Multiple sequence alignment - TraesCS1D01G278400

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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 TraesCS1D01G278400 chr1D 100.000 4783 0 0 1 4783 375958221 375953439 0.000000e+00 8833.0
1 TraesCS1D01G278400 chr1D 94.054 185 10 1 4463 4647 455642090 455642273 3.650000e-71 279.0
2 TraesCS1D01G278400 chr1D 92.000 200 12 3 4449 4646 379491646 379491449 1.310000e-70 278.0
3 TraesCS1D01G278400 chr1B 94.864 2025 81 13 2296 4306 501366799 501364784 0.000000e+00 3142.0
4 TraesCS1D01G278400 chr1B 93.137 1865 40 33 431 2238 501369013 501367180 0.000000e+00 2654.0
5 TraesCS1D01G278400 chr1B 90.452 398 28 4 1 391 501369407 501369013 2.550000e-142 516.0
6 TraesCS1D01G278400 chr1B 94.964 139 6 1 4311 4448 501364712 501364574 2.900000e-52 217.0
7 TraesCS1D01G278400 chr1B 90.728 151 1 1 4646 4783 501364583 501364433 6.320000e-44 189.0
8 TraesCS1D01G278400 chr1B 97.500 40 1 0 2261 2300 501367104 501367065 8.590000e-08 69.4
9 TraesCS1D01G278400 chr1A 90.073 2337 94 48 1 2230 474703975 474701670 0.000000e+00 2904.0
10 TraesCS1D01G278400 chr1A 95.447 1801 61 7 2296 4082 474701126 474699333 0.000000e+00 2852.0
11 TraesCS1D01G278400 chr1A 91.518 224 10 2 4234 4448 474699312 474699089 2.800000e-77 300.0
12 TraesCS1D01G278400 chr1A 88.158 152 4 2 4646 4783 474699098 474698947 8.230000e-38 169.0
13 TraesCS1D01G278400 chr1A 100.000 40 0 0 2261 2300 474701435 474701396 1.850000e-09 75.0
14 TraesCS1D01G278400 chr1A 100.000 40 0 0 2261 2300 474701568 474701529 1.850000e-09 75.0
15 TraesCS1D01G278400 chr3A 89.864 513 52 0 1000 1512 616468780 616469292 0.000000e+00 660.0
16 TraesCS1D01G278400 chr3A 84.375 128 16 4 274 399 708101163 708101288 6.500000e-24 122.0
17 TraesCS1D01G278400 chr3D 89.494 514 46 7 1000 1512 474118141 474118647 1.120000e-180 643.0
18 TraesCS1D01G278400 chr3D 95.055 182 8 1 4465 4646 24663043 24663223 7.830000e-73 285.0
19 TraesCS1D01G278400 chr3B 88.544 515 46 9 1000 1512 630363996 630364499 3.160000e-171 612.0
20 TraesCS1D01G278400 chr6D 93.970 199 11 1 4449 4647 256572499 256572302 2.800000e-77 300.0
21 TraesCS1D01G278400 chr6D 92.228 193 13 2 4456 4647 325399054 325398863 6.100000e-69 272.0
22 TraesCS1D01G278400 chrUn 94.054 185 8 3 4463 4646 98338570 98338752 1.310000e-70 278.0
23 TraesCS1D01G278400 chr7D 93.583 187 10 2 4463 4649 168413047 168412863 1.310000e-70 278.0
24 TraesCS1D01G278400 chr4D 94.022 184 10 1 4463 4646 92303757 92303575 1.310000e-70 278.0
25 TraesCS1D01G278400 chr2D 93.478 184 11 1 4463 4646 384752772 384752954 6.100000e-69 272.0
26 TraesCS1D01G278400 chr2D 100.000 31 0 0 273 303 554431937 554431967 1.860000e-04 58.4
27 TraesCS1D01G278400 chr6A 84.091 132 16 4 274 403 38757165 38757293 6.500000e-24 122.0
28 TraesCS1D01G278400 chr2B 82.443 131 21 2 274 403 243784660 243784789 3.910000e-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 TraesCS1D01G278400 chr1D 375953439 375958221 4782 True 8833.000000 8833 100.000000 1 4783 1 chr1D.!!$R1 4782
1 TraesCS1D01G278400 chr1B 501364433 501369407 4974 True 1131.233333 3142 93.607500 1 4783 6 chr1B.!!$R1 4782
2 TraesCS1D01G278400 chr1A 474698947 474703975 5028 True 1062.500000 2904 94.199333 1 4783 6 chr1A.!!$R1 4782
3 TraesCS1D01G278400 chr3A 616468780 616469292 512 False 660.000000 660 89.864000 1000 1512 1 chr3A.!!$F1 512
4 TraesCS1D01G278400 chr3D 474118141 474118647 506 False 643.000000 643 89.494000 1000 1512 1 chr3D.!!$F2 512
5 TraesCS1D01G278400 chr3B 630363996 630364499 503 False 612.000000 612 88.544000 1000 1512 1 chr3B.!!$F1 512

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
847 876 1.006639 AGTCCTCTCCTCACTTCTCCC 59.993 57.143 0.00 0.0 0.00 4.30 F
1829 1918 1.203052 CCATGGCCTTGCAGTTACAAG 59.797 52.381 13.15 0.0 45.42 3.16 F
2195 2316 0.768221 TCAGGGTGCCTTCCTCAGTT 60.768 55.000 0.00 0.0 31.06 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 2278 0.402121 AAGGAACTGAGGAAGGCACC 59.598 55.0 0.00 0.00 40.86 5.01 R
3068 3668 1.035932 CCTCTTCTTGCATGCCAGGG 61.036 60.0 17.97 11.49 0.00 4.45 R
4171 4797 0.244721 GGCATGGCTCTTGTTTCCAC 59.755 55.0 12.86 0.00 31.94 4.02 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
35 36 7.416817 GCAACACATGTTATGCTATTCATGTA 58.583 34.615 20.22 0.00 45.64 2.29
36 37 7.588854 GCAACACATGTTATGCTATTCATGTAG 59.411 37.037 20.22 11.85 45.64 2.74
37 38 8.615211 CAACACATGTTATGCTATTCATGTAGT 58.385 33.333 14.07 12.25 45.64 2.73
125 128 6.780031 TCAAGTAGATGAAAATTTTGACCCCA 59.220 34.615 8.47 0.00 0.00 4.96
128 131 7.670364 AGTAGATGAAAATTTTGACCCCAAAG 58.330 34.615 8.47 0.00 42.55 2.77
143 156 6.012333 TGACCCCAAAGTACAATTATAGGTGT 60.012 38.462 0.00 0.00 0.00 4.16
217 235 6.621737 TTCAAGCGAAGTTATAACACTACG 57.378 37.500 17.65 15.75 0.00 3.51
290 311 1.235281 GGCTCCCTCCGTTCACAAAC 61.235 60.000 0.00 0.00 0.00 2.93
362 383 9.421806 GTTTGATGTATTTGTTCATTCATTCCA 57.578 29.630 0.00 0.00 0.00 3.53
