Multiple sequence alignment - TraesCS3D01G143800

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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 TraesCS3D01G143800 chr3D 100.000 3935 0 0 1 3935 107068029 107071963 0.000000e+00 7267.0
1 TraesCS3D01G143800 chr3B 92.515 3073 156 35 894 3935 157919134 157922163 0.000000e+00 4333.0
2 TraesCS3D01G143800 chr3B 87.752 645 62 7 4 633 157914051 157914693 0.000000e+00 737.0
3 TraesCS3D01G143800 chr3B 93.750 144 9 0 659 802 157918892 157919035 2.380000e-52 217.0
4 TraesCS3D01G143800 chr3A 89.538 3116 219 47 861 3924 549622606 549619546 0.000000e+00 3849.0
5 TraesCS3D01G143800 chr3A 100.000 33 0 0 3902 3934 549619553 549619521 1.180000e-05 62.1


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 TraesCS3D01G143800 chr3D 107068029 107071963 3934 False 7267.00 7267 100.0000 1 3935 1 chr3D.!!$F1 3934
1 TraesCS3D01G143800 chr3B 157918892 157922163 3271 False 2275.00 4333 93.1325 659 3935 2 chr3B.!!$F2 3276
2 TraesCS3D01G143800 chr3B 157914051 157914693 642 False 737.00 737 87.7520 4 633 1 chr3B.!!$F1 629
3 TraesCS3D01G143800 chr3A 549619521 549622606 3085 True 1955.55 3849 94.7690 861 3934 2 chr3A.!!$R1 3073

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
649 665 0.036765 GTGTAACAGGCCGGTGATCA 60.037 55.0 10.05 6.62 36.32 2.92 F
1043 1094 0.103208 GATTCTCGTCGATGCCACCT 59.897 55.0 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 2184 0.032540 CGACCATGGATCTGATCGCA 59.967 55.0 21.47 10.58 0.0 5.10 R
3011 3071 0.038801 TCTGAACACTCTGCAGCTCG 60.039 55.0 9.47 2.20 0.0 5.03 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
24 25 5.815581 ACCTGGTTAAATCATCAGCTACAA 58.184 37.500 0.00 0.00 0.00 2.41
30 31 4.584029 AAATCATCAGCTACAACGTTCG 57.416 40.909 0.00 0.00 0.00 3.95
50 51 6.128661 CGTTCGTTACAATCTCAGGAAAATGA 60.129 38.462 0.00 0.00 0.00 2.57
65 66 4.688879 GGAAAATGACCGAACCAAATTTCC 59.311 41.667 0.00 0.00 36.90 3.13
66 67 4.946478 AAATGACCGAACCAAATTTCCA 57.054 36.364 0.00 0.00 0.00 3.53
68 69 4.946478 ATGACCGAACCAAATTTCCAAA 57.054 36.364 0.00 0.00 0.00 3.28
75 76 4.388485 GAACCAAATTTCCAAACTGCCAT 58.612 39.130 0.00 0.00 0.00 4.40
86 87 2.827921 CAAACTGCCATTCCCTAAGCTT 59.172 45.455 3.48 3.48 0.00 3.74
104 105 4.774124 AGCTTCATATGCAGCTAAGACAA 58.226 39.130 25.63 0.00 42.60 3.18
108 109 5.089970 TCATATGCAGCTAAGACAAGTGT 57.910 39.130 0.00 0.00 0.00 3.55
115 116 4.794003 GCAGCTAAGACAAGTGTTGCATTT 60.794 41.667 0.00 0.00 0.00 2.32
166 167 9.830975 AGATTAACATTACCAAAAGCAACTTTT 57.169 25.926 0.00 0.00 43.36 2.27
194 195 8.592105 TTTGAAATTTAATCTCCTGCAACAAG 57.408 30.769 0.00 0.00 0.00 3.16
196 197 4.725790 ATTTAATCTCCTGCAACAAGGC 57.274 40.909 0.00 0.00 37.24 4.35
197 198 3.439857 TTAATCTCCTGCAACAAGGCT 57.560 42.857 0.00 0.00 37.24 4.58
206 208 1.109323 GCAACAAGGCTTCCAGTGGT 61.109 55.000 9.54 0.00 0.00 4.16
216 218 2.158842 GCTTCCAGTGGTGCTAGATCAT 60.159 50.000 18.11 0.00 0.00 2.45
246 248 3.666374 GCTTGAGATCGTTTGCTTCAGTG 60.666 47.826 0.00 0.00 0.00 3.66
256 258 0.111061 TGCTTCAGTGCCATGGAGTT 59.889 50.000 18.40 0.00 0.00 3.01
266 268 3.989817 GTGCCATGGAGTTCATTTCAAAC 59.010 43.478 18.40 0.00 32.92 2.93
276 278 5.846203 AGTTCATTTCAAACATGACTTGGG 58.154 37.500 0.00 0.00 30.09 4.12
281 283 5.508200 TTTCAAACATGACTTGGGTACAC 57.492 39.130 0.00 0.00 0.00 2.90
295 297 1.202952 GGTACACCCCATGTTGGTTGA 60.203 52.381 1.53 0.00 43.19 3.18
297 299 1.631405 ACACCCCATGTTGGTTGATG 58.369 50.000 1.53 0.00 38.98 3.07
298 300 0.247185 CACCCCATGTTGGTTGATGC 59.753 55.000 1.53 0.00 35.17 3.91
319 321 3.305094 GCATTAAGCGCGTTTAGTAGTGA 59.695 43.478 15.02 0.41 0.00 3.41
321 323 2.427232 AAGCGCGTTTAGTAGTGACA 57.573 45.000 6.35 0.00 0.00 3.58
326 328 2.655474 CGCGTTTAGTAGTGACAGTGTC 59.345 50.000 16.68 16.68 0.00 3.67
328 330 3.913163 GCGTTTAGTAGTGACAGTGTCTC 59.087 47.826 23.29 19.51 33.15 3.36
356 358 4.202398 TGAAGGGCATCAGAGATATGTTCC 60.202 45.833 0.00 0.00 0.00 3.62
360 362 4.314121 GGCATCAGAGATATGTTCCAGAC 58.686 47.826 0.00 0.00 0.00 3.51
363 365 6.054295 GCATCAGAGATATGTTCCAGACTTT 58.946 40.000 0.00 0.00 0.00 2.66
