Multiple sequence alignment - TraesCS5D01G283900

Loading Multiple Alignment...

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 TraesCS5D01G283900 chr5D 100.000 2909 0 0 1 2909 384784276 384781368 0.000000e+00 5373.0
1 TraesCS5D01G283900 chr5D 82.627 472 75 6 1444 1913 384737741 384737275 7.500000e-111 411.0
2 TraesCS5D01G283900 chr5D 83.947 380 49 7 1 373 384976008 384976382 1.280000e-93 353.0
3 TraesCS5D01G283900 chr5D 96.429 196 7 0 697 892 13292948 13293143 1.010000e-84 324.0
4 TraesCS5D01G283900 chr5D 95.789 95 4 0 2448 2542 415748897 415748991 1.400000e-33 154.0
5 TraesCS5D01G283900 chr5B 95.262 1562 55 5 891 2443 461640224 461638673 0.000000e+00 2457.0
6 TraesCS5D01G283900 chr5B 96.395 1165 37 2 891 2050 461862201 461861037 0.000000e+00 1914.0
7 TraesCS5D01G283900 chr5B 96.719 701 22 1 2 701 461640934 461640234 0.000000e+00 1166.0
8 TraesCS5D01G283900 chr5B 96.581 702 23 1 1 701 461862912 461862211 0.000000e+00 1162.0
9 TraesCS5D01G283900 chr5B 92.965 398 20 4 2046 2443 461831840 461831451 9.040000e-160 573.0
10 TraesCS5D01G283900 chr5B 90.529 359 29 4 2543 2898 461831466 461831110 1.220000e-128 470.0
11 TraesCS5D01G283900 chr5B 83.691 466 61 10 1452 1913 461582049 461582503 2.680000e-115 425.0
12 TraesCS5D01G283900 chr5B 83.684 380 51 6 1 373 462309848 462310223 5.970000e-92 348.0
13 TraesCS5D01G283900 chr5B 95.789 95 4 0 2448 2542 512498213 512498119 1.400000e-33 154.0
14 TraesCS5D01G283900 chr5A 97.851 977 19 1 891 1867 485603016 485602042 0.000000e+00 1687.0
15 TraesCS5D01G283900 chr5A 97.293 702 18 1 1 701 485603727 485603026 0.000000e+00 1190.0
16 TraesCS5D01G283900 chr5A 84.211 475 65 9 1449 1917 485535621 485536091 1.230000e-123 453.0
17 TraesCS5D01G283900 chr5A 83.990 381 48 8 1 373 486748891 486749266 1.280000e-93 353.0
18 TraesCS5D01G283900 chr5A 83.721 86 13 1 1220 1304 500700376 500700291 2.400000e-11 80.5
19 TraesCS5D01G283900 chr7D 97.990 199 3 1 697 895 205951310 205951113 7.720000e-91 344.0
20 TraesCS5D01G283900 chr7D 97.949 195 4 0 698 892 566208423 566208617 3.590000e-89 339.0
21 TraesCS5D01G283900 chr7D 96.517 201 7 0 697 897 533622890 533622690 1.670000e-87 333.0
22 TraesCS5D01G283900 chr7D 95.522 201 7 2 697 896 156191442 156191641 1.300000e-83 320.0
23 TraesCS5D01G283900 chr3D 97.959 196 4 0 697 892 15906185 15906380 9.980000e-90 340.0
24 TraesCS5D01G283900 chr3D 76.280 371 62 21 1544 1905 75146321 75145968 1.070000e-39 174.0
25 TraesCS5D01G283900 chr3D 95.789 95 4 0 2448 2542 12368876 12368782 1.400000e-33 154.0
26 TraesCS5D01G283900 chr2D 96.447 197 7 0 697 893 622370912 622370716 2.800000e-85 326.0
27 TraesCS5D01G283900 chr2D 95.960 198 8 0 697 894 629724568 629724371 3.620000e-84 322.0
28 TraesCS5D01G283900 chr4B 95.500 200 8 1 697 896 643455093 643454895 4.680000e-83 318.0
29 TraesCS5D01G283900 chr1B 96.842 95 3 0 2448 2542 681451542 681451636 3.000000e-35 159.0
30 TraesCS5D01G283900 chr1B 95.789 95 4 0 2448 2542 592409216 592409310 1.400000e-33 154.0
31 TraesCS5D01G283900 chr1B 93.269 104 6 1 2440 2542 635509384 635509281 5.020000e-33 152.0
32 TraesCS5D01G283900 chr7B 95.789 95 4 0 2448 2542 717329115 717329209 1.400000e-33 154.0
33 TraesCS5D01G283900 chr6D 95.789 95 4 0 2448 2542 345048533 345048439 1.400000e-33 154.0
34 TraesCS5D01G283900 chrUn 92.381 105 7 1 2439 2542 37160748 37160644 6.490000e-32 148.0


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 TraesCS5D01G283900 chr5D 384781368 384784276 2908 True 5373.0 5373 100.0000 1 2909 1 chr5D.!!$R2 2908
1 TraesCS5D01G283900 chr5B 461638673 461640934 2261 True 1811.5 2457 95.9905 2 2443 2 chr5B.!!$R2 2441
2 TraesCS5D01G283900 chr5B 461861037 461862912 1875 True 1538.0 1914 96.4880 1 2050 2 chr5B.!!$R4 2049
3 TraesCS5D01G283900 chr5B 461831110 461831840 730 True 521.5 573 91.7470 2046 2898 2 chr5B.!!$R3 852
4 TraesCS5D01G283900 chr5A 485602042 485603727 1685 True 1438.5 1687 97.5720 1 1867 2 chr5A.!!$R2 1866

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
837 838 0.035439 CCCAGCACCTATCGTTGGTT 60.035 55.0 0.0 0.0 35.28 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 1978 0.184451 CCCAGCTGACATGGCCTTAT 59.816 55.0 17.39 0.0 36.43 1.73 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
66 67 0.457443 CCTCTACGAGATGCTGCACA 59.543 55.000 3.57 0.00 0.00 4.57
88 89 1.197492 GTTGCGTGCATGTCTCATTCA 59.803 47.619 7.93 0.00 0.00 2.57
123 124 4.996793 TGGAGATGTTTTCCCAATCTCAA 58.003 39.130 12.51 0.34 39.45 3.02
175 176 1.067071 GGGGTCGACGGAATATCATCC 60.067 57.143 9.92 0.35 36.05 3.51
274 275 7.708051 TCAAACTTGAAATACGTGAATTTCCA 58.292 30.769 17.14 8.64 42.63 3.53
490 491 2.106511 TGGAGTTGGCTGCTTAAGAAGT 59.893 45.455 12.26 0.00 33.91 3.01
