Multiple sequence alignment - TraesCS5B01G393400

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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 TraesCS5B01G393400 chr5B 100.000 5515 0 0 1 5515 571605030 571610544 0.000000e+00 10185
1 TraesCS5B01G393400 chr5B 79.170 3303 647 37 1196 4475 695814274 695810990 0.000000e+00 2250
2 TraesCS5B01G393400 chr5B 78.605 1935 385 24 2554 4475 695875784 695873866 0.000000e+00 1253
3 TraesCS5B01G393400 chr5B 97.858 607 13 0 1 607 705812369 705811763 0.000000e+00 1050
4 TraesCS5B01G393400 chr5B 77.631 1359 289 11 1163 2515 695894140 695892791 0.000000e+00 811
5 TraesCS5B01G393400 chr5D 94.509 3843 158 20 791 4618 464701452 464697648 0.000000e+00 5879
6 TraesCS5B01G393400 chr5D 79.406 3302 641 36 1196 4475 555635966 555639250 0.000000e+00 2294
7 TraesCS5B01G393400 chr5D 78.759 3305 657 41 1194 4475 555322061 555325343 0.000000e+00 2172
8 TraesCS5B01G393400 chr5D 78.253 3389 685 44 1163 4524 495551739 495548376 0.000000e+00 2128
9 TraesCS5B01G393400 chr5D 78.496 3297 662 43 1196 4466 555555642 555558917 0.000000e+00 2117
10 TraesCS5B01G393400 chr5D 77.736 3436 707 47 1063 4475 555062224 555065624 0.000000e+00 2054
11 TraesCS5B01G393400 chr5D 76.465 2184 480 32 1080 3248 555046074 555048238 0.000000e+00 1155
12 TraesCS5B01G393400 chr5D 84.017 463 34 14 4602 5036 464697634 464697184 5.140000e-110 409
13 TraesCS5B01G393400 chr5D 87.795 254 28 3 5034 5287 464695549 464695299 1.500000e-75 294
14 TraesCS5B01G393400 chr5D 93.000 200 11 1 598 794 464701682 464701483 6.990000e-74 289
15 TraesCS5B01G393400 chr5A 91.894 4182 248 49 791 4913 585202209 585198060 0.000000e+00 5760
16 TraesCS5B01G393400 chr5A 82.927 492 71 11 5034 5515 585099477 585098989 1.100000e-116 431
17 TraesCS5B01G393400 chr5A 93.434 198 8 2 598 794 585202437 585202244 6.990000e-74 289
18 TraesCS5B01G393400 chr5A 94.565 92 3 2 4944 5035 585169880 585169791 2.070000e-29 141
19 TraesCS5B01G393400 chr4A 78.970 3438 656 59 1075 4475 613744118 613740711 0.000000e+00 2281
20 TraesCS5B01G393400 chr4A 98.023 607 12 0 1 607 724630720 724630114 0.000000e+00 1055
21 TraesCS5B01G393400 chr4A 78.899 218 46 0 1190 1407 714099831 714100048 1.240000e-31 148
22 TraesCS5B01G393400 chr3A 78.772 3387 666 42 1160 4522 44605571 44608928 0.000000e+00 2222
23 TraesCS5B01G393400 chr1B 78.149 3112 637 38 1399 4486 433644484 433641392 0.000000e+00 1940
24 TraesCS5B01G393400 chr1B 97.858 607 13 0 1 607 637366408 637367014 0.000000e+00 1050
25 TraesCS5B01G393400 chr7A 98.033 610 12 0 1 610 40032650 40032041 0.000000e+00 1061
26 TraesCS5B01G393400 chr2B 97.862 608 13 0 1 608 17995142 17994535 0.000000e+00 1051
27 TraesCS5B01G393400 chr2B 97.709 611 14 0 1 611 506582404 506583014 0.000000e+00 1051
28 TraesCS5B01G393400 chr7B 97.858 607 13 0 1 607 697603335 697603941 0.000000e+00 1050
29 TraesCS5B01G393400 chr3B 97.862 608 12 1 1 608 31297792 31297186 0.000000e+00 1050
30 TraesCS5B01G393400 chr3B 97.858 607 13 0 1 607 781421139 781420533 0.000000e+00 1050
31 TraesCS5B01G393400 chr7D 73.084 2857 713 48 1189 4017 18695130 18692302 0.000000e+00 965
32 TraesCS5B01G393400 chr1A 79.270 931 179 11 1189 2112 402209008 402209931 6.020000e-179 638
33 TraesCS5B01G393400 chr2A 76.677 313 68 5 1190 1501 762741737 762741429 9.500000e-38 169
34 TraesCS5B01G393400 chr2A 77.542 236 53 0 1194 1429 715782626 715782391 5.760000e-30 143


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 TraesCS5B01G393400 chr5B 571605030 571610544 5514 False 10185.00 10185 100.00000 1 5515 1 chr5B.!!$F1 5514
1 TraesCS5B01G393400 chr5B 695810990 695814274 3284 True 2250.00 2250 79.17000 1196 4475 1 chr5B.!!$R1 3279
2 TraesCS5B01G393400 chr5B 695873866 695875784 1918 True 1253.00 1253 78.60500 2554 4475 1 chr5B.!!$R2 1921
3 TraesCS5B01G393400 chr5B 705811763 705812369 606 True 1050.00 1050 97.85800 1 607 1 chr5B.!!$R4 606
4 TraesCS5B01G393400 chr5B 695892791 695894140 1349 True 811.00 811 77.63100 1163 2515 1 chr5B.!!$R3 1352
5 TraesCS5B01G393400 chr5D 555635966 555639250 3284 False 2294.00 2294 79.40600 1196 4475 1 chr5D.!!$F5 3279
6 TraesCS5B01G393400 chr5D 555322061 555325343 3282 False 2172.00 2172 78.75900 1194 4475 1 chr5D.!!$F3 3281
7 TraesCS5B01G393400 chr5D 495548376 495551739 3363 True 2128.00 2128 78.25300 1163 4524 1 chr5D.!!$R1 3361
8 TraesCS5B01G393400 chr5D 555555642 555558917 3275 False 2117.00 2117 78.49600 1196 4466 1 chr5D.!!$F4 3270
9 TraesCS5B01G393400 chr5D 555062224 555065624 3400 False 2054.00 2054 77.73600 1063 4475 1 chr5D.!!$F2 3412
10 TraesCS5B01G393400 chr5D 464695299 464701682 6383 True 1717.75 5879 89.83025 598 5287 4 chr5D.!!$R2 4689
11 TraesCS5B01G393400 chr5D 555046074 555048238 2164 False 1155.00 1155 76.46500 1080 3248 1 chr5D.!!$F1 2168
12 TraesCS5B01G393400 chr5A 585198060 585202437 4377 True 3024.50 5760 92.66400 598 4913 2 chr5A.!!$R3 4315
13 TraesCS5B01G393400 chr4A 613740711 613744118 3407 True 2281.00 2281 78.97000 1075 4475 1 chr4A.!!$R1 3400
14 TraesCS5B01G393400 chr4A 724630114 724630720 606 True 1055.00 1055 98.02300 1 607 1 chr4A.!!$R2 606
15 TraesCS5B01G393400 chr3A 44605571 44608928 3357 False 2222.00 2222 78.77200 1160 4522 1 chr3A.!!$F1 3362
16 TraesCS5B01G393400 chr1B 433641392 433644484 3092 True 1940.00 1940 78.14900 1399 4486 1 chr1B.!!$R1 3087
17 TraesCS5B01G393400 chr1B 637366408 637367014 606 False 1050.00 1050 97.85800 1 607 1 chr1B.!!$F1 606
