Multiple sequence alignment - TraesCS5A01G155600

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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 TraesCS5A01G155600 chr5A 100.000 6573 0 0 1 6573 333737636 333744208 0.000000e+00 12139.0
1 TraesCS5A01G155600 chr5D 95.176 4726 160 30 887 5605 250415083 250419747 0.000000e+00 7402.0
2 TraesCS5A01G155600 chr5D 88.776 294 15 10 591 870 250414804 250415093 1.750000e-90 344.0
3 TraesCS5A01G155600 chr5D 89.007 282 18 4 6302 6573 250419736 250420014 2.940000e-88 337.0
4 TraesCS5A01G155600 chr5D 76.726 623 96 30 5701 6303 448169556 448168963 1.070000e-77 302.0
5 TraesCS5A01G155600 chr5B 94.123 4305 176 30 949 5238 283233876 283238118 0.000000e+00 6477.0
6 TraesCS5A01G155600 chr5B 86.445 391 31 9 200 590 283233163 283233531 6.140000e-110 409.0
7 TraesCS5A01G155600 chr5B 84.470 264 26 9 588 839 283233568 283233828 5.090000e-61 246.0
8 TraesCS5A01G155600 chr5B 88.268 179 21 0 6 184 283232999 283233177 1.440000e-51 215.0
9 TraesCS5A01G155600 chr5B 92.000 75 6 0 5311 5385 283238109 283238183 9.010000e-19 106.0
10 TraesCS5A01G155600 chr2B 85.810 1642 182 26 2143 3737 210669441 210667804 0.000000e+00 1694.0
11 TraesCS5A01G155600 chr2B 91.398 93 7 1 5228 5319 724550922 724551014 6.920000e-25 126.0
12 TraesCS5A01G155600 chr2A 89.071 1345 142 5 2388 3728 148851264 148852607 0.000000e+00 1664.0
13 TraesCS5A01G155600 chr2A 77.190 662 111 28 5661 6303 19595490 19596130 3.770000e-92 350.0
14 TraesCS5A01G155600 chr2D 88.692 1353 149 4 2388 3737 152664377 152663026 0.000000e+00 1648.0
15 TraesCS5A01G155600 chr2D 80.973 678 112 12 5604 6272 607088309 607087640 7.550000e-144 521.0
16 TraesCS5A01G155600 chrUn 89.144 654 50 14 5600 6246 327478138 327478777 0.000000e+00 795.0
17 TraesCS5A01G155600 chrUn 88.939 660 52 14 5600 6252 329940726 329940081 0.000000e+00 795.0
18 TraesCS5A01G155600 chrUn 88.939 660 52 14 5600 6252 329975538 329974893 0.000000e+00 795.0
19 TraesCS5A01G155600 chrUn 89.144 654 50 14 5600 6246 370306539 370307178 0.000000e+00 795.0
20 TraesCS5A01G155600 chr7D 86.248 669 71 7 5607 6272 479601933 479601283 0.000000e+00 706.0
21 TraesCS5A01G155600 chr7D 81.268 710 105 17 5604 6294 104918947 104918247 3.460000e-152 549.0
22 TraesCS5A01G155600 chr1A 82.622 679 94 16 5607 6272 590557475 590556808 4.420000e-161 579.0
23 TraesCS5A01G155600 chr1A 74.180 488 101 17 5828 6304 586497361 586496888 5.240000e-41 180.0
24 TraesCS5A01G155600 chr1A 100.000 85 0 0 5229 5313 587861395 587861311 2.450000e-34 158.0
25 TraesCS5A01G155600 chr3D 81.860 656 102 10 5607 6253 11455649 11455002 2.700000e-148 536.0
26 TraesCS5A01G155600 chr6D 77.301 489 90 13 5827 6303 299900061 299899582 1.090000e-67 268.0
27 TraesCS5A01G155600 chr1B 73.780 492 96 21 5828 6304 679683135 679682662 5.270000e-36 163.0
28 TraesCS5A01G155600 chr1B 93.023 86 6 0 5228 5313 480972933 480973018 6.920000e-25 126.0
29 TraesCS5A01G155600 chr1B 93.976 83 5 0 5231 5313 571427503 571427585 6.920000e-25 126.0
30 TraesCS5A01G155600 chr1B 96.875 32 1 0 904 935 665792696 665792727 3.000000e-03 54.7
31 TraesCS5A01G155600 chr1D 94.186 86 5 0 5228 5313 358222639 358222554 1.490000e-26 132.0
32 TraesCS5A01G155600 chr7A 95.122 82 4 0 5232 5313 252187683 252187602 5.350000e-26 130.0
33 TraesCS5A01G155600 chr7A 93.023 86 6 0 5228 5313 8523471 8523386 6.920000e-25 126.0
34 TraesCS5A01G155600 chr3B 92.941 85 6 0 5229 5313 135685003 135685087 2.490000e-24 124.0
35 TraesCS5A01G155600 chr3B 77.528 178 35 5 5923 6098 446703054 446703228 1.170000e-17 102.0
36 TraesCS5A01G155600 chr7B 85.000 120 9 4 5026 5145 749409571 749409681 5.390000e-21 113.0


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 TraesCS5A01G155600 chr5A 333737636 333744208 6572 False 12139.000000 12139 100.000000 1 6573 1 chr5A.!!$F1 6572
1 TraesCS5A01G155600 chr5D 250414804 250420014 5210 False 2694.333333 7402 90.986333 591 6573 3 chr5D.!!$F1 5982
2 TraesCS5A01G155600 chr5D 448168963 448169556 593 True 302.000000 302 76.726000 5701 6303 1 chr5D.!!$R1 602
3 TraesCS5A01G155600 chr5B 283232999 283238183 5184 False 1490.600000 6477 89.061200 6 5385 5 chr5B.!!$F1 5379
4 TraesCS5A01G155600 chr2B 210667804 210669441 1637 True 1694.000000 1694 85.810000 2143 3737 1 chr2B.!!$R1 1594
5 TraesCS5A01G155600 chr2A 148851264 148852607 1343 False 1664.000000 1664 89.071000 2388 3728 1 chr2A.!!$F2 1340
6 TraesCS5A01G155600 chr2A 19595490 19596130 640 False 350.000000 350 77.190000 5661 6303 1 chr2A.!!$F1 642
7 TraesCS5A01G155600 chr2D 152663026 152664377 1351 True 1648.000000 1648 88.692000 2388 3737 1 chr2D.!!$R1 1349
8 TraesCS5A01G155600 chr2D 607087640 607088309 669 True 521.000000 521 80.973000 5604 6272 1 chr2D.!!$R2 668
9 TraesCS5A01G155600 chrUn 327478138 327478777 639 False 795.000000 795 89.144000 5600 6246 1 chrUn.!!$F1 646
10 TraesCS5A01G155600 chrUn 329940081 329940726 645 True 795.000000 795 88.939000 5600 6252 1 chrUn.!!$R1 652
11 TraesCS5A01G155600 chrUn 329974893 329975538 645 True 795.000000 795 88.939000 5600 6252 1 chrUn.!!$R2 652
