Multiple sequence alignment - TraesCS5B01G115700

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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 TraesCS5B01G115700 chr5B 100.000 3738 0 0 1 3738 196235948 196239685 0.000000e+00 6903.0
1 TraesCS5B01G115700 chr5D 94.204 2778 107 17 1000 3738 191902482 191905244 0.000000e+00 4189.0
2 TraesCS5B01G115700 chr5A 93.277 2112 83 16 1672 3738 229926158 229924061 0.000000e+00 3059.0
3 TraesCS5B01G115700 chr5A 93.804 581 26 3 1000 1580 229926720 229926150 0.000000e+00 865.0
4 TraesCS5B01G115700 chr1B 85.754 723 99 3 4 725 683413395 683412676 0.000000e+00 761.0
5 TraesCS5B01G115700 chr3A 90.888 439 32 3 3304 3738 589373300 589373734 1.930000e-162 582.0
6 TraesCS5B01G115700 chr1A 81.667 660 113 7 4 661 59995052 59994399 3.280000e-150 542.0
7 TraesCS5B01G115700 chr3D 86.538 468 33 11 3272 3734 447632227 447632669 4.340000e-134 488.0
8 TraesCS5B01G115700 chr7A 85.787 197 28 0 1 197 158839475 158839671 3.780000e-50 209.0
9 TraesCS5B01G115700 chr7A 100.000 29 0 0 1796 1824 33191354 33191382 2.000000e-03 54.7
10 TraesCS5B01G115700 chr3B 83.663 202 10 12 3538 3738 586862220 586862399 6.420000e-38 169.0
11 TraesCS5B01G115700 chr7D 100.000 29 0 0 1796 1824 32944316 32944344 2.000000e-03 54.7


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 TraesCS5B01G115700 chr5B 196235948 196239685 3737 False 6903 6903 100.0000 1 3738 1 chr5B.!!$F1 3737
1 TraesCS5B01G115700 chr5D 191902482 191905244 2762 False 4189 4189 94.2040 1000 3738 1 chr5D.!!$F1 2738
2 TraesCS5B01G115700 chr5A 229924061 229926720 2659 True 1962 3059 93.5405 1000 3738 2 chr5A.!!$R1 2738
3 TraesCS5B01G115700 chr1B 683412676 683413395 719 True 761 761 85.7540 4 725 1 chr1B.!!$R1 721
4 TraesCS5B01G115700 chr1A 59994399 59995052 653 True 542 542 81.6670 4 661 1 chr1A.!!$R1 657

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
117 118 0.035630 GCACTCTTCTCCCATGCTGT 60.036 55.0 0.0 0.0 33.44 4.40 F
718 723 0.106268 TGGTCTTCCAAAGGCAGCAA 60.106 50.0 0.0 0.0 41.25 3.91 F
924 929 0.108019 CCGCTACCTTGGGGTTATCC 59.892 60.0 0.0 0.0 44.73 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 1678 0.249868 TCTTTCTCACCTGCACACGG 60.250 55.0 0.0 0.0 0.0 4.94 R
2575 2614 0.035343 AGTCGTCGTCATCCTCCTCA 60.035 55.0 0.0 0.0 0.0 3.86 R
2915 2958 6.913170 TCATAGAAACTTCAAACTGGAATGC 58.087 36.0 0.0 0.0 0.0 3.56 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
58 59 1.298014 CTGCTCCTTCTGGTGGGAC 59.702 63.158 0.00 0.00 34.23 4.46
115 116 1.220206 CGCACTCTTCTCCCATGCT 59.780 57.895 0.00 0.00 34.06 3.79
116 117 1.088340 CGCACTCTTCTCCCATGCTG 61.088 60.000 0.00 0.00 34.06 4.41
117 118 0.035630 GCACTCTTCTCCCATGCTGT 60.036 55.000 0.00 0.00 33.44 4.40
118 119 2.011046 GCACTCTTCTCCCATGCTGTC 61.011 57.143 0.00 0.00 33.44 3.51
121 122 1.411977 CTCTTCTCCCATGCTGTCGAT 59.588 52.381 0.00 0.00 0.00 3.59
123 124 0.178767 TTCTCCCATGCTGTCGATGG 59.821 55.000 0.00 0.00 40.25 3.51
192 193 3.260100 CCCCAGGCTGACAAGGGT 61.260 66.667 17.94 0.00 39.76 4.34
197 198 4.284550 GGCTGACAAGGGTGGGCA 62.285 66.667 0.00 0.00 0.00 5.36
198 199 2.985847 GCTGACAAGGGTGGGCAC 60.986 66.667 0.00 0.00 0.00 5.01
217 218 2.281070 AGTGAACTGCAGGCCGTG 60.281 61.111 19.93 0.00 0.00 4.94
231 232 3.062466 CGTGTCGGCTCTCCTGGA 61.062 66.667 0.00 0.00 0.00 3.86
266 267 3.596799 TGGGGGAGGACACGAGGA 61.597 66.667 0.00 0.00 0.00 3.71
267 268 3.075641 GGGGGAGGACACGAGGAC 61.076 72.222 0.00 0.00 0.00 3.85
367 368 1.819632 GGGCTTCGCGGACATGATT 60.820 57.895 6.13 0.00 0.00 2.57
373 374 1.748879 CGCGGACATGATTTGGGGT 60.749 57.895 0.00 0.00 0.00 4.95
376 377 0.964860 CGGACATGATTTGGGGTGCA 60.965 55.000 0.00 0.00 0.00 4.57
380 381 1.682005 ATGATTTGGGGTGCACGGG 60.682 57.895 11.45 0.00 0.00 5.28
412 413 2.483877 CGTGCAATTCTTCAGCTGGTTA 59.516 45.455 15.13 0.00 0.00 2.85
427 428 1.448013 GTTACTGGTCCAGAGGCGC 60.448 63.158 26.18 0.00 35.18 6.53
437 438 0.807667 CCAGAGGCGCATACACACTC 60.808 60.000 10.83 4.40 0.00 3.51
442 443 0.249073 GGCGCATACACACTCGAGAT 60.249 55.000 21.68 3.45 0.00 2.75
448 449 3.429547 GCATACACACTCGAGATGTCCTT 60.430 47.826 23.89 12.04 0.00 3.36
451 452 2.230025 ACACACTCGAGATGTCCTTCTG 59.770 50.000 21.68 5.86 0.00 3.02
468 469 3.478394 GCGCAAGTGCATCGTCGA 61.478 61.111 0.30 0.00 42.21 4.20
520 521 3.470888 CCCTTGGAGACGGCCGAT 61.471 66.667 35.90 20.71 0.00 4.18
527 528 1.141881 GAGACGGCCGATCACATGT 59.858 57.895 35.90 6.28 0.00 3.21
529 530 0.740868 AGACGGCCGATCACATGTTG 60.741 55.000 35.90 0.00 0.00 3.33
562 563 2.592308 GCGAGGGCCTTCTGGAAT 59.408 61.111 7.89 0.00 34.57 3.01
563 564 1.821332 GCGAGGGCCTTCTGGAATG 60.821 63.158 7.89 0.00 34.57 2.67
568 569 0.465278 GGGCCTTCTGGAATGAGCTC 60.465 60.000 6.82 6.82 34.57 4.09
574 575 1.448540 CTGGAATGAGCTCGGCGTT 60.449 57.895 9.64 1.12 0.00 4.84
575 576 0.179111 CTGGAATGAGCTCGGCGTTA 60.179 55.000 9.64 0.00 0.00 3.18
578 579 0.297820 GAATGAGCTCGGCGTTAACG 59.702 55.000 23.40 23.40 43.27 3.18
638 643 4.386951 CGGTGGGTGCGGTGATCA 62.387 66.667 0.00 0.00 0.00 2.92
667 672 0.319900 TGGAGTTCGCTCTTCTGTGC 60.320 55.000 0.00 0.00 43.59 4.57
697 702 0.534203 TCTGGAAACACAGGAACGCC 60.534 55.000 0.00 0.00 38.98 5.68
