Multiple sequence alignment - TraesCS1D01G319000

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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 TraesCS1D01G319000 chr1D 100.000 3455 0 0 1 3455 413223948 413227402 0.000000e+00 6381.0
1 TraesCS1D01G319000 chr1D 90.291 1411 128 7 1019 2423 413234467 413233060 0.000000e+00 1838.0
2 TraesCS1D01G319000 chr1D 85.888 822 103 6 1464 2283 413359804 413358994 0.000000e+00 863.0
3 TraesCS1D01G319000 chr1D 80.333 661 94 22 1391 2038 413319370 413318733 5.220000e-128 468.0
4 TraesCS1D01G319000 chr1D 82.112 464 74 8 999 1458 413373726 413373268 4.180000e-104 388.0
5 TraesCS1D01G319000 chr7A 86.680 1524 168 26 1023 2539 62279339 62277844 0.000000e+00 1657.0
6 TraesCS1D01G319000 chr7A 92.379 866 59 3 2572 3431 58987122 58986258 0.000000e+00 1227.0
7 TraesCS1D01G319000 chr7A 95.000 120 6 0 786 905 34133507 34133388 4.550000e-44 189.0
8 TraesCS1D01G319000 chr1B 87.814 1395 153 12 1019 2401 557412407 557411018 0.000000e+00 1618.0
9 TraesCS1D01G319000 chr1B 85.642 1393 180 15 999 2381 557464416 557463034 0.000000e+00 1447.0
10 TraesCS1D01G319000 chr1B 94.853 408 19 2 1 408 557393191 557393596 1.350000e-178 636.0
11 TraesCS1D01G319000 chr1B 90.488 410 26 2 908 1317 557402142 557402538 2.360000e-146 529.0
12 TraesCS1D01G319000 chr1B 88.664 247 26 1 2321 2565 557408231 557408477 2.020000e-77 300.0
13 TraesCS1D01G319000 chr1B 96.575 146 5 0 568 713 557395582 557395727 3.450000e-60 243.0
14 TraesCS1D01G319000 chr1B 92.800 125 8 1 781 905 661925226 661925349 2.740000e-41 180.0
15 TraesCS1D01G319000 chr1A 87.322 1404 164 10 1010 2401 510343198 510341797 0.000000e+00 1594.0
16 TraesCS1D01G319000 chr1A 85.714 1393 180 16 1000 2381 510354296 510352912 0.000000e+00 1452.0
17 TraesCS1D01G319000 chr1A 96.296 756 26 2 941 1696 510292895 510293648 0.000000e+00 1240.0
18 TraesCS1D01G319000 chr1A 90.741 810 45 9 1 788 510292056 510292857 0.000000e+00 1053.0
19 TraesCS1D01G319000 chr1A 95.798 119 5 0 787 905 471791931 471792049 3.520000e-45 193.0
20 TraesCS1D01G319000 chr1A 94.958 119 6 0 787 905 84725600 84725482 1.640000e-43 187.0
21 TraesCS1D01G319000 chr1A 94.118 119 7 0 787 905 353914507 353914389 7.620000e-42 182.0
22 TraesCS1D01G319000 chr1A 90.400 125 12 0 785 909 10715170 10715294 7.670000e-37 165.0
23 TraesCS1D01G319000 chr1A 94.595 37 2 0 908 944 510292851 510292887 1.340000e-04 58.4
24 TraesCS1D01G319000 chr5D 95.843 866 29 3 2572 3431 257168142 257169006 0.000000e+00 1393.0
25 TraesCS1D01G319000 chr5D 94.206 863 41 5 2575 3431 422765943 422765084 0.000000e+00 1308.0
26 TraesCS1D01G319000 chr5D 92.290 882 56 8 2558 3431 521486693 521485816 0.000000e+00 1242.0
27 TraesCS1D01G319000 chr6D 94.792 864 38 4 2574 3431 58005815 58004953 0.000000e+00 1339.0
28 TraesCS1D01G319000 chr7D 94.798 865 33 7 2574 3431 544623092 544623951 0.000000e+00 1338.0
29 TraesCS1D01G319000 chr7D 95.161 124 6 0 787 910 185770673 185770796 2.720000e-46 196.0
30 TraesCS1D01G319000 chr5A 92.370 865 59 3 2573 3431 626368310 626367447 0.000000e+00 1225.0
31 TraesCS1D01G319000 chr3A 92.184 870 61 3 2568 3431 704597780 704598648 0.000000e+00 1223.0
32 TraesCS1D01G319000 chr5B 91.972 872 61 5 2565 3431 695499259 695500126 0.000000e+00 1214.0
33 TraesCS1D01G319000 chr5B 91.304 138 9 2 782 916 613637667 613637530 5.890000e-43 185.0
34 TraesCS1D01G319000 chrUn 100.000 412 0 0 1919 2330 477522623 477523034 0.000000e+00 761.0
35 TraesCS1D01G319000 chr2A 88.535 471 47 1 1960 2423 754464720 754464250 6.470000e-157 564.0
36 TraesCS1D01G319000 chr2A 96.774 124 4 0 787 910 66088692 66088815 1.260000e-49 207.0
37 TraesCS1D01G319000 chr3D 95.968 124 5 0 787 910 10453426 10453303 5.850000e-48 202.0
38 TraesCS1D01G319000 chr6A 96.639 119 4 0 787 905 116339233 116339351 7.560000e-47 198.0
39 TraesCS1D01G319000 chr6A 96.639 119 4 0 787 905 585963368 585963250 7.560000e-47 198.0
40 TraesCS1D01G319000 chr6A 95.798 119 5 0 787 905 304956772 304956654 3.520000e-45 193.0
41 TraesCS1D01G319000 chr4B 96.639 119 4 0 787 905 12626160 12626042 7.560000e-47 198.0
