Multiple sequence alignment - TraesCS5B01G195800

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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 TraesCS5B01G195800 chr5B 100.000 3456 0 0 1 3456 353042520 353045975 0.000000e+00 6383
1 TraesCS5B01G195800 chr5B 88.482 1146 115 10 1293 2434 353920333 353921465 0.000000e+00 1369
2 TraesCS5B01G195800 chr5B 93.865 163 10 0 3282 3444 128803134 128802972 2.660000e-61 246
3 TraesCS5B01G195800 chr5D 94.054 2573 81 26 743 3287 308344272 308346800 0.000000e+00 3838
4 TraesCS5B01G195800 chr5D 88.821 1145 113 9 1293 2434 308626055 308627187 0.000000e+00 1391
5 TraesCS5B01G195800 chr5D 90.580 414 34 5 1 411 13344928 13344517 8.440000e-151 544
6 TraesCS5B01G195800 chr5A 93.673 2276 80 24 868 3107 389637493 389635246 0.000000e+00 3347
7 TraesCS5B01G195800 chr5A 85.835 1426 156 29 1043 2437 389167275 389165865 0.000000e+00 1472
8 TraesCS5B01G195800 chrUn 82.484 805 82 27 1 753 297242638 297241841 0.000000e+00 651
9 TraesCS5B01G195800 chrUn 81.463 793 90 22 3 742 75790321 75789533 6.380000e-167 597
10 TraesCS5B01G195800 chrUn 81.463 793 90 23 3 742 288475771 288474983 6.380000e-167 597
11 TraesCS5B01G195800 chrUn 85.748 421 47 7 3 411 84787390 84786971 1.910000e-117 433
12 TraesCS5B01G195800 chrUn 93.939 165 9 1 3281 3444 302184445 302184281 7.410000e-62 248
13 TraesCS5B01G195800 chr1B 82.560 797 82 23 1 742 638063405 638064199 0.000000e+00 649
14 TraesCS5B01G195800 chr1B 84.457 682 66 15 99 742 675592232 675592911 1.350000e-178 636
15 TraesCS5B01G195800 chr1B 95.706 163 7 0 3282 3444 349594162 349594324 2.650000e-66 263
16 TraesCS5B01G195800 chr1B 91.489 188 16 0 220 407 6504713 6504900 3.420000e-65 259
17 TraesCS5B01G195800 chr1B 93.865 163 10 0 3282 3444 3574572 3574734 2.660000e-61 246
18 TraesCS5B01G195800 chr1D 81.982 777 83 23 1 726 227113876 227114646 1.060000e-169 606
19 TraesCS5B01G195800 chr3D 81.193 771 105 23 1 746 563458297 563457542 4.970000e-163 584
20 TraesCS5B01G195800 chr6D 81.780 708 92 24 1 674 67688042 67688746 3.010000e-155 558
21 TraesCS5B01G195800 chr7A 80.711 788 88 25 1 741 44736704 44737474 3.900000e-154 555
22 TraesCS5B01G195800 chr7A 80.380 790 87 31 1 742 499581743 499580974 3.920000e-149 538
23 TraesCS5B01G195800 chr2B 86.364 418 44 7 1 406 772532697 772532281 8.800000e-121 444
24 TraesCS5B01G195800 chr2B 94.479 163 9 0 3282 3444 663491008 663491170 5.730000e-63 252
25 TraesCS5B01G195800 chr2B 84.328 268 28 9 1 256 146885241 146885506 2.060000e-62 250
26 TraesCS5B01G195800 chr7B 85.748 421 47 7 3 411 73291697 73291278 1.910000e-117 433
27 TraesCS5B01G195800 chr7B 94.479 163 9 0 3282 3444 330490903 330490741 5.730000e-63 252
28 TraesCS5B01G195800 chr7D 84.597 409 36 4 1 408 61292075 61292457 7.000000e-102 381
29 TraesCS5B01G195800 chr2D 82.068 474 45 15 315 751 548463864 548463394 5.450000e-98 368
30 TraesCS5B01G195800 chr2D 88.995 209 18 3 1 205 548464124 548463917 1.590000e-63 254
31 TraesCS5B01G195800 chr4D 84.483 348 35 9 409 742 489247846 489247504 3.330000e-85 326
32 TraesCS5B01G195800 chr6B 83.908 348 42 6 409 742 650056238 650055891 1.550000e-83 320
33 TraesCS5B01G195800 chr6B 93.373 166 11 0 3279 3444 189566232 189566397 2.660000e-61 246
34 TraesCS5B01G195800 chr3B 84.790 309 36 5 111 408 226782947 226783255 2.020000e-77 300
35 TraesCS5B01G195800 chr3B 94.937 158 8 0 3287 3444 216967134 216966977 7.410000e-62 248
36 TraesCS5B01G195800 chr4B 93.902 164 10 0 3281 3444 10744313 10744476 7.410000e-62 248


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 TraesCS5B01G195800 chr5B 353042520 353045975 3455 False 6383 6383 100.0000 1 3456 1 chr5B.!!$F1 3455
1 TraesCS5B01G195800 chr5B 353920333 353921465 1132 False 1369 1369 88.4820 1293 2434 1 chr5B.!!$F2 1141
2 TraesCS5B01G195800 chr5D 308344272 308346800 2528 False 3838 3838 94.0540 743 3287 1 chr5D.!!$F1 2544
3 TraesCS5B01G195800 chr5D 308626055 308627187 1132 False 1391 1391 88.8210 1293 2434 1 chr5D.!!$F2 1141
4 TraesCS5B01G195800 chr5A 389635246 389637493 2247 True 3347 3347 93.6730 868 3107 1 chr5A.!!$R2 2239
5 TraesCS5B01G195800 chr5A 389165865 389167275 1410 True 1472 1472 85.8350 1043 2437 1 chr5A.!!$R1 1394
6 TraesCS5B01G195800 chrUn 297241841 297242638 797 True 651 651 82.4840 1 753 1 chrUn.!!$R4 752
7 TraesCS5B01G195800 chrUn 75789533 75790321 788 True 597 597 81.4630 3 742 1 chrUn.!!$R1 739