367 388 6.718912 TGTATTTGTTCATTCATTCCAGTCCA 59.281 34.615 0.00 0.00 0.00 4.02
370 391 6.757897 TTGTTCATTCATTCCAGTCCATAC 57.242 37.500 0.00 0.00 0.00 2.39
427 448 5.189145 ACACTAAATTATGAACGGAGGGAGT 59.811 40.000 0.00 0.00 0.00 3.85
428 449 6.381994 ACACTAAATTATGAACGGAGGGAGTA 59.618 38.462 0.00 0.00 0.00 2.59
429 450 7.093201 ACACTAAATTATGAACGGAGGGAGTAA 60.093 37.037 0.00 0.00 0.00 2.24
500 522 1.817941 CCCTACCACATTTCGGCGG 60.818 63.158 7.21 0.00 0.00 6.13
728 753 2.203153 GTTGCGGGGTGTGTCAGT 60.203 61.111 0.00 0.00 0.00 3.41
732 757 2.972505 CGGGGTGTGTCAGTGTGC 60.973 66.667 0.00 0.00 0.00 4.57
844 873 2.534990 CCAAGTCCTCTCCTCACTTCT 58.465 52.381 0.00 0.00 0.00 2.85
845 874 2.495669 CCAAGTCCTCTCCTCACTTCTC 59.504 54.545 0.00 0.00 0.00 2.87
846 875 2.495669 CAAGTCCTCTCCTCACTTCTCC 59.504 54.545 0.00 0.00 0.00 3.71
847 876 1.006639 AGTCCTCTCCTCACTTCTCCC 59.993 57.143 0.00 0.00 0.00 4.30
1788 1855 3.845781 ATACGGTCCGTACTCTCCTAA 57.154 47.619 25.95 3.02 45.07 2.69
1819 1908 3.443045 GGTGCGACCATGGCCTTG 61.443 66.667 13.04 11.68 38.42 3.61
1828 1917 1.255882 CCATGGCCTTGCAGTTACAA 58.744 50.000 13.15 0.00 0.00 2.41
1829 1918 1.203052 CCATGGCCTTGCAGTTACAAG 59.797 52.381 13.15 0.00 45.42 3.16
1830 1919 1.888512 CATGGCCTTGCAGTTACAAGT 59.111 47.619 3.32 0.00 44.55 3.16
1895 1988 6.148150 CGTATCTACCTTGTGCCTTTTGTTTA 59.852 38.462 0.00 0.00 0.00 2.01
2091 2186 3.921677 TCGCTCGTCTTTTACTGGAATT 58.078 40.909 0.00 0.00 0.00 2.17
2146 2244 9.701098 TTGTTTCTGTTACCAGTTATACTACTG 57.299 33.333 0.00 0.00 44.07 2.74
2147 2245 8.863086 TGTTTCTGTTACCAGTTATACTACTGT 58.137 33.333 4.31 0.00 43.17 3.55
2148 2246 9.351570 GTTTCTGTTACCAGTTATACTACTGTC 57.648 37.037 4.31 0.00 43.17 3.51
2173 2271 9.132923 TCCTACTTAATTCTAGTATGGACAGTG 57.867 37.037 10.99 0.00 0.00 3.66
2175 2273 9.737427 CTACTTAATTCTAGTATGGACAGTGTG 57.263 37.037 0.00 0.00 0.00 3.82
2176 2274 8.135382 ACTTAATTCTAGTATGGACAGTGTGT 57.865 34.615 0.00 0.00 0.00 3.72
2188 2308 0.886490 CAGTGTGTCAGGGTGCCTTC 60.886 60.000 0.00 0.00 0.00 3.46
2195 2316 0.768221 TCAGGGTGCCTTCCTCAGTT 60.768 55.000 0.00 0.00 31.06 3.16
2232 2353 8.614469 ATTTGCTCTAGTTTGATAATCCTAGC 57.386 34.615 0.00 0.00 0.00 3.42
2233 2354 6.731292 TGCTCTAGTTTGATAATCCTAGCA 57.269 37.500 0.00 0.00 0.00 3.49
2234 2355 7.308450 TGCTCTAGTTTGATAATCCTAGCAT 57.692 36.000 0.00 0.00 0.00 3.79
2237 2358 7.526192 GCTCTAGTTTGATAATCCTAGCATGGA 60.526 40.741 0.00 0.13 40.82 3.41
2238 2359 7.671302 TCTAGTTTGATAATCCTAGCATGGAC 58.329 38.462 0.00 0.00 39.17 4.02
2239 2360 6.252599 AGTTTGATAATCCTAGCATGGACA 57.747 37.500 0.00 0.00 39.17 4.02
2240 2361 6.294473 AGTTTGATAATCCTAGCATGGACAG 58.706 40.000 0.00 0.00 39.17 3.51
2242 2363 6.994421 TTGATAATCCTAGCATGGACAGTA 57.006 37.500 0.00 0.00 39.17 2.74
2243 2364 6.596309 TGATAATCCTAGCATGGACAGTAG 57.404 41.667 0.00 0.00 39.17 2.57
2245 2366 3.619900 ATCCTAGCATGGACAGTAGGA 57.380 47.619 9.17 9.17 44.08 2.94
2246 2367 2.950781 TCCTAGCATGGACAGTAGGAG 58.049 52.381 0.00 0.00 36.86 3.69
2249 2370 4.106502 TCCTAGCATGGACAGTAGGAGTAT 59.893 45.833 0.00 0.00 36.86 2.12
2250 2371 4.461081 CCTAGCATGGACAGTAGGAGTATC 59.539 50.000 0.00 0.00 34.99 2.24
2251 2372 3.916035 AGCATGGACAGTAGGAGTATCA 58.084 45.455 0.00 0.00 36.25 2.15
2252 2373 3.639094 AGCATGGACAGTAGGAGTATCAC 59.361 47.826 0.00 0.00 36.25 3.06
2253 2374 3.551046 GCATGGACAGTAGGAGTATCACG 60.551 52.174 0.00 0.00 36.25 4.35
2256 2377 4.449131 TGGACAGTAGGAGTATCACGTAG 58.551 47.826 0.00 0.00 36.25 3.51
2325 2924 5.467063 AGTCCGTCTTCATTTGTTTCTCTTC 59.533 40.000 0.00 0.00 0.00 2.87
2326 2925 5.236478 GTCCGTCTTCATTTGTTTCTCTTCA 59.764 40.000 0.00 0.00 0.00 3.02
2373 2972 4.064388 CCCTGTTTTGCTTATTTTGGTGG 58.936 43.478 0.00 0.00 0.00 4.61
2379 2978 6.481644 TGTTTTGCTTATTTTGGTGGATTGTC 59.518 34.615 0.00 0.00 0.00 3.18
2831 3430 3.891366 AGCTGGATTTGCAGTACAGTTTT 59.109 39.130 13.17 0.43 0.00 2.43
2885 3484 6.966021 TGCAAAATGTCCAAACTTACTAGTC 58.034 36.000 0.00 0.00 31.99 2.59
3068 3668 0.537188 TTGAGCGAGGGGAAGATGAC 59.463 55.000 0.00 0.00 0.00 3.06
3895 4505 4.844085 TGGGTATTGTATGGATCTGGTAGG 59.156 45.833 0.00 0.00 0.00 3.18
3924 4534 3.515502 AGCTGCTGTGTACTGGAATAAGA 59.484 43.478 0.00 0.00 0.00 2.10
3988 4601 9.796180 AGGAAGATGTATACTACTGTACTAAGG 57.204 37.037 4.17 0.00 0.00 2.69
4075 4689 1.319614 GCGGCCTGCCCAAGATTTTA 61.320 55.000 0.00 0.00 37.76 1.52
4082 4696 4.081476 GCCTGCCCAAGATTTTATCTGTTT 60.081 41.667 0.00 0.00 40.13 2.83
4083 4697 5.413499 CCTGCCCAAGATTTTATCTGTTTG 58.587 41.667 0.00 0.00 40.13 2.93
4084 4698 5.404466 TGCCCAAGATTTTATCTGTTTGG 57.596 39.130 0.00 0.00 40.13 3.28
4085 4699 4.837860 TGCCCAAGATTTTATCTGTTTGGT 59.162 37.500 0.00 0.00 40.13 3.67
4086 4700 5.170748 GCCCAAGATTTTATCTGTTTGGTG 58.829 41.667 0.00 0.00 40.13 4.17
4091 4705 8.143835 CCAAGATTTTATCTGTTTGGTGAGTTT 58.856 33.333 0.00 0.00 40.13 2.66
