Multiple sequence alignment - TraesCS4D01G181000

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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 TraesCS4D01G181000 chr4D 100.000 5747 0 0 1 5747 315259553 315265299 0.000000e+00 10613
1 TraesCS4D01G181000 chr4D 91.736 121 8 2 5169 5289 509340273 509340391 3.560000e-37 167
2 TraesCS4D01G181000 chr4A 96.679 2861 60 9 2331 5169 159508754 159505907 0.000000e+00 4724
3 TraesCS4D01G181000 chr4A 93.477 1303 61 14 841 2134 159510069 159508782 0.000000e+00 1914
4 TraesCS4D01G181000 chr4A 92.557 833 50 11 10 835 159513443 159512616 0.000000e+00 1184
5 TraesCS4D01G181000 chr4A 96.242 479 12 2 5272 5747 159505903 159505428 0.000000e+00 780
6 TraesCS4D01G181000 chr4A 78.807 486 81 18 31 501 599921148 599920670 2.010000e-79 307
7 TraesCS4D01G181000 chr4B 96.571 2566 67 7 2331 4877 393157256 393159819 0.000000e+00 4231
8 TraesCS4D01G181000 chr4B 96.667 930 23 6 818 1740 393155855 393156783 0.000000e+00 1539
9 TraesCS4D01G181000 chr4B 89.563 824 68 13 15 827 393155019 393155835 0.000000e+00 1029
10 TraesCS4D01G181000 chr4B 96.218 476 12 2 5272 5747 393160280 393160749 0.000000e+00 774
11 TraesCS4D01G181000 chr4B 97.241 290 6 1 4882 5169 393159987 393160276 1.860000e-134 490
12 TraesCS4D01G181000 chr4B 86.788 386 48 2 1760 2144 393156855 393157238 1.480000e-115 427
13 TraesCS4D01G181000 chr6D 81.447 857 113 37 7 831 264451263 264450421 0.000000e+00 660
14 TraesCS4D01G181000 chr2D 82.231 529 64 16 294 814 267707167 267707673 4.110000e-116 429
15 TraesCS4D01G181000 chr2D 80.292 274 45 7 278 545 8468668 8468398 1.260000e-46 198
16 TraesCS4D01G181000 chr7D 74.379 765 137 37 83 828 530342266 530341542 7.340000e-69 272
17 TraesCS4D01G181000 chr7D 96.296 108 4 0 5169 5276 174803252 174803145 1.650000e-40 178
18 TraesCS4D01G181000 chr7D 90.769 130 10 2 5162 5290 545095913 545096041 7.660000e-39 172
19 TraesCS4D01G181000 chr1D 83.704 270 33 10 289 552 6233704 6233440 1.600000e-60 244
20 TraesCS4D01G181000 chr2A 81.298 262 42 6 263 519 7493679 7493420 7.550000e-49 206
21 TraesCS4D01G181000 chr7B 98.148 108 2 0 5169 5276 555654403 555654510 7.600000e-44 189
22 TraesCS4D01G181000 chr7B 95.192 104 5 0 5169 5272 27494498 27494395 1.280000e-36 165
23 TraesCS4D01G181000 chr3B 94.958 119 4 2 5161 5278 214560154 214560271 9.830000e-43 185
24 TraesCS4D01G181000 chr3B 95.455 110 4 1 5163 5272 805258216 805258324 2.130000e-39 174
25 TraesCS4D01G181000 chr5B 95.455 110 5 0 5169 5278 528584710 528584601 5.920000e-40 176
26 TraesCS4D01G181000 chr3D 92.437 119 7 2 5169 5286 551006276 551006393 9.900000e-38 169
27 TraesCS4D01G181000 chr5A 84.848 165 15 8 2150 2310 491296724 491296882 2.140000e-34 158


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 TraesCS4D01G181000 chr4D 315259553 315265299 5746 False 10613.0 10613 100.000000 1 5747 1 chr4D.!!$F1 5746
1 TraesCS4D01G181000 chr4A 159505428 159513443 8015 True 2150.5 4724 94.738750 10 5747 4 chr4A.!!$R2 5737
2 TraesCS4D01G181000 chr4B 393155019 393160749 5730 False 1415.0 4231 93.841333 15 5747 6 chr4B.!!$F1 5732
3 TraesCS4D01G181000 chr6D 264450421 264451263 842 True 660.0 660 81.447000 7 831 1 chr6D.!!$R1 824
4 TraesCS4D01G181000 chr2D 267707167 267707673 506 False 429.0 429 82.231000 294 814 1 chr2D.!!$F1 520
5 TraesCS4D01G181000 chr7D 530341542 530342266 724 True 272.0 272 74.379000 83 828 1 chr7D.!!$R2 745

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
896 3505 3.702048 CCGGCGGGAGGAAGAACA 61.702 66.667 20.56 0.0 34.06 3.18 F
2118 4794 0.584396 TAAGCGCAAACGACCAGTTG 59.416 50.000 11.47 0.0 43.37 3.16 F
2179 4855 0.034477 CGGGCAAACAGTAGGGGAAT 60.034 55.000 0.00 0.0 0.00 3.01 F
2265 4941 0.105246 AGATGGCCCCCAACAAAACA 60.105 50.000 0.00 0.0 36.95 2.83 F
2267 4943 0.105246 ATGGCCCCCAACAAAACAGA 60.105 50.000 0.00 0.0 36.95 3.41 F
2268 4944 0.325671 TGGCCCCCAACAAAACAGAA 60.326 50.000 0.00 0.0 0.00 3.02 F
2269 4945 0.392706 GGCCCCCAACAAAACAGAAG 59.607 55.000 0.00 0.0 0.00 2.85 F
4130 6818 0.463295 GCCGGGTTAGCCTTTCTACC 60.463 60.000 2.18 0.0 34.45 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 4836 0.034477 ATTCCCCTACTGTTTGCCCG 60.034 55.000 0.00 0.00 0.00 6.13 R
3754 6438 3.325135 CCTCCACAAACTTCAGAGGTAGT 59.675 47.826 0.00 0.00 39.45 2.73 R
4130 6818 0.386478 GCGTTGGCTCAAGCTTCTTG 60.386 55.000 0.00 0.37 41.70 3.02 R
4184 6872 2.223180 GCCCGCATTACTTACCTTTTCG 60.223 50.000 0.00 0.00 0.00 3.46 R
4232 6920 4.631377 GCATAGCATGTCAGTTTGTCTGTA 59.369 41.667 0.00 0.00 43.97 2.74 R
4273 6969 1.242076 GCCTGAATATCTGCGCCATT 58.758 50.000 4.18 0.00 0.00 3.16 R
4385 7081 1.333115 CGTAAACTGCATCACGACGA 58.667 50.000 0.00 0.00 36.53 4.20 R
5255 8127 0.033796 ATGTACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55 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
73 74 8.534778 CAACTTAAGTCAGAGAAAACAAAATGC 58.465 33.333 8.95 0.00 0.00 3.56
74 75 7.203218 ACTTAAGTCAGAGAAAACAAAATGCC 58.797 34.615 1.12 0.00 0.00 4.40
