Multiple sequence alignment - TraesCS5B01G120700

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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 TraesCS5B01G120700 chr5B 100.000 4648 0 0 1 4648 214126549 214131196 0.000000e+00 8584.0
1 TraesCS5B01G120700 chr5B 93.865 163 9 1 4458 4619 120547693 120547531 1.480000e-60 244.0
2 TraesCS5B01G120700 chr5B 100.000 73 0 0 5233 5305 214131781 214131853 9.270000e-28 135.0
3 TraesCS5B01G120700 chr5D 95.088 3644 72 30 1 3615 190495369 190498934 0.000000e+00 5638.0
4 TraesCS5B01G120700 chr5D 97.817 733 16 0 3687 4419 190498970 190499702 0.000000e+00 1266.0
5 TraesCS5B01G120700 chr5A 93.582 2680 70 36 489 3127 229501475 229498857 0.000000e+00 3903.0
6 TraesCS5B01G120700 chr5A 91.147 1299 48 12 3137 4419 229498429 229497182 0.000000e+00 1700.0
7 TraesCS5B01G120700 chr5A 96.134 388 9 3 1 388 229501997 229501616 3.490000e-176 628.0
8 TraesCS5B01G120700 chr5A 93.333 165 11 0 4455 4619 456897908 456897744 1.480000e-60 244.0
9 TraesCS5B01G120700 chr5A 95.181 83 4 0 409 491 229501502 229501584 1.200000e-26 132.0
10 TraesCS5B01G120700 chr5A 98.630 73 1 0 5233 5305 36464271 36464343 4.310000e-26 130.0
11 TraesCS5B01G120700 chr6D 93.750 160 10 0 4460 4619 66254828 66254669 1.910000e-59 241.0
12 TraesCS5B01G120700 chr6D 93.252 163 11 0 4457 4619 392896971 392897133 1.910000e-59 241.0
13 TraesCS5B01G120700 chr4B 92.308 169 13 0 4451 4619 80990823 80990655 1.910000e-59 241.0
14 TraesCS5B01G120700 chr4B 97.260 73 2 0 5233 5305 669154490 669154562 2.010000e-24 124.0
15 TraesCS5B01G120700 chr4B 88.506 87 10 0 2753 2839 105003210 105003296 7.270000e-19 106.0
16 TraesCS5B01G120700 chr4B 81.081 111 21 0 2298 2408 105002822 105002932 7.320000e-14 89.8
17 TraesCS5B01G120700 chr4D 91.379 174 14 1 4446 4619 403412895 403413067 2.470000e-58 237.0
18 TraesCS5B01G120700 chr4D 88.506 87 10 0 2753 2839 71293695 71293609 7.270000e-19 106.0
19 TraesCS5B01G120700 chr4D 81.905 105 19 0 2310 2414 71294071 71293967 7.320000e-14 89.8
20 TraesCS5B01G120700 chr2B 92.216 167 13 0 4453 4619 404425923 404425757 2.470000e-58 237.0
21 TraesCS5B01G120700 chr7A 90.909 176 13 3 4446 4619 320981353 320981179 3.190000e-57 233.0
22 TraesCS5B01G120700 chr7A 97.260 73 2 0 5233 5305 115367548 115367476 2.010000e-24 124.0
23 TraesCS5B01G120700 chr6B 89.617 183 16 3 4454 4634 696483561 696483380 4.130000e-56 230.0
24 TraesCS5B01G120700 chr4A 100.000 73 0 0 5233 5305 24494168 24494096 9.270000e-28 135.0
25 TraesCS5B01G120700 chr4A 87.755 98 12 0 2742 2839 526641572 526641669 1.210000e-21 115.0
26 TraesCS5B01G120700 chr2A 100.000 73 0 0 5233 5305 151211592 151211520 9.270000e-28 135.0
27 TraesCS5B01G120700 chr1A 100.000 73 0 0 5233 5305 103222016 103221944 9.270000e-28 135.0
28 TraesCS5B01G120700 chr3B 97.260 73 2 0 5233 5305 217771140 217771212 2.010000e-24 124.0


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 TraesCS5B01G120700 chr5B 214126549 214131853 5304 False 4359.5 8584 100.0000 1 5305 2 chr5B.!!$F1 5304
1 TraesCS5B01G120700 chr5D 190495369 190499702 4333 False 3452.0 5638 96.4525 1 4419 2 chr5D.!!$F1 4418
2 TraesCS5B01G120700 chr5A 229497182 229501997 4815 True 2077.0 3903 93.6210 1 4419 3 chr5A.!!$R2 4418

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
611 683 2.229792 AGCATGCCGTGAAAGAAAGAA 58.770 42.857 15.66 0.0 0.00 2.52 F
1773 1883 1.062488 AGGACAACAGCAAGGAGGGT 61.062 55.000 0.00 0.0 0.00 4.34 F
2031 2141 1.135721 GGCTTCATCCAAGACAATGGC 59.864 52.381 0.00 0.0 40.41 4.40 F
3646 4211 0.109781 CCAAGCCGACCAACAAATCG 60.110 55.000 0.00 0.0 38.08 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1958 2068 1.379642 CCATCCGCCCTTCTTCTTGC 61.380 60.0 0.00 0.00 0.00 4.01 R
3351 3900 0.322187 TGGACTGGACGTCGATCTGA 60.322 55.0 9.92 0.00 43.79 3.27 R
3675 4240 1.115467 TCTTTTTGCGGGCAGGAAAA 58.885 45.0 12.47 12.47 46.14 2.29 R
5244 5809 0.175989 AATCTTCCTTCTCCGCGACC 59.824 55.0 8.23 0.00 0.00 4.79 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
211 212 4.498345 GCAGGTAGATAGTCTCTGAAACCG 60.498 50.000 0.00 0.00 35.90 4.44
390 391 4.727677 AGGTAGGGAGGTAGAGTATTTCG 58.272 47.826 0.00 0.00 0.00 3.46
391 392 4.414846 AGGTAGGGAGGTAGAGTATTTCGA 59.585 45.833 0.00 0.00 0.00 3.71
532 573 6.310224 CGTGGTTCAATCATTCCATAAAAACC 59.690 38.462 0.00 0.00 35.36 3.27
611 683 2.229792 AGCATGCCGTGAAAGAAAGAA 58.770 42.857 15.66 0.00 0.00 2.52
612 684 2.622942 AGCATGCCGTGAAAGAAAGAAA 59.377 40.909 15.66 0.00 0.00 2.52
613 685 2.982470 GCATGCCGTGAAAGAAAGAAAG 59.018 45.455 6.36 0.00 0.00 2.62
614 686 3.304659 GCATGCCGTGAAAGAAAGAAAGA 60.305 43.478 6.36 0.00 0.00 2.52
615 687 4.792704 GCATGCCGTGAAAGAAAGAAAGAA 60.793 41.667 6.36 0.00 0.00 2.52
616 688 4.974368 TGCCGTGAAAGAAAGAAAGAAA 57.026 36.364 0.00 0.00 0.00 2.52
617 689 4.920376 TGCCGTGAAAGAAAGAAAGAAAG 58.080 39.130 0.00 0.00 0.00 2.62
618 690 4.638421 TGCCGTGAAAGAAAGAAAGAAAGA 59.362 37.500 0.00 0.00 0.00 2.52
619 691 5.124776 TGCCGTGAAAGAAAGAAAGAAAGAA 59.875 36.000 0.00 0.00 0.00 2.52
620 692 6.033966 GCCGTGAAAGAAAGAAAGAAAGAAA 58.966 36.000 0.00 0.00 0.00 2.52