4092 4706 9.533253 CAAGATTTTATCTGTTTGGTGAGTTTT 57.467 29.630 0.00 0.00 40.13 2.43
4101 4715 9.883142 ATCTGTTTGGTGAGTTTTTATTTTTGA 57.117 25.926 0.00 0.00 0.00 2.69
4102 4716 9.712305 TCTGTTTGGTGAGTTTTTATTTTTGAA 57.288 25.926 0.00 0.00 0.00 2.69
4103 4717 9.971744 CTGTTTGGTGAGTTTTTATTTTTGAAG 57.028 29.630 0.00 0.00 0.00 3.02
4104 4718 8.447053 TGTTTGGTGAGTTTTTATTTTTGAAGC 58.553 29.630 0.00 0.00 0.00 3.86
4105 4719 8.664798 GTTTGGTGAGTTTTTATTTTTGAAGCT 58.335 29.630 0.00 0.00 0.00 3.74
4141 4767 0.522705 GCATGCTGCACAATCTGTCG 60.523 55.000 11.37 0.00 44.26 4.35
4165 4791 4.901866 CCACAAACGGCAAATATGAAAC 57.098 40.909 0.00 0.00 0.00 2.78
4166 4792 3.363426 CCACAAACGGCAAATATGAAACG 59.637 43.478 0.00 0.00 0.00 3.60
4168 4794 4.677378 CACAAACGGCAAATATGAAACGAA 59.323 37.500 0.00 0.00 0.00 3.85
4169 4795 4.677832 ACAAACGGCAAATATGAAACGAAC 59.322 37.500 0.00 0.00 0.00 3.95
4171 4797 4.078363 ACGGCAAATATGAAACGAACTG 57.922 40.909 0.00 0.00 0.00 3.16
4183 4809 4.094294 TGAAACGAACTGTGGAAACAAGAG 59.906 41.667 0.00 0.00 46.06 2.85
4193 4819 0.961019 GAAACAAGAGCCATGCCACA 59.039 50.000 0.00 0.00 0.00 4.17
4196 4822 0.675633 ACAAGAGCCATGCCACAAAC 59.324 50.000 0.00 0.00 0.00 2.93
4212 4838 0.593128 AAACGGCAGATGCAAGACAC 59.407 50.000 7.19 0.00 44.36 3.67
4232 4858 2.625823 ATTTTGTGGTGGAGGCGCG 61.626 57.895 0.00 0.00 0.00 6.86
4388 5086 1.863454 GACGGATGAACTATGCAGCAG 59.137 52.381 0.00 0.00 0.00 4.24
4435 5138 1.689273 CAGTAGTAGCTTAGCCCAGGG 59.311 57.143 0.00 0.00 0.00 4.45
4438 5141 1.205055 AGTAGCTTAGCCCAGGGAAC 58.795 55.000 10.89 0.00 0.00 3.62
4439 5142 0.909623 GTAGCTTAGCCCAGGGAACA 59.090 55.000 10.89 0.00 0.00 3.18
4440 5143 1.280998 GTAGCTTAGCCCAGGGAACAA 59.719 52.381 10.89 0.00 0.00 2.83
4441 5144 0.329596 AGCTTAGCCCAGGGAACAAG 59.670 55.000 10.89 9.67 0.00 3.16
4442 5145 1.315981 GCTTAGCCCAGGGAACAAGC 61.316 60.000 10.89 15.89 32.51 4.01
4443 5146 0.329596 CTTAGCCCAGGGAACAAGCT 59.670 55.000 10.89 0.00 36.40 3.74
4444 5147 1.559682 CTTAGCCCAGGGAACAAGCTA 59.440 52.381 10.89 0.00 34.58 3.32
4445 5148 1.204146 TAGCCCAGGGAACAAGCTAG 58.796 55.000 10.89 0.00 34.58 3.42
4446 5149 0.842467 AGCCCAGGGAACAAGCTAGT 60.842 55.000 10.89 0.00 31.50 2.57
4447 5150 0.038310 GCCCAGGGAACAAGCTAGTT 59.962 55.000 10.89 0.00 0.00 2.24
4448 5151 1.826385 CCCAGGGAACAAGCTAGTTG 58.174 55.000 0.00 0.00 42.48 3.16
4449 5152 1.614317 CCCAGGGAACAAGCTAGTTGG 60.614 57.143 0.00 0.00 40.90 3.77
4450 5153 1.351017 CCAGGGAACAAGCTAGTTGGA 59.649 52.381 9.05 0.00 40.90 3.53
4451 5154 2.025887 CCAGGGAACAAGCTAGTTGGAT 60.026 50.000 9.05 0.00 40.90 3.41
4452 5155 3.274288 CAGGGAACAAGCTAGTTGGATC 58.726 50.000 9.05 0.00 40.90 3.36
4453 5156 2.239907 AGGGAACAAGCTAGTTGGATCC 59.760 50.000 4.20 4.20 41.91 3.36
4454 5157 2.280628 GGAACAAGCTAGTTGGATCCG 58.719 52.381 7.39 0.00 40.90 4.18
4455 5158 2.280628 GAACAAGCTAGTTGGATCCGG 58.719 52.381 7.39 0.00 40.90 5.14
4456 5159 0.107654 ACAAGCTAGTTGGATCCGGC 60.108 55.000 7.39 6.33 40.90 6.13
4457 5160 0.179000 CAAGCTAGTTGGATCCGGCT 59.821 55.000 7.39 10.04 31.82 5.52
4458 5161 0.912486 AAGCTAGTTGGATCCGGCTT 59.088 50.000 17.06 17.06 35.57 4.35
4459 5162 0.179000 AGCTAGTTGGATCCGGCTTG 59.821 55.000 7.39 9.50 0.00 4.01
4460 5163 1.440145 GCTAGTTGGATCCGGCTTGC 61.440 60.000 19.58 19.58 0.00 4.01
4461 5164 0.815615 CTAGTTGGATCCGGCTTGCC 60.816 60.000 7.39 0.75 0.00 4.52
4462 5165 1.271840 TAGTTGGATCCGGCTTGCCT 61.272 55.000 7.39 0.00 0.00 4.75
4463 5166 2.045045 TTGGATCCGGCTTGCCTG 60.045 61.111 7.39 3.29 0.00 4.85
4464 5167 4.802051 TGGATCCGGCTTGCCTGC 62.802 66.667 7.39 0.00 0.00 4.85
4465 5168 4.496336 GGATCCGGCTTGCCTGCT 62.496 66.667 10.12 0.00 0.00 4.24
4466 5169 2.899339 GATCCGGCTTGCCTGCTC 60.899 66.667 10.12 0.76 0.00 4.26
4467 5170 3.397613 GATCCGGCTTGCCTGCTCT 62.398 63.158 10.12 0.00 0.00 4.09
4468 5171 3.397613 ATCCGGCTTGCCTGCTCTC 62.398 63.158 10.12 0.00 0.00 3.20
4469 5172 4.399395 CCGGCTTGCCTGCTCTCA 62.399 66.667 10.12 0.00 0.00 3.27
4470 5173 2.124819 CGGCTTGCCTGCTCTCAT 60.125 61.111 10.12 0.00 0.00 2.90
4471 5174 2.178890 CGGCTTGCCTGCTCTCATC 61.179 63.158 10.12 0.00 0.00 2.92
4472 5175 1.823041 GGCTTGCCTGCTCTCATCC 60.823 63.158 4.11 0.00 0.00 3.51
4473 5176 2.178890 GCTTGCCTGCTCTCATCCG 61.179 63.158 0.00 0.00 0.00 4.18
4474 5177 1.220206 CTTGCCTGCTCTCATCCGT 59.780 57.895 0.00 0.00 0.00 4.69
4475 5178 1.078918 TTGCCTGCTCTCATCCGTG 60.079 57.895 0.00 0.00 0.00 4.94
4476 5179 2.894387 GCCTGCTCTCATCCGTGC 60.894 66.667 0.00 0.00 0.00 5.34
4477 5180 2.898738 CCTGCTCTCATCCGTGCT 59.101 61.111 0.00 0.00 0.00 4.40
4478 5181 1.227205 CCTGCTCTCATCCGTGCTC 60.227 63.158 0.00 0.00 0.00 4.26
4479 5182 1.227205 CTGCTCTCATCCGTGCTCC 60.227 63.158 0.00 0.00 0.00 4.70
4480 5183 2.107953 GCTCTCATCCGTGCTCCC 59.892 66.667 0.00 0.00 0.00 4.30
4481 5184 2.725312 GCTCTCATCCGTGCTCCCA 61.725 63.158 0.00 0.00 0.00 4.37
4482 5185 1.142748 CTCTCATCCGTGCTCCCAC 59.857 63.158 0.00 0.00 38.62 4.61