707 712 2.741211 GGAACGCCGTGGTCTTCC 60.741 66.667 0.00 0.00 0.00 3.46
709 714 1.595929 GAACGCCGTGGTCTTCCAA 60.596 57.895 0.00 0.00 46.15 3.53
717 722 0.823356 GTGGTCTTCCAAAGGCAGCA 60.823 55.000 0.00 0.00 46.15 4.41
718 723 0.106268 TGGTCTTCCAAAGGCAGCAA 60.106 50.000 0.00 0.00 41.25 3.91
719 724 0.315251 GGTCTTCCAAAGGCAGCAAC 59.685 55.000 0.00 0.00 33.90 4.17
720 725 0.315251 GTCTTCCAAAGGCAGCAACC 59.685 55.000 0.00 0.00 32.07 3.77
721 726 1.172180 TCTTCCAAAGGCAGCAACCG 61.172 55.000 0.00 0.00 33.69 4.44
722 727 1.454847 TTCCAAAGGCAGCAACCGT 60.455 52.632 0.00 0.00 33.69 4.83
723 728 1.452145 TTCCAAAGGCAGCAACCGTC 61.452 55.000 0.00 0.00 33.69 4.79
724 729 1.898574 CCAAAGGCAGCAACCGTCT 60.899 57.895 0.00 0.00 33.69 4.18
725 730 1.576421 CAAAGGCAGCAACCGTCTC 59.424 57.895 0.00 0.00 33.69 3.36
726 731 0.886490 CAAAGGCAGCAACCGTCTCT 60.886 55.000 0.00 0.00 33.69 3.10
727 732 0.886490 AAAGGCAGCAACCGTCTCTG 60.886 55.000 0.00 0.00 33.69 3.35
729 734 3.782244 GCAGCAACCGTCTCTGCG 61.782 66.667 8.60 0.00 42.86 5.18
736 741 4.742201 CCGTCTCTGCGGTGGGTG 62.742 72.222 0.00 0.00 46.11 4.61
738 743 4.008933 GTCTCTGCGGTGGGTGCT 62.009 66.667 0.00 0.00 0.00 4.40
739 744 3.241530 TCTCTGCGGTGGGTGCTT 61.242 61.111 0.00 0.00 0.00 3.91
740 745 3.052082 CTCTGCGGTGGGTGCTTG 61.052 66.667 0.00 0.00 0.00 4.01
741 746 4.641645 TCTGCGGTGGGTGCTTGG 62.642 66.667 0.00 0.00 0.00 3.61
742 747 4.641645 CTGCGGTGGGTGCTTGGA 62.642 66.667 0.00 0.00 0.00 3.53
743 748 3.925630 CTGCGGTGGGTGCTTGGAT 62.926 63.158 0.00 0.00 0.00 3.41
744 749 3.443045 GCGGTGGGTGCTTGGATG 61.443 66.667 0.00 0.00 0.00 3.51
745 750 3.443045 CGGTGGGTGCTTGGATGC 61.443 66.667 0.00 0.00 0.00 3.91
746 751 2.036256 GGTGGGTGCTTGGATGCT 59.964 61.111 0.00 0.00 0.00 3.79
747 752 2.345760 GGTGGGTGCTTGGATGCTG 61.346 63.158 0.00 0.00 0.00 4.41
748 753 2.677524 TGGGTGCTTGGATGCTGC 60.678 61.111 0.00 0.00 0.00 5.25
749 754 3.455469 GGGTGCTTGGATGCTGCC 61.455 66.667 0.00 0.00 0.00 4.85
750 755 3.818787 GGTGCTTGGATGCTGCCG 61.819 66.667 0.00 0.00 0.00 5.69
751 756 4.487412 GTGCTTGGATGCTGCCGC 62.487 66.667 0.00 0.00 0.00 6.53
754 759 3.570638 CTTGGATGCTGCCGCGAG 61.571 66.667 8.23 0.00 39.65 5.03
768 773 2.805353 CGAGGACGCCGTTCTGTG 60.805 66.667 0.87 0.00 0.00 3.66
769 774 2.432628 GAGGACGCCGTTCTGTGG 60.433 66.667 0.87 0.00 0.00 4.17
776 781 3.554692 CCGTTCTGTGGCGCGATC 61.555 66.667 12.10 0.51 0.00 3.69
777 782 3.902063 CGTTCTGTGGCGCGATCG 61.902 66.667 12.10 11.69 39.07 3.69
778 783 3.554692 GTTCTGTGGCGCGATCGG 61.555 66.667 18.30 8.23 35.95 4.18
808 813 2.738521 CGGAGGGTGCACGTTGAG 60.739 66.667 11.45 0.00 0.00 3.02
809 814 2.741092 GGAGGGTGCACGTTGAGA 59.259 61.111 11.45 0.00 0.00 3.27
810 815 1.070786 GGAGGGTGCACGTTGAGAA 59.929 57.895 11.45 0.00 0.00 2.87
811 816 1.228657 GGAGGGTGCACGTTGAGAAC 61.229 60.000 11.45 0.00 0.00 3.01
812 817 0.249911 GAGGGTGCACGTTGAGAACT 60.250 55.000 11.45 0.00 0.00 3.01
813 818 0.532862 AGGGTGCACGTTGAGAACTG 60.533 55.000 11.45 0.00 0.00 3.16
814 819 1.507141 GGGTGCACGTTGAGAACTGG 61.507 60.000 11.45 0.00 0.00 4.00
815 820 1.279840 GTGCACGTTGAGAACTGGC 59.720 57.895 0.00 0.00 0.00 4.85
816 821 1.146041 TGCACGTTGAGAACTGGCT 59.854 52.632 0.00 0.00 0.00 4.75
817 822 1.159713 TGCACGTTGAGAACTGGCTG 61.160 55.000 0.00 0.00 0.00 4.85
818 823 1.571460 CACGTTGAGAACTGGCTGC 59.429 57.895 0.00 0.00 0.00 5.25
819 824 1.146041 ACGTTGAGAACTGGCTGCA 59.854 52.632 0.50 0.00 0.00 4.41
820 825 0.882042 ACGTTGAGAACTGGCTGCAG 60.882 55.000 10.11 10.11 0.00 4.41
821 826 1.572085 CGTTGAGAACTGGCTGCAGG 61.572 60.000 17.12 0.73 0.00 4.85
822 827 1.601759 TTGAGAACTGGCTGCAGGC 60.602 57.895 31.92 31.92 41.50 4.85
831 836 3.397439 GCTGCAGGCCCTCTCAGA 61.397 66.667 17.12 0.00 34.27 3.27
832 837 2.964310 GCTGCAGGCCCTCTCAGAA 61.964 63.158 17.12 0.00 34.27 3.02
833 838 1.913722 CTGCAGGCCCTCTCAGAAT 59.086 57.895 5.57 0.00 0.00 2.40
834 839 1.126488 CTGCAGGCCCTCTCAGAATA 58.874 55.000 5.57 0.00 0.00 1.75
835 840 1.070445 CTGCAGGCCCTCTCAGAATAG 59.930 57.143 5.57 0.00 0.00 1.73
836 841 1.343377 TGCAGGCCCTCTCAGAATAGA 60.343 52.381 0.00 0.00 0.00 1.98
837 842 1.765314 GCAGGCCCTCTCAGAATAGAA 59.235 52.381 0.00 0.00 0.00 2.10
838 843 2.224257 GCAGGCCCTCTCAGAATAGAAG 60.224 54.545 0.00 0.00 0.00 2.85
839 844 3.037549 CAGGCCCTCTCAGAATAGAAGT 58.962 50.000 0.00 0.00 0.00 3.01
840 845 4.219115 CAGGCCCTCTCAGAATAGAAGTA 58.781 47.826 0.00 0.00 0.00 2.24
841 846 4.280677 CAGGCCCTCTCAGAATAGAAGTAG 59.719 50.000 0.00 0.00 0.00 2.57
842 847 3.006430 GGCCCTCTCAGAATAGAAGTAGC 59.994 52.174 0.00 0.00 0.00 3.58
843 848 3.006430 GCCCTCTCAGAATAGAAGTAGCC 59.994 52.174 0.00 0.00 0.00 3.93
844 849 4.479158 CCCTCTCAGAATAGAAGTAGCCT 58.521 47.826 0.00 0.00 0.00 4.58
845 850 5.636123 CCCTCTCAGAATAGAAGTAGCCTA 58.364 45.833 0.00 0.00 0.00 3.93
846 851 6.252995 CCCTCTCAGAATAGAAGTAGCCTAT 58.747 44.000 0.00 0.00 0.00 2.57
847 852 6.377146 CCCTCTCAGAATAGAAGTAGCCTATC 59.623 46.154 0.00 0.00 0.00 2.08
848 853 6.093495 CCTCTCAGAATAGAAGTAGCCTATCG 59.907 46.154 0.00 0.00 0.00 2.92
849 854 6.535540 TCTCAGAATAGAAGTAGCCTATCGT 58.464 40.000 0.00 0.00 0.00 3.73
850 855 6.651643 TCTCAGAATAGAAGTAGCCTATCGTC 59.348 42.308 0.00 0.00 0.00 4.20
