Multiple sequence alignment - TraesCS4A01G198500

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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 TraesCS4A01G198500 chr4A 100.000 4671 0 0 1 4671 484237962 484233292 0.000000e+00 8626.0
1 TraesCS4A01G198500 chr4A 97.170 742 21 0 1 742 419976603 419977344 0.000000e+00 1254.0
2 TraesCS4A01G198500 chr4D 92.643 3697 185 32 744 4391 95530339 95533997 0.000000e+00 5240.0
3 TraesCS4A01G198500 chr4B 91.488 3724 191 46 741 4391 135092209 135095879 0.000000e+00 5005.0
4 TraesCS4A01G198500 chr6A 98.116 743 13 1 1 742 194458631 194459373 0.000000e+00 1293.0
5 TraesCS4A01G198500 chr6A 97.978 742 13 2 1 742 189199014 189198275 0.000000e+00 1286.0
6 TraesCS4A01G198500 chr2A 97.978 742 14 1 1 742 474323050 474323790 0.000000e+00 1286.0
7 TraesCS4A01G198500 chr2A 97.574 742 18 0 1 742 713225759 713226500 0.000000e+00 1271.0
8 TraesCS4A01G198500 chr1A 97.844 742 16 0 1 742 513906469 513907210 0.000000e+00 1282.0
9 TraesCS4A01G198500 chr1A 98.048 666 13 0 77 742 557994674 557995339 0.000000e+00 1158.0
10 TraesCS4A01G198500 chr7A 98.209 726 13 0 1 726 299303074 299302349 0.000000e+00 1269.0
11 TraesCS4A01G198500 chr6B 93.974 697 40 2 1 696 270779760 270780455 0.000000e+00 1053.0
12 TraesCS4A01G198500 chr5B 94.444 54 2 1 699 752 295202872 295202924 1.080000e-11 82.4
13 TraesCS4A01G198500 chr3D 97.059 34 1 0 4133 4166 537634795 537634828 1.820000e-04 58.4


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 TraesCS4A01G198500 chr4A 484233292 484237962 4670 True 8626 8626 100.000 1 4671 1 chr4A.!!$R1 4670
1 TraesCS4A01G198500 chr4A 419976603 419977344 741 False 1254 1254 97.170 1 742 1 chr4A.!!$F1 741
2 TraesCS4A01G198500 chr4D 95530339 95533997 3658 False 5240 5240 92.643 744 4391 1 chr4D.!!$F1 3647
3 TraesCS4A01G198500 chr4B 135092209 135095879 3670 False 5005 5005 91.488 741 4391 1 chr4B.!!$F1 3650
4 TraesCS4A01G198500 chr6A 194458631 194459373 742 False 1293 1293 98.116 1 742 1 chr6A.!!$F1 741
5 TraesCS4A01G198500 chr6A 189198275 189199014 739 True 1286 1286 97.978 1 742 1 chr6A.!!$R1 741
6 TraesCS4A01G198500 chr2A 474323050 474323790 740 False 1286 1286 97.978 1 742 1 chr2A.!!$F1 741
7 TraesCS4A01G198500 chr2A 713225759 713226500 741 False 1271 1271 97.574 1 742 1 chr2A.!!$F2 741
8 TraesCS4A01G198500 chr1A 513906469 513907210 741 False 1282 1282 97.844 1 742 1 chr1A.!!$F1 741
9 TraesCS4A01G198500 chr1A 557994674 557995339 665 False 1158 1158 98.048 77 742 1 chr1A.!!$F2 665
10 TraesCS4A01G198500 chr7A 299302349 299303074 725 True 1269 1269 98.209 1 726 1 chr7A.!!$R1 725
11 TraesCS4A01G198500 chr6B 270779760 270780455 695 False 1053 1053 93.974 1 696 1 chr6B.!!$F1 695

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
442 444 1.069823 CAGGACATTCATCCCTCTCCG 59.930 57.143 0.00 0.00 39.91 4.63 F
1131 1139 0.249120 GTCCCCATCGTGTGATCACA 59.751 55.000 24.56 24.56 44.02 3.58 F
2490 2570 0.388294 GTACAGTGGAGGCGATACCC 59.612 60.000 0.00 0.00 40.58 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2092 1.079405 GAGGATTGGTGCCGACGAA 60.079 57.895 0.0 0.0 0.0 3.85 R
2967 3056 0.250513 AATCCTCCGAACTCTGTGGC 59.749 55.000 0.0 0.0 0.0 5.01 R
4062 4169 0.108186 TCGTCAATGCCGCTTCAGAT 60.108 50.000 0.0 0.0 0.0 2.90 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
111 112 4.822036 CCAGTACGGTCAACAATTTGAA 57.178 40.909 2.79 0.00 43.52 2.69
178 179 8.713036 AGCTTCAGATTTAGAATATTCCTCTGT 58.287 33.333 21.79 6.96 32.49 3.41
442 444 1.069823 CAGGACATTCATCCCTCTCCG 59.930 57.143 0.00 0.00 39.91 4.63
535 537 5.869649 ATTCTAGGTTGGTTTGTTTGCTT 57.130 34.783 0.00 0.00 0.00 3.91
747 750 1.740025 GGCATTTGTGCTAGTGACTCC 59.260 52.381 0.00 0.00 34.73 3.85
752 755 5.390991 GCATTTGTGCTAGTGACTCCTAAAC 60.391 44.000 0.00 0.00 0.00 2.01
763 766 4.452455 GTGACTCCTAAACACAATGTCAGG 59.548 45.833 0.00 4.06 34.32 3.86
822 825 9.999009 CGTCCACGTTATATACATATTACTGAT 57.001 33.333 0.00 0.00 34.11 2.90
851 854 2.226962 AAAGCCCTAGTCTCACGGTA 57.773 50.000 0.00 0.00 0.00 4.02
949 955 7.617041 TCCATAGATCGAGATATATATGCGG 57.383 40.000 0.00 0.00 0.00 5.69
951 957 6.094742 CCATAGATCGAGATATATATGCGGCT 59.905 42.308 0.00 7.67 0.00 5.52
952 958 5.621197 AGATCGAGATATATATGCGGCTC 57.379 43.478 0.00 0.00 0.00 4.70
954 960 3.551846 TCGAGATATATATGCGGCTCCA 58.448 45.455 0.00 0.00 0.00 3.86
955 961 4.145052 TCGAGATATATATGCGGCTCCAT 58.855 43.478 0.00 0.00 0.00 3.41
956 962 4.216472 TCGAGATATATATGCGGCTCCATC 59.784 45.833 0.00 0.00 0.00 3.51
957 963 4.217334 CGAGATATATATGCGGCTCCATCT 59.783 45.833 0.00 1.10 0.00 2.90
1070 1078 1.521457 CGTGCCATGTATCCGCAGT 60.521 57.895 0.00 0.00 32.08 4.40
1131 1139 0.249120 GTCCCCATCGTGTGATCACA 59.751 55.000 24.56 24.56 44.02 3.58
1138 1146 1.212751 CGTGTGATCACAGCGGAGA 59.787 57.895 28.54 1.90 44.02 3.71
1410 1418 3.043586 CGTCTTCATCGAGGTAAATCCG 58.956 50.000 0.00 0.00 41.99 4.18
