Multiple sequence alignment - TraesCS3B01G089300

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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 TraesCS3B01G089300 chr3B 100.000 4346 0 0 1 4346 59070673 59066328 0.000000e+00 8026
1 TraesCS3B01G089300 chr3B 89.511 696 65 8 28 717 586163402 586162709 0.000000e+00 874
2 TraesCS3B01G089300 chr3B 83.146 801 94 26 2282 3064 14237318 14236541 0.000000e+00 693
3 TraesCS3B01G089300 chr3B 82.831 664 84 18 1790 2442 59057291 59056647 6.310000e-158 568
4 TraesCS3B01G089300 chr3B 88.073 109 10 2 743 850 660994583 660994477 4.560000e-25 126
5 TraesCS3B01G089300 chr3A 93.279 3303 139 27 850 4130 46873258 46870017 0.000000e+00 4793
6 TraesCS3B01G089300 chr3A 90.722 194 8 7 4157 4346 46869954 46869767 2.590000e-62 250
7 TraesCS3B01G089300 chr3D 94.705 2814 95 18 1339 4130 36362416 36359635 0.000000e+00 4322
8 TraesCS3B01G089300 chr3D 89.343 685 69 4 28 709 419659949 419659266 0.000000e+00 857
9 TraesCS3B01G089300 chr3D 91.667 336 20 5 914 1246 36363112 36362782 3.960000e-125 459
10 TraesCS3B01G089300 chr3D 93.717 191 10 2 4157 4346 36359572 36359383 7.110000e-73 285
11 TraesCS3B01G089300 chr2D 90.073 685 63 5 28 709 495045032 495044350 0.000000e+00 883
12 TraesCS3B01G089300 chr7D 89.985 679 65 3 33 709 105641177 105640500 0.000000e+00 874
13 TraesCS3B01G089300 chr7D 89.781 685 63 6 28 709 606804748 606805428 0.000000e+00 870
14 TraesCS3B01G089300 chr7D 86.847 555 59 8 1243 1797 65640068 65639528 3.720000e-170 608
15 TraesCS3B01G089300 chr7D 88.785 107 9 2 744 849 616015924 616015820 1.270000e-25 128
16 TraesCS3B01G089300 chr4B 89.197 685 69 5 28 709 348132169 348131487 0.000000e+00 850
17 TraesCS3B01G089300 chr4B 88.613 685 73 5 28 709 348088589 348087907 0.000000e+00 828
18 TraesCS3B01G089300 chr4B 82.550 808 99 25 2300 3079 14188977 14188184 0.000000e+00 673
19 TraesCS3B01G089300 chr4B 84.778 473 45 13 2285 2744 109320678 109321136 2.380000e-122 449
20 TraesCS3B01G089300 chr4B 81.762 488 58 17 2555 3020 109321129 109321607 3.170000e-101 379
21 TraesCS3B01G089300 chr4B 86.111 108 12 2 744 850 117184144 117184039 3.550000e-21 113
22 TraesCS3B01G089300 chr5D 88.987 681 66 8 33 709 410505757 410505082 0.000000e+00 833
23 TraesCS3B01G089300 chr7B 88.807 679 71 5 33 709 568118511 568119186 0.000000e+00 828
24 TraesCS3B01G089300 chr7B 82.647 801 92 27 2278 3064 89669307 89670074 0.000000e+00 665
25 TraesCS3B01G089300 chr6B 81.250 800 102 34 2279 3064 663783551 663784316 1.730000e-168 603
26 TraesCS3B01G089300 chr4D 84.926 471 57 9 1242 1708 427884684 427884224 8.510000e-127 464
27 TraesCS3B01G089300 chr4D 90.741 162 15 0 1710 1871 427734725 427734564 2.630000e-52 217
28 TraesCS3B01G089300 chr1A 84.848 132 17 2 724 854 572746814 572746943 3.530000e-26 130
29 TraesCS3B01G089300 chr1A 88.182 110 10 2 743 851 385269110 385269217 1.270000e-25 128
30 TraesCS3B01G089300 chr5B 87.963 108 10 2 744 850 664878697 664878802 1.640000e-24 124
31 TraesCS3B01G089300 chr5A 87.156 109 11 2 744 851 700344685 700344791 2.120000e-23 121
32 TraesCS3B01G089300 chr6A 87.037 108 11 2 744 850 90213116 90213011 7.640000e-23 119
33 TraesCS3B01G089300 chr2A 86.486 111 12 2 744 853 45092566 45092458 7.640000e-23 119


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G089300 chr3B 59066328 59070673 4345 True 8026.000000 8026 100.0000 1 4346 1 chr3B.!!$R3 4345
1 TraesCS3B01G089300 chr3B 586162709 586163402 693 True 874.000000 874 89.5110 28 717 1 chr3B.!!$R4 689
2 TraesCS3B01G089300 chr3B 14236541 14237318 777 True 693.000000 693 83.1460 2282 3064 1 chr3B.!!$R1 782
3 TraesCS3B01G089300 chr3B 59056647 59057291 644 True 568.000000 568 82.8310 1790 2442 1 chr3B.!!$R2 652
4 TraesCS3B01G089300 chr3A 46869767 46873258 3491 True 2521.500000 4793 92.0005 850 4346 2 chr3A.!!$R1 3496
5 TraesCS3B01G089300 chr3D 36359383 36363112 3729 True 1688.666667 4322 93.3630 914 4346 3 chr3D.!!$R2 3432
6 TraesCS3B01G089300 chr3D 419659266 419659949 683 True 857.000000 857 89.3430 28 709 1 chr3D.!!$R1 681
7 TraesCS3B01G089300 chr2D 495044350 495045032 682 True 883.000000 883 90.0730 28 709 1 chr2D.!!$R1 681
8 TraesCS3B01G089300 chr7D 105640500 105641177 677 True 874.000000 874 89.9850 33 709 1 chr7D.!!$R2 676
9 TraesCS3B01G089300 chr7D 606804748 606805428 680 False 870.000000 870 89.7810 28 709 1 chr7D.!!$F1 681
10 TraesCS3B01G089300 chr7D 65639528 65640068 540 True 608.000000 608 86.8470 1243 1797 1 chr7D.!!$R1 554
