Multiple sequence alignment - TraesCS3B01G520200

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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 TraesCS3B01G520200 chr3B 100.000 3300 0 0 1 3300 763270818 763267519 0.000000e+00 6095
1 TraesCS3B01G520200 chr3B 97.412 657 17 0 1 657 774791740 774791084 0.000000e+00 1120
2 TraesCS3B01G520200 chr3B 78.307 1323 203 48 1009 2294 763237083 763235808 0.000000e+00 776
3 TraesCS3B01G520200 chr3B 78.643 398 76 8 1009 1403 542134995 542134604 4.230000e-64 255
4 TraesCS3B01G520200 chr3D 93.743 1694 91 4 668 2347 573844337 573846029 0.000000e+00 2527
5 TraesCS3B01G520200 chr3D 79.332 1258 193 37 1072 2294 573907031 573908256 0.000000e+00 821
6 TraesCS3B01G520200 chr3D 86.061 330 44 2 1995 2324 573878666 573878993 1.460000e-93 353
7 TraesCS3B01G520200 chr3D 78.304 401 75 10 1009 1403 415647541 415647147 7.070000e-62 248
8 TraesCS3B01G520200 chr3A 90.987 1165 64 16 1337 2489 708905755 708906890 0.000000e+00 1531
9 TraesCS3B01G520200 chr3A 90.541 962 60 17 1638 2583 708920295 708921241 0.000000e+00 1243
10 TraesCS3B01G520200 chr3A 92.405 395 29 1 948 1342 708905177 708905570 2.220000e-156 562
11 TraesCS3B01G520200 chr3A 79.969 639 93 17 1438 2053 709061724 709062350 3.910000e-119 438
12 TraesCS3B01G520200 chr5B 97.565 657 16 0 1 657 627153846 627153190 0.000000e+00 1125
13 TraesCS3B01G520200 chr5B 97.260 657 18 0 1 657 623555615 623554959 0.000000e+00 1114
14 TraesCS3B01G520200 chr2B 93.475 659 42 1 1 658 541912733 541912075 0.000000e+00 977
15 TraesCS3B01G520200 chr7B 92.157 663 49 3 1 662 639891997 639892657 0.000000e+00 933
16 TraesCS3B01G520200 chr4D 84.375 672 82 18 1 659 122706116 122706777 3.590000e-179 638
17 TraesCS3B01G520200 chr6B 83.508 667 96 10 1 658 617131447 617130786 7.830000e-171 610
18 TraesCS3B01G520200 chr4A 83.133 664 100 10 1 658 196566353 196565696 2.190000e-166 595
19 TraesCS3B01G520200 chr4A 75.976 666 90 33 2658 3294 632209849 632210473 2.510000e-71 279
20 TraesCS3B01G520200 chr7D 81.627 381 62 8 7 383 14731606 14731230 3.200000e-80 309


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 TraesCS3B01G520200 chr3B 763267519 763270818 3299 True 6095.0 6095 100.000 1 3300 1 chr3B.!!$R3 3299
1 TraesCS3B01G520200 chr3B 774791084 774791740 656 True 1120.0 1120 97.412 1 657 1 chr3B.!!$R4 656
2 TraesCS3B01G520200 chr3B 763235808 763237083 1275 True 776.0 776 78.307 1009 2294 1 chr3B.!!$R2 1285
3 TraesCS3B01G520200 chr3D 573844337 573846029 1692 False 2527.0 2527 93.743 668 2347 1 chr3D.!!$F1 1679
4 TraesCS3B01G520200 chr3D 573907031 573908256 1225 False 821.0 821 79.332 1072 2294 1 chr3D.!!$F3 1222
5 TraesCS3B01G520200 chr3A 708920295 708921241 946 False 1243.0 1243 90.541 1638 2583 1 chr3A.!!$F1 945
6 TraesCS3B01G520200 chr3A 708905177 708906890 1713 False 1046.5 1531 91.696 948 2489 2 chr3A.!!$F3 1541
7 TraesCS3B01G520200 chr3A 709061724 709062350 626 False 438.0 438 79.969 1438 2053 1 chr3A.!!$F2 615
8 TraesCS3B01G520200 chr5B 627153190 627153846 656 True 1125.0 1125 97.565 1 657 1 chr5B.!!$R2 656
9 TraesCS3B01G520200 chr5B 623554959 623555615 656 True 1114.0 1114 97.260 1 657 1 chr5B.!!$R1 656
10 TraesCS3B01G520200 chr2B 541912075 541912733 658 True 977.0 977 93.475 1 658 1 chr2B.!!$R1 657
11 TraesCS3B01G520200 chr7B 639891997 639892657 660 False 933.0 933 92.157 1 662 1 chr7B.!!$F1 661
12 TraesCS3B01G520200 chr4D 122706116 122706777 661 False 638.0 638 84.375 1 659 1 chr4D.!!$F1 658
13 TraesCS3B01G520200 chr6B 617130786 617131447 661 True 610.0 610 83.508 1 658 1 chr6B.!!$R1 657
14 TraesCS3B01G520200 chr4A 196565696 196566353 657 True 595.0 595 83.133 1 658 1 chr4A.!!$R1 657
15 TraesCS3B01G520200 chr4A 632209849 632210473 624 False 279.0 279 75.976 2658 3294 1 chr4A.!!$F1 636

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
707 715 0.462759 GGTGCTATGTGCTCTCCCAC 60.463 60.0 0.0 0.0 43.37 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2621 2897 0.034059 AGCCTCACTGTTCTTCGTGG 59.966 55.0 0.0 0.0 0.0 4.94 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
707 715 0.462759 GGTGCTATGTGCTCTCCCAC 60.463 60.000 0.00 0.00 43.37 4.61
742 750 2.041701 GGAAACATGCCATAAGCCCAT 58.958 47.619 0.00 0.00 42.71 4.00
755 763 1.823899 GCCCATAAGGTTGGAGCGG 60.824 63.158 0.00 0.00 39.25 5.52