4483 5186 1.305297 TCTCATCCGTGCTCCCACT 60.305 57.895 0.00 0.00 39.86 4.00
4484 5187 0.904865 TCTCATCCGTGCTCCCACTT 60.905 55.000 0.00 0.00 39.86 3.16
4485 5188 0.460987 CTCATCCGTGCTCCCACTTC 60.461 60.000 0.00 0.00 39.86 3.01
4486 5189 1.191489 TCATCCGTGCTCCCACTTCA 61.191 55.000 0.00 0.00 39.86 3.02
4487 5190 0.107508 CATCCGTGCTCCCACTTCAT 60.108 55.000 0.00 0.00 39.86 2.57
4488 5191 0.179000 ATCCGTGCTCCCACTTCATC 59.821 55.000 0.00 0.00 39.86 2.92
4489 5192 1.450312 CCGTGCTCCCACTTCATCC 60.450 63.158 0.00 0.00 39.86 3.51
4490 5193 1.599047 CGTGCTCCCACTTCATCCT 59.401 57.895 0.00 0.00 39.86 3.24
4491 5194 0.824109 CGTGCTCCCACTTCATCCTA 59.176 55.000 0.00 0.00 39.86 2.94
4492 5195 1.471676 CGTGCTCCCACTTCATCCTAC 60.472 57.143 0.00 0.00 39.86 3.18
4493 5196 0.824109 TGCTCCCACTTCATCCTACG 59.176 55.000 0.00 0.00 0.00 3.51
4494 5197 0.105039 GCTCCCACTTCATCCTACGG 59.895 60.000 0.00 0.00 0.00 4.02
4495 5198 0.753262 CTCCCACTTCATCCTACGGG 59.247 60.000 0.00 0.00 34.81 5.28
4496 5199 1.146263 CCCACTTCATCCTACGGGC 59.854 63.158 0.00 0.00 0.00 6.13
4497 5200 1.338136 CCCACTTCATCCTACGGGCT 61.338 60.000 0.00 0.00 0.00 5.19
4498 5201 0.179073 CCACTTCATCCTACGGGCTG 60.179 60.000 0.00 0.00 0.00 4.85
4499 5202 0.537188 CACTTCATCCTACGGGCTGT 59.463 55.000 3.57 3.57 31.27 4.40
4500 5203 1.066143 CACTTCATCCTACGGGCTGTT 60.066 52.381 3.31 0.00 31.27 3.16
4501 5204 1.207329 ACTTCATCCTACGGGCTGTTC 59.793 52.381 3.31 0.00 31.27 3.18
4502 5205 1.482593 CTTCATCCTACGGGCTGTTCT 59.517 52.381 3.31 0.00 31.27 3.01
4503 5206 1.568504 TCATCCTACGGGCTGTTCTT 58.431 50.000 3.31 0.00 31.27 2.52
4504 5207 1.906574 TCATCCTACGGGCTGTTCTTT 59.093 47.619 3.31 0.00 31.27 2.52
4505 5208 2.304761 TCATCCTACGGGCTGTTCTTTT 59.695 45.455 3.31 0.00 31.27 2.27
4506 5209 2.943036 TCCTACGGGCTGTTCTTTTT 57.057 45.000 3.31 0.00 0.00 1.94
4507 5210 2.774687 TCCTACGGGCTGTTCTTTTTC 58.225 47.619 3.31 0.00 0.00 2.29
4508 5211 1.810755 CCTACGGGCTGTTCTTTTTCC 59.189 52.381 3.31 0.00 0.00 3.13
4509 5212 2.552373 CCTACGGGCTGTTCTTTTTCCT 60.552 50.000 3.31 0.00 0.00 3.36
4510 5213 2.067365 ACGGGCTGTTCTTTTTCCTT 57.933 45.000 0.00 0.00 0.00 3.36
4511 5214 2.384828 ACGGGCTGTTCTTTTTCCTTT 58.615 42.857 0.00 0.00 0.00 3.11
4512 5215 2.764010 ACGGGCTGTTCTTTTTCCTTTT 59.236 40.909 0.00 0.00 0.00 2.27
4513 5216 3.196901 ACGGGCTGTTCTTTTTCCTTTTT 59.803 39.130 0.00 0.00 0.00 1.94
4514 5217 3.802139 CGGGCTGTTCTTTTTCCTTTTTC 59.198 43.478 0.00 0.00 0.00 2.29
4515 5218 4.441495 CGGGCTGTTCTTTTTCCTTTTTCT 60.441 41.667 0.00 0.00 0.00 2.52
4516 5219 5.428253 GGGCTGTTCTTTTTCCTTTTTCTT 58.572 37.500 0.00 0.00 0.00 2.52
4517 5220 5.880332 GGGCTGTTCTTTTTCCTTTTTCTTT 59.120 36.000 0.00 0.00 0.00 2.52
4518 5221 6.374333 GGGCTGTTCTTTTTCCTTTTTCTTTT 59.626 34.615 0.00 0.00 0.00 2.27
4519 5222 7.414098 GGGCTGTTCTTTTTCCTTTTTCTTTTC 60.414 37.037 0.00 0.00 0.00 2.29
4520 5223 7.334421 GGCTGTTCTTTTTCCTTTTTCTTTTCT 59.666 33.333 0.00 0.00 0.00 2.52
4521 5224 9.366216 GCTGTTCTTTTTCCTTTTTCTTTTCTA 57.634 29.630 0.00 0.00 0.00 2.10
4537 5240 9.853177 TTTCTTTTCTAATCTAATCATCTCCCC 57.147 33.333 0.00 0.00 0.00 4.81
4538 5241 7.978925 TCTTTTCTAATCTAATCATCTCCCCC 58.021 38.462 0.00 0.00 0.00 5.40
4559 5262 1.758862 CTGATTTTCAGGGAATGGGGC 59.241 52.381 0.00 0.00 40.71 5.80
4560 5263 1.123077 GATTTTCAGGGAATGGGGCC 58.877 55.000 0.00 0.00 0.00 5.80
4561 5264 0.687427 ATTTTCAGGGAATGGGGCCG 60.687 55.000 0.00 0.00 0.00 6.13
4562 5265 2.796734 TTTTCAGGGAATGGGGCCGG 62.797 60.000 0.00 0.00 0.00 6.13
4574 5277 4.678423 GGCCGGGCCTTATTTTCT 57.322 55.556 30.86 0.00 46.69 2.52
4575 5278 2.896278 GGCCGGGCCTTATTTTCTT 58.104 52.632 30.86 0.00 46.69 2.52
4576 5279 1.191535 GGCCGGGCCTTATTTTCTTT 58.808 50.000 30.86 0.00 46.69 2.52
4577 5280 1.136305 GGCCGGGCCTTATTTTCTTTC 59.864 52.381 30.86 0.00 46.69 2.62
4578 5281 1.822371 GCCGGGCCTTATTTTCTTTCA 59.178 47.619 8.12 0.00 0.00 2.69
4579 5282 2.232696 GCCGGGCCTTATTTTCTTTCAA 59.767 45.455 8.12 0.00 0.00 2.69
4580 5283 3.118775 GCCGGGCCTTATTTTCTTTCAAT 60.119 43.478 8.12 0.00 0.00 2.57
4581 5284 4.682787 CCGGGCCTTATTTTCTTTCAATC 58.317 43.478 0.84 0.00 0.00 2.67
4582 5285 4.159506 CCGGGCCTTATTTTCTTTCAATCA 59.840 41.667 0.84 0.00 0.00 2.57
4583 5286 5.337169 CCGGGCCTTATTTTCTTTCAATCAA 60.337 40.000 0.84 0.00 0.00 2.57
4584 5287 6.162777 CGGGCCTTATTTTCTTTCAATCAAA 58.837 36.000 0.84 0.00 0.00 2.69
4585 5288 6.818142 CGGGCCTTATTTTCTTTCAATCAAAT 59.182 34.615 0.84 0.00 0.00 2.32
4586 5289 7.334171 CGGGCCTTATTTTCTTTCAATCAAATT 59.666 33.333 0.84 0.00 0.00 1.82
4587 5290 9.665719 GGGCCTTATTTTCTTTCAATCAAATTA 57.334 29.630 0.84 0.00 0.00 1.40
4594 5297 7.636259 TTTCTTTCAATCAAATTAAGCCACG 57.364 32.000 0.00 0.00 0.00 4.94
4595 5298 6.325919 TCTTTCAATCAAATTAAGCCACGT 57.674 33.333 0.00 0.00 0.00 4.49
4596 5299 7.441890 TCTTTCAATCAAATTAAGCCACGTA 57.558 32.000 0.00 0.00 0.00 3.57