8 TraesCS5B01G195800 chrUn 288474983 288475771 788 True 597 597 81.4630 3 742 1 chrUn.!!$R3 739
9 TraesCS5B01G195800 chr1B 638063405 638064199 794 False 649 649 82.5600 1 742 1 chr1B.!!$F4 741
10 TraesCS5B01G195800 chr1B 675592232 675592911 679 False 636 636 84.4570 99 742 1 chr1B.!!$F5 643
11 TraesCS5B01G195800 chr1D 227113876 227114646 770 False 606 606 81.9820 1 726 1 chr1D.!!$F1 725
12 TraesCS5B01G195800 chr3D 563457542 563458297 755 True 584 584 81.1930 1 746 1 chr3D.!!$R1 745
13 TraesCS5B01G195800 chr6D 67688042 67688746 704 False 558 558 81.7800 1 674 1 chr6D.!!$F1 673
14 TraesCS5B01G195800 chr7A 44736704 44737474 770 False 555 555 80.7110 1 741 1 chr7A.!!$F1 740
15 TraesCS5B01G195800 chr7A 499580974 499581743 769 True 538 538 80.3800 1 742 1 chr7A.!!$R1 741
16 TraesCS5B01G195800 chr2D 548463394 548464124 730 True 311 368 85.5315 1 751 2 chr2D.!!$R1 750

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
794 854 0.107703 AATGCTCGGGATTCTCGCAA 60.108 50.0 0.0 0.0 33.94 4.85 F
960 1032 0.745845 CCCCATTCCTCTCAGCAACG 60.746 60.0 0.0 0.0 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 1989 0.100682 CGTGCTCGTAGTACATGGCT 59.899 55.0 0.00 0.00 29.68 4.75 R
2793 2920 0.178987 ACTAGGATCGATCTGCGGGT 60.179 55.0 23.96 13.03 41.33 5.28 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
61 62 4.163078 TCTCTTGATCTCCAAATCTCACCC 59.837 45.833 0.00 0.00 33.76 4.61
82 84 5.721000 ACCCATCAGCCAATTGAAAGAATAA 59.279 36.000 7.12 0.00 0.00 1.40
163 165 3.728373 GGGCTGGACGAATGGGGT 61.728 66.667 0.00 0.00 0.00 4.95
169 171 2.034999 GACGAATGGGGTTGGCCA 59.965 61.111 0.00 0.00 36.17 5.36
171 173 0.970427 GACGAATGGGGTTGGCCATT 60.970 55.000 6.09 0.00 39.05 3.16
208 213 4.143333 CAGTCCCGCAGTACCCCG 62.143 72.222 0.00 0.00 0.00 5.73
215 220 2.345991 GCAGTACCCCGTCAGCAA 59.654 61.111 0.00 0.00 0.00 3.91
241 259 2.551721 CCTTCGGATTAGATGCATGGCT 60.552 50.000 2.46 0.00 0.00 4.75
256 274 1.086696 TGGCTAGATCAAAGTTGCGC 58.913 50.000 0.00 0.00 0.00 6.09
262 280 0.810648 GATCAAAGTTGCGCCCATGA 59.189 50.000 4.18 2.70 0.00 3.07
265 283 1.599518 AAAGTTGCGCCCATGACGA 60.600 52.632 4.18 0.00 0.00 4.20
296 314 1.757682 AGAGGACGCAAACAACCAAA 58.242 45.000 0.00 0.00 0.00 3.28
299 317 2.028130 AGGACGCAAACAACCAAATGA 58.972 42.857 0.00 0.00 0.00 2.57
311 329 3.039252 ACCAAATGAGGTGTGGGAAAA 57.961 42.857 0.00 0.00 41.30 2.29
313 331 3.973305 ACCAAATGAGGTGTGGGAAAAAT 59.027 39.130 0.00 0.00 41.30 1.82
382 400 1.823899 GGGATGGCGCCGAATCTTT 60.824 57.895 23.90 0.00 0.00 2.52
388 406 3.124921 CGCCGAATCTTTGCCGGT 61.125 61.111 1.90 0.00 44.63 5.28
498 542 0.462047 CTGCCGGCGAGGAGTAAAAT 60.462 55.000 23.90 0.00 45.00 1.82
556 602 7.551617 ACGGGATAAAATCGAACTGAAAATACT 59.448 33.333 0.00 0.00 0.00 2.12
594 640 6.039382 ACCGAGAATACCCTTCAAATATTTGC 59.961 38.462 21.15 6.04 38.05 3.68
595 641 6.263168 CCGAGAATACCCTTCAAATATTTGCT 59.737 38.462 21.15 10.29 38.05 3.91
650 698 2.859165 TCTGAAAATGCCCTTCGACT 57.141 45.000 0.00 0.00 0.00 4.18
652 700 3.486383 TCTGAAAATGCCCTTCGACTTT 58.514 40.909 0.00 0.00 0.00 2.66
654 702 5.067273 TCTGAAAATGCCCTTCGACTTTTA 58.933 37.500 0.00 0.00 0.00 1.52
717 777 2.967397 GACGGACGGTCCACATCA 59.033 61.111 25.80 0.00 39.90 3.07
736 796 1.396996 CAACCGGATGGAGCGTAAAAG 59.603 52.381 9.46 0.00 39.21 2.27
794 854 0.107703 AATGCTCGGGATTCTCGCAA 60.108 50.000 0.00 0.00 33.94 4.85
799 859 1.929836 CTCGGGATTCTCGCAAAGAAG 59.070 52.381 0.00 0.00 46.95 2.85
800 860 1.548719 TCGGGATTCTCGCAAAGAAGA 59.451 47.619 0.00 0.00 46.95 2.87
801 861 2.028476 TCGGGATTCTCGCAAAGAAGAA 60.028 45.455 0.00 0.00 46.95 2.52
802 862 2.094417 CGGGATTCTCGCAAAGAAGAAC 59.906 50.000 0.00 0.45 46.95 3.01
803 863 3.339141 GGGATTCTCGCAAAGAAGAACT 58.661 45.455 4.98 0.00 46.95 3.01
804 864 4.504858 GGGATTCTCGCAAAGAAGAACTA 58.495 43.478 4.98 0.00 46.95 2.24
805 865 5.119694 GGGATTCTCGCAAAGAAGAACTAT 58.880 41.667 4.98 0.00 46.95 2.12
808 868 6.481644 GGATTCTCGCAAAGAAGAACTATGAT 59.518 38.462 4.98 0.00 46.95 2.45
820 880 8.879342 AGAAGAACTATGATTTATGAAGACGG 57.121 34.615 0.00 0.00 0.00 4.79
832 892 3.014304 TGAAGACGGTATACTCCTGCT 57.986 47.619 2.25 0.00 0.00 4.24
839 899 2.891580 CGGTATACTCCTGCTGGTACAT 59.108 50.000 9.73 4.08 38.20 2.29
840 900 3.321111 CGGTATACTCCTGCTGGTACATT 59.679 47.826 9.73 0.00 38.20 2.71
841 901 4.558898 CGGTATACTCCTGCTGGTACATTC 60.559 50.000 9.73 0.09 38.20 2.67
842 902 4.344102 GGTATACTCCTGCTGGTACATTCA 59.656 45.833 9.73 0.00 38.20 2.57