42 TraesCS1D01G319000 chr4B 94.118 119 7 0 787 905 267654187 267654069 7.620000e-42 182.0
43 TraesCS1D01G319000 chr4B 94.690 113 6 0 793 905 139778325 139778437 3.540000e-40 176.0
44 TraesCS1D01G319000 chr3B 95.122 123 6 0 787 909 560597441 560597563 9.780000e-46 195.0
45 TraesCS1D01G319000 chr7B 95.798 119 5 0 787 905 642210897 642210779 3.520000e-45 193.0
46 TraesCS1D01G319000 chr4A 94.958 119 6 0 786 904 707660719 707660837 1.640000e-43 187.0
47 TraesCS1D01G319000 chr4A 94.215 121 7 0 785 905 142343695 142343815 5.890000e-43 185.0


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 TraesCS1D01G319000 chr1D 413223948 413227402 3454 False 6381.0 6381 100.000000 1 3455 1 chr1D.!!$F1 3454
1 TraesCS1D01G319000 chr1D 413233060 413234467 1407 True 1838.0 1838 90.291000 1019 2423 1 chr1D.!!$R1 1404
2 TraesCS1D01G319000 chr1D 413358994 413359804 810 True 863.0 863 85.888000 1464 2283 1 chr1D.!!$R3 819
3 TraesCS1D01G319000 chr1D 413318733 413319370 637 True 468.0 468 80.333000 1391 2038 1 chr1D.!!$R2 647
4 TraesCS1D01G319000 chr7A 62277844 62279339 1495 True 1657.0 1657 86.680000 1023 2539 1 chr7A.!!$R3 1516
5 TraesCS1D01G319000 chr7A 58986258 58987122 864 True 1227.0 1227 92.379000 2572 3431 1 chr7A.!!$R2 859
6 TraesCS1D01G319000 chr1B 557411018 557412407 1389 True 1618.0 1618 87.814000 1019 2401 1 chr1B.!!$R1 1382
7 TraesCS1D01G319000 chr1B 557463034 557464416 1382 True 1447.0 1447 85.642000 999 2381 1 chr1B.!!$R2 1382
8 TraesCS1D01G319000 chr1B 557393191 557395727 2536 False 439.5 636 95.714000 1 713 2 chr1B.!!$F4 712
9 TraesCS1D01G319000 chr1A 510341797 510343198 1401 True 1594.0 1594 87.322000 1010 2401 1 chr1A.!!$R3 1391
10 TraesCS1D01G319000 chr1A 510352912 510354296 1384 True 1452.0 1452 85.714000 1000 2381 1 chr1A.!!$R4 1381
11 TraesCS1D01G319000 chr1A 510292056 510293648 1592 False 783.8 1240 93.877333 1 1696 3 chr1A.!!$F3 1695
12 TraesCS1D01G319000 chr5D 257168142 257169006 864 False 1393.0 1393 95.843000 2572 3431 1 chr5D.!!$F1 859
13 TraesCS1D01G319000 chr5D 422765084 422765943 859 True 1308.0 1308 94.206000 2575 3431 1 chr5D.!!$R1 856
14 TraesCS1D01G319000 chr5D 521485816 521486693 877 True 1242.0 1242 92.290000 2558 3431 1 chr5D.!!$R2 873
15 TraesCS1D01G319000 chr6D 58004953 58005815 862 True 1339.0 1339 94.792000 2574 3431 1 chr6D.!!$R1 857
16 TraesCS1D01G319000 chr7D 544623092 544623951 859 False 1338.0 1338 94.798000 2574 3431 1 chr7D.!!$F2 857
17 TraesCS1D01G319000 chr5A 626367447 626368310 863 True 1225.0 1225 92.370000 2573 3431 1 chr5A.!!$R1 858
18 TraesCS1D01G319000 chr3A 704597780 704598648 868 False 1223.0 1223 92.184000 2568 3431 1 chr3A.!!$F1 863
19 TraesCS1D01G319000 chr5B 695499259 695500126 867 False 1214.0 1214 91.972000 2565 3431 1 chr5B.!!$F1 866

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
860 2760 0.032615 AGGTTTCCAACAAGCCCACA 60.033 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2526 4472 0.03392 ACTGCTCTGCGACAATGTCA 59.966 50.0 14.24 0.0 32.09 3.58 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
132 133 2.948315 GGATTCAGAATCAGAAGCACCC 59.052 50.000 22.23 1.31 39.71 4.61
164 165 4.981806 ACTAAAAAGAGCAACTGCACAA 57.018 36.364 4.22 0.00 45.16 3.33
182 183 4.290155 CACAAGGCACAACTTATGTTCAC 58.710 43.478 0.00 0.00 41.46 3.18
185 186 1.591248 GCACAACTTATGTTCACGCG 58.409 50.000 3.53 3.53 41.46 6.01
373 374 2.719531 TGGCATATCGTTTGGGCTTA 57.280 45.000 0.00 0.00 0.00 3.09
386 387 0.394488 GGGCTTACTTGAAGGAGGCC 60.394 60.000 21.35 21.35 45.76 5.19
397 398 0.984995 AAGGAGGCCTAGTTCACCAC 59.015 55.000 4.42 0.00 31.13 4.16
449 458 6.418101 AGCATTACTTGTGTTCCATGTATCT 58.582 36.000 0.00 0.00 34.67 1.98
498 515 1.209128 GATCATACGCCACTGTTCGG 58.791 55.000 4.59 0.00 0.00 4.30
519 536 1.281867 TGCATTACCTGAACCTCCTGG 59.718 52.381 0.00 0.00 39.83 4.45
590 2476 3.310860 AAGACCCGGTGCATCGTCC 62.311 63.158 19.62 6.70 0.00 4.79
720 2614 2.287248 CGCATCTCGAGCTCACTATCAA 60.287 50.000 15.40 0.00 41.67 2.57
732 2626 2.373169 TCACTATCAATGGCCCCATCTC 59.627 50.000 0.00 0.00 35.31 2.75
