Multiple sequence alignment - TraesCS6D01G274500

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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 TraesCS6D01G274500 chr6D 100.000 4841 0 0 792 5632 382925280 382920440 0.000000e+00 8940.0
1 TraesCS6D01G274500 chr6D 100.000 478 0 0 1 478 382926071 382925594 0.000000e+00 883.0
2 TraesCS6D01G274500 chr6D 92.063 189 11 4 4860 5047 206560438 206560253 4.330000e-66 263.0
3 TraesCS6D01G274500 chr6B 94.475 4145 139 37 792 4861 573328170 573324041 0.000000e+00 6303.0
4 TraesCS6D01G274500 chr6B 91.297 563 31 10 5027 5581 573324014 573323462 0.000000e+00 752.0
5 TraesCS6D01G274500 chr6B 93.174 293 12 6 177 468 573329310 573329025 1.880000e-114 424.0
6 TraesCS6D01G274500 chr6B 81.991 422 45 13 5202 5612 573302994 573302593 4.210000e-86 329.0
7 TraesCS6D01G274500 chr6B 91.579 190 11 4 4860 5047 320413104 320412918 2.010000e-64 257.0
8 TraesCS6D01G274500 chr6B 94.643 168 3 4 301 468 573328480 573328319 7.240000e-64 255.0
9 TraesCS6D01G274500 chr6B 95.513 156 5 2 4700 4853 573313957 573313802 1.210000e-61 248.0
10 TraesCS6D01G274500 chr6B 90.683 161 10 2 2 162 573329451 573329296 5.720000e-50 209.0
11 TraesCS6D01G274500 chr6B 93.617 47 3 0 5102 5148 573301451 573301405 2.820000e-08 71.3
12 TraesCS6D01G274500 chr6A 97.001 2234 64 2 2629 4861 524994497 524992266 0.000000e+00 3751.0
13 TraesCS6D01G274500 chr6A 91.429 1855 93 28 792 2605 524996491 524994662 0.000000e+00 2484.0
14 TraesCS6D01G274500 chr6A 93.684 380 19 3 5027 5401 524992239 524991860 1.060000e-156 564.0
15 TraesCS6D01G274500 chr6A 95.794 214 5 2 236 445 524996870 524996657 5.400000e-90 342.0
16 TraesCS6D01G274500 chr6A 88.034 234 15 6 5402 5632 524991828 524991605 1.200000e-66 265.0
17 TraesCS6D01G274500 chr6A 90.741 162 14 1 1 162 524997063 524996903 1.230000e-51 215.0
18 TraesCS6D01G274500 chr5A 93.989 183 8 3 4860 5040 382566638 382566819 2.000000e-69 274.0
19 TraesCS6D01G274500 chr2B 95.322 171 6 2 4859 5027 174794987 174794817 2.590000e-68 270.0
20 TraesCS6D01G274500 chr4A 95.808 167 6 1 4860 5025 362068075 362067909 9.300000e-68 268.0
21 TraesCS6D01G274500 chr2D 94.318 176 8 2 4851 5025 516708484 516708310 9.300000e-68 268.0
22 TraesCS6D01G274500 chr2A 94.798 173 6 2 4859 5030 746757155 746756985 3.350000e-67 267.0
23 TraesCS6D01G274500 chr1D 93.785 177 9 2 4849 5023 10667835 10667659 1.200000e-66 265.0
24 TraesCS6D01G274500 chr4B 92.391 184 10 4 4858 5039 283349232 283349051 5.600000e-65 259.0


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 TraesCS6D01G274500 chr6D 382920440 382926071 5631 True 4911.500000 8940 100.0000 1 5632 2 chr6D.!!$R2 5631
1 TraesCS6D01G274500 chr6B 573323462 573329451 5989 True 1588.600000 6303 92.8544 2 5581 5 chr6B.!!$R4 5579
2 TraesCS6D01G274500 chr6B 573301405 573302994 1589 True 200.150000 329 87.8040 5102 5612 2 chr6B.!!$R3 510
3 TraesCS6D01G274500 chr6A 524991605 524997063 5458 True 1270.166667 3751 92.7805 1 5632 6 chr6A.!!$R1 5631

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
927 1652 0.716108 GAGACGTTGACATTGGCGAG 59.284 55.0 0.00 0.00 0.00 5.03 F
1555 2345 0.742281 AGTTGCAGCTATCGCACTGG 60.742 55.0 0.00 0.00 39.59 4.00 F
2648 3610 0.676736 TGGTACGTGCATGTCAGTCA 59.323 50.0 16.44 7.11 0.00 3.41 F
3962 4926 0.565674 ACCCCAAAACCCAGGAACAT 59.434 50.0 0.00 0.00 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 2518 1.202557 TGACACCGTAAACCTGTGGTC 60.203 52.381 0.00 0.0 33.12 4.02 R
3364 4328 0.669625 AGTGTCGGGCTTCTTAACGC 60.670 55.000 0.00 0.0 0.00 4.84 R
4388 5352 0.035152 TGGTGTGAGCCTTGGCTATG 60.035 55.000 14.76 0.0 0.00 2.23 R
5174 6144 1.004610 GCAACGGATGATGACGATGTG 60.005 52.381 0.00 0.0 35.66 3.21 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
25 26 5.700722 TCAGCGTCGAATAGGTATTACAT 57.299 39.130 0.00 0.00 0.00 2.29
43 44 4.916041 ACATGTGGGAATTTGAGAGAGA 57.084 40.909 0.00 0.00 0.00 3.10
45 46 3.703001 TGTGGGAATTTGAGAGAGACC 57.297 47.619 0.00 0.00 0.00 3.85
119 120 4.641541 TGACAGCATGGTCAGAAATTATGG 59.358 41.667 0.00 0.00 42.56 2.74
130 131 5.065731 GTCAGAAATTATGGTGAAGAGCCAG 59.934 44.000 0.00 0.00 39.65 4.85
