Multiple sequence alignment - TraesCS3B01G421300

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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 TraesCS3B01G421300 chr3B 100.000 3309 0 0 1 3309 658461578 658464886 0.000000e+00 6111.0
1 TraesCS3B01G421300 chr3B 89.515 887 70 10 999 1866 685639954 685639072 0.000000e+00 1101.0
2 TraesCS3B01G421300 chr3B 89.515 887 69 12 999 1866 685668446 685667565 0.000000e+00 1101.0
3 TraesCS3B01G421300 chr3B 93.177 469 30 2 2412 2879 35329203 35328736 0.000000e+00 688.0
4 TraesCS3B01G421300 chr3B 92.677 437 26 4 2847 3282 35328845 35328414 2.800000e-175 625.0
5 TraesCS3B01G421300 chr3B 79.942 344 49 15 1908 2241 685639093 685638760 5.520000e-58 235.0
6 TraesCS3B01G421300 chr3B 100.000 34 0 0 3253 3286 601378951 601378918 2.760000e-06 63.9
7 TraesCS3B01G421300 chr3D 91.838 2340 131 31 561 2859 497858691 497861011 0.000000e+00 3208.0
8 TraesCS3B01G421300 chr3D 88.000 900 72 18 999 1877 520610307 520609423 0.000000e+00 1031.0
9 TraesCS3B01G421300 chr3D 93.133 466 23 4 2847 3307 497860917 497861378 0.000000e+00 675.0
10 TraesCS3B01G421300 chr3D 87.701 187 21 2 31 217 497858512 497858696 2.000000e-52 217.0
11 TraesCS3B01G421300 chr3A 93.058 1426 85 6 563 1982 636572784 636571367 0.000000e+00 2073.0
12 TraesCS3B01G421300 chr3A 88.839 896 67 19 999 1877 655926438 655925559 0.000000e+00 1070.0
13 TraesCS3B01G421300 chr3A 88.013 901 66 20 999 1872 658195241 658196126 0.000000e+00 1027.0
14 TraesCS3B01G421300 chr3A 89.106 817 45 14 1978 2764 636566058 636565256 0.000000e+00 976.0
15 TraesCS3B01G421300 chr3A 96.020 402 14 2 2910 3309 636565250 636564849 0.000000e+00 652.0
16 TraesCS3B01G421300 chr3A 94.152 342 19 1 219 560 27005267 27005607 1.360000e-143 520.0
17 TraesCS3B01G421300 chr6B 93.133 466 30 2 2412 2876 718808199 718808663 0.000000e+00 682.0
18 TraesCS3B01G421300 chr6B 91.915 470 35 3 2412 2879 709227241 709226773 0.000000e+00 654.0
19 TraesCS3B01G421300 chr6B 92.043 465 31 4 2847 3309 709226883 709226423 0.000000e+00 649.0
20 TraesCS3B01G421300 chr6B 91.810 464 33 3 2847 3309 718808557 718809016 2.780000e-180 641.0
21 TraesCS3B01G421300 chr1B 92.964 469 31 2 2412 2879 56051494 56051027 0.000000e+00 682.0
22 TraesCS3B01G421300 chr1B 89.610 462 33 5 2847 3307 56051136 56050689 1.030000e-159 573.0
23 TraesCS3B01G421300 chr1B 94.118 357 21 0 207 563 388165222 388165578 8.080000e-151 544.0
24 TraesCS3B01G421300 chr1B 93.878 343 21 0 219 561 372155360 372155702 4.890000e-143 518.0
25 TraesCS3B01G421300 chr7B 92.704 466 32 2 2412 2876 702920257 702920721 0.000000e+00 671.0
26 TraesCS3B01G421300 chr7B 92.026 464 30 4 2847 3309 702920615 702921072 0.000000e+00 645.0
27 TraesCS3B01G421300 chr7B 96.501 343 12 0 219 561 8517106 8517448 4.790000e-158 568.0
28 TraesCS3B01G421300 chr7B 95.015 341 17 0 220 560 414158576 414158236 1.350000e-148 536.0
29 TraesCS3B01G421300 chr7B 94.220 346 20 0 219 564 427733325 427732980 2.260000e-146 529.0
30 TraesCS3B01G421300 chr5B 92.704 466 31 3 2412 2876 572031601 572032064 0.000000e+00 669.0
31 TraesCS3B01G421300 chr5B 92.457 464 29 4 2847 3309 572031959 572032417 0.000000e+00 658.0
32 TraesCS3B01G421300 chr2B 92.704 466 31 3 2412 2876 123553791 123554254 0.000000e+00 669.0
33 TraesCS3B01G421300 chr2B 92.026 464 32 3 2847 3309 123554148 123554607 0.000000e+00 647.0
34 TraesCS3B01G421300 chr2B 96.243 346 9 3 220 565 141152834 141153175 6.200000e-157 564.0
35 TraesCS3B01G421300 chr4B 91.471 469 35 3 2412 2879 515705537 515705073 1.000000e-179 640.0
36 TraesCS3B01G421300 chr4B 93.567 342 22 0 219 560 446449140 446448799 8.190000e-141 510.0
37 TraesCS3B01G421300 chr6D 95.308 341 16 0 220 560 8562840 8563180 2.900000e-150 542.0


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 TraesCS3B01G421300 chr3B 658461578 658464886 3308 False 6111.000000 6111 100.000000 1 3309 1 chr3B.!!$F1 3308
1 TraesCS3B01G421300 chr3B 685667565 685668446 881 True 1101.000000 1101 89.515000 999 1866 1 chr3B.!!$R2 867
2 TraesCS3B01G421300 chr3B 685638760 685639954 1194 True 668.000000 1101 84.728500 999 2241 2 chr3B.!!$R4 1242
3 TraesCS3B01G421300 chr3B 35328414 35329203 789 True 656.500000 688 92.927000 2412 3282 2 chr3B.!!$R3 870
4 TraesCS3B01G421300 chr3D 497858512 497861378 2866 False 1366.666667 3208 90.890667 31 3307 3 chr3D.!!$F1 3276
5 TraesCS3B01G421300 chr3D 520609423 520610307 884 True 1031.000000 1031 88.000000 999 1877 1 chr3D.!!$R1 878
6 TraesCS3B01G421300 chr3A 636571367 636572784 1417 True 2073.000000 2073 93.058000 563 1982 1 chr3A.!!$R1 1419
7 TraesCS3B01G421300 chr3A 655925559 655926438 879 True 1070.000000 1070 88.839000 999 1877 1 chr3A.!!$R2 878
8 TraesCS3B01G421300 chr3A 658195241 658196126 885 False 1027.000000 1027 88.013000 999 1872 1 chr3A.!!$F2 873
9 TraesCS3B01G421300 chr3A 636564849 636566058 1209 True 814.000000 976 92.563000 1978 3309 2 chr3A.!!$R3 1331
10 TraesCS3B01G421300 chr6B 718808199 718809016 817 False 661.500000 682 92.471500 2412 3309 2 chr6B.!!$F1 897