843 903 5.163343 GGTATACTCCTGCTGGTACATTCAA 60.163 44.000 9.73 0.00 38.20 2.69
844 904 3.340814 ACTCCTGCTGGTACATTCAAG 57.659 47.619 9.73 0.00 38.20 3.02
845 905 2.639839 ACTCCTGCTGGTACATTCAAGT 59.360 45.455 9.73 0.15 38.20 3.16
846 906 3.838317 ACTCCTGCTGGTACATTCAAGTA 59.162 43.478 9.73 0.00 38.20 2.24
847 907 4.184629 CTCCTGCTGGTACATTCAAGTAC 58.815 47.826 9.73 0.00 42.78 2.73
859 919 8.732746 GTACATTCAAGTACCTCATTTGGTAT 57.267 34.615 0.00 0.00 43.54 2.73
860 920 9.826574 GTACATTCAAGTACCTCATTTGGTATA 57.173 33.333 0.00 0.00 43.54 1.47
862 922 9.920946 ACATTCAAGTACCTCATTTGGTATAAT 57.079 29.630 0.00 0.00 43.54 1.28
922 984 4.081642 TCTCCTCCATTTGGAAACTAGTCG 60.082 45.833 0.00 0.00 44.91 4.18
955 1027 0.984961 TGAGCCCCCATTCCTCTCAG 60.985 60.000 0.00 0.00 31.07 3.35
960 1032 0.745845 CCCCATTCCTCTCAGCAACG 60.746 60.000 0.00 0.00 0.00 4.10
1119 1194 1.716826 CTCTCGCCGTCCTCCACTAC 61.717 65.000 0.00 0.00 0.00 2.73
1120 1195 2.753043 TCGCCGTCCTCCACTACC 60.753 66.667 0.00 0.00 0.00 3.18
1121 1196 2.754658 CGCCGTCCTCCACTACCT 60.755 66.667 0.00 0.00 0.00 3.08
1870 1989 1.902918 GCACTGGTTCATGCACCCA 60.903 57.895 12.25 4.99 41.65 4.51
1957 2076 2.258726 GGGCTTCTTCGGCGTGTTT 61.259 57.895 6.85 0.00 0.00 2.83
2038 2157 1.078143 GGAGAAGCTGGCGATGGTT 60.078 57.895 0.00 0.00 0.00 3.67
2302 2421 0.319083 ACATGAACGCGTCCCTGTTA 59.681 50.000 14.44 0.00 0.00 2.41
2412 2531 0.180642 ATCCTGCTGCAGATGGTCAG 59.819 55.000 30.10 14.35 32.44 3.51
2422 2541 1.596477 GATGGTCAGGCGATGGAGC 60.596 63.158 0.00 0.00 0.00 4.70
2444 2566 3.522731 CCTCCTCGTCGGCCAGAG 61.523 72.222 2.24 8.28 0.00 3.35
2448 2570 4.159266 CTCGTCGGCCAGAGGATA 57.841 61.111 16.48 1.31 42.14 2.59
2461 2583 3.429547 CCAGAGGATACCACTGAAACTCG 60.430 52.174 14.76 0.00 41.88 4.18
2524 2651 8.618952 CATTCGAAAAACTGAAACGAAAGATAC 58.381 33.333 0.00 0.00 43.89 2.24
2532 2659 9.665264 AAACTGAAACGAAAGATACAGAAATTC 57.335 29.630 0.00 0.00 34.33 2.17
2548 2675 6.597672 ACAGAAATTCCGCATATGTTTGTAGA 59.402 34.615 4.29 0.00 0.00 2.59
2602 2729 0.675633 ATTCTGTGCTTGGTTGGTGC 59.324 50.000 0.00 0.00 0.00 5.01
2648 2775 2.125512 GGCGACAAGGCTCGTGAT 60.126 61.111 0.00 0.00 42.90 3.06
2655 2782 2.707849 AAGGCTCGTGATACGGCGT 61.708 57.895 19.64 19.64 42.81 5.68
2684 2811 4.814294 CGTGGGGAGGTGTAGCGC 62.814 72.222 0.00 0.00 0.00 5.92
2685 2812 4.814294 GTGGGGAGGTGTAGCGCG 62.814 72.222 0.00 0.00 0.00 6.86
2692 2819 3.350612 GGTGTAGCGCGGTTTGCA 61.351 61.111 19.09 11.02 46.97 4.08
2711 2838 5.224821 TGCATTTTCCATTCCATTCAACA 57.775 34.783 0.00 0.00 0.00 3.33
2769 2896 0.728542 TCGCAAGAGTACGACGCATA 59.271 50.000 0.00 0.00 45.01 3.14
2788 2915 0.971959 AGAGAGAGTGGCAGGAGCAG 60.972 60.000 0.00 0.00 44.61 4.24
2789 2916 1.958902 GAGAGAGTGGCAGGAGCAGG 61.959 65.000 0.00 0.00 44.61 4.85
2790 2917 2.203907 AGAGTGGCAGGAGCAGGT 60.204 61.111 0.00 0.00 44.61 4.00
2791 2918 0.972983 GAGAGTGGCAGGAGCAGGTA 60.973 60.000 0.00 0.00 44.61 3.08
2792 2919 1.219393 GAGTGGCAGGAGCAGGTAC 59.781 63.158 0.00 0.00 44.61 3.34
2793 2920 1.536418 AGTGGCAGGAGCAGGTACA 60.536 57.895 0.00 0.00 44.61 2.90
2794 2921 1.376037 GTGGCAGGAGCAGGTACAC 60.376 63.158 0.00 0.00 44.61 2.90
2795 2922 2.269241 GGCAGGAGCAGGTACACC 59.731 66.667 0.00 0.00 44.61 4.16
2796 2923 2.269241 GCAGGAGCAGGTACACCC 59.731 66.667 0.00 0.00 41.58 4.61
2797 2924 2.579201 CAGGAGCAGGTACACCCG 59.421 66.667 0.00 0.00 38.74 5.28
2798 2925 3.391382 AGGAGCAGGTACACCCGC 61.391 66.667 0.00 0.00 38.74 6.13
2799 2926 3.702048 GGAGCAGGTACACCCGCA 61.702 66.667 9.21 0.00 38.74 5.69
2812 2939 0.178987 ACCCGCAGATCGATCCTAGT 60.179 55.000 21.66 9.67 41.67 2.57
2813 2940 0.242286 CCCGCAGATCGATCCTAGTG 59.758 60.000 21.66 16.93 41.67 2.74
2821 2948 1.109920 TCGATCCTAGTGAGCCAGGC 61.110 60.000 1.84 1.84 0.00 4.85
2931 3058 2.316792 CGACAGTGTTCAAGGAGTACG 58.683 52.381 0.00 0.00 0.00 3.67
2932 3059 2.059541 GACAGTGTTCAAGGAGTACGC 58.940 52.381 0.00 0.00 0.00 4.42
2933 3060 1.411246 ACAGTGTTCAAGGAGTACGCA 59.589 47.619 0.00 0.00 31.27 5.24
2934 3061 2.061773 CAGTGTTCAAGGAGTACGCAG 58.938 52.381 0.00 0.00 31.27 5.18
2936 3063 2.102588 AGTGTTCAAGGAGTACGCAGTT 59.897 45.455 0.00 0.00 37.78 3.16
3043 3181 1.536766 ACAATCACCGACAGTGCATTG 59.463 47.619 7.79 7.79 46.81 2.82
3046 3184 0.817229 TCACCGACAGTGCATTGCAA 60.817 50.000 13.94 0.00 46.81 4.08
3080 3218 1.849039 AGGTTCCAGATTCCCCTGATG 59.151 52.381 0.00 0.00 36.29 3.07