11 TraesCS3B01G089300 chr4B 348131487 348132169 682 True 850.000000 850 89.1970 28 709 1 chr4B.!!$R4 681
12 TraesCS3B01G089300 chr4B 348087907 348088589 682 True 828.000000 828 88.6130 28 709 1 chr4B.!!$R3 681
13 TraesCS3B01G089300 chr4B 14188184 14188977 793 True 673.000000 673 82.5500 2300 3079 1 chr4B.!!$R1 779
14 TraesCS3B01G089300 chr4B 109320678 109321607 929 False 414.000000 449 83.2700 2285 3020 2 chr4B.!!$F1 735
15 TraesCS3B01G089300 chr5D 410505082 410505757 675 True 833.000000 833 88.9870 33 709 1 chr5D.!!$R1 676
16 TraesCS3B01G089300 chr7B 568118511 568119186 675 False 828.000000 828 88.8070 33 709 1 chr7B.!!$F2 676
17 TraesCS3B01G089300 chr7B 89669307 89670074 767 False 665.000000 665 82.6470 2278 3064 1 chr7B.!!$F1 786
18 TraesCS3B01G089300 chr6B 663783551 663784316 765 False 603.000000 603 81.2500 2279 3064 1 chr6B.!!$F1 785

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
351 352 0.029567 GACGCGGAGTGAAGATCGAT 59.970 55.0 12.47 0.00 43.07 3.59 F
846 850 0.378962 CGTACTTCAGAGGAGCCTCG 59.621 60.0 10.69 6.49 46.90 4.63 F
1467 1760 0.601558 TGTGCGACTACCTGAACTCC 59.398 55.0 0.00 0.00 0.00 3.85 F
3146 3684 0.907486 ATGTTGCCTGAGCTAGCTGA 59.093 50.0 24.99 14.02 40.80 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 2144 2.161855 CACAAAGGACTGCCAATGCTA 58.838 47.619 0.0 0.0 38.71 3.49 R
2390 2711 0.881118 ACAACATACTTTGCCCTGCG 59.119 50.000 0.0 0.0 0.00 5.18 R
3180 3718 1.009675 GGCTACAAATGCATCGGCG 60.010 57.895 0.0 0.0 45.35 6.46 R
4313 4898 0.105964 TCCACCACTTGTTGTCCTCG 59.894 55.000 0.0 0.0 0.00 4.63 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
21 22 4.386867 TGGAATCCGACTATGTGAGTTC 57.613 45.455 0.00 0.00 39.06 3.01
22 23 3.132289 TGGAATCCGACTATGTGAGTTCC 59.868 47.826 0.00 0.00 39.06 3.62
23 24 3.385111 GGAATCCGACTATGTGAGTTCCT 59.615 47.826 0.00 0.00 39.06 3.36
24 25 4.141914 GGAATCCGACTATGTGAGTTCCTT 60.142 45.833 0.00 0.00 39.06 3.36
25 26 5.420409 GAATCCGACTATGTGAGTTCCTTT 58.580 41.667 0.00 0.00 39.06 3.11
26 27 4.884668 TCCGACTATGTGAGTTCCTTTT 57.115 40.909 0.00 0.00 39.06 2.27
27 28 4.817517 TCCGACTATGTGAGTTCCTTTTC 58.182 43.478 0.00 0.00 39.06 2.29
28 29 4.282449 TCCGACTATGTGAGTTCCTTTTCA 59.718 41.667 0.00 0.00 39.06 2.69
29 30 4.389077 CCGACTATGTGAGTTCCTTTTCAC 59.611 45.833 0.00 0.00 43.07 3.18
30 31 4.090066 CGACTATGTGAGTTCCTTTTCACG 59.910 45.833 0.84 0.00 45.12 4.35
31 32 4.957296 ACTATGTGAGTTCCTTTTCACGT 58.043 39.130 4.92 4.92 45.12 4.49
84 85 3.942829 TGCCGAAGAGAACAAGATCATT 58.057 40.909 0.00 0.00 0.00 2.57
94 95 8.577048 AGAGAACAAGATCATTGACATTGAAT 57.423 30.769 15.82 7.25 0.00 2.57
127 128 4.332828 TGAACGACCTCACTAGAGAATGA 58.667 43.478 0.00 0.00 44.98 2.57
273 274 1.653094 GCCGATGATTTTGGTGCCGA 61.653 55.000 0.00 0.00 0.00 5.54
297 298 1.111277 GGAACAAGTGCCAAAGGTGT 58.889 50.000 0.00 0.00 0.00 4.16
351 352 0.029567 GACGCGGAGTGAAGATCGAT 59.970 55.000 12.47 0.00 43.07 3.59
357 358 3.367607 CGGAGTGAAGATCGATCAAGAC 58.632 50.000 26.47 17.78 0.00 3.01
391 392 1.668751 GTCGTCACTTTTGCAAGACCA 59.331 47.619 10.07 0.00 33.72 4.02
393 394 1.400142 CGTCACTTTTGCAAGACCACA 59.600 47.619 10.07 0.00 33.72 4.17
400 401 5.809562 CACTTTTGCAAGACCACATTTTGTA 59.190 36.000 0.00 0.00 33.72 2.41
454 455 6.510478 GCGTGTGAACTGTGTTCTATTGTTTA 60.510 38.462 11.06 0.00 0.00 2.01
499 500 9.734620 GGAATCAATGTCAAATTCGATAATTGA 57.265 29.630 8.88 8.88 35.46 2.57
560 561 1.735920 CTCTGCATAGCCGATCCGC 60.736 63.158 0.00 0.00 0.00 5.54
617 619 0.515564 CGTTTTGCGGGGTCTAAGTG 59.484 55.000 0.00 0.00 36.85 3.16
676 678 3.392882 GCAAACTGCAAAAGCCTTATGT 58.607 40.909 0.00 0.00 44.26 2.29
683 686 2.687370 CAAAAGCCTTATGTGGGTTGC 58.313 47.619 4.42 0.00 45.79 4.17
693 696 1.370778 GTGGGTTGCCGTTTTACGC 60.371 57.895 0.00 0.00 40.91 4.42
709 713 2.161486 CGCGTCTGCTAGAGTTGCC 61.161 63.158 0.00 0.00 39.65 4.52
710 714 1.079819 GCGTCTGCTAGAGTTGCCA 60.080 57.895 0.00 0.00 38.39 4.92
711 715 0.460987 GCGTCTGCTAGAGTTGCCAT 60.461 55.000 0.00 0.00 38.39 4.40
712 716 2.009042 GCGTCTGCTAGAGTTGCCATT 61.009 52.381 0.00 0.00 38.39 3.16
713 717 2.738643 GCGTCTGCTAGAGTTGCCATTA 60.739 50.000 0.00 0.00 38.39 1.90
714 718 2.860735 CGTCTGCTAGAGTTGCCATTAC 59.139 50.000 0.00 0.00 0.00 1.89
715 719 3.429547 CGTCTGCTAGAGTTGCCATTACT 60.430 47.826 0.00 0.00 0.00 2.24
716 720 4.116238 GTCTGCTAGAGTTGCCATTACTC 58.884 47.826 0.00 0.00 41.83 2.59
722 726 3.618690 GAGTTGCCATTACTCTCCACT 57.381 47.619 0.00 0.00 39.12 4.00