1446 1472 8.752005 TGATCTTTTTGGGAGTATAAGATTGG 57.248 34.615 0.00 0.00 36.11 3.16
1613 1653 3.470567 GACTTCGCCACGCTCGTG 61.471 66.667 14.78 14.78 45.02 4.35
1702 1742 5.050972 GCGGCAGTAAGTACTAATTGATCAC 60.051 44.000 0.00 0.00 34.13 3.06
1802 1848 4.673534 TTCGAACGGAAAGGATTTTAGC 57.326 40.909 0.00 0.00 39.27 3.09
1832 1878 5.048991 ACTTGACCGTTATTTTCGCAAAGAT 60.049 36.000 0.00 0.00 0.00 2.40
1887 1934 2.724977 TTCGATCGCATCCATAGGAC 57.275 50.000 11.09 0.00 32.98 3.85
1892 1939 3.589988 GATCGCATCCATAGGACGAAAT 58.410 45.455 3.40 0.00 34.73 2.17
1912 1960 5.590530 AATAAAGTGGTTGCAGTGTCAAA 57.409 34.783 2.22 0.00 0.00 2.69
2036 2092 2.124860 GTTATTGGGGCCGTCGCT 60.125 61.111 0.00 0.00 34.44 4.93
2205 2265 2.565841 AGGAGCGCTCATTTGGTATTC 58.434 47.619 36.27 16.29 0.00 1.75
2309 2375 2.817396 GAGCTGGACAAGGCGCTC 60.817 66.667 7.64 0.00 41.60 5.03
2381 2451 1.283487 CGTGCTGCAAACATGCTCA 59.717 52.632 2.77 0.00 35.49 4.26
2418 2488 1.376543 TCGCTAGTTCCTTCGATCGT 58.623 50.000 15.94 0.00 0.00 3.73
2440 2510 7.871853 TCGTTCGATTGATGAATCTATCTGTA 58.128 34.615 3.35 0.43 37.06 2.74
2441 2511 7.803659 TCGTTCGATTGATGAATCTATCTGTAC 59.196 37.037 3.35 8.49 37.06 2.90
2442 2512 7.591426 CGTTCGATTGATGAATCTATCTGTACA 59.409 37.037 3.35 0.00 37.06 2.90
2443 2513 9.416794 GTTCGATTGATGAATCTATCTGTACAT 57.583 33.333 3.35 0.00 37.06 2.29
2460 2540 4.926832 TGTACATATATACACACGCATGCC 59.073 41.667 13.15 0.00 29.97 4.40
2490 2570 0.388294 GTACAGTGGAGGCGATACCC 59.612 60.000 0.00 0.00 40.58 3.69
2561 2641 4.097361 GTCCGGCTTCCTCACCCC 62.097 72.222 0.00 0.00 0.00 4.95
2624 2713 5.679734 TCTCTCACTTCAACTTTTCATGC 57.320 39.130 0.00 0.00 0.00 4.06
2641 2730 0.875728 TGCCGTACGTTTTGGATTGG 59.124 50.000 15.21 0.00 0.00 3.16
2642 2731 0.876399 GCCGTACGTTTTGGATTGGT 59.124 50.000 15.21 0.00 0.00 3.67
2643 2732 1.267533 GCCGTACGTTTTGGATTGGTT 59.732 47.619 15.21 0.00 0.00 3.67
2644 2733 2.918968 GCCGTACGTTTTGGATTGGTTG 60.919 50.000 15.21 0.00 0.00 3.77
2645 2734 2.548904 CCGTACGTTTTGGATTGGTTGA 59.451 45.455 15.21 0.00 0.00 3.18
2646 2735 3.189702 CCGTACGTTTTGGATTGGTTGAT 59.810 43.478 15.21 0.00 0.00 2.57
2647 2736 4.320641 CCGTACGTTTTGGATTGGTTGATT 60.321 41.667 15.21 0.00 0.00 2.57
2648 2737 4.615121 CGTACGTTTTGGATTGGTTGATTG 59.385 41.667 7.22 0.00 0.00 2.67
2652 2741 6.287525 ACGTTTTGGATTGGTTGATTGATTT 58.712 32.000 0.00 0.00 0.00 2.17
2736 2825 2.107141 CGAGGATCAAGGACGCCC 59.893 66.667 0.00 0.00 33.17 6.13
2739 2828 2.190578 GGATCAAGGACGCCCTGG 59.809 66.667 0.00 0.00 43.48 4.45
2740 2829 2.190578 GATCAAGGACGCCCTGGG 59.809 66.667 8.86 8.86 43.48 4.45
2759 2848 2.424956 GGGGGTCTACTACAACTACACG 59.575 54.545 0.00 0.00 0.00 4.49
2885 2974 3.414700 CGCAACGGCAGTGTCCTC 61.415 66.667 0.00 0.00 41.24 3.71
2910 2999 0.955919 GGAGCCCTTCAACTTCACCG 60.956 60.000 0.00 0.00 0.00 4.94
2911 3000 0.955919 GAGCCCTTCAACTTCACCGG 60.956 60.000 0.00 0.00 0.00 5.28
2967 3056 2.734723 CGCGGCCATACTGGATCG 60.735 66.667 2.24 1.59 40.96 3.69
3067 3160 5.405797 GTTCTCTTCAAATTGGGCTCAATC 58.594 41.667 13.35 0.00 42.29 2.67
3075 3168 0.612732 TTGGGCTCAATCAAGGCAGG 60.613 55.000 0.00 0.00 43.32 4.85
3204 3297 6.038382 CAGCTAGCAACATCATCTTCTTCAAT 59.962 38.462 18.83 0.00 0.00 2.57
3298 3392 8.657074 TCGGTAACTGAATTTATCATAGTTGG 57.343 34.615 0.00 0.00 37.44 3.77
3299 3393 8.262227 TCGGTAACTGAATTTATCATAGTTGGT 58.738 33.333 0.00 0.00 37.44 3.67
3329 3423 9.868277 TGTTAAAGCCTTGACCATTTATATTTG 57.132 29.630 0.00 0.00 0.00 2.32
3695 3793 4.764308 TGTATGCATGCTTTGTGTAGGAAA 59.236 37.500 20.33 0.00 0.00 3.13
3701 3799 5.125417 GCATGCTTTGTGTAGGAAAGGAATA 59.875 40.000 11.37 0.00 34.85 1.75
3706 3804 7.502226 TGCTTTGTGTAGGAAAGGAATATATGG 59.498 37.037 0.00 0.00 32.06 2.74
3716 3814 7.127955 AGGAAAGGAATATATGGTGTGTTCTCT 59.872 37.037 0.00 0.00 0.00 3.10
3840 3941 6.545666 TGGAACAAGATGAACTTACACATTGT 59.454 34.615 0.00 0.00 37.03 2.71
3851 3952 7.654116 TGAACTTACACATTGTTCACGATTCTA 59.346 33.333 0.00 0.00 43.15 2.10
3858 3959 7.549134 ACACATTGTTCACGATTCTATGTATGT 59.451 33.333 0.00 0.00 0.00 2.29
3859 3960 8.390354 CACATTGTTCACGATTCTATGTATGTT 58.610 33.333 0.00 0.00 0.00 2.71
3987 4090 3.209410 GGTTGATGATTAGGAGGCAGTG 58.791 50.000 0.00 0.00 0.00 3.66
4040 4147 5.520376 AGGTTTGAAAATCTGGTGTCTTG 57.480 39.130 0.00 0.00 0.00 3.02
4069 4176 8.921353 AGATGGGATATTCTTTCAATCTGAAG 57.079 34.615 0.00 0.00 37.70 3.02
4074 4181 2.183478 TCTTTCAATCTGAAGCGGCA 57.817 45.000 1.45 0.00 37.70 5.69
4077 4184 2.925578 TTCAATCTGAAGCGGCATTG 57.074 45.000 1.45 3.14 31.83 2.82
4078 4185 2.112380 TCAATCTGAAGCGGCATTGA 57.888 45.000 1.45 5.67 33.76 2.57
4081 4188 0.108186 ATCTGAAGCGGCATTGACGA 60.108 50.000 17.84 0.00 35.20 4.20
4117 4224 7.547019 TGTGTCTGTCATGACTTTATCAATCTC 59.453 37.037 25.55 7.57 41.93 2.75
4119 4226 7.547019 TGTCTGTCATGACTTTATCAATCTCAC 59.453 37.037 25.55 5.96 41.93 3.51
4129 4236 0.601057 TCAATCTCACGACTCGCCAA 59.399 50.000 0.00 0.00 0.00 4.52