779 2679 3.470567 GCTGTCGGTTCGCTCACG 61.471 66.667 0.00 0.00 42.01 4.35
780 2680 2.805353 CTGTCGGTTCGCTCACGG 60.805 66.667 0.00 0.00 40.63 4.94
802 2702 3.423154 CGGACACGGCTCCTTTGC 61.423 66.667 0.00 0.00 36.18 3.68
811 2711 2.434185 CTCCTTTGCCGTGCGCTA 60.434 61.111 9.73 0.00 38.78 4.26
812 2712 2.434185 TCCTTTGCCGTGCGCTAG 60.434 61.111 9.73 1.71 38.78 3.42
813 2713 3.499737 CCTTTGCCGTGCGCTAGG 61.500 66.667 9.73 13.39 38.78 3.02
814 2714 2.742372 CTTTGCCGTGCGCTAGGT 60.742 61.111 19.77 0.00 38.78 3.08
815 2715 3.027170 CTTTGCCGTGCGCTAGGTG 62.027 63.158 19.77 7.38 38.78 4.00
816 2716 3.523087 TTTGCCGTGCGCTAGGTGA 62.523 57.895 19.77 8.69 38.78 4.02
817 2717 4.735132 TGCCGTGCGCTAGGTGAC 62.735 66.667 19.77 3.61 38.78 3.67
819 2719 4.415332 CCGTGCGCTAGGTGACGT 62.415 66.667 9.73 0.00 0.00 4.34
820 2720 2.430244 CGTGCGCTAGGTGACGTT 60.430 61.111 9.73 0.00 0.00 3.99
821 2721 2.716828 CGTGCGCTAGGTGACGTTG 61.717 63.158 9.73 0.00 0.00 4.10
822 2722 2.048597 TGCGCTAGGTGACGTTGG 60.049 61.111 9.73 0.00 0.00 3.77
823 2723 2.813908 GCGCTAGGTGACGTTGGG 60.814 66.667 0.00 0.08 0.00 4.12
824 2724 2.813908 CGCTAGGTGACGTTGGGC 60.814 66.667 0.00 0.00 0.00 5.36
825 2725 2.436115 GCTAGGTGACGTTGGGCC 60.436 66.667 0.00 0.00 0.00 5.80
826 2726 2.125673 CTAGGTGACGTTGGGCCG 60.126 66.667 0.00 0.00 0.00 6.13
827 2727 4.382320 TAGGTGACGTTGGGCCGC 62.382 66.667 0.00 0.00 0.00 6.53
830 2730 4.980805 GTGACGTTGGGCCGCTGA 62.981 66.667 0.00 0.00 0.00 4.26
831 2731 4.980805 TGACGTTGGGCCGCTGAC 62.981 66.667 0.00 0.00 0.00 3.51
832 2732 4.980805 GACGTTGGGCCGCTGACA 62.981 66.667 0.00 0.00 0.00 3.58
833 2733 4.329545 ACGTTGGGCCGCTGACAT 62.330 61.111 0.00 0.00 0.00 3.06
834 2734 3.803082 CGTTGGGCCGCTGACATG 61.803 66.667 0.00 0.00 0.00 3.21
835 2735 2.672996 GTTGGGCCGCTGACATGT 60.673 61.111 0.00 0.00 0.00 3.21
836 2736 2.672651 TTGGGCCGCTGACATGTG 60.673 61.111 1.15 0.00 0.00 3.21
837 2737 4.720902 TGGGCCGCTGACATGTGG 62.721 66.667 1.15 0.00 40.36 4.17
841 2741 4.720902 CCGCTGACATGTGGGCCA 62.721 66.667 1.15 0.00 34.20 5.36
842 2742 3.129502 CGCTGACATGTGGGCCAG 61.130 66.667 6.40 5.40 0.00 4.85
843 2743 2.753043 GCTGACATGTGGGCCAGG 60.753 66.667 6.40 1.59 0.00 4.45
844 2744 2.759114 CTGACATGTGGGCCAGGT 59.241 61.111 6.40 5.66 41.63 4.00
845 2745 1.075482 CTGACATGTGGGCCAGGTT 59.925 57.895 6.40 0.00 38.40 3.50
846 2746 0.540365 CTGACATGTGGGCCAGGTTT 60.540 55.000 6.40 0.00 38.40 3.27
847 2747 0.539438 TGACATGTGGGCCAGGTTTC 60.539 55.000 6.40 1.88 38.40 2.78
848 2748 1.228862 ACATGTGGGCCAGGTTTCC 60.229 57.895 6.40 0.00 33.45 3.13
849 2749 1.228831 CATGTGGGCCAGGTTTCCA 60.229 57.895 6.40 0.00 0.00 3.53
850 2750 0.831288 CATGTGGGCCAGGTTTCCAA 60.831 55.000 6.40 0.00 31.73 3.53
851 2751 0.831711 ATGTGGGCCAGGTTTCCAAC 60.832 55.000 6.40 0.00 31.73 3.77
852 2752 1.456705 GTGGGCCAGGTTTCCAACA 60.457 57.895 6.40 0.00 31.73 3.33
853 2753 1.045911 GTGGGCCAGGTTTCCAACAA 61.046 55.000 6.40 0.00 31.73 2.83
854 2754 0.758685 TGGGCCAGGTTTCCAACAAG 60.759 55.000 0.00 0.00 0.00 3.16
855 2755 1.367471 GGCCAGGTTTCCAACAAGC 59.633 57.895 0.00 0.00 0.00 4.01
856 2756 1.367471 GCCAGGTTTCCAACAAGCC 59.633 57.895 0.00 0.00 0.00 4.35
857 2757 2.049435 CCAGGTTTCCAACAAGCCC 58.951 57.895 0.00 0.00 0.00 5.19
858 2758 0.758685 CCAGGTTTCCAACAAGCCCA 60.759 55.000 0.00 0.00 0.00 5.36
859 2759 0.389025 CAGGTTTCCAACAAGCCCAC 59.611 55.000 0.00 0.00 0.00 4.61
860 2760 0.032615 AGGTTTCCAACAAGCCCACA 60.033 50.000 0.00 0.00 0.00 4.17
861 2761 1.047801 GGTTTCCAACAAGCCCACAT 58.952 50.000 0.00 0.00 0.00 3.21
862 2762 1.270252 GGTTTCCAACAAGCCCACATG 60.270 52.381 0.00 0.00 0.00 3.21
863 2763 0.392336 TTTCCAACAAGCCCACATGC 59.608 50.000 0.00 0.00 0.00 4.06
864 2764 1.470996 TTCCAACAAGCCCACATGCC 61.471 55.000 0.00 0.00 0.00 4.40
865 2765 2.208619 CCAACAAGCCCACATGCCA 61.209 57.895 0.00 0.00 0.00 4.92
866 2766 1.290955 CAACAAGCCCACATGCCAG 59.709 57.895 0.00 0.00 0.00 4.85
867 2767 1.152483 AACAAGCCCACATGCCAGT 60.152 52.632 0.00 0.00 0.00 4.00
868 2768 1.466025 AACAAGCCCACATGCCAGTG 61.466 55.000 0.00 0.00 39.21 3.66
876 2776 1.078709 CACATGCCAGTGGTAGAACG 58.921 55.000 11.74 0.00 35.88 3.95