384 386 2.858622 GCACCTGCAGTAATGAGCA 58.141 52.632 13.81 0.00 41.59 4.26
403 405 5.300034 TGAGCATTCCGCAATCATTTCTTAT 59.700 36.000 0.00 0.00 46.13 1.73
404 406 5.526115 AGCATTCCGCAATCATTTCTTATG 58.474 37.500 0.00 0.00 46.13 1.90
463 479 7.636259 TGCACATTTTTAATAACTCACTTGC 57.364 32.000 0.00 0.00 0.00 4.01
465 481 6.090763 GCACATTTTTAATAACTCACTTGCCC 59.909 38.462 0.00 0.00 0.00 5.36
473 489 1.122019 ACTCACTTGCCCGAGGAGTT 61.122 55.000 0.00 0.00 35.41 3.01
474 490 0.390472 CTCACTTGCCCGAGGAGTTC 60.390 60.000 0.00 0.00 0.00 3.01
480 496 2.286365 TGCCCGAGGAGTTCATTTTT 57.714 45.000 0.00 0.00 0.00 1.94
504 520 7.875327 TTAGGTGCTTTTCTACTTTTGAGTT 57.125 32.000 0.00 0.00 0.00 3.01
505 521 6.136541 AGGTGCTTTTCTACTTTTGAGTTG 57.863 37.500 0.00 0.00 0.00 3.16
510 526 7.429630 GTGCTTTTCTACTTTTGAGTTGTTCTC 59.570 37.037 0.00 0.00 43.03 2.87
513 529 4.945246 TCTACTTTTGAGTTGTTCTCGCT 58.055 39.130 0.00 0.00 45.46 4.93
515 531 2.032178 ACTTTTGAGTTGTTCTCGCTGC 59.968 45.455 0.00 0.00 45.46 5.25
521 537 0.937304 GTTGTTCTCGCTGCTTGACA 59.063 50.000 0.00 0.00 0.00 3.58
582 598 7.658982 TCATCTGAGGATTTGATTTTATCTCCG 59.341 37.037 0.00 0.00 0.00 4.63
584 600 4.821805 TGAGGATTTGATTTTATCTCCGGC 59.178 41.667 0.00 0.00 0.00 6.13
600 616 0.813184 CGGCATGGCTTGATTCTTGT 59.187 50.000 18.09 0.00 0.00 3.16
604 620 2.991190 GCATGGCTTGATTCTTGTGTTG 59.009 45.455 4.32 0.00 0.00 3.33
614 630 7.487189 GCTTGATTCTTGTGTTGATTGGATAAG 59.513 37.037 0.00 0.00 0.00 1.73
619 635 4.032960 TGTGTTGATTGGATAAGTGCCT 57.967 40.909 0.00 0.00 0.00 4.75
625 641 6.382859 TGTTGATTGGATAAGTGCCTAGTCTA 59.617 38.462 0.00 0.00 0.00 2.59
628 644 8.034313 TGATTGGATAAGTGCCTAGTCTATTT 57.966 34.615 0.00 0.00 0.00 1.40
633 649 4.910458 AAGTGCCTAGTCTATTTGGTGT 57.090 40.909 0.00 0.00 0.00 4.16
634 650 7.201974 GGATAAGTGCCTAGTCTATTTGGTGTA 60.202 40.741 0.00 0.00 0.00 2.90
635 651 6.368779 AAGTGCCTAGTCTATTTGGTGTAA 57.631 37.500 0.00 0.00 0.00 2.41
636 652 5.731591 AGTGCCTAGTCTATTTGGTGTAAC 58.268 41.667 0.00 0.00 0.00 2.50
637 653 5.247564 AGTGCCTAGTCTATTTGGTGTAACA 59.752 40.000 0.00 0.00 39.98 2.41
638 654 5.581085 GTGCCTAGTCTATTTGGTGTAACAG 59.419 44.000 0.00 0.00 39.98 3.16
639 655 5.116882 GCCTAGTCTATTTGGTGTAACAGG 58.883 45.833 0.00 0.00 39.98 4.00
640 656 5.116882 CCTAGTCTATTTGGTGTAACAGGC 58.883 45.833 0.00 0.00 39.98 4.85
641 657 3.951663 AGTCTATTTGGTGTAACAGGCC 58.048 45.455 0.00 0.00 39.98 5.19
642 658 2.676342 GTCTATTTGGTGTAACAGGCCG 59.324 50.000 0.00 0.00 39.98 6.13
643 659 2.014128 CTATTTGGTGTAACAGGCCGG 58.986 52.381 0.00 0.00 39.98 6.13
644 660 0.111639 ATTTGGTGTAACAGGCCGGT 59.888 50.000 1.28 1.28 39.98 5.28
645 661 0.820074 TTTGGTGTAACAGGCCGGTG 60.820 55.000 10.05 0.00 39.98 4.94
646 662 1.697082 TTGGTGTAACAGGCCGGTGA 61.697 55.000 10.05 0.00 39.98 4.02
647 663 1.298667 GGTGTAACAGGCCGGTGAT 59.701 57.895 10.05 0.00 39.98 3.06
648 664 0.743345 GGTGTAACAGGCCGGTGATC 60.743 60.000 10.05 3.91 39.98 2.92
649 665 0.036765 GTGTAACAGGCCGGTGATCA 60.037 55.000 10.05 6.62 36.32 2.92
650 666 0.249120 TGTAACAGGCCGGTGATCAG 59.751 55.000 10.05 0.00 0.00 2.90
651 667 0.249398 GTAACAGGCCGGTGATCAGT 59.751 55.000 10.05 0.00 0.00 3.41
652 668 0.981183 TAACAGGCCGGTGATCAGTT 59.019 50.000 10.05 0.00 0.00 3.16
653 669 0.321653 AACAGGCCGGTGATCAGTTC 60.322 55.000 10.05 0.00 0.00 3.01
654 670 1.450312 CAGGCCGGTGATCAGTTCC 60.450 63.158 1.90 0.00 0.00 3.62
655 671 2.511600 GGCCGGTGATCAGTTCCG 60.512 66.667 14.61 14.61 43.30 4.30
656 672 2.577059 GCCGGTGATCAGTTCCGA 59.423 61.111 21.28 0.00 46.05 4.55
657 673 1.810030 GCCGGTGATCAGTTCCGAC 60.810 63.158 21.28 8.99 46.05 4.79
660 676 1.405526 CCGGTGATCAGTTCCGACAAT 60.406 52.381 21.28 0.00 46.05 2.71
666 682 4.213270 GTGATCAGTTCCGACAATGTTGAA 59.787 41.667 1.41 0.00 0.00 2.69
669 685 1.880027 AGTTCCGACAATGTTGAAGCC 59.120 47.619 1.41 0.00 0.00 4.35
684 700 5.945191 TGTTGAAGCCATTGAGACAATGATA 59.055 36.000 21.12 1.54 0.00 2.15
705 721 0.914644 CTGGAGGCAGATCTTTGGGA 59.085 55.000 0.00 0.00 0.00 4.37
737 753 6.400568 CAGCAATCTTCCCACAATTGTTATT 58.599 36.000 8.77 0.00 33.82 1.40