4132 4239 0.603569 ATCTCACGACTCGCCAACTT 59.396 50.000 0.00 0.00 0.00 2.66
4133 4240 1.241165 TCTCACGACTCGCCAACTTA 58.759 50.000 0.00 0.00 0.00 2.24
4148 4255 4.743955 GCCAACTTAGTCTTTCTGAGGTGT 60.744 45.833 4.50 0.00 43.28 4.16
4162 4269 4.078571 TCTGAGGTGTTCATAGGGATAGGT 60.079 45.833 0.00 0.00 34.68 3.08
4166 4273 4.788617 AGGTGTTCATAGGGATAGGTTGTT 59.211 41.667 0.00 0.00 0.00 2.83
4167 4274 5.253096 AGGTGTTCATAGGGATAGGTTGTTT 59.747 40.000 0.00 0.00 0.00 2.83
4203 4310 7.452880 TGAGTTCAATTCCACCTATTTTCAG 57.547 36.000 0.00 0.00 0.00 3.02
4216 4324 8.956426 CCACCTATTTTCAGTTGAGCTTTATTA 58.044 33.333 0.00 0.00 0.00 0.98
4229 4337 8.883731 GTTGAGCTTTATTAGAACAGATGCTAA 58.116 33.333 0.00 0.00 0.00 3.09
4236 4344 1.276421 AGAACAGATGCTAACACCGCT 59.724 47.619 0.00 0.00 0.00 5.52
4258 4368 2.749076 GCTCATTGTTGTGTGATAGGCA 59.251 45.455 0.00 0.00 0.00 4.75
4264 4374 1.885887 GTTGTGTGATAGGCAAGCCAA 59.114 47.619 14.40 0.00 38.92 4.52
4271 4381 4.080356 TGTGATAGGCAAGCCAAAGTAGAT 60.080 41.667 14.40 0.00 38.92 1.98
4272 4382 4.274459 GTGATAGGCAAGCCAAAGTAGATG 59.726 45.833 14.40 0.00 38.92 2.90
4286 4396 7.553044 GCCAAAGTAGATGTAGAAGTTTATGGT 59.447 37.037 0.00 0.00 0.00 3.55
4393 4505 2.287977 AAAAGGTAAGGTGTGGGAGC 57.712 50.000 0.00 0.00 0.00 4.70
4394 4506 0.036306 AAAGGTAAGGTGTGGGAGCG 59.964 55.000 0.00 0.00 0.00 5.03
4395 4507 0.834687 AAGGTAAGGTGTGGGAGCGA 60.835 55.000 0.00 0.00 0.00 4.93
4396 4508 1.218316 GGTAAGGTGTGGGAGCGAG 59.782 63.158 0.00 0.00 0.00 5.03
4397 4509 1.542187 GGTAAGGTGTGGGAGCGAGT 61.542 60.000 0.00 0.00 0.00 4.18
4398 4510 0.108756 GTAAGGTGTGGGAGCGAGTC 60.109 60.000 0.00 0.00 0.00 3.36
4399 4511 0.541063 TAAGGTGTGGGAGCGAGTCA 60.541 55.000 0.00 0.00 0.00 3.41
4400 4512 1.821061 AAGGTGTGGGAGCGAGTCAG 61.821 60.000 0.00 0.00 0.00 3.51
4401 4513 2.276116 GGTGTGGGAGCGAGTCAGA 61.276 63.158 0.00 0.00 0.00 3.27
4402 4514 1.080434 GTGTGGGAGCGAGTCAGAC 60.080 63.158 0.00 0.00 0.00 3.51
4403 4515 2.179517 GTGGGAGCGAGTCAGACG 59.820 66.667 0.00 0.00 0.00 4.18
4404 4516 2.282251 TGGGAGCGAGTCAGACGT 60.282 61.111 0.00 0.00 0.00 4.34
4405 4517 2.179517 GGGAGCGAGTCAGACGTG 59.820 66.667 0.00 0.00 0.00 4.49
4406 4518 2.179517 GGAGCGAGTCAGACGTGG 59.820 66.667 0.00 0.00 0.00 4.94
4407 4519 2.179517 GAGCGAGTCAGACGTGGG 59.820 66.667 0.00 0.00 0.00 4.61
4408 4520 3.973267 GAGCGAGTCAGACGTGGGC 62.973 68.421 0.00 0.00 0.00 5.36
4409 4521 4.357947 GCGAGTCAGACGTGGGCA 62.358 66.667 0.00 0.00 0.00 5.36
4410 4522 2.126307 CGAGTCAGACGTGGGCAG 60.126 66.667 0.00 0.00 0.00 4.85
4411 4523 2.433318 GAGTCAGACGTGGGCAGC 60.433 66.667 0.00 0.00 0.00 5.25
4412 4524 4.363990 AGTCAGACGTGGGCAGCG 62.364 66.667 0.00 0.00 0.00 5.18
4429 4541 3.712907 GGCCCAGGTAAGCGGTGA 61.713 66.667 0.00 0.00 0.00 4.02
4430 4542 2.590092 GCCCAGGTAAGCGGTGAT 59.410 61.111 0.00 0.00 0.00 3.06
4431 4543 1.523938 GCCCAGGTAAGCGGTGATC 60.524 63.158 0.00 0.00 0.00 2.92
4432 4544 1.972660 GCCCAGGTAAGCGGTGATCT 61.973 60.000 0.00 0.00 0.00 2.75
4433 4545 0.179073 CCCAGGTAAGCGGTGATCTG 60.179 60.000 5.15 5.15 0.00 2.90
4434 4546 0.179073 CCAGGTAAGCGGTGATCTGG 60.179 60.000 16.92 16.92 36.28 3.86
4435 4547 0.824109 CAGGTAAGCGGTGATCTGGA 59.176 55.000 4.13 0.00 0.00 3.86
4436 4548 1.207089 CAGGTAAGCGGTGATCTGGAA 59.793 52.381 4.13 0.00 0.00 3.53
4437 4549 1.906574 AGGTAAGCGGTGATCTGGAAA 59.093 47.619 0.00 0.00 0.00 3.13
4438 4550 2.505819 AGGTAAGCGGTGATCTGGAAAT 59.494 45.455 0.00 0.00 0.00 2.17
4439 4551 2.614057 GGTAAGCGGTGATCTGGAAATG 59.386 50.000 0.00 0.00 0.00 2.32
4440 4552 2.496899 AAGCGGTGATCTGGAAATGT 57.503 45.000 0.00 0.00 0.00 2.71
4441 4553 2.496899 AGCGGTGATCTGGAAATGTT 57.503 45.000 0.00 0.00 0.00 2.71
4442 4554 2.795329 AGCGGTGATCTGGAAATGTTT 58.205 42.857 0.00 0.00 0.00 2.83
4443 4555 3.157087 AGCGGTGATCTGGAAATGTTTT 58.843 40.909 0.00 0.00 0.00 2.43
4444 4556 3.191371 AGCGGTGATCTGGAAATGTTTTC 59.809 43.478 0.00 0.00 0.00 2.29
4445 4557 3.057596 GCGGTGATCTGGAAATGTTTTCA 60.058 43.478 0.00 0.00 0.00 2.69
4446 4558 4.475944 CGGTGATCTGGAAATGTTTTCAC 58.524 43.478 0.00 0.00 33.10 3.18
4447 4559 4.615912 CGGTGATCTGGAAATGTTTTCACC 60.616 45.833 12.86 12.86 45.15 4.02
4448 4560 4.475944 GTGATCTGGAAATGTTTTCACCG 58.524 43.478 0.00 0.00 0.00 4.94
4449 4561 3.057596 TGATCTGGAAATGTTTTCACCGC 60.058 43.478 0.00 0.00 0.00 5.68
4450 4562 2.582052 TCTGGAAATGTTTTCACCGCT 58.418 42.857 2.74 0.00 0.00 5.52
4451 4563 2.955660 TCTGGAAATGTTTTCACCGCTT 59.044 40.909 2.74 0.00 0.00 4.68
4452 4564 3.383185 TCTGGAAATGTTTTCACCGCTTT 59.617 39.130 2.74 0.00 0.00 3.51
4453 4565 4.119136 CTGGAAATGTTTTCACCGCTTTT 58.881 39.130 2.74 0.00 0.00 2.27
4454 4566 3.868077 TGGAAATGTTTTCACCGCTTTTG 59.132 39.130 2.74 0.00 0.00 2.44
4455 4567 3.247411 GGAAATGTTTTCACCGCTTTTGG 59.753 43.478 2.74 0.00 0.00 3.28
4456 4568 2.524569 ATGTTTTCACCGCTTTTGGG 57.475 45.000 0.00 0.00 0.00 4.12
4457 4569 1.475403 TGTTTTCACCGCTTTTGGGA 58.525 45.000 0.00 0.00 33.84 4.37