877 2777 0.036388 ACATGCCAGTGGTAGAACGG 60.036 55.000 11.74 0.00 0.00 4.44
878 2778 1.078426 ATGCCAGTGGTAGAACGGC 60.078 57.895 11.74 0.00 39.00 5.68
879 2779 1.836999 ATGCCAGTGGTAGAACGGCA 61.837 55.000 11.74 3.58 46.23 5.69
880 2780 1.741770 GCCAGTGGTAGAACGGCAG 60.742 63.158 11.74 0.00 38.65 4.85
881 2781 1.079127 CCAGTGGTAGAACGGCAGG 60.079 63.158 0.00 0.00 0.00 4.85
882 2782 1.741770 CAGTGGTAGAACGGCAGGC 60.742 63.158 0.00 0.00 0.00 4.85
883 2783 1.913762 AGTGGTAGAACGGCAGGCT 60.914 57.895 0.00 0.00 0.00 4.58
884 2784 1.741770 GTGGTAGAACGGCAGGCTG 60.742 63.158 10.94 10.94 0.00 4.85
885 2785 2.820037 GGTAGAACGGCAGGCTGC 60.820 66.667 30.93 30.93 44.08 5.25
894 2794 4.752879 GCAGGCTGCCGAACGGTA 62.753 66.667 28.87 9.39 37.42 4.02
900 2800 4.349682 TGCCGAACGGTAGAGGAT 57.650 55.556 14.63 0.00 37.65 3.24
901 2801 2.112898 TGCCGAACGGTAGAGGATC 58.887 57.895 14.63 0.00 37.65 3.36
902 2802 1.363080 GCCGAACGGTAGAGGATCC 59.637 63.158 14.63 2.48 37.65 3.36
903 2803 1.108132 GCCGAACGGTAGAGGATCCT 61.108 60.000 16.13 16.13 37.65 3.24
904 2804 0.953003 CCGAACGGTAGAGGATCCTC 59.047 60.000 31.27 31.27 43.03 3.71
912 2812 3.956377 GAGGATCCTCTTCCGCCA 58.044 61.111 31.11 0.00 40.94 5.69
955 2866 1.233019 GCATCCATTACTGCAGCGAT 58.767 50.000 15.27 4.98 38.28 4.58
959 2870 3.371102 TCCATTACTGCAGCGATACTC 57.629 47.619 15.27 0.00 0.00 2.59
965 2876 1.960040 CTGCAGCGATACTCCACCCA 61.960 60.000 0.00 0.00 0.00 4.51
971 2882 1.269831 GCGATACTCCACCCAGTGATC 60.270 57.143 0.00 0.00 35.23 2.92
988 2899 0.966179 ATCCGTTCCAAAGCCCAAAC 59.034 50.000 0.00 0.00 0.00 2.93
1597 3533 1.078848 CTGCCCGAGTTCTTGAGGG 60.079 63.158 0.00 0.00 46.44 4.30
1679 3618 1.676006 CGCCTTCAACACTTTCTTGGT 59.324 47.619 0.00 0.00 0.00 3.67
1839 3783 2.363795 CCCAGAGGCTCGGTGGTA 60.364 66.667 18.41 0.00 0.00 3.25
1854 3798 2.035066 GGTGGTATACGTATGCTTCGGT 59.965 50.000 20.79 0.00 0.00 4.69
1859 3803 4.022849 GGTATACGTATGCTTCGGTACCTT 60.023 45.833 20.79 0.00 38.88 3.50
1910 3854 4.168291 GGCTCTCGGGCTGGAAGG 62.168 72.222 0.00 0.00 37.53 3.46
1915 3859 1.219393 CTCGGGCTGGAAGGTTCTC 59.781 63.158 0.00 0.00 0.00 2.87
2386 4330 4.988598 CCTGTGACCTGCGCCGTT 62.989 66.667 4.18 0.00 0.00 4.44
2412 4356 3.954258 TCGATGATCTGGTAGAAGCAAGA 59.046 43.478 0.00 0.00 0.00 3.02
2414 4358 3.533606 TGATCTGGTAGAAGCAAGAGC 57.466 47.619 0.00 0.00 42.56 4.09
2468 4414 1.344438 ACCTTGAACATCAGCGACTGA 59.656 47.619 11.12 11.12 44.99 3.41
2477 4423 0.104855 TCAGCGACTGAAACTGCACT 59.895 50.000 7.02 0.00 37.57 4.40
2478 4424 0.234106 CAGCGACTGAAACTGCACTG 59.766 55.000 1.18 0.00 32.44 3.66
2479 4425 1.082496 GCGACTGAAACTGCACTGC 60.082 57.895 0.00 0.00 0.00 4.40
2480 4426 1.775039 GCGACTGAAACTGCACTGCA 61.775 55.000 3.11 3.11 36.92 4.41
2505 4451 2.890474 GTGGCATGGGCGTACTCG 60.890 66.667 0.00 0.00 42.47 4.18
2506 4452 4.155733 TGGCATGGGCGTACTCGG 62.156 66.667 0.00 0.00 42.47 4.63
2507 4453 4.157120 GGCATGGGCGTACTCGGT 62.157 66.667 0.00 0.00 42.47 4.69
2512 4458 2.202531 GGGCGTACTCGGTCGTTC 60.203 66.667 0.00 0.00 37.56 3.95
2521 4467 0.811915 CTCGGTCGTTCTCTGGTGAT 59.188 55.000 0.00 0.00 0.00 3.06
2522 4468 0.526211 TCGGTCGTTCTCTGGTGATG 59.474 55.000 0.00 0.00 0.00 3.07
2523 4469 0.458543 CGGTCGTTCTCTGGTGATGG 60.459 60.000 0.00 0.00 0.00 3.51
2525 4471 1.275291 GGTCGTTCTCTGGTGATGGAA 59.725 52.381 0.00 0.00 0.00 3.53
2526 4472 2.093447 GGTCGTTCTCTGGTGATGGAAT 60.093 50.000 0.00 0.00 0.00 3.01
2527 4473 2.932614 GTCGTTCTCTGGTGATGGAATG 59.067 50.000 0.00 0.00 0.00 2.67
2528 4474 2.831526 TCGTTCTCTGGTGATGGAATGA 59.168 45.455 0.00 0.00 33.20 2.57
2529 4475 2.932614 CGTTCTCTGGTGATGGAATGAC 59.067 50.000 0.00 0.00 0.00 3.06
2530 4476 3.617288 CGTTCTCTGGTGATGGAATGACA 60.617 47.826 0.00 0.00 29.31 3.58
2531 4477 4.521146 GTTCTCTGGTGATGGAATGACAT 58.479 43.478 0.00 0.00 29.31 3.06
2532 4478 4.849813 TCTCTGGTGATGGAATGACATT 57.150 40.909 0.00 0.00 29.31 2.71
2533 4479 4.520179 TCTCTGGTGATGGAATGACATTG 58.480 43.478 5.14 0.00 29.31 2.82
2534 4480 4.019051 TCTCTGGTGATGGAATGACATTGT 60.019 41.667 5.14 0.00 29.31 2.71