162 163 7.562454 TCATGCCAATCAATTTCCTTCTAATCT 59.438 33.333 0.00 0.00 0.00 2.40
163 164 7.722949 TGCCAATCAATTTCCTTCTAATCTT 57.277 32.000 0.00 0.00 0.00 2.40
164 165 8.137745 TGCCAATCAATTTCCTTCTAATCTTT 57.862 30.769 0.00 0.00 0.00 2.52
165 166 8.596293 TGCCAATCAATTTCCTTCTAATCTTTT 58.404 29.630 0.00 0.00 0.00 2.27
166 167 9.440773 GCCAATCAATTTCCTTCTAATCTTTTT 57.559 29.630 0.00 0.00 0.00 1.94
169 170 8.917415 ATCAATTTCCTTCTAATCTTTTTCGC 57.083 30.769 0.00 0.00 0.00 4.70
170 171 7.881142 TCAATTTCCTTCTAATCTTTTTCGCA 58.119 30.769 0.00 0.00 0.00 5.10
171 172 8.356657 TCAATTTCCTTCTAATCTTTTTCGCAA 58.643 29.630 0.00 0.00 0.00 4.85
172 173 8.977505 CAATTTCCTTCTAATCTTTTTCGCAAA 58.022 29.630 0.00 0.00 0.00 3.68
173 174 9.541143 AATTTCCTTCTAATCTTTTTCGCAAAA 57.459 25.926 0.00 0.00 0.00 2.44
174 175 8.934507 TTTCCTTCTAATCTTTTTCGCAAAAA 57.065 26.923 0.00 0.80 37.99 1.94
198 199 2.191981 TCCCTTCTAATCTCCACCCC 57.808 55.000 0.00 0.00 0.00 4.95
199 200 1.141185 CCCTTCTAATCTCCACCCCC 58.859 60.000 0.00 0.00 0.00 5.40
203 204 2.478872 TCTAATCTCCACCCCCTCTG 57.521 55.000 0.00 0.00 0.00 3.35
210 212 4.083080 TCTCCACCCCCTCTGTTAATAA 57.917 45.455 0.00 0.00 0.00 1.40
233 235 9.914131 ATAAAAATGAGTAAGAGTTTTTGAGGC 57.086 29.630 0.00 0.00 35.87 4.70
427 433 1.388547 GCACCGATTTCCTGGCAATA 58.611 50.000 0.00 0.00 0.00 1.90
810 1534 1.388547 TTCATTAATCCACAGCCCGC 58.611 50.000 0.00 0.00 0.00 6.13
826 1550 3.330853 GCCATCGTCGTCGCCATC 61.331 66.667 0.00 0.00 36.96 3.51
827 1551 2.104132 CCATCGTCGTCGCCATCA 59.896 61.111 0.00 0.00 36.96 3.07
845 1569 1.002857 CATCACCCCTTTCCTTCCCT 58.997 55.000 0.00 0.00 0.00 4.20
909 1634 1.063492 TCTCCCCCTACATTACTGCGA 60.063 52.381 0.00 0.00 0.00 5.10
927 1652 0.716108 GAGACGTTGACATTGGCGAG 59.284 55.000 0.00 0.00 0.00 5.03
1316 2086 1.227497 CTGCCGGAGATCTCTTGGC 60.227 63.158 34.02 34.02 45.04 4.52
1373 2149 1.221840 GGCTCTTGGCGAGATTCCA 59.778 57.895 4.57 0.00 42.62 3.53
1393 2169 2.853914 GAACACTTGGAGCGCGAC 59.146 61.111 12.10 1.97 0.00 5.19
1417 2206 1.927895 CGGCGCTCTCTAGATTGTTT 58.072 50.000 7.64 0.00 0.00 2.83
1429 2218 5.997385 TCTAGATTGTTTTCTTTTCGGCAC 58.003 37.500 0.00 0.00 0.00 5.01
1479 2269 4.274147 TGGCGGGCAAGATTTTAGAAATA 58.726 39.130 0.01 0.00 0.00 1.40
1548 2338 1.156645 CCGCTCCAGTTGCAGCTATC 61.157 60.000 1.52 0.00 33.09 2.08
1555 2345 0.742281 AGTTGCAGCTATCGCACTGG 60.742 55.000 0.00 0.00 39.59 4.00
1562 2352 3.257393 CAGCTATCGCACTGGGATATTC 58.743 50.000 14.41 10.29 36.98 1.75
1612 2402 3.559069 ACTTGGGTGCATCTTGATATGG 58.441 45.455 0.00 0.00 0.00 2.74
1613 2403 3.053395 ACTTGGGTGCATCTTGATATGGT 60.053 43.478 0.00 0.00 0.00 3.55
1614 2404 3.213206 TGGGTGCATCTTGATATGGTC 57.787 47.619 0.00 0.00 0.00 4.02
1695 2485 3.362693 CGCACCAAGTAAGAAGAACGAAC 60.363 47.826 0.00 0.00 0.00 3.95
1725 2515 5.068234 ACAAGTAACGTCTTAGCATGCTA 57.932 39.130 23.52 23.52 0.00 3.49
1753 2547 3.314080 CACAGGTTTACGGTGTCATGTTT 59.686 43.478 0.00 0.00 39.94 2.83
1906 2719 5.359009 GGTTAGGGGTTGCCTAAAAGTATTC 59.641 44.000 0.00 0.00 32.52 1.75
1978 2791 6.037786 TCTCTGGTCTTGTATTTCGTCAAT 57.962 37.500 0.00 0.00 0.00 2.57
2013 2826 6.210078 GTCTCAATACCACACTATGCTACTC 58.790 44.000 0.00 0.00 0.00 2.59
2027 2840 4.746535 TGCTACTCGGGATAACATTGAA 57.253 40.909 0.00 0.00 0.00 2.69
2030 2843 6.119536 TGCTACTCGGGATAACATTGAAAAT 58.880 36.000 0.00 0.00 0.00 1.82
2046 2859 8.071368 ACATTGAAAATTTTGCATGATTGTGTC 58.929 29.630 19.16 0.02 0.00 3.67
2059 2872 1.262417 TTGTGTCTATGCGGTGGAGA 58.738 50.000 0.00 0.00 0.00 3.71
2280 3101 4.478206 TCATCTTTAAGAGGAGGCACAG 57.522 45.455 5.15 0.00 29.09 3.66
2506 3327 9.135843 TCGTAATGTAAAACTGTCATGTCTAAG 57.864 33.333 0.00 0.00 0.00 2.18
2540 3361 8.443160 ACTTTCATACAACACGTGAATATGAAG 58.557 33.333 29.82 26.75 41.09 3.02
2562 3383 8.772250 TGAAGTCTAGTTCATTATCCTTTCCAT 58.228 33.333 0.00 0.00 31.31 3.41
2593 3414 9.891828 GTATTCATATCATATCGACATCCTCTC 57.108 37.037 0.00 0.00 0.00 3.20
2648 3610 0.676736 TGGTACGTGCATGTCAGTCA 59.323 50.000 16.44 7.11 0.00 3.41
2721 3683 1.889170 TCTGTACAGTCTGACCTGCTG 59.111 52.381 21.99 0.00 35.83 4.41
2833 3795 5.940192 ACGACAAGAATATTGCTGTTCAA 57.060 34.783 0.00 0.00 39.32 2.69
