Multiple sequence alignment - TraesCS4D01G086900

Loading Multiple Alignment...

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 TraesCS4D01G086900 chr4D 100.000 4574 0 0 1 4574 62116660 62121233 0.000000e+00 8447.0
1 TraesCS4D01G086900 chr4B 95.443 3094 98 19 758 3816 90460512 90457427 0.000000e+00 4892.0
2 TraesCS4D01G086900 chr4B 95.187 561 22 4 4016 4574 90457373 90456816 0.000000e+00 881.0
3 TraesCS4D01G086900 chr4B 86.166 759 77 9 1 733 90461595 90460839 0.000000e+00 795.0
4 TraesCS4D01G086900 chr4A 94.531 3072 125 20 742 3777 535464000 535467064 0.000000e+00 4702.0
5 TraesCS4D01G086900 chr4A 93.939 561 20 6 4016 4574 535467202 535467750 0.000000e+00 835.0
6 TraesCS4D01G086900 chr4A 95.918 49 2 0 3975 4023 535467144 535467192 3.790000e-11 80.5
7 TraesCS4D01G086900 chr7D 97.590 166 4 0 3812 3977 363148833 363148998 7.490000e-73 285.0
8 TraesCS4D01G086900 chr7A 97.006 167 5 0 3811 3977 16718367 16718201 9.690000e-72 281.0
9 TraesCS4D01G086900 chr7A 96.471 170 5 1 3811 3979 709731231 709731062 3.480000e-71 279.0
10 TraesCS4D01G086900 chr5A 96.988 166 5 0 3811 3976 389723437 389723272 3.480000e-71 279.0
11 TraesCS4D01G086900 chr2D 96.450 169 6 0 3808 3976 593801592 593801760 3.480000e-71 279.0
12 TraesCS4D01G086900 chr2B 95.930 172 7 0 3812 3983 385568874 385568703 3.480000e-71 279.0
13 TraesCS4D01G086900 chr6A 95.930 172 5 2 3809 3978 33259858 33260029 1.250000e-70 278.0
14 TraesCS4D01G086900 chr6A 94.382 178 8 2 3808 3983 546930969 546931146 5.830000e-69 272.0
15 TraesCS4D01G086900 chr6D 95.152 165 8 0 3812 3976 8921427 8921591 1.260000e-65 261.0
16 TraesCS4D01G086900 chr6B 75.820 244 45 12 223 457 538940691 538940929 1.350000e-20 111.0


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 TraesCS4D01G086900 chr4D 62116660 62121233 4573 False 8447.000000 8447 100.000000 1 4574 1 chr4D.!!$F1 4573
1 TraesCS4D01G086900 chr4B 90456816 90461595 4779 True 2189.333333 4892 92.265333 1 4574 3 chr4B.!!$R1 4573
2 TraesCS4D01G086900 chr4A 535464000 535467750 3750 False 1872.500000 4702 94.796000 742 4574 3 chr4A.!!$F1 3832

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
215 240 0.107945 AGGTGCTCATTCCGAAGCTC 60.108 55.0 0.00 0.0 0.00 4.09 F
690 717 0.181350 GGGATTTCGGACAGCCAGAT 59.819 55.0 0.41 0.0 0.00 2.90 F
1816 2186 0.396435 TTCTGATCGGCAGGTGTGTT 59.604 50.0 0.00 0.0 44.98 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 1692 1.293498 GAGCTTGGCGTTGAGGAGA 59.707 57.895 0.0 0.0 0.00 3.71 R
2027 2404 1.856629 CAAGAATTGCCACCATCCCT 58.143 50.000 0.0 0.0 40.39 4.20 R
3727 4119 3.456280 GATCAGACAGATCCAAGAGTGC 58.544 50.000 0.0 0.0 46.10 4.40 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
29 30 4.311700 TCTGTCCAGAGCACCCAA 57.688 55.556 0.00 0.00 32.82 4.12
38 39 4.395231 GTCCAGAGCACCCAAAATAACTAC 59.605 45.833 0.00 0.00 0.00 2.73
47 48 9.255029 AGCACCCAAAATAACTACAGATAAATT 57.745 29.630 0.00 0.00 0.00 1.82
166 175 7.852971 AGTTCAAATTTGATATTTGGGCATG 57.147 32.000 21.10 0.00 38.97 4.06
168 177 8.538701 AGTTCAAATTTGATATTTGGGCATGTA 58.461 29.630 21.10 0.00 38.97 2.29
170 179 9.902684 TTCAAATTTGATATTTGGGCATGTATT 57.097 25.926 21.10 0.00 38.97 1.89
171 180 9.902684 TCAAATTTGATATTTGGGCATGTATTT 57.097 25.926 16.91 0.00 38.97 1.40
198 207 0.239347 CCTTTTGAAGCGCTCACAGG 59.761 55.000 12.06 13.81 32.21 4.00
200 209 0.662619 TTTTGAAGCGCTCACAGGTG 59.337 50.000 12.06 0.00 32.21 4.00
201 210 1.785041 TTTGAAGCGCTCACAGGTGC 61.785 55.000 12.06 0.00 42.33 5.01
205 214 2.435586 GCGCTCACAGGTGCTCAT 60.436 61.111 0.00 0.00 39.35 2.90
207 216 1.975363 GCGCTCACAGGTGCTCATTC 61.975 60.000 0.00 0.00 39.35 2.67
215 240 0.107945 AGGTGCTCATTCCGAAGCTC 60.108 55.000 0.00 0.00 0.00 4.09
218 243 0.458543 TGCTCATTCCGAAGCTCGAC 60.459 55.000 7.07 0.00 43.74 4.20