723 727 3.265791 GAGTTGCCATTACTCTCCACTG 58.734 50.000 0.00 0.00 39.12 3.66
724 728 2.906389 AGTTGCCATTACTCTCCACTGA 59.094 45.455 0.00 0.00 0.00 3.41
725 729 3.003480 GTTGCCATTACTCTCCACTGAC 58.997 50.000 0.00 0.00 0.00 3.51
726 730 1.555075 TGCCATTACTCTCCACTGACC 59.445 52.381 0.00 0.00 0.00 4.02
727 731 1.555075 GCCATTACTCTCCACTGACCA 59.445 52.381 0.00 0.00 0.00 4.02
728 732 2.419297 GCCATTACTCTCCACTGACCAG 60.419 54.545 0.00 0.00 0.00 4.00
729 733 2.419297 CCATTACTCTCCACTGACCAGC 60.419 54.545 0.00 0.00 0.00 4.85
730 734 1.267121 TTACTCTCCACTGACCAGCC 58.733 55.000 0.00 0.00 0.00 4.85
731 735 0.409876 TACTCTCCACTGACCAGCCT 59.590 55.000 0.00 0.00 0.00 4.58
732 736 0.902516 ACTCTCCACTGACCAGCCTC 60.903 60.000 0.00 0.00 0.00 4.70
733 737 0.902048 CTCTCCACTGACCAGCCTCA 60.902 60.000 0.00 0.00 0.00 3.86
734 738 0.902048 TCTCCACTGACCAGCCTCAG 60.902 60.000 0.00 2.79 43.06 3.35
735 739 2.046507 CCACTGACCAGCCTCAGC 60.047 66.667 4.03 0.00 41.38 4.26
736 740 2.046507 CACTGACCAGCCTCAGCC 60.047 66.667 4.03 0.00 41.38 4.85
737 741 3.699894 ACTGACCAGCCTCAGCCG 61.700 66.667 4.03 0.00 41.38 5.52
755 759 3.967335 CGTCGAGGGAGCCGGATC 61.967 72.222 12.38 12.38 0.00 3.36
756 760 3.607661 GTCGAGGGAGCCGGATCC 61.608 72.222 31.09 31.09 38.76 3.36
762 766 3.551407 GGAGCCGGATCCCCTGAC 61.551 72.222 28.96 0.78 32.79 3.51
763 767 3.917760 GAGCCGGATCCCCTGACG 61.918 72.222 9.02 0.00 0.00 4.35
764 768 4.779733 AGCCGGATCCCCTGACGT 62.780 66.667 5.05 0.00 0.00 4.34
765 769 2.836360 GCCGGATCCCCTGACGTA 60.836 66.667 5.05 0.00 0.00 3.57
766 770 3.126528 CCGGATCCCCTGACGTAC 58.873 66.667 6.06 0.00 0.00 3.67
767 771 2.719979 CGGATCCCCTGACGTACG 59.280 66.667 15.01 15.01 0.00 3.67
768 772 2.842256 CGGATCCCCTGACGTACGG 61.842 68.421 21.06 1.19 0.00 4.02
769 773 2.416260 GATCCCCTGACGTACGGC 59.584 66.667 21.06 18.72 0.00 5.68
770 774 3.148031 GATCCCCTGACGTACGGCC 62.148 68.421 20.48 10.81 0.00 6.13
780 784 4.729856 GTACGGCCGCCTGACGTT 62.730 66.667 28.58 5.26 41.53 3.99
781 785 4.728102 TACGGCCGCCTGACGTTG 62.728 66.667 28.58 0.00 41.53 4.10
788 792 2.676471 GCCTGACGTTGGGCCATT 60.676 61.111 7.26 0.00 42.30 3.16
789 793 2.993471 GCCTGACGTTGGGCCATTG 61.993 63.158 7.26 5.36 42.30 2.82
790 794 1.303236 CCTGACGTTGGGCCATTGA 60.303 57.895 7.26 0.00 0.00 2.57
791 795 1.586154 CCTGACGTTGGGCCATTGAC 61.586 60.000 7.26 0.88 0.00 3.18
792 796 1.911293 CTGACGTTGGGCCATTGACG 61.911 60.000 23.66 23.66 41.00 4.35
793 797 2.112297 ACGTTGGGCCATTGACGT 59.888 55.556 24.89 24.89 43.12 4.34
794 798 2.258013 ACGTTGGGCCATTGACGTG 61.258 57.895 28.44 7.06 45.75 4.49
795 799 2.258013 CGTTGGGCCATTGACGTGT 61.258 57.895 18.64 0.00 0.00 4.49
796 800 1.285641 GTTGGGCCATTGACGTGTG 59.714 57.895 7.26 0.00 0.00 3.82
797 801 1.900981 TTGGGCCATTGACGTGTGG 60.901 57.895 7.26 0.00 38.55 4.17
798 802 3.061848 GGGCCATTGACGTGTGGG 61.062 66.667 4.39 1.41 36.00 4.61
799 803 2.282180 GGCCATTGACGTGTGGGT 60.282 61.111 0.00 0.00 36.00 4.51
800 804 2.332654 GGCCATTGACGTGTGGGTC 61.333 63.158 0.00 0.00 36.00 4.46
801 805 2.332654 GCCATTGACGTGTGGGTCC 61.333 63.158 11.80 0.00 36.07 4.46
802 806 2.032634 CCATTGACGTGTGGGTCCG 61.033 63.158 0.00 0.00 36.07 4.79
803 807 2.032634 CATTGACGTGTGGGTCCGG 61.033 63.158 0.00 0.00 36.07 5.14
804 808 2.211410 ATTGACGTGTGGGTCCGGA 61.211 57.895 0.00 0.00 36.07 5.14
805 809 1.550130 ATTGACGTGTGGGTCCGGAT 61.550 55.000 7.81 0.00 36.07 4.18
806 810 2.162338 TTGACGTGTGGGTCCGGATC 62.162 60.000 7.81 6.88 36.07 3.36
807 811 3.366739 GACGTGTGGGTCCGGATCC 62.367 68.421 28.04 28.04 0.00 3.36
808 812 3.387091 CGTGTGGGTCCGGATCCA 61.387 66.667 33.28 33.28 39.79 3.41
812 816 2.121832 TGGGTCCGGATCCACACT 59.878 61.111 33.28 0.00 36.49 3.55
813 817 1.987855 TGGGTCCGGATCCACACTC 60.988 63.158 33.28 7.04 36.49 3.51
814 818 1.987855 GGGTCCGGATCCACACTCA 60.988 63.158 29.68 0.00 0.00 3.41
815 819 1.517832 GGTCCGGATCCACACTCAG 59.482 63.158 7.81 0.00 0.00 3.35
816 820 1.258445 GGTCCGGATCCACACTCAGT 61.258 60.000 7.81 0.00 0.00 3.41
826 830 3.736483 CACTCAGTGTGTGTGGGC 58.264 61.111 15.60 0.00 41.53 5.36
827 831 1.893808 CACTCAGTGTGTGTGGGCC 60.894 63.158 15.60 0.00 41.53 5.80
828 832 2.666190 CTCAGTGTGTGTGGGCCG 60.666 66.667 0.00 0.00 0.00 6.13
829 833 3.460672 CTCAGTGTGTGTGGGCCGT 62.461 63.158 0.00 0.00 0.00 5.68
830 834 2.094757 CTCAGTGTGTGTGGGCCGTA 62.095 60.000 0.00 0.00 0.00 4.02
831 835 1.959226 CAGTGTGTGTGGGCCGTAC 60.959 63.158 0.00 0.29 0.00 3.67
832 836 2.138179 AGTGTGTGTGGGCCGTACT 61.138 57.895 10.72 0.90 0.00 2.73
