Multiple sequence alignment - TraesCS6B01G346800

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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 TraesCS6B01G346800 chr6B 100.000 3921 0 0 756 4676 610809947 610813867 0.000000e+00 7241
1 TraesCS6B01G346800 chr6B 100.000 2766 0 0 5078 7843 610814269 610817034 0.000000e+00 5108
2 TraesCS6B01G346800 chr6B 100.000 528 0 0 1 528 610809192 610809719 0.000000e+00 976
3 TraesCS6B01G346800 chr6A 86.413 2311 216 54 2330 4586 552759666 552761932 0.000000e+00 2438
4 TraesCS6B01G346800 chr6A 93.278 967 55 6 5489 6451 552762632 552763592 0.000000e+00 1417
5 TraesCS6B01G346800 chr6A 87.608 1041 89 19 6837 7843 552763873 552764907 0.000000e+00 1171
6 TraesCS6B01G346800 chr6A 91.768 741 27 9 756 1470 552758941 552759673 0.000000e+00 1000
7 TraesCS6B01G346800 chr6A 91.603 524 28 8 1 509 552758393 552758915 0.000000e+00 710
8 TraesCS6B01G346800 chr6A 93.651 252 16 0 6496 6747 552763590 552763841 2.070000e-100 377
9 TraesCS6B01G346800 chr6D 85.555 2326 189 83 2330 4587 406336609 406338855 0.000000e+00 2298
10 TraesCS6B01G346800 chr6D 90.619 1663 101 24 5469 7104 406339542 406341176 0.000000e+00 2156
11 TraesCS6B01G346800 chr6D 93.975 863 42 4 1470 2329 136701742 136700887 0.000000e+00 1297
12 TraesCS6B01G346800 chr6D 93.187 866 56 3 1470 2335 19640300 19641162 0.000000e+00 1269
13 TraesCS6B01G346800 chr6D 92.754 759 47 2 7088 7843 406341273 406342026 0.000000e+00 1090
14 TraesCS6B01G346800 chr6D 92.131 521 26 10 1 509 406335100 406335617 0.000000e+00 721
15 TraesCS6B01G346800 chr6D 92.442 344 21 3 1129 1470 406336276 406336616 3.290000e-133 486
16 TraesCS6B01G346800 chr6D 87.444 223 10 6 756 960 406335643 406335865 2.830000e-59 241
17 TraesCS6B01G346800 chr6D 81.919 271 20 12 5096 5349 406339178 406339436 1.330000e-47 202
18 TraesCS6B01G346800 chr5D 88.984 1634 131 19 6235 7843 435613353 435611744 0.000000e+00 1975
19 TraesCS6B01G346800 chr5D 94.077 861 43 3 1470 2329 307362235 307361382 0.000000e+00 1301
20 TraesCS6B01G346800 chr5D 93.333 105 7 0 5357 5461 176107059 176106955 1.050000e-33 156
21 TraesCS6B01G346800 chr1D 88.617 1634 137 19 6235 7843 249580462 249578853 0.000000e+00 1941
22 TraesCS6B01G346800 chr1B 94.425 861 42 3 1471 2329 683466242 683467098 0.000000e+00 1319
23 TraesCS6B01G346800 chr2A 94.186 860 40 7 1471 2329 582952629 582953479 0.000000e+00 1303
24 TraesCS6B01G346800 chr2A 95.146 103 5 0 5358 5460 482694685 482694583 6.300000e-36 163
25 TraesCS6B01G346800 chr5B 94.014 852 44 6 1471 2321 661237377 661236532 0.000000e+00 1284
26 TraesCS6B01G346800 chr5B 94.014 852 44 6 1471 2321 661238576 661237731 0.000000e+00 1284
27 TraesCS6B01G346800 chr5B 93.878 98 6 0 5358 5455 53738419 53738516 1.760000e-31 148
28 TraesCS6B01G346800 chr1A 93.264 861 55 3 1470 2329 226433894 226433036 0.000000e+00 1266
29 TraesCS6B01G346800 chr7D 93.187 866 48 4 1471 2335 160632625 160633480 0.000000e+00 1262
30 TraesCS6B01G346800 chr7D 95.098 102 5 0 5358 5459 175648248 175648349 2.260000e-35 161
31 TraesCS6B01G346800 chr7D 76.398 322 48 15 996 1309 133199650 133199951 1.760000e-31 148
32 TraesCS6B01G346800 chr7B 95.146 103 5 0 5359 5461 140933790 140933892 6.300000e-36 163
33 TraesCS6B01G346800 chr7B 76.582 316 52 11 996 1309 94267842 94268137 3.790000e-33 154
34 TraesCS6B01G346800 chr7B 93.204 103 7 0 5359 5461 446161859 446161757 1.360000e-32 152
35 TraesCS6B01G346800 chr7A 76.730 318 54 10 996 1309 131811961 131812262 8.150000e-35 159
36 TraesCS6B01G346800 chr5A 93.204 103 7 0 5359 5461 145665931 145666033 1.360000e-32 152
37 TraesCS6B01G346800 chr2D 93.069 101 7 0 5358 5458 359662921 359662821 1.760000e-31 148
38 TraesCS6B01G346800 chrUn 92.233 103 8 0 5358 5460 25042760 25042658 6.340000e-31 147


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 TraesCS6B01G346800 chr6B 610809192 610817034 7842 False 4441.666667 7241 100.000000 1 7843 3 chr6B.!!$F1 7842
1 TraesCS6B01G346800 chr6A 552758393 552764907 6514 False 1185.500000 2438 90.720167 1 7843 6 chr6A.!!$F1 7842
2 TraesCS6B01G346800 chr6D 136700887 136701742 855 True 1297.000000 1297 93.975000 1470 2329 1 chr6D.!!$R1 859
3 TraesCS6B01G346800 chr6D 19640300 19641162 862 False 1269.000000 1269 93.187000 1470 2335 1 chr6D.!!$F1 865
4 TraesCS6B01G346800 chr6D 406335100 406342026 6926 False 1027.714286 2298 88.980571 1 7843 7 chr6D.!!$F2 7842
5 TraesCS6B01G346800 chr5D 435611744 435613353 1609 True 1975.000000 1975 88.984000 6235 7843 1 chr5D.!!$R3 1608
6 TraesCS6B01G346800 chr5D 307361382 307362235 853 True 1301.000000 1301 94.077000 1470 2329 1 chr5D.!!$R2 859
7 TraesCS6B01G346800 chr1D 249578853 249580462 1609 True 1941.000000 1941 88.617000 6235 7843 1 chr1D.!!$R1 1608
8 TraesCS6B01G346800 chr1B 683466242 683467098 856 False 1319.000000 1319 94.425000 1471 2329 1 chr1B.!!$F1 858
9 TraesCS6B01G346800 chr2A 582952629 582953479 850 False 1303.000000 1303 94.186000 1471 2329 1 chr2A.!!$F1 858
10 TraesCS6B01G346800 chr5B 661236532 661238576 2044 True 1284.000000 1284 94.014000 1471 2321 2 chr5B.!!$R1 850