4597 5300 8.050778 TCTTTCAATCAAATTAAGCCACGTAT 57.949 30.769 0.00 0.00 0.00 3.06
4598 5301 7.967854 TCTTTCAATCAAATTAAGCCACGTATG 59.032 33.333 0.00 0.00 0.00 2.39
4599 5302 5.577835 TCAATCAAATTAAGCCACGTATGC 58.422 37.500 1.17 1.17 0.00 3.14
4600 5303 5.124617 TCAATCAAATTAAGCCACGTATGCA 59.875 36.000 11.32 0.00 0.00 3.96
4601 5304 4.614555 TCAAATTAAGCCACGTATGCAG 57.385 40.909 11.32 0.00 0.00 4.41
4602 5305 3.376859 TCAAATTAAGCCACGTATGCAGG 59.623 43.478 11.32 0.00 0.00 4.85
4603 5306 3.275617 AATTAAGCCACGTATGCAGGA 57.724 42.857 11.32 0.00 0.00 3.86
4604 5307 2.309528 TTAAGCCACGTATGCAGGAG 57.690 50.000 11.32 0.00 0.00 3.69
4605 5308 0.179084 TAAGCCACGTATGCAGGAGC 60.179 55.000 11.32 0.00 42.57 4.70
4615 5318 2.895680 GCAGGAGCACCGATGAGA 59.104 61.111 0.00 0.00 41.58 3.27
4616 5319 1.227205 GCAGGAGCACCGATGAGAG 60.227 63.158 0.00 0.00 41.58 3.20
4617 5320 1.227205 CAGGAGCACCGATGAGAGC 60.227 63.158 0.00 0.00 41.83 4.09
4618 5321 1.683707 AGGAGCACCGATGAGAGCA 60.684 57.895 0.00 0.00 41.83 4.26
4619 5322 1.047596 AGGAGCACCGATGAGAGCAT 61.048 55.000 0.00 0.00 41.83 3.79
4620 5323 0.879400 GGAGCACCGATGAGAGCATG 60.879 60.000 0.00 0.00 34.11 4.06
4621 5324 0.879400 GAGCACCGATGAGAGCATGG 60.879 60.000 0.00 0.00 34.11 3.66
4626 5329 3.302375 CGATGAGAGCATGGGAAGG 57.698 57.895 0.00 0.00 34.11 3.46
4627 5330 0.250209 CGATGAGAGCATGGGAAGGG 60.250 60.000 0.00 0.00 34.11 3.95
4628 5331 1.135094 GATGAGAGCATGGGAAGGGA 58.865 55.000 0.00 0.00 34.11 4.20
4629 5332 1.492176 GATGAGAGCATGGGAAGGGAA 59.508 52.381 0.00 0.00 34.11 3.97
4630 5333 0.620556 TGAGAGCATGGGAAGGGAAC 59.379 55.000 0.00 0.00 0.00 3.62
4631 5334 0.620556 GAGAGCATGGGAAGGGAACA 59.379 55.000 0.00 0.00 0.00 3.18
4632 5335 0.622665 AGAGCATGGGAAGGGAACAG 59.377 55.000 0.00 0.00 0.00 3.16
4633 5336 0.394899 GAGCATGGGAAGGGAACAGG 60.395 60.000 0.00 0.00 0.00 4.00
4634 5337 2.054453 GCATGGGAAGGGAACAGGC 61.054 63.158 0.00 0.00 34.71 4.85
4635 5338 1.383799 CATGGGAAGGGAACAGGCA 59.616 57.895 0.00 0.00 0.00 4.75
4636 5339 0.251742 CATGGGAAGGGAACAGGCAA 60.252 55.000 0.00 0.00 0.00 4.52
4637 5340 0.040204 ATGGGAAGGGAACAGGCAAG 59.960 55.000 0.00 0.00 0.00 4.01
4638 5341 1.360393 TGGGAAGGGAACAGGCAAGT 61.360 55.000 0.00 0.00 0.00 3.16
4639 5342 0.609406 GGGAAGGGAACAGGCAAGTC 60.609 60.000 0.00 0.00 0.00 3.01
4640 5343 0.402121 GGAAGGGAACAGGCAAGTCT 59.598 55.000 0.00 0.00 0.00 3.24
4641 5344 1.611936 GGAAGGGAACAGGCAAGTCTC 60.612 57.143 0.00 0.00 0.00 3.36
4642 5345 0.035458 AAGGGAACAGGCAAGTCTCG 59.965 55.000 0.00 0.00 0.00 4.04
4643 5346 1.122019 AGGGAACAGGCAAGTCTCGT 61.122 55.000 0.00 0.00 0.00 4.18
4644 5347 0.670854 GGGAACAGGCAAGTCTCGTC 60.671 60.000 0.00 0.00 0.00 4.20
4737 5454 1.024046 TGCACGCACCACATGGATAC 61.024 55.000 4.53 0.00 38.94 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 8.737168 ACTACATGAATAGCATAACATGTGTT 57.263 30.769 21.03 3.64 45.15 3.32
35 36 9.559732 TTTACAGCATGCAGTTATCAATATACT 57.440 29.630 21.46 0.00 42.53 2.12
36 37 9.817365 CTTTACAGCATGCAGTTATCAATATAC 57.183 33.333 21.46 0.00 42.53 1.47
37 38 9.559732 ACTTTACAGCATGCAGTTATCAATATA 57.440 29.630 21.46 0.00 42.53 0.86
99 102 7.288852 TGGGGTCAAAATTTTCATCTACTTGAA 59.711 33.333 0.00 0.00 33.89 2.69
116 119 7.394923 CACCTATAATTGTACTTTGGGGTCAAA 59.605 37.037 0.00 0.00 40.23 2.69
117 120 6.887545 CACCTATAATTGTACTTTGGGGTCAA 59.112 38.462 0.00 0.00 0.00 3.18
217 235 5.105392 TCCTGGCATGAAAAATGTAACCATC 60.105 40.000 0.00 0.00 0.00 3.51
270 289 1.415672 TTTGTGAACGGAGGGAGCCT 61.416 55.000 0.00 0.00 36.03 4.58
362 383 6.971726 TTCAATATGGACTACGTATGGACT 57.028 37.500 0.00 0.00 32.00 3.85
399 420 7.767198 TCCCTCCGTTCATAATTTAGTGTTAAG 59.233 37.037 0.00 0.00 0.00 1.85
403 424 5.189145 ACTCCCTCCGTTCATAATTTAGTGT 59.811 40.000 0.00 0.00 0.00 3.55
407 428 6.708949 GCATTACTCCCTCCGTTCATAATTTA 59.291 38.462 0.00 0.00 0.00 1.40
418 439 3.181487 CCAAAAATGCATTACTCCCTCCG 60.181 47.826 13.39 0.00 0.00 4.63
500 522 4.676018 GGCGTCTCTTGATCGTAGATTTAC 59.324 45.833 0.00 0.00 45.12 2.01
844 873 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
845 874 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
846 875 2.277126 ATTGGAGGGAGGGAGGGAGG 62.277 65.000 0.00 0.00 0.00 4.30
847 876 0.568192 TATTGGAGGGAGGGAGGGAG 59.432 60.000 0.00 0.00 0.00 4.30
1634 1700 1.220749 GGGACATCAACTAGCGGCA 59.779 57.895 1.45 0.00 0.00 5.69
1788 1855 2.615447 GTCGCACCATCATCATTCATGT 59.385 45.455 0.00 0.00 33.66 3.21
1819 1908 4.858692 CCATGCAAATACACTTGTAACTGC 59.141 41.667 14.65 14.65 40.06 4.40
1828 1917 0.819582 GCCAGCCATGCAAATACACT 59.180 50.000 0.00 0.00 0.00 3.55
1829 1918 0.526096 CGCCAGCCATGCAAATACAC 60.526 55.000 0.00 0.00 0.00 2.90
1830 1919 0.964860 ACGCCAGCCATGCAAATACA 60.965 50.000 0.00 0.00 0.00 2.29
2091 2186 9.872721 TGAATATTAATTCCGTACAACAGTACA 57.127 29.630 6.59 0.00 40.78 2.90
2146 2244 9.134055 ACTGTCCATACTAGAATTAAGTAGGAC 57.866 37.037 22.81 22.81 41.71 3.85