137 140 3.975168 TCCTGTAGTCCACCTTTAAGC 57.025 47.619 0.00 0.00 0.00 3.09
431 442 7.556275 CCTACTTAGGGTGCAATCTTAATCAAA 59.444 37.037 0.00 0.00 39.86 2.69
508 522 9.088987 ACACCTCAACAAAACCATATTAAAGAT 57.911 29.630 0.00 0.00 0.00 2.40
642 704 8.034215 CACCTTTGGATTAAGCATATTCAAACA 58.966 33.333 0.00 0.00 0.00 2.83
648 710 7.492020 TGGATTAAGCATATTCAAACACATTGC 59.508 33.333 0.00 0.00 38.98 3.56
774 837 4.276926 GGTCTTCAGTCATGATTATTGGGC 59.723 45.833 0.00 0.00 34.73 5.36
864 3473 8.499403 AGAGAGATAATAAACAAAACTGCCTC 57.501 34.615 0.00 0.00 0.00 4.70
896 3505 3.702048 CCGGCGGGAGGAAGAACA 61.702 66.667 20.56 0.00 34.06 3.18
1155 3764 1.344942 CGTACGTGCTGAGCAAGGAC 61.345 60.000 23.18 23.18 45.71 3.85
1386 3996 4.320567 GCTCAACTGCATATCGCTAGTAGA 60.321 45.833 0.00 0.00 43.06 2.59
1387 3997 5.763088 CTCAACTGCATATCGCTAGTAGAA 58.237 41.667 0.00 0.00 43.06 2.10
1421 4033 4.049546 AGGTCGCGTGTATTGCTTATAA 57.950 40.909 5.77 0.00 0.00 0.98
1806 4480 3.138283 TGAAATTCCTGAGTTGTGGGACT 59.862 43.478 0.00 0.00 0.00 3.85
1825 4500 6.126911 TGGGACTTTGGAGCAACTTAAAATTT 60.127 34.615 0.00 0.00 0.00 1.82
1852 4527 6.540189 CCAATTCGGTTAATTCTGATCTGACT 59.460 38.462 1.16 0.00 35.54 3.41
1865 4540 7.709149 TCTGATCTGACTCAATACTTTCAGA 57.291 36.000 2.80 2.80 46.43 3.27
1877 4552 8.539770 TCAATACTTTCAGAAACTGACTGATC 57.460 34.615 0.74 0.00 40.46 2.92
1879 4554 4.950050 ACTTTCAGAAACTGACTGATCGT 58.050 39.130 0.74 0.00 40.46 3.73
1883 4558 2.802247 CAGAAACTGACTGATCGTTGCA 59.198 45.455 0.00 0.00 37.54 4.08
1889 4564 3.187227 ACTGACTGATCGTTGCATGTTTC 59.813 43.478 0.00 0.00 0.00 2.78
1896 4571 5.927030 TGATCGTTGCATGTTTCTCTAAAC 58.073 37.500 0.00 0.00 44.40 2.01
1902 4577 6.588756 CGTTGCATGTTTCTCTAAACTAGGTA 59.411 38.462 0.00 0.00 44.44 3.08
1910 4585 5.126699 TCTCTAAACTAGGTACCCTCCAG 57.873 47.826 8.74 3.57 34.61 3.86
1943 4618 8.750515 TGTGATATTGAATTAAGCAGATCCAA 57.249 30.769 0.00 0.00 0.00 3.53
1945 4620 8.844244 GTGATATTGAATTAAGCAGATCCAACT 58.156 33.333 0.00 0.00 0.00 3.16
1978 4653 7.844009 AGATTACCTTATTTCGGTGAACAGTA 58.156 34.615 0.00 0.00 35.98 2.74
1979 4654 8.316214 AGATTACCTTATTTCGGTGAACAGTAA 58.684 33.333 0.00 0.00 35.98 2.24
2027 4702 1.333308 CACACGGACACAAAATGCAGA 59.667 47.619 0.00 0.00 0.00 4.26
2029 4704 2.622942 ACACGGACACAAAATGCAGATT 59.377 40.909 0.00 0.00 0.00 2.40
2070 4746 1.593196 TTCTTGAACACGCCTGGAAG 58.407 50.000 0.00 0.00 0.00 3.46
2089 4765 4.857037 GGAAGCGCGTCTTTGAATTAAAAT 59.143 37.500 22.38 0.00 34.56 1.82
2091 4767 5.041951 AGCGCGTCTTTGAATTAAAATGA 57.958 34.783 8.43 0.00 0.00 2.57
2118 4794 0.584396 TAAGCGCAAACGACCAGTTG 59.416 50.000 11.47 0.00 43.37 3.16
2134 4810 6.203530 CGACCAGTTGAATATGAGCATTGTAT 59.796 38.462 0.00 0.00 0.00 2.29
2135 4811 7.502120 ACCAGTTGAATATGAGCATTGTATC 57.498 36.000 0.00 0.00 0.00 2.24
2138 4814 7.176165 CCAGTTGAATATGAGCATTGTATCCAT 59.824 37.037 0.00 0.00 0.00 3.41
2157 4833 6.363167 TCCATCAATGCTGGATTTTCTTTT 57.637 33.333 1.08 0.00 37.87 2.27
2158 4834 6.771573 TCCATCAATGCTGGATTTTCTTTTT 58.228 32.000 1.08 0.00 37.87 1.94
2159 4835 7.905265 TCCATCAATGCTGGATTTTCTTTTTA 58.095 30.769 1.08 0.00 37.87 1.52
2160 4836 7.818930 TCCATCAATGCTGGATTTTCTTTTTAC 59.181 33.333 1.08 0.00 37.87 2.01
2161 4837 7.201461 CCATCAATGCTGGATTTTCTTTTTACG 60.201 37.037 0.00 0.00 35.70 3.18
2162 4838 6.155827 TCAATGCTGGATTTTCTTTTTACGG 58.844 36.000 0.00 0.00 0.00 4.02
2163 4839 4.513198 TGCTGGATTTTCTTTTTACGGG 57.487 40.909 0.00 0.00 0.00 5.28
2164 4840 3.250744 GCTGGATTTTCTTTTTACGGGC 58.749 45.455 0.00 0.00 0.00 6.13
2165 4841 3.305744 GCTGGATTTTCTTTTTACGGGCA 60.306 43.478 0.00 0.00 0.00 5.36
2166 4842 4.797933 GCTGGATTTTCTTTTTACGGGCAA 60.798 41.667 0.00 0.00 0.00 4.52
2167 4843 5.277857 TGGATTTTCTTTTTACGGGCAAA 57.722 34.783 0.00 0.00 0.00 3.68
2168 4844 5.051153 TGGATTTTCTTTTTACGGGCAAAC 58.949 37.500 0.00 0.00 0.00 2.93
2169 4845 5.051153 GGATTTTCTTTTTACGGGCAAACA 58.949 37.500 0.00 0.00 0.00 2.83
2170 4846 5.176774 GGATTTTCTTTTTACGGGCAAACAG 59.823 40.000 0.00 0.00 0.00 3.16
2171 4847 4.722361 TTTCTTTTTACGGGCAAACAGT 57.278 36.364 0.00 0.00 0.00 3.55
2172 4848 5.831702 TTTCTTTTTACGGGCAAACAGTA 57.168 34.783 0.00 0.00 0.00 2.74
2173 4849 5.427036 TTCTTTTTACGGGCAAACAGTAG 57.573 39.130 0.00 0.00 31.42 2.57
2174 4850 3.816523 TCTTTTTACGGGCAAACAGTAGG 59.183 43.478 0.00 0.00 31.42 3.18
2175 4851 2.188062 TTTACGGGCAAACAGTAGGG 57.812 50.000 0.00 0.00 31.42 3.53
2176 4852 0.325602 TTACGGGCAAACAGTAGGGG 59.674 55.000 0.00 0.00 31.42 4.79
2177 4853 0.544833 TACGGGCAAACAGTAGGGGA 60.545 55.000 0.00 0.00 0.00 4.81
2178 4854 1.377229 CGGGCAAACAGTAGGGGAA 59.623 57.895 0.00 0.00 0.00 3.97
2179 4855 0.034477 CGGGCAAACAGTAGGGGAAT 60.034 55.000 0.00 0.00 0.00 3.01
2180 4856 1.615919 CGGGCAAACAGTAGGGGAATT 60.616 52.381 0.00 0.00 0.00 2.17
2181 4857 2.100197 GGGCAAACAGTAGGGGAATTC 58.900 52.381 0.00 0.00 0.00 2.17
2182 4858 2.100197 GGCAAACAGTAGGGGAATTCC 58.900 52.381 16.74 16.74 0.00 3.01
