Multiple sequence alignment - TraesCS2A01G431400

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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 TraesCS2A01G431400 chr2A 100.000 4942 0 0 1 4942 684474107 684479048 0.000000e+00 9127
1 TraesCS2A01G431400 chr2A 78.754 353 43 16 817 1139 684461952 684462302 1.800000e-49 207
2 TraesCS2A01G431400 chr2A 92.793 111 8 0 3529 3639 445171113 445171223 1.420000e-35 161
3 TraesCS2A01G431400 chr2A 90.678 118 11 0 3525 3642 227627160 227627043 1.840000e-34 158
4 TraesCS2A01G431400 chr2B 90.000 2750 190 41 820 3531 646687442 646690144 0.000000e+00 3476
5 TraesCS2A01G431400 chr2B 90.861 1324 83 19 3633 4940 646690141 646691442 0.000000e+00 1740
6 TraesCS2A01G431400 chr2D 96.418 1312 31 7 3633 4940 541071566 541072865 0.000000e+00 2148
7 TraesCS2A01G431400 chr2D 94.542 1191 51 5 788 1977 541068414 541069591 0.000000e+00 1827
8 TraesCS2A01G431400 chr2D 92.688 930 46 9 2613 3531 541070651 541071569 0.000000e+00 1321
9 TraesCS2A01G431400 chr2D 93.536 789 47 4 1 788 476979130 476979915 0.000000e+00 1171
10 TraesCS2A01G431400 chr2D 93.393 787 49 3 1 787 1709580 1708797 0.000000e+00 1162
11 TraesCS2A01G431400 chr2D 93.401 788 47 5 1 787 520593518 520594301 0.000000e+00 1162
12 TraesCS2A01G431400 chr2D 93.375 634 34 6 1983 2613 541069765 541070393 0.000000e+00 931
13 TraesCS2A01G431400 chr2D 82.927 164 22 3 836 994 541065656 541065818 5.160000e-30 143
14 TraesCS2A01G431400 chr5D 94.162 788 42 4 1 787 229936878 229936094 0.000000e+00 1197
15 TraesCS2A01G431400 chr5D 93.393 787 49 3 1 787 441514177 441514960 0.000000e+00 1162
16 TraesCS2A01G431400 chr5D 88.189 127 15 0 3523 3649 562099915 562099789 8.570000e-33 152
17 TraesCS2A01G431400 chrUn 93.536 789 46 4 1 787 94073860 94074645 0.000000e+00 1170
18 TraesCS2A01G431400 chr1D 93.401 788 48 4 1 787 319542094 319541310 0.000000e+00 1164
19 TraesCS2A01G431400 chr1D 93.384 786 47 5 1 785 458741996 458742777 0.000000e+00 1158
20 TraesCS2A01G431400 chr1D 93.257 786 49 4 1 785 26189109 26189891 0.000000e+00 1155
21 TraesCS2A01G431400 chr7A 93.578 109 7 0 3527 3635 184652505 184652397 3.960000e-36 163
22 TraesCS2A01G431400 chr5A 93.578 109 7 0 3528 3636 392583824 392583716 3.960000e-36 163
23 TraesCS2A01G431400 chr6B 92.793 111 8 0 3525 3635 705508976 705508866 1.420000e-35 161
24 TraesCS2A01G431400 chr3A 93.519 108 7 0 3528 3635 572598296 572598403 1.420000e-35 161
25 TraesCS2A01G431400 chr7D 91.964 112 9 0 3525 3636 379324241 379324130 1.840000e-34 158
26 TraesCS2A01G431400 chr6A 91.964 112 9 0 3526 3637 475435165 475435054 1.840000e-34 158


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G431400 chr2A 684474107 684479048 4941 False 9127 9127 100.0000 1 4942 1 chr2A.!!$F3 4941
1 TraesCS2A01G431400 chr2B 646687442 646691442 4000 False 2608 3476 90.4305 820 4940 2 chr2B.!!$F1 4120
2 TraesCS2A01G431400 chr2D 541065656 541072865 7209 False 1274 2148 91.9900 788 4940 5 chr2D.!!$F3 4152
3 TraesCS2A01G431400 chr2D 476979130 476979915 785 False 1171 1171 93.5360 1 788 1 chr2D.!!$F1 787
4 TraesCS2A01G431400 chr2D 1708797 1709580 783 True 1162 1162 93.3930 1 787 1 chr2D.!!$R1 786
5 TraesCS2A01G431400 chr2D 520593518 520594301 783 False 1162 1162 93.4010 1 787 1 chr2D.!!$F2 786
6 TraesCS2A01G431400 chr5D 229936094 229936878 784 True 1197 1197 94.1620 1 787 1 chr5D.!!$R1 786
7 TraesCS2A01G431400 chr5D 441514177 441514960 783 False 1162 1162 93.3930 1 787 1 chr5D.!!$F1 786
8 TraesCS2A01G431400 chrUn 94073860 94074645 785 False 1170 1170 93.5360 1 787 1 chrUn.!!$F1 786
9 TraesCS2A01G431400 chr1D 319541310 319542094 784 True 1164 1164 93.4010 1 787 1 chr1D.!!$R1 786
10 TraesCS2A01G431400 chr1D 458741996 458742777 781 False 1158 1158 93.3840 1 785 1 chr1D.!!$F2 784
11 TraesCS2A01G431400 chr1D 26189109 26189891 782 False 1155 1155 93.2570 1 785 1 chr1D.!!$F1 784

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
995 2967 0.171455 CGCGATCCCTAGCCATCTAC 59.829 60.000 0.00 0.0 0.00 2.59 F
996 2968 0.533032 GCGATCCCTAGCCATCTACC 59.467 60.000 0.00 0.0 0.00 3.18 F
1694 3666 1.083489 CGGACCATTTTGCGCTCTAA 58.917 50.000 9.73 0.0 0.00 2.10 F
3568 6012 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.0 39.69 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2791 5209 1.418637 ACACGGGTGTTATGGTGTTCT 59.581 47.619 0.0 0.0 41.83 3.01 R
2792 5210 1.886886 ACACGGGTGTTATGGTGTTC 58.113 50.000 0.0 0.0 41.83 3.18 R
3619 6063 0.042131 ATGGTACTCCCTCCGTTCCA 59.958 55.000 0.0 0.0 36.47 3.53 R
