCGTGAAATACCC 59.124 50.000 15.70 0.00 0.00 3.69
4180 6527 3.514417 CGGGAGCTCAGATCGTCA 58.486 61.111 17.19 0.00 0.00 4.35
4192 6539 3.511595 TGCGTACGGTAGCGGGAG 61.512 66.667 19.72 9.78 35.87 4.30
4278 6625 2.167487 GTCCATGTCCTGTCTCTCTTCC 59.833 54.545 0.00 0.00 0.00 3.46
4371 6718 8.814038 AAGAATGCAAAATTATGTCCTCTAGT 57.186 30.769 0.00 0.00 0.00 2.57
4417 6765 3.436359 GCATTTCCAAAATCAAACGGCAT 59.564 39.130 0.00 0.00 0.00 4.40
4492 6841 5.051816 ACTGAAATTGAACCAAGCACAATG 58.948 37.500 0.00 0.00 35.00 2.82
4559 6908 3.885901 TCAGGTCTCATGTAATCTCTCCG 59.114 47.826 0.00 0.00 0.00 4.63
4630 6984 9.520204 CTCATATTGCGTTTCCAAATTTAATCT 57.480 29.630 0.00 0.00 0.00 2.40
4688 7043 2.826777 AATTGGGCGAGTGGCTGAGG 62.827 60.000 0.00 0.00 42.94 3.86
4915 7271 3.785859 GGTCTGCCCTCGGATGCA 61.786 66.667 0.00 0.00 35.86 3.96
4916 7272 4.899239 CGGTCTGCCCTCGGATGC 62.899 72.222 0.00 0.00 0.00 3.91
4917 7273 3.461773 ACGGTCTGCCCTCGGATG 61.462 66.667 0.00 0.00 0.00 3.51
4918 7274 3.461773 CACGGTCTGCCCTCGGAT 61.462 66.667 0.00 0.00 0.00 4.18
4921 7277 4.742201 CACCACGGTCTGCCCTCG 62.742 72.222 0.00 0.00 0.00 4.63
4927 7283 3.596066 CTCCCAGCACCACGGTCTG 62.596 68.421 8.06 8.06 0.00 3.51
4928 7284 3.314331 CTCCCAGCACCACGGTCT 61.314 66.667 0.00 0.00 0.00 3.85
4938 7294 4.555610 CTGGATTCTGCTCCCAGC 57.444 61.111 0.00 0.00 40.69 4.85
4940 7296 1.340399 ATCGCTGGATTCTGCTCCCA 61.340 55.000 0.98 0.00 35.96 4.37
4941 7297 0.883814 CATCGCTGGATTCTGCTCCC 60.884 60.000 0.98 0.00 35.96 4.30
4942 7298 0.179062 ACATCGCTGGATTCTGCTCC 60.179 55.000 0.98 0.00 35.96 4.70
4943 7299 1.329906 CAACATCGCTGGATTCTGCTC 59.670 52.381 0.98 0.00 35.96 4.26
4944 7300 1.376543 CAACATCGCTGGATTCTGCT 58.623 50.000 0.98 0.00 35.96 4.24
4945 7301 0.379669 CCAACATCGCTGGATTCTGC 59.620 55.000 0.00 0.00 35.85 4.26
4946 7302 2.028420 TCCAACATCGCTGGATTCTG 57.972 50.000 0.00 0.00 38.07 3.02
4947 7303 2.359900 GTTCCAACATCGCTGGATTCT 58.640 47.619 0.00 0.00 42.56 2.40
4948 7304 1.401905 GGTTCCAACATCGCTGGATTC 59.598 52.381 0.00 0.00 42.56 2.52
4949 7305 1.463674 GGTTCCAACATCGCTGGATT 58.536 50.000 0.00 0.00 42.56 3.01
4950 7306 0.744414 CGGTTCCAACATCGCTGGAT 60.744 55.000 0.00 0.00 42.56 3.41
4951 7307 1.375396 CGGTTCCAACATCGCTGGA 60.375 57.895 0.00 0.00 41.33 3.86
4952 7308 2.398554 CCGGTTCCAACATCGCTGG 61.399 63.158 0.00 0.00 35.05 4.85
4953 7309 3.039202 GCCGGTTCCAACATCGCTG 62.039 63.158 1.90 0.00 0.00 5.18
4954 7310 2.746277 GCCGGTTCCAACATCGCT 60.746 61.111 1.90 0.00 0.00 4.93
4955 7311 2.527547 CTTGCCGGTTCCAACATCGC 62.528 60.000 1.90 0.00 0.00 4.58