782 798 8.064222 CGCAAACTATCTTGGACATTGTTATAG 58.936 37.037 0.00 0.00 0.00 1.31
794 810 9.679661 TGGACATTGTTATAGAGAAGCAAATTA 57.320 29.630 0.00 0.00 0.00 1.40
837 884 4.377897 ACAGTAGGTTTGAAGAGTTTCCG 58.622 43.478 0.00 0.00 32.09 4.30
839 886 5.054477 CAGTAGGTTTGAAGAGTTTCCGAA 58.946 41.667 0.00 0.00 32.09 4.30
845 892 5.212934 GTTTGAAGAGTTTCCGAATGAACC 58.787 41.667 0.00 0.00 31.05 3.62
846 893 4.351874 TGAAGAGTTTCCGAATGAACCT 57.648 40.909 0.00 0.00 31.05 3.50
847 894 4.315803 TGAAGAGTTTCCGAATGAACCTC 58.684 43.478 0.00 0.00 41.48 3.85
850 897 3.835395 AGAGTTTCCGAATGAACCTCTCT 59.165 43.478 0.00 0.00 46.49 3.10
851 898 5.017490 AGAGTTTCCGAATGAACCTCTCTA 58.983 41.667 0.00 0.00 46.49 2.43
852 899 5.126384 AGAGTTTCCGAATGAACCTCTCTAG 59.874 44.000 0.00 0.00 46.49 2.43
853 900 4.773149 AGTTTCCGAATGAACCTCTCTAGT 59.227 41.667 0.00 0.00 31.05 2.57
854 901 5.950549 AGTTTCCGAATGAACCTCTCTAGTA 59.049 40.000 0.00 0.00 31.05 1.82
855 902 6.608002 AGTTTCCGAATGAACCTCTCTAGTAT 59.392 38.462 0.00 0.00 31.05 2.12
856 903 6.392625 TTCCGAATGAACCTCTCTAGTATG 57.607 41.667 0.00 0.00 0.00 2.39
857 904 4.278669 TCCGAATGAACCTCTCTAGTATGC 59.721 45.833 0.00 0.00 0.00 3.14
858 905 4.551388 CGAATGAACCTCTCTAGTATGCC 58.449 47.826 0.00 0.00 0.00 4.40
860 907 5.451937 CGAATGAACCTCTCTAGTATGCCAA 60.452 44.000 0.00 0.00 0.00 4.52
861 908 5.957771 ATGAACCTCTCTAGTATGCCAAA 57.042 39.130 0.00 0.00 0.00 3.28
862 909 5.755409 TGAACCTCTCTAGTATGCCAAAA 57.245 39.130 0.00 0.00 0.00 2.44
864 911 5.938125 TGAACCTCTCTAGTATGCCAAAAAC 59.062 40.000 0.00 0.00 0.00 2.43
866 913 3.309954 CCTCTCTAGTATGCCAAAAACGC 59.690 47.826 0.00 0.00 0.00 4.84
870 917 5.121768 TCTCTAGTATGCCAAAAACGCTTTC 59.878 40.000 0.00 0.00 0.00 2.62
876 923 7.767261 AGTATGCCAAAAACGCTTTCATATTA 58.233 30.769 0.00 0.00 0.00 0.98
879 926 6.625362 TGCCAAAAACGCTTTCATATTATGA 58.375 32.000 2.14 2.14 37.55 2.15
899 946 4.922206 TGAAACGGAGGGAGTAGTAACTA 58.078 43.478 0.00 0.00 35.56 2.24
906 953 5.359009 CGGAGGGAGTAGTAACTATTGTCAA 59.641 44.000 0.00 0.00 35.56 3.18
925 972 8.658840 TTGTCAAAAGCTAATAATAAAGGGGT 57.341 30.769 0.00 0.00 0.00 4.95
932 979 9.660544 AAAGCTAATAATAAAGGGGTGATGATT 57.339 29.630 0.00 0.00 0.00 2.57
933 980 9.660544 AAGCTAATAATAAAGGGGTGATGATTT 57.339 29.630 0.00 0.00 0.00 2.17
934 981 9.082313 AGCTAATAATAAAGGGGTGATGATTTG 57.918 33.333 0.00 0.00 0.00 2.32
935 982 9.077885 GCTAATAATAAAGGGGTGATGATTTGA 57.922 33.333 0.00 0.00 0.00 2.69
969 1019 6.524734 ACAAGAAATCTTCCCAAATGGTTTC 58.475 36.000 0.00 2.11 33.11 2.78
1043 1094 0.103208 GATTCTCGTCGATGCCACCT 59.897 55.000 0.00 0.00 0.00 4.00
1233 1284 1.541310 CGCTCCCCAACTCCTACACA 61.541 60.000 0.00 0.00 0.00 3.72
1350 1404 3.610669 CAGCTCCTCGCCGCCTAT 61.611 66.667 0.00 0.00 40.39 2.57
1422 1476 1.685224 GAAGAGGGCCACCATGTCA 59.315 57.895 6.18 0.00 40.13 3.58
1469 1523 2.594303 CTGCTGCGACCCCAACAA 60.594 61.111 0.00 0.00 0.00 2.83
1479 1533 0.837260 ACCCCAACAATGCAATGGCT 60.837 50.000 6.73 0.00 41.91 4.75
1485 1539 3.316283 CAACAATGCAATGGCTACGTTT 58.684 40.909 6.73 0.00 41.91 3.60
1487 1541 1.655099 CAATGCAATGGCTACGTTTGC 59.345 47.619 13.62 13.62 41.91 3.68
1665 1722 2.815308 CTCTCCGCGTGCCCTTAT 59.185 61.111 4.92 0.00 0.00 1.73
1749 1806 2.380410 GCGTGGCTACCTGTTCGTG 61.380 63.158 0.00 0.00 0.00 4.35
1752 1809 1.007336 GTGGCTACCTGTTCGTGACG 61.007 60.000 0.00 0.00 0.00 4.35
1897 1954 1.614227 GATGTGCGACGAAGCGTTGA 61.614 55.000 11.09 0.00 43.17 3.18
1948 2005 1.548081 CATGGTTGCTCCCAATGTGA 58.452 50.000 0.00 0.00 38.20 3.58
2083 2140 0.898326 TACCGTTCTCTCAGCCTGCA 60.898 55.000 0.00 0.00 0.00 4.41
2379 2436 2.049802 TTCGTCGCCGTTCTGTCC 60.050 61.111 0.00 0.00 35.01 4.02
2517 2574 2.045131 GGCTGGCTTGCTCAAGGAG 61.045 63.158 11.15 0.00 38.80 3.69
2523 2580 1.743252 CTTGCTCAAGGAGGCGTCC 60.743 63.158 17.88 17.88 44.33 4.79
2636 2693 1.440145 GAAGCCACCATAGCGAAGGC 61.440 60.000 0.00 0.00 45.54 4.35
2742 2799 1.517832 GGTGAGGGTGATGACGAGG 59.482 63.158 0.00 0.00 0.00 4.63
2762 2819 2.185310 GAGGCCGGCTTGAGGAAGAA 62.185 60.000 28.56 0.00 0.00 2.52
2802 2859 3.963129 TGAGGTGAAGAACAAGGTGTTT 58.037 40.909 0.00 0.00 41.28 2.83