4889 7348 0.179078 AACGCACAACAGGTTCGGTA 60.179 50.000 0.0 0.0 40.58 4.02 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
30 31 9.030452 TGGCATGTTTTCCTTACACTTATAATT 57.970 29.630 0.00 0.00 0.00 1.40
97 98 0.597637 CGCATACAGTCCCCGCTAAG 60.598 60.000 0.00 0.00 0.00 2.18
116 117 7.754924 CCGCTAAGTTTATGTCAATTGTTTCAT 59.245 33.333 5.13 10.99 0.00 2.57
149 151 5.544948 ACCCACGGGCATCTATACTATTTTA 59.455 40.000 0.69 0.00 39.32 1.52
188 190 7.947782 TGGAGGTATAATCTTATTGGTCCTT 57.052 36.000 0.00 0.00 0.00 3.36
280 282 1.535685 GCCTCTGCCCCATTGATCT 59.464 57.895 0.00 0.00 0.00 2.75
288 290 1.586422 CCCCATTGATCTGTGTAGCG 58.414 55.000 0.00 0.00 0.00 4.26
305 307 5.049267 GTGTAGCGTTCCACCAATAGAAAAA 60.049 40.000 0.00 0.00 0.00 1.94
332 334 2.125310 TGCCAACCTATCCGTGCG 60.125 61.111 0.00 0.00 0.00 5.34
380 382 4.344978 CATCCCGTCTAGGATATGAGGAA 58.655 47.826 0.00 0.00 45.21 3.36
407 409 1.986378 CGTTGACCTCTAACTCGCAAG 59.014 52.381 0.00 0.00 0.00 4.01
416 418 2.557056 TCTAACTCGCAAGCTACACTGT 59.443 45.455 0.00 0.00 37.18 3.55
497 501 6.937465 AGTTAAATTTGGTGGTTGTTTGTGTT 59.063 30.769 0.00 0.00 0.00 3.32
503 507 3.766591 TGGTGGTTGTTTGTGTTCTTCAT 59.233 39.130 0.00 0.00 0.00 2.57
509 513 5.298276 GGTTGTTTGTGTTCTTCATGGACTA 59.702 40.000 0.00 0.00 0.00 2.59
515 519 7.770366 TTGTGTTCTTCATGGACTAGTACTA 57.230 36.000 6.66 1.89 0.00 1.82
596 600 1.002624 GTGGCCGGGATCTCAAACA 60.003 57.895 2.18 0.00 0.00 2.83
600 604 0.462047 GCCGGGATCTCAAACACGAT 60.462 55.000 2.18 0.00 34.69 3.73
659 663 0.843309 TTGGTTCCAAGCTCAGGTGA 59.157 50.000 0.00 0.00 0.00 4.02
689 693 2.987149 CTGTGTAGTGAACATCGTGACC 59.013 50.000 0.00 0.00 41.10 4.02
734 738 0.685458 GGCAACAAGGATGGAGGCAT 60.685 55.000 0.00 0.00 32.64 4.40
758 762 5.536497 AGGGGTGATAATTTGTTTCTCCT 57.464 39.130 0.00 0.00 0.00 3.69
766 770 7.599998 GTGATAATTTGTTTCTCCTGTTGCAAT 59.400 33.333 0.59 0.00 0.00 3.56
774 778 2.563798 CCTGTTGCAATGCACGGGT 61.564 57.895 20.21 0.00 38.71 5.28
788 792 4.325119 TGCACGGGTAATTTTGCTAGTTA 58.675 39.130 0.00 0.00 35.91 2.24
789 793 4.760715 TGCACGGGTAATTTTGCTAGTTAA 59.239 37.500 0.00 0.00 35.91 2.01
791 795 5.122711 GCACGGGTAATTTTGCTAGTTAAGA 59.877 40.000 0.00 0.00 32.00 2.10
792 796 6.674760 GCACGGGTAATTTTGCTAGTTAAGAG 60.675 42.308 0.00 0.00 32.00 2.85
793 797 6.592607 CACGGGTAATTTTGCTAGTTAAGAGA 59.407 38.462 0.00 0.00 0.00 3.10
796 2767 8.674607 CGGGTAATTTTGCTAGTTAAGAGAAAT 58.325 33.333 0.00 0.00 0.00 2.17
940 2912 0.248134 CATCGTCTTCGTCTCCGTCC 60.248 60.000 0.00 0.00 38.33 4.79
986 2958 0.172578 CATTATCCGCGCGATCCCTA 59.827 55.000 34.63 11.61 31.92 3.53
987 2959 0.456221 ATTATCCGCGCGATCCCTAG 59.544 55.000 34.63 13.06 31.92 3.02
988 2960 2.209064 TTATCCGCGCGATCCCTAGC 62.209 60.000 34.63 0.00 31.92 3.42
991 2963 4.363990 CGCGCGATCCCTAGCCAT 62.364 66.667 28.94 0.00 0.00 4.40
992 2964 2.433318 GCGCGATCCCTAGCCATC 60.433 66.667 12.10 0.00 0.00 3.51
993 2965 2.936912 GCGCGATCCCTAGCCATCT 61.937 63.158 12.10 0.00 0.00 2.90
994 2966 1.595993 GCGCGATCCCTAGCCATCTA 61.596 60.000 12.10 0.00 0.00 1.98
995 2967 0.171455 CGCGATCCCTAGCCATCTAC 59.829 60.000 0.00 0.00 0.00 2.59
996 2968 0.533032 GCGATCCCTAGCCATCTACC 59.467 60.000 0.00 0.00 0.00 3.18
1143 3115 2.818132 GCCTCCTCCACCTCATCG 59.182 66.667 0.00 0.00 0.00 3.84
1503 3475 3.633065 TGATGATGTGTTATGGGTGCATG 59.367 43.478 0.00 0.00 0.00 4.06
1523 3495 2.818714 CTTGGAGCTGAGCTGCCG 60.819 66.667 23.20 10.51 46.33 5.69
1532 3504 1.286501 CTGAGCTGCCGCGTTTAATA 58.713 50.000 4.92 0.00 42.32 0.98
1537 3509 1.741993 CTGCCGCGTTTAATATGTGC 58.258 50.000 4.92 0.00 0.00 4.57
1568 3540 3.161450 GGGCGCATCTACCCCTGA 61.161 66.667 10.83 0.00 40.56 3.86
1621 3593 2.892374 TCAGACGCCTACAATGATGTG 58.108 47.619 0.00 0.00 40.84 3.21
1626 3598 2.927477 ACGCCTACAATGATGTGTTACG 59.073 45.455 0.00 0.00 40.84 3.18
1645 3617 3.626930 ACGATTCTCTGTCCTCTAGCTT 58.373 45.455 0.00 0.00 0.00 3.74
1691 3663 1.154225 CACGGACCATTTTGCGCTC 60.154 57.895 9.73 0.00 32.84 5.03
1694 3666 1.083489 CGGACCATTTTGCGCTCTAA 58.917 50.000 9.73 0.00 0.00 2.10
1783 3755 6.605194 TGTGCATATCATTAGCTTTGGGTTAA 59.395 34.615 0.00 0.00 0.00 2.01
1803 3777 4.836125 AAATTATGCGGTGCCTGATAAG 57.164 40.909 0.00 0.00 0.00 1.73
1858 3832 8.725405 TGGATGATTTAGTTGACGCTAAATAA 57.275 30.769 10.02 5.02 45.97 1.40
1889 3867 3.236047 TCTGCTGTACTACTTCCACCAA 58.764 45.455 0.00 0.00 0.00 3.67
1890 3868 3.838317 TCTGCTGTACTACTTCCACCAAT 59.162 43.478 0.00 0.00 0.00 3.16
1891 3869 3.935203 CTGCTGTACTACTTCCACCAATG 59.065 47.826 0.00 0.00 0.00 2.82