18 TraesCS5B01G393400 chr7A 40032041 40032650 609 True 1061.00 1061 98.03300 1 610 1 chr7A.!!$R1 609
19 TraesCS5B01G393400 chr2B 17994535 17995142 607 True 1051.00 1051 97.86200 1 608 1 chr2B.!!$R1 607
20 TraesCS5B01G393400 chr2B 506582404 506583014 610 False 1051.00 1051 97.70900 1 611 1 chr2B.!!$F1 610
21 TraesCS5B01G393400 chr7B 697603335 697603941 606 False 1050.00 1050 97.85800 1 607 1 chr7B.!!$F1 606
22 TraesCS5B01G393400 chr3B 31297186 31297792 606 True 1050.00 1050 97.86200 1 608 1 chr3B.!!$R1 607
23 TraesCS5B01G393400 chr3B 781420533 781421139 606 True 1050.00 1050 97.85800 1 607 1 chr3B.!!$R2 606
24 TraesCS5B01G393400 chr7D 18692302 18695130 2828 True 965.00 965 73.08400 1189 4017 1 chr7D.!!$R1 2828
25 TraesCS5B01G393400 chr1A 402209008 402209931 923 False 638.00 638 79.27000 1189 2112 1 chr1A.!!$F1 923

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
630 631 0.096976 CCCTAATGCGCGTCTTTGTG 59.903 55.0 8.43 3.26 0.00 3.33 F
1101 1199 0.255318 CCAGCTCAATGGCCTCTCTT 59.745 55.0 3.32 0.00 32.48 2.85 F
1467 1574 0.391263 CACCCGAACTTGGTAGGCTC 60.391 60.0 0.00 0.00 33.84 4.70 F
3294 3405 0.387565 GGTTTTCGCCTTGCCTTGAA 59.612 50.0 0.00 0.00 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2539 2650 1.915078 ATTGCTAGCGGAAGGCCACT 61.915 55.000 10.77 0.0 45.17 4.00 R
3037 3148 1.202348 GCCCGGAATTGAGTTTTCCAG 59.798 52.381 0.73 0.0 42.34 3.86 R
3431 3545 1.679032 GGCCTATGACACTGGTTGGAC 60.679 57.143 0.00 0.0 0.00 4.02 R
4723 4894 0.037326 AGTGACCGACTCCGTACGTA 60.037 55.000 15.21 0.0 0.00 3.57 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
110 111 4.548726 GCTTGCTCAAACATTTCACAAACG 60.549 41.667 0.00 0.00 0.00 3.60
558 559 2.131972 CCATTCACTCGAACAACGTCA 58.868 47.619 0.00 0.00 43.13 4.35
578 579 5.334028 CGTCACACTCAAGCAAATTCACATA 60.334 40.000 0.00 0.00 0.00 2.29
613 614 1.664873 GAGCTATTGACCCGTTTCCC 58.335 55.000 0.00 0.00 0.00 3.97
630 631 0.096976 CCCTAATGCGCGTCTTTGTG 59.903 55.000 8.43 3.26 0.00 3.33
649 650 3.187700 GTGGCCAACATCTTCTACGTAG 58.812 50.000 16.73 16.73 0.00 3.51
656 657 5.206299 CAACATCTTCTACGTAGGATCGAC 58.794 45.833 22.01 0.00 34.70 4.20
860 903 3.367703 CCCACTCCTGCATTTCATTTCAC 60.368 47.826 0.00 0.00 0.00 3.18
873 916 2.875933 TCATTTCACGGTCCACAAGTTC 59.124 45.455 0.00 0.00 0.00 3.01
881 927 2.229792 GGTCCACAAGTTCAATCAGCA 58.770 47.619 0.00 0.00 0.00 4.41
947 1005 4.450419 CGCTTGACTGACTTTGAAAGATCT 59.550 41.667 12.53 0.00 0.00 2.75
950 1008 4.067896 TGACTGACTTTGAAAGATCTGGC 58.932 43.478 12.53 11.42 0.00 4.85
951 1009 3.070018 ACTGACTTTGAAAGATCTGGCG 58.930 45.455 12.53 0.00 0.00 5.69
953 1011 2.224523 TGACTTTGAAAGATCTGGCGGT 60.225 45.455 12.53 0.00 0.00 5.68
954 1012 2.814336 GACTTTGAAAGATCTGGCGGTT 59.186 45.455 12.53 0.00 0.00 4.44
955 1013 2.554032 ACTTTGAAAGATCTGGCGGTTG 59.446 45.455 12.53 0.00 0.00 3.77
956 1014 0.881118 TTGAAAGATCTGGCGGTTGC 59.119 50.000 0.00 0.00 41.71 4.17
1026 1085 1.233019 CCTGCGATGGAATCATGGAC 58.767 55.000 0.00 0.00 45.97 4.02
1043 1112 3.684908 TGGACACATGGGACTACAAATG 58.315 45.455 0.00 0.00 0.00 2.32
1077 1146 1.836166 CCAGTCCATGATGTCCACTCT 59.164 52.381 0.00 0.00 0.00 3.24
1101 1199 0.255318 CCAGCTCAATGGCCTCTCTT 59.745 55.000 3.32 0.00 32.48 2.85
1134 1235 4.713321 ACTCCCATTCCCATCTTTTTCATG 59.287 41.667 0.00 0.00 0.00 3.07
1155 1256 1.886313 CGCGCTACTCTCGGTCCTA 60.886 63.158 5.56 0.00 0.00 2.94
1156 1257 1.648174 GCGCTACTCTCGGTCCTAC 59.352 63.158 0.00 0.00 0.00 3.18
1467 1574 0.391263 CACCCGAACTTGGTAGGCTC 60.391 60.000 0.00 0.00 33.84 4.70
2069 2177 3.860754 GCCAAATTACCACACCTTGAAGC 60.861 47.826 0.00 0.00 0.00 3.86
2610 2721 9.739276 ATAGATCTTTCAAACAACCTATTCACA 57.261 29.630 0.00 0.00 0.00 3.58
2688 2799 1.750778 CACAATCACATGTTAGGCCCC 59.249 52.381 0.00 0.00 0.00 5.80
3037 3148 5.990668 ACCTAAATCTATCCCACAACTCAC 58.009 41.667 0.00 0.00 0.00 3.51
3094 3205 7.910304 ACTAAAAAGCTTAGCATCATTAGACG 58.090 34.615 18.58 0.00 0.00 4.18
3117 3228 4.271291 GTCTCATTTAACAATCTCTCGGGC 59.729 45.833 0.00 0.00 0.00 6.13
3294 3405 0.387565 GGTTTTCGCCTTGCCTTGAA 59.612 50.000 0.00 0.00 0.00 2.69
3431 3545 6.352516 AGGAGGAGTACAATGCATCTTTAAG 58.647 40.000 0.00 0.00 0.00 1.85
3468 3582 7.978975 GTCATAGGCCATCAGATAATCTCTTAC 59.021 40.741 5.01 0.00 29.16 2.34
3696 3811 2.945008 ACTCAACACATGTTCCACACAG 59.055 45.455 0.00 0.00 39.40 3.66
3714 3829 3.759086 CACAGGACTTCAGAGCACTAGTA 59.241 47.826 0.00 0.00 0.00 1.82
3753 3868 2.828520 TGGAAGCTTAGAGACACTCCTG 59.171 50.000 0.00 0.00 0.00 3.86
3972 4096 5.812642 ACTTGACGACAACTCAATGATATCC 59.187 40.000 0.00 0.00 32.27 2.59
4026 4150 5.070047 GGCACCAGGTACTTAATTAGCTAGA 59.930 44.000 4.45 0.00 34.60 2.43
4086 4217 7.574021 TGATAATTATGGCTCCACCTAGAAT 57.426 36.000 1.78 0.00 40.22 2.40
4117 4248 6.913673 GGTTGAGCAACTACGTTTTAATTCAA 59.086 34.615 12.54 0.00 40.94 2.69
4286 4423 0.657840 GGGTTCATCGAGCATTTCCG 59.342 55.000 0.00 0.00 0.00 4.30
4385 4523 2.132517 TTGCGTCCGTGTTCGAGCTA 62.133 55.000 0.00 0.00 39.71 3.32
4519 4657 1.788258 AGTGCAACACAGTGATCGAG 58.212 50.000 7.81 0.00 41.43 4.04
4619 4789 7.915397 TGTATCTGTTCTTTTTCTTCTTGTTGC 59.085 33.333 0.00 0.00 0.00 4.17
4666 4836 3.585862 CTTAAGTAGACAGCAAAGCCGA 58.414 45.455 0.00 0.00 0.00 5.54
4683 4853 2.355818 GCCGAGGGAAATGTAGTCCTTT 60.356 50.000 0.00 0.00 35.33 3.11
4684 4854 3.270877 CCGAGGGAAATGTAGTCCTTTG 58.729 50.000 0.00 0.00 35.33 2.77
4711 4882 4.685169 ATGTATTTGCAGTTTGTCCTCG 57.315 40.909 0.00 0.00 0.00 4.63