11 TraesCS6B01G346800 chr1A 226433036 226433894 858 True 1266.000000 1266 93.264000 1470 2329 1 chr1A.!!$R1 859
12 TraesCS6B01G346800 chr7D 160632625 160633480 855 False 1262.000000 1262 93.187000 1471 2335 1 chr7D.!!$F2 864

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
346 352 1.351017 GGGATCCTGTTGGAGAACACA 59.649 52.381 12.58 0.00 46.91 3.72 F
1200 1488 0.388134 TAGTTCTGACCGTGCGCTTC 60.388 55.000 9.73 0.35 0.00 3.86 F
1433 1723 0.395686 ACGCAGCAGGCTATCATCAT 59.604 50.000 0.00 0.00 41.67 2.45 F
2096 3588 0.904649 GGAAAAGGAAGGGGGCATTG 59.095 55.000 0.00 0.00 0.00 2.82 F
2673 4198 0.603065 GCCGCCATCTTCCAAAGTTT 59.397 50.000 0.00 0.00 0.00 2.66 F
3334 4880 0.732571 CTTTGTCACACACGCTTGGT 59.267 50.000 0.00 0.00 0.00 3.67 F
3336 4882 1.092921 TTGTCACACACGCTTGGTCC 61.093 55.000 0.00 0.00 0.00 4.46 F
4334 5919 0.107703 TGCCCATGAGCTACCGAAAG 60.108 55.000 0.00 0.00 0.00 2.62 F
5389 7240 0.249699 TCCATAATGTAGTGCGCCCG 60.250 55.000 4.18 0.00 0.00 6.13 F
6510 8367 0.107654 GCGATGAGCCTGTAACCCTT 60.108 55.000 0.00 0.00 40.81 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1673 0.977627 AGACCATCACGAGGCATCCA 60.978 55.000 0.00 0.00 0.00 3.41 R
2096 3588 2.040779 AGCAGCCCTAGTACCCCC 60.041 66.667 0.00 0.00 0.00 5.40 R
2312 3804 2.462456 ATGCTCGAATGCACCGATAT 57.538 45.000 12.56 8.35 46.33 1.63 R
3484 5033 1.761784 AGTGCACCAAAGGCATTTTCA 59.238 42.857 14.63 0.00 44.11 2.69 R
4133 5704 0.036732 TCACATGCAGGTCCAAGTCC 59.963 55.000 0.00 0.00 0.00 3.85 R
4271 5843 0.169009 GAGCTTTAAGCAAGTGCCCG 59.831 55.000 19.63 0.00 45.56 6.13 R
5235 6992 0.322456 CAGGGAGAAAACCATCGCCA 60.322 55.000 0.00 0.00 40.67 5.69 R
5440 7291 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53 R
6626 8483 0.438830 CGAAGCAGTAAGTTGCCGTC 59.561 55.000 0.00 0.00 45.18 4.79 R
7603 9609 3.797353 GATGAGGCGGGCCAGGAA 61.797 66.667 12.97 0.00 38.92 3.36 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
111 114 1.564622 CAACGCGTTGGAGTGACAG 59.435 57.895 37.79 14.28 36.95 3.51
125 128 1.375908 GACAGGCATGGTGCGAGAA 60.376 57.895 2.31 0.00 46.21 2.87
346 352 1.351017 GGGATCCTGTTGGAGAACACA 59.649 52.381 12.58 0.00 46.91 3.72
373 379 2.158769 TGATGCCATTATCCACGCTCTT 60.159 45.455 0.00 0.00 0.00 2.85
456 471 3.181458 GGGGACTGCGGAGATTTATACAA 60.181 47.826 12.26 0.00 0.00 2.41
485 501 3.291584 GCTTGGGGAAGGATTTAGAAGG 58.708 50.000 0.00 0.00 0.00 3.46
802 825 1.622607 CGATGCCTGGACCCACCTAA 61.623 60.000 0.00 0.00 39.86 2.69
835 858 3.253188 CCCAATGGGCGTATAGTTCATTG 59.747 47.826 4.89 0.00 42.28 2.82
844 867 4.755123 GCGTATAGTTCATTGTAAGCCCAT 59.245 41.667 0.00 0.00 0.00 4.00
1061 1104 3.195698 GGACGGCGACATGGAAGC 61.196 66.667 16.62 0.00 0.00 3.86
1078 1121 4.470170 CCGCCGACGTCGACATGA 62.470 66.667 37.65 0.00 43.02 3.07
1155 1443 1.056700 CCATCCCTCGGATCCCTGTT 61.057 60.000 6.06 0.00 40.98 3.16
1200 1488 0.388134 TAGTTCTGACCGTGCGCTTC 60.388 55.000 9.73 0.35 0.00 3.86
1201 1489 1.664965 GTTCTGACCGTGCGCTTCT 60.665 57.895 9.73 0.00 0.00 2.85
1202 1490 1.372997 TTCTGACCGTGCGCTTCTC 60.373 57.895 9.73 0.00 0.00 2.87
1203 1491 3.175240 CTGACCGTGCGCTTCTCG 61.175 66.667 9.73 8.36 42.12 4.04
1233 1523 1.139734 GCTGGACGAGATGAAGCGA 59.860 57.895 0.00 0.00 0.00 4.93
1310 1600 0.813821 GCCAAGGAGATGCAAGGTTC 59.186 55.000 0.00 0.00 0.00 3.62
1383 1673 6.509418 TTTAGCCGCTTTTGATCTATTTGT 57.491 33.333 0.00 0.00 0.00 2.83
1420 1710 0.447801 CTTGTAATCCCACACGCAGC 59.552 55.000 0.00 0.00 0.00 5.25
1430 1720 0.812811 CACACGCAGCAGGCTATCAT 60.813 55.000 0.00 0.00 41.67 2.45
1431 1721 0.531532 ACACGCAGCAGGCTATCATC 60.532 55.000 0.00 0.00 41.67 2.92
1432 1722 0.531311 CACGCAGCAGGCTATCATCA 60.531 55.000 0.00 0.00 41.67 3.07
1433 1723 0.395686 ACGCAGCAGGCTATCATCAT 59.604 50.000 0.00 0.00 41.67 2.45
1481 1771 6.366332 GGTACTCATAAATCCTAGAATGCACG 59.634 42.308 0.00 0.00 0.00 5.34
1521 1811 3.132289 CAGTATCGGGCCAATACGGATAT 59.868 47.826 17.25 2.48 36.56 1.63
1730 3220 3.254411 TCGCATTTCCATTTAGTGTTGCA 59.746 39.130 0.00 0.00 0.00 4.08
1731 3221 3.364621 CGCATTTCCATTTAGTGTTGCAC 59.635 43.478 0.00 0.00 34.10 4.57
1767 3259 7.707624 TTTCTCTATGATTTGAACATGGCTT 57.292 32.000 0.00 0.00 0.00 4.35
1894 3386 2.586792 GGATGAGCTTCGCTGGGT 59.413 61.111 0.00 0.00 39.88 4.51
1975 3467 3.052620 GAGTAGCAGCTCGTCGCCA 62.053 63.158 0.00 0.00 40.39 5.69
2096 3588 0.904649 GGAAAAGGAAGGGGGCATTG 59.095 55.000 0.00 0.00 0.00 2.82
2109 3601 1.150764 GCATTGGGGGTACTAGGGC 59.849 63.158 0.00 0.00 0.00 5.19
2171 3663 1.092348 GCTGGGTCGTATCCAAAACC 58.908 55.000 0.00 0.00 33.36 3.27
2312 3804 1.999735 CGATTCGCTAGTTGCCTGAAA 59.000 47.619 0.00 0.00 38.78 2.69
2330 3822 2.238942 AATATCGGTGCATTCGAGCA 57.761 45.000 17.51 10.21 43.35 4.26
2395 3887 6.067263 TGCAACTATTGTAGGTGTTGTTTC 57.933 37.500 4.17 0.00 45.27 2.78
2492 4012 8.230486 CACTAGCAGTATGTTTTAAGTTCCTTG 58.770 37.037 0.00 0.00 39.31 3.61
2502 4022 5.652994 TTTAAGTTCCTTGTGCACAACTT 57.347 34.783 28.29 28.29 41.06 2.66
2534 4054 4.742438 TGCATCTTAACTTTTCGTGACC 57.258 40.909 0.00 0.00 0.00 4.02
