Multiple sequence alignment - TraesCS5D01G210400

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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 TraesCS5D01G210400 chr5D 100.000 5900 0 0 955 6854 318880256 318874357 0.000000e+00 10896.0
1 TraesCS5D01G210400 chr5D 100.000 650 0 0 1 650 318881210 318880561 0.000000e+00 1201.0
2 TraesCS5D01G210400 chr5A 95.872 5014 141 27 955 5917 413227807 413222809 0.000000e+00 8052.0
3 TraesCS5D01G210400 chr5A 89.381 452 43 5 6405 6854 549897186 549896738 1.290000e-156 564.0
4 TraesCS5D01G210400 chr5A 84.255 470 45 16 3 460 413228425 413227973 1.370000e-116 431.0
5 TraesCS5D01G210400 chr5A 94.771 153 8 0 6237 6389 549899366 549899214 8.880000e-59 239.0
6 TraesCS5D01G210400 chr5A 88.199 161 13 6 6647 6803 549897064 549896906 3.260000e-43 187.0
7 TraesCS5D01G210400 chr5A 90.625 128 9 2 525 650 413227966 413227840 4.250000e-37 167.0
8 TraesCS5D01G210400 chr5B 95.029 3802 100 27 955 4719 368667404 368663655 0.000000e+00 5891.0
9 TraesCS5D01G210400 chr5B 93.158 1447 47 19 4718 6124 368663573 368662139 0.000000e+00 2076.0
10 TraesCS5D01G210400 chr5B 84.866 674 68 13 3 650 368668102 368667437 0.000000e+00 649.0
11 TraesCS5D01G210400 chr6B 87.916 571 60 7 6292 6854 152707302 152706733 0.000000e+00 664.0
12 TraesCS5D01G210400 chr6B 89.408 321 28 6 6378 6697 3748776 3748461 3.850000e-107 399.0
13 TraesCS5D01G210400 chr6B 88.177 203 19 5 6654 6854 3748617 3748418 3.200000e-58 237.0
14 TraesCS5D01G210400 chr6B 91.176 102 9 0 1781 1882 320551132 320551031 9.270000e-29 139.0
15 TraesCS5D01G210400 chr7A 89.256 484 44 4 6373 6854 450621914 450621437 3.540000e-167 599.0
16 TraesCS5D01G210400 chr7A 96.825 63 2 0 6306 6368 450957936 450957874 9.400000e-19 106.0
17 TraesCS5D01G210400 chr1A 90.433 439 39 3 6417 6854 42191801 42191365 5.960000e-160 575.0
18 TraesCS5D01G210400 chr4A 90.187 428 38 2 6246 6673 688443696 688444119 7.770000e-154 555.0
19 TraesCS5D01G210400 chr2B 90.777 412 29 7 6451 6854 716592683 716592273 6.050000e-150 542.0
20 TraesCS5D01G210400 chr2B 81.838 468 59 17 6236 6697 563043477 563043030 3.020000e-98 370.0
21 TraesCS5D01G210400 chr2A 87.530 417 46 5 6276 6691 113189467 113189056 1.730000e-130 477.0
22 TraesCS5D01G210400 chr2A 94.792 96 4 1 1788 1882 459095818 459095913 1.540000e-31 148.0
23 TraesCS5D01G210400 chr2A 89.815 108 10 1 1789 1895 607842528 607842635 3.330000e-28 137.0
24 TraesCS5D01G210400 chr3B 87.240 337 30 7 6366 6697 772903396 772903724 8.400000e-99 372.0
25 TraesCS5D01G210400 chr3B 87.383 214 20 7 6647 6854 772903555 772903767 8.880000e-59 239.0
26 TraesCS5D01G210400 chr3B 94.737 95 5 0 1793 1887 723456001 723456095 1.540000e-31 148.0
27 TraesCS5D01G210400 chr6D 84.752 282 19 13 4456 4729 445662115 445661850 1.900000e-65 261.0
28 TraesCS5D01G210400 chr6D 85.778 225 21 6 3830 4052 445662669 445662454 1.920000e-55 228.0
29 TraesCS5D01G210400 chr6D 96.825 63 2 0 3632 3694 445662722 445662660 9.400000e-19 106.0
30 TraesCS5D01G210400 chr7D 84.397 282 20 13 4456 4729 531981762 531981497 8.820000e-64 255.0
31 TraesCS5D01G210400 chr7D 84.397 282 20 14 4456 4729 591239283 591239018 8.820000e-64 255.0
32 TraesCS5D01G210400 chr7D 85.778 225 20 7 3830 4052 591239835 591239621 1.920000e-55 228.0
33 TraesCS5D01G210400 chr7D 84.444 225 24 6 3830 4052 531982316 531982101 1.940000e-50 211.0
34 TraesCS5D01G210400 chr7D 90.654 107 8 1 1788 1894 587848129 587848233 2.580000e-29 141.0
35 TraesCS5D01G210400 chr7D 96.875 64 1 1 3632 3694 531982370 531982307 9.400000e-19 106.0
36 TraesCS5D01G210400 chr7D 95.238 63 3 0 3632 3694 591239888 591239826 4.370000e-17 100.0
37 TraesCS5D01G210400 chr1D 84.397 282 20 13 4456 4729 225945104 225944839 8.820000e-64 255.0
38 TraesCS5D01G210400 chr1D 84.043 282 21 13 4456 4729 225961578 225961313 4.100000e-62 250.0
39 TraesCS5D01G210400 chr1D 83.688 282 22 13 4456 4729 225938015 225937750 1.910000e-60 244.0