4712 4883 3.734463 TGTATTTGCAGTTTGTCCTCGA 58.266 40.909 0.00 0.00 0.00 4.04
4715 4886 2.613026 TTGCAGTTTGTCCTCGAAGA 57.387 45.000 0.00 0.00 0.00 2.87
4716 4887 1.865865 TGCAGTTTGTCCTCGAAGAC 58.134 50.000 7.24 7.24 37.28 3.01
4717 4888 0.784778 GCAGTTTGTCCTCGAAGACG 59.215 55.000 9.52 0.00 39.77 4.18
4719 4890 1.000607 CAGTTTGTCCTCGAAGACGGA 60.001 52.381 9.52 0.00 39.77 4.69
4722 4893 2.202453 GTCCTCGAAGACGGACGC 60.202 66.667 5.88 0.00 41.94 5.19
4723 4894 2.359602 TCCTCGAAGACGGACGCT 60.360 61.111 0.00 0.00 40.21 5.07
4724 4895 1.078918 TCCTCGAAGACGGACGCTA 60.079 57.895 0.00 0.00 40.21 4.26
4725 4896 1.062206 CCTCGAAGACGGACGCTAC 59.938 63.158 0.00 0.00 40.21 3.58
4726 4897 1.296722 CTCGAAGACGGACGCTACG 60.297 63.158 0.00 0.00 40.21 3.51
4728 4899 0.735978 TCGAAGACGGACGCTACGTA 60.736 55.000 0.00 0.00 45.68 3.57
4729 4900 0.585029 CGAAGACGGACGCTACGTAC 60.585 60.000 0.00 0.00 45.68 3.67
4807 4978 4.681978 GCGTTGGTGGAGCGACCT 62.682 66.667 3.36 0.00 39.86 3.85
4830 5001 4.754372 TGAGCTGATTGCAGTAAAACAG 57.246 40.909 0.00 0.00 45.94 3.16
4831 5002 4.136796 TGAGCTGATTGCAGTAAAACAGT 58.863 39.130 0.00 0.00 45.94 3.55
4835 5006 4.539870 CTGATTGCAGTAAAACAGTGTGG 58.460 43.478 0.00 0.00 37.37 4.17
4838 5009 3.562343 TGCAGTAAAACAGTGTGGGTA 57.438 42.857 0.00 0.00 0.00 3.69
4839 5010 3.207778 TGCAGTAAAACAGTGTGGGTAC 58.792 45.455 0.00 0.00 0.00 3.34
4840 5011 3.118186 TGCAGTAAAACAGTGTGGGTACT 60.118 43.478 0.00 2.28 0.00 2.73
4841 5012 4.101274 TGCAGTAAAACAGTGTGGGTACTA 59.899 41.667 11.43 0.00 0.00 1.82
4846 5019 5.362105 AAAACAGTGTGGGTACTAGTGAA 57.638 39.130 5.39 0.00 0.00 3.18
4891 5064 9.310716 CATATGCATCGATCATTAGTTAGTCAT 57.689 33.333 0.19 3.57 0.00 3.06
4898 5071 9.770097 ATCGATCATTAGTTAGTCATTGTGATT 57.230 29.630 0.00 0.00 0.00 2.57
4903 5076 7.962373 TCATTAGTTAGTCATTGTGATTTTGCG 59.038 33.333 0.00 0.00 0.00 4.85
4905 5078 4.759693 AGTTAGTCATTGTGATTTTGCGGA 59.240 37.500 0.00 0.00 0.00 5.54
4907 5080 2.228822 AGTCATTGTGATTTTGCGGACC 59.771 45.455 0.00 0.00 0.00 4.46
4916 5089 1.088340 TTTTGCGGACCGTCGAAACA 61.088 50.000 16.73 0.04 0.00 2.83
4978 5175 0.033504 AGACACGCCACAACTCGAAT 59.966 50.000 0.00 0.00 0.00 3.34
4985 5182 0.953471 CCACAACTCGAATTGGCCGA 60.953 55.000 11.74 0.00 33.63 5.54
4997 5194 0.107703 TTGGCCGACCTGATCATGTC 60.108 55.000 18.22 18.22 36.63 3.06
4998 5195 1.264045 TGGCCGACCTGATCATGTCA 61.264 55.000 24.91 8.55 36.63 3.58
5088 6922 1.134226 GCAGCAGTTCATTGTGTTGC 58.866 50.000 0.00 0.00 42.51 4.17
5100 6934 6.875948 TCATTGTGTTGCTGTGTTATAACT 57.124 33.333 16.33 0.00 0.00 2.24
5109 6943 7.700234 TGTTGCTGTGTTATAACTGAAACAAAG 59.300 33.333 16.33 3.66 41.76 2.77
5111 6945 8.165239 TGCTGTGTTATAACTGAAACAAAGAT 57.835 30.769 16.33 0.00 41.53 2.40
5149 6983 7.062322 AGAAGATGCCATGTGTTATGGAAATA 58.938 34.615 9.99 0.00 41.64 1.40
5151 6985 5.771666 AGATGCCATGTGTTATGGAAATAGG 59.228 40.000 9.99 0.00 41.64 2.57
5173 7007 6.863275 AGGAATTGATTAAAATTGGACGACC 58.137 36.000 0.00 0.00 29.89 4.79
5176 7010 3.011119 TGATTAAAATTGGACGACCGGG 58.989 45.455 6.32 0.00 39.42 5.73
5190 7024 3.801997 CGGGCCAAGGCTCCTGAT 61.802 66.667 11.40 0.00 38.65 2.90
5193 7027 2.274760 GCCAAGGCTCCTGATGCT 59.725 61.111 3.29 0.00 38.26 3.79
5200 7034 0.322816 GGCTCCTGATGCTTTCCACA 60.323 55.000 0.00 0.00 0.00 4.17
5201 7035 1.684248 GGCTCCTGATGCTTTCCACAT 60.684 52.381 0.00 0.00 0.00 3.21
5202 7036 1.404391 GCTCCTGATGCTTTCCACATG 59.596 52.381 0.00 0.00 0.00 3.21
5203 7037 1.404391 CTCCTGATGCTTTCCACATGC 59.596 52.381 0.00 0.00 0.00 4.06
5204 7038 1.005097 TCCTGATGCTTTCCACATGCT 59.995 47.619 0.00 0.00 0.00 3.79
5205 7039 1.134367 CCTGATGCTTTCCACATGCTG 59.866 52.381 0.00 0.00 0.00 4.41
5230 7064 0.670546 GGCTGCTACGAGCTGTGAAA 60.671 55.000 0.00 0.00 42.97 2.69
5231 7065 0.718343 GCTGCTACGAGCTGTGAAAG 59.282 55.000 0.00 0.00 42.97 2.62
5232 7066 1.354040 CTGCTACGAGCTGTGAAAGG 58.646 55.000 0.00 0.00 42.97 3.11
5251 7085 1.303317 CAAAAGGGAGGGGTCGGTG 60.303 63.158 0.00 0.00 0.00 4.94
5309 7143 3.084579 GCTGATCGGTGTTGCGAG 58.915 61.111 2.89 0.00 0.00 5.03
5310 7144 2.456119 GCTGATCGGTGTTGCGAGG 61.456 63.158 2.89 0.00 0.00 4.63
5311 7145 2.434185 TGATCGGTGTTGCGAGGC 60.434 61.111 0.00 0.00 0.00 4.70
5312 7146 3.195698 GATCGGTGTTGCGAGGCC 61.196 66.667 0.00 0.00 0.00 5.19
5326 7160 4.541648 GGCCGAGGGGAGGAGCTA 62.542 72.222 0.00 0.00 34.06 3.32
5327 7161 3.228017 GCCGAGGGGAGGAGCTAC 61.228 72.222 0.00 0.00 34.06 3.58
5328 7162 2.907917 CCGAGGGGAGGAGCTACG 60.908 72.222 0.00 0.00 34.06 3.51
5329 7163 2.192443 CGAGGGGAGGAGCTACGA 59.808 66.667 0.00 0.00 0.00 3.43
5330 7164 1.894756 CGAGGGGAGGAGCTACGAG 60.895 68.421 0.00 0.00 0.00 4.18
5331 7165 1.529713 GAGGGGAGGAGCTACGAGG 60.530 68.421 0.00 0.00 0.00 4.63
5332 7166 2.279408 GGGGAGGAGCTACGAGGT 59.721 66.667 0.00 0.00 0.00 3.85
5333 7167 2.128507 GGGGAGGAGCTACGAGGTG 61.129 68.421 0.00 0.00 0.00 4.00
5334 7168 2.787567 GGGAGGAGCTACGAGGTGC 61.788 68.421 0.00 0.00 34.08 5.01
5336 7170 0.465824 GGAGGAGCTACGAGGTGCTA 60.466 60.000 7.76 0.00 44.42 3.49
5337 7171 0.664224 GAGGAGCTACGAGGTGCTAC 59.336 60.000 7.76 3.68 44.42 3.58
5338 7172 0.034380 AGGAGCTACGAGGTGCTACA 60.034 55.000 6.37 0.00 42.60 2.74
5339 7173 0.815734 GGAGCTACGAGGTGCTACAA 59.184 55.000 0.00 0.00 39.77 2.41
5340 7174 1.409427 GGAGCTACGAGGTGCTACAAT 59.591 52.381 0.00 0.00 39.77 2.71
5341 7175 2.544069 GGAGCTACGAGGTGCTACAATC 60.544 54.545 0.00 0.00 39.77 2.67
