Multiple sequence alignment - TraesCS5A01G180400

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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 TraesCS5A01G180400 chr5A 100.000 5094 0 0 1 5094 379135777 379130684 0.000000e+00 9407
1 TraesCS5A01G180400 chr5B 94.642 4591 166 41 1 4557 326087850 326083306 0.000000e+00 7042
2 TraesCS5A01G180400 chr5B 86.207 116 11 1 4678 4788 326083278 326083163 2.490000e-23 121
3 TraesCS5A01G180400 chr5D 95.980 4005 112 17 821 4811 287308021 287304052 0.000000e+00 6458
4 TraesCS5A01G180400 chr5D 96.933 163 3 1 4934 5094 287304055 287303893 6.500000e-69 272
5 TraesCS5A01G180400 chr5D 96.053 76 3 0 4782 4857 498669834 498669759 1.930000e-24 124
6 TraesCS5A01G180400 chr7D 96.203 79 3 0 4786 4864 5307736 5307658 4.140000e-26 130
7 TraesCS5A01G180400 chr7D 98.611 72 1 0 4786 4857 184573430 184573359 1.490000e-25 128
8 TraesCS5A01G180400 chr4D 91.489 94 8 0 4771 4864 15786183 15786276 4.140000e-26 130
9 TraesCS5A01G180400 chr1D 98.611 72 1 0 4786 4857 370323657 370323728 1.490000e-25 128
10 TraesCS5A01G180400 chr6A 97.333 75 1 1 4783 4857 501479287 501479360 5.350000e-25 126
11 TraesCS5A01G180400 chr7A 96.053 76 2 1 4783 4858 7805386 7805312 6.930000e-24 122
12 TraesCS5A01G180400 chr7B 92.857 84 4 2 4785 4867 419032266 419032184 2.490000e-23 121
13 TraesCS5A01G180400 chr6B 96.000 75 2 1 4783 4857 541936651 541936724 2.490000e-23 121
14 TraesCS5A01G180400 chr1A 84.000 125 19 1 48 171 540155865 540155741 8.960000e-23 119


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 TraesCS5A01G180400 chr5A 379130684 379135777 5093 True 9407.0 9407 100.0000 1 5094 1 chr5A.!!$R1 5093
1 TraesCS5A01G180400 chr5B 326083163 326087850 4687 True 3581.5 7042 90.4245 1 4788 2 chr5B.!!$R1 4787
2 TraesCS5A01G180400 chr5D 287303893 287308021 4128 True 3365.0 6458 96.4565 821 5094 2 chr5D.!!$R2 4273

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
100 101 0.179156 GCTTGTTGCCATCCATGACG 60.179 55.0 0.00 0.00 35.15 4.35 F
101 102 0.179156 CTTGTTGCCATCCATGACGC 60.179 55.0 0.00 0.00 0.00 5.19 F
562 577 0.182775 ACCAGAAACTGTTTCCCGCT 59.817 50.0 25.22 8.07 40.54 5.52 F
1837 1858 0.397564 TTCAGCAGCAGACCATGTCA 59.602 50.0 0.00 0.00 34.60 3.58 F
1906 1927 2.159085 AGAAGGGATACAACGCTACTGC 60.159 50.0 0.00 0.00 39.74 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1265 1286 0.476808 TGTGGAACCTGGTGGGGTAT 60.477 55.000 0.00 0.0 38.87 2.73 R
1852 1873 0.976073 GGATGTTCTCCTCGGGGACA 60.976 60.000 0.00 0.0 41.29 4.02 R
1906 1927 2.436646 ACCTTTGCATCCGAGCCG 60.437 61.111 0.00 0.0 0.00 5.52 R
3674 3695 3.364964 CCGTTGGAATGAGGAAGAAAACG 60.365 47.826 0.00 0.0 38.97 3.60 R
4147 4171 1.493022 TCCACTTGCCCAGTAAACTGT 59.507 47.619 9.17 0.0 42.27 3.55 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 2.042686 TGAAGTTGTTGCTGCAGAGT 57.957 45.000 20.43 0.00 0.00 3.24
64 65 1.672363 TGAAGTTGTTGCTGCAGAGTG 59.328 47.619 20.43 0.00 0.00 3.51
67 68 2.579873 AGTTGTTGCTGCAGAGTGAAT 58.420 42.857 20.43 0.00 0.00 2.57
74 75 1.260033 GCTGCAGAGTGAATATCGCAC 59.740 52.381 20.43 0.00 36.53 5.34
76 77 1.206849 TGCAGAGTGAATATCGCACCA 59.793 47.619 5.36 0.00 36.95 4.17
82 83 1.004927 GTGAATATCGCACCAACGAGC 60.005 52.381 0.00 0.00 46.69 5.03
90 91 1.008538 CACCAACGAGCTTGTTGCC 60.009 57.895 33.07 0.00 46.14 4.52
91 92 1.453015 ACCAACGAGCTTGTTGCCA 60.453 52.632 33.07 0.00 46.14 4.92
96 97 0.322816 ACGAGCTTGTTGCCATCCAT 60.323 50.000 0.00 0.00 44.23 3.41
100 101 0.179156 GCTTGTTGCCATCCATGACG 60.179 55.000 0.00 0.00 35.15 4.35
101 102 0.179156 CTTGTTGCCATCCATGACGC 60.179 55.000 0.00 0.00 0.00 5.19
105 106 0.680601 TTGCCATCCATGACGCACAT 60.681 50.000 0.00 0.00 40.17 3.21
118 119 1.176527 CGCACATGTTTGGGGAGATT 58.823 50.000 0.00 0.00 0.00 2.40
119 120 1.133025 CGCACATGTTTGGGGAGATTC 59.867 52.381 0.00 0.00 0.00 2.52
120 121 1.133025 GCACATGTTTGGGGAGATTCG 59.867 52.381 0.00 0.00 0.00 3.34
121 122 2.710377 CACATGTTTGGGGAGATTCGA 58.290 47.619 0.00 0.00 0.00 3.71