495 496 3.769739 TGGCTGCTTAAGAAGTCTGAA 57.230 42.857 16.16 0.00 0.00 3.02
534 535 4.104579 TGATGTGCATATTACAGGGGATGT 59.895 41.667 0.00 0.00 46.45 3.06
652 653 3.036431 GCTTAGCCACCTGGTTGTT 57.964 52.632 0.00 0.00 37.57 2.83
704 705 1.430992 TAAGGCCCCTTATTCTCCGG 58.569 55.000 0.00 0.00 37.47 5.14
705 706 1.996070 AAGGCCCCTTATTCTCCGGC 61.996 60.000 0.00 0.00 38.96 6.13
706 707 2.752807 GGCCCCTTATTCTCCGGCA 61.753 63.158 0.00 0.00 41.58 5.69
707 708 1.227973 GCCCCTTATTCTCCGGCAG 60.228 63.158 0.00 0.00 39.50 4.85
708 709 1.451936 CCCCTTATTCTCCGGCAGG 59.548 63.158 0.00 0.00 39.46 4.85
711 712 0.815615 CCTTATTCTCCGGCAGGTGC 60.816 60.000 1.81 0.00 39.05 5.01
712 713 0.107703 CTTATTCTCCGGCAGGTGCA 60.108 55.000 1.81 0.00 44.36 4.57
713 714 0.107703 TTATTCTCCGGCAGGTGCAG 60.108 55.000 1.81 0.00 44.36 4.41
714 715 2.593468 TATTCTCCGGCAGGTGCAGC 62.593 60.000 8.11 8.11 44.36 5.25
730 731 3.876300 GCGGTTGCGAGTCATCTT 58.124 55.556 0.00 0.00 0.00 2.40
731 732 1.710339 GCGGTTGCGAGTCATCTTC 59.290 57.895 0.00 0.00 0.00 2.87
732 733 1.991430 CGGTTGCGAGTCATCTTCG 59.009 57.895 0.00 0.00 0.00 3.79
733 734 0.732880 CGGTTGCGAGTCATCTTCGT 60.733 55.000 0.00 0.00 0.00 3.85
734 735 1.429463 GGTTGCGAGTCATCTTCGTT 58.571 50.000 0.00 0.00 0.00 3.85
735 736 1.798813 GGTTGCGAGTCATCTTCGTTT 59.201 47.619 0.00 0.00 0.00 3.60
736 737 2.223377 GGTTGCGAGTCATCTTCGTTTT 59.777 45.455 0.00 0.00 0.00 2.43
737 738 3.470562 GTTGCGAGTCATCTTCGTTTTC 58.529 45.455 0.00 0.00 0.00 2.29
738 739 1.719246 TGCGAGTCATCTTCGTTTTCG 59.281 47.619 0.00 0.00 45.64 3.46
739 740 1.719780 GCGAGTCATCTTCGTTTTCGT 59.280 47.619 0.00 0.00 44.46 3.85
740 741 2.155155 GCGAGTCATCTTCGTTTTCGTT 59.845 45.455 0.00 0.00 44.46 3.85
741 742 3.711425 CGAGTCATCTTCGTTTTCGTTG 58.289 45.455 0.00 0.00 44.46 4.10
742 743 3.424198 CGAGTCATCTTCGTTTTCGTTGA 59.576 43.478 0.00 0.00 44.46 3.18
743 744 4.090066 CGAGTCATCTTCGTTTTCGTTGAT 59.910 41.667 0.00 0.00 44.46 2.57
744 745 5.517037 AGTCATCTTCGTTTTCGTTGATC 57.483 39.130 0.00 0.00 44.46 2.92
745 746 4.389077 AGTCATCTTCGTTTTCGTTGATCC 59.611 41.667 0.00 0.00 44.46 3.36
746 747 3.366724 TCATCTTCGTTTTCGTTGATCCG 59.633 43.478 0.00 0.00 44.46 4.18
747 748 1.458064 TCTTCGTTTTCGTTGATCCGC 59.542 47.619 0.00 0.00 44.46 5.54
748 749 0.513820 TTCGTTTTCGTTGATCCGCC 59.486 50.000 0.00 0.00 44.46 6.13
749 750 1.225637 CGTTTTCGTTGATCCGCCG 60.226 57.895 0.00 0.00 38.65 6.46
750 751 1.864176 GTTTTCGTTGATCCGCCGT 59.136 52.632 0.00 0.00 0.00 5.68
751 752 0.236449 GTTTTCGTTGATCCGCCGTT 59.764 50.000 0.00 0.00 0.00 4.44
752 753 0.236187 TTTTCGTTGATCCGCCGTTG 59.764 50.000 0.00 0.00 0.00 4.10
753 754 0.881159 TTTCGTTGATCCGCCGTTGT 60.881 50.000 0.00 0.00 0.00 3.32
754 755 1.286354 TTCGTTGATCCGCCGTTGTC 61.286 55.000 0.00 0.00 0.00 3.18
755 756 2.776072 GTTGATCCGCCGTTGTCG 59.224 61.111 0.00 0.00 0.00 4.35
767 768 1.963747 CGTTGTCGGCATTTTCTTCC 58.036 50.000 0.00 0.00 0.00 3.46
768 769 1.535462 CGTTGTCGGCATTTTCTTCCT 59.465 47.619 0.00 0.00 0.00 3.36
769 770 2.031157 CGTTGTCGGCATTTTCTTCCTT 60.031 45.455 0.00 0.00 0.00 3.36
770 771 3.550030 CGTTGTCGGCATTTTCTTCCTTT 60.550 43.478 0.00 0.00 0.00 3.11
771 772 4.368315 GTTGTCGGCATTTTCTTCCTTTT 58.632 39.130 0.00 0.00 0.00 2.27
772 773 3.976169 TGTCGGCATTTTCTTCCTTTTG 58.024 40.909 0.00 0.00 0.00 2.44
773 774 3.383185 TGTCGGCATTTTCTTCCTTTTGT 59.617 39.130 0.00 0.00 0.00 2.83
774 775 4.580995 TGTCGGCATTTTCTTCCTTTTGTA 59.419 37.500 0.00 0.00 0.00 2.41
775 776 5.242838 TGTCGGCATTTTCTTCCTTTTGTAT 59.757 36.000 0.00 0.00 0.00 2.29
776 777 6.156519 GTCGGCATTTTCTTCCTTTTGTATT 58.843 36.000 0.00 0.00 0.00 1.89
777 778 6.645003 GTCGGCATTTTCTTCCTTTTGTATTT 59.355 34.615 0.00 0.00 0.00 1.40
778 779 7.170828 GTCGGCATTTTCTTCCTTTTGTATTTT 59.829 33.333 0.00 0.00 0.00 1.82
779 780 7.383843 TCGGCATTTTCTTCCTTTTGTATTTTC 59.616 33.333 0.00 0.00 0.00 2.29
780 781 7.384932 CGGCATTTTCTTCCTTTTGTATTTTCT 59.615 33.333 0.00 0.00 0.00 2.52
781 782 8.712363 GGCATTTTCTTCCTTTTGTATTTTCTC 58.288 33.333 0.00 0.00 0.00 2.87
782 783 9.481340 GCATTTTCTTCCTTTTGTATTTTCTCT 57.519 29.630 0.00 0.00 0.00 3.10
797 798 9.816354 TGTATTTTCTCTTTCTTTTCTTTTGGG 57.184 29.630 0.00 0.00 0.00 4.12
798 799 7.792374 ATTTTCTCTTTCTTTTCTTTTGGGC 57.208 32.000 0.00 0.00 0.00 5.36
799 800 4.568152 TCTCTTTCTTTTCTTTTGGGCG 57.432 40.909 0.00 0.00 0.00 6.13
800 801 3.951680 TCTCTTTCTTTTCTTTTGGGCGT 59.048 39.130 0.00 0.00 0.00 5.68
801 802 4.040445 TCTTTCTTTTCTTTTGGGCGTG 57.960 40.909 0.00 0.00 0.00 5.34
802 803 2.217429 TTCTTTTCTTTTGGGCGTGC 57.783 45.000 0.00 0.00 0.00 5.34
803 804 0.387565 TCTTTTCTTTTGGGCGTGCC 59.612 50.000 1.16 1.16 0.00 5.01
804 805 0.389025 CTTTTCTTTTGGGCGTGCCT 59.611 50.000 11.25 0.00 36.10 4.75
805 806 0.103937 TTTTCTTTTGGGCGTGCCTG 59.896 50.000 11.25 0.00 36.10 4.85