3176 4140 4.638421 ACATTGTCGTTGGAAAACTTGAGA 59.362 37.500 0.00 0.00 0.00 3.27
3287 4251 5.481473 TGAGCTAATTGAAGGGCTTGAAAAT 59.519 36.000 0.00 0.00 35.01 1.82
3364 4328 2.843701 AGCAAAAGACTCACCTGACAG 58.156 47.619 0.00 0.00 0.00 3.51
3434 4398 5.239351 CCAATATCTCTTGAGCTGATGAGG 58.761 45.833 14.59 0.57 0.00 3.86
3491 4455 9.874205 AATTTCCACACCATCACTTATTATTTG 57.126 29.630 0.00 0.00 0.00 2.32
3495 4459 7.888021 TCCACACCATCACTTATTATTTGTTCT 59.112 33.333 0.00 0.00 0.00 3.01
3506 4470 5.649782 ATTATTTGTTCTCCCTGCACTTG 57.350 39.130 0.00 0.00 0.00 3.16
3689 4653 8.387813 ACCCCAAACTATGTATTGAGAAGTTTA 58.612 33.333 0.00 0.00 38.08 2.01
3962 4926 0.565674 ACCCCAAAACCCAGGAACAT 59.434 50.000 0.00 0.00 0.00 2.71
4025 4989 2.749621 CAAGGAACTGATAGTGGTTGGC 59.250 50.000 0.00 0.00 40.86 4.52
4085 5049 2.165998 AGCATGGAGGCAAGAGAAAAC 58.834 47.619 0.00 0.00 35.83 2.43
4097 5061 2.121564 GAGAAAACGCAGCTGCAGCA 62.122 55.000 38.24 0.00 45.16 4.41
4148 5112 9.717942 GATAACAAGATAATGATAGGAAGCACT 57.282 33.333 0.00 0.00 0.00 4.40
4160 5124 2.932130 GAAGCACTCCTGGGGCGATC 62.932 65.000 0.00 0.00 0.00 3.69
4388 5352 3.414700 CACGAGTGCAAGACGGCC 61.415 66.667 11.79 0.00 0.00 6.13
4867 5831 9.623000 TTTATGCCTTTTAGTTTATACTCCCTC 57.377 33.333 0.00 0.00 35.78 4.30
4868 5832 5.997843 TGCCTTTTAGTTTATACTCCCTCC 58.002 41.667 0.00 0.00 35.78 4.30
4869 5833 5.055144 GCCTTTTAGTTTATACTCCCTCCG 58.945 45.833 0.00 0.00 35.78 4.63
4871 5835 6.647229 CCTTTTAGTTTATACTCCCTCCGTT 58.353 40.000 0.00 0.00 35.78 4.44
4872 5836 6.760298 CCTTTTAGTTTATACTCCCTCCGTTC 59.240 42.308 0.00 0.00 35.78 3.95
4873 5837 5.859205 TTAGTTTATACTCCCTCCGTTCC 57.141 43.478 0.00 0.00 35.78 3.62
4874 5838 3.991683 AGTTTATACTCCCTCCGTTCCT 58.008 45.455 0.00 0.00 0.00 3.36
4875 5839 5.134725 AGTTTATACTCCCTCCGTTCCTA 57.865 43.478 0.00 0.00 0.00 2.94
4876 5840 5.522641 AGTTTATACTCCCTCCGTTCCTAA 58.477 41.667 0.00 0.00 0.00 2.69
4877 5841 5.960202 AGTTTATACTCCCTCCGTTCCTAAA 59.040 40.000 0.00 0.00 0.00 1.85
4879 5843 7.786464 AGTTTATACTCCCTCCGTTCCTAAATA 59.214 37.037 0.00 0.00 0.00 1.40
4881 5845 8.731591 TTATACTCCCTCCGTTCCTAAATATT 57.268 34.615 0.00 0.00 0.00 1.28
4882 5846 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4883 5847 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4886 5850 4.820173 CCCTCCGTTCCTAAATATTTGTCC 59.180 45.833 11.05 0.00 0.00 4.02
4887 5851 5.397559 CCCTCCGTTCCTAAATATTTGTCCT 60.398 44.000 11.05 0.00 0.00 3.85
4888 5852 6.120220 CCTCCGTTCCTAAATATTTGTCCTT 58.880 40.000 11.05 0.00 0.00 3.36
4889 5853 6.602009 CCTCCGTTCCTAAATATTTGTCCTTT 59.398 38.462 11.05 0.00 0.00 3.11
4890 5854 7.122204 CCTCCGTTCCTAAATATTTGTCCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
4891 5855 9.169592 CTCCGTTCCTAAATATTTGTCCTTTTA 57.830 33.333 11.05 0.00 0.00 1.52
4892 5856 9.169592 TCCGTTCCTAAATATTTGTCCTTTTAG 57.830 33.333 11.05 0.00 33.47 1.85
4893 5857 9.169592 CCGTTCCTAAATATTTGTCCTTTTAGA 57.830 33.333 11.05 0.00 34.90 2.10
4905 5869 9.933723 ATTTGTCCTTTTAGAGATTTCAAATGG 57.066 29.630 0.00 0.00 33.66 3.16
4906 5870 8.704849 TTGTCCTTTTAGAGATTTCAAATGGA 57.295 30.769 0.00 9.53 34.75 3.41
4907 5871 8.340618 TGTCCTTTTAGAGATTTCAAATGGAG 57.659 34.615 11.97 0.00 36.63 3.86
4908 5872 7.944554 TGTCCTTTTAGAGATTTCAAATGGAGT 59.055 33.333 11.97 0.00 36.63 3.85
4909 5873 9.449719 GTCCTTTTAGAGATTTCAAATGGAGTA 57.550 33.333 11.97 0.00 36.63 2.59
4910 5874 9.449719 TCCTTTTAGAGATTTCAAATGGAGTAC 57.550 33.333 0.00 0.00 33.17 2.73
4911 5875 8.678199 CCTTTTAGAGATTTCAAATGGAGTACC 58.322 37.037 0.00 0.00 31.44 3.34
4924 5888 3.900971 TGGAGTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
4925 5889 4.476297 TGGAGTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
4926 5890 5.633117 TGGAGTACCACATACGGATGTATA 58.367 41.667 14.23 6.38 44.82 1.47
4927 5891 6.250711 TGGAGTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
4928 5892 7.404481 TGGAGTACCACATACGGATGTATATA 58.596 38.462 14.23 3.33 44.82 0.86
4929 5893 7.555195 TGGAGTACCACATACGGATGTATATAG 59.445 40.741 14.23 0.00 44.82 1.31
4930 5894 7.772292 GGAGTACCACATACGGATGTATATAGA 59.228 40.741 14.23 0.00 44.82 1.98
4931 5895 8.503458 AGTACCACATACGGATGTATATAGAC 57.497 38.462 14.23 6.17 44.82 2.59