122 123 2.420022 CACATGTTTGGGGAGATTCGAC 59.580 50.000 0.00 0.00 0.00 4.20
123 124 1.665679 CATGTTTGGGGAGATTCGACG 59.334 52.381 0.00 0.00 0.00 5.12
132 133 2.801111 GGGAGATTCGACGGCTATTTTC 59.199 50.000 0.00 0.00 0.00 2.29
134 135 3.114065 GAGATTCGACGGCTATTTTCGT 58.886 45.455 0.00 0.00 42.67 3.85
150 151 1.449423 CGTGTCAATCGGATGGCCA 60.449 57.895 8.56 8.56 0.00 5.36
188 192 5.975693 TTTTCCTATCCACCAATGAACAC 57.024 39.130 0.00 0.00 0.00 3.32
196 200 2.487762 CCACCAATGAACACGTAGCATT 59.512 45.455 0.00 0.00 32.83 3.56
203 207 4.394439 TGAACACGTAGCATTGCCTATA 57.606 40.909 4.70 0.00 0.00 1.31
204 208 4.956085 TGAACACGTAGCATTGCCTATAT 58.044 39.130 4.70 0.00 0.00 0.86
281 292 5.615289 ACAGATCATTTCTATTCCGAAGGG 58.385 41.667 0.00 0.00 40.37 3.95
304 315 3.244805 ACAAAAACACTAGCCTAGACCCC 60.245 47.826 5.58 0.00 0.00 4.95
305 316 1.192428 AAACACTAGCCTAGACCCCG 58.808 55.000 5.58 0.00 0.00 5.73
309 320 1.229359 CTAGCCTAGACCCCGTGGA 59.771 63.158 0.00 0.00 34.81 4.02
373 384 9.887629 ACAGGATTTCAGATACATATCATCATC 57.112 33.333 1.88 0.00 35.17 2.92
380 391 8.291191 TCAGATACATATCATCATCTCACCTC 57.709 38.462 1.88 0.00 35.17 3.85
381 392 7.341512 TCAGATACATATCATCATCTCACCTCC 59.658 40.741 1.88 0.00 35.17 4.30
393 404 4.542906 TCTCACCTCCTATGATCTTCCA 57.457 45.455 0.00 0.00 0.00 3.53
414 425 5.246656 TCCAATTTCTGTGAGGCATCAAAAT 59.753 36.000 0.92 2.97 37.14 1.82
488 503 2.823984 TGTTTCACTTGGCATGCAAAG 58.176 42.857 29.57 29.57 33.35 2.77
559 574 4.081322 TGTAGACCAGAAACTGTTTCCC 57.919 45.455 25.22 14.29 40.54 3.97
562 577 0.182775 ACCAGAAACTGTTTCCCGCT 59.817 50.000 25.22 8.07 40.54 5.52
584 599 5.793457 GCTGCACGTAAAGTTTTTATACCAG 59.207 40.000 0.00 0.00 0.00 4.00
590 605 6.991531 ACGTAAAGTTTTTATACCAGTGTCCA 59.008 34.615 0.00 0.00 0.00 4.02
591 606 7.662669 ACGTAAAGTTTTTATACCAGTGTCCAT 59.337 33.333 0.00 0.00 0.00 3.41
716 735 8.769359 TGTTTGAGGGGTAAAAAGGAATAAAAA 58.231 29.630 0.00 0.00 0.00 1.94
801 820 9.767228 TTGATGATTGATTTGTTTTGAGACAAT 57.233 25.926 0.00 0.00 39.12 2.71
802 821 9.767228 TGATGATTGATTTGTTTTGAGACAATT 57.233 25.926 0.00 0.00 39.12 2.32
816 837 9.634163 TTTTGAGACAATTTGATGATTGATGAG 57.366 29.630 2.79 0.00 38.93 2.90
823 844 9.856488 ACAATTTGATGATTGATGAGAGAAAAG 57.144 29.630 2.79 0.00 38.93 2.27
829 850 9.903682 TGATGATTGATGAGAGAAAAGAAAAAC 57.096 29.630 0.00 0.00 0.00 2.43
835 856 8.931385 TGATGAGAGAAAAGAAAAACAAAAGG 57.069 30.769 0.00 0.00 0.00 3.11
836 857 8.748412 TGATGAGAGAAAAGAAAAACAAAAGGA 58.252 29.630 0.00 0.00 0.00 3.36
837 858 9.586435 GATGAGAGAAAAGAAAAACAAAAGGAA 57.414 29.630 0.00 0.00 0.00 3.36
905 926 3.560278 GTGGATACGCGGCGGTTG 61.560 66.667 27.37 0.00 42.51 3.77
906 927 3.761140 TGGATACGCGGCGGTTGA 61.761 61.111 27.37 9.12 42.51 3.18
936 957 1.941325 CAACTGGCGGAGAATAGGAC 58.059 55.000 0.00 0.00 0.00 3.85
975 996 0.618981 ACTTCGTCCCCATTCCTTCC 59.381 55.000 0.00 0.00 0.00 3.46
1083 1104 0.995675 AATGGGGGAGGTGATGGAGG 60.996 60.000 0.00 0.00 0.00 4.30
1090 1111 1.961180 GAGGTGATGGAGGTGACGGG 61.961 65.000 0.00 0.00 0.00 5.28
1121 1142 4.436998 GTGAGCGACCTCCCCGTG 62.437 72.222 0.00 0.00 37.29 4.94
1265 1286 1.890041 CGAGTGCAACAACCCCGAA 60.890 57.895 0.00 0.00 41.43 4.30
1464 1485 6.559810 CCAATTATTCGGTCATTGCAAGTTA 58.440 36.000 4.94 0.00 0.00 2.24
1493 1514 5.627499 TTTCACAGCAAGGCTATTACAAG 57.373 39.130 0.00 0.00 36.40 3.16
1495 1516 3.009033 TCACAGCAAGGCTATTACAAGGT 59.991 43.478 0.00 0.00 36.40 3.50
1564 1585 3.926821 TCGTTTGGCCCTGAAAATTAC 57.073 42.857 0.00 0.00 0.00 1.89
1618 1639 4.820173 AGGTACAGGCTTAACACAAGAAAC 59.180 41.667 0.00 0.00 0.00 2.78
1651 1672 1.738099 GCAGTCGATGCGAGGTTGT 60.738 57.895 4.48 0.00 46.99 3.32
1750 1771 5.650266 TGTCAACAAGTCTGGTTTTGTATGT 59.350 36.000 0.00 0.00 36.56 2.29
1837 1858 0.397564 TTCAGCAGCAGACCATGTCA 59.602 50.000 0.00 0.00 34.60 3.58
1852 1873 4.590647 ACCATGTCATTGATCTATCTCGGT 59.409 41.667 0.00 0.00 0.00 4.69
1906 1927 2.159085 AGAAGGGATACAACGCTACTGC 60.159 50.000 0.00 0.00 39.74 4.40
2191 2212 5.045869 TGGTGTAAGCAAGCTTAAGGTATCT 60.046 40.000 15.43 5.28 44.10 1.98
