Multiple sequence alignment - TraesCS1B01G279100

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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 TraesCS1B01G279100 chr1B 100.000 3127 0 0 1 3127 487427964 487424838 0.000000e+00 5775.0
1 TraesCS1B01G279100 chr1B 84.485 709 75 18 2366 3068 292337581 292338260 0.000000e+00 667.0
2 TraesCS1B01G279100 chr1A 93.364 1507 62 23 444 1935 463248790 463247307 0.000000e+00 2194.0
3 TraesCS1B01G279100 chr1A 85.655 725 80 16 2367 3068 592652772 592653495 0.000000e+00 741.0
4 TraesCS1B01G279100 chr1A 96.818 220 5 1 1931 2150 463247025 463246808 1.770000e-97 366.0
5 TraesCS1B01G279100 chr1D 92.593 1350 55 18 827 2169 364030536 364029225 0.000000e+00 1897.0
6 TraesCS1B01G279100 chr1D 92.674 546 28 7 284 818 364031127 364030583 0.000000e+00 776.0
7 TraesCS1B01G279100 chr1D 85.975 713 78 18 2374 3068 481728432 481727724 0.000000e+00 743.0
8 TraesCS1B01G279100 chr1D 85.211 284 23 10 1 282 364031445 364031179 1.100000e-69 274.0
9 TraesCS1B01G279100 chr1D 80.769 130 23 1 31 158 45281789 45281918 1.980000e-17 100.0
10 TraesCS1B01G279100 chr6B 98.425 762 12 0 2366 3127 10182660 10181899 0.000000e+00 1341.0
11 TraesCS1B01G279100 chr4A 97.105 760 21 1 2368 3127 693783336 693782578 0.000000e+00 1280.0
12 TraesCS1B01G279100 chr4A 77.953 127 25 2 30 153 125377483 125377357 3.340000e-10 76.8
13 TraesCS1B01G279100 chr2D 85.894 716 77 16 2370 3068 558908470 558909178 0.000000e+00 741.0
14 TraesCS1B01G279100 chr5A 84.924 723 87 19 2365 3068 666818453 666819172 0.000000e+00 712.0
15 TraesCS1B01G279100 chr4B 95.153 392 15 4 2731 3120 615158247 615157858 1.590000e-172 616.0
16 TraesCS1B01G279100 chr4B 95.935 369 14 1 2366 2733 615160737 615160369 5.770000e-167 597.0
17 TraesCS1B01G279100 chr7A 83.158 475 62 17 2359 2817 161726488 161726960 4.820000e-113 418.0
18 TraesCS1B01G279100 chr7D 82.927 123 19 2 32 152 5102008 5102130 3.300000e-20 110.0
19 TraesCS1B01G279100 chr7D 74.138 290 60 11 4 282 29728811 29728526 4.270000e-19 106.0
20 TraesCS1B01G279100 chr7D 82.301 113 18 2 31 141 218492339 218492451 2.570000e-16 97.1
21 TraesCS1B01G279100 chr4D 74.717 265 48 15 30 279 341527706 341527966 1.980000e-17 100.0
22 TraesCS1B01G279100 chrUn 79.167 144 28 1 31 172 299938105 299937962 7.140000e-17 99.0
23 TraesCS1B01G279100 chrUn 80.620 129 23 2 31 157 337008899 337009027 7.140000e-17 99.0


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 TraesCS1B01G279100 chr1B 487424838 487427964 3126 True 5775.000000 5775 100.000000 1 3127 1 chr1B.!!$R1 3126
1 TraesCS1B01G279100 chr1B 292337581 292338260 679 False 667.000000 667 84.485000 2366 3068 1 chr1B.!!$F1 702
2 TraesCS1B01G279100 chr1A 463246808 463248790 1982 True 1280.000000 2194 95.091000 444 2150 2 chr1A.!!$R1 1706
3 TraesCS1B01G279100 chr1A 592652772 592653495 723 False 741.000000 741 85.655000 2367 3068 1 chr1A.!!$F1 701
4 TraesCS1B01G279100 chr1D 364029225 364031445 2220 True 982.333333 1897 90.159333 1 2169 3 chr1D.!!$R2 2168
5 TraesCS1B01G279100 chr1D 481727724 481728432 708 True 743.000000 743 85.975000 2374 3068 1 chr1D.!!$R1 694
6 TraesCS1B01G279100 chr6B 10181899 10182660 761 True 1341.000000 1341 98.425000 2366 3127 1 chr6B.!!$R1 761
7 TraesCS1B01G279100 chr4A 693782578 693783336 758 True 1280.000000 1280 97.105000 2368 3127 1 chr4A.!!$R2 759
8 TraesCS1B01G279100 chr2D 558908470 558909178 708 False 741.000000 741 85.894000 2370 3068 1 chr2D.!!$F1 698
9 TraesCS1B01G279100 chr5A 666818453 666819172 719 False 712.000000 712 84.924000 2365 3068 1 chr5A.!!$F1 703
10 TraesCS1B01G279100 chr4B 615157858 615160737 2879 True 606.500000 616 95.544000 2366 3120 2 chr4B.!!$R1 754

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
205 206 0.166814 GCTTGTTCTAACAGCGGCAG 59.833 55.0 1.45 0.0 40.5 4.85 F
939 1046 0.319728 GTGGCAGTGCAAGAGAGAGA 59.680 55.0 18.61 0.0 0.0 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 1890 0.318441 CTTCTTCTCCCACAGCGACA 59.682 55.0 0.00 0.00 0.0 4.35 R
2222 2626 0.037139 TCCCAAACATACACGGTCCG 60.037 55.0 10.48 10.48 0.0 4.79 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
48 49 4.092091 GTCACGAGATTTGGTGTCAGATTC 59.908 45.833 0.00 0.00 34.92 2.52
74 75 7.719778 TCAGATCTATTCAATGATTCAACGG 57.280 36.000 0.00 0.00 0.00 4.44
110 111 2.271173 GGCGTTGGTCCTTAGGGG 59.729 66.667 0.00 0.00 0.00 4.79
113 114 1.607612 CGTTGGTCCTTAGGGGCAT 59.392 57.895 0.00 0.00 39.39 4.40
114 115 0.834612 CGTTGGTCCTTAGGGGCATA 59.165 55.000 0.00 0.00 39.39 3.14
115 116 1.202651 CGTTGGTCCTTAGGGGCATAG 60.203 57.143 0.00 0.00 39.39 2.23
117 118 1.802553 TGGTCCTTAGGGGCATAGAC 58.197 55.000 0.00 0.00 39.39 2.59
129 130 3.053455 GGGCATAGACGAAGATTTCTCG 58.947 50.000 0.00 0.00 0.00 4.04
130 131 3.053455 GGCATAGACGAAGATTTCTCGG 58.947 50.000 0.00 0.00 0.00 4.63
153 154 2.224281 TGTCATCGACAAAGTCAAGCCT 60.224 45.455 0.00 0.00 39.78 4.58
160 161 1.141657 ACAAAGTCAAGCCTGCTCTGA 59.858 47.619 0.00 0.00 0.00 3.27
165 166 2.170187 AGTCAAGCCTGCTCTGATAAGG 59.830 50.000 0.00 2.24 0.00 2.69
167 168 1.487976 CAAGCCTGCTCTGATAAGGGA 59.512 52.381 7.62 0.00 0.00 4.20