2535 4481 4.264253 TCTGGTGATGGAATGACATTGTC 58.736 43.478 5.14 9.93 29.31 3.18
2536 4482 3.009026 TGGTGATGGAATGACATTGTCG 58.991 45.455 5.14 0.00 29.31 4.35
2537 4483 2.223340 GGTGATGGAATGACATTGTCGC 60.223 50.000 5.14 7.45 29.31 5.19
2538 4484 2.419673 GTGATGGAATGACATTGTCGCA 59.580 45.455 5.14 0.00 34.95 5.10
2539 4485 2.679336 TGATGGAATGACATTGTCGCAG 59.321 45.455 5.14 0.00 34.95 5.18
2540 4486 2.470983 TGGAATGACATTGTCGCAGA 57.529 45.000 5.14 0.00 34.95 4.26
2541 4487 2.349590 TGGAATGACATTGTCGCAGAG 58.650 47.619 5.14 0.00 36.95 3.35
2542 4488 1.063174 GGAATGACATTGTCGCAGAGC 59.937 52.381 5.14 0.00 36.95 4.09
2543 4489 1.733912 GAATGACATTGTCGCAGAGCA 59.266 47.619 5.14 0.00 36.95 4.26
2544 4490 1.366679 ATGACATTGTCGCAGAGCAG 58.633 50.000 11.97 0.00 36.95 4.24
2545 4491 0.033920 TGACATTGTCGCAGAGCAGT 59.966 50.000 11.97 0.00 36.95 4.40
2546 4492 1.272212 TGACATTGTCGCAGAGCAGTA 59.728 47.619 11.97 0.00 36.95 2.74
2547 4493 1.923204 GACATTGTCGCAGAGCAGTAG 59.077 52.381 0.13 0.00 36.95 2.57
2548 4494 1.546029 ACATTGTCGCAGAGCAGTAGA 59.454 47.619 0.00 0.00 36.95 2.59
2549 4495 2.191802 CATTGTCGCAGAGCAGTAGAG 58.808 52.381 0.00 0.00 36.95 2.43
2550 4496 0.109086 TTGTCGCAGAGCAGTAGAGC 60.109 55.000 0.00 0.00 36.95 4.09
2552 4498 0.525242 GTCGCAGAGCAGTAGAGCTG 60.525 60.000 0.00 0.00 46.75 4.24
2553 4499 0.962855 TCGCAGAGCAGTAGAGCTGT 60.963 55.000 0.00 0.00 46.75 4.40
2554 4500 0.735471 CGCAGAGCAGTAGAGCTGTA 59.265 55.000 0.00 0.00 46.75 2.74
2555 4501 1.268488 CGCAGAGCAGTAGAGCTGTAG 60.268 57.143 0.00 0.00 46.75 2.74
2556 4502 2.020720 GCAGAGCAGTAGAGCTGTAGA 58.979 52.381 0.00 0.00 46.75 2.59
2557 4503 2.622942 GCAGAGCAGTAGAGCTGTAGAT 59.377 50.000 0.00 0.00 46.75 1.98
2558 4504 3.304659 GCAGAGCAGTAGAGCTGTAGATC 60.305 52.174 0.00 0.00 46.75 2.75
2559 4505 3.882288 CAGAGCAGTAGAGCTGTAGATCA 59.118 47.826 0.00 0.00 46.75 2.92
2560 4506 4.520111 CAGAGCAGTAGAGCTGTAGATCAT 59.480 45.833 0.00 0.00 46.75 2.45
2561 4507 4.520111 AGAGCAGTAGAGCTGTAGATCATG 59.480 45.833 0.00 0.00 46.75 3.07
2562 4508 4.214310 AGCAGTAGAGCTGTAGATCATGT 58.786 43.478 0.00 0.00 46.64 3.21
2563 4509 5.380900 AGCAGTAGAGCTGTAGATCATGTA 58.619 41.667 0.00 0.00 46.64 2.29
2564 4510 6.009589 AGCAGTAGAGCTGTAGATCATGTAT 58.990 40.000 0.00 0.00 46.64 2.29
2565 4511 7.171653 AGCAGTAGAGCTGTAGATCATGTATA 58.828 38.462 0.00 0.00 46.64 1.47
2566 4512 7.667635 AGCAGTAGAGCTGTAGATCATGTATAA 59.332 37.037 0.00 0.00 46.64 0.98
2599 4547 5.446260 TTTAGAAAAGGAGGATGTACCCC 57.554 43.478 0.00 0.00 40.05 4.95
2680 4628 5.754782 ACCAAGGTGATACATCAATAAGCA 58.245 37.500 0.00 0.00 38.75 3.91
2719 4667 1.861982 ACACCGGTGCTACTCCTATT 58.138 50.000 34.26 7.93 0.00 1.73
2773 4721 4.271049 CCTAATACCAAACAGACATCGCAG 59.729 45.833 0.00 0.00 0.00 5.18
2774 4722 2.831685 TACCAAACAGACATCGCAGT 57.168 45.000 0.00 0.00 0.00 4.40
2790 4743 3.194755 TCGCAGTCTAACATCTAAAGCCA 59.805 43.478 0.00 0.00 0.00 4.75
2986 4939 2.284258 AGCTTCCTCCTCCTGCGT 60.284 61.111 0.00 0.00 0.00 5.24
3057 5010 1.139520 GAACCGCCACCATCAATGC 59.860 57.895 0.00 0.00 0.00 3.56
3064 5017 1.468054 GCCACCATCAATGCGAAAGAC 60.468 52.381 0.00 0.00 0.00 3.01
3332 5285 3.221771 CCAGATCTGATCGAAGACCTCT 58.778 50.000 24.62 0.00 42.51 3.69
3435 5388 3.284449 GTTGTGGCCGCCGACTTT 61.284 61.111 15.15 0.00 0.00 2.66
3436 5389 1.962306 GTTGTGGCCGCCGACTTTA 60.962 57.895 15.15 0.00 0.00 1.85
3437 5390 1.003112 TTGTGGCCGCCGACTTTAT 60.003 52.632 15.15 0.00 0.00 1.40
3438 5391 0.249676 TTGTGGCCGCCGACTTTATA 59.750 50.000 15.15 0.00 0.00 0.98
3439 5392 0.249676 TGTGGCCGCCGACTTTATAA 59.750 50.000 15.15 0.00 0.00 0.98
3440 5393 1.134340 TGTGGCCGCCGACTTTATAAT 60.134 47.619 15.15 0.00 0.00 1.28
3441 5394 2.102757 TGTGGCCGCCGACTTTATAATA 59.897 45.455 15.15 0.00 0.00 0.98
3442 5395 2.477754 GTGGCCGCCGACTTTATAATAC 59.522 50.000 4.45 0.00 0.00 1.89
3443 5396 2.102757 TGGCCGCCGACTTTATAATACA 59.897 45.455 4.58 0.00 0.00 2.29
3444 5397 3.244284 TGGCCGCCGACTTTATAATACAT 60.244 43.478 4.58 0.00 0.00 2.29
3445 5398 4.021280 TGGCCGCCGACTTTATAATACATA 60.021 41.667 4.58 0.00 0.00 2.29