806 807 1.040339 TTTCTTTTGGGCGTGCCTGT 61.040 50.000 11.25 0.00 36.10 4.00
807 808 1.733402 TTCTTTTGGGCGTGCCTGTG 61.733 55.000 11.25 0.00 36.10 3.66
808 809 3.846602 CTTTTGGGCGTGCCTGTGC 62.847 63.158 11.25 0.00 36.10 4.57
809 810 4.892965 TTTGGGCGTGCCTGTGCT 62.893 61.111 11.25 0.00 38.71 4.40
814 815 4.395583 GCGTGCCTGTGCTGCTTC 62.396 66.667 0.00 0.00 38.71 3.86
815 816 3.730761 CGTGCCTGTGCTGCTTCC 61.731 66.667 0.00 0.00 38.71 3.46
816 817 3.730761 GTGCCTGTGCTGCTTCCG 61.731 66.667 0.00 0.00 38.71 4.30
828 829 3.399181 CTTCCGCCCCAGCACCTA 61.399 66.667 0.00 0.00 39.83 3.08
829 830 2.690881 TTCCGCCCCAGCACCTAT 60.691 61.111 0.00 0.00 39.83 2.57
830 831 2.666596 CTTCCGCCCCAGCACCTATC 62.667 65.000 0.00 0.00 39.83 2.08
831 832 4.609018 CCGCCCCAGCACCTATCG 62.609 72.222 0.00 0.00 39.83 2.92
832 833 3.849951 CGCCCCAGCACCTATCGT 61.850 66.667 0.00 0.00 39.83 3.73
833 834 2.590092 GCCCCAGCACCTATCGTT 59.410 61.111 0.00 0.00 39.53 3.85
834 835 1.819632 GCCCCAGCACCTATCGTTG 60.820 63.158 0.00 0.00 39.53 4.10
835 836 1.153168 CCCCAGCACCTATCGTTGG 60.153 63.158 0.00 0.00 34.73 3.77
836 837 1.602237 CCCAGCACCTATCGTTGGT 59.398 57.895 0.00 0.00 38.53 3.67
837 838 0.035439 CCCAGCACCTATCGTTGGTT 60.035 55.000 0.00 0.00 35.28 3.67
838 839 1.086696 CCAGCACCTATCGTTGGTTG 58.913 55.000 0.00 0.00 35.28 3.77
839 840 1.610624 CCAGCACCTATCGTTGGTTGT 60.611 52.381 0.00 0.00 35.28 3.32
840 841 2.354303 CCAGCACCTATCGTTGGTTGTA 60.354 50.000 0.00 0.00 35.28 2.41
841 842 3.531538 CAGCACCTATCGTTGGTTGTAT 58.468 45.455 0.00 0.00 35.28 2.29
842 843 3.555956 CAGCACCTATCGTTGGTTGTATC 59.444 47.826 0.00 0.00 35.28 2.24
843 844 2.538449 GCACCTATCGTTGGTTGTATCG 59.462 50.000 0.00 0.00 35.28 2.92
844 845 3.735820 GCACCTATCGTTGGTTGTATCGA 60.736 47.826 0.00 0.00 35.28 3.59
845 846 4.617959 CACCTATCGTTGGTTGTATCGAT 58.382 43.478 2.16 2.16 43.66 3.59
846 847 4.444388 CACCTATCGTTGGTTGTATCGATG 59.556 45.833 8.54 0.00 41.85 3.84
847 848 4.098960 ACCTATCGTTGGTTGTATCGATGT 59.901 41.667 8.54 0.00 41.85 3.06
848 849 5.047847 CCTATCGTTGGTTGTATCGATGTT 58.952 41.667 8.54 0.00 41.85 2.71
849 850 4.857871 ATCGTTGGTTGTATCGATGTTG 57.142 40.909 8.54 0.00 40.64 3.33
850 851 3.655486 TCGTTGGTTGTATCGATGTTGT 58.345 40.909 8.54 0.00 0.00 3.32
851 852 4.059511 TCGTTGGTTGTATCGATGTTGTT 58.940 39.130 8.54 0.00 0.00 2.83
852 853 4.150980 TCGTTGGTTGTATCGATGTTGTTC 59.849 41.667 8.54 0.00 0.00 3.18
853 854 4.668177 CGTTGGTTGTATCGATGTTGTTCC 60.668 45.833 8.54 3.96 0.00 3.62
854 855 4.280436 TGGTTGTATCGATGTTGTTCCT 57.720 40.909 8.54 0.00 0.00 3.36
855 856 4.647611 TGGTTGTATCGATGTTGTTCCTT 58.352 39.130 8.54 0.00 0.00 3.36
856 857 5.067273 TGGTTGTATCGATGTTGTTCCTTT 58.933 37.500 8.54 0.00 0.00 3.11
857 858 5.049060 TGGTTGTATCGATGTTGTTCCTTTG 60.049 40.000 8.54 0.00 0.00 2.77
858 859 5.048991 GGTTGTATCGATGTTGTTCCTTTGT 60.049 40.000 8.54 0.00 0.00 2.83
859 860 6.148150 GGTTGTATCGATGTTGTTCCTTTGTA 59.852 38.462 8.54 0.00 0.00 2.41
860 861 7.308109 GGTTGTATCGATGTTGTTCCTTTGTAA 60.308 37.037 8.54 0.00 0.00 2.41
861 862 7.915293 TGTATCGATGTTGTTCCTTTGTAAT 57.085 32.000 8.54 0.00 0.00 1.89
862 863 9.438228 TTGTATCGATGTTGTTCCTTTGTAATA 57.562 29.630 8.54 0.00 0.00 0.98
863 864 8.875803 TGTATCGATGTTGTTCCTTTGTAATAC 58.124 33.333 8.54 0.00 0.00 1.89
864 865 7.915293 ATCGATGTTGTTCCTTTGTAATACA 57.085 32.000 0.00 0.00 0.00 2.29
865 866 7.731882 TCGATGTTGTTCCTTTGTAATACAA 57.268 32.000 1.08 1.08 36.11 2.41
866 867 8.155821 TCGATGTTGTTCCTTTGTAATACAAA 57.844 30.769 16.57 16.57 44.91 2.83
897 898 7.268199 GGAAACCCTTTTTCGGTAATATAGG 57.732 40.000 0.00 0.00 31.69 2.57
931 932 4.307432 ACGACTATCACTTGGTGTTTCAG 58.693 43.478 0.00 0.00 34.79 3.02
1051 1052 9.472361 ACATACATTCGTCTTATGTGGTAATAC 57.528 33.333 0.00 0.00 35.56 1.89
1209 1210 0.106519 AGCATCTGTGTATTGGGGCC 60.107 55.000 0.00 0.00 0.00 5.80
1235 1236 9.277783 CTTTACCCCAGACTATGATTATTTCTG 57.722 37.037 0.00 0.00 34.63 3.02
1241 1242 6.426328 CCAGACTATGATTATTTCTGTCTGGC 59.574 42.308 21.15 0.00 46.94 4.85
1441 1443 8.548025 TCTAGCTCAGAATAGCACTATATCTCT 58.452 37.037 0.00 0.00 45.30 3.10
1442 1444 7.395190 AGCTCAGAATAGCACTATATCTCTG 57.605 40.000 9.92 9.92 45.30 3.35
1466 1472 1.338674 TGGGACCACGCATTAGTTCAG 60.339 52.381 0.00 0.00 34.12 3.02
1689 1695 6.263842 TGACATGCCATATTCTTGAGAATTCC 59.736 38.462 11.17 0.00 41.64 3.01
1791 1797 2.761208 CCCGATGAGTAGGGGTATGATC 59.239 54.545 0.00 0.00 43.90 2.92
1973 1986 1.915228 GTGGAGCAGGATAAGGCCA 59.085 57.895 5.01 0.00 0.00 5.36
2070 2087 4.685169 TGTCTCAAAGCATTCCGATTTC 57.315 40.909 0.00 0.00 28.44 2.17
2093 2110 1.227527 TGTGAGGGTGCACAAGACG 60.228 57.895 20.43 0.00 45.08 4.18
2127 2144 7.615757 ACATCCCCTAAAAATTTCAGACCTAAG 59.384 37.037 0.00 0.00 0.00 2.18