621 693 6.197282 GCCGTGAAAGAAAGAAAGAAAGAAAG 59.803 38.462 0.00 0.00 0.00 2.62
622 694 7.472543 CCGTGAAAGAAAGAAAGAAAGAAAGA 58.527 34.615 0.00 0.00 0.00 2.52
662 734 8.137437 ACTAAAGCAATGCCATGATACATTAAC 58.863 33.333 0.00 0.00 34.80 2.01
705 777 2.364002 CCCCCGCAAAAAGAAAGAAAGA 59.636 45.455 0.00 0.00 0.00 2.52
706 778 3.181470 CCCCCGCAAAAAGAAAGAAAGAA 60.181 43.478 0.00 0.00 0.00 2.52
707 779 4.438148 CCCCGCAAAAAGAAAGAAAGAAA 58.562 39.130 0.00 0.00 0.00 2.52
708 780 4.507756 CCCCGCAAAAAGAAAGAAAGAAAG 59.492 41.667 0.00 0.00 0.00 2.62
709 781 5.348164 CCCGCAAAAAGAAAGAAAGAAAGA 58.652 37.500 0.00 0.00 0.00 2.52
710 782 5.810074 CCCGCAAAAAGAAAGAAAGAAAGAA 59.190 36.000 0.00 0.00 0.00 2.52
711 783 6.312672 CCCGCAAAAAGAAAGAAAGAAAGAAA 59.687 34.615 0.00 0.00 0.00 2.52
712 784 7.148490 CCCGCAAAAAGAAAGAAAGAAAGAAAA 60.148 33.333 0.00 0.00 0.00 2.29
763 845 3.247006 TGGGATCGAAGTAGCACTTTC 57.753 47.619 0.00 0.00 38.80 2.62
936 1028 3.788708 TCCATCTCTCTCTCCCTTGTCTA 59.211 47.826 0.00 0.00 0.00 2.59
1095 1199 1.296722 CTCCGACGACGACGATGAC 60.297 63.158 20.63 1.87 42.66 3.06
1107 1211 2.586357 GATGACGAAGAGGCCCGC 60.586 66.667 0.00 0.00 0.00 6.13
1365 1469 2.809174 CGCTTCATCGACGTGCCA 60.809 61.111 0.00 0.00 0.00 4.92
1722 1832 1.834188 CGGATAAAGGCACCAAAGGT 58.166 50.000 0.00 0.00 35.62 3.50
1773 1883 1.062488 AGGACAACAGCAAGGAGGGT 61.062 55.000 0.00 0.00 0.00 4.34
2031 2141 1.135721 GGCTTCATCCAAGACAATGGC 59.864 52.381 0.00 0.00 40.41 4.40
2241 2355 2.397549 CAAGCAAGCAAGTAAGCAACC 58.602 47.619 0.00 0.00 36.85 3.77
2242 2356 1.986882 AGCAAGCAAGTAAGCAACCT 58.013 45.000 0.00 0.00 36.85 3.50
2243 2357 1.882623 AGCAAGCAAGTAAGCAACCTC 59.117 47.619 0.00 0.00 36.85 3.85
2274 2394 3.814906 TGTGGGTGTGGGTGTGGG 61.815 66.667 0.00 0.00 0.00 4.61
2275 2395 3.816090 GTGGGTGTGGGTGTGGGT 61.816 66.667 0.00 0.00 0.00 4.51
2276 2396 3.814906 TGGGTGTGGGTGTGGGTG 61.815 66.667 0.00 0.00 0.00 4.61
2277 2397 3.816090 GGGTGTGGGTGTGGGTGT 61.816 66.667 0.00 0.00 0.00 4.16
2278 2398 2.518349 GGTGTGGGTGTGGGTGTG 60.518 66.667 0.00 0.00 0.00 3.82
2279 2399 2.518349 GTGTGGGTGTGGGTGTGG 60.518 66.667 0.00 0.00 0.00 4.17
2575 2695 2.030562 CCCGACAAGGTGTTCGCT 59.969 61.111 0.00 0.00 38.74 4.93
2683 2803 6.213195 TGCCCATCTCATCATACATACATACA 59.787 38.462 0.00 0.00 0.00 2.29
2876 2998 3.427233 GCCTCTCACTCATACGTTACGTT 60.427 47.826 17.42 0.98 41.54 3.99
2890 3012 4.326548 ACGTTACGTTCGTAGTAGGAGTAC 59.673 45.833 3.95 0.00 36.35 2.73
3140 3266 2.319844 TCTCCATACATGACATCGCCT 58.680 47.619 0.00 0.00 0.00 5.52
3141 3267 3.496331 TCTCCATACATGACATCGCCTA 58.504 45.455 0.00 0.00 0.00 3.93
3142 3268 4.089361 TCTCCATACATGACATCGCCTAT 58.911 43.478 0.00 0.00 0.00 2.57
3265 3809 5.124457 CAGCAGGTAGTACATTTTGCATCTT 59.876 40.000 15.82 0.00 34.17 2.40
3275 3819 9.715121 AGTACATTTTGCATCTTCAAATTCATT 57.285 25.926 0.00 0.00 36.04 2.57
3484 4033 5.450550 CGTAGGTTACTCATCTTGATGCTCA 60.451 44.000 5.78 0.00 0.00 4.26
3543 4092 1.374758 GGAAGTGCTGGTCACCTCG 60.375 63.158 0.00 0.00 46.81 4.63
3606 4155 5.454897 GGTCCAGAAGTTCAGAGGTACTTTT 60.455 44.000 5.50 0.00 41.55 2.27
3607 4156 6.239515 GGTCCAGAAGTTCAGAGGTACTTTTA 60.240 42.308 5.50 0.00 41.55 1.52
3608 4157 6.645827 GTCCAGAAGTTCAGAGGTACTTTTAC 59.354 42.308 5.50 0.00 41.55 2.01
3610 4159 7.070821 TCCAGAAGTTCAGAGGTACTTTTACTT 59.929 37.037 5.50 0.00 41.55 2.24
3646 4211 0.109781 CCAAGCCGACCAACAAATCG 60.110 55.000 0.00 0.00 38.08 3.34
3666 4231 2.806244 CGTGTTTCGAGGAAGGAATTGT 59.194 45.455 0.00 0.00 42.86 2.71
3667 4232 3.250040 CGTGTTTCGAGGAAGGAATTGTT 59.750 43.478 0.00 0.00 42.86 2.83
3668 4233 4.261031 CGTGTTTCGAGGAAGGAATTGTTT 60.261 41.667 0.00 0.00 42.86 2.83
3669 4234 5.212934 GTGTTTCGAGGAAGGAATTGTTTC 58.787 41.667 0.00 0.00 0.00 2.78
3670 4235 5.008712 GTGTTTCGAGGAAGGAATTGTTTCT 59.991 40.000 0.00 0.00 32.16 2.52
3671 4236 5.592688 TGTTTCGAGGAAGGAATTGTTTCTT 59.407 36.000 0.00 0.00 32.16 2.52
3672 4237 6.096282 TGTTTCGAGGAAGGAATTGTTTCTTT 59.904 34.615 0.00 0.00 34.19 2.52
3673 4238 6.709018 TTCGAGGAAGGAATTGTTTCTTTT 57.291 33.333 0.00 0.00 31.88 2.27
3674 4239 6.709018 TCGAGGAAGGAATTGTTTCTTTTT 57.291 33.333 0.00 0.00 31.88 1.94
4007 4572 3.411351 GGCGTCGTGTCGTGCAAT 61.411 61.111 0.00 0.00 33.01 3.56
4243 4808 0.103208 ACCTTGAGCGGCGAGATAAG 59.897 55.000 12.98 8.80 0.00 1.73
4320 4885 0.109342 CTGATCCGCCCAGCCTAATT 59.891 55.000 0.00 0.00 0.00 1.40
4405 4970 0.648441 TTGTGTGCGACTCGTTTCAC 59.352 50.000 0.00 7.79 0.00 3.18
4415 4980 4.676018 GCGACTCGTTTCACCTAGATTATC 59.324 45.833 0.00 0.00 0.00 1.75
4419 4984 7.254692 CGACTCGTTTCACCTAGATTATCAGTA 60.255 40.741 0.00 0.00 0.00 2.74
4420 4985 8.289939 ACTCGTTTCACCTAGATTATCAGTAA 57.710 34.615 0.00 0.00 0.00 2.24
4421 4986 8.915036 ACTCGTTTCACCTAGATTATCAGTAAT 58.085 33.333 0.00 0.00 33.26 1.89
4422 4987 9.186323 CTCGTTTCACCTAGATTATCAGTAATG 57.814 37.037 0.00 0.00 30.75 1.90
4423 4988 7.652105 TCGTTTCACCTAGATTATCAGTAATGC 59.348 37.037 0.00 0.00 30.75 3.56
4424 4989 7.653713 CGTTTCACCTAGATTATCAGTAATGCT 59.346 37.037 0.00 0.00 30.75 3.79
