Multiple sequence alignment - TraesCS2A01G307400

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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 TraesCS2A01G307400 chr2A 100.000 3386 0 0 1 3386 528121107 528124492 0.000000e+00 6253.0
1 TraesCS2A01G307400 chr2D 94.969 1948 69 11 921 2845 391392243 391394184 0.000000e+00 3027.0
2 TraesCS2A01G307400 chr2D 94.059 202 10 2 2846 3046 327962405 327962205 4.240000e-79 305.0
3 TraesCS2A01G307400 chr2D 92.891 211 10 5 2830 3037 512770187 512770395 5.490000e-78 302.0
4 TraesCS2A01G307400 chr2D 88.446 251 20 5 3138 3386 391394287 391394530 9.190000e-76 294.0
5 TraesCS2A01G307400 chr2B 93.760 1939 93 15 924 2845 462949812 462951739 0.000000e+00 2885.0
6 TraesCS2A01G307400 chr2B 86.364 308 30 8 3084 3386 462951792 462952092 3.260000e-85 326.0
7 TraesCS2A01G307400 chr2B 92.958 213 12 3 2836 3047 121669506 121669716 1.180000e-79 307.0
8 TraesCS2A01G307400 chr2B 92.593 216 8 8 2837 3046 525081142 525080929 1.530000e-78 303.0
9 TraesCS2A01G307400 chr6B 88.360 945 58 16 1 902 714390579 714391514 0.000000e+00 1088.0
10 TraesCS2A01G307400 chr3B 88.303 949 57 22 1 906 512417933 512416996 0.000000e+00 1088.0
11 TraesCS2A01G307400 chr3B 95.918 49 2 0 848 896 58022154 58022202 2.800000e-11 80.5
12 TraesCS2A01G307400 chr5A 91.295 471 35 5 425 889 181022360 181021890 3.680000e-179 638.0
13 TraesCS2A01G307400 chr5A 85.593 472 28 7 1 432 181022860 181022389 3.080000e-125 459.0
14 TraesCS2A01G307400 chr1D 90.254 472 37 5 425 890 433139918 433140386 2.890000e-170 608.0
15 TraesCS2A01G307400 chr1D 88.912 478 43 6 425 896 433130043 433129570 6.300000e-162 580.0
16 TraesCS2A01G307400 chr1D 88.214 280 14 8 1 267 433130542 433130269 1.960000e-82 316.0
17 TraesCS2A01G307400 chr1D 83.099 355 17 18 118 429 433139532 433139886 1.990000e-72 283.0
18 TraesCS2A01G307400 chr1A 88.564 411 41 5 425 829 228085616 228086026 8.440000e-136 494.0
19 TraesCS2A01G307400 chr1A 85.288 469 29 12 1 429 228085116 228085584 6.660000e-122 448.0
20 TraesCS2A01G307400 chr7B 85.053 475 31 17 1 435 106925485 106925011 6.660000e-122 448.0
21 TraesCS2A01G307400 chr7B 92.857 210 12 3 2835 3043 252794258 252794465 5.490000e-78 302.0
22 TraesCS2A01G307400 chr7B 96.809 94 1 2 425 516 106924985 106924892 4.520000e-34 156.0
23 TraesCS2A01G307400 chr1B 94.146 205 8 4 2830 3033 225811776 225811977 3.280000e-80 309.0
24 TraesCS2A01G307400 chr1B 74.901 506 62 33 175 621 415109567 415109068 1.620000e-38 171.0
25 TraesCS2A01G307400 chr7A 90.638 235 14 6 2810 3039 554383097 554383328 4.240000e-79 305.0
26 TraesCS2A01G307400 chr4B 92.166 217 15 2 2815 3029 344467488 344467272 4.240000e-79 305.0
27 TraesCS2A01G307400 chr4B 94.845 194 9 1 2840 3032 588430812 588431005 5.490000e-78 302.0
28 TraesCS2A01G307400 chr4A 81.183 186 29 6 721 903 20236256 20236074 9.790000e-31 145.0
29 TraesCS2A01G307400 chr4A 84.615 117 14 4 792 906 609552384 609552498 2.760000e-21 113.0
30 TraesCS2A01G307400 chr4A 84.043 94 12 3 792 883 609552495 609552587 1.670000e-13 87.9
31 TraesCS2A01G307400 chr3D 77.663 291 23 22 175 429 30594195 30593911 4.560000e-29 139.0


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 TraesCS2A01G307400 chr2A 528121107 528124492 3385 False 6253.0 6253 100.0000 1 3386 1 chr2A.!!$F1 3385
1 TraesCS2A01G307400 chr2D 391392243 391394530 2287 False 1660.5 3027 91.7075 921 3386 2 chr2D.!!$F2 2465
2 TraesCS2A01G307400 chr2B 462949812 462952092 2280 False 1605.5 2885 90.0620 924 3386 2 chr2B.!!$F2 2462
3 TraesCS2A01G307400 chr6B 714390579 714391514 935 False 1088.0 1088 88.3600 1 902 1 chr6B.!!$F1 901
4 TraesCS2A01G307400 chr3B 512416996 512417933 937 True 1088.0 1088 88.3030 1 906 1 chr3B.!!$R1 905
5 TraesCS2A01G307400 chr5A 181021890 181022860 970 True 548.5 638 88.4440 1 889 2 chr5A.!!$R1 888
6 TraesCS2A01G307400 chr1D 433129570 433130542 972 True 448.0 580 88.5630 1 896 2 chr1D.!!$R1 895
7 TraesCS2A01G307400 chr1D 433139532 433140386 854 False 445.5 608 86.6765 118 890 2 chr1D.!!$F1 772
8 TraesCS2A01G307400 chr1A 228085116 228086026 910 False 471.0 494 86.9260 1 829 2 chr1A.!!$F1 828