756 764 1.152963 CCCATAAGGTTGGAGCGGG 60.153 63.158 0.00 0.00 39.25 6.13
789 797 6.978659 AGTTCATCGTCATTATGTAACGTGAT 59.021 34.615 6.38 0.00 37.64 3.06
911 919 3.075005 GCGCCACCTCTCCCTACA 61.075 66.667 0.00 0.00 0.00 2.74
939 947 2.523168 CCCAAAAACCCCACGCCT 60.523 61.111 0.00 0.00 0.00 5.52
955 972 4.742201 CTCGACCCGCACCACCAG 62.742 72.222 0.00 0.00 0.00 4.00
1107 1124 1.223417 GCGCCAGCAGCAAAAACATT 61.223 50.000 0.00 0.00 44.04 2.71
1152 1169 2.045926 GCGGTGATGCTCCTTGGT 60.046 61.111 0.00 0.00 0.00 3.67
1153 1170 1.220749 GCGGTGATGCTCCTTGGTA 59.779 57.895 0.00 0.00 0.00 3.25
1158 1175 1.264749 TGATGCTCCTTGGTACGGCT 61.265 55.000 0.00 0.00 0.00 5.52
1354 1561 4.124351 TCAAGGCCGACTACGCCG 62.124 66.667 0.00 0.00 39.38 6.46
1711 1949 1.733041 CGTGCCGTTCATGTCGAGT 60.733 57.895 12.77 0.00 0.00 4.18
1762 2000 2.224305 CGAGTGGAAGGTCCTGAAACTT 60.224 50.000 0.00 0.00 37.46 2.66
1764 2002 2.777692 AGTGGAAGGTCCTGAAACTTCA 59.222 45.455 5.30 0.00 41.73 3.02
1765 2003 3.395941 AGTGGAAGGTCCTGAAACTTCAT 59.604 43.478 5.30 0.00 41.73 2.57
1772 2014 1.730064 TCCTGAAACTTCATTACGCGC 59.270 47.619 5.73 0.00 36.46 6.86
2056 2310 0.753479 TCTCGGAGATGCTGGAGGAC 60.753 60.000 2.97 0.00 33.89 3.85
2238 2508 3.222603 ACCACCCTTTCATGTTCTTGAC 58.777 45.455 0.00 0.00 0.00 3.18
2275 2545 4.955774 GTCGTGGTGTTCGCCGGT 62.956 66.667 1.90 0.00 0.00 5.28
2277 2547 4.657824 CGTGGTGTTCGCCGGTCT 62.658 66.667 1.90 0.00 0.00 3.85
2282 2552 0.735287 GGTGTTCGCCGGTCTAGTTC 60.735 60.000 1.90 0.00 0.00 3.01
2330 2605 1.065273 CTCGTATTAGCCCGCGTGT 59.935 57.895 4.92 0.00 0.00 4.49
2360 2635 2.372040 TAACCGCGGTGACTTGCACT 62.372 55.000 34.95 15.59 46.86 4.40
2361 2636 2.048597 CCGCGGTGACTTGCACTA 60.049 61.111 19.50 0.00 46.86 2.74
2362 2637 1.447838 CCGCGGTGACTTGCACTAT 60.448 57.895 19.50 0.00 46.86 2.12
2388 2663 2.546899 TGTACTTATGGTGCCCTGACT 58.453 47.619 0.00 0.00 0.00 3.41
2403 2678 5.361857 TGCCCTGACTATGGTAACTAAGTAC 59.638 44.000 0.00 0.00 33.27 2.73
2472 2748 5.290885 GTGAAATTTGTTTTGAGCGGAACTT 59.709 36.000 0.00 0.00 0.00 2.66
2477 2753 1.947456 GTTTTGAGCGGAACTTGTCCT 59.053 47.619 0.00 0.00 45.36 3.85
2500 2776 8.821894 TCCTTGTTGAAAATAATTTGGAAAACG 58.178 29.630 0.00 0.00 0.00 3.60
2532 2808 6.944234 AAGTCGGAAGATTTCTTGTCTTTT 57.056 33.333 0.00 0.00 45.19 2.27
2533 2809 9.720769 ATAAGTCGGAAGATTTCTTGTCTTTTA 57.279 29.630 0.00 0.00 45.19 1.52
2534 2810 8.622948 AAGTCGGAAGATTTCTTGTCTTTTAT 57.377 30.769 0.00 0.00 45.19 1.40
2535 2811 8.257830 AGTCGGAAGATTTCTTGTCTTTTATC 57.742 34.615 0.00 0.00 45.19 1.75
2537 2813 8.504005 GTCGGAAGATTTCTTGTCTTTTATCAA 58.496 33.333 0.00 0.00 45.19 2.57
2538 2814 9.062524 TCGGAAGATTTCTTGTCTTTTATCAAA 57.937 29.630 0.00 0.00 36.13 2.69
2539 2815 9.118236 CGGAAGATTTCTTGTCTTTTATCAAAC 57.882 33.333 0.00 0.00 36.13 2.93
2540 2816 9.411801 GGAAGATTTCTTGTCTTTTATCAAACC 57.588 33.333 0.00 0.00 36.13 3.27
2542 2818 9.971922 AAGATTTCTTGTCTTTTATCAAACCTG 57.028 29.630 0.00 0.00 32.17 4.00
2546 2822 2.095969 TGTCTTTTATCAAACCTGCGCG 60.096 45.455 0.00 0.00 0.00 6.86
2584 2860 2.356913 CACGATCGTGTGGCACCA 60.357 61.111 34.48 0.00 40.91 4.17
2585 2861 2.357034 ACGATCGTGTGGCACCAC 60.357 61.111 22.06 13.03 46.33 4.16
2586 2862 3.118454 CGATCGTGTGGCACCACC 61.118 66.667 16.26 7.65 45.63 4.61
2587 2863 3.118454 GATCGTGTGGCACCACCG 61.118 66.667 16.26 17.98 45.63 4.94
2599 2875 3.124270 CCACCGCGCTGCATGTTA 61.124 61.111 5.56 0.00 0.00 2.41
2600 2876 2.098298 CACCGCGCTGCATGTTAC 59.902 61.111 5.56 0.00 0.00 2.50
2601 2877 2.358125 ACCGCGCTGCATGTTACA 60.358 55.556 5.56 0.00 0.00 2.41
2602 2878 1.963855 ACCGCGCTGCATGTTACAA 60.964 52.632 5.56 0.00 0.00 2.41
2603 2879 1.305219 ACCGCGCTGCATGTTACAAT 61.305 50.000 5.56 0.00 0.00 2.71
2604 2880 0.589729 CCGCGCTGCATGTTACAATC 60.590 55.000 5.56 0.00 0.00 2.67
2605 2881 0.096802 CGCGCTGCATGTTACAATCA 59.903 50.000 5.56 0.00 0.00 2.57
2606 2882 1.818850 GCGCTGCATGTTACAATCAG 58.181 50.000 0.00 11.17 0.00 2.90
2607 2883 1.398041 GCGCTGCATGTTACAATCAGA 59.602 47.619 17.15 0.00 0.00 3.27
2608 2884 2.538333 GCGCTGCATGTTACAATCAGAG 60.538 50.000 17.15 15.15 0.00 3.35
2609 2885 2.538333 CGCTGCATGTTACAATCAGAGC 60.538 50.000 17.15 7.83 0.00 4.09
2610 2886 2.421073 GCTGCATGTTACAATCAGAGCA 59.579 45.455 17.15 8.04 0.00 4.26