172 173 2.128729 GCTCTGATAAGGGAGCGGT 58.871 57.895 0.00 0.00 44.01 5.68
174 175 0.312416 CTCTGATAAGGGAGCGGTCG 59.688 60.000 8.77 0.00 0.00 4.79
175 176 1.300233 CTGATAAGGGAGCGGTCGC 60.300 63.158 22.56 22.56 42.33 5.19
176 177 2.016393 CTGATAAGGGAGCGGTCGCA 62.016 60.000 29.75 13.56 44.88 5.10
178 179 2.017559 GATAAGGGAGCGGTCGCAGT 62.018 60.000 29.75 20.23 44.88 4.40
179 180 2.298158 ATAAGGGAGCGGTCGCAGTG 62.298 60.000 29.75 0.00 44.88 3.66
192 193 2.972505 CAGTGTCGGCGGCTTGTT 60.973 61.111 14.51 0.00 0.00 2.83
193 194 2.665185 AGTGTCGGCGGCTTGTTC 60.665 61.111 14.51 0.00 0.00 3.18
194 195 2.665185 GTGTCGGCGGCTTGTTCT 60.665 61.111 14.51 0.00 0.00 3.01
195 196 1.373748 GTGTCGGCGGCTTGTTCTA 60.374 57.895 14.51 0.00 0.00 2.10
196 197 0.947180 GTGTCGGCGGCTTGTTCTAA 60.947 55.000 14.51 0.00 0.00 2.10
197 198 0.947180 TGTCGGCGGCTTGTTCTAAC 60.947 55.000 14.51 0.00 0.00 2.34
198 199 0.947180 GTCGGCGGCTTGTTCTAACA 60.947 55.000 3.23 0.00 37.08 2.41
199 200 0.669318 TCGGCGGCTTGTTCTAACAG 60.669 55.000 7.21 0.00 40.50 3.16
200 201 1.502190 GGCGGCTTGTTCTAACAGC 59.498 57.895 0.00 8.06 40.50 4.40
201 202 1.132640 GCGGCTTGTTCTAACAGCG 59.867 57.895 0.00 0.00 40.50 5.18
202 203 1.787847 CGGCTTGTTCTAACAGCGG 59.212 57.895 0.00 3.83 40.50 5.52
203 204 1.502190 GGCTTGTTCTAACAGCGGC 59.498 57.895 0.00 0.00 40.50 6.53
204 205 1.234615 GGCTTGTTCTAACAGCGGCA 61.235 55.000 1.45 0.00 40.50 5.69
205 206 0.166814 GCTTGTTCTAACAGCGGCAG 59.833 55.000 1.45 0.00 40.50 4.85
206 207 0.166814 CTTGTTCTAACAGCGGCAGC 59.833 55.000 0.00 0.00 40.50 5.25
326 379 3.645687 GGAGAGTCAGATAGGGCAATTCT 59.354 47.826 0.00 0.00 0.00 2.40
354 407 3.145286 TGAGATATGAGCTCAGACCTCG 58.855 50.000 24.30 0.00 37.46 4.63
384 437 4.406069 CGTTCGAATCAAACAAGATGCAT 58.594 39.130 0.00 0.00 0.00 3.96
386 439 5.156355 GTTCGAATCAAACAAGATGCATGT 58.844 37.500 2.46 0.00 0.00 3.21
395 448 9.715121 ATCAAACAAGATGCATGTATTCTTTTT 57.285 25.926 2.46 0.00 0.00 1.94
529 589 4.572389 CGGGGAAAGTTTGAGTGATCTATG 59.428 45.833 0.00 0.00 0.00 2.23
663 725 4.543689 AGTCCGTAGATTTATGGTGAGGA 58.456 43.478 1.65 0.00 37.26 3.71
713 781 0.464036 TGTGTCCTGTCAGTCACCAC 59.536 55.000 17.13 10.38 0.00 4.16
740 809 2.243407 GTCTCTAAAGTGCACGTCTCG 58.757 52.381 12.01 0.47 0.00 4.04
744 813 1.979469 CTAAAGTGCACGTCTCGTCAG 59.021 52.381 12.01 0.00 38.32 3.51
771 841 4.028993 TCCAATGGACCTGACCTAAAAC 57.971 45.455 0.00 0.00 0.00 2.43
791 861 1.131826 GAACCACATACACGCACGC 59.868 57.895 0.00 0.00 0.00 5.34
939 1046 0.319728 GTGGCAGTGCAAGAGAGAGA 59.680 55.000 18.61 0.00 0.00 3.10
940 1047 0.607112 TGGCAGTGCAAGAGAGAGAG 59.393 55.000 18.61 0.00 0.00 3.20
941 1048 0.894141 GGCAGTGCAAGAGAGAGAGA 59.106 55.000 18.61 0.00 0.00 3.10
942 1049 1.135024 GGCAGTGCAAGAGAGAGAGAG 60.135 57.143 18.61 0.00 0.00 3.20
943 1050 1.818060 GCAGTGCAAGAGAGAGAGAGA 59.182 52.381 11.09 0.00 0.00 3.10
944 1051 2.159338 GCAGTGCAAGAGAGAGAGAGAG 60.159 54.545 11.09 0.00 0.00 3.20
945 1052 3.346315 CAGTGCAAGAGAGAGAGAGAGA 58.654 50.000 0.00 0.00 0.00 3.10
946 1053 3.376234 CAGTGCAAGAGAGAGAGAGAGAG 59.624 52.174 0.00 0.00 0.00 3.20
981 1088 3.069729 GGCGATAGGATCTTTACACCTGT 59.930 47.826 0.00 0.00 35.52 4.00
1013 1122 0.465705 AAGATCATGGCGTCCGATGT 59.534 50.000 0.00 0.00 0.00 3.06
1022 1131 1.416813 GCGTCCGATGTCAAGAGCAG 61.417 60.000 0.00 0.00 0.00 4.24
1176 1285 3.649277 CTTCCAGGACTCGGGCGTG 62.649 68.421 0.00 0.00 0.00 5.34
1332 1441 2.064014 GGCAACGTGAAGGTACTGTAC 58.936 52.381 9.46 9.46 40.86 2.90
1333 1442 2.288640 GGCAACGTGAAGGTACTGTACT 60.289 50.000 16.79 0.00 40.86 2.73
1334 1443 3.057315 GGCAACGTGAAGGTACTGTACTA 60.057 47.826 16.79 0.33 40.86 1.82
1445 1558 2.363795 TCGGAGTTCGGGCTGGAT 60.364 61.111 0.00 0.00 39.77 3.41
1694 1807 4.842091 ATCGGCGCGTACACGGTC 62.842 66.667 8.43 0.00 40.23 4.79
1865 1978 3.587061 TCAAGCAGATCCAAGGTTAGGAA 59.413 43.478 0.00 0.00 38.93 3.36
1868 1981 3.846588 AGCAGATCCAAGGTTAGGAAGAA 59.153 43.478 0.00 0.00 38.93 2.52
1950 2353 5.519566 TGTTAATTCGTCTTTGTGTACGTGT 59.480 36.000 0.00 0.00 39.99 4.49
1951 2354 6.694844 TGTTAATTCGTCTTTGTGTACGTGTA 59.305 34.615 0.00 0.00 39.99 2.90
1952 2355 5.565723 AATTCGTCTTTGTGTACGTGTAC 57.434 39.130 0.00 3.21 39.99 2.90
1953 2356 2.638673 TCGTCTTTGTGTACGTGTACG 58.361 47.619 0.00 2.43 46.33 3.67
1997 2400 3.243535 TGAACATCATCTTCTCGATCGGG 60.244 47.826 16.41 13.07 0.00 5.14
2127 2530 4.282195 ACTTACTCAACAGGTTCCTCTGAG 59.718 45.833 18.44 18.44 39.53 3.35
2140 2544 1.002201 CCTCTGAGGATATGCTGCTGG 59.998 57.143 19.13 0.00 37.67 4.85
2150 2554 2.616634 ATGCTGCTGGTCTATCTGTG 57.383 50.000 0.00 0.00 0.00 3.66
2151 2555 0.107993 TGCTGCTGGTCTATCTGTGC 60.108 55.000 0.00 0.00 0.00 4.57
2152 2556 0.813210 GCTGCTGGTCTATCTGTGCC 60.813 60.000 0.00 0.00 0.00 5.01
2157 2561 2.106566 CTGGTCTATCTGTGCCTGAGT 58.893 52.381 0.00 0.00 0.00 3.41
2166 2570 1.827344 CTGTGCCTGAGTCCAGTGATA 59.173 52.381 0.00 0.00 38.74 2.15
2169 2573 2.234908 GTGCCTGAGTCCAGTGATAGTT 59.765 50.000 0.00 0.00 38.74 2.24
2170 2574 2.906389 TGCCTGAGTCCAGTGATAGTTT 59.094 45.455 0.00 0.00 38.74 2.66
2171 2575 3.327757 TGCCTGAGTCCAGTGATAGTTTT 59.672 43.478 0.00 0.00 38.74 2.43