1892 3870 3.326588 TGCTGTACTACTTCCACCAATGT 59.673 43.478 0.00 0.00 0.00 2.71
1893 3871 3.684788 GCTGTACTACTTCCACCAATGTG 59.315 47.826 0.00 0.00 42.39 3.21
1895 3873 5.147330 TGTACTACTTCCACCAATGTGAG 57.853 43.478 0.00 0.00 45.76 3.51
1936 3914 5.804639 TGCTACCTGATGAAACATGTAACT 58.195 37.500 0.00 0.00 0.00 2.24
1940 3918 9.542462 GCTACCTGATGAAACATGTAACTATAA 57.458 33.333 0.00 0.00 0.00 0.98
2027 4180 8.122952 GGGATACAGAAAACAACTGATAAATCG 58.877 37.037 0.00 0.00 38.55 3.34
2036 4189 9.796120 AAAACAACTGATAAATCGTTTTTCTCA 57.204 25.926 0.00 1.32 33.96 3.27
2041 4194 8.608844 ACTGATAAATCGTTTTTCTCAGTTCT 57.391 30.769 20.24 8.02 40.27 3.01
2065 4218 5.371115 TTTCATGCTTTTGCCTGTACTAC 57.629 39.130 0.00 0.00 46.87 2.73
2131 4286 8.236585 TGGTTATAGTATGATTGCATGCTTTT 57.763 30.769 20.33 3.05 43.71 2.27
2205 4360 3.868757 ATACGTGTCACTGTGCTGTAT 57.131 42.857 2.12 5.74 0.00 2.29
2210 4365 4.173256 CGTGTCACTGTGCTGTATTGATA 58.827 43.478 2.12 0.00 0.00 2.15
2217 4372 7.706607 GTCACTGTGCTGTATTGATAGTGATTA 59.293 37.037 2.12 0.00 43.13 1.75
2272 4429 3.620488 TCCTTTGTTAGCTTATGCAGGG 58.380 45.455 0.00 0.00 42.74 4.45
2286 4443 1.213430 TGCAGGGCATGATGATTCTCA 59.787 47.619 1.99 0.00 31.71 3.27
2387 4544 6.599638 GCCTGATGAATCTTAACAACCTAACT 59.400 38.462 0.00 0.00 0.00 2.24
2529 4686 2.037901 TGCTCTGAGATCCTCCACATC 58.962 52.381 9.28 0.00 0.00 3.06
2535 4692 4.100653 TCTGAGATCCTCCACATCATTGTC 59.899 45.833 0.00 0.00 32.34 3.18
2550 4707 9.338291 CACATCATTGTCATAAGAAAAAGACTG 57.662 33.333 0.00 0.00 32.34 3.51
2584 4741 9.388506 CATGAGGTAGTCATTTACTTTGATCTT 57.611 33.333 0.00 0.00 44.05 2.40
2626 5042 8.809066 TGTCTTGCAAGTTACTAGTAATCCTAA 58.191 33.333 25.19 9.46 0.00 2.69
2659 5075 1.497309 CCCAGGAGTGGTGCCCTTAA 61.497 60.000 0.00 0.00 43.23 1.85
2663 5079 2.505819 CAGGAGTGGTGCCCTTAAGTAT 59.494 50.000 0.97 0.00 0.00 2.12
2672 5088 4.515567 GGTGCCCTTAAGTATTAGCACATC 59.484 45.833 22.25 10.53 46.10 3.06
2700 5118 5.465724 CAGTTGGAGGTTTAACAGTCAGTAC 59.534 44.000 0.00 0.00 0.00 2.73
2719 5137 8.189460 GTCAGTACTTAGTGAGGTTATAACTGG 58.811 40.741 15.05 0.92 36.40 4.00
2720 5138 7.892241 TCAGTACTTAGTGAGGTTATAACTGGT 59.108 37.037 15.05 0.91 33.25 4.00
2721 5139 9.182214 CAGTACTTAGTGAGGTTATAACTGGTA 57.818 37.037 15.05 5.07 0.00 3.25
2722 5140 9.933240 AGTACTTAGTGAGGTTATAACTGGTAT 57.067 33.333 15.05 2.70 0.00 2.73
2723 5141 9.962783 GTACTTAGTGAGGTTATAACTGGTATG 57.037 37.037 15.05 5.79 0.00 2.39
2724 5142 8.834004 ACTTAGTGAGGTTATAACTGGTATGA 57.166 34.615 15.05 0.00 0.00 2.15
2725 5143 9.435570 ACTTAGTGAGGTTATAACTGGTATGAT 57.564 33.333 15.05 0.00 0.00 2.45
2792 5210 3.206034 TGTATGACGGTCGTACAACAG 57.794 47.619 30.91 0.00 43.57 3.16
2807 5225 3.219281 ACAACAGAACACCATAACACCC 58.781 45.455 0.00 0.00 0.00 4.61
2816 5251 1.693062 ACCATAACACCCGTGTACACA 59.307 47.619 24.98 4.62 44.13 3.72
2827 5262 3.881688 CCCGTGTACACACTATACTAGCT 59.118 47.826 24.98 0.00 44.34 3.32
2857 5292 4.621460 CCCATATATACTCACAAACGCTCG 59.379 45.833 0.00 0.00 0.00 5.03
2872 5307 1.927174 CGCTCGTCCTGTTTCTTATGG 59.073 52.381 0.00 0.00 0.00 2.74
2906 5341 9.216117 GTGTTCAGTATATGTAGGTTTTGAACT 57.784 33.333 13.17 0.00 42.05 3.01
2968 5403 5.615289 TCAAAGAGAAGAGAAAGTCCCAAG 58.385 41.667 0.00 0.00 0.00 3.61
2970 5405 5.482163 AAGAGAAGAGAAAGTCCCAAGAG 57.518 43.478 0.00 0.00 0.00 2.85
3035 5471 5.474532 TCTCTTGTTGTTTCTATGCAGCATT 59.525 36.000 14.58 0.00 0.00 3.56
3036 5472 6.654582 TCTCTTGTTGTTTCTATGCAGCATTA 59.345 34.615 14.58 0.00 0.00 1.90
3074 5510 6.707440 TGGTGAAACATTGTTGTACTTGAT 57.293 33.333 2.13 0.00 39.98 2.57
3162 5598 7.690952 AATCGGTAGACATAGAGAAGGATAC 57.309 40.000 0.00 0.00 0.00 2.24
3222 5658 4.693095 CAGGCTTCTTCTTTTCCACTCTAC 59.307 45.833 0.00 0.00 0.00 2.59
3274 5710 1.200716 CATGTGATGCCTGTTGTGTCC 59.799 52.381 0.00 0.00 0.00 4.02
3279 5715 2.289631 TGATGCCTGTTGTGTCCTACAG 60.290 50.000 0.00 0.00 42.03 2.74
3331 5767 3.952323 ACATCGTATATATAGTGGCGCCT 59.048 43.478 29.70 11.31 0.00 5.52
3337 5773 8.400184 TCGTATATATAGTGGCGCCTAAATAT 57.600 34.615 29.70 25.18 0.00 1.28
3385 5829 3.818961 AGTCATGCATTCGACAACTTG 57.181 42.857 16.86 0.00 34.48 3.16
3417 5861 4.586421 TGTTTGATAAACATTGGCTGGTGA 59.414 37.500 3.20 0.00 45.79 4.02
3460 5904 7.931015 TCCACTATGAGAATTATGTAGGGTT 57.069 36.000 0.00 0.00 0.00 4.11
3531 5975 8.141268 CCAAAATGGTTACAATTGTCTTGTACT 58.859 33.333 15.85 0.00 34.93 2.73
3532 5976 9.180678 CAAAATGGTTACAATTGTCTTGTACTC 57.819 33.333 15.85 0.00 34.93 2.59
3533 5977 7.448748 AATGGTTACAATTGTCTTGTACTCC 57.551 36.000 15.85 7.64 34.93 3.85