11 TraesCS3B01G421300 chr6B 709226423 709227241 818 True 651.500000 654 91.979000 2412 3309 2 chr6B.!!$R1 897
12 TraesCS3B01G421300 chr1B 56050689 56051494 805 True 627.500000 682 91.287000 2412 3307 2 chr1B.!!$R1 895
13 TraesCS3B01G421300 chr7B 702920257 702921072 815 False 658.000000 671 92.365000 2412 3309 2 chr7B.!!$F2 897
14 TraesCS3B01G421300 chr5B 572031601 572032417 816 False 663.500000 669 92.580500 2412 3309 2 chr5B.!!$F1 897
15 TraesCS3B01G421300 chr2B 123553791 123554607 816 False 658.000000 669 92.365000 2412 3309 2 chr2B.!!$F2 897

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
422 423 0.105408 GCCAATATGCCAAGCCCAAG 59.895 55.0 0.00 0.0 0.00 3.61 F
469 470 0.322546 AAACTTAGGCCCAAGCTCGG 60.323 55.0 11.18 0.0 39.73 4.63 F
857 873 0.370273 CGACTAGCAACAATCGTGCC 59.630 55.0 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 1886 0.909610 TGGAGGCGGACTTGAGGAAT 60.910 55.000 0.00 0.0 0.00 3.01 R
1896 1965 1.153958 CAGACGCGTGCAGAGATGA 60.154 57.895 20.70 0.0 0.00 2.92 R
2525 2637 1.212935 CCTAACAGTGGAGGATTGGGG 59.787 57.143 7.43 0.0 34.46 4.96 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
19 20 2.536761 TTTTGTGCGTAGGTAGCTGT 57.463 45.000 4.27 0.00 35.28 4.40
20 21 2.074547 TTTGTGCGTAGGTAGCTGTC 57.925 50.000 4.27 0.00 35.28 3.51
21 22 0.963225 TTGTGCGTAGGTAGCTGTCA 59.037 50.000 4.27 0.00 35.28 3.58
22 23 0.963225 TGTGCGTAGGTAGCTGTCAA 59.037 50.000 4.27 0.00 35.28 3.18
23 24 1.548719 TGTGCGTAGGTAGCTGTCAAT 59.451 47.619 4.27 0.00 35.28 2.57
24 25 2.028476 TGTGCGTAGGTAGCTGTCAATT 60.028 45.455 4.27 0.00 35.28 2.32
25 26 3.000727 GTGCGTAGGTAGCTGTCAATTT 58.999 45.455 4.27 0.00 35.28 1.82
26 27 3.000041 TGCGTAGGTAGCTGTCAATTTG 59.000 45.455 4.27 0.00 35.28 2.32
27 28 3.000727 GCGTAGGTAGCTGTCAATTTGT 58.999 45.455 4.27 0.00 0.00 2.83
28 29 3.181520 GCGTAGGTAGCTGTCAATTTGTG 60.182 47.826 4.27 0.00 0.00 3.33
29 30 3.370978 CGTAGGTAGCTGTCAATTTGTGG 59.629 47.826 4.27 0.00 0.00 4.17
30 31 2.162681 AGGTAGCTGTCAATTTGTGGC 58.837 47.619 0.00 0.47 0.00 5.01
31 32 2.162681 GGTAGCTGTCAATTTGTGGCT 58.837 47.619 0.00 14.05 30.97 4.75
32 33 3.009033 AGGTAGCTGTCAATTTGTGGCTA 59.991 43.478 0.00 12.69 30.97 3.93
33 34 3.375299 GGTAGCTGTCAATTTGTGGCTAG 59.625 47.826 15.23 0.00 33.79 3.42
34 35 3.146104 AGCTGTCAATTTGTGGCTAGT 57.854 42.857 10.09 0.00 30.97 2.57
35 36 3.490348 AGCTGTCAATTTGTGGCTAGTT 58.510 40.909 10.09 0.00 30.97 2.24
36 37 3.254166 AGCTGTCAATTTGTGGCTAGTTG 59.746 43.478 10.09 0.00 30.97 3.16
37 38 3.612479 GCTGTCAATTTGTGGCTAGTTGG 60.612 47.826 0.00 0.00 30.97 3.77
38 39 2.890311 TGTCAATTTGTGGCTAGTTGGG 59.110 45.455 0.00 0.00 30.97 4.12
39 40 2.890945 GTCAATTTGTGGCTAGTTGGGT 59.109 45.455 0.00 0.00 0.00 4.51
40 41 3.320826 GTCAATTTGTGGCTAGTTGGGTT 59.679 43.478 0.00 0.00 0.00 4.11
41 42 3.320541 TCAATTTGTGGCTAGTTGGGTTG 59.679 43.478 0.00 0.00 0.00 3.77
44 45 2.445682 TGTGGCTAGTTGGGTTGTTT 57.554 45.000 0.00 0.00 0.00 2.83
53 54 3.442076 AGTTGGGTTGTTTGGTTGGTTA 58.558 40.909 0.00 0.00 0.00 2.85
70 71 4.546829 GGTTATACCAACCACTCTCACA 57.453 45.455 1.30 0.00 38.42 3.58
91 92 7.573710 TCACATGTGGGCTTTATCTATAAAGT 58.426 34.615 25.16 1.44 46.78 2.66
92 93 8.052748 TCACATGTGGGCTTTATCTATAAAGTT 58.947 33.333 25.16 1.72 46.78 2.66
101 102 7.382759 GGCTTTATCTATAAAGTTGGTCTCTCG 59.617 40.741 18.85 0.00 46.78 4.04
104 105 8.749026 TTATCTATAAAGTTGGTCTCTCGTCT 57.251 34.615 0.00 0.00 0.00 4.18
107 108 7.536855 TCTATAAAGTTGGTCTCTCGTCTTTC 58.463 38.462 0.00 0.00 0.00 2.62
113 114 4.030314 TGGTCTCTCGTCTTTCCTCTAA 57.970 45.455 0.00 0.00 0.00 2.10
115 116 4.459685 TGGTCTCTCGTCTTTCCTCTAAAG 59.540 45.833 0.00 0.00 45.13 1.85
132 133 8.114102 TCCTCTAAAGAAAGGTAGTACATCAGA 58.886 37.037 2.06 0.00 34.12 3.27
134 135 8.880991 TCTAAAGAAAGGTAGTACATCAGAGT 57.119 34.615 2.06 0.00 0.00 3.24
140 141 4.936802 AGGTAGTACATCAGAGTCCTTGT 58.063 43.478 2.06 0.00 0.00 3.16
221 222 3.016971 TGCTGGGGCTGGCAGTAT 61.017 61.111 17.16 0.00 39.59 2.12
222 223 1.692395 TGCTGGGGCTGGCAGTATA 60.692 57.895 17.16 0.00 39.59 1.47
223 224 1.061905 TGCTGGGGCTGGCAGTATAT 61.062 55.000 17.16 0.00 39.59 0.86
224 225 0.322008 GCTGGGGCTGGCAGTATATC 60.322 60.000 17.16 0.00 35.22 1.63
225 226 1.356124 CTGGGGCTGGCAGTATATCT 58.644 55.000 17.16 0.00 0.00 1.98
226 227 2.540383 CTGGGGCTGGCAGTATATCTA 58.460 52.381 17.16 0.00 0.00 1.98
227 228 2.499289 CTGGGGCTGGCAGTATATCTAG 59.501 54.545 17.16 5.24 0.00 2.43
228 229 1.208293 GGGGCTGGCAGTATATCTAGC 59.792 57.143 17.16 0.00 0.00 3.42
234 235 3.550437 GGCAGTATATCTAGCCATGGG 57.450 52.381 15.13 0.00 46.26 4.00
268 269 2.526628 TTGGGCCCGGCCTAAAAA 59.473 55.556 27.94 14.20 45.79 1.94
287 288 4.326504 AAAAGTCCATGGCAGAAAACTG 57.673 40.909 6.96 0.00 0.00 3.16
288 289 2.957402 AGTCCATGGCAGAAAACTGA 57.043 45.000 6.96 0.00 0.00 3.41
289 290 2.787994 AGTCCATGGCAGAAAACTGAG 58.212 47.619 6.96 0.00 0.00 3.35
290 291 1.815003 GTCCATGGCAGAAAACTGAGG 59.185 52.381 6.96 0.00 0.00 3.86
291 292 0.529378 CCATGGCAGAAAACTGAGGC 59.471 55.000 0.00 0.00 0.00 4.70
292 293 0.529378 CATGGCAGAAAACTGAGGCC 59.471 55.000 0.00 0.00 44.82 5.19