2147 2245 9.132923 CACTGTCCATACTAGAATTAAGTAGGA 57.867 37.037 11.64 11.26 34.05 2.94
2148 2246 8.915036 ACACTGTCCATACTAGAATTAAGTAGG 58.085 37.037 0.00 5.94 33.15 3.18
2173 2271 1.003233 GAGGAAGGCACCCTGACAC 60.003 63.158 2.29 0.00 32.13 3.67
2175 2273 1.298014 CTGAGGAAGGCACCCTGAC 59.702 63.158 2.29 0.00 32.13 3.51
2176 2274 0.768221 AACTGAGGAAGGCACCCTGA 60.768 55.000 2.29 0.00 32.13 3.86
2178 2276 1.492993 GGAACTGAGGAAGGCACCCT 61.493 60.000 0.00 0.00 36.57 4.34
2179 2277 1.002011 GGAACTGAGGAAGGCACCC 60.002 63.158 0.00 0.00 0.00 4.61
2180 2278 0.402121 AAGGAACTGAGGAAGGCACC 59.598 55.000 0.00 0.00 40.86 5.01
2230 2351 3.639094 GTGATACTCCTACTGTCCATGCT 59.361 47.826 0.00 0.00 0.00 3.79
2231 2352 3.551046 CGTGATACTCCTACTGTCCATGC 60.551 52.174 0.00 0.00 0.00 4.06
2232 2353 3.632604 ACGTGATACTCCTACTGTCCATG 59.367 47.826 0.00 0.00 0.00 3.66
2233 2354 3.899726 ACGTGATACTCCTACTGTCCAT 58.100 45.455 0.00 0.00 0.00 3.41
2234 2355 3.361281 ACGTGATACTCCTACTGTCCA 57.639 47.619 0.00 0.00 0.00 4.02
2237 2358 4.841422 ACACTACGTGATACTCCTACTGT 58.159 43.478 0.00 0.00 36.96 3.55
2238 2359 6.238320 GGTTACACTACGTGATACTCCTACTG 60.238 46.154 0.00 0.00 36.96 2.74
2239 2360 5.819901 GGTTACACTACGTGATACTCCTACT 59.180 44.000 0.00 0.00 36.96 2.57
2240 2361 5.586243 TGGTTACACTACGTGATACTCCTAC 59.414 44.000 0.00 0.00 36.96 3.18
2242 2363 4.592942 TGGTTACACTACGTGATACTCCT 58.407 43.478 0.00 0.00 36.96 3.69
2243 2364 4.970662 TGGTTACACTACGTGATACTCC 57.029 45.455 0.00 0.00 36.96 3.85
2245 2366 6.927416 TCAATTGGTTACACTACGTGATACT 58.073 36.000 5.42 0.00 36.96 2.12
2246 2367 7.330208 ACTTCAATTGGTTACACTACGTGATAC 59.670 37.037 5.42 0.00 36.96 2.24
2249 2370 5.603596 ACTTCAATTGGTTACACTACGTGA 58.396 37.500 5.42 0.00 36.96 4.35
2250 2371 5.917541 ACTTCAATTGGTTACACTACGTG 57.082 39.130 5.42 0.00 39.75 4.49
2251 2372 6.146673 GCTTACTTCAATTGGTTACACTACGT 59.853 38.462 5.42 0.00 0.00 3.57
2252 2373 6.146510 TGCTTACTTCAATTGGTTACACTACG 59.853 38.462 5.42 0.00 0.00 3.51
2253 2374 7.429636 TGCTTACTTCAATTGGTTACACTAC 57.570 36.000 5.42 0.00 0.00 2.73
2256 2377 8.587952 AATTTGCTTACTTCAATTGGTTACAC 57.412 30.769 5.42 0.00 0.00 2.90
2379 2978 8.151141 AGTGCAGTGATTTTATCATGATACTG 57.849 34.615 21.82 21.82 42.04 2.74
2628 3227 8.606040 TGGAAAAATCCAATCAAATCTGAAAC 57.394 30.769 0.00 0.00 36.74 2.78
2831 3430 3.603532 GCAATGATCTTCAGTGGTGAGA 58.396 45.455 7.02 0.00 42.16 3.27
3068 3668 1.035932 CCTCTTCTTGCATGCCAGGG 61.036 60.000 17.97 11.49 0.00 4.45
3119 3719 1.143183 ACGGCAACCTACGGCTATG 59.857 57.895 0.00 0.00 0.00 2.23
3140 3740 1.467920 AGGCAGCTATGTTTTCCAGC 58.532 50.000 0.00 0.00 35.49 4.85
3247 3847 5.122396 GGCAAATCTGTTATCGTCTCTTGTT 59.878 40.000 0.00 0.00 0.00 2.83
3299 3899 4.673375 AGCTTGGTGCAGCCCCTG 62.673 66.667 14.36 1.93 45.94 4.45
3895 4505 3.433615 CCAGTACACAGCAGCTAGAAAAC 59.566 47.826 0.00 0.00 0.00 2.43
3924 4534 2.905736 ACCAGGCAAAAATACCAATGCT 59.094 40.909 0.00 0.00 38.79 3.79
3978 4591 4.242475 TCGCACAATGTTCCTTAGTACAG 58.758 43.478 0.00 0.00 0.00 2.74
3979 4592 4.242475 CTCGCACAATGTTCCTTAGTACA 58.758 43.478 0.00 0.00 0.00 2.90
4075 4689 9.883142 TCAAAAATAAAAACTCACCAAACAGAT 57.117 25.926 0.00 0.00 0.00 2.90
4082 4696 9.308318 GTTAGCTTCAAAAATAAAAACTCACCA 57.692 29.630 0.00 0.00 0.00 4.17
4083 4697 8.761497 GGTTAGCTTCAAAAATAAAAACTCACC 58.239 33.333 0.00 0.00 0.00 4.02
4084 4698 9.529325 AGGTTAGCTTCAAAAATAAAAACTCAC 57.471 29.630 0.00 0.00 0.00 3.51
4091 4705 9.103861 CACCAAAAGGTTAGCTTCAAAAATAAA 57.896 29.630 0.00 0.00 0.00 1.40
4092 4706 8.478877 TCACCAAAAGGTTAGCTTCAAAAATAA 58.521 29.630 0.00 0.00 0.00 1.40
4094 4708 6.883744 TCACCAAAAGGTTAGCTTCAAAAAT 58.116 32.000 0.00 0.00 0.00 1.82
4095 4709 6.071051 ACTCACCAAAAGGTTAGCTTCAAAAA 60.071 34.615 0.00 0.00 0.00 1.94
4096 4710 5.420739 ACTCACCAAAAGGTTAGCTTCAAAA 59.579 36.000 0.00 0.00 0.00 2.44
4098 4712 4.532834 ACTCACCAAAAGGTTAGCTTCAA 58.467 39.130 0.00 0.00 0.00 2.69
4099 4713 4.164843 ACTCACCAAAAGGTTAGCTTCA 57.835 40.909 0.00 0.00 0.00 3.02
4100 4714 4.793028 GCAACTCACCAAAAGGTTAGCTTC 60.793 45.833 0.00 0.00 0.00 3.86
4101 4715 3.068165 GCAACTCACCAAAAGGTTAGCTT 59.932 43.478 0.00 0.00 0.00 3.74
4102 4716 2.623416 GCAACTCACCAAAAGGTTAGCT 59.377 45.455 0.00 0.00 0.00 3.32
4103 4717 2.360801 TGCAACTCACCAAAAGGTTAGC 59.639 45.455 0.00 0.00 0.00 3.09
4104 4718 4.549458 CATGCAACTCACCAAAAGGTTAG 58.451 43.478 0.00 0.00 0.00 2.34
4105 4719 3.243704 GCATGCAACTCACCAAAAGGTTA 60.244 43.478 14.21 0.00 0.00 2.85
4124 4750 0.800631 CACGACAGATTGTGCAGCAT 59.199 50.000 0.00 0.00 33.37 3.79
4132 4758 1.660052 CGTTTGTGGCACGACAGATTG 60.660 52.381 19.54 3.96 40.20 2.67
4158 4784 5.818336 TCTTGTTTCCACAGTTCGTTTCATA 59.182 36.000 0.00 0.00 33.22 2.15
4165 4791 1.264288 GGCTCTTGTTTCCACAGTTCG 59.736 52.381 0.00 0.00 33.22 3.95
4166 4792 2.297701 TGGCTCTTGTTTCCACAGTTC 58.702 47.619 0.00 0.00 33.22 3.01
4168 4794 2.233271 CATGGCTCTTGTTTCCACAGT 58.767 47.619 0.00 0.00 33.22 3.55