2560 4080 6.151144 ACTTTACTGTTTGTAATCCTGGCATC 59.849 38.462 0.00 0.00 40.41 3.91
2564 4084 3.006940 GTTTGTAATCCTGGCATCGACA 58.993 45.455 0.00 0.00 0.00 4.35
2565 4085 2.602257 TGTAATCCTGGCATCGACAG 57.398 50.000 0.00 0.00 38.64 3.51
2636 4161 6.744537 GCACTTCAAGAATAATTGTGTGCTAG 59.255 38.462 20.92 0.00 45.86 3.42
2673 4198 0.603065 GCCGCCATCTTCCAAAGTTT 59.397 50.000 0.00 0.00 0.00 2.66
2688 4213 6.977213 TCCAAAGTTTCTCCCTTATTTTTCG 58.023 36.000 0.00 0.00 0.00 3.46
2727 4254 3.244735 GGACCCTTGCTCTTTTCTCTCTT 60.245 47.826 0.00 0.00 0.00 2.85
2843 4378 2.717639 AGATATGCCTTGTGGTGTCC 57.282 50.000 0.00 0.00 35.27 4.02
2871 4406 2.029020 TGTAGCTCAAGTAGTGGCACAG 60.029 50.000 21.41 8.23 41.80 3.66
2904 4441 6.266558 TCATGCCTTGTATTACCTTTGTTTGT 59.733 34.615 0.00 0.00 0.00 2.83
2922 4459 8.755696 TTGTTTGTCATGAATACTTATTTGGC 57.244 30.769 0.00 0.00 0.00 4.52
2936 4473 2.500509 TTTGGCGCTTGTGGTAAAAG 57.499 45.000 7.64 0.00 0.00 2.27
2968 4505 5.825679 GTGTGGGATAAATGTTATGGCTGTA 59.174 40.000 0.00 0.00 0.00 2.74
3001 4538 6.995364 TCATTTTCCATGGTTATGCATATGG 58.005 36.000 16.98 16.98 41.09 2.74
3074 4611 9.918630 CTGGATGAGTTTTAGACATTTGATTTT 57.081 29.630 0.00 0.00 0.00 1.82
3105 4642 7.008021 ACTGCCTTTTTATTTGTGATGGATT 57.992 32.000 0.00 0.00 0.00 3.01
3114 4651 8.415950 TTTATTTGTGATGGATTGGTTAGTGT 57.584 30.769 0.00 0.00 0.00 3.55
3136 4674 6.464834 GTGTTGACAGAAAGTTTTCTAACACG 59.535 38.462 22.79 9.94 44.94 4.49
3181 4719 7.241042 AGTGTTTAGTGCCTTATCTTCTACA 57.759 36.000 0.00 0.00 0.00 2.74
3287 4826 2.541762 GGATGCTCGCTCTGTTTATGTC 59.458 50.000 0.00 0.00 0.00 3.06
3330 4876 1.409064 TCTCTCTTTGTCACACACGCT 59.591 47.619 0.00 0.00 0.00 5.07
3334 4880 0.732571 CTTTGTCACACACGCTTGGT 59.267 50.000 0.00 0.00 0.00 3.67
3336 4882 1.092921 TTGTCACACACGCTTGGTCC 61.093 55.000 0.00 0.00 0.00 4.46
3411 4958 4.034279 GCGTTGCCAAGGTATTCGTATTAA 59.966 41.667 0.00 0.00 0.00 1.40
3484 5033 6.852420 TTGGATACTGACTGCTAGTTAGTT 57.148 37.500 15.26 7.07 41.55 2.24
3492 5041 6.073003 ACTGACTGCTAGTTAGTTGAAAATGC 60.073 38.462 7.57 0.00 41.55 3.56
3512 5061 4.148838 TGCCTTTGGTGCACTTAACTTAT 58.851 39.130 17.98 0.00 32.85 1.73
3522 5071 9.764363 TGGTGCACTTAACTTATATAAGAGATG 57.236 33.333 25.83 16.59 37.08 2.90
3536 5085 6.081872 ATAAGAGATGCTTATGCCAAAAGC 57.918 37.500 7.59 7.59 45.71 3.51
3626 5175 3.009473 TGCTCTGTTCCTGCCTATCTTTT 59.991 43.478 0.00 0.00 0.00 2.27
3655 5204 5.739630 CGGCAGACAATATATAGCTAGTTCG 59.260 44.000 0.00 0.00 0.00 3.95
3699 5249 4.938226 GCTCCTAACTGTAGTTCATGCTTT 59.062 41.667 0.00 0.00 39.31 3.51
3702 5252 7.926555 GCTCCTAACTGTAGTTCATGCTTTATA 59.073 37.037 0.00 0.00 39.31 0.98
3705 5255 8.204836 CCTAACTGTAGTTCATGCTTTATACCT 58.795 37.037 0.00 0.00 39.31 3.08
3716 5266 5.499004 TGCTTTATACCTTTCCTCACAGT 57.501 39.130 0.00 0.00 0.00 3.55
3774 5325 7.301054 TGTTTACATTTGTTTTTGCCTTTGTG 58.699 30.769 0.00 0.00 0.00 3.33
3808 5362 6.055588 TGCTAGTTTGCTAACTCAGAAAAGT 58.944 36.000 16.89 0.00 43.45 2.66
3915 5471 6.183347 AGGCTTTTGATATCAAGTACTTGCT 58.817 36.000 27.49 21.57 40.24 3.91
3924 5480 4.350368 TCAAGTACTTGCTGATGGTTCA 57.650 40.909 27.49 6.49 40.24 3.18
3925 5481 4.910195 TCAAGTACTTGCTGATGGTTCAT 58.090 39.130 27.49 0.00 40.24 2.57
3926 5482 6.048732 TCAAGTACTTGCTGATGGTTCATA 57.951 37.500 27.49 5.80 40.24 2.15
3927 5483 6.108687 TCAAGTACTTGCTGATGGTTCATAG 58.891 40.000 27.49 1.83 40.24 2.23
3928 5484 5.683876 AGTACTTGCTGATGGTTCATAGT 57.316 39.130 0.00 0.00 0.00 2.12
3929 5485 5.665459 AGTACTTGCTGATGGTTCATAGTC 58.335 41.667 0.00 0.00 0.00 2.59
3941 5497 7.623999 ATGGTTCATAGTCAATACCATCTCT 57.376 36.000 0.00 0.00 44.14 3.10
3942 5498 8.727100 ATGGTTCATAGTCAATACCATCTCTA 57.273 34.615 0.00 0.00 44.14 2.43
4052 5623 8.166706 GGGAAAAAGAAAAGAAAAACGAGTTTC 58.833 33.333 1.39 7.27 37.70 2.78
4064 5635 7.985752 AGAAAAACGAGTTTCCATAGTATAGGG 59.014 37.037 1.39 0.00 45.70 3.53
4087 5658 1.550976 AGTTACCTCCCTGAAGAAGCG 59.449 52.381 0.00 0.00 0.00 4.68
4147 5718 1.455849 CTTGGGACTTGGACCTGCA 59.544 57.895 0.00 0.00 0.00 4.41
4250 5822 4.225942 TCAGAATGGAGCCTTATGTTGACT 59.774 41.667 0.00 0.00 36.16 3.41
4271 5843 5.825507 ACTGTTCTTTTGCTCATTCTGAAC 58.174 37.500 0.00 0.00 34.66 3.18
4273 5845 4.222114 GTTCTTTTGCTCATTCTGAACGG 58.778 43.478 0.00 0.00 0.00 4.44
4276 5848 0.250684 TTGCTCATTCTGAACGGGCA 60.251 50.000 6.96 6.96 0.00 5.36
4285 5857 1.202710 TCTGAACGGGCACTTGCTTAA 60.203 47.619 0.38 0.00 41.70 1.85
4286 5858 1.606668 CTGAACGGGCACTTGCTTAAA 59.393 47.619 0.38 0.00 41.70 1.52
4317 5902 3.251972 CCCTCTTTTCACTTCAGAACTGC 59.748 47.826 0.00 0.00 0.00 4.40
4323 5908 1.699083 TCACTTCAGAACTGCCCATGA 59.301 47.619 0.00 0.00 0.00 3.07
4334 5919 0.107703 TGCCCATGAGCTACCGAAAG 60.108 55.000 0.00 0.00 0.00 2.62
4359 5944 2.592102 TTCATGCTGCTCCTTTTCCT 57.408 45.000 0.00 0.00 0.00 3.36
4395 5989 9.436957 GGTCTCTTTTTCTAAATGTGATGTCTA 57.563 33.333 0.00 0.00 0.00 2.59
4440 6034 6.801862 GTGTTTCTAATGGTTTTCGAGGATTG 59.198 38.462 0.00 0.00 0.00 2.67
4457 6051 6.293081 CGAGGATTGCATGTAACTCTAAATGG 60.293 42.308 0.00 0.00 0.00 3.16