4932 5896 8.105197 AGTACCACATACGGATGTATATAGACA 58.895 37.037 14.23 2.07 44.82 3.41
4933 5897 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
4935 5899 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
4963 5927 9.973450 TTAGAGTATAGATCACTCATTTTGCTC 57.027 33.333 12.69 0.00 44.03 4.26
4964 5928 7.441017 AGAGTATAGATCACTCATTTTGCTCC 58.559 38.462 12.69 0.00 44.03 4.70
4965 5929 6.219473 AGTATAGATCACTCATTTTGCTCCG 58.781 40.000 0.00 0.00 0.00 4.63
4966 5930 3.340814 AGATCACTCATTTTGCTCCGT 57.659 42.857 0.00 0.00 0.00 4.69
4967 5931 4.471904 AGATCACTCATTTTGCTCCGTA 57.528 40.909 0.00 0.00 0.00 4.02
4968 5932 5.028549 AGATCACTCATTTTGCTCCGTAT 57.971 39.130 0.00 0.00 0.00 3.06
4969 5933 4.813161 AGATCACTCATTTTGCTCCGTATG 59.187 41.667 0.00 0.00 0.00 2.39
4970 5934 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
4971 5935 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
4972 5936 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
4973 5937 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
4974 5938 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
4975 5939 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
4976 5940 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
4977 5941 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
4978 5942 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
4979 5943 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
4980 5944 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
4981 5945 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
4982 5946 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
4983 5947 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
4984 5948 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
4985 5949 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
4986 5950 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
4987 5951 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
4988 5952 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
4989 5953 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
4990 5954 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
4991 5955 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
4992 5956 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
4993 5957 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
4994 5958 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
4995 5959 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
4996 5960 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
4997 5961 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
4998 5962 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
4999 5963 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
5000 5964 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
5001 5965 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
5018 5982 9.556030 GAAAGACAAATATTTAGAAACGAAGGG 57.444 33.333 0.00 0.00 0.00 3.95
5019 5983 8.857694 AAGACAAATATTTAGAAACGAAGGGA 57.142 30.769 0.00 0.00 0.00 4.20
5020 5984 8.857694 AGACAAATATTTAGAAACGAAGGGAA 57.142 30.769 0.00 0.00 0.00 3.97
5021 5985 9.462606 AGACAAATATTTAGAAACGAAGGGAAT 57.537 29.630 0.00 0.00 0.00 3.01
5048 6012 3.895232 ACATCTATGCACGACCTCTTT 57.105 42.857 0.00 0.00 0.00 2.52
5177 6147 4.711846 ACTGAGTGCTGGTATAATCTCACA 59.288 41.667 0.00 0.00 0.00 3.58
5189 6159 6.754209 GGTATAATCTCACATCGTCATCATCC 59.246 42.308 0.00 0.00 0.00 3.51
5241 6211 3.639672 ATGCTCATCTGGACATGACAA 57.360 42.857 0.00 0.00 0.00 3.18
5350 6328 2.170397 ACGATGACATGCATGGACCTTA 59.830 45.455 29.41 6.79 37.34 2.69
5351 6329 3.205338 CGATGACATGCATGGACCTTAA 58.795 45.455 29.41 2.57 37.34 1.85
5352 6330 3.627123 CGATGACATGCATGGACCTTAAA 59.373 43.478 29.41 8.28 37.34 1.52
5353 6331 4.096231 CGATGACATGCATGGACCTTAAAA 59.904 41.667 29.41 7.65 37.34 1.52
5354 6332 5.392919 CGATGACATGCATGGACCTTAAAAA 60.393 40.000 29.41 7.01 37.34 1.94
5446 6456 1.869754 CGTGATAGCATCTCCAACCGG 60.870 57.143 0.00 0.00 0.00 5.28
5466 6476 4.634443 CCGGTTATGTATAATAGGGCAAGC 59.366 45.833 0.00 0.00 0.00 4.01
5502 6515 9.480053 ACTGTTTTTAGATCATTTGGACATTTG 57.520 29.630 0.00 0.00 0.00 2.32