3137 3275 4.580868 TGTCGTATGATGCCCTTGTTAAA 58.419 39.130 0.00 0.00 0.00 1.52
3258 3399 1.608025 CCACGTGAGAGGCAAGCTTTA 60.608 52.381 19.30 0.00 34.36 1.85
3265 3406 5.967674 CGTGAGAGGCAAGCTTTAAAATATG 59.032 40.000 0.00 0.00 0.00 1.78
3269 3410 7.176515 TGAGAGGCAAGCTTTAAAATATGACAA 59.823 33.333 0.00 0.00 0.00 3.18
3271 3412 7.177392 AGAGGCAAGCTTTAAAATATGACAACT 59.823 33.333 0.00 0.00 0.00 3.16
3272 3413 7.670364 AGGCAAGCTTTAAAATATGACAACTT 58.330 30.769 0.00 0.00 0.00 2.66
3288 3429 7.539712 TGACAACTTTTTCAGACTTAGACTG 57.460 36.000 5.40 5.40 36.80 3.51
3289 3430 6.538742 TGACAACTTTTTCAGACTTAGACTGG 59.461 38.462 11.31 0.00 36.22 4.00
3290 3431 6.415573 ACAACTTTTTCAGACTTAGACTGGT 58.584 36.000 11.31 0.00 36.22 4.00
3291 3432 6.539103 ACAACTTTTTCAGACTTAGACTGGTC 59.461 38.462 11.31 3.21 36.22 4.02
3292 3433 6.235231 ACTTTTTCAGACTTAGACTGGTCA 57.765 37.500 11.31 0.00 36.22 4.02
3293 3434 6.831976 ACTTTTTCAGACTTAGACTGGTCAT 58.168 36.000 11.31 0.00 36.22 3.06
3294 3435 7.963532 ACTTTTTCAGACTTAGACTGGTCATA 58.036 34.615 11.31 0.00 36.22 2.15
3295 3436 8.091449 ACTTTTTCAGACTTAGACTGGTCATAG 58.909 37.037 11.31 6.19 36.22 2.23
3296 3437 7.540474 TTTTCAGACTTAGACTGGTCATAGT 57.460 36.000 11.31 5.67 36.22 2.12
3297 3438 6.516739 TTCAGACTTAGACTGGTCATAGTG 57.483 41.667 11.31 3.52 36.22 2.74
3298 3439 4.950475 TCAGACTTAGACTGGTCATAGTGG 59.050 45.833 11.31 5.48 36.22 4.00
3299 3440 4.098654 CAGACTTAGACTGGTCATAGTGGG 59.901 50.000 3.88 2.55 35.18 4.61
3300 3441 3.375699 ACTTAGACTGGTCATAGTGGGG 58.624 50.000 3.51 0.00 0.00 4.96
3301 3442 3.012502 ACTTAGACTGGTCATAGTGGGGA 59.987 47.826 3.51 0.00 0.00 4.81
3302 3443 2.166907 AGACTGGTCATAGTGGGGAG 57.833 55.000 3.51 0.00 0.00 4.30
3303 3444 1.362932 AGACTGGTCATAGTGGGGAGT 59.637 52.381 3.51 0.00 0.00 3.85
3304 3445 2.585900 AGACTGGTCATAGTGGGGAGTA 59.414 50.000 3.51 0.00 0.00 2.59
3305 3446 3.012502 AGACTGGTCATAGTGGGGAGTAA 59.987 47.826 3.51 0.00 0.00 2.24
3306 3447 3.105283 ACTGGTCATAGTGGGGAGTAAC 58.895 50.000 0.00 0.00 0.00 2.50
3307 3448 3.246021 ACTGGTCATAGTGGGGAGTAACT 60.246 47.826 0.00 0.00 0.00 2.24
3308 3449 3.775316 CTGGTCATAGTGGGGAGTAACTT 59.225 47.826 0.00 0.00 0.00 2.66
3309 3450 4.950361 TGGTCATAGTGGGGAGTAACTTA 58.050 43.478 0.00 0.00 0.00 2.24
3310 3451 4.960469 TGGTCATAGTGGGGAGTAACTTAG 59.040 45.833 0.00 0.00 0.00 2.18
3311 3452 5.206587 GGTCATAGTGGGGAGTAACTTAGA 58.793 45.833 0.00 0.00 0.00 2.10
3312 3453 5.302313 GGTCATAGTGGGGAGTAACTTAGAG 59.698 48.000 0.00 0.00 0.00 2.43
3313 3454 5.892686 GTCATAGTGGGGAGTAACTTAGAGT 59.107 44.000 0.00 0.00 0.00 3.24
3314 3455 7.059156 GTCATAGTGGGGAGTAACTTAGAGTA 58.941 42.308 0.00 0.00 0.00 2.59
3315 3456 7.229106 GTCATAGTGGGGAGTAACTTAGAGTAG 59.771 44.444 0.00 0.00 0.00 2.57
3316 3457 5.533333 AGTGGGGAGTAACTTAGAGTAGT 57.467 43.478 0.00 0.00 0.00 2.73
3317 3458 6.649041 AGTGGGGAGTAACTTAGAGTAGTA 57.351 41.667 0.00 0.00 0.00 1.82
3318 3459 7.037342 AGTGGGGAGTAACTTAGAGTAGTAA 57.963 40.000 0.00 0.00 0.00 2.24
3319 3460 6.889177 AGTGGGGAGTAACTTAGAGTAGTAAC 59.111 42.308 0.00 0.00 0.00 2.50
3320 3461 6.660949 GTGGGGAGTAACTTAGAGTAGTAACA 59.339 42.308 0.00 0.00 0.00 2.41
3321 3462 7.341512 GTGGGGAGTAACTTAGAGTAGTAACAT 59.658 40.741 0.00 0.00 0.00 2.71
3322 3463 7.341256 TGGGGAGTAACTTAGAGTAGTAACATG 59.659 40.741 0.00 0.00 0.00 3.21
3323 3464 7.201835 GGGAGTAACTTAGAGTAGTAACATGC 58.798 42.308 0.00 0.00 0.00 4.06
3324 3465 7.147949 GGGAGTAACTTAGAGTAGTAACATGCA 60.148 40.741 0.00 0.00 0.00 3.96
3325 3466 8.414778 GGAGTAACTTAGAGTAGTAACATGCAT 58.585 37.037 0.00 0.00 0.00 3.96
3335 3476 7.707035 AGAGTAGTAACATGCATACTTTACTGC 59.293 37.037 24.48 23.36 37.40 4.40
3336 3477 7.556844 AGTAGTAACATGCATACTTTACTGCT 58.443 34.615 24.53 24.53 40.51 4.24
3337 3478 6.910536 AGTAACATGCATACTTTACTGCTC 57.089 37.500 19.39 1.43 39.16 4.26
3338 3479 6.644347 AGTAACATGCATACTTTACTGCTCT 58.356 36.000 19.39 3.73 39.16 4.09
3339 3480 7.782049 AGTAACATGCATACTTTACTGCTCTA 58.218 34.615 19.39 0.00 39.16 2.43
3340 3481 8.424918 AGTAACATGCATACTTTACTGCTCTAT 58.575 33.333 19.39 2.72 39.16 1.98
3341 3482 7.488187 AACATGCATACTTTACTGCTCTATG 57.512 36.000 0.00 0.00 39.16 2.23
3342 3483 6.586344 ACATGCATACTTTACTGCTCTATGT 58.414 36.000 0.00 0.00 39.16 2.29
3343 3484 7.050377 ACATGCATACTTTACTGCTCTATGTT 58.950 34.615 0.00 0.00 39.16 2.71
3344 3485 8.204160 ACATGCATACTTTACTGCTCTATGTTA 58.796 33.333 0.00 0.00 39.16 2.41