4956 7312 0.953471 TCTTGCCGGTTCCAACATCG 60.953 55.000 1.90 0.00 0.00 3.84
4957 7313 1.243902 TTCTTGCCGGTTCCAACATC 58.756 50.000 1.90 0.00 0.00 3.06
4958 7314 1.923356 ATTCTTGCCGGTTCCAACAT 58.077 45.000 1.90 0.00 0.00 2.71
4959 7315 1.698506 AATTCTTGCCGGTTCCAACA 58.301 45.000 1.90 0.00 0.00 3.33
4960 7316 2.812358 AAATTCTTGCCGGTTCCAAC 57.188 45.000 1.90 0.00 0.00 3.77
4961 7317 3.462021 CAAAAATTCTTGCCGGTTCCAA 58.538 40.909 1.90 0.00 0.00 3.53
4962 7318 2.804933 GCAAAAATTCTTGCCGGTTCCA 60.805 45.455 5.11 0.00 44.88 3.53
4963 7319 1.798223 GCAAAAATTCTTGCCGGTTCC 59.202 47.619 5.11 0.00 44.88 3.62
4971 7327 1.715519 CGTCGGCAGCAAAAATTCTTG 59.284 47.619 0.00 0.00 0.00 3.02
4972 7328 1.930371 GCGTCGGCAGCAAAAATTCTT 60.930 47.619 0.00 0.00 39.62 2.52
4973 7329 0.387239 GCGTCGGCAGCAAAAATTCT 60.387 50.000 0.00 0.00 39.62 2.40
4974 7330 1.664643 CGCGTCGGCAGCAAAAATTC 61.665 55.000 0.00 0.00 39.92 2.17
4975 7331 1.729131 CGCGTCGGCAGCAAAAATT 60.729 52.632 0.00 0.00 39.92 1.82
4976 7332 1.922135 ATCGCGTCGGCAGCAAAAAT 61.922 50.000 5.77 0.00 39.92 1.82
4977 7333 2.507322 GATCGCGTCGGCAGCAAAAA 62.507 55.000 5.77 0.00 39.92 1.94
4978 7334 3.022401 GATCGCGTCGGCAGCAAAA 62.022 57.895 5.77 0.00 39.92 2.44
4979 7335 3.487202 GATCGCGTCGGCAGCAAA 61.487 61.111 5.77 0.00 39.92 3.68
4980 7336 3.932580 AAGATCGCGTCGGCAGCAA 62.933 57.895 5.77 0.00 39.92 3.91
4981 7337 3.932580 AAAGATCGCGTCGGCAGCA 62.933 57.895 5.77 0.00 39.92 4.41
4982 7338 2.240612 AAAAAGATCGCGTCGGCAGC 62.241 55.000 5.77 0.00 39.92 5.25
4983 7339 1.787847 AAAAAGATCGCGTCGGCAG 59.212 52.632 5.77 0.00 39.92 4.85
4984 7340 3.960237 AAAAAGATCGCGTCGGCA 58.040 50.000 5.77 0.00 39.92 5.69
5004 7360 0.457443 TCTCGGCATGTGCTCACTAG 59.543 55.000 4.84 0.00 41.70 2.57
5005 7361 1.114627 ATCTCGGCATGTGCTCACTA 58.885 50.000 4.84 0.00 41.70 2.74
5006 7362 0.461516 CATCTCGGCATGTGCTCACT 60.462 55.000 4.84 0.00 41.70 3.41
5007 7363 2.012237 CATCTCGGCATGTGCTCAC 58.988 57.895 4.84 0.00 41.70 3.51
5008 7364 1.816679 GCATCTCGGCATGTGCTCA 60.817 57.895 4.84 0.00 41.70 4.26
5009 7365 1.523258 AGCATCTCGGCATGTGCTC 60.523 57.895 4.84 0.00 43.97 4.26
5010 7366 2.588439 AGCATCTCGGCATGTGCT 59.412 55.556 4.84 0.67 42.66 4.40
5011 7367 2.713770 CAGCATCTCGGCATGTGC 59.286 61.111 0.00 0.00 41.14 4.57
5012 7368 0.745486 TTCCAGCATCTCGGCATGTG 60.745 55.000 0.00 0.00 35.83 3.21
5013 7369 0.745845 GTTCCAGCATCTCGGCATGT 60.746 55.000 0.00 0.00 35.83 3.21
5014 7370 1.442526 GGTTCCAGCATCTCGGCATG 61.443 60.000 0.00 0.00 35.83 4.06
5015 7371 1.153086 GGTTCCAGCATCTCGGCAT 60.153 57.895 0.00 0.00 35.83 4.40