851 856 5.706369 TCAGAATAGAAGTAGCCTATCGTCC 59.294 44.000 0.00 0.00 0.00 4.79
852 857 5.708230 CAGAATAGAAGTAGCCTATCGTCCT 59.292 44.000 0.00 0.00 0.00 3.85
853 858 6.207810 CAGAATAGAAGTAGCCTATCGTCCTT 59.792 42.308 0.00 0.00 0.00 3.36
854 859 6.778559 AGAATAGAAGTAGCCTATCGTCCTTT 59.221 38.462 0.00 0.00 0.00 3.11
855 860 6.980416 ATAGAAGTAGCCTATCGTCCTTTT 57.020 37.500 0.00 0.00 0.00 2.27
856 861 8.474710 AATAGAAGTAGCCTATCGTCCTTTTA 57.525 34.615 0.00 0.00 0.00 1.52
857 862 6.980416 AGAAGTAGCCTATCGTCCTTTTAT 57.020 37.500 0.00 0.00 0.00 1.40
858 863 6.983984 AGAAGTAGCCTATCGTCCTTTTATC 58.016 40.000 0.00 0.00 0.00 1.75
859 864 5.725325 AGTAGCCTATCGTCCTTTTATCC 57.275 43.478 0.00 0.00 0.00 2.59
860 865 4.527427 AGTAGCCTATCGTCCTTTTATCCC 59.473 45.833 0.00 0.00 0.00 3.85
861 866 3.588569 AGCCTATCGTCCTTTTATCCCT 58.411 45.455 0.00 0.00 0.00 4.20
862 867 3.579151 AGCCTATCGTCCTTTTATCCCTC 59.421 47.826 0.00 0.00 0.00 4.30
863 868 3.579151 GCCTATCGTCCTTTTATCCCTCT 59.421 47.826 0.00 0.00 0.00 3.69
864 869 4.322123 GCCTATCGTCCTTTTATCCCTCTC 60.322 50.000 0.00 0.00 0.00 3.20
865 870 5.081032 CCTATCGTCCTTTTATCCCTCTCT 58.919 45.833 0.00 0.00 0.00 3.10
866 871 5.184287 CCTATCGTCCTTTTATCCCTCTCTC 59.816 48.000 0.00 0.00 0.00 3.20
867 872 4.252570 TCGTCCTTTTATCCCTCTCTCT 57.747 45.455 0.00 0.00 0.00 3.10
868 873 4.208746 TCGTCCTTTTATCCCTCTCTCTC 58.791 47.826 0.00 0.00 0.00 3.20
869 874 4.079672 TCGTCCTTTTATCCCTCTCTCTCT 60.080 45.833 0.00 0.00 0.00 3.10
870 875 4.277423 CGTCCTTTTATCCCTCTCTCTCTC 59.723 50.000 0.00 0.00 0.00 3.20
871 876 5.454966 GTCCTTTTATCCCTCTCTCTCTCT 58.545 45.833 0.00 0.00 0.00 3.10
872 877 5.535030 GTCCTTTTATCCCTCTCTCTCTCTC 59.465 48.000 0.00 0.00 0.00 3.20
873 878 5.435041 TCCTTTTATCCCTCTCTCTCTCTCT 59.565 44.000 0.00 0.00 0.00 3.10
874 879 5.770162 CCTTTTATCCCTCTCTCTCTCTCTC 59.230 48.000 0.00 0.00 0.00 3.20
875 880 6.410853 CCTTTTATCCCTCTCTCTCTCTCTCT 60.411 46.154 0.00 0.00 0.00 3.10
876 881 5.567037 TTATCCCTCTCTCTCTCTCTCTG 57.433 47.826 0.00 0.00 0.00 3.35
877 882 2.845659 TCCCTCTCTCTCTCTCTCTGT 58.154 52.381 0.00 0.00 0.00 3.41
878 883 2.505407 TCCCTCTCTCTCTCTCTCTGTG 59.495 54.545 0.00 0.00 0.00 3.66
879 884 2.239654 CCCTCTCTCTCTCTCTCTGTGT 59.760 54.545 0.00 0.00 0.00 3.72
880 885 3.273434 CCTCTCTCTCTCTCTCTGTGTG 58.727 54.545 0.00 0.00 0.00 3.82
881 886 3.307691 CCTCTCTCTCTCTCTCTGTGTGT 60.308 52.174 0.00 0.00 0.00 3.72
882 887 4.081142 CCTCTCTCTCTCTCTCTGTGTGTA 60.081 50.000 0.00 0.00 0.00 2.90
883 888 5.396772 CCTCTCTCTCTCTCTCTGTGTGTAT 60.397 48.000 0.00 0.00 0.00 2.29
884 889 6.061022 TCTCTCTCTCTCTCTGTGTGTATT 57.939 41.667 0.00 0.00 0.00 1.89
885 890 6.112734 TCTCTCTCTCTCTCTGTGTGTATTC 58.887 44.000 0.00 0.00 0.00 1.75
886 891 6.061022 TCTCTCTCTCTCTGTGTGTATTCT 57.939 41.667 0.00 0.00 0.00 2.40
887 892 6.112734 TCTCTCTCTCTCTGTGTGTATTCTC 58.887 44.000 0.00 0.00 0.00 2.87
888 893 4.873259 TCTCTCTCTCTGTGTGTATTCTCG 59.127 45.833 0.00 0.00 0.00 4.04
889 894 3.942115 TCTCTCTCTGTGTGTATTCTCGG 59.058 47.826 0.00 0.00 0.00 4.63
890 895 3.017442 TCTCTCTGTGTGTATTCTCGGG 58.983 50.000 0.00 0.00 0.00 5.14
891 896 1.476891 TCTCTGTGTGTATTCTCGGGC 59.523 52.381 0.00 0.00 0.00 6.13
892 897 1.204704 CTCTGTGTGTATTCTCGGGCA 59.795 52.381 0.00 0.00 0.00 5.36
893 898 1.831106 TCTGTGTGTATTCTCGGGCAT 59.169 47.619 0.00 0.00 0.00 4.40
894 899 2.159099 TCTGTGTGTATTCTCGGGCATC 60.159 50.000 0.00 0.00 0.00 3.91
895 900 1.831106 TGTGTGTATTCTCGGGCATCT 59.169 47.619 0.00 0.00 0.00 2.90
896 901 2.205074 GTGTGTATTCTCGGGCATCTG 58.795 52.381 0.00 0.00 0.00 2.90
897 902 1.831106 TGTGTATTCTCGGGCATCTGT 59.169 47.619 0.00 0.00 0.00 3.41
898 903 3.028130 TGTGTATTCTCGGGCATCTGTA 58.972 45.455 0.00 0.00 0.00 2.74
899 904 3.449377 TGTGTATTCTCGGGCATCTGTAA 59.551 43.478 0.00 0.00 0.00 2.41
900 905 4.081365 TGTGTATTCTCGGGCATCTGTAAA 60.081 41.667 0.00 0.00 0.00 2.01
901 906 4.873827 GTGTATTCTCGGGCATCTGTAAAA 59.126 41.667 0.00 0.00 0.00 1.52
902 907 5.006746 GTGTATTCTCGGGCATCTGTAAAAG 59.993 44.000 0.00 0.00 0.00 2.27
903 908 2.691409 TCTCGGGCATCTGTAAAAGG 57.309 50.000 0.00 0.00 0.00 3.11
904 909 1.209504 TCTCGGGCATCTGTAAAAGGG 59.790 52.381 0.00 0.00 0.00 3.95
905 910 0.393808 TCGGGCATCTGTAAAAGGGC 60.394 55.000 0.00 0.00 0.00 5.19
906 911 1.384222 CGGGCATCTGTAAAAGGGCC 61.384 60.000 0.00 0.00 42.65 5.80
907 912 1.384222 GGGCATCTGTAAAAGGGCCG 61.384 60.000 0.00 0.00 43.65 6.13
908 913 1.433471 GCATCTGTAAAAGGGCCGC 59.567 57.895 0.00 0.00 0.00 6.53
909 914 1.032114 GCATCTGTAAAAGGGCCGCT 61.032 55.000 0.00 0.00 0.00 5.52
910 915 1.745827 GCATCTGTAAAAGGGCCGCTA 60.746 52.381 0.00 0.00 0.00 4.26
911 916 1.940613 CATCTGTAAAAGGGCCGCTAC 59.059 52.381 0.00 1.67 0.00 3.58
912 917 0.251073 TCTGTAAAAGGGCCGCTACC 59.749 55.000 0.00 0.00 0.00 3.18
913 918 0.252197 CTGTAAAAGGGCCGCTACCT 59.748 55.000 0.00 0.00 40.96 3.08
917 922 3.728373 AAGGGCCGCTACCTTGGG 61.728 66.667 0.00 0.00 46.21 4.12
920 925 4.043100 GGCCGCTACCTTGGGGTT 62.043 66.667 0.00 0.00 44.73 4.11
921 926 2.672181 GGCCGCTACCTTGGGGTTA 61.672 63.158 0.00 0.00 44.73 2.85
922 927 1.530283 GCCGCTACCTTGGGGTTAT 59.470 57.895 0.00 0.00 44.73 1.89