40 TraesCS5D01G210400 chr1D 85.778 225 21 6 3830 4052 225962131 225961916 1.920000e-55 228.0
41 TraesCS5D01G210400 chr1D 86.667 210 20 4 3834 4042 225945651 225945449 6.920000e-55 226.0
42 TraesCS5D01G210400 chr1D 85.333 225 22 6 3830 4052 225938568 225938353 8.950000e-54 222.0
43 TraesCS5D01G210400 chr1D 90.826 109 6 4 1782 1890 338394467 338394571 7.170000e-30 143.0
44 TraesCS5D01G210400 chr1D 95.238 63 3 0 3632 3694 225938621 225938559 4.370000e-17 100.0
45 TraesCS5D01G210400 chr1D 95.238 63 3 0 3632 3694 225962184 225962122 4.370000e-17 100.0
46 TraesCS5D01G210400 chr1D 93.651 63 4 0 3632 3694 225945709 225945647 2.040000e-15 95.3
47 TraesCS5D01G210400 chr7B 86.735 196 20 2 6661 6854 131479516 131479707 5.380000e-51 213.0
48 TraesCS5D01G210400 chr3A 93.617 94 6 0 1788 1881 221948897 221948990 2.580000e-29 141.0


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 TraesCS5D01G210400 chr5D 318874357 318881210 6853 True 6048.500000 10896 100.000000 1 6854 2 chr5D.!!$R1 6853
1 TraesCS5D01G210400 chr5A 413222809 413228425 5616 True 2883.333333 8052 90.250667 3 5917 3 chr5A.!!$R1 5914
2 TraesCS5D01G210400 chr5A 549896738 549899366 2628 True 330.000000 564 90.783667 6237 6854 3 chr5A.!!$R2 617
3 TraesCS5D01G210400 chr5B 368662139 368668102 5963 True 2872.000000 5891 91.017667 3 6124 3 chr5B.!!$R1 6121
4 TraesCS5D01G210400 chr6B 152706733 152707302 569 True 664.000000 664 87.916000 6292 6854 1 chr6B.!!$R1 562

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
397 409 1.228245 GAGCACTGCCCCAGACAAA 60.228 57.895 0.00 0.0 35.18 2.83 F
1343 1377 2.028020 AGTTCCTCTGGGTCGATTGTTC 60.028 50.000 0.00 0.0 0.00 3.18 F
2498 2559 2.288640 GCAAAAGTTGGAGATGCTGCTT 60.289 45.455 0.00 0.0 34.29 3.91 F
3060 3121 0.674581 CAAAGCATGCCCGTGAGAGA 60.675 55.000 15.66 0.0 0.00 3.10 F
3817 3893 2.927580 CGACACCACTGGGCTACGT 61.928 63.158 0.00 0.0 37.90 3.57 F
3986 4063 3.058224 GCTACACAGTTCACAACCCATTC 60.058 47.826 0.00 0.0 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1444 1478 1.205657 CCGTCATGTAAATCGGACCG 58.794 55.000 7.84 7.84 44.86 4.79 R
2542 2603 0.590732 GATCAATTTGCGCTGCTCCG 60.591 55.000 9.73 0.00 0.00 4.63 R
4189 4266 0.247736 AGAGACACAATGGACGAGCC 59.752 55.000 0.00 0.00 37.10 4.70 R
4573 4651 5.025453 ACCCAACAGGAGCAATTTATTCAT 58.975 37.500 0.00 0.00 39.89 2.57 R
5343 5535 1.003928 AGCTGATGAATCTGGTGCACA 59.996 47.619 20.43 3.92 35.59 4.57 R
5924 6117 1.408702 GCACTTGAGGTTCAAAGCCAA 59.591 47.619 5.20 0.00 35.73 4.52 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
38 39 6.998258 GCATGTTGCATGATAAAGGATTAC 57.002 37.500 12.67 0.00 44.26 1.89
51 52 8.088365 TGATAAAGGATTACCATGTGTAGATCG 58.912 37.037 0.00 0.00 38.94 3.69
55 56 4.038763 GGATTACCATGTGTAGATCGGACA 59.961 45.833 0.00 0.00 35.97 4.02
85 86 7.010923 GTCAGTGGATCAAGCTTGTAAATCTAG 59.989 40.741 25.19 11.04 0.00 2.43
86 87 7.044181 CAGTGGATCAAGCTTGTAAATCTAGA 58.956 38.462 25.19 3.73 0.00 2.43
91 92 8.394121 GGATCAAGCTTGTAAATCTAGAAACTG 58.606 37.037 25.19 0.00 0.00 3.16
106 107 7.147312 TCTAGAAACTGCAACAATTTTGATGG 58.853 34.615 0.00 0.00 32.33 3.51
108 109 6.114767 AGAAACTGCAACAATTTTGATGGTT 58.885 32.000 0.00 0.00 32.33 3.67
119 120 9.612066 AACAATTTTGATGGTTTGAAAGTATGT 57.388 25.926 0.00 0.00 0.00 2.29
120 121 9.260002 ACAATTTTGATGGTTTGAAAGTATGTC 57.740 29.630 0.00 0.00 0.00 3.06
157 158 9.981460 ATTAAAAGTAGTGGGATCAAATCTCTT 57.019 29.630 0.00 0.00 0.00 2.85
160 161 6.168270 AGTAGTGGGATCAAATCTCTTAGC 57.832 41.667 0.00 0.00 0.00 3.09
184 187 8.454106 AGCGATATATGGATTCTTGCATTTTAC 58.546 33.333 0.00 0.00 35.32 2.01
193 197 8.040132 TGGATTCTTGCATTTTACCTTATTTGG 58.960 33.333 0.00 0.00 0.00 3.28
286 292 4.829064 AAAAATGAAAGAGCGTGCTACA 57.171 36.364 0.00 0.00 0.00 2.74
287 293 3.813529 AAATGAAAGAGCGTGCTACAC 57.186 42.857 0.00 0.00 0.00 2.90
303 315 3.310774 GCTACACGTACACGATAGGAGAA 59.689 47.826 9.04 0.00 43.02 2.87
397 409 1.228245 GAGCACTGCCCCAGACAAA 60.228 57.895 0.00 0.00 35.18 2.83