5016 7372 2.268920 GGTTCCAGCATCTCGGCA 59.731 61.111 0.00 0.00 35.83 5.69
5017 7373 2.892425 CGGTTCCAGCATCTCGGC 60.892 66.667 0.00 0.00 0.00 5.54
5018 7374 1.672854 TACCGGTTCCAGCATCTCGG 61.673 60.000 15.04 0.00 42.69 4.63
5019 7375 0.389391 ATACCGGTTCCAGCATCTCG 59.611 55.000 15.04 0.00 0.00 4.04
5020 7376 3.746045 TTATACCGGTTCCAGCATCTC 57.254 47.619 15.04 0.00 0.00 2.75
5021 7377 3.744530 GCTTTATACCGGTTCCAGCATCT 60.745 47.826 15.04 0.00 0.00 2.90
5022 7378 2.548480 GCTTTATACCGGTTCCAGCATC 59.452 50.000 15.04 0.00 0.00 3.91
5023 7379 2.572290 GCTTTATACCGGTTCCAGCAT 58.428 47.619 15.04 0.29 0.00 3.79
5024 7380 1.741055 CGCTTTATACCGGTTCCAGCA 60.741 52.381 15.04 0.00 0.00 4.41
5025 7381 0.935196 CGCTTTATACCGGTTCCAGC 59.065 55.000 15.04 14.74 0.00 4.85
5026 7382 2.589798 TCGCTTTATACCGGTTCCAG 57.410 50.000 15.04 5.33 0.00 3.86
5027 7383 2.828877 CATCGCTTTATACCGGTTCCA 58.171 47.619 15.04 0.00 0.00 3.53
5028 7384 1.529865 GCATCGCTTTATACCGGTTCC 59.470 52.381 15.04 0.00 0.00 3.62
5029 7385 2.221055 CAGCATCGCTTTATACCGGTTC 59.779 50.000 15.04 0.00 36.40 3.62
5030 7386 2.210116 CAGCATCGCTTTATACCGGTT 58.790 47.619 15.04 3.05 36.40 4.44
5031 7387 1.540363 CCAGCATCGCTTTATACCGGT 60.540 52.381 13.98 13.98 36.40 5.28
5032 7388 1.148310 CCAGCATCGCTTTATACCGG 58.852 55.000 0.00 0.00 36.40 5.28
5033 7389 2.148916 TCCAGCATCGCTTTATACCG 57.851 50.000 0.00 0.00 36.40 4.02
5034 7390 2.224314 GCTTCCAGCATCGCTTTATACC 59.776 50.000 0.00 0.00 41.89 2.73
5035 7391 2.224314 GGCTTCCAGCATCGCTTTATAC 59.776 50.000 0.00 0.00 44.75 1.47
5036 7392 2.104792 AGGCTTCCAGCATCGCTTTATA 59.895 45.455 0.00 0.00 44.75 0.98
5037 7393 1.133976 AGGCTTCCAGCATCGCTTTAT 60.134 47.619 0.00 0.00 44.75 1.40
5038 7394 0.253044 AGGCTTCCAGCATCGCTTTA 59.747 50.000 0.00 0.00 44.75 1.85
5039 7395 1.001641 AGGCTTCCAGCATCGCTTT 60.002 52.632 0.00 0.00 44.75 3.51
5040 7396 1.748122 CAGGCTTCCAGCATCGCTT 60.748 57.895 0.00 0.00 44.75 4.68
5041 7397 2.124819 CAGGCTTCCAGCATCGCT 60.125 61.111 0.00 0.00 44.75 4.93
5042 7398 3.207669 CCAGGCTTCCAGCATCGC 61.208 66.667 0.00 0.00 44.75 4.58
5043 7399 1.078214 TTCCAGGCTTCCAGCATCG 60.078 57.895 0.00 0.00 44.75 3.84
5044 7400 1.034292 GGTTCCAGGCTTCCAGCATC 61.034 60.000 0.00 0.00 44.75 3.91
5101 7457 2.736995 CGGAGCTCGCCGTTTTCA 60.737 61.111 7.83 0.00 46.07 2.69
5178 7534 1.165270 AAATCTACGGTTGCAGCACC 58.835 50.000 2.05 0.00 0.00 5.01
5179 7535 2.989422 AAAATCTACGGTTGCAGCAC 57.011 45.000 2.05 0.00 0.00 4.40
5199 7555 0.463620 GCAGGTGGTTCCAGCAAAAA 59.536 50.000 20.64 0.00 46.15 1.94