923 928 0.534427 GCCGCTACCTTGGGGTTATC 60.534 60.000 0.00 0.00 44.73 1.75
924 929 0.108019 CCGCTACCTTGGGGTTATCC 59.892 60.000 0.00 0.00 44.73 2.59
937 942 3.320673 GGTTATCCCCTGATCATCGTC 57.679 52.381 0.00 0.00 32.18 4.20
938 943 2.632996 GGTTATCCCCTGATCATCGTCA 59.367 50.000 0.00 0.00 32.18 4.35
939 944 3.071023 GGTTATCCCCTGATCATCGTCAA 59.929 47.826 0.00 0.00 32.18 3.18
940 945 4.263068 GGTTATCCCCTGATCATCGTCAAT 60.263 45.833 0.00 0.00 32.18 2.57
941 946 5.046591 GGTTATCCCCTGATCATCGTCAATA 60.047 44.000 0.00 0.00 32.18 1.90
942 947 6.352222 GGTTATCCCCTGATCATCGTCAATAT 60.352 42.308 0.00 0.00 32.18 1.28
943 948 7.147724 GGTTATCCCCTGATCATCGTCAATATA 60.148 40.741 0.00 0.00 32.18 0.86
944 949 8.424918 GTTATCCCCTGATCATCGTCAATATAT 58.575 37.037 0.00 0.00 32.18 0.86
945 950 6.874278 TCCCCTGATCATCGTCAATATATT 57.126 37.500 0.00 0.00 0.00 1.28
946 951 6.878317 TCCCCTGATCATCGTCAATATATTC 58.122 40.000 0.00 0.00 0.00 1.75
947 952 6.440328 TCCCCTGATCATCGTCAATATATTCA 59.560 38.462 0.00 0.00 0.00 2.57
948 953 6.760298 CCCCTGATCATCGTCAATATATTCAG 59.240 42.308 0.00 0.00 0.00 3.02
949 954 6.760298 CCCTGATCATCGTCAATATATTCAGG 59.240 42.308 13.81 13.81 39.43 3.86
950 955 7.326454 CCTGATCATCGTCAATATATTCAGGT 58.674 38.462 13.00 0.00 36.18 4.00
951 956 7.277319 CCTGATCATCGTCAATATATTCAGGTG 59.723 40.741 13.00 7.02 36.18 4.00
952 957 7.099120 TGATCATCGTCAATATATTCAGGTGG 58.901 38.462 0.00 0.00 0.00 4.61
953 958 5.793817 TCATCGTCAATATATTCAGGTGGG 58.206 41.667 0.00 0.00 0.00 4.61
954 959 4.617253 TCGTCAATATATTCAGGTGGGG 57.383 45.455 0.00 0.00 0.00 4.96
955 960 3.326588 TCGTCAATATATTCAGGTGGGGG 59.673 47.826 0.00 0.00 0.00 5.40
956 961 3.326588 CGTCAATATATTCAGGTGGGGGA 59.673 47.826 0.00 0.00 0.00 4.81
957 962 4.202419 CGTCAATATATTCAGGTGGGGGAA 60.202 45.833 0.00 0.00 0.00 3.97
958 963 5.689031 CGTCAATATATTCAGGTGGGGGAAA 60.689 44.000 0.00 0.00 0.00 3.13
959 964 5.535030 GTCAATATATTCAGGTGGGGGAAAC 59.465 44.000 0.00 0.00 0.00 2.78
960 965 5.435041 TCAATATATTCAGGTGGGGGAAACT 59.565 40.000 0.00 0.00 0.00 2.66
961 966 3.953542 ATATTCAGGTGGGGGAAACTC 57.046 47.619 0.00 0.00 0.00 3.01
962 967 1.760405 ATTCAGGTGGGGGAAACTCT 58.240 50.000 0.00 0.00 0.00 3.24
963 968 1.064825 TTCAGGTGGGGGAAACTCTC 58.935 55.000 0.00 0.00 0.00 3.20
964 969 0.840722 TCAGGTGGGGGAAACTCTCC 60.841 60.000 0.00 0.00 44.54 3.71
992 997 2.760477 CCCCCGGTGACCATTCAA 59.240 61.111 1.11 0.00 31.90 2.69
993 998 1.075836 CCCCCGGTGACCATTCAAA 59.924 57.895 1.11 0.00 31.90 2.69
994 999 0.540830 CCCCCGGTGACCATTCAAAA 60.541 55.000 1.11 0.00 31.90 2.44
995 1000 1.333177 CCCCGGTGACCATTCAAAAA 58.667 50.000 1.11 0.00 31.90 1.94
1075 1080 1.101635 CGATCACCAGGCGACCTCTA 61.102 60.000 0.00 0.00 0.00 2.43
1226 1231 1.137086 CGACTTCTCCCCAGGTACATG 59.863 57.143 0.00 0.00 0.00 3.21
1263 1268 4.237724 TCATCGTCAGTTCTGAATGTCAC 58.762 43.478 3.99 0.00 0.00 3.67
1272 1277 0.671472 CTGAATGTCACTCGCAGCCA 60.671 55.000 0.00 0.00 0.00 4.75
1288 1293 3.012518 CAGCCAATCTTCTTTCGGATGT 58.987 45.455 0.00 0.00 0.00 3.06
1304 1309 3.554544 CGGATGTAATGAGCTCTGCTGAT 60.555 47.826 16.19 1.56 39.88 2.90
1319 1324 2.815503 TGCTGATGTTGAATCCACTGTG 59.184 45.455 0.00 0.00 0.00 3.66
1344 1349 1.003051 AGAGCGGGTAGTGGGGAAT 59.997 57.895 0.00 0.00 0.00 3.01
1375 1380 0.802494 CCATGTTTACAGTGGCCGTC 59.198 55.000 0.00 0.00 0.00 4.79
1616 1621 9.727627 CTTAATTTAGTGAATTCTTCTGGATGC 57.272 33.333 7.05 0.00 38.80 3.91
1626 1631 4.147449 CTGGATGCTCCCGTCGCA 62.147 66.667 0.00 0.00 42.25 5.10
1648 1659 6.165577 GCAATGGATGTTTACAAACCTGAAT 58.834 36.000 2.55 0.00 38.11 2.57
1666 1678 3.120683 TGAATTGTTGATCGACGTTGCTC 60.121 43.478 8.59 0.00 0.00 4.26
1668 1680 1.006825 TGTTGATCGACGTTGCTCCG 61.007 55.000 8.59 0.00 0.00 4.63
1677 1689 2.591715 GTTGCTCCGTGTGCAGGT 60.592 61.111 0.00 0.00 41.71 4.00
1701 1716 2.592102 AAGAATGCAAGGGCTCAAGA 57.408 45.000 0.00 0.00 41.91 3.02
1719 1734 1.974236 AGATTAGATTGGCCGGAGAGG 59.026 52.381 5.05 0.00 44.97 3.69
1724 1739 0.744771 GATTGGCCGGAGAGGTTCAC 60.745 60.000 5.05 0.00 43.70 3.18
1766 1781 0.959553 GCCCTCGATTATCTCCACGA 59.040 55.000 0.00 0.00 0.00 4.35
1845 1860 0.391130 TCTCCCAAGATTGCGAACCG 60.391 55.000 0.00 0.00 0.00 4.44
1866 1881 3.114616 CTGTGCGACTTCGGCCTG 61.115 66.667 0.00 0.00 40.23 4.85
1965 1980 1.210931 CTTCATGCACGGCAAGGTG 59.789 57.895 2.68 0.00 43.62 4.00
1995 2010 2.562912 GACGTGTACGCCTTCGGA 59.437 61.111 4.06 0.00 44.43 4.55
1998 2013 1.513586 CGTGTACGCCTTCGGAGTC 60.514 63.158 0.00 0.00 36.95 3.36
2082 2102 3.134458 GAGCATAGTGATGTGGGTAAGC 58.866 50.000 0.00 0.00 35.30 3.09
2111 2146 3.005554 AGCATCATCAAGAAGTGGAACG 58.994 45.455 0.00 0.00 45.86 3.95
2136 2171 7.044966 CGATCGTGAATGGTGCTTTAATTTAAC 60.045 37.037 7.03 0.00 0.00 2.01
2158 2193 2.439156 GCTGGGCAGGCGAATTCT 60.439 61.111 3.52 0.00 0.00 2.40
2278 2313 4.451150 TGCATCCGTCGAGCACCC 62.451 66.667 0.00 0.00 32.55 4.61
2325 2360 6.746120 ACGTAAGATTTACTATCGCCATCTT 58.254 36.000 0.00 0.00 43.62 2.40
2511 2550 2.124903 CGAAGATTATTACAGCGCGGT 58.875 47.619 19.03 19.03 0.00 5.68
2527 2566 2.251371 GTTGCTTCGCCGGACAAC 59.749 61.111 5.05 7.31 36.03 3.32
2742 2781 5.121768 GTGCACGGATTTTTGTGTAGATACT 59.878 40.000 0.00 0.00 38.36 2.12