12 TraesCS5A01G155600 chrUn 370306539 370307178 639 False 795.000000 795 89.144000 5600 6246 1 chrUn.!!$F2 646
13 TraesCS5A01G155600 chr7D 479601283 479601933 650 True 706.000000 706 86.248000 5607 6272 1 chr7D.!!$R2 665
14 TraesCS5A01G155600 chr7D 104918247 104918947 700 True 549.000000 549 81.268000 5604 6294 1 chr7D.!!$R1 690
15 TraesCS5A01G155600 chr1A 590556808 590557475 667 True 579.000000 579 82.622000 5607 6272 1 chr1A.!!$R3 665
16 TraesCS5A01G155600 chr3D 11455002 11455649 647 True 536.000000 536 81.860000 5607 6253 1 chr3D.!!$R1 646

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
469 470 0.038343 TAACGGTGACCTGTTACGGC 60.038 55.000 12.66 0.0 0.00 5.68 F
1388 1446 0.104409 CCAGGTTAGCCCCCTCCTAT 60.104 60.000 0.00 0.0 34.57 2.57 F
1710 1770 0.407918 AAAATTCGCCCCTTCCCAGA 59.592 50.000 0.00 0.0 0.00 3.86 F
2002 2062 0.830648 TCGTATTTCAGGGCTCAGGG 59.169 55.000 0.00 0.0 0.00 4.45 F
2899 3002 1.134128 TCTGCTGCCACTTTCAACTCA 60.134 47.619 0.00 0.0 0.00 3.41 F
4230 4333 2.024918 CACGCCTGCACAGAAACTT 58.975 52.632 0.00 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 1938 0.108424 CTGCTCTCGCACCTTTAGCT 60.108 55.000 0.00 0.0 42.25 3.32 R
2882 2985 1.405105 TGTTGAGTTGAAAGTGGCAGC 59.595 47.619 0.00 0.0 0.00 5.25 R
3452 3555 0.667993 ACACAAAACATCCCGTGCAG 59.332 50.000 0.00 0.0 32.53 4.41 R
3996 4099 4.610945 ACTTGTAAAAATCTGCACTGCAC 58.389 39.130 0.00 0.0 33.79 4.57 R
4890 4997 0.601558 GTACGACTCACCTTCCTGCA 59.398 55.000 0.00 0.0 0.00 4.41 R
5614 5722 0.179111 CGAAGATAAGGGAGCGCACA 60.179 55.000 11.47 0.0 0.00 4.57 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
48 49 0.103208 GTGTCTATCGACCAGCCCAG 59.897 60.000 0.00 0.00 39.47 4.45
51 52 2.041922 TATCGACCAGCCCAGCCT 60.042 61.111 0.00 0.00 0.00 4.58
72 73 1.712018 GCGTGGGAGTATTTTCCGGC 61.712 60.000 0.00 0.00 38.17 6.13
80 81 2.104963 GAGTATTTTCCGGCAGATCCCT 59.895 50.000 0.00 0.00 0.00 4.20
81 82 2.509964 AGTATTTTCCGGCAGATCCCTT 59.490 45.455 0.00 0.00 0.00 3.95
86 87 4.993705 TTTCCGGCAGATCCCTTAATAT 57.006 40.909 0.00 0.00 0.00 1.28
93 94 6.231211 CGGCAGATCCCTTAATATGTTACTT 58.769 40.000 0.00 0.00 0.00 2.24
126 127 7.582667 TTAGTAGATCGGATGAGAAACATGA 57.417 36.000 0.00 0.00 39.56 3.07
127 128 6.083098 AGTAGATCGGATGAGAAACATGAG 57.917 41.667 0.00 0.00 39.56 2.90
130 131 3.808466 TCGGATGAGAAACATGAGAGG 57.192 47.619 0.00 0.00 39.56 3.69
135 136 5.587844 CGGATGAGAAACATGAGAGGATTTT 59.412 40.000 0.00 0.00 39.56 1.82
138 139 5.256474 TGAGAAACATGAGAGGATTTTCCC 58.744 41.667 0.00 0.00 37.19 3.97
142 143 5.779241 AACATGAGAGGATTTTCCCAGTA 57.221 39.130 0.00 0.00 37.19 2.74
145 146 4.156455 TGAGAGGATTTTCCCAGTATGC 57.844 45.455 0.00 0.00 37.19 3.14
177 178 1.200760 TAGCATGGGCCATATCCGCT 61.201 55.000 26.31 26.31 42.56 5.52
178 179 1.200760 AGCATGGGCCATATCCGCTA 61.201 55.000 23.24 0.00 42.56 4.26
179 180 0.322456 GCATGGGCCATATCCGCTAA 60.322 55.000 20.73 0.00 0.00 3.09
180 181 1.742761 CATGGGCCATATCCGCTAAG 58.257 55.000 20.73 0.00 0.00 2.18
181 182 1.003580 CATGGGCCATATCCGCTAAGT 59.996 52.381 20.73 0.00 0.00 2.24
182 183 1.136828 TGGGCCATATCCGCTAAGTT 58.863 50.000 0.00 0.00 0.00 2.66
183 184 1.493022 TGGGCCATATCCGCTAAGTTT 59.507 47.619 0.00 0.00 0.00 2.66
184 185 2.092103 TGGGCCATATCCGCTAAGTTTT 60.092 45.455 0.00 0.00 0.00 2.43
185 186 2.552743 GGGCCATATCCGCTAAGTTTTC 59.447 50.000 4.39 0.00 0.00 2.29
186 187 2.552743 GGCCATATCCGCTAAGTTTTCC 59.447 50.000 0.00 0.00 0.00 3.13
187 188 2.552743 GCCATATCCGCTAAGTTTTCCC 59.447 50.000 0.00 0.00 0.00 3.97
188 189 3.146847 CCATATCCGCTAAGTTTTCCCC 58.853 50.000 0.00 0.00 0.00 4.81
189 190 2.607631 TATCCGCTAAGTTTTCCCCG 57.392 50.000 0.00 0.00 0.00 5.73
190 191 0.746923 ATCCGCTAAGTTTTCCCCGC 60.747 55.000 0.00 0.00 0.00 6.13
191 192 1.673009 CCGCTAAGTTTTCCCCGCA 60.673 57.895 0.00 0.00 0.00 5.69
192 193 1.238625 CCGCTAAGTTTTCCCCGCAA 61.239 55.000 0.00 0.00 0.00 4.85
193 194 0.594110 CGCTAAGTTTTCCCCGCAAA 59.406 50.000 0.00 0.00 0.00 3.68
194 195 1.001158 CGCTAAGTTTTCCCCGCAAAA 60.001 47.619 0.00 0.00 0.00 2.44
195 196 2.544069 CGCTAAGTTTTCCCCGCAAAAA 60.544 45.455 0.00 0.00 0.00 1.94
227 228 4.017126 GCTAAGTTTTGACTAAGGCCCAT 58.983 43.478 0.00 0.00 0.00 4.00
228 229 4.142381 GCTAAGTTTTGACTAAGGCCCATG 60.142 45.833 0.00 0.00 0.00 3.66
229 230 3.525800 AGTTTTGACTAAGGCCCATGT 57.474 42.857 0.00 0.00 0.00 3.21
248 249 2.437897 CCTTTGACTGGGCTGGCT 59.562 61.111 0.00 0.00 0.00 4.75
279 280 4.156455 ACTAATGAGCCTGTAATGGGTG 57.844 45.455 0.00 0.00 38.02 4.61
310 311 4.160439 CAGTCCTTACTTCATAGGCTCACA 59.840 45.833 0.00 0.00 31.97 3.58
311 312 4.965532 AGTCCTTACTTCATAGGCTCACAT 59.034 41.667 0.00 0.00 29.00 3.21
327 328 1.000385 CACATTGCCCATTGTTCGTGT 60.000 47.619 0.00 0.00 0.00 4.49
329 330 1.000385 CATTGCCCATTGTTCGTGTGT 60.000 47.619 0.00 0.00 0.00 3.72
338 339 4.911610 CCATTGTTCGTGTGTCATTTCTTC 59.088 41.667 0.00 0.00 0.00 2.87
382 383 1.502231 CATCGTCCAATAGAAGGCCG 58.498 55.000 0.00 0.00 0.00 6.13
390 391 0.108329 AATAGAAGGCCGACACGTGG 60.108 55.000 21.57 2.78 0.00 4.94
419 420 3.124636 GTCAGTTGGCCACGTAGTTAATG 59.875 47.826 3.88 0.00 41.61 1.90
433 434 6.015350 ACGTAGTTAATGGGTATCAGATCCAG 60.015 42.308 0.00 0.00 37.78 3.86