4425 4990 9.982651 GTTTCACCTAGATTATCAGTAATGCTA 57.017 33.333 0.00 0.00 30.75 3.49
4427 4992 9.588096 TTCACCTAGATTATCAGTAATGCTAGA 57.412 33.333 0.00 0.00 34.37 2.43
4428 4993 9.015367 TCACCTAGATTATCAGTAATGCTAGAC 57.985 37.037 0.00 0.00 34.37 2.59
4429 4994 8.247562 CACCTAGATTATCAGTAATGCTAGACC 58.752 40.741 0.00 0.00 34.37 3.85
4430 4995 7.397761 ACCTAGATTATCAGTAATGCTAGACCC 59.602 40.741 0.00 0.00 34.37 4.46
4431 4996 7.397476 CCTAGATTATCAGTAATGCTAGACCCA 59.603 40.741 0.00 0.00 34.37 4.51
4432 4997 6.998802 AGATTATCAGTAATGCTAGACCCAC 58.001 40.000 0.00 0.00 30.75 4.61
4433 4998 3.735237 ATCAGTAATGCTAGACCCACG 57.265 47.619 0.00 0.00 0.00 4.94
4434 4999 2.453521 TCAGTAATGCTAGACCCACGT 58.546 47.619 0.00 0.00 0.00 4.49
4435 5000 3.623703 TCAGTAATGCTAGACCCACGTA 58.376 45.455 0.00 0.00 0.00 3.57
4436 5001 4.018490 TCAGTAATGCTAGACCCACGTAA 58.982 43.478 0.00 0.00 0.00 3.18
4437 5002 4.647853 TCAGTAATGCTAGACCCACGTAAT 59.352 41.667 0.00 0.00 0.00 1.89
4438 5003 4.745125 CAGTAATGCTAGACCCACGTAATG 59.255 45.833 0.00 0.00 0.00 1.90
4439 5004 2.240493 ATGCTAGACCCACGTAATGC 57.760 50.000 0.00 0.00 0.00 3.56
4440 5005 1.191535 TGCTAGACCCACGTAATGCT 58.808 50.000 0.00 0.00 0.00 3.79
4441 5006 2.380941 TGCTAGACCCACGTAATGCTA 58.619 47.619 0.00 0.00 0.00 3.49
4442 5007 2.100252 TGCTAGACCCACGTAATGCTAC 59.900 50.000 0.00 0.00 0.00 3.58
4456 5021 7.551858 CGTAATGCTACGTACAAATTTTACG 57.448 36.000 21.01 21.01 44.79 3.18
4467 5032 8.411318 CGTACAAATTTTACGTAATACTCCCT 57.589 34.615 9.18 0.00 38.00 4.20
4468 5033 8.534778 CGTACAAATTTTACGTAATACTCCCTC 58.465 37.037 9.18 0.00 38.00 4.30
4469 5034 7.854557 ACAAATTTTACGTAATACTCCCTCC 57.145 36.000 9.18 0.00 0.00 4.30
4470 5035 6.536224 ACAAATTTTACGTAATACTCCCTCCG 59.464 38.462 9.18 0.00 0.00 4.63
4471 5036 5.859205 ATTTTACGTAATACTCCCTCCGT 57.141 39.130 9.18 0.00 0.00 4.69
4472 5037 5.659440 TTTTACGTAATACTCCCTCCGTT 57.341 39.130 9.18 0.00 0.00 4.44
4473 5038 5.659440 TTTACGTAATACTCCCTCCGTTT 57.341 39.130 9.18 0.00 0.00 3.60
4474 5039 5.659440 TTACGTAATACTCCCTCCGTTTT 57.341 39.130 3.29 0.00 0.00 2.43
4475 5040 4.541973 ACGTAATACTCCCTCCGTTTTT 57.458 40.909 0.00 0.00 0.00 1.94
4476 5041 5.659440 ACGTAATACTCCCTCCGTTTTTA 57.341 39.130 0.00 0.00 0.00 1.52
4477 5042 6.036577 ACGTAATACTCCCTCCGTTTTTAA 57.963 37.500 0.00 0.00 0.00 1.52
4478 5043 6.463360 ACGTAATACTCCCTCCGTTTTTAAA 58.537 36.000 0.00 0.00 0.00 1.52
4479 5044 7.105588 ACGTAATACTCCCTCCGTTTTTAAAT 58.894 34.615 0.00 0.00 0.00 1.40
4480 5045 8.257306 ACGTAATACTCCCTCCGTTTTTAAATA 58.743 33.333 0.00 0.00 0.00 1.40
4481 5046 9.264719 CGTAATACTCCCTCCGTTTTTAAATAT 57.735 33.333 0.00 0.00 0.00 1.28
4485 5050 7.770366 ACTCCCTCCGTTTTTAAATATTTGT 57.230 32.000 11.05 0.00 0.00 2.83
4486 5051 8.185506 ACTCCCTCCGTTTTTAAATATTTGTT 57.814 30.769 11.05 0.00 0.00 2.83
4487 5052 8.644216 ACTCCCTCCGTTTTTAAATATTTGTTT 58.356 29.630 11.05 0.00 0.00 2.83
4488 5053 9.483916 CTCCCTCCGTTTTTAAATATTTGTTTT 57.516 29.630 11.05 0.00 0.00 2.43
4489 5054 9.833917 TCCCTCCGTTTTTAAATATTTGTTTTT 57.166 25.926 11.05 0.00 0.00 1.94
4509 5074 9.364989 TGTTTTTCTAGAAATTTCAACAAGTGG 57.635 29.630 22.18 0.84 29.58 4.00
4510 5075 9.366216 GTTTTTCTAGAAATTTCAACAAGTGGT 57.634 29.630 18.37 0.00 0.00 4.16
4511 5076 9.936759 TTTTTCTAGAAATTTCAACAAGTGGTT 57.063 25.926 18.37 0.00 41.47 3.67
4522 5087 7.801716 TTCAACAAGTGGTTATATATGGAGC 57.198 36.000 0.00 0.00 37.72 4.70
4523 5088 6.894682 TCAACAAGTGGTTATATATGGAGCA 58.105 36.000 0.00 0.00 37.72 4.26
4524 5089 7.342581 TCAACAAGTGGTTATATATGGAGCAA 58.657 34.615 0.00 0.00 37.72 3.91
4525 5090 7.831690 TCAACAAGTGGTTATATATGGAGCAAA 59.168 33.333 0.00 0.00 37.72 3.68
4526 5091 8.465999 CAACAAGTGGTTATATATGGAGCAAAA 58.534 33.333 0.00 0.00 37.72 2.44
4527 5092 8.766994 ACAAGTGGTTATATATGGAGCAAAAT 57.233 30.769 0.00 0.00 0.00 1.82
4528 5093 8.632679 ACAAGTGGTTATATATGGAGCAAAATG 58.367 33.333 0.00 3.52 0.00 2.32
4529 5094 8.849168 CAAGTGGTTATATATGGAGCAAAATGA 58.151 33.333 0.00 0.00 0.00 2.57
4530 5095 8.627208 AGTGGTTATATATGGAGCAAAATGAG 57.373 34.615 0.00 0.00 0.00 2.90
4531 5096 8.220559 AGTGGTTATATATGGAGCAAAATGAGT 58.779 33.333 0.00 0.00 0.00 3.41
4532 5097 8.292448 GTGGTTATATATGGAGCAAAATGAGTG 58.708 37.037 0.00 0.00 0.00 3.51
4533 5098 8.217111 TGGTTATATATGGAGCAAAATGAGTGA 58.783 33.333 0.00 0.00 0.00 3.41
4534 5099 9.066892 GGTTATATATGGAGCAAAATGAGTGAA 57.933 33.333 0.00 0.00 0.00 3.18
4539 5104 6.690194 ATGGAGCAAAATGAGTGAATCTAC 57.310 37.500 0.00 0.00 0.00 2.59
4540 5105 5.559770 TGGAGCAAAATGAGTGAATCTACA 58.440 37.500 0.00 0.00 0.00 2.74
4541 5106 5.412594 TGGAGCAAAATGAGTGAATCTACAC 59.587 40.000 0.00 0.00 40.60 2.90
4555 5120 9.469097 AGTGAATCTACACTCTAAACTATGTCT 57.531 33.333 0.00 0.00 46.36 3.41
4556 5121 9.509855 GTGAATCTACACTCTAAACTATGTCTG 57.490 37.037 0.00 0.00 37.73 3.51
4557 5122 9.244292 TGAATCTACACTCTAAACTATGTCTGT 57.756 33.333 0.00 0.00 0.00 3.41
4565 5130 9.900710 CACTCTAAACTATGTCTGTATACATCC 57.099 37.037 5.91 0.58 40.52 3.51
4566 5131 8.784994 ACTCTAAACTATGTCTGTATACATCCG 58.215 37.037 5.91 0.00 40.52 4.18