833 837 1.227734 GTGTGTGTGGGCCGTACTT 60.228 57.895 10.72 0.00 0.00 2.24
834 838 1.070105 TGTGTGTGGGCCGTACTTC 59.930 57.895 10.72 5.53 0.00 3.01
835 839 1.070105 GTGTGTGGGCCGTACTTCA 59.930 57.895 10.72 6.70 0.00 3.02
836 840 0.949105 GTGTGTGGGCCGTACTTCAG 60.949 60.000 10.72 0.00 0.00 3.02
837 841 1.116536 TGTGTGGGCCGTACTTCAGA 61.117 55.000 10.72 0.00 0.00 3.27
838 842 0.389948 GTGTGGGCCGTACTTCAGAG 60.390 60.000 9.79 0.00 0.00 3.35
839 843 1.218316 GTGGGCCGTACTTCAGAGG 59.782 63.158 0.00 0.00 0.00 3.69
840 844 1.077805 TGGGCCGTACTTCAGAGGA 59.922 57.895 0.00 0.00 0.00 3.71
841 845 0.970937 TGGGCCGTACTTCAGAGGAG 60.971 60.000 0.00 0.00 0.00 3.69
842 846 1.142097 GGCCGTACTTCAGAGGAGC 59.858 63.158 0.00 0.00 0.00 4.70
843 847 1.142097 GCCGTACTTCAGAGGAGCC 59.858 63.158 0.00 0.00 0.00 4.70
844 848 1.324005 GCCGTACTTCAGAGGAGCCT 61.324 60.000 0.00 0.00 0.00 4.58
845 849 0.741915 CCGTACTTCAGAGGAGCCTC 59.258 60.000 8.50 8.50 43.03 4.70
846 850 0.378962 CGTACTTCAGAGGAGCCTCG 59.621 60.000 10.69 6.49 46.90 4.63
847 851 1.465794 GTACTTCAGAGGAGCCTCGT 58.534 55.000 10.69 5.62 46.90 4.18
848 852 1.402613 GTACTTCAGAGGAGCCTCGTC 59.597 57.143 10.69 6.30 46.90 4.20
864 868 1.138247 GTCCCGCGTCGAGTAACAT 59.862 57.895 4.92 0.00 0.00 2.71
907 911 3.084579 CGTCGAGCAACAGGATGC 58.915 61.111 0.00 0.00 46.78 3.91
943 947 2.224113 ACGGTACTTTCAGGCGAAGAAA 60.224 45.455 5.54 4.50 34.16 2.52
947 951 4.152580 GGTACTTTCAGGCGAAGAAAAGAG 59.847 45.833 7.49 0.00 34.84 2.85
960 964 4.395959 AGAAAAGAGTGTGTTACCACGA 57.604 40.909 0.00 0.00 44.92 4.35
1254 1265 3.144193 CTCGCCGAGCTCTCCCTT 61.144 66.667 12.85 0.00 0.00 3.95
1323 1334 3.774959 CTCCCCGCTCCGATTCACG 62.775 68.421 0.00 0.00 42.18 4.35
1425 1718 4.890306 GCCTCCCCCTCCTCCTCC 62.890 77.778 0.00 0.00 0.00 4.30
1428 1721 3.742248 CTCCCCCTCCTCCTCCGTC 62.742 73.684 0.00 0.00 0.00 4.79
1467 1760 0.601558 TGTGCGACTACCTGAACTCC 59.398 55.000 0.00 0.00 0.00 3.85
1981 2289 9.314321 TCTACTTGCTGTTAATTCAGTTATAGC 57.686 33.333 0.00 0.00 37.70 2.97
1982 2290 7.321745 ACTTGCTGTTAATTCAGTTATAGCC 57.678 36.000 0.00 0.00 37.70 3.93
1983 2291 7.112779 ACTTGCTGTTAATTCAGTTATAGCCT 58.887 34.615 0.00 0.00 37.70 4.58
1984 2292 7.611855 ACTTGCTGTTAATTCAGTTATAGCCTT 59.388 33.333 0.00 0.00 37.70 4.35
1985 2293 9.109393 CTTGCTGTTAATTCAGTTATAGCCTTA 57.891 33.333 0.00 0.00 37.70 2.69
1986 2294 9.627123 TTGCTGTTAATTCAGTTATAGCCTTAT 57.373 29.630 0.00 0.00 37.70 1.73
2263 2581 1.333619 CTGTGGGAAAACAACCTCACG 59.666 52.381 0.00 0.00 34.08 4.35
2308 2626 9.199645 AGATAGATTGTCCGAATCATATCTCAT 57.800 33.333 0.00 0.00 30.43 2.90
2390 2711 7.084486 AGAAAATTTTCTGTTCCTACGAATGC 58.916 34.615 28.35 0.10 45.27 3.56
2416 2737 2.223923 GGCAAAGTATGTTGTTGGCACA 60.224 45.455 4.52 0.00 44.68 4.57
2421 2742 3.338249 AGTATGTTGTTGGCACAGCTAG 58.662 45.455 0.00 0.00 42.39 3.42
2423 2744 2.340210 TGTTGTTGGCACAGCTAGAA 57.660 45.000 0.00 0.00 42.39 2.10
2449 2770 3.971702 GCCAAGCCTGGTGGAGGT 61.972 66.667 7.49 0.00 45.53 3.85
2704 3229 5.048083 TGTCCATTCTCACAAAATTAGGTGC 60.048 40.000 4.89 0.00 35.04 5.01
2764 3289 5.359576 TCTGTTGGTTAGCAACAAGTTGAAT 59.640 36.000 26.33 6.71 42.93 2.57
2770 3295 3.004024 AGCAACAAGTTGAATGCTTCG 57.996 42.857 25.04 3.15 42.93 3.79
2775 3302 2.484264 ACAAGTTGAATGCTTCGCCTAC 59.516 45.455 10.54 0.00 0.00 3.18
2939 3477 5.530915 TGAAGTAACCAATCACCACTGAAAG 59.469 40.000 0.00 0.00 42.29 2.62
3086 3624 6.974965 AGCCTATTTTGTTTGAGTCTTCAAG 58.025 36.000 0.00 0.00 43.76 3.02
3122 3660 4.378046 GGATTTTACACAGGTTGCTACACG 60.378 45.833 0.00 0.00 0.00 4.49
3146 3684 0.907486 ATGTTGCCTGAGCTAGCTGA 59.093 50.000 24.99 14.02 40.80 4.26
3180 3718 4.202050 ACTCCAAAACTGAGCATTGTTGTC 60.202 41.667 0.00 0.00 32.98 3.18
3243 3781 3.002759 GGGCGCAGAATGTTCTCTTTATC 59.997 47.826 10.83 0.00 39.31 1.75
3249 3787 4.635765 CAGAATGTTCTCTTTATCGGCCAA 59.364 41.667 2.24 0.00 34.74 4.52
3409 3950 1.269448 CGTTGTCTTTTGGGACCATGG 59.731 52.381 11.19 11.19 35.54 3.66
3496 4037 1.498865 GGTCAGCGCATGGATTACCG 61.499 60.000 11.47 0.00 39.42 4.02
3518 4059 5.348164 CGGAAATCCTGTTGAAACAAAGTT 58.652 37.500 0.00 0.00 38.66 2.66
3522 4063 6.773976 AATCCTGTTGAAACAAAGTTCTGA 57.226 33.333 0.00 0.00 38.66 3.27
3574 4115 4.784177 TCTGAAAATGATGGCAGCTATCA 58.216 39.130 22.45 22.45 38.76 2.15
3577 4118 4.521639 TGAAAATGATGGCAGCTATCATCC 59.478 41.667 28.81 21.31 42.73 3.51
3692 4233 4.827284 TCTGATGACGGATAGCATGAGTAA 59.173 41.667 0.00 0.00 29.53 2.24