2241 4917 8.533569 AAAGGAGTTTACATATTTACATGGGG 57.466 34.615 0.00 0.00 0.00 4.96
2242 4918 6.610830 AGGAGTTTACATATTTACATGGGGG 58.389 40.000 0.00 0.00 0.00 5.40
2243 4919 6.161526 AGGAGTTTACATATTTACATGGGGGT 59.838 38.462 0.00 0.00 0.00 4.95
2244 4920 6.837048 GGAGTTTACATATTTACATGGGGGTT 59.163 38.462 0.00 0.00 0.00 4.11
2245 4921 7.201875 GGAGTTTACATATTTACATGGGGGTTG 60.202 40.741 0.00 0.00 0.00 3.77
2246 4922 7.415086 AGTTTACATATTTACATGGGGGTTGA 58.585 34.615 0.00 0.00 0.00 3.18
2247 4923 7.559897 AGTTTACATATTTACATGGGGGTTGAG 59.440 37.037 0.00 0.00 0.00 3.02
2248 4924 5.725551 ACATATTTACATGGGGGTTGAGA 57.274 39.130 0.00 0.00 0.00 3.27
2249 4925 6.279813 ACATATTTACATGGGGGTTGAGAT 57.720 37.500 0.00 0.00 0.00 2.75
2250 4926 6.070656 ACATATTTACATGGGGGTTGAGATG 58.929 40.000 0.00 0.00 0.00 2.90
2251 4927 3.380471 TTTACATGGGGGTTGAGATGG 57.620 47.619 0.00 0.00 0.00 3.51
2252 4928 0.550914 TACATGGGGGTTGAGATGGC 59.449 55.000 0.00 0.00 0.00 4.40
2253 4929 1.456331 CATGGGGGTTGAGATGGCC 60.456 63.158 0.00 0.00 0.00 5.36
2254 4930 2.704424 ATGGGGGTTGAGATGGCCC 61.704 63.158 0.00 0.00 41.62 5.80
2257 4933 3.346734 GGGTTGAGATGGCCCCCA 61.347 66.667 0.00 0.00 38.19 4.96
2258 4934 2.770130 GGTTGAGATGGCCCCCAA 59.230 61.111 0.00 0.00 36.95 4.12
2259 4935 1.682344 GGTTGAGATGGCCCCCAAC 60.682 63.158 0.00 9.07 36.95 3.77
2260 4936 1.076549 GTTGAGATGGCCCCCAACA 59.923 57.895 16.64 3.11 36.95 3.33
2261 4937 0.541764 GTTGAGATGGCCCCCAACAA 60.542 55.000 16.64 8.06 36.95 2.83
2262 4938 0.189574 TTGAGATGGCCCCCAACAAA 59.810 50.000 0.00 0.00 36.95 2.83
2263 4939 0.189574 TGAGATGGCCCCCAACAAAA 59.810 50.000 0.00 0.00 36.95 2.44
2264 4940 0.608130 GAGATGGCCCCCAACAAAAC 59.392 55.000 0.00 0.00 36.95 2.43
2265 4941 0.105246 AGATGGCCCCCAACAAAACA 60.105 50.000 0.00 0.00 36.95 2.83
2266 4942 0.321346 GATGGCCCCCAACAAAACAG 59.679 55.000 0.00 0.00 36.95 3.16
2267 4943 0.105246 ATGGCCCCCAACAAAACAGA 60.105 50.000 0.00 0.00 36.95 3.41
2268 4944 0.325671 TGGCCCCCAACAAAACAGAA 60.326 50.000 0.00 0.00 0.00 3.02
2269 4945 0.392706 GGCCCCCAACAAAACAGAAG 59.607 55.000 0.00 0.00 0.00 2.85
2270 4946 1.408969 GCCCCCAACAAAACAGAAGA 58.591 50.000 0.00 0.00 0.00 2.87
2271 4947 1.970640 GCCCCCAACAAAACAGAAGAT 59.029 47.619 0.00 0.00 0.00 2.40
2272 4948 3.161866 GCCCCCAACAAAACAGAAGATA 58.838 45.455 0.00 0.00 0.00 1.98
2273 4949 3.576550 GCCCCCAACAAAACAGAAGATAA 59.423 43.478 0.00 0.00 0.00 1.75
2274 4950 4.039852 GCCCCCAACAAAACAGAAGATAAA 59.960 41.667 0.00 0.00 0.00 1.40
2275 4951 5.783111 CCCCCAACAAAACAGAAGATAAAG 58.217 41.667 0.00 0.00 0.00 1.85
2276 4952 5.538433 CCCCCAACAAAACAGAAGATAAAGA 59.462 40.000 0.00 0.00 0.00 2.52
2277 4953 6.041523 CCCCCAACAAAACAGAAGATAAAGAA 59.958 38.462 0.00 0.00 0.00 2.52
2278 4954 7.418483 CCCCCAACAAAACAGAAGATAAAGAAA 60.418 37.037 0.00 0.00 0.00 2.52
2279 4955 7.653311 CCCCAACAAAACAGAAGATAAAGAAAG 59.347 37.037 0.00 0.00 0.00 2.62
2280 4956 8.413229 CCCAACAAAACAGAAGATAAAGAAAGA 58.587 33.333 0.00 0.00 0.00 2.52
2281 4957 9.455847 CCAACAAAACAGAAGATAAAGAAAGAG 57.544 33.333 0.00 0.00 0.00 2.85
2282 4958 9.455847 CAACAAAACAGAAGATAAAGAAAGAGG 57.544 33.333 0.00 0.00 0.00 3.69
2283 4959 7.652727 ACAAAACAGAAGATAAAGAAAGAGGC 58.347 34.615 0.00 0.00 0.00 4.70
2284 4960 7.503902 ACAAAACAGAAGATAAAGAAAGAGGCT 59.496 33.333 0.00 0.00 0.00 4.58
2285 4961 9.003658 CAAAACAGAAGATAAAGAAAGAGGCTA 57.996 33.333 0.00 0.00 0.00 3.93
2286 4962 9.574516 AAAACAGAAGATAAAGAAAGAGGCTAA 57.425 29.630 0.00 0.00 0.00 3.09
2287 4963 8.554835 AACAGAAGATAAAGAAAGAGGCTAAC 57.445 34.615 0.00 0.00 0.00 2.34
2288 4964 7.912719 ACAGAAGATAAAGAAAGAGGCTAACT 58.087 34.615 0.00 0.00 0.00 2.24
2289 4965 9.036980 ACAGAAGATAAAGAAAGAGGCTAACTA 57.963 33.333 0.00 0.00 0.00 2.24
2290 4966 9.877178 CAGAAGATAAAGAAAGAGGCTAACTAA 57.123 33.333 0.00 0.00 0.00 2.24
2344 5020 2.814805 ATAGGTGCTGGATTTGCAGT 57.185 45.000 0.97 0.00 41.41 4.40
2786 5462 2.586425 CAAGACCTTGCTTGGGAAAGA 58.414 47.619 0.00 0.00 41.15 2.52
2907 5583 9.751542 CTAATCGTTGAATAACTTCTCCTGTAT 57.248 33.333 0.00 0.00 34.60 2.29
3025 5701 2.030007 GCAACAGCAGCCATTGTTCTTA 60.030 45.455 7.81 0.00 35.46 2.10
3149 5825 9.998106 GGATGGCTTTCTTATCAAGTAGTTATA 57.002 33.333 0.00 0.00 0.00 0.98
3216 5892 8.791675 TGTGTGACTGCTAATGAATTTATGAAA 58.208 29.630 0.00 0.00 0.00 2.69
3629 6306 3.992636 GCTGCATGAGCTGTCTTTC 57.007 52.632 0.00 0.00 45.21 2.62
3705 6383 5.004922 ACTAGCTGCTCACTATTTCACTC 57.995 43.478 4.91 0.00 0.00 3.51
3754 6438 3.544684 TGAAGAGCTGCTTGACAAAGAA 58.455 40.909 2.53 0.00 36.83 2.52
3853 6537 1.380380 AGCCCAGCTTGGTATTGGC 60.380 57.895 5.61 0.00 33.89 4.52
3961 6645 3.181510 GCCAAATTAGTCATGACCGTGTC 60.182 47.826 22.21 0.13 0.00 3.67
4013 6697 3.827634 CCCTCAAGGTAATGCCGC 58.172 61.111 0.00 0.00 43.70 6.53
4026 6714 3.715628 AATGCCGCCATCTTGTAAATC 57.284 42.857 0.00 0.00 0.00 2.17
4030 6718 2.358898 GCCGCCATCTTGTAAATCATGT 59.641 45.455 0.00 0.00 0.00 3.21