4567 5132 8.687292 TCTAAACTATGTCTGTATACATCCGT 57.313 34.615 5.91 4.19 40.52 4.69
4568 5133 9.783081 TCTAAACTATGTCTGTATACATCCGTA 57.217 33.333 5.91 5.10 40.52 4.02
4572 5137 7.817641 ACTATGTCTGTATACATCCGTATGTG 58.182 38.462 5.91 0.00 45.99 3.21
4573 5138 6.894339 ATGTCTGTATACATCCGTATGTGA 57.106 37.500 5.91 0.00 45.99 3.58
4574 5139 6.894339 TGTCTGTATACATCCGTATGTGAT 57.106 37.500 5.91 0.00 45.99 3.06
4575 5140 7.989416 TGTCTGTATACATCCGTATGTGATA 57.011 36.000 5.91 0.00 45.99 2.15
4576 5141 8.040716 TGTCTGTATACATCCGTATGTGATAG 57.959 38.462 5.91 0.34 45.99 2.08
4577 5142 7.664318 TGTCTGTATACATCCGTATGTGATAGT 59.336 37.037 5.91 0.00 45.99 2.12
4578 5143 8.176365 GTCTGTATACATCCGTATGTGATAGTC 58.824 40.741 5.91 0.00 45.99 2.59
4579 5144 7.336176 TCTGTATACATCCGTATGTGATAGTCC 59.664 40.741 5.91 0.00 45.99 3.85
4580 5145 6.943718 TGTATACATCCGTATGTGATAGTCCA 59.056 38.462 3.56 0.00 45.99 4.02
4581 5146 7.614192 TGTATACATCCGTATGTGATAGTCCAT 59.386 37.037 3.56 0.00 45.99 3.41
4582 5147 5.808366 ACATCCGTATGTGATAGTCCATT 57.192 39.130 0.00 0.00 44.79 3.16
4583 5148 6.174720 ACATCCGTATGTGATAGTCCATTT 57.825 37.500 0.00 0.00 44.79 2.32
4584 5149 5.991606 ACATCCGTATGTGATAGTCCATTTG 59.008 40.000 0.00 0.00 44.79 2.32
4585 5150 5.862678 TCCGTATGTGATAGTCCATTTGA 57.137 39.130 0.00 0.00 0.00 2.69
4586 5151 6.228616 TCCGTATGTGATAGTCCATTTGAA 57.771 37.500 0.00 0.00 0.00 2.69
4587 5152 6.645306 TCCGTATGTGATAGTCCATTTGAAA 58.355 36.000 0.00 0.00 0.00 2.69
4588 5153 7.279615 TCCGTATGTGATAGTCCATTTGAAAT 58.720 34.615 0.00 0.00 0.00 2.17
4589 5154 7.441157 TCCGTATGTGATAGTCCATTTGAAATC 59.559 37.037 0.00 0.00 0.00 2.17
4590 5155 7.442364 CCGTATGTGATAGTCCATTTGAAATCT 59.558 37.037 0.00 0.00 0.00 2.40
4591 5156 8.491152 CGTATGTGATAGTCCATTTGAAATCTC 58.509 37.037 0.00 0.00 0.00 2.75
4592 5157 9.553064 GTATGTGATAGTCCATTTGAAATCTCT 57.447 33.333 0.00 0.00 0.00 3.10
4595 5160 9.958180 TGTGATAGTCCATTTGAAATCTCTAAA 57.042 29.630 0.00 0.00 0.00 1.85
4601 5166 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
4602 5167 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
4620 5185 9.729281 AAAAGACAAATATTTAGGAACGGAGTA 57.271 29.630 0.00 0.00 45.00 2.59
4621 5186 8.943909 AAGACAAATATTTAGGAACGGAGTAG 57.056 34.615 0.00 0.00 45.00 2.57
4622 5187 8.302515 AGACAAATATTTAGGAACGGAGTAGA 57.697 34.615 0.00 0.00 45.00 2.59
4623 5188 8.196103 AGACAAATATTTAGGAACGGAGTAGAC 58.804 37.037 0.00 0.00 45.00 2.59
4624 5189 8.075761 ACAAATATTTAGGAACGGAGTAGACT 57.924 34.615 0.00 0.00 45.00 3.24
4625 5190 9.193806 ACAAATATTTAGGAACGGAGTAGACTA 57.806 33.333 0.00 0.00 45.00 2.59
4629 5194 6.851222 TTTAGGAACGGAGTAGACTATACG 57.149 41.667 0.00 0.00 45.00 3.06
4630 5195 3.737850 AGGAACGGAGTAGACTATACGG 58.262 50.000 7.86 3.09 45.00 4.02
4631 5196 3.389329 AGGAACGGAGTAGACTATACGGA 59.611 47.826 7.86 0.00 45.00 4.69
4632 5197 3.745458 GGAACGGAGTAGACTATACGGAG 59.255 52.174 7.86 0.00 45.00 4.63
4633 5198 3.399440 ACGGAGTAGACTATACGGAGG 57.601 52.381 7.86 0.00 41.94 4.30
4634 5199 2.968574 ACGGAGTAGACTATACGGAGGA 59.031 50.000 7.86 0.00 41.94 3.71
4635 5200 3.582208 ACGGAGTAGACTATACGGAGGAT 59.418 47.826 7.86 0.00 41.94 3.24
4636 5201 4.041444 ACGGAGTAGACTATACGGAGGATT 59.959 45.833 7.86 0.00 41.94 3.01
4637 5202 5.002516 CGGAGTAGACTATACGGAGGATTT 58.997 45.833 0.00 0.00 0.00 2.17
4638 5203 5.106634 CGGAGTAGACTATACGGAGGATTTG 60.107 48.000 0.00 0.00 0.00 2.32
4639 5204 5.183522 GGAGTAGACTATACGGAGGATTTGG 59.816 48.000 0.00 0.00 0.00 3.28
4640 5205 5.950023 AGTAGACTATACGGAGGATTTGGA 58.050 41.667 0.00 0.00 0.00 3.53
4641 5206 6.553857 AGTAGACTATACGGAGGATTTGGAT 58.446 40.000 0.00 0.00 0.00 3.41
4642 5207 7.011382 AGTAGACTATACGGAGGATTTGGATT 58.989 38.462 0.00 0.00 0.00 3.01
4643 5208 6.102897 AGACTATACGGAGGATTTGGATTG 57.897 41.667 0.00 0.00 0.00 2.67
4644 5209 5.012148 AGACTATACGGAGGATTTGGATTGG 59.988 44.000 0.00 0.00 0.00 3.16
4645 5210 4.905456 ACTATACGGAGGATTTGGATTGGA 59.095 41.667 0.00 0.00 0.00 3.53
4646 5211 5.548056 ACTATACGGAGGATTTGGATTGGAT 59.452 40.000 0.00 0.00 0.00 3.41
4647 5212 2.936202 ACGGAGGATTTGGATTGGATG 58.064 47.619 0.00 0.00 0.00 3.51
5259 5824 3.755628 CGGGTCGCGGAGAAGGAA 61.756 66.667 6.13 0.00 0.00 3.36
5260 5825 2.184579 GGGTCGCGGAGAAGGAAG 59.815 66.667 6.13 0.00 0.00 3.46
5261 5826 2.348888 GGGTCGCGGAGAAGGAAGA 61.349 63.158 6.13 0.00 0.00 2.87
5262 5827 1.677637 GGGTCGCGGAGAAGGAAGAT 61.678 60.000 6.13 0.00 0.00 2.40
5263 5828 0.175989 GGTCGCGGAGAAGGAAGATT 59.824 55.000 6.13 0.00 0.00 2.40
5264 5829 1.405661 GGTCGCGGAGAAGGAAGATTT 60.406 52.381 6.13 0.00 0.00 2.17
5265 5830 2.347731 GTCGCGGAGAAGGAAGATTTT 58.652 47.619 6.13 0.00 0.00 1.82
5266 5831 2.094417 GTCGCGGAGAAGGAAGATTTTG 59.906 50.000 6.13 0.00 0.00 2.44
5267 5832 2.028476 TCGCGGAGAAGGAAGATTTTGA 60.028 45.455 6.13 0.00 0.00 2.69
5268 5833 2.349886 CGCGGAGAAGGAAGATTTTGAG 59.650 50.000 0.00 0.00 0.00 3.02
5269 5834 2.680339 GCGGAGAAGGAAGATTTTGAGG 59.320 50.000 0.00 0.00 0.00 3.86
5270 5835 3.274288 CGGAGAAGGAAGATTTTGAGGG 58.726 50.000 0.00 0.00 0.00 4.30
5271 5836 3.307762 CGGAGAAGGAAGATTTTGAGGGT 60.308 47.826 0.00 0.00 0.00 4.34