2611 2887 3.066342 GCTGCATGTTACAATCAGAGCAT 59.934 43.478 17.15 0.00 32.47 3.79
2612 2888 4.598062 CTGCATGTTACAATCAGAGCATG 58.402 43.478 10.32 0.00 37.39 4.06
2613 2889 4.011698 TGCATGTTACAATCAGAGCATGT 58.988 39.130 0.00 0.00 36.88 3.21
2614 2890 4.460034 TGCATGTTACAATCAGAGCATGTT 59.540 37.500 0.00 0.00 36.88 2.71
2615 2891 5.647225 TGCATGTTACAATCAGAGCATGTTA 59.353 36.000 0.00 0.00 36.88 2.41
2616 2892 5.967674 GCATGTTACAATCAGAGCATGTTAC 59.032 40.000 0.00 0.00 36.88 2.50
2617 2893 6.403527 GCATGTTACAATCAGAGCATGTTACA 60.404 38.462 7.61 7.61 39.82 2.41
2618 2894 7.529158 CATGTTACAATCAGAGCATGTTACAA 58.471 34.615 8.70 0.00 39.22 2.41
2619 2895 7.686438 TGTTACAATCAGAGCATGTTACAAT 57.314 32.000 0.00 0.00 34.74 2.71
2620 2896 7.751732 TGTTACAATCAGAGCATGTTACAATC 58.248 34.615 0.00 0.00 34.74 2.67
2621 2897 5.824904 ACAATCAGAGCATGTTACAATCC 57.175 39.130 0.00 0.00 0.00 3.01
2622 2898 4.641989 ACAATCAGAGCATGTTACAATCCC 59.358 41.667 0.00 0.00 0.00 3.85
2623 2899 3.998913 TCAGAGCATGTTACAATCCCA 57.001 42.857 0.00 0.00 0.00 4.37
2624 2900 3.609853 TCAGAGCATGTTACAATCCCAC 58.390 45.455 0.00 0.00 0.00 4.61
2625 2901 2.352651 CAGAGCATGTTACAATCCCACG 59.647 50.000 0.00 0.00 0.00 4.94
2626 2902 2.236146 AGAGCATGTTACAATCCCACGA 59.764 45.455 0.00 0.00 0.00 4.35
2627 2903 3.006940 GAGCATGTTACAATCCCACGAA 58.993 45.455 0.00 0.00 0.00 3.85
2628 2904 3.009723 AGCATGTTACAATCCCACGAAG 58.990 45.455 0.00 0.00 0.00 3.79
2629 2905 3.006940 GCATGTTACAATCCCACGAAGA 58.993 45.455 0.00 0.00 0.00 2.87
2630 2906 3.438781 GCATGTTACAATCCCACGAAGAA 59.561 43.478 0.00 0.00 0.00 2.52
2631 2907 4.671766 GCATGTTACAATCCCACGAAGAAC 60.672 45.833 0.00 0.00 0.00 3.01
2632 2908 4.074627 TGTTACAATCCCACGAAGAACA 57.925 40.909 0.00 0.00 0.00 3.18
2633 2909 4.062293 TGTTACAATCCCACGAAGAACAG 58.938 43.478 0.00 0.00 0.00 3.16
2634 2910 2.930826 ACAATCCCACGAAGAACAGT 57.069 45.000 0.00 0.00 0.00 3.55
2635 2911 2.494059 ACAATCCCACGAAGAACAGTG 58.506 47.619 0.00 0.00 38.05 3.66
2636 2912 2.104111 ACAATCCCACGAAGAACAGTGA 59.896 45.455 0.00 0.00 40.56 3.41
2637 2913 2.738846 CAATCCCACGAAGAACAGTGAG 59.261 50.000 0.00 0.00 40.56 3.51
2638 2914 0.679505 TCCCACGAAGAACAGTGAGG 59.320 55.000 0.00 0.00 40.56 3.86
2639 2915 0.951040 CCCACGAAGAACAGTGAGGC 60.951 60.000 0.00 0.00 40.56 4.70
2640 2916 0.034059 CCACGAAGAACAGTGAGGCT 59.966 55.000 0.00 0.00 40.56 4.58
2641 2917 1.541233 CCACGAAGAACAGTGAGGCTT 60.541 52.381 0.00 0.00 40.56 4.35
2642 2918 1.795286 CACGAAGAACAGTGAGGCTTC 59.205 52.381 0.00 5.80 40.56 3.86
2643 2919 1.412710 ACGAAGAACAGTGAGGCTTCA 59.587 47.619 17.69 0.00 37.25 3.02
2650 2926 4.703703 GTGAGGCTTCACCAGTCC 57.296 61.111 17.71 0.00 46.47 3.85
2651 2927 2.062070 GTGAGGCTTCACCAGTCCT 58.938 57.895 17.71 0.00 46.47 3.85
2652 2928 1.267121 GTGAGGCTTCACCAGTCCTA 58.733 55.000 17.71 0.00 46.47 2.94
2653 2929 1.066787 GTGAGGCTTCACCAGTCCTAC 60.067 57.143 17.71 0.00 46.47 3.18
2654 2930 1.267121 GAGGCTTCACCAGTCCTACA 58.733 55.000 0.00 0.00 43.14 2.74
2655 2931 1.834263 GAGGCTTCACCAGTCCTACAT 59.166 52.381 0.00 0.00 43.14 2.29
2656 2932 1.556911 AGGCTTCACCAGTCCTACATG 59.443 52.381 0.00 0.00 43.14 3.21
2663 2939 5.130705 TCACCAGTCCTACATGAGATAGT 57.869 43.478 0.00 0.00 0.00 2.12
2665 2941 4.889995 CACCAGTCCTACATGAGATAGTGA 59.110 45.833 0.00 0.00 0.00 3.41
2667 2943 4.889995 CCAGTCCTACATGAGATAGTGACA 59.110 45.833 0.00 0.00 0.00 3.58
2673 2949 5.243507 CCTACATGAGATAGTGACATGCTCT 59.756 44.000 0.00 0.00 43.21 4.09
2681 2958 1.478105 AGTGACATGCTCTGATGCGTA 59.522 47.619 0.00 0.00 35.36 4.42
2695 2972 1.292223 GCGTACTGCAAGGTGGAGA 59.708 57.895 3.61 0.00 45.45 3.71
2708 2985 3.785859 GGAGATGCAGGGACGCCA 61.786 66.667 0.00 0.00 0.00 5.69
2709 2986 2.268920 GAGATGCAGGGACGCCAA 59.731 61.111 0.00 0.00 0.00 4.52
2715 2992 4.988598 CAGGGACGCCAACACGCT 62.989 66.667 0.00 0.00 36.19 5.07
2772 3058 2.798689 CAGCCGTGCTACGAGCTA 59.201 61.111 17.09 0.00 46.05 3.32
2785 3071 1.806568 GAGCTACGAGCAGCACTCT 59.193 57.895 9.09 0.00 45.56 3.24
2786 3072 1.018148 GAGCTACGAGCAGCACTCTA 58.982 55.000 9.09 0.00 45.56 2.43
2787 3073 1.606668 GAGCTACGAGCAGCACTCTAT 59.393 52.381 9.09 0.00 45.56 1.98
2788 3074 1.606668 AGCTACGAGCAGCACTCTATC 59.393 52.381 9.09 0.00 45.56 2.08
2795 3081 1.007964 CAGCACTCTATCGAGCCGG 60.008 63.158 0.00 0.00 41.09 6.13
2796 3082 2.355244 GCACTCTATCGAGCCGGC 60.355 66.667 21.89 21.89 41.09 6.13