2195 2214 6.803320 AGCATGAATAATGTCACAAAAAGACG 59.197 34.615 0.00 0.00 38.83 4.18
2220 2239 6.662616 AGCATAAATGACACTATTCGCATTC 58.337 36.000 0.00 0.00 31.16 2.67
2222 2241 3.592381 AATGACACTATTCGCATTCGC 57.408 42.857 0.00 0.00 35.26 4.70
2241 2260 7.096065 GCATTCGCATTTGTCTTTTTAGTTTCT 60.096 33.333 0.00 0.00 38.36 2.52
2242 2261 7.908193 TTCGCATTTGTCTTTTTAGTTTCTC 57.092 32.000 0.00 0.00 0.00 2.87
2243 2262 7.022055 TCGCATTTGTCTTTTTAGTTTCTCA 57.978 32.000 0.00 0.00 0.00 3.27
2244 2263 7.476667 TCGCATTTGTCTTTTTAGTTTCTCAA 58.523 30.769 0.00 0.00 0.00 3.02
2245 2264 7.971168 TCGCATTTGTCTTTTTAGTTTCTCAAA 59.029 29.630 0.00 0.00 0.00 2.69
2246 2265 8.755018 CGCATTTGTCTTTTTAGTTTCTCAAAT 58.245 29.630 0.00 0.00 35.56 2.32
2350 2370 8.924691 TCTGGAATTTTTCGAAGCATTTAAATG 58.075 29.630 21.54 21.54 39.40 2.32
2373 2393 2.250921 TTTCCAATGGATGCATGGGT 57.749 45.000 19.34 0.00 34.89 4.51
2412 2432 6.862608 GTCACATGTCAGCTCTAGAATATGAG 59.137 42.308 0.00 0.00 0.00 2.90
2471 2491 5.876651 AAAAATCCAGGAATAATGGGAGC 57.123 39.130 0.00 0.00 38.44 4.70
2472 2492 4.541250 AAATCCAGGAATAATGGGAGCA 57.459 40.909 0.00 0.00 38.44 4.26
2473 2493 3.515602 ATCCAGGAATAATGGGAGCAC 57.484 47.619 0.00 0.00 38.44 4.40
2474 2494 2.492025 TCCAGGAATAATGGGAGCACT 58.508 47.619 0.00 0.00 38.44 4.40
2475 2495 3.664320 TCCAGGAATAATGGGAGCACTA 58.336 45.455 0.00 0.00 38.44 2.74
2476 2496 3.648067 TCCAGGAATAATGGGAGCACTAG 59.352 47.826 0.00 0.00 38.44 2.57
2477 2497 3.244700 CCAGGAATAATGGGAGCACTAGG 60.245 52.174 0.00 0.00 33.94 3.02
2478 2498 3.648067 CAGGAATAATGGGAGCACTAGGA 59.352 47.826 0.00 0.00 0.00 2.94
2479 2499 4.288105 CAGGAATAATGGGAGCACTAGGAT 59.712 45.833 0.00 0.00 0.00 3.24
2480 2500 4.916424 AGGAATAATGGGAGCACTAGGATT 59.084 41.667 0.00 0.00 0.00 3.01
2481 2501 5.373854 AGGAATAATGGGAGCACTAGGATTT 59.626 40.000 0.00 0.00 0.00 2.17
2482 2502 5.474876 GGAATAATGGGAGCACTAGGATTTG 59.525 44.000 0.00 0.00 0.00 2.32
2483 2503 5.912149 ATAATGGGAGCACTAGGATTTGA 57.088 39.130 0.00 0.00 0.00 2.69
2484 2504 4.591321 AATGGGAGCACTAGGATTTGAA 57.409 40.909 0.00 0.00 0.00 2.69
2485 2505 3.350219 TGGGAGCACTAGGATTTGAAC 57.650 47.619 0.00 0.00 0.00 3.18
2486 2506 2.026262 TGGGAGCACTAGGATTTGAACC 60.026 50.000 0.00 0.00 0.00 3.62
2487 2507 2.644676 GGAGCACTAGGATTTGAACCC 58.355 52.381 0.00 0.00 0.00 4.11
2488 2508 2.239907 GGAGCACTAGGATTTGAACCCT 59.760 50.000 0.00 0.00 36.60 4.34
2489 2509 3.274288 GAGCACTAGGATTTGAACCCTG 58.726 50.000 0.00 0.00 34.11 4.45
2490 2510 2.025887 AGCACTAGGATTTGAACCCTGG 60.026 50.000 0.00 0.00 37.12 4.45
2491 2511 2.290960 GCACTAGGATTTGAACCCTGGT 60.291 50.000 0.00 0.00 43.75 4.00
2492 2512 3.721087 ACTAGGATTTGAACCCTGGTG 57.279 47.619 0.00 0.00 41.78 4.17
2493 2513 2.308866 ACTAGGATTTGAACCCTGGTGG 59.691 50.000 0.00 0.00 41.78 4.61
2503 2523 4.179896 CCTGGTGGGTTGGGGATA 57.820 61.111 0.00 0.00 0.00 2.59
2504 2524 1.613061 CCTGGTGGGTTGGGGATAC 59.387 63.158 0.00 0.00 0.00 2.24
2520 2540 4.338379 GGATACCACTGTCCATCTAACC 57.662 50.000 0.00 0.00 34.57 2.85
2521 2541 3.709653 GGATACCACTGTCCATCTAACCA 59.290 47.826 0.00 0.00 34.57 3.67
2522 2542 4.348168 GGATACCACTGTCCATCTAACCAT 59.652 45.833 0.00 0.00 34.57 3.55
2523 2543 3.914426 ACCACTGTCCATCTAACCATC 57.086 47.619 0.00 0.00 0.00 3.51
2524 2544 3.454858 ACCACTGTCCATCTAACCATCT 58.545 45.455 0.00 0.00 0.00 2.90
2525 2545 3.452627 ACCACTGTCCATCTAACCATCTC 59.547 47.826 0.00 0.00 0.00 2.75
2526 2546 3.452264 CCACTGTCCATCTAACCATCTCA 59.548 47.826 0.00 0.00 0.00 3.27
2527 2547 4.080919 CCACTGTCCATCTAACCATCTCAA 60.081 45.833 0.00 0.00 0.00 3.02
2528 2548 4.872691 CACTGTCCATCTAACCATCTCAAC 59.127 45.833 0.00 0.00 0.00 3.18
2529 2549 4.080863 ACTGTCCATCTAACCATCTCAACC 60.081 45.833 0.00 0.00 0.00 3.77
2530 2550 3.843619 TGTCCATCTAACCATCTCAACCA 59.156 43.478 0.00 0.00 0.00 3.67
2531 2551 4.192317 GTCCATCTAACCATCTCAACCAC 58.808 47.826 0.00 0.00 0.00 4.16
2532 2552 3.843619 TCCATCTAACCATCTCAACCACA 59.156 43.478 0.00 0.00 0.00 4.17
2533 2553 4.080919 TCCATCTAACCATCTCAACCACAG 60.081 45.833 0.00 0.00 0.00 3.66
2534 2554 3.981071 TCTAACCATCTCAACCACAGG 57.019 47.619 0.00 0.00 0.00 4.00
2535 2555 3.248024 TCTAACCATCTCAACCACAGGT 58.752 45.455 0.00 0.00 37.65 4.00
2548 2568 5.964958 AACCACAGGTTGATTCATAAGTG 57.035 39.130 0.00 0.00 45.07 3.16
2549 2569 5.241403 ACCACAGGTTGATTCATAAGTGA 57.759 39.130 9.31 0.00 27.29 3.41
2550 2570 5.819991 ACCACAGGTTGATTCATAAGTGAT 58.180 37.500 9.31 0.00 29.36 3.06
2551 2571 5.882557 ACCACAGGTTGATTCATAAGTGATC 59.117 40.000 9.31 0.00 29.36 2.92
2552 2572 6.118170 CCACAGGTTGATTCATAAGTGATCT 58.882 40.000 0.00 0.00 33.56 2.75
2553 2573 6.600822 CCACAGGTTGATTCATAAGTGATCTT 59.399 38.462 0.00 0.00 37.65 2.40