5200 7556 2.123409 GCAGGTGGTTCCAGCAAAA 58.877 52.632 20.64 0.00 46.15 2.44
5201 7557 3.854856 GCAGGTGGTTCCAGCAAA 58.145 55.556 20.64 0.00 46.15 3.68
5204 7560 1.452145 TTTTCGCAGGTGGTTCCAGC 61.452 55.000 12.43 12.43 43.92 4.85
5205 7561 1.028905 TTTTTCGCAGGTGGTTCCAG 58.971 50.000 0.00 0.00 39.02 3.86
5206 7562 3.192799 TTTTTCGCAGGTGGTTCCA 57.807 47.368 0.00 0.00 39.02 3.53
5221 7577 0.459411 GCACGGTGGTTGCAGTTTTT 60.459 50.000 10.60 0.00 0.00 1.94
5222 7578 1.140804 GCACGGTGGTTGCAGTTTT 59.859 52.632 10.60 0.00 0.00 2.43
5223 7579 2.049185 TGCACGGTGGTTGCAGTTT 61.049 52.632 10.60 0.00 34.25 2.66
5224 7580 2.439338 TGCACGGTGGTTGCAGTT 60.439 55.556 10.60 0.00 34.25 3.16
5225 7581 2.318519 TAGTGCACGGTGGTTGCAGT 62.319 55.000 12.01 9.82 43.59 4.40
5226 7582 1.163420 TTAGTGCACGGTGGTTGCAG 61.163 55.000 12.01 0.00 39.39 4.41
5227 7583 0.536233 ATTAGTGCACGGTGGTTGCA 60.536 50.000 12.01 0.00 36.09 4.08
5228 7584 0.109781 CATTAGTGCACGGTGGTTGC 60.110 55.000 12.01 0.00 0.00 4.17
5240 7596 2.947652 CCATCTGGTTCCAGCATTAGTG 59.052 50.000 13.44 5.86 34.33 2.74
5241 7597 2.684927 GCCATCTGGTTCCAGCATTAGT 60.685 50.000 13.44 0.00 37.57 2.24
5242 7598 1.952296 GCCATCTGGTTCCAGCATTAG 59.048 52.381 13.44 2.81 37.57 1.73
5243 7599 1.284491 TGCCATCTGGTTCCAGCATTA 59.716 47.619 13.44 0.00 37.57 1.90
5244 7600 0.040058 TGCCATCTGGTTCCAGCATT 59.960 50.000 13.44 0.00 37.57 3.56
5245 7601 0.260816 ATGCCATCTGGTTCCAGCAT 59.739 50.000 13.44 11.24 36.18 3.79
5246 7602 0.394762 GATGCCATCTGGTTCCAGCA 60.395 55.000 13.44 9.51 37.57 4.41
5247 7603 0.394762 TGATGCCATCTGGTTCCAGC 60.395 55.000 13.44 4.19 37.57 4.85
5248 7604 2.022195 CTTGATGCCATCTGGTTCCAG 58.978 52.381 12.20 12.20 37.57 3.86
5249 7605 1.341285 CCTTGATGCCATCTGGTTCCA 60.341 52.381 6.21 0.00 37.57 3.53
5250 7606 1.064463 TCCTTGATGCCATCTGGTTCC 60.064 52.381 6.21 0.00 37.57 3.62
5251 7607 2.425143 TCCTTGATGCCATCTGGTTC 57.575 50.000 6.21 0.00 37.57 3.62
5252 7608 2.242965 TGATCCTTGATGCCATCTGGTT 59.757 45.455 6.21 3.81 37.57 3.67
5253 7609 1.848388 TGATCCTTGATGCCATCTGGT 59.152 47.619 6.21 0.45 37.57 4.00
5254 7610 2.651382 TGATCCTTGATGCCATCTGG 57.349 50.000 6.21 8.39 38.53 3.86
5255 7611 5.393135 GCATAATGATCCTTGATGCCATCTG 60.393 44.000 6.21 0.00 37.52 2.90
5256 7612 4.705507 GCATAATGATCCTTGATGCCATCT 59.294 41.667 6.21 0.00 37.52 2.90
5257 7613 4.705507 AGCATAATGATCCTTGATGCCATC 59.294 41.667 10.18 0.00 43.12 3.51
5258 7614 4.462834 CAGCATAATGATCCTTGATGCCAT 59.537 41.667 10.18 0.00 43.12 4.40
5259 7615 3.824443 CAGCATAATGATCCTTGATGCCA 59.176 43.478 10.18 0.00 43.12 4.92