2276 2297 5.202746 TGTCTAGTTATGTCTACAGGGGT 57.797 43.478 0.00 0.00 0.00 4.95
2421 2442 2.299993 TGACACTTCGAGATGGATGC 57.700 50.000 3.38 0.00 0.00 3.91
2582 2603 2.857186 TTTCCTGTGTAGATGCTGCA 57.143 45.000 4.13 4.13 0.00 4.41
2609 2630 3.749088 AGTTCATTGCCGTTGACGAAATA 59.251 39.130 4.91 0.00 43.02 1.40
2738 2759 4.767928 AGGTGCAACGGGAAATATTTACAA 59.232 37.500 12.50 0.00 38.12 2.41
3262 3283 6.053650 TGATGAGGCTGTTCTATTTGATGAG 58.946 40.000 0.00 0.00 0.00 2.90
3309 3330 2.170187 CAAGCCAGAAGGATGCTAGTCT 59.830 50.000 0.00 0.00 36.89 3.24
3580 3601 2.971095 AAGTGGCTGAGCTTGCTGCA 62.971 55.000 3.72 0.00 45.94 4.41
3936 3957 3.448660 CCTTGGATCATTTTCACCTTCCC 59.551 47.826 0.00 0.00 0.00 3.97
4147 4171 2.055689 CTGCAGTTGTGGGGTGAGGA 62.056 60.000 5.25 0.00 0.00 3.71
4150 4174 0.250467 CAGTTGTGGGGTGAGGACAG 60.250 60.000 0.00 0.00 0.00 3.51
4219 4243 6.709846 AGGCATTTCTAGTCTGCAGATTATTC 59.290 38.462 21.47 6.41 37.64 1.75
4247 4271 7.201609 GGTTTCGTTATTCTCATTACAGATGCA 60.202 37.037 0.00 0.00 0.00 3.96
4327 4351 5.835113 TTGCTTGGCCTCTTCATATTTAC 57.165 39.130 3.32 0.00 0.00 2.01
4465 4490 3.282021 CCATAGGACCTGTGAATTGTGG 58.718 50.000 19.19 0.00 0.00 4.17
4541 4579 9.636789 TTCATGATTCATTGATTCTTATCCTGT 57.363 29.630 0.00 0.00 0.00 4.00
4564 4602 1.306911 TGCATCTGGGCTGGAGGTA 60.307 57.895 0.00 0.00 34.04 3.08
4573 4616 1.070914 GGGCTGGAGGTAGATTAGCAC 59.929 57.143 0.00 0.00 36.15 4.40
4648 4691 3.244976 GAACACAGCCATGTATTTGCAC 58.755 45.455 0.00 0.00 37.65 4.57
4657 4700 4.201910 GCCATGTATTTGCACGTCTGTTAT 60.202 41.667 0.00 0.00 0.00 1.89
4669 4712 5.444745 GCACGTCTGTTATGTTCTAAGAAGC 60.445 44.000 0.00 0.00 0.00 3.86
4673 4716 5.062308 GTCTGTTATGTTCTAAGAAGCACGG 59.938 44.000 0.00 0.00 0.00 4.94
4698 4741 6.569801 GCGCTTTCTTGTTACCCTTATTTTCT 60.570 38.462 0.00 0.00 0.00 2.52
4704 4747 9.807921 TTCTTGTTACCCTTATTTTCTTGATCT 57.192 29.630 0.00 0.00 0.00 2.75
4795 4843 2.959707 AGCTCATAAAGTACTCCCTCCG 59.040 50.000 0.00 0.00 0.00 4.63
4808 4856 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4809 4857 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
4810 4858 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
4811 4859 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
4812 4860 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
4813 4861 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
4814 4862 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
4815 4863 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
4816 4864 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
4817 4865 6.209192 TCCGTCCCATAATATAAGAGCGTTTA 59.791 38.462 0.00 0.00 0.00 2.01
4818 4866 6.530534 CCGTCCCATAATATAAGAGCGTTTAG 59.469 42.308 0.00 0.00 0.00 1.85
4819 4867 7.088905 CGTCCCATAATATAAGAGCGTTTAGT 58.911 38.462 0.00 0.00 0.00 2.24
4820 4868 7.061905 CGTCCCATAATATAAGAGCGTTTAGTG 59.938 40.741 0.00 0.00 0.00 2.74
4821 4869 7.871463 GTCCCATAATATAAGAGCGTTTAGTGT 59.129 37.037 0.00 0.00 0.00 3.55
4822 4870 8.086522 TCCCATAATATAAGAGCGTTTAGTGTC 58.913 37.037 0.00 0.00 0.00 3.67
4823 4871 7.870954 CCCATAATATAAGAGCGTTTAGTGTCA 59.129 37.037 0.00 0.00 0.00 3.58
4824 4872 9.256477 CCATAATATAAGAGCGTTTAGTGTCAA 57.744 33.333 0.00 0.00 0.00 3.18
4828 4876 9.821662 AATATAAGAGCGTTTAGTGTCAAAAAC 57.178 29.630 3.12 3.12 33.26 2.43
4833 4881 4.191662 CGTTTAGTGTCAAAAACGCTCT 57.808 40.909 16.81 0.00 45.69 4.09
4834 4882 4.584394 CGTTTAGTGTCAAAAACGCTCTT 58.416 39.130 16.81 0.00 45.69 2.85
4835 4883 5.730269 CGTTTAGTGTCAAAAACGCTCTTA 58.270 37.500 16.81 0.00 45.69 2.10
4836 4884 6.360329 CGTTTAGTGTCAAAAACGCTCTTAT 58.640 36.000 16.81 0.00 45.69 1.73
4837 4885 7.503991 CGTTTAGTGTCAAAAACGCTCTTATA 58.496 34.615 16.81 0.00 45.69 0.98
4838 4886 8.166706 CGTTTAGTGTCAAAAACGCTCTTATAT 58.833 33.333 16.81 0.00 45.69 0.86
4839 4887 9.821662 GTTTAGTGTCAAAAACGCTCTTATATT 57.178 29.630 0.00 0.00 45.69 1.28
4843 4891 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
4844 4892 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