2807 3093 2.124570 AGCCGGCGATTCTGCAAT 60.125 55.556 23.20 0.00 36.28 3.56
2815 3101 1.331161 GCGATTCTGCAATGACGTACG 60.331 52.381 15.01 15.01 34.15 3.67
2827 3113 1.198408 TGACGTACGAAGAAGCACGAT 59.802 47.619 24.41 0.00 37.80 3.73
2833 3119 1.351430 CGAAGAAGCACGATGGCGAA 61.351 55.000 0.00 0.00 41.64 4.70
2837 3123 0.863119 GAAGCACGATGGCGAAATGC 60.863 55.000 0.00 0.00 45.38 3.56
2848 3134 0.039256 GCGAAATGCTGCAAGGTCAA 60.039 50.000 6.36 0.00 41.73 3.18
2849 3135 1.403249 GCGAAATGCTGCAAGGTCAAT 60.403 47.619 6.36 0.00 41.73 2.57
2852 3138 1.636148 AATGCTGCAAGGTCAATGGT 58.364 45.000 6.36 0.00 0.00 3.55
2854 3140 1.180456 TGCTGCAAGGTCAATGGTGG 61.180 55.000 0.00 0.00 0.00 4.61
2855 3141 1.880819 GCTGCAAGGTCAATGGTGGG 61.881 60.000 0.00 0.00 0.00 4.61
2856 3142 0.540365 CTGCAAGGTCAATGGTGGGT 60.540 55.000 0.00 0.00 0.00 4.51
2862 3148 1.003112 GTCAATGGTGGGTACGGCA 60.003 57.895 0.00 0.00 0.00 5.69
2863 3149 1.003112 TCAATGGTGGGTACGGCAC 60.003 57.895 0.00 0.00 0.00 5.01
2898 3184 4.722193 CAACGAGGGGAGTTGCAT 57.278 55.556 0.00 0.00 41.77 3.96
2903 3189 1.672854 CGAGGGGAGTTGCATCGGTA 61.673 60.000 0.00 0.00 0.00 4.02
2910 3196 2.171725 GTTGCATCGGTAGTCGGCC 61.172 63.158 0.00 0.00 39.77 6.13
2912 3198 1.966901 TTGCATCGGTAGTCGGCCAT 61.967 55.000 2.24 0.00 39.77 4.40
2947 3233 3.044059 GCCAGCGAGGTGATGTTGC 62.044 63.158 3.61 0.00 40.61 4.17
2948 3234 1.672030 CCAGCGAGGTGATGTTGCA 60.672 57.895 3.61 0.00 29.93 4.08
2967 3253 3.945434 GCCGATGCTGTGATGGCG 61.945 66.667 0.00 0.00 35.77 5.69
2968 3254 3.945434 CCGATGCTGTGATGGCGC 61.945 66.667 0.00 0.00 0.00 6.53
2969 3255 3.945434 CGATGCTGTGATGGCGCC 61.945 66.667 22.73 22.73 0.00 6.53
2970 3256 3.945434 GATGCTGTGATGGCGCCG 61.945 66.667 23.90 7.24 0.00 6.46
2992 3292 2.202987 GCTCCAGTGGCATCTCGG 60.203 66.667 3.51 0.00 0.00 4.63
2995 3295 1.381191 TCCAGTGGCATCTCGGCTA 60.381 57.895 3.51 0.00 41.89 3.93
3011 3311 1.500844 CTACGACGACGGCTCAACT 59.499 57.895 12.58 0.00 44.46 3.16
3012 3312 0.109873 CTACGACGACGGCTCAACTT 60.110 55.000 12.58 0.00 44.46 2.66
3014 3314 2.426183 CGACGACGGCTCAACTTCG 61.426 63.158 0.00 0.00 37.50 3.79
3020 3320 2.357034 GGCTCAACTTCGGCGACA 60.357 61.111 10.16 0.00 0.00 4.35
3028 3328 1.803334 ACTTCGGCGACATTTTGCTA 58.197 45.000 10.16 0.00 31.91 3.49
3031 3331 1.732941 TCGGCGACATTTTGCTACAT 58.267 45.000 4.99 0.00 31.91 2.29
3037 3341 2.419673 CGACATTTTGCTACATGGCTCA 59.580 45.455 0.00 0.00 0.00 4.26
3042 3346 0.393402 TTGCTACATGGCTCAGGCTG 60.393 55.000 8.58 8.58 38.73 4.85
3112 3416 3.075005 GGGAGTCTGCCGGTGCTA 61.075 66.667 1.90 0.00 38.71 3.49
3116 3420 2.005960 GAGTCTGCCGGTGCTACGAT 62.006 60.000 1.90 0.00 38.71 3.73
3141 3445 4.007644 CCCTGCTGCGAGTCCACA 62.008 66.667 0.00 0.00 0.00 4.17
3142 3446 2.267006 CCTGCTGCGAGTCCACAT 59.733 61.111 0.00 0.00 0.00 3.21
3143 3447 1.812922 CCTGCTGCGAGTCCACATC 60.813 63.158 0.00 0.00 0.00 3.06
3144 3448 2.125952 TGCTGCGAGTCCACATCG 60.126 61.111 0.00 0.00 43.00 3.84
3145 3449 2.125912 GCTGCGAGTCCACATCGT 60.126 61.111 0.00 0.00 42.13 3.73
3146 3450 1.138883 GCTGCGAGTCCACATCGTA 59.861 57.895 0.00 0.00 42.13 3.43
3147 3451 1.140407 GCTGCGAGTCCACATCGTAC 61.140 60.000 0.00 0.00 42.13 3.67
3148 3452 0.452184 CTGCGAGTCCACATCGTACT 59.548 55.000 0.00 0.00 42.13 2.73
3149 3453 0.170339 TGCGAGTCCACATCGTACTG 59.830 55.000 0.00 0.00 42.13 2.74
3150 3454 0.525668 GCGAGTCCACATCGTACTGG 60.526 60.000 0.00 0.00 42.13 4.00
3151 3455 0.809385 CGAGTCCACATCGTACTGGT 59.191 55.000 0.00 0.00 35.48 4.00
3152 3456 1.202154 CGAGTCCACATCGTACTGGTC 60.202 57.143 0.00 0.00 35.48 4.02
3153 3457 0.809385 AGTCCACATCGTACTGGTCG 59.191 55.000 0.00 0.00 0.00 4.79
3154 3458 0.524862 GTCCACATCGTACTGGTCGT 59.475 55.000 0.00 0.00 0.00 4.34
3155 3459 0.524414 TCCACATCGTACTGGTCGTG 59.476 55.000 0.00 0.00 0.00 4.35
3156 3460 0.457853 CCACATCGTACTGGTCGTGG 60.458 60.000 0.00 0.00 38.11 4.94
3157 3461 0.242825 CACATCGTACTGGTCGTGGT 59.757 55.000 0.00 0.00 0.00 4.16
3158 3462 0.242825 ACATCGTACTGGTCGTGGTG 59.757 55.000 0.00 0.00 0.00 4.17
3159 3463 0.457853 CATCGTACTGGTCGTGGTGG 60.458 60.000 0.00 0.00 0.00 4.61
3160 3464 1.601419 ATCGTACTGGTCGTGGTGGG 61.601 60.000 0.00 0.00 0.00 4.61
3161 3465 2.047560 GTACTGGTCGTGGTGGGC 60.048 66.667 0.00 0.00 0.00 5.36