510 543 2.034066 ATCCCGCCCACTGTTGTG 59.966 61.111 0.00 0.00 43.45 3.33
639 673 3.706373 GCCTCCCCGCTGAACTCA 61.706 66.667 0.00 0.00 0.00 3.41
1090 1124 2.480419 CGAAACCACTCTGATGTTGTCC 59.520 50.000 0.00 0.00 0.00 4.02
1316 1350 2.223572 GCACTTGTATGTGGGCAATAGC 60.224 50.000 0.00 0.00 38.31 2.97
1343 1377 2.028020 AGTTCCTCTGGGTCGATTGTTC 60.028 50.000 0.00 0.00 0.00 3.18
1475 1509 3.521947 ACATGACGGTAAGCCTAACTC 57.478 47.619 0.00 0.00 0.00 3.01
1477 1511 3.119101 ACATGACGGTAAGCCTAACTCTG 60.119 47.826 0.00 0.00 0.00 3.35
1478 1512 2.522185 TGACGGTAAGCCTAACTCTGT 58.478 47.619 0.00 0.00 0.00 3.41
1480 1514 3.057033 TGACGGTAAGCCTAACTCTGTTC 60.057 47.826 0.00 0.00 0.00 3.18
1757 1811 8.814038 AACTCAATCTCATTTGCTAGGTAATT 57.186 30.769 0.00 0.00 0.00 1.40
2063 2121 6.240549 AGGAAAGTAATGGTAGATCACAGG 57.759 41.667 0.00 0.00 0.00 4.00
2272 2331 7.624549 AGCAAACCATTCAAGTAGATAGAGAA 58.375 34.615 0.00 0.00 0.00 2.87
2407 2468 7.177568 TGCTTACTAATTCTCAGAGAGTTGAGT 59.822 37.037 16.55 15.95 43.96 3.41
2498 2559 2.288640 GCAAAAGTTGGAGATGCTGCTT 60.289 45.455 0.00 0.00 34.29 3.91
2542 2603 3.883830 ATGACACCAGACAGACATCTC 57.116 47.619 0.00 0.00 0.00 2.75
3036 3097 5.030295 TCTACATACGCTAAAACTGTACGC 58.970 41.667 0.00 0.00 0.00 4.42
3060 3121 0.674581 CAAAGCATGCCCGTGAGAGA 60.675 55.000 15.66 0.00 0.00 3.10
3368 3429 7.491696 GTGATAGTATGTTTTCTGTAGGTCCAC 59.508 40.741 0.00 0.00 0.00 4.02
3773 3835 6.961360 ATGTGAGACATAGAATTCGACCTA 57.039 37.500 0.00 0.00 36.99 3.08
3817 3893 2.927580 CGACACCACTGGGCTACGT 61.928 63.158 0.00 0.00 37.90 3.57
3986 4063 3.058224 GCTACACAGTTCACAACCCATTC 60.058 47.826 0.00 0.00 0.00 2.67
4077 4154 8.460831 AAAGCATTCGATTGTGTAAAAATACC 57.539 30.769 8.93 0.00 0.00 2.73
4125 4202 3.851098 AGACCTACACTTCGATCTTTGC 58.149 45.455 0.00 0.00 0.00 3.68
4189 4266 3.507622 TGGATCTGCTGGATACTATGTCG 59.492 47.826 0.00 0.00 36.27 4.35
4271 4349 6.368779 TTTGACCTAACTTAGCCTGTACAT 57.631 37.500 0.00 0.00 0.00 2.29
4448 4526 3.255888 GTGGATTTTCCCTTGAGGTGTTC 59.744 47.826 0.00 0.00 35.03 3.18
4730 4892 8.894731 TGTTGTTGCTTTATAGTTTGTACTTGA 58.105 29.630 0.00 0.00 35.78 3.02
4732 4894 7.569297 TGTTGCTTTATAGTTTGTACTTGACG 58.431 34.615 0.00 0.00 35.78 4.35
4757 4919 7.328249 CGCATTTTTCTGCTTTGGTTTCTATTA 59.672 33.333 0.00 0.00 40.06 0.98
5079 5241 4.025040 TCTTGTGCCATTTCTCATCAGT 57.975 40.909 0.00 0.00 0.00 3.41
5318 5510 9.113838 TCCTTTTCTCTGAATGTAATTATGCTC 57.886 33.333 0.00 0.00 36.07 4.26
5494 5686 5.738909 TGAAGGAGAGGATTGAATCTGAAC 58.261 41.667 5.03 0.00 0.00 3.18
5577 5769 0.800012 TGAAAATAAGCGCCACGGAC 59.200 50.000 2.29 0.00 0.00 4.79
5587 5779 0.368907 CGCCACGGACAAGTTTATCG 59.631 55.000 0.00 0.00 0.00 2.92
5602 5794 2.672961 TATCGCAAGCTGTAGCACTT 57.327 45.000 6.65 0.00 45.16 3.16
5620 5812 5.067273 GCACTTCTCAGGCTAGAGATAGTA 58.933 45.833 14.54 3.07 43.67 1.82
5634 5826 7.041644 GCTAGAGATAGTACACAGAAGTCGAAT 60.042 40.741 0.00 0.00 0.00 3.34
5776 5968 1.648467 GGGCGCAGAAGGACATTCAC 61.648 60.000 10.83 0.00 40.67 3.18
5798 5990 3.295093 TCCAATTTGAACCACTGCTTCA 58.705 40.909 0.00 0.00 0.00 3.02
5922 6115 1.696063 AGTGTTTGCTTGCACCTCAT 58.304 45.000 0.00 0.00 36.35 2.90
5923 6116 1.338973 AGTGTTTGCTTGCACCTCATG 59.661 47.619 0.00 0.00 36.35 3.07
5924 6117 1.067516 GTGTTTGCTTGCACCTCATGT 59.932 47.619 0.00 0.00 0.00 3.21
5957 6150 1.199789 TCAAGTGCCAATCGAACATGC 59.800 47.619 0.00 0.00 0.00 4.06
5964 6157 2.674954 CCAATCGAACATGCTGCAAAA 58.325 42.857 6.36 0.00 0.00 2.44
5966 6159 3.680937 CCAATCGAACATGCTGCAAAATT 59.319 39.130 6.36 0.78 0.00 1.82
6000 6193 6.363626 CGATGGTTTTATAAGGACATCTCTCG 59.636 42.308 16.48 7.30 34.20 4.04
6012 6205 5.131142 AGGACATCTCTCGGGTAAATCAAAT 59.869 40.000 0.00 0.00 0.00 2.32
6020 6213 1.202405 GGGTAAATCAAATGCCAGCCG 60.202 52.381 0.00 0.00 0.00 5.52
6049 6243 5.293079 GCATTTGCAACCAGTTTTGAAAGTA 59.707 36.000 0.00 0.00 41.59 2.24
6050 6244 6.018016 GCATTTGCAACCAGTTTTGAAAGTAT 60.018 34.615 0.00 0.00 41.59 2.12