2846 2889 6.088824 GCACAGTTTTGATGTTTCATCTAGG 58.911 40.000 10.40 0.00 0.00 3.02
2911 2954 5.959512 TCCAAGGACCAAAGGAGAAAAATA 58.040 37.500 0.00 0.00 0.00 1.40
2915 2958 8.416329 CCAAGGACCAAAGGAGAAAAATATATG 58.584 37.037 0.00 0.00 0.00 1.78
2999 3051 5.391312 AATTACTCCTCATGCAAACAACC 57.609 39.130 0.00 0.00 0.00 3.77
3000 3052 1.620822 ACTCCTCATGCAAACAACCC 58.379 50.000 0.00 0.00 0.00 4.11
3001 3053 1.145738 ACTCCTCATGCAAACAACCCT 59.854 47.619 0.00 0.00 0.00 4.34
3002 3054 2.242043 CTCCTCATGCAAACAACCCTT 58.758 47.619 0.00 0.00 0.00 3.95
3003 3055 1.962807 TCCTCATGCAAACAACCCTTG 59.037 47.619 0.00 0.00 0.00 3.61
3050 3102 7.726291 TGGGTATTTCTATCAAGTGTTCCAAAA 59.274 33.333 0.00 0.00 0.00 2.44
3124 3181 7.364939 CCATCCAAACAATACCATGGAGAATTT 60.365 37.037 21.47 9.14 44.63 1.82
3151 3208 7.094805 TGGTTCTAGAATAAATTATGCATCCGC 60.095 37.037 8.75 0.00 39.24 5.54
3163 3220 1.202568 TGCATCCGCTATGGTGAGAAG 60.203 52.381 0.00 0.00 39.64 2.85
3247 3304 7.332182 GTCTCTGATTGAACTACCCAGTTTAAG 59.668 40.741 2.00 0.00 45.18 1.85
3272 3329 7.872993 AGCGCATATTACAGAAATACATACACT 59.127 33.333 11.47 0.00 32.86 3.55
3295 3355 9.988350 CACTAATAAAACTAAATGATCGTGCTT 57.012 29.630 0.00 0.00 0.00 3.91
3299 3359 4.778842 AACTAAATGATCGTGCTTAGCG 57.221 40.909 0.00 0.00 0.00 4.26
3301 3361 2.024176 AAATGATCGTGCTTAGCGGT 57.976 45.000 0.00 0.00 0.00 5.68
3363 3423 2.151202 GCAGGTCAACGGAAATGAGAA 58.849 47.619 0.00 0.00 0.00 2.87
3442 3502 1.493134 AAGCACGACCGTCGAAAACC 61.493 55.000 27.03 9.76 43.74 3.27
3471 3531 3.093814 TCTACCATACAACGAGGCTTCA 58.906 45.455 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.465705 CACCCTGGATATCGTGCAGT 59.534 55.000 0.00 0.00 44.10 4.40
1 2 0.250038 CCACCCTGGATATCGTGCAG 60.250 60.000 0.00 0.00 45.08 4.41
2 3 0.980754 ACCACCCTGGATATCGTGCA 60.981 55.000 0.00 0.00 40.96 4.57
10 11 3.009115 CCGACCACCACCCTGGAT 61.009 66.667 0.00 0.00 40.96 3.41
46 47 1.986413 CCAGGAGTCCCACCAGAAG 59.014 63.158 5.25 0.00 33.88 2.85
93 94 2.683933 GGGAGAAGAGTGCGGGGA 60.684 66.667 0.00 0.00 0.00 4.81
100 101 0.534412 CGACAGCATGGGAGAAGAGT 59.466 55.000 0.00 0.00 43.62 3.24
154 155 4.335647 AGACAACCTGCCAGGCCG 62.336 66.667 11.63 4.36 39.63 6.13
192 193 2.203337 GCAGTTCACTGGTGCCCA 60.203 61.111 9.01 0.00 43.94 5.36
197 198 2.113986 GGCCTGCAGTTCACTGGT 59.886 61.111 13.81 0.00 43.94 4.00
198 199 3.052082 CGGCCTGCAGTTCACTGG 61.052 66.667 13.81 0.00 43.94 4.00
199 200 2.281070 ACGGCCTGCAGTTCACTG 60.281 61.111 13.81 6.76 46.40 3.66
200 201 2.281070 CACGGCCTGCAGTTCACT 60.281 61.111 13.81 0.00 0.00 3.41
217 218 3.844090 GCCTCCAGGAGAGCCGAC 61.844 72.222 19.21 0.00 41.74 4.79
246 247 2.603473 TCGTGTCCTCCCCCACAG 60.603 66.667 0.00 0.00 0.00 3.66
316 317 2.740714 GAAACGCAGCAGCCGGTAG 61.741 63.158 1.90 0.00 37.52 3.18
361 362 1.512230 CCGTGCACCCCAAATCATG 59.488 57.895 12.15 0.00 0.00 3.07
388 389 1.512734 GCTGAAGAATTGCACGCGG 60.513 57.895 12.47 0.00 0.00 6.46
391 392 0.877071 ACCAGCTGAAGAATTGCACG 59.123 50.000 17.39 0.00 0.00 5.34
397 398 3.307762 GGACCAGTAACCAGCTGAAGAAT 60.308 47.826 17.39 0.00 36.12 2.40
412 413 1.685765 TATGCGCCTCTGGACCAGT 60.686 57.895 21.06 2.57 32.61 4.00
427 428 4.097135 AGAAGGACATCTCGAGTGTGTATG 59.903 45.833 20.45 14.98 0.00 2.39
437 438 0.737367 TTGCGCAGAAGGACATCTCG 60.737 55.000 11.31 0.00 0.00 4.04
442 443 2.253758 GCACTTGCGCAGAAGGACA 61.254 57.895 11.31 0.00 0.00 4.02
448 449 2.357396 ACGATGCACTTGCGCAGA 60.357 55.556 11.31 0.62 46.99 4.26
451 452 3.478394 TCGACGATGCACTTGCGC 61.478 61.111 0.00 0.00 45.83 6.09
506 507 1.613317 ATGTGATCGGCCGTCTCCAA 61.613 55.000 27.15 13.63 0.00 3.53
511 512 1.019278 ACAACATGTGATCGGCCGTC 61.019 55.000 27.15 21.38 0.00 4.79
520 521 1.514678 GGCAGGCGAACAACATGTGA 61.515 55.000 0.00 0.00 0.00 3.58
527 528 2.975799 GAACGGGCAGGCGAACAA 60.976 61.111 0.00 0.00 0.00 2.83
590 591 4.437587 ATGCAGCCTGCCCACCTC 62.438 66.667 15.29 0.00 44.23 3.85
591 592 4.437587 GATGCAGCCTGCCCACCT 62.438 66.667 15.29 0.00 44.23 4.00
636 641 4.988716 ACTCCACCGCCGACCTGA 62.989 66.667 0.00 0.00 0.00 3.86
638 643 3.692406 GAACTCCACCGCCGACCT 61.692 66.667 0.00 0.00 0.00 3.85
667 672 1.073722 TTTCCAGAGGTGCCAGCAG 59.926 57.895 0.00 0.00 0.00 4.24
677 682 0.868406 GCGTTCCTGTGTTTCCAGAG 59.132 55.000 0.00 0.00 34.23 3.35
678 683 0.534203 GGCGTTCCTGTGTTTCCAGA 60.534 55.000 0.00 0.00 34.23 3.86
697 702 1.856265 GCTGCCTTTGGAAGACCACG 61.856 60.000 0.00 0.00 46.80 4.94
707 712 0.886490 AGAGACGGTTGCTGCCTTTG 60.886 55.000 0.00 0.00 0.00 2.77
709 714 1.302033 CAGAGACGGTTGCTGCCTT 60.302 57.895 0.00 0.00 0.00 4.35
721 726 3.537206 AAGCACCCACCGCAGAGAC 62.537 63.158 0.00 0.00 0.00 3.36
722 727 3.241530 AAGCACCCACCGCAGAGA 61.242 61.111 0.00 0.00 0.00 3.10
723 728 3.052082 CAAGCACCCACCGCAGAG 61.052 66.667 0.00 0.00 0.00 3.35
724 729 4.641645 CCAAGCACCCACCGCAGA 62.642 66.667 0.00 0.00 0.00 4.26
725 730 3.925630 ATCCAAGCACCCACCGCAG 62.926 63.158 0.00 0.00 0.00 5.18
726 731 3.965258 ATCCAAGCACCCACCGCA 61.965 61.111 0.00 0.00 0.00 5.69
727 732 3.443045 CATCCAAGCACCCACCGC 61.443 66.667 0.00 0.00 0.00 5.68
728 733 3.443045 GCATCCAAGCACCCACCG 61.443 66.667 0.00 0.00 0.00 4.94
729 734 2.036256 AGCATCCAAGCACCCACC 59.964 61.111 0.00 0.00 36.85 4.61