2554 2574 7.121759 CCACAGGTTGATTCATAAGTGATCTTT 59.878 37.037 0.00 0.00 35.36 2.52
2555 2575 9.166173 CACAGGTTGATTCATAAGTGATCTTTA 57.834 33.333 0.00 0.00 35.36 1.85
2556 2576 9.739276 ACAGGTTGATTCATAAGTGATCTTTAA 57.261 29.630 0.00 0.00 35.36 1.52
2567 2587 5.930837 AGTGATCTTTAAGCTAGCTGAGT 57.069 39.130 20.16 5.16 0.00 3.41
2575 2595 6.542370 TCTTTAAGCTAGCTGAGTGTTTTTGT 59.458 34.615 20.16 0.00 0.00 2.83
2588 2608 9.573133 CTGAGTGTTTTTGTCTTTGTAATTTCT 57.427 29.630 0.00 0.00 0.00 2.52
2604 2624 5.876651 AATTTCTCTTTCCTTGCACCTTT 57.123 34.783 0.00 0.00 0.00 3.11
2649 2670 7.717875 GGCAGGAACAAGTGGTATTTACATATA 59.282 37.037 0.00 0.00 0.00 0.86
2650 2671 9.116067 GCAGGAACAAGTGGTATTTACATATAA 57.884 33.333 0.00 0.00 0.00 0.98
2726 2747 4.201891 CGGTCTCGTATTTGTACTAGCAGT 60.202 45.833 0.00 0.00 0.00 4.40
2739 2760 8.521170 TTGTACTAGCAGTAGTGATGTATCTT 57.479 34.615 0.42 0.00 39.96 2.40
2752 2773 1.009829 GTATCTTGTTCAGCCAGCCG 58.990 55.000 0.00 0.00 0.00 5.52
2758 2779 1.448013 GTTCAGCCAGCCGGTAGTC 60.448 63.158 1.90 0.00 33.28 2.59
2770 2791 4.579340 CAGCCGGTAGTCTATAGTCAAAGA 59.421 45.833 1.90 0.00 0.00 2.52
2773 2794 7.002879 AGCCGGTAGTCTATAGTCAAAGAATA 58.997 38.462 1.90 0.00 0.00 1.75
2774 2795 7.175293 AGCCGGTAGTCTATAGTCAAAGAATAG 59.825 40.741 1.90 0.00 0.00 1.73
2801 2822 5.883685 ATGTGTCAGATGATGATAGTGGT 57.116 39.130 0.00 0.00 40.92 4.16
2859 2882 9.300681 TCCTTCACATAACAATGATCTTCTTTT 57.699 29.630 0.00 0.00 0.00 2.27
2863 2886 9.897744 TCACATAACAATGATCTTCTTTTTGTC 57.102 29.630 0.00 0.00 30.62 3.18
2877 2900 5.076182 TCTTTTTGTCTGGCATCCAACATA 58.924 37.500 0.00 0.00 30.80 2.29
2888 2911 6.422333 TGGCATCCAACATATTAGTTTCTGA 58.578 36.000 0.00 0.00 0.00 3.27
2890 2913 7.148086 TGGCATCCAACATATTAGTTTCTGAAC 60.148 37.037 0.00 0.00 35.97 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 0.950555 ATGAGACATGCACGCAACGT 60.951 50.000 0.00 0.00 42.36 3.99
73 74 4.337763 GTCGAAATGAATGAGACATGCAC 58.662 43.478 0.00 0.00 32.57 4.57
77 78 5.171476 AGAACGTCGAAATGAATGAGACAT 58.829 37.500 0.00 0.00 32.57 3.06
88 89 3.926616 ACATCTCCAAGAACGTCGAAAT 58.073 40.909 0.00 0.00 0.00 2.17
123 124 3.978672 ACCCAGTGTTTCCCTAGTTAAGT 59.021 43.478 0.00 0.00 0.00 2.24
175 176 3.761657 TGCAAGATCAAGCGCTATTTTG 58.238 40.909 12.05 14.41 0.00 2.44
274 275 4.768448 TCATCACATGAGGTGCTGAAAAAT 59.232 37.500 0.99 0.00 46.46 1.82
490 491 8.321353 ACATCATACAGTTCCAAACTATTCAGA 58.679 33.333 0.00 0.00 40.46 3.27
495 496 6.179756 TGCACATCATACAGTTCCAAACTAT 58.820 36.000 0.00 0.00 40.46 2.12
534 535 4.469657 ACTGGAAAGAAGGCACATTAACA 58.530 39.130 0.00 0.00 0.00 2.41
652 653 3.953712 TCCAGATTTAAGCAGTCGTGA 57.046 42.857 0.00 0.00 0.00 4.35
711 712 1.016130 AAGATGACTCGCAACCGCTG 61.016 55.000 0.00 0.00 35.30 5.18
712 713 0.737715 GAAGATGACTCGCAACCGCT 60.738 55.000 0.00 0.00 35.30 5.52
713 714 1.710339 GAAGATGACTCGCAACCGC 59.290 57.895 0.00 0.00 0.00 5.68
714 715 0.732880 ACGAAGATGACTCGCAACCG 60.733 55.000 0.00 0.00 0.00 4.44
715 716 1.429463 AACGAAGATGACTCGCAACC 58.571 50.000 0.00 0.00 0.00 3.77
716 717 3.470562 GAAAACGAAGATGACTCGCAAC 58.529 45.455 0.00 0.00 0.00 4.17
717 718 2.154963 CGAAAACGAAGATGACTCGCAA 59.845 45.455 0.00 0.00 0.00 4.85
718 719 1.719246 CGAAAACGAAGATGACTCGCA 59.281 47.619 0.00 0.00 0.00 5.10
719 720 1.719780 ACGAAAACGAAGATGACTCGC 59.280 47.619 0.00 0.00 0.00 5.03
720 721 3.424198 TCAACGAAAACGAAGATGACTCG 59.576 43.478 0.00 0.00 0.00 4.18
721 722 4.966850 TCAACGAAAACGAAGATGACTC 57.033 40.909 0.00 0.00 0.00 3.36
722 723 4.389077 GGATCAACGAAAACGAAGATGACT 59.611 41.667 0.00 0.00 0.00 3.41
723 724 4.638963 GGATCAACGAAAACGAAGATGAC 58.361 43.478 0.00 0.00 0.00 3.06
724 725 3.366724 CGGATCAACGAAAACGAAGATGA 59.633 43.478 0.00 0.00 35.47 2.92
725 726 3.659735 CGGATCAACGAAAACGAAGATG 58.340 45.455 0.00 0.00 35.47 2.90
726 727 2.093783 GCGGATCAACGAAAACGAAGAT 59.906 45.455 0.00 0.00 35.47 2.40
727 728 1.458064 GCGGATCAACGAAAACGAAGA 59.542 47.619 0.00 0.00 35.47 2.87
728 729 1.463528 GGCGGATCAACGAAAACGAAG 60.464 52.381 0.00 0.00 35.47 3.79
729 730 0.513820 GGCGGATCAACGAAAACGAA 59.486 50.000 0.00 0.00 35.47 3.85
730 731 1.619526 CGGCGGATCAACGAAAACGA 61.620 55.000 0.00 0.00 35.47 3.85
731 732 1.225637 CGGCGGATCAACGAAAACG 60.226 57.895 0.00 0.00 35.47 3.60
732 733 0.236449 AACGGCGGATCAACGAAAAC 59.764 50.000 13.24 0.00 35.47 2.43
733 734 0.236187 CAACGGCGGATCAACGAAAA 59.764 50.000 13.24 0.00 35.47 2.29
734 735 0.881159 ACAACGGCGGATCAACGAAA 60.881 50.000 13.24 0.00 35.47 3.46
735 736 1.286354 GACAACGGCGGATCAACGAA 61.286 55.000 13.24 0.00 35.47 3.85
736 737 1.735198 GACAACGGCGGATCAACGA 60.735 57.895 13.24 0.00 35.47 3.85
737 738 2.776072 GACAACGGCGGATCAACG 59.224 61.111 13.24 0.00 0.00 4.10
738 739 2.776072 CGACAACGGCGGATCAAC 59.224 61.111 13.24 0.00 35.72 3.18