2172 2576 4.202461 TGCCTGAGTCCAGTGATAGTTTTT 60.202 41.667 0.00 0.00 38.74 1.94
2208 2612 6.137794 ACGAGAGTCCAGTGATAGTTAATG 57.862 41.667 0.00 0.00 44.19 1.90
2209 2613 5.652891 ACGAGAGTCCAGTGATAGTTAATGT 59.347 40.000 0.00 0.00 44.19 2.71
2210 2614 6.827251 ACGAGAGTCCAGTGATAGTTAATGTA 59.173 38.462 0.00 0.00 44.19 2.29
2211 2615 7.502895 ACGAGAGTCCAGTGATAGTTAATGTAT 59.497 37.037 0.00 0.00 44.19 2.29
2212 2616 8.018520 CGAGAGTCCAGTGATAGTTAATGTATC 58.981 40.741 0.00 2.31 0.00 2.24
2213 2617 8.768501 AGAGTCCAGTGATAGTTAATGTATCA 57.231 34.615 6.45 6.45 35.06 2.15
2214 2618 9.373450 AGAGTCCAGTGATAGTTAATGTATCAT 57.627 33.333 11.58 0.00 38.76 2.45
2215 2619 9.416794 GAGTCCAGTGATAGTTAATGTATCATG 57.583 37.037 11.58 10.61 38.76 3.07
2216 2620 8.928448 AGTCCAGTGATAGTTAATGTATCATGT 58.072 33.333 11.58 3.39 38.76 3.21
2226 2630 8.589335 AGTTAATGTATCATGTATGAACGGAC 57.411 34.615 0.00 0.00 40.69 4.79
2227 2631 7.656137 AGTTAATGTATCATGTATGAACGGACC 59.344 37.037 0.00 0.00 40.69 4.46
2228 2632 3.972403 TGTATCATGTATGAACGGACCG 58.028 45.455 13.61 13.61 40.69 4.79
2229 2633 3.382227 TGTATCATGTATGAACGGACCGT 59.618 43.478 15.37 15.37 43.97 4.83
2230 2634 2.287393 TCATGTATGAACGGACCGTG 57.713 50.000 22.53 5.33 39.99 4.94
2231 2635 1.546923 TCATGTATGAACGGACCGTGT 59.453 47.619 22.53 12.42 39.99 4.49
2232 2636 2.754002 TCATGTATGAACGGACCGTGTA 59.246 45.455 22.53 13.19 39.99 2.90
2233 2637 3.382227 TCATGTATGAACGGACCGTGTAT 59.618 43.478 22.53 19.26 39.99 2.29
2234 2638 3.153676 TGTATGAACGGACCGTGTATG 57.846 47.619 22.53 0.00 39.99 2.39
2235 2639 2.492881 TGTATGAACGGACCGTGTATGT 59.507 45.455 22.53 3.57 39.99 2.29
2236 2640 2.754946 ATGAACGGACCGTGTATGTT 57.245 45.000 22.53 2.67 39.99 2.71
2237 2641 2.529780 TGAACGGACCGTGTATGTTT 57.470 45.000 22.53 1.78 39.99 2.83
2238 2642 2.136728 TGAACGGACCGTGTATGTTTG 58.863 47.619 22.53 0.00 39.99 2.93
2239 2643 1.461897 GAACGGACCGTGTATGTTTGG 59.538 52.381 22.53 0.00 39.99 3.28
2240 2644 0.320946 ACGGACCGTGTATGTTTGGG 60.321 55.000 21.02 0.00 39.18 4.12
2241 2645 0.037139 CGGACCGTGTATGTTTGGGA 60.037 55.000 5.48 0.00 0.00 4.37
2242 2646 1.445871 GGACCGTGTATGTTTGGGAC 58.554 55.000 0.00 0.00 0.00 4.46
2243 2647 1.002773 GGACCGTGTATGTTTGGGACT 59.997 52.381 0.00 0.00 0.00 3.85
2244 2648 2.073816 GACCGTGTATGTTTGGGACTG 58.926 52.381 0.00 0.00 0.00 3.51
2245 2649 1.695242 ACCGTGTATGTTTGGGACTGA 59.305 47.619 0.00 0.00 0.00 3.41
2246 2650 2.304761 ACCGTGTATGTTTGGGACTGAT 59.695 45.455 0.00 0.00 0.00 2.90
2247 2651 2.677836 CCGTGTATGTTTGGGACTGATG 59.322 50.000 0.00 0.00 0.00 3.07
2248 2652 3.595173 CGTGTATGTTTGGGACTGATGA 58.405 45.455 0.00 0.00 0.00 2.92
2249 2653 4.191544 CGTGTATGTTTGGGACTGATGAT 58.808 43.478 0.00 0.00 0.00 2.45
2250 2654 4.034394 CGTGTATGTTTGGGACTGATGATG 59.966 45.833 0.00 0.00 0.00 3.07
2251 2655 4.943705 GTGTATGTTTGGGACTGATGATGT 59.056 41.667 0.00 0.00 0.00 3.06
2252 2656 5.065218 GTGTATGTTTGGGACTGATGATGTC 59.935 44.000 0.00 0.00 0.00 3.06
2253 2657 4.581309 ATGTTTGGGACTGATGATGTCT 57.419 40.909 0.00 0.00 35.04 3.41
2254 2658 3.678289 TGTTTGGGACTGATGATGTCTG 58.322 45.455 0.00 0.00 35.04 3.51
2255 2659 3.327464 TGTTTGGGACTGATGATGTCTGA 59.673 43.478 0.00 0.00 35.04 3.27
2256 2660 4.019051 TGTTTGGGACTGATGATGTCTGAT 60.019 41.667 0.00 0.00 35.04 2.90
2257 2661 3.832615 TGGGACTGATGATGTCTGATG 57.167 47.619 0.00 0.00 35.04 3.07
2258 2662 3.377573 TGGGACTGATGATGTCTGATGA 58.622 45.455 0.00 0.00 35.04 2.92
2259 2663 3.387050 TGGGACTGATGATGTCTGATGAG 59.613 47.826 0.00 0.00 35.04 2.90
2260 2664 3.387374 GGGACTGATGATGTCTGATGAGT 59.613 47.826 0.00 0.00 35.04 3.41
2261 2665 4.501229 GGGACTGATGATGTCTGATGAGTC 60.501 50.000 0.00 0.00 35.04 3.36
2262 2666 4.289342 GACTGATGATGTCTGATGAGTCG 58.711 47.826 0.00 0.00 0.00 4.18
2263 2667 3.950395 ACTGATGATGTCTGATGAGTCGA 59.050 43.478 0.00 0.00 0.00 4.20
2264 2668 4.202000 ACTGATGATGTCTGATGAGTCGAC 60.202 45.833 7.70 7.70 0.00 4.20
2265 2669 3.696051 TGATGATGTCTGATGAGTCGACA 59.304 43.478 19.50 0.00 39.93 4.35
2266 2670 3.772060 TGATGTCTGATGAGTCGACAG 57.228 47.619 19.50 5.96 39.44 3.51
2267 2671 3.084786 TGATGTCTGATGAGTCGACAGT 58.915 45.455 19.50 2.36 39.44 3.55
2268 2672 3.507622 TGATGTCTGATGAGTCGACAGTT 59.492 43.478 19.50 0.55 39.44 3.16
2269 2673 3.288809 TGTCTGATGAGTCGACAGTTG 57.711 47.619 19.50 2.79 34.97 3.16
2270 2674 2.623416 TGTCTGATGAGTCGACAGTTGT 59.377 45.455 19.50 0.00 34.97 3.32
2271 2675 3.818773 TGTCTGATGAGTCGACAGTTGTA 59.181 43.478 19.50 0.00 34.97 2.41
2272 2676 4.459337 TGTCTGATGAGTCGACAGTTGTAT 59.541 41.667 19.50 2.29 34.97 2.29
2273 2677 4.795795 GTCTGATGAGTCGACAGTTGTATG 59.204 45.833 19.50 0.98 33.93 2.39
2274 2678 3.511699 TGATGAGTCGACAGTTGTATGC 58.488 45.455 19.50 0.00 0.00 3.14
2275 2679 3.193479 TGATGAGTCGACAGTTGTATGCT 59.807 43.478 19.50 0.00 0.00 3.79
2276 2680 2.946564 TGAGTCGACAGTTGTATGCTG 58.053 47.619 19.50 0.00 39.67 4.41
2277 2681 1.656095 GAGTCGACAGTTGTATGCTGC 59.344 52.381 19.50 0.00 37.47 5.25
2278 2682 1.273606 AGTCGACAGTTGTATGCTGCT 59.726 47.619 19.50 0.00 37.47 4.24
2279 2683 1.391485 GTCGACAGTTGTATGCTGCTG 59.609 52.381 11.55 4.33 37.47 4.41