293 294 0.613012 ATGGCAGAAAACTGAGGCCC 60.613 55.000 0.00 0.00 43.96 5.80
294 295 1.228552 GGCAGAAAACTGAGGCCCA 60.229 57.895 0.00 0.00 38.70 5.36
314 315 4.431524 CCCTCCCAGGCCCTACCA 62.432 72.222 0.00 0.00 43.14 3.25
315 316 2.039405 CCTCCCAGGCCCTACCAT 60.039 66.667 0.00 0.00 43.14 3.55
316 317 2.150051 CCTCCCAGGCCCTACCATC 61.150 68.421 0.00 0.00 43.14 3.51
317 318 2.445845 TCCCAGGCCCTACCATCG 60.446 66.667 0.00 0.00 43.14 3.84
318 319 3.560251 CCCAGGCCCTACCATCGG 61.560 72.222 0.00 0.00 43.14 4.18
319 320 3.560251 CCAGGCCCTACCATCGGG 61.560 72.222 0.00 0.00 44.89 5.14
324 325 3.468063 CCCTACCATCGGGCCTAC 58.532 66.667 0.84 0.00 37.90 3.18
325 326 1.152312 CCCTACCATCGGGCCTACT 60.152 63.158 0.84 0.00 37.90 2.57
326 327 0.763223 CCCTACCATCGGGCCTACTT 60.763 60.000 0.84 0.00 37.90 2.24
327 328 1.129058 CCTACCATCGGGCCTACTTT 58.871 55.000 0.84 0.00 37.90 2.66
328 329 1.489230 CCTACCATCGGGCCTACTTTT 59.511 52.381 0.84 0.00 37.90 2.27
329 330 2.484947 CCTACCATCGGGCCTACTTTTC 60.485 54.545 0.84 0.00 37.90 2.29
330 331 0.988832 ACCATCGGGCCTACTTTTCA 59.011 50.000 0.84 0.00 37.90 2.69
331 332 1.353022 ACCATCGGGCCTACTTTTCAA 59.647 47.619 0.84 0.00 37.90 2.69
332 333 2.017049 CCATCGGGCCTACTTTTCAAG 58.983 52.381 0.84 0.00 0.00 3.02
333 334 1.401905 CATCGGGCCTACTTTTCAAGC 59.598 52.381 0.84 0.00 0.00 4.01
334 335 0.322187 TCGGGCCTACTTTTCAAGCC 60.322 55.000 0.84 0.00 43.09 4.35
336 337 3.356814 GGCCTACTTTTCAAGCCCA 57.643 52.632 0.00 0.00 37.66 5.36
337 338 1.627864 GGCCTACTTTTCAAGCCCAA 58.372 50.000 0.00 0.00 37.66 4.12
338 339 1.546029 GGCCTACTTTTCAAGCCCAAG 59.454 52.381 0.00 0.00 37.66 3.61
339 340 1.067565 GCCTACTTTTCAAGCCCAAGC 60.068 52.381 0.00 0.00 40.32 4.01
340 341 1.546029 CCTACTTTTCAAGCCCAAGCC 59.454 52.381 0.00 0.00 41.25 4.35
341 342 1.546029 CTACTTTTCAAGCCCAAGCCC 59.454 52.381 0.00 0.00 41.25 5.19
342 343 1.290009 CTTTTCAAGCCCAAGCCCG 59.710 57.895 0.00 0.00 41.25 6.13
343 344 2.158561 CTTTTCAAGCCCAAGCCCGG 62.159 60.000 0.00 0.00 41.25 5.73
354 355 4.815973 AGCCCGGCCCATCTGGTA 62.816 66.667 5.55 0.00 39.73 3.25
355 356 3.804329 GCCCGGCCCATCTGGTAA 61.804 66.667 0.00 0.00 39.73 2.85
356 357 3.003230 CCCGGCCCATCTGGTAAA 58.997 61.111 0.00 0.00 39.73 2.01
357 358 1.304952 CCCGGCCCATCTGGTAAAA 59.695 57.895 0.00 0.00 39.73 1.52
358 359 0.323908 CCCGGCCCATCTGGTAAAAA 60.324 55.000 0.00 0.00 39.73 1.94
359 360 1.102978 CCGGCCCATCTGGTAAAAAG 58.897 55.000 0.00 0.00 36.43 2.27
360 361 0.455815 CGGCCCATCTGGTAAAAAGC 59.544 55.000 0.00 0.00 36.04 3.51
361 362 0.824109 GGCCCATCTGGTAAAAAGCC 59.176 55.000 0.00 0.00 36.04 4.35
362 363 0.824109 GCCCATCTGGTAAAAAGCCC 59.176 55.000 0.00 0.00 36.04 5.19
363 364 1.619704 GCCCATCTGGTAAAAAGCCCT 60.620 52.381 0.00 0.00 36.04 5.19
364 365 2.820178 CCCATCTGGTAAAAAGCCCTT 58.180 47.619 0.00 0.00 0.00 3.95
365 366 3.880117 GCCCATCTGGTAAAAAGCCCTTA 60.880 47.826 0.00 0.00 36.04 2.69
366 367 3.954258 CCCATCTGGTAAAAAGCCCTTAG 59.046 47.826 0.00 0.00 0.00 2.18
367 368 3.954258 CCATCTGGTAAAAAGCCCTTAGG 59.046 47.826 0.00 0.00 0.00 2.69
398 399 3.087906 GGCCGGGCCTCTTCCTTA 61.088 66.667 30.86 0.00 46.69 2.69
399 400 2.676265 GGCCGGGCCTCTTCCTTAA 61.676 63.158 30.86 0.00 46.69 1.85
400 401 1.301954 GCCGGGCCTCTTCCTTAAA 59.698 57.895 8.12 0.00 0.00 1.52
401 402 0.323087 GCCGGGCCTCTTCCTTAAAA 60.323 55.000 8.12 0.00 0.00 1.52
402 403 1.685180 GCCGGGCCTCTTCCTTAAAAT 60.685 52.381 8.12 0.00 0.00 1.82
403 404 2.024414 CCGGGCCTCTTCCTTAAAATG 58.976 52.381 0.84 0.00 0.00 2.32
404 405 1.405463 CGGGCCTCTTCCTTAAAATGC 59.595 52.381 0.84 0.00 0.00 3.56
405 406 1.757118 GGGCCTCTTCCTTAAAATGCC 59.243 52.381 0.84 0.00 36.92 4.40
406 407 2.456577 GGCCTCTTCCTTAAAATGCCA 58.543 47.619 0.00 0.00 37.58 4.92
407 408 2.831526 GGCCTCTTCCTTAAAATGCCAA 59.168 45.455 0.00 0.00 37.58 4.52
408 409 3.452264 GGCCTCTTCCTTAAAATGCCAAT 59.548 43.478 0.00 0.00 37.58 3.16
409 410 4.649218 GGCCTCTTCCTTAAAATGCCAATA 59.351 41.667 0.00 0.00 37.58 1.90
410 411 5.305386 GGCCTCTTCCTTAAAATGCCAATAT 59.695 40.000 0.00 0.00 37.58 1.28
411 412 6.218746 GCCTCTTCCTTAAAATGCCAATATG 58.781 40.000 0.00 0.00 0.00 1.78
412 413 6.218746 CCTCTTCCTTAAAATGCCAATATGC 58.781 40.000 0.00 0.00 0.00 3.14
413 414 6.160576 TCTTCCTTAAAATGCCAATATGCC 57.839 37.500 0.00 0.00 0.00 4.40
414 415 5.660417 TCTTCCTTAAAATGCCAATATGCCA 59.340 36.000 0.00 0.00 0.00 4.92
415 416 5.946942 TCCTTAAAATGCCAATATGCCAA 57.053 34.783 0.00 0.00 0.00 4.52
416 417 5.916318 TCCTTAAAATGCCAATATGCCAAG 58.084 37.500 0.00 0.00 0.00 3.61
417 418 4.512571 CCTTAAAATGCCAATATGCCAAGC 59.487 41.667 0.00 0.00 0.00 4.01
418 419 2.625695 AAATGCCAATATGCCAAGCC 57.374 45.000 0.00 0.00 0.00 4.35
419 420 0.760572 AATGCCAATATGCCAAGCCC 59.239 50.000 0.00 0.00 0.00 5.19
420 421 0.398806 ATGCCAATATGCCAAGCCCA 60.399 50.000 0.00 0.00 0.00 5.36
421 422 0.616964 TGCCAATATGCCAAGCCCAA 60.617 50.000 0.00 0.00 0.00 4.12
422 423 0.105408 GCCAATATGCCAAGCCCAAG 59.895 55.000 0.00 0.00 0.00 3.61
423 424 0.105408 CCAATATGCCAAGCCCAAGC 59.895 55.000 0.00 0.00 40.32 4.01
424 425 0.105408 CAATATGCCAAGCCCAAGCC 59.895 55.000 0.00 0.00 41.25 4.35