748 749 1.535462 AGGAAGAAAATGCCGACAACG 59.465 47.619 0.00 0.00 39.43 4.10
749 750 3.643159 AAGGAAGAAAATGCCGACAAC 57.357 42.857 0.00 0.00 0.00 3.32
750 751 4.142049 ACAAAAGGAAGAAAATGCCGACAA 60.142 37.500 0.00 0.00 0.00 3.18
751 752 3.383185 ACAAAAGGAAGAAAATGCCGACA 59.617 39.130 0.00 0.00 0.00 4.35
752 753 3.977427 ACAAAAGGAAGAAAATGCCGAC 58.023 40.909 0.00 0.00 0.00 4.79
753 754 5.975693 ATACAAAAGGAAGAAAATGCCGA 57.024 34.783 0.00 0.00 0.00 5.54
754 755 7.384932 AGAAAATACAAAAGGAAGAAAATGCCG 59.615 33.333 0.00 0.00 0.00 5.69
755 756 8.607441 AGAAAATACAAAAGGAAGAAAATGCC 57.393 30.769 0.00 0.00 0.00 4.40
756 757 9.481340 AGAGAAAATACAAAAGGAAGAAAATGC 57.519 29.630 0.00 0.00 0.00 3.56
771 772 9.816354 CCCAAAAGAAAAGAAAGAGAAAATACA 57.184 29.630 0.00 0.00 0.00 2.29
772 773 8.765219 GCCCAAAAGAAAAGAAAGAGAAAATAC 58.235 33.333 0.00 0.00 0.00 1.89
773 774 7.651704 CGCCCAAAAGAAAAGAAAGAGAAAATA 59.348 33.333 0.00 0.00 0.00 1.40
774 775 6.479990 CGCCCAAAAGAAAAGAAAGAGAAAAT 59.520 34.615 0.00 0.00 0.00 1.82
775 776 5.810074 CGCCCAAAAGAAAAGAAAGAGAAAA 59.190 36.000 0.00 0.00 0.00 2.29
776 777 5.105513 ACGCCCAAAAGAAAAGAAAGAGAAA 60.106 36.000 0.00 0.00 0.00 2.52
777 778 4.401202 ACGCCCAAAAGAAAAGAAAGAGAA 59.599 37.500 0.00 0.00 0.00 2.87
778 779 3.951680 ACGCCCAAAAGAAAAGAAAGAGA 59.048 39.130 0.00 0.00 0.00 3.10
779 780 4.044426 CACGCCCAAAAGAAAAGAAAGAG 58.956 43.478 0.00 0.00 0.00 2.85
780 781 3.736740 GCACGCCCAAAAGAAAAGAAAGA 60.737 43.478 0.00 0.00 0.00 2.52
781 782 2.539688 GCACGCCCAAAAGAAAAGAAAG 59.460 45.455 0.00 0.00 0.00 2.62
782 783 2.545731 GCACGCCCAAAAGAAAAGAAA 58.454 42.857 0.00 0.00 0.00 2.52
783 784 1.202475 GGCACGCCCAAAAGAAAAGAA 60.202 47.619 0.00 0.00 0.00 2.52
784 785 0.387565 GGCACGCCCAAAAGAAAAGA 59.612 50.000 0.00 0.00 0.00 2.52
785 786 0.389025 AGGCACGCCCAAAAGAAAAG 59.611 50.000 3.95 0.00 36.58 2.27
786 787 0.103937 CAGGCACGCCCAAAAGAAAA 59.896 50.000 3.95 0.00 36.58 2.29
787 788 1.040339 ACAGGCACGCCCAAAAGAAA 61.040 50.000 3.95 0.00 36.58 2.52
788 789 1.454847 ACAGGCACGCCCAAAAGAA 60.455 52.632 3.95 0.00 36.58 2.52
789 790 2.192861 CACAGGCACGCCCAAAAGA 61.193 57.895 3.95 0.00 36.58 2.52
790 791 2.336088 CACAGGCACGCCCAAAAG 59.664 61.111 3.95 0.00 36.58 2.27
791 792 3.910490 GCACAGGCACGCCCAAAA 61.910 61.111 3.95 0.00 40.72 2.44
792 793 4.892965 AGCACAGGCACGCCCAAA 62.893 61.111 3.95 0.00 44.61 3.28
797 798 4.395583 GAAGCAGCACAGGCACGC 62.396 66.667 0.00 0.00 44.61 5.34
798 799 3.730761 GGAAGCAGCACAGGCACG 61.731 66.667 0.00 0.00 44.61 5.34
799 800 3.730761 CGGAAGCAGCACAGGCAC 61.731 66.667 0.00 0.00 44.61 5.01
811 812 2.666596 GATAGGTGCTGGGGCGGAAG 62.667 65.000 0.00 0.00 42.25 3.46
812 813 2.690881 ATAGGTGCTGGGGCGGAA 60.691 61.111 0.00 0.00 42.25 4.30
813 814 3.161450 GATAGGTGCTGGGGCGGA 61.161 66.667 0.00 0.00 42.25 5.54
814 815 4.609018 CGATAGGTGCTGGGGCGG 62.609 72.222 0.00 0.00 42.25 6.13
815 816 3.385749 AACGATAGGTGCTGGGGCG 62.386 63.158 0.00 0.00 40.77 6.13
816 817 2.590092 AACGATAGGTGCTGGGGC 59.410 61.111 0.00 0.00 43.77 5.80
824 825 4.098960 ACATCGATACAACCAACGATAGGT 59.901 41.667 0.00 0.00 42.23 3.08
825 826 4.617959 ACATCGATACAACCAACGATAGG 58.382 43.478 0.00 0.00 42.23 2.57
826 827 5.518847 ACAACATCGATACAACCAACGATAG 59.481 40.000 0.00 0.00 42.23 2.08
827 828 5.412640 ACAACATCGATACAACCAACGATA 58.587 37.500 0.00 0.00 42.23 2.92
828 829 4.250464 ACAACATCGATACAACCAACGAT 58.750 39.130 0.00 0.00 44.37 3.73
829 830 3.655486 ACAACATCGATACAACCAACGA 58.345 40.909 0.00 0.00 39.01 3.85
830 831 4.391358 GAACAACATCGATACAACCAACG 58.609 43.478 0.00 0.00 0.00 4.10
831 832 4.454504 AGGAACAACATCGATACAACCAAC 59.545 41.667 0.00 0.00 0.00 3.77
832 833 4.647611 AGGAACAACATCGATACAACCAA 58.352 39.130 0.00 0.00 0.00 3.67
833 834 4.280436 AGGAACAACATCGATACAACCA 57.720 40.909 0.00 0.00 0.00 3.67
834 835 5.048991 ACAAAGGAACAACATCGATACAACC 60.049 40.000 0.00 0.00 0.00 3.77
835 836 5.997385 ACAAAGGAACAACATCGATACAAC 58.003 37.500 0.00 0.00 0.00 3.32
836 837 7.731882 TTACAAAGGAACAACATCGATACAA 57.268 32.000 0.00 0.00 0.00 2.41
837 838 7.915293 ATTACAAAGGAACAACATCGATACA 57.085 32.000 0.00 0.00 0.00 2.29
838 839 8.875803 TGTATTACAAAGGAACAACATCGATAC 58.124 33.333 0.00 0.00 0.00 2.24
839 840 9.438228 TTGTATTACAAAGGAACAACATCGATA 57.562 29.630 6.79 0.00 34.76 2.92
840 841 7.915293 TGTATTACAAAGGAACAACATCGAT 57.085 32.000 0.00 0.00 0.00 3.59
841 842 7.731882 TTGTATTACAAAGGAACAACATCGA 57.268 32.000 6.79 0.00 34.76 3.59
872 873 6.263842 CCTATATTACCGAAAAAGGGTTTCCC 59.736 42.308 0.00 0.00 45.90 3.97
873 874 6.263842 CCCTATATTACCGAAAAAGGGTTTCC 59.736 42.308 0.00 0.00 37.90 3.13
874 875 6.263842 CCCCTATATTACCGAAAAAGGGTTTC 59.736 42.308 3.94 0.00 40.56 2.78
875 876 6.131264 CCCCTATATTACCGAAAAAGGGTTT 58.869 40.000 3.94 0.00 40.56 3.27