442 443 4.158764 GGGTATCAGATCCAGAATCCTACG 59.841 50.000 0.00 0.00 34.67 3.51
460 461 2.754472 ACGGTTAACTTAACGGTGACC 58.246 47.619 18.92 0.00 46.22 4.02
467 468 3.017265 ACTTAACGGTGACCTGTTACG 57.983 47.619 15.17 15.39 30.74 3.18
468 469 2.288395 ACTTAACGGTGACCTGTTACGG 60.288 50.000 18.82 15.39 30.74 4.02
469 470 0.038343 TAACGGTGACCTGTTACGGC 60.038 55.000 12.66 0.00 0.00 5.68
503 504 3.855159 GGTACCCTTGACGAAGCAT 57.145 52.632 0.00 0.00 0.00 3.79
511 512 3.057315 CCCTTGACGAAGCATTTTCATGT 60.057 43.478 0.00 0.00 32.28 3.21
513 514 4.383649 CCTTGACGAAGCATTTTCATGTTG 59.616 41.667 0.00 0.00 32.28 3.33
517 518 2.060284 GAAGCATTTTCATGTTGCGCA 58.940 42.857 5.66 5.66 41.22 6.09
537 538 5.396484 CGCACATTTTCTGTCATGAAAGAT 58.604 37.500 16.48 0.00 37.27 2.40
581 582 2.806503 TTATTGTCGTGGCCCGTGGG 62.807 60.000 12.46 0.00 37.94 4.61
648 687 3.763897 GAGTATGAATGGCCCAAAACAGT 59.236 43.478 0.00 0.00 0.00 3.55
652 691 1.273327 GAATGGCCCAAAACAGTCCAG 59.727 52.381 0.00 0.00 0.00 3.86
673 712 4.330074 CAGAAGACCGAAAATTATGCGAGT 59.670 41.667 0.00 0.00 0.00 4.18
675 714 3.857052 AGACCGAAAATTATGCGAGTCA 58.143 40.909 0.00 0.00 31.96 3.41
693 732 2.164219 GTCAGCCCATTTACCATGTGTG 59.836 50.000 0.00 0.00 0.00 3.82
775 825 2.430244 CTTAGGCGCGTGTCGTGT 60.430 61.111 13.84 0.00 39.70 4.49
815 865 4.342862 CACCTATGGATCCACCTGTAAG 57.657 50.000 18.99 7.73 39.86 2.34
816 866 3.711704 CACCTATGGATCCACCTGTAAGT 59.288 47.826 18.99 2.37 39.86 2.24
818 868 3.967326 CCTATGGATCCACCTGTAAGTGA 59.033 47.826 18.99 0.00 40.34 3.41
819 869 3.914426 ATGGATCCACCTGTAAGTGAC 57.086 47.619 18.99 0.00 40.34 3.67
859 909 5.533482 CATGAGTCCTTTCTCTATTACCCG 58.467 45.833 0.00 0.00 35.68 5.28
860 910 4.863548 TGAGTCCTTTCTCTATTACCCGA 58.136 43.478 0.00 0.00 35.68 5.14
861 911 5.266788 TGAGTCCTTTCTCTATTACCCGAA 58.733 41.667 0.00 0.00 35.68 4.30
862 912 5.718130 TGAGTCCTTTCTCTATTACCCGAAA 59.282 40.000 0.00 0.00 35.68 3.46
863 913 6.127423 TGAGTCCTTTCTCTATTACCCGAAAG 60.127 42.308 0.00 0.00 41.05 2.62
864 914 4.809958 GTCCTTTCTCTATTACCCGAAAGC 59.190 45.833 0.00 0.00 40.41 3.51
865 915 4.468510 TCCTTTCTCTATTACCCGAAAGCA 59.531 41.667 0.00 0.00 40.41 3.91
866 916 5.046159 TCCTTTCTCTATTACCCGAAAGCAA 60.046 40.000 0.00 0.00 40.41 3.91
867 917 5.646360 CCTTTCTCTATTACCCGAAAGCAAA 59.354 40.000 0.00 0.00 40.41 3.68
868 918 6.150474 CCTTTCTCTATTACCCGAAAGCAAAA 59.850 38.462 0.00 0.00 40.41 2.44
869 919 6.737254 TTCTCTATTACCCGAAAGCAAAAG 57.263 37.500 0.00 0.00 0.00 2.27
870 920 5.801380 TCTCTATTACCCGAAAGCAAAAGT 58.199 37.500 0.00 0.00 0.00 2.66
871 921 6.235664 TCTCTATTACCCGAAAGCAAAAGTT 58.764 36.000 0.00 0.00 0.00 2.66
872 922 7.388437 TCTCTATTACCCGAAAGCAAAAGTTA 58.612 34.615 0.00 0.00 0.00 2.24
873 923 8.044908 TCTCTATTACCCGAAAGCAAAAGTTAT 58.955 33.333 0.00 0.00 0.00 1.89
874 924 8.570068 TCTATTACCCGAAAGCAAAAGTTATT 57.430 30.769 0.00 0.00 0.00 1.40
875 925 8.671028 TCTATTACCCGAAAGCAAAAGTTATTC 58.329 33.333 0.00 0.00 0.00 1.75
876 926 6.887626 TTACCCGAAAGCAAAAGTTATTCT 57.112 33.333 0.00 0.00 0.00 2.40
877 927 5.372547 ACCCGAAAGCAAAAGTTATTCTC 57.627 39.130 0.00 0.00 0.00 2.87
878 928 4.825085 ACCCGAAAGCAAAAGTTATTCTCA 59.175 37.500 0.00 0.00 0.00 3.27
879 929 5.300792 ACCCGAAAGCAAAAGTTATTCTCAA 59.699 36.000 0.00 0.00 0.00 3.02
880 930 6.183360 ACCCGAAAGCAAAAGTTATTCTCAAA 60.183 34.615 0.00 0.00 0.00 2.69
881 931 6.699642 CCCGAAAGCAAAAGTTATTCTCAAAA 59.300 34.615 0.00 0.00 0.00 2.44
882 932 7.223777 CCCGAAAGCAAAAGTTATTCTCAAAAA 59.776 33.333 0.00 0.00 0.00 1.94
906 956 0.109597 AAAGCAAAAGCTCGATGCCG 60.110 50.000 12.98 0.00 44.23 5.69
1026 1080 1.862123 CATATGGTGCGACGGATGC 59.138 57.895 0.00 0.00 0.00 3.91
1081 1138 1.754803 ACCTCGAGAACAAGTGTCACA 59.245 47.619 15.71 0.00 0.00 3.58
1087 1144 1.782028 GAACAAGTGTCACACGGGGC 61.782 60.000 1.22 0.00 39.64 5.80
1111 1168 1.668826 AAATGGCAGGGTGGTAGAGA 58.331 50.000 0.00 0.00 0.00 3.10
1114 1171 0.116342 TGGCAGGGTGGTAGAGAGAA 59.884 55.000 0.00 0.00 0.00 2.87
1115 1172 1.276622 GGCAGGGTGGTAGAGAGAAA 58.723 55.000 0.00 0.00 0.00 2.52
1172 1230 2.913060 ATCTCCTCCGCCGCCTAC 60.913 66.667 0.00 0.00 0.00 3.18
1383 1441 2.687566 CGACCAGGTTAGCCCCCT 60.688 66.667 0.00 0.00 34.57 4.79
1384 1442 2.732619 CGACCAGGTTAGCCCCCTC 61.733 68.421 0.00 0.00 34.57 4.30
1385 1443 2.286197 ACCAGGTTAGCCCCCTCC 60.286 66.667 0.00 0.00 34.57 4.30
1386 1444 2.042930 CCAGGTTAGCCCCCTCCT 59.957 66.667 0.00 0.00 34.57 3.69
1387 1445 1.316969 CCAGGTTAGCCCCCTCCTA 59.683 63.158 0.00 0.00 34.57 2.94
1388 1446 0.104409 CCAGGTTAGCCCCCTCCTAT 60.104 60.000 0.00 0.00 34.57 2.57
1397 1455 0.871024 CCCCCTCCTATTCCTCCTCT 59.129 60.000 0.00 0.00 0.00 3.69
1441 1499 4.208686 GTGCCTCGCCTCCGGTAG 62.209 72.222 0.00 0.00 34.56 3.18
1494 1552 1.255667 GCTCCCACTCGAACCCTGTA 61.256 60.000 0.00 0.00 0.00 2.74
1550 1608 2.663196 CGGGGACAGAAGGTGGTC 59.337 66.667 0.00 0.00 0.00 4.02
1562 1620 1.539124 GGTGGTCTGTTCCCTCCCT 60.539 63.158 0.00 0.00 30.85 4.20
1565 1623 1.982958 GTGGTCTGTTCCCTCCCTTTA 59.017 52.381 0.00 0.00 0.00 1.85
1566 1624 1.982958 TGGTCTGTTCCCTCCCTTTAC 59.017 52.381 0.00 0.00 0.00 2.01