5342 7176 1.065701 AGCTACGAGGTGCTACAATCG 59.934 52.381 0.00 9.74 37.81 3.34
5343 7177 1.065102 GCTACGAGGTGCTACAATCGA 59.935 52.381 14.93 0.00 38.50 3.59
5344 7178 2.717530 CTACGAGGTGCTACAATCGAC 58.282 52.381 14.93 0.00 38.50 4.20
5345 7179 0.179171 ACGAGGTGCTACAATCGACG 60.179 55.000 14.93 0.00 38.50 5.12
5346 7180 0.098200 CGAGGTGCTACAATCGACGA 59.902 55.000 0.00 0.00 37.35 4.20
5347 7181 1.466866 CGAGGTGCTACAATCGACGAA 60.467 52.381 0.00 0.00 37.35 3.85
5348 7182 2.186076 GAGGTGCTACAATCGACGAAG 58.814 52.381 0.00 0.00 0.00 3.79
5349 7183 0.645868 GGTGCTACAATCGACGAAGC 59.354 55.000 11.43 11.43 0.00 3.86
5350 7184 1.630148 GTGCTACAATCGACGAAGCT 58.370 50.000 17.46 0.00 34.28 3.74
5351 7185 1.584308 GTGCTACAATCGACGAAGCTC 59.416 52.381 17.46 11.70 34.28 4.09
5352 7186 0.840729 GCTACAATCGACGAAGCTCG 59.159 55.000 11.14 4.36 46.93 5.03
5353 7187 1.531264 GCTACAATCGACGAAGCTCGA 60.531 52.381 11.14 5.48 43.74 4.04
5354 7188 2.782163 CTACAATCGACGAAGCTCGAA 58.218 47.619 0.00 0.00 43.74 3.71
5355 7189 1.618861 ACAATCGACGAAGCTCGAAG 58.381 50.000 0.00 5.31 43.74 3.79
5356 7190 0.296056 CAATCGACGAAGCTCGAAGC 59.704 55.000 0.00 0.00 43.74 3.86
5368 7202 2.881074 GCTCGAAGCTTCTACATGTGA 58.119 47.619 23.50 10.74 38.45 3.58
5369 7203 3.254060 GCTCGAAGCTTCTACATGTGAA 58.746 45.455 23.50 9.30 38.45 3.18
5370 7204 3.305629 GCTCGAAGCTTCTACATGTGAAG 59.694 47.826 23.50 22.94 42.58 3.02
5380 7214 7.202016 CTTCTACATGTGAAGCTAAAAACCA 57.798 36.000 18.62 0.00 35.21 3.67
5381 7215 7.759489 TTCTACATGTGAAGCTAAAAACCAT 57.241 32.000 9.11 0.00 0.00 3.55
5382 7216 7.144722 TCTACATGTGAAGCTAAAAACCATG 57.855 36.000 9.11 0.00 0.00 3.66
5383 7217 6.939730 TCTACATGTGAAGCTAAAAACCATGA 59.060 34.615 9.11 0.00 0.00 3.07
5384 7218 6.594788 ACATGTGAAGCTAAAAACCATGAT 57.405 33.333 0.00 0.00 0.00 2.45
5385 7219 6.624423 ACATGTGAAGCTAAAAACCATGATC 58.376 36.000 0.00 0.00 0.00 2.92
5386 7220 5.295431 TGTGAAGCTAAAAACCATGATCG 57.705 39.130 0.00 0.00 0.00 3.69
5387 7221 4.155826 TGTGAAGCTAAAAACCATGATCGG 59.844 41.667 0.00 0.00 0.00 4.18
5388 7222 3.128589 TGAAGCTAAAAACCATGATCGGC 59.871 43.478 0.00 0.00 0.00 5.54
5389 7223 1.670811 AGCTAAAAACCATGATCGGCG 59.329 47.619 0.00 0.00 0.00 6.46
5390 7224 1.668751 GCTAAAAACCATGATCGGCGA 59.331 47.619 13.87 13.87 0.00 5.54
5391 7225 2.096819 GCTAAAAACCATGATCGGCGAA 59.903 45.455 15.93 0.00 0.00 4.70
5392 7226 3.426963 GCTAAAAACCATGATCGGCGAAA 60.427 43.478 15.93 5.78 0.00 3.46
5393 7227 3.866883 AAAAACCATGATCGGCGAAAT 57.133 38.095 15.93 8.29 0.00 2.17
5394 7228 3.420839 AAAACCATGATCGGCGAAATC 57.579 42.857 15.93 8.87 0.00 2.17
5395 7229 2.036958 AACCATGATCGGCGAAATCA 57.963 45.000 15.93 15.24 37.53 2.57
5396 7230 1.586422 ACCATGATCGGCGAAATCAG 58.414 50.000 15.93 5.95 36.63 2.90
5397 7231 1.138859 ACCATGATCGGCGAAATCAGA 59.861 47.619 15.93 0.00 36.63 3.27
5398 7232 2.212652 CCATGATCGGCGAAATCAGAA 58.787 47.619 15.93 0.00 36.63 3.02
5399 7233 2.222678 CCATGATCGGCGAAATCAGAAG 59.777 50.000 15.93 8.34 36.63 2.85
5400 7234 1.290203 TGATCGGCGAAATCAGAAGC 58.710 50.000 15.93 0.00 0.00 3.86
5401 7235 1.134699 TGATCGGCGAAATCAGAAGCT 60.135 47.619 15.93 0.00 0.00 3.74
5402 7236 1.260033 GATCGGCGAAATCAGAAGCTG 59.740 52.381 15.93 0.00 37.33 4.24
5403 7237 1.061570 CGGCGAAATCAGAAGCTGC 59.938 57.895 0.00 0.00 0.00 5.25
5404 7238 1.638388 CGGCGAAATCAGAAGCTGCA 61.638 55.000 0.00 0.00 0.00 4.41
5405 7239 0.523072 GGCGAAATCAGAAGCTGCAA 59.477 50.000 1.02 0.00 0.00 4.08
5406 7240 1.611043 GCGAAATCAGAAGCTGCAAC 58.389 50.000 1.02 0.00 0.00 4.17
5407 7241 1.730446 GCGAAATCAGAAGCTGCAACC 60.730 52.381 1.02 0.00 0.00 3.77
5408 7242 1.464687 CGAAATCAGAAGCTGCAACCG 60.465 52.381 1.02 0.00 0.00 4.44
5409 7243 0.883833 AAATCAGAAGCTGCAACCGG 59.116 50.000 0.00 0.00 0.00 5.28
5410 7244 0.250901 AATCAGAAGCTGCAACCGGT 60.251 50.000 0.00 0.00 0.00 5.28
5411 7245 0.613260 ATCAGAAGCTGCAACCGGTA 59.387 50.000 8.00 0.00 0.00 4.02
5412 7246 0.037326 TCAGAAGCTGCAACCGGTAG 60.037 55.000 8.00 2.11 0.00 3.18
5413 7247 1.021390 CAGAAGCTGCAACCGGTAGG 61.021 60.000 8.00 4.30 45.13 3.18
5414 7248 1.745489 GAAGCTGCAACCGGTAGGG 60.745 63.158 8.00 1.18 43.47 3.53
5415 7249 3.920093 AAGCTGCAACCGGTAGGGC 62.920 63.158 8.00 13.51 43.47 5.19
5416 7250 4.715523 GCTGCAACCGGTAGGGCA 62.716 66.667 22.33 22.33 43.47 5.36
5417 7251 2.746277 CTGCAACCGGTAGGGCAC 60.746 66.667 20.60 3.47 43.47 5.01
5418 7252 4.690719 TGCAACCGGTAGGGCACG 62.691 66.667 20.60 1.09 43.47 5.34
5424 7258 4.728102 CGGTAGGGCACGCGAACA 62.728 66.667 15.93 0.00 0.00 3.18
5425 7259 3.116531 GGTAGGGCACGCGAACAC 61.117 66.667 15.93 4.90 0.00 3.32
5426 7260 3.475774 GTAGGGCACGCGAACACG 61.476 66.667 15.93 0.00 39.50 4.49
5436 7270 3.276091 CGAACACGCTGGCAACCA 61.276 61.111 0.00 0.00 0.00 3.67
5437 7271 2.829206 CGAACACGCTGGCAACCAA 61.829 57.895 0.00 0.00 30.80 3.67
5438 7272 1.299089 GAACACGCTGGCAACCAAC 60.299 57.895 0.00 0.00 30.80 3.77
5439 7273 2.982038 GAACACGCTGGCAACCAACG 62.982 60.000 7.81 7.81 46.84 4.10
5440 7274 3.276091 CACGCTGGCAACCAACGA 61.276 61.111 15.65 0.00 44.67 3.85
5441 7275 2.281484 ACGCTGGCAACCAACGAT 60.281 55.556 15.65 0.00 44.67 3.73
5442 7276 2.176546 CGCTGGCAACCAACGATG 59.823 61.111 3.39 0.00 44.67 3.84
5443 7277 2.126346 GCTGGCAACCAACGATGC 60.126 61.111 0.00 0.00 41.82 3.91
5447 7281 4.036804 GCAACCAACGATGCCGCA 62.037 61.111 0.00 0.00 39.95 5.69
5448 7282 2.642129 CAACCAACGATGCCGCAA 59.358 55.556 0.00 0.00 39.95 4.85