4845 4893 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
4846 4894 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
4847 4895 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
4848 4896 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
4849 4897 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
4850 4898 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
4851 4899 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
4852 4900 4.710375 GCTCTTATATTATGGGACGGAGGA 59.290 45.833 0.00 0.00 0.00 3.71
4853 4901 5.187186 GCTCTTATATTATGGGACGGAGGAA 59.813 44.000 0.00 0.00 0.00 3.36
4854 4902 6.628398 GCTCTTATATTATGGGACGGAGGAAG 60.628 46.154 0.00 0.00 0.00 3.46
4855 4903 6.320518 TCTTATATTATGGGACGGAGGAAGT 58.679 40.000 0.00 0.00 0.00 3.01
4856 4904 7.472741 TCTTATATTATGGGACGGAGGAAGTA 58.527 38.462 0.00 0.00 0.00 2.24
4857 4905 5.997384 ATATTATGGGACGGAGGAAGTAC 57.003 43.478 0.00 0.00 0.00 2.73
4858 4906 2.077687 TATGGGACGGAGGAAGTACC 57.922 55.000 0.00 0.00 42.94 3.34
4876 4924 8.793592 GGAAGTACCTCTTTATTCATTTGTTGT 58.206 33.333 0.00 0.00 36.40 3.32
4882 4930 9.574516 ACCTCTTTATTCATTTGTTGTAAGAGT 57.425 29.630 0.00 0.00 36.99 3.24
4885 4933 9.677567 TCTTTATTCATTTGTTGTAAGAGTTGC 57.322 29.630 0.00 0.00 0.00 4.17
4886 4934 9.462174 CTTTATTCATTTGTTGTAAGAGTTGCA 57.538 29.630 0.00 0.00 0.00 4.08
4887 4935 9.979578 TTTATTCATTTGTTGTAAGAGTTGCAT 57.020 25.926 0.00 0.00 0.00 3.96
4888 4936 9.624697 TTATTCATTTGTTGTAAGAGTTGCATC 57.375 29.630 0.00 0.00 0.00 3.91
4889 4937 6.631971 TCATTTGTTGTAAGAGTTGCATCA 57.368 33.333 0.00 0.00 0.00 3.07
4890 4938 7.218228 TCATTTGTTGTAAGAGTTGCATCAT 57.782 32.000 0.00 0.00 0.00 2.45
4891 4939 7.660112 TCATTTGTTGTAAGAGTTGCATCATT 58.340 30.769 0.00 0.00 0.00 2.57
4892 4940 7.809331 TCATTTGTTGTAAGAGTTGCATCATTC 59.191 33.333 0.00 0.00 0.00 2.67
4893 4941 6.631971 TTGTTGTAAGAGTTGCATCATTCA 57.368 33.333 0.00 0.00 0.00 2.57
4894 4942 6.000891 TGTTGTAAGAGTTGCATCATTCAC 57.999 37.500 0.00 0.00 0.00 3.18
4895 4943 5.048782 TGTTGTAAGAGTTGCATCATTCACC 60.049 40.000 0.00 0.00 0.00 4.02
4896 4944 4.650734 TGTAAGAGTTGCATCATTCACCA 58.349 39.130 0.00 0.00 0.00 4.17
4897 4945 5.069318 TGTAAGAGTTGCATCATTCACCAA 58.931 37.500 0.00 0.00 0.00 3.67
4898 4946 5.711506 TGTAAGAGTTGCATCATTCACCAAT 59.288 36.000 0.00 0.00 0.00 3.16
4899 4947 6.883756 TGTAAGAGTTGCATCATTCACCAATA 59.116 34.615 0.00 0.00 0.00 1.90
4900 4948 6.446781 AAGAGTTGCATCATTCACCAATAG 57.553 37.500 0.00 0.00 0.00 1.73
4901 4949 5.748402 AGAGTTGCATCATTCACCAATAGA 58.252 37.500 0.00 0.00 0.00 1.98
4902 4950 5.821470 AGAGTTGCATCATTCACCAATAGAG 59.179 40.000 0.00 0.00 0.00 2.43
4903 4951 4.885907 AGTTGCATCATTCACCAATAGAGG 59.114 41.667 0.00 0.00 0.00 3.69
4904 4952 4.776435 TGCATCATTCACCAATAGAGGA 57.224 40.909 0.00 0.00 0.00 3.71
4905 4953 5.314718 TGCATCATTCACCAATAGAGGAT 57.685 39.130 0.00 0.00 0.00 3.24
4906 4954 5.698104 TGCATCATTCACCAATAGAGGATT 58.302 37.500 0.00 0.00 0.00 3.01
4907 4955 6.840527 TGCATCATTCACCAATAGAGGATTA 58.159 36.000 0.00 0.00 0.00 1.75
4908 4956 6.938596 TGCATCATTCACCAATAGAGGATTAG 59.061 38.462 0.00 0.00 0.00 1.73
4909 4957 7.164122 GCATCATTCACCAATAGAGGATTAGA 58.836 38.462 0.00 0.00 0.00 2.10
4910 4958 7.333921 GCATCATTCACCAATAGAGGATTAGAG 59.666 40.741 0.00 0.00 0.00 2.43
4911 4959 7.308450 TCATTCACCAATAGAGGATTAGAGG 57.692 40.000 0.00 0.00 0.00 3.69
4912 4960 7.075797 TCATTCACCAATAGAGGATTAGAGGA 58.924 38.462 0.00 0.00 0.00 3.71
4913 4961 6.985653 TTCACCAATAGAGGATTAGAGGAG 57.014 41.667 0.00 0.00 0.00 3.69
4914 4962 5.398236 TCACCAATAGAGGATTAGAGGAGG 58.602 45.833 0.00 0.00 0.00 4.30
4915 4963 4.530161 CACCAATAGAGGATTAGAGGAGGG 59.470 50.000 0.00 0.00 0.00 4.30
4916 4964 4.423960 ACCAATAGAGGATTAGAGGAGGGA 59.576 45.833 0.00 0.00 0.00 4.20
4917 4965 5.022787 CCAATAGAGGATTAGAGGAGGGAG 58.977 50.000 0.00 0.00 0.00 4.30
4918 4966 4.965283 ATAGAGGATTAGAGGAGGGAGG 57.035 50.000 0.00 0.00 0.00 4.30
4919 4967 1.792651 AGAGGATTAGAGGAGGGAGGG 59.207 57.143 0.00 0.00 0.00 4.30