3162 3466 3.315949 TACTGGTCGTGGTGGGCC 61.316 66.667 0.00 0.00 0.00 5.80
3194 3498 2.668457 GAGTTGTTCTGTGCTATGGTCG 59.332 50.000 0.00 0.00 0.00 4.79
3202 3506 2.890474 GCTATGGTCGTGGTGGCG 60.890 66.667 0.00 0.00 0.00 5.69
3206 3510 0.680601 TATGGTCGTGGTGGCGTAGA 60.681 55.000 0.00 0.00 0.00 2.59
3215 3519 0.458716 GGTGGCGTAGAGAAGACAGC 60.459 60.000 0.00 0.00 0.00 4.40
3229 3533 1.112113 GACAGCGGAAGGAGACCATA 58.888 55.000 0.00 0.00 0.00 2.74
3232 3536 1.115467 AGCGGAAGGAGACCATACTG 58.885 55.000 0.00 0.00 0.00 2.74
3234 3538 0.249073 CGGAAGGAGACCATACTGCG 60.249 60.000 0.00 0.00 33.57 5.18
3247 3551 3.242091 CCATACTGCGTTGACTTTCATCG 60.242 47.826 2.90 2.90 41.15 3.84
3249 3553 2.688507 ACTGCGTTGACTTTCATCGAT 58.311 42.857 10.12 0.00 40.81 3.59
3252 3556 1.732259 GCGTTGACTTTCATCGATGGT 59.268 47.619 24.61 14.87 40.81 3.55
3253 3557 2.927477 GCGTTGACTTTCATCGATGGTA 59.073 45.455 24.61 10.93 40.81 3.25
3258 3563 6.534934 GTTGACTTTCATCGATGGTAAAGAC 58.465 40.000 30.97 26.79 33.98 3.01
3264 3569 0.108520 TCGATGGTAAAGACGCCCAC 60.109 55.000 0.00 0.00 0.00 4.61
3295 3600 1.442769 CAGGAGGTGGATGTTGTTCG 58.557 55.000 0.00 0.00 0.00 3.95
3296 3601 1.001974 CAGGAGGTGGATGTTGTTCGA 59.998 52.381 0.00 0.00 0.00 3.71
3297 3602 1.909302 AGGAGGTGGATGTTGTTCGAT 59.091 47.619 0.00 0.00 0.00 3.59
3298 3603 2.305927 AGGAGGTGGATGTTGTTCGATT 59.694 45.455 0.00 0.00 0.00 3.34
3299 3604 3.081804 GGAGGTGGATGTTGTTCGATTT 58.918 45.455 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 1.435168 AGGGGCCCAATTTGTTCCTTA 59.565 47.619 27.72 0.00 0.00 2.69
657 665 8.440833 CAGTTATTCCAAGTAAACGTTTCTAGG 58.559 37.037 18.42 14.89 0.00 3.02
659 667 8.149647 TCCAGTTATTCCAAGTAAACGTTTCTA 58.850 33.333 18.42 0.00 0.00 2.10
660 668 6.993902 TCCAGTTATTCCAAGTAAACGTTTCT 59.006 34.615 18.42 11.57 0.00 2.52
661 669 7.041576 AGTCCAGTTATTCCAAGTAAACGTTTC 60.042 37.037 18.42 9.41 0.00 2.78
662 670 6.769341 AGTCCAGTTATTCCAAGTAAACGTTT 59.231 34.615 18.90 18.90 0.00 3.60
663 671 6.204108 CAGTCCAGTTATTCCAAGTAAACGTT 59.796 38.462 0.00 0.00 0.00 3.99
664 672 5.699458 CAGTCCAGTTATTCCAAGTAAACGT 59.301 40.000 0.00 0.00 0.00 3.99
665 673 5.121768 CCAGTCCAGTTATTCCAAGTAAACG 59.878 44.000 0.00 0.00 0.00 3.60
666 674 6.002082 ACCAGTCCAGTTATTCCAAGTAAAC 58.998 40.000 0.00 0.00 0.00 2.01
707 715 1.730612 GTTTCCGGCGGTCTTCTAAAG 59.269 52.381 27.32 0.00 0.00 1.85
742 750 1.474332 AACGTCCCGCTCCAACCTTA 61.474 55.000 0.00 0.00 0.00 2.69
813 821 3.916761 AGTATGTTTCGTCCTGCGTTTA 58.083 40.909 0.00 0.00 42.13 2.01
899 907 1.985895 CTGGGTTTTGTAGGGAGAGGT 59.014 52.381 0.00 0.00 0.00 3.85
911 919 2.240160 GGGTTTTTGGGTTCTGGGTTTT 59.760 45.455 0.00 0.00 0.00 2.43
946 954 1.391157 TTTCTTGGTGCTGGTGGTGC 61.391 55.000 0.00 0.00 0.00 5.01
955 972 1.959226 TCTCGCGGTTTCTTGGTGC 60.959 57.895 6.13 0.00 0.00 5.01
1086 1103 1.285641 GTTTTTGCTGCTGGCGCTA 59.714 52.632 7.64 0.00 45.43 4.26
1087 1104 2.028043 GTTTTTGCTGCTGGCGCT 59.972 55.556 7.64 0.00 45.43 5.92
1141 1158 1.221840 CAGCCGTACCAAGGAGCAT 59.778 57.895 0.00 0.00 0.00 3.79
1224 1241 3.685214 GACATCCGACGCGAGCAGT 62.685 63.158 15.93 2.89 0.00 4.40
1359 1566 4.351938 CGGAACTGGTCGGCGACA 62.352 66.667 37.13 23.27 33.68 4.35
1392 1599 1.308998 CCTTTGTTGTGAAGGACGCT 58.691 50.000 0.00 0.00 45.25 5.07
1534 1752 3.017581 AAGCCCTTGATCCGCCCT 61.018 61.111 0.00 0.00 0.00 5.19
1537 1755 1.821332 CAGGAAGCCCTTGATCCGC 60.821 63.158 0.00 0.00 42.02 5.54
1596 1822 0.635731 CTTGAAGTAGAGCGCGTTCG 59.364 55.000 17.44 0.00 39.07 3.95
1657 1883 3.615110 CGTTGAGCAGGTAGAATCTGTGT 60.615 47.826 0.00 0.00 34.89 3.72
2238 2508 2.581354 CGGTGAGCTCCTCCTTGG 59.419 66.667 12.15 0.00 37.10 3.61
2275 2545 2.943690 CGACGAAGGATCCAGAACTAGA 59.056 50.000 15.82 0.00 0.00 2.43
2277 2547 2.422479 CACGACGAAGGATCCAGAACTA 59.578 50.000 15.82 0.00 0.00 2.24
2282 2552 2.464865 GAATCACGACGAAGGATCCAG 58.535 52.381 15.82 7.44 0.00 3.86
2324 2594 0.584396 TTACAAGGCAAAGACACGCG 59.416 50.000 3.53 3.53 0.00 6.01
2330 2605 1.231958 CCGCGGTTACAAGGCAAAGA 61.232 55.000 19.50 0.00 0.00 2.52
2381 2656 7.598759 ATGTACTTAGTTACCATAGTCAGGG 57.401 40.000 0.00 0.00 0.00 4.45
2438 2714 9.276397 CTCAAAACAAATTTCACCAAATCAAAC 57.724 29.630 0.00 0.00 30.37 2.93
2439 2715 7.967303 GCTCAAAACAAATTTCACCAAATCAAA 59.033 29.630 0.00 0.00 30.37 2.69
2455 2731 2.098443 GGACAAGTTCCGCTCAAAACAA 59.902 45.455 0.00 0.00 33.46 2.83