5503 6516 8.830201 TGTTTTTAGATCATTTGGACATTTGG 57.170 30.769 0.00 0.00 0.00 3.28
5504 6517 8.646004 TGTTTTTAGATCATTTGGACATTTGGA 58.354 29.630 0.00 0.00 0.00 3.53
5505 6518 8.925700 GTTTTTAGATCATTTGGACATTTGGAC 58.074 33.333 0.00 0.00 0.00 4.02
5506 6519 7.773489 TTTAGATCATTTGGACATTTGGACA 57.227 32.000 0.00 0.00 0.00 4.02
5507 6520 7.773489 TTAGATCATTTGGACATTTGGACAA 57.227 32.000 0.00 0.00 0.00 3.18
5553 6568 5.450965 CCCTATCTTTATTTGGTGCTGCAAG 60.451 44.000 2.77 0.00 0.00 4.01
5567 6582 0.689080 TGCAAGTTTTTGGGGGCAGA 60.689 50.000 0.00 0.00 34.79 4.26
5578 6593 3.297134 TGGGGGCAGACTCATATTTTC 57.703 47.619 0.00 0.00 0.00 2.29
5599 6614 3.201930 TCCCTCCAAGTGCTGCAAATATA 59.798 43.478 2.77 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.251484 AGGTCTCTCTCAAATTCCCACA 58.749 45.455 0.00 0.00 0.00 4.17
43 44 5.768662 GCTAACCAAACTAAGGAAGAAAGGT 59.231 40.000 0.00 0.00 0.00 3.50
45 46 6.072452 CCTGCTAACCAAACTAAGGAAGAAAG 60.072 42.308 0.00 0.00 0.00 2.62
101 102 5.357878 TCTTCACCATAATTTCTGACCATGC 59.642 40.000 0.00 0.00 0.00 4.06
119 120 2.479566 TGAACATCCTGGCTCTTCAC 57.520 50.000 0.00 0.00 0.00 3.18
130 131 4.812626 GGAAATTGATTGGCATGAACATCC 59.187 41.667 0.00 0.00 0.00 3.51
173 174 5.958380 GGGTGGAGATTAGAAGGGAATTTTT 59.042 40.000 0.00 0.00 0.00 1.94
174 175 5.519808 GGGTGGAGATTAGAAGGGAATTTT 58.480 41.667 0.00 0.00 0.00 1.82
175 176 4.079154 GGGGTGGAGATTAGAAGGGAATTT 60.079 45.833 0.00 0.00 0.00 1.82
176 177 3.463704 GGGGTGGAGATTAGAAGGGAATT 59.536 47.826 0.00 0.00 0.00 2.17
177 178 3.056832 GGGGTGGAGATTAGAAGGGAAT 58.943 50.000 0.00 0.00 0.00 3.01
178 179 2.488836 GGGGTGGAGATTAGAAGGGAA 58.511 52.381 0.00 0.00 0.00 3.97
179 180 1.345112 GGGGGTGGAGATTAGAAGGGA 60.345 57.143 0.00 0.00 0.00 4.20
180 181 1.141185 GGGGGTGGAGATTAGAAGGG 58.859 60.000 0.00 0.00 0.00 3.95
181 182 2.050918 GAGGGGGTGGAGATTAGAAGG 58.949 57.143 0.00 0.00 0.00 3.46
182 183 2.703007 CAGAGGGGGTGGAGATTAGAAG 59.297 54.545 0.00 0.00 0.00 2.85
183 184 2.045885 ACAGAGGGGGTGGAGATTAGAA 59.954 50.000 0.00 0.00 0.00 2.10
184 185 1.651770 ACAGAGGGGGTGGAGATTAGA 59.348 52.381 0.00 0.00 0.00 2.10
185 186 2.182516 ACAGAGGGGGTGGAGATTAG 57.817 55.000 0.00 0.00 0.00 1.73
186 187 2.661176 AACAGAGGGGGTGGAGATTA 57.339 50.000 0.00 0.00 0.00 1.75
187 188 2.661176 TAACAGAGGGGGTGGAGATT 57.339 50.000 0.00 0.00 0.00 2.40
188 189 2.661176 TTAACAGAGGGGGTGGAGAT 57.339 50.000 0.00 0.00 0.00 2.75
189 190 2.661176 ATTAACAGAGGGGGTGGAGA 57.339 50.000 0.00 0.00 0.00 3.71
190 191 4.855298 TTTATTAACAGAGGGGGTGGAG 57.145 45.455 0.00 0.00 0.00 3.86
191 192 5.602291 TTTTTATTAACAGAGGGGGTGGA 57.398 39.130 0.00 0.00 0.00 4.02
210 212 7.068716 ACTGCCTCAAAAACTCTTACTCATTTT 59.931 33.333 0.00 0.00 0.00 1.82
229 231 8.443937 CAGTTGTACTCTTTTTATTACTGCCTC 58.556 37.037 0.00 0.00 0.00 4.70
231 233 8.095937 ACAGTTGTACTCTTTTTATTACTGCC 57.904 34.615 0.00 0.00 35.18 4.85
233 235 8.718734 GGGACAGTTGTACTCTTTTTATTACTG 58.281 37.037 0.00 0.00 37.19 2.74
809 1533 3.330853 GATGGCGACGACGATGGC 61.331 66.667 12.29 6.27 42.66 4.40
810 1534 1.278172 GATGATGGCGACGACGATGG 61.278 60.000 12.29 0.00 42.66 3.51
821 1545 0.259938 AGGAAAGGGGTGATGATGGC 59.740 55.000 0.00 0.00 0.00 4.40
825 1549 0.999712 GGGAAGGAAAGGGGTGATGA 59.000 55.000 0.00 0.00 0.00 2.92
826 1550 1.002857 AGGGAAGGAAAGGGGTGATG 58.997 55.000 0.00 0.00 0.00 3.07
827 1551 1.002857 CAGGGAAGGAAAGGGGTGAT 58.997 55.000 0.00 0.00 0.00 3.06
884 1608 3.643792 CAGTAATGTAGGGGGAGAAGGAG 59.356 52.174 0.00 0.00 0.00 3.69
885 1609 3.654273 CAGTAATGTAGGGGGAGAAGGA 58.346 50.000 0.00 0.00 0.00 3.36
889 1614 1.063492 TCGCAGTAATGTAGGGGGAGA 60.063 52.381 0.00 0.00 0.00 3.71
894 1619 1.404391 ACGTCTCGCAGTAATGTAGGG 59.596 52.381 0.00 0.00 0.00 3.53
909 1634 0.033504 ACTCGCCAATGTCAACGTCT 59.966 50.000 0.00 0.00 0.00 4.18
967 1704 4.148825 CAGGACTCCGCGGGAAGG 62.149 72.222 27.83 15.38 0.00 3.46
1301 2071 1.676678 TTCGGCCAAGAGATCTCCGG 61.677 60.000 19.30 19.69 40.42 5.14
1316 2086 3.504863 CAATGCAGAAGGTTTGATTCGG 58.495 45.455 0.00 0.00 0.00 4.30
1373 2149 2.094659 CGCGCTCCAAGTGTTCGAT 61.095 57.895 5.56 0.00 0.00 3.59