263 288 4.334481 GGATAAAATCCCGAAACATCGTGT 59.666 41.667 0.00 0.00 43.88 4.49
267 292 0.320073 TCCCGAAACATCGTGTGGAC 60.320 55.000 0.00 0.00 0.00 4.02
271 296 1.721389 CGAAACATCGTGTGGACTCTG 59.279 52.381 0.00 0.00 0.00 3.35
289 314 4.177026 CTCTGTGGTGAAAGTTCGATAGG 58.823 47.826 0.00 0.00 0.00 2.57
304 329 4.023980 TCGATAGGACCACTCATGTTCTT 58.976 43.478 0.00 0.00 0.00 2.52
311 336 6.784031 AGGACCACTCATGTTCTTAAAATCT 58.216 36.000 0.00 0.00 0.00 2.40
339 364 1.355381 TGTGAATTGCCTCACCCTCAT 59.645 47.619 7.88 0.00 44.30 2.90
388 413 5.684704 TCTATCATCACCTCCCACAATTTC 58.315 41.667 0.00 0.00 0.00 2.17
402 427 6.619437 TCCCACAATTTCTCTAGATCCCATAA 59.381 38.462 0.00 0.00 0.00 1.90
435 460 4.869861 GTCTTCAAACAACTGCAAAATGGT 59.130 37.500 0.00 0.00 0.00 3.55
442 467 4.685924 ACAACTGCAAAATGGTCTTGAAG 58.314 39.130 0.00 0.00 35.78 3.02
455 480 1.066716 TCTTGAAGCATGCCAAATGCC 60.067 47.619 15.66 0.00 45.59 4.40
457 482 1.519898 GAAGCATGCCAAATGCCCG 60.520 57.895 15.66 0.00 45.59 6.13
458 483 1.947597 GAAGCATGCCAAATGCCCGA 61.948 55.000 15.66 0.00 45.59 5.14
465 490 2.717485 CAAATGCCCGATGGAGCG 59.283 61.111 0.00 0.00 0.00 5.03
468 493 4.592192 ATGCCCGATGGAGCGACG 62.592 66.667 0.00 0.00 0.00 5.12
482 507 1.008194 CGACGGACGTCCAACAAGA 60.008 57.895 32.80 0.00 41.76 3.02
514 540 2.483288 GGCAATGGTACAACGCCG 59.517 61.111 0.00 0.00 46.87 6.46
515 541 2.036006 GGCAATGGTACAACGCCGA 61.036 57.895 0.00 0.00 46.87 5.54
527 553 3.700961 CGCCGACGTCTATTTGGG 58.299 61.111 14.70 7.27 33.53 4.12
536 562 1.417890 CGTCTATTTGGGAGGGAGCAT 59.582 52.381 0.00 0.00 0.00 3.79
541 567 5.248477 GTCTATTTGGGAGGGAGCATATACA 59.752 44.000 0.00 0.00 0.00 2.29
542 568 5.849475 TCTATTTGGGAGGGAGCATATACAA 59.151 40.000 0.00 0.00 0.00 2.41
548 574 5.430417 TGGGAGGGAGCATATACAAAGTAAA 59.570 40.000 0.00 0.00 0.00 2.01
555 581 6.931840 GGAGCATATACAAAGTAAAGGAGGAG 59.068 42.308 0.00 0.00 0.00 3.69
558 584 6.183361 GCATATACAAAGTAAAGGAGGAGGGA 60.183 42.308 0.00 0.00 0.00 4.20
559 585 7.474936 GCATATACAAAGTAAAGGAGGAGGGAT 60.475 40.741 0.00 0.00 0.00 3.85
578 604 1.191489 TGGAGTGAGAATGTGCGGGA 61.191 55.000 0.00 0.00 0.00 5.14
580 606 1.576356 GAGTGAGAATGTGCGGGATC 58.424 55.000 0.00 0.00 0.00 3.36
597 623 0.247185 ATCCGCAATGGTTTTGGCTG 59.753 50.000 0.00 0.00 39.52 4.85
603 629 2.819608 GCAATGGTTTTGGCTGAGTCTA 59.180 45.455 0.00 0.00 0.00 2.59
606 632 3.140325 TGGTTTTGGCTGAGTCTAAGG 57.860 47.619 0.00 0.00 0.00 2.69
634 661 1.227263 CTACATGGCGAAGGTCCGG 60.227 63.158 0.00 0.00 0.00 5.14
637 664 4.143333 ATGGCGAAGGTCCGGACG 62.143 66.667 27.68 17.66 0.00 4.79
646 673 2.746277 GTCCGGACGCCTGCAAAT 60.746 61.111 20.85 0.00 0.00 2.32
649 676 2.040544 CCGGACGCCTGCAAATCTT 61.041 57.895 0.00 0.00 0.00 2.40
684 711 1.539827 GGTTTGTGGGATTTCGGACAG 59.460 52.381 0.00 0.00 0.00 3.51
690 717 0.181350 GGGATTTCGGACAGCCAGAT 59.819 55.000 0.41 0.00 0.00 2.90
696 723 1.153309 CGGACAGCCAGATGCATCA 60.153 57.895 27.81 0.00 44.83 3.07
718 745 3.254166 AGTGAATGTTTGAGGCATGACAC 59.746 43.478 0.00 0.00 36.12 3.67
793 1122 1.061131 GTCATCGGTTCGTTCATGCAG 59.939 52.381 0.00 0.00 0.00 4.41
1265 1604 4.806571 CCGTGTGATCGTACAGGG 57.193 61.111 9.69 9.69 46.33 4.45
1305 1644 4.603094 TCTCTGGTACAAGGATGAGGTA 57.397 45.455 0.00 0.00 38.70 3.08
1417 1759 2.428530 TGCCTGCATGTAGTCTAGTCTG 59.571 50.000 10.09 0.00 0.00 3.51
1485 1844 4.560035 CACAGTCAGTTTTTCAAAGTGCTG 59.440 41.667 17.60 17.60 0.00 4.41
1488 1847 6.095440 ACAGTCAGTTTTTCAAAGTGCTGTAT 59.905 34.615 20.52 8.00 32.60 2.29
1555 1920 4.494091 ACTAAATGGTGCATGTAGAGCT 57.506 40.909 0.00 0.00 34.52 4.09
1652 2020 1.680735 CTGAAGGACAGCGAGCTCTAT 59.319 52.381 12.85 0.00 39.86 1.98
1661 2029 4.141287 ACAGCGAGCTCTATATGTCTCTT 58.859 43.478 12.85 0.00 0.00 2.85
1662 2030 5.309638 ACAGCGAGCTCTATATGTCTCTTA 58.690 41.667 12.85 0.00 0.00 2.10
1670 2038 8.187913 AGCTCTATATGTCTCTTATTTGCTGA 57.812 34.615 0.00 0.00 0.00 4.26