2809 2866 2.733956 AGAACAAGGTGTTTGCCTTCA 58.266 42.857 0.00 0.00 46.33 3.02
2850 2907 1.145819 GATGCCCAGAGCTGAGGAC 59.854 63.158 0.00 0.00 44.23 3.85
2851 2908 2.641439 GATGCCCAGAGCTGAGGACG 62.641 65.000 0.00 0.00 44.23 4.79
2877 2934 3.128764 TCAGAGTGCTCGACGATTTGTAT 59.871 43.478 0.00 0.00 34.09 2.29
2878 2935 3.483922 CAGAGTGCTCGACGATTTGTATC 59.516 47.826 0.00 0.00 34.09 2.24
2889 2946 4.389664 CGATTTGTATCGCGAAATGGAT 57.610 40.909 15.24 5.02 46.15 3.41
2893 2950 2.479837 TGTATCGCGAAATGGATGACC 58.520 47.619 15.24 0.00 0.00 4.02
2902 2959 2.885113 TGGATGACCAGAGACGCG 59.115 61.111 3.53 3.53 41.77 6.01
2907 2964 1.391933 ATGACCAGAGACGCGCCATA 61.392 55.000 5.73 0.00 0.00 2.74
2913 2970 1.169661 AGAGACGCGCCATAGAGGAG 61.170 60.000 5.73 0.00 41.22 3.69
2927 2987 6.688922 GCCATAGAGGAGGATCACATTGTAAA 60.689 42.308 0.00 0.00 41.22 2.01
2947 3007 7.793902 TGTAAACGTTTGATAGAAGAGAAAGC 58.206 34.615 23.46 0.00 0.00 3.51
2948 3008 7.656137 TGTAAACGTTTGATAGAAGAGAAAGCT 59.344 33.333 23.46 0.00 0.00 3.74
2992 3052 0.761187 AGCAGGCAAACAGAGTGAGA 59.239 50.000 0.00 0.00 0.00 3.27
2993 3053 1.155042 GCAGGCAAACAGAGTGAGAG 58.845 55.000 0.00 0.00 0.00 3.20
2995 3055 2.614987 GCAGGCAAACAGAGTGAGAGAT 60.615 50.000 0.00 0.00 0.00 2.75
2996 3056 3.368843 GCAGGCAAACAGAGTGAGAGATA 60.369 47.826 0.00 0.00 0.00 1.98
2999 3059 4.081752 AGGCAAACAGAGTGAGAGATACTG 60.082 45.833 0.00 0.00 35.14 2.74
3000 3060 4.081972 GGCAAACAGAGTGAGAGATACTGA 60.082 45.833 0.00 0.00 33.53 3.41
3001 3061 5.473931 GCAAACAGAGTGAGAGATACTGAA 58.526 41.667 0.00 0.00 33.53 3.02
3002 3062 5.576384 GCAAACAGAGTGAGAGATACTGAAG 59.424 44.000 0.00 0.00 33.53 3.02
3003 3063 6.571344 GCAAACAGAGTGAGAGATACTGAAGA 60.571 42.308 0.00 0.00 33.53 2.87
3004 3064 7.374272 CAAACAGAGTGAGAGATACTGAAGAA 58.626 38.462 0.00 0.00 33.53 2.52
3005 3065 6.509418 ACAGAGTGAGAGATACTGAAGAAC 57.491 41.667 0.00 0.00 33.53 3.01
3006 3066 6.245408 ACAGAGTGAGAGATACTGAAGAACT 58.755 40.000 0.00 0.00 33.53 3.01
3007 3067 6.719370 ACAGAGTGAGAGATACTGAAGAACTT 59.281 38.462 0.00 0.00 33.53 2.66
3008 3068 7.028962 CAGAGTGAGAGATACTGAAGAACTTG 58.971 42.308 0.00 0.00 0.00 3.16
3009 3069 6.152661 AGAGTGAGAGATACTGAAGAACTTGG 59.847 42.308 0.00 0.00 0.00 3.61
3010 3070 5.186797 AGTGAGAGATACTGAAGAACTTGGG 59.813 44.000 0.00 0.00 0.00 4.12
3011 3071 4.081420 TGAGAGATACTGAAGAACTTGGGC 60.081 45.833 0.00 0.00 0.00 5.36
3012 3072 3.118956 AGAGATACTGAAGAACTTGGGCG 60.119 47.826 0.00 0.00 0.00 6.13
3013 3073 2.832129 AGATACTGAAGAACTTGGGCGA 59.168 45.455 0.00 0.00 0.00 5.54
3014 3074 2.743636 TACTGAAGAACTTGGGCGAG 57.256 50.000 0.00 0.00 0.00 5.03
3015 3075 0.603975 ACTGAAGAACTTGGGCGAGC 60.604 55.000 0.00 0.00 0.00 5.03
3016 3076 0.321122 CTGAAGAACTTGGGCGAGCT 60.321 55.000 0.00 0.00 0.00 4.09
3017 3077 0.603707 TGAAGAACTTGGGCGAGCTG 60.604 55.000 0.00 0.00 0.00 4.24
3018 3078 1.916697 GAAGAACTTGGGCGAGCTGC 61.917 60.000 0.00 0.00 45.38 5.25
3035 3095 1.342496 CTGCAGAGTGTTCAGAGTGGA 59.658 52.381 8.42 0.00 0.00 4.02
3036 3096 1.762370 TGCAGAGTGTTCAGAGTGGAA 59.238 47.619 0.00 0.00 0.00 3.53
3179 3239 2.354305 GCGACGACGTCAAGGTGT 60.354 61.111 26.26 4.40 41.98 4.16
3222 3282 4.841441 TGAAGGTGTTCATGGCCC 57.159 55.556 0.00 0.00 37.79 5.80
3352 3417 0.662619 TCAAAACAGAGCAGCAACGG 59.337 50.000 0.00 0.00 0.00 4.44
3353 3418 0.662619 CAAAACAGAGCAGCAACGGA 59.337 50.000 0.00 0.00 0.00 4.69
3356 3421 0.179045 AACAGAGCAGCAACGGAACT 60.179 50.000 0.00 0.00 0.00 3.01
3368 3433 4.094684 GGAACTCCGCATGACTCG 57.905 61.111 0.00 0.00 0.00 4.18
3370 3435 1.215647 GAACTCCGCATGACTCGGT 59.784 57.895 9.63 0.00 46.49 4.69
3371 3436 1.078759 GAACTCCGCATGACTCGGTG 61.079 60.000 9.63 9.70 46.49 4.94
3372 3437 2.276116 ACTCCGCATGACTCGGTGT 61.276 57.895 10.82 10.82 45.40 4.16
3373 3438 1.079819 CTCCGCATGACTCGGTGTT 60.080 57.895 9.63 0.00 46.49 3.32
3374 3439 1.078759 CTCCGCATGACTCGGTGTTC 61.079 60.000 9.63 0.00 46.49 3.18
3375 3440 1.374125 CCGCATGACTCGGTGTTCA 60.374 57.895 0.00 0.00 41.85 3.18
3376 3441 1.354337 CCGCATGACTCGGTGTTCAG 61.354 60.000 0.00 0.00 41.85 3.02