4920 4968 0.871024 AGGATTAGAGGAGGGAGGGG 59.129 60.000 0.00 0.00 0.00 4.79
4921 4969 0.178888 GGATTAGAGGAGGGAGGGGG 60.179 65.000 0.00 0.00 0.00 5.40
4922 4970 0.868186 GATTAGAGGAGGGAGGGGGA 59.132 60.000 0.00 0.00 0.00 4.81
4923 4971 1.439143 GATTAGAGGAGGGAGGGGGAT 59.561 57.143 0.00 0.00 0.00 3.85
4924 4972 1.340502 TTAGAGGAGGGAGGGGGATT 58.659 55.000 0.00 0.00 0.00 3.01
4925 4973 2.257072 TAGAGGAGGGAGGGGGATTA 57.743 55.000 0.00 0.00 0.00 1.75
4926 4974 1.575609 AGAGGAGGGAGGGGGATTAT 58.424 55.000 0.00 0.00 0.00 1.28
4927 4975 1.439143 AGAGGAGGGAGGGGGATTATC 59.561 57.143 0.00 0.00 0.00 1.75
4928 4976 0.498685 AGGAGGGAGGGGGATTATCC 59.501 60.000 1.91 1.91 35.23 2.59
4929 4977 0.196118 GGAGGGAGGGGGATTATCCA 59.804 60.000 13.78 0.00 38.64 3.41
4930 4978 1.417506 GGAGGGAGGGGGATTATCCAA 60.418 57.143 13.78 0.00 38.64 3.53
4931 4979 1.705745 GAGGGAGGGGGATTATCCAAC 59.294 57.143 13.78 5.17 38.64 3.77
4932 4980 0.778083 GGGAGGGGGATTATCCAACC 59.222 60.000 13.78 13.93 38.64 3.77
4933 4981 1.529744 GGAGGGGGATTATCCAACCA 58.470 55.000 20.99 0.00 38.64 3.67
4957 5005 3.237268 ACAAGGGTCTTGGTATTGCAA 57.763 42.857 0.00 0.00 0.00 4.08
5059 5109 4.399395 TGGGCTTCTGGCTGCTCG 62.399 66.667 0.00 0.00 41.46 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.600557 TTGCAAAACCACCCATAGCG 59.399 50.000 0.00 0.00 0.00 4.26
28 29 2.705127 ACTTCATTGCAAAACCACCCAT 59.295 40.909 1.71 0.00 0.00 4.00
57 58 1.939974 TGGTGCGATATTCACTCTGC 58.060 50.000 8.38 0.00 34.97 4.26
63 64 1.134818 AGCTCGTTGGTGCGATATTCA 60.135 47.619 0.00 0.00 40.29 2.57
64 65 1.571919 AGCTCGTTGGTGCGATATTC 58.428 50.000 0.00 0.00 40.29 1.75
67 68 0.037697 ACAAGCTCGTTGGTGCGATA 60.038 50.000 0.00 0.00 40.90 2.92
96 97 0.888736 CTCCCCAAACATGTGCGTCA 60.889 55.000 0.00 0.00 0.00 4.35
100 101 1.133025 CGAATCTCCCCAAACATGTGC 59.867 52.381 0.00 0.00 0.00 4.57
101 102 2.420022 GTCGAATCTCCCCAAACATGTG 59.580 50.000 0.00 0.00 0.00 3.21
105 106 0.036765 CCGTCGAATCTCCCCAAACA 60.037 55.000 0.00 0.00 0.00 2.83
106 107 1.366854 GCCGTCGAATCTCCCCAAAC 61.367 60.000 0.00 0.00 0.00 2.93
118 119 1.068402 TGACACGAAAATAGCCGTCGA 60.068 47.619 0.00 0.00 38.16 4.20
119 120 1.342555 TGACACGAAAATAGCCGTCG 58.657 50.000 0.00 0.00 40.56 5.12
120 121 3.541516 CGATTGACACGAAAATAGCCGTC 60.542 47.826 0.00 0.00 36.83 4.79
121 122 2.347452 CGATTGACACGAAAATAGCCGT 59.653 45.455 0.00 0.00 39.88 5.68
122 123 2.285602 CCGATTGACACGAAAATAGCCG 60.286 50.000 0.00 0.00 0.00 5.52
123 124 2.933906 TCCGATTGACACGAAAATAGCC 59.066 45.455 0.00 0.00 0.00 3.93
132 133 1.449423 TGGCCATCCGATTGACACG 60.449 57.895 0.00 0.00 34.14 4.49
134 135 1.449423 CGTGGCCATCCGATTGACA 60.449 57.895 9.72 0.00 34.14 3.58
168 172 3.008594 ACGTGTTCATTGGTGGATAGGAA 59.991 43.478 0.00 0.00 0.00 3.36
170 174 2.985896 ACGTGTTCATTGGTGGATAGG 58.014 47.619 0.00 0.00 0.00 2.57
180 184 2.436417 AGGCAATGCTACGTGTTCATT 58.564 42.857 4.82 2.04 0.00 2.57
182 186 2.753055 TAGGCAATGCTACGTGTTCA 57.247 45.000 4.82 0.00 0.00 3.18
183 187 7.384115 TCTTTATATAGGCAATGCTACGTGTTC 59.616 37.037 4.82 0.00 0.00 3.18
184 188 7.214381 TCTTTATATAGGCAATGCTACGTGTT 58.786 34.615 4.82 0.00 0.00 3.32
187 191 9.587772 CTTATCTTTATATAGGCAATGCTACGT 57.412 33.333 4.82 0.00 0.00 3.57
188 192 9.803315 TCTTATCTTTATATAGGCAATGCTACG 57.197 33.333 4.82 0.00 0.00 3.51
260 271 5.366768 TGTCCCTTCGGAATAGAAATGATCT 59.633 40.000 0.00 0.00 40.92 2.75
261 272 5.611374 TGTCCCTTCGGAATAGAAATGATC 58.389 41.667 0.00 0.00 40.92 2.92
265 276 6.492087 TGTTTTTGTCCCTTCGGAATAGAAAT 59.508 34.615 0.00 0.00 40.92 2.17
274 285 2.225727 GCTAGTGTTTTTGTCCCTTCGG 59.774 50.000 0.00 0.00 0.00 4.30
275 286 2.225727 GGCTAGTGTTTTTGTCCCTTCG 59.774 50.000 0.00 0.00 0.00 3.79
281 292 4.001652 GGGTCTAGGCTAGTGTTTTTGTC 58.998 47.826 20.45 2.47 0.00 3.18
344 355 9.814899 GATGATATGTATCTGAAATCCTGTAGG 57.185 37.037 2.08 0.00 33.88 3.18
371 382 5.085275 TGGAAGATCATAGGAGGTGAGAT 57.915 43.478 0.00 0.00 0.00 2.75
372 383 4.542906 TGGAAGATCATAGGAGGTGAGA 57.457 45.455 0.00 0.00 0.00 3.27