9 TraesCS2A01G307400 chr7B 106924892 106925485 593 True 302.0 448 90.9310 1 516 2 chr7B.!!$R1 515

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
966 1075 0.244994 ATCTAGTGCGCATCGGGATC 59.755 55.0 15.91 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2876 3009 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.0 0.0 0.0 44.78 4.85 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
71 72 2.340078 GGCAGCAGAGTCGACACA 59.660 61.111 19.50 0.00 0.00 3.72
344 398 1.274167 TCTCCTGGTTATGTTCGCGTT 59.726 47.619 5.77 0.00 0.00 4.84
355 410 1.189403 GTTCGCGTTGGATCGTAGAG 58.811 55.000 5.77 0.00 43.63 2.43
372 427 1.544917 AGGTTCCCCATGGCTCCTT 60.545 57.895 6.09 0.00 32.91 3.36
388 443 3.118445 GCTCCTTAACCTCTCTGCTGATT 60.118 47.826 0.00 0.00 0.00 2.57
543 636 1.009389 CGAGTTCGCTGTCCAGGAAC 61.009 60.000 15.17 15.17 38.12 3.62
546 639 1.006571 TTCGCTGTCCAGGAACGAC 60.007 57.895 9.45 0.00 31.61 4.34
549 642 1.668151 GCTGTCCAGGAACGACACC 60.668 63.158 0.00 0.00 35.35 4.16
574 667 3.842923 CGTGCAGCGAGGGAGGAT 61.843 66.667 3.04 0.00 44.77 3.24
679 776 1.612950 TGTTTCTACGTGCCTTCCGTA 59.387 47.619 0.00 0.00 39.60 4.02
742 839 0.731855 GGAGTACGGTCAGTCGTTGC 60.732 60.000 0.00 0.00 43.59 4.17
783 880 6.659242 CACCATGAAACAGATTAGGTTAAGGT 59.341 38.462 0.00 0.00 0.00 3.50
808 905 9.301153 GTTAACCGTTAGATTAAGTTTATCGGA 57.699 33.333 14.81 0.00 38.92 4.55
821 918 5.597806 AGTTTATCGGATCTAATTGTGCGA 58.402 37.500 0.00 6.43 42.19 5.10
823 920 7.375834 AGTTTATCGGATCTAATTGTGCGATA 58.624 34.615 14.91 14.91 45.05 2.92
864 961 2.279935 ATGGGGTGCACGTAAGAAAA 57.720 45.000 11.45 0.00 43.62 2.29
896 993 9.974750 GTTTGATTGTTTATTAGTAGCAGAGAC 57.025 33.333 0.00 0.00 0.00 3.36
902 999 8.526667 TGTTTATTAGTAGCAGAGACAGAGAT 57.473 34.615 0.00 0.00 0.00 2.75
906 1003 9.719355 TTATTAGTAGCAGAGACAGAGATAGAG 57.281 37.037 0.00 0.00 0.00 2.43
907 1004 5.887214 AGTAGCAGAGACAGAGATAGAGA 57.113 43.478 0.00 0.00 0.00 3.10
908 1005 6.247229 AGTAGCAGAGACAGAGATAGAGAA 57.753 41.667 0.00 0.00 0.00 2.87
909 1006 6.291377 AGTAGCAGAGACAGAGATAGAGAAG 58.709 44.000 0.00 0.00 0.00 2.85
910 1007 5.372343 AGCAGAGACAGAGATAGAGAAGA 57.628 43.478 0.00 0.00 0.00 2.87
911 1008 5.371526 AGCAGAGACAGAGATAGAGAAGAG 58.628 45.833 0.00 0.00 0.00 2.85
912 1009 5.130975 AGCAGAGACAGAGATAGAGAAGAGA 59.869 44.000 0.00 0.00 0.00 3.10
913 1010 5.822519 GCAGAGACAGAGATAGAGAAGAGAA 59.177 44.000 0.00 0.00 0.00 2.87
914 1011 6.017605 GCAGAGACAGAGATAGAGAAGAGAAG 60.018 46.154 0.00 0.00 0.00 2.85
915 1012 7.275183 CAGAGACAGAGATAGAGAAGAGAAGA 58.725 42.308 0.00 0.00 0.00 2.87
916 1013 7.440556 CAGAGACAGAGATAGAGAAGAGAAGAG 59.559 44.444 0.00 0.00 0.00 2.85
917 1014 7.345653 AGAGACAGAGATAGAGAAGAGAAGAGA 59.654 40.741 0.00 0.00 0.00 3.10
918 1015 8.038862 AGACAGAGATAGAGAAGAGAAGAGAT 57.961 38.462 0.00 0.00 0.00 2.75
919 1016 9.159254 AGACAGAGATAGAGAAGAGAAGAGATA 57.841 37.037 0.00 0.00 0.00 1.98
920 1017 9.429359 GACAGAGATAGAGAAGAGAAGAGATAG 57.571 40.741 0.00 0.00 0.00 2.08
921 1018 9.159254 ACAGAGATAGAGAAGAGAAGAGATAGA 57.841 37.037 0.00 0.00 0.00 1.98
922 1019 9.650539 CAGAGATAGAGAAGAGAAGAGATAGAG 57.349 40.741 0.00 0.00 0.00 2.43
965 1074 0.681733 AATCTAGTGCGCATCGGGAT 59.318 50.000 15.91 12.47 0.00 3.85
966 1075 0.244994 ATCTAGTGCGCATCGGGATC 59.755 55.000 15.91 0.00 0.00 3.36
967 1076 0.823769 TCTAGTGCGCATCGGGATCT 60.824 55.000 15.91 6.51 0.00 2.75
968 1077 0.387878 CTAGTGCGCATCGGGATCTC 60.388 60.000 15.91 0.00 0.00 2.75
969 1078 1.806461 TAGTGCGCATCGGGATCTCC 61.806 60.000 15.91 0.00 0.00 3.71
987 1096 3.963374 TCTCCTCTCTCTCTCTCTCTCTG 59.037 52.174 0.00 0.00 0.00 3.35
1393 1502 2.885644 CGCAGACGCTAACCGCAT 60.886 61.111 0.00 0.00 41.76 4.73
1422 1531 1.433879 CGCCTCCTTCTACTCCACG 59.566 63.158 0.00 0.00 0.00 4.94
1431 1540 2.986979 TACTCCACGGTCGCAGCA 60.987 61.111 0.00 0.00 0.00 4.41
1518 1627 2.480555 CAAGACGCCGTCAATGCC 59.519 61.111 20.65 0.00 34.60 4.40
1609 1718 0.039798 TCCGTTCGAGAAGACCAACG 60.040 55.000 0.00 0.00 41.00 4.10
1623 1732 1.591327 CAACGTTTTGCTGGTGGGC 60.591 57.895 0.00 0.00 0.00 5.36
1677 1786 3.447025 GAGCGTGGGGATCGAAGGG 62.447 68.421 0.00 0.00 0.00 3.95