4507 6101 3.721087 CCATAGGGGCTGGGTTAATAG 57.279 52.381 0.00 0.00 0.00 1.73
4564 6158 8.288689 ACAAAATACTGTTGAGGTACTTGTTT 57.711 30.769 0.00 0.00 41.55 2.83
4611 6352 4.923893 TCAAGCTTTTCTTCACATGTGTG 58.076 39.130 24.63 18.02 46.91 3.82
4618 6359 6.634436 GCTTTTCTTCACATGTGTGTCTTAAG 59.366 38.462 24.63 18.49 45.76 1.85
4620 6361 6.844696 TTCTTCACATGTGTGTCTTAAGTC 57.155 37.500 24.63 0.00 45.76 3.01
4621 6362 6.161855 TCTTCACATGTGTGTCTTAAGTCT 57.838 37.500 24.63 0.00 45.76 3.24
4628 6369 8.064222 CACATGTGTGTCTTAAGTCTTAACTTG 58.936 37.037 18.03 7.89 42.01 3.16
4630 6371 9.256477 CATGTGTGTCTTAAGTCTTAACTTGTA 57.744 33.333 1.63 0.00 45.37 2.41
4631 6372 9.826574 ATGTGTGTCTTAAGTCTTAACTTGTAA 57.173 29.630 1.63 0.00 45.37 2.41
4632 6373 9.090692 TGTGTGTCTTAAGTCTTAACTTGTAAC 57.909 33.333 1.63 0.00 45.37 2.50
4634 6375 9.880157 TGTGTCTTAAGTCTTAACTTGTAACTT 57.120 29.630 1.63 0.00 45.37 2.66
4649 6390 8.409358 ACTTGTAACTTTTCCATATTTCAGCT 57.591 30.769 0.00 0.00 0.00 4.24
5125 6866 9.965902 GGATTATGTAATCTCATTTATGGTCCT 57.034 33.333 11.38 0.00 41.33 3.85
5131 6872 8.944138 TGTAATCTCATTTATGGTCCTATTGGA 58.056 33.333 0.00 0.00 40.69 3.53
5132 6873 9.965902 GTAATCTCATTTATGGTCCTATTGGAT 57.034 33.333 0.00 0.00 45.29 3.41
5183 6924 7.228706 GGTTTCTCTTGTACCTTCAAAATGAGA 59.771 37.037 0.00 0.00 30.16 3.27
5184 6925 7.969536 TTCTCTTGTACCTTCAAAATGAGAG 57.030 36.000 0.00 0.00 32.19 3.20
5215 6956 8.265055 TCCATATTGACTTTCGAGAAATAACCT 58.735 33.333 0.00 0.00 0.00 3.50
5252 7009 1.474330 ATTGGCGATGGTTTTCTCCC 58.526 50.000 0.00 0.00 0.00 4.30
5280 7038 9.582648 GGCTATAATTAATTTAACCTTCCCTCA 57.417 33.333 5.91 0.00 0.00 3.86
5345 7103 7.226128 GTGTAATAACCCAAAGACCAGCTATAC 59.774 40.741 0.00 0.00 0.00 1.47
5348 7106 4.929146 ACCCAAAGACCAGCTATACTTT 57.071 40.909 0.00 0.00 33.69 2.66
5349 7107 6.382919 AACCCAAAGACCAGCTATACTTTA 57.617 37.500 9.66 0.00 32.46 1.85
5350 7108 6.576778 ACCCAAAGACCAGCTATACTTTAT 57.423 37.500 9.66 0.20 32.46 1.40
5351 7109 6.357367 ACCCAAAGACCAGCTATACTTTATG 58.643 40.000 9.66 7.47 32.46 1.90
5352 7110 6.157994 ACCCAAAGACCAGCTATACTTTATGA 59.842 38.462 9.66 0.00 32.46 2.15
5353 7111 7.054124 CCCAAAGACCAGCTATACTTTATGAA 58.946 38.462 9.66 0.00 32.46 2.57
5354 7112 7.012421 CCCAAAGACCAGCTATACTTTATGAAC 59.988 40.741 9.66 0.00 32.46 3.18
5355 7113 7.770897 CCAAAGACCAGCTATACTTTATGAACT 59.229 37.037 9.66 0.00 32.46 3.01
5356 7114 9.817809 CAAAGACCAGCTATACTTTATGAACTA 57.182 33.333 9.66 0.00 32.46 2.24
5372 7223 5.934402 TGAACTAATACTCCCTCTGTTCC 57.066 43.478 0.00 0.00 33.57 3.62
5373 7224 5.338632 TGAACTAATACTCCCTCTGTTCCA 58.661 41.667 0.00 0.00 33.57 3.53
5374 7225 5.964477 TGAACTAATACTCCCTCTGTTCCAT 59.036 40.000 0.00 0.00 33.57 3.41
5378 7229 7.967908 ACTAATACTCCCTCTGTTCCATAATG 58.032 38.462 0.00 0.00 0.00 1.90
5381 7232 5.878406 ACTCCCTCTGTTCCATAATGTAG 57.122 43.478 0.00 0.00 0.00 2.74
5382 7233 5.281314 ACTCCCTCTGTTCCATAATGTAGT 58.719 41.667 0.00 0.00 0.00 2.73
5386 7237 3.194861 TCTGTTCCATAATGTAGTGCGC 58.805 45.455 0.00 0.00 0.00 6.09
5387 7238 2.285083 TGTTCCATAATGTAGTGCGCC 58.715 47.619 4.18 0.00 0.00 6.53
5388 7239 1.602377 GTTCCATAATGTAGTGCGCCC 59.398 52.381 4.18 0.00 0.00 6.13
5389 7240 0.249699 TCCATAATGTAGTGCGCCCG 60.250 55.000 4.18 0.00 0.00 6.13
5390 7241 1.569493 CATAATGTAGTGCGCCCGC 59.431 57.895 4.18 5.60 42.35 6.13
5403 7254 2.750888 GCCCGCGCTTTTCGAGATT 61.751 57.895 5.56 0.00 40.54 2.40
5405 7256 1.003851 CCCGCGCTTTTCGAGATTTA 58.996 50.000 5.56 0.00 40.54 1.40
5406 7257 1.395608 CCCGCGCTTTTCGAGATTTAA 59.604 47.619 5.56 0.00 40.54 1.52
5407 7258 2.159626 CCCGCGCTTTTCGAGATTTAAA 60.160 45.455 5.56 0.00 40.54 1.52
5409 7260 4.095610 CCGCGCTTTTCGAGATTTAAATT 58.904 39.130 5.56 0.00 40.54 1.82
5410 7261 4.557301 CCGCGCTTTTCGAGATTTAAATTT 59.443 37.500 5.56 0.00 40.54 1.82
5413 7264 6.450276 GCGCTTTTCGAGATTTAAATTTGAC 58.550 36.000 0.00 0.00 41.67 3.18
5416 7267 7.273381 CGCTTTTCGAGATTTAAATTTGACCAT 59.727 33.333 1.43 0.00 41.67 3.55
5431 7282 9.549078 AAATTTGACCATAAATTTAACCAACGT 57.451 25.926 1.21 0.00 44.22 3.99
5432 7283 7.932120 TTTGACCATAAATTTAACCAACGTG 57.068 32.000 1.21 0.00 0.00 4.49
5433 7284 6.015027 TGACCATAAATTTAACCAACGTGG 57.985 37.500 1.21 6.15 45.02 4.94
5434 7285 5.047943 TGACCATAAATTTAACCAACGTGGG 60.048 40.000 7.67 7.67 43.37 4.61
5435 7286 4.177783 CCATAAATTTAACCAACGTGGGC 58.822 43.478 9.56 0.00 43.37 5.36
5436 7287 2.425578 AAATTTAACCAACGTGGGCG 57.574 45.000 9.56 0.00 43.37 6.13
5437 7288 1.606903 AATTTAACCAACGTGGGCGA 58.393 45.000 9.56 0.00 43.37 5.54
5438 7289 0.876399 ATTTAACCAACGTGGGCGAC 59.124 50.000 9.56 0.00 43.37 5.19
5439 7290 0.179051 TTTAACCAACGTGGGCGACT 60.179 50.000 9.56 0.00 43.37 4.18
5440 7291 0.881159 TTAACCAACGTGGGCGACTG 60.881 55.000 9.56 0.00 43.37 3.51
5468 7319 7.316544 CGGGAGCAAAAATTATAACTACAGT 57.683 36.000 0.00 0.00 0.00 3.55
5469 7320 8.428186 CGGGAGCAAAAATTATAACTACAGTA 57.572 34.615 0.00 0.00 0.00 2.74
5470 7321 9.052759 CGGGAGCAAAAATTATAACTACAGTAT 57.947 33.333 0.00 0.00 0.00 2.12
5499 7350 3.129852 TCAAGTTCACAAGTGCAAACG 57.870 42.857 0.00 0.00 0.00 3.60