425 426 1.050421 AATATGCCAAGCCCAAGCCC 61.050 55.000 0.00 0.00 41.25 5.19
430 431 4.659172 CAAGCCCAAGCCCGTCCA 62.659 66.667 0.00 0.00 41.25 4.02
431 432 4.351054 AAGCCCAAGCCCGTCCAG 62.351 66.667 0.00 0.00 41.25 3.86
450 451 4.355720 CCCTGCTGCTGGGCTCAA 62.356 66.667 28.41 0.00 35.90 3.02
451 452 2.282674 CCTGCTGCTGGGCTCAAA 60.283 61.111 16.96 0.00 0.00 2.69
452 453 1.904865 CCTGCTGCTGGGCTCAAAA 60.905 57.895 16.96 0.00 0.00 2.44
453 454 1.288127 CTGCTGCTGGGCTCAAAAC 59.712 57.895 0.00 0.00 0.00 2.43
454 455 1.152694 TGCTGCTGGGCTCAAAACT 60.153 52.632 0.00 0.00 0.00 2.66
455 456 0.756442 TGCTGCTGGGCTCAAAACTT 60.756 50.000 0.00 0.00 0.00 2.66
456 457 1.247567 GCTGCTGGGCTCAAAACTTA 58.752 50.000 0.00 0.00 0.00 2.24
457 458 1.200948 GCTGCTGGGCTCAAAACTTAG 59.799 52.381 0.00 0.00 0.00 2.18
458 459 1.815003 CTGCTGGGCTCAAAACTTAGG 59.185 52.381 0.00 0.00 0.00 2.69
459 460 0.528017 GCTGGGCTCAAAACTTAGGC 59.472 55.000 0.00 0.00 37.55 3.93
462 463 3.356814 GGCTCAAAACTTAGGCCCA 57.643 52.632 0.00 0.00 37.12 5.36
463 464 1.627864 GGCTCAAAACTTAGGCCCAA 58.372 50.000 0.00 0.00 37.12 4.12
464 465 1.546029 GGCTCAAAACTTAGGCCCAAG 59.454 52.381 9.61 9.61 37.12 3.61
465 466 1.067565 GCTCAAAACTTAGGCCCAAGC 60.068 52.381 11.18 0.00 38.76 4.01
466 467 2.519013 CTCAAAACTTAGGCCCAAGCT 58.481 47.619 11.18 0.00 39.73 3.74
467 468 2.489722 CTCAAAACTTAGGCCCAAGCTC 59.510 50.000 11.18 0.00 39.73 4.09
468 469 1.200020 CAAAACTTAGGCCCAAGCTCG 59.800 52.381 11.18 0.00 39.73 5.03
469 470 0.322546 AAACTTAGGCCCAAGCTCGG 60.323 55.000 11.18 0.00 39.73 4.63
470 471 2.514824 CTTAGGCCCAAGCTCGGC 60.515 66.667 14.98 14.98 46.29 5.54
476 477 4.659172 CCCAAGCTCGGCCCACAA 62.659 66.667 0.00 0.00 0.00 3.33
477 478 3.058160 CCAAGCTCGGCCCACAAG 61.058 66.667 0.00 0.00 0.00 3.16
478 479 3.741476 CAAGCTCGGCCCACAAGC 61.741 66.667 0.00 1.01 36.27 4.01
479 480 4.269523 AAGCTCGGCCCACAAGCA 62.270 61.111 14.36 0.00 38.51 3.91
480 481 3.790416 AAGCTCGGCCCACAAGCAA 62.790 57.895 14.36 0.00 38.51 3.91
481 482 3.741476 GCTCGGCCCACAAGCAAG 61.741 66.667 0.00 0.00 36.06 4.01
482 483 3.741476 CTCGGCCCACAAGCAAGC 61.741 66.667 0.00 0.00 0.00 4.01
486 487 2.999063 GCCCACAAGCAAGCCCAT 60.999 61.111 0.00 0.00 0.00 4.00
487 488 3.010413 GCCCACAAGCAAGCCCATC 62.010 63.158 0.00 0.00 0.00 3.51
488 489 1.607178 CCCACAAGCAAGCCCATCA 60.607 57.895 0.00 0.00 0.00 3.07
489 490 1.601419 CCCACAAGCAAGCCCATCAG 61.601 60.000 0.00 0.00 0.00 2.90
490 491 1.601419 CCACAAGCAAGCCCATCAGG 61.601 60.000 0.00 0.00 39.47 3.86
509 510 2.278332 GCCTAGGCCCTGGATTTTAG 57.722 55.000 24.19 0.33 34.56 1.85
510 511 1.202940 GCCTAGGCCCTGGATTTTAGG 60.203 57.143 24.19 10.45 34.56 2.69
515 516 4.579127 CCTGGATTTTAGGGCCGG 57.421 61.111 0.00 0.00 0.00 6.13
516 517 1.152756 CCTGGATTTTAGGGCCGGG 60.153 63.158 2.18 0.00 41.55 5.73
517 518 1.828224 CTGGATTTTAGGGCCGGGC 60.828 63.158 22.00 22.00 0.00 6.13
581 582 1.672356 GGCGGTGACTGCAACATCT 60.672 57.895 19.20 0.00 0.00 2.90
636 637 3.058160 GCTGCCACCGATGCACTT 61.058 61.111 0.00 0.00 34.46 3.16
639 640 2.045926 GCCACCGATGCACTTCCT 60.046 61.111 0.00 0.00 0.00 3.36
659 660 1.741401 CGACCAATTCGCAGCAGGA 60.741 57.895 0.00 0.00 41.87 3.86
669 670 3.155750 CAGCAGGATAGCCCCCTC 58.844 66.667 0.00 0.00 34.66 4.30
702 703 3.198872 GGTCTCTTATGGCAAGCTACAC 58.801 50.000 0.00 0.00 0.00 2.90
714 715 2.973899 CTACACCGCAGCACTCCT 59.026 61.111 0.00 0.00 0.00 3.69
728 729 3.535629 CTCCTTGGCAGCACCGACA 62.536 63.158 0.00 0.00 43.94 4.35
796 807 2.047274 CATCGCAACACCGACCCT 60.047 61.111 0.00 0.00 40.40 4.34
857 873 0.370273 CGACTAGCAACAATCGTGCC 59.630 55.000 0.00 0.00 0.00 5.01
1817 1886 2.123854 ATCTACCAGAGCCCGCGA 60.124 61.111 8.23 0.00 0.00 5.87
1932 2001 2.873288 CGCCCAAGAAGAGCAAGC 59.127 61.111 0.00 0.00 0.00 4.01
1987 2056 0.600255 CTCCTGTTTCCGTCGTTGCT 60.600 55.000 0.00 0.00 0.00 3.91
2007 2076 0.464373 TCCTCCATCAAATCTGCCGC 60.464 55.000 0.00 0.00 0.00 6.53
2302 2407 9.141400 CTTAGTTAAACTAGTCACAGCCTTTAG 57.859 37.037 0.00 0.00 31.47 1.85
2326 2433 5.844396 GTGTTACGCTTACTGTTTGCTAAAG 59.156 40.000 0.00 0.00 0.00 1.85
2544 2656 2.092914 GTCCCCAATCCTCCACTGTTAG 60.093 54.545 0.00 0.00 0.00 2.34
2553 2665 3.907474 TCCTCCACTGTTAGGTTTGATGA 59.093 43.478 5.99 0.00 34.30 2.92
2572 2684 7.862512 TGATGATATCTTGTGTTGTGCAATA 57.137 32.000 3.98 0.00 0.00 1.90
2629 2742 3.958147 TGAACCTTGTTTCCCCTTTTCTC 59.042 43.478 0.00 0.00 0.00 2.87
2649 2762 5.982356 TCTCAATTTAGCACTGCTACTGAT 58.018 37.500 10.43 3.10 41.12 2.90
2660 2773 5.235186 GCACTGCTACTGATTCGTTGAATAT 59.765 40.000 0.00 0.00 31.89 1.28
2704 2817 6.855836 TCCATAAGCTTTGTTAATTCTGCAG 58.144 36.000 7.63 7.63 0.00 4.41
2707 2820 7.698130 CCATAAGCTTTGTTAATTCTGCAGTAC 59.302 37.037 14.67 6.22 0.00 2.73
2750 2864 4.022329 CAGTTTAGTTTTGCTTACCAGGGG 60.022 45.833 0.00 0.00 0.00 4.79
2787 2905 1.600957 CTGCAGCCGGACTTATGAATG 59.399 52.381 5.05 0.00 0.00 2.67
2788 2906 0.308993 GCAGCCGGACTTATGAATGC 59.691 55.000 5.05 0.00 0.00 3.56
2789 2907 1.959042 CAGCCGGACTTATGAATGCT 58.041 50.000 5.05 0.00 0.00 3.79
2790 2908 1.869767 CAGCCGGACTTATGAATGCTC 59.130 52.381 5.05 0.00 0.00 4.26