3377 3442 1.790387 GCATGACTCGGTGTTCAGC 59.210 57.895 0.00 0.00 0.00 4.26
3381 3446 0.464036 TGACTCGGTGTTCAGCTGTT 59.536 50.000 14.67 0.00 0.00 3.16
3391 3456 2.805671 TGTTCAGCTGTTCACGGTATTG 59.194 45.455 14.67 0.00 0.00 1.90
3489 3561 4.315122 CTCGTCGCCGATCCTCCG 62.315 72.222 0.00 0.00 43.27 4.63
3863 3974 0.772124 AGCAGGAGGGGGACAAGAAA 60.772 55.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.428253 TGTAGCTGATGATTTAACCAGGTC 58.572 41.667 0.00 0.00 38.22 3.85
2 3 5.220662 CGTTGTAGCTGATGATTTAACCAGG 60.221 44.000 0.00 0.00 0.00 4.45
15 16 3.352554 TGTAACGAACGTTGTAGCTGA 57.647 42.857 20.29 0.00 38.92 4.26
24 25 3.928727 TCCTGAGATTGTAACGAACGT 57.071 42.857 0.00 0.00 0.00 3.99
30 31 5.642063 TCGGTCATTTTCCTGAGATTGTAAC 59.358 40.000 0.00 0.00 0.00 2.50
50 51 3.739830 GCAGTTTGGAAATTTGGTTCGGT 60.740 43.478 0.00 0.00 0.00 4.69
65 66 2.450476 AGCTTAGGGAATGGCAGTTTG 58.550 47.619 0.00 0.00 0.00 2.93
66 67 2.907458 AGCTTAGGGAATGGCAGTTT 57.093 45.000 0.00 0.00 0.00 2.66
68 69 1.635487 TGAAGCTTAGGGAATGGCAGT 59.365 47.619 0.00 0.00 0.00 4.40
75 76 3.480470 GCTGCATATGAAGCTTAGGGAA 58.520 45.455 26.07 0.00 43.48 3.97
86 87 5.089970 ACACTTGTCTTAGCTGCATATGA 57.910 39.130 6.97 0.00 0.00 2.15
104 105 4.215109 AGGTCCTGTAAAAATGCAACACT 58.785 39.130 0.00 0.00 0.00 3.55
108 109 4.038642 GTCCAAGGTCCTGTAAAAATGCAA 59.961 41.667 0.00 0.00 0.00 4.08
115 116 5.772393 ATGTATGTCCAAGGTCCTGTAAA 57.228 39.130 0.00 0.00 0.00 2.01
186 187 1.108727 CCACTGGAAGCCTTGTTGCA 61.109 55.000 0.00 0.00 37.60 4.08
190 191 1.529244 GCACCACTGGAAGCCTTGT 60.529 57.895 0.71 0.00 37.60 3.16
194 195 0.543749 ATCTAGCACCACTGGAAGCC 59.456 55.000 0.71 0.00 39.62 4.35
196 197 3.834489 ATGATCTAGCACCACTGGAAG 57.166 47.619 0.71 0.00 39.62 3.46
197 198 4.290093 ACTATGATCTAGCACCACTGGAA 58.710 43.478 0.71 0.00 39.62 3.53
206 208 4.651045 TCAAGCCAGAACTATGATCTAGCA 59.349 41.667 0.00 0.00 34.53 3.49
216 218 4.245660 CAAACGATCTCAAGCCAGAACTA 58.754 43.478 0.00 0.00 0.00 2.24
246 248 4.255833 TGTTTGAAATGAACTCCATGGC 57.744 40.909 6.96 0.00 35.24 4.40
256 258 5.830457 TGTACCCAAGTCATGTTTGAAATGA 59.170 36.000 12.29 0.00 32.48 2.57
276 278 2.279935 TCAACCAACATGGGGTGTAC 57.720 50.000 11.57 0.00 46.12 2.90
281 283 1.196911 ATGCATCAACCAACATGGGG 58.803 50.000 0.00 0.14 43.37 4.96
295 297 3.869246 ACTACTAAACGCGCTTAATGCAT 59.131 39.130 5.73 0.00 43.06 3.96
297 299 3.305094 TCACTACTAAACGCGCTTAATGC 59.695 43.478 5.73 0.00 38.57 3.56
298 300 4.325204 TGTCACTACTAAACGCGCTTAATG 59.675 41.667 5.73 1.25 0.00 1.90
307 309 5.104562 TGAGACACTGTCACTACTAAACG 57.895 43.478 11.80 0.00 34.60 3.60
319 321 1.002888 CCCTTCATGCTGAGACACTGT 59.997 52.381 0.00 0.00 0.00 3.55
321 323 0.035630 GCCCTTCATGCTGAGACACT 60.036 55.000 0.00 0.00 0.00 3.55
326 328 1.134189 TCTGATGCCCTTCATGCTGAG 60.134 52.381 0.00 0.00 35.05 3.35
328 330 1.134189 TCTCTGATGCCCTTCATGCTG 60.134 52.381 0.00 0.00 35.05 4.41
374 376 3.544684 TGATTGCGGAATGCTCATTACT 58.455 40.909 6.97 0.00 46.63 2.24
384 386 7.581213 TTACCATAAGAAATGATTGCGGAAT 57.419 32.000 0.12 0.12 0.00 3.01
403 405 4.354162 GCGGGTGGGGCTTTACCA 62.354 66.667 0.00 0.00 42.05 3.25
444 455 6.127730 CCTCGGGCAAGTGAGTTATTAAAAAT 60.128 38.462 0.00 0.00 0.00 1.82
445 456 5.182380 CCTCGGGCAAGTGAGTTATTAAAAA 59.818 40.000 0.00 0.00 0.00 1.94
451 467 1.482593 CTCCTCGGGCAAGTGAGTTAT 59.517 52.381 0.00 0.00 0.00 1.89
452 468 0.895530 CTCCTCGGGCAAGTGAGTTA 59.104 55.000 0.00 0.00 0.00 2.24
454 470 1.122019 AACTCCTCGGGCAAGTGAGT 61.122 55.000 0.00 0.00 37.88 3.41
480 496 7.338449 ACAACTCAAAAGTAGAAAAGCACCTAA 59.662 33.333 0.00 0.00 33.48 2.69
487 503 6.629252 GCGAGAACAACTCAAAAGTAGAAAAG 59.371 38.462 0.00 0.00 45.14 2.27
491 507 4.745125 CAGCGAGAACAACTCAAAAGTAGA 59.255 41.667 0.00 0.00 45.14 2.59
494 510 2.032178 GCAGCGAGAACAACTCAAAAGT 59.968 45.455 0.00 0.00 45.14 2.66
504 520 1.882912 AATGTCAAGCAGCGAGAACA 58.117 45.000 0.00 0.00 0.00 3.18
505 521 2.481952 AGAAATGTCAAGCAGCGAGAAC 59.518 45.455 0.00 0.00 0.00 3.01
510 526 4.142838 TGAATACAGAAATGTCAAGCAGCG 60.143 41.667 0.00 0.00 0.00 5.18