4031 6719 3.563808 GCCGCCATCTTGTAAATCATGTA 59.436 43.478 0.00 0.00 0.00 2.29
4077 6765 4.396478 GGCTGGAGGACTTTCTTTGTTATC 59.604 45.833 0.00 0.00 0.00 1.75
4130 6818 0.463295 GCCGGGTTAGCCTTTCTACC 60.463 60.000 2.18 0.00 34.45 3.18
4184 6872 1.196127 CGTAACCCGAAGCTGGTTTTC 59.804 52.381 11.82 5.96 43.52 2.29
4232 6920 5.313712 ACCTTTTCACCAGAATATGTCGTT 58.686 37.500 0.00 0.00 32.89 3.85
4385 7081 3.118629 ACCATTATGTGACGACTCTGCAT 60.119 43.478 0.00 0.00 0.00 3.96
4484 7180 3.321111 TGTCACCTCTTAACAGAGTGGAC 59.679 47.826 11.04 11.04 44.85 4.02
4546 7242 1.673665 CACAGCACAGGAGGAAGGC 60.674 63.158 0.00 0.00 0.00 4.35
4639 7346 3.811722 GTGAATGCACGATGAAGACAA 57.188 42.857 0.00 0.00 34.94 3.18
4640 7347 4.346734 GTGAATGCACGATGAAGACAAT 57.653 40.909 0.00 0.00 34.94 2.71
4641 7348 5.469373 GTGAATGCACGATGAAGACAATA 57.531 39.130 0.00 0.00 34.94 1.90
4642 7349 5.258622 GTGAATGCACGATGAAGACAATAC 58.741 41.667 0.00 0.00 34.94 1.89
4703 7410 6.187480 CGCTTGTATCATTGTGTATGAAGTG 58.813 40.000 0.00 0.00 45.99 3.16
4816 7523 2.241176 ACAGTCAGTCACCCCAAAAAGA 59.759 45.455 0.00 0.00 0.00 2.52
5019 7891 4.848757 GGATAAACCTCTTTTATGCAGCG 58.151 43.478 0.00 0.00 44.17 5.18
5050 7922 0.695347 CCTGGAGCCAAAGGAAGAGT 59.305 55.000 0.00 0.00 35.40 3.24
5067 7939 8.115490 AGGAAGAGTTATTGAAATGGAACTTG 57.885 34.615 0.00 0.00 32.37 3.16
5169 8041 2.037251 TGATAGCGCCCTCCACTATTTC 59.963 50.000 2.29 0.00 0.00 2.17
5170 8042 0.756903 TAGCGCCCTCCACTATTTCC 59.243 55.000 2.29 0.00 0.00 3.13
5172 8044 1.984288 GCGCCCTCCACTATTTCCCT 61.984 60.000 0.00 0.00 0.00 4.20
5173 8045 0.106894 CGCCCTCCACTATTTCCCTC 59.893 60.000 0.00 0.00 0.00 4.30
5174 8046 0.474614 GCCCTCCACTATTTCCCTCC 59.525 60.000 0.00 0.00 0.00 4.30
5175 8047 0.759346 CCCTCCACTATTTCCCTCCG 59.241 60.000 0.00 0.00 0.00 4.63
5176 8048 1.497161 CCTCCACTATTTCCCTCCGT 58.503 55.000 0.00 0.00 0.00 4.69
5177 8049 1.838077 CCTCCACTATTTCCCTCCGTT 59.162 52.381 0.00 0.00 0.00 4.44
5178 8050 2.158943 CCTCCACTATTTCCCTCCGTTC 60.159 54.545 0.00 0.00 0.00 3.95
5179 8051 1.479323 TCCACTATTTCCCTCCGTTCG 59.521 52.381 0.00 0.00 0.00 3.95
5180 8052 1.472728 CCACTATTTCCCTCCGTTCGG 60.473 57.143 4.74 4.74 0.00 4.30
5181 8053 1.479323 CACTATTTCCCTCCGTTCGGA 59.521 52.381 13.34 13.34 0.00 4.55
5182 8054 2.093869 CACTATTTCCCTCCGTTCGGAA 60.094 50.000 14.79 0.44 36.35 4.30
5183 8055 2.770232 ACTATTTCCCTCCGTTCGGAAT 59.230 45.455 14.79 7.79 37.96 3.01
5184 8056 2.801077 ATTTCCCTCCGTTCGGAATT 57.199 45.000 14.79 0.00 37.96 2.17
5185 8057 3.918294 ATTTCCCTCCGTTCGGAATTA 57.082 42.857 14.79 0.88 37.96 1.40
5186 8058 2.678471 TTCCCTCCGTTCGGAATTAC 57.322 50.000 14.79 0.00 33.14 1.89
5187 8059 1.856629 TCCCTCCGTTCGGAATTACT 58.143 50.000 14.79 0.00 33.41 2.24
5188 8060 2.181975 TCCCTCCGTTCGGAATTACTT 58.818 47.619 14.79 0.00 33.41 2.24
5189 8061 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
5190 8062 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
5191 8063 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
5192 8064 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
5193 8065 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
5194 8066 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
5195 8067 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
5196 8068 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
5197 8069 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
5198 8070 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
5199 8071 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
5200 8072 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
5201 8073 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
5202 8074 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
5203 8075 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
5204 8076 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
5205 8077 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
5206 8078 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
5207 8079 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
5208 8080 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
5209 8081 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
5210 8082 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
5211 8083 6.724893 TGTCTCGGAAATGGATGTATCTAA 57.275 37.500 0.00 0.00 0.00 2.10
5212 8084 7.119709 TGTCTCGGAAATGGATGTATCTAAA 57.880 36.000 0.00 0.00 0.00 1.85
5213 8085 7.561251 TGTCTCGGAAATGGATGTATCTAAAA 58.439 34.615 0.00 0.00 0.00 1.52
5214 8086 7.494625 TGTCTCGGAAATGGATGTATCTAAAAC 59.505 37.037 0.00 0.00 0.00 2.43
5215 8087 7.711339 GTCTCGGAAATGGATGTATCTAAAACT 59.289 37.037 0.00 0.00 0.00 2.66
5216 8088 8.920174 TCTCGGAAATGGATGTATCTAAAACTA 58.080 33.333 0.00 0.00 0.00 2.24
5217 8089 9.542462 CTCGGAAATGGATGTATCTAAAACTAA 57.458 33.333 0.00 0.00 0.00 2.24
5218 8090 9.893634 TCGGAAATGGATGTATCTAAAACTAAA 57.106 29.630 0.00 0.00 0.00 1.85
5245 8117 6.705782 ACGTCTAGATACATTCATTTTTGCG 58.294 36.000 0.00 0.00 0.00 4.85