1570 1628 1.630878 CTGTTCCCTCCCTTTACTGCT 59.369 52.381 0.00 0.00 0.00 4.24
1576 1634 1.208293 CCTCCCTTTACTGCTGTCCTC 59.792 57.143 0.00 0.00 0.00 3.71
1705 1765 1.613317 CCCCCAAAATTCGCCCCTTC 61.613 60.000 0.00 0.00 0.00 3.46
1707 1767 1.613317 CCCAAAATTCGCCCCTTCCC 61.613 60.000 0.00 0.00 0.00 3.97
1710 1770 0.407918 AAAATTCGCCCCTTCCCAGA 59.592 50.000 0.00 0.00 0.00 3.86
1713 1773 1.208165 ATTCGCCCCTTCCCAGACTT 61.208 55.000 0.00 0.00 0.00 3.01
1718 1778 1.065345 GCCCCTTCCCAGACTTACTTC 60.065 57.143 0.00 0.00 0.00 3.01
1722 1782 3.328050 CCCTTCCCAGACTTACTTCTTGT 59.672 47.826 0.00 0.00 0.00 3.16
1739 1799 5.568620 TCTTGTTCTTCTCCCTTTAGCTT 57.431 39.130 0.00 0.00 0.00 3.74
1784 1844 2.494870 GCAGGGAGTGAGCAATTGAAAT 59.505 45.455 10.34 0.00 0.00 2.17
1805 1865 1.597663 CAAAACGTCACTCTTTCGCCT 59.402 47.619 0.00 0.00 0.00 5.52
1922 1982 3.281727 TCACATCCTAACCAATCCAGC 57.718 47.619 0.00 0.00 0.00 4.85
1959 2019 5.410355 AAGCATTGCTACCATTTCACATT 57.590 34.783 12.39 0.00 38.25 2.71
1986 2046 3.757270 TGTTTCCCCAATGTACATTCGT 58.243 40.909 18.25 0.00 0.00 3.85
1995 2055 5.008613 CCCAATGTACATTCGTATTTCAGGG 59.991 44.000 18.25 17.03 0.00 4.45
1996 2056 5.505654 CCAATGTACATTCGTATTTCAGGGC 60.506 44.000 18.25 0.00 0.00 5.19
1997 2057 4.481368 TGTACATTCGTATTTCAGGGCT 57.519 40.909 0.00 0.00 0.00 5.19
1998 2058 4.439057 TGTACATTCGTATTTCAGGGCTC 58.561 43.478 0.00 0.00 0.00 4.70
1999 2059 3.627395 ACATTCGTATTTCAGGGCTCA 57.373 42.857 0.00 0.00 0.00 4.26
2000 2060 3.535561 ACATTCGTATTTCAGGGCTCAG 58.464 45.455 0.00 0.00 0.00 3.35
2001 2061 2.691409 TTCGTATTTCAGGGCTCAGG 57.309 50.000 0.00 0.00 0.00 3.86
2002 2062 0.830648 TCGTATTTCAGGGCTCAGGG 59.169 55.000 0.00 0.00 0.00 4.45
2048 2108 6.795399 AGTTGTTTATGTTCTTGTTGAGTGG 58.205 36.000 0.00 0.00 0.00 4.00
2268 2334 6.149308 TGAGTGCTTTCAACATGGTTAGTATG 59.851 38.462 0.00 0.00 0.00 2.39
2272 2338 6.657117 TGCTTTCAACATGGTTAGTATGCTTA 59.343 34.615 0.00 0.00 0.00 3.09
2427 2529 9.959749 TTCCTTCACATAAATTTGTTACTGTTC 57.040 29.630 0.00 0.00 0.00 3.18
2882 2985 2.774234 TCTAAGGCATTTCCTCCCTCTG 59.226 50.000 0.00 0.00 46.94 3.35
2899 3002 1.134128 TCTGCTGCCACTTTCAACTCA 60.134 47.619 0.00 0.00 0.00 3.41
3160 3263 7.255104 GCAATGAATTTCACCGATATTCCTGTA 60.255 37.037 0.15 0.00 32.00 2.74
3452 3555 2.544069 GCTAGTACTGATTCACCGGCTC 60.544 54.545 5.39 0.00 0.00 4.70
3538 3641 2.036256 GCATGTGGCCCTGGTTCT 59.964 61.111 0.00 0.00 36.11 3.01
3658 3761 2.233271 CAAGCAAGTGGAGGAACATGT 58.767 47.619 0.00 0.00 0.00 3.21
3996 4099 5.712152 AGCTTTTTGTATCCTGTGGAAAG 57.288 39.130 0.00 0.00 34.34 2.62
4000 4103 3.500448 TTGTATCCTGTGGAAAGTGCA 57.500 42.857 0.00 0.00 34.34 4.57
4112 4215 6.407475 AATCTGCCGTCAAAAATTTATTGC 57.593 33.333 0.00 0.00 0.00 3.56
4120 4223 7.275560 GCCGTCAAAAATTTATTGCATCTTAGT 59.724 33.333 0.00 0.00 0.00 2.24
4146 4249 9.403583 TGTAAGTTTTCCTTGAAGACTTTATGT 57.596 29.630 15.20 0.00 41.87 2.29
4208 4311 3.795150 GCTCTGTCTCTAAGATTCTGCCG 60.795 52.174 0.00 0.00 0.00 5.69
4230 4333 2.024918 CACGCCTGCACAGAAACTT 58.975 52.632 0.00 0.00 0.00 2.66
4237 4340 2.553602 CCTGCACAGAAACTTGTATGCA 59.446 45.455 0.00 0.00 31.64 3.96
4277 4380 6.460953 GGCAAATCTTCCTGTTTTTAGTCACA 60.461 38.462 0.00 0.00 0.00 3.58
4522 4626 3.446442 ACCAACCAGCAAGATTCAGAT 57.554 42.857 0.00 0.00 0.00 2.90
4681 4788 2.223611 CGAAGCCAATCATCTGATCTGC 59.776 50.000 0.00 6.00 32.75 4.26
4741 4848 2.271800 AGAAAATCGCGACAGTCATCC 58.728 47.619 12.93 0.00 0.00 3.51
4758 4865 7.099764 CAGTCATCCTGTAGTTACTCACATTT 58.900 38.462 0.00 0.00 36.37 2.32
4890 4997 4.623647 GCAGGCCATGGTTCATGTAAATTT 60.624 41.667 14.67 0.00 39.94 1.82
4915 5022 3.506844 AGGAAGGTGAGTCGTACTTCTTC 59.493 47.826 16.10 8.72 39.33 2.87
4917 5024 1.811359 AGGTGAGTCGTACTTCTTCGG 59.189 52.381 0.00 0.00 0.00 4.30
4918 5025 1.538950 GGTGAGTCGTACTTCTTCGGT 59.461 52.381 0.00 0.00 0.00 4.69
4994 5101 1.219124 CTATCTGCAGCACCGGTGT 59.781 57.895 33.92 18.91 33.19 4.16
5040 5147 2.237392 ACCTGTGAGCCAAGATAGTTCC 59.763 50.000 0.00 0.00 0.00 3.62
5094 5201 2.613660 TAATCGCCATGCTGCTGCCT 62.614 55.000 13.47 0.00 38.71 4.75
5189 5296 6.116126 CCTCTTGTTGTTAGATAGAAAGGGG 58.884 44.000 0.00 0.00 0.00 4.79
5216 5324 6.349611 CCCATTTGTCTCACTTTATTGAGGTG 60.350 42.308 0.46 0.00 42.95 4.00
5217 5325 6.349611 CCATTTGTCTCACTTTATTGAGGTGG 60.350 42.308 0.46 0.00 42.95 4.61
5218 5326 4.974645 TGTCTCACTTTATTGAGGTGGT 57.025 40.909 0.46 0.00 42.95 4.16
5232 5340 3.265737 TGAGGTGGTAAATGCCATGTACT 59.734 43.478 5.05 0.00 41.08 2.73
5239 5347 3.287867 AAATGCCATGTACTCCCTCTG 57.712 47.619 0.00 0.00 0.00 3.35
5246 5354 5.427157 TGCCATGTACTCCCTCTGTAAATAA 59.573 40.000 0.00 0.00 0.00 1.40
5332 5440 7.016268 AGGGAGTGTCTCTCAATTTTAGTTGTA 59.984 37.037 4.41 0.00 44.40 2.41
5483 5591 1.668151 GGGTCTGAGTGTTGGCGTC 60.668 63.158 0.00 0.00 0.00 5.19
5492 5600 0.028902 GTGTTGGCGTCAAGGTCAAC 59.971 55.000 0.75 11.99 39.68 3.18
5493 5601 0.393132 TGTTGGCGTCAAGGTCAACA 60.393 50.000 16.32 16.32 44.57 3.33
5498 5606 1.812571 GGCGTCAAGGTCAACAATGAT 59.187 47.619 0.00 0.00 38.01 2.45
5544 5652 2.450479 AAAGGCGACAAGGAGACCCG 62.450 60.000 0.00 0.00 37.58 5.28