5272 5837 4.081087 CGGAGAAGGAAGATTTTGAGGGTA 60.081 45.833 0.00 0.00 0.00 3.69
5273 5838 5.570844 CGGAGAAGGAAGATTTTGAGGGTAA 60.571 44.000 0.00 0.00 0.00 2.85
5274 5839 6.427441 GGAGAAGGAAGATTTTGAGGGTAAT 58.573 40.000 0.00 0.00 0.00 1.89
5275 5840 6.319911 GGAGAAGGAAGATTTTGAGGGTAATG 59.680 42.308 0.00 0.00 0.00 1.90
5276 5841 6.190587 AGAAGGAAGATTTTGAGGGTAATGG 58.809 40.000 0.00 0.00 0.00 3.16
5277 5842 4.281657 AGGAAGATTTTGAGGGTAATGGC 58.718 43.478 0.00 0.00 0.00 4.40
5278 5843 4.023291 GGAAGATTTTGAGGGTAATGGCA 58.977 43.478 0.00 0.00 0.00 4.92
5279 5844 4.651045 GGAAGATTTTGAGGGTAATGGCAT 59.349 41.667 0.00 0.00 0.00 4.40
5280 5845 5.452356 GGAAGATTTTGAGGGTAATGGCATG 60.452 44.000 0.00 0.00 0.00 4.06
5281 5846 4.613437 AGATTTTGAGGGTAATGGCATGT 58.387 39.130 0.00 0.00 0.00 3.21
5282 5847 4.403432 AGATTTTGAGGGTAATGGCATGTG 59.597 41.667 0.00 0.00 0.00 3.21
5283 5848 3.448093 TTTGAGGGTAATGGCATGTGA 57.552 42.857 0.00 0.00 0.00 3.58
5284 5849 3.448093 TTGAGGGTAATGGCATGTGAA 57.552 42.857 0.00 0.00 0.00 3.18
5285 5850 3.448093 TGAGGGTAATGGCATGTGAAA 57.552 42.857 0.00 0.00 0.00 2.69
5286 5851 3.772387 TGAGGGTAATGGCATGTGAAAA 58.228 40.909 0.00 0.00 0.00 2.29
5287 5852 4.155709 TGAGGGTAATGGCATGTGAAAAA 58.844 39.130 0.00 0.00 0.00 1.94
5288 5853 4.776837 TGAGGGTAATGGCATGTGAAAAAT 59.223 37.500 0.00 0.00 0.00 1.82
5289 5854 5.954752 TGAGGGTAATGGCATGTGAAAAATA 59.045 36.000 0.00 0.00 0.00 1.40
5290 5855 6.438741 TGAGGGTAATGGCATGTGAAAAATAA 59.561 34.615 0.00 0.00 0.00 1.40
5291 5856 7.038729 TGAGGGTAATGGCATGTGAAAAATAAA 60.039 33.333 0.00 0.00 0.00 1.40
5292 5857 7.330262 AGGGTAATGGCATGTGAAAAATAAAG 58.670 34.615 0.00 0.00 0.00 1.85
5293 5858 7.038373 AGGGTAATGGCATGTGAAAAATAAAGT 60.038 33.333 0.00 0.00 0.00 2.66
5294 5859 8.254508 GGGTAATGGCATGTGAAAAATAAAGTA 58.745 33.333 0.00 0.00 0.00 2.24
5295 5860 9.646427 GGTAATGGCATGTGAAAAATAAAGTAA 57.354 29.630 0.00 0.00 0.00 2.24
5297 5862 7.810766 ATGGCATGTGAAAAATAAAGTAACG 57.189 32.000 0.00 0.00 0.00 3.18
5298 5863 5.631512 TGGCATGTGAAAAATAAAGTAACGC 59.368 36.000 0.00 0.00 0.00 4.84
5299 5864 5.631512 GGCATGTGAAAAATAAAGTAACGCA 59.368 36.000 0.00 0.00 0.00 5.24
5300 5865 6.399564 GGCATGTGAAAAATAAAGTAACGCAC 60.400 38.462 0.00 0.00 0.00 5.34
5301 5866 6.362283 GCATGTGAAAAATAAAGTAACGCACT 59.638 34.615 0.00 0.00 40.05 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.537202 GGAAGCAATTGAACTGCGAGT 59.463 47.619 10.34 0.00 44.75 4.18
260 261 4.762251 AGCAAAATGTTAGGTTGGAGACTC 59.238 41.667 0.00 0.00 0.00 3.36
334 335 2.777832 ACCTGGAGACAATTGAGCTC 57.222 50.000 13.59 16.72 42.06 4.09
417 418 2.288579 CGGTAGCAAGTCACACAAGGTA 60.289 50.000 0.00 0.00 0.00 3.08
426 427 0.830444 ACAGGACCGGTAGCAAGTCA 60.830 55.000 7.34 0.00 31.99 3.41
532 573 0.595588 TACACCATTTGCAAGGCACG 59.404 50.000 4.68 0.00 38.71 5.34
611 683 8.409371 GTTGAGATTGTCCTTTCTTTCTTTCTT 58.591 33.333 0.00 0.00 0.00 2.52
612 684 7.777440 AGTTGAGATTGTCCTTTCTTTCTTTCT 59.223 33.333 0.00 0.00 0.00 2.52
613 685 7.935520 AGTTGAGATTGTCCTTTCTTTCTTTC 58.064 34.615 0.00 0.00 0.00 2.62
614 686 7.888250 AGTTGAGATTGTCCTTTCTTTCTTT 57.112 32.000 0.00 0.00 0.00 2.52
615 687 8.980481 TTAGTTGAGATTGTCCTTTCTTTCTT 57.020 30.769 0.00 0.00 0.00 2.52
616 688 8.980481 TTTAGTTGAGATTGTCCTTTCTTTCT 57.020 30.769 0.00 0.00 0.00 2.52
617 689 7.805542 GCTTTAGTTGAGATTGTCCTTTCTTTC 59.194 37.037 0.00 0.00 0.00 2.62
618 690 7.285401 TGCTTTAGTTGAGATTGTCCTTTCTTT 59.715 33.333 0.00 0.00 0.00 2.52
619 691 6.772716 TGCTTTAGTTGAGATTGTCCTTTCTT 59.227 34.615 0.00 0.00 0.00 2.52
620 692 6.299141 TGCTTTAGTTGAGATTGTCCTTTCT 58.701 36.000 0.00 0.00 0.00 2.52
621 693 6.560253 TGCTTTAGTTGAGATTGTCCTTTC 57.440 37.500 0.00 0.00 0.00 2.62
622 694 6.959639 TTGCTTTAGTTGAGATTGTCCTTT 57.040 33.333 0.00 0.00 0.00 3.11
662 734 5.053145 GGAGATGTAGTAAGCCATCAACAG 58.947 45.833 0.00 0.00 39.92 3.16
711 783 5.591877 CCTAGATGTAGCAAGCCATCTTTTT 59.408 40.000 15.59 0.00 44.03 1.94
712 784 5.128919 CCTAGATGTAGCAAGCCATCTTTT 58.871 41.667 15.59 0.25 44.03 2.27
763 845 1.858091 ATGAGCAGCGTTAAGGATCG 58.142 50.000 0.00 0.00 0.00 3.69
1107 1211 2.131067 GGCGGAGGAGAAGGAGGAG 61.131 68.421 0.00 0.00 0.00 3.69
1365 1469 3.374402 CTCCTGGACACGCTCCGT 61.374 66.667 0.00 0.00 43.03 4.69
1958 2068 1.379642 CCATCCGCCCTTCTTCTTGC 61.380 60.000 0.00 0.00 0.00 4.01
2233 2347 6.537301 CACCGTGATTATTAAGAGGTTGCTTA 59.463 38.462 0.00 0.00 0.00 3.09
2241 2355 4.570772 CACCCACACCGTGATTATTAAGAG 59.429 45.833 5.28 0.00 35.23 2.85
2242 2356 4.020039 ACACCCACACCGTGATTATTAAGA 60.020 41.667 5.28 0.00 35.23 2.10
2243 2357 4.094294 CACACCCACACCGTGATTATTAAG 59.906 45.833 5.28 0.00 35.23 1.85
2274 2394 1.946768 AGTTGCACATACACACCACAC 59.053 47.619 0.00 0.00 0.00 3.82
2275 2395 2.340210 AGTTGCACATACACACCACA 57.660 45.000 0.00 0.00 0.00 4.17
2276 2396 3.562141 TGTTAGTTGCACATACACACCAC 59.438 43.478 0.00 0.00 0.00 4.16
2277 2397 3.809905 TGTTAGTTGCACATACACACCA 58.190 40.909 0.00 0.00 0.00 4.17
2278 2398 3.188460 CCTGTTAGTTGCACATACACACC 59.812 47.826 0.00 0.00 0.00 4.16