876 877 5.194334 ACCCCTATATTACCGAAAAAGGGTT 59.806 40.000 3.94 0.00 41.24 4.11
877 878 4.728350 ACCCCTATATTACCGAAAAAGGGT 59.272 41.667 3.94 0.00 40.56 4.34
878 879 5.067954 CACCCCTATATTACCGAAAAAGGG 58.932 45.833 0.00 0.00 41.62 3.95
879 880 4.517832 GCACCCCTATATTACCGAAAAAGG 59.482 45.833 0.00 0.00 37.30 3.11
880 881 4.517832 GGCACCCCTATATTACCGAAAAAG 59.482 45.833 0.00 0.00 0.00 2.27
881 882 4.463070 GGCACCCCTATATTACCGAAAAA 58.537 43.478 0.00 0.00 0.00 1.94
882 883 4.089408 GGCACCCCTATATTACCGAAAA 57.911 45.455 0.00 0.00 0.00 2.29
883 884 3.775261 GGCACCCCTATATTACCGAAA 57.225 47.619 0.00 0.00 0.00 3.46
931 932 3.184986 GCATCAATGTCAAGGTTTTGCAC 59.815 43.478 0.00 0.00 34.21 4.57
1209 1210 9.277783 CAGAAATAATCATAGTCTGGGGTAAAG 57.722 37.037 0.00 0.00 0.00 1.85
1235 1236 4.006319 AGCATCAAGTAAAGAAGCCAGAC 58.994 43.478 0.00 0.00 30.52 3.51
1241 1242 6.348868 GGAAGGACAAGCATCAAGTAAAGAAG 60.349 42.308 0.00 0.00 0.00 2.85
1248 1249 3.152341 CAAGGAAGGACAAGCATCAAGT 58.848 45.455 0.00 0.00 0.00 3.16
1359 1360 5.820423 ACTGTGCACAAATGTAGTAGAACAA 59.180 36.000 21.98 0.00 32.02 2.83
1466 1472 6.128742 ACGGTGAAACGACAAAACATATACTC 60.129 38.462 0.00 0.00 38.12 2.59
1791 1797 6.946649 CAAGAGAGCTTTATGGGCTTCCATG 61.947 48.000 8.06 0.00 40.91 3.66
1965 1978 0.184451 CCCAGCTGACATGGCCTTAT 59.816 55.000 17.39 0.00 36.43 1.73
1966 1979 0.913934 TCCCAGCTGACATGGCCTTA 60.914 55.000 17.39 0.00 36.43 2.69
1973 1986 3.051581 ACCTGATATTCCCAGCTGACAT 58.948 45.455 17.39 6.39 0.00 3.06
2005 2018 5.895534 AGTTGTGATCATGGGAGCATTTAAT 59.104 36.000 0.00 0.00 42.17 1.40
2093 2110 5.914898 ATTTTTAGGGGATGTAACTGCAC 57.085 39.130 0.00 0.00 0.00 4.57
2195 2214 5.657470 TGCGAATAGTGTCATTTATGCTC 57.343 39.130 0.00 0.00 0.00 4.26
2220 2239 7.678194 TTGAGAAACTAAAAAGACAAATGCG 57.322 32.000 0.00 0.00 0.00 4.73
2350 2370 2.875933 CCATGCATCCATTGGAAAATGC 59.124 45.455 18.72 18.72 36.22 3.56
2352 2372 3.116959 ACCCATGCATCCATTGGAAAAT 58.883 40.909 9.98 1.03 36.59 1.82
2412 2432 5.216566 TCACTTATTCTTGCACATTACGC 57.783 39.130 0.00 0.00 0.00 4.42
2417 2437 7.392673 ACTTCAAGATCACTTATTCTTGCACAT 59.607 33.333 7.60 0.00 45.41 3.21
2449 2469 5.129320 GTGCTCCCATTATTCCTGGATTTTT 59.871 40.000 0.00 0.00 35.70 1.94
2450 2470 4.651045 GTGCTCCCATTATTCCTGGATTTT 59.349 41.667 0.00 0.00 35.70 1.82
2451 2471 4.078980 AGTGCTCCCATTATTCCTGGATTT 60.079 41.667 0.00 0.00 35.70 2.17
2452 2472 3.464833 AGTGCTCCCATTATTCCTGGATT 59.535 43.478 0.00 0.00 35.70 3.01
2453 2473 3.059097 AGTGCTCCCATTATTCCTGGAT 58.941 45.455 0.00 0.00 35.70 3.41
2454 2474 2.492025 AGTGCTCCCATTATTCCTGGA 58.508 47.619 0.00 0.00 35.70 3.86
2455 2475 3.244700 CCTAGTGCTCCCATTATTCCTGG 60.245 52.174 0.00 0.00 0.00 4.45
2456 2476 3.648067 TCCTAGTGCTCCCATTATTCCTG 59.352 47.826 0.00 0.00 0.00 3.86
2457 2477 3.941629 TCCTAGTGCTCCCATTATTCCT 58.058 45.455 0.00 0.00 0.00 3.36
2458 2478 4.917906 ATCCTAGTGCTCCCATTATTCC 57.082 45.455 0.00 0.00 0.00 3.01
2459 2479 6.299141 TCAAATCCTAGTGCTCCCATTATTC 58.701 40.000 0.00 0.00 0.00 1.75
2460 2480 6.266131 TCAAATCCTAGTGCTCCCATTATT 57.734 37.500 0.00 0.00 0.00 1.40
2461 2481 5.912149 TCAAATCCTAGTGCTCCCATTAT 57.088 39.130 0.00 0.00 0.00 1.28
2462 2482 5.437060 GTTCAAATCCTAGTGCTCCCATTA 58.563 41.667 0.00 0.00 0.00 1.90
2463 2483 4.273318 GTTCAAATCCTAGTGCTCCCATT 58.727 43.478 0.00 0.00 0.00 3.16
2464 2484 3.372025 GGTTCAAATCCTAGTGCTCCCAT 60.372 47.826 0.00 0.00 0.00 4.00
2465 2485 2.026262 GGTTCAAATCCTAGTGCTCCCA 60.026 50.000 0.00 0.00 0.00 4.37
2466 2486 2.644676 GGTTCAAATCCTAGTGCTCCC 58.355 52.381 0.00 0.00 0.00 4.30
2467 2487 2.239907 AGGGTTCAAATCCTAGTGCTCC 59.760 50.000 0.00 0.00 37.89 4.70
2468 2488 3.274288 CAGGGTTCAAATCCTAGTGCTC 58.726 50.000 0.00 0.00 37.45 4.26
2469 2489 2.025887 CCAGGGTTCAAATCCTAGTGCT 60.026 50.000 0.00 0.00 37.45 4.40
2470 2490 2.290960 ACCAGGGTTCAAATCCTAGTGC 60.291 50.000 0.00 0.00 37.45 4.40
2471 2491 3.347216 CACCAGGGTTCAAATCCTAGTG 58.653 50.000 6.28 6.28 41.36 2.74
2472 2492 2.308866 CCACCAGGGTTCAAATCCTAGT 59.691 50.000 0.00 0.00 37.45 2.57
2473 2493 3.004752 CCACCAGGGTTCAAATCCTAG 57.995 52.381 0.00 0.00 37.45 3.02
2486 2506 1.613061 GTATCCCCAACCCACCAGG 59.387 63.158 0.00 0.00 43.78 4.45
2487 2507 1.211567 TGGTATCCCCAACCCACCAG 61.212 60.000 0.00 0.00 41.50 4.00
2488 2508 1.151565 TGGTATCCCCAACCCACCA 60.152 57.895 0.00 0.00 41.50 4.17
2489 2509 3.844063 TGGTATCCCCAACCCACC 58.156 61.111 0.00 0.00 41.50 4.61
2496 2516 1.009552 AGATGGACAGTGGTATCCCCA 59.990 52.381 0.00 0.00 42.51 4.96
2497 2517 1.807814 AGATGGACAGTGGTATCCCC 58.192 55.000 0.00 0.00 33.69 4.81
2498 2518 3.071167 GGTTAGATGGACAGTGGTATCCC 59.929 52.174 0.00 0.00 33.69 3.85
2499 2519 3.709653 TGGTTAGATGGACAGTGGTATCC 59.290 47.826 0.00 0.00 35.37 2.59