1403 2179 6.147821 TGCCGAAAAGAAAACAATCTAGAGAG 59.852 38.462 0.00 0.00 0.00 3.20
1417 2206 1.193650 CGAATCACGTGCCGAAAAGAA 59.806 47.619 11.67 0.00 37.22 2.52
1444 2234 2.288579 TGCCCGCCATACTAATCGTTAG 60.289 50.000 4.02 4.02 39.18 2.34
1446 2236 0.466543 TGCCCGCCATACTAATCGTT 59.533 50.000 0.00 0.00 0.00 3.85
1458 2248 3.801114 ATTTCTAAAATCTTGCCCGCC 57.199 42.857 0.00 0.00 0.00 6.13
1479 2269 8.674607 AGAGAAAACTAAAAGTTTCGTGAATGT 58.325 29.630 5.57 0.00 46.78 2.71
1555 2345 3.497640 CAGCTGCAGCACTTAGAATATCC 59.502 47.826 38.24 5.78 45.16 2.59
1562 2352 2.662006 TCTACAGCTGCAGCACTTAG 57.338 50.000 38.24 30.27 45.16 2.18
1571 2361 6.644592 CCAAGTCTAATAAGATCTACAGCTGC 59.355 42.308 15.27 0.00 33.30 5.25
1612 2402 0.917259 GACACGCATGATCTGACGAC 59.083 55.000 0.00 0.00 0.00 4.34
1613 2403 0.179137 GGACACGCATGATCTGACGA 60.179 55.000 0.00 0.00 0.00 4.20
1614 2404 0.179127 AGGACACGCATGATCTGACG 60.179 55.000 0.00 0.00 0.00 4.35
1695 2485 4.509915 AAGACGTTACTTGTTTGACACG 57.490 40.909 0.00 0.00 0.00 4.49
1725 2515 1.134228 ACCGTAAACCTGTGGTCCTT 58.866 50.000 0.00 0.00 33.12 3.36
1728 2518 1.202557 TGACACCGTAAACCTGTGGTC 60.203 52.381 0.00 0.00 33.12 4.02
1730 2520 1.804151 CATGACACCGTAAACCTGTGG 59.196 52.381 0.00 0.00 34.33 4.17
1731 2521 2.489971 ACATGACACCGTAAACCTGTG 58.510 47.619 0.00 0.00 36.11 3.66
1942 2755 2.238395 GACCAGAGATCAAAAGGCTCCT 59.762 50.000 0.00 0.00 0.00 3.69
2013 2826 6.718454 TGCAAAATTTTCAATGTTATCCCG 57.282 33.333 0.00 0.00 0.00 5.14
2027 2840 6.035220 CGCATAGACACAATCATGCAAAATTT 59.965 34.615 0.00 0.00 39.69 1.82
2030 2843 4.413969 CGCATAGACACAATCATGCAAAA 58.586 39.130 0.00 0.00 39.69 2.44
2046 2859 3.321497 GCTTATCTTCTCCACCGCATAG 58.679 50.000 0.00 0.00 0.00 2.23
2081 2894 7.177392 CCAATTTTAGGAGAGATGGTTTCAAGT 59.823 37.037 0.00 0.00 0.00 3.16
2506 3327 9.866936 TCACGTGTTGTATGAAAGTTTAATTAC 57.133 29.630 16.51 0.00 0.00 1.89
2540 3361 7.500559 AGCAATGGAAAGGATAATGAACTAGAC 59.499 37.037 0.00 0.00 0.00 2.59
2562 3383 9.305925 GATGTCGATATGATATGAATACAGCAA 57.694 33.333 0.00 0.00 0.00 3.91
2593 3414 5.647589 TCGTATCTAAGTTGGCAGTAACAG 58.352 41.667 0.00 0.00 33.02 3.16
2669 3631 4.194640 AGTGCATCTGTGGTCATATTCAC 58.805 43.478 0.00 0.00 29.68 3.18
2721 3683 7.116805 GCAAAATGACTATATAAAAGGGCATGC 59.883 37.037 9.90 9.90 0.00 4.06
3000 3964 3.340034 CCCGCACTAAATCAACCTACAA 58.660 45.455 0.00 0.00 0.00 2.41
3287 4251 4.476628 TGCAGAATCATCAACTCTAGCA 57.523 40.909 0.00 0.00 0.00 3.49
3364 4328 0.669625 AGTGTCGGGCTTCTTAACGC 60.670 55.000 0.00 0.00 0.00 4.84
3434 4398 3.411446 TGTTGACACAATGACAGGATCC 58.589 45.455 2.48 2.48 0.00 3.36
3506 4470 2.200373 AACATAGACAGCAACACCCC 57.800 50.000 0.00 0.00 0.00 4.95
3689 4653 5.999205 TTTCCTCACACCATTGCAATATT 57.001 34.783 12.53 0.00 0.00 1.28
3947 4911 1.688197 ACTGCATGTTCCTGGGTTTTG 59.312 47.619 0.00 0.00 0.00 2.44
3962 4926 7.164122 AGAGATTCAAAAGAGATGTAACTGCA 58.836 34.615 0.00 0.00 0.00 4.41
4085 5049 0.665068 TGAAAATTGCTGCAGCTGCG 60.665 50.000 36.61 26.07 45.83 5.18
4097 5061 6.801539 TCGATTAGTGACAAGCTGAAAATT 57.198 33.333 0.00 0.00 0.00 1.82
4148 5112 3.849951 GCTTCGATCGCCCCAGGA 61.850 66.667 11.09 0.00 0.00 3.86
4151 5115 1.819208 CAATGCTTCGATCGCCCCA 60.819 57.895 11.09 7.05 0.00 4.96
4160 5124 0.455633 GCAGCTCAACCAATGCTTCG 60.456 55.000 0.00 0.00 35.78 3.79
4235 5199 3.181487 CCTTGTTTGCCTGGTATATGCAC 60.181 47.826 0.00 0.00 34.16 4.57
4331 5295 1.446099 GATTGTGAGCGCCTCGTCA 60.446 57.895 2.29 0.00 32.35 4.35
4388 5352 0.035152 TGGTGTGAGCCTTGGCTATG 60.035 55.000 14.76 0.00 0.00 2.23
4592 5556 2.091166 ACTGAGATGCTCCAGGAGAGAT 60.091 50.000 21.89 10.81 46.50 2.75
4861 5825 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4862 5826 5.397109 GGACAAATATTTAGGAACGGAGGGA 60.397 44.000 0.00 0.00 0.00 4.20
4863 5827 4.820173 GGACAAATATTTAGGAACGGAGGG 59.180 45.833 0.00 0.00 0.00 4.30
4864 5828 5.681639 AGGACAAATATTTAGGAACGGAGG 58.318 41.667 0.00 0.00 0.00 4.30
4865 5829 7.625828 AAAGGACAAATATTTAGGAACGGAG 57.374 36.000 0.00 0.00 0.00 4.63
4866 5830 9.169592 CTAAAAGGACAAATATTTAGGAACGGA 57.830 33.333 0.00 0.00 33.69 4.69
4867 5831 9.169592 TCTAAAAGGACAAATATTTAGGAACGG 57.830 33.333 0.00 0.00 36.48 4.44