5449 7283 1.729131 CAACCAACGATGCCGCAAC 60.729 57.895 0.00 0.00 39.95 4.17
5450 7284 2.914908 AACCAACGATGCCGCAACC 61.915 57.895 0.00 0.00 39.95 3.77
5451 7285 4.459331 CCAACGATGCCGCAACCG 62.459 66.667 14.49 14.49 39.95 4.44
5461 7295 2.577059 CGCAACCGGAAGCTCCTA 59.423 61.111 9.46 0.00 33.30 2.94
5462 7296 1.810030 CGCAACCGGAAGCTCCTAC 60.810 63.158 9.46 0.00 33.30 3.18
5463 7297 1.449778 GCAACCGGAAGCTCCTACC 60.450 63.158 9.46 0.00 33.30 3.18
5464 7298 1.153628 CAACCGGAAGCTCCTACCG 60.154 63.158 9.46 12.44 45.24 4.02
5467 7301 2.494918 CGGAAGCTCCTACCGGTG 59.505 66.667 19.93 7.24 42.48 4.94
5468 7302 2.050350 CGGAAGCTCCTACCGGTGA 61.050 63.158 19.93 5.80 42.48 4.02
5469 7303 1.601419 CGGAAGCTCCTACCGGTGAA 61.601 60.000 19.93 0.00 42.48 3.18
5470 7304 0.175989 GGAAGCTCCTACCGGTGAAG 59.824 60.000 19.93 12.71 32.53 3.02
5471 7305 0.460459 GAAGCTCCTACCGGTGAAGC 60.460 60.000 19.93 21.77 0.00 3.86
5472 7306 0.905337 AAGCTCCTACCGGTGAAGCT 60.905 55.000 25.66 25.66 0.00 3.74
5473 7307 0.033405 AGCTCCTACCGGTGAAGCTA 60.033 55.000 28.33 5.46 0.00 3.32
5474 7308 0.822164 GCTCCTACCGGTGAAGCTAA 59.178 55.000 19.93 0.00 0.00 3.09
5475 7309 1.206371 GCTCCTACCGGTGAAGCTAAA 59.794 52.381 19.93 0.00 0.00 1.85
5476 7310 2.354403 GCTCCTACCGGTGAAGCTAAAA 60.354 50.000 19.93 0.00 0.00 1.52
5477 7311 3.522553 CTCCTACCGGTGAAGCTAAAAG 58.477 50.000 19.93 2.29 0.00 2.27
5478 7312 2.007608 CCTACCGGTGAAGCTAAAAGC 58.992 52.381 19.93 0.00 42.84 3.51
5490 7324 1.940613 GCTAAAAGCTATGACCGGTGG 59.059 52.381 14.63 0.00 38.45 4.61
5491 7325 2.419574 GCTAAAAGCTATGACCGGTGGA 60.420 50.000 14.63 0.00 38.45 4.02
5492 7326 2.871096 AAAAGCTATGACCGGTGGAA 57.129 45.000 14.63 0.00 0.00 3.53
5493 7327 3.366052 AAAAGCTATGACCGGTGGAAT 57.634 42.857 14.63 5.42 0.00 3.01
5494 7328 2.622064 AAGCTATGACCGGTGGAATC 57.378 50.000 14.63 0.00 0.00 2.52
5495 7329 0.389391 AGCTATGACCGGTGGAATCG 59.611 55.000 14.63 0.00 0.00 3.34
5503 7337 2.973420 CGGTGGAATCGGAAGCTAC 58.027 57.895 0.00 0.00 0.00 3.58
5504 7338 0.174845 CGGTGGAATCGGAAGCTACA 59.825 55.000 0.00 0.00 0.00 2.74
5505 7339 1.404986 CGGTGGAATCGGAAGCTACAA 60.405 52.381 0.00 0.00 0.00 2.41
5506 7340 2.007608 GGTGGAATCGGAAGCTACAAC 58.992 52.381 0.00 0.00 0.00 3.32
5507 7341 2.354805 GGTGGAATCGGAAGCTACAACT 60.355 50.000 0.00 0.00 0.00 3.16
5508 7342 2.673368 GTGGAATCGGAAGCTACAACTG 59.327 50.000 0.00 0.00 0.00 3.16
5509 7343 2.280628 GGAATCGGAAGCTACAACTGG 58.719 52.381 0.00 0.00 0.00 4.00
5510 7344 1.666189 GAATCGGAAGCTACAACTGGC 59.334 52.381 0.00 0.00 0.00 4.85
5511 7345 0.905357 ATCGGAAGCTACAACTGGCT 59.095 50.000 0.00 0.00 40.85 4.75
5512 7346 0.037326 TCGGAAGCTACAACTGGCTG 60.037 55.000 0.00 0.00 38.91 4.85
5513 7347 1.021390 CGGAAGCTACAACTGGCTGG 61.021 60.000 0.00 0.00 38.91 4.85
5514 7348 0.678048 GGAAGCTACAACTGGCTGGG 60.678 60.000 0.00 0.00 38.91 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
410 411 0.690762 ACCCACCAGTTACTCGCATT 59.309 50.000 0.00 0.00 0.00 3.56
613 614 0.521242 GCCACAAAGACGCGCATTAG 60.521 55.000 5.73 0.00 0.00 1.73
630 631 2.429610 TCCTACGTAGAAGATGTTGGCC 59.570 50.000 24.15 0.00 39.17 5.36
649 650 1.263752 GTAGCTAGTCCACGTCGATCC 59.736 57.143 0.00 0.00 0.00 3.36
860 903 1.197721 GCTGATTGAACTTGTGGACCG 59.802 52.381 0.00 0.00 0.00 4.79
873 916 1.424240 CGACTGCTGCTGCTGATTG 59.576 57.895 25.33 12.34 40.66 2.67
897 943 1.680735 TGCATGTTCCAGGAAACACAC 59.319 47.619 2.45 0.00 41.65 3.82
950 1008 2.356194 GCAAAGGCAAGGCAACCG 60.356 61.111 0.00 0.00 40.72 4.44
951 1009 2.031012 GGCAAAGGCAAGGCAACC 59.969 61.111 0.00 0.00 43.71 3.77
953 1011 2.837291 ACGGCAAAGGCAAGGCAA 60.837 55.556 0.00 0.00 43.71 4.52
954 1012 3.604667 CACGGCAAAGGCAAGGCA 61.605 61.111 0.00 0.00 43.71 4.75
956 1014 4.362476 GGCACGGCAAAGGCAAGG 62.362 66.667 0.00 0.00 43.71 3.61
986 1044 0.178981 AGCCATGACCTTGTTGCAGT 60.179 50.000 0.00 0.00 0.00 4.40
1026 1085 2.164219 GGTGCATTTGTAGTCCCATGTG 59.836 50.000 0.00 0.00 0.00 3.21
1032 1091 2.084546 GTGGAGGTGCATTTGTAGTCC 58.915 52.381 0.00 0.00 0.00 3.85
1043 1112 2.348998 CTGGGAGTGTGGAGGTGC 59.651 66.667 0.00 0.00 0.00 5.01
1077 1146 2.677524 GCCATTGAGCTGGGTGCA 60.678 61.111 0.00 0.00 45.94 4.57
1101 1199 1.700955 GAATGGGAGTAGGCGAGGTA 58.299 55.000 0.00 0.00 0.00 3.08
1155 1256 0.842635 GGCTGGGAGAAGATGATGGT 59.157 55.000 0.00 0.00 0.00 3.55
1156 1257 0.110104 GGGCTGGGAGAAGATGATGG 59.890 60.000 0.00 0.00 0.00 3.51
1817 1925 6.102897 ACCTAGACATATTGTACATGGCTC 57.897 41.667 6.58 0.00 40.99 4.70
2069 2177 7.094118 TGAGGTTATTAAAACCCAAGGAAATCG 60.094 37.037 12.92 0.00 41.18 3.34
2539 2650 1.915078 ATTGCTAGCGGAAGGCCACT 61.915 55.000 10.77 0.00 45.17 4.00
2610 2721 5.190528 TGAAATAGACTCTGGAATTGGCTCT 59.809 40.000 0.00 0.00 0.00 4.09
2886 2997 3.733443 AGTGCACCAACAAAGGAATTC 57.267 42.857 14.63 0.00 0.00 2.17
3037 3148 1.202348 GCCCGGAATTGAGTTTTCCAG 59.798 52.381 0.73 0.00 42.34 3.86
3094 3205 4.271291 GCCCGAGAGATTGTTAAATGAGAC 59.729 45.833 0.00 0.00 0.00 3.36
3117 3228 4.057406 TGCAAGAAACTTTGGAATGGTG 57.943 40.909 0.00 0.00 0.00 4.17
3276 3387 2.127251 CTTTCAAGGCAAGGCGAAAAC 58.873 47.619 0.00 0.00 0.00 2.43
3294 3405 7.072562 AGTGTATATCAGTTGAGGGAGATCTT 58.927 38.462 0.00 0.00 0.00 2.40
3431 3545 1.679032 GGCCTATGACACTGGTTGGAC 60.679 57.143 0.00 0.00 0.00 4.02
3696 3811 4.459685 TCAAGTACTAGTGCTCTGAAGTCC 59.540 45.833 14.27 0.00 0.00 3.85
3714 3829 4.032960 TCCATTTGGCATGTACTCAAGT 57.967 40.909 0.00 0.00 34.44 3.16