373 384 5.822132 ATTGGAAGATCATAGGAGGTGAG 57.178 43.478 0.00 0.00 0.00 3.51
380 391 6.485984 CCTCACAGAAATTGGAAGATCATAGG 59.514 42.308 0.00 0.00 0.00 2.57
381 392 6.017275 GCCTCACAGAAATTGGAAGATCATAG 60.017 42.308 0.00 0.00 0.00 2.23
393 404 9.558396 TTTTTATTTTGATGCCTCACAGAAATT 57.442 25.926 5.73 0.00 0.00 1.82
464 479 3.806380 TGCATGCCAAGTGAAACAAATT 58.194 36.364 16.68 0.00 41.43 1.82
529 544 6.601613 ACAGTTTCTGGTCTACATGAACAAAA 59.398 34.615 0.00 0.00 42.55 2.44
546 561 0.465460 TGCAGCGGGAAACAGTTTCT 60.465 50.000 22.60 3.15 39.59 2.52
562 577 6.260493 ACACTGGTATAAAAACTTTACGTGCA 59.740 34.615 0.00 0.00 0.00 4.57
810 831 8.748412 TCCTTTTGTTTTTCTTTTCTCTCATCA 58.252 29.630 0.00 0.00 0.00 3.07
811 832 9.586435 TTCCTTTTGTTTTTCTTTTCTCTCATC 57.414 29.630 0.00 0.00 0.00 2.92
905 926 1.095807 GCCAGTTGCGGGGAATAGTC 61.096 60.000 0.00 0.00 0.00 2.59
906 927 1.077716 GCCAGTTGCGGGGAATAGT 60.078 57.895 0.00 0.00 0.00 2.12
975 996 1.903183 AGAGAGAAAACGAAGAGGGGG 59.097 52.381 0.00 0.00 0.00 5.40
991 1012 2.233922 CCGCAAAAACCCTAGAGAGAGA 59.766 50.000 0.00 0.00 0.00 3.10
992 1013 2.622436 CCGCAAAAACCCTAGAGAGAG 58.378 52.381 0.00 0.00 0.00 3.20
1049 1070 0.804989 CCATTTTTCGCTTCTCGCCT 59.195 50.000 0.00 0.00 38.27 5.52
1090 1111 4.314440 TCACCGACTGCAGCACCC 62.314 66.667 15.27 0.00 0.00 4.61
1265 1286 0.476808 TGTGGAACCTGGTGGGGTAT 60.477 55.000 0.00 0.00 38.87 2.73
1486 1507 9.408648 CACCCTAATCATTAAGAACCTTGTAAT 57.591 33.333 0.00 0.00 0.00 1.89
1493 1514 5.823045 CAGGACACCCTAATCATTAAGAACC 59.177 44.000 0.00 0.00 42.02 3.62
1495 1516 6.636454 ACAGGACACCCTAATCATTAAGAA 57.364 37.500 0.00 0.00 42.02 2.52
1509 1530 4.280677 TGAATCAATTTGGAACAGGACACC 59.719 41.667 0.00 0.00 42.39 4.16
1564 1585 4.541648 ATCGTCCCTCCCTCCCCG 62.542 72.222 0.00 0.00 0.00 5.73
1651 1672 2.121291 TGATTGCGAAATGGCAGGTA 57.879 45.000 0.00 0.00 44.94 3.08
1750 1771 2.687200 CGGTCCAGGGGTCCATGA 60.687 66.667 2.94 0.00 30.37 3.07
1774 1795 4.007457 CTGGCACCAGGACCAATG 57.993 61.111 8.93 0.00 40.17 2.82
1837 1858 2.900546 GGGGACACCGAGATAGATCAAT 59.099 50.000 0.00 0.00 37.78 2.57
1852 1873 0.976073 GGATGTTCTCCTCGGGGACA 60.976 60.000 0.00 0.00 41.29 4.02
1906 1927 2.436646 ACCTTTGCATCCGAGCCG 60.437 61.111 0.00 0.00 0.00 5.52
2182 2203 7.602644 CAGCTTTTGTTGTAGTCAGATACCTTA 59.397 37.037 0.00 0.00 0.00 2.69
2191 2212 6.765989 ACAACTATCAGCTTTTGTTGTAGTCA 59.234 34.615 18.47 0.00 45.96 3.41
2582 2603 3.120338 CGTCAACGGCAATGAACTACATT 60.120 43.478 0.00 0.00 41.50 2.71
2900 2921 6.319658 AGACGAGGATTTGCAATTCAATGTAT 59.680 34.615 19.83 10.50 34.12 2.29
3309 3330 4.818005 CAGCATTCCATACAGTCTGCATTA 59.182 41.667 0.00 0.00 32.18 1.90
3580 3601 3.956199 CAACTTGGGCAATACCATCAGAT 59.044 43.478 0.00 0.00 40.91 2.90
3674 3695 3.364964 CCGTTGGAATGAGGAAGAAAACG 60.365 47.826 0.00 0.00 38.97 3.60
4147 4171 1.493022 TCCACTTGCCCAGTAAACTGT 59.507 47.619 9.17 0.00 42.27 3.55
4150 4174 4.947388 TGATATTCCACTTGCCCAGTAAAC 59.053 41.667 0.00 0.00 32.76 2.01
4219 4243 7.827819 TCTGTAATGAGAATAACGAAACCAG 57.172 36.000 0.00 0.00 0.00 4.00
4247 4271 7.609056 AGTAACAGAAATGATACTACCACGTT 58.391 34.615 0.00 0.00 0.00 3.99
4327 4351 9.713740 GTCATCTATGCACTTGAAGAAATAAAG 57.286 33.333 0.00 0.00 0.00 1.85
4465 4490 4.626604 GCTATGCATCATCTCTCAAGCTAC 59.373 45.833 0.19 0.00 0.00 3.58
4541 4579 0.400381 TCCAGCCCAGATGCAGGATA 60.400 55.000 0.00 0.00 41.42 2.59
4564 4602 6.302269 CCAAGAGGGAATAATGTGCTAATCT 58.698 40.000 0.00 0.00 40.01 2.40
4641 4684 6.649141 TCTTAGAACATAACAGACGTGCAAAT 59.351 34.615 0.00 0.00 0.00 2.32
4648 4691 5.220043 CGTGCTTCTTAGAACATAACAGACG 60.220 44.000 0.00 0.00 29.45 4.18
4657 4700 1.289109 GCGCCGTGCTTCTTAGAACA 61.289 55.000 0.00 0.00 41.73 3.18
4669 4712 0.110373 GGTAACAAGAAAGCGCCGTG 60.110 55.000 2.29 0.00 0.00 4.94
4673 4716 4.696899 AATAAGGGTAACAAGAAAGCGC 57.303 40.909 0.00 0.00 39.74 5.92
4795 4843 7.871463 ACACTAAACGCTCTTATATTATGGGAC 59.129 37.037 0.00 0.00 0.00 4.46
4808 4856 4.191662 CGTTTTTGACACTAAACGCTCT 57.808 40.909 16.95 0.00 46.45 4.09