4169 4795 1.068055 GCATGGCTCTTGTTTCCACAG 60.068 52.381 0.00 0.00 33.22 3.66
4171 4797 0.244721 GGCATGGCTCTTGTTTCCAC 59.755 55.000 12.86 0.00 31.94 4.02
4193 4819 0.593128 GTGTCTTGCATCTGCCGTTT 59.407 50.000 0.00 0.00 41.18 3.60
4196 4822 1.028330 ATGGTGTCTTGCATCTGCCG 61.028 55.000 0.00 0.00 41.18 5.69
4276 4906 0.804933 GCTTGGCGTAGAACTACCGG 60.805 60.000 0.00 0.00 32.61 5.28
4388 5086 1.312815 ACAGAACTGTGGCTTCTTGC 58.687 50.000 6.67 0.00 43.11 4.01
4435 5138 2.280628 CCGGATCCAACTAGCTTGTTC 58.719 52.381 13.41 0.00 0.00 3.18
4438 5141 0.179000 AGCCGGATCCAACTAGCTTG 59.821 55.000 13.41 0.00 0.00 4.01
4439 5142 0.912486 AAGCCGGATCCAACTAGCTT 59.088 50.000 13.41 13.77 35.82 3.74
4440 5143 0.179000 CAAGCCGGATCCAACTAGCT 59.821 55.000 13.41 8.39 0.00 3.32
4441 5144 1.440145 GCAAGCCGGATCCAACTAGC 61.440 60.000 13.41 6.14 0.00 3.42
4442 5145 0.815615 GGCAAGCCGGATCCAACTAG 60.816 60.000 13.41 0.00 0.00 2.57
4443 5146 1.223487 GGCAAGCCGGATCCAACTA 59.777 57.895 13.41 0.00 0.00 2.24
4444 5147 2.044946 GGCAAGCCGGATCCAACT 60.045 61.111 13.41 5.01 0.00 3.16
4445 5148 2.044946 AGGCAAGCCGGATCCAAC 60.045 61.111 13.41 2.32 41.95 3.77
4446 5149 2.045045 CAGGCAAGCCGGATCCAA 60.045 61.111 13.41 0.00 41.95 3.53
4447 5150 4.802051 GCAGGCAAGCCGGATCCA 62.802 66.667 15.46 0.00 41.95 3.41
4448 5151 4.496336 AGCAGGCAAGCCGGATCC 62.496 66.667 15.46 0.00 41.95 3.36
4449 5152 2.899339 GAGCAGGCAAGCCGGATC 60.899 66.667 15.46 14.32 39.23 3.36
4450 5153 3.397613 GAGAGCAGGCAAGCCGGAT 62.398 63.158 15.46 8.74 41.95 4.18
4451 5154 4.087892 GAGAGCAGGCAAGCCGGA 62.088 66.667 15.46 0.00 41.95 5.14
4452 5155 3.694058 ATGAGAGCAGGCAAGCCGG 62.694 63.158 6.88 6.88 41.95 6.13
4453 5156 2.124819 ATGAGAGCAGGCAAGCCG 60.125 61.111 5.28 2.12 41.95 5.52
4454 5157 1.823041 GGATGAGAGCAGGCAAGCC 60.823 63.158 2.02 2.02 34.23 4.35
4455 5158 2.178890 CGGATGAGAGCAGGCAAGC 61.179 63.158 0.00 0.00 0.00 4.01
4456 5159 1.088340 CACGGATGAGAGCAGGCAAG 61.088 60.000 0.00 0.00 0.00 4.01
4457 5160 1.078918 CACGGATGAGAGCAGGCAA 60.079 57.895 0.00 0.00 0.00 4.52
4458 5161 2.580815 CACGGATGAGAGCAGGCA 59.419 61.111 0.00 0.00 0.00 4.75
4459 5162 2.894387 GCACGGATGAGAGCAGGC 60.894 66.667 0.00 0.00 0.00 4.85
4460 5163 1.227205 GAGCACGGATGAGAGCAGG 60.227 63.158 0.00 0.00 0.00 4.85
4461 5164 1.227205 GGAGCACGGATGAGAGCAG 60.227 63.158 0.00 0.00 0.00 4.24
4462 5165 2.725312 GGGAGCACGGATGAGAGCA 61.725 63.158 0.00 0.00 0.00 4.26
4463 5166 2.107953 GGGAGCACGGATGAGAGC 59.892 66.667 0.00 0.00 0.00 4.09
4464 5167 1.142748 GTGGGAGCACGGATGAGAG 59.857 63.158 0.00 0.00 0.00 3.20
4465 5168 0.904865 AAGTGGGAGCACGGATGAGA 60.905 55.000 0.00 0.00 0.00 3.27
4466 5169 0.460987 GAAGTGGGAGCACGGATGAG 60.461 60.000 0.00 0.00 0.00 2.90
4467 5170 1.191489 TGAAGTGGGAGCACGGATGA 61.191 55.000 0.00 0.00 0.00 2.92
4468 5171 0.107508 ATGAAGTGGGAGCACGGATG 60.108 55.000 0.00 0.00 0.00 3.51
4469 5172 0.179000 GATGAAGTGGGAGCACGGAT 59.821 55.000 0.00 0.00 0.00 4.18
4470 5173 1.596934 GATGAAGTGGGAGCACGGA 59.403 57.895 0.00 0.00 0.00 4.69
4471 5174 1.450312 GGATGAAGTGGGAGCACGG 60.450 63.158 0.00 0.00 0.00 4.94
4472 5175 0.824109 TAGGATGAAGTGGGAGCACG 59.176 55.000 0.00 0.00 0.00 5.34
4473 5176 1.471676 CGTAGGATGAAGTGGGAGCAC 60.472 57.143 0.00 0.00 0.00 4.40
4474 5177 0.824109 CGTAGGATGAAGTGGGAGCA 59.176 55.000 0.00 0.00 0.00 4.26
4475 5178 3.669354 CGTAGGATGAAGTGGGAGC 57.331 57.895 0.00 0.00 0.00 4.70
4489 5192 2.779506 AGGAAAAAGAACAGCCCGTAG 58.220 47.619 0.00 0.00 0.00 3.51
4490 5193 2.943036 AGGAAAAAGAACAGCCCGTA 57.057 45.000 0.00 0.00 0.00 4.02
4491 5194 2.067365 AAGGAAAAAGAACAGCCCGT 57.933 45.000 0.00 0.00 0.00 5.28
4492 5195 3.452755 AAAAGGAAAAAGAACAGCCCG 57.547 42.857 0.00 0.00 0.00 6.13
4493 5196 5.023533 AGAAAAAGGAAAAAGAACAGCCC 57.976 39.130 0.00 0.00 0.00 5.19
4494 5197 6.985188 AAAGAAAAAGGAAAAAGAACAGCC 57.015 33.333 0.00 0.00 0.00 4.85
4495 5198 8.256611 AGAAAAGAAAAAGGAAAAAGAACAGC 57.743 30.769 0.00 0.00 0.00 4.40
4511 5214 9.853177 GGGGAGATGATTAGATTAGAAAAGAAA 57.147 33.333 0.00 0.00 0.00 2.52
4512 5215 8.440771 GGGGGAGATGATTAGATTAGAAAAGAA 58.559 37.037 0.00 0.00 0.00 2.52
4513 5216 7.978925 GGGGGAGATGATTAGATTAGAAAAGA 58.021 38.462 0.00 0.00 0.00 2.52
4539 5242 1.758862 GCCCCATTCCCTGAAAATCAG 59.241 52.381 0.32 0.32 43.91 2.90
4540 5243 1.622173 GGCCCCATTCCCTGAAAATCA 60.622 52.381 0.00 0.00 0.00 2.57
4541 5244 1.123077 GGCCCCATTCCCTGAAAATC 58.877 55.000 0.00 0.00 0.00 2.17
4542 5245 0.687427 CGGCCCCATTCCCTGAAAAT 60.687 55.000 0.00 0.00 0.00 1.82
4543 5246 1.304879 CGGCCCCATTCCCTGAAAA 60.305 57.895 0.00 0.00 0.00 2.29
4544 5247 2.358619 CGGCCCCATTCCCTGAAA 59.641 61.111 0.00 0.00 0.00 2.69
4545 5248 3.738481 CCGGCCCCATTCCCTGAA 61.738 66.667 0.00 0.00 0.00 3.02
4558 5261 1.822371 TGAAAGAAAATAAGGCCCGGC 59.178 47.619 0.00 0.00 0.00 6.13
4559 5262 4.159506 TGATTGAAAGAAAATAAGGCCCGG 59.840 41.667 0.00 0.00 0.00 5.73