3700 4241 3.511934 GGATAGCATGAGTAATCGTCCCT 59.488 47.826 0.00 0.00 0.00 4.20
3729 4270 3.543680 TTTGGAAGAGGAAGGCTATCG 57.456 47.619 0.00 0.00 0.00 2.92
3736 4277 2.952978 AGAGGAAGGCTATCGTAGTGTG 59.047 50.000 0.00 0.00 0.00 3.82
3743 4284 3.447586 AGGCTATCGTAGTGTGTGATTGT 59.552 43.478 0.00 0.00 0.00 2.71
3748 4290 5.899120 ATCGTAGTGTGTGATTGTCTACT 57.101 39.130 0.00 0.00 31.81 2.57
3767 4309 4.618920 ACTGCGTCCTATATAAAAGGGG 57.381 45.455 5.01 0.48 34.66 4.79
3852 4394 7.504238 TGTGTTGTAAATCATGTAGTTTCCCTT 59.496 33.333 0.00 0.00 0.00 3.95
3987 4532 5.175673 TCGATGCGATTTGTGAATCTGATAC 59.824 40.000 0.00 0.00 39.61 2.24
3991 4536 5.523552 TGCGATTTGTGAATCTGATACGATT 59.476 36.000 0.00 0.00 39.61 3.34
4026 4571 7.420800 GGATCAGGTGTGAATATGATTTTGAC 58.579 38.462 0.00 0.00 35.88 3.18
4049 4594 3.552699 CAGCGCCCAATTTGAATTATGTG 59.447 43.478 2.29 0.00 0.00 3.21
4052 4597 4.111916 CGCCCAATTTGAATTATGTGGTC 58.888 43.478 0.00 0.00 0.00 4.02
4053 4598 4.142182 CGCCCAATTTGAATTATGTGGTCT 60.142 41.667 0.00 0.00 0.00 3.85
4054 4599 5.067153 CGCCCAATTTGAATTATGTGGTCTA 59.933 40.000 0.00 0.00 0.00 2.59
4113 4658 0.389817 CAACGAGTGCGGGAGATTCA 60.390 55.000 0.00 0.00 43.17 2.57
4130 4675 6.127083 GGAGATTCATTCATTTTGCCCCTTTA 60.127 38.462 0.00 0.00 0.00 1.85
4131 4676 6.881570 AGATTCATTCATTTTGCCCCTTTAG 58.118 36.000 0.00 0.00 0.00 1.85
4132 4677 6.669154 AGATTCATTCATTTTGCCCCTTTAGA 59.331 34.615 0.00 0.00 0.00 2.10
4133 4678 6.872585 TTCATTCATTTTGCCCCTTTAGAT 57.127 33.333 0.00 0.00 0.00 1.98
4134 4679 7.969690 TTCATTCATTTTGCCCCTTTAGATA 57.030 32.000 0.00 0.00 0.00 1.98
4135 4680 8.551682 TTCATTCATTTTGCCCCTTTAGATAT 57.448 30.769 0.00 0.00 0.00 1.63
4136 4681 7.954835 TCATTCATTTTGCCCCTTTAGATATG 58.045 34.615 0.00 0.00 0.00 1.78
4137 4682 7.784073 TCATTCATTTTGCCCCTTTAGATATGA 59.216 33.333 0.00 0.00 0.00 2.15
4138 4683 8.591072 CATTCATTTTGCCCCTTTAGATATGAT 58.409 33.333 0.00 0.00 0.00 2.45
4139 4684 8.551682 TTCATTTTGCCCCTTTAGATATGATT 57.448 30.769 0.00 0.00 0.00 2.57
4140 4685 8.551682 TCATTTTGCCCCTTTAGATATGATTT 57.448 30.769 0.00 0.00 0.00 2.17
4141 4686 8.991275 TCATTTTGCCCCTTTAGATATGATTTT 58.009 29.630 0.00 0.00 0.00 1.82
4143 4688 7.732222 TTTGCCCCTTTAGATATGATTTTGT 57.268 32.000 0.00 0.00 0.00 2.83
4145 4690 5.833131 TGCCCCTTTAGATATGATTTTGTCC 59.167 40.000 0.00 0.00 0.00 4.02
4146 4691 6.071320 GCCCCTTTAGATATGATTTTGTCCT 58.929 40.000 0.00 0.00 0.00 3.85
4149 4694 6.992715 CCCTTTAGATATGATTTTGTCCTCGT 59.007 38.462 0.00 0.00 0.00 4.18
4150 4695 8.148351 CCCTTTAGATATGATTTTGTCCTCGTA 58.852 37.037 0.00 0.00 0.00 3.43
4151 4696 9.712305 CCTTTAGATATGATTTTGTCCTCGTAT 57.288 33.333 0.00 0.00 0.00 3.06
4203 4784 5.751243 TCTCACTACCTTTCAAGCAAAAC 57.249 39.130 0.00 0.00 0.00 2.43
4303 4888 7.821846 TGGTTTGCAATAAATATTTCTTGGGTC 59.178 33.333 21.22 10.19 0.00 4.46
4342 4927 4.696479 ACAAGTGGTGGAGATGGATATC 57.304 45.455 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.132289 GGAACTCACATAGTCGGATTCCA 59.868 47.826 3.09 0.00 37.50 3.53
1 2 3.385111 AGGAACTCACATAGTCGGATTCC 59.615 47.826 0.00 0.00 37.50 3.01
2 3 4.657436 AGGAACTCACATAGTCGGATTC 57.343 45.455 0.00 0.00 37.50 2.52
3 4 5.422214 AAAGGAACTCACATAGTCGGATT 57.578 39.130 0.00 0.00 38.49 3.01
5 6 4.282449 TGAAAAGGAACTCACATAGTCGGA 59.718 41.667 0.00 0.00 38.49 4.55
6 7 4.389077 GTGAAAAGGAACTCACATAGTCGG 59.611 45.833 0.00 0.00 41.35 4.79
7 8 4.090066 CGTGAAAAGGAACTCACATAGTCG 59.910 45.833 3.39 0.00 41.71 4.18
8 9 4.989168 ACGTGAAAAGGAACTCACATAGTC 59.011 41.667 0.00 0.00 41.71 2.59
9 10 4.957296 ACGTGAAAAGGAACTCACATAGT 58.043 39.130 0.00 0.00 41.71 2.12
10 11 4.389077 GGACGTGAAAAGGAACTCACATAG 59.611 45.833 0.00 0.00 41.71 2.23
11 12 4.312443 GGACGTGAAAAGGAACTCACATA 58.688 43.478 0.00 0.00 41.71 2.29
12 13 3.139077 GGACGTGAAAAGGAACTCACAT 58.861 45.455 0.00 0.00 41.71 3.21
13 14 2.557317 GGACGTGAAAAGGAACTCACA 58.443 47.619 0.00 0.00 41.71 3.58
14 15 1.525619 CGGACGTGAAAAGGAACTCAC 59.474 52.381 0.00 0.00 38.49 3.51
15 16 1.860676 CGGACGTGAAAAGGAACTCA 58.139 50.000 0.00 0.00 38.49 3.41
16 17 0.511653 GCGGACGTGAAAAGGAACTC 59.488 55.000 0.00 0.00 38.49 3.01
18 19 0.234884 CAGCGGACGTGAAAAGGAAC 59.765 55.000 0.00 0.00 0.00 3.62
19 20 0.105224 TCAGCGGACGTGAAAAGGAA 59.895 50.000 0.00 0.00 0.00 3.36
20 21 0.105224 TTCAGCGGACGTGAAAAGGA 59.895 50.000 0.00 0.00 30.89 3.36
21 22 0.941542 TTTCAGCGGACGTGAAAAGG 59.058 50.000 14.99 0.00 40.20 3.11
22 23 2.748461 TTTTCAGCGGACGTGAAAAG 57.252 45.000 20.36 0.00 44.89 2.27