3345 3486 8.491152 CATGCATACTTTACTGCTCTATGTTAC 58.509 37.037 0.00 0.00 39.16 2.50
3346 3487 7.782049 TGCATACTTTACTGCTCTATGTTACT 58.218 34.615 0.00 0.00 39.16 2.24
3347 3488 8.909923 TGCATACTTTACTGCTCTATGTTACTA 58.090 33.333 0.00 0.00 39.16 1.82
3348 3489 9.182933 GCATACTTTACTGCTCTATGTTACTAC 57.817 37.037 0.00 0.00 35.49 2.73
3349 3490 9.680315 CATACTTTACTGCTCTATGTTACTACC 57.320 37.037 0.00 0.00 0.00 3.18
3350 3491 7.110043 ACTTTACTGCTCTATGTTACTACCC 57.890 40.000 0.00 0.00 0.00 3.69
3351 3492 6.896307 ACTTTACTGCTCTATGTTACTACCCT 59.104 38.462 0.00 0.00 0.00 4.34
3352 3493 7.399478 ACTTTACTGCTCTATGTTACTACCCTT 59.601 37.037 0.00 0.00 0.00 3.95
3353 3494 8.827832 TTTACTGCTCTATGTTACTACCCTTA 57.172 34.615 0.00 0.00 0.00 2.69
3354 3495 9.430399 TTTACTGCTCTATGTTACTACCCTTAT 57.570 33.333 0.00 0.00 0.00 1.73
3356 3497 8.638629 ACTGCTCTATGTTACTACCCTTATAG 57.361 38.462 0.00 0.00 0.00 1.31
3357 3498 8.226112 ACTGCTCTATGTTACTACCCTTATAGT 58.774 37.037 0.00 0.00 38.89 2.12
3358 3499 8.405418 TGCTCTATGTTACTACCCTTATAGTG 57.595 38.462 0.00 0.00 36.09 2.74
3359 3500 7.450634 TGCTCTATGTTACTACCCTTATAGTGG 59.549 40.741 0.00 0.00 36.09 4.00
3375 3516 8.816894 CCTTATAGTGGGAAGTGTCATATATGT 58.183 37.037 12.42 0.00 0.00 2.29
3378 3519 8.958060 ATAGTGGGAAGTGTCATATATGTAGT 57.042 34.615 12.42 3.89 0.00 2.73
3380 3521 8.777578 AGTGGGAAGTGTCATATATGTAGTAA 57.222 34.615 12.42 0.00 0.00 2.24
3381 3522 9.381038 AGTGGGAAGTGTCATATATGTAGTAAT 57.619 33.333 12.42 0.00 0.00 1.89
3410 3551 9.836864 ACATATGCTCATTTATTGTCTTGTAGA 57.163 29.630 1.58 0.00 0.00 2.59
3413 3554 7.834068 TGCTCATTTATTGTCTTGTAGACTC 57.166 36.000 8.18 0.00 45.27 3.36
3414 3555 7.386059 TGCTCATTTATTGTCTTGTAGACTCA 58.614 34.615 8.18 0.00 45.27 3.41
3415 3556 8.043113 TGCTCATTTATTGTCTTGTAGACTCAT 58.957 33.333 8.18 3.68 45.27 2.90
3416 3557 8.887717 GCTCATTTATTGTCTTGTAGACTCATT 58.112 33.333 8.18 0.00 45.27 2.57
3432 3573 9.159470 GTAGACTCATTTTATATTGAAAAGCGC 57.841 33.333 0.00 0.00 32.06 5.92
3433 3574 7.989826 AGACTCATTTTATATTGAAAAGCGCT 58.010 30.769 2.64 2.64 32.06 5.92
3434 3575 9.109393 AGACTCATTTTATATTGAAAAGCGCTA 57.891 29.630 12.05 0.00 32.06 4.26
3435 3576 9.884465 GACTCATTTTATATTGAAAAGCGCTAT 57.116 29.630 12.05 1.76 32.06 2.97
3436 3577 9.669353 ACTCATTTTATATTGAAAAGCGCTATG 57.331 29.630 12.05 5.94 32.06 2.23
3437 3578 9.669353 CTCATTTTATATTGAAAAGCGCTATGT 57.331 29.630 12.05 0.12 32.06 2.29
3438 3579 9.449550 TCATTTTATATTGAAAAGCGCTATGTG 57.550 29.630 12.05 0.00 32.06 3.21
3439 3580 9.449550 CATTTTATATTGAAAAGCGCTATGTGA 57.550 29.630 12.05 0.00 32.06 3.58
3441 3582 9.449550 TTTTATATTGAAAAGCGCTATGTGATG 57.550 29.630 12.05 0.00 0.00 3.07
3442 3583 3.763097 TTGAAAAGCGCTATGTGATGG 57.237 42.857 12.05 0.00 0.00 3.51
3443 3584 2.710377 TGAAAAGCGCTATGTGATGGT 58.290 42.857 12.05 0.00 0.00 3.55
3444 3585 2.419673 TGAAAAGCGCTATGTGATGGTG 59.580 45.455 12.05 0.00 0.00 4.17
3445 3586 0.734889 AAAGCGCTATGTGATGGTGC 59.265 50.000 12.05 0.00 46.05 5.01
3447 3588 2.173669 GCGCTATGTGATGGTGCGT 61.174 57.895 0.00 0.00 46.94 5.24
3448 3589 1.927210 CGCTATGTGATGGTGCGTC 59.073 57.895 0.00 0.00 41.45 5.19
3449 3590 0.528466 CGCTATGTGATGGTGCGTCT 60.528 55.000 0.00 0.00 41.45 4.18
3450 3591 1.656652 GCTATGTGATGGTGCGTCTT 58.343 50.000 0.00 0.00 0.00 3.01
3451 3592 2.009774 GCTATGTGATGGTGCGTCTTT 58.990 47.619 0.00 0.00 0.00 2.52
3452 3593 2.223112 GCTATGTGATGGTGCGTCTTTG 60.223 50.000 0.00 0.00 0.00 2.77
3453 3594 2.183478 ATGTGATGGTGCGTCTTTGA 57.817 45.000 0.00 0.00 0.00 2.69
3454 3595 2.183478 TGTGATGGTGCGTCTTTGAT 57.817 45.000 0.00 0.00 0.00 2.57
3455 3596 2.503331 TGTGATGGTGCGTCTTTGATT 58.497 42.857 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.775854 GATTTGGAGATCAAGAGAGATGATAAA 57.224 33.333 0.00 0.00 37.64 1.40
41 42 4.226427 TGGGTGAGATTTGGAGATCAAG 57.774 45.455 0.00 0.00 36.62 3.02
61 62 8.712285 ACATTTATTCTTTCAATTGGCTGATG 57.288 30.769 5.42 1.75 0.00 3.07
117 119 7.066766 ACTGCAAGATCTATGAAAGTTCAATCC 59.933 37.037 0.00 0.00 37.94 3.01
126 128 3.432186 CCCCGACTGCAAGATCTATGAAA 60.432 47.826 0.00 0.00 37.43 2.69
179 181 2.367202 GGGACTGGATGAAGCCGGA 61.367 63.158 5.05 0.00 37.74 5.14
208 213 2.383527 CCGAAGGCTCGTTGCTGAC 61.384 63.158 0.00 0.00 46.14 3.51
228 246 5.933617 ACTTTGATCTAGCCATGCATCTAA 58.066 37.500 0.00 0.00 0.00 2.10
229 247 5.557576 ACTTTGATCTAGCCATGCATCTA 57.442 39.130 0.00 0.00 0.00 1.98
241 259 2.016318 CATGGGCGCAACTTTGATCTA 58.984 47.619 10.83 0.00 0.00 1.98