1679 2049 9.852091 ATGTCTCTTATTTGCTGATTTTCTTTC 57.148 29.630 0.00 0.00 0.00 2.62
1698 2068 7.502120 TCTTTCATCTTTTATCTGCTATGGC 57.498 36.000 0.00 0.00 39.26 4.40
1703 2073 8.978874 TCATCTTTTATCTGCTATGGCTTTTA 57.021 30.769 1.68 0.00 39.59 1.52
1765 2135 4.676109 TCATCCCTGTTTTCATTGGACAT 58.324 39.130 0.00 0.00 34.81 3.06
1783 2153 4.159120 GACATTCTTTTCTTTAGCCGTGC 58.841 43.478 0.00 0.00 0.00 5.34
1816 2186 0.396435 TTCTGATCGGCAGGTGTGTT 59.604 50.000 0.00 0.00 44.98 3.32
1954 2329 5.005203 CAGTTCTGAATATGAACGCTGAGAC 59.995 44.000 0.00 0.00 45.84 3.36
1980 2355 4.927267 ATAGTTGGGAAAGATGGACACA 57.073 40.909 0.00 0.00 0.00 3.72
2027 2404 7.756272 ACAAGTACACACGTATATTCATCGAAA 59.244 33.333 0.00 0.00 0.00 3.46
2038 2415 0.107214 TCATCGAAAGGGATGGTGGC 60.107 55.000 0.00 0.00 43.18 5.01
2058 2435 7.920151 TGGTGGCAATTCTTGATTTAAATATCG 59.080 33.333 0.00 0.00 0.00 2.92
2130 2507 5.894807 AGTGTTGGTGTTCAATTTCTTGAG 58.105 37.500 0.00 0.00 42.19 3.02
2209 2586 7.896383 TTTAAAATTCCATGTCATAGGGGAG 57.104 36.000 0.00 0.00 0.00 4.30
2230 2608 6.172630 GGAGTTTTGCCCATGTATCAATTTT 58.827 36.000 0.00 0.00 0.00 1.82
2343 2725 5.934781 AGATGCCTATTAGCTAGCAAGTTT 58.065 37.500 18.83 0.00 0.00 2.66
2363 2745 7.636150 AGTTTGAATAGGAGTGATTTCATGG 57.364 36.000 0.00 0.00 0.00 3.66
2402 2788 2.677875 CCAGTTGCCTGCCTTCCC 60.678 66.667 0.00 0.00 37.38 3.97
2434 2821 7.124599 ACATGCTTTGGATATCCTTTCATTTCA 59.875 33.333 22.35 9.65 36.82 2.69
2461 2848 6.653020 ACAGAATTATGCTATGAGACAACCA 58.347 36.000 0.00 0.00 0.00 3.67
2469 2856 4.655649 TGCTATGAGACAACCATGACCTAT 59.344 41.667 0.00 0.00 0.00 2.57
2652 3041 2.612721 GGCACCTGGGTTTGCATAAAAG 60.613 50.000 9.61 0.00 40.75 2.27
2694 3083 5.048782 TCAGAAATTTGATGTGAGGGAAACG 60.049 40.000 0.00 0.00 0.00 3.60
2773 3162 2.428171 GTGCACCATATCACTTTGCCAT 59.572 45.455 5.22 0.00 31.94 4.40
2879 3271 5.061853 TGCTTGCATGAGATAATTCCTCTC 58.938 41.667 3.33 9.85 39.69 3.20
2973 3365 1.347707 ACCTTTGATCTTCGCACTGGA 59.652 47.619 0.00 0.00 0.00 3.86
3107 3499 4.154347 GGGCGCTGCTAGCTCTGT 62.154 66.667 17.23 0.00 39.60 3.41
3108 3500 2.786495 GGGCGCTGCTAGCTCTGTA 61.786 63.158 17.23 0.00 39.60 2.74
3727 4119 9.453325 GGAATACAAGATAACTTCTTCTACTCG 57.547 37.037 0.00 0.00 42.98 4.18
3812 4249 2.158355 AGGGCTACGGGCTTCTCTTATA 60.158 50.000 2.91 0.00 41.46 0.98
3813 4250 2.029200 GGGCTACGGGCTTCTCTTATAC 60.029 54.545 2.91 0.00 41.46 1.47
3814 4251 2.892215 GGCTACGGGCTTCTCTTATACT 59.108 50.000 2.91 0.00 41.46 2.12
3815 4252 3.057386 GGCTACGGGCTTCTCTTATACTC 60.057 52.174 2.91 0.00 41.46 2.59
3816 4253 3.057386 GCTACGGGCTTCTCTTATACTCC 60.057 52.174 0.00 0.00 38.06 3.85
3817 4254 2.317973 ACGGGCTTCTCTTATACTCCC 58.682 52.381 0.00 0.00 0.00 4.30
3818 4255 2.091222 ACGGGCTTCTCTTATACTCCCT 60.091 50.000 0.00 0.00 0.00 4.20
3819 4256 2.559231 CGGGCTTCTCTTATACTCCCTC 59.441 54.545 0.00 0.00 0.00 4.30
3820 4257 2.901192 GGGCTTCTCTTATACTCCCTCC 59.099 54.545 0.00 0.00 0.00 4.30
3821 4258 2.559231 GGCTTCTCTTATACTCCCTCCG 59.441 54.545 0.00 0.00 0.00 4.63
3822 4259 3.224269 GCTTCTCTTATACTCCCTCCGT 58.776 50.000 0.00 0.00 0.00 4.69
3823 4260 3.637694 GCTTCTCTTATACTCCCTCCGTT 59.362 47.826 0.00 0.00 0.00 4.44
3824 4261 4.099727 GCTTCTCTTATACTCCCTCCGTTT 59.900 45.833 0.00 0.00 0.00 3.60
3825 4262 5.736777 GCTTCTCTTATACTCCCTCCGTTTC 60.737 48.000 0.00 0.00 0.00 2.78
3826 4263 5.126699 TCTCTTATACTCCCTCCGTTTCT 57.873 43.478 0.00 0.00 0.00 2.52
3827 4264 6.257994 TCTCTTATACTCCCTCCGTTTCTA 57.742 41.667 0.00 0.00 0.00 2.10
3828 4265 6.666678 TCTCTTATACTCCCTCCGTTTCTAA 58.333 40.000 0.00 0.00 0.00 2.10
3829 4266 7.121382 TCTCTTATACTCCCTCCGTTTCTAAA 58.879 38.462 0.00 0.00 0.00 1.85
3830 4267 7.783596 TCTCTTATACTCCCTCCGTTTCTAAAT 59.216 37.037 0.00 0.00 0.00 1.40