5501 7352 3.057876 TCAAGTTCACAAGTGCAAACGTT 60.058 39.130 0.00 0.00 0.00 3.99
5586 7439 6.916360 TGTTTAATCTTTCAAGCCCATTCT 57.084 33.333 0.00 0.00 0.00 2.40
5595 7448 3.084039 TCAAGCCCATTCTGTTGACATC 58.916 45.455 0.00 0.00 0.00 3.06
5795 7648 7.571919 AGGCTCTTAATCTGAATGAATCTGAA 58.428 34.615 0.00 0.00 39.17 3.02
5807 7660 3.346315 TGAATCTGAATTGCATGGTCGT 58.654 40.909 0.00 0.00 0.00 4.34
5821 7674 1.078759 GGTCGTCAGATCAAGGTGCG 61.079 60.000 0.00 0.00 0.00 5.34
5822 7675 0.109272 GTCGTCAGATCAAGGTGCGA 60.109 55.000 0.00 0.00 0.00 5.10
5858 7711 6.016777 AGCTTTTCATTCAGACATCGAGTTTT 60.017 34.615 0.00 0.00 0.00 2.43
5943 7796 3.248024 ACAGGTATCACCAAAGAGGACA 58.752 45.455 0.00 0.00 41.95 4.02
6080 7933 2.468831 GCTTTTGCAAAACGTGGATGA 58.531 42.857 20.46 0.00 46.58 2.92
6113 7966 4.036352 CGTCCGTTCTAACAGCTATCTTC 58.964 47.826 0.00 0.00 0.00 2.87
6115 7968 5.652518 GTCCGTTCTAACAGCTATCTTCTT 58.347 41.667 0.00 0.00 0.00 2.52
6116 7969 5.517054 GTCCGTTCTAACAGCTATCTTCTTG 59.483 44.000 0.00 0.00 0.00 3.02
6180 8033 0.389426 CACGCTACAGGCCGTACTTT 60.389 55.000 0.00 0.00 37.74 2.66
6215 8068 3.508762 CTTCCATGAAGCTCAATGCAAC 58.491 45.455 0.00 0.00 45.94 4.17
6230 8083 1.436983 GCAACGCCAGTAGCCATACC 61.437 60.000 0.00 0.00 38.78 2.73
6232 8085 1.324740 AACGCCAGTAGCCATACCGA 61.325 55.000 0.00 0.00 38.78 4.69
6233 8086 1.324740 ACGCCAGTAGCCATACCGAA 61.325 55.000 0.00 0.00 38.78 4.30
6297 8150 3.304525 GGTAGACATAATCTGACGACGGG 60.305 52.174 0.00 0.00 38.49 5.28
6317 8170 0.600255 CGAATGCCCCTATCGTGTCC 60.600 60.000 0.00 0.00 0.00 4.02
6353 8207 0.322816 ACTGTGGGCTTGCAGTATGG 60.323 55.000 7.20 0.00 43.30 2.74
6372 8226 5.635278 ATGGATTCAGTCATGTGGTGATA 57.365 39.130 0.00 0.00 39.48 2.15
6422 8279 3.938963 CTGACGTGGTTATTATGTTGGCT 59.061 43.478 0.00 0.00 0.00 4.75
6435 8292 4.946784 ATGTTGGCTCGAATGAAGTTAC 57.053 40.909 0.00 0.00 0.00 2.50
6510 8367 0.107654 GCGATGAGCCTGTAACCCTT 60.108 55.000 0.00 0.00 40.81 3.95
6626 8483 1.671328 CAGCTGTTGGATCTGCATCTG 59.329 52.381 5.25 0.00 35.31 2.90
6704 8561 3.557054 GCTGATGTTGGTCTTCCTGTGTA 60.557 47.826 0.00 0.00 34.23 2.90
6707 8564 2.778299 TGTTGGTCTTCCTGTGTATGC 58.222 47.619 0.00 0.00 34.23 3.14
6851 8710 2.090887 ACCGAGTATAAACCCTAGCCCT 60.091 50.000 0.00 0.00 0.00 5.19
6852 8711 3.140895 ACCGAGTATAAACCCTAGCCCTA 59.859 47.826 0.00 0.00 0.00 3.53
6862 8721 1.202818 CCCTAGCCCTAATGTTCTGGC 60.203 57.143 0.00 0.00 44.35 4.85
6931 8791 3.466836 CCACAAAGTGTGCTACTCTGAA 58.533 45.455 2.77 0.00 46.51 3.02
6939 8799 8.506437 CAAAGTGTGCTACTCTGAATGATTTTA 58.494 33.333 0.00 0.00 39.18 1.52
6976 8836 5.046231 CCCTCTTTAGTTCTTCAGGCTAGTT 60.046 44.000 0.00 0.00 0.00 2.24
7038 8918 3.623060 AGCAATTCGTCATGTGTGATACC 59.377 43.478 0.00 0.00 36.60 2.73
7139 9132 4.630111 AGTACGCTATAGCTAGTCGAGTT 58.370 43.478 21.98 0.00 39.32 3.01
7209 9203 2.033675 CGTACGTATCACCATGTGGCTA 59.966 50.000 7.22 0.00 39.32 3.93
7212 9206 2.159099 ACGTATCACCATGTGGCTACTG 60.159 50.000 0.64 0.00 39.32 2.74
7469 9469 4.704833 GCCGCTCCAGCAGACCAA 62.705 66.667 0.00 0.00 42.21 3.67
7544 9544 4.961511 GGTGACGGACGTGCAGCA 62.962 66.667 8.11 0.81 0.00 4.41
7582 9588 2.582498 GCTACAGCTACGGCGTGG 60.582 66.667 24.86 22.17 44.37 4.94
7636 9642 4.689549 TCCGCCGGGACCTCTCAA 62.690 66.667 1.90 0.00 37.43 3.02
7639 9645 3.394836 GCCGGGACCTCTCAAGCT 61.395 66.667 2.18 0.00 0.00 3.74
7757 9773 3.148279 GGTCGTGGCCTCGGAGAT 61.148 66.667 25.62 0.00 33.89 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.717707 GTGACAGAGTTGTGCTGACTTA 58.282 45.455 0.00 0.00 37.76 2.24
19 20 2.555199 GTGACAGAGTTGTGCTGACTT 58.445 47.619 0.00 0.00 37.76 3.01
73 76 0.249238 GATTCATCTCTCCGCTGCGT 60.249 55.000 21.59 0.00 0.00 5.24
111 114 2.456119 CGTCTTCTCGCACCATGCC 61.456 63.158 0.00 0.00 41.12 4.40
125 128 2.750712 GCTTCTTCTCAGGTAGTCGTCT 59.249 50.000 0.00 0.00 0.00 4.18
207 213 2.439701 CCCTCCGGAGCTACGACA 60.440 66.667 26.87 4.62 35.47 4.35
346 352 3.299503 GTGGATAATGGCATCAAGGGTT 58.700 45.455 0.00 0.00 0.00 4.11
373 379 2.636412 CCGACGAAGACAGGCAGGA 61.636 63.158 0.00 0.00 0.00 3.86
442 457 2.466846 ACGCCGTTGTATAAATCTCCG 58.533 47.619 0.00 0.00 0.00 4.63
456 471 4.572571 TTCCCCAAGCAACGCCGT 62.573 61.111 0.00 0.00 0.00 5.68
830 853 6.717997 TCGTACTATCTATGGGCTTACAATGA 59.282 38.462 0.00 0.00 0.00 2.57
835 858 4.142425 GCCTCGTACTATCTATGGGCTTAC 60.142 50.000 0.00 0.00 35.92 2.34
844 867 4.015084 GCTTATGGGCCTCGTACTATCTA 58.985 47.826 4.53 0.00 0.00 1.98
988 1031 2.418910 CGTCCATGGCCGTCTCTCT 61.419 63.158 7.10 0.00 0.00 3.10
1127 1415 4.779486 GAGGGATGGGGGTGGGGT 62.779 72.222 0.00 0.00 0.00 4.95
1133 1421 2.930562 GGATCCGAGGGATGGGGG 60.931 72.222 1.07 0.00 43.27 5.40
1155 1443 1.441738 GTTTAGGGTTTAGCGCGGAA 58.558 50.000 8.83 0.00 34.93 4.30
1218 1508 1.148759 GCCTTCGCTTCATCTCGTCC 61.149 60.000 0.00 0.00 0.00 4.79
1233 1523 1.211456 CCTCCATCTCCTTGAGCCTT 58.789 55.000 0.00 0.00 0.00 4.35
1310 1600 1.686052 AGGAGGCGCATCTAGAAAGAG 59.314 52.381 22.57 0.00 34.49 2.85
1383 1673 0.977627 AGACCATCACGAGGCATCCA 60.978 55.000 0.00 0.00 0.00 3.41