256 274 1.208052 ACATCACCTCTTCGTCATGGG 59.792 52.381 0.00 0.00 0.00 4.00
262 280 3.018149 GTCCTCTACATCACCTCTTCGT 58.982 50.000 0.00 0.00 0.00 3.85
265 283 1.751924 GCGTCCTCTACATCACCTCTT 59.248 52.381 0.00 0.00 0.00 2.85
296 314 3.244181 GCAACATTTTTCCCACACCTCAT 60.244 43.478 0.00 0.00 0.00 2.90
299 317 1.416030 GGCAACATTTTTCCCACACCT 59.584 47.619 0.00 0.00 0.00 4.00
311 329 3.447229 GCCACAAGGTTATAGGCAACATT 59.553 43.478 0.00 0.00 44.59 2.71
313 331 2.442413 GCCACAAGGTTATAGGCAACA 58.558 47.619 0.00 0.00 44.59 3.33
398 416 0.786435 ACCTTTTCAATGCCCTCCCT 59.214 50.000 0.00 0.00 0.00 4.20
498 542 0.325296 ATTCCTCGCCACCACTAGGA 60.325 55.000 0.00 0.00 38.69 2.94
507 551 1.140252 GCTAGGGTTTATTCCTCGCCA 59.860 52.381 0.00 0.00 37.19 5.69
594 640 6.509418 TTGAACCGATCAAATTTTCCCTAG 57.491 37.500 1.71 0.00 44.94 3.02
628 676 3.074412 GTCGAAGGGCATTTTCAGAAGA 58.926 45.455 0.00 0.00 0.00 2.87
633 681 5.776173 TTAAAAGTCGAAGGGCATTTTCA 57.224 34.783 0.00 0.00 0.00 2.69
674 722 3.742327 GCTGATTCGATGGTCCAGATTCA 60.742 47.826 0.00 2.11 0.00 2.57
717 777 1.677820 CCTTTTACGCTCCATCCGGTT 60.678 52.381 0.00 0.00 0.00 4.44
728 788 9.786105 GACTATATTATAGGAGTCCTTTTACGC 57.214 37.037 19.06 0.00 34.61 4.42
794 854 9.319143 CCGTCTTCATAAATCATAGTTCTTCTT 57.681 33.333 0.00 0.00 0.00 2.52
802 862 9.790389 GGAGTATACCGTCTTCATAAATCATAG 57.210 37.037 0.00 0.00 0.00 2.23
803 863 9.529823 AGGAGTATACCGTCTTCATAAATCATA 57.470 33.333 0.00 0.00 34.73 2.15
804 864 8.307483 CAGGAGTATACCGTCTTCATAAATCAT 58.693 37.037 0.00 0.00 34.73 2.45
805 865 7.658261 CAGGAGTATACCGTCTTCATAAATCA 58.342 38.462 0.00 0.00 34.73 2.57
808 868 5.597182 AGCAGGAGTATACCGTCTTCATAAA 59.403 40.000 0.00 0.00 34.73 1.40
820 880 5.531122 TGAATGTACCAGCAGGAGTATAC 57.469 43.478 0.35 0.00 38.69 1.47
844 904 9.798994 CGGAGTATATTATACCAAATGAGGTAC 57.201 37.037 9.70 0.00 46.29 3.34
846 906 8.660295 TCGGAGTATATTATACCAAATGAGGT 57.340 34.615 9.70 0.00 45.72 3.85
847 907 9.751542 GATCGGAGTATATTATACCAAATGAGG 57.248 37.037 9.70 0.00 0.00 3.86
854 914 9.562408 GAGATGAGATCGGAGTATATTATACCA 57.438 37.037 9.70 0.45 0.00 3.25
855 915 9.005777 GGAGATGAGATCGGAGTATATTATACC 57.994 40.741 9.70 3.00 0.00 2.73
856 916 9.562408 TGGAGATGAGATCGGAGTATATTATAC 57.438 37.037 5.81 5.81 0.00 1.47
857 917 9.562408 GTGGAGATGAGATCGGAGTATATTATA 57.438 37.037 0.00 0.00 0.00 0.98
858 918 8.278639 AGTGGAGATGAGATCGGAGTATATTAT 58.721 37.037 0.00 0.00 0.00 1.28
859 919 7.634718 AGTGGAGATGAGATCGGAGTATATTA 58.365 38.462 0.00 0.00 0.00 0.98
860 920 6.489603 AGTGGAGATGAGATCGGAGTATATT 58.510 40.000 0.00 0.00 0.00 1.28
861 921 6.073447 AGTGGAGATGAGATCGGAGTATAT 57.927 41.667 0.00 0.00 0.00 0.86
862 922 5.506730 AGTGGAGATGAGATCGGAGTATA 57.493 43.478 0.00 0.00 0.00 1.47
863 923 4.380843 AGTGGAGATGAGATCGGAGTAT 57.619 45.455 0.00 0.00 0.00 2.12
864 924 3.866703 AGTGGAGATGAGATCGGAGTA 57.133 47.619 0.00 0.00 0.00 2.59
865 925 2.746279 AGTGGAGATGAGATCGGAGT 57.254 50.000 0.00 0.00 0.00 3.85
866 926 3.254657 GGTTAGTGGAGATGAGATCGGAG 59.745 52.174 0.00 0.00 0.00 4.63
922 984 0.463474 GGCTCAGACTTGGATCTGGC 60.463 60.000 3.10 5.57 45.30 4.85
955 1027 4.418392 TCTTTAGGTAGATCGTTCGTTGC 58.582 43.478 0.00 0.00 0.00 4.17
960 1032 6.328641 TGGCTATCTTTAGGTAGATCGTTC 57.671 41.667 1.21 0.00 36.34 3.95
1041 1116 2.359230 AGGCGTGGAAGCTTCTGC 60.359 61.111 25.05 23.43 37.29 4.26
1119 1194 2.612251 GGAGGAGGGGAGAGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
1120 1195 2.612251 GGGAGGAGGGGAGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
1121 1196 3.430497 CGGGAGGAGGGGAGAGGA 61.430 72.222 0.00 0.00 0.00 3.71
1423 1542 1.376424 CATGCAGTTCTGCCCGTCT 60.376 57.895 19.91 0.05 0.00 4.18
1870 1989 0.100682 CGTGCTCGTAGTACATGGCT 59.899 55.000 0.00 0.00 29.68 4.75
1934 2053 2.668550 GCCGAAGAAGCCCGTGTT 60.669 61.111 0.00 0.00 0.00 3.32
1957 2076 3.676605 TTCTTGACGGCGAGGCGA 61.677 61.111 25.16 1.31 0.00 5.54
2434 2553 1.043673 AGTGGTATCCTCTGGCCGAC 61.044 60.000 0.00 0.00 0.00 4.79
2444 2566 2.734492 CGGTCGAGTTTCAGTGGTATCC 60.734 54.545 0.00 0.00 0.00 2.59
2448 2570 1.268899 CTACGGTCGAGTTTCAGTGGT 59.731 52.381 0.00 0.00 0.00 4.16
2461 2583 0.250166 ACTGGTGCCAAACTACGGTC 60.250 55.000 0.00 0.00 0.00 4.79
2524 2651 7.015226 TCTACAAACATATGCGGAATTTCTG 57.985 36.000 1.58 0.56 0.00 3.02
2532 2659 7.530525 CGTATGAATTTCTACAAACATATGCGG 59.469 37.037 1.58 0.00 0.00 5.69