2280 2684 0.723414 CGACAGTTGTATGCTGCTGG 59.277 55.000 0.00 0.00 37.47 4.85
2281 2685 1.813513 GACAGTTGTATGCTGCTGGT 58.186 50.000 0.00 0.00 37.47 4.00
2282 2686 2.154462 GACAGTTGTATGCTGCTGGTT 58.846 47.619 0.00 0.00 37.47 3.67
2283 2687 1.881973 ACAGTTGTATGCTGCTGGTTG 59.118 47.619 0.00 0.00 37.47 3.77
2284 2688 0.883833 AGTTGTATGCTGCTGGTTGC 59.116 50.000 0.00 0.00 43.25 4.17
2285 2689 0.883833 GTTGTATGCTGCTGGTTGCT 59.116 50.000 0.00 0.00 43.37 3.91
2286 2690 1.270550 GTTGTATGCTGCTGGTTGCTT 59.729 47.619 0.00 0.00 43.37 3.91
2287 2691 1.619654 TGTATGCTGCTGGTTGCTTT 58.380 45.000 0.00 0.00 43.37 3.51
2288 2692 1.962807 TGTATGCTGCTGGTTGCTTTT 59.037 42.857 0.00 0.00 43.37 2.27
2289 2693 2.288334 TGTATGCTGCTGGTTGCTTTTG 60.288 45.455 0.00 0.00 43.37 2.44
2290 2694 0.754472 ATGCTGCTGGTTGCTTTTGT 59.246 45.000 0.00 0.00 43.37 2.83
2291 2695 0.536260 TGCTGCTGGTTGCTTTTGTT 59.464 45.000 0.00 0.00 43.37 2.83
2292 2696 0.932399 GCTGCTGGTTGCTTTTGTTG 59.068 50.000 0.00 0.00 43.37 3.33
2293 2697 1.574134 CTGCTGGTTGCTTTTGTTGG 58.426 50.000 0.00 0.00 43.37 3.77
2294 2698 0.901124 TGCTGGTTGCTTTTGTTGGT 59.099 45.000 0.00 0.00 43.37 3.67
2295 2699 1.277557 TGCTGGTTGCTTTTGTTGGTT 59.722 42.857 0.00 0.00 43.37 3.67
2296 2700 2.289945 TGCTGGTTGCTTTTGTTGGTTT 60.290 40.909 0.00 0.00 43.37 3.27
2297 2701 2.095692 GCTGGTTGCTTTTGTTGGTTTG 59.904 45.455 0.00 0.00 38.95 2.93
2298 2702 3.333804 CTGGTTGCTTTTGTTGGTTTGT 58.666 40.909 0.00 0.00 0.00 2.83
2299 2703 4.499183 CTGGTTGCTTTTGTTGGTTTGTA 58.501 39.130 0.00 0.00 0.00 2.41
2300 2704 4.894784 TGGTTGCTTTTGTTGGTTTGTAA 58.105 34.783 0.00 0.00 0.00 2.41
2301 2705 5.305585 TGGTTGCTTTTGTTGGTTTGTAAA 58.694 33.333 0.00 0.00 0.00 2.01
2302 2706 5.940470 TGGTTGCTTTTGTTGGTTTGTAAAT 59.060 32.000 0.00 0.00 0.00 1.40
2303 2707 6.431234 TGGTTGCTTTTGTTGGTTTGTAAATT 59.569 30.769 0.00 0.00 0.00 1.82
2304 2708 6.744993 GGTTGCTTTTGTTGGTTTGTAAATTG 59.255 34.615 0.00 0.00 0.00 2.32
2305 2709 7.301789 GTTGCTTTTGTTGGTTTGTAAATTGT 58.698 30.769 0.00 0.00 0.00 2.71
2306 2710 8.443937 GTTGCTTTTGTTGGTTTGTAAATTGTA 58.556 29.630 0.00 0.00 0.00 2.41
2307 2711 8.723942 TGCTTTTGTTGGTTTGTAAATTGTAT 57.276 26.923 0.00 0.00 0.00 2.29
2308 2712 8.607459 TGCTTTTGTTGGTTTGTAAATTGTATG 58.393 29.630 0.00 0.00 0.00 2.39
2309 2713 8.608317 GCTTTTGTTGGTTTGTAAATTGTATGT 58.392 29.630 0.00 0.00 0.00 2.29
2311 2715 8.649973 TTTGTTGGTTTGTAAATTGTATGTCC 57.350 30.769 0.00 0.00 0.00 4.02
2312 2716 7.589958 TGTTGGTTTGTAAATTGTATGTCCT 57.410 32.000 0.00 0.00 0.00 3.85
2313 2717 7.653647 TGTTGGTTTGTAAATTGTATGTCCTC 58.346 34.615 0.00 0.00 0.00 3.71
2314 2718 6.827586 TGGTTTGTAAATTGTATGTCCTCC 57.172 37.500 0.00 0.00 0.00 4.30
2315 2719 6.548321 TGGTTTGTAAATTGTATGTCCTCCT 58.452 36.000 0.00 0.00 0.00 3.69
2316 2720 6.657541 TGGTTTGTAAATTGTATGTCCTCCTC 59.342 38.462 0.00 0.00 0.00 3.71
2317 2721 6.095021 GGTTTGTAAATTGTATGTCCTCCTCC 59.905 42.308 0.00 0.00 0.00 4.30
2318 2722 6.636454 TTGTAAATTGTATGTCCTCCTCCT 57.364 37.500 0.00 0.00 0.00 3.69
2319 2723 6.636454 TGTAAATTGTATGTCCTCCTCCTT 57.364 37.500 0.00 0.00 0.00 3.36
2320 2724 6.650120 TGTAAATTGTATGTCCTCCTCCTTC 58.350 40.000 0.00 0.00 0.00 3.46
2321 2725 5.779241 AAATTGTATGTCCTCCTCCTTCA 57.221 39.130 0.00 0.00 0.00 3.02
2322 2726 5.983333 AATTGTATGTCCTCCTCCTTCAT 57.017 39.130 0.00 0.00 0.00 2.57
2323 2727 4.760530 TTGTATGTCCTCCTCCTTCATG 57.239 45.455 0.00 0.00 0.00 3.07
2324 2728 3.041211 TGTATGTCCTCCTCCTTCATGG 58.959 50.000 0.00 0.00 37.10 3.66
2325 2729 2.575921 ATGTCCTCCTCCTTCATGGA 57.424 50.000 0.00 0.00 43.86 3.41
2326 2730 2.575921 TGTCCTCCTCCTTCATGGAT 57.424 50.000 0.00 0.00 45.16 3.41
2327 2731 2.121948 TGTCCTCCTCCTTCATGGATG 58.878 52.381 0.00 0.00 45.16 3.51
2328 2732 2.293118 TGTCCTCCTCCTTCATGGATGA 60.293 50.000 0.00 0.00 45.16 2.92
2329 2733 2.774234 GTCCTCCTCCTTCATGGATGAA 59.226 50.000 2.19 2.19 45.16 2.57
2330 2734 3.393941 GTCCTCCTCCTTCATGGATGAAT 59.606 47.826 2.56 0.00 44.92 2.57
2331 2735 4.594920 GTCCTCCTCCTTCATGGATGAATA 59.405 45.833 2.56 0.00 44.92 1.75
2332 2736 5.072329 GTCCTCCTCCTTCATGGATGAATAA 59.928 44.000 2.56 0.00 44.92 1.40
2333 2737 5.671735 TCCTCCTCCTTCATGGATGAATAAA 59.328 40.000 2.56 0.00 44.92 1.40
2334 2738 6.333702 TCCTCCTCCTTCATGGATGAATAAAT 59.666 38.462 2.56 0.00 44.92 1.40
2335 2739 7.008941 CCTCCTCCTTCATGGATGAATAAATT 58.991 38.462 2.56 0.00 44.92 1.82
2336 2740 8.166061 CCTCCTCCTTCATGGATGAATAAATTA 58.834 37.037 2.56 0.00 44.92 1.40
2337 2741 8.924511 TCCTCCTTCATGGATGAATAAATTAC 57.075 34.615 2.56 0.00 44.92 1.89
2338 2742 8.727149 TCCTCCTTCATGGATGAATAAATTACT 58.273 33.333 2.56 0.00 44.92 2.24
2339 2743 9.007901 CCTCCTTCATGGATGAATAAATTACTC 57.992 37.037 2.56 0.00 44.92 2.59
2340 2744 8.607441 TCCTTCATGGATGAATAAATTACTCG 57.393 34.615 2.56 0.00 44.92 4.18
2341 2745 7.661437 TCCTTCATGGATGAATAAATTACTCGG 59.339 37.037 2.56 0.00 44.92 4.63
2342 2746 7.094634 CCTTCATGGATGAATAAATTACTCGGG 60.095 40.741 2.56 0.00 44.92 5.14
2343 2747 7.073457 TCATGGATGAATAAATTACTCGGGA 57.927 36.000 0.00 0.00 33.08 5.14
2344 2748 7.689299 TCATGGATGAATAAATTACTCGGGAT 58.311 34.615 0.00 0.00 33.08 3.85