3831 4268 9.075678 CTCTTATACTCCCTCCGTTTCTAAATA 57.924 37.037 0.00 0.00 0.00 1.40
3832 4269 9.597681 TCTTATACTCCCTCCGTTTCTAAATAT 57.402 33.333 0.00 0.00 0.00 1.28
3836 4273 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
3837 4274 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
3838 4275 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
3839 4276 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
3840 4277 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
3841 4278 9.392259 CCCTCCGTTTCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
3882 4319 9.642343 AGACTACAACATAAGGATGTATGTAGA 57.358 33.333 26.03 9.30 45.93 2.59
3883 4320 9.680315 GACTACAACATAAGGATGTATGTAGAC 57.320 37.037 26.03 21.22 45.93 2.59
3884 4321 9.197306 ACTACAACATAAGGATGTATGTAGACA 57.803 33.333 26.03 0.00 45.93 3.41
3917 4354 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
3918 4355 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
3919 4356 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
3920 4357 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
3921 4358 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
3922 4359 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
3923 4360 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
3924 4361 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
3925 4362 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
3926 4363 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
3927 4364 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
3928 4365 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
3929 4366 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
3930 4367 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
3931 4368 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
3932 4369 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
3933 4370 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
3934 4371 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
3935 4372 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
3936 4373 4.091509 GCTTCGTATGTAGTCACTTGTTGG 59.908 45.833 0.00 0.00 0.00 3.77
3937 4374 5.456548 TTCGTATGTAGTCACTTGTTGGA 57.543 39.130 0.00 0.00 0.00 3.53
3938 4375 5.456548 TCGTATGTAGTCACTTGTTGGAA 57.543 39.130 0.00 0.00 0.00 3.53
3939 4376 6.032956 TCGTATGTAGTCACTTGTTGGAAT 57.967 37.500 0.00 0.00 0.00 3.01
3940 4377 6.097356 TCGTATGTAGTCACTTGTTGGAATC 58.903 40.000 0.00 0.00 0.00 2.52
3941 4378 6.071560 TCGTATGTAGTCACTTGTTGGAATCT 60.072 38.462 0.00 0.00 0.00 2.40
3942 4379 6.253727 CGTATGTAGTCACTTGTTGGAATCTC 59.746 42.308 0.00 0.00 0.00 2.75
3943 4380 5.808366 TGTAGTCACTTGTTGGAATCTCT 57.192 39.130 0.00 0.00 0.00 3.10
3944 4381 6.911250 TGTAGTCACTTGTTGGAATCTCTA 57.089 37.500 0.00 0.00 0.00 2.43
3945 4382 7.297936 TGTAGTCACTTGTTGGAATCTCTAA 57.702 36.000 0.00 0.00 0.00 2.10
3946 4383 7.732025 TGTAGTCACTTGTTGGAATCTCTAAA 58.268 34.615 0.00 0.00 0.00 1.85
3947 4384 8.208224 TGTAGTCACTTGTTGGAATCTCTAAAA 58.792 33.333 0.00 0.00 0.00 1.52
3948 4385 9.052759 GTAGTCACTTGTTGGAATCTCTAAAAA 57.947 33.333 0.00 0.00 0.00 1.94
3949 4386 8.159344 AGTCACTTGTTGGAATCTCTAAAAAG 57.841 34.615 2.17 2.17 37.94 2.27
3950 4387 7.993183 AGTCACTTGTTGGAATCTCTAAAAAGA 59.007 33.333 9.03 0.00 35.06 2.52
3951 4388 8.070769 GTCACTTGTTGGAATCTCTAAAAAGAC 58.929 37.037 9.03 0.00 35.06 3.01
3952 4389 7.993183 TCACTTGTTGGAATCTCTAAAAAGACT 59.007 33.333 9.03 0.00 35.06 3.24
3953 4390 8.624776 CACTTGTTGGAATCTCTAAAAAGACTT 58.375 33.333 9.03 0.00 35.06 3.01
3954 4391 9.847224 ACTTGTTGGAATCTCTAAAAAGACTTA 57.153 29.630 9.03 0.00 35.06 2.24
3967 4404 9.169592 TCTAAAAAGACTTATATTTGGGAACGG 57.830 33.333 0.00 0.00 0.00 4.44
3968 4405 9.169592 CTAAAAAGACTTATATTTGGGAACGGA 57.830 33.333 0.00 0.00 0.00 4.69
3969 4406 7.625828 AAAAGACTTATATTTGGGAACGGAG 57.374 36.000 0.00 0.00 0.00 4.63