3534 5978 5.310451 TGGTTACAATTGTCTTGTACTCCC 58.690 41.667 15.85 3.81 34.93 4.30
3535 5979 5.072600 TGGTTACAATTGTCTTGTACTCCCT 59.927 40.000 15.85 0.00 34.93 4.20
3536 5980 5.642491 GGTTACAATTGTCTTGTACTCCCTC 59.358 44.000 15.85 0.00 34.93 4.30
3537 5981 4.287766 ACAATTGTCTTGTACTCCCTCC 57.712 45.455 4.92 0.00 0.00 4.30
3538 5982 3.262420 CAATTGTCTTGTACTCCCTCCG 58.738 50.000 0.00 0.00 0.00 4.63
3539 5983 2.005370 TTGTCTTGTACTCCCTCCGT 57.995 50.000 0.00 0.00 0.00 4.69
3540 5984 2.005370 TGTCTTGTACTCCCTCCGTT 57.995 50.000 0.00 0.00 0.00 4.44
3541 5985 1.891150 TGTCTTGTACTCCCTCCGTTC 59.109 52.381 0.00 0.00 0.00 3.95
3542 5986 2.169330 GTCTTGTACTCCCTCCGTTCT 58.831 52.381 0.00 0.00 0.00 3.01
3543 5987 3.245016 TGTCTTGTACTCCCTCCGTTCTA 60.245 47.826 0.00 0.00 0.00 2.10
3544 5988 3.760684 GTCTTGTACTCCCTCCGTTCTAA 59.239 47.826 0.00 0.00 0.00 2.10
3545 5989 4.219288 GTCTTGTACTCCCTCCGTTCTAAA 59.781 45.833 0.00 0.00 0.00 1.85
3546 5990 5.021458 TCTTGTACTCCCTCCGTTCTAAAT 58.979 41.667 0.00 0.00 0.00 1.40
3547 5991 5.482878 TCTTGTACTCCCTCCGTTCTAAATT 59.517 40.000 0.00 0.00 0.00 1.82
3548 5992 6.664816 TCTTGTACTCCCTCCGTTCTAAATTA 59.335 38.462 0.00 0.00 0.00 1.40
3549 5993 6.212888 TGTACTCCCTCCGTTCTAAATTAC 57.787 41.667 0.00 0.00 0.00 1.89
3550 5994 5.954150 TGTACTCCCTCCGTTCTAAATTACT 59.046 40.000 0.00 0.00 0.00 2.24
3551 5995 5.595257 ACTCCCTCCGTTCTAAATTACTC 57.405 43.478 0.00 0.00 0.00 2.59
3552 5996 4.097589 ACTCCCTCCGTTCTAAATTACTCG 59.902 45.833 0.00 0.00 0.00 4.18
3553 5997 4.019174 TCCCTCCGTTCTAAATTACTCGT 58.981 43.478 0.00 0.00 0.00 4.18
3554 5998 4.096984 TCCCTCCGTTCTAAATTACTCGTC 59.903 45.833 0.00 0.00 0.00 4.20
3555 5999 4.033684 CCTCCGTTCTAAATTACTCGTCG 58.966 47.826 0.00 0.00 0.00 5.12
3556 6000 3.429085 TCCGTTCTAAATTACTCGTCGC 58.571 45.455 0.00 0.00 0.00 5.19
3557 6001 3.119884 TCCGTTCTAAATTACTCGTCGCA 60.120 43.478 0.00 0.00 0.00 5.10
3558 6002 3.239941 CCGTTCTAAATTACTCGTCGCAG 59.760 47.826 0.00 0.00 0.00 5.18
3559 6003 4.093514 CGTTCTAAATTACTCGTCGCAGA 58.906 43.478 0.00 0.00 0.00 4.26
3560 6004 4.556135 CGTTCTAAATTACTCGTCGCAGAA 59.444 41.667 0.00 0.00 39.69 3.02
3561 6005 5.060077 CGTTCTAAATTACTCGTCGCAGAAA 59.940 40.000 0.00 0.00 39.69 2.52
3562 6006 6.237490 CGTTCTAAATTACTCGTCGCAGAAAT 60.237 38.462 0.00 0.00 39.69 2.17
3563 6007 6.569228 TCTAAATTACTCGTCGCAGAAATG 57.431 37.500 0.00 0.00 39.69 2.32
3564 6008 4.600012 AAATTACTCGTCGCAGAAATGG 57.400 40.909 0.00 0.00 39.69 3.16
3565 6009 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
3566 6010 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
3567 6011 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
3568 6012 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
3569 6013 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
3570 6014 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
3571 6015 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
3572 6016 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
3573 6017 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
3574 6018 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
3575 6019 4.387256 GTCGCAGAAATGGATGTATCTAGC 59.613 45.833 0.00 0.00 39.69 3.42
3576 6020 4.039124 TCGCAGAAATGGATGTATCTAGCA 59.961 41.667 0.00 0.00 0.00 3.49
3577 6021 4.934001 CGCAGAAATGGATGTATCTAGCAT 59.066 41.667 0.00 0.00 0.00 3.79
3578 6022 5.410746 CGCAGAAATGGATGTATCTAGCATT 59.589 40.000 0.00 0.00 0.00 3.56
3579 6023 6.591448 CGCAGAAATGGATGTATCTAGCATTA 59.409 38.462 0.00 0.00 0.00 1.90
3580 6024 7.118245 CGCAGAAATGGATGTATCTAGCATTAA 59.882 37.037 0.00 0.00 0.00 1.40
3581 6025 8.786898 GCAGAAATGGATGTATCTAGCATTAAA 58.213 33.333 0.00 0.00 0.00 1.52
3605 6049 9.678260 AAAATGCATCTAGATACATCTATTCCC 57.322 33.333 17.09 0.00 38.60 3.97
3606 6050 7.984859 ATGCATCTAGATACATCTATTCCCA 57.015 36.000 12.00 0.00 38.60 4.37
3607 6051 7.175347 TGCATCTAGATACATCTATTCCCAC 57.825 40.000 4.54 0.00 38.60 4.61
3608 6052 6.127619 TGCATCTAGATACATCTATTCCCACG 60.128 42.308 4.54 0.00 38.60 4.94
3609 6053 6.095580 GCATCTAGATACATCTATTCCCACGA 59.904 42.308 4.54 0.00 38.60 4.35
3610 6054 7.476667 CATCTAGATACATCTATTCCCACGAC 58.523 42.308 4.54 0.00 38.60 4.34
3611 6055 6.540083 TCTAGATACATCTATTCCCACGACA 58.460 40.000 0.00 0.00 38.60 4.35
3612 6056 7.002276 TCTAGATACATCTATTCCCACGACAA 58.998 38.462 0.00 0.00 38.60 3.18
3613 6057 6.090483 AGATACATCTATTCCCACGACAAG 57.910 41.667 0.00 0.00 34.85 3.16
3614 6058 5.598830 AGATACATCTATTCCCACGACAAGT 59.401 40.000 0.00 0.00 34.85 3.16