6051 6245 7.566709 CATTTGCAACCAGTTTTGAAAGTATC 58.433 34.615 0.00 0.00 0.00 2.24
6052 6246 5.843673 TGCAACCAGTTTTGAAAGTATCA 57.156 34.783 0.00 0.00 35.85 2.15
6053 6247 6.214191 TGCAACCAGTTTTGAAAGTATCAA 57.786 33.333 0.00 0.00 46.22 2.57
6121 6324 2.115911 GGTGTTTGCGTGGTGACCA 61.116 57.895 0.00 0.00 0.00 4.02
6124 6327 0.393132 TGTTTGCGTGGTGACCAAGA 60.393 50.000 21.65 3.81 35.05 3.02
6125 6328 0.307760 GTTTGCGTGGTGACCAAGAG 59.692 55.000 21.65 9.97 35.05 2.85
6126 6329 0.179234 TTTGCGTGGTGACCAAGAGA 59.821 50.000 21.65 5.51 35.05 3.10
6127 6330 0.396435 TTGCGTGGTGACCAAGAGAT 59.604 50.000 21.65 0.00 35.05 2.75
6128 6331 0.396435 TGCGTGGTGACCAAGAGATT 59.604 50.000 21.65 0.00 35.05 2.40
6129 6332 1.202758 TGCGTGGTGACCAAGAGATTT 60.203 47.619 21.65 0.00 35.05 2.17
6130 6333 1.880027 GCGTGGTGACCAAGAGATTTT 59.120 47.619 21.65 0.00 35.05 1.82
6131 6334 2.350772 GCGTGGTGACCAAGAGATTTTG 60.351 50.000 21.65 0.00 35.05 2.44
6132 6335 2.350772 CGTGGTGACCAAGAGATTTTGC 60.351 50.000 12.36 0.00 35.05 3.68
6133 6336 2.887152 GTGGTGACCAAGAGATTTTGCT 59.113 45.455 5.57 0.00 34.18 3.91
6134 6337 3.057946 GTGGTGACCAAGAGATTTTGCTC 60.058 47.826 5.57 0.00 34.18 4.26
6135 6338 2.160417 GGTGACCAAGAGATTTTGCTCG 59.840 50.000 0.00 0.00 39.87 5.03
6136 6339 2.808543 GTGACCAAGAGATTTTGCTCGT 59.191 45.455 0.00 0.00 39.87 4.18
6137 6340 3.067106 TGACCAAGAGATTTTGCTCGTC 58.933 45.455 0.00 0.00 39.87 4.20
6138 6341 3.067106 GACCAAGAGATTTTGCTCGTCA 58.933 45.455 0.00 0.00 39.87 4.35
6139 6342 2.808543 ACCAAGAGATTTTGCTCGTCAC 59.191 45.455 0.00 0.00 39.87 3.67
6140 6343 2.160417 CCAAGAGATTTTGCTCGTCACC 59.840 50.000 0.00 0.00 39.87 4.02
6141 6344 2.100605 AGAGATTTTGCTCGTCACCC 57.899 50.000 0.00 0.00 39.87 4.61
6142 6345 1.087501 GAGATTTTGCTCGTCACCCC 58.912 55.000 0.00 0.00 0.00 4.95
6143 6346 0.400213 AGATTTTGCTCGTCACCCCA 59.600 50.000 0.00 0.00 0.00 4.96
6144 6347 0.804989 GATTTTGCTCGTCACCCCAG 59.195 55.000 0.00 0.00 0.00 4.45
6145 6348 1.244019 ATTTTGCTCGTCACCCCAGC 61.244 55.000 0.00 0.00 0.00 4.85
6146 6349 2.616797 TTTTGCTCGTCACCCCAGCA 62.617 55.000 0.00 0.00 41.45 4.41
6147 6350 3.825160 TTGCTCGTCACCCCAGCAC 62.825 63.158 0.00 0.00 42.85 4.40
6148 6351 4.314440 GCTCGTCACCCCAGCACA 62.314 66.667 0.00 0.00 33.06 4.57
6149 6352 2.357517 CTCGTCACCCCAGCACAC 60.358 66.667 0.00 0.00 0.00 3.82
6150 6353 3.157949 TCGTCACCCCAGCACACA 61.158 61.111 0.00 0.00 0.00 3.72
6151 6354 2.972505 CGTCACCCCAGCACACAC 60.973 66.667 0.00 0.00 0.00 3.82
6152 6355 2.594592 GTCACCCCAGCACACACC 60.595 66.667 0.00 0.00 0.00 4.16
6153 6356 3.884774 TCACCCCAGCACACACCC 61.885 66.667 0.00 0.00 0.00 4.61
6154 6357 3.889692 CACCCCAGCACACACCCT 61.890 66.667 0.00 0.00 0.00 4.34
6155 6358 3.570212 ACCCCAGCACACACCCTC 61.570 66.667 0.00 0.00 0.00 4.30
6156 6359 4.351054 CCCCAGCACACACCCTCC 62.351 72.222 0.00 0.00 0.00 4.30
6157 6360 3.252284 CCCAGCACACACCCTCCT 61.252 66.667 0.00 0.00 0.00 3.69
6158 6361 2.348998 CCAGCACACACCCTCCTC 59.651 66.667 0.00 0.00 0.00 3.71
6159 6362 2.348998 CAGCACACACCCTCCTCC 59.651 66.667 0.00 0.00 0.00 4.30
6160 6363 3.314331 AGCACACACCCTCCTCCG 61.314 66.667 0.00 0.00 0.00 4.63
6161 6364 3.626924 GCACACACCCTCCTCCGT 61.627 66.667 0.00 0.00 0.00 4.69
6162 6365 2.343758 CACACACCCTCCTCCGTG 59.656 66.667 0.00 0.00 36.04 4.94
6163 6366 3.626924 ACACACCCTCCTCCGTGC 61.627 66.667 0.00 0.00 33.09 5.34
6164 6367 3.314331 CACACCCTCCTCCGTGCT 61.314 66.667 0.00 0.00 33.09 4.40
6165 6368 3.314331 ACACCCTCCTCCGTGCTG 61.314 66.667 0.00 0.00 33.09 4.41
6166 6369 4.087892 CACCCTCCTCCGTGCTGG 62.088 72.222 0.00 0.00 40.09 4.85
6184 6387 4.796495 GCCGGCCGACATTTCCCT 62.796 66.667 30.73 0.00 0.00 4.20
6185 6388 2.045340 CCGGCCGACATTTCCCTT 60.045 61.111 30.73 0.00 0.00 3.95
6186 6389 1.677633 CCGGCCGACATTTCCCTTT 60.678 57.895 30.73 0.00 0.00 3.11
6187 6390 1.248101 CCGGCCGACATTTCCCTTTT 61.248 55.000 30.73 0.00 0.00 2.27
6188 6391 0.601057 CGGCCGACATTTCCCTTTTT 59.399 50.000 24.07 0.00 0.00 1.94