1420 1710 5.447624 TCAAATTGCATGATGATAGCCTG 57.552 39.130 0.00 0.00 0.00 4.85
1430 1720 8.878769 CAATCTCAAATTCATCAAATTGCATGA 58.121 29.630 0.00 0.00 37.64 3.07
1431 1721 8.122330 CCAATCTCAAATTCATCAAATTGCATG 58.878 33.333 0.00 0.00 37.64 4.06
1432 1722 7.827236 ACCAATCTCAAATTCATCAAATTGCAT 59.173 29.630 0.00 0.00 37.64 3.96
1433 1723 7.162761 ACCAATCTCAAATTCATCAAATTGCA 58.837 30.769 0.00 0.00 37.64 4.08
1481 1771 3.350833 ACTGATACCCGTATCCGTATCC 58.649 50.000 11.41 0.00 39.99 2.59
1521 1811 8.324567 GCACTTTTTCAAAATGACGAATTTACA 58.675 29.630 2.88 0.00 37.51 2.41
1584 1876 6.865205 CAGTTGACATTCTGAATCCCTTTTTC 59.135 38.462 0.00 0.00 34.02 2.29
1730 3220 5.523588 TCATAGAGAAATCACCTGGAGAGT 58.476 41.667 0.00 0.00 0.00 3.24
1731 3221 6.669125 ATCATAGAGAAATCACCTGGAGAG 57.331 41.667 0.00 0.00 0.00 3.20
1894 3386 6.078664 ACACTTCTCTTCTCCTTTTCTCCTA 58.921 40.000 0.00 0.00 0.00 2.94
1995 3487 1.992277 CAGCTACTCACCCAGGGCT 60.992 63.158 4.91 0.00 36.23 5.19
2042 3534 2.681778 CCCTCCCGAGCTCACACT 60.682 66.667 15.40 0.00 0.00 3.55
2096 3588 2.040779 AGCAGCCCTAGTACCCCC 60.041 66.667 0.00 0.00 0.00 5.40
2109 3601 3.118956 CCCAGTTAAGAGGTAGACAGCAG 60.119 52.174 0.00 0.00 0.00 4.24
2312 3804 2.462456 ATGCTCGAATGCACCGATAT 57.538 45.000 12.56 8.35 46.33 1.63
2335 3827 7.639113 AAACAAAAACAGTAATCTGGTCAGA 57.361 32.000 2.93 2.93 41.20 3.27
2336 3828 8.402472 TGTAAACAAAAACAGTAATCTGGTCAG 58.598 33.333 0.47 0.00 41.20 3.51
2395 3887 6.260936 CACTACAGAATGGGCCATAAAGTTAG 59.739 42.308 21.54 17.52 43.62 2.34
2436 3928 9.412460 GGATGCATATAAAGGATCATCCAATTA 57.588 33.333 6.42 5.46 45.55 1.40
2452 3944 6.918067 ACTGCTAGTGTAAGGATGCATATA 57.082 37.500 0.00 0.00 0.00 0.86
2453 3945 5.815233 ACTGCTAGTGTAAGGATGCATAT 57.185 39.130 0.00 0.00 0.00 1.78
2454 3946 6.267699 ACATACTGCTAGTGTAAGGATGCATA 59.732 38.462 0.00 0.00 35.95 3.14
2492 4012 4.207019 GCATGTAAGTCAAAAGTTGTGCAC 59.793 41.667 10.75 10.75 0.00 4.57
2502 4022 9.677567 GAAAAGTTAAGATGCATGTAAGTCAAA 57.322 29.630 2.46 0.00 0.00 2.69
2534 4054 5.240623 TGCCAGGATTACAAACAGTAAAGTG 59.759 40.000 0.00 0.00 45.25 3.16
2560 4080 4.201970 GGAAGAACCAGATCTCTACTGTCG 60.202 50.000 0.00 0.00 38.79 4.35
2628 4153 8.216453 CAGTTTAAAATTGAAATGCTAGCACAC 58.784 33.333 22.07 14.47 0.00 3.82
2636 4161 4.393934 GCGGCAGTTTAAAATTGAAATGC 58.606 39.130 12.74 12.74 43.85 3.56
2688 4213 6.964876 AGGGTCCCTATGGTATAAAATACC 57.035 41.667 9.39 8.83 33.07 2.73
2743 4278 8.887717 CAGTACAAGGAATAGAAAGAATGGAAG 58.112 37.037 0.00 0.00 0.00 3.46
2744 4279 8.602424 TCAGTACAAGGAATAGAAAGAATGGAA 58.398 33.333 0.00 0.00 0.00 3.53
2811 4346 3.630769 AGGCATATCTTCATTGCACACAG 59.369 43.478 0.00 0.00 38.12 3.66
2813 4348 4.142315 ACAAGGCATATCTTCATTGCACAC 60.142 41.667 0.00 0.00 38.12 3.82
2855 4390 2.545526 CACAACTGTGCCACTACTTGAG 59.454 50.000 0.00 0.00 39.39 3.02
2871 4406 5.861787 GGTAATACAAGGCATGAAACACAAC 59.138 40.000 0.00 0.00 0.00 3.32
2879 4414 6.266558 ACAAACAAAGGTAATACAAGGCATGA 59.733 34.615 0.00 0.00 0.00 3.07
2904 4441 5.356751 ACAAGCGCCAAATAAGTATTCATGA 59.643 36.000 2.29 0.00 0.00 3.07
2936 4473 3.627577 ACATTTATCCCACACTCGATTGC 59.372 43.478 2.19 0.00 0.00 3.56
2978 4515 6.761312 ACCATATGCATAACCATGGAAAATG 58.239 36.000 26.10 18.21 40.37 2.32
3074 4611 6.098409 TCACAAATAAAAAGGCAGTAAACCCA 59.902 34.615 0.00 0.00 0.00 4.51
3105 4642 6.657541 AGAAAACTTTCTGTCAACACTAACCA 59.342 34.615 3.91 0.00 45.27 3.67
3114 4651 6.971527 TCGTGTTAGAAAACTTTCTGTCAA 57.028 33.333 13.75 0.00 46.34 3.18
3154 4692 9.819267 GTAGAAGATAAGGCACTAAACACTTAT 57.181 33.333 0.00 0.00 38.49 1.73
3155 4693 8.809066 TGTAGAAGATAAGGCACTAAACACTTA 58.191 33.333 0.00 0.00 38.49 2.24
3156 4694 7.676947 TGTAGAAGATAAGGCACTAAACACTT 58.323 34.615 0.00 0.00 38.49 3.16
3157 4695 7.241042 TGTAGAAGATAAGGCACTAAACACT 57.759 36.000 0.00 0.00 38.49 3.55
3160 4698 6.763610 AGCATGTAGAAGATAAGGCACTAAAC 59.236 38.462 0.00 0.00 38.49 2.01
3177 4715 4.747108 GCATAAGACACTGGTAGCATGTAG 59.253 45.833 0.00 0.00 0.00 2.74
3181 4719 3.198635 ACTGCATAAGACACTGGTAGCAT 59.801 43.478 0.00 0.00 0.00 3.79
3360 4906 8.322091 AGTGTAAATCTATCATAATACAGCCCC 58.678 37.037 0.00 0.00 0.00 5.80
3411 4958 7.878127 ACATATTTCGCTACATAGCCAACTAAT 59.122 33.333 5.33 1.98 46.34 1.73
3484 5033 1.761784 AGTGCACCAAAGGCATTTTCA 59.238 42.857 14.63 0.00 44.11 2.69
3492 5041 9.391006 TCTTATATAAGTTAAGTGCACCAAAGG 57.609 33.333 19.58 0.00 34.93 3.11
3512 5061 7.206981 GCTTTTGGCATAAGCATCTCTTATA 57.793 36.000 29.69 0.00 44.08 0.98
3522 5071 4.382345 AATCAGAGCTTTTGGCATAAGC 57.618 40.909 28.17 28.17 46.47 3.09
3527 5076 5.711506 TGAGAATAAATCAGAGCTTTTGGCA 59.288 36.000 0.00 0.00 44.79 4.92
3590 5139 4.038271 ACAGAGCAATTTCAGGATCCAA 57.962 40.909 15.82 0.00 0.00 3.53
3655 5204 8.624776 AGGAGCAATAGCATATCAAAAAGTTAC 58.375 33.333 0.00 0.00 45.49 2.50
3661 5210 7.775093 ACAGTTAGGAGCAATAGCATATCAAAA 59.225 33.333 0.00 0.00 45.49 2.44
3699 5249 9.670442 ATTATCCTTACTGTGAGGAAAGGTATA 57.330 33.333 23.08 8.91 45.87 1.47
3702 5252 6.893020 ATTATCCTTACTGTGAGGAAAGGT 57.107 37.500 23.08 10.81 45.87 3.50