4458 4570 1.825474 TGTTTTCACCGCTTTTGGGAA 59.175 42.857 0.00 0.00 33.84 3.97
4459 4571 2.159170 TGTTTTCACCGCTTTTGGGAAG 60.159 45.455 0.00 0.00 33.84 3.46
4460 4572 1.770294 TTTCACCGCTTTTGGGAAGT 58.230 45.000 0.00 0.00 33.84 3.01
4461 4573 1.770294 TTCACCGCTTTTGGGAAGTT 58.230 45.000 0.00 0.00 33.84 2.66
4462 4574 1.770294 TCACCGCTTTTGGGAAGTTT 58.230 45.000 0.00 0.00 33.84 2.66
4463 4575 1.679153 TCACCGCTTTTGGGAAGTTTC 59.321 47.619 0.00 0.00 33.84 2.78
4464 4576 1.037493 ACCGCTTTTGGGAAGTTTCC 58.963 50.000 2.17 2.17 46.82 3.13
4476 4588 3.792401 GGAAGTTTCCAACCAGGTTTTG 58.208 45.455 0.44 0.00 46.76 2.44
4477 4589 3.196901 GGAAGTTTCCAACCAGGTTTTGT 59.803 43.478 0.44 0.00 46.76 2.83
4478 4590 4.323180 GGAAGTTTCCAACCAGGTTTTGTT 60.323 41.667 0.44 0.00 46.76 2.83
4479 4591 4.901197 AGTTTCCAACCAGGTTTTGTTT 57.099 36.364 0.44 0.00 39.02 2.83
4480 4592 4.827692 AGTTTCCAACCAGGTTTTGTTTC 58.172 39.130 0.44 0.00 39.02 2.78
4481 4593 4.530553 AGTTTCCAACCAGGTTTTGTTTCT 59.469 37.500 0.44 0.00 39.02 2.52
4482 4594 5.012664 AGTTTCCAACCAGGTTTTGTTTCTT 59.987 36.000 0.44 0.00 39.02 2.52
4483 4595 5.491323 TTCCAACCAGGTTTTGTTTCTTT 57.509 34.783 0.44 0.00 39.02 2.52
4484 4596 5.491323 TCCAACCAGGTTTTGTTTCTTTT 57.509 34.783 0.44 0.00 39.02 2.27
4485 4597 5.483811 TCCAACCAGGTTTTGTTTCTTTTC 58.516 37.500 0.44 0.00 39.02 2.29
4486 4598 5.247337 TCCAACCAGGTTTTGTTTCTTTTCT 59.753 36.000 0.44 0.00 39.02 2.52
4487 4599 5.580691 CCAACCAGGTTTTGTTTCTTTTCTC 59.419 40.000 0.44 0.00 0.00 2.87
4488 4600 6.398095 CAACCAGGTTTTGTTTCTTTTCTCT 58.602 36.000 0.44 0.00 0.00 3.10
4489 4601 7.363443 CCAACCAGGTTTTGTTTCTTTTCTCTA 60.363 37.037 0.44 0.00 0.00 2.43
4490 4602 7.898014 ACCAGGTTTTGTTTCTTTTCTCTAT 57.102 32.000 0.00 0.00 0.00 1.98
4491 4603 8.306313 ACCAGGTTTTGTTTCTTTTCTCTATT 57.694 30.769 0.00 0.00 0.00 1.73
4492 4604 8.414003 ACCAGGTTTTGTTTCTTTTCTCTATTC 58.586 33.333 0.00 0.00 0.00 1.75
4493 4605 8.413229 CCAGGTTTTGTTTCTTTTCTCTATTCA 58.587 33.333 0.00 0.00 0.00 2.57
4494 4606 9.971922 CAGGTTTTGTTTCTTTTCTCTATTCAT 57.028 29.630 0.00 0.00 0.00 2.57
4501 4613 9.748708 TGTTTCTTTTCTCTATTCATTTGTTGG 57.251 29.630 0.00 0.00 0.00 3.77
4502 4614 9.750125 GTTTCTTTTCTCTATTCATTTGTTGGT 57.250 29.630 0.00 0.00 0.00 3.67
4510 4622 9.527157 TCTCTATTCATTTGTTGGTTTTATGGA 57.473 29.630 0.00 0.00 0.00 3.41
4513 4625 9.927668 CTATTCATTTGTTGGTTTTATGGAAGT 57.072 29.630 0.00 0.00 0.00 3.01
4514 4626 8.606040 ATTCATTTGTTGGTTTTATGGAAGTG 57.394 30.769 0.00 0.00 0.00 3.16
4515 4627 7.118496 TCATTTGTTGGTTTTATGGAAGTGT 57.882 32.000 0.00 0.00 0.00 3.55
4516 4628 7.560368 TCATTTGTTGGTTTTATGGAAGTGTT 58.440 30.769 0.00 0.00 0.00 3.32
4517 4629 8.043710 TCATTTGTTGGTTTTATGGAAGTGTTT 58.956 29.630 0.00 0.00 0.00 2.83
4518 4630 7.602517 TTTGTTGGTTTTATGGAAGTGTTTG 57.397 32.000 0.00 0.00 0.00 2.93
4519 4631 6.287589 TGTTGGTTTTATGGAAGTGTTTGT 57.712 33.333 0.00 0.00 0.00 2.83
4520 4632 6.102663 TGTTGGTTTTATGGAAGTGTTTGTG 58.897 36.000 0.00 0.00 0.00 3.33
4521 4633 5.923733 TGGTTTTATGGAAGTGTTTGTGT 57.076 34.783 0.00 0.00 0.00 3.72
4522 4634 6.287589 TGGTTTTATGGAAGTGTTTGTGTT 57.712 33.333 0.00 0.00 0.00 3.32
4523 4635 6.334202 TGGTTTTATGGAAGTGTTTGTGTTC 58.666 36.000 0.00 0.00 0.00 3.18
4524 4636 6.153680 TGGTTTTATGGAAGTGTTTGTGTTCT 59.846 34.615 0.00 0.00 0.00 3.01
4525 4637 6.475402 GGTTTTATGGAAGTGTTTGTGTTCTG 59.525 38.462 0.00 0.00 0.00 3.02
4526 4638 6.767524 TTTATGGAAGTGTTTGTGTTCTGT 57.232 33.333 0.00 0.00 0.00 3.41
4527 4639 6.767524 TTATGGAAGTGTTTGTGTTCTGTT 57.232 33.333 0.00 0.00 0.00 3.16
4528 4640 5.659440 ATGGAAGTGTTTGTGTTCTGTTT 57.341 34.783 0.00 0.00 0.00 2.83
4529 4641 5.461032 TGGAAGTGTTTGTGTTCTGTTTT 57.539 34.783 0.00 0.00 0.00 2.43
4530 4642 5.848406 TGGAAGTGTTTGTGTTCTGTTTTT 58.152 33.333 0.00 0.00 0.00 1.94
4550 4662 6.966534 TTTTTCATTTCTCTGCCTCTTTCT 57.033 33.333 0.00 0.00 0.00 2.52
4551 4663 6.966534 TTTTCATTTCTCTGCCTCTTTCTT 57.033 33.333 0.00 0.00 0.00 2.52
4552 4664 6.566197 TTTCATTTCTCTGCCTCTTTCTTC 57.434 37.500 0.00 0.00 0.00 2.87
4553 4665 5.495926 TCATTTCTCTGCCTCTTTCTTCT 57.504 39.130 0.00 0.00 0.00 2.85
4554 4666 5.874093 TCATTTCTCTGCCTCTTTCTTCTT 58.126 37.500 0.00 0.00 0.00 2.52
4555 4667 6.302269 TCATTTCTCTGCCTCTTTCTTCTTT 58.698 36.000 0.00 0.00 0.00 2.52
4556 4668 6.429385 TCATTTCTCTGCCTCTTTCTTCTTTC 59.571 38.462 0.00 0.00 0.00 2.62
4557 4669 5.559148 TTCTCTGCCTCTTTCTTCTTTCT 57.441 39.130 0.00 0.00 0.00 2.52
4558 4670 4.892433 TCTCTGCCTCTTTCTTCTTTCTG 58.108 43.478 0.00 0.00 0.00 3.02
4559 4671 4.346418 TCTCTGCCTCTTTCTTCTTTCTGT 59.654 41.667 0.00 0.00 0.00 3.41
4560 4672 5.041191 TCTGCCTCTTTCTTCTTTCTGTT 57.959 39.130 0.00 0.00 0.00 3.16
4561 4673 5.440610 TCTGCCTCTTTCTTCTTTCTGTTT 58.559 37.500 0.00 0.00 0.00 2.83
4562 4674 5.888161 TCTGCCTCTTTCTTCTTTCTGTTTT 59.112 36.000 0.00 0.00 0.00 2.43
4563 4675 6.378280 TCTGCCTCTTTCTTCTTTCTGTTTTT 59.622 34.615 0.00 0.00 0.00 1.94