2457 2733 2.401017 GGACAAGTTCCGCTCAAAAC 57.599 50.000 0.00 0.00 33.46 2.43
2472 2748 9.672673 TTTTCCAAATTATTTTCAACAAGGACA 57.327 25.926 0.00 0.00 0.00 4.02
2493 2769 8.069574 TCTTCCGACTTATTTAAAACGTTTTCC 58.930 33.333 28.31 8.76 0.00 3.13
2532 2808 1.807981 CGGACGCGCAGGTTTGATA 60.808 57.895 5.73 0.00 0.00 2.15
2533 2809 3.118454 CGGACGCGCAGGTTTGAT 61.118 61.111 5.73 0.00 0.00 2.57
2554 2830 2.679132 GATCGTGTGGGATCGGACGG 62.679 65.000 0.00 0.00 34.07 4.79
2555 2831 1.299165 GATCGTGTGGGATCGGACG 60.299 63.158 0.00 0.00 34.07 4.79
2583 2859 2.098298 GTAACATGCAGCGCGGTG 59.902 61.111 32.48 32.48 0.00 4.94
2584 2860 1.305219 ATTGTAACATGCAGCGCGGT 61.305 50.000 4.23 4.23 0.00 5.68
2585 2861 0.589729 GATTGTAACATGCAGCGCGG 60.590 55.000 8.83 2.11 0.00 6.46
2586 2862 0.096802 TGATTGTAACATGCAGCGCG 59.903 50.000 0.00 0.00 0.00 6.86
2587 2863 1.398041 TCTGATTGTAACATGCAGCGC 59.602 47.619 0.00 0.00 0.00 5.92
2588 2864 2.538333 GCTCTGATTGTAACATGCAGCG 60.538 50.000 0.00 0.00 0.00 5.18
2589 2865 2.421073 TGCTCTGATTGTAACATGCAGC 59.579 45.455 0.00 0.00 0.00 5.25
2590 2866 4.095932 ACATGCTCTGATTGTAACATGCAG 59.904 41.667 0.00 0.00 38.72 4.41
2591 2867 4.011698 ACATGCTCTGATTGTAACATGCA 58.988 39.130 0.00 0.00 38.72 3.96
2592 2868 4.627611 ACATGCTCTGATTGTAACATGC 57.372 40.909 0.00 0.00 38.72 4.06
2593 2869 7.075674 TGTAACATGCTCTGATTGTAACATG 57.924 36.000 0.00 0.00 40.48 3.21
2594 2870 7.686438 TTGTAACATGCTCTGATTGTAACAT 57.314 32.000 0.00 0.00 0.00 2.71
2595 2871 7.148255 GGATTGTAACATGCTCTGATTGTAACA 60.148 37.037 0.00 0.00 0.00 2.41
2596 2872 7.189512 GGATTGTAACATGCTCTGATTGTAAC 58.810 38.462 0.00 0.00 0.00 2.50
2597 2873 6.318648 GGGATTGTAACATGCTCTGATTGTAA 59.681 38.462 0.00 0.00 0.00 2.41
2598 2874 5.822519 GGGATTGTAACATGCTCTGATTGTA 59.177 40.000 0.00 0.00 0.00 2.41
2599 2875 4.641989 GGGATTGTAACATGCTCTGATTGT 59.358 41.667 0.00 0.00 0.00 2.71
2600 2876 4.641541 TGGGATTGTAACATGCTCTGATTG 59.358 41.667 0.00 0.00 0.00 2.67
2601 2877 4.641989 GTGGGATTGTAACATGCTCTGATT 59.358 41.667 0.00 0.00 0.00 2.57
2602 2878 4.202441 GTGGGATTGTAACATGCTCTGAT 58.798 43.478 0.00 0.00 0.00 2.90
2603 2879 3.609853 GTGGGATTGTAACATGCTCTGA 58.390 45.455 0.00 0.00 0.00 3.27
2604 2880 2.352651 CGTGGGATTGTAACATGCTCTG 59.647 50.000 0.00 0.00 0.00 3.35
2605 2881 2.236146 TCGTGGGATTGTAACATGCTCT 59.764 45.455 0.00 0.00 0.00 4.09
2606 2882 2.627945 TCGTGGGATTGTAACATGCTC 58.372 47.619 0.00 0.00 0.00 4.26
2607 2883 2.779755 TCGTGGGATTGTAACATGCT 57.220 45.000 0.00 0.00 0.00 3.79
2608 2884 3.006940 TCTTCGTGGGATTGTAACATGC 58.993 45.455 0.00 0.00 0.00 4.06
2609 2885 4.454161 TGTTCTTCGTGGGATTGTAACATG 59.546 41.667 0.00 0.00 0.00 3.21
2610 2886 4.647611 TGTTCTTCGTGGGATTGTAACAT 58.352 39.130 0.00 0.00 0.00 2.71
2611 2887 4.062293 CTGTTCTTCGTGGGATTGTAACA 58.938 43.478 0.00 0.00 0.00 2.41
2612 2888 4.062991 ACTGTTCTTCGTGGGATTGTAAC 58.937 43.478 0.00 0.00 0.00 2.50
2613 2889 4.062293 CACTGTTCTTCGTGGGATTGTAA 58.938 43.478 0.00 0.00 0.00 2.41
2614 2890 3.322541 TCACTGTTCTTCGTGGGATTGTA 59.677 43.478 0.00 0.00 0.00 2.41
2615 2891 2.104111 TCACTGTTCTTCGTGGGATTGT 59.896 45.455 0.00 0.00 0.00 2.71
2616 2892 2.738846 CTCACTGTTCTTCGTGGGATTG 59.261 50.000 0.00 0.00 33.46 2.67
2617 2893 2.289694 CCTCACTGTTCTTCGTGGGATT 60.290 50.000 0.00 0.00 33.46 3.01
2618 2894 1.276421 CCTCACTGTTCTTCGTGGGAT 59.724 52.381 0.00 0.00 33.46 3.85
2619 2895 0.679505 CCTCACTGTTCTTCGTGGGA 59.320 55.000 0.00 0.00 33.46 4.37
2620 2896 0.951040 GCCTCACTGTTCTTCGTGGG 60.951 60.000 0.00 0.00 0.00 4.61
2621 2897 0.034059 AGCCTCACTGTTCTTCGTGG 59.966 55.000 0.00 0.00 0.00 4.94
2622 2898 1.795286 GAAGCCTCACTGTTCTTCGTG 59.205 52.381 0.00 0.00 0.00 4.35
2623 2899 1.412710 TGAAGCCTCACTGTTCTTCGT 59.587 47.619 0.00 0.00 38.14 3.85
2624 2900 2.154854 TGAAGCCTCACTGTTCTTCG 57.845 50.000 0.00 0.00 38.14 3.79
2634 2910 1.267121 GTAGGACTGGTGAAGCCTCA 58.733 55.000 0.00 0.00 38.35 3.86
2635 2911 1.267121 TGTAGGACTGGTGAAGCCTC 58.733 55.000 0.00 0.00 38.35 4.70
2636 2912 1.556911 CATGTAGGACTGGTGAAGCCT 59.443 52.381 0.00 0.00 38.35 4.58
2637 2913 1.555075 TCATGTAGGACTGGTGAAGCC 59.445 52.381 0.00 0.00 37.90 4.35
2638 2914 2.497675 TCTCATGTAGGACTGGTGAAGC 59.502 50.000 0.00 0.00 0.00 3.86
2639 2915 5.596361 ACTATCTCATGTAGGACTGGTGAAG 59.404 44.000 0.00 0.00 0.00 3.02