1680 1789 2.506472 GTGGGGATCGAAGGGCTC 59.494 66.667 0.00 0.00 0.00 4.70
1696 1805 0.391130 GCTCGGCACTTATGACACCA 60.391 55.000 0.00 0.00 30.51 4.17
1752 1861 4.212214 GCGAGGGATATCACATTTGAGAAC 59.788 45.833 7.92 0.00 34.35 3.01
1992 2101 4.388499 GGTTCCGGGAAGAGCGCA 62.388 66.667 10.35 0.00 0.00 6.09
2312 2421 4.436998 GGTCGGGTGGAGCAGTCG 62.437 72.222 0.00 0.00 42.75 4.18
2317 2426 2.660064 GGGTGGAGCAGTCGGACAT 61.660 63.158 11.27 0.00 0.00 3.06
2435 2545 2.005451 CGATTCTTGGTGGAGCTTCAG 58.995 52.381 0.00 0.00 0.00 3.02
2554 2672 4.142004 GGTACATAACCCGAAGTGATCTGT 60.142 45.833 0.00 0.00 43.16 3.41
2651 2779 6.483640 GTGTTTTCTGGAGTGACTACTGAAAT 59.516 38.462 24.43 0.00 40.28 2.17
2708 2836 5.880054 ATTGTAGTTGTGTGGTATTCAGC 57.120 39.130 0.00 0.00 0.00 4.26
2723 2854 9.435688 GTGGTATTCAGCATATTGTACATATGA 57.564 33.333 20.34 8.09 34.74 2.15
2780 2913 2.607499 TGCATTCCAATCCAACCTGTT 58.393 42.857 0.00 0.00 0.00 3.16
2781 2914 2.971330 TGCATTCCAATCCAACCTGTTT 59.029 40.909 0.00 0.00 0.00 2.83
2787 2920 3.509575 TCCAATCCAACCTGTTTATGTGC 59.490 43.478 0.00 0.00 0.00 4.57
2807 2940 1.332997 CGATGGAAGCATCTTTCTGCC 59.667 52.381 0.00 0.00 43.33 4.85
2812 2945 3.022406 GGAAGCATCTTTCTGCCATCTT 58.978 45.455 0.00 0.00 43.33 2.40
2813 2946 3.446516 GGAAGCATCTTTCTGCCATCTTT 59.553 43.478 0.00 0.00 43.33 2.52
2815 2948 5.126061 GGAAGCATCTTTCTGCCATCTTTTA 59.874 40.000 0.00 0.00 43.33 1.52
2820 2953 8.098912 AGCATCTTTCTGCCATCTTTTATTTTT 58.901 29.630 0.00 0.00 43.33 1.94
2822 2955 8.876790 CATCTTTCTGCCATCTTTTATTTTTCC 58.123 33.333 0.00 0.00 0.00 3.13
2827 2960 6.036577 TGCCATCTTTTATTTTTCCTGTCC 57.963 37.500 0.00 0.00 0.00 4.02
2830 2963 7.453126 TGCCATCTTTTATTTTTCCTGTCCTTA 59.547 33.333 0.00 0.00 0.00 2.69
2851 2984 9.250246 TCCTTATTTATTTGTTAGTTGAAGGGG 57.750 33.333 0.00 0.00 32.37 4.79
2852 2985 9.250246 CCTTATTTATTTGTTAGTTGAAGGGGA 57.750 33.333 0.00 0.00 0.00 4.81
2854 2987 6.584185 TTTATTTGTTAGTTGAAGGGGAGC 57.416 37.500 0.00 0.00 0.00 4.70
2855 2988 2.579410 TTGTTAGTTGAAGGGGAGCC 57.421 50.000 0.00 0.00 0.00 4.70
2856 2989 1.742308 TGTTAGTTGAAGGGGAGCCT 58.258 50.000 0.00 0.00 0.00 4.58
2857 2990 2.062636 TGTTAGTTGAAGGGGAGCCTT 58.937 47.619 0.00 0.00 0.00 4.35
2858 2991 2.224769 TGTTAGTTGAAGGGGAGCCTTG 60.225 50.000 0.00 0.00 0.00 3.61
2859 2992 0.991920 TAGTTGAAGGGGAGCCTTGG 59.008 55.000 0.00 0.00 0.00 3.61
2860 2993 1.979155 GTTGAAGGGGAGCCTTGGC 60.979 63.158 2.97 2.97 0.00 4.52
2861 2994 3.567579 TTGAAGGGGAGCCTTGGCG 62.568 63.158 5.95 0.00 0.00 5.69
2869 3002 3.958147 GAGCCTTGGCGCAGTGCTA 62.958 63.158 14.33 0.00 45.43 3.49
2870 3003 3.055719 GCCTTGGCGCAGTGCTAA 61.056 61.111 14.33 5.12 45.43 3.09
2871 3004 2.625823 GCCTTGGCGCAGTGCTAAA 61.626 57.895 14.33 3.79 44.03 1.85
2872 3005 1.503542 CCTTGGCGCAGTGCTAAAG 59.496 57.895 14.33 12.94 44.03 1.85
2873 3006 1.237285 CCTTGGCGCAGTGCTAAAGT 61.237 55.000 14.33 0.00 44.03 2.66
2874 3007 0.593128 CTTGGCGCAGTGCTAAAGTT 59.407 50.000 14.33 0.00 44.03 2.66
2875 3008 0.310543 TTGGCGCAGTGCTAAAGTTG 59.689 50.000 14.33 0.00 41.53 3.16
2876 3009 1.442688 GGCGCAGTGCTAAAGTTGC 60.443 57.895 14.33 6.95 45.43 4.17
2877 3010 1.576421 GCGCAGTGCTAAAGTTGCT 59.424 52.632 14.33 0.00 41.73 3.91
2878 3011 0.727122 GCGCAGTGCTAAAGTTGCTG 60.727 55.000 14.33 0.00 41.73 4.41
2879 3012 0.727122 CGCAGTGCTAAAGTTGCTGC 60.727 55.000 14.33 0.00 46.22 5.25
2880 3013 0.387750 GCAGTGCTAAAGTTGCTGCC 60.388 55.000 8.18 0.00 44.61 4.85
2881 3014 1.242076 CAGTGCTAAAGTTGCTGCCT 58.758 50.000 0.00 0.00 0.00 4.75
2882 3015 1.610522 CAGTGCTAAAGTTGCTGCCTT 59.389 47.619 0.00 0.00 0.00 4.35
2883 3016 1.610522 AGTGCTAAAGTTGCTGCCTTG 59.389 47.619 0.00 0.00 0.00 3.61
2884 3017 1.338020 GTGCTAAAGTTGCTGCCTTGT 59.662 47.619 0.00 0.00 0.00 3.16
2885 3018 1.337703 TGCTAAAGTTGCTGCCTTGTG 59.662 47.619 0.00 0.00 0.00 3.33
2886 3019 1.608590 GCTAAAGTTGCTGCCTTGTGA 59.391 47.619 0.00 0.00 0.00 3.58
2887 3020 2.605580 GCTAAAGTTGCTGCCTTGTGAC 60.606 50.000 0.00 0.00 0.00 3.67
2888 3021 0.746659 AAAGTTGCTGCCTTGTGACC 59.253 50.000 0.00 0.00 0.00 4.02
2889 3022 0.395586 AAGTTGCTGCCTTGTGACCA 60.396 50.000 0.00 0.00 0.00 4.02