2791 2909 1.486310 AGCCGGACTTATGAATGCTCA 59.514 47.619 5.05 0.00 35.56 4.26
2792 2910 2.105477 AGCCGGACTTATGAATGCTCAT 59.895 45.455 5.05 0.00 44.71 2.90
2793 2911 2.481952 GCCGGACTTATGAATGCTCATC 59.518 50.000 5.05 0.00 41.57 2.92
2794 2912 3.805108 GCCGGACTTATGAATGCTCATCT 60.805 47.826 5.05 0.00 41.57 2.90
2795 2913 3.744942 CCGGACTTATGAATGCTCATCTG 59.255 47.826 0.00 0.00 41.57 2.90
2796 2914 4.375272 CGGACTTATGAATGCTCATCTGT 58.625 43.478 0.00 0.00 41.57 3.41
2797 2915 4.813161 CGGACTTATGAATGCTCATCTGTT 59.187 41.667 0.00 0.00 41.57 3.16
2798 2916 5.295292 CGGACTTATGAATGCTCATCTGTTT 59.705 40.000 0.00 0.00 41.57 2.83
2799 2917 6.183360 CGGACTTATGAATGCTCATCTGTTTT 60.183 38.462 0.00 0.00 41.57 2.43
2800 2918 7.542025 GGACTTATGAATGCTCATCTGTTTTT 58.458 34.615 0.00 0.00 41.57 1.94
2822 2940 7.827819 TTTTCTGAATACAGTCGGACTTATG 57.172 36.000 8.18 0.86 43.81 1.90
2823 2941 6.769134 TTCTGAATACAGTCGGACTTATGA 57.231 37.500 8.18 2.48 43.81 2.15
2824 2942 6.769134 TCTGAATACAGTCGGACTTATGAA 57.231 37.500 8.18 2.72 43.81 2.57
2825 2943 7.348080 TCTGAATACAGTCGGACTTATGAAT 57.652 36.000 8.18 0.00 43.81 2.57
2896 3018 0.537143 TTTGTGAATGCAGCCGGACT 60.537 50.000 5.05 0.00 0.00 3.85
2897 3019 0.537143 TTGTGAATGCAGCCGGACTT 60.537 50.000 5.05 0.00 0.00 3.01
2898 3020 0.537143 TGTGAATGCAGCCGGACTTT 60.537 50.000 5.05 0.00 0.00 2.66
2899 3021 0.598065 GTGAATGCAGCCGGACTTTT 59.402 50.000 5.05 0.00 0.00 2.27
2900 3022 0.597568 TGAATGCAGCCGGACTTTTG 59.402 50.000 5.05 0.00 0.00 2.44
2901 3023 0.598065 GAATGCAGCCGGACTTTTGT 59.402 50.000 5.05 0.00 0.00 2.83
2902 3024 1.810151 GAATGCAGCCGGACTTTTGTA 59.190 47.619 5.05 0.00 0.00 2.41
2903 3025 1.904287 ATGCAGCCGGACTTTTGTAA 58.096 45.000 5.05 0.00 0.00 2.41
2904 3026 0.948678 TGCAGCCGGACTTTTGTAAC 59.051 50.000 5.05 0.00 0.00 2.50
2905 3027 1.235724 GCAGCCGGACTTTTGTAACT 58.764 50.000 5.05 0.00 0.00 2.24
2906 3028 1.607148 GCAGCCGGACTTTTGTAACTT 59.393 47.619 5.05 0.00 0.00 2.66
2907 3029 2.034179 GCAGCCGGACTTTTGTAACTTT 59.966 45.455 5.05 0.00 0.00 2.66
2908 3030 3.490249 GCAGCCGGACTTTTGTAACTTTT 60.490 43.478 5.05 0.00 0.00 2.27
2909 3031 4.678622 CAGCCGGACTTTTGTAACTTTTT 58.321 39.130 5.05 0.00 0.00 1.94
2938 3060 2.704725 TTTTCTGAATGCAGCCGAAC 57.295 45.000 0.00 0.00 42.01 3.95
2954 3118 5.681543 CAGCCGAACTTTTGTAACTTCTTTC 59.318 40.000 0.00 0.00 0.00 2.62
2979 3143 3.737559 TGGATTTCTGGGCATTACTGT 57.262 42.857 0.00 0.00 0.00 3.55
3003 3167 7.665559 TGTAGAATGGTCAAAATTTGTAGCTCT 59.334 33.333 5.56 5.72 0.00 4.09
3005 3169 8.045176 AGAATGGTCAAAATTTGTAGCTCTAC 57.955 34.615 5.56 0.27 36.63 2.59
3138 3303 6.814954 AGATGGGTCTTGTACATTCAGTAT 57.185 37.500 0.00 0.00 34.67 2.12
3298 3463 7.232534 ACACAATATGCAGTTCCCTTTTCTAAA 59.767 33.333 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.224090 TGACAGCTACCTACGCACAAAA 60.224 45.455 0.00 0.00 0.00 2.44
2 3 0.963225 TGACAGCTACCTACGCACAA 59.037 50.000 0.00 0.00 0.00 3.33
4 5 2.295253 ATTGACAGCTACCTACGCAC 57.705 50.000 0.00 0.00 0.00 5.34
5 6 3.000041 CAAATTGACAGCTACCTACGCA 59.000 45.455 0.00 0.00 0.00 5.24
6 7 3.000727 ACAAATTGACAGCTACCTACGC 58.999 45.455 0.00 0.00 0.00 4.42
7 8 3.370978 CCACAAATTGACAGCTACCTACG 59.629 47.826 0.00 0.00 0.00 3.51
8 9 3.127030 GCCACAAATTGACAGCTACCTAC 59.873 47.826 0.00 0.00 0.00 3.18
10 11 2.162681 GCCACAAATTGACAGCTACCT 58.837 47.619 0.00 0.00 0.00 3.08
11 12 2.162681 AGCCACAAATTGACAGCTACC 58.837 47.619 0.00 0.00 0.00 3.18
12 13 4.003648 ACTAGCCACAAATTGACAGCTAC 58.996 43.478 0.00 0.00 0.00 3.58
13 14 4.286297 ACTAGCCACAAATTGACAGCTA 57.714 40.909 0.00 7.90 0.00 3.32
14 15 3.146104 ACTAGCCACAAATTGACAGCT 57.854 42.857 0.00 7.15 0.00 4.24
15 16 3.568538 CAACTAGCCACAAATTGACAGC 58.431 45.455 0.00 0.00 0.00 4.40
16 17 3.057315 CCCAACTAGCCACAAATTGACAG 60.057 47.826 0.00 0.00 0.00 3.51
17 18 2.890311 CCCAACTAGCCACAAATTGACA 59.110 45.455 0.00 0.00 0.00 3.58
18 19 2.890945 ACCCAACTAGCCACAAATTGAC 59.109 45.455 0.00 0.00 0.00 3.18
19 20 3.237268 ACCCAACTAGCCACAAATTGA 57.763 42.857 0.00 0.00 0.00 2.57
20 21 3.069443 ACAACCCAACTAGCCACAAATTG 59.931 43.478 0.00 0.00 0.00 2.32
21 22 3.304829 ACAACCCAACTAGCCACAAATT 58.695 40.909 0.00 0.00 0.00 1.82
22 23 2.957474 ACAACCCAACTAGCCACAAAT 58.043 42.857 0.00 0.00 0.00 2.32
23 24 2.445682 ACAACCCAACTAGCCACAAA 57.554 45.000 0.00 0.00 0.00 2.83
24 25 2.428890 CAAACAACCCAACTAGCCACAA 59.571 45.455 0.00 0.00 0.00 3.33
25 26 2.028130 CAAACAACCCAACTAGCCACA 58.972 47.619 0.00 0.00 0.00 4.17
26 27 1.339929 CCAAACAACCCAACTAGCCAC 59.660 52.381 0.00 0.00 0.00 5.01
27 28 1.063567 ACCAAACAACCCAACTAGCCA 60.064 47.619 0.00 0.00 0.00 4.75
28 29 1.699730 ACCAAACAACCCAACTAGCC 58.300 50.000 0.00 0.00 0.00 3.93
29 30 2.223947 CCAACCAAACAACCCAACTAGC 60.224 50.000 0.00 0.00 0.00 3.42
30 31 3.028130 ACCAACCAAACAACCCAACTAG 58.972 45.455 0.00 0.00 0.00 2.57
31 32 3.103080 ACCAACCAAACAACCCAACTA 57.897 42.857 0.00 0.00 0.00 2.24
32 33 1.945580 ACCAACCAAACAACCCAACT 58.054 45.000 0.00 0.00 0.00 3.16
33 34 2.772077 AACCAACCAAACAACCCAAC 57.228 45.000 0.00 0.00 0.00 3.77