3446 5399 4.328169 GGCCGCCGACTTTATAATACATAC 59.672 45.833 0.00 0.00 0.00 2.39
3447 5400 5.166398 GCCGCCGACTTTATAATACATACT 58.834 41.667 0.00 0.00 0.00 2.12
3448 5401 5.287992 GCCGCCGACTTTATAATACATACTC 59.712 44.000 0.00 0.00 0.00 2.59
3449 5402 5.803967 CCGCCGACTTTATAATACATACTCC 59.196 44.000 0.00 0.00 0.00 3.85
3450 5403 5.803967 CGCCGACTTTATAATACATACTCCC 59.196 44.000 0.00 0.00 0.00 4.30
3451 5404 6.349944 CGCCGACTTTATAATACATACTCCCT 60.350 42.308 0.00 0.00 0.00 4.20
3452 5405 7.034397 GCCGACTTTATAATACATACTCCCTC 58.966 42.308 0.00 0.00 0.00 4.30
3453 5406 7.545489 CCGACTTTATAATACATACTCCCTCC 58.455 42.308 0.00 0.00 0.00 4.30
3454 5407 7.396623 CCGACTTTATAATACATACTCCCTCCT 59.603 40.741 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.211457 AGAAGATTGAGGCTCCGCAAT 59.789 47.619 16.00 16.00 46.21 3.56
132 133 7.649306 AGTTGCTCTTTTTAGTATGTTTGCAAG 59.351 33.333 0.00 0.00 37.37 4.01
149 150 2.036236 GCCTTGTGCAGTTGCTCTT 58.964 52.632 5.62 0.00 42.66 2.85
164 165 1.535462 GCGTGAACATAAGTTGTGCCT 59.465 47.619 0.00 0.00 38.99 4.75
373 374 2.303311 GTGAACTAGGCCTCCTTCAAGT 59.697 50.000 21.23 11.43 34.61 3.16
386 387 2.519377 TGGAACACGTGGTGAACTAG 57.481 50.000 21.57 0.00 36.96 2.57
397 398 5.106830 CATGGATGATGATACATGGAACACG 60.107 44.000 9.38 0.00 44.52 4.49
449 458 2.687935 GTTGCTTCAGTTGGGAACTTGA 59.312 45.455 0.00 0.00 40.46 3.02
478 495 1.470805 CCGAACAGTGGCGTATGATCA 60.471 52.381 0.00 0.00 0.00 2.92
481 498 0.389296 CACCGAACAGTGGCGTATGA 60.389 55.000 0.00 0.00 33.95 2.15
498 515 2.359900 CAGGAGGTTCAGGTAATGCAC 58.640 52.381 0.00 0.00 0.00 4.57
552 572 0.745845 CACAGGGCGAGAATCCAAGG 60.746 60.000 0.00 0.00 0.00 3.61
594 2480 2.356075 GCAAATGCAGCAACCGCA 60.356 55.556 0.00 0.00 44.94 5.69
720 2614 1.064824 GGGAGAAGAGATGGGGCCAT 61.065 60.000 4.39 0.00 39.69 4.40
745 2639 3.717294 CTTCGGTGGGGAGTGGGG 61.717 72.222 0.00 0.00 0.00 4.96
795 2695 3.950794 CCTAGCGCACGGCAAAGGA 62.951 63.158 11.47 0.00 45.27 3.36
802 2702 3.909258 AACGTCACCTAGCGCACGG 62.909 63.158 18.10 15.56 36.56 4.94
803 2703 2.430244 AACGTCACCTAGCGCACG 60.430 61.111 11.47 12.58 38.24 5.34
804 2704 2.380410 CCAACGTCACCTAGCGCAC 61.380 63.158 11.47 0.00 0.00 5.34
805 2705 2.048597 CCAACGTCACCTAGCGCA 60.049 61.111 11.47 0.00 0.00 6.09
806 2706 2.813908 CCCAACGTCACCTAGCGC 60.814 66.667 0.00 0.00 0.00 5.92
807 2707 2.813908 GCCCAACGTCACCTAGCG 60.814 66.667 0.00 0.00 0.00 4.26
808 2708 2.436115 GGCCCAACGTCACCTAGC 60.436 66.667 0.00 0.00 0.00 3.42
809 2709 2.125673 CGGCCCAACGTCACCTAG 60.126 66.667 0.00 0.00 0.00 3.02
810 2710 4.382320 GCGGCCCAACGTCACCTA 62.382 66.667 0.00 0.00 35.98 3.08
813 2713 4.980805 TCAGCGGCCCAACGTCAC 62.981 66.667 0.00 0.00 35.98 3.67
814 2714 4.980805 GTCAGCGGCCCAACGTCA 62.981 66.667 0.00 0.00 35.98 4.35
815 2715 4.980805 TGTCAGCGGCCCAACGTC 62.981 66.667 0.00 0.00 35.98 4.34
816 2716 4.329545 ATGTCAGCGGCCCAACGT 62.330 61.111 0.00 0.00 35.98 3.99
817 2717 3.803082 CATGTCAGCGGCCCAACG 61.803 66.667 0.00 0.00 0.00 4.10
818 2718 2.672996 ACATGTCAGCGGCCCAAC 60.673 61.111 0.00 0.00 0.00 3.77
819 2719 2.672651 CACATGTCAGCGGCCCAA 60.673 61.111 0.00 0.00 0.00 4.12
820 2720 4.720902 CCACATGTCAGCGGCCCA 62.721 66.667 0.00 0.00 0.00 5.36
824 2724 4.720902 TGGCCCACATGTCAGCGG 62.721 66.667 0.00 2.18 0.00 5.52
825 2725 3.129502 CTGGCCCACATGTCAGCG 61.130 66.667 0.00 0.00 0.00 5.18
826 2726 2.753043 CCTGGCCCACATGTCAGC 60.753 66.667 0.00 7.90 0.00 4.26
827 2727 0.540365 AAACCTGGCCCACATGTCAG 60.540 55.000 0.00 0.00 0.00 3.51
828 2728 0.539438 GAAACCTGGCCCACATGTCA 60.539 55.000 0.00 0.00 0.00 3.58
829 2729 1.250840 GGAAACCTGGCCCACATGTC 61.251 60.000 0.00 0.00 0.00 3.06
830 2730 1.228862 GGAAACCTGGCCCACATGT 60.229 57.895 0.00 0.00 0.00 3.21
831 2731 0.831288 TTGGAAACCTGGCCCACATG 60.831 55.000 0.00 0.00 0.00 3.21
832 2732 0.831711 GTTGGAAACCTGGCCCACAT 60.832 55.000 0.00 0.00 42.21 3.21
833 2733 1.456705 GTTGGAAACCTGGCCCACA 60.457 57.895 0.00 0.00 42.21 4.17
834 2734 3.455152 GTTGGAAACCTGGCCCAC 58.545 61.111 0.00 0.00 42.21 4.61
844 2744 0.392336 GCATGTGGGCTTGTTGGAAA 59.608 50.000 0.00 0.00 0.00 3.13