3753 3868 3.577649 TGTGTACTCTTAGAGCAGTGC 57.422 47.619 7.13 7.13 32.04 4.40
3972 4096 1.642037 CTGTTCCAGGCATGCTCACG 61.642 60.000 18.92 3.48 0.00 4.35
4026 4150 5.477984 AGTTGGTTGAGCAATGTAACATGAT 59.522 36.000 0.00 0.00 0.00 2.45
4286 4423 3.734293 CGACGACCTGGAAAAGATCTACC 60.734 52.174 0.00 0.94 0.00 3.18
4385 4523 5.148651 AGTCGCTAGAACATTGTAAACCT 57.851 39.130 0.00 0.00 0.00 3.50
4519 4657 2.420372 GGCAAGAAACTAGGTAGCAAGC 59.580 50.000 0.00 0.00 0.00 4.01
4598 4738 6.095377 ACAGCAACAAGAAGAAAAAGAACAG 58.905 36.000 0.00 0.00 0.00 3.16
4606 4776 5.125257 TGTGATGAACAGCAACAAGAAGAAA 59.875 36.000 0.00 0.00 33.78 2.52
4655 4825 0.171903 CATTTCCCTCGGCTTTGCTG 59.828 55.000 0.00 0.00 36.06 4.41
4666 4836 3.330701 TGCTCAAAGGACTACATTTCCCT 59.669 43.478 0.00 0.00 33.01 4.20
4707 4878 1.062206 GTAGCGTCCGTCTTCGAGG 59.938 63.158 0.00 0.00 39.71 4.63
4711 4882 0.585029 CGTACGTAGCGTCCGTCTTC 60.585 60.000 7.22 0.00 41.54 2.87
4712 4883 1.421485 CGTACGTAGCGTCCGTCTT 59.579 57.895 7.22 0.00 41.54 3.01
4715 4886 2.434185 TCCGTACGTAGCGTCCGT 60.434 61.111 15.21 3.97 37.49 4.69
4716 4887 2.322422 CTCCGTACGTAGCGTCCG 59.678 66.667 15.21 0.00 41.54 4.79
4717 4888 1.349973 GACTCCGTACGTAGCGTCC 59.650 63.158 15.21 0.00 41.54 4.79
4719 4890 2.456119 CCGACTCCGTACGTAGCGT 61.456 63.158 15.21 5.15 44.35 5.07
4720 4891 2.322422 CCGACTCCGTACGTAGCG 59.678 66.667 15.21 14.68 0.00 4.26
4722 4893 0.371645 GTGACCGACTCCGTACGTAG 59.628 60.000 15.21 10.76 0.00 3.51
4723 4894 0.037326 AGTGACCGACTCCGTACGTA 60.037 55.000 15.21 0.00 0.00 3.57
4724 4895 0.886490 AAGTGACCGACTCCGTACGT 60.886 55.000 15.21 0.00 31.73 3.57
4725 4896 1.078709 TAAGTGACCGACTCCGTACG 58.921 55.000 8.69 8.69 31.73 3.67
4726 4897 4.882671 TTATAAGTGACCGACTCCGTAC 57.117 45.455 0.00 0.00 31.73 3.67
4727 4898 5.357878 ACAATTATAAGTGACCGACTCCGTA 59.642 40.000 19.08 0.00 31.73 4.02
4728 4899 4.159135 ACAATTATAAGTGACCGACTCCGT 59.841 41.667 19.08 0.00 31.73 4.69
4729 4900 4.503007 CACAATTATAAGTGACCGACTCCG 59.497 45.833 19.08 0.00 37.97 4.63
4730 4901 4.270325 GCACAATTATAAGTGACCGACTCC 59.730 45.833 19.08 0.00 37.97 3.85
4731 4902 5.109903 AGCACAATTATAAGTGACCGACTC 58.890 41.667 19.08 1.21 37.97 3.36
4732 4903 5.086104 AGCACAATTATAAGTGACCGACT 57.914 39.130 19.08 6.13 37.97 4.18
4807 4978 5.067674 ACTGTTTTACTGCAATCAGCTCAAA 59.932 36.000 0.00 0.00 44.10 2.69
4830 5001 7.148306 CCATACAAAATTCACTAGTACCCACAC 60.148 40.741 0.00 0.00 0.00 3.82
4831 5002 6.882140 CCATACAAAATTCACTAGTACCCACA 59.118 38.462 0.00 0.00 0.00 4.17
4835 5006 6.120220 AGCCCATACAAAATTCACTAGTACC 58.880 40.000 0.00 0.00 0.00 3.34
4838 5009 6.948309 AGAAAGCCCATACAAAATTCACTAGT 59.052 34.615 0.00 0.00 0.00 2.57
4839 5010 7.253422 CAGAAAGCCCATACAAAATTCACTAG 58.747 38.462 0.00 0.00 0.00 2.57
4840 5011 6.350110 GCAGAAAGCCCATACAAAATTCACTA 60.350 38.462 0.00 0.00 37.23 2.74
4841 5012 5.567423 GCAGAAAGCCCATACAAAATTCACT 60.567 40.000 0.00 0.00 37.23 3.41
4846 5019 6.518493 CATATGCAGAAAGCCCATACAAAAT 58.482 36.000 0.00 0.00 44.83 1.82
4883 5056 4.851558 GTCCGCAAAATCACAATGACTAAC 59.148 41.667 0.00 0.00 0.00 2.34
4884 5057 4.083003 GGTCCGCAAAATCACAATGACTAA 60.083 41.667 0.00 0.00 0.00 2.24
4885 5058 3.438781 GGTCCGCAAAATCACAATGACTA 59.561 43.478 0.00 0.00 0.00 2.59
4891 5064 0.589223 GACGGTCCGCAAAATCACAA 59.411 50.000 12.28 0.00 0.00 3.33
4898 5071 0.881159 ATGTTTCGACGGTCCGCAAA 60.881 50.000 12.28 5.36 0.00 3.68
4903 5076 0.442699 GCTTGATGTTTCGACGGTCC 59.557 55.000 1.91 0.00 0.00 4.46
4905 5078 1.808411 ATGCTTGATGTTTCGACGGT 58.192 45.000 0.00 0.00 0.00 4.83
4907 5080 2.348362 TGCTATGCTTGATGTTTCGACG 59.652 45.455 0.00 0.00 0.00 5.12
4916 5089 6.211587 TGTTGCTAAATTGCTATGCTTGAT 57.788 33.333 0.00 0.00 0.00 2.57
4978 5175 0.107703 GACATGATCAGGTCGGCCAA 60.108 55.000 23.22 0.00 37.19 4.52
4997 5194 1.066257 GTTGTGTGCCCTGCAACTG 59.934 57.895 0.00 0.00 41.47 3.16
4998 5195 1.076777 AGTTGTGTGCCCTGCAACT 60.077 52.632 3.66 3.66 45.28 3.16
4999 5196 1.066257 CAGTTGTGTGCCCTGCAAC 59.934 57.895 0.00 0.00 41.47 4.17
5001 5198 1.077140 TTCAGTTGTGTGCCCTGCA 60.077 52.632 0.00 0.00 35.60 4.41
5002 5199 1.656441 CTTCAGTTGTGTGCCCTGC 59.344 57.895 0.00 0.00 0.00 4.85
5062 6896 0.541296 AATGAACTGCTGCCCTTGCT 60.541 50.000 0.00 0.00 38.71 3.91
5071 6905 2.026641 ACAGCAACACAATGAACTGCT 58.973 42.857 2.83 2.83 43.96 4.24
5109 6943 7.826690 TGGCATCTTCTACAACCTTAAAAATC 58.173 34.615 0.00 0.00 0.00 2.17
5111 6945 7.232534 ACATGGCATCTTCTACAACCTTAAAAA 59.767 33.333 0.00 0.00 0.00 1.94
5116 6950 4.012374 CACATGGCATCTTCTACAACCTT 58.988 43.478 0.00 0.00 0.00 3.50
5149 6983 6.404293 CGGTCGTCCAATTTTAATCAATTCCT 60.404 38.462 0.00 0.00 0.00 3.36
5151 6985 5.741982 CCGGTCGTCCAATTTTAATCAATTC 59.258 40.000 0.00 0.00 0.00 2.17
5173 7007 3.801997 ATCAGGAGCCTTGGCCCG 61.802 66.667 8.17 6.40 0.00 6.13
5176 7010 0.969409 AAAGCATCAGGAGCCTTGGC 60.969 55.000 2.97 2.97 0.00 4.52
5185 7019 1.134367 CAGCATGTGGAAAGCATCAGG 59.866 52.381 0.00 0.00 0.00 3.86
5200 7034 2.987596 TAGCAGCCTTGGCCAGCAT 61.988 57.895 18.35 7.08 0.00 3.79
5201 7035 3.649889 TAGCAGCCTTGGCCAGCA 61.650 61.111 18.35 0.00 0.00 4.41
5202 7036 3.136791 GTAGCAGCCTTGGCCAGC 61.137 66.667 5.11 7.31 0.00 4.85
5203 7037 2.821366 CGTAGCAGCCTTGGCCAG 60.821 66.667 5.11 0.00 0.00 4.85
5204 7038 3.315142 CTCGTAGCAGCCTTGGCCA 62.315 63.158 0.00 0.00 0.00 5.36
5205 7039 2.512515 CTCGTAGCAGCCTTGGCC 60.513 66.667 8.17 0.00 0.00 5.36
5216 7050 1.795768 TTGCCTTTCACAGCTCGTAG 58.204 50.000 0.00 0.00 0.00 3.51