6206 6409 2.588027 TTTTTCCTGTTTTCACGCCC 57.412 45.000 0.00 0.00 0.00 6.13
6207 6410 1.475403 TTTTCCTGTTTTCACGCCCA 58.525 45.000 0.00 0.00 0.00 5.36
6208 6411 1.475403 TTTCCTGTTTTCACGCCCAA 58.525 45.000 0.00 0.00 0.00 4.12
6209 6412 1.475403 TTCCTGTTTTCACGCCCAAA 58.525 45.000 0.00 0.00 0.00 3.28
6210 6413 1.475403 TCCTGTTTTCACGCCCAAAA 58.525 45.000 0.00 0.00 0.00 2.44
6211 6414 1.825474 TCCTGTTTTCACGCCCAAAAA 59.175 42.857 0.00 0.00 0.00 1.94
6212 6415 2.432510 TCCTGTTTTCACGCCCAAAAAT 59.567 40.909 0.00 0.00 0.00 1.82
6213 6416 2.799978 CCTGTTTTCACGCCCAAAAATC 59.200 45.455 0.00 0.00 0.00 2.17
6214 6417 3.492482 CCTGTTTTCACGCCCAAAAATCT 60.492 43.478 0.00 0.00 0.00 2.40
6215 6418 4.261825 CCTGTTTTCACGCCCAAAAATCTA 60.262 41.667 0.00 0.00 0.00 1.98
6216 6419 4.612943 TGTTTTCACGCCCAAAAATCTAC 58.387 39.130 0.00 0.00 0.00 2.59
6217 6420 3.546002 TTTCACGCCCAAAAATCTACG 57.454 42.857 0.00 0.00 0.00 3.51
6218 6421 0.800012 TCACGCCCAAAAATCTACGC 59.200 50.000 0.00 0.00 0.00 4.42
6219 6422 0.520412 CACGCCCAAAAATCTACGCG 60.520 55.000 3.53 3.53 44.78 6.01
6220 6423 1.582680 CGCCCAAAAATCTACGCGC 60.583 57.895 5.73 0.00 32.57 6.86
6221 6424 1.226575 GCCCAAAAATCTACGCGCC 60.227 57.895 5.73 0.00 0.00 6.53
6222 6425 1.654023 GCCCAAAAATCTACGCGCCT 61.654 55.000 5.73 0.00 0.00 5.52
6223 6426 0.098728 CCCAAAAATCTACGCGCCTG 59.901 55.000 5.73 0.00 0.00 4.85
6224 6427 0.098728 CCAAAAATCTACGCGCCTGG 59.901 55.000 5.73 0.00 0.00 4.45
6225 6428 0.802494 CAAAAATCTACGCGCCTGGT 59.198 50.000 5.73 0.00 0.00 4.00
6226 6429 1.199097 CAAAAATCTACGCGCCTGGTT 59.801 47.619 5.73 0.00 0.00 3.67
6227 6430 1.530323 AAAATCTACGCGCCTGGTTT 58.470 45.000 5.73 2.13 0.00 3.27
6228 6431 0.802494 AAATCTACGCGCCTGGTTTG 59.198 50.000 5.73 0.00 0.00 2.93
6229 6432 1.024579 AATCTACGCGCCTGGTTTGG 61.025 55.000 5.73 0.00 0.00 3.28
6230 6433 2.869503 ATCTACGCGCCTGGTTTGGG 62.870 60.000 5.73 0.00 0.00 4.12
6235 6438 3.683937 CGCCTGGTTTGGGCCTTG 61.684 66.667 4.53 0.00 46.24 3.61
6241 6444 2.997315 GTTTGGGCCTTGGGGAGC 60.997 66.667 4.53 0.00 33.58 4.70
6371 6580 2.992089 GTGGCATCACAGGGTATCG 58.008 57.895 0.00 0.00 43.13 2.92
6373 6582 0.752658 TGGCATCACAGGGTATCGAG 59.247 55.000 0.00 0.00 0.00 4.04
6376 6585 0.752658 CATCACAGGGTATCGAGCCA 59.247 55.000 10.44 0.00 46.47 4.75
6403 6620 0.449388 CTTCCGAAGATGCAAGGTGC 59.551 55.000 1.51 0.00 45.29 5.01
6409 6626 2.483877 CGAAGATGCAAGGTGCTACAAA 59.516 45.455 0.00 0.00 45.31 2.83
6417 6634 2.175878 AGGTGCTACAAACAGCTGAG 57.824 50.000 23.35 12.22 43.82 3.35
6432 8653 2.479566 CTGAGCTAGCAACCTTTCCA 57.520 50.000 18.83 0.81 0.00 3.53
6436 8657 3.202097 GAGCTAGCAACCTTTCCAGATC 58.798 50.000 18.83 0.00 0.00 2.75
6479 8700 0.519961 AACAAAACCCGAGCGCATAC 59.480 50.000 11.47 0.00 0.00 2.39
6498 8719 7.268447 GCGCATACTTGAAATATTTCCGTAATC 59.732 37.037 22.42 16.42 36.36 1.75
6505 8726 5.234757 TGAAATATTTCCGTAATCCCGAACG 59.765 40.000 22.42 0.00 36.36 3.95
6532 8753 2.892373 TTCTTAGGCAACGCAAATCG 57.108 45.000 0.00 0.00 46.39 3.34
6583 8805 6.496571 TCGTGAACAATTATTTTGAAACGGT 58.503 32.000 0.00 0.00 0.00 4.83
6741 8963 3.878160 ACAAAGTTTGGAAAAGCGGAA 57.122 38.095 19.45 0.00 34.12 4.30
6742 8964 4.400529 ACAAAGTTTGGAAAAGCGGAAT 57.599 36.364 19.45 0.00 34.12 3.01
6747 8969 5.733226 AGTTTGGAAAAGCGGAATTTTTG 57.267 34.783 0.00 0.00 32.62 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.234782 TCCGATCTACACATGGTAATCCTTTAT 59.765 37.037 0.00 0.00 34.23 1.40
30 31 4.899457 TCCGATCTACACATGGTAATCCTT 59.101 41.667 0.00 0.00 34.23 3.36
37 38 2.735151 TCTGTCCGATCTACACATGGT 58.265 47.619 0.00 0.00 0.00 3.55
38 39 3.068732 ACATCTGTCCGATCTACACATGG 59.931 47.826 13.81 0.00 30.28 3.66
51 52 3.529533 CTTGATCCACTGACATCTGTCC 58.470 50.000 7.81 0.00 44.15 4.02
55 56 3.008813 ACAAGCTTGATCCACTGACATCT 59.991 43.478 32.50 1.82 0.00 2.90
85 86 5.989551 ACCATCAAAATTGTTGCAGTTTC 57.010 34.783 0.00 0.00 0.00 2.78
86 87 6.373774 TCAAACCATCAAAATTGTTGCAGTTT 59.626 30.769 0.00 3.51 30.01 2.66