2279 2399 4.062293 TCCTGTTAGTTGCACATACACAC 58.938 43.478 0.00 0.00 0.00 3.82
2374 2494 4.007644 CGCACCAGGCAGTCCTCA 62.008 66.667 0.00 0.00 41.93 3.86
2694 2814 7.145985 AGTGTTTATACTATACCATGCGTGAG 58.854 38.462 7.72 0.00 0.00 3.51
2876 2998 4.997395 ACAAGAAACGTACTCCTACTACGA 59.003 41.667 5.06 0.00 39.50 3.43
2890 3012 7.466050 GCTCCCTCTTATTATGAACAAGAAACG 60.466 40.741 0.00 0.00 0.00 3.60
3105 3231 1.134694 GAGAAATGTCAACGGCGCC 59.865 57.895 19.07 19.07 0.00 6.53
3106 3232 1.134694 GGAGAAATGTCAACGGCGC 59.865 57.895 6.90 0.00 0.00 6.53
3107 3233 1.086696 ATGGAGAAATGTCAACGGCG 58.913 50.000 4.80 4.80 0.00 6.46
3108 3234 3.006940 TGTATGGAGAAATGTCAACGGC 58.993 45.455 0.00 0.00 0.00 5.68
3109 3235 4.875536 TCATGTATGGAGAAATGTCAACGG 59.124 41.667 0.00 0.00 0.00 4.44
3140 3266 5.753438 GGCGTGTCAGAAACATGAATAGATA 59.247 40.000 0.00 0.00 46.13 1.98
3141 3267 4.572389 GGCGTGTCAGAAACATGAATAGAT 59.428 41.667 0.00 0.00 46.13 1.98
3142 3268 3.932710 GGCGTGTCAGAAACATGAATAGA 59.067 43.478 0.00 0.00 46.13 1.98
3265 3809 6.260050 GCTCGGTCAATACCTAATGAATTTGA 59.740 38.462 0.00 0.00 44.35 2.69
3274 3818 3.196901 ACATGTGCTCGGTCAATACCTAA 59.803 43.478 0.00 0.00 44.35 2.69
3275 3819 2.764010 ACATGTGCTCGGTCAATACCTA 59.236 45.455 0.00 0.00 44.35 3.08
3318 3867 0.391228 TCTTGCAGTCTGTAACCGCA 59.609 50.000 0.00 0.00 39.52 5.69
3351 3900 0.322187 TGGACTGGACGTCGATCTGA 60.322 55.000 9.92 0.00 43.79 3.27
3497 4046 2.452064 CCCGGGGCATACTGGATGT 61.452 63.158 14.71 0.00 39.34 3.06
3498 4047 2.431683 CCCGGGGCATACTGGATG 59.568 66.667 14.71 0.00 39.34 3.51
3499 4048 2.854032 CCCCGGGGCATACTGGAT 60.854 66.667 31.01 0.00 39.34 3.41
3500 4049 3.644465 TTCCCCGGGGCATACTGGA 62.644 63.158 36.68 12.69 39.34 3.86
3501 4050 3.093835 TTCCCCGGGGCATACTGG 61.094 66.667 36.68 8.97 36.61 4.00
3502 4051 2.192175 GTTCCCCGGGGCATACTG 59.808 66.667 36.68 9.85 34.68 2.74
3543 4092 4.933064 CGGATCTGCGAGTCGGCC 62.933 72.222 15.52 0.00 0.00 6.13
3606 4155 6.563037 TGGTGGCCATGTTAATAGTAAGTA 57.437 37.500 9.72 0.00 0.00 2.24
3607 4156 5.444744 TGGTGGCCATGTTAATAGTAAGT 57.555 39.130 9.72 0.00 0.00 2.24
3608 4157 5.221048 GCTTGGTGGCCATGTTAATAGTAAG 60.221 44.000 9.72 3.22 31.53 2.34
3610 4159 4.204012 GCTTGGTGGCCATGTTAATAGTA 58.796 43.478 9.72 0.00 31.53 1.82
3646 4211 4.830826 AACAATTCCTTCCTCGAAACAC 57.169 40.909 0.00 0.00 0.00 3.32
3675 4240 1.115467 TCTTTTTGCGGGCAGGAAAA 58.885 45.000 12.47 12.47 46.14 2.29
3676 4241 1.115467 TTCTTTTTGCGGGCAGGAAA 58.885 45.000 0.00 0.00 38.42 3.13
3677 4242 1.115467 TTTCTTTTTGCGGGCAGGAA 58.885 45.000 0.00 0.00 0.00 3.36
3678 4243 1.115467 TTTTCTTTTTGCGGGCAGGA 58.885 45.000 0.00 0.00 0.00 3.86
3679 4244 1.866601 CTTTTTCTTTTTGCGGGCAGG 59.133 47.619 0.00 0.00 0.00 4.85
3680 4245 1.866601 CCTTTTTCTTTTTGCGGGCAG 59.133 47.619 0.00 0.00 0.00 4.85
3681 4246 1.482593 TCCTTTTTCTTTTTGCGGGCA 59.517 42.857 0.00 0.00 0.00 5.36
3682 4247 2.135139 CTCCTTTTTCTTTTTGCGGGC 58.865 47.619 0.00 0.00 0.00 6.13
3683 4248 3.726291 TCTCCTTTTTCTTTTTGCGGG 57.274 42.857 0.00 0.00 0.00 6.13
3684 4249 4.051237 CCTTCTCCTTTTTCTTTTTGCGG 58.949 43.478 0.00 0.00 0.00 5.69
3685 4250 4.932146 TCCTTCTCCTTTTTCTTTTTGCG 58.068 39.130 0.00 0.00 0.00 4.85
3686 4251 6.573434 TCTTCCTTCTCCTTTTTCTTTTTGC 58.427 36.000 0.00 0.00 0.00 3.68
4007 4572 2.028925 ATGCTGCACACGTCGTCA 59.971 55.556 3.57 0.00 0.00 4.35
4243 4808 0.036671 CCCGAAGTTCTGGTACACCC 60.037 60.000 5.21 0.00 34.29 4.61
4405 4970 7.397476 TGGGTCTAGCATTACTGATAATCTAGG 59.603 40.741 0.00 0.00 34.03 3.02
4415 4980 2.961526 ACGTGGGTCTAGCATTACTG 57.038 50.000 0.00 0.00 0.00 2.74
4419 4984 2.170607 AGCATTACGTGGGTCTAGCATT 59.829 45.455 0.00 0.00 0.00 3.56
4420 4985 1.762957 AGCATTACGTGGGTCTAGCAT 59.237 47.619 0.00 0.00 0.00 3.79
4421 4986 1.191535 AGCATTACGTGGGTCTAGCA 58.808 50.000 0.00 0.00 0.00 3.49
4422 4987 2.740452 GTAGCATTACGTGGGTCTAGC 58.260 52.381 0.00 0.00 0.00 3.42
4423 4988 2.996155 CGTAGCATTACGTGGGTCTAG 58.004 52.381 0.00 0.00 45.79 2.43
4443 5008 8.820933 GGAGGGAGTATTACGTAAAATTTGTAC 58.179 37.037 12.81 9.00 0.00 2.90
4444 5009 7.706179 CGGAGGGAGTATTACGTAAAATTTGTA 59.294 37.037 12.81 0.00 0.00 2.41
4445 5010 6.536224 CGGAGGGAGTATTACGTAAAATTTGT 59.464 38.462 12.81 0.00 0.00 2.83
4446 5011 6.536224 ACGGAGGGAGTATTACGTAAAATTTG 59.464 38.462 12.81 0.00 32.30 2.32
4447 5012 6.643388 ACGGAGGGAGTATTACGTAAAATTT 58.357 36.000 12.81 0.00 32.30 1.82
4448 5013 6.225981 ACGGAGGGAGTATTACGTAAAATT 57.774 37.500 12.81 0.00 32.30 1.82
4449 5014 5.859205 ACGGAGGGAGTATTACGTAAAAT 57.141 39.130 12.81 0.00 32.30 1.82
4450 5015 5.659440 AACGGAGGGAGTATTACGTAAAA 57.341 39.130 12.81 0.00 33.85 1.52
4451 5016 5.659440 AAACGGAGGGAGTATTACGTAAA 57.341 39.130 12.81 0.00 33.85 2.01
4452 5017 5.659440 AAAACGGAGGGAGTATTACGTAA 57.341 39.130 11.02 11.02 33.85 3.18
4453 5018 5.659440 AAAAACGGAGGGAGTATTACGTA 57.341 39.130 0.00 0.00 33.85 3.57
4454 5019 4.541973 AAAAACGGAGGGAGTATTACGT 57.458 40.909 0.00 0.00 35.95 3.57
4455 5020 6.966435 TTTAAAAACGGAGGGAGTATTACG 57.034 37.500 0.00 0.00 0.00 3.18