2890 3023 0.178981 AGTTGCTGCCTTGTGACCAT 60.179 50.000 0.00 0.00 0.00 3.55
2891 3024 0.038892 GTTGCTGCCTTGTGACCATG 60.039 55.000 0.00 0.00 0.00 3.66
2892 3025 0.178995 TTGCTGCCTTGTGACCATGA 60.179 50.000 0.00 0.00 0.00 3.07
2893 3026 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2894 3027 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2904 3037 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
2905 3038 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
2906 3039 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
2907 3040 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
2908 3041 0.321653 ATGAGGTCACGGGTTCAAGC 60.322 55.000 0.00 0.00 0.00 4.01
2909 3042 1.671379 GAGGTCACGGGTTCAAGCC 60.671 63.158 0.00 0.00 0.00 4.35
2910 3043 2.671963 GGTCACGGGTTCAAGCCC 60.672 66.667 0.00 0.00 45.21 5.19
2911 3044 2.430367 GTCACGGGTTCAAGCCCT 59.570 61.111 0.00 0.00 46.47 5.19
2912 3045 1.966451 GTCACGGGTTCAAGCCCTG 60.966 63.158 0.00 0.00 46.47 4.45
2913 3046 2.672996 CACGGGTTCAAGCCCTGG 60.673 66.667 0.00 0.00 46.47 4.45
2914 3047 2.852075 ACGGGTTCAAGCCCTGGA 60.852 61.111 0.00 0.00 46.47 3.86
2915 3048 2.434331 CGGGTTCAAGCCCTGGAA 59.566 61.111 0.00 0.00 46.47 3.53
2916 3049 1.228429 CGGGTTCAAGCCCTGGAAA 60.228 57.895 0.00 0.00 46.47 3.13
2917 3050 1.524008 CGGGTTCAAGCCCTGGAAAC 61.524 60.000 0.00 0.00 46.47 2.78
2918 3051 0.469144 GGGTTCAAGCCCTGGAAACA 60.469 55.000 3.08 0.00 45.22 2.83
2933 3066 5.947228 TGGAAACAGCTCTTACAGAAATG 57.053 39.130 0.00 0.00 35.01 2.32
2934 3067 5.376625 TGGAAACAGCTCTTACAGAAATGT 58.623 37.500 0.00 0.00 35.01 2.71
2935 3068 6.530120 TGGAAACAGCTCTTACAGAAATGTA 58.470 36.000 0.00 0.00 35.01 2.29
2936 3069 6.650807 TGGAAACAGCTCTTACAGAAATGTAG 59.349 38.462 0.00 0.00 35.01 2.74
2937 3070 6.092807 GGAAACAGCTCTTACAGAAATGTAGG 59.907 42.308 0.00 0.00 0.00 3.18
2938 3071 5.091261 ACAGCTCTTACAGAAATGTAGGG 57.909 43.478 0.00 0.00 0.00 3.53
2939 3072 4.777896 ACAGCTCTTACAGAAATGTAGGGA 59.222 41.667 0.00 0.00 0.00 4.20
2940 3073 5.248477 ACAGCTCTTACAGAAATGTAGGGAA 59.752 40.000 0.00 0.00 0.00 3.97
2941 3074 6.173339 CAGCTCTTACAGAAATGTAGGGAAA 58.827 40.000 0.00 0.00 0.00 3.13
2942 3075 6.314896 CAGCTCTTACAGAAATGTAGGGAAAG 59.685 42.308 0.00 0.00 0.00 2.62
2943 3076 5.586643 GCTCTTACAGAAATGTAGGGAAAGG 59.413 44.000 0.00 0.00 0.00 3.11
2944 3077 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2945 3078 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
2946 3079 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
2947 3080 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2948 3081 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2949 3082 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2950 3083 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2951 3084 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2952 3085 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
2953 3086 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
2954 3087 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
2955 3088 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
2956 3089 1.940613 GGGAAAGGCTGCGTACAATAG 59.059 52.381 0.00 0.00 0.00 1.73
2957 3090 2.419574 GGGAAAGGCTGCGTACAATAGA 60.420 50.000 0.00 0.00 0.00 1.98
2958 3091 2.608090 GGAAAGGCTGCGTACAATAGAC 59.392 50.000 0.00 0.00 0.00 2.59
2959 3092 2.311124 AAGGCTGCGTACAATAGACC 57.689 50.000 0.00 0.00 0.00 3.85
2960 3093 0.464452 AGGCTGCGTACAATAGACCC 59.536 55.000 0.00 0.00 0.00 4.46
2961 3094 0.874607 GGCTGCGTACAATAGACCCG 60.875 60.000 0.00 0.00 0.00 5.28
2962 3095 0.101759 GCTGCGTACAATAGACCCGA 59.898 55.000 0.00 0.00 0.00 5.14
2963 3096 1.470285 GCTGCGTACAATAGACCCGAA 60.470 52.381 0.00 0.00 0.00 4.30
2964 3097 2.460918 CTGCGTACAATAGACCCGAAG 58.539 52.381 0.00 0.00 0.00 3.79
2965 3098 1.820519 TGCGTACAATAGACCCGAAGT 59.179 47.619 0.00 0.00 0.00 3.01
2966 3099 2.190981 GCGTACAATAGACCCGAAGTG 58.809 52.381 0.00 0.00 0.00 3.16
2967 3100 2.805845 CGTACAATAGACCCGAAGTGG 58.194 52.381 0.00 0.00 37.55 4.00
2968 3101 2.165030 CGTACAATAGACCCGAAGTGGT 59.835 50.000 0.00 0.00 42.79 4.16