34 35 4.344390 GGTATAACCAACCAAACAACCCAA 59.656 41.667 0.00 0.00 38.42 4.12
35 36 3.896272 GGTATAACCAACCAAACAACCCA 59.104 43.478 0.00 0.00 38.42 4.51
36 37 4.524316 GGTATAACCAACCAAACAACCC 57.476 45.455 0.00 0.00 38.42 4.11
53 54 3.942829 CACATGTGAGAGTGGTTGGTAT 58.057 45.455 21.64 0.00 32.24 2.73
91 92 2.877866 AGAGGAAAGACGAGAGACCAA 58.122 47.619 0.00 0.00 0.00 3.67
92 93 2.588464 AGAGGAAAGACGAGAGACCA 57.412 50.000 0.00 0.00 0.00 4.02
104 105 9.096823 TGATGTACTACCTTTCTTTAGAGGAAA 57.903 33.333 0.00 0.00 36.84 3.13
107 108 8.294954 TCTGATGTACTACCTTTCTTTAGAGG 57.705 38.462 0.00 0.00 39.02 3.69
113 114 6.257586 AGGACTCTGATGTACTACCTTTCTT 58.742 40.000 0.00 0.00 27.52 2.52
115 116 6.071278 ACAAGGACTCTGATGTACTACCTTTC 60.071 42.308 0.00 0.00 34.83 2.62
120 121 5.394333 GGGAACAAGGACTCTGATGTACTAC 60.394 48.000 0.00 0.00 29.59 2.73
121 122 4.710375 GGGAACAAGGACTCTGATGTACTA 59.290 45.833 0.00 0.00 29.59 1.82
122 123 3.515901 GGGAACAAGGACTCTGATGTACT 59.484 47.826 0.00 0.00 31.30 2.73
123 124 3.515901 AGGGAACAAGGACTCTGATGTAC 59.484 47.826 0.00 0.00 0.00 2.90
124 125 3.769844 GAGGGAACAAGGACTCTGATGTA 59.230 47.826 0.00 0.00 0.00 2.29
132 133 1.272147 GCAATGGAGGGAACAAGGACT 60.272 52.381 0.00 0.00 0.00 3.85
134 135 0.776810 TGCAATGGAGGGAACAAGGA 59.223 50.000 0.00 0.00 0.00 3.36
140 141 1.304381 GTGGCTGCAATGGAGGGAA 60.304 57.895 3.49 0.00 0.00 3.97
209 210 1.208293 GGCTAGATATACTGCCAGCCC 59.792 57.143 0.00 0.00 40.24 5.19
211 212 3.529533 CATGGCTAGATATACTGCCAGC 58.470 50.000 16.59 4.80 46.86 4.85
212 213 3.118482 CCCATGGCTAGATATACTGCCAG 60.118 52.174 6.09 0.00 46.86 4.85
213 214 4.956508 GCCCATGGCTAGATATACTGCCA 61.957 52.174 6.09 14.68 46.69 4.92
214 215 2.420687 GCCCATGGCTAGATATACTGCC 60.421 54.545 6.09 0.00 46.69 4.85
215 216 2.911484 GCCCATGGCTAGATATACTGC 58.089 52.381 6.09 0.00 46.69 4.40
265 266 4.405358 TCAGTTTTCTGCCATGGACTTTTT 59.595 37.500 18.40 0.00 46.59 1.94
266 267 3.960102 TCAGTTTTCTGCCATGGACTTTT 59.040 39.130 18.40 0.00 46.59 2.27
267 268 3.565307 TCAGTTTTCTGCCATGGACTTT 58.435 40.909 18.40 0.00 46.59 2.66
268 269 3.152341 CTCAGTTTTCTGCCATGGACTT 58.848 45.455 18.40 0.00 46.59 3.01
269 270 2.553904 CCTCAGTTTTCTGCCATGGACT 60.554 50.000 18.40 5.72 46.59 3.85
270 271 1.815003 CCTCAGTTTTCTGCCATGGAC 59.185 52.381 18.40 7.64 46.59 4.02
271 272 1.887956 GCCTCAGTTTTCTGCCATGGA 60.888 52.381 18.40 0.00 46.59 3.41
272 273 0.529378 GCCTCAGTTTTCTGCCATGG 59.471 55.000 7.63 7.63 46.59 3.66
273 274 0.529378 GGCCTCAGTTTTCTGCCATG 59.471 55.000 0.00 0.00 46.59 3.66
274 275 0.613012 GGGCCTCAGTTTTCTGCCAT 60.613 55.000 0.84 0.00 46.59 4.40
275 276 1.228552 GGGCCTCAGTTTTCTGCCA 60.229 57.895 0.84 0.00 46.59 4.92
276 277 1.228552 TGGGCCTCAGTTTTCTGCC 60.229 57.895 4.53 0.00 46.59 4.85
277 278 1.246737 CCTGGGCCTCAGTTTTCTGC 61.247 60.000 16.96 0.00 46.59 4.26
278 279 1.246737 GCCTGGGCCTCAGTTTTCTG 61.247 60.000 16.96 5.05 41.83 3.02
279 280 1.075659 GCCTGGGCCTCAGTTTTCT 59.924 57.895 16.96 0.00 41.83 2.52
280 281 3.686760 GCCTGGGCCTCAGTTTTC 58.313 61.111 16.96 3.57 41.83 2.29
297 298 3.739080 ATGGTAGGGCCTGGGAGGG 62.739 68.421 18.53 0.00 35.37 4.30
298 299 2.039405 ATGGTAGGGCCTGGGAGG 60.039 66.667 18.53 0.00 38.80 4.30
299 300 2.511452 CGATGGTAGGGCCTGGGAG 61.511 68.421 18.53 0.00 38.35 4.30
300 301 2.445845 CGATGGTAGGGCCTGGGA 60.446 66.667 18.53 0.00 38.35 4.37
301 302 3.560251 CCGATGGTAGGGCCTGGG 61.560 72.222 18.53 3.75 38.35 4.45
302 303 3.560251 CCCGATGGTAGGGCCTGG 61.560 72.222 18.53 7.41 42.77 4.45
308 309 1.129058 AAAGTAGGCCCGATGGTAGG 58.871 55.000 0.00 0.00 0.00 3.18
309 310 2.169769 TGAAAAGTAGGCCCGATGGTAG 59.830 50.000 0.00 0.00 0.00 3.18
310 311 2.189676 TGAAAAGTAGGCCCGATGGTA 58.810 47.619 0.00 0.00 0.00 3.25
311 312 0.988832 TGAAAAGTAGGCCCGATGGT 59.011 50.000 0.00 0.00 0.00 3.55
312 313 2.017049 CTTGAAAAGTAGGCCCGATGG 58.983 52.381 0.00 0.00 39.70 3.51
325 326 2.206536 CCGGGCTTGGGCTTGAAAA 61.207 57.895 0.00 0.00 38.73 2.29
326 327 2.600173 CCGGGCTTGGGCTTGAAA 60.600 61.111 0.00 0.00 38.73 2.69
337 338 4.815973 TACCAGATGGGCCGGGCT 62.816 66.667 28.80 9.11 42.05 5.19
338 339 2.847366 TTTTACCAGATGGGCCGGGC 62.847 60.000 22.00 22.00 42.05 6.13
339 340 0.323908 TTTTTACCAGATGGGCCGGG 60.324 55.000 2.18 0.00 42.05 5.73
340 341 1.102978 CTTTTTACCAGATGGGCCGG 58.897 55.000 0.00 0.00 42.05 6.13
341 342 0.455815 GCTTTTTACCAGATGGGCCG 59.544 55.000 3.48 0.00 42.05 6.13
342 343 0.824109 GGCTTTTTACCAGATGGGCC 59.176 55.000 3.48 0.00 42.05 5.80
343 344 0.824109 GGGCTTTTTACCAGATGGGC 59.176 55.000 3.48 0.00 42.05 5.36
344 345 2.532250 AGGGCTTTTTACCAGATGGG 57.468 50.000 3.48 0.00 44.81 4.00
345 346 3.954258 CCTAAGGGCTTTTTACCAGATGG 59.046 47.826 0.00 0.00 42.17 3.51
346 347 3.954258 CCCTAAGGGCTTTTTACCAGATG 59.046 47.826 0.00 0.00 35.35 2.90
347 348 4.251103 CCCTAAGGGCTTTTTACCAGAT 57.749 45.455 0.00 0.00 35.35 2.90
348 349 3.732048 CCCTAAGGGCTTTTTACCAGA 57.268 47.619 0.00 0.00 35.35 3.86
382 383 0.323087 TTTTAAGGAAGAGGCCCGGC 60.323 55.000 0.00 0.00 0.00 6.13
383 384 2.024414 CATTTTAAGGAAGAGGCCCGG 58.976 52.381 0.00 0.00 0.00 5.73