91 92 6.784176 ACTTTCAAACCATCAAAATTGTTGC 58.216 32.000 0.00 0.00 0.00 4.17
119 120 9.667107 CCCACTACTTTTAATTATCTCAACAGA 57.333 33.333 0.00 0.00 0.00 3.41
120 121 9.667107 TCCCACTACTTTTAATTATCTCAACAG 57.333 33.333 0.00 0.00 0.00 3.16
151 152 7.925483 GCAAGAATCCATATATCGCTAAGAGAT 59.075 37.037 0.00 0.00 34.74 2.75
152 153 7.093771 TGCAAGAATCCATATATCGCTAAGAGA 60.094 37.037 0.00 0.00 0.00 3.10
153 154 7.038048 TGCAAGAATCCATATATCGCTAAGAG 58.962 38.462 0.00 0.00 0.00 2.85
154 155 6.935167 TGCAAGAATCCATATATCGCTAAGA 58.065 36.000 0.00 0.00 0.00 2.10
155 156 7.783090 ATGCAAGAATCCATATATCGCTAAG 57.217 36.000 0.00 0.00 0.00 2.18
157 158 8.565896 AAAATGCAAGAATCCATATATCGCTA 57.434 30.769 0.00 0.00 0.00 4.26
158 159 7.458409 AAAATGCAAGAATCCATATATCGCT 57.542 32.000 0.00 0.00 0.00 4.93
159 160 7.698130 GGTAAAATGCAAGAATCCATATATCGC 59.302 37.037 0.00 0.00 0.00 4.58
160 161 8.950210 AGGTAAAATGCAAGAATCCATATATCG 58.050 33.333 0.00 0.00 0.00 2.92
184 187 9.594478 GGTAAAATACAATTGTCCCAAATAAGG 57.406 33.333 15.85 0.00 0.00 2.69
280 286 2.610833 CTCCTATCGTGTACGTGTAGCA 59.389 50.000 0.00 0.00 40.80 3.49
281 287 2.868583 TCTCCTATCGTGTACGTGTAGC 59.131 50.000 0.00 0.00 40.80 3.58
282 288 4.330894 TGTTCTCCTATCGTGTACGTGTAG 59.669 45.833 0.00 8.07 40.80 2.74
284 290 3.076621 TGTTCTCCTATCGTGTACGTGT 58.923 45.455 0.00 0.00 40.80 4.49
285 291 3.752412 TGTTCTCCTATCGTGTACGTG 57.248 47.619 0.00 0.00 40.80 4.49
286 292 3.488721 GCATGTTCTCCTATCGTGTACGT 60.489 47.826 4.20 0.00 40.80 3.57
287 293 3.043586 GCATGTTCTCCTATCGTGTACG 58.956 50.000 0.00 0.00 41.45 3.67
288 294 4.041740 TGCATGTTCTCCTATCGTGTAC 57.958 45.455 0.00 0.00 0.00 2.90
361 373 3.532155 GCCTCGTCCTGAGCGGAT 61.532 66.667 0.00 0.00 45.44 4.18
367 379 3.749064 GTGCTCGCCTCGTCCTGA 61.749 66.667 0.00 0.00 0.00 3.86
429 446 4.473520 CGGCGAGGGTGAATGGCT 62.474 66.667 0.00 0.00 0.00 4.75
493 526 2.034066 CACAACAGTGGGCGGGAT 59.966 61.111 0.00 0.00 0.00 3.85
1316 1350 5.793030 ATCGACCCAGAGGAACTATAAAG 57.207 43.478 0.00 0.00 41.55 1.85
1444 1478 1.205657 CCGTCATGTAAATCGGACCG 58.794 55.000 7.84 7.84 44.86 4.79
1503 1544 5.923733 AACCACATGAACAAAACCAAGTA 57.076 34.783 0.00 0.00 0.00 2.24
1504 1545 4.817318 AACCACATGAACAAAACCAAGT 57.183 36.364 0.00 0.00 0.00 3.16
1623 1664 6.827251 ACATTCACTCACTTGCATCTATGAAT 59.173 34.615 0.00 0.00 36.28 2.57
1778 1832 5.681639 AGGTAGTACTGAATAAACCATGCC 58.318 41.667 5.39 0.00 0.00 4.40
1782 1836 8.654485 TTACAGAGGTAGTACTGAATAAACCA 57.346 34.615 5.39 0.00 37.54 3.67
1783 1837 9.363763 GTTTACAGAGGTAGTACTGAATAAACC 57.636 37.037 5.39 3.72 33.96 3.27
2063 2121 2.894765 GCTATACTGTTCCTCCTCTCCC 59.105 54.545 0.00 0.00 0.00 4.30
2272 2331 4.380531 CATAATAGGCACGGATCACAAGT 58.619 43.478 0.00 0.00 0.00 3.16
2407 2468 2.936919 AGGAAGCACAGACATGAACA 57.063 45.000 0.00 0.00 0.00 3.18
2498 2559 1.832998 GTAATCCCCGGTGTAGACCAA 59.167 52.381 10.08 0.00 43.33 3.67
2542 2603 0.590732 GATCAATTTGCGCTGCTCCG 60.591 55.000 9.73 0.00 0.00 4.63
2919 2980 7.995289 TGTTAATGCCTGATTGTAATGGTAAG 58.005 34.615 0.00 0.00 0.00 2.34
2920 2981 7.613801 ACTGTTAATGCCTGATTGTAATGGTAA 59.386 33.333 0.00 0.00 0.00 2.85
3036 3097 2.034879 ACGGGCATGCTTTGAGTCG 61.035 57.895 18.92 12.02 0.00 4.18
3060 3121 5.416271 TCCATACCGCTTTTAAGAACTCT 57.584 39.130 0.00 0.00 0.00 3.24
3244 3305 5.844004 ACTGTAAGAACTCGACAACAGATT 58.156 37.500 7.24 0.00 38.14 2.40
3282 3343 7.617041 AACTTCTCAATATAGCCAAGTCAAC 57.383 36.000 0.00 0.00 0.00 3.18
3332 3393 8.700051 AGAAAACATACTATCACTGAGTAGCAT 58.300 33.333 0.00 0.00 33.03 3.79
3368 3429 3.490348 ACCTCCTCCAGAAACACATTTG 58.510 45.455 0.00 0.00 0.00 2.32
3792 3854 4.320456 CAGTGGTGTCGCCCTGCT 62.320 66.667 0.00 0.00 36.04 4.24
3986 4063 4.387862 AGAACGTTACCATGCTTAAAGTCG 59.612 41.667 0.00 0.00 0.00 4.18
4055 4132 7.804614 TTGGTATTTTTACACAATCGAATGC 57.195 32.000 0.00 0.00 0.00 3.56
4075 4152 5.869649 AAAGGCTGAACTAAACATTTGGT 57.130 34.783 0.00 0.00 32.98 3.67
4077 4154 9.528018 TCTTTTAAAGGCTGAACTAAACATTTG 57.472 29.630 4.77 0.00 0.00 2.32