5246 8118 6.533723 ACGTCTAGATACATTCATTTTTGCGA 59.466 34.615 0.00 0.00 0.00 5.10
5247 8119 7.224753 ACGTCTAGATACATTCATTTTTGCGAT 59.775 33.333 0.00 0.00 0.00 4.58
5248 8120 8.699749 CGTCTAGATACATTCATTTTTGCGATA 58.300 33.333 0.00 0.00 0.00 2.92
5257 8129 9.301153 ACATTCATTTTTGCGATAAGTAATTCC 57.699 29.630 0.00 0.00 0.00 3.01
5258 8130 7.962934 TTCATTTTTGCGATAAGTAATTCCG 57.037 32.000 0.00 0.00 0.00 4.30
5259 8131 7.310072 TCATTTTTGCGATAAGTAATTCCGA 57.690 32.000 2.50 0.00 0.00 4.55
5260 8132 7.753659 TCATTTTTGCGATAAGTAATTCCGAA 58.246 30.769 2.50 0.00 0.00 4.30
5261 8133 7.694784 TCATTTTTGCGATAAGTAATTCCGAAC 59.305 33.333 2.50 0.00 0.00 3.95
5262 8134 4.765281 TTGCGATAAGTAATTCCGAACG 57.235 40.909 2.50 0.00 0.00 3.95
5263 8135 3.117794 TGCGATAAGTAATTCCGAACGG 58.882 45.455 6.94 6.94 0.00 4.44
5264 8136 3.181488 TGCGATAAGTAATTCCGAACGGA 60.181 43.478 12.04 12.04 43.52 4.69
5265 8137 3.424529 GCGATAAGTAATTCCGAACGGAG 59.575 47.826 15.34 2.36 46.06 4.63
5266 8138 3.979495 CGATAAGTAATTCCGAACGGAGG 59.021 47.826 15.34 0.00 46.06 4.30
5267 8139 2.685850 AAGTAATTCCGAACGGAGGG 57.314 50.000 15.34 0.00 46.06 4.30
5268 8140 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
5269 8141 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
5270 8142 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
5327 8199 2.979130 GCTAGCTAGCCAAACCTCG 58.021 57.895 31.67 0.00 43.39 4.63
5349 8221 2.286294 CAGATTATGCCGTCAACTCTGC 59.714 50.000 0.00 0.00 0.00 4.26
5350 8222 2.169352 AGATTATGCCGTCAACTCTGCT 59.831 45.455 0.00 0.00 0.00 4.24
5351 8223 2.010145 TTATGCCGTCAACTCTGCTC 57.990 50.000 0.00 0.00 0.00 4.26
5391 8263 2.690778 GCCTTCACATTTCGCCGCT 61.691 57.895 0.00 0.00 0.00 5.52
5392 8264 1.135315 CCTTCACATTTCGCCGCTG 59.865 57.895 0.00 0.00 0.00 5.18
5452 8324 3.372676 CTGCTCAATCACGCGTGCC 62.373 63.158 33.63 16.49 0.00 5.01
5513 8385 2.134287 GGATGGAGCTCCGCTACCA 61.134 63.158 27.43 10.28 39.07 3.25
5519 8394 1.079503 GAGCTCCGCTACCAAACTTG 58.920 55.000 0.87 0.00 39.88 3.16
5686 8561 0.394080 TCATGCACATTGGCCGATCA 60.394 50.000 1.06 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.918892 AAACTGGTTTTCTTTAAATGGCAC 57.081 33.333 0.00 0.00 0.00 5.01
2 3 7.980062 TCAAAAACTGGTTTTCTTTAAATGGC 58.020 30.769 11.16 0.00 41.45 4.40
73 74 6.986231 AGGTGTTTTCTCTAAAATGCAAAAGG 59.014 34.615 0.00 0.00 36.96 3.11
74 75 8.330302 CAAGGTGTTTTCTCTAAAATGCAAAAG 58.670 33.333 0.00 0.00 36.96 2.27
137 140 8.147704 ACTACAATAAACAATTTGTTTCCCTGG 58.852 33.333 26.25 16.26 46.61 4.45
233 237 5.669164 TGGTTTACAAAAATATCAGGGGC 57.331 39.130 0.00 0.00 0.00 5.80
396 406 7.457024 TTGCACCCTAAGTAGGATTTAAAAC 57.543 36.000 5.91 0.00 46.63 2.43
457 471 2.768253 TGCAATCCAGATGAACGTCT 57.232 45.000 0.00 0.00 0.00 4.18
508 522 7.821652 TGCATCGTTATTATTGGTTTCTTTCA 58.178 30.769 0.00 0.00 0.00 2.69
611 670 3.686016 TGCTTAATCCAAAGGTGTCTCC 58.314 45.455 0.00 0.00 0.00 3.71
642 704 1.100463 TGCTCACACAACCGCAATGT 61.100 50.000 0.00 0.00 0.00 2.71
801 867 1.598130 GAGGCCGTGAGTTGCAACT 60.598 57.895 31.57 31.57 43.16 3.16
840 940 8.499403 AGAGGCAGTTTTGTTTATTATCTCTC 57.501 34.615 0.00 0.00 0.00 3.20
896 3505 1.536418 TAGACTGGGCTGCACCTGT 60.536 57.895 15.69 15.69 44.19 4.00
1155 3764 4.560856 CGCTCCCGCTCCTTCTCG 62.561 72.222 0.00 0.00 0.00 4.04
1386 3996 2.308690 GCGACCTACTATCCCAGTCTT 58.691 52.381 0.00 0.00 38.80 3.01
1387 3997 1.814634 CGCGACCTACTATCCCAGTCT 60.815 57.143 0.00 0.00 38.80 3.24
1577 4190 3.956199 ACATTCTATTCGAACCTACGGGA 59.044 43.478 0.00 0.00 33.72 5.14
1825 4500 5.066375 CAGATCAGAATTAACCGAATTGGCA 59.934 40.000 0.00 0.00 43.94 4.92
1852 4527 7.329471 CGATCAGTCAGTTTCTGAAAGTATTGA 59.671 37.037 9.98 13.00 42.46 2.57
1865 4540 3.141398 ACATGCAACGATCAGTCAGTTT 58.859 40.909 0.00 0.00 0.00 2.66
1877 4552 5.408604 ACCTAGTTTAGAGAAACATGCAACG 59.591 40.000 0.00 0.00 46.30 4.10
1879 4554 6.877322 GGTACCTAGTTTAGAGAAACATGCAA 59.123 38.462 4.06 0.00 46.30 4.08
1902 4577 1.149288 TCACAGACCTAACTGGAGGGT 59.851 52.381 0.00 0.00 41.36 4.34
1910 4585 9.109393 TGCTTAATTCAATATCACAGACCTAAC 57.891 33.333 0.00 0.00 0.00 2.34
1951 4626 7.980099 ACTGTTCACCGAAATAAGGTAATCTAG 59.020 37.037 0.00 0.00 40.59 2.43
1954 4629 6.980051 ACTGTTCACCGAAATAAGGTAATC 57.020 37.500 0.00 0.00 40.59 1.75
1961 4636 6.664515 CAAAGCTTACTGTTCACCGAAATAA 58.335 36.000 0.00 0.00 0.00 1.40
1966 4641 1.871039 GCAAAGCTTACTGTTCACCGA 59.129 47.619 0.00 0.00 0.00 4.69
1968 4643 3.923017 ATGCAAAGCTTACTGTTCACC 57.077 42.857 0.00 0.00 0.00 4.02
1978 4653 4.984161 GTCACACAACAATATGCAAAGCTT 59.016 37.500 0.00 0.00 0.00 3.74
1979 4654 4.037803 TGTCACACAACAATATGCAAAGCT 59.962 37.500 0.00 0.00 0.00 3.74
2011 4686 3.557577 TGAATCTGCATTTTGTGTCCG 57.442 42.857 0.00 0.00 0.00 4.79
2053 4729 1.576421 GCTTCCAGGCGTGTTCAAG 59.424 57.895 5.57 5.77 0.00 3.02
2070 4746 5.707357 CATCATTTTAATTCAAAGACGCGC 58.293 37.500 5.73 0.00 0.00 6.86
2072 4748 6.875926 AGCATCATTTTAATTCAAAGACGC 57.124 33.333 0.00 0.00 0.00 5.19