3755 5306 4.394300 TGGTCACAAAGGCAAAAACAAATG 59.606 37.500 0.00 0.00 0.00 2.32
3774 5325 4.708726 AGCAAACTAGCAAATGATGGTC 57.291 40.909 0.00 0.00 40.93 4.02
3829 5385 4.225942 AGCATTAGACCAGAAGGACATTCA 59.774 41.667 2.27 0.00 40.67 2.57
3996 5553 4.042435 TCTTTCCCTTTTTCCCGTGATACT 59.958 41.667 0.00 0.00 0.00 2.12
3997 5554 4.329392 TCTTTCCCTTTTTCCCGTGATAC 58.671 43.478 0.00 0.00 0.00 2.24
4026 5583 7.591006 AACTCGTTTTTCTTTTCTTTTTCCC 57.409 32.000 0.00 0.00 0.00 3.97
4029 5586 8.596271 TGGAAACTCGTTTTTCTTTTCTTTTT 57.404 26.923 10.09 0.00 36.02 1.94
4087 5658 5.729510 ACAGCAGATTTCTAGACTTCCTTC 58.270 41.667 0.00 0.00 0.00 3.46
4133 5704 0.036732 TCACATGCAGGTCCAAGTCC 59.963 55.000 0.00 0.00 0.00 3.85
4147 5718 5.415701 GGTTTAGAATCACACCACATCACAT 59.584 40.000 0.00 0.00 0.00 3.21
4271 5843 0.169009 GAGCTTTAAGCAAGTGCCCG 59.831 55.000 19.63 0.00 45.56 6.13
4273 5845 1.470494 GAGGAGCTTTAAGCAAGTGCC 59.530 52.381 19.63 11.30 45.56 5.01
4276 5848 2.026729 GGGAGAGGAGCTTTAAGCAAGT 60.027 50.000 19.63 2.15 45.56 3.16
4285 5857 2.304470 GTGAAAAGAGGGAGAGGAGCTT 59.696 50.000 0.00 0.00 0.00 3.74
4286 5858 1.905894 GTGAAAAGAGGGAGAGGAGCT 59.094 52.381 0.00 0.00 0.00 4.09
4317 5902 0.815615 GGCTTTCGGTAGCTCATGGG 60.816 60.000 9.08 0.00 40.99 4.00
4323 5908 3.838244 TGAATATGGCTTTCGGTAGCT 57.162 42.857 9.08 0.00 40.99 3.32
4334 5919 1.906990 AGGAGCAGCATGAATATGGC 58.093 50.000 0.00 0.00 39.69 4.40
4385 5979 3.660501 AACGCAGAAGTAGACATCACA 57.339 42.857 0.00 0.00 0.00 3.58
4440 6034 8.947115 ACTTTACTTCCATTTAGAGTTACATGC 58.053 33.333 0.00 0.00 0.00 4.06
4457 6051 5.222631 CAGAATGTTGGGCAACTTTACTTC 58.777 41.667 0.00 0.00 41.67 3.01
4495 6089 4.584325 TGCAATTCCATCTATTAACCCAGC 59.416 41.667 0.00 0.00 0.00 4.85
4503 6097 7.707624 TTTGTCTTCTGCAATTCCATCTATT 57.292 32.000 0.00 0.00 0.00 1.73
4507 6101 5.776744 AGTTTTGTCTTCTGCAATTCCATC 58.223 37.500 0.00 0.00 0.00 3.51
4546 6140 4.772886 AGGAAACAAGTACCTCAACAGT 57.227 40.909 0.00 0.00 0.00 3.55
4564 6158 4.785376 AGCTCCCTTCAAGAATCTTAAGGA 59.215 41.667 21.82 13.62 40.85 3.36
4628 6369 6.036470 GGCAGCTGAAATATGGAAAAGTTAC 58.964 40.000 20.43 0.00 0.00 2.50
4630 6371 4.527816 TGGCAGCTGAAATATGGAAAAGTT 59.472 37.500 20.43 0.00 0.00 2.66
4631 6372 4.082026 GTGGCAGCTGAAATATGGAAAAGT 60.082 41.667 20.43 0.00 0.00 2.66
4632 6373 4.082081 TGTGGCAGCTGAAATATGGAAAAG 60.082 41.667 20.43 0.00 0.00 2.27
4634 6375 3.429492 TGTGGCAGCTGAAATATGGAAA 58.571 40.909 20.43 0.00 0.00 3.13
4636 6377 2.804986 TGTGGCAGCTGAAATATGGA 57.195 45.000 20.43 0.00 0.00 3.41
4637 6378 2.953648 TGATGTGGCAGCTGAAATATGG 59.046 45.455 20.43 0.00 0.00 2.74
4643 6384 1.985473 AAAGTGATGTGGCAGCTGAA 58.015 45.000 20.43 0.69 0.00 3.02
4647 6388 3.923017 AAGTAAAAGTGATGTGGCAGC 57.077 42.857 0.00 0.00 0.00 5.25
4649 6390 5.594725 TGGTAAAAGTAAAAGTGATGTGGCA 59.405 36.000 0.00 0.00 0.00 4.92
5183 6924 8.792830 TTCTCGAAAGTCAATATGGAAAATCT 57.207 30.769 0.00 0.00 0.00 2.40
5228 6969 5.278315 GGGAGAAAACCATCGCCAATAATAC 60.278 44.000 0.00 0.00 40.67 1.89
5235 6992 0.322456 CAGGGAGAAAACCATCGCCA 60.322 55.000 0.00 0.00 40.67 5.69
5236 6993 1.032114 CCAGGGAGAAAACCATCGCC 61.032 60.000 0.00 0.00 38.43 5.54
5252 7009 9.588096 AGGGAAGGTTAAATTAATTATAGCCAG 57.412 33.333 17.25 0.00 0.00 4.85
5324 7082 6.576778 AAGTATAGCTGGTCTTTGGGTTAT 57.423 37.500 0.00 0.00 0.00 1.89
5329 7087 7.770897 AGTTCATAAAGTATAGCTGGTCTTTGG 59.229 37.037 16.45 11.17 33.22 3.28
5345 7103 9.535878 GAACAGAGGGAGTATTAGTTCATAAAG 57.464 37.037 0.00 0.00 35.30 1.85
5348 7106 7.130099 TGGAACAGAGGGAGTATTAGTTCATA 58.870 38.462 0.00 0.00 36.52 2.15
5349 7107 5.964477 TGGAACAGAGGGAGTATTAGTTCAT 59.036 40.000 0.00 0.00 36.52 2.57
5350 7108 5.338632 TGGAACAGAGGGAGTATTAGTTCA 58.661 41.667 0.00 0.00 36.52 3.18
5351 7109 5.934402 TGGAACAGAGGGAGTATTAGTTC 57.066 43.478 0.00 0.00 34.67 3.01
5372 7223 1.569493 GCGGGCGCACTACATTATG 59.431 57.895 8.62 0.00 41.49 1.90
5373 7224 1.954146 CGCGGGCGCACTACATTAT 60.954 57.895 8.62 0.00 42.06 1.28
5374 7225 2.583868 CGCGGGCGCACTACATTA 60.584 61.111 8.62 0.00 42.06 1.90
5386 7237 1.003851 TAAATCTCGAAAAGCGCGGG 58.996 50.000 8.83 0.00 40.61 6.13
5387 7238 2.798834 TTAAATCTCGAAAAGCGCGG 57.201 45.000 8.83 0.00 40.61 6.46
5388 7239 5.282778 TCAAATTTAAATCTCGAAAAGCGCG 59.717 36.000 0.00 0.00 40.61 6.86
5389 7240 6.450276 GTCAAATTTAAATCTCGAAAAGCGC 58.550 36.000 0.00 0.00 40.61 5.92
5390 7241 6.580791 TGGTCAAATTTAAATCTCGAAAAGCG 59.419 34.615 0.10 0.00 42.69 4.68
5405 7256 9.549078 ACGTTGGTTAAATTTATGGTCAAATTT 57.451 25.926 10.40 10.40 45.45 1.82
5406 7257 8.983724 CACGTTGGTTAAATTTATGGTCAAATT 58.016 29.630 0.00 0.00 39.26 1.82
5407 7258 7.600752 CCACGTTGGTTAAATTTATGGTCAAAT 59.399 33.333 0.00 0.00 31.35 2.32
5409 7260 6.448006 CCACGTTGGTTAAATTTATGGTCAA 58.552 36.000 0.00 0.00 31.35 3.18
5410 7261 5.047943 CCCACGTTGGTTAAATTTATGGTCA 60.048 40.000 0.00 0.00 35.17 4.02
5413 7264 4.177783 GCCCACGTTGGTTAAATTTATGG 58.822 43.478 7.60 2.08 35.17 2.74
5416 7267 3.058363 GTCGCCCACGTTGGTTAAATTTA 60.058 43.478 7.60 0.00 41.18 1.40