5217 7051 2.248280 TTTGCCTTTCACAGCTCGTA 57.752 45.000 0.00 0.00 0.00 3.43
5218 7052 1.334869 CTTTTGCCTTTCACAGCTCGT 59.665 47.619 0.00 0.00 0.00 4.18
5230 7064 2.907179 CGACCCCTCCCTTTTGCCT 61.907 63.158 0.00 0.00 0.00 4.75
5231 7065 2.361230 CGACCCCTCCCTTTTGCC 60.361 66.667 0.00 0.00 0.00 4.52
5232 7066 2.361230 CCGACCCCTCCCTTTTGC 60.361 66.667 0.00 0.00 0.00 3.68
5292 7126 2.456119 CCTCGCAACACCGATCAGC 61.456 63.158 0.00 0.00 36.54 4.26
5293 7127 2.456119 GCCTCGCAACACCGATCAG 61.456 63.158 0.00 0.00 36.54 2.90
5294 7128 2.434185 GCCTCGCAACACCGATCA 60.434 61.111 0.00 0.00 36.54 2.92
5295 7129 3.195698 GGCCTCGCAACACCGATC 61.196 66.667 0.00 0.00 36.54 3.69
5309 7143 4.541648 TAGCTCCTCCCCTCGGCC 62.542 72.222 0.00 0.00 0.00 6.13
5310 7144 3.228017 GTAGCTCCTCCCCTCGGC 61.228 72.222 0.00 0.00 0.00 5.54
5311 7145 2.907917 CGTAGCTCCTCCCCTCGG 60.908 72.222 0.00 0.00 0.00 4.63
5312 7146 1.894756 CTCGTAGCTCCTCCCCTCG 60.895 68.421 0.00 0.00 0.00 4.63
5313 7147 1.529713 CCTCGTAGCTCCTCCCCTC 60.530 68.421 0.00 0.00 0.00 4.30
5314 7148 2.318172 ACCTCGTAGCTCCTCCCCT 61.318 63.158 0.00 0.00 0.00 4.79
5315 7149 2.128507 CACCTCGTAGCTCCTCCCC 61.129 68.421 0.00 0.00 0.00 4.81
5316 7150 2.787567 GCACCTCGTAGCTCCTCCC 61.788 68.421 0.00 0.00 0.00 4.30
5317 7151 0.465824 TAGCACCTCGTAGCTCCTCC 60.466 60.000 0.00 0.00 42.05 4.30
5318 7152 0.664224 GTAGCACCTCGTAGCTCCTC 59.336 60.000 0.00 0.00 42.05 3.71
5319 7153 0.034380 TGTAGCACCTCGTAGCTCCT 60.034 55.000 0.00 0.00 42.05 3.69
5320 7154 0.815734 TTGTAGCACCTCGTAGCTCC 59.184 55.000 0.00 0.00 42.05 4.70
5321 7155 2.733517 GATTGTAGCACCTCGTAGCTC 58.266 52.381 0.00 0.00 42.05 4.09
5322 7156 1.065701 CGATTGTAGCACCTCGTAGCT 59.934 52.381 0.00 0.00 44.55 3.32
5323 7157 1.065102 TCGATTGTAGCACCTCGTAGC 59.935 52.381 0.00 0.00 33.10 3.58
5324 7158 2.717530 GTCGATTGTAGCACCTCGTAG 58.282 52.381 0.00 0.00 33.10 3.51
5325 7159 1.063027 CGTCGATTGTAGCACCTCGTA 59.937 52.381 0.00 0.00 33.10 3.43
5326 7160 0.179171 CGTCGATTGTAGCACCTCGT 60.179 55.000 0.00 0.00 33.10 4.18
5327 7161 0.098200 TCGTCGATTGTAGCACCTCG 59.902 55.000 0.00 0.00 0.00 4.63
5328 7162 2.186076 CTTCGTCGATTGTAGCACCTC 58.814 52.381 0.00 0.00 0.00 3.85
5329 7163 1.736032 GCTTCGTCGATTGTAGCACCT 60.736 52.381 10.94 0.00 0.00 4.00
5330 7164 0.645868 GCTTCGTCGATTGTAGCACC 59.354 55.000 10.94 0.00 0.00 5.01
5331 7165 1.584308 GAGCTTCGTCGATTGTAGCAC 59.416 52.381 16.63 8.45 34.37 4.40
5332 7166 1.794076 CGAGCTTCGTCGATTGTAGCA 60.794 52.381 16.63 0.00 42.85 3.49
5333 7167 0.840729 CGAGCTTCGTCGATTGTAGC 59.159 55.000 8.30 8.30 42.85 3.58
5334 7168 2.453650 TCGAGCTTCGTCGATTGTAG 57.546 50.000 0.00 0.00 43.91 2.74
5348 7182 2.881074 TCACATGTAGAAGCTTCGAGC 58.119 47.619 20.43 14.39 42.84 5.03
5356 7190 7.202016 TGGTTTTTAGCTTCACATGTAGAAG 57.798 36.000 22.94 22.94 44.08 2.85
5357 7191 7.446931 TCATGGTTTTTAGCTTCACATGTAGAA 59.553 33.333 0.00 4.36 36.52 2.10
5358 7192 6.939730 TCATGGTTTTTAGCTTCACATGTAGA 59.060 34.615 0.00 0.00 36.52 2.59
5359 7193 7.144722 TCATGGTTTTTAGCTTCACATGTAG 57.855 36.000 0.00 0.00 36.52 2.74
5360 7194 7.413988 CGATCATGGTTTTTAGCTTCACATGTA 60.414 37.037 0.00 0.00 36.52 2.29
5361 7195 6.594788 ATCATGGTTTTTAGCTTCACATGT 57.405 33.333 0.00 0.00 36.52 3.21
5362 7196 5.740569 CGATCATGGTTTTTAGCTTCACATG 59.259 40.000 0.00 0.00 36.48 3.21
5363 7197 5.163622 CCGATCATGGTTTTTAGCTTCACAT 60.164 40.000 0.00 0.00 0.00 3.21
5364 7198 4.155826 CCGATCATGGTTTTTAGCTTCACA 59.844 41.667 0.00 0.00 0.00 3.58
5365 7199 4.662145 CCGATCATGGTTTTTAGCTTCAC 58.338 43.478 0.00 0.00 0.00 3.18
5366 7200 3.128589 GCCGATCATGGTTTTTAGCTTCA 59.871 43.478 0.00 0.00 0.00 3.02
5367 7201 3.695816 GCCGATCATGGTTTTTAGCTTC 58.304 45.455 0.00 0.00 0.00 3.86
5368 7202 2.097466 CGCCGATCATGGTTTTTAGCTT 59.903 45.455 0.00 0.00 0.00 3.74
5369 7203 1.670811 CGCCGATCATGGTTTTTAGCT 59.329 47.619 0.00 0.00 0.00 3.32
5370 7204 1.668751 TCGCCGATCATGGTTTTTAGC 59.331 47.619 0.00 0.00 0.00 3.09
5371 7205 4.349663 TTTCGCCGATCATGGTTTTTAG 57.650 40.909 0.00 0.00 0.00 1.85
5372 7206 4.396478 TGATTTCGCCGATCATGGTTTTTA 59.604 37.500 0.00 0.00 0.00 1.52
5373 7207 3.192422 TGATTTCGCCGATCATGGTTTTT 59.808 39.130 0.00 0.00 0.00 1.94
5374 7208 2.752354 TGATTTCGCCGATCATGGTTTT 59.248 40.909 0.00 0.00 0.00 2.43
5375 7209 2.355756 CTGATTTCGCCGATCATGGTTT 59.644 45.455 0.00 0.00 33.39 3.27
5376 7210 1.942657 CTGATTTCGCCGATCATGGTT 59.057 47.619 0.00 0.00 33.39 3.67
5377 7211 1.138859 TCTGATTTCGCCGATCATGGT 59.861 47.619 0.00 0.00 33.39 3.55
5378 7212 1.869774 TCTGATTTCGCCGATCATGG 58.130 50.000 0.00 0.00 33.39 3.66
5379 7213 2.349249 GCTTCTGATTTCGCCGATCATG 60.349 50.000 0.00 0.00 33.39 3.07
5380 7214 1.869767 GCTTCTGATTTCGCCGATCAT 59.130 47.619 0.00 0.00 33.39 2.45
5381 7215 1.134699 AGCTTCTGATTTCGCCGATCA 60.135 47.619 0.00 0.00 32.87 2.92
5382 7216 1.260033 CAGCTTCTGATTTCGCCGATC 59.740 52.381 0.00 0.00 32.44 3.69
5383 7217 1.293924 CAGCTTCTGATTTCGCCGAT 58.706 50.000 0.00 0.00 32.44 4.18
5384 7218 1.361668 GCAGCTTCTGATTTCGCCGA 61.362 55.000 0.00 0.00 32.44 5.54
5385 7219 1.061570 GCAGCTTCTGATTTCGCCG 59.938 57.895 0.00 0.00 32.44 6.46
5386 7220 0.523072 TTGCAGCTTCTGATTTCGCC 59.477 50.000 0.00 0.00 32.44 5.54
5387 7221 1.611043 GTTGCAGCTTCTGATTTCGC 58.389 50.000 0.00 0.00 32.44 4.70
5388 7222 1.464687 CGGTTGCAGCTTCTGATTTCG 60.465 52.381 0.00 0.00 32.44 3.46
5389 7223 1.135575 CCGGTTGCAGCTTCTGATTTC 60.136 52.381 0.00 0.00 32.44 2.17