5260 7616 3.192844 CCAGCATAATGATCCTTGATGCC 59.807 47.826 10.18 0.00 43.12 4.40
5261 7617 3.192844 CCCAGCATAATGATCCTTGATGC 59.807 47.826 6.89 6.89 42.57 3.91
5262 7618 4.458295 GTCCCAGCATAATGATCCTTGATG 59.542 45.833 0.00 0.00 0.00 3.07
5263 7619 4.508047 GGTCCCAGCATAATGATCCTTGAT 60.508 45.833 0.00 0.00 0.00 2.57
5264 7620 3.181440 GGTCCCAGCATAATGATCCTTGA 60.181 47.826 0.00 0.00 0.00 3.02
5265 7621 3.152341 GGTCCCAGCATAATGATCCTTG 58.848 50.000 0.00 0.00 0.00 3.61
5266 7622 2.108952 GGGTCCCAGCATAATGATCCTT 59.891 50.000 1.78 0.00 0.00 3.36
5267 7623 1.707427 GGGTCCCAGCATAATGATCCT 59.293 52.381 1.78 0.00 0.00 3.24
5268 7624 1.425066 TGGGTCCCAGCATAATGATCC 59.575 52.381 6.47 0.00 0.00 3.36
5269 7625 2.158623 TGTGGGTCCCAGCATAATGATC 60.159 50.000 12.21 0.00 32.34 2.92
5270 7626 1.852309 TGTGGGTCCCAGCATAATGAT 59.148 47.619 12.21 0.00 32.34 2.45
5271 7627 1.294041 TGTGGGTCCCAGCATAATGA 58.706 50.000 12.21 0.00 32.34 2.57
5272 7628 2.142356 TTGTGGGTCCCAGCATAATG 57.858 50.000 12.21 0.00 32.34 1.90
5273 7629 2.244510 TGATTGTGGGTCCCAGCATAAT 59.755 45.455 12.21 9.88 32.34 1.28
5274 7630 1.638070 TGATTGTGGGTCCCAGCATAA 59.362 47.619 12.21 5.07 32.34 1.90
5275 7631 1.294041 TGATTGTGGGTCCCAGCATA 58.706 50.000 12.21 4.69 32.34 3.14
5276 7632 0.409092 TTGATTGTGGGTCCCAGCAT 59.591 50.000 12.21 6.11 32.34 3.79
5277 7633 0.187117 TTTGATTGTGGGTCCCAGCA 59.813 50.000 12.21 9.97 32.34 4.41
5278 7634 1.560505 ATTTGATTGTGGGTCCCAGC 58.439 50.000 12.21 7.20 32.34 4.85
5279 7635 3.865684 GCAAATTTGATTGTGGGTCCCAG 60.866 47.826 22.31 0.00 32.34 4.45
5280 7636 2.038295 GCAAATTTGATTGTGGGTCCCA 59.962 45.455 22.31 6.47 32.80 4.37
5281 7637 2.302733 AGCAAATTTGATTGTGGGTCCC 59.697 45.455 22.31 0.00 32.80 4.46
5282 7638 3.328505 CAGCAAATTTGATTGTGGGTCC 58.671 45.455 22.31 0.00 32.80 4.46
5283 7639 3.006752 TCCAGCAAATTTGATTGTGGGTC 59.993 43.478 22.31 0.63 34.76 4.46
5284 7640 2.971330 TCCAGCAAATTTGATTGTGGGT 59.029 40.909 22.31 0.00 34.76 4.51
5285 7641 3.681593 TCCAGCAAATTTGATTGTGGG 57.318 42.857 22.31 12.70 34.76 4.61
5286 7642 3.747529 GGTTCCAGCAAATTTGATTGTGG 59.252 43.478 22.31 19.10 35.05 4.17
5287 7643 4.378774 TGGTTCCAGCAAATTTGATTGTG 58.621 39.130 22.31 11.77 32.80 3.33
5288 7644 4.634199 CTGGTTCCAGCAAATTTGATTGT 58.366 39.130 22.31 0.00 32.80 2.71
5301 7657 3.495753 GCAAAAATTCTTGCTGGTTCCAG 59.504 43.478 9.27 13.88 46.66 3.86
5302 7658 3.465871 GCAAAAATTCTTGCTGGTTCCA 58.534 40.909 9.27 0.00 46.66 3.53


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

AutoCloner maintained by Alex Coulton.