730 735 2.998279 GCAGCATCCAAGCACCCAC 61.998 63.158 0.00 0.00 36.85 4.61
731 736 2.677524 GCAGCATCCAAGCACCCA 60.678 61.111 0.00 0.00 36.85 4.51
732 737 3.455469 GGCAGCATCCAAGCACCC 61.455 66.667 0.00 0.00 36.85 4.61
733 738 3.818787 CGGCAGCATCCAAGCACC 61.819 66.667 0.00 0.00 36.85 5.01
734 739 4.487412 GCGGCAGCATCCAAGCAC 62.487 66.667 3.18 0.00 44.35 4.40
737 742 3.570638 CTCGCGGCAGCATCCAAG 61.571 66.667 10.08 0.00 45.49 3.61
751 756 2.805353 CACAGAACGGCGTCCTCG 60.805 66.667 15.17 3.33 40.37 4.63
752 757 2.432628 CCACAGAACGGCGTCCTC 60.433 66.667 15.17 8.57 0.00 3.71
753 758 4.681978 GCCACAGAACGGCGTCCT 62.682 66.667 15.17 1.16 40.35 3.85
759 764 3.554692 GATCGCGCCACAGAACGG 61.555 66.667 0.00 0.00 0.00 4.44
760 765 3.902063 CGATCGCGCCACAGAACG 61.902 66.667 0.26 0.00 0.00 3.95
761 766 3.554692 CCGATCGCGCCACAGAAC 61.555 66.667 10.32 0.00 35.83 3.01
772 777 3.665226 CTCTCGGGGAGCCGATCG 61.665 72.222 8.51 8.51 41.47 3.69
785 790 4.459089 GTGCACCCTCCGGCTCTC 62.459 72.222 5.22 0.00 0.00 3.20
790 795 4.308458 TCAACGTGCACCCTCCGG 62.308 66.667 12.15 0.00 0.00 5.14
791 796 2.709125 TTCTCAACGTGCACCCTCCG 62.709 60.000 12.15 0.95 0.00 4.63
792 797 1.070786 TTCTCAACGTGCACCCTCC 59.929 57.895 12.15 0.00 0.00 4.30
793 798 0.249911 AGTTCTCAACGTGCACCCTC 60.250 55.000 12.15 0.00 36.23 4.30
794 799 0.532862 CAGTTCTCAACGTGCACCCT 60.533 55.000 12.15 0.00 36.23 4.34
795 800 1.507141 CCAGTTCTCAACGTGCACCC 61.507 60.000 12.15 0.00 36.23 4.61
796 801 1.941812 CCAGTTCTCAACGTGCACC 59.058 57.895 12.15 0.00 36.23 5.01
797 802 1.160329 AGCCAGTTCTCAACGTGCAC 61.160 55.000 6.82 6.82 35.94 4.57
798 803 1.146041 AGCCAGTTCTCAACGTGCA 59.854 52.632 0.00 0.00 35.94 4.57
799 804 1.571460 CAGCCAGTTCTCAACGTGC 59.429 57.895 0.00 0.00 36.23 5.34
800 805 1.159713 TGCAGCCAGTTCTCAACGTG 61.160 55.000 0.00 0.00 36.23 4.49
801 806 0.882042 CTGCAGCCAGTTCTCAACGT 60.882 55.000 0.00 0.00 36.23 3.99
802 807 1.572085 CCTGCAGCCAGTTCTCAACG 61.572 60.000 8.66 0.00 37.38 4.10
803 808 1.860484 GCCTGCAGCCAGTTCTCAAC 61.860 60.000 8.66 0.00 37.38 3.18
804 809 1.601759 GCCTGCAGCCAGTTCTCAA 60.602 57.895 8.66 0.00 37.38 3.02
805 810 2.033141 GCCTGCAGCCAGTTCTCA 59.967 61.111 8.66 0.00 37.38 3.27
814 819 2.268167 ATTCTGAGAGGGCCTGCAGC 62.268 60.000 22.14 3.68 42.60 5.25
815 820 1.070445 CTATTCTGAGAGGGCCTGCAG 59.930 57.143 12.95 18.59 0.00 4.41
816 821 1.126488 CTATTCTGAGAGGGCCTGCA 58.874 55.000 12.95 8.32 0.00 4.41
817 822 1.418334 TCTATTCTGAGAGGGCCTGC 58.582 55.000 12.95 2.77 0.00 4.85
818 823 3.037549 ACTTCTATTCTGAGAGGGCCTG 58.962 50.000 12.95 0.00 0.00 4.85
819 824 3.413105 ACTTCTATTCTGAGAGGGCCT 57.587 47.619 5.25 5.25 0.00 5.19
820 825 3.006430 GCTACTTCTATTCTGAGAGGGCC 59.994 52.174 0.00 0.00 0.00 5.80
821 826 3.006430 GGCTACTTCTATTCTGAGAGGGC 59.994 52.174 0.00 0.00 0.00 5.19
822 827 4.479158 AGGCTACTTCTATTCTGAGAGGG 58.521 47.826 0.00 0.00 0.00 4.30
823 828 6.093495 CGATAGGCTACTTCTATTCTGAGAGG 59.907 46.154 0.00 0.00 0.00 3.69
824 829 6.653320 ACGATAGGCTACTTCTATTCTGAGAG 59.347 42.308 0.00 0.00 43.77 3.20
825 830 6.535540 ACGATAGGCTACTTCTATTCTGAGA 58.464 40.000 0.00 0.00 43.77 3.27
826 831 6.811253 ACGATAGGCTACTTCTATTCTGAG 57.189 41.667 0.00 0.00 43.77 3.35
827 832 6.804770 GACGATAGGCTACTTCTATTCTGA 57.195 41.667 0.00 0.00 44.90 3.27
842 847 5.081032 AGAGAGGGATAAAAGGACGATAGG 58.919 45.833 0.00 0.00 43.77 2.57
843 848 6.007703 AGAGAGAGGGATAAAAGGACGATAG 58.992 44.000 0.00 0.00 46.19 2.08
844 849 5.954757 AGAGAGAGGGATAAAAGGACGATA 58.045 41.667 0.00 0.00 0.00 2.92
845 850 4.810345 AGAGAGAGGGATAAAAGGACGAT 58.190 43.478 0.00 0.00 0.00 3.73
846 851 4.079672 AGAGAGAGAGGGATAAAAGGACGA 60.080 45.833 0.00 0.00 0.00 4.20
847 852 4.211920 AGAGAGAGAGGGATAAAAGGACG 58.788 47.826 0.00 0.00 0.00 4.79
848 853 5.454966 AGAGAGAGAGAGGGATAAAAGGAC 58.545 45.833 0.00 0.00 0.00 3.85
849 854 5.435041 AGAGAGAGAGAGAGGGATAAAAGGA 59.565 44.000 0.00 0.00 0.00 3.36
850 855 5.705400 AGAGAGAGAGAGAGGGATAAAAGG 58.295 45.833 0.00 0.00 0.00 3.11
851 856 6.488006 CAGAGAGAGAGAGAGAGGGATAAAAG 59.512 46.154 0.00 0.00 0.00 2.27
852 857 6.069088 ACAGAGAGAGAGAGAGAGGGATAAAA 60.069 42.308 0.00 0.00 0.00 1.52
853 858 5.431731 ACAGAGAGAGAGAGAGAGGGATAAA 59.568 44.000 0.00 0.00 0.00 1.40
854 859 4.975147 ACAGAGAGAGAGAGAGAGGGATAA 59.025 45.833 0.00 0.00 0.00 1.75
855 860 4.347876 CACAGAGAGAGAGAGAGAGGGATA 59.652 50.000 0.00 0.00 0.00 2.59
856 861 3.137176 CACAGAGAGAGAGAGAGAGGGAT 59.863 52.174 0.00 0.00 0.00 3.85
857 862 2.505407 CACAGAGAGAGAGAGAGAGGGA 59.495 54.545 0.00 0.00 0.00 4.20
858 863 2.239654 ACACAGAGAGAGAGAGAGAGGG 59.760 54.545 0.00 0.00 0.00 4.30
859 864 3.273434 CACACAGAGAGAGAGAGAGAGG 58.727 54.545 0.00 0.00 0.00 3.69
860 865 3.942829 ACACACAGAGAGAGAGAGAGAG 58.057 50.000 0.00 0.00 0.00 3.20
861 866 5.692115 ATACACACAGAGAGAGAGAGAGA 57.308 43.478 0.00 0.00 0.00 3.10
862 867 6.115446 AGAATACACACAGAGAGAGAGAGAG 58.885 44.000 0.00 0.00 0.00 3.20
863 868 6.061022 AGAATACACACAGAGAGAGAGAGA 57.939 41.667 0.00 0.00 0.00 3.10
864 869 5.006649 CGAGAATACACACAGAGAGAGAGAG 59.993 48.000 0.00 0.00 0.00 3.20
865 870 4.873259 CGAGAATACACACAGAGAGAGAGA 59.127 45.833 0.00 0.00 0.00 3.10