2548 2675 7.142680 ACAAACCGATGTTTTCGTATGAATTT 58.857 30.769 0.00 0.00 46.65 1.82
2602 2729 1.300971 CCGATGCACTCACCACCAAG 61.301 60.000 0.00 0.00 0.00 3.61
2643 2770 0.315059 GCATTTGACGCCGTATCACG 60.315 55.000 0.00 0.00 42.11 4.35
2648 2775 1.149361 GATCCGCATTTGACGCCGTA 61.149 55.000 0.00 0.00 0.00 4.02
2655 2782 1.451207 CCCCACGATCCGCATTTGA 60.451 57.895 0.00 0.00 0.00 2.69
2684 2811 3.037431 TGGAATGGAAAATGCAAACCG 57.963 42.857 0.00 0.00 0.00 4.44
2685 2812 5.002516 TGAATGGAATGGAAAATGCAAACC 58.997 37.500 0.00 0.00 0.00 3.27
2686 2813 6.017275 TGTTGAATGGAATGGAAAATGCAAAC 60.017 34.615 0.00 0.00 0.00 2.93
2769 2896 0.971959 CTGCTCCTGCCACTCTCTCT 60.972 60.000 0.00 0.00 38.71 3.10
2788 2915 0.318784 GATCGATCTGCGGGTGTACC 60.319 60.000 18.29 0.00 41.33 3.34
2789 2916 0.318784 GGATCGATCTGCGGGTGTAC 60.319 60.000 23.96 0.49 41.33 2.90
2790 2917 0.467474 AGGATCGATCTGCGGGTGTA 60.467 55.000 23.96 0.00 41.33 2.90
2791 2918 0.467474 TAGGATCGATCTGCGGGTGT 60.467 55.000 23.96 3.09 41.33 4.16
2792 2919 0.242286 CTAGGATCGATCTGCGGGTG 59.758 60.000 23.96 5.30 41.33 4.61
2793 2920 0.178987 ACTAGGATCGATCTGCGGGT 60.179 55.000 23.96 13.03 41.33 5.28
2794 2921 0.242286 CACTAGGATCGATCTGCGGG 59.758 60.000 23.96 10.23 41.33 6.13
2795 2922 1.198867 CTCACTAGGATCGATCTGCGG 59.801 57.143 23.96 14.01 41.33 5.69
2796 2923 1.400888 GCTCACTAGGATCGATCTGCG 60.401 57.143 23.96 14.32 42.69 5.18
2797 2924 1.067915 GGCTCACTAGGATCGATCTGC 60.068 57.143 23.96 15.33 0.00 4.26
2798 2925 2.228582 CTGGCTCACTAGGATCGATCTG 59.771 54.545 23.96 14.63 0.00 2.90
2799 2926 2.513753 CTGGCTCACTAGGATCGATCT 58.486 52.381 23.96 12.90 0.00 2.75
2987 3125 6.904498 TGAAAACTCTTTCAGTGTTTCGAAA 58.096 32.000 6.47 6.47 44.76 3.46
3043 3181 4.379918 GGAACCTGCTCTCAAGTTTATTGC 60.380 45.833 0.00 0.00 27.64 3.56
3046 3184 4.287067 TCTGGAACCTGCTCTCAAGTTTAT 59.713 41.667 0.00 0.00 27.64 1.40
3080 3218 1.154836 CGCGCAGTTCAACGAGTTC 60.155 57.895 8.75 0.00 0.00 3.01
3137 3275 6.197168 ACCAACCTGAAATGGACAATCATAT 58.803 36.000 0.00 0.00 39.12 1.78
3265 3406 6.539103 ACCAGTCTAAGTCTGAAAAAGTTGTC 59.461 38.462 0.00 0.00 35.20 3.18
3269 3410 6.235231 TGACCAGTCTAAGTCTGAAAAAGT 57.765 37.500 0.00 0.00 35.20 2.66
3271 3412 7.872993 CACTATGACCAGTCTAAGTCTGAAAAA 59.127 37.037 0.00 0.00 35.20 1.94
3272 3413 7.378966 CACTATGACCAGTCTAAGTCTGAAAA 58.621 38.462 0.00 0.00 35.20 2.29
3287 3428 3.484953 AGTTACTCCCCACTATGACCA 57.515 47.619 0.00 0.00 0.00 4.02
3288 3429 5.206587 TCTAAGTTACTCCCCACTATGACC 58.793 45.833 0.00 0.00 0.00 4.02
3289 3430 5.892686 ACTCTAAGTTACTCCCCACTATGAC 59.107 44.000 0.00 0.00 0.00 3.06
3290 3431 6.088541 ACTCTAAGTTACTCCCCACTATGA 57.911 41.667 0.00 0.00 0.00 2.15
3291 3432 7.061688 ACTACTCTAAGTTACTCCCCACTATG 58.938 42.308 0.00 0.00 0.00 2.23
3292 3433 7.223472 ACTACTCTAAGTTACTCCCCACTAT 57.777 40.000 0.00 0.00 0.00 2.12
3293 3434 6.649041 ACTACTCTAAGTTACTCCCCACTA 57.351 41.667 0.00 0.00 0.00 2.74
3294 3435 5.533333 ACTACTCTAAGTTACTCCCCACT 57.467 43.478 0.00 0.00 0.00 4.00
3295 3436 6.660949 TGTTACTACTCTAAGTTACTCCCCAC 59.339 42.308 0.00 0.00 31.82 4.61
3296 3437 6.793478 TGTTACTACTCTAAGTTACTCCCCA 58.207 40.000 0.00 0.00 31.82 4.96
3297 3438 7.683945 GCATGTTACTACTCTAAGTTACTCCCC 60.684 44.444 0.00 0.00 31.82 4.81
3298 3439 7.147949 TGCATGTTACTACTCTAAGTTACTCCC 60.148 40.741 0.00 0.00 31.82 4.30
3299 3440 7.769220 TGCATGTTACTACTCTAAGTTACTCC 58.231 38.462 0.00 0.00 31.82 3.85
3309 3450 7.707035 GCAGTAAAGTATGCATGTTACTACTCT 59.293 37.037 21.90 10.34 42.11 3.24
3310 3451 7.707035 AGCAGTAAAGTATGCATGTTACTACTC 59.293 37.037 21.90 16.49 45.01 2.59
3311 3452 7.556844 AGCAGTAAAGTATGCATGTTACTACT 58.443 34.615 21.90 19.90 45.01 2.57
3312 3453 7.707035 AGAGCAGTAAAGTATGCATGTTACTAC 59.293 37.037 21.90 18.63 45.01 2.73
3313 3454 7.782049 AGAGCAGTAAAGTATGCATGTTACTA 58.218 34.615 21.90 0.87 45.01 1.82
3314 3455 6.644347 AGAGCAGTAAAGTATGCATGTTACT 58.356 36.000 18.95 18.95 45.01 2.24
3315 3456 6.910536 AGAGCAGTAAAGTATGCATGTTAC 57.089 37.500 10.16 14.16 45.01 2.50
3316 3457 8.204160 ACATAGAGCAGTAAAGTATGCATGTTA 58.796 33.333 10.16 2.40 45.01 2.41
3317 3458 7.050377 ACATAGAGCAGTAAAGTATGCATGTT 58.950 34.615 10.16 3.42 45.01 2.71
3318 3459 6.586344 ACATAGAGCAGTAAAGTATGCATGT 58.414 36.000 10.16 0.00 45.01 3.21
3319 3460 7.488187 AACATAGAGCAGTAAAGTATGCATG 57.512 36.000 10.16 0.00 45.01 4.06
3320 3461 8.424918 AGTAACATAGAGCAGTAAAGTATGCAT 58.575 33.333 3.79 3.79 45.01 3.96