23 24 1.738350 TGTTTTCAGCGGACGTGAAAA 59.262 42.857 20.36 20.36 46.62 2.29
24 25 1.370609 TGTTTTCAGCGGACGTGAAA 58.629 45.000 14.02 14.02 41.16 2.69
25 26 1.370609 TTGTTTTCAGCGGACGTGAA 58.629 45.000 0.00 5.91 31.98 3.18
26 27 1.329292 CTTTGTTTTCAGCGGACGTGA 59.671 47.619 0.00 0.00 0.00 4.35
27 28 1.741993 CTTTGTTTTCAGCGGACGTG 58.258 50.000 0.00 0.00 0.00 4.49
28 29 0.028902 GCTTTGTTTTCAGCGGACGT 59.971 50.000 0.00 0.00 0.00 4.34
29 30 0.660300 GGCTTTGTTTTCAGCGGACG 60.660 55.000 0.00 0.00 0.00 4.79
30 31 0.383949 TGGCTTTGTTTTCAGCGGAC 59.616 50.000 0.00 0.00 0.00 4.79
31 32 1.000385 CATGGCTTTGTTTTCAGCGGA 60.000 47.619 0.00 0.00 0.00 5.54
94 95 3.244044 TGAGGTCGTTCATGTCATTGTGA 60.244 43.478 0.00 0.00 0.00 3.58
107 108 4.079970 TGTCATTCTCTAGTGAGGTCGTT 58.920 43.478 0.00 0.00 40.58 3.85
127 128 9.584008 AAGATATCTTTTCTTGCCATATCATGT 57.416 29.630 12.37 0.00 32.30 3.21
144 145 7.377696 AGCATTCTCCTCTTCAAGATATCTT 57.622 36.000 12.37 12.37 36.45 2.40
215 216 1.339929 GGCGACATTGGTTCCAAAACT 59.660 47.619 8.38 0.00 35.61 2.66
217 218 0.312416 CGGCGACATTGGTTCCAAAA 59.688 50.000 0.00 0.00 0.00 2.44
243 244 2.881539 ATCATCGGCTGGTGCACTGG 62.882 60.000 17.98 10.78 41.91 4.00
273 274 2.168313 CCTTTGGCACTTGTTCCAACTT 59.832 45.455 4.46 0.00 41.61 2.66
290 291 1.812708 GCAACCACCGAGTACACCTTT 60.813 52.381 0.00 0.00 0.00 3.11
291 292 0.250166 GCAACCACCGAGTACACCTT 60.250 55.000 0.00 0.00 0.00 3.50
297 298 0.108992 GTCATCGCAACCACCGAGTA 60.109 55.000 0.00 0.00 38.20 2.59
333 334 0.029567 GATCGATCTTCACTCCGCGT 59.970 55.000 18.29 0.00 0.00 6.01
351 352 0.388520 CACGTCTGGCATCGTCTTGA 60.389 55.000 13.34 0.00 38.23 3.02
357 358 2.880879 CGACCACGTCTGGCATCG 60.881 66.667 9.92 9.92 42.08 3.84
454 455 8.961294 TGATTCCAACAAATGAGTTCAAATTT 57.039 26.923 0.00 0.00 0.00 1.82
499 500 1.740296 CCCGCAAACCGAAGACGAT 60.740 57.895 0.00 0.00 42.66 3.73
500 501 2.356553 CCCGCAAACCGAAGACGA 60.357 61.111 0.00 0.00 42.66 4.20
543 544 2.026945 TTGCGGATCGGCTATGCAGA 62.027 55.000 23.71 1.25 37.15 4.26
545 546 0.746204 TTTTGCGGATCGGCTATGCA 60.746 50.000 23.71 6.98 0.00 3.96
635 637 4.929479 TGCAGAAAAAGGTATATGTGGGT 58.071 39.130 0.00 0.00 0.00 4.51
676 678 2.894565 CGCGTAAAACGGCAACCCA 61.895 57.895 0.00 0.00 42.82 4.51
683 686 0.638746 CTAGCAGACGCGTAAAACGG 59.361 55.000 13.97 0.71 45.49 4.44
693 696 2.015736 AATGGCAACTCTAGCAGACG 57.984 50.000 0.00 0.00 37.61 4.18
709 713 2.419297 GGCTGGTCAGTGGAGAGTAATG 60.419 54.545 0.00 0.00 0.00 1.90
710 714 1.834263 GGCTGGTCAGTGGAGAGTAAT 59.166 52.381 0.00 0.00 0.00 1.89
711 715 1.203187 AGGCTGGTCAGTGGAGAGTAA 60.203 52.381 0.00 0.00 0.00 2.24
712 716 0.409876 AGGCTGGTCAGTGGAGAGTA 59.590 55.000 0.00 0.00 0.00 2.59
713 717 0.902516 GAGGCTGGTCAGTGGAGAGT 60.903 60.000 0.00 0.00 0.00 3.24
714 718 0.902048 TGAGGCTGGTCAGTGGAGAG 60.902 60.000 0.00 0.00 0.00 3.20
715 719 0.902048 CTGAGGCTGGTCAGTGGAGA 60.902 60.000 0.00 0.00 39.39 3.71
716 720 1.595882 CTGAGGCTGGTCAGTGGAG 59.404 63.158 0.00 0.00 39.39 3.86
717 721 2.587247 GCTGAGGCTGGTCAGTGGA 61.587 63.158 0.00 0.00 45.07 4.02
718 722 2.046507 GCTGAGGCTGGTCAGTGG 60.047 66.667 0.00 0.00 45.07 4.00
719 723 2.046507 GGCTGAGGCTGGTCAGTG 60.047 66.667 0.00 0.00 45.07 3.66
720 724 3.699894 CGGCTGAGGCTGGTCAGT 61.700 66.667 4.02 0.00 45.07 3.41
738 742 3.967335 GATCCGGCTCCCTCGACG 61.967 72.222 0.00 0.00 0.00 5.12
739 743 3.607661 GGATCCGGCTCCCTCGAC 61.608 72.222 13.69 0.00 0.00 4.20
745 749 3.551407 GTCAGGGGATCCGGCTCC 61.551 72.222 16.35 16.35 38.33 4.70
746 750 3.917760 CGTCAGGGGATCCGGCTC 61.918 72.222 5.45 0.00 38.33 4.70
747 751 3.369410 TACGTCAGGGGATCCGGCT 62.369 63.158 5.45 0.00 38.33 5.52
748 752 2.836360 TACGTCAGGGGATCCGGC 60.836 66.667 5.45 0.00 38.33 6.13
749 753 2.842256 CGTACGTCAGGGGATCCGG 61.842 68.421 7.22 0.00 38.33 5.14
750 754 2.719979 CGTACGTCAGGGGATCCG 59.280 66.667 7.22 0.00 38.33 4.18
751 755 3.126528 CCGTACGTCAGGGGATCC 58.873 66.667 15.21 1.92 0.00 3.36
752 756 2.416260 GCCGTACGTCAGGGGATC 59.584 66.667 15.21 0.00 32.45 3.36
753 757 3.152400 GGCCGTACGTCAGGGGAT 61.152 66.667 15.21 0.00 32.45 3.85
763 767 4.729856 AACGTCAGGCGGCCGTAC 62.730 66.667 28.70 20.19 46.52 3.67
764 768 4.728102 CAACGTCAGGCGGCCGTA 62.728 66.667 28.70 7.31 46.52 4.02
772 776 1.303236 TCAATGGCCCAACGTCAGG 60.303 57.895 0.00 0.00 0.00 3.86
773 777 1.875963 GTCAATGGCCCAACGTCAG 59.124 57.895 0.00 0.00 0.00 3.51
774 778 1.963855 CGTCAATGGCCCAACGTCA 60.964 57.895 0.00 0.00 0.00 4.35