845 2745 1.470996 GGCATGTGGGCTTGTTGGAA 61.471 55.000 0.00 0.00 39.42 3.53
846 2746 1.907807 GGCATGTGGGCTTGTTGGA 60.908 57.895 0.00 0.00 39.42 3.53
847 2747 2.162338 CTGGCATGTGGGCTTGTTGG 62.162 60.000 0.00 0.00 43.83 3.77
848 2748 1.290955 CTGGCATGTGGGCTTGTTG 59.709 57.895 0.00 0.00 43.83 3.33
849 2749 1.152483 ACTGGCATGTGGGCTTGTT 60.152 52.632 0.00 0.00 43.83 2.83
850 2750 1.904865 CACTGGCATGTGGGCTTGT 60.905 57.895 8.60 0.00 43.83 3.16
851 2751 2.967397 CACTGGCATGTGGGCTTG 59.033 61.111 8.60 0.00 43.83 4.01
857 2757 1.078709 CGTTCTACCACTGGCATGTG 58.921 55.000 9.29 9.29 37.66 3.21
858 2758 0.036388 CCGTTCTACCACTGGCATGT 60.036 55.000 0.00 0.00 0.00 3.21
859 2759 1.369091 GCCGTTCTACCACTGGCATG 61.369 60.000 0.00 0.00 45.06 4.06
860 2760 1.078426 GCCGTTCTACCACTGGCAT 60.078 57.895 0.00 0.00 45.06 4.40
861 2761 2.345991 GCCGTTCTACCACTGGCA 59.654 61.111 0.00 0.00 45.06 4.92
862 2762 1.741770 CTGCCGTTCTACCACTGGC 60.742 63.158 0.00 0.00 45.91 4.85
863 2763 1.079127 CCTGCCGTTCTACCACTGG 60.079 63.158 0.00 0.00 0.00 4.00
864 2764 1.741770 GCCTGCCGTTCTACCACTG 60.742 63.158 0.00 0.00 0.00 3.66
865 2765 1.913762 AGCCTGCCGTTCTACCACT 60.914 57.895 0.00 0.00 0.00 4.00
866 2766 1.741770 CAGCCTGCCGTTCTACCAC 60.742 63.158 0.00 0.00 0.00 4.16
867 2767 2.662596 CAGCCTGCCGTTCTACCA 59.337 61.111 0.00 0.00 0.00 3.25
868 2768 2.820037 GCAGCCTGCCGTTCTACC 60.820 66.667 5.06 0.00 37.42 3.18
877 2777 4.752879 TACCGTTCGGCAGCCTGC 62.753 66.667 8.55 8.55 44.08 4.85
878 2778 2.509336 CTACCGTTCGGCAGCCTG 60.509 66.667 10.54 3.19 0.00 4.85
879 2779 2.678934 TCTACCGTTCGGCAGCCT 60.679 61.111 10.54 0.00 0.00 4.58
880 2780 2.202756 CTCTACCGTTCGGCAGCC 60.203 66.667 11.32 0.00 0.00 4.85
881 2781 2.017559 ATCCTCTACCGTTCGGCAGC 62.018 60.000 11.32 0.00 0.00 5.25
882 2782 0.030908 GATCCTCTACCGTTCGGCAG 59.969 60.000 11.32 8.13 0.00 4.85
883 2783 1.389609 GGATCCTCTACCGTTCGGCA 61.390 60.000 11.32 0.00 0.00 5.69
884 2784 1.108132 AGGATCCTCTACCGTTCGGC 61.108 60.000 9.02 0.00 0.00 5.54
885 2785 0.953003 GAGGATCCTCTACCGTTCGG 59.047 60.000 31.11 9.81 39.80 4.30
895 2795 1.745264 CTGGCGGAAGAGGATCCTC 59.255 63.158 31.27 31.27 43.03 3.71
896 2796 2.439104 GCTGGCGGAAGAGGATCCT 61.439 63.158 16.13 16.13 37.34 3.24
897 2797 1.977293 AAGCTGGCGGAAGAGGATCC 61.977 60.000 2.48 2.48 33.66 3.36
898 2798 0.531753 GAAGCTGGCGGAAGAGGATC 60.532 60.000 0.00 0.00 0.00 3.36
899 2799 0.980231 AGAAGCTGGCGGAAGAGGAT 60.980 55.000 0.00 0.00 0.00 3.24
900 2800 1.194781 AAGAAGCTGGCGGAAGAGGA 61.195 55.000 0.00 0.00 0.00 3.71
901 2801 0.742635 GAAGAAGCTGGCGGAAGAGG 60.743 60.000 0.00 0.00 0.00 3.69
902 2802 0.248843 AGAAGAAGCTGGCGGAAGAG 59.751 55.000 0.00 0.00 0.00 2.85
903 2803 0.247736 GAGAAGAAGCTGGCGGAAGA 59.752 55.000 0.00 0.00 0.00 2.87
904 2804 1.080995 CGAGAAGAAGCTGGCGGAAG 61.081 60.000 0.00 0.00 0.00 3.46
905 2805 1.079819 CGAGAAGAAGCTGGCGGAA 60.080 57.895 0.00 0.00 0.00 4.30
906 2806 2.573869 CGAGAAGAAGCTGGCGGA 59.426 61.111 0.00 0.00 0.00 5.54
907 2807 2.510238 CCGAGAAGAAGCTGGCGG 60.510 66.667 0.00 0.00 0.00 6.13
908 2808 2.510238 CCCGAGAAGAAGCTGGCG 60.510 66.667 0.00 0.00 0.00 5.69
909 2809 2.821810 GCCCGAGAAGAAGCTGGC 60.822 66.667 0.00 0.00 0.00 4.85
910 2810 1.153469 GAGCCCGAGAAGAAGCTGG 60.153 63.158 0.00 0.00 35.23 4.85
911 2811 0.739112 GTGAGCCCGAGAAGAAGCTG 60.739 60.000 0.00 0.00 35.23 4.24
912 2812 1.594310 GTGAGCCCGAGAAGAAGCT 59.406 57.895 0.00 0.00 38.56 3.74
955 2866 0.040646 ACGGATCACTGGGTGGAGTA 59.959 55.000 0.00 0.00 33.87 2.59
959 2870 1.078426 GGAACGGATCACTGGGTGG 60.078 63.158 0.00 0.00 33.87 4.61
965 2876 0.322546 GGGCTTTGGAACGGATCACT 60.323 55.000 0.00 0.00 0.00 3.41
971 2882 0.249280 GTGTTTGGGCTTTGGAACGG 60.249 55.000 0.00 0.00 0.00 4.44
988 2899 1.401931 CGAGGCCATTCTTTGCAAGTG 60.402 52.381 5.01 0.00 0.00 3.16
1017 2928 0.533085 GGATCCGTAGCTTCTTGCCC 60.533 60.000 0.00 0.00 44.23 5.36
1522 3457 1.471119 TGTGGTACGATCACCTCCTC 58.529 55.000 4.04 0.00 39.50 3.71
1597 3533 0.666577 CGGTCGTGTTCTTCCTGGAC 60.667 60.000 0.00 0.00 0.00 4.02
1679 3618 3.289797 CAGTACTGCCTCTCCAGGA 57.710 57.895 10.54 0.00 43.65 3.86