3615 6059 6.776116 AGATACATCTATTCCCACGACAAGTA 59.224 38.462 0.00 0.00 34.85 2.24
3616 6060 5.670792 ACATCTATTCCCACGACAAGTAA 57.329 39.130 0.00 0.00 0.00 2.24
3617 6061 6.235231 ACATCTATTCCCACGACAAGTAAT 57.765 37.500 0.00 0.00 0.00 1.89
3618 6062 6.650120 ACATCTATTCCCACGACAAGTAATT 58.350 36.000 0.00 0.00 0.00 1.40
3619 6063 7.110155 ACATCTATTCCCACGACAAGTAATTT 58.890 34.615 0.00 0.00 0.00 1.82
3620 6064 6.978343 TCTATTCCCACGACAAGTAATTTG 57.022 37.500 0.00 0.00 42.68 2.32
3621 6065 5.878116 TCTATTCCCACGACAAGTAATTTGG 59.122 40.000 0.00 0.00 41.25 3.28
3622 6066 3.773418 TCCCACGACAAGTAATTTGGA 57.227 42.857 0.00 0.00 41.25 3.53
3623 6067 4.088056 TCCCACGACAAGTAATTTGGAA 57.912 40.909 0.00 0.00 41.25 3.53
3624 6068 3.816523 TCCCACGACAAGTAATTTGGAAC 59.183 43.478 0.00 0.00 41.25 3.62
3625 6069 3.364565 CCCACGACAAGTAATTTGGAACG 60.365 47.826 0.00 0.00 41.25 3.95
3626 6070 3.364565 CCACGACAAGTAATTTGGAACGG 60.365 47.826 0.00 0.00 41.25 4.44
3627 6071 3.495377 CACGACAAGTAATTTGGAACGGA 59.505 43.478 0.00 0.00 41.25 4.69
3628 6072 3.744426 ACGACAAGTAATTTGGAACGGAG 59.256 43.478 0.00 0.00 41.25 4.63
3629 6073 3.124636 CGACAAGTAATTTGGAACGGAGG 59.875 47.826 0.00 0.00 41.25 4.30
3630 6074 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
3631 6075 3.073356 ACAAGTAATTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 41.25 4.20
3632 6076 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
3633 6077 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
3634 6078 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
3635 6079 3.345508 AATTTGGAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
3636 6080 0.978907 TTTGGAACGGAGGGAGTACC 59.021 55.000 0.00 0.00 40.67 3.34
3637 6081 0.178926 TTGGAACGGAGGGAGTACCA 60.179 55.000 0.00 0.00 43.89 3.25
3638 6082 0.042131 TGGAACGGAGGGAGTACCAT 59.958 55.000 0.00 0.00 43.89 3.55
3717 6161 5.972107 ATGTTTTGGAAGAAGTGATGGAG 57.028 39.130 0.00 0.00 0.00 3.86
3812 6257 5.749462 AGACCTTGATTGTTAGATTGGGAG 58.251 41.667 0.00 0.00 0.00 4.30
3981 6426 2.582052 CTGGGGTAAGTTTGCTCACAA 58.418 47.619 0.00 0.00 0.00 3.33
4314 6761 6.346096 AGTGTTATTACAGATAATGTGGCGT 58.654 36.000 0.00 0.00 43.80 5.68
4509 6956 2.962859 ACCTGAATGGGCTTTTGTCTT 58.037 42.857 0.00 0.00 41.11 3.01
4620 7070 1.538687 AAAACCCTGCTGATGGCTGC 61.539 55.000 0.00 0.00 42.39 5.25
4691 7141 0.460987 GCCTCATCACCCGTCTCTTG 60.461 60.000 0.00 0.00 0.00 3.02
4706 7156 3.056749 GTCTCTTGTTCGGTAGGTCATGT 60.057 47.826 0.00 0.00 0.00 3.21
4723 7174 5.385617 GTCATGTGTGCTTAAGATGAACAC 58.614 41.667 6.67 13.86 41.15 3.32
4803 7254 8.046708 TGAGCTTAAGTTGTATGATGTACCAAT 58.953 33.333 4.02 0.00 0.00 3.16
4928 7387 0.098376 GCCTCTTGCTGCAGAAATCG 59.902 55.000 20.43 7.02 36.87 3.34
4940 7399 3.810941 TGCAGAAATCGACCGTTTTAGTT 59.189 39.130 0.00 0.00 0.00 2.24
4941 7400 4.148891 GCAGAAATCGACCGTTTTAGTTG 58.851 43.478 0.00 1.43 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 1.277579 TGCCCGTGGGTTATAACAGA 58.722 50.000 17.16 0.04 37.65 3.41
122 123 3.517612 AGTATAGATGCCCGTGGGTTAT 58.482 45.455 6.82 1.66 37.65 1.89
188 190 2.092699 TGCCATGGACATACGAAATGGA 60.093 45.455 18.40 0.00 40.23 3.41
277 279 0.973632 TGGTGGAACGCTACACAGAT 59.026 50.000 3.13 0.00 39.31 2.90
280 282 2.563620 TCTATTGGTGGAACGCTACACA 59.436 45.455 3.13 0.00 39.31 3.72
305 307 0.114168 TAGGTTGGCAGGGCATTGTT 59.886 50.000 0.00 0.00 0.00 2.83
309 311 1.538666 GGATAGGTTGGCAGGGCAT 59.461 57.895 0.00 0.00 0.00 4.40
332 334 1.182385 TTGATTTGTTGGGCCGGGTC 61.182 55.000 2.18 0.00 0.00 4.46
525 529 6.964934 GTGTTTGTGTTATCCGGATTTACATC 59.035 38.462 24.71 18.89 0.00 3.06
600 604 1.743391 TGGAAAGACCAGCGAACGA 59.257 52.632 0.00 0.00 44.64 3.85
659 663 2.212869 TCACTACACAGCGAACGTTT 57.787 45.000 0.46 0.00 0.00 3.60
730 734 5.869649 AACAAATTATCACCCCTAATGCC 57.130 39.130 0.00 0.00 0.00 4.40
734 738 6.889722 CAGGAGAAACAAATTATCACCCCTAA 59.110 38.462 0.00 0.00 30.65 2.69
758 762 1.252175 ATTACCCGTGCATTGCAACA 58.748 45.000 13.94 0.00 41.47 3.33
766 770 2.785562 ACTAGCAAAATTACCCGTGCA 58.214 42.857 0.00 0.00 39.50 4.57
806 2777 8.783833 TTTCTAAGTCTCATTTCTGAAGGATG 57.216 34.615 0.00 0.00 0.00 3.51
813 2784 8.675504 AGATGCAATTTCTAAGTCTCATTTCTG 58.324 33.333 0.00 0.00 0.00 3.02
884 2856 2.562912 GCGTGTCATTGGCAGTGG 59.437 61.111 10.28 0.00 0.00 4.00
988 2960 0.250038 CGAGCCATGGTGGTAGATGG 60.250 60.000 14.67 0.00 40.46 3.51
990 2962 1.447643 GCGAGCCATGGTGGTAGAT 59.552 57.895 14.67 0.00 40.46 1.98
991 2963 2.731571 GGCGAGCCATGGTGGTAGA 61.732 63.158 14.67 0.00 40.46 2.59