2345 2749 8.821817 TCATGGATGAATAAATTACTCGGGATA 58.178 33.333 0.00 0.00 33.08 2.59
2346 2750 9.618890 CATGGATGAATAAATTACTCGGGATAT 57.381 33.333 0.00 0.00 0.00 1.63
2347 2751 9.838339 ATGGATGAATAAATTACTCGGGATATC 57.162 33.333 0.00 0.00 0.00 1.63
2348 2752 9.046846 TGGATGAATAAATTACTCGGGATATCT 57.953 33.333 2.05 0.00 0.00 1.98
2349 2753 9.535878 GGATGAATAAATTACTCGGGATATCTC 57.464 37.037 2.05 0.00 0.00 2.75
2352 2756 9.535170 TGAATAAATTACTCGGGATATCTCTCT 57.465 33.333 0.09 0.00 0.00 3.10
2353 2757 9.796120 GAATAAATTACTCGGGATATCTCTCTG 57.204 37.037 0.09 0.00 0.00 3.35
2354 2758 9.535170 AATAAATTACTCGGGATATCTCTCTGA 57.465 33.333 0.09 0.00 0.00 3.27
2355 2759 9.707957 ATAAATTACTCGGGATATCTCTCTGAT 57.292 33.333 0.09 0.00 39.11 2.90
2356 2760 8.429237 AAATTACTCGGGATATCTCTCTGATT 57.571 34.615 0.09 0.00 36.65 2.57
2357 2761 6.825944 TTACTCGGGATATCTCTCTGATTG 57.174 41.667 0.09 0.00 36.65 2.67
2358 2762 4.735369 ACTCGGGATATCTCTCTGATTGT 58.265 43.478 0.09 0.00 36.65 2.71
2359 2763 5.144100 ACTCGGGATATCTCTCTGATTGTT 58.856 41.667 0.09 0.00 36.65 2.83
2360 2764 6.307776 ACTCGGGATATCTCTCTGATTGTTA 58.692 40.000 0.09 0.00 36.65 2.41
2361 2765 6.951198 ACTCGGGATATCTCTCTGATTGTTAT 59.049 38.462 0.09 0.00 36.65 1.89
2362 2766 7.453126 ACTCGGGATATCTCTCTGATTGTTATT 59.547 37.037 0.09 0.00 36.65 1.40
2363 2767 8.195165 TCGGGATATCTCTCTGATTGTTATTT 57.805 34.615 0.09 0.00 36.65 1.40
2364 2768 8.307483 TCGGGATATCTCTCTGATTGTTATTTC 58.693 37.037 0.09 0.00 36.65 2.17
2394 2798 4.245660 TCTGCTAAAAATCAGTCGACTGG 58.754 43.478 37.82 23.85 43.91 4.00
2424 2828 5.177696 AGTGAAGTCTAAGTCGATTTGTTGC 59.822 40.000 3.04 0.00 0.00 4.17
2692 3099 5.223382 ACAAACAGATAGAGTGAAGTGACG 58.777 41.667 0.00 0.00 0.00 4.35
2873 5442 4.160642 TCAAGATCCATGCAGCTATGTT 57.839 40.909 0.00 0.00 0.00 2.71
2879 5448 3.273434 TCCATGCAGCTATGTTTGTCTC 58.727 45.455 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.024133 CACCAAATCTCGTGACACAATGAA 60.024 41.667 6.37 0.00 31.36 2.57
48 49 8.281194 CCGTTGAATCATTGAATAGATCTGAAG 58.719 37.037 5.18 0.00 0.00 3.02
74 75 1.370172 CTATAGCCACCGTCGTCGC 60.370 63.158 0.00 0.00 35.54 5.19
79 80 2.024590 AACGCCCTATAGCCACCGTC 62.025 60.000 0.00 0.00 0.00 4.79
80 81 2.062177 AACGCCCTATAGCCACCGT 61.062 57.895 0.00 0.00 0.00 4.83
110 111 2.473235 GCCGAGAAATCTTCGTCTATGC 59.527 50.000 0.00 0.00 34.02 3.14
113 114 2.753452 ACAGCCGAGAAATCTTCGTCTA 59.247 45.455 0.00 0.00 34.02 2.59
114 115 1.546476 ACAGCCGAGAAATCTTCGTCT 59.454 47.619 0.00 0.00 34.02 4.18
115 116 1.921230 GACAGCCGAGAAATCTTCGTC 59.079 52.381 0.00 0.00 34.02 4.20
117 118 1.996292 TGACAGCCGAGAAATCTTCG 58.004 50.000 0.00 0.00 34.02 3.79
129 130 1.795768 TGACTTTGTCGATGACAGCC 58.204 50.000 0.00 0.00 43.69 4.85
130 131 2.412065 GCTTGACTTTGTCGATGACAGC 60.412 50.000 0.00 0.00 43.69 4.40
160 161 2.058595 ACTGCGACCGCTCCCTTAT 61.059 57.895 15.61 0.00 42.51 1.73
175 176 2.954753 GAACAAGCCGCCGACACTG 61.955 63.158 0.00 0.00 0.00 3.66
176 177 1.812686 TAGAACAAGCCGCCGACACT 61.813 55.000 0.00 0.00 0.00 3.55
178 179 0.947180 GTTAGAACAAGCCGCCGACA 60.947 55.000 0.00 0.00 0.00 4.35
179 180 0.947180 TGTTAGAACAAGCCGCCGAC 60.947 55.000 0.00 0.00 35.67 4.79
180 181 0.669318 CTGTTAGAACAAGCCGCCGA 60.669 55.000 0.00 0.00 38.66 5.54
182 183 1.502190 GCTGTTAGAACAAGCCGCC 59.498 57.895 0.00 0.00 38.66 6.13
183 184 1.132640 CGCTGTTAGAACAAGCCGC 59.867 57.895 0.00 0.00 38.66 6.53
184 185 1.787847 CCGCTGTTAGAACAAGCCG 59.212 57.895 0.00 0.73 38.66 5.52
186 187 0.166814 CTGCCGCTGTTAGAACAAGC 59.833 55.000 0.00 1.46 38.66 4.01
187 188 0.166814 GCTGCCGCTGTTAGAACAAG 59.833 55.000 0.00 0.00 38.66 3.16
188 189 1.565156 CGCTGCCGCTGTTAGAACAA 61.565 55.000 0.00 0.00 38.66 2.83
190 191 2.740714 CCGCTGCCGCTGTTAGAAC 61.741 63.158 0.00 0.00 0.00 3.01
191 192 2.434185 CCGCTGCCGCTGTTAGAA 60.434 61.111 0.00 0.00 0.00 2.10
192 193 3.642778 GACCGCTGCCGCTGTTAGA 62.643 63.158 0.00 0.00 33.52 2.10
193 194 3.188786 GACCGCTGCCGCTGTTAG 61.189 66.667 0.00 0.00 33.52 2.34
201 202 3.414700 CACTGAACGACCGCTGCC 61.415 66.667 0.00 0.00 0.00 4.85
202 203 1.291877 AATCACTGAACGACCGCTGC 61.292 55.000 0.00 0.00 0.00 5.25
203 204 1.148310 AAATCACTGAACGACCGCTG 58.852 50.000 0.00 0.00 0.00 5.18
204 205 2.607187 CTAAATCACTGAACGACCGCT 58.393 47.619 0.00 0.00 0.00 5.52
205 206 1.659098 CCTAAATCACTGAACGACCGC 59.341 52.381 0.00 0.00 0.00 5.68
206 207 3.226346 TCCTAAATCACTGAACGACCG 57.774 47.619 0.00 0.00 0.00 4.79
207 208 3.683340 GGTTCCTAAATCACTGAACGACC 59.317 47.826 0.00 0.00 38.34 4.79
313 366 5.760253 TCTCATCGAAAAGAATTGCCCTATC 59.240 40.000 0.00 0.00 0.00 2.08
315 368 5.097742 TCTCATCGAAAAGAATTGCCCTA 57.902 39.130 0.00 0.00 0.00 3.53
316 369 3.955471 TCTCATCGAAAAGAATTGCCCT 58.045 40.909 0.00 0.00 0.00 5.19
326 379 6.212235 GTCTGAGCTCATATCTCATCGAAAA 58.788 40.000 18.63 0.00 39.56 2.29
354 407 5.285798 TGTTTGATTCGAACGGGATAAAC 57.714 39.130 0.00 6.86 30.87 2.01
384 437 4.224370 AGGCTCCCGTAGAAAAAGAATACA 59.776 41.667 0.00 0.00 0.00 2.29
386 439 5.431179 AAGGCTCCCGTAGAAAAAGAATA 57.569 39.130 0.00 0.00 0.00 1.75
395 448 1.562942 TCACTCTAAGGCTCCCGTAGA 59.437 52.381 6.72 6.72 41.04 2.59