4879 5843 9.933723 CCATTTGAAATCTCTAAAAGGACAAAT 57.066 29.630 0.00 0.00 36.38 2.32
4881 5845 8.704849 TCCATTTGAAATCTCTAAAAGGACAA 57.295 30.769 0.00 0.00 0.00 3.18
4882 5846 7.944554 ACTCCATTTGAAATCTCTAAAAGGACA 59.055 33.333 0.00 0.00 0.00 4.02
4883 5847 8.341892 ACTCCATTTGAAATCTCTAAAAGGAC 57.658 34.615 0.00 0.00 0.00 3.85
4886 5850 9.231297 TGGTACTCCATTTGAAATCTCTAAAAG 57.769 33.333 0.00 0.00 39.03 2.27
4887 5851 9.010029 GTGGTACTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
4888 5852 8.160765 TGTGGTACTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
4889 5853 7.685481 TGTGGTACTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
4890 5854 7.252612 TGTGGTACTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
4891 5855 6.126863 TGTGGTACTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
4892 5856 7.254455 CGTATGTGGTACTCCATTTGAAATCTC 60.254 40.741 3.69 0.00 46.20 2.75
4893 5857 6.538742 CGTATGTGGTACTCCATTTGAAATCT 59.461 38.462 3.69 0.00 46.20 2.40
4894 5858 6.238374 CCGTATGTGGTACTCCATTTGAAATC 60.238 42.308 3.69 0.00 46.20 2.17
4895 5859 5.588648 CCGTATGTGGTACTCCATTTGAAAT 59.411 40.000 3.69 0.00 46.20 2.17
4896 5860 4.938832 CCGTATGTGGTACTCCATTTGAAA 59.061 41.667 3.69 0.00 46.20 2.69
4897 5861 4.223255 TCCGTATGTGGTACTCCATTTGAA 59.777 41.667 3.69 0.00 46.20 2.69
4898 5862 3.770388 TCCGTATGTGGTACTCCATTTGA 59.230 43.478 3.69 0.00 46.20 2.69
4899 5863 4.131649 TCCGTATGTGGTACTCCATTTG 57.868 45.455 3.69 0.00 46.20 2.32
4900 5864 4.163458 ACATCCGTATGTGGTACTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
4901 5865 3.709653 ACATCCGTATGTGGTACTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
4902 5866 3.305720 ACATCCGTATGTGGTACTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
4903 5867 2.742348 ACATCCGTATGTGGTACTCCA 58.258 47.619 0.00 0.00 44.79 3.86
4904 5868 6.770746 ATATACATCCGTATGTGGTACTCC 57.229 41.667 3.56 0.00 45.99 3.85
4905 5869 8.610896 GTCTATATACATCCGTATGTGGTACTC 58.389 40.741 3.56 0.00 45.99 2.59
4906 5870 8.105197 TGTCTATATACATCCGTATGTGGTACT 58.895 37.037 3.56 0.00 45.99 2.73
4907 5871 8.272545 TGTCTATATACATCCGTATGTGGTAC 57.727 38.462 3.56 0.00 45.99 3.34
4909 5873 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
4937 5901 9.973450 GAGCAAAATGAGTGATCTATACTCTAA 57.027 33.333 11.67 0.00 43.79 2.10
4938 5902 8.580720 GGAGCAAAATGAGTGATCTATACTCTA 58.419 37.037 11.67 1.51 43.79 2.43
4939 5903 7.441017 GGAGCAAAATGAGTGATCTATACTCT 58.559 38.462 11.67 0.00 43.79 3.24
4940 5904 6.364706 CGGAGCAAAATGAGTGATCTATACTC 59.635 42.308 5.02 5.02 43.73 2.59
4941 5905 6.183360 ACGGAGCAAAATGAGTGATCTATACT 60.183 38.462 0.00 0.00 32.02 2.12
4942 5906 5.986135 ACGGAGCAAAATGAGTGATCTATAC 59.014 40.000 0.00 0.00 32.02 1.47
4943 5907 6.161855 ACGGAGCAAAATGAGTGATCTATA 57.838 37.500 0.00 0.00 32.02 1.31
4944 5908 5.028549 ACGGAGCAAAATGAGTGATCTAT 57.971 39.130 0.00 0.00 32.02 1.98
4945 5909 4.471904 ACGGAGCAAAATGAGTGATCTA 57.528 40.909 0.00 0.00 32.02 1.98
4946 5910 3.340814 ACGGAGCAAAATGAGTGATCT 57.659 42.857 0.00 0.00 32.02 2.75
4947 5911 4.572389 ACATACGGAGCAAAATGAGTGATC 59.428 41.667 0.00 0.00 0.00 2.92
4948 5912 4.517285 ACATACGGAGCAAAATGAGTGAT 58.483 39.130 0.00 0.00 0.00 3.06
4949 5913 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
4950 5914 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
4951 5915 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
4952 5916 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
4953 5917 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
4954 5918 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
4955 5919 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
4956 5920 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
4957 5921 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
4958 5922 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
4959 5923 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
4960 5924 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
4961 5925 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
4962 5926 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
4963 5927 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