384 385 1.405463 GCATTTTAAGGAAGAGGCCCG 59.595 52.381 0.00 0.00 0.00 6.13
385 386 1.757118 GGCATTTTAAGGAAGAGGCCC 59.243 52.381 0.00 0.00 34.17 5.80
386 387 2.456577 TGGCATTTTAAGGAAGAGGCC 58.543 47.619 0.00 0.00 40.51 5.19
387 388 4.743057 ATTGGCATTTTAAGGAAGAGGC 57.257 40.909 0.00 0.00 0.00 4.70
388 389 6.218746 GCATATTGGCATTTTAAGGAAGAGG 58.781 40.000 0.00 0.00 0.00 3.69
389 390 6.218746 GGCATATTGGCATTTTAAGGAAGAG 58.781 40.000 0.00 0.00 43.14 2.85
390 391 6.160576 GGCATATTGGCATTTTAAGGAAGA 57.839 37.500 0.00 0.00 43.14 2.87
403 404 0.105408 CTTGGGCTTGGCATATTGGC 59.895 55.000 0.00 0.00 44.03 4.52
404 405 0.105408 GCTTGGGCTTGGCATATTGG 59.895 55.000 0.00 0.00 35.22 3.16
405 406 0.105408 GGCTTGGGCTTGGCATATTG 59.895 55.000 0.00 0.00 38.73 1.90
406 407 1.050421 GGGCTTGGGCTTGGCATATT 61.050 55.000 0.00 0.00 38.73 1.28
407 408 1.458209 GGGCTTGGGCTTGGCATAT 60.458 57.895 0.00 0.00 38.73 1.78
408 409 2.043046 GGGCTTGGGCTTGGCATA 60.043 61.111 0.00 0.00 38.73 3.14
413 414 4.659172 TGGACGGGCTTGGGCTTG 62.659 66.667 0.00 0.00 38.73 4.01
414 415 4.351054 CTGGACGGGCTTGGGCTT 62.351 66.667 0.00 0.00 38.73 4.35
434 435 1.904865 TTTTGAGCCCAGCAGCAGG 60.905 57.895 0.00 0.00 34.23 4.85
435 436 1.177256 AGTTTTGAGCCCAGCAGCAG 61.177 55.000 0.00 0.00 34.23 4.24
436 437 0.756442 AAGTTTTGAGCCCAGCAGCA 60.756 50.000 0.00 0.00 34.23 4.41
437 438 1.200948 CTAAGTTTTGAGCCCAGCAGC 59.799 52.381 0.00 0.00 0.00 5.25
438 439 1.815003 CCTAAGTTTTGAGCCCAGCAG 59.185 52.381 0.00 0.00 0.00 4.24
439 440 1.909700 CCTAAGTTTTGAGCCCAGCA 58.090 50.000 0.00 0.00 0.00 4.41
440 441 0.528017 GCCTAAGTTTTGAGCCCAGC 59.472 55.000 0.00 0.00 0.00 4.85
441 442 1.177401 GGCCTAAGTTTTGAGCCCAG 58.823 55.000 0.00 0.00 37.66 4.45
442 443 3.356814 GGCCTAAGTTTTGAGCCCA 57.643 52.632 0.00 0.00 37.66 5.36
444 445 1.546029 CTTGGGCCTAAGTTTTGAGCC 59.454 52.381 20.23 0.00 43.09 4.70
445 446 1.067565 GCTTGGGCCTAAGTTTTGAGC 60.068 52.381 27.53 10.66 0.00 4.26
446 447 2.489722 GAGCTTGGGCCTAAGTTTTGAG 59.510 50.000 27.53 4.02 39.73 3.02
447 448 2.514803 GAGCTTGGGCCTAAGTTTTGA 58.485 47.619 27.53 0.00 39.73 2.69
448 449 1.200020 CGAGCTTGGGCCTAAGTTTTG 59.800 52.381 27.53 16.80 39.73 2.44
449 450 1.534729 CGAGCTTGGGCCTAAGTTTT 58.465 50.000 27.53 15.02 39.73 2.43
450 451 0.322546 CCGAGCTTGGGCCTAAGTTT 60.323 55.000 27.53 17.38 39.73 2.66
451 452 1.299976 CCGAGCTTGGGCCTAAGTT 59.700 57.895 27.53 23.21 39.73 2.66
452 453 2.990479 CCGAGCTTGGGCCTAAGT 59.010 61.111 27.53 15.67 39.73 2.24
453 454 2.514824 GCCGAGCTTGGGCCTAAG 60.515 66.667 23.78 23.78 44.97 2.18
459 460 4.659172 TTGTGGGCCGAGCTTGGG 62.659 66.667 22.06 11.19 0.00 4.12
460 461 3.058160 CTTGTGGGCCGAGCTTGG 61.058 66.667 16.53 16.53 0.00 3.61
461 462 3.741476 GCTTGTGGGCCGAGCTTG 61.741 66.667 16.29 0.00 45.75 4.01
465 466 3.741476 GCTTGCTTGTGGGCCGAG 61.741 66.667 0.00 0.00 0.00 4.63
469 470 2.999063 ATGGGCTTGCTTGTGGGC 60.999 61.111 0.00 0.00 0.00 5.36
470 471 1.601419 CTGATGGGCTTGCTTGTGGG 61.601 60.000 0.00 0.00 0.00 4.61
471 472 1.601419 CCTGATGGGCTTGCTTGTGG 61.601 60.000 0.00 0.00 0.00 4.17
472 473 1.888018 CCTGATGGGCTTGCTTGTG 59.112 57.895 0.00 0.00 0.00 3.33
473 474 4.428845 CCTGATGGGCTTGCTTGT 57.571 55.556 0.00 0.00 0.00 3.16
490 491 1.202940 CCTAAAATCCAGGGCCTAGGC 60.203 57.143 26.55 26.55 41.06 3.93
491 492 1.425448 CCCTAAAATCCAGGGCCTAGG 59.575 57.143 5.28 10.90 46.27 3.02
492 493 2.959465 CCCTAAAATCCAGGGCCTAG 57.041 55.000 5.28 0.00 46.27 3.02
498 499 1.152756 CCCGGCCCTAAAATCCAGG 60.153 63.158 0.00 0.00 0.00 4.45
499 500 1.828224 GCCCGGCCCTAAAATCCAG 60.828 63.158 0.00 0.00 0.00 3.86
500 501 2.277404 GCCCGGCCCTAAAATCCA 59.723 61.111 0.00 0.00 0.00 3.41
501 502 2.520982 GGCCCGGCCCTAAAATCC 60.521 66.667 18.83 0.00 44.06 3.01
542 543 0.392336 GCTAGTCCTGGCCATCTCAG 59.608 60.000 5.51 1.14 0.00 3.35
543 544 0.031716 AGCTAGTCCTGGCCATCTCA 60.032 55.000 5.51 0.00 37.85 3.27
544 545 0.392336 CAGCTAGTCCTGGCCATCTC 59.608 60.000 5.51 0.00 37.85 2.75
545 546 1.053264 CCAGCTAGTCCTGGCCATCT 61.053 60.000 5.51 8.22 45.28 2.90
546 547 1.449353 CCAGCTAGTCCTGGCCATC 59.551 63.158 5.51 0.00 45.28 3.51
547 548 3.652687 CCAGCTAGTCCTGGCCAT 58.347 61.111 5.51 0.00 45.28 4.40
552 553 2.185350 CACCGCCAGCTAGTCCTG 59.815 66.667 0.00 0.00 0.00 3.86
553 554 2.037367 TCACCGCCAGCTAGTCCT 59.963 61.111 0.00 0.00 0.00 3.85
554 555 2.184579 GTCACCGCCAGCTAGTCC 59.815 66.667 0.00 0.00 0.00 3.85
555 556 1.153745 CAGTCACCGCCAGCTAGTC 60.154 63.158 0.00 0.00 0.00 2.59
556 557 2.973899 CAGTCACCGCCAGCTAGT 59.026 61.111 0.00 0.00 0.00 2.57
557 558 2.510238 GCAGTCACCGCCAGCTAG 60.510 66.667 0.00 0.00 0.00 3.42
558 559 2.878089 TTGCAGTCACCGCCAGCTA 61.878 57.895 0.00 0.00 0.00 3.32
559 560 4.254709 TTGCAGTCACCGCCAGCT 62.255 61.111 0.00 0.00 0.00 4.24
581 582 1.665916 GCAGCTCGCTGAGAACACA 60.666 57.895 22.09 0.00 46.30 3.72
647 648 1.072159 GGGCTATCCTGCTGCGAAT 59.928 57.895 0.00 0.00 0.00 3.34
659 660 2.851102 ATGCTGCGAGGGGGCTAT 60.851 61.111 0.00 0.00 0.00 2.97
796 807 2.559478 CCATTGTTGGAATGGGGGAAGA 60.559 50.000 5.64 0.00 46.92 2.87
966 982 4.084888 GGACTTGGCGCGTTTCCG 62.085 66.667 8.43 0.00 37.07 4.30