5545 5653 3.692406 GGCGACAAGGAGACCCGT 61.692 66.667 0.00 0.00 37.58 5.28
5563 5671 2.539274 CCGTTGTGGCTGATTGTTTTTG 59.461 45.455 0.00 0.00 0.00 2.44
5591 5699 1.000163 CGCGGATATGTTAGCCACTCT 60.000 52.381 0.00 0.00 32.61 3.24
5592 5700 2.678324 GCGGATATGTTAGCCACTCTC 58.322 52.381 0.00 0.00 32.61 3.20
5593 5701 2.035961 GCGGATATGTTAGCCACTCTCA 59.964 50.000 0.00 0.00 32.61 3.27
5594 5702 3.306364 GCGGATATGTTAGCCACTCTCAT 60.306 47.826 0.00 0.00 32.61 2.90
5595 5703 4.082190 GCGGATATGTTAGCCACTCTCATA 60.082 45.833 0.00 0.00 32.61 2.15
5596 5704 5.645624 CGGATATGTTAGCCACTCTCATAG 58.354 45.833 0.00 0.00 32.61 2.23
5597 5705 5.415221 GGATATGTTAGCCACTCTCATAGC 58.585 45.833 0.00 0.00 33.51 2.97
5598 5706 5.047021 GGATATGTTAGCCACTCTCATAGCA 60.047 44.000 0.00 0.00 33.51 3.49
5602 5710 1.227380 GCCACTCTCATAGCACGGG 60.227 63.158 0.00 0.00 0.00 5.28
5659 5767 0.615331 GAGGCTTCATGAGGGTGTGA 59.385 55.000 6.99 0.00 0.00 3.58
5662 5770 0.320771 GCTTCATGAGGGTGTGACGT 60.321 55.000 6.99 0.00 0.00 4.34
5800 5918 3.306225 GCTTTGGTGCCAATGAAGAATGA 60.306 43.478 17.58 0.00 35.70 2.57
5849 5968 0.886043 TTGATGACTTGCTGCAGCGT 60.886 50.000 32.11 24.80 45.83 5.07
5896 6015 4.930963 CAGGTGAACTGCATTTTGTTGTA 58.069 39.130 0.00 0.00 40.97 2.41
5925 6045 1.466866 CGAGCACCGAGTCACGATTTA 60.467 52.381 0.00 0.00 45.77 1.40
5959 6080 3.364549 CCAATGTCTGGCCTTTATTGGA 58.635 45.455 24.76 4.29 46.71 3.53
6000 6122 5.321959 TGCAGAAGACATTGTTTTGTGAA 57.678 34.783 17.92 7.44 0.00 3.18
6056 6179 0.861837 GATCGGACGATGACAATGCC 59.138 55.000 12.40 0.00 34.60 4.40
6086 6209 3.074412 GTTTCCTTCTTGAAGGCATCGA 58.926 45.455 21.16 4.45 39.80 3.59
6098 6221 5.883661 TGAAGGCATCGATTTTGAAGAATC 58.116 37.500 0.00 0.00 33.64 2.52
6133 6257 0.179067 GGTGTTGTCTTCGGTGGTGA 60.179 55.000 0.00 0.00 0.00 4.02
6186 6316 3.207778 CTGTGACGGGGTCTTTGTTTTA 58.792 45.455 0.00 0.00 33.15 1.52
6191 6331 6.490721 TGTGACGGGGTCTTTGTTTTATATTT 59.509 34.615 0.00 0.00 33.15 1.40
6192 6332 7.025365 GTGACGGGGTCTTTGTTTTATATTTC 58.975 38.462 0.00 0.00 33.15 2.17
6196 6338 7.336176 ACGGGGTCTTTGTTTTATATTTCTCTC 59.664 37.037 0.00 0.00 0.00 3.20
6272 6428 1.614317 GCAGAGGCTGGGTGTAATTGT 60.614 52.381 0.00 0.00 36.96 2.71
6273 6429 2.359900 CAGAGGCTGGGTGTAATTGTC 58.640 52.381 0.00 0.00 0.00 3.18
6318 6482 5.047847 TCGAAAATAGCACGGGATAAAGAG 58.952 41.667 0.00 0.00 0.00 2.85
6348 6512 5.447818 GCCAATTTGGAGATCTTGTTCTACG 60.448 44.000 19.76 0.00 40.96 3.51
6420 6593 5.649395 CGCCTTTGTGGAATATGATATGGAT 59.351 40.000 0.00 0.00 38.35 3.41
6481 6654 4.221482 AGCAACTTTCTGGATCCAAAATCC 59.779 41.667 17.00 7.80 38.66 3.01
6496 6669 8.750515 ATCCAAAATCCAGTTTCACAAAAATT 57.249 26.923 0.00 0.00 0.00 1.82
6513 6686 8.887717 CACAAAAATTAGACCATTTGTTTTGGA 58.112 29.630 9.86 0.00 42.36 3.53
6522 6695 8.073467 AGACCATTTGTTTTGGAAAAACTAGA 57.927 30.769 14.66 3.87 37.69 2.43
6523 6696 8.197439 AGACCATTTGTTTTGGAAAAACTAGAG 58.803 33.333 14.66 5.84 37.69 2.43
6524 6697 7.847096 ACCATTTGTTTTGGAAAAACTAGAGT 58.153 30.769 14.66 5.55 37.69 3.24
6525 6698 7.979537 ACCATTTGTTTTGGAAAAACTAGAGTC 59.020 33.333 14.66 0.00 37.69 3.36
6526 6699 7.438160 CCATTTGTTTTGGAAAAACTAGAGTCC 59.562 37.037 14.66 0.00 36.26 3.85
6527 6700 5.744666 TGTTTTGGAAAAACTAGAGTCCG 57.255 39.130 14.66 0.00 32.45 4.79
6528 6701 5.430007 TGTTTTGGAAAAACTAGAGTCCGA 58.570 37.500 14.66 0.00 32.45 4.55
6531 6704 5.540400 TTGGAAAAACTAGAGTCCGAAGA 57.460 39.130 0.00 0.00 32.45 2.87
6532 6705 5.135508 TGGAAAAACTAGAGTCCGAAGAG 57.864 43.478 0.00 0.00 32.45 2.85
6533 6706 4.587684 TGGAAAAACTAGAGTCCGAAGAGT 59.412 41.667 0.00 0.00 32.45 3.24
6534 6707 5.771666 TGGAAAAACTAGAGTCCGAAGAGTA 59.228 40.000 0.00 0.00 32.45 2.59
6536 6709 6.072008 GGAAAAACTAGAGTCCGAAGAGTAGT 60.072 42.308 0.00 0.00 0.00 2.73
6537 6710 5.883503 AAACTAGAGTCCGAAGAGTAGTG 57.116 43.478 0.00 0.00 0.00 2.74
6562 6735 4.947645 ACAATTGTTTGGGTGTGAATCTG 58.052 39.130 4.92 0.00 37.15 2.90
6563 6736 4.405358 ACAATTGTTTGGGTGTGAATCTGT 59.595 37.500 4.92 0.00 37.15 3.41
6567 6740 5.703978 TGTTTGGGTGTGAATCTGTTATG 57.296 39.130 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.307121 CGATAGACACATTATTCTCAACTCTTT 57.693 33.333 0.00 0.00 39.76 2.52
48 49 0.743345 AAAATACTCCCACGCGAGGC 60.743 55.000 17.90 0.00 33.93 4.70
51 52 0.458889 CGGAAAATACTCCCACGCGA 60.459 55.000 15.93 0.00 31.03 5.87
54 55 0.391927 TGCCGGAAAATACTCCCACG 60.392 55.000 5.05 0.00 31.03 4.94
93 94 9.788889 TCTCATCCGATCTACTAATGTAACTAA 57.211 33.333 0.00 0.00 0.00 2.24
98 99 8.459911 TGTTTCTCATCCGATCTACTAATGTA 57.540 34.615 0.00 0.00 0.00 2.29
102 103 7.502561 TCTCATGTTTCTCATCCGATCTACTAA 59.497 37.037 0.00 0.00 34.09 2.24
103 104 6.998673 TCTCATGTTTCTCATCCGATCTACTA 59.001 38.462 0.00 0.00 34.09 1.82
126 127 2.852449 TGGCATACTGGGAAAATCCTCT 59.148 45.455 0.00 0.00 36.57 3.69
127 128 3.297134 TGGCATACTGGGAAAATCCTC 57.703 47.619 0.00 0.00 36.57 3.71
130 131 5.011023 CCCTTAATGGCATACTGGGAAAATC 59.989 44.000 20.34 0.00 35.40 2.17
135 136 1.780309 CCCCTTAATGGCATACTGGGA 59.220 52.381 24.30 0.39 35.40 4.37
145 146 2.242043 CCATGCTAAGCCCCTTAATGG 58.758 52.381 0.00 2.86 31.93 3.16