513 529 8.453320 CACTTATGAATACAGAAATGTCAAGCA 58.547 33.333 0.00 0.00 0.00 3.91
515 531 9.764870 CACACTTATGAATACAGAAATGTCAAG 57.235 33.333 0.00 0.00 35.93 3.02
521 537 8.862325 TTCACCACACTTATGAATACAGAAAT 57.138 30.769 0.00 0.00 0.00 2.17
561 577 4.821805 GCCGGAGATAAAATCAAATCCTCA 59.178 41.667 5.05 0.00 0.00 3.86
568 584 2.622942 GCCATGCCGGAGATAAAATCAA 59.377 45.455 5.05 0.00 36.56 2.57
582 598 1.547372 ACACAAGAATCAAGCCATGCC 59.453 47.619 0.00 0.00 0.00 4.40
584 600 4.508461 TCAACACAAGAATCAAGCCATG 57.492 40.909 0.00 0.00 0.00 3.66
600 616 5.189736 AGACTAGGCACTTATCCAATCAACA 59.810 40.000 0.00 0.00 41.75 3.33
604 620 7.389053 CCAAATAGACTAGGCACTTATCCAATC 59.611 40.741 0.00 0.00 41.75 2.67
614 630 5.484715 TGTTACACCAAATAGACTAGGCAC 58.515 41.667 0.00 0.00 0.00 5.01
619 635 4.382254 CGGCCTGTTACACCAAATAGACTA 60.382 45.833 0.00 0.00 0.00 2.59
625 641 0.111639 ACCGGCCTGTTACACCAAAT 59.888 50.000 0.00 0.00 0.00 2.32
628 644 1.485294 ATCACCGGCCTGTTACACCA 61.485 55.000 0.00 0.00 0.00 4.17
633 649 0.981183 AACTGATCACCGGCCTGTTA 59.019 50.000 0.00 0.00 0.00 2.41
634 650 0.321653 GAACTGATCACCGGCCTGTT 60.322 55.000 0.00 5.05 0.00 3.16
635 651 1.296715 GAACTGATCACCGGCCTGT 59.703 57.895 0.00 0.00 0.00 4.00
636 652 1.450312 GGAACTGATCACCGGCCTG 60.450 63.158 0.00 0.00 0.00 4.85
637 653 2.990479 GGAACTGATCACCGGCCT 59.010 61.111 0.00 0.00 0.00 5.19
638 654 2.511600 CGGAACTGATCACCGGCC 60.512 66.667 13.92 0.00 42.48 6.13
639 655 1.810030 GTCGGAACTGATCACCGGC 60.810 63.158 19.65 15.85 45.61 6.13
640 656 0.037697 TTGTCGGAACTGATCACCGG 60.038 55.000 19.65 0.00 45.61 5.28
641 657 1.660607 CATTGTCGGAACTGATCACCG 59.339 52.381 15.24 15.24 46.71 4.94
642 658 2.699954 ACATTGTCGGAACTGATCACC 58.300 47.619 0.00 0.00 0.00 4.02
643 659 3.745975 TCAACATTGTCGGAACTGATCAC 59.254 43.478 0.00 0.00 0.00 3.06
644 660 4.001618 TCAACATTGTCGGAACTGATCA 57.998 40.909 0.00 0.00 0.00 2.92
645 661 4.670221 GCTTCAACATTGTCGGAACTGATC 60.670 45.833 0.00 0.00 0.00 2.92
646 662 3.189287 GCTTCAACATTGTCGGAACTGAT 59.811 43.478 0.00 0.00 0.00 2.90
647 663 2.548057 GCTTCAACATTGTCGGAACTGA 59.452 45.455 0.00 0.00 0.00 3.41
648 664 2.350772 GGCTTCAACATTGTCGGAACTG 60.351 50.000 0.00 0.00 0.00 3.16
649 665 1.880027 GGCTTCAACATTGTCGGAACT 59.120 47.619 0.00 0.00 0.00 3.01
650 666 1.606668 TGGCTTCAACATTGTCGGAAC 59.393 47.619 0.00 0.00 0.00 3.62
651 667 1.974265 TGGCTTCAACATTGTCGGAA 58.026 45.000 0.00 0.00 0.00 4.30
652 668 2.198827 ATGGCTTCAACATTGTCGGA 57.801 45.000 0.00 0.00 0.00 4.55
653 669 2.598589 CAATGGCTTCAACATTGTCGG 58.401 47.619 9.35 0.00 46.19 4.79
660 676 4.143543 TCATTGTCTCAATGGCTTCAACA 58.856 39.130 18.26 0.00 0.00 3.33
666 682 4.135306 CAGCTATCATTGTCTCAATGGCT 58.865 43.478 18.26 16.07 0.00 4.75
669 685 4.755629 CCTCCAGCTATCATTGTCTCAATG 59.244 45.833 14.05 14.05 0.00 2.82
679 695 2.905246 AGATCTGCCTCCAGCTATCAT 58.095 47.619 0.00 0.00 44.23 2.45
684 700 0.255318 CCAAAGATCTGCCTCCAGCT 59.745 55.000 0.00 0.00 44.23 4.24
705 721 1.407989 GGGAAGATTGCTGCAGCTACT 60.408 52.381 36.61 27.56 42.66 2.57
737 753 2.690786 CGGGAATTCACAAACGAGGTA 58.309 47.619 8.74 0.00 0.00 3.08
807 853 9.531158 AACTCTTCAAACCTACTGTAGTACTAT 57.469 33.333 13.42 0.00 0.00 2.12
816 862 4.628074 TCGGAAACTCTTCAAACCTACTG 58.372 43.478 0.00 0.00 32.75 2.74
817 863 4.950205 TCGGAAACTCTTCAAACCTACT 57.050 40.909 0.00 0.00 32.75 2.57
818 864 5.699458 TCATTCGGAAACTCTTCAAACCTAC 59.301 40.000 0.00 0.00 32.75 3.18
832 879 6.683110 GCATACTAGAGAGGTTCATTCGGAAA 60.683 42.308 0.00 0.00 37.23 3.13
837 884 5.537300 TGGCATACTAGAGAGGTTCATTC 57.463 43.478 0.00 0.00 0.00 2.67
839 886 5.957771 TTTGGCATACTAGAGAGGTTCAT 57.042 39.130 0.00 0.00 0.00 2.57
845 892 4.184629 AGCGTTTTTGGCATACTAGAGAG 58.815 43.478 0.00 0.00 0.00 3.20
846 893 4.202245 AGCGTTTTTGGCATACTAGAGA 57.798 40.909 0.00 0.00 0.00 3.10
847 894 4.946784 AAGCGTTTTTGGCATACTAGAG 57.053 40.909 0.00 0.00 0.00 2.43
850 897 5.637006 ATGAAAGCGTTTTTGGCATACTA 57.363 34.783 0.00 0.00 0.00 1.82
851 898 4.519540 ATGAAAGCGTTTTTGGCATACT 57.480 36.364 0.00 0.00 0.00 2.12
852 899 6.885735 AATATGAAAGCGTTTTTGGCATAC 57.114 33.333 0.00 0.00 0.00 2.39