3970 4407 5.291905 AGACTTATATTTGGGAACGGAGG 57.708 43.478 0.00 0.00 0.00 4.30
3971 4408 4.102681 AGACTTATATTTGGGAACGGAGGG 59.897 45.833 0.00 0.00 0.00 4.30
3972 4409 4.042174 ACTTATATTTGGGAACGGAGGGA 58.958 43.478 0.00 0.00 0.00 4.20
3973 4410 4.102681 ACTTATATTTGGGAACGGAGGGAG 59.897 45.833 0.00 0.00 0.00 4.30
3974 4411 1.961133 TATTTGGGAACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
4115 4570 6.811954 TGATGGTACCAGGAAAAACTTTTTC 58.188 36.000 21.41 15.86 0.00 2.29
4255 4712 5.422012 TGCTGTATATGTCTCTTGAACCTCA 59.578 40.000 0.00 0.00 0.00 3.86
4279 4736 5.318630 TGGTATTGAAGGTTACCCAAACTC 58.681 41.667 0.00 0.00 37.63 3.01
4295 4752 6.660949 ACCCAAACTCAATCCTAAAATCTCAG 59.339 38.462 0.00 0.00 0.00 3.35
4434 4891 3.933861 AGTTTGGGCCCTATCTTACAG 57.066 47.619 25.70 0.00 0.00 2.74
4510 4967 2.238804 TGCCCTGTTAGCATACGGAGT 61.239 52.381 0.00 0.00 39.24 3.85
4549 5006 4.840115 TCTGGCTTCAGAAATCCCATTTTT 59.160 37.500 0.00 0.00 43.84 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.421844 AGTTATTTTGGGTGCTCTGGAC 58.578 45.455 0.00 0.00 0.00 4.02
18 19 5.245531 TCTGTAGTTATTTTGGGTGCTCTG 58.754 41.667 0.00 0.00 0.00 3.35
26 27 9.853555 TGTGCAATTTATCTGTAGTTATTTTGG 57.146 29.630 0.00 0.00 0.00 3.28
38 39 9.752961 TTATGGATGAATTGTGCAATTTATCTG 57.247 29.630 26.63 0.00 45.44 2.90
47 48 7.110043 TGCTATTTTATGGATGAATTGTGCA 57.890 32.000 0.00 0.00 0.00 4.57
166 175 6.087687 GCGCTTCAAAAGGACAACTAAAATAC 59.912 38.462 0.00 0.00 0.00 1.89
168 177 4.982295 GCGCTTCAAAAGGACAACTAAAAT 59.018 37.500 0.00 0.00 0.00 1.82
170 179 3.630312 AGCGCTTCAAAAGGACAACTAAA 59.370 39.130 2.64 0.00 0.00 1.85
171 180 3.211045 AGCGCTTCAAAAGGACAACTAA 58.789 40.909 2.64 0.00 0.00 2.24
198 207 0.458543 TCGAGCTTCGGAATGAGCAC 60.459 55.000 3.26 0.00 40.88 4.40
200 209 1.475441 CGTCGAGCTTCGGAATGAGC 61.475 60.000 5.87 0.00 40.88 4.26
201 210 1.475441 GCGTCGAGCTTCGGAATGAG 61.475 60.000 0.00 0.00 44.04 2.90
202 211 1.516386 GCGTCGAGCTTCGGAATGA 60.516 57.895 0.00 0.00 44.04 2.57
203 212 2.998667 GCGTCGAGCTTCGGAATG 59.001 61.111 0.00 0.00 44.04 2.67
215 240 1.590238 GGATCAACAGATTCAGCGTCG 59.410 52.381 0.00 0.00 0.00 5.12
218 243 4.348656 CAAATGGATCAACAGATTCAGCG 58.651 43.478 0.00 0.00 30.99 5.18
256 281 0.318441 ACCACAGAGTCCACACGATG 59.682 55.000 0.00 0.00 0.00 3.84
263 288 2.483013 CGAACTTTCACCACAGAGTCCA 60.483 50.000 0.00 0.00 0.00 4.02
267 292 4.082190 TCCTATCGAACTTTCACCACAGAG 60.082 45.833 0.00 0.00 0.00 3.35
271 296 3.259902 GGTCCTATCGAACTTTCACCAC 58.740 50.000 0.00 0.00 0.00 4.16
289 314 9.827411 GTTTAGATTTTAAGAACATGAGTGGTC 57.173 33.333 0.00 0.00 42.59 4.02
291 316 8.792633 TGGTTTAGATTTTAAGAACATGAGTGG 58.207 33.333 0.00 0.00 0.00 4.00
304 329 8.592809 AGGCAATTCACATTGGTTTAGATTTTA 58.407 29.630 0.00 0.00 40.36 1.52
311 336 5.132897 GTGAGGCAATTCACATTGGTTTA 57.867 39.130 9.53 0.00 45.32 2.01
325 350 3.202818 ACATGATTATGAGGGTGAGGCAA 59.797 43.478 4.20 0.00 37.73 4.52
358 383 5.070446 GTGGGAGGTGATGATAGATTGTGTA 59.930 44.000 0.00 0.00 0.00 2.90
402 427 8.637986 TGCAGTTGTTTGAAGACCTATAAAAAT 58.362 29.630 0.00 0.00 0.00 1.82
411 436 4.270808 CCATTTTGCAGTTGTTTGAAGACC 59.729 41.667 0.00 0.00 0.00 3.85
418 443 5.083533 TCAAGACCATTTTGCAGTTGTTT 57.916 34.783 0.00 0.00 0.00 2.83
423 448 2.694628 TGCTTCAAGACCATTTTGCAGT 59.305 40.909 0.00 0.00 0.00 4.40
435 460 2.373540 GCATTTGGCATGCTTCAAGA 57.626 45.000 18.92 5.95 43.97 3.02
455 480 4.907034 CGTCCGTCGCTCCATCGG 62.907 72.222 0.00 0.00 44.76 4.18
457 482 2.278013 GACGTCCGTCGCTCCATC 60.278 66.667 3.51 0.00 44.19 3.51
458 483 3.823330 GGACGTCCGTCGCTCCAT 61.823 66.667 20.85 0.00 45.41 3.41
465 490 1.067776 AGATCTTGTTGGACGTCCGTC 60.068 52.381 28.70 22.77 43.87 4.79
468 493 1.002087 ACCAGATCTTGTTGGACGTCC 59.998 52.381 28.17 28.17 37.89 4.79
471 496 1.442769 CCACCAGATCTTGTTGGACG 58.557 55.000 5.76 0.00 41.68 4.79