4601 4713 6.595772 TTTTTGGATCCGTCAACATTTTTG 57.404 33.333 7.39 0.00 0.00 2.44
4602 4714 3.932545 TGGATCCGTCAACATTTTTGG 57.067 42.857 7.39 0.00 0.00 3.28
4603 4715 3.491342 TGGATCCGTCAACATTTTTGGA 58.509 40.909 7.39 0.00 0.00 3.53
4604 4716 3.891977 TGGATCCGTCAACATTTTTGGAA 59.108 39.130 7.39 0.00 0.00 3.53
4605 4717 4.526262 TGGATCCGTCAACATTTTTGGAAT 59.474 37.500 7.39 0.00 0.00 3.01
4606 4718 5.011533 TGGATCCGTCAACATTTTTGGAATT 59.988 36.000 7.39 0.00 0.00 2.17
4607 4719 5.576774 GGATCCGTCAACATTTTTGGAATTC 59.423 40.000 0.00 0.00 0.00 2.17
4608 4720 5.521906 TCCGTCAACATTTTTGGAATTCA 57.478 34.783 7.93 0.00 0.00 2.57
4609 4721 6.095432 TCCGTCAACATTTTTGGAATTCAT 57.905 33.333 7.93 0.00 0.00 2.57
4610 4722 7.220741 TCCGTCAACATTTTTGGAATTCATA 57.779 32.000 7.93 0.00 0.00 2.15
4611 4723 7.835822 TCCGTCAACATTTTTGGAATTCATAT 58.164 30.769 7.93 0.00 0.00 1.78
4612 4724 8.961634 TCCGTCAACATTTTTGGAATTCATATA 58.038 29.630 7.93 0.00 0.00 0.86
4613 4725 9.019764 CCGTCAACATTTTTGGAATTCATATAC 57.980 33.333 7.93 0.00 0.00 1.47
4614 4726 9.787532 CGTCAACATTTTTGGAATTCATATACT 57.212 29.630 7.93 0.00 0.00 2.12
4658 4770 6.852858 TTTTTGAATTCCCGAACCATTTTC 57.147 33.333 2.27 0.00 0.00 2.29
4659 4771 5.799827 TTTGAATTCCCGAACCATTTTCT 57.200 34.783 2.27 0.00 0.00 2.52
4660 4772 5.799827 TTGAATTCCCGAACCATTTTCTT 57.200 34.783 2.27 0.00 0.00 2.52
4661 4773 6.902771 TTGAATTCCCGAACCATTTTCTTA 57.097 33.333 2.27 0.00 0.00 2.10
4662 4774 6.509418 TGAATTCCCGAACCATTTTCTTAG 57.491 37.500 2.27 0.00 0.00 2.18
4663 4775 6.242396 TGAATTCCCGAACCATTTTCTTAGA 58.758 36.000 2.27 0.00 0.00 2.10
4664 4776 6.889722 TGAATTCCCGAACCATTTTCTTAGAT 59.110 34.615 2.27 0.00 0.00 1.98
4665 4777 7.396055 TGAATTCCCGAACCATTTTCTTAGATT 59.604 33.333 2.27 0.00 0.00 2.40
4666 4778 7.718334 ATTCCCGAACCATTTTCTTAGATTT 57.282 32.000 0.00 0.00 0.00 2.17
4667 4779 6.509418 TCCCGAACCATTTTCTTAGATTTG 57.491 37.500 0.00 0.00 0.00 2.32
4668 4780 6.007703 TCCCGAACCATTTTCTTAGATTTGT 58.992 36.000 0.00 0.00 0.00 2.83
4669 4781 6.072175 TCCCGAACCATTTTCTTAGATTTGTG 60.072 38.462 0.00 0.00 0.00 3.33
4670 4782 6.072175 CCCGAACCATTTTCTTAGATTTGTGA 60.072 38.462 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 4.523943 TGAAGCTACCGGTAGTTAAGTTCA 59.476 41.667 35.78 29.44 35.65 3.18
153 154 8.900983 ACAGAGGAATATTCTAAATCTGAAGC 57.099 34.615 27.73 8.66 36.91 3.86
178 179 2.765689 AACCACCATCTGTCCCAAAA 57.234 45.000 0.00 0.00 0.00 2.44
442 444 2.456119 CGATGAGAGCGTTGTGGGC 61.456 63.158 0.00 0.00 0.00 5.36
763 766 6.183359 GCGGCTATAGTCGTATACAATGTTTC 60.183 42.308 26.19 2.79 46.15 2.78
778 781 0.524816 CGTGACAACGCGGCTATAGT 60.525 55.000 12.47 0.00 43.98 2.12
830 833 1.697982 ACCGTGAGACTAGGGCTTTTT 59.302 47.619 0.00 0.00 0.00 1.94
831 834 1.349067 ACCGTGAGACTAGGGCTTTT 58.651 50.000 0.00 0.00 0.00 2.27
832 835 2.100989 CTACCGTGAGACTAGGGCTTT 58.899 52.381 0.00 0.00 0.00 3.51
833 836 1.765230 CTACCGTGAGACTAGGGCTT 58.235 55.000 0.00 0.00 0.00 4.35
834 837 0.752376 GCTACCGTGAGACTAGGGCT 60.752 60.000 0.00 0.00 0.00 5.19
851 854 0.471617 CAGCTATAACCCAGCCAGCT 59.528 55.000 0.00 0.00 43.16 4.24
949 955 3.569701 TGGAACAGTTTTTCAGATGGAGC 59.430 43.478 0.00 0.00 0.00 4.70
951 957 4.531854 TGTGGAACAGTTTTTCAGATGGA 58.468 39.130 0.00 0.00 45.67 3.41
952 958 4.916983 TGTGGAACAGTTTTTCAGATGG 57.083 40.909 0.00 0.00 45.67 3.51
1428 1443 5.134339 AGCATCCCAATCTTATACTCCCAAA 59.866 40.000 0.00 0.00 0.00 3.28
1466 1492 4.754372 TTGCAGACACATCAAGAATCAC 57.246 40.909 0.00 0.00 0.00 3.06
1702 1742 3.338249 CACAGTACTTGGTGAATGGAGG 58.662 50.000 7.42 0.00 37.18 4.30
1741 1787 6.447084 AGATATCCTTGAGGTTTTAGGGTCAA 59.553 38.462 0.00 0.00 36.34 3.18
1802 1848 5.562623 GCGAAAATAACGGTCAAGTAACAAG 59.437 40.000 0.00 0.00 0.00 3.16
1859 1906 5.107109 TGGATGCGATCGAATATTTTTGG 57.893 39.130 21.57 0.00 0.00 3.28
1861 1908 6.878923 TCCTATGGATGCGATCGAATATTTTT 59.121 34.615 21.57 0.61 0.00 1.94
1887 1934 4.219033 GACACTGCAACCACTTTATTTCG 58.781 43.478 0.00 0.00 0.00 3.46
1892 1939 4.265893 TCTTTGACACTGCAACCACTTTA 58.734 39.130 0.00 0.00 0.00 1.85
2036 2092 1.079405 GAGGATTGGTGCCGACGAA 60.079 57.895 0.00 0.00 0.00 3.85
2134 2194 2.813754 TGAACTTATGAGTTGCAGGTGC 59.186 45.455 7.73 0.00 45.88 5.01
2177 2237 1.317613 ATGAGCGCTCCTAGAGTCAG 58.682 55.000 33.23 0.00 31.39 3.51
2187 2247 1.261619 CGGAATACCAAATGAGCGCTC 59.738 52.381 30.42 30.42 35.59 5.03
2224 2284 6.348295 GCTCTAACACAGGCATAATGATCATG 60.348 42.308 9.46 0.00 0.00 3.07
2242 2308 4.513000 CAATTCTTGCTCTCGCTCTAAC 57.487 45.455 0.00 0.00 36.97 2.34
2372 2442 2.447443 TCGTCTCTAGGTGAGCATGTT 58.553 47.619 0.00 0.00 42.38 2.71
2440 2510 3.996363 CAGGCATGCGTGTGTATATATGT 59.004 43.478 27.92 0.00 0.00 2.29
2441 2511 3.181517 GCAGGCATGCGTGTGTATATATG 60.182 47.826 33.60 11.49 43.87 1.78
2442 2512 3.002791 GCAGGCATGCGTGTGTATATAT 58.997 45.455 33.60 0.00 43.87 0.86