2640 2916 5.360999 CACTATCTCATGTAGGACTGGTGAA 59.639 44.000 0.00 0.00 0.00 3.18
2641 2917 4.889995 CACTATCTCATGTAGGACTGGTGA 59.110 45.833 0.00 0.00 0.00 4.02
2642 2918 4.889995 TCACTATCTCATGTAGGACTGGTG 59.110 45.833 0.00 0.00 0.00 4.17
2643 2919 4.890581 GTCACTATCTCATGTAGGACTGGT 59.109 45.833 0.00 0.00 0.00 4.00
2644 2920 4.889995 TGTCACTATCTCATGTAGGACTGG 59.110 45.833 0.00 0.00 0.00 4.00
2645 2921 6.445475 CATGTCACTATCTCATGTAGGACTG 58.555 44.000 0.00 0.00 35.61 3.51
2646 2922 5.010516 GCATGTCACTATCTCATGTAGGACT 59.989 44.000 0.00 0.00 40.40 3.85
2647 2923 5.010516 AGCATGTCACTATCTCATGTAGGAC 59.989 44.000 0.00 0.00 40.40 3.85
2648 2924 5.143369 AGCATGTCACTATCTCATGTAGGA 58.857 41.667 0.00 0.00 40.40 2.94
2649 2925 5.243507 AGAGCATGTCACTATCTCATGTAGG 59.756 44.000 0.00 0.00 40.40 3.18
2650 2926 6.016443 TCAGAGCATGTCACTATCTCATGTAG 60.016 42.308 0.00 0.00 40.40 2.74
2651 2927 5.829924 TCAGAGCATGTCACTATCTCATGTA 59.170 40.000 0.00 0.00 40.40 2.29
2652 2928 4.648307 TCAGAGCATGTCACTATCTCATGT 59.352 41.667 0.00 0.00 40.40 3.21
2653 2929 5.197682 TCAGAGCATGTCACTATCTCATG 57.802 43.478 0.00 0.00 40.98 3.07
2654 2930 5.785243 CATCAGAGCATGTCACTATCTCAT 58.215 41.667 0.00 0.00 0.00 2.90
2655 2931 4.501058 GCATCAGAGCATGTCACTATCTCA 60.501 45.833 0.00 0.00 0.00 3.27
2656 2932 3.989167 GCATCAGAGCATGTCACTATCTC 59.011 47.826 0.00 0.00 0.00 2.75
2663 2939 1.478105 AGTACGCATCAGAGCATGTCA 59.522 47.619 0.00 0.00 0.00 3.58
2665 2941 1.931906 CAGTACGCATCAGAGCATGT 58.068 50.000 0.00 0.00 0.00 3.21
2667 2943 2.983433 GCAGTACGCATCAGAGCAT 58.017 52.632 5.07 0.00 41.79 3.79
2681 2958 1.763120 TGCATCTCCACCTTGCAGT 59.237 52.632 0.00 0.00 41.18 4.40
2686 2963 1.903877 CGTCCCTGCATCTCCACCTT 61.904 60.000 0.00 0.00 0.00 3.50
2690 2967 3.785859 GGCGTCCCTGCATCTCCA 61.786 66.667 0.00 0.00 36.28 3.86
2695 2972 2.672996 GTGTTGGCGTCCCTGCAT 60.673 61.111 0.00 0.00 36.28 3.96
2752 3029 2.202797 CTCGTAGCACGGCTGCAT 60.203 61.111 12.72 0.00 46.97 3.96
2754 3031 3.411418 TAGCTCGTAGCACGGCTGC 62.411 63.158 21.97 16.67 45.56 5.25
2755 3032 1.586564 GTAGCTCGTAGCACGGCTG 60.587 63.158 21.97 0.00 45.56 4.85
2756 3033 2.799371 GTAGCTCGTAGCACGGCT 59.201 61.111 19.46 19.46 45.56 5.52
2757 3034 2.651232 CGTAGCTCGTAGCACGGC 60.651 66.667 16.09 10.05 45.56 5.68
2764 3050 1.025113 AGTGCTGCTCGTAGCTCGTA 61.025 55.000 8.41 0.00 42.97 3.43
2787 3073 4.873129 GCAGAATCGCCGGCTCGA 62.873 66.667 26.68 16.28 43.09 4.04
2795 3081 1.331161 CGTACGTCATTGCAGAATCGC 60.331 52.381 7.22 0.00 0.00 4.58
2796 3082 2.182014 TCGTACGTCATTGCAGAATCG 58.818 47.619 16.05 0.00 0.00 3.34
2800 3086 3.242518 CTTCTTCGTACGTCATTGCAGA 58.757 45.455 16.05 4.03 0.00 4.26
2807 3093 0.587768 TCGTGCTTCTTCGTACGTCA 59.412 50.000 16.05 2.34 42.39 4.35
2815 3101 0.796312 TTTCGCCATCGTGCTTCTTC 59.204 50.000 0.00 0.00 36.96 2.87
2827 3113 1.865788 GACCTTGCAGCATTTCGCCA 61.866 55.000 0.00 0.00 44.04 5.69
2833 3119 1.274167 CACCATTGACCTTGCAGCATT 59.726 47.619 0.00 0.00 0.00 3.56
2837 3123 0.540365 ACCCACCATTGACCTTGCAG 60.540 55.000 0.00 0.00 0.00 4.41
2848 3134 4.090588 CCGTGCCGTACCCACCAT 62.091 66.667 5.91 0.00 0.00 3.55
2852 3138 3.697747 CTTCCCGTGCCGTACCCA 61.698 66.667 0.00 0.00 0.00 4.51
2854 3140 3.887335 TTGCTTCCCGTGCCGTACC 62.887 63.158 0.00 0.00 0.00 3.34
2855 3141 2.357760 TTGCTTCCCGTGCCGTAC 60.358 61.111 0.00 0.00 0.00 3.67
2856 3142 2.357760 GTTGCTTCCCGTGCCGTA 60.358 61.111 0.00 0.00 0.00 4.02
2871 3157 2.972505 CCTCGTTGCAGCACCGTT 60.973 61.111 12.50 0.00 0.00 4.44
2878 3164 3.972227 CAACTCCCCTCGTTGCAG 58.028 61.111 0.00 0.00 35.82 4.41
2882 3168 1.079127 CGATGCAACTCCCCTCGTT 60.079 57.895 0.00 0.00 0.00 3.85
2898 3184 2.782222 GCTCATGGCCGACTACCGA 61.782 63.158 0.00 0.00 41.76 4.69
2910 3196 3.436924 TTGCTGCAGCGGCTCATG 61.437 61.111 32.11 0.00 45.83 3.07
2925 3211 2.434884 ATCACCTCGCTGGCGTTG 60.435 61.111 14.55 10.36 40.22 4.10
2932 3218 1.580845 GCTTGCAACATCACCTCGCT 61.581 55.000 0.00 0.00 0.00 4.93
2933 3219 1.154150 GCTTGCAACATCACCTCGC 60.154 57.895 0.00 0.00 0.00 5.03
2978 3278 1.227380 GTAGCCGAGATGCCACTGG 60.227 63.158 0.00 0.00 0.00 4.00
2980 3280 1.753078 TCGTAGCCGAGATGCCACT 60.753 57.895 0.00 0.00 38.40 4.00
2983 3283 2.353607 CGTCGTAGCCGAGATGCC 60.354 66.667 0.00 0.00 45.26 4.40
2992 3292 2.150837 GTTGAGCCGTCGTCGTAGC 61.151 63.158 0.71 0.00 35.01 3.58