476 501 1.002134 CCGCCCACCAGATCTTGTT 60.002 57.895 0.00 0.00 0.00 2.83
499 525 1.418367 CGTCGGCGTTGTACCATTG 59.582 57.895 6.85 0.00 0.00 2.82
500 526 3.864944 CGTCGGCGTTGTACCATT 58.135 55.556 6.85 0.00 0.00 3.16
512 538 0.104304 CCCTCCCAAATAGACGTCGG 59.896 60.000 10.46 4.60 0.00 4.79
514 540 1.202545 GCTCCCTCCCAAATAGACGTC 60.203 57.143 7.70 7.70 0.00 4.34
515 541 0.831307 GCTCCCTCCCAAATAGACGT 59.169 55.000 0.00 0.00 0.00 4.34
521 547 5.103515 ACTTTGTATATGCTCCCTCCCAAAT 60.104 40.000 0.00 0.00 0.00 2.32
526 552 5.998363 CCTTTACTTTGTATATGCTCCCTCC 59.002 44.000 0.00 0.00 0.00 4.30
527 553 6.827727 TCCTTTACTTTGTATATGCTCCCTC 58.172 40.000 0.00 0.00 0.00 4.30
536 562 6.329197 CCATCCCTCCTCCTTTACTTTGTATA 59.671 42.308 0.00 0.00 0.00 1.47
541 567 3.783082 CTCCATCCCTCCTCCTTTACTTT 59.217 47.826 0.00 0.00 0.00 2.66
542 568 3.246535 ACTCCATCCCTCCTCCTTTACTT 60.247 47.826 0.00 0.00 0.00 2.24
548 574 0.264359 CTCACTCCATCCCTCCTCCT 59.736 60.000 0.00 0.00 0.00 3.69
555 581 1.673168 GCACATTCTCACTCCATCCC 58.327 55.000 0.00 0.00 0.00 3.85
558 584 0.107508 CCCGCACATTCTCACTCCAT 60.108 55.000 0.00 0.00 0.00 3.41
559 585 1.191489 TCCCGCACATTCTCACTCCA 61.191 55.000 0.00 0.00 0.00 3.86
578 604 0.247185 CAGCCAAAACCATTGCGGAT 59.753 50.000 0.00 0.00 38.63 4.18
580 606 0.388907 CTCAGCCAAAACCATTGCGG 60.389 55.000 0.00 0.00 42.50 5.69
584 610 4.082125 CCTTAGACTCAGCCAAAACCATT 58.918 43.478 0.00 0.00 0.00 3.16
597 623 0.456628 GCCTCCGACACCTTAGACTC 59.543 60.000 0.00 0.00 0.00 3.36
603 629 0.537188 CATGTAGCCTCCGACACCTT 59.463 55.000 0.00 0.00 29.23 3.50
606 632 1.521681 GCCATGTAGCCTCCGACAC 60.522 63.158 0.00 0.00 29.23 3.67
634 661 0.881118 TTGGAAGATTTGCAGGCGTC 59.119 50.000 0.00 0.00 30.85 5.19
637 664 3.062042 CAAAGTTGGAAGATTTGCAGGC 58.938 45.455 0.00 0.00 30.85 4.85
646 673 1.028905 CCGGTTGCAAAGTTGGAAGA 58.971 50.000 0.00 0.00 39.20 2.87
649 676 1.134965 CAAACCGGTTGCAAAGTTGGA 60.135 47.619 23.08 0.00 0.00 3.53
659 686 1.335506 CGAAATCCCACAAACCGGTTG 60.336 52.381 23.08 17.07 43.43 3.77
684 711 2.022195 ACATTCACTGATGCATCTGGC 58.978 47.619 29.96 7.29 45.13 4.85
690 717 2.229543 GCCTCAAACATTCACTGATGCA 59.770 45.455 0.00 0.00 32.81 3.96
696 723 3.254166 GTGTCATGCCTCAAACATTCACT 59.746 43.478 0.00 0.00 32.11 3.41
736 763 3.645975 AACTTCAACACCGCGCGG 61.646 61.111 44.88 44.88 42.03 6.46
738 765 2.725815 GCAACTTCAACACCGCGC 60.726 61.111 0.00 0.00 0.00 6.86
739 766 1.654137 GTGCAACTTCAACACCGCG 60.654 57.895 0.00 0.00 0.00 6.46
740 767 4.302154 GTGCAACTTCAACACCGC 57.698 55.556 0.00 0.00 0.00 5.68
793 1122 0.389166 CTGAGTGGTCTGGAACGAGC 60.389 60.000 0.00 0.00 0.00 5.03
987 1320 2.441901 GCCATTGGGGGAATGCGA 60.442 61.111 4.53 0.00 40.32 5.10
1170 1509 3.532155 GTCTCTGGAGGCGCCGAT 61.532 66.667 23.20 3.63 40.66 4.18
1179 1518 4.075793 CCCCCTCCGGTCTCTGGA 62.076 72.222 0.00 0.00 0.00 3.86
1265 1604 3.934962 GCAGGATCTCCTCCCCGC 61.935 72.222 0.00 0.00 46.65 6.13
1353 1692 1.293498 GAGCTTGGCGTTGAGGAGA 59.707 57.895 0.00 0.00 0.00 3.71
1417 1759 1.544691 ACACAGATGAGTCGGGTACAC 59.455 52.381 0.00 0.00 0.00 2.90
1515 1874 9.383519 CATTTAGTATGTATCTTGTCCAAGTGT 57.616 33.333 6.90 1.08 39.38 3.55
1675 2045 7.507733 AGCCATAGCAGATAAAAGATGAAAG 57.492 36.000 0.00 0.00 43.56 2.62
1676 2046 7.886629 AAGCCATAGCAGATAAAAGATGAAA 57.113 32.000 0.00 0.00 43.56 2.69
1679 2049 9.622004 CATAAAAGCCATAGCAGATAAAAGATG 57.378 33.333 0.00 0.00 43.56 2.90
1685 2055 9.658799 GAGATACATAAAAGCCATAGCAGATAA 57.341 33.333 0.00 0.00 43.56 1.75
1698 2068 5.980116 CACACTCCGAGGAGATACATAAAAG 59.020 44.000 24.53 4.83 44.53 2.27
1703 2073 3.298686 TCACACTCCGAGGAGATACAT 57.701 47.619 24.53 0.00 44.53 2.29
1765 2135 4.846779 ATTGCACGGCTAAAGAAAAGAA 57.153 36.364 0.00 0.00 0.00 2.52
1954 2329 5.414454 TGTCCATCTTTCCCAACTATTTTCG 59.586 40.000 0.00 0.00 0.00 3.46