2977 3110 3.057337 CGAAGTGGTCGGACCCTT 58.943 61.111 23.81 23.17 46.45 3.95
2978 3111 1.080025 CGAAGTGGTCGGACCCTTC 60.080 63.158 29.43 29.43 46.45 3.46
2979 3112 1.295746 GAAGTGGTCGGACCCTTCC 59.704 63.158 29.24 19.29 38.50 3.46
2980 3113 2.181445 GAAGTGGTCGGACCCTTCCC 62.181 65.000 29.24 17.13 38.50 3.97
2981 3114 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
3015 3148 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
3016 3149 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
3017 3150 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
3018 3151 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
3019 3152 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
3020 3153 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
3026 3159 2.917227 CACCGGGCTGCCCTTTTT 60.917 61.111 33.39 13.23 42.67 1.94
3058 3191 8.459521 TTTGTTAGTTCATGTTTGTTCAGTTG 57.540 30.769 0.00 0.00 0.00 3.16
3059 3192 6.559810 TGTTAGTTCATGTTTGTTCAGTTGG 58.440 36.000 0.00 0.00 0.00 3.77
3061 3194 5.659440 AGTTCATGTTTGTTCAGTTGGTT 57.341 34.783 0.00 0.00 0.00 3.67
3074 3207 8.282455 TGTTCAGTTGGTTACTAATTTGTTGA 57.718 30.769 0.00 0.00 34.56 3.18
3128 3281 5.875359 GCTAACACAGATAACCTTAGCACTT 59.125 40.000 0.00 0.00 39.32 3.16
3135 3288 8.730680 CACAGATAACCTTAGCACTTTTACAAT 58.269 33.333 0.00 0.00 0.00 2.71
3155 3308 5.519927 ACAATAGTTTGCAAGCAAAAGTGAC 59.480 36.000 20.45 9.69 45.86 3.67
3160 3313 2.891112 TGCAAGCAAAAGTGACAAAGG 58.109 42.857 0.00 0.00 0.00 3.11
3165 3318 3.837355 AGCAAAAGTGACAAAGGGAGAT 58.163 40.909 0.00 0.00 0.00 2.75
3166 3319 4.218312 AGCAAAAGTGACAAAGGGAGATT 58.782 39.130 0.00 0.00 0.00 2.40
3227 3380 4.623932 TCACTTGAGCTATGAACAAGGT 57.376 40.909 14.52 1.02 43.28 3.50
3229 3382 4.040339 TCACTTGAGCTATGAACAAGGTGA 59.960 41.667 14.52 12.24 43.28 4.02
3279 3434 2.163818 TTACAGCCAACTCGACTTGG 57.836 50.000 16.87 16.87 43.36 3.61
3301 3456 6.019779 GGTATTGACCTGCAAAATGTTACA 57.980 37.500 0.00 0.00 43.16 2.41
3302 3457 6.630071 GGTATTGACCTGCAAAATGTTACAT 58.370 36.000 0.00 0.00 43.16 2.29
3303 3458 6.751888 GGTATTGACCTGCAAAATGTTACATC 59.248 38.462 0.00 0.00 43.16 3.06
3304 3459 4.782019 TGACCTGCAAAATGTTACATCC 57.218 40.909 0.00 0.00 0.00 3.51
3305 3460 4.406456 TGACCTGCAAAATGTTACATCCT 58.594 39.130 0.00 0.00 0.00 3.24
3312 3467 7.172868 TGCAAAATGTTACATCCTCATCATT 57.827 32.000 0.00 0.00 0.00 2.57
3313 3468 7.036829 TGCAAAATGTTACATCCTCATCATTG 58.963 34.615 0.00 0.00 0.00 2.82
3372 3527 0.639392 ATCTACCTCCCTCCAGCAGT 59.361 55.000 0.00 0.00 0.00 4.40
3374 3529 1.644337 TCTACCTCCCTCCAGCAGTTA 59.356 52.381 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 2.800159 CTACCCCCGTGTCCACCTCT 62.800 65.000 0.00 0.00 0.00 3.69
114 121 0.324923 AGTACGACACCTATGCCCCA 60.325 55.000 0.00 0.00 0.00 4.96
208 229 2.056223 GGTGCTGCAATGGCTGGAT 61.056 57.895 2.77 0.00 41.03 3.41
372 427 3.954258 TCATCGAATCAGCAGAGAGGTTA 59.046 43.478 0.00 0.00 0.00 2.85
546 639 3.705638 CTGCACGACAGCACGGTG 61.706 66.667 3.15 3.15 40.19 4.94
572 665 1.644786 CGCCCCCAAGACAACGAATC 61.645 60.000 0.00 0.00 0.00 2.52
573 666 1.674322 CGCCCCCAAGACAACGAAT 60.674 57.895 0.00 0.00 0.00 3.34
574 667 2.281208 CGCCCCCAAGACAACGAA 60.281 61.111 0.00 0.00 0.00 3.85
602 699 0.100682 ACGACGATTCCCTGTCATCG 59.899 55.000 0.00 0.14 46.33 3.84
679 776 2.275418 CCCGCAGCCCCTACAATT 59.725 61.111 0.00 0.00 0.00 2.32
805 902 6.806739 TCATTACTATCGCACAATTAGATCCG 59.193 38.462 0.00 0.00 0.00 4.18
808 905 9.935241 AGATTCATTACTATCGCACAATTAGAT 57.065 29.630 0.00 0.00 0.00 1.98
815 912 9.573133 CATACATAGATTCATTACTATCGCACA 57.427 33.333 0.00 0.00 0.00 4.57
835 932 2.948979 CGTGCACCCCATAAACATACAT 59.051 45.455 12.15 0.00 0.00 2.29
845 942 2.279935 TTTTCTTACGTGCACCCCAT 57.720 45.000 12.15 0.00 0.00 4.00
890 987 7.275183 TCTTCTCTTCTCTATCTCTGTCTCTG 58.725 42.308 0.00 0.00 0.00 3.35
896 993 9.650539 CTCTATCTCTTCTCTTCTCTATCTCTG 57.349 40.741 0.00 0.00 0.00 3.35
904 1001 9.778741 TTCAGTATCTCTATCTCTTCTCTTCTC 57.221 37.037 0.00 0.00 0.00 2.87
908 1005 9.693739 TGTTTTCAGTATCTCTATCTCTTCTCT 57.306 33.333 0.00 0.00 0.00 3.10
914 1011 9.015577 CGTCTTTGTTTTCAGTATCTCTATCTC 57.984 37.037 0.00 0.00 0.00 2.75