4813 4861 9.821662 AATATAAGAGCGTTTTTGACACTAAAC 57.178 29.630 3.38 3.38 0.00 2.01
4817 4865 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
4818 4866 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
4819 4867 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
4820 4868 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
4821 4869 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
4822 4870 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
4823 4871 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
4824 4872 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
4825 4873 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
4826 4874 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
4827 4875 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
4828 4876 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
4829 4877 4.710375 TCCTCCGTCCCATAATATAAGAGC 59.290 45.833 0.00 0.00 0.00 4.09
4830 4878 6.437793 ACTTCCTCCGTCCCATAATATAAGAG 59.562 42.308 0.00 0.00 0.00 2.85
4831 4879 6.320518 ACTTCCTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
4832 4880 6.607004 ACTTCCTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
4833 4881 6.438425 GGTACTTCCTCCGTCCCATAATATAA 59.562 42.308 0.00 0.00 0.00 0.98
4834 4882 5.954150 GGTACTTCCTCCGTCCCATAATATA 59.046 44.000 0.00 0.00 0.00 0.86
4835 4883 4.776308 GGTACTTCCTCCGTCCCATAATAT 59.224 45.833 0.00 0.00 0.00 1.28
4836 4884 4.140853 AGGTACTTCCTCCGTCCCATAATA 60.141 45.833 0.00 0.00 44.42 0.98
4837 4885 2.970640 GGTACTTCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
4838 4886 2.023695 AGGTACTTCCTCCGTCCCATAA 60.024 50.000 0.00 0.00 44.42 1.90
4839 4887 1.572415 AGGTACTTCCTCCGTCCCATA 59.428 52.381 0.00 0.00 44.42 2.74
4840 4888 0.338814 AGGTACTTCCTCCGTCCCAT 59.661 55.000 0.00 0.00 44.42 4.00
4841 4889 1.778981 AGGTACTTCCTCCGTCCCA 59.221 57.895 0.00 0.00 44.42 4.37
4842 4890 4.781264 AGGTACTTCCTCCGTCCC 57.219 61.111 0.00 0.00 44.42 4.46
4850 4898 8.793592 ACAACAAATGAATAAAGAGGTACTTCC 58.206 33.333 0.61 0.00 41.55 3.46
4856 4904 9.574516 ACTCTTACAACAAATGAATAAAGAGGT 57.425 29.630 12.00 0.00 38.27 3.85
4859 4907 9.677567 GCAACTCTTACAACAAATGAATAAAGA 57.322 29.630 0.00 0.00 0.00 2.52
4860 4908 9.462174 TGCAACTCTTACAACAAATGAATAAAG 57.538 29.630 0.00 0.00 0.00 1.85
4861 4909 9.979578 ATGCAACTCTTACAACAAATGAATAAA 57.020 25.926 0.00 0.00 0.00 1.40
4862 4910 9.624697 GATGCAACTCTTACAACAAATGAATAA 57.375 29.630 0.00 0.00 0.00 1.40
4863 4911 8.791675 TGATGCAACTCTTACAACAAATGAATA 58.208 29.630 0.00 0.00 0.00 1.75
4864 4912 7.660112 TGATGCAACTCTTACAACAAATGAAT 58.340 30.769 0.00 0.00 0.00 2.57
4865 4913 7.036996 TGATGCAACTCTTACAACAAATGAA 57.963 32.000 0.00 0.00 0.00 2.57
4866 4914 6.631971 TGATGCAACTCTTACAACAAATGA 57.368 33.333 0.00 0.00 0.00 2.57
4867 4915 7.595875 TGAATGATGCAACTCTTACAACAAATG 59.404 33.333 0.00 0.00 0.00 2.32
4868 4916 7.596248 GTGAATGATGCAACTCTTACAACAAAT 59.404 33.333 0.00 0.00 0.00 2.32
4869 4917 6.917477 GTGAATGATGCAACTCTTACAACAAA 59.083 34.615 0.00 0.00 0.00 2.83
4870 4918 6.437928 GTGAATGATGCAACTCTTACAACAA 58.562 36.000 0.00 0.00 0.00 2.83
4871 4919 5.048782 GGTGAATGATGCAACTCTTACAACA 60.049 40.000 0.00 0.00 0.00 3.33
4872 4920 5.048782 TGGTGAATGATGCAACTCTTACAAC 60.049 40.000 0.00 0.00 0.00 3.32
4873 4921 5.069318 TGGTGAATGATGCAACTCTTACAA 58.931 37.500 0.00 0.00 0.00 2.41
4874 4922 4.650734 TGGTGAATGATGCAACTCTTACA 58.349 39.130 0.00 0.00 0.00 2.41
4875 4923 5.627499 TTGGTGAATGATGCAACTCTTAC 57.373 39.130 0.00 0.00 0.00 2.34
4876 4924 7.337938 TCTATTGGTGAATGATGCAACTCTTA 58.662 34.615 0.00 0.00 0.00 2.10
4877 4925 6.182627 TCTATTGGTGAATGATGCAACTCTT 58.817 36.000 0.00 0.00 0.00 2.85
4878 4926 5.748402 TCTATTGGTGAATGATGCAACTCT 58.252 37.500 0.00 0.00 0.00 3.24
4879 4927 5.008415 CCTCTATTGGTGAATGATGCAACTC 59.992 44.000 0.00 0.00 0.00 3.01
4880 4928 4.885907 CCTCTATTGGTGAATGATGCAACT 59.114 41.667 0.00 0.00 0.00 3.16
4881 4929 4.883585 TCCTCTATTGGTGAATGATGCAAC 59.116 41.667 0.00 0.00 0.00 4.17