866 871 4.035091 CCGAGAATACACACAGAGAGAGAG 59.965 50.000 0.00 0.00 0.00 3.20
867 872 3.942115 CCGAGAATACACACAGAGAGAGA 59.058 47.826 0.00 0.00 0.00 3.10
868 873 3.066064 CCCGAGAATACACACAGAGAGAG 59.934 52.174 0.00 0.00 0.00 3.20
869 874 3.017442 CCCGAGAATACACACAGAGAGA 58.983 50.000 0.00 0.00 0.00 3.10
870 875 2.480416 GCCCGAGAATACACACAGAGAG 60.480 54.545 0.00 0.00 0.00 3.20
871 876 1.476891 GCCCGAGAATACACACAGAGA 59.523 52.381 0.00 0.00 0.00 3.10
872 877 1.204704 TGCCCGAGAATACACACAGAG 59.795 52.381 0.00 0.00 0.00 3.35
873 878 1.262417 TGCCCGAGAATACACACAGA 58.738 50.000 0.00 0.00 0.00 3.41
874 879 2.159043 AGATGCCCGAGAATACACACAG 60.159 50.000 0.00 0.00 0.00 3.66
875 880 1.831106 AGATGCCCGAGAATACACACA 59.169 47.619 0.00 0.00 0.00 3.72
876 881 2.205074 CAGATGCCCGAGAATACACAC 58.795 52.381 0.00 0.00 0.00 3.82
877 882 1.831106 ACAGATGCCCGAGAATACACA 59.169 47.619 0.00 0.00 0.00 3.72
878 883 2.604046 ACAGATGCCCGAGAATACAC 57.396 50.000 0.00 0.00 0.00 2.90
879 884 4.746535 TTTACAGATGCCCGAGAATACA 57.253 40.909 0.00 0.00 0.00 2.29
880 885 4.511826 CCTTTTACAGATGCCCGAGAATAC 59.488 45.833 0.00 0.00 0.00 1.89
881 886 4.444306 CCCTTTTACAGATGCCCGAGAATA 60.444 45.833 0.00 0.00 0.00 1.75
882 887 3.545703 CCTTTTACAGATGCCCGAGAAT 58.454 45.455 0.00 0.00 0.00 2.40
883 888 2.355716 CCCTTTTACAGATGCCCGAGAA 60.356 50.000 0.00 0.00 0.00 2.87
884 889 1.209504 CCCTTTTACAGATGCCCGAGA 59.790 52.381 0.00 0.00 0.00 4.04
885 890 1.668419 CCCTTTTACAGATGCCCGAG 58.332 55.000 0.00 0.00 0.00 4.63
886 891 0.393808 GCCCTTTTACAGATGCCCGA 60.394 55.000 0.00 0.00 0.00 5.14
887 892 1.384222 GGCCCTTTTACAGATGCCCG 61.384 60.000 0.00 0.00 35.30 6.13
888 893 1.384222 CGGCCCTTTTACAGATGCCC 61.384 60.000 0.00 0.00 37.07 5.36
889 894 2.004808 GCGGCCCTTTTACAGATGCC 62.005 60.000 0.00 0.00 37.05 4.40
890 895 1.032114 AGCGGCCCTTTTACAGATGC 61.032 55.000 0.00 0.00 0.00 3.91
891 896 1.940613 GTAGCGGCCCTTTTACAGATG 59.059 52.381 0.00 0.00 0.00 2.90
892 897 1.134189 GGTAGCGGCCCTTTTACAGAT 60.134 52.381 0.00 0.00 0.00 2.90
893 898 0.251073 GGTAGCGGCCCTTTTACAGA 59.749 55.000 0.00 0.00 0.00 3.41
894 899 0.252197 AGGTAGCGGCCCTTTTACAG 59.748 55.000 0.00 0.00 0.00 2.74
895 900 0.694196 AAGGTAGCGGCCCTTTTACA 59.306 50.000 0.00 0.00 39.27 2.41
896 901 1.092348 CAAGGTAGCGGCCCTTTTAC 58.908 55.000 7.68 0.00 40.35 2.01
897 902 0.034863 CCAAGGTAGCGGCCCTTTTA 60.035 55.000 7.68 0.00 40.35 1.52
898 903 1.304134 CCAAGGTAGCGGCCCTTTT 60.304 57.895 7.68 0.00 40.35 2.27
899 904 2.355115 CCAAGGTAGCGGCCCTTT 59.645 61.111 7.68 0.00 40.35 3.11
900 905 3.728373 CCCAAGGTAGCGGCCCTT 61.728 66.667 0.00 4.88 43.11 3.95
917 922 2.632996 TGACGATGATCAGGGGATAACC 59.367 50.000 0.09 0.00 32.67 2.85
918 923 4.336889 TTGACGATGATCAGGGGATAAC 57.663 45.455 0.09 0.00 32.67 1.89
919 924 6.874278 ATATTGACGATGATCAGGGGATAA 57.126 37.500 0.09 0.00 32.67 1.75
920 925 8.553085 AATATATTGACGATGATCAGGGGATA 57.447 34.615 0.09 0.00 32.67 2.59
921 926 7.126268 TGAATATATTGACGATGATCAGGGGAT 59.874 37.037 1.78 0.00 36.13 3.85
922 927 6.440328 TGAATATATTGACGATGATCAGGGGA 59.560 38.462 1.78 0.00 0.00 4.81
923 928 6.643388 TGAATATATTGACGATGATCAGGGG 58.357 40.000 1.78 0.00 0.00 4.79
924 929 6.760298 CCTGAATATATTGACGATGATCAGGG 59.240 42.308 13.25 0.00 36.98 4.45
925 930 7.277319 CACCTGAATATATTGACGATGATCAGG 59.723 40.741 17.19 17.19 43.70 3.86
926 931 7.277319 CCACCTGAATATATTGACGATGATCAG 59.723 40.741 1.78 0.85 0.00 2.90
927 932 7.099120 CCACCTGAATATATTGACGATGATCA 58.901 38.462 1.78 0.00 0.00 2.92
928 933 6.536582 CCCACCTGAATATATTGACGATGATC 59.463 42.308 1.78 0.00 0.00 2.92
929 934 6.409704 CCCACCTGAATATATTGACGATGAT 58.590 40.000 1.78 0.00 0.00 2.45
930 935 5.279960 CCCCACCTGAATATATTGACGATGA 60.280 44.000 1.78 0.00 0.00 2.92
931 936 4.937620 CCCCACCTGAATATATTGACGATG 59.062 45.833 1.78 0.00 0.00 3.84
932 937 4.019321 CCCCCACCTGAATATATTGACGAT 60.019 45.833 1.78 0.00 0.00 3.73
933 938 3.326588 CCCCCACCTGAATATATTGACGA 59.673 47.826 1.78 0.00 0.00 4.20
934 939 3.326588 TCCCCCACCTGAATATATTGACG 59.673 47.826 1.78 0.00 0.00 4.35
935 940 4.993705 TCCCCCACCTGAATATATTGAC 57.006 45.455 1.78 0.00 0.00 3.18
936 941 5.435041 AGTTTCCCCCACCTGAATATATTGA 59.565 40.000 1.78 0.00 0.00 2.57
937 942 5.705400 AGTTTCCCCCACCTGAATATATTG 58.295 41.667 1.78 0.00 0.00 1.90
938 943 5.676811 AGAGTTTCCCCCACCTGAATATATT 59.323 40.000 0.00 0.00 0.00 1.28
939 944 5.235534 AGAGTTTCCCCCACCTGAATATAT 58.764 41.667 0.00 0.00 0.00 0.86
940 945 4.641868 AGAGTTTCCCCCACCTGAATATA 58.358 43.478 0.00 0.00 0.00 0.86
941 946 3.459969 GAGAGTTTCCCCCACCTGAATAT 59.540 47.826 0.00 0.00 0.00 1.28
942 947 2.844348 GAGAGTTTCCCCCACCTGAATA 59.156 50.000 0.00 0.00 0.00 1.75
943 948 1.636003 GAGAGTTTCCCCCACCTGAAT 59.364 52.381 0.00 0.00 0.00 2.57
944 949 1.064825 GAGAGTTTCCCCCACCTGAA 58.935 55.000 0.00 0.00 0.00 3.02
945 950 0.840722 GGAGAGTTTCCCCCACCTGA 60.841 60.000 0.00 0.00 40.37 3.86
946 951 1.685820 GGAGAGTTTCCCCCACCTG 59.314 63.158 0.00 0.00 40.37 4.00
947 952 4.252493 GGAGAGTTTCCCCCACCT 57.748 61.111 0.00 0.00 40.37 4.00
975 980 0.540830 TTTTGAATGGTCACCGGGGG 60.541 55.000 2.42 0.00 31.90 5.40
976 981 1.333177 TTTTTGAATGGTCACCGGGG 58.667 50.000 6.32 0.00 31.90 5.73