775 779 1.964373 ACGTCAATGGCCCAACGTC 60.964 57.895 6.27 0.00 44.30 4.34
776 780 2.112297 ACGTCAATGGCCCAACGT 59.888 55.556 6.27 6.27 42.96 3.99
777 781 2.258013 ACACGTCAATGGCCCAACG 61.258 57.895 0.00 4.94 40.77 4.10
778 782 1.285641 CACACGTCAATGGCCCAAC 59.714 57.895 0.00 0.00 0.00 3.77
779 783 1.900981 CCACACGTCAATGGCCCAA 60.901 57.895 0.00 0.00 0.00 4.12
780 784 2.282110 CCACACGTCAATGGCCCA 60.282 61.111 0.00 0.00 0.00 5.36
781 785 3.061848 CCCACACGTCAATGGCCC 61.062 66.667 0.00 0.00 34.37 5.80
782 786 2.282180 ACCCACACGTCAATGGCC 60.282 61.111 0.00 0.00 34.37 5.36
783 787 2.332654 GGACCCACACGTCAATGGC 61.333 63.158 4.75 0.00 34.37 4.40
784 788 2.032634 CGGACCCACACGTCAATGG 61.033 63.158 3.46 3.46 34.24 3.16
785 789 2.032634 CCGGACCCACACGTCAATG 61.033 63.158 0.00 0.00 34.24 2.82
786 790 1.550130 ATCCGGACCCACACGTCAAT 61.550 55.000 6.12 0.00 34.24 2.57
787 791 2.162338 GATCCGGACCCACACGTCAA 62.162 60.000 6.12 0.00 34.24 3.18
788 792 2.602267 ATCCGGACCCACACGTCA 60.602 61.111 6.12 0.00 34.24 4.35
789 793 2.183555 GATCCGGACCCACACGTC 59.816 66.667 6.12 0.00 0.00 4.34
790 794 3.387947 GGATCCGGACCCACACGT 61.388 66.667 11.17 0.00 0.00 4.49
791 795 3.387091 TGGATCCGGACCCACACG 61.387 66.667 15.87 0.00 0.00 4.49
795 799 1.987855 GAGTGTGGATCCGGACCCA 60.988 63.158 15.87 15.87 0.00 4.51
796 800 1.961180 CTGAGTGTGGATCCGGACCC 61.961 65.000 8.42 8.42 0.00 4.46
797 801 1.258445 ACTGAGTGTGGATCCGGACC 61.258 60.000 6.12 11.46 0.00 4.46
798 802 0.108615 CACTGAGTGTGGATCCGGAC 60.109 60.000 6.12 6.04 42.68 4.79
799 803 2.276869 CACTGAGTGTGGATCCGGA 58.723 57.895 6.61 6.61 42.68 5.14
800 804 4.919653 CACTGAGTGTGGATCCGG 57.080 61.111 7.39 0.00 42.68 5.14
810 814 2.510906 GGCCCACACACACTGAGT 59.489 61.111 0.00 0.00 0.00 3.41
811 815 2.094757 TACGGCCCACACACACTGAG 62.095 60.000 0.00 0.00 0.00 3.35
812 816 2.134933 TACGGCCCACACACACTGA 61.135 57.895 0.00 0.00 0.00 3.41
813 817 1.959226 GTACGGCCCACACACACTG 60.959 63.158 0.00 0.00 0.00 3.66
814 818 1.692173 AAGTACGGCCCACACACACT 61.692 55.000 0.00 0.00 0.00 3.55
815 819 1.226030 GAAGTACGGCCCACACACAC 61.226 60.000 0.00 0.00 0.00 3.82
816 820 1.070105 GAAGTACGGCCCACACACA 59.930 57.895 0.00 0.00 0.00 3.72
817 821 0.949105 CTGAAGTACGGCCCACACAC 60.949 60.000 0.00 0.00 0.00 3.82
818 822 1.116536 TCTGAAGTACGGCCCACACA 61.117 55.000 0.00 0.00 0.00 3.72
819 823 0.389948 CTCTGAAGTACGGCCCACAC 60.390 60.000 0.00 0.00 0.00 3.82
820 824 1.541310 CCTCTGAAGTACGGCCCACA 61.541 60.000 0.00 0.00 0.00 4.17
821 825 1.218316 CCTCTGAAGTACGGCCCAC 59.782 63.158 0.00 0.00 0.00 4.61
822 826 0.970937 CTCCTCTGAAGTACGGCCCA 60.971 60.000 0.00 0.00 0.00 5.36
823 827 1.817209 CTCCTCTGAAGTACGGCCC 59.183 63.158 0.00 0.00 0.00 5.80
824 828 1.142097 GCTCCTCTGAAGTACGGCC 59.858 63.158 0.00 0.00 0.00 6.13
825 829 1.142097 GGCTCCTCTGAAGTACGGC 59.858 63.158 0.00 0.00 0.00 5.68
826 830 0.741915 GAGGCTCCTCTGAAGTACGG 59.258 60.000 2.15 0.00 39.80 4.02
827 831 0.378962 CGAGGCTCCTCTGAAGTACG 59.621 60.000 9.32 0.00 40.69 3.67
828 832 1.402613 GACGAGGCTCCTCTGAAGTAC 59.597 57.143 9.32 0.00 40.69 2.73
829 833 1.682394 GGACGAGGCTCCTCTGAAGTA 60.682 57.143 9.32 0.00 40.69 2.24
830 834 0.968393 GGACGAGGCTCCTCTGAAGT 60.968 60.000 9.32 4.42 40.69 3.01
831 835 1.671901 GGGACGAGGCTCCTCTGAAG 61.672 65.000 9.32 1.36 40.69 3.02
832 836 1.682684 GGGACGAGGCTCCTCTGAA 60.683 63.158 9.32 0.00 40.69 3.02
833 837 2.043852 GGGACGAGGCTCCTCTGA 60.044 66.667 9.32 0.00 40.69 3.27
846 850 1.138047 CATGTTACTCGACGCGGGAC 61.138 60.000 12.47 0.00 0.00 4.46
847 851 1.138036 CATGTTACTCGACGCGGGA 59.862 57.895 12.47 6.50 0.00 5.14
848 852 0.248907 ATCATGTTACTCGACGCGGG 60.249 55.000 12.47 1.12 0.00 6.13
859 863 1.338294 ACCGTTGGACGCATCATGTTA 60.338 47.619 0.00 0.00 40.91 2.41
864 868 1.880271 TTTTACCGTTGGACGCATCA 58.120 45.000 0.00 0.00 40.91 3.07
910 914 0.389426 AGTACCGTTGGACGCATGTC 60.389 55.000 0.00 0.00 44.72 3.06
911 915 0.034337 AAGTACCGTTGGACGCATGT 59.966 50.000 0.00 0.00 40.91 3.21
912 916 1.127951 GAAAGTACCGTTGGACGCATG 59.872 52.381 0.00 0.00 40.91 4.06
960 964 0.605319 TCAGCACGAAGGCGGAAAAT 60.605 50.000 0.00 0.00 43.17 1.82
1093 1104 4.095400 GAGGAGGGCAGGGGAGGA 62.095 72.222 0.00 0.00 0.00 3.71
1837 2144 2.161855 CACAAAGGACTGCCAATGCTA 58.838 47.619 0.00 0.00 38.71 3.49
1871 2179 3.188667 GCTACAACAAAACCAGACTAGCC 59.811 47.826 0.00 0.00 0.00 3.93
1988 2296 7.705752 GCTAAACAGAGTACATTAAGGACTACC 59.294 40.741 0.00 0.00 0.00 3.18
2114 2427 9.950496 ATCATCACTAAACAAGAATACAACTCT 57.050 29.630 0.00 0.00 0.00 3.24