2101 4777 1.092921 TTCAACTGGTCGTTTGCGCT 61.093 50.000 9.73 0.00 38.14 5.92
2135 4811 7.201461 CGTAAAAAGAAAATCCAGCATTGATGG 60.201 37.037 14.87 14.87 40.92 3.51
2138 4814 6.155827 CCGTAAAAAGAAAATCCAGCATTGA 58.844 36.000 0.00 0.00 0.00 2.57
2144 4820 4.513198 TGCCCGTAAAAAGAAAATCCAG 57.487 40.909 0.00 0.00 0.00 3.86
2145 4821 4.939052 TTGCCCGTAAAAAGAAAATCCA 57.061 36.364 0.00 0.00 0.00 3.41
2147 4823 5.751509 ACTGTTTGCCCGTAAAAAGAAAATC 59.248 36.000 2.86 0.00 30.93 2.17
2148 4824 5.666462 ACTGTTTGCCCGTAAAAAGAAAAT 58.334 33.333 2.86 0.00 30.93 1.82
2149 4825 5.074584 ACTGTTTGCCCGTAAAAAGAAAA 57.925 34.783 2.86 0.00 30.93 2.29
2150 4826 4.722361 ACTGTTTGCCCGTAAAAAGAAA 57.278 36.364 2.86 0.00 30.93 2.52
2151 4827 4.276431 CCTACTGTTTGCCCGTAAAAAGAA 59.724 41.667 2.86 0.00 30.93 2.52
2153 4829 3.057806 CCCTACTGTTTGCCCGTAAAAAG 60.058 47.826 0.00 0.00 32.34 2.27
2154 4830 2.885894 CCCTACTGTTTGCCCGTAAAAA 59.114 45.455 0.00 0.00 0.00 1.94
2155 4831 2.506444 CCCTACTGTTTGCCCGTAAAA 58.494 47.619 0.00 0.00 0.00 1.52
2156 4832 1.271488 CCCCTACTGTTTGCCCGTAAA 60.271 52.381 0.00 0.00 0.00 2.01
2157 4833 0.325602 CCCCTACTGTTTGCCCGTAA 59.674 55.000 0.00 0.00 0.00 3.18
2158 4834 0.544833 TCCCCTACTGTTTGCCCGTA 60.545 55.000 0.00 0.00 0.00 4.02
2159 4835 1.420532 TTCCCCTACTGTTTGCCCGT 61.421 55.000 0.00 0.00 0.00 5.28
2160 4836 0.034477 ATTCCCCTACTGTTTGCCCG 60.034 55.000 0.00 0.00 0.00 6.13
2161 4837 2.100197 GAATTCCCCTACTGTTTGCCC 58.900 52.381 0.00 0.00 0.00 5.36
2162 4838 2.100197 GGAATTCCCCTACTGTTTGCC 58.900 52.381 14.03 0.00 0.00 4.52
2215 4891 8.977412 CCCCATGTAAATATGTAAACTCCTTTT 58.023 33.333 0.00 0.00 0.00 2.27
2216 4892 7.563556 CCCCCATGTAAATATGTAAACTCCTTT 59.436 37.037 0.00 0.00 0.00 3.11
2217 4893 7.066781 CCCCCATGTAAATATGTAAACTCCTT 58.933 38.462 0.00 0.00 0.00 3.36
2218 4894 6.161526 ACCCCCATGTAAATATGTAAACTCCT 59.838 38.462 0.00 0.00 0.00 3.69
2219 4895 6.370453 ACCCCCATGTAAATATGTAAACTCC 58.630 40.000 0.00 0.00 0.00 3.85
2220 4896 7.558444 TCAACCCCCATGTAAATATGTAAACTC 59.442 37.037 0.00 0.00 0.00 3.01
2221 4897 7.415086 TCAACCCCCATGTAAATATGTAAACT 58.585 34.615 0.00 0.00 0.00 2.66
2222 4898 7.558444 TCTCAACCCCCATGTAAATATGTAAAC 59.442 37.037 0.00 0.00 0.00 2.01
2223 4899 7.644062 TCTCAACCCCCATGTAAATATGTAAA 58.356 34.615 0.00 0.00 0.00 2.01
2224 4900 7.214460 TCTCAACCCCCATGTAAATATGTAA 57.786 36.000 0.00 0.00 0.00 2.41
2225 4901 6.833346 TCTCAACCCCCATGTAAATATGTA 57.167 37.500 0.00 0.00 0.00 2.29
2226 4902 5.725551 TCTCAACCCCCATGTAAATATGT 57.274 39.130 0.00 0.00 0.00 2.29
2227 4903 5.477984 CCATCTCAACCCCCATGTAAATATG 59.522 44.000 0.00 0.00 0.00 1.78
2228 4904 5.644188 CCATCTCAACCCCCATGTAAATAT 58.356 41.667 0.00 0.00 0.00 1.28
2229 4905 4.691376 GCCATCTCAACCCCCATGTAAATA 60.691 45.833 0.00 0.00 0.00 1.40
2230 4906 3.914771 CCATCTCAACCCCCATGTAAAT 58.085 45.455 0.00 0.00 0.00 1.40
2231 4907 2.622977 GCCATCTCAACCCCCATGTAAA 60.623 50.000 0.00 0.00 0.00 2.01
2232 4908 1.064017 GCCATCTCAACCCCCATGTAA 60.064 52.381 0.00 0.00 0.00 2.41
2233 4909 0.550914 GCCATCTCAACCCCCATGTA 59.449 55.000 0.00 0.00 0.00 2.29
2234 4910 1.307647 GCCATCTCAACCCCCATGT 59.692 57.895 0.00 0.00 0.00 3.21
2235 4911 1.456331 GGCCATCTCAACCCCCATG 60.456 63.158 0.00 0.00 0.00 3.66
2236 4912 2.704424 GGGCCATCTCAACCCCCAT 61.704 63.158 4.39 0.00 37.70 4.00
2237 4913 3.346734 GGGCCATCTCAACCCCCA 61.347 66.667 4.39 0.00 37.70 4.96
2240 4916 2.929964 TTGGGGGCCATCTCAACCC 61.930 63.158 4.39 4.22 43.44 4.11
2241 4917 1.682344 GTTGGGGGCCATCTCAACC 60.682 63.158 12.45 0.00 34.97 3.77
2242 4918 0.541764 TTGTTGGGGGCCATCTCAAC 60.542 55.000 15.69 15.69 39.68 3.18
2243 4919 0.189574 TTTGTTGGGGGCCATCTCAA 59.810 50.000 4.39 0.00 31.53 3.02
2244 4920 0.189574 TTTTGTTGGGGGCCATCTCA 59.810 50.000 4.39 0.00 31.53 3.27
2245 4921 0.608130 GTTTTGTTGGGGGCCATCTC 59.392 55.000 4.39 0.00 31.53 2.75
2246 4922 0.105246 TGTTTTGTTGGGGGCCATCT 60.105 50.000 4.39 0.00 31.53 2.90
2247 4923 0.321346 CTGTTTTGTTGGGGGCCATC 59.679 55.000 4.39 0.00 31.53 3.51
2248 4924 0.105246 TCTGTTTTGTTGGGGGCCAT 60.105 50.000 4.39 0.00 31.53 4.40
2249 4925 0.325671 TTCTGTTTTGTTGGGGGCCA 60.326 50.000 4.39 0.00 0.00 5.36
2250 4926 0.392706 CTTCTGTTTTGTTGGGGGCC 59.607 55.000 0.00 0.00 0.00 5.80
2251 4927 1.408969 TCTTCTGTTTTGTTGGGGGC 58.591 50.000 0.00 0.00 0.00 5.80
2252 4928 5.538433 TCTTTATCTTCTGTTTTGTTGGGGG 59.462 40.000 0.00 0.00 0.00 5.40
2253 4929 6.648879 TCTTTATCTTCTGTTTTGTTGGGG 57.351 37.500 0.00 0.00 0.00 4.96
2254 4930 8.413229 TCTTTCTTTATCTTCTGTTTTGTTGGG 58.587 33.333 0.00 0.00 0.00 4.12
2255 4931 9.455847 CTCTTTCTTTATCTTCTGTTTTGTTGG 57.544 33.333 0.00 0.00 0.00 3.77
2256 4932 9.455847 CCTCTTTCTTTATCTTCTGTTTTGTTG 57.544 33.333 0.00 0.00 0.00 3.33
2257 4933 8.138074 GCCTCTTTCTTTATCTTCTGTTTTGTT 58.862 33.333 0.00 0.00 0.00 2.83
2258 4934 7.503902 AGCCTCTTTCTTTATCTTCTGTTTTGT 59.496 33.333 0.00 0.00 0.00 2.83
2259 4935 7.880105 AGCCTCTTTCTTTATCTTCTGTTTTG 58.120 34.615 0.00 0.00 0.00 2.44