992 2964 2.203070 GGCGAGCCATGGTGGTAG 60.203 66.667 14.67 2.14 40.46 3.18
993 2965 2.687200 AGGCGAGCCATGGTGGTA 60.687 61.111 17.18 0.00 40.46 3.25
994 2966 4.101448 GAGGCGAGCCATGGTGGT 62.101 66.667 17.18 0.00 40.46 4.16
995 2967 4.864334 GGAGGCGAGCCATGGTGG 62.864 72.222 17.18 3.99 41.55 4.61
996 2968 3.746949 GAGGAGGCGAGCCATGGTG 62.747 68.421 17.18 4.98 38.92 4.17
1122 3094 3.462678 GAGGTGGAGGAGGCGGAC 61.463 72.222 0.00 0.00 0.00 4.79
1365 3337 1.153429 GGTCATCGCGGCCTTAACT 60.153 57.895 6.13 0.00 0.00 2.24
1503 3475 1.744741 GCAGCTCAGCTCCAAGACC 60.745 63.158 0.00 0.00 36.40 3.85
1523 3495 2.026990 CTTCGCGCACATATTAAACGC 58.973 47.619 8.75 0.00 45.72 4.84
1568 3540 5.106555 CGGCTTTAGCATTCATTTCGGATAT 60.107 40.000 3.88 0.00 44.36 1.63
1598 3570 4.333649 CACATCATTGTAGGCGTCTGAAAT 59.666 41.667 0.00 0.00 33.76 2.17
1599 3571 3.684305 CACATCATTGTAGGCGTCTGAAA 59.316 43.478 0.00 0.00 33.76 2.69
1604 3576 3.000078 CGTAACACATCATTGTAGGCGTC 60.000 47.826 0.00 0.00 33.76 5.19
1609 3581 7.489435 ACAGAGAATCGTAACACATCATTGTAG 59.511 37.037 0.00 0.00 42.67 2.74
1621 3593 4.577283 AGCTAGAGGACAGAGAATCGTAAC 59.423 45.833 0.00 0.00 42.67 2.50
1626 3598 5.789643 ATCAAGCTAGAGGACAGAGAATC 57.210 43.478 0.00 0.00 0.00 2.52
1645 3617 4.623932 AACTGCAGAAGGTCAAGTATCA 57.376 40.909 23.35 0.00 0.00 2.15
1691 3663 9.533253 AAACAGAATTCCAAGAACATGTTTTAG 57.467 29.630 13.36 5.41 36.51 1.85
1718 3690 9.129532 GATTAGGATTGATTTCACTTGGAGAAT 57.870 33.333 0.00 0.00 0.00 2.40
1783 3755 3.820557 ACTTATCAGGCACCGCATAATT 58.179 40.909 0.00 0.00 0.00 1.40
1803 3777 2.677836 TCAAATGTCCATAGCGAGCAAC 59.322 45.455 0.00 0.00 0.00 4.17
1858 3832 8.568794 GGAAGTAGTACAGCAGAAAAGAAAATT 58.431 33.333 2.52 0.00 0.00 1.82
1889 3867 8.263640 GCATATCTCCCATACTAAATCTCACAT 58.736 37.037 0.00 0.00 0.00 3.21
1890 3868 7.455953 AGCATATCTCCCATACTAAATCTCACA 59.544 37.037 0.00 0.00 0.00 3.58
1891 3869 7.846066 AGCATATCTCCCATACTAAATCTCAC 58.154 38.462 0.00 0.00 0.00 3.51
1892 3870 8.972127 GTAGCATATCTCCCATACTAAATCTCA 58.028 37.037 0.00 0.00 0.00 3.27
1893 3871 8.417884 GGTAGCATATCTCCCATACTAAATCTC 58.582 40.741 0.00 0.00 0.00 2.75
1895 3873 8.200792 CAGGTAGCATATCTCCCATACTAAATC 58.799 40.741 0.00 0.00 20.99 2.17
1978 3956 6.464322 CCCACAAACTATGCCATCTACTATGA 60.464 42.308 0.00 0.00 0.00 2.15
2027 4180 9.468532 AAAGCATGAAATAGAACTGAGAAAAAC 57.531 29.630 0.00 0.00 0.00 2.43
2036 4189 5.244626 ACAGGCAAAAGCATGAAATAGAACT 59.755 36.000 9.20 0.00 0.00 3.01
2041 4194 6.884295 AGTAGTACAGGCAAAAGCATGAAATA 59.116 34.615 9.20 0.00 0.00 1.40
2085 4238 5.863397 ACCATGCAGTTGAATTTAATGAACG 59.137 36.000 0.00 0.00 0.00 3.95
2131 4286 8.892723 CAATCACTAACTGCACTATCCATTTTA 58.107 33.333 0.00 0.00 0.00 1.52
2249 4405 3.065925 CCTGCATAAGCTAACAAAGGAGC 59.934 47.826 0.00 0.00 42.74 4.70
2286 4443 7.106239 ACTGCATTAAAAGTACAGTCAGCTAT 58.894 34.615 0.00 0.00 36.95 2.97
2387 4544 8.778059 AGTATTTAATTGTGGATTAGGAGGTCA 58.222 33.333 0.00 0.00 32.06 4.02
2414 4571 7.734942 TCTTCAACCATAAAGGCAAAATTTCT 58.265 30.769 0.00 0.00 43.14 2.52
2448 4605 6.269315 TGTACAGTGCGTTGAATTTGAATTT 58.731 32.000 0.00 0.00 0.00 1.82
2449 4606 5.826586 TGTACAGTGCGTTGAATTTGAATT 58.173 33.333 0.00 0.00 0.00 2.17
2585 4742 9.236006 ACTTGCAAGACATAATAGAAAGACAAT 57.764 29.630 32.50 0.00 0.00 2.71
2586 4743 8.621532 ACTTGCAAGACATAATAGAAAGACAA 57.378 30.769 32.50 0.00 0.00 3.18
2626 5042 5.334421 CACTCCTGGGCCTAGTTATACTAT 58.666 45.833 15.86 0.00 29.08 2.12
2659 5075 5.189736 TCCAACTGAAGGATGTGCTAATACT 59.810 40.000 0.00 0.00 0.00 2.12
2663 5079 3.307691 CCTCCAACTGAAGGATGTGCTAA 60.308 47.826 0.00 0.00 33.99 3.09
2672 5088 4.461198 ACTGTTAAACCTCCAACTGAAGG 58.539 43.478 0.00 0.00 0.00 3.46
2722 5140 9.940166 CGAATCATTCTCATTTTCATACAATCA 57.060 29.630 0.00 0.00 0.00 2.57
2723 5141 8.899776 GCGAATCATTCTCATTTTCATACAATC 58.100 33.333 0.00 0.00 0.00 2.67
2724 5142 8.407832 TGCGAATCATTCTCATTTTCATACAAT 58.592 29.630 0.00 0.00 0.00 2.71
2725 5143 7.760437 TGCGAATCATTCTCATTTTCATACAA 58.240 30.769 0.00 0.00 0.00 2.41
2726 5144 7.319142 TGCGAATCATTCTCATTTTCATACA 57.681 32.000 0.00 0.00 0.00 2.29
2791 5209 1.418637 ACACGGGTGTTATGGTGTTCT 59.581 47.619 0.00 0.00 41.83 3.01
2792 5210 1.886886 ACACGGGTGTTATGGTGTTC 58.113 50.000 0.00 0.00 41.83 3.18
2816 5251 3.587498 TGGGCATGGAAGCTAGTATAGT 58.413 45.455 0.00 0.00 41.93 2.12
2827 5262 6.446909 TTGTGAGTATATATGGGCATGGAA 57.553 37.500 0.00 0.00 0.00 3.53
2857 5292 8.357402 ACACAAATAAACCATAAGAAACAGGAC 58.643 33.333 0.00 0.00 0.00 3.85
2906 5341 4.338118 GGATGAGTTTGTCAGACCAACAAA 59.662 41.667 17.49 7.27 42.63 2.83