4459 5024 9.470399 ACAAATATTTAAAAACGGAGGGAGTAT 57.530 29.630 0.00 0.00 0.00 2.12
4460 5025 8.866970 ACAAATATTTAAAAACGGAGGGAGTA 57.133 30.769 0.00 0.00 0.00 2.59
4461 5026 7.770366 ACAAATATTTAAAAACGGAGGGAGT 57.230 32.000 0.00 0.00 0.00 3.85
4462 5027 9.483916 AAAACAAATATTTAAAAACGGAGGGAG 57.516 29.630 0.00 0.00 0.00 4.30
4463 5028 9.833917 AAAAACAAATATTTAAAAACGGAGGGA 57.166 25.926 0.00 0.00 0.00 4.20
4483 5048 9.364989 CCACTTGTTGAAATTTCTAGAAAAACA 57.635 29.630 21.26 21.23 33.56 2.83
4484 5049 9.366216 ACCACTTGTTGAAATTTCTAGAAAAAC 57.634 29.630 21.26 19.20 33.56 2.43
4485 5050 9.936759 AACCACTTGTTGAAATTTCTAGAAAAA 57.063 25.926 21.26 8.77 35.31 1.94
4496 5061 8.850156 GCTCCATATATAACCACTTGTTGAAAT 58.150 33.333 0.00 0.00 37.83 2.17
4497 5062 7.831690 TGCTCCATATATAACCACTTGTTGAAA 59.168 33.333 0.00 0.00 37.83 2.69
4498 5063 7.342581 TGCTCCATATATAACCACTTGTTGAA 58.657 34.615 0.00 0.00 37.83 2.69
4499 5064 6.894682 TGCTCCATATATAACCACTTGTTGA 58.105 36.000 0.00 0.00 37.83 3.18
4500 5065 7.566760 TTGCTCCATATATAACCACTTGTTG 57.433 36.000 0.00 0.00 37.83 3.33
4501 5066 8.588290 TTTTGCTCCATATATAACCACTTGTT 57.412 30.769 0.00 0.00 41.11 2.83
4502 5067 8.632679 CATTTTGCTCCATATATAACCACTTGT 58.367 33.333 0.00 0.00 0.00 3.16
4503 5068 8.849168 TCATTTTGCTCCATATATAACCACTTG 58.151 33.333 0.00 0.00 0.00 3.16
4504 5069 8.995027 TCATTTTGCTCCATATATAACCACTT 57.005 30.769 0.00 0.00 0.00 3.16
4505 5070 8.220559 ACTCATTTTGCTCCATATATAACCACT 58.779 33.333 0.00 0.00 0.00 4.00
4506 5071 8.292448 CACTCATTTTGCTCCATATATAACCAC 58.708 37.037 0.00 0.00 0.00 4.16
4507 5072 8.217111 TCACTCATTTTGCTCCATATATAACCA 58.783 33.333 0.00 0.00 0.00 3.67
4508 5073 8.621532 TCACTCATTTTGCTCCATATATAACC 57.378 34.615 0.00 0.00 0.00 2.85
4513 5078 9.494271 GTAGATTCACTCATTTTGCTCCATATA 57.506 33.333 0.00 0.00 0.00 0.86
4514 5079 7.994911 TGTAGATTCACTCATTTTGCTCCATAT 59.005 33.333 0.00 0.00 0.00 1.78
4515 5080 7.280876 GTGTAGATTCACTCATTTTGCTCCATA 59.719 37.037 0.00 0.00 35.68 2.74
4516 5081 6.094603 GTGTAGATTCACTCATTTTGCTCCAT 59.905 38.462 0.00 0.00 35.68 3.41
4517 5082 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
4518 5083 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
4519 5084 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
4530 5095 9.509855 CAGACATAGTTTAGAGTGTAGATTCAC 57.490 37.037 0.00 0.00 38.46 3.18
4531 5096 9.244292 ACAGACATAGTTTAGAGTGTAGATTCA 57.756 33.333 0.00 0.00 0.00 2.57
4539 5104 9.900710 GGATGTATACAGACATAGTTTAGAGTG 57.099 37.037 11.91 0.00 40.18 3.51
4540 5105 8.784994 CGGATGTATACAGACATAGTTTAGAGT 58.215 37.037 11.91 0.00 40.18 3.24
4541 5106 8.784994 ACGGATGTATACAGACATAGTTTAGAG 58.215 37.037 11.91 0.00 40.18 2.43
4542 5107 8.687292 ACGGATGTATACAGACATAGTTTAGA 57.313 34.615 11.91 0.00 40.18 2.10
4545 5110 8.857098 ACATACGGATGTATACAGACATAGTTT 58.143 33.333 12.79 0.00 44.77 2.66
4546 5111 8.297426 CACATACGGATGTATACAGACATAGTT 58.703 37.037 14.23 0.00 44.82 2.24
4547 5112 7.664318 TCACATACGGATGTATACAGACATAGT 59.336 37.037 14.23 10.76 44.82 2.12
4548 5113 8.040716 TCACATACGGATGTATACAGACATAG 57.959 38.462 14.23 0.00 44.82 2.23
4549 5114 7.989416 TCACATACGGATGTATACAGACATA 57.011 36.000 14.23 0.11 44.82 2.29
4550 5115 6.894339 TCACATACGGATGTATACAGACAT 57.106 37.500 14.23 0.00 44.82 3.06
4551 5116 6.894339 ATCACATACGGATGTATACAGACA 57.106 37.500 14.23 0.00 44.82 3.41
4552 5117 8.041829 ACTATCACATACGGATGTATACAGAC 57.958 38.462 14.23 7.85 44.82 3.51
4553 5118 7.336176 GGACTATCACATACGGATGTATACAGA 59.664 40.741 14.23 6.57 44.82 3.41
4554 5119 7.120726 TGGACTATCACATACGGATGTATACAG 59.879 40.741 14.23 10.64 44.82 2.74
4555 5120 6.943718 TGGACTATCACATACGGATGTATACA 59.056 38.462 14.23 8.27 44.82 2.29
4556 5121 7.387119 TGGACTATCACATACGGATGTATAC 57.613 40.000 14.23 2.34 44.82 1.47
4557 5122 8.589701 AATGGACTATCACATACGGATGTATA 57.410 34.615 14.23 10.59 44.82 1.47
4558 5123 7.482169 AATGGACTATCACATACGGATGTAT 57.518 36.000 14.23 10.02 44.82 2.29
4559 5124 6.911250 AATGGACTATCACATACGGATGTA 57.089 37.500 14.23 2.61 44.82 2.29
4561 5126 6.223120 TCAAATGGACTATCACATACGGATG 58.777 40.000 5.94 5.94 39.16 3.51
4562 5127 6.419484 TCAAATGGACTATCACATACGGAT 57.581 37.500 0.00 0.00 0.00 4.18
4563 5128 5.862678 TCAAATGGACTATCACATACGGA 57.137 39.130 0.00 0.00 0.00 4.69
4564 5129 6.918892 TTTCAAATGGACTATCACATACGG 57.081 37.500 0.00 0.00 0.00 4.02
4565 5130 8.370493 AGATTTCAAATGGACTATCACATACG 57.630 34.615 0.00 0.00 0.00 3.06
4566 5131 9.553064 AGAGATTTCAAATGGACTATCACATAC 57.447 33.333 0.00 0.00 0.00 2.39
4569 5134 9.958180 TTTAGAGATTTCAAATGGACTATCACA 57.042 29.630 0.00 0.00 0.00 3.58
4575 5140 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
4576 5141 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
4593 5158 9.074576 ACTCCGTTCCTAAATATTTGTCTTTTT 57.925 29.630 11.05 0.00 0.00 1.94
4594 5159 8.631480 ACTCCGTTCCTAAATATTTGTCTTTT 57.369 30.769 11.05 0.00 0.00 2.27
4595 5160 9.379791 CTACTCCGTTCCTAAATATTTGTCTTT 57.620 33.333 11.05 0.00 0.00 2.52
4596 5161 8.755977 TCTACTCCGTTCCTAAATATTTGTCTT 58.244 33.333 11.05 0.00 0.00 3.01
4597 5162 8.196103 GTCTACTCCGTTCCTAAATATTTGTCT 58.804 37.037 11.05 0.00 0.00 3.41