2280 2598 9.944663 GAGATATGATTCGGACAATCTATCTAC 57.055 37.037 12.20 7.23 33.04 2.59
2308 2626 8.397906 GCTGCATAAACAACAGATACTCATAAA 58.602 33.333 0.00 0.00 33.10 1.40
2390 2711 0.881118 ACAACATACTTTGCCCTGCG 59.119 50.000 0.00 0.00 0.00 5.18
2416 2737 3.131755 GCTTGGCCATCAATTTTCTAGCT 59.868 43.478 6.09 0.00 34.45 3.32
2704 3229 4.871933 ACTAAAACCAGCCCATCAAAAG 57.128 40.909 0.00 0.00 0.00 2.27
2770 3295 6.374333 TCCAAACTCTTACAATTCATGTAGGC 59.626 38.462 0.00 0.00 45.00 3.93
2775 3302 6.573664 TGGTCCAAACTCTTACAATTCATG 57.426 37.500 0.00 0.00 0.00 3.07
2939 3477 7.577979 TGAACAGAACGTCCATTTTGTATAAC 58.422 34.615 0.00 0.00 0.00 1.89
2954 3492 5.155509 TGTTGTCATTTCTGAACAGAACG 57.844 39.130 15.47 10.61 46.13 3.95
3086 3624 4.020543 TGTAAAATCCACATGGTTAGGGC 58.979 43.478 0.00 0.00 36.34 5.19
3122 3660 4.869297 CAGCTAGCTCAGGCAACATATATC 59.131 45.833 16.15 0.00 41.70 1.63
3146 3684 2.173569 AGTTTTGGAGTCAGGCTCTTGT 59.826 45.455 1.07 0.00 43.62 3.16
3180 3718 1.009675 GGCTACAAATGCATCGGCG 60.010 57.895 0.00 0.00 45.35 6.46
3243 3781 1.816074 TTTTAGCAGGTAGTTGGCCG 58.184 50.000 0.00 0.00 0.00 6.13
3382 3923 4.142337 GGTCCCAAAAGACAACGAGAAAAA 60.142 41.667 0.00 0.00 38.59 1.94
3409 3950 9.228636 ACAATACAAAAATTAGTGAACGAACAC 57.771 29.630 8.22 8.22 40.60 3.32
3496 4037 6.476706 CAGAACTTTGTTTCAACAGGATTTCC 59.523 38.462 0.00 0.00 40.50 3.13
3518 4059 3.569701 GGTGGCTCAAAACATTTCTCAGA 59.430 43.478 0.00 0.00 0.00 3.27
3522 4063 2.676748 TGGGTGGCTCAAAACATTTCT 58.323 42.857 0.00 0.00 0.00 2.52
3574 4115 3.307480 CCTTCCAACAAGTTCTACCGGAT 60.307 47.826 9.46 0.00 0.00 4.18
3577 4118 3.121738 ACCTTCCAACAAGTTCTACCG 57.878 47.619 0.00 0.00 0.00 4.02
3642 4183 8.805175 AGATGTGAATGGAATGTCAAATGTTAA 58.195 29.630 0.00 0.00 0.00 2.01
3678 4219 3.511934 AGGGACGATTACTCATGCTATCC 59.488 47.826 0.00 0.00 0.00 2.59
3692 4233 7.802117 TCTTCCAAAATTAAGATAGGGACGAT 58.198 34.615 0.00 0.00 0.00 3.73
3700 4241 7.643123 AGCCTTCCTCTTCCAAAATTAAGATA 58.357 34.615 0.00 0.00 31.60 1.98
3729 4270 3.608506 CGCAGTAGACAATCACACACTAC 59.391 47.826 0.00 0.00 35.23 2.73
3767 4309 8.769359 ACAATATAATAATAGCCTCTACACCCC 58.231 37.037 0.00 0.00 0.00 4.95
3852 4394 7.397221 AGTACATGAATGGAGATCAGTTTTCA 58.603 34.615 0.00 0.00 0.00 2.69
3968 4510 5.582439 ATCGTATCAGATTCACAAATCGC 57.418 39.130 0.00 0.00 45.01 4.58
3969 4511 5.842843 GCAATCGTATCAGATTCACAAATCG 59.157 40.000 0.00 0.00 45.01 3.34
3987 4532 2.420642 CTGATCCCATACCTGCAATCG 58.579 52.381 0.00 0.00 0.00 3.34
3991 4536 0.839277 CACCTGATCCCATACCTGCA 59.161 55.000 0.00 0.00 0.00 4.41
4026 4571 2.957491 TAATTCAAATTGGGCGCTGG 57.043 45.000 7.64 0.00 0.00 4.85
4049 4594 3.767131 GCTTGGGAGAGGATAGATAGACC 59.233 52.174 0.00 0.00 0.00 3.85
4052 4597 4.321601 CGTTGCTTGGGAGAGGATAGATAG 60.322 50.000 0.00 0.00 0.00 2.08
4053 4598 3.574396 CGTTGCTTGGGAGAGGATAGATA 59.426 47.826 0.00 0.00 0.00 1.98
4054 4599 2.366916 CGTTGCTTGGGAGAGGATAGAT 59.633 50.000 0.00 0.00 0.00 1.98
4113 4658 8.731591 ATCATATCTAAAGGGGCAAAATGAAT 57.268 30.769 0.00 0.00 0.00 2.57
4130 4675 8.345565 GCAAAATACGAGGACAAAATCATATCT 58.654 33.333 0.00 0.00 0.00 1.98
4131 4676 8.345565 AGCAAAATACGAGGACAAAATCATATC 58.654 33.333 0.00 0.00 0.00 1.63
4132 4677 8.225603 AGCAAAATACGAGGACAAAATCATAT 57.774 30.769 0.00 0.00 0.00 1.78
4133 4678 7.624360 AGCAAAATACGAGGACAAAATCATA 57.376 32.000 0.00 0.00 0.00 2.15
4134 4679 6.515272 AGCAAAATACGAGGACAAAATCAT 57.485 33.333 0.00 0.00 0.00 2.45
4135 4680 5.957842 AGCAAAATACGAGGACAAAATCA 57.042 34.783 0.00 0.00 0.00 2.57
4136 4681 6.458342 CCCTAGCAAAATACGAGGACAAAATC 60.458 42.308 0.00 0.00 32.09 2.17
4137 4682 5.357032 CCCTAGCAAAATACGAGGACAAAAT 59.643 40.000 0.00 0.00 32.09 1.82
4138 4683 4.698304 CCCTAGCAAAATACGAGGACAAAA 59.302 41.667 0.00 0.00 32.09 2.44
4139 4684 4.020039 TCCCTAGCAAAATACGAGGACAAA 60.020 41.667 0.00 0.00 32.09 2.83
4140 4685 3.516300 TCCCTAGCAAAATACGAGGACAA 59.484 43.478 0.00 0.00 32.09 3.18
4141 4686 3.101437 TCCCTAGCAAAATACGAGGACA 58.899 45.455 0.00 0.00 32.09 4.02
4143 4688 3.371965 ACTCCCTAGCAAAATACGAGGA 58.628 45.455 0.00 0.00 32.09 3.71
4145 4690 4.299978 GCTACTCCCTAGCAAAATACGAG 58.700 47.826 0.00 0.00 46.56 4.18
4146 4691 4.317671 GCTACTCCCTAGCAAAATACGA 57.682 45.455 0.00 0.00 46.56 3.43
4303 4888 6.079763 CACTTGTTGTCCTCGTATTTTCATG 58.920 40.000 0.00 0.00 0.00 3.07
4313 4898 0.105964 TCCACCACTTGTTGTCCTCG 59.894 55.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.