1724 3665 3.195698 GGAAGTAGGCGCGCTTGG 61.196 66.667 32.29 0.00 0.00 3.61
1828 3772 1.668047 GCATACGTATACCACCGAGCC 60.668 57.143 7.96 0.00 0.00 4.70
1839 3783 3.304257 CGAAGGTACCGAAGCATACGTAT 60.304 47.826 6.18 1.14 0.00 3.06
1854 3798 1.063942 TCAGAGATGGAGGCGAAGGTA 60.064 52.381 0.00 0.00 0.00 3.08
1859 3803 1.959985 GATCTTCAGAGATGGAGGCGA 59.040 52.381 0.00 0.00 42.66 5.54
1902 3846 1.447945 GCTTCTGAGAACCTTCCAGC 58.552 55.000 0.00 0.00 0.00 4.85
1910 3854 1.270358 ACAGGAACGGCTTCTGAGAAC 60.270 52.381 2.29 0.00 0.00 3.01
1915 3859 1.672356 CCCACAGGAACGGCTTCTG 60.672 63.158 0.00 0.00 33.47 3.02
2386 4330 4.342092 TGCTTCTACCAGATCATCGATCAA 59.658 41.667 0.00 0.00 41.12 2.57
2437 4383 2.922950 TTCAAGGTAGCGACGGCGT 61.923 57.895 14.65 14.65 46.35 5.68
2438 4384 2.126228 TTCAAGGTAGCGACGGCG 60.126 61.111 6.12 6.12 46.35 6.46
2440 4386 1.278238 GATGTTCAAGGTAGCGACGG 58.722 55.000 0.00 0.00 0.00 4.79
2443 4389 2.010145 GCTGATGTTCAAGGTAGCGA 57.990 50.000 0.00 0.00 0.00 4.93
2444 4390 0.647410 CGCTGATGTTCAAGGTAGCG 59.353 55.000 0.00 0.00 46.09 4.26
2445 4391 1.661112 GTCGCTGATGTTCAAGGTAGC 59.339 52.381 0.00 0.00 0.00 3.58
2446 4392 2.926200 CAGTCGCTGATGTTCAAGGTAG 59.074 50.000 1.18 0.00 32.44 3.18
2448 4394 1.344438 TCAGTCGCTGATGTTCAAGGT 59.656 47.619 5.59 0.00 35.39 3.50
2451 4397 3.248363 CAGTTTCAGTCGCTGATGTTCAA 59.752 43.478 9.78 0.19 40.39 2.69
2487 4433 2.890474 GAGTACGCCCATGCCACG 60.890 66.667 0.00 0.00 0.00 4.94
2488 4434 2.890474 CGAGTACGCCCATGCCAC 60.890 66.667 0.00 0.00 0.00 5.01
2489 4435 4.155733 CCGAGTACGCCCATGCCA 62.156 66.667 0.00 0.00 38.29 4.92
2505 4451 0.895530 TCCATCACCAGAGAACGACC 59.104 55.000 0.00 0.00 0.00 4.79
2506 4452 2.743636 TTCCATCACCAGAGAACGAC 57.256 50.000 0.00 0.00 0.00 4.34
2507 4453 2.831526 TCATTCCATCACCAGAGAACGA 59.168 45.455 0.00 0.00 0.00 3.85
2512 4458 4.267536 ACAATGTCATTCCATCACCAGAG 58.732 43.478 0.00 0.00 0.00 3.35
2521 4467 2.349590 CTCTGCGACAATGTCATTCCA 58.650 47.619 14.24 3.90 32.09 3.53
2522 4468 1.063174 GCTCTGCGACAATGTCATTCC 59.937 52.381 14.24 0.00 32.09 3.01
2523 4469 1.733912 TGCTCTGCGACAATGTCATTC 59.266 47.619 14.24 2.57 32.09 2.67
2525 4471 1.338484 ACTGCTCTGCGACAATGTCAT 60.338 47.619 14.24 0.00 32.09 3.06
2526 4472 0.033920 ACTGCTCTGCGACAATGTCA 59.966 50.000 14.24 0.00 32.09 3.58
2527 4473 1.923204 CTACTGCTCTGCGACAATGTC 59.077 52.381 2.75 2.75 0.00 3.06
2528 4474 1.546029 TCTACTGCTCTGCGACAATGT 59.454 47.619 0.00 0.00 0.00 2.71
2529 4475 2.191802 CTCTACTGCTCTGCGACAATG 58.808 52.381 0.00 0.00 0.00 2.82
2530 4476 1.470632 GCTCTACTGCTCTGCGACAAT 60.471 52.381 0.00 0.00 0.00 2.71
2531 4477 0.109086 GCTCTACTGCTCTGCGACAA 60.109 55.000 0.00 0.00 0.00 3.18
2532 4478 0.962855 AGCTCTACTGCTCTGCGACA 60.963 55.000 0.00 0.00 39.34 4.35
2533 4479 0.525242 CAGCTCTACTGCTCTGCGAC 60.525 60.000 0.00 0.00 41.98 5.19
2534 4480 1.805910 CAGCTCTACTGCTCTGCGA 59.194 57.895 0.00 0.00 41.98 5.10
2535 4481 4.398631 CAGCTCTACTGCTCTGCG 57.601 61.111 0.00 0.00 41.98 5.18
2599 4547 1.521010 CGTCCAGATGCAGAGGCTG 60.521 63.158 0.00 0.00 41.91 4.85
2658 4606 6.487668 TCATGCTTATTGATGTATCACCTTGG 59.512 38.462 0.00 0.00 36.36 3.61
2680 4628 2.821969 GTTGCCAAGATGGTGACTTCAT 59.178 45.455 0.00 0.00 40.46 2.57
2706 4654 6.842437 TCATCATAGGAATAGGAGTAGCAC 57.158 41.667 0.00 0.00 0.00 4.40
2719 4667 0.106708 GGCACGCCTTCATCATAGGA 59.893 55.000 0.00 0.00 34.56 2.94
2773 4721 4.833390 ACACCTGGCTTTAGATGTTAGAC 58.167 43.478 0.00 0.00 0.00 2.59
2774 4722 4.081087 GGACACCTGGCTTTAGATGTTAGA 60.081 45.833 0.00 0.00 0.00 2.10
2866 4819 1.306654 ATGGAGGTGACGGCCCTTA 60.307 57.895 0.00 0.00 30.60 2.69
2986 4939 1.035923 GATGCGAGGAGATGGACTCA 58.964 55.000 0.00 0.00 46.54 3.41
3057 5010 1.945776 GAGCGGTGCTTCGTCTTTCG 61.946 60.000 0.00 0.00 39.88 3.46
3059 5012 1.668151 GGAGCGGTGCTTCGTCTTT 60.668 57.895 0.00 0.00 39.88 2.52
3064 5017 4.680237 TGGTGGAGCGGTGCTTCG 62.680 66.667 7.84 0.00 39.88 3.79
3332 5285 2.782222 GGCCCGTGCACGAGAGATA 61.782 63.158 39.10 0.00 43.02 1.98


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

AutoCloner maintained by Alex Coulton.