4964 5928 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
4965 5929 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
4967 5931 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
4968 5932 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
4969 5933 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
4970 5934 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
4971 5935 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
4972 5936 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
4973 5937 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
4974 5938 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
4975 5939 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
4992 5956 9.556030 CCCTTCGTTTCTAAATATTTGTCTTTC 57.444 33.333 11.05 0.00 0.00 2.62
4993 5957 9.292195 TCCCTTCGTTTCTAAATATTTGTCTTT 57.708 29.630 11.05 0.00 0.00 2.52
4994 5958 8.857694 TCCCTTCGTTTCTAAATATTTGTCTT 57.142 30.769 11.05 0.00 0.00 3.01
4995 5959 8.857694 TTCCCTTCGTTTCTAAATATTTGTCT 57.142 30.769 11.05 0.00 0.00 3.41
5002 5966 9.947433 TTTGTCTATTCCCTTCGTTTCTAAATA 57.053 29.630 0.00 0.00 0.00 1.40
5003 5967 8.727910 GTTTGTCTATTCCCTTCGTTTCTAAAT 58.272 33.333 0.00 0.00 0.00 1.40
5004 5968 7.716123 TGTTTGTCTATTCCCTTCGTTTCTAAA 59.284 33.333 0.00 0.00 0.00 1.85
5005 5969 7.218614 TGTTTGTCTATTCCCTTCGTTTCTAA 58.781 34.615 0.00 0.00 0.00 2.10
5006 5970 6.761312 TGTTTGTCTATTCCCTTCGTTTCTA 58.239 36.000 0.00 0.00 0.00 2.10
5007 5971 5.617252 TGTTTGTCTATTCCCTTCGTTTCT 58.383 37.500 0.00 0.00 0.00 2.52
5008 5972 5.934935 TGTTTGTCTATTCCCTTCGTTTC 57.065 39.130 0.00 0.00 0.00 2.78
5009 5973 6.238648 AGATGTTTGTCTATTCCCTTCGTTT 58.761 36.000 0.00 0.00 0.00 3.60
5010 5974 5.805728 AGATGTTTGTCTATTCCCTTCGTT 58.194 37.500 0.00 0.00 0.00 3.85
5011 5975 5.422214 AGATGTTTGTCTATTCCCTTCGT 57.578 39.130 0.00 0.00 0.00 3.85
5012 5976 6.073548 GCATAGATGTTTGTCTATTCCCTTCG 60.074 42.308 0.00 0.00 38.93 3.79
5013 5977 6.767902 TGCATAGATGTTTGTCTATTCCCTTC 59.232 38.462 0.00 0.00 38.93 3.46
5014 5978 6.543831 GTGCATAGATGTTTGTCTATTCCCTT 59.456 38.462 0.00 0.00 38.93 3.95
5015 5979 6.058183 GTGCATAGATGTTTGTCTATTCCCT 58.942 40.000 0.00 0.00 38.93 4.20
5016 5980 5.050091 CGTGCATAGATGTTTGTCTATTCCC 60.050 44.000 0.00 0.00 38.93 3.97
5017 5981 5.753438 TCGTGCATAGATGTTTGTCTATTCC 59.247 40.000 0.00 0.00 38.93 3.01
5018 5982 6.292381 GGTCGTGCATAGATGTTTGTCTATTC 60.292 42.308 0.00 0.00 38.93 1.75
5019 5983 5.523916 GGTCGTGCATAGATGTTTGTCTATT 59.476 40.000 0.00 0.00 38.93 1.73
5020 5984 5.050490 GGTCGTGCATAGATGTTTGTCTAT 58.950 41.667 0.00 0.00 41.03 1.98
5021 5985 4.159693 AGGTCGTGCATAGATGTTTGTCTA 59.840 41.667 0.00 0.00 35.33 2.59
5022 5986 3.055819 AGGTCGTGCATAGATGTTTGTCT 60.056 43.478 0.00 0.00 0.00 3.41
5023 5987 3.262420 AGGTCGTGCATAGATGTTTGTC 58.738 45.455 0.00 0.00 0.00 3.18
5024 5988 3.055819 AGAGGTCGTGCATAGATGTTTGT 60.056 43.478 0.00 0.00 0.00 2.83
5025 5989 3.525537 AGAGGTCGTGCATAGATGTTTG 58.474 45.455 0.00 0.00 0.00 2.93
5048 6012 2.955660 CAAACTGGTAGGCTGGAAAACA 59.044 45.455 0.00 0.00 0.00 2.83
5174 6144 1.004610 GCAACGGATGATGACGATGTG 60.005 52.381 0.00 0.00 35.66 3.21
5177 6147 2.022764 TTGCAACGGATGATGACGAT 57.977 45.000 0.00 0.00 0.00 3.73
5189 6159 4.858692 CCTCTAACAAATTGGATTGCAACG 59.141 41.667 0.00 0.00 33.52 4.10
5241 6211 2.358322 ACCGGAATCACCTTTGTTGT 57.642 45.000 9.46 0.00 36.31 3.32
5446 6456 5.929992 TGACGCTTGCCCTATTATACATAAC 59.070 40.000 0.00 0.00 0.00 1.89
5477 6487 8.928733 CCAAATGTCCAAATGATCTAAAAACAG 58.071 33.333 0.00 0.00 0.00 3.16
5478 6488 8.646004 TCCAAATGTCCAAATGATCTAAAAACA 58.354 29.630 0.00 0.00 0.00 2.83
5479 6489 8.925700 GTCCAAATGTCCAAATGATCTAAAAAC 58.074 33.333 0.00 0.00 0.00 2.43
5507 6520 4.114794 GCATCTGTTGAAGCTGTGTTTTT 58.885 39.130 0.00 0.00 34.45 1.94
5522 6537 5.829924 CACCAAATAAAGATAGGGCATCTGT 59.170 40.000 0.00 0.00 43.56 3.41
5553 6568 1.632589 ATGAGTCTGCCCCCAAAAAC 58.367 50.000 0.00 0.00 0.00 2.43
5567 6582 4.018050 AGCACTTGGAGGGAAAATATGAGT 60.018 41.667 0.00 0.00 0.00 3.41
5578 6593 1.838112 TATTTGCAGCACTTGGAGGG 58.162 50.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.