996 1001 3.215642 GCTTGGAAGCCGCATTTTT 57.784 47.368 0.00 0.00 46.20 1.94
997 1002 4.994744 GCTTGGAAGCCGCATTTT 57.005 50.000 0.00 0.00 46.20 1.82
1075 1080 4.245660 TCTGTCGAATCGCTTCTTGATTT 58.754 39.130 0.00 0.00 36.24 2.17
1124 1129 1.160989 GATCGAGATCAGCTCCGCTA 58.839 55.000 8.11 0.00 40.70 4.26
1206 1211 1.137086 CATGTACCTGGGGAGAAGTCG 59.863 57.143 0.00 0.00 0.00 4.18
1226 1231 1.921887 CGATGAAATGTTGCATGGTGC 59.078 47.619 0.00 0.00 45.29 5.01
1245 1250 2.658802 CGAGTGACATTCAGAACTGACG 59.341 50.000 3.88 2.04 39.66 4.35
1263 1268 1.061711 CGAAAGAAGATTGGCTGCGAG 59.938 52.381 0.00 0.00 0.00 5.03
1272 1277 6.352516 AGCTCATTACATCCGAAAGAAGATT 58.647 36.000 0.00 0.00 0.00 2.40
1288 1293 4.476628 TCAACATCAGCAGAGCTCATTA 57.523 40.909 17.77 0.00 36.40 1.90
1319 1324 2.352032 ACTACCCGCTCTGCTCCAC 61.352 63.158 0.00 0.00 0.00 4.02
1344 1349 2.974692 AAACATGGCTCGCACCACCA 62.975 55.000 0.00 0.00 44.17 4.17
1375 1380 3.181967 CTCCTTGCCGTCTTCGCG 61.182 66.667 0.00 0.00 35.54 5.87
1616 1621 0.744414 AACATCCATTGCGACGGGAG 60.744 55.000 0.00 0.00 33.47 4.30
1626 1631 7.734942 ACAATTCAGGTTTGTAAACATCCATT 58.265 30.769 9.44 1.09 40.63 3.16
1648 1659 1.144969 GGAGCAACGTCGATCAACAA 58.855 50.000 0.00 0.00 0.00 2.83
1666 1678 0.249868 TCTTTCTCACCTGCACACGG 60.250 55.000 0.00 0.00 0.00 4.94
1668 1680 2.351157 GCATTCTTTCTCACCTGCACAC 60.351 50.000 0.00 0.00 0.00 3.82
1677 1689 2.224843 TGAGCCCTTGCATTCTTTCTCA 60.225 45.455 0.00 0.00 41.13 3.27
1701 1716 1.807814 ACCTCTCCGGCCAATCTAAT 58.192 50.000 2.24 0.00 35.61 1.73
1753 1768 0.663568 CCGCCGTCGTGGAGATAATC 60.664 60.000 0.51 0.00 42.83 1.75
1845 1860 3.016474 GCCGAAGTCGCACAGCTTC 62.016 63.158 0.00 0.00 38.11 3.86
1965 1980 2.125512 ACGTCCATCTTGGCGCTC 60.126 61.111 7.64 0.00 39.47 5.03
1970 1985 1.082117 GGCGTACACGTCCATCTTGG 61.082 60.000 3.44 0.00 42.22 3.61
1995 2010 1.309499 CGAGCTCCAGAAGGACGACT 61.309 60.000 8.47 0.00 39.61 4.18
1998 2013 1.137825 GACGAGCTCCAGAAGGACG 59.862 63.158 8.47 0.00 39.61 4.79
2082 2102 6.238402 CCACTTCTTGATGATGCTGTAAGATG 60.238 42.308 0.00 0.00 34.07 2.90
2111 2146 7.968405 AGTTAAATTAAAGCACCATTCACGATC 59.032 33.333 0.00 0.00 0.00 3.69
2158 2193 1.227823 CTTCCCACCTTGCACGACA 60.228 57.895 0.00 0.00 0.00 4.35
2191 2226 2.417936 GTCGGAAGGCTCGGATCC 59.582 66.667 0.00 0.00 33.89 3.36
2232 2267 2.419198 CGAGGGCCATTCTCTCGG 59.581 66.667 17.59 2.93 44.40 4.63
2278 2313 4.195334 ATGCTAGGCCGGGCTTGG 62.195 66.667 37.40 27.62 0.00 3.61
2325 2360 5.050634 CGAACAAGACGACCAAGTAAAATGA 60.051 40.000 0.00 0.00 0.00 2.57
2575 2614 0.035343 AGTCGTCGTCATCCTCCTCA 60.035 55.000 0.00 0.00 0.00 3.86
2742 2781 8.514594 ACGAAAGAATCAAAAGAATTGCTGATA 58.485 29.630 0.00 0.00 32.21 2.15
2846 2889 8.511321 TGTTGTAACAAATCCATGAATGACTAC 58.489 33.333 0.00 0.00 35.67 2.73
2911 2954 7.472334 AGAAACTTCAAACTGGAATGCATAT 57.528 32.000 0.00 0.00 0.00 1.78
2915 2958 6.913170 TCATAGAAACTTCAAACTGGAATGC 58.087 36.000 0.00 0.00 0.00 3.56
2976 3027 5.417580 GGGTTGTTTGCATGAGGAGTAATTA 59.582 40.000 0.00 0.00 0.00 1.40
2979 3030 3.153919 GGGTTGTTTGCATGAGGAGTAA 58.846 45.455 0.00 0.00 0.00 2.24
2999 3051 3.640967 TCCAAACAAGGATCCAAACAAGG 59.359 43.478 15.82 9.11 31.23 3.61
3000 3052 4.935352 TCCAAACAAGGATCCAAACAAG 57.065 40.909 15.82 0.00 31.23 3.16
3001 3053 4.653341 ACATCCAAACAAGGATCCAAACAA 59.347 37.500 15.82 0.00 45.16 2.83
3002 3054 4.039004 CACATCCAAACAAGGATCCAAACA 59.961 41.667 15.82 0.00 45.16 2.83
3003 3055 4.559153 CACATCCAAACAAGGATCCAAAC 58.441 43.478 15.82 0.00 45.16 2.93
3004 3056 3.577848 CCACATCCAAACAAGGATCCAAA 59.422 43.478 15.82 0.00 45.16 3.28
3005 3057 3.164268 CCACATCCAAACAAGGATCCAA 58.836 45.455 15.82 0.00 45.16 3.53
3006 3058 2.557229 CCCACATCCAAACAAGGATCCA 60.557 50.000 15.82 0.00 45.16 3.41
3007 3059 2.102578 CCCACATCCAAACAAGGATCC 58.897 52.381 2.48 2.48 45.16 3.36
3008 3060 2.807676 ACCCACATCCAAACAAGGATC 58.192 47.619 0.00 0.00 45.16 3.36
3010 3062 4.396357 AATACCCACATCCAAACAAGGA 57.604 40.909 0.00 0.00 43.01 3.36
3067 3119 6.494893 TTTTCTTGGGATCTTATGTGTTCG 57.505 37.500 0.00 0.00 0.00 3.95
3124 3181 8.783093 CGGATGCATAATTTATTCTAGAACCAA 58.217 33.333 7.48 3.98 0.00 3.67
3151 3208 6.920758 GCATCTACAGTTACTTCTCACCATAG 59.079 42.308 0.00 0.00 0.00 2.23
3247 3304 8.018677 AGTGTATGTATTTCTGTAATATGCGC 57.981 34.615 0.00 0.00 31.61 6.09
3269 3326 9.988350 AAGCACGATCATTTAGTTTTATTAGTG 57.012 29.630 0.00 0.00 0.00 2.74
3282 3342 1.665679 CACCGCTAAGCACGATCATTT 59.334 47.619 0.00 0.00 0.00 2.32
3283 3343 1.290203 CACCGCTAAGCACGATCATT 58.710 50.000 0.00 0.00 0.00 2.57
3295 3355 7.152645 GGATTAAGATTAAGATCACACCGCTA 58.847 38.462 0.00 0.00 34.60 4.26
3299 3359 6.712547 CCAGGGATTAAGATTAAGATCACACC 59.287 42.308 0.00 0.00 34.60 4.16
3301 3361 6.183361 CCCCAGGGATTAAGATTAAGATCACA 60.183 42.308 7.25 0.00 37.50 3.58
3363 3423 4.416848 AGGCCTAATCATACAATCCACCTT 59.583 41.667 1.29 0.00 0.00 3.50
3442 3502 3.003378 TCGTTGTATGGTAGAGATGCTCG 59.997 47.826 0.00 0.00 35.36 5.03
3471 3531 7.024340 CATAATTGCACATGCTTCTCTTAGT 57.976 36.000 5.31 0.00 42.66 2.24


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

AutoCloner maintained by Alex Coulton.