2995 3295 1.371389 GAAGTTGAGCCGTCGTCGT 60.371 57.895 0.71 0.00 35.01 4.34
3011 3311 1.514003 TGTAGCAAAATGTCGCCGAA 58.486 45.000 0.00 0.00 0.00 4.30
3012 3312 1.396648 CATGTAGCAAAATGTCGCCGA 59.603 47.619 0.00 0.00 0.00 5.54
3014 3314 1.798813 GCCATGTAGCAAAATGTCGCC 60.799 52.381 0.00 0.00 0.00 5.54
3020 3320 1.753073 GCCTGAGCCATGTAGCAAAAT 59.247 47.619 0.00 0.00 34.23 1.82
3028 3328 2.271497 GAGCAGCCTGAGCCATGT 59.729 61.111 0.00 0.00 41.25 3.21
3042 3346 2.913060 ATCGTAGGAGCCCGGAGC 60.913 66.667 0.73 4.57 44.25 4.70
3049 3353 1.770085 GCTTGCAGCATCGTAGGAGC 61.770 60.000 0.00 0.00 41.89 4.70
3050 3354 1.156645 GGCTTGCAGCATCGTAGGAG 61.157 60.000 0.00 0.00 44.75 3.69
3051 3355 1.153369 GGCTTGCAGCATCGTAGGA 60.153 57.895 0.00 0.00 44.75 2.94
3052 3356 1.434622 CTGGCTTGCAGCATCGTAGG 61.435 60.000 0.00 0.00 44.75 3.18
3053 3357 0.742281 ACTGGCTTGCAGCATCGTAG 60.742 55.000 0.00 0.00 44.75 3.51
3054 3358 1.020861 CACTGGCTTGCAGCATCGTA 61.021 55.000 0.00 0.00 44.75 3.43
3055 3359 2.033141 ACTGGCTTGCAGCATCGT 59.967 55.556 0.00 1.92 44.75 3.73
3090 3394 4.767255 CCGGCAGACTCCCAGCAC 62.767 72.222 0.00 0.00 0.00 4.40
3092 3396 4.767255 CACCGGCAGACTCCCAGC 62.767 72.222 0.00 0.00 0.00 4.85
3093 3397 4.767255 GCACCGGCAGACTCCCAG 62.767 72.222 0.00 0.00 40.72 4.45
3094 3398 3.897681 TAGCACCGGCAGACTCCCA 62.898 63.158 0.00 0.00 44.61 4.37
3095 3399 3.075005 TAGCACCGGCAGACTCCC 61.075 66.667 0.00 0.00 44.61 4.30
3097 3401 2.005960 ATCGTAGCACCGGCAGACTC 62.006 60.000 0.00 0.00 44.61 3.36
3098 3402 2.052690 ATCGTAGCACCGGCAGACT 61.053 57.895 0.00 0.00 44.61 3.24
3099 3403 1.878522 CATCGTAGCACCGGCAGAC 60.879 63.158 0.00 0.00 44.61 3.51
3100 3404 2.494445 CATCGTAGCACCGGCAGA 59.506 61.111 0.00 0.00 44.61 4.26
3102 3406 4.830765 GCCATCGTAGCACCGGCA 62.831 66.667 0.00 0.00 44.61 5.69
3124 3428 3.320879 ATGTGGACTCGCAGCAGGG 62.321 63.158 0.00 0.00 36.78 4.45
3126 3430 2.163390 CGATGTGGACTCGCAGCAG 61.163 63.158 0.00 0.00 39.51 4.24
3139 3443 0.242825 CACCACGACCAGTACGATGT 59.757 55.000 0.00 0.00 34.70 3.06
3141 3445 1.601419 CCCACCACGACCAGTACGAT 61.601 60.000 0.00 0.00 34.70 3.73
3142 3446 2.270257 CCCACCACGACCAGTACGA 61.270 63.158 0.00 0.00 34.70 3.43
3143 3447 2.260434 CCCACCACGACCAGTACG 59.740 66.667 0.00 0.00 0.00 3.67
3144 3448 2.047560 GCCCACCACGACCAGTAC 60.048 66.667 0.00 0.00 0.00 2.73
3145 3449 3.315949 GGCCCACCACGACCAGTA 61.316 66.667 0.00 0.00 35.26 2.74
3163 3467 3.579626 GAACAACTCGCAGCACGGC 62.580 63.158 0.00 0.00 43.89 5.68
3164 3468 1.956170 AGAACAACTCGCAGCACGG 60.956 57.895 0.00 0.00 43.89 4.94
3165 3469 1.202568 CAGAACAACTCGCAGCACG 59.797 57.895 0.00 0.00 45.62 5.34
3166 3470 0.041839 CACAGAACAACTCGCAGCAC 60.042 55.000 0.00 0.00 0.00 4.40
3167 3471 1.775039 GCACAGAACAACTCGCAGCA 61.775 55.000 0.00 0.00 0.00 4.41
3168 3472 1.082496 GCACAGAACAACTCGCAGC 60.082 57.895 0.00 0.00 0.00 5.25
3169 3473 1.783284 TAGCACAGAACAACTCGCAG 58.217 50.000 0.00 0.00 0.00 5.18
3170 3474 2.068519 CATAGCACAGAACAACTCGCA 58.931 47.619 0.00 0.00 0.00 5.10
3171 3475 1.394917 CCATAGCACAGAACAACTCGC 59.605 52.381 0.00 0.00 0.00 5.03
3172 3476 2.668457 GACCATAGCACAGAACAACTCG 59.332 50.000 0.00 0.00 0.00 4.18
3178 3482 1.337823 ACCACGACCATAGCACAGAAC 60.338 52.381 0.00 0.00 0.00 3.01
3194 3498 0.601558 TGTCTTCTCTACGCCACCAC 59.398 55.000 0.00 0.00 0.00 4.16
3202 3506 2.093106 TCCTTCCGCTGTCTTCTCTAC 58.907 52.381 0.00 0.00 0.00 2.59
3206 3510 0.892063 GTCTCCTTCCGCTGTCTTCT 59.108 55.000 0.00 0.00 0.00 2.85
3215 3519 0.249073 CGCAGTATGGTCTCCTTCCG 60.249 60.000 0.00 0.00 35.86 4.30
3232 3536 1.732259 ACCATCGATGAAAGTCAACGC 59.268 47.619 26.86 0.00 41.51 4.84
3234 3538 6.534934 GTCTTTACCATCGATGAAAGTCAAC 58.465 40.000 26.86 16.96 32.05 3.18
3247 3551 1.940613 GATGTGGGCGTCTTTACCATC 59.059 52.381 0.00 0.00 36.54 3.51
3249 3553 0.687920 TGATGTGGGCGTCTTTACCA 59.312 50.000 0.00 0.00 0.00 3.25
3252 3556 2.482316 CCGTATGATGTGGGCGTCTTTA 60.482 50.000 0.00 0.00 0.00 1.85
3253 3557 1.651987 CGTATGATGTGGGCGTCTTT 58.348 50.000 0.00 0.00 0.00 2.52
3258 3563 1.594293 GGACCGTATGATGTGGGCG 60.594 63.158 0.00 0.00 0.00 6.13
3264 3569 1.069204 CACCTCCTGGACCGTATGATG 59.931 57.143 0.00 0.00 37.04 3.07


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

AutoCloner maintained by Alex Coulton.