4560 5263 5.323371 TGATTGAAAGAAAATAAGGCCCG 57.677 39.130 0.00 0.00 0.00 6.13
4561 5264 8.565896 AATTTGATTGAAAGAAAATAAGGCCC 57.434 30.769 0.00 0.00 0.00 5.80
4568 5271 8.711457 CGTGGCTTAATTTGATTGAAAGAAAAT 58.289 29.630 0.00 0.00 0.00 1.82
4569 5272 7.708752 ACGTGGCTTAATTTGATTGAAAGAAAA 59.291 29.630 0.00 0.00 0.00 2.29
4570 5273 7.206687 ACGTGGCTTAATTTGATTGAAAGAAA 58.793 30.769 0.00 0.00 0.00 2.52
4571 5274 6.744112 ACGTGGCTTAATTTGATTGAAAGAA 58.256 32.000 0.00 0.00 0.00 2.52
4572 5275 6.325919 ACGTGGCTTAATTTGATTGAAAGA 57.674 33.333 0.00 0.00 0.00 2.52
4573 5276 7.253750 GCATACGTGGCTTAATTTGATTGAAAG 60.254 37.037 0.00 0.00 0.00 2.62
4574 5277 6.529829 GCATACGTGGCTTAATTTGATTGAAA 59.470 34.615 0.00 0.00 0.00 2.69
4575 5278 6.033341 GCATACGTGGCTTAATTTGATTGAA 58.967 36.000 0.00 0.00 0.00 2.69
4576 5279 5.124617 TGCATACGTGGCTTAATTTGATTGA 59.875 36.000 13.98 0.00 0.00 2.57
4577 5280 5.339177 TGCATACGTGGCTTAATTTGATTG 58.661 37.500 13.98 0.00 0.00 2.67
4578 5281 5.450412 CCTGCATACGTGGCTTAATTTGATT 60.450 40.000 13.98 0.00 0.00 2.57
4579 5282 4.036734 CCTGCATACGTGGCTTAATTTGAT 59.963 41.667 13.98 0.00 0.00 2.57
4580 5283 3.376859 CCTGCATACGTGGCTTAATTTGA 59.623 43.478 13.98 0.00 0.00 2.69
4581 5284 3.376859 TCCTGCATACGTGGCTTAATTTG 59.623 43.478 13.98 0.00 0.00 2.32
4582 5285 3.616219 TCCTGCATACGTGGCTTAATTT 58.384 40.909 13.98 0.00 0.00 1.82
4583 5286 3.206150 CTCCTGCATACGTGGCTTAATT 58.794 45.455 13.98 0.00 0.00 1.40
4584 5287 2.838736 CTCCTGCATACGTGGCTTAAT 58.161 47.619 13.98 0.00 0.00 1.40
4585 5288 1.742411 GCTCCTGCATACGTGGCTTAA 60.742 52.381 13.98 0.78 39.41 1.85
4586 5289 0.179084 GCTCCTGCATACGTGGCTTA 60.179 55.000 13.98 1.05 39.41 3.09
4587 5290 1.450312 GCTCCTGCATACGTGGCTT 60.450 57.895 13.98 0.00 39.41 4.35
4588 5291 2.187946 GCTCCTGCATACGTGGCT 59.812 61.111 13.98 0.00 39.41 4.75
4589 5292 2.125147 TGCTCCTGCATACGTGGC 60.125 61.111 0.00 2.08 45.31 5.01
4598 5301 1.227205 CTCTCATCGGTGCTCCTGC 60.227 63.158 2.85 0.00 40.20 4.85
4599 5302 1.227205 GCTCTCATCGGTGCTCCTG 60.227 63.158 2.85 0.00 0.00 3.86
4600 5303 1.047596 ATGCTCTCATCGGTGCTCCT 61.048 55.000 2.85 0.00 0.00 3.69
4601 5304 0.879400 CATGCTCTCATCGGTGCTCC 60.879 60.000 0.00 0.00 0.00 4.70
4602 5305 0.879400 CCATGCTCTCATCGGTGCTC 60.879 60.000 0.00 0.00 0.00 4.26
4603 5306 1.145598 CCATGCTCTCATCGGTGCT 59.854 57.895 0.00 0.00 0.00 4.40
4604 5307 1.890979 CCCATGCTCTCATCGGTGC 60.891 63.158 0.00 0.00 0.00 5.01
4605 5308 0.178767 TTCCCATGCTCTCATCGGTG 59.821 55.000 0.00 0.00 33.36 4.94
4606 5309 0.467384 CTTCCCATGCTCTCATCGGT 59.533 55.000 0.00 0.00 33.36 4.69
4607 5310 0.250209 CCTTCCCATGCTCTCATCGG 60.250 60.000 0.00 0.00 32.94 4.18
4608 5311 0.250209 CCCTTCCCATGCTCTCATCG 60.250 60.000 0.00 0.00 0.00 3.84
4609 5312 1.135094 TCCCTTCCCATGCTCTCATC 58.865 55.000 0.00 0.00 0.00 2.92
4610 5313 1.213926 GTTCCCTTCCCATGCTCTCAT 59.786 52.381 0.00 0.00 0.00 2.90
4611 5314 0.620556 GTTCCCTTCCCATGCTCTCA 59.379 55.000 0.00 0.00 0.00 3.27
4612 5315 0.620556 TGTTCCCTTCCCATGCTCTC 59.379 55.000 0.00 0.00 0.00 3.20
4613 5316 0.622665 CTGTTCCCTTCCCATGCTCT 59.377 55.000 0.00 0.00 0.00 4.09
4614 5317 0.394899 CCTGTTCCCTTCCCATGCTC 60.395 60.000 0.00 0.00 0.00 4.26
4615 5318 1.693640 CCTGTTCCCTTCCCATGCT 59.306 57.895 0.00 0.00 0.00 3.79
4616 5319 2.054453 GCCTGTTCCCTTCCCATGC 61.054 63.158 0.00 0.00 0.00 4.06
4617 5320 0.251742 TTGCCTGTTCCCTTCCCATG 60.252 55.000 0.00 0.00 0.00 3.66
4618 5321 0.040204 CTTGCCTGTTCCCTTCCCAT 59.960 55.000 0.00 0.00 0.00 4.00
4619 5322 1.360393 ACTTGCCTGTTCCCTTCCCA 61.360 55.000 0.00 0.00 0.00 4.37
4620 5323 0.609406 GACTTGCCTGTTCCCTTCCC 60.609 60.000 0.00 0.00 0.00 3.97
4621 5324 0.402121 AGACTTGCCTGTTCCCTTCC 59.598 55.000 0.00 0.00 0.00 3.46
4622 5325 1.814793 GAGACTTGCCTGTTCCCTTC 58.185 55.000 0.00 0.00 0.00 3.46
4623 5326 0.035458 CGAGACTTGCCTGTTCCCTT 59.965 55.000 0.00 0.00 0.00 3.95
4624 5327 1.122019 ACGAGACTTGCCTGTTCCCT 61.122 55.000 0.00 0.00 0.00 4.20
4625 5328 0.670854 GACGAGACTTGCCTGTTCCC 60.671 60.000 0.00 0.00 0.00 3.97
4626 5329 0.670854 GGACGAGACTTGCCTGTTCC 60.671 60.000 0.00 0.00 0.00 3.62
4627 5330 0.033504 TGGACGAGACTTGCCTGTTC 59.966 55.000 0.00 0.00 0.00 3.18
4628 5331 0.468226 TTGGACGAGACTTGCCTGTT 59.532 50.000 0.00 0.00 0.00 3.16
4629 5332 0.034059 CTTGGACGAGACTTGCCTGT 59.966 55.000 0.00 0.00 0.00 4.00
4630 5333 1.294659 GCTTGGACGAGACTTGCCTG 61.295 60.000 0.00 1.12 0.00 4.85
4631 5334 1.004440 GCTTGGACGAGACTTGCCT 60.004 57.895 0.00 0.00 0.00 4.75
4632 5335 0.246635 TAGCTTGGACGAGACTTGCC 59.753 55.000 0.00 0.00 0.00 4.52
4633 5336 1.067495 ACTAGCTTGGACGAGACTTGC 60.067 52.381 0.00 0.00 0.00 4.01
4634 5337 3.305398 AACTAGCTTGGACGAGACTTG 57.695 47.619 0.00 0.00 0.00 3.16
4635 5338 3.654414 CAAACTAGCTTGGACGAGACTT 58.346 45.455 0.00 0.00 0.00 3.01
4636 5339 3.305398 CAAACTAGCTTGGACGAGACT 57.695 47.619 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.