915 1012 8.740906 TCGTCTTTGTTTTCAGTATCTCTATCT 58.259 33.333 0.00 0.00 0.00 1.98
916 1013 8.912787 TCGTCTTTGTTTTCAGTATCTCTATC 57.087 34.615 0.00 0.00 0.00 2.08
917 1014 9.141400 GTTCGTCTTTGTTTTCAGTATCTCTAT 57.859 33.333 0.00 0.00 0.00 1.98
918 1015 7.325338 CGTTCGTCTTTGTTTTCAGTATCTCTA 59.675 37.037 0.00 0.00 0.00 2.43
919 1016 6.144080 CGTTCGTCTTTGTTTTCAGTATCTCT 59.856 38.462 0.00 0.00 0.00 3.10
920 1017 6.289901 CGTTCGTCTTTGTTTTCAGTATCTC 58.710 40.000 0.00 0.00 0.00 2.75
921 1018 5.333111 GCGTTCGTCTTTGTTTTCAGTATCT 60.333 40.000 0.00 0.00 0.00 1.98
922 1019 4.839174 GCGTTCGTCTTTGTTTTCAGTATC 59.161 41.667 0.00 0.00 0.00 2.24
965 1074 3.963374 CAGAGAGAGAGAGAGAGAGGAGA 59.037 52.174 0.00 0.00 0.00 3.71
966 1075 3.708631 ACAGAGAGAGAGAGAGAGAGGAG 59.291 52.174 0.00 0.00 0.00 3.69
967 1076 3.706594 GACAGAGAGAGAGAGAGAGAGGA 59.293 52.174 0.00 0.00 0.00 3.71
968 1077 3.708631 AGACAGAGAGAGAGAGAGAGAGG 59.291 52.174 0.00 0.00 0.00 3.69
969 1078 4.648762 AGAGACAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
987 1096 0.171231 GCGGCATTTGGGAAAGAGAC 59.829 55.000 0.00 0.00 0.00 3.36
1074 1183 3.071206 GGCAGGAGGACGAGCAGA 61.071 66.667 0.00 0.00 0.00 4.26
1342 1451 3.760035 GAAGCGGGAGGTGAGCGA 61.760 66.667 0.00 0.00 42.46 4.93
1393 1502 3.332385 GGAGGCGGGTTTGGGGTA 61.332 66.667 0.00 0.00 0.00 3.69
1422 1531 4.179579 GCCGGAAATGCTGCGACC 62.180 66.667 5.05 0.00 42.35 4.79
1431 1540 4.157120 CGGACCCTCGCCGGAAAT 62.157 66.667 5.05 0.00 44.87 2.17
1518 1627 2.021380 GCAGTGTAATTCGGCGCG 59.979 61.111 0.00 0.00 0.00 6.86
1609 1718 2.644992 CTCGCCCACCAGCAAAAC 59.355 61.111 0.00 0.00 0.00 2.43
1623 1732 2.819284 GGTAGCCCCCATTCCCTCG 61.819 68.421 0.00 0.00 0.00 4.63
1677 1786 0.391130 TGGTGTCATAAGTGCCGAGC 60.391 55.000 0.00 0.00 0.00 5.03
1680 1789 0.389296 TCGTGGTGTCATAAGTGCCG 60.389 55.000 0.00 0.00 0.00 5.69
1977 2086 4.735132 CGTGCGCTCTTCCCGGAA 62.735 66.667 9.73 0.00 0.00 4.30
1992 2101 3.673484 GCTGCCACCACATTGCGT 61.673 61.111 0.00 0.00 0.00 5.24
2212 2321 1.512694 CAAAATCCCCTCGCCAAGC 59.487 57.895 0.00 0.00 0.00 4.01
2312 2421 2.417933 GTGACATGCTGTTCTGATGTCC 59.582 50.000 0.00 0.00 43.56 4.02
2317 2426 4.011966 AGAATGTGACATGCTGTTCTGA 57.988 40.909 4.99 0.00 0.00 3.27
2554 2672 4.381505 GGAAAACCTGTGAACAGCAGAAAA 60.382 41.667 4.87 0.00 42.47 2.29
2651 2779 5.465532 TGATATTCTGCAGCAAAACCAAA 57.534 34.783 9.47 0.00 0.00 3.28
2694 2822 6.410540 TGTACAATATGCTGAATACCACACA 58.589 36.000 0.00 0.00 0.00 3.72
2830 2963 6.154534 GGCTCCCCTTCAACTAACAAATAAAT 59.845 38.462 0.00 0.00 0.00 1.40
2834 2967 3.076032 AGGCTCCCCTTCAACTAACAAAT 59.924 43.478 0.00 0.00 38.74 2.32
2835 2968 2.445525 AGGCTCCCCTTCAACTAACAAA 59.554 45.455 0.00 0.00 38.74 2.83
2851 2984 3.958147 TAGCACTGCGCCAAGGCTC 62.958 63.158 14.78 1.20 44.04 4.70
2852 2985 3.551496 TTAGCACTGCGCCAAGGCT 62.551 57.895 4.18 11.59 44.04 4.58
2853 2986 2.533391 CTTTAGCACTGCGCCAAGGC 62.533 60.000 4.18 3.27 44.04 4.35
2854 2987 1.237285 ACTTTAGCACTGCGCCAAGG 61.237 55.000 4.18 0.00 44.04 3.61
2855 2988 0.593128 AACTTTAGCACTGCGCCAAG 59.407 50.000 4.18 0.00 44.04 3.61
2856 2989 0.310543 CAACTTTAGCACTGCGCCAA 59.689 50.000 4.18 0.00 44.04 4.52
2857 2990 1.948508 CAACTTTAGCACTGCGCCA 59.051 52.632 4.18 0.00 44.04 5.69
2858 2991 1.442688 GCAACTTTAGCACTGCGCC 60.443 57.895 4.18 0.00 44.04 6.53
2859 2992 0.727122 CAGCAACTTTAGCACTGCGC 60.727 55.000 0.00 0.00 39.80 6.09
2860 2993 0.727122 GCAGCAACTTTAGCACTGCG 60.727 55.000 0.00 0.00 43.65 5.18
2861 2994 3.098032 GCAGCAACTTTAGCACTGC 57.902 52.632 0.00 0.00 45.95 4.40
2862 2995 1.242076 AGGCAGCAACTTTAGCACTG 58.758 50.000 0.00 0.00 0.00 3.66
2863 2996 1.610522 CAAGGCAGCAACTTTAGCACT 59.389 47.619 0.00 0.00 0.00 4.40
2864 2997 1.338020 ACAAGGCAGCAACTTTAGCAC 59.662 47.619 0.00 0.00 0.00 4.40
2865 2998 1.337703 CACAAGGCAGCAACTTTAGCA 59.662 47.619 0.00 0.00 0.00 3.49
2866 2999 1.608590 TCACAAGGCAGCAACTTTAGC 59.391 47.619 0.00 0.00 0.00 3.09
2867 3000 2.030805 GGTCACAAGGCAGCAACTTTAG 60.031 50.000 0.00 0.00 0.00 1.85
2868 3001 1.953686 GGTCACAAGGCAGCAACTTTA 59.046 47.619 0.00 0.00 0.00 1.85
2869 3002 0.746659 GGTCACAAGGCAGCAACTTT 59.253 50.000 0.00 0.00 0.00 2.66