3321 3462 7.782049 AGTAACATAGAGCAGTAAAGTATGCA 58.218 34.615 0.00 0.00 45.01 3.96
3322 3463 9.182933 GTAGTAACATAGAGCAGTAAAGTATGC 57.817 37.037 0.00 0.00 42.87 3.14
3323 3464 9.680315 GGTAGTAACATAGAGCAGTAAAGTATG 57.320 37.037 0.00 0.00 0.00 2.39
3324 3465 8.858094 GGGTAGTAACATAGAGCAGTAAAGTAT 58.142 37.037 0.00 0.00 0.00 2.12
3325 3466 8.057623 AGGGTAGTAACATAGAGCAGTAAAGTA 58.942 37.037 0.00 0.00 0.00 2.24
3326 3467 6.896307 AGGGTAGTAACATAGAGCAGTAAAGT 59.104 38.462 0.00 0.00 0.00 2.66
3327 3468 7.349412 AGGGTAGTAACATAGAGCAGTAAAG 57.651 40.000 0.00 0.00 0.00 1.85
3328 3469 7.729124 AAGGGTAGTAACATAGAGCAGTAAA 57.271 36.000 0.00 0.00 0.00 2.01
3330 3471 9.736414 CTATAAGGGTAGTAACATAGAGCAGTA 57.264 37.037 0.00 0.00 0.00 2.74
3331 3472 8.226112 ACTATAAGGGTAGTAACATAGAGCAGT 58.774 37.037 0.00 0.00 33.29 4.40
3332 3473 8.516234 CACTATAAGGGTAGTAACATAGAGCAG 58.484 40.741 0.00 0.00 33.29 4.24
3333 3474 7.450634 CCACTATAAGGGTAGTAACATAGAGCA 59.549 40.741 0.00 0.00 33.29 4.26
3334 3475 7.093858 CCCACTATAAGGGTAGTAACATAGAGC 60.094 44.444 2.34 0.00 41.61 4.09
3335 3476 8.168725 TCCCACTATAAGGGTAGTAACATAGAG 58.831 40.741 9.21 0.00 46.82 2.43
3336 3477 8.060727 TCCCACTATAAGGGTAGTAACATAGA 57.939 38.462 9.21 0.00 46.82 1.98
3337 3478 8.716674 TTCCCACTATAAGGGTAGTAACATAG 57.283 38.462 9.21 0.00 46.82 2.23
3338 3479 8.716674 CTTCCCACTATAAGGGTAGTAACATA 57.283 38.462 9.21 0.00 46.82 2.29
3339 3480 7.613551 CTTCCCACTATAAGGGTAGTAACAT 57.386 40.000 9.21 0.00 46.82 2.71
3345 3486 4.960469 TGACACTTCCCACTATAAGGGTAG 59.040 45.833 12.42 12.42 46.82 3.18
3346 3487 4.950361 TGACACTTCCCACTATAAGGGTA 58.050 43.478 9.21 0.63 46.82 3.69
3347 3488 3.798515 TGACACTTCCCACTATAAGGGT 58.201 45.455 9.21 0.00 46.82 4.34
3349 3490 8.816894 ACATATATGACACTTCCCACTATAAGG 58.183 37.037 19.63 0.00 0.00 2.69
3353 3494 8.958060 ACTACATATATGACACTTCCCACTAT 57.042 34.615 19.63 0.00 0.00 2.12
3354 3495 9.871175 TTACTACATATATGACACTTCCCACTA 57.129 33.333 19.63 0.00 0.00 2.74
3355 3496 8.777578 TTACTACATATATGACACTTCCCACT 57.222 34.615 19.63 0.00 0.00 4.00
3384 3525 9.836864 TCTACAAGACAATAAATGAGCATATGT 57.163 29.630 4.29 0.00 0.00 2.29
3406 3547 9.159470 GCGCTTTTCAATATAAAATGAGTCTAC 57.841 33.333 0.00 0.00 0.00 2.59
3407 3548 9.109393 AGCGCTTTTCAATATAAAATGAGTCTA 57.891 29.630 2.64 0.00 0.00 2.59
3408 3549 7.989826 AGCGCTTTTCAATATAAAATGAGTCT 58.010 30.769 2.64 0.00 0.00 3.24
3409 3550 9.884465 ATAGCGCTTTTCAATATAAAATGAGTC 57.116 29.630 18.68 0.00 0.00 3.36
3410 3551 9.669353 CATAGCGCTTTTCAATATAAAATGAGT 57.331 29.630 18.68 0.00 0.00 3.41
3411 3552 9.669353 ACATAGCGCTTTTCAATATAAAATGAG 57.331 29.630 18.68 0.00 0.00 2.90
3412 3553 9.449550 CACATAGCGCTTTTCAATATAAAATGA 57.550 29.630 18.68 0.00 0.00 2.57
3413 3554 9.449550 TCACATAGCGCTTTTCAATATAAAATG 57.550 29.630 18.68 10.96 0.00 2.32
3415 3556 9.449550 CATCACATAGCGCTTTTCAATATAAAA 57.550 29.630 18.68 0.00 0.00 1.52
3416 3557 8.075574 CCATCACATAGCGCTTTTCAATATAAA 58.924 33.333 18.68 0.00 0.00 1.40
3417 3558 7.228507 ACCATCACATAGCGCTTTTCAATATAA 59.771 33.333 18.68 0.00 0.00 0.98
3418 3559 6.710295 ACCATCACATAGCGCTTTTCAATATA 59.290 34.615 18.68 0.00 0.00 0.86
3419 3560 5.532406 ACCATCACATAGCGCTTTTCAATAT 59.468 36.000 18.68 0.00 0.00 1.28
3420 3561 4.881273 ACCATCACATAGCGCTTTTCAATA 59.119 37.500 18.68 0.00 0.00 1.90
3421 3562 3.696051 ACCATCACATAGCGCTTTTCAAT 59.304 39.130 18.68 0.00 0.00 2.57
3422 3563 3.081061 ACCATCACATAGCGCTTTTCAA 58.919 40.909 18.68 0.00 0.00 2.69
3423 3564 2.419673 CACCATCACATAGCGCTTTTCA 59.580 45.455 18.68 0.00 0.00 2.69
3424 3565 2.792542 GCACCATCACATAGCGCTTTTC 60.793 50.000 18.68 0.00 0.00 2.29
3425 3566 1.133025 GCACCATCACATAGCGCTTTT 59.867 47.619 18.68 0.00 0.00 2.27
3426 3567 0.734889 GCACCATCACATAGCGCTTT 59.265 50.000 18.68 4.25 0.00 3.51
3427 3568 1.431488 CGCACCATCACATAGCGCTT 61.431 55.000 18.68 0.00 41.95 4.68
3428 3569 1.884464 CGCACCATCACATAGCGCT 60.884 57.895 17.26 17.26 41.95 5.92
3429 3570 2.628106 CGCACCATCACATAGCGC 59.372 61.111 0.00 0.00 41.95 5.92
3431 3572 1.656652 AAGACGCACCATCACATAGC 58.343 50.000 0.00 0.00 0.00 2.97
3432 3573 3.261580 TCAAAGACGCACCATCACATAG 58.738 45.455 0.00 0.00 0.00 2.23
3433 3574 3.326836 TCAAAGACGCACCATCACATA 57.673 42.857 0.00 0.00 0.00 2.29
3434 3575 2.183478 TCAAAGACGCACCATCACAT 57.817 45.000 0.00 0.00 0.00 3.21
3435 3576 2.183478 ATCAAAGACGCACCATCACA 57.817 45.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.