2027 2404 1.856629 CAAGAATTGCCACCATCCCT 58.143 50.000 0.00 0.00 40.39 4.20
2058 2435 7.051000 AGTTTAAGGCCTCAAATCTCTGATAC 58.949 38.462 5.23 0.00 0.00 2.24
2130 2507 5.402270 GGCAAAACTGTCAATGACATGTAAC 59.598 40.000 17.10 5.37 41.94 2.50
2209 2586 7.200778 ACAAAAATTGATACATGGGCAAAAC 57.799 32.000 0.00 0.00 0.00 2.43
2343 2725 5.114764 TGCCATGAAATCACTCCTATTCA 57.885 39.130 0.00 0.00 36.35 2.57
2363 2745 7.027778 TGGAAAGAAGAAACTAGAAAACTGC 57.972 36.000 0.00 0.00 0.00 4.40
2402 2788 4.070716 GGATATCCAAAGCATGTCTCAGG 58.929 47.826 17.34 0.00 35.64 3.86
2434 2821 8.462016 GGTTGTCTCATAGCATAATTCTGTTTT 58.538 33.333 0.00 0.00 0.00 2.43
2610 2999 5.421693 TGCCCAAAAGTTGATATAACAGCAT 59.578 36.000 0.00 0.00 0.00 3.79
2773 3162 6.481313 CAGCTTGCAGTATAAGAAATAGCAGA 59.519 38.462 0.00 0.00 0.00 4.26
2879 3271 8.378565 ACATAAGGTTACATCCTTGAGATATGG 58.621 37.037 8.06 0.00 45.96 2.74
2973 3365 8.857694 TTTTCGGATACCACTCTTTTATTTCT 57.142 30.769 0.00 0.00 0.00 2.52
3107 3499 4.958581 TGAACAGAATCTCAGCTGATCCTA 59.041 41.667 18.63 3.72 34.27 2.94
3108 3500 3.773667 TGAACAGAATCTCAGCTGATCCT 59.226 43.478 18.63 9.00 34.27 3.24
3727 4119 3.456280 GATCAGACAGATCCAAGAGTGC 58.544 50.000 0.00 0.00 46.10 4.40
3812 4249 7.564292 AGACTTATATTTAGAAACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
3813 4250 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
3814 4251 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
3815 4252 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
3856 4293 9.642343 TCTACATACATCCTTATGTTGTAGTCT 57.358 33.333 22.56 0.00 44.07 3.24
3857 4294 9.680315 GTCTACATACATCCTTATGTTGTAGTC 57.320 37.037 22.56 18.41 44.07 2.59
3858 4295 9.197306 TGTCTACATACATCCTTATGTTGTAGT 57.803 33.333 22.56 11.46 44.07 2.73
3894 4331 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
3895 4332 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
3896 4333 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
3897 4334 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
3898 4335 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
3899 4336 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
3900 4337 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
3901 4338 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
3902 4339 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
3903 4340 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
3904 4341 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
3905 4342 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
3906 4343 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
3907 4344 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
3908 4345 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
3909 4346 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
3910 4347 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
3911 4348 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
3912 4349 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
3913 4350 4.091509 CCAACAAGTGACTACATACGAAGC 59.908 45.833 0.00 0.00 0.00 3.86
3914 4351 5.466819 TCCAACAAGTGACTACATACGAAG 58.533 41.667 0.00 0.00 0.00 3.79
3915 4352 5.456548 TCCAACAAGTGACTACATACGAA 57.543 39.130 0.00 0.00 0.00 3.85
3916 4353 5.456548 TTCCAACAAGTGACTACATACGA 57.543 39.130 0.00 0.00 0.00 3.43
3917 4354 6.100004 AGATTCCAACAAGTGACTACATACG 58.900 40.000 0.00 0.00 0.00 3.06
3918 4355 7.324178 AGAGATTCCAACAAGTGACTACATAC 58.676 38.462 0.00 0.00 0.00 2.39
3919 4356 7.482169 AGAGATTCCAACAAGTGACTACATA 57.518 36.000 0.00 0.00 0.00 2.29
3920 4357 6.365970 AGAGATTCCAACAAGTGACTACAT 57.634 37.500 0.00 0.00 0.00 2.29
3921 4358 5.808366 AGAGATTCCAACAAGTGACTACA 57.192 39.130 0.00 0.00 0.00 2.74
3922 4359 8.603242 TTTTAGAGATTCCAACAAGTGACTAC 57.397 34.615 0.00 0.00 0.00 2.73