157 158 0.322456 GCGGATATGGCCCATGCTAA 60.322 55.000 6.46 0.00 37.74 3.09
196 197 8.674607 CCTTAGTCAAAACTTAGCGGATATTTT 58.325 33.333 0.00 0.00 36.92 1.82
197 198 7.201705 GCCTTAGTCAAAACTTAGCGGATATTT 60.202 37.037 0.00 0.00 36.92 1.40
198 199 6.260271 GCCTTAGTCAAAACTTAGCGGATATT 59.740 38.462 0.00 0.00 36.92 1.28
199 200 5.758784 GCCTTAGTCAAAACTTAGCGGATAT 59.241 40.000 0.00 0.00 36.92 1.63
200 201 5.114081 GCCTTAGTCAAAACTTAGCGGATA 58.886 41.667 0.00 0.00 36.92 2.59
201 202 3.939592 GCCTTAGTCAAAACTTAGCGGAT 59.060 43.478 0.00 0.00 36.92 4.18
202 203 3.332034 GCCTTAGTCAAAACTTAGCGGA 58.668 45.455 0.00 0.00 36.92 5.54
203 204 2.418976 GGCCTTAGTCAAAACTTAGCGG 59.581 50.000 0.00 0.00 36.92 5.52
204 205 2.418976 GGGCCTTAGTCAAAACTTAGCG 59.581 50.000 0.84 0.00 36.92 4.26
205 206 3.418047 TGGGCCTTAGTCAAAACTTAGC 58.582 45.455 4.53 0.00 36.92 3.09
206 207 5.010282 ACATGGGCCTTAGTCAAAACTTAG 58.990 41.667 4.53 0.00 36.92 2.18
207 208 4.764823 CACATGGGCCTTAGTCAAAACTTA 59.235 41.667 4.53 0.00 36.92 2.24
265 266 1.000896 GCACCACCCATTACAGGCT 60.001 57.895 0.00 0.00 0.00 4.58
266 267 2.052104 GGCACCACCCATTACAGGC 61.052 63.158 0.00 0.00 0.00 4.85
279 280 0.400594 AAGTAAGGACTGGTGGCACC 59.599 55.000 29.75 29.75 39.22 5.01
310 311 1.269448 GACACACGAACAATGGGCAAT 59.731 47.619 0.00 0.00 0.00 3.56
311 312 0.665835 GACACACGAACAATGGGCAA 59.334 50.000 0.00 0.00 0.00 4.52
327 328 5.362143 TGGTTGTTCATTGGAAGAAATGACA 59.638 36.000 0.00 0.28 44.26 3.58
329 330 6.477053 TTGGTTGTTCATTGGAAGAAATGA 57.523 33.333 0.00 0.00 43.20 2.57
338 339 2.437200 ACGCATTGGTTGTTCATTGG 57.563 45.000 0.00 0.00 0.00 3.16
362 363 1.884235 GGCCTTCTATTGGACGATGG 58.116 55.000 0.00 0.00 0.00 3.51
370 371 0.999406 CACGTGTCGGCCTTCTATTG 59.001 55.000 7.58 0.00 0.00 1.90
382 383 0.179161 CTGACGATCCTCCACGTGTC 60.179 60.000 15.65 3.82 42.74 3.67
390 391 0.741221 GTGGCCAACTGACGATCCTC 60.741 60.000 7.24 0.00 0.00 3.71
419 420 4.158764 CGTAGGATTCTGGATCTGATACCC 59.841 50.000 0.00 0.00 35.02 3.69
442 443 3.732212 ACAGGTCACCGTTAAGTTAACC 58.268 45.455 17.99 5.75 35.27 2.85
468 469 2.562912 CCAACATGTGGCAGTCGC 59.437 61.111 0.00 0.00 41.72 5.19
486 487 3.500680 TGAAAATGCTTCGTCAAGGGTAC 59.499 43.478 0.00 0.00 0.00 3.34
487 488 3.745799 TGAAAATGCTTCGTCAAGGGTA 58.254 40.909 0.00 0.00 0.00 3.69
488 489 2.582052 TGAAAATGCTTCGTCAAGGGT 58.418 42.857 0.00 0.00 0.00 4.34
489 490 3.057315 ACATGAAAATGCTTCGTCAAGGG 60.057 43.478 0.00 0.00 0.00 3.95
490 491 4.164822 ACATGAAAATGCTTCGTCAAGG 57.835 40.909 0.00 0.00 0.00 3.61
491 492 4.143473 GCAACATGAAAATGCTTCGTCAAG 60.143 41.667 0.00 0.00 37.12 3.02
492 493 3.735240 GCAACATGAAAATGCTTCGTCAA 59.265 39.130 0.00 0.00 37.12 3.18
493 494 3.307674 GCAACATGAAAATGCTTCGTCA 58.692 40.909 0.00 0.00 37.12 4.35
494 495 2.339400 CGCAACATGAAAATGCTTCGTC 59.661 45.455 0.00 0.00 37.92 4.20
495 496 2.318578 CGCAACATGAAAATGCTTCGT 58.681 42.857 0.00 0.00 37.92 3.85
496 497 1.058129 GCGCAACATGAAAATGCTTCG 59.942 47.619 0.30 0.00 37.92 3.79
497 498 2.060284 TGCGCAACATGAAAATGCTTC 58.940 42.857 8.16 0.71 37.92 3.86
498 499 1.794116 GTGCGCAACATGAAAATGCTT 59.206 42.857 14.00 0.00 37.92 3.91
499 500 1.269673 TGTGCGCAACATGAAAATGCT 60.270 42.857 14.00 0.00 37.92 3.79
500 501 1.138337 TGTGCGCAACATGAAAATGC 58.862 45.000 14.00 3.61 32.36 3.56
511 512 2.292845 TCATGACAGAAAATGTGCGCAA 59.707 40.909 14.00 2.60 44.17 4.85
513 514 2.617250 TCATGACAGAAAATGTGCGC 57.383 45.000 0.00 0.00 44.17 6.09
517 518 9.458727 AGTATGATCTTTCATGACAGAAAATGT 57.541 29.630 15.24 0.00 43.18 2.71
553 554 3.689649 GGCCACGACAATAATCACTTCTT 59.310 43.478 0.00 0.00 0.00 2.52
629 668 3.096092 GGACTGTTTTGGGCCATTCATA 58.904 45.455 7.26 0.00 0.00 2.15
648 687 3.621268 CGCATAATTTTCGGTCTTCTGGA 59.379 43.478 0.00 0.00 0.00 3.86
652 691 4.328983 TGACTCGCATAATTTTCGGTCTTC 59.671 41.667 0.00 0.00 0.00 2.87
667 706 0.392461 GGTAAATGGGCTGACTCGCA 60.392 55.000 0.00 0.00 0.00 5.10
673 712 2.445427 CACACATGGTAAATGGGCTGA 58.555 47.619 0.00 0.00 0.00 4.26
675 714 1.185315 GCACACATGGTAAATGGGCT 58.815 50.000 0.00 0.00 39.75 5.19
757 807 2.430244 CACGACACGCGCCTAAGT 60.430 61.111 5.73 0.00 46.04 2.24
813 863 1.174712 GCCCTGCACATGTGTCACTT 61.175 55.000 26.01 0.00 0.00 3.16
815 865 1.898094 TGCCCTGCACATGTGTCAC 60.898 57.895 26.01 11.02 31.71 3.67
816 866 2.514896 TGCCCTGCACATGTGTCA 59.485 55.556 26.01 21.42 31.71 3.58
947 997 0.037975 ACGGCCGTGTTTACACTAGG 60.038 55.000 33.75 6.95 44.34 3.02
948 998 2.634982 TACGGCCGTGTTTACACTAG 57.365 50.000 40.02 1.91 44.34 2.57
949 999 2.295909 ACTTACGGCCGTGTTTACACTA 59.704 45.455 40.02 14.84 44.34 2.74
1026 1080 3.435525 ATTACCCCCAGCCCATGCG 62.436 63.158 0.00 0.00 44.33 4.73
1039 1096 5.008118 GGTAGAAGCTCTGCAAATCATTACC 59.992 44.000 0.00 0.00 30.22 2.85
1087 1144 2.350458 CCACCCTGCCATTTTCCGG 61.350 63.158 0.00 0.00 0.00 5.14
1111 1168 2.238898 CCCCCGGTAACAATCTCTTTCT 59.761 50.000 0.00 0.00 0.00 2.52
1114 1171 0.255033 GCCCCCGGTAACAATCTCTT 59.745 55.000 0.00 0.00 0.00 2.85
1115 1172 0.620700 AGCCCCCGGTAACAATCTCT 60.621 55.000 0.00 0.00 0.00 3.10
1144 1202 2.835431 AGGAGATCGGGAGGCGTG 60.835 66.667 0.00 0.00 0.00 5.34