2500 2520 5.305644 AGATGGTTAGATGGACAGTGGTATC 59.694 44.000 0.00 0.00 0.00 2.24
2501 2521 5.219739 AGATGGTTAGATGGACAGTGGTAT 58.780 41.667 0.00 0.00 0.00 2.73
2502 2522 4.620723 AGATGGTTAGATGGACAGTGGTA 58.379 43.478 0.00 0.00 0.00 3.25
2503 2523 3.452627 GAGATGGTTAGATGGACAGTGGT 59.547 47.826 0.00 0.00 0.00 4.16
2504 2524 3.452264 TGAGATGGTTAGATGGACAGTGG 59.548 47.826 0.00 0.00 0.00 4.00
2505 2525 4.743057 TGAGATGGTTAGATGGACAGTG 57.257 45.455 0.00 0.00 0.00 3.66
2506 2526 4.080863 GGTTGAGATGGTTAGATGGACAGT 60.081 45.833 0.00 0.00 0.00 3.55
2507 2527 4.080919 TGGTTGAGATGGTTAGATGGACAG 60.081 45.833 0.00 0.00 0.00 3.51
2508 2528 3.843619 TGGTTGAGATGGTTAGATGGACA 59.156 43.478 0.00 0.00 0.00 4.02
2509 2529 4.192317 GTGGTTGAGATGGTTAGATGGAC 58.808 47.826 0.00 0.00 0.00 4.02
2510 2530 3.843619 TGTGGTTGAGATGGTTAGATGGA 59.156 43.478 0.00 0.00 0.00 3.41
2511 2531 4.194640 CTGTGGTTGAGATGGTTAGATGG 58.805 47.826 0.00 0.00 0.00 3.51
2512 2532 4.194640 CCTGTGGTTGAGATGGTTAGATG 58.805 47.826 0.00 0.00 0.00 2.90
2513 2533 3.846588 ACCTGTGGTTGAGATGGTTAGAT 59.153 43.478 0.00 0.00 27.29 1.98
2514 2534 3.248024 ACCTGTGGTTGAGATGGTTAGA 58.752 45.455 0.00 0.00 27.29 2.10
2515 2535 3.703001 ACCTGTGGTTGAGATGGTTAG 57.297 47.619 0.00 0.00 27.29 2.34
2526 2546 6.248433 ATCACTTATGAATCAACCTGTGGTT 58.752 36.000 0.00 0.00 41.98 3.67
2527 2547 5.241403 TCACTTATGAATCAACCTGTGGT 57.759 39.130 0.00 0.00 37.65 4.16
2528 2548 6.118170 AGATCACTTATGAATCAACCTGTGG 58.882 40.000 0.00 0.00 38.69 4.17
2529 2549 7.621428 AAGATCACTTATGAATCAACCTGTG 57.379 36.000 0.00 0.00 38.69 3.66
2530 2550 9.739276 TTAAAGATCACTTATGAATCAACCTGT 57.261 29.630 0.00 0.00 38.69 4.00
2532 2552 8.897752 GCTTAAAGATCACTTATGAATCAACCT 58.102 33.333 0.00 0.00 38.69 3.50
2533 2553 8.897752 AGCTTAAAGATCACTTATGAATCAACC 58.102 33.333 0.00 0.00 38.69 3.77
2536 2556 9.265901 GCTAGCTTAAAGATCACTTATGAATCA 57.734 33.333 7.70 0.00 38.69 2.57
2537 2557 9.487790 AGCTAGCTTAAAGATCACTTATGAATC 57.512 33.333 12.68 0.00 38.69 2.52
2538 2558 9.270640 CAGCTAGCTTAAAGATCACTTATGAAT 57.729 33.333 16.46 0.00 38.69 2.57
2539 2559 8.478066 TCAGCTAGCTTAAAGATCACTTATGAA 58.522 33.333 16.46 0.00 38.69 2.57
2540 2560 8.011844 TCAGCTAGCTTAAAGATCACTTATGA 57.988 34.615 16.46 0.94 39.83 2.15
2541 2561 7.925483 ACTCAGCTAGCTTAAAGATCACTTATG 59.075 37.037 16.46 0.00 35.05 1.90
2542 2562 7.925483 CACTCAGCTAGCTTAAAGATCACTTAT 59.075 37.037 16.46 0.00 35.05 1.73
2543 2563 7.093727 ACACTCAGCTAGCTTAAAGATCACTTA 60.094 37.037 16.46 0.00 35.05 2.24
2544 2564 6.105333 CACTCAGCTAGCTTAAAGATCACTT 58.895 40.000 16.46 0.00 38.05 3.16
2545 2565 5.186797 ACACTCAGCTAGCTTAAAGATCACT 59.813 40.000 16.46 0.00 0.00 3.41
2546 2566 5.415221 ACACTCAGCTAGCTTAAAGATCAC 58.585 41.667 16.46 0.00 0.00 3.06
2547 2567 5.667539 ACACTCAGCTAGCTTAAAGATCA 57.332 39.130 16.46 0.00 0.00 2.92
2548 2568 6.976636 AAACACTCAGCTAGCTTAAAGATC 57.023 37.500 16.46 0.00 0.00 2.75
2549 2569 7.229506 ACAAAAACACTCAGCTAGCTTAAAGAT 59.770 33.333 16.46 4.66 0.00 2.40
2550 2570 6.542370 ACAAAAACACTCAGCTAGCTTAAAGA 59.458 34.615 16.46 8.47 0.00 2.52
2551 2571 6.729187 ACAAAAACACTCAGCTAGCTTAAAG 58.271 36.000 16.46 15.03 0.00 1.85
2552 2572 6.542370 AGACAAAAACACTCAGCTAGCTTAAA 59.458 34.615 16.46 2.56 0.00 1.52
2553 2573 6.055588 AGACAAAAACACTCAGCTAGCTTAA 58.944 36.000 16.46 5.38 0.00 1.85
2554 2574 5.611374 AGACAAAAACACTCAGCTAGCTTA 58.389 37.500 16.46 6.45 0.00 3.09
2555 2575 4.455606 AGACAAAAACACTCAGCTAGCTT 58.544 39.130 16.46 0.00 0.00 3.74
2556 2576 4.078639 AGACAAAAACACTCAGCTAGCT 57.921 40.909 12.68 12.68 0.00 3.32
2557 2577 4.820284 AAGACAAAAACACTCAGCTAGC 57.180 40.909 6.62 6.62 0.00 3.42
2575 2595 7.425606 GTGCAAGGAAAGAGAAATTACAAAGA 58.574 34.615 0.00 0.00 0.00 2.52
2619 2639 1.181098 ACCACTTGTTCCTGCCATGC 61.181 55.000 0.00 0.00 0.00 4.06
2686 2707 3.000727 GACCGGTGACCTAAACAATCAG 58.999 50.000 14.63 0.00 0.00 2.90
2687 2708 2.635915 AGACCGGTGACCTAAACAATCA 59.364 45.455 14.63 0.00 0.00 2.57
2690 2711 1.000060 CGAGACCGGTGACCTAAACAA 60.000 52.381 14.63 0.00 0.00 2.83
2691 2712 0.599558 CGAGACCGGTGACCTAAACA 59.400 55.000 14.63 0.00 0.00 2.83
2726 2747 5.664457 CTGGCTGAACAAGATACATCACTA 58.336 41.667 0.00 0.00 0.00 2.74
2739 2760 2.167398 GACTACCGGCTGGCTGAACA 62.167 60.000 12.89 0.00 39.70 3.18
2782 2803 5.682234 AACACCACTATCATCATCTGACA 57.318 39.130 0.00 0.00 36.48 3.58
2818 2839 4.875536 TGTGAAGGATTAACATGATCACCG 59.124 41.667 0.00 0.00 35.91 4.94
2859 2882 5.754782 ACTAATATGTTGGATGCCAGACAA 58.245 37.500 0.00 0.00 33.81 3.18
2863 2886 6.543465 TCAGAAACTAATATGTTGGATGCCAG 59.457 38.462 0.00 0.00 33.81 4.85


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

AutoCloner maintained by Alex Coulton.