505 565 2.084546 GATCACTCAAACTTTCCCCGG 58.915 52.381 0.00 0.00 0.00 5.73
529 589 7.331934 TGATTTTATGCATTCTCTATAGGCGAC 59.668 37.037 3.54 0.00 0.00 5.19
573 633 1.067142 TGACACCGAAAAGAGATCCCG 60.067 52.381 0.00 0.00 0.00 5.14
663 725 2.035469 TGGGGCGTGCATCACATT 59.965 55.556 0.00 0.00 33.40 2.71
713 781 2.731976 GTGCACTTTAGAGACAGGTTCG 59.268 50.000 10.32 0.00 0.00 3.95
740 809 1.804748 GGTCCATTGGAACGAACTGAC 59.195 52.381 7.05 0.00 31.38 3.51
744 813 1.804748 GTCAGGTCCATTGGAACGAAC 59.195 52.381 15.02 12.89 45.53 3.95
771 841 0.438445 CGTGCGTGTATGTGGTTCAG 59.562 55.000 0.00 0.00 0.00 3.02
791 861 2.499289 AGCTTACCACAGAGTCTGGATG 59.501 50.000 23.79 13.59 35.51 3.51
824 894 0.389757 GCGATCTTCTGTCCCTACCC 59.610 60.000 0.00 0.00 0.00 3.69
881 988 1.398390 GAGCCTTTGATGTTACGCCTG 59.602 52.381 0.00 0.00 0.00 4.85
939 1046 0.399454 TTGGCTTGCTTGCTCTCTCT 59.601 50.000 1.96 0.00 0.00 3.10
940 1047 0.803740 CTTGGCTTGCTTGCTCTCTC 59.196 55.000 1.96 0.00 0.00 3.20
941 1048 0.608582 CCTTGGCTTGCTTGCTCTCT 60.609 55.000 1.96 0.00 0.00 3.10
942 1049 1.881602 CCTTGGCTTGCTTGCTCTC 59.118 57.895 1.96 0.00 0.00 3.20
943 1050 2.273912 GCCTTGGCTTGCTTGCTCT 61.274 57.895 4.11 0.00 0.00 4.09
944 1051 2.260743 GCCTTGGCTTGCTTGCTC 59.739 61.111 4.11 0.00 0.00 4.26
945 1052 3.677648 CGCCTTGGCTTGCTTGCT 61.678 61.111 10.12 0.00 0.00 3.91
946 1053 1.656818 TATCGCCTTGGCTTGCTTGC 61.657 55.000 10.12 0.00 0.00 4.01
981 1088 3.384789 CCATGATCTTCCTCGTACCTTGA 59.615 47.826 0.00 0.00 0.00 3.02
1013 1122 2.259917 TCACAAGGATCCTGCTCTTGA 58.740 47.619 17.02 10.62 39.97 3.02
1329 1438 4.116747 ACTGAGCTGCACAAGATAGTAC 57.883 45.455 1.02 0.00 0.00 2.73
1332 1441 6.484540 CAAATAACTGAGCTGCACAAGATAG 58.515 40.000 1.02 0.00 0.00 2.08
1333 1442 5.163723 GCAAATAACTGAGCTGCACAAGATA 60.164 40.000 1.02 0.00 33.19 1.98
1334 1443 4.380233 GCAAATAACTGAGCTGCACAAGAT 60.380 41.667 1.02 0.00 33.19 2.40
1369 1478 0.804544 GAAGCAGCCGCACGTATGTA 60.805 55.000 0.00 0.00 42.27 2.29
1372 1481 2.100631 GTGAAGCAGCCGCACGTAT 61.101 57.895 0.00 0.00 42.27 3.06
1377 1486 1.898094 AATGTGTGAAGCAGCCGCA 60.898 52.632 0.00 0.00 42.27 5.69
1777 1890 0.318441 CTTCTTCTCCCACAGCGACA 59.682 55.000 0.00 0.00 0.00 4.35
1865 1978 3.543665 AGCTTAGTATCGGTCGAGTTCT 58.456 45.455 0.00 0.65 0.00 3.01
1868 1981 2.613133 GTGAGCTTAGTATCGGTCGAGT 59.387 50.000 0.00 0.00 0.00 4.18
1925 2042 5.837191 CACGTACACAAAGACGAATTAACAC 59.163 40.000 0.89 0.00 41.60 3.32
1953 2356 2.355244 GATCGGCGCCTCTGTAGC 60.355 66.667 26.68 3.37 0.00 3.58
1997 2400 1.340465 CTTGATGTACGACGCGTGC 59.660 57.895 20.70 7.65 41.39 5.34
2127 2530 3.260380 ACAGATAGACCAGCAGCATATCC 59.740 47.826 0.00 0.00 0.00 2.59
2140 2544 2.100584 CTGGACTCAGGCACAGATAGAC 59.899 54.545 0.00 0.00 37.36 2.59
2150 2554 3.618690 AAACTATCACTGGACTCAGGC 57.381 47.619 0.00 0.00 44.99 4.85
2176 2580 2.621998 ACTGGACTCTCGTTTCGAAAGA 59.378 45.455 11.66 9.94 34.74 2.52
2177 2581 2.726760 CACTGGACTCTCGTTTCGAAAG 59.273 50.000 11.66 5.95 34.74 2.62
2178 2582 2.359848 TCACTGGACTCTCGTTTCGAAA 59.640 45.455 6.47 6.47 34.74 3.46
2179 2583 1.951602 TCACTGGACTCTCGTTTCGAA 59.048 47.619 0.00 0.00 34.74 3.71
2180 2584 1.601166 TCACTGGACTCTCGTTTCGA 58.399 50.000 0.00 0.00 0.00 3.71
2181 2585 2.638556 ATCACTGGACTCTCGTTTCG 57.361 50.000 0.00 0.00 0.00 3.46
2182 2586 4.705337 ACTATCACTGGACTCTCGTTTC 57.295 45.455 0.00 0.00 0.00 2.78
2183 2587 6.585695 TTAACTATCACTGGACTCTCGTTT 57.414 37.500 0.00 0.00 0.00 3.60
2184 2588 6.153000 ACATTAACTATCACTGGACTCTCGTT 59.847 38.462 0.00 0.00 0.00 3.85
2185 2589 5.652891 ACATTAACTATCACTGGACTCTCGT 59.347 40.000 0.00 0.00 0.00 4.18
2186 2590 6.137794 ACATTAACTATCACTGGACTCTCG 57.862 41.667 0.00 0.00 0.00 4.04
2187 2591 8.851145 TGATACATTAACTATCACTGGACTCTC 58.149 37.037 1.97 0.00 0.00 3.20
2188 2592 8.768501 TGATACATTAACTATCACTGGACTCT 57.231 34.615 1.97 0.00 0.00 3.24
2189 2593 9.416794 CATGATACATTAACTATCACTGGACTC 57.583 37.037 6.77 0.00 34.23 3.36
2190 2594 8.928448 ACATGATACATTAACTATCACTGGACT 58.072 33.333 0.00 0.00 34.23 3.85
2200 2604 9.687210 GTCCGTTCATACATGATACATTAACTA 57.313 33.333 0.00 0.00 36.56 2.24
2201 2605 7.656137 GGTCCGTTCATACATGATACATTAACT 59.344 37.037 0.00 0.00 36.56 2.24
2202 2606 7.358931 CGGTCCGTTCATACATGATACATTAAC 60.359 40.741 2.08 0.00 36.56 2.01
2203 2607 6.643360 CGGTCCGTTCATACATGATACATTAA 59.357 38.462 2.08 0.00 36.56 1.40
2204 2608 6.153756 CGGTCCGTTCATACATGATACATTA 58.846 40.000 2.08 0.00 36.56 1.90
2205 2609 4.988540 CGGTCCGTTCATACATGATACATT 59.011 41.667 2.08 0.00 36.56 2.71
2206 2610 4.038763 ACGGTCCGTTCATACATGATACAT 59.961 41.667 12.23 0.00 36.35 2.29
2207 2611 3.382227 ACGGTCCGTTCATACATGATACA 59.618 43.478 12.23 0.00 36.35 2.29
2208 2612 3.734231 CACGGTCCGTTCATACATGATAC 59.266 47.826 15.97 0.00 38.32 2.24
2209 2613 3.382227 ACACGGTCCGTTCATACATGATA 59.618 43.478 15.97 0.00 38.32 2.15
2210 2614 2.167693 ACACGGTCCGTTCATACATGAT 59.832 45.455 15.97 0.00 38.32 2.45
2211 2615 1.546923 ACACGGTCCGTTCATACATGA 59.453 47.619 15.97 0.00 38.32 3.07
2212 2616 2.004583 ACACGGTCCGTTCATACATG 57.995 50.000 15.97 3.22 38.32 3.21