1288 1346 3.916438 TTCAGGCGGGGTGGAGCTA 62.916 63.158 0.00 0.00 0.00 3.32
1358 1416 0.679002 CTAACCTGGTCGACGGAGGA 60.679 60.000 29.52 13.70 0.00 3.71
1383 1441 2.959707 GCGAGAAAGAGGAGGAATAGGA 59.040 50.000 0.00 0.00 0.00 2.94
1384 1442 2.036604 GGCGAGAAAGAGGAGGAATAGG 59.963 54.545 0.00 0.00 0.00 2.57
1385 1443 2.036604 GGGCGAGAAAGAGGAGGAATAG 59.963 54.545 0.00 0.00 0.00 1.73
1386 1444 2.040178 GGGCGAGAAAGAGGAGGAATA 58.960 52.381 0.00 0.00 0.00 1.75
1387 1445 0.833949 GGGCGAGAAAGAGGAGGAAT 59.166 55.000 0.00 0.00 0.00 3.01
1388 1446 1.265454 GGGGCGAGAAAGAGGAGGAA 61.265 60.000 0.00 0.00 0.00 3.36
1397 1455 4.760047 GCTCAGCGGGGCGAGAAA 62.760 66.667 0.00 0.00 33.54 2.52
1445 1503 1.424493 GCAGATCCAACTTCGGCTCG 61.424 60.000 0.00 0.00 32.49 5.03
1494 1552 0.321034 TCTGCTGTGAGCTGCGAAAT 60.321 50.000 0.00 0.00 42.97 2.17
1550 1608 1.630878 AGCAGTAAAGGGAGGGAACAG 59.369 52.381 0.00 0.00 0.00 3.16
1555 1613 0.253327 GGACAGCAGTAAAGGGAGGG 59.747 60.000 0.00 0.00 0.00 4.30
1562 1620 3.403038 GCAAGAAGAGGACAGCAGTAAA 58.597 45.455 0.00 0.00 0.00 2.01
1565 1623 0.320247 CGCAAGAAGAGGACAGCAGT 60.320 55.000 0.00 0.00 43.02 4.40
1566 1624 2.453843 CGCAAGAAGAGGACAGCAG 58.546 57.895 0.00 0.00 43.02 4.24
1705 1765 5.859495 AGAAGAACAAGAAGTAAGTCTGGG 58.141 41.667 0.00 0.00 0.00 4.45
1707 1767 5.929415 GGGAGAAGAACAAGAAGTAAGTCTG 59.071 44.000 0.00 0.00 0.00 3.51
1710 1770 6.502074 AAGGGAGAAGAACAAGAAGTAAGT 57.498 37.500 0.00 0.00 0.00 2.24
1713 1773 6.270231 AGCTAAAGGGAGAAGAACAAGAAGTA 59.730 38.462 0.00 0.00 0.00 2.24
1718 1778 4.083057 GCAAGCTAAAGGGAGAAGAACAAG 60.083 45.833 0.00 0.00 0.00 3.16
1722 1782 2.644798 AGGCAAGCTAAAGGGAGAAGAA 59.355 45.455 0.00 0.00 0.00 2.52
1739 1799 3.424703 CAAAGAAAGAATCCCAGAGGCA 58.575 45.455 0.00 0.00 0.00 4.75
1771 1831 5.458452 GTGACGTTTTGATTTCAATTGCTCA 59.542 36.000 0.00 0.98 35.55 4.26
1784 1844 1.595794 GGCGAAAGAGTGACGTTTTGA 59.404 47.619 0.00 0.00 0.00 2.69
1805 1865 3.974912 TGCAATGAAGCAAACAAATCGA 58.025 36.364 0.00 0.00 42.46 3.59
1875 1935 1.673033 GCTCTCGCACCTTTAGCTGAA 60.673 52.381 0.00 0.00 35.78 3.02
1876 1936 0.108615 GCTCTCGCACCTTTAGCTGA 60.109 55.000 0.00 0.00 35.78 4.26
1877 1937 0.390340 TGCTCTCGCACCTTTAGCTG 60.390 55.000 0.00 0.00 42.25 4.24
1878 1938 0.108424 CTGCTCTCGCACCTTTAGCT 60.108 55.000 0.00 0.00 42.25 3.32
1879 1939 1.700600 GCTGCTCTCGCACCTTTAGC 61.701 60.000 0.00 0.00 42.25 3.09
1880 1940 0.108424 AGCTGCTCTCGCACCTTTAG 60.108 55.000 0.00 0.00 42.25 1.85
1882 1942 0.321671 TAAGCTGCTCTCGCACCTTT 59.678 50.000 1.00 0.00 38.56 3.11
1922 1982 7.024340 AGCAATGCTTTCACATCTGTATAAG 57.976 36.000 0.00 0.00 33.89 1.73
1959 2019 8.625651 CGAATGTACATTGGGGAAACATTAATA 58.374 33.333 25.42 0.00 40.02 0.98
1977 2037 4.439057 TGAGCCCTGAAATACGAATGTAC 58.561 43.478 0.00 0.00 32.26 2.90
1986 2046 1.681229 AACCCCTGAGCCCTGAAATA 58.319 50.000 0.00 0.00 0.00 1.40
1995 2055 3.323691 ACCAACAAAAATAACCCCTGAGC 59.676 43.478 0.00 0.00 0.00 4.26
1996 2056 6.658188 TTACCAACAAAAATAACCCCTGAG 57.342 37.500 0.00 0.00 0.00 3.35
1997 2057 7.433537 TTTTACCAACAAAAATAACCCCTGA 57.566 32.000 0.00 0.00 0.00 3.86
1998 2058 8.684386 AATTTTACCAACAAAAATAACCCCTG 57.316 30.769 0.00 0.00 35.91 4.45
2000 2060 9.781633 ACTAATTTTACCAACAAAAATAACCCC 57.218 29.630 0.00 0.00 35.91 4.95
2048 2108 4.644103 ACACCTCATGCATTATTTCAGC 57.356 40.909 0.00 0.00 0.00 4.26
2137 2197 2.487762 CTGTTGGGCGACATATTGTTGT 59.512 45.455 0.00 0.00 34.26 3.32
2253 2319 8.243426 ACACAATTAAGCATACTAACCATGTTG 58.757 33.333 0.00 0.00 0.00 3.33
2268 2334 8.638685 ATCAGATTGCATTAACACAATTAAGC 57.361 30.769 6.31 0.00 36.65 3.09
2272 2338 7.550196 GGGAAATCAGATTGCATTAACACAATT 59.450 33.333 3.34 0.00 36.65 2.32
2427 2529 6.344500 ACAAATGCTCCTACATAGAACAGAG 58.656 40.000 0.00 0.00 0.00 3.35
2882 2985 1.405105 TGTTGAGTTGAAAGTGGCAGC 59.595 47.619 0.00 0.00 0.00 5.25
2899 3002 6.886459 ACTGTAACATTATTGAGCTCCATGTT 59.114 34.615 23.30 23.30 40.38 2.71
3160 3263 2.233271 CAACCAGAAGCTGTGACCATT 58.767 47.619 0.00 0.00 0.00 3.16
3452 3555 0.667993 ACACAAAACATCCCGTGCAG 59.332 50.000 0.00 0.00 32.53 4.41
3658 3761 6.978343 ATCGTTGCTGTGCTATTAAAGTTA 57.022 33.333 0.00 0.00 0.00 2.24
3996 4099 4.610945 ACTTGTAAAAATCTGCACTGCAC 58.389 39.130 0.00 0.00 33.79 4.57
4000 4103 6.096846 AGGTGAAACTTGTAAAAATCTGCACT 59.903 34.615 0.00 0.00 36.74 4.40
4112 4215 9.273016 TCTTCAAGGAAAACTTACACTAAGATG 57.727 33.333 0.00 0.00 37.29 2.90
4120 4223 9.403583 ACATAAAGTCTTCAAGGAAAACTTACA 57.596 29.630 0.00 0.00 37.29 2.41
4146 4249 6.869206 AGCTCAACCTACCAGACTAATTAA 57.131 37.500 0.00 0.00 0.00 1.40
4189 4292 4.297510 CATCGGCAGAATCTTAGAGACAG 58.702 47.826 0.00 0.00 0.00 3.51
4277 4380 1.691976 TGACACGTCTGACCATTCCTT 59.308 47.619 1.55 0.00 0.00 3.36
4424 4528 7.222000 GGTCAAACCAATACTTCCACAATTA 57.778 36.000 0.00 0.00 38.42 1.40
4522 4626 3.308595 CGCGTGGAGAATAAACAATAGCA 59.691 43.478 0.00 0.00 0.00 3.49
4576 4680 9.470399 TTCAGTACTACAACCATAGATCTGTTA 57.530 33.333 5.18 0.00 33.12 2.41
4792 4899 5.395195 CGGTAATTGCAATATTGTAACAGCG 59.605 40.000 25.13 25.13 35.65 5.18
4890 4997 0.601558 GTACGACTCACCTTCCTGCA 59.398 55.000 0.00 0.00 0.00 4.41