2260 4936 9.574516 TTAGCCTCTTTCTTTATCTTCTGTTTT 57.425 29.630 0.00 0.00 0.00 2.43
2261 4937 9.004717 GTTAGCCTCTTTCTTTATCTTCTGTTT 57.995 33.333 0.00 0.00 0.00 2.83
2262 4938 8.379331 AGTTAGCCTCTTTCTTTATCTTCTGTT 58.621 33.333 0.00 0.00 0.00 3.16
2263 4939 7.912719 AGTTAGCCTCTTTCTTTATCTTCTGT 58.087 34.615 0.00 0.00 0.00 3.41
2264 4940 9.877178 TTAGTTAGCCTCTTTCTTTATCTTCTG 57.123 33.333 0.00 0.00 0.00 3.02
2308 4984 9.710900 CAGCACCTATTTTCCTTTTTATTTCTT 57.289 29.630 0.00 0.00 0.00 2.52
2309 4985 8.314021 CCAGCACCTATTTTCCTTTTTATTTCT 58.686 33.333 0.00 0.00 0.00 2.52
2310 4986 8.311109 TCCAGCACCTATTTTCCTTTTTATTTC 58.689 33.333 0.00 0.00 0.00 2.17
2311 4987 8.201242 TCCAGCACCTATTTTCCTTTTTATTT 57.799 30.769 0.00 0.00 0.00 1.40
2312 4988 7.790782 TCCAGCACCTATTTTCCTTTTTATT 57.209 32.000 0.00 0.00 0.00 1.40
2313 4989 7.978099 ATCCAGCACCTATTTTCCTTTTTAT 57.022 32.000 0.00 0.00 0.00 1.40
2314 4990 7.790782 AATCCAGCACCTATTTTCCTTTTTA 57.209 32.000 0.00 0.00 0.00 1.52
2315 4991 6.686484 AATCCAGCACCTATTTTCCTTTTT 57.314 33.333 0.00 0.00 0.00 1.94
2316 4992 6.466812 CAAATCCAGCACCTATTTTCCTTTT 58.533 36.000 0.00 0.00 0.00 2.27
2317 4993 5.569428 GCAAATCCAGCACCTATTTTCCTTT 60.569 40.000 0.00 0.00 0.00 3.11
2318 4994 4.081476 GCAAATCCAGCACCTATTTTCCTT 60.081 41.667 0.00 0.00 0.00 3.36
2319 4995 3.448660 GCAAATCCAGCACCTATTTTCCT 59.551 43.478 0.00 0.00 0.00 3.36
2320 4996 3.195396 TGCAAATCCAGCACCTATTTTCC 59.805 43.478 0.00 0.00 37.02 3.13
2321 4997 4.082026 ACTGCAAATCCAGCACCTATTTTC 60.082 41.667 0.00 0.00 37.02 2.29
2322 4998 3.834231 ACTGCAAATCCAGCACCTATTTT 59.166 39.130 0.00 0.00 37.02 1.82
2323 4999 3.434309 ACTGCAAATCCAGCACCTATTT 58.566 40.909 0.00 0.00 37.02 1.40
2326 5002 2.040278 AGAACTGCAAATCCAGCACCTA 59.960 45.455 0.00 0.00 37.02 3.08
2329 5005 1.200948 GGAGAACTGCAAATCCAGCAC 59.799 52.381 0.00 0.00 37.02 4.40
2786 5462 2.754658 GCCTGAAGCTGCCTGCAT 60.755 61.111 0.00 0.00 45.94 3.96
3025 5701 6.239120 CCCACTGAACTGACATTCATTTTCTT 60.239 38.462 0.00 0.00 37.93 2.52
3080 5756 5.762279 ACATTGGGATTATTAACCGAGGTT 58.238 37.500 12.54 12.54 41.65 3.50
3149 5825 9.947433 AAATCATTACAATCCAATGAACACATT 57.053 25.926 2.21 0.00 43.58 2.71
3216 5892 9.023962 TGCTTTCATAAAATGACTGGTCTAAAT 57.976 29.630 2.38 0.00 39.39 1.40
3629 6306 9.170734 CCATAGTATATCAGGATCAAATTGGTG 57.829 37.037 0.00 0.00 0.00 4.17
3705 6383 5.756195 TGTTTTCTGATCAAGGTCAAGTG 57.244 39.130 0.00 0.00 0.00 3.16
3754 6438 3.325135 CCTCCACAAACTTCAGAGGTAGT 59.675 47.826 0.00 0.00 39.45 2.73
3961 6645 3.617540 AGAACTGTCGAGATATCTGCG 57.382 47.619 10.74 13.21 0.00 5.18
4013 6697 9.590451 AGCAAATTTACATGATTTACAAGATGG 57.410 29.630 0.00 0.00 0.00 3.51
4030 6718 8.621286 GCCTTAGCTATAGAAACAGCAAATTTA 58.379 33.333 3.21 0.00 40.36 1.40
4031 6719 7.484140 GCCTTAGCTATAGAAACAGCAAATTT 58.516 34.615 3.21 0.00 40.36 1.82
4077 6765 5.934625 GGTCATGGCTTAGTATCATAACCTG 59.065 44.000 0.00 0.00 28.94 4.00
4130 6818 0.386478 GCGTTGGCTCAAGCTTCTTG 60.386 55.000 0.00 0.37 41.70 3.02
4184 6872 2.223180 GCCCGCATTACTTACCTTTTCG 60.223 50.000 0.00 0.00 0.00 3.46
4232 6920 4.631377 GCATAGCATGTCAGTTTGTCTGTA 59.369 41.667 0.00 0.00 43.97 2.74
4273 6969 1.242076 GCCTGAATATCTGCGCCATT 58.758 50.000 4.18 0.00 0.00 3.16
4385 7081 1.333115 CGTAAACTGCATCACGACGA 58.667 50.000 0.00 0.00 36.53 4.20
4484 7180 5.864992 AGATACCCTCTGAACTGAGAGACAG 60.865 48.000 9.64 0.00 41.95 3.51
4552 7248 3.551454 GCTATTGCACCTATTCGTCCGTA 60.551 47.826 0.00 0.00 39.41 4.02
4632 7339 9.862371 ATCTGAATATGATACGGTATTGTCTTC 57.138 33.333 1.57 5.19 0.00 2.87
4641 7348 8.047310 GGGGAAATTATCTGAATATGATACGGT 58.953 37.037 0.00 0.00 0.00 4.83
4642 7349 8.267894 AGGGGAAATTATCTGAATATGATACGG 58.732 37.037 0.00 0.00 0.00 4.02
4703 7410 1.662026 CGCCGTTTTTCAGCACCTTAC 60.662 52.381 0.00 0.00 0.00 2.34
4816 7523 0.962356 AATGTGCGCTTAAGCCAGCT 60.962 50.000 21.53 7.82 37.68 4.24
5019 7891 4.704833 TCCAGGCAGGCGCAACTC 62.705 66.667 10.83 0.00 41.24 3.01
5041 7913 8.579863 CAAGTTCCATTTCAATAACTCTTCCTT 58.420 33.333 0.00 0.00 31.15 3.36
5050 7922 7.013846 AGACGGTTTCAAGTTCCATTTCAATAA 59.986 33.333 0.00 0.00 0.00 1.40
5067 7939 2.159435 ACACAAACAAGCAGACGGTTTC 60.159 45.455 0.00 0.00 32.79 2.78
5143 8015 1.068250 GGAGGGCGCTATCAGTGAC 59.932 63.158 7.64 0.00 31.51 3.67
5169 8041 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
5170 8042 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
5172 8044 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
5173 8045 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
5174 8046 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
5175 8047 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
5176 8048 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
5177 8049 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
5178 8050 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
5179 8051 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