2996 5431 4.872664 ACAAGAGACTCTACCAAAAGTCG 58.127 43.478 5.14 0.00 45.25 4.18
3074 5510 9.283768 CACCATTATGGCACTAATATTACTTGA 57.716 33.333 11.72 0.00 42.67 3.02
3096 5532 9.679661 TCTAGACAAATGAAAATATAAGCACCA 57.320 29.630 0.00 0.00 0.00 4.17
3222 5658 3.722147 ACCAATATCAGCAAGCTCTACG 58.278 45.455 0.00 0.00 0.00 3.51
3274 5710 9.276590 TCAATATTTCACTTATGATGGCTGTAG 57.723 33.333 0.00 0.00 33.85 2.74
3279 5715 9.754382 ATGTTTCAATATTTCACTTATGATGGC 57.246 29.630 0.00 0.00 33.85 4.40
3337 5773 7.576403 ACAACTAAACTAACCCAGGTTTTCTA 58.424 34.615 7.50 0.00 39.31 2.10
3359 5795 4.186856 TGTCGAATGCATGACTAGACAA 57.813 40.909 15.79 4.51 34.71 3.18
3360 5796 3.866883 TGTCGAATGCATGACTAGACA 57.133 42.857 15.79 15.18 36.10 3.41
3417 5861 7.472334 AGTGGAAAACAGCATCAAATAATCT 57.528 32.000 0.00 0.00 0.00 2.40
3468 5912 5.770663 CAGTAGCACAGTATACTAGACCCAT 59.229 44.000 4.74 0.00 31.10 4.00
3485 5929 1.903877 GCCTCAAGGGAGCAGTAGCA 61.904 60.000 0.00 0.00 39.96 3.49
3531 5975 4.019174 ACGAGTAATTTAGAACGGAGGGA 58.981 43.478 0.00 0.00 0.00 4.20
3532 5976 4.357996 GACGAGTAATTTAGAACGGAGGG 58.642 47.826 0.00 0.00 0.00 4.30
3533 5977 4.033684 CGACGAGTAATTTAGAACGGAGG 58.966 47.826 0.00 0.00 0.00 4.30
3534 5978 3.481388 GCGACGAGTAATTTAGAACGGAG 59.519 47.826 0.00 0.00 0.00 4.63
3535 5979 3.119884 TGCGACGAGTAATTTAGAACGGA 60.120 43.478 0.00 0.00 0.00 4.69
3536 5980 3.173599 TGCGACGAGTAATTTAGAACGG 58.826 45.455 0.00 0.00 0.00 4.44
3537 5981 4.093514 TCTGCGACGAGTAATTTAGAACG 58.906 43.478 0.00 0.00 0.00 3.95
3538 5982 6.385537 TTTCTGCGACGAGTAATTTAGAAC 57.614 37.500 0.00 0.00 0.00 3.01
3539 5983 6.035650 CCATTTCTGCGACGAGTAATTTAGAA 59.964 38.462 0.00 0.00 0.00 2.10
3540 5984 5.518847 CCATTTCTGCGACGAGTAATTTAGA 59.481 40.000 0.00 0.00 0.00 2.10
3541 5985 5.518847 TCCATTTCTGCGACGAGTAATTTAG 59.481 40.000 0.00 0.00 0.00 1.85
3542 5986 5.412640 TCCATTTCTGCGACGAGTAATTTA 58.587 37.500 0.00 0.00 0.00 1.40
3543 5987 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
3544 5988 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
3545 5989 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
3546 5990 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
3547 5991 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
3548 5992 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
3549 5993 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
3550 5994 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
3551 5995 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
3552 5996 4.387256 GCTAGATACATCCATTTCTGCGAC 59.613 45.833 0.00 0.00 0.00 5.19
3553 5997 4.039124 TGCTAGATACATCCATTTCTGCGA 59.961 41.667 0.00 0.00 0.00 5.10
3554 5998 4.309933 TGCTAGATACATCCATTTCTGCG 58.690 43.478 0.00 0.00 0.00 5.18
3555 5999 6.814506 AATGCTAGATACATCCATTTCTGC 57.185 37.500 0.00 0.00 0.00 4.26
3579 6023 9.678260 GGGAATAGATGTATCTAGATGCATTTT 57.322 33.333 29.66 23.41 42.77 1.82
3580 6024 8.829746 TGGGAATAGATGTATCTAGATGCATTT 58.170 33.333 29.66 26.60 42.77 2.32
3581 6025 8.263640 GTGGGAATAGATGTATCTAGATGCATT 58.736 37.037 29.66 22.22 42.77 3.56
3582 6026 7.417229 CGTGGGAATAGATGTATCTAGATGCAT 60.417 40.741 29.54 29.54 44.84 3.96
3583 6027 6.127619 CGTGGGAATAGATGTATCTAGATGCA 60.128 42.308 23.38 23.38 42.20 3.96
3584 6028 6.095580 TCGTGGGAATAGATGTATCTAGATGC 59.904 42.308 15.79 14.54 42.20 3.91
3585 6029 7.121315 TGTCGTGGGAATAGATGTATCTAGATG 59.879 40.741 15.79 0.00 42.20 2.90
3586 6030 7.175797 TGTCGTGGGAATAGATGTATCTAGAT 58.824 38.462 10.73 10.73 42.20 1.98
3587 6031 6.540083 TGTCGTGGGAATAGATGTATCTAGA 58.460 40.000 7.57 0.00 42.20 2.43
3588 6032 6.819397 TGTCGTGGGAATAGATGTATCTAG 57.181 41.667 7.57 0.00 42.20 2.43
3589 6033 6.776116 ACTTGTCGTGGGAATAGATGTATCTA 59.224 38.462 4.22 4.22 43.00 1.98
3590 6034 5.598830 ACTTGTCGTGGGAATAGATGTATCT 59.401 40.000 0.00 0.00 40.86 1.98
3591 6035 5.844004 ACTTGTCGTGGGAATAGATGTATC 58.156 41.667 0.00 0.00 0.00 2.24
3592 6036 5.871396 ACTTGTCGTGGGAATAGATGTAT 57.129 39.130 0.00 0.00 0.00 2.29
3593 6037 6.778834 TTACTTGTCGTGGGAATAGATGTA 57.221 37.500 0.00 0.00 0.00 2.29
3594 6038 5.670792 TTACTTGTCGTGGGAATAGATGT 57.329 39.130 0.00 0.00 0.00 3.06
3595 6039 7.409697 CAAATTACTTGTCGTGGGAATAGATG 58.590 38.462 0.00 0.00 0.00 2.90
3596 6040 6.542370 CCAAATTACTTGTCGTGGGAATAGAT 59.458 38.462 0.00 0.00 32.65 1.98
3597 6041 5.878116 CCAAATTACTTGTCGTGGGAATAGA 59.122 40.000 0.00 0.00 32.65 1.98
3598 6042 5.878116 TCCAAATTACTTGTCGTGGGAATAG 59.122 40.000 0.00 0.00 32.65 1.73