4915 5022 4.868450 TTGAACTTACAAGAACACACCG 57.132 40.909 0.00 0.00 0.00 4.94
4994 5101 0.625316 AGCCATACCACTGCCATTGA 59.375 50.000 0.00 0.00 0.00 2.57
5040 5147 5.322310 CAGAAAGATTGAGATTGTGAAGCG 58.678 41.667 0.00 0.00 0.00 4.68
5094 5201 9.337396 ACAATGTTTTACATGAGAAGTAGAACA 57.663 29.630 0.00 10.50 44.94 3.18
5121 5228 4.515944 TCATCCAAAATACAACGTTCGGTT 59.484 37.500 0.00 0.00 40.22 4.44
5124 5231 5.524511 TCTCATCCAAAATACAACGTTCG 57.475 39.130 0.00 0.00 0.00 3.95
5189 5296 4.462483 TCAATAAAGTGAGACAAATGGGCC 59.538 41.667 0.00 0.00 0.00 5.80
5216 5324 3.136626 AGAGGGAGTACATGGCATTTACC 59.863 47.826 17.75 10.62 0.00 2.85
5217 5325 4.130118 CAGAGGGAGTACATGGCATTTAC 58.870 47.826 14.47 14.47 0.00 2.01
5218 5326 3.780294 ACAGAGGGAGTACATGGCATTTA 59.220 43.478 0.00 0.00 0.00 1.40
5332 5440 4.074970 CACCTTGCCTGTTCATTTCTAGT 58.925 43.478 0.00 0.00 0.00 2.57
5365 5473 3.318839 TGAAGTTTCCCAGCTTGACATTG 59.681 43.478 0.00 0.00 0.00 2.82
5407 5515 2.662309 AAGGATTGCACCTTGCCTG 58.338 52.632 7.77 0.00 46.85 4.85
5460 5568 2.152016 GCCAACACTCAGACCCTAAAC 58.848 52.381 0.00 0.00 0.00 2.01
5492 5600 7.281774 GCCCAGAGGTAATGACATATATCATTG 59.718 40.741 17.62 2.41 46.44 2.82
5498 5606 4.498493 TGGCCCAGAGGTAATGACATATA 58.502 43.478 0.00 0.00 34.57 0.86
5510 5618 0.681175 CCTTTGTTTTGGCCCAGAGG 59.319 55.000 0.00 0.44 0.00 3.69
5544 5652 7.512297 CAATATCAAAAACAATCAGCCACAAC 58.488 34.615 0.00 0.00 0.00 3.32
5545 5653 6.147492 GCAATATCAAAAACAATCAGCCACAA 59.853 34.615 0.00 0.00 0.00 3.33
5549 5657 4.268405 CGGCAATATCAAAAACAATCAGCC 59.732 41.667 0.00 0.00 0.00 4.85
5563 5671 3.001330 GCTAACATATCCGCGGCAATATC 59.999 47.826 23.51 3.66 0.00 1.63
5591 5699 1.000843 CGGATCAATCCCGTGCTATGA 59.999 52.381 3.45 0.00 44.24 2.15
5592 5700 1.432514 CGGATCAATCCCGTGCTATG 58.567 55.000 3.45 0.00 44.24 2.23
5593 5701 0.321671 CCGGATCAATCCCGTGCTAT 59.678 55.000 0.00 0.00 45.14 2.97
5594 5702 1.046472 ACCGGATCAATCCCGTGCTA 61.046 55.000 9.46 0.00 45.14 3.49
5595 5703 1.910580 AACCGGATCAATCCCGTGCT 61.911 55.000 9.46 0.00 45.14 4.40
5596 5704 1.451387 AACCGGATCAATCCCGTGC 60.451 57.895 9.46 0.00 45.14 5.34
5597 5705 0.392461 ACAACCGGATCAATCCCGTG 60.392 55.000 9.46 2.38 45.14 4.94
5598 5706 0.392461 CACAACCGGATCAATCCCGT 60.392 55.000 9.46 0.62 45.14 5.28
5602 5710 1.062525 GCGCACAACCGGATCAATC 59.937 57.895 9.46 0.00 0.00 2.67
5614 5722 0.179111 CGAAGATAAGGGAGCGCACA 60.179 55.000 11.47 0.00 0.00 4.57
5662 5770 3.751175 CCCGTCAATAAAGTGAAGCTTCA 59.249 43.478 25.16 25.16 36.17 3.02
5714 5825 3.541996 TTCTTCACTTCTGTCAGTGCA 57.458 42.857 0.00 0.00 43.51 4.57
5821 5939 0.790207 CAAGTCATCAACACCCGACG 59.210 55.000 0.00 0.00 33.56 5.12
5849 5968 2.440599 GCCCCCTCTTGCCAAGAA 59.559 61.111 8.74 0.00 37.02 2.52
5942 6063 3.355378 CACATCCAATAAAGGCCAGACA 58.645 45.455 5.01 0.00 0.00 3.41
6056 6179 2.293122 TCAAGAAGGAAACAATGCACCG 59.707 45.455 0.00 0.00 0.00 4.94
6086 6209 6.594744 ACTGCAAAAAGGGATTCTTCAAAAT 58.405 32.000 0.00 0.00 33.94 1.82
6098 6221 1.756538 ACACCTGAACTGCAAAAAGGG 59.243 47.619 8.71 2.20 31.98 3.95
6133 6257 7.391148 AAACTCACAACAACAACACTCTAAT 57.609 32.000 0.00 0.00 0.00 1.73
6318 6482 1.966354 GATCTCCAAATTGGCCATCCC 59.034 52.381 6.09 0.00 37.47 3.85
6348 6512 4.044317 TGGATATCCCACCCTCTACTAGAC 59.956 50.000 19.34 0.00 40.82 2.59
6401 6565 8.169393 TGGCTTTATCCATATCATATTCCACAA 58.831 33.333 0.00 0.00 0.00 3.33
6435 6608 5.200483 TCAAACAGACACAAGGGAAGATTT 58.800 37.500 0.00 0.00 0.00 2.17
6442 6615 1.679139 TGCTCAAACAGACACAAGGG 58.321 50.000 0.00 0.00 0.00 3.95
6443 6616 2.684881 AGTTGCTCAAACAGACACAAGG 59.315 45.455 0.00 0.00 41.61 3.61
6481 6654 9.097257 ACAAATGGTCTAATTTTTGTGAAACTG 57.903 29.630 3.49 0.00 39.94 3.16
6496 6669 9.191479 TCTAGTTTTTCCAAAACAAATGGTCTA 57.809 29.630 13.21 0.00 39.09 2.59
6513 6686 6.489361 TCACTACTCTTCGGACTCTAGTTTTT 59.511 38.462 0.00 0.00 0.00 1.94
6518 6691 5.411977 TGTTTCACTACTCTTCGGACTCTAG 59.588 44.000 0.00 0.00 0.00 2.43
6522 6695 4.931661 TTGTTTCACTACTCTTCGGACT 57.068 40.909 0.00 0.00 0.00 3.85
6523 6696 5.465724 ACAATTGTTTCACTACTCTTCGGAC 59.534 40.000 4.92 0.00 0.00 4.79
6524 6697 5.607477 ACAATTGTTTCACTACTCTTCGGA 58.393 37.500 4.92 0.00 0.00 4.55
6525 6698 5.924475 ACAATTGTTTCACTACTCTTCGG 57.076 39.130 4.92 0.00 0.00 4.30
6526 6699 6.632834 CCAAACAATTGTTTCACTACTCTTCG 59.367 38.462 29.21 15.42 45.54 3.79
6527 6700 6.918022 CCCAAACAATTGTTTCACTACTCTTC 59.082 38.462 29.21 0.00 45.54 2.87
6528 6701 6.379988 ACCCAAACAATTGTTTCACTACTCTT 59.620 34.615 29.21 6.32 45.54 2.85
6531 6704 5.420739 ACACCCAAACAATTGTTTCACTACT 59.579 36.000 29.21 8.44 45.54 2.57
6532 6705 5.518487 CACACCCAAACAATTGTTTCACTAC 59.482 40.000 29.21 0.00 45.54 2.73
6533 6706 5.419155 TCACACCCAAACAATTGTTTCACTA 59.581 36.000 29.21 11.67 45.54 2.74
6534 6707 4.221703 TCACACCCAAACAATTGTTTCACT 59.778 37.500 29.21 13.93 45.54 3.41
6536 6709 4.808414 TCACACCCAAACAATTGTTTCA 57.192 36.364 29.21 8.47 45.54 2.69
6537 6710 6.018832 CAGATTCACACCCAAACAATTGTTTC 60.019 38.462 29.21 16.34 45.54 2.78


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

AutoCloner maintained by Alex Coulton.