4189 4266 0.247736 AGAGACACAATGGACGAGCC 59.752 55.000 0.00 0.00 37.10 4.70
4571 4649 5.127519 CCCAACAGGAGCAATTTATTCATCA 59.872 40.000 0.00 0.00 38.24 3.07
4572 4650 5.127682 ACCCAACAGGAGCAATTTATTCATC 59.872 40.000 0.00 0.00 39.89 2.92
4573 4651 5.025453 ACCCAACAGGAGCAATTTATTCAT 58.975 37.500 0.00 0.00 39.89 2.57
4732 4894 7.425577 AATAGAAACCAAAGCAGAAAAATGC 57.574 32.000 0.00 0.00 46.88 3.56
4768 4930 9.331282 CCTACTTATTTCAGTAAAAGATGAGGG 57.669 37.037 0.00 0.00 0.00 4.30
4851 5013 7.974675 ACACAATATCTGGATGAAAGTAAACG 58.025 34.615 0.00 0.00 0.00 3.60
5029 5191 9.487790 TTGAAAATTATCAACCAAAGGTCAATC 57.512 29.630 0.00 0.00 33.12 2.67
5079 5241 5.939764 AGCACTAAATGGACTAGTGATGA 57.060 39.130 12.90 0.00 46.12 2.92
5168 5359 6.752351 TGTCGAGCTAATCTGTCAAATAGTTC 59.248 38.462 0.00 0.00 0.00 3.01
5343 5535 1.003928 AGCTGATGAATCTGGTGCACA 59.996 47.619 20.43 3.92 35.59 4.57
5577 5769 3.125146 TGCTACAGCTTGCGATAAACTTG 59.875 43.478 2.44 0.00 42.66 3.16
5587 5779 1.731160 CTGAGAAGTGCTACAGCTTGC 59.269 52.381 2.44 0.00 42.66 4.01
5602 5794 5.367060 TCTGTGTACTATCTCTAGCCTGAGA 59.633 44.000 8.43 8.43 45.71 3.27
5620 5812 5.178252 CACAAATCAGATTCGACTTCTGTGT 59.822 40.000 19.01 14.73 41.13 3.72
5776 5968 3.318839 TGAAGCAGTGGTTCAAATTGGAG 59.681 43.478 30.21 0.00 45.12 3.86
5922 6115 2.426738 CACTTGAGGTTCAAAGCCAACA 59.573 45.455 0.00 0.00 35.73 3.33
5923 6116 2.799562 GCACTTGAGGTTCAAAGCCAAC 60.800 50.000 5.20 0.00 35.73 3.77
5924 6117 1.408702 GCACTTGAGGTTCAAAGCCAA 59.591 47.619 5.20 0.00 35.73 4.52
5957 6150 5.920273 ACCATCGAACTGTTAAATTTTGCAG 59.080 36.000 15.65 15.65 35.31 4.41
5966 6159 8.938906 GTCCTTATAAAACCATCGAACTGTTAA 58.061 33.333 0.00 0.00 0.00 2.01
5990 6183 5.277538 GCATTTGATTTACCCGAGAGATGTC 60.278 44.000 0.00 0.00 0.00 3.06
6000 6193 1.202405 CGGCTGGCATTTGATTTACCC 60.202 52.381 1.08 0.00 0.00 3.69
6121 6324 2.427506 GGGTGACGAGCAAAATCTCTT 58.572 47.619 0.00 0.00 0.00 2.85
6124 6327 0.400213 TGGGGTGACGAGCAAAATCT 59.600 50.000 0.00 0.00 0.00 2.40
6125 6328 0.804989 CTGGGGTGACGAGCAAAATC 59.195 55.000 0.00 0.00 0.00 2.17
6126 6329 2.946947 CTGGGGTGACGAGCAAAAT 58.053 52.632 0.00 0.00 0.00 1.82
6127 6330 4.473643 CTGGGGTGACGAGCAAAA 57.526 55.556 0.00 0.00 0.00 2.44
6132 6335 2.357517 GTGTGCTGGGGTGACGAG 60.358 66.667 0.00 0.00 0.00 4.18
6133 6336 3.157949 TGTGTGCTGGGGTGACGA 61.158 61.111 0.00 0.00 0.00 4.20
6134 6337 2.972505 GTGTGTGCTGGGGTGACG 60.973 66.667 0.00 0.00 0.00 4.35
6135 6338 2.594592 GGTGTGTGCTGGGGTGAC 60.595 66.667 0.00 0.00 0.00 3.67
6136 6339 3.884774 GGGTGTGTGCTGGGGTGA 61.885 66.667 0.00 0.00 0.00 4.02
6137 6340 3.850098 GAGGGTGTGTGCTGGGGTG 62.850 68.421 0.00 0.00 0.00 4.61
6138 6341 3.570212 GAGGGTGTGTGCTGGGGT 61.570 66.667 0.00 0.00 0.00 4.95
6139 6342 4.351054 GGAGGGTGTGTGCTGGGG 62.351 72.222 0.00 0.00 0.00 4.96
6140 6343 3.252284 AGGAGGGTGTGTGCTGGG 61.252 66.667 0.00 0.00 0.00 4.45
6141 6344 2.348998 GAGGAGGGTGTGTGCTGG 59.651 66.667 0.00 0.00 0.00 4.85
6142 6345 2.348998 GGAGGAGGGTGTGTGCTG 59.651 66.667 0.00 0.00 0.00 4.41
6143 6346 3.314331 CGGAGGAGGGTGTGTGCT 61.314 66.667 0.00 0.00 0.00 4.40
6144 6347 3.626924 ACGGAGGAGGGTGTGTGC 61.627 66.667 0.00 0.00 0.00 4.57
6145 6348 2.343758 CACGGAGGAGGGTGTGTG 59.656 66.667 0.00 0.00 0.00 3.82
6146 6349 3.626924 GCACGGAGGAGGGTGTGT 61.627 66.667 0.00 0.00 36.54 3.72
6147 6350 3.314331 AGCACGGAGGAGGGTGTG 61.314 66.667 0.00 0.00 36.54 3.82
6148 6351 3.314331 CAGCACGGAGGAGGGTGT 61.314 66.667 0.00 0.00 36.54 4.16
6149 6352 4.087892 CCAGCACGGAGGAGGGTG 62.088 72.222 0.00 0.00 36.56 4.61
6167 6370 4.796495 AGGGAAATGTCGGCCGGC 62.796 66.667 26.05 26.05 0.00 6.13
6168 6371 1.248101 AAAAGGGAAATGTCGGCCGG 61.248 55.000 27.83 6.80 0.00 6.13
6169 6372 0.601057 AAAAAGGGAAATGTCGGCCG 59.399 50.000 22.12 22.12 0.00 6.13
6187 6390 1.825474 TGGGCGTGAAAACAGGAAAAA 59.175 42.857 0.00 0.00 0.00 1.94
6188 6391 1.475403 TGGGCGTGAAAACAGGAAAA 58.525 45.000 0.00 0.00 0.00 2.29