2443 2513 2.412870 GCAGGCATGCGTGTGTATATA 58.587 47.619 33.60 0.00 43.87 0.86
2444 2514 1.229428 GCAGGCATGCGTGTGTATAT 58.771 50.000 33.60 1.42 43.87 0.86
2445 2515 2.689083 GCAGGCATGCGTGTGTATA 58.311 52.632 33.60 0.00 43.87 1.47
2446 2516 3.501396 GCAGGCATGCGTGTGTAT 58.499 55.556 33.60 3.75 43.87 2.29
2460 2540 2.425312 CTCCACTGTACTACCTCTGCAG 59.575 54.545 7.63 7.63 0.00 4.41
2608 2697 3.059188 CGTACGGCATGAAAAGTTGAAGT 60.059 43.478 7.57 0.00 0.00 3.01
2624 2713 2.548904 TCAACCAATCCAAAACGTACGG 59.451 45.455 21.06 0.68 0.00 4.02
2641 2730 8.522830 TGAGGAAGACCAAATAAATCAATCAAC 58.477 33.333 0.00 0.00 38.94 3.18
2642 2731 8.648698 TGAGGAAGACCAAATAAATCAATCAA 57.351 30.769 0.00 0.00 38.94 2.57
2643 2732 8.827832 ATGAGGAAGACCAAATAAATCAATCA 57.172 30.769 0.00 0.00 38.94 2.57
2644 2733 9.741647 GAATGAGGAAGACCAAATAAATCAATC 57.258 33.333 0.00 0.00 38.94 2.67
2645 2734 9.258629 TGAATGAGGAAGACCAAATAAATCAAT 57.741 29.630 0.00 0.00 38.94 2.57
2646 2735 8.648698 TGAATGAGGAAGACCAAATAAATCAA 57.351 30.769 0.00 0.00 38.94 2.57
2647 2736 8.108999 TCTGAATGAGGAAGACCAAATAAATCA 58.891 33.333 0.00 0.00 38.94 2.57
2648 2737 8.511604 TCTGAATGAGGAAGACCAAATAAATC 57.488 34.615 0.00 0.00 38.94 2.17
2652 2741 6.825213 CACATCTGAATGAGGAAGACCAAATA 59.175 38.462 0.00 0.00 36.08 1.40
2736 2825 3.446516 GTGTAGTTGTAGTAGACCCCCAG 59.553 52.174 0.00 0.00 0.00 4.45
2739 2828 2.424956 CCGTGTAGTTGTAGTAGACCCC 59.575 54.545 0.00 0.00 0.00 4.95
2740 2829 2.424956 CCCGTGTAGTTGTAGTAGACCC 59.575 54.545 0.00 0.00 0.00 4.46
2967 3056 0.250513 AATCCTCCGAACTCTGTGGC 59.749 55.000 0.00 0.00 0.00 5.01
3011 3104 5.822519 AGACAAGCTGTTATTCTCACAACAA 59.177 36.000 0.00 0.00 34.43 2.83
3067 3160 1.114722 TCAGCCCAAAACCTGCCTTG 61.115 55.000 0.00 0.00 0.00 3.61
3075 3168 4.252878 CCCATGTATTTTCAGCCCAAAAC 58.747 43.478 0.00 0.00 0.00 2.43
3204 3297 2.142761 CCATGGATCTCGGAGCCCA 61.143 63.158 5.56 17.21 37.30 5.36
3257 3350 9.878667 TCAGTTACCGAAATTCATCTAAACATA 57.121 29.630 0.00 0.00 0.00 2.29
3258 3351 8.786826 TCAGTTACCGAAATTCATCTAAACAT 57.213 30.769 0.00 0.00 0.00 2.71
3259 3352 8.610248 TTCAGTTACCGAAATTCATCTAAACA 57.390 30.769 0.00 0.00 0.00 2.83
3298 3392 3.153919 TGGTCAAGGCTTTAACATGGAC 58.846 45.455 0.00 0.00 0.00 4.02
3299 3393 3.517296 TGGTCAAGGCTTTAACATGGA 57.483 42.857 0.00 0.00 0.00 3.41
3329 3423 0.589729 CGCTGCGCAATATGTCCAAC 60.590 55.000 13.05 0.00 0.00 3.77
3505 3601 2.185004 TCCAACAGCCTTAGCAGAAC 57.815 50.000 0.00 0.00 43.56 3.01
3695 3793 6.146760 AGGAGAGAACACACCATATATTCCT 58.853 40.000 0.00 0.00 0.00 3.36
3701 3799 6.306987 ACAAAAAGGAGAGAACACACCATAT 58.693 36.000 0.00 0.00 0.00 1.78
3706 3804 5.560966 TGAACAAAAAGGAGAGAACACAC 57.439 39.130 0.00 0.00 0.00 3.82
3799 3897 7.224297 TCTTGTTCCAATATAAGCTGGGATAC 58.776 38.462 0.00 0.00 33.19 2.24
3825 3926 6.481976 AGAATCGTGAACAATGTGTAAGTTCA 59.518 34.615 0.00 0.00 46.53 3.18
3840 3941 9.256477 GGACATAAACATACATAGAATCGTGAA 57.744 33.333 0.00 0.00 0.00 3.18
3845 3946 7.656137 ACGTGGGACATAAACATACATAGAATC 59.344 37.037 0.00 0.00 44.52 2.52
3851 3952 5.092554 TCACGTGGGACATAAACATACAT 57.907 39.130 17.00 0.00 44.52 2.29
3858 3959 2.236146 AGCTCATCACGTGGGACATAAA 59.764 45.455 17.00 0.00 44.52 1.40
3859 3960 1.831106 AGCTCATCACGTGGGACATAA 59.169 47.619 17.00 0.00 44.52 1.90
3941 4043 0.478072 TTGGTTGTCCAGCTGGTCAT 59.522 50.000 29.38 0.00 45.22 3.06
3942 4044 0.465460 GTTGGTTGTCCAGCTGGTCA 60.465 55.000 31.58 28.74 45.22 4.02
3943 4045 2.331265 GTTGGTTGTCCAGCTGGTC 58.669 57.895 31.58 26.39 45.22 4.02
4017 4124 6.126409 ACAAGACACCAGATTTTCAAACCTA 58.874 36.000 0.00 0.00 0.00 3.08
4026 4133 5.711976 CCCATCTTTACAAGACACCAGATTT 59.288 40.000 0.00 0.00 41.01 2.17
4027 4134 5.014123 TCCCATCTTTACAAGACACCAGATT 59.986 40.000 0.00 0.00 41.01 2.40
4028 4135 4.536090 TCCCATCTTTACAAGACACCAGAT 59.464 41.667 0.00 0.00 41.01 2.90
4030 4137 4.286297 TCCCATCTTTACAAGACACCAG 57.714 45.455 0.00 0.00 41.01 4.00
4046 4153 6.206243 CGCTTCAGATTGAAAGAATATCCCAT 59.794 38.462 0.00 0.00 35.73 4.00
4047 4154 5.528690 CGCTTCAGATTGAAAGAATATCCCA 59.471 40.000 0.00 0.00 35.73 4.37
4062 4169 0.108186 TCGTCAATGCCGCTTCAGAT 60.108 50.000 0.00 0.00 0.00 2.90
4065 4172 2.379634 CGTCGTCAATGCCGCTTCA 61.380 57.895 0.00 0.00 0.00 3.02
4069 4176 1.846648 CTATCGTCGTCAATGCCGC 59.153 57.895 0.00 0.00 0.00 6.53
4074 4181 2.223502 ACACATCGCTATCGTCGTCAAT 60.224 45.455 0.00 0.00 36.96 2.57
4077 4184 1.003759 AGACACATCGCTATCGTCGTC 60.004 52.381 0.00 0.00 36.96 4.20
4078 4185 1.015109 AGACACATCGCTATCGTCGT 58.985 50.000 0.00 0.00 36.96 4.34
4081 4188 1.743394 TGACAGACACATCGCTATCGT 59.257 47.619 0.00 0.00 36.96 3.73
4117 4224 1.068472 AGACTAAGTTGGCGAGTCGTG 60.068 52.381 15.08 0.00 43.57 4.35
4119 4226 2.349297 AAGACTAAGTTGGCGAGTCG 57.651 50.000 8.54 8.54 43.57 4.18
4129 4236 5.871396 TGAACACCTCAGAAAGACTAAGT 57.129 39.130 0.00 0.00 0.00 2.24
4132 4239 5.422331 CCCTATGAACACCTCAGAAAGACTA 59.578 44.000 0.00 0.00 37.52 2.59