1083 1122 1.636769 GGGCTAGGGTTTGAGGGAGG 61.637 65.000 0.00 0.00 0.00 4.30
1170 1215 2.486966 GAACGACGGGTACGGGAG 59.513 66.667 0.00 0.00 46.48 4.30
1594 1660 4.148825 CCTTGCCTCCTCCGACGG 62.149 72.222 7.84 7.84 0.00 4.79
1817 1886 0.909610 TGGAGGCGGACTTGAGGAAT 60.910 55.000 0.00 0.00 0.00 3.01
1896 1965 1.153958 CAGACGCGTGCAGAGATGA 60.154 57.895 20.70 0.00 0.00 2.92
1987 2056 2.018644 GCGGCAGATTTGATGGAGGAA 61.019 52.381 0.00 0.00 0.00 3.36
2295 2400 3.992427 ACAGTAAGCGTAACACTAAAGGC 59.008 43.478 0.00 0.00 0.00 4.35
2302 2407 3.872560 AGCAAACAGTAAGCGTAACAC 57.127 42.857 0.00 0.00 0.00 3.32
2358 2465 8.191446 GCCATGATGTCGTAGAGTATATGTTAT 58.809 37.037 0.00 0.00 36.95 1.89
2359 2466 7.393515 AGCCATGATGTCGTAGAGTATATGTTA 59.606 37.037 0.00 0.00 36.95 2.41
2360 2467 6.209589 AGCCATGATGTCGTAGAGTATATGTT 59.790 38.462 0.00 0.00 36.95 2.71
2361 2468 5.712446 AGCCATGATGTCGTAGAGTATATGT 59.288 40.000 0.00 0.00 36.95 2.29
2375 2482 2.173519 CCCAAAACTGAGCCATGATGT 58.826 47.619 0.00 0.00 0.00 3.06
2525 2637 1.212935 CCTAACAGTGGAGGATTGGGG 59.787 57.143 7.43 0.00 34.46 4.96
2544 2656 5.801947 GCACAACACAAGATATCATCAAACC 59.198 40.000 5.32 0.00 0.00 3.27
2553 2665 7.722728 AGATCCATATTGCACAACACAAGATAT 59.277 33.333 0.00 0.00 28.41 1.63
2572 2684 9.851686 TTATGTACTGCAGAAATTAAGATCCAT 57.148 29.630 23.35 7.46 0.00 3.41
2594 2706 5.633830 ACAAGGTTCAGCTGACATTTATG 57.366 39.130 18.03 13.07 0.00 1.90
2629 2742 5.063944 ACGAATCAGTAGCAGTGCTAAATTG 59.936 40.000 26.04 21.88 43.07 2.32
2649 2762 3.805422 GGACACGGCATATATTCAACGAA 59.195 43.478 0.00 0.00 0.00 3.85
2660 2773 1.346395 AGAACAACAGGACACGGCATA 59.654 47.619 0.00 0.00 0.00 3.14
2704 2817 5.418209 TGTTTCTAGCCTAGAACAGAGGTAC 59.582 44.000 13.67 8.20 43.96 3.34
2707 2820 4.464597 ACTGTTTCTAGCCTAGAACAGAGG 59.535 45.833 29.89 16.95 43.96 3.69
2750 2864 1.936547 GCAGCATACAGTAGTTCCAGC 59.063 52.381 0.00 0.00 0.00 4.85
2797 2915 8.092068 TCATAAGTCCGACTGTATTCAGAAAAA 58.908 33.333 6.32 0.00 43.76 1.94
2798 2916 7.608153 TCATAAGTCCGACTGTATTCAGAAAA 58.392 34.615 6.32 0.00 43.76 2.29
2799 2917 7.165460 TCATAAGTCCGACTGTATTCAGAAA 57.835 36.000 6.32 0.00 43.76 2.52
2800 2918 6.769134 TCATAAGTCCGACTGTATTCAGAA 57.231 37.500 6.32 0.00 43.76 3.02
2801 2919 6.769134 TTCATAAGTCCGACTGTATTCAGA 57.231 37.500 6.32 0.00 43.76 3.27
2802 2920 6.980978 ACATTCATAAGTCCGACTGTATTCAG 59.019 38.462 0.65 0.00 46.18 3.02
2803 2921 6.873997 ACATTCATAAGTCCGACTGTATTCA 58.126 36.000 0.65 0.00 0.00 2.57
2804 2922 7.491372 TGAACATTCATAAGTCCGACTGTATTC 59.509 37.037 0.65 0.00 31.01 1.75
2805 2923 7.327975 TGAACATTCATAAGTCCGACTGTATT 58.672 34.615 0.65 0.00 31.01 1.89
2806 2924 6.873997 TGAACATTCATAAGTCCGACTGTAT 58.126 36.000 0.65 0.33 31.01 2.29
2807 2925 6.275494 TGAACATTCATAAGTCCGACTGTA 57.725 37.500 0.65 0.00 31.01 2.74
2808 2926 5.147330 TGAACATTCATAAGTCCGACTGT 57.853 39.130 0.65 0.00 31.01 3.55
2841 2959 3.521560 TCATAAGTCCGACTGCATTCAC 58.478 45.455 0.65 0.00 0.00 3.18
2880 3002 0.598065 AAAAGTCCGGCTGCATTCAC 59.402 50.000 0.50 0.00 0.00 3.18
2918 3040 2.622942 AGTTCGGCTGCATTCAGAAAAA 59.377 40.909 0.50 0.00 42.95 1.94
2919 3041 2.229792 AGTTCGGCTGCATTCAGAAAA 58.770 42.857 0.50 0.00 42.95 2.29
2920 3042 1.896220 AGTTCGGCTGCATTCAGAAA 58.104 45.000 0.50 0.00 42.95 2.52
2921 3043 1.896220 AAGTTCGGCTGCATTCAGAA 58.104 45.000 0.50 0.00 42.95 3.02
2922 3044 1.896220 AAAGTTCGGCTGCATTCAGA 58.104 45.000 0.50 0.00 42.95 3.27
2923 3045 2.287788 ACAAAAGTTCGGCTGCATTCAG 60.288 45.455 0.50 0.00 43.16 3.02
2924 3046 1.680735 ACAAAAGTTCGGCTGCATTCA 59.319 42.857 0.50 0.00 0.00 2.57
2925 3047 2.422276 ACAAAAGTTCGGCTGCATTC 57.578 45.000 0.50 0.00 0.00 2.67
2926 3048 3.317993 AGTTACAAAAGTTCGGCTGCATT 59.682 39.130 0.50 0.00 0.00 3.56
2927 3049 2.884639 AGTTACAAAAGTTCGGCTGCAT 59.115 40.909 0.50 0.00 0.00 3.96
2928 3050 2.294074 AGTTACAAAAGTTCGGCTGCA 58.706 42.857 0.50 0.00 0.00 4.41
2929 3051 3.003378 AGAAGTTACAAAAGTTCGGCTGC 59.997 43.478 0.00 0.00 45.78 5.25
2930 3052 4.813296 AGAAGTTACAAAAGTTCGGCTG 57.187 40.909 0.00 0.00 45.78 4.85
2931 3053 5.589050 AGAAAGAAGTTACAAAAGTTCGGCT 59.411 36.000 1.23 0.00 45.78 5.52
2932 3054 5.817988 AGAAAGAAGTTACAAAAGTTCGGC 58.182 37.500 1.23 0.00 45.78 5.54
2933 3055 7.248437 ACAAGAAAGAAGTTACAAAAGTTCGG 58.752 34.615 1.23 0.00 45.78 4.30
2934 3056 8.575454 CAACAAGAAAGAAGTTACAAAAGTTCG 58.425 33.333 1.23 0.00 45.78 3.95
2935 3057 8.860128 CCAACAAGAAAGAAGTTACAAAAGTTC 58.140 33.333 0.00 0.00 42.89 3.01
2936 3058 8.581578 TCCAACAAGAAAGAAGTTACAAAAGTT 58.418 29.630 0.00 0.00 0.00 2.66
2937 3059 8.117813 TCCAACAAGAAAGAAGTTACAAAAGT 57.882 30.769 0.00 0.00 0.00 2.66
2938 3060 9.586435 AATCCAACAAGAAAGAAGTTACAAAAG 57.414 29.630 0.00 0.00 0.00 2.27
2954 3118 3.967332 AATGCCCAGAAATCCAACAAG 57.033 42.857 0.00 0.00 0.00 3.16
2979 3143 9.162764 GTAGAGCTACAAATTTTGACCATTCTA 57.837 33.333 15.81 11.58 36.15 2.10
3003 3167 4.281941 ACATCTTCAGTTCACTCAGCAGTA 59.718 41.667 0.00 0.00 0.00 2.74
3005 3169 3.432592 CACATCTTCAGTTCACTCAGCAG 59.567 47.826 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.