6189 6392 1.475403 TTGGGCGTGAAAACAGGAAA 58.525 45.000 0.00 0.00 0.00 3.13
6190 6393 1.475403 TTTGGGCGTGAAAACAGGAA 58.525 45.000 0.00 0.00 0.00 3.36
6191 6394 1.475403 TTTTGGGCGTGAAAACAGGA 58.525 45.000 0.00 0.00 0.00 3.86
6192 6395 2.301577 TTTTTGGGCGTGAAAACAGG 57.698 45.000 0.00 0.00 0.00 4.00
6193 6396 3.716601 AGATTTTTGGGCGTGAAAACAG 58.283 40.909 0.00 0.00 0.00 3.16
6194 6397 3.810310 AGATTTTTGGGCGTGAAAACA 57.190 38.095 0.00 0.00 0.00 2.83
6195 6398 3.666797 CGTAGATTTTTGGGCGTGAAAAC 59.333 43.478 0.00 0.00 0.00 2.43
6196 6399 3.854045 GCGTAGATTTTTGGGCGTGAAAA 60.854 43.478 0.00 0.00 0.00 2.29
6197 6400 2.350964 GCGTAGATTTTTGGGCGTGAAA 60.351 45.455 0.00 0.00 0.00 2.69
6198 6401 1.198178 GCGTAGATTTTTGGGCGTGAA 59.802 47.619 0.00 0.00 0.00 3.18
6199 6402 0.800012 GCGTAGATTTTTGGGCGTGA 59.200 50.000 0.00 0.00 0.00 4.35
6200 6403 0.520412 CGCGTAGATTTTTGGGCGTG 60.520 55.000 0.00 0.00 38.90 5.34
6201 6404 1.791662 CGCGTAGATTTTTGGGCGT 59.208 52.632 0.00 0.00 38.90 5.68
6202 6405 1.582680 GCGCGTAGATTTTTGGGCG 60.583 57.895 8.43 0.00 45.72 6.13
6203 6406 1.226575 GGCGCGTAGATTTTTGGGC 60.227 57.895 8.43 0.00 39.30 5.36
6204 6407 0.098728 CAGGCGCGTAGATTTTTGGG 59.901 55.000 8.43 0.00 0.00 4.12
6205 6408 0.098728 CCAGGCGCGTAGATTTTTGG 59.901 55.000 8.43 0.58 0.00 3.28
6206 6409 0.802494 ACCAGGCGCGTAGATTTTTG 59.198 50.000 8.43 0.00 0.00 2.44
6207 6410 1.530323 AACCAGGCGCGTAGATTTTT 58.470 45.000 8.43 0.00 0.00 1.94
6208 6411 1.199097 CAAACCAGGCGCGTAGATTTT 59.801 47.619 8.43 0.00 0.00 1.82
6209 6412 0.802494 CAAACCAGGCGCGTAGATTT 59.198 50.000 8.43 0.85 0.00 2.17
6210 6413 1.024579 CCAAACCAGGCGCGTAGATT 61.025 55.000 8.43 0.00 0.00 2.40
6211 6414 1.449601 CCAAACCAGGCGCGTAGAT 60.450 57.895 8.43 0.00 0.00 1.98
6212 6415 2.047655 CCAAACCAGGCGCGTAGA 60.048 61.111 8.43 0.00 0.00 2.59
6213 6416 3.124921 CCCAAACCAGGCGCGTAG 61.125 66.667 8.43 0.00 0.00 3.51
6220 6423 2.604382 CCCAAGGCCCAAACCAGG 60.604 66.667 0.00 0.00 0.00 4.45
6221 6424 2.604382 CCCCAAGGCCCAAACCAG 60.604 66.667 0.00 0.00 0.00 4.00
6222 6425 3.113477 TCCCCAAGGCCCAAACCA 61.113 61.111 0.00 0.00 0.00 3.67
6223 6426 2.283894 CTCCCCAAGGCCCAAACC 60.284 66.667 0.00 0.00 0.00 3.27
6224 6427 2.997315 GCTCCCCAAGGCCCAAAC 60.997 66.667 0.00 0.00 0.00 2.93
6225 6428 3.192630 AGCTCCCCAAGGCCCAAA 61.193 61.111 0.00 0.00 0.00 3.28
6226 6429 3.661648 GAGCTCCCCAAGGCCCAA 61.662 66.667 0.87 0.00 0.00 4.12
6229 6432 2.366972 TAGGAGCTCCCCAAGGCC 60.367 66.667 29.54 1.86 36.42 5.19
6230 6433 3.113514 GCTAGGAGCTCCCCAAGGC 62.114 68.421 29.54 20.46 38.45 4.35
6231 6434 3.235369 GCTAGGAGCTCCCCAAGG 58.765 66.667 29.54 15.12 38.45 3.61
6371 6580 1.115467 TCGGAAGAGATCCTTGGCTC 58.885 55.000 1.70 0.00 46.98 4.70
6373 6582 1.482593 TCTTCGGAAGAGATCCTTGGC 59.517 52.381 16.19 0.00 46.98 4.52
6376 6585 2.768527 TGCATCTTCGGAAGAGATCCTT 59.231 45.455 23.38 5.17 46.98 3.36
6417 6634 1.936547 CGATCTGGAAAGGTTGCTAGC 59.063 52.381 8.10 8.10 0.00 3.42
6425 8646 4.389077 GTGTTGTCTTACGATCTGGAAAGG 59.611 45.833 0.00 0.00 0.00 3.11
6430 8651 4.084013 GGTTTGTGTTGTCTTACGATCTGG 60.084 45.833 0.00 0.00 0.00 3.86
6432 8653 4.062991 GGGTTTGTGTTGTCTTACGATCT 58.937 43.478 0.00 0.00 0.00 2.75
6436 8657 5.524646 TCTTAAGGGTTTGTGTTGTCTTACG 59.475 40.000 1.85 0.00 0.00 3.18
6479 8700 6.854496 TCGGGATTACGGAAATATTTCAAG 57.146 37.500 25.55 20.66 38.92 3.02
6726 8948 5.478233 ACAAAAATTCCGCTTTTCCAAAC 57.522 34.783 0.00 0.00 0.00 2.93
6741 8963 9.791801 ATATTTTGTTTGGGAGCTTACAAAAAT 57.208 25.926 19.15 15.96 46.92 1.82
6742 8964 9.050601 CATATTTTGTTTGGGAGCTTACAAAAA 57.949 29.630 19.15 12.74 46.92 1.94
6747 8969 7.870445 TGTTTCATATTTTGTTTGGGAGCTTAC 59.130 33.333 0.00 0.00 0.00 2.34
6805 9028 6.762702 TGTTTCCGTCTTTTAGGAGTTTTT 57.237 33.333 0.00 0.00 37.88 1.94
6806 9029 6.544564 TCATGTTTCCGTCTTTTAGGAGTTTT 59.455 34.615 0.00 0.00 37.88 2.43
6819 9042 8.568732 TTTTTAAGAATGTTCATGTTTCCGTC 57.431 30.769 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.