4133 4240 4.223923 CCCTATGAACACCTCAGAAAGACT 59.776 45.833 0.00 0.00 37.52 3.24
4148 4255 6.785076 TGAACAAACAACCTATCCCTATGAA 58.215 36.000 0.00 0.00 0.00 2.57
4162 4269 5.352846 TGAACTCATCTCGTTGAACAAACAA 59.647 36.000 0.00 0.00 38.84 2.83
4166 4273 6.293407 GGAATTGAACTCATCTCGTTGAACAA 60.293 38.462 0.00 0.00 0.00 2.83
4167 4274 5.179368 GGAATTGAACTCATCTCGTTGAACA 59.821 40.000 0.00 0.00 0.00 3.18
4203 4310 7.313951 AGCATCTGTTCTAATAAAGCTCAAC 57.686 36.000 0.00 0.00 0.00 3.18
4216 4324 1.276421 AGCGGTGTTAGCATCTGTTCT 59.724 47.619 0.00 0.00 37.01 3.01
4229 4337 0.819259 ACAACAATGAGCAGCGGTGT 60.819 50.000 17.07 2.78 0.00 4.16
4236 4344 2.749076 GCCTATCACACAACAATGAGCA 59.251 45.455 0.00 0.00 0.00 4.26
4258 4368 9.167311 CATAAACTTCTACATCTACTTTGGCTT 57.833 33.333 0.00 0.00 0.00 4.35
4286 4396 4.706616 AGGAAGGGAGGGATGTAGTTTAA 58.293 43.478 0.00 0.00 0.00 1.52
4299 4409 2.840651 AGTACATCACCAAGGAAGGGAG 59.159 50.000 0.00 0.00 0.00 4.30
4336 4446 7.362234 AGGGCTTTATTGATTAAACCATAGGT 58.638 34.615 0.00 0.00 37.65 3.08
4391 4503 4.057428 GCCCACGTCTGACTCGCT 62.057 66.667 6.21 0.00 0.00 4.93
4392 4504 4.357947 TGCCCACGTCTGACTCGC 62.358 66.667 6.21 2.74 0.00 5.03
4393 4505 2.126307 CTGCCCACGTCTGACTCG 60.126 66.667 6.21 0.00 0.00 4.18
4394 4506 2.433318 GCTGCCCACGTCTGACTC 60.433 66.667 6.21 0.00 0.00 3.36
4395 4507 4.363990 CGCTGCCCACGTCTGACT 62.364 66.667 6.21 0.00 0.00 3.41
4412 4524 2.942648 GATCACCGCTTACCTGGGCC 62.943 65.000 0.00 0.00 0.00 5.80
4413 4525 1.523938 GATCACCGCTTACCTGGGC 60.524 63.158 0.00 0.00 0.00 5.36
4414 4526 0.179073 CAGATCACCGCTTACCTGGG 60.179 60.000 0.00 0.00 0.00 4.45
4415 4527 0.179073 CCAGATCACCGCTTACCTGG 60.179 60.000 0.00 0.00 35.75 4.45
4416 4528 0.824109 TCCAGATCACCGCTTACCTG 59.176 55.000 0.00 0.00 0.00 4.00
4417 4529 1.568504 TTCCAGATCACCGCTTACCT 58.431 50.000 0.00 0.00 0.00 3.08
4418 4530 2.396590 TTTCCAGATCACCGCTTACC 57.603 50.000 0.00 0.00 0.00 2.85
4419 4531 3.270877 ACATTTCCAGATCACCGCTTAC 58.729 45.455 0.00 0.00 0.00 2.34
4420 4532 3.627395 ACATTTCCAGATCACCGCTTA 57.373 42.857 0.00 0.00 0.00 3.09
4421 4533 2.496899 ACATTTCCAGATCACCGCTT 57.503 45.000 0.00 0.00 0.00 4.68
4422 4534 2.496899 AACATTTCCAGATCACCGCT 57.503 45.000 0.00 0.00 0.00 5.52
4423 4535 3.057596 TGAAAACATTTCCAGATCACCGC 60.058 43.478 0.00 0.00 0.00 5.68
4424 4536 4.475944 GTGAAAACATTTCCAGATCACCG 58.524 43.478 0.00 0.00 31.81 4.94
4425 4537 4.809673 GGTGAAAACATTTCCAGATCACC 58.190 43.478 6.31 6.31 45.80 4.02
4426 4538 4.475944 CGGTGAAAACATTTCCAGATCAC 58.524 43.478 0.00 0.00 36.01 3.06
4427 4539 3.057596 GCGGTGAAAACATTTCCAGATCA 60.058 43.478 0.00 0.00 0.00 2.92
4428 4540 3.191371 AGCGGTGAAAACATTTCCAGATC 59.809 43.478 0.00 0.00 0.00 2.75
4429 4541 3.157087 AGCGGTGAAAACATTTCCAGAT 58.843 40.909 0.00 0.00 0.00 2.90
4430 4542 2.582052 AGCGGTGAAAACATTTCCAGA 58.418 42.857 0.00 0.00 0.00 3.86
4431 4543 3.369546 AAGCGGTGAAAACATTTCCAG 57.630 42.857 0.00 0.00 0.00 3.86
4432 4544 3.810310 AAAGCGGTGAAAACATTTCCA 57.190 38.095 0.00 0.00 0.00 3.53
4433 4545 3.247411 CCAAAAGCGGTGAAAACATTTCC 59.753 43.478 0.00 0.00 0.00 3.13
4434 4546 3.247411 CCCAAAAGCGGTGAAAACATTTC 59.753 43.478 0.00 0.00 0.00 2.17
4435 4547 3.118592 TCCCAAAAGCGGTGAAAACATTT 60.119 39.130 0.00 0.00 0.00 2.32
4436 4548 2.432510 TCCCAAAAGCGGTGAAAACATT 59.567 40.909 0.00 0.00 0.00 2.71
4437 4549 2.035632 TCCCAAAAGCGGTGAAAACAT 58.964 42.857 0.00 0.00 0.00 2.71
4438 4550 1.475403 TCCCAAAAGCGGTGAAAACA 58.525 45.000 0.00 0.00 0.00 2.83
4439 4551 2.159156 ACTTCCCAAAAGCGGTGAAAAC 60.159 45.455 0.00 0.00 0.00 2.43
4440 4552 2.104170 ACTTCCCAAAAGCGGTGAAAA 58.896 42.857 0.00 0.00 0.00 2.29
4441 4553 1.770294 ACTTCCCAAAAGCGGTGAAA 58.230 45.000 0.00 0.00 0.00 2.69
4442 4554 1.770294 AACTTCCCAAAAGCGGTGAA 58.230 45.000 0.00 0.00 0.00 3.18
4443 4555 1.679153 GAAACTTCCCAAAAGCGGTGA 59.321 47.619 0.00 0.00 0.00 4.02
4444 4556 1.269569 GGAAACTTCCCAAAAGCGGTG 60.270 52.381 0.00 0.00 41.62 4.94
4445 4557 1.037493 GGAAACTTCCCAAAAGCGGT 58.963 50.000 0.00 0.00 41.62 5.68
4446 4558 3.886044 GGAAACTTCCCAAAAGCGG 57.114 52.632 0.00 0.00 41.62 5.52
4460 4572 5.491323 AAGAAACAAAACCTGGTTGGAAA 57.509 34.783 13.79 0.00 34.06 3.13
4461 4573 5.491323 AAAGAAACAAAACCTGGTTGGAA 57.509 34.783 13.79 0.00 34.06 3.53
4462 4574 5.247337 AGAAAAGAAACAAAACCTGGTTGGA 59.753 36.000 13.79 0.00 34.06 3.53
4463 4575 5.487433 AGAAAAGAAACAAAACCTGGTTGG 58.513 37.500 13.79 11.12 34.06 3.77
4464 4576 6.398095 AGAGAAAAGAAACAAAACCTGGTTG 58.602 36.000 13.79 4.78 34.06 3.77
4465 4577 6.605471 AGAGAAAAGAAACAAAACCTGGTT 57.395 33.333 6.18 6.18 37.80 3.67
4466 4578 7.898014 ATAGAGAAAAGAAACAAAACCTGGT 57.102 32.000 0.00 0.00 0.00 4.00
4467 4579 8.413229 TGAATAGAGAAAAGAAACAAAACCTGG 58.587 33.333 0.00 0.00 0.00 4.45
4468 4580 9.971922 ATGAATAGAGAAAAGAAACAAAACCTG 57.028 29.630 0.00 0.00 0.00 4.00
4475 4587 9.748708 CCAACAAATGAATAGAGAAAAGAAACA 57.251 29.630 0.00 0.00 0.00 2.83