853 900 8.409371 TCATAATATGAAAGCGTTTTTGGCATA 58.591 29.630 0.00 3.22 36.11 3.14
854 901 7.264221 TCATAATATGAAAGCGTTTTTGGCAT 58.736 30.769 0.00 0.99 36.11 4.40
855 902 6.625362 TCATAATATGAAAGCGTTTTTGGCA 58.375 32.000 0.00 0.00 36.11 4.92
856 903 7.518731 TTCATAATATGAAAGCGTTTTTGGC 57.481 32.000 12.81 0.00 45.57 4.52
870 917 6.994221 ACTACTCCCTCCGTTTCATAATATG 58.006 40.000 0.00 0.00 0.00 1.78
876 923 4.351127 AGTTACTACTCCCTCCGTTTCAT 58.649 43.478 0.00 0.00 0.00 2.57
879 926 5.718607 ACAATAGTTACTACTCCCTCCGTTT 59.281 40.000 0.00 0.00 35.78 3.60
882 929 4.885907 TGACAATAGTTACTACTCCCTCCG 59.114 45.833 0.00 0.00 35.78 4.63
883 930 6.786967 TTGACAATAGTTACTACTCCCTCC 57.213 41.667 0.00 0.00 35.78 4.30
899 946 9.267071 ACCCCTTTATTATTAGCTTTTGACAAT 57.733 29.630 0.00 0.00 0.00 2.71
906 953 9.660544 AATCATCACCCCTTTATTATTAGCTTT 57.339 29.630 0.00 0.00 0.00 3.51
1225 1276 1.000019 CGAGGGGGAGTGTGTAGGA 60.000 63.158 0.00 0.00 0.00 2.94
1371 1425 3.469863 GAACACGTGGTGGGCCTCA 62.470 63.158 21.57 0.00 37.94 3.86
1422 1476 0.179100 CGGAGATGAGCGTGTTCCAT 60.179 55.000 0.00 0.00 0.00 3.41
1465 1519 3.316283 CAAACGTAGCCATTGCATTGTT 58.684 40.909 7.75 0.00 41.13 2.83
1469 1523 3.719699 GCAAACGTAGCCATTGCAT 57.280 47.368 15.19 0.00 46.57 3.96
1479 1533 4.453183 GCCATGCGCGCAAACGTA 62.453 61.111 39.68 14.53 42.83 3.57
1530 1587 2.258591 GAGAGCAGCGTCGTCCAA 59.741 61.111 0.00 0.00 0.00 3.53
1623 1680 4.424566 GCCACGGACTCGGCGTTA 62.425 66.667 6.85 0.00 38.82 3.18
1685 1742 0.393077 ATGTATCGCCCTCCCTTTCG 59.607 55.000 0.00 0.00 0.00 3.46
1731 1788 2.048503 ACGAACAGGTAGCCACGC 60.049 61.111 0.00 0.00 0.00 5.34
1749 1806 1.668151 GCACACCAGGGAGTTCGTC 60.668 63.158 0.00 0.00 0.00 4.20
1752 1809 0.250901 ACATGCACACCAGGGAGTTC 60.251 55.000 0.00 0.00 0.00 3.01
1758 1815 2.398554 GCCGTACATGCACACCAGG 61.399 63.158 0.00 0.00 0.00 4.45
2106 2163 4.530857 GCATGGACCTCCCGACCG 62.531 72.222 0.00 0.00 37.93 4.79
2127 2184 0.032540 CGACCATGGATCTGATCGCA 59.967 55.000 21.47 10.58 0.00 5.10
2424 2481 3.005155 TGTGCTCCAGTATCATCTGATCG 59.995 47.826 0.00 0.00 37.61 3.69
2499 2556 2.034687 TCCTTGAGCAAGCCAGCC 59.965 61.111 4.72 0.00 37.11 4.85
2502 2559 2.034687 GCCTCCTTGAGCAAGCCA 59.965 61.111 4.72 0.00 37.11 4.75
2545 2602 4.101448 GCACAGGTCGGCTCCCAT 62.101 66.667 0.00 0.00 0.00 4.00
2571 2628 3.485431 CAGGAGTTGAGCAGCGCG 61.485 66.667 0.00 0.00 0.00 6.86
2654 2711 3.798511 TGTGGTTGCCGGTGGTCA 61.799 61.111 1.90 0.00 0.00 4.02
2742 2799 3.689002 CTTCCTCAAGCCGGCCTCC 62.689 68.421 26.15 0.00 0.00 4.30
2779 2836 3.279434 ACACCTTGTTCTTCACCTCAAC 58.721 45.455 0.00 0.00 0.00 3.18
2781 2838 3.644966 AACACCTTGTTCTTCACCTCA 57.355 42.857 0.00 0.00 35.27 3.86
2850 2907 0.791238 CGTCGAGCACTCTGAAGACG 60.791 60.000 10.09 10.09 43.79 4.18
2851 2908 0.517755 TCGTCGAGCACTCTGAAGAC 59.482 55.000 0.00 0.00 0.00 3.01
2877 2934 0.534873 TCTGGTCATCCATTTCGCGA 59.465 50.000 3.71 3.71 43.43 5.87
2878 2935 0.933097 CTCTGGTCATCCATTTCGCG 59.067 55.000 0.00 0.00 43.43 5.87
2889 2946 2.004808 CTATGGCGCGTCTCTGGTCA 62.005 60.000 13.81 0.00 0.00 4.02
2893 2950 1.007964 CCTCTATGGCGCGTCTCTG 60.008 63.158 13.81 1.21 0.00 3.35
2902 2959 3.072184 ACAATGTGATCCTCCTCTATGGC 59.928 47.826 0.00 0.00 35.26 4.40
2907 2964 4.223032 ACGTTTACAATGTGATCCTCCTCT 59.777 41.667 0.00 0.00 0.00 3.69
2913 2970 7.970384 TCTATCAAACGTTTACAATGTGATCC 58.030 34.615 14.20 0.00 0.00 3.36
2927 2987 7.355778 CAAAAGCTTTCTCTTCTATCAAACGT 58.644 34.615 13.10 0.00 0.00 3.99
2947 3007 7.862873 TGTACGAGATACATCTATCTGCAAAAG 59.137 37.037 0.00 0.00 39.47 2.27
2948 3008 7.712797 TGTACGAGATACATCTATCTGCAAAA 58.287 34.615 0.00 0.00 39.47 2.44
2954 3014 5.645929 CCTGCTGTACGAGATACATCTATCT 59.354 44.000 0.00 0.00 43.01 1.98
2959 3019 2.034685 TGCCTGCTGTACGAGATACATC 59.965 50.000 0.00 0.00 43.01 3.06
2961 3021 1.470051 TGCCTGCTGTACGAGATACA 58.530 50.000 0.00 0.00 41.71 2.29
2962 3022 2.579207 TTGCCTGCTGTACGAGATAC 57.421 50.000 0.00 0.00 0.00 2.24
2992 3052 2.832129 TCGCCCAAGTTCTTCAGTATCT 59.168 45.455 0.00 0.00 0.00 1.98