3923 4360 9.273016 CTTTTTAGAGATTCCAACAAGTGACTA 57.727 33.333 0.00 0.00 0.00 2.59
3924 4361 7.993183 TCTTTTTAGAGATTCCAACAAGTGACT 59.007 33.333 0.00 0.00 0.00 3.41
3925 4362 8.070769 GTCTTTTTAGAGATTCCAACAAGTGAC 58.929 37.037 0.00 0.00 0.00 3.67
3926 4363 7.993183 AGTCTTTTTAGAGATTCCAACAAGTGA 59.007 33.333 0.00 0.00 0.00 3.41
3927 4364 8.159344 AGTCTTTTTAGAGATTCCAACAAGTG 57.841 34.615 0.00 0.00 0.00 3.16
3928 4365 8.753497 AAGTCTTTTTAGAGATTCCAACAAGT 57.247 30.769 0.00 0.00 0.00 3.16
3941 4378 9.169592 CCGTTCCCAAATATAAGTCTTTTTAGA 57.830 33.333 0.00 0.00 0.00 2.10
3942 4379 9.169592 TCCGTTCCCAAATATAAGTCTTTTTAG 57.830 33.333 0.00 0.00 0.00 1.85
3943 4380 9.169592 CTCCGTTCCCAAATATAAGTCTTTTTA 57.830 33.333 0.00 0.00 0.00 1.52
3944 4381 7.122204 CCTCCGTTCCCAAATATAAGTCTTTTT 59.878 37.037 0.00 0.00 0.00 1.94
3945 4382 6.602009 CCTCCGTTCCCAAATATAAGTCTTTT 59.398 38.462 0.00 0.00 0.00 2.27
3946 4383 6.120220 CCTCCGTTCCCAAATATAAGTCTTT 58.880 40.000 0.00 0.00 0.00 2.52
3947 4384 5.397559 CCCTCCGTTCCCAAATATAAGTCTT 60.398 44.000 0.00 0.00 0.00 3.01
3948 4385 4.102681 CCCTCCGTTCCCAAATATAAGTCT 59.897 45.833 0.00 0.00 0.00 3.24
3949 4386 4.102054 TCCCTCCGTTCCCAAATATAAGTC 59.898 45.833 0.00 0.00 0.00 3.01
3950 4387 4.042174 TCCCTCCGTTCCCAAATATAAGT 58.958 43.478 0.00 0.00 0.00 2.24
3951 4388 4.102681 ACTCCCTCCGTTCCCAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
3952 4389 4.042174 ACTCCCTCCGTTCCCAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
3953 4390 3.660959 ACTCCCTCCGTTCCCAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
3954 4391 2.488836 ACTCCCTCCGTTCCCAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
3955 4392 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3956 4393 1.961133 TACTCCCTCCGTTCCCAAAT 58.039 50.000 0.00 0.00 0.00 2.32
3957 4394 1.732117 TTACTCCCTCCGTTCCCAAA 58.268 50.000 0.00 0.00 0.00 3.28
3958 4395 1.835531 GATTACTCCCTCCGTTCCCAA 59.164 52.381 0.00 0.00 0.00 4.12
3959 4396 1.492764 GATTACTCCCTCCGTTCCCA 58.507 55.000 0.00 0.00 0.00 4.37
3960 4397 0.388294 CGATTACTCCCTCCGTTCCC 59.612 60.000 0.00 0.00 0.00 3.97
3961 4398 0.388294 CCGATTACTCCCTCCGTTCC 59.612 60.000 0.00 0.00 0.00 3.62
3962 4399 1.109609 ACCGATTACTCCCTCCGTTC 58.890 55.000 0.00 0.00 0.00 3.95
3963 4400 2.442236 TACCGATTACTCCCTCCGTT 57.558 50.000 0.00 0.00 0.00 4.44
3964 4401 2.442236 TTACCGATTACTCCCTCCGT 57.558 50.000 0.00 0.00 0.00 4.69
3965 4402 5.010415 AGTTTATTACCGATTACTCCCTCCG 59.990 44.000 0.00 0.00 0.00 4.63
3966 4403 6.041296 TGAGTTTATTACCGATTACTCCCTCC 59.959 42.308 0.00 0.00 31.93 4.30
3967 4404 6.922407 GTGAGTTTATTACCGATTACTCCCTC 59.078 42.308 0.00 0.00 31.93 4.30
3968 4405 6.610425 AGTGAGTTTATTACCGATTACTCCCT 59.390 38.462 0.00 0.00 31.93 4.20
3969 4406 6.814043 AGTGAGTTTATTACCGATTACTCCC 58.186 40.000 0.00 0.00 31.93 4.30
3970 4407 8.713737 AAAGTGAGTTTATTACCGATTACTCC 57.286 34.615 0.00 0.00 31.93 3.85
3972 4409 9.159364 GGAAAAGTGAGTTTATTACCGATTACT 57.841 33.333 0.00 0.00 0.00 2.24
3973 4410 8.938906 TGGAAAAGTGAGTTTATTACCGATTAC 58.061 33.333 0.00 0.00 0.00 1.89
3974 4411 9.675464 ATGGAAAAGTGAGTTTATTACCGATTA 57.325 29.630 0.00 0.00 0.00 1.75
4047 4502 7.066284 GTCATACATGCAATCTACTTTCTTGGT 59.934 37.037 0.00 0.00 0.00 3.67
4279 4736 9.565213 CTTACAAAAGCTGAGATTTTAGGATTG 57.435 33.333 8.20 0.00 0.00 2.67
4295 4752 7.280428 GGTAGAAAGGACCTATCTTACAAAAGC 59.720 40.741 0.00 0.00 33.86 3.51
4338 4795 9.927081 ACAATCTCATTTTATGGTTCCTATCTT 57.073 29.630 0.00 0.00 0.00 2.40
4434 4891 2.139118 ACGAAGAAGCTTCAGCACTTC 58.861 47.619 27.57 19.35 44.63 3.01
4549 5006 2.302733 TGAGATACAGCCAAGTGCAGAA 59.697 45.455 0.00 0.00 44.83 3.02
4550 5007 1.901833 TGAGATACAGCCAAGTGCAGA 59.098 47.619 0.00 0.00 44.83 4.26


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

AutoCloner maintained by Alex Coulton.