4476 4588 9.750125 ACCAACAAATGAATAGAGAAAAGAAAC 57.250 29.630 0.00 0.00 0.00 2.78
4484 4596 9.527157 TCCATAAAACCAACAAATGAATAGAGA 57.473 29.630 0.00 0.00 0.00 3.10
4487 4599 9.927668 ACTTCCATAAAACCAACAAATGAATAG 57.072 29.630 0.00 0.00 0.00 1.73
4488 4600 9.703892 CACTTCCATAAAACCAACAAATGAATA 57.296 29.630 0.00 0.00 0.00 1.75
4489 4601 8.210265 ACACTTCCATAAAACCAACAAATGAAT 58.790 29.630 0.00 0.00 0.00 2.57
4490 4602 7.560368 ACACTTCCATAAAACCAACAAATGAA 58.440 30.769 0.00 0.00 0.00 2.57
4491 4603 7.118496 ACACTTCCATAAAACCAACAAATGA 57.882 32.000 0.00 0.00 0.00 2.57
4492 4604 7.784633 AACACTTCCATAAAACCAACAAATG 57.215 32.000 0.00 0.00 0.00 2.32
4493 4605 7.826744 ACAAACACTTCCATAAAACCAACAAAT 59.173 29.630 0.00 0.00 0.00 2.32
4494 4606 7.118390 CACAAACACTTCCATAAAACCAACAAA 59.882 33.333 0.00 0.00 0.00 2.83
4495 4607 6.591834 CACAAACACTTCCATAAAACCAACAA 59.408 34.615 0.00 0.00 0.00 2.83
4496 4608 6.102663 CACAAACACTTCCATAAAACCAACA 58.897 36.000 0.00 0.00 0.00 3.33
4497 4609 6.103330 ACACAAACACTTCCATAAAACCAAC 58.897 36.000 0.00 0.00 0.00 3.77
4498 4610 6.287589 ACACAAACACTTCCATAAAACCAA 57.712 33.333 0.00 0.00 0.00 3.67
4499 4611 5.923733 ACACAAACACTTCCATAAAACCA 57.076 34.783 0.00 0.00 0.00 3.67
4500 4612 6.475402 CAGAACACAAACACTTCCATAAAACC 59.525 38.462 0.00 0.00 0.00 3.27
4501 4613 7.033185 ACAGAACACAAACACTTCCATAAAAC 58.967 34.615 0.00 0.00 0.00 2.43
4502 4614 7.164230 ACAGAACACAAACACTTCCATAAAA 57.836 32.000 0.00 0.00 0.00 1.52
4503 4615 6.767524 ACAGAACACAAACACTTCCATAAA 57.232 33.333 0.00 0.00 0.00 1.40
4504 4616 6.767524 AACAGAACACAAACACTTCCATAA 57.232 33.333 0.00 0.00 0.00 1.90
4505 4617 6.767524 AAACAGAACACAAACACTTCCATA 57.232 33.333 0.00 0.00 0.00 2.74
4506 4618 5.659440 AAACAGAACACAAACACTTCCAT 57.341 34.783 0.00 0.00 0.00 3.41
4507 4619 5.461032 AAAACAGAACACAAACACTTCCA 57.539 34.783 0.00 0.00 0.00 3.53
4527 4639 6.966534 AGAAAGAGGCAGAGAAATGAAAAA 57.033 33.333 0.00 0.00 0.00 1.94
4528 4640 6.774656 AGAAGAAAGAGGCAGAGAAATGAAAA 59.225 34.615 0.00 0.00 0.00 2.29
4529 4641 6.302269 AGAAGAAAGAGGCAGAGAAATGAAA 58.698 36.000 0.00 0.00 0.00 2.69
4530 4642 5.874093 AGAAGAAAGAGGCAGAGAAATGAA 58.126 37.500 0.00 0.00 0.00 2.57
4531 4643 5.495926 AGAAGAAAGAGGCAGAGAAATGA 57.504 39.130 0.00 0.00 0.00 2.57
4532 4644 6.430616 AGAAAGAAGAAAGAGGCAGAGAAATG 59.569 38.462 0.00 0.00 0.00 2.32
4533 4645 6.430616 CAGAAAGAAGAAAGAGGCAGAGAAAT 59.569 38.462 0.00 0.00 0.00 2.17
4534 4646 5.762218 CAGAAAGAAGAAAGAGGCAGAGAAA 59.238 40.000 0.00 0.00 0.00 2.52
4535 4647 5.163258 ACAGAAAGAAGAAAGAGGCAGAGAA 60.163 40.000 0.00 0.00 0.00 2.87
4536 4648 4.346418 ACAGAAAGAAGAAAGAGGCAGAGA 59.654 41.667 0.00 0.00 0.00 3.10
4537 4649 4.640364 ACAGAAAGAAGAAAGAGGCAGAG 58.360 43.478 0.00 0.00 0.00 3.35
4538 4650 4.696479 ACAGAAAGAAGAAAGAGGCAGA 57.304 40.909 0.00 0.00 0.00 4.26
4539 4651 5.764487 AAACAGAAAGAAGAAAGAGGCAG 57.236 39.130 0.00 0.00 0.00 4.85
4540 4652 6.530019 AAAAACAGAAAGAAGAAAGAGGCA 57.470 33.333 0.00 0.00 0.00 4.75
4578 4690 5.525378 CCAAAAATGTTGACGGATCCAAAAA 59.475 36.000 13.41 0.00 0.00 1.94
4579 4691 5.053145 CCAAAAATGTTGACGGATCCAAAA 58.947 37.500 13.41 0.00 0.00 2.44
4580 4692 4.342378 TCCAAAAATGTTGACGGATCCAAA 59.658 37.500 13.41 0.00 0.00 3.28
4581 4693 3.891977 TCCAAAAATGTTGACGGATCCAA 59.108 39.130 13.41 0.00 0.00 3.53
4582 4694 3.491342 TCCAAAAATGTTGACGGATCCA 58.509 40.909 13.41 0.00 0.00 3.41
4583 4695 4.513198 TTCCAAAAATGTTGACGGATCC 57.487 40.909 0.00 0.00 0.00 3.36
4584 4696 6.155827 TGAATTCCAAAAATGTTGACGGATC 58.844 36.000 2.27 0.00 0.00 3.36
4585 4697 6.095432 TGAATTCCAAAAATGTTGACGGAT 57.905 33.333 2.27 0.00 0.00 4.18
4586 4698 5.521906 TGAATTCCAAAAATGTTGACGGA 57.478 34.783 2.27 0.00 0.00 4.69
4587 4699 9.019764 GTATATGAATTCCAAAAATGTTGACGG 57.980 33.333 2.27 0.00 0.00 4.79
4588 4700 9.787532 AGTATATGAATTCCAAAAATGTTGACG 57.212 29.630 2.27 0.00 0.00 4.35
4635 4747 6.587273 AGAAAATGGTTCGGGAATTCAAAAA 58.413 32.000 7.93 0.00 0.00 1.94
4636 4748 6.168270 AGAAAATGGTTCGGGAATTCAAAA 57.832 33.333 7.93 0.00 0.00 2.44
4637 4749 5.799827 AGAAAATGGTTCGGGAATTCAAA 57.200 34.783 7.93 0.00 0.00 2.69
4638 4750 5.799827 AAGAAAATGGTTCGGGAATTCAA 57.200 34.783 7.93 0.00 0.00 2.69
4639 4751 6.242396 TCTAAGAAAATGGTTCGGGAATTCA 58.758 36.000 7.93 0.00 0.00 2.57
4640 4752 6.753107 TCTAAGAAAATGGTTCGGGAATTC 57.247 37.500 0.00 0.00 0.00 2.17
4641 4753 7.718334 AATCTAAGAAAATGGTTCGGGAATT 57.282 32.000 0.00 0.00 0.00 2.17
4642 4754 7.178451 ACAAATCTAAGAAAATGGTTCGGGAAT 59.822 33.333 0.00 0.00 0.00 3.01
4643 4755 6.492087 ACAAATCTAAGAAAATGGTTCGGGAA 59.508 34.615 0.00 0.00 0.00 3.97
4644 4756 6.007703 ACAAATCTAAGAAAATGGTTCGGGA 58.992 36.000 0.00 0.00 0.00 5.14
4645 4757 6.072175 TCACAAATCTAAGAAAATGGTTCGGG 60.072 38.462 0.00 0.00 0.00 5.14
4646 4758 6.908825 TCACAAATCTAAGAAAATGGTTCGG 58.091 36.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.