2993 3053 3.190874 CTCGCCCAAGTTCTTCAGTATC 58.809 50.000 0.00 0.00 0.00 2.24
2995 3055 1.337823 GCTCGCCCAAGTTCTTCAGTA 60.338 52.381 0.00 0.00 0.00 2.74
2996 3056 0.603975 GCTCGCCCAAGTTCTTCAGT 60.604 55.000 0.00 0.00 0.00 3.41
2999 3059 1.916697 GCAGCTCGCCCAAGTTCTTC 61.917 60.000 0.00 0.00 32.94 2.87
3000 3060 1.968540 GCAGCTCGCCCAAGTTCTT 60.969 57.895 0.00 0.00 32.94 2.52
3001 3061 2.359230 GCAGCTCGCCCAAGTTCT 60.359 61.111 0.00 0.00 32.94 3.01
3002 3062 2.669569 TGCAGCTCGCCCAAGTTC 60.670 61.111 5.82 0.00 41.33 3.01
3003 3063 2.670934 CTGCAGCTCGCCCAAGTT 60.671 61.111 0.00 0.00 41.33 2.66
3004 3064 3.602513 CTCTGCAGCTCGCCCAAGT 62.603 63.158 9.47 0.00 41.33 3.16
3005 3065 2.818714 CTCTGCAGCTCGCCCAAG 60.819 66.667 9.47 0.00 41.33 3.61
3006 3066 3.630013 ACTCTGCAGCTCGCCCAA 61.630 61.111 9.47 0.00 41.33 4.12
3007 3067 4.383861 CACTCTGCAGCTCGCCCA 62.384 66.667 9.47 0.00 41.33 5.36
3008 3068 3.890936 AACACTCTGCAGCTCGCCC 62.891 63.158 9.47 0.00 41.33 6.13
3009 3069 2.358003 AACACTCTGCAGCTCGCC 60.358 61.111 9.47 0.00 41.33 5.54
3010 3070 1.624865 CTGAACACTCTGCAGCTCGC 61.625 60.000 9.47 1.70 42.89 5.03
3011 3071 0.038801 TCTGAACACTCTGCAGCTCG 60.039 55.000 9.47 2.20 0.00 5.03
3012 3072 1.000731 ACTCTGAACACTCTGCAGCTC 59.999 52.381 9.47 0.92 0.00 4.09
3013 3073 1.047002 ACTCTGAACACTCTGCAGCT 58.953 50.000 9.47 0.00 0.00 4.24
3014 3074 1.146637 CACTCTGAACACTCTGCAGC 58.853 55.000 9.47 0.00 0.00 5.25
3015 3075 1.342496 TCCACTCTGAACACTCTGCAG 59.658 52.381 7.63 7.63 0.00 4.41
3016 3076 1.413118 TCCACTCTGAACACTCTGCA 58.587 50.000 0.00 0.00 0.00 4.41
3017 3077 2.139118 GTTCCACTCTGAACACTCTGC 58.861 52.381 0.00 0.00 43.27 4.26
3018 3078 3.742433 AGTTCCACTCTGAACACTCTG 57.258 47.619 6.67 0.00 45.62 3.35
3019 3079 3.452627 ACAAGTTCCACTCTGAACACTCT 59.547 43.478 6.67 0.00 45.62 3.24
3020 3080 3.557595 CACAAGTTCCACTCTGAACACTC 59.442 47.826 6.67 0.00 45.62 3.51
3021 3081 3.197766 TCACAAGTTCCACTCTGAACACT 59.802 43.478 6.67 0.00 45.62 3.55
3022 3082 3.531538 TCACAAGTTCCACTCTGAACAC 58.468 45.455 6.67 0.00 45.62 3.32
3023 3083 3.797039 CTCACAAGTTCCACTCTGAACA 58.203 45.455 6.67 0.00 45.62 3.18
3024 3084 2.545946 GCTCACAAGTTCCACTCTGAAC 59.454 50.000 0.00 0.00 43.95 3.18
3035 3095 2.760374 CTCTTCTTCGGCTCACAAGTT 58.240 47.619 0.00 0.00 0.00 2.66
3036 3096 1.606737 GCTCTTCTTCGGCTCACAAGT 60.607 52.381 0.00 0.00 0.00 3.16
3044 3104 1.153469 CCTCAGGCTCTTCTTCGGC 60.153 63.158 0.00 0.00 0.00 5.54
3179 3239 0.834687 ACAACCCCTTCACTAGGCGA 60.835 55.000 0.00 0.00 43.27 5.54
3329 3389 1.024271 TGCTGCTCTGTTTTGACCAC 58.976 50.000 0.00 0.00 0.00 4.16
3362 3427 0.464036 AACAGCTGAACACCGAGTCA 59.536 50.000 23.35 0.00 0.00 3.41
3364 3429 0.464036 TGAACAGCTGAACACCGAGT 59.536 50.000 23.35 0.00 0.00 4.18
3365 3430 0.861837 GTGAACAGCTGAACACCGAG 59.138 55.000 23.35 0.00 0.00 4.63
3366 3431 0.874175 CGTGAACAGCTGAACACCGA 60.874 55.000 27.61 5.83 0.00 4.69
3367 3432 1.564622 CGTGAACAGCTGAACACCG 59.435 57.895 27.61 21.83 0.00 4.94
3368 3433 0.814010 ACCGTGAACAGCTGAACACC 60.814 55.000 27.61 17.20 0.00 4.16
3369 3434 1.860676 TACCGTGAACAGCTGAACAC 58.139 50.000 23.35 24.89 0.00 3.32
3370 3435 2.805671 CAATACCGTGAACAGCTGAACA 59.194 45.455 23.35 16.46 0.00 3.18
3371 3436 2.412847 GCAATACCGTGAACAGCTGAAC 60.413 50.000 23.35 14.18 0.00 3.18
3372 3437 1.804151 GCAATACCGTGAACAGCTGAA 59.196 47.619 23.35 2.14 0.00 3.02
3373 3438 1.438651 GCAATACCGTGAACAGCTGA 58.561 50.000 23.35 0.00 0.00 4.26
3374 3439 0.447801 GGCAATACCGTGAACAGCTG 59.552 55.000 13.48 13.48 0.00 4.24
3375 3440 0.324943 AGGCAATACCGTGAACAGCT 59.675 50.000 0.00 0.00 46.52 4.24
3376 3441 1.664151 GTAGGCAATACCGTGAACAGC 59.336 52.381 0.00 0.00 46.52 4.40
3377 3442 2.277084 GGTAGGCAATACCGTGAACAG 58.723 52.381 1.94 0.00 44.61 3.16
3489 3561 3.591254 GACGAGTGGTCCACCTGGC 62.591 68.421 18.80 9.78 39.90 4.85
3541 3613 1.134965 CACTTCATCGACAGGGAGTCC 60.135 57.143 0.00 0.00 44.66 3.85
3719 3803 2.911509 AAGTGCAATGGCCACGCA 60.912 55.556 24.21 24.21 40.13 5.24
3863 3974 2.606519 TCCAGCTAACACCGGCCT 60.607 61.111 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.