2870 3003 0.395586 TGGTCACAAGGCAGCAACTT 60.396 50.000 0.00 0.00 0.00 2.66
2871 3004 0.178981 ATGGTCACAAGGCAGCAACT 60.179 50.000 0.00 0.00 0.00 3.16
2872 3005 0.038892 CATGGTCACAAGGCAGCAAC 60.039 55.000 0.00 0.00 0.00 4.17
2873 3006 0.178995 TCATGGTCACAAGGCAGCAA 60.179 50.000 0.00 0.00 0.00 3.91
2874 3007 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2875 3008 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2876 3009 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2877 3010 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2888 3021 1.442769 CTTGAACCCGTGACCTCATG 58.557 55.000 0.00 0.00 0.00 3.07
2889 3022 0.321653 GCTTGAACCCGTGACCTCAT 60.322 55.000 0.00 0.00 0.00 2.90
2890 3023 1.070786 GCTTGAACCCGTGACCTCA 59.929 57.895 0.00 0.00 0.00 3.86
2891 3024 1.671379 GGCTTGAACCCGTGACCTC 60.671 63.158 0.00 0.00 0.00 3.85
2892 3025 2.430367 GGCTTGAACCCGTGACCT 59.570 61.111 0.00 0.00 0.00 3.85
2893 3026 2.671963 GGGCTTGAACCCGTGACC 60.672 66.667 0.00 0.00 40.98 4.02
2900 3033 0.961753 CTGTTTCCAGGGCTTGAACC 59.038 55.000 0.00 0.00 34.90 3.62
2901 3034 0.315251 GCTGTTTCCAGGGCTTGAAC 59.685 55.000 0.00 0.00 39.22 3.18
2902 3035 0.185901 AGCTGTTTCCAGGGCTTGAA 59.814 50.000 0.00 0.00 39.22 2.69
2903 3036 0.250901 GAGCTGTTTCCAGGGCTTGA 60.251 55.000 0.00 0.00 39.22 3.02
2904 3037 0.251077 AGAGCTGTTTCCAGGGCTTG 60.251 55.000 0.00 0.00 39.22 4.01
2905 3038 0.480252 AAGAGCTGTTTCCAGGGCTT 59.520 50.000 0.00 0.00 39.22 4.35
2906 3039 1.003696 GTAAGAGCTGTTTCCAGGGCT 59.996 52.381 0.00 0.00 39.22 5.19
2907 3040 1.271379 TGTAAGAGCTGTTTCCAGGGC 60.271 52.381 0.00 0.00 39.22 5.19
2908 3041 2.303022 TCTGTAAGAGCTGTTTCCAGGG 59.697 50.000 17.42 1.54 38.67 4.45
2909 3042 3.685139 TCTGTAAGAGCTGTTTCCAGG 57.315 47.619 17.42 5.30 38.67 4.45
2921 3054 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
2922 3055 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
2923 3056 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
2924 3057 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
2925 3058 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
2926 3059 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2927 3060 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2928 3061 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2929 3062 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2930 3063 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2931 3064 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2932 3065 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2933 3066 0.248289 TGTACGCAGCCTTTCCCTAC 59.752 55.000 0.00 0.00 0.00 3.18
2934 3067 0.978151 TTGTACGCAGCCTTTCCCTA 59.022 50.000 0.00 0.00 0.00 3.53
2935 3068 0.328258 ATTGTACGCAGCCTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
2936 3069 1.940613 CTATTGTACGCAGCCTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
2937 3070 2.608090 GTCTATTGTACGCAGCCTTTCC 59.392 50.000 0.00 0.00 0.00 3.13
2938 3071 2.608090 GGTCTATTGTACGCAGCCTTTC 59.392 50.000 0.00 0.00 0.00 2.62
2939 3072 2.629051 GGTCTATTGTACGCAGCCTTT 58.371 47.619 0.00 0.00 0.00 3.11
2940 3073 1.134491 GGGTCTATTGTACGCAGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
2941 3074 0.464452 GGGTCTATTGTACGCAGCCT 59.536 55.000 0.00 0.00 0.00 4.58
2942 3075 0.874607 CGGGTCTATTGTACGCAGCC 60.875 60.000 0.00 0.00 0.00 4.85
2943 3076 0.101759 TCGGGTCTATTGTACGCAGC 59.898 55.000 0.00 0.00 0.00 5.25
2944 3077 2.159282 ACTTCGGGTCTATTGTACGCAG 60.159 50.000 0.00 0.00 0.00 5.18
2945 3078 1.820519 ACTTCGGGTCTATTGTACGCA 59.179 47.619 0.00 0.00 0.00 5.24
2946 3079 2.190981 CACTTCGGGTCTATTGTACGC 58.809 52.381 0.00 0.00 0.00 4.42
2947 3080 2.165030 ACCACTTCGGGTCTATTGTACG 59.835 50.000 0.00 0.00 35.96 3.67
2948 3081 3.881937 ACCACTTCGGGTCTATTGTAC 57.118 47.619 0.00 0.00 35.96 2.90
2961 3094 1.295746 GGAAGGGTCCGACCACTTC 59.704 63.158 25.81 25.81 41.02 3.01
2962 3095 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2963 3096 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2964 3097 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