5418 7269 1.267533 GTCGCCCACGTTGGTTAAATT 59.732 47.619 7.60 0.00 41.18 1.82
5419 7270 0.876399 GTCGCCCACGTTGGTTAAAT 59.124 50.000 7.60 0.00 41.18 1.40
5421 7272 0.881159 CAGTCGCCCACGTTGGTTAA 60.881 55.000 7.60 0.00 41.18 2.01
5422 7273 1.301087 CAGTCGCCCACGTTGGTTA 60.301 57.895 7.60 0.00 41.18 2.85
5423 7274 2.590575 CAGTCGCCCACGTTGGTT 60.591 61.111 7.60 0.00 41.18 3.67
5437 7288 4.947147 TTTTGCTCCCGCCGCAGT 62.947 61.111 0.00 0.00 38.80 4.40
5438 7289 2.490993 AATTTTTGCTCCCGCCGCAG 62.491 55.000 0.00 0.00 38.80 5.18
5439 7290 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
5440 7291 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53
5441 7292 3.066203 AGTTATAATTTTTGCTCCCGCCG 59.934 43.478 0.00 0.00 34.43 6.46
5442 7293 4.649088 AGTTATAATTTTTGCTCCCGCC 57.351 40.909 0.00 0.00 34.43 6.13
5443 7294 6.126568 TGTAGTTATAATTTTTGCTCCCGC 57.873 37.500 0.00 0.00 0.00 6.13
5444 7295 7.316544 ACTGTAGTTATAATTTTTGCTCCCG 57.683 36.000 0.00 0.00 0.00 5.14
5461 7312 9.263446 TGAACTTGAAGGGTAATATACTGTAGT 57.737 33.333 0.00 0.00 0.00 2.73
5462 7313 9.530633 GTGAACTTGAAGGGTAATATACTGTAG 57.469 37.037 0.00 0.00 0.00 2.74
5463 7314 9.038072 TGTGAACTTGAAGGGTAATATACTGTA 57.962 33.333 0.00 0.00 0.00 2.74
5464 7315 7.913789 TGTGAACTTGAAGGGTAATATACTGT 58.086 34.615 0.00 0.00 0.00 3.55
5465 7316 8.786826 TTGTGAACTTGAAGGGTAATATACTG 57.213 34.615 0.00 0.00 0.00 2.74
5466 7317 8.603304 ACTTGTGAACTTGAAGGGTAATATACT 58.397 33.333 0.00 0.00 0.00 2.12
5467 7318 8.665685 CACTTGTGAACTTGAAGGGTAATATAC 58.334 37.037 0.00 0.00 0.00 1.47
5468 7319 7.335924 GCACTTGTGAACTTGAAGGGTAATATA 59.664 37.037 4.79 0.00 0.00 0.86
5469 7320 6.151144 GCACTTGTGAACTTGAAGGGTAATAT 59.849 38.462 4.79 0.00 0.00 1.28
5470 7321 5.472137 GCACTTGTGAACTTGAAGGGTAATA 59.528 40.000 4.79 0.00 0.00 0.98
5577 7430 2.040813 ACAGATGTCAACAGAATGGGCT 59.959 45.455 0.00 0.00 43.62 5.19
5579 7432 5.458041 AAAACAGATGTCAACAGAATGGG 57.542 39.130 0.00 0.00 43.62 4.00
5729 7582 7.174253 TGTTCTAGAAATTCCACGTAAGCAAAT 59.826 33.333 6.78 0.00 45.62 2.32
5795 7648 2.696989 TGATCTGACGACCATGCAAT 57.303 45.000 0.00 0.00 0.00 3.56
5807 7660 4.944619 ATATCTTCGCACCTTGATCTGA 57.055 40.909 0.00 0.00 0.00 3.27
5928 7781 3.139077 GACGTTTGTCCTCTTTGGTGAT 58.861 45.455 0.00 0.00 39.30 3.06
5943 7796 0.322546 GCTTCATCCCAGGGACGTTT 60.323 55.000 11.70 0.00 32.98 3.60
6080 7933 6.334989 TGTTAGAACGGACGATACAATTGAT 58.665 36.000 13.59 1.08 0.00 2.57
6095 7948 6.326375 AGACAAGAAGATAGCTGTTAGAACG 58.674 40.000 0.00 0.00 0.00 3.95
6113 7966 6.205464 TCTCCTGAAAATAGCACAAAGACAAG 59.795 38.462 0.00 0.00 0.00 3.16
6115 7968 5.620206 TCTCCTGAAAATAGCACAAAGACA 58.380 37.500 0.00 0.00 0.00 3.41
6116 7969 5.703130 ACTCTCCTGAAAATAGCACAAAGAC 59.297 40.000 0.00 0.00 0.00 3.01
6180 8033 0.541998 TGGAAGCCTCGTCCTCTCAA 60.542 55.000 0.94 0.00 36.03 3.02
6210 8063 0.742990 GTATGGCTACTGGCGTTGCA 60.743 55.000 14.62 0.00 42.50 4.08
6215 8068 0.597637 CTTCGGTATGGCTACTGGCG 60.598 60.000 4.01 0.00 42.94 5.69
6230 8083 2.410053 GCGGCAGCTAGATTATTCTTCG 59.590 50.000 0.00 0.00 41.01 3.79
6258 8111 5.761234 TGTCTACCAGTCAAACAATGTAACC 59.239 40.000 0.00 0.00 0.00 2.85
6297 8150 3.642755 CACGATAGGGGCATTCGC 58.357 61.111 0.00 0.00 43.77 4.70
6317 8170 4.926238 CCACAGTACAACAGAGCTTAAGAG 59.074 45.833 6.67 0.00 0.00 2.85
6353 8207 5.824624 ACCAATATCACCACATGACTGAATC 59.175 40.000 0.00 0.00 41.24 2.52
6372 8226 3.832527 ACTACCAAGTCAGCAAACCAAT 58.167 40.909 0.00 0.00 0.00 3.16
6422 8279 3.239587 TGGCATCGTAACTTCATTCGA 57.760 42.857 0.00 0.00 36.77 3.71
6435 8292 2.282407 TGACATCAGAACATGGCATCG 58.718 47.619 0.00 0.00 36.83 3.84
6510 8367 9.702494 CTGACATATGCTATACTTCAGATTCAA 57.298 33.333 10.28 0.00 32.42 2.69
6626 8483 0.438830 CGAAGCAGTAAGTTGCCGTC 59.561 55.000 0.00 0.00 45.18 4.79
6685 8542 3.375299 GCATACACAGGAAGACCAACATC 59.625 47.826 0.00 0.00 38.94 3.06
6704 8561 2.481952 GCTCTTCTCGTGTTTCAAGCAT 59.518 45.455 0.00 0.00 0.00 3.79
6707 8564 3.060003 CAGTGCTCTTCTCGTGTTTCAAG 60.060 47.826 0.00 0.00 0.00 3.02
6791 8649 0.680061 CCCTCGGTATACTGGGCTTC 59.320 60.000 11.82 0.00 32.49 3.86
6851 8710 2.576191 ACTTAGGCCAGCCAGAACATTA 59.424 45.455 12.03 0.00 38.92 1.90
6852 8711 1.355720 ACTTAGGCCAGCCAGAACATT 59.644 47.619 12.03 0.00 38.92 2.71
6862 8721 0.753262 AGGATACGCACTTAGGCCAG 59.247 55.000 5.01 0.00 46.39 4.85
6931 8791 8.118600 AGAGGGGAGAAATTCAGTTAAAATCAT 58.881 33.333 0.00 0.00 0.00 2.45
6939 8799 6.455690 ACTAAAGAGGGGAGAAATTCAGTT 57.544 37.500 0.00 0.00 0.00 3.16
7038 8918 3.304928 GGACATGGCTTCAACTTCAACTG 60.305 47.826 0.00 0.00 0.00 3.16
7139 9132 2.202610 CTCACGCCGCGAGAATCA 60.203 61.111 21.79 0.00 31.84 2.57
7176 9169 2.100216 CGTACGTACGGGGTTCGG 59.900 66.667 34.54 9.16 45.30 4.30
7209 9203 3.520721 TGTGGTGGATGATCTTGATCAGT 59.479 43.478 16.86 7.18 33.59 3.41
7212 9206 4.711399 TCATGTGGTGGATGATCTTGATC 58.289 43.478 3.82 3.82 0.00 2.92
7603 9609 3.797353 GATGAGGCGGGCCAGGAA 61.797 66.667 12.97 0.00 38.92 3.36


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

AutoCloner maintained by Alex Coulton.