5180 8052 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
5181 8053 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
5182 8054 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
5183 8055 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
5184 8056 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
5185 8057 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
5186 8058 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
5187 8059 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
5188 8060 6.724893 TTAGATACATCCATTTCCGAGACA 57.275 37.500 0.00 0.00 0.00 3.41
5189 8061 7.711339 AGTTTTAGATACATCCATTTCCGAGAC 59.289 37.037 0.00 0.00 0.00 3.36
5190 8062 7.792032 AGTTTTAGATACATCCATTTCCGAGA 58.208 34.615 0.00 0.00 0.00 4.04
5191 8063 9.542462 TTAGTTTTAGATACATCCATTTCCGAG 57.458 33.333 0.00 0.00 0.00 4.63
5192 8064 9.893634 TTTAGTTTTAGATACATCCATTTCCGA 57.106 29.630 0.00 0.00 0.00 4.55
5219 8091 8.487970 CGCAAAAATGAATGTATCTAGACGTAT 58.512 33.333 0.00 0.00 0.00 3.06
5220 8092 7.703197 TCGCAAAAATGAATGTATCTAGACGTA 59.297 33.333 0.00 0.00 0.00 3.57
5221 8093 6.533723 TCGCAAAAATGAATGTATCTAGACGT 59.466 34.615 0.00 0.00 0.00 4.34
5222 8094 6.933130 TCGCAAAAATGAATGTATCTAGACG 58.067 36.000 0.00 0.00 0.00 4.18
5231 8103 9.301153 GGAATTACTTATCGCAAAAATGAATGT 57.699 29.630 0.00 0.00 0.00 2.71
5232 8104 8.471457 CGGAATTACTTATCGCAAAAATGAATG 58.529 33.333 0.00 0.00 0.00 2.67
5233 8105 8.402472 TCGGAATTACTTATCGCAAAAATGAAT 58.598 29.630 0.00 0.00 0.00 2.57
5234 8106 7.753659 TCGGAATTACTTATCGCAAAAATGAA 58.246 30.769 0.00 0.00 0.00 2.57
5235 8107 7.310072 TCGGAATTACTTATCGCAAAAATGA 57.690 32.000 0.00 0.00 0.00 2.57
5236 8108 7.304622 CGTTCGGAATTACTTATCGCAAAAATG 60.305 37.037 0.00 0.00 0.00 2.32
5237 8109 6.685403 CGTTCGGAATTACTTATCGCAAAAAT 59.315 34.615 0.00 0.00 0.00 1.82
5238 8110 6.016718 CGTTCGGAATTACTTATCGCAAAAA 58.983 36.000 0.00 0.00 0.00 1.94
5239 8111 5.446206 CCGTTCGGAATTACTTATCGCAAAA 60.446 40.000 5.19 0.00 0.00 2.44
5240 8112 4.033129 CCGTTCGGAATTACTTATCGCAAA 59.967 41.667 5.19 0.00 0.00 3.68
5241 8113 3.552699 CCGTTCGGAATTACTTATCGCAA 59.447 43.478 5.19 0.00 0.00 4.85
5242 8114 3.117794 CCGTTCGGAATTACTTATCGCA 58.882 45.455 5.19 0.00 0.00 5.10
5243 8115 3.374745 TCCGTTCGGAATTACTTATCGC 58.625 45.455 11.66 0.00 0.00 4.58
5244 8116 3.979495 CCTCCGTTCGGAATTACTTATCG 59.021 47.826 14.79 0.00 33.41 2.92
5245 8117 4.038402 TCCCTCCGTTCGGAATTACTTATC 59.962 45.833 14.79 0.00 33.41 1.75
5246 8118 3.962718 TCCCTCCGTTCGGAATTACTTAT 59.037 43.478 14.79 0.00 33.41 1.73
5247 8119 3.364549 TCCCTCCGTTCGGAATTACTTA 58.635 45.455 14.79 0.00 33.41 2.24
5248 8120 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
5249 8121 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
5250 8122 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
5251 8123 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
5252 8124 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
5253 8125 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
5254 8126 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.000 14.79 0.04 33.41 4.30
5255 8127 0.033796 ATGTACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55
5256 8128 0.102481 CATGTACTCCCTCCGTTCGG 59.898 60.000 4.74 4.74 0.00 4.30
5257 8129 0.527817 GCATGTACTCCCTCCGTTCG 60.528 60.000 0.00 0.00 0.00 3.95
5258 8130 0.535335 TGCATGTACTCCCTCCGTTC 59.465 55.000 0.00 0.00 0.00 3.95
5259 8131 0.981183 TTGCATGTACTCCCTCCGTT 59.019 50.000 0.00 0.00 0.00 4.44
5260 8132 0.981183 TTTGCATGTACTCCCTCCGT 59.019 50.000 0.00 0.00 0.00 4.69
5261 8133 1.737793 GTTTTGCATGTACTCCCTCCG 59.262 52.381 0.00 0.00 0.00 4.63
5262 8134 2.790433 TGTTTTGCATGTACTCCCTCC 58.210 47.619 0.00 0.00 0.00 4.30
5263 8135 4.009675 TGATGTTTTGCATGTACTCCCTC 58.990 43.478 0.00 0.00 38.06 4.30
5264 8136 4.032960 TGATGTTTTGCATGTACTCCCT 57.967 40.909 0.00 0.00 38.06 4.20
5265 8137 4.782019 TTGATGTTTTGCATGTACTCCC 57.218 40.909 0.00 0.00 38.06 4.30
5266 8138 5.062558 GCATTTGATGTTTTGCATGTACTCC 59.937 40.000 0.00 0.00 38.06 3.85
5267 8139 5.865552 AGCATTTGATGTTTTGCATGTACTC 59.134 36.000 0.00 0.00 38.06 2.59
5268 8140 5.786311 AGCATTTGATGTTTTGCATGTACT 58.214 33.333 0.00 0.00 38.06 2.73
5269 8141 5.865552 AGAGCATTTGATGTTTTGCATGTAC 59.134 36.000 0.00 0.00 38.06 2.90
5270 8142 6.028146 AGAGCATTTGATGTTTTGCATGTA 57.972 33.333 0.00 0.00 38.06 2.29
5349 8221 5.631512 CGTTCTGAAGAAAACTACTGAGGAG 59.368 44.000 0.00 0.00 35.58 3.69
5350 8222 5.529791 CGTTCTGAAGAAAACTACTGAGGA 58.470 41.667 0.00 0.00 35.58 3.71
5351 8223 4.150804 GCGTTCTGAAGAAAACTACTGAGG 59.849 45.833 0.00 0.00 35.58 3.86
5391 8263 1.605457 GGATCGATATGAACCGCAGCA 60.605 52.381 0.00 0.00 28.92 4.41
5392 8264 1.071605 GGATCGATATGAACCGCAGC 58.928 55.000 0.00 0.00 28.92 5.25
5452 8324 6.138761 GCTTAATTAGATGGTTCAGCAATCG 58.861 40.000 0.00 0.00 32.71 3.34


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

AutoCloner maintained by Alex Coulton.