2987 3120 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2990 3123 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2991 3124 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2992 3125 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2993 3126 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2999 3132 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
3000 3133 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
3001 3134 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
3002 3135 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
3003 3136 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
3032 3165 9.086336 CAACTGAACAAACATGAACTAACAAAT 57.914 29.630 0.00 0.00 0.00 2.32
3033 3166 7.543868 CCAACTGAACAAACATGAACTAACAAA 59.456 33.333 0.00 0.00 0.00 2.83
3034 3167 7.032580 CCAACTGAACAAACATGAACTAACAA 58.967 34.615 0.00 0.00 0.00 2.83
3035 3168 6.151985 ACCAACTGAACAAACATGAACTAACA 59.848 34.615 0.00 0.00 0.00 2.41
3036 3169 6.560711 ACCAACTGAACAAACATGAACTAAC 58.439 36.000 0.00 0.00 0.00 2.34
3037 3170 6.767524 ACCAACTGAACAAACATGAACTAA 57.232 33.333 0.00 0.00 0.00 2.24
3038 3171 6.767524 AACCAACTGAACAAACATGAACTA 57.232 33.333 0.00 0.00 0.00 2.24
3039 3172 5.659440 AACCAACTGAACAAACATGAACT 57.341 34.783 0.00 0.00 0.00 3.01
3040 3173 6.560711 AGTAACCAACTGAACAAACATGAAC 58.439 36.000 0.00 0.00 36.93 3.18
3041 3174 6.767524 AGTAACCAACTGAACAAACATGAA 57.232 33.333 0.00 0.00 36.93 2.57
3042 3175 7.867305 TTAGTAACCAACTGAACAAACATGA 57.133 32.000 0.00 0.00 39.39 3.07
3043 3176 9.528018 AAATTAGTAACCAACTGAACAAACATG 57.472 29.630 0.00 0.00 39.39 3.21
3044 3177 9.528018 CAAATTAGTAACCAACTGAACAAACAT 57.472 29.630 0.00 0.00 39.39 2.71
3045 3178 8.524487 ACAAATTAGTAACCAACTGAACAAACA 58.476 29.630 0.00 0.00 39.39 2.83
3046 3179 8.920509 ACAAATTAGTAACCAACTGAACAAAC 57.079 30.769 0.00 0.00 39.39 2.93
3047 3180 9.360093 CAACAAATTAGTAACCAACTGAACAAA 57.640 29.630 0.00 0.00 39.39 2.83
3048 3181 8.740906 TCAACAAATTAGTAACCAACTGAACAA 58.259 29.630 0.00 0.00 39.39 2.83
3049 3182 8.282455 TCAACAAATTAGTAACCAACTGAACA 57.718 30.769 0.00 0.00 39.39 3.18
3050 3183 9.744468 ATTCAACAAATTAGTAACCAACTGAAC 57.256 29.630 0.00 0.00 39.39 3.18
3078 3211 8.482852 TTGGAACATGAGAGATGTCTGATATA 57.517 34.615 0.00 0.00 39.30 0.86
3079 3212 6.990908 TGGAACATGAGAGATGTCTGATAT 57.009 37.500 0.00 0.00 30.97 1.63
3128 3281 7.761704 TCACTTTTGCTTGCAAACTATTGTAAA 59.238 29.630 18.74 0.00 40.03 2.01
3135 3288 4.710423 TGTCACTTTTGCTTGCAAACTA 57.290 36.364 18.74 6.33 0.00 2.24
3141 3294 2.159114 TCCCTTTGTCACTTTTGCTTGC 60.159 45.455 0.00 0.00 0.00 4.01
3155 3308 6.349611 CCTTGTCACATGTAAATCTCCCTTTG 60.350 42.308 0.00 0.00 0.00 2.77
3160 3313 7.770897 AGTTATCCTTGTCACATGTAAATCTCC 59.229 37.037 0.00 0.00 0.00 3.71
3165 3318 8.321353 AGATCAGTTATCCTTGTCACATGTAAA 58.679 33.333 0.00 0.00 34.90 2.01
3166 3319 7.765819 CAGATCAGTTATCCTTGTCACATGTAA 59.234 37.037 0.00 0.00 34.90 2.41
3204 3357 5.413833 CACCTTGTTCATAGCTCAAGTGAAT 59.586 40.000 10.27 0.00 37.45 2.57
3209 3362 5.335191 GGTTTCACCTTGTTCATAGCTCAAG 60.335 44.000 5.36 5.36 38.45 3.02
3279 3434 6.751888 GGATGTAACATTTTGCAGGTCAATAC 59.248 38.462 0.00 0.00 34.12 1.89
3291 3446 8.352137 TGACAATGATGAGGATGTAACATTTT 57.648 30.769 0.00 0.00 0.00 1.82
3297 3452 9.112725 CTGTTTATGACAATGATGAGGATGTAA 57.887 33.333 0.00 0.00 37.93 2.41
3299 3454 6.039047 GCTGTTTATGACAATGATGAGGATGT 59.961 38.462 0.00 0.00 37.93 3.06
3300 3455 6.262496 AGCTGTTTATGACAATGATGAGGATG 59.738 38.462 0.00 0.00 37.93 3.51
3301 3456 6.363065 AGCTGTTTATGACAATGATGAGGAT 58.637 36.000 0.00 0.00 37.93 3.24
3302 3457 5.748402 AGCTGTTTATGACAATGATGAGGA 58.252 37.500 0.00 0.00 37.93 3.71
3303 3458 5.587443 TGAGCTGTTTATGACAATGATGAGG 59.413 40.000 0.00 0.00 37.93 3.86
3304 3459 6.315642 ACTGAGCTGTTTATGACAATGATGAG 59.684 38.462 0.00 0.00 37.93 2.90
3305 3460 6.175471 ACTGAGCTGTTTATGACAATGATGA 58.825 36.000 0.00 0.00 37.93 2.92
3312 3467 5.420725 ACCATACTGAGCTGTTTATGACA 57.579 39.130 0.00 0.00 36.65 3.58
3313 3468 6.255887 GTGTACCATACTGAGCTGTTTATGAC 59.744 42.308 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.