5390 7224 0.883833 CCGGTTGCAGCTTCTGATTT 59.116 50.000 0.00 0.00 32.44 2.17
5391 7225 0.250901 ACCGGTTGCAGCTTCTGATT 60.251 50.000 0.00 0.00 32.44 2.57
5392 7226 0.613260 TACCGGTTGCAGCTTCTGAT 59.387 50.000 15.04 0.00 32.44 2.90
5393 7227 0.037326 CTACCGGTTGCAGCTTCTGA 60.037 55.000 15.04 0.00 32.44 3.27
5394 7228 1.021390 CCTACCGGTTGCAGCTTCTG 61.021 60.000 15.04 0.00 34.12 3.02
5395 7229 1.296715 CCTACCGGTTGCAGCTTCT 59.703 57.895 15.04 0.00 0.00 2.85
5396 7230 1.745489 CCCTACCGGTTGCAGCTTC 60.745 63.158 15.04 0.00 0.00 3.86
5397 7231 2.351276 CCCTACCGGTTGCAGCTT 59.649 61.111 15.04 0.00 0.00 3.74
5398 7232 4.410400 GCCCTACCGGTTGCAGCT 62.410 66.667 15.04 0.00 0.00 4.24
5399 7233 4.715523 TGCCCTACCGGTTGCAGC 62.716 66.667 15.04 16.98 0.00 5.25
5400 7234 2.746277 GTGCCCTACCGGTTGCAG 60.746 66.667 21.84 10.67 33.80 4.41
5401 7235 4.690719 CGTGCCCTACCGGTTGCA 62.691 66.667 15.04 17.40 0.00 4.08
5407 7241 4.728102 TGTTCGCGTGCCCTACCG 62.728 66.667 5.77 0.00 0.00 4.02
5408 7242 3.116531 GTGTTCGCGTGCCCTACC 61.117 66.667 5.77 0.00 0.00 3.18
5409 7243 3.475774 CGTGTTCGCGTGCCCTAC 61.476 66.667 5.77 0.00 0.00 3.18
5419 7253 2.829206 TTGGTTGCCAGCGTGTTCG 61.829 57.895 0.00 0.00 33.81 3.95
5420 7254 1.299089 GTTGGTTGCCAGCGTGTTC 60.299 57.895 0.00 0.00 33.81 3.18
5421 7255 2.804856 GTTGGTTGCCAGCGTGTT 59.195 55.556 0.00 0.00 33.81 3.32
5426 7260 2.126346 GCATCGTTGGTTGCCAGC 60.126 61.111 0.00 0.00 33.81 4.85
5430 7264 3.550339 TTGCGGCATCGTTGGTTGC 62.550 57.895 2.28 0.00 37.99 4.17
5431 7265 1.729131 GTTGCGGCATCGTTGGTTG 60.729 57.895 2.28 0.00 38.89 3.77
5432 7266 2.642700 GTTGCGGCATCGTTGGTT 59.357 55.556 2.28 0.00 38.89 3.67
5433 7267 3.361977 GGTTGCGGCATCGTTGGT 61.362 61.111 2.28 0.00 38.89 3.67
5434 7268 4.459331 CGGTTGCGGCATCGTTGG 62.459 66.667 2.28 0.00 38.89 3.77
5435 7269 4.459331 CCGGTTGCGGCATCGTTG 62.459 66.667 19.50 7.29 38.89 4.10
5436 7270 4.690719 TCCGGTTGCGGCATCGTT 62.691 61.111 19.50 0.00 38.89 3.85
5437 7271 4.690719 TTCCGGTTGCGGCATCGT 62.691 61.111 19.50 0.00 38.89 3.73
5438 7272 3.864686 CTTCCGGTTGCGGCATCG 61.865 66.667 2.28 11.22 39.81 3.84
5439 7273 4.179579 GCTTCCGGTTGCGGCATC 62.180 66.667 2.28 2.36 0.00 3.91
5440 7274 4.722700 AGCTTCCGGTTGCGGCAT 62.723 61.111 2.28 0.00 0.00 4.40
5443 7277 3.014085 TAGGAGCTTCCGGTTGCGG 62.014 63.158 0.00 0.00 42.75 5.69
5444 7278 1.810030 GTAGGAGCTTCCGGTTGCG 60.810 63.158 0.00 0.00 42.75 4.85
5445 7279 1.449778 GGTAGGAGCTTCCGGTTGC 60.450 63.158 0.00 7.39 42.75 4.17
5446 7280 1.153628 CGGTAGGAGCTTCCGGTTG 60.154 63.158 0.00 0.00 42.75 3.77
5447 7281 3.295800 CGGTAGGAGCTTCCGGTT 58.704 61.111 0.00 0.00 42.75 4.44
5450 7284 1.601419 TTCACCGGTAGGAGCTTCCG 61.601 60.000 6.87 11.66 42.75 4.30
5451 7285 0.175989 CTTCACCGGTAGGAGCTTCC 59.824 60.000 6.87 0.00 41.02 3.46
5452 7286 0.460459 GCTTCACCGGTAGGAGCTTC 60.460 60.000 22.70 0.00 41.02 3.86
5453 7287 0.905337 AGCTTCACCGGTAGGAGCTT 60.905 55.000 25.43 14.63 40.95 3.74
5454 7288 0.033405 TAGCTTCACCGGTAGGAGCT 60.033 55.000 30.27 30.27 44.44 4.09
5455 7289 0.822164 TTAGCTTCACCGGTAGGAGC 59.178 55.000 22.57 22.57 41.02 4.70
5456 7290 3.522553 CTTTTAGCTTCACCGGTAGGAG 58.477 50.000 6.87 7.42 41.02 3.69
5457 7291 2.354403 GCTTTTAGCTTCACCGGTAGGA 60.354 50.000 6.87 0.00 38.53 2.94
5458 7292 2.007608 GCTTTTAGCTTCACCGGTAGG 58.992 52.381 6.87 0.86 40.12 3.18
5470 7304 1.940613 CCACCGGTCATAGCTTTTAGC 59.059 52.381 2.59 0.00 42.84 3.09
5471 7305 3.536956 TCCACCGGTCATAGCTTTTAG 57.463 47.619 2.59 0.00 0.00 1.85
5472 7306 3.985019 TTCCACCGGTCATAGCTTTTA 57.015 42.857 2.59 0.00 0.00 1.52
5473 7307 2.871096 TTCCACCGGTCATAGCTTTT 57.129 45.000 2.59 0.00 0.00 2.27
5474 7308 2.741878 CGATTCCACCGGTCATAGCTTT 60.742 50.000 2.59 0.00 0.00 3.51
5475 7309 1.202533 CGATTCCACCGGTCATAGCTT 60.203 52.381 2.59 0.00 0.00 3.74
5476 7310 0.389391 CGATTCCACCGGTCATAGCT 59.611 55.000 2.59 0.00 0.00 3.32
5477 7311 0.600255 CCGATTCCACCGGTCATAGC 60.600 60.000 2.59 0.00 41.91 2.97
5478 7312 1.037493 TCCGATTCCACCGGTCATAG 58.963 55.000 2.59 0.00 46.53 2.23
5479 7313 1.411246 CTTCCGATTCCACCGGTCATA 59.589 52.381 2.59 0.00 46.53 2.15
5480 7314 0.178068 CTTCCGATTCCACCGGTCAT 59.822 55.000 2.59 0.00 46.53 3.06
5481 7315 1.594833 CTTCCGATTCCACCGGTCA 59.405 57.895 2.59 0.00 46.53 4.02
5482 7316 1.814169 GCTTCCGATTCCACCGGTC 60.814 63.158 2.59 0.00 46.53 4.79
5483 7317 0.974010 TAGCTTCCGATTCCACCGGT 60.974 55.000 0.00 0.00 46.53 5.28
5485 7319 0.174845 TGTAGCTTCCGATTCCACCG 59.825 55.000 0.00 0.00 0.00 4.94
5486 7320 2.007608 GTTGTAGCTTCCGATTCCACC 58.992 52.381 0.00 0.00 0.00 4.61
5487 7321 2.673368 CAGTTGTAGCTTCCGATTCCAC 59.327 50.000 0.00 0.00 0.00 4.02
5488 7322 2.354704 CCAGTTGTAGCTTCCGATTCCA 60.355 50.000 0.00 0.00 0.00 3.53
5489 7323 2.280628 CCAGTTGTAGCTTCCGATTCC 58.719 52.381 0.00 0.00 0.00 3.01
5490 7324 1.666189 GCCAGTTGTAGCTTCCGATTC 59.334 52.381 0.00 0.00 0.00 2.52
5491 7325 1.279271 AGCCAGTTGTAGCTTCCGATT 59.721 47.619 0.00 0.00 35.22 3.34
5492 7326 0.905357 AGCCAGTTGTAGCTTCCGAT 59.095 50.000 0.00 0.00 35.22 4.18
5493 7327 0.037326 CAGCCAGTTGTAGCTTCCGA 60.037 55.000 0.00 0.00 37.18 4.55
5494 7328 1.021390 CCAGCCAGTTGTAGCTTCCG 61.021 60.000 0.00 0.00 37.18 4.30
5495 7329 0.678048 CCCAGCCAGTTGTAGCTTCC 60.678 60.000 0.00 0.00 37.18 3.46
5496 7330 2.859992 CCCAGCCAGTTGTAGCTTC 58.140 57.895 0.00 0.00 37.18 3.86


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

AutoCloner maintained by Alex Coulton.