2213 2617 3.131577 ACATACACGGTCCGTTCATACAT 59.868 43.478 15.97 0.00 38.32 2.29
2214 2618 2.492881 ACATACACGGTCCGTTCATACA 59.507 45.455 15.97 0.00 38.32 2.29
2215 2619 3.155093 ACATACACGGTCCGTTCATAC 57.845 47.619 15.97 0.00 38.32 2.39
2216 2620 3.872511 AACATACACGGTCCGTTCATA 57.127 42.857 15.97 8.21 38.32 2.15
2217 2621 2.739913 CAAACATACACGGTCCGTTCAT 59.260 45.455 15.97 7.97 38.32 2.57
2218 2622 2.136728 CAAACATACACGGTCCGTTCA 58.863 47.619 15.97 5.59 38.32 3.18
2219 2623 1.461897 CCAAACATACACGGTCCGTTC 59.538 52.381 15.97 0.00 38.32 3.95
2220 2624 1.515081 CCAAACATACACGGTCCGTT 58.485 50.000 15.97 9.16 38.32 4.44
2221 2625 0.320946 CCCAAACATACACGGTCCGT 60.321 55.000 12.23 12.23 42.36 4.69
2222 2626 0.037139 TCCCAAACATACACGGTCCG 60.037 55.000 10.48 10.48 0.00 4.79
2223 2627 1.002773 AGTCCCAAACATACACGGTCC 59.997 52.381 0.00 0.00 0.00 4.46
2224 2628 2.073816 CAGTCCCAAACATACACGGTC 58.926 52.381 0.00 0.00 0.00 4.79
2225 2629 1.695242 TCAGTCCCAAACATACACGGT 59.305 47.619 0.00 0.00 0.00 4.83
2226 2630 2.465860 TCAGTCCCAAACATACACGG 57.534 50.000 0.00 0.00 0.00 4.94
2227 2631 3.595173 TCATCAGTCCCAAACATACACG 58.405 45.455 0.00 0.00 0.00 4.49
2228 2632 4.943705 ACATCATCAGTCCCAAACATACAC 59.056 41.667 0.00 0.00 0.00 2.90
2229 2633 5.045651 AGACATCATCAGTCCCAAACATACA 60.046 40.000 0.00 0.00 36.68 2.29
2230 2634 5.295292 CAGACATCATCAGTCCCAAACATAC 59.705 44.000 0.00 0.00 36.68 2.39
2231 2635 5.189539 TCAGACATCATCAGTCCCAAACATA 59.810 40.000 0.00 0.00 36.68 2.29
2232 2636 4.019051 TCAGACATCATCAGTCCCAAACAT 60.019 41.667 0.00 0.00 36.68 2.71
2233 2637 3.327464 TCAGACATCATCAGTCCCAAACA 59.673 43.478 0.00 0.00 36.68 2.83
2234 2638 3.942829 TCAGACATCATCAGTCCCAAAC 58.057 45.455 0.00 0.00 36.68 2.93
2235 2639 4.225717 TCATCAGACATCATCAGTCCCAAA 59.774 41.667 0.00 0.00 36.68 3.28
2236 2640 3.776417 TCATCAGACATCATCAGTCCCAA 59.224 43.478 0.00 0.00 36.68 4.12
2237 2641 3.377573 TCATCAGACATCATCAGTCCCA 58.622 45.455 0.00 0.00 36.68 4.37
2238 2642 3.387374 ACTCATCAGACATCATCAGTCCC 59.613 47.826 0.00 0.00 36.68 4.46
2239 2643 4.619973 GACTCATCAGACATCATCAGTCC 58.380 47.826 0.00 0.00 36.68 3.85
2240 2644 4.036144 TCGACTCATCAGACATCATCAGTC 59.964 45.833 0.00 0.00 36.26 3.51
2241 2645 3.950395 TCGACTCATCAGACATCATCAGT 59.050 43.478 0.00 0.00 0.00 3.41
2242 2646 4.201990 TGTCGACTCATCAGACATCATCAG 60.202 45.833 17.92 0.00 39.63 2.90
2243 2647 3.696051 TGTCGACTCATCAGACATCATCA 59.304 43.478 17.92 0.00 39.63 3.07
2244 2648 4.202000 ACTGTCGACTCATCAGACATCATC 60.202 45.833 17.92 0.00 42.97 2.92
2245 2649 3.698539 ACTGTCGACTCATCAGACATCAT 59.301 43.478 17.92 0.00 42.97 2.45
2246 2650 3.084786 ACTGTCGACTCATCAGACATCA 58.915 45.455 17.92 0.00 42.97 3.07
2247 2651 3.773860 ACTGTCGACTCATCAGACATC 57.226 47.619 17.92 0.00 42.97 3.06
2248 2652 3.256879 ACAACTGTCGACTCATCAGACAT 59.743 43.478 17.92 0.00 42.97 3.06
2249 2653 2.623416 ACAACTGTCGACTCATCAGACA 59.377 45.455 17.92 0.00 41.90 3.41
2250 2654 3.290308 ACAACTGTCGACTCATCAGAC 57.710 47.619 17.92 0.00 33.93 3.51
2251 2655 4.675408 GCATACAACTGTCGACTCATCAGA 60.675 45.833 17.92 0.00 33.93 3.27
2252 2656 3.549471 GCATACAACTGTCGACTCATCAG 59.451 47.826 17.92 7.79 35.60 2.90
2253 2657 3.193479 AGCATACAACTGTCGACTCATCA 59.807 43.478 17.92 0.00 0.00 3.07
2254 2658 3.549471 CAGCATACAACTGTCGACTCATC 59.451 47.826 17.92 0.00 0.00 2.92
2255 2659 3.515630 CAGCATACAACTGTCGACTCAT 58.484 45.455 17.92 0.00 0.00 2.90
2256 2660 2.926586 GCAGCATACAACTGTCGACTCA 60.927 50.000 17.92 0.00 37.47 3.41
2257 2661 1.656095 GCAGCATACAACTGTCGACTC 59.344 52.381 17.92 0.00 37.47 3.36
2258 2662 1.273606 AGCAGCATACAACTGTCGACT 59.726 47.619 17.92 0.00 37.47 4.18
2259 2663 1.391485 CAGCAGCATACAACTGTCGAC 59.609 52.381 9.11 9.11 37.47 4.20
2260 2664 1.672737 CCAGCAGCATACAACTGTCGA 60.673 52.381 0.00 0.00 37.47 4.20
2261 2665 0.723414 CCAGCAGCATACAACTGTCG 59.277 55.000 0.00 0.00 37.47 4.35
2262 2666 1.813513 ACCAGCAGCATACAACTGTC 58.186 50.000 0.00 0.00 37.47 3.51
2263 2667 1.881973 CAACCAGCAGCATACAACTGT 59.118 47.619 0.00 0.00 37.47 3.55
2264 2668 1.401931 GCAACCAGCAGCATACAACTG 60.402 52.381 0.00 0.00 44.79 3.16
2265 2669 0.883833 GCAACCAGCAGCATACAACT 59.116 50.000 0.00 0.00 44.79 3.16
2266 2670 3.406682 GCAACCAGCAGCATACAAC 57.593 52.632 0.00 0.00 44.79 3.32
2276 2680 2.022764 AACCAACAAAAGCAACCAGC 57.977 45.000 0.00 0.00 46.19 4.85
2277 2681 3.333804 ACAAACCAACAAAAGCAACCAG 58.666 40.909 0.00 0.00 0.00 4.00
2278 2682 3.409026 ACAAACCAACAAAAGCAACCA 57.591 38.095 0.00 0.00 0.00 3.67
2279 2683 5.864628 TTTACAAACCAACAAAAGCAACC 57.135 34.783 0.00 0.00 0.00 3.77
2280 2684 7.301789 ACAATTTACAAACCAACAAAAGCAAC 58.698 30.769 0.00 0.00 0.00 4.17
2281 2685 7.440523 ACAATTTACAAACCAACAAAAGCAA 57.559 28.000 0.00 0.00 0.00 3.91
2282 2686 8.607459 CATACAATTTACAAACCAACAAAAGCA 58.393 29.630 0.00 0.00 0.00 3.91
2283 2687 8.608317 ACATACAATTTACAAACCAACAAAAGC 58.392 29.630 0.00 0.00 0.00 3.51
2285 2689 9.099454 GGACATACAATTTACAAACCAACAAAA 57.901 29.630 0.00 0.00 0.00 2.44
2286 2690 8.478877 AGGACATACAATTTACAAACCAACAAA 58.521 29.630 0.00 0.00 0.00 2.83