4882 4930 5.114764 TCCTCTATTGGTGAATGATGCAA 57.885 39.130 0.00 0.00 0.00 4.08
4883 4931 4.776435 TCCTCTATTGGTGAATGATGCA 57.224 40.909 0.00 0.00 0.00 3.96
4884 4932 7.164122 TCTAATCCTCTATTGGTGAATGATGC 58.836 38.462 0.00 0.00 0.00 3.91
4885 4933 7.823310 CCTCTAATCCTCTATTGGTGAATGATG 59.177 40.741 0.00 0.00 0.00 3.07
4886 4934 7.736691 TCCTCTAATCCTCTATTGGTGAATGAT 59.263 37.037 0.00 0.00 0.00 2.45
4887 4935 7.075797 TCCTCTAATCCTCTATTGGTGAATGA 58.924 38.462 0.00 0.00 0.00 2.57
4888 4936 7.308450 TCCTCTAATCCTCTATTGGTGAATG 57.692 40.000 0.00 0.00 0.00 2.67
4889 4937 6.500049 CCTCCTCTAATCCTCTATTGGTGAAT 59.500 42.308 0.00 0.00 0.00 2.57
4890 4938 5.841237 CCTCCTCTAATCCTCTATTGGTGAA 59.159 44.000 0.00 0.00 0.00 3.18
4891 4939 5.398236 CCTCCTCTAATCCTCTATTGGTGA 58.602 45.833 0.00 0.00 0.00 4.02
4892 4940 4.530161 CCCTCCTCTAATCCTCTATTGGTG 59.470 50.000 0.00 0.00 0.00 4.17
4893 4941 4.423960 TCCCTCCTCTAATCCTCTATTGGT 59.576 45.833 0.00 0.00 0.00 3.67
4894 4942 5.017093 TCCCTCCTCTAATCCTCTATTGG 57.983 47.826 0.00 0.00 0.00 3.16
4895 4943 5.022787 CCTCCCTCCTCTAATCCTCTATTG 58.977 50.000 0.00 0.00 0.00 1.90
4896 4944 4.046618 CCCTCCCTCCTCTAATCCTCTATT 59.953 50.000 0.00 0.00 0.00 1.73
4897 4945 3.600617 CCCTCCCTCCTCTAATCCTCTAT 59.399 52.174 0.00 0.00 0.00 1.98
4898 4946 2.997463 CCCTCCCTCCTCTAATCCTCTA 59.003 54.545 0.00 0.00 0.00 2.43
4899 4947 1.792651 CCCTCCCTCCTCTAATCCTCT 59.207 57.143 0.00 0.00 0.00 3.69
4900 4948 1.203250 CCCCTCCCTCCTCTAATCCTC 60.203 61.905 0.00 0.00 0.00 3.71
4901 4949 0.871024 CCCCTCCCTCCTCTAATCCT 59.129 60.000 0.00 0.00 0.00 3.24
4902 4950 0.178888 CCCCCTCCCTCCTCTAATCC 60.179 65.000 0.00 0.00 0.00 3.01
4903 4951 0.868186 TCCCCCTCCCTCCTCTAATC 59.132 60.000 0.00 0.00 0.00 1.75
4904 4952 1.575609 ATCCCCCTCCCTCCTCTAAT 58.424 55.000 0.00 0.00 0.00 1.73
4905 4953 1.340502 AATCCCCCTCCCTCCTCTAA 58.659 55.000 0.00 0.00 0.00 2.10
4906 4954 2.257072 TAATCCCCCTCCCTCCTCTA 57.743 55.000 0.00 0.00 0.00 2.43
4907 4955 1.439143 GATAATCCCCCTCCCTCCTCT 59.561 57.143 0.00 0.00 0.00 3.69
4908 4956 1.556002 GGATAATCCCCCTCCCTCCTC 60.556 61.905 0.00 0.00 0.00 3.71
4909 4957 0.498685 GGATAATCCCCCTCCCTCCT 59.501 60.000 0.00 0.00 0.00 3.69
4910 4958 0.196118 TGGATAATCCCCCTCCCTCC 59.804 60.000 0.00 0.00 35.03 4.30
4911 4959 1.705745 GTTGGATAATCCCCCTCCCTC 59.294 57.143 0.00 0.00 35.03 4.30
4912 4960 1.702567 GGTTGGATAATCCCCCTCCCT 60.703 57.143 0.00 0.00 35.03 4.20
4913 4961 0.778083 GGTTGGATAATCCCCCTCCC 59.222 60.000 0.00 0.00 35.03 4.30
4914 4962 1.529744 TGGTTGGATAATCCCCCTCC 58.470 55.000 0.00 0.00 35.03 4.30
4915 4963 2.783510 TCTTGGTTGGATAATCCCCCTC 59.216 50.000 0.00 0.00 35.03 4.30
4916 4964 2.871796 TCTTGGTTGGATAATCCCCCT 58.128 47.619 0.00 0.00 35.03 4.79
4917 4965 3.296854 GTTCTTGGTTGGATAATCCCCC 58.703 50.000 0.00 0.00 35.03 5.40
4918 4966 3.976015 TGTTCTTGGTTGGATAATCCCC 58.024 45.455 0.00 0.00 35.03 4.81
4919 4967 4.402474 CCTTGTTCTTGGTTGGATAATCCC 59.598 45.833 0.00 0.00 35.03 3.85
4920 4968 4.402474 CCCTTGTTCTTGGTTGGATAATCC 59.598 45.833 0.00 0.00 36.96 3.01
4921 4969 5.016831 ACCCTTGTTCTTGGTTGGATAATC 58.983 41.667 0.00 0.00 0.00 1.75
4922 4970 5.010708 ACCCTTGTTCTTGGTTGGATAAT 57.989 39.130 0.00 0.00 0.00 1.28
4923 4971 4.105697 AGACCCTTGTTCTTGGTTGGATAA 59.894 41.667 0.00 0.00 30.97 1.75
4924 4972 3.655777 AGACCCTTGTTCTTGGTTGGATA 59.344 43.478 0.00 0.00 30.97 2.59
4925 4973 2.447047 AGACCCTTGTTCTTGGTTGGAT 59.553 45.455 0.00 0.00 30.97 3.41
4926 4974 1.850345 AGACCCTTGTTCTTGGTTGGA 59.150 47.619 0.00 0.00 30.97 3.53
4927 4975 2.362077 CAAGACCCTTGTTCTTGGTTGG 59.638 50.000 4.48 0.00 37.71 3.77
4928 4976 3.715628 CAAGACCCTTGTTCTTGGTTG 57.284 47.619 4.48 0.00 37.71 3.77
4932 4980 4.321230 GCAATACCAAGACCCTTGTTCTTG 60.321 45.833 5.30 5.30 40.17 3.02
4933 4981 3.826729 GCAATACCAAGACCCTTGTTCTT 59.173 43.478 6.04 0.00 0.00 2.52
5039 5089 2.749441 GCAGCCAGAAGCCCAGAC 60.749 66.667 0.00 0.00 45.47 3.51
5059 5109 2.396590 TTCGAATTAGGCACAGACCC 57.603 50.000 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.