4598 5163 8.196103 AGTCTACTCCGTTCCTAAATATTTGTC 58.804 37.037 11.05 0.00 0.00 3.18
4599 5164 8.075761 AGTCTACTCCGTTCCTAAATATTTGT 57.924 34.615 11.05 0.00 0.00 2.83
4603 5168 9.160496 CGTATAGTCTACTCCGTTCCTAAATAT 57.840 37.037 0.00 0.00 0.00 1.28
4604 5169 7.604164 CCGTATAGTCTACTCCGTTCCTAAATA 59.396 40.741 0.00 0.00 0.00 1.40
4605 5170 6.429385 CCGTATAGTCTACTCCGTTCCTAAAT 59.571 42.308 0.00 0.00 0.00 1.40
4606 5171 5.760253 CCGTATAGTCTACTCCGTTCCTAAA 59.240 44.000 0.00 0.00 0.00 1.85
4607 5172 5.070446 TCCGTATAGTCTACTCCGTTCCTAA 59.930 44.000 0.00 0.00 0.00 2.69
4608 5173 4.588951 TCCGTATAGTCTACTCCGTTCCTA 59.411 45.833 0.00 0.00 0.00 2.94
4609 5174 3.389329 TCCGTATAGTCTACTCCGTTCCT 59.611 47.826 0.00 0.00 0.00 3.36
4610 5175 3.733337 TCCGTATAGTCTACTCCGTTCC 58.267 50.000 0.00 0.00 0.00 3.62
4611 5176 3.745458 CCTCCGTATAGTCTACTCCGTTC 59.255 52.174 0.00 0.00 0.00 3.95
4612 5177 3.389329 TCCTCCGTATAGTCTACTCCGTT 59.611 47.826 0.00 0.00 0.00 4.44
4613 5178 2.968574 TCCTCCGTATAGTCTACTCCGT 59.031 50.000 0.00 0.00 0.00 4.69
4614 5179 3.674528 TCCTCCGTATAGTCTACTCCG 57.325 52.381 0.00 0.00 0.00 4.63
4615 5180 5.183522 CCAAATCCTCCGTATAGTCTACTCC 59.816 48.000 0.00 0.00 0.00 3.85
4616 5181 6.002704 TCCAAATCCTCCGTATAGTCTACTC 58.997 44.000 0.00 0.00 0.00 2.59
4617 5182 5.950023 TCCAAATCCTCCGTATAGTCTACT 58.050 41.667 0.00 0.00 0.00 2.57
4618 5183 6.837471 ATCCAAATCCTCCGTATAGTCTAC 57.163 41.667 0.00 0.00 0.00 2.59
4619 5184 6.210784 CCAATCCAAATCCTCCGTATAGTCTA 59.789 42.308 0.00 0.00 0.00 2.59
4620 5185 5.012148 CCAATCCAAATCCTCCGTATAGTCT 59.988 44.000 0.00 0.00 0.00 3.24
4621 5186 5.011738 TCCAATCCAAATCCTCCGTATAGTC 59.988 44.000 0.00 0.00 0.00 2.59
4622 5187 4.905456 TCCAATCCAAATCCTCCGTATAGT 59.095 41.667 0.00 0.00 0.00 2.12
4623 5188 5.483685 TCCAATCCAAATCCTCCGTATAG 57.516 43.478 0.00 0.00 0.00 1.31
4624 5189 5.804639 CATCCAATCCAAATCCTCCGTATA 58.195 41.667 0.00 0.00 0.00 1.47
4625 5190 4.655963 CATCCAATCCAAATCCTCCGTAT 58.344 43.478 0.00 0.00 0.00 3.06
4626 5191 4.085357 CATCCAATCCAAATCCTCCGTA 57.915 45.455 0.00 0.00 0.00 4.02
4627 5192 2.936202 CATCCAATCCAAATCCTCCGT 58.064 47.619 0.00 0.00 0.00 4.69
5242 5807 3.701604 CTTCCTTCTCCGCGACCCG 62.702 68.421 8.23 0.00 0.00 5.28
5243 5808 1.677637 ATCTTCCTTCTCCGCGACCC 61.678 60.000 8.23 0.00 0.00 4.46
5244 5809 0.175989 AATCTTCCTTCTCCGCGACC 59.824 55.000 8.23 0.00 0.00 4.79
5245 5810 2.011540 AAATCTTCCTTCTCCGCGAC 57.988 50.000 8.23 0.00 0.00 5.19
5246 5811 2.028476 TCAAAATCTTCCTTCTCCGCGA 60.028 45.455 8.23 0.00 0.00 5.87
5247 5812 2.346803 TCAAAATCTTCCTTCTCCGCG 58.653 47.619 0.00 0.00 0.00 6.46
5248 5813 2.680339 CCTCAAAATCTTCCTTCTCCGC 59.320 50.000 0.00 0.00 0.00 5.54
5249 5814 3.274288 CCCTCAAAATCTTCCTTCTCCG 58.726 50.000 0.00 0.00 0.00 4.63
5250 5815 4.308526 ACCCTCAAAATCTTCCTTCTCC 57.691 45.455 0.00 0.00 0.00 3.71
5251 5816 6.319911 CCATTACCCTCAAAATCTTCCTTCTC 59.680 42.308 0.00 0.00 0.00 2.87
5252 5817 6.190587 CCATTACCCTCAAAATCTTCCTTCT 58.809 40.000 0.00 0.00 0.00 2.85
5253 5818 5.163509 GCCATTACCCTCAAAATCTTCCTTC 60.164 44.000 0.00 0.00 0.00 3.46
5254 5819 4.711846 GCCATTACCCTCAAAATCTTCCTT 59.288 41.667 0.00 0.00 0.00 3.36
5255 5820 4.264352 TGCCATTACCCTCAAAATCTTCCT 60.264 41.667 0.00 0.00 0.00 3.36
5256 5821 4.023291 TGCCATTACCCTCAAAATCTTCC 58.977 43.478 0.00 0.00 0.00 3.46
5257 5822 5.127682 ACATGCCATTACCCTCAAAATCTTC 59.872 40.000 0.00 0.00 0.00 2.87
5258 5823 5.025453 ACATGCCATTACCCTCAAAATCTT 58.975 37.500 0.00 0.00 0.00 2.40
5259 5824 4.403432 CACATGCCATTACCCTCAAAATCT 59.597 41.667 0.00 0.00 0.00 2.40
5260 5825 4.402155 TCACATGCCATTACCCTCAAAATC 59.598 41.667 0.00 0.00 0.00 2.17
5261 5826 4.352009 TCACATGCCATTACCCTCAAAAT 58.648 39.130 0.00 0.00 0.00 1.82
5262 5827 3.772387 TCACATGCCATTACCCTCAAAA 58.228 40.909 0.00 0.00 0.00 2.44
5263 5828 3.448093 TCACATGCCATTACCCTCAAA 57.552 42.857 0.00 0.00 0.00 2.69
5264 5829 3.448093 TTCACATGCCATTACCCTCAA 57.552 42.857 0.00 0.00 0.00 3.02
5265 5830 3.448093 TTTCACATGCCATTACCCTCA 57.552 42.857 0.00 0.00 0.00 3.86
5266 5831 4.799564 TTTTTCACATGCCATTACCCTC 57.200 40.909 0.00 0.00 0.00 4.30
5267 5832 6.865834 TTATTTTTCACATGCCATTACCCT 57.134 33.333 0.00 0.00 0.00 4.34
5268 5833 7.102993 ACTTTATTTTTCACATGCCATTACCC 58.897 34.615 0.00 0.00 0.00 3.69
5269 5834 9.646427 TTACTTTATTTTTCACATGCCATTACC 57.354 29.630 0.00 0.00 0.00 2.85
5271 5836 9.347934 CGTTACTTTATTTTTCACATGCCATTA 57.652 29.630 0.00 0.00 0.00 1.90
5272 5837 7.148656 GCGTTACTTTATTTTTCACATGCCATT 60.149 33.333 0.00 0.00 0.00 3.16
5273 5838 6.310224 GCGTTACTTTATTTTTCACATGCCAT 59.690 34.615 0.00 0.00 0.00 4.40
5274 5839 5.631512 GCGTTACTTTATTTTTCACATGCCA 59.368 36.000 0.00 0.00 0.00 4.92
5275 5840 5.631512 TGCGTTACTTTATTTTTCACATGCC 59.368 36.000 0.00 0.00 0.00 4.40
5276 5841 6.362283 AGTGCGTTACTTTATTTTTCACATGC 59.638 34.615 0.00 0.00 35.67 4.06
5277 5842 7.851822 AGTGCGTTACTTTATTTTTCACATG 57.148 32.000 0.00 0.00 35.67 3.21


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

AutoCloner maintained by Alex Coulton.