2287 2691 8.012957 AGGACATACAATTTACAAACCAACAA 57.987 30.769 0.00 0.00 0.00 2.83
2288 2692 7.255660 GGAGGACATACAATTTACAAACCAACA 60.256 37.037 0.00 0.00 0.00 3.33
2289 2693 7.039993 AGGAGGACATACAATTTACAAACCAAC 60.040 37.037 0.00 0.00 0.00 3.77
2290 2694 7.007723 AGGAGGACATACAATTTACAAACCAA 58.992 34.615 0.00 0.00 0.00 3.67
2291 2695 6.548321 AGGAGGACATACAATTTACAAACCA 58.452 36.000 0.00 0.00 0.00 3.67
2292 2696 6.095021 GGAGGAGGACATACAATTTACAAACC 59.905 42.308 0.00 0.00 0.00 3.27
2293 2697 6.884836 AGGAGGAGGACATACAATTTACAAAC 59.115 38.462 0.00 0.00 0.00 2.93
2294 2698 7.027874 AGGAGGAGGACATACAATTTACAAA 57.972 36.000 0.00 0.00 0.00 2.83
2295 2699 6.636454 AGGAGGAGGACATACAATTTACAA 57.364 37.500 0.00 0.00 0.00 2.41
2296 2700 6.214615 TGAAGGAGGAGGACATACAATTTACA 59.785 38.462 0.00 0.00 0.00 2.41
2297 2701 6.650120 TGAAGGAGGAGGACATACAATTTAC 58.350 40.000 0.00 0.00 0.00 2.01
2298 2702 6.884472 TGAAGGAGGAGGACATACAATTTA 57.116 37.500 0.00 0.00 0.00 1.40
2299 2703 5.779241 TGAAGGAGGAGGACATACAATTT 57.221 39.130 0.00 0.00 0.00 1.82
2300 2704 5.398353 CCATGAAGGAGGAGGACATACAATT 60.398 44.000 0.00 0.00 41.22 2.32
2301 2705 4.103785 CCATGAAGGAGGAGGACATACAAT 59.896 45.833 0.00 0.00 41.22 2.71
2302 2706 3.455910 CCATGAAGGAGGAGGACATACAA 59.544 47.826 0.00 0.00 41.22 2.41
2303 2707 3.041211 CCATGAAGGAGGAGGACATACA 58.959 50.000 0.00 0.00 41.22 2.29
2304 2708 3.309296 TCCATGAAGGAGGAGGACATAC 58.691 50.000 0.00 0.00 43.07 2.39
2305 2709 3.706389 TCCATGAAGGAGGAGGACATA 57.294 47.619 0.00 0.00 43.07 2.29
2306 2710 2.575921 TCCATGAAGGAGGAGGACAT 57.424 50.000 0.00 0.00 43.07 3.06
2319 2723 7.073457 TCCCGAGTAATTTATTCATCCATGA 57.927 36.000 0.00 0.00 34.44 3.07
2320 2724 7.928307 ATCCCGAGTAATTTATTCATCCATG 57.072 36.000 0.66 0.00 0.00 3.66
2321 2725 9.838339 GATATCCCGAGTAATTTATTCATCCAT 57.162 33.333 0.00 0.00 0.00 3.41
2322 2726 9.046846 AGATATCCCGAGTAATTTATTCATCCA 57.953 33.333 0.00 0.00 0.00 3.41
2323 2727 9.535878 GAGATATCCCGAGTAATTTATTCATCC 57.464 37.037 0.00 0.00 0.00 3.51
2326 2730 9.535170 AGAGAGATATCCCGAGTAATTTATTCA 57.465 33.333 0.00 0.00 0.00 2.57
2327 2731 9.796120 CAGAGAGATATCCCGAGTAATTTATTC 57.204 37.037 0.00 0.00 0.00 1.75
2328 2732 9.535170 TCAGAGAGATATCCCGAGTAATTTATT 57.465 33.333 0.00 0.00 0.00 1.40
2329 2733 9.707957 ATCAGAGAGATATCCCGAGTAATTTAT 57.292 33.333 0.00 0.00 34.43 1.40
2330 2734 9.535170 AATCAGAGAGATATCCCGAGTAATTTA 57.465 33.333 0.00 0.00 35.39 1.40
2331 2735 8.310382 CAATCAGAGAGATATCCCGAGTAATTT 58.690 37.037 0.00 0.00 35.39 1.82
2332 2736 7.453126 ACAATCAGAGAGATATCCCGAGTAATT 59.547 37.037 0.00 0.00 35.39 1.40
2333 2737 6.951198 ACAATCAGAGAGATATCCCGAGTAAT 59.049 38.462 0.00 0.00 35.39 1.89
2334 2738 6.307776 ACAATCAGAGAGATATCCCGAGTAA 58.692 40.000 0.00 0.00 35.39 2.24
2335 2739 5.882040 ACAATCAGAGAGATATCCCGAGTA 58.118 41.667 0.00 0.00 35.39 2.59
2336 2740 4.735369 ACAATCAGAGAGATATCCCGAGT 58.265 43.478 0.00 0.00 35.39 4.18
2337 2741 5.720371 AACAATCAGAGAGATATCCCGAG 57.280 43.478 0.00 0.00 35.39 4.63
2338 2742 7.782897 AATAACAATCAGAGAGATATCCCGA 57.217 36.000 0.00 0.00 35.39 5.14
2339 2743 8.310382 AGAAATAACAATCAGAGAGATATCCCG 58.690 37.037 0.00 0.00 35.39 5.14
2344 2748 9.967346 CCGTTAGAAATAACAATCAGAGAGATA 57.033 33.333 0.00 0.00 35.39 1.98
2345 2749 7.439655 GCCGTTAGAAATAACAATCAGAGAGAT 59.560 37.037 0.00 0.00 39.09 2.75
2346 2750 6.757010 GCCGTTAGAAATAACAATCAGAGAGA 59.243 38.462 0.00 0.00 0.00 3.10
2347 2751 6.758886 AGCCGTTAGAAATAACAATCAGAGAG 59.241 38.462 0.00 0.00 0.00 3.20
2348 2752 6.640518 AGCCGTTAGAAATAACAATCAGAGA 58.359 36.000 0.00 0.00 0.00 3.10
2349 2753 6.758886 AGAGCCGTTAGAAATAACAATCAGAG 59.241 38.462 0.00 0.00 0.00 3.35
2350 2754 6.535150 CAGAGCCGTTAGAAATAACAATCAGA 59.465 38.462 0.00 0.00 0.00 3.27
2351 2755 6.709643 CAGAGCCGTTAGAAATAACAATCAG 58.290 40.000 0.00 0.00 0.00 2.90
2352 2756 5.064707 GCAGAGCCGTTAGAAATAACAATCA 59.935 40.000 0.00 0.00 0.00 2.57
2353 2757 5.294552 AGCAGAGCCGTTAGAAATAACAATC 59.705 40.000 0.00 0.00 0.00 2.67
2354 2758 5.186198 AGCAGAGCCGTTAGAAATAACAAT 58.814 37.500 0.00 0.00 0.00 2.71
2355 2759 4.575885 AGCAGAGCCGTTAGAAATAACAA 58.424 39.130 0.00 0.00 0.00 2.83
2356 2760 4.202245 AGCAGAGCCGTTAGAAATAACA 57.798 40.909 0.00 0.00 0.00 2.41
2357 2761 6.657836 TTTAGCAGAGCCGTTAGAAATAAC 57.342 37.500 0.00 0.00 0.00 1.89
2358 2762 7.675962 TTTTTAGCAGAGCCGTTAGAAATAA 57.324 32.000 0.00 0.00 0.00 1.40
2359 2763 7.551262 TGATTTTTAGCAGAGCCGTTAGAAATA 59.449 33.333 0.00 0.00 0.00 1.40
2360 2764 6.374333 TGATTTTTAGCAGAGCCGTTAGAAAT 59.626 34.615 0.00 0.00 0.00 2.17
2361 2765 5.703592 TGATTTTTAGCAGAGCCGTTAGAAA 59.296 36.000 0.00 0.00 0.00 2.52
2362 2766 5.242434 TGATTTTTAGCAGAGCCGTTAGAA 58.758 37.500 0.00 0.00 0.00 2.10
2363 2767 4.827692 TGATTTTTAGCAGAGCCGTTAGA 58.172 39.130 0.00 0.00 0.00 2.10
2364 2768 4.631813 ACTGATTTTTAGCAGAGCCGTTAG 59.368 41.667 0.00 0.00 36.07 2.34
2394 2798 9.582223 CAAATCGACTTAGACTTCACTAAAAAC 57.418 33.333 0.00 0.00 32.95 2.43
2424 2828 3.690460 AGCAACACAAAGATCTAAGGGG 58.310 45.455 0.00 0.00 0.00 4.79
2879 5448 9.546909 CGCACCTAAGCAATCTATTTTAATATG 57.453 33.333 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.