3599 6043 5.806818 TCCAAATTACTTGTCGTGGGAATA 58.193 37.500 0.00 0.00 32.65 1.75
3600 6044 4.658063 TCCAAATTACTTGTCGTGGGAAT 58.342 39.130 0.00 0.00 32.65 3.01
3601 6045 4.088056 TCCAAATTACTTGTCGTGGGAA 57.912 40.909 0.00 0.00 32.65 3.97
3602 6046 3.773418 TCCAAATTACTTGTCGTGGGA 57.227 42.857 0.00 0.00 32.65 4.37
3603 6047 3.364565 CGTTCCAAATTACTTGTCGTGGG 60.365 47.826 0.00 0.00 32.65 4.61
3604 6048 3.364565 CCGTTCCAAATTACTTGTCGTGG 60.365 47.826 0.00 0.00 32.65 4.94
3605 6049 3.495377 TCCGTTCCAAATTACTTGTCGTG 59.505 43.478 0.00 0.00 32.65 4.35
3606 6050 3.731089 TCCGTTCCAAATTACTTGTCGT 58.269 40.909 0.00 0.00 32.65 4.34
3607 6051 3.124636 CCTCCGTTCCAAATTACTTGTCG 59.875 47.826 0.00 0.00 32.65 4.35
3608 6052 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
3609 6053 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
3610 6054 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
3611 6055 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
3612 6056 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
3613 6057 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
3614 6058 3.198417 GGTACTCCCTCCGTTCCAAATTA 59.802 47.826 0.00 0.00 0.00 1.40
3615 6059 2.026542 GGTACTCCCTCCGTTCCAAATT 60.027 50.000 0.00 0.00 0.00 1.82
3616 6060 1.558294 GGTACTCCCTCCGTTCCAAAT 59.442 52.381 0.00 0.00 0.00 2.32
3617 6061 0.978907 GGTACTCCCTCCGTTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
3618 6062 0.178926 TGGTACTCCCTCCGTTCCAA 60.179 55.000 0.00 0.00 30.28 3.53
3619 6063 0.042131 ATGGTACTCCCTCCGTTCCA 59.958 55.000 0.00 0.00 36.47 3.53
3620 6064 2.077687 TATGGTACTCCCTCCGTTCC 57.922 55.000 0.00 0.00 0.00 3.62
3621 6065 5.014858 TCATATATGGTACTCCCTCCGTTC 58.985 45.833 12.78 0.00 0.00 3.95
3622 6066 5.006896 TCATATATGGTACTCCCTCCGTT 57.993 43.478 12.78 0.00 0.00 4.44
3623 6067 4.669866 TCATATATGGTACTCCCTCCGT 57.330 45.455 12.78 0.00 0.00 4.69
3624 6068 6.341316 CAAATCATATATGGTACTCCCTCCG 58.659 44.000 12.78 0.00 0.00 4.63
3625 6069 6.215636 ACCAAATCATATATGGTACTCCCTCC 59.784 42.308 12.78 0.00 45.37 4.30
3626 6070 7.106239 CACCAAATCATATATGGTACTCCCTC 58.894 42.308 12.78 0.00 45.45 4.30
3627 6071 6.562608 ACACCAAATCATATATGGTACTCCCT 59.437 38.462 12.78 0.00 45.45 4.20
3628 6072 6.655003 CACACCAAATCATATATGGTACTCCC 59.345 42.308 12.78 0.00 45.45 4.30
3629 6073 7.173218 CACACACCAAATCATATATGGTACTCC 59.827 40.741 12.78 0.00 45.45 3.85
3630 6074 7.931407 TCACACACCAAATCATATATGGTACTC 59.069 37.037 12.78 0.00 45.45 2.59
3631 6075 7.801104 TCACACACCAAATCATATATGGTACT 58.199 34.615 12.78 0.00 45.45 2.73
3632 6076 7.173218 CCTCACACACCAAATCATATATGGTAC 59.827 40.741 12.78 0.00 45.45 3.34
3633 6077 7.223584 CCTCACACACCAAATCATATATGGTA 58.776 38.462 12.78 0.00 45.45 3.25
3635 6079 5.048504 GCCTCACACACCAAATCATATATGG 60.049 44.000 12.78 0.21 40.16 2.74
3636 6080 5.766670 AGCCTCACACACCAAATCATATATG 59.233 40.000 6.36 6.36 0.00 1.78
3637 6081 5.945310 AGCCTCACACACCAAATCATATAT 58.055 37.500 0.00 0.00 0.00 0.86
3638 6082 5.372343 AGCCTCACACACCAAATCATATA 57.628 39.130 0.00 0.00 0.00 0.86
3717 6161 7.391148 ACCAATGTAATCAAACTACCATCAC 57.609 36.000 0.00 0.00 0.00 3.06
3812 6257 0.827507 TCACAGCCAAAAGGGGAAGC 60.828 55.000 0.00 0.00 37.04 3.86
4070 6516 6.808008 ATGACAACAATAAGACAAGACAGG 57.192 37.500 0.00 0.00 0.00 4.00
4131 6577 9.122779 TGTTAACATCATCTGATCATGCATAAA 57.877 29.630 3.59 0.00 31.21 1.40
4132 6578 8.680039 TGTTAACATCATCTGATCATGCATAA 57.320 30.769 3.59 0.00 31.21 1.90
4314 6761 0.918799 TCAATCAGCAAGGGCCCCTA 60.919 55.000 21.43 0.00 42.56 3.53
4691 7141 1.076332 GCACACATGACCTACCGAAC 58.924 55.000 0.00 0.00 0.00 3.95
4706 7156 4.565022 TCATCGTGTTCATCTTAAGCACA 58.435 39.130 0.00 0.00 0.00 4.57
4723 7174 6.468956 GGCTGTGTTGTAATACAAATTCATCG 59.531 38.462 7.48 0.00 40.15 3.84
4803 7254 9.859427 CAAGCAGAAATAATCCACAAAGAATAA 57.141 29.630 0.00 0.00 0.00 1.40
4852 7311 3.688694 TTAACATTACCCACTGACGCT 57.311 42.857 0.00 0.00 0.00 5.07
4884 7343 1.263217 CACAACAGGTTCGGTACAAGC 59.737 52.381 0.00 0.00 0.00 4.01
4885 7344 1.263217 GCACAACAGGTTCGGTACAAG 59.737 52.381 0.00 0.00 0.00 3.16
4886 7345 1.301423 GCACAACAGGTTCGGTACAA 58.699 50.000 0.00 0.00 0.00 2.41
4887 7346 0.876777 CGCACAACAGGTTCGGTACA 60.877 55.000 0.00 0.00 32.29 2.90
4888 7347 0.877213 ACGCACAACAGGTTCGGTAC 60.877 55.000 0.00 0.00 40.58 3.34
4889 7348 0.179078 AACGCACAACAGGTTCGGTA 60.179 50.000 0.00 0.00 40.58 4.02
4890 7349 1.450669 AACGCACAACAGGTTCGGT 60.451 52.632 0.00 0.00 40.58 4.69


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

AutoCloner maintained by Alex Coulton.